Multiple sequence alignment - TraesCS7D01G201400

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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 TraesCS7D01G201400 chr7D 100.000 2522 0 0 1 2522 160533157 160535678 0.000000e+00 4658.0
1 TraesCS7D01G201400 chr7D 88.428 1158 96 19 546 1683 160487244 160488383 0.000000e+00 1362.0
2 TraesCS7D01G201400 chr7A 93.730 1914 79 11 138 2018 161649766 161651671 0.000000e+00 2832.0
3 TraesCS7D01G201400 chr7A 88.579 1147 77 27 549 1665 161279428 161280550 0.000000e+00 1343.0
4 TraesCS7D01G201400 chr7A 91.649 467 38 1 2056 2522 161666016 161666481 0.000000e+00 645.0
5 TraesCS7D01G201400 chr7A 91.435 467 39 1 2056 2522 161667867 161668332 7.610000e-180 640.0
6 TraesCS7D01G201400 chr7A 91.006 467 41 1 2056 2522 161653690 161654155 1.650000e-176 628.0
7 TraesCS7D01G201400 chr7A 91.928 446 34 2 2069 2513 161651900 161652344 7.660000e-175 623.0
8 TraesCS7D01G201400 chr7A 90.538 465 43 1 2056 2520 161655493 161655956 4.610000e-172 614.0
9 TraesCS7D01G201400 chr7A 96.269 134 5 0 2 135 161648536 161648669 1.170000e-53 220.0
10 TraesCS7D01G201400 chr7B 94.543 1301 42 8 526 1805 121495562 121496854 0.000000e+00 1982.0
11 TraesCS7D01G201400 chr7B 89.080 1163 82 22 546 1678 121053046 121054193 0.000000e+00 1402.0
12 TraesCS7D01G201400 chr7B 88.215 1137 94 25 565 1683 121242114 121243228 0.000000e+00 1321.0
13 TraesCS7D01G201400 chr7B 88.029 1111 93 24 589 1683 121320386 121321472 0.000000e+00 1279.0
14 TraesCS7D01G201400 chr7B 92.837 726 47 3 1798 2520 121497280 121498003 0.000000e+00 1048.0
15 TraesCS7D01G201400 chr7B 89.538 822 59 11 877 1683 121115422 121116231 0.000000e+00 1016.0
16 TraesCS7D01G201400 chr7B 89.538 822 59 11 877 1683 121166748 121167557 0.000000e+00 1016.0
17 TraesCS7D01G201400 chr7B 95.108 511 25 0 1 511 121494492 121495002 0.000000e+00 806.0
18 TraesCS7D01G201400 chr7B 87.500 240 19 8 546 780 121113677 121113910 1.490000e-67 267.0
19 TraesCS7D01G201400 chr7B 86.250 240 22 8 546 780 121165033 121165266 1.500000e-62 250.0
20 TraesCS7D01G201400 chr7B 85.714 154 18 4 2 153 121241826 121241977 2.600000e-35 159.0
21 TraesCS7D01G201400 chr7B 84.967 153 21 2 2 153 121320070 121320221 1.210000e-33 154.0
22 TraesCS7D01G201400 chr7B 84.967 153 21 2 2 153 121385723 121385874 1.210000e-33 154.0
23 TraesCS7D01G201400 chr2B 95.556 45 1 1 336 380 53029690 53029733 1.250000e-08 71.3


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 TraesCS7D01G201400 chr7D 160533157 160535678 2521 False 4658.000000 4658 100.000000 1 2522 1 chr7D.!!$F2 2521
1 TraesCS7D01G201400 chr7D 160487244 160488383 1139 False 1362.000000 1362 88.428000 546 1683 1 chr7D.!!$F1 1137
2 TraesCS7D01G201400 chr7A 161279428 161280550 1122 False 1343.000000 1343 88.579000 549 1665 1 chr7A.!!$F1 1116
3 TraesCS7D01G201400 chr7A 161648536 161655956 7420 False 983.400000 2832 92.694200 2 2522 5 chr7A.!!$F2 2520
4 TraesCS7D01G201400 chr7A 161666016 161668332 2316 False 642.500000 645 91.542000 2056 2522 2 chr7A.!!$F3 466
