Multiple sequence alignment - TraesCS2B01G246500

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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 TraesCS2B01G246500 chr2B 100.000 9582 0 0 1 9582 250734326 250743907 0.000000e+00 17695.0
1 TraesCS2B01G246500 chr2D 96.007 8815 215 41 814 9582 194754766 194763489 0.000000e+00 14201.0
2 TraesCS2B01G246500 chr2A 96.997 6960 140 22 841 7774 209386938 209393854 0.000000e+00 11631.0
3 TraesCS2B01G246500 chr2A 95.249 1810 53 14 7780 9582 209394070 209395853 0.000000e+00 2835.0
4 TraesCS2B01G246500 chr2A 82.526 578 60 27 1 574 377154191 377154731 4.050000e-128 470.0
5 TraesCS2B01G246500 chr2A 92.788 208 13 1 607 812 377154792 377154999 5.620000e-77 300.0
6 TraesCS2B01G246500 chr2A 88.496 113 12 1 700 811 377151076 377150964 1.680000e-27 135.0
7 TraesCS2B01G246500 chrUn 98.551 414 6 0 6370 6783 477336710 477336297 0.000000e+00 732.0
8 TraesCS2B01G246500 chrUn 98.301 412 7 0 1 412 39283624 39284035 0.000000e+00 723.0
9 TraesCS2B01G246500 chrUn 93.008 472 25 7 349 819 39283930 39284394 0.000000e+00 682.0
10 TraesCS2B01G246500 chrUn 88.764 445 41 6 378 814 110705811 110705368 3.940000e-148 536.0
11 TraesCS2B01G246500 chrUn 88.218 331 24 9 4 334 110706104 110705789 1.950000e-101 381.0
12 TraesCS2B01G246500 chrUn 88.496 113 12 1 700 811 39280440 39280328 1.680000e-27 135.0
13 TraesCS2B01G246500 chr6D 88.309 479 43 10 348 818 467139875 467139402 6.500000e-156 562.0
14 TraesCS2B01G246500 chr6D 84.368 467 47 20 4 460 467140162 467139712 1.480000e-117 435.0
15 TraesCS2B01G246500 chr3B 93.048 374 24 2 440 811 81305823 81305450 6.540000e-151 545.0
16 TraesCS2B01G246500 chr3B 88.022 359 27 10 4 361 81306166 81305823 2.490000e-110 411.0
17 TraesCS2B01G246500 chr3B 89.076 119 11 2 700 817 81327039 81327156 7.750000e-31 147.0
18 TraesCS2B01G246500 chr5D 86.618 411 37 12 4 411 509554943 509554548 1.140000e-118 438.0
19 TraesCS2B01G246500 chr5D 84.804 408 45 11 415 813 509554616 509554217 2.510000e-105 394.0
20 TraesCS2B01G246500 chr7A 88.796 357 33 5 5972 6323 145457161 145456807 1.910000e-116 431.0
21 TraesCS2B01G246500 chr6B 88.136 354 35 5 5972 6320 538998818 538999169 1.930000e-111 414.0
22 TraesCS2B01G246500 chr5A 87.955 357 36 5 5972 6323 452465619 452465265 1.930000e-111 414.0
23 TraesCS2B01G246500 chr5A 86.196 326 27 14 50 374 69018839 69019147 4.290000e-88 337.0
24 TraesCS2B01G246500 chr5A 92.754 207 13 1 607 811 69019369 69019575 2.020000e-76 298.0
25 TraesCS2B01G246500 chr5A 76.371 237 38 13 348 574 69019080 69019308 2.830000e-20 111.0
26 TraesCS2B01G246500 chr4A 88.136 354 35 5 5972 6320 514233431 514233782 1.930000e-111 414.0
27 TraesCS2B01G246500 chr3A 87.879 330 25 10 5 334 17088047 17087733 3.270000e-99 374.0
