Multiple sequence alignment - TraesCS7D01G189400

Loading Multiple Alignment...

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 TraesCS7D01G189400 chr7D 100.000 4135 0 0 1 4135 142609235 142613369 0.000000e+00 7637.0
1 TraesCS7D01G189400 chr7D 76.233 446 106 0 1607 2052 576282769 576283214 1.920000e-58 237.0
2 TraesCS7D01G189400 chr7A 94.878 3085 105 26 141 3205 144602422 144605473 0.000000e+00 4772.0
3 TraesCS7D01G189400 chr7A 96.631 742 25 0 3394 4135 144606370 144607111 0.000000e+00 1232.0
4 TraesCS7D01G189400 chr7A 76.233 446 106 0 1607 2052 667211794 667212239 1.920000e-58 237.0
5 TraesCS7D01G189400 chr7A 93.431 137 8 1 1 137 144602242 144602377 7.010000e-48 202.0
6 TraesCS7D01G189400 chr7A 96.262 107 4 0 3290 3396 144606236 144606342 4.250000e-40 176.0
7 TraesCS7D01G189400 chr7A 83.607 183 18 2 634 816 144596847 144597017 1.190000e-35 161.0
8 TraesCS7D01G189400 chr7B 94.128 2793 114 19 530 3308 106952378 106949622 0.000000e+00 4204.0
9 TraesCS7D01G189400 chr7B 93.522 741 44 4 3396 4135 106949552 106948815 0.000000e+00 1099.0
10 TraesCS7D01G189400 chr7B 83.901 323 37 11 141 459 106952961 106952650 1.120000e-75 294.0
11 TraesCS7D01G189400 chr7B 74.453 548 140 0 1607 2154 638883108 638883655 1.920000e-58 237.0
12 TraesCS7D01G189400 chr4A 78.846 104 16 5 233 333 7162284 7162184 9.590000e-07 65.8
13 TraesCS7D01G189400 chr6D 100.000 30 0 0 2027 2056 452126136 452126107 5.770000e-04 56.5
14 TraesCS7D01G189400 chr5B 100.000 30 0 0 2027 2056 507801191 507801162 5.770000e-04 56.5
15 TraesCS7D01G189400 chr3D 100.000 30 0 0 2027 2056 121266954 121266925 5.770000e-04 56.5
16 TraesCS7D01G189400 chr3A 100.000 30 0 0 2027 2056 127820822 127820793 5.770000e-04 56.5


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 TraesCS7D01G189400 chr7D 142609235 142613369 4134 False 7637.000000 7637 100.0000 1 4135 1 chr7D.!!$F1 4134
1 TraesCS7D01G189400 chr7A 144602242 144607111 4869 False 1595.500000 4772 95.3005 1 4135 4 chr7A.!!$F3 4134
2 TraesCS7D01G189400 chr7B 106948815 106952961 4146 True 1865.666667 4204 90.5170 141 4135 3 chr7B.!!$R1 3994
3 TraesCS7D01G189400 chr7B 638883108 638883655 547 False 237.000000 237 74.4530 1607 2154 1 chr7B.!!$F1 547

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
530 798 0.179023 TGTTGTGTCAGCAGCCATCA 60.179 50.0 0.00 0.00 0.00 3.07 F
