Multiple sequence alignment - TraesCS7D01G330400

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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 TraesCS7D01G330400 chr7D 100.000 2581 0 0 1 2581 422153565 422150985 0.000000e+00 4767.0
1 TraesCS7D01G330400 chr7D 82.143 784 108 27 1 766 599718655 599719424 0.000000e+00 643.0
2 TraesCS7D01G330400 chr7B 89.736 1705 105 23 902 2581 438950442 438952101 0.000000e+00 2115.0
3 TraesCS7D01G330400 chr7B 96.190 105 2 2 797 900 438949969 438950072 1.230000e-38 171.0
4 TraesCS7D01G330400 chr5D 85.665 1437 97 37 776 2167 423964409 423965781 0.000000e+00 1411.0
5 TraesCS7D01G330400 chr5D 94.469 669 37 0 1 669 499061689 499061021 0.000000e+00 1031.0
6 TraesCS7D01G330400 chr5D 80.711 788 121 28 1 770 424819921 424819147 3.700000e-163 584.0
7 TraesCS7D01G330400 chr5D 83.283 329 18 17 899 1215 562709251 562708948 4.230000e-68 268.0
8 TraesCS7D01G330400 chr5B 85.268 1439 90 35 775 2167 511835216 511836578 0.000000e+00 1371.0
9 TraesCS7D01G330400 chr7A 90.471 976 56 13 1624 2581 511012792 511013748 0.000000e+00 1253.0
10 TraesCS7D01G330400 chr7A 95.060 668 31 2 1 667 15255775 15255109 0.000000e+00 1050.0
11 TraesCS7D01G330400 chr7A 87.500 848 55 15 777 1598 511011974 511012796 0.000000e+00 931.0
12 TraesCS7D01G330400 chr5A 86.491 1140 78 27 775 1877 537368757 537369857 0.000000e+00 1182.0
13 TraesCS7D01G330400 chr5A 91.248 777 58 6 1 773 631680868 631680098 0.000000e+00 1050.0
14 TraesCS7D01G330400 chr5A 90.310 774 68 4 1 773 709280469 709279702 0.000000e+00 1007.0
15 TraesCS7D01G330400 chr4D 93.077 780 47 4 1 775 224753582 224752805 0.000000e+00 1134.0
16 TraesCS7D01G330400 chr4D 94.768 669 33 1 1 669 53420071 53419405 0.000000e+00 1040.0
17 TraesCS7D01G330400 chr2A 91.214 774 67 1 1 773 760865175 760865948 0.000000e+00 1051.0
18 TraesCS7D01G330400 chr2A 90.219 777 61 9 1 770 744776721 744777489 0.000000e+00 1000.0
19 TraesCS7D01G330400 chr4B 88.761 872 73 12 1317 2167 4232185 4233052 0.000000e+00 1044.0
20 TraesCS7D01G330400 chr1D 90.968 775 62 6 1 771 467601234 467602004 0.000000e+00 1037.0
21 TraesCS7D01G330400 chr4A 88.087 873 78 12 1317 2167 663652650 663651782 0.000000e+00 1013.0
22 TraesCS7D01G330400 chr6A 81.284 732 66 43 775 1467 49550604 49551303 6.330000e-146 527.0
23 TraesCS7D01G330400 chr6A 77.503 889 65 67 775 1622 49483557 49484351 2.390000e-110 409.0
