Multiple sequence alignment - TraesCS7D01G439100

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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 TraesCS7D01G439100 chr7D 100.000 2528 0 0 1 2528 558889292 558886765 0.000000e+00 4669
1 TraesCS7D01G439100 chr7D 97.588 622 15 0 1907 2528 558865848 558865227 0.000000e+00 1066
2 TraesCS7D01G439100 chr7D 77.505 529 74 26 969 1478 7453850 7454352 2.480000e-70 276
3 TraesCS7D01G439100 chr7D 79.880 333 58 9 86 415 213103788 213104114 4.200000e-58 235
4 TraesCS7D01G439100 chr7D 78.962 366 62 14 56 415 318640569 318640925 4.200000e-58 235
5 TraesCS7D01G439100 chr6D 92.886 1715 106 9 199 1899 1540632 1538920 0.000000e+00 2477
6 TraesCS7D01G439100 chr6D 85.537 1369 165 15 546 1899 8140130 8141480 0.000000e+00 1400
7 TraesCS7D01G439100 chr6D 84.451 328 45 3 546 868 438475 438801 4.060000e-83 318
8 TraesCS7D01G439100 chr6D 93.642 173 5 3 3 169 1541419 1541247 1.160000e-63 254
9 TraesCS7D01G439100 chr6B 92.005 1751 119 16 157 1899 5716098 5714361 0.000000e+00 2438
10 TraesCS7D01G439100 chr6B 85.579 1373 147 23 546 1899 15105625 15106965 0.000000e+00 1391
11 TraesCS7D01G439100 chr6B 77.426 948 174 24 556 1498 2122535 2123447 1.720000e-146 529
12 TraesCS7D01G439100 chr6B 88.793 116 6 6 15 123 5716212 5716097 4.390000e-28 135
13 TraesCS7D01G439100 chr6A 85.142 1373 165 17 546 1899 8608627 8609979 0.000000e+00 1369
14 TraesCS7D01G439100 chr6A 85.456 1272 148 20 546 1801 8387520 8388770 0.000000e+00 1290
15 TraesCS7D01G439100 chr5B 84.949 1382 156 30 546 1899 132587809 132589166 0.000000e+00 1352
16 TraesCS7D01G439100 chr5D 84.626 1405 163 26 546 1899 119658793 119660195 0.000000e+00 1349
17 TraesCS7D01G439100 chr5D 83.264 478 63 16 78 545 206587687 206588157 8.360000e-115 424
18 TraesCS7D01G439100 chr5D 85.204 196 22 7 112 304 500356505 500356696 7.140000e-46 195
19 TraesCS7D01G439100 chr5A 84.682 1384 176 18 546 1899 129749102 129750479 0.000000e+00 1349
20 TraesCS7D01G439100 chr3D 97.910 622 13 0 1907 2528 545327258 545327879 0.000000e+00 1077
21 TraesCS7D01G439100 chr3D 97.267 622 17 0 1907 2528 22059027 22058406 0.000000e+00 1055
22 TraesCS7D01G439100 chr3D 97.267 622 17 0 1907 2528 604324896 604325517 0.000000e+00 1055
23 TraesCS7D01G439100 chr2D 97.432 623 14 2 1907 2528 386685439 386684818 0.000000e+00 1061
24 TraesCS7D01G439100 chr2D 97.111 623 16 2 1907 2528 542085126 542084505 0.000000e+00 1050
25 TraesCS7D01G439100 chr2D 96.950 623 17 2 1907 2528 641905242 641905863 0.000000e+00 1044
26 TraesCS7D01G439100 chr4D 97.106 622 18 0 1907 2528 228301557 228302178 0.000000e+00 1050
27 TraesCS7D01G439100 chr1D 97.106 622 18 0 1907 2528 385637828 385637207 0.000000e+00 1050
28 TraesCS7D01G439100 chr1D 86.313 453 55 7 99 548 100666984 100666536 1.050000e-133 486
