Multiple sequence alignment - TraesCS7B01G060600

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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 TraesCS7B01G060600 chr7B 100.000 2627 0 0 1 2627 63493088 63495714 0.000000e+00 4852
1 TraesCS7B01G060600 chr7B 92.540 496 35 2 2131 2625 63394683 63395177 0.000000e+00 710
2 TraesCS7B01G060600 chr7B 83.662 710 78 15 1668 2341 63541504 63542211 3.690000e-178 634
3 TraesCS7B01G060600 chr7B 90.380 395 30 2 1680 2066 63394282 63394676 1.800000e-141 512
4 TraesCS7B01G060600 chr7B 90.592 287 25 2 2343 2627 277705628 277705342 1.910000e-101 379
5 TraesCS7B01G060600 chr3B 97.792 1676 33 2 1 1675 773547014 773548686 0.000000e+00 2887
6 TraesCS7B01G060600 chr1B 97.733 1676 34 2 1 1675 669918195 669919867 0.000000e+00 2881
7 TraesCS7B01G060600 chr1B 97.491 1674 36 3 4 1676 418167221 418165553 0.000000e+00 2854
8 TraesCS7B01G060600 chr1B 91.103 281 24 1 2346 2625 159930705 159930425 1.910000e-101 379
9 TraesCS7B01G060600 chr5A 97.549 1673 37 2 4 1675 536712251 536710582 0.000000e+00 2859
10 TraesCS7B01G060600 chr7A 97.373 1675 38 3 4 1675 30716177 30714506 0.000000e+00 2844
11 TraesCS7B01G060600 chr7A 94.095 1304 69 5 375 1674 667967885 667966586 0.000000e+00 1975
12 TraesCS7B01G060600 chr7A 83.211 679 80 16 1685 2341 109238137 109237471 2.250000e-165 592
13 TraesCS7B01G060600 chr2A 96.294 1673 56 4 4 1675 40957564 40955897 0.000000e+00 2741
14 TraesCS7B01G060600 chr2A 95.723 1356 52 4 323 1675 722079736 722078384 0.000000e+00 2178
15 TraesCS7B01G060600 chr2A 83.500 600 95 4 1 598 407750226 407750823 8.210000e-155 556
16 TraesCS7B01G060600 chr1A 93.787 1674 91 9 4 1675 592501705 592500043 0.000000e+00 2503
17 TraesCS7B01G060600 chr7D 85.987 628 66 7 1732 2341 104741834 104741211 0.000000e+00 652
18 TraesCS7B01G060600 chr1D 91.638 287 22 1 2343 2627 409784003 409783717 1.890000e-106 396
19 TraesCS7B01G060600 chr4B 92.620 271 19 1 2340 2609 23992446 23992716 3.170000e-104 388
20 TraesCS7B01G060600 chr4B 91.166 283 25 0 2343 2625 311379112 311378830 4.100000e-103 385
21 TraesCS7B01G060600 chr4B 90.909 286 24 1 2340 2625 115356762 115357045 1.480000e-102 383
22 TraesCS7B01G060600 chr5B 90.972 288 25 1 2340 2627 313084922 313085208 1.140000e-103 387
23 TraesCS7B01G060600 chr2D 91.459 281 16 6 2346 2625 50398813 50398540 1.910000e-101 379


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 TraesCS7B01G060600 chr7B 63493088 63495714 2626 False 4852 4852 100.000 1 2627 1 chr7B.!!$F1 2626
1 TraesCS7B01G060600 chr7B 63541504 63542211 707 False 634 634 83.662 1668 2341 1 chr7B.!!$F2 673
2 TraesCS7B01G060600 chr7B 63394282 63395177 895 False 611 710 91.460 1680 2625 2 chr7B.!!$F3 945
3 TraesCS7B01G060600 chr3B 773547014 773548686 1672 False 2887 2887 97.792 1 1675 1 chr3B.!!$F1 1674
