Multiple sequence alignment - TraesCS7A01G013200

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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 TraesCS7A01G013200 chr7A 100.000 3226 0 0 1 3226 5794069 5797294 0.000000e+00 5958.0
1 TraesCS7A01G013200 chrUn 99.411 3058 18 0 1 3058 225549660 225552717 0.000000e+00 5548.0
2 TraesCS7A01G013200 chrUn 99.174 3025 15 1 1 3025 221376535 221379549 0.000000e+00 5439.0
3 TraesCS7A01G013200 chrUn 99.138 3015 16 1 44 3058 306579200 306576196 0.000000e+00 5415.0
4 TraesCS7A01G013200 chrUn 99.340 1970 13 0 1089 3058 285617356 285619325 0.000000e+00 3567.0
5 TraesCS7A01G013200 chrUn 99.634 1912 7 0 44 1955 228681447 228683358 0.000000e+00 3493.0
6 TraesCS7A01G013200 chrUn 99.365 1575 10 0 1451 3025 387971966 387970392 0.000000e+00 2854.0
7 TraesCS7A01G013200 chrUn 80.205 586 59 25 582 1163 318137661 318138193 1.400000e-103 387.0
8 TraesCS7A01G013200 chrUn 80.205 586 59 25 582 1163 322967441 322966909 1.400000e-103 387.0
9 TraesCS7A01G013200 chr3A 90.342 1812 137 19 581 2383 629063356 629065138 0.000000e+00 2342.0
10 TraesCS7A01G013200 chr3B 89.818 1817 150 20 581 2386 744541677 744539885 0.000000e+00 2298.0
11 TraesCS7A01G013200 chr3B 91.422 1632 114 20 762 2383 747099095 747100710 0.000000e+00 2215.0
12 TraesCS7A01G013200 chr3B 84.397 141 16 5 581 719 747098959 747099095 2.020000e-27 134.0
13 TraesCS7A01G013200 chr3B 87.629 97 9 3 2695 2789 146880242 146880147 3.400000e-20 110.0
14 TraesCS7A01G013200 chr3D 89.292 1821 144 27 581 2386 560281374 560279590 0.000000e+00 2235.0
15 TraesCS7A01G013200 chr2D 92.970 569 38 1 1 569 625832168 625832734 0.000000e+00 828.0
16 TraesCS7A01G013200 chr2B 88.235 578 47 2 1 578 772123550 772122994 0.000000e+00 671.0
17 TraesCS7A01G013200 chr5D 78.290 889 121 43 2388 3224 271956716 271957584 1.030000e-139 507.0
18 TraesCS7A01G013200 chr4D 84.199 443 60 8 2782 3221 148771270 148770835 3.850000e-114 422.0
19 TraesCS7A01G013200 chr4D 88.043 92 8 3 2695 2784 399953508 399953418 4.400000e-19 106.0
20 TraesCS7A01G013200 chr7D 83.784 444 61 9 2785 3224 263657872 263658308 8.330000e-111 411.0
21 TraesCS7A01G013200 chr7D 93.671 79 5 0 749 827 5007563 5007641 5.650000e-23 119.0
22 TraesCS7A01G013200 chr5B 83.596 445 61 8 2782 3221 295663681 295664118 1.080000e-109 407.0
23 TraesCS7A01G013200 chr6D 89.474 95 7 3 2695 2788 80689880 80689788 2.030000e-22 117.0
24 TraesCS7A01G013200 chr1B 87.368 95 11 1 2695 2788 667984919 667984825 1.220000e-19 108.0
25 TraesCS7A01G013200 chr2A 88.608 79 6 2 2455 2530 388243415 388243337 3.430000e-15 93.5


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 TraesCS7A01G013200 chr7A 5794069 5797294 3225 False 5958.0 5958 100.0000 1 3226 1 chr7A.!!$F1 3225
1 TraesCS7A01G013200 chrUn 225549660 225552717 3057 False 5548.0 5548 99.4110 1 3058 1 chrUn.!!$F2 3057
