Multiple sequence alignment - TraesCS4A01G430300

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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 TraesCS4A01G430300 chr4A 100.000 6905 0 0 1 6905 701702796 701695892 0.000000e+00 12752.0
1 TraesCS4A01G430300 chr4A 97.570 1029 22 1 646 1674 571068302 571067277 0.000000e+00 1759.0
2 TraesCS4A01G430300 chr4A 95.866 629 23 3 1 627 104130220 104129593 0.000000e+00 1014.0
3 TraesCS4A01G430300 chr4A 99.261 541 1 2 1 541 658634217 658634754 0.000000e+00 974.0
4 TraesCS4A01G430300 chr4A 99.621 528 2 0 1 528 658636569 658636042 0.000000e+00 965.0
5 TraesCS4A01G430300 chr2B 97.092 6396 112 24 528 6905 622903831 622910170 0.000000e+00 10713.0
6 TraesCS4A01G430300 chr2B 94.655 2320 58 23 2690 4995 690778757 690781024 0.000000e+00 3537.0
7 TraesCS4A01G430300 chr2B 92.632 2090 97 16 557 2644 690776726 690778760 0.000000e+00 2953.0
8 TraesCS4A01G430300 chr2B 99.435 531 3 0 1 531 566616914 566617444 0.000000e+00 965.0
9 TraesCS4A01G430300 chr2B 99.250 533 4 0 1 533 416059194 416058662 0.000000e+00 963.0
10 TraesCS4A01G430300 chr2B 90.787 597 35 6 6324 6902 690781209 690781803 0.000000e+00 780.0
11 TraesCS4A01G430300 chr2B 84.211 76 8 1 2623 2698 724551008 724550937 3.460000e-08 71.3
12 TraesCS4A01G430300 chr5A 99.509 3663 18 0 536 4198 544222274 544225936 0.000000e+00 6665.0
13 TraesCS4A01G430300 chr5A 95.671 3072 75 19 3265 6324 549319517 549316492 0.000000e+00 4883.0
14 TraesCS4A01G430300 chr5A 99.557 2482 10 1 4424 6905 544226351 544228831 0.000000e+00 4521.0
15 TraesCS4A01G430300 chr5A 96.312 2169 56 11 4158 6324 549298017 549295871 0.000000e+00 3541.0
16 TraesCS4A01G430300 chr5A 96.573 1488 28 10 1612 3092 549321084 549319613 0.000000e+00 2444.0
17 TraesCS4A01G430300 chr5A 94.102 1102 45 8 490 1582 549322171 549321081 0.000000e+00 1657.0
18 TraesCS4A01G430300 chr5A 89.509 591 31 9 6324 6905 549295833 549295265 0.000000e+00 719.0
19 TraesCS4A01G430300 chr5A 89.509 591 31 9 6324 6905 549316454 549315886 0.000000e+00 719.0
20 TraesCS4A01G430300 chr3B 99.671 3341 9 1 3341 6681 609330805 609327467 0.000000e+00 6107.0
21 TraesCS4A01G430300 chr3B 97.804 3461 65 8 557 4016 736485153 736488603 0.000000e+00 5960.0
22 TraesCS4A01G430300 chr3B 97.547 2813 49 7 4095 6905 736488600 736491394 0.000000e+00 4795.0
23 TraesCS4A01G430300 chr3B 99.657 1457 5 0 647 2103 609332653 609331197 0.000000e+00 2663.0
24 TraesCS4A01G430300 chr3B 99.486 972 4 1 1600 2570 609334341 609333370 0.000000e+00 1766.0
25 TraesCS4A01G430300 chr3B 99.580 714 3 0 2521 3234 609333377 609332664 0.000000e+00 1303.0
26 TraesCS4A01G430300 chr3B 92.340 235 17 1 3266 3499 466386203 466385969 3.990000e-87 333.0
27 TraesCS4A01G430300 chr3B 81.865 193 30 3 448 636 51763828 51764019 2.580000e-34 158.0
28 TraesCS4A01G430300 chr6B 97.276 3231 60 7 3687 6905 463397585 463400799 0.000000e+00 5454.0
