Multiple sequence alignment - TraesCS2B01G027500

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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 TraesCS2B01G027500 chr2B 100.000 3761 0 0 1 3761 13023308 13019548 0.000000e+00 6946.0
1 TraesCS2B01G027500 chr2B 79.093 904 170 12 1138 2026 15882835 15881936 4.160000e-169 604.0
2 TraesCS2B01G027500 chr2B 79.318 880 160 15 1138 2000 14952375 14951501 6.950000e-167 597.0
3 TraesCS2B01G027500 chr2B 77.778 963 187 17 1059 2000 15818443 15817487 5.450000e-158 568.0
4 TraesCS2B01G027500 chr2B 90.789 76 5 2 3458 3531 76822821 76822746 2.390000e-17 100.0
5 TraesCS2B01G027500 chr2D 92.111 3448 197 30 360 3761 9687500 9684082 0.000000e+00 4791.0
6 TraesCS2B01G027500 chr2D 80.592 845 147 7 1138 1969 10800298 10799458 1.470000e-178 636.0
7 TraesCS2B01G027500 chr2D 85.393 89 10 3 3446 3531 8495887 8495975 5.170000e-14 89.8
8 TraesCS2B01G027500 chr2A 92.663 3230 178 28 577 3761 8758171 8754956 0.000000e+00 4597.0
9 TraesCS2B01G027500 chr2A 83.614 653 94 13 2126 2771 11308694 11308048 5.380000e-168 601.0
10 TraesCS2B01G027500 chr2A 78.953 879 167 11 1138 2001 11025501 11024626 1.950000e-162 582.0
11 TraesCS2B01G027500 chr2A 78.802 868 171 7 1138 2000 11309669 11308810 4.210000e-159 571.0
12 TraesCS2B01G027500 chr2A 86.245 538 57 11 10 534 8772886 8772353 5.450000e-158 568.0
13 TraesCS2B01G027500 chr2A 78.454 854 165 9 1160 2000 11044917 11044070 1.190000e-149 540.0
14 TraesCS2B01G027500 chr2A 77.404 416 68 22 13 407 30751254 30750844 1.360000e-54 224.0
15 TraesCS2B01G027500 chrUn 79.385 878 160 14 1138 2000 349086999 349086128 1.930000e-167 599.0
16 TraesCS2B01G027500 chrUn 79.338 876 164 10 1138 2000 349093058 349093929 1.930000e-167 599.0
17 TraesCS2B01G027500 chrUn 79.318 880 160 15 1138 2000 303367664 303368538 6.950000e-167 597.0
18 TraesCS2B01G027500 chrUn 79.318 880 160 15 1138 2000 303430039 303430913 6.950000e-167 597.0
19 TraesCS2B01G027500 chrUn 78.872 904 172 12 1138 2026 345912634 345911735 8.990000e-166 593.0
20 TraesCS2B01G027500 chrUn 86.271 539 55 13 10 534 12044688 12045221 5.450000e-158 568.0
21 TraesCS2B01G027500 chr5B 77.751 409 71 14 15 405 391393943 391394349 2.260000e-57 233.0
22 TraesCS2B01G027500 chr6B 76.675 403 73 16 16 401 22393219 22393617 1.770000e-48 204.0
23 TraesCS2B01G027500 chr4D 76.633 398 74 15 27 407 289338477 289338082 6.370000e-48 202.0
24 TraesCS2B01G027500 chr7D 75.721 416 76 20 10 405 430228276 430228686 6.420000e-43 185.0
25 TraesCS2B01G027500 chr7D 81.208 149 12 10 268 406 182593181 182593039 5.140000e-19 106.0
26 TraesCS2B01G027500 chr1B 92.500 80 4 2 3457 3535 305291400 305291322 3.070000e-21 113.0
27 TraesCS2B01G027500 chr1B 88.750 80 6 2 3459 3538 491239654 491239730 1.110000e-15 95.3
28 TraesCS2B01G027500 chr3B 91.781 73 5 1 3458 3530 822885354 822885425 2.390000e-17 100.0
29 TraesCS2B01G027500 chr1D 80.420 143 18 8 272 405 2065366 2065507 2.390000e-17 100.0
