Multiple sequence alignment - TraesCS3A01G146100

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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 TraesCS3A01G146100 chr3A 100.000 5931 0 0 1 5931 128149125 128155055 0.000000e+00 10953.0
1 TraesCS3A01G146100 chr3A 98.582 141 1 1 2662 2802 524021197 524021336 1.280000e-61 248.0
2 TraesCS3A01G146100 chr3A 97.753 89 2 0 5721 5809 36229750 36229838 2.860000e-33 154.0
3 TraesCS3A01G146100 chr3D 95.207 4694 140 39 88 4765 121885982 121890606 0.000000e+00 7343.0
4 TraesCS3A01G146100 chr3D 92.262 336 9 2 4935 5254 121908177 121908511 1.510000e-125 460.0
5 TraesCS3A01G146100 chr3D 92.308 273 20 1 5246 5517 121921830 121922102 2.590000e-103 387.0
6 TraesCS3A01G146100 chr3D 95.322 171 8 0 5554 5724 121922105 121922275 7.570000e-69 272.0
7 TraesCS3A01G146100 chr3D 98.582 141 2 0 2662 2802 24157132 24157272 3.550000e-62 250.0
8 TraesCS3A01G146100 chr3D 100.000 125 0 0 5807 5931 121922274 121922398 1.290000e-56 231.0
9 TraesCS3A01G146100 chr3D 93.478 138 9 0 4803 4940 121890604 121890741 7.790000e-49 206.0
10 TraesCS3A01G146100 chr3D 93.913 115 7 0 2801 2915 571593686 571593572 2.200000e-39 174.0
11 TraesCS3A01G146100 chr3B 94.134 2199 81 17 88 2277 173376857 173379016 0.000000e+00 3302.0
12 TraesCS3A01G146100 chr3B 95.635 1741 66 5 3028 4765 173379529 173381262 0.000000e+00 2785.0
13 TraesCS3A01G146100 chr3B 91.527 1133 78 16 4803 5926 173381260 173382383 0.000000e+00 1544.0
14 TraesCS3A01G146100 chr3B 93.573 389 21 3 2276 2661 173379140 173379527 1.430000e-160 577.0
15 TraesCS3A01G146100 chr3B 92.308 104 6 1 5719 5822 42629628 42629527 4.790000e-31 147.0
16 TraesCS3A01G146100 chr7B 99.291 141 1 0 2662 2802 720237022 720236882 7.630000e-64 255.0
17 TraesCS3A01G146100 chr7B 95.789 95 2 1 5723 5817 450280557 450280649 1.030000e-32 152.0
18 TraesCS3A01G146100 chr2B 99.291 141 1 0 2662 2802 683738449 683738589 7.630000e-64 255.0
19 TraesCS3A01G146100 chr2B 95.402 87 4 0 5722 5808 303097265 303097351 8.010000e-29 139.0
20 TraesCS3A01G146100 chr2B 85.106 94 13 1 4263 4356 131895789 131895697 1.760000e-15 95.3
21 TraesCS3A01G146100 chr1D 99.291 141 1 0 2662 2802 254469420 254469560 7.630000e-64 255.0
22 TraesCS3A01G146100 chr1D 94.783 115 5 1 2801 2915 254418112 254417999 1.700000e-40 178.0
23 TraesCS3A01G146100 chr5D 98.582 141 1 1 2662 2802 503323505 503323644 1.280000e-61 248.0
24 TraesCS3A01G146100 chr5D 97.872 141 1 1 2662 2802 6243280 6243142 5.940000e-60 243.0
25 TraesCS3A01G146100 chr5D 94.783 115 5 1 2801 2915 512408490 512408603 1.700000e-40 178.0
26 TraesCS3A01G146100 chr5A 97.872 141 1 1 2662 2802 414823250 414823388 5.940000e-60 243.0
27 TraesCS3A01G146100 chr7D 94.783 115 5 1 2801 2915 77242301 77242188 1.700000e-40 178.0
28 TraesCS3A01G146100 chr6D 94.783 115 5 1 2801 2915 45510513 45510626 1.700000e-40 178.0
29 TraesCS3A01G146100 chr6D 93.000 100 6 1 5719 5818 383526419 383526517 1.720000e-30 145.0
30 TraesCS3A01G146100 chr2A 94.783 115 5 1 2801 2915 334595008 334595121 1.700000e-40 178.0
31 TraesCS3A01G146100 chr2A 98.889 90 1 0 5719 5808 303731196 303731285 1.710000e-35 161.0
32 TraesCS3A01G146100 chr2A 95.000 100 4 1 5719 5818 693209889 693209987 7.960000e-34 156.0
33 TraesCS3A01G146100 chr1A 94.783 115 5 1 2801 2915 554459517 554459404 1.700000e-40 178.0
34 TraesCS3A01G146100 chrUn 93.913 115 6 1 2801 2915 472679533 472679420 7.900000e-39 172.0
35 TraesCS3A01G146100 chr1B 97.753 89 2 0 5720 5808 428624077 428624165 2.860000e-33 154.0
36 TraesCS3A01G146100 chr4A 94.845 97 5 0 5715 5811 27667500 27667596 1.030000e-32 152.0
37 TraesCS3A01G146100 chr2D 72.807 342 81 10 4067 4402 80226139 80226474 8.130000e-19 106.0


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 TraesCS3A01G146100 chr3A 128149125 128155055 5930 False 10953.000000 10953 100.000000 1 5931 1 chr3A.!!$F2 5930
1 TraesCS3A01G146100 chr3D 121885982 121890741 4759 False 3774.500000 7343 94.342500 88 4940 2 chr3D.!!$F3 4852
2 TraesCS3A01G146100 chr3D 121921830 121922398 568 False 296.666667 387 95.876667 5246 5931 3 chr3D.!!$F4 685
3 TraesCS3A01G146100 chr3B 173376857 173382383 5526 False 2052.000000 3302 93.717250 88 5926 4 chr3B.!!$F1 5838

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
37 38 0.311477 GAAGCGGAGGGAGTATCGAC 59.689 60.0 0.00 0.00 34.37 4.20 F
1049 1062 0.257328 TGAACCAACACAGGAGGCAA 59.743 50.0 0.00 0.00 0.00 4.52 F
