Multiple sequence alignment - TraesCS2B01G602700

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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 TraesCS2B01G602700 chr2B 100.000 2879 0 0 1 2879 785035230 785038108 0.000000e+00 5317.0
1 TraesCS2B01G602700 chr2A 88.192 2151 109 44 481 2524 775581805 775579693 0.000000e+00 2431.0
2 TraesCS2B01G602700 chr2A 82.692 364 42 13 2536 2879 775571628 775571266 1.300000e-78 303.0
3 TraesCS2B01G602700 chr2A 83.117 308 33 11 58 361 775582277 775581985 2.200000e-66 263.0
4 TraesCS2B01G602700 chr2A 89.674 184 10 3 2699 2874 775577598 775577416 2.890000e-55 226.0
5 TraesCS2B01G602700 chr2A 83.613 238 24 8 2414 2645 775577834 775577606 2.910000e-50 209.0
6 TraesCS2B01G602700 chr2D 89.950 1801 82 40 931 2673 649104813 649106572 0.000000e+00 2231.0
7 TraesCS2B01G602700 chr2D 83.544 474 35 20 2414 2879 649108617 649109055 1.240000e-108 403.0
8 TraesCS2B01G602700 chr2D 88.194 288 28 5 77 362 649103555 649103838 3.550000e-89 339.0
9 TraesCS2B01G602700 chr2D 86.809 235 18 9 656 882 649104584 649104813 1.710000e-62 250.0
10 TraesCS2B01G602700 chr2D 86.628 172 21 2 1075 1246 67950571 67950740 3.790000e-44 189.0
11 TraesCS2B01G602700 chr2D 92.381 105 7 1 504 607 649104368 649104472 6.430000e-32 148.0
12 TraesCS2B01G602700 chr2D 90.164 61 3 2 605 662 649104495 649104555 3.080000e-10 76.8
13 TraesCS2B01G602700 chr4B 98.182 55 1 0 1475 1529 472004830 472004776 2.360000e-16 97.1
14 TraesCS2B01G602700 chr5A 95.745 47 2 0 1618 1664 608809593 608809639 3.080000e-10 76.8
15 TraesCS2B01G602700 chr6B 94.737 38 1 1 1036 1073 649866430 649866466 1.110000e-04 58.4


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 TraesCS2B01G602700 chr2B 785035230 785038108 2878 False 5317.000000 5317 100.000 1 2879 1 chr2B.!!$F1 2878
1 TraesCS2B01G602700 chr2A 775577416 775582277 4861 True 782.250000 2431 86.149 58 2874 4 chr2A.!!$R2 2816
2 TraesCS2B01G602700 chr2D 649103555 649109055 5500 False 574.633333 2231 88.507 77 2879 6 chr2D.!!$F2 2802

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
478 524 0.250124 TTTTTCGGCGCTCAAGAGGA 60.25 50.0 7.64 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 2909 0.538287 AGAAAGGGCTGGACACAAGC 60.538 55.0 0.0 0.0 0.0 4.01 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
19 20 2.642139 CATCTCGCAATGGCAGTTTT 57.358 45.000 0.00 0.00 41.24 2.43
20 21 2.950433 CATCTCGCAATGGCAGTTTTT 58.050 42.857 0.00 0.00 41.24 1.94
21 22 4.095410 CATCTCGCAATGGCAGTTTTTA 57.905 40.909 0.00 0.00 41.24 1.52
22 23 4.484236 CATCTCGCAATGGCAGTTTTTAA 58.516 39.130 0.00 0.00 41.24 1.52
23 24 4.782019 TCTCGCAATGGCAGTTTTTAAT 57.218 36.364 0.00 0.00 41.24 1.40
24 25 5.132897 TCTCGCAATGGCAGTTTTTAATT 57.867 34.783 0.00 0.00 41.24 1.40
25 26 5.537188 TCTCGCAATGGCAGTTTTTAATTT 58.463 33.333 0.00 0.00 41.24 1.82
26 27 5.633182 TCTCGCAATGGCAGTTTTTAATTTC 59.367 36.000 0.00 0.00 41.24 2.17
27 28 5.537188 TCGCAATGGCAGTTTTTAATTTCT 58.463 33.333 0.00 0.00 41.24 2.52
