Multiple sequence alignment - TraesCS2A01G015300

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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 TraesCS2A01G015300 chr2A 100.000 2246 0 0 1 2246 6242555 6244800 0.000000e+00 4148.0
1 TraesCS2A01G015300 chr2A 95.975 1292 42 4 442 1733 6056654 6055373 0.000000e+00 2089.0
2 TraesCS2A01G015300 chr2A 95.898 1292 43 4 442 1733 6112559 6111278 0.000000e+00 2084.0
3 TraesCS2A01G015300 chr2A 95.743 1292 44 5 442 1733 6021233 6019953 0.000000e+00 2071.0
4 TraesCS2A01G015300 chr2A 95.046 1292 43 5 442 1733 6164260 6162990 0.000000e+00 2012.0
5 TraesCS2A01G015300 chr2A 96.416 279 8 1 22 298 6014284 6014562 2.030000e-125 459.0
6 TraesCS2A01G015300 chr2A 96.416 279 8 1 22 298 6105005 6105283 2.030000e-125 459.0
7 TraesCS2A01G015300 chr2A 96.416 279 8 1 22 298 6152571 6152849 2.030000e-125 459.0
8 TraesCS2A01G015300 chr2A 96.057 279 9 1 22 298 6039198 6039476 9.460000e-124 453.0
9 TraesCS2A01G015300 chr2A 97.087 103 3 0 340 442 6015430 6015532 8.250000e-40 174.0
10 TraesCS2A01G015300 chr2A 97.087 103 3 0 340 442 6040327 6040429 8.250000e-40 174.0
11 TraesCS2A01G015300 chr2A 97.143 70 2 0 373 442 6158501 6158570 3.920000e-23 119.0
12 TraesCS2A01G015300 chr2A 95.714 70 3 0 373 442 6106786 6106855 1.820000e-21 113.0
13 TraesCS2A01G015300 chr2A 98.077 52 1 0 295 346 6014853 6014904 8.540000e-15 91.6
14 TraesCS2A01G015300 chr2A 98.077 52 1 0 295 346 6039767 6039818 8.540000e-15 91.6
15 TraesCS2A01G015300 chr2A 98.077 52 1 0 295 346 6105574 6105625 8.540000e-15 91.6
16 TraesCS2A01G015300 chr2A 97.959 49 1 0 295 343 6153140 6153188 3.970000e-13 86.1
17 TraesCS2A01G015300 chr2A 97.561 41 1 0 340 380 6106384 6106424 1.110000e-08 71.3
18 TraesCS2A01G015300 chr2A 97.561 41 1 0 340 380 6158099 6158139 1.110000e-08 71.3
19 TraesCS2A01G015300 chr5A 92.849 1748 98 11 1 1733 415198598 415196863 0.000000e+00 2510.0
20 TraesCS2A01G015300 chr3D 93.660 836 43 8 904 1733 126614866 126614035 0.000000e+00 1242.0
21 TraesCS2A01G015300 chr3D 92.982 570 26 2 1 568 126620743 126620186 0.000000e+00 819.0
22 TraesCS2A01G015300 chr3D 92.364 275 14 3 563 837 126615129 126614862 3.500000e-103 385.0
23 TraesCS2A01G015300 chr3D 89.894 188 15 2 790 973 575923893 575923706 2.880000e-59 239.0
24 TraesCS2A01G015300 chr2B 95.669 508 18 2 1741 2246 18010683 18010178 0.000000e+00 813.0
25 TraesCS2A01G015300 chr2B 91.256 446 28 7 1808 2246 90778858 90778417 4.130000e-167 597.0
26 TraesCS2A01G015300 chr6B 93.617 517 29 4 1733 2246 30260054 30259539 0.000000e+00 769.0
27 TraesCS2A01G015300 chr6B 82.018 456 62 12 972 1420 538368533 538368975 9.800000e-99 370.0
28 TraesCS2A01G015300 chr6B 88.031 259 25 5 1464 1721 234689312 234689565 3.630000e-78 302.0