4 TraesCS7B01G060600 chr1B 669918195 669919867 1672 False 2881 2881 97.733 1 1675 1 chr1B.!!$F1 1674
5 TraesCS7B01G060600 chr1B 418165553 418167221 1668 True 2854 2854 97.491 4 1676 1 chr1B.!!$R2 1672
6 TraesCS7B01G060600 chr5A 536710582 536712251 1669 True 2859 2859 97.549 4 1675 1 chr5A.!!$R1 1671
7 TraesCS7B01G060600 chr7A 30714506 30716177 1671 True 2844 2844 97.373 4 1675 1 chr7A.!!$R1 1671
8 TraesCS7B01G060600 chr7A 667966586 667967885 1299 True 1975 1975 94.095 375 1674 1 chr7A.!!$R3 1299
9 TraesCS7B01G060600 chr7A 109237471 109238137 666 True 592 592 83.211 1685 2341 1 chr7A.!!$R2 656
10 TraesCS7B01G060600 chr2A 40955897 40957564 1667 True 2741 2741 96.294 4 1675 1 chr2A.!!$R1 1671
11 TraesCS7B01G060600 chr2A 722078384 722079736 1352 True 2178 2178 95.723 323 1675 1 chr2A.!!$R2 1352
12 TraesCS7B01G060600 chr2A 407750226 407750823 597 False 556 556 83.500 1 598 1 chr2A.!!$F1 597
13 TraesCS7B01G060600 chr1A 592500043 592501705 1662 True 2503 2503 93.787 4 1675 1 chr1A.!!$R1 1671
14 TraesCS7B01G060600 chr7D 104741211 104741834 623 True 652 652 85.987 1732 2341 1 chr7D.!!$R1 609

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
311 312 0.401738 TCTTTGGCTCCCTGGACAAG 59.598 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2252 0.802607 CGAAGCCGAGGCAGTACTTC 60.803 60.0 17.18 9.57 44.88 3.01 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 4.603131 TGCTTGGAGAATTGCTAAATCCT 58.397 39.130 0.00 0.00 0.00 3.24
43 44 5.189736 TGCTAAATCCTCCTTTTCTCAGCTA 59.810 40.000 0.00 0.00 0.00 3.32
130 131 4.021192 CCTAAATCTGCTTTTTGGGCTTCA 60.021 41.667 0.00 0.00 29.53 3.02
311 312 0.401738 TCTTTGGCTCCCTGGACAAG 59.598 55.000 0.00 0.00 0.00 3.16
947 953 3.625649 TGTGCACATTGCTACTATGGA 57.374 42.857 17.42 0.00 45.31 3.41
1124 1134 6.808704 GCTTTCAGAAGTTCAAAAGTTCTTGT 59.191 34.615 21.91 0.00 46.33 3.16
1139 1149 7.554959 AAGTTCTTGTTCTATTACAGGGAGA 57.445 36.000 0.00 0.00 0.00 3.71
1503 1516 2.087646 GCTCACCAGGTTCTTCATTCC 58.912 52.381 0.00 0.00 0.00 3.01
1791 1824 1.201429 AGGTGGAGTAGGCCAAGTGG 61.201 60.000 5.01 0.00 40.20 4.00
1832 1865 1.880027 GAATCCGTTGAAGTTGGTGCT 59.120 47.619 0.00 0.00 0.00 4.40
1835 1868 1.082756 CGTTGAAGTTGGTGCTCGC 60.083 57.895 0.00 0.00 0.00 5.03
1961 1995 1.138247 GAACACCGTCGAGGCGTAT 59.862 57.895 0.00 0.00 46.52 3.06
1979 2013 3.615110 CGTATGTGGTGCACTTCTTCTCT 60.615 47.826 17.98 0.00 35.11 3.10
2037 2071 4.814294 GCACGTAGTCGCCCAGGG 62.814 72.222 0.00 0.00 41.61 4.45
2054 2088 2.034066 GTGGTGCAGCTAAGGGCA 59.966 61.111 18.08 0.00 44.79 5.36
2055 2089 1.379044 GTGGTGCAGCTAAGGGCAT 60.379 57.895 18.08 0.00 42.75 4.40
2056 2090 0.967380 GTGGTGCAGCTAAGGGCATT 60.967 55.000 18.08 0.00 42.75 3.56
2066 2100 3.455910 AGCTAAGGGCATTGTAGATGTCA 59.544 43.478 0.00 0.00 44.79 3.58
