Multiple sequence alignment - TraesCS1D01G384400

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 TraesCS1D01G384400 chr1D 100.000 2243 0 0 1 2243 458256300 458258542 0.000000e+00 4143
1 TraesCS1D01G384400 chr1D 90.464 1531 128 13 535 2053 458160550 458162074 0.000000e+00 2002
2 TraesCS1D01G384400 chr1D 91.654 647 39 5 1409 2053 458230724 458231357 0.000000e+00 881
3 TraesCS1D01G384400 chr1D 83.540 887 80 25 759 1599 458164345 458165211 0.000000e+00 769
4 TraesCS1D01G384400 chr1D 94.989 459 22 1 120 577 458279692 458280150 0.000000e+00 719
5 TraesCS1D01G384400 chr1D 78.673 1191 157 63 15 1143 458177612 458178767 0.000000e+00 702
6 TraesCS1D01G384400 chr1D 82.740 730 74 31 672 1382 458285703 458286399 8.860000e-169 603
7 TraesCS1D01G384400 chr1D 97.354 189 5 0 2053 2241 441199117 441199305 2.780000e-84 322
8 TraesCS1D01G384400 chr1D 96.859 191 6 0 2053 2243 261067749 261067559 9.990000e-84 320
9 TraesCS1D01G384400 chr1D 94.853 136 7 0 14 149 458168473 458168608 1.740000e-51 213
10 TraesCS1D01G384400 chr1A 88.758 1530 150 14 535 2048 550646170 550647693 0.000000e+00 1853
11 TraesCS1D01G384400 chr1A 89.147 1161 106 14 899 2053 550661201 550662347 0.000000e+00 1428
12 TraesCS1D01G384400 chr1A 91.791 938 68 5 535 1464 550684056 550684992 0.000000e+00 1297
13 TraesCS1D01G384400 chr1A 91.684 938 66 6 535 1464 550674283 550675216 0.000000e+00 1290
14 TraesCS1D01G384400 chr1A 92.408 922 36 9 15 905 550659877 550660795 0.000000e+00 1284
15 TraesCS1D01G384400 chr1A 91.578 938 62 8 535 1464 550693676 550694604 0.000000e+00 1279
16 TraesCS1D01G384400 chr1A 88.539 794 69 15 1262 2043 550721158 550721941 0.000000e+00 942
17 TraesCS1D01G384400 chr1A 92.971 626 33 2 1262 1887 550793733 550794347 0.000000e+00 902
18 TraesCS1D01G384400 chr1A 92.675 587 16 2 14 573 550673620 550674206 0.000000e+00 821
19 TraesCS1D01G384400 chr1A 92.334 587 18 2 14 573 550693013 550693599 0.000000e+00 809
20 TraesCS1D01G384400 chr1A 91.823 587 20 3 14 573 550683394 550683979 0.000000e+00 793
21 TraesCS1D01G384400 chr1A 93.464 459 27 3 120 577 550829087 550829543 0.000000e+00 678
22 TraesCS1D01G384400 chr1A 79.795 975 116 40 14 955 550792471 550793397 3.140000e-178 634
23 TraesCS1D01G384400 chr1A 82.564 585 87 13 1473 2053 550675535 550676108 3.330000e-138 501
24 TraesCS1D01G384400 chr1A 82.222 585 89 13 1473 2053 550685311 550685884 7.200000e-135 490
25 TraesCS1D01G384400 chr1A 87.108 287 28 7 1473 1758 550694923 550695201 1.290000e-82 316
26 TraesCS1D01G384400 chr1A 94.074 135 8 0 15 149 550828930 550829064 2.920000e-49 206
27 TraesCS1D01G384400 chr1B 90.355 591 29 4 14 576 628860359 628860949 0.000000e+00 750
28 TraesCS1D01G384400 chr1B 89.679 591 32 4 14 576 628903243 628903832 0.000000e+00 726
29 TraesCS1D01G384400 chr1B 89.679 591 32 4 14 576 628979354 628979943 0.000000e+00 726
