Multiple sequence alignment - TraesCS1A01G022600

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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 TraesCS1A01G022600 chr1A 100.000 1374 0 0 922 2295 11025958 11024585 0.000000e+00 2538
1 TraesCS1A01G022600 chr1A 97.587 746 18 0 923 1668 504202352 504203097 0.000000e+00 1279
2 TraesCS1A01G022600 chr1A 97.778 630 14 0 1666 2295 504203968 504204597 0.000000e+00 1086
3 TraesCS1A01G022600 chr1A 97.619 630 15 0 1666 2295 380401926 380402555 0.000000e+00 1081
4 TraesCS1A01G022600 chr1A 100.000 418 0 0 1 418 11026879 11026462 0.000000e+00 773
5 TraesCS1A01G022600 chr1A 91.786 487 25 10 922 1401 380400938 380401416 0.000000e+00 664
6 TraesCS1A01G022600 chr1A 98.182 110 2 0 309 418 380400719 380400828 2.330000e-45 193
7 TraesCS1A01G022600 chr1A 95.789 95 2 2 324 417 10358619 10358712 3.950000e-33 152
8 TraesCS1A01G022600 chr2A 98.095 630 12 0 1666 2295 23797297 23797926 0.000000e+00 1098
9 TraesCS1A01G022600 chr2A 97.460 630 16 0 1666 2295 571020245 571020874 0.000000e+00 1075
10 TraesCS1A01G022600 chr2A 97.008 635 12 3 1666 2295 600112321 600111689 0.000000e+00 1061
11 TraesCS1A01G022600 chr2A 92.577 485 25 9 923 1402 23796310 23796788 0.000000e+00 686
12 TraesCS1A01G022600 chr2A 92.213 488 25 11 922 1403 571019259 571019739 0.000000e+00 678
13 TraesCS1A01G022600 chr2A 96.632 386 12 1 1 385 23795571 23795956 6.910000e-180 640
14 TraesCS1A01G022600 chr2A 96.707 334 10 1 1 334 571018576 571018908 2.580000e-154 555
15 TraesCS1A01G022600 chr5A 97.460 630 16 0 1666 2295 507564609 507563980 0.000000e+00 1075
16 TraesCS1A01G022600 chr5A 96.912 421 9 2 1 418 603018640 603019059 0.000000e+00 702
17 TraesCS1A01G022600 chr5A 95.722 374 15 1 1 374 507566279 507565907 3.260000e-168 601
18 TraesCS1A01G022600 chr7A 97.143 630 18 0 1666 2295 707845504 707846133 0.000000e+00 1064
19 TraesCS1A01G022600 chr7A 96.989 631 18 1 1666 2295 615537946 615537316 0.000000e+00 1059
20 TraesCS1A01G022600 chr7A 96.984 630 17 2 1666 2295 650323446 650322819 0.000000e+00 1057
21 TraesCS1A01G022600 chr7A 92.843 489 20 10 922 1403 707844516 707844996 0.000000e+00 695
22 TraesCS1A01G022600 chr7A 92.355 484 21 10 923 1399 650260618 650260144 0.000000e+00 675
23 TraesCS1A01G022600 chr7A 96.000 350 14 0 1 350 650261444 650261095 9.200000e-159 569
24 TraesCS1A01G022600 chr7A 95.977 348 14 0 1 348 707843660 707844007 1.190000e-157 566
25 TraesCS1A01G022600 chr7A 96.104 154 6 0 1491 1644 689906203 689906356 3.780000e-63 252
26 TraesCS1A01G022600 chr7B 92.623 488 21 11 923 1403 544973145 544973624 0.000000e+00 688
27 TraesCS1A01G022600 chr7B 94.763 401 21 0 18 418 544972344 544972744 1.940000e-175 625
28 TraesCS1A01G022600 chr1B 92.165 485 23 10 923 1400 235897924 235898400 0.000000e+00 671
29 TraesCS1A01G022600 chr1B 91.189 488 28 11 923 1403 658504006 658503527 0.000000e+00 649
30 TraesCS1A01G022600 chr1B 95.198 354 16 1 18 371 235897031 235897383 1.990000e-155 558
31 TraesCS1A01G022600 chr6B 95.135 370 18 0 18 387 363202951 363203320 3.290000e-163 584
32 TraesCS1A01G022600 chr7D 84.479 509 43 18 1188 1668 191116170 191116670 9.600000e-129 470
33 TraesCS1A01G022600 chrUn 94.737 95 5 0 324 418 79780483 79780577 5.110000e-32 148