2068 2102 4.823989 GCTAAGGGCATTGTAGATGTCATT 59.176 41.667 0.00 0.00 41.35 2.57
2072 2106 3.947196 GGGCATTGTAGATGTCATTGTCA 59.053 43.478 0.00 0.00 0.00 3.58
2076 2110 6.039047 GGCATTGTAGATGTCATTGTCAATCT 59.961 38.462 0.00 0.00 0.00 2.40
2127 2177 2.665603 GAGCGTGAAGGCCCTCTT 59.334 61.111 0.00 0.00 38.65 2.85
2148 2198 1.296715 CGAAGTACTGCCCCAGCTT 59.703 57.895 0.00 0.00 40.80 3.74
2166 2216 4.148825 GCCGATCACCTCCACGCT 62.149 66.667 0.00 0.00 0.00 5.07
2213 2263 2.885861 CCTCGCGAAGTACTGCCT 59.114 61.111 11.33 0.00 0.00 4.75
2215 2265 1.583967 CTCGCGAAGTACTGCCTCG 60.584 63.158 11.33 10.43 0.00 4.63
2218 2268 2.885861 CGAAGTACTGCCTCGGCT 59.114 61.111 9.65 0.00 42.51 5.52
2228 2278 2.506438 CCTCGGCTTCGTCGAACC 60.506 66.667 2.90 9.64 39.77 3.62
2233 2283 2.357034 GCTTCGTCGAACCTGGCA 60.357 61.111 2.90 0.00 0.00 4.92
2296 2346 4.091939 ATGCTGAGCTGAGCGGCA 62.092 61.111 20.51 20.19 42.32 5.69
2353 2403 0.179092 GGTACACATACGGCACCTCC 60.179 60.000 0.00 0.00 31.40 4.30
2386 2436 0.802607 GTTCAGCTCGATGACGTCCC 60.803 60.000 14.12 3.95 40.69 4.46
2388 2438 0.965866 TCAGCTCGATGACGTCCCTT 60.966 55.000 14.12 0.00 40.69 3.95
2400 2450 4.253685 TGACGTCCCTTGAATTCTTGATC 58.746 43.478 14.12 0.00 0.00 2.92
2460 2510 1.206132 GACGGTGTGGTGATGGTGATA 59.794 52.381 0.00 0.00 0.00 2.15
2509 2559 5.278561 GCCTAAGCACTACGAGAATATGACT 60.279 44.000 0.00 0.00 39.53 3.41
2526 2576 0.034896 ACTGGAGGCGTAAACTGTGG 59.965 55.000 0.00 0.00 0.00 4.17
2533 2583 1.376812 CGTAAACTGTGGAGGGGGC 60.377 63.158 0.00 0.00 0.00 5.80
2572 2622 0.865769 CGTTGGTGTGTGTTCTAGGC 59.134 55.000 0.00 0.00 0.00 3.93
2576 2626 2.033194 GTGTGTGTTCTAGGCGCCC 61.033 63.158 26.15 7.94 0.00 6.13
2621 2671 1.836604 GGGGAGAGAGGCAGCCTAG 60.837 68.421 16.16 0.00 31.76 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 6.207614 GGAGGAGTCATGAAAATATTTAGCCC 59.792 42.308 0.00 0.00 0.00 5.19
311 312 8.761575 TGAACAAGCTCATTATTCCAAATTTC 57.238 30.769 0.00 0.00 0.00 2.17
392 393 1.742761 AGCAAATCTGGACCATCGTG 58.257 50.000 0.00 0.00 0.00 4.35
511 512 8.087136 AGAAGATTCTTCAATTCCAAAGAAAGC 58.913 33.333 24.51 6.82 42.86 3.51
670 674 2.447379 ATCCTCCTGATGGCCGCT 60.447 61.111 0.00 0.00 30.54 5.52
947 953 8.986991 AGTCATTATAAGAATCAGAGGACAAGT 58.013 33.333 0.00 0.00 0.00 3.16
1124 1134 6.668283 AGTAGCAACTTCTCCCTGTAATAGAA 59.332 38.462 0.00 0.00 29.00 2.10
1139 1149 3.190439 ACCCCTATTCCAGTAGCAACTT 58.810 45.455 0.00 0.00 31.97 2.66
1183 1193 7.982224 TGAATTTGCACATTGATTTCAAAACA 58.018 26.923 2.08 0.00 39.55 2.83
1503 1516 3.023832 ACAAACTTGAGGTTCAACCCTG 58.976 45.455 1.75 0.00 39.75 4.45
1676 1689 7.450627 GTCGATTGGTGTTTGTATTGTACTAC 58.549 38.462 0.00 0.00 0.00 2.73
1677 1690 6.308524 CGTCGATTGGTGTTTGTATTGTACTA 59.691 38.462 0.00 0.00 0.00 1.82
1678 1691 5.119588 CGTCGATTGGTGTTTGTATTGTACT 59.880 40.000 0.00 0.00 0.00 2.73
