Multiple sequence alignment - TraesCS4D01G196700

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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 TraesCS4D01G196700 chr4D 100.000 4434 0 0 1 4434 341411108 341406675 0.000000e+00 8152.0
1 TraesCS4D01G196700 chr4D 100.000 3534 0 0 4604 8137 341406505 341402972 0.000000e+00 6490.0
2 TraesCS4D01G196700 chr4D 96.061 1320 23 11 1653 2965 82733996 82735293 0.000000e+00 2124.0
3 TraesCS4D01G196700 chr4D 95.052 869 41 2 1 868 490422761 490421894 0.000000e+00 1365.0
4 TraesCS4D01G196700 chr2A 96.598 3557 76 14 4604 8137 657093666 657097200 0.000000e+00 5858.0
5 TraesCS4D01G196700 chr2A 97.698 1477 16 4 2966 4434 657092206 657093672 0.000000e+00 2523.0
6 TraesCS4D01G196700 chr2A 96.354 384 10 3 1274 1653 657091832 657092215 5.360000e-176 628.0
7 TraesCS4D01G196700 chr2A 92.558 215 11 5 7714 7925 520580736 520580524 3.690000e-78 303.0
8 TraesCS4D01G196700 chr2A 83.516 91 6 4 7586 7667 339090058 339089968 8.760000e-10 76.8
9 TraesCS4D01G196700 chr2A 89.286 56 3 3 7584 7637 767318868 767318814 5.270000e-07 67.6
10 TraesCS4D01G196700 chrUn 99.074 2591 9 3 1 2589 335165363 335167940 0.000000e+00 4638.0
11 TraesCS4D01G196700 chrUn 99.894 1893 2 0 4604 6496 365648887 365646995 0.000000e+00 3485.0
12 TraesCS4D01G196700 chrUn 99.007 1208 2 3 6939 8137 418950013 418951219 0.000000e+00 2156.0
13 TraesCS4D01G196700 chrUn 93.922 872 47 5 1 868 23308973 23309842 0.000000e+00 1312.0
14 TraesCS4D01G196700 chrUn 100.000 441 0 0 863 1303 475953382 475952942 0.000000e+00 815.0
15 TraesCS4D01G196700 chrUn 100.000 416 0 0 5086 5501 477180223 477180638 0.000000e+00 769.0
16 TraesCS4D01G196700 chr4B 91.460 2459 135 30 5050 7476 423055502 423053087 0.000000e+00 3310.0
17 TraesCS4D01G196700 chr4B 93.527 1483 66 16 2968 4434 423057615 423056147 0.000000e+00 2180.0
18 TraesCS4D01G196700 chr4B 92.366 786 44 6 871 1653 423058380 423057608 0.000000e+00 1105.0
19 TraesCS4D01G196700 chr4B 96.970 462 12 1 4604 5063 423056151 423055690 0.000000e+00 774.0
20 TraesCS4D01G196700 chr4B 90.769 520 46 2 1654 2172 613203275 613203793 0.000000e+00 693.0
21 TraesCS4D01G196700 chr4B 89.876 484 28 11 7674 8137 423052926 423052444 3.250000e-168 603.0
22 TraesCS4D01G196700 chr4B 91.837 49 3 1 7586 7633 533584107 533584155 5.270000e-07 67.6
23 TraesCS4D01G196700 chr4A 96.554 1480 33 10 2966 4434 125391688 125393160 0.000000e+00 2435.0
24 TraesCS4D01G196700 chr4A 92.838 1480 76 17 6021 7490 125394777 125396236 0.000000e+00 2121.0
