Multiple sequence alignment - TraesCS4B01G052600

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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 TraesCS4B01G052600 chr4B 100.000 3867 0 0 1 3867 41554171 41550305 0.000000e+00 7142
1 TraesCS4B01G052600 chr4A 93.159 2441 84 24 534 2928 574524493 574526896 0.000000e+00 3506
2 TraesCS4B01G052600 chr4A 92.804 403 21 7 3466 3867 574527579 574527974 9.320000e-161 577
3 TraesCS4B01G052600 chr4A 89.174 351 30 4 1 348 574523776 574524121 7.680000e-117 431
4 TraesCS4B01G052600 chr4A 90.230 174 16 1 2323 2495 731942513 731942686 3.890000e-55 226
5 TraesCS4B01G052600 chr4A 86.911 191 18 3 365 548 574524175 574524365 1.410000e-49 207
6 TraesCS4B01G052600 chr4D 92.941 2309 96 25 618 2891 29022416 29020140 0.000000e+00 3299
7 TraesCS4B01G052600 chr4D 91.022 401 26 7 3469 3867 28994988 28994596 2.050000e-147 532
8 TraesCS4B01G052600 chr4D 86.461 421 35 15 1 416 29022957 29022554 3.550000e-120 442
9 TraesCS4B01G052600 chr4D 87.571 177 16 6 3254 3426 28995256 28995082 2.360000e-47 200
10 TraesCS4B01G052600 chr6B 82.514 549 65 19 1025 1567 640356699 640356176 1.640000e-123 453
11 TraesCS4B01G052600 chr6B 94.615 130 6 1 1609 1738 640356169 640356041 2.360000e-47 200


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 TraesCS4B01G052600 chr4B 41550305 41554171 3866 True 7142.00 7142 100.0000 1 3867 1 chr4B.!!$R1 3866
1 TraesCS4B01G052600 chr4A 574523776 574527974 4198 False 1180.25 3506 90.5120 1 3867 4 chr4A.!!$F2 3866
2 TraesCS4B01G052600 chr4D 29020140 29022957 2817 True 1870.50 3299 89.7010 1 2891 2 chr4D.!!$R2 2890
3 TraesCS4B01G052600 chr4D 28994596 28995256 660 True 366.00 532 89.2965 3254 3867 2 chr4D.!!$R1 613
4 TraesCS4B01G052600 chr6B 640356041 640356699 658 True 326.50 453 88.5645 1025 1738 2 chr6B.!!$R1 713

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
916 1118 0.036732 CCAGGCAGAGCAGTTGGTTA 59.963 55.0 0.0 0.0 0.0 2.85 F
955 1177 0.667792 GTGACACGTTCTGCTCTCCC 60.668 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2241 1.448013 GTGGAAGTAGAGCGTGGGC 60.448 63.158 0.00 0.0 40.37 5.36 R
2953 3222 1.795872 CGCTCACAATTCGTGTTACCA 59.204 47.619 7.57 0.0 46.44 3.25 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 1.471684 CCTGGTCTGAAGCAAAGCATC 59.528 52.381 0.00 0.00 31.28 3.91
47 48 0.460987 GCATCTGAGTTGGTCTCCCG 60.461 60.000 0.00 0.00 42.12 5.14
125 128 4.332819 AGAAACACTGCAAGACACTGTAAC 59.667 41.667 0.00 0.00 37.43 2.50
162 165 1.168407 CCACCCATGATAAGCAGGCG 61.168 60.000 0.00 0.00 0.00 5.52
171 174 1.019278 ATAAGCAGGCGTGAACCGTG 61.019 55.000 11.29 0.00 39.32 4.94
189 192 1.661821 GCGTAGGCTGGCTGTATCG 60.662 63.158 14.70 13.29 35.83 2.92
190 193 2.030551 CGTAGGCTGGCTGTATCGA 58.969 57.895 14.70 0.00 0.00 3.59
191 194 0.598562 CGTAGGCTGGCTGTATCGAT 59.401 55.000 14.70 2.16 0.00 3.59
192 195 1.401670 CGTAGGCTGGCTGTATCGATC 60.402 57.143 14.70 0.00 0.00 3.69
204 207 5.119898 GGCTGTATCGATCATGAACATTCTC 59.880 44.000 0.00 0.00 0.00 2.87
215 218 1.993370 GAACATTCTCGAGTTCACCCG 59.007 52.381 13.13 0.00 42.72 5.28
244 247 1.301874 TTGCCGGGTTTGTCGTAGG 60.302 57.895 2.18 0.00 0.00 3.18
251 254 2.416747 GGGTTTGTCGTAGGGTTGTAC 58.583 52.381 0.00 0.00 0.00 2.90
261 264 6.153170 TGTCGTAGGGTTGTACTTTATCATCA 59.847 38.462 0.00 0.00 0.00 3.07
283 289 9.087424 CATCAGTCGTTCTAGTATCAAAATTGA 57.913 33.333 0.00 0.00 42.14 2.57
285 291 9.087424 TCAGTCGTTCTAGTATCAAAATTGATG 57.913 33.333 16.85 2.65 46.68 3.07
299 305 5.950965 AAATTGATGTCTATCGTGTCGTC 57.049 39.130 0.00 0.00 36.04 4.20
353 359 2.798262 CAACGCTCGCTTGCTTGC 60.798 61.111 0.00 0.00 0.00 4.01
354 360 2.974698 AACGCTCGCTTGCTTGCT 60.975 55.556 0.00 0.00 0.00 3.91
355 361 3.245948 AACGCTCGCTTGCTTGCTG 62.246 57.895 0.00 2.90 0.00 4.41
356 362 3.720193 CGCTCGCTTGCTTGCTGT 61.720 61.111 0.00 0.00 0.00 4.40
357 363 2.175322 GCTCGCTTGCTTGCTGTC 59.825 61.111 0.00 0.00 0.00 3.51
359 365 2.669569 TCGCTTGCTTGCTGTCCC 60.670 61.111 0.00 0.00 0.00 4.46
364 370 3.512154 TTGCTTGCTGTCCCCCTGG 62.512 63.158 0.00 0.00 0.00 4.45
365 371 3.650950 GCTTGCTGTCCCCCTGGA 61.651 66.667 0.00 0.00 38.75 3.86
416 459 2.431771 TTGCACGGTCGATGTCGG 60.432 61.111 2.25 0.00 40.29 4.79
418 461 3.179265 GCACGGTCGATGTCGGTG 61.179 66.667 2.25 7.56 40.29 4.94
456 499 0.179140 CGGTGTGCACAAAAGTTGCT 60.179 50.000 23.59 0.00 40.86 3.91
457 500 1.280066 GGTGTGCACAAAAGTTGCTG 58.720 50.000 23.59 0.00 40.86 4.41
466 509 4.556699 GCACAAAAGTTGCTGGTAGGTAAG 60.557 45.833 0.00 0.00 37.00 2.34
467 510 4.023193 CACAAAAGTTGCTGGTAGGTAAGG 60.023 45.833 0.00 0.00 0.00 2.69
471 514 6.576778 AAAGTTGCTGGTAGGTAAGGATAT 57.423 37.500 0.00 0.00 0.00 1.63
