Multiple sequence alignment - TraesCS3D01G159700

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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 TraesCS3D01G159700 chr3D 100.000 3235 0 0 1 3235 129396108 129399342 0.000000e+00 5975.0
1 TraesCS3D01G159700 chr3D 89.655 319 23 2 51 359 7579374 7579056 6.500000e-107 398.0
2 TraesCS3D01G159700 chr3A 95.528 2102 56 14 728 2798 141909787 141911881 0.000000e+00 3326.0
3 TraesCS3D01G159700 chr3A 90.024 421 39 3 2811 3228 371621299 371621719 2.840000e-150 542.0
4 TraesCS3D01G159700 chr3A 100.000 33 0 0 13 45 663479481 663479449 9.690000e-06 62.1
5 TraesCS3D01G159700 chr3B 95.127 1929 61 12 729 2636 183542269 183544185 0.000000e+00 3011.0
6 TraesCS3D01G159700 chr3B 96.341 82 3 0 2619 2700 183544199 183544280 5.630000e-28 135.0
7 TraesCS3D01G159700 chr3B 89.796 98 7 3 2699 2793 183544437 183544534 4.380000e-24 122.0
8 TraesCS3D01G159700 chr1D 83.478 690 89 12 51 725 377968282 377967603 1.270000e-173 619.0
9 TraesCS3D01G159700 chr1D 92.056 428 27 7 2811 3235 445288320 445288743 2.150000e-166 595.0
10 TraesCS3D01G159700 chr1D 90.164 427 34 5 2811 3235 332076028 332075608 1.700000e-152 549.0
11 TraesCS3D01G159700 chr5D 91.962 423 30 2 2814 3235 449257663 449257244 1.000000e-164 590.0
12 TraesCS3D01G159700 chr5D 84.716 229 25 2 51 269 533268501 533268729 1.510000e-53 220.0
13 TraesCS3D01G159700 chr7A 91.745 424 33 2 2814 3235 17353207 17352784 3.600000e-164 588.0
14 TraesCS3D01G159700 chr7A 88.837 430 43 4 2811 3235 434752787 434753216 1.030000e-144 523.0
15 TraesCS3D01G159700 chr7A 81.982 111 17 2 618 725 493462118 493462008 1.240000e-14 91.6
16 TraesCS3D01G159700 chr7A 88.732 71 8 0 619 689 105245424 105245354 1.600000e-13 87.9
17 TraesCS3D01G159700 chr7B 90.521 422 39 1 2814 3234 677716502 677716923 1.010000e-154 556.0
18 TraesCS3D01G159700 chr7B 100.000 37 0 0 11 47 741101659 741101695 5.790000e-08 69.4
19 TraesCS3D01G159700 chr7B 97.297 37 1 0 11 47 738394583 738394619 2.690000e-06 63.9
20 TraesCS3D01G159700 chr2D 90.187 428 39 3 2811 3235 25658293 25657866 3.650000e-154 555.0
21 TraesCS3D01G159700 chr2D 89.930 427 40 3 2811 3235 649551618 649551193 6.100000e-152 547.0
22 TraesCS3D01G159700 chr2D 89.969 319 21 3 51 359 449561710 449562027 5.030000e-108 401.0
23 TraesCS3D01G159700 chr2D 83.913 230 25 4 51 269 203456970 203457198 3.270000e-50 209.0
24 TraesCS3D01G159700 chr7D 89.688 320 21 5 51 359 70900881 70901199 6.500000e-107 398.0
25 TraesCS3D01G159700 chr7D 89.000 100 8 2 139 237 117882539 117882636 1.580000e-23 121.0
26 TraesCS3D01G159700 chr7D 89.000 100 8 2 139 237 397203659 397203756 1.580000e-23 121.0
27 TraesCS3D01G159700 chr7D 80.180 111 15 7 619 724 43662774 43662666 3.460000e-10 76.8
28 TraesCS3D01G159700 chr7D 100.000 35 0 0 13 47 531050530 531050496 7.490000e-07 65.8
29 TraesCS3D01G159700 chr2B 91.000 100 6 3 139 237 58099815 58099912 7.280000e-27 132.0
30 TraesCS3D01G159700 chr6D 86.170 94 9 3 600 691 76130689 76130780 7.390000e-17 99.0
31 TraesCS3D01G159700 chr4B 81.818 110 17 2 619 725 10968983 10968874 4.450000e-14 89.8
32 TraesCS3D01G159700 chr4B 76.282 156 28 7 575 724 10970225 10970377 1.240000e-09 75.0
33 TraesCS3D01G159700 chr1A 84.270 89 14 0 619 707 425711434 425711346 1.600000e-13 87.9
34 TraesCS3D01G159700 chr6B 86.667 75 9 1 619 692 64860446 64860372 7.440000e-12 82.4
35 TraesCS3D01G159700 chr5B 100.000 39 0 0 9 47 672192790 672192828 4.480000e-09 73.1


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 TraesCS3D01G159700 chr3D 129396108 129399342 3234 False 5975.000000 5975 100.000000 1 3235 1 chr3D.!!$F1 3234
1 TraesCS3D01G159700 chr3A 141909787 141911881 2094 False 3326.000000 3326 95.528000 728 2798 1 chr3A.!!$F1 2070
2 TraesCS3D01G159700 chr3B 183542269 183544534 2265 False 1089.333333 3011 93.754667 729 2793 3 chr3B.!!$F1 2064
3 TraesCS3D01G159700 chr1D 377967603 377968282 679 True 619.000000 619 83.478000 51 725 1 chr1D.!!$R2 674

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
547 560 0.039035 AAAAATGCTCCCGGCCACTA 59.961 50.0 2.24 0.00 40.92 2.74 F
598 611 0.319555 CGTGGGTATGGCCTATGACG 60.320 60.0 3.32 1.01 36.93 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1631 1.005450 GCCATAGGGGTTGTTGGAGAA 59.995 52.381 0.0 0.0 39.65 2.87 R
2584 2644 1.071239 CGAGCATCCGAGCAAAATACG 60.071 52.381 0.0 0.0 36.85 3.06 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
32 33 4.652679 TTTTAGAAAAGGAGGAGGACCC 57.347 45.455 0.00 0.00 36.73 4.46
