Multiple sequence alignment - TraesCS5D01G321700

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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 TraesCS5D01G321700 chr5D 100.000 2579 0 0 1 2579 413592276 413594854 0.000000e+00 4763.0
1 TraesCS5D01G321700 chr5D 97.152 2212 29 4 399 2579 413490053 413492261 0.000000e+00 3705.0
2 TraesCS5D01G321700 chr5D 98.750 400 5 0 1 400 413489592 413489991 0.000000e+00 712.0
3 TraesCS5D01G321700 chr5D 82.765 528 78 10 2045 2564 503743632 503743110 2.340000e-125 459.0
4 TraesCS5D01G321700 chr5D 79.624 319 47 13 1489 1791 413286966 413287282 2.010000e-51 213.0
5 TraesCS5D01G321700 chr5D 97.561 41 1 0 1492 1532 413491108 413491148 1.280000e-08 71.3
6 TraesCS5D01G321700 chr5D 97.561 41 1 0 1453 1493 413491147 413491187 1.280000e-08 71.3
7 TraesCS5D01G321700 chr5D 97.561 41 1 0 1492 1532 413593728 413593768 1.280000e-08 71.3
8 TraesCS5D01G321700 chr5D 97.561 41 1 0 1453 1493 413593767 413593807 1.280000e-08 71.3
9 TraesCS5D01G321700 chr5A 94.161 1096 54 4 399 1493 525918681 525919767 0.000000e+00 1661.0
10 TraesCS5D01G321700 chr5A 93.995 1099 59 7 399 1493 525724624 525725719 0.000000e+00 1657.0
11 TraesCS5D01G321700 chr5A 93.345 1097 62 5 399 1493 525830059 525831146 0.000000e+00 1611.0
12 TraesCS5D01G321700 chr5A 89.350 892 62 8 399 1285 526265262 526266125 0.000000e+00 1090.0
13 TraesCS5D01G321700 chr5A 90.094 424 32 6 1492 1913 525919727 525920142 2.260000e-150 542.0
14 TraesCS5D01G321700 chr5A 88.915 424 36 9 1492 1913 525831106 525831520 1.770000e-141 512.0
15 TraesCS5D01G321700 chr5A 92.793 333 22 2 1972 2304 525831527 525831857 4.990000e-132 481.0
16 TraesCS5D01G321700 chr5A 92.169 332 24 2 1967 2298 525726346 525726675 3.890000e-128 468.0
17 TraesCS5D01G321700 chr5A 95.172 290 11 3 112 400 525724275 525724562 3.030000e-124 455.0
18 TraesCS5D01G321700 chr5A 94.483 290 14 2 112 400 525829708 525829996 1.820000e-121 446.0
19 TraesCS5D01G321700 chr5A 94.118 289 14 3 112 400 525918333 525918618 1.100000e-118 436.0
20 TraesCS5D01G321700 chr5A 92.157 306 21 3 1492 1796 525725679 525725982 1.830000e-116 429.0
21 TraesCS5D01G321700 chr5A 90.572 297 18 4 112 400 526264904 526265198 4.030000e-103 385.0
22 TraesCS5D01G321700 chr5A 93.074 231 13 2 1492 1720 526279433 526279662 4.110000e-88 335.0
23 TraesCS5D01G321700 chr5A 93.627 204 13 0 1281 1484 526279261 526279464 3.220000e-79 305.0
24 TraesCS5D01G321700 chr5A 93.220 59 2 1 1 59 525829670 525829726 4.570000e-13 86.1
25 TraesCS5D01G321700 chr5A 93.220 59 2 1 1 59 525918295 525918351 4.570000e-13 86.1
26 TraesCS5D01G321700 chr5B 91.632 478 29 5 1016 1493 498722803 498723269 0.000000e+00 651.0
27 TraesCS5D01G321700 chr5B 91.569 427 23 8 1492 1910 498723229 498723650 6.190000e-161 577.0
28 TraesCS5D01G321700 chr5B 88.646 458 46 5 1967 2422 498723655 498724108 1.040000e-153 553.0
29 TraesCS5D01G321700 chr5B 90.777 412 24 8 1492 1899 498512092 498512493 2.920000e-149 538.0
30 TraesCS5D01G321700 chr5B 82.765 528 78 10 2045 2564 632233080 632232558 2.340000e-125 459.0
31 TraesCS5D01G321700 chr5B 93.750 288 12 3 119 400 498511395 498511682 6.590000e-116 427.0
32 TraesCS5D01G321700 chr5B 94.860 214 10 1 112 324 498722579 498722792 1.480000e-87 333.0
33 TraesCS5D01G321700 chr5B 87.607 234 24 2 1264 1493 498511900 498512132 1.520000e-67 267.0
34 TraesCS5D01G321700 chr5B 96.939 98 3 0 399 496 498511744 498511841 5.710000e-37 165.0
35 TraesCS5D01G321700 chr5B 97.059 68 2 0 522 589 498511832 498511899 5.830000e-22 115.0
36 TraesCS5D01G321700 chr5B 94.915 59 2 1 1 59 498722540 498722597 9.830000e-15 91.6
37 TraesCS5D01G321700 chr1D 82.692 468 75 6 2111 2576 385828306 385827843 6.640000e-111 411.0
38 TraesCS5D01G321700 chrUn 82.759 464 72 8 2116 2576 7353056 7353514 8.590000e-110 407.0
39 TraesCS5D01G321700 chr1B 82.759 464 72 8 2116 2576 565631567 565632025 8.590000e-110 407.0
40 TraesCS5D01G321700 chr7B 94.231 52 3 0 650 701 668204569 668204620 2.130000e-11 80.5
41 TraesCS5D01G321700 chr6A 94.872 39 2 0 658 696 504479646 504479608 7.710000e-06 62.1