472 515 5.810080 AGTTGCTGGTAGGTAAGGATATC 57.190 43.478 0.00 0.00 0.00 1.63
473 516 5.468658 AGTTGCTGGTAGGTAAGGATATCT 58.531 41.667 2.05 0.00 0.00 1.98
482 528 1.541310 TAAGGATATCTGGCCGCCGG 61.541 60.000 12.53 12.53 0.00 6.13
500 546 2.803670 CCGTCGTGTACCGCACTG 60.804 66.667 0.00 0.00 45.57 3.66
548 598 2.594541 CTCGAAATAGAGGGTGCGC 58.405 57.895 0.00 0.00 34.74 6.09
550 600 2.871427 CGAAATAGAGGGTGCGCGC 61.871 63.158 27.26 27.26 0.00 6.86
579 768 0.813210 GCTCTCCCCGATGCAGAAAG 60.813 60.000 0.00 0.00 0.00 2.62
586 775 0.962356 CCGATGCAGAAAGCTTGGGT 60.962 55.000 0.00 0.00 45.94 4.51
587 776 0.169672 CGATGCAGAAAGCTTGGGTG 59.830 55.000 0.00 0.00 45.94 4.61
603 792 3.315140 TGGCGTCGTCCAATGGGA 61.315 61.111 0.00 0.00 42.29 4.37
636 826 2.268298 CGGCAGCGTTTATTCAGTACT 58.732 47.619 0.00 0.00 0.00 2.73
638 828 3.242248 CGGCAGCGTTTATTCAGTACTAC 59.758 47.826 0.00 0.00 0.00 2.73
639 829 4.430908 GGCAGCGTTTATTCAGTACTACT 58.569 43.478 0.00 0.00 0.00 2.57
640 830 5.585390 GGCAGCGTTTATTCAGTACTACTA 58.415 41.667 0.00 0.00 0.00 1.82
670 860 1.306654 AATCCAGGGTAGGTGCGGA 60.307 57.895 0.00 0.00 0.00 5.54
671 861 1.623542 AATCCAGGGTAGGTGCGGAC 61.624 60.000 0.00 0.00 0.00 4.79
672 862 2.815684 ATCCAGGGTAGGTGCGGACA 62.816 60.000 9.96 0.00 0.00 4.02
673 863 2.579201 CAGGGTAGGTGCGGACAG 59.421 66.667 9.96 0.00 0.00 3.51
756 946 2.996621 GCATCGTACCTATCTTGGCATC 59.003 50.000 0.00 0.00 0.00 3.91
757 947 3.245797 CATCGTACCTATCTTGGCATCG 58.754 50.000 0.00 0.00 0.00 3.84
758 948 1.611977 TCGTACCTATCTTGGCATCGG 59.388 52.381 0.00 0.00 0.00 4.18
759 949 1.611977 CGTACCTATCTTGGCATCGGA 59.388 52.381 0.00 0.00 0.00 4.55
760 950 2.351835 CGTACCTATCTTGGCATCGGAG 60.352 54.545 0.00 0.00 0.00 4.63
761 951 0.394565 ACCTATCTTGGCATCGGAGC 59.605 55.000 0.00 0.00 0.00 4.70
771 966 4.208686 ATCGGAGCCGGAGCGAAC 62.209 66.667 5.05 0.00 46.67 3.95
791 986 1.339631 CCCACATCCAAAACCTAGCGA 60.340 52.381 0.00 0.00 0.00 4.93
797 992 1.084370 CCAAAACCTAGCGAGCGAGG 61.084 60.000 20.16 20.16 43.22 4.63
811 1013 1.092345 GCGAGGCATCCCTTTCACTC 61.092 60.000 0.00 0.00 43.12 3.51
902 1104 1.690633 TCTCCACCAGATCCCAGGC 60.691 63.158 0.00 0.00 0.00 4.85
907 1109 2.373707 ACCAGATCCCAGGCAGAGC 61.374 63.158 0.00 0.00 0.00 4.09
911 1113 0.913451 AGATCCCAGGCAGAGCAGTT 60.913 55.000 0.00 0.00 0.00 3.16
913 1115 2.207501 ATCCCAGGCAGAGCAGTTGG 62.208 60.000 0.00 0.00 0.00 3.77
914 1116 2.433446 CCAGGCAGAGCAGTTGGT 59.567 61.111 0.00 0.00 0.00 3.67
915 1117 1.228367 CCAGGCAGAGCAGTTGGTT 60.228 57.895 0.00 0.00 0.00 3.67
916 1118 0.036732 CCAGGCAGAGCAGTTGGTTA 59.963 55.000 0.00 0.00 0.00 2.85
917 1119 1.160137 CAGGCAGAGCAGTTGGTTAC 58.840 55.000 0.00 0.00 0.00 2.50
920 1124 1.537202 GGCAGAGCAGTTGGTTACTTG 59.463 52.381 0.00 0.00 33.85 3.16
955 1177 0.667792 GTGACACGTTCTGCTCTCCC 60.668 60.000 0.00 0.00 0.00 4.30
956 1178 1.444553 GACACGTTCTGCTCTCCCG 60.445 63.158 0.00 0.00 0.00 5.14
957 1179 2.811317 CACGTTCTGCTCTCCCGC 60.811 66.667 0.00 0.00 0.00 6.13
958 1180 2.992114 ACGTTCTGCTCTCCCGCT 60.992 61.111 0.00 0.00 0.00 5.52
959 1181 2.202676 CGTTCTGCTCTCCCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
960 1182 2.185608 GTTCTGCTCTCCCGCTCC 59.814 66.667 0.00 0.00 0.00 4.70
961 1183 3.077556 TTCTGCTCTCCCGCTCCC 61.078 66.667 0.00 0.00 0.00 4.30
1143 1365 3.375299 CCCAATCTTCGATTTCGCTTTCT 59.625 43.478 0.00 0.00 39.60 2.52
1169 1391 6.409234 CCTCCCTGCATTATTGGTTTCTACTA 60.409 42.308 0.00 0.00 0.00 1.82
1170 1392 6.354130 TCCCTGCATTATTGGTTTCTACTAC 58.646 40.000 0.00 0.00 0.00 2.73
1171 1393 6.157994 TCCCTGCATTATTGGTTTCTACTACT 59.842 38.462 0.00 0.00 0.00 2.57
1172 1394 6.260936 CCCTGCATTATTGGTTTCTACTACTG 59.739 42.308 0.00 0.00 0.00 2.74
1173 1395 6.823689 CCTGCATTATTGGTTTCTACTACTGT 59.176 38.462 0.00 0.00 0.00 3.55
1174 1396 7.201644 CCTGCATTATTGGTTTCTACTACTGTG 60.202 40.741 0.00 0.00 0.00 3.66
1315 1563 2.129555 AAATCTGCACCCTGTCGCCT 62.130 55.000 0.00 0.00 0.00 5.52
1384 1632 3.319198 GTCCCCGAGGGCTTCACA 61.319 66.667 1.76 0.00 43.94 3.58
1385 1633 3.003173 TCCCCGAGGGCTTCACAG 61.003 66.667 1.76 0.00 43.94 3.66
1390 1638 2.031516 CGAGGGCTTCACAGTGCTG 61.032 63.158 0.00 0.00 0.00 4.41
1972 2241 2.605094 CGTGATCCAGCATTACGGG 58.395 57.895 0.00 0.00 40.07 5.28
2062 2331 1.956477 GCCAAGCTGTTCAAGAAAGGA 59.044 47.619 0.00 0.00 0.00 3.36
2065 2334 2.555757 CAAGCTGTTCAAGAAAGGAGGG 59.444 50.000 0.00 0.00 0.00 4.30
2155 2424 1.414158 ACTGGATGGACATACCGGAG 58.586 55.000 9.46 0.00 42.61 4.63
2191 2460 3.630148 GTCATCCGCGGCGACATG 61.630 66.667 30.83 24.35 0.00 3.21
2607 2876 2.202362 CGTCGACTCCAGCGTCAG 60.202 66.667 14.70 0.00 33.54 3.51
