Multiple sequence alignment - TraesCS4D01G348100

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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 TraesCS4D01G348100 chr4D 100.000 2537 0 0 1 2537 502032277 502029741 0.000000e+00 4686
1 TraesCS4D01G348100 chr5A 91.938 1166 58 11 563 1700 684666975 684665818 0.000000e+00 1600
2 TraesCS4D01G348100 chr4B 89.664 1219 47 28 565 1704 646130292 646129074 0.000000e+00 1480
3 TraesCS4D01G348100 chrUn 97.236 832 21 2 1707 2537 100223398 100222568 0.000000e+00 1408
4 TraesCS4D01G348100 chrUn 91.297 563 47 2 1 562 434813839 434814400 0.000000e+00 767
5 TraesCS4D01G348100 chr6D 96.992 831 24 1 1707 2537 950959 950130 0.000000e+00 1395
6 TraesCS4D01G348100 chr6D 91.815 562 43 3 1 560 68329285 68328725 0.000000e+00 780
7 TraesCS4D01G348100 chr6D 90.909 561 50 1 1 560 27033602 27034162 0.000000e+00 752
8 TraesCS4D01G348100 chr6D 90.426 564 54 0 1 564 334239027 334238464 0.000000e+00 743
9 TraesCS4D01G348100 chr5D 96.755 832 27 0 1706 2537 88473452 88472621 0.000000e+00 1387
10 TraesCS4D01G348100 chr5D 95.427 831 37 1 1707 2537 294346793 294347622 0.000000e+00 1323
11 TraesCS4D01G348100 chr4A 92.780 831 57 2 1706 2535 710173322 710172494 0.000000e+00 1199
12 TraesCS4D01G348100 chr4A 90.893 560 49 2 1 558 709619716 709620275 0.000000e+00 750
13 TraesCS4D01G348100 chr7D 91.827 832 47 8 1707 2537 568946131 568945320 0.000000e+00 1140
14 TraesCS4D01G348100 chr5B 90.625 832 77 1 1704 2535 493514234 493515064 0.000000e+00 1103
15 TraesCS4D01G348100 chr3B 90.580 828 73 3 1708 2534 59219204 59220027 0.000000e+00 1092
16 TraesCS4D01G348100 chr2B 92.867 743 50 3 1702 2443 602049837 602049097 0.000000e+00 1075
17 TraesCS4D01G348100 chr2B 86.038 838 95 12 1705 2523 153887865 153888699 0.000000e+00 880
18 TraesCS4D01G348100 chr7A 91.844 564 45 1 1 563 670686065 670686628 0.000000e+00 785
19 TraesCS4D01G348100 chr7A 91.087 561 48 2 1 560 6799153 6799712 0.000000e+00 758
20 TraesCS4D01G348100 chr2A 91.444 561 44 4 1 560 449264581 449265138 0.000000e+00 767
21 TraesCS4D01G348100 chr1D 91.297 563 47 2 1 562 375353247 375352686 0.000000e+00 767
22 TraesCS4D01G348100 chr1B 80.479 292 46 6 1040 1330 350876442 350876161 1.980000e-51 213


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 TraesCS4D01G348100 chr4D 502029741 502032277 2536 True 4686 4686 100.000 1 2537 1 chr4D.!!$R1 2536
1 TraesCS4D01G348100 chr5A 684665818 684666975 1157 True 1600 1600 91.938 563 1700 1 chr5A.!!$R1 1137
2 TraesCS4D01G348100 chr4B 646129074 646130292 1218 True 1480 1480 89.664 565 1704 1 chr4B.!!$R1 1139
3 TraesCS4D01G348100 chrUn 100222568 100223398 830 True 1408 1408 97.236 1707 2537 1 chrUn.!!$R1 830
4 TraesCS4D01G348100 chrUn 434813839 434814400 561 False 767 767 91.297 1 562 1 chrUn.!!$F1 561
