Multiple sequence alignment - TraesCS7A01G157300

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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 TraesCS7A01G157300 chr7A 100.000 4529 0 0 1 4529 110421727 110426255 0.000000e+00 8364
1 TraesCS7A01G157300 chr7B 91.208 3617 193 58 972 4529 64068574 64072124 0.000000e+00 4802
2 TraesCS7A01G157300 chr7D 93.499 3107 133 28 972 4040 105454698 105457773 0.000000e+00 4554
3 TraesCS7A01G157300 chr7D 90.919 914 70 10 1 905 94612153 94611244 0.000000e+00 1216
4 TraesCS7A01G157300 chr7D 85.489 317 24 14 4032 4348 105459370 105459664 1.220000e-80 311
5 TraesCS7A01G157300 chr7D 95.522 67 3 0 4463 4529 105460055 105460121 1.720000e-19 108
6 TraesCS7A01G157300 chr2D 91.372 904 69 5 1 902 76869743 76870639 0.000000e+00 1229
7 TraesCS7A01G157300 chr2D 90.808 903 74 5 1 902 598001788 598002682 0.000000e+00 1199
8 TraesCS7A01G157300 chr2D 89.834 905 85 4 1 902 627641483 627642383 0.000000e+00 1155
9 TraesCS7A01G157300 chr6D 90.969 908 71 6 1 902 31823108 31824010 0.000000e+00 1212
10 TraesCS7A01G157300 chr6D 89.364 912 87 5 1 905 156436011 156435103 0.000000e+00 1138
11 TraesCS7A01G157300 chr1D 89.868 908 84 4 1 905 39968562 39967660 0.000000e+00 1160
12 TraesCS7A01G157300 chr1D 89.613 905 88 2 1 905 483964934 483964036 0.000000e+00 1146
13 TraesCS7A01G157300 chr5D 89.613 905 79 8 1 902 397007229 397008121 0.000000e+00 1136


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 TraesCS7A01G157300 chr7A 110421727 110426255 4528 False 8364.000000 8364 100.000000 1 4529 1 chr7A.!!$F1 4528
1 TraesCS7A01G157300 chr7B 64068574 64072124 3550 False 4802.000000 4802 91.208000 972 4529 1 chr7B.!!$F1 3557
2 TraesCS7A01G157300 chr7D 105454698 105460121 5423 False 1657.666667 4554 91.503333 972 4529 3 chr7D.!!$F1 3557
3 TraesCS7A01G157300 chr7D 94611244 94612153 909 True 1216.000000 1216 90.919000 1 905 1 chr7D.!!$R1 904
4 TraesCS7A01G157300 chr2D 76869743 76870639 896 False 1229.000000 1229 91.372000 1 902 1 chr2D.!!$F1 901
5 TraesCS7A01G157300 chr2D 598001788 598002682 894 False 1199.000000 1199 90.808000 1 902 1 chr2D.!!$F2 901
6 TraesCS7A01G157300 chr2D 627641483 627642383 900 False 1155.000000 1155 89.834000 1 902 1 chr2D.!!$F3 901
7 TraesCS7A01G157300 chr6D 31823108 31824010 902 False 1212.000000 1212 90.969000 1 902 1 chr6D.!!$F1 901
8 TraesCS7A01G157300 chr6D 156435103 156436011 908 True 1138.000000 1138 89.364000 1 905 1 chr6D.!!$R1 904
9 TraesCS7A01G157300 chr1D 39967660 39968562 902 True 1160.000000 1160 89.868000 1 905 1 chr1D.!!$R1 904
10 TraesCS7A01G157300 chr1D 483964036 483964934 898 True 1146.000000 1146 89.613000 1 905 1 chr1D.!!$R2 904
11 TraesCS7A01G157300 chr5D 397007229 397008121 892 False 1136.000000 1136 89.613000 1 902 1 chr5D.!!$F1 901

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
933 964 0.038526 ACGTCTTCAGTCGGCGATTT 60.039 50.0 14.79 1.16 0.00 2.17 F
1202 1233 0.039035 AGACCGCCTTTTGCCCAATA 59.961 50.0 0.00 0.00 36.24 1.90 F
2346 2393 0.456482 CACTGACTCTGAGCAGCGAG 60.456 60.0 21.16 12.29 35.57 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2660 2707 0.026544 GATCGTCGGTCTCACTCGTC 59.973 60.0 0.0 0.0 0.00 4.20 R
