Multiple sequence alignment - TraesCS1A01G092300

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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 TraesCS1A01G092300 chr1A 100.000 2954 0 0 1 2954 84797676 84794723 0.000000e+00 5456.0
1 TraesCS1A01G092300 chr1A 94.860 1576 58 14 801 2368 85006766 85005206 0.000000e+00 2440.0
2 TraesCS1A01G092300 chr1A 87.066 518 36 16 786 1272 84056038 84056555 9.250000e-155 556.0
3 TraesCS1A01G092300 chr1A 81.450 593 56 30 8 591 85007601 85007054 1.260000e-118 436.0
4 TraesCS1A01G092300 chr1A 89.091 220 14 5 2185 2394 84622323 84622542 6.280000e-67 265.0
5 TraesCS1A01G092300 chr1A 88.636 220 15 5 2185 2394 84485125 84485344 2.920000e-65 259.0
6 TraesCS1A01G092300 chr1A 85.987 157 15 6 726 879 84621093 84621245 8.470000e-36 161.0
7 TraesCS1A01G092300 chr1A 82.474 97 10 6 786 879 84483941 84484033 8.780000e-11 78.7
8 TraesCS1A01G092300 chr1A 93.750 48 2 1 2503 2550 84485526 84485572 1.470000e-08 71.3
9 TraesCS1A01G092300 chr1A 93.750 48 2 1 2503 2550 84622727 84622773 1.470000e-08 71.3
10 TraesCS1A01G092300 chr4D 88.857 2441 150 62 569 2954 464798381 464796008 0.000000e+00 2889.0
11 TraesCS1A01G092300 chr1D 90.233 1720 92 23 726 2394 88282852 88281158 0.000000e+00 2176.0
12 TraesCS1A01G092300 chr1D 91.407 1443 66 15 1558 2953 88243854 88242423 0.000000e+00 1925.0
13 TraesCS1A01G092300 chr1D 91.628 1302 67 17 720 1991 87903381 87904670 0.000000e+00 1762.0
14 TraesCS1A01G092300 chr1D 91.034 948 62 11 732 1661 88208045 88208987 0.000000e+00 1258.0
15 TraesCS1A01G092300 chr1D 91.723 737 39 11 726 1444 88244584 88243852 0.000000e+00 1003.0
16 TraesCS1A01G092300 chr1D 86.872 617 60 10 1 611 88276213 88275612 0.000000e+00 671.0
17 TraesCS1A01G092300 chr1D 80.616 779 92 33 1 767 88283703 88282972 5.570000e-152 547.0
18 TraesCS1A01G092300 chr1D 85.965 228 11 13 2178 2394 88215804 88216021 1.070000e-54 224.0
19 TraesCS1A01G092300 chr1D 94.444 54 2 1 2342 2394 87905145 87905198 6.790000e-12 82.4
20 TraesCS1A01G092300 chr1B 89.263 1723 116 33 720 2391 141844702 141846406 0.000000e+00 2093.0
21 TraesCS1A01G092300 chr1B 84.179 2326 182 66 138 2394 142135322 142133114 0.000000e+00 2085.0
22 TraesCS1A01G092300 chr1B 92.587 1295 67 15 720 1989 142037213 142038503 0.000000e+00 1832.0
23 TraesCS1A01G092300 chr1B 92.046 1295 74 15 720 1989 142093473 142094763 0.000000e+00 1794.0
24 TraesCS1A01G092300 chr1B 91.470 1102 87 4 896 1991 142086341 142087441 0.000000e+00 1507.0
