Multiple sequence alignment - TraesCS7D01G382800

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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 TraesCS7D01G382800 chr7D 100.000 4340 0 0 1 4340 496721206 496716867 0.000000e+00 8015.0
1 TraesCS7D01G382800 chr7D 91.316 380 26 3 259 635 556776821 556776446 2.990000e-141 512.0
2 TraesCS7D01G382800 chr7D 90.306 392 25 10 259 646 47118629 47118247 6.480000e-138 501.0
3 TraesCS7D01G382800 chr7D 72.917 576 143 13 3772 4340 40446062 40445493 2.060000e-43 187.0
4 TraesCS7D01G382800 chr7D 90.000 50 5 0 1110 1159 467164240 467164191 1.010000e-06 65.8
5 TraesCS7D01G382800 chr7D 100.000 30 0 0 2308 2337 568199024 568198995 6.060000e-04 56.5
6 TraesCS7D01G382800 chr4D 97.827 3681 60 5 1 3673 60174853 60178521 0.000000e+00 6336.0
7 TraesCS7D01G382800 chr4D 97.720 3684 67 6 1 3673 60171154 60167477 0.000000e+00 6322.0
8 TraesCS7D01G382800 chr4D 84.416 77 8 4 3105 3179 416867087 416867161 6.020000e-09 73.1
9 TraesCS7D01G382800 chr7B 90.209 2921 152 58 635 3484 524812315 524809458 0.000000e+00 3687.0
10 TraesCS7D01G382800 chr7B 77.287 656 143 5 3676 4327 105480665 105481318 8.810000e-102 381.0
11 TraesCS7D01G382800 chr7B 90.000 50 5 0 1110 1159 490683471 490683422 1.010000e-06 65.8
12 TraesCS7D01G382800 chr7A 90.768 2318 123 28 1595 3847 561993402 561991111 0.000000e+00 3011.0
13 TraesCS7D01G382800 chr7A 91.146 960 55 15 682 1634 561994344 561993408 0.000000e+00 1275.0
14 TraesCS7D01G382800 chr7A 85.159 694 98 5 3650 4340 529253637 529252946 0.000000e+00 706.0
15 TraesCS7D01G382800 chr7A 89.726 438 43 2 3905 4340 556471634 556471197 3.790000e-155 558.0
16 TraesCS7D01G382800 chr7A 91.573 356 24 5 3838 4189 561900281 561899928 1.810000e-133 486.0
17 TraesCS7D01G382800 chr7A 90.000 50 5 0 1110 1159 533578994 533579043 1.010000e-06 65.8
18 TraesCS7D01G382800 chr6A 88.742 453 45 4 3659 4110 46291742 46292189 2.280000e-152 549.0
19 TraesCS7D01G382800 chr6B 89.398 415 42 2 3659 4071 79428265 79428679 4.970000e-144 521.0
20 TraesCS7D01G382800 chr6B 88.647 414 45 2 3659 4070 79634098 79634511 1.800000e-138 503.0
21 TraesCS7D01G382800 chr6B 85.714 455 51 8 3888 4340 78595145 78594703 6.570000e-128 468.0
22 TraesCS7D01G382800 chr6B 90.674 193 17 1 3656 3848 78596138 78595947 5.570000e-64 255.0
23 TraesCS7D01G382800 chr6B 77.027 296 59 8 4050 4340 151678096 151678387 1.250000e-35 161.0
24 TraesCS7D01G382800 chr5A 90.601 383 32 3 259 638 287583165 287582784 5.010000e-139 505.0
