Multiple sequence alignment - TraesCS5A01G310600

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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 TraesCS5A01G310600 chr5A 100.000 2678 0 0 1 2678 522358653 522355976 0.000000e+00 4946
1 TraesCS5A01G310600 chr5A 98.313 652 9 1 1 652 492872422 492873071 0.000000e+00 1142
2 TraesCS5A01G310600 chr5A 86.383 940 81 20 1000 1906 522124619 522123694 0.000000e+00 983
3 TraesCS5A01G310600 chr5A 84.013 907 102 26 966 1856 522868860 522867981 0.000000e+00 832
4 TraesCS5A01G310600 chr5D 93.255 1883 82 11 788 2635 410638472 410636600 0.000000e+00 2732
5 TraesCS5A01G310600 chr5D 84.801 1079 101 33 1000 2045 410607141 410606093 0.000000e+00 1026
6 TraesCS5A01G310600 chr5D 84.692 908 95 23 966 1857 410874255 410873376 0.000000e+00 867
7 TraesCS5A01G310600 chr5D 79.447 579 73 27 1077 1632 410843249 410842694 4.210000e-98 368
8 TraesCS5A01G310600 chr5D 81.250 368 52 10 1077 1443 411170955 411170604 5.640000e-72 281
9 TraesCS5A01G310600 chr5D 94.286 140 8 0 657 796 410639915 410639776 5.810000e-52 215
10 TraesCS5A01G310600 chr5D 80.000 205 33 6 1506 1706 410620973 410621173 7.730000e-31 145
11 TraesCS5A01G310600 chr5D 81.212 165 28 3 1509 1673 410491443 410491604 2.160000e-26 130
12 TraesCS5A01G310600 chr5B 93.512 1418 38 14 800 2171 493125623 493124214 0.000000e+00 2060
13 TraesCS5A01G310600 chr5B 87.442 860 79 18 1000 1849 492820188 492819348 0.000000e+00 963
14 TraesCS5A01G310600 chr5B 86.327 746 71 12 966 1705 493286658 493285938 0.000000e+00 784
15 TraesCS5A01G310600 chr5B 84.601 526 52 18 2169 2678 493123928 493123416 1.850000e-136 496
16 TraesCS5A01G310600 chr5B 94.118 170 7 2 657 823 493126397 493126228 3.420000e-64 255
17 TraesCS5A01G310600 chr5B 80.303 198 32 5 1509 1706 493086034 493085844 2.780000e-30 143
18 TraesCS5A01G310600 chr5B 81.818 165 27 3 1509 1673 492783133 492783294 4.650000e-28 135
19 TraesCS5A01G310600 chrUn 98.620 652 7 2 1 652 233534689 233534040 0.000000e+00 1153
20 TraesCS5A01G310600 chrUn 98.466 652 8 1 1 652 388536517 388535868 0.000000e+00 1147
21 TraesCS5A01G310600 chr7A 98.609 647 7 1 6 652 4937331 4936687 0.000000e+00 1144
22 TraesCS5A01G310600 chr7B 97.853 652 12 1 1 652 531987451 531988100 0.000000e+00 1125
23 TraesCS5A01G310600 chr4A 97.853 652 12 1 1 652 246691333 246691982 0.000000e+00 1125
24 TraesCS5A01G310600 chr1A 97.846 650 12 1 1 650 94623516 94624163 0.000000e+00 1122
