Multiple sequence alignment - TraesCS5D01G414900

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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 TraesCS5D01G414900 chr5D 100.000 4100 0 0 1 4100 477316200 477312101 0.000000e+00 7572.0
1 TraesCS5D01G414900 chr5D 100.000 263 0 0 4368 4630 477311833 477311571 1.940000e-133 486.0
2 TraesCS5D01G414900 chr5B 94.423 3317 139 18 771 4065 584887190 584883898 0.000000e+00 5059.0
3 TraesCS5D01G414900 chr5B 83.164 493 66 11 3 491 584893494 584893015 7.110000e-118 435.0
4 TraesCS5D01G414900 chr5B 96.212 264 9 1 4368 4630 584883497 584883234 9.200000e-117 431.0
5 TraesCS5D01G414900 chr5A 92.483 3299 197 21 820 4100 596523743 596520478 0.000000e+00 4671.0
6 TraesCS5D01G414900 chr5A 85.455 495 56 5 1 492 596524541 596524060 6.920000e-138 501.0
7 TraesCS5D01G414900 chr6B 82.609 115 20 0 4516 4630 574730300 574730186 8.200000e-18 102.0
8 TraesCS5D01G414900 chr3B 88.235 68 5 3 4560 4626 656559231 656559296 1.380000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G414900 chr5D 477311571 477316200 4629 True 4029 7572 100.0000 1 4630 2 chr5D.!!$R1 4629
1 TraesCS5D01G414900 chr5B 584883234 584887190 3956 True 2745 5059 95.3175 771 4630 2 chr5B.!!$R2 3859
2 TraesCS5D01G414900 chr5A 596520478 596524541 4063 True 2586 4671 88.9690 1 4100 2 chr5A.!!$R1 4099

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
378 381 0.027979 CATGGCCATTGTTCGCGTAG 59.972 55.0 17.92 0.0 0.00 3.51 F
742 818 0.036105 TCTGTGCGATTGACCAGCAT 60.036 50.0 0.00 0.0 43.17 3.79 F
777 853 0.179054 GACCAATAAGTCCTCCCGCC 60.179 60.0 0.00 0.0 0.00 6.13 F
2340 2432 0.036306 AGGTAACCACTTTGCTCCGG 59.964 55.0 0.00 0.0 37.17 5.14 F
2948 3040 0.883833 CCACAGATTCAGTGTTGCCC 59.116 55.0 8.21 0.0 35.24 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1724 0.321653 AGAACATGTGGTCGAAGCCC 60.322 55.000 0.00 0.00 36.72 5.19 R
2250 2342 1.131826 GAAAACATCCGGTGCGACG 59.868 57.895 0.00 0.00 0.00 5.12 R
2753 2845 5.066117 AGCAAGCATTGATCTACAAGTCATG 59.934 40.000 0.00 0.00 44.15 3.07 R
3225 3318 0.316204 TCGACTTTCCTCCGACAACC 59.684 55.000 0.00 0.00 0.00 3.77 R
4506 4715 0.043481 GACGACGACGACGACCTATC 60.043 60.000 25.15 8.87 42.66 2.08 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
35 36 7.786046 TTGTAGACCTAACTAGGATCACAAA 57.214 36.000 9.83 0.00 46.63 2.83
47 48 3.007940 AGGATCACAAATGAAGTGGTCGA 59.992 43.478 0.00 0.00 45.74 4.20
61 62 1.040646 GGTCGATCCATCTAGCACCA 58.959 55.000 0.00 0.00 35.97 4.17
77 78 2.028748 GCACCATCAACTGAAGCCATTT 60.029 45.455 0.00 0.00 0.00 2.32
129 130 5.568392 AGTATACCCTTGTAGGTAGGATCG 58.432 45.833 0.00 0.00 45.46 3.69
146 147 5.003160 AGGATCGACACAAATTGAACATCA 58.997 37.500 0.00 0.00 0.00 3.07
177 178 3.070429 GCCACTTGAGCCAATAATTCG 57.930 47.619 0.00 0.00 0.00 3.34
182 183 5.327091 CACTTGAGCCAATAATTCGTTCTG 58.673 41.667 0.00 0.00 0.00 3.02
184 185 5.882557 ACTTGAGCCAATAATTCGTTCTGAT 59.117 36.000 0.00 0.00 0.00 2.90
185 186 6.375455 ACTTGAGCCAATAATTCGTTCTGATT 59.625 34.615 0.00 0.00 0.00 2.57
186 187 6.122850 TGAGCCAATAATTCGTTCTGATTG 57.877 37.500 0.00 0.00 0.00 2.67
199 200 5.091431 CGTTCTGATTGAAGCAATTTCTCC 58.909 41.667 0.00 0.00 33.90 3.71
203 204 3.125146 TGATTGAAGCAATTTCTCCGACG 59.875 43.478 0.00 0.00 33.90 5.12
