Multiple sequence alignment - TraesCS5D01G099300

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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 TraesCS5D01G099300 chr5D 100.000 3923 0 0 1 3923 111609384 111613306 0.000000e+00 7245.0
1 TraesCS5D01G099300 chr5D 92.730 674 37 9 3259 3923 129161302 129160632 0.000000e+00 963.0
2 TraesCS5D01G099300 chr5D 90.000 300 19 9 3259 3551 129156145 129155850 1.030000e-100 377.0
3 TraesCS5D01G099300 chr5B 94.487 2467 100 14 639 3088 121662960 121660513 0.000000e+00 3770.0
4 TraesCS5D01G099300 chr5B 88.648 599 47 13 1 583 121672417 121671824 0.000000e+00 710.0
5 TraesCS5D01G099300 chr5B 95.000 60 3 0 585 644 121671007 121670948 1.160000e-15 95.3
6 TraesCS5D01G099300 chr5B 83.333 102 15 1 3085 3184 477561877 477561978 4.170000e-15 93.5
7 TraesCS5D01G099300 chr5B 87.013 77 8 1 3084 3158 383538846 383538770 6.980000e-13 86.1
8 TraesCS5D01G099300 chr5A 93.952 1174 38 14 812 1974 115630947 115629796 0.000000e+00 1744.0
9 TraesCS5D01G099300 chr5A 93.050 1036 49 12 1959 2989 115624166 115623149 0.000000e+00 1493.0
10 TraesCS5D01G099300 chr5A 88.889 603 36 3 1 583 115662904 115662313 0.000000e+00 713.0
11 TraesCS5D01G099300 chr5A 88.144 194 14 5 629 820 115633782 115633596 5.100000e-54 222.0
12 TraesCS5D01G099300 chr5A 83.051 118 15 4 3089 3203 607736397 607736512 6.930000e-18 102.0
13 TraesCS5D01G099300 chr5A 94.545 55 3 0 582 636 115634130 115634076 6.980000e-13 86.1
14 TraesCS5D01G099300 chr5A 84.043 94 9 5 3069 3156 675963166 675963259 6.980000e-13 86.1
15 TraesCS5D01G099300 chr5A 79.310 116 20 3 3091 3203 616976674 616976560 1.170000e-10 78.7
16 TraesCS5D01G099300 chr3B 92.676 669 44 5 3260 3923 406750998 406750330 0.000000e+00 959.0
17 TraesCS5D01G099300 chr3B 89.453 256 24 3 3299 3551 406665762 406665507 1.760000e-83 320.0
18 TraesCS5D01G099300 chr2A 90.026 381 38 0 3543 3923 729972374 729971994 9.790000e-136 494.0
19 TraesCS5D01G099300 chr2A 82.000 100 16 1 3087 3184 763863685 763863586 2.510000e-12 84.2
20 TraesCS5D01G099300 chr3A 89.501 381 40 0 3543 3923 220651838 220651458 2.120000e-132 483.0
21 TraesCS5D01G099300 chr7B 75.833 360 83 4 3544 3901 221802842 221803199 3.110000e-41 180.0
22 TraesCS5D01G099300 chr6B 89.431 123 9 3 3086 3205 179340684 179340805 6.790000e-33 152.0
23 TraesCS5D01G099300 chr6A 86.207 116 14 1 3092 3205 497364138 497364023 1.480000e-24 124.0
24 TraesCS5D01G099300 chr6D 73.699 346 72 17 3544 3880 266786493 266786828 2.480000e-22 117.0
25 TraesCS5D01G099300 chr7A 81.818 132 16 7 3072 3200 692337069 692336943 1.930000e-18 104.0
26 TraesCS5D01G099300 chr1B 96.491 57 2 0 3545 3601 625425046 625425102 1.160000e-15 95.3
27 TraesCS5D01G099300 chr1B 91.379 58 5 0 3544 3601 625428154 625428211 3.250000e-11 80.5
28 TraesCS5D01G099300 chr1D 94.737 57 3 0 3545 3601 455014986 455015042 5.400000e-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 TraesCS5D01G099300 chr5D 111609384 111613306 3922 False 7245.000000 7245 100.000000 1 3923 1 chr5D.!!$F1 3922
1 TraesCS5D01G099300 chr5D 129160632 129161302 670 True 963.000000 963 92.730000 3259 3923 1 chr5D.!!$R2 664
2 TraesCS5D01G099300 chr5B 121660513 121662960 2447 True 3770.000000 3770 94.487000 639 3088 1 chr5B.!!$R1 2449
3 TraesCS5D01G099300 chr5B 121670948 121672417 1469 True 402.650000 710 91.824000 1 644 2 chr5B.!!$R3 643
4 TraesCS5D01G099300 chr5A 115623149 115624166 1017 True 1493.000000 1493 93.050000 1959 2989 1 chr5A.!!$R1 1030
5 TraesCS5D01G099300 chr5A 115662313 115662904 591 True 713.000000 713 88.889000 1 583 1 chr5A.!!$R2 582
6 TraesCS5D01G099300 chr5A 115629796 115634130 4334 True 684.033333 1744 92.213667 582 1974 3 chr5A.!!$R4 1392
7 TraesCS5D01G099300 chr3B 406750330 406750998 668 True 959.000000 959 92.676000 3260 3923 1 chr3B.!!$R2 663

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
402 423 1.213799 GACGTCGTCCAACCCCTAC 59.786 63.158 14.6 0.0 0.0 3.18 F
1117 4930 1.073025 AGCTTCAACATCGGTGGCA 59.927 52.632 0.0 0.0 0.0 4.92 F