5 TraesCS4D01G348100 chr6D 950130 950959 829 True 1395 1395 96.992 1707 2537 1 chr6D.!!$R1 830
6 TraesCS4D01G348100 chr6D 68328725 68329285 560 True 780 780 91.815 1 560 1 chr6D.!!$R2 559
7 TraesCS4D01G348100 chr6D 27033602 27034162 560 False 752 752 90.909 1 560 1 chr6D.!!$F1 559
8 TraesCS4D01G348100 chr6D 334238464 334239027 563 True 743 743 90.426 1 564 1 chr6D.!!$R3 563
9 TraesCS4D01G348100 chr5D 88472621 88473452 831 True 1387 1387 96.755 1706 2537 1 chr5D.!!$R1 831
10 TraesCS4D01G348100 chr5D 294346793 294347622 829 False 1323 1323 95.427 1707 2537 1 chr5D.!!$F1 830
11 TraesCS4D01G348100 chr4A 710172494 710173322 828 True 1199 1199 92.780 1706 2535 1 chr4A.!!$R1 829
12 TraesCS4D01G348100 chr4A 709619716 709620275 559 False 750 750 90.893 1 558 1 chr4A.!!$F1 557
13 TraesCS4D01G348100 chr7D 568945320 568946131 811 True 1140 1140 91.827 1707 2537 1 chr7D.!!$R1 830
14 TraesCS4D01G348100 chr5B 493514234 493515064 830 False 1103 1103 90.625 1704 2535 1 chr5B.!!$F1 831
15 TraesCS4D01G348100 chr3B 59219204 59220027 823 False 1092 1092 90.580 1708 2534 1 chr3B.!!$F1 826
16 TraesCS4D01G348100 chr2B 602049097 602049837 740 True 1075 1075 92.867 1702 2443 1 chr2B.!!$R1 741
17 TraesCS4D01G348100 chr2B 153887865 153888699 834 False 880 880 86.038 1705 2523 1 chr2B.!!$F1 818
18 TraesCS4D01G348100 chr7A 670686065 670686628 563 False 785 785 91.844 1 563 1 chr7A.!!$F2 562
19 TraesCS4D01G348100 chr7A 6799153 6799712 559 False 758 758 91.087 1 560 1 chr7A.!!$F1 559
20 TraesCS4D01G348100 chr2A 449264581 449265138 557 False 767 767 91.444 1 560 1 chr2A.!!$F1 559
21 TraesCS4D01G348100 chr1D 375352686 375353247 561 True 767 767 91.297 1 562 1 chr1D.!!$R1 561

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
45 46 0.875059 CTCCGTTTTCAGGTGCTTCC 59.125 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1702 0.385223 CAAAGTTCGCACAGCTCTGC 60.385 55.0 3.53 3.53 0.0 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
45 46 0.875059 CTCCGTTTTCAGGTGCTTCC 59.125 55.000 0.00 0.00 0.00 3.46
56 57 1.683385 AGGTGCTTCCTCAAGTTTTGC 59.317 47.619 0.00 0.00 44.42 3.68
155 156 1.674817 CCGTCCCAATGGTGTGTCTAC 60.675 57.143 0.00 0.00 0.00 2.59
199 200 3.210528 GTCTCCGGCGGATCTCGT 61.211 66.667 31.23 0.00 41.72 4.18
220 221 2.140717 GAGATTTCGTCGGTGGTTGTT 58.859 47.619 0.00 0.00 0.00 2.83
285 286 1.351017 TGTGTCTTCAGGTTGGATCCC 59.649 52.381 9.90 0.00 0.00 3.85
327 328 1.227438 GGCGGCGGTTGCTATTCTA 60.227 57.895 9.78 0.00 42.25 2.10
339 340 3.178046 TGCTATTCTAGGGTGTTGGTCA 58.822 45.455 0.00 0.00 0.00 4.02
341 342 4.130118 GCTATTCTAGGGTGTTGGTCATG 58.870 47.826 0.00 0.00 0.00 3.07
379 380 3.204526 CGACTTCCCGACTGTCTACTAT 58.795 50.000 6.21 0.00 0.00 2.12
386 387 4.337555 TCCCGACTGTCTACTATAACAAGC 59.662 45.833 6.21 0.00 0.00 4.01
421 422 4.458829 AGGGAGGGGCGATGACGA 62.459 66.667 0.00 0.00 42.66 4.20
