Multiple sequence alignment - TraesCS3A01G257100

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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 TraesCS3A01G257100 chr3A 100.000 2468 0 0 1 2468 478912874 478915341 0.000000e+00 4558.0
1 TraesCS3A01G257100 chr6A 96.066 1754 64 4 718 2468 596355510 596357261 0.000000e+00 2852.0
2 TraesCS3A01G257100 chr6A 88.459 1811 136 38 715 2468 144491466 144493260 0.000000e+00 2119.0
3 TraesCS3A01G257100 chr6A 100.000 28 0 0 488 515 176409010 176408983 4.000000e-03 52.8
4 TraesCS3A01G257100 chr7D 92.560 1801 67 18 727 2468 151511976 151513768 0.000000e+00 2521.0
5 TraesCS3A01G257100 chr5A 95.094 1488 71 1 876 2361 407700002 407701489 0.000000e+00 2342.0
6 TraesCS3A01G257100 chr5A 95.812 191 8 0 2277 2467 407701449 407701639 2.380000e-80 309.0
7 TraesCS3A01G257100 chr2D 89.928 1817 102 32 724 2468 520043086 520044893 0.000000e+00 2266.0
8 TraesCS3A01G257100 chr2D 89.375 1807 112 35 727 2468 451467953 451469744 0.000000e+00 2200.0
9 TraesCS3A01G257100 chr2D 89.901 1624 110 23 724 2317 35331898 35330299 0.000000e+00 2041.0
10 TraesCS3A01G257100 chr2D 92.258 1395 94 8 717 2104 613419776 613421163 0.000000e+00 1965.0
11 TraesCS3A01G257100 chr2D 88.011 367 26 10 2120 2468 241271382 241271748 3.800000e-113 418.0
12 TraesCS3A01G257100 chr2D 90.040 251 21 2 2120 2367 260865743 260865494 3.060000e-84 322.0
13 TraesCS3A01G257100 chr2D 84.793 217 19 8 2266 2468 613421286 613421502 3.220000e-49 206.0
14 TraesCS3A01G257100 chr6B 89.983 1787 120 23 724 2468 494076436 494078205 0.000000e+00 2254.0
15 TraesCS3A01G257100 chr7A 88.617 1801 140 28 724 2468 471263889 471262098 0.000000e+00 2130.0
16 TraesCS3A01G257100 chr5B 91.919 1386 99 7 724 2104 260234933 260236310 0.000000e+00 1927.0
17 TraesCS3A01G257100 chr6D 91.709 1387 102 7 724 2104 114017559 114016180 0.000000e+00 1912.0
18 TraesCS3A01G257100 chr3D 93.481 721 33 6 1 711 359514006 359514722 0.000000e+00 1059.0
19 TraesCS3A01G257100 chr3D 100.000 30 0 0 486 515 546168562 546168591 3.430000e-04 56.5
20 TraesCS3A01G257100 chr3B 88.091 529 38 12 192 712 465504716 465505227 2.710000e-169 604.0
21 TraesCS3A01G257100 chr5D 85.302 381 23 16 2120 2468 26958496 26958117 1.800000e-96 363.0
22 TraesCS3A01G257100 chr5D 100.000 29 0 0 487 515 522512849 522512877 1.000000e-03 54.7
23 TraesCS3A01G257100 chr7B 100.000 28 0 0 488 515 185298082 185298109 4.000000e-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 TraesCS3A01G257100 chr3A 478912874 478915341 2467 False 4558.0 4558 100.0000 1 2468 1 chr3A.!!$F1 2467
1 TraesCS3A01G257100 chr6A 596355510 596357261 1751 False 2852.0 2852 96.0660 718 2468 1 chr6A.!!$F2 1750
2 TraesCS3A01G257100 chr6A 144491466 144493260 1794 False 2119.0 2119 88.4590 715 2468 1 chr6A.!!$F1 1753
3 TraesCS3A01G257100 chr7D 151511976 151513768 1792 False 2521.0 2521 92.5600 727 2468 1 chr7D.!!$F1 1741
4 TraesCS3A01G257100 chr5A 407700002 407701639 1637 False 1325.5 2342 95.4530 876 2467 2 chr5A.!!$F1 1591
5 TraesCS3A01G257100 chr2D 520043086 520044893 1807 False 2266.0 2266 89.9280 724 2468 1 chr2D.!!$F3 1744
