Multiple sequence alignment - TraesCS2A01G238500

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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 TraesCS2A01G238500 chr2A 100.000 2741 0 0 1 2741 321742264 321745004 0.000000e+00 5062
1 TraesCS2A01G238500 chr2A 93.789 2093 125 5 1 2091 321750237 321752326 0.000000e+00 3140
2 TraesCS2A01G238500 chr2A 88.228 773 68 18 1982 2741 355473153 355473915 0.000000e+00 902
3 TraesCS2A01G238500 chr2A 89.956 677 50 12 2075 2739 121545921 121546591 0.000000e+00 857
4 TraesCS2A01G238500 chr6A 90.700 2301 166 29 115 2393 353349260 353346986 0.000000e+00 3020
5 TraesCS2A01G238500 chr6A 91.729 1995 125 22 113 2091 353341354 353339384 0.000000e+00 2734
6 TraesCS2A01G238500 chr6A 85.341 1187 132 31 1578 2741 68205991 68207158 0.000000e+00 1190
7 TraesCS2A01G238500 chr6A 87.163 927 104 12 19 935 244970176 244969255 0.000000e+00 1038
8 TraesCS2A01G238500 chr6A 80.788 1218 163 52 1523 2711 310595206 310596381 0.000000e+00 887
9 TraesCS2A01G238500 chr6A 90.000 220 18 3 1 218 115334205 115333988 5.780000e-72 281
10 TraesCS2A01G238500 chr6A 87.866 239 26 3 1 236 259285250 259285012 7.480000e-71 278
11 TraesCS2A01G238500 chr6A 88.412 233 24 3 1 230 461343132 461343364 7.480000e-71 278
12 TraesCS2A01G238500 chr6A 81.977 344 46 14 23 363 461605338 461605668 7.480000e-71 278
13 TraesCS2A01G238500 chr6A 80.992 363 53 13 3 363 461622641 461622989 9.670000e-70 274
14 TraesCS2A01G238500 chr6A 87.983 233 25 3 1 230 461293534 461293766 3.480000e-69 272
15 TraesCS2A01G238500 chr6A 81.471 340 53 9 24 363 290913893 290913564 1.250000e-68 270
16 TraesCS2A01G238500 chr6A 80.165 363 56 14 3 363 461599367 461599715 9.740000e-65 257
17 TraesCS2A01G238500 chr6A 84.746 236 32 4 128 363 568743042 568743273 1.640000e-57 233
18 TraesCS2A01G238500 chr1A 89.609 2406 196 36 3 2392 469357764 469355397 0.000000e+00 3009
19 TraesCS2A01G238500 chr1A 91.464 1851 122 23 261 2091 168235210 168237044 0.000000e+00 2510
20 TraesCS2A01G238500 chr1A 80.714 1260 178 54 1517 2739 225930854 225932085 0.000000e+00 920
21 TraesCS2A01G238500 chr1A 80.811 370 49 19 2 363 114664086 114664441 1.250000e-68 270
22 TraesCS2A01G238500 chr1A 84.871 271 33 7 1 268 204474352 204474087 1.620000e-67 267
23 TraesCS2A01G238500 chr1A 87.069 232 28 2 1 231 351721008 351721238 7.530000e-66 261
24 TraesCS2A01G238500 chr1A 86.250 240 30 3 3 239 284172783 284172544 9.740000e-65 257
25 TraesCS2A01G238500 chr1A 87.500 224 25 3 10 230 23540381 23540604 3.500000e-64 255
26 TraesCS2A01G238500 chr1A 85.950 242 31 3 1 239 123881740 123881499 3.500000e-64 255
27 TraesCS2A01G238500 chr1A 85.537 242 32 3 1 239 35603816 35603575 1.630000e-62 250
28 TraesCS2A01G238500 chr1A 85.366 246 29 5 1 239 35655242 35654997 5.860000e-62 248
