Multiple sequence alignment - TraesCS2D01G577700

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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 TraesCS2D01G577700 chr2D 100.000 3873 0 0 1 3873 640950417 640946545 0.000000e+00 7153
1 TraesCS2D01G577700 chr1B 91.657 1786 77 26 1 1759 212224389 212226129 0.000000e+00 2407
2 TraesCS2D01G577700 chr1B 95.997 1324 45 4 2555 3873 212227952 212229272 0.000000e+00 2145
3 TraesCS2D01G577700 chr1B 95.493 954 40 1 2556 3509 146425718 146424768 0.000000e+00 1520
4 TraesCS2D01G577700 chr1B 91.929 508 8 5 3392 3873 606231038 606231538 0.000000e+00 680
5 TraesCS2D01G577700 chr1B 91.372 452 10 8 3448 3873 146424798 146424350 3.330000e-165 592
6 TraesCS2D01G577700 chr1B 98.312 237 4 0 2317 2553 212226128 212226364 2.150000e-112 416
7 TraesCS2D01G577700 chr1B 98.276 116 2 0 2438 2553 606228866 606228981 1.820000e-48 204
8 TraesCS2D01G577700 chr7B 95.097 1346 37 4 2555 3873 420661244 420662587 0.000000e+00 2093
9 TraesCS2D01G577700 chr7B 94.799 1346 38 6 2555 3873 420615054 420616394 0.000000e+00 2069
10 TraesCS2D01G577700 chr7B 94.284 1347 40 8 2555 3873 656486354 656485017 0.000000e+00 2026
11 TraesCS2D01G577700 chr7B 96.643 566 18 1 1924 2489 18364310 18363746 0.000000e+00 939
12 TraesCS2D01G577700 chr7B 97.786 542 12 0 2012 2553 656488489 656487948 0.000000e+00 935
13 TraesCS2D01G577700 chr7B 95.938 517 21 0 2012 2528 615633237 615632721 0.000000e+00 839
14 TraesCS2D01G577700 chr7B 94.819 193 5 2 3684 3873 683090509 683090319 2.930000e-76 296
15 TraesCS2D01G577700 chr7B 91.176 204 13 4 1172 1370 698632173 698631970 4.930000e-69 272
16 TraesCS2D01G577700 chr2B 95.011 1323 51 9 2555 3873 321108625 321109936 0.000000e+00 2063
17 TraesCS2D01G577700 chr2B 91.010 990 40 15 1 964 321104785 321105751 0.000000e+00 1290
18 TraesCS2D01G577700 chr2B 84.650 1101 80 34 285 1304 220518546 220519638 0.000000e+00 1014
19 TraesCS2D01G577700 chr2B 89.265 680 69 3 1 677 791187125 791187803 0.000000e+00 848
20 TraesCS2D01G577700 chr2B 88.774 677 68 5 1 677 69396432 69397100 0.000000e+00 822
21 TraesCS2D01G577700 chr2B 91.833 551 16 5 3349 3873 371335330 371334783 0.000000e+00 741
22 TraesCS2D01G577700 chr2B 87.689 463 28 9 926 1370 321105755 321106206 2.670000e-141 512
23 TraesCS2D01G577700 chr2B 96.552 116 4 0 2438 2553 321106919 321107034 3.950000e-45 193
24 TraesCS2D01G577700 chr6B 94.647 1345 41 6 2555 3873 53345139 53346478 0.000000e+00 2056
25 TraesCS2D01G577700 chr6B 89.380 951 71 11 1 924 68217793 68218740 0.000000e+00 1170