2905 3052 0.391793 CTCTTTCCGCTCCCTTGGAC 60.392 60.0 0.00 0.00 32.95 4.02 F
4386 4545 0.605319 TGAACTGGTCCGGCATGTTC 60.605 55.0 16.75 16.75 37.92 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1160 1173 0.321346 TCGAGCTTTGCAGGTGATGA 59.679 50.000 0.00 0.0 0.0 2.92 R
3017 3167 0.035152 TGTGATGAGCAAGCCGGAAT 60.035 50.000 5.05 0.0 0.0 3.01 R
4496 4655 1.139654 CGCATCTCTTCCCTTGGATCA 59.860 52.381 0.00 0.0 0.0 2.92 R
5332 5507 0.035439 AGTTAGCACAATGGGGTCCG 60.035 55.000 0.00 0.0 0.0 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
25 26 8.827177 AACATCTTATTATAATTCGAAGCGGA 57.173 30.769 3.35 0.00 0.00 5.54
26 27 8.467402 ACATCTTATTATAATTCGAAGCGGAG 57.533 34.615 3.35 0.00 0.00 4.63
27 28 7.545965 ACATCTTATTATAATTCGAAGCGGAGG 59.454 37.037 3.35 0.00 0.00 4.30
28 29 6.395629 TCTTATTATAATTCGAAGCGGAGGG 58.604 40.000 3.35 0.00 0.00 4.30
29 30 4.884668 ATTATAATTCGAAGCGGAGGGA 57.115 40.909 3.35 0.00 0.00 4.20
30 31 2.821991 ATAATTCGAAGCGGAGGGAG 57.178 50.000 3.35 0.00 0.00 4.30
31 32 1.481871 TAATTCGAAGCGGAGGGAGT 58.518 50.000 3.35 0.00 0.00 3.85
32 33 1.481871 AATTCGAAGCGGAGGGAGTA 58.518 50.000 3.35 0.00 0.00 2.59
33 34 1.705873 ATTCGAAGCGGAGGGAGTAT 58.294 50.000 3.35 0.00 0.00 2.12
34 35 1.030457 TTCGAAGCGGAGGGAGTATC 58.970 55.000 0.00 0.00 0.00 2.24
35 36 1.164662 TCGAAGCGGAGGGAGTATCG 61.165 60.000 0.00 0.00 34.37 2.92
36 37 1.164662 CGAAGCGGAGGGAGTATCGA 61.165 60.000 0.00 0.00 34.37 3.59
37 38 0.311477 GAAGCGGAGGGAGTATCGAC 59.689 60.000 0.00 0.00 34.37 4.20
38 39 1.445716 AAGCGGAGGGAGTATCGACG 61.446 60.000 0.00 0.00 34.37 5.12
39 40 1.890979 GCGGAGGGAGTATCGACGA 60.891 63.158 0.00 0.00 34.37 4.20
40 41 1.442526 GCGGAGGGAGTATCGACGAA 61.443 60.000 0.00 0.00 34.37 3.85
41 42 0.587285 CGGAGGGAGTATCGACGAAG 59.413 60.000 0.00 0.00 34.37 3.79
71 72 3.744940 TCCTTCGGGTTAGGACTTAGA 57.255 47.619 0.00 0.00 36.88 2.10
72 73 3.629087 TCCTTCGGGTTAGGACTTAGAG 58.371 50.000 0.00 0.00 36.88 2.43
73 74 2.101082 CCTTCGGGTTAGGACTTAGAGC 59.899 54.545 0.00 0.00 34.56 4.09
74 75 2.519771 TCGGGTTAGGACTTAGAGCA 57.480 50.000 0.00 0.00 0.00 4.26
75 76 2.097825 TCGGGTTAGGACTTAGAGCAC 58.902 52.381 0.00 0.00 0.00 4.40
76 77 1.822990 CGGGTTAGGACTTAGAGCACA 59.177 52.381 0.00 0.00 0.00 4.57
77 78 2.232941 CGGGTTAGGACTTAGAGCACAA 59.767 50.000 0.00 0.00 0.00 3.33
78 79 3.306502 CGGGTTAGGACTTAGAGCACAAA 60.307 47.826 0.00 0.00 0.00 2.83
79 80 4.254492 GGGTTAGGACTTAGAGCACAAAG 58.746 47.826 0.00 0.00 0.00 2.77
80 81 3.685272 GGTTAGGACTTAGAGCACAAAGC 59.315 47.826 0.00 0.00 46.19 3.51
103 104 8.859517 AGCAACGAAATTTCTATAGTCTCTAC 57.140 34.615 15.92 0.00 0.00 2.59
109 110 9.227490 CGAAATTTCTATAGTCTCTACACACTG 57.773 37.037 15.92 0.00 0.00 3.66
136 137 3.192844 GTCTTGAGTGACCGATGGTAGAA 59.807 47.826 0.00 0.00 35.25 2.10
137 138 3.830178 TCTTGAGTGACCGATGGTAGAAA 59.170 43.478 0.00 0.00 35.25 2.52
169 170 9.270640 GTTGGCAATCCATATTTTAAATATGCA 57.729 29.630 24.49 15.53 43.05 3.96
303 309 5.483685 TTGCTCTAGCTTTTAGGTGAGAA 57.516 39.130 3.26 0.00 42.66 2.87
307 313 5.336849 GCTCTAGCTTTTAGGTGAGAAGTCA 60.337 44.000 0.00 0.00 38.21 3.41
326 332 4.119136 GTCATCCTCAGCTAGCTTTCTTC 58.881 47.826 16.46 0.00 0.00 2.87
435 444 3.256631 AGAACAAAGACATGCATTGACCC 59.743 43.478 0.00 2.53 0.00 4.46
465 474 1.000052 CCTGTGATTTGTGTGCATGCA 60.000 47.619 18.46 18.46 0.00 3.96
515 524 7.067859 GGTATATATTACATACAGGCCGTGAGA 59.932 40.741 10.01 0.00 31.67 3.27
626 635 5.537300 TCTCTGGGCACTCAAAGTATATC 57.463 43.478 0.00 0.00 0.00 1.63
627 636 4.962362 TCTCTGGGCACTCAAAGTATATCA 59.038 41.667 0.00 0.00 0.00 2.15
635 644 7.600752 GGGCACTCAAAGTATATCAATAGAGAC 59.399 40.741 0.00 0.00 0.00 3.36
779 790 7.703621 ACACACATATTTACGCTTACTATCGTT 59.296 33.333 0.00 0.00 39.79 3.85
828 839 5.351740 GTGTAAAGCTCAAGTAATCCTGGTC 59.648 44.000 0.00 0.00 0.00 4.02
842 853 2.174639 TCCTGGTCCATTTTGACAGTGT 59.825 45.455 0.00 0.00 36.97 3.55
915 928 6.873605 CCTAATTTGGGATCAAACCTTGTTTC 59.126 38.462 0.00 0.00 44.53 2.78
1049 1062 0.257328 TGAACCAACACAGGAGGCAA 59.743 50.000 0.00 0.00 0.00 4.52
1050 1063 1.133513 TGAACCAACACAGGAGGCAAT 60.134 47.619 0.00 0.00 0.00 3.56
1103 1116 4.464244 GCTTTAAAGCCCTTCTCCAAATCT 59.536 41.667 26.60 0.00 46.20 2.40
1160 1173 0.977395 GGAATCCGCTAGGCCAGTAT 59.023 55.000 5.01 0.00 37.47 2.12
1221 1234 4.498894 AAGATCATCCAGACATGCTTGA 57.501 40.909 6.60 0.00 0.00 3.02
1474 1487 0.553819 AAGGTGGTTAGGGTTGCACA 59.446 50.000 0.00 0.00 0.00 4.57
1478 1491 1.977009 GGTTAGGGTTGCACAGGCC 60.977 63.158 0.00 0.00 40.13 5.19
