Multiple sequence alignment - TraesCS5A01G193500

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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 TraesCS5A01G193500 chr5A 100.000 3509 0 0 1 3509 396706067 396709575 0.000000e+00 6481
1 TraesCS5A01G193500 chr5B 92.451 2676 122 38 886 3509 340718969 340721616 0.000000e+00 3749
2 TraesCS5A01G193500 chr5B 91.019 913 44 13 1 887 340717760 340718660 0.000000e+00 1197
3 TraesCS5A01G193500 chr5D 91.721 1691 79 22 1872 3509 299422914 299424596 0.000000e+00 2290
4 TraesCS5A01G193500 chr5D 96.976 992 24 5 886 1873 299420458 299421447 0.000000e+00 1661
5 TraesCS5A01G193500 chr5D 92.146 904 50 4 1 887 299419268 299420167 0.000000e+00 1256
6 TraesCS5A01G193500 chr2A 85.372 417 56 4 2086 2498 41462840 41462425 9.000000e-116 427
7 TraesCS5A01G193500 chr2B 84.675 385 58 1 2086 2470 63783369 63782986 1.980000e-102 383


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 TraesCS5A01G193500 chr5A 396706067 396709575 3508 False 6481.000000 6481 100.000000 1 3509 1 chr5A.!!$F1 3508
1 TraesCS5A01G193500 chr5B 340717760 340721616 3856 False 2473.000000 3749 91.735000 1 3509 2 chr5B.!!$F1 3508
2 TraesCS5A01G193500 chr5D 299419268 299424596 5328 False 1735.666667 2290 93.614333 1 3509 3 chr5D.!!$F1 3508

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
205 214 1.177895 TTGAATTTGCGAGCAGGCCA 61.178 50.0 5.01 0.0 0.00 5.36 F
1539 1880 0.987294 ATCCCTTGTCTGTGTCCAGG 59.013 55.0 0.00 0.0 39.31 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 3699 5.129634 TGCAAAACAGGTCAGTCAAGATAA 58.870 37.5 0.0 0.0 0.00 1.75 R
3206 5053 0.171231 TCTCAGCGTCAAGTCCGATG 59.829 55.0 0.0 0.0 42.62 3.84 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
28 33 1.361204 TGGCAGAGGGTGATCTTTGA 58.639 50.000 0.00 0.00 0.00 2.69
54 59 1.588404 CGAGACGGATTTGGTCGATTG 59.412 52.381 0.00 0.00 39.38 2.67
70 75 3.113322 CGATTGCTCAATCAATTGCCTG 58.887 45.455 19.07 0.33 45.60 4.85
71 76 3.181494 CGATTGCTCAATCAATTGCCTGA 60.181 43.478 19.07 4.95 45.60 3.86
87 92 2.201732 CCTGATGGTATCGTGGTTTCG 58.798 52.381 0.00 0.00 0.00 3.46
164 169 3.935828 GCTTTCTTGATCGCTTCTTAGGT 59.064 43.478 0.00 0.00 0.00 3.08
165 170 4.201763 GCTTTCTTGATCGCTTCTTAGGTG 60.202 45.833 0.00 0.00 0.00 4.00
166 171 4.537135 TTCTTGATCGCTTCTTAGGTGT 57.463 40.909 0.00 0.00 0.00 4.16
188 193 3.356290 AGTTATAGTTTGCAGGCCCTTG 58.644 45.455 0.00 0.00 0.00 3.61
205 214 1.177895 TTGAATTTGCGAGCAGGCCA 61.178 50.000 5.01 0.00 0.00 5.36
222 231 4.024556 CAGGCCATTAAAGAGTAGATTGCG 60.025 45.833 5.01 0.00 0.00 4.85
234 243 1.937191 AGATTGCGGAATTTTGGGGT 58.063 45.000 2.86 0.00 0.00 4.95
