Multiple sequence alignment - TraesCS2D01G322400

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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 TraesCS2D01G322400 chr2D 100.000 3077 0 0 1 3077 413778226 413775150 0.000000e+00 5683.0
1 TraesCS2D01G322400 chr2D 80.095 211 38 3 1 209 612438385 612438177 1.480000e-33 154.0
2 TraesCS2D01G322400 chr2A 91.855 2787 119 34 1 2726 580852998 580850259 0.000000e+00 3790.0
3 TraesCS2D01G322400 chr2A 85.385 390 22 10 2712 3077 580850226 580849848 3.750000e-99 372.0
4 TraesCS2D01G322400 chr2A 80.569 211 37 3 1 209 744529610 744529402 3.180000e-35 159.0
5 TraesCS2D01G322400 chr2B 93.350 1609 49 24 1 1577 486986383 486984801 0.000000e+00 2326.0
6 TraesCS2D01G322400 chr2B 92.380 1168 58 17 1579 2726 486984582 486983426 0.000000e+00 1635.0
7 TraesCS2D01G322400 chr2B 88.953 172 8 4 2753 2924 486983174 486983014 5.200000e-48 202.0
8 TraesCS2D01G322400 chr2B 93.750 80 5 0 2938 3017 486977635 486977556 1.500000e-23 121.0
9 TraesCS2D01G322400 chr2B 89.796 49 5 0 2714 2762 486983403 486983355 2.560000e-06 63.9
10 TraesCS2D01G322400 chr5D 90.476 84 6 2 9 91 332450216 332450298 3.240000e-20 110.0
11 TraesCS2D01G322400 chr5B 90.476 84 6 2 9 91 388407745 388407827 3.240000e-20 110.0
12 TraesCS2D01G322400 chr5A 90.361 83 8 0 9 91 433312029 433312111 3.240000e-20 110.0


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 TraesCS2D01G322400 chr2D 413775150 413778226 3076 True 5683.000 5683 100.00000 1 3077 1 chr2D.!!$R1 3076
1 TraesCS2D01G322400 chr2A 580849848 580852998 3150 True 2081.000 3790 88.62000 1 3077 2 chr2A.!!$R2 3076
2 TraesCS2D01G322400 chr2B 486983014 486986383 3369 True 1056.725 2326 91.11975 1 2924 4 chr2B.!!$R2 2923

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
587 598 0.887836 TACGTGACAGCACCGAGACT 60.888 55.000 0.00 0.0 42.09 3.24 F
1831 2108 1.067212 CACCGAGGTAGTAGCATCACC 59.933 57.143 1.58 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2249 0.178944 TGTCCTTCTTCTCCGGTCCA 60.179 55.0 0.00 0.0 0.00 4.02 R
2877 3408 0.385974 CCAAGAACCGAAAGCGCAAG 60.386 55.0 11.47 0.0 35.83 4.01 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
231 232 2.910977 ACCTCGGGTTCAAGGTCTAAAT 59.089 45.455 0.00 0.00 42.28 1.40
260 261 4.639824 CATATGCATGCAACGCCC 57.360 55.556 26.68 0.00 0.00 6.13
330 331 2.068519 GAACGTGTGATGACTGATGCA 58.931 47.619 0.00 0.00 0.00 3.96
554 565 9.219603 CACATCTCAACTTCTTATTTTGGACTA 57.780 33.333 0.00 0.00 0.00 2.59
587 598 0.887836 TACGTGACAGCACCGAGACT 60.888 55.000 0.00 0.00 42.09 3.24
588 599 1.730902 CGTGACAGCACCGAGACTG 60.731 63.158 0.00 0.00 42.09 3.51
589 600 1.660355 GTGACAGCACCGAGACTGA 59.340 57.895 5.68 0.00 39.14 3.41
