Multiple sequence alignment - TraesCS7D01G394200

Loading Multiple Alignment...

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 TraesCS7D01G394200 chr7D 100.000 3096 0 0 1 3096 509568429 509571524 0.000000e+00 5718.0
1 TraesCS7D01G394200 chr7D 96.721 61 2 0 2334 2394 575728775 575728835 5.460000e-18 102.0
2 TraesCS7D01G394200 chr7A 93.318 1287 73 7 960 2245 580478179 580479453 0.000000e+00 1888.0
3 TraesCS7D01G394200 chr7A 88.721 1525 104 38 749 2245 580500053 580501537 0.000000e+00 1801.0
4 TraesCS7D01G394200 chr7A 87.415 731 54 22 2395 3094 580480312 580481035 0.000000e+00 806.0
5 TraesCS7D01G394200 chr7A 84.053 602 72 14 5 589 580494843 580495437 2.700000e-155 558.0
6 TraesCS7D01G394200 chr7A 88.000 100 7 2 2213 2312 580502108 580502202 2.520000e-21 113.0
7 TraesCS7D01G394200 chr7B 92.087 1289 85 7 960 2245 537729618 537730892 0.000000e+00 1799.0
8 TraesCS7D01G394200 chr7B 87.940 738 44 22 2395 3094 537731811 537732541 0.000000e+00 828.0
9 TraesCS7D01G394200 chr7B 85.263 380 37 14 334 700 537729046 537729419 1.050000e-99 374.0
10 TraesCS7D01G394200 chr7B 89.895 287 25 2 1 283 537728763 537729049 1.750000e-97 366.0
11 TraesCS7D01G394200 chr7B 96.721 61 2 0 2334 2394 394399474 394399414 5.460000e-18 102.0
12 TraesCS7D01G394200 chr7B 91.935 62 4 1 785 846 537729477 537729537 5.500000e-13 86.1
13 TraesCS7D01G394200 chr5A 82.158 241 37 6 30 267 119438007 119438244 5.240000e-48 202.0
14 TraesCS7D01G394200 chr5A 77.833 203 28 11 77 267 650247941 650247744 3.260000e-20 110.0
15 TraesCS7D01G394200 chr5A 96.875 32 1 0 516 547 595081920 595081951 2.000000e-03 54.7
16 TraesCS7D01G394200 chr6B 80.400 250 36 12 25 268 703868113 703868355 8.820000e-41 178.0
17 TraesCS7D01G394200 chr1D 82.828 198 29 2 75 267 488547929 488548126 4.100000e-39 172.0
18 TraesCS7D01G394200 chr1D 80.851 188 25 7 85 265 62112280 62112463 1.500000e-28 137.0
19 TraesCS7D01G394200 chr1B 82.587 201 25 7 75 269 98903136 98903332 5.310000e-38 169.0
20 TraesCS7D01G394200 chr1B 96.721 61 2 0 2334 2394 5708864 5708924 5.460000e-18 102.0
21 TraesCS7D01G394200 chr3B 86.395 147 17 3 2863 3008 640657932 640657788 1.150000e-34 158.0
22 TraesCS7D01G394200 chr3B 72.832 346 70 17 1097 1424 778450918 778451257 2.540000e-16 97.1
23 TraesCS7D01G394200 chrUn 81.356 177 31 2 75 250 60962240 60962415 3.220000e-30 143.0
24 TraesCS7D01G394200 chr5D 80.000 200 25 9 77 265 522113459 522113264 1.940000e-27 134.0
25 TraesCS7D01G394200 chr5D 95.238 63 3 0 2334 2396 58507866 58507928 1.960000e-17 100.0
26 TraesCS7D01G394200 chr3D 77.236 246 26 15 2863 3087 480119371 480119135 1.950000e-22 117.0
27 TraesCS7D01G394200 chr2D 95.455 66 3 0 2334 2399 555908207 555908142 4.220000e-19 106.0
28 TraesCS7D01G394200 chr1A 96.721 61 2 0 2334 2394 7016104 7016044 5.460000e-18 102.0
29 TraesCS7D01G394200 chr5B 95.238 63 3 0 2334 2396 35695833 35695895 1.960000e-17 100.0
30 TraesCS7D01G394200 chr4D 92.857 70 3 2 2334 2402 63108225 63108157 1.960000e-17 100.0
31 TraesCS7D01G394200 chr4D 94.118 34 2 0 513 546 383792213 383792180 6.000000e-03 52.8
32 TraesCS7D01G394200 chr3A 93.846 65 4 0 2334 2398 474438889 474438825 7.070000e-17 99.0
33 TraesCS7D01G394200 chr3A 86.275 51 5 1 377 425 9359852 9359902 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 TraesCS7D01G394200 chr7D 509568429 509571524 3095 False 5718.00 5718 100.0000 1 3096 1 chr7D.!!$F1 3095
1 TraesCS7D01G394200 chr7A 580478179 580481035 2856 False 1347.00 1888 90.3665 960 3094 2 chr7A.!!$F2 2134
