Multiple sequence alignment - TraesCS1B01G149000

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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 TraesCS1B01G149000 chr1B 100.000 3903 0 0 1 3903 220750343 220754245 0.000000e+00 7208
1 TraesCS1B01G149000 chr1B 97.241 906 22 3 1 904 92337696 92336792 0.000000e+00 1531
2 TraesCS1B01G149000 chr1B 92.857 70 2 2 3214 3280 220753481 220753550 8.920000e-17 99
3 TraesCS1B01G149000 chr1B 92.857 70 2 2 3139 3208 220753556 220753622 8.920000e-17 99
4 TraesCS1B01G149000 chr1D 96.764 2287 41 10 946 3208 155346179 155343902 0.000000e+00 3783
5 TraesCS1B01G149000 chr1D 98.094 682 11 1 3224 3903 155343958 155343277 0.000000e+00 1186
6 TraesCS1B01G149000 chr1A 95.780 1256 25 7 946 2191 204826213 204827450 0.000000e+00 2001
7 TraesCS1B01G149000 chr1A 93.925 1070 21 14 2156 3206 204827555 204828599 0.000000e+00 1576
8 TraesCS1B01G149000 chr1A 96.909 906 26 2 1 904 213936973 213936068 0.000000e+00 1517
9 TraesCS1B01G149000 chr1A 96.462 424 12 2 3480 3903 204829062 204829482 0.000000e+00 697
10 TraesCS1B01G149000 chr1A 97.674 258 6 0 3224 3481 204828545 204828802 9.950000e-121 444
11 TraesCS1B01G149000 chr5B 97.792 906 18 2 1 904 59779659 59780564 0.000000e+00 1561
12 TraesCS1B01G149000 chr5B 97.241 906 23 2 1 904 677678709 677677804 0.000000e+00 1533
13 TraesCS1B01G149000 chr2B 97.461 906 21 2 1 904 793364265 793363360 0.000000e+00 1544
14 TraesCS1B01G149000 chr2B 97.461 906 19 4 1 904 390802229 390803132 0.000000e+00 1543
15 TraesCS1B01G149000 chr3B 97.020 906 25 2 1 904 772413531 772414436 0.000000e+00 1522
16 TraesCS1B01G149000 chr3B 96.909 906 26 2 1 904 161677545 161678450 0.000000e+00 1517
17 TraesCS1B01G149000 chr6B 96.909 906 26 2 1 904 257595672 257594767 0.000000e+00 1517
18 TraesCS1B01G149000 chrUn 87.174 499 48 12 1098 1593 76000718 76000233 1.580000e-153 553
19 TraesCS1B01G149000 chrUn 82.934 334 53 3 2635 2964 76000221 75999888 8.200000e-77 298
20 TraesCS1B01G149000 chr6A 86.974 499 55 5 1098 1593 5206556 5207047 1.580000e-153 553
21 TraesCS1B01G149000 chr6A 86.228 334 43 2 2634 2964 5207055 5207388 3.710000e-95 359
22 TraesCS1B01G149000 chr6D 85.932 526 54 10 1075 1593 5838544 5839056 9.540000e-151 544
23 TraesCS1B01G149000 chr6D 85.629 334 45 2 2634 2964 5839064 5839397 8.030000e-92 348
24 TraesCS1B01G149000 chr6D 78.645 487 61 20 2669 3152 4928244 4928690 2.300000e-72 283
25 TraesCS1B01G149000 chr3D 81.395 215 28 7 1851 2065 576775170 576774968 8.680000e-37 165


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 TraesCS1B01G149000 chr1B 220750343 220754245 3902 False 2468.666667 7208 95.23800 1 3903 3 chr1B.!!$F1 3902
1 TraesCS1B01G149000 chr1B 92336792 92337696 904 True 1531.000000 1531 97.24100 1 904 1 chr1B.!!$R1 903
2 TraesCS1B01G149000 chr1D 155343277 155346179 2902 True 2484.500000 3783 97.42900 946 3903 2 chr1D.!!$R1 2957
3 TraesCS1B01G149000 chr1A 213936068 213936973 905 True 1517.000000 1517 96.90900 1 904 1 chr1A.!!$R1 903
