Multiple sequence alignment - TraesCS5A01G416800

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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 TraesCS5A01G416800 chr5A 100.000 5274 0 0 1 5274 605226450 605231723 0.000000e+00 9740
1 TraesCS5A01G416800 chr5B 94.174 3965 181 29 1 3935 594915938 594919882 0.000000e+00 5997
2 TraesCS5A01G416800 chr5B 88.874 764 39 19 3936 4695 594919940 594920661 0.000000e+00 898
3 TraesCS5A01G416800 chr5B 85.294 442 41 8 4854 5274 594920660 594921098 8.110000e-118 435
4 TraesCS5A01G416800 chr5D 94.613 3694 142 33 275 3935 483711190 483714859 0.000000e+00 5666
5 TraesCS5A01G416800 chr5D 93.717 764 36 7 3936 4695 483714947 483715702 0.000000e+00 1134
6 TraesCS5A01G416800 chr5D 89.535 430 33 5 4854 5274 483715701 483716127 7.770000e-148 534
7 TraesCS5A01G416800 chr5D 94.937 237 11 1 1 236 483710952 483711188 2.320000e-98 370
8 TraesCS5A01G416800 chr3D 96.386 166 4 2 4694 4859 104025907 104026070 6.730000e-69 272
9 TraesCS5A01G416800 chr3D 96.364 165 6 0 4694 4858 449740282 449740446 6.730000e-69 272
10 TraesCS5A01G416800 chr1D 95.833 168 5 2 4694 4860 30100583 30100417 2.420000e-68 270
11 TraesCS5A01G416800 chr3B 95.783 166 7 0 4694 4859 154663044 154663209 8.710000e-68 268
12 TraesCS5A01G416800 chr3A 94.737 171 9 0 4686 4856 600920847 600921017 3.130000e-67 267
13 TraesCS5A01G416800 chr7A 93.370 181 9 2 4677 4855 494786811 494786990 1.130000e-66 265
14 TraesCS5A01G416800 chr4D 93.714 175 11 0 4688 4862 117421358 117421184 4.050000e-66 263
15 TraesCS5A01G416800 chr2A 93.678 174 10 1 4683 4855 703708436 703708263 5.240000e-65 259
16 TraesCS5A01G416800 chr4B 90.476 189 14 3 4684 4872 532435171 532434987 4.080000e-61 246


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 TraesCS5A01G416800 chr5A 605226450 605231723 5273 False 9740.000000 9740 100.000000 1 5274 1 chr5A.!!$F1 5273
1 TraesCS5A01G416800 chr5B 594915938 594921098 5160 False 2443.333333 5997 89.447333 1 5274 3 chr5B.!!$F1 5273
2 TraesCS5A01G416800 chr5D 483710952 483716127 5175 False 1926.000000 5666 93.200500 1 5274 4 chr5D.!!$F1 5273

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
388 394 0.320771 CAGTCCTACAGGCACGCTTT 60.321 55.0 0.00 0.0 34.44 3.51 F
1258 1292 0.102300 CATCGGCATGTACGTCCTGA 59.898 55.0 10.83 0.0 0.00 3.86 F
1906 1940 0.107508 CTTGGATGATGCGTGGAGGT 60.108 55.0 0.00 0.0 0.00 3.85 F