2 TraesCS7A01G013200 chrUn 221376535 221379549 3014 False 5439.0 5439 99.1740 1 3025 1 chrUn.!!$F1 3024
3 TraesCS7A01G013200 chrUn 306576196 306579200 3004 True 5415.0 5415 99.1380 44 3058 1 chrUn.!!$R1 3014
4 TraesCS7A01G013200 chrUn 285617356 285619325 1969 False 3567.0 3567 99.3400 1089 3058 1 chrUn.!!$F4 1969
5 TraesCS7A01G013200 chrUn 228681447 228683358 1911 False 3493.0 3493 99.6340 44 1955 1 chrUn.!!$F3 1911
6 TraesCS7A01G013200 chrUn 387970392 387971966 1574 True 2854.0 2854 99.3650 1451 3025 1 chrUn.!!$R3 1574
7 TraesCS7A01G013200 chrUn 318137661 318138193 532 False 387.0 387 80.2050 582 1163 1 chrUn.!!$F5 581
8 TraesCS7A01G013200 chrUn 322966909 322967441 532 True 387.0 387 80.2050 582 1163 1 chrUn.!!$R2 581
9 TraesCS7A01G013200 chr3A 629063356 629065138 1782 False 2342.0 2342 90.3420 581 2383 1 chr3A.!!$F1 1802
10 TraesCS7A01G013200 chr3B 744539885 744541677 1792 True 2298.0 2298 89.8180 581 2386 1 chr3B.!!$R2 1805
11 TraesCS7A01G013200 chr3B 747098959 747100710 1751 False 1174.5 2215 87.9095 581 2383 2 chr3B.!!$F1 1802
12 TraesCS7A01G013200 chr3D 560279590 560281374 1784 True 2235.0 2235 89.2920 581 2386 1 chr3D.!!$R1 1805
13 TraesCS7A01G013200 chr2D 625832168 625832734 566 False 828.0 828 92.9700 1 569 1 chr2D.!!$F1 568
14 TraesCS7A01G013200 chr2B 772122994 772123550 556 True 671.0 671 88.2350 1 578 1 chr2B.!!$R1 577
15 TraesCS7A01G013200 chr5D 271956716 271957584 868 False 507.0 507 78.2900 2388 3224 1 chr5D.!!$F1 836

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
1112 1140 0.599991 CAGCGTGTAACACCTGCTCA 60.6 55.0 0.0 0.0 35.74 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3101 3188 2.095919 ACGGAATGCGTAAAGAACTTGC 60.096 45.455 0.0 0.0 0.0 4.01 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
1112 1140 0.599991 CAGCGTGTAACACCTGCTCA 60.600 55.000 0.00 0.00 35.74 4.26
1955 1993 0.738389 CAAGACTTGTTTGTGGCGGT 59.262 50.000 7.05 0.00 0.00 5.68
2872 2959 0.885879 CGTGTGTGACCCTAGCTACA 59.114 55.000 0.00 0.00 0.00 2.74
3065 3152 2.497273 TCACTTGCCTGAGATTCGATCA 59.503 45.455 0.00 0.00 0.00 2.92
3068 3155 3.387374 ACTTGCCTGAGATTCGATCATCT 59.613 43.478 0.00 0.00 36.12 2.90
3069 3156 3.382048 TGCCTGAGATTCGATCATCTG 57.618 47.619 4.34 0.00 33.36 2.90
3073 3160 5.011431 TGCCTGAGATTCGATCATCTGTATT 59.989 40.000 4.34 0.00 33.36 1.89
3074 3161 5.348179 GCCTGAGATTCGATCATCTGTATTG 59.652 44.000 4.34 0.00 33.36 1.90
3076 3163 6.094193 TGAGATTCGATCATCTGTATTGCT 57.906 37.500 4.34 0.00 33.36 3.91
3078 3165 7.834803 TGAGATTCGATCATCTGTATTGCTAT 58.165 34.615 4.34 0.00 33.36 2.97
3084 3171 7.986562 TCGATCATCTGTATTGCTATACCTAC 58.013 38.462 14.47 0.00 36.58 3.18
3101 3188 5.254339 ACCTACTTAATTCTCGTTACCGG 57.746 43.478 0.00 0.00 33.95 5.28
3114 3202 2.159934 CGTTACCGGCAAGTTCTTTACG 60.160 50.000 0.00 0.00 0.00 3.18