2666 2713 0.109458 CCGTTTGATCGTCGGTCTCA 60.109 55.0 7.1 0.0 39.51 3.27 R
3818 3889 0.028505 GTGTGCATGTCGCCATCATC 59.971 55.0 0.0 0.0 41.33 2.92 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
71 73 4.471726 CGTACTTCCGTCGCCGCT 62.472 66.667 0.00 0.00 0.00 5.52
83 85 2.728817 GCCGCTATACCGAGCAGT 59.271 61.111 0.00 0.00 42.99 4.40
115 117 3.379445 GGCGTCGTCCCCTCTGAA 61.379 66.667 0.00 0.00 0.00 3.02
124 126 1.283321 GTCCCCTCTGAAAGGCTCAAT 59.717 52.381 0.00 0.00 44.71 2.57
220 222 2.442272 ACGCCGAGGCTGGAGTAT 60.442 61.111 12.70 0.00 40.50 2.12
335 338 2.710826 GGCTCTCCCTCCCTCCTCT 61.711 68.421 0.00 0.00 0.00 3.69
437 446 3.771160 CTGCCCGCCTCGTTAGGT 61.771 66.667 0.00 0.00 45.64 3.08
633 643 2.021068 ATGGTGATCCTCGACAGCGG 62.021 60.000 0.00 0.00 37.33 5.52
795 820 0.978146 ATGTAGAGCTTCAGGGCGGT 60.978 55.000 0.00 0.00 37.29 5.68
815 840 3.184003 GCGGTAAGGAACGGCGAC 61.184 66.667 16.62 7.14 43.45 5.19
894 925 5.239087 ACTCGCCGAAGTTTGGTTAAATTTA 59.761 36.000 10.98 0.00 0.00 1.40
902 933 4.986034 AGTTTGGTTAAATTTACGCCTTGC 59.014 37.500 15.18 7.98 0.00 4.01
905 936 5.961396 TGGTTAAATTTACGCCTTGCTTA 57.039 34.783 15.18 0.00 0.00 3.09
906 937 6.328641 TGGTTAAATTTACGCCTTGCTTAA 57.671 33.333 15.18 0.00 0.00 1.85
907 938 6.151004 TGGTTAAATTTACGCCTTGCTTAAC 58.849 36.000 15.18 0.00 0.00 2.01
908 939 5.284424 GGTTAAATTTACGCCTTGCTTAACG 59.716 40.000 0.00 0.00 31.58 3.18
909 940 4.492791 AAATTTACGCCTTGCTTAACGT 57.507 36.364 0.00 0.00 42.22 3.99
910 941 3.734776 ATTTACGCCTTGCTTAACGTC 57.265 42.857 0.00 0.00 39.78 4.34
911 942 1.062258 TTACGCCTTGCTTAACGTCG 58.938 50.000 0.00 0.00 39.78 5.12
912 943 0.733566 TACGCCTTGCTTAACGTCGG 60.734 55.000 0.00 0.00 39.78 4.79
913 944 2.025418 CGCCTTGCTTAACGTCGGT 61.025 57.895 0.00 0.00 0.00 4.69
914 945 0.733566 CGCCTTGCTTAACGTCGGTA 60.734 55.000 0.00 0.00 0.00 4.02
915 946 0.717784 GCCTTGCTTAACGTCGGTAC 59.282 55.000 0.00 0.00 0.00 3.34
928 959 4.472702 GGTACGTCTTCAGTCGGC 57.527 61.111 0.00 0.00 0.00 5.54
929 960 1.513586 GGTACGTCTTCAGTCGGCG 60.514 63.158 0.00 0.00 0.00 6.46
930 961 1.499056 GTACGTCTTCAGTCGGCGA 59.501 57.895 4.99 4.99 0.00 5.54
931 962 0.098376 GTACGTCTTCAGTCGGCGAT 59.902 55.000 14.79 0.00 0.00 4.58
932 963 0.806868 TACGTCTTCAGTCGGCGATT 59.193 50.000 14.79 5.78 0.00 3.34
933 964 0.038526 ACGTCTTCAGTCGGCGATTT 60.039 50.000 14.79 1.16 0.00 2.17
934 965 1.068474 CGTCTTCAGTCGGCGATTTT 58.932 50.000 14.79 0.00 0.00 1.82
935 966 1.459592 CGTCTTCAGTCGGCGATTTTT 59.540 47.619 14.79 0.00 0.00 1.94
936 967 2.664568 CGTCTTCAGTCGGCGATTTTTA 59.335 45.455 14.79 0.00 0.00 1.52
937 968 3.241678 CGTCTTCAGTCGGCGATTTTTAG 60.242 47.826 14.79 7.72 0.00 1.85
938 969 2.671396 TCTTCAGTCGGCGATTTTTAGC 59.329 45.455 14.79 0.00 0.00 3.09
939 970 0.996462 TCAGTCGGCGATTTTTAGCG 59.004 50.000 14.79 0.00 0.00 4.26
940 971 0.719465 CAGTCGGCGATTTTTAGCGT 59.281 50.000 14.79 0.00 0.00 5.07
941 972 0.997196 AGTCGGCGATTTTTAGCGTC 59.003 50.000 14.79 0.00 0.00 5.19
942 973 0.997196 GTCGGCGATTTTTAGCGTCT 59.003 50.000 14.79 0.00 0.00 4.18
