Multiple sequence alignment - TraesCS3B01G171300

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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 TraesCS3B01G171300 chr3B 100.000 4367 0 0 1 4367 172091447 172095813 0.000000e+00 8065.0
1 TraesCS3B01G171300 chr3B 97.261 3687 85 3 682 4367 172211586 172215257 0.000000e+00 6235.0
2 TraesCS3B01G171300 chr3B 90.379 2848 232 33 846 3672 146982530 146979704 0.000000e+00 3703.0
3 TraesCS3B01G171300 chr3B 89.725 2910 242 41 782 3672 172981949 172979078 0.000000e+00 3664.0
4 TraesCS3B01G171300 chr3B 93.114 2498 159 9 945 3438 172170554 172173042 0.000000e+00 3648.0
5 TraesCS3B01G171300 chr3B 91.915 2622 180 25 841 3438 172052070 172054683 0.000000e+00 3639.0
6 TraesCS3B01G171300 chr3B 98.732 631 7 1 1 631 172210961 172211590 0.000000e+00 1120.0
7 TraesCS3B01G171300 chr3B 97.952 537 11 0 3831 4367 172104859 172105395 0.000000e+00 931.0
8 TraesCS3B01G171300 chr3B 97.393 537 14 0 3831 4367 172224330 172224866 0.000000e+00 915.0
9 TraesCS3B01G171300 chr3B 92.073 492 25 3 183 667 172982451 172981967 0.000000e+00 680.0
10 TraesCS3B01G171300 chr3B 87.461 319 30 5 136 454 146983247 146982939 4.150000e-95 359.0
11 TraesCS3B01G171300 chr3B 84.249 273 23 9 3487 3754 172054697 172054954 9.380000e-62 248.0
12 TraesCS3B01G171300 chr3B 84.249 273 23 9 3487 3754 172173056 172173313 9.380000e-62 248.0
13 TraesCS3B01G171300 chr3B 94.000 100 3 2 33 129 146983456 146983357 9.790000e-32 148.0
14 TraesCS3B01G171300 chr3B 76.736 288 19 15 604 846 146982867 146982583 2.760000e-22 117.0
15 TraesCS3B01G171300 chr3D 93.262 2612 153 17 996 3597 120142574 120145172 0.000000e+00 3827.0
16 TraesCS3B01G171300 chr3D 91.436 2604 198 14 849 3433 121268889 121266292 0.000000e+00 3550.0
17 TraesCS3B01G171300 chr3D 89.308 1777 169 16 2070 3835 120132745 120134511 0.000000e+00 2209.0
18 TraesCS3B01G171300 chr3D 88.315 736 51 17 136 846 121269665 121268940 0.000000e+00 850.0
19 TraesCS3B01G171300 chr3D 87.562 201 17 3 141 334 116075101 116074902 4.390000e-55 226.0
20 TraesCS3B01G171300 chr3D 89.209 139 5 4 717 846 121335035 121334898 9.720000e-37 165.0
21 TraesCS3B01G171300 chr3D 92.079 101 5 1 32 129 121269883 121269783 5.890000e-29 139.0
22 TraesCS3B01G171300 chr1B 89.230 3092 246 48 383 3433 456714778 456711733 0.000000e+00 3784.0
23 TraesCS3B01G171300 chr1B 92.214 2453 183 6 945 3392 642701434 642698985 0.000000e+00 3465.0
24 TraesCS3B01G171300 chr1B 97.393 537 14 0 3831 4367 683366339 683366875 0.000000e+00 915.0
25 TraesCS3B01G171300 chr1B 96.852 540 17 0 3828 4367 683361241 683361780 0.000000e+00 904.0
26 TraesCS3B01G171300 chr1B 83.761 117 11 4 17 127 456726014 456725900 2.150000e-18 104.0
27 TraesCS3B01G171300 chr1D 91.755 2729 198 16 717 3433 341030159 341027446 0.000000e+00 3768.0
