Multiple sequence alignment - TraesCS5A01G193000

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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 TraesCS5A01G193000 chr5A 100.000 3263 0 0 1 3263 396414863 396418125 0.000000e+00 6026
1 TraesCS5A01G193000 chr5A 90.947 1701 113 22 851 2542 397786949 397785281 0.000000e+00 2250
2 TraesCS5A01G193000 chr5A 90.871 1676 110 17 773 2436 398051280 398049636 0.000000e+00 2207
3 TraesCS5A01G193000 chr5A 92.778 720 45 5 2548 3263 397785214 397784498 0.000000e+00 1035
4 TraesCS5A01G193000 chr5A 89.474 399 35 5 2007 2405 396490700 396491091 6.290000e-137 497
5 TraesCS5A01G193000 chr5A 82.197 264 31 7 2142 2405 398049142 398048895 2.550000e-51 213
6 TraesCS5A01G193000 chr5B 89.055 1809 111 28 789 2540 344241026 344239248 0.000000e+00 2163
7 TraesCS5A01G193000 chr5B 88.170 1809 134 28 770 2542 340134534 340136298 0.000000e+00 2082
8 TraesCS5A01G193000 chr5B 88.170 1809 134 28 770 2542 340324607 340326371 0.000000e+00 2082
9 TraesCS5A01G193000 chr5B 88.759 1708 124 23 781 2457 343952766 343951096 0.000000e+00 2028
10 TraesCS5A01G193000 chr5B 88.821 1646 120 19 924 2542 339977841 339979449 0.000000e+00 1962
11 TraesCS5A01G193000 chr5B 88.106 1589 121 30 851 2417 340609821 340611363 0.000000e+00 1825
12 TraesCS5A01G193000 chr5B 88.963 1504 110 19 924 2400 340567696 340569170 0.000000e+00 1807
13 TraesCS5A01G193000 chr5B 92.798 722 43 6 2548 3263 339979515 339980233 0.000000e+00 1037
14 TraesCS5A01G193000 chr5B 91.828 722 50 6 2548 3263 343950763 343950045 0.000000e+00 998
15 TraesCS5A01G193000 chr5B 94.301 579 27 4 2689 3263 340136533 340137109 0.000000e+00 881
16 TraesCS5A01G193000 chr5B 94.301 579 27 4 2689 3263 340326606 340327182 0.000000e+00 881
17 TraesCS5A01G193000 chr5B 91.213 239 20 1 2548 2786 344239178 344238941 1.130000e-84 324
18 TraesCS5A01G193000 chr5B 87.975 158 16 2 2548 2703 340136363 340136519 2.000000e-42 183
19 TraesCS5A01G193000 chr5B 87.975 158 16 2 2548 2703 340326436 340326592 2.000000e-42 183
20 TraesCS5A01G193000 chr5B 85.124 121 12 4 770 884 339977726 339977846 5.720000e-23 119
21 TraesCS5A01G193000 chr5D 88.700 1823 131 31 770 2542 300955524 300957321 0.000000e+00 2156
22 TraesCS5A01G193000 chr5D 88.141 1813 113 35 773 2540 300147463 300145708 0.000000e+00 2063
23 TraesCS5A01G193000 chr5D 88.663 1676 109 27 773 2400 300323362 300321720 0.000000e+00 1967
24 TraesCS5A01G193000 chr5D 87.199 1703 134 30 770 2425 299388744 299390409 0.000000e+00 1860
25 TraesCS5A01G193000 chr5D 87.547 1598 128 26 851 2417 299068571 299070128 0.000000e+00 1783
26 TraesCS5A01G193000 chr5D 86.472 1678 116 39 768 2399 300160913 300159301 0.000000e+00 1738
27 TraesCS5A01G193000 chr5D 91.413 722 53 6 2548 3263 300145641 300144923 0.000000e+00 981
