Multiple sequence alignment - TraesCS7B01G363300

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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 TraesCS7B01G363300 chr7B 100.000 2369 0 0 1 2369 625983524 625981156 0.000000e+00 4375.0
1 TraesCS7B01G363300 chr7B 83.843 1374 122 52 1011 2327 625972146 625970816 0.000000e+00 1216.0
2 TraesCS7B01G363300 chr7B 83.843 1374 122 52 1011 2327 625975319 625973989 0.000000e+00 1216.0
3 TraesCS7B01G363300 chr7A 92.984 2252 93 9 163 2369 576140785 576143016 0.000000e+00 3223.0
4 TraesCS7B01G363300 chr7A 92.297 2259 102 8 163 2369 658830824 658828586 0.000000e+00 3142.0
5 TraesCS7B01G363300 chr7A 96.880 1314 39 1 1056 2369 576226049 576227360 0.000000e+00 2198.0
6 TraesCS7B01G363300 chr7A 86.152 1011 73 38 1010 1980 658784146 658783163 0.000000e+00 1029.0
7 TraesCS7B01G363300 chr7A 85.288 1006 89 41 1010 1980 658809015 658808034 0.000000e+00 983.0
8 TraesCS7B01G363300 chr7A 87.271 817 63 20 1010 1813 576168158 576168946 0.000000e+00 894.0
9 TraesCS7B01G363300 chr7A 88.484 686 50 14 1010 1684 576232656 576233323 0.000000e+00 802.0
10 TraesCS7B01G363300 chr7A 83.955 617 55 33 1399 1980 576148937 576149544 3.440000e-153 551.0
11 TraesCS7B01G363300 chr7A 84.436 559 41 19 1010 1541 658930148 658930687 2.100000e-140 508.0
12 TraesCS7B01G363300 chr7A 85.811 444 42 6 1044 1479 575951335 575951765 3.590000e-123 451.0
13 TraesCS7B01G363300 chr7A 85.995 407 40 5 1028 1434 658891224 658890835 1.010000e-113 420.0
14 TraesCS7B01G363300 chr7A 88.169 355 27 4 1010 1364 658910645 658910306 2.190000e-110 409.0
15 TraesCS7B01G363300 chr7A 88.169 355 27 4 1010 1364 658959952 658959613 2.190000e-110 409.0
16 TraesCS7B01G363300 chr7A 86.872 358 29 3 1010 1361 659184282 659184627 3.690000e-103 385.0
17 TraesCS7B01G363300 chr7A 80.856 397 51 15 1987 2369 575443615 575443230 2.980000e-74 289.0
18 TraesCS7B01G363300 chr7A 92.929 198 14 0 2167 2364 576169227 576169424 2.980000e-74 289.0
19 TraesCS7B01G363300 chr7A 92.424 198 15 0 2167 2364 658793859 658793662 1.390000e-72 283.0
20 TraesCS7B01G363300 chr7A 91.626 203 16 1 2167 2369 576233912 576234113 1.790000e-71 279.0
21 TraesCS7B01G363300 chr7A 82.792 308 32 9 1810 2116 576233620 576233907 3.020000e-64 255.0
22 TraesCS7B01G363300 chr7A 89.011 182 15 4 1599 1780 575454770 575454594 1.100000e-53 220.0
23 TraesCS7B01G363300 chr7A 91.549 142 12 0 921 1062 576214324 576214465 1.860000e-46 196.0
24 TraesCS7B01G363300 chr7A 91.525 59 5 0 1818 1876 575444409 575444351 5.430000e-12 82.4
25 TraesCS7B01G363300 chr7D 95.170 911 44 0 1 911 569455793 569454883 0.000000e+00 1439.0
26 TraesCS7B01G363300 chr7D 91.176 850 66 4 163 1012 569708895 569708055 0.000000e+00 1146.0
27 TraesCS7B01G363300 chr7D 88.824 689 45 15 1010 1684 569403756 569403086 0.000000e+00 817.0
