Multiple sequence alignment - TraesCS7D01G337700

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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 TraesCS7D01G337700 chr7D 100.000 2359 0 0 1 2359 431121733 431119375 0.000000e+00 4357
1 TraesCS7D01G337700 chr7D 97.820 688 14 1 1 688 483549908 483549222 0.000000e+00 1186
2 TraesCS7D01G337700 chr7B 95.438 1096 36 7 686 1779 448640190 448639107 0.000000e+00 1735
3 TraesCS7D01G337700 chr7A 91.963 1095 67 11 686 1779 501921123 501922197 0.000000e+00 1515
4 TraesCS7D01G337700 chr7A 84.590 597 79 12 1770 2359 202643269 202642679 4.370000e-162 580
5 TraesCS7D01G337700 chr3D 97.974 691 12 2 1 690 346206550 346205861 0.000000e+00 1197
6 TraesCS7D01G337700 chr3D 89.231 390 37 5 1769 2154 453831513 453831901 1.270000e-132 483
7 TraesCS7D01G337700 chr3D 89.406 387 34 6 1769 2152 434085393 434085775 4.560000e-132 481
8 TraesCS7D01G337700 chr3D 88.265 392 39 7 1769 2154 339007226 339007616 1.650000e-126 462
9 TraesCS7D01G337700 chr1D 98.105 686 13 0 1 686 436995967 436996652 0.000000e+00 1195
10 TraesCS7D01G337700 chr1D 98.105 686 12 1 1 686 177909105 177908421 0.000000e+00 1194
11 TraesCS7D01G337700 chr1D 97.540 691 15 2 1 691 439995865 439995177 0.000000e+00 1181
12 TraesCS7D01G337700 chr4D 97.695 694 13 3 1 693 116324373 116325064 0.000000e+00 1190
13 TraesCS7D01G337700 chr4D 97.959 686 13 1 1 686 442995027 442995711 0.000000e+00 1188
14 TraesCS7D01G337700 chr4D 89.590 586 53 6 1781 2359 113051587 113052171 0.000000e+00 737
15 TraesCS7D01G337700 chr4D 88.295 393 38 7 1765 2154 327707560 327707173 4.590000e-127 464
16 TraesCS7D01G337700 chr5D 97.820 688 14 1 1 688 527994003 527994689 0.000000e+00 1186
17 TraesCS7D01G337700 chr5D 97.817 687 14 1 1 686 59634871 59634185 0.000000e+00 1184
18 TraesCS7D01G337700 chr5D 88.946 389 40 3 1769 2154 94075394 94075782 5.900000e-131 477
19 TraesCS7D01G337700 chr2B 89.078 586 51 12 1780 2359 88914390 88913812 0.000000e+00 715
20 TraesCS7D01G337700 chr2B 88.851 583 52 7 1781 2359 210268448 210269021 0.000000e+00 704
21 TraesCS7D01G337700 chr2B 87.724 391 43 5 1768 2154 762221142 762221531 3.580000e-123 451
22 TraesCS7D01G337700 chr6D 88.737 586 57 8 1781 2359 319459653 319459070 0.000000e+00 708
23 TraesCS7D01G337700 chr6D 89.717 389 36 4 1769 2154 457217001 457216614 5.860000e-136 494
24 TraesCS7D01G337700 chr1B 87.822 583 63 7 1781 2359 522351830 522351252 0.000000e+00 676
25 TraesCS7D01G337700 chr2D 86.500 600 54 21 1781 2359 602047573 602046980 3.310000e-178 634
26 TraesCS7D01G337700 chr2D 88.946 389 39 4 1768 2154 455226944 455227330 5.900000e-131 477
27 TraesCS7D01G337700 chr1A 86.316 570 55 17 1804 2359 263843468 263844028 1.210000e-167 599
28 TraesCS7D01G337700 chr4B 85.374 588 72 14 1780 2359 499036347 499036928 4.340000e-167 597


