Multiple sequence alignment - TraesCS7D01G136700

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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 TraesCS7D01G136700 chr7D 100.000 5244 0 0 1 5244 87994875 88000118 0.000000e+00 9684.0
1 TraesCS7D01G136700 chr7D 97.362 417 10 1 1 417 550984335 550984750 0.000000e+00 708.0
2 TraesCS7D01G136700 chr7D 92.857 42 3 0 4517 4558 39532182 39532141 1.580000e-05 62.1
3 TraesCS7D01G136700 chr7D 97.059 34 1 0 4517 4550 281083474 281083507 2.040000e-04 58.4
4 TraesCS7D01G136700 chr1D 97.266 2999 61 11 2253 5244 17628978 17631962 0.000000e+00 5064.0
5 TraesCS7D01G136700 chr1D 97.997 1298 19 4 889 2179 17627682 17628979 0.000000e+00 2246.0
6 TraesCS7D01G136700 chr1D 94.058 892 20 7 1 889 17626778 17627639 0.000000e+00 1323.0
7 TraesCS7D01G136700 chr1A 94.280 3287 133 18 1016 4297 19891571 19894807 0.000000e+00 4977.0
8 TraesCS7D01G136700 chr1A 81.931 1212 207 10 2839 4043 2937296 2938502 0.000000e+00 1014.0
9 TraesCS7D01G136700 chr1A 89.379 612 37 9 4658 5244 19895125 19895733 0.000000e+00 745.0
10 TraesCS7D01G136700 chr1A 83.333 264 18 9 632 889 19891322 19891565 2.460000e-53 220.0
11 TraesCS7D01G136700 chr1B 94.595 1517 81 1 2768 4284 25810125 25811640 0.000000e+00 2346.0
12 TraesCS7D01G136700 chr1B 91.240 1701 124 20 1016 2710 25808367 25810048 0.000000e+00 2292.0
13 TraesCS7D01G136700 chr1B 85.170 1470 178 23 2719 4182 25259942 25261377 0.000000e+00 1471.0
14 TraesCS7D01G136700 chr1B 81.997 1422 195 29 1133 2537 25258397 25259774 0.000000e+00 1151.0
15 TraesCS7D01G136700 chr1B 89.286 672 44 8 4575 5221 25812181 25812849 0.000000e+00 817.0
16 TraesCS7D01G136700 chr1B 96.403 417 14 1 1 417 565996269 565996684 0.000000e+00 686.0
17 TraesCS7D01G136700 chr1B 80.335 478 11 22 426 889 25807953 25808361 8.600000e-73 285.0
18 TraesCS7D01G136700 chr2A 81.543 1257 216 11 2792 4043 624966649 624965404 0.000000e+00 1022.0
19 TraesCS7D01G136700 chr2A 89.091 55 5 1 2096 2149 453519267 453519321 3.390000e-07 67.6
20 TraesCS7D01G136700 chrUn 81.983 1210 208 8 2839 4043 279471943 279473147 0.000000e+00 1018.0
21 TraesCS7D01G136700 chrUn 81.931 1212 207 10 2839 4043 279436279 279437485 0.000000e+00 1014.0
22 TraesCS7D01G136700 chr2B 80.699 1316 233 17 2744 4048 768059037 768057732 0.000000e+00 1003.0
23 TraesCS7D01G136700 chr2B 75.350 929 196 19 1090 2006 566403453 566402546 2.920000e-112 416.0
24 TraesCS7D01G136700 chr2B 100.000 37 0 0 2103 2139 17496247 17496211 9.420000e-08 69.4
25 TraesCS7D01G136700 chr2D 81.386 1241 214 14 2809 4043 482349731 482348502 0.000000e+00 996.0
