Multiple sequence alignment - TraesCS1A01G049500

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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 TraesCS1A01G049500 chr1A 100.000 2823 0 0 1 2823 31033293 31030471 0.000000e+00 5214
1 TraesCS1A01G049500 chr1A 92.201 1013 72 3 803 1812 31129881 31128873 0.000000e+00 1426
2 TraesCS1A01G049500 chr1A 88.257 826 90 6 1233 2052 25324484 25323660 0.000000e+00 981
3 TraesCS1A01G049500 chr1A 76.045 1077 208 31 1135 2198 35536475 35537514 5.390000e-142 514
4 TraesCS1A01G049500 chr1A 90.932 397 12 8 60 435 31130824 31130431 1.940000e-141 512
5 TraesCS1A01G049500 chr1A 82.753 574 77 13 138 692 25474455 25475025 2.530000e-135 492
6 TraesCS1A01G049500 chr1A 83.716 436 33 12 60 470 25422430 25422008 7.380000e-101 377
7 TraesCS1A01G049500 chr1A 93.496 246 15 1 501 745 31130433 31130188 5.750000e-97 364
8 TraesCS1A01G049500 chr1A 79.934 304 49 10 2529 2823 25314247 25313947 2.200000e-51 213
9 TraesCS1A01G049500 chr1A 87.342 158 16 3 612 766 25392734 25392578 8.040000e-41 178
10 TraesCS1A01G049500 chr1D 82.640 2235 322 36 306 2517 24138977 24141168 0.000000e+00 1917
11 TraesCS1A01G049500 chr1D 74.962 1314 276 43 1135 2422 36315892 36317178 3.180000e-154 555
12 TraesCS1A01G049500 chr1D 75.253 1188 244 40 872 2033 24144886 24146049 1.160000e-143 520
13 TraesCS1A01G049500 chr1D 76.689 755 144 26 1678 2421 36362354 36361621 9.480000e-105 390
14 TraesCS1A01G049500 chr1B 82.500 2080 295 37 83 2133 39671319 39673358 0.000000e+00 1760
15 TraesCS1A01G049500 chr1B 74.538 1190 274 24 861 2036 56140938 56139764 2.530000e-135 492
16 TraesCS1A01G049500 chr1B 73.900 1364 290 45 856 2199 56016970 56018287 1.180000e-133 486
17 TraesCS1A01G049500 chrUn 79.934 304 49 10 2529 2823 332913 333213 2.200000e-51 213
18 TraesCS1A01G049500 chrUn 79.934 304 49 10 2529 2823 319351553 319351253 2.200000e-51 213


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 TraesCS1A01G049500 chr1A 31030471 31033293 2822 True 5214.000000 5214 100.000000 1 2823 1 chr1A.!!$R5 2822
1 TraesCS1A01G049500 chr1A 25323660 25324484 824 True 981.000000 981 88.257000 1233 2052 1 chr1A.!!$R2 819
2 TraesCS1A01G049500 chr1A 31128873 31130824 1951 True 767.333333 1426 92.209667 60 1812 3 chr1A.!!$R6 1752
3 TraesCS1A01G049500 chr1A 35536475 35537514 1039 False 514.000000 514 76.045000 1135 2198 1 chr1A.!!$F2 1063
4 TraesCS1A01G049500 chr1A 25474455 25475025 570 False 492.000000 492 82.753000 138 692 1 chr1A.!!$F1 554
5 TraesCS1A01G049500 chr1D 24138977 24146049 7072 False 1218.500000 1917 78.946500 306 2517 2 chr1D.!!$F2 2211
6 TraesCS1A01G049500 chr1D 36315892 36317178 1286 False 555.000000 555 74.962000 1135 2422 1 chr1D.!!$F1 1287
7 TraesCS1A01G049500 chr1D 36361621 36362354 733 True 390.000000 390 76.689000 1678 2421 1 chr1D.!!$R1 743
8 TraesCS1A01G049500 chr1B 39671319 39673358 2039 False 1760.000000 1760 82.500000 83 2133 1 chr1B.!!$F1 2050
9 TraesCS1A01G049500 chr1B 56139764 56140938 1174 True 492.000000 492 74.538000 861 2036 1 chr1B.!!$R1 1175
10 TraesCS1A01G049500 chr1B 56016970 56018287 1317 False 486.000000 486 73.900000 856 2199 1 chr1B.!!$F2 1343

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
745 786 0.251877 AAACCCCATTGTAACCCCCG 60.252 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2523 2861 0.039346 CATGCGATGCACCACAAACA 60.039 50.0 0.0 0.0 43.04 2.83 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
31 32 9.528489 TCACTATATCTTATATACTGTGGTGCA 57.472 33.333 0.00 0.00 0.00 4.57
34 35 9.254133 CTATATCTTATATACTGTGGTGCATGC 57.746 37.037 11.82 11.82 0.00 4.06
35 36 4.641396 TCTTATATACTGTGGTGCATGCC 58.359 43.478 16.68 6.42 0.00 4.40
36 37 4.347876 TCTTATATACTGTGGTGCATGCCT 59.652 41.667 16.68 0.00 0.00 4.75
37 38 2.620251 TATACTGTGGTGCATGCCTC 57.380 50.000 16.68 8.35 0.00 4.70
38 39 0.620030 ATACTGTGGTGCATGCCTCA 59.380 50.000 16.68 10.64 0.00 3.86
39 40 3.587095 CTGTGGTGCATGCCTCAG 58.413 61.111 16.68 12.78 41.70 3.35
40 41 3.159615 TGTGGTGCATGCCTCAGA 58.840 55.556 16.68 9.13 0.00 3.27
41 42 1.687014 TGTGGTGCATGCCTCAGAT 59.313 52.632 16.68 0.00 0.00 2.90
42 43 0.911053 TGTGGTGCATGCCTCAGATA 59.089 50.000 16.68 0.64 0.00 1.98
43 44 1.303309 GTGGTGCATGCCTCAGATAC 58.697 55.000 16.68 4.22 0.00 2.24
44 45 0.911053 TGGTGCATGCCTCAGATACA 59.089 50.000 16.68 0.00 0.00 2.29
45 46 1.281577 TGGTGCATGCCTCAGATACAA 59.718 47.619 16.68 0.00 0.00 2.41
46 47 2.092267 TGGTGCATGCCTCAGATACAAT 60.092 45.455 16.68 0.00 0.00 2.71
47 48 2.292569 GGTGCATGCCTCAGATACAATG 59.707 50.000 16.68 0.00 0.00 2.82
48 49 3.208594 GTGCATGCCTCAGATACAATGA 58.791 45.455 16.68 0.00 0.00 2.57
