Multiple sequence alignment - TraesCS2D01G424500

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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 TraesCS2D01G424500 chr2D 100.000 3530 0 0 1 3530 537328942 537332471 0.000000e+00 6519
1 TraesCS2D01G424500 chr2D 73.429 2100 383 91 520 2533 537337833 537339843 2.990000e-175 625
2 TraesCS2D01G424500 chr2B 91.711 2461 134 25 370 2787 639497168 639499601 0.000000e+00 3350
3 TraesCS2D01G424500 chr2B 92.625 339 25 0 3192 3530 639500095 639500433 4.100000e-134 488
4 TraesCS2D01G424500 chr2B 85.932 263 27 9 3273 3530 359503831 359503574 4.490000e-69 272
5 TraesCS2D01G424500 chr2B 87.079 178 12 6 2786 2957 639499760 639499932 1.290000e-44 191
6 TraesCS2D01G424500 chr2A 90.209 1767 115 25 1051 2787 679959089 679960827 0.000000e+00 2252
7 TraesCS2D01G424500 chr2A 86.544 981 74 15 1 957 679925124 679926070 0.000000e+00 1027
8 TraesCS2D01G424500 chr2A 78.002 1241 180 37 1936 3107 679927037 679928253 0.000000e+00 693
9 TraesCS2D01G424500 chr2A 73.289 2089 382 100 520 2521 679963859 679965858 3.900000e-169 604
10 TraesCS2D01G424500 chr2A 78.068 766 137 21 986 1740 679926126 679926871 4.150000e-124 455
11 TraesCS2D01G424500 chr2A 78.175 756 117 27 835 1578 679977776 679977057 4.180000e-119 438
12 TraesCS2D01G424500 chr2A 88.856 341 33 5 3192 3530 679961294 679961631 7.050000e-112 414
13 TraesCS2D01G424500 chr2A 85.818 275 17 7 783 1054 679947407 679947662 4.490000e-69 272
14 TraesCS2D01G424500 chr2A 84.364 275 26 10 2786 3055 679960989 679961251 1.630000e-63 254
15 TraesCS2D01G424500 chr2A 92.593 108 3 4 3094 3200 597850519 597850416 2.200000e-32 150
16 TraesCS2D01G424500 chr7A 83.188 345 38 14 3201 3530 457682370 457682031 7.410000e-77 298
17 TraesCS2D01G424500 chr5B 84.669 287 34 7 3249 3530 146369384 146369665 9.650000e-71 278
18 TraesCS2D01G424500 chr5B 81.100 291 39 10 3249 3530 571524892 571524609 5.930000e-53 219
19 TraesCS2D01G424500 chr5A 85.985 264 26 10 3273 3530 476070978 476070720 4.490000e-69 272
20 TraesCS2D01G424500 chr5A 96.774 93 3 0 3103 3195 46561456 46561364 4.720000e-34 156
21 TraesCS2D01G424500 chr6D 83.333 288 40 6 3249 3530 132062062 132061777 3.500000e-65 259
22 TraesCS2D01G424500 chr6D 94.898 98 5 0 3102 3199 4556037 4555940 1.700000e-33 154
23 TraesCS2D01G424500 chr3B 82.824 262 33 8 3273 3530 561885808 561885555 1.280000e-54 224
24 TraesCS2D01G424500 chrUn 97.849 93 2 0 3107 3199 27602564 27602656 1.010000e-35 161
25 TraesCS2D01G424500 chr4B 95.833 96 3 1 3098 3193 649830909 649830815 1.700000e-33 154
26 TraesCS2D01G424500 chr1B 95.833 96 3 1 3098 3193 470881223 470881317 1.700000e-33 154
27 TraesCS2D01G424500 chr7D 96.739 92 2 1 3105 3196 11420122 11420212 6.100000e-33 152
28 TraesCS2D01G424500 chr6B 94.898 98 4 1 3102 3199 465141495 465141399 6.100000e-33 152
29 TraesCS2D01G424500 chr5D 91.818 110 6 2 3084 3193 481728925 481728819 2.200000e-32 150


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 TraesCS2D01G424500 chr2D 537328942 537332471 3529 False 6519 6519 100.000000 1 3530 1 chr2D.!!$F1 3529
1 TraesCS2D01G424500 chr2D 537337833 537339843 2010 False 625 625 73.429000 520 2533 1 chr2D.!!$F2 2013
2 TraesCS2D01G424500 chr2B 639497168 639500433 3265 False 1343 3350 90.471667 370 3530 3 chr2B.!!$F1 3160
