Multiple sequence alignment - TraesCS5B01G249600

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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 TraesCS5B01G249600 chr5B 100.000 3779 0 0 1 3779 432150946 432154724 0.000000e+00 6979
1 TraesCS5B01G249600 chr5A 95.033 3382 133 11 1 3370 467374096 467377454 0.000000e+00 5282
2 TraesCS5B01G249600 chr5A 97.101 414 10 2 3368 3779 467377557 467377970 0.000000e+00 697
3 TraesCS5B01G249600 chr5D 95.937 3126 110 12 249 3370 365690193 365693305 0.000000e+00 5053
4 TraesCS5B01G249600 chr5D 97.349 415 8 2 3368 3779 365693408 365693822 0.000000e+00 702
5 TraesCS5B01G249600 chr5D 95.294 255 8 1 1 255 365688857 365689107 5.880000e-108 401


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 TraesCS5B01G249600 chr5B 432150946 432154724 3778 False 6979.0 6979 100.000000 1 3779 1 chr5B.!!$F1 3778
1 TraesCS5B01G249600 chr5A 467374096 467377970 3874 False 2989.5 5282 96.067000 1 3779 2 chr5A.!!$F1 3778
2 TraesCS5B01G249600 chr5D 365688857 365693822 4965 False 2052.0 5053 96.193333 1 3779 3 chr5D.!!$F1 3778

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
978 2091 0.178891 AGTGGAAAGGGAGGAGCTGA 60.179 55.0 0.00 0.00 0.0 4.26 F
1630 2743 0.108186 CAAGGCGTACATGGAGCTCA 60.108 55.0 17.19 1.87 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 3537 0.035439 CGTGAAGTAAGGCACCCCAT 60.035 55.0 0.00 0.0 0.00 4.00 R
2941 4054 0.172578 CAGCGGATCTCGTGTAACCA 59.827 55.0 5.66 0.0 41.72 3.67 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
126 128 3.031660 GTGGATCACGTCGTCTTCC 57.968 57.895 13.75 13.75 0.00 3.46
176 178 1.359130 AGTACCTAACCTACCCACCGT 59.641 52.381 0.00 0.00 0.00 4.83
184 190 1.255667 CCTACCCACCGTGCTGTAGT 61.256 60.000 18.00 4.59 30.98 2.73
284 1383 0.323908 AGAGAGGACGAGGGACAAGG 60.324 60.000 0.00 0.00 0.00 3.61
288 1387 2.047179 GACGAGGGACAAGGTGGC 60.047 66.667 0.00 0.00 0.00 5.01
294 1393 2.936032 GGACAAGGTGGCCCTCCT 60.936 66.667 10.37 10.37 40.64 3.69
351 1451 2.401766 GCCCGTGCAACTGATGAGG 61.402 63.158 0.00 0.00 37.47 3.86
412 1514 1.909302 CCGGCCCATATCTATCCTTGT 59.091 52.381 0.00 0.00 0.00 3.16
450 1552 0.672401 TCGTCCCCACAAATTCTCGC 60.672 55.000 0.00 0.00 0.00 5.03
475 1577 1.973281 CACTGTCATGTGGGCCACC 60.973 63.158 32.61 18.08 34.56 4.61
516 1619 1.982395 GCTGTTGGGTAAAGGGCCC 60.982 63.158 16.46 16.46 46.26 5.80
763 1866 3.188786 CTCGCTGCAAGGTACCGC 61.189 66.667 6.18 5.47 0.00 5.68
764 1867 3.932580 CTCGCTGCAAGGTACCGCA 62.933 63.158 13.09 13.09 35.88 5.69
765 1868 3.047280 CGCTGCAAGGTACCGCAA 61.047 61.111 14.40 0.00 36.82 4.85
766 1869 2.398554 CGCTGCAAGGTACCGCAAT 61.399 57.895 14.40 0.00 36.82 3.56