30 TraesCS1D01G384400 chr1B 88.006 617 62 8 924 1536 628783907 628784515 0.000000e+00 719
31 TraesCS1D01G384400 chr1B 88.263 426 37 8 1044 1462 629074097 629074516 4.300000e-137 497
32 TraesCS1D01G384400 chr1B 77.607 911 110 49 673 1535 629064175 629065039 1.210000e-127 466
33 TraesCS1D01G384400 chr6D 98.974 195 2 0 2049 2243 428705511 428705705 1.270000e-92 350
34 TraesCS1D01G384400 chr6D 97.354 189 5 0 2053 2241 387820471 387820659 2.780000e-84 322
35 TraesCS1D01G384400 chr5D 97.382 191 5 0 2053 2243 2992815 2992625 2.150000e-85 326
36 TraesCS1D01G384400 chr5D 97.382 191 5 0 2053 2243 376961679 376961869 2.150000e-85 326
37 TraesCS1D01G384400 chr5D 97.382 191 5 0 2053 2243 443526476 443526666 2.150000e-85 326
38 TraesCS1D01G384400 chr4D 97.354 189 5 0 2053 2241 161621151 161621339 2.780000e-84 322
39 TraesCS1D01G384400 chr4D 96.825 189 6 0 2053 2241 34136965 34137153 1.290000e-82 316


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 TraesCS1D01G384400 chr1D 458256300 458258542 2242 False 4143.000000 4143 100.000000 1 2243 1 chr1D.!!$F4 2242
1 TraesCS1D01G384400 chr1D 458160550 458168608 8058 False 994.666667 2002 89.619000 14 2053 3 chr1D.!!$F7 2039
2 TraesCS1D01G384400 chr1D 458230724 458231357 633 False 881.000000 881 91.654000 1409 2053 1 chr1D.!!$F3 644
3 TraesCS1D01G384400 chr1D 458177612 458178767 1155 False 702.000000 702 78.673000 15 1143 1 chr1D.!!$F2 1128
4 TraesCS1D01G384400 chr1D 458285703 458286399 696 False 603.000000 603 82.740000 672 1382 1 chr1D.!!$F6 710
5 TraesCS1D01G384400 chr1A 550646170 550647693 1523 False 1853.000000 1853 88.758000 535 2048 1 chr1A.!!$F1 1513
6 TraesCS1D01G384400 chr1A 550659877 550662347 2470 False 1356.000000 1428 90.777500 15 2053 2 chr1A.!!$F3 2038
7 TraesCS1D01G384400 chr1A 550721158 550721941 783 False 942.000000 942 88.539000 1262 2043 1 chr1A.!!$F2 781
8 TraesCS1D01G384400 chr1A 550673620 550676108 2488 False 870.666667 1290 88.974333 14 2053 3 chr1A.!!$F4 2039
9 TraesCS1D01G384400 chr1A 550683394 550685884 2490 False 860.000000 1297 88.612000 14 2053 3 chr1A.!!$F5 2039
10 TraesCS1D01G384400 chr1A 550693013 550695201 2188 False 801.333333 1279 90.340000 14 1758 3 chr1A.!!$F6 1744
11 TraesCS1D01G384400 chr1A 550792471 550794347 1876 False 768.000000 902 86.383000 14 1887 2 chr1A.!!$F7 1873
12 TraesCS1D01G384400 chr1A 550828930 550829543 613 False 442.000000 678 93.769000 15 577 2 chr1A.!!$F8 562
13 TraesCS1D01G384400 chr1B 628860359 628860949 590 False 750.000000 750 90.355000 14 576 1 chr1B.!!$F2 562
14 TraesCS1D01G384400 chr1B 628903243 628903832 589 False 726.000000 726 89.679000 14 576 1 chr1B.!!$F3 562
15 TraesCS1D01G384400 chr1B 628979354 628979943 589 False 726.000000 726 89.679000 14 576 1 chr1B.!!$F4 562
16 TraesCS1D01G384400 chr1B 628783907 628784515 608 False 719.000000 719 88.006000 924 1536 1 chr1B.!!$F1 612
