Multiple sequence alignment - TraesCS4A01G271600

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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 TraesCS4A01G271600 chr4A 100.000 5592 0 0 1 5592 583418318 583423909 0.000000e+00 10327
1 TraesCS4A01G271600 chr4B 93.118 3618 167 39 226 3808 29271483 29267913 0.000000e+00 5227
2 TraesCS4A01G271600 chr4B 89.280 1222 65 35 3812 5001 29267876 29266689 0.000000e+00 1471
3 TraesCS4A01G271600 chr4B 83.908 522 26 23 5097 5592 29266380 29265891 3.970000e-121 446
4 TraesCS4A01G271600 chr4B 82.946 129 16 4 57 184 29272065 29271942 1.650000e-20 111
5 TraesCS4A01G271600 chr4D 91.963 3795 186 42 56 3808 17253962 17250245 0.000000e+00 5208
6 TraesCS4A01G271600 chr4D 86.877 1867 86 75 3812 5590 17250209 17248414 0.000000e+00 1943
7 TraesCS4A01G271600 chr2D 76.337 486 111 4 1135 1617 77383176 77382692 2.000000e-64 257
8 TraesCS4A01G271600 chr2B 76.434 488 107 7 1135 1617 119633681 119633197 2.000000e-64 257
9 TraesCS4A01G271600 chr5A 84.118 170 24 3 2121 2288 2104461 2104629 1.610000e-35 161
10 TraesCS4A01G271600 chr5D 83.333 174 27 2 2113 2285 2677803 2677631 5.800000e-35 159
11 TraesCS4A01G271600 chr3B 82.759 174 28 2 2113 2285 720893021 720892849 2.700000e-33 154
12 TraesCS4A01G271600 chr2A 85.816 141 14 5 1130 1267 465364064 465363927 1.620000e-30 145
13 TraesCS4A01G271600 chr5B 81.143 175 31 2 2112 2285 2573910 2573737 7.550000e-29 139
14 TraesCS4A01G271600 chr7B 84.892 139 18 3 1130 1267 197406610 197406474 2.720000e-28 137


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 TraesCS4A01G271600 chr4A 583418318 583423909 5591 False 10327.00 10327 100.000 1 5592 1 chr4A.!!$F1 5591
1 TraesCS4A01G271600 chr4B 29265891 29272065 6174 True 1813.75 5227 87.313 57 5592 4 chr4B.!!$R1 5535
2 TraesCS4A01G271600 chr4D 17248414 17253962 5548 True 3575.50 5208 89.420 56 5590 2 chr4D.!!$R1 5534

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
267 701 0.814010 AAAGAGCACGTCGCCAAACT 60.814 50.000 6.39 0.59 44.04 2.66 F
431 868 1.079127 GACCCCACATGTCGGTGAG 60.079 63.158 17.07 1.23 41.32 3.51 F
1726 2224 0.922626 GATTGGGGAGAAGGCTTCCT 59.077 55.000 23.09 10.91 40.00 3.36 F
2271 2770 1.602771 GTGGAAGGACTACTGCCCC 59.397 63.158 0.00 0.00 45.47 5.80 F
3670 4182 0.399833 TGACTGCAGGTATGTTGCCA 59.600 50.000 19.93 0.00 40.81 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 1950 0.683412 ACTCCCCAACGTACTGGTTC 59.317 55.0 5.58 0.0 34.33 3.62 R
2271 2770 0.038892 GCAAGCACCTGAACACCATG 60.039 55.0 0.00 0.0 0.00 3.66 R
2620 3127 0.318699 TCACAAGCGACAGAACCTCG 60.319 55.0 0.00 0.0 0.00 4.63 R
4143 4688 0.034896 ACAGCTAGGACCCAACAACG 59.965 55.0 0.00 0.0 0.00 4.10 R
5309 6162 0.035630 CAGCAGGTCAAGGAAGGAGG 60.036 60.0 0.00 0.0 0.00 4.30 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
122 123 4.508662 ACGGAGAGAGTTCAATGGAAATC 58.491 43.478 1.89 1.89 45.84 2.17
131 132 7.541122 GAGTTCAATGGAAATCTGTACTACC 57.459 40.000 2.97 0.00 43.04 3.18
184 185 3.310501 GGGCGTACACATAAACCATGTAC 59.689 47.826 4.11 4.11 46.47 2.90
185 186 4.186159 GGCGTACACATAAACCATGTACT 58.814 43.478 10.93 0.00 46.47 2.73
186 187 5.350633 GGCGTACACATAAACCATGTACTA 58.649 41.667 10.93 0.00 46.47 1.82
187 188 5.461078 GGCGTACACATAAACCATGTACTAG 59.539 44.000 10.93 0.00 46.47 2.57
188 189 6.038356 GCGTACACATAAACCATGTACTAGT 58.962 40.000 0.00 0.00 46.47 2.57
189 190 7.195646 GCGTACACATAAACCATGTACTAGTA 58.804 38.462 0.00 0.00 46.47 1.82
190 191 7.166473 GCGTACACATAAACCATGTACTAGTAC 59.834 40.741 23.58 23.58 46.47 2.73
191 192 8.400947 CGTACACATAAACCATGTACTAGTACT 58.599 37.037 28.56 14.70 46.47 2.73
241 671 2.442212 TCGATTTTACTGACCACGCA 57.558 45.000 0.00 0.00 0.00 5.24
267 701 0.814010 AAAGAGCACGTCGCCAAACT 60.814 50.000 6.39 0.59 44.04 2.66
309 744 1.281656 CCTCGAACAAAACGTGCCC 59.718 57.895 0.00 0.00 0.00 5.36
319 754 1.164041 AAACGTGCCCTTCCTTCGTG 61.164 55.000 0.00 0.00 35.00 4.35
