Multiple sequence alignment - TraesCS5D01G381500

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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 TraesCS5D01G381500 chr5D 100.000 3509 0 0 1 3509 451683131 451686639 0.000000e+00 6481.0
1 TraesCS5D01G381500 chr5A 92.474 2777 148 27 155 2913 570507694 570510427 0.000000e+00 3914.0
2 TraesCS5D01G381500 chr5A 92.157 255 18 2 2915 3168 570510595 570510848 3.330000e-95 359.0
3 TraesCS5D01G381500 chr5A 85.887 248 25 3 3238 3482 570517602 570517842 4.490000e-64 255.0
4 TraesCS5D01G381500 chr5A 100.000 34 0 0 3214 3247 570511053 570511086 2.920000e-06 63.9
5 TraesCS5D01G381500 chr5B 93.979 2541 112 21 387 2913 551508308 551510821 0.000000e+00 3807.0
6 TraesCS5D01G381500 chr5B 90.234 256 22 3 2915 3168 551510853 551511107 7.260000e-87 331.0
7 TraesCS5D01G381500 chr5B 86.321 212 12 8 140 345 551507975 551508175 7.630000e-52 215.0
8 TraesCS5D01G381500 chr5B 82.759 232 20 10 3213 3431 551511358 551511582 4.620000e-44 189.0
9 TraesCS5D01G381500 chr7A 89.005 573 60 3 2135 2704 635690017 635690589 0.000000e+00 706.0
10 TraesCS5D01G381500 chr7B 88.561 542 56 4 2165 2704 594961169 594961706 0.000000e+00 652.0
11 TraesCS5D01G381500 chr2D 90.681 279 24 2 1233 1510 617891116 617891393 1.540000e-98 370.0
12 TraesCS5D01G381500 chr2A 90.681 279 24 2 1233 1510 748441353 748441630 1.540000e-98 370.0
13 TraesCS5D01G381500 chr2B 90.253 277 25 2 1244 1519 753804876 753804601 9.260000e-96 361.0
14 TraesCS5D01G381500 chr3B 86.452 155 21 0 2370 2524 165911194 165911040 1.670000e-38 171.0
15 TraesCS5D01G381500 chr1B 86.452 155 21 0 2370 2524 82987653 82987807 1.670000e-38 171.0
16 TraesCS5D01G381500 chr1B 85.806 155 22 0 2370 2524 3732865 3733019 7.790000e-37 165.0
17 TraesCS5D01G381500 chr6A 85.806 155 22 0 2370 2524 239256528 239256374 7.790000e-37 165.0
18 TraesCS5D01G381500 chr6A 85.806 155 22 0 2370 2524 477475638 477475792 7.790000e-37 165.0


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 TraesCS5D01G381500 chr5D 451683131 451686639 3508 False 6481.000000 6481 100.00000 1 3509 1 chr5D.!!$F1 3508
1 TraesCS5D01G381500 chr5A 570507694 570511086 3392 False 1445.633333 3914 94.87700 155 3247 3 chr5A.!!$F2 3092
2 TraesCS5D01G381500 chr5B 551507975 551511582 3607 False 1135.500000 3807 88.32325 140 3431 4 chr5B.!!$F1 3291
3 TraesCS5D01G381500 chr7A 635690017 635690589 572 False 706.000000 706 89.00500 2135 2704 1 chr7A.!!$F1 569
4 TraesCS5D01G381500 chr7B 594961169 594961706 537 False 652.000000 652 88.56100 2165 2704 1 chr7B.!!$F1 539

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
543 641 0.108945 GGCTACCTACGACCACACAC 60.109 60.000 0.00 0.0 0.00 3.82 F
552 650 1.713246 GACCACACACACACACACG 59.287 57.895 0.00 0.0 0.00 4.49 F
1104 1223 1.925455 CCCTTGGCCTTGGGAGAGA 60.925 63.158 23.83 0.0 46.15 3.10 F
1959 2081 2.033141 GGCTCTGGTGCTGCTGAA 59.967 61.111 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1959 2081 0.761187 TCTTCAGGTCAGCAACAGCT 59.239 50.000 0.00 0.00 39.75 4.24 R
2085 2207 1.070445 CAGCTCCCCTTGCCTATCG 59.930 63.158 0.00 0.00 0.00 2.92 R
2217 2339 1.203237 TGAGGCAGAAGACCCTTCTCT 60.203 52.381 6.27 2.62 0.00 3.10 R
3253 3800 0.535335 GGTGCTTGTATCTGGGTCGA 59.465 55.000 0.00 0.00 0.00 4.20 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
33 34 9.582648 AACATTACTATTTCTGTTGTAAAGGGT 57.417 29.630 0.00 0.00 31.00 4.34
34 35 9.582648 ACATTACTATTTCTGTTGTAAAGGGTT 57.417 29.630 0.00 0.00 0.00 4.11
37 38 9.629878 TTACTATTTCTGTTGTAAAGGGTTTCA 57.370 29.630 0.00 0.00 0.00 2.69
38 39 7.937649 ACTATTTCTGTTGTAAAGGGTTTCAC 58.062 34.615 0.00 0.00 0.00 3.18
39 40 6.783708 ATTTCTGTTGTAAAGGGTTTCACA 57.216 33.333 0.00 0.00 0.00 3.58
40 41 6.783708 TTTCTGTTGTAAAGGGTTTCACAT 57.216 33.333 0.00 0.00 0.00 3.21
41 42 7.883391 TTTCTGTTGTAAAGGGTTTCACATA 57.117 32.000 0.00 0.00 0.00 2.29
42 43 8.472007 TTTCTGTTGTAAAGGGTTTCACATAT 57.528 30.769 0.00 0.00 0.00 1.78
43 44 9.575868 TTTCTGTTGTAAAGGGTTTCACATATA 57.424 29.630 0.00 0.00 0.00 0.86
44 45 9.747898 TTCTGTTGTAAAGGGTTTCACATATAT 57.252 29.630 0.00 0.00 0.00 0.86
87 88 9.897744 TTAGTAATGTGCATTTTTCTTTGAGAG 57.102 29.630 2.56 0.00 32.50 3.20
88 89 8.169977 AGTAATGTGCATTTTTCTTTGAGAGA 57.830 30.769 2.56 0.00 32.50 3.10
89 90 8.632679 AGTAATGTGCATTTTTCTTTGAGAGAA 58.367 29.630 2.56 0.00 36.17 2.87
90 91 7.704789 AATGTGCATTTTTCTTTGAGAGAAC 57.295 32.000 0.00 0.00 43.90 3.01
