Multiple sequence alignment - TraesCS1B01G135800

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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 TraesCS1B01G135800 chr1B 100.000 2421 0 0 1 2421 173123432 173121012 0.000000e+00 4471.0
1 TraesCS1B01G135800 chr1B 91.176 68 5 1 1 67 110607308 110607241 9.220000e-15 91.6
2 TraesCS1B01G135800 chr4D 90.762 1797 71 35 43 1800 123142098 123140358 0.000000e+00 2311.0
3 TraesCS1B01G135800 chr4D 94.625 614 28 3 1812 2421 123101809 123101197 0.000000e+00 946.0
4 TraesCS1B01G135800 chr4D 94.915 177 8 1 1821 1997 123101974 123101799 2.370000e-70 276.0
5 TraesCS1B01G135800 chr4B 89.376 1826 107 39 43 1824 187727868 187726086 0.000000e+00 2217.0
6 TraesCS1B01G135800 chr4B 92.698 315 20 2 2064 2376 187724513 187724200 3.670000e-123 451.0
7 TraesCS1B01G135800 chr4A 87.679 1745 99 45 87 1777 446613310 446614992 0.000000e+00 1925.0
8 TraesCS1B01G135800 chr4A 92.564 659 31 7 1765 2417 446615018 446615664 0.000000e+00 929.0
9 TraesCS1B01G135800 chr4A 93.548 62 3 1 1 62 584810899 584810959 9.220000e-15 91.6
10 TraesCS1B01G135800 chr1A 93.219 1342 28 16 745 2075 121130073 121128784 0.000000e+00 1916.0
11 TraesCS1B01G135800 chr1A 93.595 687 19 4 43 705 121130756 121130071 0.000000e+00 1002.0
12 TraesCS1B01G135800 chr1A 96.542 347 11 1 2076 2421 121128686 121128340 7.510000e-160 573.0
13 TraesCS1B01G135800 chr7B 100.000 53 0 0 1 53 735303268 735303216 5.510000e-17 99.0
14 TraesCS1B01G135800 chr7B 100.000 53 0 0 1 53 735810981 735811033 5.510000e-17 99.0
15 TraesCS1B01G135800 chr5A 98.214 56 1 0 1 56 428189387 428189442 5.510000e-17 99.0
16 TraesCS1B01G135800 chr5A 94.286 35 2 0 642 676 78965550 78965516 1.000000e-03 54.7
17 TraesCS1B01G135800 chr7A 96.491 57 1 1 1 57 461522619 461522674 2.560000e-15 93.5
18 TraesCS1B01G135800 chr3A 91.304 69 4 2 1 69 402136004 402136070 2.560000e-15 93.5
19 TraesCS1B01G135800 chr3A 93.333 60 4 0 1 60 443203622 443203681 3.320000e-14 89.8
20 TraesCS1B01G135800 chr3D 90.909 66 6 0 1 66 458620474 458620409 3.320000e-14 89.8


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 TraesCS1B01G135800 chr1B 173121012 173123432 2420 True 4471.000000 4471 100.0000 1 2421 1 chr1B.!!$R2 2420
1 TraesCS1B01G135800 chr4D 123140358 123142098 1740 True 2311.000000 2311 90.7620 43 1800 1 chr4D.!!$R1 1757
2 TraesCS1B01G135800 chr4D 123101197 123101974 777 True 611.000000 946 94.7700 1812 2421 2 chr4D.!!$R2 609
3 TraesCS1B01G135800 chr4B 187724200 187727868 3668 True 1334.000000 2217 91.0370 43 2376 2 chr4B.!!$R1 2333
4 TraesCS1B01G135800 chr4A 446613310 446615664 2354 False 1427.000000 1925 90.1215 87 2417 2 chr4A.!!$F2 2330
