Multiple sequence alignment - TraesCS3A01G040000

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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 TraesCS3A01G040000 chr3A 100.000 3249 0 0 1 3249 21005857 21009105 0.000000e+00 6000.0
1 TraesCS3A01G040000 chr3B 94.380 2331 116 8 197 2522 22426757 22424437 0.000000e+00 3565.0
2 TraesCS3A01G040000 chr3B 94.102 373 18 2 2674 3042 22404174 22403802 6.090000e-157 564.0
3 TraesCS3A01G040000 chr3B 91.209 364 28 4 2890 3249 22218915 22218552 2.910000e-135 492.0
4 TraesCS3A01G040000 chr3B 93.750 160 10 0 2520 2679 22404810 22404651 1.160000e-59 241.0
5 TraesCS3A01G040000 chr3B 88.500 200 20 2 1 199 22427459 22427262 4.190000e-59 239.0
6 TraesCS3A01G040000 chr3B 90.857 175 10 3 3027 3196 22390483 22390310 2.520000e-56 230.0
7 TraesCS3A01G040000 chr3B 92.754 69 4 1 3182 3249 22384832 22384764 7.420000e-17 99.0
8 TraesCS3A01G040000 chr6D 78.954 1625 298 29 774 2369 11070609 11069000 0.000000e+00 1066.0
9 TraesCS3A01G040000 chr6D 80.318 1382 248 18 776 2142 20760449 20759077 0.000000e+00 1024.0
10 TraesCS3A01G040000 chr6B 78.899 1635 297 35 768 2369 20879207 20877588 0.000000e+00 1064.0
11 TraesCS3A01G040000 chr6B 78.902 1621 299 30 777 2369 20961505 20959900 0.000000e+00 1059.0
12 TraesCS3A01G040000 chr6B 78.738 1632 302 35 768 2369 20835412 20833796 0.000000e+00 1050.0
13 TraesCS3A01G040000 chr6B 79.523 1509 269 28 768 2249 20700211 20698716 0.000000e+00 1038.0
14 TraesCS3A01G040000 chr7D 81.661 1096 193 6 985 2078 591009227 591008138 0.000000e+00 904.0
15 TraesCS3A01G040000 chr1A 84.615 104 15 1 2525 2628 44824807 44824909 5.730000e-18 102.0
16 TraesCS3A01G040000 chr1B 84.466 103 15 1 2525 2627 377013339 377013440 2.060000e-17 100.0
17 TraesCS3A01G040000 chr5A 81.818 110 18 2 2525 2634 246748228 246748335 1.240000e-14 91.6
18 TraesCS3A01G040000 chr6A 82.524 103 17 1 2525 2627 255290843 255290742 4.460000e-14 89.8


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 TraesCS3A01G040000 chr3A 21005857 21009105 3248 False 6000.0 6000 100.000 1 3249 1 chr3A.!!$F1 3248
1 TraesCS3A01G040000 chr3B 22424437 22427459 3022 True 1902.0 3565 91.440 1 2522 2 chr3B.!!$R5 2521
2 TraesCS3A01G040000 chr3B 22403802 22404810 1008 True 402.5 564 93.926 2520 3042 2 chr3B.!!$R4 522
3 TraesCS3A01G040000 chr6D 11069000 11070609 1609 True 1066.0 1066 78.954 774 2369 1 chr6D.!!$R1 1595
4 TraesCS3A01G040000 chr6D 20759077 20760449 1372 True 1024.0 1024 80.318 776 2142 1 chr6D.!!$R2 1366
5 TraesCS3A01G040000 chr6B 20877588 20879207 1619 True 1064.0 1064 78.899 768 2369 1 chr6B.!!$R3 1601
6 TraesCS3A01G040000 chr6B 20959900 20961505 1605 True 1059.0 1059 78.902 777 2369 1 chr6B.!!$R4 1592
7 TraesCS3A01G040000 chr6B 20833796 20835412 1616 True 1050.0 1050 78.738 768 2369 1 chr6B.!!$R2 1601
8 TraesCS3A01G040000 chr6B 20698716 20700211 1495 True 1038.0 1038 79.523 768 2249 1 chr6B.!!$R1 1481
9 TraesCS3A01G040000 chr7D 591008138 591009227 1089 True 904.0 904 81.661 985 2078 1 chr7D.!!$R1 1093

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
724 1236 0.540830 ATTAGGCACCAACCGGCAAA 60.541 50.0 0.00 0.00 34.57 3.68 F
1281 1803 0.820891 GAGGGCATGGCATGGTGTAG 60.821 60.0 27.48 2.65 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2645 1.150536 TGACCTGGCTTTGTCCACC 59.849 57.895 0.00 0.00 31.74 4.61 R
3193 4223 0.106167 TACTCGTCTGATCCCAGGGG 60.106 60.000 5.33 0.92 40.76 4.79 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
112 113 1.985622 TGGGTCTCCTCATTTCCCAT 58.014 50.000 0.00 0.00 42.52 4.00
115 116 1.566231 GGTCTCCTCATTTCCCATGGT 59.434 52.381 11.73 0.00 0.00 3.55
122 123 3.374098 CCTCATTTCCCATGGTACCCAAT 60.374 47.826 11.73 0.00 36.95 3.16
135 136 6.723298 TGGTACCCAATAGCAAAAATATGG 57.277 37.500 10.07 0.00 38.35 2.74
136 137 5.069781 TGGTACCCAATAGCAAAAATATGGC 59.930 40.000 10.07 0.00 38.35 4.40
137 138 4.687901 ACCCAATAGCAAAAATATGGCC 57.312 40.909 0.00 0.00 0.00 5.36
143 144 7.772757 CCCAATAGCAAAAATATGGCCTTTTTA 59.227 33.333 12.18 0.70 34.83 1.52
179 181 9.466497 AGCTAATTGATTGGAAAAAGAGATACA 57.534 29.630 0.00 0.00 0.00 2.29
235 743 2.401766 GGAACGCTGATGTGGCAGG 61.402 63.158 0.00 0.00 36.41 4.85
326 834 2.161609 GGCCTAAAGTGATTGGTTGTCG 59.838 50.000 0.00 0.00 0.00 4.35
364 872 6.623549 CGTGCAATCACTTTGAGTTAATGGAT 60.624 38.462 0.00 0.00 40.99 3.41
378 886 7.178274 TGAGTTAATGGATAAGTGGCACATTTT 59.822 33.333 21.41 8.14 44.52 1.82
439 947 7.989170 ACATGTGATATGAGAATAGTGCAGAAA 59.011 33.333 0.00 0.00 0.00 2.52
485 993 7.895759 TCATGGTGGAAGGAAAAAGAATAAAG 58.104 34.615 0.00 0.00 0.00 1.85
502 1010 8.613922 AGAATAAAGGGTTTTCCATGAATGAT 57.386 30.769 0.00 0.00 42.91 2.45
507 1015 4.472108 AGGGTTTTCCATGAATGATGCATT 59.528 37.500 0.00 0.00 42.91 3.56
508 1016 4.812626 GGGTTTTCCATGAATGATGCATTC 59.187 41.667 0.00 12.03 44.47 2.67