3 TraesCS2D01G424500 chr2A 679959089 679965858 6769 False 881 2252 84.179500 520 3530 4 chr2A.!!$F3 3010
4 TraesCS2D01G424500 chr2A 679925124 679928253 3129 False 725 1027 80.871333 1 3107 3 chr2A.!!$F2 3106
5 TraesCS2D01G424500 chr2A 679977057 679977776 719 True 438 438 78.175000 835 1578 1 chr2A.!!$R2 743

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
797 861 0.249741 ACAGAAAACTACGCGTGGCT 60.250 50.0 24.59 7.54 0.0 4.75 F
1754 1901 0.745845 CTCAAGGACTTCATGCCCCG 60.746 60.0 0.00 0.00 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2312 2476 1.569479 GAACAGCTTGAGTGCGTCCC 61.569 60.0 0.00 0.0 38.13 4.46 R
3019 3424 0.036022 GCACCTGCTATGGAGGGATC 59.964 60.0 9.79 0.0 38.21 3.36 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
25 26 3.070576 GGTGTCAGCCCCATTGCC 61.071 66.667 0.00 0.00 0.00 4.52
26 27 2.283101 GTGTCAGCCCCATTGCCA 60.283 61.111 0.00 0.00 0.00 4.92
28 29 1.078891 TGTCAGCCCCATTGCCAAT 59.921 52.632 0.00 0.00 0.00 3.16
29 30 0.334335 TGTCAGCCCCATTGCCAATA 59.666 50.000 0.00 0.00 0.00 1.90
63 64 5.909054 GCTGCCAAGTTTAAAATTTCTTTGC 59.091 36.000 0.00 2.38 31.98 3.68
88 107 4.833478 TTCTAAGCAGCTGAAGAAGGAT 57.167 40.909 20.43 0.00 0.00 3.24
89 108 4.134379 TCTAAGCAGCTGAAGAAGGATG 57.866 45.455 20.43 0.00 0.00 3.51
93 112 2.093553 AGCAGCTGAAGAAGGATGAGTC 60.094 50.000 20.43 0.00 0.00 3.36
96 115 2.500910 AGCTGAAGAAGGATGAGTCAGG 59.499 50.000 0.00 0.00 36.93 3.86
104 123 6.882768 AGAAGGATGAGTCAGGAAAGTATT 57.117 37.500 0.00 0.00 0.00 1.89
120 139 8.314021 AGGAAAGTATTTGGCCTTAAGAATTTG 58.686 33.333 13.25 0.00 39.27 2.32
124 143 6.665248 AGTATTTGGCCTTAAGAATTTGAGCT 59.335 34.615 3.32 0.00 0.00 4.09
146 165 0.603569 AAGGCTGTCGTCGTTCTGAT 59.396 50.000 0.00 0.00 0.00 2.90
150 169 2.033550 GGCTGTCGTCGTTCTGATAGAT 59.966 50.000 0.00 0.00 0.00 1.98
152 171 4.261072 GGCTGTCGTCGTTCTGATAGATTA 60.261 45.833 0.00 0.00 0.00 1.75
186 205 2.358957 TGGTGATCAAAGCCAGATTCG 58.641 47.619 0.00 0.00 0.00 3.34
222 241 2.494471 GTTATACCCAAACCACCTTGCC 59.506 50.000 0.00 0.00 0.00 4.52
231 250 1.528309 CCACCTTGCCACTTCGGTT 60.528 57.895 0.00 0.00 36.97 4.44
243 262 2.044758 ACTTCGGTTTACACAGGTCCT 58.955 47.619 0.00 0.00 0.00 3.85
244 263 2.036862 ACTTCGGTTTACACAGGTCCTC 59.963 50.000 0.00 0.00 0.00 3.71
245 264 0.971386 TCGGTTTACACAGGTCCTCC 59.029 55.000 0.00 0.00 0.00 4.30
246 265 0.389426 CGGTTTACACAGGTCCTCCG 60.389 60.000 0.00 0.00 39.05 4.63
247 266 0.971386 GGTTTACACAGGTCCTCCGA 59.029 55.000 0.00 0.00 39.05 4.55
273 292 4.388773 CCATCGGATCATGTGGTATTTACG 59.611 45.833 0.00 0.00 0.00 3.18
282 301 2.672381 TGTGGTATTTACGTTTAGCGGC 59.328 45.455 0.00 0.00 46.52 6.53
283 302 2.931969 GTGGTATTTACGTTTAGCGGCT 59.068 45.455 7.98 7.98 46.52 5.52
286 305 3.001634 GGTATTTACGTTTAGCGGCTTCC 59.998 47.826 8.26 0.00 46.52 3.46
299 318 1.674817 CGGCTTCCGCTTCCTAGAAAA 60.675 52.381 0.00 0.00 41.17 2.29
305 324 3.671716 TCCGCTTCCTAGAAAAACCTTC 58.328 45.455 0.00 0.00 0.00 3.46
308 327 4.010349 CGCTTCCTAGAAAAACCTTCCAT 58.990 43.478 0.00 0.00 0.00 3.41
315 334 7.066781 TCCTAGAAAAACCTTCCATGAACTTT 58.933 34.615 0.00 0.00 0.00 2.66
326 345 6.586082 CCTTCCATGAACTTTACCAAATTTCG 59.414 38.462 0.00 0.00 34.04 3.46
328 347 5.536916 TCCATGAACTTTACCAAATTTCGGT 59.463 36.000 14.19 14.19 40.73 4.69
380 400 4.021456 CCATAGCGTACATAGGGATCACAA 60.021 45.833 0.00 0.00 0.00 3.33