943 974 1.392510 GTCGGCGATTTTTAGCGTCTT 59.607 47.619 14.79 0.00 0.00 3.01
944 975 2.070783 TCGGCGATTTTTAGCGTCTTT 58.929 42.857 4.99 0.00 0.00 2.52
945 976 2.481185 TCGGCGATTTTTAGCGTCTTTT 59.519 40.909 4.99 0.00 0.00 2.27
946 977 2.588106 CGGCGATTTTTAGCGTCTTTTG 59.412 45.455 0.00 0.00 0.00 2.44
947 978 2.914838 GGCGATTTTTAGCGTCTTTTGG 59.085 45.455 0.00 0.00 0.00 3.28
948 979 2.914838 GCGATTTTTAGCGTCTTTTGGG 59.085 45.455 0.00 0.00 0.00 4.12
949 980 3.498082 CGATTTTTAGCGTCTTTTGGGG 58.502 45.455 0.00 0.00 0.00 4.96
950 981 3.672241 CGATTTTTAGCGTCTTTTGGGGG 60.672 47.826 0.00 0.00 0.00 5.40
966 997 4.115199 GGGGCAACGGCTGGAGAT 62.115 66.667 0.00 0.00 40.87 2.75
967 998 2.825836 GGGCAACGGCTGGAGATG 60.826 66.667 0.00 0.00 40.87 2.90
968 999 3.512516 GGCAACGGCTGGAGATGC 61.513 66.667 0.00 1.80 40.87 3.91
969 1000 2.437359 GCAACGGCTGGAGATGCT 60.437 61.111 0.00 0.00 36.96 3.79
970 1001 2.467826 GCAACGGCTGGAGATGCTC 61.468 63.158 0.00 0.00 36.96 4.26
1050 1081 2.286872 CCATTTCTAGCTCACTGCCAG 58.713 52.381 0.00 0.00 44.23 4.85
1164 1195 1.660560 CCAATGCCGCCCTCAGAAAG 61.661 60.000 0.00 0.00 0.00 2.62
1175 1206 0.951040 CTCAGAAAGACCACGGCCAC 60.951 60.000 2.24 0.00 0.00 5.01
1194 1225 2.983592 CCGCCAAGACCGCCTTTT 60.984 61.111 0.00 0.00 31.42 2.27
1195 1226 2.255252 CGCCAAGACCGCCTTTTG 59.745 61.111 0.00 0.00 31.42 2.44
1199 1230 2.197324 AAGACCGCCTTTTGCCCA 59.803 55.556 0.00 0.00 36.24 5.36
1200 1231 1.456705 AAGACCGCCTTTTGCCCAA 60.457 52.632 0.00 0.00 36.24 4.12
1202 1233 0.039035 AGACCGCCTTTTGCCCAATA 59.961 50.000 0.00 0.00 36.24 1.90
1235 1266 3.259314 ATCTGCAGCACCACCCCA 61.259 61.111 9.47 0.00 0.00 4.96
1757 1788 1.097547 CGGTGGCCAAGATCATCCAC 61.098 60.000 7.24 13.79 46.10 4.02
1763 1794 2.381911 GCCAAGATCATCCACCACAAT 58.618 47.619 0.00 0.00 0.00 2.71
1796 1827 1.136984 GGACGACGAAGACAGCGAT 59.863 57.895 0.00 0.00 0.00 4.58
1837 1880 2.287965 GCAACGACAACGACGACGA 61.288 57.895 15.32 0.00 42.66 4.20
1838 1881 1.475810 CAACGACAACGACGACGAC 59.524 57.895 15.32 0.00 42.66 4.34
1839 1882 1.062365 AACGACAACGACGACGACA 59.938 52.632 15.32 0.00 42.66 4.35
1865 1908 1.853319 CAACGACAACGAGGACAGC 59.147 57.895 0.00 0.00 42.66 4.40
1877 1920 4.077188 GACAGCGGCAACAGCGAC 62.077 66.667 1.45 0.00 40.31 5.19
1916 1959 4.735132 ACGGTGATCACGGTGGCG 62.735 66.667 31.21 23.78 42.19 5.69
2159 2202 1.213094 CCACCGTCGGTAATCATCGC 61.213 60.000 18.38 0.00 32.11 4.58
2168 2211 4.327357 GTCGGTAATCATCGCCTATCATTG 59.673 45.833 0.00 0.00 0.00 2.82
2192 2235 5.431765 CATCTTAACCAACTCTACCTGCAT 58.568 41.667 0.00 0.00 0.00 3.96
2247 2290 2.259204 GTGTTGCCATGCACGCAT 59.741 55.556 10.85 0.00 38.71 4.73
2321 2368 1.501169 ACACGTAACGTAACCAAGGC 58.499 50.000 0.00 0.00 38.32 4.35
2322 2369 1.069049 ACACGTAACGTAACCAAGGCT 59.931 47.619 0.00 0.00 38.32 4.58
2323 2370 1.723003 CACGTAACGTAACCAAGGCTC 59.277 52.381 0.00 0.00 38.32 4.70
2324 2371 1.340889 ACGTAACGTAACCAAGGCTCA 59.659 47.619 0.00 0.00 38.73 4.26
2346 2393 0.456482 CACTGACTCTGAGCAGCGAG 60.456 60.000 21.16 12.29 35.57 5.03
2359 2406 1.857837 GCAGCGAGAGAATAGTCAAGC 59.142 52.381 0.00 0.00 0.00 4.01