49 50 3.628942 GTGCATGCCTCAGATACAATGAA 59.371 43.478 16.68 0.00 0.00 2.57
50 51 4.277672 GTGCATGCCTCAGATACAATGAAT 59.722 41.667 16.68 0.00 0.00 2.57
51 52 4.517832 TGCATGCCTCAGATACAATGAATC 59.482 41.667 16.68 0.00 0.00 2.52
52 53 4.760715 GCATGCCTCAGATACAATGAATCT 59.239 41.667 6.36 0.00 33.94 2.40
53 54 5.241064 GCATGCCTCAGATACAATGAATCTT 59.759 40.000 6.36 0.00 31.22 2.40
54 55 6.429078 GCATGCCTCAGATACAATGAATCTTA 59.571 38.462 6.36 0.00 31.22 2.10
55 56 7.040892 GCATGCCTCAGATACAATGAATCTTAA 60.041 37.037 6.36 0.00 31.22 1.85
56 57 9.011095 CATGCCTCAGATACAATGAATCTTAAT 57.989 33.333 0.00 0.00 31.22 1.40
86 87 1.346068 GATGGTGAGGGCTCCATAGAC 59.654 57.143 0.00 0.00 45.71 2.59
441 468 8.783093 TGTTTTTAGATCGTCAATTTGACTGAT 58.217 29.630 23.98 23.98 44.85 2.90
454 481 9.214957 TCAATTTGACTGATAACTCGTGTTATT 57.785 29.630 20.40 8.17 46.05 1.40
481 515 7.170998 AGTCACTAAAACTTAGGTTCATTGTCG 59.829 37.037 0.00 0.00 34.14 4.35
489 523 5.011738 ACTTAGGTTCATTGTCGAAGGAAGA 59.988 40.000 0.00 0.00 32.72 2.87
497 531 7.377766 TCATTGTCGAAGGAAGATTTTAAGG 57.622 36.000 0.00 0.00 0.00 2.69
543 577 8.519526 GGACCATTCAACATGAAAGTAAATGTA 58.480 33.333 0.00 0.00 40.12 2.29
666 702 2.455674 TGTGGAGAAATGGAGTGTCG 57.544 50.000 0.00 0.00 0.00 4.35
669 705 1.067846 TGGAGAAATGGAGTGTCGACG 60.068 52.381 11.62 0.00 0.00 5.12
693 729 2.169832 ACAGTCCAGACATTGTTCCG 57.830 50.000 0.00 0.00 0.00 4.30
700 736 3.563808 TCCAGACATTGTTCCGTGAAAAG 59.436 43.478 0.00 0.00 0.00 2.27
701 737 3.304659 CCAGACATTGTTCCGTGAAAAGG 60.305 47.826 0.00 0.00 36.52 3.11
706 746 2.570442 TGTTCCGTGAAAAGGCAAAC 57.430 45.000 0.00 0.00 34.48 2.93
724 764 3.582714 AACAAGCCATAAAGCAGAAGC 57.417 42.857 0.00 0.00 42.56 3.86
745 786 0.251877 AAACCCCATTGTAACCCCCG 60.252 55.000 0.00 0.00 0.00 5.73
751 793 1.540267 CATTGTAACCCCCGCTGAAA 58.460 50.000 0.00 0.00 0.00 2.69
754 796 0.391927 TGTAACCCCCGCTGAAATCG 60.392 55.000 0.00 0.00 0.00 3.34
762 804 2.100797 GCTGAAATCGCGCATGCA 59.899 55.556 19.57 0.00 42.97 3.96
767 809 0.523968 GAAATCGCGCATGCACATGT 60.524 50.000 19.57 0.30 42.97 3.21
768 810 0.523968 AAATCGCGCATGCACATGTC 60.524 50.000 19.57 4.20 42.97 3.06
769 811 2.327002 AATCGCGCATGCACATGTCC 62.327 55.000 19.57 0.00 42.97 4.02
771 813 4.541482 GCGCATGCACATGTCCCG 62.541 66.667 19.57 8.29 40.80 5.14
774 816 3.520862 CATGCACATGTCCCGCCC 61.521 66.667 0.00 0.00 34.23 6.13
775 817 3.731728 ATGCACATGTCCCGCCCT 61.732 61.111 0.00 0.00 0.00 5.19
776 818 3.704231 ATGCACATGTCCCGCCCTC 62.704 63.158 0.00 0.00 0.00 4.30
778 820 4.489771 CACATGTCCCGCCCTCCC 62.490 72.222 0.00 0.00 0.00 4.30
807 1097 2.294979 GCCCCCGGTTTACTTATTCAG 58.705 52.381 0.00 0.00 0.00 3.02
882 1172 1.134438 AACCACCCTCCTCCTTGTCC 61.134 60.000 0.00 0.00 0.00 4.02
896 1186 1.069358 CTTGTCCTATCTCGCCCTTCC 59.931 57.143 0.00 0.00 0.00 3.46
1011 1301 2.405805 CGCGGCCATGGTGAATTCA 61.406 57.895 14.67 3.38 0.00 2.57
1037 1327 4.698625 ACCGACCGAGCCTCCCTT 62.699 66.667 0.00 0.00 0.00 3.95
1110 1400 0.613260 AGGCTGTGACGGCTTCATTA 59.387 50.000 16.87 0.00 36.22 1.90
1203 1493 1.663702 CACTCCCGTCAACCGTGTC 60.664 63.158 0.00 0.00 33.66 3.67
1342 1632 0.815734 ACACGAGTCCCCTAATGTCG 59.184 55.000 0.00 0.00 36.71 4.35
1382 1675 1.743623 CGTTGAAGGCGCATACCCA 60.744 57.895 10.83 0.00 0.00 4.51
1420 1716 1.066143 CGTCCCAAGCAGAAGTGGTAT 60.066 52.381 0.00 0.00 32.75 2.73
1433 1729 2.029666 GGTATCCATGAGCGCGCT 59.970 61.111 37.28 37.28 0.00 5.92
1664 1964 4.044317 ACTCCCCTTATATTCGAGCTCCTA 59.956 45.833 8.47 0.00 0.00 2.94
1693 1993 1.275010 CAACAGGGGCCCATTTGTAAC 59.725 52.381 27.72 2.59 0.00 2.50
1895 2200 5.999600 TCCATTGTGAGCTACATAATCCATG 59.000 40.000 0.00 0.00 38.04 3.66
1905 2210 8.585471 AGCTACATAATCCATGGATTAATTGG 57.415 34.615 38.37 30.37 46.20 3.16
1944 2249 6.054941 AGTTGGTATGTATGAATCGCATCAA 58.945 36.000 0.00 0.00 38.44 2.57
1951 2256 4.805719 TGTATGAATCGCATCAACAGACTC 59.194 41.667 0.00 0.00 38.44 3.36
2051 2359 8.770010 AGTAGCAGTAAGTAATATCCTGTTCT 57.230 34.615 0.00 0.00 0.00 3.01
2111 2419 5.988310 TCAGAAACTGGAAGGACGTAATA 57.012 39.130 0.00 0.00 39.30 0.98
2118 2426 4.119862 CTGGAAGGACGTAATATGGTGTG 58.880 47.826 0.00 0.00 0.00 3.82
2136 2444 4.858692 GGTGTGCTAGTAATTGCATTGTTG 59.141 41.667 2.12 0.00 41.45 3.33
2143 2451 5.878332 AGTAATTGCATTGTTGTCGATGA 57.122 34.783 0.00 0.00 37.58 2.92
2166 2477 5.337219 TCGAGTTAGTACGTTCGTTAACA 57.663 39.130 16.62 0.00 35.16 2.41
2199 2536 7.148573 CCCTATTGCAATCTTAATGCTAGTACG 60.149 40.741 16.86 0.00 44.14 3.67
2223 2560 5.220739 GGCATACATACAGTTTCTTGCTCTG 60.221 44.000 0.00 0.00 35.60 3.35
