Multiple sequence alignment - TraesCS1D01G254200

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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 TraesCS1D01G254200 chr1D 100.000 3182 0 0 1 3182 346020661 346023842 0.000000e+00 5877.0
1 TraesCS1D01G254200 chr1A 92.430 2761 100 31 58 2789 446235528 446238208 0.000000e+00 3840.0
2 TraesCS1D01G254200 chr1A 79.039 229 32 12 2787 3002 446238289 446238514 3.310000e-30 143.0
3 TraesCS1D01G254200 chr1B 93.734 2378 76 21 666 2994 463831408 463833761 0.000000e+00 3498.0
4 TraesCS1D01G254200 chr1B 92.958 568 19 4 70 634 463830862 463831411 0.000000e+00 808.0
5 TraesCS1D01G254200 chr1B 97.015 67 2 0 1 67 463823832 463823898 2.590000e-21 113.0
6 TraesCS1D01G254200 chr1B 81.513 119 18 4 3065 3182 436357399 436357514 9.400000e-16 95.3
7 TraesCS1D01G254200 chr5A 85.119 168 21 3 1637 1804 11754084 11754247 5.460000e-38 169.0
8 TraesCS1D01G254200 chr5A 84.071 113 12 5 3072 3182 303096888 303096780 1.560000e-18 104.0
9 TraesCS1D01G254200 chr7D 91.398 93 8 0 3054 3146 58994622 58994714 9.260000e-26 128.0
10 TraesCS1D01G254200 chr6B 84.298 121 12 5 3052 3169 125858734 125858618 9.330000e-21 111.0
11 TraesCS1D01G254200 chr6B 94.872 39 0 2 3011 3047 125858793 125858755 3.430000e-05 60.2
12 TraesCS1D01G254200 chr2B 84.071 113 17 1 3054 3165 717774122 717774234 1.210000e-19 108.0
13 TraesCS1D01G254200 chr2B 77.297 185 28 11 3011 3182 756101847 756101664 2.610000e-16 97.1
14 TraesCS1D01G254200 chr7A 84.762 105 15 1 3065 3169 213316680 213316577 1.560000e-18 104.0
15 TraesCS1D01G254200 chr7A 84.906 106 13 2 3079 3182 384074997 384074893 1.560000e-18 104.0
16 TraesCS1D01G254200 chr2A 82.727 110 17 2 3072 3181 366815917 366815810 2.610000e-16 97.1
17 TraesCS1D01G254200 chr6D 82.051 117 14 6 3069 3182 176638414 176638526 3.380000e-15 93.5
18 TraesCS1D01G254200 chr6A 91.071 56 3 2 3094 3149 70224672 70224619 1.220000e-09 75.0
19 TraesCS1D01G254200 chr2D 92.308 52 2 1 3011 3060 591981210 591981159 4.400000e-09 73.1


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 TraesCS1D01G254200 chr1D 346020661 346023842 3181 False 5877.0 5877 100.0000 1 3182 1 chr1D.!!$F1 3181
1 TraesCS1D01G254200 chr1A 446235528 446238514 2986 False 1991.5 3840 85.7345 58 3002 2 chr1A.!!$F1 2944
2 TraesCS1D01G254200 chr1B 463830862 463833761 2899 False 2153.0 3498 93.3460 70 2994 2 chr1B.!!$F3 2924

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
496 505 0.108329 AGTTGATTACTCCCACCGCG 60.108 55.0 0.0 0.0 28.23 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2478 2537 3.364889 TGTTCACCACTTACTCACTCG 57.635 47.619 0.0 0.0 0.0 4.18 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
20 21 3.204505 GTTGGATCCAACGACACGA 57.795 52.632 35.47 8.14 45.24 4.35
21 22 1.504359 GTTGGATCCAACGACACGAA 58.496 50.000 35.47 7.38 45.24 3.85
22 23 1.193874 GTTGGATCCAACGACACGAAC 59.806 52.381 35.47 15.64 45.24 3.95
23 24 0.389757 TGGATCCAACGACACGAACA 59.610 50.000 13.46 0.00 0.00 3.18
24 25 1.202545 TGGATCCAACGACACGAACAA 60.203 47.619 13.46 0.00 0.00 2.83
25 26 1.868498 GGATCCAACGACACGAACAAA 59.132 47.619 6.95 0.00 0.00 2.83
26 27 2.288458 GGATCCAACGACACGAACAAAA 59.712 45.455 6.95 0.00 0.00 2.44
27 28 2.810028 TCCAACGACACGAACAAAAC 57.190 45.000 0.00 0.00 0.00 2.43
28 29 2.074576 TCCAACGACACGAACAAAACA 58.925 42.857 0.00 0.00 0.00 2.83
29 30 2.094575 TCCAACGACACGAACAAAACAG 59.905 45.455 0.00 0.00 0.00 3.16
30 31 2.094575 CCAACGACACGAACAAAACAGA 59.905 45.455 0.00 0.00 0.00 3.41
31 32 3.242608 CCAACGACACGAACAAAACAGAT 60.243 43.478 0.00 0.00 0.00 2.90
32 33 4.025563 CCAACGACACGAACAAAACAGATA 60.026 41.667 0.00 0.00 0.00 1.98
33 34 4.703899 ACGACACGAACAAAACAGATAC 57.296 40.909 0.00 0.00 0.00 2.24
34 35 4.114073 ACGACACGAACAAAACAGATACA 58.886 39.130 0.00 0.00 0.00 2.29
35 36 4.026310 ACGACACGAACAAAACAGATACAC 60.026 41.667 0.00 0.00 0.00 2.90
36 37 4.442705 GACACGAACAAAACAGATACACG 58.557 43.478 0.00 0.00 0.00 4.49
37 38 4.114073 ACACGAACAAAACAGATACACGA 58.886 39.130 0.00 0.00 0.00 4.35
38 39 4.208460 ACACGAACAAAACAGATACACGAG 59.792 41.667 0.00 0.00 0.00 4.18
39 40 3.183775 ACGAACAAAACAGATACACGAGC 59.816 43.478 0.00 0.00 0.00 5.03
40 41 3.183574 CGAACAAAACAGATACACGAGCA 59.816 43.478 0.00 0.00 0.00 4.26
41 42 4.455124 GAACAAAACAGATACACGAGCAC 58.545 43.478 0.00 0.00 0.00 4.40