28 29 5.988561 TCGCAATGGCAGTTTTTAATTTCTT 59.011 32.000 0.00 0.00 41.24 2.52
29 30 6.481644 TCGCAATGGCAGTTTTTAATTTCTTT 59.518 30.769 0.00 0.00 41.24 2.52
30 31 7.011857 TCGCAATGGCAGTTTTTAATTTCTTTT 59.988 29.630 0.00 0.00 41.24 2.27
31 32 7.643371 CGCAATGGCAGTTTTTAATTTCTTTTT 59.357 29.630 0.00 0.00 41.24 1.94
32 33 8.744923 GCAATGGCAGTTTTTAATTTCTTTTTG 58.255 29.630 0.00 0.00 40.72 2.44
33 34 9.786105 CAATGGCAGTTTTTAATTTCTTTTTGT 57.214 25.926 0.00 0.00 0.00 2.83
36 37 9.660180 TGGCAGTTTTTAATTTCTTTTTGTACT 57.340 25.926 0.00 0.00 0.00 2.73
37 38 9.914923 GGCAGTTTTTAATTTCTTTTTGTACTG 57.085 29.630 0.00 0.00 33.22 2.74
38 39 9.914923 GCAGTTTTTAATTTCTTTTTGTACTGG 57.085 29.630 0.00 0.00 31.34 4.00
47 48 8.926715 ATTTCTTTTTGTACTGGTCTGTTTTC 57.073 30.769 0.00 0.00 0.00 2.29
48 49 6.445357 TCTTTTTGTACTGGTCTGTTTTCC 57.555 37.500 0.00 0.00 0.00 3.13
49 50 5.946972 TCTTTTTGTACTGGTCTGTTTTCCA 59.053 36.000 0.00 0.00 0.00 3.53
50 51 6.605594 TCTTTTTGTACTGGTCTGTTTTCCAT 59.394 34.615 0.00 0.00 33.01 3.41
51 52 5.766150 TTTGTACTGGTCTGTTTTCCATG 57.234 39.130 0.00 0.00 33.01 3.66
52 53 3.750371 TGTACTGGTCTGTTTTCCATGG 58.250 45.455 4.97 4.97 33.01 3.66
53 54 1.620822 ACTGGTCTGTTTTCCATGGC 58.379 50.000 6.96 0.00 33.01 4.40
54 55 1.133513 ACTGGTCTGTTTTCCATGGCA 60.134 47.619 6.96 0.00 33.01 4.92
55 56 2.173519 CTGGTCTGTTTTCCATGGCAT 58.826 47.619 6.96 0.00 33.01 4.40
56 57 2.564062 CTGGTCTGTTTTCCATGGCATT 59.436 45.455 6.96 0.00 33.01 3.56
57 58 3.763360 CTGGTCTGTTTTCCATGGCATTA 59.237 43.478 6.96 0.00 33.01 1.90
58 59 4.352009 TGGTCTGTTTTCCATGGCATTAT 58.648 39.130 6.96 0.00 0.00 1.28
59 60 4.776837 TGGTCTGTTTTCCATGGCATTATT 59.223 37.500 6.96 0.00 0.00 1.40
60 61 5.248020 TGGTCTGTTTTCCATGGCATTATTT 59.752 36.000 6.96 0.00 0.00 1.40
61 62 6.172630 GGTCTGTTTTCCATGGCATTATTTT 58.827 36.000 6.96 0.00 0.00 1.82
62 63 6.654582 GGTCTGTTTTCCATGGCATTATTTTT 59.345 34.615 6.96 0.00 0.00 1.94
63 64 7.361116 GGTCTGTTTTCCATGGCATTATTTTTG 60.361 37.037 6.96 0.00 0.00 2.44
86 87 4.284234 GCCATGGCAATTCCCTAACATAAT 59.716 41.667 32.08 0.00 41.49 1.28
88 89 6.225318 CCATGGCAATTCCCTAACATAATTG 58.775 40.000 0.00 0.00 41.42 2.32
118 119 3.563508 GGCAAATTTTGGAAAATTGCCG 58.436 40.909 22.20 10.42 45.16 5.69
122 123 5.277538 GCAAATTTTGGAAAATTGCCGTGTA 60.278 36.000 12.75 0.00 45.16 2.90
131 132 7.032580 TGGAAAATTGCCGTGTAATCTTTATG 58.967 34.615 0.00 0.00 0.00 1.90
210 212 8.479280 GCATTATAAAAATACAACATCTTGCCG 58.521 33.333 0.00 0.00 0.00 5.69
362 370 6.761312 TCGGTATCCTTTTCAACTTCTGTTA 58.239 36.000 0.00 0.00 34.60 2.41
364 372 6.425721 CGGTATCCTTTTCAACTTCTGTTACA 59.574 38.462 0.00 0.00 34.60 2.41
365 373 7.119262 CGGTATCCTTTTCAACTTCTGTTACAT 59.881 37.037 0.00 0.00 34.60 2.29
366 374 8.237267 GGTATCCTTTTCAACTTCTGTTACATG 58.763 37.037 0.00 0.00 34.60 3.21
367 375 7.823745 ATCCTTTTCAACTTCTGTTACATGT 57.176 32.000 2.69 2.69 34.60 3.21
368 376 7.639113 TCCTTTTCAACTTCTGTTACATGTT 57.361 32.000 2.30 0.00 34.60 2.71