24 TraesCS7D01G330400 chr6A 79.566 553 51 31 939 1467 49201970 49202484 3.180000e-89 339.0
25 TraesCS7D01G330400 chr6A 90.278 72 6 1 777 848 49201577 49201647 2.730000e-15 93.5
26 TraesCS7D01G330400 chr6D 80.495 728 63 36 775 1467 37933794 37934477 3.860000e-133 484.0
27 TraesCS7D01G330400 chr6D 78.309 899 87 57 777 1628 37927548 37928385 4.990000e-132 481.0
28 TraesCS7D01G330400 chr6B 79.277 719 71 31 775 1474 88781103 88781762 5.100000e-117 431.0
29 TraesCS7D01G330400 chr6B 79.526 591 49 38 899 1467 88717341 88717881 3.160000e-94 355.0


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 TraesCS7D01G330400 chr7D 422150985 422153565 2580 True 4767.00 4767 100.0000 1 2581 1 chr7D.!!$R1 2580
1 TraesCS7D01G330400 chr7D 599718655 599719424 769 False 643.00 643 82.1430 1 766 1 chr7D.!!$F1 765
2 TraesCS7D01G330400 chr7B 438949969 438952101 2132 False 1143.00 2115 92.9630 797 2581 2 chr7B.!!$F1 1784
3 TraesCS7D01G330400 chr5D 423964409 423965781 1372 False 1411.00 1411 85.6650 776 2167 1 chr5D.!!$F1 1391
4 TraesCS7D01G330400 chr5D 499061021 499061689 668 True 1031.00 1031 94.4690 1 669 1 chr5D.!!$R2 668
5 TraesCS7D01G330400 chr5D 424819147 424819921 774 True 584.00 584 80.7110 1 770 1 chr5D.!!$R1 769
6 TraesCS7D01G330400 chr5B 511835216 511836578 1362 False 1371.00 1371 85.2680 775 2167 1 chr5B.!!$F1 1392
7 TraesCS7D01G330400 chr7A 511011974 511013748 1774 False 1092.00 1253 88.9855 777 2581 2 chr7A.!!$F1 1804
8 TraesCS7D01G330400 chr7A 15255109 15255775 666 True 1050.00 1050 95.0600 1 667 1 chr7A.!!$R1 666
9 TraesCS7D01G330400 chr5A 537368757 537369857 1100 False 1182.00 1182 86.4910 775 1877 1 chr5A.!!$F1 1102
10 TraesCS7D01G330400 chr5A 631680098 631680868 770 True 1050.00 1050 91.2480 1 773 1 chr5A.!!$R1 772
11 TraesCS7D01G330400 chr5A 709279702 709280469 767 True 1007.00 1007 90.3100 1 773 1 chr5A.!!$R2 772
12 TraesCS7D01G330400 chr4D 224752805 224753582 777 True 1134.00 1134 93.0770 1 775 1 chr4D.!!$R2 774
13 TraesCS7D01G330400 chr4D 53419405 53420071 666 True 1040.00 1040 94.7680 1 669 1 chr4D.!!$R1 668
14 TraesCS7D01G330400 chr2A 760865175 760865948 773 False 1051.00 1051 91.2140 1 773 1 chr2A.!!$F2 772
15 TraesCS7D01G330400 chr2A 744776721 744777489 768 False 1000.00 1000 90.2190 1 770 1 chr2A.!!$F1 769
16 TraesCS7D01G330400 chr4B 4232185 4233052 867 False 1044.00 1044 88.7610 1317 2167 1 chr4B.!!$F1 850
