Multiple sequence alignment - TraesCS5B01G065500

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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 TraesCS5B01G065500 chr5B 100.000 2641 0 0 1 2641 73528083 73525443 0.000000e+00 4878.0
1 TraesCS5B01G065500 chr5B 89.203 2121 172 26 484 2579 539174351 539176439 0.000000e+00 2595.0
2 TraesCS5B01G065500 chr5B 90.639 1143 93 10 1508 2641 667472926 667474063 0.000000e+00 1506.0
3 TraesCS5B01G065500 chr5B 91.000 900 57 15 72 968 667471262 667472140 0.000000e+00 1192.0
4 TraesCS5B01G065500 chr5A 95.181 2656 111 10 1 2641 498507876 498505223 0.000000e+00 4180.0
5 TraesCS5B01G065500 chr5A 89.951 2657 199 29 1 2636 576061124 576063733 0.000000e+00 3365.0
6 TraesCS5B01G065500 chr5A 91.093 1089 55 10 578 1641 14577131 14576060 0.000000e+00 1435.0
7 TraesCS5B01G065500 chr5A 89.583 48 3 2 11 56 498507948 498507901 2.840000e-05 60.2
8 TraesCS5B01G065500 chr6A 91.962 2650 170 26 1 2636 149572081 149569461 0.000000e+00 3674.0
9 TraesCS5B01G065500 chr2A 96.010 1654 51 4 1 1639 763600501 763598848 0.000000e+00 2675.0
10 TraesCS5B01G065500 chr5D 92.936 1458 91 7 1188 2635 532475262 532476717 0.000000e+00 2111.0
11 TraesCS5B01G065500 chr5D 93.435 1310 63 7 1 1303 6681866 6683159 0.000000e+00 1921.0
12 TraesCS5B01G065500 chr5D 91.226 1060 81 6 1586 2635 6683715 6684772 0.000000e+00 1432.0
13 TraesCS5B01G065500 chr5D 90.130 385 30 4 856 1232 448112715 448112331 6.570000e-136 494.0
14 TraesCS5B01G065500 chr7B 91.612 1538 105 6 2 1535 42193352 42191835 0.000000e+00 2104.0
15 TraesCS5B01G065500 chr7B 90.473 1522 130 9 1131 2641 27766823 27768340 0.000000e+00 1993.0
16 TraesCS5B01G065500 chr7B 89.363 1523 123 13 1131 2641 707972452 707970957 0.000000e+00 1879.0
17 TraesCS5B01G065500 chr7B 90.442 1130 92 9 1524 2641 42191554 42190429 0.000000e+00 1474.0
18 TraesCS5B01G065500 chr2D 94.347 1309 58 6 1 1303 579677926 579676628 0.000000e+00 1993.0
19 TraesCS5B01G065500 chr2D 91.067 1097 85 7 1549 2635 579676158 579675065 0.000000e+00 1471.0
20 TraesCS5B01G065500 chr7A 98.250 857 11 3 1 853 717354837 717353981 0.000000e+00 1496.0
21 TraesCS5B01G065500 chr7A 94.188 757 43 1 949 1704 717345089 717344333 0.000000e+00 1153.0
22 TraesCS5B01G065500 chr4D 89.065 1198 93 28 1471 2641 505944520 505943334 0.000000e+00 1452.0


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 TraesCS5B01G065500 chr5B 73525443 73528083 2640 True 4878.0 4878 100.0000 1 2641 1 chr5B.!!$R1 2640
