Multiple sequence alignment - TraesCS4A01G460200

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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 TraesCS4A01G460200 chr4A 100.000 2208 0 0 435 2642 725752720 725750513 0.000000e+00 4078.0
1 TraesCS4A01G460200 chr4A 91.925 805 47 9 1693 2489 725799652 725798858 0.000000e+00 1110.0
2 TraesCS4A01G460200 chr4A 91.331 646 53 3 2000 2642 734768396 734769041 0.000000e+00 880.0
3 TraesCS4A01G460200 chr4A 94.762 210 10 1 1487 1696 725800164 725799956 2.540000e-85 326.0
4 TraesCS4A01G460200 chr4A 95.181 166 7 1 2477 2642 725795671 725795507 7.250000e-66 261.0
5 TraesCS4A01G460200 chr4A 100.000 43 0 0 435 477 725800202 725800160 2.180000e-11 80.5
6 TraesCS4A01G460200 chr4A 100.000 32 0 0 1 32 725753154 725753123 2.840000e-05 60.2
7 TraesCS4A01G460200 chr7A 89.288 1531 100 27 440 1946 11998797 12000287 0.000000e+00 1860.0
8 TraesCS4A01G460200 chr7D 90.762 1418 80 22 440 1829 12388127 12389521 0.000000e+00 1845.0
9 TraesCS4A01G460200 chr6B 89.545 593 49 7 2000 2582 198223469 198224058 0.000000e+00 739.0
10 TraesCS4A01G460200 chr6B 98.438 64 1 0 2579 2642 198224138 198224201 2.150000e-21 113.0
11 TraesCS4A01G460200 chr1A 85.714 77 8 3 2545 2621 19139496 19139569 7.840000e-11 78.7
12 TraesCS4A01G460200 chr6A 96.774 31 1 0 725 755 410872708 410872738 5.000000e-03 52.8


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 TraesCS4A01G460200 chr4A 725750513 725753154 2641 True 2069.100 4078 100.0000 1 2642 2 chr4A.!!$R1 2641
1 TraesCS4A01G460200 chr4A 734768396 734769041 645 False 880.000 880 91.3310 2000 2642 1 chr4A.!!$F1 642
2 TraesCS4A01G460200 chr4A 725795507 725800202 4695 True 444.375 1110 95.4670 435 2642 4 chr4A.!!$R2 2207
3 TraesCS4A01G460200 chr7A 11998797 12000287 1490 False 1860.000 1860 89.2880 440 1946 1 chr7A.!!$F1 1506
4 TraesCS4A01G460200 chr7D 12388127 12389521 1394 False 1845.000 1845 90.7620 440 1829 1 chr7D.!!$F1 1389
5 TraesCS4A01G460200 chr6B 198223469 198224201 732 False 426.000 739 93.9915 2000 2642 2 chr6B.!!$F1 642

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
31 32 0.037734 CAACACTTCACCCTACCCCC 59.962 60.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 2127 0.467384 ATGAAGAGGTGATCCAGGCG 59.533 55.0 0.0 0.0 35.89 5.52 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
23 24 6.049263 CTCTAAACAAGACAACACTTCACC 57.951 41.667 0.00 0.00 0.00 4.02
