Multiple sequence alignment - TraesCS5D01G469200

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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 TraesCS5D01G469200 chr5D 100.000 3143 0 0 1 3143 510390036 510386894 0.000000e+00 5805
1 TraesCS5D01G469200 chr5D 94.691 2901 96 17 1 2890 510627313 510624460 0.000000e+00 4451
2 TraesCS5D01G469200 chr5D 85.390 2423 275 35 1 2366 510493460 510491060 0.000000e+00 2440
3 TraesCS5D01G469200 chr5D 85.449 1024 131 13 1525 2541 510407666 510406654 0.000000e+00 1050
4 TraesCS5D01G469200 chr5D 79.271 960 168 23 997 1932 510353960 510353008 2.640000e-180 641
5 TraesCS5D01G469200 chr5D 76.937 1136 210 35 1014 2132 510904586 510905686 1.610000e-167 599
6 TraesCS5D01G469200 chr5D 75.460 1141 216 42 1016 2132 510465992 510464892 6.050000e-137 497
7 TraesCS5D01G469200 chr5D 89.027 401 39 4 997 1393 510440172 510439773 2.820000e-135 492
8 TraesCS5D01G469200 chr5D 74.912 1140 222 38 998 2115 510599630 510598533 2.210000e-126 462
9 TraesCS5D01G469200 chr5D 98.810 252 3 0 2892 3143 510374417 510374166 1.720000e-122 449
10 TraesCS5D01G469200 chr5D 97.619 252 6 0 2892 3143 510378640 510378389 1.730000e-117 433
11 TraesCS5D01G469200 chr5D 97.619 252 6 0 2892 3143 510382861 510382610 1.730000e-117 433
12 TraesCS5D01G469200 chr5D 95.635 252 11 0 2892 3143 510370227 510369976 3.770000e-109 405
13 TraesCS5D01G469200 chr5D 93.846 260 7 7 2882 3138 254481835 254482088 1.770000e-102 383
14 TraesCS5D01G469200 chr5D 90.476 126 11 1 719 844 510903715 510903839 6.970000e-37 165
15 TraesCS5D01G469200 chr5D 79.227 207 28 11 488 686 510648058 510647859 2.540000e-26 130
16 TraesCS5D01G469200 chr5B 95.431 2364 88 9 540 2890 641402154 641399798 0.000000e+00 3749
17 TraesCS5D01G469200 chr5B 95.183 436 21 0 1 436 641402616 641402181 0.000000e+00 689
18 TraesCS5D01G469200 chr5B 76.704 1159 212 38 997 2132 641412979 641411856 2.700000e-165 592
19 TraesCS5D01G469200 chr5B 76.801 1138 208 38 1014 2132 641805368 641806468 3.490000e-164 588
20 TraesCS5D01G469200 chr5B 85.905 525 65 7 998 1516 641161450 641160929 4.580000e-153 551
21 TraesCS5D01G469200 chr5B 75.629 1153 229 35 997 2132 641428270 641427153 2.780000e-145 525
22 TraesCS5D01G469200 chr5B 80.198 303 45 10 1 293 641413771 641413474 2.460000e-51 213
23 TraesCS5D01G469200 chr5A 85.331 2420 280 37 1 2366 638764201 638761803 0.000000e+00 2433
24 TraesCS5D01G469200 chr5A 77.065 1138 205 34 1014 2132 639098444 639099544 3.470000e-169 604
25 TraesCS5D01G469200 chr5A 76.404 1157 206 42 999 2132 638812425 638811313 2.120000e-156 562