25 TraesCS7D01G382800 chr6D 90.933 375 30 2 264 635 27458781 27459154 6.480000e-138 501.0
26 TraesCS7D01G382800 chr3B 90.576 382 31 3 258 635 685306406 685306026 6.480000e-138 501.0
27 TraesCS7D01G382800 chr3B 72.145 578 146 14 3772 4340 24512280 24511709 1.250000e-35 161.0
28 TraesCS7D01G382800 chr3A 90.601 383 29 5 262 639 725451573 725451953 6.480000e-138 501.0
29 TraesCS7D01G382800 chr5D 90.155 386 30 7 252 634 446307680 446308060 3.010000e-136 496.0
30 TraesCS7D01G382800 chrUn 91.030 301 24 3 3659 3958 27751017 27750719 1.880000e-108 403.0
31 TraesCS7D01G382800 chr1A 80.317 315 61 1 4022 4335 61393742 61394056 2.020000e-58 237.0
32 TraesCS7D01G382800 chr5B 71.902 694 172 20 3659 4340 666132592 666131910 3.450000e-41 180.0
33 TraesCS7D01G382800 chr1B 72.023 697 165 26 3659 4340 611788813 611789494 3.450000e-41 180.0
34 TraesCS7D01G382800 chr4A 82.927 82 12 2 3111 3191 47286730 47286650 6.020000e-09 73.1
35 TraesCS7D01G382800 chr2B 95.556 45 2 0 3105 3149 504198868 504198824 6.020000e-09 73.1


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 TraesCS7D01G382800 chr7D 496716867 496721206 4339 True 8015.0 8015 100.000 1 4340 1 chr7D.!!$R4 4339
1 TraesCS7D01G382800 chr4D 60174853 60178521 3668 False 6336.0 6336 97.827 1 3673 1 chr4D.!!$F1 3672
2 TraesCS7D01G382800 chr4D 60167477 60171154 3677 True 6322.0 6322 97.720 1 3673 1 chr4D.!!$R1 3672
3 TraesCS7D01G382800 chr7B 524809458 524812315 2857 True 3687.0 3687 90.209 635 3484 1 chr7B.!!$R2 2849
4 TraesCS7D01G382800 chr7B 105480665 105481318 653 False 381.0 381 77.287 3676 4327 1 chr7B.!!$F1 651
5 TraesCS7D01G382800 chr7A 561991111 561994344 3233 True 2143.0 3011 90.957 682 3847 2 chr7A.!!$R4 3165
6 TraesCS7D01G382800 chr7A 529252946 529253637 691 True 706.0 706 85.159 3650 4340 1 chr7A.!!$R1 690
7 TraesCS7D01G382800 chr6B 78594703 78596138 1435 True 361.5 468 88.194 3656 4340 2 chr6B.!!$R1 684

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
998 1033 0.905357 CCTTCCCCGATCAGACAACT 59.095 55.000 0.0 0.0 0.0 3.16 F
1754 1860 0.988145 GATCCACCCATCCACCTCCA 60.988 60.000 0.0 0.0 0.0 3.86 F
2081 2208 1.275010 TCTGCTTCAAGACGTATGGCA 59.725 47.619 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 2382 0.241749 TACTTGTCGCGGTACACCTG 59.758 55.0 6.13 0.0 0.00 4.00 R
3235 3434 0.173481 CGCTCTTGATCACCTTCCGA 59.827 55.0 0.00 0.0 0.00 4.55 R
4001 4972 0.664166 CCGCCCAATGATAATTGCGC 60.664 55.0 0.00 0.0 40.59 6.09 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