17 TraesCS1D01G384400 chr1B 629064175 629065039 864 False 466.000000 466 77.607000 673 1535 1 chr1B.!!$F5 862

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
840 1072 0.250124 CCCAGCCGTTGTTACTGTCA 60.25 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 3187 0.107703 CCGATGCCTACTTTGCCAGA 60.108 55.0 0.0 0.0 0.0 3.86 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
63 65 2.093447 AGTTTATGCAGAGACGAAGGGG 60.093 50.000 0.00 0.00 0.00 4.79
130 160 2.231215 ATGTCGATTGCTAGGTCTGC 57.769 50.000 0.00 0.00 0.00 4.26
204 260 6.336119 TGGATAATGGATATATGGGCCATGAT 59.664 38.462 29.14 20.71 41.36 2.45
433 498 1.552578 GCCAAATTAAAGTCGGGGGT 58.447 50.000 0.00 0.00 0.00 4.95
532 601 2.358615 GCACTGGCCGTGACATGA 60.359 61.111 25.37 0.00 46.81 3.07
533 602 1.965930 GCACTGGCCGTGACATGAA 60.966 57.895 25.37 0.00 46.81 2.57
583 768 6.664515 CCTCAAGCGAAATTACTTGTTTGTA 58.335 36.000 12.77 0.00 43.05 2.41
604 789 1.398390 GTACTATGCAACTGCCTGTGC 59.602 52.381 0.00 0.00 41.18 4.57
723 943 2.020694 GCTAGTGTAGGGTGCCGACTA 61.021 57.143 0.00 0.00 30.46 2.59
799 1029 5.991606 TCATTTTTCTCGTCAGACATGAGTT 59.008 36.000 0.00 0.00 39.04 3.01
810 1042 1.230635 ACATGAGTTGAGTGCGTGGC 61.231 55.000 0.00 0.00 0.00 5.01
840 1072 0.250124 CCCAGCCGTTGTTACTGTCA 60.250 55.000 0.00 0.00 0.00 3.58
847 1080 1.484356 GTTGTTACTGTCAGCGTCGT 58.516 50.000 0.00 0.00 0.00 4.34
1021 1670 1.480954 TGGCGTTTCTAGGAGGATCAC 59.519 52.381 0.00 0.00 36.25 3.06
1088 1737 4.096003 CCACGGCGGGTCAGGATT 62.096 66.667 13.24 0.00 0.00 3.01
1245 1896 4.096003 GCCCACCGCCTCTAGCAA 62.096 66.667 0.00 0.00 44.04 3.91
1246 1897 2.187946 CCCACCGCCTCTAGCAAG 59.812 66.667 0.00 0.00 44.04 4.01
1247 1898 2.512515 CCACCGCCTCTAGCAAGC 60.513 66.667 0.00 0.00 44.04 4.01
1248 1899 2.512515 CACCGCCTCTAGCAAGCC 60.513 66.667 0.00 0.00 44.04 4.35
1423 2146 5.880341 ACAGAAGTTGCTTACTGTTGAAAC 58.120 37.500 0.00 0.00 40.03 2.78
1725 2778 3.653122 AAGGTCCCCATACCCGGCT 62.653 63.158 0.00 0.00 40.71 5.52
1726 2779 3.094498 GGTCCCCATACCCGGCTT 61.094 66.667 0.00 0.00 33.02 4.35
1758 2811 2.225066 ACTAACCGGCAACCCCATAAAA 60.225 45.455 0.00 0.00 0.00 1.52
1767 2820 3.323691 GCAACCCCATAAAACCCATATCC 59.676 47.826 0.00 0.00 0.00 2.59
1867 2930 1.469079 CGCGATCACACACATAGACCA 60.469 52.381 0.00 0.00 0.00 4.02
1868 2931 2.616960 GCGATCACACACATAGACCAA 58.383 47.619 0.00 0.00 0.00 3.67
1979 3042 4.347000 AGGCCTATCTATTTAAGCCGAACA 59.653 41.667 1.29 0.00 45.16 3.18
1981 3044 5.298347 GCCTATCTATTTAAGCCGAACAGT 58.702 41.667 0.00 0.00 0.00 3.55
1982 3045 6.453092 GCCTATCTATTTAAGCCGAACAGTA 58.547 40.000 0.00 0.00 0.00 2.74
1986 3049 9.182933 CTATCTATTTAAGCCGAACAGTAGAAC 57.817 37.037 0.00 0.00 0.00 3.01
1989 3052 4.546829 TTAAGCCGAACAGTAGAACCAT 57.453 40.909 0.00 0.00 0.00 3.55
2023 3086 0.322008 CGCCAGCTTCCCTCTTCTTT 60.322 55.000 0.00 0.00 0.00 2.52