26 TraesCS7D01G136700 chr2D 95.981 423 10 2 1 417 60774422 60774843 0.000000e+00 680.0
27 TraesCS7D01G136700 chr2D 74.757 927 205 14 1090 2006 482382545 482381638 6.370000e-104 388.0
28 TraesCS7D01G136700 chr5D 97.381 420 11 0 1 420 468358648 468359067 0.000000e+00 715.0
29 TraesCS7D01G136700 chr5D 94.444 36 2 0 4517 4552 347364836 347364801 7.340000e-04 56.5
30 TraesCS7D01G136700 chr5B 96.429 420 14 1 1 420 562963508 562963090 0.000000e+00 691.0
31 TraesCS7D01G136700 chr5B 96.163 417 15 1 1 417 595641780 595642195 0.000000e+00 680.0
32 TraesCS7D01G136700 chr5B 94.444 36 2 0 4517 4552 403781373 403781408 7.340000e-04 56.5
33 TraesCS7D01G136700 chr6D 95.093 428 19 2 1 427 350278122 350278548 0.000000e+00 673.0
34 TraesCS7D01G136700 chr6D 100.000 28 0 0 2155 2182 245849356 245849383 9.000000e-03 52.8
35 TraesCS7D01G136700 chr6B 95.261 422 17 2 1 422 172577971 172578389 0.000000e+00 665.0
36 TraesCS7D01G136700 chr6B 93.182 44 3 0 1883 1926 460207383 460207426 1.220000e-06 65.8
37 TraesCS7D01G136700 chr3D 94.595 37 2 0 4523 4559 307228866 307228830 2.040000e-04 58.4
38 TraesCS7D01G136700 chr5A 94.286 35 2 0 4518 4552 422064097 422064063 3.000000e-03 54.7
39 TraesCS7D01G136700 chr4A 94.444 36 1 1 4516 4550 590226001 590225966 3.000000e-03 54.7
40 TraesCS7D01G136700 chr7A 94.286 35 0 2 4517 4550 2578408 2578441 9.000000e-03 52.8


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 TraesCS7D01G136700 chr7D 87994875 88000118 5243 False 9684.000000 9684 100.000000 1 5244 1 chr7D.!!$F1 5243
1 TraesCS7D01G136700 chr1D 17626778 17631962 5184 False 2877.666667 5064 96.440333 1 5244 3 chr1D.!!$F1 5243
2 TraesCS7D01G136700 chr1A 19891322 19895733 4411 False 1980.666667 4977 88.997333 632 5244 3 chr1A.!!$F2 4612
3 TraesCS7D01G136700 chr1A 2937296 2938502 1206 False 1014.000000 1014 81.931000 2839 4043 1 chr1A.!!$F1 1204
4 TraesCS7D01G136700 chr1B 25807953 25812849 4896 False 1435.000000 2346 88.864000 426 5221 4 chr1B.!!$F3 4795
5 TraesCS7D01G136700 chr1B 25258397 25261377 2980 False 1311.000000 1471 83.583500 1133 4182 2 chr1B.!!$F2 3049
6 TraesCS7D01G136700 chr2A 624965404 624966649 1245 True 1022.000000 1022 81.543000 2792 4043 1 chr2A.!!$R1 1251
7 TraesCS7D01G136700 chrUn 279471943 279473147 1204 False 1018.000000 1018 81.983000 2839 4043 1 chrUn.!!$F2 1204
8 TraesCS7D01G136700 chrUn 279436279 279437485 1206 False 1014.000000 1014 81.931000 2839 4043 1 chrUn.!!$F1 1204
9 TraesCS7D01G136700 chr2B 768057732 768059037 1305 True 1003.000000 1003 80.699000 2744 4048 1 chr2B.!!$R3 1304
10 TraesCS7D01G136700 chr2B 566402546 566403453 907 True 416.000000 416 75.350000 1090 2006 1 chr2B.!!$R2 916
