Multiple sequence alignment - TraesCS2D01G385700

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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 TraesCS2D01G385700 chr2D 100.000 3459 0 0 1 3459 490576893 490580351 0.000000e+00 6388.0
1 TraesCS2D01G385700 chr2D 84.446 1363 123 44 958 2247 490658768 490660114 0.000000e+00 1260.0
2 TraesCS2D01G385700 chr2D 85.161 930 94 14 1 923 490657899 490658791 0.000000e+00 913.0
3 TraesCS2D01G385700 chr2D 79.670 787 99 30 958 1707 490127686 490126924 8.560000e-141 510.0
4 TraesCS2D01G385700 chr2D 85.161 465 50 12 2635 3086 490660612 490661070 3.150000e-125 459.0
5 TraesCS2D01G385700 chr2D 82.341 487 39 28 1802 2247 490126217 490125737 2.520000e-101 379.0
6 TraesCS2D01G385700 chr2D 83.103 290 24 10 2316 2605 490660265 490660529 1.240000e-59 241.0
7 TraesCS2D01G385700 chr2D 83.420 193 21 8 2243 2428 490125710 490125522 5.940000e-38 169.0
8 TraesCS2D01G385700 chr2D 89.286 84 9 0 3194 3277 490124743 490124660 4.720000e-19 106.0
9 TraesCS2D01G385700 chr2D 90.909 66 6 0 3194 3259 490661208 490661273 4.750000e-14 89.8
10 TraesCS2D01G385700 chr2B 93.769 1926 75 11 1 1893 574715895 574717808 0.000000e+00 2850.0
11 TraesCS2D01G385700 chr2B 94.161 1610 57 12 911 2486 574676284 574677890 0.000000e+00 2418.0
12 TraesCS2D01G385700 chr2B 95.851 1157 39 6 1931 3086 574717805 574718953 0.000000e+00 1862.0
13 TraesCS2D01G385700 chr2B 95.942 616 20 4 190 805 574675676 574676286 0.000000e+00 994.0
14 TraesCS2D01G385700 chr2B 86.973 783 69 19 958 1712 575137646 575138423 0.000000e+00 850.0
15 TraesCS2D01G385700 chr2B 95.952 420 15 2 2668 3086 574690049 574690467 0.000000e+00 680.0
16 TraesCS2D01G385700 chr2B 95.280 339 14 2 3099 3436 574690545 574690882 1.410000e-148 536.0
17 TraesCS2D01G385700 chr2B 85.684 468 45 11 2635 3086 575141805 575142266 1.120000e-129 473.0
18 TraesCS2D01G385700 chr2B 83.762 505 64 13 1722 2219 575138471 575138964 2.430000e-126 462.0
19 TraesCS2D01G385700 chr2B 94.631 298 12 2 3099 3395 574719031 574719325 3.150000e-125 459.0
20 TraesCS2D01G385700 chr2B 89.254 335 28 2 1 335 575136707 575137033 2.480000e-111 412.0
21 TraesCS2D01G385700 chr2B 86.025 322 43 1 958 1277 574039951 574039630 9.190000e-91 344.0
22 TraesCS2D01G385700 chr2B 77.143 490 80 21 439 921 574040394 574039930 4.430000e-64 255.0
23 TraesCS2D01G385700 chr2B 93.827 162 7 2 2519 2680 574677884 574678042 1.240000e-59 241.0
24 TraesCS2D01G385700 chr2B 88.889 180 13 4 2074 2247 573941947 573941769 7.520000e-52 215.0
25 TraesCS2D01G385700 chr2B 79.767 257 26 13 3194 3436 575142407 575142651 2.760000e-36 163.0
26 TraesCS2D01G385700 chr2B 100.000 83 0 0 55 137 574675584 574675666 1.660000e-33 154.0
27 TraesCS2D01G385700 chr2B 90.476 84 8 0 3194 3277 573940775 573940692 1.010000e-20 111.0
28 TraesCS2D01G385700 chr2B 90.476 84 8 0 3194 3277 574035622 574035539 1.010000e-20 111.0
29 TraesCS2D01G385700 chr2B 88.608 79 9 0 2427 2505 573941524 573941446 2.840000e-16 97.1