4 TraesCS1B01G149000 chr1A 204826213 204829482 3269 False 1179.500000 2001 95.96025 946 3903 4 chr1A.!!$F1 2957
5 TraesCS1B01G149000 chr5B 59779659 59780564 905 False 1561.000000 1561 97.79200 1 904 1 chr5B.!!$F1 903
6 TraesCS1B01G149000 chr5B 677677804 677678709 905 True 1533.000000 1533 97.24100 1 904 1 chr5B.!!$R1 903
7 TraesCS1B01G149000 chr2B 793363360 793364265 905 True 1544.000000 1544 97.46100 1 904 1 chr2B.!!$R1 903
8 TraesCS1B01G149000 chr2B 390802229 390803132 903 False 1543.000000 1543 97.46100 1 904 1 chr2B.!!$F1 903
9 TraesCS1B01G149000 chr3B 772413531 772414436 905 False 1522.000000 1522 97.02000 1 904 1 chr3B.!!$F2 903
10 TraesCS1B01G149000 chr3B 161677545 161678450 905 False 1517.000000 1517 96.90900 1 904 1 chr3B.!!$F1 903
11 TraesCS1B01G149000 chr6B 257594767 257595672 905 True 1517.000000 1517 96.90900 1 904 1 chr6B.!!$R1 903
12 TraesCS1B01G149000 chrUn 75999888 76000718 830 True 425.500000 553 85.05400 1098 2964 2 chrUn.!!$R1 1866
13 TraesCS1B01G149000 chr6A 5206556 5207388 832 False 456.000000 553 86.60100 1098 2964 2 chr6A.!!$F1 1866
14 TraesCS1B01G149000 chr6D 5838544 5839397 853 False 446.000000 544 85.78050 1075 2964 2 chr6D.!!$F2 1889

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
923 926 0.183971 ACCGTCCACACCAAAATCCA 59.816 50.0 0.0 0.0 0.0 3.41 F
1548 1562 0.252696 ACTGCCACTCCCACATCCTA 60.253 55.0 0.0 0.0 0.0 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 2402 0.523966 TGCGGCAAAACCCTAATTCG 59.476 50.0 0.0 0.0 33.26 3.34 R
3508 3933 0.603707 AACAGGACAGCCATCACACG 60.604 55.0 0.0 0.0 36.29 4.49 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
205 206 1.550524 CCTCCTTCGTTCATGGTCTCA 59.449 52.381 0.00 0.00 0.00 3.27
387 390 2.043248 ACAGCCCGATCGTACCCT 60.043 61.111 15.09 1.39 0.00 4.34
474 477 6.011628 AGACCATCCTCCTCTTTTAATGGAAA 60.012 38.462 6.21 0.00 37.64 3.13
598 601 0.400815 TCCCACCACAAGTACCAGGT 60.401 55.000 0.00 0.00 33.91 4.00
880 883 0.638746 CGACACGAAATAGTGCCGTC 59.361 55.000 0.00 0.00 45.45 4.79
904 907 9.991388 GTCAAGTGTACGCCAAATAAATATTTA 57.009 29.630 10.27 10.27 34.36 1.40
905 908 9.991388 TCAAGTGTACGCCAAATAAATATTTAC 57.009 29.630 10.07 0.00 34.36 2.01
906 909 9.228636 CAAGTGTACGCCAAATAAATATTTACC 57.771 33.333 10.07 0.00 34.36 2.85
907 910 7.632721 AGTGTACGCCAAATAAATATTTACCG 58.367 34.615 10.07 10.10 34.36 4.02
908 911 7.280652 AGTGTACGCCAAATAAATATTTACCGT 59.719 33.333 10.07 18.41 40.83 4.83
909 912 7.583762 GTGTACGCCAAATAAATATTTACCGTC 59.416 37.037 10.07 13.38 39.70 4.79
910 913 6.063640 ACGCCAAATAAATATTTACCGTCC 57.936 37.500 10.07 0.00 37.16 4.79
911 914 5.589452 ACGCCAAATAAATATTTACCGTCCA 59.411 36.000 10.07 0.00 37.16 4.02
912 915 5.910723 CGCCAAATAAATATTTACCGTCCAC 59.089 40.000 10.07 0.00 34.36 4.02
913 916 6.458478 CGCCAAATAAATATTTACCGTCCACA 60.458 38.462 10.07 0.00 34.36 4.17
914 917 6.693978 GCCAAATAAATATTTACCGTCCACAC 59.306 38.462 10.07 0.00 34.36 3.82