1903 5719 0.465705 CCTGAGCCGAGCATTTAGGA 59.534 55.000 0.0 0.0 0.0 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 5677 0.670239 GCCCAACAATTTTCGGCCAG 60.670 55.0 2.24 0.0 33.30 4.85 R
2464 6289 0.030369 GCGTCCTTATCGTCGATGGT 59.970 55.0 17.98 0.0 0.00 3.55 R
3842 7681 0.093705 GCTTACGAGCTGAACTTGCG 59.906 55.0 0.00 0.0 45.65 4.85 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
68 69 4.649674 TCCGAAGATGTAGCCACTTATCTT 59.350 41.667 0.00 0.00 41.24 2.40
345 366 1.762460 GCACCCTAGGAGCTAGCCA 60.762 63.158 11.48 0.00 36.40 4.75
366 387 1.281867 AGCATGAGGAAACCGAATCCA 59.718 47.619 0.00 0.00 39.55 3.41
367 388 1.401905 GCATGAGGAAACCGAATCCAC 59.598 52.381 0.00 0.00 39.55 4.02
401 422 2.334946 CGACGTCGTCCAACCCCTA 61.335 63.158 29.08 0.00 34.11 3.53
402 423 1.213799 GACGTCGTCCAACCCCTAC 59.786 63.158 14.60 0.00 0.00 3.18
413 434 2.346803 CAACCCCTACGAATCACACAG 58.653 52.381 0.00 0.00 0.00 3.66
421 442 1.284297 CGAATCACACAGCGAGCACA 61.284 55.000 0.00 0.00 0.00 4.57
428 449 1.270839 ACACAGCGAGCACAATAAGGT 60.271 47.619 0.00 0.00 0.00 3.50
463 487 4.835615 GCTATAAGTGGAAGATGGAGGAGA 59.164 45.833 0.00 0.00 0.00 3.71
489 513 1.354031 TCCTTGGCAAGCCATCTGTTA 59.646 47.619 21.77 0.00 46.64 2.41
495 519 2.555199 GCAAGCCATCTGTTATCGAGT 58.445 47.619 0.00 0.00 0.00 4.18
528 552 2.284995 GTGGTGAGCCCTCCCTCT 60.285 66.667 0.00 0.00 33.02 3.69
538 562 2.286523 CCTCCCTCTGAGTTGCGGT 61.287 63.158 3.66 0.00 39.65 5.68
636 1475 8.818141 TTTATGAGACATCGATTGAGAATACC 57.182 34.615 0.00 0.00 0.00 2.73
723 1865 1.278238 GAGGCGAATGTACCAACTCG 58.722 55.000 0.00 0.00 0.00 4.18
820 1967 6.037172 CAGCTGAAGGTAGCAAATACGTTAAT 59.963 38.462 8.42 0.00 46.07 1.40
1057 4861 2.415090 GGCATTGCTGTTCTTGTGCTAG 60.415 50.000 8.82 0.00 33.38 3.42
1117 4930 1.073025 AGCTTCAACATCGGTGGCA 59.927 52.632 0.00 0.00 0.00 4.92
1189 5002 3.141398 GACAGCTTTGACCAGTTCATCA 58.859 45.455 0.00 0.00 32.84 3.07
1424 5237 1.196104 AAGCCCGGCACCTACAAGTA 61.196 55.000 13.15 0.00 0.00 2.24
1463 5276 7.806487 CGATCCCAATAGATGTTGATCAAATTG 59.194 37.037 10.35 14.87 36.17 2.32
1724 5537 6.890268 ACTAATCACCATCTTTTAGGGGAAAC 59.110 38.462 0.00 0.00 41.46 2.78
1768 5581 2.468831 TGCGAACAAAATTGAGTTGCC 58.531 42.857 0.00 0.00 0.00 4.52
1773 5586 2.742774 ACAAAATTGAGTTGCCTTCGC 58.257 42.857 0.00 0.00 0.00 4.70
1774 5587 2.061028 CAAAATTGAGTTGCCTTCGCC 58.939 47.619 0.00 0.00 0.00 5.54
1775 5588 1.327303 AAATTGAGTTGCCTTCGCCA 58.673 45.000 0.00 0.00 0.00 5.69
1806 5619 5.937540 TGCAAACAAAATCCTATCGAAGAGA 59.062 36.000 0.00 0.00 43.63 3.10
1861 5677 0.521735 GAGTTGCGGACCATGGAAAC 59.478 55.000 21.47 13.67 0.00 2.78
1903 5719 0.465705 CCTGAGCCGAGCATTTAGGA 59.534 55.000 0.00 0.00 0.00 2.94
1937 5753 5.946972 ACTCTTATAGGGAGATATCCACGTG 59.053 44.000 9.08 9.08 35.10 4.49
2040 5859 8.722480 TCTGTATTCCTGTAAACATTGATCTG 57.278 34.615 0.00 0.00 0.00 2.90
2041 5860 7.770433 TCTGTATTCCTGTAAACATTGATCTGG 59.230 37.037 0.00 0.00 0.00 3.86
2068 5887 9.926158 TGAAATTATGAGATTTTTGCTTAAGCA 57.074 25.926 26.06 26.06 38.05 3.91
2090 5909 1.600356 TGCGCTTCATGGCAGAACA 60.600 52.632 9.73 0.00 33.52 3.18
2275 6094 2.338500 GTCGACTTCATCTTCGGCTTT 58.662 47.619 8.70 0.00 36.90 3.51
2323 6144 8.556213 TTAACCAACCAAACATCTACTACATC 57.444 34.615 0.00 0.00 0.00 3.06
2370 6191 9.695526 GTAGGCAATGATATTTGATGCATTTTA 57.304 29.630 0.00 0.00 38.73 1.52
2511 6336 2.049802 GGGTTCTCGTTCGTGCGA 60.050 61.111 0.00 4.35 39.22 5.10
2526 6351 0.811219 TGCGATGCAAGATCTTCGGG 60.811 55.000 14.57 2.33 34.76 5.14
2544 6369 2.225792 GCTGGGCCAGATCTACCTT 58.774 57.895 37.07 0.00 32.44 3.50
2658 6483 2.541999 CGAGAAGCCAGATCGGTAACTC 60.542 54.545 5.66 9.24 36.97 3.01
2686 6511 5.119588 CACGTGTTTCCTCTCGCTTAATTTA 59.880 40.000 7.58 0.00 0.00 1.40
2691 6516 4.755266 TCCTCTCGCTTAATTTAGCCTT 57.245 40.909 10.66 0.00 37.90 4.35
2704 6529 4.846779 TTTAGCCTTCACCATTTCACAC 57.153 40.909 0.00 0.00 0.00 3.82
2714 6539 2.060284 CCATTTCACACCGCACAAATG 58.940 47.619 0.00 0.00 36.42 2.32
2753 6581 1.022735 GATGATGGTTGCTGCAGGAG 58.977 55.000 17.12 0.00 0.00 3.69
2905 6733 2.526873 CCTGGATCCTACCCCCGG 60.527 72.222 14.23 0.00 0.00 5.73
