Multiple sequence alignment - TraesCS3B01G240000

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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 TraesCS3B01G240000 chr3B 100.000 6028 0 0 1 6028 378686401 378692428 0.000000e+00 11132
1 TraesCS3B01G240000 chr3B 95.714 140 5 1 2756 2894 655858575 655858714 2.190000e-54 224
2 TraesCS3B01G240000 chr3B 93.333 150 8 2 2745 2892 383716469 383716618 2.830000e-53 220
3 TraesCS3B01G240000 chr3A 93.578 2834 94 35 1 2766 371630462 371627649 0.000000e+00 4145
4 TraesCS3B01G240000 chr3A 90.687 1557 99 14 3833 5374 371626589 371625064 0.000000e+00 2030
5 TraesCS3B01G240000 chr3A 88.297 957 91 8 2888 3837 371627652 371626710 0.000000e+00 1127
6 TraesCS3B01G240000 chr3A 83.603 494 57 20 5373 5855 371624903 371624423 5.540000e-120 442
7 TraesCS3B01G240000 chr3D 97.073 2221 34 5 568 2766 284213314 284211103 0.000000e+00 3712
8 TraesCS3B01G240000 chr3D 96.852 1620 40 4 2888 4507 284211106 284209498 0.000000e+00 2699
9 TraesCS3B01G240000 chr3D 98.480 1184 18 0 4664 5847 284209228 284208045 0.000000e+00 2087
10 TraesCS3B01G240000 chr3D 98.012 503 7 2 1 503 284213972 284213473 0.000000e+00 870
11 TraesCS3B01G240000 chr3D 96.571 175 5 1 5854 6028 20902644 20902471 7.640000e-74 289
12 TraesCS3B01G240000 chr3D 96.512 172 4 1 4506 4677 284209416 284209247 3.560000e-72 283
13 TraesCS3B01G240000 chr3D 97.101 138 3 1 2757 2894 283321118 283321254 1.310000e-56 231
14 TraesCS3B01G240000 chr3D 94.667 150 5 3 2759 2905 261156863 261157012 4.700000e-56 230
15 TraesCS3B01G240000 chr3D 95.714 140 6 0 2762 2901 612269560 612269699 6.080000e-55 226
16 TraesCS3B01G240000 chrUn 96.045 177 7 0 5852 6028 46155045 46154869 7.640000e-74 289
17 TraesCS3B01G240000 chr2D 96.000 175 6 1 5854 6028 527527340 527527513 3.560000e-72 283
18 TraesCS3B01G240000 chr1D 96.000 175 6 1 5854 6028 482918735 482918908 3.560000e-72 283
19 TraesCS3B01G240000 chr1D 74.930 359 75 9 4682 5025 491805744 491806102 3.760000e-32 150
20 TraesCS3B01G240000 chr4D 95.954 173 6 1 5856 6028 498967890 498967719 4.600000e-71 279
21 TraesCS3B01G240000 chr6D 95.429 175 7 1 5854 6028 314512417 314512244 1.650000e-70 278
22 TraesCS3B01G240000 chr5B 94.828 174 8 1 5855 6028 546418770 546418598 2.770000e-68 270
23 TraesCS3B01G240000 chr5B 95.139 144 3 4 2748 2891 584613662 584613523 2.190000e-54 224
24 TraesCS3B01G240000 chr4A 94.798 173 8 1 5856 6028 17398372 17398201 9.960000e-68 268
25 TraesCS3B01G240000 chr2A 94.798 173 8 1 5856 6028 734875319 734875148 9.960000e-68 268
26 TraesCS3B01G240000 chr2A 95.683 139 6 0 2756 2894 768676966 768677104 2.190000e-54 224
27 TraesCS3B01G240000 chr7B 96.403 139 4 1 2755 2892 678632495 678632357 1.690000e-55 228
28 TraesCS3B01G240000 chr7D 95.139 144 6 1 2750 2892 266214396 266214253 6.080000e-55 226
29 TraesCS3B01G240000 chr1A 75.209 359 74 9 4682 5025 589822062 589822420 8.090000e-34 156


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 TraesCS3B01G240000 chr3B 378686401 378692428 6027 False 11132.0 11132 100.00000 1 6028 1 chr3B.!!$F1 6027
1 TraesCS3B01G240000 chr3A 371624423 371630462 6039 True 1936.0 4145 89.04125 1 5855 4 chr3A.!!$R1 5854
2 TraesCS3B01G240000 chr3D 284208045 284213972 5927 True 1930.2 3712 97.38580 1 5847 5 chr3D.!!$R2 5846

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
376 379 0.037697 CGATGAACACGTCTCCCCAA 60.038 55.000 0.00 0.00 0.00 4.12 F
397 401 0.684153 GCCCACATGTAACAGCCCAT 60.684 55.000 0.00 0.00 0.00 4.00 F
1944 2063 0.604578 GTGTCACTGCAATGGCCATT 59.395 50.000 25.73 25.73 40.13 3.16 F
2781 2942 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28 F
2782 2943 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44 F
2785 2946 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17 F
3431 3593 1.260544 CCTTGCCCTGCTTTAAGCTT 58.739 50.000 18.20 3.48 42.97 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2063 0.538584 CAGGTGCTACAGGATCTGCA 59.461 55.000 0.00 0.0 37.78 4.41 R
2472 2597 0.675633 AGTGCAAGGCATTTGGTGTC 59.324 50.000 0.00 0.0 41.91 3.67 R
2874 3035 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.0 0.00 4.12 R
4085 4382 1.166531 AAAGCAACCACGCAGACTCC 61.167 55.000 0.00 0.0 0.00 3.85 R
4571 4958 4.923415 AGGAATTCACTGTAAAAGAGGGG 58.077 43.478 7.93 0.0 0.00 4.79 R
4572 4959 6.712276 AGTAGGAATTCACTGTAAAAGAGGG 58.288 40.000 7.93 0.0 0.00 4.30 R
5430 6014 0.250901 CCAGTAGGCAAAGGCACAGT 60.251 55.000 0.00 0.0 43.71 3.55 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
235 236 5.359009 AGCTACACATTCATTATTGCTGCTT 59.641 36.000 0.00 0.00 0.00 3.91
236 237 6.038356 GCTACACATTCATTATTGCTGCTTT 58.962 36.000 0.00 0.00 0.00 3.51
376 379 0.037697 CGATGAACACGTCTCCCCAA 60.038 55.000 0.00 0.00 0.00 4.12
392 396 1.176527 CCAAGGCCCACATGTAACAG 58.823 55.000 0.00 0.00 0.00 3.16
