Multiple sequence alignment - TraesCS1B01G394800

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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 TraesCS1B01G394800 chr1B 100.000 3509 0 0 1 3509 626679912 626683420 0.000000e+00 6481.0
1 TraesCS1B01G394800 chr1B 95.444 2480 112 1 865 3343 384665385 384662906 0.000000e+00 3952.0
2 TraesCS1B01G394800 chr1B 90.110 455 43 2 865 1318 625178867 625179320 1.080000e-164 590.0
3 TraesCS1B01G394800 chr1B 97.268 183 5 0 3327 3509 384661009 384660827 9.460000e-81 311.0
4 TraesCS1B01G394800 chr1B 94.340 53 2 1 814 866 626667909 626667960 2.900000e-11 80.5
5 TraesCS1B01G394800 chr1A 94.264 2493 119 9 864 3334 471876023 471873533 0.000000e+00 3790.0
6 TraesCS1B01G394800 chr1A 94.274 2218 103 11 1138 3334 471940112 471937898 0.000000e+00 3371.0
7 TraesCS1B01G394800 chr1A 90.054 744 45 12 13 744 549707537 549708263 0.000000e+00 937.0
8 TraesCS1B01G394800 chr1A 97.268 183 5 0 3327 3509 471871598 471871416 9.460000e-81 311.0
9 TraesCS1B01G394800 chr6B 93.398 2363 131 12 1004 3343 22661897 22664257 0.000000e+00 3476.0
10 TraesCS1B01G394800 chr6B 91.868 2484 183 7 865 3343 620652608 620650139 0.000000e+00 3450.0
11 TraesCS1B01G394800 chr6B 93.060 2075 131 4 1270 3343 503528420 503526358 0.000000e+00 3022.0
12 TraesCS1B01G394800 chr6B 93.012 2075 132 4 1270 3343 12737008 12734946 0.000000e+00 3016.0
13 TraesCS1B01G394800 chr6B 98.333 180 3 0 3327 3506 22666081 22666260 2.030000e-82 316.0
14 TraesCS1B01G394800 chr6B 94.652 187 9 1 3323 3509 12733045 12732860 4.430000e-74 289.0
15 TraesCS1B01G394800 chr6B 94.652 187 9 1 3323 3509 503524455 503524270 4.430000e-74 289.0
16 TraesCS1B01G394800 chr3A 93.756 2082 116 4 1263 3343 308699368 308697300 0.000000e+00 3112.0
17 TraesCS1B01G394800 chr3A 90.969 454 38 1 865 1318 308699797 308699347 3.000000e-170 608.0
18 TraesCS1B01G394800 chr5B 93.340 2072 125 3 1263 3334 37393684 37395742 0.000000e+00 3049.0
19 TraesCS1B01G394800 chr5B 93.022 2078 132 4 1267 3343 23880861 23882926 0.000000e+00 3022.0
20 TraesCS1B01G394800 chr5B 90.088 454 45 0 865 1318 37393252 37393705 1.080000e-164 590.0
21 TraesCS1B01G394800 chr5B 95.109 184 8 1 3323 3506 562367950 562368132 4.430000e-74 289.0
22 TraesCS1B01G394800 chr2A 92.974 2078 133 4 1267 3343 7962856 7964921 0.000000e+00 3016.0
23 TraesCS1B01G394800 chr7A 91.894 2122 156 5 859 2979 1132650 1134756 0.000000e+00 2952.0
24 TraesCS1B01G394800 chr5A 91.308 1162 77 15 864 2002 7023174 7022014 0.000000e+00 1565.0
25 TraesCS1B01G394800 chr6A 91.611 453 38 0 866 1318 38407541 38407993 8.270000e-176 627.0
26 TraesCS1B01G394800 chr6A 95.652 184 7 1 3323 3506 70162311 70162493 9.530000e-76 294.0
27 TraesCS1B01G394800 chr1D 80.317 630 56 34 286 866 457068764 457069374 7.010000e-112 414.0
