Multiple sequence alignment - TraesCS2B01G432600

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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 TraesCS2B01G432600 chr2B 100.000 2597 0 0 1 2597 621774206 621776802 0.000000e+00 4796.0
1 TraesCS2B01G432600 chr2A 95.120 1414 43 9 1195 2592 670881329 670882732 0.000000e+00 2206.0
2 TraesCS2B01G432600 chr2A 89.604 1087 54 26 128 1166 670880275 670881350 0.000000e+00 1327.0
3 TraesCS2B01G432600 chr2D 94.493 1362 45 19 1195 2533 525699087 525697733 0.000000e+00 2073.0
4 TraesCS2B01G432600 chr2D 89.070 1226 56 29 1 1183 525700239 525699049 0.000000e+00 1450.0
5 TraesCS2B01G432600 chr2D 97.101 69 0 1 2531 2597 525697676 525697608 5.870000e-22 115.0
6 TraesCS2B01G432600 chr2D 74.634 205 46 5 1 202 521588453 521588654 4.600000e-13 86.1
7 TraesCS2B01G432600 chr1D 77.184 206 42 3 1 202 65585277 65585481 5.870000e-22 115.0
8 TraesCS2B01G432600 chrUn 73.770 244 50 9 1 238 42330470 42330235 1.660000e-12 84.2
9 TraesCS2B01G432600 chrUn 73.770 244 50 9 1 238 449372236 449372001 1.660000e-12 84.2
10 TraesCS2B01G432600 chr4B 83.133 83 13 1 1 83 161070573 161070492 9.970000e-10 75.0


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 TraesCS2B01G432600 chr2B 621774206 621776802 2596 False 4796.000000 4796 100.000000 1 2597 1 chr2B.!!$F1 2596
1 TraesCS2B01G432600 chr2A 670880275 670882732 2457 False 1766.500000 2206 92.362000 128 2592 2 chr2A.!!$F1 2464
2 TraesCS2B01G432600 chr2D 525697608 525700239 2631 True 1212.666667 2073 93.554667 1 2597 3 chr2D.!!$R1 2596

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
807 834 0.039074 GTGTGTACTGTCTGCTCGCT 60.039 55.0 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 1705 2.205074 GTACTTGGGTCATGCTCGATG 58.795 52.381 0.0 0.0 0.0 3.84 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
24 25 6.549912 TCATATATACGCACGTACACTCTT 57.450 37.500 4.84 0.00 33.01 2.85
25 26 7.656707 TCATATATACGCACGTACACTCTTA 57.343 36.000 4.84 0.00 33.01 2.10
40 41 4.864806 ACACTCTTATGTATGAACGCACAG 59.135 41.667 0.00 0.00 0.00 3.66
43 44 5.750547 ACTCTTATGTATGAACGCACAGATG 59.249 40.000 0.00 0.00 0.00 2.90
69 70 0.336737 CTACCCCTGTGAGGACCTCT 59.663 60.000 22.14 2.79 37.67 3.69
70 71 0.041238 TACCCCTGTGAGGACCTCTG 59.959 60.000 22.14 11.88 37.67 3.35
72 73 0.545309 CCCCTGTGAGGACCTCTGAA 60.545 60.000 22.14 7.06 37.67 3.02
73 74 1.352083 CCCTGTGAGGACCTCTGAAA 58.648 55.000 22.14 0.00 37.67 2.69
102 103 5.822519 GGGCTGACACAACATCTTATGATTA 59.177 40.000 0.00 0.00 0.00 1.75
103 104 6.318648 GGGCTGACACAACATCTTATGATTAA 59.681 38.462 0.00 0.00 0.00 1.40
104 105 7.189512 GGCTGACACAACATCTTATGATTAAC 58.810 38.462 0.00 0.00 0.00 2.01
105 106 6.901887 GCTGACACAACATCTTATGATTAACG 59.098 38.462 0.00 0.00 0.00 3.18
