Multiple sequence alignment - TraesCS7D01G441300

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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 TraesCS7D01G441300 chr7D 100.000 2489 0 0 1 2489 560828482 560825994 0.000000e+00 4597.0
1 TraesCS7D01G441300 chr3D 95.232 2517 87 14 1 2489 305617886 305615375 0.000000e+00 3952.0
2 TraesCS7D01G441300 chr6D 91.959 2537 138 43 1 2489 257991963 257994481 0.000000e+00 3494.0
3 TraesCS7D01G441300 chr6D 93.523 2146 102 21 375 2489 305380477 305378338 0.000000e+00 3158.0
4 TraesCS7D01G441300 chr6D 93.238 1464 65 17 1049 2485 356212709 356211253 0.000000e+00 2124.0
5 TraesCS7D01G441300 chr5D 91.782 2531 156 32 1 2489 36561896 36564416 0.000000e+00 3474.0
6 TraesCS7D01G441300 chr5A 92.292 2478 134 29 1 2436 671452809 671455271 0.000000e+00 3465.0
7 TraesCS7D01G441300 chr2D 91.452 2527 147 42 10 2489 630081731 630079227 0.000000e+00 3406.0
8 TraesCS7D01G441300 chr2D 90.324 2284 159 40 1 2238 87947924 87950191 0.000000e+00 2937.0
9 TraesCS7D01G441300 chr2D 94.000 50 3 0 281 330 630081491 630081442 2.650000e-10 76.8
10 TraesCS7D01G441300 chr1B 89.461 2524 197 30 1 2485 476681239 476683732 0.000000e+00 3123.0
11 TraesCS7D01G441300 chr4B 88.337 2555 193 50 1 2489 15516580 15519095 0.000000e+00 2970.0
12 TraesCS7D01G441300 chr2B 88.132 2553 202 45 1 2489 655694299 655691784 0.000000e+00 2942.0
13 TraesCS7D01G441300 chr7A 93.920 1694 71 12 823 2489 635190800 635189112 0.000000e+00 2529.0
14 TraesCS7D01G441300 chr7A 90.006 1551 109 28 1 1526 130747134 130745605 0.000000e+00 1964.0
15 TraesCS7D01G441300 chr3B 93.175 1641 83 12 877 2489 16284912 16286551 0.000000e+00 2383.0
16 TraesCS7D01G441300 chr1D 93.207 1104 45 10 1411 2489 383349528 383348430 0.000000e+00 1596.0
17 TraesCS7D01G441300 chr1D 88.046 962 86 24 1 941 383359657 383358704 0.000000e+00 1112.0
18 TraesCS7D01G441300 chr1D 96.000 50 2 0 281 330 383359407 383359358 5.710000e-12 82.4
19 TraesCS7D01G441300 chr6B 92.403 803 36 10 1710 2489 470853369 470854169 0.000000e+00 1122.0
20 TraesCS7D01G441300 chr6B 86.992 492 47 11 1 490 161332830 161332354 2.820000e-149 538.0
21 TraesCS7D01G441300 chr3A 87.593 669 52 24 1 648 669776048 669775390 0.000000e+00 747.0


