Multiple sequence alignment - TraesCS5B01G332300

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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 TraesCS5B01G332300 chr5B 100.000 3287 0 0 1 3287 516465622 516462336 0.000000e+00 6071.0
1 TraesCS5B01G332300 chr5B 98.876 178 2 0 3110 3287 82237407 82237230 5.290000e-83 318.0
2 TraesCS5B01G332300 chr5B 91.011 178 14 2 3110 3286 82236449 82236625 4.240000e-59 239.0
3 TraesCS5B01G332300 chr5D 86.741 2338 125 79 371 2584 426458939 426456663 0.000000e+00 2429.0
4 TraesCS5B01G332300 chr5D 87.847 288 14 10 2738 3025 426456610 426456344 5.290000e-83 318.0
5 TraesCS5B01G332300 chr5A 88.473 1631 82 48 1110 2670 540594900 540593306 0.000000e+00 1873.0
6 TraesCS5B01G332300 chr5A 85.971 613 35 26 371 935 540595957 540595348 2.800000e-170 608.0
7 TraesCS5B01G332300 chr5A 86.869 297 23 10 2740 3035 540593155 540592874 5.290000e-83 318.0
8 TraesCS5B01G332300 chr5A 87.374 198 25 0 40 237 540596361 540596164 9.180000e-56 228.0
9 TraesCS5B01G332300 chr2A 98.343 181 3 0 3107 3287 529952213 529952033 5.290000e-83 318.0
10 TraesCS5B01G332300 chr2A 90.608 181 15 2 3107 3286 529951248 529951427 4.240000e-59 239.0
11 TraesCS5B01G332300 chr4B 96.667 180 5 1 3109 3287 588224397 588224576 6.900000e-77 298.0
12 TraesCS5B01G332300 chr4B 91.429 175 13 2 3113 3286 588225353 588225180 4.240000e-59 239.0
13 TraesCS5B01G332300 chr7B 90.173 173 17 0 3113 3285 711049929 711049757 3.300000e-55 226.0
14 TraesCS5B01G332300 chr7D 89.385 179 18 1 3109 3287 500234861 500234684 1.190000e-54 224.0
15 TraesCS5B01G332300 chr6B 89.714 175 18 0 3113 3287 588900351 588900177 1.190000e-54 224.0
16 TraesCS5B01G332300 chr1A 94.595 37 2 0 1569 1605 466897345 466897381 1.270000e-04 58.4


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 TraesCS5B01G332300 chr5B 516462336 516465622 3286 True 6071.00 6071 100.00000 1 3287 1 chr5B.!!$R2 3286
1 TraesCS5B01G332300 chr5D 426456344 426458939 2595 True 1373.50 2429 87.29400 371 3025 2 chr5D.!!$R1 2654
2 TraesCS5B01G332300 chr5A 540592874 540596361 3487 True 756.75 1873 87.17175 40 3035 4 chr5A.!!$R1 2995

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
937 1072 0.108898 GCTGTCTGATGAGTGAGCGT 60.109 55.0 0.0 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 3113 0.458716 GAAGAGAGGAAAGGACGCGG 60.459 60.0 12.47 0.0 0.0 6.46 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
17 18 2.423874 TGGTAGTGTGCACCCGTG 59.576 61.111 15.69 0.00 34.99 4.94
41 42 2.582959 GAGCATCGACGACATGGAC 58.417 57.895 0.00 0.00 0.00 4.02
42 43 0.179137 GAGCATCGACGACATGGACA 60.179 55.000 0.00 0.00 0.00 4.02
43 44 0.461548 AGCATCGACGACATGGACAT 59.538 50.000 0.00 0.00 0.00 3.06
44 45 0.578683 GCATCGACGACATGGACATG 59.421 55.000 10.57 10.57 44.15 3.21
45 46 0.578683 CATCGACGACATGGACATGC 59.421 55.000 11.96 4.77 42.39 4.06
46 47 0.530650 ATCGACGACATGGACATGCC 60.531 55.000 11.96 0.26 42.39 4.40
53 54 2.560504 GACATGGACATGCCGATGTTA 58.439 47.619 10.76 0.00 43.22 2.41
57 58 1.002544 TGGACATGCCGATGTTACACA 59.997 47.619 0.00 0.00 43.22 3.72
96 97 4.592426 GCGGAGAGCTAAAACCGT 57.408 55.556 17.16 0.00 45.91 4.83
97 98 2.836944 GCGGAGAGCTAAAACCGTT 58.163 52.632 17.16 0.00 45.91 4.44
99 100 1.792006 CGGAGAGCTAAAACCGTTGT 58.208 50.000 10.71 0.00 40.42 3.32
137 138 3.370131 CGTTTGCGCGTCTACGAT 58.630 55.556 19.15 0.00 43.02 3.73
147 148 2.590276 CGCGTCTACGATCATTCATAGC 59.410 50.000 6.71 0.00 43.02 2.97
150 151 4.613850 GCGTCTACGATCATTCATAGCAGA 60.614 45.833 6.71 0.00 43.02 4.26
169 170 0.995024 AAGCTACAAGGAGCCATGGT 59.005 50.000 14.67 0.00 43.97 3.55
170 171 0.995024 AGCTACAAGGAGCCATGGTT 59.005 50.000 14.67 7.37 43.97 3.67
178 179 3.044059 GAGCCATGGTTGAGCACGC 62.044 63.158 14.67 0.00 0.00 5.34
183 184 1.304381 ATGGTTGAGCACGCCCATT 60.304 52.632 0.00 0.00 33.99 3.16
190 191 1.228245 AGCACGCCCATTGACAACT 60.228 52.632 0.00 0.00 0.00 3.16
206 207 2.844348 ACAACTGGTGTTATAGGAGGGG 59.156 50.000 0.00 0.00 37.01 4.79
220 221 4.062032 GGGGAGGGGGAGGCAAAC 62.062 72.222 0.00 0.00 0.00 2.93
228 229 0.463833 GGGGAGGCAAACGTAGATGG 60.464 60.000 0.00 0.00 0.00 3.51
237 238 3.678806 GCAAACGTAGATGGAGATGGACA 60.679 47.826 0.00 0.00 0.00 4.02
239 240 1.683917 ACGTAGATGGAGATGGACAGC 59.316 52.381 0.00 0.00 0.00 4.40
280 317 2.688666 AGGCGATCTCCCCTGCAA 60.689 61.111 0.00 0.00 0.00 4.08
320 357 0.606604 TCGGAGAAGAAAGGGGAACG 59.393 55.000 0.00 0.00 0.00 3.95
349 386 4.227134 CAGGGGCGGTCGATCTGG 62.227 72.222 0.00 0.00 0.00 3.86
357 394 2.024871 GTCGATCTGGACGGCTCG 59.975 66.667 0.00 0.00 32.48 5.03
425 499 4.760047 CACCTTCCGGCTCGTGGG 62.760 72.222 0.00 0.00 0.00 4.61
448 535 3.537580 TGCCACGTTTACAGAAGAAGTT 58.462 40.909 0.00 0.00 0.00 2.66
450 537 4.201871 TGCCACGTTTACAGAAGAAGTTTG 60.202 41.667 0.00 0.00 0.00 2.93
484 575 2.223641 CGCAAACCTACACCTAGCGATA 60.224 50.000 0.00 0.00 45.78 2.92
528 626 1.032014 GGAGCAGAGCAGGTAGAGAG 58.968 60.000 0.00 0.00 0.00 3.20
657 757 1.294780 CACACACAGAGGAGAGCCC 59.705 63.158 0.00 0.00 33.31 5.19
