Multiple sequence alignment - TraesCS3D01G082800

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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 TraesCS3D01G082800 chr3D 100.000 2219 0 0 1 2219 42089298 42087080 0.000000e+00 4098
1 TraesCS3D01G082800 chr3B 88.545 2200 154 51 9 2148 65559154 65561315 0.000000e+00 2577
2 TraesCS3D01G082800 chr3B 96.000 75 3 0 2145 2219 65561343 65561417 2.990000e-24 122
3 TraesCS3D01G082800 chr3A 87.984 2197 149 59 1 2147 53567793 53569924 0.000000e+00 2488


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 TraesCS3D01G082800 chr3D 42087080 42089298 2218 True 4098.0 4098 100.0000 1 2219 1 chr3D.!!$R1 2218
1 TraesCS3D01G082800 chr3B 65559154 65561417 2263 False 1349.5 2577 92.2725 9 2219 2 chr3B.!!$F1 2210
2 TraesCS3D01G082800 chr3A 53567793 53569924 2131 False 2488.0 2488 87.9840 1 2147 1 chr3A.!!$F1 2146

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
852 890 0.099613 CTCGACTGATCTGGTCACGG 59.9 60.0 15.72 4.37 33.73 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 1988 1.001815 CTACCTTGTGCAACGGTTTGG 60.002 52.381 7.97 0.0 42.39 3.28 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 1.737793 CGGGCAAAATGAGTGTAGGTC 59.262 52.381 0.00 0.00 0.00 3.85
50 51 1.068585 GGGTTTGGTGTCGAGTCGT 59.931 57.895 13.12 0.00 0.00 4.34
58 59 1.668793 TGTCGAGTCGTGGTAGCGA 60.669 57.895 13.12 0.00 38.68 4.93
61 62 2.102553 GAGTCGTGGTAGCGAGCC 59.897 66.667 0.00 0.00 41.85 4.70
123 126 1.946283 GCTTTCTGGGTAGTGAGTGGC 60.946 57.143 0.00 0.00 0.00 5.01
128 131 2.646175 GGGTAGTGAGTGGCGCAGA 61.646 63.158 10.83 0.00 0.00 4.26
131 134 1.071605 GTAGTGAGTGGCGCAGAAAG 58.928 55.000 10.83 0.00 0.00 2.62
167 170 1.531423 TAGGTGAGTGTGACCTCGTC 58.469 55.000 0.00 0.00 43.15 4.20
170 173 0.110147 GTGAGTGTGACCTCGTCTCG 60.110 60.000 0.00 0.00 34.04 4.04
230 244 2.550606 GGAACTGGCGTGTGTAAATTGA 59.449 45.455 0.00 0.00 0.00 2.57
232 246 4.393680 GGAACTGGCGTGTGTAAATTGATA 59.606 41.667 0.00 0.00 0.00 2.15
261 275 7.670009 AGTGATTCAGATAATAATGCAGAGC 57.330 36.000 0.00 0.00 0.00 4.09
262 276 7.451732 AGTGATTCAGATAATAATGCAGAGCT 58.548 34.615 0.00 0.00 0.00 4.09
263 277 7.388224 AGTGATTCAGATAATAATGCAGAGCTG 59.612 37.037 0.00 0.00 0.00 4.24