28 TraesCS7B01G363300 chr7D 88.008 517 35 12 1097 1602 569706876 569706376 9.430000e-164 586.0
29 TraesCS7B01G363300 chr7D 87.992 483 35 10 1131 1600 569454495 569454023 1.240000e-152 549.0
30 TraesCS7B01G363300 chr7D 95.545 202 8 1 942 1143 569454885 569454685 2.940000e-84 322.0
31 TraesCS7B01G363300 chr7D 86.275 306 23 3 1134 1432 569585684 569585391 4.920000e-82 315.0
32 TraesCS7B01G363300 chr7D 83.390 295 27 9 1822 2116 569402766 569402494 1.090000e-63 254.0
33 TraesCS7B01G363300 chr7D 87.363 182 18 5 1599 1780 570235862 570235686 1.110000e-48 204.0
34 TraesCS7B01G363300 chr7D 88.387 155 17 1 1711 1864 570233848 570233694 4.020000e-43 185.0
35 TraesCS7B01G363300 chr5D 95.706 163 6 1 1 162 211289007 211289169 6.490000e-66 261.0
36 TraesCS7B01G363300 chr5D 94.152 171 8 2 1 170 268350742 268350573 2.340000e-65 259.0
37 TraesCS7B01G363300 chr3D 95.706 163 6 1 1 162 222951546 222951384 6.490000e-66 261.0
38 TraesCS7B01G363300 chr3D 90.761 184 15 2 1 182 366715435 366715618 6.540000e-61 244.0
39 TraesCS7B01G363300 chr2D 95.679 162 6 1 3 163 425606002 425606163 2.340000e-65 259.0
40 TraesCS7B01G363300 chr6D 95.122 164 7 1 1 163 119350677 119350840 8.400000e-65 257.0
41 TraesCS7B01G363300 chr1D 95.122 164 7 1 1 163 137584256 137584093 8.400000e-65 257.0
42 TraesCS7B01G363300 chr4D 93.567 171 9 2 1 170 353482865 353482696 1.090000e-63 254.0


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 TraesCS7B01G363300 chr7B 625981156 625983524 2368 True 4375.000000 4375 100.000000 1 2369 1 chr7B.!!$R1 2368
1 TraesCS7B01G363300 chr7B 625970816 625975319 4503 True 1216.000000 1216 83.843000 1011 2327 2 chr7B.!!$R2 1316
2 TraesCS7B01G363300 chr7A 576140785 576143016 2231 False 3223.000000 3223 92.984000 163 2369 1 chr7A.!!$F2 2206
3 TraesCS7B01G363300 chr7A 658828586 658830824 2238 True 3142.000000 3142 92.297000 163 2369 1 chr7A.!!$R5 2206
4 TraesCS7B01G363300 chr7A 576226049 576227360 1311 False 2198.000000 2198 96.880000 1056 2369 1 chr7A.!!$F5 1313
5 TraesCS7B01G363300 chr7A 658783163 658784146 983 True 1029.000000 1029 86.152000 1010 1980 1 chr7A.!!$R2 970
6 TraesCS7B01G363300 chr7A 658808034 658809015 981 True 983.000000 983 85.288000 1010 1980 1 chr7A.!!$R4 970
7 TraesCS7B01G363300 chr7A 576168158 576169424 1266 False 591.500000 894 90.100000 1010 2364 2 chr7A.!!$F8 1354
8 TraesCS7B01G363300 chr7A 576148937 576149544 607 False 551.000000 551 83.955000 1399 1980 1 chr7A.!!$F3 581
9 TraesCS7B01G363300 chr7A 658930148 658930687 539 False 508.000000 508 84.436000 1010 1541 1 chr7A.!!$F6 531
10 TraesCS7B01G363300 chr7A 576232656 576234113 1457 False 445.333333 802 87.634000 1010 2369 3 chr7A.!!$F9 1359
11 TraesCS7B01G363300 chr7D 569706376 569708895 2519 True 866.000000 1146 89.592000 163 1602 2 chr7D.!!$R4 1439
