Multiple sequence alignment - TraesCS5B01G029500

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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 TraesCS5B01G029500 chr5B 100.000 2952 0 0 1 2952 29423821 29426772 0.000000e+00 5452.0
1 TraesCS5B01G029500 chr5B 97.958 2155 42 2 799 2952 690081297 690079144 0.000000e+00 3735.0
2 TraesCS5B01G029500 chr5B 97.287 2175 42 3 795 2952 36452719 36450545 0.000000e+00 3674.0
3 TraesCS5B01G029500 chr5B 97.368 570 14 1 220 788 621788593 621788024 0.000000e+00 968.0
4 TraesCS5B01G029500 chr5B 99.490 196 1 0 1 196 690082911 690082716 1.010000e-94 357.0
5 TraesCS5B01G029500 chr5B 98.980 196 2 0 1 196 621789458 621789263 4.680000e-93 351.0
6 TraesCS5B01G029500 chr2B 97.515 2173 37 4 796 2952 563765996 563768167 0.000000e+00 3698.0
7 TraesCS5B01G029500 chr2B 97.419 2170 39 4 799 2952 257722882 257720714 0.000000e+00 3681.0
8 TraesCS5B01G029500 chr2B 97.240 2174 43 4 796 2952 106933051 106935224 0.000000e+00 3666.0
9 TraesCS5B01G029500 chr2B 97.236 2171 43 4 799 2952 327770748 327768578 0.000000e+00 3661.0
10 TraesCS5B01G029500 chr2B 97.368 570 14 1 220 788 106932398 106932967 0.000000e+00 968.0
11 TraesCS5B01G029500 chr2B 97.368 570 14 1 220 788 563765343 563765912 0.000000e+00 968.0
12 TraesCS5B01G029500 chr2B 97.193 570 15 1 220 788 257723538 257722969 0.000000e+00 963.0
13 TraesCS5B01G029500 chr2B 97.193 570 15 1 220 788 327771404 327770835 0.000000e+00 963.0
14 TraesCS5B01G029500 chr2B 98.980 196 2 0 1 196 63583304 63583499 4.680000e-93 351.0
15 TraesCS5B01G029500 chr2B 98.980 196 2 0 1 196 106931440 106931635 4.680000e-93 351.0
16 TraesCS5B01G029500 chr2B 98.980 196 2 0 1 196 297489593 297489788 4.680000e-93 351.0
17 TraesCS5B01G029500 chr3B 97.465 2170 39 3 799 2952 717599416 717597247 0.000000e+00 3688.0
18 TraesCS5B01G029500 chr3B 97.198 571 14 1 220 788 632150220 632150790 0.000000e+00 965.0
19 TraesCS5B01G029500 chr3B 97.193 570 15 1 220 788 717600072 717599503 0.000000e+00 963.0
20 TraesCS5B01G029500 chr3B 99.490 196 1 0 1 196 717601030 717600835 1.010000e-94 357.0
21 TraesCS5B01G029500 chr7B 97.499 2159 37 4 811 2952 6943047 6945205 0.000000e+00 3672.0
22 TraesCS5B01G029500 chr7B 99.490 196 1 0 1 196 6942629 6942824 1.010000e-94 357.0
23 TraesCS5B01G029500 chr1B 97.285 2173 43 3 796 2952 26650342 26652514 0.000000e+00 3672.0
24 TraesCS5B01G029500 chr1B 97.193 570 15 1 220 788 26649689 26650258 0.000000e+00 963.0
25 TraesCS5B01G029500 chr1B 98.980 196 2 0 1 196 26648731 26648926 4.680000e-93 351.0
26 TraesCS5B01G029500 chr4B 97.282 2171 40 5 799 2952 11626795 11624627 0.000000e+00 3664.0
27 TraesCS5B01G029500 chr4B 97.199 2142 42 4 828 2952 244519825 244521965 0.000000e+00 3607.0
