Multiple sequence alignment - TraesCS7B01G118200

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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 TraesCS7B01G118200 chr7B 100.000 3686 0 0 1 3686 137791401 137787716 0.000000e+00 6807
1 TraesCS7B01G118200 chr7A 93.195 3718 200 34 1 3686 174202127 174198431 0.000000e+00 5415
2 TraesCS7B01G118200 chr7D 95.356 1981 67 12 1722 3686 171307991 171306020 0.000000e+00 3125
3 TraesCS7B01G118200 chr7D 93.141 1735 74 19 1 1723 171309851 171308150 0.000000e+00 2503
4 TraesCS7B01G118200 chr6A 84.356 326 49 2 3256 3580 521458819 521459143 5.940000e-83 318
5 TraesCS7B01G118200 chr6B 83.129 326 53 2 3256 3580 567408028 567408352 2.780000e-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 TraesCS7B01G118200 chr7B 137787716 137791401 3685 True 6807 6807 100.0000 1 3686 1 chr7B.!!$R1 3685
1 TraesCS7B01G118200 chr7A 174198431 174202127 3696 True 5415 5415 93.1950 1 3686 1 chr7A.!!$R1 3685
2 TraesCS7B01G118200 chr7D 171306020 171309851 3831 True 2814 3125 94.2485 1 3686 2 chr7D.!!$R1 3685

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
727 730 0.325203 ACCCAAAGCCACCAAACACT 60.325 50.0 0.0 0.0 0.00 3.55 F
1252 1255 0.250166 GGTTGACTACCCGCACACTT 60.250 55.0 0.0 0.0 41.43 3.16 F
1271 1274 0.310543 TTTTTGCCTGCACACGCTAG 59.689 50.0 0.0 0.0 39.64 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 2027 0.035630 CTTGCCTCCTTGGAGTCCAG 60.036 60.000 12.67 6.8 38.35 3.86 R
2559 2746 1.809684 GGTCAGCCCAGTACTTGTTC 58.190 55.000 0.00 0.0 0.00 3.18 R
2718 2905 2.679336 TGCAGACAATCATCAACCATCG 59.321 45.455 0.00 0.0 0.00 3.84 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
43 44 4.015872 ACTTTGCCGATCAGTTAAAGGA 57.984 40.909 11.17 0.00 33.77 3.36
74 75 3.305813 CGGTTTACCTGCAGAACTGACTA 60.306 47.826 17.39 0.00 32.68 2.59
85 86 4.938226 GCAGAACTGACTATTAAAGGCTGT 59.062 41.667 5.97 0.00 46.71 4.40
147 148 4.010349 AGGCAAAAGCTACACAGGTATTC 58.990 43.478 0.00 0.00 0.00 1.75
162 163 4.578105 CAGGTATTCTCCTTTCATTGGCTC 59.422 45.833 0.00 0.00 35.37 4.70
214 215 5.238214 GTCTGGATTTGTAAGATCCTCATGC 59.762 44.000 4.91 0.00 42.88 4.06
382 385 9.667107 AGAATATTGGTTTCTATCTGTTCGAAA 57.333 29.630 0.00 0.00 31.75 3.46
383 386 9.922305 GAATATTGGTTTCTATCTGTTCGAAAG 57.078 33.333 0.00 0.00 0.00 2.62
