Multiple sequence alignment - TraesCS3D01G050200

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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 TraesCS3D01G050200 chr3D 100.000 3414 0 0 1 3414 19303341 19299928 0.000000e+00 6305.0
1 TraesCS3D01G050200 chr3D 86.701 2128 195 49 290 2392 19286613 19288677 0.000000e+00 2281.0
2 TraesCS3D01G050200 chr3D 92.355 811 51 8 1 808 19308803 19308001 0.000000e+00 1144.0
3 TraesCS3D01G050200 chr3D 96.571 175 5 1 2948 3121 131236268 131236094 4.310000e-74 289.0
4 TraesCS3D01G050200 chr3D 97.619 168 4 0 2949 3116 435703285 435703452 4.310000e-74 289.0
5 TraesCS3D01G050200 chr3D 95.322 171 8 0 2946 3116 562563351 562563521 4.340000e-69 272.0
6 TraesCS3D01G050200 chr3D 100.000 38 0 0 834 871 19308003 19307966 1.700000e-08 71.3
7 TraesCS3D01G050200 chr3A 90.287 2687 187 42 1 2665 26873338 26870704 0.000000e+00 3448.0
8 TraesCS3D01G050200 chr3A 86.400 2728 248 59 8 2664 26827688 26830363 0.000000e+00 2868.0
9 TraesCS3D01G050200 chr3A 93.898 295 11 4 3118 3408 26870448 26870157 4.040000e-119 438.0
10 TraesCS3D01G050200 chr3A 91.667 240 18 1 3172 3411 26831373 26831610 7.060000e-87 331.0
11 TraesCS3D01G050200 chr3A 83.088 136 20 3 269 402 64085229 64085363 1.660000e-23 121.0
12 TraesCS3D01G050200 chr3A 96.825 63 1 1 3118 3180 26830691 26830752 1.680000e-18 104.0
13 TraesCS3D01G050200 chr3A 92.857 56 4 0 2174 2229 95891687 95891742 7.850000e-12 82.4
14 TraesCS3D01G050200 chr3B 90.723 1757 98 25 963 2665 31068241 31066496 0.000000e+00 2281.0
15 TraesCS3D01G050200 chr3B 89.201 1639 114 25 954 2553 31058412 31060026 0.000000e+00 1988.0
16 TraesCS3D01G050200 chr3B 90.832 949 63 13 1 931 31069182 31068240 0.000000e+00 1249.0
17 TraesCS3D01G050200 chr3B 90.136 294 22 4 3118 3405 31066167 31065875 3.220000e-100 375.0
18 TraesCS3D01G050200 chr2A 90.496 484 42 4 1245 1728 28200529 28200050 1.340000e-178 636.0
19 TraesCS3D01G050200 chr2A 91.038 212 15 4 1517 1728 690320635 690320428 2.010000e-72 283.0
20 TraesCS3D01G050200 chr2D 98.204 167 3 0 2950 3116 18207142 18206976 3.330000e-75 292.0
21 TraesCS3D01G050200 chr2D 94.536 183 7 3 2946 3126 313809887 313809706 2.590000e-71 279.0
22 TraesCS3D01G050200 chr2D 95.152 165 8 0 1396 1560 613336810 613336646 9.400000e-66 261.0
23 TraesCS3D01G050200 chr2D 82.443 131 15 8 274 402 559398858 559398982 1.300000e-19 108.0
24 TraesCS3D01G050200 chrUn 97.041 169 5 0 2948 3116 318699534 318699366 5.580000e-73 285.0
25 TraesCS3D01G050200 chr1B 95.556 180 5 3 2953 3130 672032773 672032595 5.580000e-73 285.0
26 TraesCS3D01G050200 chr1B 81.159 138 17 8 267 402 554186306 554186436 6.030000e-18 102.0
27 TraesCS3D01G050200 chr5D 96.491 171 6 0 2950 3120 421112237 421112407 2.010000e-72 283.0
28 TraesCS3D01G050200 chr5D 83.471 121 18 2 2688 2806 419419073 419419193 1.000000e-20 111.0
29 TraesCS3D01G050200 chr6B 76.937 555 82 22 1387 1936 163653759 163653246 1.210000e-69 274.0
30 TraesCS3D01G050200 chr6B 80.556 144 19 8 261 402 116423812 116423948 6.030000e-18 102.0
31 TraesCS3D01G050200 chr6B 80.469 128 17 6 2663 2789 22814211 22814331 1.300000e-14 91.6
32 TraesCS3D01G050200 chr5A 93.514 185 11 1 2953 3136 44940927 44940743 1.210000e-69 274.0
33 TraesCS3D01G050200 chr5A 100.000 30 0 0 8 37 41166268 41166239 4.760000e-04 56.5
34 TraesCS3D01G050200 chr1A 92.121 165 13 0 1396 1560 497924740 497924576 2.050000e-57 233.0
35 TraesCS3D01G050200 chr7B 91.975 162 10 1 1396 1557 635886512 635886670 1.230000e-54 224.0
36 TraesCS3D01G050200 chr5B 80.822 146 20 6 2671 2811 562337446 562337588 1.300000e-19 108.0


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 TraesCS3D01G050200 chr3D 19299928 19303341 3413 True 6305.000000 6305 100.000000 1 3414 1 chr3D.!!$R1 3413
1 TraesCS3D01G050200 chr3D 19286613 19288677 2064 False 2281.000000 2281 86.701000 290 2392 1 chr3D.!!$F1 2102
2 TraesCS3D01G050200 chr3D 19307966 19308803 837 True 607.650000 1144 96.177500 1 871 2 chr3D.!!$R3 870
3 TraesCS3D01G050200 chr3A 26870157 26873338 3181 True 1943.000000 3448 92.092500 1 3408 2 chr3A.!!$R1 3407
4 TraesCS3D01G050200 chr3A 26827688 26831610 3922 False 1101.000000 2868 91.630667 8 3411 3 chr3A.!!$F3 3403
5 TraesCS3D01G050200 chr3B 31058412 31060026 1614 False 1988.000000 1988 89.201000 954 2553 1 chr3B.!!$F1 1599
6 TraesCS3D01G050200 chr3B 31065875 31069182 3307 True 1301.666667 2281 90.563667 1 3405 3 chr3B.!!$R1 3404
7 TraesCS3D01G050200 chr6B 163653246 163653759 513 True 274.000000 274 76.937000 1387 1936 1 chr6B.!!$R1 549

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
240 243 0.035056 CCCAGTGGTGATGGAGGTTC 60.035 60.0 8.74 0.0 40.51 3.62 F
1018 1102 0.763652 CATGTCTCCCTCCCCTGATG 59.236 60.0 0.00 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2185 0.459237 ATGTTCTTGGCGAGCGAGAG 60.459 55.0 0.0 0.0 0.0 3.20 R