861 980 4.129737 GCCACGGAGCGAGCAGTA 62.130 66.667 0.00 0.00 32.25 2.74
862 981 2.103143 CCACGGAGCGAGCAGTAG 59.897 66.667 0.00 0.00 0.00 2.57
863 982 2.407428 CCACGGAGCGAGCAGTAGA 61.407 63.158 0.00 0.00 0.00 2.59
866 985 2.840066 CGGAGCGAGCAGTAGAGGG 61.840 68.421 0.00 0.00 0.00 4.30
867 986 2.415426 GAGCGAGCAGTAGAGGGC 59.585 66.667 0.00 0.00 0.00 5.19
871 1005 3.827898 GAGCAGTAGAGGGCGCGT 61.828 66.667 8.43 0.00 34.54 6.01
935 1070 0.172127 TCGCTGTCTGATGAGTGAGC 59.828 55.000 0.00 0.00 0.00 4.26
937 1072 0.108898 GCTGTCTGATGAGTGAGCGT 60.109 55.000 0.00 0.00 0.00 5.07
1076 1218 4.180946 CGACGCACCTCCGGAGAG 62.181 72.222 33.39 24.00 40.09 3.20
1077 1219 2.750637 GACGCACCTCCGGAGAGA 60.751 66.667 33.39 0.00 43.39 3.10
1078 1220 3.053849 GACGCACCTCCGGAGAGAC 62.054 68.421 33.39 18.82 43.39 3.36
1079 1221 2.752238 CGCACCTCCGGAGAGACT 60.752 66.667 33.39 9.02 43.39 3.24
1080 1222 2.766400 CGCACCTCCGGAGAGACTC 61.766 68.421 33.39 14.76 43.39 3.36
1081 1223 2.419739 GCACCTCCGGAGAGACTCC 61.420 68.421 33.39 10.50 46.44 3.85
1103 1245 4.141228 CCTCGTAGATAGATAGGGGCCATA 60.141 50.000 4.39 1.78 33.89 2.74
1104 1246 5.050126 TCGTAGATAGATAGGGGCCATAG 57.950 47.826 4.39 0.00 0.00 2.23
1105 1247 4.141228 TCGTAGATAGATAGGGGCCATAGG 60.141 50.000 4.39 0.00 0.00 2.57
1127 1535 2.032204 CCATACTACTACCACGAGCGAC 60.032 54.545 0.00 0.00 0.00 5.19
1140 1554 2.686405 ACGAGCGACCAAGATACATACA 59.314 45.455 0.00 0.00 0.00 2.29
1154 1569 0.175760 CATACAGACACTCCCCCACG 59.824 60.000 0.00 0.00 0.00 4.94
1155 1570 0.976073 ATACAGACACTCCCCCACGG 60.976 60.000 0.00 0.00 0.00 4.94
1157 1572 2.203182 AGACACTCCCCCACGGAA 59.797 61.111 0.00 0.00 41.40 4.30
1172 1587 4.742201 GAACCAGCGAGCCAGCGA 62.742 66.667 0.00 0.00 43.00 4.93
1173 1588 4.749310 AACCAGCGAGCCAGCGAG 62.749 66.667 0.00 0.00 43.00 5.03
1175 1590 4.869440 CCAGCGAGCCAGCGAGAG 62.869 72.222 0.00 0.00 43.00 3.20
1286 1713 2.358003 GCGCTCAGCCTCAACACT 60.358 61.111 0.00 0.00 40.81 3.55
1661 2097 1.064946 GATCGAGTCGGAGGTGCAG 59.935 63.158 13.54 0.00 0.00 4.41
1712 2148 2.824341 CCTCAAGTACGACCAGGTAAGT 59.176 50.000 0.00 0.00 0.00 2.24
1764 2201 1.485066 CATTCCTGGCCGTACCTAACT 59.515 52.381 0.00 0.00 40.22 2.24
1787 2235 1.768077 CCTCTCCTCCATGGACCCC 60.768 68.421 11.44 0.00 40.56 4.95
1886 2343 0.105778 GCCCTTCTGATCCTTCCTCG 59.894 60.000 0.00 0.00 0.00 4.63
1932 2390 4.388499 CCTACAACCACCGCCGCT 62.388 66.667 0.00 0.00 0.00 5.52
1938 2396 3.346631 AACCACCGCCGCTACTACG 62.347 63.158 0.00 0.00 0.00 3.51
1939 2397 3.818787 CCACCGCCGCTACTACGT 61.819 66.667 0.00 0.00 0.00 3.57
1940 2398 2.472059 CCACCGCCGCTACTACGTA 61.472 63.158 0.00 0.00 0.00 3.57
1941 2399 1.297893 CACCGCCGCTACTACGTAC 60.298 63.158 0.00 0.00 0.00 3.67
1942 2400 1.450312 ACCGCCGCTACTACGTACT 60.450 57.895 0.00 0.00 0.00 2.73
1943 2401 1.026718 ACCGCCGCTACTACGTACTT 61.027 55.000 0.00 0.00 0.00 2.24
1944 2402 0.590732 CCGCCGCTACTACGTACTTG 60.591 60.000 0.00 0.00 0.00 3.16
1992 2452 8.014517 GCTAGCACTTACTAGTAACTATTACCG 58.985 40.741 10.63 2.39 41.49 4.02
2065 2540 9.581289 TGTTATTATGTTCTCCTTTTTCCTTGA 57.419 29.630 0.00 0.00 0.00 3.02
2066 2541 9.841880 GTTATTATGTTCTCCTTTTTCCTTGAC 57.158 33.333 0.00 0.00 0.00 3.18
2074 2550 5.602978 TCTCCTTTTTCCTTGACTCACTAGT 59.397 40.000 0.00 0.00 39.21 2.57
2138 2616 2.180017 GTGGCAATGCGCAAGGAG 59.820 61.111 17.11 5.71 45.13 3.69
2143 2621 2.117156 CAATGCGCAAGGAGAGGGG 61.117 63.158 17.11 0.00 45.13 4.79
2156 2634 2.284258 AGGGGAGAAGACGCAGCT 60.284 61.111 0.00 0.00 0.00 4.24
2161 2639 0.952984 GGAGAAGACGCAGCTGCTTT 60.953 55.000 34.22 24.65 39.32 3.51
2332 2815 7.883217 TCTAGTGCTAGTGGTATTATTACTGC 58.117 38.462 6.18 0.00 34.84 4.40
2341 2827 8.543293 AGTGGTATTATTACTGCTAGTTACCA 57.457 34.615 10.33 10.33 0.00 3.25
2388 2874 1.067582 GTCGCGTGGGAGGGATTAG 59.932 63.158 5.77 0.00 35.54 1.73
2389 2875 2.131709 TCGCGTGGGAGGGATTAGG 61.132 63.158 5.77 0.00 0.00 2.69
2390 2876 2.131709 CGCGTGGGAGGGATTAGGA 61.132 63.158 0.00 0.00 0.00 2.94
2391 2877 1.472662 CGCGTGGGAGGGATTAGGAT 61.473 60.000 0.00 0.00 0.00 3.24
2392 2878 0.765510 GCGTGGGAGGGATTAGGATT 59.234 55.000 0.00 0.00 0.00 3.01
2393 2879 1.975680 GCGTGGGAGGGATTAGGATTA 59.024 52.381 0.00 0.00 0.00 1.75
2394 2880 2.028020 GCGTGGGAGGGATTAGGATTAG 60.028 54.545 0.00 0.00 0.00 1.73
2395 2881 2.567615 CGTGGGAGGGATTAGGATTAGG 59.432 54.545 0.00 0.00 0.00 2.69
2396 2882 2.306219 GTGGGAGGGATTAGGATTAGGC 59.694 54.545 0.00 0.00 0.00 3.93
2397 2883 1.555533 GGGAGGGATTAGGATTAGGCG 59.444 57.143 0.00 0.00 0.00 5.52
2528 3036 2.687200 CGACCTCATCCCCACCCA 60.687 66.667 0.00 0.00 0.00 4.51
2531 3039 2.198304 GACCTCATCCCCACCCACAC 62.198 65.000 0.00 0.00 0.00 3.82
2547 3055 0.600255 ACACCCGCTCTGTTTTCTCG 60.600 55.000 0.00 0.00 0.00 4.04
2551 3059 1.667830 CGCTCTGTTTTCTCGGCCA 60.668 57.895 2.24 0.00 0.00 5.36
2593 3113 0.956902 ACGGCGTGGTGGAATTTACC 60.957 55.000 13.76 6.01 38.71 2.85
2594 3114 1.650314 CGGCGTGGTGGAATTTACCC 61.650 60.000 0.00 0.00 37.40 3.69
2595 3115 1.650314 GGCGTGGTGGAATTTACCCG 61.650 60.000 9.54 12.06 37.40 5.28
