Multiple sequence alignment - TraesCS6B01G247100

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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 TraesCS6B01G247100 chr6B 100.000 3143 0 0 1 3143 439381230 439384372 0.000000e+00 5805
1 TraesCS6B01G247100 chr6B 98.349 969 16 0 2175 3143 118965879 118966847 0.000000e+00 1701
2 TraesCS6B01G247100 chr6A 96.639 2202 42 7 1 2182 397525960 397523771 0.000000e+00 3627
3 TraesCS6B01G247100 chr6D 94.688 1393 27 25 1 1367 277651904 277653275 0.000000e+00 2119
4 TraesCS6B01G247100 chr3A 94.928 966 42 1 2178 3143 594018897 594017939 0.000000e+00 1506
5 TraesCS6B01G247100 chr7A 96.174 758 29 0 2175 2932 232331192 232331949 0.000000e+00 1240
6 TraesCS6B01G247100 chr7A 76.660 497 106 10 2219 2710 384403920 384404411 1.860000e-67 267
7 TraesCS6B01G247100 chr7A 76.404 267 52 8 2828 3087 383173571 383173309 1.970000e-27 134
8 TraesCS6B01G247100 chr2D 88.214 543 62 2 2175 2716 239728955 239729496 0.000000e+00 647
9 TraesCS6B01G247100 chr5B 76.706 923 194 16 2181 3089 176233349 176234264 7.830000e-136 494
10 TraesCS6B01G247100 chr1A 82.857 525 88 2 2182 2705 302630745 302630222 1.320000e-128 470
11 TraesCS6B01G247100 chr1A 77.099 131 28 2 2981 3110 264085595 264085724 1.210000e-09 75
12 TraesCS6B01G247100 chr2A 89.008 373 41 0 2353 2725 235307408 235307036 2.210000e-126 462
13 TraesCS6B01G247100 chr2A 79.493 434 86 3 2181 2612 522508257 522507825 3.940000e-79 305
14 TraesCS6B01G247100 chr2A 71.761 903 192 50 2233 3087 457910162 457911049 2.470000e-46 196
15 TraesCS6B01G247100 chr5D 76.408 284 62 3 2816 3095 10529840 10529558 7.020000e-32 148
16 TraesCS6B01G247100 chr4A 76.190 273 58 6 2816 3083 629438160 629437890 1.520000e-28 137
17 TraesCS6B01G247100 chr4A 76.569 239 49 5 2862 3095 556244425 556244661 1.180000e-24 124


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 TraesCS6B01G247100 chr6B 439381230 439384372 3142 False 5805 5805 100.000 1 3143 1 chr6B.!!$F2 3142
1 TraesCS6B01G247100 chr6B 118965879 118966847 968 False 1701 1701 98.349 2175 3143 1 chr6B.!!$F1 968
2 TraesCS6B01G247100 chr6A 397523771 397525960 2189 True 3627 3627 96.639 1 2182 1 chr6A.!!$R1 2181
3 TraesCS6B01G247100 chr6D 277651904 277653275 1371 False 2119 2119 94.688 1 1367 1 chr6D.!!$F1 1366
4 TraesCS6B01G247100 chr3A 594017939 594018897 958 True 1506 1506 94.928 2178 3143 1 chr3A.!!$R1 965
5 TraesCS6B01G247100 chr7A 232331192 232331949 757 False 1240 1240 96.174 2175 2932 1 chr7A.!!$F1 757
6 TraesCS6B01G247100 chr2D 239728955 239729496 541 False 647 647 88.214 2175 2716 1 chr2D.!!$F1 541
7 TraesCS6B01G247100 chr5B 176233349 176234264 915 False 494 494 76.706 2181 3089 1 chr5B.!!$F1 908