1923 1957 0.240945 GGTTGTTTGACCTGATGCCG 59.759 55.0 0.00 0.0 36.73 5.69 F
3177 3211 1.075601 TTTGGGGTGCTCTTCTCCAT 58.924 50.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 1957 0.392060 AGGTTACCAAATCGTCCCGC 60.392 55.000 3.51 0.0 0.00 6.13 R
2310 2344 0.690762 TGCCCACTTCCAAGAGGTAC 59.309 55.000 2.58 0.0 35.31 3.34 R
3846 3894 0.168788 CGCATTTCGGTGCATGTTCT 59.831 50.000 0.00 0.0 45.30 3.01 R
3879 3927 5.319453 TGGTTCTTAGTTCTTCGACTCCTA 58.681 41.667 0.00 0.0 0.00 2.94 R
4840 5010 0.460722 GCTTCTACTCCCTCCGTTCC 59.539 60.000 0.00 0.0 0.00 3.62 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
102 103 3.056107 GGCCTTCCCATTTTCAACCTAAC 60.056 47.826 0.00 0.00 0.00 2.34
146 151 9.216087 TCACATTTTGTTATTGCGATAAATACG 57.784 29.630 8.01 0.00 29.89 3.06
211 217 3.004002 TGAAGCAGTCATTGTTGCAAGAG 59.996 43.478 0.00 0.00 42.67 2.85
363 369 3.985279 CACTTCAAATGCAGTGACATTGG 59.015 43.478 7.32 9.76 40.87 3.16
379 385 1.568504 TTGGCCCTACAGTCCTACAG 58.431 55.000 0.00 0.00 0.00 2.74
388 394 0.320771 CAGTCCTACAGGCACGCTTT 60.321 55.000 0.00 0.00 34.44 3.51
391 397 3.028850 AGTCCTACAGGCACGCTTTATA 58.971 45.455 0.00 0.00 34.44 0.98
424 430 2.166459 CCAGTGCACGAATAGAAGGAGA 59.834 50.000 12.01 0.00 0.00 3.71
519 539 0.394938 TTCAAGCAGCGGGTTCTGTA 59.605 50.000 0.00 0.00 36.49 2.74
524 544 0.673644 GCAGCGGGTTCTGTATGTGT 60.674 55.000 0.00 0.00 36.49 3.72
848 871 2.124942 GAAGCAGGCGGGAAGAGG 60.125 66.667 0.00 0.00 0.00 3.69
849 872 4.416738 AAGCAGGCGGGAAGAGGC 62.417 66.667 0.00 0.00 0.00 4.70
877 902 2.677979 CGGCGAGAGACACACGAGA 61.678 63.158 0.00 0.00 41.50 4.04
901 926 2.911819 AGCGCGAGATAGAATAGAGC 57.088 50.000 12.10 0.00 0.00 4.09
907 932 5.090652 GCGAGATAGAATAGAGCGATAGG 57.909 47.826 0.00 0.00 0.00 2.57
908 933 4.812091 GCGAGATAGAATAGAGCGATAGGA 59.188 45.833 0.00 0.00 0.00 2.94
909 934 5.277154 GCGAGATAGAATAGAGCGATAGGAC 60.277 48.000 0.00 0.00 0.00 3.85
937 966 1.862806 GGCACGTGAGAGTTGAAGC 59.137 57.895 22.23 0.00 0.00 3.86
954 983 1.433471 GCCCATAGCGCACTTTTCC 59.567 57.895 11.47 0.00 0.00 3.13
956 985 1.024579 CCCATAGCGCACTTTTCCGT 61.025 55.000 11.47 0.00 0.00 4.69
958 987 1.359848 CATAGCGCACTTTTCCGTCT 58.640 50.000 11.47 0.00 0.00 4.18
959 988 1.324736 CATAGCGCACTTTTCCGTCTC 59.675 52.381 11.47 0.00 0.00 3.36
960 989 0.731514 TAGCGCACTTTTCCGTCTCG 60.732 55.000 11.47 0.00 0.00 4.04