2946 3196 1.031235 GAACGGAGGGAGTACTAGCC 58.969 60.0 0.0 0.0 0.0 3.93 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
57 59 8.117813 TCCTAAAACTTATTTTGGCAGGTAAG 57.882 34.615 11.59 11.59 38.50 2.34
136 138 5.278957 GGCAGGTAAATAATGGGCTAACATG 60.279 44.000 0.00 0.00 0.00 3.21
140 142 8.908903 CAGGTAAATAATGGGCTAACATGTTAA 58.091 33.333 18.55 5.06 0.00 2.01
215 217 7.063780 CAGAATTTTGGAAACATAGCCATTGTC 59.936 37.037 0.00 0.00 42.32 3.18
217 219 6.418057 TTTTGGAAACATAGCCATTGTCTT 57.582 33.333 0.00 0.00 42.32 3.01
238 241 2.606587 GCCCAGTGGTGATGGAGGT 61.607 63.158 8.74 0.00 40.51 3.85
240 243 0.035056 CCCAGTGGTGATGGAGGTTC 60.035 60.000 8.74 0.00 40.51 3.62
395 406 2.014857 AGCGACGACTATAAGCACTGA 58.985 47.619 0.00 0.00 0.00 3.41
402 413 3.376540 GACTATAAGCACTGAAGGAGCG 58.623 50.000 0.00 0.00 0.00 5.03
461 474 3.068590 CCAAAGTTGACATGGCTTTCTGT 59.931 43.478 0.00 0.00 30.96 3.41
542 567 7.558081 AGAGATTAGAGCAATCCGTAGCATATA 59.442 37.037 0.00 0.00 43.63 0.86
606 631 5.220931 GGCCAGCTAGAGTGTATTTTCAATG 60.221 44.000 0.00 0.00 0.00 2.82
609 634 7.044181 CCAGCTAGAGTGTATTTTCAATGAGA 58.956 38.462 0.00 0.00 0.00 3.27
685 710 2.029518 CTCTGGTGTCTGCACGCA 59.970 61.111 0.00 0.00 46.13 5.24
793 831 5.125417 GCTCCAGTTTTGGCACTAAATCATA 59.875 40.000 0.00 0.00 44.63 2.15
897 951 2.483714 CCAGATACATCTTCCCCACACG 60.484 54.545 0.00 0.00 34.22 4.49
924 996 5.602145 TCCAAGAAAACCAACCATTGATCTT 59.398 36.000 0.00 0.00 0.00 2.40
952 1027 2.546789 CCACACAAGTCCTTCGGTTAAC 59.453 50.000 0.00 0.00 0.00 2.01
956 1031 3.250040 CACAAGTCCTTCGGTTAACAAGG 59.750 47.826 15.46 15.46 40.69 3.61
995 1079 0.973632 TTTCGAGGCAAGAGGTAGCA 59.026 50.000 0.00 0.00 0.00 3.49
1018 1102 0.763652 CATGTCTCCCTCCCCTGATG 59.236 60.000 0.00 0.00 0.00 3.07
1048 1150 2.181777 GCGTGCTCATCGTCTCCA 59.818 61.111 0.00 0.00 0.00 3.86
1050 1152 1.226802 CGTGCTCATCGTCTCCAGG 60.227 63.158 0.00 0.00 0.00 4.45
1117 1222 6.748333 TTCTTGTTCATCACTTCATCCATC 57.252 37.500 0.00 0.00 0.00 3.51
1135 1240 3.194116 CCATCTTGGGAAAGTGTTGGATG 59.806 47.826 0.00 0.00 32.67 3.51
1159 1280 4.240096 GTTGGAAGAATGCTGACATTTGG 58.760 43.478 0.00 0.00 46.59 3.28
1160 1281 2.231964 TGGAAGAATGCTGACATTTGGC 59.768 45.455 0.00 0.00 46.59 4.52
1550 1678 1.716826 CTCGCTCTACCAGGACGTCC 61.717 65.000 27.67 27.67 0.00 4.79
1696 1824 4.717629 CTGCTCGACGGCGACCAA 62.718 66.667 10.67 0.00 42.51 3.67
1903 2031 2.283388 TTCGACTACCCCGGCTGT 60.283 61.111 0.00 0.00 0.00 4.40
2029 2157 3.347216 CGAACTGAACAGGGAAATGGAT 58.653 45.455 6.76 0.00 0.00 3.41
2086 2214 1.001378 GCCAAGAACATGCACGTCTTT 60.001 47.619 5.79 0.00 0.00 2.52
2107 2235 3.134792 AACAACACCGGCGTGCAA 61.135 55.556 6.01 0.00 44.40 4.08
2111 2239 4.539083 ACACCGGCGTGCAACAGA 62.539 61.111 6.01 0.00 44.40 3.41
2167 2295 0.171455 CGGAGTTCCTGGAGTCGAAG 59.829 60.000 0.00 0.00 0.00 3.79
2308 2436 0.392863 TCATGGCCAAGATGTCGGTG 60.393 55.000 10.96 0.00 0.00 4.94
2457 2607 4.039488 TGCTTGCTTGGTTCATCAGAAATT 59.961 37.500 0.00 0.00 35.08 1.82
2469 2619 7.041916 GGTTCATCAGAAATTCAAATGTTGCAA 60.042 33.333 0.00 0.00 35.08 4.08
2471 2621 7.435305 TCATCAGAAATTCAAATGTTGCAAGA 58.565 30.769 0.00 0.00 0.00 3.02
2510 2662 2.938451 ACCGTGATGTTGATGCATGTAG 59.062 45.455 2.46 0.00 0.00 2.74
2511 2663 2.938451 CCGTGATGTTGATGCATGTAGT 59.062 45.455 2.46 0.00 0.00 2.73
2512 2664 4.119136 CCGTGATGTTGATGCATGTAGTA 58.881 43.478 2.46 0.00 0.00 1.82
2518 2670 4.180817 TGTTGATGCATGTAGTAACTCGG 58.819 43.478 2.46 0.00 0.00 4.63
2542 2697 6.127842 GGGAAGTGTTAGTTGACTTTGTTTCA 60.128 38.462 0.00 0.00 32.47 2.69
2596 2751 2.169832 TGAGCTCAAAGGAAAGACGG 57.830 50.000 15.67 0.00 0.00 4.79
2637 2792 3.979948 TCGTTCGTAATTGAGGTGTCAA 58.020 40.909 0.00 0.00 46.81 3.18
2646 2801 2.967599 TGAGGTGTCAATCTGATCCG 57.032 50.000 0.00 0.00 31.76 4.18
2659 2814 1.766461 GATCCGGTGGTCATCCCCT 60.766 63.158 0.00 0.00 0.00 4.79
2660 2815 1.759459 GATCCGGTGGTCATCCCCTC 61.759 65.000 0.00 0.00 0.00 4.30
2661 2816 3.849951 CCGGTGGTCATCCCCTCG 61.850 72.222 0.00 0.00 0.00 4.63
2662 2817 3.075005 CGGTGGTCATCCCCTCGT 61.075 66.667 0.00 0.00 0.00 4.18
2663 2818 1.755395 CGGTGGTCATCCCCTCGTA 60.755 63.158 0.00 0.00 0.00 3.43
2664 2819 1.113517 CGGTGGTCATCCCCTCGTAT 61.114 60.000 0.00 0.00 0.00 3.06
2665 2820 1.820483 CGGTGGTCATCCCCTCGTATA 60.820 57.143 0.00 0.00 0.00 1.47
2666 2821 1.617357 GGTGGTCATCCCCTCGTATAC 59.383 57.143 0.00 0.00 0.00 1.47
2667 2822 2.313317 GTGGTCATCCCCTCGTATACA 58.687 52.381 3.32 0.00 0.00 2.29
2669 2824 3.323979 GTGGTCATCCCCTCGTATACAAT 59.676 47.826 3.32 0.00 0.00 2.71
2670 2825 4.525487 GTGGTCATCCCCTCGTATACAATA 59.475 45.833 3.32 0.00 0.00 1.90
2671 2826 5.187186 GTGGTCATCCCCTCGTATACAATAT 59.813 44.000 3.32 0.00 0.00 1.28
2672 2827 6.379133 GTGGTCATCCCCTCGTATACAATATA 59.621 42.308 3.32 0.00 0.00 0.86