29 TraesCS2A01G238500 chr1A 79.609 358 55 14 12 363 14670167 14670512 9.810000e-60 241
30 TraesCS2A01G238500 chr3A 89.493 2408 196 36 3 2392 279045780 279043412 0.000000e+00 2992
31 TraesCS2A01G238500 chr3A 91.839 1985 130 18 23 1996 279037865 279035902 0.000000e+00 2739
32 TraesCS2A01G238500 chr3A 92.442 1892 110 11 113 1996 271848125 271846259 0.000000e+00 2671
33 TraesCS2A01G238500 chr3A 91.481 1843 139 10 258 2087 254257177 254255340 0.000000e+00 2518
34 TraesCS2A01G238500 chr3A 86.805 773 78 19 1982 2741 272760581 272759820 0.000000e+00 841
35 TraesCS2A01G238500 chr3A 78.240 1250 198 51 1523 2739 393782607 393783815 0.000000e+00 734
36 TraesCS2A01G238500 chr4A 83.601 1122 145 30 1633 2739 418027619 418028716 0.000000e+00 1016
37 TraesCS2A01G238500 chr7A 87.699 691 70 13 2056 2739 490042997 490043679 0.000000e+00 791
38 TraesCS2A01G238500 chr7A 80.054 371 61 8 1 364 376776136 376775772 2.090000e-66 263
39 TraesCS2A01G238500 chr5A 86.364 352 43 5 10 361 459396679 459396333 1.990000e-101 379
40 TraesCS2A01G238500 chr5A 81.918 365 53 8 1 363 521580816 521580463 2.060000e-76 296
41 TraesCS2A01G238500 chr7D 81.435 237 36 6 10 244 105668758 105668988 1.300000e-43 187
42 TraesCS2A01G238500 chr6B 80.083 241 37 9 3 239 331535945 331536178 4.690000e-38 169
43 TraesCS2A01G238500 chr1B 80.822 219 30 9 18 231 363383939 363384150 7.860000e-36 161
44 TraesCS2A01G238500 chr1B 78.125 224 37 10 3 224 122202754 122202541 6.160000e-27 132
45 TraesCS2A01G238500 chr5D 79.464 224 38 6 10 231 315069765 315069982 4.730000e-33 152
46 TraesCS2A01G238500 chr5D 79.111 225 37 7 10 231 292279850 292280067 2.200000e-31 147
47 TraesCS2A01G238500 chr7B 77.941 272 39 17 1 262 184476766 184476506 1.700000e-32 150
48 TraesCS2A01G238500 chr4B 79.909 219 33 6 1 216 427605442 427605232 1.700000e-32 150
49 TraesCS2A01G238500 chr3D 90.351 114 8 2 248 361 49363589 49363699 2.200000e-31 147
50 TraesCS2A01G238500 chr1D 79.018 224 39 5 10 231 321935201 321935418 2.200000e-31 147
51 TraesCS2A01G238500 chr1D 78.571 224 40 5 10 231 321941247 321941464 1.020000e-29 141
52 TraesCS2A01G238500 chr1D 78.571 224 40 5 10 231 340375693 340375476 1.020000e-29 141
53 TraesCS2A01G238500 chr1D 94.872 78 4 0 425 502 230528604 230528681 3.710000e-24 122
54 TraesCS2A01G238500 chr6D 79.018 224 38 6 10 231 317381203 317381419 7.910000e-31 145
55 TraesCS2A01G238500 chr6D 78.571 224 40 5 10 231 307412124 307412341 1.020000e-29 141
56 TraesCS2A01G238500 chr6D 80.000 190 31 4 10 198 419817601 419817784 1.710000e-27 134
57 TraesCS2A01G238500 chr6D 84.559 136 17 2 3 138 102393823 102393692 6.160000e-27 132
58 TraesCS2A01G238500 chr6D 80.226 177 28 4 10 185 419809427 419809597 2.870000e-25 126
59 TraesCS2A01G238500 chr4D 81.461 178 24 6 10 185 134310060 134309890 1.320000e-28 137


