Multiple sequence alignment - TraesCS3B01G505600

Loading Multiple Alignment...

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 TraesCS3B01G505600 chr3B 100.000 2738 0 0 1 2738 749679808 749682545 0.000000e+00 5057.0
1 TraesCS3B01G505600 chr3B 78.992 1785 265 58 527 2245 749648292 749650032 0.000000e+00 1118.0
2 TraesCS3B01G505600 chr3B 79.388 1373 228 31 528 1865 749025781 749024429 0.000000e+00 917.0
3 TraesCS3B01G505600 chr3B 82.137 599 85 15 1636 2216 749650117 749650711 6.810000e-136 494.0
4 TraesCS3B01G505600 chr3B 82.051 429 67 4 2263 2691 749681421 749681839 9.320000e-95 357.0
5 TraesCS3B01G505600 chr3B 82.135 431 63 8 1614 2032 749682070 749682498 9.320000e-95 357.0
6 TraesCS3B01G505600 chr3B 76.513 694 130 22 455 1129 748787226 748786547 5.610000e-92 348.0
7 TraesCS3B01G505600 chr3B 83.483 333 32 8 2261 2570 749649387 749649719 3.450000e-74 289.0
8 TraesCS3B01G505600 chr3B 85.870 92 7 3 2524 2610 749024325 749024235 2.900000e-15 93.5
9 TraesCS3B01G505600 chr3B 93.750 48 3 0 2106 2153 749024080 749024033 3.780000e-09 73.1
10 TraesCS3B01G505600 chr3D 92.390 2142 118 21 441 2546 562459510 562461642 0.000000e+00 3011.0
11 TraesCS3B01G505600 chr3D 94.741 1179 46 7 1 1169 562378494 562379666 0.000000e+00 1820.0
12 TraesCS3B01G505600 chr3D 88.060 1273 125 16 1167 2418 562384088 562385354 0.000000e+00 1483.0
13 TraesCS3B01G505600 chr3D 78.923 1504 249 39 498 1960 561711662 561710186 0.000000e+00 959.0
14 TraesCS3B01G505600 chr3D 81.104 1196 181 21 526 1693 562348112 562349290 0.000000e+00 915.0
15 TraesCS3B01G505600 chr3D 75.957 1385 270 43 495 1856 562545149 562546493 0.000000e+00 654.0
16 TraesCS3B01G505600 chr3D 74.691 1296 260 45 495 1751 561462583 561461317 5.230000e-142 514.0
17 TraesCS3B01G505600 chr3D 82.631 593 73 17 1359 1931 562435810 562436392 5.270000e-137 497.0
18 TraesCS3B01G505600 chr3D 84.241 349 52 3 2263 2610 562460703 562461049 1.210000e-88 337.0
19 TraesCS3B01G505600 chr3D 95.918 196 7 1 2543 2737 562461717 562461912 1.580000e-82 316.0
20 TraesCS3B01G505600 chr3D 84.404 327 33 9 2261 2570 562436054 562436379 3.430000e-79 305.0
21 TraesCS3B01G505600 chr3D 82.704 318 49 5 2294 2610 561710500 561710188 7.470000e-71 278.0
22 TraesCS3B01G505600 chr3D 87.919 149 14 3 2105 2249 562355634 562355782 3.620000e-39 172.0
23 TraesCS3B01G505600 chr3D 90.789 76 4 1 2081 2153 561465809 561465734 6.240000e-17 99.0
24 TraesCS3B01G505600 chr3D 90.909 55 3 2 2106 2160 561710035 561709983 3.780000e-09 73.1
25 TraesCS3B01G505600 chr3D 97.500 40 1 0 2699 2738 562385580 562385619 4.890000e-08 69.4
26 TraesCS3B01G505600 chr3A 92.493 1039 52 6 525 1560 697567790 697568805 0.000000e+00 1463.0