1793 1826 2.821546 TCTTGATCGCCGACATAAAGG 58.178 47.619 0.00 0.00 0.00 3.11
1887 1921 4.509737 GTACGGGCTGCCGGAGAC 62.510 72.222 29.90 21.90 37.53 3.36
1900 1934 2.576832 AAGGTGGTGTCCGGGTACG 61.577 63.158 0.00 0.00 40.55 3.67
1909 1943 4.619227 CCCGCGACAAGGTGGTGT 62.619 66.667 8.23 0.00 35.78 4.16
1961 1995 1.070758 GGAGAGAAGAAGTGCACCACA 59.929 52.381 14.63 0.00 36.74 4.17
2019 2053 3.760035 CCTGGGCGACTACGTGCT 61.760 66.667 0.00 0.00 41.98 4.40
2037 2071 0.967380 AATGCCCTTAGCTGCACCAC 60.967 55.000 1.02 0.00 44.23 4.16
2055 2089 9.803315 GTACTAGATTGACAATGACATCTACAA 57.197 33.333 5.14 0.00 0.00 2.41
2056 2090 9.190317 AGTACTAGATTGACAATGACATCTACA 57.810 33.333 5.14 0.00 0.00 2.74
2066 2100 3.372954 GCGCGAGTACTAGATTGACAAT 58.627 45.455 12.10 0.00 0.00 2.71
2068 2102 1.267882 CGCGCGAGTACTAGATTGACA 60.268 52.381 28.94 0.00 0.00 3.58
2072 2106 1.008767 GGCGCGCGAGTACTAGATT 60.009 57.895 37.18 0.00 0.00 2.40
2076 2110 3.580193 GGAGGCGCGCGAGTACTA 61.580 66.667 37.18 0.00 0.00 1.82
2144 2194 2.293318 TGGAGGTGATCGGCAAGCT 61.293 57.895 0.00 0.00 0.00 3.74
2148 2198 4.451150 GCGTGGAGGTGATCGGCA 62.451 66.667 0.00 0.00 0.00 5.69
2202 2252 0.802607 CGAAGCCGAGGCAGTACTTC 60.803 60.000 17.18 9.57 44.88 3.01
2203 2253 1.215647 CGAAGCCGAGGCAGTACTT 59.784 57.895 17.18 0.80 44.88 2.24
2205 2255 1.516603 GACGAAGCCGAGGCAGTAC 60.517 63.158 17.18 3.69 44.88 2.73
2206 2256 2.882876 GACGAAGCCGAGGCAGTA 59.117 61.111 17.18 0.00 44.88 2.74
2207 2257 4.421479 CGACGAAGCCGAGGCAGT 62.421 66.667 17.18 12.61 44.88 4.40
2209 2259 3.676605 TTCGACGAAGCCGAGGCA 61.677 61.111 17.18 0.00 44.88 4.75
2210 2260 3.179939 GTTCGACGAAGCCGAGGC 61.180 66.667 11.25 5.89 37.35 4.70
2213 2263 2.257371 CAGGTTCGACGAAGCCGA 59.743 61.111 30.17 0.00 40.41 5.54
2215 2265 3.119096 GCCAGGTTCGACGAAGCC 61.119 66.667 30.17 22.89 40.41 4.35
2218 2268 2.835605 GAATGCCAGGTTCGACGAA 58.164 52.632 6.10 6.10 0.00 3.85
2238 2288 1.105457 CATTGGCGGTGGATTCATGT 58.895 50.000 0.00 0.00 0.00 3.21
2359 2409 1.010935 ATCGAGCTGAACGTGTGCAG 61.011 55.000 3.48 3.48 35.28 4.41
2386 2436 4.942483 ACTCTGCTGGATCAAGAATTCAAG 59.058 41.667 8.44 0.00 0.00 3.02
2388 2438 4.259356 CACTCTGCTGGATCAAGAATTCA 58.741 43.478 8.44 0.00 0.00 2.57
2400 2450 0.108898 CTTCCTCGACACTCTGCTGG 60.109 60.000 0.00 0.00 0.00 4.85
2436 2486 2.357034 ATCACCACACCGTCGTGC 60.357 61.111 0.00 0.00 44.40 5.34
2445 2495 3.582647 ACTTCACTATCACCATCACCACA 59.417 43.478 0.00 0.00 0.00 4.17
2460 2510 0.460311 CCTCCGCGGATAACTTCACT 59.540 55.000 31.19 0.00 33.16 3.41
2509 2559 0.320374 CTCCACAGTTTACGCCTCCA 59.680 55.000 0.00 0.00 0.00 3.86
2552 2602 1.539496 GCCTAGAACACACACCAACGA 60.539 52.381 0.00 0.00 0.00 3.85
2576 2626 2.506644 TCCTTTATTTACGTGGGGAGGG 59.493 50.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.