Multiple sequence alignment - TraesCS1D01G360700

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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 TraesCS1D01G360700 chr1D 100.000 2951 0 0 1 2951 443748979 443746029 0.000000e+00 5450.0
1 TraesCS1D01G360700 chr1D 85.855 304 26 8 238 529 443485902 443486200 1.030000e-79 307.0
2 TraesCS1D01G360700 chr1D 86.592 179 21 3 1 178 443468207 443468383 8.350000e-46 195.0
3 TraesCS1D01G360700 chr1A 92.590 1714 49 26 713 2397 539703875 539702211 0.000000e+00 2390.0
4 TraesCS1D01G360700 chr1A 87.934 663 48 11 377 1025 539706227 539705583 0.000000e+00 752.0
5 TraesCS1D01G360700 chr1A 85.625 160 19 4 242 400 32994007 32993851 6.540000e-37 165.0
6 TraesCS1D01G360700 chr1A 90.756 119 10 1 2833 2951 539701925 539701808 1.090000e-34 158.0
7 TraesCS1D01G360700 chr1A 88.372 129 14 1 242 370 305001250 305001123 1.420000e-33 154.0
8 TraesCS1D01G360700 chr1A 88.000 75 8 1 1 75 539708540 539708467 1.460000e-13 87.9
9 TraesCS1D01G360700 chr1B 90.586 1211 58 33 764 1956 603219081 603217909 0.000000e+00 1554.0
10 TraesCS1D01G360700 chr1B 90.486 925 63 14 2037 2951 603217791 603216882 0.000000e+00 1197.0
11 TraesCS1D01G360700 chr1B 91.620 179 13 2 1 178 603222634 603222457 2.270000e-61 246.0
12 TraesCS1D01G360700 chr1B 86.875 160 19 2 241 399 15240606 15240764 8.400000e-41 178.0
13 TraesCS1D01G360700 chr1B 95.402 87 4 0 667 753 603221059 603220973 3.970000e-29 139.0
14 TraesCS1D01G360700 chr7D 88.679 159 16 2 242 399 60594250 60594093 3.000000e-45 193.0
15 TraesCS1D01G360700 chr2B 87.195 164 19 2 242 404 720588738 720588900 5.020000e-43 185.0
16 TraesCS1D01G360700 chr6A 85.443 158 19 3 240 397 601271924 601271771 8.460000e-36 161.0
17 TraesCS1D01G360700 chr2D 85.350 157 19 4 246 399 176564110 176563955 3.040000e-35 159.0
18 TraesCS1D01G360700 chr2A 84.177 158 20 2 247 399 71527876 71528033 6.590000e-32 148.0


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 TraesCS1D01G360700 chr1D 443746029 443748979 2950 True 5450.000 5450 100.0000 1 2951 1 chr1D.!!$R1 2950
1 TraesCS1D01G360700 chr1A 539701808 539708540 6732 True 846.975 2390 89.8200 1 2951 4 chr1A.!!$R3 2950
2 TraesCS1D01G360700 chr1B 603216882 603222634 5752 True 784.000 1554 92.0235 1 2951 4 chr1B.!!$R1 2950

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
418 3075 0.652071 CATGTTGCAGCGCGAATCTA 59.348 50.0 12.1 0.0 0.0 1.98 F
1587 7552 0.042731 AGGAAGGGGATGGAGTTCGA 59.957 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 7869 0.040336 CTCTGCATCGATGGCATTGC 60.040 55.000 26.0 14.23 41.06 3.56 R