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 TraesCS1A01G022600 chr1A 11024585 11026879 2294 True 1655.500000 2538 100.000000 1 2295 2 chr1A.!!$R1 2294
1 TraesCS1A01G022600 chr1A 504202352 504204597 2245 False 1182.500000 1279 97.682500 923 2295 2 chr1A.!!$F3 1372
2 TraesCS1A01G022600 chr1A 380400719 380402555 1836 False 646.000000 1081 95.862333 309 2295 3 chr1A.!!$F2 1986
3 TraesCS1A01G022600 chr2A 600111689 600112321 632 True 1061.000000 1061 97.008000 1666 2295 1 chr2A.!!$R1 629
4 TraesCS1A01G022600 chr2A 23795571 23797926 2355 False 808.000000 1098 95.768000 1 2295 3 chr2A.!!$F1 2294
5 TraesCS1A01G022600 chr2A 571018576 571020874 2298 False 769.333333 1075 95.460000 1 2295 3 chr2A.!!$F2 2294
6 TraesCS1A01G022600 chr5A 507563980 507566279 2299 True 838.000000 1075 96.591000 1 2295 2 chr5A.!!$R1 2294
7 TraesCS1A01G022600 chr7A 615537316 615537946 630 True 1059.000000 1059 96.989000 1666 2295 1 chr7A.!!$R1 629
8 TraesCS1A01G022600 chr7A 650322819 650323446 627 True 1057.000000 1057 96.984000 1666 2295 1 chr7A.!!$R2 629
9 TraesCS1A01G022600 chr7A 707843660 707846133 2473 False 775.000000 1064 95.321000 1 2295 3 chr7A.!!$F2 2294
10 TraesCS1A01G022600 chr7A 650260144 650261444 1300 True 622.000000 675 94.177500 1 1399 2 chr7A.!!$R3 1398
11 TraesCS1A01G022600 chr7B 544972344 544973624 1280 False 656.500000 688 93.693000 18 1403 2 chr7B.!!$F1 1385
12 TraesCS1A01G022600 chr1B 235897031 235898400 1369 False 614.500000 671 93.681500 18 1400 2 chr1B.!!$F1 1382
13 TraesCS1A01G022600 chr7D 191116170 191116670 500 False 470.000000 470 84.479000 1188 1668 1 chr7D.!!$F1 480

