Multiple sequence alignment - TraesCS7B01G404100

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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 TraesCS7B01G404100 chr7B 100.000 2507 0 0 1 2507 672396417 672393911 0.000000e+00 4630.0
1 TraesCS7B01G404100 chr7D 91.910 2361 120 31 1 2337 591294716 591297029 0.000000e+00 3236.0
2 TraesCS7B01G404100 chr7A 93.187 1864 85 16 680 2507 681818241 681820098 0.000000e+00 2700.0
3 TraesCS7B01G404100 chr7A 91.411 652 42 8 1 646 681817605 681818248 0.000000e+00 881.0
4 TraesCS7B01G404100 chr7A 100.000 31 0 0 387 417 681817958 681817988 9.690000e-05 58.4
5 TraesCS7B01G404100 chr2D 87.460 311 30 5 1729 2039 601290062 601289761 1.430000e-92 350.0
6 TraesCS7B01G404100 chr2B 85.852 311 35 3 1729 2039 730534751 730534450 3.110000e-84 322.0


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 TraesCS7B01G404100 chr7B 672393911 672396417 2506 True 4630.000000 4630 100.000 1 2507 1 chr7B.!!$R1 2506
1 TraesCS7B01G404100 chr7D 591294716 591297029 2313 False 3236.000000 3236 91.910 1 2337 1 chr7D.!!$F1 2336
2 TraesCS7B01G404100 chr7A 681817605 681820098 2493 False 1213.133333 2700 94.866 1 2507 3 chr7A.!!$F1 2506

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
29 30 1.851021 TTGCGTGTTCAATCTGCCGG 61.851 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 1954 0.037326 TCTTCTTTGACATCGCCGCT 60.037 50.0 0.0 0.0 0.0 5.52 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
29 30 1.851021 TTGCGTGTTCAATCTGCCGG 61.851 55.000 0.00 0.00 0.00 6.13
30 31 3.039202 GCGTGTTCAATCTGCCGGG 62.039 63.158 2.18 0.00 0.00 5.73
34 35 2.751436 TTCAATCTGCCGGGCTGC 60.751 61.111 21.46 0.00 0.00 5.25
43 44 3.865383 CCGGGCTGCCAGCTATCA 61.865 66.667 22.05 0.00 41.99 2.15
44 45 2.190313 CGGGCTGCCAGCTATCAA 59.810 61.111 22.05 0.00 41.99 2.57
67 70 2.629137 TGTGTCCGCCTTACAACTAGAA 59.371 45.455 0.00 0.00 0.00 2.10
110 113 9.713740 GTGCTGAAAAATGAATACTTAGATGAG 57.286 33.333 0.00 0.00 0.00 2.90
111 114 9.453572 TGCTGAAAAATGAATACTTAGATGAGT 57.546 29.630 0.00 0.00 0.00 3.41
289 294 6.707161 TGTGTTAATAAACAGTCGCTTAACCT 59.293 34.615 0.00 0.00 46.06 3.50
325 332 5.354513 GCTACCTACTTTTGATCCAGGTTTC 59.645 44.000 0.00 0.00 40.14 2.78
430 439 7.557358 TGCATACAAAGATCCTGTGATTATGTT 59.443 33.333 8.05 0.00 0.00 2.71
435 444 7.888021 ACAAAGATCCTGTGATTATGTTAACCA 59.112 33.333 2.48 0.00 0.00 3.67
460 469 9.294030 CAATTAACTTGATTAATCTCAACCTGC 57.706 33.333 16.24 0.00 41.73 4.85
466 475 4.721776 TGATTAATCTCAACCTGCCTACCT 59.278 41.667 16.24 0.00 0.00 3.08
480 489 2.355108 GCCTACCTGCTGTTGATCTCAA 60.355 50.000 0.00 0.00 0.00 3.02
591 600 8.380867 AGATGCACATAAAGATCATAGATCCAA 58.619 33.333 3.52 0.00 0.00 3.53
592 601 7.974482 TGCACATAAAGATCATAGATCCAAG 57.026 36.000 3.52 0.00 0.00 3.61