91 92 6.455360 TGTGCATTTTTCTTTGAGAGAACT 57.545 33.333 0.00 0.00 43.90 3.01
92 93 6.267817 TGTGCATTTTTCTTTGAGAGAACTG 58.732 36.000 0.00 0.00 43.90 3.16
93 94 6.127647 TGTGCATTTTTCTTTGAGAGAACTGT 60.128 34.615 0.00 0.00 43.90 3.55
94 95 6.753744 GTGCATTTTTCTTTGAGAGAACTGTT 59.246 34.615 0.00 0.00 43.90 3.16
95 96 7.276438 GTGCATTTTTCTTTGAGAGAACTGTTT 59.724 33.333 0.00 0.00 43.90 2.83
96 97 8.465999 TGCATTTTTCTTTGAGAGAACTGTTTA 58.534 29.630 0.00 0.00 43.90 2.01
97 98 9.468532 GCATTTTTCTTTGAGAGAACTGTTTAT 57.531 29.630 0.00 0.00 43.90 1.40
103 104 8.964476 TCTTTGAGAGAACTGTTTATGAAACT 57.036 30.769 0.00 0.00 41.90 2.66
104 105 8.830580 TCTTTGAGAGAACTGTTTATGAAACTG 58.169 33.333 0.00 7.24 43.42 3.16
105 106 8.731275 TTTGAGAGAACTGTTTATGAAACTGA 57.269 30.769 13.73 0.00 41.24 3.41
106 107 8.908786 TTGAGAGAACTGTTTATGAAACTGAT 57.091 30.769 13.73 4.27 41.24 2.90
107 108 8.539770 TGAGAGAACTGTTTATGAAACTGATC 57.460 34.615 13.73 11.56 41.24 2.92
108 109 8.150296 TGAGAGAACTGTTTATGAAACTGATCA 58.850 33.333 13.73 0.00 41.36 2.92
109 110 8.316640 AGAGAACTGTTTATGAAACTGATCAC 57.683 34.615 13.73 10.47 41.36 3.06
110 111 7.933577 AGAGAACTGTTTATGAAACTGATCACA 59.066 33.333 13.73 0.00 41.36 3.58
111 112 7.865707 AGAACTGTTTATGAAACTGATCACAC 58.134 34.615 13.73 0.00 41.36 3.82
112 113 7.498900 AGAACTGTTTATGAAACTGATCACACA 59.501 33.333 13.73 0.00 41.36 3.72
113 114 7.750229 ACTGTTTATGAAACTGATCACACAT 57.250 32.000 13.73 0.00 41.24 3.21
114 115 7.587629 ACTGTTTATGAAACTGATCACACATG 58.412 34.615 13.73 0.00 41.24 3.21
115 116 7.445096 ACTGTTTATGAAACTGATCACACATGA 59.555 33.333 13.73 0.00 41.24 3.07
116 117 8.164058 TGTTTATGAAACTGATCACACATGAA 57.836 30.769 0.00 0.00 41.90 2.57
117 118 8.795513 TGTTTATGAAACTGATCACACATGAAT 58.204 29.630 0.00 0.00 41.90 2.57
118 119 9.630098 GTTTATGAAACTGATCACACATGAATT 57.370 29.630 0.00 0.00 37.09 2.17
119 120 9.628746 TTTATGAAACTGATCACACATGAATTG 57.371 29.630 0.00 0.00 38.69 2.32
120 121 6.016213 TGAAACTGATCACACATGAATTGG 57.984 37.500 0.00 0.00 38.69 3.16
121 122 4.445452 AACTGATCACACATGAATTGGC 57.555 40.909 0.00 0.00 38.69 4.52
122 123 2.421073 ACTGATCACACATGAATTGGCG 59.579 45.455 0.00 0.00 38.69 5.69
123 124 2.421073 CTGATCACACATGAATTGGCGT 59.579 45.455 0.00 0.00 38.69 5.68
124 125 2.419673 TGATCACACATGAATTGGCGTC 59.580 45.455 0.00 0.00 38.69 5.19
125 126 2.183478 TCACACATGAATTGGCGTCT 57.817 45.000 0.00 0.00 0.00 4.18
126 127 1.805943 TCACACATGAATTGGCGTCTG 59.194 47.619 0.00 0.00 0.00 3.51
127 128 0.523072 ACACATGAATTGGCGTCTGC 59.477 50.000 0.00 0.00 41.71 4.26
128 129 0.806868 CACATGAATTGGCGTCTGCT 59.193 50.000 0.00 0.00 42.25 4.24
129 130 2.009051 CACATGAATTGGCGTCTGCTA 58.991 47.619 0.00 0.00 42.25 3.49
130 131 2.419673 CACATGAATTGGCGTCTGCTAA 59.580 45.455 0.00 0.00 46.14 3.09
131 132 2.420022 ACATGAATTGGCGTCTGCTAAC 59.580 45.455 0.00 0.00 44.83 2.34
132 133 2.472695 TGAATTGGCGTCTGCTAACT 57.527 45.000 0.00 0.00 44.83 2.24
133 134 3.603158 TGAATTGGCGTCTGCTAACTA 57.397 42.857 0.00 0.00 44.83 2.24
134 135 3.259064 TGAATTGGCGTCTGCTAACTAC 58.741 45.455 0.00 0.00 44.83 2.73
135 136 3.056107 TGAATTGGCGTCTGCTAACTACT 60.056 43.478 0.00 0.00 44.83 2.57
136 137 4.158949 TGAATTGGCGTCTGCTAACTACTA 59.841 41.667 0.00 0.00 44.83 1.82
137 138 3.777465 TTGGCGTCTGCTAACTACTAG 57.223 47.619 0.00 0.00 42.25 2.57
138 139 2.995283 TGGCGTCTGCTAACTACTAGA 58.005 47.619 0.00 0.00 42.25 2.43
144 145 4.496673 CGTCTGCTAACTACTAGAAGGCAG 60.497 50.000 15.75 15.75 37.73 4.85
428 526 2.338785 GCTTGGCCTTCTCCAGCAC 61.339 63.158 3.32 0.00 37.44 4.40
474 572 0.317479 GGTGGTAGTGCTCGAACAGT 59.683 55.000 1.19 1.19 0.00 3.55
488 586 0.768221 AACAGTGCCTCCCTCTTGGA 60.768 55.000 0.00 0.00 42.41 3.53
543 641 0.108945 GGCTACCTACGACCACACAC 60.109 60.000 0.00 0.00 0.00 3.82
552 650 1.713246 GACCACACACACACACACG 59.287 57.895 0.00 0.00 0.00 4.49
553 651 2.304516 GACCACACACACACACACGC 62.305 60.000 0.00 0.00 0.00 5.34
578 676 2.619074 CCCTCAGGACAATTCAACCTCC 60.619 54.545 0.00 0.00 33.47 4.30
582 680 3.146066 CAGGACAATTCAACCTCCGAAA 58.854 45.455 0.00 0.00 31.06 3.46
720 818 5.045869 CACCAATGGAAGACCCTAGTTAGAA 60.046 44.000 6.16 0.00 35.38 2.10
721 819 5.189934 ACCAATGGAAGACCCTAGTTAGAAG 59.810 44.000 6.16 0.00 35.38 2.85
722 820 5.189934 CCAATGGAAGACCCTAGTTAGAAGT 59.810 44.000 0.00 0.00 35.38 3.01
723 821 5.941555 ATGGAAGACCCTAGTTAGAAGTG 57.058 43.478 0.00 0.00 35.38 3.16
724 822 3.514309 TGGAAGACCCTAGTTAGAAGTGC 59.486 47.826 0.00 0.00 35.38 4.40