25 TraesCS4D01G196700 chr4A 93.988 1364 57 12 4604 5957 125393153 125394501 0.000000e+00 2041.0
26 TraesCS4D01G196700 chr4A 93.281 506 20 9 1139 1639 125391148 125391644 0.000000e+00 734.0
27 TraesCS4D01G196700 chr4A 90.041 492 27 12 7663 8137 125396328 125396814 1.160000e-172 617.0
28 TraesCS4D01G196700 chr4A 92.642 299 21 1 864 1162 125390844 125391141 5.840000e-116 429.0
29 TraesCS4D01G196700 chr4A 100.000 33 0 0 7550 7582 125396290 125396322 2.450000e-05 62.1
30 TraesCS4D01G196700 chr6D 91.837 1323 72 11 1650 2967 258349407 258350698 0.000000e+00 1814.0
31 TraesCS4D01G196700 chr6D 87.405 1318 102 23 1654 2944 423179109 423180389 0.000000e+00 1459.0
32 TraesCS4D01G196700 chr6D 93.333 870 53 5 1 866 379009773 379008905 0.000000e+00 1280.0
33 TraesCS4D01G196700 chr6D 91.135 643 38 7 1653 2290 134685600 134686228 0.000000e+00 854.0
34 TraesCS4D01G196700 chr6D 91.394 581 38 2 2385 2965 134686233 134686801 0.000000e+00 787.0
35 TraesCS4D01G196700 chr7D 92.021 1153 60 18 1654 2805 636768409 636769530 0.000000e+00 1592.0
36 TraesCS4D01G196700 chr7D 88.669 706 63 6 2266 2965 408032316 408031622 0.000000e+00 846.0
37 TraesCS4D01G196700 chr7D 89.837 246 17 6 7680 7924 568325788 568326026 7.930000e-80 309.0
38 TraesCS4D01G196700 chr2D 89.942 1203 87 9 1654 2856 308901895 308903063 0.000000e+00 1522.0
39 TraesCS4D01G196700 chr2D 89.140 709 58 7 2266 2965 2488984 2489682 0.000000e+00 867.0
40 TraesCS4D01G196700 chr2D 88.293 709 64 7 2266 2965 187968141 187967443 0.000000e+00 833.0
41 TraesCS4D01G196700 chr2D 90.000 520 50 2 1654 2172 2488325 2488843 0.000000e+00 671.0
42 TraesCS4D01G196700 chr2D 82.635 167 26 2 3540 3706 453699448 453699611 2.370000e-30 145.0
43 TraesCS4D01G196700 chr2D 81.522 92 8 5 7586 7668 495786048 495785957 5.270000e-07 67.6
44 TraesCS4D01G196700 chr6A 89.992 1179 98 11 1755 2926 566423837 566422672 0.000000e+00 1507.0
45 TraesCS4D01G196700 chr6A 92.991 214 11 4 7714 7925 135573421 135573632 7.930000e-80 309.0
46 TraesCS4D01G196700 chr1B 93.995 866 47 4 4 865 95310358 95309494 0.000000e+00 1306.0
47 TraesCS4D01G196700 chr3A 93.807 872 47 6 1 867 476660749 476659880 0.000000e+00 1304.0
48 TraesCS4D01G196700 chr3A 81.188 101 9 4 7577 7667 36875000 36875100 1.130000e-08 73.1
49 TraesCS4D01G196700 chr7A 93.656 867 47 6 1 865 5013949 5013089 0.000000e+00 1290.0
50 TraesCS4D01G196700 chr7A 93.526 865 47 7 1 859 736019653 736020514 0.000000e+00 1279.0
51 TraesCS4D01G196700 chr7A 89.157 249 15 10 7680 7925 239426169 239426408 4.770000e-77 300.0
52 TraesCS4D01G196700 chr5D 93.612 861 49 6 4 860 422939950 422940808 0.000000e+00 1280.0