29 TraesCS2A01G015300 chr6B 88.718 195 16 4 790 980 148827407 148827599 1.340000e-57 233.0
30 TraesCS2A01G015300 chr6B 94.872 39 2 0 1425 1463 234689170 234689208 6.700000e-06 62.1
31 TraesCS2A01G015300 chrUn 90.962 520 29 10 1734 2246 31811111 31811619 0.000000e+00 684.0
32 TraesCS2A01G015300 chrUn 90.962 520 29 10 1734 2246 308873334 308872826 0.000000e+00 684.0
33 TraesCS2A01G015300 chrUn 96.416 279 8 1 22 298 414682418 414682140 2.030000e-125 459.0
34 TraesCS2A01G015300 chrUn 97.959 49 1 0 295 343 414681849 414681801 3.970000e-13 86.1
35 TraesCS2A01G015300 chr4B 88.462 520 39 11 1734 2246 159545913 159545408 1.910000e-170 608.0
36 TraesCS2A01G015300 chr1A 87.692 520 54 8 1733 2246 21209476 21208961 4.130000e-167 597.0
37 TraesCS2A01G015300 chr1B 89.462 446 36 7 1808 2246 565955210 565955651 9.060000e-154 553.0
38 TraesCS2A01G015300 chr3B 89.262 447 35 8 1808 2246 780820792 780820351 4.220000e-152 547.0
39 TraesCS2A01G015300 chr6D 84.579 428 45 13 1001 1420 357007891 357008305 2.690000e-109 405.0
40 TraesCS2A01G015300 chr6D 89.818 275 20 5 1462 1733 136473344 136473613 1.650000e-91 346.0
41 TraesCS2A01G015300 chr6A 90.032 311 22 6 1425 1733 177814553 177814856 5.810000e-106 394.0
42 TraesCS2A01G015300 chr6A 90.000 250 25 0 1001 1250 499402189 499402438 7.740000e-85 324.0
43 TraesCS2A01G015300 chr4D 85.088 342 44 7 154 489 57677766 57678106 2.140000e-90 342.0
44 TraesCS2A01G015300 chr7B 90.164 61 5 1 345 405 685045311 685045252 6.650000e-11 78.7


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 TraesCS2A01G015300 chr2A 6242555 6244800 2245 False 4148.000000 4148 100.000000 1 2246 1 chr2A.!!$F1 2245
1 TraesCS2A01G015300 chr2A 6055373 6056654 1281 True 2089.000000 2089 95.975000 442 1733 1 chr2A.!!$R2 1291
2 TraesCS2A01G015300 chr2A 6111278 6112559 1281 True 2084.000000 2084 95.898000 442 1733 1 chr2A.!!$R3 1291
3 TraesCS2A01G015300 chr2A 6019953 6021233 1280 True 2071.000000 2071 95.743000 442 1733 1 chr2A.!!$R1 1291
4 TraesCS2A01G015300 chr2A 6162990 6164260 1270 True 2012.000000 2012 95.046000 442 1733 1 chr2A.!!$R4 1291
5 TraesCS2A01G015300 chr2A 6152571 6153188 617 False 272.550000 459 97.187500 22 343 2 chr2A.!!$F5 321
6 TraesCS2A01G015300 chr2A 6014284 6015532 1248 False 241.533333 459 97.193333 22 442 3 chr2A.!!$F2 420
7 TraesCS2A01G015300 chr2A 6039198 6040429 1231 False 239.533333 453 97.073667 22 442 3 chr2A.!!$F3 420
8 TraesCS2A01G015300 chr5A 415196863 415198598 1735 True 2510.000000 2510 92.849000 1 1733 1 chr5A.!!$R1 1732
9 TraesCS2A01G015300 chr3D 126620186 126620743 557 True 819.000000 819 92.982000 1 568 1 chr3D.!!$R1 567
10 TraesCS2A01G015300 chr3D 126614035 126615129 1094 True 813.500000 1242 93.012000 563 1733 2 chr3D.!!$R3 1170
11 TraesCS2A01G015300 chr2B 18010178 18010683 505 True 813.000000 813 95.669000 1741 2246 1 chr2B.!!$R1 505