915 918 7.197703 CCAAATAAATATTTACCGTCCACACC 58.802 38.462 10.07 0.00 34.36 4.16
916 919 7.148052 CCAAATAAATATTTACCGTCCACACCA 60.148 37.037 10.07 0.00 34.36 4.17
917 920 7.941431 AATAAATATTTACCGTCCACACCAA 57.059 32.000 10.07 0.00 0.00 3.67
918 921 7.941431 ATAAATATTTACCGTCCACACCAAA 57.059 32.000 10.07 0.00 0.00 3.28
919 922 6.651975 AAATATTTACCGTCCACACCAAAA 57.348 33.333 0.00 0.00 0.00 2.44
920 923 6.844097 AATATTTACCGTCCACACCAAAAT 57.156 33.333 0.00 0.00 0.00 1.82
921 924 4.776795 ATTTACCGTCCACACCAAAATC 57.223 40.909 0.00 0.00 0.00 2.17
922 925 2.188062 TACCGTCCACACCAAAATCC 57.812 50.000 0.00 0.00 0.00 3.01
923 926 0.183971 ACCGTCCACACCAAAATCCA 59.816 50.000 0.00 0.00 0.00 3.41
924 927 1.203001 ACCGTCCACACCAAAATCCAT 60.203 47.619 0.00 0.00 0.00 3.41
925 928 1.202114 CCGTCCACACCAAAATCCATG 59.798 52.381 0.00 0.00 0.00 3.66
926 929 1.402720 CGTCCACACCAAAATCCATGC 60.403 52.381 0.00 0.00 0.00 4.06
927 930 1.617850 GTCCACACCAAAATCCATGCA 59.382 47.619 0.00 0.00 0.00 3.96
928 931 1.617850 TCCACACCAAAATCCATGCAC 59.382 47.619 0.00 0.00 0.00 4.57
929 932 1.619827 CCACACCAAAATCCATGCACT 59.380 47.619 0.00 0.00 0.00 4.40
930 933 2.037511 CCACACCAAAATCCATGCACTT 59.962 45.455 0.00 0.00 0.00 3.16
931 934 3.257873 CCACACCAAAATCCATGCACTTA 59.742 43.478 0.00 0.00 0.00 2.24
932 935 4.262377 CCACACCAAAATCCATGCACTTAA 60.262 41.667 0.00 0.00 0.00 1.85
933 936 4.685628 CACACCAAAATCCATGCACTTAAC 59.314 41.667 0.00 0.00 0.00 2.01
934 937 4.244862 CACCAAAATCCATGCACTTAACC 58.755 43.478 0.00 0.00 0.00 2.85
935 938 3.900601 ACCAAAATCCATGCACTTAACCA 59.099 39.130 0.00 0.00 0.00 3.67
936 939 4.346418 ACCAAAATCCATGCACTTAACCAA 59.654 37.500 0.00 0.00 0.00 3.67
937 940 5.163258 ACCAAAATCCATGCACTTAACCAAA 60.163 36.000 0.00 0.00 0.00 3.28
938 941 5.762218 CCAAAATCCATGCACTTAACCAAAA 59.238 36.000 0.00 0.00 0.00 2.44
939 942 6.261826 CCAAAATCCATGCACTTAACCAAAAA 59.738 34.615 0.00 0.00 0.00 1.94
940 943 6.859420 AAATCCATGCACTTAACCAAAAAC 57.141 33.333 0.00 0.00 0.00 2.43
941 944 3.971150 TCCATGCACTTAACCAAAAACG 58.029 40.909 0.00 0.00 0.00 3.60
942 945 2.474735 CCATGCACTTAACCAAAAACGC 59.525 45.455 0.00 0.00 0.00 4.84
943 946 2.211353 TGCACTTAACCAAAAACGCC 57.789 45.000 0.00 0.00 0.00 5.68
944 947 1.202428 TGCACTTAACCAAAAACGCCC 60.202 47.619 0.00 0.00 0.00 6.13
1288 1302 3.075005 GGGAGGAGGTGCTACGCA 61.075 66.667 0.00 0.00 35.60 5.24
1329 1343 2.256158 CTCGTTGGCGTGTACCGA 59.744 61.111 7.77 0.00 39.56 4.69
1548 1562 0.252696 ACTGCCACTCCCACATCCTA 60.253 55.000 0.00 0.00 0.00 2.94
1640 1654 8.674607 CCCATAATACAGAGTAAAACTTGGAAC 58.325 37.037 0.00 0.00 0.00 3.62
1645 1659 5.751586 ACAGAGTAAAACTTGGAACCTTGA 58.248 37.500 0.00 0.00 0.00 3.02
1680 1694 1.004292 CTGTTTCGGTCGTGGTGTTTC 60.004 52.381 0.00 0.00 0.00 2.78
1681 1695 1.292992 GTTTCGGTCGTGGTGTTTCT 58.707 50.000 0.00 0.00 0.00 2.52
1751 1765 4.802248 GCTGTCTCTCTTTCTGGTGTGATT 60.802 45.833 0.00 0.00 0.00 2.57
1752 1766 4.635223 TGTCTCTCTTTCTGGTGTGATTG 58.365 43.478 0.00 0.00 0.00 2.67