2673 2828 6.379133 TGGTCATCCCCTCGTATACAATATAC 59.621 42.308 3.32 0.00 0.00 1.47
2674 2829 6.183360 GGTCATCCCCTCGTATACAATATACC 60.183 46.154 3.32 0.00 0.00 2.73
2675 2830 6.379133 GTCATCCCCTCGTATACAATATACCA 59.621 42.308 3.32 0.00 0.00 3.25
2676 2831 6.955267 TCATCCCCTCGTATACAATATACCAA 59.045 38.462 3.32 0.00 0.00 3.67
2677 2832 7.455323 TCATCCCCTCGTATACAATATACCAAA 59.545 37.037 3.32 0.00 0.00 3.28
2678 2833 7.801893 TCCCCTCGTATACAATATACCAAAT 57.198 36.000 3.32 0.00 0.00 2.32
2681 2836 8.533657 CCCCTCGTATACAATATACCAAATACA 58.466 37.037 3.32 0.00 0.00 2.29
2708 2863 6.707440 ACTACAATGAAACACCATTTCACA 57.293 33.333 4.31 0.00 40.70 3.58
2710 2865 6.978080 ACTACAATGAAACACCATTTCACAAC 59.022 34.615 4.31 0.00 40.70 3.32
2711 2866 4.803088 ACAATGAAACACCATTTCACAACG 59.197 37.500 4.31 0.00 40.70 4.10
2712 2867 4.909696 ATGAAACACCATTTCACAACGA 57.090 36.364 4.31 0.00 40.70 3.85
2713 2868 4.703645 TGAAACACCATTTCACAACGAA 57.296 36.364 0.00 0.00 33.90 3.85
2714 2869 5.255710 TGAAACACCATTTCACAACGAAT 57.744 34.783 0.00 0.00 33.90 3.34
2715 2870 5.277825 TGAAACACCATTTCACAACGAATC 58.722 37.500 0.00 0.00 33.90 2.52
2717 2872 6.261158 TGAAACACCATTTCACAACGAATCTA 59.739 34.615 0.00 0.00 33.90 1.98
2720 2875 5.529430 ACACCATTTCACAACGAATCTAACA 59.471 36.000 0.00 0.00 32.32 2.41
2722 2877 7.083858 CACCATTTCACAACGAATCTAACAAT 58.916 34.615 0.00 0.00 32.32 2.71
2724 2879 8.956426 ACCATTTCACAACGAATCTAACAATAT 58.044 29.630 0.00 0.00 32.32 1.28
2725 2880 9.787532 CCATTTCACAACGAATCTAACAATATT 57.212 29.630 0.00 0.00 32.32 1.28
2780 3026 9.924650 TCTCTATAGTTTGGTCAAAGTAAAGAC 57.075 33.333 13.04 0.00 39.02 3.01
2782 3028 9.706691 TCTATAGTTTGGTCAAAGTAAAGACAG 57.293 33.333 13.04 7.48 39.02 3.51
2783 3029 9.490379 CTATAGTTTGGTCAAAGTAAAGACAGT 57.510 33.333 13.04 1.24 39.02 3.55
2786 3032 8.570068 AGTTTGGTCAAAGTAAAGACAGTTTA 57.430 30.769 2.27 0.00 36.50 2.01
2789 3035 8.570068 TTGGTCAAAGTAAAGACAGTTTAACT 57.430 30.769 0.00 0.00 36.50 2.24
2790 3036 8.570068 TGGTCAAAGTAAAGACAGTTTAACTT 57.430 30.769 0.00 0.00 36.50 2.66
2791 3037 8.455682 TGGTCAAAGTAAAGACAGTTTAACTTG 58.544 33.333 0.00 0.00 36.50 3.16
2792 3038 7.913821 GGTCAAAGTAAAGACAGTTTAACTTGG 59.086 37.037 0.00 0.00 36.50 3.61
2794 3040 8.671028 TCAAAGTAAAGACAGTTTAACTTGGAC 58.329 33.333 0.00 0.00 0.00 4.02
2795 3041 8.455682 CAAAGTAAAGACAGTTTAACTTGGACA 58.544 33.333 0.00 0.00 0.00 4.02
2796 3042 8.570068 AAGTAAAGACAGTTTAACTTGGACAA 57.430 30.769 0.00 0.00 0.00 3.18
2797 3043 8.570068 AGTAAAGACAGTTTAACTTGGACAAA 57.430 30.769 0.00 0.00 0.00 2.83
2798 3044 9.016438 AGTAAAGACAGTTTAACTTGGACAAAA 57.984 29.630 0.00 0.00 0.00 2.44
2799 3045 9.797556 GTAAAGACAGTTTAACTTGGACAAAAT 57.202 29.630 0.00 0.00 0.00 1.82
2801 3047 9.719355 AAAGACAGTTTAACTTGGACAAAATTT 57.281 25.926 0.00 0.00 0.00 1.82
2822 3068 8.687824 AATTTATATGCAAAAAGAACACGAGG 57.312 30.769 0.00 0.00 0.00 4.63
2823 3069 4.701956 ATATGCAAAAAGAACACGAGGG 57.298 40.909 0.00 0.00 0.00 4.30
2824 3070 2.045561 TGCAAAAAGAACACGAGGGA 57.954 45.000 0.00 0.00 0.00 4.20
2825 3071 1.946768 TGCAAAAAGAACACGAGGGAG 59.053 47.619 0.00 0.00 0.00 4.30
2826 3072 1.947456 GCAAAAAGAACACGAGGGAGT 59.053 47.619 0.00 0.00 0.00 3.85
2827 3073 3.135994 GCAAAAAGAACACGAGGGAGTA 58.864 45.455 0.00 0.00 0.00 2.59
2828 3074 3.059120 GCAAAAAGAACACGAGGGAGTAC 60.059 47.826 0.00 0.00 0.00 2.73
2829 3075 3.397849 AAAAGAACACGAGGGAGTACC 57.602 47.619 0.00 0.00 40.67 3.34
2850 3096 6.479972 ACCTCCACGTTGATAAATAGATCA 57.520 37.500 0.00 0.00 33.96 2.92
2853 3099 7.827236 ACCTCCACGTTGATAAATAGATCAAAA 59.173 33.333 0.00 0.00 45.13 2.44
2854 3100 8.673711 CCTCCACGTTGATAAATAGATCAAAAA 58.326 33.333 0.00 0.00 45.13 1.94
2896 3146 6.972328 GCTAAAACAAGTGTTGACTTCATCAA 59.028 34.615 0.00 0.00 45.39 2.57
2946 3196 3.318017 CTCCGTTCTCAAACCACTACTG 58.682 50.000 0.00 0.00 31.27 2.74
2947 3197 2.036733 TCCGTTCTCAAACCACTACTGG 59.963 50.000 0.00 0.00 44.26 4.00
2948 3198 1.798813 CGTTCTCAAACCACTACTGGC 59.201 52.381 0.00 0.00 42.08 4.85
2949 3199 2.548067 CGTTCTCAAACCACTACTGGCT 60.548 50.000 0.00 0.00 42.08 4.75
2950 3200 3.305813 CGTTCTCAAACCACTACTGGCTA 60.306 47.826 0.00 0.00 42.08 3.93
2951 3201 4.246458 GTTCTCAAACCACTACTGGCTAG 58.754 47.826 0.00 0.00 42.08 3.42
2954 3204 4.461781 TCTCAAACCACTACTGGCTAGTAC 59.538 45.833 5.74 0.00 42.08 2.73
2956 3206 4.461781 TCAAACCACTACTGGCTAGTACTC 59.538 45.833 5.74 0.00 42.08 2.59
2957 3207 3.015675 ACCACTACTGGCTAGTACTCC 57.984 52.381 5.74 0.00 42.08 3.85
2958 3208 2.308690 CCACTACTGGCTAGTACTCCC 58.691 57.143 5.74 1.65 38.36 4.30
2959 3209 2.091775 CCACTACTGGCTAGTACTCCCT 60.092 54.545 5.74 0.00 38.36 4.20
2960 3210 3.215975 CACTACTGGCTAGTACTCCCTC 58.784 54.545 5.74 0.00 38.36 4.30
2961 3211 2.175284 ACTACTGGCTAGTACTCCCTCC 59.825 54.545 5.74 0.00 38.36 4.30
2962 3212 0.106619 ACTGGCTAGTACTCCCTCCG 60.107 60.000 0.00 0.00 34.74 4.63
