Multiple sequence alignment - TraesCS3A01G282400

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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 TraesCS3A01G282400 chr3A 100.000 2645 0 0 1 2645 510832340 510829696 0.000000e+00 4885
1 TraesCS3A01G282400 chr3B 93.675 1913 83 11 763 2645 507499331 507497427 0.000000e+00 2828
2 TraesCS3A01G282400 chr3B 91.223 319 23 5 1 318 507500617 507500303 1.880000e-116 429
3 TraesCS3A01G282400 chr3B 87.861 173 15 3 481 653 507500299 507500133 5.770000e-47 198
4 TraesCS3A01G282400 chr3B 89.683 126 10 2 645 767 507499488 507499363 9.800000e-35 158
5 TraesCS3A01G282400 chr3D 92.147 955 39 10 763 1681 390414500 390413546 0.000000e+00 1315
6 TraesCS3A01G282400 chr3D 91.322 991 40 17 1674 2645 390413165 390412202 0.000000e+00 1312
7 TraesCS3A01G282400 chr3D 90.390 770 65 5 1 767 390415295 390414532 0.000000e+00 1003
8 TraesCS3A01G282400 chr5B 78.857 350 44 14 194 541 354981067 354981388 2.670000e-50 209


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 TraesCS3A01G282400 chr3A 510829696 510832340 2644 True 4885.00 4885 100.000000 1 2645 1 chr3A.!!$R1 2644
1 TraesCS3A01G282400 chr3B 507497427 507500617 3190 True 903.25 2828 90.610500 1 2645 4 chr3B.!!$R1 2644
2 TraesCS3A01G282400 chr3D 390412202 390415295 3093 True 1210.00 1315 91.286333 1 2645 3 chr3D.!!$R1 2644

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
603 604 0.033109 TCCTAGCAGTAGCAGGAGCA 60.033 55.0 0.0 0.0 45.49 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 3660 0.390472 GAGCAGGTTCCTCAAGACCG 60.39 60.0 0.0 0.0 40.89 4.79 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
27 28 8.024285 TGTTTGTAAAATCGGGCATTTAACTAG 58.976 33.333 0.00 0.00 33.16 2.57
36 37 4.371855 GGCATTTAACTAGTTTCAGCCC 57.628 45.455 14.49 6.04 33.68 5.19
52 53 1.486726 AGCCCACAATCTACCAGTAGC 59.513 52.381 0.00 0.00 33.32 3.58
94 95 9.339492 GCTCTTTCAGATTTACATTTCAGAAAG 57.661 33.333 1.28 9.99 42.32 2.62
139 140 2.169330 AGTGACGAGGTTCTTACCCTC 58.831 52.381 0.00 0.00 46.28 4.30
206 207 9.691362 AAACTTACATTATTTGTTTGCGAAGAT 57.309 25.926 0.00 0.00 39.87 2.40
242 243 7.863722 AGGACTTGAGTACATAGAGAGTAAGA 58.136 38.462 0.00 0.00 0.00 2.10
243 244 7.990886 AGGACTTGAGTACATAGAGAGTAAGAG 59.009 40.741 0.00 0.00 0.00 2.85
325 326 2.972713 ACAAGTCTCTAAAGCCCAGTCA 59.027 45.455 0.00 0.00 0.00 3.41
342 343 4.397417 CCAGTCATCCATCTTTCTTTGGTC 59.603 45.833 0.00 0.00 34.48 4.02
344 345 5.709164 CAGTCATCCATCTTTCTTTGGTCTT 59.291 40.000 0.00 0.00 34.48 3.01