12 TraesCS2A01G015300 chr6B 30259539 30260054 515 True 769.000000 769 93.617000 1733 2246 1 chr6B.!!$R1 513
13 TraesCS2A01G015300 chrUn 31811111 31811619 508 False 684.000000 684 90.962000 1734 2246 1 chrUn.!!$F1 512
14 TraesCS2A01G015300 chrUn 308872826 308873334 508 True 684.000000 684 90.962000 1734 2246 1 chrUn.!!$R1 512
15 TraesCS2A01G015300 chrUn 414681801 414682418 617 True 272.550000 459 97.187500 22 343 2 chrUn.!!$R2 321
16 TraesCS2A01G015300 chr4B 159545408 159545913 505 True 608.000000 608 88.462000 1734 2246 1 chr4B.!!$R1 512
17 TraesCS2A01G015300 chr1A 21208961 21209476 515 True 597.000000 597 87.692000 1733 2246 1 chr1A.!!$R1 513

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
101 102 0.250513 GCCATCTCTCTTTCCGTGGT 59.749 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1255 2121 1.668751 GAGACGAGACGAGCTGAGATT 59.331 52.381 0.0 0.0 0.0 2.4 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
18 19 2.030562 CAAGGGCTCGTGTCCGTT 59.969 61.111 1.88 1.81 44.16 4.44
85 86 1.596934 CCCAAGCTCTCGTAAGCCA 59.403 57.895 7.93 0.00 43.56 4.75
101 102 0.250513 GCCATCTCTCTTTCCGTGGT 59.749 55.000 0.00 0.00 0.00 4.16
114 115 1.210967 TCCGTGGTCCAGTTTTGAACT 59.789 47.619 0.00 0.00 44.06 3.01
434 1276 2.575532 CACAAGTTGAAAGAGGGCTCA 58.424 47.619 10.54 0.00 0.00 4.26
448 1290 5.128919 AGAGGGCTCATGCTTATAAAACTG 58.871 41.667 0.00 0.00 39.59 3.16
650 1492 1.076533 CTTCGACATTGACGTCCCCG 61.077 60.000 14.12 9.18 40.83 5.73
701 1543 2.710902 CCCCTCGTCATCGACAGCA 61.711 63.158 0.00 0.00 41.35 4.41
707 1549 2.592194 TCGTCATCGACAGCAGTTTAC 58.408 47.619 0.00 0.00 41.35 2.01
752 1594 7.761038 AAGTAAAGCTGGTTTTAGCATTAGT 57.239 32.000 10.36 0.00 46.07 2.24
753 1595 7.761038 AGTAAAGCTGGTTTTAGCATTAGTT 57.239 32.000 10.36 0.00 46.07 2.24
754 1596 8.178313 AGTAAAGCTGGTTTTAGCATTAGTTT 57.822 30.769 10.36 0.00 46.07 2.66
755 1597 8.082242 AGTAAAGCTGGTTTTAGCATTAGTTTG 58.918 33.333 10.36 0.00 46.07 2.93
756 1598 4.809673 AGCTGGTTTTAGCATTAGTTTGC 58.190 39.130 0.00 0.00 46.07 3.68
757 1599 4.280677 AGCTGGTTTTAGCATTAGTTTGCA 59.719 37.500 0.00 0.00 46.07 4.08
758 1600 4.385748 GCTGGTTTTAGCATTAGTTTGCAC 59.614 41.667 0.00 0.00 45.23 4.57
966 1808 9.862371 ATTTATTTTACGAATGTACATTGCCAA 57.138 25.926 25.42 12.40 0.00 4.52
1054 1909 2.930562 GGAGGGAGGTGGTGCTGT 60.931 66.667 0.00 0.00 0.00 4.40
1143 1998 1.033574 GTAGGGACCTCCTCATCGTG 58.966 60.000 0.00 0.00 44.06 4.35
1255 2121 1.133167 TCTCCAGTTGAGTCCTCCACA 60.133 52.381 1.91 0.00 42.12 4.17
1351 2218 5.513267 GGCGATCTAGGTTCCCTAATCAAAT 60.513 44.000 0.00 0.00 35.49 2.32
1355 2222 7.702772 CGATCTAGGTTCCCTAATCAAATATCG 59.297 40.741 0.00 0.00 35.49 2.92
1470 2337 7.497579 TGAGTCTCACAGCTAAATAGTAGAGAG 59.502 40.741 0.00 0.00 32.19 3.20
