Multiple sequence alignment - TraesCS2D01G462800

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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 TraesCS2D01G462800 chr2D 100.000 3035 0 0 1 3035 568775255 568772221 0.000000e+00 5605
1 TraesCS2D01G462800 chr2A 91.004 2212 107 33 482 2633 708043957 708041778 0.000000e+00 2898
2 TraesCS2D01G462800 chr2A 90.814 381 27 5 1 381 708044357 708043985 1.260000e-138 503
3 TraesCS2D01G462800 chr2A 85.946 185 24 2 2832 3015 530741839 530742022 2.390000e-46 196
4 TraesCS2D01G462800 chr2A 96.226 106 3 1 2727 2832 718971994 718971890 4.020000e-39 172
5 TraesCS2D01G462800 chr2A 88.393 112 6 5 2632 2737 708041573 708041463 8.830000e-26 128
6 TraesCS2D01G462800 chr2B 92.265 1978 81 31 251 2197 681350871 681348935 0.000000e+00 2739
7 TraesCS2D01G462800 chr2B 86.947 475 20 13 2294 2728 681348861 681348389 2.100000e-136 496
8 TraesCS2D01G462800 chr7D 88.725 204 22 1 2832 3035 547331820 547331618 6.500000e-62 248
9 TraesCS2D01G462800 chr7D 95.283 106 4 1 2727 2832 155772735 155772839 1.870000e-37 167
10 TraesCS2D01G462800 chr7D 95.283 106 4 1 2727 2832 163740234 163740130 1.870000e-37 167
11 TraesCS2D01G462800 chr1D 86.408 206 24 2 2832 3035 43284083 43283880 3.940000e-54 222
12 TraesCS2D01G462800 chr1D 95.283 106 4 1 2727 2832 270900899 270901003 1.870000e-37 167
13 TraesCS2D01G462800 chr4D 84.574 188 20 9 2832 3015 182065777 182065595 8.650000e-41 178
14 TraesCS2D01G462800 chr4D 87.603 121 14 1 2896 3015 102006632 102006512 4.080000e-29 139
15 TraesCS2D01G462800 chr4D 82.787 122 17 4 2896 3015 474448242 474448123 4.140000e-19 106
16 TraesCS2D01G462800 chr3B 93.805 113 6 1 2727 2839 699701460 699701571 5.200000e-38 169
17 TraesCS2D01G462800 chr3B 80.952 210 33 5 2832 3035 807547997 807547789 3.130000e-35 159
18 TraesCS2D01G462800 chr6D 95.283 106 4 1 2727 2832 345490407 345490303 1.870000e-37 167
19 TraesCS2D01G462800 chr3D 95.283 106 4 1 2727 2832 359257736 359257840 1.870000e-37 167
20 TraesCS2D01G462800 chr4B 93.694 111 5 2 2727 2837 588786881 588786989 6.730000e-37 165
21 TraesCS2D01G462800 chr5A 92.308 117 5 4 2727 2842 387438612 387438499 2.420000e-36 163


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 TraesCS2D01G462800 chr2D 568772221 568775255 3034 True 5605.000000 5605 100.000000 1 3035 1 chr2D.!!$R1 3034
1 TraesCS2D01G462800 chr2A 708041463 708044357 2894 True 1176.333333 2898 90.070333 1 2737 3 chr2A.!!$R2 2736
2 TraesCS2D01G462800 chr2B 681348389 681350871 2482 True 1617.500000 2739 89.606000 251 2728 2 chr2B.!!$R1 2477

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
590 611 1.518929 GTCTCTGTGACGCGCATAATC 59.481 52.381 5.73 0.0 35.81 1.75 F
1320 1374 1.770294 GTGATCTCCTCCTCCTCGTT 58.230 55.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 1968 0.955919 GGAAGAACAGGTGCCCGAAG 60.956 60.0 0.0 0.0 0.0 3.79 R
2922 3264 0.033504 GAACTTGGAGGCGTGACTGA 59.966 55.0 0.0 0.0 0.0 3.41 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
70 71 6.045459 TGCCATTACATATTGGGAGGTAAGAT 59.955 38.462 2.80 0.00 33.40 2.40
83 84 6.438741 TGGGAGGTAAGATGATGTCTATGATC 59.561 42.308 0.00 0.00 35.67 2.92
92 93 8.121305 AGATGATGTCTATGATCTTGTAGGAC 57.879 38.462 0.00 0.00 34.15 3.85
101 102 9.480861 TCTATGATCTTGTAGGACTAATATGGG 57.519 37.037 0.00 0.00 0.00 4.00
107 108 7.582719 TCTTGTAGGACTAATATGGGCATTTT 58.417 34.615 0.00 0.00 0.00 1.82
110 111 8.685838 TGTAGGACTAATATGGGCATTTTTAC 57.314 34.615 0.00 0.00 0.00 2.01
111 112 8.499406 TGTAGGACTAATATGGGCATTTTTACT 58.501 33.333 0.00 0.00 0.00 2.24
159 160 9.594038 CATATCACTAGTACAACAAAACAACAC 57.406 33.333 0.00 0.00 0.00 3.32
161 162 5.938710 TCACTAGTACAACAAAACAACACCA 59.061 36.000 0.00 0.00 0.00 4.17
169 170 9.748100 GTACAACAAAACAACACCAAATAAAAG 57.252 29.630 0.00 0.00 0.00 2.27
170 171 7.811653 ACAACAAAACAACACCAAATAAAAGG 58.188 30.769 0.00 0.00 0.00 3.11
171 172 6.429791 ACAAAACAACACCAAATAAAAGGC 57.570 33.333 0.00 0.00 0.00 4.35
286 287 7.012327 TGCTAGTATAACAAAGATTCATGTGGC 59.988 37.037 0.00 0.00 0.00 5.01
383 385 5.863397 AGACCAAAAACATGACATTAATGCG 59.137 36.000 15.48 4.52 0.00 4.73
420 423 7.083875 ACAAATGCACGCTTTAAGTACATAT 57.916 32.000 0.00 0.00 0.00 1.78
421 424 8.203937 ACAAATGCACGCTTTAAGTACATATA 57.796 30.769 0.00 0.00 0.00 0.86
576 597 8.567285 AAAAATACCACCTTTAGATGTCTCTG 57.433 34.615 0.00 0.00 32.66 3.35
590 611 1.518929 GTCTCTGTGACGCGCATAATC 59.481 52.381 5.73 0.00 35.81 1.75
670 692 8.028540 CACAACTGTATAGTGCAAGATACAAA 57.971 34.615 17.94 2.76 37.92 2.83
797 841 2.505498 CGTCGGCACACGCACTATC 61.505 63.158 0.00 0.00 43.86 2.08
884 928 4.261909 CCAGAAACGACCCGCTTATATACT 60.262 45.833 0.00 0.00 0.00 2.12
885 929 4.916249 CAGAAACGACCCGCTTATATACTC 59.084 45.833 0.00 0.00 0.00 2.59
886 930 3.930634 AACGACCCGCTTATATACTCC 57.069 47.619 0.00 0.00 0.00 3.85
887 931 2.867624 ACGACCCGCTTATATACTCCA 58.132 47.619 0.00 0.00 0.00 3.86
1125 1179 1.878522 CTTCGAGTTCCGCATCCCG 60.879 63.158 0.00 0.00 38.37 5.14
1212 1266 2.587194 CTGCTGAATCCCGCCTCG 60.587 66.667 0.00 0.00 0.00 4.63
1320 1374 1.770294 GTGATCTCCTCCTCCTCGTT 58.230 55.000 0.00 0.00 0.00 3.85
1914 1968 1.495951 GGTGATCAACGTGTTCGGC 59.504 57.895 0.00 0.00 41.85 5.54
2197 2252 1.936547 GACCTCATGCGAATCTGAACC 59.063 52.381 0.00 0.00 0.00 3.62
2198 2253 1.556911 ACCTCATGCGAATCTGAACCT 59.443 47.619 0.00 0.00 0.00 3.50
2199 2254 2.766263 ACCTCATGCGAATCTGAACCTA 59.234 45.455 0.00 0.00 0.00 3.08
