Multiple sequence alignment - TraesCS7D01G508500

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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 TraesCS7D01G508500 chr7D 100.000 4486 0 0 1 4486 612324814 612329299 0.000000e+00 8285.0
1 TraesCS7D01G508500 chr7D 91.937 1786 102 17 2714 4483 611869772 611868013 0.000000e+00 2462.0
2 TraesCS7D01G508500 chr7D 84.271 1901 207 48 840 2714 611857669 611855835 0.000000e+00 1770.0
3 TraesCS7D01G508500 chr7D 82.668 1604 206 42 983 2569 595346729 595348277 0.000000e+00 1356.0
4 TraesCS7D01G508500 chr7D 80.963 1786 263 43 922 2667 612403623 612405371 0.000000e+00 1343.0
5 TraesCS7D01G508500 chr7D 84.229 1395 163 31 1333 2711 612287028 612288381 0.000000e+00 1304.0
6 TraesCS7D01G508500 chr7D 84.032 1384 164 30 1348 2714 611871164 611869821 0.000000e+00 1279.0
7 TraesCS7D01G508500 chr7D 82.009 1573 157 67 2714 4212 611855786 611854266 0.000000e+00 1221.0
8 TraesCS7D01G508500 chr7D 81.864 1577 154 72 2714 4212 612288433 612289955 0.000000e+00 1206.0
9 TraesCS7D01G508500 chr7D 83.833 934 120 20 1713 2641 595348292 595349199 0.000000e+00 859.0
10 TraesCS7D01G508500 chr7D 81.552 580 69 20 3464 4033 612406090 612406641 1.150000e-120 444.0
11 TraesCS7D01G508500 chr7D 79.035 663 76 23 2815 3456 595349207 595349827 3.250000e-106 396.0
12 TraesCS7D01G508500 chr7D 81.352 429 47 19 850 1277 612286609 612287005 7.240000e-83 318.0
13 TraesCS7D01G508500 chr7D 87.958 191 23 0 2975 3165 612405483 612405673 4.520000e-55 226.0
14 TraesCS7D01G508500 chr7A 94.014 2723 143 12 4 2714 702406459 702409173 0.000000e+00 4108.0
15 TraesCS7D01G508500 chr7A 95.779 1777 56 7 2714 4486 702409222 702410983 0.000000e+00 2848.0
16 TraesCS7D01G508500 chr7A 82.953 1707 229 40 983 2665 688345399 688347067 0.000000e+00 1483.0
17 TraesCS7D01G508500 chr7A 84.271 1386 156 40 1344 2711 702237702 702239043 0.000000e+00 1295.0
18 TraesCS7D01G508500 chr7A 81.143 1575 171 68 2714 4212 702239095 702240619 0.000000e+00 1147.0
19 TraesCS7D01G508500 chr7A 78.061 588 84 27 1062 1640 703602005 703602556 3.350000e-86 329.0
20 TraesCS7D01G508500 chr7A 77.660 564 59 31 3591 4116 688347700 688348234 9.500000e-72 281.0
21 TraesCS7D01G508500 chr7B 91.539 1371 79 16 2714 4065 701648482 701649834 0.000000e+00 1855.0
22 TraesCS7D01G508500 chr7B 84.585 1797 202 43 926 2711 701457481 701459213 0.000000e+00 1714.0
23 TraesCS7D01G508500 chr7B 88.898 1288 94 25 5 1275 701643716 701644971 0.000000e+00 1541.0
