Multiple sequence alignment - TraesCS2A01G020100

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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 TraesCS2A01G020100 chr2A 100.000 3823 0 0 1 3823 9393916 9397738 0.000000e+00 7060.0
1 TraesCS2A01G020100 chr2A 99.166 3835 19 4 1 3823 9846384 9850217 0.000000e+00 6892.0
2 TraesCS2A01G020100 chr2A 80.020 1977 317 45 792 2732 8726910 8728844 0.000000e+00 1391.0
3 TraesCS2A01G020100 chr2A 82.215 1535 251 17 1207 2729 8707389 8708913 0.000000e+00 1303.0
4 TraesCS2A01G020100 chr2A 82.854 1079 145 19 1769 2844 9099553 9098512 0.000000e+00 931.0
5 TraesCS2A01G020100 chr2A 99.083 109 1 0 2951 3059 9396758 9396866 3.010000e-46 196.0
6 TraesCS2A01G020100 chr2A 99.083 109 1 0 2843 2951 9396866 9396974 3.010000e-46 196.0
7 TraesCS2A01G020100 chr2A 99.083 109 1 0 2951 3059 9849238 9849346 3.010000e-46 196.0
8 TraesCS2A01G020100 chr2A 98.165 109 1 1 2843 2951 9849346 9849453 5.040000e-44 189.0
9 TraesCS2A01G020100 chr2A 87.500 144 16 2 3397 3539 772654002 772653860 8.500000e-37 165.0
10 TraesCS2A01G020100 chr2A 85.443 158 20 3 3389 3544 774426725 774426569 1.100000e-35 161.0
11 TraesCS2A01G020100 chr2A 97.727 44 1 0 1091 1134 7516350 7516307 4.100000e-10 76.8
12 TraesCS2A01G020100 chr2D 89.884 2501 219 23 451 2938 9880517 9878038 0.000000e+00 3186.0
13 TraesCS2A01G020100 chr2D 79.940 1989 315 43 792 2732 9642556 9644508 0.000000e+00 1386.0
14 TraesCS2A01G020100 chr2D 82.141 1607 240 23 1141 2733 9380376 9381949 0.000000e+00 1334.0
15 TraesCS2A01G020100 chr2D 81.609 1653 251 27 1107 2733 85929700 85928075 0.000000e+00 1319.0
16 TraesCS2A01G020100 chr2D 81.684 1556 256 19 1180 2718 19586973 19588516 0.000000e+00 1267.0
17 TraesCS2A01G020100 chr2D 81.457 453 70 5 2067 2513 155450174 155450618 3.630000e-95 359.0
18 TraesCS2A01G020100 chr2D 90.299 268 24 2 3532 3798 5040527 5040261 2.190000e-92 350.0
19 TraesCS2A01G020100 chr2D 92.697 178 11 2 95 272 603994219 603994394 4.900000e-64 255.0
20 TraesCS2A01G020100 chr2D 89.116 147 15 1 3398 3544 32072233 32072378 8.440000e-42 182.0
21 TraesCS2A01G020100 chr2D 89.583 96 10 0 2951 3046 9878133 9878038 5.190000e-24 122.0
22 TraesCS2A01G020100 chr2D 81.633 147 19 3 2587 2733 9334202 9334340 8.680000e-22 115.0
23 TraesCS2A01G020100 chr2D 97.727 44 1 0 1091 1134 8480303 8480260 4.100000e-10 76.8
24 TraesCS2A01G020100 chr2B 87.298 1362 158 11 1084 2440 13181011 13179660 0.000000e+00 1543.0
25 TraesCS2A01G020100 chr2B 83.235 1533 244 10 1213 2740 768807001 768805477 0.000000e+00 1395.0
26 TraesCS2A01G020100 chr2B 82.909 1533 245 13 1207 2729 12422308 12423833 0.000000e+00 1363.0
27 TraesCS2A01G020100 chr2B 82.756 1531 254 8 1213 2740 768929421 768927898 0.000000e+00 1356.0
28 TraesCS2A01G020100 chr2B 82.482 1507 247 13 1210 2706 11518320 11516821 0.000000e+00 1304.0
29 TraesCS2A01G020100 chr2B 78.543 1990 348 40 792 2732 11454653 11452694 0.000000e+00 1236.0
30 TraesCS2A01G020100 chr2B 79.592 245 28 8 1098 1342 4759876 4759654 5.110000e-34 156.0
31 TraesCS2A01G020100 chr7D 79.831 709 124 16 2024 2724 40492405 40491708 2.050000e-137 499.0
32 TraesCS2A01G020100 chr7D 90.637 267 25 0 3532 3798 230866682 230866948 4.700000e-94 355.0
33 TraesCS2A01G020100 chr3D 91.554 296 20 4 95 389 32583547 32583838 1.650000e-108 403.0
34 TraesCS2A01G020100 chr3D 84.466 309 25 17 95 389 7919694 7919993 2.250000e-72 283.0
35 TraesCS2A01G020100 chr3D 90.345 145 13 1 3400 3544 604036411 604036554 5.040000e-44 189.0
36 TraesCS2A01G020100 chr6D 91.246 297 21 4 94 389 9019942 9020234 2.140000e-107 399.0
37 TraesCS2A01G020100 chr5D 91.760 267 22 0 3532 3798 557579151 557579417 4.660000e-99 372.0
38 TraesCS2A01G020100 chr5D 91.386 267 22 1 3532 3798 396847791 396848056 7.800000e-97 364.0
39 TraesCS2A01G020100 chr5D 91.288 264 23 0 3535 3798 12126154 12125891 1.010000e-95 361.0
40 TraesCS2A01G020100 chr5D 89.818 275 26 2 3525 3798 88922062 88921789 6.080000e-93 351.0
41 TraesCS2A01G020100 chr5D 91.803 183 13 2 90 272 35089940 35090120 1.760000e-63 254.0
42 TraesCS2A01G020100 chr4D 90.706 269 23 1 3532 3798 110250043 110250311 1.310000e-94 357.0
43 TraesCS2A01G020100 chr3A 89.324 281 29 1 3518 3798 704762160 704761881 6.080000e-93 351.0
44 TraesCS2A01G020100 chr3A 88.811 143 15 1 3403 3544 677121309 677121167 1.410000e-39 174.0
45 TraesCS2A01G020100 chr1D 96.629 178 4 1 212 389 7024950 7025125 1.040000e-75 294.0
46 TraesCS2A01G020100 chr6B 90.498 221 12 6 175 389 713775446 713775229 2.250000e-72 283.0
47 TraesCS2A01G020100 chr6B 100.000 40 0 0 265 304 6274886 6274925 1.470000e-09 75.0
48 TraesCS2A01G020100 chr4A 89.767 215 16 4 176 387 493722179 493721968 1.750000e-68 270.0
49 TraesCS2A01G020100 chr4A 88.276 145 17 0 3400 3544 222759120 222758976 1.410000e-39 174.0
50 TraesCS2A01G020100 chrUn 93.785 177 8 3 98 273 334070997 334070823 2.930000e-66 263.0
51 TraesCS2A01G020100 chrUn 93.678 174 8 3 95 267 71741481 71741652 1.360000e-64 257.0
52 TraesCS2A01G020100 chr5A 90.909 132 12 0 3413 3544 655135615 655135484 1.090000e-40 178.0
53 TraesCS2A01G020100 chr6A 86.986 146 17 2 3400 3544 54125034 54125178 3.060000e-36 163.0
54 TraesCS2A01G020100 chr4B 89.091 55 4 2 564 618 580355470 580355522 2.460000e-07 67.6


