Multiple sequence alignment - TraesCS1A01G127700

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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 TraesCS1A01G127700 chr1A 100.000 1960 0 0 1 1960 155140587 155138628 0 3620
1 TraesCS1A01G127700 chr1A 100.000 576 0 0 2295 2870 155138293 155137718 0 1064
2 TraesCS1A01G127700 chr5A 97.704 1960 41 4 1 1960 331884482 331882527 0 3367
3 TraesCS1A01G127700 chr5A 96.028 579 19 3 2295 2870 331882154 331881577 0 939


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 TraesCS1A01G127700 chr1A 155137718 155140587 2869 True 2342 3620 100.000 1 2870 2 chr1A.!!$R1 2869
1 TraesCS1A01G127700 chr5A 331881577 331884482 2905 True 2153 3367 96.866 1 2870 2 chr5A.!!$R1 2869

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
602 603 0.036732 TCTGGGTCATCCACAAGTGC 59.963 55.0 0.0 0.0 41.46 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2384 2425 0.464554 TGACATTGGAACGCACCACA 60.465 50.0 0.54 0.0 39.85 4.17 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
42 43 6.376299 CCATACCATCCCATAATCATCAACAG 59.624 42.308 0.00 0.00 0.00 3.16
50 51 6.384015 TCCCATAATCATCAACAGTAGTCACT 59.616 38.462 0.00 0.00 34.42 3.41
82 83 1.252215 TACGATTCAGGCACGGGTGA 61.252 55.000 2.38 0.00 0.00 4.02
190 191 0.732571 CATTCGCACCGCAATAACCT 59.267 50.000 0.00 0.00 0.00 3.50
191 192 0.732571 ATTCGCACCGCAATAACCTG 59.267 50.000 0.00 0.00 0.00 4.00
331 332 4.037446 TGGCCAGAGTTTTTATGAACACAC 59.963 41.667 0.00 0.00 31.94 3.82
398 399 2.045926 GCTGGTTCCGTGCCATCT 60.046 61.111 0.00 0.00 35.19 2.90
447 448 4.900635 ATAAAGGATTGGTTTGCTAGCG 57.099 40.909 10.77 0.00 0.00 4.26
476 477 7.013464 GCAGAGTGTACATTGTCTAGGTAGTAT 59.987 40.741 0.00 0.00 0.00 2.12
530 531 3.421919 TCAGATCACCAATTGTGCTCA 57.578 42.857 4.43 0.00 45.03 4.26
542 543 0.897621 TGTGCTCATCAGACGGTCAT 59.102 50.000 11.27 0.00 0.00 3.06
602 603 0.036732 TCTGGGTCATCCACAAGTGC 59.963 55.000 0.00 0.00 41.46 4.40
624 625 4.506625 GCCCAAGGCTAATATACATGACCA 60.507 45.833 0.00 0.00 46.69 4.02
751 752 2.190488 GAACCTGGGCTGAGGTGGAG 62.190 65.000 9.16 0.00 46.29 3.86
757 758 1.004745 TGGGCTGAGGTGGAGAAAATC 59.995 52.381 0.00 0.00 0.00 2.17
775 776 1.361204 TCCATGGAGCCAGACTTTGA 58.639 50.000 11.44 0.00 0.00 2.69
808 809 5.807011 CAGCCACTTGCCAGTTTTATTTATC 59.193 40.000 0.00 0.00 42.71 1.75
977 978 7.195374 AGCTAACAACAATTAGGTCTATCCA 57.805 36.000 0.00 0.00 38.23 3.41
979 980 7.048512 GCTAACAACAATTAGGTCTATCCAGT 58.951 38.462 0.00 0.00 39.02 4.00
1016 1017 5.327732 AGATCCCATGTCATTCAAAGTTGT 58.672 37.500 0.00 0.00 0.00 3.32
1020 1021 6.484288 TCCCATGTCATTCAAAGTTGTATCT 58.516 36.000 0.00 0.00 0.00 1.98
1022 1023 7.031372 CCCATGTCATTCAAAGTTGTATCTTG 58.969 38.462 0.00 0.00 0.00 3.02