369 377 7.479980 TCCTTTTCAACTTCTGTTACATGTTG 58.520 34.615 2.30 14.87 39.23 3.33
371 379 6.767524 TTTCAACTTCTGTTACATGTTGGT 57.232 33.333 2.30 0.00 38.64 3.67
375 383 8.458573 TCAACTTCTGTTACATGTTGGTATTT 57.541 30.769 2.30 0.00 38.64 1.40
376 384 9.562408 TCAACTTCTGTTACATGTTGGTATTTA 57.438 29.630 2.30 3.98 38.64 1.40
394 440 7.125053 TGGTATTTATATATCTCGGCACATGGA 59.875 37.037 0.00 0.00 0.00 3.41
403 449 3.559655 TCTCGGCACATGGAAATATTTCG 59.440 43.478 19.41 10.21 38.06 3.46
414 460 7.272515 ACATGGAAATATTTCGCTTTTTGTACG 59.727 33.333 19.41 3.21 38.06 3.67
415 461 5.569823 TGGAAATATTTCGCTTTTTGTACGC 59.430 36.000 19.41 4.27 38.06 4.42
441 487 4.455877 TGGCAATTTTTGTTCGGTTTTTGT 59.544 33.333 0.00 0.00 0.00 2.83
447 493 3.577649 TTGTTCGGTTTTTGTTGCTCA 57.422 38.095 0.00 0.00 0.00 4.26
455 501 1.938625 TTTTGTTGCTCAAAGCTGGC 58.061 45.000 0.11 0.00 45.14 4.85
477 523 2.244000 TTTTTCGGCGCTCAAGAGG 58.756 52.632 7.64 0.00 0.00 3.69
478 524 0.250124 TTTTTCGGCGCTCAAGAGGA 60.250 50.000 7.64 0.00 0.00 3.71
479 525 0.670546 TTTTCGGCGCTCAAGAGGAG 60.671 55.000 7.64 0.00 46.93 3.69
493 881 2.270858 AGAGGAGAGGAGGGGAAAAAC 58.729 52.381 0.00 0.00 0.00 2.43
507 895 4.329392 GGGAAAAACTCGTAATCAGGGAA 58.671 43.478 0.00 0.00 0.00 3.97
515 913 1.499049 GTAATCAGGGAACGGCGATC 58.501 55.000 16.62 12.28 0.00 3.69
735 1215 2.743928 CGCACCAGCACCTTCCTC 60.744 66.667 0.00 0.00 42.27 3.71
736 1216 2.360475 GCACCAGCACCTTCCTCC 60.360 66.667 0.00 0.00 41.58 4.30
737 1217 2.352805 CACCAGCACCTTCCTCCC 59.647 66.667 0.00 0.00 0.00 4.30
738 1218 2.936032 ACCAGCACCTTCCTCCCC 60.936 66.667 0.00 0.00 0.00 4.81
739 1219 2.612115 CCAGCACCTTCCTCCCCT 60.612 66.667 0.00 0.00 0.00 4.79
740 1220 2.674220 CCAGCACCTTCCTCCCCTC 61.674 68.421 0.00 0.00 0.00 4.30
741 1221 2.285743 AGCACCTTCCTCCCCTCC 60.286 66.667 0.00 0.00 0.00 4.30
742 1222 3.412408 GCACCTTCCTCCCCTCCC 61.412 72.222 0.00 0.00 0.00 4.30
743 1223 2.456840 CACCTTCCTCCCCTCCCT 59.543 66.667 0.00 0.00 0.00 4.20
744 1224 1.997874 CACCTTCCTCCCCTCCCTG 60.998 68.421 0.00 0.00 0.00 4.45
745 1225 2.367512 CCTTCCTCCCCTCCCTGG 60.368 72.222 0.00 0.00 0.00 4.45
746 1226 2.787866 CTTCCTCCCCTCCCTGGA 59.212 66.667 0.00 0.00 38.35 3.86
918 1399 1.111277 CCGTCCCAATTCCAATTCCC 58.889 55.000 0.00 0.00 0.00 3.97
919 1400 1.111277 CGTCCCAATTCCAATTCCCC 58.889 55.000 0.00 0.00 0.00 4.81
935 1429 2.301738 CCCTCCCCACAGACTTCCC 61.302 68.421 0.00 0.00 0.00 3.97
992 1486 2.750637 TCCAGTCGTCGAGAGGCC 60.751 66.667 0.00 0.00 0.00 5.19
1191 1685 2.653448 CAGCAGATCTCGGCGTCG 60.653 66.667 1.15 1.15 41.91 5.12
1194 1688 2.352915 CAGATCTCGGCGTCGCTC 60.353 66.667 18.11 6.23 36.13 5.03
1416 1916 3.144120 CTCGGAGCGGACCATCCTG 62.144 68.421 10.30 5.19 33.30 3.86
1548 2048 2.555199 GAGTGGTACATGATGAGCACC 58.445 52.381 18.74 13.03 44.52 5.01
1551 2051 1.160329 GGTACATGATGAGCACCGCC 61.160 60.000 0.00 0.00 0.00 6.13
1851 2354 1.376553 GCAGCAGTCCTTCCTCCAC 60.377 63.158 0.00 0.00 0.00 4.02
