Multiple sequence alignment - TraesCS2D01G413100

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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 TraesCS2D01G413100 chr2D 100.000 2391 0 0 1 2391 527649227 527646837 0.000000e+00 4416.0
1 TraesCS2D01G413100 chr2D 88.927 1752 123 29 1 1725 527685338 527683631 0.000000e+00 2095.0
2 TraesCS2D01G413100 chr2D 84.444 1080 116 34 795 1861 527804803 527803763 0.000000e+00 1016.0
3 TraesCS2D01G413100 chr2D 96.907 485 6 3 909 1393 528998727 528999202 0.000000e+00 804.0
4 TraesCS2D01G413100 chr2D 81.225 1012 107 44 806 1804 528994491 528995432 0.000000e+00 739.0
5 TraesCS2D01G413100 chr2D 83.152 736 91 21 58 769 614386182 614385456 2.000000e-180 641.0
6 TraesCS2D01G413100 chr2D 84.117 617 48 32 794 1391 498766714 498767299 3.470000e-153 551.0
7 TraesCS2D01G413100 chr2D 93.431 274 15 3 493 764 527677264 527676992 1.030000e-108 403.0
8 TraesCS2D01G413100 chr2D 93.066 274 15 4 493 764 527729792 527729521 4.790000e-107 398.0
9 TraesCS2D01G413100 chr2D 92.278 259 20 0 58 316 174419097 174418839 3.750000e-98 368.0
10 TraesCS2D01G413100 chr2D 87.349 166 17 4 755 917 528998304 528998468 1.130000e-43 187.0
11 TraesCS2D01G413100 chr2D 89.600 125 8 3 2002 2121 267710470 267710346 1.140000e-33 154.0
12 TraesCS2D01G413100 chr2B 90.392 1634 99 25 776 2389 625009316 625007721 0.000000e+00 2095.0
13 TraesCS2D01G413100 chr2B 89.015 619 35 12 776 1394 628156838 628157423 0.000000e+00 736.0
14 TraesCS2D01G413100 chr2B 85.270 611 42 28 799 1393 585890018 585890596 9.520000e-164 586.0
15 TraesCS2D01G413100 chr2B 86.131 137 16 2 631 764 788669992 788670128 6.890000e-31 145.0
16 TraesCS2D01G413100 chr2B 85.600 125 13 3 2002 2121 535563444 535563320 2.500000e-25 126.0
17 TraesCS2D01G413100 chr2B 90.426 94 4 1 1524 1612 627324549 627324642 4.180000e-23 119.0
18 TraesCS2D01G413100 chr2A 86.346 1582 114 26 771 2316 672645399 672643884 0.000000e+00 1631.0
19 TraesCS2D01G413100 chr2A 89.252 735 65 6 1 722 672663515 672662782 0.000000e+00 907.0
20 TraesCS2D01G413100 chr2A 92.892 619 33 7 776 1393 673451848 673452456 0.000000e+00 889.0
21 TraesCS2D01G413100 chr2A 86.649 734 51 21 1080 1804 673419996 673420691 0.000000e+00 769.0
22 TraesCS2D01G413100 chr7D 82.079 731 97 24 58 764 30248266 30247546 5.690000e-166 593.0
23 TraesCS2D01G413100 chr7B 81.124 747 92 31 52 765 679491071 679491801 9.660000e-154 553.0