26 TraesCS5D01G469200 chr5A 93.511 262 11 5 2884 3143 617245068 617245325 4.920000e-103 385
27 TraesCS5D01G469200 chr5A 76.077 627 106 25 1016 1626 638641832 638641234 1.430000e-73 287
28 TraesCS5D01G469200 chr5A 75.560 491 63 24 204 686 638813238 638812797 4.140000e-44 189
29 TraesCS5D01G469200 chr5A 90.476 126 11 1 719 844 639097595 639097719 6.970000e-37 165
30 TraesCS5D01G469200 chr7A 94.922 256 7 5 2890 3143 34304920 34304669 2.270000e-106 396
31 TraesCS5D01G469200 chr2A 94.531 256 8 5 2890 3143 2081310 2081561 1.060000e-104 390
32 TraesCS5D01G469200 chr1A 93.462 260 13 4 2885 3143 475498896 475498640 1.770000e-102 383


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 TraesCS5D01G469200 chr5D 510386894 510390036 3142 True 5805.0 5805 100.00000 1 3143 1 chr5D.!!$R2 3142
1 TraesCS5D01G469200 chr5D 510624460 510627313 2853 True 4451.0 4451 94.69100 1 2890 1 chr5D.!!$R8 2889
2 TraesCS5D01G469200 chr5D 510491060 510493460 2400 True 2440.0 2440 85.39000 1 2366 1 chr5D.!!$R6 2365
3 TraesCS5D01G469200 chr5D 510406654 510407666 1012 True 1050.0 1050 85.44900 1525 2541 1 chr5D.!!$R3 1016
4 TraesCS5D01G469200 chr5D 510353008 510353960 952 True 641.0 641 79.27100 997 1932 1 chr5D.!!$R1 935
5 TraesCS5D01G469200 chr5D 510464892 510465992 1100 True 497.0 497 75.46000 1016 2132 1 chr5D.!!$R5 1116
6 TraesCS5D01G469200 chr5D 510598533 510599630 1097 True 462.0 462 74.91200 998 2115 1 chr5D.!!$R7 1117
7 TraesCS5D01G469200 chr5D 510369976 510382861 12885 True 430.0 449 97.42075 2892 3143 4 chr5D.!!$R10 251
8 TraesCS5D01G469200 chr5D 510903715 510905686 1971 False 382.0 599 83.70650 719 2132 2 chr5D.!!$F2 1413
9 TraesCS5D01G469200 chr5B 641399798 641402616 2818 True 2219.0 3749 95.30700 1 2890 2 chr5B.!!$R3 2889
10 TraesCS5D01G469200 chr5B 641805368 641806468 1100 False 588.0 588 76.80100 1014 2132 1 chr5B.!!$F1 1118
11 TraesCS5D01G469200 chr5B 641160929 641161450 521 True 551.0 551 85.90500 998 1516 1 chr5B.!!$R1 518
12 TraesCS5D01G469200 chr5B 641427153 641428270 1117 True 525.0 525 75.62900 997 2132 1 chr5B.!!$R2 1135
13 TraesCS5D01G469200 chr5B 641411856 641413771 1915 True 402.5 592 78.45100 1 2132 2 chr5B.!!$R4 2131
14 TraesCS5D01G469200 chr5A 638761803 638764201 2398 True 2433.0 2433 85.33100 1 2366 1 chr5A.!!$R2 2365
15 TraesCS5D01G469200 chr5A 639097595 639099544 1949 False 384.5 604 83.77050 719 2132 2 chr5A.!!$F2 1413
16 TraesCS5D01G469200 chr5A 638811313 638813238 1925 True 375.5 562 75.98200 204 2132 2 chr5A.!!$R3 1928
17 TraesCS5D01G469200 chr5A 638641234 638641832 598 True 287.0 287 76.07700 1016 1626 1 chr5A.!!$R1 610