634 648 3.184379 CCAATAATCTCCACGTACGCATG 59.816 47.826 16.72 7.07 0.00 4.06
857 877 3.852536 GTCACTTCTCACTATGCACGTAC 59.147 47.826 0.00 0.00 0.00 3.67
881 901 1.913762 CCTCCCCACCGTCTCACTT 60.914 63.158 0.00 0.00 0.00 3.16
990 1010 2.106511 TCTCCCAAACTTCCCAAGTGAG 59.893 50.000 0.00 0.00 41.91 3.51
1150 1176 7.281774 ACATGAACCTATGCTCAATTTCAGTAG 59.718 37.037 0.00 0.00 0.00 2.57
1162 1188 8.713271 GCTCAATTTCAGTAGCCACTTATATAC 58.287 37.037 0.00 0.00 30.46 1.47
1223 1249 2.724358 CGGTTTCGCGCGCTTTTT 60.724 55.556 30.48 0.00 0.00 1.94
1322 1350 5.703130 GCCATAGGAAATCTGATGGTTACTC 59.297 44.000 12.58 0.00 40.88 2.59
1393 1440 1.496060 TGGATCCCTTGCTCGTATGT 58.504 50.000 9.90 0.00 0.00 2.29
1403 1450 6.437477 TCCCTTGCTCGTATGTTCATAGATAT 59.563 38.462 0.00 0.00 0.00 1.63
1690 1964 2.143122 CGCCGCACCTGTATGAATTAT 58.857 47.619 0.00 0.00 0.00 1.28
1704 1978 4.313277 TGAATTATCTCAGCGGTCTCAG 57.687 45.455 0.00 0.00 0.00 3.35
1831 2108 1.067212 CACCGAGGTAGTAGCATCACC 59.933 57.143 1.58 0.00 0.00 4.02
1930 2208 9.113876 GTTCACAAATTAAGTTCGGAAAGTATG 57.886 33.333 0.00 0.00 0.00 2.39
1971 2249 0.536460 AAGTTGACGGTCCGCCATTT 60.536 50.000 12.28 1.48 34.09 2.32
1993 2271 1.619332 GACCGGAGAAGAAGGACAAGT 59.381 52.381 9.46 0.00 0.00 3.16
2080 2358 1.900351 CCATCAGGGAAGTGAGCGA 59.100 57.895 0.00 0.00 40.01 4.93
2194 2472 1.136872 TCGCGTGTTTGTTTGCTTGC 61.137 50.000 5.77 0.00 0.00 4.01
2233 2515 1.425694 GGACCTGTATTCCTCCTCCC 58.574 60.000 0.00 0.00 0.00 4.30
2250 2532 0.810031 CCCGTGATGATCCACCGAAC 60.810 60.000 0.00 0.00 33.67 3.95
2273 2555 6.119144 CGAACCATCCATTTCGTTTAATCT 57.881 37.500 0.00 0.00 39.79 2.40
2278 2561 6.210584 ACCATCCATTTCGTTTAATCTTTGGT 59.789 34.615 0.00 0.00 0.00 3.67
2351 2634 4.690719 TCCGATGTTGGCGCGGTT 62.691 61.111 8.83 0.00 45.02 4.44
2369 2652 4.556233 CGGTTCTATTCATCGAATGCCTA 58.444 43.478 0.00 0.00 33.95 3.93
2370 2653 4.623167 CGGTTCTATTCATCGAATGCCTAG 59.377 45.833 0.00 0.00 33.95 3.02
2426 2709 2.818130 TTCACATTTGGAAGCCTTGC 57.182 45.000 0.00 0.00 0.00 4.01
2469 2757 3.330267 CCACACTCTCTAGCAAAGAACC 58.670 50.000 0.00 0.00 32.46 3.62
2535 2823 2.417924 CGCAGCACCATCTCCTATATCC 60.418 54.545 0.00 0.00 0.00 2.59
2591 2885 4.554723 GCGTGTTCTTGCTTAAGTTCATGT 60.555 41.667 4.02 0.00 0.00 3.21
2595 2889 7.642194 CGTGTTCTTGCTTAAGTTCATGTTTAA 59.358 33.333 4.02 0.00 0.00 1.52
2614 2908 1.817520 CAACGTGCACTGGTGACCA 60.818 57.895 18.02 3.40 0.00 4.02
2731 3072 3.531538 CAACCGATGTTGTAGCTATGGT 58.468 45.455 0.00 0.00 45.51 3.55
2902 3433 0.519077 CTTTCGGTTCTTGGCTGCTC 59.481 55.000 0.00 0.00 0.00 4.26
2910 3441 2.435762 TTGGCTGCTCGCGCATAA 60.436 55.556 8.75 0.00 46.74 1.90
2922 3453 2.354305 GCATAATGCCTGCGCTGC 60.354 61.111 9.73 12.54 37.42 5.25