53 TraesCS4D01G196700 chr5D 88.136 708 64 9 2266 2965 91635197 91634502 0.000000e+00 826.0
54 TraesCS4D01G196700 chr5D 90.751 519 48 0 1654 2172 91635856 91635338 0.000000e+00 693.0
55 TraesCS4D01G196700 chr1D 88.543 707 63 6 2267 2965 234834367 234833671 0.000000e+00 843.0
56 TraesCS4D01G196700 chr1D 89.734 526 50 4 1648 2172 234835031 234834509 0.000000e+00 669.0
57 TraesCS4D01G196700 chr2B 87.853 708 66 7 2266 2964 247938631 247937935 0.000000e+00 815.0
58 TraesCS4D01G196700 chr2B 87.376 705 73 6 2266 2965 662578681 662577988 0.000000e+00 797.0
59 TraesCS4D01G196700 chr2B 91.154 520 44 2 1654 2172 247939293 247938775 0.000000e+00 704.0
60 TraesCS4D01G196700 chr1A 86.383 705 79 6 2266 2965 574363484 574362792 0.000000e+00 756.0
61 TraesCS4D01G196700 chr1A 88.247 485 45 2 2489 2973 86236545 86236073 9.160000e-159 571.0
62 TraesCS4D01G196700 chr1A 97.561 41 1 0 7586 7626 407633149 407633109 4.070000e-08 71.3
63 TraesCS4D01G196700 chr7B 90.244 246 15 7 7680 7924 703109536 703109299 6.130000e-81 313.0
64 TraesCS4D01G196700 chr7B 86.207 87 3 5 7585 7662 544587844 544587758 1.460000e-12 86.1
65 TraesCS4D01G196700 chr7B 89.796 49 4 1 7586 7633 428696354 428696306 2.450000e-05 62.1
66 TraesCS4D01G196700 chr7B 100.000 28 0 0 7641 7668 392129028 392129001 1.500000e-02 52.8
67 TraesCS4D01G196700 chr5A 89.157 249 15 10 7680 7925 28638595 28638356 4.770000e-77 300.0
68 TraesCS4D01G196700 chr5A 87.449 247 21 8 7680 7924 457007493 457007731 8.040000e-70 276.0
69 TraesCS4D01G196700 chr3D 83.721 86 5 4 7586 7662 583048553 583048468 1.130000e-08 73.1
70 TraesCS4D01G196700 chr3B 97.561 41 1 0 7586 7626 732568972 732569012 4.070000e-08 71.3
71 TraesCS4D01G196700 chr3B 83.146 89 2 6 7586 7661 15492524 15492612 1.470000e-07 69.4
72 TraesCS4D01G196700 chr3B 82.353 85 6 4 7586 7661 790902245 790902161 1.900000e-06 65.8
73 TraesCS4D01G196700 chr3B 82.022 89 3 6 7586 7661 466915521 466915609 6.820000e-06 63.9
74 TraesCS4D01G196700 chr3B 81.176 85 6 4 7593 7667 578400663 578400747 8.820000e-05 60.2
75 TraesCS4D01G196700 chr3B 100.000 28 0 0 7640 7667 16404169 16404142 1.500000e-02 52.8
76 TraesCS4D01G196700 chr5B 91.304 46 2 1 7586 7629 109984909 109984864 2.450000e-05 62.1
77 TraesCS4D01G196700 chr5B 96.970 33 1 0 7641 7673 366543678 366543646 1.000000e-03 56.5


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 TraesCS4D01G196700 chr4D 341402972 341411108 8136 True 7321.000000 8152 100.000000 1 8137 2 chr4D.!!$R2 8136
