Multiple sequence alignment - TraesCS1D01G001400

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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 TraesCS1D01G001400 chr1D 100.000 1675 0 0 1719 3393 381528 379854 0.000000e+00 3094.0
1 TraesCS1D01G001400 chr1D 100.000 1367 0 0 1 1367 383246 381880 0.000000e+00 2525.0
2 TraesCS1D01G001400 chr1D 87.839 1217 121 13 1719 2909 260273 259058 0.000000e+00 1402.0
3 TraesCS1D01G001400 chr1D 85.679 1222 119 34 192 1367 252272 251061 0.000000e+00 1236.0
4 TraesCS1D01G001400 chr1D 84.026 1083 101 40 346 1367 261317 260246 0.000000e+00 976.0
5 TraesCS1D01G001400 chr1D 89.065 759 79 4 2153 2909 322068 321312 0.000000e+00 939.0
6 TraesCS1D01G001400 chr1D 86.379 881 84 15 1719 2563 251088 250208 0.000000e+00 929.0
7 TraesCS1D01G001400 chr1D 83.435 984 102 27 421 1365 323561 322600 0.000000e+00 857.0
8 TraesCS1D01G001400 chr1B 92.431 1678 91 8 1719 3391 4965980 4967626 0.000000e+00 2362.0
9 TraesCS1D01G001400 chr1B 92.066 1210 88 8 157 1362 4993556 4992351 0.000000e+00 1696.0
10 TraesCS1D01G001400 chr1B 94.974 975 34 3 394 1367 4964999 4965959 0.000000e+00 1515.0
11 TraesCS1D01G001400 chr1B 92.400 1000 74 1 1719 2718 4992340 4991343 0.000000e+00 1424.0
12 TraesCS1D01G001400 chr1B 85.852 1138 122 21 185 1287 5141129 5142262 0.000000e+00 1173.0
13 TraesCS1D01G001400 chr1B 82.053 1237 139 37 1719 2909 5142294 5143493 0.000000e+00 977.0
14 TraesCS1D01G001400 chr1B 83.756 1065 103 38 364 1367 5136320 5137375 0.000000e+00 944.0
15 TraesCS1D01G001400 chr1B 87.306 772 91 5 2141 2909 5057830 5058597 0.000000e+00 876.0
16 TraesCS1D01G001400 chr1B 87.143 770 93 5 2141 2909 5137941 5138705 0.000000e+00 869.0
17 TraesCS1D01G001400 chr1B 84.420 905 103 20 418 1287 5098629 5099530 0.000000e+00 856.0
18 TraesCS1D01G001400 chr1B 82.759 986 119 27 419 1362 5056250 5057226 0.000000e+00 832.0
19 TraesCS1D01G001400 chr1B 88.018 651 75 3 2260 2909 5100315 5100963 0.000000e+00 767.0
20 TraesCS1D01G001400 chr1B 90.798 489 41 4 2907 3393 4844037 4844523 0.000000e+00 651.0
21 TraesCS1D01G001400 chr1B 94.724 398 17 3 3 398 4961919 4962314 1.730000e-172 616.0
22 TraesCS1D01G001400 chr1B 88.889 387 43 0 1719 2105 5057345 5057731 8.520000e-131 477.0
23 TraesCS1D01G001400 chr1B 87.320 347 38 5 185 528 5055957 5056300 3.170000e-105 392.0
24 TraesCS1D01G001400 chr1B 86.455 347 41 5 185 528 5098337 5098680 3.200000e-100 375.0
25 TraesCS1D01G001400 chr1B 92.683 123 9 0 185 307 5136096 5136218 9.670000e-41 178.0
26 TraesCS1D01G001400 chr1B 84.706 170 26 0 1 170 4994561 4994392 1.620000e-38 171.0
27 TraesCS1D01G001400 chr1B 78.409 176 33 5 5 178 430620493 430620665 3.580000e-20 110.0
28 TraesCS1D01G001400 chr1A 91.107 1192 81 5 1719 2909 4033625 4034792 0.000000e+00 1591.0
29 TraesCS1D01G001400 chr1A 90.772 1192 85 5 1719 2909 4041610 4042777 0.000000e+00 1568.0
30 TraesCS1D01G001400 chr1A 90.226 1197 96 8 1719 2909 3910678 3911859 0.000000e+00 1543.0
