Multiple sequence alignment - TraesCS5D01G197100

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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 TraesCS5D01G197100 chr5D 100.000 3197 0 0 1 3197 300147896 300144700 0.000000e+00 5904
1 TraesCS5D01G197100 chr5D 88.894 2026 156 32 424 2392 300955517 300957530 0.000000e+00 2431
2 TraesCS5D01G197100 chr5D 92.052 1686 91 20 400 2050 300323396 300321719 0.000000e+00 2331
3 TraesCS5D01G197100 chr5D 89.651 1691 103 24 431 2074 299388744 299390409 0.000000e+00 2087
4 TraesCS5D01G197100 chr5D 86.432 1673 118 55 427 2048 300160915 300159301 0.000000e+00 1731
5 TraesCS5D01G197100 chr5D 84.965 1736 156 39 400 2066 299068429 299070128 0.000000e+00 1663
6 TraesCS5D01G197100 chr5D 88.443 1047 80 16 1983 3009 300314868 300313843 0.000000e+00 1225
7 TraesCS5D01G197100 chr5D 92.652 626 31 4 2385 3009 300957630 300958241 0.000000e+00 887
8 TraesCS5D01G197100 chr5D 96.758 401 13 0 1 401 300323827 300323427 0.000000e+00 669
9 TraesCS5D01G197100 chr5D 84.711 641 60 15 400 1021 299004328 299004949 9.810000e-170 606
10 TraesCS5D01G197100 chr5D 81.498 654 94 21 2552 3197 307090566 307089932 2.200000e-141 512
11 TraesCS5D01G197100 chr5B 93.425 2616 123 17 609 3197 339977862 339980455 0.000000e+00 3832
12 TraesCS5D01G197100 chr5B 89.726 2151 151 33 400 2495 344241076 344238941 0.000000e+00 2684
13 TraesCS5D01G197100 chr5B 90.554 2022 115 24 431 2412 340134534 340136519 0.000000e+00 2606
14 TraesCS5D01G197100 chr5B 90.554 2022 115 24 431 2412 340324607 340326592 0.000000e+00 2606
15 TraesCS5D01G197100 chr5B 90.034 1746 103 22 400 2106 343952809 343951096 0.000000e+00 2194
16 TraesCS5D01G197100 chr5B 98.007 1104 21 1 2095 3197 343950925 343949822 0.000000e+00 1916
17 TraesCS5D01G197100 chr5B 89.831 1475 95 23 609 2049 340567717 340569170 0.000000e+00 1842
18 TraesCS5D01G197100 chr5B 96.255 801 27 3 2398 3197 340136533 340137331 0.000000e+00 1310
19 TraesCS5D01G197100 chr5B 96.255 801 27 3 2398 3197 340326606 340327404 0.000000e+00 1310
20 TraesCS5D01G197100 chr5B 90.820 512 35 3 2498 3009 344232832 344232333 0.000000e+00 675
21 TraesCS5D01G197100 chr5B 81.335 659 86 24 2552 3197 352311049 352310415 4.760000e-138 501
22 TraesCS5D01G197100 chr5B 90.373 322 31 0 1 322 6462188 6462509 1.060000e-114 424
23 TraesCS5D01G197100 chr5B 88.509 322 37 0 1 322 543260396 543260075 1.080000e-104 390
24 TraesCS5D01G197100 chr5A 91.271 2715 158 40 522 3197 397786949 397784275 0.000000e+00 3627
25 TraesCS5D01G197100 chr5A 88.106 1816 114 36 431 2189 396415632 396417402 0.000000e+00 2063
26 TraesCS5D01G197100 chr5A 86.537 1701 138 40 427 2085 398051287 398049636 0.000000e+00 1788
27 TraesCS5D01G197100 chr5A 92.025 815 56 6 2256 3067 396417410 396418218 0.000000e+00 1136
28 TraesCS5D01G197100 chr5A 82.143 980 124 26 2245 3197 415627441 415628396 0.000000e+00 793