106 107 7.201522 GCTGACACAACATCTTATGATTAACGA 60.202 37.037 0.00 0.00 0.00 3.85
107 108 8.541133 TGACACAACATCTTATGATTAACGAA 57.459 30.769 0.00 0.00 0.00 3.85
108 109 8.655970 TGACACAACATCTTATGATTAACGAAG 58.344 33.333 0.00 0.00 0.00 3.79
110 111 8.656849 ACACAACATCTTATGATTAACGAAGTC 58.343 33.333 0.00 0.00 45.00 3.01
111 112 8.655970 CACAACATCTTATGATTAACGAAGTCA 58.344 33.333 0.00 0.00 45.00 3.41
112 113 9.383519 ACAACATCTTATGATTAACGAAGTCAT 57.616 29.630 0.00 0.00 45.00 3.06
121 122 7.290857 TGATTAACGAAGTCATTACAGAAGC 57.709 36.000 0.00 0.00 45.00 3.86
122 123 6.312918 TGATTAACGAAGTCATTACAGAAGCC 59.687 38.462 0.00 0.00 45.00 4.35
123 124 3.963428 ACGAAGTCATTACAGAAGCCT 57.037 42.857 0.00 0.00 29.74 4.58
124 125 4.273148 ACGAAGTCATTACAGAAGCCTT 57.727 40.909 0.00 0.00 29.74 4.35
125 126 4.246458 ACGAAGTCATTACAGAAGCCTTC 58.754 43.478 0.00 0.00 29.74 3.46
126 127 4.245660 CGAAGTCATTACAGAAGCCTTCA 58.754 43.478 7.29 0.00 0.00 3.02
185 186 6.855763 TCACCTGAATGCCTGAAATAAATT 57.144 33.333 0.00 0.00 0.00 1.82
208 209 0.246910 TAAATGCGAGCACGGGTGTA 59.753 50.000 5.52 0.00 40.15 2.90
228 229 4.408921 TGTATAGGAGTTGAACCCTGATGG 59.591 45.833 13.42 0.00 41.37 3.51
335 340 0.682852 TCGGTCGAAATCCAGTTGGT 59.317 50.000 0.00 0.00 36.34 3.67
394 399 2.522185 GGGGGAAAGGACACCTAAAAC 58.478 52.381 0.00 0.00 31.13 2.43
431 436 5.291128 GGTTCATCTATACAACAACACGGAG 59.709 44.000 0.00 0.00 0.00 4.63
488 500 7.019418 GTCCACTAAATGTACGTTTCATTTCC 58.981 38.462 24.19 10.69 42.21 3.13
490 502 6.019152 CACTAAATGTACGTTTCATTTCCCG 58.981 40.000 24.19 18.41 42.21 5.14
491 503 3.481112 AATGTACGTTTCATTTCCCGC 57.519 42.857 11.19 0.00 32.50 6.13
492 504 1.880271 TGTACGTTTCATTTCCCGCA 58.120 45.000 0.00 0.00 0.00 5.69
493 505 2.219458 TGTACGTTTCATTTCCCGCAA 58.781 42.857 0.00 0.00 0.00 4.85
494 506 2.617308 TGTACGTTTCATTTCCCGCAAA 59.383 40.909 0.00 0.00 0.00 3.68
602 614 3.047718 CTTCAGCGCACCCAGCATG 62.048 63.158 11.47 0.00 46.13 4.06
606 618 4.564116 GCGCACCCAGCATGCATC 62.564 66.667 21.98 0.78 46.13 3.91
607 619 2.827190 CGCACCCAGCATGCATCT 60.827 61.111 21.98 0.00 46.13 2.90
608 620 2.412323 CGCACCCAGCATGCATCTT 61.412 57.895 21.98 0.00 46.13 2.40
625 637 5.163561 TGCATCTTCCGTTTCTTTTCAACTT 60.164 36.000 0.00 0.00 0.00 2.66
662 674 1.996292 TTCTCGGCGTCTTGAATCTG 58.004 50.000 6.85 0.00 0.00 2.90
679 692 3.083997 GGATCCTGGAGCGGTGGT 61.084 66.667 3.84 0.00 0.00 4.16
680 693 2.187946 GATCCTGGAGCGGTGGTG 59.812 66.667 1.52 0.00 0.00 4.17
788 815 0.110238 CGTGCGTTGTTTGAGATGGG 60.110 55.000 0.00 0.00 0.00 4.00
802 829 1.276421 AGATGGGTGTGTACTGTCTGC 59.724 52.381 0.00 0.00 0.00 4.26
807 834 0.039074 GTGTGTACTGTCTGCTCGCT 60.039 55.000 0.00 0.00 0.00 4.93
894 921 2.685380 CCTCGGGCCCTCTTCAGT 60.685 66.667 22.43 0.00 0.00 3.41
