Multiple sequence alignment - TraesCS7B01G295300

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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 TraesCS7B01G295300 chr7B 100.000 2228 0 0 1 2228 531985653 531987880 0.000000e+00 4115
1 TraesCS7B01G295300 chr2B 96.970 1188 27 4 1 1184 449208698 449209880 0.000000e+00 1986
2 TraesCS7B01G295300 chr2B 96.465 1188 32 4 1 1184 234530530 234531711 0.000000e+00 1953
3 TraesCS7B01G295300 chr6D 96.549 1188 33 4 1 1184 458917725 458918908 0.000000e+00 1960
4 TraesCS7B01G295300 chr6D 96.552 116 4 0 1252 1367 283194731 283194616 2.260000e-45 193
5 TraesCS7B01G295300 chrUn 96.549 1188 32 4 1 1184 231559520 231560702 0.000000e+00 1958
6 TraesCS7B01G295300 chrUn 96.549 1188 32 4 1 1184 273328607 273327425 0.000000e+00 1958
7 TraesCS7B01G295300 chrUn 98.519 675 10 0 1554 2228 233534934 233534260 0.000000e+00 1192
8 TraesCS7B01G295300 chrUn 98.370 675 11 0 1554 2228 388536762 388536088 0.000000e+00 1186
9 TraesCS7B01G295300 chrUn 98.526 475 7 0 1554 2028 221554444 221553970 0.000000e+00 839
10 TraesCS7B01G295300 chrUn 98.316 475 8 0 1554 2028 229488052 229487578 0.000000e+00 833
11 TraesCS7B01G295300 chr7A 96.549 1188 31 4 1 1184 60220135 60221316 0.000000e+00 1958
12 TraesCS7B01G295300 chr3B 96.549 1188 32 4 1 1184 6000136 6001318 0.000000e+00 1958
13 TraesCS7B01G295300 chr3A 96.549 1188 31 4 1 1184 495091910 495093091 0.000000e+00 1958
14 TraesCS7B01G295300 chr4B 96.380 1188 33 4 1 1184 495577617 495578798 0.000000e+00 1947
15 TraesCS7B01G295300 chr5A 98.667 675 9 0 1554 2228 492872177 492872851 0.000000e+00 1197
16 TraesCS7B01G295300 chr5A 98.222 675 12 0 1554 2228 522358898 522358224 0.000000e+00 1181
17 TraesCS7B01G295300 chr4A 98.074 675 13 0 1554 2228 246691088 246691762 0.000000e+00 1175
18 TraesCS7B01G295300 chr4D 97.778 675 14 1 1554 2228 123678931 123679604 0.000000e+00 1162
19 TraesCS7B01G295300 chr4D 94.706 680 35 1 1172 1850 167115798 167116477 0.000000e+00 1055
20 TraesCS7B01G295300 chr4D 96.552 116 4 0 1252 1367 123696282 123696167 2.260000e-45 193
21 TraesCS7B01G295300 chr1A 98.945 474 5 0 1755 2228 94623472 94623945 0.000000e+00 848
22 TraesCS7B01G295300 chr7D 95.466 397 16 2 1172 1566 349199179 349199575 1.120000e-177 632
23 TraesCS7B01G295300 chr7D 99.094 331 3 0 1898 2228 382107650 382107320 1.470000e-166 595
24 TraesCS7B01G295300 chr1D 91.720 314 24 2 1172 1484 287101677 287101989 3.400000e-118 435
25 TraesCS7B01G295300 chr1D 96.552 116 4 0 1252 1367 212436156 212436041 2.260000e-45 193
26 TraesCS7B01G295300 chr1D 96.552 116 4 0 1252 1367 275782876 275782991 2.260000e-45 193
27 TraesCS7B01G295300 chr5B 97.414 116 3 0 1252 1367 680046899 680046784 4.850000e-47 198
