Multiple sequence alignment - TraesCS4A01G311500

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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 TraesCS4A01G311500 chr4A 100.000 2735 0 0 1 2735 603468204 603470938 0.000000e+00 5051
1 TraesCS4A01G311500 chr4A 95.833 1848 77 0 255 2102 603390556 603388709 0.000000e+00 2987
2 TraesCS4A01G311500 chr4B 89.245 2120 189 23 3 2107 1768618 1766523 0.000000e+00 2615
3 TraesCS4A01G311500 chr4D 95.433 1248 56 1 861 2107 1311737 1310490 0.000000e+00 1988
4 TraesCS4A01G311500 chr4D 90.446 785 70 4 81 864 1326103 1325323 0.000000e+00 1029
5 TraesCS4A01G311500 chr4D 74.131 518 108 18 1236 1736 1333533 1333025 1.000000e-44 191
6 TraesCS4A01G311500 chr4D 75.168 447 83 17 1421 1847 1337800 1337362 4.650000e-43 185
7 TraesCS4A01G311500 chr7A 98.730 630 7 1 2107 2735 68465862 68466491 0.000000e+00 1118
8 TraesCS4A01G311500 chr1A 98.884 627 6 1 2108 2733 390931555 390932181 0.000000e+00 1118
9 TraesCS4A01G311500 chr1A 98.569 629 8 1 2108 2735 14119607 14118979 0.000000e+00 1110
10 TraesCS4A01G311500 chr6A 98.571 630 8 1 2107 2735 135255446 135256075 0.000000e+00 1112
11 TraesCS4A01G311500 chr6A 98.569 629 8 1 2108 2735 53488173 53488801 0.000000e+00 1110
12 TraesCS4A01G311500 chr3A 98.571 630 8 1 2107 2735 725680818 725680189 0.000000e+00 1112
13 TraesCS4A01G311500 chr3A 98.571 630 8 1 2107 2735 725692862 725693491 0.000000e+00 1112
14 TraesCS4A01G311500 chr3A 76.129 465 94 11 638 1099 750697753 750698203 7.620000e-56 228
15 TraesCS4A01G311500 chr3A 75.107 466 97 13 638 1099 750671213 750671663 1.660000e-47 200
16 TraesCS4A01G311500 chr5A 98.569 629 8 1 2108 2735 633835428 633836056 0.000000e+00 1110
17 TraesCS4A01G311500 chr5A 98.104 633 10 2 2104 2735 214708218 214707587 0.000000e+00 1101
18 TraesCS4A01G311500 chr3B 75.162 1385 278 40 359 1708 825289545 825290898 2.350000e-165 592
19 TraesCS4A01G311500 chr3B 75.472 742 147 21 863 1582 823976572 823977300 2.030000e-86 329
20 TraesCS4A01G311500 chr2D 81.170 393 62 6 700 1090 426434559 426434177 3.420000e-79 305
21 TraesCS4A01G311500 chr2B 81.170 393 62 6 700 1090 503453664 503453282 3.420000e-79 305
22 TraesCS4A01G311500 chr2A 80.928 388 63 5 700 1086 562508400 562508777 2.060000e-76 296


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 TraesCS4A01G311500 chr4A 603468204 603470938 2734 False 5051 5051 100.000 1 2735 1 chr4A.!!$F1 2734
1 TraesCS4A01G311500 chr4A 603388709 603390556 1847 True 2987 2987 95.833 255 2102 1 chr4A.!!$R1 1847
2 TraesCS4A01G311500 chr4B 1766523 1768618 2095 True 2615 2615 89.245 3 2107 1 chr4B.!!$R1 2104
3 TraesCS4A01G311500 chr4D 1310490 1311737 1247 True 1988 1988 95.433 861 2107 1 chr4D.!!$R1 1246