1586 1599 2.441750 GTTGATCCCTAGGGTTATGGCA 59.558 50.000 27.58 10.51 36.47 4.92
1679 1692 6.103330 GCGTTATGTTGGTTTATTGGGAAAT 58.897 36.000 0.00 0.00 0.00 2.17
1986 1999 4.141287 TGGGTGTTCTTTGAAACGATCAT 58.859 39.130 0.00 0.00 38.03 2.45
1987 2000 5.309638 TGGGTGTTCTTTGAAACGATCATA 58.690 37.500 0.00 0.00 38.03 2.15
1988 2001 5.765677 TGGGTGTTCTTTGAAACGATCATAA 59.234 36.000 0.00 0.00 38.03 1.90
1989 2002 6.432783 TGGGTGTTCTTTGAAACGATCATAAT 59.567 34.615 0.00 0.00 38.03 1.28
2136 2150 8.956533 TTCCGAAATCAGTCATAAATACATGA 57.043 30.769 0.00 0.00 32.50 3.07
2137 2151 8.593492 TCCGAAATCAGTCATAAATACATGAG 57.407 34.615 0.00 0.00 35.63 2.90
2138 2152 8.421002 TCCGAAATCAGTCATAAATACATGAGA 58.579 33.333 0.00 0.00 35.63 3.27
2139 2153 9.212641 CCGAAATCAGTCATAAATACATGAGAT 57.787 33.333 0.00 0.00 35.63 2.75
2246 2260 1.202734 GCTAGCTTGCCTCATGGATGA 60.203 52.381 9.15 0.00 34.57 2.92
2247 2261 2.552591 GCTAGCTTGCCTCATGGATGAT 60.553 50.000 9.15 0.00 36.02 2.45
2500 2639 7.402071 AGTTAGGTAGACATTTGAATCCCACTA 59.598 37.037 0.00 0.00 0.00 2.74
2573 2712 4.885413 TGGAGAATTTGTGCTTGGAAATG 58.115 39.130 0.00 0.00 0.00 2.32
2580 2719 9.995003 AGAATTTGTGCTTGGAAATGTTAAATA 57.005 25.926 0.00 0.00 0.00 1.40
2741 2887 4.526650 TGGATCGGCTCTATTACATAAGCA 59.473 41.667 0.00 0.00 36.47 3.91
2814 2960 8.515695 TTAGTTGTATCGAAAGTGGAGAGATA 57.484 34.615 0.00 0.00 0.00 1.98
2825 2971 2.622942 GTGGAGAGATAGCTGAGTGGAG 59.377 54.545 0.00 0.00 0.00 3.86
2831 2977 4.340950 AGAGATAGCTGAGTGGAGTAAAGC 59.659 45.833 0.00 0.00 0.00 3.51
2905 3052 0.391793 CTCTTTCCGCTCCCTTGGAC 60.392 60.000 0.00 0.00 32.95 4.02
2917 3064 1.006998 CCCTTGGACCATTTGGGATCA 59.993 52.381 18.04 0.00 40.23 2.92
2959 3106 6.302535 TCGTCCTATCTATAAGAGGAGAGG 57.697 45.833 0.00 0.00 40.07 3.69
2977 3124 7.872138 AGGAGAGGATATGAAAAATGTAACCA 58.128 34.615 0.00 0.00 0.00 3.67
2978 3125 7.775561 AGGAGAGGATATGAAAAATGTAACCAC 59.224 37.037 0.00 0.00 0.00 4.16
2980 3127 8.738645 AGAGGATATGAAAAATGTAACCACTC 57.261 34.615 0.00 0.00 0.00 3.51
2981 3128 8.552296 AGAGGATATGAAAAATGTAACCACTCT 58.448 33.333 0.00 0.00 0.00 3.24
2984 3131 9.788960 GGATATGAAAAATGTAACCACTCTTTC 57.211 33.333 0.00 0.00 0.00 2.62
2985 3132 9.490663 GATATGAAAAATGTAACCACTCTTTCG 57.509 33.333 0.00 0.00 0.00 3.46
2986 3133 6.687081 TGAAAAATGTAACCACTCTTTCGT 57.313 33.333 0.00 0.00 0.00 3.85
3021 3171 1.895707 CCATCCGCTGGCAGATTCC 60.896 63.158 20.86 0.00 38.47 3.01
3120 3274 1.153086 GGAATGAGGCCACGCAGAT 60.153 57.895 5.01 0.00 0.00 2.90
3226 3380 5.473504 GGCTTCCTCACTAGTGAAAATTGAA 59.526 40.000 25.14 18.95 39.39 2.69
3229 3383 7.920682 GCTTCCTCACTAGTGAAAATTGAAAAA 59.079 33.333 25.14 8.90 39.39 1.94
3272 3426 7.012327 TGTTGTTTGGAAGAAGATAACTCTGTG 59.988 37.037 0.00 0.00 0.00 3.66
3283 3437 5.230942 AGATAACTCTGTGTTCACTTTCGG 58.769 41.667 0.00 0.00 39.89 4.30
3286 3440 3.714391 ACTCTGTGTTCACTTTCGGTAC 58.286 45.455 4.59 0.00 0.00 3.34
3431 3587 5.535029 AGTCTTATGTATGGTCCCTTGGTA 58.465 41.667 0.00 0.00 0.00 3.25
3470 3626 7.552848 TCGTAAAACAGTAAATCGTGACTAC 57.447 36.000 0.00 0.00 0.00 2.73
3528 3684 6.076981 AGATTACCTTCTGTTGTTTGCAAG 57.923 37.500 0.00 0.00 34.94 4.01
3562 3718 2.136298 TCTGGACTCTACAGGCTCAG 57.864 55.000 0.00 0.00 36.62 3.35
3582 3739 9.609346 GGCTCAGGTAAAAATTATAGTAGTTCA 57.391 33.333 0.00 0.00 0.00 3.18
3651 3810 4.911610 CAGCTTTGTCGATTTGTACTTTGG 59.088 41.667 0.00 0.00 0.00 3.28
3715 3874 0.616371 AGCGTACAAGCCATTGGGTA 59.384 50.000 8.02 0.00 40.97 3.69
3867 4026 1.132500 CCTTTAGGCCTACCCCTCAG 58.868 60.000 13.46 1.87 36.41 3.35
4035 4194 2.113986 AGTGGTCAAGTGGGCTGC 59.886 61.111 0.00 0.00 0.00 5.25
4378 4537 1.961277 GCACTGGTGAACTGGTCCG 60.961 63.158 4.79 0.00 0.00 4.79
4386 4545 0.605319 TGAACTGGTCCGGCATGTTC 60.605 55.000 16.75 16.75 37.92 3.18
4496 4655 2.173519 CAAGATGCCAACAAGGATGGT 58.826 47.619 0.00 0.00 41.22 3.55
4657 4816 8.067751 TGCTGATACAAAGTAGTGAAGTCTAT 57.932 34.615 0.00 0.00 0.00 1.98
4658 4817 9.185680 TGCTGATACAAAGTAGTGAAGTCTATA 57.814 33.333 0.00 0.00 0.00 1.31
4695 4854 2.866028 CTGGCTCTTGCTCGCAAC 59.134 61.111 0.00 0.00 39.59 4.17
4765 4924 3.490526 GCTTTTAAGGTGTGCACAATGTG 59.509 43.478 23.59 9.36 36.51 3.21
4777 4936 3.976793 CACAATGTGCAGAACTTCACT 57.023 42.857 0.00 0.00 34.49 3.41
4778 4937 4.297299 CACAATGTGCAGAACTTCACTT 57.703 40.909 0.00 0.00 34.49 3.16
4779 4938 5.422666 CACAATGTGCAGAACTTCACTTA 57.577 39.130 0.00 0.00 34.49 2.24