24 TraesCS2D01G413100 chr7B 78.596 285 30 24 502 764 679450848 679451123 2.460000e-35 159.0
25 TraesCS2D01G413100 chr7B 100.000 40 0 0 1 40 679491038 679491077 9.170000e-10 75.0
26 TraesCS2D01G413100 chr1D 81.173 733 89 27 58 764 408875882 408875173 5.810000e-151 544.0
27 TraesCS2D01G413100 chr3B 80.218 733 107 25 58 764 93620208 93620928 1.270000e-142 516.0
28 TraesCS2D01G413100 chr3B 97.143 35 1 0 1 35 93620169 93620203 2.570000e-05 60.2
29 TraesCS2D01G413100 chr6B 84.960 379 40 6 1 363 688824272 688824649 3.750000e-98 368.0
30 TraesCS2D01G413100 chr5B 88.462 130 15 0 626 755 416547825 416547954 8.850000e-35 158.0
31 TraesCS2D01G413100 chr5B 93.750 48 2 1 497 544 594931236 594931282 1.190000e-08 71.3
32 TraesCS2D01G413100 chr5A 77.903 267 38 18 512 764 706077164 706077423 1.920000e-31 147.0
33 TraesCS2D01G413100 chr1B 88.000 125 10 3 2002 2121 399624696 399624820 2.480000e-30 143.0
34 TraesCS2D01G413100 chr1A 97.059 34 1 0 484 517 580204128 580204095 9.230000e-05 58.4


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 TraesCS2D01G413100 chr2D 527646837 527649227 2390 True 4416.000000 4416 100.000000 1 2391 1 chr2D.!!$R3 2390
1 TraesCS2D01G413100 chr2D 527683631 527685338 1707 True 2095.000000 2095 88.927000 1 1725 1 chr2D.!!$R5 1724
2 TraesCS2D01G413100 chr2D 527803763 527804803 1040 True 1016.000000 1016 84.444000 795 1861 1 chr2D.!!$R7 1066
3 TraesCS2D01G413100 chr2D 614385456 614386182 726 True 641.000000 641 83.152000 58 769 1 chr2D.!!$R8 711
4 TraesCS2D01G413100 chr2D 528994491 528999202 4711 False 576.666667 804 88.493667 755 1804 3 chr2D.!!$F2 1049
5 TraesCS2D01G413100 chr2D 498766714 498767299 585 False 551.000000 551 84.117000 794 1391 1 chr2D.!!$F1 597
6 TraesCS2D01G413100 chr2B 625007721 625009316 1595 True 2095.000000 2095 90.392000 776 2389 1 chr2B.!!$R2 1613
7 TraesCS2D01G413100 chr2B 628156838 628157423 585 False 736.000000 736 89.015000 776 1394 1 chr2B.!!$F3 618
8 TraesCS2D01G413100 chr2B 585890018 585890596 578 False 586.000000 586 85.270000 799 1393 1 chr2B.!!$F1 594
9 TraesCS2D01G413100 chr2A 672643884 672645399 1515 True 1631.000000 1631 86.346000 771 2316 1 chr2A.!!$R1 1545
10 TraesCS2D01G413100 chr2A 672662782 672663515 733 True 907.000000 907 89.252000 1 722 1 chr2A.!!$R2 721
11 TraesCS2D01G413100 chr2A 673451848 673452456 608 False 889.000000 889 92.892000 776 1393 1 chr2A.!!$F2 617
12 TraesCS2D01G413100 chr2A 673419996 673420691 695 False 769.000000 769 86.649000 1080 1804 1 chr2A.!!$F1 724