767 1870 1.883021 GCTGCAAGGTACCGCAATT 59.117 52.632 14.40 0.00 36.82 2.32
768 1871 0.179163 GCTGCAAGGTACCGCAATTC 60.179 55.000 14.40 4.80 36.82 2.17
769 1872 0.451783 CTGCAAGGTACCGCAATTCC 59.548 55.000 14.40 0.00 36.82 3.01
770 1873 1.302383 TGCAAGGTACCGCAATTCCG 61.302 55.000 11.58 0.00 34.23 4.30
771 1874 1.427819 CAAGGTACCGCAATTCCGC 59.572 57.895 6.18 0.00 0.00 5.54
772 1875 1.024579 CAAGGTACCGCAATTCCGCT 61.025 55.000 6.18 0.00 0.00 5.52
792 1905 2.614057 CTCAATTCCGCTGTAATCCACC 59.386 50.000 0.00 0.00 0.00 4.61
851 1964 4.018779 AGGTTTCTCCATCCCGATTGTTTA 60.019 41.667 0.00 0.00 39.02 2.01
861 1974 6.350110 CCATCCCGATTGTTTATGTTTCTGTT 60.350 38.462 0.00 0.00 0.00 3.16
926 2039 2.811431 TCATTTTTGTACTCACAGCGGG 59.189 45.455 0.00 0.00 35.67 6.13
940 2053 3.047877 CGGGGGCAGTGTTCGTTC 61.048 66.667 0.00 0.00 0.00 3.95
941 2054 3.047877 GGGGGCAGTGTTCGTTCG 61.048 66.667 0.00 0.00 0.00 3.95
942 2055 2.280592 GGGGCAGTGTTCGTTCGT 60.281 61.111 0.00 0.00 0.00 3.85
954 2067 1.171308 TCGTTCGTGTAGAGGGAAGG 58.829 55.000 0.00 0.00 0.00 3.46
955 2068 0.886563 CGTTCGTGTAGAGGGAAGGT 59.113 55.000 0.00 0.00 0.00 3.50
978 2091 0.178891 AGTGGAAAGGGAGGAGCTGA 60.179 55.000 0.00 0.00 0.00 4.26
1105 2218 3.730761 CGCTTGCGCTCCTGCTTT 61.731 61.111 9.73 0.00 36.97 3.51
1176 2289 2.029073 CACCTGCTCGACCACGTT 59.971 61.111 0.00 0.00 40.69 3.99
1252 2365 2.829003 TGACCTCCCTAGCGCTCG 60.829 66.667 16.34 7.87 0.00 5.03
1523 2636 2.463589 ATCTCCGGGCTCGTGCAAAA 62.464 55.000 4.71 0.00 41.91 2.44
1525 2638 1.982073 CTCCGGGCTCGTGCAAAATC 61.982 60.000 4.71 0.00 41.91 2.17
1526 2639 2.331893 CCGGGCTCGTGCAAAATCA 61.332 57.895 4.71 0.00 41.91 2.57
1530 2643 0.593128 GGCTCGTGCAAAATCACAGT 59.407 50.000 12.07 0.00 41.91 3.55
1537 2650 1.962807 TGCAAAATCACAGTCCCTTGG 59.037 47.619 0.00 0.00 0.00 3.61
1630 2743 0.108186 CAAGGCGTACATGGAGCTCA 60.108 55.000 17.19 1.87 0.00 4.26
1989 3102 1.405872 TGGAGGATTATGTACGCCGT 58.594 50.000 0.00 0.00 0.00 5.68
2040 3153 4.002982 ACACAGCGTTGATTGACATGTAT 58.997 39.130 6.16 0.00 0.00 2.29
2093 3206 2.802816 GAGTCTTTGAACAGATGCGTGT 59.197 45.455 0.00 0.00 0.00 4.49
2169 3282 0.179009 GCCATCTTGCTGAGGCCATA 60.179 55.000 5.01 0.00 41.25 2.74
2325 3438 3.371097 GATCGAGCCTCGGCACCAA 62.371 63.158 15.08 0.00 44.88 3.67
2409 3522 7.468494 CGATTTATACTTGACATGCCCATCAAA 60.468 37.037 0.00 0.00 34.52 2.69
2424 3537 4.080919 CCCATCAAACCAGAGATGAGTGTA 60.081 45.833 4.12 0.00 43.28 2.90
2631 3744 0.755327 GGGGTGTCACCAAAGCAACT 60.755 55.000 23.48 0.00 41.02 3.16
2870 3983 7.142680 CAGCATTAATTGTGTCATGCATATCA 58.857 34.615 0.00 0.00 43.81 2.15
2941 4054 9.705290 GACCATCAAAATAAACAAAACATACCT 57.295 29.630 0.00 0.00 0.00 3.08
3002 4115 4.821260 GGGTTGATGATTTTTGCAAACCTT 59.179 37.500 12.39 0.00 43.15 3.50