4780 4939 5.820131 CACAATGTGCAGAACTTCACTTAA 58.180 37.500 0.00 0.00 34.49 1.85
4781 4940 6.441274 CACAATGTGCAGAACTTCACTTAAT 58.559 36.000 0.00 0.00 34.49 1.40
4782 4941 7.584108 CACAATGTGCAGAACTTCACTTAATA 58.416 34.615 0.00 0.00 34.49 0.98
4783 4942 7.535258 CACAATGTGCAGAACTTCACTTAATAC 59.465 37.037 0.00 0.00 34.49 1.89
4784 4943 6.743575 ATGTGCAGAACTTCACTTAATACC 57.256 37.500 6.23 0.00 34.49 2.73
4785 4944 5.616270 TGTGCAGAACTTCACTTAATACCA 58.384 37.500 6.23 0.00 34.49 3.25
4786 4945 6.237901 TGTGCAGAACTTCACTTAATACCAT 58.762 36.000 6.23 0.00 34.49 3.55
4787 4946 6.714810 TGTGCAGAACTTCACTTAATACCATT 59.285 34.615 6.23 0.00 34.49 3.16
4788 4947 7.094805 TGTGCAGAACTTCACTTAATACCATTC 60.095 37.037 6.23 0.00 34.49 2.67
4789 4948 7.119846 GTGCAGAACTTCACTTAATACCATTCT 59.880 37.037 0.00 0.00 0.00 2.40
4790 4949 7.119699 TGCAGAACTTCACTTAATACCATTCTG 59.880 37.037 0.00 0.00 42.09 3.02
4791 4950 7.119846 GCAGAACTTCACTTAATACCATTCTGT 59.880 37.037 10.77 0.00 41.53 3.41
4792 4951 8.446273 CAGAACTTCACTTAATACCATTCTGTG 58.554 37.037 0.00 0.00 37.06 3.66
4793 4952 6.743575 ACTTCACTTAATACCATTCTGTGC 57.256 37.500 0.00 0.00 0.00 4.57
4794 4953 6.476378 ACTTCACTTAATACCATTCTGTGCT 58.524 36.000 0.00 0.00 0.00 4.40
4795 4954 7.620880 ACTTCACTTAATACCATTCTGTGCTA 58.379 34.615 0.00 0.00 0.00 3.49
4796 4955 8.267894 ACTTCACTTAATACCATTCTGTGCTAT 58.732 33.333 0.00 0.00 0.00 2.97
4797 4956 9.113838 CTTCACTTAATACCATTCTGTGCTATT 57.886 33.333 0.00 0.00 0.00 1.73
4798 4957 8.437360 TCACTTAATACCATTCTGTGCTATTG 57.563 34.615 0.00 0.00 0.00 1.90
4799 4958 7.498900 TCACTTAATACCATTCTGTGCTATTGG 59.501 37.037 0.00 0.00 0.00 3.16
4800 4959 7.498900 CACTTAATACCATTCTGTGCTATTGGA 59.501 37.037 0.00 0.00 0.00 3.53
4801 4960 7.716998 ACTTAATACCATTCTGTGCTATTGGAG 59.283 37.037 0.00 0.00 0.00 3.86
4802 4961 5.636903 ATACCATTCTGTGCTATTGGAGT 57.363 39.130 0.00 0.00 0.00 3.85
4803 4962 3.614092 ACCATTCTGTGCTATTGGAGTG 58.386 45.455 0.00 0.00 0.00 3.51
4804 4963 2.947652 CCATTCTGTGCTATTGGAGTGG 59.052 50.000 0.00 0.00 31.32 4.00
4813 4972 5.423931 TGTGCTATTGGAGTGGTATGACTAA 59.576 40.000 0.00 0.00 0.00 2.24
4827 4986 5.944007 GGTATGACTAACTTTGTTGGACCAT 59.056 40.000 0.00 6.35 0.00 3.55
4829 4988 5.766150 TGACTAACTTTGTTGGACCATTG 57.234 39.130 0.00 0.00 0.00 2.82
4861 5020 8.576442 ACTTGTGAATGTACCAAAATAAGAAGG 58.424 33.333 0.00 0.00 0.00 3.46
4903 5062 6.270815 TGCTCGTTATGTATTAGTCAGTTCC 58.729 40.000 0.00 0.00 0.00 3.62
4905 5064 6.637658 GCTCGTTATGTATTAGTCAGTTCCTC 59.362 42.308 0.00 0.00 0.00 3.71
4984 5143 8.502387 GTGATGAGAGCATTTTAAATAGCCTAG 58.498 37.037 8.31 0.00 34.11 3.02
4985 5144 8.432013 TGATGAGAGCATTTTAAATAGCCTAGA 58.568 33.333 8.31 0.02 34.11 2.43
4986 5145 9.277783 GATGAGAGCATTTTAAATAGCCTAGAA 57.722 33.333 8.31 0.00 34.11 2.10
4987 5146 8.668510 TGAGAGCATTTTAAATAGCCTAGAAG 57.331 34.615 8.31 0.00 0.00 2.85
4988 5147 8.486210 TGAGAGCATTTTAAATAGCCTAGAAGA 58.514 33.333 8.31 0.00 0.00 2.87
4989 5148 8.900983 AGAGCATTTTAAATAGCCTAGAAGAG 57.099 34.615 8.31 0.00 0.00 2.85
4990 5149 8.490311 AGAGCATTTTAAATAGCCTAGAAGAGT 58.510 33.333 8.31 0.00 0.00 3.24
4991 5150 9.765795 GAGCATTTTAAATAGCCTAGAAGAGTA 57.234 33.333 8.31 0.00 0.00 2.59
4992 5151 9.771534 AGCATTTTAAATAGCCTAGAAGAGTAG 57.228 33.333 8.31 0.00 0.00 2.57
4993 5152 9.549078 GCATTTTAAATAGCCTAGAAGAGTAGT 57.451 33.333 0.00 0.00 0.00 2.73
4995 5154 8.943909 TTTTAAATAGCCTAGAAGAGTAGTGC 57.056 34.615 0.00 0.00 0.00 4.40
4996 5155 5.538849 AAATAGCCTAGAAGAGTAGTGCC 57.461 43.478 0.00 0.00 0.00 5.01
4997 5156 2.534042 AGCCTAGAAGAGTAGTGCCA 57.466 50.000 0.00 0.00 0.00 4.92
5038 5213 6.923199 ATGGGACTTCAAATTCAGAATGTT 57.077 33.333 0.00 0.00 37.40 2.71
5066 5241 6.476378 AGAGCAACCATACTTACTGAACAAT 58.524 36.000 0.00 0.00 0.00 2.71
5077 5252 2.648724 GAACAATGCATCGCCGCG 60.649 61.111 6.39 6.39 33.35 6.46
5142 5317 2.224606 CAAGTGCTGCTTTCTTCCAGA 58.775 47.619 0.00 0.00 34.69 3.86
5214 5389 4.321718 ACAGCTGATATCAATTCCGATGG 58.678 43.478 23.35 0.00 0.00 3.51
5332 5507 2.417586 GCAAAATGAGAAGGCCAAATGC 59.582 45.455 5.01 0.00 40.16 3.56
5341 5516 2.759560 GCCAAATGCGGACCCCAT 60.760 61.111 0.00 0.00 0.00 4.00
5348 5523 1.920734 ATGCGGACCCCATTGTGCTA 61.921 55.000 0.00 0.00 0.00 3.49
5412 5588 8.697507 AGGAAACTGTTGAACAATATCTTTCT 57.302 30.769 0.00 0.00 41.13 2.52
5470 5646 6.599244 TGCTTAAGCTGAAATATACTTGTGCT 59.401 34.615 26.90 0.00 42.66 4.40
5513 5690 4.284490 TCAGAGTAGCTTGGTTCTGAACAT 59.716 41.667 21.01 5.10 42.08 2.71