28 TraesCS5A01G193000 chr5D 90.847 590 37 5 2678 3263 300957630 300958206 0.000000e+00 774
29 TraesCS5A01G193000 chr5D 86.612 732 59 11 2548 3263 300314586 300313878 0.000000e+00 773
30 TraesCS5A01G193000 chr5D 88.982 599 44 11 770 1354 299004359 299004949 0.000000e+00 721
31 TraesCS5A01G193000 chr5D 96.667 210 7 0 2333 2542 300314868 300314659 1.860000e-92 350
32 TraesCS5A01G193000 chr5D 88.406 138 15 1 2548 2685 300957394 300957530 7.240000e-37 165
33 TraesCS5A01G193000 chr3A 84.110 1567 125 54 770 2274 456904975 456906479 0.000000e+00 1400
34 TraesCS5A01G193000 chr7A 98.960 769 8 0 1 769 634136077 634136845 0.000000e+00 1376
35 TraesCS5A01G193000 chr7A 96.851 794 12 4 1 794 624753422 624752642 0.000000e+00 1315
36 TraesCS5A01G193000 chr6A 98.960 769 8 0 1 769 12687722 12686954 0.000000e+00 1376
37 TraesCS5A01G193000 chr6A 98.575 772 10 1 1 771 570896108 570896879 0.000000e+00 1363
38 TraesCS5A01G193000 chr6A 98.571 770 10 1 1 769 591846608 591847377 0.000000e+00 1360
39 TraesCS5A01G193000 chr6A 79.907 214 28 6 1083 1296 130412851 130413049 3.390000e-30 143
40 TraesCS5A01G193000 chr4A 98.705 772 7 3 1 769 66552498 66551727 0.000000e+00 1367
41 TraesCS5A01G193000 chr4A 93.790 789 23 8 1 769 593046420 593045638 0.000000e+00 1162
42 TraesCS5A01G193000 chr1B 98.700 769 10 0 1 769 637620096 637620864 0.000000e+00 1365
43 TraesCS5A01G193000 chr6B 98.571 770 9 2 1 769 21358826 21358058 0.000000e+00 1360
44 TraesCS5A01G193000 chr7B 95.116 778 24 11 1 770 194133414 194134185 0.000000e+00 1214
45 TraesCS5A01G193000 chr3D 84.749 577 73 10 2686 3254 482005846 482006415 6.110000e-157 564
46 TraesCS5A01G193000 chr1D 83.333 576 82 11 2686 3250 18802965 18803537 1.340000e-143 520
47 TraesCS5A01G193000 chr6D 80.569 211 26 6 1086 1296 106951770 106951965 7.290000e-32 148


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 TraesCS5A01G193000 chr5A 396414863 396418125 3262 False 6026.000000 6026 100.000000 1 3263 1 chr5A.!!$F1 3262
1 TraesCS5A01G193000 chr5A 397784498 397786949 2451 True 1642.500000 2250 91.862500 851 3263 2 chr5A.!!$R1 2412
2 TraesCS5A01G193000 chr5A 398048895 398051280 2385 True 1210.000000 2207 86.534000 773 2436 2 chr5A.!!$R2 1663
3 TraesCS5A01G193000 chr5B 340609821 340611363 1542 False 1825.000000 1825 88.106000 851 2417 1 chr5B.!!$F2 1566
4 TraesCS5A01G193000 chr5B 340567696 340569170 1474 False 1807.000000 1807 88.963000 924 2400 1 chr5B.!!$F1 1476
5 TraesCS5A01G193000 chr5B 343950045 343952766 2721 True 1513.000000 2028 90.293500 781 3263 2 chr5B.!!$R1 2482
6 TraesCS5A01G193000 chr5B 344238941 344241026 2085 True 1243.500000 2163 90.134000 789 2786 2 chr5B.!!$R2 1997
7 TraesCS5A01G193000 chr5B 340134534 340137109 2575 False 1048.666667 2082 90.148667 770 3263 3 chr5B.!!$F4 2493