735 833 4.265073 AGTTAGAAGTGCAAAGCCATAGG 58.735 43.478 0.00 0.00 0.00 2.57
950 1048 4.807039 CGCGGGGTCGTAGGGTTG 62.807 72.222 0.00 0.00 38.89 3.77
1076 1195 2.032681 AGCACGAACCCCTGCTTC 59.967 61.111 0.00 0.00 41.04 3.86
1102 1221 2.941025 CCCCTTGGCCTTGGGAGA 60.941 66.667 28.00 0.00 46.15 3.71
1103 1222 2.679716 CCCTTGGCCTTGGGAGAG 59.320 66.667 23.83 1.81 46.15 3.20
1104 1223 1.925455 CCCTTGGCCTTGGGAGAGA 60.925 63.158 23.83 0.00 46.15 3.10
1723 1845 2.758327 CCTCCGACGTGGGGATCA 60.758 66.667 17.22 0.00 43.10 2.92
1728 1850 2.501610 GACGTGGGGATCAGGCTC 59.498 66.667 0.00 0.00 34.84 4.70
1792 1914 2.591429 CGCAGCACCTGTTCACCA 60.591 61.111 0.00 0.00 33.43 4.17
1855 1977 4.764172 AGACGAGATTGAGAAGGAATTGG 58.236 43.478 0.00 0.00 0.00 3.16
1874 1996 2.439701 CTCCACTGGGCTGCCATG 60.440 66.667 22.05 14.73 0.00 3.66
1959 2081 2.033141 GGCTCTGGTGCTGCTGAA 59.967 61.111 0.00 0.00 0.00 3.02
2217 2339 3.644823 TGTTATCGTCGAACTGCTGAAA 58.355 40.909 0.00 0.00 0.00 2.69
2246 2368 0.809241 CTTCTGCCTCATCTGTCGCC 60.809 60.000 0.00 0.00 0.00 5.54
2271 2393 4.819105 AATAGACGACATTGTCTTCCCA 57.181 40.909 17.01 8.21 46.85 4.37
2608 2731 3.996363 CTCCCTTTGCAACATTTTAAGCC 59.004 43.478 0.00 0.00 0.00 4.35
2698 2831 4.965119 ACCGCAACTCCAAGAAATAATC 57.035 40.909 0.00 0.00 0.00 1.75
2704 2837 7.128331 CGCAACTCCAAGAAATAATCATGTAG 58.872 38.462 0.00 0.00 0.00 2.74
2705 2838 7.201644 CGCAACTCCAAGAAATAATCATGTAGT 60.202 37.037 0.00 0.00 28.53 2.73
2804 2940 8.585881 AGTGCGTTAAGAATACTACCATGATAT 58.414 33.333 0.00 0.00 0.00 1.63
2805 2941 8.648097 GTGCGTTAAGAATACTACCATGATATG 58.352 37.037 0.00 0.00 0.00 1.78
2818 2954 8.796475 ACTACCATGATATGCATTTTTATGTCC 58.204 33.333 3.54 0.00 34.15 4.02
2824 2960 8.214721 TGATATGCATTTTTATGTCCGTTGTA 57.785 30.769 3.54 0.00 0.00 2.41
2900 3036 3.365820 GCGAAATTGATTGAACTGCCTTG 59.634 43.478 0.00 0.00 0.00 3.61
2913 3049 4.884668 ACTGCCTTGTGCTAACTACTAA 57.115 40.909 0.00 0.00 42.00 2.24
2943 3245 9.072294 GCAGAATACAAAATAATACACAACACC 57.928 33.333 0.00 0.00 0.00 4.16
2950 3252 8.784994 ACAAAATAATACACAACACCGATACAA 58.215 29.630 0.00 0.00 0.00 2.41
2968 3270 6.760298 CGATACAATGAGCTAATATGCCTGAT 59.240 38.462 0.00 0.00 0.00 2.90
3008 3310 4.097418 AGAAAGCTAGGCTCTAAAGGACA 58.903 43.478 0.00 0.00 38.25 4.02
3009 3311 4.161377 AGAAAGCTAGGCTCTAAAGGACAG 59.839 45.833 0.00 0.00 38.25 3.51
3032 3334 2.396590 ACGTACATTCACCATCACCC 57.603 50.000 0.00 0.00 0.00 4.61
3040 3342 2.350057 TCACCATCACCCGACAAAAA 57.650 45.000 0.00 0.00 0.00 1.94
3136 3439 9.709495 AAACATGTATTGACTATTGTGCATTTT 57.291 25.926 0.00 0.00 0.00 1.82
3180 3583 2.472695 TGGCACAAACTACTAGCAGG 57.527 50.000 0.00 0.00 31.92 4.85
3248 3795 1.371467 ACCTTGATCACATGACCCCA 58.629 50.000 0.00 0.00 0.00 4.96
3249 3796 1.925255 ACCTTGATCACATGACCCCAT 59.075 47.619 0.00 0.00 0.00 4.00
3263 3812 1.528824 CCCATGCTTCGACCCAGAT 59.471 57.895 0.00 0.00 0.00 2.90
3268 3817 2.672961 TGCTTCGACCCAGATACAAG 57.327 50.000 0.00 0.00 0.00 3.16
3269 3818 1.291132 GCTTCGACCCAGATACAAGC 58.709 55.000 0.00 0.00 0.00 4.01
3289 3838 3.656559 GCACCAAGCATTTGAAACTCAT 58.343 40.909 0.00 0.00 44.79 2.90
3300 3849 7.515957 CATTTGAAACTCATATGCTTCAACC 57.484 36.000 18.93 0.96 37.48 3.77
3301 3850 6.899393 TTTGAAACTCATATGCTTCAACCT 57.101 33.333 18.93 0.00 37.48 3.50
3327 3876 5.241506 CAGGAATGCAGACCTTTACAAAAGA 59.758 40.000 11.12 0.00 33.91 2.52
3331 3880 4.776349 TGCAGACCTTTACAAAAGACTGA 58.224 39.130 19.97 9.88 0.00 3.41
3333 3882 5.827797 TGCAGACCTTTACAAAAGACTGAAT 59.172 36.000 19.97 0.00 0.00 2.57
3334 3883 6.017109 TGCAGACCTTTACAAAAGACTGAATC 60.017 38.462 19.97 10.22 0.00 2.52
3338 3887 8.311836 AGACCTTTACAAAAGACTGAATCGATA 58.688 33.333 0.00 0.00 0.00 2.92
3340 3889 8.883731 ACCTTTACAAAAGACTGAATCGATATG 58.116 33.333 0.00 0.00 0.00 1.78
3386 3946 1.924524 ACAATATCGGCGTTCACTTCG 59.075 47.619 6.85 0.00 0.00 3.79
3387 3947 1.924524 CAATATCGGCGTTCACTTCGT 59.075 47.619 6.85 0.00 0.00 3.85
3431 3991 6.817765 TGTCAAACCCAAGAAGATATGTTC 57.182 37.500 4.44 4.44 0.00 3.18
3432 3992 6.303054 TGTCAAACCCAAGAAGATATGTTCA 58.697 36.000 14.46 0.00 0.00 3.18
3433 3993 6.206634 TGTCAAACCCAAGAAGATATGTTCAC 59.793 38.462 14.46 2.04 0.00 3.18
3434 3994 6.431234 GTCAAACCCAAGAAGATATGTTCACT 59.569 38.462 14.46 0.00 0.00 3.41
3435 3995 7.004086 TCAAACCCAAGAAGATATGTTCACTT 58.996 34.615 14.46 0.00 0.00 3.16
3436 3996 7.174946 TCAAACCCAAGAAGATATGTTCACTTC 59.825 37.037 14.46 4.46 39.87 3.01
3437 3997 6.126863 ACCCAAGAAGATATGTTCACTTCA 57.873 37.500 14.46 0.00 41.37 3.02
