Multiple sequence alignment - TraesCS5A01G143500

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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 TraesCS5A01G143500 chr5A 100.000 2805 0 0 1 2805 318816479 318813675 0.000000e+00 5180
1 TraesCS5A01G143500 chr5B 92.526 1619 84 18 317 1924 268497204 268495612 0.000000e+00 2285
2 TraesCS5A01G143500 chr5B 91.875 320 23 2 2 318 268497644 268497325 7.130000e-121 444
3 TraesCS5A01G143500 chr5D 94.262 610 23 5 775 1376 236448732 236449337 0.000000e+00 922
4 TraesCS5A01G143500 chr5D 86.228 806 70 23 1531 2326 236449806 236450580 0.000000e+00 835
5 TraesCS5A01G143500 chr5D 87.302 441 43 10 317 751 236448301 236448734 2.510000e-135 492
6 TraesCS5A01G143500 chr5D 91.148 305 25 1 16 318 236447879 236448183 2.010000e-111 412
7 TraesCS5A01G143500 chr5D 83.197 244 23 7 2374 2617 236450579 236450804 1.020000e-49 207


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 TraesCS5A01G143500 chr5A 318813675 318816479 2804 True 5180.0 5180 100.0000 1 2805 1 chr5A.!!$R1 2804
1 TraesCS5A01G143500 chr5B 268495612 268497644 2032 True 1364.5 2285 92.2005 2 1924 2 chr5B.!!$R1 1922
2 TraesCS5A01G143500 chr5D 236447879 236450804 2925 False 573.6 922 88.4274 16 2617 5 chr5D.!!$F1 2601

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
755 889 0.175302 AGATCTGTCGGCTGAAGCAG 59.825 55.0 0.0 1.22 44.36 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2544 3018 0.03438 AGACTACTACCGCTGCTCCA 60.034 55.0 0.0 0.0 0.0 3.86 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
100 101 0.600557 TACGGCCCTTGTTGCAATTG 59.399 50.000 0.59 0.00 0.00 2.32
291 294 2.034179 TCTCTTCTTCTCGTGTTCGCAA 59.966 45.455 0.00 0.00 36.96 4.85
307 310 0.240945 GCAACCAACCATGAACTCCG 59.759 55.000 0.00 0.00 0.00 4.63
310 313 2.046285 CCAACCATGAACTCCGGCC 61.046 63.158 0.00 0.00 0.00 6.13
311 314 1.303236 CAACCATGAACTCCGGCCA 60.303 57.895 2.24 0.00 0.00 5.36
327 374 2.357034 CACCACCACCGTCCTTCG 60.357 66.667 0.00 0.00 39.52 3.79
501 626 1.401409 CGGCGTTTCTGCAACATCATT 60.401 47.619 0.00 0.00 34.68 2.57
642 770 3.126000 GGTTTCTGCAACATGAGCTCTAC 59.874 47.826 16.19 0.00 37.07 2.59
693 827 6.337356 TGTTACAATGCTGAAGACGATGATA 58.663 36.000 0.00 0.00 0.00 2.15
711 845 1.676746 TAGCGTCAGATCTAACGGCT 58.323 50.000 19.81 17.71 39.24 5.52
712 846 1.676746 AGCGTCAGATCTAACGGCTA 58.323 50.000 19.81 0.00 39.24 3.93
713 847 1.334243 AGCGTCAGATCTAACGGCTAC 59.666 52.381 19.81 3.22 39.24 3.58
755 889 0.175302 AGATCTGTCGGCTGAAGCAG 59.825 55.000 0.00 1.22 44.36 4.24
763 897 2.968206 GCTGAAGCAGGCCCAAAG 59.032 61.111 0.00 0.00 41.59 2.77
791 925 1.750399 GTGATCGGGCATTGCAGGT 60.750 57.895 11.39 0.00 0.00 4.00
792 926 1.451927 TGATCGGGCATTGCAGGTC 60.452 57.895 11.39 9.97 0.00 3.85
793 927 1.153086 GATCGGGCATTGCAGGTCT 60.153 57.895 11.39 0.00 0.00 3.85
802 936 2.734492 GCATTGCAGGTCTTCTTCATGC 60.734 50.000 3.15 0.00 37.40 4.06
815 949 2.094390 TCTTCATGCTTGAATTGGCTGC 60.094 45.455 14.72 0.00 40.95 5.25
994 1133 6.875726 CGGATCATTAGATTAGAAAGCCATCA 59.124 38.462 0.00 0.00 33.72 3.07
995 1134 7.551974 CGGATCATTAGATTAGAAAGCCATCAT 59.448 37.037 0.00 0.00 33.72 2.45
1020 1165 4.748857 GCCATGGATGATCATCAAGAGGAA 60.749 45.833 31.49 11.92 39.54 3.36
1077 1222 0.685458 GCCCCTACGTCCTCAAGGTA 60.685 60.000 0.00 0.00 36.34 3.08
1079 1224 2.181975 CCCCTACGTCCTCAAGGTAAA 58.818 52.381 0.00 0.00 36.34 2.01
1086 1231 2.618045 CGTCCTCAAGGTAAAATGGGCT 60.618 50.000 0.00 0.00 36.34 5.19
1089 1234 3.054361 TCCTCAAGGTAAAATGGGCTCTC 60.054 47.826 0.00 0.00 36.34 3.20
1144 1289 0.390472 GGACCTGAGGAACAAGAGCG 60.390 60.000 4.99 0.00 0.00 5.03
1384 1529 2.484264 CTGTTCCCAAGTTCGATCCAAC 59.516 50.000 0.00 0.00 0.00 3.77
1399 1544 1.955778 TCCAACTCGGTTAGTTCGTCA 59.044 47.619 0.00 0.00 45.64 4.35
1433 1580 7.316640 ACGATCTGACTGAGCAATATATTACC 58.683 38.462 0.00 0.00 0.00 2.85
1434 1581 7.039714 ACGATCTGACTGAGCAATATATTACCA 60.040 37.037 0.00 0.00 0.00 3.25
1550 2015 3.672295 CTGGAGGACTTGCTCGCCC 62.672 68.421 0.00 0.00 0.00 6.13
1658 2123 1.456196 GGAGATCATCGGCGTGAGGA 61.456 60.000 6.85 0.00 42.40 3.71
1780 2245 4.530857 AGGTACCGAGCCATGCGC 62.531 66.667 6.18 0.00 37.98 6.09
1805 2270 2.019984 CCTTTCTGAACATGGGCTAGC 58.980 52.381 6.04 6.04 0.00 3.42
1812 2277 2.019984 GAACATGGGCTAGCTCAAAGG 58.980 52.381 23.69 16.43 0.00 3.11
1829 2294 4.343581 GCACTGTCTGCGTCTTCA 57.656 55.556 0.00 0.00 35.72 3.02
1830 2295 2.148687 GCACTGTCTGCGTCTTCAG 58.851 57.895 0.00 0.00 35.72 3.02
1831 2296 0.598680 GCACTGTCTGCGTCTTCAGT 60.599 55.000 0.00 0.00 41.02 3.41
1833 2298 2.862530 GCACTGTCTGCGTCTTCAGTTA 60.863 50.000 0.00 0.00 38.79 2.24
1839 2304 5.961272 TGTCTGCGTCTTCAGTTATGATTA 58.039 37.500 0.00 0.00 34.73 1.75
1840 2305 6.394809 TGTCTGCGTCTTCAGTTATGATTAA 58.605 36.000 0.00 0.00 34.73 1.40
1842 2307 7.063426 TGTCTGCGTCTTCAGTTATGATTAAAG 59.937 37.037 0.00 0.00 34.73 1.85
1927 2400 1.608055 TGGTCCAGTGCATCTTTGTG 58.392 50.000 0.00 0.00 0.00 3.33
1951 2424 7.279981 GTGTTTACATGGCTTGTACTATGATCA 59.720 37.037 12.28 0.00 40.53 2.92
1983 2456 6.903883 ATAAATGAGACACGTATTCACCAC 57.096 37.500 0.00 0.00 0.00 4.16
1985 2458 3.021269 TGAGACACGTATTCACCACAC 57.979 47.619 0.00 0.00 0.00 3.82
1988 2461 3.390135 AGACACGTATTCACCACACAAG 58.610 45.455 0.00 0.00 0.00 3.16