30 TraesCS2B01G027500 chr6D 89.610 77 7 1 3455 3530 469492335 469492411 3.090000e-16 97.1
31 TraesCS2B01G027500 chr6D 89.610 77 7 1 3455 3530 469511143 469511219 3.090000e-16 97.1


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 TraesCS2B01G027500 chr2B 13019548 13023308 3760 True 6946 6946 100.000 1 3761 1 chr2B.!!$R1 3760
1 TraesCS2B01G027500 chr2B 15881936 15882835 899 True 604 604 79.093 1138 2026 1 chr2B.!!$R4 888
2 TraesCS2B01G027500 chr2B 14951501 14952375 874 True 597 597 79.318 1138 2000 1 chr2B.!!$R2 862
3 TraesCS2B01G027500 chr2B 15817487 15818443 956 True 568 568 77.778 1059 2000 1 chr2B.!!$R3 941
4 TraesCS2B01G027500 chr2D 9684082 9687500 3418 True 4791 4791 92.111 360 3761 1 chr2D.!!$R1 3401
5 TraesCS2B01G027500 chr2D 10799458 10800298 840 True 636 636 80.592 1138 1969 1 chr2D.!!$R2 831
6 TraesCS2B01G027500 chr2A 8754956 8758171 3215 True 4597 4597 92.663 577 3761 1 chr2A.!!$R1 3184
7 TraesCS2B01G027500 chr2A 11308048 11309669 1621 True 586 601 81.208 1138 2771 2 chr2A.!!$R6 1633
8 TraesCS2B01G027500 chr2A 11024626 11025501 875 True 582 582 78.953 1138 2001 1 chr2A.!!$R3 863
9 TraesCS2B01G027500 chr2A 8772353 8772886 533 True 568 568 86.245 10 534 1 chr2A.!!$R2 524
10 TraesCS2B01G027500 chr2A 11044070 11044917 847 True 540 540 78.454 1160 2000 1 chr2A.!!$R4 840
11 TraesCS2B01G027500 chrUn 349086128 349086999 871 True 599 599 79.385 1138 2000 1 chrUn.!!$R2 862
12 TraesCS2B01G027500 chrUn 349093058 349093929 871 False 599 599 79.338 1138 2000 1 chrUn.!!$F4 862
13 TraesCS2B01G027500 chrUn 303367664 303368538 874 False 597 597 79.318 1138 2000 1 chrUn.!!$F2 862
14 TraesCS2B01G027500 chrUn 303430039 303430913 874 False 597 597 79.318 1138 2000 1 chrUn.!!$F3 862
15 TraesCS2B01G027500 chrUn 345911735 345912634 899 True 593 593 78.872 1138 2026 1 chrUn.!!$R1 888
16 TraesCS2B01G027500 chrUn 12044688 12045221 533 False 568 568 86.271 10 534 1 chrUn.!!$F1 524

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
111 113 0.035152 TCGATGCAGGCCTCATTGTT 60.035 50.0 21.97 4.73 0.00 2.83 F
134 136 0.396695 CATGCTGCTCCAGGGGAAAT 60.397 55.0 0.00 0.00 31.21 2.17 F
897 938 0.397941 TGCACCAAGAGGAAGAGTGG 59.602 55.0 0.00 0.00 38.69 4.00 F
1908 1973 0.529378 GTGAATGCAAAGAGGCCAGG 59.471 55.0 5.01 0.00 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1505 1.075896 GGACGGGGTGAGGATCTCT 60.076 63.158 0.00 0.0 34.92 3.10 R
1770 1832 1.604147 GGCCCTCCAAATCAAACCCG 61.604 60.000 0.00 0.0 0.00 5.28 R
2343 2412 0.960364 CGACATGGGGTGGGTTGAAG 60.960 60.000 0.00 0.0 0.00 3.02 R
2945 3019 1.005748 CTGCGGCTTCAGACTGTGA 60.006 57.895 1.59 0.0 36.19 3.58 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
29 30 4.344865 GATGTGTGTGGGCCGGGT 62.345 66.667 2.18 0.00 0.00 5.28
30 31 4.659172 ATGTGTGTGGGCCGGGTG 62.659 66.667 2.18 0.00 0.00 4.61
35 36 2.519780 TGTGGGCCGGGTGAAAAC 60.520 61.111 2.18 0.00 0.00 2.43
36 37 3.299977 GTGGGCCGGGTGAAAACC 61.300 66.667 2.18 0.00 0.00 3.27
