Multiple sequence alignment - TraesCS7D01G088900

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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 TraesCS7D01G088900 chr7D 100.000 2298 0 0 1 2298 53774981 53777278 0.000000e+00 4244
1 TraesCS7D01G088900 chr7D 96.674 872 22 2 1 870 53756723 53757589 0.000000e+00 1443
2 TraesCS7D01G088900 chr7D 92.423 871 55 5 1 868 221972239 221973101 0.000000e+00 1232
3 TraesCS7D01G088900 chr7D 91.514 872 66 3 2 870 221963020 221963886 0.000000e+00 1194
4 TraesCS7D01G088900 chr6D 92.966 853 52 3 20 870 395754804 395755650 0.000000e+00 1236
5 TraesCS7D01G088900 chr6D 92.299 870 60 3 1 869 292371484 292372347 0.000000e+00 1229
6 TraesCS7D01G088900 chr6D 92.723 852 55 2 20 869 395804739 395805585 0.000000e+00 1223
7 TraesCS7D01G088900 chr6D 92.497 853 57 2 20 870 395743834 395744681 0.000000e+00 1214
8 TraesCS7D01G088900 chr2D 91.696 867 65 6 3 867 219519258 219518397 0.000000e+00 1195
9 TraesCS7D01G088900 chr2D 91.514 872 67 2 1 870 219536229 219535363 0.000000e+00 1194
10 TraesCS7D01G088900 chr2D 87.600 879 79 17 871 1729 2693494 2692626 0.000000e+00 992
11 TraesCS7D01G088900 chr2D 88.514 592 51 10 871 1447 2115193 2115782 0.000000e+00 701
12 TraesCS7D01G088900 chr2D 79.960 494 76 18 1813 2297 408835858 408836337 2.190000e-90 342
13 TraesCS7D01G088900 chr2D 88.596 228 26 0 1502 1729 2115782 2116009 6.250000e-71 278
14 TraesCS7D01G088900 chr7A 86.769 1043 83 23 1296 2297 57206472 57207500 0.000000e+00 1110
15 TraesCS7D01G088900 chr7A 96.380 221 5 3 867 1086 57205718 57205936 6.040000e-96 361
16 TraesCS7D01G088900 chr7A 79.323 266 42 13 1951 2211 376180744 376181001 8.440000e-40 174
17 TraesCS7D01G088900 chr7A 93.827 81 4 1 1123 1203 57205936 57206015 1.120000e-23 121
18 TraesCS7D01G088900 chr2A 87.785 876 88 11 871 1729 2058696 2059569 0.000000e+00 1007
19 TraesCS7D01G088900 chr2A 86.986 876 95 11 871 1729 2152022 2152895 0.000000e+00 968
20 TraesCS7D01G088900 chr4A 92.575 431 25 5 867 1297 669646102 669645679 1.510000e-171 612
21 TraesCS7D01G088900 chr4A 90.749 454 26 8 1296 1735 669645046 669644595 1.970000e-165 592
22 TraesCS7D01G088900 chr4A 87.472 439 53 2 1861 2297 669644385 669643947 2.630000e-139 505
23 TraesCS7D01G088900 chr3D 81.993 572 81 17 1739 2297 531950315 531949753 1.240000e-127 466
24 TraesCS7D01G088900 chr2B 88.088 319 35 3 871 1187 31064365 31064682 2.160000e-100 375
25 TraesCS7D01G088900 chr2B 87.597 258 18 7 1311 1555 31071772 31072028 1.040000e-73 287
26 TraesCS7D01G088900 chr2B 82.000 200 29 6 1954 2151 575291434 575291628 1.830000e-36 163
27 TraesCS7D01G088900 chr7B 79.335 421 73 13 1813 2230 499258693 499259102 1.340000e-72 283
28 TraesCS7D01G088900 chr7B 80.769 312 54 6 1874 2184 626809710 626810016 2.950000e-59 239
