Multiple sequence alignment - TraesCS3A01G420400

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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 TraesCS3A01G420400 chr3A 100.000 4801 0 0 1 4801 661973730 661978530 0.000000e+00 8866
1 TraesCS3A01G420400 chr3D 88.662 4216 219 126 706 4794 527559648 527555565 0.000000e+00 4898
2 TraesCS3A01G420400 chr3D 85.714 742 57 17 1 712 527560450 527559728 0.000000e+00 737
3 TraesCS3A01G420400 chr3B 85.509 3278 240 119 1615 4799 697471336 697474471 0.000000e+00 3205
4 TraesCS3A01G420400 chr3B 90.387 801 32 17 837 1592 697470482 697471282 0.000000e+00 1011
5 TraesCS3A01G420400 chr3B 82.573 241 32 9 1 239 775837238 775837006 2.270000e-48 204
6 TraesCS3A01G420400 chr2A 83.817 241 29 9 1 239 706637402 706637170 2.250000e-53 220
7 TraesCS3A01G420400 chr6A 83.402 241 30 9 1 239 108084689 108084457 1.050000e-51 215
8 TraesCS3A01G420400 chr5D 83.402 241 30 9 1 239 2597282 2597514 1.050000e-51 215
9 TraesCS3A01G420400 chr5B 83.402 241 30 9 1 239 308572445 308572213 1.050000e-51 215
10 TraesCS3A01G420400 chr4D 83.193 238 29 10 4 239 222417720 222417492 1.750000e-49 207
11 TraesCS3A01G420400 chr1D 82.573 241 34 8 1 239 386794949 386794715 6.300000e-49 206
12 TraesCS3A01G420400 chr7B 82.573 241 32 9 1 239 193964856 193965088 2.270000e-48 204


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 TraesCS3A01G420400 chr3A 661973730 661978530 4800 False 8866.0 8866 100.000 1 4801 1 chr3A.!!$F1 4800
1 TraesCS3A01G420400 chr3D 527555565 527560450 4885 True 2817.5 4898 87.188 1 4794 2 chr3D.!!$R1 4793
2 TraesCS3A01G420400 chr3B 697470482 697474471 3989 False 2108.0 3205 87.948 837 4799 2 chr3B.!!$F1 3962

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
671 697 0.038526 ACACGTGTGAGGAATCGACC 60.039 55.0 22.71 0.0 0.00 4.79 F
1577 1764 0.177836 TCATGGCCAACGACATCGAT 59.822 50.0 10.96 0.0 43.02 3.59 F
3105 3443 0.103026 CTGCAGTGATCCGATTCCGA 59.897 55.0 5.25 0.0 38.22 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 2661 0.407139 AGGAAGTGCAAGCCCTGAAT 59.593 50.0 0.00 0.0 0.00 2.57 R
3121 3459 0.040157 ACACGCGTCGTAAGCACTTA 60.040 50.0 9.86 0.0 38.32 2.24 R
4650 5053 0.250124 TGCAACCTCAACTACACGGG 60.250 55.0 0.00 0.0 0.00 5.28 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
24 25 3.636300 TCTCAAGTTTGTCAAATGGGTGG 59.364 43.478 0.40 0.00 0.00 4.61
32 33 4.105754 TGTCAAATGGGTGGACATACAA 57.894 40.909 0.00 0.00 36.69 2.41
48 53 6.039717 GGACATACAAACATTGTGCCTATGAT 59.960 38.462 6.01 0.00 45.03 2.45
249 255 5.945191 TGAACTCATTTGCATTGAGGATACA 59.055 36.000 23.53 16.37 43.95 2.29
259 265 6.228995 TGCATTGAGGATACATTTGCAAAAA 58.771 32.000 17.19 5.33 36.81 1.94
312 321 7.801104 TCTCAAAATATCATTGGCCTACACTA 58.199 34.615 3.32 0.00 0.00 2.74
313 322 7.715249 TCTCAAAATATCATTGGCCTACACTAC 59.285 37.037 3.32 0.00 0.00 2.73
316 325 8.993121 CAAAATATCATTGGCCTACACTACTAG 58.007 37.037 3.32 0.00 0.00 2.57
317 326 8.492415 AAATATCATTGGCCTACACTACTAGA 57.508 34.615 3.32 0.00 0.00 2.43
318 327 8.671987 AATATCATTGGCCTACACTACTAGAT 57.328 34.615 3.32 0.00 0.00 1.98
319 328 5.791336 TCATTGGCCTACACTACTAGATG 57.209 43.478 3.32 0.00 0.00 2.90
417 426 1.379843 GATCAACCCAACCGCCCAT 60.380 57.895 0.00 0.00 0.00 4.00
422 431 4.431131 CCCAACCGCCCATCAGCT 62.431 66.667 0.00 0.00 0.00 4.24
423 432 2.825836 CCAACCGCCCATCAGCTC 60.826 66.667 0.00 0.00 0.00 4.09
449 474 3.790437 CTGAGCCGCCACCTCCAT 61.790 66.667 0.00 0.00 0.00 3.41
451 476 3.785859 GAGCCGCCACCTCCATCA 61.786 66.667 0.00 0.00 0.00 3.07
485 510 2.024941 CCTGGCCATTCCTCTAAACCTT 60.025 50.000 5.51 0.00 35.26 3.50
491 516 4.686396 GCCATTCCTCTAAACCTTCCTACC 60.686 50.000 0.00 0.00 0.00 3.18
502 527 4.432980 ACCTTCCTACCCCAAATATTCG 57.567 45.455 0.00 0.00 0.00 3.34
510 535 2.297701 CCCCAAATATTCGGGTGACTG 58.702 52.381 10.67 0.00 41.30 3.51
512 537 2.364632 CCAAATATTCGGGTGACTGCA 58.635 47.619 0.00 0.00 36.33 4.41
535 560 4.717313 GCACCCTCCACCCGAACC 62.717 72.222 0.00 0.00 0.00 3.62
547 572 4.073549 CCACCCGAACCAGTTAAACATAA 58.926 43.478 0.00 0.00 0.00 1.90
549 574 4.515944 CACCCGAACCAGTTAAACATAACA 59.484 41.667 2.01 0.00 32.63 2.41
555 580 4.139038 ACCAGTTAAACATAACACCGCTT 58.861 39.130 2.01 0.00 32.63 4.68
556 581 4.214758 ACCAGTTAAACATAACACCGCTTC 59.785 41.667 2.01 0.00 32.63 3.86
562 587 3.350219 ACATAACACCGCTTCTCCATT 57.650 42.857 0.00 0.00 0.00 3.16
564 589 3.270027 CATAACACCGCTTCTCCATTGA 58.730 45.455 0.00 0.00 0.00 2.57
569 594 1.278985 ACCGCTTCTCCATTGATGACA 59.721 47.619 0.00 0.00 0.00 3.58
575 600 4.669318 CTTCTCCATTGATGACATTGTGC 58.331 43.478 0.00 0.00 0.00 4.57