29 TraesCS4A01G430300 chr6B 97.610 2301 50 3 646 2945 463395289 463397585 0.000000e+00 3940.0
30 TraesCS4A01G430300 chr3D 96.129 2816 56 18 3266 6067 434919410 434916634 0.000000e+00 4547.0
31 TraesCS4A01G430300 chr3D 95.848 2288 69 18 982 3265 434921647 434919382 0.000000e+00 3675.0
32 TraesCS4A01G430300 chr3D 91.221 467 24 4 6447 6903 434916639 434916180 2.740000e-173 619.0
33 TraesCS4A01G430300 chr2D 95.703 2327 54 15 4599 6905 5937025 5934725 0.000000e+00 3701.0
34 TraesCS4A01G430300 chrUn 99.732 1493 4 0 2706 4198 394865353 394863861 0.000000e+00 2736.0
35 TraesCS4A01G430300 chrUn 92.193 602 35 8 2671 3265 42465400 42465996 0.000000e+00 841.0
36 TraesCS4A01G430300 chrUn 89.425 435 32 9 2171 2599 42464980 42465406 2.830000e-148 536.0
37 TraesCS4A01G430300 chr4D 93.609 1596 67 16 4056 5649 215155559 215153997 0.000000e+00 2350.0
38 TraesCS4A01G430300 chr4D 89.163 406 31 7 2200 2599 81335144 81335542 1.730000e-135 494.0
39 TraesCS4A01G430300 chr6A 94.360 851 33 5 4056 4905 233346665 233347501 0.000000e+00 1291.0
40 TraesCS4A01G430300 chr3A 95.591 635 23 5 1 632 177883175 177882543 0.000000e+00 1013.0
41 TraesCS4A01G430300 chr5B 99.621 528 2 0 1 528 458907530 458907003 0.000000e+00 965.0
42 TraesCS4A01G430300 chr5B 85.743 505 42 12 623 1100 416029966 416029465 2.220000e-139 507.0
43 TraesCS4A01G430300 chr5B 81.319 182 23 10 461 636 705527393 705527569 3.360000e-28 137.0
44 TraesCS4A01G430300 chr4B 99.435 531 3 0 1 531 75504669 75505199 0.000000e+00 965.0
45 TraesCS4A01G430300 chr2A 98.352 546 8 1 1 545 166765314 166765859 0.000000e+00 957.0
46 TraesCS4A01G430300 chr7B 88.964 444 35 8 2171 2608 439933847 439933412 2.830000e-148 536.0
47 TraesCS4A01G430300 chr7D 90.960 177 15 1 3492 3667 535549801 535549977 3.220000e-58 237.0
48 TraesCS4A01G430300 chr5D 88.889 63 3 2 2619 2681 453407693 453407635 2.670000e-09 75.0


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 TraesCS4A01G430300 chr4A 701695892 701702796 6904 True 12752.000000 12752 100.000000 1 6905 1 chr4A.!!$R4 6904
1 TraesCS4A01G430300 chr4A 571067277 571068302 1025 True 1759.000000 1759 97.570000 646 1674 1 chr4A.!!$R2 1028
2 TraesCS4A01G430300 chr4A 104129593 104130220 627 True 1014.000000 1014 95.866000 1 627 1 chr4A.!!$R1 626
3 TraesCS4A01G430300 chr4A 658634217 658634754 537 False 974.000000 974 99.261000 1 541 1 chr4A.!!$F1 540
4 TraesCS4A01G430300 chr4A 658636042 658636569 527 True 965.000000 965 99.621000 1 528 1 chr4A.!!$R3 527
5 TraesCS4A01G430300 chr2B 622903831 622910170 6339 False 10713.000000 10713 97.092000 528 6905 1 chr2B.!!$F2 6377
6 TraesCS4A01G430300 chr2B 690776726 690781803 5077 False 2423.333333 3537 92.691333 557 6902 3 chr2B.!!$F3 6345
7 TraesCS4A01G430300 chr2B 566616914 566617444 530 False 965.000000 965 99.435000 1 531 1 chr2B.!!$F1 530