24 25 4.879545 TCTAAACAAGACAACACTTCACCC 59.120 41.667 0.00 0.00 0.00 4.61
25 26 3.366052 AACAAGACAACACTTCACCCT 57.634 42.857 0.00 0.00 0.00 4.34
26 27 4.497291 AACAAGACAACACTTCACCCTA 57.503 40.909 0.00 0.00 0.00 3.53
27 28 3.805207 ACAAGACAACACTTCACCCTAC 58.195 45.455 0.00 0.00 0.00 3.18
28 29 3.139077 CAAGACAACACTTCACCCTACC 58.861 50.000 0.00 0.00 0.00 3.18
29 30 1.697982 AGACAACACTTCACCCTACCC 59.302 52.381 0.00 0.00 0.00 3.69
30 31 0.769247 ACAACACTTCACCCTACCCC 59.231 55.000 0.00 0.00 0.00 4.95
31 32 0.037734 CAACACTTCACCCTACCCCC 59.962 60.000 0.00 0.00 0.00 5.40
490 491 4.458397 AGTTAAGACCATCTGCATCCATG 58.542 43.478 0.00 0.00 0.00 3.66
503 505 9.752961 CATCTGCATCCATGAATTTTATTACAA 57.247 29.630 0.00 0.00 0.00 2.41
596 599 7.192913 TGTTTTACAGTTTTAGCTGACACATG 58.807 34.615 0.00 0.00 39.62 3.21
665 668 2.254546 ATTATTTGCGCCCATCTCGA 57.745 45.000 4.18 0.00 0.00 4.04
795 812 2.676176 CGATCCATGCAGAAGACACACT 60.676 50.000 0.00 0.00 0.00 3.55
796 813 2.174363 TCCATGCAGAAGACACACTG 57.826 50.000 0.00 0.00 37.22 3.66
797 814 1.693606 TCCATGCAGAAGACACACTGA 59.306 47.619 0.00 0.00 36.38 3.41
798 815 2.303890 TCCATGCAGAAGACACACTGAT 59.696 45.455 0.00 0.00 36.38 2.90
799 816 3.079578 CCATGCAGAAGACACACTGATT 58.920 45.455 0.00 0.00 36.38 2.57
800 817 4.020307 TCCATGCAGAAGACACACTGATTA 60.020 41.667 0.00 0.00 36.38 1.75
834 851 5.833131 ACAATTGTAAGTGAATCCAACCTGT 59.167 36.000 9.97 0.00 0.00 4.00
845 862 6.710295 GTGAATCCAACCTGTACATATATGCA 59.290 38.462 12.79 3.00 0.00 3.96
873 890 7.658575 ACAATGGGCATTAATCAATAGCATTTC 59.341 33.333 0.00 0.00 0.00 2.17
876 893 5.163513 GGCATTAATCAATAGCATTTCCGG 58.836 41.667 0.00 0.00 0.00 5.14
878 895 5.713025 CATTAATCAATAGCATTTCCGGGG 58.287 41.667 0.00 0.00 0.00 5.73
891 908 2.943036 TCCGGGGCCAAGATAATTAC 57.057 50.000 4.39 0.00 0.00 1.89
933 951 9.809096 CGATGCACTATATATAAATCTCAACCT 57.191 33.333 0.00 0.00 0.00 3.50
996 1014 6.112734 TGTCCAAATTGTATATTCTCGCTGT 58.887 36.000 0.00 0.00 0.00 4.40
1042 1060 0.703488 TTCCATGGCCATCTCAACCA 59.297 50.000 17.61 0.00 37.99 3.67
1047 1065 0.327924 TGGCCATCTCAACCATCGTT 59.672 50.000 0.00 0.00 0.00 3.85
1120 1141 1.507141 GGACAACACAAGCCTCGTGG 61.507 60.000 0.00 0.00 38.74 4.94
1251 1272 1.639298 GCGACCTTGCACTCATCACC 61.639 60.000 0.00 0.00 34.15 4.02
1312 1333 1.210155 GTGGACAACATGCTTCGCC 59.790 57.895 0.00 0.00 0.00 5.54
1342 1363 2.135933 GAATCGCCACGAAGGATAAGG 58.864 52.381 2.86 0.00 39.99 2.69