286 306 1.077123 CTGCTGCTGCTTCAGTGTAG 58.923 55.000 17.00 0.00 40.48 2.74
379 399 2.358898 CTGAGCCTAGTCTTGAGAGAGC 59.641 54.545 0.00 0.00 31.07 4.09
452 472 0.320073 GTGCCTGTTGTGTAGCCGTA 60.320 55.000 0.00 0.00 0.00 4.02
468 488 1.995484 CCGTACTGACAAGTGAGCATG 59.005 52.381 0.00 0.00 37.19 4.06
519 543 2.995939 AGTGACACATTATCTGCACACG 59.004 45.455 8.59 0.00 33.63 4.49
520 544 2.094258 GTGACACATTATCTGCACACGG 59.906 50.000 0.00 0.00 0.00 4.94
563 587 8.255206 CAGTCAAATATACAGTAGTGGTTGGTA 58.745 37.037 1.92 0.00 0.00 3.25
564 588 8.255905 AGTCAAATATACAGTAGTGGTTGGTAC 58.744 37.037 1.92 0.00 0.00 3.34
584 611 6.708949 TGGTACTAACAGGAAAAAGATGACAC 59.291 38.462 0.00 0.00 0.00 3.67
603 630 1.291877 CGTTCAGCTGGTGGTGTAGC 61.292 60.000 15.13 0.00 41.91 3.58
621 652 1.591703 CACACGAGGCTAAGGCAGA 59.408 57.895 0.00 0.00 40.87 4.26
624 655 1.279271 ACACGAGGCTAAGGCAGAATT 59.721 47.619 0.00 0.00 40.87 2.17
627 658 3.743396 CACGAGGCTAAGGCAGAATTATC 59.257 47.826 0.00 0.00 40.87 1.75
628 659 3.388024 ACGAGGCTAAGGCAGAATTATCA 59.612 43.478 0.00 0.00 40.87 2.15
629 660 3.993081 CGAGGCTAAGGCAGAATTATCAG 59.007 47.826 0.00 0.00 40.87 2.90
630 661 4.262207 CGAGGCTAAGGCAGAATTATCAGA 60.262 45.833 0.00 0.00 40.87 3.27
634 665 6.058183 GGCTAAGGCAGAATTATCAGAAGAA 58.942 40.000 0.00 0.00 40.87 2.52
640 671 6.373774 AGGCAGAATTATCAGAAGAAACACAG 59.626 38.462 0.00 0.00 0.00 3.66
650 681 4.453819 CAGAAGAAACACAGGTGATCTTCC 59.546 45.833 28.14 19.11 46.00 3.46
664 695 3.072915 TGATCTTCCTCCAGACTGCAAAA 59.927 43.478 0.00 0.00 0.00 2.44
690 721 5.305644 AGTTGTCTAGGTCTCACAAGATGTT 59.694 40.000 0.00 0.00 33.08 2.71
693 730 2.936919 AGGTCTCACAAGATGTTGCA 57.063 45.000 1.83 0.00 37.14 4.08
694 731 2.775890 AGGTCTCACAAGATGTTGCAG 58.224 47.619 1.83 0.00 37.14 4.41
695 732 1.198637 GGTCTCACAAGATGTTGCAGC 59.801 52.381 1.83 0.00 37.14 5.25
696 733 1.198637 GTCTCACAAGATGTTGCAGCC 59.801 52.381 1.83 0.00 37.14 4.85
719 756 1.112113 GGGTCTCAGAAGCCGTGATA 58.888 55.000 0.00 0.00 0.00 2.15
746 783 1.079503 TGCGTTTTGTTTTGTTGCCC 58.920 45.000 0.00 0.00 0.00 5.36
755 792 2.575455 TTTTGTTGCCCCGGTCCACT 62.575 55.000 0.00 0.00 0.00 4.00
852 890 0.099613 CTCGACTGATCTGGTCACGG 59.900 60.000 15.72 4.37 33.73 4.94
853 891 0.608308 TCGACTGATCTGGTCACGGT 60.608 55.000 15.72 0.00 33.73 4.83