206 207 1.061276 GAAGCAATTTCTCCGACGCTC 59.939 52.381 0.00 0.00 32.83 5.03
211 212 0.802607 ATTTCTCCGACGCTCGCTTC 60.803 55.000 0.00 0.00 38.82 3.86
220 221 3.567797 GCTCGCTTCGGCACCATC 61.568 66.667 0.00 0.00 41.88 3.51
221 222 2.892425 CTCGCTTCGGCACCATCC 60.892 66.667 0.00 0.00 41.88 3.51
222 223 3.376935 CTCGCTTCGGCACCATCCT 62.377 63.158 0.00 0.00 41.88 3.24
223 224 2.892425 CGCTTCGGCACCATCCTC 60.892 66.667 0.00 0.00 41.88 3.71
224 225 2.892425 GCTTCGGCACCATCCTCG 60.892 66.667 0.00 0.00 41.33 4.63
225 226 2.202932 CTTCGGCACCATCCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
226 227 4.467084 TTCGGCACCATCCTCGGC 62.467 66.667 0.00 0.00 0.00 5.54
235 236 1.293498 CATCCTCGGCCCCTATTCG 59.707 63.158 0.00 0.00 0.00 3.34
245 246 3.596214 GGCCCCTATTCGTGTATATGTG 58.404 50.000 0.00 0.00 0.00 3.21
248 249 3.596214 CCCTATTCGTGTATATGTGGCC 58.404 50.000 0.00 0.00 0.00 5.36
253 254 4.955925 TTCGTGTATATGTGGCCTTTTG 57.044 40.909 3.32 0.00 0.00 2.44
255 256 3.936453 TCGTGTATATGTGGCCTTTTGTC 59.064 43.478 3.32 0.00 0.00 3.18
339 342 8.758829 GTCTATTTTTATGGGAAAATGGGTTCT 58.241 33.333 5.99 0.00 39.05 3.01
350 353 5.127194 GGAAAATGGGTTCTATTCCAAGTCC 59.873 44.000 0.00 0.00 39.45 3.85
352 355 4.510167 ATGGGTTCTATTCCAAGTCCAG 57.490 45.455 0.00 0.00 36.54 3.86
354 357 3.655777 TGGGTTCTATTCCAAGTCCAGTT 59.344 43.478 0.00 0.00 0.00 3.16
374 377 2.495866 CCCATGGCCATTGTTCGC 59.504 61.111 17.92 0.00 0.00 4.70
378 381 0.027979 CATGGCCATTGTTCGCGTAG 59.972 55.000 17.92 0.00 0.00 3.51
380 383 0.320858 TGGCCATTGTTCGCGTAGAA 60.321 50.000 0.00 0.66 36.31 2.10
408 411 2.632996 TCCTATTCCTCACCTATTGCGG 59.367 50.000 0.00 0.00 0.00 5.69
436 439 2.415512 GTCGCCTATTCACACAAGGAAC 59.584 50.000 0.00 0.00 31.64 3.62
439 442 2.749621 GCCTATTCACACAAGGAACCAG 59.250 50.000 0.00 0.00 31.64 4.00
441 444 2.363306 ATTCACACAAGGAACCAGCA 57.637 45.000 0.00 0.00 0.00 4.41
447 450 0.261696 ACAAGGAACCAGCAAAGGGT 59.738 50.000 0.00 0.00 41.41 4.34
449 452 2.162681 CAAGGAACCAGCAAAGGGTAG 58.837 52.381 0.00 0.00 37.77 3.18
461 465 0.044855 AAGGGTAGGTGAGATGGCCT 59.955 55.000 3.32 0.00 38.81 5.19
480 484 4.102054 GGCCTACCCATTTAGTTAGCTACA 59.898 45.833 0.00 0.00 0.00 2.74
484 488 7.121611 GCCTACCCATTTAGTTAGCTACAAAAA 59.878 37.037 0.00 0.00 0.00 1.94
485 489 9.185680 CCTACCCATTTAGTTAGCTACAAAAAT 57.814 33.333 0.00 0.00 0.00 1.82
487 491 8.063200 ACCCATTTAGTTAGCTACAAAAATCC 57.937 34.615 0.00 0.00 0.00 3.01
488 492 7.123697 ACCCATTTAGTTAGCTACAAAAATCCC 59.876 37.037 0.00 0.00 0.00 3.85
489 493 7.342026 CCCATTTAGTTAGCTACAAAAATCCCT 59.658 37.037 0.00 0.00 0.00 4.20
490 494 8.749354 CCATTTAGTTAGCTACAAAAATCCCTT 58.251 33.333 0.00 0.00 0.00 3.95
496 500 2.500098 GCTACAAAAATCCCTTTCCCCC 59.500 50.000 0.00 0.00 0.00 5.40
501 505 4.480537 ACAAAAATCCCTTTCCCCCTTTTT 59.519 37.500 0.00 0.00 0.00 1.94
722 798 1.005450 ACTGGCCGAATTATGGGTTGT 59.995 47.619 0.00 0.00 0.00 3.32
725 801 2.291282 TGGCCGAATTATGGGTTGTTCT 60.291 45.455 0.00 0.00 0.00 3.01
738 814 1.601903 GTTGTTCTGTGCGATTGACCA 59.398 47.619 0.00 0.00 0.00 4.02
739 815 1.511850 TGTTCTGTGCGATTGACCAG 58.488 50.000 0.00 0.00 0.00 4.00
740 816 0.166814 GTTCTGTGCGATTGACCAGC 59.833 55.000 0.00 0.00 0.00 4.85
741 817 0.250252 TTCTGTGCGATTGACCAGCA 60.250 50.000 0.00 0.00 38.71 4.41