2645 2914 1.681327 GAGTACCTGGGAGACGGCA 60.681 63.158 0.00 0.00 0.00 5.69
2874 3143 4.649674 AGATGAAAGATGGTAGGCGTAGAA 59.350 41.667 0.00 0.00 0.00 2.10
2884 3153 1.726853 AGGCGTAGAATGAAGTGTGC 58.273 50.000 0.00 0.00 0.00 4.57
2920 3189 5.125417 CCTGATTGTTGGGACGATTGTATTT 59.875 40.000 0.00 0.00 29.77 1.40
2921 3190 5.948588 TGATTGTTGGGACGATTGTATTTG 58.051 37.500 0.00 0.00 29.77 2.32
2922 3191 5.475220 TGATTGTTGGGACGATTGTATTTGT 59.525 36.000 0.00 0.00 29.77 2.83
2923 3192 6.655425 TGATTGTTGGGACGATTGTATTTGTA 59.345 34.615 0.00 0.00 29.77 2.41
2924 3193 7.338196 TGATTGTTGGGACGATTGTATTTGTAT 59.662 33.333 0.00 0.00 29.77 2.29
2925 3194 7.455641 TTGTTGGGACGATTGTATTTGTATT 57.544 32.000 0.00 0.00 0.00 1.89
2926 3195 6.847400 TGTTGGGACGATTGTATTTGTATTG 58.153 36.000 0.00 0.00 0.00 1.90
2927 3196 6.431543 TGTTGGGACGATTGTATTTGTATTGT 59.568 34.615 0.00 0.00 0.00 2.71
2928 3197 7.606839 TGTTGGGACGATTGTATTTGTATTGTA 59.393 33.333 0.00 0.00 0.00 2.41
2929 3198 8.452534 GTTGGGACGATTGTATTTGTATTGTAA 58.547 33.333 0.00 0.00 0.00 2.41
2930 3199 7.976826 TGGGACGATTGTATTTGTATTGTAAC 58.023 34.615 0.00 0.00 0.00 2.50
2931 3200 7.606839 TGGGACGATTGTATTTGTATTGTAACA 59.393 33.333 0.00 0.00 0.00 2.41
2932 3201 8.617809 GGGACGATTGTATTTGTATTGTAACAT 58.382 33.333 0.00 0.00 0.00 2.71
2933 3202 9.433317 GGACGATTGTATTTGTATTGTAACATG 57.567 33.333 0.00 0.00 0.00 3.21
2935 3204 9.982291 ACGATTGTATTTGTATTGTAACATGAC 57.018 29.630 0.00 0.00 0.00 3.06
2936 3205 9.433317 CGATTGTATTTGTATTGTAACATGACC 57.567 33.333 0.00 0.00 0.00 4.02
2939 3208 9.508642 TTGTATTTGTATTGTAACATGACCAGA 57.491 29.630 0.00 0.00 0.00 3.86
2940 3209 9.508642 TGTATTTGTATTGTAACATGACCAGAA 57.491 29.630 0.00 0.00 0.00 3.02
2941 3210 9.769093 GTATTTGTATTGTAACATGACCAGAAC 57.231 33.333 0.00 0.00 0.00 3.01
2942 3211 8.635765 ATTTGTATTGTAACATGACCAGAACT 57.364 30.769 0.00 0.00 0.00 3.01
2943 3212 9.733556 ATTTGTATTGTAACATGACCAGAACTA 57.266 29.630 0.00 0.00 0.00 2.24
2944 3213 8.771920 TTGTATTGTAACATGACCAGAACTAG 57.228 34.615 0.00 0.00 0.00 2.57
2945 3214 8.129496 TGTATTGTAACATGACCAGAACTAGA 57.871 34.615 0.00 0.00 0.00 2.43
2946 3215 8.758829 TGTATTGTAACATGACCAGAACTAGAT 58.241 33.333 0.00 0.00 0.00 1.98
2947 3216 9.601217 GTATTGTAACATGACCAGAACTAGATT 57.399 33.333 0.00 0.00 0.00 2.40
2948 3217 8.723942 ATTGTAACATGACCAGAACTAGATTC 57.276 34.615 0.00 0.00 37.62 2.52
2950 3219 7.907389 TGTAACATGACCAGAACTAGATTCTT 58.093 34.615 0.00 0.00 46.05 2.52
2951 3220 7.819415 TGTAACATGACCAGAACTAGATTCTTG 59.181 37.037 0.00 1.07 46.05 3.02
2952 3221 5.181748 ACATGACCAGAACTAGATTCTTGC 58.818 41.667 0.00 0.00 46.05 4.01
2953 3222 5.046014 ACATGACCAGAACTAGATTCTTGCT 60.046 40.000 0.00 0.00 46.05 3.91
2954 3223 4.825422 TGACCAGAACTAGATTCTTGCTG 58.175 43.478 0.00 0.00 46.05 4.41
2955 3224 4.187694 GACCAGAACTAGATTCTTGCTGG 58.812 47.826 9.94 9.94 46.05 4.85
2956 3225 3.584848 ACCAGAACTAGATTCTTGCTGGT 59.415 43.478 11.05 11.05 46.05 4.00
2957 3226 4.777896 ACCAGAACTAGATTCTTGCTGGTA 59.222 41.667 14.21 0.00 46.05 3.25
2958 3227 5.248477 ACCAGAACTAGATTCTTGCTGGTAA 59.752 40.000 14.21 0.00 46.05 2.85
2959 3228 5.582665 CCAGAACTAGATTCTTGCTGGTAAC 59.417 44.000 0.00 0.00 46.05 2.50
2960 3229 6.166279 CAGAACTAGATTCTTGCTGGTAACA 58.834 40.000 0.00 0.00 46.05 2.41
2982 3251 3.124636 ACGAATTGTGAGCGTTTGTATCC 59.875 43.478 0.00 0.00 34.12 2.59
3004 3280 5.068987 TCCTCCAATGGAAGTGAAAAAGTTG 59.931 40.000 2.61 0.00 30.28 3.16
3009 3285 3.855858 TGGAAGTGAAAAAGTTGCAACC 58.144 40.909 25.62 10.69 36.68 3.77
3016 3292 4.929211 GTGAAAAAGTTGCAACCAAAGAGT 59.071 37.500 25.62 2.44 31.68 3.24
3020 3296 5.852282 AAAGTTGCAACCAAAGAGTACAT 57.148 34.783 25.62 0.00 31.68 2.29
3021 3297 6.952773 AAAGTTGCAACCAAAGAGTACATA 57.047 33.333 25.62 0.00 31.68 2.29
3022 3298 6.560253 AAGTTGCAACCAAAGAGTACATAG 57.440 37.500 25.62 0.00 31.68 2.23
3023 3299 5.865085 AGTTGCAACCAAAGAGTACATAGA 58.135 37.500 25.62 0.00 31.68 1.98
3024 3300 5.701290 AGTTGCAACCAAAGAGTACATAGAC 59.299 40.000 25.62 0.00 31.68 2.59
3025 3301 5.222079 TGCAACCAAAGAGTACATAGACA 57.778 39.130 0.00 0.00 0.00 3.41
3027 3303 6.941857 TGCAACCAAAGAGTACATAGACATA 58.058 36.000 0.00 0.00 0.00 2.29
3029 3305 6.258068 GCAACCAAAGAGTACATAGACATACC 59.742 42.308 0.00 0.00 0.00 2.73
3030 3306 6.145338 ACCAAAGAGTACATAGACATACCG 57.855 41.667 0.00 0.00 0.00 4.02
3032 3308 6.183360 ACCAAAGAGTACATAGACATACCGAC 60.183 42.308 0.00 0.00 0.00 4.79
3034 3310 5.045012 AGAGTACATAGACATACCGACCA 57.955 43.478 0.00 0.00 0.00 4.02
3035 3311 4.820716 AGAGTACATAGACATACCGACCAC 59.179 45.833 0.00 0.00 0.00 4.16
3036 3312 4.529897 AGTACATAGACATACCGACCACA 58.470 43.478 0.00 0.00 0.00 4.17