2232 2569 4.275443 CAGTTTCTTGCTCTGCTTTCTCTT 59.725 41.667 0.00 0.00 0.00 2.85
2241 2578 5.174395 GCTCTGCTTTCTCTTGAAGATGTA 58.826 41.667 0.00 0.00 32.82 2.29
2254 2591 9.553064 CTCTTGAAGATGTATTTGGTAGCTAAT 57.447 33.333 6.81 6.81 0.00 1.73
2258 2595 9.109393 TGAAGATGTATTTGGTAGCTAATTGTC 57.891 33.333 6.90 4.18 0.00 3.18
2259 2596 9.109393 GAAGATGTATTTGGTAGCTAATTGTCA 57.891 33.333 6.90 5.65 0.00 3.58
2264 2601 3.643199 TGGTAGCTAATTGTCATGGCA 57.357 42.857 0.00 0.00 0.00 4.92
2269 2606 2.756760 AGCTAATTGTCATGGCAAGTGG 59.243 45.455 22.25 20.07 0.00 4.00
2287 2624 1.352687 TGGCAATACTACTGGGTTGCA 59.647 47.619 10.57 0.00 46.46 4.08
2297 2634 1.630369 ACTGGGTTGCATTCTAGCTGA 59.370 47.619 0.00 0.00 34.99 4.26
2306 2643 2.930887 GCATTCTAGCTGACCGACACAA 60.931 50.000 0.00 0.00 0.00 3.33
2345 2682 1.067821 GTTTCGAAAACCATGGCACCA 59.932 47.619 13.10 0.00 0.00 4.17
2357 2694 2.601367 GCACCATGTGGCCTTGGT 60.601 61.111 16.85 16.85 46.92 3.67
2377 2714 4.560743 TGGGCGCTGCACAGTTCA 62.561 61.111 7.64 0.00 36.87 3.18
2379 2716 2.629656 GGGCGCTGCACAGTTCATT 61.630 57.895 7.64 0.00 0.00 2.57
2389 2727 3.947196 TGCACAGTTCATTGTCTGTTTCT 59.053 39.130 12.03 0.00 42.05 2.52
2401 2739 7.719193 TCATTGTCTGTTTCTTGATTCCTTGTA 59.281 33.333 0.00 0.00 0.00 2.41
2410 2748 0.255890 GATTCCTTGTAGGGCTGGCA 59.744 55.000 2.88 0.00 35.59 4.92
2429 2767 3.294214 GCATGTCAGGGAGATCCAAATT 58.706 45.455 0.47 0.00 38.24 1.82
2430 2768 4.464008 GCATGTCAGGGAGATCCAAATTA 58.536 43.478 0.47 0.00 38.24 1.40
2431 2769 4.889409 GCATGTCAGGGAGATCCAAATTAA 59.111 41.667 0.47 0.00 38.24 1.40
2432 2770 5.537674 GCATGTCAGGGAGATCCAAATTAAT 59.462 40.000 0.47 0.00 38.24 1.40
2439 2777 8.660435 TCAGGGAGATCCAAATTAATAAGGTAG 58.340 37.037 0.47 0.00 38.24 3.18
2455 2793 3.596214 AGGTAGTTGAATAACAGGCACG 58.404 45.455 0.00 0.00 39.30 5.34
2457 2795 4.221262 AGGTAGTTGAATAACAGGCACGTA 59.779 41.667 0.00 0.00 39.30 3.57
2461 2799 4.870426 AGTTGAATAACAGGCACGTATCTG 59.130 41.667 13.63 13.63 39.30 2.90
2464 2802 4.868171 TGAATAACAGGCACGTATCTGAAC 59.132 41.667 19.84 9.19 35.20 3.18
2466 2804 5.847111 ATAACAGGCACGTATCTGAACTA 57.153 39.130 19.84 10.60 35.20 2.24
2468 2806 5.847111 AACAGGCACGTATCTGAACTATA 57.153 39.130 19.84 0.00 35.20 1.31
2469 2807 6.406692 AACAGGCACGTATCTGAACTATAT 57.593 37.500 19.84 0.00 35.20 0.86
2475 2813 5.983720 GCACGTATCTGAACTATATGTGGTT 59.016 40.000 14.15 0.00 42.89 3.67
2477 2815 6.641314 CACGTATCTGAACTATATGTGGTTCC 59.359 42.308 14.59 0.38 43.05 3.62
2482 2820 8.727100 ATCTGAACTATATGTGGTTCCTATCA 57.273 34.615 14.59 0.00 43.05 2.15
2483 2821 7.952671 TCTGAACTATATGTGGTTCCTATCAC 58.047 38.462 14.59 0.00 43.05 3.06
2485 2823 6.613679 TGAACTATATGTGGTTCCTATCACCA 59.386 38.462 14.59 0.00 43.05 4.17
2517 2855 2.696707 GCATCCCATGATTTGGTGATGT 59.303 45.455 17.05 0.00 45.53 3.06
2519 2857 4.022589 GCATCCCATGATTTGGTGATGTAG 60.023 45.833 17.05 2.38 45.53 2.74
2522 2860 3.893200 CCCATGATTTGGTGATGTAGCAT 59.107 43.478 0.00 0.00 44.83 3.79
2523 2861 4.342951 CCCATGATTTGGTGATGTAGCATT 59.657 41.667 0.00 0.00 44.83 3.56
2524 2862 5.286438 CCATGATTTGGTGATGTAGCATTG 58.714 41.667 0.00 0.00 40.99 2.82
2525 2863 5.163488 CCATGATTTGGTGATGTAGCATTGT 60.163 40.000 0.00 0.00 40.99 2.71
2526 2864 5.981088 TGATTTGGTGATGTAGCATTGTT 57.019 34.783 0.00 0.00 36.53 2.83
2527 2865 6.343716 TGATTTGGTGATGTAGCATTGTTT 57.656 33.333 0.00 0.00 36.53 2.83
2528 2866 6.157904 TGATTTGGTGATGTAGCATTGTTTG 58.842 36.000 0.00 0.00 36.53 2.93
2529 2867 5.528043 TTTGGTGATGTAGCATTGTTTGT 57.472 34.783 0.00 0.00 36.53 2.83
2530 2868 4.502171 TGGTGATGTAGCATTGTTTGTG 57.498 40.909 0.00 0.00 0.00 3.33
2531 2869 3.255395 TGGTGATGTAGCATTGTTTGTGG 59.745 43.478 0.00 0.00 0.00 4.17
2532 2870 3.255642 GGTGATGTAGCATTGTTTGTGGT 59.744 43.478 0.00 0.00 0.00 4.16
2533 2871 4.229096 GTGATGTAGCATTGTTTGTGGTG 58.771 43.478 0.00 0.00 0.00 4.17
2534 2872 2.791383 TGTAGCATTGTTTGTGGTGC 57.209 45.000 0.00 0.00 37.84 5.01
2535 2873 2.027385 TGTAGCATTGTTTGTGGTGCA 58.973 42.857 0.00 0.00 39.94 4.57
2536 2874 2.627221 TGTAGCATTGTTTGTGGTGCAT 59.373 40.909 0.00 0.00 39.94 3.96
2537 2875 2.443887 AGCATTGTTTGTGGTGCATC 57.556 45.000 0.00 0.00 39.94 3.91
2538 2876 1.062258 GCATTGTTTGTGGTGCATCG 58.938 50.000 0.00 0.00 37.52 3.84
2539 2877 1.062258 CATTGTTTGTGGTGCATCGC 58.938 50.000 2.79 2.79 0.00 4.58
2540 2878 0.672889 ATTGTTTGTGGTGCATCGCA 59.327 45.000 9.67 9.67 35.60 5.10
2541 2879 0.672889 TTGTTTGTGGTGCATCGCAT 59.327 45.000 15.13 0.00 41.91 4.73
2542 2880 0.039346 TGTTTGTGGTGCATCGCATG 60.039 50.000 15.13 0.00 41.91 4.06
2543 2881 0.240678 GTTTGTGGTGCATCGCATGA 59.759 50.000 15.13 3.41 41.91 3.07