28 TraesCS3B01G171300 chr1D 91.935 2480 191 7 945 3419 465903095 465900620 0.000000e+00 3463.0
29 TraesCS3B01G171300 chr1D 78.378 296 23 21 405 700 341030472 341030218 2.100000e-33 154.0
30 TraesCS3B01G171300 chr5B 90.170 2584 208 15 987 3560 507802947 507800400 0.000000e+00 3323.0
31 TraesCS3B01G171300 chr5B 97.032 539 16 0 3829 4367 579143891 579144429 0.000000e+00 907.0
32 TraesCS3B01G171300 chr1A 88.835 1227 99 19 717 1916 440780750 440779535 0.000000e+00 1472.0
33 TraesCS3B01G171300 chr1A 86.479 355 31 9 136 484 440781266 440780923 1.480000e-99 374.0
34 TraesCS3B01G171300 chr1A 89.091 110 5 2 591 700 440780911 440780809 3.540000e-26 130.0
35 TraesCS3B01G171300 chr1A 85.345 116 13 2 17 129 440781489 440781375 2.760000e-22 117.0
36 TraesCS3B01G171300 chr7D 97.026 538 15 1 3831 4367 599725132 599724595 0.000000e+00 904.0
37 TraesCS3B01G171300 chr2B 96.660 539 15 2 3831 4367 13147338 13146801 0.000000e+00 893.0
38 TraesCS3B01G171300 chr2B 96.648 537 14 2 3831 4367 91615240 91615772 0.000000e+00 889.0
39 TraesCS3B01G171300 chr3A 90.909 132 12 0 136 267 127835096 127834965 1.250000e-40 178.0
40 TraesCS3B01G171300 chr3A 91.304 92 7 1 755 846 127834905 127834815 1.650000e-24 124.0
41 TraesCS3B01G171300 chr6D 77.005 187 16 6 3638 3824 452125241 452125082 1.010000e-11 82.4


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 TraesCS3B01G171300 chr3B 172091447 172095813 4366 False 8065.00 8065 100.0000 1 4367 1 chr3B.!!$F1 4366
1 TraesCS3B01G171300 chr3B 172210961 172215257 4296 False 3677.50 6235 97.9965 1 4367 2 chr3B.!!$F6 4366
2 TraesCS3B01G171300 chr3B 172979078 172982451 3373 True 2172.00 3664 90.8990 183 3672 2 chr3B.!!$R2 3489
3 TraesCS3B01G171300 chr3B 172170554 172173313 2759 False 1948.00 3648 88.6815 945 3754 2 chr3B.!!$F5 2809
4 TraesCS3B01G171300 chr3B 172052070 172054954 2884 False 1943.50 3639 88.0820 841 3754 2 chr3B.!!$F4 2913
5 TraesCS3B01G171300 chr3B 146979704 146983456 3752 True 1081.75 3703 87.1440 33 3672 4 chr3B.!!$R1 3639
6 TraesCS3B01G171300 chr3B 172104859 172105395 536 False 931.00 931 97.9520 3831 4367 1 chr3B.!!$F2 536
7 TraesCS3B01G171300 chr3B 172224330 172224866 536 False 915.00 915 97.3930 3831 4367 1 chr3B.!!$F3 536
8 TraesCS3B01G171300 chr3D 120142574 120145172 2598 False 3827.00 3827 93.2620 996 3597 1 chr3D.!!$F2 2601
9 TraesCS3B01G171300 chr3D 120132745 120134511 1766 False 2209.00 2209 89.3080 2070 3835 1 chr3D.!!$F1 1765
10 TraesCS3B01G171300 chr3D 121266292 121269883 3591 True 1513.00 3550 90.6100 32 3433 3 chr3D.!!$R3 3401
11 TraesCS3B01G171300 chr1B 456711733 456714778 3045 True 3784.00 3784 89.2300 383 3433 1 chr1B.!!$R1 3050
12 TraesCS3B01G171300 chr1B 642698985 642701434 2449 True 3465.00 3465 92.2140 945 3392 1 chr1B.!!$R3 2447
13 TraesCS3B01G171300 chr1B 683366339 683366875 536 False 915.00 915 97.3930 3831 4367 1 chr1B.!!$F2 536
