Multiple sequence alignment - TraesCS4B01G022800

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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 TraesCS4B01G022800 chr4B 100.000 2399 0 0 1 2399 16795572 16797970 0.000000e+00 4431.0
1 TraesCS4B01G022800 chr4B 91.174 1337 87 20 1072 2395 16503183 16504501 0.000000e+00 1786.0
2 TraesCS4B01G022800 chr4B 89.263 1099 70 26 4 1078 16502061 16503135 0.000000e+00 1332.0
3 TraesCS4B01G022800 chr4D 88.158 988 89 19 1427 2396 8817958 8818935 0.000000e+00 1151.0
4 TraesCS4B01G022800 chr4D 94.813 347 18 0 1072 1418 8817631 8817977 2.100000e-150 542.0
5 TraesCS4B01G022800 chr4D 90.116 344 19 7 1 335 8816592 8816929 1.320000e-117 433.0
6 TraesCS4B01G022800 chr4D 86.774 310 23 8 771 1078 8817287 8817580 1.780000e-86 329.0
7 TraesCS4B01G022800 chr4D 84.483 290 21 14 493 772 8816973 8817248 5.090000e-67 265.0
8 TraesCS4B01G022800 chr4D 89.474 57 2 1 1920 1972 8819405 8819461 4.280000e-08 69.4
9 TraesCS4B01G022800 chr4A 86.190 630 42 24 1082 1706 594460626 594460037 7.230000e-180 640.0
10 TraesCS4B01G022800 chr4A 87.436 390 24 7 4 379 594461724 594461346 2.200000e-115 425.0
11 TraesCS4B01G022800 chr4A 86.538 312 27 7 771 1081 594460978 594460681 1.780000e-86 329.0
12 TraesCS4B01G022800 chr4A 77.323 269 39 16 519 774 594461277 594461018 3.220000e-29 139.0


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 TraesCS4B01G022800 chr4B 16795572 16797970 2398 False 4431.00 4431 100.000000 1 2399 1 chr4B.!!$F1 2398
1 TraesCS4B01G022800 chr4B 16502061 16504501 2440 False 1559.00 1786 90.218500 4 2395 2 chr4B.!!$F2 2391
2 TraesCS4B01G022800 chr4D 8816592 8819461 2869 False 464.90 1151 88.969667 1 2396 6 chr4D.!!$F1 2395
3 TraesCS4B01G022800 chr4A 594460037 594461724 1687 True 383.25 640 84.371750 4 1706 4 chr4A.!!$R1 1702

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
993 1151 0.636101 AGCTGGAGAGGACAGGAGAT 59.364 55.0 0.0 0.0 36.48 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2370 2622 2.747989 TGAGTAAACAAACACGCAACCA 59.252 40.909 0.0 0.0 0.0 3.67 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
27 28 7.865385 GCCACTACATTACAAAAGAAATGTCAA 59.135 33.333 4.11 0.00 43.44 3.18
47 48 6.316140 TGTCAATATCTTTCGTTCTTCCATGG 59.684 38.462 4.97 4.97 0.00 3.66
67 71 3.448469 TCCAAAAACCGGCTTGGAT 57.552 47.368 22.89 0.00 44.87 3.41
68 72 1.710816 TCCAAAAACCGGCTTGGATT 58.289 45.000 22.89 0.00 44.87 3.01
78 82 2.159572 CCGGCTTGGATTCTACAAAACG 60.160 50.000 0.00 0.00 42.00 3.60
79 83 2.727916 CGGCTTGGATTCTACAAAACGC 60.728 50.000 0.00 0.00 0.00 4.84