5529 5706 9.416794 GTTCTGAACATGTACTATATCCATCAG 57.583 37.037 15.34 4.64 0.00 2.90
5544 5722 1.072489 CATCAGCATCCCATCTCTGCT 59.928 52.381 0.00 0.00 46.72 4.24
5575 5753 5.128205 TGCTCCAACTAATGAATCATCCAG 58.872 41.667 0.00 0.00 0.00 3.86
5595 5773 3.317711 CAGGCACAACTTGACCATGTAAA 59.682 43.478 0.00 0.00 30.55 2.01
5598 5776 4.218417 GGCACAACTTGACCATGTAAATCT 59.782 41.667 0.00 0.00 0.00 2.40
5613 5791 9.079833 CCATGTAAATCTGAAAACATCATGAAC 57.920 33.333 0.00 0.00 37.44 3.18
5655 5833 2.224161 GCATCCGTAGAGCCAAGATCTT 60.224 50.000 0.88 0.88 28.73 2.40
5679 5857 6.480763 TCAATACCTCATCTGCCAAACTAAA 58.519 36.000 0.00 0.00 0.00 1.85
5734 5912 7.970102 TGTGTTAAAGTTATACTCCCTCTGTT 58.030 34.615 0.00 0.00 0.00 3.16
5738 5916 6.697641 AAAGTTATACTCCCTCTGTTCCAA 57.302 37.500 0.00 0.00 0.00 3.53
5743 5921 8.487028 AGTTATACTCCCTCTGTTCCAAAATAG 58.513 37.037 0.00 0.00 0.00 1.73
5745 5923 7.698163 ATACTCCCTCTGTTCCAAAATAGAT 57.302 36.000 0.00 0.00 32.88 1.98
5748 5926 6.159398 ACTCCCTCTGTTCCAAAATAGATGAT 59.841 38.462 0.00 0.00 32.88 2.45
5749 5927 6.973642 TCCCTCTGTTCCAAAATAGATGATT 58.026 36.000 0.00 0.00 32.88 2.57
5750 5928 7.056635 TCCCTCTGTTCCAAAATAGATGATTC 58.943 38.462 0.00 0.00 32.88 2.52
5751 5929 6.830324 CCCTCTGTTCCAAAATAGATGATTCA 59.170 38.462 0.00 0.00 32.88 2.57
5752 5930 7.340232 CCCTCTGTTCCAAAATAGATGATTCAA 59.660 37.037 0.00 0.00 32.88 2.69
5753 5931 8.186821 CCTCTGTTCCAAAATAGATGATTCAAC 58.813 37.037 0.00 0.00 32.88 3.18
5756 5934 9.918630 CTGTTCCAAAATAGATGATTCAACTTT 57.081 29.630 1.47 0.00 0.00 2.66
5784 5962 8.983702 ACTAACTTTAATACAAAGTTGGGTCA 57.016 30.769 21.95 6.46 46.38 4.02
5785 5963 9.582648 ACTAACTTTAATACAAAGTTGGGTCAT 57.417 29.630 21.95 6.17 46.38 3.06
5787 5965 8.706322 AACTTTAATACAAAGTTGGGTCATCT 57.294 30.769 12.88 0.00 45.58 2.90
5795 5973 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.545965 CCTCCGCTTCGAATTATAATAAGATGT 59.454 37.037 0.00 0.00 0.00 3.06
2 3 7.010552 CCCTCCGCTTCGAATTATAATAAGATG 59.989 40.741 0.00 9.64 0.00 2.90
3 4 7.042335 CCCTCCGCTTCGAATTATAATAAGAT 58.958 38.462 0.00 0.00 0.00 2.40
4 5 6.209986 TCCCTCCGCTTCGAATTATAATAAGA 59.790 38.462 0.00 5.10 0.00 2.10
5 6 6.395629 TCCCTCCGCTTCGAATTATAATAAG 58.604 40.000 0.00 0.59 0.00 1.73
6 7 6.014840 ACTCCCTCCGCTTCGAATTATAATAA 60.015 38.462 0.00 0.00 0.00 1.40
7 8 5.479375 ACTCCCTCCGCTTCGAATTATAATA 59.521 40.000 0.00 0.00 0.00 0.98
8 9 4.283722 ACTCCCTCCGCTTCGAATTATAAT 59.716 41.667 0.00 0.00 0.00 1.28
9 10 3.640029 ACTCCCTCCGCTTCGAATTATAA 59.360 43.478 0.00 0.00 0.00 0.98
10 11 3.228453 ACTCCCTCCGCTTCGAATTATA 58.772 45.455 0.00 0.00 0.00 0.98
11 12 2.040178 ACTCCCTCCGCTTCGAATTAT 58.960 47.619 0.00 0.00 0.00 1.28
12 13 1.481871 ACTCCCTCCGCTTCGAATTA 58.518 50.000 0.00 0.00 0.00 1.40
13 14 1.481871 TACTCCCTCCGCTTCGAATT 58.518 50.000 0.00 0.00 0.00 2.17
14 15 1.614413 GATACTCCCTCCGCTTCGAAT 59.386 52.381 0.00 0.00 0.00 3.34
15 16 1.030457 GATACTCCCTCCGCTTCGAA 58.970 55.000 0.00 0.00 0.00 3.71
16 17 1.164662 CGATACTCCCTCCGCTTCGA 61.165 60.000 0.00 0.00 0.00 3.71
17 18 1.164662 TCGATACTCCCTCCGCTTCG 61.165 60.000 0.00 0.00 0.00 3.79
18 19 0.311477 GTCGATACTCCCTCCGCTTC 59.689 60.000 0.00 0.00 0.00 3.86
19 20 1.445716 CGTCGATACTCCCTCCGCTT 61.446 60.000 0.00 0.00 0.00 4.68
20 21 1.892862 CGTCGATACTCCCTCCGCT 60.893 63.158 0.00 0.00 0.00 5.52
21 22 1.442526 TTCGTCGATACTCCCTCCGC 61.443 60.000 0.00 0.00 0.00 5.54
22 23 0.587285 CTTCGTCGATACTCCCTCCG 59.413 60.000 0.00 0.00 0.00 4.63
23 24 1.677942 ACTTCGTCGATACTCCCTCC 58.322 55.000 0.00 0.00 0.00 4.30
24 25 4.889832 TTTACTTCGTCGATACTCCCTC 57.110 45.455 0.00 0.00 0.00 4.30
25 26 5.649782 TTTTTACTTCGTCGATACTCCCT 57.350 39.130 0.00 0.00 0.00 4.20
53 54 2.758979 TGCTCTAAGTCCTAACCCGAAG 59.241 50.000 0.00 0.00 0.00 3.79
54 55 2.494870 GTGCTCTAAGTCCTAACCCGAA 59.505 50.000 0.00 0.00 0.00 4.30
55 56 2.097825 GTGCTCTAAGTCCTAACCCGA 58.902 52.381 0.00 0.00 0.00 5.14
56 57 1.822990 TGTGCTCTAAGTCCTAACCCG 59.177 52.381 0.00 0.00 0.00 5.28
57 58 3.975168 TTGTGCTCTAAGTCCTAACCC 57.025 47.619 0.00 0.00 0.00 4.11
58 59 3.685272 GCTTTGTGCTCTAAGTCCTAACC 59.315 47.826 10.77 0.00 38.95 2.85
59 60 4.315803 TGCTTTGTGCTCTAAGTCCTAAC 58.684 43.478 10.77 0.00 43.37 2.34
60 61 4.617253 TGCTTTGTGCTCTAAGTCCTAA 57.383 40.909 10.77 0.00 43.37 2.69
61 62 4.315803 GTTGCTTTGTGCTCTAAGTCCTA 58.684 43.478 10.77 0.00 43.37 2.94
62 63 3.142174 GTTGCTTTGTGCTCTAAGTCCT 58.858 45.455 10.77 0.00 43.37 3.85
