Multiple sequence alignment - TraesCS7A01G035200

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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 TraesCS7A01G035200 chr7A 100.000 2471 0 0 1 2471 15640854 15638384 0.000000e+00 4564
1 TraesCS7A01G035200 chr7A 81.439 1126 167 18 960 2068 15689612 15688512 0.000000e+00 883
2 TraesCS7A01G035200 chr4A 91.720 2500 171 17 1 2471 718032168 718034660 0.000000e+00 3437
3 TraesCS7A01G035200 chr4A 80.665 331 55 6 1112 1433 718033648 718033978 5.280000e-62 248
4 TraesCS7A01G035200 chr7D 91.710 2473 154 17 17 2469 16692932 16690491 0.000000e+00 3384
5 TraesCS7A01G035200 chr7D 80.363 331 56 6 1112 1433 16691498 16691168 2.460000e-60 243


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 TraesCS7A01G035200 chr7A 15638384 15640854 2470 True 4564.0 4564 100.0000 1 2471 1 chr7A.!!$R1 2470
1 TraesCS7A01G035200 chr7A 15688512 15689612 1100 True 883.0 883 81.4390 960 2068 1 chr7A.!!$R2 1108
2 TraesCS7A01G035200 chr4A 718032168 718034660 2492 False 1842.5 3437 86.1925 1 2471 2 chr4A.!!$F1 2470
3 TraesCS7A01G035200 chr7D 16690491 16692932 2441 True 1813.5 3384 86.0365 17 2469 2 chr7D.!!$R1 2452

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
835 854 2.422127 GCGCCACCTAACACAACAATAT 59.578 45.455 0.0 0.0 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 1702 0.31812 CTGCCATTGTTGTTGGGGTC 59.682 55.0 0.0 0.0 34.66 4.46 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
61 62 6.818644 AGCACTTCGTTACATATTTCACTCAT 59.181 34.615 0.00 0.00 0.00 2.90
111 112 3.669557 GCATGGTTTGATTACACGTGACC 60.670 47.826 25.01 17.48 0.00 4.02
122 123 3.194005 ACACGTGACCTCAAAATGACT 57.806 42.857 25.01 0.00 0.00 3.41
134 135 6.032094 CCTCAAAATGACTGAATACATGCAC 58.968 40.000 0.00 0.00 0.00 4.57
142 143 6.108687 TGACTGAATACATGCACTAGGAAAG 58.891 40.000 0.00 0.00 0.00 2.62
179 180 9.581289 TTATATTGTACCCCTAAATGAATGTGG 57.419 33.333 0.00 0.00 0.00 4.17
259 261 3.845109 AATATGGTTTGGACAAGGGGT 57.155 42.857 0.00 0.00 0.00 4.95
260 262 4.957606 AATATGGTTTGGACAAGGGGTA 57.042 40.909 0.00 0.00 0.00 3.69
393 407 3.576078 AGTTCAGTTCCACCACATCAA 57.424 42.857 0.00 0.00 0.00 2.57
437 451 4.973168 TGACATGTAAAGGGCATCCTATC 58.027 43.478 0.00 0.00 44.07 2.08
474 488 9.481340 TGCTCTACTAATGCATGTTTATCTTAG 57.519 33.333 0.00 0.00 0.00 2.18
567 582 5.670792 AATGGTTTGCTGATGTGATCAAT 57.329 34.783 0.00 0.00 39.11 2.57
597 612 5.801947 CAGCTAATGCAAGATTACAAACCAC 59.198 40.000 0.00 0.00 42.74 4.16
604 619 5.178623 TGCAAGATTACAAACCACTAACTCG 59.821 40.000 0.00 0.00 0.00 4.18
605 620 5.178809 GCAAGATTACAAACCACTAACTCGT 59.821 40.000 0.00 0.00 0.00 4.18
609 628 8.891671 AGATTACAAACCACTAACTCGTAAAA 57.108 30.769 0.00 0.00 0.00 1.52