235 244 2.256306 AGATTGCGGAATTTTGGGGTT 58.744 42.857 2.86 0.00 0.00 4.11
325 334 9.690913 AGATTACTTTGGTAATTAAACCCCTAC 57.309 33.333 3.43 0.00 45.39 3.18
364 373 4.509600 GCTAGCCTGAGTTGTCATGTATTC 59.490 45.833 2.29 0.00 30.18 1.75
395 421 6.183360 GCTGTATCTCTCCATAGTTTGTACCA 60.183 42.308 0.00 0.00 0.00 3.25
411 437 8.458843 AGTTTGTACCATTCGATCCAAAATAAG 58.541 33.333 0.00 0.00 0.00 1.73
473 499 2.396590 TTTTGTGGATCGGAGGTAGC 57.603 50.000 0.00 0.00 0.00 3.58
498 524 4.104738 CCTATTAGCTCCCAGGAATTCCAA 59.895 45.833 26.22 9.48 38.89 3.53
502 528 1.549950 GCTCCCAGGAATTCCAACCAA 60.550 52.381 26.22 6.82 38.89 3.67
543 569 2.254546 TAAGTCACCCACTGCACTTG 57.745 50.000 0.00 0.00 34.56 3.16
576 602 5.957842 TTCACAATTCACCAATCTGTACC 57.042 39.130 0.00 0.00 0.00 3.34
694 721 6.645705 CATGTGTTGCATCATGAATTTATGC 58.354 36.000 16.71 10.63 44.94 3.14
740 767 8.500773 ACTGTTTCAACTTGTAATGGTATTACG 58.499 33.333 7.08 0.00 0.00 3.18
869 896 5.521010 TGTACAAGTTTAGCACGCCATATAC 59.479 40.000 0.00 0.00 0.00 1.47
1194 1531 7.306515 CGATGTGAAACCAAAACAAAGGTATTG 60.307 37.037 0.00 0.00 37.07 1.90
1199 1536 7.547370 TGAAACCAAAACAAAGGTATTGTCTTG 59.453 33.333 1.41 1.41 37.07 3.02
1207 1544 7.539712 ACAAAGGTATTGTCTTGTATCATCG 57.460 36.000 0.00 0.00 0.00 3.84
1257 1594 8.715088 GCTGAAGCAATCTTAACAAATGAAAAT 58.285 29.630 0.00 0.00 41.59 1.82
1317 1656 9.366216 GTTCTACAAATGAAAAACACTTTCCTT 57.634 29.630 0.00 0.00 0.00 3.36
1539 1880 0.987294 ATCCCTTGTCTGTGTCCAGG 59.013 55.000 0.00 0.00 39.31 4.45
1604 1945 7.040201 ACTGAAGCTGCAGATTTTCTATTTCAA 60.040 33.333 29.21 0.36 39.20 2.69
1643 1984 4.245660 TGAGATTCACGTGCTTCCTTTAG 58.754 43.478 11.67 0.00 0.00 1.85
1674 2015 8.745464 TTGTTAACACCAGTTTCTTGTTTAAC 57.255 30.769 8.07 0.00 39.15 2.01
1882 3693 1.895798 TGTCCTGTTGTCCTAGAGCAG 59.104 52.381 0.00 0.00 0.00 4.24
1888 3699 3.953612 CTGTTGTCCTAGAGCAGAGAGAT 59.046 47.826 0.00 0.00 0.00 2.75
2031 3843 2.424601 TCAATGCAGGCAAGTCTAATGC 59.575 45.455 0.00 0.00 43.08 3.56
2112 3924 2.905959 TTGATGCGTGCTCAGAATTG 57.094 45.000 0.00 0.00 0.00 2.32
2178 3990 2.045926 ATGAGGTCGGCAGCCAAC 60.046 61.111 13.30 2.05 0.00 3.77
2370 4182 3.245371 ACATCATGGACATGGTTCTGGTT 60.245 43.478 11.98 0.00 39.24 3.67
2409 4221 0.253044 TGAAAGAGATTGGGGCCTCG 59.747 55.000 0.84 0.00 34.75 4.63
2463 4275 2.438434 GGGGCCGTCAAGGATGTG 60.438 66.667 0.00 0.00 45.00 3.21
2490 4302 2.048601 CAGATCAGAGATGGGCTCCTT 58.951 52.381 0.00 0.00 45.10 3.36
2526 4338 4.033709 TCTAAGAGGAGGACCATGGAAAG 58.966 47.826 21.47 0.00 38.94 2.62
2636 4448 6.200475 GCAAGGTCGTGAGTAATTTATCTACC 59.800 42.308 0.00 0.00 0.00 3.18
