Multiple sequence alignment - TraesCS2B01G299600

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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 TraesCS2B01G299600 chr2B 100.000 2984 0 0 1 2984 419938627 419941610 0.000000e+00 5511
1 TraesCS2B01G299600 chr2B 93.290 2325 142 9 2 2314 528809433 528807111 0.000000e+00 3417
2 TraesCS2B01G299600 chr2B 91.563 403 19 5 2310 2711 528797549 528797161 2.620000e-150 542
3 TraesCS2B01G299600 chr7B 95.465 2999 116 11 1 2984 73168039 73171032 0.000000e+00 4767
4 TraesCS2B01G299600 chr7B 95.421 1922 71 5 1 1922 517902596 517904500 0.000000e+00 3046
5 TraesCS2B01G299600 chr6B 95.010 2966 135 8 26 2983 617031452 617034412 0.000000e+00 4645
6 TraesCS2B01G299600 chr6B 94.134 1483 81 4 932 2409 676703236 676704717 0.000000e+00 2252
7 TraesCS2B01G299600 chr6B 95.949 938 37 1 1 938 676683729 676684665 0.000000e+00 1520
8 TraesCS2B01G299600 chr6B 92.587 715 29 7 1982 2690 138658386 138659082 0.000000e+00 1005
9 TraesCS2B01G299600 chr6B 93.945 578 32 3 2407 2983 676708372 676708947 0.000000e+00 870
10 TraesCS2B01G299600 chr6B 92.334 287 18 3 2684 2967 138633787 138634072 3.580000e-109 405
11 TraesCS2B01G299600 chr6B 92.308 286 19 3 2684 2967 138672617 138672901 1.290000e-108 403
12 TraesCS2B01G299600 chr1B 93.259 2685 145 13 40 2711 344040425 344043086 0.000000e+00 3923
13 TraesCS2B01G299600 chr3B 95.141 2264 101 6 1 2257 766342005 766344266 0.000000e+00 3563
14 TraesCS2B01G299600 chr3B 93.831 697 32 7 2296 2984 766344267 766344960 0.000000e+00 1038
15 TraesCS2B01G299600 chr3B 77.626 219 32 10 2774 2984 512391487 512391696 1.880000e-22 117
16 TraesCS2B01G299600 chr4B 92.706 1796 94 15 926 2711 43564379 43562611 0.000000e+00 2556
17 TraesCS2B01G299600 chr4B 94.200 931 52 2 1 931 43573721 43572793 0.000000e+00 1419
18 TraesCS2B01G299600 chr4B 95.935 492 19 1 925 1416 43578259 43577769 0.000000e+00 797
19 TraesCS2B01G299600 chr7D 97.824 1149 24 1 1 1149 83759037 83760184 0.000000e+00 1982
20 TraesCS2B01G299600 chr7D 95.967 719 26 2 1256 1971 83760186 83760904 0.000000e+00 1164
21 TraesCS2B01G299600 chr7D 97.264 658 16 2 2328 2984 83761285 83761941 0.000000e+00 1114
22 TraesCS2B01G299600 chr7D 96.084 383 12 3 2603 2984 366437204 366436824 3.270000e-174 621
23 TraesCS2B01G299600 chr2D 97.112 658 17 2 2328 2984 238090080 238089424 0.000000e+00 1109
24 TraesCS2B01G299600 chrUn 93.089 709 25 7 1988 2690 194984898 194984208 0.000000e+00 1016


