Multiple sequence alignment - TraesCS5A01G115500

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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 TraesCS5A01G115500 chr5A 100.000 4006 0 0 1 4006 234151325 234155330 0.000000e+00 7398.0
1 TraesCS5A01G115500 chr5A 90.454 639 36 7 842 1473 309684051 309684671 0.000000e+00 819.0
2 TraesCS5A01G115500 chr5A 92.653 245 18 0 3722 3966 324477010 324477254 1.770000e-93 353.0
3 TraesCS5A01G115500 chr5A 92.143 140 11 0 3527 3666 324476865 324477004 8.780000e-47 198.0
4 TraesCS5A01G115500 chr5A 95.349 43 2 0 1 43 324476824 324476866 7.180000e-08 69.4
5 TraesCS5A01G115500 chr7A 98.095 3464 37 6 45 3484 622638578 622635120 0.000000e+00 6004.0
6 TraesCS5A01G115500 chr7A 78.406 1079 180 32 2488 3526 169766934 169767999 0.000000e+00 652.0
7 TraesCS5A01G115500 chr7A 79.098 488 79 19 43 518 206384361 206384837 8.360000e-82 315.0
8 TraesCS5A01G115500 chr5D 92.019 639 44 3 842 1473 242629793 242629155 0.000000e+00 891.0
9 TraesCS5A01G115500 chr5D 80.326 798 98 28 2764 3527 531369154 531369926 2.100000e-152 549.0
10 TraesCS5A01G115500 chr5B 91.862 639 44 4 842 1473 255968176 255968813 0.000000e+00 885.0
11 TraesCS5A01G115500 chr5B 78.771 179 36 1 324 500 58352199 58352377 7.030000e-23 119.0
12 TraesCS5A01G115500 chr6A 79.476 1335 191 56 2213 3528 52612538 52613808 0.000000e+00 870.0
13 TraesCS5A01G115500 chr6A 82.287 717 102 15 2213 2918 64998975 64998273 7.410000e-167 597.0
14 TraesCS5A01G115500 chr6A 88.503 374 27 9 3647 4006 42098557 42098186 4.750000e-119 438.0
15 TraesCS5A01G115500 chr6A 95.349 43 2 0 1 43 42098669 42098627 7.180000e-08 69.4
16 TraesCS5A01G115500 chr1A 80.128 1248 180 40 2313 3526 51831208 51829995 0.000000e+00 869.0
17 TraesCS5A01G115500 chr1A 91.645 383 19 5 3556 3925 359988861 359989243 5.930000e-143 518.0
18 TraesCS5A01G115500 chr1A 88.798 366 19 4 3534 3899 365701847 365701504 2.860000e-116 429.0
19 TraesCS5A01G115500 chr1A 78.220 753 102 28 2817 3530 81356493 81355764 3.700000e-115 425.0
20 TraesCS5A01G115500 chr3A 79.518 1245 181 37 2313 3532 725500292 725501487 0.000000e+00 819.0
21 TraesCS5A01G115500 chr3A 80.454 1013 155 29 2539 3526 47669675 47670669 0.000000e+00 734.0
22 TraesCS5A01G115500 chr3A 87.885 487 39 7 3527 4002 274058818 274059295 4.520000e-154 555.0
23 TraesCS5A01G115500 chr3A 86.199 413 39 11 3533 3945 668652694 668652300 7.950000e-117 431.0
24 TraesCS5A01G115500 chr3A 94.715 246 13 0 3721 3966 38248169 38248414 2.260000e-102 383.0