13 TraesCS2D01G413100 chr7D 30247546 30248266 720 True 593.000000 593 82.079000 58 764 1 chr7D.!!$R1 706
14 TraesCS2D01G413100 chr7B 679491038 679491801 763 False 314.000000 553 90.562000 1 765 2 chr7B.!!$F2 764
15 TraesCS2D01G413100 chr1D 408875173 408875882 709 True 544.000000 544 81.173000 58 764 1 chr1D.!!$R1 706
16 TraesCS2D01G413100 chr3B 93620169 93620928 759 False 288.100000 516 88.680500 1 764 2 chr3B.!!$F1 763

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
421 434 0.039165 CGAAGGCAAAAGCAAGGTCC 60.039 55.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 2367 0.178981 ACATCTTGCAGTTGCTGGGT 60.179 50.0 5.62 0.0 42.66 4.51 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
114 115 1.076549 GTTGGGGCATGACCAGGAA 59.923 57.895 22.13 5.82 42.05 3.36
173 174 3.322466 CTCCAGGGGAGTTGCCGT 61.322 66.667 4.08 0.00 44.25 5.68
174 175 3.316573 CTCCAGGGGAGTTGCCGTC 62.317 68.421 4.08 0.00 44.25 4.79
213 214 4.221422 GTGGAGGCGCTGGCGATA 62.221 66.667 19.31 0.00 42.83 2.92
214 215 3.466314 TGGAGGCGCTGGCGATAA 61.466 61.111 19.31 0.00 42.83 1.75
421 434 0.039165 CGAAGGCAAAAGCAAGGTCC 60.039 55.000 0.00 0.00 0.00 4.46
453 466 3.569701 GCCATTGTTCTCACCTTTCTTCA 59.430 43.478 0.00 0.00 0.00 3.02
476 489 3.632604 TCTTGGCCTATTCTCTCTGTACG 59.367 47.826 3.32 0.00 0.00 3.67
500 513 0.576798 CGATGCGTGCATGATAACGT 59.423 50.000 12.81 0.00 41.76 3.99
545 558 7.317842 AGTGAATGAGTGCTTTCATTGATAG 57.682 36.000 17.23 0.24 45.30 2.08
562 575 8.264347 TCATTGATAGTGACTGCAGGTTTTATA 58.736 33.333 19.93 3.48 0.00 0.98
569 582 6.611642 AGTGACTGCAGGTTTTATATCTCCTA 59.388 38.462 19.93 0.00 0.00 2.94
588 601 4.056050 CCTAAACAGTCGCAAGTACAAGT 58.944 43.478 0.00 0.00 39.48 3.16
589 602 4.510340 CCTAAACAGTCGCAAGTACAAGTT 59.490 41.667 0.00 0.00 39.48 2.66
591 604 2.210116 ACAGTCGCAAGTACAAGTTGG 58.790 47.619 7.96 0.00 39.48 3.77
607 620 1.071041 GTTGGTTACAGTGTTCGCGTC 60.071 52.381 5.77 1.06 0.00 5.19
614 627 1.800315 AGTGTTCGCGTCGATTCGG 60.800 57.895 5.77 0.00 35.23 4.30
628 641 2.527100 GATTCGGAAAGACACGACGAT 58.473 47.619 0.00 0.00 39.04 3.73
650 663 4.141287 TGGTTTGGAAAGACACGATGATT 58.859 39.130 0.00 0.00 0.00 2.57
651 664 4.023279 TGGTTTGGAAAGACACGATGATTG 60.023 41.667 0.00 0.00 0.00 2.67
652 665 4.023193 GGTTTGGAAAGACACGATGATTGT 60.023 41.667 0.00 0.00 0.00 2.71
908 943 2.893398 GGATCGACCCAGCGAAGT 59.107 61.111 0.00 0.00 44.22 3.01