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 TraesCS2A01G238500 chr2A 321742264 321745004 2740 False 5062 5062 100.000 1 2741 1 chr2A.!!$F2 2740
1 TraesCS2A01G238500 chr2A 321750237 321752326 2089 False 3140 3140 93.789 1 2091 1 chr2A.!!$F3 2090
2 TraesCS2A01G238500 chr2A 355473153 355473915 762 False 902 902 88.228 1982 2741 1 chr2A.!!$F4 759
3 TraesCS2A01G238500 chr2A 121545921 121546591 670 False 857 857 89.956 2075 2739 1 chr2A.!!$F1 664
4 TraesCS2A01G238500 chr6A 353346986 353349260 2274 True 3020 3020 90.700 115 2393 1 chr6A.!!$R6 2278
5 TraesCS2A01G238500 chr6A 353339384 353341354 1970 True 2734 2734 91.729 113 2091 1 chr6A.!!$R5 1978
6 TraesCS2A01G238500 chr6A 68205991 68207158 1167 False 1190 1190 85.341 1578 2741 1 chr6A.!!$F1 1163
7 TraesCS2A01G238500 chr6A 244969255 244970176 921 True 1038 1038 87.163 19 935 1 chr6A.!!$R2 916
8 TraesCS2A01G238500 chr6A 310595206 310596381 1175 False 887 887 80.788 1523 2711 1 chr6A.!!$F2 1188
9 TraesCS2A01G238500 chr1A 469355397 469357764 2367 True 3009 3009 89.609 3 2392 1 chr1A.!!$R6 2389
10 TraesCS2A01G238500 chr1A 168235210 168237044 1834 False 2510 2510 91.464 261 2091 1 chr1A.!!$F4 1830
11 TraesCS2A01G238500 chr1A 225930854 225932085 1231 False 920 920 80.714 1517 2739 1 chr1A.!!$F5 1222
12 TraesCS2A01G238500 chr3A 279043412 279045780 2368 True 2992 2992 89.493 3 2392 1 chr3A.!!$R5 2389
13 TraesCS2A01G238500 chr3A 279035902 279037865 1963 True 2739 2739 91.839 23 1996 1 chr3A.!!$R4 1973
14 TraesCS2A01G238500 chr3A 271846259 271848125 1866 True 2671 2671 92.442 113 1996 1 chr3A.!!$R2 1883
15 TraesCS2A01G238500 chr3A 254255340 254257177 1837 True 2518 2518 91.481 258 2087 1 chr3A.!!$R1 1829
16 TraesCS2A01G238500 chr3A 272759820 272760581 761 True 841 841 86.805 1982 2741 1 chr3A.!!$R3 759
17 TraesCS2A01G238500 chr3A 393782607 393783815 1208 False 734 734 78.240 1523 2739 1 chr3A.!!$F1 1216
18 TraesCS2A01G238500 chr4A 418027619 418028716 1097 False 1016 1016 83.601 1633 2739 1 chr4A.!!$F1 1106
19 TraesCS2A01G238500 chr7A 490042997 490043679 682 False 791 791 87.699 2056 2739 1 chr7A.!!$F1 683

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
278 291 0.390735 ACATGTTCGGGAAGCGGTAC 60.391 55.0 0.00 0.0 0.00 3.34 F
395 408 0.391661 ACGACGGCGGTAGAAGTAGA 60.392 55.0 18.49 0.0 43.17 2.59 F
614 633 0.396811 CGGAGTCTTCCAACTTGGGT 59.603 55.0 8.01 0.0 44.26 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 1130 0.468400 GGTATCTCCGTCCTCCAGCT 60.468 60.0 0.0 0.0 0.00 4.24 R
1464 1497 0.548682 AGAGGAGAACCCCAGTGCAT 60.549 55.0 0.0 0.0 36.73 3.96 R
2028 2114 1.349259 CCGGGATTCGTCGTGTGTTC 61.349 60.0 0.0 0.0 37.11 3.18 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
109 111 2.553602 TGCAAGCGACAATTTCAGACAT 59.446 40.909 0.00 0.00 0.00 3.06
166 169 2.594919 ATTTGGTCCACGGGCGGTA 61.595 57.895 0.00 0.00 0.00 4.02