384 387 6.743575 ATTGGTTTCTATCTGTTCGAAAGG 57.256 37.500 0.00 0.00 0.00 3.11
385 388 5.477607 TGGTTTCTATCTGTTCGAAAGGA 57.522 39.130 0.00 1.18 0.00 3.36
386 389 5.860611 TGGTTTCTATCTGTTCGAAAGGAA 58.139 37.500 0.00 0.00 0.00 3.36
463 466 3.880490 ACGTTCCAAATCAACTGCTTGTA 59.120 39.130 0.00 0.00 0.00 2.41
606 609 5.880887 AGTTCCTTTTACCTAACATAGCAGC 59.119 40.000 0.00 0.00 0.00 5.25
727 730 0.325203 ACCCAAAGCCACCAAACACT 60.325 50.000 0.00 0.00 0.00 3.55
870 873 2.548464 AGCTCATCTCCCTCTTGACT 57.452 50.000 0.00 0.00 0.00 3.41
880 883 5.258051 TCTCCCTCTTGACTAGTTTCTCTC 58.742 45.833 0.00 0.00 0.00 3.20
897 900 1.112113 CTCCATACACCACGTAGGCT 58.888 55.000 0.00 0.00 43.14 4.58
1006 1009 5.163713 GCTAAAACTAGTTTCAGGATGGCTG 60.164 44.000 20.78 4.20 36.16 4.85
1063 1066 2.335712 GCCTGTTTTCTCCTGGCCG 61.336 63.158 0.00 0.00 40.06 6.13
1128 1131 1.278985 CACTACTCCAAGACATGCCCA 59.721 52.381 0.00 0.00 0.00 5.36
1203 1206 1.143969 GCAATGCCGCTTTGATGCTC 61.144 55.000 20.10 1.51 0.00 4.26
1227 1230 2.884639 CCTCCATTTCCACGACTGTTTT 59.115 45.455 0.00 0.00 0.00 2.43
1238 1241 1.400142 CGACTGTTTTGTGCAGGTTGA 59.600 47.619 0.00 0.00 38.22 3.18
1252 1255 0.250166 GGTTGACTACCCGCACACTT 60.250 55.000 0.00 0.00 41.43 3.16
1271 1274 0.310543 TTTTTGCCTGCACACGCTAG 59.689 50.000 0.00 0.00 39.64 3.42
1273 1276 3.535629 TTGCCTGCACACGCTAGCT 62.536 57.895 13.93 0.00 39.64 3.32
1275 1278 2.328099 GCCTGCACACGCTAGCTTT 61.328 57.895 13.93 0.00 39.64 3.51
1276 1279 1.499056 CCTGCACACGCTAGCTTTG 59.501 57.895 13.93 12.11 39.64 2.77
1277 1280 1.154338 CTGCACACGCTAGCTTTGC 60.154 57.895 19.64 19.64 39.64 3.68
1278 1281 1.844771 CTGCACACGCTAGCTTTGCA 61.845 55.000 24.62 24.62 40.81 4.08
1311 1323 9.170584 GAAAGTAATTAAGTTTGCTCTGAACAC 57.829 33.333 0.00 0.00 30.60 3.32
1380 1392 3.458163 ACGGCGACCATGATCGGT 61.458 61.111 16.62 0.00 42.49 4.69
1531 1544 3.896648 ACGCAGTTGTCTTGGTAAATG 57.103 42.857 0.00 0.00 37.78 2.32
1534 1547 4.024048 ACGCAGTTGTCTTGGTAAATGAAG 60.024 41.667 0.00 0.00 37.78 3.02
1554 1567 4.373156 AGCCAAACCTATGTTCAGAGTT 57.627 40.909 0.00 0.00 32.15 3.01
1557 1570 5.241728 AGCCAAACCTATGTTCAGAGTTTTC 59.758 40.000 0.00 0.00 32.15 2.29
1577 1590 3.485394 TCATTCTTGTGCAGTGGCTTAA 58.515 40.909 0.00 0.00 41.91 1.85
