Multiple sequence alignment - TraesCS2B01G265800

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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 TraesCS2B01G265800 chr2B 100.000 3275 0 0 1 3275 357924848 357921574 0.000000e+00 6048.0
1 TraesCS2B01G265800 chr2D 93.207 3165 69 35 3 3078 302254459 302251352 0.000000e+00 4519.0
2 TraesCS2B01G265800 chr2A 93.472 2252 64 25 260 2494 379159579 379157394 0.000000e+00 3267.0
3 TraesCS2B01G265800 chr2A 94.737 684 18 8 2600 3275 379157029 379156356 0.000000e+00 1048.0
4 TraesCS2B01G265800 chr5A 86.831 243 27 3 1143 1384 609619358 609619596 1.940000e-67 267.0
5 TraesCS2B01G265800 chr5D 86.722 241 27 3 1145 1384 488677622 488677858 2.510000e-66 263.0
6 TraesCS2B01G265800 chr5B 85.892 241 29 3 1145 1384 601864722 601864958 5.420000e-63 252.0
7 TraesCS2B01G265800 chr7B 92.105 38 3 0 230 267 4006797 4006834 2.000000e-03 54.7


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 TraesCS2B01G265800 chr2B 357921574 357924848 3274 True 6048.0 6048 100.0000 1 3275 1 chr2B.!!$R1 3274
1 TraesCS2B01G265800 chr2D 302251352 302254459 3107 True 4519.0 4519 93.2070 3 3078 1 chr2D.!!$R1 3075
2 TraesCS2B01G265800 chr2A 379156356 379159579 3223 True 2157.5 3267 94.1045 260 3275 2 chr2A.!!$R1 3015

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
689 770 0.108585 CCCCTCTCTCTCTCTCTCGG 59.891 65.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2510 2624 1.356494 ATGCTCCCTCCCCCTAAAGC 61.356 60.0 0.0 0.0 0.0 3.51 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
18 19 1.667830 GCTTGCACTGACTACCGCA 60.668 57.895 0.00 0.00 0.00 5.69
19 20 1.227999 GCTTGCACTGACTACCGCAA 61.228 55.000 0.00 0.00 41.79 4.85
53 54 1.468520 CCAAGGCACAATACGGTTCTG 59.531 52.381 0.00 0.00 0.00 3.02
72 73 2.043252 CTGGGGGTTTATGGGGTTTACA 59.957 50.000 0.00 0.00 0.00 2.41
74 75 3.079226 TGGGGGTTTATGGGGTTTACATT 59.921 43.478 0.00 0.00 0.00 2.71
127 128 0.675633 TTTACCTACCTATCGCCGGC 59.324 55.000 19.07 19.07 0.00 6.13
129 130 2.072874 TACCTACCTATCGCCGGCCT 62.073 60.000 23.46 11.53 0.00 5.19
130 131 2.637383 CCTACCTATCGCCGGCCTC 61.637 68.421 23.46 0.00 0.00 4.70
132 133 1.587933 CTACCTATCGCCGGCCTCTC 61.588 65.000 23.46 0.00 0.00 3.20
158 184 1.112113 TAAGACAGGAGATGACGGCC 58.888 55.000 0.00 0.00 0.00 6.13
180 207 5.746065 GCCATGCCTTAACATACCACTATCT 60.746 44.000 0.00 0.00 0.00 1.98
232 268 7.403312 TTTTCAAACCAGAGTCAGATCAAAA 57.597 32.000 0.00 0.00 0.00 2.44
233 269 6.624352 TTCAAACCAGAGTCAGATCAAAAG 57.376 37.500 0.00 0.00 0.00 2.27
234 270 5.065914 TCAAACCAGAGTCAGATCAAAAGG 58.934 41.667 0.00 0.00 0.00 3.11
255 305 4.133078 GGGTCAAAACATCAAATTTGGCA 58.867 39.130 17.90 0.00 41.65 4.92
302 352 2.076207 TCATGGGCATTTCCAGGATG 57.924 50.000 0.00 0.00 41.90 3.51