5 TraesCS7D01G201400 chr7B 121053046 121054193 1147 False 1402.000000 1402 89.080000 546 1678 1 chr7B.!!$F1 1132
6 TraesCS7D01G201400 chr7B 121494492 121498003 3511 False 1278.666667 1982 94.162667 1 2520 3 chr7B.!!$F7 2519
7 TraesCS7D01G201400 chr7B 121241826 121243228 1402 False 740.000000 1321 86.964500 2 1683 2 chr7B.!!$F5 1681
8 TraesCS7D01G201400 chr7B 121320070 121321472 1402 False 716.500000 1279 86.498000 2 1683 2 chr7B.!!$F6 1681
9 TraesCS7D01G201400 chr7B 121113677 121116231 2554 False 641.500000 1016 88.519000 546 1683 2 chr7B.!!$F3 1137
10 TraesCS7D01G201400 chr7B 121165033 121167557 2524 False 633.000000 1016 87.894000 546 1683 2 chr7B.!!$F4 1137

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
950 4049 1.133884 GTCCCCAGGCTACAAATACCC 60.134 57.143 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 9806 0.107831 TGGTGTTCTGGAAACGAGGG 59.892 55.0 0.0 0.0 0.0 4.3 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
213 1308 4.817318 TTACATATCCGGCATCTGCATA 57.183 40.909 0.00 0.00 44.36 3.14
250 1345 4.678509 ACCAACATAAACATACACGCAG 57.321 40.909 0.00 0.00 0.00 5.18
265 1361 5.186996 ACACGCAGAAAAGAAAATGTGAT 57.813 34.783 0.00 0.00 0.00 3.06
387 1483 2.094906 TGATCACCGAGACGTAGGTTTG 60.095 50.000 7.06 0.00 39.00 2.93
740 2402 4.000325 TGTATATCGGGAAATCGCATTGG 59.000 43.478 0.00 0.00 0.00 3.16
842 3844 8.913487 TGAACTCATGATACATGCATCTATTT 57.087 30.769 7.44 0.00 0.00 1.40
843 3845 9.346005 TGAACTCATGATACATGCATCTATTTT 57.654 29.630 7.44 0.00 0.00 1.82
950 4049 1.133884 GTCCCCAGGCTACAAATACCC 60.134 57.143 0.00 0.00 0.00 3.69
986 4088 1.685517 TCTTCATCCATCTCGAGCCAG 59.314 52.381 7.81 0.00 0.00 4.85
1458 4564 4.697352 GTCTTCATCACCTGCAACTACAAT 59.303 41.667 0.00 0.00 0.00 2.71
1530 4639 1.426621 CGAAGCCTAGTACGTGCGA 59.573 57.895 0.00 0.00 0.00 5.10
1563 4676 1.468895 TACATGCATACGTACGTGCG 58.531 50.000 30.25 24.57 44.11 5.34
1748 4889 2.771372 AGCCAAACAAATTGTGAACCCT 59.229 40.909 0.00 0.00 37.32 4.34
1789 4930 5.458891 CCTTCGTCCTATAATGTAAGACCG 58.541 45.833 0.00 0.00 0.00 4.79
1793 4934 5.410746 TCGTCCTATAATGTAAGACCGCTAG 59.589 44.000 0.00 0.00 0.00 3.42
1833 5409 2.044758 GTTATGGGACGGTGGGAGTAT 58.955 52.381 0.00 0.00 0.00 2.12
1877 5453 1.587034 CGTTCGAAGATAAGAACCCGC 59.413 52.381 0.00 0.00 42.57 6.13
1891 5467 5.975693 AGAACCCGCAATTCTTGAAATAA 57.024 34.783 0.00 0.00 32.32 1.40
1899 5475 6.747280 CCGCAATTCTTGAAATAAGATTTCGT 59.253 34.615 7.28 0.00 0.00 3.85
1976 5552 9.905713 AGTGTGAAAAATAGAATAGCCTATTGA 57.094 29.630 0.71 0.00 38.82 2.57
1997 5573 1.398451 GGCAACATCACAAACTCGACG 60.398 52.381 0.00 0.00 0.00 5.12
2111 5865 1.059098 TCGCATCCATCATAAGGCCT 58.941 50.000 0.00 0.00 0.00 5.19
2167 5921 0.582482 CAGCGCTGCAAAAATGCAAA 59.418 45.000 26.68 0.00 44.88 3.68
2200 5954 7.979786 AGATTAAGTCAGATGTCCTCCTAAA 57.020 36.000 0.00 0.00 0.00 1.85
2342 6096 2.988839 GCAAGGTCCAGGGCCTCAT 61.989 63.158 14.99 0.00 34.81 2.90
