Multiple sequence alignment - TraesCS4B01G341700

Loading Multiple Alignment...

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 TraesCS4B01G341700 chr4B 100.000 3161 0 0 1 3161 634464226 634467386 0.000000e+00 5838.0
1 TraesCS4B01G341700 chr4B 97.011 3145 61 19 1 3144 634964351 634961239 0.000000e+00 5256.0
2 TraesCS4B01G341700 chr4B 95.170 766 36 1 628 1393 610532038 610532802 0.000000e+00 1208.0
3 TraesCS4B01G341700 chr4B 100.000 90 0 0 3508 3597 634467733 634467822 2.220000e-37 167.0
4 TraesCS4B01G341700 chr4B 93.333 90 5 1 3508 3597 634961357 634961269 8.100000e-27 132.0
5 TraesCS4B01G341700 chr4B 93.590 78 3 2 1394 1470 610554079 610554003 8.160000e-22 115.0
6 TraesCS4B01G341700 chr4B 90.000 90 8 1 3508 3597 634961405 634961317 8.160000e-22 115.0
7 TraesCS4B01G341700 chr4B 100.000 61 0 0 3537 3597 634960913 634960853 2.940000e-21 113.0
8 TraesCS4B01G341700 chr4B 91.026 78 5 2 1394 1470 634956511 634956587 1.770000e-18 104.0
9 TraesCS4B01G341700 chr4B 97.436 39 1 0 3509 3547 634467348 634467386 2.320000e-07 67.6
10 TraesCS4B01G341700 chr3B 97.588 1700 38 3 1463 3161 544828370 544830067 0.000000e+00 2909.0
11 TraesCS4B01G341700 chr3B 96.822 1699 54 0 1463 3161 31138183 31139881 0.000000e+00 2839.0
12 TraesCS4B01G341700 chr3B 97.128 766 21 1 628 1393 544827637 544828401 0.000000e+00 1291.0
13 TraesCS4B01G341700 chr3B 93.506 770 45 5 628 1396 31137452 31138217 0.000000e+00 1140.0
14 TraesCS4B01G341700 chr3B 92.511 227 16 1 2935 3161 544829890 544830115 1.250000e-84 324.0
15 TraesCS4B01G341700 chr3B 91.630 227 19 0 2935 3161 31139703 31139929 7.500000e-82 315.0
16 TraesCS4B01G341700 chr3B 90.749 227 21 0 2935 3161 31139751 31139977 1.620000e-78 303.0
17 TraesCS4B01G341700 chr3B 92.179 179 14 0 2983 3161 31139655 31139833 1.660000e-63 254.0
18 TraesCS4B01G341700 chr3B 93.333 90 5 1 3508 3597 544829885 544829973 8.100000e-27 132.0
19 TraesCS4B01G341700 chr3B 93.590 78 3 2 1394 1470 31141959 31141883 8.160000e-22 115.0
20 TraesCS4B01G341700 chr2B 95.393 1411 63 1 1751 3161 760246412 760245004 0.000000e+00 2244.0
21 TraesCS4B01G341700 chr2B 94.805 770 38 2 628 1396 760247470 760246702 0.000000e+00 1199.0
22 TraesCS4B01G341700 chr2B 95.423 284 13 0 1463 1746 760246736 760246453 1.520000e-123 453.0
23 TraesCS4B01G341700 chr2B 90.045 221 22 0 2935 3155 760245182 760244962 1.630000e-73 287.0
24 TraesCS4B01G341700 chr2B 97.561 41 0 1 1408 1447 760240440 760240480 6.440000e-08 69.4
25 TraesCS4B01G341700 chr1D 93.047 1352 69 13 1810 3161 491850091 491848765 0.000000e+00 1953.0
26 TraesCS4B01G341700 chr1D 92.825 1352 73 13 1810 3161 386435771 386437098 0.000000e+00 1938.0