397 401 0.684153 GCCCACATGTAACAGCCCAT 60.684 55.000 0.00 0.00 0.00 4.00
765 869 2.895372 GGATTTGGATCCGCGCGT 60.895 61.111 29.95 11.62 42.36 6.01
1714 1833 4.513442 AGTTAGATTTTGCGTCATGCCTA 58.487 39.130 0.00 0.00 45.60 3.93
1821 1940 1.062488 ACCTGGGAGCTGTGGAGTTT 61.062 55.000 0.00 0.00 0.00 2.66
1836 1955 3.137544 TGGAGTTTAAGAAGCAGTGGGAA 59.862 43.478 0.00 0.00 0.00 3.97
1881 2000 3.272716 AGGGTGGATGATGAGATAGCT 57.727 47.619 0.00 0.00 0.00 3.32
1944 2063 0.604578 GTGTCACTGCAATGGCCATT 59.395 50.000 25.73 25.73 40.13 3.16
2415 2536 5.191722 TCCATCAGTTCCTATTAAGCCTTGT 59.808 40.000 0.00 0.00 0.00 3.16
2472 2597 7.697691 ACGATTCTGATTTAATTGCTTACCAG 58.302 34.615 0.00 0.00 0.00 4.00
2475 2600 7.994425 TTCTGATTTAATTGCTTACCAGACA 57.006 32.000 0.00 0.00 0.00 3.41
2484 2609 1.202348 GCTTACCAGACACCAAATGCC 59.798 52.381 0.00 0.00 0.00 4.40
2706 2867 6.302269 ACCAGATGGCTTTTCTAATATCCTG 58.698 40.000 0.00 0.00 39.32 3.86
2717 2878 9.189156 CTTTTCTAATATCCTGGGAATTCAACA 57.811 33.333 7.93 4.90 0.00 3.33
2762 2923 6.156256 AGGACTGCATAGTTTGGTGTAATCTA 59.844 38.462 0.00 0.00 37.25 1.98
2763 2924 6.480320 GGACTGCATAGTTTGGTGTAATCTAG 59.520 42.308 0.00 0.00 37.25 2.43
2764 2925 6.947464 ACTGCATAGTTTGGTGTAATCTAGT 58.053 36.000 0.00 0.00 31.66 2.57
2765 2926 8.074613 ACTGCATAGTTTGGTGTAATCTAGTA 57.925 34.615 0.00 0.00 31.66 1.82
2766 2927 7.980099 ACTGCATAGTTTGGTGTAATCTAGTAC 59.020 37.037 0.00 0.00 31.66 2.73
2767 2928 8.074613 TGCATAGTTTGGTGTAATCTAGTACT 57.925 34.615 0.00 0.00 0.00 2.73
2768 2929 8.195436 TGCATAGTTTGGTGTAATCTAGTACTC 58.805 37.037 0.00 0.00 0.00 2.59
2769 2930 7.652507 GCATAGTTTGGTGTAATCTAGTACTCC 59.347 40.741 0.00 5.18 37.88 3.85
2770 2931 6.541934 AGTTTGGTGTAATCTAGTACTCCC 57.458 41.667 0.00 2.73 36.99 4.30
2771 2932 6.262207 AGTTTGGTGTAATCTAGTACTCCCT 58.738 40.000 0.00 0.00 36.99 4.20
2772 2933 6.380560 AGTTTGGTGTAATCTAGTACTCCCTC 59.619 42.308 0.00 0.00 36.99 4.30
2773 2934 4.801164 TGGTGTAATCTAGTACTCCCTCC 58.199 47.826 0.00 0.00 36.99 4.30
2774 2935 3.819902 GGTGTAATCTAGTACTCCCTCCG 59.180 52.174 0.00 0.00 33.40 4.63
2775 2936 4.459330 GTGTAATCTAGTACTCCCTCCGT 58.541 47.826 0.00 0.00 0.00 4.69
2776 2937 4.514816 GTGTAATCTAGTACTCCCTCCGTC 59.485 50.000 0.00 0.00 0.00 4.79
2777 2938 2.955342 ATCTAGTACTCCCTCCGTCC 57.045 55.000 0.00 0.00 0.00 4.79
2778 2939 0.842635 TCTAGTACTCCCTCCGTCCC 59.157 60.000 0.00 0.00 0.00 4.46
2779 2940 0.549950 CTAGTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
2780 2941 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
2781 2942 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2782 2943 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2783 2944 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2784 2945 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2785 2946 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2786 2947 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2787 2948 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2788 2949 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2789 2950 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2790 2951 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2791 2952 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2792 2953 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2793 2954 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2794 2955 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2795 2956 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2796 2957 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2797 2958 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2798 2959 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2799 2960 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2800 2961 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2801 2962 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2802 2963 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2818 2979 7.962964 GATTTGTCTAAATCCGGATGTATCA 57.037 36.000 19.95 15.35 44.08 2.15
2819 2980 8.378172 GATTTGTCTAAATCCGGATGTATCAA 57.622 34.615 19.95 19.78 44.08 2.57
2820 2981 7.786178 TTTGTCTAAATCCGGATGTATCAAG 57.214 36.000 19.95 6.76 0.00 3.02
2821 2982 6.479972 TGTCTAAATCCGGATGTATCAAGT 57.520 37.500 19.95 0.00 0.00 3.16
2822 2983 6.513180 TGTCTAAATCCGGATGTATCAAGTC 58.487 40.000 19.95 5.11 0.00 3.01
2823 2984 6.097696 TGTCTAAATCCGGATGTATCAAGTCA 59.902 38.462 19.95 7.79 0.00 3.41
2824 2985 6.421202 GTCTAAATCCGGATGTATCAAGTCAC 59.579 42.308 19.95 0.00 0.00 3.67
2825 2986 2.863401 TCCGGATGTATCAAGTCACG 57.137 50.000 0.00 0.00 0.00 4.35
2826 2987 2.097036 TCCGGATGTATCAAGTCACGT 58.903 47.619 0.00 0.00 0.00 4.49
2827 2988 2.494471 TCCGGATGTATCAAGTCACGTT 59.506 45.455 0.00 0.00 0.00 3.99
2828 2989 3.056393 TCCGGATGTATCAAGTCACGTTT 60.056 43.478 0.00 0.00 0.00 3.60
