Multiple sequence alignment - TraesCS7B01G045200

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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 TraesCS7B01G045200 chr7B 100.000 3445 0 0 1 3445 44306297 44302853 0.000000e+00 6362.0
1 TraesCS7B01G045200 chr7B 98.820 763 9 0 2682 3444 440826590 440827352 0.000000e+00 1360.0
2 TraesCS7B01G045200 chr7B 94.609 742 38 2 2680 3419 610224139 610224880 0.000000e+00 1147.0
3 TraesCS7B01G045200 chr7B 84.000 550 75 11 955 1493 44382564 44382017 1.830000e-142 516.0
4 TraesCS7B01G045200 chr7B 86.168 441 47 10 2226 2659 44394022 44393589 6.730000e-127 464.0
5 TraesCS7B01G045200 chr7B 84.816 461 57 5 1723 2181 44394480 44394031 5.240000e-123 451.0
6 TraesCS7B01G045200 chr7B 86.396 419 48 6 2226 2637 44361989 44361573 1.890000e-122 449.0
7 TraesCS7B01G045200 chr7B 90.536 317 27 3 950 1264 44395106 44394791 1.910000e-112 416.0
8 TraesCS7B01G045200 chr7B 83.333 318 32 11 1312 1621 44394784 44394480 1.220000e-69 274.0
9 TraesCS7B01G045200 chr7A 98.432 1658 25 1 1 1658 94431957 94430301 0.000000e+00 2916.0
10 TraesCS7B01G045200 chr7A 94.439 1007 27 11 1656 2660 94426914 94425935 0.000000e+00 1522.0
11 TraesCS7B01G045200 chr7A 84.050 558 77 10 951 1498 94450749 94450194 8.470000e-146 527.0
12 TraesCS7B01G045200 chr7A 83.603 433 56 11 2226 2650 94449546 94449121 3.220000e-105 392.0
13 TraesCS7B01G045200 chr7D 97.893 1424 24 4 1 1421 92254488 92253068 0.000000e+00 2459.0
14 TraesCS7B01G045200 chr7D 94.627 1247 30 8 1416 2660 92249369 92248158 0.000000e+00 1897.0
15 TraesCS7B01G045200 chr7D 81.415 721 91 22 951 1660 92273205 92272517 1.810000e-152 549.0
16 TraesCS7B01G045200 chr7D 86.538 416 48 8 2226 2637 92272070 92271659 5.240000e-123 451.0
17 TraesCS7B01G045200 chr3A 98.953 764 8 0 2682 3445 10265366 10266129 0.000000e+00 1367.0
18 TraesCS7B01G045200 chr3A 97.775 764 17 0 2680 3443 623360549 623359786 0.000000e+00 1317.0
19 TraesCS7B01G045200 chr5B 98.560 764 11 0 2682 3445 319325906 319326669 0.000000e+00 1351.0
20 TraesCS7B01G045200 chr5B 94.779 747 36 2 2674 3419 54552191 54551447 0.000000e+00 1160.0
21 TraesCS7B01G045200 chr1B 98.556 762 11 0 2684 3445 119769476 119770237 0.000000e+00 1347.0
22 TraesCS7B01G045200 chr1B 98.175 767 14 0 2679 3445 567368287 567367521 0.000000e+00 1339.0
23 TraesCS7B01G045200 chr4B 94.309 738 41 1 2683 3419 536847426 536848163 0.000000e+00 1129.0