2043 3106 2.125269 ACCGCCTCGTAACCATGC 60.125 61.111 0.00 0.00 0.00 4.06
2059 3122 4.162690 GCCCCGGCAGACTACAGG 62.163 72.222 0.00 0.00 41.49 4.00
2060 3123 2.363795 CCCCGGCAGACTACAGGA 60.364 66.667 0.00 0.00 0.00 3.86
2062 3125 1.338136 CCCCGGCAGACTACAGGAAT 61.338 60.000 0.00 0.00 0.00 3.01
2064 3127 0.824109 CCGGCAGACTACAGGAATCA 59.176 55.000 0.00 0.00 0.00 2.57
2065 3128 1.202463 CCGGCAGACTACAGGAATCAG 60.202 57.143 0.00 0.00 0.00 2.90
2066 3129 1.804372 CGGCAGACTACAGGAATCAGC 60.804 57.143 0.00 0.00 0.00 4.26
2067 3130 1.484240 GGCAGACTACAGGAATCAGCT 59.516 52.381 0.00 0.00 0.00 4.24
2068 3131 2.695666 GGCAGACTACAGGAATCAGCTA 59.304 50.000 0.00 0.00 0.00 3.32
2069 3132 3.491792 GGCAGACTACAGGAATCAGCTAC 60.492 52.174 0.00 0.00 0.00 3.58
2070 3133 3.383185 GCAGACTACAGGAATCAGCTACT 59.617 47.826 0.00 0.00 0.00 2.57
2072 3135 5.625656 GCAGACTACAGGAATCAGCTACTTT 60.626 44.000 0.00 0.00 0.00 2.66
2073 3136 5.809562 CAGACTACAGGAATCAGCTACTTTG 59.190 44.000 0.00 0.00 0.00 2.77
2074 3137 4.508662 ACTACAGGAATCAGCTACTTTGC 58.491 43.478 0.00 0.00 0.00 3.68
2075 3138 2.716217 ACAGGAATCAGCTACTTTGCC 58.284 47.619 0.00 0.00 0.00 4.52
2076 3139 1.667724 CAGGAATCAGCTACTTTGCCG 59.332 52.381 0.00 0.00 0.00 5.69
2078 3141 1.666189 GGAATCAGCTACTTTGCCGTC 59.334 52.381 0.00 0.00 0.00 4.79
2079 3142 2.622436 GAATCAGCTACTTTGCCGTCT 58.378 47.619 0.00 0.00 0.00 4.18
2080 3143 2.015736 ATCAGCTACTTTGCCGTCTG 57.984 50.000 0.00 0.00 0.00 3.51
2081 3144 0.670546 TCAGCTACTTTGCCGTCTGC 60.671 55.000 0.00 0.00 41.77 4.26
2082 3145 1.376037 AGCTACTTTGCCGTCTGCC 60.376 57.895 0.00 0.00 40.16 4.85
2084 3147 1.912371 GCTACTTTGCCGTCTGCCAC 61.912 60.000 0.00 0.00 40.16 5.01
2104 3167 2.956987 CAGACGGCAAAGGCAAGG 59.043 61.111 0.00 0.00 43.71 3.61
2105 3168 1.600636 CAGACGGCAAAGGCAAGGA 60.601 57.895 0.00 0.00 43.71 3.36
2106 3169 0.962356 CAGACGGCAAAGGCAAGGAT 60.962 55.000 0.00 0.00 43.71 3.24
2107 3170 0.962356 AGACGGCAAAGGCAAGGATG 60.962 55.000 0.00 0.00 43.71 3.51
2126 3189 2.358737 CGGACGGCAAAAGGCTCT 60.359 61.111 0.00 0.00 44.01 4.09
2128 3191 2.335712 GGACGGCAAAAGGCTCTGG 61.336 63.158 0.00 0.00 44.01 3.86
2129 3192 2.982744 GACGGCAAAAGGCTCTGGC 61.983 63.158 11.70 11.70 44.01 4.85
2130 3193 2.985282 CGGCAAAAGGCTCTGGCA 60.985 61.111 18.94 0.00 44.01 4.92
2131 3194 2.563798 CGGCAAAAGGCTCTGGCAA 61.564 57.895 18.94 0.00 44.01 4.52
2132 3195 1.747774 GGCAAAAGGCTCTGGCAAA 59.252 52.632 15.53 0.00 44.01 3.68
2135 3198 1.613437 GCAAAAGGCTCTGGCAAAGTA 59.387 47.619 0.00 0.00 40.87 2.24
2137 3200 2.206576 AAAGGCTCTGGCAAAGTAGG 57.793 50.000 0.00 0.00 40.87 3.18
2138 3201 0.322906 AAGGCTCTGGCAAAGTAGGC 60.323 55.000 0.00 0.00 40.87 3.93
2139 3202 1.002134 GGCTCTGGCAAAGTAGGCA 60.002 57.895 7.27 0.00 42.25 4.75
2140 3203 0.394899 GGCTCTGGCAAAGTAGGCAT 60.395 55.000 7.27 0.00 43.56 4.40