984 1029 0.814457 CTCGCTCTTGTGCTACCTCT 59.186 55.000 0.00 0.00 0.00 3.69
990 1035 3.491792 GCTCTTGTGCTACCTCTACATCC 60.492 52.174 0.00 0.00 0.00 3.51
1104 1149 1.805945 CCGCTTCCAGCACTCGTAC 60.806 63.158 0.00 0.00 42.58 3.67
1133 1207 1.681486 CTTCTTCCTCCCCCTCGCTC 61.681 65.000 0.00 0.00 0.00 5.03
1134 1208 2.042435 CTTCCTCCCCCTCGCTCT 60.042 66.667 0.00 0.00 0.00 4.09
1183 1257 0.603569 AGTCACCGTCACTCACCATC 59.396 55.000 0.00 0.00 0.00 3.51
1184 1258 0.389948 GTCACCGTCACTCACCATCC 60.390 60.000 0.00 0.00 0.00 3.51
1185 1259 1.079127 CACCGTCACTCACCATCCC 60.079 63.158 0.00 0.00 0.00 3.85
1186 1260 1.535444 ACCGTCACTCACCATCCCA 60.535 57.895 0.00 0.00 0.00 4.37
1187 1261 1.125093 ACCGTCACTCACCATCCCAA 61.125 55.000 0.00 0.00 0.00 4.12
1188 1262 0.673644 CCGTCACTCACCATCCCAAC 60.674 60.000 0.00 0.00 0.00 3.77
1189 1263 0.034756 CGTCACTCACCATCCCAACA 59.965 55.000 0.00 0.00 0.00 3.33
1191 1265 1.072331 GTCACTCACCATCCCAACACT 59.928 52.381 0.00 0.00 0.00 3.55
1193 1267 2.567169 TCACTCACCATCCCAACACTAG 59.433 50.000 0.00 0.00 0.00 2.57
1292 1366 7.648039 AGCTAATCTTGCAGTAGTAGTAGTT 57.352 36.000 6.69 0.00 0.00 2.24
1442 1516 4.831307 CGCGTCGACTTCCGGGAG 62.831 72.222 8.71 8.71 39.09 4.30
1648 1727 2.159099 TCATCGAGCATGACCCAAGTAC 60.159 50.000 0.00 0.00 36.51 2.73
1988 2069 7.640240 CCTCTTCTCAACTTTGTTCTTAAAACG 59.360 37.037 0.00 0.00 0.00 3.60
2152 2241 2.103042 CACTAGCTGCTGTTCCCGC 61.103 63.158 13.43 0.00 0.00 6.13
2433 2529 3.550436 GCTAGCTCGGTCGTTAATTAGCT 60.550 47.826 7.70 0.00 42.58 3.32
2533 2629 6.097696 GCTCACTCTTCTCCTCCTTTTATACT 59.902 42.308 0.00 0.00 0.00 2.12
2534 2630 7.285858 GCTCACTCTTCTCCTCCTTTTATACTA 59.714 40.741 0.00 0.00 0.00 1.82
2536 2632 9.716556 TCACTCTTCTCCTCCTTTTATACTAAT 57.283 33.333 0.00 0.00 0.00 1.73
2537 2633 9.974980 CACTCTTCTCCTCCTTTTATACTAATC 57.025 37.037 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.224592 CAGGGGTAGGGTGTGCATC 59.775 63.158 0.00 0.00 0.00 3.91
43 44 2.185310 CTCACAGGGGTAGGGTGTGC 62.185 65.000 0.00 0.00 41.17 4.57
50 51 0.336737 AGAGGTCCTCACAGGGGTAG 59.663 60.000 21.26 0.00 35.59 3.18
53 54 0.545309 TTCAGAGGTCCTCACAGGGG 60.545 60.000 21.26 3.43 35.59 4.79
69 70 0.836606 TGTGTCAGCCCAGTCTTTCA 59.163 50.000 0.00 0.00 0.00 2.69
70 71 1.604278 GTTGTGTCAGCCCAGTCTTTC 59.396 52.381 0.00 0.00 0.00 2.62
72 73 0.546122 TGTTGTGTCAGCCCAGTCTT 59.454 50.000 0.00 0.00 0.00 3.01
73 74 0.767375 ATGTTGTGTCAGCCCAGTCT 59.233 50.000 0.00 0.00 0.00 3.24
102 103 4.273148 AGGCTTCTGTAATGACTTCGTT 57.727 40.909 0.00 0.00 0.00 3.85
103 104 3.963428 AGGCTTCTGTAATGACTTCGT 57.037 42.857 0.00 0.00 0.00 3.85
104 105 4.245660 TGAAGGCTTCTGTAATGACTTCG 58.754 43.478 26.26 0.00 36.54 3.79
