Multiple sequence alignment - TraesCS4B01G164700

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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 TraesCS4B01G164700 chr4B 100.000 2686 0 0 1 2686 343787035 343789720 0.000000e+00 4961.0
1 TraesCS4B01G164700 chr4B 89.846 1950 144 28 789 2686 288476720 288474773 0.000000e+00 2455.0
2 TraesCS4B01G164700 chr4B 93.754 1601 59 13 1 1560 343639666 343641266 0.000000e+00 2364.0
3 TraesCS4B01G164700 chr4B 94.584 1237 65 2 1451 2686 343641184 343642419 0.000000e+00 1912.0
4 TraesCS4B01G164700 chr4B 91.763 1214 95 4 1475 2686 200933711 200934921 0.000000e+00 1683.0
5 TraesCS4B01G164700 chr4B 92.139 1183 85 7 1509 2686 368726016 368727195 0.000000e+00 1663.0
6 TraesCS4B01G164700 chr6B 90.007 1521 103 9 1214 2686 238437118 238435599 0.000000e+00 1921.0
7 TraesCS4B01G164700 chr6B 89.873 474 31 7 1 458 4666720 4667192 6.400000e-166 593.0
8 TraesCS4B01G164700 chr6B 89.005 191 20 1 91 280 692624818 692625008 4.470000e-58 235.0
9 TraesCS4B01G164700 chr5B 92.016 1215 91 5 1475 2686 291687831 291686620 0.000000e+00 1701.0
10 TraesCS4B01G164700 chr5B 90.954 1216 91 6 1475 2686 345109475 345110675 0.000000e+00 1618.0
11 TraesCS4B01G164700 chr5B 90.240 1127 88 9 452 1556 291688954 291687828 0.000000e+00 1452.0
12 TraesCS4B01G164700 chr3B 90.453 1215 107 5 1475 2686 762524901 762523693 0.000000e+00 1592.0
13 TraesCS4B01G164700 chr4D 91.460 1089 77 5 474 1562 261239222 261238150 0.000000e+00 1482.0
14 TraesCS4B01G164700 chr4D 93.993 283 17 0 44 326 261239829 261239547 1.910000e-116 429.0
15 TraesCS4B01G164700 chr7A 91.008 1101 90 5 452 1546 583641342 583642439 0.000000e+00 1476.0
16 TraesCS4B01G164700 chr7A 85.122 1351 141 38 631 1926 633711933 633710588 0.000000e+00 1327.0
17 TraesCS4B01G164700 chr6D 90.288 1112 91 6 452 1562 297179049 297177954 0.000000e+00 1439.0
18 TraesCS4B01G164700 chr6D 94.898 98 5 0 311 408 297179481 297179384 1.290000e-33 154.0
19 TraesCS4B01G164700 chr7D 93.362 919 59 2 474 1392 501731759 501732675 0.000000e+00 1358.0
20 TraesCS4B01G164700 chr7D 90.612 948 86 2 1741 2686 152023502 152022556 0.000000e+00 1254.0
21 TraesCS4B01G164700 chr7D 94.419 215 12 0 112 326 501731221 501731435 5.540000e-87 331.0
22 TraesCS4B01G164700 chr3D 91.195 954 74 8 1737 2686 571759138 571758191 0.000000e+00 1288.0
23 TraesCS4B01G164700 chr5A 90.295 948 75 10 631 1562 345672215 345671269 0.000000e+00 1225.0
24 TraesCS4B01G164700 chr5A 88.450 987 85 17 598 1560 178868307 178867326 0.000000e+00 1164.0
25 TraesCS4B01G164700 chr5A 95.758 165 7 0 452 616 133818233 133818397 1.590000e-67 267.0
26 TraesCS4B01G164700 chr5A 95.758 165 7 0 452 616 168399780 168399616 1.590000e-67 267.0
27 TraesCS4B01G164700 chr5A 90.196 51 3 2 600 649 242484157 242484108 6.210000e-07 65.8
28 TraesCS4B01G164700 chr5A 86.207 58 5 3 601 657 501869098 501869153 2.890000e-05 60.2
29 TraesCS4B01G164700 chr1A 89.568 949 81 11 631 1562 580783694 580784641 0.000000e+00 1188.0