25 TraesCS5A01G115500 chr3A 95.683 139 6 0 3527 3665 38248025 38248163 1.450000e-54 224.0
26 TraesCS5A01G115500 chr3A 85.088 114 17 0 45 158 397994461 397994348 2.530000e-22 117.0
27 TraesCS5A01G115500 chr3A 98.113 53 1 0 3954 4006 668652311 668652259 4.260000e-15 93.5
28 TraesCS5A01G115500 chr3A 97.674 43 1 0 1 43 38247984 38248026 1.540000e-09 75.0
29 TraesCS5A01G115500 chr3A 97.674 43 1 0 1 43 274058777 274058819 1.540000e-09 75.0
30 TraesCS5A01G115500 chr3A 97.674 43 1 0 1 43 668652741 668652699 1.540000e-09 75.0
31 TraesCS5A01G115500 chr2A 79.398 1262 183 47 2313 3528 575198548 575197318 0.000000e+00 819.0
32 TraesCS5A01G115500 chr2A 80.296 812 132 18 2751 3537 434077836 434078644 4.460000e-164 588.0
33 TraesCS5A01G115500 chr2A 77.494 782 117 36 2791 3527 130064797 130064030 8.010000e-112 414.0
34 TraesCS5A01G115500 chr2A 78.175 504 73 19 36 516 18480513 18481002 1.820000e-73 287.0
35 TraesCS5A01G115500 chr2A 84.348 115 18 0 45 159 8200634 8200520 3.270000e-21 113.0
36 TraesCS5A01G115500 chr7D 81.434 1018 151 25 2213 3218 63968804 63967813 0.000000e+00 798.0
37 TraesCS5A01G115500 chr7D 81.944 144 14 3 3669 3800 412164408 412164265 1.180000e-20 111.0
38 TraesCS5A01G115500 chr6B 79.868 1058 166 33 2495 3527 520732597 520731562 0.000000e+00 730.0
39 TraesCS5A01G115500 chr6B 90.329 486 27 6 3533 4006 710445257 710444780 1.580000e-173 619.0
40 TraesCS5A01G115500 chr6B 84.644 534 64 17 1469 1996 427638660 427638139 2.130000e-142 516.0
41 TraesCS5A01G115500 chr6B 80.928 194 29 8 329 516 682856586 682856777 3.230000e-31 147.0
42 TraesCS5A01G115500 chr6B 76.987 239 46 7 329 558 683131909 683131671 1.170000e-25 128.0
43 TraesCS5A01G115500 chr6B 81.818 110 19 1 45 154 42160020 42159912 1.530000e-14 91.6
44 TraesCS5A01G115500 chr1B 80.380 999 147 38 2561 3526 54232965 54231983 0.000000e+00 713.0
45 TraesCS5A01G115500 chr1B 78.598 1070 173 38 2486 3527 513247049 513246008 0.000000e+00 656.0
46 TraesCS5A01G115500 chr2B 79.900 1000 154 36 2561 3527 645421202 645420217 0.000000e+00 689.0
47 TraesCS5A01G115500 chr2B 79.800 1000 153 38 2561 3526 644731133 644730149 0.000000e+00 682.0
48 TraesCS5A01G115500 chr2B 87.292 480 45 9 3527 4006 74817611 74818074 5.890000e-148 534.0
49 TraesCS5A01G115500 chr2B 87.398 492 28 11 3527 4006 303911632 303912101 5.890000e-148 534.0
50 TraesCS5A01G115500 chr2B 77.958 803 115 36 2769 3526 432922 433707 2.840000e-121 446.0
51 TraesCS5A01G115500 chr2B 85.401 411 44 10 3535 3945 622265120 622264726 2.880000e-111 412.0