17 TraesCS7D01G330400 chr1D 467601234 467602004 770 False 1037.00 1037 90.9680 1 771 1 chr1D.!!$F1 770
18 TraesCS7D01G330400 chr4A 663651782 663652650 868 True 1013.00 1013 88.0870 1317 2167 1 chr4A.!!$R1 850
19 TraesCS7D01G330400 chr6A 49550604 49551303 699 False 527.00 527 81.2840 775 1467 1 chr6A.!!$F2 692
20 TraesCS7D01G330400 chr6A 49483557 49484351 794 False 409.00 409 77.5030 775 1622 1 chr6A.!!$F1 847
21 TraesCS7D01G330400 chr6A 49201577 49202484 907 False 216.25 339 84.9220 777 1467 2 chr6A.!!$F3 690
22 TraesCS7D01G330400 chr6D 37933794 37934477 683 False 484.00 484 80.4950 775 1467 1 chr6D.!!$F2 692
23 TraesCS7D01G330400 chr6D 37927548 37928385 837 False 481.00 481 78.3090 777 1628 1 chr6D.!!$F1 851
24 TraesCS7D01G330400 chr6B 88781103 88781762 659 False 431.00 431 79.2770 775 1474 1 chr6B.!!$F2 699
25 TraesCS7D01G330400 chr6B 88717341 88717881 540 False 355.00 355 79.5260 899 1467 1 chr6B.!!$F1 568

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
738 782 0.042188 CGTGAAACCGTTCAGTGCAG 60.042 55.0 0.0 0.0 44.44 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 3082 0.112412 ACCCAATGAAAACCGCCTCT 59.888 50.0 0.0 0.0 0.0 3.69 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
685 728 1.264672 GCGGACGCGCAATTATTTTT 58.735 45.000 5.73 0.00 34.62 1.94
687 730 2.510874 CGGACGCGCAATTATTTTTCA 58.489 42.857 5.73 0.00 0.00 2.69
734 777 2.877974 GCGCGTGAAACCGTTCAGT 61.878 57.895 8.43 0.00 44.44 3.41
737 780 2.010670 CGTGAAACCGTTCAGTGCA 58.989 52.632 0.00 0.00 44.44 4.57
738 782 0.042188 CGTGAAACCGTTCAGTGCAG 60.042 55.000 0.00 0.00 44.44 4.41
879 930 1.608025 GCAGGAAACACAGATCCGTCA 60.608 52.381 0.00 0.00 40.78 4.35
929 1349 5.252630 ACTCAAATCTTTTCATCCTCCTCCT 59.747 40.000 0.00 0.00 0.00 3.69
960 1387 4.776837 TCCTACCTTCGTTACAAATACCCA 59.223 41.667 0.00 0.00 0.00 4.51
961 1388 5.426185 TCCTACCTTCGTTACAAATACCCAT 59.574 40.000 0.00 0.00 0.00 4.00
962 1389 5.526111 CCTACCTTCGTTACAAATACCCATG 59.474 44.000 0.00 0.00 0.00 3.66
963 1390 4.266714 ACCTTCGTTACAAATACCCATGG 58.733 43.478 4.14 4.14 0.00 3.66
1099 1554 0.107945 GCCGACAAGGAGAATCTGCT 60.108 55.000 0.00 0.00 45.00 4.24
1105 1560 0.394080 AAGGAGAATCTGCTGCCAGC 60.394 55.000 10.45 10.45 42.82 4.85
1106 1561 2.178890 GGAGAATCTGCTGCCAGCG 61.179 63.158 12.80 7.19 46.26 5.18
1107 1562 1.153489 GAGAATCTGCTGCCAGCGA 60.153 57.895 12.80 12.52 46.26 4.93
