Multiple sequence alignment - TraesCS7A01G281400

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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 TraesCS7A01G281400 chr7A 100.000 2467 0 0 1 2467 305701160 305698694 0.000000e+00 4556
1 TraesCS7A01G281400 chr7A 94.454 2236 102 8 3 2217 630248270 630246036 0.000000e+00 3422
2 TraesCS7A01G281400 chr7A 87.580 934 76 22 677 1582 675230335 675231256 0.000000e+00 1046
3 TraesCS7A01G281400 chr6A 93.938 2491 118 17 1 2467 546622173 546619692 0.000000e+00 3733
4 TraesCS7A01G281400 chr6A 92.096 873 47 11 1617 2467 409119737 409120609 0.000000e+00 1210
5 TraesCS7A01G281400 chr6A 91.418 536 43 3 113 647 409119171 409119704 0.000000e+00 732
6 TraesCS7A01G281400 chr6A 87.678 422 46 6 715 1133 376681346 376680928 1.030000e-133 486
7 TraesCS7A01G281400 chr7B 93.883 1831 104 5 1 1826 660061383 660063210 0.000000e+00 2754
8 TraesCS7A01G281400 chr7B 88.803 902 81 16 678 1564 653019128 653018232 0.000000e+00 1088
9 TraesCS7A01G281400 chr7B 92.540 563 22 5 1925 2467 660063211 660063773 0.000000e+00 789
10 TraesCS7A01G281400 chr1D 92.644 870 41 10 1620 2467 412547959 412547091 0.000000e+00 1230
11 TraesCS7A01G281400 chr1D 92.642 530 37 2 119 647 412548523 412547995 0.000000e+00 761
12 TraesCS7A01G281400 chr1D 90.401 573 32 6 1915 2467 14566451 14565882 0.000000e+00 732
13 TraesCS7A01G281400 chr1D 90.227 573 33 6 1915 2467 14633797 14634366 0.000000e+00 726
14 TraesCS7A01G281400 chr6B 92.078 871 48 9 1617 2467 553538699 553539568 0.000000e+00 1206
15 TraesCS7A01G281400 chr6B 93.860 114 6 1 1 113 216317937 216318050 1.170000e-38 171
16 TraesCS7A01G281400 chr2A 92.075 858 59 6 1617 2467 92978509 92979364 0.000000e+00 1199
17 TraesCS7A01G281400 chr4A 91.514 872 51 9 1617 2467 66422151 66421282 0.000000e+00 1179
18 TraesCS7A01G281400 chr4A 90.909 550 49 1 119 667 66422717 66422168 0.000000e+00 737
19 TraesCS7A01G281400 chrUn 91.389 871 54 6 1617 2467 316628276 316629145 0.000000e+00 1173
20 TraesCS7A01G281400 chr3B 91.045 871 57 7 1617 2467 565037379 565038248 0.000000e+00 1157
21 TraesCS7A01G281400 chr7D 89.183 906 70 15 677 1564 584855246 584854351 0.000000e+00 1105
22 TraesCS7A01G281400 chr7D 89.466 674 57 8 718 1383 92809591 92808924 0.000000e+00 839
23 TraesCS7A01G281400 chr2D 90.138 872 40 15 1617 2467 154509546 154508700 0.000000e+00 1092
24 TraesCS7A01G281400 chr2D 92.830 530 36 2 119 647 154510107 154509579 0.000000e+00 767
25 TraesCS7A01G281400 chr2D 91.546 414 33 2 718 1130 87982037 87981625 9.900000e-159 569
26 TraesCS7A01G281400 chr4D 92.639 557 32 5 113 667 165302474 165303023 0.000000e+00 793
27 TraesCS7A01G281400 chr4D 89.982 549 28 11 1617 2143 165303040 165303583 0.000000e+00 684