2963 3213 0.106619 CTGGCTAGTACTCCCTCCGT 60.107 60.000 0.00 0.00 0.00 4.69
2964 3214 0.333993 TGGCTAGTACTCCCTCCGTT 59.666 55.000 0.00 0.00 0.00 4.44
2965 3215 1.031235 GGCTAGTACTCCCTCCGTTC 58.969 60.000 0.00 0.00 0.00 3.95
2966 3216 1.031235 GCTAGTACTCCCTCCGTTCC 58.969 60.000 0.00 0.00 0.00 3.62
2967 3217 1.409942 GCTAGTACTCCCTCCGTTCCT 60.410 57.143 0.00 0.00 0.00 3.36
2968 3218 2.158696 GCTAGTACTCCCTCCGTTCCTA 60.159 54.545 0.00 0.00 0.00 2.94
2969 3219 3.686691 GCTAGTACTCCCTCCGTTCCTAA 60.687 52.174 0.00 0.00 0.00 2.69
2970 3220 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2971 3221 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2972 3222 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2973 3223 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2974 3224 6.141790 AGTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2975 3225 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2976 3226 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2977 3227 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2978 3228 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2979 3229 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2980 3230 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2981 3231 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2982 3232 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2983 3233 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2984 3234 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2985 3235 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2986 3236 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3001 3251 9.948964 TGTCTTTCTAGAGATTTCAAATGATCA 57.051 29.630 0.00 0.00 0.00 2.92
3003 3253 9.388506 TCTTTCTAGAGATTTCAAATGATCACC 57.611 33.333 0.00 0.00 0.00 4.02
3004 3254 9.170734 CTTTCTAGAGATTTCAAATGATCACCA 57.829 33.333 0.00 0.00 0.00 4.17
3005 3255 8.498054 TTCTAGAGATTTCAAATGATCACCAC 57.502 34.615 0.00 0.00 0.00 4.16
3006 3256 7.623630 TCTAGAGATTTCAAATGATCACCACA 58.376 34.615 0.00 0.00 0.00 4.17
3007 3257 8.270030 TCTAGAGATTTCAAATGATCACCACAT 58.730 33.333 0.00 0.00 0.00 3.21
3008 3258 9.551734 CTAGAGATTTCAAATGATCACCACATA 57.448 33.333 0.00 0.00 0.00 2.29
3009 3259 8.218338 AGAGATTTCAAATGATCACCACATAC 57.782 34.615 0.00 0.00 0.00 2.39
3010 3260 7.011763 AGAGATTTCAAATGATCACCACATACG 59.988 37.037 0.00 0.00 0.00 3.06
3011 3261 5.559427 TTTCAAATGATCACCACATACGG 57.441 39.130 0.00 0.00 0.00 4.02
3012 3262 4.479786 TCAAATGATCACCACATACGGA 57.520 40.909 0.00 0.00 0.00 4.69
3013 3263 5.034852 TCAAATGATCACCACATACGGAT 57.965 39.130 0.00 0.00 0.00 4.18
3014 3264 4.815846 TCAAATGATCACCACATACGGATG 59.184 41.667 5.94 5.94 39.16 3.51
3016 3266 5.545063 AATGATCACCACATACGGATGTA 57.455 39.130 14.23 0.00 44.82 2.29
3017 3267 5.745312 ATGATCACCACATACGGATGTAT 57.255 39.130 14.23 2.79 44.82 2.29
3018 3268 6.850752 ATGATCACCACATACGGATGTATA 57.149 37.500 14.23 0.00 44.82 1.47
3019 3269 6.850752 TGATCACCACATACGGATGTATAT 57.149 37.500 14.23 4.54 44.82 0.86
3020 3270 7.948034 TGATCACCACATACGGATGTATATA 57.052 36.000 14.23 0.00 44.82 0.86
3021 3271 7.996385 TGATCACCACATACGGATGTATATAG 58.004 38.462 14.23 0.00 44.82 1.31
3022 3272 7.832187 TGATCACCACATACGGATGTATATAGA 59.168 37.037 14.23 7.88 44.82 1.98
3023 3273 7.387119 TCACCACATACGGATGTATATAGAC 57.613 40.000 14.23 0.00 44.82 2.59
3024 3274 6.943718 TCACCACATACGGATGTATATAGACA 59.056 38.462 14.23 2.07 44.82 3.41
3025 3275 7.614192 TCACCACATACGGATGTATATAGACAT 59.386 37.037 14.23 12.70 44.82 3.06
3026 3276 8.899771 CACCACATACGGATGTATATAGACATA 58.100 37.037 14.23 0.00 44.82 2.29
3027 3277 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
3057 3307 7.440523 AGTGTAGATTCACTCATTTTGTTCC 57.559 36.000 0.00 0.00 44.07 3.62
3058 3308 6.147821 AGTGTAGATTCACTCATTTTGTTCCG 59.852 38.462 0.00 0.00 44.07 4.30
3059 3309 5.995282 TGTAGATTCACTCATTTTGTTCCGT 59.005 36.000 0.00 0.00 0.00 4.69
3060 3310 7.117236 GTGTAGATTCACTCATTTTGTTCCGTA 59.883 37.037 0.00 0.00 35.68 4.02
3061 3311 7.822334 TGTAGATTCACTCATTTTGTTCCGTAT 59.178 33.333 0.00 0.00 0.00 3.06
3062 3312 7.076842 AGATTCACTCATTTTGTTCCGTATG 57.923 36.000 0.00 0.00 0.00 2.39
3063 3313 6.655003 AGATTCACTCATTTTGTTCCGTATGT 59.345 34.615 0.00 0.00 0.00 2.29
3064 3314 7.822334 AGATTCACTCATTTTGTTCCGTATGTA 59.178 33.333 0.00 0.00 0.00 2.29
3065 3315 6.961359 TCACTCATTTTGTTCCGTATGTAG 57.039 37.500 0.00 0.00 0.00 2.74
3066 3316 6.460781 TCACTCATTTTGTTCCGTATGTAGT 58.539 36.000 0.00 0.00 0.00 2.73
3067 3317 6.588756 TCACTCATTTTGTTCCGTATGTAGTC 59.411 38.462 0.00 0.00 0.00 2.59
3068 3318 6.367695 CACTCATTTTGTTCCGTATGTAGTCA 59.632 38.462 0.00 0.00 0.00 3.41
3069 3319 7.064609 CACTCATTTTGTTCCGTATGTAGTCAT 59.935 37.037 0.00 0.00 38.00 3.06
3070 3320 7.277981 ACTCATTTTGTTCCGTATGTAGTCATC 59.722 37.037 0.00 0.00 35.70 2.92