29 TraesCS5D01G197100 chr5A 81.164 653 98 18 2552 3197 390366210 390366844 4.760000e-138 501
30 TraesCS5D01G197100 chr3D 85.337 832 97 16 2385 3197 482005835 482006660 0.000000e+00 837
31 TraesCS5D01G197100 chr4D 91.445 339 25 4 1 338 59512443 59512108 2.250000e-126 462
32 TraesCS5D01G197100 chr1B 90.031 321 30 2 1 321 518792375 518792693 6.380000e-112 414
33 TraesCS5D01G197100 chr1B 89.342 319 34 0 4 322 29286877 29287195 4.970000e-108 401
34 TraesCS5D01G197100 chr3A 87.926 323 38 1 1 322 440510533 440510855 2.330000e-101 379
35 TraesCS5D01G197100 chr3A 87.578 322 39 1 1 322 632735110 632734790 3.890000e-99 372
36 TraesCS5D01G197100 chr6B 88.050 318 34 3 4 321 520856901 520856588 1.080000e-99 374


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 TraesCS5D01G197100 chr5D 300144700 300147896 3196 True 5904.0 5904 100.0000 1 3197 1 chr5D.!!$R1 3196
1 TraesCS5D01G197100 chr5D 299388744 299390409 1665 False 2087.0 2087 89.6510 431 2074 1 chr5D.!!$F3 1643
2 TraesCS5D01G197100 chr5D 300159301 300160915 1614 True 1731.0 1731 86.4320 427 2048 1 chr5D.!!$R2 1621
3 TraesCS5D01G197100 chr5D 299068429 299070128 1699 False 1663.0 1663 84.9650 400 2066 1 chr5D.!!$F2 1666
4 TraesCS5D01G197100 chr5D 300955517 300958241 2724 False 1659.0 2431 90.7730 424 3009 2 chr5D.!!$F4 2585
5 TraesCS5D01G197100 chr5D 300321719 300323827 2108 True 1500.0 2331 94.4050 1 2050 2 chr5D.!!$R5 2049
6 TraesCS5D01G197100 chr5D 300313843 300314868 1025 True 1225.0 1225 88.4430 1983 3009 1 chr5D.!!$R3 1026
7 TraesCS5D01G197100 chr5D 299004328 299004949 621 False 606.0 606 84.7110 400 1021 1 chr5D.!!$F1 621
8 TraesCS5D01G197100 chr5D 307089932 307090566 634 True 512.0 512 81.4980 2552 3197 1 chr5D.!!$R4 645
9 TraesCS5D01G197100 chr5B 339977862 339980455 2593 False 3832.0 3832 93.4250 609 3197 1 chr5B.!!$F2 2588
10 TraesCS5D01G197100 chr5B 344238941 344241076 2135 True 2684.0 2684 89.7260 400 2495 1 chr5B.!!$R2 2095
11 TraesCS5D01G197100 chr5B 343949822 343952809 2987 True 2055.0 2194 94.0205 400 3197 2 chr5B.!!$R5 2797
12 TraesCS5D01G197100 chr5B 340134534 340137331 2797 False 1958.0 2606 93.4045 431 3197 2 chr5B.!!$F4 2766
13 TraesCS5D01G197100 chr5B 340324607 340327404 2797 False 1958.0 2606 93.4045 431 3197 2 chr5B.!!$F5 2766
14 TraesCS5D01G197100 chr5B 340567717 340569170 1453 False 1842.0 1842 89.8310 609 2049 1 chr5B.!!$F3 1440
15 TraesCS5D01G197100 chr5B 352310415 352311049 634 True 501.0 501 81.3350 2552 3197 1 chr5B.!!$R3 645
16 TraesCS5D01G197100 chr5A 397784275 397786949 2674 True 3627.0 3627 91.2710 522 3197 1 chr5A.!!$R1 2675
17 TraesCS5D01G197100 chr5A 398049636 398051287 1651 True 1788.0 1788 86.5370 427 2085 1 chr5A.!!$R2 1658
18 TraesCS5D01G197100 chr5A 396415632 396418218 2586 False 1599.5 2063 90.0655 431 3067 2 chr5A.!!$F3 2636
19 TraesCS5D01G197100 chr5A 415627441 415628396 955 False 793.0 793 82.1430 2245 3197 1 chr5A.!!$F2 952