854 892 0.179161 CGACTGATCTGGTCACGGTC 60.179 60.000 15.72 0.00 33.73 4.79
865 904 2.194889 TCACGGTCACGCCACACTA 61.195 57.895 0.00 0.00 46.04 2.74
889 928 2.031516 ACCGTCGTCGTCATCGTCT 61.032 57.895 0.71 0.00 38.33 4.18
950 990 4.688021 AGCAGCACTAGCATTAGTAAGAC 58.312 43.478 0.00 0.00 45.49 3.01
951 991 3.487574 GCAGCACTAGCATTAGTAAGACG 59.512 47.826 0.00 0.00 45.49 4.18
963 1003 2.361789 AGTAAGACGGACAGAGAGCTC 58.638 52.381 5.27 5.27 0.00 4.09
969 1018 0.455410 CGGACAGAGAGCTCTTGAGG 59.545 60.000 19.36 10.21 37.98 3.86
1237 1294 2.579657 CCCTCCGGCGCCATACATA 61.580 63.158 28.98 3.10 0.00 2.29
1242 1299 0.315886 CCGGCGCCATACATACTACA 59.684 55.000 28.98 0.00 0.00 2.74
1243 1300 1.668919 CCGGCGCCATACATACTACAG 60.669 57.143 28.98 4.53 0.00 2.74
1376 1461 2.364632 TGGTTGATTTGAGCCATACCG 58.635 47.619 0.00 0.00 0.00 4.02
1513 1619 6.096141 TGTTCCAGTTTCACAGCTTTGATTTA 59.904 34.615 2.84 0.00 0.00 1.40
1514 1620 6.317789 TCCAGTTTCACAGCTTTGATTTAG 57.682 37.500 2.84 0.00 0.00 1.85
1515 1621 5.241506 TCCAGTTTCACAGCTTTGATTTAGG 59.758 40.000 2.84 4.74 0.00 2.69
1649 1764 2.796031 CAACAATTGCATTGAACTGCGT 59.204 40.909 5.05 0.00 45.30 5.24
1680 1795 3.057315 CACAAAATTCAGGGCTACCACAG 60.057 47.826 0.00 0.00 40.13 3.66
1687 1802 0.983378 AGGGCTACCACAGACATCCC 60.983 60.000 0.00 0.00 40.13 3.85
1709 1824 0.249120 AGCGAATCAATCACCGGTCA 59.751 50.000 2.59 0.00 0.00 4.02
1725 1840 2.197605 TCAGTCACCGGCGTCTTCA 61.198 57.895 6.01 0.00 0.00 3.02
1826 1941 1.406903 CCTTGGGCCCTGAATTCATC 58.593 55.000 25.70 1.48 0.00 2.92
1873 1988 0.674895 ACTCCGGCAAGTTCTCATGC 60.675 55.000 0.00 0.00 41.82 4.06
1978 2095 2.040606 GGCCACCTCCTCTACCCA 59.959 66.667 0.00 0.00 0.00 4.51
1990 2107 1.218316 CTACCCACAACGCCCTCTC 59.782 63.158 0.00 0.00 0.00 3.20
2071 2188 9.920826 GAGATTTTCTTTTAAACAAAAGGCAAG 57.079 29.630 9.34 0.00 39.56 4.01
2129 2246 8.299570 GCTAAAATCTTCAAACAGGATTCTCAA 58.700 33.333 0.00 0.00 0.00 3.02
2133 2250 8.413309 AATCTTCAAACAGGATTCTCAATGAA 57.587 30.769 0.00 0.00 39.24 2.57
2148 2265 7.009179 TCTCAATGAAGATGAGTTAACAGGT 57.991 36.000 8.61 0.00 43.77 4.00
2199 2347 7.307160 GGTTTTAATTTAGTGTTGAAAGCCAGC 60.307 37.037 0.00 0.00 30.84 4.85