567 1075 7.117379 GGTATACACAGGCGAGGTAATTAAATC 59.883 40.741 5.01 0.00 0.00 2.17
649 1158 8.783093 TCAAATTTACTCTTGATCAACGAACAT 58.217 29.630 3.38 0.00 0.00 2.71
724 1236 0.540830 ATTAGGCACCAACCGGCAAA 60.541 50.000 0.00 0.00 34.57 3.68
893 1405 6.480651 ACAACGTATGACACTACAACAATGAA 59.519 34.615 0.00 0.00 0.00 2.57
1062 1584 6.398918 TGGTGTTCTACTTCTTATCTTGAGC 58.601 40.000 0.00 0.00 0.00 4.26
1140 1662 4.332828 AGTATTTCCGAAAGAACCAAGGG 58.667 43.478 0.00 0.00 32.95 3.95
1220 1742 3.340814 TTCCTTGGCAGAGCTAGAAAG 57.659 47.619 0.00 0.00 0.00 2.62
1242 1764 4.023193 AGGGCAACAAATAACTTTGACTCG 60.023 41.667 5.17 0.00 43.71 4.18
1281 1803 0.820891 GAGGGCATGGCATGGTGTAG 60.821 60.000 27.48 2.65 0.00 2.74
1511 2033 0.894835 CCATGCTAACCCAACCAACC 59.105 55.000 0.00 0.00 0.00 3.77
1536 2058 3.011595 TCCATGTTGTCCTGGGATGATTT 59.988 43.478 0.00 0.00 33.13 2.17
1600 2122 2.168106 CCACTCAGCTGCTTCAGTATCT 59.832 50.000 9.47 0.00 33.43 1.98
1958 2480 1.548357 GCTGGAGGAGGCAACAGAGA 61.548 60.000 0.00 0.00 41.41 3.10
1977 2499 5.119279 CAGAGAAAGAAATTCGTGATGTCGT 59.881 40.000 0.00 0.00 43.15 4.34
2046 2568 6.983307 CCTACTATGAAACAAGTGGAGATGAG 59.017 42.308 0.00 0.00 0.00 2.90
2114 2636 5.803967 GCTCCAAGAAATGAAAGTATGCAAG 59.196 40.000 0.00 0.00 0.00 4.01
2123 2645 8.922058 AAATGAAAGTATGCAAGCATTCTTAG 57.078 30.769 21.74 0.00 41.14 2.18
2158 2695 4.735132 ACACGTCGGCCGGTGATG 62.735 66.667 32.48 23.83 42.24 3.07
2230 2767 1.666189 GAGCAAGAGTTTATGGCGTCC 59.334 52.381 0.00 0.00 0.00 4.79
2249 2790 4.230603 CGACCCTACCACGCTAGA 57.769 61.111 0.00 0.00 0.00 2.43
2255 2796 1.337260 CCCTACCACGCTAGATCATGC 60.337 57.143 0.00 0.00 0.00 4.06
2270 2811 3.827008 TCATGCAGTCCTCTTGGTATC 57.173 47.619 0.00 0.00 34.23 2.24
2321 2865 8.634335 TCAAATTCTATCATTGTTGTCCTTCA 57.366 30.769 0.00 0.00 0.00 3.02
2343 2887 7.864108 TCAATGGAAATGGTGAAGTATACAG 57.136 36.000 5.50 0.00 0.00 2.74
2589 3133 0.394565 GCAATCCTACCATCGGAGCT 59.605 55.000 0.00 0.00 33.29 4.09
2596 3140 0.458669 TACCATCGGAGCTTCGTTCC 59.541 55.000 15.46 0.00 0.00 3.62
2616 3160 5.229921 TCCAATTCGGAATCACGATTTTC 57.770 39.130 3.28 0.00 42.52 2.29
2632 3176 5.047802 ACGATTTTCGACTACCTTGTTAGGA 60.048 40.000 3.62 0.00 42.75 2.94
2705 3731 7.117236 CAGTTGTGCTACGGAATTTACTTCTAA 59.883 37.037 0.00 0.00 34.08 2.10
2764 3790 7.865385 GTGCCAAAAACTTGAGTAATGTAATGA 59.135 33.333 0.00 0.00 0.00 2.57
2790 3816 7.228308 ACGTGAGAGTAGTGTTATATCTTACCC 59.772 40.741 0.00 0.00 0.00 3.69
2806 3832 3.443045 CCGCTTGGTGGGTCATGC 61.443 66.667 0.00 0.00 35.35 4.06
2819 3845 4.280929 GTGGGTCATGCCTTTAACTTTCTT 59.719 41.667 6.20 0.00 37.43 2.52
2820 3846 4.522789 TGGGTCATGCCTTTAACTTTCTTC 59.477 41.667 6.20 0.00 37.43 2.87
2890 3920 2.560542 TGTGGGTTACATGTGGCATTTC 59.439 45.455 9.11 0.00 33.42 2.17
2913 3943 4.201930 CGCCAAGTAGTCTAAGGTACAGAG 60.202 50.000 0.00 0.00 0.00 3.35
2919 3949 8.614346 CAAGTAGTCTAAGGTACAGAGATGTAC 58.386 40.741 9.52 9.52 42.72 2.90
2927 3957 7.914427 AAGGTACAGAGATGTACATTATCCA 57.086 36.000 14.60 0.00 44.18 3.41
2928 3958 7.291411 AGGTACAGAGATGTACATTATCCAC 57.709 40.000 10.30 9.27 44.60 4.02
3013 4043 1.818060 GCATGTTGCTCATTGTACCCA 59.182 47.619 0.00 0.00 40.96 4.51
3018 4048 0.747644 TGCTCATTGTACCCATGGCG 60.748 55.000 6.09 2.02 0.00 5.69
3047 4077 9.770097 TTTATCTTCTTCTCTTATGTATGCCTG 57.230 33.333 0.00 0.00 0.00 4.85
3048 4078 6.798427 TCTTCTTCTCTTATGTATGCCTGT 57.202 37.500 0.00 0.00 0.00 4.00
3049 4079 7.187824 TCTTCTTCTCTTATGTATGCCTGTT 57.812 36.000 0.00 0.00 0.00 3.16
3050 4080 7.044181 TCTTCTTCTCTTATGTATGCCTGTTG 58.956 38.462 0.00 0.00 0.00 3.33
3051 4081 6.299805 TCTTCTCTTATGTATGCCTGTTGT 57.700 37.500 0.00 0.00 0.00 3.32
3052 4082 6.108687 TCTTCTCTTATGTATGCCTGTTGTG 58.891 40.000 0.00 0.00 0.00 3.33
3053 4083 5.675684 TCTCTTATGTATGCCTGTTGTGA 57.324 39.130 0.00 0.00 0.00 3.58
3054 4084 6.048732 TCTCTTATGTATGCCTGTTGTGAA 57.951 37.500 0.00 0.00 0.00 3.18
3055 4085 5.874810 TCTCTTATGTATGCCTGTTGTGAAC 59.125 40.000 0.00 0.00 0.00 3.18
3056 4086 5.804639 TCTTATGTATGCCTGTTGTGAACT 58.195 37.500 0.00 0.00 0.00 3.01
3057 4087 5.874810 TCTTATGTATGCCTGTTGTGAACTC 59.125 40.000 0.00 0.00 0.00 3.01
3058 4088 2.412870 TGTATGCCTGTTGTGAACTCG 58.587 47.619 0.00 0.00 0.00 4.18
3059 4089 1.732259 GTATGCCTGTTGTGAACTCGG 59.268 52.381 0.00 0.00 0.00 4.63
3060 4090 1.237285 ATGCCTGTTGTGAACTCGGC 61.237 55.000 11.17 11.17 43.88 5.54
3061 4091 2.617274 GCCTGTTGTGAACTCGGCC 61.617 63.158 0.00 0.00 40.42 6.13
3062 4092 1.071471 CCTGTTGTGAACTCGGCCT 59.929 57.895 0.00 0.00 0.00 5.19
3063 4093 1.230635 CCTGTTGTGAACTCGGCCTG 61.231 60.000 0.00 0.00 0.00 4.85
3064 4094 0.532862 CTGTTGTGAACTCGGCCTGT 60.533 55.000 0.00 0.00 0.00 4.00
3065 4095 0.107410 TGTTGTGAACTCGGCCTGTT 60.107 50.000 10.21 10.21 0.00 3.16
