Multiple sequence alignment - TraesCS1D01G055000

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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 TraesCS1D01G055000 chr1D 100.000 2756 0 0 1 2756 36364001 36361246 0.000000e+00 5090
1 TraesCS1D01G055000 chr1D 93.996 916 45 8 1628 2538 36316423 36317333 0.000000e+00 1378
2 TraesCS1D01G055000 chr1D 93.233 798 54 0 849 1646 36315606 36316403 0.000000e+00 1175
3 TraesCS1D01G055000 chr1A 90.495 1536 127 13 120 1646 35579377 35577852 0.000000e+00 2010
4 TraesCS1D01G055000 chr1A 93.839 1120 65 3 1637 2756 35577823 35576708 0.000000e+00 1683
5 TraesCS1D01G055000 chr1A 93.771 899 49 3 1641 2538 35526471 35527363 0.000000e+00 1343
6 TraesCS1D01G055000 chr1A 92.990 913 58 6 1628 2538 35486805 35487713 0.000000e+00 1327
7 TraesCS1D01G055000 chr1A 92.702 781 57 0 866 1646 35536206 35536986 0.000000e+00 1127
8 TraesCS1D01G055000 chr1A 85.810 1043 88 31 1628 2654 35537006 35538004 0.000000e+00 1051
9 TraesCS1D01G055000 chr1A 89.179 804 75 6 844 1646 35485993 35486785 0.000000e+00 992
10 TraesCS1D01G055000 chr1A 85.457 667 75 12 18 668 35535241 35535901 0.000000e+00 675
11 TraesCS1D01G055000 chr1A 82.222 810 87 29 17 782 35484809 35485605 0.000000e+00 645
12 TraesCS1D01G055000 chr1A 85.314 606 65 14 124 713 35514441 35515038 3.040000e-169 604
13 TraesCS1D01G055000 chr1B 86.929 1423 154 17 245 1644 55976421 55977834 0.000000e+00 1568
14 TraesCS1D01G055000 chr1B 93.782 788 48 1 859 1646 56140945 56140159 0.000000e+00 1182
15 TraesCS1D01G055000 chr1B 90.712 829 75 2 819 1646 55998277 55999104 0.000000e+00 1103
16 TraesCS1D01G055000 chr1B 88.889 909 60 20 1628 2532 55977865 55978736 0.000000e+00 1081
17 TraesCS1D01G055000 chr1B 90.262 801 78 0 846 1646 56016955 56017755 0.000000e+00 1048
18 TraesCS1D01G055000 chr1B 92.918 706 45 3 2053 2756 56139746 56139044 0.000000e+00 1022
19 TraesCS1D01G055000 chr1B 86.320 826 76 28 1628 2433 56017775 56018583 0.000000e+00 865
20 TraesCS1D01G055000 chr1B 85.280 822 112 8 829 1646 55964135 55964951 0.000000e+00 839
21 TraesCS1D01G055000 chr1B 89.159 618 53 7 120 729 56141871 56141260 0.000000e+00 758
22 TraesCS1D01G055000 chr1B 93.154 482 31 2 2053 2532 55999514 55999995 0.000000e+00 706
23 TraesCS1D01G055000 chr1B 98.201 389 6 1 1637 2025 56140130 56139743 0.000000e+00 678
24 TraesCS1D01G055000 chr1B 94.486 399 16 4 1628 2025 55999124 55999517 6.530000e-171 610
25 TraesCS1D01G055000 chr1B 88.320 488 43 9 245 728 56016177 56016654 8.560000e-160 573