25 TraesCS5A01G310600 chr4D 97.546 652 13 2 1 652 123679176 123679824 0.000000e+00 1112
26 TraesCS5A01G310600 chr3D 98.192 553 8 1 100 652 145414051 145414601 0.000000e+00 965
27 TraesCS5A01G310600 chr2B 91.925 161 13 0 1 161 797714979 797715139 2.680000e-55 226


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 TraesCS5A01G310600 chr5A 522355976 522358653 2677 True 4946.0 4946 100.000000 1 2678 1 chr5A.!!$R2 2677
1 TraesCS5A01G310600 chr5A 492872422 492873071 649 False 1142.0 1142 98.313000 1 652 1 chr5A.!!$F1 651
2 TraesCS5A01G310600 chr5A 522123694 522124619 925 True 983.0 983 86.383000 1000 1906 1 chr5A.!!$R1 906
3 TraesCS5A01G310600 chr5A 522867981 522868860 879 True 832.0 832 84.013000 966 1856 1 chr5A.!!$R3 890
4 TraesCS5A01G310600 chr5D 410636600 410639915 3315 True 1473.5 2732 93.770500 657 2635 2 chr5D.!!$R5 1978
5 TraesCS5A01G310600 chr5D 410606093 410607141 1048 True 1026.0 1026 84.801000 1000 2045 1 chr5D.!!$R1 1045
6 TraesCS5A01G310600 chr5D 410873376 410874255 879 True 867.0 867 84.692000 966 1857 1 chr5D.!!$R3 891
7 TraesCS5A01G310600 chr5D 410842694 410843249 555 True 368.0 368 79.447000 1077 1632 1 chr5D.!!$R2 555
8 TraesCS5A01G310600 chr5B 492819348 492820188 840 True 963.0 963 87.442000 1000 1849 1 chr5B.!!$R1 849
9 TraesCS5A01G310600 chr5B 493123416 493126397 2981 True 937.0 2060 90.743667 657 2678 3 chr5B.!!$R4 2021
10 TraesCS5A01G310600 chr5B 493285938 493286658 720 True 784.0 784 86.327000 966 1705 1 chr5B.!!$R3 739
11 TraesCS5A01G310600 chrUn 233534040 233534689 649 True 1153.0 1153 98.620000 1 652 1 chrUn.!!$R1 651
12 TraesCS5A01G310600 chrUn 388535868 388536517 649 True 1147.0 1147 98.466000 1 652 1 chrUn.!!$R2 651
13 TraesCS5A01G310600 chr7A 4936687 4937331 644 True 1144.0 1144 98.609000 6 652 1 chr7A.!!$R1 646
14 TraesCS5A01G310600 chr7B 531987451 531988100 649 False 1125.0 1125 97.853000 1 652 1 chr7B.!!$F1 651
15 TraesCS5A01G310600 chr4A 246691333 246691982 649 False 1125.0 1125 97.853000 1 652 1 chr4A.!!$F1 651
16 TraesCS5A01G310600 chr1A 94623516 94624163 647 False 1122.0 1122 97.846000 1 650 1 chr1A.!!$F1 649
17 TraesCS5A01G310600 chr4D 123679176 123679824 648 False 1112.0 1112 97.546000 1 652 1 chr4D.!!$F1 651
18 TraesCS5A01G310600 chr3D 145414051 145414601 550 False 965.0 965 98.192000 100 652 1 chr3D.!!$F1 552

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