27 TraesCS4B01G341700 chr1D 95.423 1136 46 4 1751 2885 416512932 416514062 0.000000e+00 1805.0
28 TraesCS4B01G341700 chr1D 93.170 776 50 3 621 1396 491851257 491850485 0.000000e+00 1136.0
29 TraesCS4B01G341700 chr1D 92.527 281 19 1 1463 1743 386435343 386435621 5.590000e-108 401.0
30 TraesCS4B01G341700 chr1D 92.115 279 20 1 1463 1741 491850519 491850243 3.370000e-105 392.0
31 TraesCS4B01G341700 chr1D 94.444 90 4 1 3508 3597 386436963 386437051 1.740000e-28 137.0
32 TraesCS4B01G341700 chr1D 92.222 90 6 1 3508 3597 386437613 386437701 3.770000e-25 126.0
33 TraesCS4B01G341700 chr1D 93.103 87 5 1 3511 3597 491848945 491848860 3.770000e-25 126.0
34 TraesCS4B01G341700 chr1D 92.941 85 5 1 3513 3597 386437064 386437147 4.880000e-24 122.0
35 TraesCS4B01G341700 chr1D 91.954 87 6 1 3511 3597 491848849 491848764 1.750000e-23 121.0
36 TraesCS4B01G341700 chr5D 95.863 1136 41 4 1751 2885 292686685 292687815 0.000000e+00 1832.0
37 TraesCS4B01G341700 chr5D 95.914 465 16 2 1 464 119741857 119742319 0.000000e+00 750.0
38 TraesCS4B01G341700 chr5D 97.191 178 4 1 454 630 119743339 119743516 2.100000e-77 300.0
39 TraesCS4B01G341700 chrUn 95.599 1136 43 5 1751 2885 10230138 10229009 0.000000e+00 1814.0
40 TraesCS4B01G341700 chrUn 83.697 779 99 20 628 1398 100590702 100591460 0.000000e+00 710.0
41 TraesCS4B01G341700 chrUn 92.473 279 19 1 1463 1741 10230460 10230184 7.240000e-107 398.0
42 TraesCS4B01G341700 chr6A 94.366 1136 58 4 1751 2885 592857907 592859037 0.000000e+00 1738.0
43 TraesCS4B01G341700 chr6A 95.032 1107 50 3 1751 2857 561584751 561583650 0.000000e+00 1735.0
44 TraesCS4B01G341700 chr6B 95.189 769 32 3 628 1396 468286351 468285588 0.000000e+00 1210.0
45 TraesCS4B01G341700 chr6B 93.750 208 13 0 2954 3161 468283449 468283242 2.700000e-81 313.0
46 TraesCS4B01G341700 chr6B 93.243 74 3 2 1394 1466 468256004 468256076 1.370000e-19 108.0
47 TraesCS4B01G341700 chr6B 91.837 49 3 1 1394 1442 468256106 468256153 2.320000e-07 67.6
48 TraesCS4B01G341700 chr2D 96.355 631 22 1 1 630 54197125 54196495 0.000000e+00 1037.0
49 TraesCS4B01G341700 chr2D 95.667 300 12 1 628 927 622905170 622905468 6.980000e-132 481.0
50 TraesCS4B01G341700 chr2D 95.238 42 0 1 1408 1447 622909299 622909258 8.340000e-07 65.8
51 TraesCS4B01G341700 chr3A 93.978 631 37 1 1 630 621351037 621350407 0.000000e+00 953.0
52 TraesCS4B01G341700 chr5B 87.613 775 84 8 628 1399 186149889 186150654 0.000000e+00 889.0
53 TraesCS4B01G341700 chr4A 95.164 517 23 2 1 517 429539052 429538538 0.000000e+00 815.0
54 TraesCS4B01G341700 chr4A 96.831 284 8 1 1463 1746 722382961 722382679 1.170000e-129 473.0
55 TraesCS4B01G341700 chr4A 94.488 127 6 1 505 630 429534203 429534077 1.020000e-45 195.0