1398 1419 2.983030 GGCGGCATGGTGAACACA 60.983 61.111 3.07 0.00 0.00 3.72
1432 1453 3.559811 CCACAACATCATCCAGGACTTCA 60.560 47.826 0.00 0.00 0.00 3.02
1480 1501 3.363787 TCTGAGCTACCAGAGTGCA 57.636 52.632 1.08 0.00 38.18 4.57
1493 1514 3.320626 CAGAGTGCATTGAGAAGACGAA 58.679 45.455 0.00 0.00 0.00 3.85
1495 1516 2.413453 GAGTGCATTGAGAAGACGAACC 59.587 50.000 0.00 0.00 0.00 3.62
1599 1626 0.890542 TGGCAATCGTCAGCAAAGCT 60.891 50.000 0.00 0.00 40.77 3.74
1620 1647 6.186234 AGCTTTGATAAATCTCTTCTTGGCT 58.814 36.000 0.00 0.00 0.00 4.75
1670 1697 9.307121 GCTATCTATAATTAGCATCGTGTGATT 57.693 33.333 8.15 0.00 40.42 2.57
1771 2110 0.324460 CTCTCCACCTCCTACCCGTT 60.324 60.000 0.00 0.00 0.00 4.44
1788 2127 0.458370 GTTCGATTTGGGCATGCACC 60.458 55.000 19.33 17.30 0.00 5.01
1829 2169 2.836981 CCATCCCTGCCCAATTTTTACA 59.163 45.455 0.00 0.00 0.00 2.41
1898 2240 0.320374 TCGCCGATTTCCTGTGAAGT 59.680 50.000 0.00 0.00 0.00 3.01
1900 2242 1.808411 GCCGATTTCCTGTGAAGTGA 58.192 50.000 0.00 0.00 0.00 3.41
1917 2259 1.053835 TGAGCCAACCACACTCTGGA 61.054 55.000 0.00 0.00 43.95 3.86
1918 2260 0.108585 GAGCCAACCACACTCTGGAA 59.891 55.000 0.00 0.00 43.95 3.53
1946 2288 0.949105 CTACGTTCGCAAACCCAGCT 60.949 55.000 0.00 0.00 31.27 4.24
1947 2289 0.947180 TACGTTCGCAAACCCAGCTC 60.947 55.000 0.00 0.00 31.27 4.09
2221 2567 8.852135 CACTTACAAATTACCAAGTAGGGAAAA 58.148 33.333 0.00 0.00 45.57 2.29
2241 2587 7.361799 GGGAAAAGTTTCTTCATATAACGCACT 60.362 37.037 3.92 0.00 37.35 4.40
2391 2737 7.811236 TGTAGAACACGTCATTCCTAGTTAAAG 59.189 37.037 5.63 0.00 0.00 1.85
2433 2784 7.977789 TTTGTCAAATAGAGTACATGCAGAA 57.022 32.000 0.00 0.00 0.00 3.02
2491 6042 1.003839 CGTCCCTTACAGCTGCCAA 60.004 57.895 15.27 7.43 0.00 4.52
2500 6051 1.376942 CAGCTGCCAACAGGAGAGG 60.377 63.158 0.00 0.00 44.63 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.007724 GGGTGAAGTGTTGTCTTGTTTAGAG 59.992 44.000 0.00 0.00 32.23 2.43
1 2 4.879545 GGGTGAAGTGTTGTCTTGTTTAGA 59.120 41.667 0.00 0.00 0.00 2.10
2 3 4.881850 AGGGTGAAGTGTTGTCTTGTTTAG 59.118 41.667 0.00 0.00 0.00 1.85
4 5 3.697166 AGGGTGAAGTGTTGTCTTGTTT 58.303 40.909 0.00 0.00 0.00 2.83
5 6 3.366052 AGGGTGAAGTGTTGTCTTGTT 57.634 42.857 0.00 0.00 0.00 2.83
6 7 3.433173 GGTAGGGTGAAGTGTTGTCTTGT 60.433 47.826 0.00 0.00 0.00 3.16
7 8 3.139077 GGTAGGGTGAAGTGTTGTCTTG 58.861 50.000 0.00 0.00 0.00 3.02
8 9 2.105993 GGGTAGGGTGAAGTGTTGTCTT 59.894 50.000 0.00 0.00 0.00 3.01
9 10 1.697982 GGGTAGGGTGAAGTGTTGTCT 59.302 52.381 0.00 0.00 0.00 3.41