1585 1598 5.371115 TGTGCAGTGGCTTAATTACTTTC 57.629 39.130 0.00 0.00 41.91 2.62
1622 1635 2.592102 ATCAGGCTTGCCTTTTGAGA 57.408 45.000 11.99 6.27 0.00 3.27
1696 1710 3.244215 TGCTACCTGATATAACCTGCTGC 60.244 47.826 0.00 0.00 0.00 5.25
1723 1737 6.017605 CCATTTGGATGCTGTTTAGCTACTAG 60.018 42.308 0.00 0.00 43.69 2.57
1724 1738 9.323484 CCATTTGGATGCTGTTTAGCTACTAGC 62.323 44.444 13.43 13.43 43.69 3.42
1756 1930 8.394971 ACAAAGAACATGACAGATACATTTCA 57.605 30.769 0.00 0.00 0.00 2.69
1775 1949 8.084073 ACATTTCATGAAAATAGAACACCACAG 58.916 33.333 23.91 3.66 35.77 3.66
2004 2181 7.327214 GGTATGATCTTCTCTCTTTTGACAGT 58.673 38.462 0.00 0.00 0.00 3.55
2008 2185 3.804325 TCTTCTCTCTTTTGACAGTTGCG 59.196 43.478 0.00 0.00 0.00 4.85
2019 2196 7.593273 TCTTTTGACAGTTGCGGTTTATATTTG 59.407 33.333 0.00 0.00 0.00 2.32
2067 2252 1.883638 GCAGAACCAGACAATCAGGCA 60.884 52.381 0.00 0.00 0.00 4.75
2068 2253 2.719739 CAGAACCAGACAATCAGGCAT 58.280 47.619 0.00 0.00 0.00 4.40
2070 2255 4.264253 CAGAACCAGACAATCAGGCATTA 58.736 43.478 0.00 0.00 0.00 1.90
2136 2321 7.879160 AGTAGGATCTACAGATACTCCTTTACG 59.121 40.741 7.25 0.00 41.82 3.18
2141 2326 7.934855 TCTACAGATACTCCTTTACGTCTTT 57.065 36.000 0.00 0.00 0.00 2.52
2206 2392 7.046652 CCTTCTGAATTCTGATATGTGTGAGT 58.953 38.462 14.89 0.00 0.00 3.41
2240 2426 7.174946 CCCTTGTTATCTTCTTAAGCTGAACAA 59.825 37.037 14.56 14.56 35.15 2.83
2286 2473 2.691409 TTGAAGGATCCCACACGATC 57.309 50.000 8.55 0.00 38.36 3.69
2295 2482 2.237751 CCACACGATCGGATTCGCC 61.238 63.158 20.98 0.00 42.82 5.54
2427 2614 0.944311 GTGGCGACGACAACATCAGT 60.944 55.000 4.13 0.00 0.00 3.41
2457 2644 1.597027 CCACACTTCCGCGACCTTT 60.597 57.895 8.23 0.00 0.00 3.11
2718 2905 3.304057 CCTTTGTTTGCGTCTTCTCCTTC 60.304 47.826 0.00 0.00 0.00 3.46
2803 2990 4.746951 CCGTCGTCGCGCTACACA 62.747 66.667 12.90 0.00 35.54 3.72
2914 3104 6.918569 CAGCAATGGATTCTGATCAGATTTTC 59.081 38.462 25.64 20.27 37.29 2.29
3105 3300 1.509548 CCATTCCAGGGAGTTGGGGT 61.510 60.000 10.15 0.00 38.81 4.95
3306 3501 1.293924 CCAGCAACGATGAGTCATCC 58.706 55.000 24.23 12.18 37.57 3.51
3369 3564 0.531974 TGAACTTGTGTGAGTCGGCC 60.532 55.000 0.00 0.00 0.00 6.13
3429 3624 1.376424 CAGCATGCGAACCACCTCT 60.376 57.895 13.01 0.00 0.00 3.69