5 TraesCS1B01G135800 chr1A 121128340 121130756 2416 True 1163.666667 1916 94.4520 43 2421 3 chr1A.!!$R1 2378

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
603 641 0.391263 AACCAGCTACCGCAGTAAGC 60.391 55.0 0.0 0.0 39.1 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 1621 1.529438 CGAAGTAAACCACACGCACAT 59.471 47.619 0.0 0.0 0.0 3.21 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
45 46 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
46 47 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
47 48 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
48 49 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
287 291 3.309682 CGTCTTGCAGTTGAGAAAGTCAA 59.690 43.478 0.00 0.00 43.26 3.18
534 547 5.597806 CGTGCTGAACTATTATTAGTGGGA 58.402 41.667 0.00 0.00 38.69 4.37
588 626 6.761099 TTGTCTTTGTGCTTAACTTAACCA 57.239 33.333 0.00 0.00 0.00 3.67
589 627 6.371809 TGTCTTTGTGCTTAACTTAACCAG 57.628 37.500 0.00 0.00 0.00 4.00
590 628 5.212934 GTCTTTGTGCTTAACTTAACCAGC 58.787 41.667 0.00 0.00 0.00 4.85
591 629 5.008712 GTCTTTGTGCTTAACTTAACCAGCT 59.991 40.000 0.00 0.00 33.15 4.24
592 630 6.204108 GTCTTTGTGCTTAACTTAACCAGCTA 59.796 38.462 0.00 0.00 33.15 3.32
593 631 5.934935 TTGTGCTTAACTTAACCAGCTAC 57.065 39.130 0.00 0.00 33.15 3.58
594 632 4.320870 TGTGCTTAACTTAACCAGCTACC 58.679 43.478 0.00 0.00 33.15 3.18
595 633 3.370061 GTGCTTAACTTAACCAGCTACCG 59.630 47.826 0.00 0.00 33.15 4.02
596 634 2.350804 GCTTAACTTAACCAGCTACCGC 59.649 50.000 0.00 0.00 0.00 5.68
597 635 3.592059 CTTAACTTAACCAGCTACCGCA 58.408 45.455 0.00 0.00 39.10 5.69
598 636 2.094762 AACTTAACCAGCTACCGCAG 57.905 50.000 0.00 0.00 39.10 5.18
599 637 0.974383 ACTTAACCAGCTACCGCAGT 59.026 50.000 0.00 0.00 39.10 4.40
600 638 2.173519 ACTTAACCAGCTACCGCAGTA 58.826 47.619 0.00 0.00 39.10 2.74
601 639 2.564062 ACTTAACCAGCTACCGCAGTAA 59.436 45.455 0.00 0.00 39.10 2.24
602 640 2.953466 TAACCAGCTACCGCAGTAAG 57.047 50.000 0.00 0.00 39.10 2.34
603 641 0.391263 AACCAGCTACCGCAGTAAGC 60.391 55.000 0.00 0.00 39.10 3.09
604 642 1.258445 ACCAGCTACCGCAGTAAGCT 61.258 55.000 0.00 0.00 42.61 3.74
607 645 1.405821 CAGCTACCGCAGTAAGCTAGT 59.594 52.381 0.00 0.00 42.61 2.57
608 646 2.617308 CAGCTACCGCAGTAAGCTAGTA 59.383 50.000 0.00 0.00 42.61 1.82
612 650 2.454538 ACCGCAGTAAGCTAGTAACCT 58.545 47.619 0.00 0.00 42.61 3.50
613 651 3.624777 ACCGCAGTAAGCTAGTAACCTA 58.375 45.455 0.00 0.00 42.61 3.08
671 739 9.364653 GTACTCCCTCTGTAAAGAATTATAGGA 57.635 37.037 0.00 0.00 32.71 2.94
710 780 6.072119 CCGCCCCTAAGGATAATCAAAATTAC 60.072 42.308 0.00 0.00 38.24 1.89
712 782 6.780522 GCCCCTAAGGATAATCAAAATTACCA 59.219 38.462 0.00 0.00 38.24 3.25
714 784 8.638873 CCCCTAAGGATAATCAAAATTACCAAC 58.361 37.037 0.00 0.00 38.24 3.77
