Multiple sequence alignment - TraesCS1A01G068900

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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 TraesCS1A01G068900 chr1A 100.000 3791 0 0 1 3791 50541079 50537289 0.000000e+00 7001.0
1 TraesCS1A01G068900 chr1A 97.797 2451 48 2 509 2958 589112791 589115236 0.000000e+00 4222.0
2 TraesCS1A01G068900 chr1A 94.915 177 7 2 1 175 544170784 544170960 3.730000e-70 276.0
3 TraesCS1A01G068900 chr1A 94.318 176 9 1 1 175 444429460 444429635 6.240000e-68 268.0
4 TraesCS1A01G068900 chr1A 75.591 254 37 14 1831 2080 521671854 521671622 6.700000e-18 102.0
5 TraesCS1A01G068900 chr4B 92.362 2998 161 36 4 2957 58970446 58973419 0.000000e+00 4205.0
6 TraesCS1A01G068900 chr4B 80.348 748 85 29 2956 3655 457871852 457872585 9.390000e-141 510.0
7 TraesCS1A01G068900 chr7B 94.772 2257 94 7 707 2959 743663367 743661131 0.000000e+00 3493.0
8 TraesCS1A01G068900 chr7B 84.581 454 46 12 65 505 743663805 743663363 2.710000e-116 429.0
9 TraesCS1A01G068900 chr1B 93.683 2248 79 15 753 2956 667284154 667286382 0.000000e+00 3306.0
10 TraesCS1A01G068900 chr1B 81.095 767 81 27 2952 3668 491728874 491729626 4.280000e-154 555.0
11 TraesCS1A01G068900 chr1B 80.341 763 87 26 2956 3668 161314466 161315215 1.560000e-143 520.0
12 TraesCS1A01G068900 chr7A 97.460 1181 17 4 1778 2957 15675975 15677143 0.000000e+00 2002.0
13 TraesCS1A01G068900 chr7A 99.137 1043 8 1 714 1755 15674937 15675979 0.000000e+00 1875.0
14 TraesCS1A01G068900 chr7A 96.267 643 11 5 1 635 15668756 15669393 0.000000e+00 1042.0
15 TraesCS1A01G068900 chr7A 97.778 90 2 0 631 720 15674712 15674801 5.070000e-34 156.0
16 TraesCS1A01G068900 chr4A 95.018 843 21 2 2969 3791 65656039 65655198 0.000000e+00 1304.0
17 TraesCS1A01G068900 chr4A 95.455 176 7 1 1 175 430273630 430273455 2.880000e-71 279.0
18 TraesCS1A01G068900 chr4A 92.655 177 11 2 1 175 543404681 543404505 1.750000e-63 254.0
19 TraesCS1A01G068900 chr4A 80.297 269 40 8 1 257 690247254 690246987 1.390000e-44 191.0
20 TraesCS1A01G068900 chr5D 89.524 525 47 5 2450 2967 560484109 560484632 0.000000e+00 658.0
21 TraesCS1A01G068900 chr5D 83.088 136 16 2 1618 1753 501504090 501503962 2.390000e-22 117.0
22 TraesCS1A01G068900 chr3B 80.183 767 83 31 2956 3668 42267613 42268364 9.390000e-141 510.0
23 TraesCS1A01G068900 chr6B 80.267 750 83 29 2971 3668 95573136 95572400 4.370000e-139 505.0
24 TraesCS1A01G068900 chr6B 87.069 116 10 5 2970 3085 461154828 461154718 3.980000e-25 126.0
25 TraesCS1A01G068900 chr2D 86.429 420 48 4 2544 2959 23162390 23162804 5.770000e-123 451.0
26 TraesCS1A01G068900 chr3D 85.882 425 51 4 2539 2959 589558498 589558079 9.660000e-121 444.0
27 TraesCS1A01G068900 chr3D 84.969 326 34 7 3346 3668 15453747 15454060 2.200000e-82 316.0
28 TraesCS1A01G068900 chr5B 84.742 426 55 5 2539 2960 280594433 280594014 5.860000e-113 418.0