367 419 0.685660 GAGAGACCTTGGACCGGTTT 59.314 55.000 9.42 0.00 34.19 3.27
372 424 1.057851 ACCTTGGACCGGTTTGAGGA 61.058 55.000 27.69 6.11 0.00 3.71
406 462 1.783284 GTGATGAACGTCTGACAGCA 58.217 50.000 8.73 2.87 0.00 4.41
456 512 1.658717 GCGATGGATGGACGAGACG 60.659 63.158 0.00 0.00 0.00 4.18
503 572 2.048597 TGCCGATTCGTTGCGACT 60.049 55.556 5.20 0.00 34.89 4.18
504 573 1.666553 TGCCGATTCGTTGCGACTT 60.667 52.632 5.20 0.00 34.89 3.01
680 761 1.011545 TCCTCCTCTACCCCTCTCTCT 59.988 57.143 0.00 0.00 0.00 3.10
681 762 1.423921 CCTCCTCTACCCCTCTCTCTC 59.576 61.905 0.00 0.00 0.00 3.20
682 763 2.418669 CTCCTCTACCCCTCTCTCTCT 58.581 57.143 0.00 0.00 0.00 3.10
683 764 2.372172 CTCCTCTACCCCTCTCTCTCTC 59.628 59.091 0.00 0.00 0.00 3.20
684 765 2.021441 TCCTCTACCCCTCTCTCTCTCT 60.021 54.545 0.00 0.00 0.00 3.10
685 766 2.372172 CCTCTACCCCTCTCTCTCTCTC 59.628 59.091 0.00 0.00 0.00 3.20
686 767 3.318313 CTCTACCCCTCTCTCTCTCTCT 58.682 54.545 0.00 0.00 0.00 3.10
687 768 3.314693 TCTACCCCTCTCTCTCTCTCTC 58.685 54.545 0.00 0.00 0.00 3.20
688 769 0.837272 ACCCCTCTCTCTCTCTCTCG 59.163 60.000 0.00 0.00 0.00 4.04
689 770 0.108585 CCCCTCTCTCTCTCTCTCGG 59.891 65.000 0.00 0.00 0.00 4.63
690 771 1.128200 CCCTCTCTCTCTCTCTCGGA 58.872 60.000 0.00 0.00 0.00 4.55
691 772 1.202651 CCCTCTCTCTCTCTCTCGGAC 60.203 61.905 0.00 0.00 0.00 4.79
692 773 1.762957 CCTCTCTCTCTCTCTCGGACT 59.237 57.143 0.00 0.00 0.00 3.85
693 774 2.224066 CCTCTCTCTCTCTCTCGGACTC 60.224 59.091 0.00 0.00 0.00 3.36
734 819 0.825840 CTCCCTCCCTCCATCGTCTC 60.826 65.000 0.00 0.00 0.00 3.36
735 820 2.196925 CCCTCCCTCCATCGTCTCG 61.197 68.421 0.00 0.00 0.00 4.04
736 821 1.454111 CCTCCCTCCATCGTCTCGT 60.454 63.158 0.00 0.00 0.00 4.18
737 822 1.448922 CCTCCCTCCATCGTCTCGTC 61.449 65.000 0.00 0.00 0.00 4.20
738 823 0.464735 CTCCCTCCATCGTCTCGTCT 60.465 60.000 0.00 0.00 0.00 4.18
930 1020 1.098050 CTGGCTGGCTTAATTTCGCT 58.902 50.000 2.00 0.00 0.00 4.93
995 1085 2.686816 CCGGCGGACCAATTCACAC 61.687 63.158 24.41 0.00 34.57 3.82
1065 1167 4.487412 CGCCCCGACGACCAGTAC 62.487 72.222 0.00 0.00 34.06 2.73
1066 1168 4.139234 GCCCCGACGACCAGTACC 62.139 72.222 0.00 0.00 0.00 3.34
1067 1169 2.677524 CCCCGACGACCAGTACCA 60.678 66.667 0.00 0.00 0.00 3.25
1068 1170 2.707849 CCCCGACGACCAGTACCAG 61.708 68.421 0.00 0.00 0.00 4.00
1069 1171 2.707849 CCCGACGACCAGTACCAGG 61.708 68.421 0.00 0.58 0.00 4.45
1070 1172 1.676635 CCGACGACCAGTACCAGGA 60.677 63.158 8.83 0.00 0.00 3.86
1071 1173 1.654954 CCGACGACCAGTACCAGGAG 61.655 65.000 8.83 5.17 0.00 3.69
1072 1174 1.511768 GACGACCAGTACCAGGAGC 59.488 63.158 8.83 0.54 0.00 4.70
1073 1175 1.228769 ACGACCAGTACCAGGAGCA 60.229 57.895 8.83 0.00 0.00 4.26
1074 1176 1.251527 ACGACCAGTACCAGGAGCAG 61.252 60.000 8.83 0.70 0.00 4.24