2644 4456 7.432545 CGTGAGTAATTTATCTACCTGTGTGAG 59.567 40.741 0.00 0.00 0.00 3.51
2747 4566 3.950395 AGTTTAGCCAGATTCCTGAATGC 59.050 43.478 0.00 0.00 43.02 3.56
2780 4599 1.246056 TTGCAAGTGAGCCTGGATGC 61.246 55.000 0.00 0.00 0.00 3.91
2782 4601 1.654954 GCAAGTGAGCCTGGATGCTG 61.655 60.000 0.00 0.00 42.95 4.41
2853 4676 6.485313 TGTTTTGTGATGAGTTTATCTCGGTT 59.515 34.615 0.00 0.00 45.46 4.44
2863 4686 3.904800 TTATCTCGGTTGGATTGAGCA 57.095 42.857 0.00 0.00 0.00 4.26
2864 4687 2.322355 ATCTCGGTTGGATTGAGCAG 57.678 50.000 0.00 0.00 0.00 4.24
2867 4690 1.938577 CTCGGTTGGATTGAGCAGATG 59.061 52.381 0.00 0.00 0.00 2.90
2868 4691 1.554617 TCGGTTGGATTGAGCAGATGA 59.445 47.619 0.00 0.00 0.00 2.92
2869 4692 1.667724 CGGTTGGATTGAGCAGATGAC 59.332 52.381 0.00 0.00 0.00 3.06
2870 4693 2.679059 CGGTTGGATTGAGCAGATGACT 60.679 50.000 0.00 0.00 0.00 3.41
2871 4694 3.350833 GGTTGGATTGAGCAGATGACTT 58.649 45.455 0.00 0.00 0.00 3.01
2911 4745 1.800805 ATGAGGTGCAGTTGTTCTCG 58.199 50.000 0.00 0.00 0.00 4.04
2914 4748 0.687354 AGGTGCAGTTGTTCTCGGAT 59.313 50.000 0.00 0.00 0.00 4.18
2916 4750 2.501723 AGGTGCAGTTGTTCTCGGATAT 59.498 45.455 0.00 0.00 0.00 1.63
3080 4927 6.237901 ACACATGATAAAGCTTGGTCTTGTA 58.762 36.000 21.84 4.08 30.71 2.41
3100 4947 1.615883 ACTGGTAGCACTGACACTGAG 59.384 52.381 0.00 0.00 0.00 3.35
3111 4958 2.998670 CTGACACTGAGTATGCTTGTGG 59.001 50.000 17.19 5.12 35.40 4.17
3195 5042 0.895100 TGATGGAGCAAGTTGGGCAC 60.895 55.000 4.75 0.00 0.00 5.01
3220 5067 3.195698 GGGCATCGGACTTGACGC 61.196 66.667 0.00 0.00 0.00 5.19
3346 5194 4.542735 GGGTTACCGATCAAAAACAACTG 58.457 43.478 0.00 0.00 0.00 3.16
3361 5213 3.198068 ACAACTGCTCCTATTGCATACG 58.802 45.455 0.00 0.00 39.86 3.06
3366 5218 2.158971 TGCTCCTATTGCATACGCTGAA 60.159 45.455 0.00 0.00 39.64 3.02
3404 5261 3.254166 TCAAGATTTTGTGCCTCAGAAGC 59.746 43.478 0.00 0.00 35.73 3.86
3417 5274 1.068474 CAGAAGCCGTCCGTAAGTTG 58.932 55.000 0.00 0.00 0.00 3.16
3423 5280 1.143969 CCGTCCGTAAGTTGATCGGC 61.144 60.000 9.89 6.02 43.35 5.54
3424 5281 0.457166 CGTCCGTAAGTTGATCGGCA 60.457 55.000 9.89 0.00 43.35 5.69
3425 5282 0.997196 GTCCGTAAGTTGATCGGCAC 59.003 55.000 9.89 6.83 43.35 5.01
3426 5283 0.604073 TCCGTAAGTTGATCGGCACA 59.396 50.000 9.89 0.00 43.35 4.57
3427 5284 1.001068 TCCGTAAGTTGATCGGCACAA 59.999 47.619 9.89 0.00 43.35 3.33
3430 5310 2.412325 CGTAAGTTGATCGGCACAAACC 60.412 50.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.496899 TTCAAAGATCACCCTCTGCC 57.503 50.000 0.00 0.00 0.00 4.85
14 15 5.643777 TCTCGAATTTTCAAAGATCACCCTC 59.356 40.000 0.00 0.00 0.00 4.30