42 43 2.806244 ACAAAACAGATACACGAGCACC 59.194 45.455 0.00 0.00 0.00 5.01
43 44 1.710013 AAACAGATACACGAGCACCG 58.290 50.000 0.00 0.00 45.44 4.94
44 45 0.736325 AACAGATACACGAGCACCGC 60.736 55.000 0.00 0.00 43.32 5.68
45 46 1.153842 CAGATACACGAGCACCGCA 60.154 57.895 0.00 0.00 43.32 5.69
46 47 1.153823 AGATACACGAGCACCGCAC 60.154 57.895 0.00 0.00 43.32 5.34
47 48 2.125673 ATACACGAGCACCGCACC 60.126 61.111 0.00 0.00 43.32 5.01
48 49 2.558554 GATACACGAGCACCGCACCT 62.559 60.000 0.00 0.00 43.32 4.00
49 50 2.835701 ATACACGAGCACCGCACCTG 62.836 60.000 0.00 0.00 43.32 4.00
50 51 4.662961 CACGAGCACCGCACCTGA 62.663 66.667 0.00 0.00 43.32 3.86
51 52 4.664677 ACGAGCACCGCACCTGAC 62.665 66.667 0.00 0.00 43.32 3.51
52 53 4.662961 CGAGCACCGCACCTGACA 62.663 66.667 0.00 0.00 0.00 3.58
53 54 2.280797 GAGCACCGCACCTGACAA 60.281 61.111 0.00 0.00 0.00 3.18
54 55 2.281070 AGCACCGCACCTGACAAG 60.281 61.111 0.00 0.00 0.00 3.16
55 56 2.591715 GCACCGCACCTGACAAGT 60.592 61.111 0.00 0.00 0.00 3.16
56 57 2.607892 GCACCGCACCTGACAAGTC 61.608 63.158 0.00 0.00 0.00 3.01
57 58 1.227527 CACCGCACCTGACAAGTCA 60.228 57.895 2.56 2.56 38.06 3.41
58 59 1.227556 ACCGCACCTGACAAGTCAC 60.228 57.895 0.00 0.00 35.46 3.67
59 60 1.227527 CCGCACCTGACAAGTCACA 60.228 57.895 0.00 0.00 35.46 3.58
60 61 1.498865 CCGCACCTGACAAGTCACAC 61.499 60.000 0.00 0.00 35.46 3.82
61 62 0.809636 CGCACCTGACAAGTCACACA 60.810 55.000 0.00 0.00 35.46 3.72
148 152 4.572571 GCAACCCCCACGACCACA 62.573 66.667 0.00 0.00 0.00 4.17
154 158 2.030562 CCCACGACCACAGTCACC 59.969 66.667 0.00 0.00 43.73 4.02
187 191 3.931247 CGGAACACGGACCCACCA 61.931 66.667 0.00 0.00 39.42 4.17
193 197 4.954118 ACGGACCCACCAGAGGCA 62.954 66.667 0.00 0.00 38.90 4.75
336 340 3.774599 GACCCGCATGTCATCCCCC 62.775 68.421 0.00 0.00 35.29 5.40
496 505 0.108329 AGTTGATTACTCCCACCGCG 60.108 55.000 0.00 0.00 28.23 6.46
497 506 1.448893 TTGATTACTCCCACCGCGC 60.449 57.895 0.00 0.00 0.00 6.86
498 507 2.588034 GATTACTCCCACCGCGCC 60.588 66.667 0.00 0.00 0.00 6.53
499 508 3.379865 GATTACTCCCACCGCGCCA 62.380 63.158 0.00 0.00 0.00 5.69
500 509 3.675619 ATTACTCCCACCGCGCCAC 62.676 63.158 0.00 0.00 0.00 5.01
598 607 2.435069 GCTAGTTTCTTACTCCTCCCCC 59.565 54.545 0.00 0.00 38.33 5.40
642 651 4.737177 GCTGGCTGGCTGGCTTCT 62.737 66.667 18.27 0.00 42.34 2.85
666 675 3.560239 GCCAAAGCCTTCCTTCTTCTACT 60.560 47.826 0.00 0.00 31.99 2.57
672 681 3.262151 GCCTTCCTTCTTCTACTGGAGTT 59.738 47.826 0.00 0.00 0.00 3.01
987 1035 0.465460 TTGCAAGCTTGAACCGAGGT 60.465 50.000 30.39 0.00 0.00 3.85
1041 1093 3.670377 GTGGTGTTCTTGGCGGCC 61.670 66.667 13.32 13.32 0.00 6.13
1125 1177 4.129737 CTCGACGACATGCCGGGT 62.130 66.667 6.33 0.00 0.00 5.28
1392 1444 0.895530 CCGTCAGCAAGAACCTCCTA 59.104 55.000 0.00 0.00 0.00 2.94
1980 2032 3.640407 GTGCAGGAGCTGGTGGGA 61.640 66.667 0.00 0.00 42.74 4.37
2187 2239 0.920763 AATGGAGGGGCTGACATGGA 60.921 55.000 0.00 0.00 0.00 3.41
2406 2464 8.515414 ACAGAAGAAGTTGGTGCTTTAATAATC 58.485 33.333 0.00 0.00 0.00 1.75
2504 2563 3.137544 TGAGTAAGTGGTGAACATTGGGT 59.862 43.478 0.00 0.00 0.00 4.51
2515 2574 4.037923 GTGAACATTGGGTCTTGATGTTGT 59.962 41.667 5.75 0.00 42.31 3.32
2556 2615 4.215613 GGTGTTAGGATCAGTGGTGTTTTC 59.784 45.833 0.00 0.00 0.00 2.29
2583 2642 6.394809 TGATGATCATCAAATATGGCAATGC 58.605 36.000 31.46 0.00 44.14 3.56
2601 2660 3.044305 GGCAAGCGTTCGCTGTCT 61.044 61.111 20.05 2.24 41.76 3.41
2607 2666 3.155998 CAAGCGTTCGCTGTCTAAATTG 58.844 45.455 20.05 8.43 41.76 2.32
2608 2667 2.413837 AGCGTTCGCTGTCTAAATTGT 58.586 42.857 18.75 0.00 40.32 2.71
2609 2668 3.581755 AGCGTTCGCTGTCTAAATTGTA 58.418 40.909 18.75 0.00 40.32 2.41
2610 2669 3.367025 AGCGTTCGCTGTCTAAATTGTAC 59.633 43.478 18.75 0.00 40.32 2.90
2669 2728 6.072112 ACAATGGTTACAAGCTTACAGTTG 57.928 37.500 0.00 5.88 0.00 3.16
2794 2936 1.852895 GTACTTGGCTTCTACGCGATG 59.147 52.381 15.93 4.70 0.00 3.84
2845 2987 2.429971 TGCAGATCTCAAGCCTGACTAG 59.570 50.000 0.00 0.00 0.00 2.57
2873 3025 7.100458 ACCTGATTTGTGATTACTTATTGCC 57.900 36.000 0.00 0.00 0.00 4.52
2877 3029 8.121305 TGATTTGTGATTACTTATTGCCAGTT 57.879 30.769 0.00 0.00 0.00 3.16
2879 3031 5.309323 TGTGATTACTTATTGCCAGTTGC 57.691 39.130 0.00 0.00 41.77 4.17
2893 3045 2.288948 CCAGTTGCAATTGCTTGGCTTA 60.289 45.455 29.37 6.12 42.66 3.09
2899 3051 3.119388 TGCAATTGCTTGGCTTACAGATC 60.119 43.478 29.37 0.00 42.66 2.75