742 818 0.036105 TCTGTGCGATTGACCAGCAT 60.036 50.000 0.00 0.00 43.17 3.79
743 819 0.806868 CTGTGCGATTGACCAGCATT 59.193 50.000 0.00 0.00 43.17 3.56
744 820 1.200716 CTGTGCGATTGACCAGCATTT 59.799 47.619 0.00 0.00 43.17 2.32
745 821 2.419673 CTGTGCGATTGACCAGCATTTA 59.580 45.455 0.00 0.00 43.17 1.40
746 822 2.419673 TGTGCGATTGACCAGCATTTAG 59.580 45.455 0.00 0.00 43.17 1.85
747 823 2.420022 GTGCGATTGACCAGCATTTAGT 59.580 45.455 0.00 0.00 43.17 2.24
748 824 2.677836 TGCGATTGACCAGCATTTAGTC 59.322 45.455 0.00 0.00 35.81 2.59
749 825 2.285834 GCGATTGACCAGCATTTAGTCG 60.286 50.000 0.00 0.00 33.09 4.18
750 826 2.285834 CGATTGACCAGCATTTAGTCGC 60.286 50.000 0.00 0.00 33.09 5.19
751 827 2.177394 TTGACCAGCATTTAGTCGCA 57.823 45.000 0.00 0.00 33.09 5.10
752 828 2.177394 TGACCAGCATTTAGTCGCAA 57.823 45.000 0.00 0.00 33.09 4.85
753 829 2.499197 TGACCAGCATTTAGTCGCAAA 58.501 42.857 0.00 0.00 33.09 3.68
754 830 2.483877 TGACCAGCATTTAGTCGCAAAG 59.516 45.455 0.00 0.00 33.09 2.77
755 831 2.742053 GACCAGCATTTAGTCGCAAAGA 59.258 45.455 0.00 0.00 0.00 2.52
756 832 2.744202 ACCAGCATTTAGTCGCAAAGAG 59.256 45.455 0.00 0.00 0.00 2.85
757 833 2.476854 CCAGCATTTAGTCGCAAAGAGC 60.477 50.000 0.00 0.00 40.87 4.09
769 845 3.391227 GCAAAGAGCGACCAATAAGTC 57.609 47.619 0.00 0.00 0.00 3.01
770 846 2.096013 GCAAAGAGCGACCAATAAGTCC 59.904 50.000 0.00 0.00 32.91 3.85
771 847 3.600388 CAAAGAGCGACCAATAAGTCCT 58.400 45.455 0.00 0.00 32.91 3.85
772 848 3.528597 AAGAGCGACCAATAAGTCCTC 57.471 47.619 0.00 0.00 35.77 3.71
773 849 1.757699 AGAGCGACCAATAAGTCCTCC 59.242 52.381 0.00 0.00 35.97 4.30
774 850 0.831307 AGCGACCAATAAGTCCTCCC 59.169 55.000 0.00 0.00 32.91 4.30
775 851 0.529992 GCGACCAATAAGTCCTCCCG 60.530 60.000 0.00 0.00 32.91 5.14
776 852 0.529992 CGACCAATAAGTCCTCCCGC 60.530 60.000 0.00 0.00 32.91 6.13
777 853 0.179054 GACCAATAAGTCCTCCCGCC 60.179 60.000 0.00 0.00 0.00 6.13
778 854 1.227556 CCAATAAGTCCTCCCGCCG 60.228 63.158 0.00 0.00 0.00 6.46
794 870 2.660612 CCGTAAACACGCCGTCACC 61.661 63.158 0.00 0.00 0.00 4.02
803 879 2.813908 GCCGTCACCAACTAGGCG 60.814 66.667 0.00 0.00 43.14 5.52
818 894 2.813908 GCGTTGTAGCCCACGAGG 60.814 66.667 0.00 0.00 39.47 4.63
897 973 4.775236 AGATATTTGCCTCTCACTTCACC 58.225 43.478 0.00 0.00 0.00 4.02
905 981 2.280797 TCACTTCACCTGTGCGCC 60.281 61.111 4.18 0.00 35.58 6.53
931 1011 1.217244 GGCACGACACCTTATCCGT 59.783 57.895 0.00 0.00 35.46 4.69
991 1071 2.750637 GTCGCCACTCCTCCTCGA 60.751 66.667 0.00 0.00 0.00 4.04
995 1075 2.419739 GCCACTCCTCCTCGACTCC 61.420 68.421 0.00 0.00 0.00 3.85
1005 1085 3.273654 TCGACTCCCCCACTCCCT 61.274 66.667 0.00 0.00 0.00 4.20
1459 1539 2.421619 GTGCTTGTTCCTCCTTCTGAG 58.578 52.381 0.00 0.00 41.07 3.35
1483 1563 3.857854 CACCGCGCTGCTGATGTC 61.858 66.667 5.56 0.00 0.00 3.06
1774 1854 3.560068 GGCGAAAAGGTATGTATGTCCTG 59.440 47.826 0.00 0.00 0.00 3.86
1808 1888 4.059511 CTCAATGATCAGACATCAGAGGC 58.940 47.826 0.09 0.00 33.15 4.70
2187 2279 2.160205 GGAAGCTTTAAAGGCTCGGTT 58.840 47.619 16.78 3.15 39.30 4.44
2250 2342 3.070878 TGAAACCCAAAGGCATTTTCTCC 59.929 43.478 0.00 0.00 36.11 3.71
2338 2430 2.615747 GGAGAGGTAACCACTTTGCTCC 60.616 54.545 0.00 0.00 34.55 4.70
2340 2432 0.036306 AGGTAACCACTTTGCTCCGG 59.964 55.000 0.00 0.00 37.17 5.14