726 745 7.663081 ACTCTTGACATGTAAAGTGATGATTGT 59.337 33.333 25.25 10.14 0.00 2.71
774 793 3.790091 CTGACAGTCAGGTGATATGTGG 58.210 50.000 21.46 0.00 40.71 4.17
835 854 2.422127 GCGCCACCTAACACAACAATAT 59.578 45.455 0.00 0.00 0.00 1.28
901 921 3.634504 TGTAGGATGGAATGCAGCAAAT 58.365 40.909 0.00 0.00 36.98 2.32
910 930 3.243636 GGAATGCAGCAAATAGACCATGG 60.244 47.826 11.19 11.19 0.00 3.66
940 960 7.986085 ATAAATAGGCATGTACCATGAAGAC 57.014 36.000 8.34 0.00 0.00 3.01
1063 1086 1.606885 CGCCATTGCCCAGTTGGAAT 61.607 55.000 0.00 0.00 37.39 3.01
1068 1091 0.541764 TTGCCCAGTTGGAATCCACC 60.542 55.000 0.00 0.00 37.39 4.61
1098 1121 2.460757 GCTTTGGACAATGCCAACAT 57.539 45.000 10.73 0.00 46.99 2.71
1120 1146 3.223589 AACCGGGGCAACAACAGC 61.224 61.111 6.32 0.00 39.74 4.40
1196 1222 3.703052 GTGAGAATGCCATTCCTCCAAAT 59.297 43.478 13.69 0.00 40.13 2.32
1204 1230 2.689983 CCATTCCTCCAAATACAGGTGC 59.310 50.000 0.00 0.00 0.00 5.01
1228 1254 0.463295 GCTTAGCAGCTGCCAGATCA 60.463 55.000 34.39 11.54 43.51 2.92
1266 1292 1.593750 GCAGCTAGCACAGATCCCG 60.594 63.158 18.83 0.00 44.79 5.14
1374 1400 4.095334 CAGCAAGCACAACATAAGAGCATA 59.905 41.667 0.00 0.00 0.00 3.14
1409 1435 5.121105 TGAGAACCTATCATTGATGTGCAG 58.879 41.667 9.46 0.00 0.00 4.41
1447 1473 2.873472 CAATGCCAGCAACAACAACAAT 59.127 40.909 0.00 0.00 0.00 2.71
1452 1478 1.598601 CAGCAACAACAACAATTGGGC 59.401 47.619 10.83 0.63 35.45 5.36
1468 1494 1.556911 TGGGCCAACAACAACAACAAT 59.443 42.857 2.13 0.00 0.00 2.71
1509 1538 1.499056 GTGTGCGACATTCCTGCAG 59.501 57.895 6.78 6.78 39.67 4.41
1550 1579 1.852157 TGCCATTCCCCCAGACACT 60.852 57.895 0.00 0.00 0.00 3.55
1584 1613 1.529152 CCAGCTGCCAGAATGTGCAA 61.529 55.000 8.66 0.00 40.72 4.08
1603 1632 2.203480 ACCAATGTTGCCGGCAGT 60.203 55.556 30.75 20.10 0.00 4.40
1611 1640 1.094785 GTTGCCGGCAGTTATCACAT 58.905 50.000 30.75 0.00 0.00 3.21
1673 1702 1.009829 GAGGCTATCAGGCAACAACG 58.990 55.000 2.39 0.00 44.19 4.10
1734 1763 1.467734 CCAGCACAACTTGAGAGCATC 59.532 52.381 0.00 0.00 0.00 3.91
1830 1865 1.298953 ACATTCCCATGGTGGCTACT 58.701 50.000 11.73 0.00 35.79 2.57
1834 1869 1.209621 TCCCATGGTGGCTACTTACC 58.790 55.000 11.73 0.00 35.79 2.85
1976 2012 9.463443 AAAGCATTTGTCTGAATAAAACTACAC 57.537 29.630 0.00 0.00 36.60 2.90
2049 2086 4.899457 ACCGAATTCTGTATGTCTCCCATA 59.101 41.667 3.52 0.00 34.86 2.74
2050 2087 5.011125 ACCGAATTCTGTATGTCTCCCATAG 59.989 44.000 3.52 0.00 36.71 2.23
2051 2088 5.473931 CGAATTCTGTATGTCTCCCATAGG 58.526 45.833 3.52 0.00 36.71 2.57
2056 2093 4.140686 TCTGTATGTCTCCCATAGGACCAT 60.141 45.833 0.00 0.00 37.19 3.55
2094 2131 4.389890 AACAGTAGTTGGTACACACGAA 57.610 40.909 0.00 0.00 39.29 3.85
2109 2146 9.304731 GGTACACACGAAGAAAATACACATATA 57.695 33.333 0.00 0.00 0.00 0.86
