Multiple sequence alignment - TraesCS2D01G553500

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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 TraesCS2D01G553500 chr2D 100.000 3236 0 0 1 3236 628251326 628254561 0.000000e+00 5976.0
1 TraesCS2D01G553500 chr2D 89.816 1738 116 31 519 2241 628593686 628591995 0.000000e+00 2172.0
2 TraesCS2D01G553500 chr2D 85.476 1921 205 39 519 2405 628587546 628585666 0.000000e+00 1934.0
3 TraesCS2D01G553500 chr2D 81.112 1943 261 54 521 2430 628264619 628266488 0.000000e+00 1458.0
4 TraesCS2D01G553500 chr2D 82.468 1175 142 34 519 1680 628258678 628259801 0.000000e+00 970.0
5 TraesCS2D01G553500 chr2D 84.559 952 115 18 1496 2430 628995452 628994516 0.000000e+00 915.0
6 TraesCS2D01G553500 chr2D 86.967 821 88 9 2431 3236 628579116 628578300 0.000000e+00 905.0
7 TraesCS2D01G553500 chr2D 86.707 820 88 12 2430 3233 628266320 628267134 0.000000e+00 891.0
8 TraesCS2D01G553500 chr2D 85.036 822 100 15 2430 3236 628994684 628993871 0.000000e+00 815.0
9 TraesCS2D01G553500 chr2D 79.419 1239 159 41 1217 2430 628580115 628578948 0.000000e+00 787.0
10 TraesCS2D01G553500 chr2D 93.786 515 30 2 1 515 331912301 331912813 0.000000e+00 773.0
11 TraesCS2D01G553500 chr2D 93.945 512 28 3 1 512 174379781 174380289 0.000000e+00 771.0
12 TraesCS2D01G553500 chr2D 93.922 510 30 1 3 512 411490285 411490793 0.000000e+00 769.0
13 TraesCS2D01G553500 chr2D 82.207 888 148 7 521 1401 628996535 628995651 0.000000e+00 756.0
14 TraesCS2D01G553500 chr2D 95.167 269 12 1 2968 3236 628590983 628590716 1.070000e-114 424.0
15 TraesCS2D01G553500 chr2D 83.215 423 48 17 2028 2430 628260015 628260434 1.830000e-97 366.0
16 TraesCS2D01G553500 chr2D 87.195 164 8 10 2896 3050 628585665 628585506 1.190000e-39 174.0
17 TraesCS2D01G553500 chr2D 96.512 86 3 0 3151 3236 628585462 628585377 3.370000e-30 143.0
18 TraesCS2D01G553500 chr2D 97.222 72 2 0 3076 3147 628585509 628585438 4.380000e-24 122.0
19 TraesCS2D01G553500 chr5D 94.680 2763 89 22 513 3236 15570280 15567537 0.000000e+00 4235.0
20 TraesCS2D01G553500 chr5D 85.905 823 88 17 2430 3236 15561725 15560915 0.000000e+00 852.0
21 TraesCS2D01G553500 chr5D 80.578 1004 130 34 1451 2430 15562518 15561556 0.000000e+00 713.0
22 TraesCS2D01G553500 chr5D 94.097 288 11 3 2949 3236 15567318 15567037 1.780000e-117 433.0
23 TraesCS2D01G553500 chr5D 86.364 66 5 3 1399 1460 277244649 277244584 5.790000e-08 69.4
24 TraesCS2D01G553500 chr2B 91.997 2774 130 42 513 3233 771281599 771284333 0.000000e+00 3808.0