2 TraesCS7D01G394200 chr7A 580500053 580502202 2149 False 957.00 1801 88.3605 749 2312 2 chr7A.!!$F3 1563
3 TraesCS7D01G394200 chr7A 580494843 580495437 594 False 558.00 558 84.0530 5 589 1 chr7A.!!$F1 584
4 TraesCS7D01G394200 chr7B 537728763 537732541 3778 False 690.62 1799 89.4240 1 3094 5 chr7B.!!$F1 3093

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
948 996 0.389817 TGAGGATGTCAAACTCGCCG 60.39 55.0 3.56 0.0 34.03 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2364 3138 0.179029 AAAATGGAGGCGTATCCCCG 60.179 55.0 5.71 0.0 38.72 5.73 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
45 46 9.768215 TTTCCCTAAGTATCATTCCTTTGAAAT 57.232 29.630 0.00 0.00 33.32 2.17
48 49 9.413734 CCCTAAGTATCATTCCTTTGAAATCTT 57.586 33.333 0.00 0.00 33.32 2.40
62 63 6.509418 TTGAAATCTTCCTTAATTGTCCCG 57.491 37.500 0.00 0.00 0.00 5.14
66 67 4.360951 TCTTCCTTAATTGTCCCGTGTT 57.639 40.909 0.00 0.00 0.00 3.32
72 73 5.182380 TCCTTAATTGTCCCGTGTTTGATTC 59.818 40.000 0.00 0.00 0.00 2.52
97 99 9.698309 TCGCCAAATAAAATTATGTTTCTTTGA 57.302 25.926 9.00 0.00 37.01 2.69
153 159 7.769970 CCTAAAATACGGGTAGGTAAATCACAA 59.230 37.037 0.00 0.00 31.43 3.33
164 170 3.306019 GGTAAATCACAAGCAGGGTTTGG 60.306 47.826 0.00 0.00 0.00 3.28
248 254 7.040755 CCAGAATATTTATATCCCGTTGCAACA 60.041 37.037 28.01 10.43 0.00 3.33
256 262 2.177580 CCGTTGCAACACACGGTCT 61.178 57.895 28.01 0.00 37.83 3.85
276 291 8.600668 ACGGTCTATTATCTAGTGATGTACCTA 58.399 37.037 0.00 0.00 34.32 3.08
307 322 9.868277 TTAAAAAGAGTGTTCATGTGTTTCAAT 57.132 25.926 0.00 0.00 0.00 2.57
319 334 4.041049 TGTGTTTCAATCAAATGTGTCGC 58.959 39.130 0.00 0.00 0.00 5.19
590 614 9.258826 TGAAGAAAATGTACATCATGTTTTTGG 57.741 29.630 9.23 0.00 34.45 3.28
597 621 9.820725 AATGTACATCATGTTTTTGGAATATGG 57.179 29.630 9.23 0.00 36.81 2.74
601 625 7.322664 ACATCATGTTTTTGGAATATGGTCAC 58.677 34.615 0.00 0.00 0.00 3.67
602 626 7.178983 ACATCATGTTTTTGGAATATGGTCACT 59.821 33.333 0.00 0.00 0.00 3.41
607 631 6.773200 TGTTTTTGGAATATGGTCACTGTGTA 59.227 34.615 7.79 0.00 0.00 2.90
664 690 6.691754 TGTGCATTGAAAGAAACTAGACAA 57.308 33.333 0.00 0.00 0.00 3.18
676 702 7.321745 AGAAACTAGACAAGTGTTGGAAAAG 57.678 36.000 0.00 0.00 38.88 2.27
679 705 2.666317 AGACAAGTGTTGGAAAAGGGG 58.334 47.619 0.00 0.00 34.12 4.79
684 710 4.287326 ACAAGTGTTGGAAAAGGGGAAAAA 59.713 37.500 0.00 0.00 34.12 1.94
720 746 6.969669 AAGAAAATAAACAGCGAAGAAACG 57.030 33.333 0.00 0.00 0.00 3.60
735 761 6.872608 CGAAGAAACGCATAAAAACCAAAAT 58.127 32.000 0.00 0.00 0.00 1.82
738 764 4.740741 AACGCATAAAAACCAAAATGCC 57.259 36.364 0.00 0.00 41.29 4.40
741 767 3.616379 CGCATAAAAACCAAAATGCCGAT 59.384 39.130 0.00 0.00 41.29 4.18
743 769 4.629200 GCATAAAAACCAAAATGCCGATGA 59.371 37.500 0.00 0.00 39.01 2.92
760 791 5.059710 GCCGATGAAGAAATGAAGAAAAACG 59.940 40.000 0.00 0.00 0.00 3.60
847 883 4.692475 GCCCGCGTTACCACCAGT 62.692 66.667 4.92 0.00 0.00 4.00
849 885 2.433664 CCGCGTTACCACCAGTCC 60.434 66.667 4.92 0.00 0.00 3.85
850 886 2.340809 CGCGTTACCACCAGTCCA 59.659 61.111 0.00 0.00 0.00 4.02
851 887 2.025418 CGCGTTACCACCAGTCCAC 61.025 63.158 0.00 0.00 0.00 4.02
855 903 0.470766 GTTACCACCAGTCCACCACA 59.529 55.000 0.00 0.00 0.00 4.17
867 915 2.108514 CACCACAGTGCCGGCTATG 61.109 63.158 29.70 26.49 37.14 2.23
916 964 1.820581 CCGATTCGGTGAAGGGCTA 59.179 57.895 17.08 0.00 42.73 3.93
931 979 3.935993 GCTACTGGCCTGAGTTTGA 57.064 52.632 17.64 0.00 34.27 2.69
932 980 1.731720 GCTACTGGCCTGAGTTTGAG 58.268 55.000 17.64 1.99 34.27 3.02