30 TraesCS2D01G385700 chr2B 88.608 79 9 0 2427 2505 574036371 574036293 2.840000e-16 97.1
31 TraesCS2D01G385700 chr2A 97.315 1676 39 5 1415 3086 634107950 634109623 0.000000e+00 2841.0
32 TraesCS2D01G385700 chr2A 97.129 1428 29 4 1 1425 634106468 634107886 0.000000e+00 2399.0
33 TraesCS2D01G385700 chr2A 84.500 1329 131 42 977 2247 634607205 634608516 0.000000e+00 1243.0
34 TraesCS2D01G385700 chr2A 85.684 929 85 12 1 923 634606317 634607203 0.000000e+00 935.0
35 TraesCS2D01G385700 chr2A 95.873 315 10 2 3122 3436 634109705 634110016 1.110000e-139 507.0
36 TraesCS2D01G385700 chr2A 85.288 469 47 13 2635 3086 634609103 634609566 6.760000e-127 464.0
37 TraesCS2D01G385700 chr2A 83.754 357 31 11 2250 2605 634608577 634608907 2.590000e-81 313.0
38 TraesCS2D01G385700 chr2A 89.011 91 8 2 3196 3286 634609709 634609797 1.010000e-20 111.0
39 TraesCS2D01G385700 chrUn 79.615 780 103 24 962 1706 259671365 259670607 3.080000e-140 508.0
40 TraesCS2D01G385700 chrUn 82.062 485 36 26 1802 2247 259669930 259669458 1.960000e-97 366.0
41 TraesCS2D01G385700 chr5D 92.000 50 3 1 920 969 269578722 269578674 6.190000e-08 69.4
42 TraesCS2D01G385700 chr3D 95.238 42 2 0 925 966 127334673 127334714 2.230000e-07 67.6
43 TraesCS2D01G385700 chr3D 93.023 43 1 2 925 965 506698394 506698352 1.040000e-05 62.1
44 TraesCS2D01G385700 chr4B 95.238 42 1 1 925 966 95188074 95188114 8.010000e-07 65.8
45 TraesCS2D01G385700 chr1D 95.122 41 2 0 925 965 326287728 326287768 8.010000e-07 65.8
46 TraesCS2D01G385700 chr1A 93.333 45 2 1 921 965 412460385 412460428 8.010000e-07 65.8


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 TraesCS2D01G385700 chr2D 490576893 490580351 3458 False 6388.000000 6388 100.000000 1 3459 1 chr2D.!!$F1 3458
1 TraesCS2D01G385700 chr2D 490657899 490661273 3374 False 592.560000 1260 85.756000 1 3259 5 chr2D.!!$F2 3258
2 TraesCS2D01G385700 chr2D 490124660 490127686 3026 True 291.000000 510 83.679250 958 3277 4 chr2D.!!$R1 2319
3 TraesCS2D01G385700 chr2B 574715895 574719325 3430 False 1723.666667 2850 94.750333 1 3395 3 chr2B.!!$F3 3394
4 TraesCS2D01G385700 chr2B 574675584 574678042 2458 False 951.750000 2418 95.982500 55 2680 4 chr2B.!!$F1 2625
5 TraesCS2D01G385700 chr2B 574690049 574690882 833 False 608.000000 680 95.616000 2668 3436 2 chr2B.!!$F2 768
6 TraesCS2D01G385700 chr2B 575136707 575142651 5944 False 472.000000 850 85.088000 1 3436 5 chr2B.!!$F4 3435
7 TraesCS2D01G385700 chr2B 574035539 574040394 4855 True 201.775000 344 85.563000 439 3277 4 chr2B.!!$R2 2838
8 TraesCS2D01G385700 chr2A 634106468 634110016 3548 False 1915.666667 2841 96.772333 1 3436 3 chr2A.!!$F1 3435
9 TraesCS2D01G385700 chr2A 634606317 634609797 3480 False 613.200000 1243 85.647400 1 3286 5 chr2A.!!$F2 3285
10 TraesCS2D01G385700 chrUn 259669458 259671365 1907 True 437.000000 508 80.838500 962 2247 2 chrUn.!!$R1 1285

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