1753 1767 3.999663 GTCTCTCTTTCTGGTGTGATTGG 59.000 47.826 0.00 0.00 0.00 3.16
1754 1768 3.903714 TCTCTCTTTCTGGTGTGATTGGA 59.096 43.478 0.00 0.00 0.00 3.53
1755 1769 4.533707 TCTCTCTTTCTGGTGTGATTGGAT 59.466 41.667 0.00 0.00 0.00 3.41
1876 1890 3.117663 TGTTTTGGGTCAAGACTAAGGCT 60.118 43.478 0.00 0.00 31.11 4.58
1877 1891 2.859165 TTGGGTCAAGACTAAGGCTG 57.141 50.000 0.00 0.00 0.00 4.85
1878 1892 2.024176 TGGGTCAAGACTAAGGCTGA 57.976 50.000 0.00 0.00 0.00 4.26
1879 1893 2.551270 TGGGTCAAGACTAAGGCTGAT 58.449 47.619 0.00 0.00 0.00 2.90
2022 2036 5.488262 TCAGTGAGATGAATGACAGGAAA 57.512 39.130 0.00 0.00 0.00 3.13
2129 2143 9.310449 TCTCAGTACTTTGGTTATCTAAACTCT 57.690 33.333 0.00 0.00 0.00 3.24
2130 2144 9.575783 CTCAGTACTTTGGTTATCTAAACTCTC 57.424 37.037 0.00 0.00 0.00 3.20
2136 2150 5.717078 TGGTTATCTAAACTCTCACGTGT 57.283 39.130 16.51 0.00 0.00 4.49
2245 2402 9.127277 TGCTCTAAACATAAATAATTGTACCCC 57.873 33.333 0.00 0.00 0.00 4.95
2277 2434 0.677414 TGCCGCAATGCTTGATCTCA 60.677 50.000 2.94 0.00 0.00 3.27
2406 2563 9.768662 ATCTGAAAACAGAAATGTTTATGCTTT 57.231 25.926 6.78 0.00 40.67 3.51
2509 2666 6.494842 TCAAAGTACAGCAATTCAAGTGTTC 58.505 36.000 0.00 0.00 0.00 3.18
2546 2703 7.630513 GCTGCCACCAATGTACTTAATTATGTT 60.631 37.037 9.08 0.00 0.00 2.71
2594 2751 9.267084 CTAGGCCTCTTTCTATTTACTGAAATC 57.733 37.037 9.68 0.00 36.62 2.17
2758 2918 6.121776 TCACAGGCTTATAAGAAAGTTGGA 57.878 37.500 16.85 1.82 0.00 3.53
2812 2972 5.940470 CCCAGATTTTAGTGTCTTAGTTGCT 59.060 40.000 0.00 0.00 0.00 3.91
3158 3322 4.319177 AGTGTCAAGTATCAAGGTTGAGC 58.681 43.478 0.00 0.00 41.08 4.26
3159 3323 4.065088 GTGTCAAGTATCAAGGTTGAGCA 58.935 43.478 0.00 0.00 41.08 4.26
3160 3324 4.065088 TGTCAAGTATCAAGGTTGAGCAC 58.935 43.478 0.00 0.00 41.08 4.40
3161 3325 4.065088 GTCAAGTATCAAGGTTGAGCACA 58.935 43.478 0.00 0.00 41.08 4.57
3163 3327 3.769739 AGTATCAAGGTTGAGCACACA 57.230 42.857 0.00 0.00 41.08 3.72
3164 3328 4.292186 AGTATCAAGGTTGAGCACACAT 57.708 40.909 0.00 0.00 41.08 3.21
3165 3329 4.005650 AGTATCAAGGTTGAGCACACATG 58.994 43.478 0.00 0.00 41.08 3.21
3166 3330 2.346766 TCAAGGTTGAGCACACATGT 57.653 45.000 0.00 0.00 32.50 3.21
3167 3331 2.221169 TCAAGGTTGAGCACACATGTC 58.779 47.619 0.00 0.00 32.50 3.06
3168 3332 1.948834 CAAGGTTGAGCACACATGTCA 59.051 47.619 0.00 0.00 0.00 3.58
3169 3333 1.888215 AGGTTGAGCACACATGTCAG 58.112 50.000 0.00 0.00 0.00 3.51
3170 3334 0.877071 GGTTGAGCACACATGTCAGG 59.123 55.000 0.00 0.00 0.00 3.86
3171 3335 1.543208 GGTTGAGCACACATGTCAGGA 60.543 52.381 0.00 0.00 0.00 3.86
3172 3336 1.802960 GTTGAGCACACATGTCAGGAG 59.197 52.381 0.00 0.00 0.00 3.69
3173 3337 1.341080 TGAGCACACATGTCAGGAGA 58.659 50.000 0.00 0.00 0.00 3.71
3174 3338 1.274447 TGAGCACACATGTCAGGAGAG 59.726 52.381 0.00 0.00 0.00 3.20
3175 3339 0.036577 AGCACACATGTCAGGAGAGC 60.037 55.000 0.00 0.00 0.00 4.09
3176 3340 0.321034 GCACACATGTCAGGAGAGCA 60.321 55.000 0.00 0.00 0.00 4.26
3177 3341 1.678123 GCACACATGTCAGGAGAGCAT 60.678 52.381 0.00 0.00 0.00 3.79