933 981 1.677217 GCTACTGGCCTGAGTTTGAGG 60.677 57.143 17.64 0.00 34.27 3.86
935 983 1.366319 ACTGGCCTGAGTTTGAGGAT 58.634 50.000 17.64 0.00 31.48 3.24
936 984 1.004044 ACTGGCCTGAGTTTGAGGATG 59.996 52.381 17.64 0.00 31.48 3.51
937 985 1.004044 CTGGCCTGAGTTTGAGGATGT 59.996 52.381 3.32 0.00 31.48 3.06
939 987 1.003580 GGCCTGAGTTTGAGGATGTCA 59.996 52.381 0.00 0.00 31.48 3.58
940 988 2.553028 GGCCTGAGTTTGAGGATGTCAA 60.553 50.000 0.00 0.00 43.82 3.18
947 995 1.808411 TTGAGGATGTCAAACTCGCC 58.192 50.000 3.56 0.00 42.49 5.54
948 996 0.389817 TGAGGATGTCAAACTCGCCG 60.390 55.000 3.56 0.00 34.03 6.46
949 997 0.389948 GAGGATGTCAAACTCGCCGT 60.390 55.000 0.00 0.00 0.00 5.68
950 998 0.389948 AGGATGTCAAACTCGCCGTC 60.390 55.000 0.00 0.00 0.00 4.79
951 999 0.669318 GGATGTCAAACTCGCCGTCA 60.669 55.000 0.00 0.00 0.00 4.35
952 1000 0.716108 GATGTCAAACTCGCCGTCAG 59.284 55.000 0.00 0.00 0.00 3.51
953 1001 0.670546 ATGTCAAACTCGCCGTCAGG 60.671 55.000 0.00 0.00 41.62 3.86
954 1002 1.006571 GTCAAACTCGCCGTCAGGA 60.007 57.895 0.00 0.00 41.02 3.86
955 1003 1.009389 GTCAAACTCGCCGTCAGGAG 61.009 60.000 0.00 0.00 41.02 3.69
956 1004 2.048127 AAACTCGCCGTCAGGAGC 60.048 61.111 0.00 0.00 41.02 4.70
957 1005 2.867855 AAACTCGCCGTCAGGAGCA 61.868 57.895 0.00 0.00 41.02 4.26
958 1006 2.377628 AAACTCGCCGTCAGGAGCAA 62.378 55.000 0.00 0.00 41.02 3.91
963 1021 3.003173 CCGTCAGGAGCAAGGGGA 61.003 66.667 0.00 0.00 41.02 4.81
965 1023 1.376037 CGTCAGGAGCAAGGGGAAC 60.376 63.158 0.00 0.00 0.00 3.62
982 1040 1.798813 GAACTGAATCAAACTCGCCGT 59.201 47.619 0.00 0.00 0.00 5.68
992 1050 2.507992 CTCGCCGTCAGGAGCAAG 60.508 66.667 0.00 0.00 41.02 4.01
1032 1090 4.189188 CTGCCGCTTCAGCCATGC 62.189 66.667 0.00 0.00 37.91 4.06
1122 1180 1.661463 ATCTGGTGGTGGATGACTGT 58.339 50.000 0.00 0.00 0.00 3.55
1149 1207 1.000607 GGATACAGCGTCCGCAAGATA 60.001 52.381 14.70 1.03 44.88 1.98
1438 1496 2.588620 ACATGATAGTCGAGTCCTCCC 58.411 52.381 0.00 0.00 0.00 4.30
1504 1562 2.276740 CATGGGCCTGGACCTTCC 59.723 66.667 21.75 0.00 36.96 3.46
1533 1591 1.141881 CCTCCCATCGTTCCAGTCG 59.858 63.158 0.00 0.00 0.00 4.18
1640 1698 4.778415 CCTCGAGTGGACGTGCCG 62.778 72.222 12.31 0.63 40.66 5.69
1702 1760 2.692368 GGGACCTGGATGCCTGGA 60.692 66.667 15.23 0.00 44.09 3.86
1830 1888 4.980805 GACCGGCTGTTCCACGCA 62.981 66.667 0.00 0.00 34.01 5.24
1848 1906 3.138798 GACCGCGAGAGGCACCTA 61.139 66.667 8.23 0.00 43.84 3.08
1877 1935 0.687757 CTCCTCTTCATGGGGGACGA 60.688 60.000 0.00 0.00 0.00 4.20
1878 1936 0.976073 TCCTCTTCATGGGGGACGAC 60.976 60.000 0.00 0.00 0.00 4.34
1879 1937 1.264749 CCTCTTCATGGGGGACGACA 61.265 60.000 0.00 0.00 0.00 4.35
1880 1938 0.108138 CTCTTCATGGGGGACGACAC 60.108 60.000 0.00 0.00 0.00 3.67
1881 1939 0.834261 TCTTCATGGGGGACGACACA 60.834 55.000 0.00 0.00 0.00 3.72
1882 1940 0.673644 CTTCATGGGGGACGACACAC 60.674 60.000 0.00 0.00 0.00 3.82
1884 1942 2.602267 ATGGGGGACGACACACGA 60.602 61.111 0.00 0.00 45.77 4.35
1918 1976 2.126424 GAGTGTGTCTCGGCCGAC 60.126 66.667 27.28 17.65 33.25 4.79
1963 2021 1.808891 GCCCACCGTGTGTACCATATC 60.809 57.143 0.00 0.00 0.00 1.63
1981 2039 5.507482 CCATATCACTACGTTCGGTCTCAAT 60.507 44.000 0.00 0.00 0.00 2.57
2047 2105 1.067669 GCCTATGAGATGACAGACGCA 59.932 52.381 0.00 0.00 0.00 5.24
2099 2157 6.889177 TCCAACTGCATTCTGGATGTAATTAA 59.111 34.615 7.32 0.00 38.07 1.40
2139 2197 6.096846 GGACTTAATTGTGCTGGAAATGGTAT 59.903 38.462 0.00 0.00 0.00 2.73
2155 2216 8.362639 GGAAATGGTATTATGATTTGTGCTGAT 58.637 33.333 0.00 0.00 0.00 2.90