37 38 3.503839 TGGGCCGGGTGAAAACCT 61.504 61.111 2.18 0.00 0.00 3.50
38 39 2.989253 GGGCCGGGTGAAAACCTG 60.989 66.667 2.18 0.00 35.93 4.00
39 40 2.203437 GGCCGGGTGAAAACCTGT 60.203 61.111 2.18 0.00 34.36 4.00
41 42 1.658114 GCCGGGTGAAAACCTGTTC 59.342 57.895 2.18 0.00 34.36 3.18
49 51 2.687935 GTGAAAACCTGTTCTGCCTTCA 59.312 45.455 0.00 0.00 0.00 3.02
63 65 0.466124 CCTTCAGGTAGGCTGGTAGC 59.534 60.000 0.00 0.00 41.46 3.58
82 84 2.750888 GGCGATGTTCGTGCCCTTC 61.751 63.158 0.00 0.00 42.81 3.46
83 85 1.741770 GCGATGTTCGTGCCCTTCT 60.742 57.895 0.00 0.00 42.81 2.85
84 86 1.298859 GCGATGTTCGTGCCCTTCTT 61.299 55.000 0.00 0.00 42.81 2.52
85 87 0.721718 CGATGTTCGTGCCCTTCTTC 59.278 55.000 0.00 0.00 34.72 2.87
88 90 2.270352 TGTTCGTGCCCTTCTTCAAT 57.730 45.000 0.00 0.00 0.00 2.57
95 97 1.019278 GCCCTTCTTCAATGCGTCGA 61.019 55.000 0.00 0.00 0.00 4.20
97 99 1.328680 CCCTTCTTCAATGCGTCGATG 59.671 52.381 0.00 0.00 0.00 3.84
98 100 1.267732 CCTTCTTCAATGCGTCGATGC 60.268 52.381 22.77 22.77 0.00 3.91
106 108 4.819761 GCGTCGATGCAGGCCTCA 62.820 66.667 24.45 4.56 34.15 3.86
110 112 0.745845 GTCGATGCAGGCCTCATTGT 60.746 55.000 21.97 5.01 0.00 2.71
111 113 0.035152 TCGATGCAGGCCTCATTGTT 60.035 50.000 21.97 4.73 0.00 2.83
116 118 1.272037 TGCAGGCCTCATTGTTCATCA 60.272 47.619 0.00 0.00 0.00 3.07
119 121 2.029623 AGGCCTCATTGTTCATCATGC 58.970 47.619 0.00 0.00 0.00 4.06
134 136 0.396695 CATGCTGCTCCAGGGGAAAT 60.397 55.000 0.00 0.00 31.21 2.17
158 160 4.227134 CCTCGGATCAGGCGGTGG 62.227 72.222 0.00 0.00 0.00 4.61
182 184 1.342672 ACACTGGTGTCCGACCCTTT 61.343 55.000 0.01 0.00 45.45 3.11
207 209 1.081840 GCGCCACTTTTGAGCTCAC 60.082 57.895 18.03 1.60 0.00 3.51
209 211 1.576421 GCCACTTTTGAGCTCACGG 59.424 57.895 18.03 12.84 0.00 4.94
212 214 1.002468 CCACTTTTGAGCTCACGGTTG 60.002 52.381 18.03 11.41 0.00 3.77
221 223 1.693083 GCTCACGGTTGGTCGTATGC 61.693 60.000 0.00 0.00 41.86 3.14
240 242 1.962306 GGTTTACTTCGCGGTGGCA 60.962 57.895 6.13 0.00 39.92 4.92
245 247 1.017177 TACTTCGCGGTGGCATGTTC 61.017 55.000 6.13 0.00 39.92 3.18
254 256 1.888512 GGTGGCATGTTCACAGTTGAT 59.111 47.619 18.27 0.00 36.90 2.57
259 261 3.505680 GGCATGTTCACAGTTGATAACCA 59.494 43.478 0.00 0.00 0.00 3.67
260 262 4.158394 GGCATGTTCACAGTTGATAACCAT 59.842 41.667 0.00 0.00 0.00 3.55
262 264 5.335897 GCATGTTCACAGTTGATAACCATGT 60.336 40.000 0.00 0.00 32.26 3.21
263 265 5.940192 TGTTCACAGTTGATAACCATGTC 57.060 39.130 0.00 0.00 0.00 3.06
294 296 2.746277 GTAGGGGTGGCGTTGCTG 60.746 66.667 0.00 0.00 0.00 4.41
295 297 3.246112 TAGGGGTGGCGTTGCTGT 61.246 61.111 0.00 0.00 0.00 4.40
302 304 2.655044 GGCGTTGCTGTGCACAAC 60.655 61.111 21.98 17.54 43.15 3.32
303 305 2.101965 GCGTTGCTGTGCACAACA 59.898 55.556 21.98 20.26 46.14 3.33
322 325 0.623723 ACATTGTATCCGCCTTGGGT 59.376 50.000 0.00 0.00 38.76 4.51
323 326 1.308998 CATTGTATCCGCCTTGGGTC 58.691 55.000 0.00 0.00 38.76 4.46
326 331 0.616395 TGTATCCGCCTTGGGTCTGA 60.616 55.000 0.00 0.00 38.76 3.27
354 359 1.530323 GTGGGGCGTGAGTTTGTATT 58.470 50.000 0.00 0.00 0.00 1.89