29 TraesCS7D01G088900 chr3B 81.548 336 56 6 1868 2201 524096665 524096996 2.910000e-69 272
30 TraesCS7D01G088900 chr1B 85.385 260 33 5 1974 2230 207442473 207442730 4.870000e-67 265
31 TraesCS7D01G088900 chr5D 79.598 348 62 9 1948 2291 294940649 294940307 8.200000e-60 241
32 TraesCS7D01G088900 chr5B 78.927 261 45 10 1954 2211 143693441 143693694 3.930000e-38 169


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 TraesCS7D01G088900 chr7D 53774981 53777278 2297 False 4244.000000 4244 100.000000 1 2298 1 chr7D.!!$F2 2297
1 TraesCS7D01G088900 chr7D 53756723 53757589 866 False 1443.000000 1443 96.674000 1 870 1 chr7D.!!$F1 869
2 TraesCS7D01G088900 chr7D 221972239 221973101 862 False 1232.000000 1232 92.423000 1 868 1 chr7D.!!$F4 867
3 TraesCS7D01G088900 chr7D 221963020 221963886 866 False 1194.000000 1194 91.514000 2 870 1 chr7D.!!$F3 868
4 TraesCS7D01G088900 chr6D 395754804 395755650 846 False 1236.000000 1236 92.966000 20 870 1 chr6D.!!$F3 850
5 TraesCS7D01G088900 chr6D 292371484 292372347 863 False 1229.000000 1229 92.299000 1 869 1 chr6D.!!$F1 868
6 TraesCS7D01G088900 chr6D 395804739 395805585 846 False 1223.000000 1223 92.723000 20 869 1 chr6D.!!$F4 849
7 TraesCS7D01G088900 chr6D 395743834 395744681 847 False 1214.000000 1214 92.497000 20 870 1 chr6D.!!$F2 850
8 TraesCS7D01G088900 chr2D 219518397 219519258 861 True 1195.000000 1195 91.696000 3 867 1 chr2D.!!$R2 864
9 TraesCS7D01G088900 chr2D 219535363 219536229 866 True 1194.000000 1194 91.514000 1 870 1 chr2D.!!$R3 869
10 TraesCS7D01G088900 chr2D 2692626 2693494 868 True 992.000000 992 87.600000 871 1729 1 chr2D.!!$R1 858
11 TraesCS7D01G088900 chr2D 2115193 2116009 816 False 489.500000 701 88.555000 871 1729 2 chr2D.!!$F2 858
12 TraesCS7D01G088900 chr7A 57205718 57207500 1782 False 530.666667 1110 92.325333 867 2297 3 chr7A.!!$F2 1430
13 TraesCS7D01G088900 chr2A 2058696 2059569 873 False 1007.000000 1007 87.785000 871 1729 1 chr2A.!!$F1 858
14 TraesCS7D01G088900 chr2A 2152022 2152895 873 False 968.000000 968 86.986000 871 1729 1 chr2A.!!$F2 858
15 TraesCS7D01G088900 chr4A 669643947 669646102 2155 True 569.666667 612 90.265333 867 2297 3 chr4A.!!$R1 1430
16 TraesCS7D01G088900 chr3D 531949753 531950315 562 True 466.000000 466 81.993000 1739 2297 1 chr3D.!!$R1 558

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
415 417 0.72379 GCTCGACGAGACGAAACGAA 60.724 55.0 28.43 0.0 41.67 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 3340 1.078426 ATGACCCCTGCGCACTTAC 60.078 57.895 5.66 0.0 0.0 2.34 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
61 63 1.266178 TCACTCGGAAGGCAATCTCA 58.734 50.000 0.00 0.00 0.00 3.27
88 90 4.071423 TCGATCAGCAAGTTTTCATTCCA 58.929 39.130 0.00 0.00 0.00 3.53
148 150 4.094590 TCGGAAGACAATCTCTTACTCGAC 59.905 45.833 0.00 0.00 39.53 4.20