28 TraesCS2B01G246500 chr1A 89.773 88 8 1 1223 1310 34933778 34933864 2.830000e-20 111.0
29 TraesCS2B01G246500 chr7B 85.417 96 12 2 1215 1310 458530685 458530778 2.200000e-16 99.0
30 TraesCS2B01G246500 chr3D 94.231 52 3 0 1220 1271 560151668 560151719 7.980000e-11 80.5
31 TraesCS2B01G246500 chr1D 90.741 54 5 0 1215 1268 364473096 364473149 1.330000e-08 73.1


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 TraesCS2B01G246500 chr2B 250734326 250743907 9581 False 17695.000000 17695 100.0000 1 9582 1 chr2B.!!$F1 9581
1 TraesCS2B01G246500 chr2D 194754766 194763489 8723 False 14201.000000 14201 96.0070 814 9582 1 chr2D.!!$F1 8768
2 TraesCS2B01G246500 chr2A 209386938 209395853 8915 False 7233.000000 11631 96.1230 841 9582 2 chr2A.!!$F1 8741
3 TraesCS2B01G246500 chr2A 377154191 377154999 808 False 385.000000 470 87.6570 1 812 2 chr2A.!!$F2 811
4 TraesCS2B01G246500 chrUn 39283624 39284394 770 False 702.500000 723 95.6545 1 819 2 chrUn.!!$F1 818
5 TraesCS2B01G246500 chrUn 110705368 110706104 736 True 458.500000 536 88.4910 4 814 2 chrUn.!!$R3 810
6 TraesCS2B01G246500 chr6D 467139402 467140162 760 True 498.500000 562 86.3385 4 818 2 chr6D.!!$R1 814
7 TraesCS2B01G246500 chr3B 81305450 81306166 716 True 478.000000 545 90.5350 4 811 2 chr3B.!!$R1 807
8 TraesCS2B01G246500 chr5D 509554217 509554943 726 True 416.000000 438 85.7110 4 813 2 chr5D.!!$R1 809
9 TraesCS2B01G246500 chr5A 69018839 69019575 736 False 248.666667 337 85.1070 50 811 3 chr5A.!!$F1 761

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
942 1068 1.352352 CTCACACCACTTCCTCCCAAT 59.648 52.381 0.00 0.0 0.00 3.16 F
1659 1797 1.479323 TGTAGATACGGGAAGTGCCAC 59.521 52.381 0.00 0.0 38.95 5.01 F
1789 1934 0.535102 GGTGTATAGCTTGGCGCCAT 60.535 55.000 33.25 19.1 40.39 4.40 F
2159 2305 1.188863 TACGACCCCTTAGTGCCTTC 58.811 55.000 0.00 0.0 0.00 3.46 F
2359 2505 3.135994 GGTTGAACTAACTCGCCTTTCA 58.864 45.455 0.00 0.0 39.31 2.69 F
4108 4255 0.250901 GAGCAAGGAACTGGGAAGCA 60.251 55.000 0.00 0.0 40.86 3.91 F
4834 4990 0.945099 CTATCAGCGTCCTCGTGCTA 59.055 55.000 0.00 0.0 40.03 3.49 F
4945 5101 2.426024 CAGGAATGGCAGAAAGTCCATG 59.574 50.000 0.00 0.0 41.92 3.66 F
5535 5702 2.455674 TATCACGCAACAGAGCACTT 57.544 45.000 0.00 0.0 0.00 3.16 F
6594 6767 1.271597 ACTGCACTCCCAACTCCAATC 60.272 52.381 0.00 0.0 0.00 2.67 F
8110 8497 1.439644 GTCATCTGTCGAGCCTCCC 59.560 63.158 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1909 1.151777 CCAAGCTATACACCCGTGCG 61.152 60.000 0.00 0.00 0.00 5.34 R
2774 2920 2.354510 TGCGGGAAATCGACAATGAATC 59.645 45.455 0.00 0.00 0.00 2.52 R
3664 3811 1.551329 GCCCCCAGTGGTTATCCAAAA 60.551 52.381 8.74 0.00 46.15 2.44 R
3986 4133 1.482593 ACTGGTCTCCCTCTTATTGCG 59.517 52.381 0.00 0.00 0.00 4.85 R