3037 3313 3.795623 ACATAGACATACCGACCACAC 57.204 47.619 0.00 0.00 0.00 3.82
3039 3315 0.452987 TAGACATACCGACCACACGC 59.547 55.000 0.00 0.00 0.00 5.34
3040 3316 1.080366 GACATACCGACCACACGCA 60.080 57.895 0.00 0.00 0.00 5.24
3041 3317 1.349259 GACATACCGACCACACGCAC 61.349 60.000 0.00 0.00 0.00 5.34
3042 3318 1.373622 CATACCGACCACACGCACA 60.374 57.895 0.00 0.00 0.00 4.57
3043 3319 1.373748 ATACCGACCACACGCACAC 60.374 57.895 0.00 0.00 0.00 3.82
3046 3322 2.550772 CGACCACACGCACACATG 59.449 61.111 0.00 0.00 0.00 3.21
3074 3350 5.070981 CCTATGGAAGATTGGAGTAGCTTCA 59.929 44.000 0.00 0.00 38.72 3.02
3080 3356 6.428385 AAGATTGGAGTAGCTTCAAAATCG 57.572 37.500 0.00 0.00 32.23 3.34
3082 3358 5.582665 AGATTGGAGTAGCTTCAAAATCGAC 59.417 40.000 0.00 0.00 32.23 4.20
3083 3359 4.537135 TGGAGTAGCTTCAAAATCGACT 57.463 40.909 0.00 0.00 0.00 4.18
3084 3360 4.495422 TGGAGTAGCTTCAAAATCGACTC 58.505 43.478 0.00 0.00 33.58 3.36
3085 3361 3.548268 GGAGTAGCTTCAAAATCGACTCG 59.452 47.826 0.00 0.00 34.64 4.18
3086 3362 2.924290 AGTAGCTTCAAAATCGACTCGC 59.076 45.455 0.00 0.00 0.00 5.03
3087 3363 2.086054 AGCTTCAAAATCGACTCGCT 57.914 45.000 0.00 0.00 0.00 4.93
3088 3364 1.996191 AGCTTCAAAATCGACTCGCTC 59.004 47.619 0.00 0.00 0.00 5.03
3093 3371 5.418310 TTCAAAATCGACTCGCTCTTTTT 57.582 34.783 0.00 0.00 0.00 1.94
3114 3392 2.551912 AAACAACTCCCGCGCTTGG 61.552 57.895 5.56 6.11 0.00 3.61
3123 3401 0.377203 CCCGCGCTTGGTTAGAAATC 59.623 55.000 5.56 0.00 0.00 2.17
3133 3414 5.524281 GCTTGGTTAGAAATCCTAGTACAGC 59.476 44.000 0.00 0.00 0.00 4.40
3134 3415 5.258456 TGGTTAGAAATCCTAGTACAGCG 57.742 43.478 0.00 0.00 0.00 5.18
3174 3633 8.519492 AAAGAACAAAATCCAATACACATTCG 57.481 30.769 0.00 0.00 0.00 3.34
3182 3641 4.992688 TCCAATACACATTCGGCAAAATC 58.007 39.130 0.00 0.00 0.00 2.17
3194 3653 3.081804 CGGCAAAATCTAGGAGGTTGTT 58.918 45.455 0.00 0.00 0.00 2.83
3195 3654 3.119849 CGGCAAAATCTAGGAGGTTGTTG 60.120 47.826 0.00 0.00 0.00 3.33
3197 3656 4.706962 GGCAAAATCTAGGAGGTTGTTGAT 59.293 41.667 0.00 0.00 0.00 2.57
3198 3657 5.163612 GGCAAAATCTAGGAGGTTGTTGATC 60.164 44.000 0.00 0.00 0.00 2.92
3199 3658 5.415701 GCAAAATCTAGGAGGTTGTTGATCA 59.584 40.000 0.00 0.00 0.00 2.92
3200 3659 6.071952 GCAAAATCTAGGAGGTTGTTGATCAA 60.072 38.462 3.38 3.38 0.00 2.57
3201 3660 7.523709 GCAAAATCTAGGAGGTTGTTGATCAAA 60.524 37.037 10.35 0.00 37.81 2.69
3202 3661 7.693969 AAATCTAGGAGGTTGTTGATCAAAG 57.306 36.000 10.35 0.56 37.81 2.77
3203 3662 6.627087 ATCTAGGAGGTTGTTGATCAAAGA 57.373 37.500 10.35 6.44 37.81 2.52
3204 3663 6.042638 TCTAGGAGGTTGTTGATCAAAGAG 57.957 41.667 10.35 0.00 37.81 2.85
3205 3664 4.713792 AGGAGGTTGTTGATCAAAGAGT 57.286 40.909 10.35 0.00 37.81 3.24
3206 3665 4.646572 AGGAGGTTGTTGATCAAAGAGTC 58.353 43.478 10.35 3.86 37.81 3.36
3207 3666 4.349342 AGGAGGTTGTTGATCAAAGAGTCT 59.651 41.667 10.35 4.64 37.81 3.24
3208 3667 5.544176 AGGAGGTTGTTGATCAAAGAGTCTA 59.456 40.000 10.35 0.00 37.81 2.59
3209 3668 6.043243 AGGAGGTTGTTGATCAAAGAGTCTAA 59.957 38.462 10.35 0.00 37.81 2.10
3210 3669 6.370166 GGAGGTTGTTGATCAAAGAGTCTAAG 59.630 42.308 10.35 0.00 37.81 2.18
3211 3670 5.703130 AGGTTGTTGATCAAAGAGTCTAAGC 59.297 40.000 10.35 6.84 37.81 3.09
3212 3671 5.106515 GGTTGTTGATCAAAGAGTCTAAGCC 60.107 44.000 10.35 0.00 37.81 4.35
3213 3672 4.579869 TGTTGATCAAAGAGTCTAAGCCC 58.420 43.478 10.35 0.00 0.00 5.19
3214 3673 4.041567 TGTTGATCAAAGAGTCTAAGCCCA 59.958 41.667 10.35 0.00 0.00 5.36
3215 3674 4.207891 TGATCAAAGAGTCTAAGCCCAC 57.792 45.455 0.00 0.00 0.00 4.61
3216 3675 2.743636 TCAAAGAGTCTAAGCCCACG 57.256 50.000 0.00 0.00 0.00 4.94
3217 3676 1.275291 TCAAAGAGTCTAAGCCCACGG 59.725 52.381 0.00 0.00 0.00 4.94
3218 3677 1.275291 CAAAGAGTCTAAGCCCACGGA 59.725 52.381 0.00 0.00 0.00 4.69
3219 3678 1.187087 AAGAGTCTAAGCCCACGGAG 58.813 55.000 0.00 0.00 0.00 4.63
3220 3679 0.331954 AGAGTCTAAGCCCACGGAGA 59.668 55.000 0.00 0.00 0.00 3.71
3221 3680 0.741915 GAGTCTAAGCCCACGGAGAG 59.258 60.000 0.00 0.00 0.00 3.20
3222 3681 0.039911 AGTCTAAGCCCACGGAGAGT 59.960 55.000 0.00 0.00 0.00 3.24
3223 3682 0.896226 GTCTAAGCCCACGGAGAGTT 59.104 55.000 0.00 0.00 0.00 3.01
3227 3686 3.319198 GCCCACGGAGAGTTGGGA 61.319 66.667 10.98 0.00 41.04 4.37
3229 3688 2.261671 CCACGGAGAGTTGGGACG 59.738 66.667 0.00 0.00 0.00 4.79
3236 3695 2.182030 GAGTTGGGACGAGAGGCG 59.818 66.667 0.00 0.00 43.44 5.52
3247 3706 1.509004 GAGAGGCGTCAGGTGAGAC 59.491 63.158 9.41 0.00 35.19 3.36
3248 3707 1.228583 AGAGGCGTCAGGTGAGACA 60.229 57.895 9.41 0.00 38.43 3.41
3249 3708 0.827925 AGAGGCGTCAGGTGAGACAA 60.828 55.000 9.41 0.00 38.43 3.18
3250 3709 0.247736 GAGGCGTCAGGTGAGACAAT 59.752 55.000 0.52 0.00 38.43 2.71