961 990 2.308039 GCGCACTTTTCCGTCTCGT 61.308 57.895 0.30 0.00 0.00 4.18
962 991 1.828331 GCGCACTTTTCCGTCTCGTT 61.828 55.000 0.30 0.00 0.00 3.85
976 1005 1.271656 TCTCGTTTCGTTTCCCTCCTC 59.728 52.381 0.00 0.00 0.00 3.71
979 1008 1.373748 TTTCGTTTCCCTCCTCGCG 60.374 57.895 0.00 0.00 0.00 5.87
982 1014 2.506438 GTTTCCCTCCTCGCGTCG 60.506 66.667 5.77 0.00 0.00 5.12
983 1015 4.430765 TTTCCCTCCTCGCGTCGC 62.431 66.667 7.29 7.29 0.00 5.19
1258 1292 0.102300 CATCGGCATGTACGTCCTGA 59.898 55.000 10.83 0.00 0.00 3.86
1407 1441 0.172578 TCTACGTCAAGATGTGGGCG 59.827 55.000 5.22 0.00 34.00 6.13
1791 1825 1.271982 ACGGAGGCTGACTTACTCTCA 60.272 52.381 0.00 0.00 0.00 3.27
1795 1829 0.827368 GGCTGACTTACTCTCAGGGG 59.173 60.000 0.00 0.00 36.43 4.79
1906 1940 0.107508 CTTGGATGATGCGTGGAGGT 60.108 55.000 0.00 0.00 0.00 3.85
1923 1957 0.240945 GGTTGTTTGACCTGATGCCG 59.759 55.000 0.00 0.00 36.73 5.69
2052 2086 2.875672 GCCTGATTCAGTTACACTGGCA 60.876 50.000 12.54 0.00 45.94 4.92
2250 2284 4.703897 CCATCGATGTGGTTATTGGTAGT 58.296 43.478 23.27 0.00 34.46 2.73
2310 2344 1.685302 CGGCAGTGAAAATGTTTCGG 58.315 50.000 0.00 0.00 32.28 4.30
2605 2639 3.244387 GGAACCTGAAGAAGCTCTTGAGT 60.244 47.826 9.97 1.45 36.22 3.41
2724 2758 5.373555 TGGAAAGGAGATCCATGGTATCATT 59.626 40.000 12.58 9.37 41.98 2.57
3177 3211 1.075601 TTTGGGGTGCTCTTCTCCAT 58.924 50.000 0.00 0.00 0.00 3.41
3339 3373 8.517878 TCAAAAATGAGAAGATTGATGAAGGAC 58.482 33.333 0.00 0.00 0.00 3.85
3429 3463 1.915141 CAGACAAAAGCCACCCTGAT 58.085 50.000 0.00 0.00 0.00 2.90
3486 3520 9.780413 CTTCTTCTAGAATTAAAACATGAAGGC 57.220 33.333 5.44 0.00 33.13 4.35
3681 3715 7.926018 ACAAAAATGAACTATTTGGACAAGGTC 59.074 33.333 0.00 0.00 38.93 3.85
3714 3748 4.080413 TGCTGATCCATCCATGTCAAACTA 60.080 41.667 0.00 0.00 0.00 2.24
3715 3749 4.883585 GCTGATCCATCCATGTCAAACTAA 59.116 41.667 0.00 0.00 0.00 2.24
3724 3758 7.414873 CCATCCATGTCAAACTAAATGAGACAG 60.415 40.741 0.00 0.00 41.85 3.51
3753 3788 7.816995 GGAATCAGGATCAGTATACTGTCATTC 59.183 40.741 27.83 23.42 43.65 2.67
3809 3856 8.377034 TCCTTTAACATAGTTTGCAGGTTAGTA 58.623 33.333 0.00 0.00 0.00 1.82
3858 3906 3.849911 TCTTCTTCTAGAACATGCACCG 58.150 45.455 0.00 0.00 29.89 4.94
3911 3964 3.071167 AGAACTAAGAACCAAAGCCGACT 59.929 43.478 0.00 0.00 0.00 4.18
3986 4125 3.058224 AGTCGTTTAGTGATTTGCTTGCC 60.058 43.478 0.00 0.00 0.00 4.52