3066 4096 1.139256 TGTTGTGAACTCGGCCTGTTA 59.861 47.619 10.37 0.00 0.00 2.41
3067 4097 2.224426 TGTTGTGAACTCGGCCTGTTAT 60.224 45.455 10.37 0.00 0.00 1.89
3068 4098 3.007074 TGTTGTGAACTCGGCCTGTTATA 59.993 43.478 10.37 2.07 0.00 0.98
3069 4099 3.965379 TGTGAACTCGGCCTGTTATAA 57.035 42.857 10.37 0.00 0.00 0.98
3070 4100 3.592059 TGTGAACTCGGCCTGTTATAAC 58.408 45.455 8.75 8.75 0.00 1.89
3071 4101 3.007074 TGTGAACTCGGCCTGTTATAACA 59.993 43.478 17.16 17.16 37.37 2.41
3072 4102 4.189231 GTGAACTCGGCCTGTTATAACAT 58.811 43.478 18.35 1.34 38.41 2.71
3073 4103 5.105269 TGTGAACTCGGCCTGTTATAACATA 60.105 40.000 18.35 0.00 38.41 2.29
3074 4104 5.813672 GTGAACTCGGCCTGTTATAACATAA 59.186 40.000 18.35 0.00 38.41 1.90
3075 4105 6.018994 GTGAACTCGGCCTGTTATAACATAAG 60.019 42.308 18.35 11.41 38.41 1.73
3076 4106 5.864418 ACTCGGCCTGTTATAACATAAGA 57.136 39.130 18.35 13.63 38.41 2.10
3077 4107 5.598769 ACTCGGCCTGTTATAACATAAGAC 58.401 41.667 18.35 11.53 38.41 3.01
3078 4108 4.952460 TCGGCCTGTTATAACATAAGACC 58.048 43.478 18.35 13.47 38.41 3.85
3079 4109 4.406326 TCGGCCTGTTATAACATAAGACCA 59.594 41.667 18.35 0.00 38.41 4.02
3080 4110 5.071250 TCGGCCTGTTATAACATAAGACCAT 59.929 40.000 18.35 0.00 38.41 3.55
3081 4111 5.179368 CGGCCTGTTATAACATAAGACCATG 59.821 44.000 18.35 4.05 38.41 3.66
3082 4112 6.296026 GGCCTGTTATAACATAAGACCATGA 58.704 40.000 18.35 0.00 38.41 3.07
3083 4113 6.204882 GGCCTGTTATAACATAAGACCATGAC 59.795 42.308 18.35 0.00 38.41 3.06
3084 4114 6.204882 GCCTGTTATAACATAAGACCATGACC 59.795 42.308 18.35 0.00 38.41 4.02
3085 4115 6.710744 CCTGTTATAACATAAGACCATGACCC 59.289 42.308 18.35 0.00 38.41 4.46
3086 4116 7.201702 TGTTATAACATAAGACCATGACCCA 57.798 36.000 14.35 0.00 33.17 4.51
3087 4117 7.811282 TGTTATAACATAAGACCATGACCCAT 58.189 34.615 14.35 0.00 33.17 4.00
3088 4118 8.278639 TGTTATAACATAAGACCATGACCCATT 58.721 33.333 14.35 0.00 33.17 3.16
3089 4119 8.567948 GTTATAACATAAGACCATGACCCATTG 58.432 37.037 10.81 0.00 0.00 2.82
3090 4120 4.591321 ACATAAGACCATGACCCATTGT 57.409 40.909 0.00 0.00 0.00 2.71
3091 4121 5.708736 ACATAAGACCATGACCCATTGTA 57.291 39.130 0.00 0.00 0.00 2.41
3092 4122 6.073447 ACATAAGACCATGACCCATTGTAA 57.927 37.500 0.00 0.00 0.00 2.41
3093 4123 5.885912 ACATAAGACCATGACCCATTGTAAC 59.114 40.000 0.00 0.00 0.00 2.50
3094 4124 3.366052 AGACCATGACCCATTGTAACC 57.634 47.619 0.00 0.00 0.00 2.85
3095 4125 2.025321 AGACCATGACCCATTGTAACCC 60.025 50.000 0.00 0.00 0.00 4.11
3096 4126 1.713647 ACCATGACCCATTGTAACCCA 59.286 47.619 0.00 0.00 0.00 4.51
3097 4127 2.099405 CCATGACCCATTGTAACCCAC 58.901 52.381 0.00 0.00 0.00 4.61
3098 4128 2.291540 CCATGACCCATTGTAACCCACT 60.292 50.000 0.00 0.00 0.00 4.00
3099 4129 2.871096 TGACCCATTGTAACCCACTC 57.129 50.000 0.00 0.00 0.00 3.51
3100 4130 2.344592 TGACCCATTGTAACCCACTCT 58.655 47.619 0.00 0.00 0.00 3.24
3101 4131 3.522759 TGACCCATTGTAACCCACTCTA 58.477 45.455 0.00 0.00 0.00 2.43
3102 4132 3.517901 TGACCCATTGTAACCCACTCTAG 59.482 47.826 0.00 0.00 0.00 2.43
3103 4133 3.518303 GACCCATTGTAACCCACTCTAGT 59.482 47.826 0.00 0.00 0.00 2.57
3104 4134 3.263425 ACCCATTGTAACCCACTCTAGTG 59.737 47.826 3.02 3.02 45.23 2.74
3118 4148 4.717233 CTCTAGTGAGTCATGACTTGCT 57.283 45.455 28.46 26.83 42.66 3.91
3119 4149 5.070770 CTCTAGTGAGTCATGACTTGCTT 57.929 43.478 28.46 16.56 42.66 3.91
3120 4150 5.474578 TCTAGTGAGTCATGACTTGCTTT 57.525 39.130 28.46 14.99 42.66 3.51
3121 4151 5.473931 TCTAGTGAGTCATGACTTGCTTTC 58.526 41.667 28.46 15.50 42.66 2.62
3122 4152 3.062763 AGTGAGTCATGACTTGCTTTCG 58.937 45.455 28.46 0.00 42.66 3.46
3123 4153 1.800586 TGAGTCATGACTTGCTTTCGC 59.199 47.619 28.46 13.91 42.66 4.70
3124 4154 2.072298 GAGTCATGACTTGCTTTCGCT 58.928 47.619 28.46 3.10 42.66 4.93
3125 4155 2.481952 GAGTCATGACTTGCTTTCGCTT 59.518 45.455 28.46 2.55 42.66 4.68
3126 4156 2.225019 AGTCATGACTTGCTTTCGCTTG 59.775 45.455 22.89 0.00 38.83 4.01
3127 4157 2.031682 GTCATGACTTGCTTTCGCTTGT 60.032 45.455 18.83 0.00 36.97 3.16
3128 4158 2.618241 TCATGACTTGCTTTCGCTTGTT 59.382 40.909 0.00 0.00 36.97 2.83
3129 4159 2.473530 TGACTTGCTTTCGCTTGTTG 57.526 45.000 0.00 0.00 36.97 3.33
3130 4160 1.123655 GACTTGCTTTCGCTTGTTGC 58.876 50.000 0.00 0.00 36.97 4.17
3131 4161 0.740737 ACTTGCTTTCGCTTGTTGCT 59.259 45.000 0.00 0.00 40.11 3.91
3132 4162 1.268743 ACTTGCTTTCGCTTGTTGCTC 60.269 47.619 0.00 0.00 40.11 4.26
3133 4163 0.030638 TTGCTTTCGCTTGTTGCTCC 59.969 50.000 0.00 0.00 40.11 4.70
3134 4164 1.100463 TGCTTTCGCTTGTTGCTCCA 61.100 50.000 0.00 0.00 40.11 3.86
3135 4165 0.030638 GCTTTCGCTTGTTGCTCCAA 59.969 50.000 0.00 0.00 40.11 3.53
3136 4166 1.758783 CTTTCGCTTGTTGCTCCAAC 58.241 50.000 1.33 1.33 43.78 3.77
3137 4167 0.028770 TTTCGCTTGTTGCTCCAACG 59.971 50.000 3.93 0.00 46.13 4.10
3138 4168 1.092921 TTCGCTTGTTGCTCCAACGT 61.093 50.000 3.93 0.00 46.13 3.99