2200 2255 3.126831 CCTCATGCGAATCTGAACCTAC 58.873 50.000 0.00 0.00 0.00 3.18
2201 2256 3.181471 CCTCATGCGAATCTGAACCTACT 60.181 47.826 0.00 0.00 0.00 2.57
2202 2257 4.046938 TCATGCGAATCTGAACCTACTC 57.953 45.455 0.00 0.00 0.00 2.59
2203 2258 3.701542 TCATGCGAATCTGAACCTACTCT 59.298 43.478 0.00 0.00 0.00 3.24
2204 2259 3.510388 TGCGAATCTGAACCTACTCTG 57.490 47.619 0.00 0.00 0.00 3.35
2205 2260 3.089284 TGCGAATCTGAACCTACTCTGA 58.911 45.455 0.00 0.00 0.00 3.27
2206 2261 3.509967 TGCGAATCTGAACCTACTCTGAA 59.490 43.478 0.00 0.00 0.00 3.02
2207 2262 3.860536 GCGAATCTGAACCTACTCTGAAC 59.139 47.826 0.00 0.00 0.00 3.18
2208 2263 4.381079 GCGAATCTGAACCTACTCTGAACT 60.381 45.833 0.00 0.00 0.00 3.01
2211 2266 6.426646 AATCTGAACCTACTCTGAACTTGT 57.573 37.500 0.00 0.00 0.00 3.16
2213 2268 5.141182 TCTGAACCTACTCTGAACTTGTCT 58.859 41.667 0.00 0.00 0.00 3.41
2225 2280 3.380320 TGAACTTGTCTTCAGAGTGTCGA 59.620 43.478 0.00 0.00 0.00 4.20
2226 2281 4.038042 TGAACTTGTCTTCAGAGTGTCGAT 59.962 41.667 0.00 0.00 0.00 3.59
2227 2282 3.906998 ACTTGTCTTCAGAGTGTCGATG 58.093 45.455 0.00 0.00 0.00 3.84
2228 2283 3.319405 ACTTGTCTTCAGAGTGTCGATGT 59.681 43.478 0.00 0.00 0.00 3.06
2229 2284 4.519350 ACTTGTCTTCAGAGTGTCGATGTA 59.481 41.667 0.00 0.00 0.00 2.29
2230 2285 5.184096 ACTTGTCTTCAGAGTGTCGATGTAT 59.816 40.000 0.00 0.00 0.00 2.29
2237 2299 9.653287 TCTTCAGAGTGTCGATGTATAAAATTT 57.347 29.630 0.00 0.00 0.00 1.82
2257 2319 7.814264 AATTTCTCATGAACAGAAGAACACT 57.186 32.000 0.00 0.00 31.48 3.55
2258 2320 7.814264 ATTTCTCATGAACAGAAGAACACTT 57.186 32.000 0.00 0.00 31.48 3.16
2259 2321 7.630242 TTTCTCATGAACAGAAGAACACTTT 57.370 32.000 0.00 0.00 31.48 2.66
2260 2322 6.609237 TCTCATGAACAGAAGAACACTTTG 57.391 37.500 0.00 0.00 0.00 2.77
2261 2323 5.528690 TCTCATGAACAGAAGAACACTTTGG 59.471 40.000 0.00 0.00 0.00 3.28
2262 2324 5.192927 TCATGAACAGAAGAACACTTTGGT 58.807 37.500 0.00 0.00 0.00 3.67
2263 2325 5.652014 TCATGAACAGAAGAACACTTTGGTT 59.348 36.000 0.00 0.00 0.00 3.67
2264 2326 5.560966 TGAACAGAAGAACACTTTGGTTC 57.439 39.130 1.15 1.15 45.87 3.62
2265 2327 4.398044 TGAACAGAAGAACACTTTGGTTCC 59.602 41.667 16.71 0.00 46.52 3.62
2266 2328 3.963129 ACAGAAGAACACTTTGGTTCCA 58.037 40.909 2.68 0.00 46.52 3.53
2267 2329 4.340617 ACAGAAGAACACTTTGGTTCCAA 58.659 39.130 0.00 0.00 46.52 3.53
2268 2330 4.770010 ACAGAAGAACACTTTGGTTCCAAA 59.230 37.500 14.99 14.99 46.52 3.28
2269 2331 5.245075 ACAGAAGAACACTTTGGTTCCAAAA 59.755 36.000 16.25 3.30 46.52 2.44
2270 2332 5.576774 CAGAAGAACACTTTGGTTCCAAAAC 59.423 40.000 16.25 7.40 46.52 2.43
2308 2370 4.707105 TCAAGCTGAAGATCACTGTGAAA 58.293 39.130 15.31 0.00 0.00 2.69
2309 2371 4.512944 TCAAGCTGAAGATCACTGTGAAAC 59.487 41.667 15.31 11.75 37.35 2.78
2322 2422 1.017387 GTGAAACCGGATGAGGATGC 58.983 55.000 9.46 0.00 34.73 3.91
2323 2423 0.617935 TGAAACCGGATGAGGATGCA 59.382 50.000 9.46 0.00 34.73 3.96
2325 2425 0.749454 AAACCGGATGAGGATGCAGC 60.749 55.000 9.46 0.00 34.73 5.25
2347 2448 8.917655 GCAGCGTACTTTTTAAATTTGGAAATA 58.082 29.630 0.00 0.00 0.00 1.40
2365 2466 5.298276 GGAAATAAGGATGTGGCGTCAAATA 59.702 40.000 0.00 0.00 0.00 1.40
2612 2738 2.036346 GGAACTGACAAGCCTGCATTTT 59.964 45.455 0.00 0.00 0.00 1.82
2614 2740 1.342174 ACTGACAAGCCTGCATTTTGG 59.658 47.619 9.04 0.00 0.00 3.28
2615 2741 1.614903 CTGACAAGCCTGCATTTTGGA 59.385 47.619 9.04 0.00 0.00 3.53
2616 2742 1.614903 TGACAAGCCTGCATTTTGGAG 59.385 47.619 9.04 0.00 35.43 3.86
2624 2750 5.299949 AGCCTGCATTTTGGAGTTTTAAAG 58.700 37.500 0.00 0.00 33.66 1.85
2626 2752 5.757808 GCCTGCATTTTGGAGTTTTAAAGAA 59.242 36.000 0.00 0.00 33.66 2.52
2628 2754 7.041167 GCCTGCATTTTGGAGTTTTAAAGAAAT 60.041 33.333 0.00 0.00 33.66 2.17
2629 2755 9.487790 CCTGCATTTTGGAGTTTTAAAGAAATA 57.512 29.630 0.00 0.00 33.66 1.40
2680 3016 8.961294 TGATTTGATTTGAAACCATTTTGACT 57.039 26.923 0.00 0.00 0.00 3.41
2711 3053 3.584406 TCATATCACACATGGGGATCTCC 59.416 47.826 3.99 3.99 0.00 3.71
2732 3074 1.134491 GGGGACGTGATGGTTTAGAGG 60.134 57.143 0.00 0.00 0.00 3.69
2733 3075 1.653151 GGACGTGATGGTTTAGAGGC 58.347 55.000 0.00 0.00 0.00 4.70
2734 3076 1.066430 GGACGTGATGGTTTAGAGGCA 60.066 52.381 0.00 0.00 0.00 4.75
2736 3078 1.338769 ACGTGATGGTTTAGAGGCACC 60.339 52.381 0.00 0.00 0.00 5.01
2737 3079 1.066143 CGTGATGGTTTAGAGGCACCT 60.066 52.381 0.00 0.00 33.76 4.00
2738 3080 2.167693 CGTGATGGTTTAGAGGCACCTA 59.832 50.000 0.00 0.00 33.76 3.08
2739 3081 3.532542 GTGATGGTTTAGAGGCACCTAC 58.467 50.000 0.00 0.00 33.76 3.18
2740 3082 2.504175 TGATGGTTTAGAGGCACCTACC 59.496 50.000 0.13 0.13 33.76 3.18
2741 3083 2.032965 TGGTTTAGAGGCACCTACCA 57.967 50.000 5.15 5.15 33.76 3.25
2742 3084 2.557869 TGGTTTAGAGGCACCTACCAT 58.442 47.619 5.15 0.00 33.76 3.55
2743 3085 2.916934 TGGTTTAGAGGCACCTACCATT 59.083 45.455 5.15 0.00 33.76 3.16
2744 3086 3.279434 GGTTTAGAGGCACCTACCATTG 58.721 50.000 2.09 0.00 0.00 2.82
2745 3087 3.308188 GGTTTAGAGGCACCTACCATTGT 60.308 47.826 2.09 0.00 0.00 2.71
2746 3088 3.627395 TTAGAGGCACCTACCATTGTG 57.373 47.619 0.00 0.00 35.58 3.33
2747 3089 1.362224 AGAGGCACCTACCATTGTGT 58.638 50.000 0.00 0.00 34.94 3.72
2748 3090 1.279271 AGAGGCACCTACCATTGTGTC 59.721 52.381 0.00 0.00 37.36 3.67
2749 3091 1.362224 AGGCACCTACCATTGTGTCT 58.638 50.000 0.00 0.00 42.30 3.41
2750 3092 2.500098 GAGGCACCTACCATTGTGTCTA 59.500 50.000 0.00 0.00 46.72 2.59
2751 3093 3.115390 AGGCACCTACCATTGTGTCTAT 58.885 45.455 0.00 0.00 45.05 1.98