20 TraesCS5D01G197100 chr5A 390366210 390366844 634 False 501.0 501 81.1640 2552 3197 1 chr5A.!!$F1 645
21 TraesCS5D01G197100 chr3D 482005835 482006660 825 False 837.0 837 85.3370 2385 3197 1 chr3D.!!$F1 812

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
387 388 1.202533 CCAATCGCAACGATAGGAGGT 60.203 52.381 2.52 0.0 46.3 3.85 F
1424 1610 0.968901 TCCCCGTTACTGATCGTGCT 60.969 55.000 1.23 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 1999 0.179034 ATCAATGCCGAGCCTCTTCC 60.179 55.000 0.0 0.0 0.0 3.46 R
2658 3296 1.824852 TCTTTCTCGGCAGCATACTCA 59.175 47.619 0.0 0.0 0.0 3.41 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 3.326747 ACACTCGCCACAATAGTCTTTC 58.673 45.455 0.00 0.00 0.00 2.62
99 100 8.927675 TTCTGTTATGGCTCCTTTACTTTTAA 57.072 30.769 0.00 0.00 0.00 1.52
168 169 3.991773 TGTAAACAGATCAGCCAACGTAC 59.008 43.478 0.00 0.00 0.00 3.67
313 314 2.403252 AAGCTACCAGATTGGAACGG 57.597 50.000 1.40 0.00 40.96 4.44
357 358 1.446099 CCGATGGGATACGCCGATG 60.446 63.158 0.00 0.00 34.93 3.84
360 361 2.521958 GATGGGATACGCCGATGGGG 62.522 65.000 0.00 0.00 41.67 4.96
361 362 2.920912 GGGATACGCCGATGGGGA 60.921 66.667 6.92 0.00 39.07 4.81
387 388 1.202533 CCAATCGCAACGATAGGAGGT 60.203 52.381 2.52 0.00 46.30 3.85
388 389 1.860950 CAATCGCAACGATAGGAGGTG 59.139 52.381 2.52 0.00 46.30 4.00
467 501 4.439700 CGCAAGCAAATCTGATTTCCTGAT 60.440 41.667 12.50 0.00 35.32 2.90
487 528 2.549926 TGGATCACATCACATACGCAC 58.450 47.619 0.00 0.00 0.00 5.34
488 529 1.522676 GGATCACATCACATACGCACG 59.477 52.381 0.00 0.00 0.00 5.34
507 567 1.331447 CGCATGCTCGATTTGGAATCA 59.669 47.619 17.13 0.00 0.00 2.57
519 579 2.118313 TGGAATCAGCATCACACCTG 57.882 50.000 0.00 0.00 0.00 4.00
520 580 1.340308 TGGAATCAGCATCACACCTGG 60.340 52.381 0.00 0.00 0.00 4.45
971 1135 2.168106 CTCCTCCAGTTCCTGTGATCAG 59.832 54.545 0.00 0.00 41.01 2.90
973 1137 2.304180 CCTCCAGTTCCTGTGATCAGTT 59.696 50.000 0.00 0.00 39.82 3.16
991 1155 2.434359 GCAAGAAGGCGCCTACGT 60.434 61.111 33.07 15.67 42.83 3.57
1177 1341 2.490903 GTCGAGTTACAGGAGCAGGTTA 59.509 50.000 0.00 0.00 0.00 2.85
1415 1601 1.623542 GGTGGCATCTCCCCGTTACT 61.624 60.000 0.00 0.00 0.00 2.24
1424 1610 0.968901 TCCCCGTTACTGATCGTGCT 60.969 55.000 1.23 0.00 0.00 4.40
1460 1658 1.153353 GTCGAAGATGAAACCGCCAA 58.847 50.000 0.00 0.00 40.67 4.52
1538 1771 1.639298 GACACTGATTCCGGCAGCAC 61.639 60.000 7.41 0.00 36.86 4.40
1623 1856 4.720902 CCAGCACCGGCCATCACA 62.721 66.667 0.00 0.00 42.56 3.58
1852 2091 2.490115 CTCTACCTCAAGCTTGACGACT 59.510 50.000 25.16 9.07 32.90 4.18
1933 2204 0.393077 AGTCGTTGCTAGCAAGGTGT 59.607 50.000 36.01 25.99 41.08 4.16
1938 2209 4.267928 GTCGTTGCTAGCAAGGTGTTATAG 59.732 45.833 36.01 18.12 41.08 1.31
2468 3092 5.222631 GTTTTGTGCCTGAATTTCCTACTG 58.777 41.667 0.00 0.00 0.00 2.74
2520 3148 8.106462 TGACATTCTCATTCTTTATACAACCCA 58.894 33.333 0.00 0.00 0.00 4.51