404 405 0.251787 GGGGAAGAATGCCACAACCT 60.252 55.0 0.0 0.0 36.91 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 4575 0.462225 TTGGACGTTGCTTTCACGGA 60.462 50.0 0.0 0.0 0.0 4.69 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
279 280 5.186992 TCTTCCATCATGAAAGTCGGTAAGA 59.813 40.000 0.00 4.90 0.00 2.10
404 405 0.251787 GGGGAAGAATGCCACAACCT 60.252 55.000 0.00 0.00 36.91 3.50
498 499 3.825328 ACCTTCAACTTCTCAAGTGCAT 58.175 40.909 0.00 0.00 41.91 3.96
555 556 3.775654 CCCCGCCCACTGTCTCTC 61.776 72.222 0.00 0.00 0.00 3.20
569 570 1.335496 GTCTCTCAGGTATCCACTCGC 59.665 57.143 0.00 0.00 0.00 5.03
712 713 8.929827 TTTTAAGTTATAATGATCGACGGTCA 57.070 30.769 14.13 14.13 0.00 4.02
713 714 9.537192 TTTTAAGTTATAATGATCGACGGTCAT 57.463 29.630 17.79 17.79 37.91 3.06
727 728 7.158099 TCGACGGTCATGATATGAGATATTT 57.842 36.000 9.10 0.00 40.53 1.40
944 2914 4.237843 TCCTATCATCCATTCCAAGCTCT 58.762 43.478 0.00 0.00 0.00 4.09
956 2926 4.342862 TCCAAGCTCTGAATATACAGCC 57.657 45.455 0.00 0.00 37.75 4.85
1010 2980 2.047655 GCGACCGATGGACACCAA 60.048 61.111 0.00 0.00 36.95 3.67
1362 3341 4.094646 ATGATGCCCGTCCACGCA 62.095 61.111 0.00 0.00 39.79 5.24
1706 3727 9.230122 TGATCAACTGATTAAGCAATGTAAAGA 57.770 29.630 0.00 0.00 34.37 2.52
1851 3889 7.386025 GGCACAAATGAGCTTCTTTCTTTATTT 59.614 33.333 2.97 0.00 0.00 1.40
1959 4018 4.998672 CGACCCTACCACTAATGTTTTTGA 59.001 41.667 0.00 0.00 0.00 2.69
1960 4019 5.121768 CGACCCTACCACTAATGTTTTTGAG 59.878 44.000 0.00 0.00 0.00 3.02
1978 4043 2.882761 TGAGCTGCCATGCAATAGAATC 59.117 45.455 0.00 0.00 38.41 2.52
2060 4125 1.355381 TGAAGTCGACCAGGGGTAGTA 59.645 52.381 13.01 0.00 35.25 1.82
2209 4575 4.559300 CGCCATTGGTCATGTCTTCTTTTT 60.559 41.667 4.26 0.00 0.00 1.94
2250 4616 6.095440 CCAAAATATCTACACAGGGTTCTTGG 59.905 42.308 0.00 0.00 0.00 3.61
2316 4684 1.073125 TGATGAACTCCCCGAAAAGCA 59.927 47.619 0.00 0.00 0.00 3.91
2390 4758 0.541063 TTAGTGGTGAGGACGGAGCA 60.541 55.000 0.00 0.00 0.00 4.26
2396 4764 1.378646 TGAGGACGGAGCATCGACT 60.379 57.895 5.74 3.65 34.37 4.18
2397 4765 0.107361 TGAGGACGGAGCATCGACTA 60.107 55.000 5.74 0.00 34.37 2.59
2403 4771 0.456221 CGGAGCATCGACTAGTTGGT 59.544 55.000 10.33 3.84 34.37 3.67
2410 4778 0.759959 TCGACTAGTTGGTTGGGCAA 59.240 50.000 10.33 0.00 0.00 4.52
2413 4781 2.161609 CGACTAGTTGGTTGGGCAATTC 59.838 50.000 1.70 0.00 0.00 2.17
2464 4832 2.667318 CGGCTTGAACGCGTGATGT 61.667 57.895 14.98 0.00 0.00 3.06
2465 4833 1.132640 GGCTTGAACGCGTGATGTC 59.867 57.895 14.98 7.20 0.00 3.06