1902 2409 3.646650 CGCCCGTCGGTTAATTAGA 57.353 52.632 11.06 0.00 33.78 2.10
1905 2412 2.207590 GCCCGTCGGTTAATTAGAAGG 58.792 52.381 11.06 0.09 34.14 3.46
1907 2414 3.679639 GCCCGTCGGTTAATTAGAAGGAA 60.680 47.826 11.06 0.00 35.95 3.36
1908 2415 4.117685 CCCGTCGGTTAATTAGAAGGAAG 58.882 47.826 11.06 0.00 35.95 3.46
1909 2416 3.554731 CCGTCGGTTAATTAGAAGGAAGC 59.445 47.826 2.08 0.00 35.95 3.86
1911 2418 4.179298 GTCGGTTAATTAGAAGGAAGCGT 58.821 43.478 7.58 0.00 41.94 5.07
1912 2419 5.343249 GTCGGTTAATTAGAAGGAAGCGTA 58.657 41.667 7.58 0.00 41.94 4.42
1917 2424 6.922407 GGTTAATTAGAAGGAAGCGTAGTAGG 59.078 42.308 0.00 0.00 0.00 3.18
1923 2430 1.134560 AGGAAGCGTAGTAGGAAAGCG 59.865 52.381 0.00 0.00 0.00 4.68
1936 2443 2.167662 GGAAAGCGAAAGGGGAATTGA 58.832 47.619 0.00 0.00 0.00 2.57
1937 2444 2.560981 GGAAAGCGAAAGGGGAATTGAA 59.439 45.455 0.00 0.00 0.00 2.69
1938 2445 3.006430 GGAAAGCGAAAGGGGAATTGAAA 59.994 43.478 0.00 0.00 0.00 2.69
1939 2446 4.322725 GGAAAGCGAAAGGGGAATTGAAAT 60.323 41.667 0.00 0.00 0.00 2.17
1940 2447 4.456280 AAGCGAAAGGGGAATTGAAATC 57.544 40.909 0.00 0.00 0.00 2.17
1941 2448 2.423538 AGCGAAAGGGGAATTGAAATCG 59.576 45.455 0.00 0.00 0.00 3.34
1942 2449 2.479560 GCGAAAGGGGAATTGAAATCGG 60.480 50.000 0.00 0.00 0.00 4.18
1943 2450 2.099098 CGAAAGGGGAATTGAAATCGGG 59.901 50.000 0.00 0.00 0.00 5.14
1944 2451 1.485124 AAGGGGAATTGAAATCGGGC 58.515 50.000 0.00 0.00 0.00 6.13
1945 2452 0.751643 AGGGGAATTGAAATCGGGCG 60.752 55.000 0.00 0.00 0.00 6.13
1946 2453 1.065764 GGGAATTGAAATCGGGCGC 59.934 57.895 0.00 0.00 0.00 6.53
1976 2483 2.197324 GGTTTGTGCAGTGGGGGA 59.803 61.111 0.00 0.00 0.00 4.81
2020 2528 0.098025 CGACGACTCCAGAGAAGAGC 59.902 60.000 0.70 0.00 34.56 4.09
2021 2529 1.459450 GACGACTCCAGAGAAGAGCT 58.541 55.000 0.70 0.00 34.56 4.09
2023 2531 0.179140 CGACTCCAGAGAAGAGCTGC 60.179 60.000 0.70 0.00 34.56 5.25
2059 2591 2.264794 GACACGTTCCGGCTGGAT 59.735 61.111 16.96 0.00 45.91 3.41
2060 2592 2.047274 ACACGTTCCGGCTGGATG 60.047 61.111 16.96 13.75 45.91 3.51
2061 2593 2.819595 CACGTTCCGGCTGGATGG 60.820 66.667 16.96 12.88 45.91 3.51
2062 2594 3.000819 ACGTTCCGGCTGGATGGA 61.001 61.111 16.96 0.00 45.91 3.41
2063 2595 2.202932 CGTTCCGGCTGGATGGAG 60.203 66.667 16.96 3.36 45.91 3.86
2190 2737 0.326618 TCCATCCCTCCCTCTGGAAC 60.327 60.000 0.00 0.00 41.17 3.62
2192 2739 1.383248 ATCCCTCCCTCTGGAACCG 60.383 63.158 0.00 0.00 41.17 4.44
2197 2744 0.033405 CTCCCTCTGGAACCGTCCTA 60.033 60.000 0.00 0.00 45.22 2.94
2200 2747 0.753262 CCTCTGGAACCGTCCTATGG 59.247 60.000 0.00 0.00 45.22 2.74
2249 2799 5.189736 AGTGAGAGAGAGATAGTGAGTGAGT 59.810 44.000 0.00 0.00 0.00 3.41
2259 2809 3.071874 AGTGAGTGAGTGAGAGAGAGG 57.928 52.381 0.00 0.00 0.00 3.69
2264 2818 2.043450 AGTGAGAGAGAGGGCCCG 60.043 66.667 18.44 0.00 0.00 6.13
2265 2819 2.043852 GTGAGAGAGAGGGCCCGA 60.044 66.667 18.44 0.00 0.00 5.14
2346 2900 5.000591 TGAAGCAAGATGAATTTCACCGTA 58.999 37.500 0.15 0.00 0.00 4.02