590 615 1.005037 GTGCCTGACACGGTCATGA 60.005 57.895 11.48 0.00 41.94 3.07
591 616 0.602638 GTGCCTGACACGGTCATGAA 60.603 55.000 0.00 1.23 41.94 2.57
592 617 0.324614 TGCCTGACACGGTCATGAAT 59.675 50.000 0.00 0.00 41.94 2.57
593 618 1.271325 TGCCTGACACGGTCATGAATT 60.271 47.619 0.00 0.00 41.94 2.17
594 619 1.131126 GCCTGACACGGTCATGAATTG 59.869 52.381 0.00 0.00 41.94 2.32
671 697 0.038526 ACACGTGTGAGGAATCGACC 60.039 55.000 22.71 0.00 0.00 4.79
732 849 4.511826 ACACTAGAGCAAAGTAAGCAACAC 59.488 41.667 0.00 0.00 0.00 3.32
744 861 6.780706 AGTAAGCAACACGCCAATATATAC 57.219 37.500 0.00 0.00 44.04 1.47
775 894 2.202892 GAACATCGGGCTCGGACC 60.203 66.667 5.94 0.00 36.95 4.46
939 1063 3.917760 GCTCGCTATCGCCAGGGT 61.918 66.667 0.00 0.00 35.26 4.34
1052 1200 2.004120 TCGCTCTCCTCCTCCTCCT 61.004 63.158 0.00 0.00 0.00 3.69
1053 1201 1.528309 CGCTCTCCTCCTCCTCCTC 60.528 68.421 0.00 0.00 0.00 3.71
1054 1202 1.152546 GCTCTCCTCCTCCTCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
1107 1264 0.596577 TCAACACCGAGTTCGAGGAG 59.403 55.000 2.59 0.00 43.02 3.69
1209 1367 0.458669 TCCCGGCGAGTTCACTAATC 59.541 55.000 9.30 0.00 0.00 1.75
1376 1556 4.785453 GGCTGCCAGAAGTCCCCG 62.785 72.222 15.17 0.00 0.00 5.73
1399 1579 2.100197 GGCAATTAAACCACTCTCCCC 58.900 52.381 0.00 0.00 0.00 4.81
1577 1764 0.177836 TCATGGCCAACGACATCGAT 59.822 50.000 10.96 0.00 43.02 3.59
1584 1771 0.647410 CAACGACATCGATGGTCAGC 59.353 55.000 28.09 11.38 43.02 4.26
1612 1801 7.389232 TCTGCTTCGATCATTATCCATTACAT 58.611 34.615 0.00 0.00 0.00 2.29
1613 1802 7.879677 TCTGCTTCGATCATTATCCATTACATT 59.120 33.333 0.00 0.00 0.00 2.71
1746 1967 1.518572 GATCGTGTCGCGGTCCAAT 60.519 57.895 6.13 0.00 44.46 3.16
1792 2013 3.491652 GCGCGAAGAAGGGTGAGC 61.492 66.667 12.10 0.00 0.00 4.26
1815 2040 5.334879 GCACACCTGAATCGTAAATCAGTTT 60.335 40.000 2.51 0.00 41.16 2.66
1844 2074 9.689976 CGCCATATATACTACTACTCGTATACT 57.310 37.037 0.56 0.00 33.00 2.12
1924 2154 1.300542 GATGCAGCTCTACTCGCCC 60.301 63.158 0.00 0.00 0.00 6.13
1966 2196 1.511613 CCATCCCTTTCCTCTGGCTA 58.488 55.000 0.00 0.00 0.00 3.93
2076 2309 5.375417 TCGTTTCAACAGATTTCATGCAT 57.625 34.783 0.00 0.00 0.00 3.96
2183 2422 1.671901 CGAAGGAGACCAGGAGGCTC 61.672 65.000 5.78 5.78 39.06 4.70
2314 2553 3.799755 GCGTGGTTGATGGTCGGC 61.800 66.667 0.00 0.00 0.00 5.54
2464 2742 8.932610 ACTCATTGTCAGGTATAGATCTCAAAT 58.067 33.333 0.00 0.00 0.00 2.32
2495 2773 9.298250 CTGAATTCTTGGATCATTATCTTCCAT 57.702 33.333 7.05 0.00 39.22 3.41
2496 2774 9.293404 TGAATTCTTGGATCATTATCTTCCATC 57.707 33.333 7.05 0.00 39.22 3.51
2497 2775 9.517868 GAATTCTTGGATCATTATCTTCCATCT 57.482 33.333 0.00 0.00 39.22 2.90
2498 2776 9.878737 AATTCTTGGATCATTATCTTCCATCTT 57.121 29.630 0.00 0.00 39.22 2.40
2499 2777 8.915057 TTCTTGGATCATTATCTTCCATCTTC 57.085 34.615 0.00 0.00 39.22 2.87
2500 2778 8.272659 TCTTGGATCATTATCTTCCATCTTCT 57.727 34.615 0.00 0.00 39.22 2.85
2501 2779 9.384849 TCTTGGATCATTATCTTCCATCTTCTA 57.615 33.333 0.00 0.00 39.22 2.10
2526 2804 3.319137 TTTTCTGAGGGACATCGTCTG 57.681 47.619 0.00 0.00 32.47 3.51
2527 2805 1.186200 TTCTGAGGGACATCGTCTGG 58.814 55.000 0.00 0.00 32.47 3.86
2528 2806 1.142748 CTGAGGGACATCGTCTGGC 59.857 63.158 0.00 0.00 32.47 4.85
2529 2807 2.105128 GAGGGACATCGTCTGGCG 59.895 66.667 0.00 0.00 43.01 5.69
2546 2824 2.752354 TGGCGTCTTAATTTGATGTGGG 59.248 45.455 0.00 0.00 0.00 4.61
2698 2976 4.636435 CCGTTCGCCTGGGTTGGT 62.636 66.667 0.00 0.00 0.00 3.67
2729 3007 4.992319 TCATGGTACGTCGTCAAAGAAAAT 59.008 37.500 0.00 0.00 0.00 1.82
2734 3028 5.618395 GGTACGTCGTCAAAGAAAATTTGTC 59.382 40.000 0.00 0.00 0.00 3.18
2743 3037 8.057742 CGTCAAAGAAAATTTGTCAAATTCCAG 58.942 33.333 20.98 10.26 40.05 3.86
2750 3044 2.132740 TGTCAAATTCCAGCGTTTGC 57.867 45.000 0.00 0.00 43.24 3.68
2786 3089 5.771469 TCCATGTGTTTTACTTGATGCTTG 58.229 37.500 0.00 0.00 36.76 4.01
2790 3093 7.062605 CCATGTGTTTTACTTGATGCTTGATTC 59.937 37.037 0.00 0.00 36.76 2.52
2791 3094 7.275888 TGTGTTTTACTTGATGCTTGATTCT 57.724 32.000 0.00 0.00 0.00 2.40
2795 3100 9.598517 TGTTTTACTTGATGCTTGATTCTTTTT 57.401 25.926 0.00 0.00 0.00 1.94
2828 3133 1.616159 TCGGCATGATGATCCTCGTA 58.384 50.000 0.00 0.00 0.00 3.43
2834 3139 3.124806 GCATGATGATCCTCGTATTGCAG 59.875 47.826 0.00 0.00 0.00 4.41
2865 3170 6.584563 GCAAATGCCGAACATAAAAGTAAGAA 59.415 34.615 0.00 0.00 38.34 2.52
2866 3171 7.201350 GCAAATGCCGAACATAAAAGTAAGAAG 60.201 37.037 0.00 0.00 38.34 2.85
2868 3173 6.476243 TGCCGAACATAAAAGTAAGAAGAC 57.524 37.500 0.00 0.00 0.00 3.01
2870 3175 5.410439 GCCGAACATAAAAGTAAGAAGACCA 59.590 40.000 0.00 0.00 0.00 4.02
2871 3176 6.620089 GCCGAACATAAAAGTAAGAAGACCAC 60.620 42.308 0.00 0.00 0.00 4.16