28 TraesCS7A01G281400 chr3A 91.231 536 44 3 113 647 356687376 356687909 0.000000e+00 726
29 TraesCS7A01G281400 chr1A 91.228 114 9 1 1 113 344786515 344786628 1.180000e-33 154


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 TraesCS7A01G281400 chr7A 305698694 305701160 2466 True 4556.0 4556 100.0000 1 2467 1 chr7A.!!$R1 2466
1 TraesCS7A01G281400 chr7A 630246036 630248270 2234 True 3422.0 3422 94.4540 3 2217 1 chr7A.!!$R2 2214
2 TraesCS7A01G281400 chr7A 675230335 675231256 921 False 1046.0 1046 87.5800 677 1582 1 chr7A.!!$F1 905
3 TraesCS7A01G281400 chr6A 546619692 546622173 2481 True 3733.0 3733 93.9380 1 2467 1 chr6A.!!$R2 2466
4 TraesCS7A01G281400 chr6A 409119171 409120609 1438 False 971.0 1210 91.7570 113 2467 2 chr6A.!!$F1 2354
5 TraesCS7A01G281400 chr7B 660061383 660063773 2390 False 1771.5 2754 93.2115 1 2467 2 chr7B.!!$F1 2466
6 TraesCS7A01G281400 chr7B 653018232 653019128 896 True 1088.0 1088 88.8030 678 1564 1 chr7B.!!$R1 886
7 TraesCS7A01G281400 chr1D 412547091 412548523 1432 True 995.5 1230 92.6430 119 2467 2 chr1D.!!$R2 2348
8 TraesCS7A01G281400 chr1D 14565882 14566451 569 True 732.0 732 90.4010 1915 2467 1 chr1D.!!$R1 552
9 TraesCS7A01G281400 chr1D 14633797 14634366 569 False 726.0 726 90.2270 1915 2467 1 chr1D.!!$F1 552
10 TraesCS7A01G281400 chr6B 553538699 553539568 869 False 1206.0 1206 92.0780 1617 2467 1 chr6B.!!$F2 850
11 TraesCS7A01G281400 chr2A 92978509 92979364 855 False 1199.0 1199 92.0750 1617 2467 1 chr2A.!!$F1 850
12 TraesCS7A01G281400 chr4A 66421282 66422717 1435 True 958.0 1179 91.2115 119 2467 2 chr4A.!!$R1 2348
13 TraesCS7A01G281400 chrUn 316628276 316629145 869 False 1173.0 1173 91.3890 1617 2467 1 chrUn.!!$F1 850
14 TraesCS7A01G281400 chr3B 565037379 565038248 869 False 1157.0 1157 91.0450 1617 2467 1 chr3B.!!$F1 850
15 TraesCS7A01G281400 chr7D 584854351 584855246 895 True 1105.0 1105 89.1830 677 1564 1 chr7D.!!$R2 887
16 TraesCS7A01G281400 chr7D 92808924 92809591 667 True 839.0 839 89.4660 718 1383 1 chr7D.!!$R1 665
17 TraesCS7A01G281400 chr2D 154508700 154510107 1407 True 929.5 1092 91.4840 119 2467 2 chr2D.!!$R2 2348
18 TraesCS7A01G281400 chr4D 165302474 165303583 1109 False 738.5 793 91.3105 113 2143 2 chr4D.!!$F1 2030
19 TraesCS7A01G281400 chr3A 356687376 356687909 533 False 726.0 726 91.2310 113 647 1 chr3A.!!$F1 534

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
537 546 0.468226 ACTTCGACTCACTGCCCAAA 59.532 50.0 0.0 0.0 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2061 0.033781 TTGGAATTTCGTCCGTCCGT 59.966 50.0 0.0 0.0 40.96 4.69 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
164 166 1.293062 ATCAAGATCACCCCTGCTGT 58.707 50.000 0.00 0.00 0.00 4.40
