Multiple sequence alignment - TraesCS4D01G104300

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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 TraesCS4D01G104300 chr4D 100.000 2793 0 0 1 2793 82740051 82737259 0.000000e+00 5158.0
1 TraesCS4D01G104300 chr4D 98.099 684 12 1 2110 2793 320277284 320277966 0.000000e+00 1190.0
2 TraesCS4D01G104300 chr4D 87.174 499 57 6 1360 1857 82819884 82819392 6.760000e-156 560.0
3 TraesCS4D01G104300 chr4D 87.107 318 33 4 335 651 421335511 421335201 1.230000e-93 353.0
4 TraesCS4D01G104300 chr4B 92.573 1306 46 17 817 2097 117083882 117082603 0.000000e+00 1827.0
5 TraesCS4D01G104300 chr4B 89.266 1239 81 25 856 2082 71753654 71754852 0.000000e+00 1504.0
6 TraesCS4D01G104300 chr4B 89.247 930 49 21 685 1594 117106455 117105557 0.000000e+00 1116.0
7 TraesCS4D01G104300 chr4B 85.593 590 66 11 1290 1870 117183059 117182480 3.980000e-168 601.0
8 TraesCS4D01G104300 chr4B 89.489 333 25 3 9 331 71707253 71707585 2.000000e-111 412.0
9 TraesCS4D01G104300 chr4B 87.202 336 27 4 9 334 117085452 117085123 4.390000e-98 368.0
10 TraesCS4D01G104300 chr4B 87.342 316 30 6 335 646 396704004 396703695 1.230000e-93 353.0
11 TraesCS4D01G104300 chr4B 95.210 167 6 1 1933 2097 117105210 117105044 2.130000e-66 263.0
12 TraesCS4D01G104300 chr4B 90.741 108 9 1 228 334 117106569 117106462 2.900000e-30 143.0
13 TraesCS4D01G104300 chr4B 89.381 113 8 3 225 334 71707262 71707373 3.750000e-29 139.0
14 TraesCS4D01G104300 chr4B 86.726 113 11 3 225 334 117085443 117085332 3.780000e-24 122.0
15 TraesCS4D01G104300 chr4A 94.831 1180 37 11 758 1927 494045902 494044737 0.000000e+00 1820.0
16 TraesCS4D01G104300 chr4A 91.775 766 51 7 1 759 494046903 494046143 0.000000e+00 1055.0
17 TraesCS4D01G104300 chr4A 84.036 783 96 20 1127 1903 494457899 494457140 0.000000e+00 726.0
18 TraesCS4D01G104300 chr4A 87.829 304 31 2 335 637 154521127 154521425 4.430000e-93 351.0
19 TraesCS4D01G104300 chr4A 97.931 145 3 0 1938 2082 494039436 494039292 4.620000e-63 252.0
20 TraesCS4D01G104300 chr7D 98.246 684 12 0 2110 2793 579134932 579134249 0.000000e+00 1197.0
21 TraesCS4D01G104300 chr7D 98.102 685 13 0 2109 2793 624775998 624775314 0.000000e+00 1194.0
22 TraesCS4D01G104300 chr7D 97.661 684 13 2 2110 2793 614485606 614484926 0.000000e+00 1171.0
23 TraesCS4D01G104300 chr7D 97.515 684 15 2 2110 2793 575154079 575153398 0.000000e+00 1168.0