28 33 3.124636 CGACCAAATCCGTCTCGAATTTT 59.875 43.478 0.00 0.00 0.00 1.82
54 59 2.429610 ACCATCAGGCAATTGATTGAGC 59.570 45.455 10.34 0.00 39.46 4.26
70 75 2.199236 GGACGAAACCACGATACCATC 58.801 52.381 0.00 0.00 37.03 3.51
71 76 1.551430 TGGACGAAACCACGATACCAT 59.449 47.619 0.00 0.00 34.77 3.55
87 92 3.747976 GGGGCGCACATGTTGGAC 61.748 66.667 13.89 0.00 0.00 4.02
116 121 2.726241 CGCATAACACATCACGATCGAT 59.274 45.455 24.34 0.00 0.00 3.59
164 169 3.521937 AGGGCCTGCAAACTATAACTACA 59.478 43.478 4.50 0.00 0.00 2.74
165 170 4.152284 AGGGCCTGCAAACTATAACTAC 57.848 45.455 4.50 0.00 0.00 2.73
166 171 4.226394 TCAAGGGCCTGCAAACTATAACTA 59.774 41.667 6.92 0.00 0.00 2.24
188 193 0.174162 AATGGCCTGCTCGCAAATTC 59.826 50.000 3.32 0.00 0.00 2.17
205 214 8.190784 CCAAAATTCCGCAATCTACTCTTTAAT 58.809 33.333 0.00 0.00 0.00 1.40
259 268 9.897744 CTTAAAAATCTGCAATTAGACACTGAA 57.102 29.630 0.00 0.00 0.00 3.02
261 270 8.025445 AGCTTAAAAATCTGCAATTAGACACTG 58.975 33.333 0.00 0.00 0.00 3.66
364 373 4.702612 ACTATGGAGAGATACAGCCATACG 59.297 45.833 0.00 0.00 41.19 3.06
395 421 5.515106 TGGGGAACTTATTTTGGATCGAAT 58.485 37.500 0.00 0.00 0.00 3.34
473 499 4.505742 GGAATTCCTGGGAGCTAATAGGTG 60.506 50.000 17.73 0.00 0.00 4.00
498 524 2.520968 GTGAAGGGGCCACTTGGT 59.479 61.111 29.04 0.00 37.57 3.67
502 528 2.208349 AGAGGTGAAGGGGCCACT 59.792 61.111 0.00 0.00 35.05 4.00
543 569 6.454795 TGGTGAATTGTGAAAGAAATAAGCC 58.545 36.000 0.00 0.00 0.00 4.35
576 602 6.109359 AGTACAGCTTTGCCAGAATAACTAG 58.891 40.000 0.00 0.00 0.00 2.57
694 721 6.169094 ACAGTGAGACCTCTGAAAATACATG 58.831 40.000 0.00 0.00 37.35 3.21
869 896 7.967908 AGGATAACCATCAATAAGACTACAGG 58.032 38.462 0.00 0.00 38.94 4.00
1044 1381 6.323739 ACTTCCCAAAAGTTTCTTTGATAGCA 59.676 34.615 0.00 0.00 38.35 3.49
1539 1880 9.911980 GATAAAAGTACGAACATAAGGCTAAAC 57.088 33.333 0.00 0.00 0.00 2.01
1604 1945 8.299570 GTGAATCTCAGTAAATTGACAACCATT 58.700 33.333 0.00 0.00 0.00 3.16
1643 1984 6.313744 AGAAACTGGTGTTAACAAGCATAC 57.686 37.500 10.51 0.00 34.96 2.39
1703 2044 6.676237 AATTGCACACAAAAGGGTAAAAAG 57.324 33.333 0.00 0.00 39.77 2.27
1882 3693 6.463995 ACAGGTCAGTCAAGATAATCTCTC 57.536 41.667 0.00 0.00 31.03 3.20
1888 3699 5.129634 TGCAAAACAGGTCAGTCAAGATAA 58.870 37.500 0.00 0.00 0.00 1.75
2031 3843 6.623486 TGTATGTGGATTGAAAGCAAATGAG 58.377 36.000 0.00 0.00 37.59 2.90
2112 3924 9.229784 CACATTCATGTTAGATATGCAAAAGAC 57.770 33.333 0.00 0.00 39.39 3.01
2370 4182 2.291209 TGGTGTCGAAGTACTGGGTA 57.709 50.000 0.00 0.00 0.00 3.69
2409 4221 2.528041 ACACCGAAGAAGACTTGGAC 57.472 50.000 0.00 0.00 36.39 4.02
2448 4260 3.134127 GCCACATCCTTGACGGCC 61.134 66.667 0.00 0.00 38.33 6.13