27 TraesCS3B01G505600 chr3A 92.864 1009 49 6 1560 2546 697569219 697570226 0.000000e+00 1443.0
28 TraesCS3B01G505600 chr3A 78.745 1482 247 44 531 1965 697457440 697455980 0.000000e+00 929.0
29 TraesCS3B01G505600 chr3A 75.465 1129 227 29 498 1593 697673472 697674583 3.150000e-139 505.0
30 TraesCS3B01G505600 chr3A 87.644 348 42 1 2263 2610 697569273 697569619 1.180000e-108 403.0
31 TraesCS3B01G505600 chr3A 94.444 108 6 0 2543 2650 697570301 697570408 1.690000e-37 167.0
32 TraesCS3B01G505600 chr3A 95.402 87 4 0 2651 2737 697575432 697575518 3.680000e-29 139.0


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 TraesCS3B01G505600 chr3B 749679808 749682545 2737 False 1923.666667 5057 88.062000 1 2738 3 chr3B.!!$F2 2737
1 TraesCS3B01G505600 chr3B 749648292 749650711 2419 False 633.666667 1118 81.537333 527 2570 3 chr3B.!!$F1 2043
2 TraesCS3B01G505600 chr3B 749024033 749025781 1748 True 361.200000 917 86.336000 528 2610 3 chr3B.!!$R2 2082
3 TraesCS3B01G505600 chr3B 748786547 748787226 679 True 348.000000 348 76.513000 455 1129 1 chr3B.!!$R1 674
4 TraesCS3B01G505600 chr3D 562378494 562379666 1172 False 1820.000000 1820 94.741000 1 1169 1 chr3D.!!$F3 1168
5 TraesCS3B01G505600 chr3D 562459510 562461912 2402 False 1221.333333 3011 90.849667 441 2737 3 chr3D.!!$F7 2296
6 TraesCS3B01G505600 chr3D 562348112 562349290 1178 False 915.000000 915 81.104000 526 1693 1 chr3D.!!$F1 1167
7 TraesCS3B01G505600 chr3D 562384088 562385619 1531 False 776.200000 1483 92.780000 1167 2738 2 chr3D.!!$F5 1571
8 TraesCS3B01G505600 chr3D 562545149 562546493 1344 False 654.000000 654 75.957000 495 1856 1 chr3D.!!$F4 1361
9 TraesCS3B01G505600 chr3D 561709983 561711662 1679 True 436.700000 959 84.178667 498 2610 3 chr3D.!!$R2 2112
10 TraesCS3B01G505600 chr3D 562435810 562436392 582 False 401.000000 497 83.517500 1359 2570 2 chr3D.!!$F6 1211
11 TraesCS3B01G505600 chr3D 561461317 561465809 4492 True 306.500000 514 82.740000 495 2153 2 chr3D.!!$R1 1658
12 TraesCS3B01G505600 chr3A 697455980 697457440 1460 True 929.000000 929 78.745000 531 1965 1 chr3A.!!$R1 1434
13 TraesCS3B01G505600 chr3A 697567790 697570408 2618 False 869.000000 1463 91.861250 525 2650 4 chr3A.!!$F3 2125
14 TraesCS3B01G505600 chr3A 697673472 697674583 1111 False 505.000000 505 75.465000 498 1593 1 chr3A.!!$F2 1095

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
212 213 0.535328 TCCAACGCGGAAAATGGTCA 60.535 50.0 12.47 0.0 42.52 4.02 F
1001 3806 0.912486 GCTGGAGGGGTGTTCACTAT 59.088 55.0 2.98 0.0 0.00 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 4857 1.630369 TGCCTGCTCATACACCTTCTT 59.370 47.619 0.0 0.0 0.0 2.52 R