355 790 4.343323 TAGCAGCGCTGGCCCAAA 62.343 61.111 36.47 11.37 40.10 3.28
410 847 3.314541 AAGAAACGCCACAGTAGTAGG 57.685 47.619 0.00 0.00 0.00 3.18
431 868 1.079127 GACCCCACATGTCGGTGAG 60.079 63.158 17.07 1.23 41.32 3.51
735 1221 2.046604 GTAAAAGCGCCCGTCCCT 60.047 61.111 2.29 0.00 0.00 4.20
761 1247 2.060980 CCCCCTCACTCCTCTTCCG 61.061 68.421 0.00 0.00 0.00 4.30
778 1264 2.520536 CGTCCATCCCCATCCCCTC 61.521 68.421 0.00 0.00 0.00 4.30
786 1272 2.778717 CCATCCCCTCCCCCTTCC 60.779 72.222 0.00 0.00 0.00 3.46
787 1273 2.044450 CATCCCCTCCCCCTTCCA 59.956 66.667 0.00 0.00 0.00 3.53
788 1274 2.044620 ATCCCCTCCCCCTTCCAC 59.955 66.667 0.00 0.00 0.00 4.02
789 1275 4.733725 TCCCCTCCCCCTTCCACG 62.734 72.222 0.00 0.00 0.00 4.94
902 1394 3.339093 AGGCGAAAAGGGGAGGGG 61.339 66.667 0.00 0.00 0.00 4.79
913 1405 2.684499 GGGAGGGGGAGAGGCTTTG 61.684 68.421 0.00 0.00 0.00 2.77
937 1429 4.467107 GAGGGAGGCGGAGGAGGT 62.467 72.222 0.00 0.00 0.00 3.85
982 1477 4.802051 ATCTGCAATGCCGGCGGT 62.802 61.111 28.82 10.60 38.75 5.68
1476 1974 3.697747 TACGTTGGGGAGTGGCGG 61.698 66.667 0.00 0.00 0.00 6.13
1521 2019 2.124570 CTGATCTGGGCCAACGGG 60.125 66.667 8.04 0.00 37.18 5.28
1623 2121 4.704103 TCCTGGCCGAGGAGCTGT 62.704 66.667 17.12 0.00 46.96 4.40
1722 2220 2.009302 GGGGATTGGGGAGAAGGCT 61.009 63.158 0.00 0.00 0.00 4.58
1723 2221 1.584717 GGGGATTGGGGAGAAGGCTT 61.585 60.000 0.00 0.00 0.00 4.35
1726 2224 0.922626 GATTGGGGAGAAGGCTTCCT 59.077 55.000 23.09 10.91 40.00 3.36
1914 2412 3.680786 CCGTGCTGGTCGTCCTCA 61.681 66.667 0.00 0.00 34.23 3.86
1987 2485 4.363999 GCATAAGAACTACGAGCTCATGT 58.636 43.478 15.40 7.02 0.00 3.21
2035 2533 7.118680 GGTGATTCCTCGTTATTTAGTTGTTGA 59.881 37.037 0.00 0.00 0.00 3.18
2036 2534 8.500773 GTGATTCCTCGTTATTTAGTTGTTGAA 58.499 33.333 0.00 0.00 0.00 2.69
2042 2541 7.271223 CCTCGTTATTTAGTTGTTGAAATGCTG 59.729 37.037 0.00 0.00 0.00 4.41
2050 2549 5.362263 AGTTGTTGAAATGCTGAAATGCTT 58.638 33.333 0.00 0.00 0.00 3.91
2063 2562 2.554370 AATGCTTGCAATGTGGCTTT 57.446 40.000 0.00 1.55 34.04 3.51
2078 2577 4.922692 TGTGGCTTTTATTTCAGCGAATTG 59.077 37.500 0.00 0.00 36.85 2.32
2139 2638 3.140814 GTGGGGAAATCTGCGGCC 61.141 66.667 0.00 0.00 0.00 6.13
2271 2770 1.602771 GTGGAAGGACTACTGCCCC 59.397 63.158 0.00 0.00 45.47 5.80
2334 2833 6.707440 TGTTCTCTGGATTGCTTTGTTTTA 57.293 33.333 0.00 0.00 0.00 1.52
2335 2834 7.106439 TGTTCTCTGGATTGCTTTGTTTTAA 57.894 32.000 0.00 0.00 0.00 1.52
2337 2836 8.203485 TGTTCTCTGGATTGCTTTGTTTTAATT 58.797 29.630 0.00 0.00 0.00 1.40
2338 2837 8.490355 GTTCTCTGGATTGCTTTGTTTTAATTG 58.510 33.333 0.00 0.00 0.00 2.32
2341 2840 9.474920 CTCTGGATTGCTTTGTTTTAATTGTTA 57.525 29.630 0.00 0.00 0.00 2.41
2344 2843 9.039870 TGGATTGCTTTGTTTTAATTGTTACTG 57.960 29.630 0.00 0.00 0.00 2.74
2389 2893 5.951148 TGGATTATGCAGACATTTGAGGAAA 59.049 36.000 0.00 0.00 37.74 3.13
2396 2900 7.048629 TGCAGACATTTGAGGAAATTGTTTA 57.951 32.000 0.00 0.00 28.65 2.01
2632 3139 2.363788 TTGGATTCGAGGTTCTGTCG 57.636 50.000 0.00 0.00 38.84 4.35
2651 3158 2.492881 TCGCTTGTGAAATGATTGGCAT 59.507 40.909 0.00 0.00 39.43 4.40
2652 3159 2.601314 CGCTTGTGAAATGATTGGCATG 59.399 45.455 0.00 0.00 37.28 4.06
2653 3160 2.933906 GCTTGTGAAATGATTGGCATGG 59.066 45.455 0.00 0.00 37.28 3.66
2671 3181 3.023946 TGGTTGTTTGAATTGCATCGG 57.976 42.857 0.00 0.00 0.00 4.18
2736 3246 1.171549 TCAAGCCTTGCGAATGTGCA 61.172 50.000 0.00 0.00 44.61 4.57
2829 3339 8.103305 TGCCAAGTAGAAATACTTTGAGAGAAT 58.897 33.333 4.05 0.00 38.14 2.40
3028 3539 5.750650 CAATTCCTTGCCACAAAATGTTTC 58.249 37.500 0.00 0.00 0.00 2.78
3030 3541 4.057406 TCCTTGCCACAAAATGTTTCTG 57.943 40.909 0.00 0.00 0.00 3.02
3048 3559 8.138365 TGTTTCTGTGTTAGTTACTGATCAAC 57.862 34.615 0.00 0.00 0.00 3.18
3233 3744 0.949588 TTGTATTTCGGTTGCGGCGA 60.950 50.000 12.98 0.00 0.00 5.54
3242 3753 1.702491 GGTTGCGGCGATCTTGGTAC 61.702 60.000 12.98 0.00 0.00 3.34
3272 3783 3.009033 TCCATGAGTAAGTTCAACCCCTG 59.991 47.826 0.00 0.00 0.00 4.45
3280 3791 7.092444 TGAGTAAGTTCAACCCCTGATGATATT 60.092 37.037 0.00 0.00 32.78 1.28