2902 3054 3.423539 TTGCTTGGCTTACAGATCTGT 57.576 42.857 30.11 30.11 46.87 3.41
2905 3057 2.938756 GCTTGGCTTACAGATCTGTGCT 60.939 50.000 33.76 13.52 44.63 4.40
2906 3058 3.341823 CTTGGCTTACAGATCTGTGCTT 58.658 45.455 33.76 13.16 44.63 3.91
2909 3076 3.198872 GGCTTACAGATCTGTGCTTACC 58.801 50.000 33.76 23.27 44.63 2.85
2929 3096 3.209410 CCACTTATGGCAGAGTGATTCC 58.791 50.000 26.27 0.00 44.65 3.01
2935 3102 0.749454 GGCAGAGTGATTCCGGCAAT 60.749 55.000 0.00 0.00 0.00 3.56
2974 3146 7.663827 TCTTGAAGTGAATTCTGCATCATTTT 58.336 30.769 7.05 0.00 38.83 1.82
2975 3147 8.145767 TCTTGAAGTGAATTCTGCATCATTTTT 58.854 29.630 7.05 0.00 38.83 1.94
3002 3174 9.829507 ATTGATTTTCTTTTTGACACCACATTA 57.170 25.926 0.00 0.00 0.00 1.90
3003 3175 8.870160 TGATTTTCTTTTTGACACCACATTAG 57.130 30.769 0.00 0.00 0.00 1.73
3004 3176 7.437862 TGATTTTCTTTTTGACACCACATTAGC 59.562 33.333 0.00 0.00 0.00 3.09
3005 3177 6.463995 TTTCTTTTTGACACCACATTAGCT 57.536 33.333 0.00 0.00 0.00 3.32
3006 3178 7.575414 TTTCTTTTTGACACCACATTAGCTA 57.425 32.000 0.00 0.00 0.00 3.32
3007 3179 7.575414 TTCTTTTTGACACCACATTAGCTAA 57.425 32.000 8.99 8.99 0.00 3.09
3008 3180 7.575414 TCTTTTTGACACCACATTAGCTAAA 57.425 32.000 10.85 0.00 0.00 1.85
3009 3181 7.422399 TCTTTTTGACACCACATTAGCTAAAC 58.578 34.615 10.85 0.00 0.00 2.01
3010 3182 5.351233 TTTGACACCACATTAGCTAAACG 57.649 39.130 10.85 7.46 0.00 3.60
3011 3183 2.739913 TGACACCACATTAGCTAAACGC 59.260 45.455 10.85 0.00 39.57 4.84
3023 3195 2.629051 GCTAAACGCTAATGGGTCAGT 58.371 47.619 0.00 0.00 38.46 3.41
3024 3196 2.608090 GCTAAACGCTAATGGGTCAGTC 59.392 50.000 0.00 0.00 38.46 3.51
3025 3197 1.722011 AAACGCTAATGGGTCAGTCG 58.278 50.000 0.00 0.00 38.46 4.18
3026 3198 0.892755 AACGCTAATGGGTCAGTCGA 59.107 50.000 0.00 0.00 38.46 4.20
3027 3199 1.112113 ACGCTAATGGGTCAGTCGAT 58.888 50.000 0.00 0.00 33.98 3.59
3028 3200 1.480954 ACGCTAATGGGTCAGTCGATT 59.519 47.619 0.00 0.00 33.98 3.34
3029 3201 2.093658 ACGCTAATGGGTCAGTCGATTT 60.094 45.455 0.00 0.00 33.98 2.17
3030 3202 2.936498 CGCTAATGGGTCAGTCGATTTT 59.064 45.455 0.00 0.00 0.00 1.82
3031 3203 3.242413 CGCTAATGGGTCAGTCGATTTTG 60.242 47.826 0.00 0.00 0.00 2.44
3032 3204 3.938963 GCTAATGGGTCAGTCGATTTTGA 59.061 43.478 0.00 0.00 0.00 2.69
3033 3205 4.034510 GCTAATGGGTCAGTCGATTTTGAG 59.965 45.833 0.00 0.00 0.00 3.02
3034 3206 3.981071 ATGGGTCAGTCGATTTTGAGA 57.019 42.857 0.00 0.00 0.00 3.27
3035 3207 3.981071 TGGGTCAGTCGATTTTGAGAT 57.019 42.857 0.00 0.00 0.00 2.75
3036 3208 4.286297 TGGGTCAGTCGATTTTGAGATT 57.714 40.909 0.00 0.00 0.00 2.40
3037 3209 4.253685 TGGGTCAGTCGATTTTGAGATTC 58.746 43.478 0.00 0.00 0.00 2.52
3038 3210 3.623510 GGGTCAGTCGATTTTGAGATTCC 59.376 47.826 0.00 0.00 0.00 3.01
3039 3211 3.623510 GGTCAGTCGATTTTGAGATTCCC 59.376 47.826 0.00 0.00 0.00 3.97
3040 3212 4.253685 GTCAGTCGATTTTGAGATTCCCA 58.746 43.478 0.00 0.00 0.00 4.37
3041 3213 4.331168 GTCAGTCGATTTTGAGATTCCCAG 59.669 45.833 0.00 0.00 0.00 4.45
3042 3214 4.222810 TCAGTCGATTTTGAGATTCCCAGA 59.777 41.667 0.00 0.00 0.00 3.86
3043 3215 4.937620 CAGTCGATTTTGAGATTCCCAGAA 59.062 41.667 0.00 0.00 0.00 3.02
3044 3216 5.412594 CAGTCGATTTTGAGATTCCCAGAAA 59.587 40.000 0.00 0.00 0.00 2.52
3045 3217 6.094603 CAGTCGATTTTGAGATTCCCAGAAAT 59.905 38.462 0.00 0.00 0.00 2.17
3046 3218 6.660949 AGTCGATTTTGAGATTCCCAGAAATT 59.339 34.615 0.00 0.00 0.00 1.82
3047 3219 6.969473 GTCGATTTTGAGATTCCCAGAAATTC 59.031 38.462 0.00 0.00 0.00 2.17
3048 3220 6.658816 TCGATTTTGAGATTCCCAGAAATTCA 59.341 34.615 0.00 0.00 0.00 2.57
3049 3221 6.749118 CGATTTTGAGATTCCCAGAAATTCAC 59.251 38.462 0.00 0.00 0.00 3.18
3050 3222 5.982890 TTTGAGATTCCCAGAAATTCACC 57.017 39.130 0.00 0.00 0.00 4.02
3051 3223 3.609853 TGAGATTCCCAGAAATTCACCG 58.390 45.455 0.00 0.00 0.00 4.94
3052 3224 2.945668 GAGATTCCCAGAAATTCACCGG 59.054 50.000 0.00 0.00 0.00 5.28
3053 3225 2.576191 AGATTCCCAGAAATTCACCGGA 59.424 45.455 9.46 0.00 0.00 5.14
3054 3226 2.489938 TTCCCAGAAATTCACCGGAG 57.510 50.000 9.46 0.00 0.00 4.63
3069 3241 0.827368 CGGAGGAAGGAGAAGGAAGG 59.173 60.000 0.00 0.00 0.00 3.46
3070 3242 1.897647 CGGAGGAAGGAGAAGGAAGGT 60.898 57.143 0.00 0.00 0.00 3.50
3071 3243 1.557371 GGAGGAAGGAGAAGGAAGGTG 59.443 57.143 0.00 0.00 0.00 4.00
3072 3244 0.988063 AGGAAGGAGAAGGAAGGTGC 59.012 55.000 0.00 0.00 0.00 5.01