2369 2416 4.938080 AGAATAGTCAAGCGTAGGACATG 58.062 43.478 0.00 0.00 36.50 3.21
2406 2453 1.141657 TGCATCACCTAGGAATCTGGC 59.858 52.381 17.98 11.41 0.00 4.85
2461 2508 1.889105 CATGCGGGTCCAGATTCCG 60.889 63.158 0.00 7.69 45.84 4.30
2489 2536 1.037579 TGAGTCGAGTCGGATGCCAT 61.038 55.000 13.54 0.00 0.00 4.40
2544 2591 3.062234 CCTCGAGCTAAAATCCGAAACAC 59.938 47.826 6.99 0.00 0.00 3.32
2596 2643 1.810151 GAATGTTGGCCGCTCTTAACA 59.190 47.619 6.54 6.54 37.43 2.41
2644 2691 5.890334 ACAACAACTCATCGACAAAAACAT 58.110 33.333 0.00 0.00 0.00 2.71
2659 2706 3.721087 AAACATCATTCTTCCGGTCCT 57.279 42.857 0.00 0.00 0.00 3.85
2660 2707 2.698855 ACATCATTCTTCCGGTCCTG 57.301 50.000 0.00 0.00 0.00 3.86
2666 2713 0.538977 TTCTTCCGGTCCTGACGAGT 60.539 55.000 0.00 0.00 0.00 4.18
2668 2715 1.228337 TTCCGGTCCTGACGAGTGA 60.228 57.895 0.00 0.00 0.00 3.41
2702 2749 1.832912 GGCCGGGATTGACTGATCT 59.167 57.895 2.18 0.00 0.00 2.75
2705 2752 1.071385 GCCGGGATTGACTGATCTGAT 59.929 52.381 2.18 0.00 0.00 2.90
2706 2753 2.869636 GCCGGGATTGACTGATCTGATC 60.870 54.545 10.72 10.72 0.00 2.92
2707 2754 2.366590 CCGGGATTGACTGATCTGATCA 59.633 50.000 18.61 18.61 37.76 2.92
2716 2763 2.284263 TGATCTGATCAGACGTGCAC 57.716 50.000 27.37 6.82 40.75 4.57
3178 3229 1.890894 CGGTGGTCATCGAGTCCTT 59.109 57.895 0.00 0.00 37.01 3.36
3424 3475 1.410004 CCCTACGACCAAGGCATCTA 58.590 55.000 0.00 0.00 32.34 1.98
3437 3492 4.708726 AGGCATCTAAACTACGTACGTT 57.291 40.909 27.92 11.11 0.00 3.99
3476 3532 7.159372 TCAGAGGTTAATCTTGAACTGTTACC 58.841 38.462 0.00 0.00 0.00 2.85
3515 3571 8.507249 GCAAGATGTTCAGTAAGTTCTGTTAAT 58.493 33.333 0.00 0.00 36.85 1.40
3518 3574 9.429359 AGATGTTCAGTAAGTTCTGTTAATCTG 57.571 33.333 0.00 0.00 36.85 2.90
3520 3576 8.958119 TGTTCAGTAAGTTCTGTTAATCTGTT 57.042 30.769 0.00 0.00 36.85 3.16
3588 3645 6.067263 GTGTACAACCAATCAGCAGTTTTA 57.933 37.500 0.00 0.00 0.00 1.52
3591 3648 5.852282 ACAACCAATCAGCAGTTTTAACT 57.148 34.783 0.00 0.00 40.60 2.24
3592 3649 6.952773 ACAACCAATCAGCAGTTTTAACTA 57.047 33.333 0.00 0.00 37.08 2.24
3593 3650 6.735130 ACAACCAATCAGCAGTTTTAACTAC 58.265 36.000 0.00 0.00 37.08 2.73
3594 3651 6.546034 ACAACCAATCAGCAGTTTTAACTACT 59.454 34.615 0.00 0.00 37.08 2.57
3595 3652 6.560253 ACCAATCAGCAGTTTTAACTACTG 57.440 37.500 14.11 14.11 46.87 2.74
3602 3659 8.896320 TCAGCAGTTTTAACTACTGTATTTGA 57.104 30.769 17.87 11.65 46.04 2.69
3616 3673 7.035840 ACTGTATTTGAAATGCAGATGATCC 57.964 36.000 32.62 0.00 35.69 3.36
3675 3740 2.173356 CTGATCTGTTGGGGCCAGATAA 59.827 50.000 4.39 0.00 46.84 1.75
3678 3743 2.204463 TCTGTTGGGGCCAGATAATGA 58.796 47.619 4.39 0.00 34.12 2.57
3682 3747 2.887152 GTTGGGGCCAGATAATGACATC 59.113 50.000 4.39 0.00 0.00 3.06
3747 3818 3.625764 TGAGTTTTGTAACGCTGAAGCTT 59.374 39.130 0.00 0.00 39.31 3.74
3818 3889 1.200252 CTACTGTCTGGACTGTCCACG 59.800 57.143 25.12 19.59 42.67 4.94
3849 3920 1.509644 ATGCACACAACGTCCAGCTG 61.510 55.000 6.78 6.78 0.00 4.24
3852 3923 1.451207 ACACAACGTCCAGCTGCAA 60.451 52.632 8.66 0.00 0.00 4.08
4005 4127 5.935206 TGGTCGACATAATTTTGCTAACTGA 59.065 36.000 18.91 0.00 0.00 3.41
4008 4130 7.968405 GGTCGACATAATTTTGCTAACTGAAAT 59.032 33.333 18.91 0.00 0.00 2.17