29 TraesCS7D01G439100 chr3B 84.928 418 50 11 137 548 123673783 123673373 6.510000e-111 411
30 TraesCS7D01G439100 chr3B 74.312 436 78 30 98 516 491261151 491260733 1.210000e-33 154
31 TraesCS7D01G439100 chr3A 82.522 452 54 16 100 545 91460653 91461085 8.540000e-100 374
32 TraesCS7D01G439100 chr3A 83.851 322 48 4 1581 1899 623942460 623942780 1.140000e-78 303
33 TraesCS7D01G439100 chr7A 81.311 412 59 12 951 1358 8381207 8381604 4.060000e-83 318


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 TraesCS7D01G439100 chr7D 558886765 558889292 2527 True 4669.0 4669 100.000 1 2528 1 chr7D.!!$R2 2527
1 TraesCS7D01G439100 chr7D 558865227 558865848 621 True 1066.0 1066 97.588 1907 2528 1 chr7D.!!$R1 621
2 TraesCS7D01G439100 chr7D 7453850 7454352 502 False 276.0 276 77.505 969 1478 1 chr7D.!!$F1 509
3 TraesCS7D01G439100 chr6D 8140130 8141480 1350 False 1400.0 1400 85.537 546 1899 1 chr6D.!!$F2 1353
4 TraesCS7D01G439100 chr6D 1538920 1541419 2499 True 1365.5 2477 93.264 3 1899 2 chr6D.!!$R1 1896
5 TraesCS7D01G439100 chr6B 15105625 15106965 1340 False 1391.0 1391 85.579 546 1899 1 chr6B.!!$F2 1353
6 TraesCS7D01G439100 chr6B 5714361 5716212 1851 True 1286.5 2438 90.399 15 1899 2 chr6B.!!$R1 1884
7 TraesCS7D01G439100 chr6B 2122535 2123447 912 False 529.0 529 77.426 556 1498 1 chr6B.!!$F1 942
8 TraesCS7D01G439100 chr6A 8608627 8609979 1352 False 1369.0 1369 85.142 546 1899 1 chr6A.!!$F2 1353
9 TraesCS7D01G439100 chr6A 8387520 8388770 1250 False 1290.0 1290 85.456 546 1801 1 chr6A.!!$F1 1255
10 TraesCS7D01G439100 chr5B 132587809 132589166 1357 False 1352.0 1352 84.949 546 1899 1 chr5B.!!$F1 1353
11 TraesCS7D01G439100 chr5D 119658793 119660195 1402 False 1349.0 1349 84.626 546 1899 1 chr5D.!!$F1 1353
12 TraesCS7D01G439100 chr5A 129749102 129750479 1377 False 1349.0 1349 84.682 546 1899 1 chr5A.!!$F1 1353
13 TraesCS7D01G439100 chr3D 545327258 545327879 621 False 1077.0 1077 97.910 1907 2528 1 chr3D.!!$F1 621
14 TraesCS7D01G439100 chr3D 22058406 22059027 621 True 1055.0 1055 97.267 1907 2528 1 chr3D.!!$R1 621
15 TraesCS7D01G439100 chr3D 604324896 604325517 621 False 1055.0 1055 97.267 1907 2528 1 chr3D.!!$F2 621
16 TraesCS7D01G439100 chr2D 386684818 386685439 621 True 1061.0 1061 97.432 1907 2528 1 chr2D.!!$R1 621
17 TraesCS7D01G439100 chr2D 542084505 542085126 621 True 1050.0 1050 97.111 1907 2528 1 chr2D.!!$R2 621
18 TraesCS7D01G439100 chr2D 641905242 641905863 621 False 1044.0 1044 96.950 1907 2528 1 chr2D.!!$F1 621
19 TraesCS7D01G439100 chr4D 228301557 228302178 621 False 1050.0 1050 97.106 1907 2528 1 chr4D.!!$F1 621
20 TraesCS7D01G439100 chr1D 385637207 385637828 621 True 1050.0 1050 97.106 1907 2528 1 chr1D.!!$R2 621

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