3073 3245 0.988063 GGAAGGAGAAGGAAGGTGCT 59.012 55.000 0.00 0.00 0.00 4.40
3074 3246 1.065782 GGAAGGAGAAGGAAGGTGCTC 60.066 57.143 0.00 0.00 0.00 4.26
3075 3247 1.625818 GAAGGAGAAGGAAGGTGCTCA 59.374 52.381 0.00 0.00 0.00 4.26
3076 3248 0.980423 AGGAGAAGGAAGGTGCTCAC 59.020 55.000 0.00 0.00 0.00 3.51
3077 3249 0.980423 GGAGAAGGAAGGTGCTCACT 59.020 55.000 0.00 0.00 0.00 3.41
3078 3250 1.338579 GGAGAAGGAAGGTGCTCACTG 60.339 57.143 0.00 0.00 0.00 3.66
3079 3251 0.689623 AGAAGGAAGGTGCTCACTGG 59.310 55.000 0.00 0.00 0.00 4.00
3080 3252 0.687354 GAAGGAAGGTGCTCACTGGA 59.313 55.000 0.00 0.00 0.00 3.86
3081 3253 0.689623 AAGGAAGGTGCTCACTGGAG 59.310 55.000 0.00 0.00 44.33 3.86
3082 3254 1.197430 AGGAAGGTGCTCACTGGAGG 61.197 60.000 0.00 0.00 41.67 4.30
3083 3255 1.298014 GAAGGTGCTCACTGGAGGG 59.702 63.158 0.00 0.00 41.67 4.30
3084 3256 2.811542 GAAGGTGCTCACTGGAGGGC 62.812 65.000 0.00 0.00 41.67 5.19
3085 3257 3.325753 GGTGCTCACTGGAGGGCT 61.326 66.667 0.00 0.00 41.67 5.19
3086 3258 1.990060 GGTGCTCACTGGAGGGCTA 60.990 63.158 0.00 0.00 41.67 3.93
3087 3259 1.219393 GTGCTCACTGGAGGGCTAC 59.781 63.158 0.00 0.00 41.67 3.58
3088 3260 1.990060 TGCTCACTGGAGGGCTACC 60.990 63.158 0.00 0.00 41.67 3.18
3102 3274 5.608798 AGGGCTACCTCAGTATCTATCTT 57.391 43.478 0.00 0.00 46.95 2.40
3103 3275 6.721843 AGGGCTACCTCAGTATCTATCTTA 57.278 41.667 0.00 0.00 46.95 2.10
3104 3276 6.727394 AGGGCTACCTCAGTATCTATCTTAG 58.273 44.000 0.00 0.00 46.95 2.18
3105 3277 5.889289 GGGCTACCTCAGTATCTATCTTAGG 59.111 48.000 0.00 0.00 33.84 2.69
3106 3278 5.889289 GGCTACCTCAGTATCTATCTTAGGG 59.111 48.000 0.00 0.00 32.42 3.53
3107 3279 6.486941 GCTACCTCAGTATCTATCTTAGGGT 58.513 44.000 0.00 0.00 32.42 4.34
3108 3280 6.949463 GCTACCTCAGTATCTATCTTAGGGTT 59.051 42.308 0.00 0.00 32.42 4.11
3109 3281 7.452189 GCTACCTCAGTATCTATCTTAGGGTTT 59.548 40.741 0.00 0.00 32.42 3.27
3111 3283 8.943594 ACCTCAGTATCTATCTTAGGGTTTAG 57.056 38.462 0.00 0.00 32.42 1.85
3112 3284 7.951245 ACCTCAGTATCTATCTTAGGGTTTAGG 59.049 40.741 0.00 0.00 32.42 2.69
3113 3285 7.397761 CCTCAGTATCTATCTTAGGGTTTAGGG 59.602 44.444 0.00 0.00 0.00 3.53
3114 3286 7.834046 TCAGTATCTATCTTAGGGTTTAGGGT 58.166 38.462 0.00 0.00 0.00 4.34
3115 3287 7.728981 TCAGTATCTATCTTAGGGTTTAGGGTG 59.271 40.741 0.00 0.00 0.00 4.61
3116 3288 7.017531 AGTATCTATCTTAGGGTTTAGGGTGG 58.982 42.308 0.00 0.00 0.00 4.61
3117 3289 4.563782 TCTATCTTAGGGTTTAGGGTGGG 58.436 47.826 0.00 0.00 0.00 4.61
3118 3290 1.975471 TCTTAGGGTTTAGGGTGGGG 58.025 55.000 0.00 0.00 0.00 4.96
3119 3291 0.924090 CTTAGGGTTTAGGGTGGGGG 59.076 60.000 0.00 0.00 0.00 5.40
3120 3292 1.216368 TTAGGGTTTAGGGTGGGGGC 61.216 60.000 0.00 0.00 0.00 5.80
3121 3293 4.435970 GGGTTTAGGGTGGGGGCG 62.436 72.222 0.00 0.00 0.00 6.13
3122 3294 4.435970 GGTTTAGGGTGGGGGCGG 62.436 72.222 0.00 0.00 0.00 6.13
3123 3295 3.654143 GTTTAGGGTGGGGGCGGT 61.654 66.667 0.00 0.00 0.00 5.68
3124 3296 3.653078 TTTAGGGTGGGGGCGGTG 61.653 66.667 0.00 0.00 0.00 4.94
3138 3310 4.712425 GGTGGTCGACGACGGTGG 62.712 72.222 22.07 0.00 40.21 4.61
3139 3311 3.969802 GTGGTCGACGACGGTGGT 61.970 66.667 20.92 0.00 40.21 4.16
3140 3312 3.968568 TGGTCGACGACGGTGGTG 61.969 66.667 20.92 0.00 40.21 4.17
3141 3313 3.969802 GGTCGACGACGGTGGTGT 61.970 66.667 20.92 0.00 40.21 4.16
3142 3314 2.728383 GTCGACGACGGTGGTGTG 60.728 66.667 12.94 0.00 40.21 3.82
3143 3315 3.968568 TCGACGACGGTGGTGTGG 61.969 66.667 7.55 0.00 40.21 4.17
3145 3317 4.675029 GACGACGGTGGTGTGGGG 62.675 72.222 0.00 0.00 0.00 4.96
3148 3320 4.265056 GACGGTGGTGTGGGGCTT 62.265 66.667 0.00 0.00 0.00 4.35
3149 3321 4.265056 ACGGTGGTGTGGGGCTTC 62.265 66.667 0.00 0.00 0.00 3.86
3151 3323 4.265056 GGTGGTGTGGGGCTTCGT 62.265 66.667 0.00 0.00 0.00 3.85
3152 3324 2.668550 GTGGTGTGGGGCTTCGTC 60.669 66.667 0.00 0.00 0.00 4.20
3153 3325 4.308458 TGGTGTGGGGCTTCGTCG 62.308 66.667 0.00 0.00 0.00 5.12
3154 3326 3.998672 GGTGTGGGGCTTCGTCGA 61.999 66.667 0.00 0.00 0.00 4.20
3155 3327 2.029964 GTGTGGGGCTTCGTCGAA 59.970 61.111 7.57 7.57 0.00 3.71
3156 3328 2.027625 GTGTGGGGCTTCGTCGAAG 61.028 63.158 27.01 27.01 42.03 3.79
3157 3329 2.204461 TGTGGGGCTTCGTCGAAGA 61.204 57.895 33.52 13.72 41.71 2.87
3158 3330 1.005394 GTGGGGCTTCGTCGAAGAA 60.005 57.895 33.52 13.19 41.71 2.52
3159 3331 0.601841 GTGGGGCTTCGTCGAAGAAA 60.602 55.000 33.52 15.10 41.71 2.52
3160 3332 0.107081 TGGGGCTTCGTCGAAGAAAA 59.893 50.000 33.52 15.41 41.71 2.29