25 TraesCS1A01G092300 chr1B 90.847 590 30 6 2388 2954 142133063 142132475 0.000000e+00 769.0
26 TraesCS1A01G092300 chr1B 82.533 229 27 10 2178 2395 142102864 142103090 3.890000e-44 189.0
27 TraesCS1A01G092300 chr3B 93.983 964 58 0 1028 1991 535705558 535704595 0.000000e+00 1459.0
28 TraesCS1A01G092300 chr3B 83.111 225 14 15 2181 2394 535555350 535555139 1.810000e-42 183.0


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 TraesCS1A01G092300 chr1A 84794723 84797676 2953 True 5456.0 5456 100.0000 1 2954 1 chr1A.!!$R1 2953
1 TraesCS1A01G092300 chr1A 85005206 85007601 2395 True 1438.0 2440 88.1550 8 2368 2 chr1A.!!$R2 2360
2 TraesCS1A01G092300 chr1A 84056038 84056555 517 False 556.0 556 87.0660 786 1272 1 chr1A.!!$F1 486
3 TraesCS1A01G092300 chr4D 464796008 464798381 2373 True 2889.0 2889 88.8570 569 2954 1 chr4D.!!$R1 2385
4 TraesCS1A01G092300 chr1D 88242423 88244584 2161 True 1464.0 1925 91.5650 726 2953 2 chr1D.!!$R2 2227
5 TraesCS1A01G092300 chr1D 88281158 88283703 2545 True 1361.5 2176 85.4245 1 2394 2 chr1D.!!$R3 2393
6 TraesCS1A01G092300 chr1D 88208045 88208987 942 False 1258.0 1258 91.0340 732 1661 1 chr1D.!!$F1 929
7 TraesCS1A01G092300 chr1D 87903381 87905198 1817 False 922.2 1762 93.0360 720 2394 2 chr1D.!!$F3 1674
8 TraesCS1A01G092300 chr1D 88275612 88276213 601 True 671.0 671 86.8720 1 611 1 chr1D.!!$R1 610
9 TraesCS1A01G092300 chr1B 141844702 141846406 1704 False 2093.0 2093 89.2630 720 2391 1 chr1B.!!$F1 1671
10 TraesCS1A01G092300 chr1B 142037213 142038503 1290 False 1832.0 1832 92.5870 720 1989 1 chr1B.!!$F2 1269
11 TraesCS1A01G092300 chr1B 142093473 142094763 1290 False 1794.0 1794 92.0460 720 1989 1 chr1B.!!$F4 1269
12 TraesCS1A01G092300 chr1B 142086341 142087441 1100 False 1507.0 1507 91.4700 896 1991 1 chr1B.!!$F3 1095
13 TraesCS1A01G092300 chr1B 142132475 142135322 2847 True 1427.0 2085 87.5130 138 2954 2 chr1B.!!$R1 2816
14 TraesCS1A01G092300 chr3B 535704595 535705558 963 True 1459.0 1459 93.9830 1028 1991 1 chr3B.!!$R2 963


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
709 863 0.251916 AAAGATGAACGGCCGGATGA 59.748 50.0 31.76 12.96 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 3125 4.082463 GCGGATGTTCCCTTTTTCATTGTA 60.082 41.667 0.0 0.0 31.13 2.41 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
221 233 4.733850 TGTGTGTTAAAAATGTTCACGCA 58.266 34.783 5.89 5.89 43.74 5.24
350 364 8.520351 GTTTGTATAACTAAAAGAAGTGCCCAT 58.480 33.333 0.00 0.00 0.00 4.00