4 TraesCS4A01G311500 chr4D 1325323 1326103 780 True 1029 1029 90.446 81 864 1 chr4D.!!$R2 783
5 TraesCS4A01G311500 chr7A 68465862 68466491 629 False 1118 1118 98.730 2107 2735 1 chr7A.!!$F1 628
6 TraesCS4A01G311500 chr1A 390931555 390932181 626 False 1118 1118 98.884 2108 2733 1 chr1A.!!$F1 625
7 TraesCS4A01G311500 chr1A 14118979 14119607 628 True 1110 1110 98.569 2108 2735 1 chr1A.!!$R1 627
8 TraesCS4A01G311500 chr6A 135255446 135256075 629 False 1112 1112 98.571 2107 2735 1 chr6A.!!$F2 628
9 TraesCS4A01G311500 chr6A 53488173 53488801 628 False 1110 1110 98.569 2108 2735 1 chr6A.!!$F1 627
10 TraesCS4A01G311500 chr3A 725680189 725680818 629 True 1112 1112 98.571 2107 2735 1 chr3A.!!$R1 628
11 TraesCS4A01G311500 chr3A 725692862 725693491 629 False 1112 1112 98.571 2107 2735 1 chr3A.!!$F1 628
12 TraesCS4A01G311500 chr5A 633835428 633836056 628 False 1110 1110 98.569 2108 2735 1 chr5A.!!$F1 627
13 TraesCS4A01G311500 chr5A 214707587 214708218 631 True 1101 1101 98.104 2104 2735 1 chr5A.!!$R1 631
14 TraesCS4A01G311500 chr3B 825289545 825290898 1353 False 592 592 75.162 359 1708 1 chr3B.!!$F2 1349
15 TraesCS4A01G311500 chr3B 823976572 823977300 728 False 329 329 75.472 863 1582 1 chr3B.!!$F1 719

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
305 319 0.331616 GTGAAACCCTAGGCCCACAT 59.668 55.0 2.05 0.0 0.0 3.21 F
1325 1369 0.108585 ACCGTCACTTTGCATCTGGT 59.891 50.0 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1463 0.909623 CAAACACCGAGTATCCCCCT 59.090 55.000 0.0 0.0 0.00 4.79 R
2211 2259 9.151471 AGTTTGTCTATGTATTCACACATGTAC 57.849 33.333 0.0 0.0 39.46 2.90 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
24 25 2.009302 AAGGAAGGATGGAGGGGGC 61.009 63.158 0.00 0.00 0.00 5.80
25 26 3.878667 GGAAGGATGGAGGGGGCG 61.879 72.222 0.00 0.00 0.00 6.13
53 59 4.821589 CGGCGGGCAGTCTCTTCC 62.822 72.222 0.00 0.00 0.00 3.46
54 60 4.475135 GGCGGGCAGTCTCTTCCC 62.475 72.222 0.00 0.00 36.68 3.97
55 61 3.394836 GCGGGCAGTCTCTTCCCT 61.395 66.667 3.35 0.00 37.89 4.20
57 63 1.679898 CGGGCAGTCTCTTCCCTTT 59.320 57.895 3.35 0.00 37.89 3.11
60 66 1.065782 GGGCAGTCTCTTCCCTTTCTC 60.066 57.143 0.00 0.00 37.08 2.87
61 67 1.905894 GGCAGTCTCTTCCCTTTCTCT 59.094 52.381 0.00 0.00 0.00 3.10
63 69 3.244735 GGCAGTCTCTTCCCTTTCTCTTT 60.245 47.826 0.00 0.00 0.00 2.52
67 73 4.103943 AGTCTCTTCCCTTTCTCTTTTGCT 59.896 41.667 0.00 0.00 0.00 3.91
71 77 2.423577 TCCCTTTCTCTTTTGCTACGC 58.576 47.619 0.00 0.00 0.00 4.42
72 78 2.151202 CCCTTTCTCTTTTGCTACGCA 58.849 47.619 0.00 0.00 36.47 5.24
97 108 7.125536 ACGACGGAGGAAAGTTTTAATTTAG 57.874 36.000 0.00 0.00 0.00 1.85
150 161 5.992217 AGGAGCGAATATGGTAAGATTTGAC 59.008 40.000 0.00 0.00 0.00 3.18
164 175 8.336080 GGTAAGATTTGACTTGATTTCCGTATC 58.664 37.037 0.00 0.00 0.00 2.24
