Multiple sequence alignment - TraesCS2B01G312700

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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 TraesCS2B01G312700 chr2B 100.000 3647 0 0 1 3647 448111906 448115552 0.000000e+00 6735.0
1 TraesCS2B01G312700 chr2B 100.000 35 0 0 250 284 750129699 750129665 8.450000e-07 65.8
2 TraesCS2B01G312700 chr2D 94.778 3351 133 22 20 3348 376690890 376694220 0.000000e+00 5180.0
3 TraesCS2B01G312700 chr2D 92.891 211 13 2 3343 3553 376696485 376696693 4.580000e-79 305.0
4 TraesCS2B01G312700 chr2D 94.253 87 5 0 3561 3647 376698949 376699035 2.280000e-27 134.0
5 TraesCS2B01G312700 chr2D 87.838 74 5 3 17 87 138296468 138296540 2.330000e-12 84.2
6 TraesCS2B01G312700 chr2A 92.268 3298 154 47 254 3482 510424786 510428051 0.000000e+00 4584.0
7 TraesCS2B01G312700 chr2A 95.679 162 7 0 3486 3647 510431437 510431598 1.000000e-65 261.0
8 TraesCS2B01G312700 chr1B 80.000 150 25 4 17 163 642732512 642732659 4.980000e-19 106.0
9 TraesCS2B01G312700 chr7A 81.188 101 13 4 184 284 696556235 696556329 3.910000e-10 76.8
10 TraesCS2B01G312700 chr6D 87.879 66 5 3 220 284 310412887 310412950 1.400000e-09 75.0
11 TraesCS2B01G312700 chrUn 90.909 55 2 2 231 284 21311768 21311820 1.820000e-08 71.3
12 TraesCS2B01G312700 chr4D 86.207 58 6 2 227 284 486528309 486528254 1.090000e-05 62.1
13 TraesCS2B01G312700 chr4D 79.070 86 13 4 200 284 486534318 486534237 2.000000e-03 54.7
14 TraesCS2B01G312700 chr5B 75.172 145 24 10 255 393 505562176 505562038 1.410000e-04 58.4
15 TraesCS2B01G312700 chr4B 100.000 28 0 0 257 284 620376456 620376483 7.000000e-03 52.8


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 TraesCS2B01G312700 chr2B 448111906 448115552 3646 False 6735.0 6735 100.0000 1 3647 1 chr2B.!!$F1 3646
1 TraesCS2B01G312700 chr2D 376690890 376699035 8145 False 1873.0 5180 93.9740 20 3647 3 chr2D.!!$F2 3627
2 TraesCS2B01G312700 chr2A 510424786 510431598 6812 False 2422.5 4584 93.9735 254 3647 2 chr2A.!!$F1 3393

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
887 925 0.804989 CAGCTACTTTTCTTGGGCCG 59.195 55.0 0.0 0.0 0.00 6.13 F
1307 1375 0.249699 TTCAATATCGTCCGCCGCAT 60.250 50.0 0.0 0.0 36.19 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 1856 0.175760 ATGAGAACACATCCCGGTCG 59.824 55.0 0.0 0.0 0.00 4.79 R
3037 3106 1.957668 TCATCTCATCGGCAATGGTG 58.042 50.0 0.0 0.0 35.94 4.17 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
78 79 7.160726 TGATGTCTATTTTCTCACACACATCA 58.839 34.615 7.21 7.21 44.03 3.07
