Multiple sequence alignment - TraesCS2A01G365500

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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 TraesCS2A01G365500 chr2A 100.000 2971 0 0 1 2971 610176197 610179167 0.000000e+00 5487.0
1 TraesCS2A01G365500 chr2A 94.732 2050 61 4 239 2261 607512473 607514502 0.000000e+00 3144.0
2 TraesCS2A01G365500 chr2A 93.491 338 16 3 1 332 607512166 607512503 5.720000e-137 497.0
3 TraesCS2A01G365500 chr2A 82.866 321 55 0 32 352 138528265 138527945 3.750000e-74 289.0
4 TraesCS2A01G365500 chr2A 91.852 135 10 1 257 391 610176372 610176505 1.410000e-43 187.0
5 TraesCS2A01G365500 chr2A 91.852 135 10 1 176 309 610176453 610176587 1.410000e-43 187.0
6 TraesCS2A01G365500 chr2B 94.896 2018 85 12 176 2178 545152126 545154140 0.000000e+00 3140.0
7 TraesCS2A01G365500 chr2B 97.238 181 5 0 152 332 545152021 545152201 1.030000e-79 307.0
8 TraesCS2A01G365500 chr2B 90.129 233 8 1 2032 2264 545154368 545154585 3.750000e-74 289.0
9 TraesCS2A01G365500 chr2B 82.555 321 56 0 32 352 185762927 185762607 1.740000e-72 283.0
10 TraesCS2A01G365500 chr2B 93.985 133 8 0 257 389 545152045 545152177 5.020000e-48 202.0
11 TraesCS2A01G365500 chr2B 81.818 187 34 0 32 218 186402883 186403069 1.100000e-34 158.0
12 TraesCS2A01G365500 chr2D 97.056 1019 22 2 1235 2251 462240872 462241884 0.000000e+00 1709.0
13 TraesCS2A01G365500 chr2D 98.686 609 8 0 630 1238 462240184 462240792 0.000000e+00 1081.0
14 TraesCS2A01G365500 chr2D 82.307 1283 181 32 730 1991 131642937 131641680 0.000000e+00 1070.0
15 TraesCS2A01G365500 chr2D 93.056 216 15 0 1 216 462229307 462229522 1.720000e-82 316.0
16 TraesCS2A01G365500 chr2D 99.296 142 1 0 320 461 462240042 462240183 1.060000e-64 257.0
17 TraesCS2A01G365500 chr2D 84.298 242 36 2 32 272 131643434 131643194 4.950000e-58 235.0
18 TraesCS2A01G365500 chr2D 91.818 110 9 0 223 332 462238092 462238201 1.430000e-33 154.0
19 TraesCS2A01G365500 chr2D 93.421 76 5 0 176 251 462238126 462238201 2.420000e-21 113.0
20 TraesCS2A01G365500 chr1B 83.533 1585 207 28 428 2006 275553324 275554860 0.000000e+00 1432.0
21 TraesCS2A01G365500 chr1B 83.207 1584 211 30 430 2006 275671947 275673482 0.000000e+00 1400.0
22 TraesCS2A01G365500 chr1B 83.104 1598 203 34 428 2006 275358367 275359916 0.000000e+00 1393.0
23 TraesCS2A01G365500 chr1B 82.979 1598 205 34 428 2006 275458357 275459906 0.000000e+00 1382.0
24 TraesCS2A01G365500 chr1B 91.781 73 4 2 2192 2262 480973023 480972951 1.880000e-17 100.0
25 TraesCS2A01G365500 chr1A 83.176 1587 209 35 428 2006 246129303 246127767 0.000000e+00 1399.0
26 TraesCS2A01G365500 chr6B 93.530 711 27 9 2265 2971 661998752 661998057 0.000000e+00 1040.0