2353 2907 6.009115 AGATGAATTTCACCGTACCAAAAC 57.991 37.500 0.15 0.00 0.00 2.43
2355 2909 5.176407 TGAATTTCACCGTACCAAAACAG 57.824 39.130 0.00 0.00 0.00 3.16
2357 2911 2.335316 TTCACCGTACCAAAACAGCT 57.665 45.000 0.00 0.00 0.00 4.24
2365 2919 1.846007 ACCAAAACAGCTTGTGTCCA 58.154 45.000 0.00 0.00 39.03 4.02
2367 2921 1.536709 CCAAAACAGCTTGTGTCCAGC 60.537 52.381 0.00 0.00 39.03 4.85
2369 2923 1.109323 AAACAGCTTGTGTCCAGCCC 61.109 55.000 0.00 0.00 39.03 5.19
2401 2963 5.874810 TCCTCTGATATTTTCTTTCACACCG 59.125 40.000 0.00 0.00 0.00 4.94
2402 2964 5.874810 CCTCTGATATTTTCTTTCACACCGA 59.125 40.000 0.00 0.00 0.00 4.69
2403 2965 6.540189 CCTCTGATATTTTCTTTCACACCGAT 59.460 38.462 0.00 0.00 0.00 4.18
2406 2968 7.224753 TCTGATATTTTCTTTCACACCGATAGC 59.775 37.037 0.00 0.00 0.00 2.97
2407 2969 7.047891 TGATATTTTCTTTCACACCGATAGCT 58.952 34.615 0.00 0.00 0.00 3.32
2408 2970 5.803020 ATTTTCTTTCACACCGATAGCTC 57.197 39.130 0.00 0.00 0.00 4.09
2409 2971 2.961526 TCTTTCACACCGATAGCTCC 57.038 50.000 0.00 0.00 0.00 4.70
2410 2972 2.176045 TCTTTCACACCGATAGCTCCA 58.824 47.619 0.00 0.00 0.00 3.86
2413 2975 1.557099 TCACACCGATAGCTCCAAGT 58.443 50.000 0.00 0.00 0.00 3.16
2450 3020 1.414378 GAAAATGGGCGTTGGTTTCG 58.586 50.000 0.00 0.00 0.00 3.46
2475 3045 1.359848 GAGGCTGATGTGTTGGTACG 58.640 55.000 0.00 0.00 0.00 3.67
2476 3046 0.685097 AGGCTGATGTGTTGGTACGT 59.315 50.000 0.00 0.00 0.00 3.57
2477 3047 1.897133 AGGCTGATGTGTTGGTACGTA 59.103 47.619 0.00 0.00 0.00 3.57
2479 3049 1.652124 GCTGATGTGTTGGTACGTACG 59.348 52.381 18.98 15.01 0.00 3.67
2511 3081 1.002366 GACGTTGAGCGATTGCAGAT 58.998 50.000 7.90 0.00 46.23 2.90
2539 3134 4.337763 CGTAGTAGTACGTGATGGTGTTC 58.662 47.826 19.78 0.00 45.84 3.18
2601 5890 2.043980 CCACCCAATTTCCCGTCCG 61.044 63.158 0.00 0.00 0.00 4.79
2625 5914 6.634436 CGTTTCTAGGATATTTAAGCGTACGT 59.366 38.462 17.90 0.00 0.00 3.57
2631 5925 6.211515 AGGATATTTAAGCGTACGTTCGATT 58.788 36.000 21.07 21.07 42.00 3.34
2648 5942 1.125021 GATTGCGACGCATATTCTCCG 59.875 52.381 25.09 0.00 38.76 4.63
2651 5945 1.548973 GCGACGCATATTCTCCGTGG 61.549 60.000 16.42 0.00 35.06 4.94
2653 5947 1.488527 GACGCATATTCTCCGTGGAC 58.511 55.000 0.00 0.00 35.06 4.02
2654 5948 0.248907 ACGCATATTCTCCGTGGACG 60.249 55.000 0.00 0.00 39.44 4.79
2671 5965 3.521605 GGAATAAACCGGCTGGCC 58.478 61.111 12.89 0.00 39.70 5.36
2756 6052 8.715088 GCTAGCAAAACAATTGAAATGAAATCT 58.285 29.630 13.59 3.13 0.00 2.40
2787 6091 1.597937 GGCTACGTTACGTATGGTCCG 60.598 57.143 18.06 6.65 41.53 4.79
2795 6099 0.388907 ACGTATGGTCCGTGAAACCG 60.389 55.000 0.00 0.00 39.81 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.642139 AAAACTGCCATTGCGAGATG 57.358 45.000 0.00 0.00 41.78 2.90
1 2 4.782019 TTAAAAACTGCCATTGCGAGAT 57.218 36.364 0.00 0.00 41.78 2.75
3 4 5.634859 AGAAATTAAAAACTGCCATTGCGAG 59.365 36.000 0.00 0.00 41.78 5.03
5 6 5.844301 AGAAATTAAAAACTGCCATTGCG 57.156 34.783 0.00 0.00 41.78 4.85
6 7 8.744923 CAAAAAGAAATTAAAAACTGCCATTGC 58.255 29.630 0.00 0.00 38.26 3.56