593 602 6.429078 TGCACATAAAGATCATAGATCCAAGC 59.571 38.462 3.52 0.00 0.00 4.01
616 625 5.629849 GCAGCCTGTCATAGTTATTACTACG 59.370 44.000 0.00 0.00 39.59 3.51
685 694 7.192148 TGGAAAGAAAAATATTGTTCGTCGA 57.808 32.000 11.85 8.56 0.00 4.20
739 748 5.072600 TGGGGACTAAACTCTAAACACACAT 59.927 40.000 0.00 0.00 0.00 3.21
877 886 7.630242 TTAAAGATCTTCATGGTGGAATCAC 57.370 36.000 8.78 0.00 42.91 3.06
1054 1063 0.244994 CTTCACTCTCCTGACCACGG 59.755 60.000 0.00 0.00 0.00 4.94
1056 1065 3.374402 ACTCTCCTGACCACGGCG 61.374 66.667 4.80 4.80 0.00 6.46
1212 1221 4.335647 ACACCCGGCAGCAAGGAG 62.336 66.667 6.94 1.69 0.00 3.69
1225 1234 0.809385 CAAGGAGTACGAGCTTCGGA 59.191 55.000 9.75 0.00 45.59 4.55
1257 1272 1.012562 CGACGACGACGATGACGAT 60.013 57.895 15.32 0.00 41.06 3.73
1392 1413 3.963687 CTCGTGCATCTGCCAGGCA 62.964 63.158 15.23 15.23 41.18 4.75
1523 1544 4.391216 GGGCTGATCTCATTACATTGATCG 59.609 45.833 0.00 0.00 38.40 3.69
1543 1564 5.580911 TCGATTGATTGCGATTATGTCTG 57.419 39.130 0.00 0.00 0.00 3.51
1556 1577 5.523552 CGATTATGTCTGCTACACCAAATCA 59.476 40.000 15.93 0.00 42.09 2.57
1589 1610 7.966753 CACATTCCTTACACAGAGATTGAATTG 59.033 37.037 0.00 0.00 0.00 2.32
1590 1611 7.884877 ACATTCCTTACACAGAGATTGAATTGA 59.115 33.333 0.00 0.00 0.00 2.57
1591 1612 8.900781 CATTCCTTACACAGAGATTGAATTGAT 58.099 33.333 0.00 0.00 0.00 2.57
1593 1614 7.050377 TCCTTACACAGAGATTGAATTGATCC 58.950 38.462 0.00 0.00 0.00 3.36
1594 1615 6.825213 CCTTACACAGAGATTGAATTGATCCA 59.175 38.462 0.00 0.00 0.00 3.41
1595 1616 7.501559 CCTTACACAGAGATTGAATTGATCCAT 59.498 37.037 0.00 0.00 0.00 3.41
1596 1617 9.551734 CTTACACAGAGATTGAATTGATCCATA 57.448 33.333 0.00 0.00 0.00 2.74
1830 1860 2.315246 GATGAGATCGTTGCTGGCC 58.685 57.895 0.00 0.00 0.00 5.36
1956 1986 3.121030 GAAGACATGCACGGCGCT 61.121 61.111 6.90 0.00 43.06 5.92
2030 2063 6.266330 TGATTCGACTCATCAGATACAGGATT 59.734 38.462 0.65 0.00 0.00 3.01
2052 2100 3.011085 CTTGTGGCTCAAGTCTGCA 57.989 52.632 18.61 0.00 45.89 4.41
2055 2103 1.372683 GTGGCTCAAGTCTGCAGGA 59.627 57.895 15.13 1.70 0.00 3.86
2071 2122 3.554692 GAGACGCCGACGCAATGG 61.555 66.667 0.00 0.00 45.53 3.16
2092 2143 0.949105 AACCTGAACGTAGCCGCTTG 60.949 55.000 0.00 0.00 37.70 4.01
2121 2172 1.057285 CGCGTCACAAAGTCATCGTAC 59.943 52.381 0.00 0.00 0.00 3.67
2165 2216 1.526887 GGAAGGTGCCGATCCATCA 59.473 57.895 10.04 0.00 33.30 3.07
2245 2296 5.243060 TCATAGACTCCACGAAACTTTCTCA 59.757 40.000 0.00 0.00 0.00 3.27
2252 2303 3.202906 CACGAAACTTTCTCAAGGGTGA 58.797 45.455 0.00 0.00 33.82 4.02
2341 2396 5.106118 GCTTGAAGAATGGTTAGGGTTTCTC 60.106 44.000 0.00 0.00 0.00 2.87
2343 2398 5.805728 TGAAGAATGGTTAGGGTTTCTCTC 58.194 41.667 0.00 0.00 0.00 3.20
2365 2420 4.456911 TCGTGAGGAAGTTACGATAAGTGT 59.543 41.667 0.00 0.00 41.33 3.55