27 TraesCS2A01G365500 chr7B 81.709 995 158 12 981 1969 2907582 2908558 0.000000e+00 808.0
28 TraesCS2A01G365500 chr3D 88.336 643 53 10 2341 2969 62069488 62068854 0.000000e+00 752.0
29 TraesCS2A01G365500 chr3D 91.667 72 4 1 2195 2264 85447128 85447057 6.780000e-17 99.0
30 TraesCS2A01G365500 chr3D 91.549 71 4 2 2193 2262 611501135 611501066 2.440000e-16 97.1
31 TraesCS2A01G365500 chr3A 88.354 644 52 11 2341 2969 71148263 71147628 0.000000e+00 752.0
32 TraesCS2A01G365500 chr3B 88.553 629 50 12 2341 2956 100967358 100966739 0.000000e+00 743.0
33 TraesCS2A01G365500 chr3B 86.458 96 8 3 2192 2282 86108414 86108319 1.880000e-17 100.0
34 TraesCS2A01G365500 chr1D 91.549 71 4 2 2194 2262 358222551 358222621 2.440000e-16 97.1
35 TraesCS2A01G365500 chr1D 91.045 67 4 2 2199 2263 28194202 28194136 4.080000e-14 89.8


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 TraesCS2A01G365500 chr2A 610176197 610179167 2970 False 1953.666667 5487 94.5680 1 2971 3 chr2A.!!$F2 2970
1 TraesCS2A01G365500 chr2A 607512166 607514502 2336 False 1820.500000 3144 94.1115 1 2261 2 chr2A.!!$F1 2260
2 TraesCS2A01G365500 chr2B 545152021 545154585 2564 False 984.500000 3140 94.0620 152 2264 4 chr2B.!!$F2 2112
3 TraesCS2A01G365500 chr2D 462238092 462241884 3792 False 662.800000 1709 96.0554 176 2251 5 chr2D.!!$F2 2075
4 TraesCS2A01G365500 chr2D 131641680 131643434 1754 True 652.500000 1070 83.3025 32 1991 2 chr2D.!!$R1 1959
5 TraesCS2A01G365500 chr1B 275553324 275554860 1536 False 1432.000000 1432 83.5330 428 2006 1 chr1B.!!$F3 1578
6 TraesCS2A01G365500 chr1B 275671947 275673482 1535 False 1400.000000 1400 83.2070 430 2006 1 chr1B.!!$F4 1576
7 TraesCS2A01G365500 chr1B 275358367 275359916 1549 False 1393.000000 1393 83.1040 428 2006 1 chr1B.!!$F1 1578
8 TraesCS2A01G365500 chr1B 275458357 275459906 1549 False 1382.000000 1382 82.9790 428 2006 1 chr1B.!!$F2 1578
9 TraesCS2A01G365500 chr1A 246127767 246129303 1536 True 1399.000000 1399 83.1760 428 2006 1 chr1A.!!$R1 1578
10 TraesCS2A01G365500 chr6B 661998057 661998752 695 True 1040.000000 1040 93.5300 2265 2971 1 chr6B.!!$R1 706
11 TraesCS2A01G365500 chr7B 2907582 2908558 976 False 808.000000 808 81.7090 981 1969 1 chr7B.!!$F1 988
12 TraesCS2A01G365500 chr3D 62068854 62069488 634 True 752.000000 752 88.3360 2341 2969 1 chr3D.!!$R1 628
13 TraesCS2A01G365500 chr3A 71147628 71148263 635 True 752.000000 752 88.3540 2341 2969 1 chr3A.!!$R1 628
14 TraesCS2A01G365500 chr3B 100966739 100967358 619 True 743.000000 743 88.5530 2341 2956 1 chr3B.!!$R2 615

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