396 416 2.159761 TCACAAATAAGCACGCGTTAGC 60.160 45.455 10.22 12.04 40.74 3.09
434 454 2.568956 TGAGGACATGACTCTTCCTTGG 59.431 50.000 18.22 0.00 40.02 3.61
480 500 1.329256 CCTTATGGACCGTCGGATCT 58.671 55.000 20.51 0.00 34.57 2.75
509 533 1.784062 CGAGAAGCGCTTTGTCAGG 59.216 57.895 25.84 8.74 0.00 3.86
594 618 5.823045 TGAAGAAGTTGAAAAGGTTCCTCTC 59.177 40.000 0.00 0.00 32.28 3.20
606 630 2.158696 GGTTCCTCTCTTATGCAGGCAT 60.159 50.000 11.94 11.94 40.19 4.40
697 735 3.195610 TCGAACATGTCTCTAGCAATGGT 59.804 43.478 0.00 0.00 0.00 3.55
698 736 3.308053 CGAACATGTCTCTAGCAATGGTG 59.692 47.826 0.00 0.00 0.00 4.17
797 861 0.249741 ACAGAAAACTACGCGTGGCT 60.250 50.000 24.59 7.54 0.00 4.75
893 959 8.994429 TTTTCTCTTTTCAGTCTCTGCTATAG 57.006 34.615 0.00 0.00 0.00 1.31
894 960 6.142818 TCTCTTTTCAGTCTCTGCTATAGC 57.857 41.667 18.18 18.18 42.50 2.97
895 961 5.068460 TCTCTTTTCAGTCTCTGCTATAGCC 59.932 44.000 21.84 6.06 41.18 3.93
896 962 4.959210 TCTTTTCAGTCTCTGCTATAGCCT 59.041 41.667 21.84 8.36 41.18 4.58
897 963 6.129874 TCTTTTCAGTCTCTGCTATAGCCTA 58.870 40.000 21.84 8.93 41.18 3.93
898 964 6.780031 TCTTTTCAGTCTCTGCTATAGCCTAT 59.220 38.462 21.84 0.00 41.18 2.57
899 965 7.945109 TCTTTTCAGTCTCTGCTATAGCCTATA 59.055 37.037 21.84 2.21 41.18 1.31
1017 1146 2.667473 ACATGCAGGTACCTTACGAC 57.333 50.000 13.15 0.01 0.00 4.34
1018 1147 2.176889 ACATGCAGGTACCTTACGACT 58.823 47.619 13.15 0.00 0.00 4.18
1019 1148 3.359033 ACATGCAGGTACCTTACGACTA 58.641 45.455 13.15 0.00 0.00 2.59
1020 1149 3.958798 ACATGCAGGTACCTTACGACTAT 59.041 43.478 13.15 0.00 0.00 2.12
1021 1150 4.037684 ACATGCAGGTACCTTACGACTATC 59.962 45.833 13.15 0.00 0.00 2.08
1022 1151 3.623703 TGCAGGTACCTTACGACTATCA 58.376 45.455 13.15 0.00 0.00 2.15
1092 1224 1.405105 CCAAATGTATGGGTTCCTGCG 59.595 52.381 0.00 0.00 36.79 5.18
1155 1287 1.954362 ATCTGGTCGTCAGCTCCAGC 61.954 60.000 12.50 0.00 45.67 4.85
1370 1505 2.652530 GTACCACCACGGCTCGAA 59.347 61.111 1.50 0.00 39.03 3.71
1437 1572 1.328680 CACTTCATCAAGGAATCGCGG 59.671 52.381 6.13 0.00 33.37 6.46
1511 1646 1.297451 GCTACTACGACGCGGACAG 60.297 63.158 12.47 4.27 0.00 3.51
1602 1743 8.066595 CAGTATATGCTATTTTTGTGCAGAGAC 58.933 37.037 0.00 0.00 39.45 3.36
1640 1787 1.607801 CCGACAGCTGAGGTGGATCA 61.608 60.000 23.35 0.00 35.13 2.92
1754 1901 0.745845 CTCAAGGACTTCATGCCCCG 60.746 60.000 0.00 0.00 0.00 5.73
2070 2226 1.089920 AGAAGATGCGCATCACCAAC 58.910 50.000 42.35 28.70 40.22 3.77
2103 2259 3.639099 CAAGCTCTTCTTGCCTCCA 57.361 52.632 0.00 0.00 44.85 3.86
2312 2476 3.322466 AGGAGGCCTCACCAACGG 61.322 66.667 33.29 0.00 43.14 4.44
2340 2504 1.898574 CAAGCTGTTCACCGGGCTT 60.899 57.895 6.32 7.02 44.43 4.35
2383 2547 5.822519 GGGAACTGCTATGACAACATCATTA 59.177 40.000 0.00 0.00 46.54 1.90
2542 2710 0.807667 CCAGTAAGCTAGCTGCACCG 60.808 60.000 20.16 11.57 45.94 4.94
2568 2736 4.465512 GCCATGGCGAGCGTTGTG 62.466 66.667 23.48 0.00 0.00 3.33
2570 2738 2.616330 CCATGGCGAGCGTTGTGTT 61.616 57.895 0.00 0.00 0.00 3.32
2571 2739 1.440850 CATGGCGAGCGTTGTGTTG 60.441 57.895 0.00 0.00 0.00 3.33
2572 2740 1.891919 ATGGCGAGCGTTGTGTTGT 60.892 52.632 0.00 0.00 0.00 3.32
2573 2741 0.601576 ATGGCGAGCGTTGTGTTGTA 60.602 50.000 0.00 0.00 0.00 2.41
2574 2742 1.203313 GGCGAGCGTTGTGTTGTAC 59.797 57.895 0.00 0.00 0.00 2.90