2356 2448 3.251571 CTCCGGAGTTTACTACACTTGC 58.748 50.000 24.04 0.00 0.00 4.01
2380 2472 2.917971 GCTCACGTGACACTAGATTGAC 59.082 50.000 15.76 0.00 0.00 3.18
2686 2778 4.764823 TGTCAAGGGAATGTATGTTCAACC 59.235 41.667 0.00 0.00 0.00 3.77
2753 2845 7.555306 AGGAGATTATTAACCGCTTTTCTTC 57.445 36.000 0.00 0.00 0.00 2.87
2942 3034 2.693069 GTCAGGACCACAGATTCAGTG 58.307 52.381 2.40 2.40 36.76 3.66
2945 3037 2.810274 CAGGACCACAGATTCAGTGTTG 59.190 50.000 8.21 0.00 35.24 3.33
2948 3040 0.883833 CCACAGATTCAGTGTTGCCC 59.116 55.000 8.21 0.00 35.24 5.36
2956 3048 3.518634 TTCAGTGTTGCCCTTTTGAAC 57.481 42.857 0.00 0.00 0.00 3.18
2969 3062 3.058777 CCTTTTGAACCATTTGTGCATGC 60.059 43.478 11.82 11.82 30.56 4.06
2987 3080 5.210715 GCATGCTGCATGAGTTACTAAATC 58.789 41.667 38.70 17.21 43.81 2.17
2990 3083 5.491070 TGCTGCATGAGTTACTAAATCTGT 58.509 37.500 0.00 0.00 0.00 3.41
2991 3084 5.939883 TGCTGCATGAGTTACTAAATCTGTT 59.060 36.000 0.00 0.00 0.00 3.16
3021 3114 4.494091 TCTTTTCCATCAGACTGATCCC 57.506 45.455 15.24 0.00 34.28 3.85
3036 3129 3.762288 CTGATCCCGGAATTCCTATCGTA 59.238 47.826 22.05 6.96 0.00 3.43
3109 3202 1.008079 GCTCAGGTGTGTGCAAAGC 60.008 57.895 0.00 0.00 41.84 3.51
3110 3203 1.450531 GCTCAGGTGTGTGCAAAGCT 61.451 55.000 0.00 0.00 41.84 3.74
3111 3204 1.027357 CTCAGGTGTGTGCAAAGCTT 58.973 50.000 0.00 0.00 0.00 3.74
3114 3207 1.134753 CAGGTGTGTGCAAAGCTTCAA 59.865 47.619 0.00 0.00 0.00 2.69
3116 3209 2.431782 AGGTGTGTGCAAAGCTTCAAAT 59.568 40.909 0.00 0.00 0.00 2.32
3118 3211 3.735746 GGTGTGTGCAAAGCTTCAAATAC 59.264 43.478 0.00 0.00 0.00 1.89
3119 3212 3.421888 GTGTGTGCAAAGCTTCAAATACG 59.578 43.478 0.00 0.00 0.00 3.06
3120 3213 2.405025 GTGTGCAAAGCTTCAAATACGC 59.595 45.455 0.00 0.00 0.00 4.42
3121 3214 2.293122 TGTGCAAAGCTTCAAATACGCT 59.707 40.909 0.00 0.00 35.09 5.07
3127 3220 5.390991 GCAAAGCTTCAAATACGCTACTTCT 60.391 40.000 0.00 0.00 32.90 2.85
3149 3242 3.870723 TTTTCATGGTTGTCTTCGACG 57.129 42.857 0.00 0.00 34.95 5.12
3151 3244 3.313012 TTCATGGTTGTCTTCGACGAT 57.687 42.857 0.00 0.00 34.95 3.73
3160 3253 4.274421 TGTCTTCGACGATCACTGTATC 57.726 45.455 0.00 0.00 34.95 2.24
3171 3264 4.500837 CGATCACTGTATCAACTGCTACAC 59.499 45.833 0.00 0.00 0.00 2.90
3176 3269 7.382898 TCACTGTATCAACTGCTACACATTTA 58.617 34.615 0.00 0.00 0.00 1.40
3184 3277 8.397575 TCAACTGCTACACATTTATGGTTTAA 57.602 30.769 0.00 0.00 0.00 1.52
3186 3279 9.289303 CAACTGCTACACATTTATGGTTTAATC 57.711 33.333 0.00 0.00 0.00 1.75
3189 3282 8.574251 TGCTACACATTTATGGTTTAATCTGT 57.426 30.769 0.00 0.00 0.00 3.41
3213 3306 2.749044 CTGTGGGCGCTGCAAGAT 60.749 61.111 7.64 0.00 34.07 2.40
3225 3318 2.417933 GCTGCAAGATGGAACTACAGTG 59.582 50.000 0.00 0.00 34.07 3.66
3358 3455 2.560981 TCAAGTACTGCGTGAGGATTCA 59.439 45.455 0.00 0.00 32.08 2.57
3380 3477 5.538053 TCATTTTGTTGGGTTGAGATTGCTA 59.462 36.000 0.00 0.00 0.00 3.49
3427 3526 3.515502 TGGTTCATAGACAAGTCCCTCTG 59.484 47.826 0.00 0.00 0.00 3.35
3466 3566 9.219603 TCTTACATTCTATTTGGTGAAGACAAG 57.780 33.333 0.00 0.00 0.00 3.16
3479 3579 5.468746 GGTGAAGACAAGTACTGTTGCAATA 59.531 40.000 0.59 0.00 38.84 1.90
3506 3606 6.236409 ACTATGTATTCATCATTGAGGCCAG 58.764 40.000 5.01 0.00 35.70 4.85
3526 3626 4.153475 CCAGATTTGCTTGCAAGGAAAATG 59.847 41.667 38.43 34.94 46.83 2.32