460 461 2.862530 GCTTCAGTGCTTGTAGTCGTCA 60.863 50.000 0.00 0.00 0.00 4.35
471 472 4.019792 TGTAGTCGTCACTAGGTGGTTA 57.980 45.455 0.00 0.00 35.67 2.85
526 527 5.636121 GGTGTTCGTTGTACTGTCATGATTA 59.364 40.000 0.00 0.00 0.00 1.75
552 554 4.182693 TGAATACATCGACAGTTTCCGT 57.817 40.909 0.00 0.00 0.00 4.69
593 596 2.509548 TCTTCCCTGTGGTGGATTATGG 59.490 50.000 0.00 0.00 0.00 2.74
603 606 3.117587 TGGTGGATTATGGTCATGCATGA 60.118 43.478 25.42 25.42 0.00 3.07
622 625 2.541547 ATACTGTCGTCGGTCGGGGA 62.542 60.000 0.00 0.00 40.32 4.81
977 997 1.963464 TAAACCCTCGCCGTGATCCC 61.963 60.000 0.00 0.00 0.00 3.85
989 1009 2.410939 CGTGATCCCAGTAGCATCATG 58.589 52.381 0.00 0.00 0.00 3.07
993 1013 3.455543 TGATCCCAGTAGCATCATGACAA 59.544 43.478 0.00 0.00 0.00 3.18
1605 1693 2.094762 ACTTGAACGGGCAGACATAC 57.905 50.000 0.00 0.00 0.00 2.39
1606 1694 1.346395 ACTTGAACGGGCAGACATACA 59.654 47.619 0.00 0.00 0.00 2.29
1607 1695 1.732259 CTTGAACGGGCAGACATACAC 59.268 52.381 0.00 0.00 0.00 2.90
1608 1696 0.682292 TGAACGGGCAGACATACACA 59.318 50.000 0.00 0.00 0.00 3.72
1609 1697 1.076332 GAACGGGCAGACATACACAC 58.924 55.000 0.00 0.00 0.00 3.82
1610 1698 0.669318 AACGGGCAGACATACACACG 60.669 55.000 0.00 0.00 0.00 4.49
1612 1700 0.802222 CGGGCAGACATACACACGAG 60.802 60.000 0.00 0.00 0.00 4.18
1613 1701 0.246635 GGGCAGACATACACACGAGT 59.753 55.000 0.00 0.00 0.00 4.18
1647 1738 1.834188 ACTTTGCGGTTCCCCTTATG 58.166 50.000 0.00 0.00 0.00 1.90
1683 1774 6.348498 TGTTGATCTCGTCATATTGGTCATT 58.652 36.000 0.00 0.00 36.54 2.57
1752 1844 8.465322 GGCGTACCATAGCTTTATAGAAGGCT 62.465 46.154 11.67 11.67 42.50 4.58
1786 1878 0.388649 AGAAACTACACTCGCTGCGG 60.389 55.000 23.03 15.00 0.00 5.69
1830 1937 1.040339 ACCCAAACACAACACCGCAT 61.040 50.000 0.00 0.00 0.00 4.73
1831 1938 0.597118 CCCAAACACAACACCGCATG 60.597 55.000 0.00 0.00 0.00 4.06
2214 2324 2.914379 GGAGACAACCACAACTCCG 58.086 57.895 0.00 0.00 39.27 4.63
2333 2443 0.739462 AGATTTTCATCCGCGCGTCA 60.739 50.000 29.95 15.60 0.00 4.35
2450 2561 2.024868 CATCGACCGGACGCACAAA 61.025 57.895 21.57 4.18 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.842381 CTGAAAACGGAGCCCTCCCT 61.842 60.000 8.68 0.00 46.96 4.20
45 46 3.058914 CACGAACCCTAGCAAAACTTGAG 60.059 47.826 0.00 0.00 0.00 3.02
56 57 0.173708 GAGCAGGACACGAACCCTAG 59.826 60.000 0.00 0.00 0.00 3.02
178 179 1.739338 GAGATCCGCCGGAGACACAT 61.739 60.000 13.12 0.00 34.05 3.21
199 200 1.069513 ACAACCACCGACGAAATCTCA 59.930 47.619 0.00 0.00 0.00 3.27
207 208 0.452585 ACCAAAAACAACCACCGACG 59.547 50.000 0.00 0.00 0.00 5.12
220 221 1.376683 CCGAGCGGATCCACCAAAA 60.377 57.895 13.41 0.00 38.90 2.44
285 286 7.332003 CGATGAAGAGAATTTTAGATCGGAG 57.668 40.000 0.00 0.00 0.00 4.63
327 328 1.065410 TCCCACATGACCAACACCCT 61.065 55.000 0.00 0.00 0.00 4.34