24 TraesCS7D01G508500 chr7B 82.256 1702 245 32 982 2667 672770098 672771758 0.000000e+00 1417.0
25 TraesCS7D01G508500 chr7B 97.305 742 20 0 1268 2009 701645934 701646675 0.000000e+00 1260.0
26 TraesCS7D01G508500 chr7B 91.725 713 44 7 2002 2711 701647730 701648430 0.000000e+00 976.0
27 TraesCS7D01G508500 chr7B 81.211 793 80 34 3272 4012 701459812 701460587 3.890000e-160 575.0
28 TraesCS7D01G508500 chr7B 92.204 372 23 2 4112 4483 701649834 701650199 5.140000e-144 521.0
29 TraesCS7D01G508500 chr7B 89.702 369 22 9 2714 3070 701459265 701459629 1.470000e-124 457.0
30 TraesCS7D01G508500 chr7B 79.350 431 56 24 2825 3244 701012129 701011721 5.720000e-69 272.0
31 TraesCS7D01G508500 chr7B 78.189 486 42 27 3591 4029 672772392 672772860 7.450000e-63 252.0
32 TraesCS7D01G508500 chr7B 78.761 226 32 10 279 491 701456904 701457126 2.180000e-28 137.0
33 TraesCS7D01G508500 chrUn 84.021 751 86 22 830 1576 324305048 324304328 0.000000e+00 691.0
34 TraesCS7D01G508500 chrUn 83.888 751 87 22 830 1576 324358663 324357943 0.000000e+00 686.0
35 TraesCS7D01G508500 chrUn 86.175 651 62 18 926 1576 87707672 87708294 0.000000e+00 678.0
36 TraesCS7D01G508500 chrUn 87.084 511 48 11 1066 1576 445548116 445547624 3.030000e-156 562.0
37 TraesCS7D01G508500 chrUn 80.457 788 87 32 3272 4007 368811829 368812601 1.420000e-149 540.0
38 TraesCS7D01G508500 chrUn 79.111 225 31 10 280 491 324305541 324305320 1.680000e-29 141.0
39 TraesCS7D01G508500 chrUn 79.111 225 31 10 280 491 324359153 324358932 1.680000e-29 141.0
40 TraesCS7D01G508500 chrUn 78.761 226 32 10 279 491 87707095 87707317 2.180000e-28 137.0
41 TraesCS7D01G508500 chrUn 78.761 226 32 10 279 491 375666083 375666305 2.180000e-28 137.0
42 TraesCS7D01G508500 chrUn 94.915 59 1 1 4116 4172 465862360 465862302 1.720000e-14 91.6


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 TraesCS7D01G508500 chr7D 612324814 612329299 4485 False 8285.000000 8285 100.000000 1 4486 1 chr7D.!!$F1 4485
1 TraesCS7D01G508500 chr7D 611868013 611871164 3151 True 1870.500000 2462 87.984500 1348 4483 2 chr7D.!!$R2 3135
2 TraesCS7D01G508500 chr7D 611854266 611857669 3403 True 1495.500000 1770 83.140000 840 4212 2 chr7D.!!$R1 3372
3 TraesCS7D01G508500 chr7D 612286609 612289955 3346 False 942.666667 1304 82.481667 850 4212 3 chr7D.!!$F3 3362
4 TraesCS7D01G508500 chr7D 595346729 595349827 3098 False 870.333333 1356 81.845333 983 3456 3 chr7D.!!$F2 2473