909 944 1.227002 GGATCGACCCAGCGAAGTC 60.227 63.158 0.00 0.00 44.22 3.01
993 1041 4.888325 CCCCGCCCTCAGATCCCT 62.888 72.222 0.00 0.00 0.00 4.20
1030 1078 0.035630 CAGACTCCCTCCAAAGCAGG 60.036 60.000 0.00 0.00 0.00 4.85
1031 1079 1.377856 GACTCCCTCCAAAGCAGGC 60.378 63.158 0.00 0.00 0.00 4.85
1032 1080 2.129555 GACTCCCTCCAAAGCAGGCA 62.130 60.000 0.00 0.00 0.00 4.75
1033 1081 1.378250 CTCCCTCCAAAGCAGGCAG 60.378 63.158 0.00 0.00 0.00 4.85
1034 1082 3.066814 CCCTCCAAAGCAGGCAGC 61.067 66.667 0.00 0.00 46.19 5.25
1394 1776 0.105039 CGGCTTCGGAGGCTAGATTT 59.895 55.000 16.26 0.00 45.73 2.17
1403 1785 2.027192 GGAGGCTAGATTTGTGTGGTGA 60.027 50.000 0.00 0.00 0.00 4.02
1430 1814 2.370281 TCCTCGTTTGCTCTGTGATC 57.630 50.000 0.00 0.00 0.00 2.92
1447 1832 3.016736 TGATCTGTGCTGTCGTAGATGA 58.983 45.455 0.00 0.00 40.67 2.92
1515 1901 3.871594 CAGTAGGCTGTGTAATACCTTGC 59.128 47.826 0.00 0.00 37.92 4.01
1516 1902 3.775316 AGTAGGCTGTGTAATACCTTGCT 59.225 43.478 0.00 0.00 33.60 3.91
1517 1903 3.268023 AGGCTGTGTAATACCTTGCTC 57.732 47.619 0.00 0.00 0.00 4.26
1518 1904 2.840651 AGGCTGTGTAATACCTTGCTCT 59.159 45.455 0.00 0.00 0.00 4.09
1519 1905 2.939103 GGCTGTGTAATACCTTGCTCTG 59.061 50.000 0.00 0.00 0.00 3.35
1520 1906 3.600388 GCTGTGTAATACCTTGCTCTGT 58.400 45.455 0.00 0.00 0.00 3.41
1521 1907 4.382685 GGCTGTGTAATACCTTGCTCTGTA 60.383 45.833 0.00 0.00 0.00 2.74
1522 1908 4.567159 GCTGTGTAATACCTTGCTCTGTAC 59.433 45.833 0.00 0.00 0.00 2.90
1545 1935 5.533903 ACTTCTGTTCAATGCAATCACTTCT 59.466 36.000 0.00 0.00 0.00 2.85
1670 2104 9.520204 CACTGAATCAGTCTTTTATTTGTTTGT 57.480 29.630 13.72 0.00 43.43 2.83
1705 2139 0.039256 TGCTTGCCAGTTTTGATCGC 60.039 50.000 0.00 0.00 0.00 4.58
1767 2201 5.095691 TGAAACTCGTTGCTTCTCATTTC 57.904 39.130 0.00 0.00 0.00 2.17
1885 2332 1.209504 GTGACATGCCCCTAGCTGTAA 59.790 52.381 0.00 0.00 44.23 2.41
1912 2367 0.911769 CATGCCCCTACCTGAAGACA 59.088 55.000 0.00 0.00 0.00 3.41
1939 2404 4.038282 AGCAACTGCAAGATGTTGAAATGA 59.962 37.500 17.87 0.00 44.29 2.57
1945 2410 4.240096 GCAAGATGTTGAAATGACCAAGG 58.760 43.478 6.80 0.00 35.46 3.61
2099 2659 6.620877 TCTCACATATTGTCCTGTTAACCT 57.379 37.500 2.48 0.00 0.00 3.50
2140 2700 5.230942 AGTTGTCATCGAGTCACTAAAAGG 58.769 41.667 0.00 0.00 0.00 3.11
2193 2762 2.919666 ATTTTGTATCTGCGCACACC 57.080 45.000 5.66 0.00 0.00 4.16
2238 2807 3.189495 ACTCATAGTCTCGTATCCATGCG 59.811 47.826 0.00 0.00 37.23 4.73
2278 3166 8.352201 TCCAATTTGTTTCTGTCACTATTCTTG 58.648 33.333 0.00 0.00 0.00 3.02