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
116 119 2.909662 TCCACACCATACAGATCCAACA 59.09 45.455 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 2779 0.464036 ACAGCACGAGACAACAGGAA 59.536 50.0 0.0 0.0 0.0 3.36 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
116 119 2.909662 TCCACACCATACAGATCCAACA 59.090 45.455 0.00 0.00 0.00 3.33
1137 1932 0.534203 GCTCTCCTCGTCTCGGATCT 60.534 60.000 0.00 0.00 0.00 2.75
1147 2564 2.412089 CGTCTCGGATCTGGTTTGTTTC 59.588 50.000 0.62 0.00 0.00 2.78
1169 2592 2.736719 CGTCCAGATCTGACGCTGATTT 60.737 50.000 24.62 0.00 35.56 2.17
1314 2737 4.415332 GCGAACGCGTCTCCTCCA 62.415 66.667 14.44 0.00 40.36 3.86
1356 2779 3.181463 TGCACGGTTTAGTTAGACTTGGT 60.181 43.478 0.00 0.00 0.00 3.67
1441 2864 1.969862 GCTGCAGGCCTGTGAAATT 59.030 52.632 32.81 0.00 34.27 1.82
1448 2871 2.229784 CAGGCCTGTGAAATTGAGTTCC 59.770 50.000 25.53 0.00 0.00 3.62
1451 2874 2.293399 GCCTGTGAAATTGAGTTCCGTT 59.707 45.455 0.00 0.00 0.00 4.44
1455 2878 3.942115 TGTGAAATTGAGTTCCGTTGACA 59.058 39.130 0.00 0.00 0.00 3.58
1458 2881 5.625311 GTGAAATTGAGTTCCGTTGACATTC 59.375 40.000 0.00 0.00 0.00 2.67
1461 2884 0.442699 GAGTTCCGTTGACATTCGGC 59.557 55.000 12.74 3.12 45.44 5.54
1462 2885 0.034896 AGTTCCGTTGACATTCGGCT 59.965 50.000 12.74 4.93 45.44 5.52
1465 2888 1.600023 TCCGTTGACATTCGGCTTTT 58.400 45.000 12.74 0.00 45.44 2.27
1469 2892 3.564511 CGTTGACATTCGGCTTTTGAAT 58.435 40.909 0.00 0.00 36.52 2.57
1485 2908 6.873605 GCTTTTGAATATGTTGGGTTTTAGCT 59.126 34.615 0.00 0.00 0.00 3.32
1491 2914 7.615365 TGAATATGTTGGGTTTTAGCTCATCTT 59.385 33.333 0.00 0.00 0.00 2.40
1553 3007 7.497773 AAGTTAGGTTTTAGTAGATCCTGCT 57.502 36.000 1.39 0.00 0.00 4.24
1589 3043 7.645058 TTGTTAGGAGAATTGGGATGAATTC 57.355 36.000 0.00 0.00 41.02 2.17
1596 3050 5.699143 AGAATTGGGATGAATTCAGGGTAG 58.301 41.667 14.54 0.00 42.50 3.18
1804 3582 9.091220 GGTACTACTAATTCTCATACCAGGAAT 57.909 37.037 0.00 0.00 32.52 3.01
2035 3818 7.821359 GTGCCTCATATATGAATGCTCTTTCTA 59.179 37.037 25.54 10.46 36.29 2.10
2038 3821 7.986320 CCTCATATATGAATGCTCTTTCTAGGG 59.014 40.741 16.08 5.39 36.18 3.53
2091 3874 6.493458 TGCTGACTACACTGATTATATGCCTA 59.507 38.462 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 119 0.460284 CCAGCGTGCGTTTAGGAGAT 60.460 55.000 0.00 0.00 0.00 2.75
203 206 2.363361 GGTCGGGGAGAGGAAGGA 59.637 66.667 0.00 0.00 0.00 3.36
207 210 2.299727 GATCTGGGTCGGGGAGAGGA 62.300 65.000 0.00 0.00 0.00 3.71
303 306 0.396435 TGGTCGTTGCAGGTCAAGAT 59.604 50.000 0.00 0.00 34.91 2.40
1007 1802 1.303806 TCCACCATGGAGTCGACGA 60.304 57.895 21.47 0.00 42.67 4.20
1137 1932 2.105821 AGATCTGGACGGAAACAAACCA 59.894 45.455 0.00 0.00 0.00 3.67
1149 2566 2.593346 AATCAGCGTCAGATCTGGAC 57.407 50.000 22.42 16.69 0.00 4.02
1314 2737 0.618968 AGCAAGAGGGAGACGGGATT 60.619 55.000 0.00 0.00 0.00 3.01
1356 2779 0.464036 ACAGCACGAGACAACAGGAA 59.536 50.000 0.00 0.00 0.00 3.36
1428 2851 2.519013 GGAACTCAATTTCACAGGCCT 58.481 47.619 0.00 0.00 0.00 5.19
1430 2853 1.880027 ACGGAACTCAATTTCACAGGC 59.120 47.619 0.00 0.00 0.00 4.85
1431 2854 3.563808 TCAACGGAACTCAATTTCACAGG 59.436 43.478 0.00 0.00 0.00 4.00
1432 2855 4.035091 TGTCAACGGAACTCAATTTCACAG 59.965 41.667 0.00 0.00 0.00 3.66
1437 2860 4.783242 CGAATGTCAACGGAACTCAATTT 58.217 39.130 0.00 0.00 0.00 1.82
1448 2871 2.679355 TCAAAAGCCGAATGTCAACG 57.321 45.000 0.00 0.00 0.00 4.10
1451 2874 5.895636 ACATATTCAAAAGCCGAATGTCA 57.104 34.783 0.00 0.00 34.89 3.58
1455 2878 4.466015 ACCCAACATATTCAAAAGCCGAAT 59.534 37.500 0.00 0.00 36.97 3.34
1458 2881 3.866883 ACCCAACATATTCAAAAGCCG 57.133 42.857 0.00 0.00 0.00 5.52
1461 2884 8.087750 TGAGCTAAAACCCAACATATTCAAAAG 58.912 33.333 0.00 0.00 0.00 2.27
1462 2885 7.957002 TGAGCTAAAACCCAACATATTCAAAA 58.043 30.769 0.00 0.00 0.00 2.44
1465 2888 7.118723 AGATGAGCTAAAACCCAACATATTCA 58.881 34.615 0.00 0.00 0.00 2.57
1469 2892 6.721318 AGAAGATGAGCTAAAACCCAACATA 58.279 36.000 0.00 0.00 0.00 2.29
1527 2952 9.214962 AGCAGGATCTACTAAAACCTAACTTAT 57.785 33.333 0.00 0.00 0.00 1.73
1589 3043 1.599047 CCCACAGCTGACTACCCTG 59.401 63.158 23.35 5.94 0.00 4.45
1596 3050 1.302832 CCAGTTCCCCACAGCTGAC 60.303 63.158 23.35 6.81 0.00 3.51
1787 3565 9.479549 AAACACAATATTCCTGGTATGAGAATT 57.520 29.630 0.00 0.00 32.64 2.17
1804 3582 4.041567 TGGAAGAGCTCAGGAAACACAATA 59.958 41.667 17.77 0.00 0.00 1.90
1910 3693 6.169094 ACCACATGAAACAGATAGAACAGAG 58.831 40.000 0.00 0.00 0.00 3.35
2035 3818 4.160329 GGGGAAGAGAAATTGAAAACCCT 58.840 43.478 0.00 0.00 35.62 4.34
2038 3821 6.892456 AGATAGGGGGAAGAGAAATTGAAAAC 59.108 38.462 0.00 0.00 0.00 2.43
2091 3874 2.698855 AAGCAGCATCGGTGTAGAAT 57.301 45.000 0.00 0.00 33.19 2.40


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

AutoCloner maintained by Alex Coulton.