3062 4176 1.626356 TAGCTGTGAGGGTGGATGCC 61.626 60.000 0.00 0.00 0.00 4.40
3205 4319 8.553459 AACTCCTGTAGTTTGTTCATAAGATG 57.447 34.615 0.00 0.00 46.61 2.90
3259 4373 9.944376 TGTTCCATGGTAATTAGATATCTAAGC 57.056 33.333 25.30 18.24 41.24 3.09
3297 4411 7.857569 TGTGTTGGAGAAATTTTAGTTAGTCG 58.142 34.615 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 110 0.458025 GGGAAGACGACGTGATCCAC 60.458 60.000 22.99 12.93 31.63 4.02
126 128 1.908793 ACTGACGTGGTGAGAGGGG 60.909 63.158 0.00 0.00 0.00 4.79
176 178 1.448365 CATGCCAGCGACTACAGCA 60.448 57.895 0.00 0.00 37.94 4.41
184 190 4.002506 ACGGACACATGCCAGCGA 62.003 61.111 0.00 0.00 0.00 4.93
257 1356 1.096416 CTCGTCCTCTCTGTGGTACC 58.904 60.000 4.43 4.43 0.00 3.34
259 1358 0.034380 CCCTCGTCCTCTCTGTGGTA 60.034 60.000 0.00 0.00 0.00 3.25
262 1361 0.609406 TGTCCCTCGTCCTCTCTGTG 60.609 60.000 0.00 0.00 0.00 3.66
269 1368 1.913762 CCACCTTGTCCCTCGTCCT 60.914 63.158 0.00 0.00 0.00 3.85
272 1371 3.637273 GGCCACCTTGTCCCTCGT 61.637 66.667 0.00 0.00 0.00 4.18
284 1383 2.282462 CCACACAAGGAGGGCCAC 60.282 66.667 6.18 0.00 36.29 5.01
288 1387 4.722700 CGGCCCACACAAGGAGGG 62.723 72.222 0.00 0.00 45.68 4.30
294 1393 1.000270 ATTATGCCGGCCCACACAA 60.000 52.632 26.77 2.60 0.00 3.33
351 1451 1.376553 GGGTGAGCAGGACAAGAGC 60.377 63.158 0.00 0.00 0.00 4.09
424 1526 4.595538 TGTGGGGACGACGTGTGC 62.596 66.667 4.58 0.00 38.37 4.57
450 1552 2.032528 ACATGACAGTGGGCACGG 59.967 61.111 0.00 0.00 36.20 4.94
462 1564 1.133199 AGAAAAAGGTGGCCCACATGA 60.133 47.619 17.22 0.00 35.86 3.07
464 1566 1.341080 CAGAAAAAGGTGGCCCACAT 58.659 50.000 17.22 5.46 35.86 3.21
516 1619 0.531200 ACTCCTTTAGCTCGTTCCCG 59.469 55.000 0.00 0.00 0.00 5.14
763 1866 0.734889 AGCGGAATTGAGCGGAATTG 59.265 50.000 1.21 0.00 38.61 2.32
764 1867 0.734889 CAGCGGAATTGAGCGGAATT 59.265 50.000 0.00 0.00 38.61 2.17
765 1868 0.392998 ACAGCGGAATTGAGCGGAAT 60.393 50.000 8.43 0.00 38.61 3.01
766 1869 0.248012 TACAGCGGAATTGAGCGGAA 59.752 50.000 8.43 0.00 38.61 4.30
767 1870 0.248012 TTACAGCGGAATTGAGCGGA 59.752 50.000 8.43 0.00 38.61 5.54
768 1871 1.261619 GATTACAGCGGAATTGAGCGG 59.738 52.381 0.00 0.00 38.61 5.52
769 1872 1.261619 GGATTACAGCGGAATTGAGCG 59.738 52.381 0.00 0.00 38.61 5.03
770 1873 2.032178 GTGGATTACAGCGGAATTGAGC 59.968 50.000 0.00 0.00 0.00 4.26
771 1874 2.614057 GGTGGATTACAGCGGAATTGAG 59.386 50.000 0.00 0.00 37.90 3.02
772 1875 2.639065 GGTGGATTACAGCGGAATTGA 58.361 47.619 0.00 0.00 37.90 2.57
831 1944 5.505780 ACATAAACAATCGGGATGGAGAAA 58.494 37.500 0.00 0.00 0.00 2.52
870 1983 5.560966 AGCAAAAACGAAACAGAAGAAGA 57.439 34.783 0.00 0.00 0.00 2.87
926 2039 0.598158 TACACGAACGAACACTGCCC 60.598 55.000 0.14 0.00 0.00 5.36
