Multiple sequence alignment - TraesCS2D01G085600

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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 TraesCS2D01G085600 chr2D 100.000 3460 0 0 1 3460 37034734 37031275 0.000000e+00 6390.0
1 TraesCS2D01G085600 chr2D 93.104 3495 138 35 1 3416 202200262 202196792 0.000000e+00 5024.0
2 TraesCS2D01G085600 chr2D 92.362 2959 127 30 510 3416 568478482 568481393 0.000000e+00 4120.0
3 TraesCS2D01G085600 chr3D 93.748 3471 144 23 1 3416 552501878 552498426 0.000000e+00 5140.0
4 TraesCS2D01G085600 chr3D 92.939 3470 178 24 1 3417 610828764 610832219 0.000000e+00 4988.0
5 TraesCS2D01G085600 chr3D 93.802 2388 89 24 1084 3416 225880716 225878333 0.000000e+00 3535.0
6 TraesCS2D01G085600 chr7D 93.631 3470 151 23 1 3417 514081813 514085265 0.000000e+00 5120.0
7 TraesCS2D01G085600 chr7D 93.176 3473 161 32 1 3416 576372131 576368678 0.000000e+00 5031.0
8 TraesCS2D01G085600 chr7D 92.383 3479 160 32 1 3416 322689643 322686207 0.000000e+00 4859.0
9 TraesCS2D01G085600 chr7D 95.164 2047 82 10 1388 3418 73271914 73269869 0.000000e+00 3216.0
10 TraesCS2D01G085600 chr7D 89.800 902 38 12 828 1684 581331231 581332123 0.000000e+00 1107.0
11 TraesCS2D01G085600 chr6D 93.543 3469 149 30 1 3416 446852704 446856150 0.000000e+00 5096.0
12 TraesCS2D01G085600 chr6D 93.308 3482 153 35 2 3416 11397633 11401101 0.000000e+00 5066.0
13 TraesCS2D01G085600 chr5D 93.172 3471 138 31 1 3417 340549945 340546520 0.000000e+00 5005.0
14 TraesCS2D01G085600 chr5D 92.740 3471 163 30 1 3416 527308836 527312272 0.000000e+00 4931.0
15 TraesCS2D01G085600 chr5D 92.540 3472 148 38 1 3416 177627275 177630691 0.000000e+00 4874.0
16 TraesCS2D01G085600 chr4D 92.796 3484 173 28 1 3417 405164919 405161447 0.000000e+00 4972.0
17 TraesCS2D01G085600 chr4D 91.024 1827 110 19 1 1785 83237541 83239355 0.000000e+00 2416.0
18 TraesCS2D01G085600 chr1D 92.905 3467 172 26 5 3417 90262145 90265591 0.000000e+00 4972.0
19 TraesCS2D01G085600 chr1D 93.156 2367 100 18 1105 3416 314679754 314682113 0.000000e+00 3417.0
20 TraesCS2D01G085600 chr7A 89.594 3469 271 45 1 3416 181562597 181566028 0.000000e+00 4324.0
21 TraesCS2D01G085600 chr1B 89.364 3460 279 36 1 3417 190540082 190543495 0.000000e+00 4268.0
22 TraesCS2D01G085600 chr5A 93.454 2368 95 17 1101 3416 377285114 377282755 0.000000e+00 3459.0
23 TraesCS2D01G085600 chr4A 92.318 2226 130 12 1225 3416 413144737 413146955 0.000000e+00 3125.0