737 807 2.825532 GGAGAGCTTTCTGTCTCTGTCT 59.174 50.000 4.01 0.00 39.57 3.41
1111 1196 3.167485 TGGATGCTTCTCCTTGCAAAAT 58.833 40.909 0.00 0.00 42.74 1.82
1112 1197 4.343231 TGGATGCTTCTCCTTGCAAAATA 58.657 39.130 0.00 0.00 42.74 1.40
1113 1198 4.400251 TGGATGCTTCTCCTTGCAAAATAG 59.600 41.667 0.00 0.00 42.74 1.73
1114 1199 4.400567 GGATGCTTCTCCTTGCAAAATAGT 59.599 41.667 0.00 0.00 42.74 2.12
1115 1200 5.590259 GGATGCTTCTCCTTGCAAAATAGTA 59.410 40.000 0.00 0.00 42.74 1.82
1116 1201 6.238593 GGATGCTTCTCCTTGCAAAATAGTAG 60.239 42.308 0.00 2.97 42.74 2.57
1117 1202 4.943705 TGCTTCTCCTTGCAAAATAGTAGG 59.056 41.667 0.00 0.00 36.15 3.18
1118 1203 5.186198 GCTTCTCCTTGCAAAATAGTAGGA 58.814 41.667 0.00 0.12 34.07 2.94
1142 1227 6.968250 AGTACTCTCGTGCTATTTATGTACC 58.032 40.000 0.00 0.00 34.12 3.34
1145 1230 5.593095 ACTCTCGTGCTATTTATGTACCTCA 59.407 40.000 0.00 0.00 0.00 3.86
1148 1233 5.779922 TCGTGCTATTTATGTACCTCATCC 58.220 41.667 0.00 0.00 37.91 3.51
1149 1234 4.621460 CGTGCTATTTATGTACCTCATCCG 59.379 45.833 0.00 0.00 37.91 4.18
1204 1289 5.353956 TCAATTCCTATTGTGGTGATGAACG 59.646 40.000 0.00 0.00 41.54 3.95
1250 1335 4.697756 TCGCCCGTTGCAGGAAGG 62.698 66.667 0.00 0.00 41.33 3.46
1438 1534 1.021390 AAGCTGCATGCACTCGTACC 61.021 55.000 18.46 0.00 45.94 3.34
1439 1535 2.802667 GCTGCATGCACTCGTACCG 61.803 63.158 18.46 5.54 42.31 4.02
1440 1536 1.446099 CTGCATGCACTCGTACCGT 60.446 57.895 18.46 0.00 0.00 4.83
1441 1537 1.413767 CTGCATGCACTCGTACCGTC 61.414 60.000 18.46 0.00 0.00 4.79
1540 1640 2.916111 CATGTGCGTGTGGTTTACTTC 58.084 47.619 0.00 0.00 0.00 3.01
1751 1870 8.370940 TCAGCTATTTATCCTCTAACATGAAGG 58.629 37.037 0.00 0.63 0.00 3.46
1936 2147 1.072332 TTGTTTCTGGGCAGCGCTA 59.928 52.632 10.99 0.00 0.00 4.26
1950 2161 1.591594 CGCTATGTGCCGGTCGATT 60.592 57.895 1.90 0.00 38.78 3.34
2311 4085 5.163237 GGTGCTATAGGTAGACCAAAATGGA 60.163 44.000 2.85 0.00 40.96 3.41
2316 4090 3.624777 AGGTAGACCAAAATGGAGCATG 58.375 45.455 2.85 0.00 40.96 4.06
2406 4180 6.846283 CGATGTTAAGACACTGTGAAAAGTTC 59.154 38.462 15.86 0.00 38.91 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
20 21 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
21 22 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
22 23 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
23 24 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
24 25 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
25 26 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
26 27 9.294614 ACTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
29 30 9.646522 TTTACTACTCCCTCCGTAAACTAATAT 57.353 33.333 0.00 0.00 29.71 1.28
30 31 9.474313 TTTTACTACTCCCTCCGTAAACTAATA 57.526 33.333 0.00 0.00 33.18 0.98