26 TraesCS2D01G577700 chr6B 91.549 213 9 4 2012 2216 703944806 703945017 6.330000e-73 285
27 TraesCS2D01G577700 chr2A 91.802 1415 69 12 1 1370 59859353 59860765 0.000000e+00 1927
28 TraesCS2D01G577700 chr2A 96.481 824 27 1 2555 3378 59862687 59863508 0.000000e+00 1360
29 TraesCS2D01G577700 chr2A 97.388 268 5 2 3392 3658 675945789 675946055 4.560000e-124 455
30 TraesCS2D01G577700 chr2A 98.276 116 1 1 2438 2553 59861431 59861545 6.560000e-48 202
31 TraesCS2D01G577700 chr4A 91.378 1415 72 16 1 1370 79414345 79415754 0.000000e+00 1892
32 TraesCS2D01G577700 chr4A 97.126 835 23 1 1655 2489 699840785 699841618 0.000000e+00 1408
33 TraesCS2D01G577700 chr4A 89.497 676 67 4 3 677 644927995 644927323 0.000000e+00 852
34 TraesCS2D01G577700 chr4A 88.938 678 71 4 1 677 644926699 644926025 0.000000e+00 833
35 TraesCS2D01G577700 chr4A 86.306 628 48 10 1379 1987 677935160 677935768 0.000000e+00 649
36 TraesCS2D01G577700 chr4A 91.584 202 11 5 1172 1368 661809306 661809106 1.370000e-69 274
37 TraesCS2D01G577700 chr5A 90.941 1413 82 16 1 1370 506440276 506441685 0.000000e+00 1858
38 TraesCS2D01G577700 chr5A 88.198 1432 80 30 1 1370 564683494 564682090 0.000000e+00 1626
39 TraesCS2D01G577700 chr5A 95.690 116 4 1 2438 2553 506442351 506442465 6.610000e-43 185
40 TraesCS2D01G577700 chr7A 89.619 1416 90 19 1 1370 921565 920161 0.000000e+00 1748
41 TraesCS2D01G577700 chr7A 90.265 678 57 6 1 677 77887242 77887911 0.000000e+00 878
42 TraesCS2D01G577700 chr7A 89.866 671 60 8 1 669 386213051 386213715 0.000000e+00 856
43 TraesCS2D01G577700 chr7A 99.138 116 0 1 2438 2553 919617 919503 1.410000e-49 207
44 TraesCS2D01G577700 chr5B 89.007 1410 100 18 4 1370 186353135 186351738 0.000000e+00 1694
45 TraesCS2D01G577700 chr5B 95.899 829 33 1 1661 2489 34585539 34584712 0.000000e+00 1341
46 TraesCS2D01G577700 chr5B 93.433 533 5 3 3365 3871 444448882 444448354 0.000000e+00 763
47 TraesCS2D01G577700 chr3A 96.723 824 25 1 2555 3378 373434224 373435045 0.000000e+00 1371
48 TraesCS2D01G577700 chr3A 87.076 619 33 7 784 1370 346428778 346428175 0.000000e+00 656
49 TraesCS2D01G577700 chr3A 90.883 351 15 5 1037 1370 373431952 373432302 4.560000e-124 455
50 TraesCS2D01G577700 chr3A 98.276 116 1 1 2438 2553 373432968 373433082 6.560000e-48 202
51 TraesCS2D01G577700 chr4B 90.574 679 60 4 1 677 618128490 618127814 0.000000e+00 896
52 TraesCS2D01G577700 chr4B 88.954 679 69 6 1 677 564759335 564758661 0.000000e+00 833
53 TraesCS2D01G577700 chr4B 90.000 630 38 13 1379 1987 591497487 591498112 0.000000e+00 791