8 TraesCS4A01G430300 chr2B 416058662 416059194 532 True 963.000000 963 99.250000 1 533 1 chr2B.!!$R1 532
9 TraesCS4A01G430300 chr5A 544222274 544228831 6557 False 5593.000000 6665 99.533000 536 6905 2 chr5A.!!$F1 6369
10 TraesCS4A01G430300 chr5A 549315886 549322171 6285 True 2425.750000 4883 93.963750 490 6905 4 chr5A.!!$R2 6415
11 TraesCS4A01G430300 chr5A 549295265 549298017 2752 True 2130.000000 3541 92.910500 4158 6905 2 chr5A.!!$R1 2747
12 TraesCS4A01G430300 chr3B 736485153 736491394 6241 False 5377.500000 5960 97.675500 557 6905 2 chr3B.!!$F2 6348
13 TraesCS4A01G430300 chr3B 609327467 609334341 6874 True 2959.750000 6107 99.598500 647 6681 4 chr3B.!!$R2 6034
14 TraesCS4A01G430300 chr6B 463395289 463400799 5510 False 4697.000000 5454 97.443000 646 6905 2 chr6B.!!$F1 6259
15 TraesCS4A01G430300 chr3D 434916180 434921647 5467 True 2947.000000 4547 94.399333 982 6903 3 chr3D.!!$R1 5921
16 TraesCS4A01G430300 chr2D 5934725 5937025 2300 True 3701.000000 3701 95.703000 4599 6905 1 chr2D.!!$R1 2306
17 TraesCS4A01G430300 chrUn 394863861 394865353 1492 True 2736.000000 2736 99.732000 2706 4198 1 chrUn.!!$R1 1492
18 TraesCS4A01G430300 chrUn 42464980 42465996 1016 False 688.500000 841 90.809000 2171 3265 2 chrUn.!!$F1 1094
19 TraesCS4A01G430300 chr4D 215153997 215155559 1562 True 2350.000000 2350 93.609000 4056 5649 1 chr4D.!!$R1 1593
20 TraesCS4A01G430300 chr6A 233346665 233347501 836 False 1291.000000 1291 94.360000 4056 4905 1 chr6A.!!$F1 849
21 TraesCS4A01G430300 chr3A 177882543 177883175 632 True 1013.000000 1013 95.591000 1 632 1 chr3A.!!$R1 631
22 TraesCS4A01G430300 chr5B 458907003 458907530 527 True 965.000000 965 99.621000 1 528 1 chr5B.!!$R2 527
23 TraesCS4A01G430300 chr5B 416029465 416029966 501 True 507.000000 507 85.743000 623 1100 1 chr5B.!!$R1 477
24 TraesCS4A01G430300 chr4B 75504669 75505199 530 False 965.000000 965 99.435000 1 531 1 chr4B.!!$F1 530
25 TraesCS4A01G430300 chr2A 166765314 166765859 545 False 957.000000 957 98.352000 1 545 1 chr2A.!!$F1 544

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
565 567 2.956964 CCGATCGCTTCTGGTCGC 60.957 66.667 10.32 0.0 33.06 5.19 F
1638 1681 1.600663 GCCGTCGAGATCGTTGATGAT 60.601 52.381 1.70 0.0 40.80 2.45 F
2480 2528 1.034838 TTGGCCTGTTGTGCTTTCGT 61.035 50.000 3.32 0.0 0.00 3.85 F
3533 5420 3.963129 TGAACTGGCTAACCCTTATTGG 58.037 45.455 0.00 0.0 33.59 3.16 F
3862 5749 3.964411 TCTTCTCCCTCGAACACATCTA 58.036 45.455 0.00 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2126 3.305964 CGTCGATCGGCTTGTATGTATT 58.694 45.455 18.81 0.00 35.71 1.89 R
3533 5420 5.078411 AGTCAGTTCAGGACATATGACAC 57.922 43.478 10.38 0.00 39.54 3.67 R
3862 5749 1.475392 GCAGCAGAGGATCAGAAGCAT 60.475 52.381 0.00 0.00 37.82 3.79 R
4864 6956 5.474578 AATGTACTGTCACAGACTCACAT 57.525 39.130 13.14 11.75 33.75 3.21 R