3161 3333 1.232119 GGGGCTTCGTCGAAGAAAAA 58.768 50.000 33.52 0.30 41.71 1.94
3175 3347 4.468007 AAAAACTCGACGTGGGGG 57.532 55.556 1.47 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.202545 TGTTCGTGTCGTTGGATCCAA 60.203 47.619 23.63 23.63 0.00 3.53
4 5 0.389757 TGTTCGTGTCGTTGGATCCA 59.610 50.000 11.44 11.44 0.00 3.41
5 6 1.504359 TTGTTCGTGTCGTTGGATCC 58.496 50.000 4.20 4.20 0.00 3.36
6 7 3.242478 TGTTTTGTTCGTGTCGTTGGATC 60.242 43.478 0.00 0.00 0.00 3.36
7 8 2.678836 TGTTTTGTTCGTGTCGTTGGAT 59.321 40.909 0.00 0.00 0.00 3.41
8 9 2.074576 TGTTTTGTTCGTGTCGTTGGA 58.925 42.857 0.00 0.00 0.00 3.53
9 10 2.094575 TCTGTTTTGTTCGTGTCGTTGG 59.905 45.455 0.00 0.00 0.00 3.77
10 11 3.377434 TCTGTTTTGTTCGTGTCGTTG 57.623 42.857 0.00 0.00 0.00 4.10
11 12 4.567558 TGTATCTGTTTTGTTCGTGTCGTT 59.432 37.500 0.00 0.00 0.00 3.85
12 13 4.026310 GTGTATCTGTTTTGTTCGTGTCGT 60.026 41.667 0.00 0.00 0.00 4.34
13 14 4.442705 GTGTATCTGTTTTGTTCGTGTCG 58.557 43.478 0.00 0.00 0.00 4.35
14 15 4.207635 TCGTGTATCTGTTTTGTTCGTGTC 59.792 41.667 0.00 0.00 0.00 3.67
15 16 4.114073 TCGTGTATCTGTTTTGTTCGTGT 58.886 39.130 0.00 0.00 0.00 4.49
16 17 4.688063 CTCGTGTATCTGTTTTGTTCGTG 58.312 43.478 0.00 0.00 0.00 4.35
17 18 3.183775 GCTCGTGTATCTGTTTTGTTCGT 59.816 43.478 0.00 0.00 0.00 3.85
18 19 3.183574 TGCTCGTGTATCTGTTTTGTTCG 59.816 43.478 0.00 0.00 0.00 3.95
19 20 4.455124 GTGCTCGTGTATCTGTTTTGTTC 58.545 43.478 0.00 0.00 0.00 3.18
20 21 3.250040 GGTGCTCGTGTATCTGTTTTGTT 59.750 43.478 0.00 0.00 0.00 2.83
21 22 2.806244 GGTGCTCGTGTATCTGTTTTGT 59.194 45.455 0.00 0.00 0.00 2.83
22 23 2.159841 CGGTGCTCGTGTATCTGTTTTG 60.160 50.000 0.00 0.00 0.00 2.44
23 24 2.066262 CGGTGCTCGTGTATCTGTTTT 58.934 47.619 0.00 0.00 0.00 2.43
24 25 1.710013 CGGTGCTCGTGTATCTGTTT 58.290 50.000 0.00 0.00 0.00 2.83
25 26 0.736325 GCGGTGCTCGTGTATCTGTT 60.736 55.000 2.43 0.00 41.72 3.16
26 27 1.153823 GCGGTGCTCGTGTATCTGT 60.154 57.895 2.43 0.00 41.72 3.41
27 28 1.153842 TGCGGTGCTCGTGTATCTG 60.154 57.895 2.43 0.00 41.72 2.90
28 29 1.153823 GTGCGGTGCTCGTGTATCT 60.154 57.895 2.43 0.00 41.72 1.98
29 30 2.165301 GGTGCGGTGCTCGTGTATC 61.165 63.158 2.43 0.00 41.72 2.24
30 31 2.125673 GGTGCGGTGCTCGTGTAT 60.126 61.111 2.43 0.00 41.72 2.29
31 32 3.299977 AGGTGCGGTGCTCGTGTA 61.300 61.111 2.43 0.00 41.72 2.90
32 33 4.969196 CAGGTGCGGTGCTCGTGT 62.969 66.667 5.64 0.00 41.72 4.49
33 34 4.662961 TCAGGTGCGGTGCTCGTG 62.663 66.667 7.09 7.09 41.72 4.35
34 35 4.664677 GTCAGGTGCGGTGCTCGT 62.665 66.667 2.43 0.00 41.72 4.18
35 36 4.662961 TGTCAGGTGCGGTGCTCG 62.663 66.667 0.00 0.00 42.76 5.03
36 37 2.280797 TTGTCAGGTGCGGTGCTC 60.281 61.111 0.00 0.00 0.00 4.26
37 38 2.281070 CTTGTCAGGTGCGGTGCT 60.281 61.111 0.00 0.00 0.00 4.40
38 39 2.591715 ACTTGTCAGGTGCGGTGC 60.592 61.111 0.00 0.00 0.00 5.01
39 40 1.227527 TGACTTGTCAGGTGCGGTG 60.228 57.895 0.00 0.00 0.00 4.94
40 41 1.227556 GTGACTTGTCAGGTGCGGT 60.228 57.895 3.45 0.00 0.00 5.68
41 42 1.227527 TGTGACTTGTCAGGTGCGG 60.228 57.895 3.45 0.00 0.00 5.69
42 43 0.809636 TGTGTGACTTGTCAGGTGCG 60.810 55.000 3.45 0.00 0.00 5.34
43 44 0.657840 GTGTGTGACTTGTCAGGTGC 59.342 55.000 3.45 0.00 0.00 5.01
44 45 1.665679 GTGTGTGTGACTTGTCAGGTG 59.334 52.381 3.45 0.00 0.00 4.00
45 46 1.406887 GGTGTGTGTGACTTGTCAGGT 60.407 52.381 3.45 0.00 0.00 4.00
46 47 1.299541 GGTGTGTGTGACTTGTCAGG 58.700 55.000 3.45 0.00 0.00 3.86
47 48 2.022764 TGGTGTGTGTGACTTGTCAG 57.977 50.000 3.45 0.00 0.00 3.51
48 49 2.481289 TTGGTGTGTGTGACTTGTCA 57.519 45.000 0.00 0.00 0.00 3.58
49 50 2.159435 GGTTTGGTGTGTGTGACTTGTC 60.159 50.000 0.00 0.00 0.00 3.18
50 51 1.816224 GGTTTGGTGTGTGTGACTTGT 59.184 47.619 0.00 0.00 0.00 3.16
51 52 1.134175 GGGTTTGGTGTGTGTGACTTG 59.866 52.381 0.00 0.00 0.00 3.16
52 53 1.470051 GGGTTTGGTGTGTGTGACTT 58.530 50.000 0.00 0.00 0.00 3.01
53 54 0.746563 CGGGTTTGGTGTGTGTGACT 60.747 55.000 0.00 0.00 0.00 3.41
54 55 1.027792 ACGGGTTTGGTGTGTGTGAC 61.028 55.000 0.00 0.00 0.00 3.67
55 56 0.745128 GACGGGTTTGGTGTGTGTGA 60.745 55.000 0.00 0.00 0.00 3.58
56 57 1.720694 GGACGGGTTTGGTGTGTGTG 61.721 60.000 0.00 0.00 0.00 3.82
57 58 1.452470 GGACGGGTTTGGTGTGTGT 60.452 57.895 0.00 0.00 0.00 3.72
58 59 0.107081 TAGGACGGGTTTGGTGTGTG 59.893 55.000 0.00 0.00 0.00 3.82
59 60 0.838608 TTAGGACGGGTTTGGTGTGT 59.161 50.000 0.00 0.00 0.00 3.72