8 TraesCS6B01G247100 chr1A 302630222 302630745 523 True 470 470 82.857 2182 2705 1 chr1A.!!$R1 523

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
894 924 0.107897 TGTCACACCTGTGTCACCAC 60.108 55.0 1.93 0.0 45.76 4.16 F
897 927 0.177836 CACACCTGTGTCACCACTCA 59.822 55.0 0.00 0.0 42.83 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 2018 1.301479 ACTTCCACTTCGCCGTTCC 60.301 57.895 0.00 0.0 0.00 3.62 R
2865 2903 1.885388 TTCGTGACTGCACCAACGG 60.885 57.895 9.62 0.0 42.09 4.44 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
139 142 5.921408 CGTATTTAGGAACAGAGGTAGCATC 59.079 44.000 0.00 0.00 0.00 3.91
220 223 7.995663 ACTATGGTAAATAATGCCCTATTGGA 58.004 34.615 0.00 0.00 35.39 3.53
223 226 5.480073 TGGTAAATAATGCCCTATTGGATGC 59.520 40.000 0.00 0.00 35.39 3.91
527 537 2.294512 CCTTTCTTTCAGGTGTCTTGCC 59.705 50.000 0.00 0.00 0.00 4.52
540 550 3.088532 TGTCTTGCCAAAAAGTGACAGT 58.911 40.909 0.00 0.00 31.87 3.55
894 924 0.107897 TGTCACACCTGTGTCACCAC 60.108 55.000 1.93 0.00 45.76 4.16
895 925 0.178068 GTCACACCTGTGTCACCACT 59.822 55.000 0.00 0.00 45.76 4.00
896 926 0.464036 TCACACCTGTGTCACCACTC 59.536 55.000 0.00 0.00 45.76 3.51
897 927 0.177836 CACACCTGTGTCACCACTCA 59.822 55.000 0.00 0.00 42.83 3.41
898 928 0.178068 ACACCTGTGTCACCACTCAC 59.822 55.000 0.00 0.00 40.24 3.51
899 929 0.532862 CACCTGTGTCACCACTCACC 60.533 60.000 0.00 0.00 42.34 4.02
900 930 0.980754 ACCTGTGTCACCACTCACCA 60.981 55.000 0.00 0.00 42.34 4.17
1342 1372 9.994432 AATTTCGAAAGATGCAATTTAGAGTAG 57.006 29.630 16.80 0.00 41.60 2.57
1527 1557 2.765122 AGCAGTCAACTCAGAGCTTTC 58.235 47.619 0.00 0.00 0.00 2.62
1529 1559 2.748605 CAGTCAACTCAGAGCTTTCGT 58.251 47.619 0.00 0.00 0.00 3.85
1559 1589 4.574828 TGATATCGATGACTGTTCAGACGA 59.425 41.667 8.54 11.11 43.51 4.20
1564 1594 0.591659 TGACTGTTCAGACGAGGACG 59.408 55.000 6.83 0.00 45.75 4.79
1595 1625 2.693069 CTTAGGGAGTGTCAACTGCAG 58.307 52.381 13.48 13.48 46.04 4.41
1596 1626 0.321671 TAGGGAGTGTCAACTGCAGC 59.678 55.000 15.27 0.00 46.04 5.25
1644 1674 6.700520 CCGAGACCAACTATTTCCACTATAAC 59.299 42.308 0.00 0.00 0.00 1.89
1684 1714 4.245660 TGAGCCTTGTTCTTCGAATAGTG 58.754 43.478 0.00 0.00 0.00 2.74
1858 1888 2.301346 ACAGAGACAACCTTGCTTTGG 58.699 47.619 0.00 0.00 0.00 3.28
1988 2018 7.639113 TTTTGGATAAATGGCTACTTGTAGG 57.361 36.000 9.49 0.00 0.00 3.18
2006 2036 1.301479 GGAACGGCGAAGTGGAAGT 60.301 57.895 16.62 0.00 0.00 3.01
2056 2086 2.650322 TGGTTTCTGAAGGTCCACAAC 58.350 47.619 0.00 0.00 0.00 3.32
2074 2104 1.940758 CGTACGTTGCGGGGTATCG 60.941 63.158 7.22 0.00 0.00 2.92