2596 3116 1.798087 CGTGGTGGAATTTACCCGC 59.202 57.895 9.54 0.00 37.40 6.13
2597 3117 1.798087 GTGGTGGAATTTACCCGCG 59.202 57.895 0.00 0.00 37.40 6.46
2598 3118 0.956902 GTGGTGGAATTTACCCGCGT 60.957 55.000 4.92 0.00 37.40 6.01
2606 3126 0.616891 ATTTACCCGCGTCCTTTCCT 59.383 50.000 4.92 0.00 0.00 3.36
2627 3147 9.543783 TTTCCTCTCTTCTTTTTAGTAGACAAC 57.456 33.333 0.00 0.00 0.00 3.32
2628 3148 8.246430 TCCTCTCTTCTTTTTAGTAGACAACA 57.754 34.615 0.00 0.00 0.00 3.33
2629 3149 8.361139 TCCTCTCTTCTTTTTAGTAGACAACAG 58.639 37.037 0.00 0.00 0.00 3.16
2630 3150 8.361139 CCTCTCTTCTTTTTAGTAGACAACAGA 58.639 37.037 0.00 0.00 0.00 3.41
2667 3192 5.123936 ACAAAGTTGACACTTACTTCCTCC 58.876 41.667 0.00 0.00 42.89 4.30
2670 3195 4.147321 AGTTGACACTTACTTCCTCCGTA 58.853 43.478 0.00 0.00 0.00 4.02
2671 3196 4.586001 AGTTGACACTTACTTCCTCCGTAA 59.414 41.667 0.00 0.00 0.00 3.18
2672 3197 5.069516 AGTTGACACTTACTTCCTCCGTAAA 59.930 40.000 0.00 0.00 0.00 2.01
2673 3198 5.733620 TGACACTTACTTCCTCCGTAAAT 57.266 39.130 0.00 0.00 0.00 1.40
2674 3199 6.839124 TGACACTTACTTCCTCCGTAAATA 57.161 37.500 0.00 0.00 0.00 1.40
2678 3268 8.488651 ACACTTACTTCCTCCGTAAATAAATG 57.511 34.615 0.00 0.00 0.00 2.32
2687 3277 5.981315 CCTCCGTAAATAAATGTAAGAGCGA 59.019 40.000 0.00 0.00 0.00 4.93
2688 3278 6.074463 CCTCCGTAAATAAATGTAAGAGCGAC 60.074 42.308 0.00 0.00 0.00 5.19
2689 3279 5.456497 TCCGTAAATAAATGTAAGAGCGACG 59.544 40.000 0.00 0.00 0.00 5.12
2693 3283 0.721718 AAATGTAAGAGCGACGCTGC 59.278 50.000 29.85 18.18 39.88 5.25
2703 3293 3.099267 AGCGACGCTGCTCTTATATTT 57.901 42.857 23.84 0.00 42.95 1.40
2704 3294 3.053455 AGCGACGCTGCTCTTATATTTC 58.947 45.455 23.84 0.00 42.95 2.17
2706 3296 3.491267 GCGACGCTGCTCTTATATTTCTT 59.509 43.478 13.73 0.00 0.00 2.52
2707 3297 4.375506 GCGACGCTGCTCTTATATTTCTTC 60.376 45.833 13.73 0.00 0.00 2.87
2708 3298 4.740205 CGACGCTGCTCTTATATTTCTTCA 59.260 41.667 0.00 0.00 0.00 3.02
2709 3299 5.331905 CGACGCTGCTCTTATATTTCTTCAC 60.332 44.000 0.00 0.00 0.00 3.18
2711 3301 5.292101 ACGCTGCTCTTATATTTCTTCACAC 59.708 40.000 0.00 0.00 0.00 3.82
2713 3303 6.509199 CGCTGCTCTTATATTTCTTCACACAG 60.509 42.308 0.00 0.00 0.00 3.66
2714 3304 6.238320 GCTGCTCTTATATTTCTTCACACAGG 60.238 42.308 0.00 0.00 0.00 4.00
2715 3305 6.946340 TGCTCTTATATTTCTTCACACAGGA 58.054 36.000 0.00 0.00 0.00 3.86
2751 3369 1.134220 ACACACACAACCAACGATCCT 60.134 47.619 0.00 0.00 0.00 3.24
2843 3461 2.820479 CGACGTCGCTCTCTCCCT 60.820 66.667 26.59 0.00 0.00 4.20
2844 3462 2.795297 GACGTCGCTCTCTCCCTG 59.205 66.667 0.00 0.00 0.00 4.45
2845 3463 3.404141 GACGTCGCTCTCTCCCTGC 62.404 68.421 0.00 0.00 0.00 4.85
2876 3494 2.754946 TGGCCTTTCCGTTGTACTAG 57.245 50.000 3.32 0.00 37.80 2.57
2880 3498 4.223477 TGGCCTTTCCGTTGTACTAGTAAT 59.777 41.667 3.32 0.00 37.80 1.89
2882 3500 5.064325 GGCCTTTCCGTTGTACTAGTAATTG 59.936 44.000 3.61 0.00 0.00 2.32
2883 3501 5.064325 GCCTTTCCGTTGTACTAGTAATTGG 59.936 44.000 3.61 4.92 0.00 3.16
2884 3502 5.064325 CCTTTCCGTTGTACTAGTAATTGGC 59.936 44.000 3.61 0.00 0.00 4.52
2887 3505 5.172934 TCCGTTGTACTAGTAATTGGCTTG 58.827 41.667 3.61 0.00 0.00 4.01
2888 3506 4.933400 CCGTTGTACTAGTAATTGGCTTGT 59.067 41.667 3.61 0.00 0.00 3.16
2890 3508 6.401796 CCGTTGTACTAGTAATTGGCTTGTTC 60.402 42.308 3.61 2.13 0.00 3.18
2973 3592 6.565999 CGTTTCACAGGAGAAAAATCAGGTAC 60.566 42.308 0.00 0.00 39.05 3.34
2978 3597 7.672660 TCACAGGAGAAAAATCAGGTACTACTA 59.327 37.037 0.00 0.00 36.02 1.82
2984 3603 9.406113 GAGAAAAATCAGGTACTACTACTCCTA 57.594 37.037 0.00 0.00 36.02 2.94
2988 3607 9.850198 AAAATCAGGTACTACTACTCCTACTAG 57.150 37.037 0.00 0.00 36.02 2.57
2989 3608 8.565780 AATCAGGTACTACTACTCCTACTAGT 57.434 38.462 0.00 0.00 36.02 2.57
2990 3609 7.358770 TCAGGTACTACTACTCCTACTAGTG 57.641 44.000 5.39 0.00 36.02 2.74
3037 3656 4.445699 CGCAGGGAGTAGCCAATC 57.554 61.111 0.00 0.00 38.95 2.67
3038 3657 1.227674 CGCAGGGAGTAGCCAATCC 60.228 63.158 0.00 0.00 38.95 3.01
3039 3658 1.690219 CGCAGGGAGTAGCCAATCCT 61.690 60.000 0.00 0.00 38.95 3.24
3040 3659 0.548510 GCAGGGAGTAGCCAATCCTT 59.451 55.000 0.00 0.00 38.95 3.36
3041 3660 1.748591 GCAGGGAGTAGCCAATCCTTG 60.749 57.143 6.38 6.38 43.60 3.61
3042 3661 1.561542 CAGGGAGTAGCCAATCCTTGT 59.438 52.381 2.64 0.00 37.77 3.16
3043 3662 1.561542 AGGGAGTAGCCAATCCTTGTG 59.438 52.381 0.00 0.00 38.95 3.33
3044 3663 1.408822 GGGAGTAGCCAATCCTTGTGG 60.409 57.143 0.00 0.00 38.95 4.17
3045 3664 1.408822 GGAGTAGCCAATCCTTGTGGG 60.409 57.143 0.00 0.00 36.58 4.61
3046 3665 0.034089 AGTAGCCAATCCTTGTGGGC 60.034 55.000 0.00 0.00 46.77 5.36
3048 3667 2.283821 GCCAATCCTTGTGGGCCA 60.284 61.111 0.00 0.00 40.55 5.36
3049 3668 2.649129 GCCAATCCTTGTGGGCCAC 61.649 63.158 29.75 29.75 40.55 5.01
3050 3669 2.342650 CCAATCCTTGTGGGCCACG 61.343 63.158 30.14 17.51 37.14 4.94
3051 3670 1.603455 CAATCCTTGTGGGCCACGT 60.603 57.895 30.14 11.76 37.14 4.49
3052 3671 0.322098 CAATCCTTGTGGGCCACGTA 60.322 55.000 30.14 19.84 37.14 3.57
3053 3672 0.322187 AATCCTTGTGGGCCACGTAC 60.322 55.000 30.14 8.62 37.14 3.67