3586 3686 5.505173 AAAGGAAACTGATGTTGTCACTG 57.495 39.130 0.00 0.00 42.68 3.66
3702 3803 5.885912 TGGTCTCTTACTTTCTTTGTTTGCT 59.114 36.000 0.00 0.00 0.00 3.91
4052 4163 2.613474 GGCCCGTGTTGTACTCAATGTA 60.613 50.000 0.00 0.00 35.92 2.29
4054 4165 3.863400 GCCCGTGTTGTACTCAATGTAGT 60.863 47.826 0.00 0.00 35.92 2.73
4070 4181 4.857130 TGTAGTCTAGAACCTGGCTCTA 57.143 45.455 6.65 6.65 0.00 2.43
4072 4183 4.473922 TGTAGTCTAGAACCTGGCTCTAGA 59.526 45.833 25.69 25.69 45.85 2.43
4077 4188 2.462723 AGAACCTGGCTCTAGAGGAAC 58.537 52.381 21.23 4.65 33.16 3.62
4086 4197 3.526534 GCTCTAGAGGAACGCTTGAATT 58.473 45.455 21.23 0.00 39.41 2.17
4088 4199 4.748892 CTCTAGAGGAACGCTTGAATTCA 58.251 43.478 12.27 3.38 39.41 2.57
4089 4200 4.748892 TCTAGAGGAACGCTTGAATTCAG 58.251 43.478 8.41 4.57 40.42 3.02
4096 4207 4.368315 GAACGCTTGAATTCAGGGTTTTT 58.632 39.130 25.86 14.35 38.51 1.94
4097 4208 3.977427 ACGCTTGAATTCAGGGTTTTTC 58.023 40.909 18.18 0.84 0.00 2.29
4098 4209 3.383185 ACGCTTGAATTCAGGGTTTTTCA 59.617 39.130 18.18 0.00 0.00 2.69
4099 4210 4.039124 ACGCTTGAATTCAGGGTTTTTCAT 59.961 37.500 18.18 0.00 0.00 2.57
4422 4631 3.426859 GGCAATGACGACTTAGATCATCG 59.573 47.826 0.00 1.27 41.60 3.84
4450 4659 4.083862 GTGCTCCTCCCCACCGTC 62.084 72.222 0.00 0.00 0.00 4.79
4488 4697 3.382832 CCCGTCTCCGTCTTGCCT 61.383 66.667 0.00 0.00 0.00 4.75
4506 4715 1.078918 TGCCTTGTCTCCAGCATCG 60.079 57.895 0.00 0.00 0.00 3.84
4555 4764 0.748005 ACAAGCATCATACGGCCACC 60.748 55.000 2.24 0.00 0.00 4.61
4556 4765 1.152963 AAGCATCATACGGCCACCC 60.153 57.895 2.24 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.786046 TTTGTGATCCTAGTTAGGTCTACAA 57.214 36.000 5.16 10.75 44.02 2.41
12 13 7.618117 TCATTTGTGATCCTAGTTAGGTCTACA 59.382 37.037 5.16 6.21 44.02 2.74
14 15 8.603898 TTCATTTGTGATCCTAGTTAGGTCTA 57.396 34.615 5.16 0.00 44.02 2.59
27 28 4.034510 GGATCGACCACTTCATTTGTGATC 59.965 45.833 0.00 0.00 37.60 2.92
47 48 3.713248 TCAGTTGATGGTGCTAGATGGAT 59.287 43.478 0.00 0.00 0.00 3.41
129 130 8.170553 GCCAAATATTGATGTTCAATTTGTGTC 58.829 33.333 7.94 0.00 44.03 3.67
146 147 1.750778 CTCAAGTGGCCGCCAAATATT 59.249 47.619 15.39 4.13 34.18 1.28
177 178 5.091431 CGGAGAAATTGCTTCAATCAGAAC 58.909 41.667 0.00 0.00 36.40 3.01
182 183 3.674423 CGTCGGAGAAATTGCTTCAATC 58.326 45.455 0.00 0.00 39.69 2.67
184 185 1.196808 GCGTCGGAGAAATTGCTTCAA 59.803 47.619 0.00 0.00 39.69 2.69
185 186 0.796312 GCGTCGGAGAAATTGCTTCA 59.204 50.000 0.00 0.00 39.69 3.02
186 187 1.061276 GAGCGTCGGAGAAATTGCTTC 59.939 52.381 0.00 0.00 39.69 3.86
203 204 3.567797 GATGGTGCCGAAGCGAGC 61.568 66.667 0.00 0.00 44.31 5.03
206 207 2.892425 GAGGATGGTGCCGAAGCG 60.892 66.667 0.00 0.00 44.31 4.68
215 216 1.073706 AATAGGGGCCGAGGATGGT 60.074 57.895 0.00 0.00 0.00 3.55
219 220 2.131709 CACGAATAGGGGCCGAGGA 61.132 63.158 0.00 0.00 0.00 3.71
220 221 1.111116 TACACGAATAGGGGCCGAGG 61.111 60.000 0.00 0.00 0.00 4.63
221 222 0.966920 ATACACGAATAGGGGCCGAG 59.033 55.000 0.00 0.00 0.00 4.63
222 223 2.291209 TATACACGAATAGGGGCCGA 57.709 50.000 0.00 0.00 0.00 5.54
223 224 2.232941 ACATATACACGAATAGGGGCCG 59.767 50.000 0.00 0.00 0.00 6.13
224 225 3.596214 CACATATACACGAATAGGGGCC 58.404 50.000 0.00 0.00 0.00 5.80
225 226 3.596214 CCACATATACACGAATAGGGGC 58.404 50.000 0.00 0.00 0.00 5.80