7 8 9.786105 ACAAAAAGAAATTAAAAACTGCCATTG 57.214 25.926 0.00 0.00 0.00 2.82
10 11 9.660180 AGTACAAAAAGAAATTAAAAACTGCCA 57.340 25.926 0.00 0.00 0.00 4.92
11 12 9.914923 CAGTACAAAAAGAAATTAAAAACTGCC 57.085 29.630 0.00 0.00 0.00 4.85
12 13 9.914923 CCAGTACAAAAAGAAATTAAAAACTGC 57.085 29.630 0.00 0.00 0.00 4.40
21 22 9.366216 GAAAACAGACCAGTACAAAAAGAAATT 57.634 29.630 0.00 0.00 0.00 1.82
22 23 7.979537 GGAAAACAGACCAGTACAAAAAGAAAT 59.020 33.333 0.00 0.00 0.00 2.17
23 24 7.039644 TGGAAAACAGACCAGTACAAAAAGAAA 60.040 33.333 0.00 0.00 0.00 2.52
24 25 6.434652 TGGAAAACAGACCAGTACAAAAAGAA 59.565 34.615 0.00 0.00 0.00 2.52
25 26 5.946972 TGGAAAACAGACCAGTACAAAAAGA 59.053 36.000 0.00 0.00 0.00 2.52
26 27 6.202516 TGGAAAACAGACCAGTACAAAAAG 57.797 37.500 0.00 0.00 0.00 2.27
27 28 6.406400 CCATGGAAAACAGACCAGTACAAAAA 60.406 38.462 5.56 0.00 39.62 1.94
28 29 5.068460 CCATGGAAAACAGACCAGTACAAAA 59.932 40.000 5.56 0.00 39.62 2.44
29 30 4.582656 CCATGGAAAACAGACCAGTACAAA 59.417 41.667 5.56 0.00 39.62 2.83
30 31 4.141287 CCATGGAAAACAGACCAGTACAA 58.859 43.478 5.56 0.00 39.62 2.41
31 32 3.750371 CCATGGAAAACAGACCAGTACA 58.250 45.455 5.56 0.00 39.62 2.90
32 33 2.488153 GCCATGGAAAACAGACCAGTAC 59.512 50.000 18.40 0.00 39.62 2.73
33 34 2.107378 TGCCATGGAAAACAGACCAGTA 59.893 45.455 18.40 0.00 39.62 2.74
34 35 1.133513 TGCCATGGAAAACAGACCAGT 60.134 47.619 18.40 0.00 39.62 4.00
35 36 1.619654 TGCCATGGAAAACAGACCAG 58.380 50.000 18.40 0.00 39.62 4.00
36 37 2.307496 ATGCCATGGAAAACAGACCA 57.693 45.000 18.40 0.00 40.57 4.02
37 38 5.343307 AATAATGCCATGGAAAACAGACC 57.657 39.130 18.40 0.00 0.00 3.85
38 39 7.520686 CAAAAATAATGCCATGGAAAACAGAC 58.479 34.615 18.40 0.00 0.00 3.51
39 40 6.149142 GCAAAAATAATGCCATGGAAAACAGA 59.851 34.615 18.40 0.00 37.85 3.41
40 41 6.316319 GCAAAAATAATGCCATGGAAAACAG 58.684 36.000 18.40 0.00 37.85 3.16
41 42 6.251655 GCAAAAATAATGCCATGGAAAACA 57.748 33.333 18.40 3.68 37.85 2.83
63 64 1.484038 TGTTAGGGAATTGCCATGGC 58.516 50.000 30.54 30.54 38.95 4.40
86 87 2.540265 AAATTTGCCATGGCGAACAA 57.460 40.000 36.51 23.48 45.94 2.83
88 89 1.464219 CCAAAATTTGCCATGGCGAAC 59.536 47.619 36.51 10.81 45.94 3.95
205 207 9.482627 AGAACAAAATATTTACAAATTCGGCAA 57.517 25.926 0.01 0.00 0.00 4.52
326 334 9.196139 TGAAAAGGATACCGAAAATGGATTATT 57.804 29.630 0.00 0.00 37.17 1.40
327 335 8.760980 TGAAAAGGATACCGAAAATGGATTAT 57.239 30.769 0.00 0.00 37.17 1.28
328 336 8.463607 GTTGAAAAGGATACCGAAAATGGATTA 58.536 33.333 0.00 0.00 37.17 1.75
345 353 6.697019 CCAACATGTAACAGAAGTTGAAAAGG 59.303 38.462 0.00 0.00 41.41 3.11
362 370 8.318412 TGCCGAGATATATAAATACCAACATGT 58.682 33.333 0.00 0.00 0.00 3.21
364 372 8.318412 TGTGCCGAGATATATAAATACCAACAT 58.682 33.333 0.00 0.00 0.00 2.71
365 373 7.672240 TGTGCCGAGATATATAAATACCAACA 58.328 34.615 0.00 0.00 0.00 3.33
366 374 8.604035 CATGTGCCGAGATATATAAATACCAAC 58.396 37.037 0.00 0.00 0.00 3.77
367 375 7.768582 CCATGTGCCGAGATATATAAATACCAA 59.231 37.037 0.00 0.00 0.00 3.67