3634 3833 2.916703 ATGGCAGGGCGTTTGCAA 60.917 55.556 0.00 0.00 45.35 4.08
3683 3882 3.940209 TCATTTCAGGTTGTTCCATGC 57.060 42.857 0.00 0.00 39.02 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.729690 GATCGGCAAAGTTCCTGCTC 59.270 55.000 0.00 0.00 39.82 4.26
25 26 3.008594 TCCTTCCTTTAACTGATCGGCAA 59.991 43.478 0.00 0.00 0.00 4.52
43 44 2.369532 TGCAGGTAAACCGTAACTCCTT 59.630 45.455 0.00 0.00 42.08 3.36
74 75 7.041721 GCTTAATGCCTAAAACAGCCTTTAAT 58.958 34.615 0.00 0.00 35.15 1.40
85 86 4.016444 CCCTGTCTGCTTAATGCCTAAAA 58.984 43.478 0.00 0.00 42.00 1.52
108 109 3.002791 TGCCTCTGAATGCTTCTTAACG 58.997 45.455 1.28 0.00 0.00 3.18
147 148 1.101331 GCCAGAGCCAATGAAAGGAG 58.899 55.000 0.00 0.00 0.00 3.69
162 163 3.002656 CAGTACAACAAGTGTCTTGCCAG 59.997 47.826 9.06 3.11 41.98 4.85
214 215 5.518865 TGGAATATCTGGAAAGAAAAGGGG 58.481 41.667 0.00 0.00 0.00 4.79
316 318 4.104696 ACCAGTGAGGAAAACAAAAACG 57.895 40.909 0.00 0.00 41.22 3.60
463 466 5.715439 TGTTAGATCACCTTCCCATGAAT 57.285 39.130 0.00 0.00 0.00 2.57
540 543 8.190122 TGAATGCCAACTAACAAAATATGCTAG 58.810 33.333 0.00 0.00 34.51 3.42
541 544 8.060931 TGAATGCCAACTAACAAAATATGCTA 57.939 30.769 0.00 0.00 0.00 3.49
542 545 6.934056 TGAATGCCAACTAACAAAATATGCT 58.066 32.000 0.00 0.00 0.00 3.79
606 609 6.589523 TGTTTTAAATCATTTGGATGCTTCCG 59.410 34.615 13.54 0.04 45.89 4.30
727 730 4.030216 TCTCTCTCTCTCTCTCTGTAGCA 58.970 47.826 0.00 0.00 0.00 3.49
870 873 4.084287 ACGTGGTGTATGGAGAGAAACTA 58.916 43.478 0.00 0.00 0.00 2.24
880 883 1.066430 ACAAGCCTACGTGGTGTATGG 60.066 52.381 0.00 0.00 38.35 2.74
919 922 3.243501 GGCAAGTTTCTTGTTCTGCATGA 60.244 43.478 0.00 0.00 0.00 3.07
1006 1009 2.428071 GAAGCACAACGCAGCTGC 60.428 61.111 29.12 29.12 46.13 5.25
1149 1152 4.819761 GCGCACTCCATCTCGGCA 62.820 66.667 0.30 0.00 33.14 5.69
1203 1206 2.106683 GTCGTGGAAATGGAGGCGG 61.107 63.158 0.00 0.00 0.00 6.13
1252 1255 0.310543 CTAGCGTGTGCAGGCAAAAA 59.689 50.000 17.32 1.69 46.23 1.94
1258 1261 1.499056 CAAAGCTAGCGTGTGCAGG 59.501 57.895 9.55 0.00 46.23 4.85
1271 1274 1.731969 CTTTCGCTGGCTGCAAAGC 60.732 57.895 16.76 14.49 43.06 3.51
1273 1276 1.313772 TTACTTTCGCTGGCTGCAAA 58.686 45.000 16.76 13.47 43.06 3.68
1275 1278 1.533625 AATTACTTTCGCTGGCTGCA 58.466 45.000 16.76 1.04 43.06 4.41