1990 2463 3.799366 ACACGTATTCACCACACAAGAA 58.201 40.909 0.00 0.00 0.00 2.52
1991 2464 4.193090 ACACGTATTCACCACACAAGAAA 58.807 39.130 0.00 0.00 0.00 2.52
1993 2466 5.298276 ACACGTATTCACCACACAAGAAAAT 59.702 36.000 0.00 0.00 0.00 1.82
1994 2467 5.624900 CACGTATTCACCACACAAGAAAATG 59.375 40.000 0.00 0.00 0.00 2.32
1995 2468 5.529430 ACGTATTCACCACACAAGAAAATGA 59.471 36.000 0.00 0.00 0.00 2.57
1996 2469 5.851177 CGTATTCACCACACAAGAAAATGAC 59.149 40.000 0.00 0.00 0.00 3.06
1997 2470 6.293407 CGTATTCACCACACAAGAAAATGACT 60.293 38.462 0.00 0.00 0.00 3.41
1998 2471 5.499139 TTCACCACACAAGAAAATGACTC 57.501 39.130 0.00 0.00 0.00 3.36
1999 2472 4.780815 TCACCACACAAGAAAATGACTCT 58.219 39.130 0.00 0.00 0.00 3.24
2000 2473 5.192927 TCACCACACAAGAAAATGACTCTT 58.807 37.500 0.00 0.00 33.31 2.85
2026 2499 8.359642 TGTTTCCGATGAAATTTCAGAAATTCT 58.640 29.630 24.91 11.12 42.20 2.40
2036 2509 8.970691 AAATTTCAGAAATTCTAATCACCACG 57.029 30.769 19.41 0.00 40.05 4.94
2038 2511 3.938963 TCAGAAATTCTAATCACCACGGC 59.061 43.478 0.00 0.00 0.00 5.68
2041 2514 2.332063 ATTCTAATCACCACGGCAGG 57.668 50.000 0.00 0.00 0.00 4.85
2044 2517 1.479323 TCTAATCACCACGGCAGGTAC 59.521 52.381 0.00 0.00 40.77 3.34
2062 2535 5.118664 CAGGTACCGAATATACGCATTTCAG 59.881 44.000 6.18 0.00 0.00 3.02
2066 2539 3.363970 CCGAATATACGCATTTCAGGCAC 60.364 47.826 0.00 0.00 0.00 5.01
2077 2550 5.278414 CGCATTTCAGGCACAATATTATGGA 60.278 40.000 0.00 0.00 0.00 3.41
2118 2591 9.447157 TCAGATTTCAACAGAAACCAAATTTTT 57.553 25.926 0.00 0.00 34.36 1.94
2119 2592 9.493206 CAGATTTCAACAGAAACCAAATTTTTG 57.507 29.630 0.00 0.00 38.17 2.44
2126 2600 1.213491 AACCAAATTTTTGACGCGGC 58.787 45.000 12.47 8.67 40.55 6.53
2127 2601 0.387565 ACCAAATTTTTGACGCGGCT 59.612 45.000 15.80 0.00 40.55 5.52
2145 2619 3.181490 CGGCTACTCTGCAACTACATGTA 60.181 47.826 5.25 5.25 34.04 2.29
2151 2625 7.653713 GCTACTCTGCAACTACATGTATATTGT 59.346 37.037 21.88 9.72 0.00 2.71
2152 2626 9.186323 CTACTCTGCAACTACATGTATATTGTC 57.814 37.037 21.88 16.88 0.00 3.18
2153 2627 7.555965 ACTCTGCAACTACATGTATATTGTCA 58.444 34.615 21.88 19.10 0.00 3.58
2174 2648 7.322664 TGTCATCATTGGAAAAAGAAATAGCC 58.677 34.615 0.00 0.00 0.00 3.93
2175 2649 6.758416 GTCATCATTGGAAAAAGAAATAGCCC 59.242 38.462 0.00 0.00 0.00 5.19
2176 2650 6.669154 TCATCATTGGAAAAAGAAATAGCCCT 59.331 34.615 0.00 0.00 0.00 5.19
2177 2651 6.284891 TCATTGGAAAAAGAAATAGCCCTG 57.715 37.500 0.00 0.00 0.00 4.45
2178 2652 5.779771 TCATTGGAAAAAGAAATAGCCCTGT 59.220 36.000 0.00 0.00 0.00 4.00
2179 2653 5.467035 TTGGAAAAAGAAATAGCCCTGTG 57.533 39.130 0.00 0.00 0.00 3.66
2180 2654 4.735369 TGGAAAAAGAAATAGCCCTGTGA 58.265 39.130 0.00 0.00 0.00 3.58
2181 2655 4.522789 TGGAAAAAGAAATAGCCCTGTGAC 59.477 41.667 0.00 0.00 0.00 3.67
2182 2656 4.522789 GGAAAAAGAAATAGCCCTGTGACA 59.477 41.667 0.00 0.00 0.00 3.58
2183 2657 5.185828 GGAAAAAGAAATAGCCCTGTGACAT 59.814 40.000 0.00 0.00 0.00 3.06
2223 2697 6.328641 ACTCGTGTAAGAACATCTACAACT 57.671 37.500 0.00 0.00 38.08 3.16
2224 2698 6.150318 ACTCGTGTAAGAACATCTACAACTG 58.850 40.000 0.00 0.00 38.08 3.16
2225 2699 6.016527 ACTCGTGTAAGAACATCTACAACTGA 60.017 38.462 0.00 0.00 38.08 3.41
2231 2705 8.988934 TGTAAGAACATCTACAACTGAAATGTC 58.011 33.333 0.00 0.00 30.56 3.06
2240 2714 8.335532 TCTACAACTGAAATGTCCTAATTTGG 57.664 34.615 0.00 0.00 29.89 3.28
2254 2728 0.400594 ATTTGGGCCCTATAGCGTCC 59.599 55.000 25.70 0.74 0.00 4.79
2258 2732 1.408453 GGGCCCTATAGCGTCCAGTT 61.408 60.000 17.04 0.00 0.00 3.16
2273 2747 2.642311 TCCAGTTACCTCTCATTTGGCA 59.358 45.455 0.00 0.00 0.00 4.92
2275 2749 3.191371 CCAGTTACCTCTCATTTGGCAAC 59.809 47.826 0.00 0.00 31.54 4.17
2277 2751 2.812011 GTTACCTCTCATTTGGCAACGT 59.188 45.455 0.00 0.00 42.51 3.99
2279 2753 0.804989 CCTCTCATTTGGCAACGTCC 59.195 55.000 0.00 0.00 42.51 4.79
2280 2754 1.522668 CTCTCATTTGGCAACGTCCA 58.477 50.000 0.00 0.00 42.51 4.02
2282 2756 0.950836 CTCATTTGGCAACGTCCACA 59.049 50.000 0.00 0.00 42.51 4.17
2283 2757 0.950836 TCATTTGGCAACGTCCACAG 59.049 50.000 0.00 0.00 42.51 3.66
2284 2758 0.664166 CATTTGGCAACGTCCACAGC 60.664 55.000 0.00 0.00 42.51 4.40
2288 2762 3.712881 GCAACGTCCACAGCCGTC 61.713 66.667 0.00 0.00 36.04 4.79
2289 2763 3.041940 CAACGTCCACAGCCGTCC 61.042 66.667 0.00 0.00 36.04 4.79
2290 2764 4.309950 AACGTCCACAGCCGTCCC 62.310 66.667 0.00 0.00 36.04 4.46
2300 2774 0.613777 CAGCCGTCCCCCTTATATCC 59.386 60.000 0.00 0.00 0.00 2.59
2301 2775 0.903454 AGCCGTCCCCCTTATATCCG 60.903 60.000 0.00 0.00 0.00 4.18
2326 2800 3.569491 CTCTAAATCCATGCAACCCCAT 58.431 45.455 0.00 0.00 0.00 4.00
2327 2801 3.298619 TCTAAATCCATGCAACCCCATG 58.701 45.455 0.00 0.00 41.71 3.66
2328 2802 0.542805 AAATCCATGCAACCCCATGC 59.457 50.000 0.00 0.00 46.58 4.06
2336 2810 4.424711 AACCCCATGCGGCGTGAT 62.425 61.111 23.18 5.81 0.00 3.06
2337 2811 4.856801 ACCCCATGCGGCGTGATC 62.857 66.667 23.18 0.00 0.00 2.92
2338 2812 4.854924 CCCCATGCGGCGTGATCA 62.855 66.667 23.18 0.00 0.00 2.92
2339 2813 2.823593 CCCATGCGGCGTGATCAA 60.824 61.111 23.18 0.00 0.00 2.57
2340 2814 2.405805 CCCATGCGGCGTGATCAAA 61.406 57.895 23.18 0.00 0.00 2.69
2341 2815 1.505807 CCATGCGGCGTGATCAAAA 59.494 52.632 23.18 0.00 0.00 2.44
2342 2816 0.101040 CCATGCGGCGTGATCAAAAT 59.899 50.000 23.18 0.00 0.00 1.82