30 TraesCS4B01G164700 chr3A 88.394 965 78 16 631 1561 513295587 513296551 0.000000e+00 1131.0
31 TraesCS4B01G164700 chr3A 96.364 165 6 0 452 616 513295446 513295610 3.410000e-69 272.0
32 TraesCS4B01G164700 chr2A 87.831 945 84 15 631 1562 655909228 655908302 0.000000e+00 1079.0
33 TraesCS4B01G164700 chr2B 84.270 267 20 9 91 354 786389682 786389929 9.610000e-60 241.0
34 TraesCS4B01G164700 chr7B 83.521 267 22 9 91 354 688413017 688413264 2.080000e-56 230.0
35 TraesCS4B01G164700 chr7B 81.967 183 11 9 175 354 632610832 632610995 4.660000e-28 135.0
36 TraesCS4B01G164700 chr7B 80.874 183 13 9 175 354 421499917 421499754 1.010000e-24 124.0
37 TraesCS4B01G164700 chr1B 82.772 267 24 9 91 354 39180912 39180665 4.500000e-53 219.0
38 TraesCS4B01G164700 chr5D 93.878 98 6 0 311 408 140961260 140961163 5.990000e-32 148.0


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 TraesCS4B01G164700 chr4B 343787035 343789720 2685 False 4961.0 4961 100.0000 1 2686 1 chr4B.!!$F2 2685
1 TraesCS4B01G164700 chr4B 288474773 288476720 1947 True 2455.0 2455 89.8460 789 2686 1 chr4B.!!$R1 1897
2 TraesCS4B01G164700 chr4B 343639666 343642419 2753 False 2138.0 2364 94.1690 1 2686 2 chr4B.!!$F4 2685
3 TraesCS4B01G164700 chr4B 200933711 200934921 1210 False 1683.0 1683 91.7630 1475 2686 1 chr4B.!!$F1 1211
4 TraesCS4B01G164700 chr4B 368726016 368727195 1179 False 1663.0 1663 92.1390 1509 2686 1 chr4B.!!$F3 1177
5 TraesCS4B01G164700 chr6B 238435599 238437118 1519 True 1921.0 1921 90.0070 1214 2686 1 chr6B.!!$R1 1472
6 TraesCS4B01G164700 chr5B 345109475 345110675 1200 False 1618.0 1618 90.9540 1475 2686 1 chr5B.!!$F1 1211
7 TraesCS4B01G164700 chr5B 291686620 291688954 2334 True 1576.5 1701 91.1280 452 2686 2 chr5B.!!$R1 2234
8 TraesCS4B01G164700 chr3B 762523693 762524901 1208 True 1592.0 1592 90.4530 1475 2686 1 chr3B.!!$R1 1211
9 TraesCS4B01G164700 chr4D 261238150 261239829 1679 True 955.5 1482 92.7265 44 1562 2 chr4D.!!$R1 1518
10 TraesCS4B01G164700 chr7A 583641342 583642439 1097 False 1476.0 1476 91.0080 452 1546 1 chr7A.!!$F1 1094
11 TraesCS4B01G164700 chr7A 633710588 633711933 1345 True 1327.0 1327 85.1220 631 1926 1 chr7A.!!$R1 1295
12 TraesCS4B01G164700 chr6D 297177954 297179481 1527 True 796.5 1439 92.5930 311 1562 2 chr6D.!!$R1 1251
13 TraesCS4B01G164700 chr7D 152022556 152023502 946 True 1254.0 1254 90.6120 1741 2686 1 chr7D.!!$R1 945
14 TraesCS4B01G164700 chr7D 501731221 501732675 1454 False 844.5 1358 93.8905 112 1392 2 chr7D.!!$F1 1280
15 TraesCS4B01G164700 chr3D 571758191 571759138 947 True 1288.0 1288 91.1950 1737 2686 1 chr3D.!!$R1 949
16 TraesCS4B01G164700 chr5A 345671269 345672215 946 True 1225.0 1225 90.2950 631 1562 1 chr5A.!!$R4 931
17 TraesCS4B01G164700 chr5A 178867326 178868307 981 True 1164.0 1164 88.4500 598 1560 1 chr5A.!!$R2 962
18 TraesCS4B01G164700 chr1A 580783694 580784641 947 False 1188.0 1188 89.5680 631 1562 1 chr1A.!!$F1 931