11 TraesCS7D01G136700 chr2D 482348502 482349731 1229 True 996.000000 996 81.386000 2809 4043 1 chr2D.!!$R1 1234
12 TraesCS7D01G136700 chr2D 482381638 482382545 907 True 388.000000 388 74.757000 1090 2006 1 chr2D.!!$R2 916

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
139 140 0.543749 CTTCTACCCCCTGCTTCCTG 59.456 60.000 0.00 0.0 0.00 3.86 F
956 1019 0.906756 AGAAGCTCACTGGCCTAGCA 60.907 55.000 18.01 0.0 38.75 3.49 F
2449 2544 1.067354 GGATACCGGTGTTCTTGTCGT 60.067 52.381 19.93 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2242 7.041372 TGACCAAGTTCATAGAAAACTAGCAAC 60.041 37.037 0.0 0.0 35.96 4.17 R
2635 2731 3.134262 CCACACACTGATCCTCATCTGAT 59.866 47.826 0.0 0.0 33.29 2.90 R
4397 4645 6.461110 AAGGAGCTGGTTTTCATTATCATG 57.539 37.500 0.0 0.0 0.00 3.07 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
97 98 2.791655 TGAGTCCAAGACGAAGCTCTA 58.208 47.619 0.00 0.00 37.67 2.43
121 122 2.683933 ATCGACCAAGTCCCGGCT 60.684 61.111 0.00 0.00 0.00 5.52
130 131 3.477346 GTCCCGGCTTCTACCCCC 61.477 72.222 0.00 0.00 0.00 5.40
131 132 3.691326 TCCCGGCTTCTACCCCCT 61.691 66.667 0.00 0.00 0.00 4.79
132 133 3.480133 CCCGGCTTCTACCCCCTG 61.480 72.222 0.00 0.00 0.00 4.45
133 134 4.176752 CCGGCTTCTACCCCCTGC 62.177 72.222 0.00 0.00 0.00 4.85
134 135 3.083997 CGGCTTCTACCCCCTGCT 61.084 66.667 0.00 0.00 0.00 4.24
135 136 2.670148 CGGCTTCTACCCCCTGCTT 61.670 63.158 0.00 0.00 0.00 3.91
136 137 1.224870 GGCTTCTACCCCCTGCTTC 59.775 63.158 0.00 0.00 0.00 3.86
137 138 1.224870 GCTTCTACCCCCTGCTTCC 59.775 63.158 0.00 0.00 0.00 3.46
138 139 1.275421 GCTTCTACCCCCTGCTTCCT 61.275 60.000 0.00 0.00 0.00 3.36
139 140 0.543749 CTTCTACCCCCTGCTTCCTG 59.456 60.000 0.00 0.00 0.00 3.86
140 141 0.914417 TTCTACCCCCTGCTTCCTGG 60.914 60.000 0.00 0.00 0.00 4.45
141 142 2.286121 TACCCCCTGCTTCCTGGG 60.286 66.667 0.00 0.00 46.78 4.45
142 143 4.617595 ACCCCCTGCTTCCTGGGT 62.618 66.667 0.00 0.00 46.03 4.51
143 144 4.052518 CCCCCTGCTTCCTGGGTG 62.053 72.222 0.00 0.00 46.03 4.61
144 145 4.052518 CCCCTGCTTCCTGGGTGG 62.053 72.222 0.00 0.00 46.03 4.61
145 146 2.935481 CCCTGCTTCCTGGGTGGA 60.935 66.667 0.00 0.00 43.34 4.02
146 147 2.311854 CCCTGCTTCCTGGGTGGAT 61.312 63.158 0.00 0.00 45.68 3.41
147 148 1.077212 CCTGCTTCCTGGGTGGATG 60.077 63.158 0.00 0.00 45.68 3.51
148 149 1.077212 CTGCTTCCTGGGTGGATGG 60.077 63.158 0.00 0.00 45.68 3.51
242 243 2.837591 TGGTGATGCTTAGCTTAGGACA 59.162 45.455 5.60 0.00 0.00 4.02
260 261 1.148310 CAGGTGCTTCGGTTGTGTAG 58.852 55.000 0.00 0.00 0.00 2.74
287 288 1.235724 GTTTGTGGTGGGTGTAGCTC 58.764 55.000 0.00 0.00 0.00 4.09