357 358 3.374042 TTGGTCTTGTTGGTTTCTCCA 57.626 42.857 0.00 0.00 45.60 3.86
376 377 2.423373 CCAATCCGATCCAATGGACCTT 60.423 50.000 3.09 0.00 37.02 3.50
396 397 8.023706 GGACCTTGTTCTCTTTATCAATTTGAC 58.976 37.037 0.15 0.00 0.00 3.18
398 399 8.571336 ACCTTGTTCTCTTTATCAATTTGACTG 58.429 33.333 0.15 0.00 0.00 3.51
406 407 7.453393 TCTTTATCAATTTGACTGACTCCACT 58.547 34.615 0.15 0.00 0.00 4.00
409 410 4.569943 TCAATTTGACTGACTCCACTAGC 58.430 43.478 0.00 0.00 0.00 3.42
412 413 3.876274 TTGACTGACTCCACTAGCATC 57.124 47.619 0.00 0.00 0.00 3.91
501 502 5.222316 TGGCATATAAAGGGATGGCTTATGT 60.222 40.000 9.44 0.00 46.05 2.29
502 503 5.358160 GGCATATAAAGGGATGGCTTATGTC 59.642 44.000 1.55 0.00 43.38 3.06
536 537 6.096673 TGTTTTAATCCTTTTTCCAGCCTC 57.903 37.500 0.00 0.00 0.00 4.70
551 552 3.006110 CCAGCCTCTGATGAGAATCTCTC 59.994 52.174 11.92 7.20 42.73 3.20
562 563 7.772166 TGATGAGAATCTCTCGCTAAAGTTTA 58.228 34.615 11.92 0.00 46.25 2.01
570 571 1.076332 CGCTAAAGTTTAGCCGCAGT 58.924 50.000 32.03 0.00 37.26 4.40
603 604 0.033109 TCCTAGCAGTAGCAGGAGCA 60.033 55.000 0.00 0.00 45.49 4.26
606 607 0.176680 TAGCAGTAGCAGGAGCAAGC 59.823 55.000 0.00 0.00 45.49 4.01
632 633 2.352960 GGCAAAGAGAAGATGGCTTACG 59.647 50.000 0.00 0.00 36.76 3.18
665 1319 4.152938 GCATTGCAGATTTTGGTTCCTTTC 59.847 41.667 3.15 0.00 0.00 2.62
674 1328 0.323629 TGGTTCCTTTCAGCCTACCG 59.676 55.000 0.00 0.00 0.00 4.02
676 1330 1.079405 TTCCTTTCAGCCTACCGCG 60.079 57.895 0.00 0.00 44.76 6.46
685 1339 0.462047 AGCCTACCGCGATTTTCAGG 60.462 55.000 8.23 5.46 44.76 3.86
719 1373 3.084786 AGCCGAAAATCCTTGAAAGAGG 58.915 45.455 0.00 0.00 38.20 3.69
729 1386 1.795286 CTTGAAAGAGGAGTGCGTGTC 59.205 52.381 0.00 0.00 0.00 3.67
739 1396 0.528466 AGTGCGTGTCATATGAGGCG 60.528 55.000 18.91 18.91 0.00 5.52
740 1397 0.806102 GTGCGTGTCATATGAGGCGT 60.806 55.000 22.02 0.00 0.00 5.68
846 1539 6.371809 AAGTTTCAGTTCTTGCATTAACGA 57.628 33.333 0.00 4.82 0.00 3.85
847 1540 5.990408 AGTTTCAGTTCTTGCATTAACGAG 58.010 37.500 0.00 4.31 0.00 4.18
848 1541 5.527582 AGTTTCAGTTCTTGCATTAACGAGT 59.472 36.000 0.00 0.00 0.00 4.18
853 1546 6.365247 TCAGTTCTTGCATTAACGAGTAGTTC 59.635 38.462 0.00 0.00 43.06 3.01
857 1553 8.373992 GTTCTTGCATTAACGAGTAGTTCTAAG 58.626 37.037 0.00 0.00 43.06 2.18
946 1650 3.837731 TCACACATCACCTGAACCAGATA 59.162 43.478 0.00 0.00 32.44 1.98
952 1656 2.906389 TCACCTGAACCAGATAGCAAGT 59.094 45.455 0.00 0.00 32.44 3.16
1036 1740 1.512926 CACTTTGGTGTCCCTTCTCG 58.487 55.000 0.00 0.00 38.54 4.04
1177 1899 2.986979 TGCACGCCTCCGACTACA 60.987 61.111 0.00 0.00 38.29 2.74