2213 2361 5.590259 TGAAAGCCAGCTTCCTAATATGTTC 59.410 40.000 5.17 0.00 34.84 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.204012 CAAACCCTTCTTTGTGACCTACA 58.796 43.478 0.00 0.00 37.56 2.74
23 24 2.223479 CGACACCAAACCCTTCTTTGTG 60.223 50.000 0.00 0.00 30.33 3.33
30 31 0.249741 CGACTCGACACCAAACCCTT 60.250 55.000 0.00 0.00 0.00 3.95
50 51 3.774528 CAGCAGGGCTCGCTACCA 61.775 66.667 2.62 0.00 37.72 3.25
61 62 2.821969 AGATAAAAGCCAACACAGCAGG 59.178 45.455 0.00 0.00 0.00 4.85
123 126 2.295909 TGGATTTTGTTCCCTTTCTGCG 59.704 45.455 0.00 0.00 34.67 5.18
128 131 4.528206 CCTAAGCTGGATTTTGTTCCCTTT 59.472 41.667 0.00 0.00 34.67 3.11
131 134 3.193479 CACCTAAGCTGGATTTTGTTCCC 59.807 47.826 0.00 0.00 34.67 3.97
167 170 6.577427 CGTTTTTATTCCTGTTCCTTTTCGAG 59.423 38.462 0.00 0.00 0.00 4.04
170 173 6.358822 CGACGTTTTTATTCCTGTTCCTTTTC 59.641 38.462 0.00 0.00 0.00 2.29
217 220 9.773328 AATCACTTTCATATCAATTTACACACG 57.227 29.630 0.00 0.00 0.00 4.49
264 278 1.966972 ACTGAAGCAGCAGCAGCAG 60.967 57.895 12.92 17.46 45.49 4.24
265 279 2.112507 ACTGAAGCAGCAGCAGCA 59.887 55.556 12.92 0.00 45.49 4.41
348 368 1.552792 ACTAGGCTCAGCTCTTTCACC 59.447 52.381 0.00 0.00 0.00 4.02
352 372 3.169099 TCAAGACTAGGCTCAGCTCTTT 58.831 45.455 0.00 0.00 0.00 2.52
379 399 2.366916 GTCCACCATATCCTCACTCTGG 59.633 54.545 0.00 0.00 0.00 3.86
452 472 1.810755 CATGCATGCTCACTTGTCAGT 59.189 47.619 20.33 0.00 0.00 3.41
519 543 2.143122 CTGGTGTATGTGTGTGTGTCC 58.857 52.381 0.00 0.00 0.00 4.02
520 544 2.800544 GACTGGTGTATGTGTGTGTGTC 59.199 50.000 0.00 0.00 0.00 3.67
563 587 5.365619 ACGTGTCATCTTTTTCCTGTTAGT 58.634 37.500 0.00 0.00 0.00 2.24
564 588 5.924475 ACGTGTCATCTTTTTCCTGTTAG 57.076 39.130 0.00 0.00 0.00 2.34
567 592 4.196193 TGAACGTGTCATCTTTTTCCTGT 58.804 39.130 0.00 0.00 0.00 4.00
584 611 1.291877 GCTACACCACCAGCTGAACG 61.292 60.000 17.39 0.15 34.86 3.95
603 630 0.037326 TTCTGCCTTAGCCTCGTGTG 60.037 55.000 0.00 0.00 38.69 3.82
621 652 8.105829 AGATCACCTGTGTTTCTTCTGATAATT 58.894 33.333 0.00 0.00 0.00 1.40
624 655 6.611613 AGATCACCTGTGTTTCTTCTGATA 57.388 37.500 0.00 0.00 0.00 2.15
627 658 4.453819 GGAAGATCACCTGTGTTTCTTCTG 59.546 45.833 26.05 0.00 42.88 3.02
628 659 4.349342 AGGAAGATCACCTGTGTTTCTTCT 59.651 41.667 26.05 17.60 42.88 2.85
629 660 4.646572 AGGAAGATCACCTGTGTTTCTTC 58.353 43.478 22.85 22.85 42.75 2.87