24 TraesCS4D01G104300 chr7D 88.026 309 34 2 333 641 45802730 45803035 2.040000e-96 363.0
25 TraesCS4D01G104300 chr3D 98.099 684 13 0 2110 2793 1941446 1940763 0.000000e+00 1192.0
26 TraesCS4D01G104300 chr3D 88.779 303 24 6 335 634 69501424 69501719 2.040000e-96 363.0
27 TraesCS4D01G104300 chr3D 92.188 64 5 0 928 991 614624769 614624832 1.070000e-14 91.6
28 TraesCS4D01G104300 chr1D 97.953 684 14 0 2110 2793 11499620 11500303 0.000000e+00 1186.0
29 TraesCS4D01G104300 chr2D 97.525 687 15 1 2107 2793 642959106 642959790 0.000000e+00 1173.0
30 TraesCS4D01G104300 chr2D 97.518 685 16 1 2110 2793 630956313 630956997 0.000000e+00 1170.0
31 TraesCS4D01G104300 chr6A 78.310 793 131 23 1127 1903 16071753 16072520 9.050000e-130 473.0
32 TraesCS4D01G104300 chr6A 88.852 305 28 2 335 638 189538481 189538780 1.220000e-98 370.0
33 TraesCS4D01G104300 chr6D 77.427 793 117 30 1127 1903 15400685 15401431 1.550000e-112 416.0
34 TraesCS4D01G104300 chr5B 87.869 305 30 3 335 637 303229398 303229099 4.430000e-93 351.0
35 TraesCS4D01G104300 chr2A 87.419 310 31 5 335 643 478912062 478911760 1.590000e-92 350.0
36 TraesCS4D01G104300 chr2A 85.000 60 7 2 1588 1646 37199654 37199596 3.000000e-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 TraesCS4D01G104300 chr4D 82737259 82740051 2792 True 5158.000000 5158 100.000000 1 2793 1 chr4D.!!$R1 2792
1 TraesCS4D01G104300 chr4D 320277284 320277966 682 False 1190.000000 1190 98.099000 2110 2793 1 chr4D.!!$F1 683
2 TraesCS4D01G104300 chr4B 71753654 71754852 1198 False 1504.000000 1504 89.266000 856 2082 1 chr4B.!!$F1 1226
3 TraesCS4D01G104300 chr4B 117082603 117085452 2849 True 772.333333 1827 88.833667 9 2097 3 chr4B.!!$R3 2088
4 TraesCS4D01G104300 chr4B 117182480 117183059 579 True 601.000000 601 85.593000 1290 1870 1 chr4B.!!$R1 580
5 TraesCS4D01G104300 chr4B 117105044 117106569 1525 True 507.333333 1116 91.732667 228 2097 3 chr4B.!!$R4 1869
6 TraesCS4D01G104300 chr4A 494044737 494046903 2166 True 1437.500000 1820 93.303000 1 1927 2 chr4A.!!$R3 1926
7 TraesCS4D01G104300 chr4A 494457140 494457899 759 True 726.000000 726 84.036000 1127 1903 1 chr4A.!!$R2 776
8 TraesCS4D01G104300 chr7D 579134249 579134932 683 True 1197.000000 1197 98.246000 2110 2793 1 chr7D.!!$R2 683
9 TraesCS4D01G104300 chr7D 624775314 624775998 684 True 1194.000000 1194 98.102000 2109 2793 1 chr7D.!!$R4 684
10 TraesCS4D01G104300 chr7D 614484926 614485606 680 True 1171.000000 1171 97.661000 2110 2793 1 chr7D.!!$R3 683