42 43 3.791586 GAGGACCCTGGCCTCTGC 61.792 72.222 8.79 0.00 46.70 4.26
43 44 4.664267 AGGACCCTGGCCTCTGCA 62.664 66.667 3.32 0.00 40.13 4.41
44 45 3.415087 GGACCCTGGCCTCTGCAT 61.415 66.667 3.32 0.00 40.13 3.96
45 46 2.191641 GACCCTGGCCTCTGCATC 59.808 66.667 3.32 0.00 40.13 3.91
46 47 2.285969 ACCCTGGCCTCTGCATCT 60.286 61.111 3.32 0.00 40.13 2.90
47 48 1.919600 GACCCTGGCCTCTGCATCTT 61.920 60.000 3.32 0.00 40.13 2.40
48 49 0.621571 ACCCTGGCCTCTGCATCTTA 60.622 55.000 3.32 0.00 40.13 2.10
49 50 0.108207 CCCTGGCCTCTGCATCTTAG 59.892 60.000 3.32 0.00 40.13 2.18
59 60 6.071108 GGCCTCTGCATCTTAGTATCTCATTA 60.071 42.308 0.00 0.00 40.13 1.90
64 65 6.159293 TGCATCTTAGTATCTCATTAAGGCG 58.841 40.000 0.00 0.00 29.65 5.52
79 80 1.238439 AGGCGTCAAATGGTGTCTTG 58.762 50.000 0.00 0.00 0.00 3.02
96 97 3.002348 GTCTTGTCTGTTGGTTAGCACAC 59.998 47.826 0.00 0.00 0.00 3.82
99 100 1.260561 GTCTGTTGGTTAGCACACACG 59.739 52.381 0.00 0.00 0.00 4.49
102 103 2.887889 TTGGTTAGCACACACGCGC 61.888 57.895 5.73 0.00 36.85 6.86
126 127 2.300967 TAGCACCAAGAGGGCCCTG 61.301 63.158 34.59 18.36 42.05 4.45
129 130 4.617595 ACCAAGAGGGCCCTGGGT 62.618 66.667 34.59 29.54 42.05 4.51
144 145 4.803452 CCCTGGGTGAACAATATAACCAT 58.197 43.478 3.97 0.00 34.18 3.55
160 161 1.742880 CATGAGGCAGGACACCACG 60.743 63.158 0.00 0.00 0.00 4.94
306 318 1.289066 CTGAGCTCGTGGGTTCGAA 59.711 57.895 9.64 0.00 39.34 3.71
307 319 0.319555 CTGAGCTCGTGGGTTCGAAA 60.320 55.000 9.64 0.00 39.34 3.46
323 335 3.741805 CGAAACTTCGGATCCCTTTTC 57.258 47.619 6.06 8.73 46.30 2.29
337 350 7.201741 CGGATCCCTTTTCCTTTCTTATTTCTC 60.202 40.741 6.06 0.00 0.00 2.87
373 386 9.938670 TCACACGGTATTATTATTACAAATTGC 57.061 29.630 0.00 0.00 0.00 3.56
391 404 7.220683 ACAAATTGCGTTATATCTGTGATTTGC 59.779 33.333 0.00 0.00 36.14 3.68
393 406 6.375945 TTGCGTTATATCTGTGATTTGCAT 57.624 33.333 0.00 0.00 0.00 3.96
398 411 8.655970 GCGTTATATCTGTGATTTGCATATACA 58.344 33.333 0.00 0.00 0.00 2.29
399 412 9.958285 CGTTATATCTGTGATTTGCATATACAC 57.042 33.333 10.50 10.50 0.00 2.90
402 415 5.109500 TCTGTGATTTGCATATACACCCA 57.891 39.130 13.08 0.00 0.00 4.51
423 436 2.564771 TGCTTGGTGTAGCTGATATGC 58.435 47.619 0.00 0.00 41.76 3.14
432 445 1.148273 GCTGATATGCGGGACCCAA 59.852 57.895 12.15 0.00 0.00 4.12
441 454 1.302511 CGGGACCCAAACCTGACAG 60.303 63.158 12.15 0.00 35.98 3.51
455 468 2.430465 CTGACAGGTTGAACCCATCAG 58.570 52.381 23.19 23.19 41.47 2.90
457 470 2.224523 TGACAGGTTGAACCCATCAGTC 60.225 50.000 11.41 11.68 39.75 3.51
470 483 2.224137 CCATCAGTCTGCATCCGTATGT 60.224 50.000 0.00 0.00 35.38 2.29
488 501 9.990360 TCCGTATGTGATACAATTATGTGTAAT 57.010 29.630 0.00 0.00 40.84 1.89
529 542 2.569853 TGAGGGGATTCTCGCTGTAAAA 59.430 45.455 0.00 0.00 36.61 1.52
547 560 0.039035 AAAAATGCTCCCGGCCACTA 59.961 50.000 2.24 0.00 40.92 2.74
556 569 2.435938 CGGCCACTAACATGCGGT 60.436 61.111 2.24 0.00 0.00 5.68
558 571 2.112815 GGCCACTAACATGCGGTCC 61.113 63.158 0.00 0.00 0.00 4.46
579 592 1.815421 CACCATACTGGCTCGCCAC 60.815 63.158 6.52 0.00 42.67 5.01
581 594 2.184322 CATACTGGCTCGCCACGT 59.816 61.111 6.52 11.54 41.89 4.49
587 600 4.157120 GGCTCGCCACGTGGGTAT 62.157 66.667 34.58 0.00 39.65 2.73
589 602 2.202878 CTCGCCACGTGGGTATGG 60.203 66.667 34.58 10.08 39.65 2.74
596 609 0.756294 CACGTGGGTATGGCCTATGA 59.244 55.000 7.95 0.00 38.05 2.15
598 611 0.319555 CGTGGGTATGGCCTATGACG 60.320 60.000 3.32 1.01 36.93 4.35
604 617 3.039011 GGTATGGCCTATGACGGGATAT 58.961 50.000 3.32 0.00 0.00 1.63
605 618 3.181465 GGTATGGCCTATGACGGGATATG 60.181 52.174 3.32 0.00 0.00 1.78
609 622 2.835764 GGCCTATGACGGGATATGGTAA 59.164 50.000 0.00 0.00 0.00 2.85
610 623 3.454812 GGCCTATGACGGGATATGGTAAT 59.545 47.826 0.00 0.00 0.00 1.89
613 626 5.597182 GCCTATGACGGGATATGGTAATAGA 59.403 44.000 0.00 0.00 31.72 1.98
616 629 7.287927 CCTATGACGGGATATGGTAATAGACAT 59.712 40.741 0.00 0.00 31.72 3.06
617 630 6.928348 TGACGGGATATGGTAATAGACATT 57.072 37.500 0.00 0.00 0.00 2.71
629 642 7.757526 TGGTAATAGACATTGTATTTGCACAC 58.242 34.615 0.00 0.00 0.00 3.82
630 643 7.609918 TGGTAATAGACATTGTATTTGCACACT 59.390 33.333 0.00 0.00 0.00 3.55
631 644 8.458843 GGTAATAGACATTGTATTTGCACACTT 58.541 33.333 0.00 0.00 0.00 3.16
693 706 1.804151 GGCACTAAACTGATCGCACAA 59.196 47.619 0.00 0.00 0.00 3.33
699 712 6.402118 GCACTAAACTGATCGCACAAGATAAA 60.402 38.462 0.00 0.00 0.00 1.40
705 718 8.492673 AACTGATCGCACAAGATAAATTAAGA 57.507 30.769 0.00 0.00 0.00 2.10
711 727 5.062934 CGCACAAGATAAATTAAGACCGTGA 59.937 40.000 0.00 0.00 0.00 4.35
731 747 9.578439 ACCGTGATGTATTTAACTCTAGTAAAC 57.422 33.333 0.00 0.00 0.00 2.01