24 TraesCS7B01G045200 chr4B 81.503 173 15 15 1003 1170 568340006 568340166 3.610000e-25 126.0
25 TraesCS7B01G045200 chr4B 78.035 173 21 11 1003 1170 568410461 568410621 3.660000e-15 93.5
26 TraesCS7B01G045200 chr4D 77.907 172 23 9 1003 1170 455319013 455319173 3.660000e-15 93.5
27 TraesCS7B01G045200 chr3D 95.349 43 2 0 901 943 73896451 73896409 6.170000e-08 69.4


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 TraesCS7B01G045200 chr7B 44302853 44306297 3444 True 6362.00 6362 100.00000 1 3445 1 chr7B.!!$R1 3444
1 TraesCS7B01G045200 chr7B 440826590 440827352 762 False 1360.00 1360 98.82000 2682 3444 1 chr7B.!!$F1 762
2 TraesCS7B01G045200 chr7B 610224139 610224880 741 False 1147.00 1147 94.60900 2680 3419 1 chr7B.!!$F2 739
3 TraesCS7B01G045200 chr7B 44382017 44382564 547 True 516.00 516 84.00000 955 1493 1 chr7B.!!$R3 538
4 TraesCS7B01G045200 chr7B 44393589 44395106 1517 True 401.25 464 86.21325 950 2659 4 chr7B.!!$R4 1709
5 TraesCS7B01G045200 chr7A 94425935 94431957 6022 True 2219.00 2916 96.43550 1 2660 2 chr7A.!!$R1 2659
6 TraesCS7B01G045200 chr7A 94449121 94450749 1628 True 459.50 527 83.82650 951 2650 2 chr7A.!!$R2 1699
7 TraesCS7B01G045200 chr7D 92248158 92254488 6330 True 2178.00 2459 96.26000 1 2660 2 chr7D.!!$R1 2659
8 TraesCS7B01G045200 chr7D 92271659 92273205 1546 True 500.00 549 83.97650 951 2637 2 chr7D.!!$R2 1686
9 TraesCS7B01G045200 chr3A 10265366 10266129 763 False 1367.00 1367 98.95300 2682 3445 1 chr3A.!!$F1 763
10 TraesCS7B01G045200 chr3A 623359786 623360549 763 True 1317.00 1317 97.77500 2680 3443 1 chr3A.!!$R1 763
11 TraesCS7B01G045200 chr5B 319325906 319326669 763 False 1351.00 1351 98.56000 2682 3445 1 chr5B.!!$F1 763
12 TraesCS7B01G045200 chr5B 54551447 54552191 744 True 1160.00 1160 94.77900 2674 3419 1 chr5B.!!$R1 745
13 TraesCS7B01G045200 chr1B 119769476 119770237 761 False 1347.00 1347 98.55600 2684 3445 1 chr1B.!!$F1 761
14 TraesCS7B01G045200 chr1B 567367521 567368287 766 True 1339.00 1339 98.17500 2679 3445 1 chr1B.!!$R1 766
15 TraesCS7B01G045200 chr4B 536847426 536848163 737 False 1129.00 1129 94.30900 2683 3419 1 chr4B.!!$F1 736

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
679 680 3.340814 ACTTAGACTTCCAGGCATGTG 57.659 47.619 0.00 0.0 0.00 3.21 F
1449 5166 1.734465 GCGCTCAGCTGTTTCTACATT 59.266 47.619 14.67 0.0 44.04 2.71 F