2991 6819 2.497675 TGTATCAGAGACCTCCACTTGC 59.502 50.000 0.00 0.00 0.00 4.01
2992 6820 0.908198 ATCAGAGACCTCCACTTGCC 59.092 55.000 0.00 0.00 0.00 4.52
3108 6939 8.761575 AATATCAGTTTTGTTAAAGCACATGG 57.238 30.769 0.00 0.00 0.00 3.66
3109 6940 5.843673 TCAGTTTTGTTAAAGCACATGGA 57.156 34.783 0.00 0.00 0.00 3.41
3110 6941 5.587289 TCAGTTTTGTTAAAGCACATGGAC 58.413 37.500 0.00 0.00 0.00 4.02
3111 6942 4.440758 CAGTTTTGTTAAAGCACATGGACG 59.559 41.667 0.00 0.00 0.00 4.79
3112 6943 4.097286 AGTTTTGTTAAAGCACATGGACGT 59.903 37.500 0.00 0.00 0.00 4.34
3113 6944 3.617540 TTGTTAAAGCACATGGACGTG 57.382 42.857 0.00 0.00 40.00 4.49
3121 6952 2.370281 CACATGGACGTGCTCTAAGT 57.630 50.000 8.99 0.00 0.00 2.24
3122 6953 3.503827 CACATGGACGTGCTCTAAGTA 57.496 47.619 8.99 0.00 0.00 2.24
3123 6954 4.046938 CACATGGACGTGCTCTAAGTAT 57.953 45.455 8.99 0.00 0.00 2.12
3124 6955 4.433615 CACATGGACGTGCTCTAAGTATT 58.566 43.478 8.99 0.00 0.00 1.89
3125 6956 4.268644 CACATGGACGTGCTCTAAGTATTG 59.731 45.833 8.99 0.00 0.00 1.90
3126 6957 4.081642 ACATGGACGTGCTCTAAGTATTGT 60.082 41.667 8.99 0.00 0.00 2.71
3127 6958 5.126545 ACATGGACGTGCTCTAAGTATTGTA 59.873 40.000 8.99 0.00 0.00 2.41
3128 6959 4.990257 TGGACGTGCTCTAAGTATTGTAC 58.010 43.478 8.99 0.00 0.00 2.90
3129 6960 4.460034 TGGACGTGCTCTAAGTATTGTACA 59.540 41.667 8.99 0.00 0.00 2.90
3130 6961 5.126545 TGGACGTGCTCTAAGTATTGTACAT 59.873 40.000 8.99 0.00 0.00 2.29
3131 6962 5.686397 GGACGTGCTCTAAGTATTGTACATC 59.314 44.000 0.00 0.00 0.00 3.06
3132 6963 6.452494 ACGTGCTCTAAGTATTGTACATCT 57.548 37.500 0.00 0.00 0.00 2.90
3133 6964 7.255035 GGACGTGCTCTAAGTATTGTACATCTA 60.255 40.741 0.00 0.00 0.00 1.98
3134 6965 7.993101 ACGTGCTCTAAGTATTGTACATCTAA 58.007 34.615 0.00 0.00 0.00 2.10
3135 6966 8.129840 ACGTGCTCTAAGTATTGTACATCTAAG 58.870 37.037 0.00 0.00 0.00 2.18
3136 6967 8.129840 CGTGCTCTAAGTATTGTACATCTAAGT 58.870 37.037 0.00 0.00 0.00 2.24
3137 6968 9.453325 GTGCTCTAAGTATTGTACATCTAAGTC 57.547 37.037 0.00 0.00 0.00 3.01
3138 6969 8.630917 TGCTCTAAGTATTGTACATCTAAGTCC 58.369 37.037 0.00 0.00 0.00 3.85
3139 6970 8.852135 GCTCTAAGTATTGTACATCTAAGTCCT 58.148 37.037 0.00 0.00 0.00 3.85
3145 6976 9.642343 AGTATTGTACATCTAAGTCCTATGTCA 57.358 33.333 0.00 0.00 35.54 3.58
3148 6979 9.770097 ATTGTACATCTAAGTCCTATGTCATTG 57.230 33.333 0.00 0.00 35.54 2.82
3149 6980 8.533569 TGTACATCTAAGTCCTATGTCATTGA 57.466 34.615 0.00 0.00 35.54 2.57
3150 6981 9.147732 TGTACATCTAAGTCCTATGTCATTGAT 57.852 33.333 0.00 0.00 35.54 2.57
3151 6982 9.988815 GTACATCTAAGTCCTATGTCATTGATT 57.011 33.333 0.00 0.00 35.54 2.57
3152 6983 8.899427 ACATCTAAGTCCTATGTCATTGATTG 57.101 34.615 0.00 0.00 0.00 2.67
3153 6984 8.489489 ACATCTAAGTCCTATGTCATTGATTGT 58.511 33.333 0.00 0.00 0.00 2.71
3154 6985 9.987272 CATCTAAGTCCTATGTCATTGATTGTA 57.013 33.333 0.00 0.00 0.00 2.41
3155 6986 9.988815 ATCTAAGTCCTATGTCATTGATTGTAC 57.011 33.333 0.00 0.00 0.00 2.90
3156 6987 8.135529 TCTAAGTCCTATGTCATTGATTGTACG 58.864 37.037 0.00 0.00 0.00 3.67
3157 6988 5.050490 AGTCCTATGTCATTGATTGTACGC 58.950 41.667 0.00 0.00 0.00 4.42
3158 6989 5.050490 GTCCTATGTCATTGATTGTACGCT 58.950 41.667 0.00 0.00 0.00 5.07
3159 6990 6.040504 AGTCCTATGTCATTGATTGTACGCTA 59.959 38.462 0.00 0.00 0.00 4.26
3160 6991 6.700081 GTCCTATGTCATTGATTGTACGCTAA 59.300 38.462 0.00 0.00 0.00 3.09
3161 6992 7.223971 GTCCTATGTCATTGATTGTACGCTAAA 59.776 37.037 0.00 0.00 0.00 1.85
3162 6993 7.766738 TCCTATGTCATTGATTGTACGCTAAAA 59.233 33.333 0.00 0.00 0.00 1.52
3163 6994 8.559536 CCTATGTCATTGATTGTACGCTAAAAT 58.440 33.333 0.00 0.00 0.00 1.82
3164 6995 9.935682 CTATGTCATTGATTGTACGCTAAAATT 57.064 29.630 0.00 0.00 0.00 1.82
3166 6997 8.446489 TGTCATTGATTGTACGCTAAAATTTG 57.554 30.769 0.00 0.00 0.00 2.32
3167 6998 8.079203 TGTCATTGATTGTACGCTAAAATTTGT 58.921 29.630 0.00 0.00 0.00 2.83
3168 6999 8.365210 GTCATTGATTGTACGCTAAAATTTGTG 58.635 33.333 0.00 0.00 0.00 3.33
3169 7000 6.683090 TTGATTGTACGCTAAAATTTGTGC 57.317 33.333 0.00 0.00 0.00 4.57
3170 7001 5.763088 TGATTGTACGCTAAAATTTGTGCA 58.237 33.333 13.64 5.17 0.00 4.57