2144 3207 0.392998 CTGGCAAAGTAGGCATCGGT 60.393 55.000 0.00 0.00 43.56 4.69
2145 3208 0.906066 TGGCAAAGTAGGCATCGGTA 59.094 50.000 0.00 0.00 39.34 4.02
2146 3209 1.279558 TGGCAAAGTAGGCATCGGTAA 59.720 47.619 0.00 0.00 39.34 2.85
2147 3210 2.290387 TGGCAAAGTAGGCATCGGTAAA 60.290 45.455 0.00 0.00 39.34 2.01
2148 3211 2.354821 GGCAAAGTAGGCATCGGTAAAG 59.645 50.000 0.00 0.00 0.00 1.85
2149 3212 3.267483 GCAAAGTAGGCATCGGTAAAGA 58.733 45.455 0.00 0.00 0.00 2.52
2150 3213 3.309954 GCAAAGTAGGCATCGGTAAAGAG 59.690 47.826 0.00 0.00 0.00 2.85
2152 3215 2.389715 AGTAGGCATCGGTAAAGAGCT 58.610 47.619 0.00 0.00 0.00 4.09
2153 3216 2.766828 AGTAGGCATCGGTAAAGAGCTT 59.233 45.455 0.00 0.00 0.00 3.74
2154 3217 2.317530 AGGCATCGGTAAAGAGCTTC 57.682 50.000 0.00 0.00 0.00 3.86
2155 3218 1.834263 AGGCATCGGTAAAGAGCTTCT 59.166 47.619 0.00 0.00 0.00 2.85
2158 3221 3.181506 GGCATCGGTAAAGAGCTTCTTTG 60.182 47.826 16.59 5.54 45.45 2.77
2159 3222 3.729163 GCATCGGTAAAGAGCTTCTTTGC 60.729 47.826 16.59 15.29 45.45 3.68
2163 3226 3.457198 GTAAAGAGCTTCTTTGCCGTC 57.543 47.619 16.59 4.17 45.45 4.79
2164 3227 2.262423 AAAGAGCTTCTTTGCCGTCT 57.738 45.000 9.46 0.00 44.34 4.18
2167 3230 0.952984 GAGCTTCTTTGCCGTCTGCT 60.953 55.000 0.00 0.00 42.00 4.24
2168 3231 0.536006 AGCTTCTTTGCCGTCTGCTT 60.536 50.000 0.00 0.00 42.00 3.91
2169 3232 0.312102 GCTTCTTTGCCGTCTGCTTT 59.688 50.000 0.00 0.00 42.00 3.51
2170 3233 1.269257 GCTTCTTTGCCGTCTGCTTTT 60.269 47.619 0.00 0.00 42.00 2.27
2171 3234 2.799562 GCTTCTTTGCCGTCTGCTTTTT 60.800 45.455 0.00 0.00 42.00 1.94
2174 3237 2.425312 TCTTTGCCGTCTGCTTTTTGAA 59.575 40.909 0.00 0.00 42.00 2.69
2176 3239 0.030638 TGCCGTCTGCTTTTTGAAGC 59.969 50.000 4.27 4.27 45.67 3.86
2183 3246 3.072953 GCTTTTTGAAGCGGACGAC 57.927 52.632 0.00 0.00 35.93 4.34
2184 3247 0.306533 GCTTTTTGAAGCGGACGACA 59.693 50.000 0.00 0.00 35.93 4.35
2185 3248 1.268335 GCTTTTTGAAGCGGACGACAA 60.268 47.619 0.00 0.00 35.93 3.18
2186 3249 2.793237 GCTTTTTGAAGCGGACGACAAA 60.793 45.455 0.00 2.41 35.93 2.83
2188 3251 0.941542 TTTGAAGCGGACGACAAAGG 59.058 50.000 0.00 0.00 0.00 3.11
2203 4618 2.149973 AAAGGGGCCTTTGCTATCAG 57.850 50.000 0.00 0.00 43.72 2.90
2204 4619 0.396278 AAGGGGCCTTTGCTATCAGC 60.396 55.000 0.84 0.00 42.82 4.26
2205 4620 2.189499 GGGGCCTTTGCTATCAGCG 61.189 63.158 0.84 0.00 46.26 5.18
2206 4621 2.189499 GGGCCTTTGCTATCAGCGG 61.189 63.158 0.84 0.00 46.26 5.52
2207 4622 2.718107 GCCTTTGCTATCAGCGGC 59.282 61.111 0.00 0.00 46.26 6.53
2208 4623 1.821332 GCCTTTGCTATCAGCGGCT 60.821 57.895 0.00 0.00 46.26 5.52
2209 4624 0.532862 GCCTTTGCTATCAGCGGCTA 60.533 55.000 0.26 0.00 46.26 3.93
2210 4625 1.953559 CCTTTGCTATCAGCGGCTAA 58.046 50.000 0.26 0.00 46.26 3.09
2211 4626 1.599542 CCTTTGCTATCAGCGGCTAAC 59.400 52.381 0.26 0.00 46.26 2.34
2212 4627 1.258982 CTTTGCTATCAGCGGCTAACG 59.741 52.381 0.26 0.00 46.26 3.18