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 TraesCS7D01G337700 chr7D 431119375 431121733 2358 True 4357 4357 100.000 1 2359 1 chr7D.!!$R1 2358
1 TraesCS7D01G337700 chr7D 483549222 483549908 686 True 1186 1186 97.820 1 688 1 chr7D.!!$R2 687
2 TraesCS7D01G337700 chr7B 448639107 448640190 1083 True 1735 1735 95.438 686 1779 1 chr7B.!!$R1 1093
3 TraesCS7D01G337700 chr7A 501921123 501922197 1074 False 1515 1515 91.963 686 1779 1 chr7A.!!$F1 1093
4 TraesCS7D01G337700 chr7A 202642679 202643269 590 True 580 580 84.590 1770 2359 1 chr7A.!!$R1 589
5 TraesCS7D01G337700 chr3D 346205861 346206550 689 True 1197 1197 97.974 1 690 1 chr3D.!!$R1 689
6 TraesCS7D01G337700 chr1D 436995967 436996652 685 False 1195 1195 98.105 1 686 1 chr1D.!!$F1 685
7 TraesCS7D01G337700 chr1D 177908421 177909105 684 True 1194 1194 98.105 1 686 1 chr1D.!!$R1 685
8 TraesCS7D01G337700 chr1D 439995177 439995865 688 True 1181 1181 97.540 1 691 1 chr1D.!!$R2 690
9 TraesCS7D01G337700 chr4D 116324373 116325064 691 False 1190 1190 97.695 1 693 1 chr4D.!!$F2 692
10 TraesCS7D01G337700 chr4D 442995027 442995711 684 False 1188 1188 97.959 1 686 1 chr4D.!!$F3 685
11 TraesCS7D01G337700 chr4D 113051587 113052171 584 False 737 737 89.590 1781 2359 1 chr4D.!!$F1 578
12 TraesCS7D01G337700 chr5D 527994003 527994689 686 False 1186 1186 97.820 1 688 1 chr5D.!!$F2 687
13 TraesCS7D01G337700 chr5D 59634185 59634871 686 True 1184 1184 97.817 1 686 1 chr5D.!!$R1 685
14 TraesCS7D01G337700 chr2B 88913812 88914390 578 True 715 715 89.078 1780 2359 1 chr2B.!!$R1 579
15 TraesCS7D01G337700 chr2B 210268448 210269021 573 False 704 704 88.851 1781 2359 1 chr2B.!!$F1 578
16 TraesCS7D01G337700 chr6D 319459070 319459653 583 True 708 708 88.737 1781 2359 1 chr6D.!!$R1 578
17 TraesCS7D01G337700 chr1B 522351252 522351830 578 True 676 676 87.822 1781 2359 1 chr1B.!!$R1 578
18 TraesCS7D01G337700 chr2D 602046980 602047573 593 True 634 634 86.500 1781 2359 1 chr2D.!!$R1 578
19 TraesCS7D01G337700 chr1A 263843468 263844028 560 False 599 599 86.316 1804 2359 1 chr1A.!!$F1 555
20 TraesCS7D01G337700 chr4B 499036347 499036928 581 False 597 597 85.374 1780 2359 1 chr4B.!!$F1 579

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
254 255 1.384191 GAATGGGCCTCTGTTGGGT 59.616 57.895 4.53 0.0 0.0 4.51 F
1153 1155 0.035056 GGCAGTATTGGAGCACACCT 60.035 55.000 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1262 1264 0.178068 ATGTACCGTGTGAGCCATCC 59.822 55.000 0.00 0.0 0.00 3.51 R
2057 2080 1.134640 ACTGTAACCACGCTGTTGTGA 60.135 47.619 4.15 0.0 42.55 3.58 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
245 246 1.550869 CCTTTTCACAGGAATGGGCCT 60.551 52.381 4.53 0.00 39.37 5.19
254 255 1.384191 GAATGGGCCTCTGTTGGGT 59.616 57.895 4.53 0.00 0.00 4.51
