Multiple sequence alignment - TraesCS2B01G589200

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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 TraesCS2B01G589200 chr2B 100.000 6041 0 0 1 6041 775596236 775602276 0.000000e+00 11156.0
1 TraesCS2B01G589200 chr2B 74.649 1566 214 82 657 2102 655630891 655632393 1.930000e-144 523.0
2 TraesCS2B01G589200 chr2B 90.071 141 14 0 5894 6034 655633383 655633523 3.720000e-42 183.0
3 TraesCS2B01G589200 chr2B 85.106 141 16 4 2563 2699 175537425 175537286 8.160000e-29 139.0
4 TraesCS2B01G589200 chr5B 98.384 5385 65 7 647 6030 707890833 707896196 0.000000e+00 9443.0
5 TraesCS2B01G589200 chr5B 91.003 778 61 8 4895 5668 71644567 71643795 0.000000e+00 1040.0
6 TraesCS2B01G589200 chr5B 79.399 898 147 18 2406 3294 356186586 356187454 3.120000e-167 599.0
7 TraesCS2B01G589200 chr5B 86.139 404 30 20 1992 2375 71645246 71644849 4.360000e-111 412.0
8 TraesCS2B01G589200 chr5B 82.586 379 34 19 5681 6036 71643672 71643303 7.610000e-79 305.0
9 TraesCS2B01G589200 chr4A 86.257 2423 313 14 2658 5073 729041392 729043801 0.000000e+00 2612.0
10 TraesCS2B01G589200 chr2D 85.539 1791 158 31 651 2375 520506741 520504986 0.000000e+00 1779.0
11 TraesCS2B01G589200 chr2D 91.248 777 61 7 4895 5668 520504704 520503932 0.000000e+00 1051.0
12 TraesCS2B01G589200 chr2D 82.368 380 35 21 5678 6033 520503813 520503442 9.840000e-78 302.0
13 TraesCS2B01G589200 chr2D 88.406 138 14 2 2563 2699 122702563 122702427 1.350000e-36 165.0
14 TraesCS2B01G589200 chr3A 85.601 1764 158 37 678 2375 636821305 636823038 0.000000e+00 1762.0
15 TraesCS2B01G589200 chr3A 89.402 887 76 16 4966 5847 636824354 636825227 0.000000e+00 1101.0
16 TraesCS2B01G589200 chr3A 88.156 895 76 17 4895 5782 62444447 62445318 0.000000e+00 1038.0
17 TraesCS2B01G589200 chr3A 87.500 616 51 17 1779 2375 62443559 62444167 0.000000e+00 688.0
18 TraesCS2B01G589200 chr3A 91.855 221 14 1 1556 1776 62438539 62438755 7.610000e-79 305.0
19 TraesCS2B01G589200 chr3A 87.895 190 21 2 5844 6033 636827608 636827795 7.880000e-54 222.0
20 TraesCS2B01G589200 chr3A 77.593 241 45 7 2415 2650 416166128 416165892 2.940000e-28 137.0
21 TraesCS2B01G589200 chr3A 92.188 64 5 0 654 717 636821242 636821305 2.320000e-14 91.6
22 TraesCS2B01G589200 chr1A 87.550 1253 151 5 2658 3906 1201364 1202615 0.000000e+00 1445.0
23 TraesCS2B01G589200 chr1A 83.237 173 23 5 2450 2617 537535537 537535366 2.920000e-33 154.0
24 TraesCS2B01G589200 chr5A 86.969 1036 96 28 5025 6034 490034915 490035937 0.000000e+00 1129.0
25 TraesCS2B01G589200 chr5A 89.721 574 43 6 2374 2931 490034327 490034900 0.000000e+00 719.0
26 TraesCS2B01G589200 chr5A 86.232 552 63 4 650 1190 490033180 490033729 2.430000e-163 586.0
27 TraesCS2B01G589200 chr5A 92.093 215 11 4 2162 2375 490033799 490034008 1.270000e-76 298.0
28 TraesCS2B01G589200 chr3B 83.863 1196 108 30 1229 2375 597051156 597052315 0.000000e+00 1061.0
29 TraesCS2B01G589200 chr3B 80.146 962 156 17 3970 4928 787987732 787986803 0.000000e+00 686.0
30 TraesCS2B01G589200 chr3B 91.549 426 31 3 4926 5351 597057554 597057974 3.140000e-162 582.0