2166 2207 3.311486 CCACCGTTGGCATAAACAAAT 57.689 42.857 0.00 0.00 35.56 2.32
2167 2208 4.442375 CCACCGTTGGCATAAACAAATA 57.558 40.909 0.00 0.00 35.56 1.40
2169 2210 5.415221 CCACCGTTGGCATAAACAAATATT 58.585 37.500 0.00 0.00 35.56 1.28
2206 2247 8.388484 ACATGATAAACCTCATAAGCATCTTC 57.612 34.615 0.00 0.00 34.11 2.87
2222 2263 1.067142 TCTTCCCGAACTGAACCATCG 60.067 52.381 0.00 0.00 36.39 3.84
2230 2271 3.865745 CGAACTGAACCATCGCTTAGATT 59.134 43.478 0.00 0.00 37.52 2.40
2310 2351 1.694696 AGGAACAGAGTCCTGGTGAAC 59.305 52.381 0.00 0.00 46.75 3.18
2367 2408 2.900122 ATGACAGGATTTGAAACGCG 57.100 45.000 3.53 3.53 0.00 6.01
2369 2410 1.529438 TGACAGGATTTGAAACGCGTC 59.471 47.619 14.44 0.25 0.00 5.19
2439 2480 4.376413 GCTACATCACAAGCGGATTAATCG 60.376 45.833 9.32 6.21 0.00 3.34
2440 2481 3.792401 ACATCACAAGCGGATTAATCGA 58.208 40.909 9.32 0.00 0.00 3.59
2465 2506 2.285602 GCCATAGTTATTGCGACGTGTG 60.286 50.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 6.403333 TGAGTGAAATATGTAACGAAGTGC 57.597 37.500 0.00 0.00 45.00 4.40
111 112 6.849502 AGTGCATGTATTCAGTCATTTTGAG 58.150 36.000 0.00 0.00 0.00 3.02
122 123 7.882791 TCTTTTCTTTCCTAGTGCATGTATTCA 59.117 33.333 0.00 0.00 0.00 2.57
142 143 7.510407 AGGGGTACAATATAAGAGCTCTTTTC 58.490 38.462 32.70 12.23 37.40 2.29
176 177 3.606687 AGGTAACATCGAAATGGTCCAC 58.393 45.455 0.00 0.00 37.19 4.02
179 180 4.332819 CCTGAAGGTAACATCGAAATGGTC 59.667 45.833 0.00 0.00 37.01 4.02
229 230 9.620660 CTTGTCCAAACCATATTTAGTGTTTAC 57.379 33.333 0.00 0.00 30.29 2.01
231 232 7.256154 CCCTTGTCCAAACCATATTTAGTGTTT 60.256 37.037 0.00 0.00 0.00 2.83
277 279 2.849943 TGGTTGCTACCCATCCATACTT 59.150 45.455 15.00 0.00 44.35 2.24
393 407 5.190528 TCAAGAGATTTCCATGGAGCTACTT 59.809 40.000 15.53 14.27 0.00 2.24
437 451 2.929531 AGTAGAGCACGACATGACTG 57.070 50.000 0.00 0.00 0.00 3.51
567 582 8.560355 TTGTAATCTTGCATTAGCTGTTTAGA 57.440 30.769 0.00 0.00 42.74 2.10
597 612 6.978343 TGATCCATGGTTTTTACGAGTTAG 57.022 37.500 12.58 0.00 0.00 2.34
604 619 6.256321 GCATTCACATGATCCATGGTTTTTAC 59.744 38.462 12.58 0.00 45.16 2.01
605 620 6.070938 TGCATTCACATGATCCATGGTTTTTA 60.071 34.615 12.58 0.00 45.16 1.52
609 628 3.367321 TGCATTCACATGATCCATGGTT 58.633 40.909 12.58 2.52 45.16 3.67
683 702 3.305720 AGAGTTCGGGTGGCATATCTTA 58.694 45.455 0.00 0.00 0.00 2.10
726 745 8.996271 GTGAGATTGATAATGCATATGACTCAA 58.004 33.333 6.97 5.77 32.71 3.02
774 793 5.181690 TGGCCATCAAATATACTTTTCGC 57.818 39.130 0.00 0.00 0.00 4.70
835 854 8.225603 GGATGCTTTCCAAACTAATAATCTCA 57.774 34.615 1.83 0.00 44.74 3.27
901 921 5.338381 GCCTATTTATAGCTGCCATGGTCTA 60.338 44.000 14.67 12.54 0.00 2.59
910 930 5.245531 TGGTACATGCCTATTTATAGCTGC 58.754 41.667 0.00 0.00 0.00 5.25
940 960 2.573462 TCTGAAGGTTGATGAAGGAGGG 59.427 50.000 0.00 0.00 0.00 4.30