28 TraesCS1B01G394800 chr1D 85.870 276 31 5 3 277 457067070 457067338 1.590000e-73 287.0
29 TraesCS1B01G394800 chr1D 96.078 51 2 0 815 865 457063857 457063907 2.240000e-12 84.2
30 TraesCS1B01G394800 chr2B 96.739 184 5 1 3323 3506 775411560 775411742 4.400000e-79 305.0
31 TraesCS1B01G394800 chr3B 95.187 187 8 1 3323 3509 169244495 169244310 9.530000e-76 294.0


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 TraesCS1B01G394800 chr1B 626679912 626683420 3508 False 6481.000000 6481 100.000000 1 3509 1 chr1B.!!$F3 3508
1 TraesCS1B01G394800 chr1B 384660827 384665385 4558 True 2131.500000 3952 96.356000 865 3509 2 chr1B.!!$R1 2644
2 TraesCS1B01G394800 chr1A 471937898 471940112 2214 True 3371.000000 3371 94.274000 1138 3334 1 chr1A.!!$R1 2196
3 TraesCS1B01G394800 chr1A 471871416 471876023 4607 True 2050.500000 3790 95.766000 864 3509 2 chr1A.!!$R2 2645
4 TraesCS1B01G394800 chr1A 549707537 549708263 726 False 937.000000 937 90.054000 13 744 1 chr1A.!!$F1 731
5 TraesCS1B01G394800 chr6B 620650139 620652608 2469 True 3450.000000 3450 91.868000 865 3343 1 chr6B.!!$R1 2478
6 TraesCS1B01G394800 chr6B 22661897 22666260 4363 False 1896.000000 3476 95.865500 1004 3506 2 chr6B.!!$F1 2502
7 TraesCS1B01G394800 chr6B 503524270 503528420 4150 True 1655.500000 3022 93.856000 1270 3509 2 chr6B.!!$R3 2239
8 TraesCS1B01G394800 chr6B 12732860 12737008 4148 True 1652.500000 3016 93.832000 1270 3509 2 chr6B.!!$R2 2239
9 TraesCS1B01G394800 chr3A 308697300 308699797 2497 True 1860.000000 3112 92.362500 865 3343 2 chr3A.!!$R1 2478
10 TraesCS1B01G394800 chr5B 23880861 23882926 2065 False 3022.000000 3022 93.022000 1267 3343 1 chr5B.!!$F1 2076
11 TraesCS1B01G394800 chr5B 37393252 37395742 2490 False 1819.500000 3049 91.714000 865 3334 2 chr5B.!!$F3 2469
12 TraesCS1B01G394800 chr2A 7962856 7964921 2065 False 3016.000000 3016 92.974000 1267 3343 1 chr2A.!!$F1 2076
13 TraesCS1B01G394800 chr7A 1132650 1134756 2106 False 2952.000000 2952 91.894000 859 2979 1 chr7A.!!$F1 2120
14 TraesCS1B01G394800 chr5A 7022014 7023174 1160 True 1565.000000 1565 91.308000 864 2002 1 chr5A.!!$R1 1138
15 TraesCS1B01G394800 chr1D 457063857 457069374 5517 False 261.733333 414 87.421667 3 866 3 chr1D.!!$F1 863

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
249 3461 0.036164 CTTCCACCCCGTGTTGATCA 59.964 55.0 0.0 0.0 0.0 2.92 F
250 3462 0.036164 TTCCACCCCGTGTTGATCAG 59.964 55.0 0.0 0.0 0.0 2.90 F
1999 6776 0.809241 GCTCCTTGACCTCAGCATCG 60.809 60.0 0.0 0.0 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 6419 0.450583 AGATGCGCGAAGTAGAACGA 59.549 50.000 12.10 0.0 0.00 3.85 R
2149 6926 1.271102 GAGCTCACGAGGTTCAAGAGT 59.729 52.381 9.40 0.0 39.57 3.24 R
3071 7850 1.205655 GCTGACAGGCATCACAGACTA 59.794 52.381 4.26 0.0 32.90 2.59 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