25 TraesCS2D01G553500 chr2B 84.885 741 86 12 2465 3188 771973652 771972921 0.000000e+00 725.0
26 TraesCS2D01G553500 chr2B 83.951 729 104 9 521 1243 771380510 771381231 0.000000e+00 686.0
27 TraesCS2D01G553500 chr2B 79.668 782 106 23 1449 2193 771381369 771382134 6.190000e-142 514.0
28 TraesCS2D01G553500 chr2B 86.751 317 34 5 2924 3233 771382141 771382456 2.390000e-91 346.0
29 TraesCS2D01G553500 chr2B 87.692 65 4 2 1556 1616 771505824 771505888 4.480000e-09 73.1
30 TraesCS2D01G553500 chr2B 86.957 69 4 3 1556 1620 771821870 771821803 4.480000e-09 73.1
31 TraesCS2D01G553500 chr2A 95.894 1851 63 5 1399 3236 758564385 758566235 0.000000e+00 2985.0
32 TraesCS2D01G553500 chr2A 80.948 1963 262 53 521 2430 758583617 758585520 0.000000e+00 1450.0
33 TraesCS2D01G553500 chr2A 85.053 1425 142 28 521 1924 758575725 758577099 0.000000e+00 1386.0
34 TraesCS2D01G553500 chr2A 94.190 895 38 7 513 1402 758563411 758564296 0.000000e+00 1352.0
35 TraesCS2D01G553500 chr2A 88.683 1131 93 16 2127 3233 758577310 758578429 0.000000e+00 1347.0
36 TraesCS2D01G553500 chr2A 87.561 820 82 9 2430 3233 758585351 758586166 0.000000e+00 931.0
37 TraesCS2D01G553500 chr2A 79.386 912 138 25 524 1402 758516869 758515975 5.980000e-167 597.0
38 TraesCS2D01G553500 chr2A 86.364 66 5 2 1556 1617 758599235 758599300 5.790000e-08 69.4
39 TraesCS2D01G553500 chr7D 94.553 514 27 1 1 514 141109825 141110337 0.000000e+00 793.0
40 TraesCS2D01G553500 chr7D 94.336 512 28 1 1 512 558416645 558416135 0.000000e+00 784.0
41 TraesCS2D01G553500 chr7D 94.325 511 28 1 1 511 582069476 582068967 0.000000e+00 782.0
42 TraesCS2D01G553500 chr7D 94.152 513 28 2 1 512 43286125 43286636 0.000000e+00 780.0
43 TraesCS2D01G553500 chr4D 94.336 512 29 0 1 512 39472278 39472789 0.000000e+00 785.0
44 TraesCS2D01G553500 chr4D 94.152 513 26 3 1 512 355931040 355931549 0.000000e+00 778.0
45 TraesCS2D01G553500 chr4D 88.136 59 3 3 1399 1453 484149232 484149290 2.080000e-07 67.6
46 TraesCS2D01G553500 chr1D 78.571 910 140 34 521 1401 460176950 460177833 1.700000e-152 549.0
47 TraesCS2D01G553500 chr1D 89.091 55 6 0 1399 1453 408924547 408924493 5.790000e-08 69.4
48 TraesCS2D01G553500 chr5B 89.286 56 5 1 1399 1453 271145830 271145885 5.790000e-08 69.4
49 TraesCS2D01G553500 chr5B 87.097 62 7 1 1399 1460 315165330 315165270 5.790000e-08 69.4
50 TraesCS2D01G553500 chr3A 89.091 55 5 1 1399 1452 430526451 430526505 2.080000e-07 67.6