24 TraesCS2D01G085600 chr2A 89.463 1509 98 18 1 1464 434762382 434763874 0.000000e+00 1849.0
25 TraesCS2D01G085600 chr2A 97.727 44 1 0 3417 3460 41644117 41644074 3.700000e-10 76.8
26 TraesCS2D01G085600 chr6A 88.466 945 53 18 757 1656 215253560 215252627 0.000000e+00 1090.0
27 TraesCS2D01G085600 chr2B 100.000 44 0 0 3417 3460 64070504 64070547 7.960000e-12 82.4
28 TraesCS2D01G085600 chr2B 100.000 44 0 0 3417 3460 64230167 64230124 7.960000e-12 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 TraesCS2D01G085600 chr2D 37031275 37034734 3459 True 6390 6390 100.000 1 3460 1 chr2D.!!$R1 3459
1 TraesCS2D01G085600 chr2D 202196792 202200262 3470 True 5024 5024 93.104 1 3416 1 chr2D.!!$R2 3415
2 TraesCS2D01G085600 chr2D 568478482 568481393 2911 False 4120 4120 92.362 510 3416 1 chr2D.!!$F1 2906
3 TraesCS2D01G085600 chr3D 552498426 552501878 3452 True 5140 5140 93.748 1 3416 1 chr3D.!!$R2 3415
4 TraesCS2D01G085600 chr3D 610828764 610832219 3455 False 4988 4988 92.939 1 3417 1 chr3D.!!$F1 3416
5 TraesCS2D01G085600 chr3D 225878333 225880716 2383 True 3535 3535 93.802 1084 3416 1 chr3D.!!$R1 2332
6 TraesCS2D01G085600 chr7D 514081813 514085265 3452 False 5120 5120 93.631 1 3417 1 chr7D.!!$F1 3416
7 TraesCS2D01G085600 chr7D 576368678 576372131 3453 True 5031 5031 93.176 1 3416 1 chr7D.!!$R3 3415
8 TraesCS2D01G085600 chr7D 322686207 322689643 3436 True 4859 4859 92.383 1 3416 1 chr7D.!!$R2 3415
9 TraesCS2D01G085600 chr7D 73269869 73271914 2045 True 3216 3216 95.164 1388 3418 1 chr7D.!!$R1 2030
10 TraesCS2D01G085600 chr7D 581331231 581332123 892 False 1107 1107 89.800 828 1684 1 chr7D.!!$F2 856
11 TraesCS2D01G085600 chr6D 446852704 446856150 3446 False 5096 5096 93.543 1 3416 1 chr6D.!!$F2 3415
12 TraesCS2D01G085600 chr6D 11397633 11401101 3468 False 5066 5066 93.308 2 3416 1 chr6D.!!$F1 3414
13 TraesCS2D01G085600 chr5D 340546520 340549945 3425 True 5005 5005 93.172 1 3417 1 chr5D.!!$R1 3416
14 TraesCS2D01G085600 chr5D 527308836 527312272 3436 False 4931 4931 92.740 1 3416 1 chr5D.!!$F2 3415
15 TraesCS2D01G085600 chr5D 177627275 177630691 3416 False 4874 4874 92.540 1 3416 1 chr5D.!!$F1 3415
16 TraesCS2D01G085600 chr4D 405161447 405164919 3472 True 4972 4972 92.796 1 3417 1 chr4D.!!$R1 3416
17 TraesCS2D01G085600 chr4D 83237541 83239355 1814 False 2416 2416 91.024 1 1785 1 chr4D.!!$F1 1784
18 TraesCS2D01G085600 chr1D 90262145 90265591 3446 False 4972 4972 92.905 5 3417 1 chr1D.!!$F1 3412