3054 3673 2.515996 ATCCTTGTGGGCCACGTACG 62.516 60.000 30.14 15.01 37.14 3.67
3055 3674 2.340809 CTTGTGGGCCACGTACGA 59.659 61.111 30.14 10.98 37.14 3.43
3056 3675 2.025418 CTTGTGGGCCACGTACGAC 61.025 63.158 30.14 9.00 37.14 4.34
3058 3677 4.041917 GTGGGCCACGTACGACGA 62.042 66.667 22.83 3.54 46.05 4.20
3059 3678 3.293714 TGGGCCACGTACGACGAA 61.294 61.111 24.41 0.00 46.05 3.85
3060 3679 2.049248 GGGCCACGTACGACGAAA 60.049 61.111 24.41 0.00 46.05 3.46
3061 3680 1.446618 GGGCCACGTACGACGAAAT 60.447 57.895 24.41 0.00 46.05 2.17
3062 3681 1.689352 GGGCCACGTACGACGAAATG 61.689 60.000 24.41 8.36 46.05 2.32
3063 3682 1.010419 GGCCACGTACGACGAAATGT 61.010 55.000 24.41 0.00 46.05 2.71
3064 3683 0.092351 GCCACGTACGACGAAATGTG 59.908 55.000 24.41 10.69 46.05 3.21
3065 3684 1.411394 CCACGTACGACGAAATGTGT 58.589 50.000 24.41 0.00 46.05 3.72
3066 3685 2.583739 CCACGTACGACGAAATGTGTA 58.416 47.619 24.41 0.00 46.05 2.90
3067 3686 2.339400 CCACGTACGACGAAATGTGTAC 59.661 50.000 24.41 3.91 46.05 2.90
3068 3687 3.228749 CACGTACGACGAAATGTGTACT 58.771 45.455 24.41 0.00 46.05 2.73
3069 3688 4.393934 CACGTACGACGAAATGTGTACTA 58.606 43.478 24.41 0.00 46.05 1.82
3070 3689 4.258359 CACGTACGACGAAATGTGTACTAC 59.742 45.833 24.41 0.00 46.05 2.73
3071 3690 4.152402 ACGTACGACGAAATGTGTACTACT 59.848 41.667 24.41 0.00 46.05 2.57
3072 3691 5.347635 ACGTACGACGAAATGTGTACTACTA 59.652 40.000 24.41 0.00 46.05 1.82
3073 3692 5.893187 CGTACGACGAAATGTGTACTACTAG 59.107 44.000 10.44 0.00 46.05 2.57
3074 3693 4.656041 ACGACGAAATGTGTACTACTAGC 58.344 43.478 0.00 0.00 0.00 3.42
3075 3694 3.717890 CGACGAAATGTGTACTACTAGCG 59.282 47.826 0.00 0.00 0.00 4.26
3076 3695 4.493057 CGACGAAATGTGTACTACTAGCGA 60.493 45.833 0.00 0.00 0.00 4.93
3077 3696 4.906423 ACGAAATGTGTACTACTAGCGAG 58.094 43.478 0.00 0.00 0.00 5.03
3078 3697 4.633126 ACGAAATGTGTACTACTAGCGAGA 59.367 41.667 0.00 0.00 0.00 4.04
3079 3698 5.122869 ACGAAATGTGTACTACTAGCGAGAA 59.877 40.000 0.00 0.00 0.00 2.87
3080 3699 6.183360 ACGAAATGTGTACTACTAGCGAGAAT 60.183 38.462 0.00 0.00 0.00 2.40
3081 3700 6.140895 CGAAATGTGTACTACTAGCGAGAATG 59.859 42.308 0.00 0.00 0.00 2.67
3082 3701 4.895224 TGTGTACTACTAGCGAGAATGG 57.105 45.455 0.00 0.00 0.00 3.16
3083 3702 4.267536 TGTGTACTACTAGCGAGAATGGT 58.732 43.478 0.00 0.00 0.00 3.55
3084 3703 4.334759 TGTGTACTACTAGCGAGAATGGTC 59.665 45.833 0.00 0.00 0.00 4.02
3085 3704 3.881688 TGTACTACTAGCGAGAATGGTCC 59.118 47.826 0.00 0.00 0.00 4.46
3086 3705 1.948145 ACTACTAGCGAGAATGGTCCG 59.052 52.381 0.00 0.00 0.00 4.79
3087 3706 1.948145 CTACTAGCGAGAATGGTCCGT 59.052 52.381 0.00 0.00 0.00 4.69
3088 3707 0.739561 ACTAGCGAGAATGGTCCGTC 59.260 55.000 0.00 0.00 0.00 4.79
3089 3708 0.030908 CTAGCGAGAATGGTCCGTCC 59.969 60.000 0.00 0.00 0.00 4.79
3090 3709 0.395311 TAGCGAGAATGGTCCGTCCT 60.395 55.000 0.00 0.00 37.07 3.85
3091 3710 1.218316 GCGAGAATGGTCCGTCCTT 59.782 57.895 0.00 0.00 37.07 3.36
3092 3711 1.084370 GCGAGAATGGTCCGTCCTTG 61.084 60.000 0.00 0.00 37.07 3.61
3093 3712 0.530744 CGAGAATGGTCCGTCCTTGA 59.469 55.000 0.00 0.00 37.07 3.02
3094 3713 1.736032 CGAGAATGGTCCGTCCTTGAC 60.736 57.143 0.00 0.00 37.07 3.18
3095 3714 1.550976 GAGAATGGTCCGTCCTTGACT 59.449 52.381 0.00 0.00 37.07 3.41
3096 3715 1.978580 AGAATGGTCCGTCCTTGACTT 59.021 47.619 0.00 0.00 37.07 3.01
3097 3716 2.076863 GAATGGTCCGTCCTTGACTTG 58.923 52.381 0.00 0.00 37.07 3.16
3098 3717 1.348064 ATGGTCCGTCCTTGACTTGA 58.652 50.000 0.00 0.00 37.07 3.02
3099 3718 1.348064 TGGTCCGTCCTTGACTTGAT 58.652 50.000 0.00 0.00 37.07 2.57
3100 3719 1.697432 TGGTCCGTCCTTGACTTGATT 59.303 47.619 0.00 0.00 37.07 2.57
3101 3720 2.901192 TGGTCCGTCCTTGACTTGATTA 59.099 45.455 0.00 0.00 37.07 1.75
3102 3721 3.517901 TGGTCCGTCCTTGACTTGATTAT 59.482 43.478 0.00 0.00 37.07 1.28
3103 3722 4.019681 TGGTCCGTCCTTGACTTGATTATT 60.020 41.667 0.00 0.00 37.07 1.40
3104 3723 4.941873 GGTCCGTCCTTGACTTGATTATTT 59.058 41.667 0.00 0.00 33.22 1.40
3105 3724 5.064834 GGTCCGTCCTTGACTTGATTATTTC 59.935 44.000 0.00 0.00 33.22 2.17
3106 3725 5.875359 GTCCGTCCTTGACTTGATTATTTCT 59.125 40.000 0.00 0.00 0.00 2.52
3107 3726 5.874810 TCCGTCCTTGACTTGATTATTTCTG 59.125 40.000 0.00 0.00 0.00 3.02
3108 3727 5.065218 CCGTCCTTGACTTGATTATTTCTGG 59.935 44.000 0.00 0.00 0.00 3.86
3109 3728 5.065218 CGTCCTTGACTTGATTATTTCTGGG 59.935 44.000 0.00 0.00 0.00 4.45
3110 3729 6.180472 GTCCTTGACTTGATTATTTCTGGGA 58.820 40.000 0.00 0.00 0.00 4.37
3111 3730 6.830838 GTCCTTGACTTGATTATTTCTGGGAT 59.169 38.462 0.00 0.00 0.00 3.85
3112 3731 7.340487 GTCCTTGACTTGATTATTTCTGGGATT 59.660 37.037 0.00 0.00 0.00 3.01
3113 3732 7.895429 TCCTTGACTTGATTATTTCTGGGATTT 59.105 33.333 0.00 0.00 0.00 2.17
3114 3733 8.534496 CCTTGACTTGATTATTTCTGGGATTTT 58.466 33.333 0.00 0.00 0.00 1.82
3115 3734 9.933723 CTTGACTTGATTATTTCTGGGATTTTT 57.066 29.630 0.00 0.00 0.00 1.94
3132 3751 3.897141 TTTTTGTCCAAAAGGACCACC 57.103 42.857 11.79 0.00 40.83 4.61
3146 3765 5.520748 AGGACCACCTATCAAGTTGAATT 57.479 39.130 10.14 0.00 45.83 2.17
3147 3766 5.256474 AGGACCACCTATCAAGTTGAATTG 58.744 41.667 10.14 4.75 45.83 2.32