5 TraesCS7D01G508500 chr7D 612403623 612406641 3018 False 671.000000 1343 83.491000 922 4033 3 chr7D.!!$F4 3111
6 TraesCS7D01G508500 chr7A 702406459 702410983 4524 False 3478.000000 4108 94.896500 4 4486 2 chr7A.!!$F4 4482
7 TraesCS7D01G508500 chr7A 702237702 702240619 2917 False 1221.000000 1295 82.707000 1344 4212 2 chr7A.!!$F3 2868
8 TraesCS7D01G508500 chr7A 688345399 688348234 2835 False 882.000000 1483 80.306500 983 4116 2 chr7A.!!$F2 3133
9 TraesCS7D01G508500 chr7A 703602005 703602556 551 False 329.000000 329 78.061000 1062 1640 1 chr7A.!!$F1 578
10 TraesCS7D01G508500 chr7B 701643716 701650199 6483 False 1230.600000 1855 92.334200 5 4483 5 chr7B.!!$F3 4478
11 TraesCS7D01G508500 chr7B 672770098 672772860 2762 False 834.500000 1417 80.222500 982 4029 2 chr7B.!!$F1 3047
12 TraesCS7D01G508500 chr7B 701456904 701460587 3683 False 720.750000 1714 83.564750 279 4012 4 chr7B.!!$F2 3733
13 TraesCS7D01G508500 chrUn 368811829 368812601 772 False 540.000000 540 80.457000 3272 4007 1 chrUn.!!$F1 735
14 TraesCS7D01G508500 chrUn 324304328 324305541 1213 True 416.000000 691 81.566000 280 1576 2 chrUn.!!$R3 1296
15 TraesCS7D01G508500 chrUn 324357943 324359153 1210 True 413.500000 686 81.499500 280 1576 2 chrUn.!!$R4 1296
16 TraesCS7D01G508500 chrUn 87707095 87708294 1199 False 407.500000 678 82.468000 279 1576 2 chrUn.!!$F3 1297

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
686 709 0.545071 TGCCCTCATCACCTCTGTCA 60.545 55.000 0.0 0.0 0.0 3.58 F
1439 2487 1.302832 GCATCCCCTCCGGCATAAG 60.303 63.158 0.0 0.0 0.0 1.73 F
2186 4331 1.234821 GGAGCGTTTGTGGTTCATCA 58.765 50.000 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 2538 0.796312 GGAAAAGTTGAGCGCGATGA 59.204 50.000 12.10 0.0 0.00 2.92 R
2333 5361 1.204941 AGTGTGTCGGGCATACTTCTC 59.795 52.381 6.15 0.0 45.43 2.87 R
3791 7104 1.526887 CGTCGTCACAATGAAACAGCT 59.473 47.619 0.00 0.0 0.00 4.24 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
40 41 2.967946 GCCGCCTAGGAACAACCCT 61.968 63.158 14.75 0.00 45.00 4.34
41 42 1.619807 GCCGCCTAGGAACAACCCTA 61.620 60.000 14.75 0.00 45.00 3.53
80 82 2.104792 CACCAAGAACAACTGAGAGGGA 59.895 50.000 0.00 0.00 0.00 4.20
178 191 2.363172 GGGTGAGGGAGAGCTGGAC 61.363 68.421 0.00 0.00 0.00 4.02
190 203 3.068881 CTGGACGAAGAAGGGCCA 58.931 61.111 6.18 0.00 0.00 5.36
257 270 2.294078 GGGGAGGAGGTGAGGTGTG 61.294 68.421 0.00 0.00 0.00 3.82