28 TraesCS7B01G295300 chr2D 95.652 115 5 0 1253 1367 291777541 291777655 3.780000e-43 185
29 TraesCS7B01G295300 chr2A 92.373 118 5 1 1175 1288 24962693 24962576 4.920000e-37 165


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 TraesCS7B01G295300 chr7B 531985653 531987880 2227 False 4115 4115 100.000 1 2228 1 chr7B.!!$F1 2227
1 TraesCS7B01G295300 chr2B 449208698 449209880 1182 False 1986 1986 96.970 1 1184 1 chr2B.!!$F2 1183
2 TraesCS7B01G295300 chr2B 234530530 234531711 1181 False 1953 1953 96.465 1 1184 1 chr2B.!!$F1 1183
3 TraesCS7B01G295300 chr6D 458917725 458918908 1183 False 1960 1960 96.549 1 1184 1 chr6D.!!$F1 1183
4 TraesCS7B01G295300 chrUn 231559520 231560702 1182 False 1958 1958 96.549 1 1184 1 chrUn.!!$F1 1183
5 TraesCS7B01G295300 chrUn 273327425 273328607 1182 True 1958 1958 96.549 1 1184 1 chrUn.!!$R4 1183
6 TraesCS7B01G295300 chrUn 233534260 233534934 674 True 1192 1192 98.519 1554 2228 1 chrUn.!!$R3 674
7 TraesCS7B01G295300 chrUn 388536088 388536762 674 True 1186 1186 98.370 1554 2228 1 chrUn.!!$R5 674
8 TraesCS7B01G295300 chr7A 60220135 60221316 1181 False 1958 1958 96.549 1 1184 1 chr7A.!!$F1 1183
9 TraesCS7B01G295300 chr3B 6000136 6001318 1182 False 1958 1958 96.549 1 1184 1 chr3B.!!$F1 1183
10 TraesCS7B01G295300 chr3A 495091910 495093091 1181 False 1958 1958 96.549 1 1184 1 chr3A.!!$F1 1183
11 TraesCS7B01G295300 chr4B 495577617 495578798 1181 False 1947 1947 96.380 1 1184 1 chr4B.!!$F1 1183
12 TraesCS7B01G295300 chr5A 492872177 492872851 674 False 1197 1197 98.667 1554 2228 1 chr5A.!!$F1 674
13 TraesCS7B01G295300 chr5A 522358224 522358898 674 True 1181 1181 98.222 1554 2228 1 chr5A.!!$R1 674
14 TraesCS7B01G295300 chr4A 246691088 246691762 674 False 1175 1175 98.074 1554 2228 1 chr4A.!!$F1 674
15 TraesCS7B01G295300 chr4D 123678931 123679604 673 False 1162 1162 97.778 1554 2228 1 chr4D.!!$F1 674
16 TraesCS7B01G295300 chr4D 167115798 167116477 679 False 1055 1055 94.706 1172 1850 1 chr4D.!!$F2 678

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
379 383 0.399091 AGAGAGGCATCCGAATCCCA 60.399 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1549 1559 1.103803 CTACCGTCTGCCTCTGCTAA 58.896 55.0 0.0 0.0 38.71 3.09 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 3.799366 TGGAGAGTTTGCTTTTACACGA 58.201 40.909 0.00 0.00 0.00 4.35
71 72 9.615660 AAATAGAGGAAAGGGGAAAAAGTAAAT 57.384 29.630 0.00 0.00 0.00 1.40
78 79 8.311836 GGAAAGGGGAAAAAGTAAATTCTAAGG 58.688 37.037 0.00 0.00 0.00 2.69
248 249 2.851045 GGACCCAGGCCCTTCAAA 59.149 61.111 0.00 0.00 0.00 2.69
273 274 1.688311 CCCTCCGGATCCACTAACTCA 60.688 57.143 13.41 0.00 0.00 3.41
333 334 2.769621 TCTGCATCCCGGGAGCAT 60.770 61.111 33.61 17.15 37.68 3.79