3148 3767 5.010282 GGACCACCTATCAAGTTGAATTGT 58.990 41.667 10.14 4.30 0.00 2.71
3149 3768 5.123979 GGACCACCTATCAAGTTGAATTGTC 59.876 44.000 10.14 10.32 0.00 3.18
3150 3769 5.630121 ACCACCTATCAAGTTGAATTGTCA 58.370 37.500 10.14 0.00 0.00 3.58
3151 3770 6.068010 ACCACCTATCAAGTTGAATTGTCAA 58.932 36.000 10.14 0.00 41.57 3.18
3152 3771 6.549364 ACCACCTATCAAGTTGAATTGTCAAA 59.451 34.615 10.14 0.00 45.29 2.69
3153 3772 7.069331 ACCACCTATCAAGTTGAATTGTCAAAA 59.931 33.333 10.14 0.00 45.29 2.44
3154 3773 7.925483 CCACCTATCAAGTTGAATTGTCAAAAA 59.075 33.333 10.14 0.00 45.29 1.94
3175 3794 7.881775 AAAAAGACTACCTCTGAAACACATT 57.118 32.000 0.00 0.00 0.00 2.71
3176 3795 6.867662 AAAGACTACCTCTGAAACACATTG 57.132 37.500 0.00 0.00 0.00 2.82
3177 3796 5.808366 AGACTACCTCTGAAACACATTGA 57.192 39.130 0.00 0.00 0.00 2.57
3178 3797 5.542779 AGACTACCTCTGAAACACATTGAC 58.457 41.667 0.00 0.00 0.00 3.18
3179 3798 5.070446 AGACTACCTCTGAAACACATTGACA 59.930 40.000 0.00 0.00 0.00 3.58
3180 3799 5.680619 ACTACCTCTGAAACACATTGACAA 58.319 37.500 0.00 0.00 0.00 3.18
3181 3800 6.119536 ACTACCTCTGAAACACATTGACAAA 58.880 36.000 0.00 0.00 0.00 2.83
3182 3801 5.913137 ACCTCTGAAACACATTGACAAAA 57.087 34.783 0.00 0.00 0.00 2.44
3183 3802 6.279513 ACCTCTGAAACACATTGACAAAAA 57.720 33.333 0.00 0.00 0.00 1.94
3198 3817 2.032981 AAAAAGACCACCTGCAGCG 58.967 52.632 8.66 4.27 0.00 5.18
3199 3818 0.751643 AAAAAGACCACCTGCAGCGT 60.752 50.000 8.66 4.99 0.00 5.07
3200 3819 1.447317 AAAAGACCACCTGCAGCGTG 61.447 55.000 21.62 21.62 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.423874 CACGGGTGCACACTACCA 59.576 61.111 18.70 0.00 40.03 3.25
13 14 3.250323 CGATGCTCGTCTGCACGG 61.250 66.667 0.00 0.00 46.70 4.94
14 15 2.202479 TCGATGCTCGTCTGCACG 60.202 61.111 5.66 8.64 46.33 5.34
15 16 2.500442 CGTCGATGCTCGTCTGCAC 61.500 63.158 0.00 0.00 46.33 4.57
17 18 2.100410 TCGTCGATGCTCGTCTGC 59.900 61.111 0.00 0.00 41.35 4.26
18 19 0.248255 ATGTCGTCGATGCTCGTCTG 60.248 55.000 0.00 0.00 41.35 3.51
19 20 0.248255 CATGTCGTCGATGCTCGTCT 60.248 55.000 0.00 0.00 41.35 4.18
20 21 1.202973 CCATGTCGTCGATGCTCGTC 61.203 60.000 0.00 0.00 41.35 4.20
21 22 1.226688 CCATGTCGTCGATGCTCGT 60.227 57.895 0.00 0.00 41.35 4.18
22 23 1.064134 TCCATGTCGTCGATGCTCG 59.936 57.895 0.00 0.00 42.10 5.03
23 24 0.179137 TGTCCATGTCGTCGATGCTC 60.179 55.000 0.00 0.00 0.00 4.26
24 25 0.461548 ATGTCCATGTCGTCGATGCT 59.538 50.000 0.00 0.00 0.00 3.79
25 26 0.578683 CATGTCCATGTCGTCGATGC 59.421 55.000 0.00 0.00 34.23 3.91
26 27 0.578683 GCATGTCCATGTCGTCGATG 59.421 55.000 8.91 0.00 40.80 3.84
27 28 0.530650 GGCATGTCCATGTCGTCGAT 60.531 55.000 8.91 0.00 40.80 3.59
28 29 1.153647 GGCATGTCCATGTCGTCGA 60.154 57.895 8.91 0.00 40.80 4.20
29 30 3.398920 GGCATGTCCATGTCGTCG 58.601 61.111 8.91 0.00 40.80 5.12
33 34 1.382522 AACATCGGCATGTCCATGTC 58.617 50.000 11.07 5.52 42.89 3.06
34 35 2.288666 GTAACATCGGCATGTCCATGT 58.711 47.619 4.58 4.58 42.89 3.21
35 36 2.032054 GTGTAACATCGGCATGTCCATG 59.968 50.000 3.14 3.14 42.89 3.66
36 37 2.288666 GTGTAACATCGGCATGTCCAT 58.711 47.619 6.92 0.00 42.89 3.41
37 38 1.002544 TGTGTAACATCGGCATGTCCA 59.997 47.619 6.92 0.00 45.67 4.02
38 39 1.732941 TGTGTAACATCGGCATGTCC 58.267 50.000 0.00 0.00 45.67 4.02
53 54 1.741525 GCTGCAACATTGGGTGTGT 59.258 52.632 0.00 0.00 41.14 3.72
57 58 1.047596 TTGTGGCTGCAACATTGGGT 61.048 50.000 11.25 0.00 0.00 4.51
89 90 2.124236 TCGGCCCACAACGGTTTT 60.124 55.556 0.00 0.00 0.00 2.43
90 91 2.593436 CTCGGCCCACAACGGTTT 60.593 61.111 0.00 0.00 0.00 3.27
147 148 2.286872 CATGGCTCCTTGTAGCTTCTG 58.713 52.381 0.00 0.00 42.37 3.02
150 151 0.995024 ACCATGGCTCCTTGTAGCTT 59.005 50.000 13.04 0.00 42.37 3.74
155 156 0.610232 GCTCAACCATGGCTCCTTGT 60.610 55.000 13.04 0.00 0.00 3.16
159 160 2.401766 CGTGCTCAACCATGGCTCC 61.402 63.158 13.04 0.00 0.00 4.70
169 170 0.821301 TTGTCAATGGGCGTGCTCAA 60.821 50.000 0.00 0.00 0.00 3.02
170 171 1.228094 TTGTCAATGGGCGTGCTCA 60.228 52.632 0.00 0.00 0.00 4.26
178 179 4.640201 CCTATAACACCAGTTGTCAATGGG 59.360 45.833 14.63 10.11 41.13 4.00
183 184 3.517901 CCCTCCTATAACACCAGTTGTCA 59.482 47.826 0.00 0.00 37.51 3.58
190 191 1.061657 CCCTCCCCTCCTATAACACCA 60.062 57.143 0.00 0.00 0.00 4.17
206 207 1.221021 CTACGTTTGCCTCCCCCTC 59.779 63.158 0.00 0.00 0.00 4.30
220 221 1.335415 CGCTGTCCATCTCCATCTACG 60.335 57.143 0.00 0.00 0.00 3.51
296 333 1.014564 CCCTTTCTTCTCCGACGCAC 61.015 60.000 0.00 0.00 0.00 5.34
304 341 0.325272 AGCCGTTCCCCTTTCTTCTC 59.675 55.000 0.00 0.00 0.00 2.87
338 375 3.471244 GAGCCGTCCAGATCGACCG 62.471 68.421 0.00 0.00 0.00 4.79
361 398 0.442699 GAAAACGCCAGGTCGATCAC 59.557 55.000 9.87 0.00 0.00 3.06
365 402 0.680618 TAAGGAAAACGCCAGGTCGA 59.319 50.000 9.87 0.00 0.00 4.20
368 405 0.251033 GGGTAAGGAAAACGCCAGGT 60.251 55.000 0.00 0.00 0.00 4.00
424 498 0.517316 CTTCTGTAAACGTGGCAGCC 59.483 55.000 3.66 3.66 0.00 4.85
425 499 1.508632 TCTTCTGTAAACGTGGCAGC 58.491 50.000 8.76 0.00 0.00 5.25
448 535 3.580916 GCGTGGGTTATTCGCCAA 58.419 55.556 0.00 0.00 43.41 4.52