1506 2373 6.831976 AGTAAATGGATCTAATCTGGTGTCC 58.168 40.000 0.00 0.00 0.00 4.02
1547 2414 0.593128 GAGGTTGCTTCATGCGTGTT 59.407 50.000 5.68 0.00 46.63 3.32
1651 2518 5.532557 GATGACTGGCTTTAAGTTGCTTTT 58.467 37.500 0.00 0.00 0.00 2.27
1652 2519 5.337578 TGACTGGCTTTAAGTTGCTTTTT 57.662 34.783 0.00 0.00 0.00 1.94
1653 2520 5.108517 TGACTGGCTTTAAGTTGCTTTTTG 58.891 37.500 0.00 0.00 0.00 2.44
1742 2610 4.744795 ATGGTTGCTGGTTGTTAAACAA 57.255 36.364 0.00 0.00 38.10 2.83
1944 2817 1.806542 CGCACCCCTGCATATAACATC 59.193 52.381 0.00 0.00 44.50 3.06
1945 2818 2.162681 GCACCCCTGCATATAACATCC 58.837 52.381 0.00 0.00 43.62 3.51
1950 2823 2.038426 CCCTGCATATAACATCCACGGA 59.962 50.000 0.00 0.00 0.00 4.69
2048 2924 2.170607 GTCAAACCCATCTAGCCTAGCA 59.829 50.000 0.00 0.00 0.00 3.49
2084 2960 1.272147 GCCTCCTCACCAAACCTCAAT 60.272 52.381 0.00 0.00 0.00 2.57
2103 2979 6.127225 CCTCAATAATCAGGTCACAGAGAAGA 60.127 42.308 0.00 0.00 0.00 2.87
2110 2986 3.006217 CAGGTCACAGAGAAGATGTCACA 59.994 47.826 0.00 0.00 0.00 3.58
2151 3027 0.244721 CACGCAGATCACACCTCAGA 59.755 55.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 1.827969 CTGGACCACGGAAAGAGAGAT 59.172 52.381 0.00 0.0 0.00 2.75
144 145 1.734388 AACAACGCCTTCCCTGCAAC 61.734 55.000 0.00 0.0 0.00 4.17
245 258 2.162408 CGGAACTGGAAGAAGAAATGCC 59.838 50.000 0.00 0.0 37.43 4.40
434 1276 7.775093 TGGCTCTACATTCAGTTTTATAAGCAT 59.225 33.333 0.00 0.0 0.00 3.79
448 1290 1.929836 CGCTGTTCTGGCTCTACATTC 59.070 52.381 0.00 0.0 0.00 2.67
650 1492 0.036732 TGTCAGAACCCCATGAGCAC 59.963 55.000 0.00 0.0 0.00 4.40
755 1597 7.019774 TCAGAATTCATATACTGCAAAGTGC 57.980 36.000 8.44 0.0 45.29 4.40
966 1808 1.152963 GGTGCCAGGACCGCAATAT 60.153 57.895 0.00 0.0 38.13 1.28
1054 1909 2.046023 CACCAGGATGAGGCGCAA 60.046 61.111 10.83 0.0 39.69 4.85
1143 1998 2.031465 TTTGGGCCGAAGTCGACC 59.969 61.111 13.01 0.0 41.35 4.79
1255 2121 1.668751 GAGACGAGACGAGCTGAGATT 59.331 52.381 0.00 0.0 0.00 2.40
1351 2218 9.961265 ATTCGAGTTATCAAATTCACTACGATA 57.039 29.630 0.00 0.0 0.00 2.92
1582 2449 4.759693 GTGTAATTGAGTTGTCCACATGGA 59.240 41.667 0.00 0.0 43.08 3.41
1583 2450 4.082787 GGTGTAATTGAGTTGTCCACATGG 60.083 45.833 0.00 0.0 0.00 3.66
1584 2451 4.518590 TGGTGTAATTGAGTTGTCCACATG 59.481 41.667 0.00 0.0 0.00 3.21
1651 2518 5.929415 TGCGTCTACAACTCAATATTGTCAA 59.071 36.000 14.97 0.0 40.68 3.18
1652 2519 5.474825 TGCGTCTACAACTCAATATTGTCA 58.525 37.500 14.97 0.0 40.68 3.58
1653 2520 6.403333 TTGCGTCTACAACTCAATATTGTC 57.597 37.500 14.97 0.0 40.68 3.18
1742 2610 3.695830 ATGAAGGTTGACACATACGGT 57.304 42.857 0.00 0.0 0.00 4.83
2084 2960 5.716703 TGACATCTTCTCTGTGACCTGATTA 59.283 40.000 0.00 0.0 0.00 1.75
2163 3039 2.484203 GACGTAGCCGAAGACGCT 59.516 61.111 0.00 0.0 42.81 5.07


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

AutoCloner maintained by Alex Coulton.