339 340 0.249398 GTCGTGCTAAGGTCCCACAT 59.751 55.000 0.00 0.00 0.00 3.21
341 342 1.445582 CGTCGTGCTAAGGTCCCAC 60.446 63.158 0.00 0.00 0.00 4.61
379 380 2.671619 GCCGGGCACAGCTTGTTA 60.672 61.111 15.62 0.00 0.00 2.41
402 403 2.764128 GTCATCGCCCCTCCCTCA 60.764 66.667 0.00 0.00 0.00 3.86
460 461 6.158695 ACATCCAGATTCATTAACCACCTAGT 59.841 38.462 0.00 0.00 0.00 2.57
526 527 6.036083 CGGAAACTGTCGATGTATTCATCTTT 59.964 38.462 10.20 4.06 45.76 2.52
593 596 2.469147 CGACGACAGTATCATGCATGAC 59.531 50.000 30.92 19.73 40.03 3.06
603 606 2.117156 CCCCGACCGACGACAGTAT 61.117 63.158 0.00 0.00 45.77 2.12
622 625 1.475682 GGTTGACTCGTTCTACCGGAT 59.524 52.381 9.46 0.00 39.86 4.18
864 873 2.439507 TGCTTCCTTGGCTAGGGATTAG 59.560 50.000 15.05 0.00 44.86 1.73
977 997 2.030091 CGCACTTGTCATGATGCTACTG 59.970 50.000 15.13 1.76 35.88 2.74
989 1009 0.460987 CTCCTCCATCCGCACTTGTC 60.461 60.000 0.00 0.00 0.00 3.18
993 1013 1.760086 CTCCTCCTCCATCCGCACT 60.760 63.158 0.00 0.00 0.00 4.40
1293 1343 4.501714 GCCGCCCGTATGTCGTCA 62.502 66.667 0.00 0.00 37.94 4.35
1519 1599 3.692257 ATCTCAAGAGTGTTCCCACAG 57.308 47.619 0.00 0.00 44.39 3.66
1605 1693 1.300465 ACAGCTCTGCACTCGTGTG 60.300 57.895 13.13 13.13 46.37 3.82
1606 1694 1.300465 CACAGCTCTGCACTCGTGT 60.300 57.895 0.00 0.00 0.00 4.49
1607 1695 2.665395 GCACAGCTCTGCACTCGTG 61.665 63.158 9.30 0.50 37.11 4.35
1608 1696 2.356793 GCACAGCTCTGCACTCGT 60.357 61.111 9.30 0.00 37.11 4.18
1609 1697 3.476646 CGCACAGCTCTGCACTCG 61.477 66.667 14.60 0.00 36.94 4.18
1610 1698 1.665916 TTCGCACAGCTCTGCACTC 60.666 57.895 14.60 0.00 36.94 3.51
1612 1700 1.502163 AAGTTCGCACAGCTCTGCAC 61.502 55.000 14.60 5.61 36.94 4.57
1613 1701 0.815213 AAAGTTCGCACAGCTCTGCA 60.815 50.000 14.60 0.00 36.94 4.41
1614 1702 0.385223 CAAAGTTCGCACAGCTCTGC 60.385 55.000 3.53 3.53 0.00 4.26
1615 1703 0.385223 GCAAAGTTCGCACAGCTCTG 60.385 55.000 0.00 0.00 0.00 3.35
1647 1738 2.802816 GAGATCAACATGCCACGTATCC 59.197 50.000 0.00 0.00 0.00 2.59
1683 1774 5.160607 ACATTTTATCTTGGACTGGACGA 57.839 39.130 0.00 0.00 0.00 4.20
1752 1844 9.391006 AGTGTAGTTTCTTGTAACTCAAATTCA 57.609 29.630 0.00 0.00 39.08 2.57
1786 1878 1.798223 TGTTGTGCTATGCTCGTTGTC 59.202 47.619 0.00 0.00 0.00 3.18
1830 1937 1.680735 CCTTTGTGTTGTAGCTTGCCA 59.319 47.619 0.00 0.00 0.00 4.92
1831 1938 1.000274 CCCTTTGTGTTGTAGCTTGCC 60.000 52.381 0.00 0.00 0.00 4.52
2055 2164 0.539051 CGCTGTCCTCCTTGATCCTT 59.461 55.000 0.00 0.00 0.00 3.36
2214 2324 3.775654 CACCTCCCTCACTCGCCC 61.776 72.222 0.00 0.00 0.00 6.13
2333 2443 4.317530 TCTAGATGGTGTAGTGAGGTGT 57.682 45.455 0.00 0.00 0.00 4.16
2342 2452 4.018870 TGTTGCCCAATTCTAGATGGTGTA 60.019 41.667 10.77 1.09 34.79 2.90
2450 2561 1.308998 CGTGGCTGGTGTTCTTCTTT 58.691 50.000 0.00 0.00 0.00 2.52
2498 2611 4.767255 GAGGTGCGGTGAGGCTGG 62.767 72.222 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.