2652 8735 1.394917 GTGACATCAACATCACCGAGC 59.605 52.381 0.0 0.00 39.49 5.03 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
30 31 1.594331 AGTTCTTCCGCTGTTCAACC 58.406 50.000 0.00 0.00 0.00 3.77
36 37 3.047877 CGCTGTTCAACCCGACCC 61.048 66.667 0.00 0.00 0.00 4.46
38 39 2.258726 GCTGTTCAACCCGACCCAC 61.259 63.158 0.00 0.00 0.00 4.61
45 46 2.763645 AACCCGACCCACAAAGGCT 61.764 57.895 0.00 0.00 35.39 4.58
128 1845 0.690762 GAAGTCACCCCAGCCAGTAA 59.309 55.000 0.00 0.00 0.00 2.24
228 1962 3.500680 GTGGCGGTGTCAGAAATTAAAGA 59.499 43.478 0.00 0.00 0.00 2.52
232 1966 5.007724 GGCGGTGTCAGAAATTAAAGATAGG 59.992 44.000 0.00 0.00 0.00 2.57
233 1967 5.007724 GCGGTGTCAGAAATTAAAGATAGGG 59.992 44.000 0.00 0.00 0.00 3.53
234 1968 6.113411 CGGTGTCAGAAATTAAAGATAGGGT 58.887 40.000 0.00 0.00 0.00 4.34
302 2313 6.912591 GCCAAACTACACTAATGCATGTATTC 59.087 38.462 12.62 0.00 31.10 1.75
381 3038 2.041265 CCAGGGCCCTAGTGGTCT 59.959 66.667 28.13 0.00 39.39 3.85
418 3075 0.652071 CATGTTGCAGCGCGAATCTA 59.348 50.000 12.10 0.00 0.00 1.98
438 3095 1.673920 ACTCGTTGTCACGCCAAATTT 59.326 42.857 0.00 0.00 46.70 1.82
602 3273 7.162082 TCTTATCCAAGACAAGAAAAGGAGAC 58.838 38.462 0.00 0.00 35.82 3.36
619 3290 3.119352 GGAGACATTCCAAACAATCAGGC 60.119 47.826 0.00 0.00 46.01 4.85
625 3296 2.302260 TCCAAACAATCAGGCGTCAAA 58.698 42.857 0.00 0.00 0.00 2.69
629 3300 3.575965 AACAATCAGGCGTCAAAATCC 57.424 42.857 0.00 0.00 0.00 3.01
631 3302 1.737236 CAATCAGGCGTCAAAATCCGA 59.263 47.619 0.00 0.00 0.00 4.55
637 3308 1.467374 GGCGTCAAAATCCGAACATGG 60.467 52.381 0.00 0.00 0.00 3.66
638 3309 1.895051 CGTCAAAATCCGAACATGGC 58.105 50.000 0.00 0.00 0.00 4.40
657 3328 6.039270 ACATGGCGCTTATTGCTTCTTTAATA 59.961 34.615 7.64 0.00 40.11 0.98
658 3329 6.060028 TGGCGCTTATTGCTTCTTTAATAG 57.940 37.500 7.64 0.00 40.11 1.73
659 3330 5.588648 TGGCGCTTATTGCTTCTTTAATAGT 59.411 36.000 7.64 0.00 40.11 2.12
702 3373 2.942804 TGAGAAACATGAAACCTGGCA 58.057 42.857 0.00 0.00 0.00 4.92
844 3559 4.436332 TCATTCGTGTCCATCTCATCAAG 58.564 43.478 0.00 0.00 0.00 3.02
853 3568 7.520453 CGTGTCCATCTCATCAAGAAAGAAAAA 60.520 37.037 0.00 0.00 37.61 1.94
911 3626 1.670406 CTGCCTTTGCTCGCTGTCT 60.670 57.895 0.00 0.00 38.71 3.41
913 3628 2.394563 GCCTTTGCTCGCTGTCTCC 61.395 63.158 0.00 0.00 33.53 3.71
927 3642 2.103143 CTCCGCTCGCCACTGTAG 59.897 66.667 0.00 0.00 0.00 2.74
970 3685 2.167281 CTCGAGCTCCCAAATCTCAGAA 59.833 50.000 8.47 0.00 0.00 3.02
981 4513 2.654749 ATCTCAGAACGAACATCGCA 57.345 45.000 0.00 0.00 45.12 5.10
983 4515 2.328473 TCTCAGAACGAACATCGCAAG 58.672 47.619 0.00 0.00 45.12 4.01
984 4516 2.061773 CTCAGAACGAACATCGCAAGT 58.938 47.619 0.00 0.00 45.12 3.16