4018 4140 4.930963 TGCTAACTGAAATGTTGTTGTGG 58.069 39.130 0.00 0.00 0.00 4.17
4019 4141 4.400884 TGCTAACTGAAATGTTGTTGTGGT 59.599 37.500 0.00 0.00 0.00 4.16
4020 4142 5.105554 TGCTAACTGAAATGTTGTTGTGGTT 60.106 36.000 0.00 0.00 0.00 3.67
4079 5806 2.625790 ACTCTCTGTCCAGTGAGAACAC 59.374 50.000 25.16 0.00 46.44 3.32
4093 5820 4.160439 GTGAGAACACAGGATGATACCTCA 59.840 45.833 0.00 0.00 45.32 3.86
4095 5826 3.452627 AGAACACAGGATGATACCTCACC 59.547 47.826 0.00 0.00 39.69 4.02
4125 5856 3.565307 CCACATATTGCAATGGGGTAGT 58.435 45.455 22.27 8.06 44.20 2.73
4170 5903 3.112263 TCCCCACCTATCTTTTCATCGT 58.888 45.455 0.00 0.00 0.00 3.73
4172 5905 3.123804 CCCACCTATCTTTTCATCGTCG 58.876 50.000 0.00 0.00 0.00 5.12
4173 5906 3.181479 CCCACCTATCTTTTCATCGTCGA 60.181 47.826 0.00 0.00 0.00 4.20
4174 5907 3.797256 CCACCTATCTTTTCATCGTCGAC 59.203 47.826 5.18 5.18 0.00 4.20
4175 5908 3.482472 CACCTATCTTTTCATCGTCGACG 59.518 47.826 31.30 31.30 41.45 5.12
4224 5957 6.937436 TCAGAAACCTTTCTAACTGTTTCC 57.063 37.500 0.00 0.00 45.23 3.13
4225 5958 6.419791 TCAGAAACCTTTCTAACTGTTTCCA 58.580 36.000 0.00 0.00 45.23 3.53
4247 5980 9.904198 TTCCATATAAAAAGATCATCACTGTCA 57.096 29.630 0.00 0.00 0.00 3.58
4269 6002 7.755373 TGTCATATAACTGATTCGTATGCTAGC 59.245 37.037 8.10 8.10 0.00 3.42
4279 6014 2.734606 TCGTATGCTAGCACACAACAAC 59.265 45.455 24.85 11.32 0.00 3.32
4294 6029 2.855963 CAACAACAGCAAAGCAGAAGTG 59.144 45.455 0.00 0.00 0.00 3.16
4298 6033 3.637998 ACAGCAAAGCAGAAGTGATTG 57.362 42.857 0.00 0.00 30.96 2.67
4299 6034 2.954318 ACAGCAAAGCAGAAGTGATTGT 59.046 40.909 0.00 0.00 30.96 2.71
4361 6096 3.427161 CTAGTTAAGCAGGGCATTTGC 57.573 47.619 0.00 0.00 41.83 3.68
4391 6126 0.830648 TGCTCCTCCGGTTATTCCAG 59.169 55.000 0.00 0.00 35.57 3.86
4476 6487 0.033504 TCTTGTGCAGAAGACCGTCC 59.966 55.000 21.46 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 187 3.499737 GTTGCCGCCCTCGATGTG 61.500 66.667 0.00 0.00 38.10 3.21
220 222 4.332543 AAGGTGGAGGGAGCGGGA 62.333 66.667 0.00 0.00 0.00 5.14
230 233 2.606519 CCGGTGGGAGAAGGTGGA 60.607 66.667 0.00 0.00 34.06 4.02
286 289 2.196229 CCGGACGAGGAGGAGGAT 59.804 66.667 0.00 0.00 0.00 3.24
314 317 2.835895 GAGGGAGGGAGAGCCGTC 60.836 72.222 0.00 0.00 46.03 4.79
315 318 4.467107 GGAGGGAGGGAGAGCCGT 62.467 72.222 0.00 0.00 33.83 5.68
433 442 0.406750 TGGACTCCACCTTCGACCTA 59.593 55.000 0.00 0.00 0.00 3.08
437 446 2.283529 GGCTGGACTCCACCTTCGA 61.284 63.158 0.00 0.00 0.00 3.71
459 468 2.946172 TATGGCCTCGTACTCCGCGA 62.946 60.000 8.23 0.00 36.19 5.87
511 521 4.308458 TCGTCCCACGCCCACTTG 62.308 66.667 0.00 0.00 42.21 3.16
612 622 0.461548 GCTGTCGAGGATCACCATGA 59.538 55.000 0.00 0.00 38.94 3.07
714 724 2.044555 TCGTCGTCGCCTCCTTCAT 61.045 57.895 0.00 0.00 36.96 2.57
715 725 2.670592 TCGTCGTCGCCTCCTTCA 60.671 61.111 0.00 0.00 36.96 3.02
717 727 4.099170 CGTCGTCGTCGCCTCCTT 62.099 66.667 0.00 0.00 36.96 3.36
749 774 0.319900 AGCCTGTAGAACTGCGTGTG 60.320 55.000 0.00 0.00 0.00 3.82
795 820 4.397832 GCCGTTCCTTACCGCCCA 62.398 66.667 0.00 0.00 0.00 5.36
894 925 2.025418 CCGACGTTAAGCAAGGCGT 61.025 57.895 0.00 0.00 40.44 5.68