240 251 5.658190 AGTTAATCCATGAGGTGATTTTGGG 59.342 40.000 0.00 0.00 35.89 4.12
241 252 4.335735 AATCCATGAGGTGATTTTGGGA 57.664 40.909 0.00 0.00 35.89 4.37
252 266 5.823045 AGGTGATTTTGGGAAAGTATCGATC 59.177 40.000 0.00 0.00 0.00 3.69
253 267 5.588648 GGTGATTTTGGGAAAGTATCGATCA 59.411 40.000 0.00 0.00 0.00 2.92
305 319 0.331616 GTGAAACCCTAGGCCCACAT 59.668 55.000 2.05 0.00 0.00 3.21
346 361 3.075134 ACAGAAAAAGAGGCAGGAATCCT 59.925 43.478 0.00 0.00 36.46 3.24
356 373 1.045350 CAGGAATCCTCTCCTCCGCA 61.045 60.000 0.00 0.00 44.46 5.69
367 384 4.790962 CTCCGCAGCCAGCCATGT 62.791 66.667 0.00 0.00 41.38 3.21
629 650 4.660938 GTCCTGCCCCAACGCCTT 62.661 66.667 0.00 0.00 0.00 4.35
661 683 1.289380 GGCTCCTTCGAGTTCACGT 59.711 57.895 0.00 0.00 38.49 4.49
780 802 4.814294 GTCACCGCCGCCGAGATT 62.814 66.667 0.00 0.00 36.29 2.40
833 855 1.133407 GCTCTCCAAGATCGTCTTCGT 59.867 52.381 0.00 0.00 33.78 3.85
844 866 2.525629 TCTTCGTGCCTGACCCCA 60.526 61.111 0.00 0.00 0.00 4.96
1043 1065 3.448093 TGGGAATGTTTATGTGCTCCA 57.552 42.857 0.00 0.00 0.00 3.86
1094 1116 3.033909 TCATCATCGAGGACCAGACATT 58.966 45.455 0.00 0.00 0.00 2.71
1239 1283 2.900122 ACATCGCTGTTTCGGATTTG 57.100 45.000 0.00 0.00 28.70 2.32
1325 1369 0.108585 ACCGTCACTTTGCATCTGGT 59.891 50.000 0.00 0.00 0.00 4.00
1419 1463 2.260434 GACGCGGTGGCTGACTTA 59.740 61.111 12.47 0.00 36.88 2.24
1542 1586 2.054799 GGTAGGGATCAAGGCATGGTA 58.945 52.381 0.00 0.00 0.00 3.25
1582 1626 1.972588 ATCTACACCTTGCCTTCCCT 58.027 50.000 0.00 0.00 0.00 4.20
1590 1634 2.595009 CTTGCCTTCCCTCTACGGCC 62.595 65.000 0.00 0.00 41.80 6.13
1621 1665 1.604378 GGGCCTCTACAGTGCACAT 59.396 57.895 21.04 9.36 0.00 3.21
1690 1737 4.519213 TGAATTAGGTGTTTATGGGACCG 58.481 43.478 0.00 0.00 34.72 4.79
1714 1761 2.281276 GGGTTCGGGCTCAACGTT 60.281 61.111 0.00 0.00 0.00 3.99
2113 2161 4.403432 CCATGCTTGGATTATGTTGAAGGT 59.597 41.667 13.33 0.00 46.92 3.50
2276 2324 4.276431 GCCTCTACTTGACTAGCTCGTTAT 59.724 45.833 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.101331 CTCCATCCTTCCTTGCTTGC 58.899 55.000 0.00 0.00 0.00 4.01
1 2 1.684248 CCCTCCATCCTTCCTTGCTTG 60.684 57.143 0.00 0.00 0.00 4.01
36 42 4.821589 GGAAGAGACTGCCCGCCG 62.822 72.222 0.00 0.00 0.00 6.46
49 55 4.670227 CGTAGCAAAAGAGAAAGGGAAG 57.330 45.455 0.00 0.00 0.00 3.46
67 73 0.387622 CTTTCCTCCGTCGTTGCGTA 60.388 55.000 0.00 0.00 0.00 4.42
71 77 4.799419 TTAAAACTTTCCTCCGTCGTTG 57.201 40.909 0.00 0.00 0.00 4.10
72 78 6.381481 AAATTAAAACTTTCCTCCGTCGTT 57.619 33.333 0.00 0.00 0.00 3.85
74 80 7.117379 AGACTAAATTAAAACTTTCCTCCGTCG 59.883 37.037 0.00 0.00 0.00 5.12
75 81 8.320396 AGACTAAATTAAAACTTTCCTCCGTC 57.680 34.615 0.00 0.00 0.00 4.79
76 82 8.565416 CAAGACTAAATTAAAACTTTCCTCCGT 58.435 33.333 0.00 0.00 0.00 4.69
