Multiple sequence alignment - TraesCS7A01G330600

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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 TraesCS7A01G330600 chr7A 100.000 3681 0 0 1 3681 483815130 483811450 0.000000e+00 6798.0
1 TraesCS7A01G330600 chr7A 89.489 352 34 2 1436 1785 309672329 309672679 3.370000e-120 442.0
2 TraesCS7A01G330600 chr7A 84.555 382 35 10 2212 2588 309672677 309673039 1.260000e-94 357.0
3 TraesCS7A01G330600 chr7A 90.574 244 19 2 1205 1444 309666171 309666414 1.650000e-83 320.0
4 TraesCS7A01G330600 chr7A 88.043 184 20 2 1 182 309582643 309582826 2.230000e-52 217.0
5 TraesCS7A01G330600 chr7A 100.000 35 0 0 2977 3011 483812123 483812089 8.530000e-07 65.8
6 TraesCS7A01G330600 chr5A 99.601 3011 12 0 1 3011 13418357 13415347 0.000000e+00 5494.0
7 TraesCS7A01G330600 chr5A 99.407 675 3 1 3008 3681 13415381 13414707 0.000000e+00 1223.0
8 TraesCS7A01G330600 chr5A 87.827 994 95 10 229 1205 688510611 688511595 0.000000e+00 1142.0
9 TraesCS7A01G330600 chr5A 88.014 292 31 3 2715 3003 688513487 688513777 3.520000e-90 342.0
10 TraesCS7A01G330600 chr5A 91.209 91 7 1 1878 1968 688512347 688512436 4.990000e-24 122.0
11 TraesCS7A01G330600 chr3B 99.369 3011 17 2 1 3011 769886651 769883643 0.000000e+00 5454.0
12 TraesCS7A01G330600 chr3B 98.963 675 6 1 3008 3681 769883677 769883003 0.000000e+00 1206.0
13 TraesCS7A01G330600 chr3B 85.768 801 86 8 422 1205 74183785 74184574 0.000000e+00 822.0
14 TraesCS7A01G330600 chr3B 84.943 704 78 17 1283 1968 74184809 74185502 0.000000e+00 688.0
15 TraesCS7A01G330600 chr3B 84.945 631 67 7 1 616 74183169 74183786 6.760000e-172 614.0
16 TraesCS7A01G330600 chr3B 85.507 483 57 8 3009 3480 74199180 74199660 3.300000e-135 492.0
17 TraesCS7A01G330600 chr3B 84.706 255 23 11 2166 2415 74186317 74186560 1.320000e-59 241.0
18 TraesCS7A01G330600 chr3B 84.337 83 13 0 3598 3680 74199720 74199802 8.470000e-12 82.4
19 TraesCS7A01G330600 chrUn 98.783 2712 28 3 1 2708 82493161 82495871 0.000000e+00 4820.0
20 TraesCS7A01G330600 chrUn 98.370 675 10 1 3008 3681 377699844 377699170 0.000000e+00 1184.0
21 TraesCS7A01G330600 chrUn 97.706 218 5 0 2794 3011 377700027 377699810 3.470000e-100 375.0
22 TraesCS7A01G330600 chr1D 93.686 681 34 7 3008 3680 276748588 276747909 0.000000e+00 1011.0
23 TraesCS7A01G330600 chr1D 88.152 422 35 4 2591 3011 111967555 111967148 4.270000e-134 488.0
24 TraesCS7A01G330600 chr1D 94.286 210 11 1 2794 3003 276748771 276748563 1.650000e-83 320.0
25 TraesCS7A01G330600 chr1D 95.122 82 4 0 1973 2054 111968359 111968278 2.980000e-26 130.0
26 TraesCS7A01G330600 chr1D 100.000 28 0 0 3641 3668 408539352 408539325 7.000000e-03 52.8
27 TraesCS7A01G330600 chr6A 89.227 789 65 11 1283 2054 171412046 171412831 0.000000e+00 968.0
28 TraesCS7A01G330600 chr6A 84.009 469 56 14 3218 3681 171413694 171414148 2.030000e-117 433.0
29 TraesCS7A01G330600 chr6A 90.090 222 18 3 2591 2812 171413350 171413567 6.020000e-73 285.0
30 TraesCS7A01G330600 chr1B 87.568 740 80 7 470 1205 213332612 213333343 0.000000e+00 846.0
31 TraesCS7A01G330600 chr1B 79.128 436 68 11 1205 1628 562211617 562211193 2.800000e-71 279.0
32 TraesCS7A01G330600 chr4B 86.267 801 82 8 422 1205 111987972 111988761 0.000000e+00 845.0
33 TraesCS7A01G330600 chr4B 85.556 630 74 3 1 616 111987347 111987973 0.000000e+00 643.0
34 TraesCS7A01G330600 chr4B 89.130 414 44 1 2591 3003 111991544 111991957 7.050000e-142 514.0
35 TraesCS7A01G330600 chr4B 85.124 484 59 7 3009 3480 111991932 111992414 1.990000e-132 483.0
36 TraesCS7A01G330600 chr7B 86.142 801 82 9 422 1205 707759809 707759021 0.000000e+00 837.0
37 TraesCS7A01G330600 chr7B 85.646 627 70 4 4 616 707760428 707759808 3.100000e-180 641.0
38 TraesCS7A01G330600 chr7B 90.097 414 40 1 2591 3003 707756439 707756026 1.500000e-148 536.0
39 TraesCS7A01G330600 chr7B 86.279 481 54 7 3009 3479 707756051 707755573 2.540000e-141 512.0
40 TraesCS7A01G330600 chr7B 85.542 83 12 0 3598 3680 707755517 707755435 1.820000e-13 87.9
41 TraesCS7A01G330600 chr2B 85.893 801 85 8 422 1205 53571326 53572115 0.000000e+00 828.0
42 TraesCS7A01G330600 chr2B 85.079 630 68 5 1 616 53570710 53571327 1.450000e-173 619.0
43 TraesCS7A01G330600 chr2B 89.737 380 37 1 2591 2968 53574996 53575375 5.530000e-133 484.0
44 TraesCS7A01G330600 chr2B 85.714 469 56 6 3022 3480 53575389 53575856 5.530000e-133 484.0
45 TraesCS7A01G330600 chr2B 79.634 437 69 11 1205 1631 108993078 108992652 2.780000e-76 296.0
46 TraesCS7A01G330600 chr2B 83.529 255 27 9 2166 2415 53573861 53574105 1.330000e-54 224.0
47 TraesCS7A01G330600 chr2B 84.524 84 12 1 3598 3680 53575916 53575999 8.470000e-12 82.4
48 TraesCS7A01G330600 chr3A 86.050 724 69 9 1 701 410121201 410121915 0.000000e+00 749.0
49 TraesCS7A01G330600 chr3A 88.889 432 41 3 3009 3434 410124283 410124713 3.260000e-145 525.0
50 TraesCS7A01G330600 chr3A 86.256 422 36 6 2591 3011 410123916 410124316 4.360000e-119 438.0
51 TraesCS7A01G330600 chr3A 95.294 85 4 0 1970 2054 410122460 410122544 6.410000e-28 135.0
52 TraesCS7A01G330600 chr4A 89.014 355 37 2 4 358 623994158 623993806 4.360000e-119 438.0
53 TraesCS7A01G330600 chr4A 79.405 437 70 11 1205 1631 743701929 743701503 1.290000e-74 291.0
54 TraesCS7A01G330600 chr5B 87.719 114 6 2 2166 2279 516091325 516091220 3.860000e-25 126.0
55 TraesCS7A01G330600 chr4D 88.288 111 5 3 2170 2280 24333952 24333850 3.860000e-25 126.0
56 TraesCS7A01G330600 chr5D 87.500 112 6 2 2166 2277 426294270 426294167 4.990000e-24 122.0
57 TraesCS7A01G330600 chr6D 89.773 88 9 0 1967 2054 455904126 455904213 3.000000e-21 113.0
58 TraesCS7A01G330600 chr6B 89.773 88 9 0 1967 2054 693274107 693274194 3.000000e-21 113.0