52 TraesCS5A01G115500 chr2B 100.000 43 0 0 1 43 303911591 303911633 3.320000e-11 80.5
53 TraesCS5A01G115500 chr2B 97.674 43 1 0 1 43 622265169 622265127 1.540000e-09 75.0
54 TraesCS5A01G115500 chr4D 79.916 712 112 18 2488 3177 206298159 206297457 1.000000e-135 494.0
55 TraesCS5A01G115500 chr4A 89.822 393 26 5 3556 3934 261414883 261414491 3.600000e-135 492.0
56 TraesCS5A01G115500 chr4A 88.491 391 22 7 3556 3945 329684199 329684567 6.110000e-123 451.0
57 TraesCS5A01G115500 chr4A 80.936 577 78 15 2313 2868 404266224 404266789 1.030000e-115 427.0
58 TraesCS5A01G115500 chr4A 81.651 109 16 4 42 148 611328670 611328776 1.980000e-13 87.9
59 TraesCS5A01G115500 chr4A 92.857 56 4 0 3927 3982 512973899 512973844 9.230000e-12 82.4
60 TraesCS5A01G115500 chr4A 97.674 43 1 0 1 43 329684150 329684192 1.540000e-09 75.0
61 TraesCS5A01G115500 chr4A 95.122 41 1 1 4 43 261414930 261414890 3.340000e-06 63.9
62 TraesCS5A01G115500 chr3B 79.477 497 79 18 44 528 608530476 608529991 8.300000e-87 331.0
63 TraesCS5A01G115500 chr3B 75.783 479 67 22 45 501 482572729 482573180 3.160000e-46 196.0
64 TraesCS5A01G115500 chr7B 82.301 339 53 6 193 528 513721397 513721063 1.820000e-73 287.0


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 TraesCS5A01G115500 chr5A 234151325 234155330 4005 False 7398.00 7398 100.0000 1 4006 1 chr5A.!!$F1 4005
1 TraesCS5A01G115500 chr5A 309684051 309684671 620 False 819.00 819 90.4540 842 1473 1 chr5A.!!$F2 631
2 TraesCS5A01G115500 chr7A 622635120 622638578 3458 True 6004.00 6004 98.0950 45 3484 1 chr7A.!!$R1 3439
3 TraesCS5A01G115500 chr7A 169766934 169767999 1065 False 652.00 652 78.4060 2488 3526 1 chr7A.!!$F1 1038
4 TraesCS5A01G115500 chr5D 242629155 242629793 638 True 891.00 891 92.0190 842 1473 1 chr5D.!!$R1 631
5 TraesCS5A01G115500 chr5D 531369154 531369926 772 False 549.00 549 80.3260 2764 3527 1 chr5D.!!$F1 763
6 TraesCS5A01G115500 chr5B 255968176 255968813 637 False 885.00 885 91.8620 842 1473 1 chr5B.!!$F2 631
7 TraesCS5A01G115500 chr6A 52612538 52613808 1270 False 870.00 870 79.4760 2213 3528 1 chr6A.!!$F1 1315
8 TraesCS5A01G115500 chr6A 64998273 64998975 702 True 597.00 597 82.2870 2213 2918 1 chr6A.!!$R1 705
9 TraesCS5A01G115500 chr1A 51829995 51831208 1213 True 869.00 869 80.1280 2313 3526 1 chr1A.!!$R1 1213
10 TraesCS5A01G115500 chr1A 81355764 81356493 729 True 425.00 425 78.2200 2817 3530 1 chr1A.!!$R2 713