1 TraesCS5B01G065500 chr5B 539174351 539176439 2088 False 2595.0 2595 89.2030 484 2579 1 chr5B.!!$F1 2095
2 TraesCS5B01G065500 chr5B 667471262 667474063 2801 False 1349.0 1506 90.8195 72 2641 2 chr5B.!!$F2 2569
3 TraesCS5B01G065500 chr5A 576061124 576063733 2609 False 3365.0 3365 89.9510 1 2636 1 chr5A.!!$F1 2635
4 TraesCS5B01G065500 chr5A 498505223 498507948 2725 True 2120.1 4180 92.3820 1 2641 2 chr5A.!!$R2 2640
5 TraesCS5B01G065500 chr5A 14576060 14577131 1071 True 1435.0 1435 91.0930 578 1641 1 chr5A.!!$R1 1063
6 TraesCS5B01G065500 chr6A 149569461 149572081 2620 True 3674.0 3674 91.9620 1 2636 1 chr6A.!!$R1 2635
7 TraesCS5B01G065500 chr2A 763598848 763600501 1653 True 2675.0 2675 96.0100 1 1639 1 chr2A.!!$R1 1638
8 TraesCS5B01G065500 chr5D 532475262 532476717 1455 False 2111.0 2111 92.9360 1188 2635 1 chr5D.!!$F1 1447
9 TraesCS5B01G065500 chr5D 6681866 6684772 2906 False 1676.5 1921 92.3305 1 2635 2 chr5D.!!$F2 2634
10 TraesCS5B01G065500 chr7B 27766823 27768340 1517 False 1993.0 1993 90.4730 1131 2641 1 chr7B.!!$F1 1510
11 TraesCS5B01G065500 chr7B 707970957 707972452 1495 True 1879.0 1879 89.3630 1131 2641 1 chr7B.!!$R1 1510
12 TraesCS5B01G065500 chr7B 42190429 42193352 2923 True 1789.0 2104 91.0270 2 2641 2 chr7B.!!$R2 2639
13 TraesCS5B01G065500 chr2D 579675065 579677926 2861 True 1732.0 1993 92.7070 1 2635 2 chr2D.!!$R1 2634
14 TraesCS5B01G065500 chr7A 717353981 717354837 856 True 1496.0 1496 98.2500 1 853 1 chr7A.!!$R2 852
15 TraesCS5B01G065500 chr7A 717344333 717345089 756 True 1153.0 1153 94.1880 949 1704 1 chr7A.!!$R1 755
16 TraesCS5B01G065500 chr4D 505943334 505944520 1186 True 1452.0 1452 89.0650 1471 2641 1 chr4D.!!$R1 1170

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
892 978 1.229359 CCATCCATCCTTGCTGCCT 59.771 57.895 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 2786 2.284699 CCAACCCCTCCCTCTCGT 60.285 66.667 0.0 0.0 0.0 4.18 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
78 151 8.816894 TGTATTTTGTGAGGAATCTAGAACTCT 58.183 33.333 17.83 7.58 0.00 3.24
171 244 7.063934 AGCAGAATACTCATTGATGATCTGA 57.936 36.000 19.15 0.00 40.23 3.27
862 948 2.036256 GCCATGGTTGAGCACCCT 59.964 61.111 14.67 0.00 46.68 4.34
888 974 2.517875 GCGCCATCCATCCTTGCT 60.518 61.111 0.00 0.00 0.00 3.91
892 978 1.229359 CCATCCATCCTTGCTGCCT 59.771 57.895 0.00 0.00 0.00 4.75
1073 1212 0.684805 GACAGATGTCGGGGAGGAGT 60.685 60.000 0.00 0.00 35.12 3.85
1112 1251 1.076332 GTGTTGACGATTAAGGCGCT 58.924 50.000 7.64 0.00 0.00 5.92
1362 1541 4.626081 GTGGCTGGGCGTCAGTGT 62.626 66.667 9.08 0.00 45.08 3.55