2610 2790 3.826729 GTGTTCCCTTTCCTTGCTACAAT 59.173 43.478 0.00 0.00 0.00 2.71
2612 2792 5.475564 GTGTTCCCTTTCCTTGCTACAATTA 59.524 40.000 0.00 0.00 0.00 1.40
2613 2793 6.015772 GTGTTCCCTTTCCTTGCTACAATTAA 60.016 38.462 0.00 0.00 0.00 1.40
2614 2794 6.551601 TGTTCCCTTTCCTTGCTACAATTAAA 59.448 34.615 0.00 0.00 0.00 1.52
2615 2795 7.070074 TGTTCCCTTTCCTTGCTACAATTAAAA 59.930 33.333 0.00 0.00 0.00 1.52
2649 2829 7.288852 AGTTCCATGTATATGACTGAGCTAGTT 59.711 37.037 0.25 0.00 40.53 2.24
2659 2839 4.006319 GACTGAGCTAGTTCCATTTGCTT 58.994 43.478 3.94 0.00 40.53 3.91
2691 2876 4.155826 TCTCGGTTATTGCATTTCACAAGG 59.844 41.667 0.00 0.00 0.00 3.61
2720 2905 4.319177 AGTTTGTGCTGATCTAGTGTTCC 58.681 43.478 0.00 0.00 0.00 3.62
2951 3335 8.455903 AAACGATATTGAGTGAATGGATGATT 57.544 30.769 0.00 0.00 0.00 2.57
3008 3413 2.053627 GTTGCTGAAAGAATTGGTGCG 58.946 47.619 0.00 0.00 34.07 5.34
3019 3424 0.179056 ATTGGTGCGTATTCGGAGGG 60.179 55.000 0.00 0.00 38.20 4.30
3037 3442 0.689623 GGATCCCTCCATAGCAGGTG 59.310 60.000 0.00 0.00 41.64 4.00
3057 3462 1.539157 CCTTTTGGCAGAGAAGGGAC 58.461 55.000 14.88 0.00 37.00 4.46
3058 3463 1.202927 CCTTTTGGCAGAGAAGGGACA 60.203 52.381 14.88 0.00 37.00 4.02
3059 3464 2.556114 CCTTTTGGCAGAGAAGGGACAT 60.556 50.000 14.88 0.00 37.00 3.06
3061 3466 1.361204 TTGGCAGAGAAGGGACATGA 58.639 50.000 0.00 0.00 0.00 3.07
3062 3467 1.588239 TGGCAGAGAAGGGACATGAT 58.412 50.000 0.00 0.00 0.00 2.45
3064 3469 2.295885 GGCAGAGAAGGGACATGATTG 58.704 52.381 0.00 0.00 0.00 2.67
3065 3470 2.356535 GGCAGAGAAGGGACATGATTGT 60.357 50.000 0.00 0.00 39.32 2.71
3066 3471 3.350833 GCAGAGAAGGGACATGATTGTT 58.649 45.455 0.00 0.00 35.79 2.83
3067 3472 3.376546 GCAGAGAAGGGACATGATTGTTC 59.623 47.826 0.00 0.00 35.79 3.18
3068 3473 3.620374 CAGAGAAGGGACATGATTGTTCG 59.380 47.826 0.00 0.00 35.79 3.95
3070 3475 2.571653 AGAAGGGACATGATTGTTCGGA 59.428 45.455 0.00 0.00 35.79 4.55
3071 3476 2.698855 AGGGACATGATTGTTCGGAG 57.301 50.000 0.00 0.00 35.79 4.63
3072 3477 1.909302 AGGGACATGATTGTTCGGAGT 59.091 47.619 0.00 0.00 35.79 3.85
3073 3478 2.305927 AGGGACATGATTGTTCGGAGTT 59.694 45.455 0.00 0.00 35.79 3.01
3074 3479 2.420022 GGGACATGATTGTTCGGAGTTG 59.580 50.000 0.00 0.00 35.79 3.16
3095 3500 1.067635 CACACACCCCTTTGCTAATGC 60.068 52.381 0.00 0.00 40.20 3.56
3098 3503 1.075374 ACACCCCTTTGCTAATGCTGA 59.925 47.619 0.00 0.00 40.48 4.26
3107 3512 6.311200 CCCTTTGCTAATGCTGATTTGTTAAC 59.689 38.462 0.00 0.00 40.48 2.01
3108 3513 7.092716 CCTTTGCTAATGCTGATTTGTTAACT 58.907 34.615 7.22 0.00 40.48 2.24
3109 3514 8.243426 CCTTTGCTAATGCTGATTTGTTAACTA 58.757 33.333 7.22 0.00 40.48 2.24
3110 3515 8.964420 TTTGCTAATGCTGATTTGTTAACTAC 57.036 30.769 7.22 0.00 40.48 2.73
3111 3516 7.921786 TGCTAATGCTGATTTGTTAACTACT 57.078 32.000 7.22 0.00 40.48 2.57
3112 3517 7.974675 TGCTAATGCTGATTTGTTAACTACTC 58.025 34.615 7.22 3.92 40.48 2.59
3113 3518 7.065803 TGCTAATGCTGATTTGTTAACTACTCC 59.934 37.037 7.22 0.00 40.48 3.85
3114 3519 6.759497 AATGCTGATTTGTTAACTACTCCC 57.241 37.500 7.22 0.00 0.00 4.30
3115 3520 5.499004 TGCTGATTTGTTAACTACTCCCT 57.501 39.130 7.22 0.00 0.00 4.20
3116 3521 5.488341 TGCTGATTTGTTAACTACTCCCTC 58.512 41.667 7.22 0.00 0.00 4.30
3117 3522 4.876679 GCTGATTTGTTAACTACTCCCTCC 59.123 45.833 7.22 0.00 0.00 4.30
3118 3523 5.080969 TGATTTGTTAACTACTCCCTCCG 57.919 43.478 7.22 0.00 0.00 4.63