3139 4169 0.249531 TCGCTTGTTGCTCCAACGTA 60.250 50.000 0.00 0.00 46.13 3.57
3140 4170 0.796312 CGCTTGTTGCTCCAACGTAT 59.204 50.000 0.00 0.00 46.13 3.06
3141 4171 1.464023 CGCTTGTTGCTCCAACGTATG 60.464 52.381 0.00 0.00 46.13 2.39
3142 4172 1.804151 GCTTGTTGCTCCAACGTATGA 59.196 47.619 0.00 0.00 46.13 2.15
3143 4173 2.412847 GCTTGTTGCTCCAACGTATGAC 60.413 50.000 0.00 0.00 46.13 3.06
3144 4174 1.424403 TGTTGCTCCAACGTATGACG 58.576 50.000 0.00 0.00 46.13 4.35
3158 4188 5.006649 CGTATGACGTTCCTATTGAATGC 57.993 43.478 0.00 0.00 42.68 3.56
3159 4189 4.506288 CGTATGACGTTCCTATTGAATGCA 59.494 41.667 0.00 0.00 42.68 3.96
3160 4190 5.006261 CGTATGACGTTCCTATTGAATGCAA 59.994 40.000 0.00 0.00 42.68 4.08
3161 4191 4.678509 TGACGTTCCTATTGAATGCAAC 57.321 40.909 0.00 0.00 42.68 4.17
3162 4192 4.323417 TGACGTTCCTATTGAATGCAACT 58.677 39.130 0.00 0.00 42.68 3.16
3163 4193 4.759693 TGACGTTCCTATTGAATGCAACTT 59.240 37.500 0.00 0.00 42.68 2.66
3164 4194 5.935206 TGACGTTCCTATTGAATGCAACTTA 59.065 36.000 0.00 0.00 42.68 2.24
3165 4195 6.092122 TGACGTTCCTATTGAATGCAACTTAG 59.908 38.462 0.00 0.00 42.68 2.18
3166 4196 5.938125 ACGTTCCTATTGAATGCAACTTAGT 59.062 36.000 0.00 0.00 42.68 2.24
3167 4197 6.128282 ACGTTCCTATTGAATGCAACTTAGTG 60.128 38.462 0.00 0.00 42.68 2.74
3168 4198 6.555315 GTTCCTATTGAATGCAACTTAGTGG 58.445 40.000 0.00 0.00 36.72 4.00
3169 4199 5.815581 TCCTATTGAATGCAACTTAGTGGT 58.184 37.500 0.00 0.00 36.72 4.16
3170 4200 6.245408 TCCTATTGAATGCAACTTAGTGGTT 58.755 36.000 0.00 0.00 36.72 3.67
3171 4201 7.398829 TCCTATTGAATGCAACTTAGTGGTTA 58.601 34.615 0.00 0.00 36.72 2.85
3172 4202 7.335924 TCCTATTGAATGCAACTTAGTGGTTAC 59.664 37.037 0.00 0.00 36.72 2.50
3173 4203 7.336931 CCTATTGAATGCAACTTAGTGGTTACT 59.663 37.037 0.00 0.00 37.62 2.24
3174 4204 6.952773 TTGAATGCAACTTAGTGGTTACTT 57.047 33.333 0.00 0.00 38.36 2.24
3175 4205 6.554334 TGAATGCAACTTAGTGGTTACTTC 57.446 37.500 0.00 0.00 38.36 3.01
3176 4206 6.296026 TGAATGCAACTTAGTGGTTACTTCT 58.704 36.000 0.00 0.00 38.36 2.85
3177 4207 6.426937 TGAATGCAACTTAGTGGTTACTTCTC 59.573 38.462 0.00 0.00 38.36 2.87
3178 4208 5.546621 TGCAACTTAGTGGTTACTTCTCT 57.453 39.130 0.00 0.00 38.36 3.10
3179 4209 5.925509 TGCAACTTAGTGGTTACTTCTCTT 58.074 37.500 0.00 0.00 38.36 2.85
3180 4210 7.058023 TGCAACTTAGTGGTTACTTCTCTTA 57.942 36.000 0.00 0.00 38.36 2.10
3181 4211 7.676947 TGCAACTTAGTGGTTACTTCTCTTAT 58.323 34.615 0.00 0.00 38.36 1.73
3182 4212 7.602644 TGCAACTTAGTGGTTACTTCTCTTATG 59.397 37.037 0.00 0.00 38.36 1.90
3183 4213 7.603024 GCAACTTAGTGGTTACTTCTCTTATGT 59.397 37.037 0.00 0.00 38.36 2.29
3184 4214 9.490379 CAACTTAGTGGTTACTTCTCTTATGTT 57.510 33.333 0.00 0.00 38.36 2.71
3185 4215 9.708092 AACTTAGTGGTTACTTCTCTTATGTTC 57.292 33.333 0.00 0.00 38.36 3.18
3186 4216 8.867097 ACTTAGTGGTTACTTCTCTTATGTTCA 58.133 33.333 0.00 0.00 38.36 3.18
3187 4217 9.877178 CTTAGTGGTTACTTCTCTTATGTTCAT 57.123 33.333 0.00 0.00 38.36 2.57
3188 4218 9.653287 TTAGTGGTTACTTCTCTTATGTTCATG 57.347 33.333 0.00 0.00 38.36 3.07
3189 4219 7.680730 AGTGGTTACTTCTCTTATGTTCATGT 58.319 34.615 0.00 0.00 31.66 3.21
3190 4220 7.604164 AGTGGTTACTTCTCTTATGTTCATGTG 59.396 37.037 0.00 0.00 31.66 3.21
3191 4221 7.387948 GTGGTTACTTCTCTTATGTTCATGTGT 59.612 37.037 0.00 0.00 0.00 3.72
3192 4222 7.936847 TGGTTACTTCTCTTATGTTCATGTGTT 59.063 33.333 0.00 0.00 0.00 3.32
3193 4223 8.443937 GGTTACTTCTCTTATGTTCATGTGTTC 58.556 37.037 0.00 0.00 0.00 3.18
3194 4224 8.443937 GTTACTTCTCTTATGTTCATGTGTTCC 58.556 37.037 0.00 0.00 0.00 3.62
3195 4225 5.940470 ACTTCTCTTATGTTCATGTGTTCCC 59.060 40.000 0.00 0.00 0.00 3.97
3196 4226 4.843728 TCTCTTATGTTCATGTGTTCCCC 58.156 43.478 0.00 0.00 0.00 4.81
3197 4227 4.536090 TCTCTTATGTTCATGTGTTCCCCT 59.464 41.667 0.00 0.00 0.00 4.79
3198 4228 4.588899 TCTTATGTTCATGTGTTCCCCTG 58.411 43.478 0.00 0.00 0.00 4.45
3199 4229 2.220653 ATGTTCATGTGTTCCCCTGG 57.779 50.000 0.00 0.00 0.00 4.45
3200 4230 0.112218 TGTTCATGTGTTCCCCTGGG 59.888 55.000 5.50 5.50 0.00 4.45
3201 4231 0.404040 GTTCATGTGTTCCCCTGGGA 59.596 55.000 16.20 3.95 43.52 4.37
3202 4232 1.005924 GTTCATGTGTTCCCCTGGGAT 59.994 52.381 16.20 0.00 44.74 3.85
3203 4233 0.918983 TCATGTGTTCCCCTGGGATC 59.081 55.000 16.20 6.04 44.74 3.36
3204 4234 0.625316 CATGTGTTCCCCTGGGATCA 59.375 55.000 16.20 11.21 44.74 2.92
3205 4235 0.921896 ATGTGTTCCCCTGGGATCAG 59.078 55.000 16.20 0.00 44.74 2.90
3206 4236 0.178876 TGTGTTCCCCTGGGATCAGA 60.179 55.000 16.20 11.70 44.74 3.27
3207 4237 0.253327 GTGTTCCCCTGGGATCAGAC 59.747 60.000 16.20 6.97 44.74 3.51
3208 4238 1.264749 TGTTCCCCTGGGATCAGACG 61.265 60.000 16.20 0.00 44.74 4.18
3209 4239 0.976073 GTTCCCCTGGGATCAGACGA 60.976 60.000 16.20 0.00 44.74 4.20
3210 4240 0.687757 TTCCCCTGGGATCAGACGAG 60.688 60.000 16.20 0.00 44.74 4.18
3211 4241 1.381872 CCCCTGGGATCAGACGAGT 60.382 63.158 16.20 0.00 43.49 4.18