195 196 7.617533 ATGTTAACAAAGTTCAAATACACGC 57.382 32.000 13.23 0.00 0.00 5.34
291 292 9.426837 ACATTTTCTAAAAATGTCATGACCATG 57.573 29.630 22.85 3.70 44.83 3.66
371 372 9.624697 TGTATGAAACACTTTTCTGAATTATGC 57.375 29.630 0.00 0.00 41.64 3.14
426 427 6.027131 TGTGACAAACATATTTTAGATGCGC 58.973 36.000 0.00 0.00 32.36 6.09
427 428 6.128035 TGTGACAAACATATTTTAGATGCGCT 60.128 34.615 9.73 0.00 32.36 5.92
429 430 8.070171 GTGACAAACATATTTTAGATGCGCTAT 58.930 33.333 9.73 0.00 0.00 2.97
464 465 2.951457 TTCTGCATGCCATCAACATG 57.049 45.000 16.68 0.00 46.19 3.21
524 536 8.918961 TTTTACGAAAATGATAAATGCCGAAT 57.081 26.923 0.00 0.00 0.00 3.34
525 537 7.906611 TTACGAAAATGATAAATGCCGAATG 57.093 32.000 0.00 0.00 0.00 2.67
583 596 7.697710 TCGATGACAATTTTAATGATGCAAGAC 59.302 33.333 0.00 0.00 0.00 3.01
596 609 1.601903 TGCAAGACGGCAAGTTTAGTG 59.398 47.619 0.00 0.00 41.65 2.74
688 701 1.027792 TCCCCGCGCCACTAAATTTC 61.028 55.000 0.00 0.00 0.00 2.17
694 707 2.351418 CGCGCCACTAAATTTCTCATCA 59.649 45.455 0.00 0.00 0.00 3.07
696 709 4.346129 GCGCCACTAAATTTCTCATCAAG 58.654 43.478 0.00 0.00 0.00 3.02
701 714 7.247019 GCCACTAAATTTCTCATCAAGAACTC 58.753 38.462 0.00 0.00 43.75 3.01
703 716 8.663911 CCACTAAATTTCTCATCAAGAACTCTC 58.336 37.037 0.00 0.00 43.75 3.20
744 757 0.812412 AATGTTCGGGCGTTATCGGG 60.812 55.000 0.00 0.00 37.56 5.14
864 900 3.192844 AGTGATCTAAAGGAAGCGAACGA 59.807 43.478 0.00 0.00 0.00 3.85
887 925 0.804989 CAGCTACTTTTCTTGGGCCG 59.195 55.000 0.00 0.00 0.00 6.13
911 949 1.540363 CCTTGACCACAACGCTGTAGT 60.540 52.381 0.00 0.00 33.22 2.73
923 961 3.075005 TGTAGTCGAGCCCAGGCC 61.075 66.667 4.70 0.00 43.17 5.19
924 962 3.851128 GTAGTCGAGCCCAGGCCC 61.851 72.222 4.70 0.00 43.17 5.80
929 967 4.676951 CGAGCCCAGGCCCCAAAA 62.677 66.667 4.70 0.00 43.17 2.44
930 968 2.681421 GAGCCCAGGCCCCAAAAG 60.681 66.667 4.70 0.00 43.17 2.27
932 970 4.638895 GCCCAGGCCCCAAAAGGT 62.639 66.667 0.00 0.00 34.56 3.50
935 973 1.462928 CCAGGCCCCAAAAGGTACA 59.537 57.895 0.00 0.00 0.00 2.90
937 975 0.898326 CAGGCCCCAAAAGGTACACC 60.898 60.000 0.00 0.00 0.00 4.16
939 977 1.154221 GCCCCAAAAGGTACACCCA 59.846 57.895 0.00 0.00 36.42 4.51
940 978 0.898326 GCCCCAAAAGGTACACCCAG 60.898 60.000 0.00 0.00 36.42 4.45
1254 1322 2.574399 GTCCTCGCCTCACACTCC 59.426 66.667 0.00 0.00 0.00 3.85
1307 1375 0.249699 TTCAATATCGTCCGCCGCAT 60.250 50.000 0.00 0.00 36.19 4.73
1309 1377 0.943835 CAATATCGTCCGCCGCATCA 60.944 55.000 0.00 0.00 36.19 3.07