19 TraesCS4B01G164700 chr3A 513295446 513296551 1105 False 701.5 1131 92.3790 452 1561 2 chr3A.!!$F1 1109
20 TraesCS4B01G164700 chr2A 655908302 655909228 926 True 1079.0 1079 87.8310 631 1562 1 chr2A.!!$R1 931

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
22 23 0.610687 AGTCAGTCTAGGGTTGCTGC 59.389 55.0 0.0 0.0 0.0 5.25 F
1388 1835 1.333177 GGGATGACGAGGAGCATAGT 58.667 55.0 0.0 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 1839 0.248843 CCGCTCTGCTCCTCTTCTTT 59.751 55.0 0.00 0.0 0.00 2.52 R
2532 3289 0.529992 CTACGAGGGTCGGAAATGCC 60.530 60.0 0.86 0.0 45.59 4.40 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
22 23 0.610687 AGTCAGTCTAGGGTTGCTGC 59.389 55.000 0.00 0.00 0.00 5.25
33 34 1.474077 GGGTTGCTGCTCCATGTTTAG 59.526 52.381 14.10 0.00 0.00 1.85
39 40 3.503363 TGCTGCTCCATGTTTAGAACAAG 59.497 43.478 0.00 0.00 45.86 3.16
65 66 2.614983 GTTGCTTCTCCGTGGTGTTAAA 59.385 45.455 0.00 0.00 0.00 1.52
67 68 3.482436 TGCTTCTCCGTGGTGTTAAATT 58.518 40.909 0.00 0.00 0.00 1.82
206 207 5.936956 GCTTAGCTGCAGAATCCAGTATATT 59.063 40.000 20.43 0.00 32.93 1.28
209 210 5.933617 AGCTGCAGAATCCAGTATATTTGA 58.066 37.500 20.43 0.00 32.93 2.69
213 214 7.201767 GCTGCAGAATCCAGTATATTTGAAGTT 60.202 37.037 20.43 0.00 32.93 2.66
367 368 2.098614 TGCACTTTTCACTTCAGGCAA 58.901 42.857 0.00 0.00 0.00 4.52
546 838 6.586344 AGATATGATCCTGATGTCGTGTTTT 58.414 36.000 0.00 0.00 0.00 2.43
559 851 9.607988 TGATGTCGTGTTTTCCATTTATAGTAT 57.392 29.630 0.00 0.00 0.00 2.12
721 1061 3.791245 TCCACAAGTGCATTGGTTTTTC 58.209 40.909 11.76 0.00 43.68 2.29
771 1112 5.762179 TTCATTCCAACTATGTCCAGTCT 57.238 39.130 0.00 0.00 0.00 3.24
854 1215 3.830744 TGGAAGGTTTCGAGTTCTTCA 57.169 42.857 18.56 8.01 37.82 3.02
1201 1562 3.047280 GCGACGCCATGTTCACCA 61.047 61.111 9.14 0.00 0.00 4.17
1385 1832 2.502492 CGGGGATGACGAGGAGCAT 61.502 63.158 0.00 0.00 0.00 3.79
1388 1835 1.333177 GGGATGACGAGGAGCATAGT 58.667 55.000 0.00 0.00 0.00 2.12
1392 1839 0.033503 TGACGAGGAGCATAGTGGGA 60.034 55.000 0.00 0.00 0.00 4.37
1394 1841 1.480954 GACGAGGAGCATAGTGGGAAA 59.519 52.381 0.00 0.00 0.00 3.13
1397 1907 2.168521 CGAGGAGCATAGTGGGAAAGAA 59.831 50.000 0.00 0.00 0.00 2.52
1419 1944 2.685017 AGCAGAGCGGGGATGACA 60.685 61.111 0.00 0.00 0.00 3.58
1425 1965 2.514824 GCGGGGATGACAAGGAGC 60.515 66.667 0.00 0.00 0.00 4.70
1434 1974 1.078567 GACAAGGAGCAGAGCAGGG 60.079 63.158 0.00 0.00 0.00 4.45
1562 2251 2.494445 CTCGCGATGGTAGTGGCA 59.506 61.111 10.36 0.00 0.00 4.92
1876 2622 6.672266 TGAAATTATGGGGTTTTGTGCTTA 57.328 33.333 0.00 0.00 0.00 3.09
2259 3014 5.745227 ACCTACCATGAACGAAGATTCATT 58.255 37.500 0.00 0.00 45.10 2.57
2362 3117 4.232221 CTGTCTTGTGATGGCAAACAATC 58.768 43.478 16.50 13.48 35.82 2.67
2482 3239 0.039618 ACCCCAAATGGCGTCATTCT 59.960 50.000 16.85 3.69 42.29 2.40
2532 3289 1.202177 CGGATGGTCGCCAAAAATCAG 60.202 52.381 2.68 0.00 36.95 2.90
2607 3364 2.115291 GCTGGAACCGGCTGGAATC 61.115 63.158 21.41 15.70 44.39 2.52
2620 3377 1.207089 CTGGAATCTGAACTGCGGGTA 59.793 52.381 0.00 0.00 0.00 3.69