368 376 7.125053 TCCATGTGCCGAGATATATAAATACCA 59.875 37.037 0.00 0.00 0.00 3.25
369 377 7.497595 TCCATGTGCCGAGATATATAAATACC 58.502 38.462 0.00 0.00 0.00 2.73
376 384 9.113838 GAAATATTTCCATGTGCCGAGATATAT 57.886 33.333 16.05 0.00 0.00 0.86
394 440 6.994868 TTGCGTACAAAAAGCGAAATATTT 57.005 29.167 0.00 0.00 35.02 1.40
403 449 1.777101 TGCCATTGCGTACAAAAAGC 58.223 45.000 0.00 0.00 39.77 3.51
414 460 2.547634 ACCGAACAAAAATTGCCATTGC 59.452 40.909 0.00 0.00 38.26 3.56
415 461 4.809815 AACCGAACAAAAATTGCCATTG 57.190 36.364 0.00 0.00 0.00 2.82
460 506 0.670546 CTCCTCTTGAGCGCCGAAAA 60.671 55.000 2.29 0.00 33.47 2.29
466 512 1.437160 CTCCTCTCCTCTTGAGCGC 59.563 63.158 0.00 0.00 41.18 5.92
474 520 2.237643 GAGTTTTTCCCCTCCTCTCCTC 59.762 54.545 0.00 0.00 0.00 3.71
475 521 2.270858 GAGTTTTTCCCCTCCTCTCCT 58.729 52.381 0.00 0.00 0.00 3.69
476 522 1.066071 CGAGTTTTTCCCCTCCTCTCC 60.066 57.143 0.00 0.00 0.00 3.71
477 523 1.624312 ACGAGTTTTTCCCCTCCTCTC 59.376 52.381 0.00 0.00 0.00 3.20
478 524 1.730851 ACGAGTTTTTCCCCTCCTCT 58.269 50.000 0.00 0.00 0.00 3.69
479 525 3.690475 TTACGAGTTTTTCCCCTCCTC 57.310 47.619 0.00 0.00 0.00 3.71
486 874 4.142966 CGTTCCCTGATTACGAGTTTTTCC 60.143 45.833 0.00 0.00 37.47 3.13
487 875 4.142966 CCGTTCCCTGATTACGAGTTTTTC 60.143 45.833 0.00 0.00 37.47 2.29
493 881 0.870307 CGCCGTTCCCTGATTACGAG 60.870 60.000 0.00 0.00 37.47 4.18
734 1214 1.240129 GATCCATCCAGGGAGGGGA 59.760 63.158 18.20 15.02 45.20 4.81
735 1215 1.849823 GGATCCATCCAGGGAGGGG 60.850 68.421 18.20 10.34 45.20 4.79
736 1216 3.913107 GGATCCATCCAGGGAGGG 58.087 66.667 12.74 12.74 46.38 4.30
738 1218 1.762522 CACGGGATCCATCCAGGGAG 61.763 65.000 15.23 0.00 46.79 4.30
739 1219 1.766059 CACGGGATCCATCCAGGGA 60.766 63.158 15.23 0.00 46.79 4.20
770 1250 4.112341 CTTGCGAGCCAAGGCAGC 62.112 66.667 19.86 19.86 45.78 5.25
918 1399 1.538876 TGGGAAGTCTGTGGGGAGG 60.539 63.158 0.00 0.00 0.00 4.30
919 1400 1.986413 CTGGGAAGTCTGTGGGGAG 59.014 63.158 0.00 0.00 0.00 4.30
958 1452 1.457009 GGACTAGACTAGCAGCGGGG 61.457 65.000 9.52 0.00 0.00 5.73
1397 1897 4.593864 GGATGGTCCGCTCCGAGC 62.594 72.222 10.59 10.59 38.02 5.03
1836 2339 2.671682 GGGTGGAGGAAGGACTGC 59.328 66.667 0.00 0.00 0.00 4.40
1837 2340 2.660064 CGGGGTGGAGGAAGGACTG 61.660 68.421 0.00 0.00 0.00 3.51
1838 2341 2.284699 CGGGGTGGAGGAAGGACT 60.285 66.667 0.00 0.00 0.00 3.85
1892 2399 6.922407 CCTACTACGCTTCCTTCTAATTAACC 59.078 42.308 0.00 0.00 0.00 2.85
1902 2409 2.416972 CGCTTTCCTACTACGCTTCCTT 60.417 50.000 0.00 0.00 0.00 3.36
1905 2412 2.556534 TCGCTTTCCTACTACGCTTC 57.443 50.000 0.00 0.00 0.00 3.86
1907 2414 2.416972 CCTTTCGCTTTCCTACTACGCT 60.417 50.000 0.00 0.00 0.00 5.07
1908 2415 1.925185 CCTTTCGCTTTCCTACTACGC 59.075 52.381 0.00 0.00 0.00 4.42
1909 2416 2.537401 CCCTTTCGCTTTCCTACTACG 58.463 52.381 0.00 0.00 0.00 3.51
1911 2418 2.823959 TCCCCTTTCGCTTTCCTACTA 58.176 47.619 0.00 0.00 0.00 1.82
1912 2419 1.652947 TCCCCTTTCGCTTTCCTACT 58.347 50.000 0.00 0.00 0.00 2.57