3282 3793 8.116026 AGTAAGTTCAACCCCTGATGATATTTT 58.884 33.333 0.00 0.00 32.78 1.82
3283 3794 6.780457 AGTTCAACCCCTGATGATATTTTG 57.220 37.500 0.00 0.00 32.78 2.44
3289 3800 3.891366 CCCCTGATGATATTTTGGGTGTC 59.109 47.826 0.00 0.00 33.13 3.67
3290 3801 4.535781 CCCTGATGATATTTTGGGTGTCA 58.464 43.478 0.00 0.00 0.00 3.58
3339 3850 4.430007 TCGGTAATACTGACTTGATGTGC 58.570 43.478 0.00 0.00 0.00 4.57
3344 3855 2.015736 ACTGACTTGATGTGCGGATC 57.984 50.000 0.00 0.00 0.00 3.36
3351 3862 5.028549 ACTTGATGTGCGGATCTATTCTT 57.971 39.130 0.00 0.00 0.00 2.52
3403 3914 7.451731 TTTGGAGTCTGAAGGTATTATGGAT 57.548 36.000 0.00 0.00 0.00 3.41
3418 3929 8.154856 GGTATTATGGATTACAGCTTCTTGGTA 58.845 37.037 0.00 0.00 0.00 3.25
3430 3941 3.997681 GCTTCTTGGTAGGAGTTCACTTC 59.002 47.826 0.00 0.00 28.80 3.01
3495 4006 2.347731 CGCTTCTCCAAGTAAGTTCCC 58.652 52.381 0.00 0.00 31.45 3.97
3509 4020 4.741928 AAGTTCCCTGTTCTTTACCCAT 57.258 40.909 0.00 0.00 0.00 4.00
3658 4170 6.725834 TGATTATGATAGGATACCTGACTGCA 59.274 38.462 0.00 0.00 34.61 4.41
3670 4182 0.399833 TGACTGCAGGTATGTTGCCA 59.600 50.000 19.93 0.00 40.81 4.92
3692 4204 6.313658 GCCATGTTTTCTTTTGAACTGTTTCT 59.686 34.615 0.00 0.00 38.30 2.52
3711 4223 8.785329 TGTTTCTTACCTTTTTCTTGCAAAAT 57.215 26.923 0.00 0.00 0.00 1.82
3754 4266 2.969821 AACAAGCCTGGGTTCATGTA 57.030 45.000 8.43 0.00 0.00 2.29
3796 4308 8.040132 ACTTTTCTCAAAATGACCACATGAAAA 58.960 29.630 0.00 0.00 36.79 2.29
3808 4320 6.072728 TGACCACATGAAAAGGAAGTAATTCG 60.073 38.462 0.00 0.00 0.00 3.34
3810 4322 6.072673 ACCACATGAAAAGGAAGTAATTCGTC 60.073 38.462 0.00 0.00 0.00 4.20
3816 4361 6.647481 TGAAAAGGAAGTAATTCGTCGATTCA 59.353 34.615 12.96 12.96 0.00 2.57
3820 4365 7.611213 AGGAAGTAATTCGTCGATTCATTTT 57.389 32.000 0.00 0.00 0.00 1.82
3882 4427 9.809096 TTACAACTGCATGTTAGAAAATTGAAA 57.191 25.926 0.00 0.00 37.07 2.69
3883 4428 8.356533 ACAACTGCATGTTAGAAAATTGAAAG 57.643 30.769 6.18 0.00 37.07 2.62
4019 4564 1.003118 GGGTTCTACACATGGCTCACA 59.997 52.381 0.00 0.00 0.00 3.58
4130 4675 2.482721 CCGTCCACTTGGTTAACACATC 59.517 50.000 8.10 0.00 36.34 3.06
4133 4678 4.134563 GTCCACTTGGTTAACACATCTGT 58.865 43.478 8.10 1.30 36.34 3.41
4134 4679 4.024048 GTCCACTTGGTTAACACATCTGTG 60.024 45.833 8.10 8.74 42.99 3.66
4135 4680 5.518036 TCCACTTGGTTAACACATCTGTGC 61.518 45.833 10.16 0.00 42.00 4.57
4143 4688 3.975992 CACATCTGTGCGTTTAGGC 57.024 52.632 0.00 0.00 39.39 3.93
4144 4689 0.095245 CACATCTGTGCGTTTAGGCG 59.905 55.000 0.00 0.00 39.39 5.52
4366 4918 0.317479 AGTTCGACCCGTTTCTCCTG 59.683 55.000 0.00 0.00 0.00 3.86
4429 4981 5.412594 AGTGCATGACGTGATTCTGTATTTT 59.587 36.000 0.00 0.00 0.00 1.82
4591 5143 6.327934 CAGAATTTTTGTGGAAGATGGCTAG 58.672 40.000 0.00 0.00 0.00 3.42
4592 5144 6.151648 CAGAATTTTTGTGGAAGATGGCTAGA 59.848 38.462 0.00 0.00 0.00 2.43
4594 5146 7.398332 AGAATTTTTGTGGAAGATGGCTAGAAT 59.602 33.333 0.00 0.00 0.00 2.40
4595 5147 6.916360 TTTTTGTGGAAGATGGCTAGAATT 57.084 33.333 0.00 0.00 0.00 2.17
4628 5185 4.730949 AGATGCAACAGGAATTCCATTG 57.269 40.909 26.22 26.17 38.89 2.82
4664 5242 0.547075 TTCCGAGGTGGTTTTGGTCA 59.453 50.000 0.00 0.00 39.52 4.02
4667 5245 1.539827 CCGAGGTGGTTTTGGTCAATC 59.460 52.381 0.00 0.00 0.00 2.67
4676 5254 4.344679 TGGTTTTGGTCAATCTTCTGCATT 59.655 37.500 0.00 0.00 0.00 3.56
4705 5283 8.364142 CAAAGGAACTCCATTGTTAAATACCAA 58.636 33.333 5.70 0.00 38.49 3.67
4730 5308 0.250209 ATCATCATCAGCCGCTGGAC 60.250 55.000 20.23 0.00 31.51 4.02
4739 5317 2.183555 CCGCTGGACTCCGGTAAC 59.816 66.667 0.00 0.00 39.67 2.50
4765 5344 1.226773 CGTCGACCGGGTAATCACC 60.227 63.158 10.58 0.00 44.96 4.02
4789 5368 0.888619 AACGAACCTCGATCAGCAGA 59.111 50.000 2.59 0.00 43.74 4.26
4802 5382 1.110442 CAGCAGAGAAGGGAGACGAT 58.890 55.000 0.00 0.00 0.00 3.73
4860 5445 1.582610 GGCTGGATTTTGGAACGCGA 61.583 55.000 15.93 0.00 0.00 5.87
4918 5508 0.112218 TGATTTGGTGGGTGGTGAGG 59.888 55.000 0.00 0.00 0.00 3.86