2393 9806 3.507233 TGTCCAAAAGAAGATGATGTGGC 59.493 43.478 0.00 0.00 0.00 5.01
2482 9895 2.286872 CCAGCAATTGCCAAACACAAA 58.713 42.857 26.45 0.00 43.38 2.83
2487 9900 5.230306 CAGCAATTGCCAAACACAAATTTTG 59.770 36.000 26.45 9.27 43.38 2.44
2513 9926 5.239744 TCTTTTCAATGGTAAGTGCGCTTTA 59.760 36.000 19.18 5.82 36.22 1.85
2514 9927 4.678509 TTCAATGGTAAGTGCGCTTTAG 57.321 40.909 19.18 2.64 36.22 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 6.091577 GGACATCACACATTATAACGTGTTGA 59.908 38.462 18.42 16.43 43.71 3.18
197 1292 6.538945 TTATAGTTATGCAGATGCCGGATA 57.461 37.500 5.05 0.00 41.18 2.59
227 1322 5.932883 TCTGCGTGTATGTTTATGTTGGTTA 59.067 36.000 0.00 0.00 0.00 2.85
248 1343 9.699985 CTTATCGAGATCACATTTTCTTTTCTG 57.300 33.333 0.00 0.00 0.00 3.02
250 1345 7.641802 GGCTTATCGAGATCACATTTTCTTTTC 59.358 37.037 0.00 0.00 0.00 2.29
265 1361 0.459585 GTGGTTGCGGCTTATCGAGA 60.460 55.000 0.00 0.00 0.00 4.04
310 1406 3.276857 AGGTCTAGCGTCGTCTTTGATA 58.723 45.455 0.00 0.00 0.00 2.15
445 1541 2.027625 CCTCGCAAGGACGAACACC 61.028 63.158 0.00 0.00 46.67 4.16
515 2163 5.647589 TCTCGCGAATACACAATAGACTTT 58.352 37.500 11.33 0.00 0.00 2.66
740 2402 5.049398 ACTACTTCTGACAACGAGTGATC 57.951 43.478 0.00 0.00 0.00 2.92
950 4049 2.807967 TGAAGAGTGCTGGAATTTGACG 59.192 45.455 0.00 0.00 0.00 4.35
998 4104 2.431954 ACTCTTGGAAGATGCCATGG 57.568 50.000 7.63 7.63 37.86 3.66
1032 4138 0.107066 CCATGACTATGGCCAGTGCA 60.107 55.000 13.05 7.23 46.84 4.57
1140 4246 1.285641 GTTGTTGTCCCATGCCACG 59.714 57.895 0.00 0.00 0.00 4.94
1458 4564 3.179339 TTGAAGTTGCCCGGGGGA 61.179 61.111 25.28 9.87 37.50 4.81
1530 4639 4.476628 TGCATGTATGATCACACTCACT 57.523 40.909 5.59 0.00 0.00 3.41
1563 4676 5.864474 TCAAACCACACAAACATAAACACAC 59.136 36.000 0.00 0.00 0.00 3.82
1769 4910 4.139786 AGCGGTCTTACATTATAGGACGA 58.860 43.478 0.00 0.00 0.00 4.20
1813 5389 1.488390 TACTCCCACCGTCCCATAAC 58.512 55.000 0.00 0.00 0.00 1.89
1833 5409 7.148573 ACGCAAATTCAAATTTTGTGTGTAACA 60.149 29.630 12.86 0.00 39.73 2.41
1857 5433 1.587034 GCGGGTTCTTATCTTCGAACG 59.413 52.381 0.00 0.00 40.21 3.95
1976 5552 1.873591 GTCGAGTTTGTGATGTTGCCT 59.126 47.619 0.00 0.00 0.00 4.75
2111 5865 2.903350 TGCGACCGCGATAGGCTA 60.903 61.111 8.23 0.00 45.51 3.93
2116 5870 1.091197 TAGACAGTGCGACCGCGATA 61.091 55.000 8.23 0.00 45.51 2.92
2167 5921 9.171877 GGACATCTGACTTAATCTTCAAATTCT 57.828 33.333 0.00 0.00 0.00 2.40
2200 5954 2.571212 TGGTGATTGAGCGTGTCTTTT 58.429 42.857 0.00 0.00 0.00 2.27
2208 5962 4.333649 ACACAATAAGATGGTGATTGAGCG 59.666 41.667 0.94 0.00 36.42 5.03
2307 6061 2.593956 GCCGGGTTCCTTCAGACCT 61.594 63.158 2.18 0.00 36.18 3.85
2337 6091 4.144297 TCTTTGGAGTTTTGTCCATGAGG 58.856 43.478 0.00 0.00 46.31 3.86
2342 6096 4.855340 AGAGTTCTTTGGAGTTTTGTCCA 58.145 39.130 0.00 0.00 45.37 4.02
2393 9806 0.107831 TGGTGTTCTGGAAACGAGGG 59.892 55.000 0.00 0.00 0.00 4.30
2487 9900 4.098416 GCGCACTTACCATTGAAAAGATC 58.902 43.478 0.30 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.