528 626 3.044305 ACGTGCTCGCTGCCTTTC 61.044 61.111 8.29 0.00 42.00 2.62
608 706 1.435515 GCACTGGTCAAACGCCAAA 59.564 52.632 0.00 0.00 35.32 3.28
609 707 2.485795 GGCACTGGTCAAACGCCAA 61.486 57.895 0.00 0.00 42.50 4.52
937 1072 4.660611 TTACCTCCCCCGCACCCA 62.661 66.667 0.00 0.00 0.00 4.51
1072 1214 6.406624 CCCTATCTATCTACGAGGAGTCTCTC 60.407 50.000 0.00 0.00 37.86 3.20
1073 1215 5.424252 CCCTATCTATCTACGAGGAGTCTCT 59.576 48.000 0.00 0.00 37.86 3.10
1074 1216 5.395990 CCCCTATCTATCTACGAGGAGTCTC 60.396 52.000 0.00 0.00 36.69 3.36
1075 1217 4.472108 CCCCTATCTATCTACGAGGAGTCT 59.528 50.000 0.00 0.00 0.00 3.24
1076 1218 4.773013 CCCCTATCTATCTACGAGGAGTC 58.227 52.174 0.00 0.00 0.00 3.36
1077 1219 3.054213 GCCCCTATCTATCTACGAGGAGT 60.054 52.174 0.00 0.00 0.00 3.85
1078 1220 3.547746 GCCCCTATCTATCTACGAGGAG 58.452 54.545 0.00 0.00 0.00 3.69
1079 1221 2.241685 GGCCCCTATCTATCTACGAGGA 59.758 54.545 0.00 0.00 0.00 3.71
1080 1222 2.025226 TGGCCCCTATCTATCTACGAGG 60.025 54.545 0.00 0.00 0.00 4.63
1081 1223 3.367646 TGGCCCCTATCTATCTACGAG 57.632 52.381 0.00 0.00 0.00 4.18
1082 1224 4.141228 CCTATGGCCCCTATCTATCTACGA 60.141 50.000 0.00 0.00 0.00 3.43
1083 1225 4.145807 CCTATGGCCCCTATCTATCTACG 58.854 52.174 0.00 0.00 0.00 3.51
1084 1226 3.898741 GCCTATGGCCCCTATCTATCTAC 59.101 52.174 0.00 0.00 44.06 2.59
1085 1227 4.200447 GCCTATGGCCCCTATCTATCTA 57.800 50.000 0.00 0.00 44.06 1.98
1086 1228 3.053359 GCCTATGGCCCCTATCTATCT 57.947 52.381 0.00 0.00 44.06 1.98
1103 1245 2.584236 CTCGTGGTAGTAGTATGGCCT 58.416 52.381 3.32 0.00 0.00 5.19
1104 1246 1.000496 GCTCGTGGTAGTAGTATGGCC 60.000 57.143 0.00 0.00 0.00 5.36
1105 1247 1.334779 CGCTCGTGGTAGTAGTATGGC 60.335 57.143 0.00 0.00 0.00 4.40
1106 1248 2.032204 GTCGCTCGTGGTAGTAGTATGG 60.032 54.545 0.00 0.00 0.00 2.74
1108 1250 2.216898 GGTCGCTCGTGGTAGTAGTAT 58.783 52.381 0.00 0.00 0.00 2.12
1115 1523 1.402968 GTATCTTGGTCGCTCGTGGTA 59.597 52.381 0.00 0.00 0.00 3.25
1127 1535 4.202264 GGGGAGTGTCTGTATGTATCTTGG 60.202 50.000 0.00 0.00 0.00 3.61
1155 1570 4.742201 TCGCTGGCTCGCTGGTTC 62.742 66.667 0.00 0.00 0.00 3.62
1484 1920 1.218047 GTGGCCGTAGCACATCTCA 59.782 57.895 0.00 0.00 42.56 3.27
1631 2067 1.517257 CTCGATCTGGGTGACGTGC 60.517 63.158 0.00 0.00 0.00 5.34
1712 2148 2.696893 GGAGAGAGGGGGTGCCTA 59.303 66.667 0.00 0.00 0.00 3.93
1764 2201 1.075970 CCATGGAGGAGAGGGACGA 60.076 63.158 5.56 0.00 41.22 4.20
1886 2343 2.915775 TCGATCTCGATCCCTCGTC 58.084 57.895 0.00 0.00 44.22 4.20
1932 2390 6.202379 CACTCTAGCTATGCAAGTACGTAGTA 59.798 42.308 2.72 0.00 45.11 1.82
1938 2396 4.268884 GCAACACTCTAGCTATGCAAGTAC 59.731 45.833 9.36 0.00 34.10 2.73
1939 2397 4.081697 TGCAACACTCTAGCTATGCAAGTA 60.082 41.667 13.60 0.00 40.47 2.24
1940 2398 3.265791 GCAACACTCTAGCTATGCAAGT 58.734 45.455 9.36 2.08 34.10 3.16
1941 2399 3.264947 TGCAACACTCTAGCTATGCAAG 58.735 45.455 13.60 3.64 40.47 4.01
1942 2400 3.264947 CTGCAACACTCTAGCTATGCAA 58.735 45.455 16.01 3.81 42.53 4.08
1943 2401 2.234661 ACTGCAACACTCTAGCTATGCA 59.765 45.455 14.83 14.83 41.08 3.96
1944 2402 2.898705 ACTGCAACACTCTAGCTATGC 58.101 47.619 7.63 7.63 0.00 3.14
1992 2452 4.158579 TGATGGATGATCATCGTAGTAGCC 59.841 45.833 25.60 12.98 44.68 3.93
2065 2540 2.754658 CCGGCCGGACTAGTGAGT 60.755 66.667 41.82 0.00 39.20 3.41
2066 2541 3.528370 CCCGGCCGGACTAGTGAG 61.528 72.222 45.44 22.17 37.50 3.51
2088 2564 3.190118 GCTGAGTGACCAAAAGATTGAGG 59.810 47.826 0.00 0.00 38.94 3.86
2138 2616 2.185608 GCTGCGTCTTCTCCCCTC 59.814 66.667 0.00 0.00 0.00 4.30
2156 2634 1.066502 TGCCGCTGTACAGATAAAGCA 60.067 47.619 27.08 20.80 41.25 3.91
2161 2639 2.504920 AGCTGCCGCTGTACAGATA 58.495 52.632 27.08 7.72 46.86 1.98
2183 2661 5.310331 GGAGATCTACTACTGGTAGGTAGGT 59.690 48.000 11.73 7.46 45.78 3.08
2295 2773 6.374894 CCACTAGCACTAGAACTAACAGTACT 59.625 42.308 11.59 0.00 36.97 2.73
2296 2774 6.150809 ACCACTAGCACTAGAACTAACAGTAC 59.849 42.308 11.59 0.00 36.97 2.73
2332 2815 9.583765 CACAGATCATATCATCATGGTAACTAG 57.416 37.037 0.00 0.00 37.61 2.57
2341 2827 6.296803 ACAGCAACACAGATCATATCATCAT 58.703 36.000 0.00 0.00 0.00 2.45
2388 2874 0.819666 CTTTCTGCCCCGCCTAATCC 60.820 60.000 0.00 0.00 0.00 3.01
2389 2875 0.819666 CCTTTCTGCCCCGCCTAATC 60.820 60.000 0.00 0.00 0.00 1.75
2390 2876 1.227383 CCTTTCTGCCCCGCCTAAT 59.773 57.895 0.00 0.00 0.00 1.73
2391 2877 2.674754 CCTTTCTGCCCCGCCTAA 59.325 61.111 0.00 0.00 0.00 2.69
2392 2878 3.407967 CCCTTTCTGCCCCGCCTA 61.408 66.667 0.00 0.00 0.00 3.93
2394 2880 4.803908 CTCCCTTTCTGCCCCGCC 62.804 72.222 0.00 0.00 0.00 6.13
2395 2881 4.803908 CCTCCCTTTCTGCCCCGC 62.804 72.222 0.00 0.00 0.00 6.13
2396 2882 4.803908 GCCTCCCTTTCTGCCCCG 62.804 72.222 0.00 0.00 0.00 5.73
2397 2883 4.803908 CGCCTCCCTTTCTGCCCC 62.804 72.222 0.00 0.00 0.00 5.80
2528 3036 0.600255 CGAGAAAACAGAGCGGGTGT 60.600 55.000 0.00 0.00 0.00 4.16
2531 3039 2.391389 GCCGAGAAAACAGAGCGGG 61.391 63.158 0.00 0.00 42.09 6.13
2551 3059 3.717294 GTCCATGGACCACGGCCT 61.717 66.667 31.37 0.00 39.08 5.19
2586 3106 1.003928 AGGAAAGGACGCGGGTAAATT 59.996 47.619 12.47 0.15 0.00 1.82
