Multiple sequence alignment - TraesCS4A01G285100

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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 TraesCS4A01G285100 chr4A 100.000 2886 0 0 1 2886 591507486 591504601 0.000000e+00 5330.0
1 TraesCS4A01G285100 chr4A 98.700 2539 27 3 352 2886 593105126 593107662 0.000000e+00 4501.0
2 TraesCS4A01G285100 chr4A 98.684 2051 26 1 836 2886 592823362 592825411 0.000000e+00 3637.0
3 TraesCS4A01G285100 chr4A 98.899 1908 20 1 980 2886 592537384 592539291 0.000000e+00 3406.0
4 TraesCS4A01G285100 chr4A 98.585 636 8 1 352 987 592536582 592537216 0.000000e+00 1123.0
5 TraesCS4A01G285100 chr4A 99.715 351 1 0 1 351 592536201 592536551 0.000000e+00 643.0
6 TraesCS4A01G285100 chr4A 99.145 351 0 1 1 351 593104748 593105095 1.890000e-176 628.0
7 TraesCS4A01G285100 chr4A 100.000 257 0 0 1 257 592822548 592822804 2.600000e-130 475.0
8 TraesCS4A01G285100 chr3B 92.990 970 63 4 416 1385 144083370 144084334 0.000000e+00 1410.0
9 TraesCS4A01G285100 chr3B 93.470 536 30 2 1378 1912 144097550 144098081 0.000000e+00 791.0
10 TraesCS4A01G285100 chr3B 98.165 109 2 0 1986 2094 144098081 144098189 1.060000e-44 191.0
11 TraesCS4A01G285100 chr3B 81.437 167 25 5 199 360 163865377 163865212 6.490000e-27 132.0
12 TraesCS4A01G285100 chr3B 80.838 167 26 5 199 360 163846949 163846784 3.020000e-25 126.0
13 TraesCS4A01G285100 chr6A 86.385 639 72 10 966 1599 495442301 495441673 0.000000e+00 684.0
14 TraesCS4A01G285100 chr6A 85.423 638 79 9 969 1601 431760615 431759987 0.000000e+00 651.0
15 TraesCS4A01G285100 chr6A 80.656 579 76 23 417 975 495442918 495442356 1.600000e-112 416.0
16 TraesCS4A01G285100 chr6A 79.894 567 86 15 425 975 431761226 431760672 9.700000e-105 390.0
17 TraesCS4A01G285100 chr7A 86.228 639 74 9 966 1599 561606829 561607458 0.000000e+00 680.0
18 TraesCS4A01G285100 chr7A 89.337 347 31 2 1602 1946 561607535 561607877 5.710000e-117 431.0
19 TraesCS4A01G285100 chr7A 80.927 561 73 21 425 966 561606220 561606765 2.070000e-111 412.0
20 TraesCS4A01G285100 chr7A 90.698 86 7 1 267 351 138380919 138381004 2.350000e-21 113.0
21 TraesCS4A01G285100 chr6B 86.228 639 74 9 966 1599 142691103 142691732 0.000000e+00 680.0
22 TraesCS4A01G285100 chr6B 80.824 558 75 18 425 964 142690494 142691037 2.680000e-110 409.0
23 TraesCS4A01G285100 chr6B 87.342 158 19 1 195 351 543845432 543845589 2.280000e-41 180.0
24 TraesCS4A01G285100 chr3A 85.915 639 76 9 966 1599 661662616 661661987 0.000000e+00 669.0
25 TraesCS4A01G285100 chr3A 89.914 347 29 2 1602 1946 661661910 661661568 2.640000e-120 442.0
26 TraesCS4A01G285100 chr3A 80.662 574 76 22 423 975 661663230 661662671 2.070000e-111 412.0
27 TraesCS4A01G285100 chr5A 85.803 641 77 9 966 1601 492997057 492996426 0.000000e+00 667.0
28 TraesCS4A01G285100 chr5A 89.625 347 30 2 1602 1946 492992307 492991965 1.230000e-118 436.0
29 TraesCS4A01G285100 chr5A 80.035 566 80 23 425 972 492997664 492997114 3.490000e-104 388.0
30 TraesCS4A01G285100 chr5A 90.000 160 14 2 202 360 8807902 8807744 3.770000e-49 206.0
31 TraesCS4A01G285100 chr5A 89.865 148 15 0 204 351 229515787 229515934 1.060000e-44 191.0
32 TraesCS4A01G285100 chr7B 87.609 460 51 3 1722 2181 19119437 19119890 1.970000e-146 529.0
33 TraesCS4A01G285100 chr7B 93.506 154 9 1 199 351 185622891 185623044 8.040000e-56 228.0
34 TraesCS4A01G285100 chr7B 93.464 153 9 1 200 351 678205436 678205588 2.890000e-55 226.0
35 TraesCS4A01G285100 chr7B 96.667 60 1 1 2216 2274 232248205 232248264 6.580000e-17 99.0
36 TraesCS4A01G285100 chr7B 85.393 89 10 2 2183 2271 497254064 497253979 3.960000e-14 89.8
37 TraesCS4A01G285100 chr2B 82.624 564 61 16 417 975 732884171 732883640 5.630000e-127 464.0
38 TraesCS4A01G285100 chr2B 85.177 452 58 5 1731 2180 250725693 250725249 3.390000e-124 455.0
39 TraesCS4A01G285100 chr2B 88.312 154 15 3 205 357 555365678 555365829 6.350000e-42 182.0
40 TraesCS4A01G285100 chr2B 86.517 89 9 2 2183 2271 27859809 27859724 8.510000e-16 95.3
41 TraesCS4A01G285100 chrUn 77.208 566 85 20 413 970 46035059 46035588 1.010000e-74 291.0
42 TraesCS4A01G285100 chrUn 100.000 33 0 0 2183 2215 168288515 168288483 8.630000e-06 62.1
43 TraesCS4A01G285100 chr5D 94.000 150 9 0 202 351 66671950 66671801 8.040000e-56 228.0
44 TraesCS4A01G285100 chr6D 92.405 158 12 0 194 351 469057457 469057614 2.890000e-55 226.0
45 TraesCS4A01G285100 chr4B 92.903 155 11 0 197 351 549133710 549133864 2.890000e-55 226.0
46 TraesCS4A01G285100 chr4B 89.691 97 5 4 2176 2272 307108582 307108673 5.050000e-23 119.0
47 TraesCS4A01G285100 chr4B 88.764 89 7 2 2183 2271 8980482 8980567 3.930000e-19 106.0
48 TraesCS4A01G285100 chr3D 89.831 177 15 3 177 351 142632731 142632556 1.040000e-54 224.0
49 TraesCS4A01G285100 chr1B 91.358 162 14 0 190 351 268402686 268402847 3.740000e-54 222.0
50 TraesCS4A01G285100 chr1B 86.517 89 9 2 2183 2271 63708486 63708401 8.510000e-16 95.3
51 TraesCS4A01G285100 chr2A 83.648 159 23 3 204 361 450143194 450143350 2.320000e-31 147.0
52 TraesCS4A01G285100 chr4D 93.333 75 5 0 2271 2345 334178734 334178808 8.450000e-21 111.0