3438 3998 6.542821 ACCCAAGAAGATATGTTCACTTCAA 58.457 36.000 14.46 0.00 41.37 2.69
3439 3999 6.656693 ACCCAAGAAGATATGTTCACTTCAAG 59.343 38.462 14.46 1.93 41.37 3.02
3440 4000 6.094603 CCCAAGAAGATATGTTCACTTCAAGG 59.905 42.308 14.46 9.17 41.37 3.61
3441 4001 6.094603 CCAAGAAGATATGTTCACTTCAAGGG 59.905 42.308 14.46 4.14 41.37 3.95
3442 4002 6.380079 AGAAGATATGTTCACTTCAAGGGT 57.620 37.500 14.46 0.00 41.37 4.34
3443 4003 6.784031 AGAAGATATGTTCACTTCAAGGGTT 58.216 36.000 14.46 0.00 41.37 4.11
3444 4004 7.918076 AGAAGATATGTTCACTTCAAGGGTTA 58.082 34.615 14.46 0.00 41.37 2.85
3445 4005 8.383175 AGAAGATATGTTCACTTCAAGGGTTAA 58.617 33.333 14.46 0.00 41.37 2.01
3446 4006 7.923414 AGATATGTTCACTTCAAGGGTTAAC 57.077 36.000 0.00 0.00 0.00 2.01
3447 4007 6.884836 AGATATGTTCACTTCAAGGGTTAACC 59.115 38.462 16.85 16.85 40.67 2.85
3448 4008 4.237976 TGTTCACTTCAAGGGTTAACCA 57.762 40.909 25.71 2.37 43.89 3.67
3449 4009 4.798882 TGTTCACTTCAAGGGTTAACCAT 58.201 39.130 25.71 17.07 43.89 3.55
3450 4010 5.942961 TGTTCACTTCAAGGGTTAACCATA 58.057 37.500 25.71 1.98 43.89 2.74
3451 4011 6.366340 TGTTCACTTCAAGGGTTAACCATAA 58.634 36.000 25.71 10.36 43.89 1.90
3452 4012 6.263617 TGTTCACTTCAAGGGTTAACCATAAC 59.736 38.462 25.71 17.12 43.89 1.89
3465 4025 7.916914 GTTAACCATAACCATACACTGACTT 57.083 36.000 0.00 0.00 36.25 3.01
3466 4026 7.748847 GTTAACCATAACCATACACTGACTTG 58.251 38.462 0.00 0.00 36.25 3.16
3467 4027 5.499004 ACCATAACCATACACTGACTTGT 57.501 39.130 0.00 0.00 0.00 3.16
3468 4028 6.614694 ACCATAACCATACACTGACTTGTA 57.385 37.500 0.00 0.00 36.41 2.41
3469 4029 6.403878 ACCATAACCATACACTGACTTGTAC 58.596 40.000 0.00 0.00 34.79 2.90
3470 4030 5.518847 CCATAACCATACACTGACTTGTACG 59.481 44.000 0.00 0.00 34.79 3.67
3471 4031 4.595762 AACCATACACTGACTTGTACGT 57.404 40.909 0.00 0.00 34.79 3.57
3472 4032 4.595762 ACCATACACTGACTTGTACGTT 57.404 40.909 0.00 0.00 34.79 3.99
3473 4033 5.710513 ACCATACACTGACTTGTACGTTA 57.289 39.130 0.00 0.00 34.79 3.18
3474 4034 6.088016 ACCATACACTGACTTGTACGTTAA 57.912 37.500 0.00 0.00 34.79 2.01
3475 4035 6.514947 ACCATACACTGACTTGTACGTTAAA 58.485 36.000 0.00 0.00 34.79 1.52
3476 4036 7.156673 ACCATACACTGACTTGTACGTTAAAT 58.843 34.615 0.00 0.00 34.79 1.40
3477 4037 7.117236 ACCATACACTGACTTGTACGTTAAATG 59.883 37.037 0.00 0.00 34.79 2.32
3478 4038 5.338614 ACACTGACTTGTACGTTAAATGC 57.661 39.130 0.00 0.00 0.00 3.56
3479 4039 5.054477 ACACTGACTTGTACGTTAAATGCT 58.946 37.500 0.00 0.00 0.00 3.79
3480 4040 5.176958 ACACTGACTTGTACGTTAAATGCTC 59.823 40.000 0.00 0.00 0.00 4.26
3481 4041 5.405571 CACTGACTTGTACGTTAAATGCTCT 59.594 40.000 0.00 0.00 0.00 4.09
3482 4042 6.584942 CACTGACTTGTACGTTAAATGCTCTA 59.415 38.462 0.00 0.00 0.00 2.43
3483 4043 6.807230 ACTGACTTGTACGTTAAATGCTCTAG 59.193 38.462 0.00 0.00 0.00 2.43
3484 4044 5.575606 TGACTTGTACGTTAAATGCTCTAGC 59.424 40.000 0.00 0.00 42.50 3.42
3485 4045 4.868734 ACTTGTACGTTAAATGCTCTAGCC 59.131 41.667 0.00 0.00 41.18 3.93
3486 4046 4.730949 TGTACGTTAAATGCTCTAGCCT 57.269 40.909 0.00 0.00 41.18 4.58
3487 4047 4.679662 TGTACGTTAAATGCTCTAGCCTC 58.320 43.478 0.00 0.00 41.18 4.70
3488 4048 4.401519 TGTACGTTAAATGCTCTAGCCTCT 59.598 41.667 0.00 0.00 41.18 3.69
3489 4049 5.591472 TGTACGTTAAATGCTCTAGCCTCTA 59.409 40.000 0.00 0.00 41.18 2.43
3490 4050 5.189659 ACGTTAAATGCTCTAGCCTCTAG 57.810 43.478 0.00 0.00 41.18 2.43
3491 4051 4.645588 ACGTTAAATGCTCTAGCCTCTAGT 59.354 41.667 0.00 0.00 41.18 2.57
3492 4052 5.826737 ACGTTAAATGCTCTAGCCTCTAGTA 59.173 40.000 0.00 0.00 41.18 1.82
3493 4053 6.016943 ACGTTAAATGCTCTAGCCTCTAGTAG 60.017 42.308 0.00 0.00 41.18 2.57
3494 4054 6.016943 CGTTAAATGCTCTAGCCTCTAGTAGT 60.017 42.308 0.00 0.00 41.18 2.73
3495 4055 7.172875 CGTTAAATGCTCTAGCCTCTAGTAGTA 59.827 40.741 0.00 0.00 41.18 1.82
3496 4056 8.848182 GTTAAATGCTCTAGCCTCTAGTAGTAA 58.152 37.037 0.00 0.00 41.18 2.24
3497 4057 6.887626 AATGCTCTAGCCTCTAGTAGTAAC 57.112 41.667 0.00 0.00 41.18 2.50
3498 4058 5.369409 TGCTCTAGCCTCTAGTAGTAACA 57.631 43.478 0.00 0.00 41.18 2.41
3499 4059 5.752650 TGCTCTAGCCTCTAGTAGTAACAA 58.247 41.667 0.00 0.00 41.18 2.83
3500 4060 5.589452 TGCTCTAGCCTCTAGTAGTAACAAC 59.411 44.000 0.00 0.00 41.18 3.32
3501 4061 5.589452 GCTCTAGCCTCTAGTAGTAACAACA 59.411 44.000 0.00 0.00 34.31 3.33
3502 4062 6.263617 GCTCTAGCCTCTAGTAGTAACAACAT 59.736 42.308 0.00 0.00 34.31 2.71
3503 4063 7.569639 TCTAGCCTCTAGTAGTAACAACATG 57.430 40.000 0.00 0.00 0.00 3.21