226 227 3.596214 GCCACATATACACGAATAGGGG 58.404 50.000 0.00 0.00 0.00 4.79
227 228 3.260884 AGGCCACATATACACGAATAGGG 59.739 47.826 5.01 0.00 0.00 3.53
228 229 4.537135 AGGCCACATATACACGAATAGG 57.463 45.455 5.01 0.00 0.00 2.57
229 230 6.260050 ACAAAAGGCCACATATACACGAATAG 59.740 38.462 5.01 0.00 0.00 1.73
230 231 6.116806 ACAAAAGGCCACATATACACGAATA 58.883 36.000 5.01 0.00 0.00 1.75
235 236 3.936453 TCGACAAAAGGCCACATATACAC 59.064 43.478 5.01 0.00 0.00 2.90
245 246 5.560953 GCACATAATCTATCGACAAAAGGCC 60.561 44.000 0.00 0.00 0.00 5.19
310 311 9.722317 ACCCATTTTCCCATAAAAATAGACATA 57.278 29.630 0.00 0.00 36.86 2.29
311 312 8.622572 ACCCATTTTCCCATAAAAATAGACAT 57.377 30.769 0.00 0.00 36.86 3.06
312 313 8.442660 AACCCATTTTCCCATAAAAATAGACA 57.557 30.769 0.00 0.00 36.86 3.41
313 314 8.758829 AGAACCCATTTTCCCATAAAAATAGAC 58.241 33.333 0.00 0.00 36.86 2.59
335 338 4.876679 GGCTAACTGGACTTGGAATAGAAC 59.123 45.833 0.00 0.00 0.00 3.01
339 342 3.186283 TGGGCTAACTGGACTTGGAATA 58.814 45.455 0.00 0.00 0.00 1.75
368 371 2.602878 GATTCACCTTCTACGCGAACA 58.397 47.619 15.93 0.00 0.00 3.18
370 373 2.288961 GGATTCACCTTCTACGCGAA 57.711 50.000 15.93 0.00 35.41 4.70
418 421 2.749621 CTGGTTCCTTGTGTGAATAGGC 59.250 50.000 0.00 0.00 0.00 3.93
421 424 3.500448 TGCTGGTTCCTTGTGTGAATA 57.500 42.857 0.00 0.00 0.00 1.75
436 439 0.984230 TCTCACCTACCCTTTGCTGG 59.016 55.000 0.00 0.00 0.00 4.85
439 442 2.019156 GCCATCTCACCTACCCTTTGC 61.019 57.143 0.00 0.00 0.00 3.68
441 444 0.919710 GGCCATCTCACCTACCCTTT 59.080 55.000 0.00 0.00 0.00 3.11
447 450 0.639943 TGGGTAGGCCATCTCACCTA 59.360 55.000 5.01 0.00 37.50 3.08
449 452 0.846693 AATGGGTAGGCCATCTCACC 59.153 55.000 5.01 3.58 36.17 4.02
461 465 9.181061 GGATTTTTGTAGCTAACTAAATGGGTA 57.819 33.333 10.99 0.00 33.72 3.69
472 476 5.020795 GGGGAAAGGGATTTTTGTAGCTAA 58.979 41.667 0.00 0.00 0.00 3.09
564 610 8.868522 TGTGGACATTCTTTAAGAATTCTGAT 57.131 30.769 16.59 0.00 41.90 2.90
565 611 8.690203 TTGTGGACATTCTTTAAGAATTCTGA 57.310 30.769 16.59 0.00 41.90 3.27
566 612 9.918630 AATTGTGGACATTCTTTAAGAATTCTG 57.081 29.630 16.59 10.63 41.90 3.02
685 759 6.431543 TCGGCCAGTCAAGATTTTACATTAAA 59.568 34.615 2.24 0.00 0.00 1.52
688 762 4.331968 TCGGCCAGTCAAGATTTTACATT 58.668 39.130 2.24 0.00 0.00 2.71
689 763 3.950397 TCGGCCAGTCAAGATTTTACAT 58.050 40.909 2.24 0.00 0.00 2.29
691 765 4.965119 ATTCGGCCAGTCAAGATTTTAC 57.035 40.909 2.24 0.00 0.00 2.01
722 798 0.250252 TGCTGGTCAATCGCACAGAA 60.250 50.000 0.00 0.00 32.86 3.02
725 801 1.246649 AAATGCTGGTCAATCGCACA 58.753 45.000 0.00 0.00 36.37 4.57
749 825 2.096013 GGACTTATTGGTCGCTCTTTGC 59.904 50.000 0.00 0.00 37.12 3.68
750 826 3.600388 AGGACTTATTGGTCGCTCTTTG 58.400 45.455 0.00 0.00 37.12 2.77
751 827 3.369576 GGAGGACTTATTGGTCGCTCTTT 60.370 47.826 0.00 0.00 37.12 2.52
752 828 2.168728 GGAGGACTTATTGGTCGCTCTT 59.831 50.000 0.00 0.00 37.12 2.85
753 829 1.757699 GGAGGACTTATTGGTCGCTCT 59.242 52.381 0.00 0.00 37.12 4.09
754 830 1.202545 GGGAGGACTTATTGGTCGCTC 60.203 57.143 0.00 0.00 37.12 5.03
755 831 0.831307 GGGAGGACTTATTGGTCGCT 59.169 55.000 0.00 0.00 37.12 4.93
756 832 0.529992 CGGGAGGACTTATTGGTCGC 60.530 60.000 0.00 0.00 37.12 5.19
757 833 0.529992 GCGGGAGGACTTATTGGTCG 60.530 60.000 0.00 0.00 37.12 4.79
758 834 0.179054 GGCGGGAGGACTTATTGGTC 60.179 60.000 0.00 0.00 35.66 4.02