2296 3184 6.428083 TTCTTGTCCTGGAACATTAGTACA 57.572 37.500 0.00 0.00 38.20 2.90
2353 3241 3.758554 GGCAAAGCTTTACCATCTCTTGA 59.241 43.478 21.51 0.00 0.00 3.02
2365 3253 5.605534 ACCATCTCTTGAAACATAGATCGG 58.394 41.667 0.00 0.00 0.00 4.18
2389 3277 4.521130 ACATGGTACTCATATGCTACCG 57.479 45.455 17.87 11.02 33.78 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.060326 TGTCGACGAACAGGTTGATC 57.940 50.000 11.62 0.00 33.11 2.92
96 97 1.076549 TTCCTGGTCATGCCCCAAC 59.923 57.895 5.58 0.00 36.04 3.77
114 115 3.011517 ATGCGCCCAGGGAAGAGT 61.012 61.111 10.89 0.00 0.00 3.24
213 214 4.408821 TCCTTCGCCGCCATGCTT 62.409 61.111 0.00 0.00 0.00 3.91
214 215 4.845580 CTCCTTCGCCGCCATGCT 62.846 66.667 0.00 0.00 0.00 3.79
331 344 2.280592 GGTCTGGCCGTTGTTCGT 60.281 61.111 0.00 0.00 37.94 3.85
358 371 0.239347 GTCGTTTCCGTCTTCCTCGA 59.761 55.000 0.00 0.00 35.01 4.04
372 385 2.579201 CCAGGGAGCATCGTCGTT 59.421 61.111 0.00 0.00 34.37 3.85
453 466 4.279671 CGTACAGAGAGAATAGGCCAAGAT 59.720 45.833 5.01 0.00 0.00 2.40
476 489 1.220169 ATCATGCACGCATCGCTCTC 61.220 55.000 0.44 0.00 33.90 3.20
500 513 8.737168 TCACTTCAATCTTTCTTTTCTTCTCA 57.263 30.769 0.00 0.00 0.00 3.27
545 558 5.675538 AGGAGATATAAAACCTGCAGTCAC 58.324 41.667 13.81 0.00 0.00 3.67
562 575 3.963428 ACTTGCGACTGTTTAGGAGAT 57.037 42.857 0.00 0.00 0.00 2.75
569 582 3.064820 CCAACTTGTACTTGCGACTGTTT 59.935 43.478 0.00 0.00 0.00 2.83
588 601 1.210870 GACGCGAACACTGTAACCAA 58.789 50.000 15.93 0.00 0.00 3.67
589 602 0.935831 CGACGCGAACACTGTAACCA 60.936 55.000 15.93 0.00 0.00 3.67
591 604 1.334054 ATCGACGCGAACACTGTAAC 58.666 50.000 15.93 0.00 39.99 2.50
607 620 0.633733 CGTCGTGTCTTTCCGAATCG 59.366 55.000 0.00 0.00 34.47 3.34
614 627 2.096417 CCAAACCATCGTCGTGTCTTTC 60.096 50.000 0.00 0.00 0.00 2.62
628 641 3.201353 TCATCGTGTCTTTCCAAACCA 57.799 42.857 0.00 0.00 0.00 3.67
760 775 9.332301 CGGTTGTTTTATCGTATATGTTTTGTT 57.668 29.630 0.00 0.00 0.00 2.83
761 776 7.482428 GCGGTTGTTTTATCGTATATGTTTTGT 59.518 33.333 0.00 0.00 0.00 2.83
762 777 7.044576 GGCGGTTGTTTTATCGTATATGTTTTG 60.045 37.037 0.00 0.00 0.00 2.44
924 964 0.779997 ACTGCAAGATTTGGGGGACT 59.220 50.000 0.00 0.00 37.43 3.85
993 1041 2.104622 TCTGATGCTTGCGATGGGATTA 59.895 45.455 0.00 0.00 0.00 1.75
1030 1078 0.744057 GGAAGAAGAGGAGCTGCTGC 60.744 60.000 14.48 13.74 30.78 5.25
1031 1079 0.903942 AGGAAGAAGAGGAGCTGCTG 59.096 55.000 14.48 0.00 30.78 4.41