3212 4242 0.106167 CCCCTGGGATCAGACGAGTA 60.106 60.000 16.20 0.00 43.49 2.59
3213 4243 1.033574 CCCTGGGATCAGACGAGTAC 58.966 60.000 7.01 0.00 43.49 2.73
3214 4244 1.685180 CCCTGGGATCAGACGAGTACA 60.685 57.143 7.01 0.00 43.49 2.90
3215 4245 2.100197 CCTGGGATCAGACGAGTACAA 58.900 52.381 0.00 0.00 43.49 2.41
3216 4246 2.099921 CCTGGGATCAGACGAGTACAAG 59.900 54.545 0.00 0.00 43.49 3.16
3217 4247 3.017442 CTGGGATCAGACGAGTACAAGA 58.983 50.000 0.00 0.00 43.49 3.02
3218 4248 3.427573 TGGGATCAGACGAGTACAAGAA 58.572 45.455 0.00 0.00 0.00 2.52
3219 4249 3.830178 TGGGATCAGACGAGTACAAGAAA 59.170 43.478 0.00 0.00 0.00 2.52
3220 4250 4.082190 TGGGATCAGACGAGTACAAGAAAG 60.082 45.833 0.00 0.00 0.00 2.62
3221 4251 4.158025 GGGATCAGACGAGTACAAGAAAGA 59.842 45.833 0.00 0.00 0.00 2.52
3222 4252 5.336744 GGATCAGACGAGTACAAGAAAGAG 58.663 45.833 0.00 0.00 0.00 2.85
3223 4253 4.162096 TCAGACGAGTACAAGAAAGAGC 57.838 45.455 0.00 0.00 0.00 4.09
3224 4254 3.568430 TCAGACGAGTACAAGAAAGAGCA 59.432 43.478 0.00 0.00 0.00 4.26
3225 4255 4.037565 TCAGACGAGTACAAGAAAGAGCAA 59.962 41.667 0.00 0.00 0.00 3.91
3226 4256 4.149046 CAGACGAGTACAAGAAAGAGCAAC 59.851 45.833 0.00 0.00 0.00 4.17
3227 4257 4.038162 AGACGAGTACAAGAAAGAGCAACT 59.962 41.667 0.00 0.00 0.00 3.16
3228 4258 4.694339 ACGAGTACAAGAAAGAGCAACTT 58.306 39.130 0.00 0.00 40.98 2.66
3229 4259 4.745620 ACGAGTACAAGAAAGAGCAACTTC 59.254 41.667 0.00 0.00 37.93 3.01
3230 4260 4.150804 CGAGTACAAGAAAGAGCAACTTCC 59.849 45.833 0.00 0.00 37.93 3.46
3231 4261 5.036117 AGTACAAGAAAGAGCAACTTCCA 57.964 39.130 0.00 0.00 37.93 3.53
3232 4262 5.625150 AGTACAAGAAAGAGCAACTTCCAT 58.375 37.500 0.00 0.00 37.93 3.41
3233 4263 5.703130 AGTACAAGAAAGAGCAACTTCCATC 59.297 40.000 0.00 0.00 37.93 3.51
3234 4264 4.464008 ACAAGAAAGAGCAACTTCCATCA 58.536 39.130 0.00 0.00 37.93 3.07
3235 4265 4.518211 ACAAGAAAGAGCAACTTCCATCAG 59.482 41.667 0.00 0.00 37.93 2.90
3236 4266 4.363991 AGAAAGAGCAACTTCCATCAGT 57.636 40.909 0.00 0.00 37.93 3.41
3237 4267 4.070716 AGAAAGAGCAACTTCCATCAGTG 58.929 43.478 0.00 0.00 37.93 3.66
3238 4268 3.777106 AAGAGCAACTTCCATCAGTGA 57.223 42.857 0.00 0.00 32.91 3.41
3239 4269 3.996921 AGAGCAACTTCCATCAGTGAT 57.003 42.857 0.00 0.00 0.00 3.06
3240 4270 5.426689 AAGAGCAACTTCCATCAGTGATA 57.573 39.130 5.03 0.00 32.91 2.15
3241 4271 5.426689 AGAGCAACTTCCATCAGTGATAA 57.573 39.130 5.03 0.00 0.00 1.75
3242 4272 5.809001 AGAGCAACTTCCATCAGTGATAAA 58.191 37.500 5.03 2.83 0.00 1.40
3243 4273 5.879223 AGAGCAACTTCCATCAGTGATAAAG 59.121 40.000 18.94 18.94 0.00 1.85
3244 4274 4.946157 AGCAACTTCCATCAGTGATAAAGG 59.054 41.667 22.15 14.07 0.00 3.11
3245 4275 4.439289 GCAACTTCCATCAGTGATAAAGGC 60.439 45.833 22.15 16.11 0.00 4.35
3246 4276 4.574674 ACTTCCATCAGTGATAAAGGCA 57.425 40.909 22.15 6.35 0.00 4.75
3247 4277 5.121380 ACTTCCATCAGTGATAAAGGCAT 57.879 39.130 22.15 7.39 0.00 4.40
3248 4278 5.128919 ACTTCCATCAGTGATAAAGGCATC 58.871 41.667 22.15 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 8.374743 TCAGTTATGGCATGTGATTATTAGCTA 58.625 33.333 10.98 0.00 0.00 3.32
45 46 7.439157 TCAGTTATGGCATGTGATTATTAGC 57.561 36.000 10.98 0.00 0.00 3.09
83 84 2.587777 TGAGGAGACCCACCTATCTCTT 59.412 50.000 1.61 0.00 41.05 2.85
93 94 3.511552 TGGGAAATGAGGAGACCCA 57.488 52.632 0.00 0.00 46.74 4.51
115 116 5.463154 AGGCCATATTTTTGCTATTGGGTA 58.537 37.500 5.01 0.00 0.00 3.69
135 136 9.045223 CAATTAGCTGGGAATAAATAAAAAGGC 57.955 33.333 0.00 0.00 0.00 4.35
143 144 8.551682 TTCCAATCAATTAGCTGGGAATAAAT 57.448 30.769 0.00 0.00 0.00 1.40
190 192 6.228258 TGACCGCTTTCAAACTAACTTCTAT 58.772 36.000 0.00 0.00 0.00 1.98
192 194 4.448210 TGACCGCTTTCAAACTAACTTCT 58.552 39.130 0.00 0.00 0.00 2.85
194 196 5.449999 CCTTTGACCGCTTTCAAACTAACTT 60.450 40.000 5.69 0.00 39.94 2.66
199 201 2.650322 TCCTTTGACCGCTTTCAAACT 58.350 42.857 5.69 0.00 39.94 2.66
200 202 3.113322 GTTCCTTTGACCGCTTTCAAAC 58.887 45.455 5.69 0.00 39.94 2.93
201 203 2.223386 CGTTCCTTTGACCGCTTTCAAA 60.223 45.455 8.73 8.73 42.04 2.69
202 204 1.332375 CGTTCCTTTGACCGCTTTCAA 59.668 47.619 0.00 0.00 33.55 2.69
204 206 0.385598 GCGTTCCTTTGACCGCTTTC 60.386 55.000 0.00 0.00 42.66 2.62
206 208 3.340789 GCGTTCCTTTGACCGCTT 58.659 55.556 0.00 0.00 42.66 4.68
208 210 1.298859 ATCAGCGTTCCTTTGACCGC 61.299 55.000 0.00 0.00 46.07 5.68
209 211 0.443869 CATCAGCGTTCCTTTGACCG 59.556 55.000 0.00 0.00 0.00 4.79
210 212 1.197721 CACATCAGCGTTCCTTTGACC 59.802 52.381 0.00 0.00 0.00 4.02
255 763 4.462834 GGTCAAAATCAACTTAAGAGGGGG 59.537 45.833 10.09 0.00 0.00 5.40
299 807 5.914898 ACCAATCACTTTAGGCCATAAAC 57.085 39.130 5.01 0.00 30.16 2.01
304 812 3.153919 GACAACCAATCACTTTAGGCCA 58.846 45.455 5.01 0.00 0.00 5.36
326 834 2.050985 GCACGCTGCCAACAACTC 60.051 61.111 0.00 0.00 37.42 3.01
364 872 7.172342 ACTAATGGAGTAAAATGTGCCACTTA 58.828 34.615 0.00 0.00 36.27 2.24