609 1202 0.324645 GAGGGATGGGGTTGCATGTT 60.325 55.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2973 0.593128 GTTGTCGCAACCAGATGCTT 59.407 50.0 10.43 0.0 44.21 3.91 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
94 101 7.502561 CCAGGTTTCTTCTTTCCTTTTCTCTTA 59.497 37.037 0.00 0.0 0.00 2.10
169 176 3.450457 ACAAGATTCAAAACCAGTGCCAA 59.550 39.130 0.00 0.0 0.00 4.52
208 800 1.423541 TGTTGCCACAATGGACCTAGT 59.576 47.619 0.00 0.0 40.96 2.57
368 960 2.926778 TCAAAACCCTTGCCCAAATG 57.073 45.000 0.00 0.0 0.00 2.32
401 993 9.472361 CATCAATGAAGGAATTTATGGAATCAC 57.528 33.333 0.00 0.0 0.00 3.06
442 1034 9.073475 GGGTGCTTTTCCCTTTTATTTAATTTT 57.927 29.630 0.00 0.0 41.58 1.82
470 1062 9.352191 TGTTTTGAAAAATTCCATCAATTCCAT 57.648 25.926 0.00 0.0 33.16 3.41
478 1070 9.577222 AAAATTCCATCAATTCCATTTTCTTGT 57.423 25.926 0.00 0.0 33.16 3.16
498 1090 8.929827 TCTTGTATTTAAACATGATGCAATGG 57.070 30.769 0.00 0.0 30.93 3.16
499 1091 8.530311 TCTTGTATTTAAACATGATGCAATGGT 58.470 29.630 0.00 0.0 30.93 3.55
537 1129 4.654091 TTTGCTGGCAATATTCTAAGGC 57.346 40.909 8.86 0.0 35.70 4.35
608 1201 1.307647 GAGGGATGGGGTTGCATGT 59.692 57.895 0.00 0.0 0.00 3.21
609 1202 0.324645 GAGGGATGGGGTTGCATGTT 60.325 55.000 0.00 0.0 0.00 2.71
678 1276 7.207383 GCATTCTTTTTGTAAAAGTACCACCT 58.793 34.615 10.65 0.0 0.00 4.00
824 1425 4.171005 TCGTTTCCTTGTGATGTACGATC 58.829 43.478 0.00 0.0 31.19 3.69
921 1533 3.829026 GCAACCAAATCTTTCCTCTCCTT 59.171 43.478 0.00 0.0 0.00 3.36
923 1535 5.221521 GCAACCAAATCTTTCCTCTCCTTTT 60.222 40.000 0.00 0.0 0.00 2.27
924 1536 6.218746 CAACCAAATCTTTCCTCTCCTTTTG 58.781 40.000 0.00 0.0 0.00 2.44
927 1539 2.185004 TCTTTCCTCTCCTTTTGCGG 57.815 50.000 0.00 0.0 0.00 5.69
928 1540 1.420138 TCTTTCCTCTCCTTTTGCGGT 59.580 47.619 0.00 0.0 0.00 5.68
1012 1640 2.885113 CAGTGATGGCGACCTCGA 59.115 61.111 0.00 0.0 43.02 4.04
1129 1780 3.275999 CACATGATTGAGGATGACTGCA 58.724 45.455 0.00 0.0 0.00 4.41
1309 1960 0.250234 CCTCAAGATCTGGGACGCAA 59.750 55.000 0.00 0.0 0.00 4.85
1323 1974 3.306019 GGGACGCAAAATTCATCAAGGTT 60.306 43.478 0.00 0.0 0.00 3.50
1389 2040 5.385509 TGATTCGACCATTTCCTTTTTCC 57.614 39.130 0.00 0.0 0.00 3.13
1446 2113 1.517242 GATCTAGATTGGGCTTGCGG 58.483 55.000 6.70 0.0 0.00 5.69
1485 2152 2.820728 TAGATTGGACGGACTCCTCA 57.179 50.000 0.00 0.0 40.26 3.86
1666 2345 9.435688 ACATGTGTATATCATTGTTATGCGTAT 57.564 29.630 0.00 0.0 0.00 3.06
1881 2569 5.106197 TGGCTTGTAACACATCTTAATGCAG 60.106 40.000 0.00 0.0 36.26 4.41
1901 2589 9.717942 AATGCAGGACAATCTATCTAATTACTC 57.282 33.333 0.00 0.0 0.00 2.59
1902 2590 8.250143 TGCAGGACAATCTATCTAATTACTCA 57.750 34.615 0.00 0.0 0.00 3.41
1903 2591 8.874156 TGCAGGACAATCTATCTAATTACTCAT 58.126 33.333 0.00 0.0 0.00 2.90
1946 2634 4.383774 CACACAAACGTGTACGATCAAT 57.616 40.909 11.79 0.0 45.90 2.57