4346 4502 1.908619 TCCTTCCATGTAGCAGCTTCA 59.091 47.619 0.00 0.90 0.00 3.02 R
4945 5101 1.866925 GTTCCAACTGCGCCAGTAC 59.133 57.895 4.18 0.08 44.62 2.73 R
6159 6332 1.455383 CGGTTGCAGCCTCCAACTTT 61.455 55.000 18.19 0.00 41.64 2.66 R
6594 6767 2.290323 CCCAGTAAACAAGGGAGAGGTG 60.290 54.545 5.03 0.00 45.80 4.00 R
7196 7369 1.212935 AGCATACCCAATGACCTGTCC 59.787 52.381 0.00 0.00 37.86 4.02 R
8323 8710 0.859232 CCTCACGGAACAACTTGTCG 59.141 55.000 0.00 0.00 0.00 4.35 R
8930 9319 1.797025 CCGGTCAACAGTTCTTCCTC 58.203 55.000 0.00 0.00 0.00 3.71 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
335 336 1.704082 CCTCCAGGTCCACCCTCTA 59.296 63.158 0.00 0.00 43.86 2.43
377 378 3.013932 CTCCAGGCCTGCCCTCTT 61.014 66.667 28.39 0.00 44.09 2.85
378 379 3.011517 TCCAGGCCTGCCCTCTTC 61.012 66.667 28.39 0.00 44.09 2.87
379 380 4.120755 CCAGGCCTGCCCTCTTCC 62.121 72.222 28.39 0.00 44.09 3.46
380 381 4.479993 CAGGCCTGCCCTCTTCCG 62.480 72.222 22.33 0.00 44.09 4.30
551 640 2.046314 GCCGCTGCTAGGGTTTCA 60.046 61.111 0.00 0.00 33.53 2.69
619 737 1.482593 CGATAAGGTGAGGAAGGCTGT 59.517 52.381 0.00 0.00 0.00 4.40
820 942 7.757941 AGAAGGAATTCTCTCAAAGAAAAGG 57.242 36.000 5.23 0.00 46.85 3.11
942 1068 1.352352 CTCACACCACTTCCTCCCAAT 59.648 52.381 0.00 0.00 0.00 3.16
961 1089 2.190578 CCCCCGTGCTCTGATTCC 59.809 66.667 0.00 0.00 0.00 3.01
1320 1458 4.735132 CTCAAGCCCGCCGACGAA 62.735 66.667 0.00 0.00 43.93 3.85
1659 1797 1.479323 TGTAGATACGGGAAGTGCCAC 59.521 52.381 0.00 0.00 38.95 5.01
1789 1934 0.535102 GGTGTATAGCTTGGCGCCAT 60.535 55.000 33.25 19.10 40.39 4.40
1810 1956 2.942376 TGTTACTGTGCTTTGTGGTGAG 59.058 45.455 0.00 0.00 0.00 3.51
1910 2056 2.512885 CAGCGTGAAATTCAGCATCAC 58.487 47.619 15.78 0.00 39.98 3.06
1911 2057 2.095617 CAGCGTGAAATTCAGCATCACA 60.096 45.455 15.78 0.00 42.76 3.58
1975 2121 4.763793 AGCTGTCTGTTTGATGCTTAATGT 59.236 37.500 0.00 0.00 35.12 2.71
2006 2152 2.284190 GTAGGAAGATGCCTGTTCTGC 58.716 52.381 0.00 0.00 39.08 4.26
2097 2243 9.737427 AATGAGTGAGATCTTATAGTTAACGTG 57.263 33.333 0.00 0.00 0.00 4.49
2098 2244 7.194278 TGAGTGAGATCTTATAGTTAACGTGC 58.806 38.462 0.00 0.00 0.00 5.34
2099 2245 6.505272 AGTGAGATCTTATAGTTAACGTGCC 58.495 40.000 0.00 0.00 0.00 5.01
2100 2246 6.096423 AGTGAGATCTTATAGTTAACGTGCCA 59.904 38.462 0.00 0.00 0.00 4.92
2101 2247 6.755141 GTGAGATCTTATAGTTAACGTGCCAA 59.245 38.462 0.00 0.00 0.00 4.52
2102 2248 7.438459 GTGAGATCTTATAGTTAACGTGCCAAT 59.562 37.037 0.00 0.00 0.00 3.16
2103 2249 7.985184 TGAGATCTTATAGTTAACGTGCCAATT 59.015 33.333 0.00 0.00 0.00 2.32
2104 2250 9.472361 GAGATCTTATAGTTAACGTGCCAATTA 57.528 33.333 0.00 0.00 0.00 1.40
2105 2251 9.998106 AGATCTTATAGTTAACGTGCCAATTAT 57.002 29.630 0.00 0.00 0.00 1.28
