Multiple sequence alignment - TraesCS7D01G327200

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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 TraesCS7D01G327200 chr7D 100.000 6686 0 0 1 6686 417932341 417925656 0.000000e+00 12347.0
1 TraesCS7D01G327200 chr7D 98.111 3441 28 10 3271 6686 418054078 418050650 0.000000e+00 5960.0
2 TraesCS7D01G327200 chr7D 98.695 2145 15 3 1134 3277 418057180 418055048 0.000000e+00 3794.0
3 TraesCS7D01G327200 chr7D 94.825 2029 56 22 2 2023 418618003 418616017 0.000000e+00 3120.0
4 TraesCS7D01G327200 chr7D 93.602 1438 80 5 3282 4711 418902206 418900773 0.000000e+00 2135.0
5 TraesCS7D01G327200 chr7D 93.394 1438 82 6 3282 4711 418614364 418612932 0.000000e+00 2117.0
6 TraesCS7D01G327200 chr7D 91.995 1499 71 21 528 2023 418904812 418903360 0.000000e+00 2058.0
7 TraesCS7D01G327200 chr7D 96.332 1145 33 6 1 1143 418070272 418069135 0.000000e+00 1873.0
8 TraesCS7D01G327200 chr7D 90.267 1161 58 21 2081 3194 418903361 418902209 0.000000e+00 1467.0
9 TraesCS7D01G327200 chr7D 91.868 787 50 7 3931 4711 418394478 418393700 0.000000e+00 1086.0
10 TraesCS7D01G327200 chr7D 90.065 775 52 11 4695 5448 418900758 418899988 0.000000e+00 981.0
11 TraesCS7D01G327200 chr7D 89.935 775 52 12 4695 5448 418612917 418612148 0.000000e+00 976.0
12 TraesCS7D01G327200 chr7D 87.485 815 69 17 4695 5488 418393685 418392883 0.000000e+00 909.0
13 TraesCS7D01G327200 chr7D 88.551 690 54 7 5880 6548 418390028 418389343 0.000000e+00 813.0
14 TraesCS7D01G327200 chr7D 87.983 699 50 7 5880 6548 418899542 418898848 0.000000e+00 795.0
15 TraesCS7D01G327200 chr7D 91.754 570 39 5 3378 3943 418396271 418395706 0.000000e+00 785.0
16 TraesCS7D01G327200 chr7D 90.034 592 34 9 2081 2655 418616018 418615435 0.000000e+00 743.0
17 TraesCS7D01G327200 chr7D 89.428 577 29 13 2648 3194 418614941 418614367 0.000000e+00 699.0
18 TraesCS7D01G327200 chr7D 84.533 653 69 6 5880 6501 449508701 449508050 9.530000e-173 617.0
19 TraesCS7D01G327200 chr7D 84.394 487 43 7 6092 6548 418597301 418596818 1.320000e-121 448.0
20 TraesCS7D01G327200 chr7D 83.333 150 19 5 6540 6686 529914194 529914340 4.210000e-27 134.0
21 TraesCS7D01G327200 chr7B 93.036 5184 261 50 528 5681 433872395 433867282 0.000000e+00 7481.0
22 TraesCS7D01G327200 chr7B 92.663 4825 188 63 528 5254 434365319 434360563 0.000000e+00 6796.0
23 TraesCS7D01G327200 chr7B 90.794 1662 87 22 937 2569 212775890 212777514 0.000000e+00 2161.0
24 TraesCS7D01G327200 chr7B 91.467 750 28 7 5835 6548 433866714 433865965 0.000000e+00 998.0
25 TraesCS7D01G327200 chr7B 88.314 676 45 7 5880 6525 434358581 434357910 0.000000e+00 780.0
26 TraesCS7D01G327200 chr7B 79.017 1139 183 36 3516 4612 212778618 212779742 0.000000e+00 728.0
27 TraesCS7D01G327200 chr7B 85.694 699 67 6 5877 6545 212781003 212781698 0.000000e+00 706.0