19 TraesCS2D01G085600 chr1D 314679754 314682113 2359 False 3417 3417 93.156 1105 3416 1 chr1D.!!$F2 2311
20 TraesCS2D01G085600 chr7A 181562597 181566028 3431 False 4324 4324 89.594 1 3416 1 chr7A.!!$F1 3415
21 TraesCS2D01G085600 chr1B 190540082 190543495 3413 False 4268 4268 89.364 1 3417 1 chr1B.!!$F1 3416
22 TraesCS2D01G085600 chr5A 377282755 377285114 2359 True 3459 3459 93.454 1101 3416 1 chr5A.!!$R1 2315
23 TraesCS2D01G085600 chr4A 413144737 413146955 2218 False 3125 3125 92.318 1225 3416 1 chr4A.!!$F1 2191
24 TraesCS2D01G085600 chr2A 434762382 434763874 1492 False 1849 1849 89.463 1 1464 1 chr2A.!!$F1 1463
25 TraesCS2D01G085600 chr6A 215252627 215253560 933 True 1090 1090 88.466 757 1656 1 chr6A.!!$R1 899

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
447 451 0.405198 TGGAGCAGGCAAAATCCAGA 59.595 50.0 0.0 0.0 36.92 3.86 F
1276 1385 0.034896 GAGACCGAGGAAAGGCAACA 59.965 55.0 0.0 0.0 41.41 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 1903 1.734655 AGGGGATGATAAGGCACGAT 58.265 50.0 0.00 0.0 0.0 3.73 R
3204 3429 0.108520 CCGGAAGCGCTACTGGTAAA 60.109 55.0 12.05 0.0 0.0 2.01 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
94 97 0.675837 GAGAGCAGCACAGGATTGCA 60.676 55.000 0.00 0.00 45.62 4.08
120 123 2.033602 TGACTCGCCGTCTGAGGA 59.966 61.111 0.00 0.00 43.25 3.71
260 263 3.505293 GTGGAAGAAGTACTACCGTGAGT 59.495 47.826 0.00 0.00 0.00 3.41
362 365 2.035832 TCATCTGAGACAGTCGCAACAA 59.964 45.455 8.46 0.00 32.61 2.83
445 449 1.941377 ATTGGAGCAGGCAAAATCCA 58.059 45.000 0.00 0.00 40.04 3.41
446 450 1.259609 TTGGAGCAGGCAAAATCCAG 58.740 50.000 0.00 0.00 42.54 3.86
447 451 0.405198 TGGAGCAGGCAAAATCCAGA 59.595 50.000 0.00 0.00 36.92 3.86
539 565 4.340246 CAGCTGCACCTGCTCCCA 62.340 66.667 0.00 0.00 42.66 4.37
717 782 1.503818 TTCTTTGCAGGCCGACGAAC 61.504 55.000 0.00 0.00 0.00 3.95
942 1009 2.288948 GCTTGGTGATTGTTGCAATGGA 60.289 45.455 0.59 0.00 0.00 3.41
1226 1295 2.751436 GCCTGAATTGCCGCCTCA 60.751 61.111 0.00 0.00 0.00 3.86
1228 1297 2.768492 CCTGAATTGCCGCCTCAGC 61.768 63.158 8.15 0.00 36.14 4.26
1231 1300 3.407046 GAATTGCCGCCTCAGCAGC 62.407 63.158 0.00 0.00 43.07 5.25
1276 1385 0.034896 GAGACCGAGGAAAGGCAACA 59.965 55.000 0.00 0.00 41.41 3.33
1277 1386 0.472471 AGACCGAGGAAAGGCAACAA 59.528 50.000 0.00 0.00 41.41 2.83
1278 1387 0.591659 GACCGAGGAAAGGCAACAAC 59.408 55.000 0.00 0.00 41.41 3.32