31 TraesCS2B01G589200 chr3B 93.082 159 11 0 653 811 597050978 597051136 3.640000e-57 233.0
32 TraesCS2B01G589200 chr6D 93.778 659 26 8 3 651 460482031 460482684 0.000000e+00 976.0
33 TraesCS2B01G589200 chr1B 88.179 829 80 16 5025 5848 454928513 454929328 0.000000e+00 972.0
34 TraesCS2B01G589200 chr1B 89.721 574 43 6 2374 2931 454927925 454928498 0.000000e+00 719.0
35 TraesCS2B01G589200 chr1B 86.364 550 62 4 652 1190 454926780 454927327 6.740000e-164 588.0
36 TraesCS2B01G589200 chr1B 92.093 215 11 4 2162 2375 454927397 454927606 1.270000e-76 298.0
37 TraesCS2B01G589200 chr2A 83.996 1056 117 14 902 1924 625939078 625940114 0.000000e+00 966.0
38 TraesCS2B01G589200 chr2A 97.111 450 13 0 3051 3500 625953041 625953490 0.000000e+00 760.0
39 TraesCS2B01G589200 chr2A 93.617 329 17 2 5111 5439 625953489 625953813 7.040000e-134 488.0
40 TraesCS2B01G589200 chr2A 85.396 404 44 13 5630 6033 625954093 625954481 7.290000e-109 405.0
41 TraesCS2B01G589200 chr2A 90.452 199 13 4 2153 2348 625952772 625952967 2.160000e-64 257.0
42 TraesCS2B01G589200 chr2A 87.432 183 19 4 651 831 625938527 625938707 2.210000e-49 207.0
43 TraesCS2B01G589200 chr4B 97.838 370 5 1 1 370 147073622 147073988 2.370000e-178 636.0
44 TraesCS2B01G589200 chr4B 96.181 288 9 1 366 651 147075654 147075941 2.550000e-128 470.0
45 TraesCS2B01G589200 chrUn 79.000 700 115 22 2406 3097 274275923 274275248 3.320000e-122 449.0
46 TraesCS2B01G589200 chrUn 75.594 463 71 27 5605 6033 21277010 21277464 2.220000e-44 191.0
47 TraesCS2B01G589200 chr1D 83.488 430 67 4 5177 5604 89601795 89601368 1.220000e-106 398.0
48 TraesCS2B01G589200 chr7B 87.500 128 16 0 5903 6030 701299536 701299409 1.360000e-31 148.0
49 TraesCS2B01G589200 chr7B 78.125 224 40 7 2432 2650 327254462 327254681 3.800000e-27 134.0
50 TraesCS2B01G589200 chr6A 84.921 126 11 3 1 118 563271629 563271754 2.960000e-23 121.0


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 TraesCS2B01G589200 chr2B 775596236 775602276 6040 False 11156.000000 11156 100.00000 1 6041 1 chr2B.!!$F1 6040
1 TraesCS2B01G589200 chr2B 655630891 655633523 2632 False 353.000000 523 82.36000 657 6034 2 chr2B.!!$F2 5377
2 TraesCS2B01G589200 chr5B 707890833 707896196 5363 False 9443.000000 9443 98.38400 647 6030 1 chr5B.!!$F2 5383
3 TraesCS2B01G589200 chr5B 356186586 356187454 868 False 599.000000 599 79.39900 2406 3294 1 chr5B.!!$F1 888
4 TraesCS2B01G589200 chr5B 71643303 71645246 1943 True 585.666667 1040 86.57600 1992 6036 3 chr5B.!!$R1 4044
5 TraesCS2B01G589200 chr4A 729041392 729043801 2409 False 2612.000000 2612 86.25700 2658 5073 1 chr4A.!!$F1 2415
6 TraesCS2B01G589200 chr2D 520503442 520506741 3299 True 1044.000000 1779 86.38500 651 6033 3 chr2D.!!$R2 5382
7 TraesCS2B01G589200 chr3A 62443559 62445318 1759 False 863.000000 1038 87.82800 1779 5782 2 chr3A.!!$F2 4003
8 TraesCS2B01G589200 chr3A 636821242 636827795 6553 False 794.150000 1762 88.77150 654 6033 4 chr3A.!!$F3 5379
9 TraesCS2B01G589200 chr1A 1201364 1202615 1251 False 1445.000000 1445 87.55000 2658 3906 1 chr1A.!!$F1 1248