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 TraesCS7A01G330600 chr7A 483811450 483815130 3680 True 3431.900000 6798 100.000000 1 3681 2 chr7A.!!$R1 3680
1 TraesCS7A01G330600 chr7A 309672329 309673039 710 False 399.500000 442 87.022000 1436 2588 2 chr7A.!!$F3 1152
2 TraesCS7A01G330600 chr5A 13414707 13418357 3650 True 3358.500000 5494 99.504000 1 3681 2 chr5A.!!$R1 3680
3 TraesCS7A01G330600 chr5A 688510611 688513777 3166 False 535.333333 1142 89.016667 229 3003 3 chr5A.!!$F1 2774
4 TraesCS7A01G330600 chr3B 769883003 769886651 3648 True 3330.000000 5454 99.166000 1 3681 2 chr3B.!!$R1 3680
5 TraesCS7A01G330600 chr3B 74183169 74186560 3391 False 591.250000 822 85.090500 1 2415 4 chr3B.!!$F1 2414
6 TraesCS7A01G330600 chr3B 74199180 74199802 622 False 287.200000 492 84.922000 3009 3680 2 chr3B.!!$F2 671
7 TraesCS7A01G330600 chrUn 82493161 82495871 2710 False 4820.000000 4820 98.783000 1 2708 1 chrUn.!!$F1 2707
8 TraesCS7A01G330600 chrUn 377699170 377700027 857 True 779.500000 1184 98.038000 2794 3681 2 chrUn.!!$R1 887
9 TraesCS7A01G330600 chr1D 276747909 276748771 862 True 665.500000 1011 93.986000 2794 3680 2 chr1D.!!$R3 886
10 TraesCS7A01G330600 chr1D 111967148 111968359 1211 True 309.000000 488 91.637000 1973 3011 2 chr1D.!!$R2 1038
11 TraesCS7A01G330600 chr6A 171412046 171414148 2102 False 562.000000 968 87.775333 1283 3681 3 chr6A.!!$F1 2398
12 TraesCS7A01G330600 chr1B 213332612 213333343 731 False 846.000000 846 87.568000 470 1205 1 chr1B.!!$F1 735
13 TraesCS7A01G330600 chr4B 111987347 111992414 5067 False 621.250000 845 86.519250 1 3480 4 chr4B.!!$F1 3479
14 TraesCS7A01G330600 chr7B 707755435 707760428 4993 True 522.780000 837 86.741200 4 3680 5 chr7B.!!$R1 3676
15 TraesCS7A01G330600 chr2B 53570710 53575999 5289 False 453.566667 828 85.746000 1 3680 6 chr2B.!!$F1 3679
16 TraesCS7A01G330600 chr3A 410121201 410124713 3512 False 461.750000 749 89.122250 1 3434 4 chr3A.!!$F1 3433