414 415 2.237893 ACGGGTTATCGGATCCAAAACT 59.762 45.455 13.41 0.00 0.00 2.66
518 519 4.808895 CGATTTATCGTCATGGAAGTGGAA 59.191 41.667 4.03 0.00 44.74 3.53
610 611 8.352137 TGATTCTGTCATAAATTTGTCATGGT 57.648 30.769 0.00 0.00 0.00 3.55
916 918 8.716674 ATATAATGTCATCTTCTTTGCCCATT 57.283 30.769 0.00 0.00 0.00 3.16
1065 1067 2.554272 GTTGCTACGCCAACCACG 59.446 61.111 3.58 0.00 39.27 4.94
1153 1155 0.035056 GGCAGTATTGGAGCACACCT 60.035 55.000 0.00 0.00 0.00 4.00
1159 1161 2.496899 ATTGGAGCACACCTAACTGG 57.503 50.000 0.00 0.00 42.93 4.00
1160 1162 0.400213 TTGGAGCACACCTAACTGGG 59.600 55.000 0.00 0.00 41.11 4.45
1162 1164 1.299976 GAGCACACCTAACTGGGGG 59.700 63.158 0.00 0.00 45.72 5.40
1227 1229 3.430790 CGAGGAGCAGATTGTGAATGGTA 60.431 47.826 0.00 0.00 0.00 3.25
1242 1244 6.183360 TGTGAATGGTATAAACTATCGGCTCA 60.183 38.462 0.00 0.00 0.00 4.26
1262 1264 4.196971 TCATCATTGATGCCTTGAGACTG 58.803 43.478 19.74 0.00 39.63 3.51
1434 1436 6.694447 AGGAAATGTCAAGGAATTGATGTTG 58.306 36.000 0.00 0.00 33.02 3.33
1442 1444 7.284261 TGTCAAGGAATTGATGTTGTGTTTCTA 59.716 33.333 0.00 0.00 33.02 2.10
1444 1446 6.575162 AGGAATTGATGTTGTGTTTCTACC 57.425 37.500 0.00 0.00 0.00 3.18
1445 1447 6.306987 AGGAATTGATGTTGTGTTTCTACCT 58.693 36.000 0.00 0.00 0.00 3.08
1446 1448 6.207417 AGGAATTGATGTTGTGTTTCTACCTG 59.793 38.462 0.00 0.00 0.00 4.00
1493 1495 1.003223 GGCAACTCGCAACGTTTTACT 60.003 47.619 0.00 0.00 45.17 2.24
1639 1642 1.478631 TGGTTGTGAAATGTGCACCA 58.521 45.000 15.69 1.28 35.43 4.17
1644 1647 0.523072 GTGAAATGTGCACCATCGCT 59.477 50.000 15.69 0.00 31.75 4.93
1678 1681 4.871933 AACACAAGATGGCCCTAAAAAG 57.128 40.909 0.00 0.00 0.00 2.27
1683 1686 4.017130 ACAAGATGGCCCTAAAAAGGAGAT 60.017 41.667 0.00 0.00 0.00 2.75
1715 1718 7.428472 GGCGTTTCACTTTAAGATAACTATTGC 59.572 37.037 0.00 0.00 0.00 3.56
1720 1723 7.324935 TCACTTTAAGATAACTATTGCGGTCA 58.675 34.615 0.00 0.00 0.00 4.02
1751 1754 9.077885 TCTTCTTGCTATTTATGTCCTTTTGTT 57.922 29.630 0.00 0.00 0.00 2.83
1779 1782 6.821665 GGTGTTGGTATATGTGACTGTGTATT 59.178 38.462 0.00 0.00 0.00 1.89
1886 1900 2.742053 GTGTGTCTACGTACCCTCGTAA 59.258 50.000 0.00 0.00 43.89 3.18
1974 1995 1.971962 GTACCGAACGTACGACACTTG 59.028 52.381 24.41 7.44 38.17 3.16
1983 2004 0.238025 TACGACACTTGCGCGTTCTA 59.762 50.000 8.43 0.00 39.24 2.10
2019 2040 1.292541 GACGTCCTCCGCCTTCTTT 59.707 57.895 3.51 0.00 41.42 2.52
2057 2080 2.628657 GGTAGTAGATGAGTTCCGGCAT 59.371 50.000 0.00 0.00 0.00 4.40
2072 2095 1.654220 GCATCACAACAGCGTGGTT 59.346 52.632 0.00 0.00 37.50 3.67
2090 2115 2.484264 GGTTACAGTGATGGTGAAGTGC 59.516 50.000 0.00 0.00 0.00 4.40
2129 2155 5.405571 CGCCTAAGCACTACGAAAATATGAT 59.594 40.000 0.00 0.00 39.83 2.45
2197 2237 4.659111 TCTTCTTGTAGACGTTGTTGGA 57.341 40.909 0.00 0.00 0.00 3.53
2212 2252 2.538790 TGGACCTCCAAGTGCAGAA 58.461 52.632 0.00 0.00 44.35 3.02