2752 3094 3.118261 AGGCACCTACCATTGTGTCTATG 60.118 47.826 0.00 0.00 45.05 2.23
2753 3095 3.118408 GGCACCTACCATTGTGTCTATGA 60.118 47.826 0.00 0.00 34.34 2.15
2754 3096 3.871594 GCACCTACCATTGTGTCTATGAC 59.128 47.826 0.00 0.00 34.94 3.06
2755 3097 4.622933 GCACCTACCATTGTGTCTATGACA 60.623 45.833 0.00 0.00 40.50 3.58
2756 3098 5.674525 CACCTACCATTGTGTCTATGACAT 58.325 41.667 3.65 0.00 44.63 3.06
2757 3099 5.525012 CACCTACCATTGTGTCTATGACATG 59.475 44.000 3.65 0.00 44.63 3.21
2758 3100 5.189736 ACCTACCATTGTGTCTATGACATGT 59.810 40.000 0.00 0.00 44.63 3.21
2759 3101 6.115446 CCTACCATTGTGTCTATGACATGTT 58.885 40.000 0.00 0.00 44.63 2.71
2760 3102 5.885230 ACCATTGTGTCTATGACATGTTG 57.115 39.130 0.00 2.73 44.63 3.33
2761 3103 4.701651 ACCATTGTGTCTATGACATGTTGG 59.298 41.667 0.00 16.68 44.63 3.77
2762 3104 4.439153 CCATTGTGTCTATGACATGTTGGC 60.439 45.833 0.00 0.00 44.63 4.52
2763 3105 3.701205 TGTGTCTATGACATGTTGGCT 57.299 42.857 0.00 0.00 44.63 4.75
2764 3106 3.599343 TGTGTCTATGACATGTTGGCTC 58.401 45.455 0.00 0.00 44.63 4.70
2765 3107 3.007831 TGTGTCTATGACATGTTGGCTCA 59.992 43.478 0.00 0.00 44.63 4.26
2766 3108 4.002982 GTGTCTATGACATGTTGGCTCAA 58.997 43.478 0.00 0.00 44.63 3.02
2767 3109 4.002982 TGTCTATGACATGTTGGCTCAAC 58.997 43.478 0.00 10.15 39.84 3.18
2774 3116 3.042560 GTTGGCTCAACAGGTGGC 58.957 61.111 11.69 0.00 43.09 5.01
2775 3117 1.529244 GTTGGCTCAACAGGTGGCT 60.529 57.895 11.69 0.00 43.09 4.75
2776 3118 1.529010 TTGGCTCAACAGGTGGCTG 60.529 57.895 0.00 0.00 36.59 4.85
2777 3119 2.674380 GGCTCAACAGGTGGCTGG 60.674 66.667 0.00 0.00 33.22 4.85
2778 3120 3.368571 GCTCAACAGGTGGCTGGC 61.369 66.667 0.00 0.00 0.00 4.85
2779 3121 2.674380 CTCAACAGGTGGCTGGCC 60.674 66.667 4.43 4.43 0.00 5.36
2780 3122 4.284550 TCAACAGGTGGCTGGCCC 62.285 66.667 9.28 0.00 34.56 5.80
2781 3123 4.601794 CAACAGGTGGCTGGCCCA 62.602 66.667 9.28 0.00 42.79 5.36
2788 3130 3.578286 TGGCTGGCCCACATGTCA 61.578 61.111 9.28 0.00 39.18 3.58
2789 3131 2.753043 GGCTGGCCCACATGTCAG 60.753 66.667 0.00 7.70 0.00 3.51
2790 3132 2.034687 GCTGGCCCACATGTCAGT 59.965 61.111 12.37 0.00 0.00 3.41
2791 3133 2.338015 GCTGGCCCACATGTCAGTG 61.338 63.158 12.37 0.00 39.21 3.66
2792 3134 1.376086 CTGGCCCACATGTCAGTGA 59.624 57.895 0.00 0.00 42.05 3.41
2793 3135 0.957395 CTGGCCCACATGTCAGTGAC 60.957 60.000 16.68 16.68 42.05 3.67
2794 3136 1.073025 GGCCCACATGTCAGTGACA 59.927 57.895 27.35 27.35 46.90 3.58
2795 3137 1.237285 GGCCCACATGTCAGTGACAC 61.237 60.000 27.70 13.72 45.65 3.67
2796 3138 0.534877 GCCCACATGTCAGTGACACA 60.535 55.000 27.70 7.67 45.65 3.72
2797 3139 1.965935 CCCACATGTCAGTGACACAA 58.034 50.000 27.70 6.16 45.65 3.33
2798 3140 2.296792 CCCACATGTCAGTGACACAAA 58.703 47.619 27.70 5.76 45.65 2.83
2799 3141 2.291465 CCCACATGTCAGTGACACAAAG 59.709 50.000 27.70 18.82 45.65 2.77
2800 3142 2.291465 CCACATGTCAGTGACACAAAGG 59.709 50.000 27.70 21.15 45.65 3.11
2801 3143 1.949525 ACATGTCAGTGACACAAAGGC 59.050 47.619 27.70 0.00 45.65 4.35
2802 3144 1.948834 CATGTCAGTGACACAAAGGCA 59.051 47.619 27.70 3.06 45.65 4.75
2803 3145 1.667236 TGTCAGTGACACAAAGGCAG 58.333 50.000 22.06 0.00 37.67 4.85
2804 3146 0.947244 GTCAGTGACACAAAGGCAGG 59.053 55.000 18.54 0.00 34.37 4.85
2805 3147 0.546122 TCAGTGACACAAAGGCAGGT 59.454 50.000 8.59 0.00 34.37 4.00
2806 3148 0.664761 CAGTGACACAAAGGCAGGTG 59.335 55.000 8.59 2.29 34.37 4.00
2807 3149 1.103398 AGTGACACAAAGGCAGGTGC 61.103 55.000 8.59 0.00 34.37 5.01
2825 3167 3.249687 CCTTTAAGGCACCGAAGCT 57.750 52.632 0.00 0.00 34.17 3.74
2826 3168 0.804989 CCTTTAAGGCACCGAAGCTG 59.195 55.000 0.00 0.00 34.17 4.24
2827 3169 0.169009 CTTTAAGGCACCGAAGCTGC 59.831 55.000 0.00 0.00 34.17 5.25
2828 3170 1.573829 TTTAAGGCACCGAAGCTGCG 61.574 55.000 7.28 7.28 35.31 5.18
2829 3171 2.725203 TTAAGGCACCGAAGCTGCGT 62.725 55.000 14.34 0.00 35.31 5.24
2833 3175 2.434884 CACCGAAGCTGCGTCCAT 60.435 61.111 14.34 0.00 0.00 3.41
2834 3176 2.125512 ACCGAAGCTGCGTCCATC 60.126 61.111 14.34 0.00 0.00 3.51
2835 3177 2.185350 CCGAAGCTGCGTCCATCT 59.815 61.111 14.34 0.00 0.00 2.90
2836 3178 1.880340 CCGAAGCTGCGTCCATCTC 60.880 63.158 14.34 0.00 0.00 2.75
2837 3179 1.880340 CGAAGCTGCGTCCATCTCC 60.880 63.158 5.73 0.00 0.00 3.71
2838 3180 1.219124 GAAGCTGCGTCCATCTCCA 59.781 57.895 4.11 0.00 0.00 3.86
2839 3181 1.078848 AAGCTGCGTCCATCTCCAC 60.079 57.895 0.00 0.00 0.00 4.02
2840 3182 1.548357 AAGCTGCGTCCATCTCCACT 61.548 55.000 0.00 0.00 0.00 4.00
2841 3183 1.520342 GCTGCGTCCATCTCCACTC 60.520 63.158 0.00 0.00 0.00 3.51
2842 3184 1.226802 CTGCGTCCATCTCCACTCG 60.227 63.158 0.00 0.00 0.00 4.18
2843 3185 1.938657 CTGCGTCCATCTCCACTCGT 61.939 60.000 0.00 0.00 0.00 4.18
2844 3186 1.215647 GCGTCCATCTCCACTCGTT 59.784 57.895 0.00 0.00 0.00 3.85
2845 3187 0.802607 GCGTCCATCTCCACTCGTTC 60.803 60.000 0.00 0.00 0.00 3.95
2846 3188 0.523546 CGTCCATCTCCACTCGTTCG 60.524 60.000 0.00 0.00 0.00 3.95
2847 3189 0.179134 GTCCATCTCCACTCGTTCGG 60.179 60.000 0.00 0.00 0.00 4.30
2848 3190 1.519455 CCATCTCCACTCGTTCGGC 60.519 63.158 0.00 0.00 0.00 5.54
2849 3191 1.519455 CATCTCCACTCGTTCGGCC 60.519 63.158 0.00 0.00 0.00 6.13
2850 3192 2.722201 ATCTCCACTCGTTCGGCCC 61.722 63.158 0.00 0.00 0.00 5.80
2851 3193 3.382832 CTCCACTCGTTCGGCCCT 61.383 66.667 0.00 0.00 0.00 5.19
2852 3194 3.358076 CTCCACTCGTTCGGCCCTC 62.358 68.421 0.00 0.00 0.00 4.30
2853 3195 3.691342 CCACTCGTTCGGCCCTCA 61.691 66.667 0.00 0.00 0.00 3.86