2463 4275 1.430479 CATCTCTGATCTGCGATGCC 58.570 55.000 16.50 0.00 0.00 4.40
2490 4302 2.828520 CTCTTAGAGAGTGTTGGCCTGA 59.171 50.000 2.53 0.00 37.57 3.86
2526 4338 3.758554 TCTTGCAAAACAGAAGCTATCCC 59.241 43.478 0.00 0.00 0.00 3.85
2596 4408 3.067106 ACCTTGCCAAATATCTATCGCG 58.933 45.455 0.00 0.00 0.00 5.87
2636 4448 5.044428 ACTTAACGTAGTAGCTCACACAG 57.956 43.478 0.00 0.00 45.00 3.66
2644 4456 9.737025 CTAAAATTCACAACTTAACGTAGTAGC 57.263 33.333 0.00 0.00 45.00 3.58
2823 4646 9.683069 GAGATAAACTCATCACAAAACACAAAT 57.317 29.630 0.00 0.00 44.36 2.32
2837 4660 5.989477 TCAATCCAACCGAGATAAACTCAT 58.011 37.500 0.00 0.00 45.14 2.90
2853 4676 2.026542 AGCAAGTCATCTGCTCAATCCA 60.027 45.455 0.00 0.00 32.98 3.41
2896 4730 2.380084 TATCCGAGAACAACTGCACC 57.620 50.000 0.00 0.00 0.00 5.01
2911 4745 6.985117 TCAAAATCTGCTATTGCCAATATCC 58.015 36.000 0.00 0.00 38.71 2.59
2914 4748 6.550481 TCCATCAAAATCTGCTATTGCCAATA 59.450 34.615 0.00 0.00 38.71 1.90
2916 4750 4.710865 TCCATCAAAATCTGCTATTGCCAA 59.289 37.500 0.00 0.00 38.71 4.52
3069 4916 3.006967 AGTGCTACCAGTACAAGACCAAG 59.993 47.826 0.00 0.00 32.98 3.61
3080 4927 1.615883 CTCAGTGTCAGTGCTACCAGT 59.384 52.381 2.50 0.00 0.00 4.00
3111 4958 1.610522 ACTGGAGTTGCATCAGTTTGC 59.389 47.619 6.67 0.00 38.44 3.68
3114 4961 1.242076 GCACTGGAGTTGCATCAGTT 58.758 50.000 8.98 0.00 39.43 3.16
3115 4962 0.607489 GGCACTGGAGTTGCATCAGT 60.607 55.000 6.67 6.67 41.81 3.41
3116 4963 1.310933 GGGCACTGGAGTTGCATCAG 61.311 60.000 0.00 1.93 34.91 2.90
3117 4964 1.303561 GGGCACTGGAGTTGCATCA 60.304 57.895 0.00 0.00 0.00 3.07
3118 4965 1.001641 AGGGCACTGGAGTTGCATC 60.002 57.895 0.00 0.00 0.00 3.91
3129 4976 2.703675 CTTCAACCAGGCAGGGCACT 62.704 60.000 0.00 0.00 43.89 4.40
3206 5053 0.171231 TCTCAGCGTCAAGTCCGATG 59.829 55.000 0.00 0.00 42.62 3.84
3220 5067 1.078567 GGAAGCTGCAGGGTCTCAG 60.079 63.158 17.12 0.00 0.00 3.35
3234 5081 0.537188 AGTACATGGACGCCTGGAAG 59.463 55.000 1.41 0.00 0.00 3.46
3341 5189 2.032549 GCGTATGCAATAGGAGCAGTTG 60.033 50.000 0.89 0.00 46.36 3.16
3346 5194 2.154854 TCAGCGTATGCAATAGGAGC 57.845 50.000 10.11 0.00 46.23 4.70
3361 5213 3.253230 AGCTGTTTGTGTTTTGTTCAGC 58.747 40.909 0.00 0.00 44.44 4.26
3366 5218 4.782019 TCTTGAGCTGTTTGTGTTTTGT 57.218 36.364 0.00 0.00 0.00 2.83
3396 5249 0.526662 ACTTACGGACGGCTTCTGAG 59.473 55.000 6.84 0.00 34.26 3.35
3417 5274 0.727398 GCTGTAGGTTTGTGCCGATC 59.273 55.000 0.00 0.00 0.00 3.69
3430 5310 1.134995 TCGACAGATTGCCTGCTGTAG 60.135 52.381 0.00 0.00 46.81 2.74


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

AutoCloner maintained by Alex Coulton.