887 922 2.539547 CGCACACAAGAAAGAACCAGTG 60.540 50.000 0.00 0.00 0.00 3.66
998 1033 0.905357 CCTTCCCCGATCAGACAACT 59.095 55.000 0.00 0.00 0.00 3.16
1108 1143 1.381872 CACTGACCTCTCCCGGGAT 60.382 63.158 27.07 9.39 0.00 3.85
1432 1478 2.943653 CAAGTGGTTTCCGGTCGC 59.056 61.111 0.00 0.00 0.00 5.19
1481 1527 1.404717 CCTTCAGGACGATGTGGACAG 60.405 57.143 0.00 0.00 37.39 3.51
1541 1587 2.098298 CTGGTCGCGCATTTTCCG 59.902 61.111 8.75 0.00 0.00 4.30
1598 1695 2.943033 CAGTTCCCTGACGTGTTTTCTT 59.057 45.455 0.00 0.00 41.50 2.52
1599 1696 3.002348 CAGTTCCCTGACGTGTTTTCTTC 59.998 47.826 0.00 0.00 41.50 2.87
1600 1697 3.118371 AGTTCCCTGACGTGTTTTCTTCT 60.118 43.478 0.00 0.00 0.00 2.85
1601 1698 3.553828 TCCCTGACGTGTTTTCTTCTT 57.446 42.857 0.00 0.00 0.00 2.52
1602 1699 3.463944 TCCCTGACGTGTTTTCTTCTTC 58.536 45.455 0.00 0.00 0.00 2.87
1603 1700 3.134081 TCCCTGACGTGTTTTCTTCTTCT 59.866 43.478 0.00 0.00 0.00 2.85
1754 1860 0.988145 GATCCACCCATCCACCTCCA 60.988 60.000 0.00 0.00 0.00 3.86
1801 1912 4.020218 TCCGTCCAAATCTCTCTGTTGAAT 60.020 41.667 0.00 0.00 0.00 2.57
1809 1920 7.930325 CCAAATCTCTCTGTTGAATAGCTGATA 59.070 37.037 0.00 0.00 0.00 2.15
2046 2173 2.463589 TTTCGCAGGCCCGACTTCAT 62.464 55.000 0.00 0.00 36.90 2.57
2077 2204 3.502920 CGACTTCTGCTTCAAGACGTAT 58.497 45.455 0.00 0.00 35.30 3.06
2081 2208 1.275010 TCTGCTTCAAGACGTATGGCA 59.725 47.619 0.00 0.00 0.00 4.92
2290 2417 1.450312 GTACCAGCGCAGGCAGAAT 60.450 57.895 20.03 0.90 43.41 2.40
2363 2490 2.046988 TGGAGGACGAGTACGCGA 60.047 61.111 25.90 0.00 43.96 5.87
2538 2692 2.363795 CTGGTGGGGTCGAGGCTA 60.364 66.667 0.00 0.00 0.00 3.93
2782 2951 1.537202 GTCCTTTCAGTTGAGCGCAAT 59.463 47.619 11.47 0.00 36.22 3.56
2987 3185 1.332195 TGATCCTCATCGGCGAGAAT 58.668 50.000 17.22 3.86 34.79 2.40
3235 3434 2.665185 GACTCCACGCGCTGGTTT 60.665 61.111 21.61 12.91 41.52 3.27
3488 3690 4.417426 AGGTAAGGTTGATATCCGGTTG 57.583 45.455 0.00 0.00 0.00 3.77
3527 3729 4.505808 CTGCCATGGTAAATTTTGCATGA 58.494 39.130 14.67 0.00 0.00 3.07
3544 3746 1.080772 GACCGCGCGATATGGATCA 60.081 57.895 34.63 0.00 31.78 2.92
3624 3831 5.701290 CGGAGTCAAAAGGAGAAACTTACAT 59.299 40.000 0.00 0.00 0.00 2.29
3699 3906 4.565236 CCCCATCAATCTCTAATCTCCTGC 60.565 50.000 0.00 0.00 0.00 4.85
3735 3943 8.195436 ACTCATTGATCCTTATGAAAGCAAATG 58.805 33.333 0.00 0.00 30.90 2.32
3789 3997 4.136796 GGACTTATATTGTGCTGCATCCA 58.863 43.478 5.27 0.00 0.00 3.41
3858 4066 8.686334 CAAATACTAATGTTAATGTGAAGGCCT 58.314 33.333 0.00 0.00 0.00 5.19
3875 4093 5.391312 AGGCCTAAATTTGTGCTTTACTG 57.609 39.130 1.29 0.00 0.00 2.74