165 167 1.535462 CGACCGGCAAGTTTTCATTCT 59.465 47.619 0.00 0.00 0.00 2.40
328 330 2.009774 CCGACTGAAAACATAGCCTGG 58.990 52.381 0.00 0.00 0.00 4.45
413 415 1.154450 AGCTCGACGAGACGAAACG 60.154 57.895 28.43 0.24 41.67 3.60
414 416 1.154525 GCTCGACGAGACGAAACGA 60.155 57.895 28.43 0.00 41.67 3.85
415 417 0.723790 GCTCGACGAGACGAAACGAA 60.724 55.000 28.43 0.00 41.67 3.85
416 418 1.666904 CTCGACGAGACGAAACGAAA 58.333 50.000 20.25 0.00 41.67 3.46
417 419 2.039085 CTCGACGAGACGAAACGAAAA 58.961 47.619 20.25 0.00 41.67 2.29
449 451 4.023193 GCTGAAGGTTTTTCGATTCAAGGA 60.023 41.667 0.00 0.00 31.70 3.36
821 827 2.814336 GCTGAAAACCCTTTCACTCGAT 59.186 45.455 0.00 0.00 44.76 3.59
1010 1017 4.972733 AACGTGCATGCAGCCCCA 62.973 61.111 23.41 0.00 44.83 4.96
1222 1633 2.564771 CCGGTGTACTACGGTGATAGA 58.435 52.381 17.15 0.00 44.85 1.98
1245 1656 1.353694 AGATGCCTTCACCTTCAGCTT 59.646 47.619 0.00 0.00 0.00 3.74
1282 1693 6.373774 ACATCATTAAGAGCCTCTTTGTCAAG 59.626 38.462 13.04 2.58 37.89 3.02
1301 2345 4.533707 TCAAGCCCATTCCCATCTAGATAG 59.466 45.833 4.54 0.00 0.00 2.08
1476 2537 5.468409 TGTTTCGATGTGTGACATGTATGTT 59.532 36.000 0.00 0.00 39.27 2.71
1586 2648 5.277634 CGGTCCAGTTTTTATTGAAACGTCT 60.278 40.000 0.00 0.00 42.78 4.18
1623 2685 6.520021 AATTTATGTGGGAGAGGATGATCA 57.480 37.500 0.00 0.00 0.00 2.92
1791 2881 2.422093 GCCAGAGTAGAGGGGGAAAATG 60.422 54.545 0.00 0.00 0.00 2.32
1839 2936 2.357323 CAGCATCAGAAGAGAGTAGCGA 59.643 50.000 0.00 0.00 0.00 4.93
1845 2942 7.339212 AGCATCAGAAGAGAGTAGCGAATATAT 59.661 37.037 0.00 0.00 0.00 0.86
1846 2943 7.973388 GCATCAGAAGAGAGTAGCGAATATATT 59.027 37.037 0.00 0.00 0.00 1.28
1891 3050 0.473326 AGCAATGCCCTGAGATCCTC 59.527 55.000 0.00 0.00 0.00 3.71
1921 3080 2.378547 ACCCTACAAGAAAGCAATCCCA 59.621 45.455 0.00 0.00 0.00 4.37
1922 3081 3.181423 ACCCTACAAGAAAGCAATCCCAA 60.181 43.478 0.00 0.00 0.00 4.12
1934 3093 5.099042 AGCAATCCCAAAGTAGTTATCGT 57.901 39.130 0.00 0.00 0.00 3.73
2006 3165 1.592400 CTCCGAGCGTCCTGTTACCA 61.592 60.000 0.00 0.00 0.00 3.25
2022 3181 0.180406 ACCATGGACACGGCTATTCC 59.820 55.000 21.47 0.00 0.00 3.01
2089 3248 2.746472 GCTCAATTAACTCTGGCCGGAT 60.746 50.000 16.52 3.37 0.00 4.18
2168 3328 3.099267 CTCTCCAAAGAGTCAACACGT 57.901 47.619 0.00 0.00 43.52 4.49
2180 3340 2.340577 GTCAACACGTCGGTCTAAATCG 59.659 50.000 0.00 0.00 0.00 3.34
2189 3349 1.254570 CGGTCTAAATCGTAAGTGCGC 59.745 52.381 0.00 0.00 39.48 6.09
2217 3379 2.203015 GCCGATCGCCCTAAGCAA 60.203 61.111 10.32 0.00 44.04 3.91
2297 3459 0.755327 AACCAGCTCACCCCAACAAC 60.755 55.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.567138 ATGGTCATCCGAGTGAAAATTTC 57.433 39.130 0.00 0.00 36.30 2.17
16 17 7.645058 AATATGGTCATCCGAGTGAAAATTT 57.355 32.000 0.00 0.00 36.30 1.82
61 63 6.992063 ATGAAAACTTGCTGATCGAGTAAT 57.008 33.333 0.00 0.00 38.47 1.89
88 90 4.261578 TCCGAGTGAAAAGATTACCGTT 57.738 40.909 0.00 0.00 0.00 4.44