3251 3710 0.036952 AGGCGTCAGGTGAGACAATG 60.037 55.000 0.00 0.00 38.43 2.82
3291 3760 0.603975 AAACGGAGAGCACTGGAAGC 60.604 55.000 0.00 0.00 37.60 3.86
3316 3785 6.403527 CGATCCATACTTTCAGATTGCAACAA 60.404 38.462 0.00 0.00 0.00 2.83
3332 3801 4.272991 TGCAACAATGATTGGCAAGTTTTC 59.727 37.500 10.27 0.00 34.12 2.29
3334 3803 5.007921 GCAACAATGATTGGCAAGTTTTCTT 59.992 36.000 10.27 0.00 36.28 2.52
3366 3835 5.105752 GCAGAGTCGATTGTTCTATGAACT 58.894 41.667 11.06 0.00 0.00 3.01
3369 3838 7.679875 GCAGAGTCGATTGTTCTATGAACTAGA 60.680 40.741 11.06 3.83 34.56 2.43
3395 3864 6.018016 ACCATATTCTTGCTTGCAAAACAAAC 60.018 34.615 13.72 0.00 37.96 2.93
3416 3914 2.273908 CAATGCTGCAGCCTCCTTT 58.726 52.632 34.64 17.30 41.18 3.11
3436 3934 2.211250 ATGCAAGTGCTCAACCTCAT 57.789 45.000 4.69 0.00 42.66 2.90
3446 3944 5.536161 AGTGCTCAACCTCATGTAAATGTTT 59.464 36.000 0.00 0.00 0.00 2.83
3514 4035 5.993748 ATATAAACAACACCAACCCCTTG 57.006 39.130 0.00 0.00 0.00 3.61
3528 4049 4.267341 ACCCCTTGCTCTAGTACTGTAT 57.733 45.455 5.39 0.00 0.00 2.29
3529 4050 3.961408 ACCCCTTGCTCTAGTACTGTATG 59.039 47.826 5.39 0.00 0.00 2.39
3563 4084 3.188460 CGGTGTTTTACATCAAGGGTCAG 59.812 47.826 0.00 0.00 0.00 3.51
3593 4114 1.686355 TGACCACGCTGTTCCATTTT 58.314 45.000 0.00 0.00 0.00 1.82
3650 4171 3.317449 AAAAACGTCCTTCCGAGGG 57.683 52.632 0.00 0.00 43.72 4.30
3746 4268 5.451798 GCCATGGAAAAGAAGTTCAAGTTCA 60.452 40.000 18.40 0.00 30.04 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.183492 TGCTTTGCTTCAGACCAGGT 59.817 50.000 0.00 0.00 0.00 4.00
16 17 3.072944 ACTCAGATGCTTTGCTTCAGAC 58.927 45.455 7.90 0.00 35.57 3.51
47 48 0.250901 TCAGGGCAGCAACTCTTTCC 60.251 55.000 0.00 0.00 0.00 3.13
162 165 2.048503 AGCCTACGCACGGTTCAC 60.049 61.111 0.00 0.00 37.52 3.18
171 174 1.661821 CGATACAGCCAGCCTACGC 60.662 63.158 0.00 0.00 0.00 4.42
204 207 0.721718 GATTGCTTCGGGTGAACTCG 59.278 55.000 0.00 0.00 0.00 4.18
229 232 0.952010 CAACCCTACGACAAACCCGG 60.952 60.000 0.00 0.00 0.00 5.73
244 247 6.812160 AGAACGACTGATGATAAAGTACAACC 59.188 38.462 0.00 0.00 0.00 3.77
251 254 9.952188 TTGATACTAGAACGACTGATGATAAAG 57.048 33.333 0.00 0.00 0.00 1.85
261 264 9.088512 GACATCAATTTTGATACTAGAACGACT 57.911 33.333 5.52 0.00 45.62 4.18
283 289 0.029035 GGCGACGACACGATAGACAT 59.971 55.000 0.00 0.00 41.38 3.06
285 291 0.860618 GTGGCGACGACACGATAGAC 60.861 60.000 19.65 0.00 41.38 2.59
299 305 4.025401 GCAACCTTGTCCGTGGCG 62.025 66.667 0.00 0.00 0.00 5.69
343 349 3.741476 GGGGACAGCAAGCAAGCG 61.741 66.667 0.00 0.00 40.15 4.68
348 354 3.635268 CTCCAGGGGGACAGCAAGC 62.635 68.421 0.00 0.00 38.64 4.01
349 355 2.227036 ACTCCAGGGGGACAGCAAG 61.227 63.158 0.00 0.00 38.64 4.01
353 359 3.721706 GGCACTCCAGGGGGACAG 61.722 72.222 0.00 0.00 38.64 3.51
359 365 3.190738 TTGAACCGGCACTCCAGGG 62.191 63.158 0.00 0.00 32.61 4.45
364 370 4.090057 GCGCTTGAACCGGCACTC 62.090 66.667 0.00 0.00 0.00 3.51
389 432 1.269102 CGACCGTGCAAGGTAGATAGG 60.269 57.143 24.86 6.23 46.09 2.57
416 459 3.490759 CGGCTGCCATGTCGACAC 61.491 66.667 22.71 9.19 37.20 3.67
456 499 3.517612 GGCCAGATATCCTTACCTACCA 58.482 50.000 0.00 0.00 0.00 3.25
457 500 2.496470 CGGCCAGATATCCTTACCTACC 59.504 54.545 2.24 0.00 0.00 3.18
586 775 3.315140 TCCCATTGGACGACGCCA 61.315 61.111 3.62 6.88 35.03 5.69
603 792 2.515057 TGCCGTGCACTTTTCCGT 60.515 55.556 16.19 0.00 31.71 4.69
636 826 6.183361 ACCCTGGATTGGTGGATATACTAGTA 60.183 42.308 4.77 4.77 33.94 1.82
638 828 5.094387 ACCCTGGATTGGTGGATATACTAG 58.906 45.833 0.00 0.00 33.94 2.57
639 829 5.101254 ACCCTGGATTGGTGGATATACTA 57.899 43.478 0.00 0.00 33.94 1.82
640 830 3.954662 ACCCTGGATTGGTGGATATACT 58.045 45.455 0.00 0.00 33.94 2.12
670 860 0.330604 AATGCAGATGCCCTGTCTGT 59.669 50.000 1.72 0.00 43.86 3.41
671 861 1.134367 CAAATGCAGATGCCCTGTCTG 59.866 52.381 1.72 0.00 44.71 3.51
672 862 1.471119 CAAATGCAGATGCCCTGTCT 58.529 50.000 1.72 0.00 44.71 3.41
673 863 0.179119 GCAAATGCAGATGCCCTGTC 60.179 55.000 13.95 0.00 44.71 3.51
734 924 1.070134 TGCCAAGATAGGTACGATGCC 59.930 52.381 0.00 0.00 0.00 4.40
735 925 2.526304 TGCCAAGATAGGTACGATGC 57.474 50.000 0.00 0.00 0.00 3.91
736 926 3.245797 CGATGCCAAGATAGGTACGATG 58.754 50.000 0.00 0.00 0.00 3.84
737 927 2.231478 CCGATGCCAAGATAGGTACGAT 59.769 50.000 0.00 0.00 0.00 3.73
740 930 2.610727 GCTCCGATGCCAAGATAGGTAC 60.611 54.545 0.00 0.00 0.00 3.34
760 950 4.778143 ATGTGGGTTCGCTCCGGC 62.778 66.667 0.00 0.00 0.00 6.13
761 951 2.511600 GATGTGGGTTCGCTCCGG 60.512 66.667 0.00 0.00 0.00 5.14
768 958 2.492088 GCTAGGTTTTGGATGTGGGTTC 59.508 50.000 0.00 0.00 0.00 3.62
771 966 1.094785 CGCTAGGTTTTGGATGTGGG 58.905 55.000 0.00 0.00 0.00 4.61
791 986 1.078143 GTGAAAGGGATGCCTCGCT 60.078 57.895 6.10 2.62 45.85 4.93