2854 3196 2.125912 CACTCGTTCGGCCCTCAG 60.126 66.667 0.00 0.00 0.00 3.35
2855 3197 3.382832 ACTCGTTCGGCCCTCAGG 61.383 66.667 0.00 0.00 0.00 3.86
2872 3214 3.105157 GCGCAACCGGCAATTGTG 61.105 61.111 0.30 6.95 45.17 3.33
2873 3215 2.430582 CGCAACCGGCAATTGTGG 60.431 61.111 14.90 14.90 45.17 4.17
2874 3216 2.733945 GCAACCGGCAATTGTGGT 59.266 55.556 16.02 16.02 43.97 4.16
2875 3217 1.068921 GCAACCGGCAATTGTGGTT 59.931 52.632 23.41 23.41 46.57 3.67
2876 3218 0.531753 GCAACCGGCAATTGTGGTTT 60.532 50.000 25.37 13.82 43.23 3.27
2877 3219 1.216122 CAACCGGCAATTGTGGTTTG 58.784 50.000 25.37 18.94 43.23 2.93
2878 3220 0.105778 AACCGGCAATTGTGGTTTGG 59.894 50.000 23.41 12.39 43.23 3.28
2879 3221 1.667510 CCGGCAATTGTGGTTTGGC 60.668 57.895 7.40 0.37 43.87 4.52
2880 3222 1.667510 CGGCAATTGTGGTTTGGCC 60.668 57.895 7.40 0.00 44.30 5.36
2881 3223 1.302431 GGCAATTGTGGTTTGGCCC 60.302 57.895 7.40 0.00 42.13 5.80
2882 3224 1.754107 GCAATTGTGGTTTGGCCCT 59.246 52.632 7.40 0.00 36.04 5.19
2883 3225 0.108396 GCAATTGTGGTTTGGCCCTT 59.892 50.000 7.40 0.00 36.04 3.95
2884 3226 1.877680 GCAATTGTGGTTTGGCCCTTC 60.878 52.381 7.40 0.00 36.04 3.46
2885 3227 0.678950 AATTGTGGTTTGGCCCTTCG 59.321 50.000 0.00 0.00 36.04 3.79
2886 3228 1.184970 ATTGTGGTTTGGCCCTTCGG 61.185 55.000 0.00 0.00 36.04 4.30
2898 3240 4.025401 CTTCGGCCAGCGCGTTTT 62.025 61.111 8.43 0.00 35.02 2.43
2899 3241 3.536498 CTTCGGCCAGCGCGTTTTT 62.536 57.895 8.43 0.00 35.02 1.94
2900 3242 3.815569 TTCGGCCAGCGCGTTTTTG 62.816 57.895 8.43 1.32 35.02 2.44
2908 3250 4.398598 CGCGTTTTTGGCCCCGAG 62.399 66.667 0.00 0.00 0.00 4.63
2909 3251 4.050934 GCGTTTTTGGCCCCGAGG 62.051 66.667 0.00 0.00 0.00 4.63
2919 3261 2.203509 CCCCGAGGGCGATCTAGT 60.204 66.667 1.76 0.00 40.82 2.57
2920 3262 1.833049 CCCCGAGGGCGATCTAGTT 60.833 63.158 1.76 0.00 40.82 2.24
2921 3263 1.400530 CCCCGAGGGCGATCTAGTTT 61.401 60.000 1.76 0.00 40.82 2.66
2922 3264 0.464452 CCCGAGGGCGATCTAGTTTT 59.536 55.000 0.00 0.00 40.82 2.43
2923 3265 1.538419 CCCGAGGGCGATCTAGTTTTC 60.538 57.143 0.00 0.00 40.82 2.29
2924 3266 1.136305 CCGAGGGCGATCTAGTTTTCA 59.864 52.381 0.00 0.00 40.82 2.69
2925 3267 2.464865 CGAGGGCGATCTAGTTTTCAG 58.535 52.381 0.00 0.00 40.82 3.02
2926 3268 2.159226 CGAGGGCGATCTAGTTTTCAGT 60.159 50.000 0.00 0.00 40.82 3.41
2927 3269 3.449632 GAGGGCGATCTAGTTTTCAGTC 58.550 50.000 0.00 0.00 0.00 3.51
2928 3270 2.832129 AGGGCGATCTAGTTTTCAGTCA 59.168 45.455 0.00 0.00 0.00 3.41
2929 3271 2.930682 GGGCGATCTAGTTTTCAGTCAC 59.069 50.000 0.00 0.00 0.00 3.67
2930 3272 2.599082 GGCGATCTAGTTTTCAGTCACG 59.401 50.000 0.00 0.00 0.00 4.35
2931 3273 2.028165 GCGATCTAGTTTTCAGTCACGC 59.972 50.000 0.00 0.00 36.06 5.34
2932 3274 2.599082 CGATCTAGTTTTCAGTCACGCC 59.401 50.000 0.00 0.00 0.00 5.68
2933 3275 3.673594 CGATCTAGTTTTCAGTCACGCCT 60.674 47.826 0.00 0.00 0.00 5.52
2934 3276 3.299340 TCTAGTTTTCAGTCACGCCTC 57.701 47.619 0.00 0.00 0.00 4.70
2935 3277 2.029290 TCTAGTTTTCAGTCACGCCTCC 60.029 50.000 0.00 0.00 0.00 4.30
2936 3278 0.468226 AGTTTTCAGTCACGCCTCCA 59.532 50.000 0.00 0.00 0.00 3.86
2937 3279 1.134220 AGTTTTCAGTCACGCCTCCAA 60.134 47.619 0.00 0.00 0.00 3.53
2938 3280 1.264288 GTTTTCAGTCACGCCTCCAAG 59.736 52.381 0.00 0.00 0.00 3.61
2939 3281 0.468226 TTTCAGTCACGCCTCCAAGT 59.532 50.000 0.00 0.00 0.00 3.16
2940 3282 0.468226 TTCAGTCACGCCTCCAAGTT 59.532 50.000 0.00 0.00 0.00 2.66
2941 3283 0.033504 TCAGTCACGCCTCCAAGTTC 59.966 55.000 0.00 0.00 0.00 3.01
2942 3284 1.006102 AGTCACGCCTCCAAGTTCG 60.006 57.895 0.00 0.00 0.00 3.95
2943 3285 2.027625 GTCACGCCTCCAAGTTCGG 61.028 63.158 0.00 0.00 0.00 4.30
2944 3286 3.423154 CACGCCTCCAAGTTCGGC 61.423 66.667 0.00 0.00 40.40 5.54
2945 3287 4.699522 ACGCCTCCAAGTTCGGCC 62.700 66.667 0.00 0.00 40.70 6.13
2948 3290 3.646715 CCTCCAAGTTCGGCCCCA 61.647 66.667 0.00 0.00 0.00 4.96
2949 3291 2.434331 CTCCAAGTTCGGCCCCAA 59.566 61.111 0.00 0.00 0.00 4.12
2950 3292 1.675641 CTCCAAGTTCGGCCCCAAG 60.676 63.158 0.00 0.00 0.00 3.61
2951 3293 2.124507 CTCCAAGTTCGGCCCCAAGA 62.125 60.000 0.00 0.00 0.00 3.02
2952 3294 1.971695 CCAAGTTCGGCCCCAAGAC 60.972 63.158 0.00 0.00 0.00 3.01
2953 3295 2.032071 AAGTTCGGCCCCAAGACG 59.968 61.111 0.00 0.00 0.00 4.18
2954 3296 4.699522 AGTTCGGCCCCAAGACGC 62.700 66.667 0.00 0.00 0.00 5.19
2958 3300 4.524318 CGGCCCCAAGACGCGTAT 62.524 66.667 13.97 5.94 0.00 3.06
2959 3301 2.816718 GGCCCCAAGACGCGTATA 59.183 61.111 13.97 0.00 0.00 1.47
2960 3302 1.144496 GGCCCCAAGACGCGTATAA 59.856 57.895 13.97 0.00 0.00 0.98
2961 3303 0.462403 GGCCCCAAGACGCGTATAAA 60.462 55.000 13.97 0.00 0.00 1.40
2962 3304 1.589803 GCCCCAAGACGCGTATAAAT 58.410 50.000 13.97 0.00 0.00 1.40
2963 3305 1.944709 GCCCCAAGACGCGTATAAATT 59.055 47.619 13.97 0.00 0.00 1.82
2964 3306 2.032290 GCCCCAAGACGCGTATAAATTC 60.032 50.000 13.97 0.00 0.00 2.17
2965 3307 3.199677 CCCCAAGACGCGTATAAATTCA 58.800 45.455 13.97 0.00 0.00 2.57
2966 3308 3.623960 CCCCAAGACGCGTATAAATTCAA 59.376 43.478 13.97 0.00 0.00 2.69
2967 3309 4.095185 CCCCAAGACGCGTATAAATTCAAA 59.905 41.667 13.97 0.00 0.00 2.69
2968 3310 5.025826 CCCAAGACGCGTATAAATTCAAAC 58.974 41.667 13.97 0.00 0.00 2.93
2969 3311 5.391097 CCCAAGACGCGTATAAATTCAAACA 60.391 40.000 13.97 0.00 0.00 2.83
2970 3312 6.255215 CCAAGACGCGTATAAATTCAAACAT 58.745 36.000 13.97 0.00 0.00 2.71
2971 3313 6.194508 CCAAGACGCGTATAAATTCAAACATG 59.805 38.462 13.97 0.00 0.00 3.21
2972 3314 6.656314 AGACGCGTATAAATTCAAACATGA 57.344 33.333 13.97 0.00 0.00 3.07