64 3276 2.986728 ACAAGGAACCTAACCACCTCAT 59.013 45.455 0.00 0.00 31.89 2.90
65 3277 4.019681 CACAAGGAACCTAACCACCTCATA 60.020 45.833 0.00 0.00 31.89 2.15
73 3285 4.220821 ACCTAACCACCTCATATATGCTCG 59.779 45.833 7.92 0.51 0.00 5.03
249 3461 0.036164 CTTCCACCCCGTGTTGATCA 59.964 55.000 0.00 0.00 0.00 2.92
250 3462 0.036164 TTCCACCCCGTGTTGATCAG 59.964 55.000 0.00 0.00 0.00 2.90
279 3497 1.940613 ACTCGACCTGCAAGTTTTCAC 59.059 47.619 0.00 0.00 0.00 3.18
288 4922 4.441913 CCTGCAAGTTTTCACAAATGAGGT 60.442 41.667 0.00 0.00 35.83 3.85
299 4933 4.154015 TCACAAATGAGGTTGAAGTATGCG 59.846 41.667 0.00 0.00 32.59 4.73
313 4947 5.129815 TGAAGTATGCGGGTTATTTCCTACT 59.870 40.000 0.00 0.00 0.00 2.57
314 4948 5.625568 AGTATGCGGGTTATTTCCTACTT 57.374 39.130 0.00 0.00 0.00 2.24
315 4949 6.736110 AGTATGCGGGTTATTTCCTACTTA 57.264 37.500 0.00 0.00 0.00 2.24
316 4950 7.128234 AGTATGCGGGTTATTTCCTACTTAA 57.872 36.000 0.00 0.00 0.00 1.85
374 5008 1.313812 ACTCTAGGACTTGACCGGCG 61.314 60.000 0.00 0.00 34.73 6.46
381 5015 1.566018 GACTTGACCGGCGGAAACTG 61.566 60.000 35.78 19.43 0.00 3.16
401 5040 1.802337 GCGAACCCCTGTGTTTTCCC 61.802 60.000 0.00 0.00 0.00 3.97
417 5056 2.478872 TCCCTAGCTAGGAGCACAAT 57.521 50.000 36.80 0.00 46.63 2.71
425 5072 2.349886 GCTAGGAGCACAATCTGAAACG 59.650 50.000 0.00 0.00 41.89 3.60
565 5246 2.032377 CCGAATGTAAACGTGTGCAAGT 60.032 45.455 0.00 0.00 0.00 3.16
566 5247 3.547214 CCGAATGTAAACGTGTGCAAGTT 60.547 43.478 0.00 0.00 34.60 2.66
577 5259 3.425625 CGTGTGCAAGTTAATGGCGTTAT 60.426 43.478 0.00 0.00 0.00 1.89
629 5315 4.976116 CGTGTTCATTTTTGTTTCTCTCCC 59.024 41.667 0.00 0.00 0.00 4.30
632 5318 5.660864 TGTTCATTTTTGTTTCTCTCCCCTT 59.339 36.000 0.00 0.00 0.00 3.95
633 5319 5.789643 TCATTTTTGTTTCTCTCCCCTTG 57.210 39.130 0.00 0.00 0.00 3.61
634 5320 4.039124 TCATTTTTGTTTCTCTCCCCTTGC 59.961 41.667 0.00 0.00 0.00 4.01
647 5333 1.273327 CCCCTTGCGCAAAGAAAGAAT 59.727 47.619 25.01 0.00 37.73 2.40
648 5334 2.599659 CCCTTGCGCAAAGAAAGAATC 58.400 47.619 25.01 0.00 37.73 2.52
678 5364 9.231297 TGTTCTTTGATTATTAGACAAGGAAGG 57.769 33.333 0.00 0.00 39.14 3.46
722 5408 8.417176 GTGTTCGACAATGTTAAAAATGTGATC 58.583 33.333 0.00 0.00 0.00 2.92
744 5434 5.909477 TCACAACTTTAGACGAGAAAAGGA 58.091 37.500 11.00 0.01 37.09 3.36
980 5678 2.264005 TATGGGTGTCGTGCAGTTTT 57.736 45.000 0.00 0.00 0.00 2.43
1091 5793 2.126071 CGTCACGCCGAATCCTGT 60.126 61.111 0.00 0.00 0.00 4.00
1359 6094 4.476752 GCCCCGTACGGATTGCCA 62.477 66.667 35.41 0.00 37.50 4.92
1714 6491 2.979676 CATGGCGTGCACAGGTGT 60.980 61.111 18.64 0.00 0.00 4.16
1770 6547 2.484062 CGATGGTTCCCTGCCATGC 61.484 63.158 1.16 0.00 45.87 4.06
1817 6594 2.037620 GCATGGGTCGCTCAGGATCT 62.038 60.000 0.00 0.00 0.00 2.75
1999 6776 0.809241 GCTCCTTGACCTCAGCATCG 60.809 60.000 0.00 0.00 0.00 3.84