4024 4163 2.638480 TGTTGCTGTAGAAGGCAAGT 57.362 45.000 0.48 0.00 46.87 3.16
4046 4185 1.087501 GGGCGATTTGGAAGACTGTC 58.912 55.000 0.00 0.00 0.00 3.51
4063 4202 3.073062 ACTGTCCCATGCAGTTAGTTCTT 59.927 43.478 0.00 0.00 43.87 2.52
4074 4213 6.112734 TGCAGTTAGTTCTTTTGTCTTCTCA 58.887 36.000 0.00 0.00 0.00 3.27
4152 4291 5.887598 TGATTGTGATTTATCCCAGTGGAAG 59.112 40.000 11.95 0.00 45.98 3.46
4153 4292 4.927267 TGTGATTTATCCCAGTGGAAGT 57.073 40.909 11.95 0.00 45.98 3.01
4154 4293 5.255397 TGTGATTTATCCCAGTGGAAGTT 57.745 39.130 11.95 0.00 45.98 2.66
4155 4294 6.381498 TGTGATTTATCCCAGTGGAAGTTA 57.619 37.500 11.95 0.00 45.98 2.24
4185 4325 9.213799 GATATTCTGATGGTGATAAAGGAGAAC 57.786 37.037 0.00 0.00 0.00 3.01
4331 4472 6.985188 ATTCGTAATGCAGTAAGAACACAT 57.015 33.333 21.55 6.33 0.00 3.21
4366 4507 8.766151 TGTTTTGTTTGTTTTCTGGTTAACTTC 58.234 29.630 5.42 0.00 0.00 3.01
4490 4660 3.936453 CACAGAAATTCAAATGGCCATGG 59.064 43.478 21.63 15.23 0.00 3.66
4491 4661 3.839490 ACAGAAATTCAAATGGCCATGGA 59.161 39.130 21.63 17.49 0.00 3.41
4492 4662 4.286549 ACAGAAATTCAAATGGCCATGGAA 59.713 37.500 26.44 26.44 0.00 3.53
4493 4663 5.045432 ACAGAAATTCAAATGGCCATGGAAT 60.045 36.000 27.87 27.87 31.25 3.01
4494 4664 5.295787 CAGAAATTCAAATGGCCATGGAATG 59.704 40.000 31.29 22.23 46.21 2.67
4495 4665 4.847990 AATTCAAATGGCCATGGAATGT 57.152 36.364 31.29 22.52 44.81 2.71
4496 4666 3.613494 TTCAAATGGCCATGGAATGTG 57.387 42.857 21.63 13.45 44.81 3.21
4497 4667 2.538222 TCAAATGGCCATGGAATGTGT 58.462 42.857 21.63 0.00 44.81 3.72
4498 4668 2.496871 TCAAATGGCCATGGAATGTGTC 59.503 45.455 21.63 0.00 44.81 3.67
4499 4669 2.234168 CAAATGGCCATGGAATGTGTCA 59.766 45.455 21.63 0.00 44.81 3.58
4500 4670 1.771565 ATGGCCATGGAATGTGTCAG 58.228 50.000 20.04 0.00 44.81 3.51
4501 4671 0.323633 TGGCCATGGAATGTGTCAGG 60.324 55.000 18.40 0.00 44.81 3.86
4502 4672 0.323725 GGCCATGGAATGTGTCAGGT 60.324 55.000 18.40 0.00 44.81 4.00
4503 4673 1.098050 GCCATGGAATGTGTCAGGTC 58.902 55.000 18.40 0.00 44.81 3.85
4504 4674 1.755179 CCATGGAATGTGTCAGGTCC 58.245 55.000 5.56 0.00 44.81 4.46
4505 4675 1.004628 CCATGGAATGTGTCAGGTCCA 59.995 52.381 5.56 7.19 44.81 4.02
4507 4677 2.787473 TGGAATGTGTCAGGTCCATC 57.213 50.000 0.00 0.00 35.22 3.51
4508 4678 2.269023 TGGAATGTGTCAGGTCCATCT 58.731 47.619 0.00 0.00 35.22 2.90
4509 4679 2.644299 TGGAATGTGTCAGGTCCATCTT 59.356 45.455 0.00 0.00 35.22 2.40