2638 3276 4.276926 CAGAATCTGTTTAATAGCAGGGGC 59.723 45.833 1.31 0.00 41.61 5.80
2658 3296 5.716703 GGGGCAGCTTATAACAAATCCATAT 59.283 40.000 0.00 0.00 0.00 1.78
2843 3484 6.428385 AGTGAAAACAAGAGAGTGTTGAAG 57.572 37.500 0.00 0.00 40.86 3.02
2969 3612 9.382244 CAAAATGCACTACAAAACTTAGTAGAC 57.618 33.333 6.60 0.06 40.02 2.59
3028 3686 2.427095 GCCAGAACAACCAAGAGTGTTT 59.573 45.455 0.00 0.00 0.00 2.83
3033 3691 4.881850 AGAACAACCAAGAGTGTTTACCTG 59.118 41.667 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.489481 ACGATCTCCAGGCAATCTGA 58.511 50.000 0.00 0.00 46.18 3.27
76 77 9.974980 TTTTTAAAAGTAAAGGAGCCATAACAG 57.025 29.630 0.14 0.00 30.92 3.16
99 100 5.814481 AGAGGAAGCTAGCTCTTCAATTTT 58.186 37.500 19.65 0.00 43.14 1.82
106 107 5.497464 AGAAAAAGAGGAAGCTAGCTCTT 57.503 39.130 19.65 14.17 37.72 2.85
357 358 4.833811 GCGATTGGCATTTTCCCC 57.166 55.556 0.00 0.00 42.87 4.81
387 388 2.042842 TGAGGCCATCATTTCTTTCCCA 59.957 45.455 5.01 0.00 31.12 4.37
388 389 2.738743 TGAGGCCATCATTTCTTTCCC 58.261 47.619 5.01 0.00 31.12 3.97
467 501 2.549926 GTGCGTATGTGATGTGATCCA 58.450 47.619 0.00 0.00 0.00 3.41
487 528 1.331447 TGATTCCAAATCGAGCATGCG 59.669 47.619 13.01 0.00 0.00 4.73
488 529 2.857489 GCTGATTCCAAATCGAGCATGC 60.857 50.000 10.51 10.51 0.00 4.06
507 567 2.194388 CTCAGGCCAGGTGTGATGCT 62.194 60.000 5.01 0.00 0.00 3.79
519 579 3.317430 CCTTTTATTGATCAGCTCAGGCC 59.683 47.826 0.00 0.00 39.73 5.19
520 580 3.243334 GCCTTTTATTGATCAGCTCAGGC 60.243 47.826 15.28 15.28 34.68 4.85
687 848 1.827399 GCTTCCTCGTGAACTCCCCA 61.827 60.000 0.00 0.00 0.00 4.96
971 1135 1.502190 GTAGGCGCCTTCTTGCAAC 59.498 57.895 37.74 21.34 0.00 4.17
973 1137 1.879737 TACGTAGGCGCCTTCTTGCA 61.880 55.000 37.74 13.33 42.83 4.08
991 1155 2.690497 CAGAGGCCGTCATCTTCTTCTA 59.310 50.000 0.00 0.00 0.00 2.10
1177 1341 2.293677 TCTTCTCTCGAGCGAACTTGTT 59.706 45.455 13.66 0.00 0.00 2.83
1402 1588 1.681793 CACGATCAGTAACGGGGAGAT 59.318 52.381 0.00 0.00 0.00 2.75
1538 1771 0.389166 GTGCTCTGAACCTGAGTCGG 60.389 60.000 0.00 0.00 33.06 4.79
1600 1833 4.643387 GGCCGGTGCTGGACTGTT 62.643 66.667 1.90 0.00 37.74 3.16
1623 1856 0.607489 GCTGCTCACATGTTGGAGGT 60.607 55.000 13.43 0.00 0.00 3.85
1766 1999 0.179034 ATCAATGCCGAGCCTCTTCC 60.179 55.000 0.00 0.00 0.00 3.46
1852 2091 1.671850 GCGTTGCTGCTTCCAGTAGTA 60.672 52.381 0.00 0.00 41.26 1.82
2342 2816 4.234550 AGGTGATGCTATCATTCAGGGTA 58.765 43.478 2.80 0.00 42.04 3.69
2520 3148 2.225091 TGGGAATGAGAATGGTGCAAGT 60.225 45.455 0.00 0.00 0.00 3.16
2658 3296 1.824852 TCTTTCTCGGCAGCATACTCA 59.175 47.619 0.00 0.00 0.00 3.41
2843 3484 7.432869 TCTACAGAACCTCGTACTACTATCTC 58.567 42.308 0.00 0.00 0.00 2.75
2969 3612 7.792374 TTACCTGATTAGAAAGCAGCATTAG 57.208 36.000 0.00 0.00 43.32 1.73
3028 3686 3.039011 GGATCCTAAGAAGCACCAGGTA 58.961 50.000 3.84 0.00 0.00 3.08
3033 3691 3.914426 TTCTGGATCCTAAGAAGCACC 57.086 47.619 14.23 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.