1 TraesCS4D01G196700 chr4D 82733996 82735293 1297 False 2124.000000 2124 96.061000 1653 2965 1 chr4D.!!$F1 1312
2 TraesCS4D01G196700 chr4D 490421894 490422761 867 True 1365.000000 1365 95.052000 1 868 1 chr4D.!!$R1 867
3 TraesCS4D01G196700 chr2A 657091832 657097200 5368 False 3003.000000 5858 96.883333 1274 8137 3 chr2A.!!$F1 6863
4 TraesCS4D01G196700 chrUn 335165363 335167940 2577 False 4638.000000 4638 99.074000 1 2589 1 chrUn.!!$F2 2588
5 TraesCS4D01G196700 chrUn 365646995 365648887 1892 True 3485.000000 3485 99.894000 4604 6496 1 chrUn.!!$R1 1892
6 TraesCS4D01G196700 chrUn 418950013 418951219 1206 False 2156.000000 2156 99.007000 6939 8137 1 chrUn.!!$F3 1198
7 TraesCS4D01G196700 chrUn 23308973 23309842 869 False 1312.000000 1312 93.922000 1 868 1 chrUn.!!$F1 867
8 TraesCS4D01G196700 chr4B 423052444 423058380 5936 True 1594.400000 3310 92.839800 871 8137 5 chr4B.!!$R1 7266
9 TraesCS4D01G196700 chr4B 613203275 613203793 518 False 693.000000 693 90.769000 1654 2172 1 chr4B.!!$F2 518
10 TraesCS4D01G196700 chr4A 125390844 125396814 5970 False 1205.585714 2435 94.192000 864 8137 7 chr4A.!!$F1 7273
11 TraesCS4D01G196700 chr6D 258349407 258350698 1291 False 1814.000000 1814 91.837000 1650 2967 1 chr6D.!!$F1 1317
12 TraesCS4D01G196700 chr6D 423179109 423180389 1280 False 1459.000000 1459 87.405000 1654 2944 1 chr6D.!!$F2 1290
13 TraesCS4D01G196700 chr6D 379008905 379009773 868 True 1280.000000 1280 93.333000 1 866 1 chr6D.!!$R1 865
14 TraesCS4D01G196700 chr6D 134685600 134686801 1201 False 820.500000 854 91.264500 1653 2965 2 chr6D.!!$F3 1312
15 TraesCS4D01G196700 chr7D 636768409 636769530 1121 False 1592.000000 1592 92.021000 1654 2805 1 chr7D.!!$F2 1151
16 TraesCS4D01G196700 chr7D 408031622 408032316 694 True 846.000000 846 88.669000 2266 2965 1 chr7D.!!$R1 699
17 TraesCS4D01G196700 chr2D 308901895 308903063 1168 False 1522.000000 1522 89.942000 1654 2856 1 chr2D.!!$F1 1202
18 TraesCS4D01G196700 chr2D 187967443 187968141 698 True 833.000000 833 88.293000 2266 2965 1 chr2D.!!$R1 699
19 TraesCS4D01G196700 chr2D 2488325 2489682 1357 False 769.000000 867 89.570000 1654 2965 2 chr2D.!!$F3 1311
20 TraesCS4D01G196700 chr6A 566422672 566423837 1165 True 1507.000000 1507 89.992000 1755 2926 1 chr6A.!!$R1 1171
21 TraesCS4D01G196700 chr1B 95309494 95310358 864 True 1306.000000 1306 93.995000 4 865 1 chr1B.!!$R1 861
22 TraesCS4D01G196700 chr3A 476659880 476660749 869 True 1304.000000 1304 93.807000 1 867 1 chr3A.!!$R1 866
23 TraesCS4D01G196700 chr7A 5013089 5013949 860 True 1290.000000 1290 93.656000 1 865 1 chr7A.!!$R1 864