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 TraesCS2D01G553500 chr2D 628251326 628254561 3235 False 5976.000000 5976 100.000000 1 3236 1 chr2D.!!$F4 3235
1 TraesCS2D01G553500 chr2D 628264619 628267134 2515 False 1174.500000 1458 83.909500 521 3233 2 chr2D.!!$F6 2712
2 TraesCS2D01G553500 chr2D 628578300 628580115 1815 True 846.000000 905 83.193000 1217 3236 2 chr2D.!!$R1 2019
3 TraesCS2D01G553500 chr2D 628993871 628996535 2664 True 828.666667 915 83.934000 521 3236 3 chr2D.!!$R3 2715
4 TraesCS2D01G553500 chr2D 628585377 628593686 8309 True 828.166667 2172 91.898000 519 3236 6 chr2D.!!$R2 2717
5 TraesCS2D01G553500 chr2D 331912301 331912813 512 False 773.000000 773 93.786000 1 515 1 chr2D.!!$F2 514
6 TraesCS2D01G553500 chr2D 174379781 174380289 508 False 771.000000 771 93.945000 1 512 1 chr2D.!!$F1 511
7 TraesCS2D01G553500 chr2D 411490285 411490793 508 False 769.000000 769 93.922000 3 512 1 chr2D.!!$F3 509
8 TraesCS2D01G553500 chr2D 628258678 628260434 1756 False 668.000000 970 82.841500 519 2430 2 chr2D.!!$F5 1911
9 TraesCS2D01G553500 chr5D 15567037 15570280 3243 True 2334.000000 4235 94.388500 513 3236 2 chr5D.!!$R3 2723
10 TraesCS2D01G553500 chr5D 15560915 15562518 1603 True 782.500000 852 83.241500 1451 3236 2 chr5D.!!$R2 1785
11 TraesCS2D01G553500 chr2B 771281599 771284333 2734 False 3808.000000 3808 91.997000 513 3233 1 chr2B.!!$F1 2720
12 TraesCS2D01G553500 chr2B 771972921 771973652 731 True 725.000000 725 84.885000 2465 3188 1 chr2B.!!$R2 723
13 TraesCS2D01G553500 chr2B 771380510 771382456 1946 False 515.333333 686 83.456667 521 3233 3 chr2B.!!$F3 2712
14 TraesCS2D01G553500 chr2A 758563411 758566235 2824 False 2168.500000 2985 95.042000 513 3236 2 chr2A.!!$F2 2723
15 TraesCS2D01G553500 chr2A 758575725 758578429 2704 False 1366.500000 1386 86.868000 521 3233 2 chr2A.!!$F3 2712
16 TraesCS2D01G553500 chr2A 758583617 758586166 2549 False 1190.500000 1450 84.254500 521 3233 2 chr2A.!!$F4 2712
17 TraesCS2D01G553500 chr2A 758515975 758516869 894 True 597.000000 597 79.386000 524 1402 1 chr2A.!!$R1 878
18 TraesCS2D01G553500 chr7D 141109825 141110337 512 False 793.000000 793 94.553000 1 514 1 chr7D.!!$F2 513
19 TraesCS2D01G553500 chr7D 558416135 558416645 510 True 784.000000 784 94.336000 1 512 1 chr7D.!!$R1 511
20 TraesCS2D01G553500 chr7D 582068967 582069476 509 True 782.000000 782 94.325000 1 511 1 chr7D.!!$R2 510
21 TraesCS2D01G553500 chr7D 43286125 43286636 511 False 780.000000 780 94.152000 1 512 1 chr7D.!!$F1 511