2124 9316 0.106419 CGAGGAGGAGGAAGCTAGGT 60.106 60.000 0.00 0.0 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 9295 0.106419 CTAGCTTCCTCCTCCTCGGT 60.106 60.000 0.00 0.00 0.00 4.69 R
2389 9592 0.321919 TGTTGCATGCTGAGGACCTC 60.322 55.000 20.33 15.13 0.00 3.85 R
3372 10585 4.785512 CTCGCCGAAGACGCAGCT 62.786 66.667 0.00 0.00 38.29 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
26 27 9.996554 TCACTTAAAAACTGATTGAGAGATGTA 57.003 29.630 0.00 0.00 0.00 2.29
679 680 3.340814 ACTTAGACTTCCAGGCATGTG 57.659 47.619 0.00 0.00 0.00 3.21
828 829 5.395657 CCTTATGTCCTGCTTATGTCTGACA 60.396 44.000 13.60 13.60 0.00 3.58
1151 1153 9.699410 ATATAATGAAGACCACAATCTTTTGGA 57.301 29.630 2.22 0.00 39.08 3.53
1197 1204 5.174395 CACTCTCACTCCCTTTATTGTCTG 58.826 45.833 0.00 0.00 0.00 3.51
1198 1206 4.841246 ACTCTCACTCCCTTTATTGTCTGT 59.159 41.667 0.00 0.00 0.00 3.41
1449 5166 1.734465 GCGCTCAGCTGTTTCTACATT 59.266 47.619 14.67 0.00 44.04 2.71
1702 8870 2.629051 CCCAAAACTCGGTAAGGCTAG 58.371 52.381 0.00 0.00 0.00 3.42
1895 9086 6.151312 TGCCGTGGTTGTACATATAACAAAAT 59.849 34.615 0.00 0.00 38.50 1.82
2103 9295 4.642885 CACCCTTCTTTTTACAGTTGGACA 59.357 41.667 0.00 0.00 0.00 4.02
2124 9316 0.106419 CGAGGAGGAGGAAGCTAGGT 60.106 60.000 0.00 0.00 0.00 3.08
2186 9383 8.839310 ACGCGGTAATATATAGTATAGTAGGG 57.161 38.462 12.47 0.00 0.00 3.53
2187 9384 8.651389 ACGCGGTAATATATAGTATAGTAGGGA 58.349 37.037 12.47 0.00 0.00 4.20
2188 9385 9.494271 CGCGGTAATATATAGTATAGTAGGGAA 57.506 37.037 0.00 0.00 0.00 3.97
2219 9416 8.277720 AGTATAGTAGGAGGTGACTAGAATGA 57.722 38.462 0.00 0.00 44.43 2.57
2220 9417 8.380099 AGTATAGTAGGAGGTGACTAGAATGAG 58.620 40.741 0.00 0.00 44.43 2.90
2221 9418 5.718801 AGTAGGAGGTGACTAGAATGAGA 57.281 43.478 0.00 0.00 44.43 3.27
2222 9419 6.274322 AGTAGGAGGTGACTAGAATGAGAT 57.726 41.667 0.00 0.00 44.43 2.75
2223 9420 6.303839 AGTAGGAGGTGACTAGAATGAGATC 58.696 44.000 0.00 0.00 44.43 2.75
2224 9421 5.136068 AGGAGGTGACTAGAATGAGATCA 57.864 43.478 0.00 0.00 44.43 2.92
2491 9694 8.762426 CCTACTTATTTGCCTCGTACTAATTTC 58.238 37.037 0.00 0.00 0.00 2.17
2660 9871 8.542497 AATTGTCATCAGAAACATTTCAATGG 57.458 30.769 14.63 1.94 40.70 3.16
2661 9872 6.897706 TGTCATCAGAAACATTTCAATGGA 57.102 33.333 14.63 5.68 40.70 3.41
2662 9873 6.680810 TGTCATCAGAAACATTTCAATGGAC 58.319 36.000 14.63 12.34 40.70 4.02
2663 9874 6.491062 TGTCATCAGAAACATTTCAATGGACT 59.509 34.615 14.63 0.00 40.70 3.85
2664 9875 7.665145 TGTCATCAGAAACATTTCAATGGACTA 59.335 33.333 14.63 4.86 40.70 2.59