2544 2882 1.135315 GTTTGTGGTGCATCGCATGAT 60.135 47.619 15.13 0.00 41.91 2.45
2545 2883 2.035530 TTGTGGTGCATCGCATGATA 57.964 45.000 15.13 0.00 41.91 2.15
2546 2884 2.259266 TGTGGTGCATCGCATGATAT 57.741 45.000 9.67 0.00 41.91 1.63
2547 2885 1.874872 TGTGGTGCATCGCATGATATG 59.125 47.619 9.67 0.00 41.91 1.78
2548 2886 1.198408 GTGGTGCATCGCATGATATGG 59.802 52.381 5.43 0.00 41.91 2.74
2549 2887 1.202794 TGGTGCATCGCATGATATGGT 60.203 47.619 0.00 0.00 41.91 3.55
2550 2888 1.198408 GGTGCATCGCATGATATGGTG 59.802 52.381 0.00 0.00 41.91 4.17
2551 2889 2.145536 GTGCATCGCATGATATGGTGA 58.854 47.619 0.00 0.00 41.91 4.02
2552 2890 2.745821 GTGCATCGCATGATATGGTGAT 59.254 45.455 0.00 0.00 41.91 3.06
2556 2894 5.713822 CATCGCATGATATGGTGATGTAG 57.286 43.478 0.00 0.00 43.53 2.74
2557 2895 3.588955 TCGCATGATATGGTGATGTAGC 58.411 45.455 0.00 0.00 0.00 3.58
2558 2896 3.006752 TCGCATGATATGGTGATGTAGCA 59.993 43.478 0.00 0.00 41.72 3.49
2559 2897 3.124128 CGCATGATATGGTGATGTAGCAC 59.876 47.826 0.00 0.00 40.04 4.40
2560 2898 4.321718 GCATGATATGGTGATGTAGCACT 58.678 43.478 0.00 0.00 40.04 4.40
2568 2906 5.357742 TGGTGATGTAGCACTGTTCATAT 57.642 39.130 0.00 0.00 38.78 1.78
2583 2921 2.368439 TCATATGCTTTCTGGGTGTGC 58.632 47.619 0.00 0.00 0.00 4.57
2595 2933 3.520862 GTGTGCGGCCCATGGATG 61.521 66.667 15.22 3.14 0.00 3.51
2617 2960 4.406326 TGGGCTCCGTCACATATTTAGTTA 59.594 41.667 0.00 0.00 0.00 2.24
2623 2966 6.399743 TCCGTCACATATTTAGTTACTTGCA 58.600 36.000 0.00 0.00 0.00 4.08
2628 2971 6.657117 TCACATATTTAGTTACTTGCAGGCAA 59.343 34.615 6.53 6.53 0.00 4.52
2632 2975 8.840321 CATATTTAGTTACTTGCAGGCAATAGT 58.160 33.333 7.21 5.55 35.20 2.12
2642 2985 2.825532 GCAGGCAATAGTCCCAAAAAGA 59.174 45.455 0.00 0.00 0.00 2.52
2647 2990 6.378280 CAGGCAATAGTCCCAAAAAGATTACT 59.622 38.462 0.00 0.00 0.00 2.24
2648 2991 6.603599 AGGCAATAGTCCCAAAAAGATTACTC 59.396 38.462 0.00 0.00 0.00 2.59
2649 2992 6.458342 GGCAATAGTCCCAAAAAGATTACTCG 60.458 42.308 0.00 0.00 0.00 4.18
2654 2997 5.011738 AGTCCCAAAAAGATTACTCGTGAGA 59.988 40.000 3.44 0.00 39.12 3.27
2669 3014 7.849804 ACTCGTGAGATTTATTTGTTAGCAT 57.150 32.000 3.44 0.00 40.84 3.79
2671 3016 8.818057 ACTCGTGAGATTTATTTGTTAGCATAC 58.182 33.333 3.44 0.00 40.84 2.39
2672 3017 8.138365 TCGTGAGATTTATTTGTTAGCATACC 57.862 34.615 0.00 0.00 33.31 2.73
2690 3035 5.798434 GCATACCTTAACGAATTTGGTTCAC 59.202 40.000 0.00 0.00 36.60 3.18
2751 5885 9.699410 AGATGGTTTAATTGATTGATTAGTCCA 57.301 29.630 0.00 0.00 34.20 4.02
2762 5896 8.868522 TGATTGATTAGTCCATTAATGATCCC 57.131 34.615 17.23 1.82 0.00 3.85
2763 5897 7.890127 TGATTGATTAGTCCATTAATGATCCCC 59.110 37.037 17.23 4.47 0.00 4.81
2765 5899 7.347319 TGATTAGTCCATTAATGATCCCCAT 57.653 36.000 17.23 1.91 36.99 4.00
2767 5901 4.664688 AGTCCATTAATGATCCCCATCC 57.335 45.455 17.23 0.00 33.53 3.51
2771 5905 4.290459 TCCATTAATGATCCCCATCCTCTG 59.710 45.833 17.23 0.00 33.53 3.35
2772 5906 3.795688 TTAATGATCCCCATCCTCTGC 57.204 47.619 0.00 0.00 33.53 4.26
2773 5907 1.830486 AATGATCCCCATCCTCTGCT 58.170 50.000 0.00 0.00 33.53 4.24
2774 5908 1.360185 ATGATCCCCATCCTCTGCTC 58.640 55.000 0.00 0.00 0.00 4.26
2775 5909 0.267054 TGATCCCCATCCTCTGCTCT 59.733 55.000 0.00 0.00 0.00 4.09
2776 5910 0.975887 GATCCCCATCCTCTGCTCTC 59.024 60.000 0.00 0.00 0.00 3.20
2777 5911 0.473501 ATCCCCATCCTCTGCTCTCC 60.474 60.000 0.00 0.00 0.00 3.71
2778 5912 1.383664 CCCCATCCTCTGCTCTCCA 60.384 63.158 0.00 0.00 0.00 3.86
2780 5914 0.469070 CCCATCCTCTGCTCTCCAAG 59.531 60.000 0.00 0.00 0.00 3.61
2789 5923 3.076092 CTCTCCAAGCAGCCTGGT 58.924 61.111 10.02 0.00 0.00 4.00
2790 5924 1.377994 CTCTCCAAGCAGCCTGGTT 59.622 57.895 10.02 2.71 38.82 3.67
2792 5926 0.185901 TCTCCAAGCAGCCTGGTTTT 59.814 50.000 6.38 0.00 35.69 2.43
2793 5927 1.043022 CTCCAAGCAGCCTGGTTTTT 58.957 50.000 6.38 0.00 35.69 1.94
2794 5928 1.000171 CTCCAAGCAGCCTGGTTTTTC 60.000 52.381 6.38 0.00 35.69 2.29
2796 5930 1.138661 CCAAGCAGCCTGGTTTTTCAA 59.861 47.619 6.38 0.00 35.69 2.69
2798 5932 2.803956 CAAGCAGCCTGGTTTTTCAATG 59.196 45.455 6.38 0.00 35.69 2.82
2799 5933 1.345415 AGCAGCCTGGTTTTTCAATGG 59.655 47.619 0.00 0.00 0.00 3.16
2801 5935 2.027837 GCAGCCTGGTTTTTCAATGGAT 60.028 45.455 0.00 0.00 0.00 3.41
2802 5936 3.592059 CAGCCTGGTTTTTCAATGGATG 58.408 45.455 0.00 0.00 0.00 3.51
2803 5937 2.568509 AGCCTGGTTTTTCAATGGATGG 59.431 45.455 0.00 0.00 0.00 3.51
2805 5939 3.617288 GCCTGGTTTTTCAATGGATGGTC 60.617 47.826 0.00 0.00 0.00 4.02
2806 5940 3.367292 CCTGGTTTTTCAATGGATGGTCG 60.367 47.826 0.00 0.00 0.00 4.79
2808 5942 3.505680 TGGTTTTTCAATGGATGGTCGAG 59.494 43.478 0.00 0.00 0.00 4.04
2810 5944 4.142600 GGTTTTTCAATGGATGGTCGAGAG 60.143 45.833 0.00 0.00 0.00 3.20