80 84 2.415491 GGCTTGGATTCTACAAAACGCC 60.415 50.000 0.00 0.00 32.12 5.68
81 85 2.727916 GCTTGGATTCTACAAAACGCCG 60.728 50.000 0.00 0.00 0.00 6.46
119 123 2.329379 GTGAGCCGCGATTAGAATAGG 58.671 52.381 8.23 0.00 0.00 2.57
264 293 3.575351 GAAGTCGTGCCCTGCGTCT 62.575 63.158 0.00 0.00 0.00 4.18
399 428 1.373748 GCACGTTCCTCGGTTGCTA 60.374 57.895 0.00 0.00 44.69 3.49
402 431 1.290955 CGTTCCTCGGTTGCTACCA 59.709 57.895 17.63 3.99 45.31 3.25
423 452 5.310068 ACCAAGATCAAGATCAGATAGGCAT 59.690 40.000 12.21 0.00 40.22 4.40
586 620 2.115911 TGCGCGGTTCTGTTTTGGT 61.116 52.632 8.83 0.00 0.00 3.67
591 625 1.235724 CGGTTCTGTTTTGGTCTCCC 58.764 55.000 0.00 0.00 0.00 4.30
592 626 1.476110 CGGTTCTGTTTTGGTCTCCCA 60.476 52.381 0.00 0.00 39.65 4.37
911 1062 2.342648 GGACCACGCCGTCTCTTT 59.657 61.111 0.00 0.00 33.07 2.52
915 1066 2.551270 CACGCCGTCTCTTTGTGC 59.449 61.111 0.00 0.00 0.00 4.57
936 1087 2.554462 CTCTTCGTCTCAGACAGTTCCA 59.446 50.000 5.45 0.00 32.09 3.53
967 1125 2.656002 AGGAGCTAGCGTGATTCACTA 58.344 47.619 14.54 1.00 31.34 2.74
972 1130 5.048643 GGAGCTAGCGTGATTCACTAATCTA 60.049 44.000 14.54 9.12 41.83 1.98
985 1143 6.455690 TCACTAATCTATAGCTGGAGAGGA 57.544 41.667 0.00 0.00 0.00 3.71
986 1144 6.242396 TCACTAATCTATAGCTGGAGAGGAC 58.758 44.000 0.00 0.00 0.00 3.85
987 1145 6.007076 CACTAATCTATAGCTGGAGAGGACA 58.993 44.000 0.00 0.00 0.00 4.02
988 1146 6.150976 CACTAATCTATAGCTGGAGAGGACAG 59.849 46.154 0.00 0.00 38.95 3.51
989 1147 3.517296 TCTATAGCTGGAGAGGACAGG 57.483 52.381 0.00 0.00 36.48 4.00
991 1149 2.380064 ATAGCTGGAGAGGACAGGAG 57.620 55.000 0.00 0.00 36.48 3.69
992 1150 1.299939 TAGCTGGAGAGGACAGGAGA 58.700 55.000 0.00 0.00 36.48 3.71
993 1151 0.636101 AGCTGGAGAGGACAGGAGAT 59.364 55.000 0.00 0.00 36.48 2.75
994 1152 1.856259 AGCTGGAGAGGACAGGAGATA 59.144 52.381 0.00 0.00 36.48 1.98
995 1153 1.960689 GCTGGAGAGGACAGGAGATAC 59.039 57.143 0.00 0.00 36.48 2.24
1023 1183 3.062466 CCCGGAGCTGTCTCGACA 61.062 66.667 0.73 0.00 40.26 4.35
1024 1184 2.636412 CCCGGAGCTGTCTCGACAA 61.636 63.158 0.73 0.00 41.33 3.18
1027 1187 1.290324 GGAGCTGTCTCGACAAGCA 59.710 57.895 17.40 0.00 41.33 3.91
1078 1238 2.224159 GGGGTGTCCAAGGAGAGCA 61.224 63.158 15.95 0.00 37.59 4.26
1362 1579 0.532862 AGACCTCTTGTGGTGTTGCG 60.533 55.000 0.00 0.00 41.00 4.85
1542 1769 5.233050 CAGATCATGTTCGTTAGTGGATGAC 59.767 44.000 0.00 0.00 0.00 3.06
1558 1787 4.039852 TGGATGACAAGTACAGTAGCAACA 59.960 41.667 0.00 0.00 0.00 3.33
1573 1802 7.831193 ACAGTAGCAACAAAATCAGAATCCTAT 59.169 33.333 0.00 0.00 0.00 2.57
1648 1880 7.811236 ACCTTAATTTTTAGCTAAAAAGGCGAC 59.189 33.333 35.04 0.00 45.11 5.19