591 682 2.579787 CGTTAGGACTCAGCGCGG 60.580 66.667 8.83 0.0 0.0 6.46 F
1641 3156 3.001026 TGTGTTGCGCAAATTTTCATGTG 59.999 39.130 26.87 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 4490 1.685355 AACTGGTTGGGTTTGCTGGC 61.685 55.0 0.0 0.0 0.0 4.85 R
3301 8594 1.731720 ATTCTTCTTCAGGAGCACGC 58.268 50.0 0.0 0.0 0.0 5.34 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
137 138 3.316308 CACCCAAGTTTGAGTCTTTGGAG 59.684 47.826 14.03 8.98 33.63 3.86
138 139 3.053619 ACCCAAGTTTGAGTCTTTGGAGT 60.054 43.478 14.03 9.39 33.63 3.85
140 141 4.402474 CCCAAGTTTGAGTCTTTGGAGTTT 59.598 41.667 14.03 0.00 31.83 2.66
141 142 5.592688 CCCAAGTTTGAGTCTTTGGAGTTTA 59.407 40.000 14.03 0.00 31.83 2.01
281 292 6.439636 TCCATTCCCTATTTGGTCTCATAG 57.560 41.667 0.00 0.00 0.00 2.23
436 524 6.149474 AGGTAGTTTTTGATGGAATTGAGACG 59.851 38.462 0.00 0.00 0.00 4.18
485 576 7.762159 TGTTTGACGATGCACTATTTATGAGTA 59.238 33.333 0.00 0.00 0.00 2.59
591 682 2.579787 CGTTAGGACTCAGCGCGG 60.580 66.667 8.83 0.00 0.00 6.46
1309 2714 4.949856 ACATCTTTGGAATTATTGCGACCT 59.050 37.500 0.00 0.00 0.00 3.85
1325 2730 3.857052 CGACCTCATGGCTAAAGTAACA 58.143 45.455 0.00 0.00 36.63 2.41
1641 3156 3.001026 TGTGTTGCGCAAATTTTCATGTG 59.999 39.130 26.87 0.00 0.00 3.21
1927 4093 4.248058 GGGAGTGCAAAATCAAATTCCTG 58.752 43.478 0.00 0.00 0.00 3.86
2090 4428 9.302345 CACTGATTCTTACATGTCGTACTATTT 57.698 33.333 0.00 0.00 0.00 1.40
2150 4490 4.659922 CGAAACAAGTACGTGTAGAAAGCG 60.660 45.833 14.94 8.68 0.00 4.68
2362 7218 0.679640 TTGTTAATGGAGGCAGCCCG 60.680 55.000 8.22 0.00 35.76 6.13
2506 7399 6.377327 AAATCATGGCATAAACCTAGTTCG 57.623 37.500 0.00 0.00 0.00 3.95
2512 7405 4.155280 TGGCATAAACCTAGTTCGCTTTTC 59.845 41.667 0.00 0.00 0.00 2.29
2518 7411 2.223377 ACCTAGTTCGCTTTTCGCAAAG 59.777 45.455 2.96 2.96 42.26 2.77
2665 7830 3.768757 TCCCTAACAAATGGCCAATTCTG 59.231 43.478 10.96 7.39 0.00 3.02
2703 7872 9.031537 CATTTTCCCTTATTTGGTTAGTTAGGT 57.968 33.333 0.00 0.00 0.00 3.08
2727 7896 5.527214 TCAACTGAATTTACTGACCTGTGTG 59.473 40.000 0.00 0.00 0.00 3.82
2747 7916 4.192317 GTGCCTAACAATCTACTCCCTTG 58.808 47.826 0.00 0.00 0.00 3.61
2864 8034 8.956426 TCACAAACAGAATTACAGAAGAGTTTT 58.044 29.630 0.00 0.00 0.00 2.43
3002 8174 5.163499 GCTGATGCTACCAGAAACTAGTAGT 60.163 44.000 0.00 0.00 36.64 2.73
3071 8255 5.723295 AGTTTGCTCAGCTTTTTCTTTCAA 58.277 33.333 0.00 0.00 0.00 2.69
3140 8425 1.969923 CAGCCTTTGGATGGGAAAACA 59.030 47.619 0.00 0.00 35.19 2.83
3227 8520 5.298777 GGATCTAGCTGCTGTTGAATTTGAT 59.701 40.000 13.43 2.24 0.00 2.57
3358 8662 6.479001 GGCTCGATTTATACAGAAAACTAGCA 59.521 38.462 0.00 0.00 33.95 3.49
3436 8742 9.663904 TGATAACGAAAAGAAACAAGAAAGATG 57.336 29.630 0.00 0.00 0.00 2.90
3437 8743 9.878599 GATAACGAAAAGAAACAAGAAAGATGA 57.121 29.630 0.00 0.00 0.00 2.92
3438 8744 9.884465 ATAACGAAAAGAAACAAGAAAGATGAG 57.116 29.630 0.00 0.00 0.00 2.90
3439 8745 7.321745 ACGAAAAGAAACAAGAAAGATGAGT 57.678 32.000 0.00 0.00 0.00 3.41
3440 8746 7.410485 ACGAAAAGAAACAAGAAAGATGAGTC 58.590 34.615 0.00 0.00 0.00 3.36