56 TraesCS4B01G341700 chr4A 88.235 102 12 0 1 102 725936658 725936557 4.880000e-24 122.0
57 TraesCS4B01G341700 chr4A 94.521 73 3 1 1394 1466 722382057 722382128 1.060000e-20 111.0
58 TraesCS4B01G341700 chr2A 85.806 310 34 8 1504 1812 770555592 770555292 1.610000e-83 320.0


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 TraesCS4B01G341700 chr4B 634464226 634467822 3596 False 2024.20 5838 99.145333 1 3597 3 chr4B.!!$F3 3596
1 TraesCS4B01G341700 chr4B 634960853 634964351 3498 True 1404.00 5256 95.086000 1 3597 4 chr4B.!!$R2 3596
2 TraesCS4B01G341700 chr4B 610532038 610532802 764 False 1208.00 1208 95.170000 628 1393 1 chr4B.!!$F1 765
3 TraesCS4B01G341700 chr3B 544827637 544830115 2478 False 1164.00 2909 95.140000 628 3597 4 chr3B.!!$F2 2969
4 TraesCS4B01G341700 chr3B 31137452 31139977 2525 False 970.20 2839 92.977200 628 3161 5 chr3B.!!$F1 2533
5 TraesCS4B01G341700 chr2B 760244962 760247470 2508 True 1045.75 2244 93.916500 628 3161 4 chr2B.!!$R1 2533
6 TraesCS4B01G341700 chr1D 416512932 416514062 1130 False 1805.00 1805 95.423000 1751 2885 1 chr1D.!!$F1 1134
7 TraesCS4B01G341700 chr1D 491848764 491851257 2493 True 745.60 1953 92.677800 621 3597 5 chr1D.!!$R1 2976
8 TraesCS4B01G341700 chr1D 386435343 386437701 2358 False 544.80 1938 92.991800 1463 3597 5 chr1D.!!$F2 2134
9 TraesCS4B01G341700 chr5D 292686685 292687815 1130 False 1832.00 1832 95.863000 1751 2885 1 chr5D.!!$F1 1134
10 TraesCS4B01G341700 chr5D 119741857 119743516 1659 False 525.00 750 96.552500 1 630 2 chr5D.!!$F2 629
11 TraesCS4B01G341700 chrUn 10229009 10230460 1451 True 1106.00 1814 94.036000 1463 2885 2 chrUn.!!$R1 1422
12 TraesCS4B01G341700 chrUn 100590702 100591460 758 False 710.00 710 83.697000 628 1398 1 chrUn.!!$F1 770
13 TraesCS4B01G341700 chr6A 592857907 592859037 1130 False 1738.00 1738 94.366000 1751 2885 1 chr6A.!!$F1 1134
14 TraesCS4B01G341700 chr6A 561583650 561584751 1101 True 1735.00 1735 95.032000 1751 2857 1 chr6A.!!$R1 1106
15 TraesCS4B01G341700 chr6B 468283242 468286351 3109 True 761.50 1210 94.469500 628 3161 2 chr6B.!!$R1 2533
16 TraesCS4B01G341700 chr2D 54196495 54197125 630 True 1037.00 1037 96.355000 1 630 1 chr2D.!!$R1 629
17 TraesCS4B01G341700 chr3A 621350407 621351037 630 True 953.00 953 93.978000 1 630 1 chr3A.!!$R1 629
18 TraesCS4B01G341700 chr5B 186149889 186150654 765 False 889.00 889 87.613000 628 1399 1 chr5B.!!$F1 771
19 TraesCS4B01G341700 chr4A 429538538 429539052 514 True 815.00 815 95.164000 1 517 1 chr4A.!!$R2 516

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
957 969 0.905337 CTCTGTTCTTCTCCCCCGGT 60.905 60.000 0.0 0.0 0.00 5.28 F
1060 1075 3.636679 CTGAACATCTCCTCCTCCTACA 58.363 50.000 0.0 0.0 0.00 2.74 F