3119 3524 4.529377 TGATTTGTTAACTACTCCCTCCGT 59.471 41.667 7.22 0.00 0.00 4.69
3120 3525 5.716228 TGATTTGTTAACTACTCCCTCCGTA 59.284 40.000 7.22 0.00 0.00 4.02
3121 3526 6.211184 TGATTTGTTAACTACTCCCTCCGTAA 59.789 38.462 7.22 0.00 0.00 3.18
3122 3527 6.418057 TTTGTTAACTACTCCCTCCGTAAA 57.582 37.500 7.22 0.00 0.00 2.01
3123 3528 5.391312 TGTTAACTACTCCCTCCGTAAAC 57.609 43.478 7.22 0.00 0.00 2.01
3124 3529 5.079643 TGTTAACTACTCCCTCCGTAAACT 58.920 41.667 7.22 0.00 0.00 2.66
3125 3530 6.245408 TGTTAACTACTCCCTCCGTAAACTA 58.755 40.000 7.22 0.00 0.00 2.24
3126 3531 6.719370 TGTTAACTACTCCCTCCGTAAACTAA 59.281 38.462 7.22 0.00 0.00 2.24
3127 3532 7.397192 TGTTAACTACTCCCTCCGTAAACTAAT 59.603 37.037 7.22 0.00 0.00 1.73
3128 3533 8.903820 GTTAACTACTCCCTCCGTAAACTAATA 58.096 37.037 0.00 0.00 0.00 0.98
3129 3534 9.646522 TTAACTACTCCCTCCGTAAACTAATAT 57.353 33.333 0.00 0.00 0.00 1.28
3131 3536 9.646522 AACTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
3132 3537 9.294614 ACTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
3133 3538 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
3134 3539 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3135 3540 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
3136 3541 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
3137 3542 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
3138 3543 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
3139 3544 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
3140 3545 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
3141 3546 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
3142 3547 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
3188 3593 9.490379 AACGCTCTTATATTATTTTACAGAGGG 57.510 33.333 8.36 8.36 42.53 4.30
3189 3594 8.867097 ACGCTCTTATATTATTTTACAGAGGGA 58.133 33.333 14.96 0.00 40.49 4.20
3190 3595 9.360093 CGCTCTTATATTATTTTACAGAGGGAG 57.640 37.037 4.76 0.00 40.49 4.30
3224 3629 4.957684 ATTAATTCCTACCACTCCTCGG 57.042 45.455 0.00 0.00 0.00 4.63
3232 3637 1.004918 CCACTCCTCGGACAACACC 60.005 63.158 0.00 0.00 0.00 4.16
3318 3723 8.336235 TCATTTGTATAATCTTGAGTTTCCCCT 58.664 33.333 0.00 0.00 0.00 4.79
3325 3731 4.799715 TCTTGAGTTTCCCCTAAAACCA 57.200 40.909 0.00 0.00 39.46 3.67
3352 3758 9.918630 CATGGAAAAATCTGAGAAAAATAGTGT 57.081 29.630 0.00 0.00 0.00 3.55
3445 3851 7.679659 TGATTATCGTCTGTTTGATAACTCG 57.320 36.000 0.00 0.00 39.23 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.940209 TGGCAGCCAAGTTCTTTATTG 57.060 42.857 13.33 0.00 0.00 1.90
63 64 5.413833 TCCTTCTTCAGCTGCTTAGAAAATG 59.586 40.000 18.92 12.95 0.00 2.32
69 70 4.121317 CTCATCCTTCTTCAGCTGCTTAG 58.879 47.826 9.47 6.42 0.00 2.18
70 71 3.517100 ACTCATCCTTCTTCAGCTGCTTA 59.483 43.478 9.47 0.00 0.00 3.09
71 72 2.305343 ACTCATCCTTCTTCAGCTGCTT 59.695 45.455 9.47 0.00 0.00 3.91
88 107 3.330701 AGGCCAAATACTTTCCTGACTCA 59.669 43.478 5.01 0.00 0.00 3.41
89 108 3.956744 AGGCCAAATACTTTCCTGACTC 58.043 45.455 5.01 0.00 0.00 3.36
93 112 6.834168 TTCTTAAGGCCAAATACTTTCCTG 57.166 37.500 5.01 0.00 0.00 3.86
96 115 9.358872 CTCAAATTCTTAAGGCCAAATACTTTC 57.641 33.333 5.01 0.00 0.00 2.62
104 123 4.406456 TGAGCTCAAATTCTTAAGGCCAA 58.594 39.130 15.67 0.00 0.00 4.52
120 139 1.347817 CGACGACAGCCTTTGAGCTC 61.348 60.000 6.82 6.82 42.61 4.09
