Multiple sequence alignment - TraesCS7A01G383000

Loading Multiple Alignment...

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 TraesCS7A01G383000 chr7A 100.000 3437 0 0 1 3437 558082517 558079081 0.000000e+00 6348.0
1 TraesCS7A01G383000 chr7A 94.634 2404 110 6 352 2740 558093050 558090651 0.000000e+00 3707.0
2 TraesCS7A01G383000 chr7A 87.823 2628 262 32 9 2604 558102120 558099519 0.000000e+00 3027.0
3 TraesCS7A01G383000 chr7A 92.072 391 22 5 2739 3123 558090365 558089978 3.020000e-150 542.0
4 TraesCS7A01G383000 chr7A 90.284 422 29 7 1 410 558093440 558093019 3.020000e-150 542.0
5 TraesCS7A01G383000 chr7A 76.607 731 153 16 1634 2355 735763296 735762575 1.500000e-103 387.0
6 TraesCS7A01G383000 chr7A 76.254 299 49 9 2606 2888 558099636 558099344 4.630000e-29 139.0
7 TraesCS7A01G383000 chr7A 83.206 131 15 4 2603 2727 558090917 558090788 2.800000e-21 113.0
8 TraesCS7A01G383000 chr7D 98.488 3440 47 2 1 3435 491790920 491787481 0.000000e+00 6059.0
9 TraesCS7A01G383000 chr7D 93.016 3150 179 18 1 3123 491800972 491797837 0.000000e+00 4560.0
10 TraesCS7A01G383000 chr7D 88.588 2620 255 27 7 2604 491864470 491861873 0.000000e+00 3142.0
11 TraesCS7A01G383000 chr7D 79.208 303 45 8 2603 2888 491861999 491861698 9.730000e-46 195.0
12 TraesCS7A01G383000 chr7D 83.688 141 15 5 2594 2727 491798499 491798360 3.600000e-25 126.0
13 TraesCS7A01G383000 chr7D 84.298 121 8 7 2494 2603 491788314 491788194 1.300000e-19 108.0
14 TraesCS7A01G383000 chr7B 93.728 3141 170 11 7 3123 521133692 521130555 0.000000e+00 4684.0
15 TraesCS7A01G383000 chr7B 97.386 2640 69 0 13 2652 521123709 521121070 0.000000e+00 4494.0
16 TraesCS7A01G383000 chr7B 89.074 2343 216 22 7 2335 521142816 521140500 0.000000e+00 2872.0
17 TraesCS7A01G383000 chr7B 96.086 792 24 6 2650 3435 521120874 521120084 0.000000e+00 1284.0
18 TraesCS7A01G383000 chr7B 83.471 121 9 7 2494 2603 521131074 521130954 6.070000e-18 102.0
19 TraesCS7A01G383000 chr7B 84.286 70 7 3 3362 3429 617555094 617555027 7.960000e-07 65.8
20 TraesCS7A01G383000 chr2B 75.531 1696 339 52 794 2430 729767415 729769093 0.000000e+00 763.0
21 TraesCS7A01G383000 chr4A 75.085 293 61 9 57 340 738514089 738514378 3.600000e-25 126.0


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 TraesCS7A01G383000 chr7A 558079081 558082517 3436 True 6348.0 6348 100.0000 1 3437 1 chr7A.!!$R1 3436
1 TraesCS7A01G383000 chr7A 558099344 558102120 2776 True 1583.0 3027 82.0385 9 2888 2 chr7A.!!$R4 2879
2 TraesCS7A01G383000 chr7A 558089978 558093440 3462 True 1226.0 3707 90.0490 1 3123 4 chr7A.!!$R3 3122
3 TraesCS7A01G383000 chr7A 735762575 735763296 721 True 387.0 387 76.6070 1634 2355 1 chr7A.!!$R2 721
4 TraesCS7A01G383000 chr7D 491787481 491790920 3439 True 3083.5 6059 91.3930 1 3435 2 chr7D.!!$R1 3434
5 TraesCS7A01G383000 chr7D 491797837 491800972 3135 True 2343.0 4560 88.3520 1 3123 2 chr7D.!!$R2 3122
6 TraesCS7A01G383000 chr7D 491861698 491864470 2772 True 1668.5 3142 83.8980 7 2888 2 chr7D.!!$R3 2881
7 TraesCS7A01G383000 chr7B 521120084 521123709 3625 True 2889.0 4494 96.7360 13 3435 2 chr7B.!!$R3 3422
8 TraesCS7A01G383000 chr7B 521140500 521142816 2316 True 2872.0 2872 89.0740 7 2335 1 chr7B.!!$R1 2328
9 TraesCS7A01G383000 chr7B 521130555 521133692 3137 True 2393.0 4684 88.5995 7 3123 2 chr7B.!!$R4 3116
10 TraesCS7A01G383000 chr2B 729767415 729769093 1678 False 763.0 763 75.5310 794 2430 1 chr2B.!!$F1 1636