210 213 1.677217 GGAGCATTCTCAGAGCGGTTT 60.677 52.381 0.00 0.00 41.13 3.27
216 219 2.910688 TCTCAGAGCGGTTTGAGTTT 57.089 45.000 27.88 0.00 41.21 2.66
242 246 1.278238 GAAGTAGTCATTCACGGCCG 58.722 55.000 26.86 26.86 0.00 6.13
278 291 0.390735 ACATGTTCGGGAAGCGGTAC 60.391 55.000 0.00 0.00 0.00 3.34
376 389 4.157289 GGTAGTGGAAGTAGATGTTCACGA 59.843 45.833 0.00 0.00 0.00 4.35
395 408 0.391661 ACGACGGCGGTAGAAGTAGA 60.392 55.000 18.49 0.00 43.17 2.59
502 521 3.803886 GGCGACGGTAATGGAACC 58.196 61.111 0.00 0.00 36.08 3.62
512 531 4.164221 ACGGTAATGGAACCTCATGAATCT 59.836 41.667 0.00 0.00 37.39 2.40
606 625 1.067142 GTACATGCACGGAGTCTTCCA 60.067 52.381 0.00 0.00 41.61 3.53
614 633 0.396811 CGGAGTCTTCCAACTTGGGT 59.603 55.000 8.01 0.00 44.26 4.51
624 643 0.607217 CAACTTGGGTTCCGGGTACC 60.607 60.000 14.02 14.02 38.39 3.34
648 667 2.750637 GACGAGCTCGGGGAGACA 60.751 66.667 36.93 0.00 44.95 3.41
662 681 4.013050 GGGGAGACAATGGAGAAAGAAAG 58.987 47.826 0.00 0.00 0.00 2.62
694 713 4.801330 TCAATAGACACGAAGACCACAT 57.199 40.909 0.00 0.00 0.00 3.21
701 720 4.021456 AGACACGAAGACCACATACATGAA 60.021 41.667 0.00 0.00 0.00 2.57
844 869 2.520020 AGCAGCAAGGCACAGCAA 60.520 55.556 0.00 0.00 35.83 3.91
976 1003 0.921256 AGAGGGGAAGGATTGGGTGG 60.921 60.000 0.00 0.00 0.00 4.61
1133 1162 2.235016 GAGATACCAGAGACGCATCCT 58.765 52.381 0.00 0.00 0.00 3.24
1222 1251 4.008933 GCGTCCTGCTGGTGGTCT 62.009 66.667 9.73 0.00 41.73 3.85
1268 1297 4.796495 GTCAGGGCCGCGGGAATT 62.796 66.667 29.38 0.00 0.00 2.17
1357 1387 4.483243 GGGATCGGGAAAGCGGCA 62.483 66.667 1.45 0.00 0.00 5.69
1397 1430 1.881709 GGGCTCGCTAGGTTTACGC 60.882 63.158 0.00 0.00 0.00 4.42
1402 1435 2.580815 GCTAGGTTTACGCGGGGT 59.419 61.111 12.47 2.46 0.00 4.95
1464 1497 3.466881 CCAACTGACCGACTGGGA 58.533 61.111 0.00 0.00 40.75 4.37
1505 1538 3.117474 TCTCCCTCATTCTCTCGTACCAT 60.117 47.826 0.00 0.00 0.00 3.55
1828 1898 3.043340 GCAAGTGTGTTTGCGGTTT 57.957 47.368 0.00 0.00 43.36 3.27
1955 2026 6.887545 AGATCCATACGGTTTATTTGGTTGAA 59.112 34.615 0.00 0.00 0.00 2.69
2144 2232 1.964223 GATCTAGAATGGCACCGGAGA 59.036 52.381 9.46 0.00 0.00 3.71
2172 2270 6.137559 ACGGAAGAGGAAGATAAGAGGTAAT 58.862 40.000 0.00 0.00 0.00 1.89
2191 2289 9.216117 GAGGTAATACTAAGTTGCTTCTTTGAA 57.784 33.333 8.93 0.00 0.00 2.69
2192 2290 9.569122 AGGTAATACTAAGTTGCTTCTTTGAAA 57.431 29.630 8.93 0.00 0.00 2.69
2349 2450 6.250344 TGAAAAGAGATGCAAGACTTGATG 57.750 37.500 19.51 0.00 0.00 3.07
2471 2575 5.248640 TGGAAGGAACTGAACATGATCTTC 58.751 41.667 0.00 0.00 40.86 2.87
2559 2674 7.283580 TGGAATCAAAAGAACGGAGTAGAAAAA 59.716 33.333 0.00 0.00 45.00 1.94
2644 2765 4.522722 TGGAAAACCAACAACGAAAAGT 57.477 36.364 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 4.386951 CATGCCGTCCACCCGTGA 62.387 66.667 0.00 0.00 0.00 4.35