3881 4099 9.237846 GCCTAAATTTGTGCTTTACTGAATATC 57.762 33.333 0.00 0.00 0.00 1.63
3951 4921 4.955450 TGGGGATGGATAAAACAGATTGTG 59.045 41.667 0.00 0.00 0.00 3.33
4001 4972 2.171003 GGGTGAATGGTTGGAAAGAGG 58.829 52.381 0.00 0.00 0.00 3.69
4002 4973 1.546029 GGTGAATGGTTGGAAAGAGGC 59.454 52.381 0.00 0.00 0.00 4.70
4061 5032 3.125316 GTCAGTTGCACAAGCTATACCAC 59.875 47.826 0.00 0.00 42.74 4.16
4094 5065 9.855021 CAATGTCGGTCTTTAAAATTCCTAAAT 57.145 29.630 0.00 0.00 0.00 1.40
4142 5114 0.395173 GTCGCAATATTGGTGGGGGT 60.395 55.000 17.02 0.00 0.00 4.95
4159 5131 2.158726 GGGGTACAGTGACAACCAGAAA 60.159 50.000 13.48 0.00 34.83 2.52
4189 5161 2.549082 TGGATGGCATGGTGGAAATTT 58.451 42.857 3.81 0.00 0.00 1.82
4195 5167 3.643320 TGGCATGGTGGAAATTTTGTGTA 59.357 39.130 0.00 0.00 0.00 2.90
4196 5168 4.101585 TGGCATGGTGGAAATTTTGTGTAA 59.898 37.500 0.00 0.00 0.00 2.41
4221 5194 1.005450 TGCAAAGGAGGTATGGGGTTC 59.995 52.381 0.00 0.00 0.00 3.62
4237 5210 2.232941 GGGTTCAGAGACATCCGTTGTA 59.767 50.000 0.00 0.00 39.18 2.41
4286 5259 9.554053 ACAGGCATAGAGGTTAATAGATAATCT 57.446 33.333 0.00 0.00 37.67 2.40
4302 5275 6.529220 AGATAATCTAGATTCCTTGTGTGGC 58.471 40.000 21.17 1.28 32.50 5.01
4311 5284 1.765904 TCCTTGTGTGGCACTGTTCTA 59.234 47.619 19.83 0.00 35.11 2.10
4323 5296 5.303078 TGGCACTGTTCTAAAGGCAAAATAA 59.697 36.000 0.00 0.00 0.00 1.40
4329 5302 8.094548 ACTGTTCTAAAGGCAAAATAATTTCCC 58.905 33.333 0.00 0.00 0.00 3.97
4330 5303 7.093992 TGTTCTAAAGGCAAAATAATTTCCCG 58.906 34.615 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
282 290 8.597167 CATGTTGAGATAAATAGGATAGTGGGA 58.403 37.037 0.00 0.00 0.00 4.37
317 325 0.251341 GTGGGCCTTTGATGAGGTGT 60.251 55.000 4.53 0.00 39.11 4.16
998 1033 0.956633 GTGTCGAGTGTGGTAGGTCA 59.043 55.000 0.00 0.00 0.00 4.02
1093 1128 1.152525 GCTATCCCGGGAGAGGTCA 60.153 63.158 39.03 12.91 34.37 4.02
1481 1527 3.590466 AAGCCCACCCTCACCATGC 62.590 63.158 0.00 0.00 0.00 4.06
1541 1587 1.668751 CAGGAGAGAGAGACGTACTGC 59.331 57.143 0.00 0.00 0.00 4.40
1598 1695 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1599 1696 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1600 1697 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1601 1698 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1602 1699 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1603 1700 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1754 1860 3.127548 TCGTAAATAGCTCGAGGAAACGT 59.872 43.478 15.58 0.00 34.70 3.99