1290 1392 1.072159 GCAGGATCGCCTTGGCTAT 59.928 57.895 10.12 4.14 43.90 2.97
1396 1504 4.722700 CCAACCACCCGGCCTCAG 62.723 72.222 0.00 0.00 34.57 3.35
1524 1638 3.453679 GGCTCCGTCCTCTCGCTT 61.454 66.667 0.00 0.00 0.00 4.68
1765 1879 2.408022 CGGACTACCTCGGCTTCG 59.592 66.667 0.00 0.00 0.00 3.79
1846 1960 3.737172 GCAACATTGCGCCCGTCT 61.737 61.111 4.18 0.00 45.11 4.18
2570 2684 4.687948 CAGGTGTCAATTCACTACTCACTG 59.312 45.833 0.00 0.00 38.28 3.66
2580 2694 3.786450 TCACTACTCACTGGAGAGGGATA 59.214 47.826 0.00 0.00 44.26 2.59
2598 2712 5.476945 AGGGATATGTTTTGGTGTTCTGTTC 59.523 40.000 0.00 0.00 0.00 3.18
2661 3034 0.963355 TTCTGGTTACCCGGCATTGC 60.963 55.000 0.00 0.00 37.01 3.56
2749 3122 7.307632 GGTCAGCTATATGAACAAATGCACTAG 60.308 40.741 0.00 0.00 36.86 2.57
2750 3123 7.225538 GTCAGCTATATGAACAAATGCACTAGT 59.774 37.037 0.00 0.00 0.00 2.57
2751 3124 8.421002 TCAGCTATATGAACAAATGCACTAGTA 58.579 33.333 0.00 0.00 0.00 1.82
2756 3129 5.356882 TGAACAAATGCACTAGTAACAGC 57.643 39.130 0.00 0.00 0.00 4.40
2763 3136 6.436843 AATGCACTAGTAACAGCAAATACC 57.563 37.500 9.40 0.00 40.76 2.73
2849 3225 9.850628 GCTTTTACTAGGTTTAATTGTTTAGGG 57.149 33.333 0.00 0.00 0.00 3.53
3115 3496 6.766467 ACTATTTCCTTTTGTCGAGAACTTGT 59.234 34.615 0.00 0.00 0.00 3.16
3125 3506 4.039973 TGTCGAGAACTTGTAGACCCAATT 59.960 41.667 0.00 0.00 0.00 2.32
3142 3523 4.207165 CCAATTATCCCTCATTTGTCCGT 58.793 43.478 0.00 0.00 0.00 4.69
3203 3584 8.923609 ATCAACATAGCATAGTTCATAGATCG 57.076 34.615 0.00 0.00 0.00 3.69
3270 3651 2.204013 TCCCAATCCACGGGGTCA 60.204 61.111 2.12 0.00 44.62 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.227999 TTGCGGTAGTCAGTGCAAGC 61.228 55.000 0.00 0.00 41.95 4.01
1 2 1.225855 TTTGCGGTAGTCAGTGCAAG 58.774 50.000 0.00 0.00 46.68 4.01
9 10 2.422479 GGGGAAGAATTTTGCGGTAGTC 59.578 50.000 0.00 0.00 0.00 2.59
18 19 2.827003 GCCTTGGGAGGGGAAGAATTTT 60.827 50.000 0.00 0.00 43.75 1.82
19 20 1.273267 GCCTTGGGAGGGGAAGAATTT 60.273 52.381 0.00 0.00 43.75 1.82
53 54 2.923898 TGTAAACCCCATAAACCCCC 57.076 50.000 0.00 0.00 0.00 5.40
72 73 1.348775 GCTGGCAGTAGGGAGGGAAT 61.349 60.000 17.16 0.00 0.00 3.01
74 75 2.365635 GCTGGCAGTAGGGAGGGA 60.366 66.667 17.16 0.00 0.00 4.20
129 130 4.592997 TCTCCTGTCTTATGACCAGAGA 57.407 45.455 17.15 17.15 42.69 3.10
130 131 4.892345 TCATCTCCTGTCTTATGACCAGAG 59.108 45.833 14.31 14.31 42.28 3.35
132 133 4.498850 CGTCATCTCCTGTCTTATGACCAG 60.499 50.000 6.32 4.39 43.34 4.00
158 184 7.441836 TGTAGATAGTGGTATGTTAAGGCATG 58.558 38.462 0.00 0.00 0.00 4.06
211 247 5.065914 CCTTTTGATCTGACTCTGGTTTGA 58.934 41.667 0.00 0.00 0.00 2.69
212 248 4.217118 CCCTTTTGATCTGACTCTGGTTTG 59.783 45.833 0.00 0.00 0.00 2.93
229 265 6.183360 GCCAAATTTGATGTTTTGACCCTTTT 60.183 34.615 19.86 0.00 35.34 2.27