630 661 4.505742 GGAGGAAGATCACCTGTGTTTCTT 60.506 45.833 14.70 13.91 37.93 2.52
634 665 2.304180 CTGGAGGAAGATCACCTGTGTT 59.696 50.000 14.70 0.00 37.93 3.32
640 671 1.134551 GCAGTCTGGAGGAAGATCACC 60.135 57.143 1.14 0.00 0.00 4.02
664 695 5.871396 TCTTGTGAGACCTAGACAACTTT 57.129 39.130 0.00 0.00 0.00 2.66
690 721 2.853542 TGAGACCCCAAGGCTGCA 60.854 61.111 0.50 0.00 36.11 4.41
693 730 1.846712 GCTTCTGAGACCCCAAGGCT 61.847 60.000 0.00 0.00 36.11 4.58
694 731 1.377856 GCTTCTGAGACCCCAAGGC 60.378 63.158 0.00 0.00 36.11 4.35
695 732 1.301293 GGCTTCTGAGACCCCAAGG 59.699 63.158 0.00 0.00 40.04 3.61
696 733 1.078848 CGGCTTCTGAGACCCCAAG 60.079 63.158 0.00 0.00 0.00 3.61
719 756 4.630111 ACAAAACAAAACGCATCCATCAT 58.370 34.783 0.00 0.00 0.00 2.45
746 783 0.105964 TCAAGTGTTGAGTGGACCGG 59.894 55.000 0.00 0.00 34.08 5.28
755 792 1.581934 CAGGCGAGTTCAAGTGTTGA 58.418 50.000 0.00 0.00 38.04 3.18
837 875 0.603569 GTGACCGTGACCAGATCAGT 59.396 55.000 0.00 0.00 38.28 3.41
839 877 1.584495 CGTGACCGTGACCAGATCA 59.416 57.895 0.00 0.00 33.79 2.92
852 890 1.927174 GTGATGATAGTGTGGCGTGAC 59.073 52.381 0.00 0.00 0.00 3.67
853 891 1.134818 GGTGATGATAGTGTGGCGTGA 60.135 52.381 0.00 0.00 0.00 4.35
854 892 1.290203 GGTGATGATAGTGTGGCGTG 58.710 55.000 0.00 0.00 0.00 5.34
865 904 0.738975 ATGACGACGACGGTGATGAT 59.261 50.000 12.58 0.00 44.46 2.45
923 963 0.179936 AATGCTAGTGCTGCTCTCCC 59.820 55.000 7.59 1.52 40.48 4.30
950 990 0.455410 CCTCAAGAGCTCTCTGTCCG 59.545 60.000 18.55 10.00 40.36 4.79
951 991 0.823460 CCCTCAAGAGCTCTCTGTCC 59.177 60.000 18.55 0.00 40.36 4.02
1237 1294 0.035458 GCTGGTGGTCTTGCTGTAGT 59.965 55.000 0.00 0.00 0.00 2.73
1242 1299 1.197430 AGCTAGCTGGTGGTCTTGCT 61.197 55.000 18.57 0.00 36.77 3.91
1243 1300 0.537188 TAGCTAGCTGGTGGTCTTGC 59.463 55.000 27.68 0.00 0.00 4.01
1307 1391 6.098838 ACTGACAGACAATCCTGAGCATATTA 59.901 38.462 10.08 0.00 37.59 0.98
1395 1480 6.618811 CCCTCTTTCACTGATGAATTTCTTG 58.381 40.000 0.00 0.00 44.36 3.02
1399 1484 4.670765 AGCCCTCTTTCACTGATGAATTT 58.329 39.130 0.00 0.00 44.36 1.82
1400 1485 4.313020 AGCCCTCTTTCACTGATGAATT 57.687 40.909 0.00 0.00 44.36 2.17
1401 1486 5.441718 TTAGCCCTCTTTCACTGATGAAT 57.558 39.130 0.00 0.00 44.36 2.57
1402 1487 4.908601 TTAGCCCTCTTTCACTGATGAA 57.091 40.909 0.00 0.00 43.28 2.57