1047 1048 7.876068 TGTCGTATGGTTAGTTCATCTCTTTTT 59.124 33.333 0.00 0.00 0.00 1.94
1085 1086 4.090588 CCTAAAGGCACGCCCGGA 62.091 66.667 0.73 0.00 39.21 5.14
1259 1260 2.885135 TACCGTTCTAGACCCACTCA 57.115 50.000 0.00 0.00 0.00 3.41
1377 1378 1.886542 CTCCAACTGGCCCTACAAAAC 59.113 52.381 0.00 0.00 34.44 2.43
1616 1617 7.545615 ACTTTCTTATCCAAAATTTTCGATGGC 59.454 33.333 18.00 0.00 32.87 4.40
1662 1663 1.280710 AGGTACGCCCATCACAATCAA 59.719 47.619 0.00 0.00 34.66 2.57
1668 1669 2.019984 GCCCATCACAATCAAGACTCC 58.980 52.381 0.00 0.00 0.00 3.85
1717 1718 3.969117 TTTATCATCCAGCATGAACGC 57.031 42.857 0.00 0.00 45.06 4.84
1780 1781 2.439960 TTGCACCGACACACCCTCT 61.440 57.895 0.00 0.00 0.00 3.69
1827 1828 1.037579 ACATCTCGCTCGTCCCATCA 61.038 55.000 0.00 0.00 0.00 3.07
1932 1933 2.972505 CGCGAAGGCACCACAACT 60.973 61.111 0.00 0.00 39.92 3.16
1942 1943 2.351350 GGCACCACAACTGATTTTACGG 60.351 50.000 0.00 0.00 0.00 4.02
2350 2389 1.164411 CATTCTTGTTGCACCCGCTA 58.836 50.000 0.00 0.00 39.64 4.26
2361 2400 2.234168 TGCACCCGCTATGTTAGTTGTA 59.766 45.455 0.00 0.00 39.64 2.41
2367 2408 6.092944 CACCCGCTATGTTAGTTGTATTTTCA 59.907 38.462 0.00 0.00 0.00 2.69
2399 2440 1.271652 TGGTATGTGGTGCGTTCCAAT 60.272 47.619 2.55 2.96 39.34 3.16
2418 2459 6.612741 TCCAATGTCAATATCCATGATCCAA 58.387 36.000 0.00 0.00 0.00 3.53
2482 2523 2.033141 GCTGAAGCTCCCTGTGCA 59.967 61.111 0.00 0.00 38.21 4.57
2508 2549 2.520968 GTTGCAAGTGGGGAGGGT 59.479 61.111 0.00 0.00 0.00 4.34
2538 2579 6.965500 CATGAATGTCATTGTTCTAGCAGAAC 59.035 38.462 17.11 17.11 43.69 3.01
2586 2627 3.136443 TCACCAGTGTCCATGAAAGAAGT 59.864 43.478 0.00 0.00 0.00 3.01
2647 2688 8.696374 TCCAATGTTTACCACAATGTCTTTTTA 58.304 29.630 0.00 0.00 39.50 1.52
2648 2689 8.760569 CCAATGTTTACCACAATGTCTTTTTAC 58.239 33.333 0.00 0.00 39.50 2.01
2686 2728 0.543277 AGCATTTGAGCTCGGGATCA 59.457 50.000 0.00 0.00 42.18 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.247676 TGTTGATGATTATGGGATGGTATGG 58.752 40.000 0.00 0.00 0.00 2.74
82 83 9.125026 GGATACATATTCTCTTCATGTTTGGTT 57.875 33.333 0.00 0.00 34.78 3.67
149 150 5.488341 TGACTTGTCTTCCCTTTGCTATAC 58.512 41.667 2.35 0.00 0.00 1.47
190 191 0.677414 TTCAGCGCATGAAGCATCCA 60.677 50.000 11.47 0.00 43.09 3.41
191 192 2.100846 TTCAGCGCATGAAGCATCC 58.899 52.632 11.47 0.00 43.09 3.51
331 332 3.118482 TCCAGCTAGCAGGATTTTCTCAG 60.118 47.826 23.85 0.00 0.00 3.35
398 399 3.372730 GCAATTGCTGACGGGGCA 61.373 61.111 23.21 0.00 38.21 5.36
447 448 2.693069 AGACAATGTACACTCTGCTGC 58.307 47.619 0.00 0.00 0.00 5.25
602 603 5.241403 TGGTCATGTATATTAGCCTTGGG 57.759 43.478 0.00 0.00 0.00 4.12
624 625 0.473755 TGGTCAGCAATGTGTGTCCT 59.526 50.000 0.00 0.00 0.00 3.85