2593 3113 0.458716 GAAGAGAGGAAAGGACGCGG 60.459 60.000 12.47 0.00 0.00 6.46
2594 3114 0.528470 AGAAGAGAGGAAAGGACGCG 59.472 55.000 3.53 3.53 0.00 6.01
2595 3115 2.753055 AAGAAGAGAGGAAAGGACGC 57.247 50.000 0.00 0.00 0.00 5.19
2596 3116 6.224584 ACTAAAAAGAAGAGAGGAAAGGACG 58.775 40.000 0.00 0.00 0.00 4.79
2597 3117 8.586744 TCTACTAAAAAGAAGAGAGGAAAGGAC 58.413 37.037 0.00 0.00 0.00 3.85
2598 3118 8.586744 GTCTACTAAAAAGAAGAGAGGAAAGGA 58.413 37.037 0.00 0.00 0.00 3.36
2606 3126 8.915036 ACTCTGTTGTCTACTAAAAAGAAGAGA 58.085 33.333 0.00 0.00 32.35 3.10
2639 3164 8.142551 AGGAAGTAAGTGTCAACTTTGTACTAG 58.857 37.037 0.00 0.00 44.47 2.57
2662 3187 5.981315 CGCTCTTACATTTATTTACGGAGGA 59.019 40.000 0.00 0.00 0.00 3.71
2667 3192 5.051907 AGCGTCGCTCTTACATTTATTTACG 60.052 40.000 15.47 0.00 30.62 3.18
2670 3195 4.494199 GCAGCGTCGCTCTTACATTTATTT 60.494 41.667 18.76 0.00 36.40 1.40
2671 3196 3.001330 GCAGCGTCGCTCTTACATTTATT 59.999 43.478 18.76 0.00 36.40 1.40
2672 3197 2.540101 GCAGCGTCGCTCTTACATTTAT 59.460 45.455 18.76 0.00 36.40 1.40
2673 3198 1.924524 GCAGCGTCGCTCTTACATTTA 59.075 47.619 18.76 0.00 36.40 1.40
2674 3199 0.721718 GCAGCGTCGCTCTTACATTT 59.278 50.000 18.76 0.00 36.40 2.32
2687 3277 5.292101 GTGTGAAGAAATATAAGAGCAGCGT 59.708 40.000 0.00 0.00 0.00 5.07
2688 3278 5.291858 TGTGTGAAGAAATATAAGAGCAGCG 59.708 40.000 0.00 0.00 0.00 5.18
2689 3279 6.238320 CCTGTGTGAAGAAATATAAGAGCAGC 60.238 42.308 0.00 0.00 0.00 5.25
2726 3344 6.044046 GGATCGTTGGTTGTGTGTGTATATA 58.956 40.000 0.00 0.00 0.00 0.86
2727 3345 4.873827 GGATCGTTGGTTGTGTGTGTATAT 59.126 41.667 0.00 0.00 0.00 0.86
2728 3346 4.020928 AGGATCGTTGGTTGTGTGTGTATA 60.021 41.667 0.00 0.00 0.00 1.47
2729 3347 3.071479 GGATCGTTGGTTGTGTGTGTAT 58.929 45.455 0.00 0.00 0.00 2.29
2730 3348 2.103432 AGGATCGTTGGTTGTGTGTGTA 59.897 45.455 0.00 0.00 0.00 2.90
2731 3349 1.134220 AGGATCGTTGGTTGTGTGTGT 60.134 47.619 0.00 0.00 0.00 3.72
2732 3350 1.264020 CAGGATCGTTGGTTGTGTGTG 59.736 52.381 0.00 0.00 0.00 3.82
2733 3351 1.593196 CAGGATCGTTGGTTGTGTGT 58.407 50.000 0.00 0.00 0.00 3.72
2734 3352 0.874390 CCAGGATCGTTGGTTGTGTG 59.126 55.000 6.70 0.00 0.00 3.82
2735 3353 0.889186 GCCAGGATCGTTGGTTGTGT 60.889 55.000 14.30 0.00 38.02 3.72
2736 3354 0.606401 AGCCAGGATCGTTGGTTGTG 60.606 55.000 14.30 0.00 38.02 3.33
2751 3369 2.876879 CGACGTGCGAACAAAGCCA 61.877 57.895 0.00 0.00 44.57 4.75
2843 3461 3.661648 GCCAAAGGGAGGGAGGCA 61.662 66.667 0.00 0.00 44.59 4.75
2844 3462 4.448976 GGCCAAAGGGAGGGAGGC 62.449 72.222 0.00 0.00 44.48 4.70
2845 3463 1.804530 AAAGGCCAAAGGGAGGGAGG 61.805 60.000 5.01 0.00 35.59 4.30
2876 3494 4.145756 CGTGTTTTCGAACAAGCCAATTAC 59.854 41.667 0.00 0.00 34.01 1.89
2880 3498 1.738350 TCGTGTTTTCGAACAAGCCAA 59.262 42.857 0.00 0.00 36.89 4.52
2882 3500 2.461897 TTCGTGTTTTCGAACAAGCC 57.538 45.000 0.00 0.00 43.36 4.35
2883 3501 3.165124 TGTTTCGTGTTTTCGAACAAGC 58.835 40.909 0.00 0.00 46.89 4.01
2884 3502 5.717491 GCTTTGTTTCGTGTTTTCGAACAAG 60.717 40.000 0.00 0.00 46.89 3.16
2887 3505 3.849708 AGCTTTGTTTCGTGTTTTCGAAC 59.150 39.130 0.00 0.00 46.89 3.95
2888 3506 3.849145 CAGCTTTGTTTCGTGTTTTCGAA 59.151 39.130 0.00 0.00 45.87 3.71
2890 3508 2.035756 GCAGCTTTGTTTCGTGTTTTCG 60.036 45.455 0.00 0.00 0.00 3.46
2907 3526 1.372087 CCATTTCTGGACTCGGCAGC 61.372 60.000 0.00 0.00 46.37 5.25
2948 3567 4.275936 ACCTGATTTTTCTCCTGTGAAACG 59.724 41.667 0.00 0.00 42.39 3.60
2973 3592 6.678409 GCAAACAGCACTAGTAGGAGTAGTAG 60.678 46.154 1.45 0.00 44.79 2.57
2978 3597 3.320673 GCAAACAGCACTAGTAGGAGT 57.679 47.619 1.45 0.00 44.79 3.85
2990 3609 0.110192 GCGTGGTCTAAGCAAACAGC 60.110 55.000 0.00 0.00 46.19 4.40
3034 3653 0.322187 GTACGTGGCCCACAAGGATT 60.322 55.000 15.45 0.00 38.24 3.01
3035 3654 1.298667 GTACGTGGCCCACAAGGAT 59.701 57.895 15.45 0.00 38.24 3.24
3036 3655 2.745037 GTACGTGGCCCACAAGGA 59.255 61.111 15.45 0.00 38.24 3.36
3037 3656 2.740826 CGTACGTGGCCCACAAGG 60.741 66.667 15.45 3.11 33.40 3.61
3038 3657 2.025418 GTCGTACGTGGCCCACAAG 61.025 63.158 15.45 0.38 33.40 3.16
3039 3658 2.029369 GTCGTACGTGGCCCACAA 59.971 61.111 15.45 0.00 33.40 3.33
3040 3659 4.345962 CGTCGTACGTGGCCCACA 62.346 66.667 15.45 0.00 36.74 4.17
3041 3660 3.556543 TTCGTCGTACGTGGCCCAC 62.557 63.158 16.05 2.98 43.14 4.61
3042 3661 2.157305 ATTTCGTCGTACGTGGCCCA 62.157 55.000 16.05 0.00 43.14 5.36
3043 3662 1.446618 ATTTCGTCGTACGTGGCCC 60.447 57.895 16.05 0.00 43.14 5.80
3044 3663 1.010419 ACATTTCGTCGTACGTGGCC 61.010 55.000 16.05 0.00 43.14 5.36
3045 3664 0.092351 CACATTTCGTCGTACGTGGC 59.908 55.000 16.05 6.20 43.14 5.01
3046 3665 1.411394 ACACATTTCGTCGTACGTGG 58.589 50.000 16.05 8.51 43.14 4.94
3047 3666 3.228749 AGTACACATTTCGTCGTACGTG 58.771 45.455 16.05 9.46 43.14 4.49
3048 3667 3.542712 AGTACACATTTCGTCGTACGT 57.457 42.857 16.05 0.00 43.14 3.57
3049 3668 4.641954 AGTAGTACACATTTCGTCGTACG 58.358 43.478 9.53 9.53 44.19 3.67
3050 3669 5.674580 GCTAGTAGTACACATTTCGTCGTAC 59.325 44.000 2.52 0.00 34.76 3.67
3051 3670 5.500771 CGCTAGTAGTACACATTTCGTCGTA 60.501 44.000 2.52 0.00 0.00 3.43