791 808 0.465287 TGCTCAGTGCTTCAGTGTCA 59.535 50.000 2.08 0.23 43.37 3.58
792 809 1.146637 GCTCAGTGCTTCAGTGTCAG 58.853 55.000 2.08 0.00 36.33 3.51
793 810 1.539929 GCTCAGTGCTTCAGTGTCAGT 60.540 52.381 2.08 0.00 36.33 3.41
794 811 2.288457 GCTCAGTGCTTCAGTGTCAGTA 60.288 50.000 2.08 0.00 36.33 2.74
1224 1264 1.431440 CTCTTCCTCCTCGTGCTCG 59.569 63.158 0.81 0.81 38.55 5.03
1585 1628 0.320771 GGGCGACAAGAGCAAGAAGA 60.321 55.000 0.00 0.00 36.08 2.87
1588 1631 2.072298 GCGACAAGAGCAAGAAGATGT 58.928 47.619 0.00 0.00 34.19 3.06
1780 1826 5.888161 AGCAAGAAGAAGAAACCAAAGAAGA 59.112 36.000 0.00 0.00 0.00 2.87
1781 1827 6.378280 AGCAAGAAGAAGAAACCAAAGAAGAA 59.622 34.615 0.00 0.00 0.00 2.52
1782 1828 6.694844 GCAAGAAGAAGAAACCAAAGAAGAAG 59.305 38.462 0.00 0.00 0.00 2.85
2229 2282 5.507637 TCCTTAACTACCAGTAGGACTCTG 58.492 45.833 9.53 0.00 37.49 3.35
2236 2289 6.674573 ACTACCAGTAGGACTCTGTCATAAT 58.325 40.000 9.53 0.00 37.49 1.28
2286 2339 3.501828 TCCAACGATGTTCATCAGTTTGG 59.498 43.478 20.26 20.26 35.87 3.28
2536 2596 0.755327 ACTTTGGGTTTGCGCTTCCT 60.755 50.000 9.73 0.00 0.00 3.36
2562 2622 2.869101 TGCCACCACTGCACTATTTA 57.131 45.000 0.00 0.00 32.85 1.40
2564 2624 3.696045 TGCCACCACTGCACTATTTAAT 58.304 40.909 0.00 0.00 32.85 1.40
2584 2644 2.695359 TCCTTTGTGTCGGCAAGTATC 58.305 47.619 0.00 0.00 0.00 2.24
2590 2650 3.852286 TGTGTCGGCAAGTATCGTATTT 58.148 40.909 0.00 0.00 0.00 1.40
2614 2677 1.521457 GGATGCTCGCCATGTCGAA 60.521 57.895 0.00 0.00 38.08 3.71
2710 2962 8.388103 CGTATCATGTAGACTTAACCTTTTTGG 58.612 37.037 0.00 0.00 42.93 3.28
2805 3061 9.083080 TCACATAAGAAGTATAATTGACACACG 57.917 33.333 0.00 0.00 0.00 4.49
2806 3062 9.083080 CACATAAGAAGTATAATTGACACACGA 57.917 33.333 0.00 0.00 0.00 4.35
2807 3063 9.302345 ACATAAGAAGTATAATTGACACACGAG 57.698 33.333 0.00 0.00 0.00 4.18
2808 3064 9.516314 CATAAGAAGTATAATTGACACACGAGA 57.484 33.333 0.00 0.00 0.00 4.04
2809 3065 9.737427 ATAAGAAGTATAATTGACACACGAGAG 57.263 33.333 0.00 0.00 0.00 3.20
2810 3066 6.565234 AGAAGTATAATTGACACACGAGAGG 58.435 40.000 0.00 0.00 0.00 3.69
2811 3067 4.683832 AGTATAATTGACACACGAGAGGC 58.316 43.478 0.00 0.00 0.00 4.70
2812 3068 3.895232 ATAATTGACACACGAGAGGCT 57.105 42.857 0.00 0.00 0.00 4.58
2813 3069 2.086054 AATTGACACACGAGAGGCTC 57.914 50.000 6.34 6.34 0.00 4.70
2814 3070 0.247736 ATTGACACACGAGAGGCTCC 59.752 55.000 11.71 1.69 0.00 4.70
2815 3071 1.816863 TTGACACACGAGAGGCTCCC 61.817 60.000 11.71 0.00 0.00 4.30
2816 3072 2.997897 ACACACGAGAGGCTCCCC 60.998 66.667 11.71 2.46 0.00 4.81
2817 3073 3.775654 CACACGAGAGGCTCCCCC 61.776 72.222 11.71 0.00 0.00 5.40
2882 3138 4.806339 CCGCCCCTCTTCTCCCCT 62.806 72.222 0.00 0.00 0.00 4.79
2883 3139 3.157949 CGCCCCTCTTCTCCCCTC 61.158 72.222 0.00 0.00 0.00 4.30
2884 3140 3.157949 GCCCCTCTTCTCCCCTCG 61.158 72.222 0.00 0.00 0.00 4.63
2885 3141 3.157949 CCCCTCTTCTCCCCTCGC 61.158 72.222 0.00 0.00 0.00 5.03
2886 3142 3.157949 CCCTCTTCTCCCCTCGCC 61.158 72.222 0.00 0.00 0.00 5.54
2887 3143 3.532155 CCTCTTCTCCCCTCGCCG 61.532 72.222 0.00 0.00 0.00 6.46
2888 3144 4.214327 CTCTTCTCCCCTCGCCGC 62.214 72.222 0.00 0.00 0.00 6.53
2924 3180 2.750237 GGCAAAGCCCGGTAGGTG 60.750 66.667 0.00 0.00 44.06 4.00
2925 3181 3.440415 GCAAAGCCCGGTAGGTGC 61.440 66.667 0.00 0.61 38.26 5.01
2926 3182 2.351276 CAAAGCCCGGTAGGTGCT 59.649 61.111 0.00 0.00 43.00 4.40
2927 3183 2.040544 CAAAGCCCGGTAGGTGCTG 61.041 63.158 0.00 0.00 41.22 4.41
2928 3184 3.268103 AAAGCCCGGTAGGTGCTGG 62.268 63.158 0.00 0.00 41.22 4.85
2953 3209 4.523282 GGGGCCCCATCTCCTCCT 62.523 72.222 37.61 0.00 35.81 3.69
2954 3210 2.851588 GGGCCCCATCTCCTCCTC 60.852 72.222 12.23 0.00 0.00 3.71
2955 3211 3.237741 GGCCCCATCTCCTCCTCG 61.238 72.222 0.00 0.00 0.00 4.63
2956 3212 3.934962 GCCCCATCTCCTCCTCGC 61.935 72.222 0.00 0.00 0.00 5.03
2957 3213 3.610669 CCCCATCTCCTCCTCGCG 61.611 72.222 0.00 0.00 0.00 5.87
2958 3214 4.292178 CCCATCTCCTCCTCGCGC 62.292 72.222 0.00 0.00 0.00 6.86
2959 3215 3.531207 CCATCTCCTCCTCGCGCA 61.531 66.667 8.75 0.00 0.00 6.09
2960 3216 2.496341 CATCTCCTCCTCGCGCAA 59.504 61.111 8.75 0.00 0.00 4.85
2961 3217 1.591059 CATCTCCTCCTCGCGCAAG 60.591 63.158 8.75 0.00 43.44 4.01
2962 3218 2.790791 ATCTCCTCCTCGCGCAAGG 61.791 63.158 8.50 8.50 37.81 3.61
3044 3300 4.436998 GCAGGTCCGACGGAGGTG 62.437 72.222 18.98 18.08 29.39 4.00
3045 3301 4.436998 CAGGTCCGACGGAGGTGC 62.437 72.222 18.98 5.12 29.39 5.01
3046 3302 4.680537 AGGTCCGACGGAGGTGCT 62.681 66.667 18.98 0.00 29.39 4.40