2872 3177 6.128363 CCGAACATAAAAGTAAGAAGACCACC 60.128 42.308 0.00 0.00 0.00 4.61
2873 3178 6.425721 CGAACATAAAAGTAAGAAGACCACCA 59.574 38.462 0.00 0.00 0.00 4.17
2874 3179 7.119262 CGAACATAAAAGTAAGAAGACCACCAT 59.881 37.037 0.00 0.00 0.00 3.55
2875 3180 7.923414 ACATAAAAGTAAGAAGACCACCATC 57.077 36.000 0.00 0.00 0.00 3.51
2876 3181 6.594159 ACATAAAAGTAAGAAGACCACCATCG 59.406 38.462 0.00 0.00 0.00 3.84
2877 3182 2.674796 AGTAAGAAGACCACCATCGC 57.325 50.000 0.00 0.00 0.00 4.58
2878 3183 1.207329 AGTAAGAAGACCACCATCGCC 59.793 52.381 0.00 0.00 0.00 5.54
2879 3184 1.066430 GTAAGAAGACCACCATCGCCA 60.066 52.381 0.00 0.00 0.00 5.69
2882 3187 1.153369 AAGACCACCATCGCCATCG 60.153 57.895 0.00 0.00 0.00 3.84
2898 3203 3.007979 CATCGCCATGGACATTCATTG 57.992 47.619 18.40 0.00 0.00 2.82
2913 3226 5.363868 ACATTCATTGTAGCTACTCTGGCTA 59.636 40.000 23.84 10.69 40.74 3.93
2914 3227 5.932619 TTCATTGTAGCTACTCTGGCTAA 57.067 39.130 23.84 9.00 42.79 3.09
2915 3228 5.521906 TCATTGTAGCTACTCTGGCTAAG 57.478 43.478 23.84 5.00 42.79 2.18
2922 3235 2.615912 GCTACTCTGGCTAAGCAATTGG 59.384 50.000 7.72 0.00 35.05 3.16
2924 3237 2.996631 ACTCTGGCTAAGCAATTGGAG 58.003 47.619 7.72 5.17 0.00 3.86
3049 3387 4.466370 TCATGATCACGGTAGGTTTTCTCT 59.534 41.667 0.00 0.00 0.00 3.10
3078 3416 2.107366 CAAACTGGACAAAACCCCTGT 58.893 47.619 0.00 0.00 36.38 4.00
3084 3422 4.014406 CTGGACAAAACCCCTGTATAACC 58.986 47.826 0.00 0.00 0.00 2.85
3092 3430 1.213296 CCCTGTATAACCCCTGCAGT 58.787 55.000 13.81 0.00 0.00 4.40
3093 3431 1.134098 CCCTGTATAACCCCTGCAGTG 60.134 57.143 13.81 0.00 0.00 3.66
3095 3433 2.439507 CCTGTATAACCCCTGCAGTGAT 59.560 50.000 13.81 0.64 0.00 3.06
3096 3434 3.495100 CCTGTATAACCCCTGCAGTGATC 60.495 52.174 13.81 0.00 0.00 2.92
3101 3439 1.274703 ACCCCTGCAGTGATCCGATT 61.275 55.000 13.81 0.00 0.00 3.34
3102 3440 0.533755 CCCCTGCAGTGATCCGATTC 60.534 60.000 13.81 0.00 0.00 2.52
3103 3441 0.533755 CCCTGCAGTGATCCGATTCC 60.534 60.000 13.81 0.00 0.00 3.01
3104 3442 0.877649 CCTGCAGTGATCCGATTCCG 60.878 60.000 13.81 0.00 0.00 4.30
3105 3443 0.103026 CTGCAGTGATCCGATTCCGA 59.897 55.000 5.25 0.00 38.22 4.55
3107 3445 1.269778 TGCAGTGATCCGATTCCGATC 60.270 52.381 7.74 7.74 38.22 3.69
3108 3446 1.269778 GCAGTGATCCGATTCCGATCA 60.270 52.381 11.99 11.99 38.22 2.92
3109 3447 2.398498 CAGTGATCCGATTCCGATCAC 58.602 52.381 27.02 27.02 44.26 3.06
3111 3449 2.430694 AGTGATCCGATTCCGATCACAA 59.569 45.455 31.54 9.05 45.14 3.33
3112 3450 2.540101 GTGATCCGATTCCGATCACAAC 59.460 50.000 28.27 12.57 43.88 3.32
3113 3451 1.787155 GATCCGATTCCGATCACAACG 59.213 52.381 9.32 0.00 38.22 4.10
3114 3452 0.804544 TCCGATTCCGATCACAACGC 60.805 55.000 0.00 0.00 38.22 4.84
3116 3454 1.137459 CGATTCCGATCACAACGCGA 61.137 55.000 15.93 0.00 38.22 5.87
3117 3455 1.209128 GATTCCGATCACAACGCGAT 58.791 50.000 15.93 0.00 32.33 4.58
3119 3457 0.109039 TTCCGATCACAACGCGATCA 60.109 50.000 15.93 0.00 39.43 2.92
3120 3458 0.525455 TCCGATCACAACGCGATCAG 60.525 55.000 15.93 1.12 39.43 2.90
3121 3459 0.802222 CCGATCACAACGCGATCAGT 60.802 55.000 15.93 1.87 39.43 3.41
3122 3460 1.533129 CCGATCACAACGCGATCAGTA 60.533 52.381 15.93 0.00 39.43 2.74
3123 3461 2.182014 CGATCACAACGCGATCAGTAA 58.818 47.619 15.93 0.00 39.43 2.24
3124 3462 2.214244 CGATCACAACGCGATCAGTAAG 59.786 50.000 15.93 0.00 39.43 2.34
3125 3463 2.717580 TCACAACGCGATCAGTAAGT 57.282 45.000 15.93 0.00 0.00 2.24
3126 3464 2.324860 TCACAACGCGATCAGTAAGTG 58.675 47.619 15.93 4.32 32.56 3.16
3127 3465 1.068474 ACAACGCGATCAGTAAGTGC 58.932 50.000 15.93 0.00 0.00 4.40
3128 3466 1.336887 ACAACGCGATCAGTAAGTGCT 60.337 47.619 15.93 0.00 0.00 4.40
3129 3467 1.726791 CAACGCGATCAGTAAGTGCTT 59.273 47.619 15.93 0.00 0.00 3.91
3130 3468 2.921121 CAACGCGATCAGTAAGTGCTTA 59.079 45.455 15.93 0.00 0.00 3.09
3131 3469 2.527100 ACGCGATCAGTAAGTGCTTAC 58.473 47.619 15.93 12.71 44.22 2.34
3142 3480 3.399770 TGCTTACGACGCGTGTGC 61.400 61.111 20.70 15.61 41.39 4.57
3331 3669 1.002857 CCTGAATCCCCACCTTCCTT 58.997 55.000 0.00 0.00 0.00 3.36
3336 3674 0.423544 ATCCCCACCTTCCTTCCTCT 59.576 55.000 0.00 0.00 0.00 3.69
3339 3677 1.068121 CCCACCTTCCTTCCTCTGTT 58.932 55.000 0.00 0.00 0.00 3.16
3340 3678 1.271597 CCCACCTTCCTTCCTCTGTTG 60.272 57.143 0.00 0.00 0.00 3.33
3341 3679 1.271597 CCACCTTCCTTCCTCTGTTGG 60.272 57.143 0.00 0.00 0.00 3.77
3342 3680 1.699634 CACCTTCCTTCCTCTGTTGGA 59.300 52.381 0.00 0.00 0.00 3.53
3343 3681 1.700186 ACCTTCCTTCCTCTGTTGGAC 59.300 52.381 0.00 0.00 35.58 4.02
3344 3682 1.699634 CCTTCCTTCCTCTGTTGGACA 59.300 52.381 0.00 0.00 35.58 4.02
3345 3683 2.551071 CCTTCCTTCCTCTGTTGGACAC 60.551 54.545 0.00 0.00 35.58 3.67