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
405 422 1.066286 GCACCTGTCTCAGCTTCTCAT 60.066 52.381 0.00 0.0 0.0 2.90 F
1219 1877 1.499368 TGGCAGTGCTATCCATCTCA 58.501 50.000 16.11 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1957 0.967380 GTAGGCCATTGCAGCAACCT 60.967 55.0 17.52 17.52 40.13 3.50 R
2730 3450 1.032014 GAACAGCCAAAGCCAACTGA 58.968 50.0 0.00 0.00 41.25 3.41 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
29 30 3.589654 CTCCGCAGCCTCGTTTCCA 62.590 63.158 0.00 0.00 0.00 3.53
64 65 3.494336 CGTACTCGCCGACGACCT 61.494 66.667 0.00 0.00 45.12 3.85
105 106 1.810532 CTCCCGTTCCTCTTCCTCG 59.189 63.158 0.00 0.00 0.00 4.63
109 110 1.153745 CGTTCCTCTTCCTCGCCTG 60.154 63.158 0.00 0.00 0.00 4.85
120 121 1.443407 CTCGCCTGGGTGTCTATGG 59.557 63.158 0.00 0.00 0.00 2.74
164 172 5.330455 TGTTTCTAATCTGAGCTCATCGT 57.670 39.130 18.63 7.62 0.00 3.73
185 193 5.009110 TCGTAGATGCAACCTAGATCTCAAG 59.991 44.000 0.00 0.00 0.00 3.02
227 235 4.771577 TGGTGTGCCATCTTGTAAATTGAT 59.228 37.500 0.00 0.00 40.46 2.57
298 314 7.264221 GGTTAGGAGCATATACATGATCTGAG 58.736 42.308 0.00 0.00 45.12 3.35
405 422 1.066286 GCACCTGTCTCAGCTTCTCAT 60.066 52.381 0.00 0.00 0.00 2.90
513 543 7.376866 GCATTGTAGCAACATGTGTATTATGTC 59.623 37.037 0.00 0.00 37.77 3.06
702 746 2.241176 TGTTCTTTCCTGTGACCCACTT 59.759 45.455 0.00 0.00 35.11 3.16
725 769 7.837689 ACTTAGTACAGGTCATAAGTCCATACA 59.162 37.037 0.00 0.00 34.22 2.29
1023 1679 3.257375 TGTCCACATGTGTACTACCTGAC 59.743 47.826 23.79 19.36 0.00 3.51
1189 1847 2.472695 ATTTGAGCGTGGCAGAGTTA 57.527 45.000 0.00 0.00 0.00 2.24
1219 1877 1.499368 TGGCAGTGCTATCCATCTCA 58.501 50.000 16.11 0.00 0.00 3.27
1299 1957 5.864418 ATAAGTACCCAATACAGCTTCGA 57.136 39.130 0.00 0.00 36.09 3.71
1331 1989 5.358160 GCAATGGCCTACTTCTTTGTTATCT 59.642 40.000 3.32 0.00 0.00 1.98
1415 2085 2.637382 TGGCACTTCCAGATACTGAACA 59.363 45.455 0.00 0.00 40.72 3.18
1527 2209 2.604914 GGTCATGAGCTGTATCAACACG 59.395 50.000 17.59 0.00 31.76 4.49
1541 2223 6.814644 TGTATCAACACGGAAGTTAAGGTATG 59.185 38.462 0.00 0.00 46.40 2.39
1603 2303 7.394641 GGAAAACTAGAGATCCATTTGAAGGTT 59.605 37.037 0.00 0.00 32.08 3.50
1710 2410 2.916934 ACAAGGGCTCAACCATAGGTTA 59.083 45.455 0.40 0.00 45.01 2.85
1753 2456 4.150627 CAGATAGGACCGACATATTTTGCG 59.849 45.833 0.00 0.00 0.00 4.85
1829 2532 0.251634 TTGGATGGCTGTGCGATACA 59.748 50.000 0.00 0.00 35.87 2.29
1920 2623 0.743345 GGGACATGTTACTCCGCACC 60.743 60.000 0.00 0.00 0.00 5.01
2242 2951 3.704061 AGGTGCACCAAACTGTTGTTATT 59.296 39.130 36.39 8.73 38.89 1.40
2270 2989 7.891498 TGTACTAGATTGTTGGCTATCTGTA 57.109 36.000 0.00 0.00 37.65 2.74