360 363 3.138304 TCTTCACCATGTTGTTCTTCCG 58.862 45.455 0.00 0.00 0.00 4.30
397 400 4.182693 TCTGAATCAAGCCAGCAATTTG 57.817 40.909 0.00 0.00 0.00 2.32
556 565 7.286508 GCTTATTCTTTTGCAAAAAGAGAAGC 58.713 34.615 29.96 29.96 42.68 3.86
773 791 4.263911 GCAAGCACAAATTAATTCTCGAGC 59.736 41.667 7.81 4.23 0.00 5.03
778 796 3.932710 ACAAATTAATTCTCGAGCGAGCA 59.067 39.130 14.61 4.81 41.71 4.26
820 838 1.529152 TACGTGCGGCTTCTCCAAGA 61.529 55.000 0.00 0.00 34.01 3.02
821 839 2.097038 CGTGCGGCTTCTCCAAGAG 61.097 63.158 0.00 0.00 34.01 2.85
913 975 4.267536 TGAGATCCATTCTGCTTTCTTGG 58.732 43.478 0.00 0.00 33.74 3.61
915 977 2.291209 TCCATTCTGCTTTCTTGGCA 57.709 45.000 0.00 0.00 38.10 4.92
956 1019 0.906756 AGAAGCTCACTGGCCTAGCA 60.907 55.000 18.01 0.00 38.75 3.49
2449 2544 1.067354 GGATACCGGTGTTCTTGTCGT 60.067 52.381 19.93 0.00 0.00 4.34
2471 2566 5.389516 CGTGTAGGAAGAAAAATGGAAGACG 60.390 44.000 0.00 0.00 0.00 4.18
2518 2613 8.456471 GGCTTAATACTAGGTAACACAAAAAGG 58.544 37.037 0.00 0.00 41.41 3.11
2688 2784 9.232473 GGACATGAGAAATAGACTAAAACCTTT 57.768 33.333 0.00 0.00 0.00 3.11
2767 2881 5.006941 TGTTAGCGAAAGAACACCAACTAAC 59.993 40.000 0.00 0.00 38.96 2.34
2804 2927 4.352893 TCTCTCTCTCTCTCTCTCACTCA 58.647 47.826 0.00 0.00 0.00 3.41
3194 3358 2.962859 AGGAATTTGGCCAAGAGTTGT 58.037 42.857 19.48 1.29 0.00 3.32
3200 3364 4.320608 TTTGGCCAAGAGTTGTTCATTC 57.679 40.909 19.48 0.00 0.00 2.67
3254 3418 2.485814 CTCTTAGGTTGTTGCCTTGAGC 59.514 50.000 0.00 0.00 39.94 4.26
3351 3515 6.872547 CGATCATCACATATCTCCTTCAACAT 59.127 38.462 0.00 0.00 0.00 2.71
4017 4186 9.082313 AGAAAATGAGAACCAACACATAAATCT 57.918 29.630 0.00 0.00 0.00 2.40
4104 4275 3.060272 CGTGCATAGCTTCTTTCCATACG 60.060 47.826 0.00 0.00 0.00 3.06
4420 4668 6.189859 TCATGATAATGAAAACCAGCTCCTT 58.810 36.000 0.00 0.00 0.00 3.36
4520 4774 9.263538 TGTGGCCTAGTAATATTATTGTAAACG 57.736 33.333 3.32 0.00 0.00 3.60
4808 5375 6.039047 CATCAAGTTGATCAACCTATTCCAGG 59.961 42.308 30.34 12.38 42.11 4.45
4829 5406 4.076394 GGCATCCAGTAAACCAGTGTAAA 58.924 43.478 0.00 0.00 0.00 2.01
4984 5576 2.483889 GGCAGCTACTTTATCCGAAGCT 60.484 50.000 0.00 0.00 44.08 3.74
5071 5664 4.059511 TGCATGCAGTTGGATTTGAAAAG 58.940 39.130 18.46 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.149578 CTGGAGCTTCACCTTGAACAG 58.850 52.381 0.00 0.00 32.21 3.16
97 98 1.265454 GGACTTGGTCGATCCCAGGT 61.265 60.000 9.26 9.26 46.45 4.00
117 118 2.595009 GAAGCAGGGGGTAGAAGCCG 62.595 65.000 0.00 0.00 36.39 5.52
121 122 0.914417 CCAGGAAGCAGGGGGTAGAA 60.914 60.000 0.00 0.00 0.00 2.10
136 137 3.567579 AACGCACCATCCACCCAGG 62.568 63.158 0.00 0.00 39.47 4.45