1653 1885 0.034337 AGCTAAAAAGGCGACGACCA 59.966 50.000 0.00 0.00 34.52 4.02
1725 1964 6.683286 CGAATGAGATTATACCGAGATACACG 59.317 42.308 0.00 0.00 0.00 4.49
1726 1965 5.292671 TGAGATTATACCGAGATACACGC 57.707 43.478 0.00 0.00 0.00 5.34
1727 1966 4.142966 TGAGATTATACCGAGATACACGCG 60.143 45.833 3.53 3.53 41.18 6.01
1835 2080 1.000394 GTGGCTTTTTGGCGGTACAAT 60.000 47.619 0.00 0.00 45.14 2.71
1837 2082 2.891580 TGGCTTTTTGGCGGTACAATAA 59.108 40.909 0.00 0.00 45.14 1.40
1972 2222 8.201464 TGAACGCCTTATCTAACTCATATGAAA 58.799 33.333 6.90 0.00 0.00 2.69
1974 2224 8.958119 ACGCCTTATCTAACTCATATGAAAAA 57.042 30.769 6.90 0.00 0.00 1.94
2105 2357 8.854117 ACTACTTTTCATCAGCTTCAAGAAAAT 58.146 29.630 11.33 6.89 37.50 1.82
2259 2511 8.301002 CCATTCATGATTTTGAAAGGCAAATTT 58.699 29.630 0.00 0.00 45.30 1.82
2299 2551 3.391506 TTGGCTCATCGACATCCATAG 57.608 47.619 0.00 0.00 0.00 2.23
2318 2570 6.821665 TCCATAGCTTACCACATCTACAAAAC 59.178 38.462 0.00 0.00 0.00 2.43
2342 2594 5.106673 CGAATTACTCCCTCCTTTCACAAAC 60.107 44.000 0.00 0.00 0.00 2.93
2376 2628 6.924111 TCTATCCTTTTTCTGATTTGGTTGC 58.076 36.000 0.00 0.00 0.00 4.17
2386 2638 3.589988 TGATTTGGTTGCGTGTTTGTTT 58.410 36.364 0.00 0.00 0.00 2.83
2396 2648 5.236655 TGCGTGTTTGTTTACTCATTTCA 57.763 34.783 0.00 0.00 0.00 2.69
2397 2649 5.270083 TGCGTGTTTGTTTACTCATTTCAG 58.730 37.500 0.00 0.00 0.00 3.02
2398 2650 5.163703 TGCGTGTTTGTTTACTCATTTCAGT 60.164 36.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.183361 TGGATCCATGGAAGAACGAAAGATAT 60.183 38.462 20.67 0.00 0.00 1.63
47 48 1.253100 TCCAAGCCGGTTTTTGGATC 58.747 50.000 24.27 0.00 45.87 3.36
67 71 2.319096 CGGCCGGCGTTTTGTAGAA 61.319 57.895 22.54 0.00 0.00 2.10
68 72 2.739287 CGGCCGGCGTTTTGTAGA 60.739 61.111 22.54 0.00 0.00 2.59
100 104 1.336887 GCCTATTCTAATCGCGGCTCA 60.337 52.381 6.13 0.00 34.80 4.26
255 284 3.322466 AGGGGTCAAGACGCAGGG 61.322 66.667 17.34 0.00 44.89 4.45
256 285 2.046892 CAGGGGTCAAGACGCAGG 60.047 66.667 17.34 6.37 44.89 4.85
264 293 1.302192 GTTACAGCGCAGGGGTCAA 60.302 57.895 11.47 0.00 0.00 3.18
399 428 4.657504 TGCCTATCTGATCTTGATCTTGGT 59.342 41.667 11.31 4.37 0.00 3.67
402 431 6.499699 TGGTATGCCTATCTGATCTTGATCTT 59.500 38.462 11.31 0.92 35.27 2.40
423 452 2.435234 GCAATCGGCGTGGTGGTA 60.435 61.111 6.85 0.00 0.00 3.25
517 546 3.573558 CGGCAATACGGTTGCAGT 58.426 55.556 23.30 0.00 46.58 4.40
586 620 0.329261 CCTTTGTGGCATCTGGGAGA 59.671 55.000 0.00 0.00 0.00 3.71
868 1013 0.461163 GAAGAAGAAGAGCCGAGGCC 60.461 60.000 10.95 0.00 43.17 5.19
