Multiple sequence alignment - TraesCS1B01G177200

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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 TraesCS1B01G177200 chr1B 100.000 2683 0 0 1 2683 321692960 321690278 0.000000e+00 4955.0
1 TraesCS1B01G177200 chr1B 81.746 378 50 16 1444 1816 573328701 573328338 5.620000e-77 298.0
2 TraesCS1B01G177200 chr2D 96.065 2643 67 15 73 2683 47216258 47213621 0.000000e+00 4270.0
3 TraesCS1B01G177200 chr2D 91.080 213 15 4 228 439 47216311 47216102 4.370000e-73 285.0
4 TraesCS1B01G177200 chr2D 97.297 74 2 0 1 74 47216401 47216328 2.800000e-25 126.0
5 TraesCS1B01G177200 chr1A 95.803 2192 73 10 503 2683 157962604 157964787 0.000000e+00 3520.0
6 TraesCS1B01G177200 chr1A 96.568 437 15 0 73 509 157960337 157960773 0.000000e+00 725.0
7 TraesCS1B01G177200 chr1A 95.946 74 3 0 1 74 157960194 157960267 1.300000e-23 121.0
8 TraesCS1B01G177200 chr1A 94.118 51 3 0 2037 2087 150064427 150064477 7.960000e-11 78.7
9 TraesCS1B01G177200 chr6A 96.440 1601 56 1 73 1672 92404967 92406567 0.000000e+00 2639.0
10 TraesCS1B01G177200 chr6A 97.297 74 2 0 1 74 92404824 92404897 2.800000e-25 126.0
11 TraesCS1B01G177200 chr2B 95.350 1656 68 6 73 1725 783705794 783704145 0.000000e+00 2623.0
12 TraesCS1B01G177200 chr2B 93.300 806 38 7 1888 2683 783950197 783949398 0.000000e+00 1175.0
13 TraesCS1B01G177200 chr2B 95.690 696 30 0 1030 1725 783960227 783959532 0.000000e+00 1120.0
14 TraesCS1B01G177200 chr2B 92.486 346 19 2 73 418 783960869 783960531 3.100000e-134 488.0
15 TraesCS1B01G177200 chr2B 93.590 312 17 3 673 983 783960535 783960226 1.880000e-126 462.0
16 TraesCS1B01G177200 chr2B 94.944 178 6 1 1707 1881 783704131 783703954 2.630000e-70 276.0
17 TraesCS1B01G177200 chr2B 93.820 178 8 1 1707 1881 783959518 783959341 5.700000e-67 265.0
18 TraesCS1B01G177200 chr2B 94.595 74 4 0 1 74 783961012 783960939 6.070000e-22 115.0
19 TraesCS1B01G177200 chr5B 94.147 1196 43 10 1346 2518 384737743 384736552 0.000000e+00 1796.0
20 TraesCS1B01G177200 chr5B 94.667 825 41 3 523 1344 384739521 384738697 0.000000e+00 1277.0
21 TraesCS1B01G177200 chr5B 94.737 456 22 2 73 527 384740417 384739963 0.000000e+00 708.0
22 TraesCS1B01G177200 chr5B 92.814 167 8 1 2516 2682 384725276 384725114 3.450000e-59 239.0
23 TraesCS1B01G177200 chr5B 94.595 74 4 0 1 74 384740560 384740487 6.070000e-22 115.0
24 TraesCS1B01G177200 chr5B 97.917 48 1 0 2040 2087 461643355 461643308 1.710000e-12 84.2
25 TraesCS1B01G177200 chr1D 94.954 1090 34 7 73 1152 468418959 468420037 0.000000e+00 1688.0
26 TraesCS1B01G177200 chr1D 97.876 565 12 0 1150 1714 468424715 468425279 0.000000e+00 977.0
27 TraesCS1B01G177200 chr1D 94.426 610 24 5 2081 2683 468432001 468432607 0.000000e+00 929.0
28 TraesCS1B01G177200 chr1D 80.174 459 60 21 1453 1902 423805141 423804705 5.580000e-82 315.0
29 TraesCS1B01G177200 chr1D 97.297 74 2 0 1 74 468418831 468418904 2.800000e-25 126.0
30 TraesCS1B01G177200 chr1D 88.636 88 8 2 2088 2175 468747603 468747518 3.650000e-19 106.0
31 TraesCS1B01G177200 chr3B 92.585 971 43 10 1084 2041 462053547 462054501 0.000000e+00 1367.0
32 TraesCS1B01G177200 chr3B 94.553 514 20 4 2177 2683 462054502 462055014 0.000000e+00 787.0
33 TraesCS1B01G177200 chr3B 91.538 520 30 8 234 747 461711556 461711045 0.000000e+00 704.0
34 TraesCS1B01G177200 chr3B 94.167 120 5 2 963 1082 462048592 462048709 5.900000e-42 182.0