1077 1092 4.411869 TCCTACAATGGCATCATCAAGGTA 59.588 41.667 0.0 0.0 32.62 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 3169 2.235402 CTGGGCATCCAAAAGAGCATTT 59.765 45.455 0.0 0.0 43.51 2.32 R
2195 3314 7.971722 GTCATAGTTCTCCTGTAGTTTCTTCTC 59.028 40.741 0.0 0.0 0.00 2.87 R
3121 5403 7.328277 GATAAGTCGATGATATGAGGCTAGT 57.672 40.000 0.0 0.0 0.00 2.57 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
404 408 1.292992 GGACCGACGAACAGTTTGTT 58.707 50.000 7.65 0.00 44.37 2.83
513 517 5.130145 GGAGAAAAGAATCCTGAGGATGAGA 59.870 44.000 15.97 0.00 42.27 3.27
541 545 3.809832 GCTCAAGCTTTTGTGTCTGACTA 59.190 43.478 9.51 0.00 38.21 2.59
583 587 4.569719 TCCAATTTACCAAGGAGGAGAC 57.430 45.455 0.00 0.00 41.22 3.36
608 612 5.393027 CGATGCATTTATTAAGGTATGGGGC 60.393 44.000 0.00 0.00 0.00 5.80
616 620 2.917713 AAGGTATGGGGCAAACATCA 57.082 45.000 0.00 0.00 0.00 3.07
626 630 2.429610 GGGCAAACATCAGAGCATTCAT 59.570 45.455 0.00 0.00 0.00 2.57
892 896 4.098914 ACTGGATCGATCTAGCTCTCTT 57.901 45.455 31.70 13.70 38.79 2.85
957 969 0.905337 CTCTGTTCTTCTCCCCCGGT 60.905 60.000 0.00 0.00 0.00 5.28
1060 1075 3.636679 CTGAACATCTCCTCCTCCTACA 58.363 50.000 0.00 0.00 0.00 2.74
1077 1092 4.411869 TCCTACAATGGCATCATCAAGGTA 59.588 41.667 0.00 0.00 32.62 3.08
1435 1556 9.990360 TGAAACTGTATGTATGAACTTAACTGA 57.010 29.630 0.00 0.00 0.00 3.41
1482 1603 6.753279 TGAATATGCTTTGTTTATGAAGCTGC 59.247 34.615 9.19 0.00 46.39 5.25
1486 1607 6.271488 TGCTTTGTTTATGAAGCTGCTAAT 57.729 33.333 0.90 2.61 46.39 1.73
1642 2627 6.704050 TCTTTGTTTAATTTGCTTTAGCCACC 59.296 34.615 0.00 0.00 41.18 4.61
2014 3133 5.467035 ACCTCACAGAAGAGAAGAAGAAG 57.533 43.478 0.00 0.00 37.87 2.85
2050 3169 8.962884 ATTATGACAGTTTGTATGCTGATGTA 57.037 30.769 0.00 0.00 36.62 2.29
2195 3314 3.867984 GCTGTCAAAGAAAGAGGAGGAGG 60.868 52.174 0.00 0.00 0.00 4.30
3098 4922 5.282055 AGCCTCATTTCATCGACTTATCA 57.718 39.130 0.00 0.00 0.00 2.15
3102 4926 6.510799 GCCTCATTTCATCGACTTATCAACAG 60.511 42.308 0.00 0.00 0.00 3.16
3159 5441 4.657436 GACTTATCGACAGAATGACCCT 57.343 45.455 0.42 0.00 39.69 4.34
3160 5442 5.769484 GACTTATCGACAGAATGACCCTA 57.231 43.478 0.42 0.00 39.69 3.53
3527 5809 3.742433 CCTAGCCTCATTTCATCGACT 57.258 47.619 0.00 0.00 0.00 4.18
3528 5810 4.065321 CCTAGCCTCATTTCATCGACTT 57.935 45.455 0.00 0.00 0.00 3.01
3529 5811 5.201713 CCTAGCCTCATTTCATCGACTTA 57.798 43.478 0.00 0.00 0.00 2.24
3530 5812 5.788450 CCTAGCCTCATTTCATCGACTTAT 58.212 41.667 0.00 0.00 0.00 1.73
3531 5813 5.866633 CCTAGCCTCATTTCATCGACTTATC 59.133 44.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 197 5.505654 CGCAACACAAGGATTTTGAGTTAGT 60.506 40.000 3.14 0.00 32.85 2.24
404 408 3.417069 AACATGATTTCAGGGACGTCA 57.583 42.857 18.91 0.00 30.95 4.35