3047 3303 2.753043 GGTCCGACGGAGGTGCTA 60.753 66.667 18.98 0.00 29.39 3.49
3048 3304 2.345760 GGTCCGACGGAGGTGCTAA 61.346 63.158 18.98 0.00 29.39 3.09
3049 3305 1.139095 GTCCGACGGAGGTGCTAAG 59.861 63.158 18.98 0.00 29.39 2.18
3050 3306 1.001764 TCCGACGGAGGTGCTAAGA 60.002 57.895 13.88 0.00 0.00 2.10
3051 3307 0.395311 TCCGACGGAGGTGCTAAGAT 60.395 55.000 13.88 0.00 0.00 2.40
3052 3308 0.249073 CCGACGGAGGTGCTAAGATG 60.249 60.000 8.64 0.00 0.00 2.90
3053 3309 0.872021 CGACGGAGGTGCTAAGATGC 60.872 60.000 0.00 0.00 0.00 3.91
3054 3310 0.530870 GACGGAGGTGCTAAGATGCC 60.531 60.000 0.00 0.00 0.00 4.40
3055 3311 0.978146 ACGGAGGTGCTAAGATGCCT 60.978 55.000 0.00 0.00 0.00 4.75
3056 3312 0.249657 CGGAGGTGCTAAGATGCCTC 60.250 60.000 0.00 0.00 44.93 4.70
3057 3313 0.249657 GGAGGTGCTAAGATGCCTCG 60.250 60.000 0.00 0.00 46.20 4.63
3058 3314 0.461961 GAGGTGCTAAGATGCCTCGT 59.538 55.000 0.00 0.00 38.22 4.18
3059 3315 0.461961 AGGTGCTAAGATGCCTCGTC 59.538 55.000 0.00 0.00 0.00 4.20
3060 3316 0.530870 GGTGCTAAGATGCCTCGTCC 60.531 60.000 0.00 0.00 0.00 4.79
3061 3317 0.461961 GTGCTAAGATGCCTCGTCCT 59.538 55.000 0.00 0.00 0.00 3.85
3062 3318 0.461548 TGCTAAGATGCCTCGTCCTG 59.538 55.000 0.00 0.00 0.00 3.86
3063 3319 0.878086 GCTAAGATGCCTCGTCCTGC 60.878 60.000 0.00 0.00 0.00 4.85
3064 3320 0.596083 CTAAGATGCCTCGTCCTGCG 60.596 60.000 0.00 0.00 43.01 5.18
3065 3321 1.320344 TAAGATGCCTCGTCCTGCGT 61.320 55.000 0.00 0.00 42.13 5.24
3066 3322 2.842394 AAGATGCCTCGTCCTGCGTG 62.842 60.000 0.00 0.00 42.13 5.34
3067 3323 3.649277 GATGCCTCGTCCTGCGTGT 62.649 63.158 0.00 0.00 42.13 4.49
3068 3324 3.939837 ATGCCTCGTCCTGCGTGTG 62.940 63.158 0.00 0.00 42.13 3.82
3070 3326 3.680786 CCTCGTCCTGCGTGTGGA 61.681 66.667 0.00 0.00 42.13 4.02
3071 3327 2.126307 CTCGTCCTGCGTGTGGAG 60.126 66.667 0.00 0.00 42.13 3.86
3077 3333 4.742201 CTGCGTGTGGAGGGACGG 62.742 72.222 0.00 0.00 36.09 4.79
3079 3335 4.736896 GCGTGTGGAGGGACGGTC 62.737 72.222 0.00 0.00 36.09 4.79
3080 3336 3.299977 CGTGTGGAGGGACGGTCA 61.300 66.667 10.76 0.00 31.84 4.02
3081 3337 2.342648 GTGTGGAGGGACGGTCAC 59.657 66.667 10.76 6.34 0.00 3.67
3083 3339 4.065281 GTGGAGGGACGGTCACGG 62.065 72.222 10.76 0.00 46.48 4.94
3120 3376 4.776322 CGGAGGCAACATGGGCGA 62.776 66.667 0.00 0.00 38.57 5.54
3121 3377 3.134127 GGAGGCAACATGGGCGAC 61.134 66.667 0.00 0.00 38.57 5.19
3122 3378 2.045926 GAGGCAACATGGGCGACT 60.046 61.111 0.00 0.00 38.57 4.18
3123 3379 2.045926 AGGCAACATGGGCGACTC 60.046 61.111 0.00 0.00 38.57 3.36
3124 3380 3.134127 GGCAACATGGGCGACTCC 61.134 66.667 0.00 0.00 0.00 3.85
3125 3381 3.499737 GCAACATGGGCGACTCCG 61.500 66.667 0.00 0.00 39.16 4.63
3126 3382 2.819595 CAACATGGGCGACTCCGG 60.820 66.667 0.00 0.00 36.06 5.14
3127 3383 3.319198 AACATGGGCGACTCCGGT 61.319 61.111 0.00 0.00 36.06 5.28
3128 3384 3.605749 AACATGGGCGACTCCGGTG 62.606 63.158 0.00 0.00 36.06 4.94
3129 3385 4.082523 CATGGGCGACTCCGGTGT 62.083 66.667 9.33 9.33 36.06 4.16
3130 3386 3.319198 ATGGGCGACTCCGGTGTT 61.319 61.111 11.06 0.00 36.06 3.32
3131 3387 3.605749 ATGGGCGACTCCGGTGTTG 62.606 63.158 17.90 17.90 36.06 3.33
3133 3389 3.998672 GGCGACTCCGGTGTTGGA 61.999 66.667 22.28 0.00 36.37 3.53
3134 3390 2.264794 GCGACTCCGGTGTTGGAT 59.735 61.111 22.28 0.00 37.41 3.41
3135 3391 1.810030 GCGACTCCGGTGTTGGATC 60.810 63.158 22.28 5.36 37.41 3.36
3136 3392 1.153628 CGACTCCGGTGTTGGATCC 60.154 63.158 14.99 4.20 37.41 3.36
3137 3393 1.153628 GACTCCGGTGTTGGATCCG 60.154 63.158 11.06 0.00 45.42 4.18
3138 3394 2.511600 CTCCGGTGTTGGATCCGC 60.512 66.667 7.39 3.05 44.63 5.54
3139 3395 4.444838 TCCGGTGTTGGATCCGCG 62.445 66.667 7.39 0.00 44.63 6.46
3140 3396 4.444838 CCGGTGTTGGATCCGCGA 62.445 66.667 8.23 0.00 44.63 5.87
3141 3397 2.885644 CGGTGTTGGATCCGCGAG 60.886 66.667 8.23 0.00 40.28 5.03
3142 3398 3.195698 GGTGTTGGATCCGCGAGC 61.196 66.667 8.23 0.00 0.00 5.03
3143 3399 2.434185 GTGTTGGATCCGCGAGCA 60.434 61.111 8.23 0.00 0.00 4.26
3144 3400 2.125552 TGTTGGATCCGCGAGCAG 60.126 61.111 8.23 0.00 0.00 4.24
3145 3401 3.567797 GTTGGATCCGCGAGCAGC 61.568 66.667 8.23 0.00 43.95 5.25
3155 3411 4.880537 CGAGCAGCAGGTAGGGCG 62.881 72.222 0.00 0.00 36.08 6.13
3156 3412 4.537433 GAGCAGCAGGTAGGGCGG 62.537 72.222 0.00 0.00 36.08 6.13
3198 3454 4.193893 CCAGATCCATGGCCGGCA 62.194 66.667 30.85 15.30 32.48 5.69
3199 3455 2.114625 CAGATCCATGGCCGGCAT 59.885 61.111 30.85 17.04 0.00 4.40
3200 3456 2.114625 AGATCCATGGCCGGCATG 59.885 61.111 30.85 26.48 0.00 4.06
3210 3466 4.864334 CCGGCATGGTGCTCCTCC 62.864 72.222 6.34 4.10 44.28 4.30