2829 2990 3.682858 CCGGATGTATCAAGTCACGTTTT 59.317 43.478 0.00 0.00 0.00 2.43
2830 2991 4.865925 CCGGATGTATCAAGTCACGTTTTA 59.134 41.667 0.00 0.00 0.00 1.52
2831 2992 5.005394 CCGGATGTATCAAGTCACGTTTTAG 59.995 44.000 0.00 0.00 0.00 1.85
2832 2993 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
2833 2994 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
2834 2995 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
2835 2996 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
2845 3006 9.962783 AGTCACGTTTTAGTATTAGATACATCC 57.037 33.333 0.00 0.00 38.21 3.51
2846 3007 8.899776 GTCACGTTTTAGTATTAGATACATCCG 58.100 37.037 0.00 0.00 38.21 4.18
2847 3008 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
2848 3009 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
2865 3026 8.234136 ACATCCGTATCTAGACAAATGTAAGA 57.766 34.615 0.00 1.82 0.00 2.10
2866 3027 8.136165 ACATCCGTATCTAGACAAATGTAAGAC 58.864 37.037 0.00 0.00 0.00 3.01
2867 3028 7.634671 TCCGTATCTAGACAAATGTAAGACA 57.365 36.000 0.00 0.00 0.00 3.41
2868 3029 8.058667 TCCGTATCTAGACAAATGTAAGACAA 57.941 34.615 0.00 0.00 0.00 3.18
2869 3030 8.188799 TCCGTATCTAGACAAATGTAAGACAAG 58.811 37.037 0.00 0.00 0.00 3.16
2870 3031 8.188799 CCGTATCTAGACAAATGTAAGACAAGA 58.811 37.037 0.00 0.00 0.00 3.02
2871 3032 9.569167 CGTATCTAGACAAATGTAAGACAAGAA 57.431 33.333 0.00 0.00 0.00 2.52
2878 3039 8.143835 AGACAAATGTAAGACAAGAATTTTGGG 58.856 33.333 7.26 0.00 31.16 4.12
2879 3040 8.017418 ACAAATGTAAGACAAGAATTTTGGGA 57.983 30.769 7.26 0.00 31.16 4.37
2880 3041 7.926018 ACAAATGTAAGACAAGAATTTTGGGAC 59.074 33.333 7.26 0.00 31.16 4.46
2881 3042 5.682943 TGTAAGACAAGAATTTTGGGACG 57.317 39.130 5.68 0.00 0.00 4.79
2882 3043 4.517453 TGTAAGACAAGAATTTTGGGACGG 59.483 41.667 0.00 0.00 0.00 4.79
2883 3044 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2884 3045 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2885 3046 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2886 3047 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2971 3133 6.550843 CCTTTATTGCAATATCGAACACACA 58.449 36.000 19.51 0.00 0.00 3.72
3048 3210 7.951347 ATCTTGATTCAAGCTTCTATTGGTT 57.049 32.000 19.53 0.00 40.84 3.67
3141 3303 9.745018 AGTATACATTATCCTGAAATGGAATGG 57.255 33.333 5.50 0.00 39.85 3.16
3215 3377 6.102615 TCCTGATATTTAATAACCCACAGCCT 59.897 38.462 0.00 0.00 0.00 4.58
3237 3399 3.375699 TGGACTAGAATCTTGACCCCTC 58.624 50.000 10.00 0.00 0.00 4.30
3259 3421 7.339466 CCCTCATAAACCTAGTTGCTGTTTTAT 59.661 37.037 0.35 0.00 34.33 1.40
3383 3545 8.257602 TCAAAGGTGGTATTGATAGCTATACA 57.742 34.615 6.13 4.11 35.36 2.29
3431 3593 1.260544 CCTTGCCCTGCTTTAAGCTT 58.739 50.000 18.20 3.48 42.97 3.74
3592 3759 4.734398 TTTTGGCTCACAACATTTGACT 57.266 36.364 0.00 0.00 39.19 3.41
3678 3845 7.189693 TGGCTTCAATATATGCTTTTAGTCG 57.810 36.000 0.00 0.00 0.00 4.18
3824 3992 7.175293 GTCCTGTATAAATTGTGTTGGTAACCA 59.825 37.037 0.00 0.00 0.00 3.67
3864 4157 5.400485 GGTACGGTACTTATGCAAATACTCG 59.600 44.000 17.14 0.71 0.00 4.18
4043 4340 6.881065 TGATCTTGACTATTCCCTGTTTTGAG 59.119 38.462 0.00 0.00 0.00 3.02
4080 4377 6.707290 TCCTAGTTCCAAATTCGAATCAAGA 58.293 36.000 11.83 5.53 0.00 3.02
4085 4382 4.009675 TCCAAATTCGAATCAAGACCCAG 58.990 43.478 11.83 0.00 0.00 4.45
4127 4424 7.799918 CTTTAGCCATAAAGTCCTGGTTTAGGA 60.800 40.741 3.80 0.00 44.26 2.94
4181 4478 3.696051 GAGCATAAGAAGAATGGTTGCCA 59.304 43.478 0.00 0.00 35.31 4.92
4193 4490 7.961326 AGAATGGTTGCCAATTCTTAACTAT 57.039 32.000 0.00 0.00 36.95 2.12
4449 4746 2.373502 AGTTCACCTCTTTTAGCCTGCT 59.626 45.455 0.00 0.00 0.00 4.24
4499 4803 6.536447 TCTTGCCATTGAATATGCATCTCTA 58.464 36.000 0.19 0.00 33.08 2.43
4536 4923 2.027469 TGGTGAGCTACTACAGTCGAGA 60.027 50.000 0.00 0.00 0.00 4.04
4571 4958 6.560253 ATTTGGTACACTCACTGTTTGATC 57.440 37.500 0.00 0.00 39.29 2.92
4572 4959 4.002906 TGGTACACTCACTGTTTGATCC 57.997 45.455 0.00 0.00 33.91 3.36
5218 5640 9.740239 GTATACAGTACAGATTACGAAATTCCA 57.260 33.333 0.00 0.00 0.00 3.53
5408 5992 8.267183 TGCCTTCTCTGATACTATGAAATTCAA 58.733 33.333 0.00 0.00 0.00 2.69
5430 6014 6.013206 TCAAGTGGCAAACCTTCCTACTTATA 60.013 38.462 0.00 0.00 36.63 0.98
5770 6389 2.228822 CGCCTGTATTTGTCCAAAGCTT 59.771 45.455 0.00 0.00 33.32 3.74
5851 6470 1.086696 CAATGCGTCGGTTCTCCAAT 58.913 50.000 0.00 0.00 0.00 3.16
5855 6474 1.950909 TGCGTCGGTTCTCCAATTTTT 59.049 42.857 0.00 0.00 0.00 1.94
5877 6496 6.787085 TTTTTCTTTTGAAACGAAGGCAAA 57.213 29.167 0.00 0.00 46.80 3.68
5878 6497 6.787085 TTTTCTTTTGAAACGAAGGCAAAA 57.213 29.167 0.00 0.00 46.80 2.44
5883 6502 6.976636 TTTTGAAACGAAGGCAAAAGATTT 57.023 29.167 0.00 0.00 36.80 2.17
5884 6503 5.964887 TTGAAACGAAGGCAAAAGATTTG 57.035 34.783 0.00 0.00 0.00 2.32
5885 6504 3.801594 TGAAACGAAGGCAAAAGATTTGC 59.198 39.130 17.18 17.18 44.22 3.68
5894 6513 4.445452 GCAAAAGATTTGCCTCATCTCA 57.555 40.909 15.12 0.00 39.38 3.27