165 167 0.615331 TCAAGATCACCCCTGCTGTC 59.385 55.000 0.00 0.00 0.00 3.51
196 201 2.158871 TCTACTCGGTTGCTGGTGTTTT 60.159 45.455 0.00 0.00 0.00 2.43
300 309 4.500035 GGTTGCCGGATTTTGTGTTTCTTA 60.500 41.667 5.05 0.00 0.00 2.10
343 352 6.124088 TCTTCTCTTGTTTCTGCAGTTTTC 57.876 37.500 14.67 4.00 0.00 2.29
416 425 2.280797 GCTGCAAGGGTGTCACGA 60.281 61.111 0.00 0.00 0.00 4.35
418 427 1.367471 CTGCAAGGGTGTCACGAGA 59.633 57.895 0.00 0.00 0.00 4.04
486 495 2.226200 CCATGTCGTTCAACTCATGCAA 59.774 45.455 13.65 0.00 37.09 4.08
536 545 1.272490 CTACTTCGACTCACTGCCCAA 59.728 52.381 0.00 0.00 0.00 4.12
537 546 0.468226 ACTTCGACTCACTGCCCAAA 59.532 50.000 0.00 0.00 0.00 3.28
607 616 3.962718 TCCATAGTCTCATGTGCTGATGA 59.037 43.478 0.00 0.00 32.10 2.92
690 700 3.683937 GGCACGCCATTGCTGGTT 61.684 61.111 2.36 0.00 45.10 3.67
771 787 3.006133 TACTGCATGCCGGACCCA 61.006 61.111 16.68 0.00 0.00 4.51
772 788 3.323758 TACTGCATGCCGGACCCAC 62.324 63.158 16.68 0.00 0.00 4.61
834 850 2.579201 GAGAACCTGCGGCAGCTA 59.421 61.111 24.27 0.00 45.42 3.32
1020 1036 3.771160 GGCGACCCCGACACTGAT 61.771 66.667 0.00 0.00 44.91 2.90
1036 1052 0.606130 TGATGCTGACAATGCCGTGT 60.606 50.000 0.00 0.00 0.00 4.49
1058 1074 2.581354 CAAGGAGCAGGAGGACCG 59.419 66.667 0.00 0.00 41.83 4.79
1060 1076 4.787280 AGGAGCAGGAGGACCGGG 62.787 72.222 6.32 0.00 41.83 5.73
1111 1127 2.494445 CTGCCCACGCTCGTCATA 59.506 61.111 0.00 0.00 35.36 2.15
1112 1128 1.878522 CTGCCCACGCTCGTCATAC 60.879 63.158 0.00 0.00 35.36 2.39
1114 1130 1.227263 GCCCACGCTCGTCATACAT 60.227 57.895 0.00 0.00 0.00 2.29
1130 1146 4.887655 TCATACATGACGTCCAGTACAGAT 59.112 41.667 14.12 0.00 0.00 2.90
1138 1159 2.289444 CGTCCAGTACAGATGTGGGTTT 60.289 50.000 0.00 0.00 31.70 3.27
1326 1363 1.620323 GAGCACCAAGGCCTTCATTTT 59.380 47.619 17.29 0.97 0.00 1.82
1327 1364 1.345415 AGCACCAAGGCCTTCATTTTG 59.655 47.619 17.29 9.33 0.00 2.44
1364 1416 4.800993 GTGAATCGACGATGAACTTCTGAT 59.199 41.667 11.83 0.00 0.00 2.90
1466 1518 1.374252 GGTGTGCAGGGACACGTAG 60.374 63.158 16.18 0.00 46.13 3.51
1858 1916 2.097825 AGAAGGCCACATTTCTCATGC 58.902 47.619 5.01 0.00 0.00 4.06
1932 1993 3.117512 ACCACCACATTTAGGGATCCATC 60.118 47.826 15.23 0.00 0.00 3.51
2000 2061 2.159099 CGAAGTTCACAGGCCATAGCTA 60.159 50.000 5.01 0.00 39.73 3.32
2038 2099 0.687354 ACTGTACTGCAACCCCTCAG 59.313 55.000 0.00 0.00 36.45 3.35
2072 2155 6.096846 GGTAAAATGATCCACAAGCTACCATT 59.903 38.462 0.00 0.00 33.66 3.16
2170 2253 2.742348 TCGGTGTAATGCCTAAGGAGA 58.258 47.619 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.325753 GCAGGGGAGCCTGAGTGT 61.326 66.667 0.00 0.00 39.96 3.55
51 52 0.667487 CAGGAGCAAGAAGTTCGCGA 60.667 55.000 3.71 3.71 0.00 5.87
165 167 3.262420 CAACCGAGTAGATCCAAACAGG 58.738 50.000 0.00 0.00 39.47 4.00