54 TraesCS2D01G577700 chr4B 95.337 193 4 2 3684 3873 626668769 626668579 6.290000e-78 302
55 TraesCS2D01G577700 chr1D 89.265 680 67 6 1 677 411407497 411408173 0.000000e+00 846
56 TraesCS2D01G577700 chr4D 88.871 638 40 5 1379 1987 470112557 470113192 0.000000e+00 756
57 TraesCS2D01G577700 chr6A 91.253 423 22 7 2012 2427 608503036 608503450 2.610000e-156 562
58 TraesCS2D01G577700 chr6D 89.305 374 29 6 2012 2384 461687214 461687577 3.530000e-125 459
59 TraesCS2D01G577700 chr3B 96.957 230 6 1 2012 2241 16868791 16868563 6.070000e-103 385


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 TraesCS2D01G577700 chr2D 640946545 640950417 3872 True 7153.0 7153 100.000000 1 3873 1 chr2D.!!$R1 3872
1 TraesCS2D01G577700 chr1B 212224389 212229272 4883 False 1656.0 2407 95.322000 1 3873 3 chr1B.!!$F1 3872
2 TraesCS2D01G577700 chr1B 146424350 146425718 1368 True 1056.0 1520 93.432500 2556 3873 2 chr1B.!!$R1 1317
3 TraesCS2D01G577700 chr1B 606228866 606231538 2672 False 442.0 680 95.102500 2438 3873 2 chr1B.!!$F2 1435
4 TraesCS2D01G577700 chr7B 420661244 420662587 1343 False 2093.0 2093 95.097000 2555 3873 1 chr7B.!!$F2 1318
5 TraesCS2D01G577700 chr7B 420615054 420616394 1340 False 2069.0 2069 94.799000 2555 3873 1 chr7B.!!$F1 1318
6 TraesCS2D01G577700 chr7B 656485017 656488489 3472 True 1480.5 2026 96.035000 2012 3873 2 chr7B.!!$R5 1861
7 TraesCS2D01G577700 chr7B 18363746 18364310 564 True 939.0 939 96.643000 1924 2489 1 chr7B.!!$R1 565
8 TraesCS2D01G577700 chr7B 615632721 615633237 516 True 839.0 839 95.938000 2012 2528 1 chr7B.!!$R2 516
9 TraesCS2D01G577700 chr2B 321104785 321109936 5151 False 1014.5 2063 92.565500 1 3873 4 chr2B.!!$F4 3872
10 TraesCS2D01G577700 chr2B 220518546 220519638 1092 False 1014.0 1014 84.650000 285 1304 1 chr2B.!!$F2 1019
11 TraesCS2D01G577700 chr2B 791187125 791187803 678 False 848.0 848 89.265000 1 677 1 chr2B.!!$F3 676
12 TraesCS2D01G577700 chr2B 69396432 69397100 668 False 822.0 822 88.774000 1 677 1 chr2B.!!$F1 676
13 TraesCS2D01G577700 chr2B 371334783 371335330 547 True 741.0 741 91.833000 3349 3873 1 chr2B.!!$R1 524
14 TraesCS2D01G577700 chr6B 53345139 53346478 1339 False 2056.0 2056 94.647000 2555 3873 1 chr6B.!!$F1 1318
15 TraesCS2D01G577700 chr6B 68217793 68218740 947 False 1170.0 1170 89.380000 1 924 1 chr6B.!!$F2 923
16 TraesCS2D01G577700 chr2A 59859353 59863508 4155 False 1163.0 1927 95.519667 1 3378 3 chr2A.!!$F2 3377
17 TraesCS2D01G577700 chr4A 79414345 79415754 1409 False 1892.0 1892 91.378000 1 1370 1 chr4A.!!$F1 1369