797 992 2.290577 ACTTGAGGAGTGAAAGGGATGC 60.291 50.000 0.00 0.00 37.17 3.91
811 1013 2.484417 CCATCCGGATGAGAACTTGAGG 60.484 54.545 40.01 19.23 41.20 3.86
902 1104 1.537202 GCCAAGTAACCAACTGCTCTG 59.463 52.381 0.00 0.00 38.88 3.35
907 1109 2.749621 GGATCAGCCAAGTAACCAACTG 59.250 50.000 0.00 0.00 38.88 3.16
911 1113 0.251916 CCGGATCAGCCAAGTAACCA 59.748 55.000 0.00 0.00 35.94 3.67
913 1115 0.252197 ACCCGGATCAGCCAAGTAAC 59.748 55.000 0.73 0.00 35.94 2.50
914 1116 0.988832 AACCCGGATCAGCCAAGTAA 59.011 50.000 0.73 0.00 35.94 2.24
915 1117 0.251916 CAACCCGGATCAGCCAAGTA 59.748 55.000 0.73 0.00 35.94 2.24
916 1118 1.002134 CAACCCGGATCAGCCAAGT 60.002 57.895 0.73 0.00 35.94 3.16
917 1119 1.750399 CCAACCCGGATCAGCCAAG 60.750 63.158 0.73 0.00 36.56 3.61
920 1124 3.728373 ACCCAACCCGGATCAGCC 61.728 66.667 0.73 0.00 36.56 4.85
957 1179 2.997315 TGGTGTCTGGAGCGGGAG 60.997 66.667 0.00 0.00 0.00 4.30
958 1180 3.311110 GTGGTGTCTGGAGCGGGA 61.311 66.667 0.00 0.00 0.00 5.14
959 1181 4.394712 GGTGGTGTCTGGAGCGGG 62.395 72.222 0.00 0.00 0.00 6.13
960 1182 4.742201 CGGTGGTGTCTGGAGCGG 62.742 72.222 0.00 0.00 0.00 5.52
962 1184 4.314440 TGCGGTGGTGTCTGGAGC 62.314 66.667 0.00 0.00 0.00 4.70
963 1185 2.357517 GTGCGGTGGTGTCTGGAG 60.358 66.667 0.00 0.00 0.00 3.86
964 1186 4.293648 CGTGCGGTGGTGTCTGGA 62.294 66.667 0.00 0.00 0.00 3.86
965 1187 3.800685 TTCGTGCGGTGGTGTCTGG 62.801 63.158 0.00 0.00 0.00 3.86
966 1188 2.279851 TTCGTGCGGTGGTGTCTG 60.280 61.111 0.00 0.00 0.00 3.51
967 1189 2.279918 GTTCGTGCGGTGGTGTCT 60.280 61.111 0.00 0.00 0.00 3.41
968 1190 3.343421 GGTTCGTGCGGTGGTGTC 61.343 66.667 0.00 0.00 0.00 3.67
1124 1346 4.508662 AGGAGAAAGCGAAATCGAAGATT 58.491 39.130 7.06 0.00 45.12 2.40
1143 1365 3.269381 AGAAACCAATAATGCAGGGAGGA 59.731 43.478 0.00 0.00 0.00 3.71
1169 1391 1.348036 GAAACCAGAGCCTACCACAGT 59.652 52.381 0.00 0.00 0.00 3.55
1170 1392 1.339151 GGAAACCAGAGCCTACCACAG 60.339 57.143 0.00 0.00 0.00 3.66
1171 1393 0.690762 GGAAACCAGAGCCTACCACA 59.309 55.000 0.00 0.00 0.00 4.17
1172 1394 0.690762 TGGAAACCAGAGCCTACCAC 59.309 55.000 0.00 0.00 0.00 4.16
1173 1395 1.668826 ATGGAAACCAGAGCCTACCA 58.331 50.000 0.00 0.00 36.75 3.25
1174 1396 2.026262 TCAATGGAAACCAGAGCCTACC 60.026 50.000 0.00 0.00 36.75 3.18
1384 1632 3.072476 CAGTAGTGGCCCAGCACT 58.928 61.111 0.00 0.00 35.60 4.40
1385 1633 2.747855 GCAGTAGTGGCCCAGCAC 60.748 66.667 0.00 0.00 0.00 4.40
1972 2241 1.448013 GTGGAAGTAGAGCGTGGGC 60.448 63.158 0.00 0.00 40.37 5.36
2155 2424 4.811364 GCCTGCCTCCTCTTGCCC 62.811 72.222 0.00 0.00 0.00 5.36
2304 2573 2.989639 CCAGCGGGAGGTTGATGA 59.010 61.111 0.00 0.00 39.46 2.92
2874 3143 2.211250 ATCAAGCCAGCACACTTCAT 57.789 45.000 0.00 0.00 0.00 2.57
2884 3153 4.277672 CCAACAATCAGGATATCAAGCCAG 59.722 45.833 4.83 0.00 31.71 4.85
2920 3189 8.129496 TCTAGTTCTGGTCATGTTACAATACA 57.871 34.615 0.00 0.00 0.00 2.29
2921 3190 9.601217 AATCTAGTTCTGGTCATGTTACAATAC 57.399 33.333 0.00 0.00 0.00 1.89
2922 3191 9.817809 GAATCTAGTTCTGGTCATGTTACAATA 57.182 33.333 0.00 0.00 33.89 1.90
2923 3192 8.543774 AGAATCTAGTTCTGGTCATGTTACAAT 58.456 33.333 6.74 0.00 45.38 2.71
2924 3193 7.907389 AGAATCTAGTTCTGGTCATGTTACAA 58.093 34.615 6.74 0.00 45.38 2.41
2925 3194 7.482169 AGAATCTAGTTCTGGTCATGTTACA 57.518 36.000 6.74 0.00 45.38 2.41
2926 3195 7.201565 GCAAGAATCTAGTTCTGGTCATGTTAC 60.202 40.741 7.92 0.00 46.39 2.50
2927 3196 6.818644 GCAAGAATCTAGTTCTGGTCATGTTA 59.181 38.462 7.92 0.00 46.39 2.41
2928 3197 5.645497 GCAAGAATCTAGTTCTGGTCATGTT 59.355 40.000 7.92 0.00 46.39 2.71
2929 3198 5.046014 AGCAAGAATCTAGTTCTGGTCATGT 60.046 40.000 7.92 0.00 46.39 3.21
2930 3199 5.293814 CAGCAAGAATCTAGTTCTGGTCATG 59.706 44.000 7.92 0.00 46.39 3.07
2931 3200 5.426504 CAGCAAGAATCTAGTTCTGGTCAT 58.573 41.667 7.92 0.00 46.39 3.06
2932 3201 4.323028 CCAGCAAGAATCTAGTTCTGGTCA 60.323 45.833 7.92 0.00 46.39 4.02
2933 3202 4.187694 CCAGCAAGAATCTAGTTCTGGTC 58.812 47.826 7.92 3.59 46.39 4.02
2934 3203 3.584848 ACCAGCAAGAATCTAGTTCTGGT 59.415 43.478 15.17 15.17 46.39 4.00
2935 3204 4.213564 ACCAGCAAGAATCTAGTTCTGG 57.786 45.455 14.24 14.24 46.39 3.86
2936 3205 6.091441 GTGTTACCAGCAAGAATCTAGTTCTG 59.909 42.308 7.92 5.07 46.39 3.02
2938 3207 5.062308 CGTGTTACCAGCAAGAATCTAGTTC 59.938 44.000 0.00 0.00 37.08 3.01
2939 3208 4.929808 CGTGTTACCAGCAAGAATCTAGTT 59.070 41.667 0.00 0.00 0.00 2.24
2940 3209 4.219944 TCGTGTTACCAGCAAGAATCTAGT 59.780 41.667 0.00 0.00 0.00 2.57
2941 3210 4.744570 TCGTGTTACCAGCAAGAATCTAG 58.255 43.478 0.00 0.00 0.00 2.43
2942 3211 4.794278 TCGTGTTACCAGCAAGAATCTA 57.206 40.909 0.00 0.00 0.00 1.98