3171 7002 5.627367 TGATTGTACGCTAAAATTTGTGCAC 59.373 36.000 10.75 10.75 0.00 4.57
3172 7003 4.553756 TGTACGCTAAAATTTGTGCACA 57.446 36.364 17.42 17.42 0.00 4.57
3173 7004 4.283678 TGTACGCTAAAATTTGTGCACAC 58.716 39.130 21.56 4.23 0.00 3.82
3174 7005 3.428746 ACGCTAAAATTTGTGCACACA 57.571 38.095 21.56 14.78 39.98 3.72
3175 7006 3.976169 ACGCTAAAATTTGTGCACACAT 58.024 36.364 21.56 16.74 41.52 3.21
3176 7007 4.367450 ACGCTAAAATTTGTGCACACATT 58.633 34.783 22.44 22.44 41.52 2.71
3177 7008 4.808364 ACGCTAAAATTTGTGCACACATTT 59.192 33.333 29.45 29.45 41.52 2.32
3178 7009 5.293079 ACGCTAAAATTTGTGCACACATTTT 59.707 32.000 38.33 38.33 44.00 1.82
3179 7010 5.840267 CGCTAAAATTTGTGCACACATTTTC 59.160 36.000 39.60 30.17 42.10 2.29
3180 7011 6.292274 CGCTAAAATTTGTGCACACATTTTCT 60.292 34.615 39.60 28.18 42.10 2.52
3181 7012 7.408910 GCTAAAATTTGTGCACACATTTTCTT 58.591 30.769 39.60 27.66 42.10 2.52
3182 7013 7.909641 GCTAAAATTTGTGCACACATTTTCTTT 59.090 29.630 39.60 27.40 42.10 2.52
3183 7014 9.771915 CTAAAATTTGTGCACACATTTTCTTTT 57.228 25.926 39.60 27.56 42.10 2.27
3186 7017 9.934190 AAATTTGTGCACACATTTTCTTTTATC 57.066 25.926 29.45 0.00 41.52 1.75
3187 7018 8.891671 ATTTGTGCACACATTTTCTTTTATCT 57.108 26.923 21.56 0.00 41.52 1.98
3188 7019 8.715191 TTTGTGCACACATTTTCTTTTATCTT 57.285 26.923 21.56 0.00 41.52 2.40
3189 7020 9.809096 TTTGTGCACACATTTTCTTTTATCTTA 57.191 25.926 21.56 0.00 41.52 2.10
3190 7021 9.979578 TTGTGCACACATTTTCTTTTATCTTAT 57.020 25.926 21.56 0.00 41.52 1.73
3191 7022 9.979578 TGTGCACACATTTTCTTTTATCTTATT 57.020 25.926 17.42 0.00 36.21 1.40
3215 7046 9.750125 ATTTCATTTTCTTTCTGTTAGGTGTTC 57.250 29.630 0.00 0.00 0.00 3.18
3216 7047 6.954944 TCATTTTCTTTCTGTTAGGTGTTCG 58.045 36.000 0.00 0.00 0.00 3.95
3217 7048 6.764085 TCATTTTCTTTCTGTTAGGTGTTCGA 59.236 34.615 0.00 0.00 0.00 3.71
3218 7049 7.444183 TCATTTTCTTTCTGTTAGGTGTTCGAT 59.556 33.333 0.00 0.00 0.00 3.59
3219 7050 6.780706 TTTCTTTCTGTTAGGTGTTCGATC 57.219 37.500 0.00 0.00 0.00 3.69
3220 7051 5.723672 TCTTTCTGTTAGGTGTTCGATCT 57.276 39.130 0.00 0.00 0.00 2.75
3221 7052 5.710984 TCTTTCTGTTAGGTGTTCGATCTC 58.289 41.667 0.00 0.00 0.00 2.75
3222 7053 5.243060 TCTTTCTGTTAGGTGTTCGATCTCA 59.757 40.000 0.00 0.00 0.00 3.27
3223 7054 4.436242 TCTGTTAGGTGTTCGATCTCAC 57.564 45.455 7.17 7.17 0.00 3.51
3224 7055 4.079970 TCTGTTAGGTGTTCGATCTCACT 58.920 43.478 12.96 4.10 35.26 3.41
3225 7056 4.523173 TCTGTTAGGTGTTCGATCTCACTT 59.477 41.667 12.96 9.54 35.26 3.16
3226 7057 5.010719 TCTGTTAGGTGTTCGATCTCACTTT 59.989 40.000 12.96 7.04 35.26 2.66
3227 7058 5.227908 TGTTAGGTGTTCGATCTCACTTTC 58.772 41.667 12.96 6.18 35.26 2.62
3228 7059 5.221362 TGTTAGGTGTTCGATCTCACTTTCA 60.221 40.000 12.96 7.88 35.26 2.69
3229 7060 3.919216 AGGTGTTCGATCTCACTTTCAG 58.081 45.455 12.96 0.00 35.26 3.02
3230 7061 3.574396 AGGTGTTCGATCTCACTTTCAGA 59.426 43.478 12.96 0.00 35.26 3.27
3231 7062 4.221703 AGGTGTTCGATCTCACTTTCAGAT 59.778 41.667 12.96 0.00 35.26 2.90
3232 7063 5.419155 AGGTGTTCGATCTCACTTTCAGATA 59.581 40.000 12.96 0.00 35.26 1.98
3233 7064 5.517054 GGTGTTCGATCTCACTTTCAGATAC 59.483 44.000 12.96 0.00 35.26 2.24
3234 7065 6.093404 GTGTTCGATCTCACTTTCAGATACA 58.907 40.000 8.11 0.00 30.30 2.29
3235 7066 6.034044 GTGTTCGATCTCACTTTCAGATACAC 59.966 42.308 8.11 0.00 33.44 2.90
3236 7067 5.897377 TCGATCTCACTTTCAGATACACA 57.103 39.130 0.00 0.00 30.30 3.72
3237 7068 6.456795 TCGATCTCACTTTCAGATACACAT 57.543 37.500 0.00 0.00 30.30 3.21
3238 7069 6.499172 TCGATCTCACTTTCAGATACACATC 58.501 40.000 0.00 0.00 30.30 3.06
3239 7070 6.095440 TCGATCTCACTTTCAGATACACATCA 59.905 38.462 0.00 0.00 33.21 3.07
3240 7071 6.922407 CGATCTCACTTTCAGATACACATCAT 59.078 38.462 0.00 0.00 33.21 2.45
3241 7072 8.078596 CGATCTCACTTTCAGATACACATCATA 58.921 37.037 0.00 0.00 33.21 2.15
3242 7073 9.409312 GATCTCACTTTCAGATACACATCATAG 57.591 37.037 0.00 0.00 33.21 2.23
3243 7074 8.525290 TCTCACTTTCAGATACACATCATAGA 57.475 34.615 0.00 0.00 33.21 1.98
3244 7075 8.628280 TCTCACTTTCAGATACACATCATAGAG 58.372 37.037 0.00 0.00 33.21 2.43
3245 7076 8.298729 TCACTTTCAGATACACATCATAGAGT 57.701 34.615 0.00 0.00 33.21 3.24