695 2603 0.033208 AGGCAGAGGAGACTGAGGAG 60.033 60.0 0.0 0.0 44.43 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 4723 2.691409 GGCACTCTGGCAGTACATTA 57.309 50.0 15.27 0.0 43.14 1.9 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
23 24 0.518636 CAAACATGGAGACGCACCAG 59.481 55.000 0.00 0.0 40.89 4.00
99 100 5.627735 GCAGATCTGATAAGTGGTCTTTCCA 60.628 44.000 27.04 0.0 45.01 3.53
235 236 3.303938 TGGACCAAGGAAAATCAAGCAA 58.696 40.909 0.00 0.0 0.00 3.91
243 244 3.579586 AGGAAAATCAAGCAATGAAGGCA 59.420 39.130 0.00 0.0 42.54 4.75
352 2212 5.376854 AGTAACGAAAGCAAATCAAGCAT 57.623 34.783 0.00 0.0 0.00 3.79
607 2482 0.669318 CAAAAGGACGCGCTGAGGTA 60.669 55.000 5.73 0.0 0.00 3.08
614 2489 2.818132 GCGCTGAGGTAGGAGCAT 59.182 61.111 0.00 0.0 34.69 3.79
679 2587 0.603569 TTCTCACTTCAGGACGAGGC 59.396 55.000 0.00 0.0 0.00 4.70
680 2588 0.539669 TCTCACTTCAGGACGAGGCA 60.540 55.000 0.00 0.0 0.00 4.75
681 2589 0.108898 CTCACTTCAGGACGAGGCAG 60.109 60.000 0.00 0.0 0.00 4.85
682 2590 0.539669 TCACTTCAGGACGAGGCAGA 60.540 55.000 0.00 0.0 0.00 4.26
683 2591 0.108898 CACTTCAGGACGAGGCAGAG 60.109 60.000 0.00 0.0 0.00 3.35
684 2592 1.254284 ACTTCAGGACGAGGCAGAGG 61.254 60.000 0.00 0.0 0.00 3.69
685 2593 0.967887 CTTCAGGACGAGGCAGAGGA 60.968 60.000 0.00 0.0 0.00 3.71
686 2594 0.967887 TTCAGGACGAGGCAGAGGAG 60.968 60.000 0.00 0.0 0.00 3.69
687 2595 1.379176 CAGGACGAGGCAGAGGAGA 60.379 63.158 0.00 0.0 0.00 3.71
688 2596 1.379309 AGGACGAGGCAGAGGAGAC 60.379 63.158 0.00 0.0 0.00 3.36
690 2598 1.662438 GGACGAGGCAGAGGAGACTG 61.662 65.000 0.00 0.0 44.43 3.51
691 2599 0.678366 GACGAGGCAGAGGAGACTGA 60.678 60.000 0.00 0.0 44.43 3.41
692 2600 0.679640 ACGAGGCAGAGGAGACTGAG 60.680 60.000 0.00 0.0 44.43 3.35
693 2601 1.383456 CGAGGCAGAGGAGACTGAGG 61.383 65.000 0.00 0.0 44.43 3.86
694 2602 0.033601 GAGGCAGAGGAGACTGAGGA 60.034 60.000 0.00 0.0 44.43 3.71
695 2603 0.033208 AGGCAGAGGAGACTGAGGAG 60.033 60.000 0.00 0.0 44.43 3.69
696 2604 1.042559 GGCAGAGGAGACTGAGGAGG 61.043 65.000 0.00 0.0 44.43 4.30
790 2698 3.744214 CGTAAAGGCTGGGAATCTGCATA 60.744 47.826 0.00 0.0 41.38 3.14
1180 3100 3.409026 ACCGCAACATTCTCTTCTCTT 57.591 42.857 0.00 0.0 0.00 2.85
1217 3137 1.882623 CCAAAAACTCACTCCAGAGGC 59.117 52.381 0.00 0.0 39.97 4.70
1345 3363 1.391157 TTTTTGCGCTTGACTGGCCT 61.391 50.000 9.73 0.0 0.00 5.19
1368 3386 1.359833 CGTGCAATTGTGGCTGTGT 59.640 52.632 7.40 0.0 0.00 3.72
1382 3400 3.894427 TGGCTGTGTACCATGTTGATTTT 59.106 39.130 0.00 0.0 30.29 1.82
1888 3907 3.565902 AGTCGAGCGATATGTGAGATTGA 59.434 43.478 0.00 0.0 0.00 2.57
1995 4014 0.238289 CTTGTGCCGTGGATGTTGTC 59.762 55.000 0.00 0.0 0.00 3.18
2063 4087 5.639082 CCTGTTGCCCAATTTTATCTGTTTC 59.361 40.000 0.00 0.0 0.00 2.78