3178 3342 2.708051 CACACATGTCAGGAGAGCATT 58.292 47.619 0.00 0.00 0.00 3.56
3179 3343 3.079578 CACACATGTCAGGAGAGCATTT 58.920 45.455 0.00 0.00 0.00 2.32
3180 3344 4.256110 CACACATGTCAGGAGAGCATTTA 58.744 43.478 0.00 0.00 0.00 1.40
3181 3345 4.880120 CACACATGTCAGGAGAGCATTTAT 59.120 41.667 0.00 0.00 0.00 1.40
3182 3346 4.880120 ACACATGTCAGGAGAGCATTTATG 59.120 41.667 0.00 0.00 0.00 1.90
3183 3347 4.880120 CACATGTCAGGAGAGCATTTATGT 59.120 41.667 0.00 0.00 0.00 2.29
3184 3348 6.051074 CACATGTCAGGAGAGCATTTATGTA 58.949 40.000 0.00 0.00 0.00 2.29
3185 3349 6.709397 CACATGTCAGGAGAGCATTTATGTAT 59.291 38.462 0.00 0.00 0.00 2.29
3186 3350 6.933521 ACATGTCAGGAGAGCATTTATGTATC 59.066 38.462 0.00 0.00 0.00 2.24
3187 3351 6.484364 TGTCAGGAGAGCATTTATGTATCA 57.516 37.500 0.00 0.00 0.00 2.15
3188 3352 6.888105 TGTCAGGAGAGCATTTATGTATCAA 58.112 36.000 0.00 0.00 0.00 2.57
3189 3353 7.337938 TGTCAGGAGAGCATTTATGTATCAAA 58.662 34.615 0.00 0.00 0.00 2.69
3190 3354 7.828717 TGTCAGGAGAGCATTTATGTATCAAAA 59.171 33.333 0.00 0.00 0.00 2.44
3191 3355 8.844244 GTCAGGAGAGCATTTATGTATCAAAAT 58.156 33.333 0.00 0.00 0.00 1.82
3192 3356 8.843262 TCAGGAGAGCATTTATGTATCAAAATG 58.157 33.333 3.93 3.93 43.05 2.32
3204 3368 7.876936 ATGTATCAAAATGCTTCTGATGACT 57.123 32.000 7.16 0.00 32.22 3.41
3205 3369 7.692460 TGTATCAAAATGCTTCTGATGACTT 57.308 32.000 7.16 0.00 32.22 3.01
3206 3370 7.532571 TGTATCAAAATGCTTCTGATGACTTG 58.467 34.615 7.16 0.00 32.22 3.16
3207 3371 4.801891 TCAAAATGCTTCTGATGACTTGC 58.198 39.130 0.00 0.00 0.00 4.01
3208 3372 4.278919 TCAAAATGCTTCTGATGACTTGCA 59.721 37.500 0.00 0.00 34.88 4.08
3209 3373 3.844577 AATGCTTCTGATGACTTGCAC 57.155 42.857 0.00 0.00 33.16 4.57
3210 3374 2.259266 TGCTTCTGATGACTTGCACA 57.741 45.000 0.00 0.00 0.00 4.57
3211 3375 1.875514 TGCTTCTGATGACTTGCACAC 59.124 47.619 0.00 0.00 0.00 3.82
3212 3376 1.875514 GCTTCTGATGACTTGCACACA 59.124 47.619 0.00 0.00 0.00 3.72
3213 3377 2.486982 GCTTCTGATGACTTGCACACAT 59.513 45.455 0.00 0.00 0.00 3.21
3214 3378 3.669824 GCTTCTGATGACTTGCACACATG 60.670 47.826 4.54 0.00 0.00 3.21
3215 3379 3.130280 TCTGATGACTTGCACACATGT 57.870 42.857 0.00 0.00 36.91 3.21
3216 3380 3.069289 TCTGATGACTTGCACACATGTC 58.931 45.455 0.00 5.42 46.19 3.06
3562 3987 9.747898 TGGTGTTTCTTTAGATATGTTATTGGT 57.252 29.630 0.00 0.00 0.00 3.67
3588 4013 5.755409 TGTCCACCTTGTGAAGTATACAT 57.245 39.130 5.50 0.00 35.23 2.29
3685 4110 0.106569 TGTGCCAAGGATGCTATGGG 60.107 55.000 14.18 6.41 34.71 4.00
3689 4114 0.250467 CCAAGGATGCTATGGGGACG 60.250 60.000 7.32 0.00 0.00 4.79
3765 4192 6.204301 AGAGAATAGCATGTACATGTTGATGC 59.796 38.462 31.10 24.22 41.29 3.91
3809 4236 5.125417 AGGGCATGTACATGTTGATGTTTAC 59.875 40.000 31.10 14.02 40.05 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 9.211485 CAAGTTGGCTAGATTTTCATTCATTTT 57.789 29.630 0.00 0.00 0.00 1.82
205 206 6.688073 AACTCGGATAATATGGAGGTGATT 57.312 37.500 3.85 0.00 0.00 2.57
387 390 4.956085 TCTTTTGATCACGACCTTCTCAA 58.044 39.130 0.00 0.00 0.00 3.02