2331 7058 1.228124 CCGTTCAGTGCAGGGGAAA 60.228 57.895 0.0 0.0 0.0 3.13 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
124 125 3.486383 CTGAAACATGGGTGTGGTAACT 58.514 45.455 0.00 0.00 38.92 2.24
163 164 5.591099 TCTTTGCAAGATGTCCAAAGAAAC 58.409 37.500 13.05 0.00 46.57 2.78
175 176 5.357314 TGTCCAAAGAAACGTAACCAAATGA 59.643 36.000 0.00 0.00 0.00 2.57
212 213 0.535328 TCCAACGCGGAAAATGGTCA 60.535 50.000 12.47 0.00 42.52 4.02
347 348 7.864379 AGTTGAACTATTCTCATGCAAAGTTTG 59.136 33.333 11.41 11.41 0.00 2.93
954 3740 2.177518 AGGTGGTCCTCTCCTCCCA 61.178 63.158 0.00 0.00 40.58 4.37
963 3749 3.227276 CTCCTCCCACCGATCCCG 61.227 72.222 0.00 0.00 0.00 5.14
1001 3806 0.912486 GCTGGAGGGGTGTTCACTAT 59.088 55.000 2.98 0.00 0.00 2.12
1064 3875 2.047061 GGTATATCTGTGGCAGGTCCA 58.953 52.381 0.00 0.00 44.18 4.02
1393 4242 3.422303 GCAACAGCGATGGTGCGA 61.422 61.111 29.41 0.00 42.97 5.10
1581 4853 1.280421 GTTCATCTGAGGAGCAGGGTT 59.720 52.381 1.23 0.00 44.98 4.11
1585 4857 2.024176 TCTGAGGAGCAGGGTTGTTA 57.976 50.000 0.00 0.00 44.98 2.41
1669 4941 5.301835 ACATGTCTCTCCCTTTATGATGG 57.698 43.478 0.00 0.00 0.00 3.51
1693 4965 2.199652 CCGCCTGTTTTCCCTGCAA 61.200 57.895 0.00 0.00 0.00 4.08
1694 4966 1.739049 CGCCTGTTTTCCCTGCAAA 59.261 52.632 0.00 0.00 0.00 3.68
1745 5021 2.313234 CGCTGTGCTTTGATCTTTGTG 58.687 47.619 0.00 0.00 0.00 3.33
1753 5029 6.071784 TGTGCTTTGATCTTTGTGCTATCATT 60.072 34.615 0.00 0.00 30.17 2.57
1955 6623 8.405531 GTCTGCTATTTTGCCAATAAGTATGAA 58.594 33.333 0.00 0.00 0.00 2.57
2034 6739 2.094390 GTGCAGATGTTCATGCCACATT 60.094 45.455 10.65 1.35 41.85 2.71
2100 6811 6.136541 ACCTCTGTTCATTTCACTGAAAAC 57.863 37.500 8.28 3.54 36.92 2.43
2243 6958 4.397420 TGCAGTCAATTGGTCATGTAAGT 58.603 39.130 5.42 0.00 0.00 2.24
2268 6983 4.651503 GGGTCTTAGAACCTCTGATCATCA 59.348 45.833 9.43 0.00 36.31 3.07
2331 7058 6.028131 TCTTTATGATGATCTGGCCTCCTAT 58.972 40.000 3.32 0.00 0.00 2.57
2396 7123 4.019174 CCCCTGTGCTTTGATCTTTGTAT 58.981 43.478 0.00 0.00 0.00 2.29
2527 7259 3.690460 AGCTAGTGCATGCCTTTTTACT 58.310 40.909 16.68 13.07 42.74 2.24
2614 7502 5.925509 TGGCCAATAAGTATGAGTAGGAAC 58.074 41.667 0.61 0.00 0.00 3.62
2635 7523 7.611079 AGGAACAATAGTCTCGTACTTAGTTCT 59.389 37.037 18.95 10.89 39.47 3.01
2706 7595 2.661866 ACGTCGCACAACCTCTGC 60.662 61.111 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 157 6.635239 CGTGAATCATTTGGTTACGTTTCTTT 59.365 34.615 0.00 0.00 0.00 2.52
163 164 4.671880 TTCCGTGAATCATTTGGTTACG 57.328 40.909 0.00 0.00 0.00 3.18
175 176 3.696045 TGGACATCCATTTTCCGTGAAT 58.304 40.909 0.00 0.00 42.01 2.57
212 213 2.357836 CTTGGTGCAGGGCATCCT 59.642 61.111 0.00 0.00 46.26 3.24