2811 5945 4.551702 TTTTCAATGGATGGTCGAGAGA 57.448 40.909 0.00 0.00 38.16 3.10
2812 5946 3.808466 TTCAATGGATGGTCGAGAGAG 57.192 47.619 0.00 0.00 43.49 3.20
2813 5947 2.034878 TCAATGGATGGTCGAGAGAGG 58.965 52.381 0.00 0.00 43.49 3.69
2814 5948 0.755686 AATGGATGGTCGAGAGAGGC 59.244 55.000 0.00 0.00 43.49 4.70
2816 5950 1.039785 TGGATGGTCGAGAGAGGCAG 61.040 60.000 0.00 0.00 43.49 4.85
2817 5951 0.753479 GGATGGTCGAGAGAGGCAGA 60.753 60.000 0.00 0.00 43.49 4.26
2818 5952 1.327303 GATGGTCGAGAGAGGCAGAT 58.673 55.000 0.00 0.00 43.49 2.90
2819 5953 1.269448 GATGGTCGAGAGAGGCAGATC 59.731 57.143 0.00 0.00 43.49 2.75
2820 5954 1.098129 TGGTCGAGAGAGGCAGATCG 61.098 60.000 0.00 0.00 43.49 3.69
2821 5955 1.098712 GGTCGAGAGAGGCAGATCGT 61.099 60.000 0.00 0.00 43.49 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.528489 TGCACCACAGTATATAAGATATAGTGA 57.472 33.333 20.60 2.88 35.48 3.41
8 9 9.254133 GCATGCACCACAGTATATAAGATATAG 57.746 37.037 14.21 0.00 0.00 1.31
9 10 8.204160 GGCATGCACCACAGTATATAAGATATA 58.796 37.037 21.36 0.00 0.00 0.86
10 11 7.050377 GGCATGCACCACAGTATATAAGATAT 58.950 38.462 21.36 0.00 0.00 1.63
11 12 6.213397 AGGCATGCACCACAGTATATAAGATA 59.787 38.462 21.36 0.00 0.00 1.98
12 13 5.013495 AGGCATGCACCACAGTATATAAGAT 59.987 40.000 21.36 0.00 0.00 2.40
13 14 4.347876 AGGCATGCACCACAGTATATAAGA 59.652 41.667 21.36 0.00 0.00 2.10
14 15 4.645535 AGGCATGCACCACAGTATATAAG 58.354 43.478 21.36 0.00 0.00 1.73
15 16 4.102367 TGAGGCATGCACCACAGTATATAA 59.898 41.667 21.36 0.00 0.00 0.98
16 17 3.645687 TGAGGCATGCACCACAGTATATA 59.354 43.478 21.36 0.00 0.00 0.86
17 18 2.439135 TGAGGCATGCACCACAGTATAT 59.561 45.455 21.36 0.00 0.00 0.86
18 19 1.836802 TGAGGCATGCACCACAGTATA 59.163 47.619 21.36 0.00 0.00 1.47
19 20 0.620030 TGAGGCATGCACCACAGTAT 59.380 50.000 21.36 0.00 0.00 2.12
20 21 0.036105 CTGAGGCATGCACCACAGTA 60.036 55.000 21.36 0.00 41.80 2.74
21 22 1.303074 CTGAGGCATGCACCACAGT 60.303 57.895 21.36 0.00 41.80 3.55
22 23 0.393944 ATCTGAGGCATGCACCACAG 60.394 55.000 21.36 20.00 46.34 3.66
23 24 0.911053 TATCTGAGGCATGCACCACA 59.089 50.000 21.36 11.93 0.00 4.17
24 25 1.303309 GTATCTGAGGCATGCACCAC 58.697 55.000 21.36 7.80 0.00 4.16
25 26 0.911053 TGTATCTGAGGCATGCACCA 59.089 50.000 21.36 14.97 0.00 4.17
26 27 2.042686 TTGTATCTGAGGCATGCACC 57.957 50.000 21.36 10.81 0.00 5.01
27 28 3.208594 TCATTGTATCTGAGGCATGCAC 58.791 45.455 21.36 13.34 0.00 4.57
28 29 3.564053 TCATTGTATCTGAGGCATGCA 57.436 42.857 21.36 0.00 0.00 3.96
29 30 4.760715 AGATTCATTGTATCTGAGGCATGC 59.239 41.667 9.90 9.90 31.32 4.06
30 31 6.879276 AAGATTCATTGTATCTGAGGCATG 57.121 37.500 6.56 0.00 32.82 4.06
45 46 9.872684 ACCATCTCCATGTTTATTAAGATTCAT 57.127 29.630 0.00 0.00 0.00 2.57
46 47 9.123902 CACCATCTCCATGTTTATTAAGATTCA 57.876 33.333 0.00 0.00 0.00 2.57
47 48 9.342308 TCACCATCTCCATGTTTATTAAGATTC 57.658 33.333 0.00 0.00 0.00 2.52
48 49 9.347240 CTCACCATCTCCATGTTTATTAAGATT 57.653 33.333 0.00 0.00 0.00 2.40
49 50 7.941238 CCTCACCATCTCCATGTTTATTAAGAT 59.059 37.037 0.00 0.00 0.00 2.40
50 51 7.282585 CCTCACCATCTCCATGTTTATTAAGA 58.717 38.462 0.00 0.00 0.00 2.10
51 52 6.488006 CCCTCACCATCTCCATGTTTATTAAG 59.512 42.308 0.00 0.00 0.00 1.85
52 53 6.364701 CCCTCACCATCTCCATGTTTATTAA 58.635 40.000 0.00 0.00 0.00 1.40
53 54 5.690097 GCCCTCACCATCTCCATGTTTATTA 60.690 44.000 0.00 0.00 0.00 0.98
54 55 4.796606 CCCTCACCATCTCCATGTTTATT 58.203 43.478 0.00 0.00 0.00 1.40
55 56 3.435601 GCCCTCACCATCTCCATGTTTAT 60.436 47.826 0.00 0.00 0.00 1.40
56 57 2.092429 GCCCTCACCATCTCCATGTTTA 60.092 50.000 0.00 0.00 0.00 2.01
57 58 1.341383 GCCCTCACCATCTCCATGTTT 60.341 52.381 0.00 0.00 0.00 2.83
58 59 0.257039 GCCCTCACCATCTCCATGTT 59.743 55.000 0.00 0.00 0.00 2.71
59 60 0.622738 AGCCCTCACCATCTCCATGT 60.623 55.000 0.00 0.00 0.00 3.21
60 61 0.108207 GAGCCCTCACCATCTCCATG 59.892 60.000 0.00 0.00 0.00 3.66
61 62 1.059006 GGAGCCCTCACCATCTCCAT 61.059 60.000 2.53 0.00 43.42 3.41
62 63 1.690633 GGAGCCCTCACCATCTCCA 60.691 63.158 2.53 0.00 43.42 3.86
63 64 1.059006 ATGGAGCCCTCACCATCTCC 61.059 60.000 0.00 0.00 42.35 3.71
64 65 1.622811 CTATGGAGCCCTCACCATCTC 59.377 57.143 0.00 0.00 44.45 2.75
86 87 6.890663 TTACAATTACCGTTGATTAGACCG 57.109 37.500 0.00 0.00 33.37 4.79
245 248 9.984190 TTTGTGTTTCTTTACTAACTTTTTGGT 57.016 25.926 0.00 0.00 0.00 3.67
454 481 9.485206 GACAATGAACCTAAGTTTTAGTGACTA 57.515 33.333 0.00 0.00 35.94 2.59
455 482 7.170998 CGACAATGAACCTAAGTTTTAGTGACT 59.829 37.037 0.00 0.00 35.94 3.41
456 483 7.170320 TCGACAATGAACCTAAGTTTTAGTGAC 59.830 37.037 0.00 0.00 35.94 3.67
474 508 7.377766 TCCTTAAAATCTTCCTTCGACAATG 57.622 36.000 0.00 0.00 0.00 2.82