29 TraesCS1A01G068900 chr5B 76.127 377 29 19 1620 1956 633142923 633143278 1.420000e-29 141.0
30 TraesCS1A01G068900 chr7D 75.658 760 124 39 1053 1761 476109821 476110570 4.720000e-84 322.0
31 TraesCS1A01G068900 chr7D 74.307 541 91 30 1053 1550 49288339 49287804 6.470000e-43 185.0
32 TraesCS1A01G068900 chr7D 74.307 541 91 30 1053 1550 49309888 49309353 6.470000e-43 185.0
33 TraesCS1A01G068900 chr7D 89.344 122 12 1 2956 3076 72067468 72067589 6.560000e-33 152.0
34 TraesCS1A01G068900 chr7D 83.217 143 16 4 1053 1189 593881739 593881879 1.430000e-24 124.0
35 TraesCS1A01G068900 chr4D 80.244 410 46 10 2969 3352 295417317 295417717 3.730000e-70 276.0
36 TraesCS1A01G068900 chrUn 78.870 407 69 10 1349 1745 69739359 69738960 3.760000e-65 259.0
37 TraesCS1A01G068900 chr3A 82.132 319 41 6 3351 3668 731513677 731513374 3.760000e-65 259.0
38 TraesCS1A01G068900 chr2A 77.860 271 48 9 1 261 192132419 192132151 1.410000e-34 158.0
39 TraesCS1A01G068900 chr5A 80.882 136 19 6 1618 1753 599487118 599486990 2.410000e-17 100.0
40 TraesCS1A01G068900 chr5A 75.862 145 20 7 1609 1753 625702704 625702833 4.090000e-05 60.2


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 TraesCS1A01G068900 chr1A 50537289 50541079 3790 True 7001.000000 7001 100.0000 1 3791 1 chr1A.!!$R1 3790
1 TraesCS1A01G068900 chr1A 589112791 589115236 2445 False 4222.000000 4222 97.7970 509 2958 1 chr1A.!!$F3 2449
2 TraesCS1A01G068900 chr4B 58970446 58973419 2973 False 4205.000000 4205 92.3620 4 2957 1 chr4B.!!$F1 2953
3 TraesCS1A01G068900 chr4B 457871852 457872585 733 False 510.000000 510 80.3480 2956 3655 1 chr4B.!!$F2 699
4 TraesCS1A01G068900 chr7B 743661131 743663805 2674 True 1961.000000 3493 89.6765 65 2959 2 chr7B.!!$R1 2894
5 TraesCS1A01G068900 chr1B 667284154 667286382 2228 False 3306.000000 3306 93.6830 753 2956 1 chr1B.!!$F3 2203
6 TraesCS1A01G068900 chr1B 491728874 491729626 752 False 555.000000 555 81.0950 2952 3668 1 chr1B.!!$F2 716
7 TraesCS1A01G068900 chr1B 161314466 161315215 749 False 520.000000 520 80.3410 2956 3668 1 chr1B.!!$F1 712
8 TraesCS1A01G068900 chr7A 15674712 15677143 2431 False 1344.333333 2002 98.1250 631 2957 3 chr7A.!!$F2 2326
9 TraesCS1A01G068900 chr7A 15668756 15669393 637 False 1042.000000 1042 96.2670 1 635 1 chr7A.!!$F1 634
10 TraesCS1A01G068900 chr4A 65655198 65656039 841 True 1304.000000 1304 95.0180 2969 3791 1 chr4A.!!$R1 822
11 TraesCS1A01G068900 chr5D 560484109 560484632 523 False 658.000000 658 89.5240 2450 2967 1 chr5D.!!$F1 517
12 TraesCS1A01G068900 chr3B 42267613 42268364 751 False 510.000000 510 80.1830 2956 3668 1 chr3B.!!$F1 712
13 TraesCS1A01G068900 chr6B 95572400 95573136 736 True 505.000000 505 80.2670 2971 3668 1 chr6B.!!$R1 697
14 TraesCS1A01G068900 chr7D 476109821 476110570 749 False 322.000000 322 75.6580 1053 1761 1 chr7D.!!$F2 708

