Multiple sequence alignment - TraesCS3B01G224300

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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 TraesCS3B01G224300 chr3B 100.000 3498 0 0 1 3498 300391158 300394655 0 6460
1 TraesCS3B01G224300 chr3B 96.338 2785 88 11 723 3498 603030135 603027356 0 4566
2 TraesCS3B01G224300 chr3B 96.222 2779 92 6 723 3498 129925464 129922696 0 4538
3 TraesCS3B01G224300 chr3B 97.095 723 21 0 1 723 129926237 129925515 0 1219
4 TraesCS3B01G224300 chr3B 96.961 724 20 2 1 723 603030908 603030186 0 1214
5 TraesCS3B01G224300 chr3B 95.310 725 24 5 1 723 236257119 236256403 0 1142
6 TraesCS3B01G224300 chr7B 96.259 2780 96 6 723 3498 475125015 475122240 0 4551
7 TraesCS3B01G224300 chr7B 93.047 2790 165 20 723 3498 202721701 202718927 0 4050
8 TraesCS3B01G224300 chr7B 96.542 723 22 2 1 723 475125785 475125066 0 1194
9 TraesCS3B01G224300 chr7B 95.436 723 28 5 1 723 463804456 463805173 0 1147
10 TraesCS3B01G224300 chr4B 96.223 2780 96 7 723 3498 494454614 494457388 0 4543
11 TraesCS3B01G224300 chr4B 92.931 2787 170 20 723 3496 310221436 310218664 0 4030
12 TraesCS3B01G224300 chr4B 95.297 723 30 4 1 723 224376009 224376727 0 1144
13 TraesCS3B01G224300 chr4B 95.297 723 30 4 1 723 310222204 310221486 0 1144
14 TraesCS3B01G224300 chr2B 92.829 2789 167 23 723 3498 506419876 506417108 0 4012
15 TraesCS3B01G224300 chr2B 92.760 2790 171 21 723 3498 300239132 300236360 0 4004
16 TraesCS3B01G224300 chr1B 92.716 2787 177 20 723 3498 256711429 256714200 0 3999
17 TraesCS3B01G224300 chr6B 96.547 724 23 2 1 723 489233717 489234439 0 1197
18 TraesCS3B01G224300 chr5B 95.297 723 30 4 1 723 299224982 299224264 0 1144


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 TraesCS3B01G224300 chr3B 300391158 300394655 3497 False 6460.0 6460 100.0000 1 3498 1 chr3B.!!$F1 3497
1 TraesCS3B01G224300 chr3B 603027356 603030908 3552 True 2890.0 4566 96.6495 1 3498 2 chr3B.!!$R3 3497
2 TraesCS3B01G224300 chr3B 129922696 129926237 3541 True 2878.5 4538 96.6585 1 3498 2 chr3B.!!$R2 3497
3 TraesCS3B01G224300 chr3B 236256403 236257119 716 True 1142.0 1142 95.3100 1 723 1 chr3B.!!$R1 722
4 TraesCS3B01G224300 chr7B 202718927 202721701 2774 True 4050.0 4050 93.0470 723 3498 1 chr7B.!!$R1 2775
5 TraesCS3B01G224300 chr7B 475122240 475125785 3545 True 2872.5 4551 96.4005 1 3498 2 chr7B.!!$R2 3497
6 TraesCS3B01G224300 chr7B 463804456 463805173 717 False 1147.0 1147 95.4360 1 723 1 chr7B.!!$F1 722
7 TraesCS3B01G224300 chr4B 494454614 494457388 2774 False 4543.0 4543 96.2230 723 3498 1 chr4B.!!$F2 2775
8 TraesCS3B01G224300 chr4B 310218664 310222204 3540 True 2587.0 4030 94.1140 1 3496 2 chr4B.!!$R1 3495
9 TraesCS3B01G224300 chr4B 224376009 224376727 718 False 1144.0 1144 95.2970 1 723 1 chr4B.!!$F1 722
