Multiple sequence alignment - TraesCS5B01G144700

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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 TraesCS5B01G144700 chr5B 100.000 3533 0 0 1 3533 271953527 271949995 0.000000e+00 6525
1 TraesCS5B01G144700 chr5D 95.135 3515 109 24 33 3533 233035090 233038556 0.000000e+00 5487
2 TraesCS5B01G144700 chr5D 90.182 275 25 1 3051 3325 175767573 175767301 1.210000e-94 357
3 TraesCS5B01G144700 chr5A 95.443 3182 95 18 1 3165 321928413 321925265 0.000000e+00 5027
4 TraesCS5B01G144700 chr5A 95.181 332 12 1 3202 3533 321924763 321924436 4.040000e-144 521
5 TraesCS5B01G144700 chr5A 89.003 291 28 2 3050 3340 352899992 352899706 1.210000e-94 357
6 TraesCS5B01G144700 chr5A 88.927 289 30 1 3052 3340 275102295 275102009 4.340000e-94 355
7 TraesCS5B01G144700 chr6A 89.796 294 26 3 3051 3343 591650320 591650030 1.200000e-99 374
8 TraesCS5B01G144700 chr6A 90.217 276 24 1 3050 3325 398132947 398132675 1.210000e-94 357
9 TraesCS5B01G144700 chr7A 90.876 274 24 1 3051 3324 503448774 503449046 2.000000e-97 366
10 TraesCS5B01G144700 chr7A 87.960 299 30 3 3046 3344 109457889 109458181 7.260000e-92 348
11 TraesCS5B01G144700 chr3A 90.217 276 25 1 3050 3325 541673 541946 3.350000e-95 359


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 TraesCS5B01G144700 chr5B 271949995 271953527 3532 True 6525 6525 100.000 1 3533 1 chr5B.!!$R1 3532
1 TraesCS5B01G144700 chr5D 233035090 233038556 3466 False 5487 5487 95.135 33 3533 1 chr5D.!!$F1 3500
2 TraesCS5B01G144700 chr5A 321924436 321928413 3977 True 2774 5027 95.312 1 3533 2 chr5A.!!$R3 3532

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
155 167 0.170561 CAATTCCGACGTCGTCCTCT 59.829 55.000 33.49 13.27 37.74 3.69 F
157 169 0.450983 ATTCCGACGTCGTCCTCTTC 59.549 55.000 33.49 0.00 37.74 2.87 F
435 456 0.587489 GCTGCTCGTTAATGAAGCGC 60.587 55.000 0.00 0.00 0.00 5.92 F
604 626 1.303074 GGAAAACACGGGGGACTCC 60.303 63.158 0.00 0.00 0.00 3.85 F
1821 1844 0.547471 TGGAAGGGCCAGATGTCAGA 60.547 55.000 6.18 0.00 43.33 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1407 0.745486 TCATCTGAAGCATGCCACCG 60.745 55.000 15.66 5.46 0.00 4.94 R
1694 1717 1.514657 CCAATGCCACGTGATTGCG 60.515 57.895 19.30 9.93 37.94 4.85 R
1821 1844 1.970640 GGATTCCCAACAAAAGGTGCT 59.029 47.619 0.00 0.00 0.00 4.40 R
2356 2379 2.047274 CAGCCATCGACGGTGGTT 60.047 61.111 27.18 19.89 39.01 3.67 R
3408 3897 2.492088 GGATGGTAGCAAACTGGTTTCC 59.508 50.000 0.00 0.00 0.00 3.13 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