2149 6926 7.243332 TGAAAATATCAATGGTCGTGACACCA 61.243 38.462 8.85 8.85 41.19 4.17
2280 7058 0.110486 GGAAGCCCTTCAAGTCACCA 59.890 55.000 9.95 0.00 41.20 4.17
2506 7284 0.465460 TGGCAAAGGCAACGAGAAGT 60.465 50.000 0.00 0.00 43.71 3.01
2783 7561 8.162085 TGTTCTTAGAGTTCCTTCTACTACTCA 58.838 37.037 0.00 0.00 39.51 3.41
3065 7844 5.825532 TCCCATTGTGTCCAATAAAGATGA 58.174 37.500 0.00 0.00 39.28 2.92
3071 7850 5.202765 TGTGTCCAATAAAGATGATGCCAT 58.797 37.500 0.00 0.00 35.29 4.40
3136 7915 0.876399 TTCGGATTCGAGTCGTGTCA 59.124 50.000 13.12 0.00 46.75 3.58
3352 10153 7.175104 ACATAAGTACTCCATGGATTTGTTGT 58.825 34.615 16.63 11.08 0.00 3.32
3401 10202 1.764723 TGCCATGACTCCTATGTCTGG 59.235 52.381 0.00 0.00 37.82 3.86
3506 10307 1.409064 GTATCTGACCATCACTCGGCA 59.591 52.381 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.055891 GGTTTATGTCTTGGGCTTTGCAT 60.056 43.478 0.00 0.00 0.00 3.96
2 3 2.298729 GGTTTATGTCTTGGGCTTTGCA 59.701 45.455 0.00 0.00 0.00 4.08
3 4 2.353704 GGGTTTATGTCTTGGGCTTTGC 60.354 50.000 0.00 0.00 0.00 3.68
6 7 2.557452 CCAGGGTTTATGTCTTGGGCTT 60.557 50.000 0.00 0.00 0.00 4.35
7 8 1.005924 CCAGGGTTTATGTCTTGGGCT 59.994 52.381 0.00 0.00 0.00 5.19
8 9 1.272480 ACCAGGGTTTATGTCTTGGGC 60.272 52.381 0.00 0.00 0.00 5.36
10 11 2.446435 CCACCAGGGTTTATGTCTTGG 58.554 52.381 0.00 0.00 0.00 3.61
64 3276 5.972935 TCAAGTGAAAGAACCGAGCATATA 58.027 37.500 0.00 0.00 0.00 0.86
65 3277 4.832248 TCAAGTGAAAGAACCGAGCATAT 58.168 39.130 0.00 0.00 0.00 1.78
73 3285 6.986231 ACCAATGAAAATCAAGTGAAAGAACC 59.014 34.615 0.00 0.00 0.00 3.62
160 3372 4.026475 CGCTCGTTGGAGAAAGAATATGAC 60.026 45.833 0.00 0.00 43.27 3.06
161 3373 4.112634 CGCTCGTTGGAGAAAGAATATGA 58.887 43.478 0.00 0.00 43.27 2.15
163 3375 3.865745 CACGCTCGTTGGAGAAAGAATAT 59.134 43.478 0.00 0.00 43.27 1.28
164 3376 3.250744 CACGCTCGTTGGAGAAAGAATA 58.749 45.455 0.00 0.00 43.27 1.75
249 3461 1.540267 CAGGTCGAGTTCACCTCTCT 58.460 55.000 0.00 0.00 42.85 3.10
250 3462 0.109039 GCAGGTCGAGTTCACCTCTC 60.109 60.000 0.00 0.00 42.85 3.20
279 3497 3.181497 CCCGCATACTTCAACCTCATTTG 60.181 47.826 0.00 0.00 0.00 2.32
288 4922 4.850680 AGGAAATAACCCGCATACTTCAA 58.149 39.130 0.00 0.00 0.00 2.69
313 4947 8.012241 GCGCCAAATAAAACATCAACAAATTAA 58.988 29.630 0.00 0.00 0.00 1.40
314 4948 7.386299 AGCGCCAAATAAAACATCAACAAATTA 59.614 29.630 2.29 0.00 0.00 1.40
315 4949 6.204495 AGCGCCAAATAAAACATCAACAAATT 59.796 30.769 2.29 0.00 0.00 1.82
316 4950 5.700373 AGCGCCAAATAAAACATCAACAAAT 59.300 32.000 2.29 0.00 0.00 2.32
330 4964 2.356135 GTCTTGGAGAAGCGCCAAATA 58.644 47.619 2.29 0.00 42.26 1.40
374 5008 1.971695 CAGGGGTTCGCCAGTTTCC 60.972 63.158 8.53 0.00 39.65 3.13
381 5015 1.658114 GAAAACACAGGGGTTCGCC 59.342 57.895 0.00 0.00 0.00 5.54
401 5040 4.662468 TTCAGATTGTGCTCCTAGCTAG 57.338 45.455 14.20 14.20 42.97 3.42