10 TraesCS2B01G589200 chr5A 490033180 490035937 2757 False 683.000000 1129 88.75375 650 6034 4 chr5A.!!$F1 5384
11 TraesCS2B01G589200 chr3B 787986803 787987732 929 True 686.000000 686 80.14600 3970 4928 1 chr3B.!!$R1 958
12 TraesCS2B01G589200 chr3B 597050978 597052315 1337 False 647.000000 1061 88.47250 653 2375 2 chr3B.!!$F2 1722
13 TraesCS2B01G589200 chr6D 460482031 460482684 653 False 976.000000 976 93.77800 3 651 1 chr6D.!!$F1 648
14 TraesCS2B01G589200 chr1B 454926780 454929328 2548 False 644.250000 972 89.08925 652 5848 4 chr1B.!!$F1 5196
15 TraesCS2B01G589200 chr2A 625938527 625940114 1587 False 586.500000 966 85.71400 651 1924 2 chr2A.!!$F1 1273
16 TraesCS2B01G589200 chr2A 625952772 625954481 1709 False 477.500000 760 91.64400 2153 6033 4 chr2A.!!$F2 3880
17 TraesCS2B01G589200 chr4B 147073622 147075941 2319 False 553.000000 636 97.00950 1 651 2 chr4B.!!$F1 650
18 TraesCS2B01G589200 chrUn 274275248 274275923 675 True 449.000000 449 79.00000 2406 3097 1 chrUn.!!$R1 691

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
454 2126 0.747283 GGCTGCTCCAGGTGAGATTG 60.747 60.000 0.00 0.0 44.42 2.67 F
634 2316 2.666508 CGTACAAAGAGATGGAACGGTG 59.333 50.000 0.00 0.0 33.12 4.94 F
1303 3354 1.680735 CCTACAGCTGAGCTCGATCTT 59.319 52.381 23.35 0.0 36.40 2.40 F
2393 4913 1.819928 TGAAATGTGTATGCCGCTGT 58.180 45.000 0.00 0.0 0.00 4.40 F
3529 6085 1.250328 CTGATGGTGCCTGCAGAAAA 58.750 50.000 17.39 0.0 0.00 2.29 F
3950 6506 5.885449 ATTTGAGGAAAAATGGTCCACAA 57.115 34.783 0.00 0.0 41.95 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 3354 2.646719 GCCGCGATATGTACCGGA 59.353 61.111 9.46 0.0 43.20 5.14 R
2393 4913 2.698803 AGCATCTGACGCAACATACAA 58.301 42.857 0.00 0.0 0.00 2.41 R
3136 5692 1.202580 GCGACCTCATACTTGCCATCT 60.203 52.381 0.00 0.0 0.00 2.90 R
3707 6263 0.482446 ACACCTCCCATTGCCTTGAA 59.518 50.000 0.00 0.0 0.00 2.69 R
4887 7445 0.106769 TCCACTTGTTGCTGGCTGAA 60.107 50.000 0.00 0.0 0.00 3.02 R
5194 8722 4.351111 GGTGGGTCCATATTCTCCTTGTAT 59.649 45.833 0.00 0.0 35.97 2.29 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
215 216 8.786826 TGGACATAGGTTAAGTTAACTTCATG 57.213 34.615 23.76 21.22 38.68 3.07
453 2125 1.203441 TGGCTGCTCCAGGTGAGATT 61.203 55.000 0.00 0.00 44.42 2.40
454 2126 0.747283 GGCTGCTCCAGGTGAGATTG 60.747 60.000 0.00 0.00 44.42 2.67
630 2312 3.120304 GCAACCGTACAAAGAGATGGAAC 60.120 47.826 0.00 0.00 0.00 3.62
634 2316 2.666508 CGTACAAAGAGATGGAACGGTG 59.333 50.000 0.00 0.00 33.12 4.94
1303 3354 1.680735 CCTACAGCTGAGCTCGATCTT 59.319 52.381 23.35 0.00 36.40 2.40
1336 3404 2.202892 GCGGTCGGACCTCAATCC 60.203 66.667 23.86 2.93 35.66 3.01
1735 3832 6.468543 AGGAAACCTTGTATGAAAGACTCTC 58.531 40.000 0.00 0.00 0.00 3.20
1933 4077 5.948162 AGTGGAAAAATCATGCAGATACAGT 59.052 36.000 0.00 0.00 35.39 3.55
2393 4913 1.819928 TGAAATGTGTATGCCGCTGT 58.180 45.000 0.00 0.00 0.00 4.40
3136 5692 9.703892 GCTATGATTAGCTTGAAGATAAGAGAA 57.296 33.333 8.92 0.00 46.13 2.87
3350 5906 6.493458 ACCAGAAAATATTGGTTGCACTAAGT 59.507 34.615 0.00 0.00 45.16 2.24
3518 6074 2.882761 CACATATTCTGGGCTGATGGTG 59.117 50.000 0.00 0.00 0.00 4.17