153 165 1.214589 CCAATTCCGACGTCGTCCT 59.785 57.895 33.49 16.21 37.74 3.85
155 167 0.170561 CAATTCCGACGTCGTCCTCT 59.829 55.000 33.49 13.27 37.74 3.69
156 168 0.886563 AATTCCGACGTCGTCCTCTT 59.113 50.000 33.49 17.41 37.74 2.85
157 169 0.450983 ATTCCGACGTCGTCCTCTTC 59.549 55.000 33.49 0.00 37.74 2.87
158 170 1.580845 TTCCGACGTCGTCCTCTTCC 61.581 60.000 33.49 0.00 37.74 3.46
159 171 2.484203 CGACGTCGTCCTCTTCCC 59.516 66.667 29.08 0.00 34.11 3.97
160 172 2.883621 GACGTCGTCCTCTTCCCC 59.116 66.667 14.60 0.00 0.00 4.81
161 173 1.678300 GACGTCGTCCTCTTCCCCT 60.678 63.158 14.60 0.00 0.00 4.79
197 209 0.591741 CGCCGAGATTGGTCTACGAC 60.592 60.000 0.00 0.00 33.97 4.34
294 307 2.612000 TCTTCGAACCCTTGGACCTTA 58.388 47.619 0.00 0.00 0.00 2.69
366 386 4.564769 TCCAAATCCGCGCAAAATATTTTC 59.435 37.500 10.53 5.59 0.00 2.29
381 401 2.476126 TTTTCCCCTCGCGTTTGATA 57.524 45.000 5.77 0.00 0.00 2.15
426 446 2.707849 GGGAGTCGGCTGCTCGTTA 61.708 63.158 8.88 0.00 34.00 3.18
427 447 1.214589 GGAGTCGGCTGCTCGTTAA 59.785 57.895 0.00 0.00 34.00 2.01
435 456 0.587489 GCTGCTCGTTAATGAAGCGC 60.587 55.000 0.00 0.00 0.00 5.92
459 480 1.475392 CGATCTCGGTACCTCTCCTGT 60.475 57.143 10.90 0.00 35.37 4.00
460 481 1.950909 GATCTCGGTACCTCTCCTGTG 59.049 57.143 10.90 0.00 0.00 3.66
519 540 2.293318 TGGATCTCTTGCGGCAGGT 61.293 57.895 12.05 0.00 0.00 4.00
532 553 1.816074 GGCAGGTTGTTCCGTGATAA 58.184 50.000 0.00 0.00 41.99 1.75
604 626 1.303074 GGAAAACACGGGGGACTCC 60.303 63.158 0.00 0.00 0.00 3.85
674 696 4.000325 TCCAGTTTGGTCATGTGAATACG 59.000 43.478 0.00 0.00 39.03 3.06
682 704 4.576873 TGGTCATGTGAATACGTTGTTTGT 59.423 37.500 0.00 0.00 0.00 2.83
689 711 4.611366 GTGAATACGTTGTTTGTTAGCTGC 59.389 41.667 0.00 0.00 0.00 5.25
727 749 6.259608 GCAGATATGCTTAATCGCTTATCCAT 59.740 38.462 4.74 0.00 42.99 3.41
731 753 9.846248 GATATGCTTAATCGCTTATCCATTTTT 57.154 29.630 9.65 0.00 39.35 1.94
773 795 7.496263 TGGTTTAATGTACGCTGCATATTTCTA 59.504 33.333 0.00 0.00 0.00 2.10
782 804 3.496130 GCTGCATATTTCTACTGCGTCAT 59.504 43.478 0.00 0.00 38.75 3.06
794 816 1.662629 CTGCGTCATTAACTGGAGCAG 59.337 52.381 0.10 0.10 43.66 4.24
867 890 7.121911 CGTGCTCAACAATGTATCTGATAAAG 58.878 38.462 0.00 0.00 0.00 1.85
877 900 5.529289 TGTATCTGATAAAGACCTGACCCT 58.471 41.667 0.00 0.00 37.88 4.34
914 937 6.539103 GGACATACCTCTGTTTCCATTTAGAC 59.461 42.308 0.00 0.00 35.41 2.59
917 940 4.652822 ACCTCTGTTTCCATTTAGACCAC 58.347 43.478 0.00 0.00 0.00 4.16
931 954 6.554334 TTTAGACCACTTGTTATCTGCAAC 57.446 37.500 0.00 0.00 0.00 4.17
1037 1060 4.727507 ATCAGACACAATCTAGCGACTT 57.272 40.909 0.00 0.00 35.15 3.01