485 993 3.891422 TGCATCATTCATGGAAAACCC 57.109 42.857 0.00 0.00 32.37 4.11
527 1035 7.445402 GCCTGTGTATACCAAAGATTCACATAT 59.555 37.037 0.00 0.00 34.62 1.78
538 1046 1.903860 ACCTCGCCTGTGTATACCAAA 59.096 47.619 0.00 0.00 0.00 3.28
544 1052 5.995897 GGATTTAATTACCTCGCCTGTGTAT 59.004 40.000 0.00 0.00 0.00 2.29
549 1057 5.308825 AGATGGATTTAATTACCTCGCCTG 58.691 41.667 0.00 0.00 0.00 4.85
674 1183 5.747565 CGACACTAGATTTTGTTTTCAGCA 58.252 37.500 0.00 0.00 0.00 4.41
756 1268 4.450080 TCTGCAATATAAGAGATGCGCAAG 59.550 41.667 17.11 1.13 41.61 4.01
893 1405 9.101655 GATTTTGGCTTTTTATTGATATGCACT 57.898 29.630 0.00 0.00 0.00 4.40
995 1517 7.872993 CGATGGTAATACCTGTAATGAAGATGT 59.127 37.037 11.16 0.00 39.58 3.06
1062 1584 0.179137 TGCGGATGAGAACTGTAGCG 60.179 55.000 0.00 0.00 0.00 4.26
1140 1662 7.435068 TGAAATTAGTTGTTCCAGTAGAAGC 57.565 36.000 0.00 0.00 34.29 3.86
1220 1742 4.023536 TCGAGTCAAAGTTATTTGTTGCCC 60.024 41.667 1.08 0.00 45.06 5.36
1242 1764 0.092351 CGCGACCAACAATACGTGTC 59.908 55.000 0.00 0.00 40.60 3.67
1281 1803 4.985409 CGCTGGTCAGATAAGATACCTTTC 59.015 45.833 1.65 0.00 33.94 2.62
1600 2122 6.096846 TGGACTTGACATCTCGATGAAAGATA 59.903 38.462 22.01 11.82 41.20 1.98
1798 2320 6.649557 GCAACTCTACAAGTACTACACCAAAT 59.350 38.462 0.00 0.00 37.17 2.32
1958 2480 3.122948 CCGACGACATCACGAATTTCTTT 59.877 43.478 0.00 0.00 37.03 2.52
2114 2636 2.164422 GGCTTTGTCCACCTAAGAATGC 59.836 50.000 0.00 0.00 0.00 3.56
2123 2645 1.150536 TGACCTGGCTTTGTCCACC 59.849 57.895 0.00 0.00 31.74 4.61
2249 2790 3.713248 TGATACCAAGAGGACTGCATGAT 59.287 43.478 0.00 0.00 38.69 2.45
2255 2796 5.491070 TGAAACATGATACCAAGAGGACTG 58.509 41.667 0.00 0.00 38.69 3.51
2270 2811 8.560576 AACGAAAAATACAGACTTGAAACATG 57.439 30.769 0.00 0.00 0.00 3.21
2463 3007 9.835389 TTACATGATGATCACAAGTTCATATCA 57.165 29.630 8.13 0.41 35.01 2.15
2554 3098 7.602644 GGTAGGATTGCAAATCGTAGAATGATA 59.397 37.037 1.71 0.00 43.58 2.15
2557 3101 5.527214 TGGTAGGATTGCAAATCGTAGAATG 59.473 40.000 1.71 0.00 43.58 2.67
2564 3108 2.224079 CCGATGGTAGGATTGCAAATCG 59.776 50.000 16.64 16.64 36.19 3.34
2571 3115 2.760374 GAAGCTCCGATGGTAGGATTG 58.240 52.381 0.00 0.00 37.13 2.67
2572 3116 1.341531 CGAAGCTCCGATGGTAGGATT 59.658 52.381 0.00 0.00 37.13 3.01
2596 3140 4.723862 GTCGAAAATCGTGATTCCGAATTG 59.276 41.667 16.24 0.00 41.35 2.32
2616 3160 5.068234 TGATGTTCCTAACAAGGTAGTCG 57.932 43.478 0.00 0.00 45.86 4.18
2632 3176 7.385752 CCTGAATACAAATTGCAAACTGATGTT 59.614 33.333 15.79 8.36 38.16 2.71
2705 3731 3.118531 ACCATGGCATCCTCTTTACTCT 58.881 45.455 13.04 0.00 0.00 3.24
2764 3790 7.228308 GGGTAAGATATAACACTACTCTCACGT 59.772 40.741 0.00 0.00 0.00 4.49
2790 3816 3.443045 GGCATGACCCACCAAGCG 61.443 66.667 0.00 0.00 32.13 4.68
2864 3894 3.085533 GCCACATGTAACCCACATTACA 58.914 45.455 0.00 1.16 46.01 2.41
2865 3895 3.085533 TGCCACATGTAACCCACATTAC 58.914 45.455 0.00 0.00 46.01 1.89
2890 3920 3.693085 TCTGTACCTTAGACTACTTGGCG 59.307 47.826 0.00 0.00 0.00 5.69
2919 3949 9.485591 GTAACAAGATTTTGTACGTGGATAATG 57.514 33.333 1.50 0.00 46.54 1.90
2927 3957 8.388103 GCATATGAGTAACAAGATTTTGTACGT 58.612 33.333 6.97 0.00 46.54 3.57
2928 3958 7.850982 GGCATATGAGTAACAAGATTTTGTACG 59.149 37.037 6.97 0.00 46.54 3.67
2973 4003 8.884124 ACATGCATAATATAAGGGCACTAATT 57.116 30.769 0.00 0.00 37.30 1.40
3013 4043 8.997323 CATAAGAGAAGAAGATAAATTCGCCAT 58.003 33.333 0.00 0.00 34.27 4.40
3042 4072 4.454948 CCGAGTTCACAACAGGCA 57.545 55.556 0.00 0.00 0.00 4.75
3043 4073 2.946762 GCCGAGTTCACAACAGGC 59.053 61.111 9.23 9.23 45.31 4.85
3044 4074 1.071471 AGGCCGAGTTCACAACAGG 59.929 57.895 0.00 0.00 35.45 4.00
3045 4075 0.532862 ACAGGCCGAGTTCACAACAG 60.533 55.000 0.00 0.00 0.00 3.16
3046 4076 0.107410 AACAGGCCGAGTTCACAACA 60.107 50.000 10.38 0.00 0.00 3.33
3047 4077 1.873698 TAACAGGCCGAGTTCACAAC 58.126 50.000 18.11 0.00 0.00 3.32
3048 4078 2.851263 ATAACAGGCCGAGTTCACAA 57.149 45.000 18.11 3.77 0.00 3.33
3049 4079 3.007074 TGTTATAACAGGCCGAGTTCACA 59.993 43.478 18.11 15.85 34.30 3.58
3050 4080 3.592059 TGTTATAACAGGCCGAGTTCAC 58.408 45.455 18.11 13.96 34.30 3.18
3051 4081 3.965379 TGTTATAACAGGCCGAGTTCA 57.035 42.857 18.11 8.93 34.30 3.18
3052 4082 6.200475 GTCTTATGTTATAACAGGCCGAGTTC 59.800 42.308 22.03 6.72 43.04 3.01
3053 4083 6.047231 GTCTTATGTTATAACAGGCCGAGTT 58.953 40.000 22.03 18.51 43.04 3.01
3054 4084 5.452917 GGTCTTATGTTATAACAGGCCGAGT 60.453 44.000 22.03 7.52 43.04 4.18
3055 4085 4.989168 GGTCTTATGTTATAACAGGCCGAG 59.011 45.833 22.03 14.35 43.04 4.63
3056 4086 4.406326 TGGTCTTATGTTATAACAGGCCGA 59.594 41.667 22.03 13.04 43.04 5.54
3057 4087 4.699637 TGGTCTTATGTTATAACAGGCCG 58.300 43.478 22.03 11.23 43.04 6.13
3058 4088 6.204882 GTCATGGTCTTATGTTATAACAGGCC 59.795 42.308 22.03 18.91 43.04 5.19
3059 4089 6.204882 GGTCATGGTCTTATGTTATAACAGGC 59.795 42.308 22.03 11.14 43.04 4.85