1432 1569 0.179073 GCTGCGGATAGAGAAAGGCA 60.179 55.000 0.00 0.00 0.00 4.75
1603 1741 0.037590 TGTCCGCCTTTATGCCTTGT 59.962 50.000 0.00 0.00 0.00 3.16
1645 1783 4.323104 GGGTTGAGCAGATACCTCATATCC 60.323 50.000 0.00 0.00 40.74 2.59
1760 1898 1.065418 CGCCAATAAGGACAAGGAGGT 60.065 52.381 0.00 0.00 41.22 3.85
1765 1903 5.631481 GCCAATAAGGACAAGGAGGTGATTA 60.631 44.000 0.00 0.00 41.22 1.75
1960 2100 7.749126 GGAATCGTCGAAGAACATTAACAAAAT 59.251 33.333 4.85 0.00 39.69 1.82
1990 2130 2.341257 CCACATCAAGTCTGTTCTCGG 58.659 52.381 0.00 0.00 0.00 4.63
2148 2290 1.347062 TGTCCTACACCACATGCTGA 58.653 50.000 0.00 0.00 0.00 4.26
2447 2590 1.133575 CCTGACTTGGATGGATGGCAT 60.134 52.381 0.00 0.00 0.00 4.40
2872 3049 2.672961 TGCGAGAGGGATACAAACTG 57.327 50.000 0.00 0.00 39.74 3.16
2885 3062 6.202954 GGGATACAAACTGATGTACTGCATAC 59.797 42.308 0.00 0.00 38.53 2.39
2945 3144 9.423061 CGTATATCATTGTTTAGATGGATGACA 57.577 33.333 0.00 0.00 30.37 3.58
3222 3448 1.278238 CTTTACCAGTAGCGCTTCCG 58.722 55.000 18.68 1.74 37.57 4.30
3254 3480 1.888215 TGCAGATATTAGCAGCAGCC 58.112 50.000 0.00 0.00 43.56 4.85
3418 3644 2.414994 GGTTTTCCCTAGTAGTGGCC 57.585 55.000 0.00 0.00 0.00 5.36
3419 3645 1.064906 GGTTTTCCCTAGTAGTGGCCC 60.065 57.143 0.00 0.00 0.00 5.80
3420 3646 1.914108 GTTTTCCCTAGTAGTGGCCCT 59.086 52.381 0.00 0.00 0.00 5.19
3421 3647 2.307980 GTTTTCCCTAGTAGTGGCCCTT 59.692 50.000 0.00 0.00 0.00 3.95
3422 3648 1.580059 TTCCCTAGTAGTGGCCCTTG 58.420 55.000 0.00 0.00 0.00 3.61
3423 3649 0.714180 TCCCTAGTAGTGGCCCTTGA 59.286 55.000 0.00 0.00 0.00 3.02
3424 3650 1.079825 TCCCTAGTAGTGGCCCTTGAA 59.920 52.381 0.00 0.00 0.00 2.69
3425 3651 1.209747 CCCTAGTAGTGGCCCTTGAAC 59.790 57.143 0.00 0.00 0.00 3.18
3426 3652 1.209747 CCTAGTAGTGGCCCTTGAACC 59.790 57.143 0.00 0.00 0.00 3.62
3427 3653 1.906574 CTAGTAGTGGCCCTTGAACCA 59.093 52.381 0.00 0.00 0.00 3.67
3428 3654 0.693049 AGTAGTGGCCCTTGAACCAG 59.307 55.000 0.00 0.00 36.38 4.00
3429 3655 0.322546 GTAGTGGCCCTTGAACCAGG 60.323 60.000 0.00 0.00 36.38 4.45
3430 3656 0.474854 TAGTGGCCCTTGAACCAGGA 60.475 55.000 0.00 0.00 36.38 3.86
3431 3657 1.152830 GTGGCCCTTGAACCAGGAA 59.847 57.895 0.00 0.00 36.38 3.36
3432 3658 0.895559 GTGGCCCTTGAACCAGGAAG 60.896 60.000 0.00 0.00 36.38 3.46
3433 3659 1.304464 GGCCCTTGAACCAGGAAGG 60.304 63.158 0.00 0.00 45.67 3.46
3434 3660 1.767692 GCCCTTGAACCAGGAAGGA 59.232 57.895 6.95 0.00 41.26 3.36
3435 3661 0.332972 GCCCTTGAACCAGGAAGGAT 59.667 55.000 6.95 0.00 41.26 3.24