1045 1068 2.483583 ATCTAGCGACTTTGAGCTCG 57.516 50.000 9.64 0.00 43.44 5.03
1173 1196 4.636249 AGGCTACTGTGCTTAATGATAGC 58.364 43.478 0.00 0.00 39.10 2.97
1233 1256 2.159028 ACAAAGAAGGCGGAGATCTAGC 60.159 50.000 12.76 12.76 0.00 3.42
1384 1407 2.158726 TCTACACCAAACCAGTCCCAAC 60.159 50.000 0.00 0.00 0.00 3.77
1508 1531 3.129462 TCAGATGCTTCTCTAGGTCAACG 59.871 47.826 0.00 0.00 0.00 4.10
1821 1844 0.547471 TGGAAGGGCCAGATGTCAGA 60.547 55.000 6.18 0.00 43.33 3.27
2076 2099 6.184789 ACCATGCATGCATCTATATCATTCA 58.815 36.000 30.07 0.00 33.90 2.57
2356 2379 1.068588 AGCAGTCAAACAGAGCACGTA 59.931 47.619 0.00 0.00 0.00 3.57
2357 2380 1.864711 GCAGTCAAACAGAGCACGTAA 59.135 47.619 0.00 0.00 0.00 3.18
2442 2465 3.658757 TTGTGCTTTGCAAATCCTACC 57.341 42.857 13.23 0.00 41.47 3.18
2651 2674 5.112686 GGTCAATGTGATAAGTGAGGAGAC 58.887 45.833 0.00 0.00 0.00 3.36
2795 2818 5.104776 TCCTCTGCTTCATATTGCTGTAACT 60.105 40.000 0.00 0.00 0.00 2.24
2887 2910 1.001406 CCAGACTCCAGTTCACCTCAC 59.999 57.143 0.00 0.00 0.00 3.51
2960 2983 4.635765 TGCTCATGTATAGGTTTGTCTTGC 59.364 41.667 0.00 0.00 0.00 4.01
3196 3413 5.957771 TCCATTGAGTCTAGGCTAATGTT 57.042 39.130 17.62 0.00 0.00 2.71
3198 3415 6.349300 TCCATTGAGTCTAGGCTAATGTTTC 58.651 40.000 17.62 0.06 0.00 2.78
3284 3773 2.001076 ACCAAAGGGCTCCAAAGAAG 57.999 50.000 0.00 0.00 37.90 2.85
3285 3774 1.217942 ACCAAAGGGCTCCAAAGAAGT 59.782 47.619 0.00 0.00 37.90 3.01
3385 3874 1.474077 CATGAGGTAAAACAGGGCAGC 59.526 52.381 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 139 1.381076 GTCGGAATTGGGGGTTGGA 59.619 57.895 0.00 0.00 0.00 3.53
153 165 2.444140 GGCTCGGCTAGGGGAAGA 60.444 66.667 0.00 0.00 0.00 2.87
197 209 1.144936 GGGAACAGCGATCTGGGAG 59.855 63.158 0.00 0.00 44.54 4.30
294 307 2.033299 CAGCAAACAATCAGTTGACGGT 59.967 45.455 0.00 0.00 41.19 4.83
366 386 1.798813 GCTAATATCAAACGCGAGGGG 59.201 52.381 15.93 0.00 0.00 4.79
381 401 0.461339 CACTACAACGGGGCGCTAAT 60.461 55.000 7.64 0.00 0.00 1.73
422 442 0.909174 TCGTACGCGCTTCATTAACG 59.091 50.000 11.24 2.40 38.14 3.18
423 443 2.787680 AGATCGTACGCGCTTCATTAAC 59.212 45.455 11.24 0.00 38.14 2.01
426 446 1.478137 GAGATCGTACGCGCTTCATT 58.522 50.000 11.24 0.00 38.14 2.57
427 447 0.657659 CGAGATCGTACGCGCTTCAT 60.658 55.000 11.24 0.00 38.14 2.57
435 456 1.791785 GAGAGGTACCGAGATCGTACG 59.208 57.143 9.53 9.53 37.74 3.67
519 540 4.517453 CACCCTCTTTTTATCACGGAACAA 59.483 41.667 0.00 0.00 0.00 2.83
532 553 4.770010 TCAATTTAATCGCCACCCTCTTTT 59.230 37.500 0.00 0.00 0.00 2.27
573 594 5.009210 CCCGTGTTTTCCTTCATTAGTTTCA 59.991 40.000 0.00 0.00 0.00 2.69
