Multiple sequence alignment - TraesCS2D01G252500

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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 TraesCS2D01G252500 chr2D 100.000 2414 0 0 1 2414 303516136 303513723 0.000000e+00 4458.0
1 TraesCS2D01G252500 chr2B 90.920 1597 53 36 1 1548 372090267 372088714 0.000000e+00 2061.0
2 TraesCS2D01G252500 chr2B 89.889 633 46 11 1543 2170 372088684 372088065 0.000000e+00 798.0
3 TraesCS2D01G252500 chr2B 93.798 258 8 4 2160 2414 372088033 372087781 4.870000e-102 381.0
4 TraesCS2D01G252500 chr2A 87.507 1833 48 56 482 2170 381504062 381502267 0.000000e+00 1949.0
5 TraesCS2D01G252500 chr2A 93.674 411 11 6 1 396 381504707 381504297 3.430000e-168 601.0
6 TraesCS2D01G252500 chr2A 90.830 229 11 5 2160 2384 381502240 381502018 5.050000e-77 298.0
7 TraesCS2D01G252500 chr1A 82.051 117 19 2 1299 1414 562902784 562902899 5.490000e-17 99.0
8 TraesCS2D01G252500 chr3B 81.356 118 20 2 1299 1415 379654015 379654131 7.100000e-16 95.3
9 TraesCS2D01G252500 chr1B 82.143 112 18 2 1307 1417 649670511 649670621 7.100000e-16 95.3
10 TraesCS2D01G252500 chr1B 81.356 118 20 2 1299 1415 651286856 651286740 7.100000e-16 95.3
11 TraesCS2D01G252500 chr5B 81.481 108 18 2 1306 1412 328274092 328274198 1.190000e-13 87.9
12 TraesCS2D01G252500 chr1D 80.000 120 22 2 1299 1417 469795849 469795967 1.190000e-13 87.9
13 TraesCS2D01G252500 chr6D 79.661 118 22 2 1299 1415 17042690 17042574 1.540000e-12 84.2


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 TraesCS2D01G252500 chr2D 303513723 303516136 2413 True 4458.000000 4458 100.000000 1 2414 1 chr2D.!!$R1 2413
1 TraesCS2D01G252500 chr2B 372087781 372090267 2486 True 1080.000000 2061 91.535667 1 2414 3 chr2B.!!$R1 2413
2 TraesCS2D01G252500 chr2A 381502018 381504707 2689 True 949.333333 1949 90.670333 1 2384 3 chr2A.!!$R1 2383

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
91 95 0.100503 GTTGGTTGTGTGGTGTGAGC 59.899 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2510 0.108089 TACGTACCGGTACCAGCGTA 60.108 55.0 33.52 28.1 37.4 4.42 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
91 95 0.100503 GTTGGTTGTGTGGTGTGAGC 59.899 55.000 0.00 0.00 0.00 4.26
101 105 1.961277 GGTGTGAGCCGTTGGTGAG 60.961 63.158 0.00 0.00 0.00 3.51
297 310 3.376914 CTGCCGTGACGATCGACGA 62.377 63.158 25.39 0.00 45.77 4.20
338 363 3.471806 GCTCCGTTCCCTCCCTCC 61.472 72.222 0.00 0.00 0.00 4.30
339 364 2.764547 CTCCGTTCCCTCCCTCCC 60.765 72.222 0.00 0.00 0.00 4.30