2467 4835 1.565156 GCTTGAACGCGTGATGTCCA 61.565 55.000 14.98 0.00 0.00 4.02
2469 4837 0.530870 TTGAACGCGTGATGTCCACA 60.531 50.000 14.98 0.52 45.98 4.17
2470 4838 0.943835 TGAACGCGTGATGTCCACAG 60.944 55.000 14.98 0.00 45.98 3.66
2516 4885 9.778741 ATTATCAACAAGTGTTAGTTCTTGAGA 57.221 29.630 11.07 8.75 42.22 3.27
2571 4941 6.539103 GGTGTTAGTGGAGATGGAGAAATAAC 59.461 42.308 0.00 0.00 0.00 1.89
2597 4967 0.526096 CAATGCCTGAAAATCCGCGG 60.526 55.000 22.12 22.12 0.00 6.46
2600 4970 3.089784 CCTGAAAATCCGCGGACG 58.910 61.111 33.75 14.14 39.67 4.79
2629 4999 0.104855 GCATGTCGGAGGTGCTCATA 59.895 55.000 7.15 0.00 36.02 2.15
2648 5018 7.015974 TGCTCATATCTCTCAAACCTATGACAT 59.984 37.037 0.00 0.00 0.00 3.06
2656 5026 7.500892 TCTCTCAAACCTATGACATCTCTAGTC 59.499 40.741 0.00 0.00 36.55 2.59
2659 5029 6.773200 TCAAACCTATGACATCTCTAGTCGAT 59.227 38.462 0.00 0.00 38.83 3.59
2660 5030 7.285629 TCAAACCTATGACATCTCTAGTCGATT 59.714 37.037 0.00 0.00 38.83 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 280 1.906574 TCCCTGTTGCCGACTAGATTT 59.093 47.619 0.00 0.00 0.00 2.17
404 405 2.619590 GGCCCAAAGTATCGGAAGGAAA 60.620 50.000 0.00 0.00 0.00 3.13
498 499 5.867716 GCTTAGAGACGTGAAAAATACAGGA 59.132 40.000 0.00 0.00 0.00 3.86
554 555 2.029623 GGTAAGCGAGTGGATACCTGA 58.970 52.381 0.00 0.00 35.88 3.86
555 556 1.754803 TGGTAAGCGAGTGGATACCTG 59.245 52.381 8.37 0.00 38.85 4.00
564 565 2.425312 CAGTCTCAGATGGTAAGCGAGT 59.575 50.000 0.00 0.00 0.00 4.18
569 570 5.355596 GGATTGTCAGTCTCAGATGGTAAG 58.644 45.833 0.00 0.00 0.00 2.34
655 656 9.910511 CGCGTCTAACATTTTTATACATTTACT 57.089 29.630 0.00 0.00 0.00 2.24
705 706 7.030165 ACGAAATATCTCATATCATGACCGTC 58.970 38.462 0.00 0.00 35.06 4.79
727 728 2.223735 GGCCGTCTGATCTGATTTACGA 60.224 50.000 16.71 0.49 32.35 3.43
944 2914 4.403113 TGTAACGAGGTGGCTGTATATTCA 59.597 41.667 0.00 0.00 0.00 2.57
956 2926 1.600485 GGTTTGTGGTGTAACGAGGTG 59.400 52.381 0.00 0.00 38.12 4.00
998 2968 3.487202 CGGCGTTGGTGTCCATCG 61.487 66.667 12.90 12.90 45.92 3.84
1362 3341 1.597027 CAACTTGAACGACCCGGCT 60.597 57.895 0.00 0.00 0.00 5.52
1416 3395 1.301293 CTGGAACTCCTTGAGGGCC 59.699 63.158 0.00 0.00 36.82 5.80
1533 3544 4.147449 CCGCCGATCCAGTGCTCA 62.147 66.667 0.00 0.00 0.00 4.26
1706 3727 5.304686 AGCACTAGCAGTACTCTCTAGAT 57.695 43.478 24.71 13.35 45.49 1.98
1950 4009 1.345089 TGCATGGCAGCTCAAAAACAT 59.655 42.857 9.68 0.00 33.32 2.71
1959 4018 2.236766 GGATTCTATTGCATGGCAGCT 58.763 47.619 9.68 0.00 40.61 4.24