987 1007 1.131638 CCTTCATGGTGGCTAGCCTA 58.868 55.000 33.07 19.96 36.94 3.93
1098 1121 1.379977 TTGTTGCCCCGGTTGTTGA 60.380 52.632 0.00 0.00 0.00 3.18
1196 1222 0.391661 GCTAAGCTGCTGCACCTGTA 60.392 55.000 18.42 1.32 42.74 2.74
1228 1254 1.411246 CTGGCAGCATTGGTATTGCAT 59.589 47.619 0.00 0.00 42.62 3.96
1257 1283 1.742768 GATTCGCTCCGGGATCTGT 59.257 57.895 0.00 0.00 0.00 3.41
1266 1292 3.757248 ATGGCACCGGATTCGCTCC 62.757 63.158 9.46 0.00 41.07 4.70
1374 1400 3.515602 AGGTTCTCAAGCAACATCCTT 57.484 42.857 0.00 0.00 0.00 3.36
1447 1473 0.976641 TGTTGTTGTTGTTGGCCCAA 59.023 45.000 0.00 0.00 0.00 4.12
1452 1478 6.355397 TGCAATTATTGTTGTTGTTGTTGG 57.645 33.333 6.81 0.00 0.00 3.77
1518 1547 0.968901 ATGGCACTGTCATTGGGCTG 60.969 55.000 0.00 0.00 0.00 4.85
1550 1579 1.626356 GCTGGTAGGCTGATCCACCA 61.626 60.000 5.98 5.98 40.97 4.17
1584 1613 2.520500 TGCCGGCAACATTGGTGT 60.521 55.556 30.74 0.00 41.28 4.16
1603 1632 4.908601 ATTGCTCCGGGATATGTGATAA 57.091 40.909 0.00 0.00 0.00 1.75
1673 1702 0.318120 CTGCCATTGTTGTTGGGGTC 59.682 55.000 0.00 0.00 34.66 4.46
1734 1763 1.817099 GGCCTGAAGCGACATCCTG 60.817 63.158 0.00 0.00 45.17 3.86
1834 1869 0.606604 AACTAGTACGCACCACCAGG 59.393 55.000 0.00 0.00 42.21 4.45
1847 1882 4.433615 CACCGCTACATTGATCAACTAGT 58.566 43.478 11.07 12.14 0.00 2.57
2030 2067 5.308237 GGTCCTATGGGAGACATACAGAATT 59.692 44.000 0.00 0.00 43.12 2.17
2049 2086 3.713248 TCATGCTATGAACTGATGGTCCT 59.287 43.478 0.00 0.00 36.11 3.85
2050 2087 4.077300 TCATGCTATGAACTGATGGTCC 57.923 45.455 0.00 0.00 36.11 4.46
2077 2114 5.971895 TTTTCTTCGTGTGTACCAACTAC 57.028 39.130 0.00 0.00 0.00 2.73
2078 2115 7.169645 GTGTATTTTCTTCGTGTGTACCAACTA 59.830 37.037 0.00 0.00 0.00 2.24
2153 2194 7.385267 ACTGAGCAAAATATTTGTTTATGCCA 58.615 30.769 15.04 12.28 31.51 4.92
2167 2208 8.806146 AGGTTTATCATGTTTACTGAGCAAAAT 58.194 29.630 0.00 0.00 0.00 1.82
2169 2210 7.446931 TGAGGTTTATCATGTTTACTGAGCAAA 59.553 33.333 0.00 0.00 0.00 3.68
2206 2247 0.673644 AAGCGATGGTTCAGTTCGGG 60.674 55.000 0.00 0.00 33.62 5.14
2222 2263 3.492102 TGGGCTCCATACAATCTAAGC 57.508 47.619 0.00 0.00 0.00 3.09
2230 2271 3.949586 TGATTTGATGGGCTCCATACA 57.050 42.857 6.69 5.00 45.26 2.29
2300 2341 0.537653 TGTGTGTTCGTTCACCAGGA 59.462 50.000 0.00 0.00 37.51 3.86
2310 2351 2.354510 ACATGTTCTGGTTGTGTGTTCG 59.645 45.455 0.00 0.00 0.00 3.95
2350 2391 1.798813 AGACGCGTTTCAAATCCTGTC 59.201 47.619 15.53 0.00 0.00 3.51
2353 2394 1.535462 CCAAGACGCGTTTCAAATCCT 59.465 47.619 15.53 0.00 0.00 3.24
2439 2480 3.121944 CGTCGCAATAACTATGGCTCATC 59.878 47.826 0.00 0.00 30.28 2.92
2440 2481 3.059884 CGTCGCAATAACTATGGCTCAT 58.940 45.455 0.00 0.00 30.28 2.90


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

AutoCloner maintained by Alex Coulton.