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 TraesCS7D01G441300 chr7D 560825994 560828482 2488 True 4597.0 4597 100.000 1 2489 1 chr7D.!!$R1 2488
1 TraesCS7D01G441300 chr3D 305615375 305617886 2511 True 3952.0 3952 95.232 1 2489 1 chr3D.!!$R1 2488
2 TraesCS7D01G441300 chr6D 257991963 257994481 2518 False 3494.0 3494 91.959 1 2489 1 chr6D.!!$F1 2488
3 TraesCS7D01G441300 chr6D 305378338 305380477 2139 True 3158.0 3158 93.523 375 2489 1 chr6D.!!$R1 2114
4 TraesCS7D01G441300 chr6D 356211253 356212709 1456 True 2124.0 2124 93.238 1049 2485 1 chr6D.!!$R2 1436
5 TraesCS7D01G441300 chr5D 36561896 36564416 2520 False 3474.0 3474 91.782 1 2489 1 chr5D.!!$F1 2488
6 TraesCS7D01G441300 chr5A 671452809 671455271 2462 False 3465.0 3465 92.292 1 2436 1 chr5A.!!$F1 2435
7 TraesCS7D01G441300 chr2D 87947924 87950191 2267 False 2937.0 2937 90.324 1 2238 1 chr2D.!!$F1 2237
8 TraesCS7D01G441300 chr2D 630079227 630081731 2504 True 1741.4 3406 92.726 10 2489 2 chr2D.!!$R1 2479
9 TraesCS7D01G441300 chr1B 476681239 476683732 2493 False 3123.0 3123 89.461 1 2485 1 chr1B.!!$F1 2484
10 TraesCS7D01G441300 chr4B 15516580 15519095 2515 False 2970.0 2970 88.337 1 2489 1 chr4B.!!$F1 2488
11 TraesCS7D01G441300 chr2B 655691784 655694299 2515 True 2942.0 2942 88.132 1 2489 1 chr2B.!!$R1 2488
12 TraesCS7D01G441300 chr7A 635189112 635190800 1688 True 2529.0 2529 93.920 823 2489 1 chr7A.!!$R2 1666
13 TraesCS7D01G441300 chr7A 130745605 130747134 1529 True 1964.0 1964 90.006 1 1526 1 chr7A.!!$R1 1525
14 TraesCS7D01G441300 chr3B 16284912 16286551 1639 False 2383.0 2383 93.175 877 2489 1 chr3B.!!$F1 1612
15 TraesCS7D01G441300 chr1D 383348430 383349528 1098 True 1596.0 1596 93.207 1411 2489 1 chr1D.!!$R1 1078
16 TraesCS7D01G441300 chr1D 383358704 383359657 953 True 597.2 1112 92.023 1 941 2 chr1D.!!$R2 940
17 TraesCS7D01G441300 chr6B 470853369 470854169 800 False 1122.0 1122 92.403 1710 2489 1 chr6B.!!$F1 779
18 TraesCS7D01G441300 chr3A 669775390 669776048 658 True 747.0 747 87.593 1 648 1 chr3A.!!$R1 647