2973 3315 7.246674 AGACGCGTATAAATTCAAACATGAT 57.753 32.000 13.97 0.00 0.00 2.45
2974 3316 8.360325 AGACGCGTATAAATTCAAACATGATA 57.640 30.769 13.97 0.00 0.00 2.15
2975 3317 8.988934 AGACGCGTATAAATTCAAACATGATAT 58.011 29.630 13.97 0.00 0.00 1.63
2976 3318 9.594038 GACGCGTATAAATTCAAACATGATATT 57.406 29.630 13.97 0.00 0.00 1.28
2977 3319 9.944663 ACGCGTATAAATTCAAACATGATATTT 57.055 25.926 11.67 0.00 0.00 1.40
2982 3324 8.816640 ATAAATTCAAACATGATATTTCCCGC 57.183 30.769 0.00 0.00 0.00 6.13
2983 3325 6.469782 AATTCAAACATGATATTTCCCGCT 57.530 33.333 0.00 0.00 0.00 5.52
2984 3326 7.581213 AATTCAAACATGATATTTCCCGCTA 57.419 32.000 0.00 0.00 0.00 4.26
2985 3327 6.371809 TTCAAACATGATATTTCCCGCTAC 57.628 37.500 0.00 0.00 0.00 3.58
2986 3328 5.432645 TCAAACATGATATTTCCCGCTACA 58.567 37.500 0.00 0.00 0.00 2.74
2987 3329 5.883115 TCAAACATGATATTTCCCGCTACAA 59.117 36.000 0.00 0.00 0.00 2.41
2988 3330 6.375736 TCAAACATGATATTTCCCGCTACAAA 59.624 34.615 0.00 0.00 0.00 2.83
2989 3331 6.767524 AACATGATATTTCCCGCTACAAAA 57.232 33.333 0.00 0.00 0.00 2.44
2990 3332 6.767524 ACATGATATTTCCCGCTACAAAAA 57.232 33.333 0.00 0.00 0.00 1.94
3007 3349 2.468532 AAAAAGACGCCACAAGTTCG 57.531 45.000 0.00 0.00 0.00 3.95
3008 3350 0.661020 AAAAGACGCCACAAGTTCGG 59.339 50.000 0.00 0.00 0.00 4.30
3009 3351 1.782028 AAAGACGCCACAAGTTCGGC 61.782 55.000 3.13 3.13 45.28 5.54
3013 3355 2.785258 GCCACAAGTTCGGCGATC 59.215 61.111 11.76 10.67 38.82 3.69
3014 3356 2.032634 GCCACAAGTTCGGCGATCA 61.033 57.895 19.04 0.00 38.82 2.92
3015 3357 1.787847 CCACAAGTTCGGCGATCAC 59.212 57.895 19.04 11.84 0.00 3.06
3016 3358 1.635663 CCACAAGTTCGGCGATCACC 61.636 60.000 19.04 4.72 0.00 4.02
3017 3359 0.948623 CACAAGTTCGGCGATCACCA 60.949 55.000 19.04 0.00 0.00 4.17
3018 3360 0.036388 ACAAGTTCGGCGATCACCAT 60.036 50.000 19.04 1.77 0.00 3.55
3019 3361 1.206132 ACAAGTTCGGCGATCACCATA 59.794 47.619 19.04 0.00 0.00 2.74
3020 3362 1.593006 CAAGTTCGGCGATCACCATAC 59.407 52.381 19.04 8.95 0.00 2.39
3021 3363 0.104304 AGTTCGGCGATCACCATACC 59.896 55.000 19.04 0.00 0.00 2.73
3022 3364 0.179094 GTTCGGCGATCACCATACCA 60.179 55.000 11.76 0.00 0.00 3.25
3023 3365 0.179094 TTCGGCGATCACCATACCAC 60.179 55.000 11.76 0.00 0.00 4.16
3024 3366 1.142965 CGGCGATCACCATACCACA 59.857 57.895 0.00 0.00 0.00 4.17
3025 3367 0.461163 CGGCGATCACCATACCACAA 60.461 55.000 0.00 0.00 0.00 3.33
3026 3368 1.810031 CGGCGATCACCATACCACAAT 60.810 52.381 0.00 0.00 0.00 2.71
3027 3369 2.297701 GGCGATCACCATACCACAATT 58.702 47.619 0.00 0.00 0.00 2.32
3028 3370 2.290641 GGCGATCACCATACCACAATTC 59.709 50.000 0.00 0.00 0.00 2.17
3029 3371 2.032894 GCGATCACCATACCACAATTCG 60.033 50.000 0.00 0.00 0.00 3.34
3030 3372 3.453424 CGATCACCATACCACAATTCGA 58.547 45.455 0.00 0.00 0.00 3.71
3031 3373 3.245284 CGATCACCATACCACAATTCGAC 59.755 47.826 0.00 0.00 0.00 4.20
3032 3374 2.612604 TCACCATACCACAATTCGACG 58.387 47.619 0.00 0.00 0.00 5.12
3033 3375 2.231721 TCACCATACCACAATTCGACGA 59.768 45.455 0.00 0.00 0.00 4.20
3034 3376 3.118920 TCACCATACCACAATTCGACGAT 60.119 43.478 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.917887 ATGGCAATATTTCCATTGGATTTAAAA 57.082 25.926 13.21 0.00 39.95 1.52
39 40 7.734410 ACCTCCCAATATGTAATGGCAATATTT 59.266 33.333 0.00 0.00 35.28 1.40
46 47 5.876357 TCTTACCTCCCAATATGTAATGGC 58.124 41.667 0.00 0.00 35.28 4.40
70 71 8.996651 TTAGTCCTACAAGATCATAGACATCA 57.003 34.615 0.00 0.00 0.00 3.07
83 84 7.823745 AAAATGCCCATATTAGTCCTACAAG 57.176 36.000 0.00 0.00 0.00 3.16
138 139 6.184580 TGGTGTTGTTTTGTTGTACTAGTG 57.815 37.500 5.39 0.00 0.00 2.74
139 140 6.821031 TTGGTGTTGTTTTGTTGTACTAGT 57.179 33.333 0.00 0.00 0.00 2.57
196 197 8.511604 ACACAACCAAAATGGAAGATATAGAG 57.488 34.615 2.85 0.00 40.96 2.43
225 226 8.632679 ACCATGTGCCAATACTGAAAATTATAG 58.367 33.333 0.00 0.00 0.00 1.31
383 385 7.298122 AGCGTGCATTTGTAAGTATTATATGC 58.702 34.615 0.00 0.00 40.22 3.14
397 399 9.497030 TTTATATGTACTTAAAGCGTGCATTTG 57.503 29.630 0.00 0.00 38.40 2.32
558 579 4.499183 GTCACAGAGACATCTAAAGGTGG 58.501 47.826 0.00 0.00 46.77 4.61
576 597 1.457303 GATGGAGATTATGCGCGTCAC 59.543 52.381 4.79 0.00 0.00 3.67
623 645 4.335647 CGTGCAGGCCTCACCCTT 62.336 66.667 22.03 0.00 40.58 3.95
706 728 7.503566 ACCTGTTTGTACTCACTGTTAGTAGTA 59.496 37.037 2.22 0.00 30.26 1.82
707 729 6.323225 ACCTGTTTGTACTCACTGTTAGTAGT 59.677 38.462 2.22 0.00 30.26 2.73
708 730 6.746120 ACCTGTTTGTACTCACTGTTAGTAG 58.254 40.000 2.22 0.00 30.26 2.57
709 731 6.720112 ACCTGTTTGTACTCACTGTTAGTA 57.280 37.500 0.00 0.00 0.00 1.82
710 732 5.609533 ACCTGTTTGTACTCACTGTTAGT 57.390 39.130 0.00 0.00 0.00 2.24
711 733 6.238374 CCAAACCTGTTTGTACTCACTGTTAG 60.238 42.308 18.49 0.00 46.19 2.34
797 841 1.604693 GGTATACGAGGCAACCGATGG 60.605 57.143 0.00 0.00 34.83 3.51
845 889 0.249398 CTGGGTTACCGGGTCTGAAG 59.751 60.000 6.32 0.00 39.64 3.02
884 928 4.021650 GTGTCAACGAACGCTGGA 57.978 55.556 0.00 0.00 0.00 3.86
1320 1374 1.243902 CGGCTTTGGGCTTCTTTGTA 58.756 50.000 0.00 0.00 41.46 2.41
1914 1968 0.955919 GGAAGAACAGGTGCCCGAAG 60.956 60.000 0.00 0.00 0.00 3.79
2133 2188 1.198637 CTAAACAACAGGAGCAGCAGC 59.801 52.381 0.00 0.00 42.56 5.25
2134 2189 2.771089 TCTAAACAACAGGAGCAGCAG 58.229 47.619 0.00 0.00 0.00 4.24
2135 2190 2.878406 GTTCTAAACAACAGGAGCAGCA 59.122 45.455 0.00 0.00 0.00 4.41
2203 2258 3.380320 TCGACACTCTGAAGACAAGTTCA 59.620 43.478 0.00 0.00 35.16 3.18
2204 2259 3.966154 TCGACACTCTGAAGACAAGTTC 58.034 45.455 0.00 0.00 0.00 3.01