10 TraesCS3B01G224300 chr2B 506417108 506419876 2768 True 4012.0 4012 92.8290 723 3498 1 chr2B.!!$R2 2775
11 TraesCS3B01G224300 chr2B 300236360 300239132 2772 True 4004.0 4004 92.7600 723 3498 1 chr2B.!!$R1 2775
12 TraesCS3B01G224300 chr1B 256711429 256714200 2771 False 3999.0 3999 92.7160 723 3498 1 chr1B.!!$F1 2775
13 TraesCS3B01G224300 chr6B 489233717 489234439 722 False 1197.0 1197 96.5470 1 723 1 chr6B.!!$F1 722
14 TraesCS3B01G224300 chr5B 299224264 299224982 718 True 1144.0 1144 95.2970 1 723 1 chr5B.!!$R1 722

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
741 851 3.386402 GGGAAAAACATTTGTCCTGGACA 59.614 43.478 25.12 25.12 42.96 4.02 F
1198 1310 0.600518 CCAGATGATGAGCAGGCTCG 60.601 60.000 15.83 0.61 45.48 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 2509 0.362179 CATGACTCGTACGTTGCGTG 59.638 55.0 16.05 12.39 41.39 5.34 R
3009 3145 2.490328 TCTTTGCTTTTCCTGTTGCG 57.510 45.0 0.00 0.00 0.00 4.85 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
307 308 8.607713 TCTAGTGGTAAAATAATCTCAAACCCA 58.392 33.333 0.00 0.00 0.00 4.51
741 851 3.386402 GGGAAAAACATTTGTCCTGGACA 59.614 43.478 25.12 25.12 42.96 4.02
1004 1116 2.436646 CCGAAGCAAGGCGATGGT 60.437 61.111 0.00 0.00 0.00 3.55
1198 1310 0.600518 CCAGATGATGAGCAGGCTCG 60.601 60.000 15.83 0.61 45.48 5.03
1212 1324 3.470888 CTCGGGATGAAGGGCGGT 61.471 66.667 0.00 0.00 0.00 5.68
1217 1329 2.514824 GATGAAGGGCGGTGGCTC 60.515 66.667 0.00 0.00 41.19 4.70
1266 1378 2.323059 GAGTACACCGACGAGGAAAAC 58.677 52.381 8.56 3.71 45.00 2.43
1459 1571 7.789202 ACTATAGTCTATGAAGTGGATGCAT 57.211 36.000 0.00 0.00 0.00 3.96
1464 1576 6.363065 AGTCTATGAAGTGGATGCATGATTT 58.637 36.000 2.46 0.00 0.00 2.17
1669 1782 8.754991 TTAAAAGATCTTTGGTGAAGTGGTAA 57.245 30.769 21.15 9.05 36.70 2.85
1682 1795 6.099269 GGTGAAGTGGTAAAGGTCCATATCTA 59.901 42.308 0.00 0.00 37.30 1.98
1753 1866 4.154737 TGCACAAAGATGTATCAAGCACTC 59.845 41.667 0.00 0.00 37.82 3.51
1809 1924 2.440409 ACTTGAATCAAGGAGCGCATT 58.560 42.857 24.77 0.00 44.81 3.56
1856 1971 8.587608 TGATTCTCTAATTTGGTGAAGCATTTT 58.412 29.630 10.24 0.00 31.06 1.82
2200 2328 2.420022 CCCCAACAACTTCATCGACATC 59.580 50.000 0.00 0.00 0.00 3.06
2204 2332 3.685139 ACAACTTCATCGACATCCAGT 57.315 42.857 0.00 0.00 0.00 4.00
2454 2582 5.196695 GGATATTTCAAAAGAGCAGGAGGT 58.803 41.667 0.00 0.00 0.00 3.85
2528 2656 6.152492 TGCATTCATTATGTTGAACCAGCTAA 59.848 34.615 0.00 0.00 38.37 3.09
2557 2685 6.631016 TGATATGTGTGTCCTTAGTCTTGTC 58.369 40.000 0.00 0.00 0.00 3.18
2840 2972 4.702131 CAGGCTAACTAAGGACAAAAGCAT 59.298 41.667 0.00 0.00 0.00 3.79
2880 3012 3.260632 TCAGTACAGCTTAGGCATGAACA 59.739 43.478 0.00 0.00 41.70 3.18
2983 3118 8.604035 CATTCAGTACTAAAAACATCGTGCTAT 58.396 33.333 0.00 0.00 0.00 2.97
3171 3310 5.991861 TCCCTAAAACAGTGACACACTAAA 58.008 37.500 8.59 0.00 43.43 1.85
3223 3362 5.994250 TCAGTACAACTAGGACTATACGGT 58.006 41.667 0.00 0.00 0.00 4.83