908 939 0.179205 CCGACTGAAGACGTACCGAC 60.179 60.000 0.00 0.00 0.00 4.79
909 940 1.915614 GCCGACTGAAGACGTACCGA 61.916 60.000 0.00 0.00 0.00 4.69
910 941 1.513586 GCCGACTGAAGACGTACCG 60.514 63.158 0.00 0.00 0.00 4.02
911 942 1.513586 CGCCGACTGAAGACGTACC 60.514 63.158 0.00 0.00 0.00 3.34
912 943 0.098376 ATCGCCGACTGAAGACGTAC 59.902 55.000 0.00 0.00 0.00 3.67
913 944 0.806868 AATCGCCGACTGAAGACGTA 59.193 50.000 0.00 0.00 0.00 3.57
914 945 0.038526 AAATCGCCGACTGAAGACGT 60.039 50.000 0.00 0.00 0.00 4.34
915 946 1.068474 AAAATCGCCGACTGAAGACG 58.932 50.000 0.00 0.00 0.00 4.18
916 947 3.483738 GCTAAAAATCGCCGACTGAAGAC 60.484 47.826 0.00 0.00 0.00 3.01
917 948 2.671396 GCTAAAAATCGCCGACTGAAGA 59.329 45.455 0.00 0.00 0.00 2.87
918 949 2.534939 CGCTAAAAATCGCCGACTGAAG 60.535 50.000 0.00 0.00 0.00 3.02
919 950 1.392168 CGCTAAAAATCGCCGACTGAA 59.608 47.619 0.00 0.00 0.00 3.02
920 951 0.996462 CGCTAAAAATCGCCGACTGA 59.004 50.000 0.00 0.00 0.00 3.41
921 952 0.719465 ACGCTAAAAATCGCCGACTG 59.281 50.000 0.00 0.00 0.00 3.51
922 953 0.997196 GACGCTAAAAATCGCCGACT 59.003 50.000 0.00 0.00 0.00 4.18
923 954 0.997196 AGACGCTAAAAATCGCCGAC 59.003 50.000 0.00 0.00 0.00 4.79
924 955 1.717194 AAGACGCTAAAAATCGCCGA 58.283 45.000 0.00 0.00 0.00 5.54
925 956 2.520686 AAAGACGCTAAAAATCGCCG 57.479 45.000 0.00 0.00 0.00 6.46
926 957 2.914838 CCAAAAGACGCTAAAAATCGCC 59.085 45.455 0.00 0.00 0.00 5.54
927 958 2.914838 CCCAAAAGACGCTAAAAATCGC 59.085 45.455 0.00 0.00 0.00 4.58
928 959 3.498082 CCCCAAAAGACGCTAAAAATCG 58.502 45.455 0.00 0.00 0.00 3.34
929 960 3.845178 CCCCCAAAAGACGCTAAAAATC 58.155 45.455 0.00 0.00 0.00 2.17
930 961 3.953712 CCCCCAAAAGACGCTAAAAAT 57.046 42.857 0.00 0.00 0.00 1.82
949 980 4.115199 ATCTCCAGCCGTTGCCCC 62.115 66.667 0.00 0.00 38.69 5.80
950 981 2.825836 CATCTCCAGCCGTTGCCC 60.826 66.667 0.00 0.00 38.69 5.36
951 982 3.512516 GCATCTCCAGCCGTTGCC 61.513 66.667 0.00 0.00 38.69 4.52
952 983 2.437359 AGCATCTCCAGCCGTTGC 60.437 61.111 0.00 0.00 37.95 4.17
953 984 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
967 998 0.315706 CTTGCGCGAATGCTAAGAGC 60.316 55.000 12.10 0.00 42.82 4.09
968 999 0.315706 GCTTGCGCGAATGCTAAGAG 60.316 55.000 17.27 0.00 39.65 2.85
969 1000 1.018752 TGCTTGCGCGAATGCTAAGA 61.019 50.000 23.79 2.67 39.65 2.10
970 1001 0.858961 GTGCTTGCGCGAATGCTAAG 60.859 55.000 23.79 11.59 39.65 2.18
987 1018 4.336433 AGTTCTCATGGTTTGTGAGTTGTG 59.664 41.667 0.00 0.00 42.82 3.33
1050 1081 1.534175 CGGGAAGAGTGTGCGAGTATC 60.534 57.143 0.00 0.00 0.00 2.24
1179 1210 2.049156 GCAAAAGGCGGTCTTGGC 60.049 61.111 0.00 0.00 35.55 4.52
1195 1226 2.516225 GGACGGTGGCTATTGGGC 60.516 66.667 0.00 0.00 41.27 5.36
1199 1230 2.125269 GCGTGGACGGTGGCTATT 60.125 61.111 0.71 0.00 40.23 1.73
1200 1231 4.157120 GGCGTGGACGGTGGCTAT 62.157 66.667 0.71 0.00 40.23 2.97
1296 1327 2.509336 GGTGATGGACGACGCCAG 60.509 66.667 14.66 0.00 42.15 4.85
1796 1827 3.359523 CTGTCGTCGTCGTCCCCA 61.360 66.667 1.33 0.00 38.33 4.96
1837 1880 2.109739 TTGTCGTTGCGGCTGTTGT 61.110 52.632 0.00 0.00 30.55 3.32
1838 1881 1.654137 GTTGTCGTTGCGGCTGTTG 60.654 57.895 0.00 0.00 30.55 3.33