2205 2260 4.202161 ACATCGACACTCTGAAGACAAGTT 60.202 41.667 0.00 0.00 0.00 2.66
2206 2261 3.319405 ACATCGACACTCTGAAGACAAGT 59.681 43.478 0.00 0.00 0.00 3.16
2207 2262 3.906998 ACATCGACACTCTGAAGACAAG 58.093 45.455 0.00 0.00 0.00 3.16
2208 2263 5.644977 ATACATCGACACTCTGAAGACAA 57.355 39.130 0.00 0.00 0.00 3.18
2211 2266 9.653287 AAATTTTATACATCGACACTCTGAAGA 57.347 29.630 0.00 0.00 0.00 2.87
2213 2268 9.653287 AGAAATTTTATACATCGACACTCTGAA 57.347 29.630 0.00 0.00 0.00 3.02
2230 2285 9.950680 GTGTTCTTCTGTTCATGAGAAATTTTA 57.049 29.630 0.00 0.00 35.08 1.52
2237 2299 5.528690 CCAAAGTGTTCTTCTGTTCATGAGA 59.471 40.000 0.00 0.00 32.90 3.27
2261 2323 4.665833 AAAACTAGCTGGGTTTTGGAAC 57.334 40.909 22.57 0.00 42.76 3.62
2266 2328 3.704061 TGAAGCAAAACTAGCTGGGTTTT 59.296 39.130 10.82 16.38 44.45 2.43
2267 2329 3.295973 TGAAGCAAAACTAGCTGGGTTT 58.704 40.909 7.37 7.37 42.53 3.27
2268 2330 2.944129 TGAAGCAAAACTAGCTGGGTT 58.056 42.857 0.85 0.00 42.53 4.11
2269 2331 2.656947 TGAAGCAAAACTAGCTGGGT 57.343 45.000 0.85 0.00 42.53 4.51
2270 2332 2.352127 GCTTGAAGCAAAACTAGCTGGG 60.352 50.000 13.09 0.00 42.53 4.45
2271 2333 2.555757 AGCTTGAAGCAAAACTAGCTGG 59.444 45.455 20.45 0.00 45.56 4.85
2272 2334 3.911661 AGCTTGAAGCAAAACTAGCTG 57.088 42.857 20.45 0.00 45.56 4.24
2273 2335 3.480470 TCAGCTTGAAGCAAAACTAGCT 58.520 40.909 20.45 0.00 45.56 3.32
2274 2336 3.904136 TCAGCTTGAAGCAAAACTAGC 57.096 42.857 20.45 0.00 45.56 3.42
2308 2370 2.507944 GCTGCATCCTCATCCGGT 59.492 61.111 0.00 0.00 0.00 5.28
2309 2371 2.087462 TACGCTGCATCCTCATCCGG 62.087 60.000 0.00 0.00 0.00 5.14
2347 2448 2.017049 GCTATTTGACGCCACATCCTT 58.983 47.619 0.00 0.00 0.00 3.36
2365 2466 1.447317 CCGTTGCTCCAACTGTTGCT 61.447 55.000 14.94 0.00 41.62 3.91
2518 2644 1.533625 TGAATTGTAGCACCACAGGC 58.466 50.000 0.00 0.00 0.00 4.85
2573 2699 3.842732 TCCACACATGTGTACTCTACG 57.157 47.619 30.11 16.01 42.83 3.51
2592 2718 3.054878 CAAAATGCAGGCTTGTCAGTTC 58.945 45.455 0.00 0.00 0.00 3.01
2593 2719 2.224113 CCAAAATGCAGGCTTGTCAGTT 60.224 45.455 0.00 0.00 0.00 3.16
2624 2750 7.350744 TGCCATATTGCCATCCATATATTTC 57.649 36.000 0.00 0.00 0.00 2.17
2626 2752 8.229605 ACTATGCCATATTGCCATCCATATATT 58.770 33.333 0.00 0.00 0.00 1.28
2628 2754 6.999871 CACTATGCCATATTGCCATCCATATA 59.000 38.462 0.00 0.00 0.00 0.86
2629 2755 5.831525 CACTATGCCATATTGCCATCCATAT 59.168 40.000 0.00 0.00 0.00 1.78
2630 2756 5.195185 CACTATGCCATATTGCCATCCATA 58.805 41.667 0.00 0.00 0.00 2.74
2650 2985 5.534207 TGGTTTCAAATCAAATCAGCACT 57.466 34.783 0.00 0.00 0.00 4.40
2680 3016 8.498575 TCCCCATGTGTGATATGAGTAAAATAA 58.501 33.333 0.00 0.00 0.00 1.40
2691 3027 2.568956 CGGAGATCCCCATGTGTGATAT 59.431 50.000 0.00 0.00 0.00 1.63
2694 3036 1.337384 CCGGAGATCCCCATGTGTGA 61.337 60.000 0.00 0.00 0.00 3.58
2711 3053 0.533491 TCTAAACCATCACGTCCCCG 59.467 55.000 0.00 0.00 40.83 5.73
2730 3072 1.362224 AGACACAATGGTAGGTGCCT 58.638 50.000 0.00 0.00 38.57 4.75
2732 3074 3.871594 GTCATAGACACAATGGTAGGTGC 59.128 47.826 0.00 0.00 38.57 5.01
2733 3075 5.084818 TGTCATAGACACAATGGTAGGTG 57.915 43.478 0.00 0.00 37.67 4.00
2734 3076 5.189736 ACATGTCATAGACACAATGGTAGGT 59.810 40.000 1.43 0.00 45.65 3.08
2736 3078 6.037500 CCAACATGTCATAGACACAATGGTAG 59.962 42.308 0.00 0.00 45.65 3.18
2737 3079 5.879777 CCAACATGTCATAGACACAATGGTA 59.120 40.000 0.00 0.00 45.65 3.25
2738 3080 4.701651 CCAACATGTCATAGACACAATGGT 59.298 41.667 0.00 0.00 45.65 3.55
2739 3081 4.439153 GCCAACATGTCATAGACACAATGG 60.439 45.833 16.38 16.38 45.65 3.16
2740 3082 4.397103 AGCCAACATGTCATAGACACAATG 59.603 41.667 0.00 0.24 45.65 2.82
2741 3083 4.592942 AGCCAACATGTCATAGACACAAT 58.407 39.130 0.00 0.00 45.65 2.71
2742 3084 4.002982 GAGCCAACATGTCATAGACACAA 58.997 43.478 0.00 0.00 45.65 3.33
2743 3085 3.007831 TGAGCCAACATGTCATAGACACA 59.992 43.478 0.00 0.00 45.65 3.72
2744 3086 3.599343 TGAGCCAACATGTCATAGACAC 58.401 45.455 0.00 0.00 45.65 3.67
2745 3087 3.979101 TGAGCCAACATGTCATAGACA 57.021 42.857 0.00 1.95 46.90 3.41
2746 3088 4.606457 GTTGAGCCAACATGTCATAGAC 57.394 45.455 0.00 0.00 43.09 2.59
2757 3099 1.529244 AGCCACCTGTTGAGCCAAC 60.529 57.895 10.15 10.15 43.78 3.77
2758 3100 1.529010 CAGCCACCTGTTGAGCCAA 60.529 57.895 0.00 0.00 34.31 4.52
2759 3101 2.113774 CAGCCACCTGTTGAGCCA 59.886 61.111 0.00 0.00 34.31 4.75
2760 3102 2.674380 CCAGCCACCTGTTGAGCC 60.674 66.667 0.00 0.00 37.38 4.70
2761 3103 3.368571 GCCAGCCACCTGTTGAGC 61.369 66.667 0.00 0.00 37.38 4.26
2762 3104 2.674380 GGCCAGCCACCTGTTGAG 60.674 66.667 3.12 0.00 37.38 3.02
2763 3105 4.284550 GGGCCAGCCACCTGTTGA 62.285 66.667 11.50 0.00 37.38 3.18
2764 3106 4.601794 TGGGCCAGCCACCTGTTG 62.602 66.667 11.50 0.00 37.38 3.33
2765 3107 4.603535 GTGGGCCAGCCACCTGTT 62.604 66.667 6.40 0.00 37.38 3.16
2767 3109 4.371417 ATGTGGGCCAGCCACCTG 62.371 66.667 6.40 0.00 37.38 4.00
2768 3110 4.371417 CATGTGGGCCAGCCACCT 62.371 66.667 6.40 0.00 37.38 4.00
2769 3111 4.684134 ACATGTGGGCCAGCCACC 62.684 66.667 6.40 0.00 37.38 4.61
2770 3112 3.064324 GACATGTGGGCCAGCCAC 61.064 66.667 6.40 4.05 37.98 5.01
2771 3113 3.572447 CTGACATGTGGGCCAGCCA 62.572 63.158 6.40 1.84 37.98 4.75
2772 3114 2.753043 CTGACATGTGGGCCAGCC 60.753 66.667 6.40 0.00 0.00 4.85
2773 3115 2.034687 ACTGACATGTGGGCCAGC 59.965 61.111 6.40 2.28 0.00 4.85
2774 3116 0.957395 GTCACTGACATGTGGGCCAG 60.957 60.000 6.40 6.93 38.40 4.85
2775 3117 1.073025 GTCACTGACATGTGGGCCA 59.927 57.895 1.15 0.00 38.40 5.36