11 TraesCS5A01G115500 chr3A 725500292 725501487 1195 False 819.00 819 79.5180 2313 3532 1 chr3A.!!$F2 1219
12 TraesCS5A01G115500 chr3A 47669675 47670669 994 False 734.00 734 80.4540 2539 3526 1 chr3A.!!$F1 987
13 TraesCS5A01G115500 chr3A 274058777 274059295 518 False 315.00 555 92.7795 1 4002 2 chr3A.!!$F4 4001
14 TraesCS5A01G115500 chr2A 575197318 575198548 1230 True 819.00 819 79.3980 2313 3528 1 chr2A.!!$R3 1215
15 TraesCS5A01G115500 chr2A 434077836 434078644 808 False 588.00 588 80.2960 2751 3537 1 chr2A.!!$F2 786
16 TraesCS5A01G115500 chr2A 130064030 130064797 767 True 414.00 414 77.4940 2791 3527 1 chr2A.!!$R2 736
17 TraesCS5A01G115500 chr7D 63967813 63968804 991 True 798.00 798 81.4340 2213 3218 1 chr7D.!!$R1 1005
18 TraesCS5A01G115500 chr6B 520731562 520732597 1035 True 730.00 730 79.8680 2495 3527 1 chr6B.!!$R3 1032
19 TraesCS5A01G115500 chr6B 427638139 427638660 521 True 516.00 516 84.6440 1469 1996 1 chr6B.!!$R2 527
20 TraesCS5A01G115500 chr1B 54231983 54232965 982 True 713.00 713 80.3800 2561 3526 1 chr1B.!!$R1 965
21 TraesCS5A01G115500 chr1B 513246008 513247049 1041 True 656.00 656 78.5980 2486 3527 1 chr1B.!!$R2 1041
22 TraesCS5A01G115500 chr2B 645420217 645421202 985 True 689.00 689 79.9000 2561 3527 1 chr2B.!!$R2 966
23 TraesCS5A01G115500 chr2B 644730149 644731133 984 True 682.00 682 79.8000 2561 3526 1 chr2B.!!$R1 965
24 TraesCS5A01G115500 chr2B 432922 433707 785 False 446.00 446 77.9580 2769 3526 1 chr2B.!!$F1 757
25 TraesCS5A01G115500 chr2B 303911591 303912101 510 False 307.25 534 93.6990 1 4006 2 chr2B.!!$F3 4005
26 TraesCS5A01G115500 chr4D 206297457 206298159 702 True 494.00 494 79.9160 2488 3177 1 chr4D.!!$R1 689
27 TraesCS5A01G115500 chr4A 404266224 404266789 565 False 427.00 427 80.9360 2313 2868 1 chr4A.!!$F1 555

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
225 226 0.030235 GTTGGCTTTCACGGTTGACC 59.970 55.000 0.00 0.0 0.0 4.02 F
240 241 0.617820 TGACCTAGGCTTCCCTGTCC 60.618 60.000 9.30 0.0 42.9 4.02 F
424 425 1.002624 GATCCTTTGTCCCGGTGCA 60.003 57.895 0.00 0.0 0.0 4.57 F
1826 1860 1.882912 TGTTCGTCTGCATGCTCTTT 58.117 45.000 20.33 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1623 4.159506 ACAGTAGCCTGAATCTTGACTCTC 59.840 45.833 0.0 0.0 41.50 3.20 R
1826 1860 4.564782 ATGGAGAAGACTGCTTGAATCA 57.435 40.909 0.0 0.0 35.49 2.57 R
2291 2325 1.747355 GCTGGATTGTTGAGGTCCATG 59.253 52.381 0.0 0.0 40.96 3.66 R
3719 3955 0.809385 CACCATCGTAGTCGTCCTGT 59.191 55.000 0.0 0.0 38.33 4.00 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