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 TraesCS2B01G299600 chr2B 419938627 419941610 2983 False 5511.0 5511 100.000000 1 2984 1 chr2B.!!$F1 2983
1 TraesCS2B01G299600 chr2B 528807111 528809433 2322 True 3417.0 3417 93.290000 2 2314 1 chr2B.!!$R2 2312
2 TraesCS2B01G299600 chr7B 73168039 73171032 2993 False 4767.0 4767 95.465000 1 2984 1 chr7B.!!$F1 2983
3 TraesCS2B01G299600 chr7B 517902596 517904500 1904 False 3046.0 3046 95.421000 1 1922 1 chr7B.!!$F2 1921
4 TraesCS2B01G299600 chr6B 617031452 617034412 2960 False 4645.0 4645 95.010000 26 2983 1 chr6B.!!$F4 2957
5 TraesCS2B01G299600 chr6B 676703236 676708947 5711 False 1561.0 2252 94.039500 932 2983 2 chr6B.!!$F6 2051
6 TraesCS2B01G299600 chr6B 676683729 676684665 936 False 1520.0 1520 95.949000 1 938 1 chr6B.!!$F5 937
7 TraesCS2B01G299600 chr6B 138658386 138659082 696 False 1005.0 1005 92.587000 1982 2690 1 chr6B.!!$F2 708
8 TraesCS2B01G299600 chr1B 344040425 344043086 2661 False 3923.0 3923 93.259000 40 2711 1 chr1B.!!$F1 2671
9 TraesCS2B01G299600 chr3B 766342005 766344960 2955 False 2300.5 3563 94.486000 1 2984 2 chr3B.!!$F2 2983
10 TraesCS2B01G299600 chr4B 43562611 43564379 1768 True 2556.0 2556 92.706000 926 2711 1 chr4B.!!$R1 1785
11 TraesCS2B01G299600 chr4B 43572793 43573721 928 True 1419.0 1419 94.200000 1 931 1 chr4B.!!$R2 930
12 TraesCS2B01G299600 chr7D 83759037 83761941 2904 False 1420.0 1982 97.018333 1 2984 3 chr7D.!!$F1 2983
13 TraesCS2B01G299600 chr2D 238089424 238090080 656 True 1109.0 1109 97.112000 2328 2984 1 chr2D.!!$R1 656
14 TraesCS2B01G299600 chrUn 194984208 194984898 690 True 1016.0 1016 93.089000 1988 2690 1 chrUn.!!$R1 702

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
125 126 0.179137 TCTTGTCGATGCTGGCTACG 60.179 55.0 0.0 0.53 0.00 3.51 F
859 867 0.252103 AGACCCGAGGTGGAAAGCTA 60.252 55.0 0.0 0.00 42.00 3.32 F
1636 1650 0.953727 GCGATCCATTTGCAGCCATA 59.046 50.0 0.0 0.00 34.56 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 1445 0.327591 CTGCCTCTCCAAAGCCTTCT 59.672 55.000 0.0 0.0 0.0 2.85 R
1721 1735 0.595095 GGGTCTTCTTGTGCTGCTTG 59.405 55.000 0.0 0.0 0.0 4.01 R
2546 6435 4.361783 TGGTGGAAAGGATGAGATCTACA 58.638 43.478 0.0 0.0 0.0 2.74 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
125 126 0.179137 TCTTGTCGATGCTGGCTACG 60.179 55.000 0.00 0.53 0.00 3.51
207 209 4.735369 ACACCACAAAATCCACCTCATAA 58.265 39.130 0.00 0.00 0.00 1.90
215 217 3.845781 ATCCACCTCATAACGCAGAAT 57.154 42.857 0.00 0.00 0.00 2.40
312 314 3.010696 GGGATTTTGAGGTCTCCTTCCTT 59.989 47.826 4.24 0.00 35.20 3.36