2245 2308 1.160137 AGCTCGGTCTGCAAAATGAC 58.840 50.000 0.00 0.00 0.00 3.06
2246 2309 0.169009 GCTCGGTCTGCAAAATGACC 59.831 55.000 11.84 11.84 46.69 4.02
2251 2314 2.519013 GGTCTGCAAAATGACCCTCTT 58.481 47.619 10.97 0.00 45.03 2.85
2252 2315 3.686016 GGTCTGCAAAATGACCCTCTTA 58.314 45.455 10.97 0.00 45.03 2.10
2253 2316 3.691609 GGTCTGCAAAATGACCCTCTTAG 59.308 47.826 10.97 0.00 45.03 2.18
2255 2318 3.009473 TCTGCAAAATGACCCTCTTAGCT 59.991 43.478 0.00 0.00 0.00 3.32
2256 2319 4.225042 TCTGCAAAATGACCCTCTTAGCTA 59.775 41.667 0.00 0.00 0.00 3.32
2257 2320 4.517285 TGCAAAATGACCCTCTTAGCTAG 58.483 43.478 0.00 0.00 0.00 3.42
2267 3041 6.553476 TGACCCTCTTAGCTAGCACATATAAA 59.447 38.462 18.83 0.00 0.00 1.40
2304 3078 5.067283 GTGTTTCTTAAGCCTCCTTTGTTCA 59.933 40.000 0.00 0.00 32.47 3.18
2306 3080 7.001674 TGTTTCTTAAGCCTCCTTTGTTCATA 58.998 34.615 0.00 0.00 32.47 2.15
2312 3086 5.559148 AGCCTCCTTTGTTCATAGGATAG 57.441 43.478 11.24 8.13 39.72 2.08
2313 3087 4.349342 AGCCTCCTTTGTTCATAGGATAGG 59.651 45.833 11.24 10.98 39.72 2.57
2314 3088 4.348168 GCCTCCTTTGTTCATAGGATAGGA 59.652 45.833 15.96 0.00 39.72 2.94
2315 3089 5.013599 GCCTCCTTTGTTCATAGGATAGGAT 59.986 44.000 15.96 0.00 39.72 3.24
2316 3090 6.213600 GCCTCCTTTGTTCATAGGATAGGATA 59.786 42.308 15.96 0.00 39.72 2.59
2317 3091 7.092668 GCCTCCTTTGTTCATAGGATAGGATAT 60.093 40.741 15.96 0.00 39.72 1.63
2318 3092 8.263640 CCTCCTTTGTTCATAGGATAGGATATG 58.736 40.741 11.24 0.00 39.72 1.78
2319 3093 8.972662 TCCTTTGTTCATAGGATAGGATATGA 57.027 34.615 7.68 0.00 35.66 2.15
2320 3094 8.816894 TCCTTTGTTCATAGGATAGGATATGAC 58.183 37.037 7.68 0.00 37.96 3.06
2321 3095 8.820831 CCTTTGTTCATAGGATAGGATATGACT 58.179 37.037 3.76 0.00 37.96 3.41
2337 3111 8.317679 AGGATATGACTAACTAAATCTCATGGC 58.682 37.037 0.00 0.00 0.00 4.40
2338 3112 8.317679 GGATATGACTAACTAAATCTCATGGCT 58.682 37.037 0.00 0.00 0.00 4.75
2339 3113 9.149225 GATATGACTAACTAAATCTCATGGCTG 57.851 37.037 0.00 0.00 0.00 4.85
2340 3114 5.118990 TGACTAACTAAATCTCATGGCTGC 58.881 41.667 0.00 0.00 0.00 5.25
2341 3115 5.102953 ACTAACTAAATCTCATGGCTGCA 57.897 39.130 0.50 0.00 0.00 4.41
2342 3116 5.688807 ACTAACTAAATCTCATGGCTGCAT 58.311 37.500 0.50 0.00 0.00 3.96
2344 3118 2.621998 ACTAAATCTCATGGCTGCATGC 59.378 45.455 11.82 11.82 41.94 4.06
2346 3120 1.704641 AATCTCATGGCTGCATGCAT 58.295 45.000 22.97 2.59 45.15 3.96
2347 3121 1.248486 ATCTCATGGCTGCATGCATC 58.752 50.000 22.97 17.75 45.15 3.91
2349 3123 0.961753 CTCATGGCTGCATGCATCAT 59.038 50.000 22.97 22.96 45.15 2.45
2351 3125 2.556622 CTCATGGCTGCATGCATCATTA 59.443 45.455 22.97 16.99 45.15 1.90
2352 3126 3.161866 TCATGGCTGCATGCATCATTAT 58.838 40.909 22.97 9.82 45.15 1.28
2355 3129 3.161866 TGGCTGCATGCATCATTATGAT 58.838 40.909 22.97 1.25 45.15 2.45
2366 3140 1.162698 CATTATGATGCAGAGGCCGG 58.837 55.000 0.00 0.00 40.13 6.13
2367 3141 0.037303 ATTATGATGCAGAGGCCGGG 59.963 55.000 2.18 0.00 40.13 5.73
2368 3142 2.055689 TTATGATGCAGAGGCCGGGG 62.056 60.000 2.18 0.00 40.13 5.73
2369 3143 2.963391 TATGATGCAGAGGCCGGGGA 62.963 60.000 2.18 0.00 40.13 4.81
2370 3144 3.564218 GATGCAGAGGCCGGGGAT 61.564 66.667 2.18 0.00 40.13 3.85
2371 3145 2.122413 ATGCAGAGGCCGGGGATA 60.122 61.111 2.18 0.00 40.13 2.59
2372 3146 2.456287 GATGCAGAGGCCGGGGATAC 62.456 65.000 2.18 0.00 40.13 2.24
2373 3147 4.301027 GCAGAGGCCGGGGATACG 62.301 72.222 2.18 0.00 37.60 3.06
2384 3158 1.605753 GGGGATACGCCTCCATTTTC 58.394 55.000 6.23 0.00 45.38 2.29
2385 3159 1.133915 GGGGATACGCCTCCATTTTCA 60.134 52.381 6.23 0.00 45.38 2.69