1801 1912 5.508153 GCAGAGAAGGAATCGTTATCAGCTA 60.508 44.000 16.51 0.00 32.36 3.32
1809 1920 3.865745 CGTTATGCAGAGAAGGAATCGTT 59.134 43.478 0.00 0.00 0.00 3.85
1929 2040 0.248907 CACGAACACTCACACGACCT 60.249 55.000 0.00 0.00 0.00 3.85
2021 2148 2.040544 CGGGCCTGCGAAAAGATGT 61.041 57.895 0.84 0.00 0.00 3.06
2077 2204 1.527380 GTTCTTCACCCGGTTGCCA 60.527 57.895 0.00 0.00 0.00 4.92
2081 2208 0.549469 AACCAGTTCTTCACCCGGTT 59.451 50.000 0.00 0.00 37.01 4.44
2255 2382 0.241749 TACTTGTCGCGGTACACCTG 59.758 55.000 6.13 0.00 0.00 4.00
2290 2417 3.405093 GAGGATGCCGATGGTGCCA 62.405 63.158 0.00 0.00 0.00 4.92
2538 2692 3.530910 CTCCGCGGTGAAGTTGGGT 62.531 63.158 27.15 0.00 0.00 4.51
3235 3434 0.173481 CGCTCTTGATCACCTTCCGA 59.827 55.000 0.00 0.00 0.00 4.55
3488 3690 5.168526 TGGCAGCAATACGATGAATTTAC 57.831 39.130 0.00 0.00 30.38 2.01
3527 3729 0.667487 CTTGATCCATATCGCGCGGT 60.667 55.000 31.69 27.77 34.60 5.68
3699 3906 4.452825 AGGATCAATGAGTCATCTGCAAG 58.547 43.478 5.98 0.00 0.00 4.01
3735 3943 4.864704 TTAAAGTTTGGGCATTCTCCAC 57.135 40.909 0.00 0.00 33.43 4.02
3789 3997 7.671398 AGATTTATCCAAACTCACCAATTGTCT 59.329 33.333 4.43 0.00 0.00 3.41
3833 4041 8.823220 AGGCCTTCACATTAACATTAGTATTT 57.177 30.769 0.00 0.00 0.00 1.40
3875 4093 6.957984 TTGAGCGCTTCTATCATGATATTC 57.042 37.500 13.26 5.08 0.00 1.75
3881 4099 6.368243 ACTTATCATTGAGCGCTTCTATCATG 59.632 38.462 13.26 8.12 0.00 3.07
3951 4921 5.633601 TGACACGATCAATCAAGTACTGAAC 59.366 40.000 0.00 0.00 32.34 3.18
4001 4972 0.664166 CCGCCCAATGATAATTGCGC 60.664 55.000 0.00 0.00 40.59 6.09
4002 4973 0.667993 ACCGCCCAATGATAATTGCG 59.332 50.000 0.00 0.00 41.51 4.85
4061 5032 5.749596 TTAAAGACCGACATTGCATATGG 57.250 39.130 4.56 2.60 0.00 2.74
4129 5100 2.508300 GTCACTGTACCCCCACCAATAT 59.492 50.000 0.00 0.00 0.00 1.28
4142 5114 5.008613 GCATTCTTTTCTGGTTGTCACTGTA 59.991 40.000 0.00 0.00 0.00 2.74
4159 5131 2.104111 CCATGCCATCCAATGCATTCTT 59.896 45.455 9.53 0.00 45.52 2.52
4189 5161 3.882888 CCTCCTTTGCACTTCTTACACAA 59.117 43.478 0.00 0.00 0.00 3.33
4195 5167 3.562176 CCCATACCTCCTTTGCACTTCTT 60.562 47.826 0.00 0.00 0.00 2.52
4196 5168 2.025887 CCCATACCTCCTTTGCACTTCT 60.026 50.000 0.00 0.00 0.00 2.85
4221 5194 7.409697 CCAAATTAATACAACGGATGTCTCTG 58.590 38.462 0.00 0.00 42.70 3.35
4286 5259 2.371841 ACAGTGCCACACAAGGAATCTA 59.628 45.455 0.00 0.00 36.74 1.98
4293 5266 3.003689 CCTTTAGAACAGTGCCACACAAG 59.996 47.826 0.00 0.00 36.74 3.16
4302 5275 8.925700 GGAAATTATTTTGCCTTTAGAACAGTG 58.074 33.333 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.