28 TraesCS7D01G327200 chr7B 80.204 980 137 28 4733 5681 212779783 212780736 0.000000e+00 682.0
29 TraesCS7D01G327200 chr7B 87.454 542 36 14 6039 6548 434160890 434160349 4.460000e-166 595.0
30 TraesCS7D01G327200 chr7B 83.658 514 46 15 528 1010 434173119 434172613 3.680000e-122 449.0
31 TraesCS7D01G327200 chr7B 85.588 340 27 11 2571 2888 212777600 212777939 2.990000e-88 337.0
32 TraesCS7D01G327200 chr7B 87.701 187 19 2 16 201 212774610 212774793 1.460000e-51 215.0
33 TraesCS7D01G327200 chr7B 94.215 121 7 0 388 508 212774809 212774929 1.140000e-42 185.0
34 TraesCS7D01G327200 chr7B 87.209 86 7 3 3309 3390 212778020 212778105 1.980000e-15 95.3
35 TraesCS7D01G327200 chr7A 93.027 3542 149 36 1873 5368 483946286 483942797 0.000000e+00 5083.0
36 TraesCS7D01G327200 chr7A 95.785 2135 66 8 3558 5681 483488808 483486687 0.000000e+00 3422.0
37 TraesCS7D01G327200 chr7A 96.125 1316 43 7 2254 3562 483494288 483492974 0.000000e+00 2141.0
38 TraesCS7D01G327200 chr7A 95.754 895 26 3 929 1819 483495738 483494852 0.000000e+00 1432.0
39 TraesCS7D01G327200 chr7A 95.642 895 26 4 929 1819 483947170 483946285 0.000000e+00 1424.0
40 TraesCS7D01G327200 chr7A 90.358 643 55 3 3303 3943 483746833 483746196 0.000000e+00 837.0
41 TraesCS7D01G327200 chr7A 91.708 603 37 7 3928 4524 483744968 483744373 0.000000e+00 824.0
42 TraesCS7D01G327200 chr7A 87.639 720 55 12 5860 6548 483486188 483485472 0.000000e+00 806.0
43 TraesCS7D01G327200 chr7A 90.674 386 21 9 1873 2258 483494853 483494483 3.600000e-137 499.0
44 TraesCS7D01G327200 chr7A 90.132 304 16 4 4964 5254 483654903 483654601 3.780000e-102 383.0
45 TraesCS7D01G327200 chr7A 90.566 265 23 2 5880 6144 483653538 483653276 3.840000e-92 350.0
46 TraesCS7D01G327200 chr7A 89.394 66 7 0 5616 5681 514706529 514706594 4.300000e-12 84.2
47 TraesCS7D01G327200 chr5B 90.491 326 20 7 1359 1681 101893622 101893939 2.880000e-113 420.0
48 TraesCS7D01G327200 chr5B 94.118 187 11 0 1697 1883 290922982 290922796 1.100000e-72 285.0
49 TraesCS7D01G327200 chr5B 81.757 148 14 4 19 159 73395132 73394991 1.970000e-20 111.0
50 TraesCS7D01G327200 chr2B 93.462 260 17 0 1119 1378 42564790 42565049 2.920000e-103 387.0
51 TraesCS7D01G327200 chr5A 100.000 157 0 0 5678 5834 31738902 31739058 2.360000e-74 291.0
52 TraesCS7D01G327200 chr5A 100.000 157 0 0 5678 5834 31828107 31828263 2.360000e-74 291.0
53 TraesCS7D01G327200 chr5A 100.000 157 0 0 5678 5834 31919506 31919662 2.360000e-74 291.0
54 TraesCS7D01G327200 chrUn 100.000 155 0 0 5680 5834 40097882 40097728 3.050000e-73 287.0
55 TraesCS7D01G327200 chrUn 100.000 155 0 0 5680 5834 399744423 399744269 3.050000e-73 287.0
56 TraesCS7D01G327200 chr4D 100.000 155 0 0 5680 5834 123627423 123627577 3.050000e-73 287.0
57 TraesCS7D01G327200 chr4D 100.000 155 0 0 5680 5834 135017481 135017327 3.050000e-73 287.0