1917 2424 3.934457 TTCAATTCCCCTTTCGCTTTC 57.066 42.857 0.00 0.00 0.00 2.62
1923 2430 2.159099 GCCCGATTTCAATTCCCCTTTC 60.159 50.000 0.00 0.00 0.00 2.62
1976 2483 1.274712 CTTGTCCTCTGCTCCTCCTT 58.725 55.000 0.00 0.00 0.00 3.36
2059 2591 6.790232 ACAAAAACAGAAAGAAATCCTCCA 57.210 33.333 0.00 0.00 0.00 3.86
2060 2592 6.701841 GGAACAAAAACAGAAAGAAATCCTCC 59.298 38.462 0.00 0.00 0.00 4.30
2061 2593 6.417930 CGGAACAAAAACAGAAAGAAATCCTC 59.582 38.462 0.00 0.00 0.00 3.71
2062 2594 6.127451 ACGGAACAAAAACAGAAAGAAATCCT 60.127 34.615 0.00 0.00 0.00 3.24
2063 2595 6.019881 CACGGAACAAAAACAGAAAGAAATCC 60.020 38.462 0.00 0.00 0.00 3.01
2163 2706 2.746359 GAGGGATGGATCTGCGGG 59.254 66.667 0.00 0.00 0.00 6.13
2249 2799 1.456518 CATCGGGCCCTCTCTCTCA 60.457 63.158 22.43 0.00 0.00 3.27
2259 2809 1.000896 CCCCATAATCCATCGGGCC 60.001 63.158 0.00 0.00 37.36 5.80
2264 2818 3.885297 CCAATATCGCCCCATAATCCATC 59.115 47.826 0.00 0.00 0.00 3.51
2265 2819 3.269381 ACCAATATCGCCCCATAATCCAT 59.731 43.478 0.00 0.00 0.00 3.41
2346 2900 1.750778 CTGGACACAAGCTGTTTTGGT 59.249 47.619 0.00 0.00 31.03 3.67
2353 2907 0.825010 AAAGGGCTGGACACAAGCTG 60.825 55.000 0.00 0.00 0.00 4.24
2355 2909 0.538287 AGAAAGGGCTGGACACAAGC 60.538 55.000 0.00 0.00 0.00 4.01
2357 2911 2.452600 AAAGAAAGGGCTGGACACAA 57.547 45.000 0.00 0.00 0.00 3.33
2365 2919 5.723860 ATATCAGAGGAAAAGAAAGGGCT 57.276 39.130 0.00 0.00 0.00 5.19
2367 2921 8.586879 AGAAAATATCAGAGGAAAAGAAAGGG 57.413 34.615 0.00 0.00 0.00 3.95
2395 2957 2.002586 CAACTTGGAGCTATCGGTGTG 58.997 52.381 0.00 0.00 0.00 3.82
2396 2958 1.066143 CCAACTTGGAGCTATCGGTGT 60.066 52.381 0.92 0.00 40.96 4.16
2407 2969 2.281484 GCGTGCCTCCAACTTGGA 60.281 61.111 10.23 10.23 45.98 3.53
2408 2970 2.192861 TTGCGTGCCTCCAACTTGG 61.193 57.895 0.74 0.74 39.43 3.61
2409 2971 1.008538 GTTGCGTGCCTCCAACTTG 60.009 57.895 0.00 0.00 38.55 3.16
2410 2972 2.542907 CGTTGCGTGCCTCCAACTT 61.543 57.895 8.26 0.00 39.24 2.66
2422 2992 1.732683 GCCCATTTTCCACGTTGCG 60.733 57.895 0.00 0.00 0.00 4.85
2475 3045 3.777925 CACACGGCAGCAGCGTAC 61.778 66.667 0.00 0.00 43.41 3.67
2476 3046 3.984749 TCACACGGCAGCAGCGTA 61.985 61.111 0.00 0.00 43.41 4.42
2534 3129 3.672767 TTCTAGAACGGGGAAGAACAC 57.327 47.619 0.00 0.00 0.00 3.32
2539 3134 2.354805 CCACCTTTCTAGAACGGGGAAG 60.355 54.545 27.46 15.32 35.33 3.46
2601 5890 7.920908 ACGTACGCTTAAATATCCTAGAAAC 57.079 36.000 16.72 0.00 0.00 2.78
2631 5925 4.319249 CGGAGAATATGCGTCGCA 57.681 55.556 24.05 24.05 44.86 5.10
2654 5948 3.521605 GGCCAGCCGGTTTATTCC 58.478 61.111 1.90 0.00 33.28 3.01
2697 5993 7.967854 TCGGTTTTGATCATGCACTATTAAAAG 59.032 33.333 11.03 4.27 0.00 2.27
2756 6052 1.196104 AACGTAGCCCACTGCCCTAA 61.196 55.000 0.00 0.00 42.71 2.69
2815 6119 1.673665 GCACCACTTGGAGGAGCAG 60.674 63.158 1.14 0.00 41.59 4.24
2816 6120 2.431683 GCACCACTTGGAGGAGCA 59.568 61.111 1.14 0.00 41.59 4.26


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

AutoCloner maintained by Alex Coulton.