1605 1673 2.610232 GCTTTTTGACCGAATGCCACAT 60.610 45.455 0.00 0.00 0.00 3.21
1708 1776 1.720781 AATGCCCCAAAGAACTGCTT 58.279 45.000 0.00 0.00 38.88 3.91
1745 1813 0.623723 ATCGGTGGGTATGCAAAGGT 59.376 50.000 0.00 0.00 0.00 3.50
1890 1958 7.795482 TTTTAATGAGTTCCGTGAGAAAGAA 57.205 32.000 0.00 0.00 35.85 2.52
1921 1989 4.388773 CAGACGAGCTTGTTATTGTTGCTA 59.611 41.667 8.34 0.00 33.83 3.49
2412 2480 2.029918 GTCAATGCCAGGAAAACCTCAC 60.030 50.000 0.00 0.00 0.00 3.51
2486 2554 1.862827 GCTTGGAAAAGTTGCAGCAAG 59.137 47.619 8.49 0.00 30.85 4.01
2604 2672 5.936956 AGTTAGAGCTGAAATGACTGGAAAG 59.063 40.000 0.00 0.00 0.00 2.62
2669 2737 9.109393 GTAAGGCATTTGTTGAGACTATTGATA 57.891 33.333 0.00 0.00 0.00 2.15
2700 2768 4.718940 TTTATCTTGCCTTAGCTTTGCC 57.281 40.909 0.00 0.00 40.80 4.52
3037 3106 4.125703 CTGGTGAGATTTCATCTACTGCC 58.874 47.826 0.00 0.00 40.38 4.85
3038 3107 3.519107 TGGTGAGATTTCATCTACTGCCA 59.481 43.478 0.00 0.00 40.38 4.92
3060 3129 1.877443 CATTGCCGATGAGATGATGCA 59.123 47.619 0.00 0.00 38.03 3.96
3125 3194 9.781633 TTCTTTACTACCTATTTAGTTTGTGCA 57.218 29.630 0.00 0.00 34.10 4.57
3129 3198 7.668525 ACTACCTATTTAGTTTGTGCACTTC 57.331 36.000 19.41 8.28 0.00 3.01
3258 3331 8.830580 CATTTCAGGTATAATGAACTCGTGAAT 58.169 33.333 1.98 0.00 36.44 2.57
3259 3332 7.770801 TTCAGGTATAATGAACTCGTGAATG 57.229 36.000 0.00 0.00 31.86 2.67
3260 3333 6.873997 TCAGGTATAATGAACTCGTGAATGT 58.126 36.000 0.00 0.00 0.00 2.71
3261 3334 8.002984 TCAGGTATAATGAACTCGTGAATGTA 57.997 34.615 0.00 0.00 0.00 2.29
3265 3338 9.698617 GGTATAATGAACTCGTGAATGTAAAAC 57.301 33.333 0.00 0.00 0.00 2.43
3281 3354 9.659830 GAATGTAAAACGGACATATATTTCACC 57.340 33.333 1.49 0.00 36.50 4.02
3317 3390 4.721977 GCGCATACTTTTGTACAATGTACG 59.278 41.667 17.47 17.92 37.78 3.67
3401 5752 9.546428 TGTACATGTATGGATTGTCTATCTTTG 57.454 33.333 9.18 0.00 33.53 2.77
3417 5768 4.357918 TCTTTGAACTCCTAGCTTTGCT 57.642 40.909 0.00 0.00 43.41 3.91
3501 9234 2.322658 TCACTTTACCCCTTCGACTGT 58.677 47.619 0.00 0.00 0.00 3.55
3560 9293 3.598693 TGCCCCATCATCACACATTAT 57.401 42.857 0.00 0.00 0.00 1.28
3583 11564 7.958053 ATCTGAAAAATCAGCAAAAAGGAAG 57.042 32.000 0.97 0.00 37.63 3.46
3586 11567 6.877236 TGAAAAATCAGCAAAAAGGAAGAGT 58.123 32.000 0.00 0.00 0.00 3.24
3629 11610 0.251386 AGTGCTCGTCAAGGAGGAGA 60.251 55.000 17.34 3.12 44.32 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 177 5.493133 TCAGCGTGTATTTGAACTTTGTT 57.507 34.783 0.00 0.00 0.00 2.83
178 179 5.741510 TGTTTCAGCGTGTATTTGAACTTTG 59.258 36.000 0.00 0.00 31.11 2.77