60 61 1.605232 GTTTAGGACGGGTTTGGTGTG 59.395 52.381 0.00 0.00 0.00 3.82
61 62 1.477377 GGTTTAGGACGGGTTTGGTGT 60.477 52.381 0.00 0.00 0.00 4.16
114 118 0.179100 TGCTGGATCTACTTGCGCTC 60.179 55.000 9.73 0.00 0.00 5.03
121 125 0.253160 TGGGGGTTGCTGGATCTACT 60.253 55.000 0.00 0.00 0.00 2.57
187 191 2.039624 ATCCGTGGTCCTGCCTCT 59.960 61.111 0.00 0.00 38.35 3.69
193 197 0.747255 CGAGATTCATCCGTGGTCCT 59.253 55.000 0.00 0.00 0.00 3.85
497 506 4.183858 ACGTGGTGGTGGTGGTGG 62.184 66.667 0.00 0.00 0.00 4.61
498 507 2.590575 GACGTGGTGGTGGTGGTG 60.591 66.667 0.00 0.00 0.00 4.17
499 508 4.230002 CGACGTGGTGGTGGTGGT 62.230 66.667 0.00 0.00 0.00 4.16
500 509 4.230002 ACGACGTGGTGGTGGTGG 62.230 66.667 1.11 0.00 0.00 4.61
501 510 2.660552 GACGACGTGGTGGTGGTG 60.661 66.667 8.32 0.00 0.00 4.17
502 511 2.836360 AGACGACGTGGTGGTGGT 60.836 61.111 8.32 0.00 0.00 4.16
503 512 2.049433 GAGACGACGTGGTGGTGG 60.049 66.667 8.32 0.00 0.00 4.61
504 513 2.049433 GGAGACGACGTGGTGGTG 60.049 66.667 8.32 0.00 0.00 4.17
505 514 2.520020 TGGAGACGACGTGGTGGT 60.520 61.111 8.32 0.00 0.00 4.16
506 515 2.049433 GTGGAGACGACGTGGTGG 60.049 66.667 8.32 0.00 0.00 4.61
507 516 2.049433 GGTGGAGACGACGTGGTG 60.049 66.667 8.32 0.00 0.00 4.17
508 517 2.203451 AGGTGGAGACGACGTGGT 60.203 61.111 4.58 1.66 0.00 4.16
509 518 2.567049 GAGGTGGAGACGACGTGG 59.433 66.667 4.58 0.00 0.00 4.94
510 519 2.567049 GGAGGTGGAGACGACGTG 59.433 66.667 4.58 0.00 0.00 4.49
511 520 3.054503 CGGAGGTGGAGACGACGT 61.055 66.667 0.00 0.00 0.00 4.34
512 521 2.745100 TCGGAGGTGGAGACGACG 60.745 66.667 0.00 0.00 0.00 5.12
513 522 2.876219 GTCGGAGGTGGAGACGAC 59.124 66.667 0.00 0.00 46.89 4.34
627 636 4.399395 CGAGAAGCCAGCCAGCCA 62.399 66.667 0.00 0.00 0.00 4.75
637 646 1.503994 GAAGGCTTTGGCGAGAAGC 59.496 57.895 0.00 10.46 46.71 3.86
642 651 0.110486 AAGAAGGAAGGCTTTGGCGA 59.890 50.000 0.00 0.00 39.81 5.54
645 654 4.006319 CAGTAGAAGAAGGAAGGCTTTGG 58.994 47.826 0.00 0.00 0.00 3.28
666 675 0.681733 GCTCACTCCACTCAACTCCA 59.318 55.000 0.00 0.00 0.00 3.86
672 681 4.724602 GCGCGCTCACTCCACTCA 62.725 66.667 26.67 0.00 0.00 3.41
708 717 1.077068 TGAGCGCCTTTAATGGGGG 60.077 57.895 21.38 14.42 40.00 5.40
987 1035 2.361104 GCCATCCCCACGAAAGCA 60.361 61.111 0.00 0.00 0.00 3.91
1023 1072 4.025401 GCCGCCAAGAACACCACG 62.025 66.667 0.00 0.00 0.00 4.94
1125 1177 2.431942 GCGTCGAAGAAGGCGGAA 60.432 61.111 1.37 0.00 39.69 4.30
2187 2239 4.959399 GCTTCTGAGAGCAGCCAT 57.041 55.556 0.00 0.00 42.01 4.40
2439 2498 5.551233 AGACACAAGCACATACACTTACAT 58.449 37.500 0.00 0.00 0.00 2.29
2478 2537 3.364889 TGTTCACCACTTACTCACTCG 57.635 47.619 0.00 0.00 0.00 4.18
2504 2563 3.258123 TCATCGTCAGGACAACATCAAGA 59.742 43.478 0.00 0.00 0.00 3.02
2515 2574 1.114627 CCACCATCTCATCGTCAGGA 58.885 55.000 0.00 0.00 0.00 3.86
2556 2615 9.736023 CATTGCCATATTTGATGATCATCATAG 57.264 33.333 33.23 21.42 46.12 2.23
2591 2650 4.898328 ACGTACAATTTAGACAGCGAAC 57.102 40.909 0.00 0.00 0.00 3.95
2669 2728 1.310904 TAGACCACGCCAACCAAAAC 58.689 50.000 0.00 0.00 0.00 2.43
2794 2936 2.645838 TTATGATTGCTCAGAGGGCC 57.354 50.000 0.00 0.00 34.12 5.80
2845 2987 9.573133 CAATAAGTAATCACAAATCAGGTTTCC 57.427 33.333 0.00 0.00 0.00 3.13
2873 3025 1.873698 AAGCCAAGCAATTGCAACTG 58.126 45.000 30.89 22.58 45.16 3.16
2877 3029 2.237643 TCTGTAAGCCAAGCAATTGCA 58.762 42.857 30.89 6.74 45.16 4.08
2879 3031 4.157289 ACAGATCTGTAAGCCAAGCAATTG 59.843 41.667 26.87 0.00 42.90 2.32
2881 3033 3.693085 CACAGATCTGTAAGCCAAGCAAT 59.307 43.478 27.44 0.00 42.83 3.56
2893 3045 5.423015 CATAAGTGGTAAGCACAGATCTGT 58.577 41.667 22.89 22.89 46.17 3.41
2909 3076 2.868583 CGGAATCACTCTGCCATAAGTG 59.131 50.000 1.91 1.91 43.41 3.16
2928 3095 2.711542 AGACCACTTTCTTATTGCCGG 58.288 47.619 0.00 0.00 0.00 6.13
2929 3096 4.003648 AGAAGACCACTTTCTTATTGCCG 58.996 43.478 0.00 0.00 35.90 5.69
2935 3102 6.884832 TCACTTCAAGAAGACCACTTTCTTA 58.115 36.000 16.16 0.00 40.79 2.10
2974 3146 9.829507 ATGTGGTGTCAAAAAGAAAATCAATAA 57.170 25.926 0.00 0.00 0.00 1.40
2975 3147 9.829507 AATGTGGTGTCAAAAAGAAAATCAATA 57.170 25.926 0.00 0.00 0.00 1.90
3004 3176 2.858344 CGACTGACCCATTAGCGTTTAG 59.142 50.000 0.00 0.00 0.00 1.85
3005 3177 2.492881 TCGACTGACCCATTAGCGTTTA 59.507 45.455 0.00 0.00 0.00 2.01
3006 3178 1.274167 TCGACTGACCCATTAGCGTTT 59.726 47.619 0.00 0.00 0.00 3.60