28 TraesCS5B01G029500 chr4B 97.368 570 14 1 220 788 11627451 11626882 0.000000e+00 968.0
29 TraesCS5B01G029500 chr4B 98.611 144 2 0 1 144 244504273 244504416 3.780000e-64 255.0
30 TraesCS5B01G029500 chr6B 97.189 2170 45 3 799 2952 21616960 21614791 0.000000e+00 3655.0
31 TraesCS5B01G029500 chr6B 97.143 2170 46 3 799 2952 586281073 586278904 0.000000e+00 3650.0
32 TraesCS5B01G029500 chr6B 99.490 196 1 0 1 196 21618423 21618228 1.010000e-94 357.0
33 TraesCS5B01G029500 chr4A 95.844 1131 43 4 1824 2952 643217355 643216227 0.000000e+00 1825.0
34 TraesCS5B01G029500 chr1D 99.457 184 1 0 13 196 456488461 456488644 4.710000e-88 335.0
35 TraesCS5B01G029500 chr6D 98.370 184 3 0 13 196 467271899 467272082 1.020000e-84 324.0
36 TraesCS5B01G029500 chr3D 98.370 184 3 0 13 196 49427190 49427007 1.020000e-84 324.0
37 TraesCS5B01G029500 chr5D 97.283 184 5 0 13 196 544759422 544759239 2.210000e-81 313.0
38 TraesCS5B01G029500 chr5D 98.485 132 2 0 13 144 540480570 540480701 1.770000e-57 233.0
39 TraesCS5B01G029500 chr7D 88.235 51 3 3 193 241 289817399 289817448 1.140000e-04 58.4
40 TraesCS5B01G029500 chr2D 97.059 34 0 1 193 225 67949740 67949707 4.110000e-04 56.5


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 TraesCS5B01G029500 chr5B 29423821 29426772 2951 False 5452.000000 5452 100.000000 1 2952 1 chr5B.!!$F1 2951
1 TraesCS5B01G029500 chr5B 36450545 36452719 2174 True 3674.000000 3674 97.287000 795 2952 1 chr5B.!!$R1 2157
2 TraesCS5B01G029500 chr5B 690079144 690082911 3767 True 2046.000000 3735 98.724000 1 2952 2 chr5B.!!$R3 2951
3 TraesCS5B01G029500 chr5B 621788024 621789458 1434 True 659.500000 968 98.174000 1 788 2 chr5B.!!$R2 787
4 TraesCS5B01G029500 chr2B 563765343 563768167 2824 False 2333.000000 3698 97.441500 220 2952 2 chr2B.!!$F4 2732
5 TraesCS5B01G029500 chr2B 257720714 257723538 2824 True 2322.000000 3681 97.306000 220 2952 2 chr2B.!!$R1 2732
6 TraesCS5B01G029500 chr2B 327768578 327771404 2826 True 2312.000000 3661 97.214500 220 2952 2 chr2B.!!$R2 2732
7 TraesCS5B01G029500 chr2B 106931440 106935224 3784 False 1661.666667 3666 97.862667 1 2952 3 chr2B.!!$F3 2951
8 TraesCS5B01G029500 chr3B 717597247 717601030 3783 True 1669.333333 3688 98.049333 1 2952 3 chr3B.!!$R1 2951
9 TraesCS5B01G029500 chr3B 632150220 632150790 570 False 965.000000 965 97.198000 220 788 1 chr3B.!!$F1 568
10 TraesCS5B01G029500 chr7B 6942629 6945205 2576 False 2014.500000 3672 98.494500 1 2952 2 chr7B.!!$F1 2951
11 TraesCS5B01G029500 chr1B 26648731 26652514 3783 False 1662.000000 3672 97.819333 1 2952 3 chr1B.!!$F1 2951
12 TraesCS5B01G029500 chr4B 244519825 244521965 2140 False 3607.000000 3607 97.199000 828 2952 1 chr4B.!!$F2 2124