2343 2817 1.333308 CCATGCGGCGTGATCAAAATA 59.667 47.619 23.18 0.00 0.00 1.40
2344 2818 2.602933 CCATGCGGCGTGATCAAAATAG 60.603 50.000 23.18 0.00 0.00 1.73
2345 2819 0.376852 TGCGGCGTGATCAAAATAGC 59.623 50.000 9.37 0.55 0.00 2.97
2346 2820 0.376852 GCGGCGTGATCAAAATAGCA 59.623 50.000 9.37 0.00 0.00 3.49
2347 2821 1.856014 GCGGCGTGATCAAAATAGCAC 60.856 52.381 9.37 0.00 0.00 4.40
2348 2822 1.396648 CGGCGTGATCAAAATAGCACA 59.603 47.619 0.00 0.00 0.00 4.57
2349 2823 2.032054 CGGCGTGATCAAAATAGCACAT 59.968 45.455 0.00 0.00 0.00 3.21
2350 2824 3.247411 CGGCGTGATCAAAATAGCACATA 59.753 43.478 0.00 0.00 0.00 2.29
2351 2825 4.609113 CGGCGTGATCAAAATAGCACATAG 60.609 45.833 0.00 0.00 0.00 2.23
2352 2826 4.511454 GGCGTGATCAAAATAGCACATAGA 59.489 41.667 0.00 0.00 0.00 1.98
2353 2827 5.180117 GGCGTGATCAAAATAGCACATAGAT 59.820 40.000 0.00 0.00 0.00 1.98
2354 2828 6.368791 GGCGTGATCAAAATAGCACATAGATA 59.631 38.462 0.00 0.00 0.00 1.98
2355 2829 7.095229 GGCGTGATCAAAATAGCACATAGATAA 60.095 37.037 0.00 0.00 0.00 1.75
2356 2830 8.446273 GCGTGATCAAAATAGCACATAGATAAT 58.554 33.333 0.00 0.00 0.00 1.28
2367 2841 9.910267 ATAGCACATAGATAATTCAATATGGCA 57.090 29.630 0.00 0.00 31.34 4.92
2368 2842 8.818622 AGCACATAGATAATTCAATATGGCAT 57.181 30.769 4.88 4.88 31.34 4.40
2369 2843 9.910267 AGCACATAGATAATTCAATATGGCATA 57.090 29.630 10.07 10.07 31.34 3.14
2380 2854 7.933215 TTCAATATGGCATAGATCAGATTGG 57.067 36.000 13.39 0.00 40.73 3.16
2381 2855 7.261688 TCAATATGGCATAGATCAGATTGGA 57.738 36.000 13.39 0.00 40.73 3.53
2389 2863 5.581479 GCATAGATCAGATTGGACATAGCAG 59.419 44.000 0.00 0.00 0.00 4.24
2390 2864 6.573876 GCATAGATCAGATTGGACATAGCAGA 60.574 42.308 0.00 0.00 0.00 4.26
2401 2875 8.757982 ATTGGACATAGCAGAGTTCAATTTAT 57.242 30.769 3.85 0.00 40.19 1.40
2415 2889 4.242475 TCAATTTATAGCCGGACATAGCG 58.758 43.478 5.05 0.00 0.00 4.26
2417 2891 2.717580 TTATAGCCGGACATAGCGTG 57.282 50.000 5.05 0.00 0.00 5.34
2418 2892 0.242825 TATAGCCGGACATAGCGTGC 59.757 55.000 5.05 0.00 0.00 5.34
2427 2901 1.059264 GACATAGCGTGCGAAGTTCAC 59.941 52.381 3.32 0.00 0.00 3.18
2469 2943 9.734620 GCATAGCATATTCACAAAAGTTTATCA 57.265 29.630 0.00 0.00 0.00 2.15
2495 2969 7.171630 ACGATACATAAATTAGAGCTAGGGG 57.828 40.000 0.00 0.00 0.00 4.79
2497 2971 6.154706 CGATACATAAATTAGAGCTAGGGGGT 59.845 42.308 0.00 0.00 0.00 4.95
2498 2972 5.568620 ACATAAATTAGAGCTAGGGGGTG 57.431 43.478 0.00 0.00 0.00 4.61
2499 2973 4.202472 ACATAAATTAGAGCTAGGGGGTGC 60.202 45.833 0.00 0.00 0.00 5.01
2500 2974 1.141185 AATTAGAGCTAGGGGGTGCC 58.859 55.000 0.00 0.00 0.00 5.01
2501 2975 1.122019 ATTAGAGCTAGGGGGTGCCG 61.122 60.000 0.00 0.00 0.00 5.69
2502 2976 3.751049 TAGAGCTAGGGGGTGCCGG 62.751 68.421 0.00 0.00 0.00 6.13
2504 2978 4.499116 AGCTAGGGGGTGCCGGAT 62.499 66.667 5.05 0.00 0.00 4.18
2505 2979 3.489513 GCTAGGGGGTGCCGGATT 61.490 66.667 5.05 0.00 0.00 3.01
2538 3012 3.628646 CTGGTCCCTTCCCCTTGCG 62.629 68.421 0.00 0.00 0.00 4.85
2541 3015 3.327404 TCCCTTCCCCTTGCGGTC 61.327 66.667 0.00 0.00 0.00 4.79
2544 3018 1.074951 CCTTCCCCTTGCGGTCTTT 59.925 57.895 0.00 0.00 0.00 2.52
2557 3031 0.741221 GGTCTTTGGAGCAGCGGTAG 60.741 60.000 0.00 0.00 39.51 3.18
2567 3041 0.731417 GCAGCGGTAGTAGTCTTCGA 59.269 55.000 0.00 0.00 0.00 3.71
2569 3043 1.005340 AGCGGTAGTAGTCTTCGACG 58.995 55.000 0.00 0.00 37.67 5.12
2570 3044 0.723981 GCGGTAGTAGTCTTCGACGT 59.276 55.000 0.00 0.00 37.67 4.34
2571 3045 1.927174 GCGGTAGTAGTCTTCGACGTA 59.073 52.381 0.00 0.00 37.67 3.57
2572 3046 2.285313 GCGGTAGTAGTCTTCGACGTAC 60.285 54.545 0.00 0.00 37.67 3.67
2573 3047 2.923655 CGGTAGTAGTCTTCGACGTACA 59.076 50.000 0.00 0.00 37.67 2.90
2574 3048 3.241804 CGGTAGTAGTCTTCGACGTACAC 60.242 52.174 0.00 0.00 37.67 2.90
2575 3049 3.679980 GGTAGTAGTCTTCGACGTACACA 59.320 47.826 0.00 0.00 37.67 3.72
2576 3050 4.331168 GGTAGTAGTCTTCGACGTACACAT 59.669 45.833 0.00 0.00 37.67 3.21
2577 3051 4.596801 AGTAGTCTTCGACGTACACATC 57.403 45.455 0.00 0.00 37.67 3.06
2578 3052 2.522372 AGTCTTCGACGTACACATCG 57.478 50.000 5.12 5.12 37.67 3.84
2579 3053 1.129998 AGTCTTCGACGTACACATCGG 59.870 52.381 10.28 0.00 38.86 4.18
2580 3054 1.135859 GTCTTCGACGTACACATCGGT 60.136 52.381 10.28 0.00 38.86 4.69
2602 3076 1.763968 ACGGAGAGGAATCGTCATCA 58.236 50.000 5.72 0.00 37.02 3.07
2603 3077 2.311463 ACGGAGAGGAATCGTCATCAT 58.689 47.619 5.72 0.00 37.02 2.45
2608 3082 2.952310 AGAGGAATCGTCATCATCGTCA 59.048 45.455 5.72 0.00 37.02 4.35
2617 3091 2.413112 GTCATCATCGTCAGTGGTTGTG 59.587 50.000 0.00 0.00 0.00 3.33
2618 3092 1.129251 CATCATCGTCAGTGGTTGTGC 59.871 52.381 0.00 0.00 0.00 4.57
2619 3093 0.602638 TCATCGTCAGTGGTTGTGCC 60.603 55.000 0.00 0.00 37.90 5.01
2620 3094 1.667830 ATCGTCAGTGGTTGTGCCG 60.668 57.895 0.00 0.00 41.21 5.69
2621 3095 2.377628 ATCGTCAGTGGTTGTGCCGT 62.378 55.000 0.00 0.00 41.21 5.68
2622 3096 2.177580 CGTCAGTGGTTGTGCCGTT 61.178 57.895 0.00 0.00 41.21 4.44
2623 3097 1.355210 GTCAGTGGTTGTGCCGTTG 59.645 57.895 0.00 0.00 41.21 4.10
2624 3098 1.078072 TCAGTGGTTGTGCCGTTGT 60.078 52.632 0.00 0.00 41.21 3.32
2625 3099 1.092921 TCAGTGGTTGTGCCGTTGTC 61.093 55.000 0.00 0.00 41.21 3.18
2626 3100 2.177580 AGTGGTTGTGCCGTTGTCG 61.178 57.895 0.00 0.00 41.21 4.35
2636 3110 4.814900 CGTTGTCGGATGAGGGAG 57.185 61.111 0.00 0.00 0.00 4.30
2637 3111 2.189833 CGTTGTCGGATGAGGGAGA 58.810 57.895 0.00 0.00 0.00 3.71