2386 3160 2.650322 GGGATACGCCTCCATTTTCAA 58.350 47.619 6.23 0.00 37.01 2.69
2388 3162 3.445805 GGGATACGCCTCCATTTTCAAAA 59.554 43.478 6.23 0.00 37.01 2.44
2568 3700 6.861065 TTGATAAACTGAAGAACACTGGAC 57.139 37.500 0.00 0.00 0.00 4.02
2577 3709 4.635765 TGAAGAACACTGGACAAAACTGAG 59.364 41.667 0.00 0.00 0.00 3.35
2589 3722 8.786826 TGGACAAAACTGAGTAAATATACTGG 57.213 34.615 0.00 0.00 42.47 4.00
2610 3744 6.609212 ACTGGATATGACTGAGTACATGACTT 59.391 38.462 0.00 0.00 39.06 3.01
2629 3763 5.296780 TGACTTAAACACAGCAGAAAAGAGG 59.703 40.000 0.00 0.00 0.00 3.69
2635 3769 4.381411 ACACAGCAGAAAAGAGGAACTAC 58.619 43.478 0.00 0.00 41.55 2.73
2644 3782 5.602978 AGAAAAGAGGAACTACTGGAAGACA 59.397 40.000 0.00 0.00 41.55 3.41
2703 3841 8.787852 AGATGGAGTGAAGAAGAACAAATTTAC 58.212 33.333 0.00 0.00 0.00 2.01
2706 3844 7.070183 GGAGTGAAGAAGAACAAATTTACGAC 58.930 38.462 0.00 0.00 0.00 4.34
2748 3886 5.000012 AGTAGCTGAGGAAATCTAACACG 58.000 43.478 0.00 0.00 0.00 4.49
2799 3937 4.739046 ACAGACTTGAAGAAAGATTGCG 57.261 40.909 0.00 0.00 39.38 4.85
2882 4020 4.380843 TCATTTGGGGAACAAGAGCTTA 57.619 40.909 0.00 0.00 40.82 3.09
2885 4025 5.243730 TCATTTGGGGAACAAGAGCTTAAAG 59.756 40.000 0.00 0.00 40.82 1.85
2892 4032 6.439599 GGGAACAAGAGCTTAAAGAGAAAAC 58.560 40.000 0.00 0.00 0.00 2.43
2901 4041 8.348507 AGAGCTTAAAGAGAAAACATGAAACAG 58.651 33.333 0.00 0.00 0.00 3.16
2936 4078 7.170965 TCTCAGAATATTATCCCCAATGCTTC 58.829 38.462 0.00 0.00 0.00 3.86
2995 4137 2.936919 ACAGAGGAAGCACATCACAA 57.063 45.000 0.00 0.00 0.00 3.33
3034 4177 5.730550 TCAAAGCGTATACCACAAAGAGAT 58.269 37.500 0.00 0.00 0.00 2.75
3035 4178 5.810587 TCAAAGCGTATACCACAAAGAGATC 59.189 40.000 0.00 0.00 0.00 2.75
3036 4179 5.339008 AAGCGTATACCACAAAGAGATCA 57.661 39.130 0.00 0.00 0.00 2.92
3037 4180 5.537300 AGCGTATACCACAAAGAGATCAT 57.463 39.130 0.00 0.00 0.00 2.45
3053 4196 9.539825 AAAGAGATCATAATGCTAGTGTGTTAG 57.460 33.333 0.00 0.00 0.00 2.34
3079 4222 0.394216 TGCACAACACAAGCAGAGGT 60.394 50.000 0.00 0.00 33.75 3.85
3080 4223 0.308993 GCACAACACAAGCAGAGGTC 59.691 55.000 0.00 0.00 0.00 3.85
3094 4237 4.816925 AGCAGAGGTCAAAGACTGTTTAAC 59.183 41.667 0.00 0.00 32.47 2.01
3095 4238 4.574828 GCAGAGGTCAAAGACTGTTTAACA 59.425 41.667 0.00 0.00 32.47 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.688073 ATGATACTTAGGGAAACGATGGAT 57.312 37.500 0.00 0.00 0.00 3.41
22 23 8.986929 AGATTTCAAAGGAATGATACTTAGGG 57.013 34.615 0.00 0.00 31.93 3.53
45 46 4.360951 AACACGGGACAATTAAGGAAGA 57.639 40.909 0.00 0.00 0.00 2.87
48 49 4.088056 TCAAACACGGGACAATTAAGGA 57.912 40.909 0.00 0.00 0.00 3.36
62 63 9.687717 CATAATTTTATTTGGCGAATCAAACAC 57.312 29.630 2.50 0.00 39.13 3.32
140 146 4.650972 AACCCTGCTTGTGATTTACCTA 57.349 40.909 0.00 0.00 0.00 3.08
236 242 2.897846 CCGTGTGTTGCAACGGGA 60.898 61.111 23.79 7.92 37.78 5.14
248 254 7.174599 GGTACATCACTAGATAATAGACCGTGT 59.825 40.741 0.00 0.00 31.88 4.49
276 291 9.651913 AACACATGAACACTCTTTTTAAATGTT 57.348 25.926 0.00 4.25 36.24 2.71
282 297 9.515020 GATTGAAACACATGAACACTCTTTTTA 57.485 29.630 0.00 0.00 0.00 1.52
283 298 8.034215 TGATTGAAACACATGAACACTCTTTTT 58.966 29.630 0.00 0.00 0.00 1.94
288 303 7.436080 ACATTTGATTGAAACACATGAACACTC 59.564 33.333 8.30 0.00 32.16 3.51
290 305 7.010367 ACACATTTGATTGAAACACATGAACAC 59.990 33.333 8.30 0.00 32.16 3.32
616 640 7.682593 TTGTACATAATATACGTGTGAACCG 57.317 36.000 0.00 0.00 0.00 4.44
630 654 9.926158 TTTCTTTCAATGCACATTGTACATAAT 57.074 25.926 19.81 0.00 46.15 1.28