8 TraesCS5A01G193000 chr5B 340324607 340327182 2575 False 1048.666667 2082 90.148667 770 3263 3 chr5B.!!$F5 2493
9 TraesCS5A01G193000 chr5B 339977726 339980233 2507 False 1039.333333 1962 88.914333 770 3263 3 chr5B.!!$F3 2493
10 TraesCS5A01G193000 chr5D 300321720 300323362 1642 True 1967.000000 1967 88.663000 773 2400 1 chr5D.!!$R2 1627
11 TraesCS5A01G193000 chr5D 299388744 299390409 1665 False 1860.000000 1860 87.199000 770 2425 1 chr5D.!!$F3 1655
12 TraesCS5A01G193000 chr5D 299068571 299070128 1557 False 1783.000000 1783 87.547000 851 2417 1 chr5D.!!$F2 1566
13 TraesCS5A01G193000 chr5D 300159301 300160913 1612 True 1738.000000 1738 86.472000 768 2399 1 chr5D.!!$R1 1631
14 TraesCS5A01G193000 chr5D 300144923 300147463 2540 True 1522.000000 2063 89.777000 773 3263 2 chr5D.!!$R3 2490
15 TraesCS5A01G193000 chr5D 300955524 300958206 2682 False 1031.666667 2156 89.317667 770 3263 3 chr5D.!!$F4 2493
16 TraesCS5A01G193000 chr5D 299004359 299004949 590 False 721.000000 721 88.982000 770 1354 1 chr5D.!!$F1 584
17 TraesCS5A01G193000 chr5D 300313878 300314868 990 True 561.500000 773 91.639500 2333 3263 2 chr5D.!!$R4 930
18 TraesCS5A01G193000 chr3A 456904975 456906479 1504 False 1400.000000 1400 84.110000 770 2274 1 chr3A.!!$F1 1504
19 TraesCS5A01G193000 chr7A 634136077 634136845 768 False 1376.000000 1376 98.960000 1 769 1 chr7A.!!$F1 768
20 TraesCS5A01G193000 chr7A 624752642 624753422 780 True 1315.000000 1315 96.851000 1 794 1 chr7A.!!$R1 793
21 TraesCS5A01G193000 chr6A 12686954 12687722 768 True 1376.000000 1376 98.960000 1 769 1 chr6A.!!$R1 768
22 TraesCS5A01G193000 chr6A 570896108 570896879 771 False 1363.000000 1363 98.575000 1 771 1 chr6A.!!$F2 770
23 TraesCS5A01G193000 chr6A 591846608 591847377 769 False 1360.000000 1360 98.571000 1 769 1 chr6A.!!$F3 768
24 TraesCS5A01G193000 chr4A 66551727 66552498 771 True 1367.000000 1367 98.705000 1 769 1 chr4A.!!$R1 768
25 TraesCS5A01G193000 chr4A 593045638 593046420 782 True 1162.000000 1162 93.790000 1 769 1 chr4A.!!$R2 768
26 TraesCS5A01G193000 chr1B 637620096 637620864 768 False 1365.000000 1365 98.700000 1 769 1 chr1B.!!$F1 768
27 TraesCS5A01G193000 chr6B 21358058 21358826 768 True 1360.000000 1360 98.571000 1 769 1 chr6B.!!$R1 768
28 TraesCS5A01G193000 chr7B 194133414 194134185 771 False 1214.000000 1214 95.116000 1 770 1 chr7B.!!$F1 769
29 TraesCS5A01G193000 chr3D 482005846 482006415 569 False 564.000000 564 84.749000 2686 3254 1 chr3D.!!$F1 568
30 TraesCS5A01G193000 chr1D 18802965 18803537 572 False 520.000000 520 83.333000 2686 3250 1 chr1D.!!$F1 564

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
825 860 1.136110 ACGGATCACATCACATACGCA 59.864 47.619 0.00 0.0 0.00 5.24 F