12 TraesCS7B01G363300 chr7D 569454023 569455793 1770 True 770.000000 1439 92.902333 1 1600 3 chr7D.!!$R3 1599
13 TraesCS7B01G363300 chr7D 569402494 569403756 1262 True 535.500000 817 86.107000 1010 2116 2 chr7D.!!$R2 1106

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
815 816 0.460284 ATACAGCGTTGGAGAAGCCG 60.46 55.0 3.74 0.0 40.66 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 6276 5.308014 AGTGTTATGACTTCACATTGAGCA 58.692 37.5 0.0 0.0 34.94 4.26 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
56 57 5.914033 TGGCACTATGTCAATAGGTTAGAC 58.086 41.667 0.00 0.00 40.23 2.59
176 177 0.464916 TATCAGAGACGTAGGCGCCA 60.465 55.000 31.54 12.31 42.83 5.69
295 296 1.452651 CCATCAAGGCCATGCTCGT 60.453 57.895 5.01 0.00 0.00 4.18
377 378 4.530857 CAACTAGGCGGAGGGCGG 62.531 72.222 0.00 0.00 44.92 6.13
419 420 2.815647 GGAGGCGAACGCTTGGAG 60.816 66.667 18.14 0.00 41.60 3.86
426 427 0.667487 CGAACGCTTGGAGAGAGCAA 60.667 55.000 0.00 0.00 40.13 3.91
433 434 2.482664 GCTTGGAGAGAGCAATCGATCA 60.483 50.000 0.00 0.00 39.89 2.92
551 552 1.302431 CCACCGGCAGTGTCAATGA 60.302 57.895 0.00 0.00 45.74 2.57
763 764 6.353323 TGATTGACTCCGGCTAAAATATTCA 58.647 36.000 0.00 0.00 0.00 2.57
765 766 6.861065 TTGACTCCGGCTAAAATATTCATC 57.139 37.500 0.00 0.00 0.00 2.92
815 816 0.460284 ATACAGCGTTGGAGAAGCCG 60.460 55.000 3.74 0.00 40.66 5.52
872 893 9.996554 AAAAAGAAAAAGGAATACATTTCCGAT 57.003 25.926 0.00 0.00 43.23 4.18
930 951 2.355108 CCGGAAGAACACCAGACATCAT 60.355 50.000 0.00 0.00 0.00 2.45
950 971 2.604629 TATCCACGCCCCCGGTTTT 61.605 57.895 0.00 0.00 39.22 2.43
954 975 4.960866 ACGCCCCCGGTTTTGACC 62.961 66.667 0.00 0.00 39.22 4.02
1067 1121 0.974383 CCGTATGAGGGGTATGGGAC 59.026 60.000 0.00 0.00 0.00 4.46
1166 2482 4.285790 TCCCCTGCCCAACCTCCT 62.286 66.667 0.00 0.00 0.00 3.69
1180 2496 3.125573 TCCTCGAGGAGTCACGCG 61.126 66.667 30.49 3.53 39.78 6.01
1181 2497 3.125573 CCTCGAGGAGTCACGCGA 61.126 66.667 28.21 7.11 37.39 5.87
1182 2498 2.687805 CCTCGAGGAGTCACGCGAA 61.688 63.158 28.21 0.00 37.39 4.70
1183 2499 1.226156 CTCGAGGAGTCACGCGAAG 60.226 63.158 15.93 4.76 31.89 3.79
1184 2500 1.636570 CTCGAGGAGTCACGCGAAGA 61.637 60.000 15.93 7.66 31.89 2.87
1185 2501 1.226156 CGAGGAGTCACGCGAAGAG 60.226 63.158 15.93 0.00 0.00 2.85
1186 2502 1.877367 GAGGAGTCACGCGAAGAGT 59.123 57.895 15.93 13.53 45.01 3.24
1187 2503 1.085091 GAGGAGTCACGCGAAGAGTA 58.915 55.000 15.93 0.00 39.58 2.59
1239 2573 1.676635 CGACCACCACGAGAGGGTA 60.677 63.158 0.00 0.00 36.72 3.69
1332 2666 0.324091 AACTCCCCGACGACCAGTAT 60.324 55.000 0.00 0.00 0.00 2.12
1373 2707 2.786578 GCGACGAAGAAGCTTGATCTAG 59.213 50.000 2.10 0.00 0.00 2.43
1529 2920 6.654959 TGTGTAACCAGGCAAAGCTATATTA 58.345 36.000 0.00 0.00 34.36 0.98
1799 6726 4.868171 TCATGGCTTTAACTACGCACTAAG 59.132 41.667 0.00 0.00 0.00 2.18