24 TraesCS4D01G196700 chr7A 736019653 736020514 861 False 1279.000000 1279 93.526000 1 859 1 chr7A.!!$F2 858
25 TraesCS4D01G196700 chr5D 422939950 422940808 858 False 1280.000000 1280 93.612000 4 860 1 chr5D.!!$F1 856
26 TraesCS4D01G196700 chr5D 91634502 91635856 1354 True 759.500000 826 89.443500 1654 2965 2 chr5D.!!$R1 1311
27 TraesCS4D01G196700 chr1D 234833671 234835031 1360 True 756.000000 843 89.138500 1648 2965 2 chr1D.!!$R1 1317
28 TraesCS4D01G196700 chr2B 662577988 662578681 693 True 797.000000 797 87.376000 2266 2965 1 chr2B.!!$R1 699
29 TraesCS4D01G196700 chr2B 247937935 247939293 1358 True 759.500000 815 89.503500 1654 2964 2 chr2B.!!$R2 1310
30 TraesCS4D01G196700 chr1A 574362792 574363484 692 True 756.000000 756 86.383000 2266 2965 1 chr1A.!!$R3 699

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
39 40 1.045350 CCAGATCTGGGCTCTTCGGA 61.045 60.000 31.14 0.00 46.81 4.55 F
186 187 3.060000 GCTTAGCGGGCCCGTTTT 61.060 61.111 42.53 29.89 42.09 2.43 F
1303 1363 2.614481 GCTCACTTGTTAATCCCCGTGA 60.614 50.000 0.00 0.00 0.00 4.35 F
2656 2915 2.048023 CAAGCCCGGATGCACACAT 61.048 57.895 0.73 0.00 39.98 3.21 F
4207 4508 0.604578 TCGTTAGCACCACCCAGTAC 59.395 55.000 0.00 0.00 0.00 2.73 F
5501 6039 1.239347 GGGTTCTGTGTCCTGCTTTC 58.761 55.000 0.00 0.00 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 1363 2.299326 ATGCAAAAGGAGAAGGCAGT 57.701 45.000 0.00 0.0 37.96 4.40 R
2656 2915 0.109532 TGGCATTTCCTCGAACACCA 59.890 50.000 0.00 0.0 35.26 4.17 R
2970 3253 0.386605 CGCGTGGCTTACAATGCAAA 60.387 50.000 0.00 0.0 33.59 3.68 R
5084 5593 4.123497 AGATTTGTGCGCTACATGTCTA 57.877 40.909 9.73 0.0 39.48 2.59 R
6647 7406 1.482182 TGCTTCCTCGTGCACTGATAT 59.518 47.619 16.19 0.0 33.94 1.63 R
7967 8787 0.105913 GTGTAGAGAGGGAGGGAGGG 60.106 65.000 0.00 0.0 0.00 4.30 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
39 40 1.045350 CCAGATCTGGGCTCTTCGGA 61.045 60.000 31.14 0.00 46.81 4.55
186 187 3.060000 GCTTAGCGGGCCCGTTTT 61.060 61.111 42.53 29.89 42.09 2.43
1303 1363 2.614481 GCTCACTTGTTAATCCCCGTGA 60.614 50.000 0.00 0.00 0.00 4.35
2656 2915 2.048023 CAAGCCCGGATGCACACAT 61.048 57.895 0.73 0.00 39.98 3.21
2983 3266 7.816945 ATACTCATGTTTTTGCATTGTAAGC 57.183 32.000 0.00 0.00 0.00 3.09
2991 3274 0.670854 TGCATTGTAAGCCACGCGTA 60.671 50.000 13.44 0.00 0.00 4.42
3170 3453 9.096160 GTTTCCTTTATGTTAGTAGCTACCTTC 57.904 37.037 20.31 10.88 0.00 3.46
3490 3784 5.106317 GCAAATCTTGGTACCGATTTTCAGA 60.106 40.000 19.43 6.93 36.04 3.27
4207 4508 0.604578 TCGTTAGCACCACCCAGTAC 59.395 55.000 0.00 0.00 0.00 2.73