656 657 3.448660 ACATCTCATGACTCATCGGTTGA 59.551 43.478 0.00 0.00 0.00 3.18
751 752 3.010200 AGTCTGGCTCCATGGATTTTC 57.990 47.619 16.63 5.90 0.00 2.29
757 758 2.022195 CATCAAAGTCTGGCTCCATGG 58.978 52.381 4.97 4.97 0.00 3.66
775 776 1.614317 GGCAAGTGGCTGGTCTTACAT 60.614 52.381 0.00 0.00 44.01 2.29
808 809 5.760253 AGCATTGAAAACCGATGGAGTATAG 59.240 40.000 0.00 0.00 37.18 1.31
939 940 2.139118 GTTAGCTCTCCATCGGCAATC 58.861 52.381 0.00 0.00 0.00 2.67
977 978 5.324409 TGGGATCTTGCTTGAATTGTTACT 58.676 37.500 0.00 0.00 0.00 2.24
979 980 5.716228 ACATGGGATCTTGCTTGAATTGTTA 59.284 36.000 0.00 0.00 0.00 2.41
1016 1017 8.234136 AGATGAACTAACCATACGACAAGATA 57.766 34.615 0.00 0.00 0.00 1.98
1020 1021 6.525578 AGAGATGAACTAACCATACGACAA 57.474 37.500 0.00 0.00 0.00 3.18
1022 1023 7.829378 AAAAGAGATGAACTAACCATACGAC 57.171 36.000 0.00 0.00 0.00 4.34
1047 1048 3.886505 GGGTTGGTAAGAACACATGTCAA 59.113 43.478 0.00 0.00 0.00 3.18
1085 1086 3.636764 GGTGGTCAAAAACATGAGAGGTT 59.363 43.478 0.00 0.00 0.00 3.50
1259 1260 1.238439 CTGAAACCAGTCGTGCCAAT 58.762 50.000 0.00 0.00 0.00 3.16
1377 1378 1.912043 AGTCCCTGGTCCATCTTTCTG 59.088 52.381 0.00 0.00 0.00 3.02
1454 1455 2.094390 TCTACATAGGTGACCGTGCAAC 60.094 50.000 9.47 0.00 0.00 4.17
1662 1663 2.299326 AATGGCTGCAAAAGGAGTCT 57.701 45.000 0.50 0.00 0.00 3.24
1749 1750 1.269051 CGGTGCAACTCCAAGTTTTCC 60.269 52.381 0.00 0.00 36.03 3.13
1932 1933 4.821260 ACATGCTGATATGCCGTAAAATCA 59.179 37.500 0.00 0.00 0.00 2.57
2361 2400 9.859427 CACATACCATACAGAAATTGTGAAAAT 57.141 29.630 0.00 0.00 41.10 1.82
2367 2408 5.125417 GCACCACATACCATACAGAAATTGT 59.875 40.000 0.00 0.00 43.96 2.71
2375 2416 2.623535 GAACGCACCACATACCATACA 58.376 47.619 0.00 0.00 0.00 2.29
2384 2425 0.464554 TGACATTGGAACGCACCACA 60.465 50.000 0.54 0.00 39.85 4.17
2399 2440 4.768448 GCCATTGGATCATGGATATTGACA 59.232 41.667 14.72 0.00 40.30 3.58
2441 2482 1.996898 AGCGCAAACATCATGCATTTG 59.003 42.857 11.47 0.19 44.01 2.32
2482 2523 1.533753 CACTTGCAACCCACCCCAT 60.534 57.895 0.00 0.00 0.00 4.00
2508 2549 2.234896 ACAATGACATTCATGGCCCA 57.765 45.000 0.00 0.00 37.15 5.36
2544 2585 5.702209 GGTGAAAGATTTTCATTGTGGCAAT 59.298 36.000 7.42 0.00 0.00 3.56
2603 2644 1.552254 GGAATCAAGGGGGAAAAGGCA 60.552 52.381 0.00 0.00 0.00 4.75
2647 2688 9.632638 AAATGCTACCTGATGTGAATAATTAGT 57.367 29.630 0.00 0.00 0.00 2.24
2648 2689 9.888878 CAAATGCTACCTGATGTGAATAATTAG 57.111 33.333 0.00 0.00 0.00 1.73
2686 2728 5.047590 AGCGATTTACCGAAAAAGGGATTTT 60.048 36.000 0.00 0.00 43.85 1.82
2698 2740 2.431419 TGGGTAATCAGCGATTTACCGA 59.569 45.455 7.91 2.25 33.95 4.69
2701 2743 2.876550 GGGTGGGTAATCAGCGATTTAC 59.123 50.000 8.65 3.81 36.14 2.01


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

AutoCloner maintained by Alex Coulton.