2107 2253 9.998106 ATCTTATAGTTAACGTGCCAATTATCT 57.002 29.630 0.00 0.00 0.00 1.98
2108 2254 9.826574 TCTTATAGTTAACGTGCCAATTATCTT 57.173 29.630 0.00 0.00 0.00 2.40
2112 2258 6.768078 AGTTAACGTGCCAATTATCTTAACG 58.232 36.000 0.00 0.00 35.78 3.18
2153 2299 2.100989 CTGAGCTTACGACCCCTTAGT 58.899 52.381 0.00 0.00 0.00 2.24
2159 2305 1.188863 TACGACCCCTTAGTGCCTTC 58.811 55.000 0.00 0.00 0.00 3.46
2190 2336 7.529519 CGTTATTAACAGTTTCACTAGTGTTGC 59.470 37.037 21.99 12.70 40.79 4.17
2359 2505 3.135994 GGTTGAACTAACTCGCCTTTCA 58.864 45.455 0.00 0.00 39.31 2.69
2486 2632 3.910627 AGTTTCTGTCCCTGGTTAGTGAT 59.089 43.478 0.00 0.00 0.00 3.06
2606 2752 5.356190 CCTTGCAATGATCTAAGCTTTCTCA 59.644 40.000 3.20 6.02 0.00 3.27
2658 2804 3.731652 TGTGTTTTGCTGGAGGAATTG 57.268 42.857 0.00 0.00 0.00 2.32
2774 2920 9.438291 CTATTAATTTGTGCTATTTTCCTCACG 57.562 33.333 0.00 0.00 32.48 4.35
3546 3693 7.163682 GTCACGTTAACTTTTGTTTCTGATCAC 59.836 37.037 3.71 0.00 43.32 3.06
3663 3810 5.882557 ACTCTGGTTGATGGTTGATATGTTC 59.117 40.000 0.00 0.00 0.00 3.18
3664 3811 6.065976 TCTGGTTGATGGTTGATATGTTCT 57.934 37.500 0.00 0.00 0.00 3.01
3986 4133 1.128015 GAACGAGAACTTGCGTCGC 59.872 57.895 11.10 11.10 40.23 5.19
4108 4255 0.250901 GAGCAAGGAACTGGGAAGCA 60.251 55.000 0.00 0.00 40.86 3.91
4346 4502 1.497161 CGGAACCTGTCCCTAAGGAT 58.503 55.000 0.00 0.00 46.41 3.24
4461 4617 4.638421 TGAACGATTGAACTTCTTTGTGGT 59.362 37.500 0.00 0.00 0.00 4.16
4834 4990 0.945099 CTATCAGCGTCCTCGTGCTA 59.055 55.000 0.00 0.00 40.03 3.49
4945 5101 2.426024 CAGGAATGGCAGAAAGTCCATG 59.574 50.000 0.00 0.00 41.92 3.66
5114 5270 7.279313 GGTAAACATTCCTAAACTCGCTATTGA 59.721 37.037 0.00 0.00 0.00 2.57
5116 5272 6.910536 ACATTCCTAAACTCGCTATTGAAG 57.089 37.500 0.00 0.00 0.00 3.02
5396 5561 4.389890 TGAATTTGCTGCTTCAACAACT 57.610 36.364 0.00 0.00 0.00 3.16
5401 5566 3.631145 TGCTGCTTCAACAACTTCATC 57.369 42.857 0.00 0.00 0.00 2.92
5402 5567 2.950975 TGCTGCTTCAACAACTTCATCA 59.049 40.909 0.00 0.00 0.00 3.07
5403 5568 3.570975 TGCTGCTTCAACAACTTCATCAT 59.429 39.130 0.00 0.00 0.00 2.45
5535 5702 2.455674 TATCACGCAACAGAGCACTT 57.544 45.000 0.00 0.00 0.00 3.16
5592 5759 7.593875 TTTTCAATTAATGCAGGATTTTCCG 57.406 32.000 0.00 0.00 42.75 4.30
5605 5772 4.157840 AGGATTTTCCGTTAAGTGGCATTC 59.842 41.667 0.00 0.00 42.75 2.67
5634 5801 8.200792 AGTAATTTATCAGTCTAACCTGCTCTG 58.799 37.037 0.00 0.00 32.32 3.35
5644 5811 6.663953 AGTCTAACCTGCTCTGTATTTAGTGA 59.336 38.462 0.00 0.00 0.00 3.41
5678 5845 6.789268 TCCCTCTTCCAGAAATAACAAATCA 58.211 36.000 0.00 0.00 0.00 2.57
5820 5987 8.153550 ACACTGTTCTCATAGAATTCTGTTCTT 58.846 33.333 18.47 0.00 36.50 2.52
6061 6234 8.409358 AGTCATTTTGGCACTTTTAGAGTAAT 57.591 30.769 0.00 0.00 36.65 1.89
6159 6332 3.075005 GACCCGGCTGTCTGGCTA 61.075 66.667 0.00 0.00 37.42 3.93