1276 1279 3.127030 ACTTAATTACTTTCGCTGGCTGC 59.873 43.478 6.26 6.26 38.57 5.25
1277 1280 4.946784 ACTTAATTACTTTCGCTGGCTG 57.053 40.909 0.00 0.00 0.00 4.85
1278 1281 5.699839 CAAACTTAATTACTTTCGCTGGCT 58.300 37.500 0.00 0.00 0.00 4.75
1281 1284 6.521133 CAGAGCAAACTTAATTACTTTCGCTG 59.479 38.462 11.96 0.00 0.00 5.18
1282 1285 6.426937 TCAGAGCAAACTTAATTACTTTCGCT 59.573 34.615 0.00 0.00 0.00 4.93
1283 1286 6.599437 TCAGAGCAAACTTAATTACTTTCGC 58.401 36.000 0.00 0.00 0.00 4.70
1284 1287 8.067784 TGTTCAGAGCAAACTTAATTACTTTCG 58.932 33.333 0.00 0.00 0.00 3.46
1285 1288 9.170584 GTGTTCAGAGCAAACTTAATTACTTTC 57.829 33.333 0.00 0.00 0.00 2.62
1286 1289 8.135529 GGTGTTCAGAGCAAACTTAATTACTTT 58.864 33.333 0.00 0.00 0.00 2.66
1287 1290 7.502561 AGGTGTTCAGAGCAAACTTAATTACTT 59.497 33.333 0.00 0.00 0.00 2.24
1288 1291 6.998673 AGGTGTTCAGAGCAAACTTAATTACT 59.001 34.615 0.00 0.00 0.00 2.24
1289 1292 7.041372 TCAGGTGTTCAGAGCAAACTTAATTAC 60.041 37.037 0.00 0.00 0.00 1.89
1290 1293 6.995686 TCAGGTGTTCAGAGCAAACTTAATTA 59.004 34.615 0.00 0.00 0.00 1.40
1291 1294 5.827797 TCAGGTGTTCAGAGCAAACTTAATT 59.172 36.000 0.00 0.00 0.00 1.40
1295 1307 3.281727 TCAGGTGTTCAGAGCAAACTT 57.718 42.857 0.00 0.00 0.00 2.66
1311 1323 3.556775 CCTGCAACAAACAAACATTCAGG 59.443 43.478 0.00 0.00 33.57 3.86
1380 1392 0.833409 TCTGGTCTGCCTGCTTCTCA 60.833 55.000 0.00 0.00 34.18 3.27
1531 1544 4.327680 ACTCTGAACATAGGTTTGGCTTC 58.672 43.478 0.00 0.00 37.36 3.86
1534 1547 5.009610 TGAAAACTCTGAACATAGGTTTGGC 59.990 40.000 7.71 0.00 37.36 4.52
1554 1567 2.309613 AGCCACTGCACAAGAATGAAA 58.690 42.857 0.00 0.00 41.13 2.69
1557 1570 3.921119 TTAAGCCACTGCACAAGAATG 57.079 42.857 0.00 0.00 41.13 2.67
1577 1590 2.504367 AGTGGTGCAAGCGAAAGTAAT 58.496 42.857 0.00 0.00 36.92 1.89
1585 1598 2.419673 TGATATGAAAGTGGTGCAAGCG 59.580 45.455 0.00 0.00 36.92 4.68
1647 1661 9.801873 GCAGGTTATAATGAAATACATGTTTGT 57.198 29.630 2.30 0.00 39.39 2.83
1655 1669 7.661847 AGGTAGCAGCAGGTTATAATGAAATAC 59.338 37.037 0.00 0.00 0.00 1.89
1696 1710 2.801063 CTAAACAGCATCCAAATGGCG 58.199 47.619 0.00 0.00 33.19 5.69
1723 1737 3.803231 TGTCATGTTCTTTGTTTGCATGC 59.197 39.130 11.82 11.82 37.44 4.06
1724 1738 5.283294 TCTGTCATGTTCTTTGTTTGCATG 58.717 37.500 0.00 0.00 38.49 4.06