1839 1882 2.713154 GTTGTCGTTGCGGCTGTT 59.287 55.556 0.00 0.00 30.55 3.16
1898 1941 3.118454 GCCACCGTGATCACCGTG 61.118 66.667 29.38 29.38 39.26 4.94
1916 1959 2.999063 TTCCCCGACCCGTCCTTC 60.999 66.667 0.00 0.00 0.00 3.46
2159 2202 6.769822 AGAGTTGGTTAAGATGCAATGATAGG 59.230 38.462 0.00 0.00 0.00 2.57
2168 2211 3.623510 GCAGGTAGAGTTGGTTAAGATGC 59.376 47.826 0.00 0.00 0.00 3.91
2317 2364 1.617850 CAGAGTCAGTGAGTGAGCCTT 59.382 52.381 4.86 0.00 35.13 4.35
2321 2368 1.885233 TGCTCAGAGTCAGTGAGTGAG 59.115 52.381 17.33 17.33 43.00 3.51
2322 2369 1.885233 CTGCTCAGAGTCAGTGAGTGA 59.115 52.381 4.86 2.51 43.00 3.41
2323 2370 1.669502 GCTGCTCAGAGTCAGTGAGTG 60.670 57.143 17.83 0.00 43.00 3.51
2324 2371 0.602562 GCTGCTCAGAGTCAGTGAGT 59.397 55.000 17.83 0.00 43.00 3.41
2346 2393 4.634184 TGTCCTACGCTTGACTATTCTC 57.366 45.455 0.00 0.00 32.67 2.87
2359 2406 1.262417 GTGCATGCATCATGTCCTACG 59.738 52.381 25.64 0.00 43.10 3.51
2369 2416 1.267533 TGCATTATCCGTGCATGCATC 59.732 47.619 25.64 16.09 46.53 3.91
2406 2453 7.061210 CGTAAATTTAGATAGATCTGCGTCAGG 59.939 40.741 5.18 0.00 37.76 3.86
2461 2508 0.179124 GACTCGACTCATGCACCTCC 60.179 60.000 0.00 0.00 0.00 4.30
2544 2591 2.420568 GCATGCAGGTCCATGGTGG 61.421 63.158 14.21 1.00 42.18 4.61
2644 2691 0.530744 CGTCAGGACCGGAAGAATGA 59.469 55.000 9.46 1.59 0.00 2.57
2659 2706 0.672711 ATCGTCGGTCTCACTCGTCA 60.673 55.000 0.00 0.00 0.00 4.35
2660 2707 0.026544 GATCGTCGGTCTCACTCGTC 59.973 60.000 0.00 0.00 0.00 4.20
2666 2713 0.109458 CCGTTTGATCGTCGGTCTCA 60.109 55.000 7.10 0.00 39.51 3.27
2668 2715 1.445582 GCCGTTTGATCGTCGGTCT 60.446 57.895 18.97 0.00 45.11 3.85
2687 2734 3.740631 TGATCAGATCAGTCAATCCCG 57.259 47.619 9.21 0.00 33.59 5.14
2702 2749 1.079888 ATGCGTGCACGTCTGATCA 60.080 52.632 36.80 25.81 42.22 2.92
2705 2752 1.300542 TTCATGCGTGCACGTCTGA 60.301 52.632 36.80 32.58 42.22 3.27
2706 2753 1.154599 GTTCATGCGTGCACGTCTG 60.155 57.895 36.80 31.13 42.22 3.51
2707 2754 0.950555 ATGTTCATGCGTGCACGTCT 60.951 50.000 36.80 23.09 42.22 4.18
2708 2755 0.790495 CATGTTCATGCGTGCACGTC 60.790 55.000 36.80 28.50 42.22 4.34
2709 2756 1.207339 CATGTTCATGCGTGCACGT 59.793 52.632 36.80 18.68 42.22 4.49
2710 2757 4.045526 CATGTTCATGCGTGCACG 57.954 55.556 34.01 34.01 43.27 5.34
3161 3212 0.175989 GGAAGGACTCGATGACCACC 59.824 60.000 0.00 0.00 32.90 4.61
3424 3475 4.771590 TGAGATCCAACGTACGTAGTTT 57.228 40.909 23.12 7.45 37.78 2.66
3437 3492 5.768980 AACCTCTGAATTCTTGAGATCCA 57.231 39.130 22.01 0.00 0.00 3.41
3476 3532 2.101125 CATCTTGCCGAAATTAACGCG 58.899 47.619 3.53 3.53 0.00 6.01
3515 3571 3.006859 AGTTGGATCATGACACGAACAGA 59.993 43.478 21.77 0.00 0.00 3.41
3516 3572 3.124128 CAGTTGGATCATGACACGAACAG 59.876 47.826 21.77 14.84 0.00 3.16
3517 3573 3.066380 CAGTTGGATCATGACACGAACA 58.934 45.455 21.77 5.86 0.00 3.18
3518 3574 3.325870 TCAGTTGGATCATGACACGAAC 58.674 45.455 16.15 16.15 0.00 3.95
3520 3576 3.676291 TTCAGTTGGATCATGACACGA 57.324 42.857 0.00 0.00 0.00 4.35
3588 3645 8.565896 TCATCTGCATTTCAAATACAGTAGTT 57.434 30.769 9.74 0.00 0.00 2.24
3591 3648 7.994911 AGGATCATCTGCATTTCAAATACAGTA 59.005 33.333 9.74 0.00 0.00 2.74