26 TraesCS1D01G055000 chr1B 85.849 318 29 6 107 415 55955781 55956091 9.520000e-85 324
27 TraesCS1D01G055000 chr1B 85.535 318 30 6 107 415 55944528 55944838 4.430000e-83 318
28 TraesCS1D01G055000 chr1B 88.298 94 9 1 641 734 55963662 55963753 8.070000e-21 111
29 TraesCS1D01G055000 chr7B 90.476 105 10 0 2652 2756 176002830 176002934 3.700000e-29 139
30 TraesCS1D01G055000 chr4D 90.476 105 9 1 2653 2756 421405113 421405009 1.330000e-28 137
31 TraesCS1D01G055000 chr4D 76.491 285 33 13 68 347 455095022 455095277 1.040000e-24 124
32 TraesCS1D01G055000 chr4A 89.623 106 11 0 2651 2756 577977981 577978086 4.790000e-28 135
33 TraesCS1D01G055000 chr5B 89.524 105 11 0 2652 2756 90185856 90185752 1.720000e-27 134
34 TraesCS1D01G055000 chr5B 89.524 105 9 2 2653 2756 358271831 358271934 6.190000e-27 132
35 TraesCS1D01G055000 chr5B 88.182 110 12 1 2647 2755 34915546 34915437 2.230000e-26 130
36 TraesCS1D01G055000 chr7A 89.524 105 10 1 2652 2756 636896497 636896394 6.190000e-27 132
37 TraesCS1D01G055000 chr4B 79.661 177 19 7 164 335 567599024 567599188 8.070000e-21 111


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 TraesCS1D01G055000 chr1D 36361246 36364001 2755 True 5090.000000 5090 100.000000 1 2756 1 chr1D.!!$R1 2755
1 TraesCS1D01G055000 chr1D 36315606 36317333 1727 False 1276.500000 1378 93.614500 849 2538 2 chr1D.!!$F1 1689
2 TraesCS1D01G055000 chr1A 35576708 35579377 2669 True 1846.500000 2010 92.167000 120 2756 2 chr1A.!!$R1 2636
3 TraesCS1D01G055000 chr1A 35526471 35527363 892 False 1343.000000 1343 93.771000 1641 2538 1 chr1A.!!$F2 897
4 TraesCS1D01G055000 chr1A 35484809 35487713 2904 False 988.000000 1327 88.130333 17 2538 3 chr1A.!!$F3 2521
5 TraesCS1D01G055000 chr1A 35535241 35538004 2763 False 951.000000 1127 87.989667 18 2654 3 chr1A.!!$F4 2636
6 TraesCS1D01G055000 chr1A 35514441 35515038 597 False 604.000000 604 85.314000 124 713 1 chr1A.!!$F1 589
7 TraesCS1D01G055000 chr1B 55976421 55978736 2315 False 1324.500000 1568 87.909000 245 2532 2 chr1B.!!$F4 2287
8 TraesCS1D01G055000 chr1B 56139044 56141871 2827 True 910.000000 1182 93.515000 120 2756 4 chr1B.!!$R1 2636
9 TraesCS1D01G055000 chr1B 56016177 56018583 2406 False 828.666667 1048 88.300667 245 2433 3 chr1B.!!$F6 2188
10 TraesCS1D01G055000 chr1B 55998277 55999995 1718 False 806.333333 1103 92.784000 819 2532 3 chr1B.!!$F5 1713
11 TraesCS1D01G055000 chr1B 55963662 55964951 1289 False 475.000000 839 86.789000 641 1646 2 chr1B.!!$F3 1005

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