3211 3467 4.864334 CGGCATGGTGCTCCTCCC 62.864 72.222 6.34 3.01 44.28 4.30
3212 3468 4.512914 GGCATGGTGCTCCTCCCC 62.513 72.222 6.34 0.00 44.28 4.81
3213 3469 3.415087 GCATGGTGCTCCTCCCCT 61.415 66.667 6.34 0.00 40.96 4.79
3214 3470 2.914289 CATGGTGCTCCTCCCCTC 59.086 66.667 6.34 0.00 34.23 4.30
3215 3471 2.765807 ATGGTGCTCCTCCCCTCG 60.766 66.667 6.34 0.00 34.23 4.63
3222 3478 4.475444 TCCTCCCCTCGGCGGAAT 62.475 66.667 7.21 0.00 40.24 3.01
3223 3479 3.930012 CCTCCCCTCGGCGGAATC 61.930 72.222 7.21 0.00 35.88 2.52
3224 3480 2.840102 CTCCCCTCGGCGGAATCT 60.840 66.667 7.21 0.00 33.16 2.40
3225 3481 1.530891 CTCCCCTCGGCGGAATCTA 60.531 63.158 7.21 0.00 33.16 1.98
3226 3482 0.900647 CTCCCCTCGGCGGAATCTAT 60.901 60.000 7.21 0.00 33.16 1.98
3227 3483 1.185618 TCCCCTCGGCGGAATCTATG 61.186 60.000 7.21 0.00 33.16 2.23
3228 3484 1.472662 CCCCTCGGCGGAATCTATGT 61.473 60.000 7.21 0.00 33.16 2.29
3229 3485 0.038159 CCCTCGGCGGAATCTATGTC 60.038 60.000 7.21 0.00 33.16 3.06
3230 3486 0.962489 CCTCGGCGGAATCTATGTCT 59.038 55.000 7.21 0.00 33.16 3.41
3231 3487 1.336332 CCTCGGCGGAATCTATGTCTG 60.336 57.143 7.21 0.00 33.16 3.51
3232 3488 0.673985 TCGGCGGAATCTATGTCTGG 59.326 55.000 7.21 0.00 0.00 3.86
3233 3489 0.673985 CGGCGGAATCTATGTCTGGA 59.326 55.000 0.00 0.00 0.00 3.86
3234 3490 1.336332 CGGCGGAATCTATGTCTGGAG 60.336 57.143 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.668335 AGGGTCCTCCTCCTTTTCTAAAAA 59.332 41.667 0.00 0.00 44.06 1.94
11 12 4.042934 CAGGGTCCTCCTCCTTTTCTAAAA 59.957 45.833 0.00 0.00 46.12 1.52
12 13 3.587506 CAGGGTCCTCCTCCTTTTCTAAA 59.412 47.826 0.00 0.00 46.12 1.85
13 14 3.182152 CAGGGTCCTCCTCCTTTTCTAA 58.818 50.000 0.00 0.00 46.12 2.10
14 15 2.562214 CCAGGGTCCTCCTCCTTTTCTA 60.562 54.545 0.00 0.00 46.12 2.10
15 16 1.662686 CAGGGTCCTCCTCCTTTTCT 58.337 55.000 0.00 0.00 46.12 2.52
16 17 0.621082 CCAGGGTCCTCCTCCTTTTC 59.379 60.000 0.00 0.00 46.12 2.29
17 18 1.501654 GCCAGGGTCCTCCTCCTTTT 61.502 60.000 0.00 0.00 46.12 2.27
18 19 1.925972 GCCAGGGTCCTCCTCCTTT 60.926 63.158 0.00 0.00 46.12 3.11
19 20 2.285743 GCCAGGGTCCTCCTCCTT 60.286 66.667 0.00 0.00 46.12 3.36
20 21 4.423209 GGCCAGGGTCCTCCTCCT 62.423 72.222 0.00 0.00 46.12 3.69
21 22 4.423209 AGGCCAGGGTCCTCCTCC 62.423 72.222 5.01 0.00 46.12 4.30
22 23 2.766229 GAGGCCAGGGTCCTCCTC 60.766 72.222 5.01 8.45 46.12 3.71
26 27 3.958629 ATGCAGAGGCCAGGGTCCT 62.959 63.158 5.01 1.61 40.13 3.85
27 28 3.412624 GATGCAGAGGCCAGGGTCC 62.413 68.421 5.01 0.00 40.13 4.46
28 29 1.919600 AAGATGCAGAGGCCAGGGTC 61.920 60.000 5.01 0.00 40.13 4.46
29 30 0.621571 TAAGATGCAGAGGCCAGGGT 60.622 55.000 5.01 0.00 40.13 4.34
30 31 0.108207 CTAAGATGCAGAGGCCAGGG 59.892 60.000 5.01 0.00 40.13 4.45
31 32 0.835941 ACTAAGATGCAGAGGCCAGG 59.164 55.000 5.01 0.00 40.13 4.45
32 33 3.577848 AGATACTAAGATGCAGAGGCCAG 59.422 47.826 5.01 0.00 40.13 4.85
33 34 3.576118 GAGATACTAAGATGCAGAGGCCA 59.424 47.826 5.01 0.00 40.13 5.36
34 35 3.576118 TGAGATACTAAGATGCAGAGGCC 59.424 47.826 0.00 0.00 40.13 5.19
35 36 4.862902 TGAGATACTAAGATGCAGAGGC 57.137 45.455 0.00 0.00 41.68 4.70
36 37 8.034215 CCTTAATGAGATACTAAGATGCAGAGG 58.966 40.741 0.00 0.00 0.00 3.69
37 38 7.545265 GCCTTAATGAGATACTAAGATGCAGAG 59.455 40.741 0.00 0.00 0.00 3.35
38 39 7.382110 GCCTTAATGAGATACTAAGATGCAGA 58.618 38.462 0.00 0.00 0.00 4.26
39 40 6.309980 CGCCTTAATGAGATACTAAGATGCAG 59.690 42.308 0.00 0.00 0.00 4.41
40 41 6.159293 CGCCTTAATGAGATACTAAGATGCA 58.841 40.000 0.00 0.00 0.00 3.96
41 42 6.159988 ACGCCTTAATGAGATACTAAGATGC 58.840 40.000 0.00 0.00 0.00 3.91
42 43 7.371159 TGACGCCTTAATGAGATACTAAGATG 58.629 38.462 0.00 0.00 0.00 2.90
43 44 7.526142 TGACGCCTTAATGAGATACTAAGAT 57.474 36.000 0.00 0.00 0.00 2.40
44 45 6.954487 TGACGCCTTAATGAGATACTAAGA 57.046 37.500 0.00 0.00 0.00 2.10
45 46 8.491152 CATTTGACGCCTTAATGAGATACTAAG 58.509 37.037 0.00 0.00 32.36 2.18
46 47 7.441157 CCATTTGACGCCTTAATGAGATACTAA 59.559 37.037 0.00 0.00 32.36 2.24
47 48 6.929049 CCATTTGACGCCTTAATGAGATACTA 59.071 38.462 0.00 0.00 32.36 1.82
48 49 5.760253 CCATTTGACGCCTTAATGAGATACT 59.240 40.000 0.00 0.00 32.36 2.12
49 50 5.527582 ACCATTTGACGCCTTAATGAGATAC 59.472 40.000 0.00 0.00 32.36 2.24
59 60 1.608590 CAAGACACCATTTGACGCCTT 59.391 47.619 0.00 0.00 0.00 4.35
64 65 4.498009 CCAACAGACAAGACACCATTTGAC 60.498 45.833 0.00 0.00 0.00 3.18
79 80 1.260561 CGTGTGTGCTAACCAACAGAC 59.739 52.381 0.00 0.00 0.00 3.51
96 97 4.424430 GTGCTACCAACGCGCGTG 62.424 66.667 38.44 27.05 0.00 5.34
115 116 2.121506 TTCACCCAGGGCCCTCTT 60.122 61.111 25.77 5.77 0.00 2.85