14 TraesCS3B01G171300 chr1B 683361241 683361780 539 False 904.00 904 96.8520 3828 4367 1 chr1B.!!$F1 539
15 TraesCS3B01G171300 chr1D 465900620 465903095 2475 True 3463.00 3463 91.9350 945 3419 1 chr1D.!!$R1 2474
16 TraesCS3B01G171300 chr1D 341027446 341030472 3026 True 1961.00 3768 85.0665 405 3433 2 chr1D.!!$R2 3028
17 TraesCS3B01G171300 chr5B 507800400 507802947 2547 True 3323.00 3323 90.1700 987 3560 1 chr5B.!!$R1 2573
18 TraesCS3B01G171300 chr5B 579143891 579144429 538 False 907.00 907 97.0320 3829 4367 1 chr5B.!!$F1 538
19 TraesCS3B01G171300 chr1A 440779535 440781489 1954 True 523.25 1472 87.4375 17 1916 4 chr1A.!!$R1 1899
20 TraesCS3B01G171300 chr7D 599724595 599725132 537 True 904.00 904 97.0260 3831 4367 1 chr7D.!!$R1 536
21 TraesCS3B01G171300 chr2B 13146801 13147338 537 True 893.00 893 96.6600 3831 4367 1 chr2B.!!$R1 536
22 TraesCS3B01G171300 chr2B 91615240 91615772 532 False 889.00 889 96.6480 3831 4367 1 chr2B.!!$F1 536

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
875 1142 2.564062 TCCAACCCGAGTCGTATTCTTT 59.436 45.455 12.31 0.00 0.00 2.52 F
1570 1883 0.532573 GGAGAGGCTTGACGTCATCA 59.467 55.000 20.80 4.16 35.56 3.07 F
2144 2457 0.036010 AACATGAAGCTGGACGAGGG 60.036 55.000 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 2130 0.402121 GAAGGCCTTCCTCAGGTTGT 59.598 55.000 31.91 0.0 46.07 3.32 R
2433 2747 0.531200 GGTACTGGACGGTCTCTTGG 59.469 60.000 8.23 0.0 0.00 3.61 R
3575 3979 3.120130 AGCTAGTTTTCAGAGTCTCGTCG 60.120 47.826 0.00 0.0 0.00 5.12 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
627 760 6.100424 AGAGGGAGAAGAAAAGAAGAAACTCA 59.900 38.462 0.00 0.00 0.00 3.41
628 761 6.295249 AGGGAGAAGAAAAGAAGAAACTCAG 58.705 40.000 0.00 0.00 0.00 3.35
629 762 5.471797 GGGAGAAGAAAAGAAGAAACTCAGG 59.528 44.000 0.00 0.00 0.00 3.86
630 763 6.058833 GGAGAAGAAAAGAAGAAACTCAGGT 58.941 40.000 0.00 0.00 0.00 4.00
631 764 6.203915 GGAGAAGAAAAGAAGAAACTCAGGTC 59.796 42.308 0.00 0.00 0.00 3.85
632 765 5.755861 AGAAGAAAAGAAGAAACTCAGGTCG 59.244 40.000 0.00 0.00 0.00 4.79
633 766 4.381411 AGAAAAGAAGAAACTCAGGTCGG 58.619 43.478 0.00 0.00 0.00 4.79
875 1142 2.564062 TCCAACCCGAGTCGTATTCTTT 59.436 45.455 12.31 0.00 0.00 2.52
882 1149 3.243771 CCGAGTCGTATTCTTTAGGCCAT 60.244 47.826 12.31 0.00 0.00 4.40
970 1273 2.751166 ATACACGAGAGCAGCAACTT 57.249 45.000 0.00 0.00 0.00 2.66
1098 1402 1.198094 TCTGCAATCTCCACCCCGAA 61.198 55.000 0.00 0.00 0.00 4.30
1172 1476 2.340809 CCGCCACAACACGGTCTA 59.659 61.111 0.00 0.00 44.46 2.59
1278 1589 2.646719 GTCGTGTCCGTGCACCTA 59.353 61.111 12.15 0.00 36.08 3.08
1320 1632 4.457496 CGCGTGCACATCCTCCCT 62.457 66.667 18.64 0.00 0.00 4.20
1389 1702 3.037549 CCTCAAGCTCTACTTCCTGGAT 58.962 50.000 0.00 0.00 36.04 3.41
1428 1741 2.490685 GGCGACCTCTTCCTCGTC 59.509 66.667 0.00 0.00 32.30 4.20