347 348 3.306703 CGCCAAATGGTATCATGTTTTGC 59.693 43.478 0.71 0.00 37.57 3.68
348 349 4.742417 TCGCCAAATGGTATCATGTTTTG 58.258 39.130 0.71 0.00 37.57 2.44
349 350 4.677779 GCTCGCCAAATGGTATCATGTTTT 60.678 41.667 0.71 0.00 37.57 2.43
350 351 3.181487 GCTCGCCAAATGGTATCATGTTT 60.181 43.478 0.71 0.00 37.57 2.83
352 353 1.949525 GCTCGCCAAATGGTATCATGT 59.050 47.619 0.71 0.00 37.57 3.21
353 354 2.224606 AGCTCGCCAAATGGTATCATG 58.775 47.619 0.71 0.00 37.57 3.07
356 357 6.554334 TTTATTAGCTCGCCAAATGGTATC 57.446 37.500 0.71 0.00 37.57 2.24
357 358 6.952773 TTTTATTAGCTCGCCAAATGGTAT 57.047 33.333 0.71 0.00 37.57 2.73
452 462 2.846827 TCAGAGGAAAGGGGATTTCTCC 59.153 50.000 0.86 0.00 45.62 3.71
963 3749 3.134127 GACTCAATGTGGGGCGGC 61.134 66.667 0.00 0.00 0.00 6.53
974 3760 3.003173 CCCCTCCAGCGGACTCAA 61.003 66.667 0.00 0.00 0.00 3.02
975 3761 4.316823 ACCCCTCCAGCGGACTCA 62.317 66.667 0.00 0.00 0.00 3.41
1581 4853 4.832248 CCTGCTCATACACCTTCTTAACA 58.168 43.478 0.00 0.00 0.00 2.41
1585 4857 1.630369 TGCCTGCTCATACACCTTCTT 59.370 47.619 0.00 0.00 0.00 2.52
1630 4902 2.897271 TGTATGTGGCTCAAACCCAT 57.103 45.000 0.00 0.00 34.34 4.00
1669 4941 2.626780 GGAAAACAGGCGGCCAGAC 61.627 63.158 23.09 7.78 0.00 3.51
1693 4965 4.279420 GCTCTTGATTGTGTCCCTTTTCTT 59.721 41.667 0.00 0.00 0.00 2.52
1694 4966 3.823304 GCTCTTGATTGTGTCCCTTTTCT 59.177 43.478 0.00 0.00 0.00 2.52
1745 5021 4.506886 AGTCGTACCTAGCAATGATAGC 57.493 45.455 0.00 0.00 0.00 2.97
1753 5029 6.766429 TCTATCATAGAAGTCGTACCTAGCA 58.234 40.000 0.00 0.00 0.00 3.49
1833 5836 3.776969 AGATGAGATGTAGTCAAGCCCAA 59.223 43.478 0.00 0.00 0.00 4.12
1955 6623 4.202326 CGGAACCAGGTACAAGCCTATTAT 60.202 45.833 0.00 0.00 37.04 1.28
2034 6739 4.014406 TCCGCAGAATCTAGTGTTCTACA 58.986 43.478 11.12 0.00 34.32 2.74
2100 6811 9.764870 CAATACACTTCTGTAAACATCAGAATG 57.235 33.333 8.46 10.62 46.30 2.67
2113 6824 6.237901 TGGATAACTTGCAATACACTTCTGT 58.762 36.000 0.00 0.00 0.00 3.41
2206 6921 9.069078 CAATTGACTGCAATATCTACTGTTTTG 57.931 33.333 0.00 0.00 43.71 2.44
2243 6958 4.425772 TGATCAGAGGTTCTAAGACCCAA 58.574 43.478 0.00 0.00 40.73 4.12
2268 6983 4.818005 GGTTCATACCCGGACGAATAAAAT 59.182 41.667 0.73 0.00 38.60 1.82
2309 7036 6.708885 AATAGGAGGCCAGATCATCATAAA 57.291 37.500 5.01 0.00 0.00 1.40
2331 7058 1.228124 CCGTTCAGTGCAGGGGAAA 60.228 57.895 0.00 0.00 0.00 3.13
2396 7123 4.525487 AGAAGTTGTACCCAGTGACGATAA 59.475 41.667 0.00 0.00 0.00 1.75
2614 7502 9.790389 AAATCAGAACTAAGTACGAGACTATTG 57.210 33.333 5.00 0.00 37.44 1.90
2662 7551 8.009974 GGCATGAACGTCTATACATTTGTATTC 58.990 37.037 8.41 1.59 41.18 1.75
2695 7584 3.058432 CAGTGAAATGAGCAGAGGTTGTG 60.058 47.826 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.