2665 9876 8.180267 GTCATCAGAAACATTTCAATGGACTAG 58.820 37.037 14.63 0.00 40.70 2.57
2666 9877 8.102676 TCATCAGAAACATTTCAATGGACTAGA 58.897 33.333 14.63 0.00 40.70 2.43
2667 9878 8.733458 CATCAGAAACATTTCAATGGACTAGAA 58.267 33.333 7.10 0.00 40.70 2.10
2668 9879 8.868522 TCAGAAACATTTCAATGGACTAGAAT 57.131 30.769 7.10 0.00 40.70 2.40
2669 9880 9.300681 TCAGAAACATTTCAATGGACTAGAATT 57.699 29.630 7.10 0.00 40.70 2.17
2673 9884 9.753674 AAACATTTCAATGGACTAGAATTAGGA 57.246 29.630 0.00 0.00 40.70 2.94
2674 9885 8.738645 ACATTTCAATGGACTAGAATTAGGAC 57.261 34.615 0.00 0.00 40.70 3.85
2675 9886 8.552296 ACATTTCAATGGACTAGAATTAGGACT 58.448 33.333 0.00 0.00 40.70 3.85
2676 9887 9.401058 CATTTCAATGGACTAGAATTAGGACTT 57.599 33.333 0.00 0.00 32.78 3.01
2677 9888 9.620259 ATTTCAATGGACTAGAATTAGGACTTC 57.380 33.333 0.00 0.00 0.00 3.01
2945 10157 2.122099 ACCCTCCGTTCCCTTGGT 60.122 61.111 0.00 0.00 0.00 3.67
3084 10297 0.683504 ATCTGGTCGTCGGTAGCCTT 60.684 55.000 0.00 0.00 0.00 4.35
3132 10345 0.527600 CGGAGATGCGGTTCGAATCA 60.528 55.000 9.48 4.80 43.74 2.57
3167 10380 3.221222 GGGTGCTCTAGCCACGAT 58.779 61.111 0.00 0.00 46.44 3.73
3246 10459 4.804420 TCCCTCCCGCTCCATGCT 62.804 66.667 0.00 0.00 40.11 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.873591 GCTTGTGTTGTTCTCCGTGAT 59.126 47.619 0.00 0.00 0.00 3.06
603 604 6.209391 CCTTTTAAAGACACCATGTTCATCCT 59.791 38.462 6.24 0.00 0.00 3.24
647 648 5.877012 TGGAAGTCTAAGTTCTCAATGCATC 59.123 40.000 0.00 0.00 0.00 3.91
679 680 9.274065 CAAACACTACACTAAACTGAACTTTTC 57.726 33.333 0.00 0.00 0.00 2.29
828 829 9.453572 ACACAAATTACTCTGTCAATGATACAT 57.546 29.630 0.00 0.00 0.00 2.29
1151 1153 0.988063 GGGAGGAAGAGAGCAAACCT 59.012 55.000 0.00 0.00 0.00 3.50
1702 8870 5.646606 TGAACCACTTTGCTGAGTTTTAAC 58.353 37.500 0.00 0.00 0.00 2.01
1895 9086 1.145571 AGGGTGCTTCAGGTTTACCA 58.854 50.000 1.13 0.00 38.89 3.25
2103 9295 0.106419 CTAGCTTCCTCCTCCTCGGT 60.106 60.000 0.00 0.00 0.00 4.69
2124 9316 1.352352 AGCCTCCTCTTTAGCTTGCAA 59.648 47.619 0.00 0.00 29.27 4.08
2194 9391 8.277720 TCATTCTAGTCACCTCCTACTATACT 57.722 38.462 0.00 0.00 0.00 2.12
2195 9392 8.377034 TCTCATTCTAGTCACCTCCTACTATAC 58.623 40.741 0.00 0.00 0.00 1.47
2196 9393 8.507582 TCTCATTCTAGTCACCTCCTACTATA 57.492 38.462 0.00 0.00 0.00 1.31
2197 9394 7.395525 TCTCATTCTAGTCACCTCCTACTAT 57.604 40.000 0.00 0.00 0.00 2.12
2198 9395 6.826632 TCTCATTCTAGTCACCTCCTACTA 57.173 41.667 0.00 0.00 0.00 1.82