63 64 2.096218 CGTTGCTTTGTGCTCTAAGTCC 60.096 50.000 10.77 0.00 43.37 3.85
64 65 2.800544 TCGTTGCTTTGTGCTCTAAGTC 59.199 45.455 10.77 5.16 43.37 3.01
65 66 2.833794 TCGTTGCTTTGTGCTCTAAGT 58.166 42.857 10.77 0.00 43.37 2.24
66 67 3.878086 TTCGTTGCTTTGTGCTCTAAG 57.122 42.857 5.73 5.73 43.37 2.18
67 68 4.829064 ATTTCGTTGCTTTGTGCTCTAA 57.171 36.364 0.00 0.00 43.37 2.10
68 69 4.829064 AATTTCGTTGCTTTGTGCTCTA 57.171 36.364 0.00 0.00 43.37 2.43
69 70 3.715628 AATTTCGTTGCTTTGTGCTCT 57.284 38.095 0.00 0.00 43.37 4.09
70 71 4.044426 AGAAATTTCGTTGCTTTGTGCTC 58.956 39.130 12.42 0.00 43.37 4.26
71 72 4.045636 AGAAATTTCGTTGCTTTGTGCT 57.954 36.364 12.42 0.00 43.37 4.40
72 73 6.801862 ACTATAGAAATTTCGTTGCTTTGTGC 59.198 34.615 12.42 0.00 43.25 4.57
73 74 8.230486 AGACTATAGAAATTTCGTTGCTTTGTG 58.770 33.333 12.42 0.07 0.00 3.33
74 75 8.324163 AGACTATAGAAATTTCGTTGCTTTGT 57.676 30.769 12.42 5.29 0.00 2.83
75 76 8.660373 AGAGACTATAGAAATTTCGTTGCTTTG 58.340 33.333 12.42 2.50 0.00 2.77
76 77 8.779354 AGAGACTATAGAAATTTCGTTGCTTT 57.221 30.769 12.42 0.00 0.00 3.51
77 78 9.303537 GTAGAGACTATAGAAATTTCGTTGCTT 57.696 33.333 12.42 0.00 0.00 3.91
78 79 8.467598 TGTAGAGACTATAGAAATTTCGTTGCT 58.532 33.333 12.42 6.76 0.00 3.91
79 80 8.533153 GTGTAGAGACTATAGAAATTTCGTTGC 58.467 37.037 12.42 2.34 0.00 4.17
80 81 9.569167 TGTGTAGAGACTATAGAAATTTCGTTG 57.431 33.333 12.42 8.97 0.00 4.10
81 82 9.570488 GTGTGTAGAGACTATAGAAATTTCGTT 57.430 33.333 12.42 6.82 0.00 3.85
82 83 8.958506 AGTGTGTAGAGACTATAGAAATTTCGT 58.041 33.333 12.42 8.22 0.00 3.85
83 84 9.227490 CAGTGTGTAGAGACTATAGAAATTTCG 57.773 37.037 12.42 1.19 0.00 3.46
86 87 9.862371 CAACAGTGTGTAGAGACTATAGAAATT 57.138 33.333 6.78 0.00 0.00 1.82
87 88 9.244292 TCAACAGTGTGTAGAGACTATAGAAAT 57.756 33.333 6.78 0.00 0.00 2.17
88 89 8.631480 TCAACAGTGTGTAGAGACTATAGAAA 57.369 34.615 6.78 0.00 0.00 2.52
89 90 7.883833 ACTCAACAGTGTGTAGAGACTATAGAA 59.116 37.037 20.92 0.00 29.78 2.10
90 91 7.395617 ACTCAACAGTGTGTAGAGACTATAGA 58.604 38.462 20.92 0.00 29.78 1.98
91 92 7.551262 AGACTCAACAGTGTGTAGAGACTATAG 59.449 40.741 20.92 0.00 31.71 1.31
92 93 7.395617 AGACTCAACAGTGTGTAGAGACTATA 58.604 38.462 20.92 0.00 31.71 1.31
93 94 6.242396 AGACTCAACAGTGTGTAGAGACTAT 58.758 40.000 20.92 5.01 31.71 2.12
103 104 3.553511 GTCACTCAAGACTCAACAGTGTG 59.446 47.826 0.00 0.00 36.61 3.82
109 110 2.795175 TCGGTCACTCAAGACTCAAC 57.205 50.000 0.00 0.00 38.57 3.18
178 179 8.924691 CATGGGTACACAAAGTAATTTGATTTG 58.075 33.333 21.48 11.97 39.32 2.32
194 200 5.009210 TGCTTTTAACTTCACATGGGTACAC 59.991 40.000 0.00 0.00 0.00 2.90
197 203 6.096987 TGTTTGCTTTTAACTTCACATGGGTA 59.903 34.615 0.00 0.00 0.00 3.69
240 246 1.682451 CCTGCTGGCCATTGATTGGG 61.682 60.000 5.51 0.00 46.55 4.12
303 309 3.373830 AGAAAGCTAGCTGAGGATGACT 58.626 45.455 20.16 6.26 0.00 3.41
307 313 3.110705 TGGAAGAAAGCTAGCTGAGGAT 58.889 45.455 20.16 3.88 0.00 3.24
326 332 1.815003 GTCTCCATTGTTCAAGCCTGG 59.185 52.381 0.00 0.00 0.00 4.45
435 444 5.122869 CACACAAATCACAGGATCTAACAGG 59.877 44.000 0.00 0.00 31.88 4.00
515 524 6.015180 AGTGTTTGCTATTGATGTGGTTTGAT 60.015 34.615 0.00 0.00 0.00 2.57
626 635 7.269297 CGTGTATGATATGACGTGTCTCTATTG 59.731 40.741 0.00 0.00 0.00 1.90
627 636 7.172703 TCGTGTATGATATGACGTGTCTCTATT 59.827 37.037 0.00 0.00 33.56 1.73
635 644 7.477733 GTGTATAGTCGTGTATGATATGACGTG 59.522 40.741 0.00 0.00 38.71 4.49
779 790 5.774690 AGAAGTTAAGGACATTGATTTGCCA 59.225 36.000 0.00 0.00 0.00 4.92
842 853 7.319646 ACACTCTTAATTTTGTTGCTTGACAA 58.680 30.769 0.00 0.00 37.73 3.18
967 980 6.701145 AGAGGTGTCGTATATATATGCAGG 57.299 41.667 10.87 0.00 0.00 4.85
981 994 3.119101 AGGTGCAACTATAAGAGGTGTCG 60.119 47.826 0.00 0.00 45.59 4.35
1049 1062 4.222810 GCACCTTGAACCCCAAAGAATTAT 59.777 41.667 0.00 0.00 33.76 1.28
1050 1063 3.576550 GCACCTTGAACCCCAAAGAATTA 59.423 43.478 0.00 0.00 33.76 1.40
1103 1116 0.614979 AGCGGTAGAAGGCAAGGAGA 60.615 55.000 0.00 0.00 0.00 3.71
1160 1173 0.321346 TCGAGCTTTGCAGGTGATGA 59.679 50.000 0.00 0.00 0.00 2.92
1221 1234 3.244665 TGTTCATCATCTTGTGGCACTCT 60.245 43.478 19.83 0.00 0.00 3.24
1478 1491 7.575265 CCTCTAGGAAATACTTGGGCAAAGTG 61.575 46.154 17.63 0.00 42.94 3.16
1586 1599 8.207545 CCTGTATACTCCTTAAGAAATGCTTCT 58.792 37.037 3.36 0.00 44.11 2.85
1679 1692 1.552337 CCTAGCCTTGCTTCACTCTCA 59.448 52.381 0.00 0.00 40.44 3.27
2018 2031 9.500864 GCAAATAACAACAATGAAACACATTTT 57.499 25.926 0.00 0.00 45.60 1.82
2134 2148 8.972127 GCTGGGTATATGTATTTAGAGATCTCA 58.028 37.037 24.39 8.03 0.00 3.27