270 283 5.248477 AGGTGAGGTGTGTATAATCACTTGT 59.752 40.000 3.91 0.00 40.07 3.16
284 297 2.378547 TCACTTGTATCCCCCTTTGCTT 59.621 45.455 0.00 0.00 0.00 3.91
430 450 2.135139 GTCAGCGTGATGTCAAACTCA 58.865 47.619 0.00 0.00 0.00 3.41
468 491 0.891373 CTGCTCTTCGTCTTCCTCCA 59.109 55.000 0.00 0.00 0.00 3.86
508 531 3.264052 CCCACCCCACACCCATCA 61.264 66.667 0.00 0.00 0.00 3.07
512 535 2.162906 ACCCCACACCCATCAAGCT 61.163 57.895 0.00 0.00 0.00 3.74
546 569 2.184066 GCCGCCGAATTTGCCAAT 59.816 55.556 0.00 0.00 0.00 3.16
554 577 1.737236 CGAATTTGCCAATGACCTCGA 59.263 47.619 0.00 0.00 0.00 4.04
686 709 0.545071 TGCCCTCATCACCTCTGTCA 60.545 55.000 0.00 0.00 0.00 3.58
693 716 3.176411 TCATCACCTCTGTCATTCACCT 58.824 45.455 0.00 0.00 0.00 4.00
698 721 3.259374 CACCTCTGTCATTCACCTACACT 59.741 47.826 0.00 0.00 0.00 3.55
701 724 3.239449 TCTGTCATTCACCTACACTGGT 58.761 45.455 0.00 0.00 41.77 4.00
702 725 3.646162 TCTGTCATTCACCTACACTGGTT 59.354 43.478 0.00 0.00 38.45 3.67
824 850 1.468520 CAACGCTGGTCTGGGTTTATG 59.531 52.381 7.37 0.00 40.36 1.90
829 855 2.879756 GCTGGTCTGGGTTTATGCTTGA 60.880 50.000 0.00 0.00 0.00 3.02
838 864 7.542130 GTCTGGGTTTATGCTTGAAACAATAAG 59.458 37.037 9.75 0.00 38.32 1.73
1439 2487 1.302832 GCATCCCCTCCGGCATAAG 60.303 63.158 0.00 0.00 0.00 1.73
1887 2957 1.338020 GTGTTTGGTCTTTGGAGCCTG 59.662 52.381 0.00 0.00 39.02 4.85
2010 3092 8.023128 TGCAAGCTCTGACTGAATTAATTTTAC 58.977 33.333 1.43 0.00 0.00 2.01
2186 4331 1.234821 GGAGCGTTTGTGGTTCATCA 58.765 50.000 0.00 0.00 0.00 3.07
2190 4335 2.744202 AGCGTTTGTGGTTCATCATCTC 59.256 45.455 0.00 0.00 0.00 2.75
2191 4336 2.159517 GCGTTTGTGGTTCATCATCTCC 60.160 50.000 0.00 0.00 0.00 3.71
2192 4337 3.338249 CGTTTGTGGTTCATCATCTCCT 58.662 45.455 0.00 0.00 0.00 3.69
2409 5437 1.397672 TCTCCTTGGATGCTCTCGAG 58.602 55.000 5.93 5.93 0.00 4.04
2569 5600 6.026513 GCAAAGATAGTCAACATCTTCAAGC 58.973 40.000 0.00 1.28 40.92 4.01
2570 5601 6.348786 GCAAAGATAGTCAACATCTTCAAGCA 60.349 38.462 0.00 0.00 40.92 3.91
2571 5602 6.981762 AAGATAGTCAACATCTTCAAGCAG 57.018 37.500 0.00 0.00 38.11 4.24
2576 5607 2.751259 TCAACATCTTCAAGCAGGCATC 59.249 45.455 0.00 0.00 0.00 3.91
2593 5624 4.225942 AGGCATCTTCTTCTGTGGAATGTA 59.774 41.667 0.00 0.00 0.00 2.29
2797 5880 6.662414 TGACTTGAGATAAAATTGTAGGCG 57.338 37.500 0.00 0.00 0.00 5.52
2870 5962 3.306973 CGAATATGTGTCGTTGACATGCT 59.693 43.478 2.62 0.00 44.63 3.79
3371 6601 9.577110 CTCAGCATATTGTGTTTTATTTGACAT 57.423 29.630 0.00 0.00 0.00 3.06