4919 5509 0.112412 GATTTGGTGGGTGGTGAGGT 59.888 55.000 0.00 0.00 0.00 3.85
4920 5510 0.560688 ATTTGGTGGGTGGTGAGGTT 59.439 50.000 0.00 0.00 0.00 3.50
4921 5511 0.396417 TTTGGTGGGTGGTGAGGTTG 60.396 55.000 0.00 0.00 0.00 3.77
4922 5512 2.115266 GGTGGGTGGTGAGGTTGG 59.885 66.667 0.00 0.00 0.00 3.77
4923 5513 2.763645 GGTGGGTGGTGAGGTTGGT 61.764 63.158 0.00 0.00 0.00 3.67
4936 5539 2.557869 AGGTTGGTCCTTGGTAGCATA 58.442 47.619 0.00 0.00 45.67 3.14
5059 5671 5.104941 GGGGATAGGGAATTTTTGTTTCCAG 60.105 44.000 4.96 0.00 43.72 3.86
5062 5674 7.256511 GGGATAGGGAATTTTTGTTTCCAGAAA 60.257 37.037 4.96 0.00 43.72 2.52
5079 5691 5.253096 TCCAGAAAGAGGGTAATTTAAGGCT 59.747 40.000 0.00 0.00 0.00 4.58
5081 5693 4.950475 AGAAAGAGGGTAATTTAAGGCTGC 59.050 41.667 0.00 0.00 0.00 5.25
5083 5695 1.947456 GAGGGTAATTTAAGGCTGCGG 59.053 52.381 0.00 0.00 0.00 5.69
5084 5696 0.384309 GGGTAATTTAAGGCTGCGGC 59.616 55.000 9.72 9.72 37.82 6.53
5085 5697 1.099689 GGTAATTTAAGGCTGCGGCA 58.900 50.000 21.31 1.29 40.87 5.69
5087 5699 2.479560 GGTAATTTAAGGCTGCGGCAAG 60.480 50.000 21.31 0.00 40.87 4.01
5181 6007 5.902613 TCAGAATTGAATTCGGCATCTTT 57.097 34.783 12.27 0.00 43.92 2.52
5182 6008 5.883661 TCAGAATTGAATTCGGCATCTTTC 58.116 37.500 12.27 0.00 43.92 2.62
5184 6010 6.151648 TCAGAATTGAATTCGGCATCTTTCTT 59.848 34.615 12.27 0.00 43.92 2.52
5186 6012 4.701956 TTGAATTCGGCATCTTTCTTCC 57.298 40.909 0.04 0.00 0.00 3.46
5188 6014 2.058593 ATTCGGCATCTTTCTTCCCC 57.941 50.000 0.00 0.00 0.00 4.81
5191 6017 0.543749 CGGCATCTTTCTTCCCCTCT 59.456 55.000 0.00 0.00 0.00 3.69
5193 6019 1.133945 GGCATCTTTCTTCCCCTCTCC 60.134 57.143 0.00 0.00 0.00 3.71
5194 6020 1.133945 GCATCTTTCTTCCCCTCTCCC 60.134 57.143 0.00 0.00 0.00 4.30
5195 6021 2.486716 CATCTTTCTTCCCCTCTCCCT 58.513 52.381 0.00 0.00 0.00 4.20
5196 6022 2.255770 TCTTTCTTCCCCTCTCCCTC 57.744 55.000 0.00 0.00 0.00 4.30
5197 6023 1.437149 TCTTTCTTCCCCTCTCCCTCA 59.563 52.381 0.00 0.00 0.00 3.86
5229 6074 2.218603 GTCGTTGGCTTCTTCCTTTCA 58.781 47.619 0.00 0.00 0.00 2.69
5234 6079 3.297134 TGGCTTCTTCCTTTCACAGTT 57.703 42.857 0.00 0.00 0.00 3.16
5249 6102 2.233676 CACAGTTTTTATTGGCCCCTCC 59.766 50.000 0.00 0.00 0.00 4.30
5250 6103 1.831106 CAGTTTTTATTGGCCCCTCCC 59.169 52.381 0.00 0.00 0.00 4.30
5251 6104 1.435168 AGTTTTTATTGGCCCCTCCCA 59.565 47.619 0.00 0.00 0.00 4.37
5252 6105 1.553248 GTTTTTATTGGCCCCTCCCAC 59.447 52.381 0.00 0.00 33.82 4.61
5296 6149 3.530149 AGAGAGAAGGTAGGGTAGAGCTT 59.470 47.826 0.00 0.00 37.34 3.74
5332 6185 1.004044 CCTTCCTTGACCTGCTGTGAT 59.996 52.381 0.00 0.00 0.00 3.06
5333 6186 2.082231 CTTCCTTGACCTGCTGTGATG 58.918 52.381 0.00 0.00 0.00 3.07
5334 6187 1.351076 TCCTTGACCTGCTGTGATGA 58.649 50.000 0.00 0.00 0.00 2.92
5335 6188 1.002430 TCCTTGACCTGCTGTGATGAC 59.998 52.381 0.00 0.00 0.00 3.06
5336 6189 1.446907 CTTGACCTGCTGTGATGACC 58.553 55.000 0.00 0.00 0.00 4.02
5338 6191 1.184970 TGACCTGCTGTGATGACCGA 61.185 55.000 0.00 0.00 0.00 4.69
5339 6192 0.459237 GACCTGCTGTGATGACCGAG 60.459 60.000 0.00 0.00 0.00 4.63
5372 6234 2.098614 GCCTGTGATGTCTCAGAGAGA 58.901 52.381 12.32 0.00 43.71 3.10
5373 6235 2.099592 GCCTGTGATGTCTCAGAGAGAG 59.900 54.545 12.32 0.00 43.71 3.20
5446 6314 3.151912 AGAGAAAGGAAAGCACAGCAT 57.848 42.857 0.00 0.00 0.00 3.79
5447 6315 4.292186 AGAGAAAGGAAAGCACAGCATA 57.708 40.909 0.00 0.00 0.00 3.14
5448 6316 4.260170 AGAGAAAGGAAAGCACAGCATAG 58.740 43.478 0.00 0.00 0.00 2.23
5449 6317 2.751806 AGAAAGGAAAGCACAGCATAGC 59.248 45.455 0.00 0.00 0.00 2.97
5450 6318 2.205022 AAGGAAAGCACAGCATAGCA 57.795 45.000 0.00 0.00 0.00 3.49
5472 6340 2.693069 GGAACAGCCGATGGATAGATG 58.307 52.381 0.00 0.00 0.00 2.90
5535 6410 3.636764 CCTATAATGCCCAAACCTGGAAC 59.363 47.826 0.00 0.00 46.92 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.851686 TTTTGCAGGAAGTATTATATCTGATGT 57.148 29.630 0.00 0.00 0.00 3.06
76 77 7.042321 CGTCCCGAATTACTTATTGCAGAAATA 60.042 37.037 0.00 0.00 0.00 1.40
85 86 4.891756 TCTCTCCGTCCCGAATTACTTATT 59.108 41.667 0.00 0.00 0.00 1.40