5895 6514 5.007385 GCAAAAGATTTGCCTCATCTCAT 57.993 39.130 15.12 0.00 39.38 2.90
5896 6515 5.416947 GCAAAAGATTTGCCTCATCTCATT 58.583 37.500 15.12 0.00 39.38 2.57
5897 6516 6.567050 GCAAAAGATTTGCCTCATCTCATTA 58.433 36.000 15.12 0.00 39.38 1.90
5898 6517 7.037438 GCAAAAGATTTGCCTCATCTCATTAA 58.963 34.615 15.12 0.00 39.38 1.40
5899 6518 7.709613 GCAAAAGATTTGCCTCATCTCATTAAT 59.290 33.333 15.12 0.00 39.38 1.40
5900 6519 9.595823 CAAAAGATTTGCCTCATCTCATTAATT 57.404 29.630 0.00 0.00 30.19 1.40
5904 6523 9.857656 AGATTTGCCTCATCTCATTAATTAAGA 57.142 29.630 3.94 0.00 0.00 2.10
5907 6526 9.685276 TTTGCCTCATCTCATTAATTAAGAAGA 57.315 29.630 12.30 12.30 0.00 2.87
5908 6527 8.899427 TGCCTCATCTCATTAATTAAGAAGAG 57.101 34.615 16.17 16.17 35.61 2.85
5909 6528 8.489489 TGCCTCATCTCATTAATTAAGAAGAGT 58.511 33.333 19.02 8.41 34.60 3.24
5910 6529 9.336171 GCCTCATCTCATTAATTAAGAAGAGTT 57.664 33.333 19.02 11.08 34.60 3.01
5925 6544 7.497925 AAGAAGAGTTTTGAGTTACATGACC 57.502 36.000 0.00 0.00 0.00 4.02
5926 6545 5.696724 AGAAGAGTTTTGAGTTACATGACCG 59.303 40.000 0.00 0.00 0.00 4.79
5927 6546 5.209818 AGAGTTTTGAGTTACATGACCGA 57.790 39.130 0.00 0.00 0.00 4.69
5928 6547 4.989168 AGAGTTTTGAGTTACATGACCGAC 59.011 41.667 0.00 0.00 0.00 4.79
5929 6548 4.062991 AGTTTTGAGTTACATGACCGACC 58.937 43.478 0.00 0.00 0.00 4.79
5930 6549 2.357327 TTGAGTTACATGACCGACCG 57.643 50.000 0.00 0.00 0.00 4.79
5931 6550 0.108992 TGAGTTACATGACCGACCGC 60.109 55.000 0.00 0.00 0.00 5.68
5932 6551 0.804933 GAGTTACATGACCGACCGCC 60.805 60.000 0.00 0.00 0.00 6.13
5933 6552 1.812507 GTTACATGACCGACCGCCC 60.813 63.158 0.00 0.00 0.00 6.13
5934 6553 3.359515 TTACATGACCGACCGCCCG 62.360 63.158 0.00 0.00 0.00 6.13
5936 6555 3.829044 CATGACCGACCGCCCGTA 61.829 66.667 0.00 0.00 0.00 4.02
5937 6556 3.524606 ATGACCGACCGCCCGTAG 61.525 66.667 0.00 0.00 0.00 3.51
5938 6557 4.720902 TGACCGACCGCCCGTAGA 62.721 66.667 0.00 0.00 0.00 2.59
5939 6558 4.185059 GACCGACCGCCCGTAGAC 62.185 72.222 0.00 0.00 0.00 2.59
5950 6569 2.507769 CGTAGACGGCCCGAAACC 60.508 66.667 11.71 0.00 35.37 3.27
5957 6576 4.948257 GGCCCGAAACCGATAAGT 57.052 55.556 0.00 0.00 0.00 2.24
5958 6577 2.686602 GGCCCGAAACCGATAAGTC 58.313 57.895 0.00 0.00 0.00 3.01
5959 6578 0.177373 GGCCCGAAACCGATAAGTCT 59.823 55.000 0.00 0.00 0.00 3.24
5960 6579 1.410153 GGCCCGAAACCGATAAGTCTA 59.590 52.381 0.00 0.00 0.00 2.59
5961 6580 2.467838 GCCCGAAACCGATAAGTCTAC 58.532 52.381 0.00 0.00 0.00 2.59
5962 6581 2.100418 GCCCGAAACCGATAAGTCTACT 59.900 50.000 0.00 0.00 0.00 2.57
5963 6582 3.794812 GCCCGAAACCGATAAGTCTACTC 60.795 52.174 0.00 0.00 0.00 2.59
5964 6583 3.631227 CCCGAAACCGATAAGTCTACTCT 59.369 47.826 0.00 0.00 0.00 3.24
5965 6584 4.261114 CCCGAAACCGATAAGTCTACTCTC 60.261 50.000 0.00 0.00 0.00 3.20
5966 6585 4.516359 CGAAACCGATAAGTCTACTCTCG 58.484 47.826 7.65 7.65 33.52 4.04
5967 6586 3.967203 AACCGATAAGTCTACTCTCGC 57.033 47.619 8.68 0.00 32.85 5.03
5968 6587 1.865970 ACCGATAAGTCTACTCTCGCG 59.134 52.381 0.00 0.00 32.85 5.87
5969 6588 1.194997 CCGATAAGTCTACTCTCGCGG 59.805 57.143 6.13 0.00 32.85 6.46
5970 6589 1.398705 CGATAAGTCTACTCTCGCGGC 60.399 57.143 6.13 0.00 0.00 6.53
5971 6590 1.602851 GATAAGTCTACTCTCGCGGCA 59.397 52.381 6.13 0.00 0.00 5.69
5972 6591 1.676746 TAAGTCTACTCTCGCGGCAT 58.323 50.000 6.13 0.00 0.00 4.40
5973 6592 1.676746 AAGTCTACTCTCGCGGCATA 58.323 50.000 6.13 0.00 0.00 3.14
5974 6593 1.676746 AGTCTACTCTCGCGGCATAA 58.323 50.000 6.13 0.00 0.00 1.90
5975 6594 1.604755 AGTCTACTCTCGCGGCATAAG 59.395 52.381 6.13 0.00 0.00 1.73
5976 6595 1.602851 GTCTACTCTCGCGGCATAAGA 59.397 52.381 6.13 0.00 0.00 2.10
5977 6596 1.874231 TCTACTCTCGCGGCATAAGAG 59.126 52.381 17.39 17.39 41.84 2.85
5978 6597 1.874231 CTACTCTCGCGGCATAAGAGA 59.126 52.381 23.71 15.02 39.09 3.10
5979 6598 1.103803 ACTCTCGCGGCATAAGAGAA 58.896 50.000 23.71 0.00 40.09 2.87
5980 6599 1.202313 ACTCTCGCGGCATAAGAGAAC 60.202 52.381 23.71 0.00 40.09 3.01
5981 6600 1.066303 CTCTCGCGGCATAAGAGAACT 59.934 52.381 14.71 0.00 40.09 3.01
5982 6601 1.065701 TCTCGCGGCATAAGAGAACTC 59.934 52.381 6.13 0.00 38.00 3.01
5983 6602 0.815095 TCGCGGCATAAGAGAACTCA 59.185 50.000 6.13 0.00 0.00 3.41
5984 6603 1.202302 TCGCGGCATAAGAGAACTCAG 60.202 52.381 6.13 0.00 0.00 3.35
5985 6604 1.202302 CGCGGCATAAGAGAACTCAGA 60.202 52.381 0.00 0.00 0.00 3.27
5986 6605 2.197577 GCGGCATAAGAGAACTCAGAC 58.802 52.381 4.64 0.00 0.00 3.51
5987 6606 2.455032 CGGCATAAGAGAACTCAGACG 58.545 52.381 4.64 1.88 0.00 4.18
5988 6607 2.159366 CGGCATAAGAGAACTCAGACGT 60.159 50.000 4.64 0.00 0.00 4.34
5989 6608 3.673594 CGGCATAAGAGAACTCAGACGTT 60.674 47.826 4.64 0.00 0.00 3.99
5990 6609 4.246458 GGCATAAGAGAACTCAGACGTTT 58.754 43.478 4.64 0.00 0.00 3.60
5991 6610 4.092091 GGCATAAGAGAACTCAGACGTTTG 59.908 45.833 0.00 0.00 0.00 2.93
5992 6611 4.092091 GCATAAGAGAACTCAGACGTTTGG 59.908 45.833 6.21 0.00 0.00 3.28