11 TraesCS4D01G104300 chr7D 575153398 575154079 681 True 1168.000000 1168 97.515000 2110 2793 1 chr7D.!!$R1 683
12 TraesCS4D01G104300 chr3D 1940763 1941446 683 True 1192.000000 1192 98.099000 2110 2793 1 chr3D.!!$R1 683
13 TraesCS4D01G104300 chr1D 11499620 11500303 683 False 1186.000000 1186 97.953000 2110 2793 1 chr1D.!!$F1 683
14 TraesCS4D01G104300 chr2D 642959106 642959790 684 False 1173.000000 1173 97.525000 2107 2793 1 chr2D.!!$F2 686
15 TraesCS4D01G104300 chr2D 630956313 630956997 684 False 1170.000000 1170 97.518000 2110 2793 1 chr2D.!!$F1 683
16 TraesCS4D01G104300 chr6A 16071753 16072520 767 False 473.000000 473 78.310000 1127 1903 1 chr6A.!!$F1 776
17 TraesCS4D01G104300 chr6D 15400685 15401431 746 False 416.000000 416 77.427000 1127 1903 1 chr6D.!!$F1 776

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
459 470 0.395724 CCCAACCCCCAATGAGCTAC 60.396 60.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 3404 0.31812 CTGACAAAATGGTGGCCCAC 59.682 55.0 4.93 4.93 45.65 4.61 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
142 152 2.288458 GTGTGTTTAAGCGCTACAACCA 59.712 45.455 22.41 17.79 0.00 3.67
196 206 5.398169 GCAATCAAACGACCATACAAATCA 58.602 37.500 0.00 0.00 0.00 2.57
198 208 7.192913 GCAATCAAACGACCATACAAATCATA 58.807 34.615 0.00 0.00 0.00 2.15
341 352 4.460948 TGTGTTTTATCCTACTCCGTCC 57.539 45.455 0.00 0.00 0.00 4.79
459 470 0.395724 CCCAACCCCCAATGAGCTAC 60.396 60.000 0.00 0.00 0.00 3.58
460 471 0.625849 CCAACCCCCAATGAGCTACT 59.374 55.000 0.00 0.00 0.00 2.57
461 472 1.843851 CCAACCCCCAATGAGCTACTA 59.156 52.381 0.00 0.00 0.00 1.82
507 518 9.342308 AGAAGACCATGTGTATAATGTTATTGG 57.658 33.333 0.00 0.00 0.00 3.16
539 550 8.786826 TTACCGTGTGATGAGAGAAAAATATT 57.213 30.769 0.00 0.00 0.00 1.28
567 578 5.530519 TTACTCTAAAGTGCATTGCGAAG 57.469 39.130 3.84 0.00 36.92 3.79
574 585 5.627499 AAAGTGCATTGCGAAGATAGAAA 57.373 34.783 3.84 0.00 0.00 2.52
624 635 6.737254 ACTCAAATATACACTTTTCACCGG 57.263 37.500 0.00 0.00 0.00 5.28
628 639 6.370442 TCAAATATACACTTTTCACCGGACAG 59.630 38.462 9.46 0.00 0.00 3.51
654 665 5.999600 GGAAGTAAGTGTGTTTAAGGGCTAA 59.000 40.000 0.00 0.00 0.00 3.09
675 686 7.280356 GCTAAAACCCTATGTGAAGAATCCTA 58.720 38.462 0.00 0.00 0.00 2.94
676 687 7.939588 GCTAAAACCCTATGTGAAGAATCCTAT 59.060 37.037 0.00 0.00 0.00 2.57
707 718 2.350057 TCCCACGATCAAACAACCAA 57.650 45.000 0.00 0.00 0.00 3.67