1274 1996 1.226746 GTCGGAAGGTTGGTTGTGAG 58.773 55.000 0.00 0.00 0.00 3.51
1351 2073 7.102993 TCTTAGGTGATCGATGACATTTTTGA 58.897 34.615 16.93 4.36 0.00 2.69
1359 2081 7.751793 TGATCGATGACATTTTTGATGTTTCTG 59.248 33.333 0.54 0.00 31.52 3.02
1454 2176 0.037326 TCAAGCGGACCAGTTAGCAG 60.037 55.000 0.00 0.00 0.00 4.24
1485 2208 4.339247 CGGCTGATTATCCACCAATTTCTT 59.661 41.667 0.00 0.00 0.00 2.52
1504 2227 4.686972 TCTTCCGTTAGATGCATTCAGAG 58.313 43.478 0.00 0.00 0.00 3.35
1523 2246 1.444119 GAGCTGGTGTCGGTTTTGCA 61.444 55.000 0.00 0.00 0.00 4.08
1525 2248 0.031994 GCTGGTGTCGGTTTTGCATT 59.968 50.000 0.00 0.00 0.00 3.56
1670 2425 6.891908 AGATCAAATGTTTACCCAACTGCTAT 59.108 34.615 0.00 0.00 36.21 2.97
1753 2897 6.937436 AGTTTGTACTGTACCCTGAAAAAG 57.063 37.500 14.91 0.00 31.99 2.27
1755 2899 7.114095 AGTTTGTACTGTACCCTGAAAAAGAA 58.886 34.615 14.91 0.00 31.99 2.52
1772 2923 2.797491 AGAAAACGCTTGCAAGTTCAC 58.203 42.857 26.55 9.80 0.00 3.18
1785 2937 4.819088 TGCAAGTTCACAGCAAATAGTACA 59.181 37.500 0.00 0.00 34.97 2.90
1814 2979 2.799126 ATGAATAAAGCACCACCGGA 57.201 45.000 9.46 0.00 0.00 5.14
1856 3021 8.371699 AGAAAGTTCTACTTCATGTCTAAGCTT 58.628 33.333 3.48 3.48 37.47 3.74
1877 3042 2.196742 TGATATCTGAGGGCCCTGTT 57.803 50.000 34.59 13.76 0.00 3.16
1910 3075 1.668419 CAGATTTTCGGTAGCCCAGG 58.332 55.000 0.00 0.00 0.00 4.45
1929 3094 5.464168 CCAGGTGATCTGATTTGTTTGAAC 58.536 41.667 0.00 0.00 46.18 3.18
1939 3104 6.030548 TGATTTGTTTGAACCACAGTCAAA 57.969 33.333 0.00 0.00 37.33 2.69
1970 3136 5.733655 GCAATTTCCTCTGATTCATGCTCAG 60.734 44.000 15.30 15.30 41.23 3.35
2022 3188 0.176680 CAGACGGCAGAGCTATGGTT 59.823 55.000 10.92 0.00 0.00 3.67
2030 3196 2.012673 CAGAGCTATGGTTGGTTGAGC 58.987 52.381 0.00 0.00 0.00 4.26
2222 3391 9.005777 AGTCGCTATAAGAAAACCACAATAAAA 57.994 29.630 0.00 0.00 0.00 1.52
2268 3437 6.382570 ACTCTATGCAGATAACAGACTCCTTT 59.617 38.462 0.00 0.00 0.00 3.11
2513 3682 0.979665 TCTTGAGGAACCTGCTCCTG 59.020 55.000 0.00 0.00 46.33 3.86
2516 3685 2.530151 AGGAACCTGCTCCTGCCA 60.530 61.111 0.00 0.00 44.56 4.92
2611 3780 0.617935 TCCATGCAAGGAACGGATGA 59.382 50.000 8.54 0.00 33.93 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.499004 AGATTGTGGGCTGAAACTAGTTA 57.501 39.130 8.92 0.00 0.00 2.24
27 28 2.749621 CTGGTAGATTGTGGGCTGAAAC 59.250 50.000 0.00 0.00 0.00 2.78
36 37 2.348666 GCAACGCTACTGGTAGATTGTG 59.651 50.000 11.44 4.92 35.24 3.33
139 140 0.395862 TAGAAGAGCCACCTCCCGAG 60.396 60.000 0.00 0.00 38.96 4.63
182 183 9.691362 AAATCTTCGCAAACAAATAATGTAAGT 57.309 25.926 0.00 0.00 42.99 2.24