137 138 8.425577 ACCATAGATACGAATATAAGCATTGC 57.574 34.615 0.00 0.00 0.00 3.56
202 203 3.072184 CCAACATCTTATCTAGCCCAGCT 59.928 47.826 0.00 0.00 43.41 4.24
225 226 0.030235 GTTGGCTTTCACGGTTGACC 59.970 55.000 0.00 0.00 0.00 4.02
240 241 0.617820 TGACCTAGGCTTCCCTGTCC 60.618 60.000 9.30 0.00 42.90 4.02
261 262 3.777522 CCACAACCTCCTCTATTCCTCTT 59.222 47.826 0.00 0.00 0.00 2.85
337 338 1.618487 CTACGACCTACCTCCATCCC 58.382 60.000 0.00 0.00 0.00 3.85
424 425 1.002624 GATCCTTTGTCCCGGTGCA 60.003 57.895 0.00 0.00 0.00 4.57
756 757 5.104693 TCACGTCAATTCATATAACCTGGGT 60.105 40.000 0.00 0.00 0.00 4.51
893 914 7.378966 ACGGACCTTGTAGTATTGATGATATG 58.621 38.462 0.00 0.00 0.00 1.78
1075 1096 4.489737 TGTTCTGGAGGAAAGGAGTTCTA 58.510 43.478 0.00 0.00 36.40 2.10
1415 1439 6.766429 ACGAAAACTGTTCCCTTTAGTCTAT 58.234 36.000 0.00 0.00 0.00 1.98
1535 1567 7.328249 TGTCTGTTTTTGTTTCTTGCTGTTTAG 59.672 33.333 0.00 0.00 0.00 1.85
1826 1860 1.882912 TGTTCGTCTGCATGCTCTTT 58.117 45.000 20.33 0.00 0.00 2.52
2035 2069 3.007182 CCCGGTCAACTAAGTTCCAAGTA 59.993 47.826 0.00 0.00 0.00 2.24
2291 2325 5.861787 GGTGCTACATATTTGTTTGTTGGTC 59.138 40.000 0.00 0.00 37.28 4.02
2318 2352 1.200020 CTCAACAATCCAGCGTTTCCC 59.800 52.381 0.00 0.00 0.00 3.97
2689 2738 3.810941 TCTTGGTACGAAGTCGCAAAAAT 59.189 39.130 16.08 0.00 43.93 1.82
2887 2994 7.011763 GCAAGTACACTACAATGATGATGATGT 59.988 37.037 0.00 0.00 0.00 3.06
2889 2996 8.654230 AGTACACTACAATGATGATGATGTTC 57.346 34.615 0.00 0.00 0.00 3.18
3268 3458 1.166531 ACAAGACTTGAAGCGGTGCC 61.167 55.000 21.95 0.00 0.00 5.01
3545 3781 6.002062 AGTGAATGACGAAAATTTCAGACC 57.998 37.500 6.53 0.00 0.00 3.85
3549 3785 2.552315 TGACGAAAATTTCAGACCTGGC 59.448 45.455 6.53 0.00 0.00 4.85
3569 3805 3.821033 GGCAGTACAAATTCAGACTTGGT 59.179 43.478 0.00 0.00 0.00 3.67
3616 3852 0.754957 AGAGAGAGGATGGCTCACCG 60.755 60.000 0.00 0.00 39.70 4.94
3650 3886 4.451150 GAGGGTGCGTCGATGGCA 62.451 66.667 6.79 8.41 38.25 4.92
3718 3954 1.700042 CCCCTTCTCCTCCCAATCGG 61.700 65.000 0.00 0.00 0.00 4.18
3719 3955 0.691078 CCCTTCTCCTCCCAATCGGA 60.691 60.000 0.00 0.00 38.83 4.55
3729 3977 1.605058 CCCAATCGGACAGGACGACT 61.605 60.000 0.00 0.00 43.78 4.18
3730 3978 1.100510 CCAATCGGACAGGACGACTA 58.899 55.000 0.00 0.00 43.78 2.59
3862 4110 2.379972 CAGGGGAGTCGAGTCAGTTAT 58.620 52.381 21.38 0.23 0.00 1.89
3866 4114 2.100989 GGAGTCGAGTCAGTTATGGGT 58.899 52.381 21.38 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 7.202066 GCTTTATAGGGGGTATTCTTGTAGTGA 60.202 40.741 0.00 0.00 0.00 3.41