124 143 0.387929 AGAACGACGACAGCCTTTGA 59.612 50.000 0.00 0.00 0.00 2.69
131 150 6.579292 GGAATAATCTATCAGAACGACGACAG 59.421 42.308 0.00 0.00 0.00 3.51
171 190 4.334759 CAGAATCACGAATCTGGCTTTGAT 59.665 41.667 4.48 0.00 39.48 2.57
186 205 6.296026 TGGGTATAACTAATGCCAGAATCAC 58.704 40.000 0.00 0.00 41.93 3.06
196 215 6.405397 GCAAGGTGGTTTGGGTATAACTAATG 60.405 42.308 0.00 0.00 0.00 1.90
222 241 2.140717 GGACCTGTGTAAACCGAAGTG 58.859 52.381 0.00 0.00 0.00 3.16
231 250 1.481871 GGATCGGAGGACCTGTGTAA 58.518 55.000 0.00 0.00 0.00 2.41
282 301 3.676093 AGGTTTTTCTAGGAAGCGGAAG 58.324 45.455 0.00 0.00 0.00 3.46
283 302 3.782656 AGGTTTTTCTAGGAAGCGGAA 57.217 42.857 0.00 0.00 0.00 4.30
286 305 3.408634 TGGAAGGTTTTTCTAGGAAGCG 58.591 45.455 0.00 0.00 0.00 4.68
299 318 6.994421 ATTTGGTAAAGTTCATGGAAGGTT 57.006 33.333 0.00 0.00 0.00 3.50
305 324 5.778862 ACCGAAATTTGGTAAAGTTCATGG 58.221 37.500 2.39 9.65 43.49 3.66
308 327 6.452494 TCAACCGAAATTTGGTAAAGTTCA 57.548 33.333 5.15 0.00 43.49 3.18
315 334 2.892215 GGGGTTCAACCGAAATTTGGTA 59.108 45.455 5.15 0.00 39.83 3.25
326 345 1.202722 TCTTCGTGAAGGGGTTCAACC 60.203 52.381 9.58 0.00 38.88 3.77
328 347 3.502123 ATTCTTCGTGAAGGGGTTCAA 57.498 42.857 9.58 0.00 38.18 2.69
413 433 2.568956 CCAAGGAAGAGTCATGTCCTCA 59.431 50.000 14.61 0.00 41.03 3.86
454 474 3.068560 CGACGGTCCATAAGGTCAAAAA 58.931 45.455 1.91 0.00 35.89 1.94
458 478 0.323633 TCCGACGGTCCATAAGGTCA 60.324 55.000 14.79 0.00 35.89 4.02
480 500 1.516386 GCTTCTCGCGTCGGATTGA 60.516 57.895 5.77 0.00 0.00 2.57
606 630 7.085476 ACCAGGTAACCATAATATATGTGCA 57.915 36.000 0.00 0.00 37.17 4.57
608 632 9.739276 ATCAACCAGGTAACCATAATATATGTG 57.261 33.333 0.00 0.00 37.17 3.21
610 634 9.958180 TCATCAACCAGGTAACCATAATATATG 57.042 33.333 0.00 0.00 37.17 1.78
779 843 0.163788 CAGCCACGCGTAGTTTTCTG 59.836 55.000 13.44 9.14 0.00 3.02
797 861 2.050144 CTCCTCTTTATAGGCCAGCCA 58.950 52.381 12.03 0.00 38.92 4.75
894 960 8.225603 AGAAACATGTACAAATGCCTTATAGG 57.774 34.615 0.00 0.00 38.80 2.57
899 965 9.206870 CAAAATAGAAACATGTACAAATGCCTT 57.793 29.630 0.00 0.00 0.00 4.35
1017 1146 1.615883 ACGGCCAGCTGATACTGATAG 59.384 52.381 17.39 0.00 40.25 2.08
1018 1147 1.341209 CACGGCCAGCTGATACTGATA 59.659 52.381 17.39 0.00 40.25 2.15
1019 1148 0.105593 CACGGCCAGCTGATACTGAT 59.894 55.000 17.39 0.00 40.25 2.90
1020 1149 1.517361 CACGGCCAGCTGATACTGA 59.483 57.895 17.39 0.00 40.25 3.41
1021 1150 1.522355 CCACGGCCAGCTGATACTG 60.522 63.158 17.39 11.74 37.42 2.74
1022 1151 2.903357 CCACGGCCAGCTGATACT 59.097 61.111 17.39 0.00 0.00 2.12
1044 1176 2.446802 GCCCTCCCCTCCCAGTAG 60.447 72.222 0.00 0.00 0.00 2.57
1092 1224 1.093159 CTGTCATCTGCAAAGGGAGC 58.907 55.000 0.00 0.00 31.59 4.70
1209 1344 5.111989 TCGAAGTCTTCAATAGGATTGCTG 58.888 41.667 12.99 0.00 0.00 4.41
1370 1505 0.463295 CATCTGCTGGATGGCTTCGT 60.463 55.000 10.86 0.00 45.85 3.85
1441 1576 0.178068 CCATACACCTCCTCAACGGG 59.822 60.000 0.00 0.00 0.00 5.28
1602 1743 1.945776 GCTTCTCTTCGTCGCCGTTG 61.946 60.000 0.00 0.00 35.01 4.10
1640 1787 2.816087 CTGAAAGCATTGTACAGCCACT 59.184 45.455 3.63 0.00 0.00 4.00
2070 2226 2.280524 TTGCCGGTGAACCACTCG 60.281 61.111 1.90 0.00 34.40 4.18
2103 2259 2.711922 GGCATCGTCGAGGGACACT 61.712 63.158 9.19 0.00 43.61 3.55
2312 2476 1.569479 GAACAGCTTGAGTGCGTCCC 61.569 60.000 0.00 0.00 38.13 4.46