578 599 2.752903 CCCCCGTGTTTTCCTTCATTAG 59.247 50.000 0.00 0.00 0.00 1.73
604 626 2.475864 CACACCAACCAAATCATTTGCG 59.524 45.455 4.40 1.22 39.31 4.85
674 696 2.490328 TGCAGCAGCTAACAAACAAC 57.510 45.000 1.76 0.00 42.74 3.32
682 704 4.297299 GCAAATAGAATGCAGCAGCTAA 57.703 40.909 10.79 0.00 43.29 3.09
734 756 9.908152 CGTACATTAAACCAGATGACTATGATA 57.092 33.333 0.00 0.00 0.00 2.15
794 816 3.038710 CTGACAAAGAAAAGCAAGCGAC 58.961 45.455 0.00 0.00 0.00 5.19
828 850 2.163412 TGAGCACGCACAAAAGTTCTTT 59.837 40.909 0.00 0.00 0.00 2.52
867 890 2.026262 TGCTTAATTCCAGGGTCAGGTC 60.026 50.000 0.00 0.00 0.00 3.85
914 937 2.413239 CGCTGTTGCAGATAACAAGTGG 60.413 50.000 0.00 0.00 39.81 4.00
917 940 1.466360 GGCGCTGTTGCAGATAACAAG 60.466 52.381 7.64 0.00 39.81 3.16
931 954 0.039165 GAAAAGAACAAGGGGCGCTG 60.039 55.000 7.64 0.00 0.00 5.18
978 1001 7.222999 GGCATCTTGTACTAGTAAATCTGACAC 59.777 40.741 3.61 0.00 0.00 3.67
979 1002 7.265673 GGCATCTTGTACTAGTAAATCTGACA 58.734 38.462 3.61 0.00 0.00 3.58
1037 1060 2.669569 GGCTGGCAACGAGCTCAA 60.670 61.111 15.40 0.00 44.79 3.02
1045 1068 1.588082 CATCTGGTTGGCTGGCAAC 59.412 57.895 31.81 31.81 0.00 4.17
1173 1196 3.820467 TGCTGGTTGTTACATCTCTTTGG 59.180 43.478 0.00 0.00 0.00 3.28
1233 1256 5.181009 TCATTAGATTCCAGACTTGCAGTG 58.819 41.667 0.00 0.00 0.00 3.66
1245 1268 6.149142 GTGAGAATGCATCCTCATTAGATTCC 59.851 42.308 19.28 0.00 40.95 3.01
1384 1407 0.745486 TCATCTGAAGCATGCCACCG 60.745 55.000 15.66 5.46 0.00 4.94
1508 1531 2.050144 TCTCCCTTCCCATCATGCTAC 58.950 52.381 0.00 0.00 0.00 3.58
1694 1717 1.514657 CCAATGCCACGTGATTGCG 60.515 57.895 19.30 9.93 37.94 4.85
1774 1797 4.160065 TGCCATCAAGTTGGTCATATTTGG 59.840 41.667 2.34 0.00 39.11 3.28
1821 1844 1.970640 GGATTCCCAACAAAAGGTGCT 59.029 47.619 0.00 0.00 0.00 4.40
2261 2284 7.873719 TTAAACATGTCCTGAGTTTCTTCAA 57.126 32.000 0.00 0.00 36.85 2.69
2356 2379 2.047274 CAGCCATCGACGGTGGTT 60.047 61.111 27.18 19.89 39.01 3.67
2357 2380 2.391724 AAACAGCCATCGACGGTGGT 62.392 55.000 27.18 12.17 39.01 4.16
2442 2465 2.093106 AGTCGCCTTCTACCACTACTG 58.907 52.381 0.00 0.00 0.00 2.74
2651 2674 3.506067 GGTTACAGGAACAACTCAATGGG 59.494 47.826 0.00 0.00 40.09 4.00
2795 2818 6.579666 ACTTTGAAGCAGAGATTAATTGCA 57.420 33.333 12.02 0.00 40.22 4.08
2887 2910 4.088648 CAGCGCTGGTTAAATTTCTAACG 58.911 43.478 29.88 0.00 33.36 3.18
2960 2983 4.890158 ACTTATGGAAAAGCAAAAGGGG 57.110 40.909 0.00 0.00 0.00 4.79
3385 3874 2.535984 CCTTCTGCTTGCGTACTATTCG 59.464 50.000 0.00 0.00 0.00 3.34
3408 3897 2.492088 GGATGGTAGCAAACTGGTTTCC 59.508 50.000 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.