2776 3118 1.073025 TGTCACTGACATGTGGGCC 59.927 57.895 1.15 0.00 37.67 5.80
2777 3119 0.534877 TGTGTCACTGACATGTGGGC 60.535 55.000 14.95 2.12 44.63 5.36
2778 3120 1.965935 TTGTGTCACTGACATGTGGG 58.034 50.000 14.95 0.00 44.63 4.61
2779 3121 2.291465 CCTTTGTGTCACTGACATGTGG 59.709 50.000 14.95 10.90 44.63 4.17
2780 3122 2.287188 GCCTTTGTGTCACTGACATGTG 60.287 50.000 14.95 6.36 44.63 3.21
2781 3123 1.949525 GCCTTTGTGTCACTGACATGT 59.050 47.619 14.95 0.00 44.63 3.21
2782 3124 1.948834 TGCCTTTGTGTCACTGACATG 59.051 47.619 14.95 6.36 44.63 3.21
2783 3125 2.224606 CTGCCTTTGTGTCACTGACAT 58.775 47.619 14.95 0.00 44.63 3.06
2784 3126 1.667236 CTGCCTTTGTGTCACTGACA 58.333 50.000 7.84 7.84 40.50 3.58
2785 3127 0.947244 CCTGCCTTTGTGTCACTGAC 59.053 55.000 4.27 1.86 0.00 3.51
2786 3128 0.546122 ACCTGCCTTTGTGTCACTGA 59.454 50.000 4.27 0.00 0.00 3.41
2787 3129 0.664761 CACCTGCCTTTGTGTCACTG 59.335 55.000 4.27 0.00 0.00 3.66
2788 3130 1.103398 GCACCTGCCTTTGTGTCACT 61.103 55.000 4.27 0.00 34.94 3.41
2789 3131 1.360192 GCACCTGCCTTTGTGTCAC 59.640 57.895 0.00 0.00 34.94 3.67
2790 3132 3.840437 GCACCTGCCTTTGTGTCA 58.160 55.556 0.00 0.00 34.94 3.58
2807 3149 0.804989 CAGCTTCGGTGCCTTAAAGG 59.195 55.000 0.00 0.00 38.80 3.11
2816 3158 2.434884 ATGGACGCAGCTTCGGTG 60.435 61.111 11.19 0.00 0.00 4.94
2817 3159 2.125512 GATGGACGCAGCTTCGGT 60.126 61.111 11.19 0.00 0.00 4.69
2818 3160 1.880340 GAGATGGACGCAGCTTCGG 60.880 63.158 11.19 0.00 0.00 4.30
2819 3161 1.880340 GGAGATGGACGCAGCTTCG 60.880 63.158 3.63 3.63 0.00 3.79
2820 3162 1.086634 GTGGAGATGGACGCAGCTTC 61.087 60.000 0.00 0.00 0.00 3.86
2821 3163 1.078848 GTGGAGATGGACGCAGCTT 60.079 57.895 0.00 0.00 0.00 3.74
2822 3164 1.954362 GAGTGGAGATGGACGCAGCT 61.954 60.000 0.00 0.00 0.00 4.24
2823 3165 1.520342 GAGTGGAGATGGACGCAGC 60.520 63.158 0.00 0.00 0.00 5.25
2824 3166 1.226802 CGAGTGGAGATGGACGCAG 60.227 63.158 0.00 0.00 0.00 5.18
2825 3167 1.532604 AACGAGTGGAGATGGACGCA 61.533 55.000 0.00 0.00 0.00 5.24
2826 3168 0.802607 GAACGAGTGGAGATGGACGC 60.803 60.000 0.00 0.00 0.00 5.19
2827 3169 0.523546 CGAACGAGTGGAGATGGACG 60.524 60.000 0.00 0.00 0.00 4.79
2828 3170 0.179134 CCGAACGAGTGGAGATGGAC 60.179 60.000 0.00 0.00 0.00 4.02
2829 3171 1.945354 GCCGAACGAGTGGAGATGGA 61.945 60.000 0.00 0.00 0.00 3.41
2830 3172 1.519455 GCCGAACGAGTGGAGATGG 60.519 63.158 0.00 0.00 0.00 3.51
2831 3173 1.519455 GGCCGAACGAGTGGAGATG 60.519 63.158 0.00 0.00 0.00 2.90
2832 3174 2.722201 GGGCCGAACGAGTGGAGAT 61.722 63.158 0.00 0.00 0.00 2.75
2833 3175 3.379445 GGGCCGAACGAGTGGAGA 61.379 66.667 0.00 0.00 0.00 3.71
2834 3176 3.358076 GAGGGCCGAACGAGTGGAG 62.358 68.421 0.00 0.00 0.00 3.86
2835 3177 3.379445 GAGGGCCGAACGAGTGGA 61.379 66.667 0.00 0.00 0.00 4.02
2836 3178 3.649277 CTGAGGGCCGAACGAGTGG 62.649 68.421 0.00 0.00 0.00 4.00
2837 3179 2.125912 CTGAGGGCCGAACGAGTG 60.126 66.667 0.00 0.00 0.00 3.51
2838 3180 3.382832 CCTGAGGGCCGAACGAGT 61.383 66.667 0.00 0.00 0.00 4.18
2852 3194 4.054825 AATTGCCGGTTGCGCCTG 62.055 61.111 4.18 0.00 45.60 4.85
2853 3195 4.054825 CAATTGCCGGTTGCGCCT 62.055 61.111 4.18 0.00 45.60 5.52
2854 3196 4.356442 ACAATTGCCGGTTGCGCC 62.356 61.111 4.18 0.00 45.60 6.53
2855 3197 3.105157 CACAATTGCCGGTTGCGC 61.105 61.111 5.05 0.00 45.60 6.09
2856 3198 2.430582 CCACAATTGCCGGTTGCG 60.431 61.111 5.05 0.00 45.60 4.85
2857 3199 0.531753 AAACCACAATTGCCGGTTGC 60.532 50.000 25.60 0.00 42.18 4.17
2858 3200 1.216122 CAAACCACAATTGCCGGTTG 58.784 50.000 25.60 17.50 42.18 3.77
2859 3201 0.105778 CCAAACCACAATTGCCGGTT 59.894 50.000 21.48 21.48 44.90 4.44
2860 3202 1.745264 CCAAACCACAATTGCCGGT 59.255 52.632 13.14 13.14 33.32 5.28
2861 3203 1.667510 GCCAAACCACAATTGCCGG 60.668 57.895 5.05 9.16 0.00 6.13
2862 3204 1.667510 GGCCAAACCACAATTGCCG 60.668 57.895 5.05 0.00 38.86 5.69
2863 3205 1.302431 GGGCCAAACCACAATTGCC 60.302 57.895 4.39 0.00 42.05 4.52
2864 3206 0.108396 AAGGGCCAAACCACAATTGC 59.892 50.000 6.18 0.00 42.05 3.56
2865 3207 1.605202 CGAAGGGCCAAACCACAATTG 60.605 52.381 6.18 3.24 42.05 2.32
2866 3208 0.678950 CGAAGGGCCAAACCACAATT 59.321 50.000 6.18 0.00 42.05 2.32
2867 3209 2.350738 CGAAGGGCCAAACCACAAT 58.649 52.632 6.18 0.00 42.05 2.71
2868 3210 3.849064 CGAAGGGCCAAACCACAA 58.151 55.556 6.18 0.00 42.05 3.33
2881 3223 3.536498 AAAAACGCGCTGGCCGAAG 62.536 57.895 5.73 0.00 40.02 3.79
2882 3224 3.587933 AAAAACGCGCTGGCCGAA 61.588 55.556 5.73 0.00 40.02 4.30
2883 3225 4.320928 CAAAAACGCGCTGGCCGA 62.321 61.111 5.73 0.00 40.02 5.54
2891 3233 4.398598 CTCGGGGCCAAAAACGCG 62.399 66.667 3.53 3.53 43.27 6.01
2892 3234 4.050934 CCTCGGGGCCAAAAACGC 62.051 66.667 4.39 0.00 0.00 4.84
2893 3235 3.370231 CCCTCGGGGCCAAAAACG 61.370 66.667 4.39 0.00 35.35 3.60
2903 3245 0.464452 AAAACTAGATCGCCCTCGGG 59.536 55.000 0.00 0.00 36.13 5.14
2904 3246 1.136305 TGAAAACTAGATCGCCCTCGG 59.864 52.381 0.00 0.00 36.13 4.63
2905 3247 2.159226 ACTGAAAACTAGATCGCCCTCG 60.159 50.000 0.00 0.00 0.00 4.63
2906 3248 3.119101 TGACTGAAAACTAGATCGCCCTC 60.119 47.826 0.00 0.00 0.00 4.30
2907 3249 2.832129 TGACTGAAAACTAGATCGCCCT 59.168 45.455 0.00 0.00 0.00 5.19
2908 3250 2.930682 GTGACTGAAAACTAGATCGCCC 59.069 50.000 0.00 0.00 0.00 6.13
2909 3251 2.599082 CGTGACTGAAAACTAGATCGCC 59.401 50.000 0.00 0.00 0.00 5.54
2910 3252 2.028165 GCGTGACTGAAAACTAGATCGC 59.972 50.000 0.00 0.00 0.00 4.58
2911 3253 2.599082 GGCGTGACTGAAAACTAGATCG 59.401 50.000 0.00 0.00 0.00 3.69