2638 3112 0.101399 CGTTGTCGGATGAGGGAGAG 59.899 60.000 0.00 0.00 0.00 3.20
2639 3113 0.461961 GTTGTCGGATGAGGGAGAGG 59.538 60.000 0.00 0.00 0.00 3.69
2640 3114 0.335019 TTGTCGGATGAGGGAGAGGA 59.665 55.000 0.00 0.00 0.00 3.71
2641 3115 0.335019 TGTCGGATGAGGGAGAGGAA 59.665 55.000 0.00 0.00 0.00 3.36
2642 3116 0.747852 GTCGGATGAGGGAGAGGAAC 59.252 60.000 0.00 0.00 0.00 3.62
2643 3117 0.752009 TCGGATGAGGGAGAGGAACG 60.752 60.000 0.00 0.00 0.00 3.95
2644 3118 1.739338 CGGATGAGGGAGAGGAACGG 61.739 65.000 0.00 0.00 0.00 4.44
2645 3119 0.397254 GGATGAGGGAGAGGAACGGA 60.397 60.000 0.00 0.00 0.00 4.69
2646 3120 1.710816 GATGAGGGAGAGGAACGGAT 58.289 55.000 0.00 0.00 0.00 4.18
2647 3121 1.616374 GATGAGGGAGAGGAACGGATC 59.384 57.143 0.00 0.00 0.00 3.36
2659 3133 2.505982 CGGATCCCGGCTTGACAT 59.494 61.111 6.06 0.00 44.15 3.06
2660 3134 1.595382 CGGATCCCGGCTTGACATC 60.595 63.158 6.06 0.00 44.15 3.06
2661 3135 1.595382 GGATCCCGGCTTGACATCG 60.595 63.158 0.00 0.00 0.00 3.84
2662 3136 1.595382 GATCCCGGCTTGACATCGG 60.595 63.158 0.00 0.00 43.05 4.18
2667 3141 4.778143 GGCTTGACATCGGGCCGT 62.778 66.667 27.32 10.72 35.08 5.68
2668 3142 3.499737 GCTTGACATCGGGCCGTG 61.500 66.667 27.32 23.82 0.00 4.94
2669 3143 2.264480 CTTGACATCGGGCCGTGA 59.736 61.111 27.32 8.03 0.00 4.35
2670 3144 1.811266 CTTGACATCGGGCCGTGAG 60.811 63.158 27.32 18.52 0.00 3.51
2691 3165 4.394712 CGAGGTGGGCGGCTTTCT 62.395 66.667 9.56 3.43 0.00 2.52
2692 3166 2.436824 GAGGTGGGCGGCTTTCTC 60.437 66.667 9.56 9.38 0.00 2.87
2693 3167 3.978571 GAGGTGGGCGGCTTTCTCC 62.979 68.421 9.56 2.66 0.00 3.71
2703 3177 3.494336 CTTTCTCCGCGGCAGCTG 61.494 66.667 23.51 10.11 42.32 4.24
2714 3188 3.588336 GCAGCTGCCTTCTCCTTG 58.412 61.111 28.76 0.00 34.31 3.61
2715 3189 2.045131 GCAGCTGCCTTCTCCTTGG 61.045 63.158 28.76 0.00 34.31 3.61
2723 3197 2.795231 CCTTCTCCTTGGCAATCAGA 57.205 50.000 0.00 2.03 0.00 3.27
2724 3198 2.363683 CCTTCTCCTTGGCAATCAGAC 58.636 52.381 0.00 0.00 0.00 3.51
2725 3199 2.363683 CTTCTCCTTGGCAATCAGACC 58.636 52.381 0.00 0.00 0.00 3.85
2726 3200 1.361204 TCTCCTTGGCAATCAGACCA 58.639 50.000 0.00 0.00 0.00 4.02
2727 3201 1.003580 TCTCCTTGGCAATCAGACCAC 59.996 52.381 0.00 0.00 35.10 4.16
2728 3202 0.038166 TCCTTGGCAATCAGACCACC 59.962 55.000 0.00 0.00 35.10 4.61
2729 3203 0.038744 CCTTGGCAATCAGACCACCT 59.961 55.000 0.00 0.00 35.10 4.00
2730 3204 1.548582 CCTTGGCAATCAGACCACCTT 60.549 52.381 0.00 0.00 35.10 3.50
2731 3205 1.815003 CTTGGCAATCAGACCACCTTC 59.185 52.381 0.00 0.00 35.10 3.46
2732 3206 0.321564 TGGCAATCAGACCACCTTCG 60.322 55.000 0.00 0.00 0.00 3.79
2733 3207 1.648467 GGCAATCAGACCACCTTCGC 61.648 60.000 0.00 0.00 0.00 4.70
2734 3208 0.955428 GCAATCAGACCACCTTCGCA 60.955 55.000 0.00 0.00 0.00 5.10
2735 3209 1.742761 CAATCAGACCACCTTCGCAT 58.257 50.000 0.00 0.00 0.00 4.73
2736 3210 2.086869 CAATCAGACCACCTTCGCATT 58.913 47.619 0.00 0.00 0.00 3.56
2737 3211 2.489329 CAATCAGACCACCTTCGCATTT 59.511 45.455 0.00 0.00 0.00 2.32
2738 3212 2.270352 TCAGACCACCTTCGCATTTT 57.730 45.000 0.00 0.00 0.00 1.82
2739 3213 1.879380 TCAGACCACCTTCGCATTTTG 59.121 47.619 0.00 0.00 0.00 2.44
2740 3214 1.608590 CAGACCACCTTCGCATTTTGT 59.391 47.619 0.00 0.00 0.00 2.83
2741 3215 1.880027 AGACCACCTTCGCATTTTGTC 59.120 47.619 0.00 0.00 0.00 3.18
2742 3216 0.591170 ACCACCTTCGCATTTTGTCG 59.409 50.000 0.00 0.00 0.00 4.35
2743 3217 0.591170 CCACCTTCGCATTTTGTCGT 59.409 50.000 0.00 0.00 0.00 4.34
2744 3218 1.399727 CCACCTTCGCATTTTGTCGTC 60.400 52.381 0.00 0.00 0.00 4.20
2745 3219 0.511221 ACCTTCGCATTTTGTCGTCG 59.489 50.000 0.00 0.00 0.00 5.12
2746 3220 0.787787 CCTTCGCATTTTGTCGTCGA 59.212 50.000 0.00 0.00 0.00 4.20
2747 3221 1.461888 CCTTCGCATTTTGTCGTCGAC 60.462 52.381 18.51 18.51 0.00 4.20
2748 3222 0.159973 TTCGCATTTTGTCGTCGACG 59.840 50.000 31.30 31.30 41.45 5.12
2769 3243 4.554036 GGGGGCATCTGTCTCCGC 62.554 72.222 0.00 0.00 26.17 5.54
2770 3244 4.554036 GGGGCATCTGTCTCCGCC 62.554 72.222 0.00 0.00 44.10 6.13
2771 3245 4.899239 GGGCATCTGTCTCCGCCG 62.899 72.222 0.00 0.00 45.85 6.46
2772 3246 3.838271 GGCATCTGTCTCCGCCGA 61.838 66.667 0.00 0.00 34.26 5.54
2773 3247 2.583593 GCATCTGTCTCCGCCGAC 60.584 66.667 0.00 0.00 34.52 4.79
2774 3248 2.885113 CATCTGTCTCCGCCGACA 59.115 61.111 5.16 5.16 41.33 4.35
2775 3249 1.439228 CATCTGTCTCCGCCGACAT 59.561 57.895 5.63 0.00 42.51 3.06
2776 3250 0.873312 CATCTGTCTCCGCCGACATG 60.873 60.000 5.63 0.00 42.51 3.21
2777 3251 1.037579 ATCTGTCTCCGCCGACATGA 61.038 55.000 0.00 6.32 42.51 3.07
2778 3252 1.215382 CTGTCTCCGCCGACATGAA 59.785 57.895 0.00 0.00 42.51 2.57
2779 3253 0.803768 CTGTCTCCGCCGACATGAAG 60.804 60.000 0.00 0.00 42.51 3.02
2780 3254 1.519455 GTCTCCGCCGACATGAAGG 60.519 63.158 0.00 2.96 34.11 3.46
2781 3255 1.680989 TCTCCGCCGACATGAAGGA 60.681 57.895 13.84 7.15 0.00 3.36
2782 3256 1.227089 CTCCGCCGACATGAAGGAG 60.227 63.158 13.84 11.95 41.91 3.69
2783 3257 1.949847 CTCCGCCGACATGAAGGAGT 61.950 60.000 13.84 0.00 42.48 3.85
2784 3258 1.811266 CCGCCGACATGAAGGAGTG 60.811 63.158 13.84 4.27 0.00 3.51
2785 3259 1.811266 CGCCGACATGAAGGAGTGG 60.811 63.158 13.84 0.17 0.00 4.00
2786 3260 1.596934 GCCGACATGAAGGAGTGGA 59.403 57.895 13.84 0.00 0.00 4.02
2787 3261 0.460987 GCCGACATGAAGGAGTGGAG 60.461 60.000 13.84 0.00 0.00 3.86