22 TraesCS2D01G553500 chr4D 39472278 39472789 511 False 785.000000 785 94.336000 1 512 1 chr4D.!!$F1 511
23 TraesCS2D01G553500 chr4D 355931040 355931549 509 False 778.000000 778 94.152000 1 512 1 chr4D.!!$F2 511
24 TraesCS2D01G553500 chr1D 460176950 460177833 883 False 549.000000 549 78.571000 521 1401 1 chr1D.!!$F1 880

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
517 521 0.684805 GACCGGTCCTGACATCCTCT 60.685 60.0 24.75 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2504 9132 1.137513 GTTTCAGGAAGACACGACGG 58.862 55.0 0.0 0.0 0.0 4.79 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
64 66 6.791887 ATATTTCATGACAGGCGTTATGAG 57.208 37.500 13.35 0.00 45.63 2.90
87 90 6.233434 AGCATAGAATATTTCGGAGCATGAA 58.767 36.000 0.00 0.00 34.02 2.57
91 94 9.979270 CATAGAATATTTCGGAGCATGAATTAC 57.021 33.333 0.00 0.00 34.02 1.89
184 187 3.549794 GCTATTGTCTTGGCCAGATTCT 58.450 45.455 5.11 0.00 32.60 2.40
233 236 2.480555 CGGAACCTGCGCAATGAC 59.519 61.111 13.05 3.55 0.00 3.06
315 319 2.224378 CCCATAGACGCAGATGAACCAT 60.224 50.000 0.00 0.00 0.00 3.55
345 349 2.238646 TCCGCCATCAACCACTAGAAAT 59.761 45.455 0.00 0.00 0.00 2.17
347 351 3.535561 CGCCATCAACCACTAGAAATCT 58.464 45.455 0.00 0.00 0.00 2.40
348 352 3.941483 CGCCATCAACCACTAGAAATCTT 59.059 43.478 0.00 0.00 0.00 2.40
349 353 4.396166 CGCCATCAACCACTAGAAATCTTT 59.604 41.667 0.00 0.00 0.00 2.52
409 413 9.777297 ACATATTTTGTACTTTGCTTGGAATTT 57.223 25.926 0.00 0.00 36.57 1.82
421 425 7.945033 TTGCTTGGAATTTTTGTATCAAGTC 57.055 32.000 0.00 0.00 35.43 3.01
426 430 5.533154 TGGAATTTTTGTATCAAGTCGGTGT 59.467 36.000 0.00 0.00 0.00 4.16
487 491 4.634411 AGGGCCATTTTCTGGGAAATTAT 58.366 39.130 6.18 0.00 46.06 1.28
517 521 0.684805 GACCGGTCCTGACATCCTCT 60.685 60.000 24.75 0.00 0.00 3.69
823 858 2.095415 GCTTGAAAATAAACCGGTCGCT 60.095 45.455 8.04 0.00 0.00 4.93
872 907 1.153168 CGAGCCATTACACCCCTGG 60.153 63.158 0.00 0.00 0.00 4.45
912 959 6.270815 GCTTACAGTTATCGACATGGAAGTA 58.729 40.000 12.12 0.00 0.00 2.24
927 974 2.550606 GGAAGTATTGGTTTGTGTCGCA 59.449 45.455 0.00 0.00 0.00 5.10
1199 1277 4.187694 GAGAAGACAATCTCGCTGGATTT 58.812 43.478 0.00 0.00 36.77 2.17
1230 1308 4.459089 GAGGGTGCAGTCGGGAGC 62.459 72.222 0.00 0.00 34.18 4.70
1302 1380 0.455464 CGCAGGACGTCGACACATTA 60.455 55.000 17.16 0.00 36.87 1.90
1315 1393 3.367395 CGACACATTACAGCTTGAGAGGA 60.367 47.826 0.00 0.00 0.00 3.71
1423 7753 1.672881 GCGTTTAGATCCTTGCTGCAT 59.327 47.619 1.84 0.00 0.00 3.96
1547 8016 1.613437 ACATAGTTTGGTGGTTGCTGC 59.387 47.619 0.00 0.00 0.00 5.25