361 362 8.446489 TGTAAACAAATGTTCGCATAATTCAG 57.554 30.769 0.00 0.00 37.25 3.02
402 403 6.027131 GCGCATCTAAAATATGTTTGTCACA 58.973 36.000 0.30 0.00 40.71 3.58
464 465 8.682710 TGCAGTGTTAAAATGATATTCCTAACC 58.317 33.333 0.00 0.00 0.00 2.85
535 547 7.205992 TCGAAAATGTTCAATTTTCCATGACA 58.794 30.769 14.64 0.00 42.12 3.58
536 548 7.636259 TCGAAAATGTTCAATTTTCCATGAC 57.364 32.000 14.64 0.00 42.12 3.06
558 570 7.305019 CGTCTTGCATCATTAAAATTGTCATCG 60.305 37.037 0.00 0.00 0.00 3.84
583 596 1.263217 GTGTGTCCACTAAACTTGCCG 59.737 52.381 0.00 0.00 38.61 5.69
596 609 8.056593 TTTTCCAGAAAATTGACAAGTGTGTCC 61.057 37.037 1.45 0.00 42.63 4.02
688 701 5.182570 TGGCAAATTGAGAGTTCTTGATGAG 59.817 40.000 0.00 0.00 0.00 2.90
694 707 4.154942 ACCATGGCAAATTGAGAGTTCTT 58.845 39.130 13.04 0.00 0.00 2.52
696 709 3.507233 TGACCATGGCAAATTGAGAGTTC 59.493 43.478 13.04 0.00 0.00 3.01
829 843 7.281324 TCCTTTAGATCACTCGTTTGTTTCAAA 59.719 33.333 0.00 0.00 0.00 2.69
864 900 2.297315 GCCCAAGAAAAGTAGCTGCTTT 59.703 45.455 22.34 22.34 40.07 3.51
892 930 1.865865 ACTACAGCGTTGTGGTCAAG 58.134 50.000 15.44 6.58 44.63 3.02
923 961 1.271926 CCTCTGGGTGTACCTTTTGGG 60.272 57.143 0.44 0.00 46.08 4.12
924 962 1.886655 GCCTCTGGGTGTACCTTTTGG 60.887 57.143 0.44 1.08 41.11 3.28
929 967 2.285442 GGGCCTCTGGGTGTACCT 60.285 66.667 0.84 0.00 41.11 3.08
930 968 3.408853 GGGGCCTCTGGGTGTACC 61.409 72.222 0.84 0.00 40.81 3.34
932 970 1.464395 TTTGGGGCCTCTGGGTGTA 60.464 57.895 3.07 0.00 34.45 2.90
935 973 3.966543 CGTTTGGGGCCTCTGGGT 61.967 66.667 3.07 0.00 34.45 4.51
937 975 4.659172 TGCGTTTGGGGCCTCTGG 62.659 66.667 3.07 0.00 0.00 3.86
1095 1163 3.565214 TGGAGGCCAAGGCGAACA 61.565 61.111 5.01 0.67 43.06 3.18
1578 1646 0.179040 TTCGGTCAAAAAGCTCCCGT 60.179 50.000 0.00 0.00 39.62 5.28
1605 1673 3.404899 GTTCCAATGAACCACGTTCCTA 58.595 45.455 2.26 0.00 44.20 2.94
1708 1776 1.667212 GATCAATGATGTGTGCGCTGA 59.333 47.619 9.73 0.00 0.00 4.26
1745 1813 5.888691 TTTCGCAACTTGCATATTTCCTA 57.111 34.783 14.10 0.00 45.36 2.94
1764 1832 8.005466 TCGTGTAACTTATCGAACAACATTTTC 58.995 33.333 0.00 0.00 31.75 2.29
1788 1856 0.175760 ATGAGAACACATCCCGGTCG 59.824 55.000 0.00 0.00 0.00 4.79
1890 1958 1.210478 ACAAGCTCGTCTGGGCATATT 59.790 47.619 0.00 0.00 0.00 1.28
1921 1989 1.153289 GGGAGCACGCTGTCATCAT 60.153 57.895 0.00 0.00 0.00 2.45
2412 2480 4.586235 GCACCCCATGATCCCGGG 62.586 72.222 16.85 16.85 43.05 5.73
2486 2554 6.048509 TCTGGTTCAATTTCAAAAAGCTTCC 58.951 36.000 0.00 0.00 0.00 3.46