1108 1563 1.427592 GAGAATCTGCTGCCAGCGAC 61.428 60.000 12.80 1.53 46.26 5.19
1109 1564 2.437359 AATCTGCTGCCAGCGACC 60.437 61.111 12.80 0.00 46.26 4.79
1110 1565 3.258228 AATCTGCTGCCAGCGACCA 62.258 57.895 12.80 0.00 46.26 4.02
1111 1566 3.965539 ATCTGCTGCCAGCGACCAC 62.966 63.158 12.80 0.00 46.26 4.16
1147 1614 4.034246 CCGTCCTCATGGGAGTCA 57.966 61.111 0.00 0.00 46.10 3.41
1148 1615 2.521103 CCGTCCTCATGGGAGTCAT 58.479 57.895 0.00 0.00 46.10 3.06
1172 1642 4.315588 GCTGTCAGGAGCTGCAAT 57.684 55.556 8.35 0.00 35.95 3.56
1337 1825 2.358247 GAGCCGGCCGTGAAGAAA 60.358 61.111 26.15 0.00 0.00 2.52
1344 1832 1.600916 GCCGTGAAGAAAGGGCTGT 60.601 57.895 0.83 0.00 45.59 4.40
1556 2112 7.597386 AGAGAAAACTCAAAATGGATGCTTAC 58.403 34.615 0.00 0.00 0.00 2.34
1647 2206 0.106318 ATTTGGAGCTGGGATCTGCC 60.106 55.000 0.00 0.00 38.41 4.85
1714 2277 0.825010 CAAGCCACTCCCTTTGCAGT 60.825 55.000 0.00 0.00 0.00 4.40
1715 2278 0.771127 AAGCCACTCCCTTTGCAGTA 59.229 50.000 0.00 0.00 0.00 2.74
1801 2364 2.350772 GGATGTTGAAACTGCTTCGGTG 60.351 50.000 0.00 0.00 36.78 4.94
1808 2371 1.032014 AACTGCTTCGGTGCAACAAT 58.968 45.000 0.98 0.00 42.83 2.71
1817 2380 1.876799 CGGTGCAACAATTACTGTGGA 59.123 47.619 0.98 0.00 38.67 4.02
1831 2394 1.043116 TGTGGATGCGGTAGAGGGAG 61.043 60.000 0.00 0.00 0.00 4.30
1841 2404 1.625879 TAGAGGGAGGCAGGAGGGA 60.626 63.158 0.00 0.00 0.00 4.20
1889 2452 9.309516 ACAATATACCAGTATACTTTCGTTGTG 57.690 33.333 1.56 0.44 29.69 3.33
1934 2497 9.600646 GTACTTGAGTCTAGCAAAATTTTCTTC 57.399 33.333 0.00 0.00 0.00 2.87
2026 2589 7.172361 GGCATTAGGAAGATAACAGAGTTGATC 59.828 40.741 0.00 0.00 0.00 2.92
2076 2650 6.152323 TGAGATAGCTTAGTTCCGTTAACAGT 59.848 38.462 6.39 0.00 40.83 3.55
2082 2656 6.152323 AGCTTAGTTCCGTTAACAGTATCTGA 59.848 38.462 6.39 0.00 40.83 3.27
2159 2737 2.159099 TGACTATGCTCCTTAACAGGCG 60.159 50.000 0.00 0.00 40.58 5.52
2167 2745 3.381949 CTCCTTAACAGGCGTATAGTGC 58.618 50.000 0.00 0.00 40.58 4.40
2180 2767 4.440525 GCGTATAGTGCCAACTTGTAGGTA 60.441 45.833 0.00 0.00 37.88 3.08
2182 2769 5.066893 CGTATAGTGCCAACTTGTAGGTAGA 59.933 44.000 0.00 0.00 37.88 2.59
2206 2793 9.129870 AGATAACTAGTATTCTCTCTATCCCCA 57.870 37.037 0.00 0.00 0.00 4.96
2218 2805 4.984268 TCTCTATCCCCATCCAAATTTCCT 59.016 41.667 0.00 0.00 0.00 3.36
2229 2816 9.018582 CCCATCCAAATTTCCTTCTATAAGATC 57.981 37.037 0.00 0.00 34.37 2.75