58 TraesCS7D01G327200 chr1D 100.000 155 0 0 5680 5834 185752390 185752544 3.050000e-73 287.0
59 TraesCS7D01G327200 chr1D 86.986 146 15 2 6541 6686 72467639 72467498 1.930000e-35 161.0
60 TraesCS7D01G327200 chr5D 90.604 149 8 5 6540 6686 377869383 377869527 6.840000e-45 193.0
61 TraesCS7D01G327200 chr5D 89.262 149 10 6 6540 6686 520506521 520506665 1.480000e-41 182.0
62 TraesCS7D01G327200 chr5D 84.066 182 26 2 208 389 470464919 470465097 8.910000e-39 172.0
63 TraesCS7D01G327200 chr5D 82.301 113 14 5 48 157 67348940 67348831 7.140000e-15 93.5
64 TraesCS7D01G327200 chr2D 89.404 151 10 5 6539 6686 11497633 11497780 1.140000e-42 185.0
65 TraesCS7D01G327200 chr2D 88.000 150 10 6 6540 6686 112309983 112310127 3.210000e-38 171.0
66 TraesCS7D01G327200 chr1A 82.759 203 24 9 190 389 349338513 349338707 3.210000e-38 171.0
67 TraesCS7D01G327200 chr1A 90.698 129 8 4 6559 6686 405547774 405547649 1.150000e-37 169.0
68 TraesCS7D01G327200 chr1A 92.188 64 2 3 2021 2082 53412015 53412077 3.320000e-13 87.9
69 TraesCS7D01G327200 chr6A 93.578 109 4 2 6543 6650 616113695 616113589 6.940000e-35 159.0
70 TraesCS7D01G327200 chr4B 80.000 170 27 5 198 366 412507887 412508050 1.180000e-22 119.0
71 TraesCS7D01G327200 chr4B 81.481 81 2 7 319 390 506616840 506616764 3.000000e-03 54.7
72 TraesCS7D01G327200 chr3A 79.137 139 18 5 17 153 611936451 611936322 1.190000e-12 86.1


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 TraesCS7D01G327200 chr7D 417925656 417932341 6685 True 12347.000000 12347 100.000000 1 6686 1 chr7D.!!$R1 6685
1 TraesCS7D01G327200 chr7D 418050650 418057180 6530 True 4877.000000 5960 98.403000 1134 6686 2 chr7D.!!$R5 5552
2 TraesCS7D01G327200 chr7D 418069135 418070272 1137 True 1873.000000 1873 96.332000 1 1143 1 chr7D.!!$R2 1142
3 TraesCS7D01G327200 chr7D 418612148 418618003 5855 True 1531.000000 3120 91.523200 2 5448 5 chr7D.!!$R7 5446
4 TraesCS7D01G327200 chr7D 418898848 418904812 5964 True 1487.200000 2135 90.782400 528 6548 5 chr7D.!!$R8 6020
5 TraesCS7D01G327200 chr7D 418389343 418396271 6928 True 898.250000 1086 89.914500 3378 6548 4 chr7D.!!$R6 3170
6 TraesCS7D01G327200 chr7D 449508050 449508701 651 True 617.000000 617 84.533000 5880 6501 1 chr7D.!!$R4 621
7 TraesCS7D01G327200 chr7B 433865965 433872395 6430 True 4239.500000 7481 92.251500 528 6548 2 chr7B.!!$R3 6020
8 TraesCS7D01G327200 chr7B 434357910 434365319 7409 True 3788.000000 6796 90.488500 528 6525 2 chr7B.!!$R4 5997
9 TraesCS7D01G327200 chr7B 212774610 212781698 7088 False 638.662500 2161 86.302750 16 6545 8 chr7B.!!$F1 6529
10 TraesCS7D01G327200 chr7B 434160349 434160890 541 True 595.000000 595 87.454000 6039 6548 1 chr7B.!!$R1 509
11 TraesCS7D01G327200 chr7B 434172613 434173119 506 True 449.000000 449 83.658000 528 1010 1 chr7B.!!$R2 482