3529 6085 1.250328 CTGATGGTGCCTGCAGAAAA 58.750 50.000 17.39 0.00 0.00 2.29
3707 6263 6.048732 ACAAATGGTTGTTCAAGACCTTTT 57.951 33.333 0.00 0.00 46.01 2.27
3709 6265 6.593770 ACAAATGGTTGTTCAAGACCTTTTTC 59.406 34.615 4.30 0.00 46.01 2.29
3950 6506 5.885449 ATTTGAGGAAAAATGGTCCACAA 57.115 34.783 0.00 0.00 41.95 3.33
4887 7445 2.036346 GCACAAAGATGAAGCAGGGTTT 59.964 45.455 0.00 0.00 33.46 3.27
5428 8960 1.899617 CCATCCCACACCATTTGCC 59.100 57.895 0.00 0.00 0.00 4.52
5854 12018 6.491745 TCCTTGTTGGTAAAACTGATGCATAA 59.508 34.615 0.00 0.00 37.07 1.90
5892 12056 5.757850 ACAAAAGACAGCCTGTTCTTAAG 57.242 39.130 0.00 0.00 0.00 1.85
6036 12200 6.239772 CCGTATCACCTGATATTTTCCCCTAA 60.240 42.308 0.00 0.00 39.03 2.69
6037 12201 6.874134 CGTATCACCTGATATTTTCCCCTAAG 59.126 42.308 0.00 0.00 39.03 2.18
6038 12202 6.848562 ATCACCTGATATTTTCCCCTAAGT 57.151 37.500 0.00 0.00 32.01 2.24
6039 12203 7.947782 ATCACCTGATATTTTCCCCTAAGTA 57.052 36.000 0.00 0.00 32.01 2.24
6040 12204 7.133133 TCACCTGATATTTTCCCCTAAGTAC 57.867 40.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
275 276 8.199176 TGTGTCAGTCAAAAATTAACGAGTTA 57.801 30.769 0.00 0.00 0.00 2.24
330 331 8.523915 TGGATCGGTAATTCTAGTTTGTAGTA 57.476 34.615 0.00 0.00 0.00 1.82
331 332 7.414222 TGGATCGGTAATTCTAGTTTGTAGT 57.586 36.000 0.00 0.00 0.00 2.73
332 333 8.712285 TTTGGATCGGTAATTCTAGTTTGTAG 57.288 34.615 0.00 0.00 0.00 2.74
630 2312 1.274167 TGTACTTAGCCCAACTCACCG 59.726 52.381 0.00 0.00 0.00 4.94
634 2316 2.832733 ACTCCTGTACTTAGCCCAACTC 59.167 50.000 0.00 0.00 0.00 3.01
964 2988 1.754803 TCGTACCGGATCTGAGCAAAT 59.245 47.619 9.46 0.00 0.00 2.32
1028 3052 0.741326 CTTAGTCGGCTCTAGCTGCA 59.259 55.000 5.89 0.00 46.62 4.41
1303 3354 2.646719 GCCGCGATATGTACCGGA 59.353 61.111 9.46 0.00 43.20 5.14
1735 3832 8.746922 ATACTTTTGCACATCAACACTTATTG 57.253 30.769 0.00 0.00 33.73 1.90
1776 3880 4.336433 CCCTTCTTGTGTGCCTATATGTTG 59.664 45.833 0.00 0.00 0.00 3.33
2393 4913 2.698803 AGCATCTGACGCAACATACAA 58.301 42.857 0.00 0.00 0.00 2.41
2831 5385 3.962063 TCAGGCACGTATATTGAACCCTA 59.038 43.478 0.00 0.00 0.00 3.53
3136 5692 1.202580 GCGACCTCATACTTGCCATCT 60.203 52.381 0.00 0.00 0.00 2.90
3350 5906 8.541133 TCACGACAATAATTCTGTAAATCACA 57.459 30.769 0.00 0.00 35.30 3.58
3529 6085 3.627577 CCTCGCCAAATAGTGCATAGTTT 59.372 43.478 0.00 0.00 0.00 2.66
3707 6263 0.482446 ACACCTCCCATTGCCTTGAA 59.518 50.000 0.00 0.00 0.00 2.69
3709 6265 0.604578 CAACACCTCCCATTGCCTTG 59.395 55.000 0.00 0.00 0.00 3.61
4410 6968 1.227234 GCAACCTTGGTTGTGGTGC 60.227 57.895 26.99 14.16 36.57 5.01
4765 7323 2.619931 TCCTGGATCTTTGTCTGTCCA 58.380 47.619 0.00 0.00 38.37 4.02
4887 7445 0.106769 TCCACTTGTTGCTGGCTGAA 60.107 50.000 0.00 0.00 0.00 3.02
5194 8722 4.351111 GGTGGGTCCATATTCTCCTTGTAT 59.649 45.833 0.00 0.00 35.97 2.29
5428 8960 7.202016 TCTCCAAAAACAATAGTACAAGCTG 57.798 36.000 0.00 0.00 0.00 4.24
5854 12018 7.607250 TGTCTTTTGTAAAACCACAACAGATT 58.393 30.769 7.78 0.00 43.42 2.40


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

AutoCloner maintained by Alex Coulton.