35 TraesCS1B01G177200 chr3B 94.595 74 4 0 1 74 461711652 461711579 6.070000e-22 115.0
36 TraesCS1B01G177200 chr3D 80.672 1221 151 45 283 1461 255525243 255524066 0.000000e+00 869.0
37 TraesCS1B01G177200 chr3D 89.247 93 9 1 2534 2625 103812142 103812050 6.070000e-22 115.0
38 TraesCS1B01G177200 chr3A 81.420 1141 139 37 351 1462 272780084 272778988 0.000000e+00 865.0
39 TraesCS1B01G177200 chr3A 95.833 48 2 0 2040 2087 8255537 8255584 7.960000e-11 78.7
40 TraesCS1B01G177200 chr4A 86.207 174 21 2 1290 1461 444153284 444153456 4.560000e-43 185.0
41 TraesCS1B01G177200 chr4A 95.833 48 2 0 2040 2087 548783353 548783306 7.960000e-11 78.7
42 TraesCS1B01G177200 chr4B 88.889 99 7 4 2088 2184 664792814 664792910 4.690000e-23 119.0
43 TraesCS1B01G177200 chr4B 90.698 86 6 2 2088 2173 234685836 234685919 2.180000e-21 113.0
44 TraesCS1B01G177200 chr4B 89.535 86 7 2 2088 2173 377376906 377376989 1.020000e-19 108.0
45 TraesCS1B01G177200 chr2A 82.069 145 19 7 2534 2672 62217693 62217550 1.690000e-22 117.0
46 TraesCS1B01G177200 chr7B 82.143 140 18 7 2539 2672 606356478 606356616 2.180000e-21 113.0
47 TraesCS1B01G177200 chr4D 95.833 48 2 0 2040 2087 227998239 227998192 7.960000e-11 78.7
48 TraesCS1B01G177200 chr5A 76.230 122 24 3 1734 1854 703161054 703161171 2.880000e-05 60.2


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 TraesCS1B01G177200 chr1B 321690278 321692960 2682 True 4955.000000 4955 100.000000 1 2683 1 chr1B.!!$R1 2682
1 TraesCS1B01G177200 chr2D 47213621 47216401 2780 True 1560.333333 4270 94.814000 1 2683 3 chr2D.!!$R1 2682
2 TraesCS1B01G177200 chr1A 157960194 157964787 4593 False 1455.333333 3520 96.105667 1 2683 3 chr1A.!!$F2 2682
3 TraesCS1B01G177200 chr6A 92404824 92406567 1743 False 1382.500000 2639 96.868500 1 1672 2 chr6A.!!$F1 1671
4 TraesCS1B01G177200 chr2B 783703954 783705794 1840 True 1449.500000 2623 95.147000 73 1881 2 chr2B.!!$R2 1808
5 TraesCS1B01G177200 chr2B 783949398 783950197 799 True 1175.000000 1175 93.300000 1888 2683 1 chr2B.!!$R1 795
6 TraesCS1B01G177200 chr2B 783959341 783961012 1671 True 490.000000 1120 94.036200 1 1881 5 chr2B.!!$R3 1880
7 TraesCS1B01G177200 chr5B 384736552 384740560 4008 True 974.000000 1796 94.536500 1 2518 4 chr5B.!!$R3 2517
8 TraesCS1B01G177200 chr1D 468424715 468425279 564 False 977.000000 977 97.876000 1150 1714 1 chr1D.!!$F1 564
9 TraesCS1B01G177200 chr1D 468432001 468432607 606 False 929.000000 929 94.426000 2081 2683 1 chr1D.!!$F2 602
10 TraesCS1B01G177200 chr1D 468418831 468420037 1206 False 907.000000 1688 96.125500 1 1152 2 chr1D.!!$F3 1151
11 TraesCS1B01G177200 chr3B 462053547 462055014 1467 False 1077.000000 1367 93.569000 1084 2683 2 chr3B.!!$F2 1599
12 TraesCS1B01G177200 chr3B 461711045 461711652 607 True 409.500000 704 93.066500 1 747 2 chr3B.!!$R1 746
13 TraesCS1B01G177200 chr3D 255524066 255525243 1177 True 869.000000 869 80.672000 283 1461 1 chr3D.!!$R2 1178
14 TraesCS1B01G177200 chr3A 272778988 272780084 1096 True 865.000000 865 81.420000 351 1462 1 chr3A.!!$R1 1111

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
43 44 0.035630 GCTTGATGCTCTCCACCACT 60.036 55.0 0.0 0.0 38.95 4.00 F
800 2748 0.040067 GACCGCAAAGAAAGTGCAGG 60.040 55.0 0.0 0.0 42.33 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1038 2997 2.057137 AACTTTTGCCAGAGACAGCA 57.943 45.0 0.0 0.0 37.18 4.41 R