5993 6612 2.156343 AGAGAACTCAGACGTTTGGC 57.844 50.000 6.21 0.00 0.00 4.52
5994 6613 1.149148 GAGAACTCAGACGTTTGGCC 58.851 55.000 6.21 0.00 0.00 5.36
5995 6614 0.250338 AGAACTCAGACGTTTGGCCC 60.250 55.000 6.21 0.00 0.00 5.80
5996 6615 1.228154 AACTCAGACGTTTGGCCCC 60.228 57.895 6.21 0.00 0.00 5.80
5997 6616 1.705997 AACTCAGACGTTTGGCCCCT 61.706 55.000 6.21 0.00 0.00 4.79
5998 6617 1.672356 CTCAGACGTTTGGCCCCTG 60.672 63.158 6.21 0.00 0.00 4.45
5999 6618 3.365265 CAGACGTTTGGCCCCTGC 61.365 66.667 0.00 0.00 0.00 4.85
6010 6629 4.247130 CCCCTGCCAACCCCCAAA 62.247 66.667 0.00 0.00 0.00 3.28
6011 6630 2.604382 CCCTGCCAACCCCCAAAG 60.604 66.667 0.00 0.00 0.00 2.77
6012 6631 2.201210 CCTGCCAACCCCCAAAGT 59.799 61.111 0.00 0.00 0.00 2.66
6013 6632 1.908299 CCTGCCAACCCCCAAAGTC 60.908 63.158 0.00 0.00 0.00 3.01
6014 6633 1.153756 CTGCCAACCCCCAAAGTCT 59.846 57.895 0.00 0.00 0.00 3.24
6015 6634 1.152567 TGCCAACCCCCAAAGTCTG 60.153 57.895 0.00 0.00 0.00 3.51
6016 6635 1.152830 GCCAACCCCCAAAGTCTGA 59.847 57.895 0.00 0.00 0.00 3.27
6017 6636 1.179174 GCCAACCCCCAAAGTCTGAC 61.179 60.000 0.00 0.00 0.00 3.51
6018 6637 0.539669 CCAACCCCCAAAGTCTGACC 60.540 60.000 3.76 0.00 0.00 4.02
6019 6638 0.478507 CAACCCCCAAAGTCTGACCT 59.521 55.000 3.76 0.00 0.00 3.85
6020 6639 0.771755 AACCCCCAAAGTCTGACCTC 59.228 55.000 3.76 0.00 0.00 3.85
6021 6640 1.134438 ACCCCCAAAGTCTGACCTCC 61.134 60.000 3.76 0.00 0.00 4.30
6022 6641 1.296715 CCCCAAAGTCTGACCTCCG 59.703 63.158 3.76 0.00 0.00 4.63
6023 6642 1.376037 CCCAAAGTCTGACCTCCGC 60.376 63.158 3.76 0.00 0.00 5.54
6024 6643 1.376037 CCAAAGTCTGACCTCCGCC 60.376 63.158 3.76 0.00 0.00 6.13
6025 6644 1.674057 CAAAGTCTGACCTCCGCCT 59.326 57.895 3.76 0.00 0.00 5.52
6026 6645 0.035458 CAAAGTCTGACCTCCGCCTT 59.965 55.000 3.76 0.00 0.00 4.35
6027 6646 0.035458 AAAGTCTGACCTCCGCCTTG 59.965 55.000 3.76 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
376 379 1.000896 GGCTGTTACATGTGGGCCT 60.001 57.895 9.11 0.00 36.96 5.19
765 869 4.479156 AAACAAGGGGAAATCCAAGGTA 57.521 40.909 1.22 0.00 37.91 3.08
884 988 3.678056 ACTTGCTTCACATCCTCGTAA 57.322 42.857 0.00 0.00 0.00 3.18
1200 1304 2.879490 TCTCCCCCTTCCCCTCCA 60.879 66.667 0.00 0.00 0.00 3.86
1510 1614 2.372890 TGAGCATCCAGAGGGGCAG 61.373 63.158 0.00 0.00 36.21 4.85
1821 1940 2.514803 GCCTTTTCCCACTGCTTCTTA 58.485 47.619 0.00 0.00 0.00 2.10
1836 1955 1.039856 AGCAATCCACAAACGCCTTT 58.960 45.000 0.00 0.00 0.00 3.11
1944 2063 0.538584 CAGGTGCTACAGGATCTGCA 59.461 55.000 0.00 0.00 37.78 4.41
2472 2597 0.675633 AGTGCAAGGCATTTGGTGTC 59.324 50.000 0.00 0.00 41.91 3.67
2475 2600 1.342174 CTGAAGTGCAAGGCATTTGGT 59.658 47.619 3.63 0.00 41.91 3.67
2484 2609 1.528586 CGACCAGAACTGAAGTGCAAG 59.471 52.381 3.19 0.00 0.00 4.01
2571 2719 7.324935 TGATTTTTCTGCATGCATTAGTTCAT 58.675 30.769 22.97 7.68 0.00 2.57
2651 2812 7.172361 GGAAGATAAATCAGTCATGCTAAGACC 59.828 40.741 0.00 0.00 36.68 3.85
2717 2878 8.091449 CAGTCCTCTAGAATCTAACAACAAACT 58.909 37.037 0.00 0.00 0.00 2.66
2762 2923 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
2763 2924 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
2764 2925 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2765 2926 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2766 2927 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2767 2928 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2768 2929 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2769 2930 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2770 2931 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2771 2932 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2772 2933 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2773 2934 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2774 2935 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2775 2936 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2776 2937 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2783 2944 9.151471 CGGATTTAGACAAATCTAAGACAAGAA 57.849 33.333 9.31 0.00 45.93 2.52
2784 2945 7.764443 CCGGATTTAGACAAATCTAAGACAAGA 59.236 37.037 0.00 0.00 45.93 3.02
2785 2946 7.764443 TCCGGATTTAGACAAATCTAAGACAAG 59.236 37.037 0.00 0.00 45.93 3.16
2786 2947 7.617225 TCCGGATTTAGACAAATCTAAGACAA 58.383 34.615 0.00 0.00 45.93 3.18
2787 2948 7.177832 TCCGGATTTAGACAAATCTAAGACA 57.822 36.000 0.00 0.00 45.93 3.41
2788 2949 7.711339 ACATCCGGATTTAGACAAATCTAAGAC 59.289 37.037 16.19 0.00 45.93 3.01
2789 2950 7.792032 ACATCCGGATTTAGACAAATCTAAGA 58.208 34.615 16.19 5.41 45.93 2.10
2790 2951 9.712305 ATACATCCGGATTTAGACAAATCTAAG 57.288 33.333 16.19 0.00 45.93 2.18
2791 2952 9.706691 GATACATCCGGATTTAGACAAATCTAA 57.293 33.333 16.19 0.00 46.26 2.10
2792 2953 8.866093 TGATACATCCGGATTTAGACAAATCTA 58.134 33.333 16.19 0.00 46.26 1.98