631 655 9.190858 GTTTCTTTCAATGCACATTGTACATAA 57.809 29.630 19.81 6.76 46.15 1.90
632 656 8.575589 AGTTTCTTTCAATGCACATTGTACATA 58.424 29.630 19.81 1.23 46.15 2.29
634 658 6.804677 AGTTTCTTTCAATGCACATTGTACA 58.195 32.000 19.81 0.00 46.15 2.90
635 659 8.289618 TCTAGTTTCTTTCAATGCACATTGTAC 58.710 33.333 19.81 11.04 46.15 2.90
661 687 2.838637 TCCCCTTTTCCAACACTTGT 57.161 45.000 0.00 0.00 0.00 3.16
694 720 8.318167 CGTTTCTTCGCTGTTTATTTTCTTTTT 58.682 29.630 0.00 0.00 0.00 1.94
695 721 7.827619 CGTTTCTTCGCTGTTTATTTTCTTTT 58.172 30.769 0.00 0.00 0.00 2.27
696 722 7.376530 CGTTTCTTCGCTGTTTATTTTCTTT 57.623 32.000 0.00 0.00 0.00 2.52
697 723 6.969669 CGTTTCTTCGCTGTTTATTTTCTT 57.030 33.333 0.00 0.00 0.00 2.52
711 737 5.874892 TTTGGTTTTTATGCGTTTCTTCG 57.125 34.783 0.00 0.00 0.00 3.79
712 738 6.573357 GCATTTTGGTTTTTATGCGTTTCTTC 59.427 34.615 0.00 0.00 34.70 2.87
713 739 6.426327 GCATTTTGGTTTTTATGCGTTTCTT 58.574 32.000 0.00 0.00 34.70 2.52
714 740 5.049749 GGCATTTTGGTTTTTATGCGTTTCT 60.050 36.000 0.00 0.00 43.22 2.52
715 741 5.143660 GGCATTTTGGTTTTTATGCGTTTC 58.856 37.500 0.00 0.00 43.22 2.78
716 742 4.319118 CGGCATTTTGGTTTTTATGCGTTT 60.319 37.500 0.00 0.00 43.22 3.60
717 743 3.185391 CGGCATTTTGGTTTTTATGCGTT 59.815 39.130 0.00 0.00 43.22 4.84
718 744 2.734079 CGGCATTTTGGTTTTTATGCGT 59.266 40.909 0.00 0.00 43.22 5.24
719 745 2.989840 TCGGCATTTTGGTTTTTATGCG 59.010 40.909 0.00 0.00 43.22 4.73
720 746 4.629200 TCATCGGCATTTTGGTTTTTATGC 59.371 37.500 0.00 0.00 41.94 3.14
721 747 6.589523 TCTTCATCGGCATTTTGGTTTTTATG 59.410 34.615 0.00 0.00 0.00 1.90
722 748 6.696411 TCTTCATCGGCATTTTGGTTTTTAT 58.304 32.000 0.00 0.00 0.00 1.40
723 749 6.090483 TCTTCATCGGCATTTTGGTTTTTA 57.910 33.333 0.00 0.00 0.00 1.52
735 761 5.703978 TTTTCTTCATTTCTTCATCGGCA 57.296 34.783 0.00 0.00 0.00 5.69
738 764 6.370593 TCCGTTTTTCTTCATTTCTTCATCG 58.629 36.000 0.00 0.00 0.00 3.84
741 767 7.276878 GGTTTTCCGTTTTTCTTCATTTCTTCA 59.723 33.333 0.00 0.00 0.00 3.02
743 769 6.537301 GGGTTTTCCGTTTTTCTTCATTTCTT 59.463 34.615 0.00 0.00 41.82 2.52
797 833 2.811431 TCTTGCGTTCAGGGTAATGTTG 59.189 45.455 0.00 0.00 0.00 3.33
849 885 2.108514 CATAGCCGGCACTGTGGTG 61.109 63.158 31.54 11.89 45.53 4.17
850 886 2.268920 CATAGCCGGCACTGTGGT 59.731 61.111 31.54 8.51 0.00 4.16
851 887 2.514592 CCATAGCCGGCACTGTGG 60.515 66.667 31.54 24.65 41.75 4.17
916 964 1.004044 CATCCTCAAACTCAGGCCAGT 59.996 52.381 5.01 0.00 0.00 4.00
930 978 0.389948 ACGGCGAGTTTGACATCCTC 60.390 55.000 16.62 0.00 0.00 3.71
931 979 0.389948 GACGGCGAGTTTGACATCCT 60.390 55.000 16.62 0.00 0.00 3.24
932 980 0.669318 TGACGGCGAGTTTGACATCC 60.669 55.000 16.62 0.00 0.00 3.51
933 981 0.716108 CTGACGGCGAGTTTGACATC 59.284 55.000 16.62 0.00 0.00 3.06
935 983 1.300620 CCTGACGGCGAGTTTGACA 60.301 57.895 16.62 1.05 0.00 3.58
936 984 1.006571 TCCTGACGGCGAGTTTGAC 60.007 57.895 16.62 0.00 0.00 3.18
937 985 1.289066 CTCCTGACGGCGAGTTTGA 59.711 57.895 16.62 2.15 0.00 2.69
939 987 2.048127 GCTCCTGACGGCGAGTTT 60.048 61.111 16.62 0.00 0.00 2.66
940 988 2.771763 CTTGCTCCTGACGGCGAGTT 62.772 60.000 16.62 0.00 35.78 3.01
941 989 3.288308 CTTGCTCCTGACGGCGAGT 62.288 63.158 16.62 0.00 35.78 4.18
943 991 4.069232 CCTTGCTCCTGACGGCGA 62.069 66.667 16.62 0.00 0.00 5.54
946 994 2.592993 TTCCCCTTGCTCCTGACGG 61.593 63.158 0.00 0.00 0.00 4.79
947 995 1.376037 GTTCCCCTTGCTCCTGACG 60.376 63.158 0.00 0.00 0.00 4.35
948 996 0.322008 CAGTTCCCCTTGCTCCTGAC 60.322 60.000 0.00 0.00 0.00 3.51