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
331 342 0.474660 AGGGATGGATAGCTGGGTCC 60.475 60.000 0.00 1.71 35.02 4.46 F
333 344 1.140312 GGATGGATAGCTGGGTCCAA 58.860 55.000 17.68 5.68 46.78 3.53 F
638 678 1.825474 TCTTTCCTCATCGGGTCACTC 59.175 52.381 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 1974 0.468226 CGGCAGGGCTAAACTGGATA 59.532 55.0 0.00 0.0 36.48 2.59 R
2231 2510 5.610398 TGCTTCTCACTAATGAAACTCACA 58.390 37.5 0.00 0.0 33.30 3.58 R
2937 3242 0.820482 TACTAGCATAGCCCGCGTGA 60.820 55.0 4.92 0.0 44.39 4.35 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
26 27 2.905415 TTGCCTCAAGATTCACCCAT 57.095 45.000 0.00 0.00 0.00 4.00
100 103 1.682394 GGGTGTGGTGGTGTACAAACA 60.682 52.381 0.00 0.00 0.00 2.83
205 210 2.555547 GGCAGGTTGCTGTGGTCAC 61.556 63.158 0.67 0.00 44.28 3.67
226 237 3.242518 CTCGCTGTCACGTTGAGATTTA 58.757 45.455 0.00 0.00 0.00 1.40
229 240 3.612423 CGCTGTCACGTTGAGATTTATGA 59.388 43.478 0.00 0.00 0.00 2.15
237 248 5.582269 CACGTTGAGATTTATGACCTGACAT 59.418 40.000 0.00 0.00 0.00 3.06
249 260 5.310409 TGACCTGACATCTTTCCTTCTTT 57.690 39.130 0.00 0.00 0.00 2.52
320 331 3.399181 GCGGTGACCAGGGATGGA 61.399 66.667 1.11 0.00 0.00 3.41
329 340 0.769776 CCAGGGATGGATAGCTGGGT 60.770 60.000 0.00 0.00 0.00 4.51
330 341 0.689623 CAGGGATGGATAGCTGGGTC 59.310 60.000 0.00 0.00 0.00 4.46
331 342 0.474660 AGGGATGGATAGCTGGGTCC 60.475 60.000 0.00 1.71 35.02 4.46
333 344 1.140312 GGATGGATAGCTGGGTCCAA 58.860 55.000 17.68 5.68 46.78 3.53
518 558 3.065371 GGATGTTTCCAGTTAATGCTCGG 59.935 47.826 0.00 0.00 42.12 4.63
638 678 1.825474 TCTTTCCTCATCGGGTCACTC 59.175 52.381 0.00 0.00 0.00 3.51
1437 1695 4.200874 ACTTCATCTACTAGGAGACGGTG 58.799 47.826 6.88 1.91 0.00 4.94
1576 1835 2.049985 CGAGATCCGCGTCATCCC 60.050 66.667 4.92 0.00 0.00 3.85
2016 2283 9.844790 CTTTTCAATATGATCTTTGTTAGTGCA 57.155 29.630 0.00 0.00 0.00 4.57
2025 2292 8.703604 TGATCTTTGTTAGTGCATAGAGTTAC 57.296 34.615 0.00 0.00 31.85 2.50
2184 2462 3.383185 TGGTCGCTGGTTTTCATTCTTTT 59.617 39.130 0.00 0.00 0.00 2.27
2254 2533 5.466728 GTGTGAGTTTCATTAGTGAGAAGCA 59.533 40.000 0.00 0.00 35.39 3.91
2255 2534 6.017934 GTGTGAGTTTCATTAGTGAGAAGCAA 60.018 38.462 0.00 0.00 35.39 3.91
2256 2535 6.542005 TGTGAGTTTCATTAGTGAGAAGCAAA 59.458 34.615 0.00 0.00 35.39 3.68
2871 3176 8.928733 GGTTTTAGTCACGTACAATTCTATCAA 58.071 33.333 0.00 0.00 0.00 2.57
2963 3268 5.411977 ACGCGGGCTATGCTAGTATATATAG 59.588 44.000 12.47 0.00 0.00 1.31
2965 3270 6.183360 CGCGGGCTATGCTAGTATATATAGAG 60.183 46.154 0.00 0.00 0.00 2.43
2967 3272 7.065324 GCGGGCTATGCTAGTATATATAGAGAG 59.935 44.444 0.62 0.36 0.00 3.20
3036 3341 3.807538 TCAGTCGGCCGCGTACTC 61.808 66.667 23.51 6.23 0.00 2.59
3376 3724 3.758554 CGAACCAGATTTTCCATGTCCTT 59.241 43.478 0.00 0.00 0.00 3.36
3388 3736 1.808945 CATGTCCTTGACAGCTGGTTC 59.191 52.381 19.93 8.09 46.04 3.62