2213 4628 0.529773 TTGCTATCAGCGGCTAACGG 60.530 55.000 0.26 0.00 46.26 4.44
2214 4629 2.310966 GCTATCAGCGGCTAACGGC 61.311 63.158 0.26 1.71 44.51 5.68
2215 4630 1.067416 CTATCAGCGGCTAACGGCA 59.933 57.895 0.26 0.00 44.14 5.69
2217 4632 0.108089 TATCAGCGGCTAACGGCAAA 60.108 50.000 0.26 0.00 44.14 3.68
2218 4633 1.369091 ATCAGCGGCTAACGGCAAAG 61.369 55.000 0.26 0.00 44.14 2.77
2219 4634 2.032634 CAGCGGCTAACGGCAAAGA 61.033 57.895 0.26 0.00 44.14 2.52
2220 4635 1.302192 AGCGGCTAACGGCAAAGAA 60.302 52.632 0.00 0.00 44.14 2.52
2221 4636 0.887387 AGCGGCTAACGGCAAAGAAA 60.887 50.000 0.00 0.00 44.14 2.52
2222 4637 0.454452 GCGGCTAACGGCAAAGAAAG 60.454 55.000 0.00 0.00 44.51 2.62
2229 4644 2.561373 GGCAAAGAAAGCCGACGG 59.439 61.111 10.29 10.29 43.15 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.438108 TGACTTGCAGTATAAAGGTACAGGTA 59.562 38.462 0.00 0.00 0.00 3.08
9 10 5.247564 TGACTTGCAGTATAAAGGTACAGGT 59.752 40.000 0.00 0.00 0.00 4.00
10 11 5.730550 TGACTTGCAGTATAAAGGTACAGG 58.269 41.667 0.00 0.00 0.00 4.00
11 12 5.292101 GCTGACTTGCAGTATAAAGGTACAG 59.708 44.000 0.00 0.00 46.62 2.74
12 13 5.175859 GCTGACTTGCAGTATAAAGGTACA 58.824 41.667 0.00 0.00 46.62 2.90
63 65 5.646577 AGTACCTACTGACACATCTGTTC 57.353 43.478 0.00 0.00 38.01 3.18
130 160 5.758296 TCAGTAAGCACTTTCTACTTTGGTG 59.242 40.000 0.00 0.00 30.46 4.17
433 498 2.483714 GCTCATGCTCAGGTTCGGATAA 60.484 50.000 0.00 0.00 36.03 1.75
532 601 2.088423 TCGACAAGTGTTGGTGCTTTT 58.912 42.857 0.00 0.00 34.12 2.27
533 602 1.745232 TCGACAAGTGTTGGTGCTTT 58.255 45.000 0.00 0.00 34.12 3.51
583 768 2.936993 GCACAGGCAGTTGCATAGTACT 60.937 50.000 6.43 0.00 44.36 2.73
723 943 9.846248 CAAAATCTTATTTCGGACATCTTTTCT 57.154 29.630 0.00 0.00 0.00 2.52
799 1029 4.994471 CCAGCAGCCACGCACTCA 62.994 66.667 0.00 0.00 0.00 3.41
830 1062 1.400629 GCTACGACGCTGACAGTAACA 60.401 52.381 3.99 0.00 0.00 2.41
1021 1670 3.260483 GCTCCTCGTCATGCGCAG 61.260 66.667 18.32 8.46 41.07 5.18
1423 2146 5.084722 GTCATTTCATTCGCAGTTTCAGAG 58.915 41.667 0.00 0.00 0.00 3.35
1598 2645 9.715121 ACGGTAAGATCTGAAAAACAATAGTAA 57.285 29.630 0.00 0.00 0.00 2.24
1783 2839 1.889829 GTCCGAGTCTCCCCATATCTG 59.110 57.143 0.00 0.00 0.00 2.90
1784 2840 1.545875 CGTCCGAGTCTCCCCATATCT 60.546 57.143 0.00 0.00 0.00 1.98
1815 2878 2.590575 CAGTCCAACGTGGCGGTT 60.591 61.111 0.00 0.00 37.47 4.44
1816 2879 3.542676 TCAGTCCAACGTGGCGGT 61.543 61.111 0.00 0.00 37.47 5.68
1867 2930 4.324991 GGTGCCCTTCGGACCGTT 62.325 66.667 14.79 0.00 0.00 4.44
1877 2940 0.616111 AGAACTGATCGAGGTGCCCT 60.616 55.000 0.00 0.00 36.03 5.19
1882 2945 1.338200 GCACCAAGAACTGATCGAGGT 60.338 52.381 0.00 0.00 39.64 3.85
1887 2950 2.097142 GCATCTGCACCAAGAACTGATC 59.903 50.000 0.00 0.00 41.59 2.92
1957 3020 4.638304 TGTTCGGCTTAAATAGATAGGCC 58.362 43.478 0.00 0.00 42.82 5.19