869 1014 0.461163 GGAAGAAGAAGAGCCGAGGC 60.461 60.000 5.89 5.89 42.33 4.70
911 1062 1.268079 CTGTCTGAGACGAAGAGCACA 59.732 52.381 8.23 0.00 34.95 4.57
915 1066 2.554462 TGGAACTGTCTGAGACGAAGAG 59.446 50.000 8.23 2.15 34.95 2.85
947 1105 1.479709 AGTGAATCACGCTAGCTCCT 58.520 50.000 13.93 0.26 39.64 3.69
967 1125 4.107149 TCCTGTCCTCTCCAGCTATAGATT 59.893 45.833 3.21 0.00 0.00 2.40
972 1130 1.856259 TCTCCTGTCCTCTCCAGCTAT 59.144 52.381 0.00 0.00 0.00 2.97
985 1143 2.045524 CTCCATGCCTGTATCTCCTGT 58.954 52.381 0.00 0.00 0.00 4.00
986 1144 1.270732 GCTCCATGCCTGTATCTCCTG 60.271 57.143 0.00 0.00 35.15 3.86
987 1145 1.055040 GCTCCATGCCTGTATCTCCT 58.945 55.000 0.00 0.00 35.15 3.69
988 1146 3.621953 GCTCCATGCCTGTATCTCC 57.378 57.895 0.00 0.00 35.15 3.71
1018 1178 4.680237 CACCGCCCTGCTTGTCGA 62.680 66.667 0.00 0.00 0.00 4.20
1078 1238 1.371558 GTGCCTCCACCTTCTTCGT 59.628 57.895 0.00 0.00 35.92 3.85
1362 1579 2.807045 CTGACGACGCTGTGCTCC 60.807 66.667 0.00 0.00 0.00 4.70
1366 1583 3.108289 CAGGCTGACGACGCTGTG 61.108 66.667 9.42 0.00 0.00 3.66
1435 1659 9.466497 AACACCAGAAATAGTCAATGTAATGAT 57.534 29.630 0.00 0.00 0.00 2.45
1440 1664 8.908903 ACAAAAACACCAGAAATAGTCAATGTA 58.091 29.630 0.00 0.00 0.00 2.29
1542 1769 7.189693 TCTGATTTTGTTGCTACTGTACTTG 57.810 36.000 0.00 0.00 0.00 3.16
1558 1787 9.981460 AACTCCAAACTATAGGATTCTGATTTT 57.019 29.630 4.43 0.00 32.53 1.82
1573 1802 9.179909 TGTGACTGAATTTAAAACTCCAAACTA 57.820 29.630 0.00 0.00 0.00 2.24
1648 1880 2.150390 TGGTCACATGTTCATTGGTCG 58.850 47.619 0.00 0.00 0.00 4.79
1653 1885 5.132502 TCAGAAGTTGGTCACATGTTCATT 58.867 37.500 0.00 0.00 0.00 2.57
1725 1964 0.440758 TTACACAACTATGCGTGCGC 59.559 50.000 9.85 9.85 42.35 6.09
1726 1965 2.865556 TTTACACAACTATGCGTGCG 57.134 45.000 0.00 0.00 36.57 5.34
1727 1966 5.007234 TCCATATTTACACAACTATGCGTGC 59.993 40.000 0.00 0.00 36.57 5.34
2083 2335 7.042321 TGCAATTTTCTTGAAGCTGATGAAAAG 60.042 33.333 17.57 10.75 39.11 2.27
2105 2357 3.994392 GTCGGTCTCAAATTCTAGTGCAA 59.006 43.478 0.00 0.00 0.00 4.08
2274 2526 4.522114 TGGATGTCGATGAGCCAAATAAA 58.478 39.130 2.14 0.00 0.00 1.40
2287 2539 3.028130 TGTGGTAAGCTATGGATGTCGA 58.972 45.455 0.00 0.00 0.00 4.20
2290 2542 5.602561 TGTAGATGTGGTAAGCTATGGATGT 59.397 40.000 0.00 0.00 0.00 3.06
2299 2551 5.600908 TTCGTTTTGTAGATGTGGTAAGC 57.399 39.130 0.00 0.00 0.00 3.09
2318 2570 4.202245 TGTGAAAGGAGGGAGTAATTCG 57.798 45.455 0.00 0.00 0.00 3.34
2358 2610 4.111916 ACACGCAACCAAATCAGAAAAAG 58.888 39.130 0.00 0.00 0.00 2.27
2370 2622 2.747989 TGAGTAAACAAACACGCAACCA 59.252 40.909 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.