2788 3262 0.176680 CCGACATGAAGGAGTGGAGG 59.823 60.000 0.00 0.00 0.00 4.30
2789 3263 1.186200 CGACATGAAGGAGTGGAGGA 58.814 55.000 0.00 0.00 0.00 3.71
2790 3264 1.759445 CGACATGAAGGAGTGGAGGAT 59.241 52.381 0.00 0.00 0.00 3.24
2791 3265 2.482664 CGACATGAAGGAGTGGAGGATG 60.483 54.545 0.00 0.00 0.00 3.51
2792 3266 2.768527 GACATGAAGGAGTGGAGGATGA 59.231 50.000 0.00 0.00 0.00 2.92
2793 3267 2.503356 ACATGAAGGAGTGGAGGATGAC 59.497 50.000 0.00 0.00 0.00 3.06
2794 3268 1.186200 TGAAGGAGTGGAGGATGACG 58.814 55.000 0.00 0.00 0.00 4.35
2795 3269 1.187087 GAAGGAGTGGAGGATGACGT 58.813 55.000 0.00 0.00 0.00 4.34
2796 3270 2.291346 TGAAGGAGTGGAGGATGACGTA 60.291 50.000 0.00 0.00 0.00 3.57
2797 3271 2.060050 AGGAGTGGAGGATGACGTAG 57.940 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.660938 GTGGTGCAGGGGGTGGAC 62.661 72.222 0.00 0.00 46.52 4.02
6 7 4.351054 GAGGTGGTGCAGGGGGTG 62.351 72.222 0.00 0.00 0.00 4.61
100 101 7.969536 ATGTCTGATATACCTGTATTGCAAC 57.030 36.000 0.00 0.00 0.00 4.17
114 115 9.988815 GTTTGAGACCTGTATTATGTCTGATAT 57.011 33.333 0.00 0.00 39.36 1.63
174 177 2.666526 GGAATCGGGCGATGAGGC 60.667 66.667 0.00 0.00 45.91 4.70
228 231 4.166011 GCAACGATGGACGCAGGC 62.166 66.667 0.00 0.00 46.94 4.85
261 264 2.107366 GAGAAGAAGAGAGGTGGAGGG 58.893 57.143 0.00 0.00 0.00 4.30
291 294 1.303317 GCCGGAGTTCATGGTTGGT 60.303 57.895 5.05 0.00 0.00 3.67
310 313 2.357034 CGAAGGACGGTGGTGGTG 60.357 66.667 0.00 0.00 38.46 4.17
387 512 2.060980 GTCATGGAGGAGGTCGGCT 61.061 63.158 0.00 0.00 0.00 5.52
438 563 2.322081 AACCCGGTCGTCGCAATTG 61.322 57.895 0.00 0.00 37.59 2.32
478 603 3.959975 GTTGCAGAAACGCCGCCA 61.960 61.111 0.00 0.00 0.00 5.69
558 683 3.248125 CACATTTTTGCAACATGGGTGTC 59.752 43.478 18.00 0.00 37.67 3.67
606 734 8.801299 TGTTGCAGAAACCATTTGAAATATAGA 58.199 29.630 0.00 0.00 38.06 1.98
614 742 4.796946 GCTCATGTTGCAGAAACCATTTGA 60.797 41.667 8.20 0.00 38.06 2.69
693 827 1.334243 GTAGCCGTTAGATCTGACGCT 59.666 52.381 28.97 27.75 40.59 5.07
769 903 0.611618 TGCAATGCCCGATCACCTTT 60.612 50.000 1.53 0.00 0.00 3.11
771 905 1.452651 CTGCAATGCCCGATCACCT 60.453 57.895 1.53 0.00 0.00 4.00
815 949 4.378616 CGTTTTCACAGTTAATGAAAGGCG 59.621 41.667 11.18 11.18 44.57 5.52
874 1008 1.966451 GTCCGGTGGCTTGACTTGG 60.966 63.158 0.00 0.00 0.00 3.61
875 1009 1.966451 GGTCCGGTGGCTTGACTTG 60.966 63.158 0.00 0.00 0.00 3.16
994 1133 3.008704 TCTTGATGATCATCCATGGCGAT 59.991 43.478 28.61 14.39 37.02 4.58
995 1134 2.369532 TCTTGATGATCATCCATGGCGA 59.630 45.455 28.61 11.66 37.02 5.54
1020 1165 3.302347 CTTCACCTTCTCCGGCGCT 62.302 63.158 7.64 0.00 0.00 5.92
1077 1222 2.519771 TGATGCTGAGAGCCCATTTT 57.480 45.000 0.00 0.00 41.51 1.82
1079 1224 1.409802 CCTTGATGCTGAGAGCCCATT 60.410 52.381 0.00 0.00 41.51 3.16
1086 1231 1.078918 CACGCCCTTGATGCTGAGA 60.079 57.895 0.00 0.00 0.00 3.27
1089 1234 2.046023 TCCACGCCCTTGATGCTG 60.046 61.111 0.00 0.00 0.00 4.41
1144 1289 1.816863 TTGTGCTCCAGGAGGTCGTC 61.817 60.000 18.83 1.23 35.89 4.20
1384 1529 2.983402 TCTGTGACGAACTAACCGAG 57.017 50.000 0.00 0.00 0.00 4.63
1399 1544 4.023279 GCTCAGTCAGATCGTATCATCTGT 60.023 45.833 10.59 0.00 46.91 3.41
1550 2015 1.026718 AAGAAATCCTTGCCGCCGAG 61.027 55.000 0.00 0.00 32.92 4.63
1625 2090 2.224793 TGATCTCCTCGTACATCGGGAT 60.225 50.000 0.00 0.00 43.64 3.85
1658 2123 0.252284 AACCTCTCCTCGGTGACCAT 60.252 55.000 1.11 0.00 34.33 3.55
1705 2170 3.119096 GGCGGCGAGTCCAAGAAC 61.119 66.667 12.98 0.00 34.01 3.01
1780 2245 1.470098 CCCATGTTCAGAAAGGCTTCG 59.530 52.381 0.00 0.00 36.61 3.79
1897 2370 7.890515 AGATGCACTGGACCATATATATATCG 58.109 38.462 2.03 0.00 0.00 2.92
1899 2372 9.842775 CAAAGATGCACTGGACCATATATATAT 57.157 33.333 0.00 0.00 0.00 0.86
1900 2373 8.825774 ACAAAGATGCACTGGACCATATATATA 58.174 33.333 0.00 0.00 0.00 0.86
1908 2381 1.133823 ACACAAAGATGCACTGGACCA 60.134 47.619 0.00 0.00 0.00 4.02
1927 2400 7.786178 TGATCATAGTACAAGCCATGTAAAC 57.214 36.000 0.00 0.00 45.81 2.01
1955 2428 9.256477 GGTGAATACGTGTCTCATTTATATCAA 57.744 33.333 0.00 0.00 0.00 2.57
1956 2429 8.417884 TGGTGAATACGTGTCTCATTTATATCA 58.582 33.333 0.00 0.00 0.00 2.15
1966 2439 3.021269 TGTGTGGTGAATACGTGTCTC 57.979 47.619 0.00 0.00 0.00 3.36
1973 2446 6.970484 AGTCATTTTCTTGTGTGGTGAATAC 58.030 36.000 0.00 0.00 0.00 1.89
1978 2451 5.276270 CAAGAGTCATTTTCTTGTGTGGTG 58.724 41.667 6.79 0.00 44.05 4.17
1988 2461 6.241207 TCATCGGAAACAAGAGTCATTTTC 57.759 37.500 0.00 0.00 0.00 2.29
1990 2463 6.633500 TTTCATCGGAAACAAGAGTCATTT 57.367 33.333 0.00 0.00 38.07 2.32
1991 2464 6.824305 ATTTCATCGGAAACAAGAGTCATT 57.176 33.333 0.00 0.00 45.22 2.57
1993 2466 6.262049 TGAAATTTCATCGGAAACAAGAGTCA 59.738 34.615 16.91 0.00 45.22 3.41
1994 2467 6.668323 TGAAATTTCATCGGAAACAAGAGTC 58.332 36.000 16.91 0.00 45.22 3.36
1995 2468 6.486657 TCTGAAATTTCATCGGAAACAAGAGT 59.513 34.615 20.76 0.00 45.22 3.24
1996 2469 6.902341 TCTGAAATTTCATCGGAAACAAGAG 58.098 36.000 20.76 5.28 45.22 2.85
1997 2470 6.875948 TCTGAAATTTCATCGGAAACAAGA 57.124 33.333 20.76 8.12 45.22 3.02
1998 2471 7.928908 TTTCTGAAATTTCATCGGAAACAAG 57.071 32.000 20.76 5.95 45.22 3.16
2026 2499 0.538118 GGTACCTGCCGTGGTGATTA 59.462 55.000 4.06 0.00 41.05 1.75
2028 2501 2.987125 GGTACCTGCCGTGGTGAT 59.013 61.111 4.06 0.00 41.05 3.06
2036 2509 1.000060 TGCGTATATTCGGTACCTGCC 60.000 52.381 10.90 0.00 0.00 4.85