1570 1883 0.532573 GGAGAGGCTTGACGTCATCA 59.467 55.000 20.80 4.16 35.56 3.07
1817 2130 3.141488 GGCCGGAGAGAGCGAGAA 61.141 66.667 5.05 0.00 0.00 2.87
1906 2219 4.812476 CCATCGCGCCGAACAGGA 62.812 66.667 0.00 0.00 45.00 3.86
1951 2264 1.103803 GTGTATCGTCTCCCAGCTGA 58.896 55.000 17.39 0.00 0.00 4.26
2144 2457 0.036010 AACATGAAGCTGGACGAGGG 60.036 55.000 0.00 0.00 0.00 4.30
2393 2707 2.167398 GAGGTGCCCAACGTCAGCTA 62.167 60.000 6.66 0.00 42.17 3.32
2397 2711 0.613260 TGCCCAACGTCAGCTAGAAT 59.387 50.000 0.00 0.00 0.00 2.40
2433 2747 2.185608 GGCGTCAAGAGGGAGCTC 59.814 66.667 4.71 4.71 0.00 4.09
2677 2991 2.954684 AAGGCCCGTCAATCTGCGA 61.955 57.895 0.00 0.00 0.00 5.10
2859 3173 1.837439 AGGCCCGACATAATTGACTCA 59.163 47.619 0.00 0.00 0.00 3.41
3004 3318 2.594303 CGCTGGCAAGGTTCACCA 60.594 61.111 0.00 0.00 38.89 4.17
3162 3483 1.210478 GAGGTGGCTCAGATTAAGGCA 59.790 52.381 0.00 0.00 45.89 4.75
3190 3511 5.746245 CACTTCGAGGAGTCAATGAAGTATC 59.254 44.000 17.44 0.00 45.35 2.24
3393 3715 9.137459 TCCAGTAACCATTGTTAGAAAATGAAA 57.863 29.630 0.00 0.00 37.62 2.69
3575 3979 7.415318 GGTGCTTTCCTTTTATTTCTAGGTAGC 60.415 40.741 0.00 0.00 37.82 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
411 538 4.289410 TCCTTCATGTTCTCTCCCAATTCA 59.711 41.667 0.00 0.00 0.00 2.57
685 826 1.870941 TACGGGGAAGAGCTCTCCCA 61.871 60.000 33.79 21.01 42.62 4.37
970 1273 2.074576 CTCTCGTAGTCTCGTTGGTCA 58.925 52.381 0.00 0.00 0.00 4.02
1817 2130 0.402121 GAAGGCCTTCCTCAGGTTGT 59.598 55.000 31.91 0.00 46.07 3.32
1906 2219 1.179814 ACCTCGCCGTGAGTCTTCTT 61.180 55.000 8.14 0.00 43.64 2.52
1951 2264 2.202932 GCCGTCCATGAGCGTCAT 60.203 61.111 0.00 0.00 37.65 3.06
2093 2406 2.876645 GGAGCACTTCGAGACGCG 60.877 66.667 3.53 3.53 42.69 6.01
2144 2457 2.030946 GCAATCACCTCTATGTTGACGC 59.969 50.000 0.00 0.00 0.00 5.19
2361 2675 0.596083 GCACCTCGATGATGGTCTCG 60.596 60.000 0.00 0.00 33.75 4.04
2393 2707 0.674895 GAGGCTGCCAACGTCATTCT 60.675 55.000 22.65 0.00 0.00 2.40
2397 2711 3.573772 CTCGAGGCTGCCAACGTCA 62.574 63.158 27.34 14.99 0.00 4.35
2433 2747 0.531200 GGTACTGGACGGTCTCTTGG 59.469 60.000 8.23 0.00 0.00 3.61
2677 2991 2.585869 CGAAGAACAGCACGCACGT 61.586 57.895 0.00 0.00 0.00 4.49
2887 3201 2.634940 GCAAGGGGATGTAGATGAGCTA 59.365 50.000 0.00 0.00 0.00 3.32
2922 3236 1.066858 GCCTTGAAGATCTGGTGACGA 60.067 52.381 0.00 0.00 0.00 4.20
3162 3483 3.574396 TCATTGACTCCTCGAAGTGAACT 59.426 43.478 0.00 0.00 0.00 3.01
3190 3511 4.200283 GCTCACGCTCCTCCTCGG 62.200 72.222 0.00 0.00 0.00 4.63
3281 3602 4.373116 GTGTCTGCGCCGGGAAGA 62.373 66.667 4.18 0.00 0.00 2.87
3575 3979 3.120130 AGCTAGTTTTCAGAGTCTCGTCG 60.120 47.826 0.00 0.00 0.00 5.12
4264 4678 5.186198 ACTACTTTGTTCTGAAACTGCAGT 58.814 37.500 15.25 15.25 37.20 4.40


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

AutoCloner maintained by Alex Coulton.