6 TraesCS3A01G257100 chr2D 451467953 451469744 1791 False 2200.0 2200 89.3750 727 2468 1 chr2D.!!$F2 1741
7 TraesCS3A01G257100 chr2D 35330299 35331898 1599 True 2041.0 2041 89.9010 724 2317 1 chr2D.!!$R1 1593
8 TraesCS3A01G257100 chr2D 613419776 613421502 1726 False 1085.5 1965 88.5255 717 2468 2 chr2D.!!$F4 1751
9 TraesCS3A01G257100 chr6B 494076436 494078205 1769 False 2254.0 2254 89.9830 724 2468 1 chr6B.!!$F1 1744
10 TraesCS3A01G257100 chr7A 471262098 471263889 1791 True 2130.0 2130 88.6170 724 2468 1 chr7A.!!$R1 1744
11 TraesCS3A01G257100 chr5B 260234933 260236310 1377 False 1927.0 1927 91.9190 724 2104 1 chr5B.!!$F1 1380
12 TraesCS3A01G257100 chr6D 114016180 114017559 1379 True 1912.0 1912 91.7090 724 2104 1 chr6D.!!$R1 1380
13 TraesCS3A01G257100 chr3D 359514006 359514722 716 False 1059.0 1059 93.4810 1 711 1 chr3D.!!$F1 710
14 TraesCS3A01G257100 chr3B 465504716 465505227 511 False 604.0 604 88.0910 192 712 1 chr3B.!!$F1 520

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
919 942 1.282157 GGCCTACTTGTCAGGTTGGAT 59.718 52.381 17.67 0.0 35.45 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 1920 0.244994 CTTGTGAGTCAGGTCCTCGG 59.755 60.0 0.0 0.0 0.0 4.63 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
54 55 8.947055 ATTCATTTTGTATTGCTATTTGGTCC 57.053 30.769 0.00 0.00 0.00 4.46
59 60 2.755952 ATTGCTATTTGGTCCCTCCC 57.244 50.000 0.00 0.00 34.77 4.30
92 93 1.822990 GTCGTAGTTCCCATCACCAGA 59.177 52.381 0.00 0.00 0.00 3.86
96 97 3.676324 CGTAGTTCCCATCACCAGACTTC 60.676 52.174 0.00 0.00 0.00 3.01
113 117 5.598005 CAGACTTCTATCATCTCCTTGGACT 59.402 44.000 0.00 0.00 0.00 3.85
136 140 6.039047 ACTGATTGTCAATATCTGAACATGGC 59.961 38.462 0.00 0.00 35.22 4.40
172 176 3.004734 ACTGTTTGTTGCCATTGTAGAGC 59.995 43.478 0.00 0.00 0.00 4.09
289 300 8.412456 TGATTTGCTTCTTTCAACTTCATTGTA 58.588 29.630 0.00 0.00 39.54 2.41
290 301 9.248291 GATTTGCTTCTTTCAACTTCATTGTAA 57.752 29.630 0.00 0.00 39.54 2.41
301 312 9.585099 TTCAACTTCATTGTAATTGAATATGGC 57.415 29.630 0.00 0.00 39.54 4.40
380 396 8.627403 CATTTGTCAGGCTACTTCATTTGATAT 58.373 33.333 0.00 0.00 0.00 1.63
550 567 1.363744 AATTGCTCACGTGCTCTAGC 58.636 50.000 17.46 17.46 42.50 3.42
712 731 6.054860 AGGCTGATGTGTGTCTTTTACTAT 57.945 37.500 0.00 0.00 0.00 2.12
713 732 7.182817 AGGCTGATGTGTGTCTTTTACTATA 57.817 36.000 0.00 0.00 0.00 1.31
714 733 7.796054 AGGCTGATGTGTGTCTTTTACTATAT 58.204 34.615 0.00 0.00 0.00 0.86
715 734 8.267894 AGGCTGATGTGTGTCTTTTACTATATT 58.732 33.333 0.00 0.00 0.00 1.28
716 735 8.893727 GGCTGATGTGTGTCTTTTACTATATTT 58.106 33.333 0.00 0.00 0.00 1.40
919 942 1.282157 GGCCTACTTGTCAGGTTGGAT 59.718 52.381 17.67 0.00 35.45 3.41
938 961 3.877508 GGATTGTTATAGAGCTGCCGTTT 59.122 43.478 0.00 0.00 0.00 3.60
967 991 2.636893 CGATCTGGATCAGAAATCCCCT 59.363 50.000 10.62 0.00 44.04 4.79
998 1023 6.329197 CAGTCCAAATCCCTAACCCTATTCTA 59.671 42.308 0.00 0.00 0.00 2.10
1119 1144 1.374252 CCGTAGCTTGCTGGAACGT 60.374 57.895 13.12 0.00 31.87 3.99
1466 1491 3.363182 CGTTGGATTCAGTTTTCGCGTTA 60.363 43.478 5.77 0.00 0.00 3.18
1589 1614 0.250467 GTTCTCAAGCAGCTGGGTGA 60.250 55.000 17.12 0.00 0.00 4.02