538 636 7.605449 ACTTGATGGAAAATAAGTGTTCATGG 58.395 34.615 0.00 0.00 32.56 3.66
539 637 7.451255 ACTTGATGGAAAATAAGTGTTCATGGA 59.549 33.333 0.00 0.00 32.56 3.41
540 638 7.959658 TGATGGAAAATAAGTGTTCATGGAT 57.040 32.000 0.00 0.00 0.00 3.41
541 639 9.473007 TTGATGGAAAATAAGTGTTCATGGATA 57.527 29.630 0.00 0.00 0.00 2.59
542 640 9.645128 TGATGGAAAATAAGTGTTCATGGATAT 57.355 29.630 0.00 0.00 0.00 1.63
584 721 8.296713 TGCATATGACTTTTAAGAAGTGTTTCC 58.703 33.333 6.97 0.00 33.64 3.13
666 806 6.377080 AGGGAACAAAAAGGAGAGAGAAAAT 58.623 36.000 0.00 0.00 0.00 1.82
674 814 5.619625 AAGGAGAGAGAAAATGCGAAAAG 57.380 39.130 0.00 0.00 0.00 2.27
709 863 0.251916 AAAGATGAACGGCCGGATGA 59.748 50.000 31.76 12.96 0.00 2.92
743 1061 1.516386 CGTACGAGATGGCTTGCGT 60.516 57.895 10.44 0.00 40.42 5.24
864 1195 4.172772 CGCGCGCTGCCCATAAAA 62.173 61.111 30.48 0.00 42.08 1.52
865 1196 2.278142 GCGCGCTGCCCATAAAAG 60.278 61.111 26.67 0.00 37.76 2.27
880 1227 4.392940 CATAAAAGGCCTCGATCCTCATT 58.607 43.478 5.23 7.95 32.45 2.57
883 1230 1.207791 AGGCCTCGATCCTCATTGTT 58.792 50.000 0.00 0.00 0.00 2.83
885 1232 1.134401 GGCCTCGATCCTCATTGTTCA 60.134 52.381 0.00 0.00 0.00 3.18
886 1233 2.486191 GGCCTCGATCCTCATTGTTCAT 60.486 50.000 0.00 0.00 0.00 2.57
887 1234 3.209410 GCCTCGATCCTCATTGTTCATT 58.791 45.455 0.00 0.00 0.00 2.57
888 1235 3.003068 GCCTCGATCCTCATTGTTCATTG 59.997 47.826 0.00 0.00 0.00 2.82
890 1237 4.637534 CCTCGATCCTCATTGTTCATTGTT 59.362 41.667 0.00 0.00 0.00 2.83
893 1240 5.352293 TCGATCCTCATTGTTCATTGTTCTG 59.648 40.000 0.00 0.00 0.00 3.02
897 1244 6.479006 TCCTCATTGTTCATTGTTCTGATCT 58.521 36.000 0.00 0.00 0.00 2.75
898 1245 6.373495 TCCTCATTGTTCATTGTTCTGATCTG 59.627 38.462 0.00 0.00 0.00 2.90
902 1249 4.005650 TGTTCATTGTTCTGATCTGCCTC 58.994 43.478 0.00 0.00 0.00 4.70
950 1310 1.955529 CTCCCAACGCACACGAATCG 61.956 60.000 0.00 0.00 43.93 3.34
975 1336 0.390124 CCTCTGCTCTGATCTGCTCC 59.610 60.000 0.00 0.00 0.00 4.70
977 1338 1.047596 TCTGCTCTGATCTGCTCCCC 61.048 60.000 0.00 0.00 0.00 4.81
2108 2539 2.096496 GCAATCAGTGATTCACCCTTCG 59.904 50.000 15.60 3.56 34.49 3.79
2215 2844 2.093658 GGTTGAGCTTTCTATGACCGGA 60.094 50.000 9.46 0.00 0.00 5.14
2232 2870 3.452627 ACCGGACTGAATCTGCTAATCTT 59.547 43.478 9.46 0.00 31.52 2.40
2405 3101 7.128331 CACAACAGTAACAGATTTCACTGAAG 58.872 38.462 7.52 2.52 40.67 3.02
2429 3125 8.814038 AGAAAAGATGGCACTAACAGATAATT 57.186 30.769 0.00 0.00 0.00 1.40