2199 9396 5.718801 TCTCATTCTAGTCACCTCCTACT 57.281 43.478 0.00 0.00 0.00 2.57
2200 9397 6.065374 TGATCTCATTCTAGTCACCTCCTAC 58.935 44.000 0.00 0.00 0.00 3.18
2201 9398 6.267492 TGATCTCATTCTAGTCACCTCCTA 57.733 41.667 0.00 0.00 0.00 2.94
2202 9399 5.136068 TGATCTCATTCTAGTCACCTCCT 57.864 43.478 0.00 0.00 0.00 3.69
2203 9400 4.280677 CCTGATCTCATTCTAGTCACCTCC 59.719 50.000 0.00 0.00 0.00 4.30
2204 9401 5.136828 TCCTGATCTCATTCTAGTCACCTC 58.863 45.833 0.00 0.00 0.00 3.85
2205 9402 5.136068 TCCTGATCTCATTCTAGTCACCT 57.864 43.478 0.00 0.00 0.00 4.00
2206 9403 6.719370 ACTATCCTGATCTCATTCTAGTCACC 59.281 42.308 0.00 0.00 0.00 4.02
2207 9404 7.230510 ACACTATCCTGATCTCATTCTAGTCAC 59.769 40.741 0.00 0.00 0.00 3.67
2208 9405 7.293828 ACACTATCCTGATCTCATTCTAGTCA 58.706 38.462 0.00 0.00 0.00 3.41
2209 9406 7.446931 TGACACTATCCTGATCTCATTCTAGTC 59.553 40.741 0.00 0.00 0.00 2.59
2210 9407 7.293828 TGACACTATCCTGATCTCATTCTAGT 58.706 38.462 0.00 0.00 0.00 2.57
2211 9408 7.757941 TGACACTATCCTGATCTCATTCTAG 57.242 40.000 0.00 0.00 0.00 2.43
2212 9409 8.718158 AATGACACTATCCTGATCTCATTCTA 57.282 34.615 0.00 0.00 0.00 2.10
2213 9410 7.510001 AGAATGACACTATCCTGATCTCATTCT 59.490 37.037 18.23 18.23 43.93 2.40
2214 9411 7.669427 AGAATGACACTATCCTGATCTCATTC 58.331 38.462 15.46 15.46 41.14 2.67
2215 9412 7.615039 AGAATGACACTATCCTGATCTCATT 57.385 36.000 0.00 0.00 31.21 2.57
2216 9413 7.949565 AGTAGAATGACACTATCCTGATCTCAT 59.050 37.037 0.00 0.00 0.00 2.90
2217 9414 7.293828 AGTAGAATGACACTATCCTGATCTCA 58.706 38.462 0.00 0.00 0.00 3.27
2218 9415 7.759489 AGTAGAATGACACTATCCTGATCTC 57.241 40.000 0.00 0.00 0.00 2.75
2219 9416 7.393234 GCTAGTAGAATGACACTATCCTGATCT 59.607 40.741 0.00 0.00 0.00 2.75
2220 9417 7.175816 TGCTAGTAGAATGACACTATCCTGATC 59.824 40.741 0.00 0.00 0.00 2.92
2221 9418 7.007116 TGCTAGTAGAATGACACTATCCTGAT 58.993 38.462 0.00 0.00 0.00 2.90
2222 9419 6.365520 TGCTAGTAGAATGACACTATCCTGA 58.634 40.000 0.00 0.00 0.00 3.86
2223 9420 6.641169 TGCTAGTAGAATGACACTATCCTG 57.359 41.667 0.00 0.00 0.00 3.86
2224 9421 6.210385 CCATGCTAGTAGAATGACACTATCCT 59.790 42.308 18.53 0.00 32.78 3.24
2389 9592 0.321919 TGTTGCATGCTGAGGACCTC 60.322 55.000 20.33 15.13 0.00 3.85
2655 9866 5.463724 GCGAAGTCCTAATTCTAGTCCATTG 59.536 44.000 0.00 0.00 0.00 2.82
3372 10585 4.785512 CTCGCCGAAGACGCAGCT 62.786 66.667 0.00 0.00 38.29 4.24


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

AutoCloner maintained by Alex Coulton.