1356 1532 0.111446 CGGGCTCTGAGAGGGAGATA 59.889 60.000 12.01 0.0 33.03 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2471 0.035317 TGCTGCTTCCAGTCATCGTT 59.965 50.000 0.0 0.0 41.26 3.85 R
2802 3581 1.065053 TGGTGCAAGCGGGTTGTATAT 60.065 47.619 19.8 0.0 38.55 0.86 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
130 132 9.566432 TTGGCTTTTAATCATGTTTTAATTGGT 57.434 25.926 0.00 0.00 0.00 3.67
187 189 3.117284 ACATCCAGGTGGTAGTTTTTGGT 60.117 43.478 0.00 0.00 36.34 3.67
693 724 1.605058 CCTCTTTTCGCTCGAGGGGA 61.605 60.000 27.01 18.16 40.47 4.81
825 860 1.136110 ACGGATCACATCACATACGCA 59.864 47.619 0.00 0.00 0.00 5.24
826 861 2.224042 ACGGATCACATCACATACGCAT 60.224 45.455 0.00 0.00 0.00 4.73
827 862 2.409715 CGGATCACATCACATACGCATC 59.590 50.000 0.00 0.00 0.00 3.91
828 863 2.738846 GGATCACATCACATACGCATCC 59.261 50.000 0.00 0.00 0.00 3.51
829 864 2.977772 TCACATCACATACGCATCCA 57.022 45.000 0.00 0.00 0.00 3.41
831 866 1.258720 CACATCACATACGCATCCACG 59.741 52.381 0.00 0.00 39.50 4.94
1203 1373 2.501128 GTGCTAGCTCCCGCATCA 59.499 61.111 17.23 0.00 38.56 3.07
1356 1532 0.111446 CGGGCTCTGAGAGGGAGATA 59.889 60.000 12.01 0.00 33.03 1.98
1372 1548 1.022735 GATACTCGCGGAAGACCTGA 58.977 55.000 6.13 0.00 0.00 3.86
1560 1747 2.486636 ATCCGTCGCTGCAAGAACGA 62.487 55.000 13.98 6.38 44.20 3.85
1602 1795 2.371259 GGCCCAAGAGGAGGAGGAC 61.371 68.421 0.00 0.00 38.24 3.85
1651 1845 1.107538 CGTCTCCCCCTTAGCGATCA 61.108 60.000 0.00 0.00 0.00 2.92
1761 1958 0.825010 GCGTCTCCCCCTTACCGATA 60.825 60.000 0.00 0.00 0.00 2.92
2040 2332 3.461773 GCCCGTCAGGAGCTGCTA 61.462 66.667 7.70 0.00 41.02 3.49
2179 2471 0.106708 ACTCTTCCGCAAGCTTGACA 59.893 50.000 30.39 9.42 0.00 3.58
2631 3196 4.122046 TCACGATGTAAGATTGATGCCTG 58.878 43.478 0.00 0.00 0.00 4.85
2638 3203 5.748402 TGTAAGATTGATGCCTGAAGACAT 58.252 37.500 0.00 0.00 0.00 3.06
2645 3210 3.697542 TGATGCCTGAAGACATTGAATGG 59.302 43.478 10.27 0.00 33.60 3.16
2660 3225 3.812262 TGAATGGTAGCATCACCTCATG 58.188 45.455 8.07 0.00 39.50 3.07
2674 3304 3.009723 ACCTCATGCATTCGGTTTACAG 58.990 45.455 10.21 0.00 0.00 2.74
2736 3515 6.469782 AGATTCAAGCCTTTTCAGTTTTCA 57.530 33.333 0.00 0.00 0.00 2.69
2773 3552 9.692325 GAATTTCCTCCTAATGGATATGCTAAT 57.308 33.333 0.00 0.00 42.29 1.73
2801 3580 6.131972 TCCTCCTTGACATTCTCATTCTTT 57.868 37.500 0.00 0.00 0.00 2.52
2802 3581 7.257790 TCCTCCTTGACATTCTCATTCTTTA 57.742 36.000 0.00 0.00 0.00 1.85
2845 3628 1.466167 CTCATTCCCAACTGCGAACTG 59.534 52.381 0.00 0.00 0.00 3.16
3061 3858 4.042062 ACATGACCTCTGGACTGAATTTGA 59.958 41.667 0.00 0.00 0.00 2.69
3062 3859 4.008074 TGACCTCTGGACTGAATTTGAC 57.992 45.455 0.00 0.00 0.00 3.18
3066 3863 4.288105 ACCTCTGGACTGAATTTGACTGAT 59.712 41.667 0.00 0.00 0.00 2.90
3070 3867 5.246883 TCTGGACTGAATTTGACTGATGAGA 59.753 40.000 0.00 0.00 0.00 3.27