2331 3050 4.741342 CCGGTCAACTAGTATCGAACTTT 58.259 43.478 0.00 0.00 39.80 2.66
2337 3056 5.867716 TCAACTAGTATCGAACTTTTGCTCC 59.132 40.000 0.00 0.00 39.80 4.70
2357 3076 6.377146 TGCTCCCTTAATTTGGAAATCTACAC 59.623 38.462 0.00 0.00 0.00 2.90
2404 3123 3.921119 TGAACATGTGGAGTGAAATGC 57.079 42.857 0.00 0.00 0.00 3.56
2566 3285 2.816672 AGCTGGCTTTCTTCTTGTTAGC 59.183 45.455 0.00 0.00 0.00 3.09
2590 3309 6.187682 CCTTCTTTATGCCTTTCCTTCCTTA 58.812 40.000 0.00 0.00 0.00 2.69
2656 3375 5.843019 TCATAGGTTCTCTTCACCCTTTT 57.157 39.130 0.00 0.00 34.44 2.27
2658 3377 5.309543 TCATAGGTTCTCTTCACCCTTTTCA 59.690 40.000 0.00 0.00 34.44 2.69
2661 3380 2.543777 TCTCTTCACCCTTTTCACCG 57.456 50.000 0.00 0.00 0.00 4.94
2664 3383 0.593128 CTTCACCCTTTTCACCGCTG 59.407 55.000 0.00 0.00 0.00 5.18
2672 3392 3.119849 CCCTTTTCACCGCTGTAGAATTG 60.120 47.826 0.00 0.00 0.00 2.32
2726 3446 3.131396 AGCACCAACTGTTCTAACTTCG 58.869 45.455 0.00 0.00 0.00 3.79
2730 3450 5.235516 CACCAACTGTTCTAACTTCGGTAT 58.764 41.667 0.00 0.00 0.00 2.73
2819 3542 5.838531 ATACTTAGAAGAAGAGACCCGTG 57.161 43.478 0.00 0.00 0.00 4.94
2875 3598 3.074412 ACCAAATCGCGAAGAAGACAAT 58.926 40.909 15.24 0.00 0.00 2.71
2883 3606 4.748102 TCGCGAAGAAGACAATGTTTAGTT 59.252 37.500 6.20 0.00 0.00 2.24
2890 3613 7.678947 AGAAGACAATGTTTAGTTGGAGATG 57.321 36.000 0.00 0.00 0.00 2.90
3138 12305 0.823356 ACCAACGCAAAGGCTCACAT 60.823 50.000 0.00 0.00 38.10 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 0.604243 ACCGCGTAATGGTTGCTTCA 60.604 50.000 4.92 0.00 35.82 3.02
105 106 2.203070 CGCCATAGACACCCAGGC 60.203 66.667 0.00 0.00 41.86 4.85
109 110 0.748005 AACATGCGCCATAGACACCC 60.748 55.000 4.18 0.00 0.00 4.61
120 121 1.154413 CACGAGGACAAACATGCGC 60.154 57.895 0.00 0.00 0.00 6.09
164 172 4.039730 GCCTTGAGATCTAGGTTGCATCTA 59.960 45.833 12.28 0.00 40.32 1.98
185 193 3.508840 CTGGCGAAACGGATGGCC 61.509 66.667 8.48 8.48 45.76 5.36
298 314 3.654414 ACAGAAACGAACTCATCAGACC 58.346 45.455 0.00 0.00 0.00 3.85
405 422 2.307768 CTAAGGACCTATCAGACGCCA 58.692 52.381 0.00 0.00 0.00 5.69
480 510 1.612950 TGTTGCTACAATGCACCTTGG 59.387 47.619 0.00 0.00 43.20 3.61
481 511 3.247442 CATGTTGCTACAATGCACCTTG 58.753 45.455 4.79 0.00 43.20 3.61
482 512 2.892852 ACATGTTGCTACAATGCACCTT 59.107 40.909 4.79 0.00 43.20 3.50
483 513 2.229543 CACATGTTGCTACAATGCACCT 59.770 45.455 4.79 0.00 43.20 4.00
484 514 2.030007 ACACATGTTGCTACAATGCACC 60.030 45.455 4.79 0.00 43.20 5.01
485 515 3.287312 ACACATGTTGCTACAATGCAC 57.713 42.857 4.79 0.00 43.20 4.57
486 516 5.641783 AATACACATGTTGCTACAATGCA 57.358 34.783 4.79 0.00 41.65 3.96