800 1068 0.554305 ACCGGAGAAACCCCAAACTT 59.446 50.0 9.46 0.00 34.64 2.66 F
1291 1578 0.818296 CAGGTTCCTGGAGTACCTCG 59.182 60.0 15.69 9.05 40.24 4.63 F
1725 2012 1.140312 TGCAGTTCCTCAAGTTCCCT 58.860 50.0 0.00 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1781 1.224870 GAGGTTAAGCAGGAGGCCC 59.775 63.158 7.52 0.0 46.50 5.80 R
1725 2012 1.885388 CACCGCCGTGAACTTGTCA 60.885 57.895 0.00 0.0 43.14 3.58 R
3068 3356 1.022982 TGCCGATGTCGACGTACTCT 61.023 55.000 10.95 0.0 43.02 3.24 R
3617 4651 0.101219 CTCTGCGATGTCGGTCATGA 59.899 55.000 4.44 0.0 40.23 3.07 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
120 121 4.694982 TCACTTATGCGTGTGATTGTGATT 59.305 37.500 0.00 0.00 38.15 2.57
128 129 4.221342 CGTGTGATTGTGATTTTCCACTG 58.779 43.478 0.00 0.00 37.89 3.66
137 138 6.925610 TGTGATTTTCCACTGCTATGTATC 57.074 37.500 0.00 0.00 37.89 2.24
138 139 6.413892 TGTGATTTTCCACTGCTATGTATCA 58.586 36.000 0.00 0.00 37.89 2.15
186 228 3.014623 GCCCCTTTGCTTCGTAGTAAAT 58.985 45.455 5.83 0.00 35.78 1.40
187 229 3.181500 GCCCCTTTGCTTCGTAGTAAATG 60.181 47.826 5.83 3.84 35.78 2.32
239 281 3.129113 TGTCATGTGCATGCAAATCCTAC 59.871 43.478 24.58 18.99 38.65 3.18
312 357 6.981722 AGAATTTGGTGTGGTTGTAGATTTC 58.018 36.000 0.00 0.00 0.00 2.17
314 359 4.447138 TTGGTGTGGTTGTAGATTTCCT 57.553 40.909 0.00 0.00 0.00 3.36
393 438 5.613329 ACACCTACTAATCAAACGACCAAA 58.387 37.500 0.00 0.00 0.00 3.28
394 439 5.467735 ACACCTACTAATCAAACGACCAAAC 59.532 40.000 0.00 0.00 0.00 2.93
395 440 5.467399 CACCTACTAATCAAACGACCAAACA 59.533 40.000 0.00 0.00 0.00 2.83
396 441 6.148811 CACCTACTAATCAAACGACCAAACAT 59.851 38.462 0.00 0.00 0.00 2.71
397 442 7.332430 CACCTACTAATCAAACGACCAAACATA 59.668 37.037 0.00 0.00 0.00 2.29
398 443 7.548075 ACCTACTAATCAAACGACCAAACATAG 59.452 37.037 0.00 0.00 0.00 2.23
405 451 8.742554 ATCAAACGACCAAACATAGATTTTTC 57.257 30.769 0.00 0.00 0.00 2.29
424 470 9.600646 GATTTTTCCTTTCTTTCTAAGACTTCG 57.399 33.333 0.00 0.00 37.23 3.79
446 492 7.753309 TCGTTCAAATCCTCCAATTCTTTTA 57.247 32.000 0.00 0.00 0.00 1.52
479 743 6.127897 CCTTTGTATAGAAAAGGCCACTTGAG 60.128 42.308 5.01 0.00 45.28 3.02
530 798 0.179023 TGTTGTGTCAGCAGCCATCA 60.179 50.000 0.00 0.00 0.00 3.07
531 799 1.171308 GTTGTGTCAGCAGCCATCAT 58.829 50.000 0.00 0.00 0.00 2.45
532 800 1.131883 GTTGTGTCAGCAGCCATCATC 59.868 52.381 0.00 0.00 0.00 2.92