598 601 3.003585 GCGTGACATGATTGCCATATCAA 59.996 43.478 0.00 0.00 40.08 2.57
676 679 0.326595 TGCGGGTGAGGCAATCTTAA 59.673 50.000 0.00 0.00 37.49 1.85
677 680 0.546122 ATGCGGGTGAGGCAATCTTA 59.454 50.000 0.00 0.00 44.66 2.10
880 883 9.228636 GGTAAATATTTATTTGGCGTACACTTG 57.771 33.333 11.00 0.00 36.62 3.16
904 907 0.183971 TGGATTTTGGTGTGGACGGT 59.816 50.000 0.00 0.00 0.00 4.83
905 908 1.202114 CATGGATTTTGGTGTGGACGG 59.798 52.381 0.00 0.00 0.00 4.79
906 909 1.402720 GCATGGATTTTGGTGTGGACG 60.403 52.381 0.00 0.00 0.00 4.79
907 910 1.617850 TGCATGGATTTTGGTGTGGAC 59.382 47.619 0.00 0.00 0.00 4.02
908 911 1.617850 GTGCATGGATTTTGGTGTGGA 59.382 47.619 0.00 0.00 0.00 4.02
909 912 1.619827 AGTGCATGGATTTTGGTGTGG 59.380 47.619 0.00 0.00 0.00 4.17
910 913 3.389925 AAGTGCATGGATTTTGGTGTG 57.610 42.857 0.00 0.00 0.00 3.82
911 914 4.262420 GGTTAAGTGCATGGATTTTGGTGT 60.262 41.667 0.00 0.00 0.00 4.16
912 915 4.244862 GGTTAAGTGCATGGATTTTGGTG 58.755 43.478 0.00 0.00 0.00 4.17
913 916 3.900601 TGGTTAAGTGCATGGATTTTGGT 59.099 39.130 0.00 0.00 0.00 3.67
914 917 4.533919 TGGTTAAGTGCATGGATTTTGG 57.466 40.909 0.00 0.00 0.00 3.28
915 918 6.857777 TTTTGGTTAAGTGCATGGATTTTG 57.142 33.333 0.00 0.00 0.00 2.44
916 919 6.018343 CGTTTTTGGTTAAGTGCATGGATTTT 60.018 34.615 0.00 0.00 0.00 1.82
917 920 5.465056 CGTTTTTGGTTAAGTGCATGGATTT 59.535 36.000 0.00 0.00 0.00 2.17
918 921 4.987912 CGTTTTTGGTTAAGTGCATGGATT 59.012 37.500 0.00 0.00 0.00 3.01
919 922 4.555262 CGTTTTTGGTTAAGTGCATGGAT 58.445 39.130 0.00 0.00 0.00 3.41
920 923 3.797184 GCGTTTTTGGTTAAGTGCATGGA 60.797 43.478 0.00 0.00 0.00 3.41
921 924 2.474735 GCGTTTTTGGTTAAGTGCATGG 59.525 45.455 0.00 0.00 0.00 3.66
922 925 2.474735 GGCGTTTTTGGTTAAGTGCATG 59.525 45.455 0.00 0.00 0.00 4.06
923 926 2.547007 GGGCGTTTTTGGTTAAGTGCAT 60.547 45.455 0.00 0.00 0.00 3.96
924 927 1.202428 GGGCGTTTTTGGTTAAGTGCA 60.202 47.619 0.00 0.00 0.00 4.57
925 928 1.493772 GGGCGTTTTTGGTTAAGTGC 58.506 50.000 0.00 0.00 0.00 4.40
926 929 1.684450 AGGGGCGTTTTTGGTTAAGTG 59.316 47.619 0.00 0.00 0.00 3.16
927 930 1.958579 GAGGGGCGTTTTTGGTTAAGT 59.041 47.619 0.00 0.00 0.00 2.24
928 931 1.957877 TGAGGGGCGTTTTTGGTTAAG 59.042 47.619 0.00 0.00 0.00 1.85
929 932 1.682323 GTGAGGGGCGTTTTTGGTTAA 59.318 47.619 0.00 0.00 0.00 2.01
930 933 1.320507 GTGAGGGGCGTTTTTGGTTA 58.679 50.000 0.00 0.00 0.00 2.85
931 934 1.730451 CGTGAGGGGCGTTTTTGGTT 61.730 55.000 0.00 0.00 0.00 3.67
932 935 2.190841 CGTGAGGGGCGTTTTTGGT 61.191 57.895 0.00 0.00 0.00 3.67
933 936 2.190841 ACGTGAGGGGCGTTTTTGG 61.191 57.895 0.00 0.00 39.79 3.28
934 937 1.008995 CACGTGAGGGGCGTTTTTG 60.009 57.895 10.90 0.00 40.90 2.44
935 938 3.427670 CACGTGAGGGGCGTTTTT 58.572 55.556 10.90 0.00 40.90 1.94
943 946 1.503818 CCGTTTGTTCCACGTGAGGG 61.504 60.000 19.30 7.08 35.81 4.30
944 947 0.812412 ACCGTTTGTTCCACGTGAGG 60.812 55.000 19.30 0.09 35.81 3.86
1329 1343 3.075005 ATCGCCCAGTACAGCCGT 61.075 61.111 0.00 0.00 0.00 5.68
1548 1562 1.763770 GGCCTGATTGGGATCGGAT 59.236 57.895 0.00 0.00 40.48 4.18