121 122 2.956333 GGTTATATTGTTCACCCAGGGC 59.044 50.000 4.91 0.00 0.00 5.19
126 127 4.278419 GCCTCATGGTTATATTGTTCACCC 59.722 45.833 0.00 0.00 35.27 4.61
129 130 5.104151 TCCTGCCTCATGGTTATATTGTTCA 60.104 40.000 0.00 0.00 35.27 3.18
144 145 2.842462 ACGTGGTGTCCTGCCTCA 60.842 61.111 0.00 0.00 0.00 3.86
160 161 7.945134 ACATTATTTCTCCATTTAGGCATCAC 58.055 34.615 0.00 0.00 37.29 3.06
189 191 5.591472 TCCTGCTGATTTAATTGTCTCCATG 59.409 40.000 0.00 0.00 0.00 3.66
192 194 6.515272 TTTCCTGCTGATTTAATTGTCTCC 57.485 37.500 0.00 0.00 0.00 3.71
209 221 7.829211 TTAGACCATCTAGTTGGAATTTTCCTG 59.171 37.037 23.87 0.00 37.98 3.86
211 223 8.753497 ATTAGACCATCTAGTTGGAATTTTCC 57.247 34.615 23.87 2.23 39.25 3.13
239 251 7.759433 CCGGTAAATCAAGCAAGATTTTATGTT 59.241 33.333 17.77 0.59 43.67 2.71
252 264 3.304057 GCAATCTAGCCGGTAAATCAAGC 60.304 47.826 1.90 0.00 0.00 4.01
256 268 3.251004 CCTTGCAATCTAGCCGGTAAATC 59.749 47.826 1.90 0.00 0.00 2.17
257 269 3.214328 CCTTGCAATCTAGCCGGTAAAT 58.786 45.455 1.90 0.00 0.00 1.40
262 274 1.097547 CACCCTTGCAATCTAGCCGG 61.098 60.000 0.00 0.00 0.00 6.13
290 302 0.319641 AGTTTCGAACCCACGAGCTC 60.320 55.000 2.73 2.73 43.04 4.09
306 318 3.808834 AAGGAAAAGGGATCCGAAGTT 57.191 42.857 5.45 0.00 42.03 2.66
307 319 3.330998 AGAAAGGAAAAGGGATCCGAAGT 59.669 43.478 5.45 0.00 42.03 3.01
366 379 7.220491 TGCAAATCACAGATATAACGCAATTTG 59.780 33.333 0.00 0.00 35.65 2.32
373 386 9.958285 GTGTATATGCAAATCACAGATATAACG 57.042 33.333 0.00 0.00 0.00 3.18
402 415 3.144506 GCATATCAGCTACACCAAGCAT 58.855 45.455 0.00 0.00 45.30 3.79
423 436 1.302511 CTGTCAGGTTTGGGTCCCG 60.303 63.158 2.65 0.00 0.00 5.14
441 454 1.168714 GCAGACTGATGGGTTCAACC 58.831 55.000 6.65 0.00 37.60 3.77
446 459 0.107508 CGGATGCAGACTGATGGGTT 60.108 55.000 6.65 0.00 0.00 4.11
450 463 2.798847 CACATACGGATGCAGACTGATG 59.201 50.000 7.78 1.60 36.43 3.07
455 468 3.977427 TGTATCACATACGGATGCAGAC 58.023 45.455 7.78 2.64 38.59 3.51
457 470 5.929697 AATTGTATCACATACGGATGCAG 57.070 39.130 7.78 0.23 38.35 4.41
495 508 8.850156 CGAGAATCCCCTCACATTTTATTTAAT 58.150 33.333 0.00 0.00 32.86 1.40
496 509 7.201785 GCGAGAATCCCCTCACATTTTATTTAA 60.202 37.037 0.00 0.00 32.86 1.52
529 542 0.039035 TTAGTGGCCGGGAGCATTTT 59.961 50.000 2.18 0.00 46.50 1.82
532 545 1.635817 ATGTTAGTGGCCGGGAGCAT 61.636 55.000 2.18 0.00 46.50 3.79
537 550 3.202001 CGCATGTTAGTGGCCGGG 61.202 66.667 2.18 0.00 0.00 5.73
542 555 3.794270 CGGACCGCATGTTAGTGG 58.206 61.111 0.00 0.00 44.72 4.00
572 585 2.202878 CCATACCCACGTGGCGAG 60.203 66.667 29.75 18.03 37.83 5.03
579 592 0.319555 CGTCATAGGCCATACCCACG 60.320 60.000 5.01 1.08 40.58 4.94
581 594 1.125093 CCCGTCATAGGCCATACCCA 61.125 60.000 5.01 0.00 40.58 4.51
585 598 3.038280 CCATATCCCGTCATAGGCCATA 58.962 50.000 5.01 0.00 0.00 2.74
587 600 1.275666 CCATATCCCGTCATAGGCCA 58.724 55.000 5.01 0.00 0.00 5.36
589 602 4.755266 ATTACCATATCCCGTCATAGGC 57.245 45.455 0.00 0.00 0.00 3.93
591 604 7.640597 TGTCTATTACCATATCCCGTCATAG 57.359 40.000 0.00 0.00 0.00 2.23
596 609 6.681729 ACAATGTCTATTACCATATCCCGT 57.318 37.500 0.00 0.00 0.00 5.28
604 617 7.609918 AGTGTGCAAATACAATGTCTATTACCA 59.390 33.333 0.00 0.00 31.36 3.25
605 618 7.985476 AGTGTGCAAATACAATGTCTATTACC 58.015 34.615 0.00 0.00 31.36 2.85
609 622 6.658816 TCCAAGTGTGCAAATACAATGTCTAT 59.341 34.615 0.00 0.00 31.36 1.98
610 623 6.000840 TCCAAGTGTGCAAATACAATGTCTA 58.999 36.000 0.00 0.00 31.36 2.59
613 626 4.340666 TGTCCAAGTGTGCAAATACAATGT 59.659 37.500 0.00 0.00 31.36 2.71
616 629 4.930963 CTTGTCCAAGTGTGCAAATACAA 58.069 39.130 0.00 0.00 33.87 2.41
617 630 4.566545 CTTGTCCAAGTGTGCAAATACA 57.433 40.909 0.00 0.00 33.87 2.29
629 642 8.479280 CGAAAATGATGTTTTAACTTGTCCAAG 58.521 33.333 5.51 5.51 43.79 3.61
630 643 7.976734 ACGAAAATGATGTTTTAACTTGTCCAA 59.023 29.630 0.00 0.00 0.00 3.53
631 644 7.433719 CACGAAAATGATGTTTTAACTTGTCCA 59.566 33.333 0.00 0.00 0.00 4.02
644 657 9.959749 AAGTTGTAAAATACACGAAAATGATGT 57.040 25.926 0.00 0.00 38.63 3.06
650 663 8.404000 TGCCTAAAGTTGTAAAATACACGAAAA 58.596 29.630 0.00 0.00 38.63 2.29
686 699 5.062934 CACGGTCTTAATTTATCTTGTGCGA 59.937 40.000 0.00 0.00 0.00 5.10
689 702 7.974675 ACATCACGGTCTTAATTTATCTTGTG 58.025 34.615 0.00 0.00 0.00 3.33
705 718 9.578439 GTTTACTAGAGTTAAATACATCACGGT 57.422 33.333 0.00 0.00 0.00 4.83
791 808 5.585047 GCTTTCGGTTATGGAATCACTTACT 59.415 40.000 0.00 0.00 0.00 2.24
792 809 5.585047 AGCTTTCGGTTATGGAATCACTTAC 59.415 40.000 0.00 0.00 0.00 2.34
793 810 5.741011 AGCTTTCGGTTATGGAATCACTTA 58.259 37.500 0.00 0.00 0.00 2.24
794 811 4.589908 AGCTTTCGGTTATGGAATCACTT 58.410 39.130 0.00 0.00 0.00 3.16