3060 4090 6.710744 GGGTCATGGTCTTATGTTATAACAGG 59.289 42.308 22.03 14.60 43.04 4.00
3061 4091 7.279615 TGGGTCATGGTCTTATGTTATAACAG 58.720 38.462 22.03 10.16 43.04 3.16
3062 4092 7.201702 TGGGTCATGGTCTTATGTTATAACA 57.798 36.000 20.14 20.14 44.06 2.41
3063 4093 8.567948 CAATGGGTCATGGTCTTATGTTATAAC 58.432 37.037 8.75 8.75 0.00 1.89
3064 4094 8.278639 ACAATGGGTCATGGTCTTATGTTATAA 58.721 33.333 0.00 0.00 0.00 0.98
3065 4095 7.811282 ACAATGGGTCATGGTCTTATGTTATA 58.189 34.615 0.00 0.00 0.00 0.98
3066 4096 6.672593 ACAATGGGTCATGGTCTTATGTTAT 58.327 36.000 0.00 0.00 0.00 1.89
3067 4097 6.073447 ACAATGGGTCATGGTCTTATGTTA 57.927 37.500 0.00 0.00 0.00 2.41
3068 4098 4.934356 ACAATGGGTCATGGTCTTATGTT 58.066 39.130 0.00 0.00 0.00 2.71
3069 4099 4.591321 ACAATGGGTCATGGTCTTATGT 57.409 40.909 0.00 0.00 0.00 2.29
3070 4100 5.299279 GGTTACAATGGGTCATGGTCTTATG 59.701 44.000 0.00 0.00 29.91 1.90
3071 4101 5.445964 GGTTACAATGGGTCATGGTCTTAT 58.554 41.667 0.00 0.00 29.91 1.73
3072 4102 4.324719 GGGTTACAATGGGTCATGGTCTTA 60.325 45.833 0.00 0.00 29.91 2.10
3073 4103 3.563479 GGGTTACAATGGGTCATGGTCTT 60.563 47.826 0.00 0.00 29.91 3.01
3074 4104 2.025321 GGGTTACAATGGGTCATGGTCT 60.025 50.000 0.00 0.00 29.91 3.85
3075 4105 2.291282 TGGGTTACAATGGGTCATGGTC 60.291 50.000 0.00 0.00 29.91 4.02
3076 4106 1.713647 TGGGTTACAATGGGTCATGGT 59.286 47.619 0.00 0.00 32.23 3.55
3077 4107 2.099405 GTGGGTTACAATGGGTCATGG 58.901 52.381 0.00 0.00 0.00 3.66
3078 4108 3.016736 GAGTGGGTTACAATGGGTCATG 58.983 50.000 0.00 0.00 0.00 3.07
3079 4109 2.919602 AGAGTGGGTTACAATGGGTCAT 59.080 45.455 0.00 0.00 0.00 3.06
3080 4110 2.344592 AGAGTGGGTTACAATGGGTCA 58.655 47.619 0.00 0.00 0.00 4.02
3081 4111 3.518303 ACTAGAGTGGGTTACAATGGGTC 59.482 47.826 0.00 0.00 0.00 4.46
3082 4112 3.263425 CACTAGAGTGGGTTACAATGGGT 59.737 47.826 0.00 0.00 42.10 4.51
3083 4113 3.517901 TCACTAGAGTGGGTTACAATGGG 59.482 47.826 9.73 0.00 45.65 4.00
3084 4114 4.759782 CTCACTAGAGTGGGTTACAATGG 58.240 47.826 9.73 0.00 45.65 3.16
3098 4128 5.473931 GAAAGCAAGTCATGACTCACTAGA 58.526 41.667 28.01 0.00 41.58 2.43
3099 4129 4.325741 CGAAAGCAAGTCATGACTCACTAG 59.674 45.833 28.01 17.14 41.58 2.57
3100 4130 4.237724 CGAAAGCAAGTCATGACTCACTA 58.762 43.478 28.01 0.00 41.58 2.74
3101 4131 3.062763 CGAAAGCAAGTCATGACTCACT 58.937 45.455 28.01 23.27 41.58 3.41
3102 4132 3.446184 CGAAAGCAAGTCATGACTCAC 57.554 47.619 28.01 21.53 41.58 3.51
3122 4152 1.804151 TCATACGTTGGAGCAACAAGC 59.196 47.619 0.00 0.00 43.70 4.01
3123 4153 2.159841 CGTCATACGTTGGAGCAACAAG 60.160 50.000 0.00 0.00 43.70 3.16
3124 4154 1.795872 CGTCATACGTTGGAGCAACAA 59.204 47.619 0.00 0.00 43.70 2.83
3125 4155 1.424403 CGTCATACGTTGGAGCAACA 58.576 50.000 0.00 0.00 43.70 3.33
3135 4165 9.252326 GTTGCATTCAATAGGAACGTCATACGT 62.252 40.741 0.00 0.00 45.03 3.57
3136 4166 6.992814 GTTGCATTCAATAGGAACGTCATACG 60.993 42.308 0.00 0.00 40.03 3.06
3137 4167 5.984233 TGCATTCAATAGGAACGTCATAC 57.016 39.130 0.00 0.00 38.60 2.39
3138 4168 6.112734 AGTTGCATTCAATAGGAACGTCATA 58.887 36.000 0.00 0.00 40.43 2.15
3139 4169 4.943705 AGTTGCATTCAATAGGAACGTCAT 59.056 37.500 0.00 0.00 40.43 3.06
3140 4170 4.323417 AGTTGCATTCAATAGGAACGTCA 58.677 39.130 0.00 0.00 40.43 4.35
3141 4171 4.946784 AGTTGCATTCAATAGGAACGTC 57.053 40.909 0.00 0.00 40.43 4.34
3142 4172 5.938125 ACTAAGTTGCATTCAATAGGAACGT 59.062 36.000 0.00 0.00 40.43 3.99
3143 4173 6.250819 CACTAAGTTGCATTCAATAGGAACG 58.749 40.000 0.00 0.00 40.43 3.95
3144 4174 6.151144 ACCACTAAGTTGCATTCAATAGGAAC 59.849 38.462 0.00 0.00 38.60 3.62
3145 4175 6.245408 ACCACTAAGTTGCATTCAATAGGAA 58.755 36.000 0.00 0.00 40.46 3.36
3146 4176 5.815581 ACCACTAAGTTGCATTCAATAGGA 58.184 37.500 0.00 0.00 34.29 2.94
3147 4177 6.515272 AACCACTAAGTTGCATTCAATAGG 57.485 37.500 0.00 0.00 34.29 2.57
3148 4178 8.268850 AGTAACCACTAAGTTGCATTCAATAG 57.731 34.615 0.00 0.00 35.10 1.73
3149 4179 8.630054 AAGTAACCACTAAGTTGCATTCAATA 57.370 30.769 0.00 0.00 35.10 1.90
3150 4180 7.448469 AGAAGTAACCACTAAGTTGCATTCAAT 59.552 33.333 0.00 0.00 35.10 2.57
3151 4181 6.770785 AGAAGTAACCACTAAGTTGCATTCAA 59.229 34.615 0.00 0.00 35.10 2.69
3152 4182 6.296026 AGAAGTAACCACTAAGTTGCATTCA 58.704 36.000 0.00 0.00 35.10 2.57
3153 4183 6.651225 AGAGAAGTAACCACTAAGTTGCATTC 59.349 38.462 0.00 0.00 35.10 2.67
3154 4184 6.534634 AGAGAAGTAACCACTAAGTTGCATT 58.465 36.000 0.00 0.00 35.10 3.56
3155 4185 6.115448 AGAGAAGTAACCACTAAGTTGCAT 57.885 37.500 0.00 0.00 35.10 3.96
3156 4186 5.546621 AGAGAAGTAACCACTAAGTTGCA 57.453 39.130 0.00 0.00 35.10 4.08
3157 4187 7.603024 ACATAAGAGAAGTAACCACTAAGTTGC 59.397 37.037 0.00 0.00 33.48 4.17
3158 4188 9.490379 AACATAAGAGAAGTAACCACTAAGTTG 57.510 33.333 0.00 0.00 33.48 3.16
3159 4189 9.708092 GAACATAAGAGAAGTAACCACTAAGTT 57.292 33.333 0.00 0.00 33.48 2.66