3504 4064 5.599999 AGCCTCTAGTAGTAACAACATGG 57.400 43.478 0.00 0.00 0.00 3.66
3505 4065 5.269991 AGCCTCTAGTAGTAACAACATGGA 58.730 41.667 0.00 0.00 0.00 3.41
3506 4066 5.900123 AGCCTCTAGTAGTAACAACATGGAT 59.100 40.000 0.00 0.00 0.00 3.41
3507 4067 5.986135 GCCTCTAGTAGTAACAACATGGATG 59.014 44.000 0.00 0.00 0.00 3.51
3508 4068 6.183360 GCCTCTAGTAGTAACAACATGGATGA 60.183 42.308 7.66 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.582648 ACCCTTTACAACAGAAATAGTAATGTT 57.417 29.630 0.00 0.00 36.34 2.71
8 9 9.582648 AACCCTTTACAACAGAAATAGTAATGT 57.417 29.630 0.00 0.00 0.00 2.71
11 12 9.629878 TGAAACCCTTTACAACAGAAATAGTAA 57.370 29.630 0.00 0.00 0.00 2.24
12 13 9.059260 GTGAAACCCTTTACAACAGAAATAGTA 57.941 33.333 0.00 0.00 0.00 1.82
13 14 7.558444 TGTGAAACCCTTTACAACAGAAATAGT 59.442 33.333 0.00 0.00 34.36 2.12
14 15 7.936584 TGTGAAACCCTTTACAACAGAAATAG 58.063 34.615 0.00 0.00 34.36 1.73
15 16 7.883391 TGTGAAACCCTTTACAACAGAAATA 57.117 32.000 0.00 0.00 34.36 1.40
16 17 6.783708 TGTGAAACCCTTTACAACAGAAAT 57.216 33.333 0.00 0.00 34.36 2.17
17 18 6.783708 ATGTGAAACCCTTTACAACAGAAA 57.216 33.333 0.00 0.00 34.36 2.52
18 19 9.747898 ATATATGTGAAACCCTTTACAACAGAA 57.252 29.630 0.00 0.00 34.36 3.02
61 62 9.897744 CTCTCAAAGAAAAATGCACATTACTAA 57.102 29.630 0.00 0.00 0.00 2.24
62 63 9.283768 TCTCTCAAAGAAAAATGCACATTACTA 57.716 29.630 0.00 0.00 0.00 1.82
63 64 8.169977 TCTCTCAAAGAAAAATGCACATTACT 57.830 30.769 0.00 0.00 0.00 2.24
64 65 8.694394 GTTCTCTCAAAGAAAAATGCACATTAC 58.306 33.333 0.00 0.00 45.50 1.89
65 66 8.632679 AGTTCTCTCAAAGAAAAATGCACATTA 58.367 29.630 0.00 0.00 45.50 1.90
66 67 7.437267 CAGTTCTCTCAAAGAAAAATGCACATT 59.563 33.333 0.00 0.00 45.50 2.71
67 68 6.921857 CAGTTCTCTCAAAGAAAAATGCACAT 59.078 34.615 0.00 0.00 45.50 3.21
68 69 6.127647 ACAGTTCTCTCAAAGAAAAATGCACA 60.128 34.615 0.00 0.00 45.50 4.57
69 70 6.268566 ACAGTTCTCTCAAAGAAAAATGCAC 58.731 36.000 0.00 0.00 45.50 4.57
70 71 6.455360 ACAGTTCTCTCAAAGAAAAATGCA 57.545 33.333 0.00 0.00 45.50 3.96
71 72 7.761651 AAACAGTTCTCTCAAAGAAAAATGC 57.238 32.000 0.00 0.00 45.50 3.56
77 78 9.396022 AGTTTCATAAACAGTTCTCTCAAAGAA 57.604 29.630 5.42 0.00 43.79 2.52
78 79 8.830580 CAGTTTCATAAACAGTTCTCTCAAAGA 58.169 33.333 5.42 0.00 43.79 2.52
79 80 8.830580 TCAGTTTCATAAACAGTTCTCTCAAAG 58.169 33.333 5.42 0.00 43.79 2.77
80 81 8.731275 TCAGTTTCATAAACAGTTCTCTCAAA 57.269 30.769 5.42 0.00 43.79 2.69
81 82 8.908786 ATCAGTTTCATAAACAGTTCTCTCAA 57.091 30.769 5.42 0.00 43.79 3.02
82 83 8.150296 TGATCAGTTTCATAAACAGTTCTCTCA 58.850 33.333 5.42 0.00 43.79 3.27
83 84 8.439286 GTGATCAGTTTCATAAACAGTTCTCTC 58.561 37.037 0.00 0.00 43.79 3.20
84 85 7.933577 TGTGATCAGTTTCATAAACAGTTCTCT 59.066 33.333 0.00 0.00 43.79 3.10
85 86 8.012241 GTGTGATCAGTTTCATAAACAGTTCTC 58.988 37.037 0.00 4.13 43.79 2.87
86 87 7.498900 TGTGTGATCAGTTTCATAAACAGTTCT 59.501 33.333 0.00 0.00 43.79 3.01
87 88 7.639039 TGTGTGATCAGTTTCATAAACAGTTC 58.361 34.615 0.00 3.11 43.79 3.01
88 89 7.566760 TGTGTGATCAGTTTCATAAACAGTT 57.433 32.000 0.00 0.00 43.79 3.16
89 90 7.445096 TCATGTGTGATCAGTTTCATAAACAGT 59.555 33.333 0.00 0.00 43.79 3.55
90 91 7.809665 TCATGTGTGATCAGTTTCATAAACAG 58.190 34.615 0.00 0.00 43.79 3.16
91 92 7.742556 TCATGTGTGATCAGTTTCATAAACA 57.257 32.000 0.00 0.00 43.79 2.83
92 93 9.630098 AATTCATGTGTGATCAGTTTCATAAAC 57.370 29.630 0.00 0.00 36.57 2.01
93 94 9.628746 CAATTCATGTGTGATCAGTTTCATAAA 57.371 29.630 0.00 0.00 33.56 1.40
94 95 8.245491 CCAATTCATGTGTGATCAGTTTCATAA 58.755 33.333 0.00 0.00 33.56 1.90
95 96 7.629008 GCCAATTCATGTGTGATCAGTTTCATA 60.629 37.037 0.00 0.00 33.56 2.15
96 97 6.627243 CCAATTCATGTGTGATCAGTTTCAT 58.373 36.000 0.00 0.00 33.56 2.57
97 98 5.565242 GCCAATTCATGTGTGATCAGTTTCA 60.565 40.000 0.00 0.00 33.56 2.69
98 99 4.860907 GCCAATTCATGTGTGATCAGTTTC 59.139 41.667 0.00 0.00 33.56 2.78
99 100 4.616604 CGCCAATTCATGTGTGATCAGTTT 60.617 41.667 0.00 0.00 33.56 2.66
100 101 3.119743 CGCCAATTCATGTGTGATCAGTT 60.120 43.478 0.00 0.00 33.56 3.16
101 102 2.421073 CGCCAATTCATGTGTGATCAGT 59.579 45.455 0.00 0.00 33.56 3.41
102 103 2.421073 ACGCCAATTCATGTGTGATCAG 59.579 45.455 0.00 0.00 33.56 2.90
103 104 2.419673 GACGCCAATTCATGTGTGATCA 59.580 45.455 0.00 0.00 33.56 2.92
104 105 2.679837 AGACGCCAATTCATGTGTGATC 59.320 45.455 0.00 0.00 33.56 2.92
105 106 2.421073 CAGACGCCAATTCATGTGTGAT 59.579 45.455 0.00 0.00 33.56 3.06
106 107 1.805943 CAGACGCCAATTCATGTGTGA 59.194 47.619 0.00 0.00 0.00 3.58
107 108 1.730121 GCAGACGCCAATTCATGTGTG 60.730 52.381 0.00 0.00 0.00 3.82