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 TraesCS4A01G285100 chr4A 591504601 591507486 2885 True 5330.000000 5330 100.000000 1 2886 1 chr4A.!!$R1 2885
1 TraesCS4A01G285100 chr4A 593104748 593107662 2914 False 2564.500000 4501 98.922500 1 2886 2 chr4A.!!$F3 2885
2 TraesCS4A01G285100 chr4A 592822548 592825411 2863 False 2056.000000 3637 99.342000 1 2886 2 chr4A.!!$F2 2885
3 TraesCS4A01G285100 chr4A 592536201 592539291 3090 False 1724.000000 3406 99.066333 1 2886 3 chr4A.!!$F1 2885
4 TraesCS4A01G285100 chr3B 144083370 144084334 964 False 1410.000000 1410 92.990000 416 1385 1 chr3B.!!$F1 969
5 TraesCS4A01G285100 chr3B 144097550 144098189 639 False 491.000000 791 95.817500 1378 2094 2 chr3B.!!$F2 716
6 TraesCS4A01G285100 chr6A 495441673 495442918 1245 True 550.000000 684 83.520500 417 1599 2 chr6A.!!$R2 1182
7 TraesCS4A01G285100 chr6A 431759987 431761226 1239 True 520.500000 651 82.658500 425 1601 2 chr6A.!!$R1 1176
8 TraesCS4A01G285100 chr7A 561606220 561607877 1657 False 507.666667 680 85.497333 425 1946 3 chr7A.!!$F2 1521
9 TraesCS4A01G285100 chr6B 142690494 142691732 1238 False 544.500000 680 83.526000 425 1599 2 chr6B.!!$F2 1174
10 TraesCS4A01G285100 chr3A 661661568 661663230 1662 True 507.666667 669 85.497000 423 1946 3 chr3A.!!$R1 1523
11 TraesCS4A01G285100 chr5A 492996426 492997664 1238 True 527.500000 667 82.919000 425 1601 2 chr5A.!!$R3 1176
12 TraesCS4A01G285100 chr2B 732883640 732884171 531 True 464.000000 464 82.624000 417 975 1 chr2B.!!$R3 558
13 TraesCS4A01G285100 chrUn 46035059 46035588 529 False 291.000000 291 77.208000 413 970 1 chrUn.!!$F1 557