3160 4190 8.867097 TGAACATAAGAGAAGTAACCACTAAGT 58.133 33.333 0.00 0.00 33.48 2.24
3161 4191 9.877178 ATGAACATAAGAGAAGTAACCACTAAG 57.123 33.333 0.00 0.00 33.48 2.18
3162 4192 9.653287 CATGAACATAAGAGAAGTAACCACTAA 57.347 33.333 0.00 0.00 33.48 2.24
3163 4193 8.812972 ACATGAACATAAGAGAAGTAACCACTA 58.187 33.333 0.00 0.00 33.48 2.74
3164 4194 7.604164 CACATGAACATAAGAGAAGTAACCACT 59.396 37.037 0.00 0.00 36.19 4.00
3165 4195 7.387948 ACACATGAACATAAGAGAAGTAACCAC 59.612 37.037 0.00 0.00 0.00 4.16
3166 4196 7.450074 ACACATGAACATAAGAGAAGTAACCA 58.550 34.615 0.00 0.00 0.00 3.67
3167 4197 7.907214 ACACATGAACATAAGAGAAGTAACC 57.093 36.000 0.00 0.00 0.00 2.85
3168 4198 8.443937 GGAACACATGAACATAAGAGAAGTAAC 58.556 37.037 0.00 0.00 0.00 2.50
3169 4199 7.606456 GGGAACACATGAACATAAGAGAAGTAA 59.394 37.037 0.00 0.00 0.00 2.24
3170 4200 7.103641 GGGAACACATGAACATAAGAGAAGTA 58.896 38.462 0.00 0.00 0.00 2.24
3171 4201 5.940470 GGGAACACATGAACATAAGAGAAGT 59.060 40.000 0.00 0.00 0.00 3.01
3172 4202 5.355350 GGGGAACACATGAACATAAGAGAAG 59.645 44.000 0.00 0.00 0.00 2.85
3173 4203 5.014123 AGGGGAACACATGAACATAAGAGAA 59.986 40.000 0.00 0.00 0.00 2.87
3174 4204 4.536090 AGGGGAACACATGAACATAAGAGA 59.464 41.667 0.00 0.00 0.00 3.10
3175 4205 4.637534 CAGGGGAACACATGAACATAAGAG 59.362 45.833 0.00 0.00 0.00 2.85
3176 4206 4.567537 CCAGGGGAACACATGAACATAAGA 60.568 45.833 0.00 0.00 0.00 2.10
3177 4207 3.696051 CCAGGGGAACACATGAACATAAG 59.304 47.826 0.00 0.00 0.00 1.73
3178 4208 3.563261 CCCAGGGGAACACATGAACATAA 60.563 47.826 0.00 0.00 37.50 1.90
3179 4209 2.025416 CCCAGGGGAACACATGAACATA 60.025 50.000 0.00 0.00 37.50 2.29
3180 4210 1.272648 CCCAGGGGAACACATGAACAT 60.273 52.381 0.00 0.00 37.50 2.71
3181 4211 0.112218 CCCAGGGGAACACATGAACA 59.888 55.000 0.00 0.00 37.50 3.18
3182 4212 0.404040 TCCCAGGGGAACACATGAAC 59.596 55.000 5.33 0.00 42.05 3.18
3183 4213 2.875704 TCCCAGGGGAACACATGAA 58.124 52.632 5.33 0.00 42.05 2.57
3184 4214 4.679500 TCCCAGGGGAACACATGA 57.321 55.556 5.33 0.00 42.05 3.07
3193 4223 0.106167 TACTCGTCTGATCCCAGGGG 60.106 60.000 5.33 0.92 40.76 4.79
3194 4224 1.033574 GTACTCGTCTGATCCCAGGG 58.966 60.000 0.00 0.00 40.76 4.45
3195 4225 1.763968 TGTACTCGTCTGATCCCAGG 58.236 55.000 0.00 0.00 40.76 4.45
3196 4226 3.017442 TCTTGTACTCGTCTGATCCCAG 58.983 50.000 0.00 0.00 41.74 4.45
3197 4227 3.081710 TCTTGTACTCGTCTGATCCCA 57.918 47.619 0.00 0.00 0.00 4.37
3198 4228 4.158025 TCTTTCTTGTACTCGTCTGATCCC 59.842 45.833 0.00 0.00 0.00 3.85
3199 4229 5.312120 TCTTTCTTGTACTCGTCTGATCC 57.688 43.478 0.00 0.00 0.00 3.36
3200 4230 4.796312 GCTCTTTCTTGTACTCGTCTGATC 59.204 45.833 0.00 0.00 0.00 2.92
3201 4231 4.218635 TGCTCTTTCTTGTACTCGTCTGAT 59.781 41.667 0.00 0.00 0.00 2.90
3202 4232 3.568430 TGCTCTTTCTTGTACTCGTCTGA 59.432 43.478 0.00 0.00 0.00 3.27
3203 4233 3.902150 TGCTCTTTCTTGTACTCGTCTG 58.098 45.455 0.00 0.00 0.00 3.51
3204 4234 4.038162 AGTTGCTCTTTCTTGTACTCGTCT 59.962 41.667 0.00 0.00 0.00 4.18
3205 4235 4.299978 AGTTGCTCTTTCTTGTACTCGTC 58.700 43.478 0.00 0.00 0.00 4.20
3206 4236 4.323553 AGTTGCTCTTTCTTGTACTCGT 57.676 40.909 0.00 0.00 0.00 4.18
3207 4237 4.150804 GGAAGTTGCTCTTTCTTGTACTCG 59.849 45.833 0.00 0.00 36.40 4.18
3208 4238 5.057149 TGGAAGTTGCTCTTTCTTGTACTC 58.943 41.667 0.00 0.00 36.40 2.59
3209 4239 5.036117 TGGAAGTTGCTCTTTCTTGTACT 57.964 39.130 0.00 0.00 36.40 2.73
3210 4240 5.470098 TGATGGAAGTTGCTCTTTCTTGTAC 59.530 40.000 0.00 0.00 36.40 2.90
3211 4241 5.620206 TGATGGAAGTTGCTCTTTCTTGTA 58.380 37.500 0.00 0.00 36.40 2.41
3212 4242 4.464008 TGATGGAAGTTGCTCTTTCTTGT 58.536 39.130 0.00 0.00 36.40 3.16
3213 4243 4.518211 ACTGATGGAAGTTGCTCTTTCTTG 59.482 41.667 0.00 0.00 36.40 3.02
3214 4244 4.518211 CACTGATGGAAGTTGCTCTTTCTT 59.482 41.667 0.00 0.00 36.40 2.52
3215 4245 4.070716 CACTGATGGAAGTTGCTCTTTCT 58.929 43.478 0.00 0.00 36.40 2.52
3216 4246 4.067896 TCACTGATGGAAGTTGCTCTTTC 58.932 43.478 0.00 0.00 36.40 2.62
3217 4247 4.090761 TCACTGATGGAAGTTGCTCTTT 57.909 40.909 0.00 0.00 36.40 2.52
3218 4248 3.777106 TCACTGATGGAAGTTGCTCTT 57.223 42.857 0.00 0.00 39.32 2.85
3219 4249 3.996921 ATCACTGATGGAAGTTGCTCT 57.003 42.857 0.00 0.00 0.00 4.09
3220 4250 5.065731 CCTTTATCACTGATGGAAGTTGCTC 59.934 44.000 1.42 0.00 0.00 4.26
3221 4251 4.946157 CCTTTATCACTGATGGAAGTTGCT 59.054 41.667 1.42 0.00 0.00 3.91
3222 4252 4.439289 GCCTTTATCACTGATGGAAGTTGC 60.439 45.833 1.42 3.25 0.00 4.17
3223 4253 4.701651 TGCCTTTATCACTGATGGAAGTTG 59.298 41.667 1.42 0.00 0.00 3.16
3224 4254 4.922206 TGCCTTTATCACTGATGGAAGTT 58.078 39.130 1.42 0.00 0.00 2.66
3225 4255 4.574674 TGCCTTTATCACTGATGGAAGT 57.425 40.909 1.42 0.00 0.00 3.01
3226 4256 5.686159 GATGCCTTTATCACTGATGGAAG 57.314 43.478 1.42 6.03 0.00 3.46


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

AutoCloner maintained by Alex Coulton.