543 811 2.027325 CCATCATCGGGCATGTGTG 58.973 57.895 0.00 0.00 33.66 3.82
557 825 4.019312 TGTGCAGCCCATGAGCGA 62.019 61.111 0.00 0.00 38.01 4.93
559 827 4.478371 TGCAGCCCATGAGCGAGG 62.478 66.667 0.00 0.00 38.01 4.63
560 828 4.166888 GCAGCCCATGAGCGAGGA 62.167 66.667 0.00 0.00 38.01 3.71
584 852 1.368019 CAACAAGTGTGCGTGCGAG 60.368 57.895 0.00 0.00 0.00 5.03
800 1068 0.554305 ACCGGAGAAACCCCAAACTT 59.446 50.000 9.46 0.00 34.64 2.66
801 1069 1.063492 ACCGGAGAAACCCCAAACTTT 60.063 47.619 9.46 0.00 34.64 2.66
878 1146 6.543831 CCTCAATCTATTTAAACACAGGAGGG 59.456 42.308 12.43 0.00 34.76 4.30
906 1174 3.552684 CGTACTACGTTCCCTCCAAAACA 60.553 47.826 0.00 0.00 36.74 2.83
907 1175 3.564053 ACTACGTTCCCTCCAAAACAA 57.436 42.857 0.00 0.00 0.00 2.83
909 1177 1.029681 ACGTTCCCTCCAAAACAAGC 58.970 50.000 0.00 0.00 0.00 4.01
912 1180 1.679153 GTTCCCTCCAAAACAAGCGAA 59.321 47.619 0.00 0.00 0.00 4.70
914 1182 1.133915 TCCCTCCAAAACAAGCGAACT 60.134 47.619 0.00 0.00 0.00 3.01
915 1183 1.001378 CCCTCCAAAACAAGCGAACTG 60.001 52.381 0.00 0.00 0.00 3.16
964 1243 2.076863 CAGTTGCCACTAGCCAAGTAC 58.923 52.381 0.00 0.00 42.71 2.73
983 1262 5.378332 AGTACAGTAGTAGCCTGATCGATT 58.622 41.667 0.00 0.00 34.04 3.34
984 1263 5.828859 AGTACAGTAGTAGCCTGATCGATTT 59.171 40.000 0.00 0.00 34.04 2.17
988 1267 6.265649 ACAGTAGTAGCCTGATCGATTTGTAT 59.734 38.462 0.00 0.00 34.04 2.29
994 1275 5.300752 AGCCTGATCGATTTGTATGTAAGG 58.699 41.667 0.00 0.00 0.00 2.69
1291 1578 0.818296 CAGGTTCCTGGAGTACCTCG 59.182 60.000 15.69 9.05 40.24 4.63
1494 1781 4.436998 GTCGGGCTGGACGTCCTG 62.437 72.222 33.39 32.12 34.28 3.86
1557 1844 2.182030 CTCTTCCTGCGGTCGTCC 59.818 66.667 0.00 0.00 0.00 4.79
1725 2012 1.140312 TGCAGTTCCTCAAGTTCCCT 58.860 50.000 0.00 0.00 0.00 4.20
2499 2787 1.339610 CACATCATCCCTCTCCTCGTC 59.660 57.143 0.00 0.00 0.00 4.20
2501 2789 1.885887 CATCATCCCTCTCCTCGTCTC 59.114 57.143 0.00 0.00 0.00 3.36
2633 2921 2.047179 GGCCTGACGTGGTTCCTC 60.047 66.667 0.00 0.00 0.00 3.71
2636 2924 2.663196 CTGACGTGGTTCCTCCCC 59.337 66.667 0.00 0.00 34.77 4.81
2892 3180 2.825836 GGATGCTGGCCAGGAACG 60.826 66.667 31.97 7.96 30.94 3.95
2912 3200 2.103143 ATGTCGGAGAAGCTCGCG 59.897 61.111 0.00 0.00 39.69 5.87
2943 3231 1.918293 AGGACGGTGAAGGCCATCA 60.918 57.895 6.57 6.57 43.43 3.07
3060 3348 2.892425 GCGATGAGTTCAGGGCGG 60.892 66.667 0.00 0.00 0.00 6.13