1960 4019 1.958579 TGGATTCTATTGCATGGCAGC 59.041 47.619 0.00 0.00 40.61 5.25
1978 4043 1.270550 ACGAACAGTACCTACCGTTGG 59.729 52.381 0.00 0.00 31.38 3.77
2060 4125 6.493166 TCAGAAATAAACATCTGGTCCCATT 58.507 36.000 3.23 0.00 0.00 3.16
2092 4157 5.837979 TGTCTTTCCCCTCAATCAATCAAAA 59.162 36.000 0.00 0.00 0.00 2.44
2209 4575 0.462225 TTGGACGTTGCTTTCACGGA 60.462 50.000 0.00 0.00 0.00 4.69
2302 4669 0.693049 ACAGATGCTTTTCGGGGAGT 59.307 50.000 0.00 0.00 0.00 3.85
2361 4729 5.614013 CGTCCTCACCACTAACGAATTTTTC 60.614 44.000 0.00 0.00 35.45 2.29
2390 4758 0.981183 TGCCCAACCAACTAGTCGAT 59.019 50.000 0.00 0.00 0.00 3.59
2396 4764 1.540267 CCGAATTGCCCAACCAACTA 58.460 50.000 0.00 0.00 0.00 2.24
2397 4765 1.184970 CCCGAATTGCCCAACCAACT 61.185 55.000 0.00 0.00 0.00 3.16
2403 4771 0.679640 CAGCTACCCGAATTGCCCAA 60.680 55.000 0.00 0.00 0.00 4.12
2410 4778 2.190578 GCTGGCAGCTACCCGAAT 59.809 61.111 31.37 0.00 38.45 3.34
2413 4781 2.441822 GATAGGCTGGCAGCTACCCG 62.442 65.000 35.73 0.80 41.99 5.28
2429 4797 2.191513 CGGGGCTCGAACTCGGATA 61.192 63.158 0.00 0.00 42.43 2.59
2451 4819 3.945436 GTGGACATCACGCGTTCA 58.055 55.556 10.22 0.00 36.56 3.18
2458 4826 4.636249 AGAAGAAACTCTGTGGACATCAC 58.364 43.478 0.00 0.00 46.23 3.06
2459 4827 4.963318 AGAAGAAACTCTGTGGACATCA 57.037 40.909 0.00 0.00 0.00 3.07
2461 4829 9.793259 TTTTTATAGAAGAAACTCTGTGGACAT 57.207 29.630 0.00 0.00 0.00 3.06
2493 4862 7.173907 CCATCTCAAGAACTAACACTTGTTGAT 59.826 37.037 4.82 0.00 42.50 2.57
2494 4863 6.483307 CCATCTCAAGAACTAACACTTGTTGA 59.517 38.462 4.82 0.00 42.50 3.18
2530 4900 9.226606 CCACTAACACCACTAATGAATTTTAGA 57.773 33.333 4.30 0.00 34.08 2.10
2540 4910 5.030147 TCCATCTCCACTAACACCACTAAT 58.970 41.667 0.00 0.00 0.00 1.73
2546 4916 4.553330 TTTCTCCATCTCCACTAACACC 57.447 45.455 0.00 0.00 0.00 4.16
2552 4922 3.134804 CCGGTTATTTCTCCATCTCCACT 59.865 47.826 0.00 0.00 0.00 4.00
2554 4924 3.380393 TCCGGTTATTTCTCCATCTCCA 58.620 45.455 0.00 0.00 0.00 3.86
2555 4925 4.417426 TTCCGGTTATTTCTCCATCTCC 57.583 45.455 0.00 0.00 0.00 3.71
2571 4941 2.810439 TTTTCAGGCATTGTTTCCGG 57.190 45.000 0.00 0.00 0.00 5.14
2597 4967 3.159298 ACATGCATGTCCCTTCGTC 57.841 52.632 26.61 0.00 35.87 4.20
2621 4991 6.644592 GTCATAGGTTTGAGAGATATGAGCAC 59.355 42.308 0.00 0.00 34.46 4.40
2629 4999 8.004215 ACTAGAGATGTCATAGGTTTGAGAGAT 58.996 37.037 0.00 0.00 0.00 2.75
2648 5018 9.417561 TCTAAAATTTAGGGAATCGACTAGAGA 57.582 33.333 12.29 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.