13 TraesCS5B01G029500 chr4B 11624627 11627451 2824 True 2316.000000 3664 97.325000 220 2952 2 chr4B.!!$R1 2732
14 TraesCS5B01G029500 chr6B 586278904 586281073 2169 True 3650.000000 3650 97.143000 799 2952 1 chr6B.!!$R1 2153
15 TraesCS5B01G029500 chr6B 21614791 21618423 3632 True 2006.000000 3655 98.339500 1 2952 2 chr6B.!!$R2 2951
16 TraesCS5B01G029500 chr4A 643216227 643217355 1128 True 1825.000000 1825 95.844000 1824 2952 1 chr4A.!!$R1 1128

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
653 1486 0.381801 GCAGACTTGTGGTGTTGGTG 59.618 55.000 0.0 0.0 0.0 4.17 F
907 1818 1.407851 CCCTGCTCATCTTGCTGCTTA 60.408 52.381 0.0 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 2634 4.359971 TGTCATGCAGAATTCAAATCGG 57.640 40.909 8.44 0.0 0.0 4.18 R
2892 3824 0.179129 GCCGAGCCCAACAATTCATG 60.179 55.000 0.00 0.0 0.0 3.07 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
215 249 9.927081 ATAATATTGGTCCTTCTTTTGACAGAT 57.073 29.630 0.00 0.00 33.09 2.90
490 1323 6.768483 TGTCCTTTGTCTCATCATCTTAACA 58.232 36.000 0.00 0.00 0.00 2.41
554 1387 8.475331 AGTAGGAGTATTTTACATGTTGTTCG 57.525 34.615 2.30 0.00 0.00 3.95
564 1397 2.687935 ACATGTTGTTCGTTTCTTGGCT 59.312 40.909 0.00 0.00 0.00 4.75
653 1486 0.381801 GCAGACTTGTGGTGTTGGTG 59.618 55.000 0.00 0.00 0.00 4.17
661 1494 3.444703 TGTGGTGTTGGTGCAATTTAC 57.555 42.857 0.00 0.00 0.00 2.01
791 1626 9.367160 TCATCTTATCTCTATGACAACCATACA 57.633 33.333 0.00 0.00 36.71 2.29
797 1708 8.670521 ATCTCTATGACAACCATACATCCATA 57.329 34.615 0.00 0.00 36.71 2.74
809 1720 5.884232 CCATACATCCATAAGTATGCTGCAT 59.116 40.000 20.18 20.18 43.81 3.96
907 1818 1.407851 CCCTGCTCATCTTGCTGCTTA 60.408 52.381 0.00 0.00 0.00 3.09
1036 1947 5.752892 AACAGAGATTGCTAGCATCATTG 57.247 39.130 20.13 18.81 0.00 2.82
1215 2126 2.668212 GCACGGCAGTAGCACCAA 60.668 61.111 6.55 0.00 44.61 3.67
1338 2249 4.704833 TGCTGCTCGGCCTCAACC 62.705 66.667 0.00 0.00 0.00 3.77
1453 2364 5.710513 TCCGTCTGCAGTTAACTAAGTTA 57.289 39.130 14.67 0.00 0.00 2.24
1581 2492 5.537188 ACAGTTCTAGCTTTTCTGACTCAG 58.463 41.667 12.44 0.00 0.00 3.35
1722 2634 6.220930 TCACCTTCGTATGCATAGGTTTATC 58.779 40.000 22.18 2.74 38.93 1.75
1725 2637 5.456548 TTCGTATGCATAGGTTTATCCGA 57.543 39.130 22.18 14.80 41.99 4.55
2080 2992 6.037098 GCTGACGAGTATTGTTAGATCTTGT 58.963 40.000 0.00 0.00 38.30 3.16
2274 3188 5.648092 GGTACTAGCTGAATGTTGAATGGTT 59.352 40.000 0.00 0.00 0.00 3.67
2574 3504 1.599797 GCCCTTTGTACTGGCACGT 60.600 57.895 10.19 0.00 44.70 4.49
2726 3656 6.488683 CCACTTACCTGACAAATTGAAACCTA 59.511 38.462 0.00 0.00 0.00 3.08
2851 3781 1.479389 GCTACCATATTGGGCTTGGCT 60.479 52.381 0.00 0.00 43.37 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