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
919 1015 1.384191 GGCAGAGGGTGGAAATGGT 59.616 57.895 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2622 2.334838 GCGAGTAAAACCACGATGAGT 58.665 47.619 0.0 0.0 0.0 3.41 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
919 1015 1.384191 GGCAGAGGGTGGAAATGGT 59.616 57.895 0.00 0.0 0.00 3.55
1107 1446 3.138798 GAGGCGGACGTCCTGCTA 61.139 66.667 33.97 0.0 36.36 3.49
1299 1638 3.063180 CGGCATCAATTCTCTGTCTTGTC 59.937 47.826 0.00 0.0 0.00 3.18
1369 1708 0.846427 TTCTTGGCCAGATCACCCCT 60.846 55.000 5.11 0.0 0.00 4.79
1804 2220 7.838771 AGTACCATCTTCACGTATTTTTACC 57.161 36.000 0.00 0.0 0.00 2.85
2163 2583 5.215252 TCATATACTCTTGGTGGCTTAGC 57.785 43.478 0.00 0.0 0.00 3.09
2221 2641 6.642683 AATTACTCATCGTGGTTTTACTCG 57.357 37.500 0.00 0.0 0.00 4.18
2437 2857 3.181516 GCTGCTACTTTGATTCAGAACGG 60.182 47.826 0.00 0.0 0.00 4.44
2488 2908 1.822990 GTACTACACTGCTACCCTGCA 59.177 52.381 0.00 0.0 41.05 4.41
2548 2968 6.375455 TGCTATTTCTCAGTTCTCAAAATCCC 59.625 38.462 0.00 0.0 0.00 3.85
2878 3299 9.915629 GTTATCTTCTCAGTTAATCGATATGGT 57.084 33.333 0.00 0.0 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
522 559 6.462487 CGGTGTAATATGGACAGTAGGATGTT 60.462 42.308 0.0 0.0 32.25 2.71
812 861 1.169661 CGGCAAACAACCTACAGGCA 61.170 55.000 0.0 0.0 39.32 4.75
869 965 0.335019 TGGGGATGAGAGAAGACGGA 59.665 55.000 0.0 0.0 0.00 4.69
919 1015 1.643286 AGAGGAGAGAGATGGTGGTCA 59.357 52.381 0.0 0.0 0.00 4.02
1107 1446 2.529744 GGGTGGAGACCAAGGCAGT 61.530 63.158 0.0 0.0 45.25 4.40
1369 1708 1.076187 TGCCATGGACAATACACCCAA 59.924 47.619 18.4 0.0 33.15 4.12
1623 2039 7.307751 CCTTCGTACAAAATCTACAAAGAGCAA 60.308 37.037 0.0 0.0 34.49 3.91
1804 2220 8.937634 AACCATCTAGTATAAACCAACTAACG 57.062 34.615 0.0 0.0 0.00 3.18
2192 2612 6.642707 AAACCACGATGAGTAATTTGGAAA 57.357 33.333 0.0 0.0 0.00 3.13
2202 2622 2.334838 GCGAGTAAAACCACGATGAGT 58.665 47.619 0.0 0.0 0.00 3.41
2437 2857 5.431765 TGATCAAGAGAATTAGGCAAGACC 58.568 41.667 0.0 0.0 39.61 3.85
2483 2903 7.951530 ATCTAAGTTTTTGTTTTCATGCAGG 57.048 32.000 0.0 0.0 0.00 4.85


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

AutoCloner maintained by Alex Coulton.