2340 2504 2.656069 GGGGCGCAGGTACTTCTCA 61.656 63.158 10.83 0.00 34.60 3.27
2383 2547 5.116882 GGACCTGTAGTTTTCAATCGCTAT 58.883 41.667 0.00 0.00 0.00 2.97
2567 2735 6.530120 ACACCAAGATACAAGATGTACAACA 58.470 36.000 0.00 0.00 35.42 3.33
2568 2736 7.360946 GGAACACCAAGATACAAGATGTACAAC 60.361 40.741 0.00 0.00 35.42 3.32
2570 2738 6.170506 GGAACACCAAGATACAAGATGTACA 58.829 40.000 0.00 0.00 35.42 2.90
2571 2739 5.585047 GGGAACACCAAGATACAAGATGTAC 59.415 44.000 0.00 0.00 35.85 2.90
2572 2740 5.487488 AGGGAACACCAAGATACAAGATGTA 59.513 40.000 0.00 0.00 43.89 2.29
2573 2741 4.289672 AGGGAACACCAAGATACAAGATGT 59.710 41.667 0.00 0.00 43.89 3.06
2574 2742 4.848357 AGGGAACACCAAGATACAAGATG 58.152 43.478 0.00 0.00 43.89 2.90
2629 2809 7.789202 ATGGAACTAGCTCAGTCATATACAT 57.211 36.000 0.00 0.00 36.04 2.29
2639 2819 4.260170 AGAAGCAAATGGAACTAGCTCAG 58.740 43.478 0.00 0.00 33.83 3.35
2649 2829 6.208599 ACCGAGAATTTTAAGAAGCAAATGGA 59.791 34.615 0.00 0.00 0.00 3.41
2659 2839 9.567848 GAAATGCAATAACCGAGAATTTTAAGA 57.432 29.630 0.00 0.00 0.00 2.10
2691 2876 3.397482 AGATCAGCACAAACTCACTGAC 58.603 45.455 0.00 0.00 41.63 3.51
2720 2905 3.883489 AGGGACGTCAAGAAAAGAAAAGG 59.117 43.478 18.91 0.00 0.00 3.11
2807 3185 1.551883 ACGGGGCAGTTTACGACTAAT 59.448 47.619 0.00 0.00 36.65 1.73
2809 3187 0.244450 CACGGGGCAGTTTACGACTA 59.756 55.000 0.00 0.00 36.65 2.59
2810 3188 1.005394 CACGGGGCAGTTTACGACT 60.005 57.895 0.00 0.00 39.89 4.18
2811 3189 0.390735 ATCACGGGGCAGTTTACGAC 60.391 55.000 0.00 0.00 0.00 4.34
2812 3190 0.390603 CATCACGGGGCAGTTTACGA 60.391 55.000 0.00 0.00 0.00 3.43
2813 3191 1.366111 CCATCACGGGGCAGTTTACG 61.366 60.000 0.00 0.00 0.00 3.18
2814 3192 2.477880 CCATCACGGGGCAGTTTAC 58.522 57.895 0.00 0.00 0.00 2.01
2835 3213 0.179134 GTGCCAGCTACGTACCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
2973 3378 9.935241 TCTTTCAGCAACTTCCAGATATATATC 57.065 33.333 13.95 13.95 0.00 1.63
2985 3390 3.737774 GCACCAATTCTTTCAGCAACTTC 59.262 43.478 0.00 0.00 0.00 3.01
2989 3394 1.680735 ACGCACCAATTCTTTCAGCAA 59.319 42.857 0.00 0.00 0.00 3.91
2990 3395 1.317613 ACGCACCAATTCTTTCAGCA 58.682 45.000 0.00 0.00 0.00 4.41
2991 3396 3.764885 ATACGCACCAATTCTTTCAGC 57.235 42.857 0.00 0.00 0.00 4.26
2992 3397 4.334443 CGAATACGCACCAATTCTTTCAG 58.666 43.478 0.00 0.00 31.29 3.02
3001 3406 1.219664 CCCTCCGAATACGCACCAA 59.780 57.895 0.00 0.00 38.29 3.67
3019 3424 0.036022 GCACCTGCTATGGAGGGATC 59.964 60.000 9.79 0.00 38.21 3.36
3037 3442 0.251341 TCCCTTCTCTGCCAAAAGGC 60.251 55.000 0.00 0.00 38.59 4.35
3046 3451 3.620374 CGAACAATCATGTCCCTTCTCTG 59.380 47.826 0.00 0.00 39.40 3.35
3047 3452 3.369892 CCGAACAATCATGTCCCTTCTCT 60.370 47.826 0.00 0.00 39.40 3.10
3048 3453 2.939103 CCGAACAATCATGTCCCTTCTC 59.061 50.000 0.00 0.00 39.40 2.87
3049 3454 2.571653 TCCGAACAATCATGTCCCTTCT 59.428 45.455 0.00 0.00 39.40 2.85
3050 3455 2.939103 CTCCGAACAATCATGTCCCTTC 59.061 50.000 0.00 0.00 39.40 3.46
3051 3456 2.305927 ACTCCGAACAATCATGTCCCTT 59.694 45.455 0.00 0.00 39.40 3.95
3054 3459 2.159517 GCAACTCCGAACAATCATGTCC 60.160 50.000 0.00 0.00 39.40 4.02
3057 3462 2.226200 TGTGCAACTCCGAACAATCATG 59.774 45.455 0.00 0.00 38.04 3.07
3058 3463 2.226437 GTGTGCAACTCCGAACAATCAT 59.774 45.455 0.00 0.00 38.04 2.45
3059 3464 1.601903 GTGTGCAACTCCGAACAATCA 59.398 47.619 0.00 0.00 38.04 2.57