118 119 0.243636 CCAAACAGAATCGGTTGGGC 59.756 55.0 6.75 0.0 32.82 5.36 F
301 316 0.455815 GTTTTTGGGCAGCTATCGGG 59.544 55.0 0.00 0.0 0.00 5.14 F
1107 1523 0.174845 CGAAGGTAGATCCAACGCCA 59.825 55.0 0.00 0.0 39.02 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1090 1506 1.202533 CGATGGCGTTGGATCTACCTT 60.203 52.381 0.00 0.0 39.86 3.50 R
1206 1623 1.218316 GTCCGGAGCGATGGTTTCT 59.782 57.895 3.06 0.0 0.00 2.52 R
2469 2980 0.539986 AAGGGTATGAATCGTGCGGT 59.460 50.000 0.00 0.0 0.00 5.68 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
65 66 4.643387 GTGGCAGACCCAGGCGTT 62.643 66.667 0.00 0.00 46.54 4.84
79 80 4.636435 CGTTGGGGAGGTGCGGTT 62.636 66.667 0.00 0.00 0.00 4.44
94 95 3.605664 GTTGTGCTGGTGGTGGCC 61.606 66.667 0.00 0.00 0.00 5.36
102 103 4.041762 GGTGGTGGCCGGATCCAA 62.042 66.667 13.41 0.00 37.96 3.53
105 106 2.034999 GGTGGCCGGATCCAAACA 59.965 61.111 13.41 3.74 37.96 2.83
117 118 1.904287 TCCAAACAGAATCGGTTGGG 58.096 50.000 12.66 12.66 40.15 4.12
118 119 0.243636 CCAAACAGAATCGGTTGGGC 59.756 55.000 6.75 0.00 32.82 5.36
149 151 3.216292 GGCGGCGGCATATTTGGT 61.216 61.111 29.41 0.00 42.47 3.67
170 172 1.385915 TGGGGAGCTATGGGAAGGG 60.386 63.158 0.00 0.00 0.00 3.95
173 175 1.386057 GGAGCTATGGGAAGGGGGT 60.386 63.158 0.00 0.00 0.00 4.95
174 176 0.994050 GGAGCTATGGGAAGGGGGTT 60.994 60.000 0.00 0.00 0.00 4.11
298 313 2.446435 TGGAGTTTTTGGGCAGCTATC 58.554 47.619 0.00 0.00 0.00 2.08
301 316 0.455815 GTTTTTGGGCAGCTATCGGG 59.544 55.000 0.00 0.00 0.00 5.14
306 321 2.844839 GGCAGCTATCGGGGAGGT 60.845 66.667 0.00 0.00 0.00 3.85
368 384 5.416952 CCTTTTGTTGGAGATGCTCTTATGT 59.583 40.000 0.00 0.00 0.00 2.29
439 457 3.059461 TCAATTTGACTACCGAAACACGC 60.059 43.478 0.00 0.00 41.07 5.34
457 476 2.227865 ACGCCTTGCACGTCATTAAAAT 59.772 40.909 0.00 0.00 40.28 1.82
458 477 2.593775 CGCCTTGCACGTCATTAAAATG 59.406 45.455 0.00 0.00 37.75 2.32
545 568 9.952030 TTCAACATGAAGGTAAATGTGTAGATA 57.048 29.630 0.00 0.00 37.11 1.98
637 667 5.598830 TCCATACAATGACTAGAGGGAGAAC 59.401 44.000 0.00 0.00 0.00 3.01
663 693 7.239763 TCATAGAGAAATGGAGTGTACACAA 57.760 36.000 27.06 12.98 0.00 3.33
678 735 1.066908 ACACAAACGAAAGCCCACATG 59.933 47.619 0.00 0.00 0.00 3.21
686 743 1.340889 GAAAGCCCACATGAAACAGCA 59.659 47.619 0.00 0.00 0.00 4.41
771 859 3.754976 TGTACCCTCCCCCTAAATTCAT 58.245 45.455 0.00 0.00 0.00 2.57
782 870 3.687212 CCCTAAATTCATGCGTACACACA 59.313 43.478 0.00 0.00 0.00 3.72
789 877 2.047560 GCGTACACACACTCCCCC 60.048 66.667 0.00 0.00 0.00 5.40