77 83 8.021396 CCAAGACTAAATTAAAACTTTCCTCCG 58.979 37.037 0.00 0.00 0.00 4.63
78 84 8.857098 ACCAAGACTAAATTAAAACTTTCCTCC 58.143 33.333 0.00 0.00 0.00 4.30
130 141 7.246674 TCAAGTCAAATCTTACCATATTCGC 57.753 36.000 0.00 0.00 0.00 4.70
139 150 8.336080 GGATACGGAAATCAAGTCAAATCTTAC 58.664 37.037 0.00 0.00 0.00 2.34
164 175 4.096382 CACAATCAAAACTTATCCCTCCGG 59.904 45.833 0.00 0.00 0.00 5.14
217 228 5.656416 TCCCAAAATCACCTCATGGATTAAC 59.344 40.000 0.00 0.00 33.57 2.01
223 234 3.834231 ACTTTCCCAAAATCACCTCATGG 59.166 43.478 0.00 0.00 39.83 3.66
228 239 5.174037 TCGATACTTTCCCAAAATCACCT 57.826 39.130 0.00 0.00 0.00 4.00
229 240 5.588648 TGATCGATACTTTCCCAAAATCACC 59.411 40.000 0.00 0.00 0.00 4.02
230 241 6.677781 TGATCGATACTTTCCCAAAATCAC 57.322 37.500 0.00 0.00 0.00 3.06
240 251 9.134734 CCTTCTTTATAGCTGATCGATACTTTC 57.865 37.037 0.00 0.00 0.00 2.62
241 252 8.861086 TCCTTCTTTATAGCTGATCGATACTTT 58.139 33.333 0.00 0.00 0.00 2.66
252 266 4.813697 GCCTGACTTCCTTCTTTATAGCTG 59.186 45.833 0.00 0.00 0.00 4.24
253 267 4.141597 GGCCTGACTTCCTTCTTTATAGCT 60.142 45.833 0.00 0.00 0.00 3.32
284 298 1.536907 TGGGCCTAGGGTTTCACGA 60.537 57.895 11.72 0.00 0.00 4.35
305 319 3.455910 CTGTGAGGAATGGAGGGATTGTA 59.544 47.826 0.00 0.00 0.00 2.41
356 373 3.240134 AACGACGACATGGCTGGCT 62.240 57.895 0.00 0.00 0.00 4.75
661 683 1.756690 GCTCCTAATCGGGTAGGTGGA 60.757 57.143 10.86 0.00 41.40 4.02
712 734 1.068055 GTCGTAGAGGCAGACGGAAAA 60.068 52.381 6.10 0.00 39.53 2.29
714 736 2.177950 GTCGTAGAGGCAGACGGAA 58.822 57.895 6.10 0.00 39.53 4.30
780 802 2.123854 ATGAGCGGCGGTAGGAGA 60.124 61.111 13.22 0.00 0.00 3.71
844 866 1.593296 GCGGTGAAGTCGTCCCTAGT 61.593 60.000 0.00 0.00 0.00 2.57
925 947 3.352338 GACGGACGCGGTCAAGGAT 62.352 63.158 12.47 0.00 34.54 3.24
1065 1087 0.595053 CCTCGATGATGACGGGTTCG 60.595 60.000 0.00 0.00 43.02 3.95
1094 1116 2.223502 CGCGTTACAAGATCCTCTGCTA 60.224 50.000 0.00 0.00 0.00 3.49
1239 1283 0.951040 CCAGGTTCTTGGCACTCGTC 60.951 60.000 0.00 0.00 0.00 4.20
1419 1463 0.909623 CAAACACCGAGTATCCCCCT 59.090 55.000 0.00 0.00 0.00 4.79
1542 1586 1.211567 TCCCGGTCCCCATGTCAAAT 61.212 55.000 0.00 0.00 0.00 2.32
1582 1626 2.981560 GAACGACACCGGCCGTAGA 61.982 63.158 26.12 0.00 38.13 2.59
1621 1665 1.275291 CCTCGGAAAGTACCAGCAGAA 59.725 52.381 0.00 0.00 0.00 3.02
1690 1737 3.978571 GAGCCCGAACCCTTGCTCC 62.979 68.421 0.00 0.00 43.40 4.70
1714 1761 5.065235 ACATCATTGTGACATGTCTTGTGA 58.935 37.500 25.55 21.52 39.18 3.58
1818 1865 4.400884 TGGACACAACAAGCAATTACACTT 59.599 37.500 0.00 0.00 0.00 3.16
2071 2118 2.683867 TGGGAACTAAACCAACACAACG 59.316 45.455 0.00 0.00 32.89 4.10
2211 2259 9.151471 AGTTTGTCTATGTATTCACACATGTAC 57.849 33.333 0.00 0.00 39.46 2.90


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

AutoCloner maintained by Alex Coulton.