949 997 0.473694 TCAGTTCCCCTTGCTCCTGA 60.474 55.000 0.00 0.00 0.00 3.86
950 998 0.401738 TTCAGTTCCCCTTGCTCCTG 59.598 55.000 0.00 0.00 0.00 3.86
951 999 1.283321 GATTCAGTTCCCCTTGCTCCT 59.717 52.381 0.00 0.00 0.00 3.69
952 1000 1.004745 TGATTCAGTTCCCCTTGCTCC 59.995 52.381 0.00 0.00 0.00 4.70
953 1001 2.496899 TGATTCAGTTCCCCTTGCTC 57.503 50.000 0.00 0.00 0.00 4.26
954 1002 2.893489 GTTTGATTCAGTTCCCCTTGCT 59.107 45.455 0.00 0.00 0.00 3.91
955 1003 2.893489 AGTTTGATTCAGTTCCCCTTGC 59.107 45.455 0.00 0.00 0.00 4.01
956 1004 3.189287 CGAGTTTGATTCAGTTCCCCTTG 59.811 47.826 0.00 0.00 0.00 3.61
957 1005 3.412386 CGAGTTTGATTCAGTTCCCCTT 58.588 45.455 0.00 0.00 0.00 3.95
958 1006 2.876079 GCGAGTTTGATTCAGTTCCCCT 60.876 50.000 0.00 0.00 0.00 4.79
963 1021 1.798813 GACGGCGAGTTTGATTCAGTT 59.201 47.619 16.62 0.00 0.00 3.16
965 1023 1.391485 CTGACGGCGAGTTTGATTCAG 59.609 52.381 16.62 9.85 0.00 3.02
982 1040 0.904865 ATGTCGTCCCTTGCTCCTGA 60.905 55.000 0.00 0.00 0.00 3.86
992 1050 3.195698 GCTTCGGCATGTCGTCCC 61.196 66.667 20.64 5.08 41.33 4.46
1050 1108 2.032071 CGGTGGTTCCCTCGCTTT 59.968 61.111 0.00 0.00 0.00 3.51
1122 1180 1.681538 GGACGCTGTATCCTCTCTCA 58.318 55.000 0.00 0.00 33.03 3.27
1149 1207 2.651361 CTGAAGGTGCCGACGTCT 59.349 61.111 14.70 0.00 0.00 4.18
1411 1469 2.287069 ACTCGACTATCATGTACAGCGC 60.287 50.000 0.00 0.00 0.00 5.92
1412 1470 3.546617 GACTCGACTATCATGTACAGCG 58.453 50.000 0.33 0.00 0.00 5.18
1486 1544 2.440980 GAAGGTCCAGGCCCATGC 60.441 66.667 0.00 0.00 0.00 4.06
1521 1579 1.215647 GTCTGGCGACTGGAACGAT 59.784 57.895 0.00 0.00 37.19 3.73
1533 1591 0.165944 CCAACGATTTGACGTCTGGC 59.834 55.000 17.92 2.83 45.83 4.85
1612 1670 1.534235 ACTCGAGGCTCCTGGTGTT 60.534 57.895 18.41 0.00 0.00 3.32
1674 1732 2.759355 TCCAGGTCCCGATCAAAGTAT 58.241 47.619 0.00 0.00 0.00 2.12
1685 1743 2.081161 ATCCAGGCATCCAGGTCCC 61.081 63.158 0.00 0.00 31.65 4.46
1702 1760 1.153061 CATGGATGCAGAGCCCCAT 59.847 57.895 0.00 7.05 40.00 4.00
1830 1888 3.640257 TAGGTGCCTCTCGCGGTCT 62.640 63.158 6.13 0.00 42.08 3.85
1877 1935 1.006102 GGCAGTAGCTGTCGTGTGT 60.006 57.895 0.00 0.00 41.70 3.72
1878 1936 1.010935 CAGGCAGTAGCTGTCGTGTG 61.011 60.000 0.00 0.00 41.46 3.82
1879 1937 1.290324 CAGGCAGTAGCTGTCGTGT 59.710 57.895 0.00 0.00 41.46 4.49
1880 1938 2.097038 GCAGGCAGTAGCTGTCGTG 61.097 63.158 0.00 0.00 41.46 4.35
1881 1939 2.219325 GAGCAGGCAGTAGCTGTCGT 62.219 60.000 0.00 0.00 41.46 4.34
1882 1940 1.518133 GAGCAGGCAGTAGCTGTCG 60.518 63.158 0.00 0.00 41.46 4.35
1883 1941 1.518133 CGAGCAGGCAGTAGCTGTC 60.518 63.158 0.00 0.00 42.04 3.51
1884 1942 1.943116 CTCGAGCAGGCAGTAGCTGT 61.943 60.000 0.00 0.00 42.04 4.40
1918 1976 1.032657 ACTCATCCTCGTCCTGGTCG 61.033 60.000 7.02 7.02 0.00 4.79
1963 2021 3.541130 CGTAATTGAGACCGAACGTAGTG 59.459 47.826 0.00 0.00 45.00 2.74
1981 2039 5.828328 TCTCAGCTCTCCATCTTTATCGTAA 59.172 40.000 0.00 0.00 0.00 3.18
2047 2105 7.170489 CGCTTGTATAGTTCATTCATCTCATGT 59.830 37.037 0.00 0.00 0.00 3.21
2157 2218 9.965824 GATGAAACTTTGTAGGAAAATCTGAAA 57.034 29.630 0.00 0.00 0.00 2.69
2159 2220 8.924511 AGATGAAACTTTGTAGGAAAATCTGA 57.075 30.769 0.00 0.00 0.00 3.27
2245 2308 7.880195 ACATTTTATATGTGCTAGCTAAGAGGG 59.120 37.037 17.23 1.30 0.00 4.30
2246 2309 8.839310 ACATTTTATATGTGCTAGCTAAGAGG 57.161 34.615 17.23 5.43 0.00 3.69
2274 3048 6.731292 AGGAGGCTTAAGAAACACAAAAAT 57.269 33.333 6.67 0.00 0.00 1.82
2275 3049 6.538945 AAGGAGGCTTAAGAAACACAAAAA 57.461 33.333 6.67 0.00 0.00 1.94
2312 3086 8.317679 AGCCATGAGATTTAGTTAGTCATATCC 58.682 37.037 0.00 0.00 0.00 2.59