2372 2427 7.439381 AGGAAGTTACGATAAGTGTCTCAAAA 58.561 34.615 0.00 0.00 0.00 2.44
2377 2432 2.671396 CGATAAGTGTCTCAAAACCCGG 59.329 50.000 0.00 0.00 0.00 5.73
2406 2461 1.795162 CGCGTTCTGAATTTGGCATCC 60.795 52.381 0.00 0.00 0.00 3.51
2447 2504 4.626172 CCTCACTGCATATTCATCGAGATG 59.374 45.833 6.74 6.74 40.09 2.90
2475 2532 2.013563 GCCCATCATGTTTCTCGCTCA 61.014 52.381 0.00 0.00 0.00 4.26
2476 2533 2.569059 CCCATCATGTTTCTCGCTCAT 58.431 47.619 0.00 0.00 0.00 2.90
2485 2542 3.002246 TGTTTCTCGCTCATGTGAACAAC 59.998 43.478 0.00 0.69 31.75 3.32
2500 2557 4.097892 GTGAACAACCATTAATAGGCCTGG 59.902 45.833 17.99 10.61 34.84 4.45
2503 2560 5.142806 ACAACCATTAATAGGCCTGGATT 57.857 39.130 17.99 11.03 32.92 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.393537 ACACTTGATAGCTGGCAGCC 60.394 55.000 34.33 20.40 43.77 4.85
30 31 0.731417 CACACTTGATAGCTGGCAGC 59.269 55.000 31.56 31.56 42.84 5.25
34 35 1.645034 CGGACACACTTGATAGCTGG 58.355 55.000 0.00 0.00 0.00 4.85
41 42 0.753867 TGTAAGGCGGACACACTTGA 59.246 50.000 0.00 0.00 0.00 3.02
42 43 1.263217 GTTGTAAGGCGGACACACTTG 59.737 52.381 0.00 0.00 0.00 3.16
43 44 1.140252 AGTTGTAAGGCGGACACACTT 59.860 47.619 0.00 0.00 0.00 3.16
44 45 0.756903 AGTTGTAAGGCGGACACACT 59.243 50.000 0.00 0.57 0.00 3.55
67 70 2.142319 GCACGGTTTGAATGCCAAATT 58.858 42.857 0.00 0.00 45.48 1.82
110 113 0.606604 TAGAAAGGAGCCGGACACAC 59.393 55.000 5.05 0.00 0.00 3.82
111 114 0.895530 CTAGAAAGGAGCCGGACACA 59.104 55.000 5.05 0.00 0.00 3.72
207 212 0.319297 CCACTTTGGCTGCAGCTTTC 60.319 55.000 35.82 21.24 41.70 2.62
265 270 7.013529 CAGGTTAAGCGACTGTTTATTAACAC 58.986 38.462 17.03 10.67 39.29 3.32
289 294 2.174210 AGTAGGTAGCTATGTCGGGACA 59.826 50.000 4.71 3.69 46.44 4.02
325 332 1.442148 GCCAAGAGGGGTAGCTACG 59.558 63.158 17.48 2.51 37.04 3.51
363 372 7.976135 ACTGGATCTTTATATGCATCTTGTC 57.024 36.000 0.19 0.00 0.00 3.18
433 442 9.793252 CAGGTTGAGATTAATCAAGTTAATTGG 57.207 33.333 17.56 0.00 41.82 3.16
435 444 8.470002 GGCAGGTTGAGATTAATCAAGTTAATT 58.530 33.333 17.56 0.00 41.82 1.40
460 469 3.616956 TTGAGATCAACAGCAGGTAGG 57.383 47.619 0.00 0.00 0.00 3.18
466 475 2.294233 GGCAGTTTTGAGATCAACAGCA 59.706 45.455 11.41 0.00 37.19 4.41
480 489 2.745968 TGAAACAAAGAGGGGCAGTTT 58.254 42.857 0.00 0.00 35.33 2.66
591 600 5.878406 AGTAATAACTATGACAGGCTGCT 57.122 39.130 15.89 1.32 32.84 4.24
592 601 5.629849 CGTAGTAATAACTATGACAGGCTGC 59.370 44.000 15.89 8.22 44.74 5.25
593 602 6.967135 TCGTAGTAATAACTATGACAGGCTG 58.033 40.000 14.16 14.16 45.27 4.85
640 649 7.643569 TCCATAATGACATGCTACATTTGTT 57.356 32.000 15.06 3.40 37.75 2.83
685 694 2.038557 ACGTATTCTTGCACCTGAGGTT 59.961 45.455 0.00 0.00 31.02 3.50
739 748 9.628500 ATGCACGGTATATCTAGTGATAATCTA 57.372 33.333 0.00 0.00 38.50 1.98
847 856 8.421249 TCCACCATGAAGATCTTTAAACAATT 57.579 30.769 9.87 0.00 0.00 2.32