2649 3406 4.126437 AGTTTGCCTGTTATTTTTGCCAC 58.874 39.130 0.00 0.00 0.00 5.01
2654 3412 5.128919 TGCCTGTTATTTTTGCCACAAATT 58.871 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.538678 GCAACATTACTTGTTCTAAACATGGAG 59.461 37.037 0.00 0.00 45.55 3.86
33 34 4.213482 ACGGAGAAGCAACATTACTTGTTC 59.787 41.667 0.00 0.00 45.55 3.18
39 40 2.159627 CACCACGGAGAAGCAACATTAC 59.840 50.000 0.00 0.00 0.00 1.89
50 51 2.156098 GCCAATTTAACACCACGGAGA 58.844 47.619 0.00 0.00 0.00 3.71
65 66 7.446625 CCTGCAAGATAGACTATTTAAGCCAAT 59.553 37.037 0.00 0.00 34.07 3.16
67 68 6.126768 ACCTGCAAGATAGACTATTTAAGCCA 60.127 38.462 0.00 0.00 34.07 4.75
206 207 3.423539 ACAGAGCCAGCATAACTTCAA 57.576 42.857 0.00 0.00 0.00 2.69
209 210 3.084786 GGAAACAGAGCCAGCATAACTT 58.915 45.455 0.00 0.00 0.00 2.66
367 368 6.407525 GCATTCCTTTACCACTCTCATACTCT 60.408 42.308 0.00 0.00 0.00 3.24
426 465 2.799562 GCCAAAGGTCAAAACTGAGCAC 60.800 50.000 7.04 0.00 38.64 4.40
546 838 7.323052 TGTGCCCATGTATACTATAAATGGA 57.677 36.000 20.85 5.18 40.23 3.41
559 851 1.076850 CTGCCCATGTGCCCATGTA 60.077 57.895 8.41 0.00 45.83 2.29
721 1061 8.025445 CCAAGTTTATGATGGAAAAAGTGAGAG 58.975 37.037 0.00 0.00 36.27 3.20
854 1215 9.442047 ACTTCAAGATTTCTCAATTACGATCTT 57.558 29.630 0.00 0.00 35.01 2.40
877 1238 9.105844 AGTGATGATAAATATACCTGCCTACTT 57.894 33.333 0.00 0.00 0.00 2.24
1023 1384 1.301677 CCTCCCGCAGCTTCACTTTC 61.302 60.000 0.00 0.00 0.00 2.62
1072 1433 1.301401 CGTCGAACACCACCACCAT 60.301 57.895 0.00 0.00 0.00 3.55
1138 1499 0.395311 CCAAGATGCAGCTCATGGGT 60.395 55.000 13.83 0.00 35.05 4.51
1201 1562 3.738982 TGGTGTTGTCGAACATCTTCAT 58.261 40.909 2.41 0.00 42.82 2.57
1385 1832 2.834549 CTGCTCCTCTTCTTTCCCACTA 59.165 50.000 0.00 0.00 0.00 2.74
1388 1835 1.905215 CTCTGCTCCTCTTCTTTCCCA 59.095 52.381 0.00 0.00 0.00 4.37
1392 1839 0.248843 CCGCTCTGCTCCTCTTCTTT 59.751 55.000 0.00 0.00 0.00 2.52
1394 1841 2.057408 CCCGCTCTGCTCCTCTTCT 61.057 63.158 0.00 0.00 0.00 2.85
1397 1907 3.387609 ATCCCCGCTCTGCTCCTCT 62.388 63.158 0.00 0.00 0.00 3.69
1419 1944 1.994507 CCTCCCTGCTCTGCTCCTT 60.995 63.158 0.00 0.00 0.00 3.36
1425 1965 2.268280 CTGCACCTCCCTGCTCTG 59.732 66.667 0.00 0.00 38.07 3.35
1562 2251 1.973281 CAGCTGTGGAATTGCCGGT 60.973 57.895 5.25 0.00 40.66 5.28
2152 2904 2.035066 GGTAGGCCACATTTGATGATGC 59.965 50.000 5.01 0.00 34.09 3.91
2339 3094 1.955778 TGTTTGCCATCACAAGACAGG 59.044 47.619 0.00 0.00 0.00 4.00
2362 3117 1.172180 TGGAACCTCGCTTTGGCAAG 61.172 55.000 0.00 0.00 38.60 4.01
2500 3257 3.243839 GCGACCATCCGTAAAATAGGGTA 60.244 47.826 0.00 0.00 35.31 3.69
2532 3289 0.529992 CTACGAGGGTCGGAAATGCC 60.530 60.000 0.86 0.00 45.59 4.40
2607 3364 0.537188 ATGGAGTACCCGCAGTTCAG 59.463 55.000 0.00 0.00 37.93 3.02
2620 3377 7.378181 CAAAAATAACAGGCAAACTATGGAGT 58.622 34.615 0.00 0.00 37.59 3.85
2649 3406 9.573133 CCTACCTGTGAAGCTAAAAATAATTTG 57.427 33.333 0.00 0.00 0.00 2.32
2654 3412 5.811190 TGCCTACCTGTGAAGCTAAAAATA 58.189 37.500 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.