210 244 8.492415 TGAACAAGGCCTACTATTATATCTGT 57.508 34.615 5.16 0.00 0.00 3.41
328 1161 0.036306 GTGGTCGTCCTGGTCCATTT 59.964 55.000 0.00 0.00 32.45 2.32
329 1162 1.677552 GTGGTCGTCCTGGTCCATT 59.322 57.895 0.00 0.00 32.45 3.16
408 1241 2.359107 CGGCTGCACCACACTGAT 60.359 61.111 0.50 0.00 39.03 2.90
490 1323 5.233083 TGATGAGACAAAGGACAACAGAT 57.767 39.130 0.00 0.00 0.00 2.90
544 1377 3.044986 CAGCCAAGAAACGAACAACATG 58.955 45.455 0.00 0.00 0.00 3.21
564 1397 1.477700 GATTAGCAAACATGCTGGGCA 59.522 47.619 13.27 0.00 45.81 5.36
693 1526 8.978472 AGGATTAAATGCAGACAGTAGTAGTAA 58.022 33.333 0.00 0.00 0.00 2.24
788 1623 6.212187 AGAGATGCAGCATACTTATGGATGTA 59.788 38.462 8.22 0.00 34.32 2.29
789 1624 5.012871 AGAGATGCAGCATACTTATGGATGT 59.987 40.000 8.22 0.00 34.32 3.06
790 1625 5.489249 AGAGATGCAGCATACTTATGGATG 58.511 41.667 8.22 0.00 34.32 3.51
791 1626 5.338219 GGAGAGATGCAGCATACTTATGGAT 60.338 44.000 8.22 0.00 34.32 3.41
792 1627 4.020751 GGAGAGATGCAGCATACTTATGGA 60.021 45.833 8.22 0.00 34.32 3.41
793 1628 4.252073 GGAGAGATGCAGCATACTTATGG 58.748 47.826 8.22 0.00 34.32 2.74
797 1708 2.368221 GAGGGAGAGATGCAGCATACTT 59.632 50.000 8.22 0.00 0.00 2.24
809 1720 1.313889 ATGGAGTGAGGAGGGAGAGA 58.686 55.000 0.00 0.00 0.00 3.10
907 1818 2.769209 ACAGAGAGTATTCCCTGCCAT 58.231 47.619 0.00 0.00 0.00 4.40
1017 1928 4.815308 GTGTCAATGATGCTAGCAATCTCT 59.185 41.667 23.54 4.08 0.00 3.10
1036 1947 6.206634 TCAATTCAAAGGGTGTATCTTGTGTC 59.793 38.462 0.00 0.00 0.00 3.67
1215 2126 0.698238 TCCCAACAGCAGCAAGGTAT 59.302 50.000 0.00 0.00 0.00 2.73
1453 2364 2.138542 AGTAGGACATCAATGGGGCAT 58.861 47.619 0.00 0.00 0.00 4.40
1561 2472 5.778862 ACTCTGAGTCAGAAAAGCTAGAAC 58.221 41.667 22.83 0.00 40.18 3.01
1581 2492 5.468746 TCATGCAGTACCAAGTTAACAACTC 59.531 40.000 8.61 0.00 41.91 3.01
1722 2634 4.359971 TGTCATGCAGAATTCAAATCGG 57.640 40.909 8.44 0.00 0.00 4.18
1725 2637 9.529325 CTATTTCATGTCATGCAGAATTCAAAT 57.471 29.630 8.44 8.54 0.00 2.32
2080 2992 4.529109 TCACGACCATACATTCAACTGA 57.471 40.909 0.00 0.00 0.00 3.41
2209 3122 9.388346 CGAGCTAGTTAAAATGAGATAGTAGTG 57.612 37.037 0.00 0.00 0.00 2.74
2274 3188 8.546083 AACTGGGGCAAATATATTATGAACAA 57.454 30.769 0.00 0.00 0.00 2.83
2726 3656 3.244911 CCCAGTTGTCAGGTTCTGGTAAT 60.245 47.826 8.83 0.00 43.96 1.89
2834 3764 0.630673 TGAGCCAAGCCCAATATGGT 59.369 50.000 0.00 0.00 35.17 3.55
2851 3781 6.664384 TCATCAATTTTTGGTCAGGATCATGA 59.336 34.615 5.84 5.84 0.00 3.07
2892 3824 0.179129 GCCGAGCCCAACAATTCATG 60.179 55.000 0.00 0.00 0.00 3.07
2893 3825 1.322538 GGCCGAGCCCAACAATTCAT 61.323 55.000 3.73 0.00 44.06 2.57


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

AutoCloner maintained by Alex Coulton.