2943 3212 3.678056 TCGTGTTACCAGCAAGAATCT 57.322 42.857 0.00 0.00 0.00 2.40
2944 3213 4.946784 ATTCGTGTTACCAGCAAGAATC 57.053 40.909 0.00 0.00 39.55 2.52
2945 3214 4.518970 ACAATTCGTGTTACCAGCAAGAAT 59.481 37.500 0.00 0.00 43.26 2.40
2946 3215 3.880490 ACAATTCGTGTTACCAGCAAGAA 59.120 39.130 0.00 0.00 37.01 2.52
2947 3216 3.249799 CACAATTCGTGTTACCAGCAAGA 59.750 43.478 0.00 0.00 38.92 3.02
2948 3217 3.249799 TCACAATTCGTGTTACCAGCAAG 59.750 43.478 7.57 0.00 46.44 4.01
2949 3218 3.206964 TCACAATTCGTGTTACCAGCAA 58.793 40.909 7.57 0.00 46.44 3.91
2950 3219 2.805671 CTCACAATTCGTGTTACCAGCA 59.194 45.455 7.57 0.00 46.44 4.41
2951 3220 2.412847 GCTCACAATTCGTGTTACCAGC 60.413 50.000 7.57 5.80 46.44 4.85
2952 3221 2.159841 CGCTCACAATTCGTGTTACCAG 60.160 50.000 7.57 1.03 46.44 4.00
2953 3222 1.795872 CGCTCACAATTCGTGTTACCA 59.204 47.619 7.57 0.00 46.44 3.25
2954 3223 1.796459 ACGCTCACAATTCGTGTTACC 59.204 47.619 7.57 0.00 46.44 2.85
2955 3224 3.515071 AACGCTCACAATTCGTGTTAC 57.485 42.857 7.57 0.00 46.44 2.50
2956 3225 3.310227 ACAAACGCTCACAATTCGTGTTA 59.690 39.130 7.57 0.00 46.44 2.41
2957 3226 2.096819 ACAAACGCTCACAATTCGTGTT 59.903 40.909 7.57 0.00 46.44 3.32
2958 3227 1.668751 ACAAACGCTCACAATTCGTGT 59.331 42.857 7.57 0.00 46.44 4.49
2959 3228 7.086687 AGGATACAAACGCTCACAATTCGTG 62.087 44.000 2.68 2.68 43.86 4.35
2960 3229 3.124636 GGATACAAACGCTCACAATTCGT 59.875 43.478 0.00 0.00 38.15 3.85
2982 3251 4.746611 GCAACTTTTTCACTTCCATTGGAG 59.253 41.667 5.36 3.33 31.21 3.86
3004 3280 6.258068 GGTATGTCTATGTACTCTTTGGTTGC 59.742 42.308 0.00 0.00 0.00 4.17
3009 3285 6.183360 TGGTCGGTATGTCTATGTACTCTTTG 60.183 42.308 0.00 0.00 0.00 2.77
3016 3292 3.313249 CGTGTGGTCGGTATGTCTATGTA 59.687 47.826 0.00 0.00 0.00 2.29
3020 3296 0.452987 GCGTGTGGTCGGTATGTCTA 59.547 55.000 0.00 0.00 0.00 2.59
3021 3297 1.214589 GCGTGTGGTCGGTATGTCT 59.785 57.895 0.00 0.00 0.00 3.41
3022 3298 1.080366 TGCGTGTGGTCGGTATGTC 60.080 57.895 0.00 0.00 0.00 3.06
3023 3299 1.373748 GTGCGTGTGGTCGGTATGT 60.374 57.895 0.00 0.00 0.00 2.29
3024 3300 1.373622 TGTGCGTGTGGTCGGTATG 60.374 57.895 0.00 0.00 0.00 2.39
3025 3301 1.373748 GTGTGCGTGTGGTCGGTAT 60.374 57.895 0.00 0.00 0.00 2.73
3027 3303 3.454587 ATGTGTGCGTGTGGTCGGT 62.455 57.895 0.00 0.00 0.00 4.69
3029 3305 2.550772 CATGTGTGCGTGTGGTCG 59.449 61.111 0.00 0.00 0.00 4.79
3030 3306 2.945984 CCATGTGTGCGTGTGGTC 59.054 61.111 0.00 0.00 0.00 4.02
3032 3308 4.388080 CGCCATGTGTGCGTGTGG 62.388 66.667 6.66 0.00 46.59 4.17
3039 3315 0.747644 TTCCATAGGCGCCATGTGTG 60.748 55.000 31.54 16.49 0.00 3.82
3040 3316 0.464373 CTTCCATAGGCGCCATGTGT 60.464 55.000 31.54 10.27 0.00 3.72
3041 3317 0.179048 TCTTCCATAGGCGCCATGTG 60.179 55.000 31.54 22.50 0.00 3.21
3042 3318 0.767375 ATCTTCCATAGGCGCCATGT 59.233 50.000 31.54 11.17 0.00 3.21
3043 3319 1.538512 CAATCTTCCATAGGCGCCATG 59.461 52.381 31.54 26.73 0.00 3.66
3046 3322 0.108585 TCCAATCTTCCATAGGCGCC 59.891 55.000 21.89 21.89 0.00 6.53
3049 3325 3.326297 AGCTACTCCAATCTTCCATAGGC 59.674 47.826 0.00 0.00 0.00 3.93
3054 3330 4.908601 TTGAAGCTACTCCAATCTTCCA 57.091 40.909 0.00 0.00 35.35 3.53
3074 3350 3.003275 TGCAAAAAGAGCGAGTCGATTTT 59.997 39.130 18.61 15.76 32.50 1.82
3080 3356 3.065019 TGTTTGCAAAAAGAGCGAGTC 57.935 42.857 14.67 0.00 33.85 3.36
3082 3358 3.438360 AGTTGTTTGCAAAAAGAGCGAG 58.562 40.909 14.67 0.00 36.22 5.03
3083 3359 3.434637 GAGTTGTTTGCAAAAAGAGCGA 58.565 40.909 14.67 0.00 36.22 4.93
3084 3360 2.535574 GGAGTTGTTTGCAAAAAGAGCG 59.464 45.455 14.67 0.00 36.22 5.03
3085 3361 2.866156 GGGAGTTGTTTGCAAAAAGAGC 59.134 45.455 14.67 1.27 36.22 4.09
3086 3362 3.115554 CGGGAGTTGTTTGCAAAAAGAG 58.884 45.455 14.67 0.00 36.22 2.85
3087 3363 2.737039 GCGGGAGTTGTTTGCAAAAAGA 60.737 45.455 14.67 0.00 36.22 2.52
3088 3364 1.592543 GCGGGAGTTGTTTGCAAAAAG 59.407 47.619 14.67 0.00 36.22 2.27
3093 3371 3.959975 GCGCGGGAGTTGTTTGCA 61.960 61.111 8.83 0.00 0.00 4.08
3114 3392 5.507650 CCTCCGCTGTACTAGGATTTCTAAC 60.508 48.000 0.00 0.00 33.04 2.34
3123 3401 1.316651 GGTACCTCCGCTGTACTAGG 58.683 60.000 4.06 0.00 38.84 3.02
3145 3426 6.163476 GTGTATTGGATTTTGTTCTTTCCCC 58.837 40.000 0.00 0.00 0.00 4.81
3146 3427 6.754193 TGTGTATTGGATTTTGTTCTTTCCC 58.246 36.000 0.00 0.00 0.00 3.97
3148 3429 8.638565 CGAATGTGTATTGGATTTTGTTCTTTC 58.361 33.333 0.00 0.00 0.00 2.62
3159 3618 5.360714 AGATTTTGCCGAATGTGTATTGGAT 59.639 36.000 0.00 0.00 0.00 3.41
3162 3621 6.038161 TCCTAGATTTTGCCGAATGTGTATTG 59.962 38.462 0.00 0.00 0.00 1.90
3174 3633 4.079253 TCAACAACCTCCTAGATTTTGCC 58.921 43.478 0.00 0.00 0.00 4.52
3182 3641 5.799213 ACTCTTTGATCAACAACCTCCTAG 58.201 41.667 7.89 0.00 38.29 3.02
3194 3653 3.368427 CGTGGGCTTAGACTCTTTGATCA 60.368 47.826 0.00 0.00 0.00 2.92