3246 7077 9.408648 TCACTTTCAGATACACATCATAGAGTA 57.591 33.333 0.00 0.00 33.21 2.59
3252 7083 9.746457 TCAGATACACATCATAGAGTATTAGCT 57.254 33.333 0.00 0.00 33.21 3.32
3292 7123 3.329225 AGAGGAGGGAAAGAAGAAAGTGG 59.671 47.826 0.00 0.00 0.00 4.00
3297 7128 5.221263 GGAGGGAAAGAAGAAAGTGGAAAAC 60.221 44.000 0.00 0.00 0.00 2.43
3298 7129 5.269189 AGGGAAAGAAGAAAGTGGAAAACA 58.731 37.500 0.00 0.00 0.00 2.83
3301 7132 6.535150 GGGAAAGAAGAAAGTGGAAAACAAAG 59.465 38.462 0.00 0.00 0.00 2.77
3306 7137 6.813649 AGAAGAAAGTGGAAAACAAAGAAAGC 59.186 34.615 0.00 0.00 0.00 3.51
3307 7138 5.419542 AGAAAGTGGAAAACAAAGAAAGCC 58.580 37.500 0.00 0.00 0.00 4.35
3312 7143 0.249280 AAAACAAAGAAAGCCGCCGG 60.249 50.000 0.00 0.00 0.00 6.13
3313 7144 1.388837 AAACAAAGAAAGCCGCCGGT 61.389 50.000 4.45 0.00 0.00 5.28
3315 7146 3.670377 AAAGAAAGCCGCCGGTGC 61.670 61.111 10.27 9.98 0.00 5.01
3454 7293 0.462759 CGCACCCCTCTCCTTGATTC 60.463 60.000 0.00 0.00 0.00 2.52
3507 7346 2.666190 GTCAGCTGTTGCGGCAGA 60.666 61.111 14.67 0.00 45.42 4.26
3534 7373 1.621672 CCACTTCCCTCTCCAGGCTC 61.622 65.000 0.00 0.00 38.72 4.70
3591 7430 3.577334 CTTGCCCCCAAGCCGGTAA 62.577 63.158 1.90 0.00 41.72 2.85
3602 7441 3.081804 CAAGCCGGTAAATGAGGAAAGT 58.918 45.455 1.90 0.00 0.00 2.66
3613 7452 2.113243 GAGGAAAGTGGTGGCGGAGT 62.113 60.000 0.00 0.00 0.00 3.85
3686 7525 0.892755 TAGGATTTGCTCACGACGGT 59.107 50.000 0.00 0.00 0.00 4.83
3715 7554 2.036006 GTGGCGCCATCGGTTGTTA 61.036 57.895 35.23 0.86 35.95 2.41
3782 7621 1.065926 TCGAAGAGACAGCCGTACCTA 60.066 52.381 0.00 0.00 0.00 3.08
3786 7625 1.134037 AGAGACAGCCGTACCTAGAGG 60.134 57.143 0.00 0.00 42.17 3.69
3837 7676 3.884037 AACAGGGTGAATCTTGGAGTT 57.116 42.857 0.00 0.00 0.00 3.01
3838 7677 3.146104 ACAGGGTGAATCTTGGAGTTG 57.854 47.619 0.00 0.00 0.00 3.16
3842 7681 2.820197 GGGTGAATCTTGGAGTTGGTTC 59.180 50.000 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 5.516044 TCAGACCTAAGATAAGTGGCTACA 58.484 41.667 2.02 0.00 0.00 2.74
68 69 2.107378 TGCATTGGGTTGTTCAGACCTA 59.893 45.455 0.00 0.00 37.34 3.08
240 261 6.016777 GCATCGGTCTTTCAAAGGATTATGAT 60.017 38.462 0.00 0.00 0.00 2.45
328 349 0.755686 CTTGGCTAGCTCCTAGGGTG 59.244 60.000 15.72 3.54 34.88 4.61
345 366 2.290896 TGGATTCGGTTTCCTCATGCTT 60.291 45.455 0.00 0.00 34.17 3.91
349 370 1.553248 TCGTGGATTCGGTTTCCTCAT 59.447 47.619 0.00 0.00 34.17 2.90
366 387 1.079819 CGCCACTCACATCCTTCGT 60.080 57.895 0.00 0.00 0.00 3.85
367 388 1.078759 GTCGCCACTCACATCCTTCG 61.079 60.000 0.00 0.00 0.00 3.79
399 420 0.917259 GCTCGCTGTGTGATTCGTAG 59.083 55.000 0.00 0.00 0.00 3.51
401 422 1.006220 TGCTCGCTGTGTGATTCGT 60.006 52.632 0.00 0.00 0.00 3.85
402 423 1.284297 TGTGCTCGCTGTGTGATTCG 61.284 55.000 0.00 0.00 0.00 3.34
413 434 1.327764 GCAGTACCTTATTGTGCTCGC 59.672 52.381 0.00 0.00 0.00 5.03
421 442 4.510167 AGCAAGATGGCAGTACCTTATT 57.490 40.909 0.00 0.00 40.22 1.40
428 449 4.653801 TCCACTTATAGCAAGATGGCAGTA 59.346 41.667 0.00 0.00 35.83 2.74
463 487 1.000396 GGCTTGCCAAGGAGGATGT 60.000 57.895 6.57 0.00 41.22 3.06
473 497 1.209261 TCGATAACAGATGGCTTGCCA 59.791 47.619 17.19 17.19 0.00 4.92
475 499 2.555199 ACTCGATAACAGATGGCTTGC 58.445 47.619 0.00 0.00 0.00 4.01
478 502 5.777802 CATCTAACTCGATAACAGATGGCT 58.222 41.667 14.16 0.00 39.16 4.75
489 513 1.689273 GAGGTGGGCATCTAACTCGAT 59.311 52.381 0.00 0.00 28.65 3.59
528 552 1.112916 TCACTCTCCACCGCAACTCA 61.113 55.000 0.00 0.00 0.00 3.41
538 562 1.699730 TGACGTTCCTTCACTCTCCA 58.300 50.000 0.00 0.00 0.00 3.86
647 1789 1.740025 CTCCACGCCTCCTTGATTTTC 59.260 52.381 0.00 0.00 0.00 2.29
648 1790 1.351017 TCTCCACGCCTCCTTGATTTT 59.649 47.619 0.00 0.00 0.00 1.82
777 1919 1.104577 TGTTTGGAAACCAGGACGGC 61.105 55.000 0.00 0.00 39.03 5.68
778 1920 0.951558 CTGTTTGGAAACCAGGACGG 59.048 55.000 0.00 0.00 38.11 4.79
786 1933 3.304726 GCTACCTTCAGCTGTTTGGAAAC 60.305 47.826 22.19 11.00 38.57 2.78
1057 4861 0.980423 GGGGAGATGGATGCTAGGAC 59.020 60.000 0.00 0.00 0.00 3.85
1189 5002 0.104304 AAGTGCTCGACGTTCTTGGT 59.896 50.000 0.00 0.00 0.00 3.67
1424 5237 7.061054 TCTATTGGGATCGACCGAGATATATT 58.939 38.462 0.00 0.00 40.11 1.28