988 1006 5.338365 CGTTATATATAGCCGTGGGAGAAC 58.662 45.833 1.44 0.00 0.00 3.01
989 1007 4.142315 GCGTTATATATAGCCGTGGGAGAA 60.142 45.833 12.61 0.00 0.00 2.87
1585 1628 3.309121 CCATAGGGGTTGTTGGAGAACAT 60.309 47.826 0.00 0.00 41.77 2.71
1588 1631 1.005450 GCCATAGGGGTTGTTGGAGAA 59.995 52.381 0.00 0.00 39.65 2.87
1780 1826 4.335647 CACTGCGGCAGGGGACTT 62.336 66.667 31.38 8.79 40.21 3.01
2229 2282 6.233430 ACGCAGAGCATGATTAATTATGAC 57.767 37.500 21.00 14.10 0.00 3.06
2236 2289 4.190772 TCATGAACGCAGAGCATGATTAA 58.809 39.130 0.00 0.00 42.66 1.40
2286 2339 9.000486 AGTTACAGCCAAGATTAAAACTAAGAC 58.000 33.333 0.00 0.00 0.00 3.01
2536 2596 2.034532 CAGTGGTGGCATGGCAGA 59.965 61.111 24.03 9.64 0.00 4.26
2562 2622 1.981256 ACTTGCCGACACAAAGGATT 58.019 45.000 0.00 0.00 0.00 3.01
2564 2624 2.695359 GATACTTGCCGACACAAAGGA 58.305 47.619 0.00 0.00 0.00 3.36
2584 2644 1.071239 CGAGCATCCGAGCAAAATACG 60.071 52.381 0.00 0.00 36.85 3.06
2590 2650 3.390183 ATGGCGAGCATCCGAGCAA 62.390 57.895 0.00 0.00 36.85 3.91
2793 3049 2.094182 GGAGCCTCTCGTGTGTCAATTA 60.094 50.000 0.00 0.00 0.00 1.40
2794 3050 1.338200 GGAGCCTCTCGTGTGTCAATT 60.338 52.381 0.00 0.00 0.00 2.32
2797 3053 2.276116 GGGAGCCTCTCGTGTGTCA 61.276 63.158 0.00 0.00 0.00 3.58
2798 3054 2.574399 GGGAGCCTCTCGTGTGTC 59.426 66.667 0.00 0.00 0.00 3.67
2799 3055 2.997897 GGGGAGCCTCTCGTGTGT 60.998 66.667 0.00 0.00 0.00 3.72
2800 3056 3.775654 GGGGGAGCCTCTCGTGTG 61.776 72.222 0.00 0.00 0.00 3.82
2865 3121 4.806339 AGGGGAGAAGAGGGGCGG 62.806 72.222 0.00 0.00 0.00 6.13
2866 3122 3.157949 GAGGGGAGAAGAGGGGCG 61.158 72.222 0.00 0.00 0.00 6.13
2867 3123 3.157949 CGAGGGGAGAAGAGGGGC 61.158 72.222 0.00 0.00 0.00 5.80
2868 3124 3.157949 GCGAGGGGAGAAGAGGGG 61.158 72.222 0.00 0.00 0.00 4.79
2869 3125 3.157949 GGCGAGGGGAGAAGAGGG 61.158 72.222 0.00 0.00 0.00 4.30
2870 3126 3.532155 CGGCGAGGGGAGAAGAGG 61.532 72.222 0.00 0.00 0.00 3.69
2871 3127 4.214327 GCGGCGAGGGGAGAAGAG 62.214 72.222 12.98 0.00 0.00 2.85
2908 3164 3.440415 GCACCTACCGGGCTTTGC 61.440 66.667 6.32 5.41 39.10 3.68
2909 3165 2.040544 CAGCACCTACCGGGCTTTG 61.041 63.158 6.32 0.00 35.48 2.77
2910 3166 2.351276 CAGCACCTACCGGGCTTT 59.649 61.111 6.32 0.00 35.48 3.51
2911 3167 3.717294 CCAGCACCTACCGGGCTT 61.717 66.667 6.32 0.00 35.48 4.35
2936 3192 4.523282 AGGAGGAGATGGGGCCCC 62.523 72.222 36.14 36.14 0.00 5.80
2937 3193 2.851588 GAGGAGGAGATGGGGCCC 60.852 72.222 18.17 18.17 0.00 5.80
2938 3194 3.237741 CGAGGAGGAGATGGGGCC 61.238 72.222 0.00 0.00 0.00 5.80
2939 3195 3.934962 GCGAGGAGGAGATGGGGC 61.935 72.222 0.00 0.00 0.00 5.80
2940 3196 3.610669 CGCGAGGAGGAGATGGGG 61.611 72.222 0.00 0.00 0.00 4.96
2941 3197 4.292178 GCGCGAGGAGGAGATGGG 62.292 72.222 12.10 0.00 0.00 4.00
2942 3198 2.967929 CTTGCGCGAGGAGGAGATGG 62.968 65.000 17.45 0.00 0.00 3.51
2943 3199 1.591059 CTTGCGCGAGGAGGAGATG 60.591 63.158 17.45 0.00 0.00 2.90
2944 3200 2.790791 CCTTGCGCGAGGAGGAGAT 61.791 63.158 36.40 0.00 39.25 2.75
2945 3201 3.452786 CCTTGCGCGAGGAGGAGA 61.453 66.667 36.40 0.00 39.25 3.71
2946 3202 4.521062 CCCTTGCGCGAGGAGGAG 62.521 72.222 40.07 22.21 39.25 3.69
3027 3283 4.436998 CACCTCCGTCGGACCTGC 62.437 72.222 10.71 0.00 0.00 4.85
3028 3284 4.436998 GCACCTCCGTCGGACCTG 62.437 72.222 10.71 9.36 0.00 4.00
3029 3285 2.776370 TTAGCACCTCCGTCGGACCT 62.776 60.000 10.71 7.02 0.00 3.85
3030 3286 2.280823 CTTAGCACCTCCGTCGGACC 62.281 65.000 10.71 0.00 0.00 4.46
3031 3287 1.139095 CTTAGCACCTCCGTCGGAC 59.861 63.158 10.71 0.00 0.00 4.79
3032 3288 0.395311 ATCTTAGCACCTCCGTCGGA 60.395 55.000 14.54 14.54 0.00 4.55
3033 3289 0.249073 CATCTTAGCACCTCCGTCGG 60.249 60.000 4.39 4.39 0.00 4.79
3034 3290 0.872021 GCATCTTAGCACCTCCGTCG 60.872 60.000 0.00 0.00 0.00 5.12
3035 3291 0.530870 GGCATCTTAGCACCTCCGTC 60.531 60.000 0.00 0.00 35.83 4.79
3036 3292 0.978146 AGGCATCTTAGCACCTCCGT 60.978 55.000 0.00 0.00 35.83 4.69
3037 3293 0.249657 GAGGCATCTTAGCACCTCCG 60.250 60.000 0.00 0.00 42.44 4.63
3038 3294 0.249657 CGAGGCATCTTAGCACCTCC 60.250 60.000 0.00 0.00 44.89 4.30
3039 3295 0.461961 ACGAGGCATCTTAGCACCTC 59.538 55.000 0.00 0.00 44.37 3.85
3040 3296 0.461961 GACGAGGCATCTTAGCACCT 59.538 55.000 0.00 0.00 35.83 4.00
3041 3297 0.530870 GGACGAGGCATCTTAGCACC 60.531 60.000 0.00 0.00 35.83 5.01
3042 3298 0.461961 AGGACGAGGCATCTTAGCAC 59.538 55.000 0.00 0.00 35.83 4.40
3043 3299 0.461548 CAGGACGAGGCATCTTAGCA 59.538 55.000 0.00 0.00 35.83 3.49
3044 3300 0.878086 GCAGGACGAGGCATCTTAGC 60.878 60.000 0.00 0.00 0.00 3.09