340 365 3.281787 TCCGTTCCCTCCCTCCCT 61.282 66.667 0.00 0.00 0.00 4.20
341 366 2.764547 CCGTTCCCTCCCTCCCTC 60.765 72.222 0.00 0.00 0.00 4.30
342 367 2.764547 CGTTCCCTCCCTCCCTCC 60.765 72.222 0.00 0.00 0.00 4.30
343 368 2.367107 GTTCCCTCCCTCCCTCCC 60.367 72.222 0.00 0.00 0.00 4.30
344 369 2.543637 TTCCCTCCCTCCCTCCCT 60.544 66.667 0.00 0.00 0.00 4.20
345 370 2.647949 TTCCCTCCCTCCCTCCCTC 61.648 68.421 0.00 0.00 0.00 4.30
396 421 6.148480 GCCTGCAGATACATGTAAATTCCTAG 59.852 42.308 17.39 3.32 0.00 3.02
397 422 7.220030 CCTGCAGATACATGTAAATTCCTAGT 58.780 38.462 17.39 0.00 0.00 2.57
398 423 8.367911 CCTGCAGATACATGTAAATTCCTAGTA 58.632 37.037 17.39 0.00 0.00 1.82
399 424 9.197694 CTGCAGATACATGTAAATTCCTAGTAC 57.802 37.037 8.42 0.00 0.00 2.73
420 457 5.968387 ACTTAGAATTCGCCTGTAAATCG 57.032 39.130 0.00 0.00 0.00 3.34
430 467 3.531538 GCCTGTAAATCGAGATGGACAA 58.468 45.455 0.00 0.00 0.00 3.18
448 485 6.403049 TGGACAATATTTTCTGAGAGCGTTA 58.597 36.000 1.82 0.00 0.00 3.18
479 529 8.757877 CCCATTGGTTCATTATAAAGAAAAGGA 58.242 33.333 4.78 0.00 0.00 3.36
510 756 2.197283 TGCTGATGTGCCACAACATA 57.803 45.000 8.31 0.00 40.87 2.29
715 974 2.669240 GGGTGGAGTAGTGGTGGC 59.331 66.667 0.00 0.00 0.00 5.01
716 975 1.918800 GGGTGGAGTAGTGGTGGCT 60.919 63.158 0.00 0.00 0.00 4.75
784 1043 1.936547 GCGATCCATGTCTCTTTGACC 59.063 52.381 0.00 0.00 44.75 4.02
848 1109 2.365617 ACACTTCCATTCGAGACACACT 59.634 45.455 0.00 0.00 0.00 3.55
904 1169 2.047179 GTCCACCGCTCCCTGTTC 60.047 66.667 0.00 0.00 0.00 3.18
905 1170 3.319198 TCCACCGCTCCCTGTTCC 61.319 66.667 0.00 0.00 0.00 3.62
1179 1469 4.437587 CTCCTGCTTGGCCTGGGG 62.438 72.222 3.32 0.00 35.26 4.96
1242 1532 4.637489 CGAGAGATCCAGGCGGCG 62.637 72.222 0.51 0.51 0.00 6.46
1533 1841 3.663176 CTTGTGCCGTGCCTGTGG 61.663 66.667 0.00 0.00 0.00 4.17
1650 2020 4.555747 CGTGTGTTTGTTTTTGTAGGTGAC 59.444 41.667 0.00 0.00 0.00 3.67
1726 2132 1.462616 ATGCAATGACGCCTAGCAAA 58.537 45.000 0.00 0.00 38.85 3.68
1740 2146 3.379372 CCTAGCAAACTAGCATGCACATT 59.621 43.478 21.98 7.50 44.00 2.71
1792 2198 3.880047 TCTGTCCACCGTAAACCATAG 57.120 47.619 0.00 0.00 0.00 2.23
1794 2200 3.194116 TCTGTCCACCGTAAACCATAGAC 59.806 47.826 0.00 0.00 0.00 2.59
1827 2233 6.262273 TCTCTATGCATGTTCGTGTATACTGA 59.738 38.462 10.16 0.00 0.00 3.41
1829 2235 5.912360 ATGCATGTTCGTGTATACTGATG 57.088 39.130 0.00 0.05 0.00 3.07
1831 2262 3.362014 GCATGTTCGTGTATACTGATGCG 60.362 47.826 4.17 1.94 0.00 4.73
1847 2278 1.705256 TGCGTACTCAATTGGACGTC 58.295 50.000 21.30 7.13 37.61 4.34