2100 2130 2.829120 AGCTTCTCTGTTGTCCTACTCC 59.171 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 226 3.030291 ACAGAAGATCCCAGCTAGACAG 58.970 50.000 0.00 0.00 0.00 3.51
278 282 4.578516 TGTAACCATGCCGATAAATCAAGG 59.421 41.667 0.00 0.00 0.00 3.61
369 373 5.163602 ACCACGTGTCAAACATGTTTTGTAT 60.164 36.000 21.10 0.00 45.33 2.29
527 537 3.688272 CTGCAGACACTGTCACTTTTTG 58.312 45.455 8.42 1.24 34.60 2.44
894 924 2.028294 AGATGACAGAAGCAGTGGTGAG 60.028 50.000 0.00 0.00 0.00 3.51
895 925 1.973515 AGATGACAGAAGCAGTGGTGA 59.026 47.619 0.00 0.00 0.00 4.02
896 926 2.469274 AGATGACAGAAGCAGTGGTG 57.531 50.000 0.00 0.00 0.00 4.17
897 927 3.771479 TGATAGATGACAGAAGCAGTGGT 59.229 43.478 0.00 0.00 0.00 4.16
898 928 4.397481 TGATAGATGACAGAAGCAGTGG 57.603 45.455 0.00 0.00 0.00 4.00
899 929 4.569966 GGTTGATAGATGACAGAAGCAGTG 59.430 45.833 0.00 0.00 0.00 3.66
900 930 4.223700 TGGTTGATAGATGACAGAAGCAGT 59.776 41.667 0.00 0.00 0.00 4.40
1019 1049 1.030488 TCTACTGGAAGACCGAGGCG 61.030 60.000 0.00 0.00 39.42 5.52
1342 1372 7.522374 CATTCTAACAAGTACTTCCTCAAAGC 58.478 38.462 4.77 0.00 38.67 3.51
1508 1538 1.458827 CGAAAGCTCTGAGTTGACTGC 59.541 52.381 6.53 0.00 0.00 4.40
1541 1571 1.468914 CCTCGTCTGAACAGTCATCGA 59.531 52.381 1.73 0.00 37.53 3.59
1559 1589 2.428890 CCTAAGCTCATCAACTCGTCCT 59.571 50.000 0.00 0.00 0.00 3.85
1564 1594 3.196685 ACACTCCCTAAGCTCATCAACTC 59.803 47.826 0.00 0.00 0.00 3.01
1595 1625 4.636206 GGAGTATGAAATCATTATCCCCGC 59.364 45.833 0.55 0.00 37.76 6.13
1596 1626 5.186198 GGGAGTATGAAATCATTATCCCCG 58.814 45.833 22.93 0.00 45.16 5.73
1620 1650 7.490000 AGTTATAGTGGAAATAGTTGGTCTCG 58.510 38.462 0.00 0.00 0.00 4.04
1644 1674 3.058155 GCTCATCCATATGCTGCTCAAAG 60.058 47.826 0.00 0.00 32.90 2.77
1684 1714 3.509575 TCCATATCAACAACTTTGGGTGC 59.490 43.478 0.00 0.00 0.00 5.01
1765 1795 9.462606 GAAAACCTCCTCTAATTTGGAATCTAA 57.537 33.333 0.00 0.00 31.23 2.10
1769 1799 6.665248 CCTGAAAACCTCCTCTAATTTGGAAT 59.335 38.462 0.00 0.00 31.23 3.01
1858 1888 3.118261 TGATTGGTATCAACAGCCTCCTC 60.118 47.826 0.00 0.00 37.83 3.71
1920 1950 4.558095 GCTGCTGTTGAAGTTTCATCACAT 60.558 41.667 0.00 0.00 37.00 3.21
1988 2018 1.301479 ACTTCCACTTCGCCGTTCC 60.301 57.895 0.00 0.00 0.00 3.62
2006 2036 3.519107 TCCAAGATAATGTCTGGTGAGCA 59.481 43.478 0.00 0.00 37.23 4.26
2056 2086 1.940758 CGATACCCCGCAACGTACG 60.941 63.158 15.01 15.01 0.00 3.67
2074 2104 3.996480 AGGACAACAGAGAAGCTACAAC 58.004 45.455 0.00 0.00 0.00 3.32
2100 2130 5.235831 CACACATGCAACATATACCTGAGAG 59.764 44.000 0.00 0.00 0.00 3.20
2865 2903 1.885388 TTCGTGACTGCACCAACGG 60.885 57.895 9.62 0.00 42.09 4.44
2959 2997 4.380945 GGATGCCAAGCCCCACCA 62.381 66.667 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.