108 109 0.523072 GCAGACGCCAATTCATGTGT 59.477 50.000 0.00 0.00 0.00 3.72
109 110 0.806868 AGCAGACGCCAATTCATGTG 59.193 50.000 0.00 0.00 39.83 3.21
110 111 2.401583 TAGCAGACGCCAATTCATGT 57.598 45.000 0.00 0.00 39.83 3.21
111 112 2.679837 AGTTAGCAGACGCCAATTCATG 59.320 45.455 0.00 0.00 39.83 3.07
112 113 2.991250 AGTTAGCAGACGCCAATTCAT 58.009 42.857 0.00 0.00 39.83 2.57
113 114 2.472695 AGTTAGCAGACGCCAATTCA 57.527 45.000 0.00 0.00 39.83 2.57
114 115 3.522553 AGTAGTTAGCAGACGCCAATTC 58.477 45.455 0.00 0.00 39.83 2.17
115 116 3.611766 AGTAGTTAGCAGACGCCAATT 57.388 42.857 0.00 0.00 39.83 2.32
116 117 3.952323 TCTAGTAGTTAGCAGACGCCAAT 59.048 43.478 0.00 0.00 39.83 3.16
117 118 3.349927 TCTAGTAGTTAGCAGACGCCAA 58.650 45.455 0.00 0.00 39.83 4.52
118 119 2.995283 TCTAGTAGTTAGCAGACGCCA 58.005 47.619 0.00 0.00 39.83 5.69
119 120 3.243134 CCTTCTAGTAGTTAGCAGACGCC 60.243 52.174 0.00 0.00 39.83 5.68
120 121 3.792794 GCCTTCTAGTAGTTAGCAGACGC 60.793 52.174 0.00 0.00 38.99 5.19
121 122 3.377485 TGCCTTCTAGTAGTTAGCAGACG 59.623 47.826 0.00 0.00 0.00 4.18
122 123 4.985538 TGCCTTCTAGTAGTTAGCAGAC 57.014 45.455 0.00 0.00 0.00 3.51
124 125 3.131223 TGCTGCCTTCTAGTAGTTAGCAG 59.869 47.826 22.55 22.55 46.87 4.24
125 126 3.096852 TGCTGCCTTCTAGTAGTTAGCA 58.903 45.455 15.87 15.87 37.56 3.49
126 127 3.381908 TCTGCTGCCTTCTAGTAGTTAGC 59.618 47.826 12.31 12.31 31.00 3.09
127 128 5.584253 TTCTGCTGCCTTCTAGTAGTTAG 57.416 43.478 0.00 0.00 31.00 2.34
128 129 6.605995 TGTATTCTGCTGCCTTCTAGTAGTTA 59.394 38.462 0.00 0.00 31.00 2.24
129 130 5.422331 TGTATTCTGCTGCCTTCTAGTAGTT 59.578 40.000 0.00 0.00 31.00 2.24
130 131 4.956700 TGTATTCTGCTGCCTTCTAGTAGT 59.043 41.667 0.00 0.00 31.00 2.73
131 132 5.521906 TGTATTCTGCTGCCTTCTAGTAG 57.478 43.478 0.00 0.00 0.00 2.57
132 133 5.932619 TTGTATTCTGCTGCCTTCTAGTA 57.067 39.130 0.00 0.00 0.00 1.82
133 134 4.826274 TTGTATTCTGCTGCCTTCTAGT 57.174 40.909 0.00 0.00 0.00 2.57
134 135 6.690194 ATTTTGTATTCTGCTGCCTTCTAG 57.310 37.500 0.00 0.00 0.00 2.43
135 136 7.564793 TCTATTTTGTATTCTGCTGCCTTCTA 58.435 34.615 0.00 0.00 0.00 2.10
136 137 6.418101 TCTATTTTGTATTCTGCTGCCTTCT 58.582 36.000 0.00 0.00 0.00 2.85
137 138 6.683974 TCTATTTTGTATTCTGCTGCCTTC 57.316 37.500 0.00 0.00 0.00 3.46
138 139 7.651027 ATTCTATTTTGTATTCTGCTGCCTT 57.349 32.000 0.00 0.00 0.00 4.35
173 174 9.799106 AGGCATAATAGCTTTTTGTATCAGTAT 57.201 29.630 0.00 0.00 34.17 2.12
174 175 9.056005 CAGGCATAATAGCTTTTTGTATCAGTA 57.944 33.333 0.00 0.00 34.17 2.74
195 196 0.827089 CCCACATGGTTTGTCAGGCA 60.827 55.000 0.00 0.00 36.00 4.75
488 586 2.234908 CAGGGGAATGAAGAGTTCGACT 59.765 50.000 0.00 0.00 0.00 4.18
543 641 2.969806 GAGGGCATGCGTGTGTGTG 61.970 63.158 12.44 0.00 0.00 3.82
552 650 0.743097 GAATTGTCCTGAGGGCATGC 59.257 55.000 6.62 9.90 0.00 4.06
553 651 2.133281 TGAATTGTCCTGAGGGCATG 57.867 50.000 6.62 0.00 0.00 4.06
578 676 3.118592 AGACTTGGGAGCTTAGGATTTCG 60.119 47.826 0.00 0.00 0.00 3.46
582 680 2.769095 GTCAGACTTGGGAGCTTAGGAT 59.231 50.000 0.00 0.00 0.00 3.24
720 818 3.813443 CATCTACCTATGGCTTTGCACT 58.187 45.455 0.00 0.00 0.00 4.40
721 819 2.291741 GCATCTACCTATGGCTTTGCAC 59.708 50.000 0.00 0.00 0.00 4.57
722 820 2.575532 GCATCTACCTATGGCTTTGCA 58.424 47.619 0.00 0.00 0.00 4.08
723 821 1.882623 GGCATCTACCTATGGCTTTGC 59.117 52.381 3.41 0.00 46.09 3.68
1073 1192 1.341209 GCCAAGGGGAACAAACAGAAG 59.659 52.381 0.00 0.00 35.59 2.85
1076 1195 0.469892 AGGCCAAGGGGAACAAACAG 60.470 55.000 5.01 0.00 35.59 3.16
1102 1221 1.153823 CCGCCGACGACATTCTTCT 60.154 57.895 0.00 0.00 43.93 2.85
1103 1222 2.799540 GCCGCCGACGACATTCTTC 61.800 63.158 0.00 0.00 43.93 2.87
1104 1223 2.813908 GCCGCCGACGACATTCTT 60.814 61.111 0.00 0.00 43.93 2.52
1410 1532 1.358402 CTGCTCCGTGATCTCCTCG 59.642 63.158 0.00 0.00 0.00 4.63
1792 1914 3.884895 TGTCAACAATCACACAGACCTT 58.115 40.909 0.00 0.00 0.00 3.50
1855 1977 2.976490 ATGGCAGCCCAGTGGAGAC 61.976 63.158 11.95 2.61 46.24 3.36
1874 1996 1.930908 GATGCCCTGCACAGCTTCAC 61.931 60.000 11.98 0.00 43.04 3.18
1959 2081 0.761187 TCTTCAGGTCAGCAACAGCT 59.239 50.000 0.00 0.00 39.75 4.24
2085 2207 1.070445 CAGCTCCCCTTGCCTATCG 59.930 63.158 0.00 0.00 0.00 2.92
2217 2339 1.203237 TGAGGCAGAAGACCCTTCTCT 60.203 52.381 6.27 2.62 0.00 3.10
2246 2368 4.332819 GGAAGACAATGTCGTCTATTTGGG 59.667 45.833 24.00 0.00 45.56 4.12
2271 2393 2.781757 TCCCTGAAGCTCATCATCCAAT 59.218 45.455 0.00 0.00 0.00 3.16
2646 2771 5.615289 ACATAAGCCTCAACTATCATGGTC 58.385 41.667 0.00 0.00 0.00 4.02