1724 5537 7.065563 GCAATTGCATAGATAGGATCAGGTTAG 59.934 40.741 25.36 0.00 41.59 2.34
1768 5581 3.573598 TGTTTGCATACATTTGGCGAAG 58.426 40.909 5.83 0.00 31.93 3.79
1773 5586 8.721019 ATAGGATTTTGTTTGCATACATTTGG 57.279 30.769 10.90 0.00 0.00 3.28
1774 5587 8.533965 CGATAGGATTTTGTTTGCATACATTTG 58.466 33.333 10.90 0.00 0.00 2.32
1775 5588 8.465999 TCGATAGGATTTTGTTTGCATACATTT 58.534 29.630 10.90 0.00 0.00 2.32
1806 5619 7.676393 CATGCATGCAAAAACAAAACAAAAAT 58.324 26.923 26.68 0.00 0.00 1.82
1861 5677 0.670239 GCCCAACAATTTTCGGCCAG 60.670 55.000 2.24 0.00 33.30 4.85
1933 5749 3.129792 GCTCTTAGAAGCTGCACGT 57.870 52.632 1.02 0.00 39.27 4.49
2002 5818 8.250143 ACAGGAATACAGAAATGTTTCCTTTT 57.750 30.769 15.79 8.41 42.69 2.27
2006 5822 8.573035 TGTTTACAGGAATACAGAAATGTTTCC 58.427 33.333 2.04 11.26 37.92 3.13
2016 5832 7.554118 ACCAGATCAATGTTTACAGGAATACAG 59.446 37.037 0.00 0.00 0.00 2.74
2075 5894 0.730494 GCGTTGTTCTGCCATGAAGC 60.730 55.000 0.00 0.00 0.00 3.86
2090 5909 1.367102 CCTTTGCCAATGGTGCGTT 59.633 52.632 0.00 0.00 0.00 4.84
2323 6144 2.168521 CCTCACCTAGGTACATGTGTGG 59.831 54.545 15.80 7.77 40.94 4.17
2370 6191 0.742990 CGCGTGGGTGTCACCATAAT 60.743 55.000 23.48 0.00 43.59 1.28
2464 6289 0.030369 GCGTCCTTATCGTCGATGGT 59.970 55.000 17.98 0.00 0.00 3.55
2511 6336 0.465097 CCAGCCCGAAGATCTTGCAT 60.465 55.000 14.00 0.00 0.00 3.96
2526 6351 0.179034 CAAGGTAGATCTGGCCCAGC 60.179 60.000 5.66 0.00 0.00 4.85
2658 6483 1.618861 CGAGAGGAAACACGTGCTAG 58.381 55.000 17.22 0.00 0.00 3.42
2686 6511 1.620822 GGTGTGAAATGGTGAAGGCT 58.379 50.000 0.00 0.00 0.00 4.58
2691 6516 0.464554 TGTGCGGTGTGAAATGGTGA 60.465 50.000 0.00 0.00 0.00 4.02
2704 6529 1.154488 CGTCGGTTCATTTGTGCGG 60.154 57.895 0.00 0.00 0.00 5.69
2729 6557 0.171903 GCAGCAACCATCATCACCAC 59.828 55.000 0.00 0.00 0.00 4.16
2753 6581 0.466963 CCCGTAGAATACACCACCCC 59.533 60.000 0.00 0.00 43.24 4.95
2905 6733 3.642705 CAACCTAGAAGTTGCTTTTGGC 58.357 45.455 0.00 0.00 40.60 4.52
2992 6820 0.933509 GCTATCGCCGTGTAACCTCG 60.934 60.000 0.00 0.00 0.00 4.63
2996 6827 1.254570 CTTTCGCTATCGCCGTGTAAC 59.745 52.381 0.00 0.00 35.26 2.50
3088 6919 4.440758 CGTCCATGTGCTTTAACAAAACTG 59.559 41.667 0.00 0.00 32.81 3.16
3089 6920 4.097286 ACGTCCATGTGCTTTAACAAAACT 59.903 37.500 0.00 0.00 32.81 2.66
3090 6921 4.206200 CACGTCCATGTGCTTTAACAAAAC 59.794 41.667 0.00 0.00 32.81 2.43
3091 6922 4.355437 CACGTCCATGTGCTTTAACAAAA 58.645 39.130 0.00 0.00 32.81 2.44
3092 6923 3.958704 CACGTCCATGTGCTTTAACAAA 58.041 40.909 0.00 0.00 32.81 2.83
3093 6924 3.617540 CACGTCCATGTGCTTTAACAA 57.382 42.857 0.00 0.00 32.81 2.83
3102 6933 2.370281 ACTTAGAGCACGTCCATGTG 57.630 50.000 0.00 0.00 42.81 3.21
3103 6934 4.081642 ACAATACTTAGAGCACGTCCATGT 60.082 41.667 0.00 0.00 0.00 3.21
3104 6935 4.433615 ACAATACTTAGAGCACGTCCATG 58.566 43.478 0.00 0.00 0.00 3.66
3105 6936 4.737855 ACAATACTTAGAGCACGTCCAT 57.262 40.909 0.00 0.00 0.00 3.41
3106 6937 4.460034 TGTACAATACTTAGAGCACGTCCA 59.540 41.667 0.00 0.00 0.00 4.02
3107 6938 4.990257 TGTACAATACTTAGAGCACGTCC 58.010 43.478 0.00 0.00 0.00 4.79
3108 6939 6.496571 AGATGTACAATACTTAGAGCACGTC 58.503 40.000 0.00 0.00 0.00 4.34
3109 6940 6.452494 AGATGTACAATACTTAGAGCACGT 57.548 37.500 0.00 0.00 0.00 4.49
3110 6941 8.129840 ACTTAGATGTACAATACTTAGAGCACG 58.870 37.037 0.00 0.00 0.00 5.34
3111 6942 9.453325 GACTTAGATGTACAATACTTAGAGCAC 57.547 37.037 0.00 0.00 0.00 4.40
3112 6943 8.630917 GGACTTAGATGTACAATACTTAGAGCA 58.369 37.037 0.00 0.00 0.00 4.26
3113 6944 8.852135 AGGACTTAGATGTACAATACTTAGAGC 58.148 37.037 0.00 2.61 0.00 4.09
3119 6950 9.642343 TGACATAGGACTTAGATGTACAATACT 57.358 33.333 0.00 2.76 33.99 2.12
3122 6953 9.770097 CAATGACATAGGACTTAGATGTACAAT 57.230 33.333 0.00 0.00 33.99 2.71
3123 6954 8.977412 TCAATGACATAGGACTTAGATGTACAA 58.023 33.333 0.00 0.00 33.99 2.41
3124 6955 8.533569 TCAATGACATAGGACTTAGATGTACA 57.466 34.615 0.00 0.00 33.99 2.90
3125 6956 9.988815 AATCAATGACATAGGACTTAGATGTAC 57.011 33.333 0.00 0.00 33.99 2.90
3126 6957 9.987272 CAATCAATGACATAGGACTTAGATGTA 57.013 33.333 0.00 0.00 33.99 2.29