18 TraesCS2D01G577700 chr4A 699840785 699841618 833 False 1408.0 1408 97.126000 1655 2489 1 chr4A.!!$F3 834
19 TraesCS2D01G577700 chr4A 644926025 644927995 1970 True 842.5 852 89.217500 1 677 2 chr4A.!!$R2 676
20 TraesCS2D01G577700 chr4A 677935160 677935768 608 False 649.0 649 86.306000 1379 1987 1 chr4A.!!$F2 608
21 TraesCS2D01G577700 chr5A 564682090 564683494 1404 True 1626.0 1626 88.198000 1 1370 1 chr5A.!!$R1 1369
22 TraesCS2D01G577700 chr5A 506440276 506442465 2189 False 1021.5 1858 93.315500 1 2553 2 chr5A.!!$F1 2552
23 TraesCS2D01G577700 chr7A 919503 921565 2062 True 977.5 1748 94.378500 1 2553 2 chr7A.!!$R1 2552
24 TraesCS2D01G577700 chr7A 77887242 77887911 669 False 878.0 878 90.265000 1 677 1 chr7A.!!$F1 676
25 TraesCS2D01G577700 chr7A 386213051 386213715 664 False 856.0 856 89.866000 1 669 1 chr7A.!!$F2 668
26 TraesCS2D01G577700 chr5B 186351738 186353135 1397 True 1694.0 1694 89.007000 4 1370 1 chr5B.!!$R2 1366
27 TraesCS2D01G577700 chr5B 34584712 34585539 827 True 1341.0 1341 95.899000 1661 2489 1 chr5B.!!$R1 828
28 TraesCS2D01G577700 chr5B 444448354 444448882 528 True 763.0 763 93.433000 3365 3871 1 chr5B.!!$R3 506
29 TraesCS2D01G577700 chr3A 373431952 373435045 3093 False 676.0 1371 95.294000 1037 3378 3 chr3A.!!$F1 2341
30 TraesCS2D01G577700 chr3A 346428175 346428778 603 True 656.0 656 87.076000 784 1370 1 chr3A.!!$R1 586
31 TraesCS2D01G577700 chr4B 618127814 618128490 676 True 896.0 896 90.574000 1 677 1 chr4B.!!$R2 676
32 TraesCS2D01G577700 chr4B 564758661 564759335 674 True 833.0 833 88.954000 1 677 1 chr4B.!!$R1 676
33 TraesCS2D01G577700 chr4B 591497487 591498112 625 False 791.0 791 90.000000 1379 1987 1 chr4B.!!$F1 608
34 TraesCS2D01G577700 chr1D 411407497 411408173 676 False 846.0 846 89.265000 1 677 1 chr1D.!!$F1 676
35 TraesCS2D01G577700 chr4D 470112557 470113192 635 False 756.0 756 88.871000 1379 1987 1 chr4D.!!$F1 608

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
776 2108 1.841919 TGACATGGCATCCATCTGACT 59.158 47.619 0.00 0.0 43.15 3.41 F
1305 2742 0.469144 AAGCCTCGATCTCCTCCTCC 60.469 60.000 0.00 0.0 0.00 4.30 F
1545 3224 0.678048 GAAGACTTCGCATTGCCCCT 60.678 55.000 2.41 0.0 0.00 4.79 F
1789 3666 0.804364 TGCTATGCTTTTGGACTGCG 59.196 50.000 0.00 0.0 0.00 5.18 F
1875 3753 1.780309 TGTTGGTGGGATTCTTGGACT 59.220 47.619 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 3434 0.423544 ACCTCTTCCCCATCTTCCCT 59.576 55.000 0.0 0.0 0.00 4.20 R
2204 4091 2.093310 CGTCAACATGATCAGAGTGCAC 59.907 50.000 9.4 9.4 0.00 4.57 R