196 201 1.174783 GGTGTGAGTAGCCTCGAAGA 58.825 55.000 0.00 0.00 40.85 2.87
300 309 7.889469 AGAAGAAATGCATCAGTTTTGTACAT 58.111 30.769 0.00 0.00 0.00 2.29
343 352 6.696148 AGTCGACACAGTAAAGTTCAGTTAAG 59.304 38.462 19.50 0.00 0.00 1.85
536 545 2.648059 GACACATGCCCAGAAGCTATT 58.352 47.619 0.00 0.00 0.00 1.73
537 546 1.473965 CGACACATGCCCAGAAGCTAT 60.474 52.381 0.00 0.00 0.00 2.97
607 616 2.548464 AAGAGAGACTGAGAGGGCAT 57.452 50.000 0.00 0.00 0.00 4.40
690 700 2.567615 GGTACCAGAGAAAGCTTCCTCA 59.432 50.000 15.68 0.00 32.07 3.86
771 787 1.305381 CTCCCCGAAGTCCTCCTGT 60.305 63.158 0.00 0.00 0.00 4.00
772 788 2.060980 CCTCCCCGAAGTCCTCCTG 61.061 68.421 0.00 0.00 0.00 3.86
1015 1031 0.321919 ACGGCATTGTCAGCATCAGT 60.322 50.000 0.00 0.00 0.00 3.41
1017 1033 0.606130 ACACGGCATTGTCAGCATCA 60.606 50.000 0.00 0.00 0.00 3.07
1020 1036 1.100463 ACAACACGGCATTGTCAGCA 61.100 50.000 0.00 0.00 35.32 4.41
1036 1052 0.473694 TCCTCCTGCTCCTTGGACAA 60.474 55.000 0.00 0.00 0.00 3.18
1111 1127 2.826128 ACATCTGTACTGGACGTCATGT 59.174 45.455 18.91 16.71 0.00 3.21
1112 1128 3.182182 CACATCTGTACTGGACGTCATG 58.818 50.000 18.91 11.83 0.00 3.07
1114 1130 1.544246 CCACATCTGTACTGGACGTCA 59.456 52.381 18.91 2.63 0.00 4.35
1165 1190 0.094730 CGTCGCCGGAGAAATGAAAC 59.905 55.000 10.32 0.00 0.00 2.78
1255 1289 2.097038 CCTCCTTGAAGCTGACGCG 61.097 63.158 3.53 3.53 42.32 6.01
1259 1293 1.201429 GGTCCCCTCCTTGAAGCTGA 61.201 60.000 0.00 0.00 0.00 4.26
1261 1295 2.294078 CGGTCCCCTCCTTGAAGCT 61.294 63.158 0.00 0.00 0.00 3.74
1326 1363 1.124780 TTCACCCTTCTTGTCGTCCA 58.875 50.000 0.00 0.00 0.00 4.02
1327 1364 2.347731 GATTCACCCTTCTTGTCGTCC 58.652 52.381 0.00 0.00 0.00 4.79
1364 1416 2.916702 TGTCTGCAGAGAAAAGCTCA 57.083 45.000 18.89 5.93 46.45 4.26
1431 1483 1.736645 CCGTCATGTTCGTCGCCTT 60.737 57.895 10.74 0.00 0.00 4.35
1606 1660 1.386533 GCTAAGCATCAGCACATGGT 58.613 50.000 0.00 0.00 45.49 3.55
1607 1661 0.666913 GGCTAAGCATCAGCACATGG 59.333 55.000 0.00 0.00 45.49 3.66
1881 1942 7.597369 GCCTAAACACCCTTTTTACATACAAAG 59.403 37.037 0.00 0.00 0.00 2.77
1932 1993 0.176680 CATGGTGGAGGAGACCGAAG 59.823 60.000 0.00 0.00 36.12 3.79
2000 2061 0.033781 TTGGAATTTCGTCCGTCCGT 59.966 50.000 0.00 0.00 40.96 4.69
2038 2099 4.580580 GTGGATCATTTTACCTGTGGATCC 59.419 45.833 4.20 4.20 46.93 3.36
2072 2155 0.746204 TGGACACTTCGTTGCAGCAA 60.746 50.000 2.83 2.83 0.00 3.91
2138 2221 3.478857 TTACACCGAACAACTGTGGAT 57.521 42.857 0.00 0.00 37.89 3.41
2170 2253 7.396540 ACAAAAGTGAGAGAGACATTGTTTT 57.603 32.000 0.00 0.00 0.00 2.43
2272 2356 1.603236 CGAGACTTCTCCCAGCTGCT 61.603 60.000 8.66 0.00 39.79 4.24


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

AutoCloner maintained by Alex Coulton.