985 4517 2.058798 TCAGAACGAACATCGCAAGTC 58.941 47.619 0.00 0.00 45.12 3.01
986 4518 1.792367 CAGAACGAACATCGCAAGTCA 59.208 47.619 0.00 0.00 45.12 3.41
1153 7116 0.854853 CGGCGTCGACAAGTACTACG 60.855 60.000 17.16 10.14 39.00 3.51
1478 7443 2.622436 CGGAGGACATTCAGAAGTTCC 58.378 52.381 0.00 5.07 0.00 3.62
1586 7551 0.466124 GAGGAAGGGGATGGAGTTCG 59.534 60.000 0.00 0.00 0.00 3.95
1587 7552 0.042731 AGGAAGGGGATGGAGTTCGA 59.957 55.000 0.00 0.00 0.00 3.71
1656 7621 2.183555 CCCACTTCGGCCTACGTC 59.816 66.667 0.00 0.00 44.69 4.34
1904 7869 2.852431 GAAGACCTCGAGACCGCACG 62.852 65.000 15.71 0.00 35.37 5.34
1978 7980 5.452777 GTTTGTGAAGGTTCTATCTTGTGC 58.547 41.667 0.00 0.00 0.00 4.57
2120 8133 6.317642 TCGAATAAAATGGTGATACTGGTTGG 59.682 38.462 0.00 0.00 0.00 3.77
2303 8325 3.189702 TGTTTTAGGCTATCGGCAAACAC 59.810 43.478 14.38 0.00 38.51 3.32
2312 8334 2.612567 CGGCAAACACGCTTGGCTA 61.613 57.895 14.36 0.00 46.70 3.93
2330 8352 5.376625 TGGCTAGATTTGTTTTGTGACTCT 58.623 37.500 0.00 0.00 0.00 3.24
2331 8353 5.827797 TGGCTAGATTTGTTTTGTGACTCTT 59.172 36.000 0.00 0.00 0.00 2.85
2376 8400 3.253188 TGGTCTGCATTCAAAAGCTGTAC 59.747 43.478 0.00 0.00 0.00 2.90
2393 8473 3.670625 TGTACATTTTTCGGGTGGAGAG 58.329 45.455 0.00 0.00 0.00 3.20
2398 8478 2.060050 TTTTCGGGTGGAGAGCAAAA 57.940 45.000 0.00 0.00 0.00 2.44
2498 8579 6.715347 ATTGTCCCCATTTTGTAGCTTATC 57.285 37.500 0.00 0.00 0.00 1.75
2597 8680 5.654650 TGATGGTTCCAGTTTTGTAAACACT 59.345 36.000 5.23 0.00 0.00 3.55
2602 8685 7.976734 TGGTTCCAGTTTTGTAAACACTTTATG 59.023 33.333 5.23 0.00 0.00 1.90
2650 8733 1.141657 AGGAGAAGCTGTTGTTCTGCA 59.858 47.619 6.64 0.00 42.98 4.41
2652 8735 2.095364 GGAGAAGCTGTTGTTCTGCATG 60.095 50.000 0.00 0.00 40.90 4.06
2673 8756 2.687370 CTCGGTGATGTTGATGTCACA 58.313 47.619 7.67 0.00 44.99 3.58
2675 8758 4.432712 CTCGGTGATGTTGATGTCACATA 58.567 43.478 7.67 0.00 44.99 2.29
2690 8773 9.891828 TGATGTCACATAAATTTTGTAACAGAC 57.108 29.630 12.15 11.49 29.10 3.51
2694 8777 8.349983 GTCACATAAATTTTGTAACAGACTGGT 58.650 33.333 7.51 1.99 0.00 4.00
2695 8778 8.564574 TCACATAAATTTTGTAACAGACTGGTC 58.435 33.333 7.51 0.00 0.00 4.02
2696 8779 8.567948 CACATAAATTTTGTAACAGACTGGTCT 58.432 33.333 7.51 0.00 41.37 3.85
2697 8780 9.131791 ACATAAATTTTGTAACAGACTGGTCTT 57.868 29.630 7.51 0.00 37.98 3.01
2778 8861 5.836358 TGTATTTAGTGGCAGTTTTCCCTTT 59.164 36.000 0.00 0.00 0.00 3.11
2823 8906 6.095440 GCTAAAATCTCAGGGCACTCAAAATA 59.905 38.462 0.00 0.00 0.00 1.40
2830 8913 6.024552 TCAGGGCACTCAAAATAAAACATC 57.975 37.500 0.00 0.00 0.00 3.06
2884 8967 5.801947 AGCTGATTTTCATGTATTTGCGTTC 59.198 36.000 0.00 0.00 0.00 3.95