3127 6958 8.489489 ACAATCAATGACATAGGACTTAGATGT 58.511 33.333 0.00 0.00 36.52 3.06
3128 6959 8.899427 ACAATCAATGACATAGGACTTAGATG 57.101 34.615 0.00 0.00 0.00 2.90
3129 6960 9.988815 GTACAATCAATGACATAGGACTTAGAT 57.011 33.333 0.00 0.00 0.00 1.98
3130 6961 8.135529 CGTACAATCAATGACATAGGACTTAGA 58.864 37.037 0.00 0.00 0.00 2.10
3131 6962 7.096023 GCGTACAATCAATGACATAGGACTTAG 60.096 40.741 0.00 0.00 0.00 2.18
3132 6963 6.700081 GCGTACAATCAATGACATAGGACTTA 59.300 38.462 0.00 0.00 0.00 2.24
3133 6964 5.523916 GCGTACAATCAATGACATAGGACTT 59.476 40.000 0.00 0.00 0.00 3.01
3134 6965 5.050490 GCGTACAATCAATGACATAGGACT 58.950 41.667 0.00 0.00 0.00 3.85
3135 6966 5.050490 AGCGTACAATCAATGACATAGGAC 58.950 41.667 0.00 0.00 0.00 3.85
3136 6967 5.276461 AGCGTACAATCAATGACATAGGA 57.724 39.130 0.00 0.00 0.00 2.94
3137 6968 7.477144 TTTAGCGTACAATCAATGACATAGG 57.523 36.000 0.00 0.00 0.00 2.57
3138 6969 9.935682 AATTTTAGCGTACAATCAATGACATAG 57.064 29.630 0.00 0.00 0.00 2.23
3140 6971 9.075519 CAAATTTTAGCGTACAATCAATGACAT 57.924 29.630 0.00 0.00 0.00 3.06
3141 6972 8.079203 ACAAATTTTAGCGTACAATCAATGACA 58.921 29.630 0.00 0.00 0.00 3.58
3142 6973 8.365210 CACAAATTTTAGCGTACAATCAATGAC 58.635 33.333 0.00 0.00 0.00 3.06
3143 6974 7.061673 GCACAAATTTTAGCGTACAATCAATGA 59.938 33.333 0.00 0.00 0.00 2.57
3144 6975 7.148836 TGCACAAATTTTAGCGTACAATCAATG 60.149 33.333 7.01 0.00 0.00 2.82
3145 6976 6.865726 TGCACAAATTTTAGCGTACAATCAAT 59.134 30.769 7.01 0.00 0.00 2.57
3146 6977 6.143118 GTGCACAAATTTTAGCGTACAATCAA 59.857 34.615 13.17 0.00 0.00 2.57
3147 6978 5.627367 GTGCACAAATTTTAGCGTACAATCA 59.373 36.000 13.17 0.00 0.00 2.57
3148 6979 5.627367 TGTGCACAAATTTTAGCGTACAATC 59.373 36.000 19.28 0.00 0.00 2.67
3149 6980 5.401079 GTGTGCACAAATTTTAGCGTACAAT 59.599 36.000 23.59 0.00 0.00 2.71
3150 6981 4.735822 GTGTGCACAAATTTTAGCGTACAA 59.264 37.500 23.59 0.00 0.00 2.41
3151 6982 4.201920 TGTGTGCACAAATTTTAGCGTACA 60.202 37.500 23.59 7.50 38.56 2.90
3152 6983 4.283678 TGTGTGCACAAATTTTAGCGTAC 58.716 39.130 23.59 4.62 38.56 3.67
3153 6984 4.553756 TGTGTGCACAAATTTTAGCGTA 57.446 36.364 23.59 0.00 38.56 4.42
3154 6985 3.428746 TGTGTGCACAAATTTTAGCGT 57.571 38.095 23.59 0.00 38.56 5.07
3155 6986 4.970472 AATGTGTGCACAAATTTTAGCG 57.030 36.364 26.43 0.00 45.41 4.26
3160 6991 9.934190 GATAAAAGAAAATGTGTGCACAAATTT 57.066 25.926 33.04 33.04 43.58 1.82
3161 6992 9.328845 AGATAAAAGAAAATGTGTGCACAAATT 57.671 25.926 26.43 26.43 45.41 1.82
3162 6993 8.891671 AGATAAAAGAAAATGTGTGCACAAAT 57.108 26.923 23.59 20.18 45.41 2.32
3163 6994 8.715191 AAGATAAAAGAAAATGTGTGCACAAA 57.285 26.923 23.59 18.43 45.41 2.83
3164 6995 9.979578 ATAAGATAAAAGAAAATGTGTGCACAA 57.020 25.926 23.59 12.53 45.41 3.33
3165 6996 9.979578 AATAAGATAAAAGAAAATGTGTGCACA 57.020 25.926 17.42 17.42 46.44 4.57
3189 7020 9.750125 GAACACCTAACAGAAAGAAAATGAAAT 57.250 29.630 0.00 0.00 0.00 2.17
3190 7021 7.913297 CGAACACCTAACAGAAAGAAAATGAAA 59.087 33.333 0.00 0.00 0.00 2.69
3191 7022 7.281324 TCGAACACCTAACAGAAAGAAAATGAA 59.719 33.333 0.00 0.00 0.00 2.57
3192 7023 6.764085 TCGAACACCTAACAGAAAGAAAATGA 59.236 34.615 0.00 0.00 0.00 2.57
3193 7024 6.954944 TCGAACACCTAACAGAAAGAAAATG 58.045 36.000 0.00 0.00 0.00 2.32
3194 7025 7.661847 AGATCGAACACCTAACAGAAAGAAAAT 59.338 33.333 0.00 0.00 0.00 1.82
3195 7026 6.990349 AGATCGAACACCTAACAGAAAGAAAA 59.010 34.615 0.00 0.00 0.00 2.29
3196 7027 6.522054 AGATCGAACACCTAACAGAAAGAAA 58.478 36.000 0.00 0.00 0.00 2.52
3197 7028 6.097915 AGATCGAACACCTAACAGAAAGAA 57.902 37.500 0.00 0.00 0.00 2.52
3198 7029 5.243060 TGAGATCGAACACCTAACAGAAAGA 59.757 40.000 0.00 0.00 0.00 2.52
3199 7030 5.346281 GTGAGATCGAACACCTAACAGAAAG 59.654 44.000 8.79 0.00 0.00 2.62
3200 7031 5.010719 AGTGAGATCGAACACCTAACAGAAA 59.989 40.000 14.09 0.00 37.69 2.52
3201 7032 4.523173 AGTGAGATCGAACACCTAACAGAA 59.477 41.667 14.09 0.00 37.69 3.02
3202 7033 4.079970 AGTGAGATCGAACACCTAACAGA 58.920 43.478 14.09 0.00 37.69 3.41
3203 7034 4.442375 AGTGAGATCGAACACCTAACAG 57.558 45.455 14.09 0.00 37.69 3.16