12 TraesCS7D01G327200 chr7A 483942797 483947170 4373 True 3253.500000 5083 94.334500 929 5368 2 chr7A.!!$R5 4439
13 TraesCS7D01G327200 chr7A 483485472 483488808 3336 True 2114.000000 3422 91.712000 3558 6548 2 chr7A.!!$R1 2990
14 TraesCS7D01G327200 chr7A 483492974 483495738 2764 True 1357.333333 2141 94.184333 929 3562 3 chr7A.!!$R2 2633
15 TraesCS7D01G327200 chr7A 483744373 483746833 2460 True 830.500000 837 91.033000 3303 4524 2 chr7A.!!$R4 1221
16 TraesCS7D01G327200 chr7A 483653276 483654903 1627 True 366.500000 383 90.349000 4964 6144 2 chr7A.!!$R3 1180

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
431 436 0.036732 GTTGGCCTGATGAGGTGACA 59.963 55.000 3.32 0.0 42.15 3.58 F
908 1544 2.609459 CCGCTAGAATGAATCGTTGCTT 59.391 45.455 0.00 0.0 0.00 3.91 F
1409 2078 2.725008 GGAGCGTCATCCTCCTCG 59.275 66.667 0.33 0.0 44.40 4.63 F
2045 2725 6.144845 ACTCCCTCCATCCCAAATATAATG 57.855 41.667 0.00 0.0 0.00 1.90 F
2955 4486 0.107831 AGCTACGCTTGGTGGTTTCA 59.892 50.000 0.00 0.0 33.89 2.69 F
4303 9803 3.287222 TGTGGGCTTTATACTGGAATGC 58.713 45.455 0.00 0.0 0.00 3.56 F
5403 11057 5.069516 AGTTCCATTTGTTCTCAGCACATTT 59.930 36.000 0.00 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1306 1966 1.260825 GCTCGTCGTCGTCATCAGATA 59.739 52.381 1.33 0.00 38.33 1.98 R
2045 2725 5.448632 CCCACAATATAGCTTGGAAAACGAC 60.449 44.000 1.24 0.00 0.00 4.34 R
2955 4486 6.378280 CCCAATGGACTAAGCAAGAAATTACT 59.622 38.462 0.00 0.00 0.00 2.24 R
4303 9803 7.095271 ACTGACAGTTTTTGTTTTTGTTCCATG 60.095 33.333 1.07 0.00 41.05 3.66 R
4854 10398 6.839124 TCAAAAACACATAAGGCATCTGAT 57.161 33.333 0.00 0.00 0.00 2.90 R
5403 11057 2.300152 CAGGTCCAGAGTTGACTAGCAA 59.700 50.000 0.00 0.00 33.22 3.91 R
6568 16375 6.183360 TGCTTCAATCTATAAAATTGGGGCAG 60.183 38.462 15.56 7.55 37.23 4.85 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
95 100 1.143969 GCCGACCCGATAACTTCGTG 61.144 60.000 0.00 0.00 46.65 4.35
225 230 2.577606 TGGTTTGTGGGATCGTCATT 57.422 45.000 0.00 0.00 0.00 2.57
334 339 8.033038 ACAATCCATTATGCATCTTCATATTGC 58.967 33.333 0.19 0.00 32.85 3.56
431 436 0.036732 GTTGGCCTGATGAGGTGACA 59.963 55.000 3.32 0.00 42.15 3.58
464 469 2.899339 GCCAGAATCTGCGAGGCC 60.899 66.667 4.40 0.00 39.42 5.19
653 1250 9.713740 TCGGAATTTCAAAATTTTGTTTCATTG 57.286 25.926 25.98 18.76 38.64 2.82
908 1544 2.609459 CCGCTAGAATGAATCGTTGCTT 59.391 45.455 0.00 0.00 0.00 3.91
1409 2078 2.725008 GGAGCGTCATCCTCCTCG 59.275 66.667 0.33 0.00 44.40 4.63
1829 2509 6.818281 ACCCTGCAAATATACAACCTACTA 57.182 37.500 0.00 0.00 0.00 1.82
2045 2725 6.144845 ACTCCCTCCATCCCAAATATAATG 57.855 41.667 0.00 0.00 0.00 1.90
2955 4486 0.107831 AGCTACGCTTGGTGGTTTCA 59.892 50.000 0.00 0.00 33.89 2.69
3102 4633 5.144100 TCTTTCAGGCATAAGGTGGAAAAA 58.856 37.500 0.00 0.00 0.00 1.94