3083 3890 4.621991 ACTGATGAGAATCCGGTAAATCG 58.378 43.478 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 132 6.228258 AGCCAACTAAAAACGAGTTATCTGA 58.772 36.000 0.00 0.00 35.36 3.27
396 400 1.682684 CCTCCTCCTACACAGCCGT 60.683 63.158 0.00 0.00 0.00 5.68
825 860 4.371975 CAAACCGTGGACGTGGAT 57.628 55.556 0.00 0.00 37.74 3.41
1065 1235 2.548295 GCCGGTCTTGGCGTCAAAA 61.548 57.895 3.10 0.00 46.75 2.44
1200 1370 3.234730 GGAGCCGACGGGGATGAT 61.235 66.667 17.22 0.00 38.47 2.45
1356 1532 1.587054 CTTCAGGTCTTCCGCGAGT 59.413 57.895 8.23 0.00 39.05 4.18
1372 1548 0.320771 ATCTCCGCAACGAACAGCTT 60.321 50.000 0.00 0.00 0.00 3.74
1550 1737 1.295792 GTCTTGGTGTCGTTCTTGCA 58.704 50.000 0.00 0.00 0.00 4.08
1560 1747 1.677552 CTTAGGGCCGTCTTGGTGT 59.322 57.895 0.00 0.00 41.21 4.16
1602 1795 1.750351 TGTCAACTTCTTCGTCGTCG 58.250 50.000 0.00 0.00 38.55 5.12
2040 2332 2.438795 GCCGTCCTCTCCGTCTCT 60.439 66.667 0.00 0.00 0.00 3.10
2132 2424 1.064952 GCCGCAACAAGTTGTAGTTGT 59.935 47.619 9.37 0.00 45.16 3.32
2133 2425 1.064803 TGCCGCAACAAGTTGTAGTTG 59.935 47.619 9.37 5.36 45.91 3.16
2134 2426 1.333619 CTGCCGCAACAAGTTGTAGTT 59.666 47.619 9.37 0.00 42.31 2.24
2135 2427 0.944386 CTGCCGCAACAAGTTGTAGT 59.056 50.000 9.37 0.00 42.31 2.73
2136 2428 1.225855 TCTGCCGCAACAAGTTGTAG 58.774 50.000 9.37 1.79 42.31 2.74
2137 2429 1.890876 ATCTGCCGCAACAAGTTGTA 58.109 45.000 9.37 0.00 42.31 2.41
2179 2471 0.035317 TGCTGCTTCCAGTCATCGTT 59.965 50.000 0.00 0.00 41.26 3.85
2440 2754 7.394016 TGGACATCTCTGTTAAACATGTGTAT 58.606 34.615 0.00 0.00 35.14 2.29
2542 3040 5.067805 CCGAGCCTCCAAGCTATAAATTTTT 59.932 40.000 0.00 0.00 45.15 1.94
2543 3041 4.580580 CCGAGCCTCCAAGCTATAAATTTT 59.419 41.667 0.00 0.00 45.15 1.82
2544 3042 4.137543 CCGAGCCTCCAAGCTATAAATTT 58.862 43.478 0.00 0.00 45.15 1.82
2546 3044 2.706190 ACCGAGCCTCCAAGCTATAAAT 59.294 45.455 0.00 0.00 45.15 1.40
2553 3118 1.134371 AGAAATACCGAGCCTCCAAGC 60.134 52.381 0.00 0.00 0.00 4.01
2631 3196 5.220931 GGTGATGCTACCATTCAATGTCTTC 60.221 44.000 0.00 0.00 40.54 2.87
2638 3203 3.998913 TGAGGTGATGCTACCATTCAA 57.001 42.857 7.85 0.00 43.37 2.69
2660 3225 7.302524 TGTATCTTTTTCTGTAAACCGAATGC 58.697 34.615 0.00 0.00 0.00 3.56
2666 3296 9.010029 TCCTTGATGTATCTTTTTCTGTAAACC 57.990 33.333 0.00 0.00 0.00 3.27
2674 3304 6.765915 AAGCCTCCTTGATGTATCTTTTTC 57.234 37.500 0.00 0.00 0.00 2.29
2736 3515 4.162651 AGGAGGAAATTCAGGCACAAAAT 58.837 39.130 0.00 0.00 0.00 1.82
2773 3552 6.627087 ATGAGAATGTCAAGGAGGAACTAA 57.373 37.500 0.00 0.00 37.57 2.24
2801 3580 2.170817 TGGTGCAAGCGGGTTGTATATA 59.829 45.455 19.80 5.08 38.55 0.86
2802 3581 1.065053 TGGTGCAAGCGGGTTGTATAT 60.065 47.619 19.80 0.00 38.55 0.86
2845 3628 5.932303 TGGATGCTTAACTGAAGAACTGTAC 59.068 40.000 0.00 0.00 37.33 2.90
3061 3858 4.621991 CGATTTACCGGATTCTCATCAGT 58.378 43.478 9.46 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.