2021 2710 9.618890 AAGTCATACAAGCATCATAATACAAGT 57.381 29.630 0.00 0.0 0.00 3.16
2160 2849 2.365617 GGGATACAGATCGAAAGAGGCA 59.634 50.000 0.00 0.0 41.83 4.75
2284 2973 3.005539 GTCTGGCTCCTGGGCTCA 61.006 66.667 7.03 0.0 41.48 4.26
2524 3213 3.570540 TGCAGCATGTAGGAGAGAGTAT 58.429 45.455 0.00 0.0 39.31 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.264749 TGCTAGGAGGACGGCAACAT 61.265 55.000 0.00 0.00 31.86 2.71
2 3 1.153549 CTGCTAGGAGGACGGCAAC 60.154 63.158 2.75 0.00 33.76 4.17
3 4 3.019003 GCTGCTAGGAGGACGGCAA 62.019 63.158 13.67 0.00 35.72 4.52
5 6 3.438017 CTGCTGCTAGGAGGACGGC 62.438 68.421 13.67 2.30 36.21 5.68
6 7 2.811101 CTGCTGCTAGGAGGACGG 59.189 66.667 13.67 0.00 29.18 4.79
36 37 2.825982 CAACCGGTCCAGTCCACA 59.174 61.111 8.04 0.00 0.00 4.17
169 176 9.851686 TGGCAACATATATATTTCAGAGAAGTT 57.148 29.630 0.00 0.00 46.17 2.66
208 800 8.881743 GCCTTGAAATAATTTATGTGCATTTGA 58.118 29.630 0.00 0.00 0.00 2.69
401 993 7.148423 GGAAAAGCACCCTAAAAATGCATTTAG 60.148 37.037 24.35 18.04 39.55 1.85
444 1036 8.743085 TGGAATTGATGGAATTTTTCAAAACA 57.257 26.923 3.69 0.00 34.18 2.83
533 1125 0.037303 CATGGAGGTGTCACAGCCTT 59.963 55.000 2.57 1.03 34.81 4.35
534 1126 1.681666 CATGGAGGTGTCACAGCCT 59.318 57.895 2.57 0.56 37.91 4.58
537 1129 1.827344 TCTAGCATGGAGGTGTCACAG 59.173 52.381 5.12 0.00 0.00 3.66
678 1276 0.108804 GTAGCGCACACAAGGCTAGA 60.109 55.000 11.47 0.00 39.72 2.43
786 1387 4.638865 GGAAACGAAGCCAAGTATTACCAT 59.361 41.667 0.00 0.00 0.00 3.55
824 1425 2.794910 ACGCGTGATTGGAAATCTATCG 59.205 45.455 12.93 5.43 31.66 2.92
1012 1640 0.247736 ATCTTCTTCTCGCCTGCGTT 59.752 50.000 11.68 0.00 40.74 4.84
1103 1754 0.548031 ATCCTCAATCATGTGGCGGT 59.452 50.000 0.00 0.00 39.54 5.68
1129 1780 0.620556 ATCGGGATGGCTTTGTCAGT 59.379 50.000 0.00 0.00 0.00 3.41
1281 1932 0.827368 AGATCTTGAGGTCTTCGGCC 59.173 55.000 0.00 0.00 0.00 6.13
1309 1960 5.248020 TGGCATGGTTAACCTTGATGAATTT 59.752 36.000 33.54 4.26 42.04 1.82
1323 1974 0.251916 CGAAGAGGGTGGCATGGTTA 59.748 55.000 0.00 0.00 0.00 2.85
1403 2054 0.776810 TGCCAGAAGGGGAACATGAA 59.223 50.000 0.00 0.00 37.04 2.57
1405 2056 0.038744 AGTGCCAGAAGGGGAACATG 59.961 55.000 0.00 0.00 39.14 3.21
1576 2248 2.572290 ACTAGGATTTTGTATGGCCGC 58.428 47.619 0.00 0.00 0.00 6.53
1666 2345 8.370940 CACTGATCATAATAAAGCTTCCTAGGA 58.629 37.037 7.62 7.62 0.00 2.94
1903 2591 9.292846 GTGTGTATGATTAGTGTACGATTGTTA 57.707 33.333 0.00 0.00 0.00 2.41
1904 2592 7.815549 TGTGTGTATGATTAGTGTACGATTGTT 59.184 33.333 0.00 0.00 0.00 2.83
1905 2593 7.317390 TGTGTGTATGATTAGTGTACGATTGT 58.683 34.615 0.00 0.00 0.00 2.71
1946 2634 1.286849 TCTTCCCGTGAGTCCCTGATA 59.713 52.381 0.00 0.00 0.00 2.15
2284 2973 0.593128 GTTGTCGCAACCAGATGCTT 59.407 50.000 10.43 0.00 44.21 3.91


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

AutoCloner maintained by Alex Coulton.