87 88 3.881688 CTCTCTCCGTCCCGAATTACTTA 59.118 47.826 0.00 0.00 0.00 2.24
111 112 5.964477 AGGAGGTAGTACAGATTTCCATTGA 59.036 40.000 2.06 0.00 0.00 2.57
122 123 5.105310 ACTTGCACATAAGGAGGTAGTACAG 60.105 44.000 2.06 0.00 31.94 2.74
124 125 5.105473 TGACTTGCACATAAGGAGGTAGTAC 60.105 44.000 0.00 0.00 31.94 2.73
129 130 4.307032 AATGACTTGCACATAAGGAGGT 57.693 40.909 0.00 0.00 31.94 3.85
130 131 5.649782 AAAATGACTTGCACATAAGGAGG 57.350 39.130 0.00 0.00 31.94 4.30
131 132 8.915654 GTTTTAAAATGACTTGCACATAAGGAG 58.084 33.333 3.52 0.00 31.94 3.69
184 185 7.431249 TCTGTTTGGCGGAATATAAGTACTAG 58.569 38.462 0.00 0.00 0.00 2.57
185 186 7.350744 TCTGTTTGGCGGAATATAAGTACTA 57.649 36.000 0.00 0.00 0.00 1.82
186 187 6.229936 TCTGTTTGGCGGAATATAAGTACT 57.770 37.500 0.00 0.00 0.00 2.73
187 188 6.913873 TTCTGTTTGGCGGAATATAAGTAC 57.086 37.500 0.00 0.00 37.54 2.73
241 671 1.209128 CGACGTGCTCTTTGTCACTT 58.791 50.000 0.00 0.00 32.91 3.16
251 684 1.082756 CAAGTTTGGCGACGTGCTC 60.083 57.895 0.00 0.00 45.43 4.26
267 701 0.959553 TTTGATTTTACCGCGGCCAA 59.040 45.000 28.58 17.52 0.00 4.52
309 744 3.479269 GCGCGACCACGAAGGAAG 61.479 66.667 12.10 0.93 42.66 3.46
338 773 4.343323 TTTGGGCCAGCGCTGCTA 62.343 61.111 31.96 14.44 36.40 3.49
552 996 4.452733 CTTCTGGGTCGGGTCGGC 62.453 72.222 0.00 0.00 0.00 5.54
553 997 2.678934 TCTTCTGGGTCGGGTCGG 60.679 66.667 0.00 0.00 0.00 4.79
555 999 1.605971 GACCTCTTCTGGGTCGGGTC 61.606 65.000 0.00 0.00 42.84 4.46
556 1000 1.609794 GACCTCTTCTGGGTCGGGT 60.610 63.158 0.00 0.00 42.84 5.28
557 1001 3.300013 GACCTCTTCTGGGTCGGG 58.700 66.667 0.00 0.00 42.84 5.14
704 1190 2.801483 TTTTACCGTACTGCCCCCGC 62.801 60.000 0.00 0.00 0.00 6.13
705 1191 0.741927 CTTTTACCGTACTGCCCCCG 60.742 60.000 0.00 0.00 0.00 5.73
735 1221 3.216371 AGTGAGGGGGAGGGGGAA 61.216 66.667 0.00 0.00 0.00 3.97
742 1228 1.392534 GGAAGAGGAGTGAGGGGGA 59.607 63.158 0.00 0.00 0.00 4.81
743 1229 2.060980 CGGAAGAGGAGTGAGGGGG 61.061 68.421 0.00 0.00 0.00 5.40
744 1230 1.305381 ACGGAAGAGGAGTGAGGGG 60.305 63.158 0.00 0.00 0.00 4.79
745 1231 1.324005 GGACGGAAGAGGAGTGAGGG 61.324 65.000 0.00 0.00 0.00 4.30
761 1247 2.156774 GGAGGGGATGGGGATGGAC 61.157 68.421 0.00 0.00 0.00 4.02
786 1272 1.804326 GTAGTACTGTGCGGGCGTG 60.804 63.158 5.39 0.00 0.00 5.34
787 1273 0.677731 TAGTAGTACTGTGCGGGCGT 60.678 55.000 13.29 0.00 0.00 5.68
788 1274 0.248377 GTAGTAGTACTGTGCGGGCG 60.248 60.000 13.29 0.00 0.00 6.13
789 1275 1.101331 AGTAGTAGTACTGTGCGGGC 58.899 55.000 13.29 0.00 38.14 6.13
790 1276 2.290093 GCTAGTAGTAGTACTGTGCGGG 59.710 54.545 18.75 4.96 39.96 6.13
791 1277 2.290093 GGCTAGTAGTAGTACTGTGCGG 59.710 54.545 18.75 6.38 39.96 5.69
792 1278 2.941064 TGGCTAGTAGTAGTACTGTGCG 59.059 50.000 18.75 7.02 39.96 5.34
793 1279 3.243134 GCTGGCTAGTAGTAGTACTGTGC 60.243 52.174 18.75 19.64 39.96 4.57
836 1326 1.173913 GTTTGATTTGGGCTAGCGGT 58.826 50.000 9.00 0.00 0.00 5.68
902 1394 2.684499 CCCCTCCCAAAGCCTCTCC 61.684 68.421 0.00 0.00 0.00 3.71
931 1423 1.550130 TTTGCGATTCGGGACCTCCT 61.550 55.000 8.34 0.00 35.95 3.69
937 1429 0.177141 CTAGGGTTTGCGATTCGGGA 59.823 55.000 8.34 0.00 0.00 5.14
958 1453 3.599704 GCATTGCAGATCGGGGCC 61.600 66.667 3.15 0.00 0.00 5.80
1104 1602 3.687102 CCGCTGTACACGTCCCCA 61.687 66.667 13.98 0.00 0.00 4.96
1218 1716 2.437359 CAGGAGAAGCGGCCCTTG 60.437 66.667 10.77 0.00 32.78 3.61
1452 1950 0.683412 ACTCCCCAACGTACTGGTTC 59.317 55.000 5.58 0.00 34.33 3.62
1594 2092 2.754658 CCAGGAGCCGACGTACCT 60.755 66.667 0.00 0.00 0.00 3.08
1920 2418 3.612247 CTTCCCCTCAGGCGTGGTG 62.612 68.421 6.56 0.17 34.51 4.17
2035 2533 4.069304 ACATTGCAAGCATTTCAGCATTT 58.931 34.783 4.94 0.00 36.80 2.32
2036 2534 3.435327 CACATTGCAAGCATTTCAGCATT 59.565 39.130 4.94 0.00 36.80 3.56
2042 2541 2.088950 AGCCACATTGCAAGCATTTC 57.911 45.000 4.94 0.00 0.00 2.17
2050 2549 3.995705 GCTGAAATAAAAGCCACATTGCA 59.004 39.130 0.00 0.00 33.12 4.08
2078 2577 6.092748 CACAATAAACACCCACAATTCTAGC 58.907 40.000 0.00 0.00 0.00 3.42