232 268 4.141528 TGCCAAATTTGATGTTTTGACCCT 60.142 37.500 19.86 0.00 35.34 4.34
233 269 4.133078 TGCCAAATTTGATGTTTTGACCC 58.867 39.130 19.86 0.00 35.34 4.46
234 270 5.106594 GGATGCCAAATTTGATGTTTTGACC 60.107 40.000 19.86 6.52 35.34 4.02
302 352 0.317519 AACAAACAAACGCTAGCCGC 60.318 50.000 9.66 0.00 41.76 6.53
406 462 2.034687 ATGGCAACTGGCTCGCTT 59.965 55.556 4.78 0.00 44.01 4.68
680 761 4.276183 CCGATTTTATGAGTCCGAGAGAGA 59.724 45.833 0.00 0.00 0.00 3.10
681 762 4.541779 CCGATTTTATGAGTCCGAGAGAG 58.458 47.826 0.00 0.00 0.00 3.20
682 763 3.318275 CCCGATTTTATGAGTCCGAGAGA 59.682 47.826 0.00 0.00 0.00 3.10
683 764 3.318275 TCCCGATTTTATGAGTCCGAGAG 59.682 47.826 0.00 0.00 0.00 3.20
684 765 3.293337 TCCCGATTTTATGAGTCCGAGA 58.707 45.455 0.00 0.00 0.00 4.04
685 766 3.318275 TCTCCCGATTTTATGAGTCCGAG 59.682 47.826 0.00 0.00 0.00 4.63
686 767 3.067742 GTCTCCCGATTTTATGAGTCCGA 59.932 47.826 0.00 0.00 0.00 4.55
687 768 3.381949 GTCTCCCGATTTTATGAGTCCG 58.618 50.000 0.00 0.00 0.00 4.79
688 769 3.388350 AGGTCTCCCGATTTTATGAGTCC 59.612 47.826 0.00 0.00 34.54 3.85
689 770 4.674281 AGGTCTCCCGATTTTATGAGTC 57.326 45.455 0.00 0.00 35.12 3.36
690 771 5.437191 AAAGGTCTCCCGATTTTATGAGT 57.563 39.130 0.00 0.00 35.12 3.41
691 772 5.297029 GGAAAAGGTCTCCCGATTTTATGAG 59.703 44.000 0.00 0.00 35.12 2.90
692 773 5.045140 AGGAAAAGGTCTCCCGATTTTATGA 60.045 40.000 0.00 0.00 32.95 2.15
693 774 5.193679 AGGAAAAGGTCTCCCGATTTTATG 58.806 41.667 0.00 0.00 32.95 1.90
713 794 2.299727 GACGATGGAGGGAGGGAGGA 62.300 65.000 0.00 0.00 0.00 3.71
734 819 0.922717 GAGTAGGACGAGACGAGACG 59.077 60.000 0.00 0.00 0.00 4.18
735 820 1.660104 GTGAGTAGGACGAGACGAGAC 59.340 57.143 0.00 0.00 0.00 3.36
736 821 1.274447 TGTGAGTAGGACGAGACGAGA 59.726 52.381 0.00 0.00 0.00 4.04
737 822 1.394227 GTGTGAGTAGGACGAGACGAG 59.606 57.143 0.00 0.00 0.00 4.18
738 823 1.001746 AGTGTGAGTAGGACGAGACGA 59.998 52.381 0.00 0.00 0.00 4.20
930 1020 0.464036 CTACCCAGAGCGCATTGGTA 59.536 55.000 23.33 18.91 32.40 3.25
995 1085 4.598894 CGCTGAGCTCCATCCGGG 62.599 72.222 12.15 0.00 38.37 5.73
1063 1165 1.306141 CCTGGTCCTGCTCCTGGTA 60.306 63.158 0.00 0.00 38.64 3.25
1064 1166 2.608988 CCTGGTCCTGCTCCTGGT 60.609 66.667 0.00 0.00 38.64 4.00
1065 1167 2.284921 TCCTGGTCCTGCTCCTGG 60.285 66.667 0.00 0.00 42.80 4.45
1066 1168 2.664081 GGTCCTGGTCCTGCTCCTG 61.664 68.421 2.47 0.00 0.00 3.86
1067 1169 2.284995 GGTCCTGGTCCTGCTCCT 60.285 66.667 2.47 0.00 0.00 3.69
1068 1170 2.607750 TGGTCCTGGTCCTGCTCC 60.608 66.667 11.28 0.00 0.00 4.70
1069 1171 2.665603 GTGGTCCTGGTCCTGCTC 59.334 66.667 11.28 0.00 0.00 4.26
1070 1172 3.314331 CGTGGTCCTGGTCCTGCT 61.314 66.667 11.28 0.00 0.00 4.24
1071 1173 4.394712 CCGTGGTCCTGGTCCTGC 62.395 72.222 11.28 3.78 0.00 4.85