3071 3321 7.100409 TCATTTTGTTCCGTATGTAGTCATCA 58.900 34.615 0.00 0.00 35.70 3.07
3072 3322 7.768582 TCATTTTGTTCCGTATGTAGTCATCAT 59.231 33.333 0.00 0.00 35.70 2.45
3073 3323 7.915293 TTTTGTTCCGTATGTAGTCATCATT 57.085 32.000 0.00 0.00 35.70 2.57
3074 3324 7.915293 TTTGTTCCGTATGTAGTCATCATTT 57.085 32.000 0.00 0.00 35.70 2.32
3075 3325 6.902224 TGTTCCGTATGTAGTCATCATTTG 57.098 37.500 0.00 0.00 35.70 2.32
3076 3326 6.635755 TGTTCCGTATGTAGTCATCATTTGA 58.364 36.000 0.00 0.00 35.70 2.69
3077 3327 7.100409 TGTTCCGTATGTAGTCATCATTTGAA 58.900 34.615 0.00 0.00 35.70 2.69
3078 3328 7.604545 TGTTCCGTATGTAGTCATCATTTGAAA 59.395 33.333 0.00 0.00 35.70 2.69
3079 3329 7.534085 TCCGTATGTAGTCATCATTTGAAAC 57.466 36.000 0.00 0.00 35.70 2.78
3080 3330 6.537301 TCCGTATGTAGTCATCATTTGAAACC 59.463 38.462 0.00 0.00 35.70 3.27
3081 3331 6.538742 CCGTATGTAGTCATCATTTGAAACCT 59.461 38.462 0.00 0.00 35.70 3.50
3082 3332 7.254455 CCGTATGTAGTCATCATTTGAAACCTC 60.254 40.741 0.00 0.00 35.70 3.85
3083 3333 7.492669 CGTATGTAGTCATCATTTGAAACCTCT 59.507 37.037 0.00 0.00 35.70 3.69
3084 3334 9.817809 GTATGTAGTCATCATTTGAAACCTCTA 57.182 33.333 0.00 0.00 35.70 2.43
3085 3335 8.954950 ATGTAGTCATCATTTGAAACCTCTAG 57.045 34.615 0.00 0.00 35.70 2.43
3086 3336 8.134202 TGTAGTCATCATTTGAAACCTCTAGA 57.866 34.615 0.00 0.00 35.70 2.43
3087 3337 8.593679 TGTAGTCATCATTTGAAACCTCTAGAA 58.406 33.333 0.00 0.00 35.70 2.10
3088 3338 9.436957 GTAGTCATCATTTGAAACCTCTAGAAA 57.563 33.333 0.00 0.00 35.70 2.52
3089 3339 8.558973 AGTCATCATTTGAAACCTCTAGAAAG 57.441 34.615 0.00 0.00 35.70 2.62
3090 3340 8.378565 AGTCATCATTTGAAACCTCTAGAAAGA 58.621 33.333 0.00 0.00 35.70 2.52
3091 3341 8.447053 GTCATCATTTGAAACCTCTAGAAAGAC 58.553 37.037 0.00 0.00 35.70 3.01
3092 3342 8.156820 TCATCATTTGAAACCTCTAGAAAGACA 58.843 33.333 0.00 0.00 0.00 3.41
3093 3343 8.786898 CATCATTTGAAACCTCTAGAAAGACAA 58.213 33.333 0.00 0.00 0.00 3.18
3094 3344 8.746052 TCATTTGAAACCTCTAGAAAGACAAA 57.254 30.769 0.00 4.41 0.00 2.83
3095 3345 9.354673 TCATTTGAAACCTCTAGAAAGACAAAT 57.645 29.630 13.64 13.64 36.38 2.32
3107 3357 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3108 3358 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3109 3359 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3110 3360 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3111 3361 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3112 3362 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3113 3363 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3114 3364 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3115 3365 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3116 3366 7.092757 ACAAATATTTAGGAACGGAGGGAGTAA 60.093 37.037 0.00 0.00 0.00 2.24
3117 3367 7.628501 AATATTTAGGAACGGAGGGAGTAAT 57.371 36.000 0.00 0.00 0.00 1.89
3118 3368 8.731591 AATATTTAGGAACGGAGGGAGTAATA 57.268 34.615 0.00 0.00 0.00 0.98
3119 3369 6.667558 ATTTAGGAACGGAGGGAGTAATAG 57.332 41.667 0.00 0.00 0.00 1.73
3120 3370 3.684408 AGGAACGGAGGGAGTAATAGT 57.316 47.619 0.00 0.00 0.00 2.12
3121 3371 4.803329 AGGAACGGAGGGAGTAATAGTA 57.197 45.455 0.00 0.00 0.00 1.82
3301 4178 3.686916 ACTTGGGAAGAGAACTGCTAC 57.313 47.619 0.00 0.00 0.00 3.58
3332 4209 2.994417 TGCCGGGGAAAATGCACC 60.994 61.111 2.18 0.00 0.00 5.01
3343 4220 3.305110 GAAAATGCACCAACGAACGAAT 58.695 40.909 0.14 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.736126 ATTTGGTAAGCACTTATTGGCC 57.264 40.909 0.00 0.00 0.00 5.36
140 142 7.790027 TGCATTGCAACAGGGTATAAATATTT 58.210 30.769 9.33 5.89 34.76 1.40
215 217 0.107017 CCATCACCACTGGGCCTAAG 60.107 60.000 4.53 3.18 37.90 2.18
217 219 0.982852 CTCCATCACCACTGGGCCTA 60.983 60.000 4.53 0.00 37.90 3.93
238 241 1.751351 CTCGCACCATCCTCTACTGAA 59.249 52.381 0.00 0.00 0.00 3.02
240 243 0.249238 GCTCGCACCATCCTCTACTG 60.249 60.000 0.00 0.00 0.00 2.74
278 281 7.356089 AGGTTAAAAGTTTTTCCGGAAGAAT 57.644 32.000 21.70 9.77 33.44 2.40
297 301 5.356426 CCACGACACATGATGAATAGGTTA 58.644 41.667 0.00 0.00 0.00 2.85
395 406 5.548406 ACTTTGAGTTTGTATACGCTCCTT 58.452 37.500 14.96 0.00 0.00 3.36
542 567 1.486997 ATCCAGCAGTCCAGCACAGT 61.487 55.000 0.00 0.00 36.85 3.55
685 710 2.261671 CAACACCGTCTAGCCGCT 59.738 61.111 0.00 0.00 0.00 5.52
793 831 7.201679 CGAAATCATCCTTGCTCTGAGTAAAAT 60.202 37.037 9.45 3.96 0.00 1.82
897 951 5.852827 TCAATGGTTGGTTTTCTTGGATTC 58.147 37.500 0.00 0.00 0.00 2.52
924 996 1.507140 AGGACTTGTGTGGAGGTTGA 58.493 50.000 0.00 0.00 0.00 3.18
952 1027 4.645535 TCTCAACCAGAAGTGATTCCTTG 58.354 43.478 0.00 0.00 0.00 3.61
956 1031 6.147821 TCGAAATTCTCAACCAGAAGTGATTC 59.852 38.462 0.00 0.00 44.71 2.52
995 1079 2.003548 GGGGAGGGAGACATGGCTT 61.004 63.158 0.41 0.00 0.00 4.35
1018 1102 4.530857 CACGCGGGGGAGGATCAC 62.531 72.222 12.47 0.00 38.30 3.06