2081 2580 4.283212 CCCACAATAAACACCCACAATTCT 59.717 41.667 0.00 0.00 0.00 2.40
2084 2583 2.301583 GCCCACAATAAACACCCACAAT 59.698 45.455 0.00 0.00 0.00 2.71
2220 2719 2.332654 GGAATGTGGTGGCGTGACC 61.333 63.158 0.00 0.00 39.84 4.02
2271 2770 0.038892 GCAAGCACCTGAACACCATG 60.039 55.000 0.00 0.00 0.00 3.66
2334 2833 7.559897 CCCCCAGTCAATAATACAGTAACAATT 59.440 37.037 0.00 0.00 0.00 2.32
2335 2834 7.060421 CCCCCAGTCAATAATACAGTAACAAT 58.940 38.462 0.00 0.00 0.00 2.71
2337 2836 5.727279 TCCCCCAGTCAATAATACAGTAACA 59.273 40.000 0.00 0.00 0.00 2.41
2338 2837 6.243216 TCCCCCAGTCAATAATACAGTAAC 57.757 41.667 0.00 0.00 0.00 2.50
2341 2840 4.446311 GCATCCCCCAGTCAATAATACAGT 60.446 45.833 0.00 0.00 0.00 3.55
2344 2843 4.074970 CAGCATCCCCCAGTCAATAATAC 58.925 47.826 0.00 0.00 0.00 1.89
2347 2846 1.215173 CCAGCATCCCCCAGTCAATAA 59.785 52.381 0.00 0.00 0.00 1.40
2349 2848 0.920763 TCCAGCATCCCCCAGTCAAT 60.921 55.000 0.00 0.00 0.00 2.57
2352 2851 1.140312 TAATCCAGCATCCCCCAGTC 58.860 55.000 0.00 0.00 0.00 3.51
2354 2853 1.889699 GCATAATCCAGCATCCCCCAG 60.890 57.143 0.00 0.00 0.00 4.45
2356 2855 0.112995 TGCATAATCCAGCATCCCCC 59.887 55.000 0.00 0.00 35.51 5.40
2357 2856 1.074405 TCTGCATAATCCAGCATCCCC 59.926 52.381 0.00 0.00 40.42 4.81
2389 2893 2.418628 CGCCGGATCAACAGTAAACAAT 59.581 45.455 5.05 0.00 0.00 2.71
2396 2900 0.828022 TAATCCGCCGGATCAACAGT 59.172 50.000 20.67 4.93 42.27 3.55
2452 2956 0.832135 TCTTCCCAGGCGAAGACAGT 60.832 55.000 13.62 0.00 42.58 3.55
2620 3127 0.318699 TCACAAGCGACAGAACCTCG 60.319 55.000 0.00 0.00 0.00 4.63
2632 3139 2.933906 CCATGCCAATCATTTCACAAGC 59.066 45.455 0.00 0.00 31.79 4.01
2651 3158 2.288702 CCCGATGCAATTCAAACAACCA 60.289 45.455 0.00 0.00 0.00 3.67
2652 3159 2.336667 CCCGATGCAATTCAAACAACC 58.663 47.619 0.00 0.00 0.00 3.77
2653 3160 2.029470 TCCCCGATGCAATTCAAACAAC 60.029 45.455 0.00 0.00 0.00 3.32
2671 3181 8.978874 ATTTTCCTAATTTAATGCCATTTCCC 57.021 30.769 0.00 0.00 0.00 3.97
2707 3217 1.134995 GCAAGGCTTGAAACCCTATGC 60.135 52.381 30.45 8.11 32.42 3.14
2736 3246 4.101430 AGAAGACAATGCCAAAACAATGGT 59.899 37.500 0.00 0.00 42.75 3.55
2829 3339 7.228906 TGAGATACCATTTAACAAACAAACCGA 59.771 33.333 0.00 0.00 0.00 4.69
3028 3539 5.918576 TGTCGTTGATCAGTAACTAACACAG 59.081 40.000 0.00 0.00 0.00 3.66
3030 3541 6.420008 AGTTGTCGTTGATCAGTAACTAACAC 59.580 38.462 0.00 0.00 0.00 3.32
3045 3556 2.135933 GACCTGGAGAAGTTGTCGTTG 58.864 52.381 0.00 0.00 0.00 4.10
3048 3559 0.388649 CGGACCTGGAGAAGTTGTCG 60.389 60.000 0.00 0.00 0.00 4.35
3233 3744 5.462240 TCATGGAGATCTCTGTACCAAGAT 58.538 41.667 21.81 6.77 34.96 2.40
3242 3753 6.462552 TGAACTTACTCATGGAGATCTCTG 57.537 41.667 21.81 13.44 33.32 3.35
3280 3791 7.841956 TCTTGAAAGTAATTTTGACACCCAAA 58.158 30.769 0.00 0.00 42.56 3.28
3282 3793 7.411486 TTCTTGAAAGTAATTTTGACACCCA 57.589 32.000 0.00 0.00 0.00 4.51
3283 3794 8.710835 TTTTCTTGAAAGTAATTTTGACACCC 57.289 30.769 0.00 0.00 0.00 4.61
3312 3823 7.277760 CACATCAAGTCAGTATTACCGATTCAA 59.722 37.037 0.00 0.00 0.00 2.69
3328 3839 4.626042 AGAATAGATCCGCACATCAAGTC 58.374 43.478 0.00 0.00 0.00 3.01
3339 3850 4.065321 AGTTGCCTGAAGAATAGATCCG 57.935 45.455 0.00 0.00 0.00 4.18
3344 3855 6.096141 TCTCTCTGTAGTTGCCTGAAGAATAG 59.904 42.308 0.00 0.00 0.00 1.73
3351 3862 3.834813 ACAATCTCTCTGTAGTTGCCTGA 59.165 43.478 0.00 0.00 0.00 3.86
3361 3872 6.774656 ACTCCAAAAATTCACAATCTCTCTGT 59.225 34.615 0.00 0.00 0.00 3.41
3403 3914 4.591498 TGAACTCCTACCAAGAAGCTGTAA 59.409 41.667 0.00 0.00 0.00 2.41
3430 3941 0.529833 AGGCAGAGACATCGTCACAG 59.470 55.000 0.00 0.00 34.60 3.66
3436 3947 0.735471 TCTTCGAGGCAGAGACATCG 59.265 55.000 0.00 0.00 44.64 3.84
3541 4053 5.565834 GCTCTGCTTAAGGATAATCGCTAGT 60.566 44.000 4.29 0.00 0.00 2.57
3542 4054 4.862018 GCTCTGCTTAAGGATAATCGCTAG 59.138 45.833 4.29 0.00 0.00 3.42
3543 4055 4.524714 AGCTCTGCTTAAGGATAATCGCTA 59.475 41.667 4.29 0.00 33.89 4.26
3670 4182 9.366216 GGTAAGAAACAGTTCAAAAGAAAACAT 57.634 29.630 0.00 0.00 36.09 2.71