2793 2954 7.735917 TGATACATCCGGATTTAGACAAATCT 58.264 34.615 16.19 0.00 46.26 2.40
2794 2955 7.962964 TGATACATCCGGATTTAGACAAATC 57.037 36.000 16.19 7.95 46.30 2.17
2795 2956 7.993183 ACTTGATACATCCGGATTTAGACAAAT 59.007 33.333 16.19 10.66 37.06 2.32
2796 2957 7.335627 ACTTGATACATCCGGATTTAGACAAA 58.664 34.615 16.19 5.69 0.00 2.83
2797 2958 6.884832 ACTTGATACATCCGGATTTAGACAA 58.115 36.000 16.19 19.60 0.00 3.18
2798 2959 6.097696 TGACTTGATACATCCGGATTTAGACA 59.902 38.462 16.19 14.08 0.00 3.41
2799 2960 6.421202 GTGACTTGATACATCCGGATTTAGAC 59.579 42.308 16.19 11.72 0.00 2.59
2800 2961 6.513180 GTGACTTGATACATCCGGATTTAGA 58.487 40.000 16.19 0.94 0.00 2.10
2801 2962 5.402568 CGTGACTTGATACATCCGGATTTAG 59.597 44.000 16.19 6.45 0.00 1.85
2802 2963 5.163488 ACGTGACTTGATACATCCGGATTTA 60.163 40.000 16.19 14.15 0.00 1.40
2803 2964 4.119862 CGTGACTTGATACATCCGGATTT 58.880 43.478 16.19 11.96 0.00 2.17
2804 2965 3.132289 ACGTGACTTGATACATCCGGATT 59.868 43.478 16.19 9.22 0.00 3.01
2805 2966 2.693591 ACGTGACTTGATACATCCGGAT 59.306 45.455 12.38 12.38 0.00 4.18
2806 2967 2.097036 ACGTGACTTGATACATCCGGA 58.903 47.619 6.61 6.61 0.00 5.14
2807 2968 2.579207 ACGTGACTTGATACATCCGG 57.421 50.000 0.00 0.00 0.00 5.14
2808 2969 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
2809 2970 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
2819 2980 9.962783 GGATGTATCTAATACTAAAACGTGACT 57.037 33.333 0.00 0.00 36.70 3.41
2820 2981 8.899776 CGGATGTATCTAATACTAAAACGTGAC 58.100 37.037 0.00 0.00 36.70 3.67
2821 2982 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
2822 2983 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
2839 3000 9.346005 TCTTACATTTGTCTAGATACGGATGTA 57.654 33.333 11.94 11.94 32.86 2.29
2840 3001 8.136165 GTCTTACATTTGTCTAGATACGGATGT 58.864 37.037 13.29 13.29 34.19 3.06
2841 3002 8.135529 TGTCTTACATTTGTCTAGATACGGATG 58.864 37.037 0.00 0.85 0.00 3.51
2842 3003 8.234136 TGTCTTACATTTGTCTAGATACGGAT 57.766 34.615 0.00 0.00 0.00 4.18
2843 3004 7.634671 TGTCTTACATTTGTCTAGATACGGA 57.365 36.000 0.00 0.00 0.00 4.69
2844 3005 8.188799 TCTTGTCTTACATTTGTCTAGATACGG 58.811 37.037 0.00 0.00 0.00 4.02
2845 3006 9.569167 TTCTTGTCTTACATTTGTCTAGATACG 57.431 33.333 0.00 0.00 0.00 3.06
2852 3013 8.143835 CCCAAAATTCTTGTCTTACATTTGTCT 58.856 33.333 0.00 0.00 27.14 3.41
2853 3014 8.141268 TCCCAAAATTCTTGTCTTACATTTGTC 58.859 33.333 0.00 0.00 27.14 3.18
2854 3015 7.926018 GTCCCAAAATTCTTGTCTTACATTTGT 59.074 33.333 0.00 0.00 27.14 2.83
2855 3016 7.114811 CGTCCCAAAATTCTTGTCTTACATTTG 59.885 37.037 0.00 0.00 0.00 2.32
2856 3017 7.145323 CGTCCCAAAATTCTTGTCTTACATTT 58.855 34.615 0.00 0.00 0.00 2.32
2857 3018 6.294508 CCGTCCCAAAATTCTTGTCTTACATT 60.295 38.462 0.00 0.00 0.00 2.71
2858 3019 5.183140 CCGTCCCAAAATTCTTGTCTTACAT 59.817 40.000 0.00 0.00 0.00 2.29
2859 3020 4.517453 CCGTCCCAAAATTCTTGTCTTACA 59.483 41.667 0.00 0.00 0.00 2.41
2860 3021 4.758165 TCCGTCCCAAAATTCTTGTCTTAC 59.242 41.667 0.00 0.00 0.00 2.34
2861 3022 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2862 3023 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2863 3024 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2864 3025 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2865 3026 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2866 3027 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2867 3028 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2868 3029 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2869 3030 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2870 3031 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2871 3032 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2872 3033 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
2873 3034 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
2874 3035 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2875 3036 0.686441 CACATACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
2876 3037 1.400530 CCACATACTCCCTCCGTCCC 61.401 65.000 0.00 0.00 0.00 4.46
2877 3038 0.686769 ACCACATACTCCCTCCGTCC 60.687 60.000 0.00 0.00 0.00 4.79
2878 3039 2.062971 TACCACATACTCCCTCCGTC 57.937 55.000 0.00 0.00 0.00 4.79
2879 3040 2.698797 CAATACCACATACTCCCTCCGT 59.301 50.000 0.00 0.00 0.00 4.69
2880 3041 2.037251 CCAATACCACATACTCCCTCCG 59.963 54.545 0.00 0.00 0.00 4.63
2881 3042 2.372172 CCCAATACCACATACTCCCTCC 59.628 54.545 0.00 0.00 0.00 4.30
2882 3043 3.046374 ACCCAATACCACATACTCCCTC 58.954 50.000 0.00 0.00 0.00 4.30
2883 3044 3.145559 ACCCAATACCACATACTCCCT 57.854 47.619 0.00 0.00 0.00 4.20
2884 3045 4.745783 GCTTACCCAATACCACATACTCCC 60.746 50.000 0.00 0.00 0.00 4.30
2885 3046 4.141574 TGCTTACCCAATACCACATACTCC 60.142 45.833 0.00 0.00 0.00 3.85
2886 3047 5.031066 TGCTTACCCAATACCACATACTC 57.969 43.478 0.00 0.00 0.00 2.59
2971 3133 5.917462 ACCTTTGAAGCATAAGCAACTTTT 58.083 33.333 0.00 0.00 45.49 2.27