1403 1488 4.908601 TTTAGCCCTCTTTCACTGATGA 57.091 40.909 0.00 0.00 0.00 2.92
1404 1489 6.327934 CAATTTTAGCCCTCTTTCACTGATG 58.672 40.000 0.00 0.00 0.00 3.07
1405 1490 5.105595 GCAATTTTAGCCCTCTTTCACTGAT 60.106 40.000 0.00 0.00 0.00 2.90
1406 1491 4.218417 GCAATTTTAGCCCTCTTTCACTGA 59.782 41.667 0.00 0.00 0.00 3.41
1411 1504 4.460731 ACTCAGCAATTTTAGCCCTCTTTC 59.539 41.667 0.00 0.00 0.00 2.62
1472 1568 3.084039 GGAACATGCCAATCTTGTCTCA 58.916 45.455 0.00 0.00 32.59 3.27
1478 1584 3.896888 TGAAACTGGAACATGCCAATCTT 59.103 39.130 0.00 0.00 38.20 2.40
1649 1764 4.504689 GCCCTGAATTTTGTGGGAATTCAA 60.505 41.667 7.93 0.00 46.78 2.69
1670 1785 1.144057 CGGGATGTCTGTGGTAGCC 59.856 63.158 0.00 0.00 0.00 3.93
1680 1795 1.089481 TTGATTCGCTGCGGGATGTC 61.089 55.000 23.03 12.91 0.00 3.06
1687 1802 1.011904 CGGTGATTGATTCGCTGCG 60.012 57.895 17.25 17.25 34.59 5.18
1709 1824 2.023414 TTGTGAAGACGCCGGTGACT 62.023 55.000 24.59 19.14 0.00 3.41
1725 1840 2.044353 AGGAGGCAATAACCCCATTTGT 59.956 45.455 0.00 0.00 0.00 2.83
1770 1885 1.602237 GTCGAGGGAAAGATGGCCA 59.398 57.895 8.56 8.56 0.00 5.36
1826 1941 8.813282 GGTTTAACTAAACAATTGTGTCTTTGG 58.187 33.333 12.82 7.17 45.50 3.28
1862 1977 1.981256 ACGGTTTGGCATGAGAACTT 58.019 45.000 0.00 0.00 0.00 2.66
1873 1988 1.001815 CTACCTTGTGCAACGGTTTGG 60.002 52.381 7.97 0.00 42.39 3.28
1978 2095 2.357517 CTTGCGAGAGGGCGTTGT 60.358 61.111 0.00 0.00 35.06 3.32
1990 2107 1.712977 GGAGCAGATGGAAGCTTGCG 61.713 60.000 13.65 0.00 42.04 4.85
2059 2176 6.758254 ACTTGCAATATACTTGCCTTTTGTT 58.242 32.000 0.00 0.00 44.32 2.83
2061 2178 6.308766 GTGACTTGCAATATACTTGCCTTTTG 59.691 38.462 0.00 0.00 44.32 2.44
2071 2188 7.251704 AGCATTACTGTGACTTGCAATATAC 57.748 36.000 0.00 0.00 35.79 1.47
2129 2246 6.611613 TCTGACCTGTTAACTCATCTTCAT 57.388 37.500 7.22 0.00 0.00 2.57
2130 2247 6.611613 ATCTGACCTGTTAACTCATCTTCA 57.388 37.500 7.22 0.89 0.00 3.02
2131 2248 8.035394 TGTAATCTGACCTGTTAACTCATCTTC 58.965 37.037 7.22 0.00 0.00 2.87
2133 2250 7.364232 CCTGTAATCTGACCTGTTAACTCATCT 60.364 40.741 7.22 0.00 0.00 2.90
2148 2265 3.273434 GAGTGCAATGCCTGTAATCTGA 58.727 45.455 1.53 0.00 32.69 3.27


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

AutoCloner maintained by Alex Coulton.