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
385 462 1.447317 CGACCATGCCCATAACTGCC 61.447 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1793 4.226846 ACCTCCCATCTGCCATCTATTATG 59.773 45.833 0.0 0.0 0.0 1.9 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
126 142 3.009916 AGCATATCCTTCACCATGATCCC 59.990 47.826 0.00 0.00 0.00 3.85
234 252 7.525526 GCCATATACCAACAACTATCTCAGCTA 60.526 40.741 0.00 0.00 0.00 3.32
273 292 8.705810 TCAACCAATTGTGCAAAAATGGAAACA 61.706 33.333 27.31 7.76 40.18 2.83
385 462 1.447317 CGACCATGCCCATAACTGCC 61.447 60.000 0.00 0.00 0.00 4.85
428 508 6.939163 ACACAAAACATGCTCTATTCTCTCTT 59.061 34.615 0.00 0.00 0.00 2.85
465 546 7.587037 ATTCCATTCTGAAGACACTTCAAAA 57.413 32.000 13.78 8.71 0.00 2.44
801 899 2.664916 CTTGCATGTGTTTAGTGTGGC 58.335 47.619 0.00 0.00 0.00 5.01
846 944 9.471084 GCTAACTTGCTTTAATTTTTCTGGTTA 57.529 29.630 0.00 0.00 0.00 2.85
1047 1148 9.135189 CCAGATGAAAATAATGGTGATCCTTTA 57.865 33.333 0.00 0.00 37.61 1.85
1087 1188 3.321396 TGCTGGAAATGCAGAATTTGTGA 59.679 39.130 6.08 0.00 38.64 3.58
1294 1407 3.158676 GTTGGTAATGGTTTGGGTGCTA 58.841 45.455 0.00 0.00 0.00 3.49
1395 1508 7.637968 AAGGAGCACTACAATGCATATTCCTTA 60.638 37.037 14.07 0.00 46.59 2.69
1449 1562 4.226394 TCAAGGAAGGATATGAAAACCGGA 59.774 41.667 9.46 0.00 0.00 5.14
1530 1643 1.064979 GGGGCAGAAAAGATTCCCGTA 60.065 52.381 0.00 0.00 37.85 4.02
1627 1740 3.899980 AGGCAAAAAGAGGAGCAAGAAAT 59.100 39.130 0.00 0.00 0.00 2.17
1633 1746 7.517893 GCAAAAAGAGGAGCAAGAAATGAAAAG 60.518 37.037 0.00 0.00 0.00 2.27
1680 1793 5.702865 TGCAAAGCTAAGATGATTGTGAAC 58.297 37.500 0.00 0.00 0.00 3.18
1681 1794 5.241285 TGCAAAGCTAAGATGATTGTGAACA 59.759 36.000 0.00 0.00 0.00 3.18
1919 2060 2.357154 GGCCCATCAACAACTACCTGAT 60.357 50.000 0.00 0.00 0.00 2.90
2048 2197 0.253044 TGGATGCTGGACTTGCCTAC 59.747 55.000 0.00 0.00 37.63 3.18
2093 2249 4.009675 TGCAAATTCCTACTTGCCTAGTG 58.990 43.478 4.48 0.00 45.92 2.74
2098 2258 6.819397 AATTCCTACTTGCCTAGTGTTTTC 57.181 37.500 0.00 0.00 37.73 2.29
2101 2262 5.245531 TCCTACTTGCCTAGTGTTTTCATG 58.754 41.667 0.00 0.00 37.73 3.07
2102 2263 5.003804 CCTACTTGCCTAGTGTTTTCATGT 58.996 41.667 0.00 0.00 37.73 3.21
2103 2264 4.836125 ACTTGCCTAGTGTTTTCATGTG 57.164 40.909 0.00 0.00 35.19 3.21
2104 2265 4.207165 ACTTGCCTAGTGTTTTCATGTGT 58.793 39.130 0.00 0.00 35.19 3.72
2108 2269 6.701145 TGCCTAGTGTTTTCATGTGTAAAA 57.299 33.333 0.00 0.00 0.00 1.52
2271 2448 7.427895 GGTTTGTTTTGTGTATTTTGTTCATGC 59.572 33.333 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 252 5.163733 ACAATTGGTTGAAGTAACGTTTCGT 60.164 36.000 5.91 0.0 40.28 3.85
273 292 5.297776 GGCTATGCTCACTATGTTCAATGTT 59.702 40.000 0.00 0.0 0.00 2.71
465 546 2.697751 CTCCTGCCATAGAAGTGCTACT 59.302 50.000 0.00 0.0 0.00 2.57
604 697 9.768662 GCAATATATTTTTCAGGAAATCCATGT 57.231 29.630 1.67 0.0 38.89 3.21
801 899 3.959573 GCTTATTGAGGCAAGCTAGTG 57.040 47.619 0.00 0.0 43.07 2.74
993 1094 8.222637 TCCTCATTCAGGTCAATCATTATCAAT 58.777 33.333 0.00 0.0 43.95 2.57
998 1099 6.122277 GGTTCCTCATTCAGGTCAATCATTA 58.878 40.000 0.00 0.0 43.95 1.90
1087 1188 1.137697 GGGGGATTAGGTGATTCCGT 58.862 55.000 0.00 0.0 41.99 4.69
1294 1407 6.161381 GTGACCAAGCTTCATCATCATTTTT 58.839 36.000 11.39 0.0 0.00 1.94
1395 1508 5.885449 TTTTGATTGAAAACCCCATCTGT 57.115 34.783 0.00 0.0 0.00 3.41
1530 1643 4.394300 GCTTGCTCAACAATGTCATCTAGT 59.606 41.667 0.00 0.0 37.72 2.57
1627 1740 8.203485 AGTTTGCACAATTTTATCTCCTTTTCA 58.797 29.630 0.00 0.0 0.00 2.69
1633 1746 5.783111 ACCAGTTTGCACAATTTTATCTCC 58.217 37.500 0.00 0.0 0.00 3.71
1680 1793 4.226846 ACCTCCCATCTGCCATCTATTATG 59.773 45.833 0.00 0.0 0.00 1.90
1681 1794 4.226846 CACCTCCCATCTGCCATCTATTAT 59.773 45.833 0.00 0.0 0.00 1.28
1919 2060 5.477510 ACAGTCACATGTTTCAAGCAAAAA 58.522 33.333 0.00 0.0 0.00 1.94
2009 2154 7.470424 GCATCCAGAAACAAATCAGGCATTATA 60.470 37.037 0.00 0.0 0.00 0.98
2048 2197 4.630894 TGAGCAACAAACAGGTAAACAG 57.369 40.909 0.00 0.0 0.00 3.16
2108 2269 7.682021 GCAAGTCTAGAGTCAACACCAATTTTT 60.682 37.037 0.00 0.0 0.00 1.94
2112 2273 4.319177 GCAAGTCTAGAGTCAACACCAAT 58.681 43.478 0.00 0.0 0.00 3.16


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

AutoCloner maintained by Alex Coulton.