833 1199 6.543465 TCACCAATGACACATCCATCTATTTC 59.457 38.462 0.00 0.00 0.00 2.17
837 1203 4.047166 TGACACATCCATCTATTTCCCCT 58.953 43.478 0.00 0.00 0.00 4.79
882 1297 2.033602 CAAACCCACCCTCGTCCC 59.966 66.667 0.00 0.00 0.00 4.46
914 1329 2.167281 CAGATCTCGTCCTCACCACATT 59.833 50.000 0.00 0.00 0.00 2.71
936 1351 0.617820 ACCGTACCCCTCTCATTGCT 60.618 55.000 0.00 0.00 0.00 3.91
1107 1523 0.174845 CGAAGGTAGATCCAACGCCA 59.825 55.000 0.00 0.00 39.02 5.69
1206 1623 4.402528 CCCGTCAACCGCCATGGA 62.403 66.667 18.40 0.00 42.00 3.41
1257 1674 4.832823 TCCTCGAATCAGCAATATGAGGTA 59.167 41.667 14.15 4.82 38.84 3.08
1287 1704 1.178534 TACAGCTTGGCCTTGGCAAC 61.179 55.000 14.04 3.78 42.98 4.17
1338 1755 2.805295 CGCTGTCAACAAGTACCCTGAA 60.805 50.000 0.00 0.00 0.00 3.02
1416 1833 1.981951 TTGCTATGCCATCCCTCGCA 61.982 55.000 0.00 0.00 39.79 5.10
1421 1838 4.575973 GCCATCCCTCGCAGCCAT 62.576 66.667 0.00 0.00 0.00 4.40
1507 1924 2.359169 AAGAGGCCGCGATTCTCCA 61.359 57.895 8.23 0.00 0.00 3.86
1520 1937 4.262207 GCGATTCTCCATATCACTCTCCAA 60.262 45.833 0.00 0.00 0.00 3.53
2042 2508 7.318141 ACTTTGGTATCATCAGCAATTGAAAG 58.682 34.615 10.34 7.81 39.77 2.62
2060 2527 3.323751 AAGGACGTAATGTGGTGTACC 57.676 47.619 0.00 0.00 0.00 3.34
2118 2613 4.868171 TGTTCGTTGATGCTAGTACATTCC 59.132 41.667 0.00 0.00 0.00 3.01
2183 2692 4.893608 TCAGTGCATACAGTTTCTTGCTA 58.106 39.130 0.00 0.00 36.10 3.49
2243 2753 0.038251 CGAGTGCCAGTACTGCTTGA 60.038 55.000 17.86 0.00 0.00 3.02
2453 2964 0.179076 TATCGTCGTCCTGGAGCGTA 60.179 55.000 15.00 6.22 0.00 4.42
2469 2980 0.528924 CGTACCAGGGTTCGATGACA 59.471 55.000 11.45 0.00 40.47 3.58
2477 2988 1.731613 GTTCGATGACACCGCACGA 60.732 57.895 0.00 0.00 0.00 4.35
2485 2996 0.928229 GACACCGCACGATTCATACC 59.072 55.000 0.00 0.00 0.00 2.73
2490 3001 2.014128 CCGCACGATTCATACCCTTTT 58.986 47.619 0.00 0.00 0.00 2.27
2727 3239 9.630098 CTACATACAAAGCAAAATGAGTGAATT 57.370 29.630 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.641645 CAACGCCTGGGTCTGCCA 62.642 66.667 0.00 0.00 36.17 4.92
64 65 3.494254 ACAACCGCACCTCCCCAA 61.494 61.111 0.00 0.00 0.00 4.12
65 66 4.263572 CACAACCGCACCTCCCCA 62.264 66.667 0.00 0.00 0.00 4.96
83 84 4.489771 GGATCCGGCCACCACCAG 62.490 72.222 2.24 0.00 0.00 4.00
94 95 2.024176 ACCGATTCTGTTTGGATCCG 57.976 50.000 7.39 0.00 0.00 4.18
101 102 1.202879 TGAGCCCAACCGATTCTGTTT 60.203 47.619 0.00 0.00 0.00 2.83
102 103 0.400213 TGAGCCCAACCGATTCTGTT 59.600 50.000 0.00 0.00 0.00 3.16
105 106 0.036010 CACTGAGCCCAACCGATTCT 60.036 55.000 0.00 0.00 0.00 2.40
139 140 1.136891 GCTCCCCACAACCAAATATGC 59.863 52.381 0.00 0.00 0.00 3.14