3695 4207 9.570488 TTTCAAATGAATTTTGCAAGAAAAAGG 57.430 25.926 0.00 0.00 43.68 3.11
3727 4239 1.693606 ACCCAGGCTTGTTTTGAATGG 59.306 47.619 0.00 0.00 0.00 3.16
3733 4245 2.397597 ACATGAACCCAGGCTTGTTTT 58.602 42.857 0.00 0.00 0.00 2.43
3754 4266 8.974060 TGAGAAAAGTTGGTAGAATTACACTT 57.026 30.769 0.00 0.00 31.16 3.16
3796 4308 7.333423 TCAAAATGAATCGACGAATTACTTCCT 59.667 33.333 0.00 0.00 0.00 3.36
3808 4320 7.393551 ACAACAAATGTCAAAATGAATCGAC 57.606 32.000 0.00 0.00 37.96 4.20
3810 4322 7.110490 GCAAACAACAAATGTCAAAATGAATCG 59.890 33.333 0.00 0.00 42.99 3.34
3816 4361 6.981762 TCAGCAAACAACAAATGTCAAAAT 57.018 29.167 0.00 0.00 42.99 1.82
3820 4365 5.321959 TCTTCAGCAAACAACAAATGTCA 57.678 34.783 0.00 0.00 42.99 3.58
3882 4427 4.757149 GGTTGTTGAAGTTGCACTATCTCT 59.243 41.667 0.00 0.00 0.00 3.10
3883 4428 4.757149 AGGTTGTTGAAGTTGCACTATCTC 59.243 41.667 0.00 0.00 0.00 2.75
3936 4481 5.041191 CACAAGGATGGGCTAGTAAGATT 57.959 43.478 0.00 0.00 0.00 2.40
4019 4564 8.263854 ACAGCTTGTATGAGTTATATAAGGGT 57.736 34.615 11.67 0.00 39.52 4.34
4110 4655 3.186409 CAGATGTGTTAACCAAGTGGACG 59.814 47.826 3.83 0.00 38.94 4.79
4111 4656 4.024048 CACAGATGTGTTAACCAAGTGGAC 60.024 45.833 3.83 0.00 40.96 4.02
4130 4675 0.306533 AACAACGCCTAAACGCACAG 59.693 50.000 0.00 0.00 36.19 3.66
4133 4678 1.649815 CCAACAACGCCTAAACGCA 59.350 52.632 0.00 0.00 36.19 5.24
4134 4679 1.081708 CCCAACAACGCCTAAACGC 60.082 57.895 0.00 0.00 36.19 4.84
4135 4680 0.236449 GACCCAACAACGCCTAAACG 59.764 55.000 0.00 0.00 39.50 3.60
4136 4681 0.594602 GGACCCAACAACGCCTAAAC 59.405 55.000 0.00 0.00 0.00 2.01
4137 4682 0.475044 AGGACCCAACAACGCCTAAA 59.525 50.000 0.00 0.00 0.00 1.85
4138 4683 1.276989 CTAGGACCCAACAACGCCTAA 59.723 52.381 0.00 0.00 31.34 2.69
4139 4684 0.899720 CTAGGACCCAACAACGCCTA 59.100 55.000 0.00 0.00 0.00 3.93
4140 4685 1.677552 CTAGGACCCAACAACGCCT 59.322 57.895 0.00 0.00 0.00 5.52
4141 4686 2.038837 GCTAGGACCCAACAACGCC 61.039 63.158 0.00 0.00 0.00 5.68
4142 4687 1.003718 AGCTAGGACCCAACAACGC 60.004 57.895 0.00 0.00 0.00 4.84
4143 4688 0.034896 ACAGCTAGGACCCAACAACG 59.965 55.000 0.00 0.00 0.00 4.10
4144 4689 2.271944 AACAGCTAGGACCCAACAAC 57.728 50.000 0.00 0.00 0.00 3.32
4222 4767 9.736023 CAGATTAATGGAGTTAACAAATAAGCC 57.264 33.333 8.61 0.00 35.23 4.35
4378 4930 3.961414 TGGTTCGGGGCCAGGAAC 61.961 66.667 23.82 23.82 41.33 3.62
4411 4963 4.900684 TCCCAAAATACAGAATCACGTCA 58.099 39.130 0.00 0.00 0.00 4.35
4429 4981 3.324846 CCTGGAGAATGTCGATTATCCCA 59.675 47.826 9.37 6.99 45.82 4.37
4501 5053 2.427506 GCAGATATCGAATTGGGGTCC 58.572 52.381 0.00 0.00 0.00 4.46
4594 5146 3.198635 TGTTGCATCTTTTGACCCCAAAA 59.801 39.130 0.00 0.00 46.55 2.44
4595 5147 2.768527 TGTTGCATCTTTTGACCCCAAA 59.231 40.909 0.00 0.00 40.24 3.28
4607 5159 3.449737 CCAATGGAATTCCTGTTGCATCT 59.550 43.478 24.73 0.00 38.91 2.90
4608 5160 3.448301 TCCAATGGAATTCCTGTTGCATC 59.552 43.478 24.73 0.00 38.91 3.91
4628 5185 1.587547 GAATCATCCGCTGGACTTCC 58.412 55.000 0.00 0.00 32.98 3.46
4642 5199 1.144093 ACCAAAACCACCTCGGAATCA 59.856 47.619 0.00 0.00 38.63 2.57
4664 5242 5.537674 AGTTCCTTTGACAATGCAGAAGATT 59.462 36.000 0.00 0.00 0.00 2.40
4667 5245 4.320788 GGAGTTCCTTTGACAATGCAGAAG 60.321 45.833 0.00 0.00 0.00 2.85
4705 5283 1.575244 CGGCTGATGATGATCGTTGT 58.425 50.000 0.00 0.00 0.00 3.32
4730 5308 0.456221 ACGAGCTGATGTTACCGGAG 59.544 55.000 9.46 0.00 0.00 4.63
4765 5344 1.649171 CTGATCGAGGTTCGTTCAACG 59.351 52.381 2.64 2.64 44.66 4.10
4789 5368 0.976641 TGCAACATCGTCTCCCTTCT 59.023 50.000 0.00 0.00 0.00 2.85
4802 5382 0.248580 CTGCGACTTGCTTTGCAACA 60.249 50.000 0.00 0.00 43.99 3.33
4820 5400 0.036952 CAGTCCACATTCTGGTCGCT 60.037 55.000 0.00 0.00 41.52 4.93
4860 5445 2.444421 ACTAGTTTCGATCCTCGTGGT 58.556 47.619 2.99 0.00 41.35 4.16
4873 5458 7.883311 ACAAAATGTACAGATGCCTACTAGTTT 59.117 33.333 0.00 0.00 0.00 2.66
4918 5508 4.130118 CTGATATGCTACCAAGGACCAAC 58.870 47.826 0.00 0.00 0.00 3.77