1548 8017 1.888512 CATAGTTTGGTGGTTGCTGCT 59.111 47.619 0.00 0.00 0.00 4.24
1549 8018 2.065899 TAGTTTGGTGGTTGCTGCTT 57.934 45.000 0.00 0.00 0.00 3.91
1550 8019 1.194218 AGTTTGGTGGTTGCTGCTTT 58.806 45.000 0.00 0.00 0.00 3.51
1551 8020 1.554617 AGTTTGGTGGTTGCTGCTTTT 59.445 42.857 0.00 0.00 0.00 2.27
1681 8161 3.771577 AGAATTCTAGGGGTATTGCGG 57.228 47.619 6.06 0.00 0.00 5.69
1814 8322 9.832445 ATCTTTGTAGTGTTCTTTCTTAGACAA 57.168 29.630 0.00 0.00 30.90 3.18
1962 8568 7.650104 GTCTTTTTGGTTTCCGATGTGAAAATA 59.350 33.333 0.00 0.00 36.09 1.40
2036 8647 6.237755 GCAGAATCACAAGCTATTTTGAATGC 60.238 38.462 2.51 4.79 0.00 3.56
2048 8659 4.592485 TTTTGAATGCCGTACCAAATGT 57.408 36.364 0.00 0.00 0.00 2.71
2062 8673 8.751335 CCGTACCAAATGTTATTATTTGCATTC 58.249 33.333 0.00 0.00 43.40 2.67
2475 9097 1.557099 TGGTCAGTAGGCCACACTAG 58.443 55.000 5.01 3.33 0.00 2.57
2476 9098 1.203137 TGGTCAGTAGGCCACACTAGT 60.203 52.381 5.01 0.00 0.00 2.57
2504 9132 5.539048 TGCTTAGTCACTGTCTTAACCTTC 58.461 41.667 0.00 0.00 0.00 3.46
2581 9382 3.541632 GCCATTCACCGGAGATTTAAGA 58.458 45.455 9.46 0.00 0.00 2.10
2932 9780 9.388506 GATGGTAATTATGGACAGATGGATTAG 57.611 37.037 0.00 0.00 0.00 1.73
2933 9781 8.275187 TGGTAATTATGGACAGATGGATTAGT 57.725 34.615 0.00 0.00 0.00 2.24
3050 10407 1.789576 AAACCCCTTCACTCGGCCAT 61.790 55.000 2.24 0.00 0.00 4.40
3092 10449 1.063006 CGCCACAATCCTTGCATCG 59.937 57.895 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 30 6.262049 TGTCATGAAATATACGAAACCCATGG 59.738 38.462 4.14 4.14 33.16 3.66
64 66 6.486253 TTCATGCTCCGAAATATTCTATGC 57.514 37.500 0.00 0.00 0.00 3.14
91 94 8.871125 AGAGCACGGATATAATATAATAAGGGG 58.129 37.037 0.00 0.00 0.00 4.79
108 111 1.463056 CGCAAACATTAAGAGCACGGA 59.537 47.619 0.00 0.00 0.00 4.69
150 153 0.257039 CAATAGCCAGGGACAAGCCT 59.743 55.000 0.00 0.00 36.66 4.58
233 236 2.013483 CTTCGCGAGGCTGCTATCG 61.013 63.158 9.59 18.76 41.79 2.92
345 349 5.001232 GTGGCCTATGAGTACAACAAAAGA 58.999 41.667 3.32 0.00 0.00 2.52
347 351 4.720046 TGTGGCCTATGAGTACAACAAAA 58.280 39.130 3.32 0.00 0.00 2.44
348 352 4.359434 TGTGGCCTATGAGTACAACAAA 57.641 40.909 3.32 0.00 0.00 2.83
349 353 4.359434 TTGTGGCCTATGAGTACAACAA 57.641 40.909 3.32 0.00 0.00 2.83
409 413 4.594123 TGAGACACCGACTTGATACAAA 57.406 40.909 0.00 0.00 0.00 2.83
421 425 2.094494 ACTGTTAGCTGATGAGACACCG 60.094 50.000 0.00 0.00 0.00 4.94
426 430 5.069648 CCAGGATTACTGTTAGCTGATGAGA 59.930 44.000 0.00 0.00 46.06 3.27