3195 3654 3.190874 CGTGGGCTTAGACTCTTTGATC 58.809 50.000 0.00 0.00 0.00 2.92
3197 3656 1.275291 CCGTGGGCTTAGACTCTTTGA 59.725 52.381 0.00 0.00 0.00 2.69
3198 3657 1.275291 TCCGTGGGCTTAGACTCTTTG 59.725 52.381 0.00 0.00 0.00 2.77
3199 3658 1.550976 CTCCGTGGGCTTAGACTCTTT 59.449 52.381 0.00 0.00 0.00 2.52
3200 3659 1.187087 CTCCGTGGGCTTAGACTCTT 58.813 55.000 0.00 0.00 0.00 2.85
3201 3660 0.331954 TCTCCGTGGGCTTAGACTCT 59.668 55.000 0.00 0.00 0.00 3.24
3202 3661 0.741915 CTCTCCGTGGGCTTAGACTC 59.258 60.000 0.00 0.00 0.00 3.36
3203 3662 0.039911 ACTCTCCGTGGGCTTAGACT 59.960 55.000 0.00 0.00 0.00 3.24
3204 3663 0.896226 AACTCTCCGTGGGCTTAGAC 59.104 55.000 0.00 0.00 0.00 2.59
3205 3664 0.895530 CAACTCTCCGTGGGCTTAGA 59.104 55.000 0.00 0.00 0.00 2.10
3206 3665 0.108138 CCAACTCTCCGTGGGCTTAG 60.108 60.000 0.00 0.00 27.49 2.18
3207 3666 1.550130 CCCAACTCTCCGTGGGCTTA 61.550 60.000 0.00 0.00 35.14 3.09
3208 3667 2.750350 CCAACTCTCCGTGGGCTT 59.250 61.111 0.00 0.00 27.49 4.35
3209 3668 3.322466 CCCAACTCTCCGTGGGCT 61.322 66.667 0.00 0.00 35.14 5.19
3210 3669 3.319198 TCCCAACTCTCCGTGGGC 61.319 66.667 3.73 0.00 41.24 5.36
3211 3670 2.663196 GTCCCAACTCTCCGTGGG 59.337 66.667 2.09 2.09 42.78 4.61
3212 3671 2.214181 CTCGTCCCAACTCTCCGTGG 62.214 65.000 0.00 0.00 0.00 4.94
3213 3672 1.213013 CTCGTCCCAACTCTCCGTG 59.787 63.158 0.00 0.00 0.00 4.94
3214 3673 0.961358 CTCTCGTCCCAACTCTCCGT 60.961 60.000 0.00 0.00 0.00 4.69
3215 3674 1.658686 CCTCTCGTCCCAACTCTCCG 61.659 65.000 0.00 0.00 0.00 4.63
3216 3675 1.950973 GCCTCTCGTCCCAACTCTCC 61.951 65.000 0.00 0.00 0.00 3.71
3217 3676 1.513622 GCCTCTCGTCCCAACTCTC 59.486 63.158 0.00 0.00 0.00 3.20
3218 3677 2.344203 CGCCTCTCGTCCCAACTCT 61.344 63.158 0.00 0.00 0.00 3.24
3219 3678 2.182030 CGCCTCTCGTCCCAACTC 59.818 66.667 0.00 0.00 0.00 3.01
3229 3688 1.244697 TGTCTCACCTGACGCCTCTC 61.245 60.000 0.00 0.00 39.64 3.20
3236 3695 4.493547 CTTCTCTCATTGTCTCACCTGAC 58.506 47.826 0.00 0.00 37.47 3.51
3239 3698 2.094286 CGCTTCTCTCATTGTCTCACCT 60.094 50.000 0.00 0.00 0.00 4.00
3241 3700 2.266554 CCGCTTCTCTCATTGTCTCAC 58.733 52.381 0.00 0.00 0.00 3.51
3247 3706 0.731417 CCTTGCCGCTTCTCTCATTG 59.269 55.000 0.00 0.00 0.00 2.82
3248 3707 0.393537 CCCTTGCCGCTTCTCTCATT 60.394 55.000 0.00 0.00 0.00 2.57
3249 3708 1.222936 CCCTTGCCGCTTCTCTCAT 59.777 57.895 0.00 0.00 0.00 2.90
3250 3709 1.892819 CTCCCTTGCCGCTTCTCTCA 61.893 60.000 0.00 0.00 0.00 3.27
3251 3710 1.153469 CTCCCTTGCCGCTTCTCTC 60.153 63.158 0.00 0.00 0.00 3.20
3291 3760 5.065090 TGTTGCAATCTGAAAGTATGGATCG 59.935 40.000 0.59 0.00 33.76 3.69
3300 3769 5.163893 GCCAATCATTGTTGCAATCTGAAAG 60.164 40.000 0.59 3.73 0.00 2.62
3316 3785 7.230849 TGATACAAGAAAACTTGCCAATCAT 57.769 32.000 9.44 0.00 37.83 2.45
3332 3801 3.443099 TCGACTCTGCCATGATACAAG 57.557 47.619 0.00 0.00 0.00 3.16
3334 3803 3.132824 ACAATCGACTCTGCCATGATACA 59.867 43.478 0.00 0.00 0.00 2.29
3366 3835 6.832520 TTTGCAAGCAAGAATATGGTTCTA 57.167 33.333 7.60 0.00 38.87 2.10
3369 3838 5.609423 TGTTTTGCAAGCAAGAATATGGTT 58.391 33.333 7.60 0.00 41.40 3.67
3374 3843 5.006552 GCTGTTTGTTTTGCAAGCAAGAATA 59.993 36.000 14.98 2.26 45.33 1.75
3408 3877 1.403323 GAGCACTTGCATAAAGGAGGC 59.597 52.381 3.62 0.00 45.16 4.70
3413 3882 3.503363 TGAGGTTGAGCACTTGCATAAAG 59.497 43.478 3.62 0.00 45.16 1.85
3416 3914 2.857186 TGAGGTTGAGCACTTGCATA 57.143 45.000 3.62 0.00 45.16 3.14
3455 3953 5.398169 TGAACAATGTTGATGTAAATCGGC 58.602 37.500 2.20 0.00 0.00 5.54
3456 3954 8.374728 CAAATGAACAATGTTGATGTAAATCGG 58.625 33.333 2.20 0.00 0.00 4.18
3457 3955 8.914654 ACAAATGAACAATGTTGATGTAAATCG 58.085 29.630 2.20 0.00 0.00 3.34
3463 3961 9.897744 CTTAGTACAAATGAACAATGTTGATGT 57.102 29.630 2.20 0.00 0.00 3.06
3485 4006 8.248253 GGGGTTGGTGTTGTTTATATTTCTTAG 58.752 37.037 0.00 0.00 0.00 2.18
3506 4027 2.903926 ACAGTACTAGAGCAAGGGGTT 58.096 47.619 0.00 0.00 0.00 4.11
3514 4035 7.884816 TTTTGACAACATACAGTACTAGAGC 57.115 36.000 0.00 0.00 0.00 4.09
3540 4061 3.143728 GACCCTTGATGTAAAACACCGT 58.856 45.455 0.00 0.00 0.00 4.83
3541 4062 3.142951 TGACCCTTGATGTAAAACACCG 58.857 45.455 0.00 0.00 0.00 4.94
3543 4064 4.455877 CCTCTGACCCTTGATGTAAAACAC 59.544 45.833 0.00 0.00 0.00 3.32
3544 4065 4.651778 CCTCTGACCCTTGATGTAAAACA 58.348 43.478 0.00 0.00 0.00 2.83
3545 4066 3.440522 GCCTCTGACCCTTGATGTAAAAC 59.559 47.826 0.00 0.00 0.00 2.43
3546 4067 3.073798 TGCCTCTGACCCTTGATGTAAAA 59.926 43.478 0.00 0.00 0.00 1.52
3563 4084 1.000274 AGCGTGGTCAATTTTTGCCTC 60.000 47.619 0.00 0.00 0.00 4.70
3664 4185 1.834263 GACAGGAGGGCATAGACACTT 59.166 52.381 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.