3436 3662 1.683319 GCCCTTGAACCAGGAAGGATC 60.683 57.143 6.95 0.00 41.26 3.36
3437 3663 1.635487 CCCTTGAACCAGGAAGGATCA 59.365 52.381 6.95 0.00 46.32 2.92
3442 3668 4.387026 TGAACCAGGAAGGATCACATTT 57.613 40.909 0.00 0.00 43.51 2.32
3443 3669 4.081406 TGAACCAGGAAGGATCACATTTG 58.919 43.478 0.00 0.00 43.51 2.32
3444 3670 4.202556 TGAACCAGGAAGGATCACATTTGA 60.203 41.667 0.00 0.00 43.51 2.69
3445 3671 4.598036 ACCAGGAAGGATCACATTTGAT 57.402 40.909 0.00 0.00 45.78 2.57
3446 3672 4.275810 ACCAGGAAGGATCACATTTGATG 58.724 43.478 0.00 0.00 42.95 3.07
3447 3673 4.018141 ACCAGGAAGGATCACATTTGATGA 60.018 41.667 0.00 0.00 42.95 2.92
3448 3674 4.579340 CCAGGAAGGATCACATTTGATGAG 59.421 45.833 0.00 0.00 42.95 2.90
3449 3675 5.434408 CAGGAAGGATCACATTTGATGAGA 58.566 41.667 0.00 0.00 42.95 3.27
3450 3676 5.884232 CAGGAAGGATCACATTTGATGAGAA 59.116 40.000 0.00 0.00 42.95 2.87
3451 3677 6.038382 CAGGAAGGATCACATTTGATGAGAAG 59.962 42.308 0.00 0.00 42.95 2.85
3452 3678 6.069789 AGGAAGGATCACATTTGATGAGAAGA 60.070 38.462 0.00 0.00 42.95 2.87
3453 3679 6.771749 GGAAGGATCACATTTGATGAGAAGAT 59.228 38.462 0.00 0.00 42.95 2.40
3454 3680 7.255173 GGAAGGATCACATTTGATGAGAAGATG 60.255 40.741 0.00 0.00 42.95 2.90
3455 3681 6.062749 AGGATCACATTTGATGAGAAGATGG 58.937 40.000 0.00 0.00 42.95 3.51
3456 3682 6.060136 GGATCACATTTGATGAGAAGATGGA 58.940 40.000 0.00 0.00 42.95 3.41
3457 3683 6.205076 GGATCACATTTGATGAGAAGATGGAG 59.795 42.308 0.00 0.00 42.95 3.86
3458 3684 6.303903 TCACATTTGATGAGAAGATGGAGA 57.696 37.500 0.00 0.00 0.00 3.71
3459 3685 6.896883 TCACATTTGATGAGAAGATGGAGAT 58.103 36.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 139 1.826385 GGTTGAATGGAGTGTCCCAG 58.174 55.000 0.00 0.00 39.97 4.45
224 227 1.537814 TTCCACGTGGCACCGTCTAT 61.538 55.000 30.25 0.00 39.45 1.98
260 263 0.251033 TCGTTTCTCTCCTCCGTGGA 60.251 55.000 0.00 0.00 43.86 4.02
277 280 3.293311 TCAGTTAACCTCCGTCTTTCG 57.707 47.619 0.88 0.00 39.52 3.46
717 782 0.181587 TACAATATGGTGCACGGGGG 59.818 55.000 11.45 0.53 0.00 5.40
942 1009 2.017668 TTGGCCACAACAGGACCCAT 62.018 55.000 3.88 0.00 35.02 4.00
1276 1385 4.592942 TGGATCATAGAAGCAGCTTTGTT 58.407 39.130 9.62 0.00 0.00 2.83
1277 1386 4.197750 CTGGATCATAGAAGCAGCTTTGT 58.802 43.478 9.62 2.54 0.00 2.83
1278 1387 3.003482 GCTGGATCATAGAAGCAGCTTTG 59.997 47.826 9.62 3.91 35.69 2.77
1603 1741 2.963101 CCCCGATGAGGTAGTTCATGTA 59.037 50.000 0.00 0.00 37.90 2.29