3363 3701 5.049336 TGGACACAACACAACATAATTACCG 60.049 40.000 0.00 0.00 0.00 4.02
3399 3746 4.930463 GCATGATGCAGATATGACAGAG 57.070 45.455 13.36 0.00 44.26 3.35
3455 3802 2.357543 CGTCATGATCGGCTACGCG 61.358 63.158 3.53 3.53 40.69 6.01
3487 3834 2.484264 CCAATTTCCTGAACCTCGTGAC 59.516 50.000 0.00 0.00 0.00 3.67
3493 3840 1.597663 CCTGAACCTCGTGACAACAAC 59.402 52.381 0.00 0.00 0.00 3.32
3495 3842 1.208535 TGAACCTCGTGACAACAACCT 59.791 47.619 0.00 0.00 0.00 3.50
3497 3844 2.814280 ACCTCGTGACAACAACCTAG 57.186 50.000 0.00 0.00 0.00 3.02
3498 3845 2.037144 ACCTCGTGACAACAACCTAGT 58.963 47.619 0.00 0.00 0.00 2.57
3499 3846 2.223971 ACCTCGTGACAACAACCTAGTG 60.224 50.000 0.00 0.00 0.00 2.74
3500 3847 1.792949 CTCGTGACAACAACCTAGTGC 59.207 52.381 0.00 0.00 0.00 4.40
3501 3848 0.865769 CGTGACAACAACCTAGTGCC 59.134 55.000 0.00 0.00 0.00 5.01
3502 3849 1.808512 CGTGACAACAACCTAGTGCCA 60.809 52.381 0.00 0.00 0.00 4.92
3503 3850 2.504367 GTGACAACAACCTAGTGCCAT 58.496 47.619 0.00 0.00 0.00 4.40
3504 3851 2.484264 GTGACAACAACCTAGTGCCATC 59.516 50.000 0.00 0.00 0.00 3.51
3506 3853 3.146066 GACAACAACCTAGTGCCATCAA 58.854 45.455 0.00 0.00 0.00 2.57
3512 3859 4.943705 ACAACCTAGTGCCATCAACATTAG 59.056 41.667 0.00 0.00 0.00 1.73
3556 3903 4.028993 ACTACCCCAAAATTGACGATGT 57.971 40.909 0.00 0.00 0.00 3.06
3653 4000 1.014352 CGCTAGGTACCATTGCCAAC 58.986 55.000 15.94 0.00 0.00 3.77
3698 4046 1.479730 ACATGCAGAATCTCGAGCTCA 59.520 47.619 15.40 0.00 0.00 4.26
3727 4088 5.464168 GTTGATCTTGTGGTCTGAAATTGG 58.536 41.667 0.00 0.00 0.00 3.16
3745 4106 0.321653 GGTCTTGCAGGAACCATCGT 60.322 55.000 1.61 0.00 0.00 3.73
3807 4171 1.596477 GCCAAGGCATAGGAGAGCG 60.596 63.158 6.14 0.00 41.49 5.03
3823 4187 2.388232 GCGTCACCGTGGATGGAAC 61.388 63.158 0.00 0.00 36.15 3.62
3846 4219 3.433615 ACTCCGTAGTACGTAGTTGACAC 59.566 47.826 20.60 0.00 37.51 3.67
3851 4224 1.271656 AGTACGTAGTTGACACCCAGC 59.728 52.381 0.00 0.00 37.78 4.85
3933 4306 7.327032 GGCAAAAGAAAGATGAAACATCTGTAC 59.673 37.037 13.77 9.02 0.00 2.90
3935 4308 9.390795 CAAAAGAAAGATGAAACATCTGTACTG 57.609 33.333 13.77 0.00 0.00 2.74
3936 4309 8.682936 AAAGAAAGATGAAACATCTGTACTGT 57.317 30.769 13.77 7.23 0.00 3.55
3937 4310 9.778741 AAAGAAAGATGAAACATCTGTACTGTA 57.221 29.630 13.77 0.00 0.00 2.74
3938 4311 9.778741 AAGAAAGATGAAACATCTGTACTGTAA 57.221 29.630 13.77 0.00 0.00 2.41
3948 4321 5.742453 ACATCTGTACTGTAATTTCGTAGCG 59.258 40.000 0.00 0.00 0.00 4.26
3994 4371 6.769134 AATTGTAGGGTGCAGGTTAATTAC 57.231 37.500 0.00 0.00 0.00 1.89
4091 4472 2.280797 GGCACGCAACTCTGTCCA 60.281 61.111 0.00 0.00 0.00 4.02
4092 4473 1.891919 GGCACGCAACTCTGTCCAA 60.892 57.895 0.00 0.00 0.00 3.53
4093 4474 1.237285 GGCACGCAACTCTGTCCAAT 61.237 55.000 0.00 0.00 0.00 3.16
4094 4475 0.166814 GCACGCAACTCTGTCCAATC 59.833 55.000 0.00 0.00 0.00 2.67
4095 4476 1.800805 CACGCAACTCTGTCCAATCT 58.199 50.000 0.00 0.00 0.00 2.40
4096 4477 2.146342 CACGCAACTCTGTCCAATCTT 58.854 47.619 0.00 0.00 0.00 2.40
4097 4478 2.158449 CACGCAACTCTGTCCAATCTTC 59.842 50.000 0.00 0.00 0.00 2.87
4098 4479 1.734465 CGCAACTCTGTCCAATCTTCC 59.266 52.381 0.00 0.00 0.00 3.46
4099 4480 2.087646 GCAACTCTGTCCAATCTTCCC 58.912 52.381 0.00 0.00 0.00 3.97
4106 4487 5.046231 ACTCTGTCCAATCTTCCCTAAGAAC 60.046 44.000 0.00 0.00 44.75 3.01
4128 4519 6.939132 ACAAGCTCTTGATCCAAATCATAG 57.061 37.500 15.74 0.00 41.49 2.23
4141 4532 7.526142 TCCAAATCATAGCCACTAGTAGTAG 57.474 40.000 1.57 2.87 0.00 2.57
4142 4533 7.067421 TCCAAATCATAGCCACTAGTAGTAGT 58.933 38.462 1.57 4.29 40.38 2.73
4143 4534 8.222637 TCCAAATCATAGCCACTAGTAGTAGTA 58.777 37.037 9.94 0.00 37.40 1.82
4145 4536 9.900710 CAAATCATAGCCACTAGTAGTAGTAAG 57.099 37.037 9.94 6.30 37.40 2.34
4146 4537 9.643735 AAATCATAGCCACTAGTAGTAGTAAGT 57.356 33.333 9.94 0.88 37.40 2.24
4148 4539 9.947433 ATCATAGCCACTAGTAGTAGTAAGTAG 57.053 37.037 9.94 0.00 37.40 2.57
4150 4541 9.947433 CATAGCCACTAGTAGTAGTAAGTAGAT 57.053 37.037 9.94 0.00 37.40 1.98
4153 4544 9.777297 AGCCACTAGTAGTAGTAAGTAGATTAC 57.223 37.037 9.94 0.00 43.58 1.89
4181 4572 0.384309 TACATGCCGGAGATCGTGTC 59.616 55.000 5.05 0.00 37.11 3.67
4192 4595 1.079503 GATCGTGTCAACTTGGCTCC 58.920 55.000 0.00 0.00 0.00 4.70
4196 4599 1.168714 GTGTCAACTTGGCTCCATCC 58.831 55.000 0.00 0.00 0.00 3.51
4200 4603 1.064463 TCAACTTGGCTCCATCCATCC 60.064 52.381 0.00 0.00 35.77 3.51
4201 4604 1.002069 AACTTGGCTCCATCCATCCA 58.998 50.000 0.00 0.00 35.77 3.41
4203 4606 1.144503 ACTTGGCTCCATCCATCCATC 59.855 52.381 0.00 0.00 35.77 3.51
4204 4607 1.144298 CTTGGCTCCATCCATCCATCA 59.856 52.381 0.00 0.00 35.77 3.07