712 723 4.320202 CCCACGATCAAACAACCAAACTAG 60.320 45.833 0.00 0.00 0.00 2.57
732 749 2.167900 AGTCCGGCCTGTTGTAGTAATC 59.832 50.000 0.00 0.00 0.00 1.75
773 1032 6.381498 TCATTCCTATGGTTTACAAGTCCA 57.619 37.500 0.00 0.00 35.64 4.02
822 2190 1.579932 CTCGACGTGTACCAGCTGT 59.420 57.895 13.81 3.45 0.00 4.40
842 2210 0.713329 GCCGGCGTTTAATTTGCAAG 59.287 50.000 12.58 0.00 0.00 4.01
922 2291 5.586877 TGGGACTTCACCACTAGTAGTATT 58.413 41.667 1.57 0.00 31.83 1.89
1032 2401 4.074970 GGTAGTATAAGTAGGCACGCCTA 58.925 47.826 13.86 13.86 46.14 3.93
1209 2581 0.107017 TCCAGGCTTGCTATGAAGGC 60.107 55.000 0.00 0.00 46.35 4.35
1696 3081 0.037605 AGTACGGCAACTCCTTTCCG 60.038 55.000 0.00 0.00 46.61 4.30
1735 3120 0.108615 CCGCCTCCTGTGACTGTAAG 60.109 60.000 0.00 0.00 42.29 2.34
1848 3247 4.098196 GGATCTTACTTTCGGAGCTACTGT 59.902 45.833 0.00 0.00 0.00 3.55
1849 3248 4.436242 TCTTACTTTCGGAGCTACTGTG 57.564 45.455 0.00 0.00 0.00 3.66
1927 3342 4.433186 TCGTTGCTATGAAATGTTTGGG 57.567 40.909 0.00 0.00 0.00 4.12
1928 3343 2.923020 CGTTGCTATGAAATGTTTGGGC 59.077 45.455 0.00 0.00 0.00 5.36
1930 3345 2.533916 TGCTATGAAATGTTTGGGCCA 58.466 42.857 0.00 0.00 0.00 5.36
1931 3346 2.233431 TGCTATGAAATGTTTGGGCCAC 59.767 45.455 5.23 0.00 0.00 5.01
1942 3371 2.082834 TGGGCCACCATTGCTAAGA 58.917 52.632 0.00 0.00 43.37 2.10
1975 3404 5.072055 TGAGGTATCCAATTGCACCATATG 58.928 41.667 18.68 0.00 33.27 1.78
2097 3530 0.178767 TCCTAGCTGCATGCAATCGT 59.821 50.000 22.88 8.79 45.94 3.73
2098 3531 1.412343 TCCTAGCTGCATGCAATCGTA 59.588 47.619 22.88 9.47 45.94 3.43
2099 3532 2.158971 TCCTAGCTGCATGCAATCGTAA 60.159 45.455 22.88 3.58 45.94 3.18
2100 3533 2.810274 CCTAGCTGCATGCAATCGTAAT 59.190 45.455 22.88 5.13 45.94 1.89
2101 3534 3.996363 CCTAGCTGCATGCAATCGTAATA 59.004 43.478 22.88 5.99 45.94 0.98
2102 3535 3.885484 AGCTGCATGCAATCGTAATAC 57.115 42.857 22.88 2.90 45.94 1.89
2103 3536 3.470709 AGCTGCATGCAATCGTAATACT 58.529 40.909 22.88 5.11 45.94 2.12
2104 3537 3.496130 AGCTGCATGCAATCGTAATACTC 59.504 43.478 22.88 0.00 45.94 2.59
2105 3538 3.248363 GCTGCATGCAATCGTAATACTCA 59.752 43.478 22.88 0.00 42.31 3.41
2106 3539 4.083643 GCTGCATGCAATCGTAATACTCAT 60.084 41.667 22.88 0.00 42.31 2.90
2107 3540 5.561532 GCTGCATGCAATCGTAATACTCATT 60.562 40.000 22.88 0.00 42.31 2.57
2270 3703 6.609212 GCTACTCCTATCCAATATGATGAGGA 59.391 42.308 0.00 0.00 34.12 3.71
2400 3833 1.532604 AATCCGGTCAGACGCACTCA 61.533 55.000 0.00 0.00 0.00 3.41