5084 5593 4.829492 GCAGGAGATGGCATTAATTAAGGT 59.171 41.667 11.20 0.00 0.00 3.50
5225 5736 2.518112 TGCTGTTGCCTGGCGAAA 60.518 55.556 10.93 4.01 38.71 3.46
5226 5737 2.124060 TGCTGTTGCCTGGCGAAAA 61.124 52.632 10.93 0.00 38.71 2.29
5501 6039 1.239347 GGGTTCTGTGTCCTGCTTTC 58.761 55.000 0.00 0.00 0.00 2.62
6772 7532 7.609760 ATTTTTGTCGATGCAGTTATAGTCA 57.390 32.000 0.00 0.00 0.00 3.41
7697 8497 7.444299 TGTACTAGTATTCCGAACCAAGTTTT 58.556 34.615 5.75 0.00 0.00 2.43
7968 8788 4.530857 CGGCGACACCATCCCTCC 62.531 72.222 0.00 0.00 39.03 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
809 838 1.346395 AGCAACCAACACCGATACAGA 59.654 47.619 0.00 0.00 0.00 3.41
1303 1363 2.299326 ATGCAAAAGGAGAAGGCAGT 57.701 45.000 0.00 0.00 37.96 4.40
2656 2915 0.109532 TGGCATTTCCTCGAACACCA 59.890 50.000 0.00 0.00 35.26 4.17
2715 2988 1.011333 CGTTATTACAAGTGGGGCCG 58.989 55.000 0.00 0.00 0.00 6.13
2805 3080 6.255215 AGACGATTTAAACATGTTTATGGCG 58.745 36.000 27.14 27.23 38.66 5.69
2915 3196 2.112297 TTGCCGTCCCACAGAACC 59.888 61.111 0.00 0.00 0.00 3.62
2967 3250 2.096958 GCGTGGCTTACAATGCAAAAAC 60.097 45.455 0.00 0.00 34.02 2.43
2968 3251 2.131183 GCGTGGCTTACAATGCAAAAA 58.869 42.857 0.00 0.00 34.02 1.94
2969 3252 1.777101 GCGTGGCTTACAATGCAAAA 58.223 45.000 0.00 0.00 34.02 2.44
2970 3253 0.386605 CGCGTGGCTTACAATGCAAA 60.387 50.000 0.00 0.00 33.59 3.68
2971 3254 1.208870 CGCGTGGCTTACAATGCAA 59.791 52.632 0.00 0.00 33.59 4.08
2983 3266 5.564768 TCATTTGTATTTCAATACGCGTGG 58.435 37.500 24.59 11.65 43.24 4.94
2991 3274 8.533657 TCTCAATGCCTTCATTTGTATTTCAAT 58.466 29.630 0.00 0.00 40.74 2.57
5084 5593 4.123497 AGATTTGTGCGCTACATGTCTA 57.877 40.909 9.73 0.00 39.48 2.59
5225 5736 4.718961 AGCTATTCATGTAGGCGGAATTT 58.281 39.130 0.00 0.00 33.59 1.82
5226 5737 4.319177 GAGCTATTCATGTAGGCGGAATT 58.681 43.478 0.00 0.00 33.59 2.17
6647 7406 1.482182 TGCTTCCTCGTGCACTGATAT 59.518 47.619 16.19 0.00 33.94 1.63
7697 8497 4.733850 TGTTCATACGCAACAACAACAAA 58.266 34.783 0.00 0.00 30.67 2.83
7700 8500 4.347813 ACTTGTTCATACGCAACAACAAC 58.652 39.130 0.00 0.00 38.53 3.32
7703 8503 5.031578 TCAAACTTGTTCATACGCAACAAC 58.968 37.500 0.00 0.00 38.53 3.32
7706 8513 5.387342 GCATTCAAACTTGTTCATACGCAAC 60.387 40.000 0.00 0.00 0.00 4.17
7965 8785 0.481128 GTAGAGAGGGAGGGAGGGAG 59.519 65.000 0.00 0.00 0.00 4.30
7966 8786 0.254154 TGTAGAGAGGGAGGGAGGGA 60.254 60.000 0.00 0.00 0.00 4.20
7967 8787 0.105913 GTGTAGAGAGGGAGGGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
7968 8788 0.105913 GGTGTAGAGAGGGAGGGAGG 60.106 65.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.