496 500 0.684805 AGGATGTCAGGACCGGTCTC 60.685 60.000 32.52 22.35 0.00 3.36
498 502 0.684805 AGAGGATGTCAGGACCGGTC 60.685 60.000 27.04 27.04 0.00 4.79
517 521 2.280524 CGCACGGTCCAGTCCAAA 60.281 61.111 0.00 0.00 0.00 3.28
596 609 1.070134 CACCACCGTCTCCTTGAAGAA 59.930 52.381 0.00 0.00 0.00 2.52
667 680 3.350377 GCAACCAAAGCGGCTACA 58.650 55.556 1.35 0.00 39.03 2.74
748 774 1.664649 CGTTGCGTCTGCCTCTTCA 60.665 57.895 0.00 0.00 41.78 3.02
823 858 3.038280 TGTGTGGGAAGAGAAGACAAGA 58.962 45.455 0.00 0.00 0.00 3.02
872 907 1.911057 AAGCCAGGTAAGCTCCAAAC 58.089 50.000 0.00 0.00 40.49 2.93
912 959 1.327303 ATGGTGCGACACAAACCAAT 58.673 45.000 11.20 0.00 46.59 3.16
927 974 2.124736 AGCCATGCGCGTAATGGT 60.125 55.556 30.69 20.35 45.46 3.55
947 994 7.282585 TCAATCGAACCTGAAATCCAATAGAT 58.717 34.615 0.00 0.00 36.48 1.98
1199 1277 2.935238 GCACCCTCGATTAAGCAGTCAA 60.935 50.000 0.00 0.00 0.00 3.18
1230 1308 5.047306 TCCGACATAATATAGGAGCAAGTGG 60.047 44.000 0.00 0.00 0.00 4.00
1302 1380 4.833478 ATAACACATCCTCTCAAGCTGT 57.167 40.909 0.00 0.00 0.00 4.40
1315 1393 7.014134 TGACTGTTTTGGACATGAATAACACAT 59.986 33.333 0.00 0.00 37.69 3.21
1423 7753 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
1492 7822 9.486497 CTTACTGATCACATTAATGAGCTATGT 57.514 33.333 22.16 14.29 35.97 2.29
1493 7823 9.486497 ACTTACTGATCACATTAATGAGCTATG 57.514 33.333 22.16 9.31 35.97 2.23
1536 7998 2.602257 AAAGAAAAGCAGCAACCACC 57.398 45.000 0.00 0.00 0.00 4.61
1814 8322 5.574188 AGTCCTGCTTGACTGGAATAAATT 58.426 37.500 7.74 0.00 46.85 1.82
2005 8615 8.804743 CAAAATAGCTTGTGATTCTGCATTTAG 58.195 33.333 0.00 0.00 0.00 1.85
2036 8647 8.641499 AATGCAAATAATAACATTTGGTACGG 57.359 30.769 9.81 0.00 43.23 4.02
2416 9038 3.487372 ACCAAAAGCACTTAAGGACTCC 58.513 45.455 7.53 0.00 0.00 3.85
2475 9097 3.983741 AGACAGTGACTAAGCAGACAAC 58.016 45.455 0.00 0.00 0.00 3.32
2476 9098 4.672587 AAGACAGTGACTAAGCAGACAA 57.327 40.909 0.00 0.00 0.00 3.18
2504 9132 1.137513 GTTTCAGGAAGACACGACGG 58.862 55.000 0.00 0.00 0.00 4.79
2581 9382 5.724328 TGAGTTCATTTAATGACTCGAGCT 58.276 37.500 13.61 0.00 39.39 4.09
2848 9663 8.306761 TCTCTGGAAAAGCCTTCATTAAAAATC 58.693 33.333 0.00 0.00 37.63 2.17
2933 9781 9.368674 CCATCTGCACATGACAAAAATTATTAA 57.631 29.630 3.19 0.00 0.00 1.40
2939 9787 4.619863 GCTCCATCTGCACATGACAAAAAT 60.620 41.667 3.19 0.00 0.00 1.82
3050 10407 2.549064 TAGAGCAGAAAAGTGCAGCA 57.451 45.000 0.00 0.00 46.60 4.41
3092 10449 1.740025 GGCTTCACTTATGCAGGACAC 59.260 52.381 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.