142 144 3.372566 CCATAGCTCCCCACAACCAAATA 60.373 47.826 0.00 0.00 0.00 1.40
149 151 0.918983 CTTCCCATAGCTCCCCACAA 59.081 55.000 0.00 0.00 0.00 3.33
368 384 8.978874 ACAAAACTGGATATAGTAATCATGCA 57.021 30.769 0.00 0.00 0.00 3.96
439 457 5.971202 GGATACATTTTAATGACGTGCAAGG 59.029 40.000 9.32 0.00 39.67 3.61
637 667 7.323420 TGTGTACACTCCATTTCTCTATGAAG 58.677 38.462 25.60 0.00 35.89 3.02
663 693 2.028130 TGTTTCATGTGGGCTTTCGTT 58.972 42.857 0.00 0.00 0.00 3.85
729 808 4.133078 CAATGAGGTTTCTCCCTATGCTC 58.867 47.826 0.00 0.00 39.23 4.26
739 818 2.576648 GGGAGGGTACAATGAGGTTTCT 59.423 50.000 0.00 0.00 0.00 2.52
771 859 2.738480 GGGGAGTGTGTGTACGCA 59.262 61.111 4.65 4.65 39.77 5.24
882 1297 3.304123 GGACGAGATCTGAGATACAACGG 60.304 52.174 0.00 0.00 0.00 4.44
914 1329 2.104967 CAATGAGAGGGGTACGGTGTA 58.895 52.381 0.00 0.00 0.00 2.90
936 1351 0.461548 CTCTAGATCTGGTTGCGGCA 59.538 55.000 5.18 0.00 0.00 5.69
997 1413 2.264480 CGCCGAGTTCACCATGGA 59.736 61.111 21.47 0.00 0.00 3.41
1039 1455 1.912043 ACCTTCCTTGGTGAGATCTGG 59.088 52.381 0.00 0.00 39.17 3.86
1090 1506 1.202533 CGATGGCGTTGGATCTACCTT 60.203 52.381 0.00 0.00 39.86 3.50
1107 1523 3.461773 CCTCGGTGGGCACTCGAT 61.462 66.667 5.53 0.00 34.98 3.59
1206 1623 1.218316 GTCCGGAGCGATGGTTTCT 59.782 57.895 3.06 0.00 0.00 2.52
1320 1737 3.452990 TGACTTCAGGGTACTTGTTGACA 59.547 43.478 0.00 0.00 0.00 3.58
1416 1833 2.182791 CTCGCGACAGTCATGGCT 59.817 61.111 3.71 0.00 29.20 4.75
1520 1937 3.481559 TGTCTTCCTCAATCTCCTCCT 57.518 47.619 0.00 0.00 0.00 3.69
1716 2182 2.963101 CCGGTAGGACTCCATGTTGATA 59.037 50.000 0.00 0.00 41.02 2.15
2042 2508 2.028748 ACTGGTACACCACATTACGTCC 60.029 50.000 0.00 0.00 42.01 4.79
2060 2527 4.503007 GCATCAAGAGCAATGCAATTACTG 59.497 41.667 8.35 3.97 45.97 2.74
2118 2613 6.713903 AGATTGCAATAGGGATGTATGTGAAG 59.286 38.462 12.97 0.00 0.00 3.02
2243 2753 1.959226 CAACCAGCTACAACGCGGT 60.959 57.895 12.47 0.00 38.04 5.68
2320 2830 1.421410 GACGAACTATGCAGCACCCG 61.421 60.000 0.00 0.00 0.00 5.28
2330 2840 5.209818 TCAGGAAACAAGTGACGAACTAT 57.790 39.130 0.00 0.00 38.56 2.12
2453 2964 1.677552 GGTGTCATCGAACCCTGGT 59.322 57.895 0.00 0.00 0.00 4.00
2469 2980 0.539986 AAGGGTATGAATCGTGCGGT 59.460 50.000 0.00 0.00 0.00 5.68
2485 2996 1.039856 CCCACTCACACCCAAAAAGG 58.960 55.000 0.00 0.00 37.03 3.11
2490 3001 2.776526 AGCCCCACTCACACCCAA 60.777 61.111 0.00 0.00 0.00 4.12
2641 3153 7.714703 AGAACGGAAGGAGTATTTCATAGTAC 58.285 38.462 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.