4510 4680 3.012518 GGAATGTGTCAGGTCCATCTTG 58.987 50.000 0.00 0.00 0.00 3.02
4511 4681 2.795231 ATGTGTCAGGTCCATCTTGG 57.205 50.000 0.00 0.00 39.43 3.61
4512 4682 1.434188 TGTGTCAGGTCCATCTTGGT 58.566 50.000 0.00 0.00 39.03 3.67
4513 4683 1.347707 TGTGTCAGGTCCATCTTGGTC 59.652 52.381 0.00 0.00 39.03 4.02
4514 4684 1.347707 GTGTCAGGTCCATCTTGGTCA 59.652 52.381 0.00 0.00 39.03 4.02
4515 4685 2.026822 GTGTCAGGTCCATCTTGGTCAT 60.027 50.000 0.00 0.00 39.03 3.06
4516 4686 2.026915 TGTCAGGTCCATCTTGGTCATG 60.027 50.000 0.00 0.08 38.39 3.07
4521 4691 3.392616 AGGTCCATCTTGGTCATGTATCC 59.607 47.826 0.00 0.00 39.03 2.59
4542 4712 0.102481 CTGTACATAGGCGCGGTCTT 59.898 55.000 8.83 0.00 0.00 3.01
4547 4717 1.411246 ACATAGGCGCGGTCTTATCAA 59.589 47.619 8.83 0.00 0.00 2.57
4555 4725 3.732943 CGCGGTCTTATCAACAAAGTTC 58.267 45.455 0.00 0.00 0.00 3.01
4573 4743 7.968405 ACAAAGTTCATATAATTCTTTGACGGC 59.032 33.333 18.37 0.00 44.04 5.68
4605 4775 6.149973 TCTCAATGCTGACAGTTTATTCCTTG 59.850 38.462 3.99 0.00 0.00 3.61
4645 4815 5.391312 CAAGCTAACTTGTATGGCCTTTT 57.609 39.130 3.32 0.00 46.84 2.27
4656 4826 2.341846 TGGCCTTTTCGTCTTGAACT 57.658 45.000 3.32 0.00 35.97 3.01
4663 4833 4.260784 CCTTTTCGTCTTGAACTTGGACAG 60.261 45.833 0.00 0.00 35.97 3.51
4680 4850 7.394359 ACTTGGACAGCATTATTCTATTTGTGT 59.606 33.333 0.00 0.00 0.00 3.72
4693 4863 7.701539 TTCTATTTGTGTGCCATAATGTTCT 57.298 32.000 0.00 0.00 0.00 3.01
4694 4864 8.800370 TTCTATTTGTGTGCCATAATGTTCTA 57.200 30.769 0.00 0.00 0.00 2.10
4695 4865 8.208718 TCTATTTGTGTGCCATAATGTTCTAC 57.791 34.615 0.00 0.00 0.00 2.59
4696 4866 8.046708 TCTATTTGTGTGCCATAATGTTCTACT 58.953 33.333 0.00 0.00 0.00 2.57
4697 4867 6.494893 TTTGTGTGCCATAATGTTCTACTC 57.505 37.500 0.00 0.00 0.00 2.59
4698 4868 4.513442 TGTGTGCCATAATGTTCTACTCC 58.487 43.478 0.00 0.00 0.00 3.85
4699 4869 3.877508 GTGTGCCATAATGTTCTACTCCC 59.122 47.826 0.00 0.00 0.00 4.30
4700 4870 3.780294 TGTGCCATAATGTTCTACTCCCT 59.220 43.478 0.00 0.00 0.00 4.20
4701 4871 4.141711 TGTGCCATAATGTTCTACTCCCTC 60.142 45.833 0.00 0.00 0.00 4.30
4702 4872 4.101741 GTGCCATAATGTTCTACTCCCTCT 59.898 45.833 0.00 0.00 0.00 3.69
4703 4873 4.101585 TGCCATAATGTTCTACTCCCTCTG 59.898 45.833 0.00 0.00 0.00 3.35
4704 4874 4.101741 GCCATAATGTTCTACTCCCTCTGT 59.898 45.833 0.00 0.00 0.00 3.41
4705 4875 5.396884 GCCATAATGTTCTACTCCCTCTGTT 60.397 44.000 0.00 0.00 0.00 3.16