3104 3392 1.896694 CAGAGAGCAGAGGGACACC 59.103 63.158 0.00 0.00 0.00 4.16
3173 3462 1.119684 TGTGTAGTGCAGACTGTGGT 58.880 50.000 3.99 0.00 33.21 4.16
3175 3464 2.296190 TGTGTAGTGCAGACTGTGGTAG 59.704 50.000 3.99 0.00 33.21 3.18
3180 3469 2.761208 AGTGCAGACTGTGGTAGGATAC 59.239 50.000 3.99 0.00 42.04 2.24
3181 3470 4.325109 TAGTGCAGACTGTGGTAGGATACT 60.325 45.833 3.99 0.00 41.73 2.12
3182 3471 5.104235 TAGTGCAGACTGTGGTAGGATACTA 60.104 44.000 3.99 0.00 40.11 1.82
3238 4235 1.660560 GGTGCCTCACATCACATGCC 61.661 60.000 0.00 0.00 35.86 4.40
3245 4242 3.181457 CCTCACATCACATGCCTGATAGT 60.181 47.826 0.00 0.00 29.28 2.12
3250 4247 5.923114 CACATCACATGCCTGATAGTACTAC 59.077 44.000 4.31 0.35 29.28 2.73
3253 4250 7.175816 ACATCACATGCCTGATAGTACTACTAG 59.824 40.741 4.31 6.51 33.66 2.57
3287 4284 2.423538 CCATACAAGCAGGTGTTTAGCC 59.576 50.000 0.00 0.00 32.75 3.93
3300 4297 3.507622 GTGTTTAGCCCAATTCTTCTGCT 59.492 43.478 0.00 0.00 36.11 4.24
3320 4317 8.791327 TCTGCTATCATAATTTGTGTTCTTCA 57.209 30.769 0.00 0.00 0.00 3.02
3435 4469 1.065410 TGCCTCCCCAGGTTCAAGAA 61.065 55.000 0.00 0.00 42.74 2.52
3576 4610 4.172512 CCATCGCCCTCAGCTGCT 62.173 66.667 9.47 0.00 40.39 4.24
3645 4679 2.285256 CGACATCGCAGAGCATTTACAC 60.285 50.000 0.00 0.00 43.63 2.90
3646 4680 2.672874 GACATCGCAGAGCATTTACACA 59.327 45.455 0.00 0.00 43.63 3.72
3666 4700 5.236478 ACACAGAGAAACAACGGATGTAAAG 59.764 40.000 0.00 0.00 42.99 1.85
3683 4717 2.803030 AAGTGCTGGCAGATTCAGAT 57.197 45.000 20.86 0.00 34.36 2.90
3709 4743 8.466617 TCAGAGATAGGAAAACTAGTATGGAC 57.533 38.462 0.00 0.00 34.56 4.02
3749 4784 1.609061 CGTTGATGAGGGTCTGCAAGT 60.609 52.381 0.00 0.00 33.76 3.16
3796 4831 1.133853 GGAATCCCAAGCTCTCTGCAT 60.134 52.381 0.00 0.00 45.94 3.96
3797 4832 2.652590 GAATCCCAAGCTCTCTGCATT 58.347 47.619 0.00 0.00 45.94 3.56
3808 4843 4.020396 AGCTCTCTGCATTTCTTCTTCAGA 60.020 41.667 0.00 0.00 45.94 3.27
3941 4976 3.843240 CGTTCGAAGCTGCTCCGC 61.843 66.667 2.48 0.00 0.00 5.54
3982 5017 2.283173 GGCAACCCCTTCCCACTG 60.283 66.667 0.00 0.00 0.00 3.66
4117 5152 3.122111 GCGAGCTCTACAACTTCAGAAAC 59.878 47.826 12.85 0.00 0.00 2.78
4120 5155 5.569823 CGAGCTCTACAACTTCAGAAACTAC 59.430 44.000 12.85 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 6.183360 GCATAAGTGACAGAGATTTACCAACC 60.183 42.308 0.00 0.00 0.00 3.77
86 87 5.577164 ACACGCATAAGTGACAGAGATTTAC 59.423 40.000 4.00 0.00 44.43 2.01