2733 2869 6.756542 TGATCAGTTGTCCAGTATACAATTCG 59.243 38.462 5.50 0.00 38.95 3.34
2804 2940 6.504398 TGTTTACAACGGACATAAAAATGCA 58.496 32.000 0.00 0.00 0.00 3.96
2805 2941 6.639279 ACTGTTTACAACGGACATAAAAATGC 59.361 34.615 2.41 0.00 40.26 3.56
2879 3015 4.383649 CACAAGGCAGTTCAATCAATTTCG 59.616 41.667 0.00 0.00 0.00 3.46
2900 3036 8.404000 TGTATTCTGCTACTTAGTAGTTAGCAC 58.596 37.037 19.12 14.72 38.30 4.40
2943 3245 6.101997 TCAGGCATATTAGCTCATTGTATCG 58.898 40.000 0.00 0.00 34.17 2.92
2950 3252 6.124316 AGTTCATCAGGCATATTAGCTCAT 57.876 37.500 0.00 0.00 34.17 2.90
2968 3270 4.698201 TTCTTGTGACCCACATAGTTCA 57.302 40.909 0.27 0.00 44.16 3.18
3008 3310 2.290008 TGATGGTGAATGTACGTTGGCT 60.290 45.455 4.71 0.00 0.00 4.75
3009 3311 2.080693 TGATGGTGAATGTACGTTGGC 58.919 47.619 4.71 0.00 0.00 4.52
3147 3450 6.581712 AGTTTGTGCCATCAATTTTACAACT 58.418 32.000 0.00 0.00 0.00 3.16
3148 3451 6.843069 AGTTTGTGCCATCAATTTTACAAC 57.157 33.333 0.00 0.00 0.00 3.32
3187 3590 5.350504 AAGTGATGATGCTAACTGCTAGT 57.649 39.130 0.00 0.00 43.37 2.57
3188 3591 6.983307 ACTAAAGTGATGATGCTAACTGCTAG 59.017 38.462 0.00 0.00 43.37 3.42
3189 3592 6.878317 ACTAAAGTGATGATGCTAACTGCTA 58.122 36.000 0.00 0.00 43.37 3.49
3191 3594 6.758886 AGTACTAAAGTGATGATGCTAACTGC 59.241 38.462 0.00 0.00 43.25 4.40
3192 3595 8.194104 AGAGTACTAAAGTGATGATGCTAACTG 58.806 37.037 0.00 0.00 0.00 3.16
3194 3597 7.436673 CCAGAGTACTAAAGTGATGATGCTAAC 59.563 40.741 0.00 0.00 0.00 2.34
3195 3598 7.342026 TCCAGAGTACTAAAGTGATGATGCTAA 59.658 37.037 0.00 0.00 0.00 3.09
3196 3599 6.833933 TCCAGAGTACTAAAGTGATGATGCTA 59.166 38.462 0.00 0.00 0.00 3.49
3197 3600 5.658634 TCCAGAGTACTAAAGTGATGATGCT 59.341 40.000 0.00 0.00 0.00 3.79
3198 3601 5.907207 TCCAGAGTACTAAAGTGATGATGC 58.093 41.667 0.00 0.00 0.00 3.91
3199 3602 7.551585 AGTTCCAGAGTACTAAAGTGATGATG 58.448 38.462 0.00 0.00 0.00 3.07
3200 3603 7.415765 CGAGTTCCAGAGTACTAAAGTGATGAT 60.416 40.741 0.00 0.00 0.00 2.45
3202 3605 6.030849 CGAGTTCCAGAGTACTAAAGTGATG 58.969 44.000 0.00 0.00 0.00 3.07
3203 3606 5.393243 GCGAGTTCCAGAGTACTAAAGTGAT 60.393 44.000 0.00 0.00 0.00 3.06
3205 3608 4.167268 GCGAGTTCCAGAGTACTAAAGTG 58.833 47.826 0.00 0.00 0.00 3.16
3207 3610 4.436242 TGCGAGTTCCAGAGTACTAAAG 57.564 45.455 0.00 0.00 0.00 1.85
3208 3611 4.553323 GTTGCGAGTTCCAGAGTACTAAA 58.447 43.478 0.00 0.00 0.00 1.85
3209 3612 3.057033 GGTTGCGAGTTCCAGAGTACTAA 60.057 47.826 0.00 0.00 0.00 2.24
3210 3613 2.490903 GGTTGCGAGTTCCAGAGTACTA 59.509 50.000 0.00 0.00 0.00 1.82
3248 3795 2.743183 GCTTGTATCTGGGTCGAAGCAT 60.743 50.000 0.00 0.00 36.62 3.79
3249 3796 1.405526 GCTTGTATCTGGGTCGAAGCA 60.406 52.381 0.00 0.00 36.62 3.91
3250 3797 1.291132 GCTTGTATCTGGGTCGAAGC 58.709 55.000 0.00 0.00 0.00 3.86
3251 3798 2.271800 GTGCTTGTATCTGGGTCGAAG 58.728 52.381 0.00 0.00 0.00 3.79
3252 3799 1.066430 GGTGCTTGTATCTGGGTCGAA 60.066 52.381 0.00 0.00 0.00 3.71
3253 3800 0.535335 GGTGCTTGTATCTGGGTCGA 59.465 55.000 0.00 0.00 0.00 4.20
3263 3812 4.099266 AGTTTCAAATGCTTGGTGCTTGTA 59.901 37.500 0.00 0.00 43.37 2.41
3268 3817 3.096489 TGAGTTTCAAATGCTTGGTGC 57.904 42.857 0.00 0.00 43.25 5.01
3269 3818 5.290158 GCATATGAGTTTCAAATGCTTGGTG 59.710 40.000 6.97 0.00 33.01 4.17
3289 3838 3.696051 GCATTCCTGAAGGTTGAAGCATA 59.304 43.478 0.00 0.00 36.34 3.14
3294 3843 3.149196 GTCTGCATTCCTGAAGGTTGAA 58.851 45.455 0.00 0.00 36.34 2.69
3295 3844 2.553028 GGTCTGCATTCCTGAAGGTTGA 60.553 50.000 0.00 0.00 36.34 3.18
3296 3845 1.815003 GGTCTGCATTCCTGAAGGTTG 59.185 52.381 0.00 0.00 36.34 3.77
3297 3846 1.707427 AGGTCTGCATTCCTGAAGGTT 59.293 47.619 8.71 0.00 36.34 3.50
3298 3847 1.366319 AGGTCTGCATTCCTGAAGGT 58.634 50.000 8.71 0.00 36.34 3.50
3299 3848 2.503895 AAGGTCTGCATTCCTGAAGG 57.496 50.000 10.02 0.00 33.97 3.46
3300 3849 4.326826 TGTAAAGGTCTGCATTCCTGAAG 58.673 43.478 10.02 0.00 33.97 3.02
3301 3850 4.365514 TGTAAAGGTCTGCATTCCTGAA 57.634 40.909 10.02 0.64 33.97 3.02
3327 3876 3.667497 ATGTCGCCATATCGATTCAGT 57.333 42.857 1.71 0.00 40.84 3.41
3331 3880 9.684448 CTTATCTAATATGTCGCCATATCGATT 57.316 33.333 1.71 0.00 42.23 3.34
3333 3882 7.139392 GCTTATCTAATATGTCGCCATATCGA 58.861 38.462 0.00 0.77 42.23 3.59
3334 3883 6.918022 TGCTTATCTAATATGTCGCCATATCG 59.082 38.462 0.00 0.00 42.23 2.92
3338 3887 6.286240 TCTGCTTATCTAATATGTCGCCAT 57.714 37.500 0.00 0.00 34.97 4.40
3340 3889 6.333416 TGATCTGCTTATCTAATATGTCGCC 58.667 40.000 0.00 0.00 0.00 5.54