3052 3671 4.656041 GCTAGTAGTACACATTTCGTCGT 58.344 43.478 2.52 0.00 0.00 4.34
3053 3672 3.717890 CGCTAGTAGTACACATTTCGTCG 59.282 47.826 2.52 0.00 0.00 5.12
3054 3673 4.901814 TCGCTAGTAGTACACATTTCGTC 58.098 43.478 2.52 0.00 0.00 4.20
3055 3674 4.633126 TCTCGCTAGTAGTACACATTTCGT 59.367 41.667 2.52 0.00 0.00 3.85
3056 3675 5.152923 TCTCGCTAGTAGTACACATTTCG 57.847 43.478 2.52 0.00 0.00 3.46
3057 3676 6.418226 CCATTCTCGCTAGTAGTACACATTTC 59.582 42.308 2.52 0.00 0.00 2.17
3058 3677 6.127423 ACCATTCTCGCTAGTAGTACACATTT 60.127 38.462 2.52 0.00 0.00 2.32
3059 3678 5.360144 ACCATTCTCGCTAGTAGTACACATT 59.640 40.000 2.52 0.00 0.00 2.71
3060 3679 4.888239 ACCATTCTCGCTAGTAGTACACAT 59.112 41.667 2.52 0.00 0.00 3.21
3061 3680 4.267536 ACCATTCTCGCTAGTAGTACACA 58.732 43.478 2.52 0.00 0.00 3.72
3062 3681 4.261114 GGACCATTCTCGCTAGTAGTACAC 60.261 50.000 2.52 0.00 0.00 2.90
3063 3682 3.881688 GGACCATTCTCGCTAGTAGTACA 59.118 47.826 2.52 0.00 0.00 2.90
3064 3683 3.059051 CGGACCATTCTCGCTAGTAGTAC 60.059 52.174 0.00 0.00 0.00 2.73
3065 3684 3.136763 CGGACCATTCTCGCTAGTAGTA 58.863 50.000 0.00 0.00 0.00 1.82
3066 3685 1.948145 CGGACCATTCTCGCTAGTAGT 59.052 52.381 0.00 0.00 0.00 2.73
3067 3686 1.948145 ACGGACCATTCTCGCTAGTAG 59.052 52.381 0.00 0.00 0.00 2.57
3068 3687 1.945394 GACGGACCATTCTCGCTAGTA 59.055 52.381 0.00 0.00 0.00 1.82
3069 3688 0.739561 GACGGACCATTCTCGCTAGT 59.260 55.000 0.00 0.00 0.00 2.57
3070 3689 0.030908 GGACGGACCATTCTCGCTAG 59.969 60.000 0.00 0.00 38.79 3.42
3071 3690 0.395311 AGGACGGACCATTCTCGCTA 60.395 55.000 0.00 0.00 42.04 4.26
3072 3691 1.258445 AAGGACGGACCATTCTCGCT 61.258 55.000 0.00 0.00 42.04 4.93
3073 3692 1.084370 CAAGGACGGACCATTCTCGC 61.084 60.000 0.00 0.00 42.04 5.03
3074 3693 0.530744 TCAAGGACGGACCATTCTCG 59.469 55.000 0.00 0.00 42.04 4.04
3075 3694 1.550976 AGTCAAGGACGGACCATTCTC 59.449 52.381 0.00 0.00 42.04 2.87
3076 3695 1.645710 AGTCAAGGACGGACCATTCT 58.354 50.000 0.00 0.00 42.04 2.40
3077 3696 2.076863 CAAGTCAAGGACGGACCATTC 58.923 52.381 0.00 0.00 42.04 2.67
3078 3697 1.697432 TCAAGTCAAGGACGGACCATT 59.303 47.619 0.00 0.00 42.04 3.16
3079 3698 1.348064 TCAAGTCAAGGACGGACCAT 58.652 50.000 0.00 0.00 42.04 3.55
3080 3699 1.348064 ATCAAGTCAAGGACGGACCA 58.652 50.000 0.00 0.00 42.04 4.02
3081 3700 2.474410 AATCAAGTCAAGGACGGACC 57.526 50.000 0.00 0.00 37.67 4.46
3082 3701 5.875359 AGAAATAATCAAGTCAAGGACGGAC 59.125 40.000 0.00 0.00 37.67 4.79
3083 3702 5.874810 CAGAAATAATCAAGTCAAGGACGGA 59.125 40.000 0.00 0.00 37.67 4.69
3084 3703 5.065218 CCAGAAATAATCAAGTCAAGGACGG 59.935 44.000 0.00 0.00 37.67 4.79
3085 3704 5.065218 CCCAGAAATAATCAAGTCAAGGACG 59.935 44.000 0.00 0.00 37.67 4.79
3086 3705 6.180472 TCCCAGAAATAATCAAGTCAAGGAC 58.820 40.000 0.00 0.00 0.00 3.85
3087 3706 6.387192 TCCCAGAAATAATCAAGTCAAGGA 57.613 37.500 0.00 0.00 0.00 3.36
3088 3707 7.651027 AATCCCAGAAATAATCAAGTCAAGG 57.349 36.000 0.00 0.00 0.00 3.61
3089 3708 9.933723 AAAAATCCCAGAAATAATCAAGTCAAG 57.066 29.630 0.00 0.00 0.00 3.02
3118 3737 5.980964 CAACTTGATAGGTGGTCCTTTTGGA 60.981 44.000 0.00 0.00 42.12 3.53
3119 3738 4.034285 ACTTGATAGGTGGTCCTTTTGG 57.966 45.455 0.00 0.00 42.12 3.28
3120 3739 5.070001 TCAACTTGATAGGTGGTCCTTTTG 58.930 41.667 0.00 0.00 42.12 2.44
3121 3740 5.319043 TCAACTTGATAGGTGGTCCTTTT 57.681 39.130 0.00 0.00 42.12 2.27
3122 3741 4.993705 TCAACTTGATAGGTGGTCCTTT 57.006 40.909 0.00 0.00 42.12 3.11
3123 3742 4.993705 TTCAACTTGATAGGTGGTCCTT 57.006 40.909 0.00 0.00 42.12 3.36
3125 3744 5.010282 ACAATTCAACTTGATAGGTGGTCC 58.990 41.667 0.00 0.00 39.67 4.46
3126 3745 5.705441 TGACAATTCAACTTGATAGGTGGTC 59.295 40.000 0.00 0.00 39.67 4.02
3127 3746 5.630121 TGACAATTCAACTTGATAGGTGGT 58.370 37.500 0.00 0.00 39.67 4.16
3128 3747 6.573664 TTGACAATTCAACTTGATAGGTGG 57.426 37.500 0.00 0.00 39.67 4.61
3129 3748 8.870160 TTTTTGACAATTCAACTTGATAGGTG 57.130 30.769 0.00 0.00 41.64 4.00
3151 3770 7.556275 TCAATGTGTTTCAGAGGTAGTCTTTTT 59.444 33.333 0.00 0.00 30.64 1.94
3152 3771 7.012421 GTCAATGTGTTTCAGAGGTAGTCTTTT 59.988 37.037 0.00 0.00 30.64 2.27
3153 3772 6.483640 GTCAATGTGTTTCAGAGGTAGTCTTT 59.516 38.462 0.00 0.00 30.64 2.52
3154 3773 5.992217 GTCAATGTGTTTCAGAGGTAGTCTT 59.008 40.000 0.00 0.00 30.64 3.01
3155 3774 5.070446 TGTCAATGTGTTTCAGAGGTAGTCT 59.930 40.000 0.00 0.00 35.00 3.24
3156 3775 5.297547 TGTCAATGTGTTTCAGAGGTAGTC 58.702 41.667 0.00 0.00 0.00 2.59
3157 3776 5.290493 TGTCAATGTGTTTCAGAGGTAGT 57.710 39.130 0.00 0.00 0.00 2.73
3158 3777 6.618287 TTTGTCAATGTGTTTCAGAGGTAG 57.382 37.500 0.00 0.00 0.00 3.18
3159 3778 7.397892 TTTTTGTCAATGTGTTTCAGAGGTA 57.602 32.000 0.00 0.00 0.00 3.08
3160 3779 5.913137 TTTTGTCAATGTGTTTCAGAGGT 57.087 34.783 0.00 0.00 0.00 3.85
3180 3799 0.751643 ACGCTGCAGGTGGTCTTTTT 60.752 50.000 17.12 0.00 0.00 1.94
3181 3800 1.152963 ACGCTGCAGGTGGTCTTTT 60.153 52.632 17.12 0.00 0.00 2.27
3182 3801 1.893808 CACGCTGCAGGTGGTCTTT 60.894 57.895 17.12 0.00 0.00 2.52
3183 3802 2.281070 CACGCTGCAGGTGGTCTT 60.281 61.111 17.12 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.