1760 1898 4.323485 GGGGATGATAAGGCACGATAATCA 60.323 45.833 0.00 0.00 0.00 2.57
1765 1903 1.734655 AGGGGATGATAAGGCACGAT 58.265 50.000 0.00 0.00 0.00 3.73
1960 2100 3.587061 AGACTTGATGTGGGTGTAATCCA 59.413 43.478 0.00 0.00 0.00 3.41
1990 2130 3.242316 GCCGTAGTAAAACATAGCACTGC 60.242 47.826 0.00 0.00 0.00 4.40
2148 2290 1.825474 CTGGTGATCCCGTCTGTACTT 59.175 52.381 0.00 0.00 35.15 2.24
2447 2590 3.893326 ATCGACAATCACTCCATGTCA 57.107 42.857 6.03 0.00 42.76 3.58
2872 3049 3.053455 GAGCGGAAGTATGCAGTACATC 58.947 50.000 0.00 0.00 40.38 3.06
2885 3062 2.447244 ACTTTGAGTGAGAGCGGAAG 57.553 50.000 0.00 0.00 0.00 3.46
2945 3144 7.986085 AGTCTTGATTACTTGCAACTACATT 57.014 32.000 0.00 0.00 0.00 2.71
3204 3429 0.108520 CCGGAAGCGCTACTGGTAAA 60.109 55.000 12.05 0.00 0.00 2.01
3222 3448 0.453390 ATCTGCAGCGCTTTTTAGCC 59.547 50.000 7.50 0.00 0.00 3.93
3254 3480 1.512926 AGCGTGTTTTAGTGCAGAGG 58.487 50.000 0.00 0.00 0.00 3.69
3418 3644 2.040278 TGTGATCCTTCCTGGTTCAAGG 59.960 50.000 6.36 6.36 43.76 3.61
3419 3645 3.423539 TGTGATCCTTCCTGGTTCAAG 57.576 47.619 0.00 0.00 43.76 3.02
3420 3646 4.387026 AATGTGATCCTTCCTGGTTCAA 57.613 40.909 0.00 0.00 43.76 2.69
3421 3647 4.081406 CAAATGTGATCCTTCCTGGTTCA 58.919 43.478 0.00 0.00 41.00 3.18
3422 3648 4.335416 TCAAATGTGATCCTTCCTGGTTC 58.665 43.478 0.00 0.00 37.07 3.62
3423 3649 4.387026 TCAAATGTGATCCTTCCTGGTT 57.613 40.909 0.00 0.00 37.07 3.67
3424 3650 4.018141 TCATCAAATGTGATCCTTCCTGGT 60.018 41.667 0.00 0.00 42.88 4.00
3425 3651 4.529897 TCATCAAATGTGATCCTTCCTGG 58.470 43.478 0.00 0.00 42.88 4.45
3426 3652 5.434408 TCTCATCAAATGTGATCCTTCCTG 58.566 41.667 0.00 0.00 42.88 3.86
3427 3653 5.705397 TCTCATCAAATGTGATCCTTCCT 57.295 39.130 0.00 0.00 42.88 3.36
3428 3654 6.118170 TCTTCTCATCAAATGTGATCCTTCC 58.882 40.000 0.00 0.00 42.88 3.46
3429 3655 7.255173 CCATCTTCTCATCAAATGTGATCCTTC 60.255 40.741 0.00 0.00 42.88 3.46
3430 3656 6.546403 CCATCTTCTCATCAAATGTGATCCTT 59.454 38.462 0.00 0.00 42.88 3.36
3431 3657 6.062749 CCATCTTCTCATCAAATGTGATCCT 58.937 40.000 0.00 0.00 42.88 3.24
3432 3658 6.060136 TCCATCTTCTCATCAAATGTGATCC 58.940 40.000 0.00 0.00 42.88 3.36
3433 3659 6.990939 TCTCCATCTTCTCATCAAATGTGATC 59.009 38.462 0.00 0.00 42.88 2.92
3434 3660 6.896883 TCTCCATCTTCTCATCAAATGTGAT 58.103 36.000 0.00 0.00 45.80 3.06
3435 3661 6.303903 TCTCCATCTTCTCATCAAATGTGA 57.696 37.500 0.00 0.00 38.41 3.58


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

AutoCloner maintained by Alex Coulton.