10 11 1.271217 GGGGTAGGGTGAAGTGTTGTC 60.271 57.143 0.00 0.00 0.00 3.18
11 12 0.769247 GGGGTAGGGTGAAGTGTTGT 59.231 55.000 0.00 0.00 0.00 3.32
12 13 0.037734 GGGGGTAGGGTGAAGTGTTG 59.962 60.000 0.00 0.00 0.00 3.33
13 14 2.471462 GGGGGTAGGGTGAAGTGTT 58.529 57.895 0.00 0.00 0.00 3.32
14 15 4.245333 GGGGGTAGGGTGAAGTGT 57.755 61.111 0.00 0.00 0.00 3.55
474 475 4.931661 AAATTCATGGATGCAGATGGTC 57.068 40.909 0.00 0.00 0.00 4.02
546 548 7.897575 TGCTGTCAAAGTTTTATTTGTTTGT 57.102 28.000 0.00 0.00 40.36 2.83
555 557 8.247562 ACTGTAAAACATGCTGTCAAAGTTTTA 58.752 29.630 0.00 0.00 41.00 1.52
578 581 6.257411 CCTCTATCATGTGTCAGCTAAAACTG 59.743 42.308 0.00 0.00 39.12 3.16
579 582 6.344500 CCTCTATCATGTGTCAGCTAAAACT 58.656 40.000 0.00 0.00 0.00 2.66
580 583 5.007136 GCCTCTATCATGTGTCAGCTAAAAC 59.993 44.000 0.00 0.00 0.00 2.43
581 584 5.118990 GCCTCTATCATGTGTCAGCTAAAA 58.881 41.667 0.00 0.00 0.00 1.52
582 585 4.162131 TGCCTCTATCATGTGTCAGCTAAA 59.838 41.667 0.00 0.00 0.00 1.85
583 586 3.706086 TGCCTCTATCATGTGTCAGCTAA 59.294 43.478 0.00 0.00 0.00 3.09
584 587 3.299503 TGCCTCTATCATGTGTCAGCTA 58.700 45.455 0.00 0.00 0.00 3.32
585 588 2.113807 TGCCTCTATCATGTGTCAGCT 58.886 47.619 0.00 0.00 0.00 4.24
586 589 2.609427 TGCCTCTATCATGTGTCAGC 57.391 50.000 0.00 0.00 0.00 4.26
587 590 4.134379 ACTTGCCTCTATCATGTGTCAG 57.866 45.455 0.00 0.00 0.00 3.51
596 599 2.555199 ACGCATGAACTTGCCTCTATC 58.445 47.619 0.00 0.00 39.52 2.08
618 621 5.319140 AGGTTACAATATTTTTCCGGTGC 57.681 39.130 0.00 0.00 0.00 5.01
645 648 2.571212 TCGAGATGGGCGCAAATAATT 58.429 42.857 10.83 0.00 0.00 1.40
682 699 4.789012 AATCAGGTTACCAAATGTGCAG 57.211 40.909 3.51 0.00 0.00 4.41
749 766 9.734620 CGATTTCCAATAAAATAAAGAGCATCA 57.265 29.630 0.00 0.00 37.82 3.07
834 851 9.692325 TTAATGCCCATTGTATGCATATATGTA 57.308 29.630 21.00 10.24 44.49 2.29
845 862 7.779754 TGCTATTGATTAATGCCCATTGTAT 57.220 32.000 3.85 0.00 32.50 2.29
873 890 2.649531 TGTAATTATCTTGGCCCCGG 57.350 50.000 0.00 0.00 0.00 5.73
876 893 6.868339 GTGCATAAATGTAATTATCTTGGCCC 59.132 38.462 0.00 0.00 33.67 5.80
878 895 7.432869 TGGTGCATAAATGTAATTATCTTGGC 58.567 34.615 0.00 0.00 33.67 4.52
891 908 5.299582 TGCATCGATATGGTGCATAAATG 57.700 39.130 6.54 0.00 43.30 2.32
906 923 9.803315 GGTTGAGATTTATATATAGTGCATCGA 57.197 33.333 0.00 0.00 0.00 3.59
933 951 3.371965 GAGATGGTTGGAGGTGTAGGTA 58.628 50.000 0.00 0.00 0.00 3.08
938 956 1.280457 GAGGAGATGGTTGGAGGTGT 58.720 55.000 0.00 0.00 0.00 4.16