2135 2149 8.972127 TGCTGGGTATATGTATTTAGAGATCTC 58.028 37.037 15.29 15.29 0.00 2.75
2136 2150 8.901472 TGCTGGGTATATGTATTTAGAGATCT 57.099 34.615 0.00 0.00 0.00 2.75
2140 2154 9.265901 GCATATGCTGGGTATATGTATTTAGAG 57.734 37.037 20.64 0.00 39.57 2.43
2141 2155 8.767436 TGCATATGCTGGGTATATGTATTTAGA 58.233 33.333 27.13 0.00 39.57 2.10
2142 2156 8.830580 GTGCATATGCTGGGTATATGTATTTAG 58.169 37.037 27.13 0.00 39.57 1.85
2143 2157 8.325046 TGTGCATATGCTGGGTATATGTATTTA 58.675 33.333 27.13 0.00 39.57 1.40
2144 2158 7.121168 GTGTGCATATGCTGGGTATATGTATTT 59.879 37.037 27.13 0.00 39.57 1.40
2145 2159 6.599244 GTGTGCATATGCTGGGTATATGTATT 59.401 38.462 27.13 0.00 39.57 1.89
2146 2160 6.115446 GTGTGCATATGCTGGGTATATGTAT 58.885 40.000 27.13 0.00 39.57 2.29
2147 2161 5.012561 TGTGTGCATATGCTGGGTATATGTA 59.987 40.000 27.13 0.47 39.57 2.29
2148 2162 4.202451 TGTGTGCATATGCTGGGTATATGT 60.202 41.667 27.13 0.00 39.57 2.29
2149 2163 4.325972 TGTGTGCATATGCTGGGTATATG 58.674 43.478 27.13 9.97 40.08 1.78
2150 2164 4.639078 TGTGTGCATATGCTGGGTATAT 57.361 40.909 27.13 0.00 42.66 0.86
2191 2205 8.492673 TTCAGGCTTTCAGTTACATATAGTTG 57.507 34.615 0.00 0.00 0.00 3.16
2500 2639 1.145571 TGGGGCTTTCAACTACCACT 58.854 50.000 0.00 0.00 0.00 4.00
2611 2757 8.105097 TGCAAAGCTATTGTTAACAAGACATA 57.895 30.769 24.22 12.02 39.47 2.29
2618 2764 7.810766 GCTAATTGCAAAGCTATTGTTAACA 57.189 32.000 14.55 3.59 42.31 2.41
2674 2820 7.233757 GGTGTAGTATCAGATCCCAAAGATAGT 59.766 40.741 0.00 0.00 34.42 2.12
2741 2887 7.075148 TGATATGGGGCAAAATTTAGGAATCT 58.925 34.615 0.00 0.00 0.00 2.40
2814 2960 0.247736 CCGCTTTACTCCACTCAGCT 59.752 55.000 0.00 0.00 0.00 4.24
2825 2971 1.011333 TTAGCAATCCGCCGCTTTAC 58.989 50.000 0.00 0.00 44.04 2.01
2867 3014 3.306379 GGGATTCGAACCCTCGGT 58.694 61.111 21.61 0.00 45.49 4.69
2927 3074 8.167605 TCTTATAGATAGGACGAACCAAGAAG 57.832 38.462 0.00 0.00 42.04 2.85
2959 3106 9.490663 CGAAAGAGTGGTTACATTTTTCATATC 57.509 33.333 0.00 0.00 0.00 1.63
3016 3166 0.659957 GTGATGAGCAAGCCGGAATC 59.340 55.000 5.05 0.00 0.00 2.52
3017 3167 0.035152 TGTGATGAGCAAGCCGGAAT 60.035 50.000 5.05 0.00 0.00 3.01
3021 3171 0.445436 GTCTTGTGATGAGCAAGCCG 59.555 55.000 0.00 0.00 42.06 5.52
3166 3320 4.241590 TGCACAAGGTGATCATTTTGAC 57.758 40.909 21.79 15.48 35.23 3.18
3229 3383 9.052759 CCAAACAACAAGTATCAAGTAACTAGT 57.947 33.333 0.00 0.00 0.00 2.57
3431 3587 6.220930 TGTTTTACGAGCTATGTGTCTCTTT 58.779 36.000 1.45 0.00 0.00 2.52
3498 3654 7.639113 AACAACAGAAGGTAATCTTTTGTGA 57.361 32.000 8.97 0.00 46.16 3.58
3528 3684 9.036671 GTAGAGTCCAGAATTCTATAAGCAAAC 57.963 37.037 7.86 0.00 0.00 2.93
3901 4060 2.037367 CACGGTGAGAGGGAGGGA 59.963 66.667 0.74 0.00 0.00 4.20
4035 4194 1.996786 GCTGGGCATGTGGTTCATCG 61.997 60.000 0.00 0.00 34.09 3.84
4378 4537 3.747976 GGTGCCGTGGAACATGCC 61.748 66.667 0.00 0.00 45.46 4.40
4496 4655 1.139654 CGCATCTCTTCCCTTGGATCA 59.860 52.381 0.00 0.00 0.00 2.92
4657 4816 5.121611 CCAGCAACGTCTTATGTTCACAATA 59.878 40.000 0.00 0.00 0.00 1.90
4658 4817 4.083324 CCAGCAACGTCTTATGTTCACAAT 60.083 41.667 0.00 0.00 0.00 2.71
4765 4924 7.119846 ACAGAATGGTATTAAGTGAAGTTCTGC 59.880 37.037 4.17 0.00 43.62 4.26
4766 4925 8.446273 CACAGAATGGTATTAAGTGAAGTTCTG 58.554 37.037 4.17 9.08 43.62 3.02
4767 4926 7.119846 GCACAGAATGGTATTAAGTGAAGTTCT 59.880 37.037 4.17 0.00 43.62 3.01
4768 4927 7.119846 AGCACAGAATGGTATTAAGTGAAGTTC 59.880 37.037 0.00 0.00 43.62 3.01
4769 4928 6.942576 AGCACAGAATGGTATTAAGTGAAGTT 59.057 34.615 0.00 0.00 43.62 2.66
4770 4929 6.476378 AGCACAGAATGGTATTAAGTGAAGT 58.524 36.000 0.00 0.00 43.62 3.01
4771 4930 6.992063 AGCACAGAATGGTATTAAGTGAAG 57.008 37.500 0.00 0.00 43.62 3.02
4781 4940 4.384098 CCACTCCAATAGCACAGAATGGTA 60.384 45.833 0.00 0.00 45.14 3.25
4782 4941 3.614092 CACTCCAATAGCACAGAATGGT 58.386 45.455 0.00 0.00 43.62 3.55
4783 4942 2.947652 CCACTCCAATAGCACAGAATGG 59.052 50.000 0.00 0.00 43.62 3.16
4784 4943 3.614092 ACCACTCCAATAGCACAGAATG 58.386 45.455 0.00 0.00 46.00 2.67
4785 4944 5.130975 TCATACCACTCCAATAGCACAGAAT 59.869 40.000 0.00 0.00 0.00 2.40
4786 4945 4.469586 TCATACCACTCCAATAGCACAGAA 59.530 41.667 0.00 0.00 0.00 3.02
4787 4946 4.030216 TCATACCACTCCAATAGCACAGA 58.970 43.478 0.00 0.00 0.00 3.41
4788 4947 4.122776 GTCATACCACTCCAATAGCACAG 58.877 47.826 0.00 0.00 0.00 3.66
4789 4948 3.774766 AGTCATACCACTCCAATAGCACA 59.225 43.478 0.00 0.00 0.00 4.57
4790 4949 4.408182 AGTCATACCACTCCAATAGCAC 57.592 45.455 0.00 0.00 0.00 4.40