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
367 377 1.545582 GGTCCACCAACATCACCAATG 59.454 52.381 0.0 0.0 37.40 2.82 F
1119 1192 1.208535 AGTTCCACAGACGTGTTCCAA 59.791 47.619 0.0 0.0 41.93 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1593 4.469657 TCTAAAGGCAACAACTCCAACAT 58.530 39.13 0.00 0.0 41.41 2.71 R
2879 3505 2.751166 AATAGCTAGCATGTAGGCGG 57.249 50.00 18.83 0.0 39.27 6.13 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
55 59 2.945668 CCTCCTAGCATAGCCACAAAAC 59.054 50.000 0.00 0.0 37.37 2.43
367 377 1.545582 GGTCCACCAACATCACCAATG 59.454 52.381 0.00 0.0 37.40 2.82
1067 1122 2.224159 GGACAGGAGGGTGCTCCAA 61.224 63.158 7.20 0.0 45.66 3.53
1119 1192 1.208535 AGTTCCACAGACGTGTTCCAA 59.791 47.619 0.00 0.0 41.93 3.53
1221 1300 1.757306 CCTCACCAACTGCTCCTGT 59.243 57.895 0.00 0.0 0.00 4.00
1511 1593 1.427368 ACAGGCCACCAATCAAGGTAA 59.573 47.619 5.01 0.0 40.77 2.85
2374 2482 3.323979 GGGTGAAGTGGTCAGAGTTCTTA 59.676 47.826 0.00 0.0 36.74 2.10
2879 3505 9.088512 CACTTATAAACTAGTCATCAACCTGTC 57.911 37.037 0.00 0.0 0.00 3.51
3141 3775 8.040716 GTGTAATAAATGCACTAAACCTGACT 57.959 34.615 0.00 0.0 41.01 3.41
3266 3900 4.593206 TCTTCACACCTGGAACACTTCTAT 59.407 41.667 0.00 0.0 0.00 1.98
3268 3902 3.901222 TCACACCTGGAACACTTCTATCA 59.099 43.478 0.00 0.0 0.00 2.15
3435 4069 8.731605 TGAACAGATTACAAAAACAACACACTA 58.268 29.630 0.00 0.0 0.00 2.74
3436 4070 9.730420 GAACAGATTACAAAAACAACACACTAT 57.270 29.630 0.00 0.0 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 162 0.035630 AGAGGTGGATGACTTGCTGC 60.036 55.000 0.00 0.0 0.00 5.25
240 247 1.376812 GATTGGCGTCTCCCGGTTT 60.377 57.895 0.00 0.0 36.94 3.27
367 377 3.412386 AGATGTTGGTGTTGGTTCTAGC 58.588 45.455 0.00 0.0 0.00 3.42
765 814 3.181464 TGTTGTTGACGTATTCTGGGACA 60.181 43.478 0.00 0.0 0.00 4.02
817 866 4.531854 AGGAACGAAGAGATCTCATCTGA 58.468 43.478 24.39 0.0 40.38 3.27
957 1012 2.047274 CCGGTGCAGACGGTGAAT 60.047 61.111 18.91 0.0 46.03 2.57
1119 1192 1.195115 ATGTCACACGAGCTATGGGT 58.805 50.000 0.00 0.0 0.00 4.51
1221 1300 4.606210 TGTCATGGTAGGAGTAAGCAGTA 58.394 43.478 0.00 0.0 0.00 2.74
1511 1593 4.469657 TCTAAAGGCAACAACTCCAACAT 58.530 39.130 0.00 0.0 41.41 2.71
2374 2482 5.747248 GCATATCAAGCTCCATTAGACCCTT 60.747 44.000 0.00 0.0 0.00 3.95
2822 3448 5.227569 TGTGAGTTCAGATAGCCTTCAAA 57.772 39.130 0.00 0.0 0.00 2.69
2879 3505 2.751166 AATAGCTAGCATGTAGGCGG 57.249 50.000 18.83 0.0 39.27 6.13
3141 3775 1.792757 AAGGGGCCTCAGATGCAACA 61.793 55.000 4.79 0.0 0.00 3.33
3266 3900 3.446873 AGCATTTGTGTTGTTCTTGGTGA 59.553 39.130 0.00 0.0 0.00 4.02
3268 3902 3.181476 GGAGCATTTGTGTTGTTCTTGGT 60.181 43.478 0.00 0.0 0.00 3.67


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

AutoCloner maintained by Alex Coulton.