487 517 7.195646 ACATAATACACATGTTGCTACAATGC 58.804 34.615 4.79 0.00 37.91 3.56
488 518 8.615211 AGACATAATACACATGTTGCTACAATG 58.385 33.333 4.79 9.42 36.76 2.82
489 519 8.737168 AGACATAATACACATGTTGCTACAAT 57.263 30.769 4.79 0.00 36.76 2.71
490 520 8.560355 AAGACATAATACACATGTTGCTACAA 57.440 30.769 4.79 0.00 36.76 2.41
491 521 7.821846 TGAAGACATAATACACATGTTGCTACA 59.178 33.333 2.82 2.82 36.76 2.74
492 522 8.116753 GTGAAGACATAATACACATGTTGCTAC 58.883 37.037 0.00 0.00 36.76 3.58
513 543 1.238439 ACAAGTCGGCAATGGTGAAG 58.762 50.000 0.00 0.00 0.00 3.02
582 614 9.781834 GCTATCTAGTAGTTATGTGCAAGATAG 57.218 37.037 15.59 15.59 42.05 2.08
702 746 8.598202 TTTGTATGGACTTATGACCTGTACTA 57.402 34.615 0.00 0.00 0.00 1.82
1023 1679 0.103208 GGATGTCTACCACCAGCTCG 59.897 60.000 0.00 0.00 0.00 5.03
1219 1877 2.205462 ACCTGAGGGCAGTCTGGT 59.795 61.111 2.38 10.66 42.33 4.00
1299 1957 0.967380 GTAGGCCATTGCAGCAACCT 60.967 55.000 17.52 17.52 40.13 3.50
1527 2209 8.537858 TCCTTAGAGAAACATACCTTAACTTCC 58.462 37.037 0.00 0.00 0.00 3.46
1541 2223 4.020128 ACCATGTGGAGTCCTTAGAGAAAC 60.020 45.833 11.33 0.00 38.94 2.78
1603 2303 7.027874 ACACCCCATTTACAAAGAGAGAATA 57.972 36.000 0.00 0.00 0.00 1.75
1710 2410 2.444388 TGGATATCCTGGCAGCTGAATT 59.556 45.455 20.43 0.00 36.82 2.17
1753 2456 2.130395 GCTAAGACGGCCGTTATAACC 58.870 52.381 34.65 18.69 0.00 2.85
1776 2479 1.739562 GCACAAGACGCCTGAGGAG 60.740 63.158 0.65 0.00 0.00 3.69
1829 2532 2.529632 GGCCTTCCAAACTCCAAATCT 58.470 47.619 0.00 0.00 0.00 2.40
1920 2623 2.934887 TGCCAATATCCATCACTGTGG 58.065 47.619 8.11 0.00 40.76 4.17
2242 2951 9.764363 CAGATAGCCAACAATCTAGTACATTAA 57.236 33.333 0.00 0.00 31.25 1.40
2331 3050 6.951198 TGTAGATTTCCAAATTAAGGGAGCAA 59.049 34.615 0.00 0.00 34.02 3.91
2404 3123 4.779987 CACATCCACGCAGAATATTCATG 58.220 43.478 17.56 11.94 0.00 3.07
2566 3285 4.604156 AGGAAGGAAAGGCATAAAGAAGG 58.396 43.478 0.00 0.00 0.00 3.46
2590 3309 2.047830 CCCCTCTACCGAAAATAGCCT 58.952 52.381 0.00 0.00 0.00 4.58
2656 3375 3.006430 TCAGAACAATTCTACAGCGGTGA 59.994 43.478 23.44 4.04 38.11 4.02
2658 3377 3.678056 TCAGAACAATTCTACAGCGGT 57.322 42.857 0.00 0.00 38.11 5.68
2661 3380 7.588512 ACAAAGATTCAGAACAATTCTACAGC 58.411 34.615 0.00 0.00 38.11 4.40
2726 3446 1.474077 CAGCCAAAGCCAACTGATACC 59.526 52.381 0.00 0.00 41.25 2.73
2730 3450 1.032014 GAACAGCCAAAGCCAACTGA 58.968 50.000 0.00 0.00 41.25 3.41
2775 3497 9.661954 AGTATATAGATCATGTATTACAGGGGG 57.338 37.037 8.48 0.00 29.72 5.40
3033 12200 6.433093 TCATATATACCACATGTAGTCGCACT 59.567 38.462 0.00 0.00 31.61 4.40


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

AutoCloner maintained by Alex Coulton.