3349 3898 9.208022 CCGATATTGTTTGATCTGCTTATCTAA 57.792 33.333 0.00 0.00 0.00 2.10
3350 3899 7.331934 GCCGATATTGTTTGATCTGCTTATCTA 59.668 37.037 0.00 0.00 31.71 1.98
3351 3900 6.148480 GCCGATATTGTTTGATCTGCTTATCT 59.852 38.462 0.00 0.00 31.71 1.98
3352 3901 6.310197 GCCGATATTGTTTGATCTGCTTATC 58.690 40.000 0.00 0.00 31.71 1.75
3353 3902 5.106948 CGCCGATATTGTTTGATCTGCTTAT 60.107 40.000 0.00 0.00 32.09 1.73
3354 3903 4.211164 CGCCGATATTGTTTGATCTGCTTA 59.789 41.667 0.00 0.00 32.09 3.09
3355 3904 3.002656 CGCCGATATTGTTTGATCTGCTT 59.997 43.478 0.00 0.00 32.09 3.91
3356 3905 2.545526 CGCCGATATTGTTTGATCTGCT 59.454 45.455 0.00 0.00 32.09 4.24
3357 3906 2.287915 ACGCCGATATTGTTTGATCTGC 59.712 45.455 0.00 0.00 0.00 4.26
3373 3933 3.058351 CGTACGAAGTGAACGCCG 58.942 61.111 10.44 0.00 45.73 6.46
3386 3946 4.468689 GGCTGGGGTGGAGCGTAC 62.469 72.222 0.00 0.00 37.32 3.67
3441 4001 7.389607 ACAAGTCAGTGTATGGTTATGGTTAAC 59.610 37.037 0.00 0.00 37.55 2.01
3442 4002 7.455058 ACAAGTCAGTGTATGGTTATGGTTAA 58.545 34.615 0.00 0.00 0.00 2.01
3443 4003 7.011499 ACAAGTCAGTGTATGGTTATGGTTA 57.989 36.000 0.00 0.00 0.00 2.85
3444 4004 5.876357 ACAAGTCAGTGTATGGTTATGGTT 58.124 37.500 0.00 0.00 0.00 3.67
3445 4005 5.499004 ACAAGTCAGTGTATGGTTATGGT 57.501 39.130 0.00 0.00 0.00 3.55
3446 4006 5.518847 CGTACAAGTCAGTGTATGGTTATGG 59.481 44.000 0.00 0.00 37.35 2.74
3447 4007 6.097356 ACGTACAAGTCAGTGTATGGTTATG 58.903 40.000 8.87 0.00 42.77 1.90
3448 4008 6.276832 ACGTACAAGTCAGTGTATGGTTAT 57.723 37.500 8.87 0.00 42.77 1.89
3449 4009 5.710513 ACGTACAAGTCAGTGTATGGTTA 57.289 39.130 8.87 0.00 42.77 2.85
3450 4010 4.595762 ACGTACAAGTCAGTGTATGGTT 57.404 40.909 8.87 0.00 42.77 3.67
3451 4011 4.595762 AACGTACAAGTCAGTGTATGGT 57.404 40.909 8.87 0.24 42.77 3.55
3452 4012 7.453034 CATTTAACGTACAAGTCAGTGTATGG 58.547 38.462 8.87 0.00 42.77 2.74
3453 4013 6.953743 GCATTTAACGTACAAGTCAGTGTATG 59.046 38.462 0.00 3.58 43.66 2.39
3454 4014 6.872020 AGCATTTAACGTACAAGTCAGTGTAT 59.128 34.615 0.00 0.00 36.42 2.29
3455 4015 6.218019 AGCATTTAACGTACAAGTCAGTGTA 58.782 36.000 0.00 0.00 32.75 2.90
3456 4016 5.054477 AGCATTTAACGTACAAGTCAGTGT 58.946 37.500 0.00 0.00 35.43 3.55
3457 4017 5.405571 AGAGCATTTAACGTACAAGTCAGTG 59.594 40.000 0.00 0.00 0.00 3.66
3458 4018 5.539048 AGAGCATTTAACGTACAAGTCAGT 58.461 37.500 0.00 0.00 0.00 3.41
3459 4019 6.237595 GCTAGAGCATTTAACGTACAAGTCAG 60.238 42.308 0.00 0.00 41.59 3.51
3460 4020 5.575606 GCTAGAGCATTTAACGTACAAGTCA 59.424 40.000 0.00 0.00 41.59 3.41
3461 4021 5.005490 GGCTAGAGCATTTAACGTACAAGTC 59.995 44.000 3.54 0.00 44.36 3.01
3462 4022 4.868734 GGCTAGAGCATTTAACGTACAAGT 59.131 41.667 3.54 0.00 44.36 3.16
3463 4023 5.109903 AGGCTAGAGCATTTAACGTACAAG 58.890 41.667 3.54 0.00 44.36 3.16
3464 4024 5.080969 AGGCTAGAGCATTTAACGTACAA 57.919 39.130 3.54 0.00 44.36 2.41
3465 4025 4.401519 AGAGGCTAGAGCATTTAACGTACA 59.598 41.667 3.54 0.00 44.36 2.90
3466 4026 4.934515 AGAGGCTAGAGCATTTAACGTAC 58.065 43.478 3.54 0.00 44.36 3.67
3467 4027 5.826737 ACTAGAGGCTAGAGCATTTAACGTA 59.173 40.000 8.36 0.00 44.36 3.57
3468 4028 4.645588 ACTAGAGGCTAGAGCATTTAACGT 59.354 41.667 8.36 0.00 44.36 3.99
3469 4029 5.189659 ACTAGAGGCTAGAGCATTTAACG 57.810 43.478 8.36 0.00 44.36 3.18
3470 4030 7.279750 ACTACTAGAGGCTAGAGCATTTAAC 57.720 40.000 8.36 0.00 44.36 2.01
3471 4031 8.848182 GTTACTACTAGAGGCTAGAGCATTTAA 58.152 37.037 8.36 0.00 44.36 1.52
3472 4032 7.997223 TGTTACTACTAGAGGCTAGAGCATTTA 59.003 37.037 8.36 0.00 44.36 1.40
3473 4033 6.834451 TGTTACTACTAGAGGCTAGAGCATTT 59.166 38.462 8.36 0.00 44.36 2.32
3474 4034 6.366340 TGTTACTACTAGAGGCTAGAGCATT 58.634 40.000 8.36 0.00 44.36 3.56
3475 4035 5.942961 TGTTACTACTAGAGGCTAGAGCAT 58.057 41.667 8.36 0.00 44.36 3.79
3476 4036 5.369409 TGTTACTACTAGAGGCTAGAGCA 57.631 43.478 8.36 0.00 44.36 4.26
3477 4037 5.589452 TGTTGTTACTACTAGAGGCTAGAGC 59.411 44.000 8.36 0.00 41.14 4.09
3478 4038 7.255312 CCATGTTGTTACTACTAGAGGCTAGAG 60.255 44.444 8.36 4.53 0.00 2.43
3479 4039 6.546403 CCATGTTGTTACTACTAGAGGCTAGA 59.454 42.308 8.36 0.00 0.00 2.43
3480 4040 6.546403 TCCATGTTGTTACTACTAGAGGCTAG 59.454 42.308 0.00 0.00 0.00 3.42
3481 4041 6.429151 TCCATGTTGTTACTACTAGAGGCTA 58.571 40.000 0.00 0.00 0.00 3.93
3482 4042 5.269991 TCCATGTTGTTACTACTAGAGGCT 58.730 41.667 0.00 0.00 0.00 4.58
3483 4043 5.593679 TCCATGTTGTTACTACTAGAGGC 57.406 43.478 0.00 0.00 0.00 4.70
3484 4044 7.348080 TCATCCATGTTGTTACTACTAGAGG 57.652 40.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.