2413 3846 1.080501 CACTCATGTGTCGTCGCCT 60.081 57.895 0.00 0.00 39.24 5.52
2421 3854 0.389948 GTGTCGTCGCCTCCATCTTT 60.390 55.000 0.00 0.00 0.00 2.52
2707 4140 3.009584 GGAAGACCCAGATCTGAGGTTTT 59.990 47.826 26.83 26.25 35.34 2.43
2769 4202 0.175760 GCCTCGACCATCAGCAGTAA 59.824 55.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 123 3.684788 AGCGCTTAAACACACTTAGGATG 59.315 43.478 2.64 0.00 0.00 3.51
142 152 6.072673 GGAAAACCGTAGAATTCTTCACATGT 60.073 38.462 14.36 4.25 0.00 3.21
168 178 0.785378 TGGTCGTTTGATTGCGTACG 59.215 50.000 11.84 11.84 35.46 3.67
173 183 5.398169 TGATTTGTATGGTCGTTTGATTGC 58.602 37.500 0.00 0.00 0.00 3.56
196 206 9.793252 GCATGACATCTTCAAAAACTACAATAT 57.207 29.630 0.00 0.00 37.92 1.28
198 208 7.092716 GGCATGACATCTTCAAAAACTACAAT 58.907 34.615 0.00 0.00 37.92 2.71
221 231 3.258971 ACAACTAGAGATGCTCTTGGC 57.741 47.619 1.88 0.00 41.50 4.52
235 245 5.654650 ACATGAAGTTTTGTGGGAACAACTA 59.345 36.000 0.00 0.00 46.06 2.24
273 284 4.040755 ACACACTCCATTAGCCCTTAGAT 58.959 43.478 0.00 0.00 0.00 1.98
337 348 1.855513 TGTACACTTTTCACCGGACG 58.144 50.000 9.46 0.00 0.00 4.79
381 392 9.546428 CTTTTCAATCCATTTTTACTCCACTTT 57.454 29.630 0.00 0.00 0.00 2.66
387 398 6.928492 TGCACCTTTTCAATCCATTTTTACTC 59.072 34.615 0.00 0.00 0.00 2.59
398 409 5.125100 TGATGACTTGCACCTTTTCAATC 57.875 39.130 0.00 0.00 0.00 2.67
402 413 5.776744 AGAAATGATGACTTGCACCTTTTC 58.223 37.500 0.00 0.00 0.00 2.29
483 494 9.120538 GACCAATAACATTATACACATGGTCTT 57.879 33.333 17.62 0.00 46.71 3.01
495 506 8.836413 CACGGTAATCAAGACCAATAACATTAT 58.164 33.333 0.00 0.00 36.72 1.28
507 518 4.744570 TCTCATCACACGGTAATCAAGAC 58.255 43.478 0.00 0.00 0.00 3.01
546 557 4.816392 TCTTCGCAATGCACTTTAGAGTA 58.184 39.130 5.91 0.00 33.90 2.59
547 558 3.664107 TCTTCGCAATGCACTTTAGAGT 58.336 40.909 5.91 0.00 36.25 3.24
548 559 4.871993 ATCTTCGCAATGCACTTTAGAG 57.128 40.909 5.91 0.00 0.00 2.43
550 561 5.973651 TCTATCTTCGCAATGCACTTTAG 57.026 39.130 5.91 0.00 0.00 1.85
563 574 9.140286 TCACAAAAGAGTGTATTTCTATCTTCG 57.860 33.333 0.00 0.00 40.37 3.79
604 615 6.370442 TCTGTCCGGTGAAAAGTGTATATTTG 59.630 38.462 0.00 0.00 0.00 2.32
616 627 1.420430 ACTTCCTCTGTCCGGTGAAA 58.580 50.000 0.00 0.00 0.00 2.69
618 629 2.168496 CTTACTTCCTCTGTCCGGTGA 58.832 52.381 0.00 0.00 0.00 4.02
621 632 1.893801 ACACTTACTTCCTCTGTCCGG 59.106 52.381 0.00 0.00 0.00 5.14
624 635 6.424207 CCTTAAACACACTTACTTCCTCTGTC 59.576 42.308 0.00 0.00 0.00 3.51