4208 4611 1.202903 GCTCCATCCATCCATCAAGCT 60.203 52.381 0.00 0.00 0.00 3.74
4209 4612 2.752154 GCTCCATCCATCCATCAAGCTT 60.752 50.000 0.00 0.00 0.00 3.74
4210 4613 3.147629 CTCCATCCATCCATCAAGCTTC 58.852 50.000 0.00 0.00 0.00 3.86
4211 4614 2.781757 TCCATCCATCCATCAAGCTTCT 59.218 45.455 0.00 0.00 0.00 2.85
4213 4616 3.434596 CCATCCATCCATCAAGCTTCTCA 60.435 47.826 0.00 0.00 0.00 3.27
4214 4617 4.399219 CATCCATCCATCAAGCTTCTCAT 58.601 43.478 0.00 0.00 0.00 2.90
4215 4618 3.816994 TCCATCCATCAAGCTTCTCATG 58.183 45.455 0.00 0.00 0.00 3.07
4216 4619 2.885266 CCATCCATCAAGCTTCTCATGG 59.115 50.000 17.43 17.43 37.70 3.66
4217 4620 2.048444 TCCATCAAGCTTCTCATGGC 57.952 50.000 18.26 0.00 36.49 4.40
4218 4621 0.661552 CCATCAAGCTTCTCATGGCG 59.338 55.000 13.29 0.00 29.71 5.69
4219 4622 1.660167 CATCAAGCTTCTCATGGCGA 58.340 50.000 0.00 0.00 0.00 5.54
4220 4623 1.598132 CATCAAGCTTCTCATGGCGAG 59.402 52.381 0.00 0.00 43.80 5.03
4221 4624 0.742281 TCAAGCTTCTCATGGCGAGC 60.742 55.000 0.00 6.92 41.98 5.03
4222 4625 0.743701 CAAGCTTCTCATGGCGAGCT 60.744 55.000 0.00 10.52 46.71 4.09
4223 4626 1.601171 AGCTTCTCATGGCGAGCTT 59.399 52.632 10.52 0.00 42.46 3.74
4224 4627 0.743701 AGCTTCTCATGGCGAGCTTG 60.744 55.000 10.52 0.00 42.46 4.01
4225 4628 1.720301 CTTCTCATGGCGAGCTTGC 59.280 57.895 18.32 18.32 41.98 4.01
4226 4629 1.003476 TTCTCATGGCGAGCTTGCA 60.003 52.632 27.02 13.69 41.98 4.08
4227 4630 0.393402 TTCTCATGGCGAGCTTGCAT 60.393 50.000 27.02 15.29 41.98 3.96
4228 4631 0.393402 TCTCATGGCGAGCTTGCATT 60.393 50.000 27.02 11.00 41.98 3.56
4229 4632 0.248498 CTCATGGCGAGCTTGCATTG 60.248 55.000 27.02 21.51 34.18 2.82
4230 4633 1.876714 CATGGCGAGCTTGCATTGC 60.877 57.895 27.02 10.44 36.28 3.56
4231 4634 2.344981 ATGGCGAGCTTGCATTGCA 61.345 52.632 27.02 15.81 36.47 4.08
4277 4680 3.771160 ACCACGATCGGGCTCACC 61.771 66.667 20.98 0.00 0.00 4.02
4331 4734 3.307445 CTCCTCACCAGGGAGCTG 58.693 66.667 0.00 0.00 42.95 4.24
4502 4905 2.663852 CCCACGTTGGTCACCGTC 60.664 66.667 0.00 0.00 35.17 4.79
4524 4927 2.122768 GGATGAAGTGGGTCCTCATCT 58.877 52.381 15.05 0.21 37.79 2.90
4530 4933 2.367202 TGGGTCCTCATCTTCGCCC 61.367 63.158 0.00 0.00 36.73 6.13
4650 5053 3.757248 ATCGCCCGGATGTTCTGCC 62.757 63.158 0.73 0.00 32.92 4.85
4677 5080 0.877743 GTTGAGGTTGCAGAGGAAGC 59.122 55.000 0.00 0.00 0.00 3.86
4799 5202 1.226717 GGTGGACTCGTCGAGCATC 60.227 63.158 22.00 12.67 36.15 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.105754 TGTATGTCCACCCATTTGACAA 57.894 40.909 0.00 0.00 41.85 3.18
20 21 3.574614 GCACAATGTTTGTATGTCCACC 58.425 45.455 0.00 0.00 43.23 4.61
24 25 6.435430 TCATAGGCACAATGTTTGTATGTC 57.565 37.500 0.00 0.00 43.23 3.06
32 33 3.966979 TGGTCATCATAGGCACAATGTT 58.033 40.909 0.00 0.00 0.00 2.71
48 53 6.814644 CGACTATATGTTTGTAGGTTTGGTCA 59.185 38.462 0.00 0.00 0.00 4.02
236 242 6.724694 TTTTTGCAAATGTATCCTCAATGC 57.275 33.333 13.65 0.00 35.93 3.56
265 271 9.521841 TGAGATAATTAGGAGATTACGTGAGAT 57.478 33.333 0.00 0.00 0.00 2.75
283 292 9.812347 TGTAGGCCAATGATATTTTGAGATAAT 57.188 29.630 5.01 0.00 0.00 1.28
289 298 7.573710 AGTAGTGTAGGCCAATGATATTTTGA 58.426 34.615 5.01 0.00 0.00 2.69
399 408 1.379843 ATGGGCGGTTGGGTTGATC 60.380 57.895 0.00 0.00 0.00 2.92
417 426 1.605971 CTCAGGCAGAGCAGAGCTGA 61.606 60.000 0.85 0.00 39.88 4.26
442 467 1.750399 GCAACGGCATGATGGAGGT 60.750 57.895 0.00 0.00 40.72 3.85
467 492 2.242452 AGGAAGGTTTAGAGGAATGGCC 59.758 50.000 0.00 0.00 0.00 5.36
535 560 5.390567 GGAGAAGCGGTGTTATGTTTAACTG 60.391 44.000 0.00 0.00 38.81 3.16
547 572 1.278985 TCATCAATGGAGAAGCGGTGT 59.721 47.619 0.00 0.00 0.00 4.16
549 574 1.278985 TGTCATCAATGGAGAAGCGGT 59.721 47.619 0.00 0.00 0.00 5.68
555 580 3.018856 GGCACAATGTCATCAATGGAGA 58.981 45.455 0.00 0.00 0.00 3.71
556 581 3.021695 AGGCACAATGTCATCAATGGAG 58.978 45.455 0.00 0.00 0.00 3.86
562 587 2.153645 GTGTCAGGCACAATGTCATCA 58.846 47.619 0.00 0.00 46.91 3.07
569 594 0.036732 ATGACCGTGTCAGGCACAAT 59.963 50.000 5.87 0.00 46.04 2.71
575 600 1.739466 CCAATTCATGACCGTGTCAGG 59.261 52.381 11.02 11.02 46.04 3.86
590 615 2.203209 GGCGAGGCCGATCCAATT 60.203 61.111 0.00 0.00 39.62 2.32
656 682 1.560923 CATCGGTCGATTCCTCACAC 58.439 55.000 2.84 0.00 31.62 3.82
683 714 8.026607 TCAACATTTTCGGATTTCCTAAACATC 58.973 33.333 0.00 0.00 31.47 3.06
685 716 7.142680 GTCAACATTTTCGGATTTCCTAAACA 58.857 34.615 0.00 0.00 31.47 2.83
689 720 6.001460 AGTGTCAACATTTTCGGATTTCCTA 58.999 36.000 0.00 0.00 0.00 2.94
690 721 4.827284 AGTGTCAACATTTTCGGATTTCCT 59.173 37.500 0.00 0.00 0.00 3.36
691 722 5.121221 AGTGTCAACATTTTCGGATTTCC 57.879 39.130 0.00 0.00 0.00 3.13
732 849 6.247582 CCGCGTTAATTTTGTATATATTGGCG 59.752 38.462 4.92 0.00 36.52 5.69