3269 3408 1.202818 GCCTGGAGAAGAACCACAACT 60.203 52.381 0.00 0.00 33.57 3.16
3307 3446 7.381323 AGGCCAAAAACTAAATCAAAGAGATG 58.619 34.615 5.01 0.00 36.96 2.90
3333 3472 9.159470 GTAAGTTCGACAAAAGAGAAAAATCAG 57.841 33.333 0.00 0.00 0.00 2.90
3355 3494 5.063438 CAGAAGAAACACAACAGAAAGACGA 59.937 40.000 0.00 0.00 0.00 4.20
3378 3517 2.844122 AGCCTCGAACAACACAAAAC 57.156 45.000 0.00 0.00 0.00 2.43
3468 3607 9.371136 AGTGCTATGATGATACCAATTAATACG 57.629 33.333 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 137 8.637986 AGGAAACTTAGCATAATTGACAAACAA 58.362 29.630 0.00 0.00 39.59 2.83
307 308 5.864198 TTTATAACTTAGGTTGGGGGTGT 57.136 39.130 0.00 0.00 36.92 4.16
355 359 5.865085 TCCTGCTGTTTTAGTACTGATGTT 58.135 37.500 5.39 0.00 0.00 2.71
741 851 1.275573 GGTGGCCTCGAAGAACTAACT 59.724 52.381 3.32 0.00 34.09 2.24
790 900 0.179150 GCCGTTTTTGCAGTGTGTCA 60.179 50.000 0.00 0.00 0.00 3.58
956 1068 6.430000 GTGGGCTTGTGATAGAGAAGTTTTTA 59.570 38.462 0.00 0.00 0.00 1.52
1038 1150 2.800544 GTTGCTGCTCTTGTTCGAAGTA 59.199 45.455 0.00 0.00 0.00 2.24
1082 1194 1.411246 TGGTGTACTCGTGCTTCTTGT 59.589 47.619 0.00 0.00 0.00 3.16
1538 1651 9.565090 TGCATAAAGTTCAGAATGCTATAATCT 57.435 29.630 7.12 0.00 43.98 2.40
1669 1782 5.309020 ACATGTGCATCTAGATATGGACCTT 59.691 40.000 13.48 1.58 44.83 3.50
1682 1795 6.882610 TTAGTTTGAGAAACATGTGCATCT 57.117 33.333 0.00 3.77 43.79 2.90
1801 1916 4.319333 CCAGAGTCAATGATTAATGCGCTC 60.319 45.833 9.73 0.00 0.00 5.03
1856 1971 6.612247 TTTTTCTATCTTCGTTGCTTCACA 57.388 33.333 0.00 0.00 0.00 3.58
2200 2328 1.815003 GGATCTTTCCACTTGCACTGG 59.185 52.381 3.47 3.47 42.12 4.00
2381 2509 0.362179 CATGACTCGTACGTTGCGTG 59.638 55.000 16.05 12.39 41.39 5.34
2393 2521 3.849911 TGTCGATTGTCTTCCATGACTC 58.150 45.455 0.00 0.00 37.79 3.36
2454 2582 2.827755 TGCAGTGGTAGTAGGGATCAA 58.172 47.619 0.00 0.00 0.00 2.57
2528 2656 8.484214 AGACTAAGGACACACATATCATATGT 57.516 34.615 4.29 4.29 0.00 2.29
2557 2685 6.129717 CGAAAGCAAACTACAAATCTGAAACG 60.130 38.462 0.00 0.00 0.00 3.60
2668 2796 3.490348 AGCTAGCAAACTTGTTGGATGT 58.510 40.909 18.83 0.00 0.00 3.06
2808 2939 5.070047 GTCCTTAGTTAGCCTGCCACTATTA 59.930 44.000 0.95 0.00 0.00 0.98
2840 2972 2.885266 CTGAGCGTCCAAGGCTACTATA 59.115 50.000 0.00 0.00 39.71 1.31
2931 3064 3.955551 TCCTTGGCCGAAACTTAGTTTTT 59.044 39.130 11.88 0.00 35.77 1.94
3009 3145 2.490328 TCTTTGCTTTTCCTGTTGCG 57.510 45.000 0.00 0.00 0.00 4.85
3212 3351 4.392940 TCCTAGCACTTACCGTATAGTCC 58.607 47.826 0.00 0.00 0.00 3.85
3223 3362 9.337396 CATTGTTTGGTATAATCCTAGCACTTA 57.663 33.333 0.00 0.00 0.00 2.24
3307 3446 9.159470 CTGATTTTTCTCTTTTGTCGAACTTAC 57.841 33.333 0.00 0.00 0.00 2.34
3333 3472 5.464965 TCGTCTTTCTGTTGTGTTTCTTC 57.535 39.130 0.00 0.00 0.00 2.87
3355 3494 2.902705 TGTGTTGTTCGAGGCTAGTT 57.097 45.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.