2300 2340 4.582656 CGTAGGATGAAGATGGTCTCTCTT 59.417 45.833 0.00 0.00 35.69 2.85
2301 2341 5.507149 CGTAGGATGAAGATGGTCTCTCTTG 60.507 48.000 0.00 0.00 33.18 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.795638 GACGTCTTTCGGCCCATC 58.204 61.111 8.70 0.00 42.54 3.51
245 246 1.302431 CGTGGCATGACCCAACAGA 60.302 57.895 0.00 0.00 36.46 3.41
254 255 2.430075 CGTCGACACGTGGCATGA 60.430 61.111 23.63 8.75 41.42 3.07
414 415 0.664761 CCGTTAAGCTATCGGGTCGA 59.335 55.000 13.87 0.00 40.49 4.20
836 838 9.899226 GGGCAAGAATCAATTACATATCTTTAC 57.101 33.333 0.00 0.00 0.00 2.01
916 918 0.602562 GGCTTGCAATGGTTGTGCTA 59.397 50.000 0.00 0.00 42.69 3.49
1227 1229 6.093219 GCATCAATGATGAGCCGATAGTTTAT 59.907 38.462 25.77 0.00 42.09 1.40
1242 1244 3.201487 TCCAGTCTCAAGGCATCAATGAT 59.799 43.478 0.00 0.00 0.00 2.45
1262 1264 0.178068 ATGTACCGTGTGAGCCATCC 59.822 55.000 0.00 0.00 0.00 3.51
1411 1413 6.366877 CACAACATCAATTCCTTGACATTTCC 59.633 38.462 0.00 0.00 43.92 3.13
1434 1436 6.640518 TCCATAATCTGTCAGGTAGAAACAC 58.359 40.000 0.00 0.00 0.00 3.32
1442 1444 9.872684 ATGAATAATTTCCATAATCTGTCAGGT 57.127 29.630 0.00 0.00 0.00 4.00
1577 1580 1.815003 GCCATCTTTGTGAAGGGACTG 59.185 52.381 0.00 0.00 40.86 3.51
1578 1581 2.815589 GTGCCATCTTTGTGAAGGGACT 60.816 50.000 4.73 0.00 46.68 3.85
1639 1642 9.431887 TCTTGTGTTTCTTAACTTTATAGCGAT 57.568 29.630 0.00 0.00 35.24 4.58
1644 1647 8.736244 GGCCATCTTGTGTTTCTTAACTTTATA 58.264 33.333 0.00 0.00 35.24 0.98
1678 1681 3.798202 AGTGAAACGCCATCTAATCTCC 58.202 45.455 0.00 0.00 45.86 3.71
1683 1686 8.662141 GTTATCTTAAAGTGAAACGCCATCTAA 58.338 33.333 0.00 0.00 45.86 2.10
1715 1718 1.446907 AGCAAGAAGAGCAATGACCG 58.553 50.000 0.00 0.00 0.00 4.79
1720 1723 7.059156 AGGACATAAATAGCAAGAAGAGCAAT 58.941 34.615 0.00 0.00 0.00 3.56
1751 1754 5.471797 CACAGTCACATATACCAACACCAAA 59.528 40.000 0.00 0.00 0.00 3.28
1779 1782 2.323599 TCCATGCAACATTCCCAACAA 58.676 42.857 0.00 0.00 0.00 2.83
1886 1900 5.310451 TGTTAAATGCTTCCTCTTACGGTT 58.690 37.500 0.00 0.00 0.00 4.44
1983 2004 1.591594 CACCGAGCTGAACGTGTGT 60.592 57.895 0.00 0.00 32.15 3.72
2019 2040 1.289160 ACCTTGCCTCTTGCTGGATA 58.711 50.000 0.00 0.00 42.00 2.59
2034 2057 2.694109 GCCGGAACTCATCTACTACCTT 59.306 50.000 5.05 0.00 0.00 3.50
2057 2080 1.134640 ACTGTAACCACGCTGTTGTGA 60.135 47.619 4.15 0.00 42.55 3.58
2072 2095 2.899900 AGAGCACTTCACCATCACTGTA 59.100 45.455 0.00 0.00 0.00 2.74
2129 2155 2.742403 CACCGTTTACACCCCCGA 59.258 61.111 0.00 0.00 0.00 5.14
2197 2237 2.301346 CAAACTTCTGCACTTGGAGGT 58.699 47.619 0.00 0.00 34.00 3.85
2212 2252 6.206829 GGAAATTTGCTACTGTCCTACAAACT 59.793 38.462 1.93 0.00 33.46 2.66
2300 2340 1.561643 TTTGGTTGCAGGGTTGTTCA 58.438 45.000 0.00 0.00 0.00 3.18
2301 2341 2.908688 ATTTGGTTGCAGGGTTGTTC 57.091 45.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.