2923 3454 2.842256 GCATAATGCCTGCGCTGCT 61.842 57.895 20.27 6.73 37.42 4.24
2925 3456 1.153107 ATAATGCCTGCGCTGCTCA 60.153 52.632 20.27 14.69 35.36 4.26
2926 3457 1.442526 ATAATGCCTGCGCTGCTCAC 61.443 55.000 20.27 6.09 35.36 3.51
2935 3487 2.507992 GCTGCTCACTCGTCGCAT 60.508 61.111 0.00 0.00 32.62 4.73
2999 3551 5.410067 TCCTCAAAGTCAACTTTTTGCTTG 58.590 37.500 5.41 0.00 43.07 4.01
3000 3552 5.184864 TCCTCAAAGTCAACTTTTTGCTTGA 59.815 36.000 5.41 0.00 43.07 3.02
3012 3564 1.484038 TTGCTTGAACAAGTTGGGCT 58.516 45.000 14.62 0.00 40.45 5.19
3018 3573 1.305201 GAACAAGTTGGGCTCGTTGA 58.695 50.000 7.96 0.00 0.00 3.18
3050 3605 4.659172 CCAGCCAGCCCCGTTTGA 62.659 66.667 0.00 0.00 0.00 2.69
3068 3623 5.121768 CGTTTGAAAAGAAGATACCCGATGT 59.878 40.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 261 0.105593 ATCTCATGTACAGGGCGCAG 59.894 55.000 10.83 0.00 0.00 5.18
264 265 1.961394 TCGGTATCTCATGTACAGGGC 59.039 52.381 7.81 0.00 0.00 5.19
330 331 3.624861 CGAAGGTTTAGCTGATCTTGCAT 59.375 43.478 12.40 2.72 0.00 3.96
587 598 0.828762 TTCGGTCGGTCCCTTCTTCA 60.829 55.000 0.00 0.00 0.00 3.02
588 599 0.389556 GTTCGGTCGGTCCCTTCTTC 60.390 60.000 0.00 0.00 0.00 2.87
589 600 1.670015 GTTCGGTCGGTCCCTTCTT 59.330 57.895 0.00 0.00 0.00 2.52
634 648 0.879090 CCCGGGTTAAACACAAGCTC 59.121 55.000 14.18 0.00 0.00 4.09
765 785 3.071874 TGCAGTTTGTAATCTCCCTGG 57.928 47.619 0.00 0.00 0.00 4.45
944 964 2.261729 GGAAAGGGGATAGCTAGGGAG 58.738 57.143 0.00 0.00 0.00 4.30
1005 1025 1.786937 ACTCCTGCCTCTTGATCGAT 58.213 50.000 0.00 0.00 0.00 3.59
1150 1176 6.128902 CGATTCAAGAACCGTATATAAGTGGC 60.129 42.308 0.00 0.00 0.00 5.01
1162 1188 1.340465 CGACGCGATTCAAGAACCG 59.660 57.895 15.93 0.00 0.00 4.44
1250 1276 9.577110 CTACAATCATAACACAAAAATGCAGAT 57.423 29.630 0.00 0.00 0.00 2.90
1268 1294 8.712228 ACTGTATGGATCTATGACTACAATCA 57.288 34.615 1.10 0.00 0.00 2.57
1292 1318 5.936956 CCATCAGATTTCCTATGGCTAGAAC 59.063 44.000 0.00 0.00 33.02 3.01
1335 1363 3.640967 ACCAACTGCAATCTGCCTAAAAA 59.359 39.130 0.00 0.00 44.23 1.94
1336 1364 3.230134 ACCAACTGCAATCTGCCTAAAA 58.770 40.909 0.00 0.00 44.23 1.52
1337 1365 2.875296 ACCAACTGCAATCTGCCTAAA 58.125 42.857 0.00 0.00 44.23 1.85
1338 1366 2.584835 ACCAACTGCAATCTGCCTAA 57.415 45.000 0.00 0.00 44.23 2.69
1339 1367 2.584835 AACCAACTGCAATCTGCCTA 57.415 45.000 0.00 0.00 44.23 3.93
1349 1377 3.507233 TCTGAATCCATGAAACCAACTGC 59.493 43.478 0.00 0.00 0.00 4.40
1403 1450 6.017440 GTGCTAGACTGGATAACACAAACAAA 60.017 38.462 0.00 0.00 0.00 2.83
1577 1849 8.797350 TTTTGCATCTACTCCATATATGATGG 57.203 34.615 14.54 0.00 40.48 3.51
1690 1964 0.603569 GGAAACTGAGACCGCTGAGA 59.396 55.000 0.00 0.00 0.00 3.27
1831 2108 7.387673 GGAATCAAAGGTAAAACAATCAAAGGG 59.612 37.037 0.00 0.00 0.00 3.95