6498 6671 9.314321 GGAAAGAAGATAAATCATACTCGTTCA 57.686 33.333 0.00 0.00 0.00 3.18
6506 6679 9.088512 GATAAATCATACTCGTTCACTTGAAGT 57.911 33.333 0.00 0.00 34.27 3.01
6507 6680 7.730364 AAATCATACTCGTTCACTTGAAGTT 57.270 32.000 0.00 0.00 34.27 2.66
6513 6686 4.201822 ACTCGTTCACTTGAAGTTTTCTGC 60.202 41.667 0.00 0.00 34.27 4.26
6594 6767 1.271597 ACTGCACTCCCAACTCCAATC 60.272 52.381 0.00 0.00 0.00 2.67
6864 7037 5.657474 TCAACTGGTTCGATATTGAGGTAC 58.343 41.667 0.00 0.00 0.00 3.34
7102 7275 3.192541 TGCTTGTCTGAGTTAGTTGCA 57.807 42.857 0.00 0.00 0.00 4.08
7114 7287 2.754552 GTTAGTTGCAGAATGGCCATCA 59.245 45.455 21.08 9.99 35.86 3.07
7196 7369 5.294306 GCCTTTTCCTTTTCTTTGTTTCCTG 59.706 40.000 0.00 0.00 0.00 3.86
7230 7403 4.042311 TGGGTATGCTAAGTTTCCTTGTCA 59.958 41.667 0.00 0.00 31.89 3.58
7591 7764 5.180117 ACTCGAAAGATTTGTCATGAACCAG 59.820 40.000 0.00 0.00 40.84 4.00
7656 7829 4.081642 AGGCACTGTTCACGTATAAGACAT 60.082 41.667 0.00 0.00 37.18 3.06
7688 7861 2.578480 TGGGTATATTCACACCAGCCAA 59.422 45.455 0.00 0.00 36.48 4.52
7770 7943 8.773033 CCTAAAGTAGGGGTGTTAGATACTAA 57.227 38.462 0.00 0.00 42.42 2.24
7837 8221 2.332063 CTGGTAGCATAACCTGGGTG 57.668 55.000 0.00 0.00 40.44 4.61
7902 8286 2.320367 CTGCCATATCGTAGCGTCTTC 58.680 52.381 0.00 0.00 0.00 2.87
7937 8322 7.149973 GCATGTTTTCTACAATGCATATCCAT 58.850 34.615 0.00 0.00 40.89 3.41
7948 8333 2.076863 GCATATCCATAGTTCACGGCC 58.923 52.381 0.00 0.00 0.00 6.13
8110 8497 1.439644 GTCATCTGTCGAGCCTCCC 59.560 63.158 0.00 0.00 0.00 4.30
8197 8584 2.425143 TTGGGGATGATGAAGCTGAC 57.575 50.000 0.00 0.00 0.00 3.51
8290 8677 7.707624 AGGCAACAAAGATATTGATGAAGAA 57.292 32.000 3.08 0.00 41.41 2.52
8320 8707 2.941720 GGCTCAGTTTATCTGCCTCTTG 59.058 50.000 0.00 0.00 43.32 3.02
8323 8710 4.568760 GCTCAGTTTATCTGCCTCTTGTAC 59.431 45.833 0.00 0.00 43.32 2.90
8371 8758 2.105477 AGTGGACACTGCTCTTCAACAT 59.895 45.455 3.82 0.00 40.75 2.71
8380 8767 1.941209 GCTCTTCAACATGCACTCCGA 60.941 52.381 0.00 0.00 0.00 4.55
8416 8803 1.866015 AGTACAGCTGCCATCTACCA 58.134 50.000 15.27 0.00 0.00 3.25
8522 8909 8.221944 TGGATTCGTAATGGGGTTATAGAATTT 58.778 33.333 0.00 0.00 35.04 1.82
8595 8982 0.909623 AGGTAGGTGAATGTTCCCCG 59.090 55.000 0.00 0.00 29.33 5.73
8738 9127 0.674895 AGATTCAAGTGCCTGCGGTC 60.675 55.000 0.00 0.00 0.00 4.79
8763 9152 9.771534 TCTTATTGTTGAATTTTGGGTTTTAGG 57.228 29.630 0.00 0.00 0.00 2.69
8802 9191 3.719924 TCTCAGCAAATGTGGCAAAAAG 58.280 40.909 0.00 0.00 0.00 2.27
8926 9315 0.170339 GGCGTTTTGGTGTAGATGCC 59.830 55.000 0.00 0.00 37.06 4.40
8930 9319 1.199097 GTTTTGGTGTAGATGCCGGTG 59.801 52.381 1.90 0.00 0.00 4.94
8951 9340 0.534203 GGAAGAACTGTTGACCGGCA 60.534 55.000 0.00 0.00 0.00 5.69