2038 2511 4.986034 TGAAATGCGTATATTCGGTACCTG 59.014 41.667 10.90 3.80 0.00 4.00
2041 2514 4.143179 GCCTGAAATGCGTATATTCGGTAC 60.143 45.833 3.84 0.00 0.00 3.34
2044 2517 2.805671 TGCCTGAAATGCGTATATTCGG 59.194 45.455 3.84 8.94 0.00 4.30
2046 2519 4.811555 TGTGCCTGAAATGCGTATATTC 57.188 40.909 0.00 0.00 0.00 1.75
2088 2561 7.873719 TTGGTTTCTGTTGAAATCTGACTTA 57.126 32.000 3.88 0.00 42.24 2.24
2118 2591 2.926420 TTGCAGAGTAGCCGCGTCA 61.926 57.895 4.92 0.00 0.00 4.35
2119 2592 2.126071 TTGCAGAGTAGCCGCGTC 60.126 61.111 4.92 0.00 0.00 5.19
2126 2600 9.186323 GACAATATACATGTAGTTGCAGAGTAG 57.814 37.037 23.38 7.39 0.00 2.57
2127 2601 8.691797 TGACAATATACATGTAGTTGCAGAGTA 58.308 33.333 23.38 6.60 0.00 2.59
2151 2625 6.669154 AGGGCTATTTCTTTTTCCAATGATGA 59.331 34.615 0.00 0.00 0.00 2.92
2152 2626 6.759827 CAGGGCTATTTCTTTTTCCAATGATG 59.240 38.462 0.00 0.00 0.00 3.07
2153 2627 6.441604 ACAGGGCTATTTCTTTTTCCAATGAT 59.558 34.615 0.00 0.00 0.00 2.45
2195 2669 9.701098 TTGTAGATGTTCTTACACGAGTATTTT 57.299 29.630 0.00 0.00 37.03 1.82
2223 2697 3.103742 GGGCCCAAATTAGGACATTTCA 58.896 45.455 19.95 0.00 32.01 2.69
2224 2698 3.374764 AGGGCCCAAATTAGGACATTTC 58.625 45.455 27.56 0.00 32.01 2.17
2225 2699 3.490060 AGGGCCCAAATTAGGACATTT 57.510 42.857 27.56 0.00 32.01 2.32
2231 2705 2.039879 ACGCTATAGGGCCCAAATTAGG 59.960 50.000 27.56 9.89 0.00 2.69
2240 2714 1.000618 GTAACTGGACGCTATAGGGCC 59.999 57.143 16.22 17.05 0.00 5.80
2258 2732 2.614481 GGACGTTGCCAAATGAGAGGTA 60.614 50.000 0.00 0.00 0.00 3.08
2277 2751 2.833151 ATAAGGGGGACGGCTGTGGA 62.833 60.000 0.80 0.00 0.00 4.02
2279 2753 1.002087 GATATAAGGGGGACGGCTGTG 59.998 57.143 0.80 0.00 0.00 3.66
2280 2754 1.349067 GATATAAGGGGGACGGCTGT 58.651 55.000 0.00 0.00 0.00 4.40
2282 2756 0.903454 CGGATATAAGGGGGACGGCT 60.903 60.000 0.00 0.00 0.00 5.52
2283 2757 0.901580 TCGGATATAAGGGGGACGGC 60.902 60.000 0.00 0.00 0.00 5.68
2284 2758 1.274447 GTTCGGATATAAGGGGGACGG 59.726 57.143 0.00 0.00 0.00 4.79
2285 2759 1.274447 GGTTCGGATATAAGGGGGACG 59.726 57.143 0.00 0.00 0.00 4.79
2286 2760 2.566279 GAGGTTCGGATATAAGGGGGAC 59.434 54.545 0.00 0.00 0.00 4.46
2287 2761 2.453601 AGAGGTTCGGATATAAGGGGGA 59.546 50.000 0.00 0.00 0.00 4.81
2288 2762 2.903926 AGAGGTTCGGATATAAGGGGG 58.096 52.381 0.00 0.00 0.00 5.40
2289 2763 6.351966 GGATTTAGAGGTTCGGATATAAGGGG 60.352 46.154 0.00 0.00 0.00 4.79
2290 2764 6.212791 TGGATTTAGAGGTTCGGATATAAGGG 59.787 42.308 0.00 0.00 0.00 3.95
2291 2765 7.241042 TGGATTTAGAGGTTCGGATATAAGG 57.759 40.000 0.00 0.00 0.00 2.69
2300 2774 3.065371 GGTTGCATGGATTTAGAGGTTCG 59.935 47.826 0.00 0.00 0.00 3.95
2301 2775 3.381590 GGGTTGCATGGATTTAGAGGTTC 59.618 47.826 0.00 0.00 0.00 3.62
2326 2800 0.376852 GCTATTTTGATCACGCCGCA 59.623 50.000 0.00 0.00 0.00 5.69
2327 2801 0.376852 TGCTATTTTGATCACGCCGC 59.623 50.000 0.00 0.00 0.00 6.53
2328 2802 1.396648 TGTGCTATTTTGATCACGCCG 59.603 47.619 0.00 0.00 32.48 6.46
2329 2803 3.698029 ATGTGCTATTTTGATCACGCC 57.302 42.857 0.00 0.00 32.48 5.68
2330 2804 5.657470 TCTATGTGCTATTTTGATCACGC 57.343 39.130 0.00 0.00 32.48 5.34
2341 2815 9.910267 TGCCATATTGAATTATCTATGTGCTAT 57.090 29.630 0.00 0.00 31.77 2.97
2342 2816 9.910267 ATGCCATATTGAATTATCTATGTGCTA 57.090 29.630 0.00 0.00 31.77 3.49
2343 2817 8.818622 ATGCCATATTGAATTATCTATGTGCT 57.181 30.769 0.00 0.00 31.77 4.40
2354 2828 8.967918 CCAATCTGATCTATGCCATATTGAATT 58.032 33.333 0.00 0.00 32.17 2.17
2355 2829 8.333984 TCCAATCTGATCTATGCCATATTGAAT 58.666 33.333 0.00 0.00 32.17 2.57
2356 2830 7.609146 GTCCAATCTGATCTATGCCATATTGAA 59.391 37.037 0.00 0.00 32.17 2.69
2357 2831 7.108194 GTCCAATCTGATCTATGCCATATTGA 58.892 38.462 0.00 0.00 32.17 2.57
2358 2832 6.882678 TGTCCAATCTGATCTATGCCATATTG 59.117 38.462 0.00 0.00 31.05 1.90
2359 2833 7.024345 TGTCCAATCTGATCTATGCCATATT 57.976 36.000 0.00 0.00 0.00 1.28
2360 2834 6.631763 TGTCCAATCTGATCTATGCCATAT 57.368 37.500 0.00 0.00 0.00 1.78
2361 2835 6.631763 ATGTCCAATCTGATCTATGCCATA 57.368 37.500 0.00 0.00 0.00 2.74
2362 2836 4.987963 TGTCCAATCTGATCTATGCCAT 57.012 40.909 0.00 0.00 0.00 4.40
2363 2837 4.987963 ATGTCCAATCTGATCTATGCCA 57.012 40.909 0.00 0.00 0.00 4.92
2364 2838 4.874966 GCTATGTCCAATCTGATCTATGCC 59.125 45.833 0.00 0.00 0.00 4.40
2365 2839 5.485620 TGCTATGTCCAATCTGATCTATGC 58.514 41.667 0.00 0.00 0.00 3.14
2366 2840 6.932947 TCTGCTATGTCCAATCTGATCTATG 58.067 40.000 0.00 0.00 0.00 2.23
2367 2841 6.725369 ACTCTGCTATGTCCAATCTGATCTAT 59.275 38.462 0.00 0.00 0.00 1.98
2368 2842 6.073981 ACTCTGCTATGTCCAATCTGATCTA 58.926 40.000 0.00 0.00 0.00 1.98
2369 2843 4.900652 ACTCTGCTATGTCCAATCTGATCT 59.099 41.667 0.00 0.00 0.00 2.75
2370 2844 5.212532 ACTCTGCTATGTCCAATCTGATC 57.787 43.478 0.00 0.00 0.00 2.92
2371 2845 5.129980 TGAACTCTGCTATGTCCAATCTGAT 59.870 40.000 0.00 0.00 0.00 2.90
2372 2846 4.467438 TGAACTCTGCTATGTCCAATCTGA 59.533 41.667 0.00 0.00 0.00 3.27
2373 2847 4.763073 TGAACTCTGCTATGTCCAATCTG 58.237 43.478 0.00 0.00 0.00 2.90
2374 2848 5.426689 TTGAACTCTGCTATGTCCAATCT 57.573 39.130 0.00 0.00 0.00 2.40
2375 2849 6.690194 AATTGAACTCTGCTATGTCCAATC 57.310 37.500 0.00 0.00 0.00 2.67
2376 2850 8.757982 ATAAATTGAACTCTGCTATGTCCAAT 57.242 30.769 0.00 0.00 0.00 3.16
2377 2851 9.330063 CTATAAATTGAACTCTGCTATGTCCAA 57.670 33.333 0.00 0.00 0.00 3.53