3061 3466 1.333619 GTGTGTGCAACTCCGAACAAT 59.666 47.619 0.00 0.00 38.04 2.71
3062 3467 0.730265 GTGTGTGCAACTCCGAACAA 59.270 50.000 0.00 0.00 38.04 2.83
3064 3469 1.647084 GGTGTGTGCAACTCCGAAC 59.353 57.895 0.00 0.00 38.04 3.95
3065 3470 1.525077 GGGTGTGTGCAACTCCGAA 60.525 57.895 11.42 0.00 42.40 4.30
3066 3471 2.110213 GGGTGTGTGCAACTCCGA 59.890 61.111 11.42 0.00 42.40 4.55
3067 3472 2.958578 AAGGGGTGTGTGCAACTCCG 62.959 60.000 0.17 0.00 42.40 4.63
3068 3473 0.755327 AAAGGGGTGTGTGCAACTCC 60.755 55.000 0.00 0.00 41.02 3.85
3070 3475 1.675720 GCAAAGGGGTGTGTGCAACT 61.676 55.000 0.00 0.00 38.04 3.16
3071 3476 1.227234 GCAAAGGGGTGTGTGCAAC 60.227 57.895 0.00 0.00 36.97 4.17
3072 3477 0.106469 TAGCAAAGGGGTGTGTGCAA 60.106 50.000 0.00 0.00 39.50 4.08
3073 3478 0.106469 TTAGCAAAGGGGTGTGTGCA 60.106 50.000 0.00 0.00 39.50 4.57
3074 3479 1.067635 CATTAGCAAAGGGGTGTGTGC 60.068 52.381 0.00 0.00 37.26 4.57
3095 3500 5.109903 CGGAGGGAGTAGTTAACAAATCAG 58.890 45.833 8.61 0.00 0.00 2.90
3098 3503 6.610075 TTACGGAGGGAGTAGTTAACAAAT 57.390 37.500 8.61 0.00 0.00 2.32
3107 3512 9.512588 TCTTATATTAGTTTACGGAGGGAGTAG 57.487 37.037 0.00 0.00 0.00 2.57
3108 3513 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
3109 3514 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
3110 3515 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
3111 3516 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
3112 3517 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
3113 3518 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
3114 3519 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
3115 3520 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
3116 3521 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
3162 3567 9.490379 CCCTCTGTAAAATAATATAAGAGCGTT 57.510 33.333 0.00 0.00 0.00 4.84
3163 3568 8.867097 TCCCTCTGTAAAATAATATAAGAGCGT 58.133 33.333 0.00 0.00 0.00 5.07
3164 3569 9.360093 CTCCCTCTGTAAAATAATATAAGAGCG 57.640 37.037 0.00 0.00 0.00 5.03
3174 3579 9.998106 GCATATTCTACTCCCTCTGTAAAATAA 57.002 33.333 0.00 0.00 0.00 1.40
3175 3580 9.381038 AGCATATTCTACTCCCTCTGTAAAATA 57.619 33.333 0.00 0.00 0.00 1.40
3176 3581 8.268878 AGCATATTCTACTCCCTCTGTAAAAT 57.731 34.615 0.00 0.00 0.00 1.82
3177 3582 7.676683 AGCATATTCTACTCCCTCTGTAAAA 57.323 36.000 0.00 0.00 0.00 1.52
3178 3583 8.777578 TTAGCATATTCTACTCCCTCTGTAAA 57.222 34.615 0.00 0.00 0.00 2.01
3179 3584 8.958060 ATTAGCATATTCTACTCCCTCTGTAA 57.042 34.615 0.00 0.00 0.00 2.41
3180 3585 8.958060 AATTAGCATATTCTACTCCCTCTGTA 57.042 34.615 0.00 0.00 0.00 2.74
3181 3586 7.863901 AATTAGCATATTCTACTCCCTCTGT 57.136 36.000 0.00 0.00 0.00 3.41
3197 3602 7.394144 AGGAGTGGTAGGAATTAATTAGCAT 57.606 36.000 0.00 0.00 0.00 3.79
3214 3619 1.004918 GGTGTTGTCCGAGGAGTGG 60.005 63.158 0.00 0.00 0.00 4.00
3224 3629 4.545823 TCATTCAAGAAACGGTGTTGTC 57.454 40.909 0.00 0.00 32.34 3.18
3312 3717 3.905493 TTCCATGTGGTTTTAGGGGAA 57.095 42.857 0.00 0.00 36.34 3.97
3318 3723 7.831691 TCTCAGATTTTTCCATGTGGTTTTA 57.168 32.000 0.00 0.00 36.34 1.52
3325 3731 9.918630 CACTATTTTTCTCAGATTTTTCCATGT 57.081 29.630 0.00 0.00 0.00 3.21
3428 3834 8.610855 TTCTTATACGAGTTATCAAACAGACG 57.389 34.615 0.00 0.00 38.12 4.18


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

AutoCloner maintained by Alex Coulton.