94 95 3.433274 ACAATCACACGCATAAGTGACAG 59.567 43.478 4.00 0.00 46.38 3.51
96 97 3.431912 TCACAATCACACGCATAAGTGAC 59.568 43.478 4.00 0.00 46.38 3.67
128 129 7.639162 AACTACGCATAAACTGATACATAGC 57.361 36.000 0.00 0.00 0.00 2.97
137 138 3.917985 GGCCAAAAACTACGCATAAACTG 59.082 43.478 0.00 0.00 0.00 3.16
138 139 3.824443 AGGCCAAAAACTACGCATAAACT 59.176 39.130 5.01 0.00 0.00 2.66
186 228 6.871844 TCATGTGTTTTTCATTCCTGTTTCA 58.128 32.000 0.00 0.00 0.00 2.69
187 229 7.769272 TTCATGTGTTTTTCATTCCTGTTTC 57.231 32.000 0.00 0.00 0.00 2.78
239 281 6.511416 AGTCATCAAATAGACTCGAATCCTG 58.489 40.000 0.00 0.00 40.96 3.86
295 339 5.741011 TCATAGGAAATCTACAACCACACC 58.259 41.667 0.00 0.00 0.00 4.16
362 407 5.515797 TTGATTAGTAGGTGTCGATCCTG 57.484 43.478 18.30 0.00 36.60 3.86
398 443 9.600646 CGAAGTCTTAGAAAGAAAGGAAAAATC 57.399 33.333 0.00 0.00 39.67 2.17
405 451 7.478520 TTGAACGAAGTCTTAGAAAGAAAGG 57.521 36.000 0.00 0.00 45.00 3.11
417 463 4.351874 TTGGAGGATTTGAACGAAGTCT 57.648 40.909 0.00 0.00 45.00 3.24
418 464 5.412904 AGAATTGGAGGATTTGAACGAAGTC 59.587 40.000 0.00 0.00 45.00 3.01
420 466 5.886960 AGAATTGGAGGATTTGAACGAAG 57.113 39.130 0.00 0.00 0.00 3.79
421 467 6.648879 AAAGAATTGGAGGATTTGAACGAA 57.351 33.333 0.00 0.00 0.00 3.85
422 468 6.648879 AAAAGAATTGGAGGATTTGAACGA 57.351 33.333 0.00 0.00 0.00 3.85
423 469 8.243426 TCATAAAAGAATTGGAGGATTTGAACG 58.757 33.333 0.00 0.00 0.00 3.95
424 470 9.927668 TTCATAAAAGAATTGGAGGATTTGAAC 57.072 29.630 0.00 0.00 0.00 3.18
460 724 4.568072 TGCTCAAGTGGCCTTTTCTATA 57.432 40.909 3.32 0.00 0.00 1.31
543 811 4.166888 TCCTCGCTCATGGGCTGC 62.167 66.667 17.16 3.55 0.00 5.25
557 825 0.109342 CACACTTGTTGGGCTCTCCT 59.891 55.000 0.00 0.00 36.20 3.69
584 852 1.540607 CTATCCACGTCGCGATGCAC 61.541 60.000 27.52 6.94 0.00 4.57
800 1068 2.102578 TGTGGATGAGAGATCGCTGAA 58.897 47.619 2.76 0.00 0.00 3.02
801 1069 1.406898 GTGTGGATGAGAGATCGCTGA 59.593 52.381 2.76 0.00 0.00 4.26
906 1174 1.029408 TGTGGTGTTGCAGTTCGCTT 61.029 50.000 0.00 0.00 43.06 4.68
907 1175 1.451207 TGTGGTGTTGCAGTTCGCT 60.451 52.632 0.00 0.00 43.06 4.93
909 1177 0.304705 GAGTGTGGTGTTGCAGTTCG 59.695 55.000 0.00 0.00 0.00 3.95
912 1180 0.035534 TGTGAGTGTGGTGTTGCAGT 60.036 50.000 0.00 0.00 0.00 4.40
914 1182 1.761449 AATGTGAGTGTGGTGTTGCA 58.239 45.000 0.00 0.00 0.00 4.08