3116 3278 8.960591 CCCATTCCATTTCAGGATAATGTATAC 58.039 37.037 0.00 0.00 37.56 1.47
3208 3370 3.902881 AGATTCTAGTCCAAGGCTGTG 57.097 47.619 0.00 0.00 0.00 3.66
3215 3377 3.775316 GAGGGGTCAAGATTCTAGTCCAA 59.225 47.826 0.00 0.00 0.00 3.53
3259 3421 1.034838 AAGCACTCACACGGCCAAAA 61.035 50.000 2.24 0.00 0.00 2.44
3383 3545 9.981114 CAAACTGGGATTTAGTACAAAAAGAAT 57.019 29.630 0.00 0.00 0.00 2.40
3431 3593 6.071784 ACACGTGAACAGTTAGGATATACACA 60.072 38.462 25.01 0.00 0.00 3.72
3550 3717 7.485913 CCAAAATAAAGATTTCACACAGGATCG 59.514 37.037 0.00 0.00 34.01 3.69
3720 3887 5.469479 ACAGAAGAAAACAACAAACCACAG 58.531 37.500 0.00 0.00 0.00 3.66
3824 3992 3.562973 CCGTACCGATGTACTACATGAGT 59.437 47.826 6.41 6.25 44.27 3.41
4015 4312 3.776969 ACAGGGAATAGTCAAGATCAGCA 59.223 43.478 0.00 0.00 0.00 4.41
4043 4340 6.786967 TGGAACTAGGAATACCAGAGTAAC 57.213 41.667 0.00 0.00 38.94 2.50
4085 4382 1.166531 AAAGCAACCACGCAGACTCC 61.167 55.000 0.00 0.00 0.00 3.85
4193 4490 8.594550 ACTCTAGGTTTAAACAGAGCTTATGAA 58.405 33.333 24.89 5.34 38.46 2.57
4499 4803 9.765795 GTAGCTCACCAAACAATACTATCTTAT 57.234 33.333 0.00 0.00 0.00 1.73
4536 4923 8.349983 GTGAGTGTACCAAATAAATGAAACTGT 58.650 33.333 0.00 0.00 0.00 3.55
4571 4958 4.923415 AGGAATTCACTGTAAAAGAGGGG 58.077 43.478 7.93 0.00 0.00 4.79
4572 4959 6.712276 AGTAGGAATTCACTGTAAAAGAGGG 58.288 40.000 7.93 0.00 0.00 4.30
5408 5992 4.929146 ATAAGTAGGAAGGTTTGCCACT 57.071 40.909 0.00 0.00 37.19 4.00
5430 6014 0.250901 CCAGTAGGCAAAGGCACAGT 60.251 55.000 0.00 0.00 43.71 3.55
5657 6276 5.858049 ACGTTGTGCATTCATTCTGTTAATG 59.142 36.000 0.00 0.00 34.45 1.90
5660 6279 5.211454 CAACGTTGTGCATTCATTCTGTTA 58.789 37.500 20.21 0.00 0.00 2.41
5719 6338 6.198687 ACAACGTTGTGTATTCATTCTGTTG 58.801 36.000 31.87 1.14 40.49 3.33
5770 6389 0.038166 GTGGATCAACCTGCCCAAGA 59.962 55.000 0.00 0.00 39.86 3.02
5826 6445 1.732259 AGAACCGACGCATTGATGTTC 59.268 47.619 3.61 3.61 33.94 3.18
5855 6474 6.787085 TTTTGCCTTCGTTTCAAAAGAAAA 57.213 29.167 0.05 0.00 35.53 2.29
5860 6479 6.674278 GCAAATCTTTTGCCTTCGTTTCAAAA 60.674 34.615 12.74 0.00 39.38 2.44
5861 6480 5.220567 GCAAATCTTTTGCCTTCGTTTCAAA 60.221 36.000 12.74 0.00 39.38 2.69
5862 6481 4.269844 GCAAATCTTTTGCCTTCGTTTCAA 59.730 37.500 12.74 0.00 39.38 2.69
5863 6482 3.801594 GCAAATCTTTTGCCTTCGTTTCA 59.198 39.130 12.74 0.00 39.38 2.69
5864 6483 4.374990 GCAAATCTTTTGCCTTCGTTTC 57.625 40.909 12.74 0.00 39.38 2.78
5873 6492 4.445452 TGAGATGAGGCAAATCTTTTGC 57.555 40.909 14.88 14.88 44.22 3.68
5874 6493 9.595823 AATTAATGAGATGAGGCAAATCTTTTG 57.404 29.630 3.79 0.00 34.50 2.44
5878 6497 9.857656 TCTTAATTAATGAGATGAGGCAAATCT 57.142 29.630 0.00 1.97 37.09 2.40
5881 6500 9.685276 TCTTCTTAATTAATGAGATGAGGCAAA 57.315 29.630 0.00 0.00 0.00 3.68
5882 6501 9.334947 CTCTTCTTAATTAATGAGATGAGGCAA 57.665 33.333 22.19 3.87 37.73 4.52
5883 6502 8.489489 ACTCTTCTTAATTAATGAGATGAGGCA 58.511 33.333 27.23 8.22 41.92 4.75
5884 6503 8.900983 ACTCTTCTTAATTAATGAGATGAGGC 57.099 34.615 27.23 0.00 41.92 4.70
5899 6518 9.052759 GGTCATGTAACTCAAAACTCTTCTTAA 57.947 33.333 0.00 0.00 0.00 1.85
5900 6519 7.384115 CGGTCATGTAACTCAAAACTCTTCTTA 59.616 37.037 0.00 0.00 0.00 2.10
5901 6520 6.202954 CGGTCATGTAACTCAAAACTCTTCTT 59.797 38.462 0.00 0.00 0.00 2.52
5902 6521 5.696724 CGGTCATGTAACTCAAAACTCTTCT 59.303 40.000 0.00 0.00 0.00 2.85
5903 6522 5.694910 TCGGTCATGTAACTCAAAACTCTTC 59.305 40.000 0.00 0.00 0.00 2.87
5904 6523 5.465724 GTCGGTCATGTAACTCAAAACTCTT 59.534 40.000 0.00 0.00 0.00 2.85
5905 6524 4.989168 GTCGGTCATGTAACTCAAAACTCT 59.011 41.667 0.00 0.00 0.00 3.24
5906 6525 4.151867 GGTCGGTCATGTAACTCAAAACTC 59.848 45.833 0.00 0.00 0.00 3.01
5907 6526 4.062991 GGTCGGTCATGTAACTCAAAACT 58.937 43.478 0.00 0.00 0.00 2.66
5908 6527 3.120786 CGGTCGGTCATGTAACTCAAAAC 60.121 47.826 0.00 0.00 0.00 2.43
5909 6528 3.061322 CGGTCGGTCATGTAACTCAAAA 58.939 45.455 0.00 0.00 0.00 2.44
5910 6529 2.679450 CGGTCGGTCATGTAACTCAAA 58.321 47.619 0.00 0.00 0.00 2.69
5911 6530 1.670674 GCGGTCGGTCATGTAACTCAA 60.671 52.381 0.00 0.00 0.00 3.02
5912 6531 0.108992 GCGGTCGGTCATGTAACTCA 60.109 55.000 0.00 0.00 0.00 3.41
5913 6532 0.804933 GGCGGTCGGTCATGTAACTC 60.805 60.000 0.00 0.00 0.00 3.01
5914 6533 1.217244 GGCGGTCGGTCATGTAACT 59.783 57.895 0.00 0.00 0.00 2.24
5915 6534 1.812507 GGGCGGTCGGTCATGTAAC 60.813 63.158 0.00 0.00 0.00 2.50
5916 6535 2.580276 GGGCGGTCGGTCATGTAA 59.420 61.111 0.00 0.00 0.00 2.41
5917 6536 3.829044 CGGGCGGTCGGTCATGTA 61.829 66.667 0.00 0.00 0.00 2.29
5919 6538 3.768185 CTACGGGCGGTCGGTCATG 62.768 68.421 0.00 0.00 0.00 3.07
5920 6539 3.524606 CTACGGGCGGTCGGTCAT 61.525 66.667 0.00 0.00 0.00 3.06
5921 6540 4.720902 TCTACGGGCGGTCGGTCA 62.721 66.667 0.00 0.00 0.00 4.02
5922 6541 4.185059 GTCTACGGGCGGTCGGTC 62.185 72.222 0.00 0.00 0.00 4.79