3204 7035 4.866508 AAGTGAGATCGAACACCTAACA 57.133 40.909 14.09 0.00 37.69 2.41
3205 7036 5.227908 TGAAAGTGAGATCGAACACCTAAC 58.772 41.667 14.09 3.10 37.69 2.34
3206 7037 5.243060 TCTGAAAGTGAGATCGAACACCTAA 59.757 40.000 14.09 2.14 37.69 2.69
3207 7038 4.765339 TCTGAAAGTGAGATCGAACACCTA 59.235 41.667 14.09 2.48 37.69 3.08
3208 7039 3.574396 TCTGAAAGTGAGATCGAACACCT 59.426 43.478 14.09 2.72 37.69 4.00
3209 7040 3.914312 TCTGAAAGTGAGATCGAACACC 58.086 45.455 14.09 0.00 37.69 4.16
3210 7041 6.034044 GTGTATCTGAAAGTGAGATCGAACAC 59.966 42.308 11.10 11.10 37.30 3.32
3211 7042 6.093404 GTGTATCTGAAAGTGAGATCGAACA 58.907 40.000 0.00 0.00 32.32 3.18
3212 7043 6.093404 TGTGTATCTGAAAGTGAGATCGAAC 58.907 40.000 0.00 0.00 32.32 3.95
3213 7044 6.267496 TGTGTATCTGAAAGTGAGATCGAA 57.733 37.500 0.00 0.00 32.32 3.71
3214 7045 5.897377 TGTGTATCTGAAAGTGAGATCGA 57.103 39.130 0.00 0.00 32.32 3.59
3215 7046 6.268566 TGATGTGTATCTGAAAGTGAGATCG 58.731 40.000 0.00 0.00 34.31 3.69
3216 7047 9.409312 CTATGATGTGTATCTGAAAGTGAGATC 57.591 37.037 0.00 0.00 34.31 2.75
3217 7048 9.140874 TCTATGATGTGTATCTGAAAGTGAGAT 57.859 33.333 0.00 0.00 34.31 2.75
3218 7049 8.525290 TCTATGATGTGTATCTGAAAGTGAGA 57.475 34.615 0.00 0.00 34.31 3.27
3219 7050 8.412456 ACTCTATGATGTGTATCTGAAAGTGAG 58.588 37.037 0.00 0.00 34.31 3.51
3220 7051 8.298729 ACTCTATGATGTGTATCTGAAAGTGA 57.701 34.615 0.00 0.00 34.31 3.41
3226 7057 9.746457 AGCTAATACTCTATGATGTGTATCTGA 57.254 33.333 0.00 0.00 34.31 3.27
3243 7074 9.988815 CCAAGTTGTATCAGATAAGCTAATACT 57.011 33.333 1.45 0.00 0.00 2.12
3244 7075 9.982651 TCCAAGTTGTATCAGATAAGCTAATAC 57.017 33.333 1.45 0.00 0.00 1.89
3246 7077 8.928448 TCTCCAAGTTGTATCAGATAAGCTAAT 58.072 33.333 1.45 0.00 0.00 1.73
3247 7078 8.306313 TCTCCAAGTTGTATCAGATAAGCTAA 57.694 34.615 1.45 0.00 0.00 3.09
3248 7079 7.014711 CCTCTCCAAGTTGTATCAGATAAGCTA 59.985 40.741 1.45 0.00 0.00 3.32
3249 7080 6.183360 CCTCTCCAAGTTGTATCAGATAAGCT 60.183 42.308 1.45 0.00 0.00 3.74
3250 7081 5.988561 CCTCTCCAAGTTGTATCAGATAAGC 59.011 44.000 1.45 0.00 0.00 3.09
3251 7082 7.353414 TCCTCTCCAAGTTGTATCAGATAAG 57.647 40.000 1.45 0.00 0.00 1.73
3252 7083 6.325028 CCTCCTCTCCAAGTTGTATCAGATAA 59.675 42.308 1.45 0.00 0.00 1.75
3253 7084 5.835819 CCTCCTCTCCAAGTTGTATCAGATA 59.164 44.000 1.45 0.00 0.00 1.98
3254 7085 4.653341 CCTCCTCTCCAAGTTGTATCAGAT 59.347 45.833 1.45 0.00 0.00 2.90
3255 7086 4.026744 CCTCCTCTCCAAGTTGTATCAGA 58.973 47.826 1.45 0.00 0.00 3.27
3256 7087 3.133721 CCCTCCTCTCCAAGTTGTATCAG 59.866 52.174 1.45 0.00 0.00 2.90
3257 7088 3.107601 CCCTCCTCTCCAAGTTGTATCA 58.892 50.000 1.45 0.00 0.00 2.15
3292 7123 1.128513 CGGCGGCTTTCTTTGTTTTC 58.871 50.000 7.61 0.00 0.00 2.29
3297 7128 2.255252 CACCGGCGGCTTTCTTTG 59.745 61.111 28.71 11.33 0.00 2.77
3298 7129 3.670377 GCACCGGCGGCTTTCTTT 61.670 61.111 28.71 0.15 0.00 2.52
3312 7143 0.244721 GTTGGATCAGGCAAAGGCAC 59.755 55.000 0.00 0.00 43.71 5.01
3313 7144 0.112995 AGTTGGATCAGGCAAAGGCA 59.887 50.000 0.00 0.00 43.71 4.75
3315 7146 1.547372 CCAAGTTGGATCAGGCAAAGG 59.453 52.381 17.60 0.00 40.96 3.11
3316 7147 2.517959 TCCAAGTTGGATCAGGCAAAG 58.482 47.619 21.05 0.00 42.67 2.77
3345 7183 0.174845 TAAACCACGCGATCCAGAGG 59.825 55.000 15.93 5.12 0.00 3.69
3438 7277 1.196012 GACGAATCAAGGAGAGGGGT 58.804 55.000 0.00 0.00 0.00 4.95
3454 7293 3.047877 GGGAACGCCAAGTGGACG 61.048 66.667 0.18 7.04 39.44 4.79
3507 7346 1.903183 GAGAGGGAAGTGGCAGTAACT 59.097 52.381 0.00 0.00 0.00 2.24
3591 7430 0.609131 CCGCCACCACTTTCCTCATT 60.609 55.000 0.00 0.00 0.00 2.57
3602 7441 2.429930 CCTTTCACTCCGCCACCA 59.570 61.111 0.00 0.00 0.00 4.17
3710 7549 7.340743 TCTTGTTCCAGTGGAAATCTTTAACAA 59.659 33.333 26.19 20.66 43.86 2.83
3715 7554 5.694995 TCTCTTGTTCCAGTGGAAATCTTT 58.305 37.500 26.19 0.00 43.86 2.52
3837 7676 1.221466 CGAGCTGAACTTGCGAACCA 61.221 55.000 0.00 0.00 35.28 3.67
3838 7677 1.222115 ACGAGCTGAACTTGCGAACC 61.222 55.000 0.00 0.00 32.28 3.62
3842 7681 0.093705 GCTTACGAGCTGAACTTGCG 59.906 55.000 0.00 0.00 45.65 4.85


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

AutoCloner maintained by Alex Coulton.