939 2052 3.009916 ACTCTAACCTTCCCTCTACACGA 59.990 47.826 0.00 0.00 0.00 4.35
940 2053 3.128938 CACTCTAACCTTCCCTCTACACG 59.871 52.174 0.00 0.00 0.00 4.49
941 2054 3.447944 CCACTCTAACCTTCCCTCTACAC 59.552 52.174 0.00 0.00 0.00 2.90
942 2055 3.335786 TCCACTCTAACCTTCCCTCTACA 59.664 47.826 0.00 0.00 0.00 2.74
954 2067 2.093394 GCTCCTCCCTTTCCACTCTAAC 60.093 54.545 0.00 0.00 0.00 2.34
955 2068 2.188817 GCTCCTCCCTTTCCACTCTAA 58.811 52.381 0.00 0.00 0.00 2.10
1227 2340 3.375443 TAGGGAGGTCAGGCGGAGG 62.375 68.421 0.00 0.00 0.00 4.30
1252 2365 2.787567 GGAGAGCGAGGTAGTGGCC 61.788 68.421 0.00 0.00 0.00 5.36
1356 2469 3.467043 GTCAGTGAGACGTAACGCA 57.533 52.632 0.00 0.00 37.53 5.24
1446 2559 0.669318 GCATTCCCTCGAACACACGA 60.669 55.000 0.00 0.00 40.00 4.35
1523 2636 0.036010 CGCTTCCAAGGGACTGTGAT 60.036 55.000 0.00 0.00 40.86 3.06
1525 2638 0.535102 AACGCTTCCAAGGGACTGTG 60.535 55.000 10.15 0.00 40.86 3.66
1526 2639 1.053424 TAACGCTTCCAAGGGACTGT 58.947 50.000 10.15 0.00 40.86 3.55
1530 2643 1.294138 CCGTAACGCTTCCAAGGGA 59.706 57.895 10.15 0.00 41.06 4.20
1537 2650 0.724785 GCAAACAGCCGTAACGCTTC 60.725 55.000 0.00 0.00 36.82 3.86
1788 2901 2.360165 GGCATTCCACAGGATCACATTC 59.640 50.000 0.00 0.00 0.00 2.67
1855 2968 4.081406 ACCTGCATCTGCTTGAACAAATA 58.919 39.130 3.53 0.00 42.66 1.40
1959 3072 2.847327 AATCCTCCATCCATACTGCG 57.153 50.000 0.00 0.00 0.00 5.18
1989 3102 1.273267 ACATCCTCCCTGCACTCACTA 60.273 52.381 0.00 0.00 0.00 2.74
2040 3153 0.609957 CAATGCTCCCTGACTTGGCA 60.610 55.000 0.00 0.00 37.32 4.92
2093 3206 1.621672 TACCACATCCCGCTCATGCA 61.622 55.000 0.00 0.00 39.64 3.96
2169 3282 1.067295 TCATGTCCTCAAACAGGCCT 58.933 50.000 0.00 0.00 43.08 5.19
2409 3522 2.293184 ACCCCATACACTCATCTCTGGT 60.293 50.000 0.00 0.00 0.00 4.00
2424 3537 0.035439 CGTGAAGTAAGGCACCCCAT 60.035 55.000 0.00 0.00 0.00 4.00
2706 3819 3.262420 GCAGAGTAAGGCGAAAATCTCA 58.738 45.455 0.00 0.00 0.00 3.27
2870 3983 2.099592 CGCAATTGCATTGTAGGGACAT 59.900 45.455 28.77 0.00 42.20 3.06
2900 4013 1.067416 GGTCACAGTGCTCACGACA 59.933 57.895 0.00 0.00 36.20 4.35
2941 4054 0.172578 CAGCGGATCTCGTGTAACCA 59.827 55.000 5.66 0.00 41.72 3.67
3027 4141 7.254590 CCTCACAGCTAATTCTGCTACATAAAC 60.255 40.741 5.69 0.00 38.92 2.01
3041 4155 1.133976 GCATCCACCCTCACAGCTAAT 60.134 52.381 0.00 0.00 0.00 1.73
3205 4319 7.141363 GCCAATACAATACTGATGGATTGTTC 58.859 38.462 11.24 0.01 44.26 3.18
3259 4373 3.213506 TCCAACACAATTGAGGTCACAG 58.786 45.455 13.59 0.00 0.00 3.66
3536 4758 6.394025 AAGCTCCTTCTAATAAGTACTCCG 57.606 41.667 0.00 0.00 0.00 4.63
3573 4796 1.879380 CCGCTCACAAATGGTCTTGAA 59.121 47.619 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.