744 861 2.843643 CGATGTTCCCGCGTTAATTTTG 59.156 45.455 4.92 0.00 0.00 2.44
794 914 0.806492 GCTACTTGCTCTGGTACCGC 60.806 60.000 7.57 5.31 38.95 5.68
814 934 3.160872 CATGCATGCCAATTGCCAA 57.839 47.368 14.93 0.00 39.39 4.52
815 935 4.943822 CATGCATGCCAATTGCCA 57.056 50.000 14.93 0.00 39.39 4.92
1052 1200 4.075793 CCAGGAGGAGGACGGGGA 62.076 72.222 0.00 0.00 36.89 4.81
1083 1240 0.878523 CGAACTCGGTGTTGAAGCCA 60.879 55.000 0.00 0.00 39.30 4.75
1107 1264 1.657751 GGAGCTTGGGCGATTTGTCC 61.658 60.000 0.00 0.00 45.24 4.02
1167 1324 5.862678 TGGATGATTGATAGTACAACCGA 57.137 39.130 0.00 0.00 32.50 4.69
1169 1326 5.940470 GGGATGGATGATTGATAGTACAACC 59.060 44.000 0.00 0.00 32.50 3.77
1173 1331 4.759782 CCGGGATGGATGATTGATAGTAC 58.240 47.826 0.00 0.00 42.00 2.73
1178 1336 0.321919 CGCCGGGATGGATGATTGAT 60.322 55.000 2.18 0.00 42.00 2.57
1209 1367 0.515127 TTCACCTGCGCGTAAATGTG 59.485 50.000 8.43 11.17 0.00 3.21
1376 1556 2.164422 GGAGAGTGGTTTAATTGCCTGC 59.836 50.000 0.00 0.00 0.00 4.85
1433 1616 2.783609 ATGCAGCTCAGAACAGATGT 57.216 45.000 0.00 0.00 32.07 3.06
1584 1771 4.572909 TGGATAATGATCGAAGCAGATGG 58.427 43.478 0.00 0.00 32.28 3.51
1596 1783 8.886719 CGCACTGATAATGTAATGGATAATGAT 58.113 33.333 0.00 0.00 0.00 2.45
1601 1790 5.408299 GCACGCACTGATAATGTAATGGATA 59.592 40.000 0.00 0.00 0.00 2.59
1612 1801 2.158330 CGCTCGCACGCACTGATAA 61.158 57.895 0.00 0.00 0.00 1.75
1613 1802 2.579518 CGCTCGCACGCACTGATA 60.580 61.111 0.00 0.00 0.00 2.15
1746 1967 0.826715 CCTCGAAGATCTTGAGCCCA 59.173 55.000 14.00 0.00 33.89 5.36
1792 2013 5.862924 AACTGATTTACGATTCAGGTGTG 57.137 39.130 5.08 0.00 42.93 3.82
1815 2040 8.200120 ATACGAGTAGTAGTATATATGGCGACA 58.800 37.037 0.00 0.00 41.60 4.35
1831 2056 9.775854 AATCACATGTACTAGTATACGAGTAGT 57.224 33.333 21.79 15.10 44.89 2.73
1844 2074 1.930503 CGCCGCAAATCACATGTACTA 59.069 47.619 0.00 0.00 0.00 1.82
1846 2076 0.724549 TCGCCGCAAATCACATGTAC 59.275 50.000 0.00 0.00 0.00 2.90
1924 2154 2.668212 TCGAAGGCCGCCTTGTTG 60.668 61.111 29.60 17.65 44.82 3.33
1966 2196 2.672996 GTGGTGCTGACGGCCATT 60.673 61.111 2.24 0.00 40.92 3.16
2076 2309 1.140652 TGAATGATGATACTGCCGCCA 59.859 47.619 0.00 0.00 0.00 5.69
2165 2404 1.334384 GGAGCCTCCTGGTCTCCTTC 61.334 65.000 18.34 2.66 45.20 3.46
2183 2422 1.675641 CAGGCTCCTCGGTTTTGGG 60.676 63.158 0.00 0.00 0.00 4.12
2314 2553 4.521062 CCGCCGAGGCAGAAGAGG 62.521 72.222 15.03 2.03 42.06 3.69
2400 2652 2.613691 CAAGCCCTGAATGTGAAATGC 58.386 47.619 0.00 0.00 0.00 3.56
2409 2661 0.407139 AGGAAGTGCAAGCCCTGAAT 59.593 50.000 0.00 0.00 0.00 2.57
2505 2783 3.557054 CCAGACGATGTCCCTCAGAAAAA 60.557 47.826 0.00 0.00 32.18 1.94
2506 2784 2.028112 CCAGACGATGTCCCTCAGAAAA 60.028 50.000 0.00 0.00 32.18 2.29
2507 2785 1.550524 CCAGACGATGTCCCTCAGAAA 59.449 52.381 0.00 0.00 32.18 2.52
2508 2786 1.186200 CCAGACGATGTCCCTCAGAA 58.814 55.000 0.00 0.00 32.18 3.02
2509 2787 1.323271 GCCAGACGATGTCCCTCAGA 61.323 60.000 0.00 0.00 32.18 3.27
2510 2788 1.142748 GCCAGACGATGTCCCTCAG 59.857 63.158 0.00 0.00 32.18 3.35
2511 2789 3.298958 GCCAGACGATGTCCCTCA 58.701 61.111 0.00 0.00 32.18 3.86
2522 2800 4.437390 CCACATCAAATTAAGACGCCAGAC 60.437 45.833 0.00 0.00 0.00 3.51
2523 2801 3.689161 CCACATCAAATTAAGACGCCAGA 59.311 43.478 0.00 0.00 0.00 3.86
2524 2802 3.181497 CCCACATCAAATTAAGACGCCAG 60.181 47.826 0.00 0.00 0.00 4.85
2525 2803 2.752354 CCCACATCAAATTAAGACGCCA 59.248 45.455 0.00 0.00 0.00 5.69
2526 2804 2.752903 ACCCACATCAAATTAAGACGCC 59.247 45.455 0.00 0.00 0.00 5.68
2527 2805 3.427503 CCACCCACATCAAATTAAGACGC 60.428 47.826 0.00 0.00 0.00 5.19
2528 2806 3.128589 CCCACCCACATCAAATTAAGACG 59.871 47.826 0.00 0.00 0.00 4.18
2529 2807 3.119137 GCCCACCCACATCAAATTAAGAC 60.119 47.826 0.00 0.00 0.00 3.01
2719 2997 7.254387 CGCTGGAATTTGACAAATTTTCTTTGA 60.254 33.333 23.46 6.58 40.97 2.69
2729 3007 2.863137 GCAAACGCTGGAATTTGACAAA 59.137 40.909 2.48 2.48 37.91 2.83
2734 3028 3.122297 TGAAAGCAAACGCTGGAATTTG 58.878 40.909 0.00 0.00 40.49 2.32
2743 3037 4.210955 TGGAAATCAAATGAAAGCAAACGC 59.789 37.500 0.00 0.00 0.00 4.84
2754 3052 9.258826 TCAAGTAAAACACATGGAAATCAAATG 57.741 29.630 0.00 0.00 0.00 2.32
2795 3100 0.329931 TGCCGATGCCCTAGGAAAAA 59.670 50.000 11.48 0.00 36.33 1.94
2800 3105 0.675837 CATCATGCCGATGCCCTAGG 60.676 60.000 0.06 0.06 44.95 3.02
2834 3139 3.698029 ATGTTCGGCATTTGCACTATC 57.302 42.857 4.74 0.00 44.36 2.08
2849 3154 7.739498 TGGTGGTCTTCTTACTTTTATGTTC 57.261 36.000 0.00 0.00 0.00 3.18
2865 3170 2.501128 CGATGGCGATGGTGGTCT 59.499 61.111 0.00 0.00 40.82 3.85
2866 3171 3.272334 GCGATGGCGATGGTGGTC 61.272 66.667 0.00 0.00 40.82 4.02