1979 3042 3.315596 GGGCTAGGGTTATGGTTCTACT 58.684 50.000 0.00 0.00 0.00 2.57
1981 3044 2.322658 CGGGCTAGGGTTATGGTTCTA 58.677 52.381 0.00 0.00 0.00 2.10
1982 3045 1.129058 CGGGCTAGGGTTATGGTTCT 58.871 55.000 0.00 0.00 0.00 3.01
1986 3049 1.752833 GGACGGGCTAGGGTTATGG 59.247 63.158 0.00 0.00 0.00 2.74
1989 3052 3.149648 GCGGACGGGCTAGGGTTA 61.150 66.667 0.00 0.00 0.00 2.85
2023 3086 1.985662 ATGGTTACGAGGCGGTGGA 60.986 57.895 0.00 0.00 0.00 4.02
2043 3106 1.338136 ATTCCTGTAGTCTGCCGGGG 61.338 60.000 2.18 0.00 0.00 5.73
2053 3116 3.873952 GGCAAAGTAGCTGATTCCTGTAG 59.126 47.826 0.00 0.00 34.17 2.74
2054 3117 3.678806 CGGCAAAGTAGCTGATTCCTGTA 60.679 47.826 0.00 0.00 43.63 2.74
2056 3119 1.667724 CGGCAAAGTAGCTGATTCCTG 59.332 52.381 0.00 0.00 43.63 3.86
2057 3120 1.279271 ACGGCAAAGTAGCTGATTCCT 59.721 47.619 0.00 0.00 43.63 3.36
2058 3121 1.666189 GACGGCAAAGTAGCTGATTCC 59.334 52.381 0.00 0.00 43.63 3.01
2059 3122 2.349886 CAGACGGCAAAGTAGCTGATTC 59.650 50.000 0.00 0.00 43.63 2.52
2060 3123 2.350522 CAGACGGCAAAGTAGCTGATT 58.649 47.619 0.00 0.00 43.63 2.57
2062 3125 0.670546 GCAGACGGCAAAGTAGCTGA 60.671 55.000 0.00 0.00 43.63 4.26
2064 3127 2.111999 TGGCAGACGGCAAAGTAGCT 62.112 55.000 0.00 0.00 46.20 3.32
2065 3128 1.671054 TGGCAGACGGCAAAGTAGC 60.671 57.895 0.00 0.00 46.20 3.58
2066 3129 4.693532 TGGCAGACGGCAAAGTAG 57.306 55.556 0.00 0.00 46.20 2.57
2081 3144 3.726517 CTTTGCCGTCTGCCGTGG 61.727 66.667 0.00 0.00 40.16 4.94
2082 3145 3.726517 CCTTTGCCGTCTGCCGTG 61.727 66.667 0.00 0.00 40.16 4.94
2085 3148 3.273080 CTTGCCTTTGCCGTCTGCC 62.273 63.158 0.00 0.00 40.16 4.85
2086 3149 2.256461 CTTGCCTTTGCCGTCTGC 59.744 61.111 0.00 0.00 41.77 4.26
2088 3151 0.962356 CATCCTTGCCTTTGCCGTCT 60.962 55.000 0.00 0.00 36.33 4.18
2090 3153 1.978617 CCATCCTTGCCTTTGCCGT 60.979 57.895 0.00 0.00 36.33 5.68
2091 3154 2.887360 CCATCCTTGCCTTTGCCG 59.113 61.111 0.00 0.00 36.33 5.69
2092 3155 2.580815 GCCATCCTTGCCTTTGCC 59.419 61.111 0.00 0.00 36.33 4.52
2096 3159 2.044946 GTCCGCCATCCTTGCCTT 60.045 61.111 0.00 0.00 0.00 4.35
2100 3163 4.776322 TGCCGTCCGCCATCCTTG 62.776 66.667 0.00 0.00 36.24 3.61
2102 3165 3.561120 TTTTGCCGTCCGCCATCCT 62.561 57.895 0.00 0.00 36.24 3.24
2104 3167 2.485122 CTTTTGCCGTCCGCCATC 59.515 61.111 0.00 0.00 36.24 3.51
2105 3168 3.061848 CCTTTTGCCGTCCGCCAT 61.062 61.111 0.00 0.00 36.24 4.40
2109 3172 2.358737 AGAGCCTTTTGCCGTCCG 60.359 61.111 0.00 0.00 42.71 4.79
2110 3173 2.335712 CCAGAGCCTTTTGCCGTCC 61.336 63.158 0.00 0.00 42.71 4.79
2111 3174 2.982744 GCCAGAGCCTTTTGCCGTC 61.983 63.158 0.00 0.00 42.71 4.79
2113 3176 2.086251 TTTGCCAGAGCCTTTTGCCG 62.086 55.000 0.00 0.00 42.71 5.69
2117 3180 2.519013 CCTACTTTGCCAGAGCCTTTT 58.481 47.619 0.00 0.00 38.69 2.27
2120 3183 1.301293 GCCTACTTTGCCAGAGCCT 59.699 57.895 0.00 0.00 38.69 4.58
2121 3184 0.394899 ATGCCTACTTTGCCAGAGCC 60.395 55.000 0.00 0.00 38.69 4.70