1417 1597 3.953652 TCTGGGGGAGAAGGGGCA 61.954 66.667 0.00 0.00 0.00 5.36
1532 1995 0.109342 GCGGGTGGATGGATCTGAAT 59.891 55.000 0.00 0.00 0.00 2.57
1537 2292 2.707791 GGTGGATGGATCTGAATGGAGA 59.292 50.000 0.00 0.00 0.00 3.71
1557 2312 2.415608 GGAGATGACGAGGTGGCGA 61.416 63.158 0.00 0.00 34.83 5.54
1626 2693 1.302511 GGGTTGATCTGCCACGTGT 60.303 57.895 15.65 0.00 0.00 4.49
1652 2721 2.363925 GGGTAGGAGGTCGCTGGT 60.364 66.667 0.00 0.00 0.00 4.00
1706 2786 2.299727 GATCGGGGGAGAGGAGGTCA 62.300 65.000 0.00 0.00 0.00 4.02
2009 3116 3.963665 TCAAGTGCCGAAAATGAGTTTG 58.036 40.909 0.00 0.00 0.00 2.93
2130 3237 5.043248 GTGTCAAAAGTTTTGATCCACCTG 58.957 41.667 28.69 3.37 0.00 4.00
2415 3533 9.764363 GTCATTATATGTGATCAAGTTACCAGA 57.236 33.333 0.00 0.00 0.00 3.86
2569 3688 9.346005 TGTTCAAATGATCTCATATTATGCACT 57.654 29.630 0.00 0.00 35.10 4.40
2622 3741 5.768317 TGCCTAAGGAAGTTTTCATTTTCG 58.232 37.500 0.00 0.00 35.11 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 244 2.038557 CCTAGCACCTTGGTACACAACT 59.961 50.000 0.00 0.00 39.29 3.16
862 948 3.157252 GGATGGCGCCTGAGGAGA 61.157 66.667 29.70 5.17 0.00 3.71
888 974 5.706447 AGGATGTTGTAGATAGACTAGGCA 58.294 41.667 0.00 0.00 0.00 4.75
892 978 5.770663 GCAGGAGGATGTTGTAGATAGACTA 59.229 44.000 0.00 0.00 0.00 2.59
1041 1180 4.248842 CTGTCGTGCCCCCACACA 62.249 66.667 0.00 0.00 42.17 3.72
1332 1473 0.735978 CAGCCACAATAGCGTCACGA 60.736 55.000 0.00 0.00 34.64 4.35
1335 1476 1.078497 CCCAGCCACAATAGCGTCA 60.078 57.895 0.00 0.00 34.64 4.35
1362 1541 0.460459 TCACGCAACGGAGACAACAA 60.460 50.000 0.00 0.00 0.00 2.83
1417 1597 0.622738 AGATCCATCCACCCACTGCT 60.623 55.000 0.00 0.00 0.00 4.24
1532 1995 1.006043 ACCTCGTCATCTCCTTCTCCA 59.994 52.381 0.00 0.00 0.00 3.86
1537 2292 1.901085 GCCACCTCGTCATCTCCTT 59.099 57.895 0.00 0.00 0.00 3.36
1557 2312 0.761187 CCCATCAGATCCATCACCGT 59.239 55.000 0.00 0.00 0.00 4.83
1626 2693 1.611261 CCTCCTACCCCAACACCGA 60.611 63.158 0.00 0.00 0.00 4.69
1680 2757 4.547367 CTCCCCCGATCCCAACGC 62.547 72.222 0.00 0.00 0.00 4.84
1683 2760 2.040884 CCTCTCCCCCGATCCCAA 60.041 66.667 0.00 0.00 0.00 4.12
1706 2786 2.284699 CCAACCCCTCCCTCTCGT 60.285 66.667 0.00 0.00 0.00 4.18
2009 3116 9.174166 ACAAATATATTGTAGGTCCTTCACAAC 57.826 33.333 9.04 0.00 35.17 3.32
2130 3237 4.026062 GCGGAAATTTGTCTTTTTCACCAC 60.026 41.667 0.00 0.00 34.29 4.16
2381 3499 7.804843 TGATCACATATAATGACACAATGCA 57.195 32.000 0.00 0.00 0.00 3.96
2569 3688 4.991789 TGCCATTCTAATATGCACCCTA 57.008 40.909 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.