2070 4468 7.450014 TGCCCAATTTTATCTGTTTCTGTCTTA 59.550 33.333 0.00 0.0 0.00 2.10
2107 4505 9.410556 GCAAAACTGCAGAATTATTTCTCTTTA 57.589 29.630 23.35 0.0 40.28 1.85
2171 4572 8.400947 TGTTATCCGACTATTTGTGTCTACTAC 58.599 37.037 0.00 0.0 32.70 2.73
2210 4611 4.883083 TGTGAAGTACTGCCTCTGTAAAG 58.117 43.478 0.00 0.0 0.00 1.85
2334 4737 8.995027 AAAATGGAATATAATGTACTGCCAGA 57.005 30.769 0.00 0.0 0.00 3.86
2335 4738 8.627208 AAATGGAATATAATGTACTGCCAGAG 57.373 34.615 0.00 0.0 0.00 3.35
2336 4739 6.747414 TGGAATATAATGTACTGCCAGAGT 57.253 37.500 0.00 0.0 38.88 3.24
2337 4740 6.524734 TGGAATATAATGTACTGCCAGAGTG 58.475 40.000 0.00 0.0 35.96 3.51
2338 4741 5.409826 GGAATATAATGTACTGCCAGAGTGC 59.590 44.000 0.00 0.0 37.78 4.40
2339 4742 2.691409 TAATGTACTGCCAGAGTGCC 57.309 50.000 0.00 0.0 36.50 5.01
2634 5043 2.972713 ACAGACCCTAAACTGCAAGAGA 59.027 45.455 0.00 0.0 37.61 3.10
2639 5048 4.985538 ACCCTAAACTGCAAGAGAAATGA 58.014 39.130 0.00 0.0 37.43 2.57
2730 5150 3.420893 AGAAATCAAGAACATCCGCCAA 58.579 40.909 0.00 0.0 0.00 4.52
2850 5270 5.845734 TGTAAGAACTGGAGGTAATAGGGA 58.154 41.667 0.00 0.0 0.00 4.20
2912 5332 1.278537 TGATGACTGACCTCATGGCA 58.721 50.000 0.00 0.0 36.63 4.92
2958 5378 4.942761 AACATTGTGAAGCAACAGGAAT 57.057 36.364 0.00 0.0 40.28 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 1.141657 ACAGTGCACAGTCATCTGGTT 59.858 47.619 21.04 0.00 45.14 3.67
235 236 5.106157 CCTTCGTTACTTGATTTGCCTTCAT 60.106 40.000 0.00 0.00 0.00 2.57
243 244 6.325919 TGATTTGCCTTCGTTACTTGATTT 57.674 33.333 0.00 0.00 0.00 2.17
287 357 3.652057 TTTCCTTGGTCCATCATCCTC 57.348 47.619 0.00 0.00 0.00 3.71
352 2212 3.068064 TCGAGGCATGCGTCTCCA 61.068 61.111 31.12 16.39 41.08 3.86
507 2382 9.185680 GAATTTGTTATACATCCTTACACCCTT 57.814 33.333 0.00 0.00 0.00 3.95
607 2482 4.157289 GTGTGTCAATTTGATCATGCTCCT 59.843 41.667 1.78 0.00 0.00 3.69
614 2489 2.483877 GCTCGGTGTGTCAATTTGATCA 59.516 45.455 1.78 0.00 0.00 2.92
679 2587 1.383456 CGCCTCCTCAGTCTCCTCTG 61.383 65.000 0.00 0.00 36.85 3.35
680 2588 1.077068 CGCCTCCTCAGTCTCCTCT 60.077 63.158 0.00 0.00 0.00 3.69
681 2589 2.124693 CCGCCTCCTCAGTCTCCTC 61.125 68.421 0.00 0.00 0.00 3.71
682 2590 2.043450 CCGCCTCCTCAGTCTCCT 60.043 66.667 0.00 0.00 0.00 3.69
683 2591 2.043852 TCCGCCTCCTCAGTCTCC 60.044 66.667 0.00 0.00 0.00 3.71
684 2592 2.124693 CCTCCGCCTCCTCAGTCTC 61.125 68.421 0.00 0.00 0.00 3.36
685 2593 2.043450 CCTCCGCCTCCTCAGTCT 60.043 66.667 0.00 0.00 0.00 3.24
686 2594 2.043852 TCCTCCGCCTCCTCAGTC 60.044 66.667 0.00 0.00 0.00 3.51
687 2595 2.043450 CTCCTCCGCCTCCTCAGT 60.043 66.667 0.00 0.00 0.00 3.41