2610 3306 3.243704 CGATCAATCCTCACCTCTTCTCC 60.244 52.174 0.00 0.00 0.00 3.71
2628 3324 2.860735 CTCCGCAGTTGCAAGTCTATAC 59.139 50.000 3.08 0.00 42.21 1.47
2716 3414 1.347378 GAGATGGCTCTTCCTCATCCC 59.653 57.143 0.00 0.00 38.33 3.85
2738 3436 0.450983 GCTTCTGTCCTGCATCTTGC 59.549 55.000 0.00 0.00 45.29 4.01
2768 3482 0.392193 CCCAGGTGACTCATCAGTGC 60.392 60.000 0.00 0.00 40.21 4.40
2771 3485 1.374631 GGTGACTCATCAGTGCGCA 60.375 57.895 5.66 5.66 34.75 6.09
2783 3497 0.241749 AGTGCGCATGTGAAATGTGG 59.758 50.000 15.91 0.00 0.00 4.17
2790 3504 2.557924 GCATGTGAAATGTGGTGAAGGA 59.442 45.455 0.00 0.00 0.00 3.36
2799 3513 2.457598 TGTGGTGAAGGACTAGCTAGG 58.542 52.381 24.35 7.13 0.00 3.02
2847 3568 1.850377 TGTGCAGCGTTTCATTTTGG 58.150 45.000 0.00 0.00 0.00 3.28
2854 3575 1.269517 GCGTTTCATTTTGGTGCAGGA 60.270 47.619 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.225981 ACAAAGAGGAAAGAAACAGCAAAT 57.774 33.333 0.00 0.00 0.00 2.32
46 47 9.191995 CATTTCGGAAATATATACAAAAAGGCC 57.808 33.333 15.13 0.00 0.00 5.19
47 48 9.744468 ACATTTCGGAAATATATACAAAAAGGC 57.256 29.630 15.13 0.00 0.00 4.35
464 479 9.825972 CACTTCTTTTTCGCTTTTCTATATGAA 57.174 29.630 0.00 0.00 0.00 2.57
465 480 8.999431 ACACTTCTTTTTCGCTTTTCTATATGA 58.001 29.630 0.00 0.00 0.00 2.15
466 481 9.612620 AACACTTCTTTTTCGCTTTTCTATATG 57.387 29.630 0.00 0.00 0.00 1.78
467 482 9.827411 GAACACTTCTTTTTCGCTTTTCTATAT 57.173 29.630 0.00 0.00 0.00 0.86
468 483 8.832521 TGAACACTTCTTTTTCGCTTTTCTATA 58.167 29.630 0.00 0.00 0.00 1.31
478 493 3.998522 ACGTGTGAACACTTCTTTTTCG 58.001 40.909 11.55 0.00 44.34 3.46
514 612 7.829725 TCCATGAACACTTATTTTCCATCAAG 58.170 34.615 0.00 0.00 0.00 3.02
542 640 9.836864 AGTCATATGCATATTTCTGTTCTGTAA 57.163 29.630 16.71 0.00 0.00 2.41
559 657 8.296713 TGGAAACACTTCTTAAAAGTCATATGC 58.703 33.333 0.00 0.00 33.40 3.14
640 780 4.718961 TCTCTCTCCTTTTTGTTCCCTTG 58.281 43.478 0.00 0.00 0.00 3.61
654 794 6.481954 TTACTTTTCGCATTTTCTCTCTCC 57.518 37.500 0.00 0.00 0.00 3.71
682 822 3.668656 CGGCCGTTCATCTTTTTCTTTTC 59.331 43.478 19.50 0.00 0.00 2.29
687 827 1.161843 TCCGGCCGTTCATCTTTTTC 58.838 50.000 26.12 0.00 0.00 2.29
709 863 4.057432 TCGTACGGGTTTTCTTTTCGATT 58.943 39.130 16.52 0.00 0.00 3.34
743 1061 2.869801 ACTTTGAAATCGCTTCGTCACA 59.130 40.909 0.00 0.00 36.78 3.58
858 1178 3.475566 TGAGGATCGAGGCCTTTTATG 57.524 47.619 6.77 0.00 38.61 1.90
859 1179 4.141390 ACAATGAGGATCGAGGCCTTTTAT 60.141 41.667 6.77 0.00 38.61 1.40
864 1195 1.139853 GAACAATGAGGATCGAGGCCT 59.860 52.381 3.86 3.86 38.61 5.19