1615 1629 8.674607 GGTTCCAAGTTTTACTCTGTATTATGG 58.325 37.037 0.00 0.00 0.00 2.74
1640 1654 4.223923 ACAGGAACTCTAACCAGATCAAGG 59.776 45.833 0.00 0.00 34.60 3.61
1645 1659 4.322801 CCGAAACAGGAACTCTAACCAGAT 60.323 45.833 0.00 0.00 34.60 2.90
1680 1694 3.768757 CCCTAGATGGCTAGATCCAGAAG 59.231 52.174 0.00 0.00 45.71 2.85
1681 1695 3.402708 TCCCTAGATGGCTAGATCCAGAA 59.597 47.826 0.00 0.00 45.71 3.02
1751 1765 9.527157 TTCAAATAAAACTACTGATCCAATCCA 57.473 29.630 0.00 0.00 0.00 3.41
2055 2069 5.476091 AGGCTAAGGTGTATATTCAGAGC 57.524 43.478 0.00 0.00 0.00 4.09
2104 2118 9.575783 GAGAGTTTAGATAACCAAAGTACTGAG 57.424 37.037 0.00 0.00 0.00 3.35
2222 2379 9.902684 TTCGGGGTACAATTATTTATGTTTAGA 57.097 29.630 0.00 0.00 0.00 2.10
2245 2402 0.523966 TGCGGCAAAACCCTAATTCG 59.476 50.000 0.00 0.00 33.26 3.34
2277 2434 3.633525 ACATCAGTGCACAAACAAGACAT 59.366 39.130 21.04 0.00 0.00 3.06
2406 2563 3.798515 ACCTAGGTAATCCCACAACTCA 58.201 45.455 14.41 0.00 34.66 3.41
2476 2633 8.486210 TGAATTGCTGTACTTTGATATAGGAGT 58.514 33.333 0.00 0.00 0.00 3.85
2509 2666 3.383620 TGGTGGCAGCAAAAATTACAG 57.616 42.857 18.31 0.00 0.00 2.74
2546 2703 4.520874 AGAGAAGTGATGACTCGTTCTCAA 59.479 41.667 12.99 0.00 36.58 3.02
2594 2751 6.150396 ACCTAGTTAGCATTGCTACTGTAG 57.850 41.667 17.79 16.20 41.12 2.74
2758 2918 2.177016 GCCAGTAGGGGGTGGATTAAAT 59.823 50.000 0.00 0.00 35.67 1.40
2812 2972 1.899142 TGGATCTGACGGACACATTCA 59.101 47.619 0.00 0.00 0.00 2.57
3158 3322 2.398252 ATGCTCTCCTGACATGTGTG 57.602 50.000 1.15 0.00 0.00 3.82
3159 3323 3.430042 AAATGCTCTCCTGACATGTGT 57.570 42.857 1.15 0.00 0.00 3.72
3160 3324 4.880120 ACATAAATGCTCTCCTGACATGTG 59.120 41.667 1.15 0.00 0.00 3.21
3161 3325 5.108187 ACATAAATGCTCTCCTGACATGT 57.892 39.130 0.00 0.00 0.00 3.21
3163 3327 7.071069 TGATACATAAATGCTCTCCTGACAT 57.929 36.000 0.00 0.00 0.00 3.06
3164 3328 6.484364 TGATACATAAATGCTCTCCTGACA 57.516 37.500 0.00 0.00 0.00 3.58
3165 3329 7.792374 TTTGATACATAAATGCTCTCCTGAC 57.208 36.000 0.00 0.00 0.00 3.51
3166 3330 8.843262 CATTTTGATACATAAATGCTCTCCTGA 58.157 33.333 0.00 0.00 35.64 3.86
3178 3342 9.399797 AGTCATCAGAAGCATTTTGATACATAA 57.600 29.630 0.00 0.00 30.77 1.90
3179 3343 8.969260 AGTCATCAGAAGCATTTTGATACATA 57.031 30.769 0.00 0.00 30.77 2.29
3180 3344 7.876936 AGTCATCAGAAGCATTTTGATACAT 57.123 32.000 0.00 0.00 30.77 2.29
3181 3345 7.532571 CAAGTCATCAGAAGCATTTTGATACA 58.467 34.615 0.00 0.00 30.77 2.29
3182 3346 6.471519 GCAAGTCATCAGAAGCATTTTGATAC 59.528 38.462 0.00 0.00 30.77 2.24
3183 3347 6.151480 TGCAAGTCATCAGAAGCATTTTGATA 59.849 34.615 0.00 0.00 30.77 2.15
3184 3348 5.047590 TGCAAGTCATCAGAAGCATTTTGAT 60.048 36.000 0.00 0.00 32.01 2.57
3185 3349 4.278919 TGCAAGTCATCAGAAGCATTTTGA 59.721 37.500 0.00 0.00 0.00 2.69
3186 3350 4.384846 GTGCAAGTCATCAGAAGCATTTTG 59.615 41.667 0.00 0.00 33.06 2.44
3187 3351 4.038282 TGTGCAAGTCATCAGAAGCATTTT 59.962 37.500 0.00 0.00 33.06 1.82
3188 3352 3.570975 TGTGCAAGTCATCAGAAGCATTT 59.429 39.130 0.00 0.00 33.06 2.32