688 2596 2.124693 GTCTCCTCCGCCTCCTCAG 61.125 68.421 0.00 0.00 0.00 3.35
689 2597 2.043852 GTCTCCTCCGCCTCCTCA 60.044 66.667 0.00 0.00 0.00 3.86
690 2598 3.213402 CGTCTCCTCCGCCTCCTC 61.213 72.222 0.00 0.00 0.00 3.71
691 2599 4.824515 CCGTCTCCTCCGCCTCCT 62.825 72.222 0.00 0.00 0.00 3.69
692 2600 4.816984 TCCGTCTCCTCCGCCTCC 62.817 72.222 0.00 0.00 0.00 4.30
693 2601 1.677637 AATTCCGTCTCCTCCGCCTC 61.678 60.000 0.00 0.00 0.00 4.70
694 2602 1.677637 GAATTCCGTCTCCTCCGCCT 61.678 60.000 0.00 0.00 0.00 5.52
695 2603 1.227292 GAATTCCGTCTCCTCCGCC 60.227 63.158 0.00 0.00 0.00 6.13
696 2604 0.806492 GTGAATTCCGTCTCCTCCGC 60.806 60.000 2.27 0.00 0.00 5.54
790 2698 1.303888 TTACCGCAGTCGTCTCCCT 60.304 57.895 0.00 0.00 0.00 4.20
1180 3100 1.901464 GGCAGTTTTCCCTTCGCCA 60.901 57.895 0.00 0.00 39.38 5.69
1244 3248 4.081642 GCAGGAAGAAAAGGGGGAAATTAC 60.082 45.833 0.00 0.00 0.00 1.89
1345 3363 2.560119 GCCACAATTGCACGGGACA 61.560 57.895 5.05 0.00 0.00 4.02
1368 3386 6.549364 AGTTGGACTTCAAAATCAACATGGTA 59.451 34.615 0.00 0.00 39.84 3.25
1382 3400 5.130350 CCCTTTACTTTCAGTTGGACTTCA 58.870 41.667 0.00 0.00 0.00 3.02
1888 3907 6.198639 ACAGTTATCTCCACCTTAGAGTCAT 58.801 40.000 0.00 0.00 32.93 3.06
1995 4014 6.602179 TCAAAGACAAATAATTCTGCAGTCG 58.398 36.000 14.67 0.00 0.00 4.18
2063 4087 4.566545 TTGCAAACCACATGTAAGACAG 57.433 40.909 0.00 0.00 0.00 3.51
2283 4686 6.180472 ACCTCAAATACAATGTCCAGTTAGG 58.820 40.000 0.00 0.00 39.47 2.69
2320 4723 2.691409 GGCACTCTGGCAGTACATTA 57.309 50.000 15.27 0.00 43.14 1.90
2333 4736 6.743575 ATTTCTTTGTGTATACTGGCACTC 57.256 37.500 4.17 0.00 36.63 3.51
2334 4737 7.336931 CCTTATTTCTTTGTGTATACTGGCACT 59.663 37.037 4.17 0.00 36.63 4.40
2335 4738 7.472543 CCTTATTTCTTTGTGTATACTGGCAC 58.527 38.462 4.17 0.00 36.26 5.01
2336 4739 6.094881 GCCTTATTTCTTTGTGTATACTGGCA 59.905 38.462 4.17 0.00 34.00 4.92
2337 4740 6.094881 TGCCTTATTTCTTTGTGTATACTGGC 59.905 38.462 4.17 0.00 0.00 4.85
2338 4741 7.336931 AGTGCCTTATTTCTTTGTGTATACTGG 59.663 37.037 4.17 0.00 0.00 4.00
2339 4742 8.177663 CAGTGCCTTATTTCTTTGTGTATACTG 58.822 37.037 4.17 0.00 0.00 2.74
2505 4910 5.982465 TTTGACTTTGGCTAACAATTTGC 57.018 34.783 0.00 0.00 39.21 3.68
2560 4967 8.930760 CCTATATGCTTATCTTCTTTGCAGTAC 58.069 37.037 0.00 0.00 37.07 2.73
2634 5043 8.627208 AGTTCTCTGATGTTATTGTGTCATTT 57.373 30.769 0.00 0.00 0.00 2.32
2639 5048 6.365970 AGGAGTTCTCTGATGTTATTGTGT 57.634 37.500 0.00 0.00 0.00 3.72
2690 5101 8.686334 TGATTTCTTCAGGTAATAATTGGCTTC 58.314 33.333 0.00 0.00 0.00 3.86
2730 5150 3.181490 TGTTGATAAGCTCGCGTATCAGT 60.181 43.478 20.80 0.00 43.96 3.41


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

AutoCloner maintained by Alex Coulton.