2928 9013 6.932400 CGCCATGGACCAAAGTAGTATATTAA 59.068 38.462 18.40 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.047877 GGGTCGGGTTGAACAGCG 61.048 66.667 0.00 0.00 35.31 5.18
30 31 0.323629 TTCTAGCCTTTGTGGGTCGG 59.676 55.000 0.00 0.00 44.42 4.79
36 37 5.890334 TGAAAACTTGTTCTAGCCTTTGTG 58.110 37.500 0.00 0.00 0.00 3.33
38 39 7.042523 CCAAATGAAAACTTGTTCTAGCCTTTG 60.043 37.037 0.00 0.00 0.00 2.77
45 46 8.231692 TCATGTCCAAATGAAAACTTGTTCTA 57.768 30.769 0.00 0.00 33.63 2.10
128 1845 5.416271 AACAACTATGTTCTACGGTGGAT 57.584 39.130 0.00 0.00 46.78 3.41
210 1944 6.037172 CACCCTATCTTTAATTTCTGACACCG 59.963 42.308 0.00 0.00 0.00 4.94
213 1947 6.423182 CCCACCCTATCTTTAATTTCTGACA 58.577 40.000 0.00 0.00 0.00 3.58
215 1949 5.103686 CCCCCACCCTATCTTTAATTTCTGA 60.104 44.000 0.00 0.00 0.00 3.27
217 1951 5.403558 CCCCCACCCTATCTTTAATTTCT 57.596 43.478 0.00 0.00 0.00 2.52
240 1974 2.119391 TGTCAATTGCCCCACCCC 59.881 61.111 0.00 0.00 0.00 4.95
241 1975 1.118356 TTGTGTCAATTGCCCCACCC 61.118 55.000 15.52 0.00 0.00 4.61
242 1976 0.755686 TTTGTGTCAATTGCCCCACC 59.244 50.000 15.52 0.79 0.00 4.61
243 1977 1.412343 AGTTTGTGTCAATTGCCCCAC 59.588 47.619 0.00 8.01 0.00 4.61
244 1978 1.786937 AGTTTGTGTCAATTGCCCCA 58.213 45.000 0.00 0.00 0.00 4.96
245 1979 2.908688 AAGTTTGTGTCAATTGCCCC 57.091 45.000 0.00 0.00 0.00 5.80
246 1980 4.187694 TCAAAAGTTTGTGTCAATTGCCC 58.812 39.130 0.00 0.00 39.18 5.36
247 1981 5.989551 ATCAAAAGTTTGTGTCAATTGCC 57.010 34.783 0.00 0.00 39.18 4.52
252 2263 6.406400 CCCCTGTAATCAAAAGTTTGTGTCAA 60.406 38.462 3.82 0.00 39.18 3.18
302 2313 5.757886 TGAACAGTGCGGAATTTAGAAAAG 58.242 37.500 0.00 0.00 0.00 2.27
363 3020 3.798511 GACCACTAGGGCCCTGGC 61.799 72.222 35.81 16.80 42.05 4.85
381 3038 2.587247 GCAGTGGCAGAGACAGGGA 61.587 63.158 0.00 0.00 40.72 4.20
438 3095 1.412079 AACAAGCCACAAAGATGCCA 58.588 45.000 0.00 0.00 0.00 4.92
517 3187 6.421377 AACTCATTTTGCCAACTTTTTCAC 57.579 33.333 0.00 0.00 0.00 3.18
546 3216 8.979534 AGGATAGACTAAAGAACGGAAATAAGT 58.020 33.333 0.00 0.00 0.00 2.24
554 3224 6.546772 AGACCTTAGGATAGACTAAAGAACGG 59.453 42.308 4.77 0.00 32.92 4.44
555 3225 7.571080 AGACCTTAGGATAGACTAAAGAACG 57.429 40.000 4.77 0.00 32.92 3.95
596 3267 4.338879 CCTGATTGTTTGGAATGTCTCCT 58.661 43.478 0.00 0.00 45.64 3.69
602 3273 2.228582 TGACGCCTGATTGTTTGGAATG 59.771 45.455 0.00 0.00 0.00 2.67
613 3284 1.737793 GTTCGGATTTTGACGCCTGAT 59.262 47.619 0.00 0.00 0.00 2.90
619 3290 1.790123 CGCCATGTTCGGATTTTGACG 60.790 52.381 0.00 0.00 0.00 4.35
625 3296 1.967319 ATAAGCGCCATGTTCGGATT 58.033 45.000 2.29 0.00 0.00 3.01
629 3300 2.858729 GCAATAAGCGCCATGTTCG 58.141 52.632 2.29 0.00 0.00 3.95
664 3335 9.195411 TGTTTCTCATAACTCATTTGCATTTTC 57.805 29.630 0.00 0.00 0.00 2.29