2312 2900 7.332182 TGTTTTCGCTTTTGTTATTTTTCTGGT 59.668 29.630 0.00 0.00 0.00 4.00
2313 2901 6.820470 TTCGCTTTTGTTATTTTTCTGGTG 57.180 33.333 0.00 0.00 0.00 4.17
2337 2925 5.479716 TTGAACTTTGTTTCTTCTCGGTC 57.520 39.130 0.00 0.00 0.00 4.79
2349 2937 0.594602 TCTCGGTCGATTTCACGTGT 59.405 50.000 16.51 0.00 34.70 4.49
2353 2941 1.724623 CGGTCGATTTCACGTGTGATT 59.275 47.619 16.51 2.31 39.64 2.57
2426 3015 2.416836 GCCCGATAAAAGTTTGGAAGGC 60.417 50.000 0.00 0.00 0.00 4.35
2489 3081 1.080298 GGTGTAGTAGCGTTGCCGT 60.080 57.895 0.00 0.00 36.15 5.68
2490 3082 0.171007 GGTGTAGTAGCGTTGCCGTA 59.829 55.000 0.00 0.00 36.15 4.02
2508 3100 1.743394 GTAGAGGCGGTTTTCATTGGG 59.257 52.381 0.00 0.00 0.00 4.12
2553 3152 9.604626 CTTTTTGTGTTCTTTGCATTGTTTTTA 57.395 25.926 0.00 0.00 0.00 1.52
2559 3158 6.697019 TGTTCTTTGCATTGTTTTTAGAGCTC 59.303 34.615 5.27 5.27 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.217231 CGGAGCGGTTGGATAGGT 58.783 61.111 0.00 0.00 0.00 3.08
669 710 2.906161 ACGTGAAAAATAATTGCGCGTC 59.094 40.909 8.43 0.00 36.68 5.19
670 711 2.654528 CACGTGAAAAATAATTGCGCGT 59.345 40.909 10.90 2.12 39.72 6.01
680 723 3.917985 GGAAATAAGCGCACGTGAAAAAT 59.082 39.130 22.23 2.26 0.00 1.82
685 728 1.075542 CTGGAAATAAGCGCACGTGA 58.924 50.000 22.23 0.00 0.00 4.35
687 730 1.644786 GGCTGGAAATAAGCGCACGT 61.645 55.000 11.47 0.00 41.78 4.49
734 777 3.319689 GGTAACTTGGTTTTTAGCCTGCA 59.680 43.478 0.00 0.00 0.00 4.41
737 780 2.555325 GCGGTAACTTGGTTTTTAGCCT 59.445 45.455 0.00 0.00 0.00 4.58
738 782 2.666344 CGCGGTAACTTGGTTTTTAGCC 60.666 50.000 0.00 0.00 0.00 3.93
879 930 2.236959 GAGAGGAGTGGGAGGGAGCT 62.237 65.000 0.00 0.00 0.00 4.09
929 1349 2.617840 ACGAAGGTAGGAGGGAAGAA 57.382 50.000 0.00 0.00 0.00 2.52
963 1390 2.105649 GGGACTGGAAGGATCTTCCATC 59.894 54.545 24.30 21.34 46.47 3.51
1041 1487 1.408702 GAAGAAGATCTGCCGCTCTCT 59.591 52.381 0.00 0.00 0.00 3.10
1142 1609 0.173481 TGACAGCTACGCCATGACTC 59.827 55.000 0.00 0.00 0.00 3.36
1143 1610 0.174389 CTGACAGCTACGCCATGACT 59.826 55.000 0.00 0.00 0.00 3.41
1144 1611 0.807667 CCTGACAGCTACGCCATGAC 60.808 60.000 0.00 0.00 0.00 3.06
1145 1612 0.970427 TCCTGACAGCTACGCCATGA 60.970 55.000 0.00 0.00 0.00 3.07
1146 1613 0.529337 CTCCTGACAGCTACGCCATG 60.529 60.000 0.00 0.00 0.00 3.66
1147 1614 1.819229 CTCCTGACAGCTACGCCAT 59.181 57.895 0.00 0.00 0.00 4.40
1148 1615 3.006756 GCTCCTGACAGCTACGCCA 62.007 63.158 0.00 0.00 36.38 5.69