3007 3179 0.892755 TCGACTGACCCATTAGCGTT 59.107 50.000 0.00 0.00 0.00 4.84
3008 3180 1.112113 ATCGACTGACCCATTAGCGT 58.888 50.000 0.00 0.00 0.00 5.07
3009 3181 2.225068 AATCGACTGACCCATTAGCG 57.775 50.000 0.00 0.00 0.00 4.26
3010 3182 3.938963 TCAAAATCGACTGACCCATTAGC 59.061 43.478 0.00 0.00 0.00 3.09
3011 3183 5.419542 TCTCAAAATCGACTGACCCATTAG 58.580 41.667 0.00 0.00 0.00 1.73
3012 3184 5.414789 TCTCAAAATCGACTGACCCATTA 57.585 39.130 0.00 0.00 0.00 1.90
3013 3185 4.286297 TCTCAAAATCGACTGACCCATT 57.714 40.909 0.00 0.00 0.00 3.16
3014 3186 3.981071 TCTCAAAATCGACTGACCCAT 57.019 42.857 0.00 0.00 0.00 4.00
3015 3187 3.981071 ATCTCAAAATCGACTGACCCA 57.019 42.857 0.00 0.00 0.00 4.51
3016 3188 3.623510 GGAATCTCAAAATCGACTGACCC 59.376 47.826 0.00 0.00 0.00 4.46
3017 3189 3.623510 GGGAATCTCAAAATCGACTGACC 59.376 47.826 0.00 0.00 0.00 4.02
3018 3190 4.253685 TGGGAATCTCAAAATCGACTGAC 58.746 43.478 0.00 0.00 0.00 3.51
3019 3191 4.222810 TCTGGGAATCTCAAAATCGACTGA 59.777 41.667 0.00 0.00 0.00 3.41
3020 3192 4.507710 TCTGGGAATCTCAAAATCGACTG 58.492 43.478 0.00 0.00 0.00 3.51
3021 3193 4.826274 TCTGGGAATCTCAAAATCGACT 57.174 40.909 0.00 0.00 0.00 4.18
3022 3194 5.880054 TTTCTGGGAATCTCAAAATCGAC 57.120 39.130 0.00 0.00 0.00 4.20
3023 3195 6.658816 TGAATTTCTGGGAATCTCAAAATCGA 59.341 34.615 0.00 0.00 0.00 3.59
3024 3196 6.749118 GTGAATTTCTGGGAATCTCAAAATCG 59.251 38.462 0.00 0.00 0.00 3.34
3025 3197 7.038048 GGTGAATTTCTGGGAATCTCAAAATC 58.962 38.462 0.00 0.00 0.00 2.17
3026 3198 6.350445 CGGTGAATTTCTGGGAATCTCAAAAT 60.350 38.462 0.00 0.00 0.00 1.82
3027 3199 5.048083 CGGTGAATTTCTGGGAATCTCAAAA 60.048 40.000 0.00 0.00 0.00 2.44
3028 3200 4.458989 CGGTGAATTTCTGGGAATCTCAAA 59.541 41.667 0.00 0.00 0.00 2.69
3029 3201 4.009675 CGGTGAATTTCTGGGAATCTCAA 58.990 43.478 0.00 0.00 0.00 3.02
3030 3202 3.609853 CGGTGAATTTCTGGGAATCTCA 58.390 45.455 0.00 0.00 0.00 3.27
3031 3203 2.945668 CCGGTGAATTTCTGGGAATCTC 59.054 50.000 0.00 0.00 0.00 2.75
3032 3204 2.576191 TCCGGTGAATTTCTGGGAATCT 59.424 45.455 0.00 0.00 32.62 2.40
3033 3205 2.945668 CTCCGGTGAATTTCTGGGAATC 59.054 50.000 0.00 0.00 32.62 2.52
3034 3206 2.357154 CCTCCGGTGAATTTCTGGGAAT 60.357 50.000 4.76 0.00 32.62 3.01
3035 3207 1.004277 CCTCCGGTGAATTTCTGGGAA 59.996 52.381 4.76 0.00 32.62 3.97
3036 3208 0.618458 CCTCCGGTGAATTTCTGGGA 59.382 55.000 4.76 1.55 32.62 4.37
3037 3209 0.618458 TCCTCCGGTGAATTTCTGGG 59.382 55.000 4.76 0.00 32.62 4.45
3038 3210 2.359900 CTTCCTCCGGTGAATTTCTGG 58.640 52.381 4.76 3.84 0.00 3.86
3039 3211 2.027192 TCCTTCCTCCGGTGAATTTCTG 60.027 50.000 4.76 0.00 0.00 3.02
3040 3212 2.237392 CTCCTTCCTCCGGTGAATTTCT 59.763 50.000 4.76 0.00 0.00 2.52
3041 3213 2.236395 TCTCCTTCCTCCGGTGAATTTC 59.764 50.000 4.76 0.00 0.00 2.17
3042 3214 2.266279 TCTCCTTCCTCCGGTGAATTT 58.734 47.619 4.76 0.00 0.00 1.82
3043 3215 1.952621 TCTCCTTCCTCCGGTGAATT 58.047 50.000 4.76 0.00 0.00 2.17
3044 3216 1.834263 CTTCTCCTTCCTCCGGTGAAT 59.166 52.381 4.76 0.00 34.60 2.57
3045 3217 1.267121 CTTCTCCTTCCTCCGGTGAA 58.733 55.000 4.76 7.03 34.13 3.18
3046 3218 0.614979 CCTTCTCCTTCCTCCGGTGA 60.615 60.000 4.76 0.00 0.00 4.02
3047 3219 0.614979 TCCTTCTCCTTCCTCCGGTG 60.615 60.000 0.00 0.00 0.00 4.94
3048 3220 0.116541 TTCCTTCTCCTTCCTCCGGT 59.883 55.000 0.00 0.00 0.00 5.28
3049 3221 0.827368 CTTCCTTCTCCTTCCTCCGG 59.173 60.000 0.00 0.00 0.00 5.14
3050 3222 0.827368 CCTTCCTTCTCCTTCCTCCG 59.173 60.000 0.00 0.00 0.00 4.63
3051 3223 1.557371 CACCTTCCTTCTCCTTCCTCC 59.443 57.143 0.00 0.00 0.00 4.30
3052 3224 1.065782 GCACCTTCCTTCTCCTTCCTC 60.066 57.143 0.00 0.00 0.00 3.71
3053 3225 0.988063 GCACCTTCCTTCTCCTTCCT 59.012 55.000 0.00 0.00 0.00 3.36
3054 3226 0.988063 AGCACCTTCCTTCTCCTTCC 59.012 55.000 0.00 0.00 0.00 3.46
3055 3227 1.625818 TGAGCACCTTCCTTCTCCTTC 59.374 52.381 0.00 0.00 0.00 3.46
3056 3228 1.349357 GTGAGCACCTTCCTTCTCCTT 59.651 52.381 0.00 0.00 0.00 3.36
3057 3229 0.980423 GTGAGCACCTTCCTTCTCCT 59.020 55.000 0.00 0.00 0.00 3.69
3058 3230 0.980423 AGTGAGCACCTTCCTTCTCC 59.020 55.000 0.00 0.00 0.00 3.71
3059 3231 1.338579 CCAGTGAGCACCTTCCTTCTC 60.339 57.143 0.00 0.00 0.00 2.87
3060 3232 0.689623 CCAGTGAGCACCTTCCTTCT 59.310 55.000 0.00 0.00 0.00 2.85
3061 3233 0.687354 TCCAGTGAGCACCTTCCTTC 59.313 55.000 0.00 0.00 0.00 3.46
3062 3234 0.689623 CTCCAGTGAGCACCTTCCTT 59.310 55.000 0.00 0.00 0.00 3.36