2124 3187 0.107703 CCGATGCCTACTTTGCCAGA 60.108 55.000 0.00 0.00 0.00 3.86
2126 3189 0.906066 TACCGATGCCTACTTTGCCA 59.094 50.000 0.00 0.00 0.00 4.92
2128 3191 3.267483 TCTTTACCGATGCCTACTTTGC 58.733 45.455 0.00 0.00 0.00 3.68
2129 3192 3.309954 GCTCTTTACCGATGCCTACTTTG 59.690 47.826 0.00 0.00 0.00 2.77
2130 3193 3.197983 AGCTCTTTACCGATGCCTACTTT 59.802 43.478 0.00 0.00 0.00 2.66
2131 3194 2.766828 AGCTCTTTACCGATGCCTACTT 59.233 45.455 0.00 0.00 0.00 2.24
2132 3195 2.389715 AGCTCTTTACCGATGCCTACT 58.610 47.619 0.00 0.00 0.00 2.57
2135 3198 1.834263 AGAAGCTCTTTACCGATGCCT 59.166 47.619 0.00 0.00 0.00 4.75
2137 3200 3.729163 GCAAAGAAGCTCTTTACCGATGC 60.729 47.826 9.78 6.56 44.23 3.91
2138 3201 3.181506 GGCAAAGAAGCTCTTTACCGATG 60.182 47.826 10.34 2.38 44.23 3.84
2139 3202 3.010420 GGCAAAGAAGCTCTTTACCGAT 58.990 45.455 10.34 0.00 44.23 4.18
2140 3203 2.423577 GGCAAAGAAGCTCTTTACCGA 58.576 47.619 10.34 0.00 44.23 4.69
2144 3207 3.067106 CAGACGGCAAAGAAGCTCTTTA 58.933 45.455 9.78 0.00 44.23 1.85
2145 3208 1.876156 CAGACGGCAAAGAAGCTCTTT 59.124 47.619 0.00 5.61 46.75 2.52
2146 3209 1.517242 CAGACGGCAAAGAAGCTCTT 58.483 50.000 0.00 0.00 38.59 2.85
2147 3210 0.952984 GCAGACGGCAAAGAAGCTCT 60.953 55.000 0.00 0.00 43.97 4.09
2148 3211 1.499502 GCAGACGGCAAAGAAGCTC 59.500 57.895 0.00 0.00 43.97 4.09
2149 3212 3.660621 GCAGACGGCAAAGAAGCT 58.339 55.556 0.00 0.00 43.97 3.74
2167 3230 2.223386 CCTTTGTCGTCCGCTTCAAAAA 60.223 45.455 0.00 0.00 31.07 1.94
2168 3231 1.332375 CCTTTGTCGTCCGCTTCAAAA 59.668 47.619 0.00 0.00 31.07 2.44
2169 3232 0.941542 CCTTTGTCGTCCGCTTCAAA 59.058 50.000 0.00 0.00 0.00 2.69
2170 3233 0.882927 CCCTTTGTCGTCCGCTTCAA 60.883 55.000 0.00 0.00 0.00 2.69
2171 3234 1.301401 CCCTTTGTCGTCCGCTTCA 60.301 57.895 0.00 0.00 0.00 3.02
2174 3237 4.699522 GCCCCTTTGTCGTCCGCT 62.700 66.667 0.00 0.00 0.00 5.52
2176 3239 3.546714 AAGGCCCCTTTGTCGTCCG 62.547 63.158 0.00 0.00 31.29 4.79
2184 3247 1.961919 GCTGATAGCAAAGGCCCCTTT 60.962 52.381 6.48 6.48 45.98 3.11
2185 3248 0.396278 GCTGATAGCAAAGGCCCCTT 60.396 55.000 0.00 0.00 41.89 3.95
2186 3249 1.228510 GCTGATAGCAAAGGCCCCT 59.771 57.895 0.00 0.00 41.89 4.79
2188 3251 2.189499 CCGCTGATAGCAAAGGCCC 61.189 63.158 0.00 0.00 42.58 5.80
2202 4617 0.887387 TTTCTTTGCCGTTAGCCGCT 60.887 50.000 0.00 0.00 42.71 5.52
2203 4618 0.454452 CTTTCTTTGCCGTTAGCCGC 60.454 55.000 0.00 0.00 42.71 6.53
2204 4619 0.454452 GCTTTCTTTGCCGTTAGCCG 60.454 55.000 0.00 0.00 42.71 5.52
2205 4620 0.109272 GGCTTTCTTTGCCGTTAGCC 60.109 55.000 0.00 0.00 42.71 3.93
2206 4621 3.401577 GGCTTTCTTTGCCGTTAGC 57.598 52.632 0.00 0.00 41.03 3.09
2212 4627 2.561373 CCGTCGGCTTTCTTTGCC 59.439 61.111 0.00 0.00 46.42 4.52
2213 4628 2.126850 GCCGTCGGCTTTCTTTGC 60.127 61.111 28.98 0.00 46.69 3.68


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

AutoCloner maintained by Alex Coulton.