3189 3353 3.057736 GTGTGCAAGTCATCAGAAGCATT 60.058 43.478 0.00 0.00 33.06 3.56
3190 3354 2.486982 GTGTGCAAGTCATCAGAAGCAT 59.513 45.455 0.00 0.00 33.06 3.79
3191 3355 1.875514 GTGTGCAAGTCATCAGAAGCA 59.124 47.619 0.00 0.00 0.00 3.91
3192 3356 1.875514 TGTGTGCAAGTCATCAGAAGC 59.124 47.619 0.00 0.00 0.00 3.86
3193 3357 3.501062 ACATGTGTGCAAGTCATCAGAAG 59.499 43.478 0.00 0.00 0.00 2.85
3194 3358 3.479489 ACATGTGTGCAAGTCATCAGAA 58.521 40.909 0.00 0.00 0.00 3.02
3195 3359 3.069289 GACATGTGTGCAAGTCATCAGA 58.931 45.455 1.15 0.00 41.44 3.27
3196 3360 2.809696 TGACATGTGTGCAAGTCATCAG 59.190 45.455 1.15 0.00 44.97 2.90
3197 3361 2.848691 TGACATGTGTGCAAGTCATCA 58.151 42.857 1.15 0.00 44.97 3.07
3201 3365 4.452114 TGATACTTGACATGTGTGCAAGTC 59.548 41.667 26.01 17.13 44.20 3.01
3202 3366 4.388485 TGATACTTGACATGTGTGCAAGT 58.612 39.130 25.70 25.70 45.62 3.16
3203 3367 5.361135 TTGATACTTGACATGTGTGCAAG 57.639 39.130 19.08 19.08 41.28 4.01
3204 3368 5.764487 TTTGATACTTGACATGTGTGCAA 57.236 34.783 1.15 0.00 0.00 4.08
3205 3369 5.764487 TTTTGATACTTGACATGTGTGCA 57.236 34.783 1.15 0.00 0.00 4.57
3206 3370 5.061311 GCATTTTGATACTTGACATGTGTGC 59.939 40.000 1.15 0.00 0.00 4.57
3207 3371 6.088483 GTGCATTTTGATACTTGACATGTGTG 59.912 38.462 1.15 0.00 0.00 3.82
3208 3372 6.151691 GTGCATTTTGATACTTGACATGTGT 58.848 36.000 1.15 0.00 0.00 3.72
3209 3373 6.088483 GTGTGCATTTTGATACTTGACATGTG 59.912 38.462 1.15 0.00 0.00 3.21
3210 3374 6.151691 GTGTGCATTTTGATACTTGACATGT 58.848 36.000 0.00 0.00 0.00 3.21
3211 3375 6.151004 TGTGTGCATTTTGATACTTGACATG 58.849 36.000 0.00 0.00 0.00 3.21
3212 3376 6.330004 TGTGTGCATTTTGATACTTGACAT 57.670 33.333 0.00 0.00 0.00 3.06
3213 3377 5.764487 TGTGTGCATTTTGATACTTGACA 57.236 34.783 0.00 0.00 0.00 3.58
3214 3378 6.151691 ACATGTGTGCATTTTGATACTTGAC 58.848 36.000 0.00 0.00 31.99 3.18
3215 3379 6.016443 TGACATGTGTGCATTTTGATACTTGA 60.016 34.615 1.15 0.00 31.99 3.02
3216 3380 6.151004 TGACATGTGTGCATTTTGATACTTG 58.849 36.000 1.15 0.00 31.99 3.16
3217 3381 6.330004 TGACATGTGTGCATTTTGATACTT 57.670 33.333 1.15 0.00 31.99 2.24
3218 3382 5.106038 CCTGACATGTGTGCATTTTGATACT 60.106 40.000 1.15 0.00 31.99 2.12
3219 3383 5.097529 CCTGACATGTGTGCATTTTGATAC 58.902 41.667 1.15 0.00 31.99 2.24
3220 3384 5.008980 TCCTGACATGTGTGCATTTTGATA 58.991 37.500 1.15 0.00 31.99 2.15
3221 3385 3.827876 TCCTGACATGTGTGCATTTTGAT 59.172 39.130 1.15 0.00 31.99 2.57
3222 3386 3.220940 TCCTGACATGTGTGCATTTTGA 58.779 40.909 1.15 0.00 31.99 2.69
3496 3921 3.427528 GCCATCACACGGTATACATTACG 59.572 47.826 5.01 1.46 0.00 3.18
3508 3933 0.603707 AACAGGACAGCCATCACACG 60.604 55.000 0.00 0.00 36.29 4.49
3562 3987 7.681679 TGTATACTTCACAAGGTGGACATTTA 58.318 34.615 4.17 0.00 33.87 1.40
3685 4110 2.122167 TGGCACAAAACCACCGTCC 61.122 57.895 0.00 0.00 31.92 4.79
3765 4192 4.020396 CCCTCTCCTCATCCATGTCATAAG 60.020 50.000 0.00 0.00 0.00 1.73
3809 4236 5.870978 CCATTCCAACTAAATCAGGCAAAAG 59.129 40.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.