186 187 6.399880 CGCAAATCTTCGCAAACAAATAATGT 60.400 34.615 0.00 0.00 46.82 2.71
200 201 1.464608 TCCTTTCAGCGCAAATCTTCG 59.535 47.619 11.47 0.00 0.00 3.79
205 206 2.227388 CTCAAGTCCTTTCAGCGCAAAT 59.773 45.455 11.47 0.00 0.00 2.32
206 207 1.603802 CTCAAGTCCTTTCAGCGCAAA 59.396 47.619 11.47 0.56 0.00 3.68
242 243 5.061179 AGGCACGAAAAAGTACACATAACT 58.939 37.500 0.00 0.00 0.00 2.24
243 244 5.352643 AGGCACGAAAAAGTACACATAAC 57.647 39.130 0.00 0.00 0.00 1.89
286 287 6.712547 AGACTTGTACTCTTCCAAATTTCCAG 59.287 38.462 0.00 0.00 0.00 3.86
325 326 5.244626 CCAACAAGACCAAAGAAAGATGGAT 59.755 40.000 0.00 0.00 39.12 3.41
357 358 2.242196 ACAAGGTCCATTGGATCGGATT 59.758 45.455 9.01 0.00 38.00 3.01
362 363 4.227864 AGAGAACAAGGTCCATTGGATC 57.772 45.455 9.01 8.48 32.73 3.36
376 377 8.908786 AGTCAGTCAAATTGATAAAGAGAACA 57.091 30.769 0.00 0.00 0.00 3.18
396 397 2.223688 CGGAAGATGCTAGTGGAGTCAG 60.224 54.545 0.00 0.00 0.00 3.51
398 399 2.025155 TCGGAAGATGCTAGTGGAGTC 58.975 52.381 0.00 0.00 33.31 3.36
412 413 5.052481 TGCTATCAGTTCAATGATCGGAAG 58.948 41.667 0.00 0.87 40.40 3.46
453 454 1.030457 CCATGGCCTGCTTTGATCTC 58.970 55.000 3.32 0.00 0.00 2.75
455 456 1.440476 GCCATGGCCTGCTTTGATC 59.560 57.895 27.24 0.00 34.56 2.92
474 475 2.762327 GCCATCCCTTTATATGCCATGG 59.238 50.000 7.63 7.63 33.72 3.66
501 502 4.947388 AGGATTAAAACATAAAGGCAGCGA 59.053 37.500 0.00 0.00 0.00 4.93
502 503 5.248870 AGGATTAAAACATAAAGGCAGCG 57.751 39.130 0.00 0.00 0.00 5.18
536 537 5.830912 ACTTTAGCGAGAGATTCTCATCAG 58.169 41.667 15.83 5.18 43.55 2.90
551 552 1.076332 ACTGCGGCTAAACTTTAGCG 58.924 50.000 21.85 18.28 41.24 4.26
593 594 1.144716 CGATGGCTTGCTCCTGCTA 59.855 57.895 0.00 0.00 40.48 3.49
594 595 2.124819 CGATGGCTTGCTCCTGCT 60.125 61.111 0.00 0.00 40.48 4.24
595 596 3.207669 CCGATGGCTTGCTCCTGC 61.208 66.667 0.00 0.00 40.20 4.85
606 607 1.945394 CCATCTTCTCTTTGCCGATGG 59.055 52.381 0.00 0.00 43.42 3.51
665 1319 0.652592 CTGAAAATCGCGGTAGGCTG 59.347 55.000 6.13 0.00 40.44 4.85
674 1328 3.740321 TGTTGCAAAATCCTGAAAATCGC 59.260 39.130 0.00 0.00 0.00 4.58
676 1330 6.036408 GGCTATGTTGCAAAATCCTGAAAATC 59.964 38.462 5.08 0.00 34.04 2.17
685 1339 5.005682 GGATTTTCGGCTATGTTGCAAAATC 59.994 40.000 5.08 5.11 40.57 2.17
719 1373 1.212616 GCCTCATATGACACGCACTC 58.787 55.000 0.00 0.00 0.00 3.51
846 1539 2.748532 ACTTCGAGCGCTTAGAACTACT 59.251 45.455 20.50 5.70 0.00 2.57
847 1540 3.134021 ACTTCGAGCGCTTAGAACTAC 57.866 47.619 20.50 2.19 0.00 2.73
848 1541 4.952262 TTACTTCGAGCGCTTAGAACTA 57.048 40.909 20.50 14.71 0.00 2.24
853 1546 2.027688 CGGTTTTACTTCGAGCGCTTAG 59.972 50.000 13.26 12.44 0.00 2.18