3441 8747 7.065803 ACGAAAAGAAACAAGAAAGATGAGTCA 59.934 33.333 0.00 0.00 0.00 3.41
3442 8748 7.910162 CGAAAAGAAACAAGAAAGATGAGTCAA 59.090 33.333 0.00 0.00 0.00 3.18
3443 8749 9.573133 GAAAAGAAACAAGAAAGATGAGTCAAA 57.427 29.630 0.00 0.00 0.00 2.69
3447 8753 9.342308 AGAAACAAGAAAGATGAGTCAAATACA 57.658 29.630 0.00 0.00 0.00 2.29
3450 8756 8.853077 ACAAGAAAGATGAGTCAAATACATCA 57.147 30.769 0.00 0.00 41.64 3.07
3451 8757 8.725148 ACAAGAAAGATGAGTCAAATACATCAC 58.275 33.333 0.00 0.00 41.64 3.06
3452 8758 8.724229 CAAGAAAGATGAGTCAAATACATCACA 58.276 33.333 0.00 0.00 41.64 3.58
3453 8759 8.489990 AGAAAGATGAGTCAAATACATCACAG 57.510 34.615 0.00 0.00 41.64 3.66
3454 8760 7.551974 AGAAAGATGAGTCAAATACATCACAGG 59.448 37.037 0.00 0.00 41.64 4.00
3455 8761 6.305272 AGATGAGTCAAATACATCACAGGT 57.695 37.500 0.00 0.00 41.64 4.00
3456 8762 7.423844 AGATGAGTCAAATACATCACAGGTA 57.576 36.000 0.00 0.00 41.64 3.08
3457 8763 7.268586 AGATGAGTCAAATACATCACAGGTAC 58.731 38.462 0.00 0.00 41.64 3.34
3458 8764 5.730550 TGAGTCAAATACATCACAGGTACC 58.269 41.667 2.73 2.73 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.768215 ATTTAGGAAGGAATGATGAAGGTTTTA 57.232 29.630 0.00 0.00 0.00 1.52
137 138 1.468736 CGTACCCAGCGAGGTCTAAAC 60.469 57.143 3.76 0.00 41.58 2.01
138 139 0.813184 CGTACCCAGCGAGGTCTAAA 59.187 55.000 3.76 0.00 41.58 1.85
140 141 2.117156 GCGTACCCAGCGAGGTCTA 61.117 63.158 3.76 0.00 41.58 2.59
141 142 3.450115 GCGTACCCAGCGAGGTCT 61.450 66.667 3.76 0.00 41.58 3.85
281 292 0.988678 AGAGGCCATGGTAGGAACCC 60.989 60.000 14.67 3.72 46.16 4.11
502 593 6.629182 GTATTCAACGGACAACTCTCTTAC 57.371 41.667 0.00 0.00 0.00 2.34
591 682 2.407428 GGGCTAGGCTTCGCAAACC 61.407 63.158 16.80 0.00 0.00 3.27
611 702 5.624159 CCATTCCTGAATTCACATAGGCTA 58.376 41.667 3.38 0.00 0.00 3.93
1309 2714 7.637631 TGCATAAATGTTACTTTAGCCATGA 57.362 32.000 0.00 0.00 0.00 3.07
1927 4093 8.675705 ATTATGGCAAATAAAATAAACCTGCC 57.324 30.769 3.24 3.24 46.44 4.85
2150 4490 1.685355 AACTGGTTGGGTTTGCTGGC 61.685 55.000 0.00 0.00 0.00 4.85
2362 7218 6.480320 AGCGTGATCTTTAACAGGTCAATATC 59.520 38.462 0.00 0.00 44.78 1.63
2512 7405 6.236017 TGTGAACTAGTTTTATCCTTTGCG 57.764 37.500 10.02 0.00 0.00 4.85
2518 7411 5.930569 ACTCCGTTGTGAACTAGTTTTATCC 59.069 40.000 10.02 0.00 0.00 2.59
2703 7872 5.527214 CACACAGGTCAGTAAATTCAGTTGA 59.473 40.000 0.00 0.00 0.00 3.18
2727 7896 3.118223 AGCAAGGGAGTAGATTGTTAGGC 60.118 47.826 0.00 0.00 0.00 3.93
2747 7916 4.214437 GTGATGCGCAATATTCTACAAGC 58.786 43.478 17.11 0.00 0.00 4.01
2864 8034 2.416747 CACCTCAATCGAGAAAGCACA 58.583 47.619 0.00 0.00 42.34 4.57
3071 8255 3.134574 TGACCGCATAAACCTTCTGTT 57.865 42.857 0.00 0.00 39.43 3.16
3182 8475 6.140303 TCCCAGATGTAAACAGACGTATAC 57.860 41.667 0.00 0.00 0.00 1.47
3301 8594 1.731720 ATTCTTCTTCAGGAGCACGC 58.268 50.000 0.00 0.00 0.00 5.34
3358 8662 4.331968 TCATCCCTTGTATGCTTTTTCGT 58.668 39.130 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.