166 169 4.255510 TGTAAGGTATAACCCCGAGACT 57.744 45.455 0.00 0.00 39.75 3.24
210 213 7.232737 TGAATGACTACTTCCTCTACAAACTCA 59.767 37.037 0.00 0.00 0.00 3.41
216 219 4.398358 CCGTGAATGACTACTTCCTCTACA 59.602 45.833 0.00 0.00 0.00 2.74
242 246 3.119245 ACATGTACCACGACTACCATGAC 60.119 47.826 0.00 0.00 0.00 3.06
376 389 0.391661 TCTACTTCTACCGCCGTCGT 60.392 55.000 0.00 0.00 0.00 4.34
495 508 3.267812 ACCACAGATTCATGAGGTTCCAT 59.732 43.478 0.00 0.00 40.73 3.41
502 521 2.482664 CCGGAGACCACAGATTCATGAG 60.483 54.545 0.00 0.00 0.00 2.90
512 531 1.985662 ATTACGCCCGGAGACCACA 60.986 57.895 0.73 0.00 0.00 4.17
583 602 3.181479 GGAAGACTCCGTGCATGTACATA 60.181 47.826 14.55 0.11 30.03 2.29
592 611 0.868406 CAAGTTGGAAGACTCCGTGC 59.132 55.000 0.00 0.00 45.85 5.34
606 625 1.763120 GGTACCCGGAACCCAAGTT 59.237 57.895 0.73 0.00 39.54 2.66
624 643 1.878522 CCCGAGCTCGTCAAATCCG 60.879 63.158 32.41 15.54 37.74 4.18
648 667 1.815003 CCGCTGCTTTCTTTCTCCATT 59.185 47.619 0.00 0.00 0.00 3.16
662 681 0.864455 GTCTATTGATGCTCCGCTGC 59.136 55.000 0.00 0.00 0.00 5.25
844 869 2.736236 CTGCAGCTTCGAGTGCGT 60.736 61.111 0.00 0.00 42.96 5.24
896 921 2.571757 CTTGCCTCGTGCGACCTA 59.428 61.111 0.00 0.00 45.60 3.08
1025 1054 2.770475 GCCCTCTCCTTCCCCCTC 60.770 72.222 0.00 0.00 0.00 4.30
1098 1127 3.385384 CTCCGTCCTCCAGCTGCA 61.385 66.667 8.66 0.00 0.00 4.41
1101 1130 0.468400 GGTATCTCCGTCCTCCAGCT 60.468 60.000 0.00 0.00 0.00 4.24
1357 1387 0.605589 CCTCCTCGTTCACTTCTGCT 59.394 55.000 0.00 0.00 0.00 4.24
1365 1395 2.683933 GCCCCTCCTCCTCGTTCA 60.684 66.667 0.00 0.00 0.00 3.18
1397 1430 2.291043 AAGGCCTAGTCACACCCCG 61.291 63.158 5.16 0.00 0.00 5.73
1402 1435 3.077907 GCCCAAGGCCTAGTCACA 58.922 61.111 5.16 0.00 44.06 3.58
1464 1497 0.548682 AGAGGAGAACCCCAGTGCAT 60.549 55.000 0.00 0.00 36.73 3.96
1717 1776 3.766676 TCGAGACTCTTCCTGATTTCG 57.233 47.619 0.03 0.00 0.00 3.46
1955 2026 6.147000 GTCATCATGCAACCCGTTTTAAAAAT 59.853 34.615 1.31 0.00 0.00 1.82
2028 2114 1.349259 CCGGGATTCGTCGTGTGTTC 61.349 60.000 0.00 0.00 37.11 3.18
2144 2232 5.128008 CCTCTTATCTTCCTCTTCCGTTTCT 59.872 44.000 0.00 0.00 0.00 2.52
2192 2290 3.219052 TCTTTGGTTTCACGCGTTTTT 57.781 38.095 10.22 0.00 0.00 1.94
2193 2291 2.918600 GTTCTTTGGTTTCACGCGTTTT 59.081 40.909 10.22 0.00 0.00 2.43
2199 2297 4.364415 TTCAAGGTTCTTTGGTTTCACG 57.636 40.909 0.00 0.00 0.00 4.35
2349 2450 2.767505 TCCTCAACTTCTTTTCGCCTC 58.232 47.619 0.00 0.00 0.00 4.70
2471 2575 4.852134 TCAACCCATCATCTTGTTTGTG 57.148 40.909 0.00 0.00 0.00 3.33
2552 2667 9.621629 TTTGAGGTAGAAGATGTTGTTTTTCTA 57.378 29.630 0.00 0.00 32.54 2.10
2559 2674 5.703130 GCTCTTTTGAGGTAGAAGATGTTGT 59.297 40.000 0.00 0.00 46.30 3.32
2644 2765 2.584835 AAGCCCACATCAAGCTTACA 57.415 45.000 0.00 0.00 44.72 2.41


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

AutoCloner maintained by Alex Coulton.