1117 1222 1.068333 CGCATCCAACACTTTCCCAAG 60.068 52.381 0.00 0.00 35.92 3.61
1135 1240 0.874390 TGTCAGCATTCTTCCAACGC 59.126 50.000 0.00 0.00 0.00 4.84
1696 1824 1.977854 TGGTAGCTGTTCACCATCAGT 59.022 47.619 1.76 0.00 39.91 3.41
1903 2031 2.204074 TCCTGGTAGGCCTTGGCA 60.204 61.111 12.58 0.00 34.61 4.92
2009 2137 5.163612 GCTTATCCATTTCCCTGTTCAGTTC 60.164 44.000 0.00 0.00 0.00 3.01
2018 2146 1.972872 CGCTGCTTATCCATTTCCCT 58.027 50.000 0.00 0.00 0.00 4.20
2029 2157 1.079127 GAGGACCTTGCGCTGCTTA 60.079 57.895 9.73 0.00 0.00 3.09
2044 2172 3.213402 GAGAGGCTCCGGACGAGG 61.213 72.222 11.71 0.00 39.22 4.63
2045 2173 3.578272 CGAGAGGCTCCGGACGAG 61.578 72.222 11.71 0.00 42.04 4.18
2057 2185 0.459237 ATGTTCTTGGCGAGCGAGAG 60.459 55.000 0.00 0.00 0.00 3.20
2457 2607 4.143543 TCAGGATGTCTTGCAACATTTGA 58.856 39.130 5.52 9.55 39.93 2.69
2469 2619 7.827236 TCACGGTTTAATTAATTCAGGATGTCT 59.173 33.333 3.39 0.00 37.40 3.41
2471 2621 7.931578 TCACGGTTTAATTAATTCAGGATGT 57.068 32.000 3.39 0.00 37.40 3.06
2510 2662 4.683320 GTCAACTAACACTTCCCGAGTTAC 59.317 45.833 0.00 0.00 36.10 2.50
2511 2663 4.586001 AGTCAACTAACACTTCCCGAGTTA 59.414 41.667 0.00 0.00 36.10 2.24
2512 2664 3.387050 AGTCAACTAACACTTCCCGAGTT 59.613 43.478 0.00 0.00 36.10 3.01
2518 2670 6.848451 TGAAACAAAGTCAACTAACACTTCC 58.152 36.000 0.00 0.00 31.38 3.46
2542 2697 1.267121 AGATGCCTTGTACGGACACT 58.733 50.000 0.00 0.00 34.48 3.55
2596 2751 7.306167 CGAACGATCTACACTACTTACTCTCTC 60.306 44.444 0.00 0.00 0.00 3.20
2637 2792 1.051812 GGATGACCACCGGATCAGAT 58.948 55.000 9.46 0.00 35.97 2.90
2646 2801 1.617357 GTATACGAGGGGATGACCACC 59.383 57.143 0.00 0.00 41.27 4.61
2683 2838 8.402798 TGTGAAATGGTGTTTCATTGTAGTAT 57.597 30.769 6.50 0.00 40.12 2.12
2685 2840 6.707440 TGTGAAATGGTGTTTCATTGTAGT 57.293 33.333 6.50 0.00 40.12 2.73
2686 2841 6.142161 CGTTGTGAAATGGTGTTTCATTGTAG 59.858 38.462 6.50 0.00 40.12 2.74
2687 2842 5.974158 CGTTGTGAAATGGTGTTTCATTGTA 59.026 36.000 6.50 0.00 40.12 2.41
2688 2843 4.803088 CGTTGTGAAATGGTGTTTCATTGT 59.197 37.500 6.50 0.00 40.12 2.71
2691 2846 4.909696 TCGTTGTGAAATGGTGTTTCAT 57.090 36.364 6.50 0.00 40.12 2.57
2692 2847 4.703645 TTCGTTGTGAAATGGTGTTTCA 57.296 36.364 0.00 0.00 36.21 2.69
2694 2849 5.514274 AGATTCGTTGTGAAATGGTGTTT 57.486 34.783 0.00 0.00 40.71 2.83
2695 2850 6.038825 TGTTAGATTCGTTGTGAAATGGTGTT 59.961 34.615 0.00 0.00 40.71 3.32
2696 2851 5.529430 TGTTAGATTCGTTGTGAAATGGTGT 59.471 36.000 0.00 0.00 40.71 4.16
2698 2853 6.627395 TTGTTAGATTCGTTGTGAAATGGT 57.373 33.333 0.00 0.00 40.71 3.55
2699 2854 9.787532 AATATTGTTAGATTCGTTGTGAAATGG 57.212 29.630 0.00 0.00 40.71 3.16
2754 3000 9.924650 GTCTTTACTTTGACCAAACTATAGAGA 57.075 33.333 6.78 0.00 0.00 3.10
2755 3001 9.706691 TGTCTTTACTTTGACCAAACTATAGAG 57.293 33.333 6.78 0.00 32.67 2.43
2757 3003 9.490379 ACTGTCTTTACTTTGACCAAACTATAG 57.510 33.333 0.00 0.00 32.67 1.31
2759 3005 8.747538 AACTGTCTTTACTTTGACCAAACTAT 57.252 30.769 0.00 0.00 32.67 2.12
2761 3007 7.462571 AAACTGTCTTTACTTTGACCAAACT 57.537 32.000 0.00 0.00 32.67 2.66
2762 3008 9.069078 GTTAAACTGTCTTTACTTTGACCAAAC 57.931 33.333 0.00 0.00 32.67 2.93
2764 3010 8.570068 AGTTAAACTGTCTTTACTTTGACCAA 57.430 30.769 0.00 0.00 32.67 3.67
2767 3013 8.671028 TCCAAGTTAAACTGTCTTTACTTTGAC 58.329 33.333 0.00 0.00 0.00 3.18
2769 3015 8.455682 TGTCCAAGTTAAACTGTCTTTACTTTG 58.544 33.333 0.00 0.00 0.00 2.77
2770 3016 8.570068 TGTCCAAGTTAAACTGTCTTTACTTT 57.430 30.769 0.00 0.00 0.00 2.66
2771 3017 8.570068 TTGTCCAAGTTAAACTGTCTTTACTT 57.430 30.769 0.00 0.00 0.00 2.24
2772 3018 8.570068 TTTGTCCAAGTTAAACTGTCTTTACT 57.430 30.769 0.00 0.00 0.00 2.24
2773 3019 9.797556 ATTTTGTCCAAGTTAAACTGTCTTTAC 57.202 29.630 0.00 0.00 0.00 2.01
2775 3021 9.719355 AAATTTTGTCCAAGTTAAACTGTCTTT 57.281 25.926 0.00 0.00 0.00 2.52
2796 3042 9.139174 CCTCGTGTTCTTTTTGCATATAAATTT 57.861 29.630 0.00 0.00 0.00 1.82
2797 3043 7.759433 CCCTCGTGTTCTTTTTGCATATAAATT 59.241 33.333 0.00 0.00 0.00 1.82
2798 3044 7.122055 TCCCTCGTGTTCTTTTTGCATATAAAT 59.878 33.333 0.00 0.00 0.00 1.40
2799 3045 6.431543 TCCCTCGTGTTCTTTTTGCATATAAA 59.568 34.615 0.00 0.00 0.00 1.40
2800 3046 5.941058 TCCCTCGTGTTCTTTTTGCATATAA 59.059 36.000 0.00 0.00 0.00 0.98
2801 3047 5.492895 TCCCTCGTGTTCTTTTTGCATATA 58.507 37.500 0.00 0.00 0.00 0.86
2802 3048 4.331968 TCCCTCGTGTTCTTTTTGCATAT 58.668 39.130 0.00 0.00 0.00 1.78
2803 3049 3.745799 TCCCTCGTGTTCTTTTTGCATA 58.254 40.909 0.00 0.00 0.00 3.14
2804 3050 2.554032 CTCCCTCGTGTTCTTTTTGCAT 59.446 45.455 0.00 0.00 0.00 3.96
2805 3051 1.946768 CTCCCTCGTGTTCTTTTTGCA 59.053 47.619 0.00 0.00 0.00 4.08
2806 3052 1.947456 ACTCCCTCGTGTTCTTTTTGC 59.053 47.619 0.00 0.00 0.00 3.68
2807 3053 3.497262 GGTACTCCCTCGTGTTCTTTTTG 59.503 47.826 0.00 0.00 0.00 2.44
2808 3054 3.390311 AGGTACTCCCTCGTGTTCTTTTT 59.610 43.478 0.00 0.00 40.71 1.94
2809 3055 2.970640 AGGTACTCCCTCGTGTTCTTTT 59.029 45.455 0.00 0.00 40.71 2.27