31 TraesCS1D01G001400 chr1A 90.934 1114 78 9 254 1362 4040504 4041599 0.000000e+00 1476.0
32 TraesCS1D01G001400 chr1A 90.754 1114 80 9 254 1362 4032519 4033614 0.000000e+00 1465.0
33 TraesCS1D01G001400 chr1A 86.106 1130 100 24 272 1362 3847965 3846854 0.000000e+00 1164.0
34 TraesCS1D01G001400 chr1A 90.552 815 75 2 2096 2909 3845998 3845185 0.000000e+00 1077.0
35 TraesCS1D01G001400 chr4D 92.553 94 7 0 3298 3391 12629883 12629790 5.910000e-28 135.0
36 TraesCS1D01G001400 chr6A 86.667 105 13 1 85 189 594960277 594960174 7.690000e-22 115.0
37 TraesCS1D01G001400 chr6D 86.275 102 14 0 88 189 448813124 448813023 9.950000e-21 111.0
38 TraesCS1D01G001400 chr4B 86.301 73 10 0 90 162 520517889 520517817 2.810000e-11 80.5


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 TraesCS1D01G001400 chr1D 379854 383246 3392 True 2809.500000 3094 100.000000 1 3393 2 chr1D.!!$R4 3392
1 TraesCS1D01G001400 chr1D 259058 261317 2259 True 1189.000000 1402 85.932500 346 2909 2 chr1D.!!$R2 2563
2 TraesCS1D01G001400 chr1D 250208 252272 2064 True 1082.500000 1236 86.029000 192 2563 2 chr1D.!!$R1 2371
3 TraesCS1D01G001400 chr1D 321312 323561 2249 True 898.000000 939 86.250000 421 2909 2 chr1D.!!$R3 2488
4 TraesCS1D01G001400 chr1B 4961919 4967626 5707 False 1497.666667 2362 94.043000 3 3391 3 chr1B.!!$F3 3388
5 TraesCS1D01G001400 chr1B 4991343 4994561 3218 True 1097.000000 1696 89.724000 1 2718 3 chr1B.!!$R1 2717
6 TraesCS1D01G001400 chr1B 5136096 5143493 7397 False 828.200000 1173 86.297400 185 2909 5 chr1B.!!$F6 2724
7 TraesCS1D01G001400 chr1B 5098337 5100963 2626 False 666.000000 856 86.297667 185 2909 3 chr1B.!!$F5 2724
8 TraesCS1D01G001400 chr1B 5055957 5058597 2640 False 644.250000 876 86.568500 185 2909 4 chr1B.!!$F4 2724
9 TraesCS1D01G001400 chr1A 3910678 3911859 1181 False 1543.000000 1543 90.226000 1719 2909 1 chr1A.!!$F1 1190
10 TraesCS1D01G001400 chr1A 4032519 4034792 2273 False 1528.000000 1591 90.930500 254 2909 2 chr1A.!!$F2 2655
11 TraesCS1D01G001400 chr1A 4040504 4042777 2273 False 1522.000000 1568 90.853000 254 2909 2 chr1A.!!$F3 2655
12 TraesCS1D01G001400 chr1A 3845185 3847965 2780 True 1120.500000 1164 88.329000 272 2909 2 chr1A.!!$R1 2637

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
883 4703 3.407698 TGTATGTAGTGCCACCAAACAG 58.592 45.455 0.0 0.0 0.0 3.16 F
1244 5120 0.540830 TTCCCCAACCCCATCAAACG 60.541 55.000 0.0 0.0 0.0 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 6475 0.837691 ATGGTGGAGCAGTCAGGTGA 60.838 55.000 0.0 0.0 0.00 4.02 R
2400 6666 1.377202 GGGTCACACATGATGGCGT 60.377 57.895 0.0 0.0 37.14 5.68 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
73 74 7.607250 TGCAAATTTGGTTGTTACCCTATTAG 58.393 34.615 19.47 0.00 44.35 1.73
143 144 4.895961 ACTCCACTAAAGGTTTACTCTGC 58.104 43.478 0.00 0.00 0.00 4.26
153 154 3.967987 AGGTTTACTCTGCCGAATCCTAT 59.032 43.478 0.00 0.00 0.00 2.57
265 1116 5.416083 TCTTAGTAATCACGGTTGTCATGG 58.584 41.667 0.00 0.00 0.00 3.66
518 4266 8.794335 ACTACCCTTGACATAAAAGAAGAATC 57.206 34.615 0.00 0.00 0.00 2.52