328 330 2.926838 GCCTCGAGAGACAAATCAAGAC 59.073 50.000 15.71 0.00 35.39 3.01
413 415 3.977427 ACCTTCAGCACGGAAAATTTTC 58.023 40.909 20.51 20.51 36.46 2.29
414 416 4.400529 AACCTTCAGCACGGAAAATTTT 57.599 36.364 2.28 2.28 0.00 1.82
415 417 4.400529 AAACCTTCAGCACGGAAAATTT 57.599 36.364 0.00 0.00 0.00 1.82
416 418 4.400529 AAAACCTTCAGCACGGAAAATT 57.599 36.364 0.00 0.00 0.00 1.82
417 419 4.368315 GAAAAACCTTCAGCACGGAAAAT 58.632 39.130 0.00 0.00 0.00 1.82
449 451 1.755179 CAATTCGGCCCTCAAGATGT 58.245 50.000 0.00 0.00 0.00 3.06
821 827 5.068198 GGCATAAAAAGAGAATGAGATGGCA 59.932 40.000 0.00 0.00 38.21 4.92
1010 1017 1.922447 TGGCCACATCCCTATTGTTCT 59.078 47.619 0.00 0.00 0.00 3.01
1090 1097 7.360861 CCACTCATCTTCTATCATCGAGTCTAC 60.361 44.444 0.00 0.00 30.12 2.59
1222 1633 2.560105 GCTGAAGGTGAAGGCATCTTTT 59.440 45.455 0.00 0.00 45.25 2.27
1245 1656 5.418676 TCTTAATGATGTCGTCAAGATGCA 58.581 37.500 0.00 0.00 40.97 3.96
1282 1693 5.026790 AGTACTATCTAGATGGGAATGGGC 58.973 45.833 19.12 0.00 0.00 5.36
1301 2345 1.542108 GCCTGCATGAGGATGGAGTAC 60.542 57.143 13.48 0.00 46.33 2.73
1350 2397 5.668558 ACACGAGATTGGAAAACAACTAC 57.331 39.130 0.00 0.00 42.94 2.73
1353 2410 7.924103 ATTAAACACGAGATTGGAAAACAAC 57.076 32.000 0.00 0.00 42.94 3.32
1476 2537 3.004629 GGTTCATCTGACATGCAACACAA 59.995 43.478 0.00 0.00 0.00 3.33
1586 2648 6.543465 CCCACATAAATTTAGTGATCTGAGCA 59.457 38.462 20.27 0.00 35.33 4.26
1639 2701 7.361201 CCGAAAATCCGAATCACATATTAGCAT 60.361 37.037 0.00 0.00 0.00 3.79
1791 2881 7.910441 AGATACTAGTCTTCGTTAGGATAGC 57.090 40.000 0.00 0.00 0.00 2.97
1856 2953 5.813672 GGCATTGCTGATATGAAAACATTGT 59.186 36.000 8.82 0.00 0.00 2.71
1857 2954 5.235616 GGGCATTGCTGATATGAAAACATTG 59.764 40.000 8.82 0.00 0.00 2.82
1863 3022 3.887110 CTCAGGGCATTGCTGATATGAAA 59.113 43.478 8.82 0.00 0.00 2.69
1866 3025 3.136009 TCTCAGGGCATTGCTGATATG 57.864 47.619 8.82 1.31 0.00 1.78
1891 3050 2.431954 TCTTGTAGGGTAGTCGAGGG 57.568 55.000 0.00 0.00 0.00 4.30
1959 3118 8.500238 TGTATCCTGATCTACTACACCTAGAAA 58.500 37.037 0.00 0.00 0.00 2.52
1966 3125 6.293516 CGGAGTTGTATCCTGATCTACTACAC 60.294 46.154 0.00 0.00 37.20 2.90
2006 3165 3.646162 TCTATTGGAATAGCCGTGTCCAT 59.354 43.478 2.02 0.00 41.05 3.41
2056 3215 5.985781 AGTTAATTGAGCGTGTTGTGTAAG 58.014 37.500 0.00 0.00 0.00 2.34
2061 3220 3.498397 CCAGAGTTAATTGAGCGTGTTGT 59.502 43.478 0.00 0.00 0.00 3.32
2089 3248 5.765576 TGGGCATTACCTAGAAAAGTGTA 57.234 39.130 0.00 0.00 39.10 2.90
2168 3328 2.789208 CGCACTTACGATTTAGACCGA 58.211 47.619 0.00 0.00 34.06 4.69
2180 3340 1.078426 ATGACCCCTGCGCACTTAC 60.078 57.895 5.66 0.00 0.00 2.34
2189 3349 2.111878 GATCGGCCATGACCCCTG 59.888 66.667 2.24 0.00 0.00 4.45
2217 3379 1.672356 GCCAGACAACGTGCAGGAT 60.672 57.895 14.38 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.