2810 3056 2.606378 AGGTACTCCCTCGTGTTCTTT 58.394 47.619 0.00 0.00 40.71 2.52
2811 3057 2.305858 AGGTACTCCCTCGTGTTCTT 57.694 50.000 0.00 0.00 40.71 2.52
2824 3070 7.287005 TGATCTATTTATCAACGTGGAGGTACT 59.713 37.037 0.00 0.00 35.16 2.73
2825 3071 7.431249 TGATCTATTTATCAACGTGGAGGTAC 58.569 38.462 0.00 0.00 32.97 3.34
2826 3072 7.591421 TGATCTATTTATCAACGTGGAGGTA 57.409 36.000 0.00 0.00 32.97 3.08
2827 3073 6.479972 TGATCTATTTATCAACGTGGAGGT 57.520 37.500 0.00 0.00 32.97 3.85
2828 3074 7.786178 TTTGATCTATTTATCAACGTGGAGG 57.214 36.000 0.00 0.00 43.69 4.30
2869 3119 6.509418 TGAAGTCAACACTTGTTTTAGCTT 57.491 33.333 0.00 0.00 43.37 3.74
2917 3167 3.135994 GTTTGAGAACGGAGGTTGCTAA 58.864 45.455 0.00 0.00 36.24 3.09
2918 3168 2.549349 GGTTTGAGAACGGAGGTTGCTA 60.549 50.000 0.00 0.00 36.24 3.49
2924 3174 2.299297 AGTAGTGGTTTGAGAACGGAGG 59.701 50.000 0.00 0.00 36.61 4.30
2925 3175 3.318017 CAGTAGTGGTTTGAGAACGGAG 58.682 50.000 0.00 0.00 36.61 4.63
2946 3196 1.031235 GAACGGAGGGAGTACTAGCC 58.969 60.000 0.00 0.00 0.00 3.93
2947 3197 1.031235 GGAACGGAGGGAGTACTAGC 58.969 60.000 0.00 0.00 0.00 3.42
2948 3198 2.732844 AGGAACGGAGGGAGTACTAG 57.267 55.000 0.00 0.00 0.00 2.57
2949 3199 4.591321 TTTAGGAACGGAGGGAGTACTA 57.409 45.455 0.00 0.00 0.00 1.82
2950 3200 3.463048 TTTAGGAACGGAGGGAGTACT 57.537 47.619 0.00 0.00 0.00 2.73
2951 3201 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
2954 3204 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2956 3206 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2957 3207 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2958 3208 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2959 3209 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2960 3210 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2975 3225 9.948964 TGATCATTTGAAATCTCTAGAAAGACA 57.051 29.630 0.00 0.00 0.00 3.41
2977 3227 9.388506 GGTGATCATTTGAAATCTCTAGAAAGA 57.611 33.333 0.00 0.00 0.00 2.52
2978 3228 9.170734 TGGTGATCATTTGAAATCTCTAGAAAG 57.829 33.333 0.00 0.00 0.00 2.62
2979 3229 8.950210 GTGGTGATCATTTGAAATCTCTAGAAA 58.050 33.333 0.00 0.00 0.00 2.52
2980 3230 8.102676 TGTGGTGATCATTTGAAATCTCTAGAA 58.897 33.333 0.00 0.00 0.00 2.10
2981 3231 7.623630 TGTGGTGATCATTTGAAATCTCTAGA 58.376 34.615 0.00 0.00 0.00 2.43
2982 3232 7.854557 TGTGGTGATCATTTGAAATCTCTAG 57.145 36.000 0.00 0.00 0.00 2.43
2983 3233 9.330063 GTATGTGGTGATCATTTGAAATCTCTA 57.670 33.333 0.00 0.00 0.00 2.43
2984 3234 7.011763 CGTATGTGGTGATCATTTGAAATCTCT 59.988 37.037 0.00 0.00 0.00 3.10
2985 3235 7.128331 CGTATGTGGTGATCATTTGAAATCTC 58.872 38.462 0.00 0.00 0.00 2.75
2986 3236 6.038603 CCGTATGTGGTGATCATTTGAAATCT 59.961 38.462 0.00 0.00 0.00 2.40
2987 3237 6.038161 TCCGTATGTGGTGATCATTTGAAATC 59.962 38.462 0.00 0.00 0.00 2.17
2988 3238 5.885352 TCCGTATGTGGTGATCATTTGAAAT 59.115 36.000 0.00 0.00 0.00 2.17
2989 3239 5.249420 TCCGTATGTGGTGATCATTTGAAA 58.751 37.500 0.00 0.00 0.00 2.69
2990 3240 4.837972 TCCGTATGTGGTGATCATTTGAA 58.162 39.130 0.00 0.00 0.00 2.69
2991 3241 4.479786 TCCGTATGTGGTGATCATTTGA 57.520 40.909 0.00 0.00 0.00 2.69
2992 3242 4.576053 ACATCCGTATGTGGTGATCATTTG 59.424 41.667 0.00 0.00 44.79 2.32
2993 3243 4.780815 ACATCCGTATGTGGTGATCATTT 58.219 39.130 0.00 0.00 44.79 2.32
2994 3244 4.422073 ACATCCGTATGTGGTGATCATT 57.578 40.909 0.00 0.00 44.79 2.57
2995 3245 5.745312 ATACATCCGTATGTGGTGATCAT 57.255 39.130 3.56 0.00 45.99 2.45
2996 3246 6.850752 ATATACATCCGTATGTGGTGATCA 57.149 37.500 3.56 0.00 45.99 2.92
2997 3247 8.129840 GTCTATATACATCCGTATGTGGTGATC 58.870 40.741 3.56 0.00 45.99 2.92
2998 3248 7.614192 TGTCTATATACATCCGTATGTGGTGAT 59.386 37.037 3.56 0.00 45.99 3.06
2999 3249 6.943718 TGTCTATATACATCCGTATGTGGTGA 59.056 38.462 3.56 0.00 45.99 4.02
3000 3250 7.153217 TGTCTATATACATCCGTATGTGGTG 57.847 40.000 3.56 0.00 45.99 4.17
3001 3251 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
3034 3284 6.073222 ACGGAACAAAATGAGTGAATCTACAC 60.073 38.462 0.00 0.00 40.60 2.90
3035 3285 5.995282 ACGGAACAAAATGAGTGAATCTACA 59.005 36.000 0.00 0.00 0.00 2.74
3036 3286 6.481954 ACGGAACAAAATGAGTGAATCTAC 57.518 37.500 0.00 0.00 0.00 2.59
3037 3287 7.822334 ACATACGGAACAAAATGAGTGAATCTA 59.178 33.333 0.00 0.00 0.00 1.98
3038 3288 6.655003 ACATACGGAACAAAATGAGTGAATCT 59.345 34.615 0.00 0.00 0.00 2.40
3039 3289 6.842163 ACATACGGAACAAAATGAGTGAATC 58.158 36.000 0.00 0.00 0.00 2.52
3040 3290 6.817765 ACATACGGAACAAAATGAGTGAAT 57.182 33.333 0.00 0.00 0.00 2.57
3041 3291 6.932400 ACTACATACGGAACAAAATGAGTGAA 59.068 34.615 0.00 0.00 0.00 3.18
3042 3292 6.460781 ACTACATACGGAACAAAATGAGTGA 58.539 36.000 0.00 0.00 0.00 3.41
3043 3293 6.367695 TGACTACATACGGAACAAAATGAGTG 59.632 38.462 0.00 0.00 0.00 3.51
3044 3294 6.460781 TGACTACATACGGAACAAAATGAGT 58.539 36.000 0.00 0.00 0.00 3.41