3397 3745 2.930562 AGCTGGTTCCGGGCTTCT 60.931 61.111 0.00 0.00 31.81 2.85
3506 3854 0.968405 GTTGCCTTGCAGGGATGAAA 59.032 50.000 20.85 3.85 40.61 2.69
3520 3868 2.615493 GGATGAAAGTCATGGTCGGTGT 60.615 50.000 0.00 0.00 37.20 4.16
3609 3966 6.777091 TGTTTGATTTCTGATCTCTTCCCAAA 59.223 34.615 0.00 0.00 0.00 3.28
3610 3967 7.040201 TGTTTGATTTCTGATCTCTTCCCAAAG 60.040 37.037 0.00 0.00 0.00 2.77
3767 4128 9.764870 CAATCTGTTATTAGTTGACATGAAGTG 57.235 33.333 0.00 0.00 0.00 3.16
3768 4129 7.364522 TCTGTTATTAGTTGACATGAAGTGC 57.635 36.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.561735 CGTAAGGTCTTTTTCAGCCAAA 57.438 40.909 0.00 0.00 0.00 3.28
100 103 5.110814 TGAAATAAATGGATCCACGAGGT 57.889 39.130 18.99 0.00 35.89 3.85
205 210 1.702886 AATCTCAACGTGACAGCGAG 58.297 50.000 0.00 0.00 35.59 5.03
226 237 5.511386 AAGAAGGAAAGATGTCAGGTCAT 57.489 39.130 0.00 0.00 0.00 3.06
229 240 4.141158 ACCAAAGAAGGAAAGATGTCAGGT 60.141 41.667 0.00 0.00 0.00 4.00
237 248 4.137543 GAGAAGCACCAAAGAAGGAAAGA 58.862 43.478 0.00 0.00 0.00 2.52
249 260 1.945354 GATCGACCGGAGAAGCACCA 61.945 60.000 9.46 0.00 0.00 4.17
320 331 5.280011 CCGTCTTATAATTGGACCCAGCTAT 60.280 44.000 0.00 0.00 0.00 2.97
329 340 5.105567 TCCTTTGCCGTCTTATAATTGGA 57.894 39.130 2.81 0.00 0.00 3.53
330 341 5.124776 TGTTCCTTTGCCGTCTTATAATTGG 59.875 40.000 0.00 0.00 0.00 3.16
331 342 6.189677 TGTTCCTTTGCCGTCTTATAATTG 57.810 37.500 0.00 0.00 0.00 2.32
332 343 6.183360 CCATGTTCCTTTGCCGTCTTATAATT 60.183 38.462 0.00 0.00 0.00 1.40
333 344 5.299279 CCATGTTCCTTTGCCGTCTTATAAT 59.701 40.000 0.00 0.00 0.00 1.28
518 558 6.605194 AGAGAAAAATATCTGAAGGAAAGGGC 59.395 38.462 0.00 0.00 0.00 5.19
638 678 3.782244 GCAACGCAGGTGAGCTCG 61.782 66.667 9.64 0.00 0.00 5.03
1709 1974 0.468226 CGGCAGGGCTAAACTGGATA 59.532 55.000 0.00 0.00 36.48 2.59
2018 2285 9.696572 TGTCCATTTGTATACTCTAGTAACTCT 57.303 33.333 4.17 0.00 33.76 3.24
2231 2510 5.610398 TGCTTCTCACTAATGAAACTCACA 58.390 37.500 0.00 0.00 33.30 3.58
2937 3242 0.820482 TACTAGCATAGCCCGCGTGA 60.820 55.000 4.92 0.00 44.39 4.35
2939 3244 1.830279 TATACTAGCATAGCCCGCGT 58.170 50.000 4.92 0.00 44.39 6.01
2965 3270 7.269316 CCTGGGTCTTAAATAGAGTTTCTCTC 58.731 42.308 2.41 0.00 40.34 3.20
2967 3272 6.070136 ACCCTGGGTCTTAAATAGAGTTTCTC 60.070 42.308 14.05 0.00 32.23 2.87
3036 3341 2.839486 TGTGCTAGGTTGAACCAGAG 57.161 50.000 17.83 13.86 41.95 3.35
3267 3615 1.007271 CAGTCGCACAAGAGGACGT 60.007 57.895 0.00 0.00 35.87 4.34
3376 3724 4.329545 GCCCGGAACCAGCTGTCA 62.330 66.667 13.81 0.00 0.00 3.58
3397 3745 1.978455 AACGTGGAGAACCTGTGCCA 61.978 55.000 0.00 0.00 37.04 4.92
3506 3854 0.524862 GTACGACACCGACCATGACT 59.475 55.000 0.00 0.00 39.50 3.41
3520 3868 1.990799 CATTGCTTCTGGACGTACGA 58.009 50.000 24.41 0.00 0.00 3.43


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

AutoCloner maintained by Alex Coulton.