3134 3222 3.966154 CGCATTCCGTAGTACAAGATCT 58.034 45.455 0.38 0.00 0.00 2.75
3137 3225 4.537965 CATTCCGTAGTACAAGATCTCCG 58.462 47.826 0.00 0.00 0.00 4.63
3151 3239 5.923733 AGATCTCCGTGACTAAACTCATT 57.076 39.130 0.00 0.00 0.00 2.57
3153 3241 7.033530 AGATCTCCGTGACTAAACTCATTAG 57.966 40.000 0.00 0.00 45.48 1.73
3165 3253 7.601073 CTAAACTCATTAGTCACATGCTTGA 57.399 36.000 6.60 0.00 36.94 3.02
3168 3256 6.882610 ACTCATTAGTCACATGCTTGAAAA 57.117 33.333 6.60 0.00 0.00 2.29
3169 3257 7.458409 ACTCATTAGTCACATGCTTGAAAAT 57.542 32.000 6.60 0.00 0.00 1.82
3171 3259 8.362639 ACTCATTAGTCACATGCTTGAAAATTT 58.637 29.630 6.60 0.00 0.00 1.82
3172 3260 8.746922 TCATTAGTCACATGCTTGAAAATTTC 57.253 30.769 6.60 0.00 0.00 2.17
3173 3261 8.358895 TCATTAGTCACATGCTTGAAAATTTCA 58.641 29.630 4.03 4.03 38.04 2.69
3174 3262 9.146984 CATTAGTCACATGCTTGAAAATTTCAT 57.853 29.630 9.41 0.00 39.84 2.57
3209 3297 2.516227 CGAGAGGGCCCAGAGATATA 57.484 55.000 27.56 0.00 0.00 0.86
3211 3299 3.370104 CGAGAGGGCCCAGAGATATATT 58.630 50.000 27.56 0.00 0.00 1.28
3224 3312 5.349817 CAGAGATATATTTCCGTCACATGGC 59.650 44.000 0.00 0.00 0.00 4.40
3225 3313 4.245660 AGATATATTTCCGTCACATGGCG 58.754 43.478 0.00 0.00 43.72 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1112 1140 1.207791 CCAGAGTAGCCCTTGACCAT 58.792 55.000 0.00 0.00 0.00 3.55
1955 1993 3.570125 CCGCTGGAGATTGTATCTGTCTA 59.430 47.826 0.00 0.00 40.38 2.59
2455 2499 4.677983 TCCCTCACCCCTATATAAAGAGGA 59.322 45.833 7.12 0.00 42.87 3.71
2872 2959 6.331061 GTTATGTCTACATGTTCTCGAACCT 58.669 40.000 2.30 0.00 40.46 3.50
3073 3160 8.571336 GGTAACGAGAATTAAGTAGGTATAGCA 58.429 37.037 4.48 0.00 0.00 3.49
3074 3161 8.962857 GGTAACGAGAATTAAGTAGGTATAGC 57.037 38.462 0.00 0.00 0.00 2.97
3101 3188 2.095919 ACGGAATGCGTAAAGAACTTGC 60.096 45.455 0.00 0.00 0.00 4.01
3114 3202 4.299978 GGAGATCTTGTACTACGGAATGC 58.700 47.826 0.00 0.00 0.00 3.56
3124 3212 5.952033 AGTTTAGTCACGGAGATCTTGTAC 58.048 41.667 0.00 0.00 0.00 2.90
3130 3218 6.797454 ACTAATGAGTTTAGTCACGGAGATC 58.203 40.000 0.00 0.00 46.04 2.75
3151 3239 9.791820 CATATGAAATTTTCAAGCATGTGACTA 57.208 29.630 15.34 0.96 43.95 2.59
3153 3241 8.692110 TCATATGAAATTTTCAAGCATGTGAC 57.308 30.769 15.34 0.00 43.95 3.67
3168 3256 9.996554 TCTCGGTAATACAACATCATATGAAAT 57.003 29.630 9.99 0.00 0.00 2.17
3169 3257 9.476202 CTCTCGGTAATACAACATCATATGAAA 57.524 33.333 9.99 0.00 0.00 2.69
3171 3259 7.309805 CCCTCTCGGTAATACAACATCATATGA 60.310 40.741 8.10 8.10 0.00 2.15
3172 3260 6.813649 CCCTCTCGGTAATACAACATCATATG 59.186 42.308 0.00 0.00 0.00 1.78
3173 3261 6.574465 GCCCTCTCGGTAATACAACATCATAT 60.574 42.308 0.00 0.00 0.00 1.78
3174 3262 5.279306 GCCCTCTCGGTAATACAACATCATA 60.279 44.000 0.00 0.00 0.00 2.15
3202 3290 4.327357 CGCCATGTGACGGAAATATATCTC 59.673 45.833 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.