3670 6976 9.929180 CTATATACAAGGTGCACAGTTATATGT 57.071 33.333 20.43 10.81 0.00 2.29
3791 7104 6.377146 GCCTATGGTTTCAGTTCCTATTTTGA 59.623 38.462 0.00 0.00 0.00 2.69
3933 7307 8.536175 CCTCTGTTTCCTCTCTTTTCTAACTAT 58.464 37.037 0.00 0.00 0.00 2.12
3959 7333 5.645497 GCACCCTATATGATGGATTGAAGAC 59.355 44.000 0.00 0.00 0.00 3.01
4068 7442 2.470990 AGTGTGAGATATGCAGGGTGA 58.529 47.619 0.00 0.00 0.00 4.02
4216 7628 1.671845 GTCAAAGCGGTTGTAACACCA 59.328 47.619 0.00 0.00 38.47 4.17
4316 7728 0.487325 TGACAGGAAGGAGAGGACCA 59.513 55.000 0.00 0.00 0.00 4.02
4345 7757 3.013921 TCCATCAGGCCGTGTAAAATTC 58.986 45.455 0.00 0.00 33.74 2.17
4435 8076 3.489180 ACGGTAAGATGAGTTCGTCAG 57.511 47.619 4.32 0.00 39.07 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.349755 GGTTGTTCCTAGGCGGCA 59.650 61.111 13.08 0.00 0.00 5.69
60 61 2.408565 TCCCTCTCAGTTGTTCTTGGT 58.591 47.619 0.00 0.00 0.00 3.67
67 69 1.272147 GGCCATTTCCCTCTCAGTTGT 60.272 52.381 0.00 0.00 0.00 3.32
152 154 3.695825 TCCCTCACCCCTCCCTCC 61.696 72.222 0.00 0.00 0.00 4.30
161 163 2.716017 CGTCCAGCTCTCCCTCACC 61.716 68.421 0.00 0.00 0.00 4.02
178 191 4.033776 TGCCCTGGCCCTTCTTCG 62.034 66.667 5.57 0.00 41.09 3.79
222 235 2.681778 CCCCCAGCTCTCGTGACT 60.682 66.667 0.00 0.00 0.00 3.41
243 256 4.406003 GTGATTATACACACCTCACCTCCT 59.594 45.833 0.00 0.00 40.11 3.69
257 270 6.206829 GCAAAGGGGGATACAAGTGATTATAC 59.793 42.308 0.00 0.00 39.74 1.47
270 283 2.815158 GGAAACAAGCAAAGGGGGATA 58.185 47.619 0.00 0.00 0.00 2.59
284 297 5.221884 TGGGTATAAAAGGAAGACGGAAACA 60.222 40.000 0.00 0.00 0.00 2.83
430 450 0.107654 GACGTGGCATCCTAAGGCTT 60.108 55.000 4.58 4.58 31.41 4.35
468 491 0.892063 GGAGAAGCGTCAAGGAGTCT 59.108 55.000 1.61 0.00 0.00 3.24
508 531 2.286523 CGGAGGAGGTGGTGAGCTT 61.287 63.158 0.00 0.00 0.00 3.74
530 553 0.801836 GTCATTGGCAAATTCGGCGG 60.802 55.000 7.21 0.00 0.00 6.13
531 554 0.801836 GGTCATTGGCAAATTCGGCG 60.802 55.000 3.01 0.00 0.00 6.46
532 555 0.532115 AGGTCATTGGCAAATTCGGC 59.468 50.000 3.01 0.00 0.00 5.54
546 569 1.592400 CGCTAGTGGGTTCGAGGTCA 61.592 60.000 0.00 0.00 0.00 4.02
554 577 1.153628 GATGCGACGCTAGTGGGTT 60.154 57.895 22.08 0.00 39.55 4.11
656 679 0.400213 ATGAGGGCAAAAGGTCGACA 59.600 50.000 18.91 0.00 0.00 4.35
686 709 1.610624 CGGCAACCAGTGTAGGTGAAT 60.611 52.381 0.00 0.00 42.25 2.57
693 716 2.437518 TTAGCGCGGCAACCAGTGTA 62.438 55.000 8.83 0.00 0.00 2.90
698 721 2.740826 GACTTAGCGCGGCAACCA 60.741 61.111 8.83 0.00 0.00 3.67