6631 8871 1.384502 CCTAGGCCCCCATCAGTGA 60.385 63.158 0.00 0.00 0.00 3.41 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
228 229 7.624360 TCGATTATAGAATGTTTGCCAGTTT 57.376 32.000 0.00 0.00 0.00 2.66
565 567 2.956964 CCGATCGCTTCTGGTCGC 60.957 66.667 10.32 0.00 33.06 5.19
1638 1681 1.600663 GCCGTCGAGATCGTTGATGAT 60.601 52.381 1.70 0.00 40.80 2.45
2083 2126 5.243954 GTCCTGCATGTATGGACATCTACTA 59.756 44.000 20.89 0.00 44.82 1.82
2480 2528 1.034838 TTGGCCTGTTGTGCTTTCGT 61.035 50.000 3.32 0.00 0.00 3.85
2585 2682 4.072131 GTTGGGAGTGCTCAAGTATTCAA 58.928 43.478 1.41 0.00 34.53 2.69
2704 2804 5.607171 ACAGGTCCTATATTTGTTAGAGGGG 59.393 44.000 0.00 0.00 39.40 4.79
3533 5420 3.963129 TGAACTGGCTAACCCTTATTGG 58.037 45.455 0.00 0.00 33.59 3.16
3862 5749 3.964411 TCTTCTCCCTCGAACACATCTA 58.036 45.455 0.00 0.00 0.00 1.98
4864 6956 6.207221 CAGAAAATATGGCATGCTACATACCA 59.793 38.462 18.92 5.25 32.87 3.25
6105 8204 2.851263 TCCATGTACCAAGTGGACAC 57.149 50.000 3.83 2.35 37.12 3.67
6639 8879 2.202797 CGGGAGCCGTCACTGATG 60.203 66.667 0.00 0.00 42.73 3.07
6640 8880 2.187946 GGGAGCCGTCACTGATGG 59.812 66.667 12.47 12.47 41.35 3.51
6641 8881 2.187946 GGAGCCGTCACTGATGGG 59.812 66.667 17.54 7.01 39.01 4.00
6642 8882 2.187946 GAGCCGTCACTGATGGGG 59.812 66.667 17.54 4.73 39.01 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 229 9.823647 TGTGAACATTTTTAAGCAATTTTCCTA 57.176 25.926 0.00 0.00 0.00 2.94
565 567 1.136474 TGCAAAATTAGCGACGACGTG 60.136 47.619 4.58 0.00 41.98 4.49
2083 2126 3.305964 CGTCGATCGGCTTGTATGTATT 58.694 45.455 18.81 0.00 35.71 1.89
2704 2804 7.659186 AGTTGACGGATATCTAGAAACATACC 58.341 38.462 2.05 0.00 0.00 2.73
3533 5420 5.078411 AGTCAGTTCAGGACATATGACAC 57.922 43.478 10.38 0.00 39.54 3.67
3862 5749 1.475392 GCAGCAGAGGATCAGAAGCAT 60.475 52.381 0.00 0.00 37.82 3.79
4864 6956 5.474578 AATGTACTGTCACAGACTCACAT 57.525 39.130 13.14 11.75 33.75 3.21
6626 8866 3.402681 CCCCCATCAGTGACGGCT 61.403 66.667 0.00 0.00 0.00 5.52
6628 8868 4.489771 GGCCCCCATCAGTGACGG 62.490 72.222 0.00 0.00 0.00 4.79
6629 8869 2.032860 CTAGGCCCCCATCAGTGACG 62.033 65.000 0.00 0.00 0.00 4.35
6630 8870 1.700042 CCTAGGCCCCCATCAGTGAC 61.700 65.000 0.00 0.00 0.00 3.67
6631 8871 1.384502 CCTAGGCCCCCATCAGTGA 60.385 63.158 0.00 0.00 0.00 3.41
6632 8872 1.694169 ACCTAGGCCCCCATCAGTG 60.694 63.158 9.30 0.00 0.00 3.66
6633 8873 1.384643 GACCTAGGCCCCCATCAGT 60.385 63.158 9.30 0.00 0.00 3.41
6634 8874 2.150051 GGACCTAGGCCCCCATCAG 61.150 68.421 9.30 0.00 0.00 2.90
6635 8875 2.039831 GGACCTAGGCCCCCATCA 60.040 66.667 9.30 0.00 0.00 3.07
6636 8876 3.242291 CGGACCTAGGCCCCCATC 61.242 72.222 8.79 0.00 0.00 3.51
6637 8877 4.900259 CCGGACCTAGGCCCCCAT 62.900 72.222 8.79 0.00 0.00 4.00
6642 8882 3.525545 GACGACCGGACCTAGGCC 61.526 72.222 9.46 10.43 0.00 5.19


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

AutoCloner maintained by Alex Coulton.