3045 3301 3.280920 GCAGGACGAGGCATCTTAG 57.719 57.895 0.00 0.00 0.00 2.18
3057 3313 3.311110 TCCCTCCACACGCAGGAC 61.311 66.667 0.00 0.00 30.32 3.85
3058 3314 3.311110 GTCCCTCCACACGCAGGA 61.311 66.667 0.00 0.00 30.32 3.86
3059 3315 4.742201 CGTCCCTCCACACGCAGG 62.742 72.222 0.00 0.00 0.00 4.85
3060 3316 4.742201 CCGTCCCTCCACACGCAG 62.742 72.222 0.00 0.00 34.58 5.18
3062 3318 4.736896 GACCGTCCCTCCACACGC 62.737 72.222 0.00 0.00 34.58 5.34
3063 3319 3.299977 TGACCGTCCCTCCACACG 61.300 66.667 0.00 0.00 35.72 4.49
3064 3320 2.342648 GTGACCGTCCCTCCACAC 59.657 66.667 0.00 0.00 0.00 3.82
3065 3321 3.299977 CGTGACCGTCCCTCCACA 61.300 66.667 0.00 0.00 0.00 4.17
3066 3322 4.065281 CCGTGACCGTCCCTCCAC 62.065 72.222 0.00 0.00 0.00 4.02
3095 3351 2.124695 GTTGCCTCCGGGTGATCC 60.125 66.667 0.00 0.00 34.45 3.36
3096 3352 1.097547 CATGTTGCCTCCGGGTGATC 61.098 60.000 0.00 0.00 34.45 2.92
3097 3353 1.077501 CATGTTGCCTCCGGGTGAT 60.078 57.895 0.00 0.00 34.45 3.06
3098 3354 2.350895 CATGTTGCCTCCGGGTGA 59.649 61.111 0.00 0.00 34.45 4.02
3099 3355 2.751436 CCATGTTGCCTCCGGGTG 60.751 66.667 0.00 0.00 34.45 4.61
3100 3356 4.047125 CCCATGTTGCCTCCGGGT 62.047 66.667 0.00 0.00 34.45 5.28
3103 3359 4.776322 TCGCCCATGTTGCCTCCG 62.776 66.667 0.00 0.00 0.00 4.63
3104 3360 3.134127 GTCGCCCATGTTGCCTCC 61.134 66.667 0.00 0.00 0.00 4.30
3105 3361 2.045926 AGTCGCCCATGTTGCCTC 60.046 61.111 0.00 0.00 0.00 4.70
3106 3362 2.045926 GAGTCGCCCATGTTGCCT 60.046 61.111 0.00 0.00 0.00 4.75
3107 3363 3.134127 GGAGTCGCCCATGTTGCC 61.134 66.667 0.00 0.00 0.00 4.52
3108 3364 3.499737 CGGAGTCGCCCATGTTGC 61.500 66.667 0.00 0.00 0.00 4.17
3109 3365 2.819595 CCGGAGTCGCCCATGTTG 60.820 66.667 0.00 0.00 34.56 3.33
3110 3366 3.319198 ACCGGAGTCGCCCATGTT 61.319 61.111 9.46 0.00 34.56 2.71
3111 3367 4.082523 CACCGGAGTCGCCCATGT 62.083 66.667 9.46 0.00 34.56 3.21
3112 3368 3.605749 AACACCGGAGTCGCCCATG 62.606 63.158 9.46 0.00 34.56 3.66
3113 3369 3.319198 AACACCGGAGTCGCCCAT 61.319 61.111 9.46 0.00 34.56 4.00
3114 3370 4.308458 CAACACCGGAGTCGCCCA 62.308 66.667 9.46 0.00 34.56 5.36
3116 3372 3.310860 ATCCAACACCGGAGTCGCC 62.311 63.158 9.46 0.00 38.83 5.54
3117 3373 1.810030 GATCCAACACCGGAGTCGC 60.810 63.158 9.46 0.00 38.83 5.19
3118 3374 1.153628 GGATCCAACACCGGAGTCG 60.154 63.158 9.46 0.00 38.83 4.18
3119 3375 1.153628 CGGATCCAACACCGGAGTC 60.154 63.158 9.46 0.00 44.59 3.36
3120 3376 2.978824 CGGATCCAACACCGGAGT 59.021 61.111 9.46 2.22 44.59 3.85
3125 3381 3.195698 GCTCGCGGATCCAACACC 61.196 66.667 13.41 0.00 0.00 4.16
3126 3382 2.434185 TGCTCGCGGATCCAACAC 60.434 61.111 13.41 0.00 0.00 3.32
3127 3383 2.125552 CTGCTCGCGGATCCAACA 60.126 61.111 13.41 0.85 0.00 3.33
3128 3384 3.567797 GCTGCTCGCGGATCCAAC 61.568 66.667 13.41 1.69 0.00 3.77
3129 3385 4.081185 TGCTGCTCGCGGATCCAA 62.081 61.111 13.41 0.00 43.27 3.53
3135 3391 4.880537 CCTACCTGCTGCTCGCGG 62.881 72.222 6.13 0.00 44.89 6.46
3136 3392 4.880537 CCCTACCTGCTGCTCGCG 62.881 72.222 0.00 0.00 43.27 5.87
3138 3394 4.880537 CGCCCTACCTGCTGCTCG 62.881 72.222 0.00 0.00 0.00 5.03
3139 3395 4.537433 CCGCCCTACCTGCTGCTC 62.537 72.222 0.00 0.00 0.00 4.26
3181 3437 3.502621 ATGCCGGCCATGGATCTGG 62.503 63.158 26.77 14.48 39.45 3.86
3182 3438 2.114625 ATGCCGGCCATGGATCTG 59.885 61.111 26.77 3.22 31.48 2.90
3183 3439 2.114625 CATGCCGGCCATGGATCT 59.885 61.111 26.77 0.00 46.09 2.75
3193 3449 4.864334 GGAGGAGCACCATGCCGG 62.864 72.222 2.07 0.00 46.52 6.13
3194 3450 4.864334 GGGAGGAGCACCATGCCG 62.864 72.222 2.07 0.00 46.52 5.69
3195 3451 4.512914 GGGGAGGAGCACCATGCC 62.513 72.222 2.07 2.41 46.52 4.40
3196 3452 3.412624 GAGGGGAGGAGCACCATGC 62.413 68.421 2.07 0.00 45.20 4.06
3197 3453 2.914289 GAGGGGAGGAGCACCATG 59.086 66.667 2.07 0.00 45.20 3.66
3198 3454 2.765807 CGAGGGGAGGAGCACCAT 60.766 66.667 2.07 0.00 45.20 3.55
3207 3463 0.900647 ATAGATTCCGCCGAGGGGAG 60.901 60.000 7.83 0.00 45.17 4.30
3208 3464 1.155390 ATAGATTCCGCCGAGGGGA 59.845 57.895 7.83 0.32 42.93 4.81
3209 3465 1.293498 CATAGATTCCGCCGAGGGG 59.707 63.158 0.00 0.00 41.52 4.79
3210 3466 0.038159 GACATAGATTCCGCCGAGGG 60.038 60.000 0.00 0.00 41.52 4.30
3211 3467 0.962489 AGACATAGATTCCGCCGAGG 59.038 55.000 0.00 0.00 42.97 4.63
3212 3468 1.336332 CCAGACATAGATTCCGCCGAG 60.336 57.143 0.00 0.00 0.00 4.63
3213 3469 0.673985 CCAGACATAGATTCCGCCGA 59.326 55.000 0.00 0.00 0.00 5.54
3214 3470 0.673985 TCCAGACATAGATTCCGCCG 59.326 55.000 0.00 0.00 0.00 6.46
3215 3471 2.447244 CTCCAGACATAGATTCCGCC 57.553 55.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.