1853 2284 4.625742 CGTACTCAATTGGACGTCTTGATT 59.374 41.667 16.46 13.52 0.00 2.57
1871 2302 2.238942 TTGGTATACATGCCTCGCAG 57.761 50.000 5.01 0.00 43.65 5.18
1889 2320 2.033407 GCAGTCGCATGCATACTTGTAG 60.033 50.000 19.57 9.25 45.77 2.74
1892 2323 4.442403 CAGTCGCATGCATACTTGTAGTAG 59.558 45.833 19.57 3.16 33.66 2.57
1893 2324 4.098044 AGTCGCATGCATACTTGTAGTAGT 59.902 41.667 19.57 0.00 33.66 2.73
1894 2325 5.298527 AGTCGCATGCATACTTGTAGTAGTA 59.701 40.000 19.57 0.00 33.66 1.82
1980 2445 8.517062 TTGTTGGTGGAAAATTGAATTTTGAT 57.483 26.923 19.47 0.00 42.15 2.57
2000 2465 3.703001 TTTGATGGAGAGTGGGAAGAC 57.297 47.619 0.00 0.00 0.00 3.01
2042 2507 1.367659 GCGACTGTCCGTAGTAGAGT 58.632 55.000 1.55 0.00 0.00 3.24
2043 2508 2.544685 GCGACTGTCCGTAGTAGAGTA 58.455 52.381 1.55 0.00 0.00 2.59
2044 2509 2.539274 GCGACTGTCCGTAGTAGAGTAG 59.461 54.545 1.55 0.00 0.00 2.57
2045 2510 3.779759 CGACTGTCCGTAGTAGAGTAGT 58.220 50.000 1.55 0.00 0.00 2.73
2046 2511 4.734989 GCGACTGTCCGTAGTAGAGTAGTA 60.735 50.000 1.55 0.00 0.00 1.82
2047 2512 4.737765 CGACTGTCCGTAGTAGAGTAGTAC 59.262 50.000 1.55 0.00 0.00 2.73
2132 2597 1.608590 CCATGAAACGTGACTTGCCTT 59.391 47.619 0.00 0.00 0.00 4.35
2133 2598 2.034558 CCATGAAACGTGACTTGCCTTT 59.965 45.455 0.00 0.00 0.00 3.11
2134 2599 3.490761 CCATGAAACGTGACTTGCCTTTT 60.491 43.478 0.00 0.00 0.00 2.27
2170 2637 0.685097 TTCAAAGGCGTGAGGTAGCT 59.315 50.000 0.00 0.00 0.00 3.32
2171 2638 0.685097 TCAAAGGCGTGAGGTAGCTT 59.315 50.000 0.00 0.00 0.00 3.74
2172 2639 1.071699 TCAAAGGCGTGAGGTAGCTTT 59.928 47.619 0.00 0.00 34.07 3.51
2173 2640 2.300723 TCAAAGGCGTGAGGTAGCTTTA 59.699 45.455 0.00 0.00 32.33 1.85
2174 2641 3.071479 CAAAGGCGTGAGGTAGCTTTAA 58.929 45.455 0.00 0.00 32.33 1.52
2175 2642 2.381725 AGGCGTGAGGTAGCTTTAAC 57.618 50.000 0.00 0.00 0.00 2.01
2176 2643 1.066358 AGGCGTGAGGTAGCTTTAACC 60.066 52.381 0.00 0.00 37.27 2.85
2195 2699 0.603569 CTCACTCACTGTACCGGCTT 59.396 55.000 0.00 0.00 0.00 4.35
2303 2814 1.990799 TCGTGTGACGATCCACAATC 58.009 50.000 6.40 0.00 46.73 2.67
2399 2910 7.495901 TGACACGTAGTAGTACTAGCTAGAAT 58.504 38.462 27.45 13.87 41.61 2.40
2403 2914 9.689976 CACGTAGTAGTACTAGCTAGAATAAGA 57.310 37.037 27.45 4.44 41.61 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 95 1.003718 GGGTCTTCCTCACCAACGG 60.004 63.158 0.00 0.00 35.35 4.44
101 105 0.462759 CCATCGCTCTTGGGTCTTCC 60.463 60.000 0.00 0.00 0.00 3.46
297 310 0.531974 ACACGGCGTGACAAGACAAT 60.532 50.000 42.65 17.26 36.96 2.71
345 370 8.603495 CAAGAATTTGAACGCCGACTATACGG 62.603 46.154 0.00 0.00 44.83 4.02