105 106 7.044798 ACTATGAAGGCTTCTGTAATGACTTC 58.955 38.462 26.26 0.00 34.88 3.01
106 107 6.951971 ACTATGAAGGCTTCTGTAATGACTT 58.048 36.000 26.26 0.31 0.00 3.01
107 108 6.552445 ACTATGAAGGCTTCTGTAATGACT 57.448 37.500 26.26 4.50 0.00 3.41
108 109 5.460419 CGACTATGAAGGCTTCTGTAATGAC 59.540 44.000 26.26 10.31 0.00 3.06
109 110 5.359860 TCGACTATGAAGGCTTCTGTAATGA 59.640 40.000 26.26 15.05 0.00 2.57
110 111 5.460419 GTCGACTATGAAGGCTTCTGTAATG 59.540 44.000 26.26 13.20 0.00 1.90
111 112 5.593010 GTCGACTATGAAGGCTTCTGTAAT 58.407 41.667 26.26 14.57 0.00 1.89
112 113 4.438336 CGTCGACTATGAAGGCTTCTGTAA 60.438 45.833 26.26 8.09 0.00 2.41
113 114 3.064958 CGTCGACTATGAAGGCTTCTGTA 59.935 47.826 26.26 17.61 0.00 2.74
114 115 2.159366 CGTCGACTATGAAGGCTTCTGT 60.159 50.000 26.26 20.77 0.00 3.41
115 116 2.455032 CGTCGACTATGAAGGCTTCTG 58.545 52.381 26.26 18.11 0.00 3.02
116 117 1.405821 CCGTCGACTATGAAGGCTTCT 59.594 52.381 26.26 14.89 30.82 2.85
117 118 1.404391 TCCGTCGACTATGAAGGCTTC 59.596 52.381 20.27 20.27 37.42 3.86
118 119 1.471119 TCCGTCGACTATGAAGGCTT 58.529 50.000 14.70 0.00 37.42 4.35
119 120 1.134560 GTTCCGTCGACTATGAAGGCT 59.865 52.381 14.70 0.00 37.42 4.58
120 121 1.557651 GTTCCGTCGACTATGAAGGC 58.442 55.000 14.70 0.04 37.42 4.35
121 122 1.131883 ACGTTCCGTCGACTATGAAGG 59.868 52.381 14.70 18.53 33.69 3.46
122 123 2.539346 ACGTTCCGTCGACTATGAAG 57.461 50.000 14.70 9.58 33.69 3.02
123 124 4.621068 AATACGTTCCGTCGACTATGAA 57.379 40.909 14.70 10.56 41.54 2.57
124 125 4.621068 AAATACGTTCCGTCGACTATGA 57.379 40.909 14.70 4.61 41.54 2.15
125 126 4.205792 GGAAAATACGTTCCGTCGACTATG 59.794 45.833 14.70 6.90 41.54 2.23
126 127 4.354587 GGAAAATACGTTCCGTCGACTAT 58.645 43.478 14.70 0.29 41.54 2.12
142 143 1.626686 TGTGCATTCGGTGGGAAAAT 58.373 45.000 0.00 0.00 38.36 1.82
152 153 2.793585 GCATTCAGGTGATGTGCATTCG 60.794 50.000 11.09 0.00 36.60 3.34
185 186 1.013596 CCCGTGCTCGCATTTATTGA 58.986 50.000 1.89 0.00 35.54 2.57
394 399 4.112256 GAACCGTGCACGTACGCG 62.112 66.667 34.81 22.44 42.44 6.01
431 436 4.698575 ACTCTAATTGCCTAAGCTGCTAC 58.301 43.478 0.90 0.00 40.80 3.58
471 480 2.814919 TGCGGGAAATGAAACGTACATT 59.185 40.909 12.89 12.89 39.25 2.71
472 481 2.428491 TGCGGGAAATGAAACGTACAT 58.572 42.857 0.00 0.00 0.00 2.29
497 509 3.982576 AGAAACTGCCGAACGATTTTT 57.017 38.095 0.00 0.00 0.00 1.94
498 510 3.628017 CAAGAAACTGCCGAACGATTTT 58.372 40.909 0.00 0.00 0.00 1.82
499 511 2.604614 GCAAGAAACTGCCGAACGATTT 60.605 45.455 0.00 0.00 36.25 2.17
533 545 8.850156 ACGTCTTTCCAGTTTTACTACTAGTAA 58.150 33.333 3.76 4.76 38.79 2.24
602 614 4.860072 AGTTGAAAAGAAACGGAAGATGC 58.140 39.130 0.00 0.00 32.65 3.91
603 615 6.414987 GTCAAGTTGAAAAGAAACGGAAGATG 59.585 38.462 7.25 0.00 32.65 2.90
604 616 6.318900 AGTCAAGTTGAAAAGAAACGGAAGAT 59.681 34.615 7.25 0.00 32.65 2.40