8954 9343 0.108585 AGAACTGTTGACCGGCACAT 59.891 50.000 0.00 0.00 0.00 3.21
8997 9387 4.726416 CCGGCTCAAATATACATGAATGC 58.274 43.478 0.00 0.00 0.00 3.56
9001 9391 6.919662 CGGCTCAAATATACATGAATGCTTTT 59.080 34.615 0.00 0.00 0.00 2.27
9106 9498 8.154649 AGCAAGTAAATATATGCACCTACAAC 57.845 34.615 0.00 0.00 41.18 3.32
9163 9558 3.145286 GCTGAAGCAAGGTTCTTCTTCT 58.855 45.455 12.54 0.00 40.31 2.85
9164 9559 3.567585 GCTGAAGCAAGGTTCTTCTTCTT 59.432 43.478 12.54 0.00 40.31 2.52
9165 9560 4.320129 GCTGAAGCAAGGTTCTTCTTCTTC 60.320 45.833 12.54 0.00 40.31 2.87
9223 9618 1.495584 GACGCAACGAAACCTGCTCA 61.496 55.000 0.00 0.00 36.38 4.26
9247 9642 3.251004 CAGGTTCAGCAACTACTCAAACC 59.749 47.826 0.00 0.00 34.70 3.27
9250 9645 4.338400 GGTTCAGCAACTACTCAAACCTTT 59.662 41.667 0.00 0.00 33.00 3.11
9286 9681 2.033801 CCTTCACAAAGCAAGGTCAGTG 59.966 50.000 0.00 0.00 35.34 3.66
9348 9743 0.608582 AAGCTCACTCTACCGACCGT 60.609 55.000 0.00 0.00 0.00 4.83
9461 9856 3.826754 CTGACCTCGCCGCTAGCA 61.827 66.667 16.45 0.00 44.04 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 2.982488 ACTGTGATCCCTCCAAAGAAGT 59.018 45.455 0.00 0.00 0.00 3.01
232 233 1.228154 GCTTCGTGACCCCCACTTT 60.228 57.895 0.00 0.00 43.53 2.66
570 659 2.294078 CCTTTCTCACCCCGAGCCT 61.294 63.158 0.00 0.00 41.98 4.58
619 737 0.601057 TTTGACTCGATCGAGCACCA 59.399 50.000 38.12 29.75 45.54 4.17
757 879 9.979578 TTAAATTTGATGCTTTATGTGACACTT 57.020 25.926 7.20 3.00 0.00 3.16
789 911 8.766476 TCTTTGAGAGAATTCCTTCTATGACAT 58.234 33.333 0.65 0.00 41.87 3.06
820 942 0.789383 CGCGTCATTTCTTTGCGTCC 60.789 55.000 0.00 0.00 43.50 4.79
949 1077 2.911484 CTAGGGTTGGAATCAGAGCAC 58.089 52.381 0.00 0.00 0.00 4.40
950 1078 1.210478 GCTAGGGTTGGAATCAGAGCA 59.790 52.381 0.00 0.00 0.00 4.26
953 1081 0.178068 GCGCTAGGGTTGGAATCAGA 59.822 55.000 8.77 0.00 0.00 3.27
956 1084 1.526225 GGGCGCTAGGGTTGGAATC 60.526 63.158 7.64 0.00 0.00 2.52
957 1085 2.595655 GGGCGCTAGGGTTGGAAT 59.404 61.111 7.64 0.00 0.00 3.01
958 1086 4.090588 CGGGCGCTAGGGTTGGAA 62.091 66.667 7.64 0.00 0.00 3.53
1167 1305 1.514087 GAGGTCGCCGTTCATGGTA 59.486 57.895 0.00 0.00 0.00 3.25
1659 1797 0.316841 CACAAATCCCAAACCCACGG 59.683 55.000 0.00 0.00 0.00 4.94
1764 1909 1.151777 CCAAGCTATACACCCGTGCG 61.152 60.000 0.00 0.00 0.00 5.34
1789 1934 2.942376 CTCACCACAAAGCACAGTAACA 59.058 45.455 0.00 0.00 0.00 2.41
1893 2039 4.087510 ACATGTGATGCTGAATTTCACG 57.912 40.909 0.00 0.00 42.07 4.35
1910 2056 3.820467 ACCACCAGTCATTACACAACATG 59.180 43.478 0.00 0.00 0.00 3.21
1911 2057 3.820467 CACCACCAGTCATTACACAACAT 59.180 43.478 0.00 0.00 0.00 2.71
1975 2121 6.095860 CAGGCATCTTCCTACAAAATGATCAA 59.904 38.462 0.00 0.00 33.95 2.57
2006 2152 6.033831 GGTTTGATTGTTCAATACTGAATGCG 59.966 38.462 0.00 0.00 43.39 4.73