544 558 7.792032 AGATTTCAGAGGTTATAATTCGGACA 58.208 34.615 0.00 0.00 0.00 4.02
554 568 9.310449 AGGTTATAATTCGGACACACTATAGAT 57.690 33.333 6.78 0.00 0.00 1.98
570 584 7.720074 ACACTATAGATTCACGGTGAAGATAGA 59.280 37.037 31.59 22.34 40.05 1.98
584 602 5.683743 GTGAAGATAGATTAGCACAGACGAC 59.316 44.000 0.00 0.00 0.00 4.34
597 615 2.488153 ACAGACGACGAGATGAACATGA 59.512 45.455 0.00 0.00 0.00 3.07
604 622 4.309933 GACGAGATGAACATGATGGCATA 58.690 43.478 0.00 0.00 32.27 3.14
725 755 7.831753 TGTGAGTTAATCTAAAGAGTCTCCAG 58.168 38.462 0.00 0.00 0.00 3.86
837 878 3.404773 GGCCAGTTGGAGCCTAGT 58.595 61.111 0.00 0.00 46.14 2.57
848 889 1.562017 GAGCCTAGTTAGCACTTCGC 58.438 55.000 0.00 0.00 42.91 4.70
889 930 1.537776 CGAGCTAGATGCACCAAGAGG 60.538 57.143 0.00 0.00 45.94 3.69
897 938 0.397941 TGCACCAAGAGGAAGAGTGG 59.602 55.000 0.00 0.00 38.69 4.00
998 1042 1.203928 CGTACAGCTAGCTCATGCAC 58.796 55.000 16.15 4.98 42.74 4.57
999 1043 1.202348 CGTACAGCTAGCTCATGCACT 60.202 52.381 16.15 0.00 42.74 4.40
1284 1334 3.016736 CCGTCTTGGAGCCATTTATGTT 58.983 45.455 0.00 0.00 42.00 2.71
1423 1473 2.038690 GTGACACCACACGGAGAGA 58.961 57.895 0.00 0.00 42.72 3.10
1539 1589 4.213270 CACCTTGTGACGTACATCAACAAT 59.787 41.667 0.00 0.00 39.48 2.71
1770 1832 1.414550 GACTACTTCCCAGCCCTCATC 59.585 57.143 0.00 0.00 0.00 2.92
1812 1874 3.754965 TGAGAAGGTTTCCAAGGATGTG 58.245 45.455 0.00 0.00 0.00 3.21
1894 1959 3.652057 ATCTTCGGAATGGTGGTGAAT 57.348 42.857 0.00 0.00 0.00 2.57
1908 1973 0.529378 GTGAATGCAAAGAGGCCAGG 59.471 55.000 5.01 0.00 0.00 4.45
1971 2036 3.806316 CAACCATTGTTGTCCGTAGAC 57.194 47.619 1.51 0.00 45.51 2.59
1983 2048 2.025727 GTAGACGACATCCGGGCG 59.974 66.667 0.00 3.29 43.93 6.13
2001 2066 2.100252 GGCGCAGATAGTGGTTAGTACA 59.900 50.000 10.83 0.00 0.00 2.90
2064 2131 1.521580 TGCATGCATTCGTGAAGTGA 58.478 45.000 18.46 0.00 0.00 3.41
2095 2162 4.594123 TTGATCCCCCGTTTTTCTTTTC 57.406 40.909 0.00 0.00 0.00 2.29
2097 2164 3.319689 TGATCCCCCGTTTTTCTTTTCAC 59.680 43.478 0.00 0.00 0.00 3.18
2099 2166 2.427812 TCCCCCGTTTTTCTTTTCACAC 59.572 45.455 0.00 0.00 0.00 3.82
2343 2412 1.247567 GCATACACCCATACCATGCC 58.752 55.000 0.00 0.00 36.78 4.40
2346 2415 3.149196 CATACACCCATACCATGCCTTC 58.851 50.000 0.00 0.00 0.00 3.46
2388 2457 1.749634 GTAGACACCACTATCGCTGGT 59.250 52.381 0.00 0.00 43.22 4.00
2532 2601 0.601558 TCAGTGAACCAGGACTACGC 59.398 55.000 0.00 0.00 0.00 4.42
2612 2681 2.545946 TCACAATGATGTTGTTCGCGAA 59.454 40.909 19.38 19.38 37.82 4.70
2644 2713 2.521958 ATTCACCTGGACGAAGCCCG 62.522 60.000 0.00 0.00 45.44 6.13
2661 2730 0.739462 CCGCTGGCGTTGACAGAATA 60.739 55.000 13.84 0.00 42.14 1.75
2682 2751 8.325046 AGAATAAGTCTCCAAGAAAGCAATACT 58.675 33.333 0.00 0.00 0.00 2.12
2713 2782 1.075536 CCTTAGCTGAACCCCTGGTTT 59.924 52.381 0.00 0.00 46.95 3.27
2730 2799 2.804647 GTTTTGCAAGCTAAACCACGT 58.195 42.857 17.31 0.00 36.29 4.49
2736 2805 0.396811 AAGCTAAACCACGTCTGGCT 59.603 50.000 0.00 0.00 42.08 4.75