865 1196 1.134401 TGAACAATGAGGATCGAGGCC 60.134 52.381 0.00 0.00 38.61 5.19
880 1227 4.005650 GAGGCAGATCAGAACAATGAACA 58.994 43.478 0.00 0.00 31.76 3.18
883 1230 3.118482 GGAGAGGCAGATCAGAACAATGA 60.118 47.826 0.00 0.00 0.00 2.57
885 1232 3.113824 AGGAGAGGCAGATCAGAACAAT 58.886 45.455 0.00 0.00 0.00 2.71
886 1233 2.544721 AGGAGAGGCAGATCAGAACAA 58.455 47.619 0.00 0.00 0.00 2.83
887 1234 2.244486 AGGAGAGGCAGATCAGAACA 57.756 50.000 0.00 0.00 0.00 3.18
888 1235 2.158971 GGAAGGAGAGGCAGATCAGAAC 60.159 54.545 0.00 0.00 0.00 3.01
890 1237 1.290431 AGGAAGGAGAGGCAGATCAGA 59.710 52.381 0.00 0.00 0.00 3.27
893 1240 1.047801 GGAGGAAGGAGAGGCAGATC 58.952 60.000 0.00 0.00 0.00 2.75
897 1244 0.692419 GATGGGAGGAAGGAGAGGCA 60.692 60.000 0.00 0.00 0.00 4.75
898 1245 1.414866 GGATGGGAGGAAGGAGAGGC 61.415 65.000 0.00 0.00 0.00 4.70
902 1249 0.105964 TCGAGGATGGGAGGAAGGAG 60.106 60.000 0.00 0.00 0.00 3.69
1045 1406 3.818787 CTTGCTGCCATGGACGCC 61.819 66.667 18.40 0.00 0.00 5.68
1057 1418 1.144057 CGTATCGGGGCTTCTTGCT 59.856 57.895 0.00 0.00 42.39 3.91
1272 1633 2.544686 CTCGATAATCGACTCGTGACCT 59.455 50.000 12.00 0.00 44.82 3.85
2108 2539 8.629158 TCATGTAATTTCCATGCTACAATAACC 58.371 33.333 11.14 0.00 39.60 2.85
2215 2844 7.750229 TTTCAACAAGATTAGCAGATTCAGT 57.250 32.000 0.00 0.00 0.00 3.41
2397 3093 4.090761 AGTGCCATCTTTTCTTCAGTGA 57.909 40.909 0.00 0.00 0.00 3.41
2405 3101 9.937175 GTAATTATCTGTTAGTGCCATCTTTTC 57.063 33.333 0.00 0.00 0.00 2.29
2429 3125 4.082463 GCGGATGTTCCCTTTTTCATTGTA 60.082 41.667 0.00 0.00 31.13 2.41
2610 3306 4.394795 GTTTGTATAGACTTGCAACTGCG 58.605 43.478 0.00 0.00 45.83 5.18
2628 3324 6.480524 TGAACTGATATGAAACGAGGTTTG 57.519 37.500 0.00 0.00 35.77 2.93
2709 3407 0.179936 GGACAGAAGCAGGGGATGAG 59.820 60.000 0.00 0.00 0.00 2.90
2712 3410 1.919600 GCAGGACAGAAGCAGGGGAT 61.920 60.000 0.00 0.00 0.00 3.85
2716 3414 0.252479 AGATGCAGGACAGAAGCAGG 59.748 55.000 0.00 0.00 42.14 4.85
2738 3436 3.007920 ACCTGGGAGAGCCAGCAG 61.008 66.667 0.00 0.00 35.15 4.24
2768 3482 2.587956 CTTCACCACATTTCACATGCG 58.412 47.619 0.00 0.00 0.00 4.73
2771 3485 4.104383 AGTCCTTCACCACATTTCACAT 57.896 40.909 0.00 0.00 0.00 3.21
2783 3497 3.560896 CGAGTACCTAGCTAGTCCTTCAC 59.439 52.174 19.31 7.55 0.00 3.18
2790 3504 2.171027 AGCAGTCGAGTACCTAGCTAGT 59.829 50.000 19.31 10.02 31.68 2.57
2799 3513 0.435008 CAAACGCAGCAGTCGAGTAC 59.565 55.000 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.