493 499 6.556212 TCATCACTTCTATCTCAACTTCGAC 58.444 40.000 0.00 0.00 0.00 4.20
793 801 6.153510 AGGCAAGAATAAAAGGAATTGGTCTC 59.846 38.462 0.00 0.00 0.00 3.36
859 867 0.252103 AGACCCGAGGTGGAAAGCTA 60.252 55.000 0.00 0.00 42.00 3.32
1116 1124 6.605594 ACTTGAACCACTAAAACTGAATTCCA 59.394 34.615 2.27 0.00 0.00 3.53
1178 1186 7.016465 ACCTTGGTTACCTGTTATTGTAGTGTA 59.984 37.037 2.07 0.00 0.00 2.90
1266 1276 7.513371 AGATATTCCAGGAGAAAGTAGTACG 57.487 40.000 0.00 0.00 38.21 3.67
1267 1277 7.061688 AGATATTCCAGGAGAAAGTAGTACGT 58.938 38.462 0.00 0.00 38.21 3.57
1280 1290 9.247861 AGAAAGTAGTACGTTTTCTATCCCTTA 57.752 33.333 13.22 0.00 38.88 2.69
1298 1308 6.489603 TCCCTTATTTTTGTCCTTGCTATCA 58.510 36.000 0.00 0.00 0.00 2.15
1506 1519 4.946772 GGAAGAAGAAAATGAGGAAGAGGG 59.053 45.833 0.00 0.00 0.00 4.30
1510 1523 4.328118 AGAAAATGAGGAAGAGGGCATT 57.672 40.909 0.00 0.00 32.75 3.56
1636 1650 0.953727 GCGATCCATTTGCAGCCATA 59.046 50.000 0.00 0.00 34.56 2.74
1651 1665 5.123820 TGCAGCCATACTTCAAGATGTTAAC 59.876 40.000 0.00 0.00 0.00 2.01
1877 1891 0.319405 GCTTGTGCTTCCAGGCATTT 59.681 50.000 0.00 0.00 44.34 2.32
2101 2119 7.274468 GTGATGTCTAGACTGCCATATAAATCG 59.726 40.741 23.01 0.00 0.00 3.34
2138 2318 9.797642 TGATAAATTATGCTCCTGTTACATCAT 57.202 29.630 0.00 0.00 0.00 2.45
2211 2441 3.817647 GGGTTGATAGCATCCTGACATTC 59.182 47.826 7.95 0.00 34.83 2.67
2343 2573 0.248866 GTGGTGTTTTTGGCTGGTCG 60.249 55.000 0.00 0.00 0.00 4.79
2401 2633 7.125811 TCCTTGTATCTAACTCCTGCTTATTGT 59.874 37.037 0.00 0.00 0.00 2.71
2480 6369 5.730550 TCCAGTAATGGTGTGACATAACTC 58.269 41.667 9.41 0.00 0.00 3.01
2546 6435 4.869861 GTCAAAAGTGTTGAAAAGCATGGT 59.130 37.500 0.00 0.00 0.00 3.55
2736 6629 3.243068 CCTTTCCTTCGTCAAAGTGTTGG 60.243 47.826 0.00 0.00 35.29 3.77
2846 6743 5.981088 TGCTTATTGGCAGATGAGAAAAA 57.019 34.783 5.91 0.00 37.29 1.94
2899 6796 0.396435 TGTGGCGTGGAAGATGAAGT 59.604 50.000 0.00 0.00 0.00 3.01
2920 6822 6.469782 AGTTCAATGGAAAAGCTTCTTTGA 57.530 33.333 0.00 5.22 34.62 2.69
2936 6838 6.753744 GCTTCTTTGAAAGATTGTGAACTTGT 59.246 34.615 8.64 0.00 37.38 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 3.181544 GCTAAAAATCCTTTCGCGTTTGC 60.182 43.478 5.77 0.00 37.91 3.68
133 134 7.095017 CCTCGATATGGAGCTAAAAATCCTTTC 60.095 40.741 9.12 0.00 36.50 2.62
207 209 5.107337 CGCATGTTGAGATATTATTCTGCGT 60.107 40.000 0.00 0.00 35.28 5.24
215 217 2.799978 CGTGGCGCATGTTGAGATATTA 59.200 45.455 10.83 0.00 0.00 0.98
493 499 4.829064 TTCCGAAAATTTGTCCACTCAG 57.171 40.909 0.00 0.00 0.00 3.35
708 716 4.584688 GCACAAGCAAGAATGGGC 57.415 55.556 0.00 0.00 39.03 5.36