2250 7255 6.757237 TGAAACTTTACACCATGATTTGCAT 58.243 32.000 0.00 0.00 37.85 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.533625 TTGACATAGTGCCAAGTGCC 58.466 50.000 0.00 0.00 40.16 5.01
155 156 0.661552 GCGCCTACGTCTCTGATACA 59.338 55.000 0.00 0.00 42.83 2.29
176 177 2.915659 TGGAACGCGGAGACCAGT 60.916 61.111 12.47 0.00 0.00 4.00
266 267 0.247460 CCTTGATGGTCTGCTCGTCA 59.753 55.000 0.00 0.00 0.00 4.35
295 296 4.448720 TCCACGATACCTAGATTCTCCA 57.551 45.455 0.00 0.00 0.00 3.86
377 378 3.567797 GCTCCTCGAACATGCGGC 61.568 66.667 0.00 0.00 0.00 6.53
419 420 1.482278 GTCCGTGATCGATTGCTCTC 58.518 55.000 0.00 0.00 39.71 3.20
426 427 0.100682 CGTTCTGGTCCGTGATCGAT 59.899 55.000 0.00 0.00 39.71 3.59
433 434 4.681978 GGCAGCGTTCTGGTCCGT 62.682 66.667 0.00 0.00 40.65 4.69
551 552 2.210013 TCAGAGTTCGCTGCCTGGT 61.210 57.895 0.00 0.00 35.86 4.00
638 639 2.617308 CGCCCTAGTCTATTCTTCGTCA 59.383 50.000 0.00 0.00 0.00 4.35
763 764 6.127168 TGGACACTAAGTTCGGATATGTTGAT 60.127 38.462 0.00 0.00 0.00 2.57
765 766 5.416083 TGGACACTAAGTTCGGATATGTTG 58.584 41.667 0.00 0.00 0.00 3.33
864 885 1.657804 CCCTAGGCCCTATCGGAAAT 58.342 55.000 2.05 0.00 0.00 2.17
899 920 2.946346 TTCTTCCGGGTGCCGTACC 61.946 63.158 0.00 0.00 46.80 3.34
913 934 5.045651 TGGATACATGATGTCTGGTGTTCTT 60.046 40.000 0.00 0.00 46.17 2.52
914 935 4.471025 TGGATACATGATGTCTGGTGTTCT 59.529 41.667 0.00 0.00 46.17 3.01
915 936 4.769688 TGGATACATGATGTCTGGTGTTC 58.230 43.478 0.00 0.00 46.17 3.18
950 971 3.751518 TCCATCGAGATCTATTCGGTCA 58.248 45.455 0.00 0.00 38.54 4.02
954 975 3.376859 CCTCCTCCATCGAGATCTATTCG 59.623 52.174 0.00 0.00 38.52 3.34
1023 1077 2.359967 CCTCAACCTCTCGGGGGAC 61.360 68.421 0.00 0.00 40.03 4.46
1042 1096 4.192950 CCCCTCATACGGGTCGAT 57.807 61.111 0.00 0.00 43.06 3.59
1067 1121 2.995283 TCACCATCATCTGCTTCTTGG 58.005 47.619 0.00 0.00 0.00 3.61
1166 2482 1.636570 CTCTTCGCGTGACTCCTCGA 61.637 60.000 5.77 0.00 0.00 4.04
1180 2496 2.017559 ATGGCCTCGCGGTACTCTTC 62.018 60.000 6.13 0.00 0.00 2.87
1181 2497 2.058595 ATGGCCTCGCGGTACTCTT 61.059 57.895 6.13 0.00 0.00 2.85
1182 2498 2.442272 ATGGCCTCGCGGTACTCT 60.442 61.111 6.13 0.00 0.00 3.24
1183 2499 2.279517 CATGGCCTCGCGGTACTC 60.280 66.667 6.13 0.00 0.00 2.59
1184 2500 3.849951 CCATGGCCTCGCGGTACT 61.850 66.667 6.13 0.00 0.00 2.73
1185 2501 3.845259 TCCATGGCCTCGCGGTAC 61.845 66.667 6.96 0.00 0.00 3.34
1186 2502 3.845259 GTCCATGGCCTCGCGGTA 61.845 66.667 6.96 0.00 0.00 4.02
1332 2666 1.467342 CTGTCGTAGTGGATGACGTCA 59.533 52.381 22.48 22.48 45.75 4.35
1373 2707 9.138062 CACATTAGATAGATAGATGTTGCTCAC 57.862 37.037 0.00 0.00 0.00 3.51
1696 6276 5.308014 AGTGTTATGACTTCACATTGAGCA 58.692 37.500 0.00 0.00 34.94 4.26
2250 7255 5.915758 CGGTCAAAATAAACCATCGTGAAAA 59.084 36.000 0.00 0.00 35.13 2.29


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

AutoCloner maintained by Alex Coulton.