506 540 5.975693 GTTGAATGGTCCCTCATTAAACA 57.024 39.130 11.05 0.00 43.23 2.83
568 602 9.516788 AGGTATACCTTTCTACTTAGGGAAAAT 57.483 33.333 19.27 0.00 46.09 1.82
682 718 2.034053 TGCCTTTTCACGGAACAATGTC 59.966 45.455 0.00 0.00 0.00 3.06
701 737 3.302365 TCTGCTTTATGGCTTGTTTGC 57.698 42.857 0.00 0.00 0.00 3.68
706 746 1.739466 TCGCTTCTGCTTTATGGCTTG 59.261 47.619 0.00 0.00 36.97 4.01
712 752 2.092323 GGGGTTTCGCTTCTGCTTTAT 58.908 47.619 0.00 0.00 36.97 1.40
724 764 1.179152 GGGGTTACAATGGGGTTTCG 58.821 55.000 0.00 0.00 0.00 3.46
745 786 2.100797 TGCATGCGCGATTTCAGC 59.899 55.556 12.10 4.75 42.97 4.26
751 793 2.711311 GACATGTGCATGCGCGAT 59.289 55.556 25.08 16.55 42.39 4.58
754 796 4.541482 CGGGACATGTGCATGCGC 62.541 66.667 24.25 24.25 42.39 6.09
784 826 1.986632 ATAAGTAAACCGGGGGCGGG 61.987 60.000 6.32 0.00 0.00 6.13
785 827 0.107066 AATAAGTAAACCGGGGGCGG 60.107 55.000 6.32 0.00 0.00 6.13
786 828 1.302366 GAATAAGTAAACCGGGGGCG 58.698 55.000 6.32 0.00 0.00 6.13
787 829 2.294979 CTGAATAAGTAAACCGGGGGC 58.705 52.381 6.32 0.00 0.00 5.80
788 830 2.294979 GCTGAATAAGTAAACCGGGGG 58.705 52.381 6.32 0.00 0.00 5.40
789 831 2.943033 CTGCTGAATAAGTAAACCGGGG 59.057 50.000 6.32 0.00 0.00 5.73
790 832 2.354821 GCTGCTGAATAAGTAAACCGGG 59.645 50.000 6.32 0.00 0.00 5.73
791 833 2.030457 CGCTGCTGAATAAGTAAACCGG 59.970 50.000 0.00 0.00 0.00 5.28
792 834 2.927477 TCGCTGCTGAATAAGTAAACCG 59.073 45.455 0.00 0.00 0.00 4.44
793 835 4.786609 GCATCGCTGCTGAATAAGTAAACC 60.787 45.833 3.51 0.00 45.32 3.27
794 836 4.274865 GCATCGCTGCTGAATAAGTAAAC 58.725 43.478 3.51 0.00 45.32 2.01
795 837 4.536364 GCATCGCTGCTGAATAAGTAAA 57.464 40.909 3.51 0.00 45.32 2.01
882 1172 1.548269 GAGGATGGAAGGGCGAGATAG 59.452 57.143 0.00 0.00 0.00 2.08
896 1186 1.134280 GTGGATGTGGTGAGGAGGATG 60.134 57.143 0.00 0.00 0.00 3.51
971 1261 2.147958 GTAAAGTCGCACCATCAACCA 58.852 47.619 0.00 0.00 0.00 3.67
1037 1327 1.381165 TTCGATCGCGGGATCTGACA 61.381 55.000 31.85 19.68 45.66 3.58
1231 1521 0.324738 TCCAGATCTTGCGAGGAGGT 60.325 55.000 0.00 0.00 0.00 3.85
1323 1613 0.815734 CGACATTAGGGGACTCGTGT 59.184 55.000 0.00 0.00 43.67 4.49
1342 1632 3.028366 GCGAAGAAACCGCCTCAGC 62.028 63.158 0.00 0.00 46.22 4.26
1420 1716 3.457263 TGGTAGCGCGCTCATGGA 61.457 61.111 40.23 18.17 0.00 3.41
1433 1729 3.755628 GCTCGGACGCCTGTGGTA 61.756 66.667 0.00 0.00 0.00 3.25
1479 1775 3.222354 GAACCGTGGCCTGTCGAGT 62.222 63.158 3.32 4.37 0.00 4.18
1589 1887 2.029020 ACGTTGAGCTGATTCTGCACTA 60.029 45.455 16.56 5.80 0.00 2.74
1664 1964 1.566298 GGCCCCTGTTGAGGAGTGAT 61.566 60.000 0.00 0.00 42.93 3.06
1693 1993 4.651778 TGGGGACAAGAACATTTACAGAG 58.348 43.478 0.00 0.00 37.44 3.35
1895 2200 9.482627 CTCTTACTCTATGTGACCAATTAATCC 57.517 37.037 0.00 0.00 0.00 3.01
1905 2210 7.773149 ACATACCAACTCTTACTCTATGTGAC 58.227 38.462 0.00 0.00 0.00 3.67
2030 2338 8.414778 ACTACAGAACAGGATATTACTTACTGC 58.585 37.037 0.00 0.00 32.60 4.40
2039 2347 5.661312 TGGTGCTACTACAGAACAGGATATT 59.339 40.000 0.00 0.00 33.90 1.28
2043 2351 2.884320 TGGTGCTACTACAGAACAGGA 58.116 47.619 0.00 0.00 33.90 3.86
2044 2352 3.678056 TTGGTGCTACTACAGAACAGG 57.322 47.619 0.00 0.00 33.90 4.00
2111 2419 4.706476 ACAATGCAATTACTAGCACACCAT 59.294 37.500 0.00 0.00 44.49 3.55
2118 2426 5.216566 TCGACAACAATGCAATTACTAGC 57.783 39.130 0.00 0.00 32.46 3.42
2136 2444 4.449870 ACGTACTAACTCGATCATCGAC 57.550 45.455 5.39 0.00 44.82 4.20
2143 2451 5.927030 TGTTAACGAACGTACTAACTCGAT 58.073 37.500 11.66 2.90 38.51 3.59
2166 2477 4.754411 AAGATTGCAATAGGGGATGGAT 57.246 40.909 12.97 0.00 0.00 3.41
2199 2536 4.878397 AGAGCAAGAAACTGTATGTATGCC 59.122 41.667 0.00 0.00 0.00 4.40
2207 2544 4.708177 AGAAAGCAGAGCAAGAAACTGTA 58.292 39.130 0.00 0.00 34.60 2.74
2208 2545 3.549794 AGAAAGCAGAGCAAGAAACTGT 58.450 40.909 0.00 0.00 34.60 3.55
2209 2546 3.814283 AGAGAAAGCAGAGCAAGAAACTG 59.186 43.478 0.00 0.00 35.14 3.16
2210 2547 4.084011 AGAGAAAGCAGAGCAAGAAACT 57.916 40.909 0.00 0.00 0.00 2.66
2223 2560 7.150783 ACCAAATACATCTTCAAGAGAAAGC 57.849 36.000 0.00 0.00 38.06 3.51
2232 2569 9.109393 GACAATTAGCTACCAAATACATCTTCA 57.891 33.333 0.00 0.00 0.00 3.02
2241 2578 4.955450 TGCCATGACAATTAGCTACCAAAT 59.045 37.500 0.00 0.00 0.00 2.32
2254 2591 1.340088 ATTGCCACTTGCCATGACAA 58.660 45.000 0.00 0.00 40.16 3.18
2258 2595 3.065786 CAGTAGTATTGCCACTTGCCATG 59.934 47.826 0.00 0.00 40.16 3.66
2259 2596 3.282021 CAGTAGTATTGCCACTTGCCAT 58.718 45.455 0.00 0.00 40.16 4.40
2264 2601 3.686016 CAACCCAGTAGTATTGCCACTT 58.314 45.455 0.00 0.00 0.00 3.16
2269 2606 3.947834 AGAATGCAACCCAGTAGTATTGC 59.052 43.478 0.00 0.94 46.08 3.56