4791 4950 5.661312 AGTTAGTCATACCACTCCAATAGCA 59.339 40.000 0.00 0.00 0.00 3.49
4792 4951 6.163135 AGTTAGTCATACCACTCCAATAGC 57.837 41.667 0.00 0.00 0.00 2.97
4793 4952 8.041323 ACAAAGTTAGTCATACCACTCCAATAG 58.959 37.037 0.00 0.00 0.00 1.73
4794 4953 7.913789 ACAAAGTTAGTCATACCACTCCAATA 58.086 34.615 0.00 0.00 0.00 1.90
4795 4954 6.779860 ACAAAGTTAGTCATACCACTCCAAT 58.220 36.000 0.00 0.00 0.00 3.16
4796 4955 6.182507 ACAAAGTTAGTCATACCACTCCAA 57.817 37.500 0.00 0.00 0.00 3.53
4797 4956 5.818678 ACAAAGTTAGTCATACCACTCCA 57.181 39.130 0.00 0.00 0.00 3.86
4798 4957 5.411669 CCAACAAAGTTAGTCATACCACTCC 59.588 44.000 0.00 0.00 0.00 3.85
4799 4958 6.147328 GTCCAACAAAGTTAGTCATACCACTC 59.853 42.308 0.00 0.00 0.00 3.51
4800 4959 5.995897 GTCCAACAAAGTTAGTCATACCACT 59.004 40.000 0.00 0.00 0.00 4.00
4801 4960 5.180680 GGTCCAACAAAGTTAGTCATACCAC 59.819 44.000 0.00 0.00 0.00 4.16
4802 4961 5.163184 TGGTCCAACAAAGTTAGTCATACCA 60.163 40.000 0.00 0.00 0.00 3.25
4803 4962 5.310451 TGGTCCAACAAAGTTAGTCATACC 58.690 41.667 0.00 0.00 0.00 2.73
4804 4963 7.174253 TCAATGGTCCAACAAAGTTAGTCATAC 59.826 37.037 0.00 0.00 0.00 2.39
4813 4972 5.422012 AGTTTTCTCAATGGTCCAACAAAGT 59.578 36.000 0.00 0.00 0.00 2.66
4827 4986 7.397892 TTGGTACATTCACAAGTTTTCTCAA 57.602 32.000 0.00 0.00 39.30 3.02
4829 4988 8.871686 ATTTTGGTACATTCACAAGTTTTCTC 57.128 30.769 0.00 0.00 39.30 2.87
4861 5020 7.121974 ACGAGCATGCTAACATTAACATATC 57.878 36.000 22.74 1.69 32.87 1.63
4877 5036 7.096023 GGAACTGACTAATACATAACGAGCATG 60.096 40.741 0.00 0.00 0.00 4.06
4903 5062 6.939132 AAGATCTGCATTTATCAAGTGGAG 57.061 37.500 0.00 0.00 33.27 3.86
4905 5064 9.459640 CATAAAAGATCTGCATTTATCAAGTGG 57.540 33.333 0.00 0.00 30.32 4.00
4993 5152 4.527509 TTTTTGTTCTCTGTGTTTGGCA 57.472 36.364 0.00 0.00 0.00 4.92
5066 5241 4.961511 GGATACCGCGGCGATGCA 62.962 66.667 28.58 3.57 34.15 3.96
5077 5252 0.532862 CTGGTGGTCGCATGGATACC 60.533 60.000 0.00 4.61 36.09 2.73
5155 5330 7.384439 TGGTTGATTGCTTTGATCGTTATAA 57.616 32.000 0.00 0.00 0.00 0.98
5162 5337 8.706492 TTCAATATTGGTTGATTGCTTTGATC 57.294 30.769 15.36 0.00 37.88 2.92
5332 5507 0.035439 AGTTAGCACAATGGGGTCCG 60.035 55.000 0.00 0.00 0.00 4.79
5348 5523 0.469705 TCATTTGCACCTGGGCAGTT 60.470 50.000 9.31 0.77 45.88 3.16
5412 5588 7.929245 TGAAGTGCTTACAGTAAGAAACACATA 59.071 33.333 22.50 9.30 38.02 2.29
5476 5652 9.160496 CAAGCTACTCTGAACTCAATTAAAGAT 57.840 33.333 0.00 0.00 0.00 2.40
5481 5658 6.360370 ACCAAGCTACTCTGAACTCAATTA 57.640 37.500 0.00 0.00 0.00 1.40
5513 5690 5.341169 TGGGATGCTGATGGATATAGTACA 58.659 41.667 0.00 0.00 0.00 2.90
5529 5706 1.415659 ACACTAGCAGAGATGGGATGC 59.584 52.381 0.00 0.00 40.29 3.91
5544 5722 7.446931 TGATTCATTAGTTGGAGCAAAACACTA 59.553 33.333 0.00 0.00 0.00 2.74
5575 5753 4.218417 AGATTTACATGGTCAAGTTGTGCC 59.782 41.667 2.11 7.43 0.00 5.01
5595 5773 7.819644 TGATTTCGTTCATGATGTTTTCAGAT 58.180 30.769 0.00 0.00 37.89 2.90
5598 5776 6.969366 ACTGATTTCGTTCATGATGTTTTCA 58.031 32.000 0.00 0.00 39.12 2.69
5613 5791 4.100529 GCATGACATTGGAACTGATTTCG 58.899 43.478 0.00 0.00 34.67 3.46
5655 5833 4.574674 AGTTTGGCAGATGAGGTATTGA 57.425 40.909 0.00 0.00 0.00 2.57
5679 5857 1.113517 GCAGCCATCAGCCCATCAAT 61.114 55.000 0.00 0.00 45.47 2.57
5763 5941 9.975218 ATAGATGACCCAACTTTGTATTAAAGT 57.025 29.630 0.00 0.00 41.82 2.66
5768 5946 8.531146 CCAAAATAGATGACCCAACTTTGTATT 58.469 33.333 0.00 0.00 0.00 1.89
5769 5947 7.893302 TCCAAAATAGATGACCCAACTTTGTAT 59.107 33.333 0.00 0.00 0.00 2.29
5770 5948 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
5771 5949 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
5776 5954 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
5777 5955 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
5778 5956 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
5780 5958 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
5781 5959 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
5782 5960 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
5783 5961 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
5784 5962 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
5785 5963 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
5787 5965 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
5791 5969 2.291996 TGATCTACTCCCTCCGTTCCAA 60.292 50.000 0.00 0.00 0.00 3.53
5795 5973 5.015391 ACCTATATGATCTACTCCCTCCGTT 59.985 44.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.