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
343 351 1.344438 TGTCGTCACTTGCATCTCCTT 59.656 47.619 0.00 0.0 0.00 3.36 F
999 1233 3.057548 CTGGATTGCACAGCGGCA 61.058 61.111 1.45 0.0 43.19 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 2201 4.111577 TCTAACCCAGGGAGATTCACATT 58.888 43.478 14.54 0.0 0.00 2.71 R
3292 5754 4.873259 GGAGTCAAAGAAACTCTCATAGGC 59.127 45.833 3.55 0.0 42.28 3.93 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
174 175 3.243334 TGTCATTTTTCAGCGATGCACAA 60.243 39.130 0.00 0.0 0.00 3.33
343 351 1.344438 TGTCGTCACTTGCATCTCCTT 59.656 47.619 0.00 0.0 0.00 3.36
999 1233 3.057548 CTGGATTGCACAGCGGCA 61.058 61.111 1.45 0.0 43.19 5.69
1843 2424 5.430886 TGCTCGCTTCTATACCCGTATATA 58.569 41.667 0.00 0.0 0.00 0.86
3292 5754 3.718723 TGATGGGAAATGTTTTAGGGGG 58.281 45.455 0.00 0.0 0.00 5.40
3308 5770 1.847088 GGGGGCCTATGAGAGTTTCTT 59.153 52.381 0.84 0.0 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 8.812972 TGATGACTATAAACCTGACAGTAAAGT 58.187 33.333 0.93 0.0 0.00 2.66
508 736 3.130516 CAGCTTGCACTTCCATGAATCAT 59.869 43.478 0.00 0.0 0.00 2.45
1630 2201 4.111577 TCTAACCCAGGGAGATTCACATT 58.888 43.478 14.54 0.0 0.00 2.71
3292 5754 4.873259 GGAGTCAAAGAAACTCTCATAGGC 59.127 45.833 3.55 0.0 42.28 3.93
3308 5770 1.275291 GGAGTCATGAACCGGAGTCAA 59.725 52.381 9.46 0.0 35.61 3.18


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

AutoCloner maintained by Alex Coulton.