364 368 0.681733 GGCTGTGGTCAGTCAAGAGA 59.318 55.000 0.00 0.00 44.73 3.10
379 383 0.399091 AGAGAGGCATCCGAATCCCA 60.399 55.000 0.00 0.00 0.00 4.37
565 569 3.490078 GGAGCTCCGTGAAGAAGACTATG 60.490 52.174 19.06 0.00 0.00 2.23
602 607 0.827925 TGTTGAGCCGACTCCAGTCT 60.828 55.000 5.21 0.00 42.74 3.24
802 807 1.725641 TGTGATGTGATCGGCAAGAC 58.274 50.000 0.00 0.00 0.00 3.01
812 817 2.559698 TCGGCAAGACAAAGATGGAA 57.440 45.000 0.00 0.00 0.00 3.53
813 818 3.071874 TCGGCAAGACAAAGATGGAAT 57.928 42.857 0.00 0.00 0.00 3.01
814 819 3.420893 TCGGCAAGACAAAGATGGAATT 58.579 40.909 0.00 0.00 0.00 2.17
815 820 3.440173 TCGGCAAGACAAAGATGGAATTC 59.560 43.478 0.00 0.00 0.00 2.17
842 851 8.713708 TTTGGTATAAGGAAGGAAATCAAACA 57.286 30.769 0.00 0.00 0.00 2.83
1124 1133 8.549338 TTGAACTTTTTGGTATTTTCCGTTTT 57.451 26.923 0.00 0.00 0.00 2.43
1125 1134 7.965045 TGAACTTTTTGGTATTTTCCGTTTTG 58.035 30.769 0.00 0.00 0.00 2.44
1195 1204 1.072505 GCTCCGGTTCCAGGTTTCA 59.927 57.895 0.00 0.00 0.00 2.69
1203 1212 3.119495 CGGTTCCAGGTTTCAATTCCATC 60.119 47.826 0.00 0.00 0.00 3.51
1205 1214 2.722094 TCCAGGTTTCAATTCCATCCG 58.278 47.619 0.00 0.00 0.00 4.18
1209 1218 4.262420 CCAGGTTTCAATTCCATCCGTTTT 60.262 41.667 0.00 0.00 0.00 2.43
1212 1221 7.147983 CCAGGTTTCAATTCCATCCGTTTTATA 60.148 37.037 0.00 0.00 0.00 0.98
1248 1257 9.897744 AAGTGATGTTATGTTACATTTTGACTG 57.102 29.630 2.23 0.00 38.80 3.51
1262 1271 8.641498 ACATTTTGACTGAGGATTGAATAAGT 57.359 30.769 0.00 0.00 0.00 2.24
1264 1273 9.350357 CATTTTGACTGAGGATTGAATAAGTTG 57.650 33.333 0.00 0.00 0.00 3.16
1435 1445 4.973168 TCTGGAATAGGTGGATATGTTGC 58.027 43.478 0.00 0.00 0.00 4.17
1457 1467 4.802563 GCAGAGGAAACGTACAAGGTATAC 59.197 45.833 0.00 0.00 0.00 1.47
1459 1469 6.034591 CAGAGGAAACGTACAAGGTATACAG 58.965 44.000 5.01 0.00 0.00 2.74
1461 1471 6.435277 AGAGGAAACGTACAAGGTATACAGAA 59.565 38.462 5.01 0.00 0.00 3.02
1523 1533 6.292919 GCACCATGTAAAACCGATTAGAGATC 60.293 42.308 0.00 0.00 0.00 2.75
1549 1559 5.463154 AGGATACAGATCTAGTTCCTTGCT 58.537 41.667 11.79 1.94 41.41 3.91
1563 1573 1.367659 CTTGCTTAGCAGAGGCAGAC 58.632 55.000 7.08 0.00 44.61 3.51
1641 1651 0.108585 GGCAGAAGGAACACTCACCA 59.891 55.000 0.00 0.00 0.00 4.17
1814 1824 4.229353 TGATACCTTCACAAATCCCCATCA 59.771 41.667 0.00 0.00 0.00 3.07
1878 1888 3.861840 TCTGAAACCTGCTATCTTTCCG 58.138 45.455 0.00 0.00 0.00 4.30
1963 1973 2.168936 TCGAGACTAGGACTCTCAGGTC 59.831 54.545 14.23 0.00 34.85 3.85
2070 2080 6.540189 CGGTATCTTCTTCCATCATGAAAGTT 59.460 38.462 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.087031 TGTTCGATAGGGTCTTCGTCTT 58.913 45.455 0.00 0.00 36.74 3.01
71 72 8.605947 CCTTATTGATCCATATGTCCCTTAGAA 58.394 37.037 1.24 0.00 0.00 2.10
78 79 7.890127 TGGATTTCCTTATTGATCCATATGTCC 59.110 37.037 1.24 0.00 42.21 4.02