2604 2672 4.380128 CGACCTGCTATTTTTGTTAACCCC 60.380 45.833 2.48 0.00 0.00 4.95
2700 2768 6.338146 TCTACTCAACATTCCAATAAGGTCG 58.662 40.000 0.00 0.00 39.02 4.79
2759 2827 3.899734 TGACAATGCAAAGCACACATAC 58.100 40.909 0.00 0.00 43.04 2.39
2811 2879 3.747529 CCAAACTTGGGTGCAAATCATTC 59.252 43.478 0.09 0.00 44.70 2.67
2840 2908 3.954258 GCAACCTTCTACCATAAAGGCAT 59.046 43.478 1.13 0.00 44.93 4.40
2841 2909 3.010138 AGCAACCTTCTACCATAAAGGCA 59.990 43.478 1.13 0.00 44.93 4.75
2842 2910 3.378427 CAGCAACCTTCTACCATAAAGGC 59.622 47.826 1.13 0.00 44.93 4.35
2843 2911 3.378427 GCAGCAACCTTCTACCATAAAGG 59.622 47.826 0.00 0.00 46.21 3.11
2844 2912 4.265073 AGCAGCAACCTTCTACCATAAAG 58.735 43.478 0.00 0.00 0.00 1.85
2845 2913 4.301072 AGCAGCAACCTTCTACCATAAA 57.699 40.909 0.00 0.00 0.00 1.40
2846 2914 4.301072 AAGCAGCAACCTTCTACCATAA 57.699 40.909 0.00 0.00 0.00 1.90
2847 2915 4.301072 AAAGCAGCAACCTTCTACCATA 57.699 40.909 0.00 0.00 0.00 2.74
2953 3021 8.863872 TGTCAGCATATACTAGAAGCACTATA 57.136 34.615 0.00 0.00 0.00 1.31
3037 3106 1.957668 TCATCTCATCGGCAATGGTG 58.042 50.000 0.00 0.00 35.94 4.17
3038 3107 2.501261 CATCATCTCATCGGCAATGGT 58.499 47.619 0.00 0.00 35.94 3.55
3115 3184 5.789521 TGTATGCTAGAAGTGCACAAACTA 58.210 37.500 21.04 16.55 43.59 2.24
3125 3194 4.141914 GGCACTACCTTGTATGCTAGAAGT 60.142 45.833 0.00 0.00 38.18 3.01
3129 3198 2.743938 CGGCACTACCTTGTATGCTAG 58.256 52.381 0.00 0.00 38.18 3.42
3258 3331 8.795842 AAGGTGAAATATATGTCCGTTTTACA 57.204 30.769 0.23 0.00 0.00 2.41
3259 3332 9.498307 CAAAGGTGAAATATATGTCCGTTTTAC 57.502 33.333 0.23 0.00 0.00 2.01
3260 3333 9.233649 ACAAAGGTGAAATATATGTCCGTTTTA 57.766 29.630 0.23 0.00 0.00 1.52
3261 3334 8.117813 ACAAAGGTGAAATATATGTCCGTTTT 57.882 30.769 0.23 0.00 0.00 2.43
3265 3338 7.985476 AGAAACAAAGGTGAAATATATGTCCG 58.015 34.615 0.23 0.00 0.00 4.79
3281 3354 7.114811 ACAAAAGTATGCGCATAAGAAACAAAG 59.885 33.333 30.50 16.04 0.00 2.77
3317 3390 2.953640 TCACGGAAAAACGTATGCAC 57.046 45.000 0.00 0.00 46.75 4.57
3358 5709 4.537751 TGTACATTGTGTGGGAAAAAGGA 58.462 39.130 0.00 0.00 0.00 3.36
3401 5752 3.669536 ACTCAAGCAAAGCTAGGAGTTC 58.330 45.455 15.96 0.00 44.88 3.01
3501 9234 5.186797 ACATCAGTGAAAACAACTTTGGGAA 59.813 36.000 0.00 0.00 0.00 3.97
3560 9293 7.111247 TCTTCCTTTTTGCTGATTTTTCAGA 57.889 32.000 7.16 0.00 39.99 3.27
3583 11564 4.067896 TGCAGACCTTTTCATCTTCACTC 58.932 43.478 0.00 0.00 0.00 3.51
3586 11567 6.417258 TGATATGCAGACCTTTTCATCTTCA 58.583 36.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.