1042 1060 3.340814 AGAAAGGAGCATGACAACGAT 57.659 42.857 0.00 0.00 0.00 3.73
1047 1065 2.430465 GCAGAAGAAAGGAGCATGACA 58.570 47.619 0.00 0.00 0.00 3.58
1120 1141 1.237285 ATGTTCTTGCACGCCTCCAC 61.237 55.000 0.00 0.00 0.00 4.02
1251 1272 1.269166 GCACCTTGAGTATGTCGACG 58.731 55.000 11.62 0.00 0.00 5.12
1342 1363 2.202810 GAGGGCACGAGCTGCTAC 60.203 66.667 0.15 0.00 46.25 3.58
1398 1419 2.363306 TGTTGTGGCAGATTTGGAGT 57.637 45.000 0.00 0.00 0.00 3.85
1432 1453 1.315257 CCATGCTTACCTTTGCGGCT 61.315 55.000 0.00 0.00 35.61 5.52
1464 1485 1.901833 TCAATGCACTCTGGTAGCTCA 59.098 47.619 0.00 0.00 0.00 4.26
1480 1501 3.804036 TGTTGTGGTTCGTCTTCTCAAT 58.196 40.909 0.00 0.00 0.00 2.57
1493 1514 1.133823 TGCAGTCCTTGATGTTGTGGT 60.134 47.619 0.00 0.00 0.00 4.16
1495 1516 2.031420 CAGTGCAGTCCTTGATGTTGTG 60.031 50.000 0.00 0.00 0.00 3.33
1541 1562 2.818169 GCCATAGCCATCGTCCCCA 61.818 63.158 0.00 0.00 0.00 4.96
1599 1626 5.126061 GCCAGCCAAGAAGAGATTTATCAAA 59.874 40.000 0.00 0.00 0.00 2.69
1620 1647 3.199946 CCTAGTTACCATCCTTCTTGCCA 59.800 47.826 0.00 0.00 0.00 4.92
1771 2110 2.405805 CGGTGCATGCCCAAATCGA 61.406 57.895 16.68 0.00 0.00 3.59
1788 2127 0.467384 ATGAAGAGGTGATCCAGGCG 59.533 55.000 0.00 0.00 35.89 5.52
1829 2169 0.745128 CGTCCGGTAGCTGTCTCTCT 60.745 60.000 0.00 0.00 0.00 3.10
1898 2240 1.451504 CCAGAGTGTGGTTGGCTCA 59.548 57.895 0.00 0.00 42.17 4.26
2024 2367 1.961793 TCCGTTCTTTGGTGACCAAG 58.038 50.000 17.50 11.65 44.84 3.61
2113 2458 6.073112 CCAAATAATTTTTGTGCCCACTCTTG 60.073 38.462 0.00 0.00 0.00 3.02
2191 2537 9.675464 CCCTACTTGGTAATTTGTAAGTGATTA 57.325 33.333 9.72 0.00 35.26 1.75
2221 2567 7.667043 TTTCAGTGCGTTATATGAAGAAACT 57.333 32.000 0.00 0.00 33.53 2.66
2256 2602 9.822185 ATGAAATTTGTAATTTCTAAGGATGGC 57.178 29.630 19.71 0.00 38.47 4.40
2324 2670 5.697178 TGTTTGTGCGCTCTACTAATTGTTA 59.303 36.000 9.73 0.00 0.00 2.41
2409 2755 7.977789 TTCTGCATGTACTCTATTTGACAAA 57.022 32.000 2.48 2.48 0.00 2.83
2433 2784 3.445805 CACCGCCCCAATTGTTACTTATT 59.554 43.478 4.43 0.00 0.00 1.40
2442 2793 2.470983 AAAAATCACCGCCCCAATTG 57.529 45.000 0.00 0.00 0.00 2.32
2491 6042 3.334054 GCCCCTTGCCTCTCCTGT 61.334 66.667 0.00 0.00 0.00 4.00
2500 6051 2.387757 TCCATTATCTTTGCCCCTTGC 58.612 47.619 0.00 0.00 41.77 4.01
2511 6062 6.786461 TCTTCTCATGGTCTCATCCATTATCT 59.214 38.462 0.00 0.00 44.75 1.98


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

AutoCloner maintained by Alex Coulton.