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 TraesCS5D01G321700 chr5D 413592276 413594854 2578 False 1635.200 4763 98.37400 1 2579 3 chr5D.!!$F3 2578
1 TraesCS5D01G321700 chr5D 413489592 413492261 2669 False 1139.900 3705 97.75600 1 2579 4 chr5D.!!$F2 2578
2 TraesCS5D01G321700 chr5D 503743110 503743632 522 True 459.000 459 82.76500 2045 2564 1 chr5D.!!$R1 519
3 TraesCS5D01G321700 chr5A 525724275 525726675 2400 False 752.250 1657 93.37325 112 2298 4 chr5A.!!$F1 2186
4 TraesCS5D01G321700 chr5A 526264904 526266125 1221 False 737.500 1090 89.96100 112 1285 2 chr5A.!!$F4 1173
5 TraesCS5D01G321700 chr5A 525918295 525920142 1847 False 681.275 1661 92.89825 1 1913 4 chr5A.!!$F3 1912
6 TraesCS5D01G321700 chr5A 525829670 525831857 2187 False 627.220 1611 92.55120 1 2304 5 chr5A.!!$F2 2303
7 TraesCS5D01G321700 chr5B 632232558 632233080 522 True 459.000 459 82.76500 2045 2564 1 chr5B.!!$R1 519
8 TraesCS5D01G321700 chr5B 498722540 498724108 1568 False 441.120 651 92.32440 1 2422 5 chr5B.!!$F2 2421
9 TraesCS5D01G321700 chr5B 498511395 498512493 1098 False 302.400 538 93.22640 119 1899 5 chr5B.!!$F1 1780

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
421 498 7.389053 CCCATATTGACTACTCAAATTCTAGGC 59.611 40.741 0.0 0.0 39.9 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 2732 4.202556 TGAGGGTGTGATTGAGGATTTTGA 60.203 41.667 0.0 0.0 0.0 2.69 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
388 399 8.441312 AGATGTGAATTTTGCAAAGTTTCATT 57.559 26.923 27.89 21.9 30.16 2.57
421 498 7.389053 CCCATATTGACTACTCAAATTCTAGGC 59.611 40.741 0.00 0.0 39.90 3.93
1802 1895 6.642683 GTGTAACACGTACTAATTGATGCT 57.357 37.500 0.00 0.0 36.32 3.79
2300 2702 4.386312 GGGGATGAGGTTTTGATCATGGTA 60.386 45.833 0.00 0.0 0.00 3.25
2312 2714 6.925610 TTGATCATGGTATAACTGCTCAAC 57.074 37.500 0.00 0.0 0.00 3.18
2330 2732 5.526846 GCTCAACTGCTTAGAGATATTGCTT 59.473 40.000 0.00 0.0 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 7.826260 TTTCACAGAAGAAAAACATGTTTCC 57.174 32.000 23.47 17.44 38.10 3.13
388 399 7.194112 TTGAGTAGTCAATATGGGAACATCA 57.806 36.000 8.98 0.00 41.94 3.07
421 498 6.314784 GTGTCTCGGATGGAAAAACAATAAG 58.685 40.000 0.00 0.00 0.00 1.73
720 801 4.522405 TGGAAATGTATGTGGTGGACTTTG 59.478 41.667 0.00 0.00 0.00 2.77
2061 2456 4.861196 TGAATTACCAAAATCATCCGGGA 58.139 39.130 0.00 0.00 0.00 5.14
2300 2702 5.667539 TCTCTAAGCAGTTGAGCAGTTAT 57.332 39.130 0.00 0.00 36.85 1.89
2312 2714 8.074972 GGATTTTGAAGCAATATCTCTAAGCAG 58.925 37.037 9.37 0.00 34.12 4.24
2330 2732 4.202556 TGAGGGTGTGATTGAGGATTTTGA 60.203 41.667 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.