605 617 5.646360 AGTCAAGTTGAAAAGAAACGGAAGA 59.354 36.000 7.25 0.00 32.65 2.87
606 618 5.880341 AGTCAAGTTGAAAAGAAACGGAAG 58.120 37.500 7.25 0.00 32.65 3.46
607 619 5.890424 AGTCAAGTTGAAAAGAAACGGAA 57.110 34.783 7.25 0.00 32.65 4.30
608 620 5.392595 CCAAGTCAAGTTGAAAAGAAACGGA 60.393 40.000 7.25 0.00 32.65 4.69
625 637 4.750098 CGAGAAAAACTTCTAGCCAAGTCA 59.250 41.667 0.00 0.00 35.45 3.41
662 674 3.083997 ACCACCGCTCCAGGATCC 61.084 66.667 2.48 2.48 34.73 3.36
788 815 0.039074 AGCGAGCAGACAGTACACAC 60.039 55.000 0.00 0.00 0.00 3.82
802 829 1.439679 GACAACCTTAACCCAGCGAG 58.560 55.000 0.00 0.00 0.00 5.03
807 834 1.956297 CACACGACAACCTTAACCCA 58.044 50.000 0.00 0.00 0.00 4.51
894 921 2.540910 AGGGGAGAGGGGTGAGGA 60.541 66.667 0.00 0.00 0.00 3.71
921 962 1.913419 GGACAGAAGATGGGTTGGGTA 59.087 52.381 0.00 0.00 0.00 3.69
984 1029 1.225431 TCCATGGGGAGATGGGATGTA 59.775 52.381 13.02 0.00 42.95 2.29
990 1035 2.831770 CCGTCCATGGGGAGATGG 59.168 66.667 13.02 3.21 46.12 3.51
1104 1149 3.319689 GGGGAGGAAGAAGAAGAGATACG 59.680 52.174 0.00 0.00 0.00 3.06
1133 1207 0.539051 ATCAAGAAGTGGCGGAGGAG 59.461 55.000 0.00 0.00 0.00 3.69
1134 1208 1.860641 TATCAAGAAGTGGCGGAGGA 58.139 50.000 0.00 0.00 0.00 3.71
1183 1257 5.674525 TCATATCAAGAAGCTAGTGTTGGG 58.325 41.667 0.00 0.00 0.00 4.12
1184 1258 7.255035 CCATTCATATCAAGAAGCTAGTGTTGG 60.255 40.741 0.00 0.00 0.00 3.77
1185 1259 7.496920 TCCATTCATATCAAGAAGCTAGTGTTG 59.503 37.037 0.00 0.00 0.00 3.33
1186 1260 7.568349 TCCATTCATATCAAGAAGCTAGTGTT 58.432 34.615 0.00 0.00 0.00 3.32
1187 1261 7.129457 TCCATTCATATCAAGAAGCTAGTGT 57.871 36.000 0.00 0.00 0.00 3.55
1188 1262 7.876582 TCATCCATTCATATCAAGAAGCTAGTG 59.123 37.037 0.00 0.00 0.00 2.74
1189 1263 7.971201 TCATCCATTCATATCAAGAAGCTAGT 58.029 34.615 0.00 0.00 0.00 2.57
1191 1265 7.236225 TCCTCATCCATTCATATCAAGAAGCTA 59.764 37.037 0.00 0.00 0.00 3.32
1193 1267 6.236409 TCCTCATCCATTCATATCAAGAAGC 58.764 40.000 0.00 0.00 0.00 3.86
1292 1366 4.931601 GCACCGCATATATGAGAAAGATGA 59.068 41.667 17.10 0.00 0.00 2.92
1374 1448 0.461870 GGCACCAGTCGCACATATCA 60.462 55.000 0.00 0.00 0.00 2.15
1377 1451 1.218047 GAGGCACCAGTCGCACATA 59.782 57.895 0.00 0.00 0.00 2.29
1431 1505 3.672295 CTGCTGCCTCCCGGAAGTC 62.672 68.421 0.73 0.00 38.36 3.01
1536 1610 2.995574 ACCTTGGTCGACCCTCGG 60.996 66.667 31.19 27.14 40.88 4.63
1628 1705 2.205074 GTACTTGGGTCATGCTCGATG 58.795 52.381 0.00 0.00 0.00 3.84
1648 1727 2.952978 ACTCCTCATAACTAGCTGGTCG 59.047 50.000 2.06 0.00 0.00 4.79
1743 1824 8.357290 TGCTTACTCCTAAGTAACACATAAGA 57.643 34.615 0.00 0.00 41.88 2.10
2295 2391 2.577593 GTCCTGCCTGGTACGACC 59.422 66.667 3.23 0.00 39.22 4.79


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

AutoCloner maintained by Alex Coulton.