857 1553 0.365859 CTCGGTTTTACTTCGAGCGC 59.634 55.000 0.00 0.00 42.70 5.92
878 1574 3.629142 AGGGTGATAGCCAGTTACAAC 57.371 47.619 0.00 0.00 38.48 3.32
952 1656 0.106769 TCTGCCTTTCACTTGCACCA 60.107 50.000 0.00 0.00 0.00 4.17
1036 1740 1.385528 GAGAGGAGGAAGAGGACGAC 58.614 60.000 0.00 0.00 0.00 4.34
1177 1899 4.684703 GCTGACAAAGACTATGTACACGTT 59.315 41.667 0.00 0.00 0.00 3.99
1274 1996 1.938625 AATGTTGCTTGCCACACAAC 58.061 45.000 1.62 2.78 43.10 3.32
1351 2073 0.957395 CCTCCGTGCTGCAGAAACAT 60.957 55.000 20.43 0.00 0.00 2.71
1359 2081 4.704833 TTGCCTCCTCCGTGCTGC 62.705 66.667 0.00 0.00 0.00 5.25
1454 2176 1.560860 GATAATCAGCCGCGCTCACC 61.561 60.000 5.56 0.00 36.40 4.02
1485 2208 3.491619 GCTCTCTGAATGCATCTAACGGA 60.492 47.826 0.00 2.35 0.00 4.69
1504 2227 1.282875 GCAAAACCGACACCAGCTC 59.717 57.895 0.00 0.00 0.00 4.09
1546 2298 1.676967 CCTCCTTCCCTGCACAAGC 60.677 63.158 0.00 0.00 42.57 4.01
1670 2425 3.319689 TGACATGTTTCAGGTCGTAGTGA 59.680 43.478 0.00 0.00 46.33 3.41
1753 2897 2.525055 TGTGAACTTGCAAGCGTTTTC 58.475 42.857 26.27 20.65 0.00 2.29
1755 2899 1.798813 GCTGTGAACTTGCAAGCGTTT 60.799 47.619 26.27 13.28 0.00 3.60
1772 2923 8.849168 TCATTATTTCCCATGTACTATTTGCTG 58.151 33.333 0.00 0.00 0.00 4.41
1785 2937 7.418942 GGTGGTGCTTTATTCATTATTTCCCAT 60.419 37.037 0.00 0.00 0.00 4.00
1814 2979 8.174733 AGAACTTTCTGAATCATTTGTCACAT 57.825 30.769 0.00 0.00 35.89 3.21
1856 3021 3.567375 ACAGGGCCCTCAGATATCATA 57.433 47.619 25.77 0.00 0.00 2.15
1900 3065 1.428869 ATCAGATCACCTGGGCTACC 58.571 55.000 0.00 0.00 43.12 3.18
1910 3075 5.830912 TGTGGTTCAAACAAATCAGATCAC 58.169 37.500 0.00 0.00 0.00 3.06
1929 3094 6.293027 GGAAATTGCTGAAAATTTGACTGTGG 60.293 38.462 0.00 0.00 39.31 4.17
1939 3104 7.235935 TGAATCAGAGGAAATTGCTGAAAAT 57.764 32.000 0.00 0.00 41.48 1.82
2011 3177 1.912043 AGCTCAACCAACCATAGCTCT 59.088 47.619 0.00 0.00 39.23 4.09
2030 3196 0.440371 GGCTCGTCGCTTTCTTCAAG 59.560 55.000 0.00 0.00 39.13 3.02
2118 3284 1.020437 GCTGAAGCATAGGGAGTTGC 58.980 55.000 0.00 0.00 41.59 4.17
2222 3391 6.546034 AGAGTTGGCACACTTAAGTTACATTT 59.454 34.615 5.07 0.00 39.29 2.32
2312 3481 4.200838 TCATGAGTTCAGCCATAACGAA 57.799 40.909 0.00 0.00 32.00 3.85
2491 3660 0.390472 GAGCAGGTTCCTCAAGACCG 60.390 60.000 0.00 0.00 40.89 4.79
2516 3685 2.450476 GACATGGCCAAGTTCCTTCAT 58.550 47.619 15.98 0.00 0.00 2.57
2611 3780 3.300765 GGTCGTGGGACGTCCTGT 61.301 66.667 32.52 0.00 44.36 4.00


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

AutoCloner maintained by Alex Coulton.