678 3349 5.048083 TGCCAGGTTTCATGTTTCTCATAAC 60.048 40.000 0.00 0.00 34.67 1.89
681 3352 3.499338 TGCCAGGTTTCATGTTTCTCAT 58.501 40.909 0.00 0.00 37.22 2.90
702 3373 3.183801 AGGGATGCAAATTTGGAACCAT 58.816 40.909 30.69 24.97 42.03 3.55
844 3559 3.372060 CGCAAGTGGACCTTTTTCTTTC 58.628 45.455 0.00 0.00 0.00 2.62
853 3568 3.222354 GACGACCGCAAGTGGACCT 62.222 63.158 6.67 0.00 0.00 3.85
911 3626 2.675423 ACTACAGTGGCGAGCGGA 60.675 61.111 0.00 0.00 0.00 5.54
913 3628 0.798771 GAAGACTACAGTGGCGAGCG 60.799 60.000 0.00 0.00 0.00 5.03
970 3685 0.865769 GGTTGACTTGCGATGTTCGT 59.134 50.000 0.00 0.00 42.81 3.85
1031 6994 0.741221 GGCCGCGAAGATCTTGAAGT 60.741 55.000 14.00 0.00 0.00 3.01
1561 7526 1.574526 CCATCCCCTTCCTCAGGCAA 61.575 60.000 0.00 0.00 42.29 4.52
1586 7551 0.531532 CATGATGTCCACCGGCTCTC 60.532 60.000 0.00 0.00 0.00 3.20
1587 7552 1.524002 CATGATGTCCACCGGCTCT 59.476 57.895 0.00 0.00 0.00 4.09
1656 7621 1.581447 GCTTCCAGCTTTGAACCGG 59.419 57.895 0.00 0.00 38.45 5.28
1818 7783 2.673833 GTGTCCTCCAAGTACTTGACG 58.326 52.381 32.50 22.18 42.93 4.35
1904 7869 0.040336 CTCTGCATCGATGGCATTGC 60.040 55.000 26.00 14.23 41.06 3.56
2150 8163 8.087136 TGCATTTTATTCAGCAAACACAGATTA 58.913 29.630 0.00 0.00 33.48 1.75
2303 8325 3.670055 CACAAAACAAATCTAGCCAAGCG 59.330 43.478 0.00 0.00 0.00 4.68
2312 8334 8.517878 CATGGATAAGAGTCACAAAACAAATCT 58.482 33.333 0.00 0.00 0.00 2.40
2330 8352 9.964354 CCAGAAGATTAATATGTCCATGGATAA 57.036 33.333 19.62 12.32 0.00 1.75
2331 8353 9.116080 ACCAGAAGATTAATATGTCCATGGATA 57.884 33.333 19.62 16.79 0.00 2.59
2376 8400 1.533625 TGCTCTCCACCCGAAAAATG 58.466 50.000 0.00 0.00 0.00 2.32
2393 8473 8.275632 GTGGTCAGATAAACATTTTCTTTTTGC 58.724 33.333 0.00 0.00 0.00 3.68
2398 8478 7.138736 CGTTGTGGTCAGATAAACATTTTCTT 58.861 34.615 0.00 0.00 0.00 2.52
2498 8579 7.925483 TCCAACAGAAAAACAAATACCAGAATG 59.075 33.333 0.00 0.00 0.00 2.67
2597 8680 5.241285 TGCAGAACAGAAAGCACATCATAAA 59.759 36.000 0.00 0.00 31.05 1.40
2602 8685 3.631145 TTGCAGAACAGAAAGCACATC 57.369 42.857 0.00 0.00 36.62 3.06
2650 8733 2.283298 GACATCAACATCACCGAGCAT 58.717 47.619 0.00 0.00 0.00 3.79
2652 8735 1.394917 GTGACATCAACATCACCGAGC 59.605 52.381 0.00 0.00 39.49 5.03
2716 8799 1.828595 TCTGCCGTATGCTTTACCTGA 59.171 47.619 0.00 0.00 42.00 3.86
2722 8805 3.146066 TGAACTTTCTGCCGTATGCTTT 58.854 40.909 0.00 0.00 42.00 3.51
2808 8891 6.029346 AGATGTTTTATTTTGAGTGCCCTG 57.971 37.500 0.00 0.00 0.00 4.45
2884 8967 4.749598 TGGCGTACTAGCAATCATGTATTG 59.250 41.667 11.35 11.35 46.62 1.90


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

AutoCloner maintained by Alex Coulton.