417 5056 7.103641 AGAGTCCATTATTTTAGCGTTTCAGA 58.896 34.615 0.00 0.00 0.00 3.27
498 5145 2.767445 CGCCCACGGATAGACGACA 61.767 63.158 0.00 0.00 37.61 4.35
547 5228 5.918011 CCATTAACTTGCACACGTTTACATT 59.082 36.000 0.00 0.00 0.00 2.71
595 5281 4.500703 AAATGAACACGTTCGATCGATC 57.499 40.909 20.18 17.13 42.28 3.69
596 5282 4.921470 AAAATGAACACGTTCGATCGAT 57.079 36.364 20.18 1.82 42.28 3.59
597 5283 4.025563 ACAAAAATGAACACGTTCGATCGA 60.026 37.500 21.80 15.15 42.28 3.59
629 5315 3.565905 AGATTCTTTCTTTGCGCAAGG 57.434 42.857 24.86 24.86 32.64 3.61
632 5318 3.565482 ACAGAAGATTCTTTCTTTGCGCA 59.435 39.130 5.66 5.66 44.88 6.09
633 5319 4.152607 ACAGAAGATTCTTTCTTTGCGC 57.847 40.909 0.00 0.00 44.88 6.09
634 5320 5.995055 AGAACAGAAGATTCTTTCTTTGCG 58.005 37.500 0.00 0.00 44.88 4.85
676 5362 6.947644 ACACCTTTAATAAACACGTTTCCT 57.052 33.333 0.00 0.00 34.23 3.36
677 5363 6.357766 CGAACACCTTTAATAAACACGTTTCC 59.642 38.462 0.00 0.00 34.23 3.13
678 5364 7.110628 GTCGAACACCTTTAATAAACACGTTTC 59.889 37.037 0.00 0.00 34.23 2.78
722 5408 6.598753 TTCCTTTTCTCGTCTAAAGTTGTG 57.401 37.500 0.00 0.00 31.07 3.33
744 5434 0.107897 CCATGGCTGCATGCACATTT 60.108 50.000 18.46 0.00 45.15 2.32
798 5495 0.400213 ATCTGTGTTTCCCTTCGGCA 59.600 50.000 0.00 0.00 0.00 5.69
803 5500 2.289694 CGACCTCATCTGTGTTTCCCTT 60.290 50.000 0.00 0.00 0.00 3.95
854 5551 2.249139 ACAGTCTAACAGGTGGGTCTC 58.751 52.381 0.00 0.00 0.00 3.36
932 5630 8.934697 GGGGTGTGGCTATCTCATATATATAAA 58.065 37.037 0.00 0.00 0.00 1.40
1084 5786 3.706373 AGGCGCCGTGACAGGATT 61.706 61.111 23.20 0.00 0.00 3.01
1085 5787 4.457496 CAGGCGCCGTGACAGGAT 62.457 66.667 23.20 0.00 0.00 3.24
1642 6419 0.450583 AGATGCGCGAAGTAGAACGA 59.549 50.000 12.10 0.00 0.00 3.85
1770 6547 4.489771 GGATGGTGCGGTGGAGGG 62.490 72.222 0.00 0.00 0.00 4.30
1999 6776 2.682856 TCATCTTGCCAAAATAGTCGGC 59.317 45.455 0.00 0.00 46.43 5.54
2149 6926 1.271102 GAGCTCACGAGGTTCAAGAGT 59.729 52.381 9.40 0.00 39.57 3.24
2280 7058 4.250305 ACTGACTTGCCGCCGGTT 62.250 61.111 4.45 0.00 0.00 4.44
2776 7554 9.594936 AGGAACAGATAATAAGCTATGAGTAGT 57.405 33.333 0.00 0.00 0.00 2.73
2793 7571 4.523173 TCACGAGTAAGTTGAGGAACAGAT 59.477 41.667 0.00 0.00 34.17 2.90
3065 7844 2.267174 GGCATCACAGACTATGGCAT 57.733 50.000 4.88 4.88 45.31 4.40
3071 7850 1.205655 GCTGACAGGCATCACAGACTA 59.794 52.381 4.26 0.00 32.90 2.59
3166 7945 3.781760 GGCATGCCCCCATACATG 58.218 61.111 27.24 0.00 45.19 3.21
3185 7964 6.808008 AATTATGACCACTCACAGAAGTTG 57.192 37.500 0.00 0.00 0.00 3.16
3238 8017 6.964464 TGATAAGGTAAAGCCAGGTAAATCA 58.036 36.000 0.00 0.00 40.61 2.57
3401 10202 4.928661 AATGCAGACAAACGATCAGTAC 57.071 40.909 0.00 0.00 0.00 2.73
3464 10265 2.158682 TGCAGACCACCAACAATACTGT 60.159 45.455 0.00 0.00 37.39 3.55


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

AutoCloner maintained by Alex Coulton.