2756 2829 4.637534 GGCTGCACATCTCTATGAGAAAAA 59.362 41.667 0.50 0.00 42.27 1.94
2790 2863 9.961265 AGTCAATGCATGTTTTATCTGATTATG 57.039 29.630 0.00 0.00 0.00 1.90
2857 2930 0.953960 GGTCGTGCATTCCTCGGTTT 60.954 55.000 0.00 0.00 0.00 3.27
2863 2937 3.308530 GTGCATTCCTCGGTTTTTCAAG 58.691 45.455 0.00 0.00 0.00 3.02
2864 2938 2.295909 TGCATTCCTCGGTTTTTCAAGG 59.704 45.455 0.00 0.00 0.00 3.61
2933 3007 5.702865 ACAATGCTAATGTGATGTGTGTTC 58.297 37.500 0.00 0.00 0.00 3.18
2945 3019 2.520069 TGTGTGTTCTTGGGTTGTGTT 58.480 42.857 0.00 0.00 0.00 3.32
2949 3023 2.490115 GTGTTCTTGGGTTGTGTTCACA 59.510 45.455 1.23 1.23 0.00 3.58
2955 3029 1.557371 TGGGTTGTGTTCACAGTCTGA 59.443 47.619 6.91 0.00 0.00 3.27
2956 3030 2.026729 TGGGTTGTGTTCACAGTCTGAA 60.027 45.455 6.91 0.00 36.46 3.02
2957 3031 2.614057 GGGTTGTGTTCACAGTCTGAAG 59.386 50.000 6.91 0.00 39.69 3.02
2958 3032 2.032178 GGTTGTGTTCACAGTCTGAAGC 59.968 50.000 6.91 0.00 39.69 3.86
2959 3033 1.953559 TGTGTTCACAGTCTGAAGCC 58.046 50.000 6.91 0.00 39.69 4.35
2967 3041 1.018226 CAGTCTGAAGCCGCAGAAGG 61.018 60.000 7.60 0.67 45.69 3.46
2986 3060 5.462068 AGAAGGCGCAAAAGTTGTTATTTTC 59.538 36.000 10.83 0.00 0.00 2.29
2988 3062 6.079424 AGGCGCAAAAGTTGTTATTTTCTA 57.921 33.333 10.83 0.00 0.00 2.10
3054 3128 9.836864 ATTATGATACTCTGCAAACAGTTCATA 57.163 29.630 13.66 13.66 44.77 2.15
3136 3210 6.039829 TGTTTATTACAATGTGACAACCAGCA 59.960 34.615 0.00 0.00 32.64 4.41
3322 3396 4.334481 GTCGTGGAAAGAAAAGAAGGACAA 59.666 41.667 0.00 0.00 0.00 3.18
3377 3451 9.513906 TGACATCTTGTATTCCTTCAATGTTTA 57.486 29.630 0.00 0.00 0.00 2.01
3416 3492 8.906636 TTATATCGACACTTCACTTTCAGTAC 57.093 34.615 0.00 0.00 0.00 2.73
3456 3532 1.736681 GCTCTCTTCTTTCGCTTGCAT 59.263 47.619 0.00 0.00 0.00 3.96
3464 3540 2.995939 TCTTTCGCTTGCATGTACTCTG 59.004 45.455 1.14 0.00 0.00 3.35
3503 3579 6.830114 AAGTACATTTAGATCACTAAGCGC 57.170 37.500 0.00 0.00 39.36 5.92
3505 3581 6.210078 AGTACATTTAGATCACTAAGCGCTC 58.790 40.000 12.06 0.00 39.36 5.03
3506 3582 5.269505 ACATTTAGATCACTAAGCGCTCT 57.730 39.130 12.06 4.00 39.36 4.09
3576 3665 3.171277 GGTGCAAGAATAACATTCGCAC 58.829 45.455 16.83 16.83 45.68 5.34
3598 3687 3.610242 CACACGATTGCTTCTAGAGACAC 59.390 47.826 0.00 0.00 0.00 3.67
3600 3689 3.856521 CACGATTGCTTCTAGAGACACAG 59.143 47.826 0.00 0.00 0.00 3.66
3618 3707 4.202441 CACAGGGTAGGATTCCAATTCAG 58.798 47.826 5.29 0.00 0.00 3.02
3625 3714 6.890268 GGGTAGGATTCCAATTCAGTTTAACT 59.110 38.462 5.29 0.00 0.00 2.24
3634 3723 7.685481 TCCAATTCAGTTTAACTATGGAGTCA 58.315 34.615 13.41 0.00 33.58 3.41
3636 3725 8.960591 CCAATTCAGTTTAACTATGGAGTCATT 58.039 33.333 10.78 0.00 33.58 2.57
3749 3844 9.897744 CTTACAAATATTTTCTTGTCAAGCTCA 57.102 29.630 7.78 0.00 37.05 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.742372 ACACACATCGCCTTCGGC 60.742 61.111 0.00 0.00 46.75 5.54
4 5 2.390599 CCACACACATCGCCTTCGG 61.391 63.158 0.00 0.00 36.13 4.30
5 6 2.390599 CCCACACACATCGCCTTCG 61.391 63.158 0.00 0.00 0.00 3.79