1032 1080 2.541233 TAGGAAGAAGAGGAGCTGCT 57.459 50.000 7.79 7.79 32.08 4.24
1033 1081 3.133721 TGATTAGGAAGAAGAGGAGCTGC 59.866 47.826 0.00 0.00 0.00 5.25
1034 1082 4.161189 TGTGATTAGGAAGAAGAGGAGCTG 59.839 45.833 0.00 0.00 0.00 4.24
1035 1083 4.161377 GTGTGATTAGGAAGAAGAGGAGCT 59.839 45.833 0.00 0.00 0.00 4.09
1036 1084 4.161377 AGTGTGATTAGGAAGAAGAGGAGC 59.839 45.833 0.00 0.00 0.00 4.70
1394 1776 1.064758 AGGAAGTTGCTTCACCACACA 60.065 47.619 10.51 0.00 41.77 3.72
1403 1785 1.604278 GAGCAAACGAGGAAGTTGCTT 59.396 47.619 11.09 0.00 38.02 3.91
1430 1814 3.706802 ATCTCATCTACGACAGCACAG 57.293 47.619 0.00 0.00 0.00 3.66
1447 1832 2.095853 CGCACGCCAAATCAGTAAATCT 59.904 45.455 0.00 0.00 0.00 2.40
1471 1856 3.366052 ACCCCATGACAGAATACAACC 57.634 47.619 0.00 0.00 0.00 3.77
1515 1901 5.929697 TTGCATTGAACAGAAGTACAGAG 57.070 39.130 0.00 0.00 0.00 3.35
1516 1902 5.997129 TGATTGCATTGAACAGAAGTACAGA 59.003 36.000 0.00 0.00 0.00 3.41
1517 1903 6.072838 AGTGATTGCATTGAACAGAAGTACAG 60.073 38.462 0.00 0.00 0.00 2.74
1518 1904 5.764686 AGTGATTGCATTGAACAGAAGTACA 59.235 36.000 0.00 0.00 0.00 2.90
1519 1905 6.246420 AGTGATTGCATTGAACAGAAGTAC 57.754 37.500 0.00 0.00 0.00 2.73
1520 1906 6.712095 AGAAGTGATTGCATTGAACAGAAGTA 59.288 34.615 0.00 0.00 0.00 2.24
1521 1907 5.533903 AGAAGTGATTGCATTGAACAGAAGT 59.466 36.000 0.00 0.00 0.00 3.01
1522 1908 6.010294 AGAAGTGATTGCATTGAACAGAAG 57.990 37.500 0.00 0.00 0.00 2.85
1545 1935 3.565482 GCATTTCGCCAGGATTCAGAATA 59.435 43.478 0.00 0.00 32.94 1.75
1670 2104 4.988540 GGCAAGCAACGAGTGACATATATA 59.011 41.667 0.00 0.00 0.00 0.86
1740 2174 6.228273 TGAGAAGCAACGAGTTTCAAATAG 57.772 37.500 10.47 0.00 39.64 1.73
1885 2332 2.092212 CAGGTAGGGGCATGACAGATTT 60.092 50.000 0.00 0.00 0.00 2.17
1912 2367 0.178981 ACATCTTGCAGTTGCTGGGT 60.179 50.000 5.62 0.00 42.66 4.51
1939 2404 2.957402 TCAAATCAGCAGACCTTGGT 57.043 45.000 0.00 0.00 38.24 3.67
1945 2410 6.691818 CAGAGCAAATAATCAAATCAGCAGAC 59.308 38.462 0.00 0.00 0.00 3.51
2168 2736 4.142513 TGTGCGCAGATACAAAATAATGCA 60.143 37.500 12.22 0.00 33.33 3.96
2278 3166 5.411669 CCAAGTTGTACTAATGTTCCAGGAC 59.588 44.000 1.45 0.00 0.00 3.85
2296 3184 4.289672 ACATATGTGACCTCTTCCCAAGTT 59.710 41.667 7.78 0.00 0.00 2.66
2353 3241 4.689612 ACCATGTAGCCGATCTATGTTT 57.310 40.909 0.00 0.00 0.00 2.83
2365 3253 5.411781 GGTAGCATATGAGTACCATGTAGC 58.588 45.833 21.54 7.69 36.89 3.58


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

AutoCloner maintained by Alex Coulton.