628 639 4.454847 GCCCTTAAACACACTTACTTCCTC 59.545 45.833 0.00 0.00 0.00 3.71
694 705 4.083484 CCGGACTAGTTTGGTTGTTTGATC 60.083 45.833 0.00 0.00 0.00 2.92
707 718 1.549170 CTACAACAGGCCGGACTAGTT 59.451 52.381 11.18 14.77 0.00 2.24
712 723 2.547826 GATTACTACAACAGGCCGGAC 58.452 52.381 10.86 0.00 0.00 4.79
732 749 1.442526 GAAGTGGCATGGCATCCTCG 61.443 60.000 26.07 0.00 0.00 4.63
773 1032 2.160721 TTAGGGCCTCTCTGATTCGT 57.839 50.000 10.74 0.00 0.00 3.85
822 2190 0.032130 TTGCAAATTAAACGCCGGCA 59.968 45.000 28.98 6.55 0.00 5.69
842 2210 3.693578 ACTAGTACTCGTAGCAAGTTCCC 59.306 47.826 0.00 0.00 0.00 3.97
974 2343 6.933521 CCATCCAGACCTAAATTGTATCTCAG 59.066 42.308 0.00 0.00 0.00 3.35
1010 2379 2.889678 AGGCGTGCCTACTTATACTACC 59.110 50.000 12.68 0.00 46.14 3.18
1031 2400 3.024547 CTGCTAGCCTGACTTACCACTA 58.975 50.000 13.29 0.00 0.00 2.74
1032 2401 1.827969 CTGCTAGCCTGACTTACCACT 59.172 52.381 13.29 0.00 0.00 4.00
1037 2406 2.212327 GCCCTGCTAGCCTGACTTA 58.788 57.895 13.29 0.00 0.00 2.24
1696 3081 1.585521 CGCGACTGTCATCGGGTAC 60.586 63.158 0.00 0.00 46.57 3.34
1848 3247 6.147656 CAGCGCCATTACATTGATAGATAACA 59.852 38.462 2.29 0.00 0.00 2.41
1849 3248 6.368791 TCAGCGCCATTACATTGATAGATAAC 59.631 38.462 2.29 0.00 0.00 1.89
1927 3342 3.205784 AGAGATCTTAGCAATGGTGGC 57.794 47.619 0.00 0.00 0.00 5.01
1928 3343 5.543507 AGTAGAGATCTTAGCAATGGTGG 57.456 43.478 0.00 0.00 0.00 4.61
1930 3345 7.187824 TCAAAGTAGAGATCTTAGCAATGGT 57.812 36.000 0.00 0.00 0.00 3.55
1931 3346 6.705381 CCTCAAAGTAGAGATCTTAGCAATGG 59.295 42.308 0.00 0.00 37.87 3.16
1936 3365 7.231722 TGGATACCTCAAAGTAGAGATCTTAGC 59.768 40.741 0.00 0.00 37.87 3.09
1942 3371 6.995091 GCAATTGGATACCTCAAAGTAGAGAT 59.005 38.462 7.72 0.00 37.87 2.75
1975 3404 0.318120 CTGACAAAATGGTGGCCCAC 59.682 55.000 4.93 4.93 45.65 4.61
2270 3703 2.822643 TAGTGGCCCAGCTAGCACCT 62.823 60.000 18.83 4.00 0.00 4.00
2295 3728 1.278127 TGTTAGGCTTAGGTGAGTGGC 59.722 52.381 0.00 0.00 0.00 5.01
2400 3833 1.141881 GATGGAGGCGACGACACAT 59.858 57.895 10.22 10.22 0.00 3.21
2413 3846 3.903714 TCTGAAGACCTGTGAAAGATGGA 59.096 43.478 0.00 0.00 0.00 3.41
2421 3854 6.183360 CCTCAATATGATCTGAAGACCTGTGA 60.183 42.308 0.00 0.00 0.00 3.58
2762 4195 0.603569 CGTCTGGTGGAGTTACTGCT 59.396 55.000 5.34 0.00 0.00 4.24
2769 4202 2.597805 ACGCTCGTCTGGTGGAGT 60.598 61.111 0.00 0.00 32.83 3.85


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

AutoCloner maintained by Alex Coulton.