5933 6552 2.507769 GGTTTCGGGCCGTCTACG 60.508 66.667 27.32 0.00 39.44 3.51
5934 6553 2.507769 CGGTTTCGGGCCGTCTAC 60.508 66.667 27.32 20.37 43.84 2.59
5940 6559 0.177373 AGACTTATCGGTTTCGGGCC 59.823 55.000 0.00 0.00 36.95 5.80
5941 6560 2.100418 AGTAGACTTATCGGTTTCGGGC 59.900 50.000 0.00 0.00 36.95 6.13
5942 6561 3.631227 AGAGTAGACTTATCGGTTTCGGG 59.369 47.826 0.00 0.00 36.95 5.14
5943 6562 4.552378 CGAGAGTAGACTTATCGGTTTCGG 60.552 50.000 9.26 0.00 34.17 4.30
5944 6563 4.516359 CGAGAGTAGACTTATCGGTTTCG 58.484 47.826 9.26 0.00 34.17 3.46
5945 6564 4.281264 GCGAGAGTAGACTTATCGGTTTC 58.719 47.826 15.63 1.48 36.57 2.78
5946 6565 3.242673 CGCGAGAGTAGACTTATCGGTTT 60.243 47.826 0.00 0.00 36.57 3.27
5947 6566 2.287373 CGCGAGAGTAGACTTATCGGTT 59.713 50.000 0.00 0.00 36.57 4.44
5948 6567 1.865970 CGCGAGAGTAGACTTATCGGT 59.134 52.381 0.00 0.00 36.57 4.69
5949 6568 1.194997 CCGCGAGAGTAGACTTATCGG 59.805 57.143 8.23 8.79 36.57 4.18
5950 6569 1.398705 GCCGCGAGAGTAGACTTATCG 60.399 57.143 8.23 11.69 38.03 2.92
5951 6570 1.602851 TGCCGCGAGAGTAGACTTATC 59.397 52.381 8.23 0.00 0.00 1.75
5952 6571 1.676746 TGCCGCGAGAGTAGACTTAT 58.323 50.000 8.23 0.00 0.00 1.73
5953 6572 1.676746 ATGCCGCGAGAGTAGACTTA 58.323 50.000 8.23 0.00 0.00 2.24
5954 6573 1.676746 TATGCCGCGAGAGTAGACTT 58.323 50.000 8.23 0.00 0.00 3.01
5955 6574 1.604755 CTTATGCCGCGAGAGTAGACT 59.395 52.381 8.23 0.00 0.00 3.24
5956 6575 1.602851 TCTTATGCCGCGAGAGTAGAC 59.397 52.381 8.23 0.00 0.00 2.59
5957 6576 1.874231 CTCTTATGCCGCGAGAGTAGA 59.126 52.381 8.23 3.77 33.81 2.59
5958 6577 1.874231 TCTCTTATGCCGCGAGAGTAG 59.126 52.381 18.00 6.45 38.41 2.57
5959 6578 1.963172 TCTCTTATGCCGCGAGAGTA 58.037 50.000 18.00 5.96 38.41 2.59
5960 6579 1.103803 TTCTCTTATGCCGCGAGAGT 58.896 50.000 18.00 0.90 38.41 3.24
5961 6580 1.066303 AGTTCTCTTATGCCGCGAGAG 59.934 52.381 8.23 11.90 38.57 3.20
5962 6581 1.065701 GAGTTCTCTTATGCCGCGAGA 59.934 52.381 8.23 0.00 32.36 4.04
5963 6582 1.202302 TGAGTTCTCTTATGCCGCGAG 60.202 52.381 8.23 0.00 0.00 5.03
5964 6583 0.815095 TGAGTTCTCTTATGCCGCGA 59.185 50.000 8.23 0.00 0.00 5.87
5965 6584 1.202302 TCTGAGTTCTCTTATGCCGCG 60.202 52.381 0.00 0.00 0.00 6.46
5966 6585 2.197577 GTCTGAGTTCTCTTATGCCGC 58.802 52.381 1.53 0.00 0.00 6.53
5967 6586 2.159366 ACGTCTGAGTTCTCTTATGCCG 60.159 50.000 1.53 0.00 0.00 5.69
5968 6587 3.512033 ACGTCTGAGTTCTCTTATGCC 57.488 47.619 1.53 0.00 0.00 4.40
5969 6588 4.092091 CCAAACGTCTGAGTTCTCTTATGC 59.908 45.833 0.00 0.00 32.43 3.14
5970 6589 4.092091 GCCAAACGTCTGAGTTCTCTTATG 59.908 45.833 0.00 0.00 32.43 1.90
5971 6590 4.246458 GCCAAACGTCTGAGTTCTCTTAT 58.754 43.478 0.00 0.00 32.43 1.73
5972 6591 3.554337 GGCCAAACGTCTGAGTTCTCTTA 60.554 47.826 0.00 0.00 32.43 2.10
5973 6592 2.484889 GCCAAACGTCTGAGTTCTCTT 58.515 47.619 0.00 0.00 32.43 2.85
5974 6593 1.270358 GGCCAAACGTCTGAGTTCTCT 60.270 52.381 0.00 0.00 32.43 3.10
5975 6594 1.149148 GGCCAAACGTCTGAGTTCTC 58.851 55.000 0.00 0.00 32.43 2.87
5976 6595 0.250338 GGGCCAAACGTCTGAGTTCT 60.250 55.000 4.39 0.00 32.43 3.01
5977 6596 1.235281 GGGGCCAAACGTCTGAGTTC 61.235 60.000 4.39 0.00 32.43 3.01
5978 6597 1.228154 GGGGCCAAACGTCTGAGTT 60.228 57.895 4.39 0.00 35.59 3.01
5979 6598 2.147387 AGGGGCCAAACGTCTGAGT 61.147 57.895 4.39 0.00 0.00 3.41
5980 6599 1.672356 CAGGGGCCAAACGTCTGAG 60.672 63.158 4.39 0.00 0.00 3.35
5981 6600 2.429930 CAGGGGCCAAACGTCTGA 59.570 61.111 4.39 0.00 0.00 3.27
5982 6601 3.365265 GCAGGGGCCAAACGTCTG 61.365 66.667 4.39 3.02 0.00 3.51
5993 6612 4.247130 TTTGGGGGTTGGCAGGGG 62.247 66.667 0.00 0.00 0.00 4.79
5994 6613 2.604382 CTTTGGGGGTTGGCAGGG 60.604 66.667 0.00 0.00 0.00 4.45
5995 6614 1.908299 GACTTTGGGGGTTGGCAGG 60.908 63.158 0.00 0.00 0.00 4.85
5996 6615 1.153756 AGACTTTGGGGGTTGGCAG 59.846 57.895 0.00 0.00 0.00 4.85
5997 6616 1.152567 CAGACTTTGGGGGTTGGCA 60.153 57.895 0.00 0.00 0.00 4.92
5998 6617 1.152830 TCAGACTTTGGGGGTTGGC 59.847 57.895 0.00 0.00 0.00 4.52
5999 6618 0.539669 GGTCAGACTTTGGGGGTTGG 60.540 60.000 0.00 0.00 0.00 3.77
6000 6619 0.478507 AGGTCAGACTTTGGGGGTTG 59.521 55.000 0.00 0.00 0.00 3.77
6001 6620 0.771755 GAGGTCAGACTTTGGGGGTT 59.228 55.000 0.00 0.00 0.00 4.11
6002 6621 1.134438 GGAGGTCAGACTTTGGGGGT 61.134 60.000 0.00 0.00 0.00 4.95
6003 6622 1.685820 GGAGGTCAGACTTTGGGGG 59.314 63.158 0.00 0.00 0.00 5.40
6004 6623 1.296715 CGGAGGTCAGACTTTGGGG 59.703 63.158 0.00 0.00 0.00 4.96
6005 6624 1.376037 GCGGAGGTCAGACTTTGGG 60.376 63.158 0.00 0.00 0.00 4.12
6006 6625 1.376037 GGCGGAGGTCAGACTTTGG 60.376 63.158 0.00 0.00 0.00 3.28
6007 6626 0.035458 AAGGCGGAGGTCAGACTTTG 59.965 55.000 0.00 0.00 35.91 2.77
6008 6627 0.035458 CAAGGCGGAGGTCAGACTTT 59.965 55.000 0.00 0.00 37.29 2.66
6009 6628 1.674057 CAAGGCGGAGGTCAGACTT 59.326 57.895 0.00 0.00 40.02 3.01
6010 6629 3.382111 CAAGGCGGAGGTCAGACT 58.618 61.111 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.