2868 3173 4.854924 TGGCGATGGCGATGGTGG 62.855 66.667 0.00 0.00 41.24 4.61
2878 3183 2.359848 ACAATGAATGTCCATGGCGATG 59.640 45.455 6.96 1.01 37.96 3.84
2879 3184 2.658285 ACAATGAATGTCCATGGCGAT 58.342 42.857 6.96 0.00 37.96 4.58
2882 3187 2.954318 AGCTACAATGAATGTCCATGGC 59.046 45.455 6.96 2.72 42.70 4.40
2898 3203 3.802948 TTGCTTAGCCAGAGTAGCTAC 57.197 47.619 16.43 16.43 42.37 3.58
2913 3226 3.057033 GTGCAAGATCACTCCAATTGCTT 60.057 43.478 12.90 0.00 44.99 3.91
2914 3227 2.490903 GTGCAAGATCACTCCAATTGCT 59.509 45.455 12.90 0.00 44.99 3.91
2915 3228 2.229543 TGTGCAAGATCACTCCAATTGC 59.770 45.455 0.00 6.63 44.97 3.56
2922 3235 6.259550 ACCTAAAAATGTGCAAGATCACTC 57.740 37.500 0.00 0.00 37.81 3.51
2924 3237 5.119125 GCAACCTAAAAATGTGCAAGATCAC 59.881 40.000 0.00 0.00 37.48 3.06
3065 3403 3.010920 AGGGGTTATACAGGGGTTTTGTC 59.989 47.826 0.00 0.00 0.00 3.18
3066 3404 2.998186 AGGGGTTATACAGGGGTTTTGT 59.002 45.455 0.00 0.00 0.00 2.83
3067 3405 3.361786 CAGGGGTTATACAGGGGTTTTG 58.638 50.000 0.00 0.00 0.00 2.44
3068 3406 2.291996 GCAGGGGTTATACAGGGGTTTT 60.292 50.000 0.00 0.00 0.00 2.43
3072 3410 0.474184 CTGCAGGGGTTATACAGGGG 59.526 60.000 5.57 0.00 0.00 4.79
3078 3416 1.691976 CGGATCACTGCAGGGGTTATA 59.308 52.381 17.80 0.00 0.00 0.98
3084 3422 0.533755 GGAATCGGATCACTGCAGGG 60.534 60.000 19.93 15.69 0.00 4.45
3092 3430 2.798145 CGTTGTGATCGGAATCGGATCA 60.798 50.000 23.74 23.74 34.39 2.92
3093 3431 1.787155 CGTTGTGATCGGAATCGGATC 59.213 52.381 19.80 19.80 34.39 3.36
3095 3433 0.804544 GCGTTGTGATCGGAATCGGA 60.805 55.000 0.00 0.00 34.39 4.55
3096 3434 1.636340 GCGTTGTGATCGGAATCGG 59.364 57.895 0.00 0.00 34.39 4.18
3101 3439 4.395080 GATCGCGTTGTGATCGGA 57.605 55.556 5.77 0.00 39.28 4.55
3104 3442 3.000674 CACTTACTGATCGCGTTGTGATC 60.001 47.826 5.77 12.23 46.15 2.92
3105 3443 2.923655 CACTTACTGATCGCGTTGTGAT 59.076 45.455 5.77 0.00 35.33 3.06
3107 3445 1.201812 GCACTTACTGATCGCGTTGTG 60.202 52.381 5.77 2.28 0.00 3.33
3108 3446 1.068474 GCACTTACTGATCGCGTTGT 58.932 50.000 5.77 3.66 0.00 3.32
3109 3447 1.350193 AGCACTTACTGATCGCGTTG 58.650 50.000 5.77 0.00 0.00 4.10
3111 3449 2.527100 GTAAGCACTTACTGATCGCGT 58.473 47.619 5.77 0.00 41.51 6.01
3112 3450 1.513178 CGTAAGCACTTACTGATCGCG 59.487 52.381 16.31 0.00 42.31 5.87
3113 3451 2.530700 GTCGTAAGCACTTACTGATCGC 59.469 50.000 16.31 3.68 42.31 4.58
3114 3452 2.776765 CGTCGTAAGCACTTACTGATCG 59.223 50.000 16.31 15.06 42.31 3.69
3116 3454 2.527100 GCGTCGTAAGCACTTACTGAT 58.473 47.619 16.31 0.00 42.31 2.90
3117 3455 1.726892 CGCGTCGTAAGCACTTACTGA 60.727 52.381 16.31 12.59 42.31 3.41
3119 3457 0.239347 ACGCGTCGTAAGCACTTACT 59.761 50.000 5.58 0.00 42.31 2.24
3120 3458 0.361184 CACGCGTCGTAAGCACTTAC 59.639 55.000 9.86 9.98 38.32 2.34
3121 3459 0.040157 ACACGCGTCGTAAGCACTTA 60.040 50.000 9.86 0.00 38.32 2.24
3122 3460 1.299620 ACACGCGTCGTAAGCACTT 60.300 52.632 9.86 0.00 38.32 3.16
3123 3461 2.014554 CACACGCGTCGTAAGCACT 61.015 57.895 9.86 0.00 38.32 4.40
3124 3462 2.464189 CACACGCGTCGTAAGCAC 59.536 61.111 9.86 0.00 38.32 4.40
3125 3463 3.399770 GCACACGCGTCGTAAGCA 61.400 61.111 9.86 0.00 38.32 3.91
3142 3480 1.665679 GGCAACCTACATCACATGTCG 59.334 52.381 0.00 0.00 43.67 4.35
3143 3481 2.710377 TGGCAACCTACATCACATGTC 58.290 47.619 0.00 0.00 43.67 3.06
3145 3483 2.424601 CCTTGGCAACCTACATCACATG 59.575 50.000 0.00 0.00 0.00 3.21
3339 3677 5.049336 CGGTAATTATGTTGTGTTGTGTCCA 60.049 40.000 0.00 0.00 0.00 4.02
3340 3678 5.387279 CGGTAATTATGTTGTGTTGTGTCC 58.613 41.667 0.00 0.00 0.00 4.02
3341 3679 5.387279 CCGGTAATTATGTTGTGTTGTGTC 58.613 41.667 0.00 0.00 0.00 3.67
3342 3680 4.320641 GCCGGTAATTATGTTGTGTTGTGT 60.321 41.667 1.90 0.00 0.00 3.72
3343 3681 4.083003 AGCCGGTAATTATGTTGTGTTGTG 60.083 41.667 1.90 0.00 0.00 3.33
3344 3682 4.076394 AGCCGGTAATTATGTTGTGTTGT 58.924 39.130 1.90 0.00 0.00 3.32
3345 3683 4.411327 CAGCCGGTAATTATGTTGTGTTG 58.589 43.478 1.90 0.00 0.00 3.33
3487 3834 2.884012 TGTTGATGGCACTAGGTTGTTG 59.116 45.455 0.00 0.00 0.00 3.33
3493 3840 4.422073 TCCTAATGTTGATGGCACTAGG 57.578 45.455 0.00 0.00 0.00 3.02
3495 3842 4.080356 AGCTTCCTAATGTTGATGGCACTA 60.080 41.667 0.00 0.00 0.00 2.74
3497 3844 3.019564 AGCTTCCTAATGTTGATGGCAC 58.980 45.455 0.00 0.00 0.00 5.01
3498 3845 3.018856 CAGCTTCCTAATGTTGATGGCA 58.981 45.455 0.00 0.00 0.00 4.92
3499 3846 3.019564 ACAGCTTCCTAATGTTGATGGC 58.980 45.455 0.00 0.00 0.00 4.40
3506 3853 4.697352 CAGTTAGCAACAGCTTCCTAATGT 59.303 41.667 0.00 0.00 39.77 2.71
3512 3859 6.763610 AGTTATATCAGTTAGCAACAGCTTCC 59.236 38.462 0.00 0.00 39.77 3.46
3531 3878 7.340256 ACATCGTCAATTTTGGGGTAGTTATA 58.660 34.615 0.00 0.00 0.00 0.98