793 801 1.006805 GCTCATCGTCCTCATCGGG 60.007 63.158 0.00 0.00 0.00 5.14
840 848 0.252103 TAGCTTTCCACCTCGGGTCT 60.252 55.000 0.00 0.00 31.02 3.85
859 867 0.542702 CCACCCTTGAAGGCACCATT 60.543 55.000 5.50 0.00 32.73 3.16
1250 1260 7.701501 GGATAGAAAACGTACTACTTTCTCCTG 59.298 40.741 13.86 0.00 39.50 3.86
1266 1276 9.639601 CAAGGACAAAAATAAGGGATAGAAAAC 57.360 33.333 0.00 0.00 0.00 2.43
1267 1277 8.311109 GCAAGGACAAAAATAAGGGATAGAAAA 58.689 33.333 0.00 0.00 0.00 2.29
1280 1290 7.278875 TGGTTTTTGATAGCAAGGACAAAAAT 58.721 30.769 15.83 0.00 46.26 1.82
1283 1293 5.860941 TGGTTTTTGATAGCAAGGACAAA 57.139 34.783 9.69 0.00 35.04 2.83
1411 1424 8.311836 CCTTCTACACTTTCTCCTGTTACAATA 58.688 37.037 0.00 0.00 0.00 1.90
1416 1429 4.838986 AGCCTTCTACACTTTCTCCTGTTA 59.161 41.667 0.00 0.00 0.00 2.41
1432 1445 0.327591 CTGCCTCTCCAAAGCCTTCT 59.672 55.000 0.00 0.00 0.00 2.85
1506 1519 3.944015 AGCTGTTCCTGTTGAGATAATGC 59.056 43.478 0.00 0.00 0.00 3.56
1510 1523 3.089284 TCGAGCTGTTCCTGTTGAGATA 58.911 45.455 0.00 0.00 0.00 1.98
1606 1619 2.746277 GGATCGCTTGGTGCCGTT 60.746 61.111 0.00 0.00 38.78 4.44
1611 1624 0.527113 TGCAAATGGATCGCTTGGTG 59.473 50.000 0.00 0.00 0.00 4.17
1636 1650 3.503748 GCTGGCTGTTAACATCTTGAAGT 59.496 43.478 9.13 0.00 0.00 3.01
1651 1665 1.159713 TCACGTTGTTCAGCTGGCTG 61.160 55.000 15.13 15.58 44.86 4.85
1706 1720 2.667874 TTGTCGCGCCATTGCTGA 60.668 55.556 0.00 0.00 34.43 4.26
1721 1735 0.595095 GGGTCTTCTTGTGCTGCTTG 59.405 55.000 0.00 0.00 0.00 4.01
2080 2098 6.026947 ACCGATTTATATGGCAGTCTAGAC 57.973 41.667 15.41 15.41 0.00 2.59
2101 2119 9.331282 GGAGCATAATTTATCACCTATCATACC 57.669 37.037 0.00 0.00 0.00 2.73
2319 2549 2.613977 CCAGCCAAAAACACCACAACAA 60.614 45.455 0.00 0.00 0.00 2.83
2343 2573 6.677781 TCAGCACAAGTTTGGCTTATATAC 57.322 37.500 5.48 0.00 35.27 1.47
2401 2633 3.520721 TCTTTCATCTGCCAATGAGGAGA 59.479 43.478 8.34 8.34 41.22 3.71
2546 6435 4.361783 TGGTGGAAAGGATGAGATCTACA 58.638 43.478 0.00 0.00 0.00 2.74
2823 6720 6.534475 TTTTTCTCATCTGCCAATAAGCAT 57.466 33.333 0.00 0.00 43.09 3.79
2846 6743 8.655901 TCCCATTTTCTAATTAACCTTGCTTTT 58.344 29.630 0.00 0.00 0.00 2.27
2847 6744 8.201242 TCCCATTTTCTAATTAACCTTGCTTT 57.799 30.769 0.00 0.00 0.00 3.51
2858 6755 6.153340 CACACCACTGATCCCATTTTCTAATT 59.847 38.462 0.00 0.00 0.00 1.40
2899 6796 7.555087 TCTTTCAAAGAAGCTTTTCCATTGAA 58.445 30.769 11.00 11.00 36.43 2.69
2920 6822 8.697507 ATAGAAAGGACAAGTTCACAATCTTT 57.302 30.769 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.