6 7 2.690778 GCCCACACACATCGCCTTC 61.691 63.158 0.00 0.00 0.00 3.46
7 8 2.672996 GCCCACACACATCGCCTT 60.673 61.111 0.00 0.00 0.00 4.35
8 9 4.722700 GGCCCACACACATCGCCT 62.723 66.667 0.00 0.00 36.65 5.52
29 30 2.951642 CTGAAGGCAGAACAGGTTTTCA 59.048 45.455 0.00 0.00 45.17 2.69
30 31 2.294512 CCTGAAGGCAGAACAGGTTTTC 59.705 50.000 0.00 0.00 45.17 2.29
31 32 2.310538 CCTGAAGGCAGAACAGGTTTT 58.689 47.619 0.00 0.00 45.17 2.43
36 37 2.393271 CCTACCTGAAGGCAGAACAG 57.607 55.000 0.00 0.00 45.17 3.16
49 51 3.155167 GCCGCTACCAGCCTACCT 61.155 66.667 0.00 0.00 38.18 3.08
52 54 2.520982 ATCGCCGCTACCAGCCTA 60.521 61.111 0.00 0.00 38.18 3.93
57 59 2.202690 CGAACATCGCCGCTACCA 60.203 61.111 0.00 0.00 31.14 3.25
60 62 2.883730 GCACGAACATCGCCGCTA 60.884 61.111 0.00 0.00 45.12 4.26
82 84 0.027194 CCTGCATCGACGCATTGAAG 59.973 55.000 6.63 0.00 42.06 3.02
83 85 1.980951 GCCTGCATCGACGCATTGAA 61.981 55.000 6.63 0.00 42.06 2.69
84 86 2.463620 GCCTGCATCGACGCATTGA 61.464 57.895 6.63 0.00 42.06 2.57
85 87 2.023741 GCCTGCATCGACGCATTG 59.976 61.111 6.63 2.35 42.06 2.82
88 90 4.819761 GAGGCCTGCATCGACGCA 62.820 66.667 12.00 5.84 40.32 5.24
95 97 2.029623 GATGAACAATGAGGCCTGCAT 58.970 47.619 12.00 11.18 0.00 3.96
97 99 1.466856 TGATGAACAATGAGGCCTGC 58.533 50.000 12.00 1.89 0.00 4.85
98 100 2.223735 GCATGATGAACAATGAGGCCTG 60.224 50.000 12.00 0.00 0.00 4.85
99 101 2.029623 GCATGATGAACAATGAGGCCT 58.970 47.619 3.86 3.86 0.00 5.19
101 103 2.798499 GCAGCATGATGAACAATGAGGC 60.798 50.000 16.67 0.00 39.69 4.70
106 108 2.688446 CTGGAGCAGCATGATGAACAAT 59.312 45.455 16.67 0.00 39.69 2.71
110 112 0.106868 CCCTGGAGCAGCATGATGAA 60.107 55.000 16.67 0.00 39.69 2.57
111 113 1.530283 CCCTGGAGCAGCATGATGA 59.470 57.895 16.67 0.00 39.69 2.92
116 118 0.106318 GATTTCCCCTGGAGCAGCAT 60.106 55.000 0.00 0.00 31.21 3.79
119 121 2.315443 AGGATTTCCCCTGGAGCAG 58.685 57.895 0.00 0.00 34.68 4.24
161 163 2.665185 GGTCGGACACCAGTGTGC 60.665 66.667 8.43 10.39 46.86 4.57
182 184 0.179032 TCAAAAGTGGCGCCTTCAGA 60.179 50.000 29.70 14.84 0.00 3.27
191 193 1.166531 ACCGTGAGCTCAAAAGTGGC 61.167 55.000 20.19 2.78 0.00 5.01
207 209 1.293267 AAACCGCATACGACCAACCG 61.293 55.000 0.00 0.00 43.93 4.44
209 211 2.340337 AGTAAACCGCATACGACCAAC 58.660 47.619 0.00 0.00 43.93 3.77
212 214 1.585214 CGAAGTAAACCGCATACGACC 59.415 52.381 0.00 0.00 43.93 4.79
221 223 3.018840 GCCACCGCGAAGTAAACCG 62.019 63.158 8.23 0.00 0.00 4.44
240 242 6.149973 CAGACATGGTTATCAACTGTGAACAT 59.850 38.462 0.00 0.00 37.30 2.71
245 247 4.005650 AGCAGACATGGTTATCAACTGTG 58.994 43.478 0.00 0.00 31.66 3.66
254 256 4.322725 CCACTACAAGAGCAGACATGGTTA 60.323 45.833 0.00 0.00 37.25 2.85
259 261 3.449018 CCTACCACTACAAGAGCAGACAT 59.551 47.826 0.00 0.00 0.00 3.06
260 262 2.826128 CCTACCACTACAAGAGCAGACA 59.174 50.000 0.00 0.00 0.00 3.41
262 264 2.457598 CCCTACCACTACAAGAGCAGA 58.542 52.381 0.00 0.00 0.00 4.26
263 265 1.482593 CCCCTACCACTACAAGAGCAG 59.517 57.143 0.00 0.00 0.00 4.24
302 304 1.024271 CCCAAGGCGGATACAATGTG 58.976 55.000 0.00 0.00 36.56 3.21