109 110 5.347124 ACCTATATGGGATTCGGATTACCA 58.653 41.667 12.81 6.32 41.11 3.25
180 181 3.726557 AGCATCTCCCAACAAGATTCA 57.273 42.857 0.00 0.00 31.05 2.57
292 293 1.277557 GTCCTCACAGTCAGCCAGAAT 59.722 52.381 0.00 0.00 0.00 2.40
364 368 1.700042 GGAGTGGGATTCGGATGCCT 61.700 60.000 16.14 0.00 43.69 4.75
412 416 5.542251 CCCAATCAAAAGAAGGAGGGTTTTA 59.458 40.000 0.00 0.00 0.00 1.52
414 418 3.903714 CCCAATCAAAAGAAGGAGGGTTT 59.096 43.478 0.00 0.00 0.00 3.27
565 569 1.479323 ACATGAATCAAGCATGGTGCC 59.521 47.619 0.00 0.00 46.52 5.01
602 607 4.090588 GCCCGGGGATTGACGTCA 62.091 66.667 25.28 15.76 0.00 4.35
770 775 3.833650 TCACATCACATCCAAGGCATTTT 59.166 39.130 0.00 0.00 0.00 1.82
802 807 9.754382 CCTTATACCAAATGAATTCCATCTTTG 57.246 33.333 2.27 7.71 33.53 2.77
812 817 9.713684 TGATTTCCTTCCTTATACCAAATGAAT 57.286 29.630 0.00 0.00 0.00 2.57
813 818 9.540538 TTGATTTCCTTCCTTATACCAAATGAA 57.459 29.630 0.00 0.00 0.00 2.57
814 819 9.540538 TTTGATTTCCTTCCTTATACCAAATGA 57.459 29.630 0.00 0.00 0.00 2.57
815 820 9.586435 GTTTGATTTCCTTCCTTATACCAAATG 57.414 33.333 0.00 0.00 0.00 2.32
842 851 3.428862 CCTTTTTCCTGCTCAAACAACGT 60.429 43.478 0.00 0.00 0.00 3.99
854 863 8.459911 TTTTTCTCTAGTTACCCTTTTTCCTG 57.540 34.615 0.00 0.00 0.00 3.86
882 891 3.137360 GTCCAGGGAGAGCCTATTTTGAT 59.863 47.826 0.00 0.00 0.00 2.57
1124 1133 5.385628 TTGACCCATCATATCATCCAACA 57.614 39.130 0.00 0.00 33.85 3.33
1125 1134 6.005823 TGATTGACCCATCATATCATCCAAC 58.994 40.000 0.00 0.00 33.85 3.77
1221 1230 9.897744 AGTCAAAATGTAACATAACATCACTTG 57.102 29.630 0.00 0.00 39.16 3.16
1248 1257 6.122277 TCATGACCCAACTTATTCAATCCTC 58.878 40.000 0.00 0.00 0.00 3.71
1262 1271 4.081406 CAACTTCCATTCTCATGACCCAA 58.919 43.478 0.00 0.00 31.07 4.12
1264 1273 3.944015 CTCAACTTCCATTCTCATGACCC 59.056 47.826 0.00 0.00 31.07 4.46
1320 1329 3.429543 CGTGCATTGGAATGGAAAAGTTG 59.570 43.478 0.00 0.00 38.50 3.16
1321 1330 3.320541 TCGTGCATTGGAATGGAAAAGTT 59.679 39.130 0.00 0.00 38.50 2.66
1325 1334 4.269183 AGTATCGTGCATTGGAATGGAAA 58.731 39.130 0.00 0.00 38.50 3.13
1435 1445 5.957798 TGTATACCTTGTACGTTTCCTCTG 58.042 41.667 0.00 0.00 0.00 3.35
1523 1533 6.516527 GCAAGGAACTAGATCTGTATCCTCTG 60.517 46.154 19.39 18.53 38.49 3.35
1549 1559 1.103803 CTACCGTCTGCCTCTGCTAA 58.896 55.000 0.00 0.00 38.71 3.09
1641 1651 7.976734 GCATCTATAGAGTTACGAATTGCCTAT 59.023 37.037 8.70 0.00 0.00 2.57
1814 1824 4.227197 AGATTACCTCCATCTCGGTCAAT 58.773 43.478 0.00 0.00 34.76 2.57
1878 1888 2.301577 AGTTGTGAGCCGATAGAAGC 57.698 50.000 0.00 0.00 39.76 3.86
1963 1973 5.600908 TTTCTGTTTTCCGAATCTTACCG 57.399 39.130 0.00 0.00 0.00 4.02
2070 2080 1.828595 TGCCGACTAGATTGCTTACCA 59.171 47.619 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.