2096 2242 3.348119 TGGCACGTTAAGATAATTGGCA 58.652 40.909 0.00 0.00 37.21 4.92
2097 2243 4.364415 TTGGCACGTTAAGATAATTGGC 57.636 40.909 0.00 0.00 0.00 4.52
2098 2244 8.567948 AGATAATTGGCACGTTAAGATAATTGG 58.432 33.333 0.00 0.00 0.00 3.16
2099 2245 9.950680 AAGATAATTGGCACGTTAAGATAATTG 57.049 29.630 0.00 0.00 0.00 2.32
2108 2254 9.787435 AGGATTAATAAGATAATTGGCACGTTA 57.213 29.630 0.00 0.00 0.00 3.18
2109 2255 8.567948 CAGGATTAATAAGATAATTGGCACGTT 58.432 33.333 0.00 0.00 0.00 3.99
2110 2256 7.936847 TCAGGATTAATAAGATAATTGGCACGT 59.063 33.333 0.00 0.00 0.00 4.49
2111 2257 8.322906 TCAGGATTAATAAGATAATTGGCACG 57.677 34.615 0.00 0.00 0.00 5.34
2112 2258 8.239998 GCTCAGGATTAATAAGATAATTGGCAC 58.760 37.037 0.00 0.00 0.00 5.01
2153 2299 4.457603 ACTGTTAATAACGCATTGAAGGCA 59.542 37.500 1.88 0.00 0.00 4.75
2190 2336 1.784856 CACGTAACAAGTCACAGTCGG 59.215 52.381 0.00 0.00 0.00 4.79
2658 2804 4.332819 ACAAGCTTGTTGTGTTCTAGTGAC 59.667 41.667 26.36 0.00 38.47 3.67
2773 2919 2.599848 GCGGGAAATCGACAATGAATCG 60.600 50.000 0.00 0.00 41.00 3.34
2774 2920 2.354510 TGCGGGAAATCGACAATGAATC 59.645 45.455 0.00 0.00 0.00 2.52
3663 3810 2.456577 CCCCCAGTGGTTATCCAAAAG 58.543 52.381 8.74 0.00 46.15 2.27
3664 3811 1.551329 GCCCCCAGTGGTTATCCAAAA 60.551 52.381 8.74 0.00 46.15 2.44
3894 4041 4.708868 TCACGAGAAAACAAGTCAATCG 57.291 40.909 0.00 0.00 35.00 3.34
3986 4133 1.482593 ACTGGTCTCCCTCTTATTGCG 59.517 52.381 0.00 0.00 0.00 4.85
4108 4255 7.707624 ATGAGGTCAAACATTTCATGTATGT 57.292 32.000 9.44 9.44 44.07 2.29
4346 4502 1.908619 TCCTTCCATGTAGCAGCTTCA 59.091 47.619 0.00 0.90 0.00 3.02
4461 4617 2.358582 CCACACTGCAGAACATGAAACA 59.641 45.455 23.35 0.00 0.00 2.83
4834 4990 4.674281 AAAAGAGAAGACAGAGAACGGT 57.326 40.909 0.00 0.00 0.00 4.83
4945 5101 1.866925 GTTCCAACTGCGCCAGTAC 59.133 57.895 4.18 0.08 44.62 2.73
5209 5371 4.991056 GCCAGCGATTTACATCTGATAAGA 59.009 41.667 0.00 0.00 0.00 2.10
5403 5568 9.729023 CCTATCGCACAACATTGAATATTTTAA 57.271 29.630 0.00 0.00 0.00 1.52
5535 5702 8.196378 ACCTTAACCATAAAATTTACAAGCCA 57.804 30.769 0.00 0.00 0.00 4.75
5634 5801 7.232534 AGAGGGAGATCTGTGATCACTAAATAC 59.767 40.741 25.55 13.05 0.00 1.89
5644 5811 3.052262 TCTGGAAGAGGGAGATCTGTGAT 60.052 47.826 0.00 0.00 38.67 3.06
5678 5845 8.052748 TGTTTCCTCATAGTACATTTATGCCTT 58.947 33.333 0.00 0.00 0.00 4.35
5791 5958 5.873712 CAGAATTCTATGAGAACAGTGTGCT 59.126 40.000 2.39 2.39 37.00 4.40
5820 5987 2.690497 CTCCGGCTCTAGATGAAGACAA 59.310 50.000 0.00 0.00 0.00 3.18
6061 6234 9.465199 TTTCACTCATTTGAATATCCAAGATCA 57.535 29.630 0.00 0.00 35.42 2.92
6159 6332 1.455383 CGGTTGCAGCCTCCAACTTT 61.455 55.000 18.19 0.00 41.64 2.66
6513 6686 7.232534 AGAGTAAGCCTAATACCATTCTGAGAG 59.767 40.741 0.00 0.00 0.00 3.20
6594 6767 2.290323 CCCAGTAAACAAGGGAGAGGTG 60.290 54.545 5.03 0.00 45.80 4.00