303 305 0.623723 ACCCAAGGCGGATACAATGT 59.376 50.000 0.00 0.00 36.56 2.71
322 325 1.836391 CCCCACCAACACACTCAGA 59.164 57.895 0.00 0.00 0.00 3.27
323 326 1.898574 GCCCCACCAACACACTCAG 60.899 63.158 0.00 0.00 0.00 3.35
326 331 3.804329 ACGCCCCACCAACACACT 61.804 61.111 0.00 0.00 0.00 3.55
434 446 4.579340 ACTCTGTCTTGTCTACGACTTTCA 59.421 41.667 0.00 0.00 33.15 2.69
439 451 9.649024 GTAATATAACTCTGTCTTGTCTACGAC 57.351 37.037 0.00 0.00 0.00 4.34
440 452 9.387257 TGTAATATAACTCTGTCTTGTCTACGA 57.613 33.333 0.00 0.00 0.00 3.43
544 558 6.716934 ATCTTCACCGTGAATCTATAGTGT 57.283 37.500 14.29 0.00 35.59 3.55
554 568 5.105513 TGTGCTAATCTATCTTCACCGTGAA 60.106 40.000 13.29 13.29 34.79 3.18
570 584 2.683362 TCATCTCGTCGTCTGTGCTAAT 59.317 45.455 0.00 0.00 0.00 1.73
584 602 5.874895 AATATGCCATCATGTTCATCTCG 57.125 39.130 0.00 0.00 29.53 4.04
604 622 8.738645 TTAAATTACCAAAACAAGTGGCAAAT 57.261 26.923 0.00 0.00 40.02 2.32
837 878 5.511888 GGGTATTAATAGGGCGAAGTGCTAA 60.512 44.000 0.00 0.00 45.43 3.09
848 889 6.415206 TCGTTTCAGAGGGTATTAATAGGG 57.585 41.667 0.00 0.00 0.00 3.53
897 938 4.044426 GTGTTGAGATTTGTGTTGGAAGC 58.956 43.478 0.00 0.00 0.00 3.86
998 1042 5.248087 CGTACATTGTTTGCGAACTCATAG 58.752 41.667 17.65 6.17 36.70 2.23
999 1043 4.092237 CCGTACATTGTTTGCGAACTCATA 59.908 41.667 17.65 3.06 36.70 2.15
1238 1288 2.941064 CACATGATGTCTGTGTCCATCC 59.059 50.000 0.00 0.00 39.30 3.51
1423 1473 1.677217 GCGCCTCATCTTCTTCCACTT 60.677 52.381 0.00 0.00 0.00 3.16
1455 1505 1.075896 GGACGGGGTGAGGATCTCT 60.076 63.158 0.00 0.00 34.92 3.10
1589 1651 8.492673 TCTTATCATGTTACCACAGAAATGTC 57.507 34.615 0.00 0.00 35.94 3.06
1770 1832 1.604147 GGCCCTCCAAATCAAACCCG 61.604 60.000 0.00 0.00 0.00 5.28
1812 1874 2.943033 CAACCGGTTGAGTATTCCCATC 59.057 50.000 38.61 0.00 42.93 3.51
1894 1959 1.719063 AAGTCCCTGGCCTCTTTGCA 61.719 55.000 3.32 0.00 0.00 4.08
1971 2036 3.207547 TATCTGCGCCCGGATGTCG 62.208 63.158 0.73 1.52 37.62 4.35
1974 2039 1.665916 CACTATCTGCGCCCGGATG 60.666 63.158 0.73 0.00 37.62 3.51
1983 2048 6.816640 TGAAATGTGTACTAACCACTATCTGC 59.183 38.462 0.00 0.00 33.92 4.26
2001 2066 9.911788 ACTGAATATTGATAGAGGTTGAAATGT 57.088 29.630 0.00 0.00 0.00 2.71
2064 2131 4.047627 ACGGGGGATCAAATTCTTCTTT 57.952 40.909 0.00 0.00 0.00 2.52
2124 2193 7.643569 TGTTGCATACATCATTTCCTACATT 57.356 32.000 0.00 0.00 0.00 2.71
2242 2311 6.319658 TGGACTAGTTTATCTTTACCGACGAT 59.680 38.462 0.00 0.00 0.00 3.73
2343 2412 0.960364 CGACATGGGGTGGGTTGAAG 60.960 60.000 0.00 0.00 0.00 3.02
2346 2415 3.061848 GCGACATGGGGTGGGTTG 61.062 66.667 0.00 0.00 0.00 3.77
2461 2530 2.035832 CGGGCTGAAAATCAAGTGGTTT 59.964 45.455 0.00 0.00 0.00 3.27
2499 2568 4.065088 GTTCACTGAGGAGTACATTTGCA 58.935 43.478 0.00 0.00 0.00 4.08
2532 2601 9.331282 CTCCTCCCACTACTAAATGAAATAAAG 57.669 37.037 0.00 0.00 0.00 1.85
2612 2681 1.637553 AGGTGAATCCCTGCAACATCT 59.362 47.619 0.00 0.00 36.75 2.90
2644 2713 2.076863 ACTTATTCTGTCAACGCCAGC 58.923 47.619 0.00 0.00 0.00 4.85