528 4276 7.607250 ACATAAAAGAAGAATCTGACGAGTCT 58.393 34.615 4.78 0.00 45.71 3.24
792 4610 9.664332 GATAAGATGAGTCAGTGCCAATTATAT 57.336 33.333 0.00 0.00 0.00 0.86
883 4703 3.407698 TGTATGTAGTGCCACCAAACAG 58.592 45.455 0.00 0.00 0.00 3.16
1017 4844 5.516062 CCATACCATCATCCATCCTTCACAT 60.516 44.000 0.00 0.00 0.00 3.21
1032 4860 5.480422 TCCTTCACATAACTAGAGCACAAGA 59.520 40.000 0.00 0.00 0.00 3.02
1089 4917 4.115516 CACCATGAAGACCTTACTCATCG 58.884 47.826 0.00 0.00 0.00 3.84
1146 4974 0.937304 CAATATGCAAGTCGACCCCG 59.063 55.000 13.01 1.67 37.07 5.73
1160 4988 0.619543 ACCCCGGCTACCAAGTACAT 60.620 55.000 0.00 0.00 0.00 2.29
1244 5120 0.540830 TTCCCCAACCCCATCAAACG 60.541 55.000 0.00 0.00 0.00 3.60
1829 5906 1.341080 CAGCCCCAACAACAATTCCT 58.659 50.000 0.00 0.00 0.00 3.36
1966 6043 1.984424 TGTCATTGGTGTCATCCCTCA 59.016 47.619 0.00 0.00 0.00 3.86
1968 6045 3.779738 TGTCATTGGTGTCATCCCTCATA 59.220 43.478 0.00 0.00 0.00 2.15
2070 6147 0.914644 AGTGTGCAGCCATCCATAGT 59.085 50.000 0.00 0.00 0.00 2.12
2105 6266 2.095617 TCATCATGCAGCAAGAACAACG 60.096 45.455 4.06 0.00 0.00 4.10
2123 6329 2.434884 ACAAGGCGTGCAGATCCG 60.435 61.111 0.00 0.00 0.00 4.18
2145 6375 1.166531 GGCCACTGTTTCAGCTCGTT 61.167 55.000 0.00 0.00 34.37 3.85
2291 6553 1.340017 ACCATTTGCCAGCATAGTCGT 60.340 47.619 0.00 0.00 0.00 4.34
2400 6666 3.062909 GCGATGACAAATAAAGTGGCGTA 59.937 43.478 0.00 0.00 0.00 4.42
2402 6668 4.574759 GATGACAAATAAAGTGGCGTACG 58.425 43.478 11.84 11.84 0.00 3.67
2538 6809 4.556697 TCATCCCTAACTGCAATCCTAGA 58.443 43.478 0.00 0.00 0.00 2.43
2771 7043 0.785979 GCAAAACAAGCGCCTGATTG 59.214 50.000 14.09 16.90 46.72 2.67
2782 7054 1.202177 CGCCTGATTGGAAACCATTCG 60.202 52.381 0.00 0.00 36.88 3.34
2877 11935 5.838521 TCAAAAGCAATTCTTTAGGGGACTT 59.161 36.000 4.13 0.00 43.84 3.01
2978 12036 0.380378 GTGAGCACCGAAAAGCAACA 59.620 50.000 0.00 0.00 0.00 3.33
2985 12043 1.172180 CCGAAAAGCAACAGGAGCCA 61.172 55.000 0.00 0.00 0.00 4.75
2996 12054 3.795688 ACAGGAGCCAGAAAATGAAGA 57.204 42.857 0.00 0.00 0.00 2.87
2998 12056 4.268359 ACAGGAGCCAGAAAATGAAGATC 58.732 43.478 0.00 0.00 0.00 2.75
3027 12085 7.715249 ACAAGAGAACAACACTTTTATAGAGCA 59.285 33.333 0.00 0.00 0.00 4.26
3064 12123 7.481275 AGCAAACATGTATCAAAGGTTTTTG 57.519 32.000 0.00 0.00 44.03 2.44
3087 12146 1.404035 GCAAAATAGCCCCAACTACCG 59.596 52.381 0.00 0.00 0.00 4.02
3168 12231 2.256591 GCATGGCCTAGGATGCGTG 61.257 63.158 14.75 4.39 35.95 5.34
3228 12291 6.877556 ATACTAATATCATCTGCGCGAAAG 57.122 37.500 12.10 6.60 0.00 2.62
3246 12309 5.772521 CGAAAGAACACCCTTGATTTTCAT 58.227 37.500 0.00 0.00 0.00 2.57
3249 12312 7.224557 CGAAAGAACACCCTTGATTTTCATTTT 59.775 33.333 0.00 0.00 0.00 1.82
3292 12355 7.406031 ACAGAGAACGTTATTATCTTCCTCA 57.594 36.000 0.00 0.00 0.00 3.86
3335 12398 7.976734 CCTTATAGGATTTCACTATTAGGAGCG 59.023 40.741 10.43 0.00 44.56 5.03
3369 12432 2.951745 CGCTCCTGCTAACTCGCG 60.952 66.667 0.00 0.00 36.97 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 3.449632 GACCTAGCCGAACTCTGAAATC 58.550 50.000 0.00 0.00 0.00 2.17