2378 2852 7.442364 GCTATAAATTGAACTCTGCTATGTCCA 59.558 37.037 0.00 0.00 0.00 4.02
2379 2853 7.095017 GGCTATAAATTGAACTCTGCTATGTCC 60.095 40.741 0.00 0.00 0.00 4.02
2380 2854 7.359598 CGGCTATAAATTGAACTCTGCTATGTC 60.360 40.741 0.00 0.00 0.00 3.06
2381 2855 6.425114 CGGCTATAAATTGAACTCTGCTATGT 59.575 38.462 0.00 0.00 0.00 2.29
2389 2863 6.128526 GCTATGTCCGGCTATAAATTGAACTC 60.129 42.308 0.00 0.00 0.00 3.01
2390 2864 5.701290 GCTATGTCCGGCTATAAATTGAACT 59.299 40.000 0.00 0.00 0.00 3.01
2401 2875 2.415843 GCACGCTATGTCCGGCTA 59.584 61.111 0.00 0.00 0.00 3.93
2415 2889 3.218398 CGATCTTTTGTGAACTTCGCAC 58.782 45.455 4.46 0.00 36.51 5.34
2417 2891 2.478894 TCCGATCTTTTGTGAACTTCGC 59.521 45.455 0.00 0.00 0.00 4.70
2418 2892 3.493129 TGTCCGATCTTTTGTGAACTTCG 59.507 43.478 0.00 0.00 0.00 3.79
2427 2901 4.751600 TGCTATGCTATGTCCGATCTTTTG 59.248 41.667 0.00 0.00 0.00 2.44
2469 2943 8.915036 CCCCTAGCTCTAATTTATGTATCGTAT 58.085 37.037 0.00 0.00 0.00 3.06
2489 2963 1.148498 GAAATCCGGCACCCCCTAG 59.852 63.158 0.00 0.00 0.00 3.02
2495 2969 0.958822 AAAGTGTGAAATCCGGCACC 59.041 50.000 0.00 0.00 34.19 5.01
2497 2971 1.202879 AGGAAAGTGTGAAATCCGGCA 60.203 47.619 0.00 0.00 37.05 5.69
2498 2972 1.468914 GAGGAAAGTGTGAAATCCGGC 59.531 52.381 0.00 0.00 37.05 6.13
2499 2973 1.732259 CGAGGAAAGTGTGAAATCCGG 59.268 52.381 0.00 0.00 37.05 5.14
2500 2974 1.128692 GCGAGGAAAGTGTGAAATCCG 59.871 52.381 0.00 0.00 37.05 4.18
2501 2975 2.160417 CAGCGAGGAAAGTGTGAAATCC 59.840 50.000 0.00 0.00 0.00 3.01
2502 2976 2.160417 CCAGCGAGGAAAGTGTGAAATC 59.840 50.000 0.00 0.00 41.22 2.17
2503 2977 2.154462 CCAGCGAGGAAAGTGTGAAAT 58.846 47.619 0.00 0.00 41.22 2.17
2504 2978 1.134220 ACCAGCGAGGAAAGTGTGAAA 60.134 47.619 5.19 0.00 41.22 2.69
2505 2979 0.468226 ACCAGCGAGGAAAGTGTGAA 59.532 50.000 5.19 0.00 41.22 3.18
2538 3012 0.741221 CTACCGCTGCTCCAAAGACC 60.741 60.000 0.00 0.00 0.00 3.85
2541 3015 1.204941 ACTACTACCGCTGCTCCAAAG 59.795 52.381 0.00 0.00 0.00 2.77
2544 3018 0.034380 AGACTACTACCGCTGCTCCA 60.034 55.000 0.00 0.00 0.00 3.86
2567 3041 1.210931 CGTCCACCGATGTGTACGT 59.789 57.895 3.12 0.00 46.10 3.57
2569 3043 0.179145 CTCCGTCCACCGATGTGTAC 60.179 60.000 0.00 0.00 41.09 2.90
2570 3044 0.322726 TCTCCGTCCACCGATGTGTA 60.323 55.000 0.00 0.00 41.09 2.90
2571 3045 1.595993 CTCTCCGTCCACCGATGTGT 61.596 60.000 0.00 0.00 41.09 3.72
2572 3046 1.139734 CTCTCCGTCCACCGATGTG 59.860 63.158 0.00 0.00 42.39 3.21
2573 3047 2.052690 CCTCTCCGTCCACCGATGT 61.053 63.158 0.00 0.00 39.56 3.06
2574 3048 1.320344 TTCCTCTCCGTCCACCGATG 61.320 60.000 0.00 0.00 39.56 3.84
2575 3049 0.397254 ATTCCTCTCCGTCCACCGAT 60.397 55.000 0.00 0.00 39.56 4.18
2576 3050 1.000019 ATTCCTCTCCGTCCACCGA 60.000 57.895 0.00 0.00 39.56 4.69
2577 3051 1.437986 GATTCCTCTCCGTCCACCG 59.562 63.158 0.00 0.00 0.00 4.94
2578 3052 1.321074 ACGATTCCTCTCCGTCCACC 61.321 60.000 0.00 0.00 29.82 4.61
2579 3053 0.100861 GACGATTCCTCTCCGTCCAC 59.899 60.000 0.00 0.00 44.67 4.02
2580 3054 2.490165 GACGATTCCTCTCCGTCCA 58.510 57.895 0.00 0.00 44.67 4.02
2585 3059 2.294791 ACGATGATGACGATTCCTCTCC 59.705 50.000 0.00 0.00 34.70 3.71
2602 3076 1.667830 CGGCACAACCACTGACGAT 60.668 57.895 0.00 0.00 39.03 3.73
2603 3077 2.279851 CGGCACAACCACTGACGA 60.280 61.111 0.00 0.00 39.03 4.20
2608 3082 2.177580 CGACAACGGCACAACCACT 61.178 57.895 0.00 0.00 39.03 4.00
2619 3093 0.101399 CTCTCCCTCATCCGACAACG 59.899 60.000 0.00 0.00 39.43 4.10
2620 3094 0.461961 CCTCTCCCTCATCCGACAAC 59.538 60.000 0.00 0.00 0.00 3.32
2621 3095 0.335019 TCCTCTCCCTCATCCGACAA 59.665 55.000 0.00 0.00 0.00 3.18
2622 3096 0.335019 TTCCTCTCCCTCATCCGACA 59.665 55.000 0.00 0.00 0.00 4.35
2623 3097 0.747852 GTTCCTCTCCCTCATCCGAC 59.252 60.000 0.00 0.00 0.00 4.79
2624 3098 0.752009 CGTTCCTCTCCCTCATCCGA 60.752 60.000 0.00 0.00 0.00 4.55
2625 3099 1.736586 CGTTCCTCTCCCTCATCCG 59.263 63.158 0.00 0.00 0.00 4.18
2626 3100 0.397254 TCCGTTCCTCTCCCTCATCC 60.397 60.000 0.00 0.00 0.00 3.51
2627 3101 1.616374 GATCCGTTCCTCTCCCTCATC 59.384 57.143 0.00 0.00 0.00 2.92
2628 3102 1.710816 GATCCGTTCCTCTCCCTCAT 58.289 55.000 0.00 0.00 0.00 2.90
2629 3103 0.397254 GGATCCGTTCCTCTCCCTCA 60.397 60.000 0.00 0.00 41.78 3.86
2630 3104 1.116536 GGGATCCGTTCCTCTCCCTC 61.117 65.000 5.45 0.00 44.75 4.30
2631 3105 1.075151 GGGATCCGTTCCTCTCCCT 60.075 63.158 5.45 0.00 44.75 4.20
2632 3106 2.499827 CGGGATCCGTTCCTCTCCC 61.500 68.421 5.45 0.00 44.75 4.30
2633 3107 2.499827 CCGGGATCCGTTCCTCTCC 61.500 68.421 5.45 0.00 46.80 3.71
2634 3108 3.130227 CCGGGATCCGTTCCTCTC 58.870 66.667 5.45 0.00 46.80 3.20
2635 3109 3.155167 GCCGGGATCCGTTCCTCT 61.155 66.667 2.18 0.00 46.80 3.69
2636 3110 2.732619 AAGCCGGGATCCGTTCCTC 61.733 63.158 2.18 0.00 46.80 3.71
2637 3111 2.687566 AAGCCGGGATCCGTTCCT 60.688 61.111 2.18 0.00 46.80 3.36
2638 3112 2.513897 CAAGCCGGGATCCGTTCC 60.514 66.667 2.18 0.00 46.80 3.62
2639 3113 1.814169 GTCAAGCCGGGATCCGTTC 60.814 63.158 2.18 0.00 46.80 3.95
2640 3114 1.910580 ATGTCAAGCCGGGATCCGTT 61.911 55.000 2.18 0.00 46.80 4.44
2641 3115 2.311688 GATGTCAAGCCGGGATCCGT 62.312 60.000 2.18 0.00 46.80 4.69
2643 3117 1.595382 CGATGTCAAGCCGGGATCC 60.595 63.158 1.92 1.92 0.00 3.36
2644 3118 1.595382 CCGATGTCAAGCCGGGATC 60.595 63.158 2.18 0.00 39.59 3.36