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 TraesCS2A01G020100 chr2A 9393916 9397738 3822 False 2484.000000 7060 99.388667 1 3823 3 chr2A.!!$F3 3822
1 TraesCS2A01G020100 chr2A 9846384 9850217 3833 False 2425.666667 6892 98.804667 1 3823 3 chr2A.!!$F4 3822
2 TraesCS2A01G020100 chr2A 8726910 8728844 1934 False 1391.000000 1391 80.020000 792 2732 1 chr2A.!!$F2 1940
3 TraesCS2A01G020100 chr2A 8707389 8708913 1524 False 1303.000000 1303 82.215000 1207 2729 1 chr2A.!!$F1 1522
4 TraesCS2A01G020100 chr2A 9098512 9099553 1041 True 931.000000 931 82.854000 1769 2844 1 chr2A.!!$R2 1075
5 TraesCS2A01G020100 chr2D 9878038 9880517 2479 True 1654.000000 3186 89.733500 451 3046 2 chr2D.!!$R4 2595
6 TraesCS2A01G020100 chr2D 9642556 9644508 1952 False 1386.000000 1386 79.940000 792 2732 1 chr2D.!!$F3 1940
7 TraesCS2A01G020100 chr2D 9380376 9381949 1573 False 1334.000000 1334 82.141000 1141 2733 1 chr2D.!!$F2 1592
8 TraesCS2A01G020100 chr2D 85928075 85929700 1625 True 1319.000000 1319 81.609000 1107 2733 1 chr2D.!!$R3 1626
9 TraesCS2A01G020100 chr2D 19586973 19588516 1543 False 1267.000000 1267 81.684000 1180 2718 1 chr2D.!!$F4 1538
10 TraesCS2A01G020100 chr2B 13179660 13181011 1351 True 1543.000000 1543 87.298000 1084 2440 1 chr2B.!!$R4 1356
11 TraesCS2A01G020100 chr2B 768805477 768807001 1524 True 1395.000000 1395 83.235000 1213 2740 1 chr2B.!!$R5 1527
12 TraesCS2A01G020100 chr2B 12422308 12423833 1525 False 1363.000000 1363 82.909000 1207 2729 1 chr2B.!!$F1 1522
13 TraesCS2A01G020100 chr2B 768927898 768929421 1523 True 1356.000000 1356 82.756000 1213 2740 1 chr2B.!!$R6 1527
14 TraesCS2A01G020100 chr2B 11516821 11518320 1499 True 1304.000000 1304 82.482000 1210 2706 1 chr2B.!!$R3 1496
15 TraesCS2A01G020100 chr2B 11452694 11454653 1959 True 1236.000000 1236 78.543000 792 2732 1 chr2B.!!$R2 1940
16 TraesCS2A01G020100 chr7D 40491708 40492405 697 True 499.000000 499 79.831000 2024 2724 1 chr7D.!!$R1 700