701 724 1.005512 TCTTGACTTAGCGCGGCAA 60.006 52.632 8.83 1.00 0.00 4.52
702 725 1.736645 GTCTTGACTTAGCGCGGCA 60.737 57.895 8.83 0.00 0.00 5.69
787 813 5.175673 CAGCGTTGATGTGTGGTATATGTAG 59.824 44.000 0.00 0.00 0.00 2.74
824 850 5.629435 CCGGTCTTTTCTTATTGTTTCAAGC 59.371 40.000 0.00 0.00 0.00 4.01
829 855 5.243060 CCCTTCCGGTCTTTTCTTATTGTTT 59.757 40.000 0.00 0.00 0.00 2.83
838 864 2.092323 CATTCCCCTTCCGGTCTTTTC 58.908 52.381 0.00 0.00 0.00 2.29
1322 2355 2.356667 GCTCCTTGTCCTTGGGGG 59.643 66.667 0.00 0.00 0.00 5.40
1487 2538 0.796312 GGAAAAGTTGAGCGCGATGA 59.204 50.000 12.10 0.00 0.00 2.92
1887 2957 0.951040 ACTGTAGCCGCAGTTTGCTC 60.951 55.000 5.09 0.00 46.45 4.26
2186 4331 2.405618 TCGATCCATCCCAAGGAGAT 57.594 50.000 0.00 0.00 38.83 2.75
2190 4335 4.357918 ACTAATTCGATCCATCCCAAGG 57.642 45.455 0.00 0.00 0.00 3.61
2191 4336 5.928839 CAGTACTAATTCGATCCATCCCAAG 59.071 44.000 0.00 0.00 0.00 3.61
2192 4337 5.741964 GCAGTACTAATTCGATCCATCCCAA 60.742 44.000 0.00 0.00 0.00 4.12
2333 5361 1.204941 AGTGTGTCGGGCATACTTCTC 59.795 52.381 6.15 0.00 45.43 2.87
2409 5437 3.375299 CGAATCCATTGAACTCCACTTCC 59.625 47.826 0.00 0.00 0.00 3.46
2438 5466 8.592529 TTCCAATAAATCAAACTCATGATCCA 57.407 30.769 0.00 0.00 39.08 3.41
2569 5600 2.775911 TCCACAGAAGAAGATGCCTG 57.224 50.000 0.00 0.00 0.00 4.85
2570 5601 3.009916 ACATTCCACAGAAGAAGATGCCT 59.990 43.478 0.00 0.00 34.86 4.75
2571 5602 3.350833 ACATTCCACAGAAGAAGATGCC 58.649 45.455 0.00 0.00 34.86 4.40
2576 5607 9.994432 GATAAACATTACATTCCACAGAAGAAG 57.006 33.333 0.00 0.00 34.86 2.85
2593 5624 3.009723 CACCCGAGCTGTGATAAACATT 58.990 45.455 0.00 0.00 38.39 2.71
2797 5880 2.299297 TCTCTCCGTCTCCCAAAAGAAC 59.701 50.000 0.00 0.00 0.00 3.01
3371 6601 7.669089 TGTGGAGTAATATGTGTAGGAATGA 57.331 36.000 0.00 0.00 0.00 2.57
3670 6976 5.047731 TCAAATGTCACAGAAACCACACAAA 60.048 36.000 0.00 0.00 0.00 2.83
3791 7104 1.526887 CGTCGTCACAATGAAACAGCT 59.473 47.619 0.00 0.00 0.00 4.24
3933 7307 5.581350 TCAATCCATCATATAGGGTGCAA 57.419 39.130 0.00 0.00 0.00 4.08
3959 7333 1.991264 CAGAAGTGACACAGAGATGCG 59.009 52.381 8.59 0.00 0.00 4.73
4068 7442 2.501723 AGTGTCGCCAGGAATCAACTAT 59.498 45.455 0.00 0.00 0.00 2.12
4275 7687 0.541530 TTAAGCATGGGCCAACAGCA 60.542 50.000 24.56 7.96 46.50 4.41
4316 7728 0.471617 CGGCCTGATGGAGGAATCTT 59.528 55.000 0.00 0.00 46.33 2.40


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

AutoCloner maintained by Alex Coulton.