759 835 1.912971 GGCGGGAGGACTTATTGGT 59.087 57.895 0.00 0.00 0.00 3.67
760 836 1.227556 CGGCGGGAGGACTTATTGG 60.228 63.158 0.00 0.00 0.00 3.16
761 837 0.748450 TACGGCGGGAGGACTTATTG 59.252 55.000 13.24 0.00 0.00 1.90
762 838 1.488390 TTACGGCGGGAGGACTTATT 58.512 50.000 13.24 0.00 0.00 1.40
763 839 1.137675 GTTTACGGCGGGAGGACTTAT 59.862 52.381 13.24 0.00 0.00 1.73
764 840 0.532115 GTTTACGGCGGGAGGACTTA 59.468 55.000 13.24 0.00 0.00 2.24
765 841 1.294459 GTTTACGGCGGGAGGACTT 59.706 57.895 13.24 0.00 0.00 3.01
766 842 1.909781 TGTTTACGGCGGGAGGACT 60.910 57.895 13.24 0.00 0.00 3.85
767 843 1.739196 GTGTTTACGGCGGGAGGAC 60.739 63.158 13.24 3.00 0.00 3.85
768 844 2.658422 GTGTTTACGGCGGGAGGA 59.342 61.111 13.24 0.00 0.00 3.71
769 845 2.812178 CGTGTTTACGGCGGGAGG 60.812 66.667 13.24 0.00 46.23 4.30
778 854 0.041926 GTTGGTGACGGCGTGTTTAC 60.042 55.000 21.19 10.99 0.00 2.01
817 893 0.460459 GGTTCTAGCTTCTCGTGGCC 60.460 60.000 0.00 0.00 0.00 5.36
818 894 0.460459 GGGTTCTAGCTTCTCGTGGC 60.460 60.000 0.00 0.00 0.00 5.01
819 895 0.179134 CGGGTTCTAGCTTCTCGTGG 60.179 60.000 0.00 0.00 0.00 4.94
820 896 0.526662 ACGGGTTCTAGCTTCTCGTG 59.473 55.000 0.00 0.00 0.00 4.35
821 897 2.119801 TACGGGTTCTAGCTTCTCGT 57.880 50.000 0.00 10.32 0.00 4.18
822 898 4.320348 CCTTATACGGGTTCTAGCTTCTCG 60.320 50.000 0.00 0.00 0.00 4.04
823 899 4.826183 TCCTTATACGGGTTCTAGCTTCTC 59.174 45.833 0.00 0.00 0.00 2.87
824 900 4.801164 TCCTTATACGGGTTCTAGCTTCT 58.199 43.478 0.00 0.00 0.00 2.85
955 1035 2.099062 CATCGTTGGCTCGCTTGC 59.901 61.111 0.00 0.00 0.00 4.01
956 1036 2.099062 GCATCGTTGGCTCGCTTG 59.901 61.111 0.00 0.00 0.00 4.01
988 1068 3.273654 AGGGAGTGGGGGAGTCGA 61.274 66.667 0.00 0.00 0.00 4.20
991 1071 2.876858 AGGAGGGAGTGGGGGAGT 60.877 66.667 0.00 0.00 0.00 3.85
995 1075 2.041405 GAGGAGGAGGGAGTGGGG 60.041 72.222 0.00 0.00 0.00 4.96
1351 1431 2.853914 GACAGCGTTCGCTTGGTC 59.146 61.111 17.05 17.09 39.76 4.02
1360 1440 2.338984 GACAGGACCGACAGCGTT 59.661 61.111 0.00 0.00 35.23 4.84
1483 1563 0.677731 TCCCGGAAGCATTTGAGCAG 60.678 55.000 0.73 0.00 36.85 4.24
1644 1724 0.321653 AGAACATGTGGTCGAAGCCC 60.322 55.000 0.00 0.00 36.72 5.19
1704 1784 2.182842 GGTGCAGGCCATTAGCGAG 61.183 63.158 5.01 0.00 45.17 5.03
1710 1790 1.607467 GGTGAAGGTGCAGGCCATT 60.607 57.895 5.01 0.00 0.00 3.16
1774 1854 3.867493 TGATCATTGAGCTCGTGATGAAC 59.133 43.478 28.69 23.55 33.03 3.18
1808 1888 5.048643 ACCTGATATTAACAGTCGATCCTCG 60.049 44.000 0.00 0.00 35.59 4.63
2088 2180 2.900273 GCATACCGACCAGCCAGA 59.100 61.111 0.00 0.00 0.00 3.86
2202 2294 4.889832 ATCTCCAATGACGAAATTCAGC 57.110 40.909 0.00 0.00 0.00 4.26
2250 2342 1.131826 GAAAACATCCGGTGCGACG 59.868 57.895 0.00 0.00 0.00 5.12
2396 2488 8.558973 AAAATTGTGAAACCTGACAAATTCAA 57.441 26.923 0.00 0.00 35.76 2.69
2686 2778 8.160106 ACATTATTAGCTCAGGATAGGGAAAAG 58.840 37.037 0.00 0.00 0.00 2.27
2753 2845 5.066117 AGCAAGCATTGATCTACAAGTCATG 59.934 40.000 0.00 0.00 44.15 3.07
2930 3022 1.901591 AGGGCAACACTGAATCTGTG 58.098 50.000 16.95 16.95 38.85 3.66
2942 3034 3.312146 CACAAATGGTTCAAAAGGGCAAC 59.688 43.478 0.00 0.00 0.00 4.17
2945 3037 1.872952 GCACAAATGGTTCAAAAGGGC 59.127 47.619 0.00 0.00 0.00 5.19
2948 3040 3.810941 AGCATGCACAAATGGTTCAAAAG 59.189 39.130 21.98 0.00 34.71 2.27