265 1116 5.530519 TGATGCATTTAGTCGAAGTTGTC 57.469 39.130 0.00 0.00 0.00 3.18
465 4092 6.091577 TGTTGTACACGAATCAATACATGACC 59.908 38.462 0.00 0.00 41.93 4.02
518 4266 6.093404 TGAACAAGCTAATAAGACTCGTCAG 58.907 40.000 0.00 0.00 0.00 3.51
528 4276 9.851686 ATGATGGTAAGATGAACAAGCTAATAA 57.148 29.630 0.00 0.00 0.00 1.40
792 4610 5.654603 TCATCTAAGAGTGGCGAAAACTA 57.345 39.130 0.00 0.00 0.00 2.24
839 4659 2.433239 ACGTACTTTTGGAGTGGTCAGT 59.567 45.455 0.00 0.00 39.48 3.41
1017 4844 7.394016 TGGATTTGATTCTTGTGCTCTAGTTA 58.606 34.615 0.00 0.00 0.00 2.24
1054 4882 2.364632 TCATGGTGGATTTGCGTTAGG 58.635 47.619 0.00 0.00 0.00 2.69
1160 4988 1.198713 ATGGTTGTTGTTGTGGCCAA 58.801 45.000 7.24 0.00 0.00 4.52
1244 5120 2.028130 TGTTGTGGTTGATGGTGGAAC 58.972 47.619 0.00 0.00 0.00 3.62
1886 5963 6.351881 GGGGTTCATCTGTTGTTGTAGAGATA 60.352 42.308 0.00 0.00 0.00 1.98
1966 6043 5.237996 CACTTCGTGGCAAGATCATTGATAT 59.762 40.000 3.45 0.00 0.00 1.63
1968 6045 3.376234 CACTTCGTGGCAAGATCATTGAT 59.624 43.478 3.45 0.00 0.00 2.57
2028 6105 1.375098 GCTGCTGAGGAATCTGTGCC 61.375 60.000 0.00 0.00 0.00 5.01
2070 6147 2.399916 TGATGATGGAATGCACGACA 57.600 45.000 0.00 0.00 0.00 4.35
2105 6266 2.456119 CGGATCTGCACGCCTTGTC 61.456 63.158 0.00 0.00 0.00 3.18
2123 6329 4.043200 GCTGAAACAGTGGCCGCC 62.043 66.667 14.07 1.04 33.43 6.13
2145 6375 1.348008 GGATGATGCCCTGACCCTGA 61.348 60.000 0.00 0.00 0.00 3.86
2245 6475 0.837691 ATGGTGGAGCAGTCAGGTGA 60.838 55.000 0.00 0.00 0.00 4.02
2400 6666 1.377202 GGGTCACACATGATGGCGT 60.377 57.895 0.00 0.00 37.14 5.68
2402 6668 2.114670 CGGGGTCACACATGATGGC 61.115 63.158 0.00 0.00 37.14 4.40
2538 6809 5.053145 GCAGCTAGCTATTGATGTGTAAGT 58.947 41.667 18.86 0.00 41.15 2.24
2565 6836 8.846423 ATAGATTATATAGTAACCTGCCAGCT 57.154 34.615 0.00 0.00 0.00 4.24
2742 7014 3.059665 GCGCTTGTTTTGCTGCTAAAATT 60.060 39.130 10.65 0.00 32.71 1.82
2771 7043 5.411669 ACATTTAGAGTGACGAATGGTTTCC 59.588 40.000 0.00 0.00 34.07 3.13
2969 12027 2.071778 TTCTGGCTCCTGTTGCTTTT 57.928 45.000 0.00 0.00 0.00 2.27
2978 12036 4.226846 TGAGATCTTCATTTTCTGGCTCCT 59.773 41.667 0.00 0.00 0.00 3.69
2998 12056 9.261180 TCTATAAAAGTGTTGTTCTCTTGTGAG 57.739 33.333 0.00 0.00 41.51 3.51
3009 12067 7.817418 TTTCCTTGCTCTATAAAAGTGTTGT 57.183 32.000 0.00 0.00 0.00 3.32
3049 12108 7.728847 ATTTTGCTCCAAAAACCTTTGATAC 57.271 32.000 7.15 0.00 44.68 2.24
3218 12281 1.507141 AAGGGTGTTCTTTCGCGCAG 61.507 55.000 8.75 0.00 34.10 5.18
3257 12320 2.037251 ACGTTCTCTGTACCTGTGCAAT 59.963 45.455 0.00 0.00 0.00 3.56
3260 12323 2.150397 AACGTTCTCTGTACCTGTGC 57.850 50.000 0.00 0.00 0.00 4.57
3262 12325 7.642082 AGATAATAACGTTCTCTGTACCTGT 57.358 36.000 2.82 0.00 0.00 4.00
3322 12385 3.119101 AGTTGTGGACGCTCCTAATAGTG 60.119 47.826 5.77 0.00 37.46 2.74
3369 12432 2.772189 CACGCTGCTCGCTGTTAC 59.228 61.111 0.00 0.00 43.23 2.50


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

AutoCloner maintained by Alex Coulton.