2313 3087 9.149225 CAGCCATGAGATTTAGTTAGTCATATC 57.851 37.037 0.00 0.00 0.00 1.63
2314 3088 7.605691 GCAGCCATGAGATTTAGTTAGTCATAT 59.394 37.037 0.00 0.00 0.00 1.78
2315 3089 6.931281 GCAGCCATGAGATTTAGTTAGTCATA 59.069 38.462 0.00 0.00 0.00 2.15
2316 3090 5.762218 GCAGCCATGAGATTTAGTTAGTCAT 59.238 40.000 0.00 0.00 0.00 3.06
2317 3091 5.118990 GCAGCCATGAGATTTAGTTAGTCA 58.881 41.667 0.00 0.00 0.00 3.41
2318 3092 5.118990 TGCAGCCATGAGATTTAGTTAGTC 58.881 41.667 0.00 0.00 0.00 2.59
2319 3093 5.102953 TGCAGCCATGAGATTTAGTTAGT 57.897 39.130 0.00 0.00 0.00 2.24
2330 3104 8.292011 ATCATAATGATGCATGCAGCCATGAG 62.292 42.308 30.88 23.87 42.31 2.90
2335 3109 3.511699 CATCATAATGATGCATGCAGCC 58.488 45.455 31.30 22.02 46.37 4.85
2346 3120 1.271001 CCGGCCTCTGCATCATAATGA 60.271 52.381 0.00 0.00 40.13 2.57
2347 3121 1.162698 CCGGCCTCTGCATCATAATG 58.837 55.000 0.00 0.00 40.13 1.90
2349 3123 1.451504 CCCGGCCTCTGCATCATAA 59.548 57.895 0.00 0.00 40.13 1.90
2351 3125 3.882326 CCCCGGCCTCTGCATCAT 61.882 66.667 0.00 0.00 40.13 2.45
2352 3126 2.963391 TATCCCCGGCCTCTGCATCA 62.963 60.000 0.00 0.00 40.13 3.07
2355 3129 3.161450 GTATCCCCGGCCTCTGCA 61.161 66.667 0.00 0.00 40.13 4.41
2364 3138 0.179029 AAAATGGAGGCGTATCCCCG 60.179 55.000 5.71 0.00 38.72 5.73
2366 3140 2.341846 TGAAAATGGAGGCGTATCCC 57.658 50.000 5.71 0.00 38.72 3.85
2367 3141 4.712122 TTTTGAAAATGGAGGCGTATCC 57.288 40.909 1.46 1.46 40.03 2.59
2425 3526 9.230932 GCTATTTCTTCAGTTGCTCAATATTTC 57.769 33.333 0.00 0.00 0.00 2.17
2429 3530 7.686438 TTGCTATTTCTTCAGTTGCTCAATA 57.314 32.000 0.00 0.00 0.00 1.90
2435 3543 8.965172 CATATTCATTGCTATTTCTTCAGTTGC 58.035 33.333 0.00 0.00 0.00 4.17
2516 3624 9.591792 TCTCTTGAGTCATATTCAGTGTAATTG 57.408 33.333 0.00 0.00 0.00 2.32
2589 3722 9.803315 TGTTTAAGTCATGTACTCAGTCATATC 57.197 33.333 0.00 0.00 37.50 1.63
2610 3744 5.437060 AGTTCCTCTTTTCTGCTGTGTTTA 58.563 37.500 0.00 0.00 0.00 2.01
2629 3763 6.049790 AGTTTGTTCTGTCTTCCAGTAGTTC 58.950 40.000 0.00 0.00 42.19 3.01
2635 3769 7.065803 TCAGTTTAAGTTTGTTCTGTCTTCCAG 59.934 37.037 0.00 0.00 42.97 3.86
2674 3812 5.551305 TGTTCTTCTTCACTCCATCTTCA 57.449 39.130 0.00 0.00 0.00 3.02
2732 3870 8.610248 TTCAAATTACGTGTTAGATTTCCTCA 57.390 30.769 0.00 0.00 0.00 3.86
2799 3937 9.010029 TCCTCAAGTAAATAAAACCATGTCTTC 57.990 33.333 0.00 0.00 0.00 2.87
2833 3971 6.082031 AGTAAGTTCTTGGCCCCTAATTTTT 58.918 36.000 0.00 0.00 0.00 1.94
2835 3973 5.222254 TGAGTAAGTTCTTGGCCCCTAATTT 60.222 40.000 0.00 0.00 0.00 1.82
2836 3974 4.291249 TGAGTAAGTTCTTGGCCCCTAATT 59.709 41.667 0.00 0.00 0.00 1.40
2837 3975 3.850173 TGAGTAAGTTCTTGGCCCCTAAT 59.150 43.478 0.00 0.00 0.00 1.73
2882 4020 8.066612 TCCTTTCTGTTTCATGTTTTCTCTTT 57.933 30.769 0.00 0.00 0.00 2.52
2885 4025 5.917447 GCTCCTTTCTGTTTCATGTTTTCTC 59.083 40.000 0.00 0.00 0.00 2.87
2892 4032 4.698780 TGAGATGCTCCTTTCTGTTTCATG 59.301 41.667 0.00 0.00 0.00 3.07
2901 4041 7.552330 GGGATAATATTCTGAGATGCTCCTTTC 59.448 40.741 0.00 0.00 0.00 2.62
2936 4078 4.254492 GAGCTAAGGTTTACCAGTGAAGG 58.746 47.826 1.13 0.00 38.89 3.46
2995 4137 6.681777 ACGCTTTGATTCTTTTTAGAGCATT 58.318 32.000 0.00 0.00 0.00 3.56
3036 4179 9.046296 GCAATCTTACTAACACACTAGCATTAT 57.954 33.333 0.00 0.00 0.00 1.28
3037 4180 8.038351 TGCAATCTTACTAACACACTAGCATTA 58.962 33.333 0.00 0.00 0.00 1.90
3053 4196 3.963665 TGCTTGTGTTGTGCAATCTTAC 58.036 40.909 0.00 0.00 33.48 2.34


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

AutoCloner maintained by Alex Coulton.