1072 1174 3.706373 CCCGTGGTCCTGGTCCTG 61.706 72.222 11.28 4.05 0.00 3.86
1395 1503 2.932194 TTGGCTGAGGCTGAGGCT 60.932 61.111 26.27 8.79 42.48 4.58
1396 1504 2.749441 GTTGGCTGAGGCTGAGGC 60.749 66.667 20.36 20.36 38.73 4.70
1397 1505 0.538057 TTTGTTGGCTGAGGCTGAGG 60.538 55.000 7.74 0.00 38.73 3.86
1398 1506 0.595095 GTTTGTTGGCTGAGGCTGAG 59.405 55.000 7.74 0.00 38.73 3.35
1399 1507 0.106769 TGTTTGTTGGCTGAGGCTGA 60.107 50.000 7.74 0.00 38.73 4.26
1400 1508 0.313043 CTGTTTGTTGGCTGAGGCTG 59.687 55.000 7.74 0.00 38.73 4.85
1401 1509 0.106519 ACTGTTTGTTGGCTGAGGCT 60.107 50.000 7.74 0.00 38.73 4.58
1402 1510 0.312102 GACTGTTTGTTGGCTGAGGC 59.688 55.000 0.00 0.00 37.82 4.70
1403 1511 1.972872 AGACTGTTTGTTGGCTGAGG 58.027 50.000 0.00 0.00 0.00 3.86
1404 1512 3.003068 CAGAAGACTGTTTGTTGGCTGAG 59.997 47.826 0.00 0.00 39.11 3.35
1405 1513 2.945008 CAGAAGACTGTTTGTTGGCTGA 59.055 45.455 0.00 0.00 39.11 4.26
1406 1514 2.542411 GCAGAAGACTGTTTGTTGGCTG 60.542 50.000 0.00 0.00 45.04 4.85
1457 1565 1.153208 GATCTGGTGAGCTGCTGGG 60.153 63.158 7.01 0.00 0.00 4.45
1572 1686 1.446966 GTCCTTCACAGAGGCGCTC 60.447 63.158 7.64 2.67 36.71 5.03
2073 2187 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
2074 2188 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
2075 2189 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
2076 2190 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
2077 2191 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
2078 2192 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
2510 2624 1.356494 ATGCTCCCTCCCCCTAAAGC 61.356 60.000 0.00 0.00 0.00 3.51
2570 2684 4.236527 ACACCAAAACATATCCCTCTCC 57.763 45.455 0.00 0.00 0.00 3.71
2580 2694 2.698274 GGGGAACAGAACACCAAAACAT 59.302 45.455 0.00 0.00 0.00 2.71
2749 3122 5.751243 ATCCATTCGGTATTTGCTGTTAC 57.249 39.130 0.00 0.00 0.00 2.50
2750 3123 7.867305 TTTATCCATTCGGTATTTGCTGTTA 57.133 32.000 0.00 0.00 0.00 2.41
2751 3124 6.767524 TTTATCCATTCGGTATTTGCTGTT 57.232 33.333 0.00 0.00 0.00 3.16
2849 3225 0.102663 GGACTGCGCCTCTACTTACC 59.897 60.000 4.18 0.00 0.00 2.85
3098 3479 4.448060 GGGTCTACAAGTTCTCGACAAAAG 59.552 45.833 0.00 0.00 0.00 2.27
3106 3487 6.056236 GGGATAATTGGGTCTACAAGTTCTC 58.944 44.000 0.00 0.00 33.23 2.87
3115 3496 6.410388 GGACAAATGAGGGATAATTGGGTCTA 60.410 42.308 0.00 0.00 0.00 2.59
3125 3506 2.169769 GGACACGGACAAATGAGGGATA 59.830 50.000 0.00 0.00 0.00 2.59
3245 3626 3.781307 TGGATTGGGACGCCCTCG 61.781 66.667 14.76 0.00 45.70 4.63
3246 3627 2.124695 GTGGATTGGGACGCCCTC 60.125 66.667 14.76 6.16 45.70 4.30
3247 3628 4.096003 CGTGGATTGGGACGCCCT 62.096 66.667 14.76 0.00 45.70 5.19


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

AutoCloner maintained by Alex Coulton.