2350 4237 2.164624 CGGTGTTCCAGGTTTTGTTTCA 59.835 45.455 0.0 0.0 0.00 2.69 R
2799 6279 2.308570 TCTTTGCCCCTGAAGAAGCATA 59.691 45.455 0.0 0.0 34.72 3.14 R
3216 6699 6.582636 TGTCACCAGAGGTAAATAGCAATAG 58.417 40.000 0.0 0.0 32.11 1.73 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
76 77 3.133691 TCACGCATGATAGCTCATTTCC 58.866 45.455 0.00 0.00 40.20 3.13
94 96 9.463443 CTCATTTCCGAGAACACTTTTTAAAAT 57.537 29.630 0.55 0.00 34.79 1.82
573 1878 9.528847 GCACTCGAAAAATGGAAAATAAAATTC 57.471 29.630 0.00 0.00 0.00 2.17
776 2108 1.841919 TGACATGGCATCCATCTGACT 59.158 47.619 0.00 0.00 43.15 3.41
902 2238 4.162690 GCATTCCTCCCTCGCCGT 62.163 66.667 0.00 0.00 0.00 5.68
1284 2721 4.436998 GTCCAGCACCCGGAGTCG 62.437 72.222 0.73 0.00 31.65 4.18
1303 2740 1.398958 GCAAGCCTCGATCTCCTCCT 61.399 60.000 0.00 0.00 0.00 3.69
1304 2741 0.673437 CAAGCCTCGATCTCCTCCTC 59.327 60.000 0.00 0.00 0.00 3.71
1305 2742 0.469144 AAGCCTCGATCTCCTCCTCC 60.469 60.000 0.00 0.00 0.00 4.30
1370 2816 3.812019 CGACGACACCTCCTCGGG 61.812 72.222 0.00 0.00 36.97 5.14
1374 2820 2.663196 GACACCTCCTCGGGTTGG 59.337 66.667 0.00 0.00 37.52 3.77
1375 2821 1.911766 GACACCTCCTCGGGTTGGA 60.912 63.158 0.00 0.00 37.52 3.53
1545 3224 0.678048 GAAGACTTCGCATTGCCCCT 60.678 55.000 2.41 0.00 0.00 4.79
1746 3561 5.941058 TGTGGCTTTGGTTTAGATCGAATTA 59.059 36.000 0.00 0.00 0.00 1.40
1789 3666 0.804364 TGCTATGCTTTTGGACTGCG 59.196 50.000 0.00 0.00 0.00 5.18
1868 3746 5.652014 TGTGAGAATTATGTTGGTGGGATTC 59.348 40.000 0.00 0.00 0.00 2.52
1875 3753 1.780309 TGTTGGTGGGATTCTTGGACT 59.220 47.619 0.00 0.00 0.00 3.85
2056 3943 6.274579 TGTGCTAAAATGTATCCATGCATTG 58.725 36.000 0.00 0.00 41.26 2.82
2204 4091 3.376859 TGTTACCTGCTGTGTGTTTGAAG 59.623 43.478 0.00 0.00 0.00 3.02
2350 4237 6.206829 GTCCTTTCCTTGCTTGTGTTTATACT 59.793 38.462 0.00 0.00 0.00 2.12
2372 4259 1.842052 AACAAAACCTGGAACACCGT 58.158 45.000 0.00 0.00 0.00 4.83
2553 4440 4.317530 AGTGATGTGAGTGGGACTACTA 57.682 45.455 0.00 0.00 0.00 1.82
2673 6153 7.383102 AGGTTCATCATAGTTTTAGTGCAAG 57.617 36.000 0.00 0.00 0.00 4.01
3081 6564 9.618890 CATCTCCTAGTCATAAATTTCCTGAAA 57.381 33.333 0.00 0.00 34.46 2.69
3088 6571 7.697691 AGTCATAAATTTCCTGAAATAGTGCG 58.302 34.615 5.60 0.00 39.88 5.34
3092 6575 5.705609 AATTTCCTGAAATAGTGCGTGTT 57.294 34.783 5.60 0.00 39.88 3.32
3153 6636 6.569179 TTTCTAACTTGATTGTTGTAGGCC 57.431 37.500 0.00 0.00 0.00 5.19
3216 6699 5.953183 TGCCACTGTTCATTCATTTATGTC 58.047 37.500 0.00 0.00 0.00 3.06