2661 2730 5.006386 CCAGTATTGCTTTCTTGGAGACTT 58.994 41.667 0.00 0.00 0.00 3.01
2713 2782 1.601903 CAGACGTGGTTTAGCTTGCAA 59.398 47.619 0.00 0.00 0.00 4.08
2730 2799 2.364647 CTCATAGAGATGTGCAGCCAGA 59.635 50.000 0.00 0.00 34.41 3.86
2767 2840 9.406828 CCTCATAATCAGATAAAACATGCATTG 57.593 33.333 0.00 0.00 0.00 2.82
2823 2896 1.604378 GACCACTGAGGACATGGGG 59.396 63.158 0.00 0.00 41.22 4.96
2871 2945 3.312421 CAGACACACGTTGTTTCCATCTT 59.688 43.478 5.14 0.00 39.17 2.40
2872 2946 2.872245 CAGACACACGTTGTTTCCATCT 59.128 45.455 5.14 0.00 39.17 2.90
2874 2948 2.639065 ACAGACACACGTTGTTTCCAT 58.361 42.857 5.14 0.00 39.17 3.41
2875 2949 2.102070 ACAGACACACGTTGTTTCCA 57.898 45.000 5.14 0.00 39.17 3.53
2876 2950 2.931325 TGTACAGACACACGTTGTTTCC 59.069 45.455 0.00 0.00 39.17 3.13
2877 2951 4.587211 TTGTACAGACACACGTTGTTTC 57.413 40.909 0.00 0.00 39.17 2.78
2878 2952 5.554822 ATTTGTACAGACACACGTTGTTT 57.445 34.783 0.00 0.00 39.17 2.83
2923 2997 2.687935 ACACAACCCAAGAACACACATC 59.312 45.455 0.00 0.00 0.00 3.06
2933 3007 2.355756 CAGACTGTGAACACAACCCAAG 59.644 50.000 8.93 0.00 41.33 3.61
2945 3019 1.005748 CTGCGGCTTCAGACTGTGA 60.006 57.895 1.59 0.00 36.19 3.58
2949 3023 1.294780 CCTTCTGCGGCTTCAGACT 59.705 57.895 0.00 0.00 42.27 3.24
2967 3041 6.986424 ACTAGAAAATAACAACTTTTGCGC 57.014 33.333 0.00 0.00 0.00 6.09
3024 3098 6.259608 ACTGTTTGCAGAGTATCATAATGCTC 59.740 38.462 1.30 0.00 45.28 4.26
3076 3150 4.746535 TTTATGATGCGAAGGTGGTAGA 57.253 40.909 0.00 0.00 0.00 2.59
3184 3258 9.007901 CACCAGTCTTCATCTTATTTTCTCTTT 57.992 33.333 0.00 0.00 0.00 2.52
3186 3260 7.911651 TCACCAGTCTTCATCTTATTTTCTCT 58.088 34.615 0.00 0.00 0.00 3.10
3219 3293 9.627123 CAAAACTATTTATCTTCCCTCCATACA 57.373 33.333 0.00 0.00 0.00 2.29
3310 3384 9.802039 TTACCAGTATATGTTTGTCCTTCTTTT 57.198 29.630 0.00 0.00 0.00 2.27
3322 3396 9.290988 TGACAATGTGTTTTACCAGTATATGTT 57.709 29.630 0.00 0.00 0.00 2.71
3382 3456 9.249053 AGTGAAGTGTCGATATAATATGATCCT 57.751 33.333 0.00 0.00 0.00 3.24
3383 3457 9.862371 AAGTGAAGTGTCGATATAATATGATCC 57.138 33.333 0.00 0.00 0.00 3.36
3416 3492 1.645034 CGGAAGAGCACCATGTACAG 58.355 55.000 0.33 0.00 0.00 2.74
3485 3561 7.881643 ATAAGAGCGCTTAGTGATCTAAATG 57.118 36.000 13.26 0.00 37.84 2.32
3500 3576 6.146347 CCCTCTGTAAAGAAATATAAGAGCGC 59.854 42.308 0.00 0.00 0.00 5.92
3501 3577 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
3502 3578 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
3505 3581 9.984190 GGTACTCCCTCTGTAAAGAAATATAAG 57.016 37.037 0.00 0.00 0.00 1.73
3506 3582 9.496710 TGGTACTCCCTCTGTAAAGAAATATAA 57.503 33.333 0.00 0.00 0.00 0.98
3573 3662 2.337583 TCTAGAAGCAATCGTGTGTGC 58.662 47.619 0.00 0.00 41.22 4.57
3576 3665 3.610242 GTGTCTCTAGAAGCAATCGTGTG 59.390 47.826 0.00 0.00 0.00 3.82
3598 3687 4.510167 ACTGAATTGGAATCCTACCCTG 57.490 45.455 0.00 0.00 0.00 4.45
3600 3689 6.890268 AGTTAAACTGAATTGGAATCCTACCC 59.110 38.462 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.