4303 9803 3.287222 TGTGGGCTTTATACTGGAATGC 58.713 45.455 0.00 0.00 0.00 3.56
5403 11057 5.069516 AGTTCCATTTGTTCTCAGCACATTT 59.930 36.000 0.00 0.00 0.00 2.32
6037 15790 1.078848 GACAGCTCCTTGACGCCAT 60.079 57.895 0.00 0.00 0.00 4.40
6218 15980 4.410400 CCAGCCGTCCTTGGACCC 62.410 72.222 13.53 5.76 0.00 4.46
6422 16226 4.379243 CCACAGCTCGCCGTTCCT 62.379 66.667 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 100 2.421248 CCCTGAAGATCTTTCCTCTGCC 60.421 54.545 9.87 0.00 0.00 4.85
206 211 2.577606 AATGACGATCCCACAAACCA 57.422 45.000 0.00 0.00 0.00 3.67
244 249 3.130280 TGAGTCAGTGTAGACCGTACA 57.870 47.619 0.00 0.00 39.34 2.90
334 339 1.687123 CCCTATACGGTCACCCAGAAG 59.313 57.143 0.00 0.00 0.00 2.85
383 388 2.280797 GCCACGCAGACCTGTTGA 60.281 61.111 0.00 0.00 0.00 3.18
464 469 3.244665 TGCATAGGGGCTCTGACATTATG 60.245 47.826 0.00 0.00 34.04 1.90
599 1176 6.088719 TGTTTTCAAAGCACGAACATTTTC 57.911 33.333 0.00 0.00 0.00 2.29
662 1278 8.073768 ACGTTTTTAGAAAAATGACGATGTGAT 58.926 29.630 20.98 0.00 43.95 3.06
706 1334 6.524734 GGGAGAATTCCTGAAAACACAATTT 58.475 36.000 0.65 0.00 43.49 1.82
707 1335 6.101650 GGGAGAATTCCTGAAAACACAATT 57.898 37.500 0.65 0.00 43.49 2.32
708 1336 5.728637 GGGAGAATTCCTGAAAACACAAT 57.271 39.130 0.65 0.00 43.49 2.71
908 1544 0.970640 TCGATTTGGGTCCGTTCTGA 59.029 50.000 0.00 0.00 0.00 3.27
1305 1965 2.660631 GCTCGTCGTCGTCATCAGATAG 60.661 54.545 1.33 0.00 38.33 2.08
1306 1966 1.260825 GCTCGTCGTCGTCATCAGATA 59.739 52.381 1.33 0.00 38.33 1.98
1517 2186 3.355378 ACATCCACTCAGAGTCTCAGAG 58.645 50.000 18.10 18.10 36.28 3.35
1518 2187 3.448093 ACATCCACTCAGAGTCTCAGA 57.552 47.619 0.00 0.00 0.00 3.27
1519 2188 6.951062 TTATACATCCACTCAGAGTCTCAG 57.049 41.667 0.00 0.00 0.00 3.35
1520 2189 7.062957 TGATTATACATCCACTCAGAGTCTCA 58.937 38.462 0.00 0.00 0.00 3.27
1521 2190 7.309133 CCTGATTATACATCCACTCAGAGTCTC 60.309 44.444 0.00 0.00 33.59 3.36
1522 2191 6.493115 CCTGATTATACATCCACTCAGAGTCT 59.507 42.308 0.00 0.00 33.59 3.24
1523 2192 6.266558 ACCTGATTATACATCCACTCAGAGTC 59.733 42.308 0.00 0.00 33.59 3.36
1524 2193 6.139671 ACCTGATTATACATCCACTCAGAGT 58.860 40.000 0.00 0.00 33.59 3.24
2045 2725 5.448632 CCCACAATATAGCTTGGAAAACGAC 60.449 44.000 1.24 0.00 0.00 4.34
2300 3181 8.950210 CCATAAGAAGTGACTATGAACAAATGT 58.050 33.333 0.00 0.00 0.00 2.71
2955 4486 6.378280 CCCAATGGACTAAGCAAGAAATTACT 59.622 38.462 0.00 0.00 0.00 2.24
4303 9803 7.095271 ACTGACAGTTTTTGTTTTTGTTCCATG 60.095 33.333 1.07 0.00 41.05 3.66
4854 10398 6.839124 TCAAAAACACATAAGGCATCTGAT 57.161 33.333 0.00 0.00 0.00 2.90
5403 11057 2.300152 CAGGTCCAGAGTTGACTAGCAA 59.700 50.000 0.00 0.00 33.22 3.91
6568 16375 6.183360 TGCTTCAATCTATAAAATTGGGGCAG 60.183 38.462 15.56 7.55 37.23 4.85
6576 16383 9.578439 GCTTTGTTCTGCTTCAATCTATAAAAT 57.422 29.630 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.