2272 2609 4.656112 AGCTAGAATGCAACCCAGTAGTAT 59.344 41.667 0.00 0.00 34.99 2.12
2287 2624 2.093973 CCTTGTGTCGGTCAGCTAGAAT 60.094 50.000 0.00 0.00 0.00 2.40
2297 2634 4.619227 CCACGCCCTTGTGTCGGT 62.619 66.667 0.00 0.00 38.20 4.69
2320 2657 2.657184 CCATGGTTTTCGAAACCGTTC 58.343 47.619 10.79 0.00 43.15 3.95
2323 2660 0.312416 TGCCATGGTTTTCGAAACCG 59.688 50.000 14.67 4.69 43.15 4.44
2337 2674 1.985662 CAAGGCCACATGGTGCCAT 60.986 57.895 24.40 13.59 37.57 4.40
2345 2682 2.118076 CCACCACCAAGGCCACAT 59.882 61.111 5.01 0.00 43.14 3.21
2377 2714 6.966534 ACAAGGAATCAAGAAACAGACAAT 57.033 33.333 0.00 0.00 0.00 2.71
2379 2716 5.997746 CCTACAAGGAATCAAGAAACAGACA 59.002 40.000 0.00 0.00 37.67 3.41
2389 2727 1.340991 GCCAGCCCTACAAGGAATCAA 60.341 52.381 0.00 0.00 37.67 2.57
2401 2739 3.736224 CCCTGACATGCCAGCCCT 61.736 66.667 3.04 0.00 32.97 5.19
2410 2748 7.946776 CCTTATTAATTTGGATCTCCCTGACAT 59.053 37.037 0.00 0.00 35.38 3.06
2429 2767 7.493320 CGTGCCTGTTATTCAACTACCTTATTA 59.507 37.037 0.00 0.00 35.56 0.98
2430 2768 6.315393 CGTGCCTGTTATTCAACTACCTTATT 59.685 38.462 0.00 0.00 35.56 1.40
2431 2769 5.815740 CGTGCCTGTTATTCAACTACCTTAT 59.184 40.000 0.00 0.00 35.56 1.73
2432 2770 5.172934 CGTGCCTGTTATTCAACTACCTTA 58.827 41.667 0.00 0.00 35.56 2.69
2439 2777 4.868171 TCAGATACGTGCCTGTTATTCAAC 59.132 41.667 15.49 0.00 35.06 3.18
2446 2784 4.737855 ATAGTTCAGATACGTGCCTGTT 57.262 40.909 15.49 8.04 0.00 3.16
2450 2788 4.923871 CCACATATAGTTCAGATACGTGCC 59.076 45.833 0.00 0.00 0.00 5.01
2457 2795 8.589338 GTGATAGGAACCACATATAGTTCAGAT 58.411 37.037 12.11 6.48 43.37 2.90
2461 2799 7.062749 TGGTGATAGGAACCACATATAGTTC 57.937 40.000 0.00 0.00 42.82 3.01
2483 2821 1.524621 GGATGCACCACGAGGATGG 60.525 63.158 5.68 0.00 46.10 3.51
2485 2823 1.348008 ATGGGATGCACCACGAGGAT 61.348 55.000 5.68 0.00 44.72 3.24
2517 2855 2.095314 CGATGCACCACAAACAATGCTA 60.095 45.455 0.00 0.00 38.90 3.49
2519 2857 1.062258 CGATGCACCACAAACAATGC 58.938 50.000 0.00 0.00 38.59 3.56
2522 2860 0.672889 ATGCGATGCACCACAAACAA 59.327 45.000 0.00 0.00 43.04 2.83
2523 2861 0.039346 CATGCGATGCACCACAAACA 60.039 50.000 0.00 0.00 43.04 2.83
2524 2862 0.240678 TCATGCGATGCACCACAAAC 59.759 50.000 0.00 0.00 43.04 2.93
2525 2863 1.175654 ATCATGCGATGCACCACAAA 58.824 45.000 0.00 0.00 43.04 2.83
2526 2864 2.035530 TATCATGCGATGCACCACAA 57.964 45.000 0.00 0.00 43.04 3.33
2527 2865 1.874872 CATATCATGCGATGCACCACA 59.125 47.619 0.00 0.00 43.04 4.17
2528 2866 1.198408 CCATATCATGCGATGCACCAC 59.802 52.381 0.00 0.00 43.04 4.16
2529 2867 1.202794 ACCATATCATGCGATGCACCA 60.203 47.619 0.00 0.00 43.04 4.17
2530 2868 1.198408 CACCATATCATGCGATGCACC 59.802 52.381 0.00 0.00 43.04 5.01
2531 2869 2.145536 TCACCATATCATGCGATGCAC 58.854 47.619 0.00 0.00 43.04 4.57
2532 2870 2.547299 TCACCATATCATGCGATGCA 57.453 45.000 0.00 0.00 44.86 3.96
2533 2871 2.745821 ACATCACCATATCATGCGATGC 59.254 45.455 12.83 0.00 39.92 3.91
2534 2872 4.033702 GCTACATCACCATATCATGCGATG 59.966 45.833 11.93 11.93 41.03 3.84
2535 2873 4.186926 GCTACATCACCATATCATGCGAT 58.813 43.478 0.00 0.00 35.50 4.58
2536 2874 3.006752 TGCTACATCACCATATCATGCGA 59.993 43.478 0.00 0.00 0.00 5.10
2537 2875 3.124128 GTGCTACATCACCATATCATGCG 59.876 47.826 0.00 0.00 0.00 4.73
2538 2876 4.153655 CAGTGCTACATCACCATATCATGC 59.846 45.833 0.00 0.00 37.68 4.06
2539 2877 5.303165 ACAGTGCTACATCACCATATCATG 58.697 41.667 0.00 0.00 37.68 3.07
2540 2878 5.557576 ACAGTGCTACATCACCATATCAT 57.442 39.130 0.00 0.00 37.68 2.45
2541 2879 5.104982 TGAACAGTGCTACATCACCATATCA 60.105 40.000 0.00 0.00 37.68 2.15
2542 2880 5.359756 TGAACAGTGCTACATCACCATATC 58.640 41.667 0.00 0.00 37.68 1.63
2543 2881 5.357742 TGAACAGTGCTACATCACCATAT 57.642 39.130 0.00 0.00 37.68 1.78
2544 2882 4.817318 TGAACAGTGCTACATCACCATA 57.183 40.909 0.00 0.00 37.68 2.74
2545 2883 3.701205 TGAACAGTGCTACATCACCAT 57.299 42.857 0.00 0.00 37.68 3.55
2546 2884 3.701205 ATGAACAGTGCTACATCACCA 57.299 42.857 0.00 0.00 37.68 4.17
2547 2885 4.024556 GCATATGAACAGTGCTACATCACC 60.025 45.833 6.97 0.00 37.68 4.02
2548 2886 4.813161 AGCATATGAACAGTGCTACATCAC 59.187 41.667 6.97 0.00 46.54 3.06
2549 2887 5.027293 AGCATATGAACAGTGCTACATCA 57.973 39.130 6.97 0.00 46.54 3.07
2556 2894 3.181493 CCCAGAAAGCATATGAACAGTGC 60.181 47.826 6.97 6.79 39.10 4.40
2557 2895 4.012374 ACCCAGAAAGCATATGAACAGTG 58.988 43.478 6.97 0.00 0.00 3.66
2558 2896 4.012374 CACCCAGAAAGCATATGAACAGT 58.988 43.478 6.97 0.00 0.00 3.55
2559 2897 4.012374 ACACCCAGAAAGCATATGAACAG 58.988 43.478 6.97 0.00 0.00 3.16
2560 2898 3.758023 CACACCCAGAAAGCATATGAACA 59.242 43.478 6.97 0.00 0.00 3.18
2568 2906 2.594303 CCGCACACCCAGAAAGCA 60.594 61.111 0.00 0.00 0.00 3.91