3045 3295 6.961359 TGACTACATACGGAACAAAATGAG 57.039 37.500 0.00 0.00 0.00 2.90
3046 3296 7.100409 TGATGACTACATACGGAACAAAATGA 58.900 34.615 0.00 0.00 36.82 2.57
3047 3297 7.302350 TGATGACTACATACGGAACAAAATG 57.698 36.000 0.00 0.00 36.82 2.32
3048 3298 8.506168 AATGATGACTACATACGGAACAAAAT 57.494 30.769 0.00 0.00 36.82 1.82
3049 3299 7.915293 AATGATGACTACATACGGAACAAAA 57.085 32.000 0.00 0.00 36.82 2.44
3050 3300 7.604545 TCAAATGATGACTACATACGGAACAAA 59.395 33.333 0.00 0.00 36.82 2.83
3051 3301 7.100409 TCAAATGATGACTACATACGGAACAA 58.900 34.615 0.00 0.00 36.82 2.83
3052 3302 6.635755 TCAAATGATGACTACATACGGAACA 58.364 36.000 0.00 0.00 36.82 3.18
3053 3303 7.534085 TTCAAATGATGACTACATACGGAAC 57.466 36.000 0.00 0.00 37.92 3.62
3054 3304 7.065324 GGTTTCAAATGATGACTACATACGGAA 59.935 37.037 0.00 0.00 37.92 4.30
3055 3305 6.537301 GGTTTCAAATGATGACTACATACGGA 59.463 38.462 0.00 0.00 37.92 4.69
3056 3306 6.538742 AGGTTTCAAATGATGACTACATACGG 59.461 38.462 0.00 0.00 37.92 4.02
3057 3307 7.492669 AGAGGTTTCAAATGATGACTACATACG 59.507 37.037 0.00 0.00 37.92 3.06
3058 3308 8.723942 AGAGGTTTCAAATGATGACTACATAC 57.276 34.615 0.00 0.00 37.92 2.39
3060 3310 8.762645 TCTAGAGGTTTCAAATGATGACTACAT 58.237 33.333 0.00 0.00 37.92 2.29
3061 3311 8.134202 TCTAGAGGTTTCAAATGATGACTACA 57.866 34.615 0.00 0.00 37.92 2.74
3062 3312 9.436957 TTTCTAGAGGTTTCAAATGATGACTAC 57.563 33.333 0.00 0.00 37.92 2.73
3063 3313 9.658799 CTTTCTAGAGGTTTCAAATGATGACTA 57.341 33.333 0.00 0.00 37.92 2.59
3064 3314 8.378565 TCTTTCTAGAGGTTTCAAATGATGACT 58.621 33.333 0.00 0.00 37.92 3.41
3065 3315 8.447053 GTCTTTCTAGAGGTTTCAAATGATGAC 58.553 37.037 0.00 0.00 37.92 3.06
3066 3316 8.156820 TGTCTTTCTAGAGGTTTCAAATGATGA 58.843 33.333 0.00 0.00 35.85 2.92
3067 3317 8.327941 TGTCTTTCTAGAGGTTTCAAATGATG 57.672 34.615 0.00 0.00 0.00 3.07
3068 3318 8.924511 TTGTCTTTCTAGAGGTTTCAAATGAT 57.075 30.769 0.00 0.00 0.00 2.45
3069 3319 8.746052 TTTGTCTTTCTAGAGGTTTCAAATGA 57.254 30.769 0.00 0.00 0.00 2.57
3081 3331 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3082 3332 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3083 3333 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3084 3334 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3085 3335 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3086 3336 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3087 3337 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3088 3338 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3089 3339 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3090 3340 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3091 3341 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3092 3342 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3093 3343 7.628501 ATTACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
3094 3344 7.954620 ACTATTACTCCCTCCGTTCCTAAATAT 59.045 37.037 0.00 0.00 0.00 1.28
3095 3345 7.300658 ACTATTACTCCCTCCGTTCCTAAATA 58.699 38.462 0.00 0.00 0.00 1.40
3096 3346 6.141790 ACTATTACTCCCTCCGTTCCTAAAT 58.858 40.000 0.00 0.00 0.00 1.40
3097 3347 5.522641 ACTATTACTCCCTCCGTTCCTAAA 58.477 41.667 0.00 0.00 0.00 1.85
3098 3348 5.134725 ACTATTACTCCCTCCGTTCCTAA 57.865 43.478 0.00 0.00 0.00 2.69
3099 3349 4.803329 ACTATTACTCCCTCCGTTCCTA 57.197 45.455 0.00 0.00 0.00 2.94
3100 3350 3.684408 ACTATTACTCCCTCCGTTCCT 57.316 47.619 0.00 0.00 0.00 3.36
3101 3351 4.892345 ACTTACTATTACTCCCTCCGTTCC 59.108 45.833 0.00 0.00 0.00 3.62
3102 3352 7.067494 TGTTACTTACTATTACTCCCTCCGTTC 59.933 40.741 0.00 0.00 0.00 3.95
3103 3353 6.891908 TGTTACTTACTATTACTCCCTCCGTT 59.108 38.462 0.00 0.00 0.00 4.44
3104 3354 6.426587 TGTTACTTACTATTACTCCCTCCGT 58.573 40.000 0.00 0.00 0.00 4.69
3105 3355 6.949352 TGTTACTTACTATTACTCCCTCCG 57.051 41.667 0.00 0.00 0.00 4.63
3106 3356 8.921205 TGAATGTTACTTACTATTACTCCCTCC 58.079 37.037 0.00 0.00 0.00 4.30
3107 3357 9.968870 CTGAATGTTACTTACTATTACTCCCTC 57.031 37.037 0.00 0.00 0.00 4.30
3108 3358 9.490083 ACTGAATGTTACTTACTATTACTCCCT 57.510 33.333 0.00 0.00 0.00 4.20
3115 3365 9.787435 TTGTCCAACTGAATGTTACTTACTATT 57.213 29.630 0.00 0.00 37.07 1.73
3116 3366 9.787435 TTTGTCCAACTGAATGTTACTTACTAT 57.213 29.630 0.00 0.00 37.07 2.12
3117 3367 9.616156 TTTTGTCCAACTGAATGTTACTTACTA 57.384 29.630 0.00 0.00 37.07 1.82
3118 3368 8.403236 GTTTTGTCCAACTGAATGTTACTTACT 58.597 33.333 0.00 0.00 37.07 2.24
3119 3369 8.185505 TGTTTTGTCCAACTGAATGTTACTTAC 58.814 33.333 0.00 0.00 37.07 2.34
3120 3370 8.282455 TGTTTTGTCCAACTGAATGTTACTTA 57.718 30.769 0.00 0.00 37.07 2.24
3121 3371 7.164230 TGTTTTGTCCAACTGAATGTTACTT 57.836 32.000 0.00 0.00 37.07 2.24
3285 4162 1.406205 GCCAGTAGCAGTTCTCTTCCC 60.406 57.143 0.00 0.00 42.97 3.97
3332 4209 0.309302 TGCCACCAATTCGTTCGTTG 59.691 50.000 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.