1683 1708 1.380403 TTGTTGGCAAGGTGGTGACG 61.380 55.000 0.00 0.00 0.00 4.35
1893 1920 2.749441 GTGGCTGCCAGGAGAAGC 60.749 66.667 24.10 4.31 32.34 3.86
1908 1935 1.228894 AAGCCGAGGACCTGACTCA 60.229 57.895 0.00 0.00 34.66 3.41
2018 2046 2.151502 TTGGCTTTCCACTTGGTTCA 57.848 45.000 0.00 0.00 43.33 3.18
2084 2114 3.884169 TCTATTTTGTGCTCGTTGTTGC 58.116 40.909 0.00 0.00 0.00 4.17
2100 2130 3.623848 TGCGGTGAAGCAACTGTAT 57.376 47.368 0.00 0.00 45.06 2.29
2113 2176 5.367302 AGCAACTGTATTGCCAAAATTGTT 58.633 33.333 7.97 0.00 45.98 2.83
2274 2406 7.793902 AGTAAACAGTAGCATTCAACTAAACG 58.206 34.615 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.153489 CATGCAGACACTCGGGAGG 60.153 63.158 0.00 0.00 0.00 4.30
59 60 1.135660 ACTACGACATGCAGACACTCG 60.136 52.381 0.00 0.00 36.07 4.18
92 93 5.523588 TCAGTCCAAGGAGATGATAGAAGT 58.476 41.667 0.00 0.00 0.00 3.01
96 97 6.172136 ACAATCAGTCCAAGGAGATGATAG 57.828 41.667 14.04 0.73 33.35 2.08
113 117 6.038936 CAGCCATGTTCAGATATTGACAATCA 59.961 38.462 3.36 0.00 34.94 2.57
136 140 5.200368 ACAAACAGTAAAGGCAAATCCAG 57.800 39.130 0.00 0.00 37.29 3.86
172 176 6.741992 TGCTAACAACCATGATACAGAAAG 57.258 37.500 0.00 0.00 0.00 2.62
289 300 7.448469 GGTACCTATTGACAGCCATATTCAATT 59.552 37.037 4.06 0.00 39.92 2.32
290 301 6.942576 GGTACCTATTGACAGCCATATTCAAT 59.057 38.462 4.06 5.23 41.67 2.57
301 312 3.689649 GCTTTGGTGGTACCTATTGACAG 59.310 47.826 14.36 1.93 39.58 3.51
385 401 5.527214 CAGGCGGTAATTACATTCAGATGAA 59.473 40.000 17.16 0.00 36.73 2.57
518 535 4.114794 GTGAGCAATTAATTGGCATGGTC 58.885 43.478 25.61 16.78 38.21 4.02
552 569 3.460672 ATATGGGCTGCGACGGTGG 62.461 63.158 0.00 0.00 0.00 4.61
556 573 0.514255 CATTCATATGGGCTGCGACG 59.486 55.000 2.13 0.00 0.00 5.12
601 618 4.573900 AGAATGAAACTAGGAGTGCACAG 58.426 43.478 21.04 10.09 0.00 3.66
833 854 2.448582 TGGAGACAAACCAGCGGGT 61.449 57.895 1.28 1.28 43.40 5.28
919 942 3.055385 AGGAAACGGCAGCTCTATAACAA 60.055 43.478 0.00 0.00 0.00 2.83
938 961 1.137675 CTGATCCAGATCGCAACAGGA 59.862 52.381 3.33 0.00 40.63 3.86
967 991 2.059756 AGGGATTTGGACTGGGAAGA 57.940 50.000 0.00 0.00 0.00 2.87
1171 1196 0.749649 GAGATCAGGACATGGCTCGT 59.250 55.000 0.00 0.00 0.00 4.18
1264 1289 3.168604 CGTCACTGTCTGCTCGCG 61.169 66.667 0.00 0.00 0.00 5.87
1466 1491 2.234661 TGAGATCGAACCATTCTGCACT 59.765 45.455 0.00 0.00 0.00 4.40
1498 1523 3.059884 CGAGCTTGCTCTTGTACTTCAA 58.940 45.455 18.75 0.00 34.61 2.69
1589 1614 1.273048 GCAGGATCTCGATCAGCTCAT 59.727 52.381 8.97 0.00 39.54 2.90
1683 1708 2.054232 TCGACTCAGGTATCTCCACC 57.946 55.000 0.00 0.00 39.02 4.61
1893 1920 0.244994 CTTGTGAGTCAGGTCCTCGG 59.755 60.000 0.00 0.00 0.00 4.63
1908 1935 4.394300 GCACAGTCTTGAAGATATGCTTGT 59.606 41.667 16.27 5.71 36.83 3.16
2018 2046 7.117236 CACTACAGATTGTTAACACGGTACAAT 59.883 37.037 8.07 6.69 43.19 2.71
2084 2114 1.135689 GGCAATACAGTTGCTTCACCG 60.136 52.381 11.92 0.00 44.36 4.94
2113 2176 6.210385 ACCAGCACATTACACAAATATTTGGA 59.790 34.615 27.43 12.80 42.34 3.53
2168 2265 4.870123 TGGCACAAACAAATAAGCTCAT 57.130 36.364 0.00 0.00 31.92 2.90


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

AutoCloner maintained by Alex Coulton.