1149 1616 2.202810 GCTCCTGACAGCTACGCC 60.203 66.667 0.00 0.00 36.38 5.68
1172 1642 3.452786 CTCCCGAGCCGCTTCAGA 61.453 66.667 0.00 0.00 0.00 3.27
1344 1832 2.203139 CAGTGCAACACCACCGGA 60.203 61.111 9.46 0.00 41.43 5.14
1556 2112 4.816385 AGTATGCCACACCTTTAATCGATG 59.184 41.667 0.00 0.00 0.00 3.84
1639 2198 2.364002 GGAGAACTGTAGAGGCAGATCC 59.636 54.545 0.00 1.64 38.53 3.36
1647 2206 3.192422 CACAGTCCTGGAGAACTGTAGAG 59.808 52.174 16.53 4.58 40.94 2.43
1773 2336 4.154942 AGCAGTTTCAACATCCTTCCATT 58.845 39.130 0.00 0.00 0.00 3.16
1780 2343 1.880027 ACCGAAGCAGTTTCAACATCC 59.120 47.619 0.00 0.00 35.43 3.51
1801 2364 2.518949 CGCATCCACAGTAATTGTTGC 58.481 47.619 0.00 0.00 38.16 4.17
1808 2371 1.754803 CCTCTACCGCATCCACAGTAA 59.245 52.381 0.00 0.00 0.00 2.24
1817 2380 2.041922 TGCCTCCCTCTACCGCAT 60.042 61.111 0.00 0.00 0.00 4.73
1831 2394 0.749049 GCAAATCATTCCCTCCTGCC 59.251 55.000 0.00 0.00 0.00 4.85
1841 2404 3.202906 GCTGAATGCCATGCAAATCATT 58.797 40.909 9.48 9.48 43.62 2.57
1889 2452 3.409026 ACACCTGAAATCACTGAGACC 57.591 47.619 0.00 0.00 0.00 3.85
2026 2589 3.119316 GCTGGGATAGTCAGATGTATCCG 60.119 52.174 12.59 4.92 44.03 4.18
2130 2708 2.826488 AGGAGCATAGTCAAGACTGGT 58.174 47.619 12.77 3.64 42.52 4.00
2159 2737 6.461110 TCTACCTACAAGTTGGCACTATAC 57.539 41.667 7.96 0.00 30.68 1.47
2180 2767 9.129870 TGGGGATAGAGAGAATACTAGTTATCT 57.870 37.037 0.00 5.19 32.71 1.98
2182 2769 9.930158 GATGGGGATAGAGAGAATACTAGTTAT 57.070 37.037 0.00 0.00 0.00 1.89
2206 2793 8.736675 TGGGATCTTATAGAAGGAAATTTGGAT 58.263 33.333 0.00 0.00 33.09 3.41
2312 2900 5.182380 ACCGAGAAGAAACAAAGTTCAAACA 59.818 36.000 0.00 0.00 0.00 2.83
2313 2901 5.637809 ACCGAGAAGAAACAAAGTTCAAAC 58.362 37.500 0.00 0.00 0.00 2.93
2337 2925 5.763444 AGAAGTAATCACACGTGAAATCG 57.237 39.130 25.01 4.99 43.58 3.34
2349 2937 7.609760 AATGCACAAATCGTAGAAGTAATCA 57.390 32.000 0.00 0.00 43.58 2.57
2379 2967 2.854963 AGAACAAGCTTCACATCAGCA 58.145 42.857 0.00 0.00 39.99 4.41
2380 2968 3.911661 AAGAACAAGCTTCACATCAGC 57.088 42.857 0.00 0.00 37.56 4.26
2426 3015 2.159128 AGGCGAGACATGAACATCTCAG 60.159 50.000 0.00 0.00 41.28 3.35
2463 3055 0.384669 CGCTACTACACCTGGCCTAC 59.615 60.000 3.32 0.00 0.00 3.18
2489 3081 1.353022 ACCCAATGAAAACCGCCTCTA 59.647 47.619 0.00 0.00 0.00 2.43
2490 3082 0.112412 ACCCAATGAAAACCGCCTCT 59.888 50.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.