3063 3235 1.197430 CCTCCAGTGAGCACCTTCCT 61.197 60.000 0.00 0.00 37.29 3.36
3064 3236 1.298014 CCTCCAGTGAGCACCTTCC 59.702 63.158 0.00 0.00 37.29 3.46
3065 3237 1.298014 CCCTCCAGTGAGCACCTTC 59.702 63.158 0.00 0.00 37.29 3.46
3066 3238 2.900106 GCCCTCCAGTGAGCACCTT 61.900 63.158 0.00 0.00 37.29 3.50
3067 3239 2.461986 TAGCCCTCCAGTGAGCACCT 62.462 60.000 0.00 0.00 37.29 4.00
3068 3240 1.990060 TAGCCCTCCAGTGAGCACC 60.990 63.158 0.00 0.00 37.29 5.01
3069 3241 1.219393 GTAGCCCTCCAGTGAGCAC 59.781 63.158 0.00 0.00 37.29 4.40
3070 3242 1.990060 GGTAGCCCTCCAGTGAGCA 60.990 63.158 0.00 0.00 37.29 4.26
3071 3243 1.687493 AGGTAGCCCTCCAGTGAGC 60.687 63.158 0.00 0.00 35.62 4.26
3072 3244 4.796408 AGGTAGCCCTCCAGTGAG 57.204 61.111 0.00 0.00 35.62 3.51
3080 3252 5.608798 AAGATAGATACTGAGGTAGCCCT 57.391 43.478 0.00 0.00 46.66 5.19
3081 3253 5.889289 CCTAAGATAGATACTGAGGTAGCCC 59.111 48.000 0.00 0.00 35.17 5.19
3082 3254 5.889289 CCCTAAGATAGATACTGAGGTAGCC 59.111 48.000 0.00 0.00 34.92 3.93
3083 3255 6.486941 ACCCTAAGATAGATACTGAGGTAGC 58.513 44.000 0.00 0.00 34.92 3.58
3084 3256 8.943594 AAACCCTAAGATAGATACTGAGGTAG 57.056 38.462 0.00 0.00 34.92 3.18
3086 3258 7.951245 CCTAAACCCTAAGATAGATACTGAGGT 59.049 40.741 0.00 0.00 34.92 3.85
3087 3259 7.397761 CCCTAAACCCTAAGATAGATACTGAGG 59.602 44.444 0.00 0.00 36.13 3.86
3088 3260 7.951245 ACCCTAAACCCTAAGATAGATACTGAG 59.049 40.741 0.00 0.00 0.00 3.35
3089 3261 7.728981 CACCCTAAACCCTAAGATAGATACTGA 59.271 40.741 0.00 0.00 0.00 3.41
3090 3262 7.038941 CCACCCTAAACCCTAAGATAGATACTG 60.039 44.444 0.00 0.00 0.00 2.74
3091 3263 7.017531 CCACCCTAAACCCTAAGATAGATACT 58.982 42.308 0.00 0.00 0.00 2.12
3092 3264 6.212993 CCCACCCTAAACCCTAAGATAGATAC 59.787 46.154 0.00 0.00 0.00 2.24
3093 3265 6.328592 CCCACCCTAAACCCTAAGATAGATA 58.671 44.000 0.00 0.00 0.00 1.98
3094 3266 5.163390 CCCACCCTAAACCCTAAGATAGAT 58.837 45.833 0.00 0.00 0.00 1.98
3095 3267 4.563782 CCCACCCTAAACCCTAAGATAGA 58.436 47.826 0.00 0.00 0.00 1.98
3096 3268 3.651423 CCCCACCCTAAACCCTAAGATAG 59.349 52.174 0.00 0.00 0.00 2.08
3097 3269 3.636855 CCCCCACCCTAAACCCTAAGATA 60.637 52.174 0.00 0.00 0.00 1.98
3098 3270 2.499515 CCCCACCCTAAACCCTAAGAT 58.500 52.381 0.00 0.00 0.00 2.40
3099 3271 1.558622 CCCCCACCCTAAACCCTAAGA 60.559 57.143 0.00 0.00 0.00 2.10
3100 3272 0.924090 CCCCCACCCTAAACCCTAAG 59.076 60.000 0.00 0.00 0.00 2.18
3101 3273 1.216368 GCCCCCACCCTAAACCCTAA 61.216 60.000 0.00 0.00 0.00 2.69
3102 3274 1.620282 GCCCCCACCCTAAACCCTA 60.620 63.158 0.00 0.00 0.00 3.53
3103 3275 2.944954 GCCCCCACCCTAAACCCT 60.945 66.667 0.00 0.00 0.00 4.34
3104 3276 4.435970 CGCCCCCACCCTAAACCC 62.436 72.222 0.00 0.00 0.00 4.11
3105 3277 4.435970 CCGCCCCCACCCTAAACC 62.436 72.222 0.00 0.00 0.00 3.27
3106 3278 3.654143 ACCGCCCCCACCCTAAAC 61.654 66.667 0.00 0.00 0.00 2.01
3107 3279 3.653078 CACCGCCCCCACCCTAAA 61.653 66.667 0.00 0.00 0.00 1.85
3121 3293 4.712425 CCACCGTCGTCGACCACC 62.712 72.222 19.29 0.00 39.71 4.61
3122 3294 3.969802 ACCACCGTCGTCGACCAC 61.970 66.667 19.29 6.61 39.71 4.16
3123 3295 3.968568 CACCACCGTCGTCGACCA 61.969 66.667 19.29 0.00 39.71 4.02
3124 3296 3.969802 ACACCACCGTCGTCGACC 61.970 66.667 19.29 2.53 39.71 4.79
3125 3297 2.728383 CACACCACCGTCGTCGAC 60.728 66.667 15.51 15.51 39.71 4.20
3126 3298 3.968568 CCACACCACCGTCGTCGA 61.969 66.667 2.98 0.00 39.71 4.20
3128 3300 4.675029 CCCCACACCACCGTCGTC 62.675 72.222 0.00 0.00 0.00 4.20
3131 3303 4.265056 AAGCCCCACACCACCGTC 62.265 66.667 0.00 0.00 0.00 4.79
3132 3304 4.265056 GAAGCCCCACACCACCGT 62.265 66.667 0.00 0.00 0.00 4.83
3134 3306 4.265056 ACGAAGCCCCACACCACC 62.265 66.667 0.00 0.00 0.00 4.61
3135 3307 2.668550 GACGAAGCCCCACACCAC 60.669 66.667 0.00 0.00 0.00 4.16
3136 3308 4.308458 CGACGAAGCCCCACACCA 62.308 66.667 0.00 0.00 0.00 4.17
3137 3309 3.524648 TTCGACGAAGCCCCACACC 62.525 63.158 6.10 0.00 0.00 4.16
3138 3310 2.027625 CTTCGACGAAGCCCCACAC 61.028 63.158 23.46 0.00 32.78 3.82
3139 3311 1.750341 TTCTTCGACGAAGCCCCACA 61.750 55.000 28.65 11.00 39.29 4.17
3140 3312 0.601841 TTTCTTCGACGAAGCCCCAC 60.602 55.000 28.65 0.00 39.29 4.61
3141 3313 0.107081 TTTTCTTCGACGAAGCCCCA 59.893 50.000 28.65 12.04 39.29 4.96
3142 3314 1.232119 TTTTTCTTCGACGAAGCCCC 58.768 50.000 28.65 0.00 39.29 5.80
3158 3330 4.468007 CCCCCACGTCGAGTTTTT 57.532 55.556 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.