1756 1930 5.940470 GGAGTCTGTGGTGTTCTATTTTCAT 59.060 40.000 0.00 0.00 0.00 2.57
1763 1937 5.519808 AGATATGGAGTCTGTGGTGTTCTA 58.480 41.667 0.00 0.00 0.00 2.10
1765 1939 4.744795 AGATATGGAGTCTGTGGTGTTC 57.255 45.455 0.00 0.00 0.00 3.18
1771 1945 6.890979 TGTCAGATAGATATGGAGTCTGTG 57.109 41.667 0.00 0.00 37.96 3.66
1775 1949 5.186797 CCCCTTGTCAGATAGATATGGAGTC 59.813 48.000 0.00 0.00 35.47 3.36
1801 1977 2.037121 CCCACCAACCTGAAACATTTCC 59.963 50.000 2.00 0.00 36.36 3.13
1802 1978 2.547855 GCCCACCAACCTGAAACATTTC 60.548 50.000 0.00 0.00 37.69 2.17
1850 2027 0.035630 CTTGCCTCCTTGGAGTCCAG 60.036 60.000 12.67 6.80 38.35 3.86
2036 2213 6.484364 TGTCTGGTTCTGCTGATATGAATA 57.516 37.500 0.00 0.00 0.00 1.75
2037 2214 5.363562 TGTCTGGTTCTGCTGATATGAAT 57.636 39.130 0.00 0.00 0.00 2.57
2045 2230 2.082231 CCTGATTGTCTGGTTCTGCTG 58.918 52.381 0.00 0.00 31.65 4.41
2047 2232 0.807496 GCCTGATTGTCTGGTTCTGC 59.193 55.000 5.04 0.00 37.74 4.26
2108 2293 8.700439 AAAGGAGTATCTGTAGATCCTACTTC 57.300 38.462 11.09 3.75 39.74 3.01
2240 2426 7.716560 TGCAAATGTCATATGTCTAGTAAGCAT 59.283 33.333 1.90 0.00 0.00 3.79
2250 2437 6.798482 TCCTTCAATGCAAATGTCATATGTC 58.202 36.000 1.90 0.00 0.00 3.06
2295 2482 4.383602 CGGAAGTTTGCGCACCGG 62.384 66.667 24.14 0.00 39.92 5.28
2304 2491 3.069158 CGTATATCCTGTCCCGGAAGTTT 59.931 47.826 0.73 0.00 36.49 2.66
2427 2614 2.282391 GTGTGGCTGTCCATGGCA 60.282 61.111 6.96 7.80 45.62 4.92
2457 2644 2.602878 GTCTCGAAATAGGCGTTGTCA 58.397 47.619 0.00 0.00 0.00 3.58
2559 2746 1.809684 GGTCAGCCCAGTACTTGTTC 58.190 55.000 0.00 0.00 0.00 3.18
2718 2905 2.679336 TGCAGACAATCATCAACCATCG 59.321 45.455 0.00 0.00 0.00 3.84
2786 2973 4.746951 TGTGTAGCGCGACGACGG 62.747 66.667 12.10 0.48 40.15 4.79
2803 2990 9.646522 ATTACTCCATACAGCCAAAATATTTCT 57.353 29.630 0.10 0.00 0.00 2.52
2914 3104 3.624326 TTTCAGATTGAAACAGGTGCG 57.376 42.857 0.36 0.00 41.02 5.34
3105 3300 5.571285 AGATGAAGTGTACACAGGAGAGTA 58.429 41.667 27.06 5.62 0.00 2.59
3306 3501 0.179150 GCTGCTACTCTGACCTGACG 60.179 60.000 0.00 0.00 0.00 4.35
3429 3624 3.770040 CACCGGCCGAGGATGTCA 61.770 66.667 30.73 0.00 34.73 3.58
3634 3833 6.636850 GCACTTTTGTCGAAACTGTTCATAAT 59.363 34.615 0.00 0.00 32.89 1.28


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

AutoCloner maintained by Alex Coulton.