2912 3254 3.851098 AGGCGTGACTGAAAACTAGATC 58.149 45.455 0.00 0.00 0.00 2.75
2913 3255 3.368531 GGAGGCGTGACTGAAAACTAGAT 60.369 47.826 0.00 0.00 0.00 1.98
2914 3256 2.029290 GGAGGCGTGACTGAAAACTAGA 60.029 50.000 0.00 0.00 0.00 2.43
2915 3257 2.288825 TGGAGGCGTGACTGAAAACTAG 60.289 50.000 0.00 0.00 0.00 2.57
2916 3258 1.689813 TGGAGGCGTGACTGAAAACTA 59.310 47.619 0.00 0.00 0.00 2.24
2917 3259 0.468226 TGGAGGCGTGACTGAAAACT 59.532 50.000 0.00 0.00 0.00 2.66
2918 3260 1.264288 CTTGGAGGCGTGACTGAAAAC 59.736 52.381 0.00 0.00 0.00 2.43
2919 3261 1.134220 ACTTGGAGGCGTGACTGAAAA 60.134 47.619 0.00 0.00 0.00 2.29
2920 3262 0.468226 ACTTGGAGGCGTGACTGAAA 59.532 50.000 0.00 0.00 0.00 2.69
2921 3263 0.468226 AACTTGGAGGCGTGACTGAA 59.532 50.000 0.00 0.00 0.00 3.02
2922 3264 0.033504 GAACTTGGAGGCGTGACTGA 59.966 55.000 0.00 0.00 0.00 3.41
2923 3265 1.284982 CGAACTTGGAGGCGTGACTG 61.285 60.000 0.00 0.00 0.00 3.51
2924 3266 1.006102 CGAACTTGGAGGCGTGACT 60.006 57.895 0.00 0.00 0.00 3.41
2925 3267 2.027625 CCGAACTTGGAGGCGTGAC 61.028 63.158 0.00 0.00 0.00 3.67
2926 3268 2.342279 CCGAACTTGGAGGCGTGA 59.658 61.111 0.00 0.00 0.00 4.35
2927 3269 3.423154 GCCGAACTTGGAGGCGTG 61.423 66.667 0.00 0.00 41.53 5.34
2931 3273 3.204467 TTGGGGCCGAACTTGGAGG 62.204 63.158 0.00 0.00 0.00 4.30
2932 3274 1.675641 CTTGGGGCCGAACTTGGAG 60.676 63.158 0.00 0.00 0.00 3.86
2933 3275 2.150719 TCTTGGGGCCGAACTTGGA 61.151 57.895 0.00 0.00 0.00 3.53
2934 3276 1.971695 GTCTTGGGGCCGAACTTGG 60.972 63.158 0.00 0.00 0.00 3.61
2935 3277 2.325082 CGTCTTGGGGCCGAACTTG 61.325 63.158 0.00 0.00 0.00 3.16
2936 3278 2.032071 CGTCTTGGGGCCGAACTT 59.968 61.111 0.00 0.00 0.00 2.66
2937 3279 4.699522 GCGTCTTGGGGCCGAACT 62.700 66.667 0.00 0.00 0.00 3.01
2941 3283 2.632136 TTATACGCGTCTTGGGGCCG 62.632 60.000 18.63 0.00 34.15 6.13
2942 3284 0.462403 TTTATACGCGTCTTGGGGCC 60.462 55.000 18.63 0.00 34.15 5.80
2943 3285 1.589803 ATTTATACGCGTCTTGGGGC 58.410 50.000 18.63 0.00 34.15 5.80
2944 3286 3.199677 TGAATTTATACGCGTCTTGGGG 58.800 45.455 18.63 0.00 34.15 4.96
2945 3287 4.868450 TTGAATTTATACGCGTCTTGGG 57.132 40.909 18.63 0.00 0.00 4.12
2946 3288 5.623335 TGTTTGAATTTATACGCGTCTTGG 58.377 37.500 18.63 0.00 0.00 3.61
2947 3289 6.958752 TCATGTTTGAATTTATACGCGTCTTG 59.041 34.615 18.63 5.37 0.00 3.02
2948 3290 7.067532 TCATGTTTGAATTTATACGCGTCTT 57.932 32.000 18.63 7.57 0.00 3.01
2949 3291 6.656314 TCATGTTTGAATTTATACGCGTCT 57.344 33.333 18.63 9.26 0.00 4.18
2950 3292 9.594038 AATATCATGTTTGAATTTATACGCGTC 57.406 29.630 18.63 0.00 34.96 5.19
2951 3293 9.944663 AAATATCATGTTTGAATTTATACGCGT 57.055 25.926 19.17 19.17 34.96 6.01
2956 3298 9.906660 GCGGGAAATATCATGTTTGAATTTATA 57.093 29.630 0.00 0.00 34.96 0.98
2957 3299 8.641541 AGCGGGAAATATCATGTTTGAATTTAT 58.358 29.630 0.00 0.00 34.96 1.40
2958 3300 8.006298 AGCGGGAAATATCATGTTTGAATTTA 57.994 30.769 0.00 0.00 34.96 1.40
2959 3301 6.877236 AGCGGGAAATATCATGTTTGAATTT 58.123 32.000 0.00 0.00 34.96 1.82
2960 3302 6.469782 AGCGGGAAATATCATGTTTGAATT 57.530 33.333 0.00 0.00 34.96 2.17
2961 3303 6.545666 TGTAGCGGGAAATATCATGTTTGAAT 59.454 34.615 0.00 0.00 34.96 2.57
2962 3304 5.883115 TGTAGCGGGAAATATCATGTTTGAA 59.117 36.000 0.00 0.00 34.96 2.69
2963 3305 5.432645 TGTAGCGGGAAATATCATGTTTGA 58.567 37.500 0.00 0.00 36.00 2.69
2964 3306 5.749596 TGTAGCGGGAAATATCATGTTTG 57.250 39.130 0.00 0.00 0.00 2.93
2965 3307 6.767524 TTTGTAGCGGGAAATATCATGTTT 57.232 33.333 0.00 0.00 0.00 2.83
2966 3308 6.767524 TTTTGTAGCGGGAAATATCATGTT 57.232 33.333 0.00 0.00 0.00 2.71
2967 3309 6.767524 TTTTTGTAGCGGGAAATATCATGT 57.232 33.333 0.00 0.00 0.00 3.21
2988 3330 1.064952 CCGAACTTGTGGCGTCTTTTT 59.935 47.619 0.00 0.00 0.00 1.94
2989 3331 0.661020 CCGAACTTGTGGCGTCTTTT 59.339 50.000 0.00 0.00 0.00 2.27
2990 3332 1.782028 GCCGAACTTGTGGCGTCTTT 61.782 55.000 0.00 0.00 42.22 2.52
2991 3333 2.251642 GCCGAACTTGTGGCGTCTT 61.252 57.895 0.00 0.00 42.22 3.01
2992 3334 2.665185 GCCGAACTTGTGGCGTCT 60.665 61.111 0.00 0.00 42.22 4.18
2997 3339 1.635663 GGTGATCGCCGAACTTGTGG 61.636 60.000 10.09 0.00 0.00 4.17
2998 3340 0.948623 TGGTGATCGCCGAACTTGTG 60.949 55.000 20.16 0.00 0.00 3.33
2999 3341 0.036388 ATGGTGATCGCCGAACTTGT 60.036 50.000 20.16 0.00 0.00 3.16
3000 3342 1.593006 GTATGGTGATCGCCGAACTTG 59.407 52.381 20.16 0.00 0.00 3.16
3001 3343 1.472728 GGTATGGTGATCGCCGAACTT 60.473 52.381 20.16 5.45 0.00 2.66
3002 3344 0.104304 GGTATGGTGATCGCCGAACT 59.896 55.000 20.16 7.63 0.00 3.01
3003 3345 0.179094 TGGTATGGTGATCGCCGAAC 60.179 55.000 20.16 18.58 0.00 3.95
3004 3346 0.179094 GTGGTATGGTGATCGCCGAA 60.179 55.000 20.16 8.01 0.00 4.30
3005 3347 1.324005 TGTGGTATGGTGATCGCCGA 61.324 55.000 20.16 8.18 0.00 5.54
3006 3348 0.461163 TTGTGGTATGGTGATCGCCG 60.461 55.000 20.16 0.00 0.00 6.46
3007 3349 1.967319 ATTGTGGTATGGTGATCGCC 58.033 50.000 18.84 18.84 0.00 5.54
3008 3350 2.032894 CGAATTGTGGTATGGTGATCGC 60.033 50.000 0.00 0.00 0.00 4.58
3009 3351 3.245284 GTCGAATTGTGGTATGGTGATCG 59.755 47.826 0.00 0.00 0.00 3.69
3010 3352 3.245284 CGTCGAATTGTGGTATGGTGATC 59.755 47.826 0.00 0.00 0.00 2.92
3011 3353 3.118920 TCGTCGAATTGTGGTATGGTGAT 60.119 43.478 0.00 0.00 0.00 3.06
3012 3354 2.231721 TCGTCGAATTGTGGTATGGTGA 59.768 45.455 0.00 0.00 0.00 4.02
3013 3355 2.612604 TCGTCGAATTGTGGTATGGTG 58.387 47.619 0.00 0.00 0.00 4.17
3014 3356 3.536956 ATCGTCGAATTGTGGTATGGT 57.463 42.857 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.