396 421 6.694411 TCGATTTACAGGCGAATTCTAAGTAC 59.306 38.462 3.52 0.00 0.00 2.73
397 422 6.798482 TCGATTTACAGGCGAATTCTAAGTA 58.202 36.000 3.52 0.00 0.00 2.24
398 423 5.657474 TCGATTTACAGGCGAATTCTAAGT 58.343 37.500 3.52 0.00 0.00 2.24
399 424 5.977725 TCTCGATTTACAGGCGAATTCTAAG 59.022 40.000 3.52 0.00 33.26 2.18
420 457 6.073873 CGCTCTCAGAAAATATTGTCCATCTC 60.074 42.308 1.75 0.00 0.00 2.75
430 467 5.297029 GGCCTTTAACGCTCTCAGAAAATAT 59.703 40.000 0.00 0.00 0.00 1.28
448 485 6.671779 TCTTTATAATGAACCAATGGGCCTTT 59.328 34.615 4.53 0.76 37.90 3.11
479 529 4.082571 GGCACATCAGCAAAATCAGTTACT 60.083 41.667 0.00 0.00 35.83 2.24
484 730 2.029739 TGTGGCACATCAGCAAAATCAG 60.030 45.455 17.96 0.00 44.52 2.90
510 756 0.104304 CACGGCCGCCTAATCTACTT 59.896 55.000 28.58 0.00 0.00 2.24
545 791 2.947542 CGAGCCGATCCTACTCCG 59.052 66.667 0.00 0.00 0.00 4.63
547 793 1.528292 ATGGCGAGCCGATCCTACTC 61.528 60.000 9.78 0.00 39.42 2.59
548 794 1.531840 ATGGCGAGCCGATCCTACT 60.532 57.895 9.78 0.00 39.42 2.57
549 795 1.373497 CATGGCGAGCCGATCCTAC 60.373 63.158 9.78 0.00 39.42 3.18
576 825 0.106569 ATGGCCGAAAGATGGATGCA 60.107 50.000 0.00 0.00 0.00 3.96
577 826 0.595095 GATGGCCGAAAGATGGATGC 59.405 55.000 0.00 0.00 0.00 3.91
715 974 1.153823 CGAACCCGGCACACTCTAG 60.154 63.158 0.00 0.00 0.00 2.43
716 975 1.466025 AACGAACCCGGCACACTCTA 61.466 55.000 0.00 0.00 40.78 2.43
751 1010 1.028868 GGATCGCTTTTGGCAGAGCT 61.029 55.000 18.64 0.00 41.91 4.09
848 1109 2.273179 CGGACAGGTCGAAGGGTGA 61.273 63.158 0.00 0.00 0.00 4.02
904 1169 0.462759 GCAAGGGAACGAGGATGAGG 60.463 60.000 0.00 0.00 0.00 3.86
905 1170 0.250234 TGCAAGGGAACGAGGATGAG 59.750 55.000 0.00 0.00 0.00 2.90
978 1256 3.855853 GCGCCTCCTTCTCCCTCC 61.856 72.222 0.00 0.00 0.00 4.30
1296 1586 3.802418 GACGAACACCACGGGCACT 62.802 63.158 0.00 0.00 34.93 4.40
1461 1751 0.250124 GTCGTTGATCACCACCACCA 60.250 55.000 0.00 0.00 0.00 4.17
1462 1752 1.289109 CGTCGTTGATCACCACCACC 61.289 60.000 0.00 0.00 0.00 4.61
1463 1753 1.289109 CCGTCGTTGATCACCACCAC 61.289 60.000 0.00 0.00 0.00 4.16
1533 1841 4.988486 GCAACGCACAGCCACAGC 62.988 66.667 0.00 0.00 40.32 4.40
1650 2020 5.180492 CCTCCACTCTCTAACTAGATAAGCG 59.820 48.000 0.00 0.00 0.00 4.68
1726 2132 5.902613 AATAACACAATGTGCATGCTAGT 57.097 34.783 20.33 4.36 36.98 2.57
1792 2198 6.307558 CGAACATGCATAGAGATGATAGTGTC 59.692 42.308 0.00 0.00 34.73 3.67
1794 2200 6.089150 CACGAACATGCATAGAGATGATAGTG 59.911 42.308 0.00 0.00 34.73 2.74
1827 2233 2.094182 AGACGTCCAATTGAGTACGCAT 60.094 45.455 20.53 11.28 38.87 4.73