2645 3119 2.505982 CCGATGTCAAGCCGGGAT 59.494 61.111 2.18 0.00 39.59 3.85
2650 3124 4.778143 ACGGCCCGATGTCAAGCC 62.778 66.667 11.71 0.00 42.18 4.35
2651 3125 3.499737 CACGGCCCGATGTCAAGC 61.500 66.667 11.71 0.00 0.00 4.01
2652 3126 1.811266 CTCACGGCCCGATGTCAAG 60.811 63.158 11.71 0.00 0.00 3.02
2653 3127 2.264480 CTCACGGCCCGATGTCAA 59.736 61.111 11.71 0.00 0.00 3.18
2654 3128 3.770040 CCTCACGGCCCGATGTCA 61.770 66.667 11.71 0.00 0.00 3.58
2674 3148 4.394712 AGAAAGCCGCCCACCTCG 62.395 66.667 0.00 0.00 0.00 4.63
2675 3149 2.436824 GAGAAAGCCGCCCACCTC 60.437 66.667 0.00 0.00 0.00 3.85
2676 3150 4.035102 GGAGAAAGCCGCCCACCT 62.035 66.667 0.00 0.00 0.00 4.00
2686 3160 3.494336 CAGCTGCCGCGGAGAAAG 61.494 66.667 33.48 20.41 42.32 2.62
2697 3171 2.045131 CCAAGGAGAAGGCAGCTGC 61.045 63.158 30.88 30.88 41.14 5.25
2698 3172 4.315588 CCAAGGAGAAGGCAGCTG 57.684 61.111 10.11 10.11 0.00 4.24
2704 3178 2.363683 GTCTGATTGCCAAGGAGAAGG 58.636 52.381 0.00 0.00 0.00 3.46
2705 3179 2.290514 TGGTCTGATTGCCAAGGAGAAG 60.291 50.000 0.00 0.00 0.00 2.85
2706 3180 1.704628 TGGTCTGATTGCCAAGGAGAA 59.295 47.619 0.00 0.00 0.00 2.87
2707 3181 1.003580 GTGGTCTGATTGCCAAGGAGA 59.996 52.381 0.00 0.00 36.41 3.71
2708 3182 1.457346 GTGGTCTGATTGCCAAGGAG 58.543 55.000 0.00 0.00 36.41 3.69
2709 3183 0.038166 GGTGGTCTGATTGCCAAGGA 59.962 55.000 0.00 0.00 36.41 3.36
2710 3184 0.038744 AGGTGGTCTGATTGCCAAGG 59.961 55.000 0.00 0.00 36.41 3.61
2711 3185 1.815003 GAAGGTGGTCTGATTGCCAAG 59.185 52.381 0.00 0.00 36.41 3.61
2712 3186 1.881925 CGAAGGTGGTCTGATTGCCAA 60.882 52.381 0.00 0.00 36.41 4.52
2713 3187 0.321564 CGAAGGTGGTCTGATTGCCA 60.322 55.000 0.00 0.00 0.00 4.92
2714 3188 1.648467 GCGAAGGTGGTCTGATTGCC 61.648 60.000 0.00 0.00 0.00 4.52
2715 3189 0.955428 TGCGAAGGTGGTCTGATTGC 60.955 55.000 0.00 0.00 0.00 3.56
2716 3190 1.742761 ATGCGAAGGTGGTCTGATTG 58.257 50.000 0.00 0.00 0.00 2.67
2717 3191 2.496899 AATGCGAAGGTGGTCTGATT 57.503 45.000 0.00 0.00 0.00 2.57
2718 3192 2.489329 CAAAATGCGAAGGTGGTCTGAT 59.511 45.455 0.00 0.00 0.00 2.90
2719 3193 1.879380 CAAAATGCGAAGGTGGTCTGA 59.121 47.619 0.00 0.00 0.00 3.27
2720 3194 1.608590 ACAAAATGCGAAGGTGGTCTG 59.391 47.619 0.00 0.00 0.00 3.51
2721 3195 1.880027 GACAAAATGCGAAGGTGGTCT 59.120 47.619 0.00 0.00 0.00 3.85
2722 3196 1.399727 CGACAAAATGCGAAGGTGGTC 60.400 52.381 0.00 0.00 0.00 4.02
2723 3197 0.591170 CGACAAAATGCGAAGGTGGT 59.409 50.000 0.00 0.00 0.00 4.16
2724 3198 0.591170 ACGACAAAATGCGAAGGTGG 59.409 50.000 0.00 0.00 0.00 4.61
2725 3199 1.721489 CGACGACAAAATGCGAAGGTG 60.721 52.381 0.00 0.00 0.00 4.00
2726 3200 0.511221 CGACGACAAAATGCGAAGGT 59.489 50.000 0.00 0.00 0.00 3.50
2727 3201 0.787787 TCGACGACAAAATGCGAAGG 59.212 50.000 0.00 0.00 0.00 3.46
2728 3202 1.778568 CGTCGACGACAAAATGCGAAG 60.779 52.381 33.35 3.52 43.02 3.79
2729 3203 0.159973 CGTCGACGACAAAATGCGAA 59.840 50.000 33.35 0.00 43.02 4.70
2730 3204 0.660891 TCGTCGACGACAAAATGCGA 60.661 50.000 34.97 13.73 44.22 5.10
2731 3205 1.770432 TCGTCGACGACAAAATGCG 59.230 52.632 34.97 11.62 44.22 4.73
2752 3226 4.554036 GCGGAGACAGATGCCCCC 62.554 72.222 0.00 0.00 0.00 5.40
2753 3227 4.554036 GGCGGAGACAGATGCCCC 62.554 72.222 0.00 0.00 41.70 5.80
2754 3228 4.899239 CGGCGGAGACAGATGCCC 62.899 72.222 0.00 0.00 44.71 5.36
2755 3229 3.838271 TCGGCGGAGACAGATGCC 61.838 66.667 7.21 0.00 44.09 4.40
2756 3230 2.583593 GTCGGCGGAGACAGATGC 60.584 66.667 7.21 0.00 40.65 3.91
2757 3231 2.885113 TGTCGGCGGAGACAGATG 59.115 61.111 7.21 0.00 45.18 2.90
2762 3236 1.519455 CCTTCATGTCGGCGGAGAC 60.519 63.158 7.21 0.00 41.30 3.36
2763 3237 1.667154 CTCCTTCATGTCGGCGGAGA 61.667 60.000 7.21 0.00 43.02 3.71
2764 3238 1.227089 CTCCTTCATGTCGGCGGAG 60.227 63.158 7.21 0.00 35.75 4.63
2765 3239 1.982395 ACTCCTTCATGTCGGCGGA 60.982 57.895 7.21 0.00 0.00 5.54
2766 3240 1.811266 CACTCCTTCATGTCGGCGG 60.811 63.158 7.21 0.00 0.00 6.13
2767 3241 1.811266 CCACTCCTTCATGTCGGCG 60.811 63.158 0.00 0.00 0.00 6.46
2768 3242 0.460987 CTCCACTCCTTCATGTCGGC 60.461 60.000 0.00 0.00 0.00 5.54
2769 3243 0.176680 CCTCCACTCCTTCATGTCGG 59.823 60.000 0.00 0.00 0.00 4.79
2770 3244 1.186200 TCCTCCACTCCTTCATGTCG 58.814 55.000 0.00 0.00 0.00 4.35
2771 3245 2.768527 TCATCCTCCACTCCTTCATGTC 59.231 50.000 0.00 0.00 0.00 3.06
2772 3246 2.503356 GTCATCCTCCACTCCTTCATGT 59.497 50.000 0.00 0.00 0.00 3.21
2773 3247 2.482664 CGTCATCCTCCACTCCTTCATG 60.483 54.545 0.00 0.00 0.00 3.07
2774 3248 1.759445 CGTCATCCTCCACTCCTTCAT 59.241 52.381 0.00 0.00 0.00 2.57
2775 3249 1.186200 CGTCATCCTCCACTCCTTCA 58.814 55.000 0.00 0.00 0.00 3.02
2776 3250 1.187087 ACGTCATCCTCCACTCCTTC 58.813 55.000 0.00 0.00 0.00 3.46
2777 3251 2.291670 ACTACGTCATCCTCCACTCCTT 60.292 50.000 0.00 0.00 0.00 3.36
2778 3252 1.285373 ACTACGTCATCCTCCACTCCT 59.715 52.381 0.00 0.00 0.00 3.69
2779 3253 1.405821 CACTACGTCATCCTCCACTCC 59.594 57.143 0.00 0.00 0.00 3.85
2780 3254 1.405821 CCACTACGTCATCCTCCACTC 59.594 57.143 0.00 0.00 0.00 3.51
2781 3255 1.005569 TCCACTACGTCATCCTCCACT 59.994 52.381 0.00 0.00 0.00 4.00
2782 3256 1.405821 CTCCACTACGTCATCCTCCAC 59.594 57.143 0.00 0.00 0.00 4.02
2783 3257 1.283905 TCTCCACTACGTCATCCTCCA 59.716 52.381 0.00 0.00 0.00 3.86
2784 3258 2.054232 TCTCCACTACGTCATCCTCC 57.946 55.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.