4919 5509 3.780294 ACTGATATGCTACCAAGGACCAA 59.220 43.478 0.00 0.00 0.00 3.67
4920 5510 3.384168 ACTGATATGCTACCAAGGACCA 58.616 45.455 0.00 0.00 0.00 4.02
4921 5511 3.244249 GGACTGATATGCTACCAAGGACC 60.244 52.174 0.00 0.00 0.00 4.46
4922 5512 3.643792 AGGACTGATATGCTACCAAGGAC 59.356 47.826 0.00 0.00 0.00 3.85
4923 5513 3.928754 AGGACTGATATGCTACCAAGGA 58.071 45.455 0.00 0.00 0.00 3.36
4964 5567 5.012893 CCAGCCAAGAAAAGAATCCTAACT 58.987 41.667 0.00 0.00 0.00 2.24
4965 5568 4.767409 ACCAGCCAAGAAAAGAATCCTAAC 59.233 41.667 0.00 0.00 0.00 2.34
5038 5650 8.585018 TCTTTCTGGAAACAAAAATTCCCTATC 58.415 33.333 3.06 0.00 44.72 2.08
5059 5671 4.201920 CGCAGCCTTAAATTACCCTCTTTC 60.202 45.833 0.00 0.00 0.00 2.62
5062 5674 2.421529 CCGCAGCCTTAAATTACCCTCT 60.422 50.000 0.00 0.00 0.00 3.69
5081 5693 3.763097 TTATTCATTCACTGCTTGCCG 57.237 42.857 0.00 0.00 0.00 5.69
5083 5695 6.037940 TCTCTCATTATTCATTCACTGCTTGC 59.962 38.462 0.00 0.00 0.00 4.01
5084 5696 7.494952 TCTCTCTCATTATTCATTCACTGCTTG 59.505 37.037 0.00 0.00 0.00 4.01
5085 5697 7.563020 TCTCTCTCATTATTCATTCACTGCTT 58.437 34.615 0.00 0.00 0.00 3.91
5087 5699 7.656542 TGATCTCTCTCATTATTCATTCACTGC 59.343 37.037 0.00 0.00 0.00 4.40
5088 5700 9.713713 ATGATCTCTCTCATTATTCATTCACTG 57.286 33.333 0.00 0.00 31.82 3.66
5089 5701 9.713713 CATGATCTCTCTCATTATTCATTCACT 57.286 33.333 0.00 0.00 33.59 3.41
5090 5702 9.491675 ACATGATCTCTCTCATTATTCATTCAC 57.508 33.333 0.00 0.00 33.59 3.18
5095 5707 9.359653 TCTGTACATGATCTCTCTCATTATTCA 57.640 33.333 0.00 0.00 33.59 2.57
5181 6007 0.336737 GAGTGAGGGAGAGGGGAAGA 59.663 60.000 0.00 0.00 0.00 2.87
5182 6008 0.338120 AGAGTGAGGGAGAGGGGAAG 59.662 60.000 0.00 0.00 0.00 3.46
5184 6010 0.553862 AGAGAGTGAGGGAGAGGGGA 60.554 60.000 0.00 0.00 0.00 4.81
5186 6012 2.235898 CAAAAGAGAGTGAGGGAGAGGG 59.764 54.545 0.00 0.00 0.00 4.30
5188 6014 2.673610 CGCAAAAGAGAGTGAGGGAGAG 60.674 54.545 0.00 0.00 0.00 3.20
5191 6017 1.000955 GACGCAAAAGAGAGTGAGGGA 59.999 52.381 0.00 0.00 0.00 4.20
5193 6019 1.063806 CGACGCAAAAGAGAGTGAGG 58.936 55.000 0.00 0.00 0.00 3.86
5194 6020 1.772182 ACGACGCAAAAGAGAGTGAG 58.228 50.000 0.00 0.00 0.00 3.51
5195 6021 1.858458 CAACGACGCAAAAGAGAGTGA 59.142 47.619 0.00 0.00 0.00 3.41
5196 6022 1.070577 CCAACGACGCAAAAGAGAGTG 60.071 52.381 0.00 0.00 0.00 3.51
5197 6023 1.217882 CCAACGACGCAAAAGAGAGT 58.782 50.000 0.00 0.00 0.00 3.24
5229 6074 2.536066 GGAGGGGCCAATAAAAACTGT 58.464 47.619 4.39 0.00 36.34 3.55
5234 6079 0.323908 CGTGGGAGGGGCCAATAAAA 60.324 55.000 4.39 0.00 38.95 1.52
5249 6102 1.133025 CCTGCAAAAAGCTATCCGTGG 59.867 52.381 0.00 0.00 45.94 4.94
5250 6103 1.468054 GCCTGCAAAAAGCTATCCGTG 60.468 52.381 0.00 0.00 45.94 4.94
5251 6104 0.811281 GCCTGCAAAAAGCTATCCGT 59.189 50.000 0.00 0.00 45.94 4.69
5252 6105 0.101219 GGCCTGCAAAAAGCTATCCG 59.899 55.000 0.00 0.00 45.94 4.18
5308 6161 1.204113 AGCAGGTCAAGGAAGGAGGG 61.204 60.000 0.00 0.00 0.00 4.30
5309 6162 0.035630 CAGCAGGTCAAGGAAGGAGG 60.036 60.000 0.00 0.00 0.00 4.30
5372 6234 4.202567 ACTTCCAACACTCTCTCTCTCTCT 60.203 45.833 0.00 0.00 0.00 3.10
5373 6235 4.079253 ACTTCCAACACTCTCTCTCTCTC 58.921 47.826 0.00 0.00 0.00 3.20
5374 6236 3.826157 CACTTCCAACACTCTCTCTCTCT 59.174 47.826 0.00 0.00 0.00 3.10
5375 6237 3.056891 CCACTTCCAACACTCTCTCTCTC 60.057 52.174 0.00 0.00 0.00 3.20
5376 6238 2.896685 CCACTTCCAACACTCTCTCTCT 59.103 50.000 0.00 0.00 0.00 3.10
5377 6239 2.028567 CCCACTTCCAACACTCTCTCTC 60.029 54.545 0.00 0.00 0.00 3.20
5378 6240 1.974236 CCCACTTCCAACACTCTCTCT 59.026 52.381 0.00 0.00 0.00 3.10
5379 6241 1.002544 CCCCACTTCCAACACTCTCTC 59.997 57.143 0.00 0.00 0.00 3.20
5380 6242 1.059913 CCCCACTTCCAACACTCTCT 58.940 55.000 0.00 0.00 0.00 3.10
5381 6243 1.056660 TCCCCACTTCCAACACTCTC 58.943 55.000 0.00 0.00 0.00 3.20
5382 6244 1.518367 TTCCCCACTTCCAACACTCT 58.482 50.000 0.00 0.00 0.00 3.24
5472 6340 1.205417 TCACCGTTCCGATCTTAACCC 59.795 52.381 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.