3766 7743 3.681034 CGAAGGAGCTCCATGTTGAAGAT 60.681 47.826 33.90 6.77 38.89 2.40
3767 7744 4.268359 GAAGGAGCTCCATGTTGAAGATT 58.732 43.478 33.90 15.42 38.89 2.40
3768 7745 3.618351 AGGAGCTCCATGTTGAAGATTG 58.382 45.455 33.90 0.00 38.89 2.67
3769 7746 3.265221 AGGAGCTCCATGTTGAAGATTGA 59.735 43.478 33.90 0.00 38.89 2.57
3773 7750 4.699257 AGCTCCATGTTGAAGATTGAAGAC 59.301 41.667 0.00 0.00 0.00 3.01
3777 7755 6.005823 TCCATGTTGAAGATTGAAGACACAT 58.994 36.000 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.010314 TCAGGCCAAATGATCAATCTTATGC 59.990 40.000 5.01 0.87 0.00 3.14
573 1878 7.307337 GGAATGACAAACAATGTTGCTAAAAGG 60.307 37.037 0.00 0.00 44.12 3.11
776 2108 0.758734 GATGGATGGACGGATGGACA 59.241 55.000 0.00 0.00 0.00 4.02
1110 2510 2.437895 ACGACGGGAGAGCGATGA 60.438 61.111 0.00 0.00 35.76 2.92
1284 2721 1.068921 GGAGGAGATCGAGGCTTGC 59.931 63.158 0.00 0.00 0.00 4.01
1318 2763 3.971702 AGGGAGGCAAAGGCGCTT 61.972 61.111 7.64 0.00 42.47 4.68
1370 2816 1.078708 TCCTCCGGCGAAATCCAAC 60.079 57.895 9.30 0.00 0.00 3.77
1374 2820 1.521681 CAGGTCCTCCGGCGAAATC 60.522 63.158 9.30 0.00 39.05 2.17
1375 2821 2.584608 CAGGTCCTCCGGCGAAAT 59.415 61.111 9.30 0.00 39.05 2.17
1619 3434 0.423544 ACCTCTTCCCCATCTTCCCT 59.576 55.000 0.00 0.00 0.00 4.20
1746 3561 3.613910 GCACGAAACAACAGGGCATTAAT 60.614 43.478 0.00 0.00 0.00 1.40
1789 3666 2.801111 GCCTGCTAAATTCCGTACTAGC 59.199 50.000 3.30 3.30 37.79 3.42
1927 3814 3.788227 ATCCCAACAGAAGCACTAACA 57.212 42.857 0.00 0.00 0.00 2.41
2204 4091 2.093310 CGTCAACATGATCAGAGTGCAC 59.907 50.000 9.40 9.40 0.00 4.57
2350 4237 2.164624 CGGTGTTCCAGGTTTTGTTTCA 59.835 45.455 0.00 0.00 0.00 2.69
2372 4259 9.653287 AATATTTGAGAATGAAACTACGAGTGA 57.347 29.630 0.00 0.00 0.00 3.41
2583 6063 7.399245 ACAACAACAATACCAACTAACAAGT 57.601 32.000 0.00 0.00 0.00 3.16
2799 6279 2.308570 TCTTTGCCCCTGAAGAAGCATA 59.691 45.455 0.00 0.00 34.72 3.14
2936 6419 7.426929 ACTAGCTATTGACAGAAAAACACAG 57.573 36.000 0.00 0.00 0.00 3.66
3081 6564 6.990349 AGCACCTAAATATAAACACGCACTAT 59.010 34.615 0.00 0.00 0.00 2.12
3153 6636 8.899427 ATGAACCAACAGAGATATATCTTGTG 57.101 34.615 16.37 17.42 37.25 3.33
3216 6699 6.582636 TGTCACCAGAGGTAAATAGCAATAG 58.417 40.000 0.00 0.00 32.11 1.73
3766 7743 9.890629 ATTTACAAGCTCTATATGTGTCTTCAA 57.109 29.630 0.00 0.00 0.00 2.69
3767 7744 9.890629 AATTTACAAGCTCTATATGTGTCTTCA 57.109 29.630 0.00 0.00 0.00 3.02
3777 7755 8.696374 ACAGCTACAGAATTTACAAGCTCTATA 58.304 33.333 0.00 0.00 38.20 1.31


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

AutoCloner maintained by Alex Coulton.