3556 3903 2.764010 ACATACGTGAATGACAGGCCTA 59.236 45.455 3.98 0.00 37.84 3.93
3680 4027 4.496360 CATATGAGCTCGAGATTCTGCAT 58.504 43.478 18.75 12.08 0.00 3.96
3683 4030 3.257873 ACCCATATGAGCTCGAGATTCTG 59.742 47.826 18.75 6.21 0.00 3.02
3698 4046 4.474651 TCAGACCACAAGATCAACCCATAT 59.525 41.667 0.00 0.00 0.00 1.78
3727 4088 1.197721 CAACGATGGTTCCTGCAAGAC 59.802 52.381 0.00 0.00 31.02 3.01
3762 4123 3.847602 CTGGCTGAGCTCCCCTCG 61.848 72.222 12.15 3.98 43.82 4.63
3807 4171 0.034896 AGTGTTCCATCCACGGTGAC 59.965 55.000 10.28 0.00 37.88 3.67
3830 4194 2.489329 GCTGGGTGTCAACTACGTACTA 59.511 50.000 0.00 0.00 0.00 1.82
3832 4196 1.670967 GGCTGGGTGTCAACTACGTAC 60.671 57.143 0.00 0.00 0.00 3.67
3834 4198 1.119574 AGGCTGGGTGTCAACTACGT 61.120 55.000 0.00 0.00 0.00 3.57
3836 4200 1.523758 CAAGGCTGGGTGTCAACTAC 58.476 55.000 0.00 0.00 0.00 2.73
3851 4224 4.832608 GTACGCCCGGAGCCAAGG 62.833 72.222 0.73 0.00 38.78 3.61
3933 4306 7.111139 CACTAACAATCGCTACGAAATTACAG 58.889 38.462 0.00 0.00 39.99 2.74
3935 4308 6.892951 CACACTAACAATCGCTACGAAATTAC 59.107 38.462 0.00 0.00 39.99 1.89
3936 4309 6.587226 ACACACTAACAATCGCTACGAAATTA 59.413 34.615 0.00 0.00 39.99 1.40
3937 4310 5.407387 ACACACTAACAATCGCTACGAAATT 59.593 36.000 0.00 0.00 39.99 1.82
3938 4311 4.927425 ACACACTAACAATCGCTACGAAAT 59.073 37.500 0.00 0.00 39.99 2.17
4091 4472 5.770685 AGAGCTTGTTCTTAGGGAAGATT 57.229 39.130 0.00 0.00 41.40 2.40
4092 4473 5.249393 TCAAGAGCTTGTTCTTAGGGAAGAT 59.751 40.000 9.79 0.00 39.06 2.40
4093 4474 4.593206 TCAAGAGCTTGTTCTTAGGGAAGA 59.407 41.667 9.79 0.00 41.16 2.87
4094 4475 4.899502 TCAAGAGCTTGTTCTTAGGGAAG 58.100 43.478 9.79 0.00 41.16 3.46
4095 4476 4.974645 TCAAGAGCTTGTTCTTAGGGAA 57.025 40.909 9.79 0.00 41.16 3.97
4096 4477 4.080863 GGATCAAGAGCTTGTTCTTAGGGA 60.081 45.833 16.50 0.00 41.16 4.20
4097 4478 4.195416 GGATCAAGAGCTTGTTCTTAGGG 58.805 47.826 16.50 0.00 41.16 3.53
4098 4479 4.836825 TGGATCAAGAGCTTGTTCTTAGG 58.163 43.478 16.50 0.00 41.16 2.69
4099 4480 6.808008 TTTGGATCAAGAGCTTGTTCTTAG 57.192 37.500 16.50 0.00 41.16 2.18
4106 4487 5.278364 GGCTATGATTTGGATCAAGAGCTTG 60.278 44.000 18.23 3.87 45.50 4.01
4128 4519 8.707839 CGTAATCTACTTACTACTACTAGTGGC 58.292 40.741 5.39 0.00 38.05 5.01
4142 4533 8.986847 GCATGTAGAGACTACGTAATCTACTTA 58.013 37.037 26.37 16.56 42.91 2.24
4143 4534 7.041235 GGCATGTAGAGACTACGTAATCTACTT 60.041 40.741 26.37 21.61 42.91 2.24
4145 4536 6.601264 GGCATGTAGAGACTACGTAATCTAC 58.399 44.000 22.96 22.96 42.83 2.59
4146 4537 5.407691 CGGCATGTAGAGACTACGTAATCTA 59.592 44.000 6.52 7.08 0.00 1.98
4147 4538 4.213694 CGGCATGTAGAGACTACGTAATCT 59.786 45.833 6.20 6.20 0.00 2.40
4148 4539 4.465016 CGGCATGTAGAGACTACGTAATC 58.535 47.826 0.00 0.00 0.00 1.75
4150 4541 2.615447 CCGGCATGTAGAGACTACGTAA 59.385 50.000 0.00 0.00 0.00 3.18
4151 4542 2.158914 TCCGGCATGTAGAGACTACGTA 60.159 50.000 0.00 0.00 0.00 3.57
4152 4543 1.022735 CCGGCATGTAGAGACTACGT 58.977 55.000 0.00 0.00 0.00 3.57
4153 4544 1.264557 CTCCGGCATGTAGAGACTACG 59.735 57.143 0.00 0.00 0.00 3.51
4155 4546 3.413327 GATCTCCGGCATGTAGAGACTA 58.587 50.000 11.92 0.00 39.36 2.59
4156 4547 2.235016 GATCTCCGGCATGTAGAGACT 58.765 52.381 11.92 4.49 39.36 3.24
4157 4548 1.068885 CGATCTCCGGCATGTAGAGAC 60.069 57.143 11.92 7.16 39.36 3.36
4158 4549 1.239347 CGATCTCCGGCATGTAGAGA 58.761 55.000 12.03 12.03 40.73 3.10
4159 4550 0.955178 ACGATCTCCGGCATGTAGAG 59.045 55.000 0.00 0.00 43.93 2.43
4181 4572 1.341285 TGGATGGATGGAGCCAAGTTG 60.341 52.381 0.00 0.00 42.16 3.16
4192 4595 3.816994 TGAGAAGCTTGATGGATGGATG 58.183 45.455 2.10 0.00 0.00 3.51
4196 4599 2.293677 GCCATGAGAAGCTTGATGGATG 59.706 50.000 23.82 11.22 38.10 3.51
4200 4603 1.660167 TCGCCATGAGAAGCTTGATG 58.340 50.000 2.10 3.13 0.00 3.07
4211 4614 1.804598 CAATGCAAGCTCGCCATGA 59.195 52.632 0.00 0.00 0.00 3.07
4213 4616 1.672854 ATGCAATGCAAGCTCGCCAT 61.673 50.000 13.45 0.00 43.62 4.40
4214 4617 2.344981 ATGCAATGCAAGCTCGCCA 61.345 52.632 13.45 0.00 43.62 5.69
4215 4618 1.876714 CATGCAATGCAAGCTCGCC 60.877 57.895 13.45 0.00 43.62 5.54
4216 4619 3.688136 CATGCAATGCAAGCTCGC 58.312 55.556 13.45 0.00 43.62 5.03
4502 4905 1.264749 TGAGGACCCACTTCATCCGG 61.265 60.000 0.00 0.00 37.60 5.14
4554 4957 2.147433 AACTACCCGTCCCTCTCCGT 62.147 60.000 0.00 0.00 0.00 4.69
4559 4962 0.614134 ACCTCAACTACCCGTCCCTC 60.614 60.000 0.00 0.00 0.00 4.30
4650 5053 0.250124 TGCAACCTCAACTACACGGG 60.250 55.000 0.00 0.00 0.00 5.28
4691 5094 3.017314 GTCTACGACATCGCGCCG 61.017 66.667 0.00 0.60 44.43 6.46


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

AutoCloner maintained by Alex Coulton.