1930 2208 7.392418 ACTTTGTAATAGGAACCCTAGAACAC 58.608 38.462 8.75 1.68 39.70 3.32
1971 2249 0.178944 TGTCCTTCTTCTCCGGTCCA 60.179 55.000 0.00 0.00 0.00 4.02
1993 2271 4.308458 CGTTGCAGTGGTCGGGGA 62.308 66.667 0.00 0.00 0.00 4.81
2080 2358 2.733301 CCGGATCGCTCATGCTCT 59.267 61.111 0.00 0.00 36.97 4.09
2091 2369 1.432270 CTTCTTGAAGCGGCCGGATC 61.432 60.000 29.38 10.66 0.00 3.36
2194 2472 5.420409 GTCCCTCTTAGGTTCACATACAAG 58.580 45.833 0.00 0.00 31.93 3.16
2233 2515 0.179148 TCGTTCGGTGGATCATCACG 60.179 55.000 0.00 0.00 38.46 4.35
2272 2554 5.397240 GGAACGAACGAAATAAACACCAAAG 59.603 40.000 0.14 0.00 0.00 2.77
2273 2555 5.163683 TGGAACGAACGAAATAAACACCAAA 60.164 36.000 0.14 0.00 0.00 3.28
2278 2561 4.912766 GCATTGGAACGAACGAAATAAACA 59.087 37.500 0.14 0.00 0.00 2.83
2287 2570 0.450482 GACACGCATTGGAACGAACG 60.450 55.000 0.00 0.00 0.00 3.95
2351 2634 9.809096 GAAATATCTAGGCATTCGATGAATAGA 57.191 33.333 0.00 0.00 35.07 1.98
2426 2709 6.091713 GTGGCTTGAAGATTGGATTTTTCATG 59.908 38.462 0.00 0.00 30.45 3.07
2469 2757 4.206843 GCGAAATGCTATCGTGATTTCTG 58.793 43.478 0.00 0.00 42.15 3.02
2498 2786 2.350772 GCTGCGTTTTCAGTTATGTGCT 60.351 45.455 0.00 0.00 36.49 4.40
2553 2847 2.186826 ACGCAAGAGGGTTGTGTGC 61.187 57.895 3.26 0.00 41.07 4.57
2591 2885 2.096174 GTCACCAGTGCACGTTGTTAAA 59.904 45.455 12.01 0.00 0.00 1.52
2595 2889 1.817941 GGTCACCAGTGCACGTTGT 60.818 57.895 12.01 7.17 0.00 3.32
2726 3020 1.876263 CATGACGCGCGACACCATA 60.876 57.895 39.36 14.74 0.00 2.74
2791 3322 4.409218 GACGACCCGCTACGTGCA 62.409 66.667 0.00 0.00 42.74 4.57
2807 3338 2.432456 GCGCATCAGGTGACACGA 60.432 61.111 0.30 0.00 0.00 4.35
2874 3405 2.978018 GAACCGAAAGCGCAAGGGG 61.978 63.158 11.47 8.21 35.83 4.79
2877 3408 0.385974 CCAAGAACCGAAAGCGCAAG 60.386 55.000 11.47 0.00 35.83 4.01
2910 3441 4.405671 AGTGAGCAGCGCAGGCAT 62.406 61.111 23.22 10.42 43.41 4.40
2920 3451 1.801512 CGAATGCGACGAGTGAGCA 60.802 57.895 0.00 5.66 45.46 4.26
2921 3452 2.508891 CCGAATGCGACGAGTGAGC 61.509 63.158 0.00 0.00 40.82 4.26
2922 3453 1.154016 ACCGAATGCGACGAGTGAG 60.154 57.895 0.00 0.00 40.82 3.51
2923 3454 1.443702 CACCGAATGCGACGAGTGA 60.444 57.895 0.00 0.00 40.82 3.41
2925 3456 2.809601 GCACCGAATGCGACGAGT 60.810 61.111 0.00 0.00 46.55 4.18
2969 3521 9.740134 CAAAAAGTTGACTTTGAGGATCACGCT 62.740 40.741 9.67 0.00 44.69 5.07
2982 3534 6.223120 ACTTGTTCAAGCAAAAAGTTGACTT 58.777 32.000 11.79 0.00 36.83 3.01
3012 3564 1.006086 CCGTATGCTGCAATCAACGA 58.994 50.000 22.79 0.00 32.35 3.85
3018 3573 1.825191 CTGGCCCGTATGCTGCAAT 60.825 57.895 6.36 0.00 0.00 3.56
3050 3605 4.384208 CCAGGACATCGGGTATCTTCTTTT 60.384 45.833 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.