31 32 7.961326 TTTACTACTCCCTCCGTAAACTAAT 57.039 36.000 0.00 0.00 29.71 1.73
32 33 7.775053 TTTTACTACTCCCTCCGTAAACTAA 57.225 36.000 0.00 0.00 33.18 2.24
33 34 7.961326 ATTTTACTACTCCCTCCGTAAACTA 57.039 36.000 0.00 0.00 33.18 2.24
34 35 6.864151 ATTTTACTACTCCCTCCGTAAACT 57.136 37.500 0.00 0.00 33.18 2.66
35 36 8.470002 TCTTATTTTACTACTCCCTCCGTAAAC 58.530 37.037 0.00 0.00 33.18 2.01
36 37 8.593945 TCTTATTTTACTACTCCCTCCGTAAA 57.406 34.615 0.00 0.00 32.00 2.01
37 38 8.593945 TTCTTATTTTACTACTCCCTCCGTAA 57.406 34.615 0.00 0.00 0.00 3.18
38 39 8.055181 TCTTCTTATTTTACTACTCCCTCCGTA 58.945 37.037 0.00 0.00 0.00 4.02
39 40 6.894103 TCTTCTTATTTTACTACTCCCTCCGT 59.106 38.462 0.00 0.00 0.00 4.69
40 41 7.344095 TCTTCTTATTTTACTACTCCCTCCG 57.656 40.000 0.00 0.00 0.00 4.63
41 42 9.602568 CTTTCTTCTTATTTTACTACTCCCTCC 57.397 37.037 0.00 0.00 0.00 4.30
534 547 9.198475 AGCTGATCTTTCTGAAAAATATCCAAT 57.802 29.630 4.18 0.00 0.00 3.16
595 633 6.396450 AGTGTTTAGGTTACTAGCTTACTGC 58.604 40.000 0.00 0.00 43.29 4.40
596 634 8.828688 AAAGTGTTTAGGTTACTAGCTTACTG 57.171 34.615 0.00 0.00 33.36 2.74
597 635 9.842775 AAAAAGTGTTTAGGTTACTAGCTTACT 57.157 29.630 0.00 0.00 33.36 2.24
671 739 1.208776 GGGGCGGTTACATGTTACTCT 59.791 52.381 14.15 0.00 0.00 3.24
681 749 3.325716 TGATTATCCTTAGGGGCGGTTAC 59.674 47.826 0.00 0.00 34.39 2.50
710 780 2.038295 AGACAGAAAGCTCTCCAGTTGG 59.962 50.000 0.00 0.00 0.00 3.77
712 782 3.006752 CAGAGACAGAAAGCTCTCCAGTT 59.993 47.826 0.00 0.00 39.36 3.16
714 784 2.562298 ACAGAGACAGAAAGCTCTCCAG 59.438 50.000 0.00 0.00 39.36 3.86
1069 1146 8.859156 CATCCATTAACGTCAAAAACTAATTGG 58.141 33.333 0.00 0.00 0.00 3.16
1076 1153 6.149633 AGAAGCATCCATTAACGTCAAAAAC 58.850 36.000 0.00 0.00 0.00 2.43
1204 1289 2.599848 CGGTCGGCGAATCAAATCAATC 60.600 50.000 12.92 0.00 0.00 2.67
1250 1335 1.405821 CTCCGTCAGATCAGGGTACAC 59.594 57.143 0.00 0.00 0.00 2.90
1336 1421 2.584391 GGCCACCTCGAACTGACCT 61.584 63.158 0.00 0.00 0.00 3.85
1339 1424 4.373116 GCGGCCACCTCGAACTGA 62.373 66.667 2.24 0.00 0.00 3.41
1521 1621 1.529438 CGAAGTAAACCACACGCACAT 59.471 47.619 0.00 0.00 0.00 3.21
1751 1870 4.098416 GCAATTTGTTCCTTCGCTGTATC 58.902 43.478 0.00 0.00 0.00 2.24
1936 2147 2.202878 CCGAATCGACCGGCACAT 60.203 61.111 14.03 0.00 40.54 3.21
1950 2161 3.138930 GATGTAGAGCCTGCGCCGA 62.139 63.158 4.18 0.00 34.57 5.54
2311 4085 6.719370 TGGAAAACCATTTACTTAGACATGCT 59.281 34.615 0.00 0.00 30.12 3.79
2316 4090 9.419297 GGAAATTGGAAAACCATTTACTTAGAC 57.581 33.333 0.00 0.00 30.12 2.59
2338 4112 8.848474 AAAAATCTCAGACTATTTCTCGGAAA 57.152 30.769 2.25 2.25 28.96 3.13


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

AutoCloner maintained by Alex Coulton.