2150 5150 2.101415 GGCCCTGTTTGATTTCCTATGC 59.899 50.0 0.0 0.0 0.00 3.14 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
43 44 0.035630 GCTTGATGCTCTCCACCACT 60.036 55.000 0.00 0.00 38.95 4.00
232 304 0.530744 TTGTGCTCCTACTGCCGTAG 59.469 55.000 8.24 8.24 42.24 3.51
353 442 2.507944 CTGGCTCCTCATTCGGGG 59.492 66.667 0.00 0.00 0.00 5.73
604 2546 6.900189 TCAATTAGTTAAACCGCGAATTGAA 58.100 32.000 19.60 7.17 40.78 2.69
681 2625 7.315142 GCAACACATTCTATGATTTTCTTCCA 58.685 34.615 0.00 0.00 0.00 3.53
762 2709 3.843619 TGGTCTGGTCTATGGATGTTGAA 59.156 43.478 0.00 0.00 0.00 2.69
800 2748 0.040067 GACCGCAAAGAAAGTGCAGG 60.040 55.000 0.00 0.00 42.33 4.85
855 2805 7.864379 ACATCAAATTTCAGTGACAAGAACATC 59.136 33.333 0.00 0.00 0.00 3.06
1038 2997 2.995872 GCCACTCTCTTCCGCGAGT 61.996 63.158 8.23 0.00 40.92 4.18
1289 3258 3.009473 ACTCCACCTATGAGCACATGTTT 59.991 43.478 6.91 0.00 37.87 2.83
1569 4491 2.159667 TGAATTCGTTTGAGATGCTGCG 60.160 45.455 0.04 0.00 0.00 5.18
1877 4866 6.746120 ACGGCCTATAATTCTACACTTACTG 58.254 40.000 0.00 0.00 0.00 2.74
2132 5131 5.161943 ACTAGCGACTTTTTAGTTGGGAT 57.838 39.130 0.00 0.00 0.00 3.85
2235 5239 8.764558 TGTACAGTTTTAGGAGCATAGGAAATA 58.235 33.333 0.00 0.00 0.00 1.40
2381 5385 9.995003 TTCATACAAATTTAGGAGCACAAAAAT 57.005 25.926 0.00 0.00 0.00 1.82
2499 5514 9.744468 ACACACAAAAGAAACATAGATAAAACC 57.256 29.630 0.00 0.00 0.00 3.27
2563 5578 5.136220 AGGGGATAAATTTTAGGAGGAAGGG 59.864 44.000 0.00 0.00 0.00 3.95
2656 5675 7.222999 CAGGAGACGAAGAATTATCCTGTTAAC 59.777 40.741 10.24 0.00 45.67 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 153 1.293498 GCCTCGTCTGGAAGCAAGA 59.707 57.895 0.00 0.00 32.13 3.02
353 442 2.352960 GCAAGATGGAGGTCAAATCGAC 59.647 50.000 0.00 0.00 44.57 4.20
604 2546 3.493176 GCTCCTGCACCAAGAAACAAATT 60.493 43.478 0.00 0.00 39.41 1.82
681 2625 5.093677 AGGGGCCAAATAGTTTCAGATTTT 58.906 37.500 4.39 0.00 0.00 1.82
762 2709 1.622811 TCCCGGCTGCAATCAAATTTT 59.377 42.857 0.50 0.00 0.00 1.82
800 2748 3.643763 CAGATATCTACAACGGTGAGCC 58.356 50.000 7.88 0.00 0.00 4.70
1038 2997 2.057137 AACTTTTGCCAGAGACAGCA 57.943 45.000 0.00 0.00 37.18 4.41
1176 3144 3.242349 CCGTCGACACTGTCAGTATAGTC 60.242 52.174 17.16 8.37 32.09 2.59
1747 4736 9.515020 TTTTTGTCAGATATCACTTGTGAAAAC 57.485 29.630 7.57 2.72 0.00 2.43
1877 4866 8.181487 TGTTTCGTAGAACAATGACTTATAGC 57.819 34.615 0.00 0.00 45.90 2.97
2041 5040 2.512476 AGTCCCTGTAAACAAACACCCT 59.488 45.455 0.00 0.00 0.00 4.34
2150 5150 2.101415 GGCCCTGTTTGATTTCCTATGC 59.899 50.000 0.00 0.00 0.00 3.14
2151 5151 3.635591 AGGCCCTGTTTGATTTCCTATG 58.364 45.455 0.00 0.00 0.00 2.23
2152 5152 5.466127 TTAGGCCCTGTTTGATTTCCTAT 57.534 39.130 0.00 0.00 0.00 2.57
2153 5153 4.938575 TTAGGCCCTGTTTGATTTCCTA 57.061 40.909 0.00 0.00 0.00 2.94
2154 5154 3.825908 TTAGGCCCTGTTTGATTTCCT 57.174 42.857 0.00 0.00 0.00 3.36
2156 5156 7.404671 TTCTATTTAGGCCCTGTTTGATTTC 57.595 36.000 0.00 0.00 0.00 2.17
2157 5157 7.790782 TTTCTATTTAGGCCCTGTTTGATTT 57.209 32.000 0.00 0.00 0.00 2.17
2235 5239 5.416952 GGCACTAATAAGCTTCCATGCATAT 59.583 40.000 0.00 0.00 33.48 1.78
2381 5385 8.103305 GCCACCCAGAAATCTCATAAATAGATA 58.897 37.037 0.00 0.00 33.32 1.98
2499 5514 7.600375 AGAACACATGATTACGCCATATCTAAG 59.400 37.037 0.00 0.00 0.00 2.18
2563 5578 4.020662 ACTTCAGAAACTCACCTCATCTCC 60.021 45.833 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.