3592 3649 6.832384 AGGATCATCTGCATTTCAAATACAGT 59.168 34.615 9.74 0.00 0.00 3.55
3593 3650 7.273320 AGGATCATCTGCATTTCAAATACAG 57.727 36.000 4.14 4.14 0.00 2.74
3594 3651 7.649533 AAGGATCATCTGCATTTCAAATACA 57.350 32.000 0.00 0.00 0.00 2.29
3595 3652 8.937634 AAAAGGATCATCTGCATTTCAAATAC 57.062 30.769 0.00 0.00 0.00 1.89
3602 3659 9.193806 ACATTACTAAAAGGATCATCTGCATTT 57.806 29.630 0.00 0.00 0.00 2.32
3662 3724 2.785269 AGATGTCATTATCTGGCCCCAA 59.215 45.455 0.00 0.00 36.12 4.12
3675 3740 5.171476 CACGAACCACTTAGAAGATGTCAT 58.829 41.667 0.00 0.00 0.00 3.06
3678 3743 3.326747 GCACGAACCACTTAGAAGATGT 58.673 45.455 0.00 0.00 0.00 3.06
3682 3747 1.779569 ACGCACGAACCACTTAGAAG 58.220 50.000 0.00 0.00 0.00 2.85
3747 3818 3.127589 CGCCGTGTCATCACCAATTATA 58.872 45.455 0.00 0.00 41.09 0.98
3818 3889 0.028505 GTGTGCATGTCGCCATCATC 59.971 55.000 0.00 0.00 41.33 2.92
3841 3912 2.908073 CGTGGGTTTGCAGCTGGAC 61.908 63.158 17.12 0.92 0.00 4.02
3849 3920 1.149148 GAACTCTCTCGTGGGTTTGC 58.851 55.000 0.00 0.00 0.00 3.68
3852 3923 2.169330 GGTAGAACTCTCTCGTGGGTT 58.831 52.381 0.00 0.00 32.70 4.11
4020 4142 7.569677 AAAGTGATTTTCGTCGAAACAAAAA 57.430 28.000 19.59 5.74 30.83 1.94
4079 5806 2.031870 TGACGGTGAGGTATCATCCTG 58.968 52.381 0.00 0.00 37.87 3.86
4093 5820 0.618458 AATATGTGGCCTGTGACGGT 59.382 50.000 3.32 0.00 0.00 4.83
4095 5826 0.378257 GCAATATGTGGCCTGTGACG 59.622 55.000 3.32 0.00 0.00 4.35
4121 5852 7.205992 TCTGAATATCTGATCACTGCAACTAC 58.794 38.462 0.00 0.00 0.00 2.73
4123 5854 6.231258 TCTGAATATCTGATCACTGCAACT 57.769 37.500 0.00 0.00 0.00 3.16
4170 5903 4.575236 AGATCTTGATACTACTTGCGTCGA 59.425 41.667 0.00 0.00 0.00 4.20
4172 5905 4.907010 CGAGATCTTGATACTACTTGCGTC 59.093 45.833 3.60 0.00 0.00 5.19
4173 5906 4.790123 GCGAGATCTTGATACTACTTGCGT 60.790 45.833 14.59 0.00 0.00 5.24
4174 5907 3.666334 GCGAGATCTTGATACTACTTGCG 59.334 47.826 14.59 0.74 0.00 4.85
4175 5908 3.984633 GGCGAGATCTTGATACTACTTGC 59.015 47.826 14.59 0.00 35.01 4.01
4237 5970 7.936950 ACGAATCAGTTATATGACAGTGATG 57.063 36.000 0.00 0.00 30.46 3.07
4240 5973 7.596621 AGCATACGAATCAGTTATATGACAGTG 59.403 37.037 0.00 0.00 30.46 3.66
4241 5974 7.661968 AGCATACGAATCAGTTATATGACAGT 58.338 34.615 0.00 0.00 30.46 3.55
4242 5975 9.283420 CTAGCATACGAATCAGTTATATGACAG 57.717 37.037 0.00 0.00 30.46 3.51
4243 5976 7.755373 GCTAGCATACGAATCAGTTATATGACA 59.245 37.037 10.63 0.00 30.46 3.58
4247 5980 7.542477 GTGTGCTAGCATACGAATCAGTTATAT 59.458 37.037 25.95 0.00 0.00 0.86
4269 6002 1.921887 CTGCTTTGCTGTTGTTGTGTG 59.078 47.619 0.00 0.00 0.00 3.82
4279 6014 3.305964 CACAATCACTTCTGCTTTGCTG 58.694 45.455 0.00 0.00 0.00 4.41
4294 6029 6.095440 ACAGCTTGGTTAATATCACCACAATC 59.905 38.462 6.28 0.00 44.34 2.67
4298 6033 5.897377 AACAGCTTGGTTAATATCACCAC 57.103 39.130 6.28 0.00 44.34 4.16
4299 6034 5.336372 GCAAACAGCTTGGTTAATATCACCA 60.336 40.000 3.09 3.09 42.90 4.17
4314 6049 7.972277 CAGTGATATTTTATTCTGCAAACAGCT 59.028 33.333 0.00 0.00 44.10 4.24
4391 6126 5.234543 GGACCGATCAAGTAAGAGCAATAAC 59.765 44.000 0.00 0.00 0.00 1.89
4428 6164 0.034616 AGTGGCAGCTCTGAAGTGAC 59.965 55.000 0.29 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.