137 138 2.034066 AACGCACCATCCACCCAG 59.966 61.111 0.00 0.00 0.00 4.45
138 139 2.282110 CAACGCACCATCCACCCA 60.282 61.111 0.00 0.00 0.00 4.51
139 140 3.061848 CCAACGCACCATCCACCC 61.062 66.667 0.00 0.00 0.00 4.61
140 141 3.747976 GCCAACGCACCATCCACC 61.748 66.667 0.00 0.00 34.03 4.61
141 142 4.101790 CGCCAACGCACCATCCAC 62.102 66.667 0.00 0.00 34.03 4.02
142 143 4.321966 TCGCCAACGCACCATCCA 62.322 61.111 0.00 0.00 39.84 3.41
143 144 3.499737 CTCGCCAACGCACCATCC 61.500 66.667 0.00 0.00 39.84 3.51
144 145 3.499737 CCTCGCCAACGCACCATC 61.500 66.667 0.00 0.00 39.84 3.51
148 149 3.423154 CTTCCCTCGCCAACGCAC 61.423 66.667 0.00 0.00 39.84 5.34
242 243 0.756903 ACTACACAACCGAAGCACCT 59.243 50.000 0.00 0.00 0.00 4.00
260 261 1.754226 ACCCACCACAAACAACATGAC 59.246 47.619 0.00 0.00 0.00 3.06
316 319 5.984695 TCCGAAGATCAGAAAGAGAAAGA 57.015 39.130 0.00 0.00 0.00 2.52
426 430 7.401080 CAAAACTTTGAGATTCGTGCATTTTT 58.599 30.769 0.00 0.00 40.55 1.94
773 791 2.579249 GCTGCTCTCTCGTGCTCG 60.579 66.667 0.81 0.81 38.55 5.03
778 796 1.752694 GGAGGAGCTGCTCTCTCGT 60.753 63.158 30.98 5.60 41.60 4.18
820 838 7.147585 ACAGCATAGAACTCACCTGATAAATCT 60.148 37.037 0.00 0.00 0.00 2.40
821 839 6.989169 ACAGCATAGAACTCACCTGATAAATC 59.011 38.462 0.00 0.00 0.00 2.17
913 975 3.795101 GCATGATCACAAGTAAAGCATGC 59.205 43.478 10.51 10.51 46.56 4.06
915 977 5.416639 TCTTGCATGATCACAAGTAAAGCAT 59.583 36.000 19.83 0.00 43.05 3.79
2153 2242 7.041372 TGACCAAGTTCATAGAAAACTAGCAAC 60.041 37.037 0.00 0.00 35.96 4.17
2449 2544 5.860611 TCGTCTTCCATTTTTCTTCCTACA 58.139 37.500 0.00 0.00 0.00 2.74
2471 2566 3.935203 CCGATATCAGGGTTGCATGTATC 59.065 47.826 3.12 0.00 0.00 2.24
2551 2646 5.396548 GGACTTAAAGGTCAAGGGATAGGAC 60.397 48.000 0.00 0.00 37.91 3.85
2635 2731 3.134262 CCACACACTGATCCTCATCTGAT 59.866 47.826 0.00 0.00 33.29 2.90
2735 2848 6.427150 GTGTTCTTTCGCTAACAAAAGATGA 58.573 36.000 0.00 0.00 40.25 2.92
2767 2881 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2804 2927 5.762179 TGGGATGAGACAACTATTTCAGT 57.238 39.130 0.00 0.00 40.05 3.41
2958 3119 3.237268 ACAAAAGCAACCCTCCATGTA 57.763 42.857 0.00 0.00 0.00 2.29
3037 3198 5.048364 GTCAAAGTTGTTGGTGGCATGTATA 60.048 40.000 0.00 0.00 0.00 1.47
3351 3515 7.397221 TGCTTCATGAGAAATCCTTAAGAGAA 58.603 34.615 3.36 0.00 32.35 2.87
4017 4186 8.585881 GTCACCTAGCATAATATGAACTTCCTA 58.414 37.037 4.14 0.00 0.00 2.94
4397 4645 6.461110 AAGGAGCTGGTTTTCATTATCATG 57.539 37.500 0.00 0.00 0.00 3.07
4520 4774 6.127897 CCCTCTGATCCAAAATAAGTGTTGTC 60.128 42.308 0.00 0.00 0.00 3.18
4808 5375 4.379499 GCTTTACACTGGTTTACTGGATGC 60.379 45.833 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.