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
175 185 4.155462 GGTTTGGGTTAGCTAGCTTTGTAC 59.845 45.833 24.88 15.2 0.00 2.9 F
1753 1845 1.172180 ATGTTTGGCCGACACACTGG 61.172 55.000 13.34 0.0 31.07 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2065 3.259625 TCAATCACTACCAACATCGTCCA 59.740 43.478 0.0 0.0 0.00 4.02 R
3450 3583 0.464735 CCCGGTTTGTGAGTGAACCA 60.465 55.000 0.0 0.0 44.37 3.67 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
175 185 4.155462 GGTTTGGGTTAGCTAGCTTTGTAC 59.845 45.833 24.88 15.2 0.00 2.90
205 215 5.683876 AATATAGCTGTACCCTATGCCTG 57.316 43.478 0.00 0.0 0.00 4.85
1753 1845 1.172180 ATGTTTGGCCGACACACTGG 61.172 55.000 13.34 0.0 31.07 4.00
3013 3146 3.187227 CAGCACAATTCTGCTACTCGTTT 59.813 43.478 7.96 0.0 46.14 3.60
3184 3317 2.939103 GCTCTATGTGTTGTGTGGATCC 59.061 50.000 4.20 4.2 0.00 3.36
3450 3583 3.335711 GGCCAGCCCATTAGTCCT 58.664 61.111 0.00 0.0 0.00 3.85
3462 3595 3.007940 CCATTAGTCCTGGTTCACTCACA 59.992 47.826 0.00 0.0 0.00 3.58
3490 3623 1.153756 CCATGGGGGCAACTATCCC 59.846 63.158 2.85 0.0 43.15 3.85
3589 3722 2.674420 TGCCTATATATACCCCCTCGC 58.326 52.381 0.00 0.0 0.00 5.03
3611 3744 1.575576 GCAAGCAGAGCAGTGGAGTG 61.576 60.000 0.00 0.0 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 205 4.422073 TGATCTGTTTACAGGCATAGGG 57.578 45.455 9.82 0.0 43.91 3.53
1971 2065 3.259625 TCAATCACTACCAACATCGTCCA 59.740 43.478 0.00 0.0 0.00 4.02
2756 2888 1.135689 GCCACGTGAACACATCCATTC 60.136 52.381 19.30 0.0 0.00 2.67
3341 3474 3.965539 CTCCTCAAGGGCTGGCGTG 62.966 68.421 0.00 0.0 35.41 5.34
3450 3583 0.464735 CCCGGTTTGTGAGTGAACCA 60.465 55.000 0.00 0.0 44.37 3.67
3462 3595 3.668142 CCCCATGGGTCCCGGTTT 61.668 66.667 29.33 0.0 38.25 3.27
3490 3623 4.760047 CCCTGGCCTCACGAACCG 62.760 72.222 3.32 0.0 0.00 4.44
3589 3722 3.429141 CACTGCTCTGCTTGCGGG 61.429 66.667 1.30 0.0 40.81 6.13
3611 3744 1.581447 CCGGCCAGAAAAACAGAGC 59.419 57.895 2.24 0.0 0.00 4.09


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

AutoCloner maintained by Alex Coulton.