513 517 4.823989 AGACACAAAAGCTTGAGCATAACT 59.176 37.500 0.00 0.00 45.16 2.24
583 587 5.125417 CCCCATACCTTAATAAATGCATCGG 59.875 44.000 0.00 0.00 0.00 4.18
608 612 6.673154 TCACTATGAATGCTCTGATGTTTG 57.327 37.500 0.00 0.00 0.00 2.93
616 620 5.434408 TCTGCAATTCACTATGAATGCTCT 58.566 37.500 18.23 0.06 45.57 4.09
626 630 4.037446 GTGGTGGTTTTCTGCAATTCACTA 59.963 41.667 0.00 0.00 0.00 2.74
754 758 7.645340 CACCTGTCATAATAGTGCTTAAAATGC 59.355 37.037 0.00 0.00 0.00 3.56
892 896 0.613292 GCAGAGGAGAGAGTGTGGGA 60.613 60.000 0.00 0.00 0.00 4.37
1060 1075 4.336433 CGAACTTACCTTGATGATGCCATT 59.664 41.667 0.00 0.00 32.09 3.16
1409 1530 9.990360 TCAGTTAAGTTCATACATACAGTTTCA 57.010 29.630 0.00 0.00 0.00 2.69
1453 1574 9.787532 GCTTCATAAACAAAGCATATTCAGTTA 57.212 29.630 2.41 0.00 38.12 2.24
1454 1575 8.526147 AGCTTCATAAACAAAGCATATTCAGTT 58.474 29.630 9.49 0.00 40.51 3.16
1455 1576 7.972277 CAGCTTCATAAACAAAGCATATTCAGT 59.028 33.333 9.49 0.00 40.51 3.41
1456 1577 7.043590 GCAGCTTCATAAACAAAGCATATTCAG 60.044 37.037 9.49 0.00 40.51 3.02
1457 1578 6.753279 GCAGCTTCATAAACAAAGCATATTCA 59.247 34.615 9.49 0.00 40.51 2.57
1458 1579 6.976925 AGCAGCTTCATAAACAAAGCATATTC 59.023 34.615 9.49 0.00 40.51 1.75
1459 1580 6.870769 AGCAGCTTCATAAACAAAGCATATT 58.129 32.000 9.49 0.00 40.51 1.28
1460 1581 6.461110 AGCAGCTTCATAAACAAAGCATAT 57.539 33.333 9.49 0.00 40.51 1.78
1461 1582 5.902613 AGCAGCTTCATAAACAAAGCATA 57.097 34.783 9.49 0.00 40.51 3.14
1642 2627 1.934589 TGAGAACACACTCCAACACG 58.065 50.000 0.00 0.00 36.22 4.49
1779 2800 5.010282 GGTATCATCAAACCAACAGGTTCT 58.990 41.667 0.00 0.00 44.72 3.01
2014 3133 6.595716 ACAAACTGTCATAATTCTCCTGTAGC 59.404 38.462 0.00 0.00 0.00 3.58
2050 3169 2.235402 CTGGGCATCCAAAAGAGCATTT 59.765 45.455 0.00 0.00 43.51 2.32
2195 3314 7.971722 GTCATAGTTCTCCTGTAGTTTCTTCTC 59.028 40.741 0.00 0.00 0.00 2.87
3121 5403 7.328277 GATAAGTCGATGATATGAGGCTAGT 57.672 40.000 0.00 0.00 0.00 2.57
3507 5789 3.742433 AGTCGATGAAATGAGGCTAGG 57.258 47.619 0.00 0.00 0.00 3.02
3508 5790 6.942886 GATAAGTCGATGAAATGAGGCTAG 57.057 41.667 0.00 0.00 0.00 3.42
3524 5806 4.657436 AGGGTCATTCTGTCGATAAGTC 57.343 45.455 0.00 0.00 0.00 3.01
3525 5807 4.585162 CCTAGGGTCATTCTGTCGATAAGT 59.415 45.833 0.00 0.00 0.00 2.24
3526 5808 4.021894 CCCTAGGGTCATTCTGTCGATAAG 60.022 50.000 20.88 0.00 0.00 1.73
3527 5809 3.895656 CCCTAGGGTCATTCTGTCGATAA 59.104 47.826 20.88 0.00 0.00 1.75
3528 5810 3.497332 CCCTAGGGTCATTCTGTCGATA 58.503 50.000 20.88 0.00 0.00 2.92
3529 5811 2.320781 CCCTAGGGTCATTCTGTCGAT 58.679 52.381 20.88 0.00 0.00 3.59
3530 5812 1.776662 CCCTAGGGTCATTCTGTCGA 58.223 55.000 20.88 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.