6618 6791 5.413309 ACAGAAGTGGACTAGATGGAAAG 57.587 43.478 0.00 0.00 0.00 2.62
7102 7275 4.202182 CCGATTTCAAATGATGGCCATTCT 60.202 41.667 21.84 7.48 44.28 2.40
7114 7287 5.299279 GTGATGTATCCCACCGATTTCAAAT 59.701 40.000 0.00 0.00 31.92 2.32
7196 7369 1.212935 AGCATACCCAATGACCTGTCC 59.787 52.381 0.00 0.00 37.86 4.02
7230 7403 4.536090 TCTTGGTTATCTTCCATCACCTGT 59.464 41.667 0.00 0.00 34.75 4.00
7591 7764 3.190535 ACCACCAATGTTTCGCTACAATC 59.809 43.478 0.00 0.00 0.00 2.67
7639 7812 4.629634 CCTGCAATGTCTTATACGTGAACA 59.370 41.667 0.00 0.00 0.00 3.18
7656 7829 3.465210 TGAATATACCCATTCCCCTGCAA 59.535 43.478 0.00 0.00 34.59 4.08
7688 7861 1.971357 CGCTCTAGGTCCACCCATATT 59.029 52.381 0.00 0.00 36.42 1.28
7837 8221 2.731968 CGCAACACATATTTCTGGGTGC 60.732 50.000 0.00 0.00 31.73 5.01
7902 8286 7.754069 TTGTAGAAAACATGCAAACAGAAAG 57.246 32.000 0.00 0.00 38.10 2.62
7937 8322 1.568504 ATCAAGAGGGCCGTGAACTA 58.431 50.000 0.65 0.00 36.87 2.24
7948 8333 8.391075 TGAGTTTAAGGTAACAAATCAAGAGG 57.609 34.615 0.00 0.00 41.41 3.69
8065 8452 1.202976 ACTGCTTTGGCACCAGAATCT 60.203 47.619 13.85 0.00 44.28 2.40
8197 8584 2.182030 GGTTCAGGCTCCGACTCG 59.818 66.667 0.00 0.00 0.00 4.18
8320 8707 2.462889 TCACGGAACAACTTGTCGTAC 58.537 47.619 7.98 0.00 30.62 3.67
8323 8710 0.859232 CCTCACGGAACAACTTGTCG 59.141 55.000 0.00 0.00 0.00 4.35
8380 8767 3.838317 TGTACTTCAACCTAGGATGTGCT 59.162 43.478 17.98 3.27 0.00 4.40
8484 8871 6.368791 CCATTACGAATCCACACGATCATTAT 59.631 38.462 0.00 0.00 0.00 1.28
8488 8875 3.453424 CCATTACGAATCCACACGATCA 58.547 45.455 0.00 0.00 0.00 2.92
8595 8982 4.766969 GCATTCGCCAAAAGATTCAATC 57.233 40.909 0.00 0.00 0.00 2.67
8649 9036 5.201713 TGCTTTCCTATTAGTCTCCATCG 57.798 43.478 0.00 0.00 0.00 3.84
8738 9127 9.554395 ACCTAAAACCCAAAATTCAACAATAAG 57.446 29.630 0.00 0.00 0.00 1.73
8763 9152 5.396654 GCTGAGAACGAAGAAATCACAAAAC 59.603 40.000 0.00 0.00 0.00 2.43
8802 9191 8.743714 AGGAAAATGAAATCCAGACAGTATTTC 58.256 33.333 0.00 0.00 39.16 2.17
8870 9259 3.953712 TTCTACAAGCACCTCGAATCA 57.046 42.857 0.00 0.00 0.00 2.57
8926 9315 2.135933 GTCAACAGTTCTTCCTCACCG 58.864 52.381 0.00 0.00 0.00 4.94
8930 9319 1.797025 CCGGTCAACAGTTCTTCCTC 58.203 55.000 0.00 0.00 0.00 3.71
9001 9391 8.461222 CCTCACATAAAAGTGAAGCATATCAAA 58.539 33.333 0.00 0.00 46.90 2.69
9106 9498 4.393680 TGCAACTATGTAACCGGCTTTAAG 59.606 41.667 0.00 0.00 0.00 1.85
9223 9618 4.623932 TTGAGTAGTTGCTGAACCTGAT 57.376 40.909 0.00 0.00 31.81 2.90
9247 9642 4.080695 TGAAGGACCTGATCTCCATGAAAG 60.081 45.833 0.00 0.00 0.00 2.62
9250 9645 2.768527 GTGAAGGACCTGATCTCCATGA 59.231 50.000 0.00 0.00 0.00 3.07
9348 9743 3.587797 AGATTCTCGTCCGTTTTGCTA 57.412 42.857 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.