137 138 4.965762 CACAAATCTACAACGCATATGCTG 59.034 41.667 24.56 18.83 39.32 4.41
202 203 1.403679 CAACCGTGAAAGCCAACTTGA 59.596 47.619 0.00 0.00 35.85 3.02
225 226 0.984230 TTGTGGACAGGGAAGCCTAG 59.016 55.000 0.00 0.00 0.00 3.02
240 241 4.467795 TCAAGAGGAATAGAGGAGGTTGTG 59.532 45.833 0.00 0.00 0.00 3.33
424 425 3.300765 GTGGTGTCGAGGGACGGT 61.301 66.667 0.00 0.00 46.49 4.83
756 757 4.100963 TGCTTGTTGGAGTAGAGTTTGAGA 59.899 41.667 0.00 0.00 0.00 3.27
918 939 8.098912 ACGTAAACAAAGACAGGGTAAGATTAT 58.901 33.333 0.00 0.00 0.00 1.28
1415 1439 8.918202 AGTTTTGTTATTTGAGATCCAGTACA 57.082 30.769 0.00 0.00 0.00 2.90
1535 1567 7.437862 TCAGCATGTCCAGATTTTAAACAAAAC 59.562 33.333 0.00 0.00 37.40 2.43
1591 1623 4.159506 ACAGTAGCCTGAATCTTGACTCTC 59.840 45.833 0.00 0.00 41.50 3.20
1694 1726 5.458595 TGCTTAGATGGATTAGGAGTCTCA 58.541 41.667 1.47 0.00 0.00 3.27
1826 1860 4.564782 ATGGAGAAGACTGCTTGAATCA 57.435 40.909 0.00 0.00 35.49 2.57
2291 2325 1.747355 GCTGGATTGTTGAGGTCCATG 59.253 52.381 0.00 0.00 40.96 3.66
2318 2352 4.053983 CCTCGATCAGACACCAACATATG 58.946 47.826 0.00 0.00 0.00 1.78
2689 2738 4.637977 TCTGCATTACCACGAATATTGCAA 59.362 37.500 0.00 0.00 38.04 4.08
2887 2994 6.655930 TCATCATCATCATCAGGAACAAGAA 58.344 36.000 0.00 0.00 0.00 2.52
2889 2996 6.710744 TCATCATCATCATCATCAGGAACAAG 59.289 38.462 0.00 0.00 0.00 3.16
3268 3458 1.514873 GCCGCGCAAAGGAGAATTG 60.515 57.895 8.75 0.00 0.00 2.32
3463 3696 8.869897 CGTATCTAAATGTCCATATATGCGTTT 58.130 33.333 7.24 10.47 0.00 3.60
3545 3781 4.083110 CCAAGTCTGAATTTGTACTGCCAG 60.083 45.833 0.00 0.00 0.00 4.85
3549 3785 7.870954 TGTACTACCAAGTCTGAATTTGTACTG 59.129 37.037 14.76 5.15 37.15 2.74
3569 3805 6.681729 ACTCCCTGTTCTGAATTTGTACTA 57.318 37.500 0.00 0.00 0.00 1.82
3616 3852 1.304217 TCGTCCTCCACTCCTCCAC 60.304 63.158 0.00 0.00 0.00 4.02
3650 3886 2.681778 CACCCTCGTCCTCAGCCT 60.682 66.667 0.00 0.00 0.00 4.58
3718 3954 1.093159 ACCATCGTAGTCGTCCTGTC 58.907 55.000 0.00 0.00 38.33 3.51
3719 3955 0.809385 CACCATCGTAGTCGTCCTGT 59.191 55.000 0.00 0.00 38.33 4.00
3729 3977 1.435925 CTGCTACGCCACCATCGTA 59.564 57.895 0.00 0.00 40.89 3.43
3730 3978 2.184322 CTGCTACGCCACCATCGT 59.816 61.111 0.00 0.00 43.20 3.73
3840 4088 2.037367 TGACTCGACTCCCCTGGG 59.963 66.667 5.50 5.50 0.00 4.45
3862 4110 2.365105 CCTTCGGCCTCCTACCCA 60.365 66.667 0.00 0.00 0.00 4.51
3982 4237 4.657408 TGCCGCCATGACTGCCAA 62.657 61.111 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.