915 1183 2.859538 CAAAATGTGAGTGTGGTGTTGC 59.140 45.455 0.00 0.00 0.00 4.17
918 1186 2.358898 GAGCAAAATGTGAGTGTGGTGT 59.641 45.455 0.00 0.00 0.00 4.16
964 1243 4.938080 ACAAATCGATCAGGCTACTACTG 58.062 43.478 0.00 0.00 37.30 2.74
983 1262 3.687212 CGACATGCCAACCTTACATACAA 59.313 43.478 0.00 0.00 0.00 2.41
984 1263 3.266636 CGACATGCCAACCTTACATACA 58.733 45.455 0.00 0.00 0.00 2.29
988 1267 2.550487 GCGACATGCCAACCTTACA 58.450 52.632 0.00 0.00 37.76 2.41
1494 1781 1.224870 GAGGTTAAGCAGGAGGCCC 59.775 63.158 7.52 0.00 46.50 5.80
1725 2012 1.885388 CACCGCCGTGAACTTGTCA 60.885 57.895 0.00 0.00 43.14 3.58
2892 3180 1.880340 CGAGCTTCTCCGACATGGC 60.880 63.158 0.00 0.00 37.80 4.40
2912 3200 2.202756 GTCCTGTCGATGTCGGCC 60.203 66.667 4.43 0.00 44.42 6.13
2943 3231 2.532256 CCTCGTACGCCTCGTCGAT 61.532 63.158 11.24 0.00 41.54 3.59
3060 3348 1.128321 GTCGACGTACTCTGACAGGAC 59.872 57.143 0.00 0.00 31.47 3.85
3068 3356 1.022982 TGCCGATGTCGACGTACTCT 61.023 55.000 10.95 0.00 43.02 3.24
3173 3462 9.220767 CATCACGCTATATATGCTAGTATCCTA 57.779 37.037 0.00 0.00 0.00 2.94
3175 3464 7.877003 ACATCACGCTATATATGCTAGTATCC 58.123 38.462 0.00 0.00 0.00 2.59
3250 4247 8.673711 TGCTTGTATGGCAAAAATTACTACTAG 58.326 33.333 0.00 0.00 36.53 2.57
3253 4250 6.751888 CCTGCTTGTATGGCAAAAATTACTAC 59.248 38.462 0.00 0.00 39.30 2.73
3287 4284 9.459640 CACAAATTATGATAGCAGAAGAATTGG 57.540 33.333 12.70 5.37 29.26 3.16
3443 4477 2.143925 GCCAGCTACAAAAAGAGACGT 58.856 47.619 0.00 0.00 0.00 4.34
3617 4651 0.101219 CTCTGCGATGTCGGTCATGA 59.899 55.000 4.44 0.00 40.23 3.07
3645 4679 5.679906 CACTTTACATCCGTTGTTTCTCTG 58.320 41.667 0.00 0.00 39.87 3.35
3646 4680 4.213482 GCACTTTACATCCGTTGTTTCTCT 59.787 41.667 0.00 0.00 39.87 3.10
3666 4700 2.355132 CTGAATCTGAATCTGCCAGCAC 59.645 50.000 0.00 0.00 0.00 4.40
3683 4717 8.915036 GTCCATACTAGTTTTCCTATCTCTGAA 58.085 37.037 0.00 0.00 0.00 3.02
3749 4784 1.638388 CCGCATCGCAAGCTGAAGAA 61.638 55.000 0.00 0.00 34.90 2.52
3796 4831 3.131396 GCTCACCGTTCTGAAGAAGAAA 58.869 45.455 0.00 0.00 46.51 2.52
3797 4832 2.548067 GGCTCACCGTTCTGAAGAAGAA 60.548 50.000 0.00 0.00 42.83 2.52
3941 4976 1.478510 ACTGTGTTATGGCGAGGAGAG 59.521 52.381 0.00 0.00 0.00 3.20
3982 5017 3.309961 TCTGATGACAGCACAGAAGAC 57.690 47.619 0.00 0.00 43.17 3.01


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

AutoCloner maintained by Alex Coulton.