2969 3062 8.292448 ACAAAACAGATTTAGTAACTCATGCAG 58.708 33.333 3.39 0.00 0.00 4.41
2987 3080 9.748708 TCTGATGGAAAAGAAAATACAAAACAG 57.251 29.630 0.00 0.00 0.00 3.16
2990 3083 9.748708 CAGTCTGATGGAAAAGAAAATACAAAA 57.251 29.630 0.00 0.00 0.00 2.44
2991 3084 9.130661 TCAGTCTGATGGAAAAGAAAATACAAA 57.869 29.630 0.00 0.00 0.00 2.83
3021 3114 5.043903 CCAGCATATACGATAGGAATTCCG 58.956 45.833 18.82 9.38 42.08 4.30
3036 3129 2.029288 CGCGCCGAATCCAGCATAT 61.029 57.895 0.00 0.00 0.00 1.78
3149 3242 5.410924 TGTGTAGCAGTTGATACAGTGATC 58.589 41.667 10.21 0.38 45.99 2.92
3151 3244 4.864704 TGTGTAGCAGTTGATACAGTGA 57.135 40.909 10.21 0.00 45.99 3.41
3160 3253 9.289303 GATTAAACCATAAATGTGTAGCAGTTG 57.711 33.333 0.00 0.00 36.00 3.16
3176 3269 6.375455 CCACAGCTAAGAACAGATTAAACCAT 59.625 38.462 0.00 0.00 0.00 3.55
3184 3277 1.406069 CGCCCACAGCTAAGAACAGAT 60.406 52.381 0.00 0.00 40.39 2.90
3186 3279 1.639298 GCGCCCACAGCTAAGAACAG 61.639 60.000 0.00 0.00 40.39 3.16
3189 3282 1.375908 CAGCGCCCACAGCTAAGAA 60.376 57.895 2.29 0.00 44.06 2.52
3196 3289 2.749044 ATCTTGCAGCGCCCACAG 60.749 61.111 2.29 2.98 0.00 3.66
3198 3291 3.818787 CCATCTTGCAGCGCCCAC 61.819 66.667 2.29 0.00 0.00 4.61
3213 3306 1.069513 CCGACAACCACTGTAGTTCCA 59.930 52.381 0.00 0.00 38.84 3.53
3225 3318 0.316204 TCGACTTTCCTCCGACAACC 59.684 55.000 0.00 0.00 0.00 3.77
3358 3455 4.961438 AGCAATCTCAACCCAACAAAAT 57.039 36.364 0.00 0.00 0.00 1.82
3380 3477 1.608590 CAATCCAACACCTGCGTCTTT 59.391 47.619 0.00 0.00 0.00 2.52
3427 3526 9.620259 AATAGAATGTAAGATTTCCTGTTCTCC 57.380 33.333 0.00 0.00 0.00 3.71
3466 3566 8.888579 AATACATAGTCCTATTGCAACAGTAC 57.111 34.615 0.00 0.00 0.00 2.73
3468 3568 7.564793 TGAATACATAGTCCTATTGCAACAGT 58.435 34.615 0.00 0.00 0.00 3.55
3479 3579 6.471146 GCCTCAATGATGAATACATAGTCCT 58.529 40.000 0.00 0.00 36.82 3.85
3506 3606 5.007921 ACAACATTTTCCTTGCAAGCAAATC 59.992 36.000 21.43 0.00 35.33 2.17
3526 3626 5.760253 CCATAGACCCATGAGAATGTACAAC 59.240 44.000 0.00 0.00 0.00 3.32
3702 3803 7.724490 ACATGATCTCCTCCGATGAATATAA 57.276 36.000 0.00 0.00 0.00 0.98
4052 4163 3.117663 CCTCTAGAGCCAGGTTCTAGACT 60.118 52.174 30.14 3.42 43.78 3.24
4054 4165 3.124066 TCCTCTAGAGCCAGGTTCTAGA 58.876 50.000 31.03 31.03 45.44 2.43
4070 4181 2.616510 CCCTGAATTCAAGCGTTCCTCT 60.617 50.000 9.88 0.00 0.00 3.69
4072 4183 1.073923 ACCCTGAATTCAAGCGTTCCT 59.926 47.619 9.88 0.00 0.00 3.36
4077 4188 3.976169 TGAAAAACCCTGAATTCAAGCG 58.024 40.909 9.88 2.30 0.00 4.68
4398 4607 2.128035 GATCTAAGTCGTCATTGCCGG 58.872 52.381 0.00 0.00 0.00 6.13
4403 4612 5.066634 AGTGTCGATGATCTAAGTCGTCATT 59.933 40.000 10.92 6.67 36.27 2.57
4405 4614 3.939592 AGTGTCGATGATCTAAGTCGTCA 59.060 43.478 0.00 0.94 34.50 4.35
4422 4631 2.665603 GGAGCACCTCCCAGTGTC 59.334 66.667 0.00 0.00 44.36 3.67
4450 4659 2.097038 CGAAGGGAGCGAGCAACTG 61.097 63.158 0.00 0.00 0.00 3.16
4488 4697 1.078918 CGATGCTGGAGACAAGGCA 60.079 57.895 0.00 0.00 44.39 4.75
4506 4715 0.043481 GACGACGACGACGACCTATC 60.043 60.000 25.15 8.87 42.66 2.08
4555 4764 3.203040 ACCTAAAAGTGGAGGGATGATGG 59.797 47.826 0.00 0.00 37.14 3.51
4556 4765 4.455606 GACCTAAAAGTGGAGGGATGATG 58.544 47.826 0.00 0.00 37.14 3.07


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

AutoCloner maintained by Alex Coulton.