1056 1065 3.640000 CCATCCGCGAACCGATGC 61.640 66.667 8.23 0.00 40.02 3.91
1212 1221 2.101770 CGGGTCCGAAGCTCGTAC 59.898 66.667 2.83 0.00 42.83 3.67
1247 1262 1.137086 CCCCTTCTTCATCGTCATCGT 59.863 52.381 0.00 0.00 38.33 3.73
1248 1263 1.539065 CCCCCTTCTTCATCGTCATCG 60.539 57.143 0.00 0.00 38.55 3.84
1249 1264 1.762957 TCCCCCTTCTTCATCGTCATC 59.237 52.381 0.00 0.00 0.00 2.92
1257 1272 0.685097 CGTGTTCTCCCCCTTCTTCA 59.315 55.000 0.00 0.00 0.00 3.02
1314 1329 4.980805 GGGTCGCTGTTGTCGGCA 62.981 66.667 0.00 0.00 45.42 5.69
1404 1425 2.100631 CGAGGTCATGAACACCGGC 61.101 63.158 14.46 1.19 39.13 6.13
1523 1544 5.354054 AGCAGACATAATCGCAATCAATC 57.646 39.130 0.00 0.00 31.70 2.67
1543 1564 4.455533 TGTGAACTGATGATTTGGTGTAGC 59.544 41.667 0.00 0.00 0.00 3.58
1556 1577 6.014242 TCTCTGTGTAAGGAATGTGAACTGAT 60.014 38.462 0.00 0.00 0.00 2.90
1659 1685 6.094603 TCCGACTTCAGTTAAGGATGTAGTAC 59.905 42.308 0.00 0.00 39.73 2.73
1660 1686 6.182627 TCCGACTTCAGTTAAGGATGTAGTA 58.817 40.000 0.00 0.00 39.73 1.82
1661 1687 5.014858 TCCGACTTCAGTTAAGGATGTAGT 58.985 41.667 0.00 0.00 39.73 2.73
1662 1688 5.578005 TCCGACTTCAGTTAAGGATGTAG 57.422 43.478 0.00 0.00 39.73 2.74
1663 1689 5.220989 CGATCCGACTTCAGTTAAGGATGTA 60.221 44.000 13.80 0.00 39.73 2.29
1664 1690 4.440250 CGATCCGACTTCAGTTAAGGATGT 60.440 45.833 13.80 0.00 39.73 3.06
1668 1694 3.777465 TCGATCCGACTTCAGTTAAGG 57.223 47.619 0.00 0.00 39.73 2.69
1720 1750 1.658717 CGCTCGCTAGTTCCGGATG 60.659 63.158 4.15 0.00 0.00 3.51
1875 1905 1.666011 CCATGAGGCGCTACCGTAT 59.334 57.895 7.64 0.00 46.52 3.06
1924 1954 0.037326 TCTTCTTTGACATCGCCGCT 60.037 50.000 0.00 0.00 0.00 5.52
2052 2100 3.760035 ATTGCGTCGGCGTCTCCT 61.760 61.111 12.58 0.00 44.10 3.69
2065 2116 0.878416 TACGTTCAGGTTGCCATTGC 59.122 50.000 0.00 0.00 38.26 3.56
2071 2122 3.023591 GCGGCTACGTTCAGGTTGC 62.024 63.158 0.00 0.00 43.45 4.17
2165 2216 3.760035 ATCGCCTCAACGTCCGCT 61.760 61.111 0.00 0.00 0.00 5.52
2220 2271 5.715070 AGAAAGTTTCGTGGAGTCTATGAG 58.285 41.667 9.91 0.00 34.02 2.90
2229 2280 2.171870 ACCCTTGAGAAAGTTTCGTGGA 59.828 45.455 9.91 0.00 34.02 4.02
2245 2296 3.165071 CCAAAGTGGCTAAATCACCCTT 58.835 45.455 0.00 0.00 35.87 3.95
2341 2396 5.029014 CACTTATCGTAACTTCCTCACGAG 58.971 45.833 2.41 0.00 46.60 4.18
2343 2398 4.730657 ACACTTATCGTAACTTCCTCACG 58.269 43.478 0.00 0.00 37.03 4.35
2365 2420 0.322322 ATGCGTACCGGGTTTTGAGA 59.678 50.000 4.31 0.00 0.00 3.27
2406 2461 0.385390 GGCAACAACAACAGGTCCAG 59.615 55.000 0.00 0.00 0.00 3.86
2447 2504 2.283145 AACATGATGGGCCTATGCTC 57.717 50.000 6.22 0.00 38.98 4.26
2475 2532 5.360714 CAGGCCTATTAATGGTTGTTCACAT 59.639 40.000 3.98 0.00 0.00 3.21
2476 2533 4.704540 CAGGCCTATTAATGGTTGTTCACA 59.295 41.667 3.98 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.