1829 2235 1.992170 AGACGTCCAATTGAGTACGC 58.008 50.000 20.53 15.33 38.87 4.42
1831 2262 5.163854 CCAATCAAGACGTCCAATTGAGTAC 60.164 44.000 25.11 1.36 36.47 2.73
1847 2278 3.187227 GCGAGGCATGTATACCAATCAAG 59.813 47.826 0.00 0.00 0.00 3.02
1853 2284 1.068588 GACTGCGAGGCATGTATACCA 59.931 52.381 0.00 0.00 38.13 3.25
1871 2302 4.360563 ACTACTACAAGTATGCATGCGAC 58.639 43.478 14.09 13.62 29.08 5.19
1942 2373 4.759693 TCCACCAACAAAATGCTACTACAG 59.240 41.667 0.00 0.00 0.00 2.74
1980 2445 2.028112 CGTCTTCCCACTCTCCATCAAA 60.028 50.000 0.00 0.00 0.00 2.69
2000 2465 1.079819 ATCACCTTCTGTGGACGCG 60.080 57.895 3.53 3.53 45.48 6.01
2042 2507 1.663695 GTACCGGTACCAGCGTACTA 58.336 55.000 30.84 0.00 43.78 1.82
2043 2508 1.369091 CGTACCGGTACCAGCGTACT 61.369 60.000 33.52 0.00 43.78 2.73
2044 2509 1.062525 CGTACCGGTACCAGCGTAC 59.937 63.158 33.52 16.29 43.60 3.67
2045 2510 0.108089 TACGTACCGGTACCAGCGTA 60.108 55.000 33.52 28.10 37.40 4.42
2046 2511 1.376683 TACGTACCGGTACCAGCGT 60.377 57.895 33.52 29.04 37.40 5.07
2047 2512 1.062525 GTACGTACCGGTACCAGCG 59.937 63.158 33.52 25.49 37.41 5.18
2048 2513 1.062525 CGTACGTACCGGTACCAGC 59.937 63.158 33.52 22.75 39.65 4.85
2049 2514 1.062525 GCGTACGTACCGGTACCAG 59.937 63.158 33.52 24.33 39.65 4.00
2050 2515 1.672682 TGCGTACGTACCGGTACCA 60.673 57.895 33.52 23.66 39.65 3.25
2051 2516 1.226295 GTGCGTACGTACCGGTACC 60.226 63.158 33.52 21.57 39.65 3.34
2141 2606 1.866853 CGCCTTTGAACCAAGCCTCC 61.867 60.000 0.00 0.00 0.00 4.30
2170 2637 3.006110 CCGGTACAGTGAGTGAGGTTAAA 59.994 47.826 0.00 0.00 0.00 1.52
2171 2638 2.559668 CCGGTACAGTGAGTGAGGTTAA 59.440 50.000 0.00 0.00 0.00 2.01
2172 2639 2.165167 CCGGTACAGTGAGTGAGGTTA 58.835 52.381 0.00 0.00 0.00 2.85
2173 2640 0.966920 CCGGTACAGTGAGTGAGGTT 59.033 55.000 0.00 0.00 0.00 3.50
2174 2641 1.533469 GCCGGTACAGTGAGTGAGGT 61.533 60.000 1.90 0.00 0.00 3.85
2175 2642 1.215647 GCCGGTACAGTGAGTGAGG 59.784 63.158 1.90 0.00 0.00 3.86
2176 2643 0.603569 AAGCCGGTACAGTGAGTGAG 59.396 55.000 1.90 0.00 0.00 3.51
2177 2644 0.317160 CAAGCCGGTACAGTGAGTGA 59.683 55.000 1.90 0.00 0.00 3.41
2178 2645 0.033504 ACAAGCCGGTACAGTGAGTG 59.966 55.000 1.90 0.00 0.00 3.51
2179 2646 0.756903 AACAAGCCGGTACAGTGAGT 59.243 50.000 1.90 0.00 0.00 3.41
2303 2814 8.406297 TGTATTACTACTAGTGCAGATGAGTTG 58.594 37.037 5.39 0.00 0.00 3.16
2340 2851 1.062002 CGTAGCAAATAACCGTGCCTG 59.938 52.381 0.00 0.00 41.88 4.85


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

AutoCloner maintained by Alex Coulton.