2595 2933 3.470645 ACTAAATATGTGACGGAGCCC 57.529 47.619 0.00 0.00 0.00 5.19
2617 2960 0.698238 TGGGACTATTGCCTGCAAGT 59.302 50.000 10.64 3.49 39.47 3.16
2623 2966 6.494059 AGTAATCTTTTTGGGACTATTGCCT 58.506 36.000 0.00 0.00 33.27 4.75
2628 2971 6.942976 TCACGAGTAATCTTTTTGGGACTAT 58.057 36.000 0.00 0.00 0.00 2.12
2632 2975 5.477607 TCTCACGAGTAATCTTTTTGGGA 57.522 39.130 0.00 0.00 0.00 4.37
2642 2985 9.378551 TGCTAACAAATAAATCTCACGAGTAAT 57.621 29.630 0.00 0.00 0.00 1.89
2647 2990 7.985184 AGGTATGCTAACAAATAAATCTCACGA 59.015 33.333 0.00 0.00 0.00 4.35
2648 2991 8.142994 AGGTATGCTAACAAATAAATCTCACG 57.857 34.615 0.00 0.00 0.00 4.35
2662 3007 7.080353 ACCAAATTCGTTAAGGTATGCTAAC 57.920 36.000 0.00 0.00 0.00 2.34
2669 3014 6.711194 TGATGTGAACCAAATTCGTTAAGGTA 59.289 34.615 0.00 0.00 40.56 3.08
2671 3016 6.007936 TGATGTGAACCAAATTCGTTAAGG 57.992 37.500 0.00 0.00 40.56 2.69
2672 3017 7.807433 TGATTGATGTGAACCAAATTCGTTAAG 59.193 33.333 0.00 0.00 40.56 1.85
2677 3022 8.686397 TTTATGATTGATGTGAACCAAATTCG 57.314 30.769 0.00 0.00 40.56 3.34
2707 3052 9.975218 AAACCATCTATTTTCAAGTAGTATGGT 57.025 29.630 14.00 14.00 38.72 3.55
2737 5871 7.890127 GGGGATCATTAATGGACTAATCAATCA 59.110 37.037 15.36 0.00 0.00 2.57
2738 5872 7.890127 TGGGGATCATTAATGGACTAATCAATC 59.110 37.037 15.36 7.37 0.00 2.67
2741 5875 6.778542 TGGGGATCATTAATGGACTAATCA 57.221 37.500 15.36 3.79 0.00 2.57
2744 5878 5.857283 AGGATGGGGATCATTAATGGACTAA 59.143 40.000 15.36 0.00 35.97 2.24
2748 5882 4.290459 CAGAGGATGGGGATCATTAATGGA 59.710 45.833 15.36 3.14 35.97 3.41
2749 5883 4.597004 CAGAGGATGGGGATCATTAATGG 58.403 47.826 15.36 0.00 35.97 3.16
2750 5884 4.015084 GCAGAGGATGGGGATCATTAATG 58.985 47.826 9.29 9.29 35.97 1.90
2751 5885 3.921486 AGCAGAGGATGGGGATCATTAAT 59.079 43.478 0.00 0.00 35.97 1.40
2752 5886 3.328931 GAGCAGAGGATGGGGATCATTAA 59.671 47.826 0.00 0.00 35.97 1.40
2755 5889 1.132462 AGAGCAGAGGATGGGGATCAT 60.132 52.381 0.00 0.00 39.13 2.45
2756 5890 0.267054 AGAGCAGAGGATGGGGATCA 59.733 55.000 0.00 0.00 0.00 2.92
2757 5891 0.975887 GAGAGCAGAGGATGGGGATC 59.024 60.000 0.00 0.00 0.00 3.36
2758 5892 0.473501 GGAGAGCAGAGGATGGGGAT 60.474 60.000 0.00 0.00 0.00 3.85
2759 5893 1.074926 GGAGAGCAGAGGATGGGGA 60.075 63.158 0.00 0.00 0.00 4.81
2760 5894 0.984961 TTGGAGAGCAGAGGATGGGG 60.985 60.000 0.00 0.00 0.00 4.96
2761 5895 0.469070 CTTGGAGAGCAGAGGATGGG 59.531 60.000 0.00 0.00 0.00 4.00
2772 5906 0.251077 AAACCAGGCTGCTTGGAGAG 60.251 55.000 33.91 10.65 39.08 3.20
2773 5907 0.185901 AAAACCAGGCTGCTTGGAGA 59.814 50.000 33.91 0.00 39.08 3.71
2774 5908 1.000171 GAAAAACCAGGCTGCTTGGAG 60.000 52.381 33.91 11.72 39.08 3.86
2775 5909 1.039856 GAAAAACCAGGCTGCTTGGA 58.960 50.000 33.91 0.00 39.08 3.53
2776 5910 0.752054 TGAAAAACCAGGCTGCTTGG 59.248 50.000 27.02 27.02 41.60 3.61
2777 5911 2.600470 TTGAAAAACCAGGCTGCTTG 57.400 45.000 9.56 4.57 0.00 4.01
2778 5912 2.224354 CCATTGAAAAACCAGGCTGCTT 60.224 45.455 9.56 0.00 0.00 3.91
2780 5914 1.344114 TCCATTGAAAAACCAGGCTGC 59.656 47.619 9.56 0.00 0.00 5.25
2781 5915 3.592059 CATCCATTGAAAAACCAGGCTG 58.408 45.455 7.75 7.75 0.00 4.85
2782 5916 2.568509 CCATCCATTGAAAAACCAGGCT 59.431 45.455 0.00 0.00 0.00 4.58
2783 5917 2.302733 ACCATCCATTGAAAAACCAGGC 59.697 45.455 0.00 0.00 0.00 4.85
2784 5918 3.367292 CGACCATCCATTGAAAAACCAGG 60.367 47.826 0.00 0.00 0.00 4.45
2785 5919 3.505680 TCGACCATCCATTGAAAAACCAG 59.494 43.478 0.00 0.00 0.00 4.00
2786 5920 3.491342 TCGACCATCCATTGAAAAACCA 58.509 40.909 0.00 0.00 0.00 3.67
2787 5921 3.756434 TCTCGACCATCCATTGAAAAACC 59.244 43.478 0.00 0.00 0.00 3.27
2788 5922 4.695455 TCTCTCGACCATCCATTGAAAAAC 59.305 41.667 0.00 0.00 0.00 2.43
2789 5923 4.905429 TCTCTCGACCATCCATTGAAAAA 58.095 39.130 0.00 0.00 0.00 1.94
2790 5924 4.507710 CTCTCTCGACCATCCATTGAAAA 58.492 43.478 0.00 0.00 0.00 2.29
2792 5926 2.432146 CCTCTCTCGACCATCCATTGAA 59.568 50.000 0.00 0.00 0.00 2.69
2793 5927 2.034878 CCTCTCTCGACCATCCATTGA 58.965 52.381 0.00 0.00 0.00 2.57
2794 5928 1.539929 GCCTCTCTCGACCATCCATTG 60.540 57.143 0.00 0.00 0.00 2.82
2796 5930 0.397675 TGCCTCTCTCGACCATCCAT 60.398 55.000 0.00 0.00 0.00 3.41
2798 5932 0.753479 TCTGCCTCTCTCGACCATCC 60.753 60.000 0.00 0.00 0.00 3.51
2799 5933 1.269448 GATCTGCCTCTCTCGACCATC 59.731 57.143 0.00 0.00 0.00 3.51
2801 5935 1.098129 CGATCTGCCTCTCTCGACCA 61.098 60.000 0.00 0.00 33.07 4.02
2802 5936 1.098712 ACGATCTGCCTCTCTCGACC 61.099 60.000 0.00 0.00 35.24 4.79
2803 5937 1.584175 TACGATCTGCCTCTCTCGAC 58.416 55.000 0.00 0.00 35.24 4.20


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

AutoCloner maintained by Alex Coulton.