4706 4876 6.284459 CCATAATGTTCTACTCCCTCTGTTC 58.716 44.000 0.00 0.00 0.00 3.18
4707 4877 4.828072 AATGTTCTACTCCCTCTGTTCC 57.172 45.455 0.00 0.00 0.00 3.62
4708 4878 3.544698 TGTTCTACTCCCTCTGTTCCT 57.455 47.619 0.00 0.00 0.00 3.36
4709 4879 4.669866 TGTTCTACTCCCTCTGTTCCTA 57.330 45.455 0.00 0.00 0.00 2.94
4710 4880 5.006896 TGTTCTACTCCCTCTGTTCCTAA 57.993 43.478 0.00 0.00 0.00 2.69
4711 4881 5.399991 TGTTCTACTCCCTCTGTTCCTAAA 58.600 41.667 0.00 0.00 0.00 1.85
4712 4882 6.023603 TGTTCTACTCCCTCTGTTCCTAAAT 58.976 40.000 0.00 0.00 0.00 1.40
4713 4883 7.186972 TGTTCTACTCCCTCTGTTCCTAAATA 58.813 38.462 0.00 0.00 0.00 1.40
4714 4884 7.844779 TGTTCTACTCCCTCTGTTCCTAAATAT 59.155 37.037 0.00 0.00 0.00 1.28
4715 4885 9.364653 GTTCTACTCCCTCTGTTCCTAAATATA 57.635 37.037 0.00 0.00 0.00 0.86
4716 4886 9.947189 TTCTACTCCCTCTGTTCCTAAATATAA 57.053 33.333 0.00 0.00 0.00 0.98
4717 4887 9.589461 TCTACTCCCTCTGTTCCTAAATATAAG 57.411 37.037 0.00 0.00 0.00 1.73
4718 4888 9.369672 CTACTCCCTCTGTTCCTAAATATAAGT 57.630 37.037 0.00 0.00 0.00 2.24
4719 4889 8.252624 ACTCCCTCTGTTCCTAAATATAAGTC 57.747 38.462 0.00 0.00 0.00 3.01
4720 4890 8.068733 ACTCCCTCTGTTCCTAAATATAAGTCT 58.931 37.037 0.00 0.00 0.00 3.24
4721 4891 8.855804 TCCCTCTGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
4722 4892 9.280456 TCCCTCTGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
4723 4893 9.907229 CCCTCTGTTCCTAAATATAAGTCTTTT 57.093 33.333 0.00 0.00 0.00 2.27
4751 4921 9.698309 AGAGATTTGAATATGAACTACATACGG 57.302 33.333 0.00 0.00 43.12 4.02
4752 4922 9.692749 GAGATTTGAATATGAACTACATACGGA 57.307 33.333 0.00 0.00 43.12 4.69
4755 4925 9.996554 ATTTGAATATGAACTACATACGGATGA 57.003 29.630 16.36 0.00 43.12 2.92
4756 4926 9.825109 TTTGAATATGAACTACATACGGATGAA 57.175 29.630 16.36 0.00 43.12 2.57
4757 4927 9.996554 TTGAATATGAACTACATACGGATGAAT 57.003 29.630 16.36 0.00 43.12 2.57
4764 4934 8.448615 TGAACTACATACGGATGAATATAGACG 58.551 37.037 16.36 0.00 36.48 4.18
4765 4935 7.918536 ACTACATACGGATGAATATAGACGT 57.081 36.000 16.36 0.00 36.48 4.34
4766 4936 9.440773 AACTACATACGGATGAATATAGACGTA 57.559 33.333 16.36 0.00 40.43 3.57
4767 4937 9.610705 ACTACATACGGATGAATATAGACGTAT 57.389 33.333 16.36 0.00 45.07 3.06
4797 4967 6.681777 AGTGTAAATTCACTCATTTTGCTCC 58.318 36.000 0.00 0.00 44.07 4.70
4798 4968 5.569059 GTGTAAATTCACTCATTTTGCTCCG 59.431 40.000 0.00 0.00 35.68 4.63
4799 4969 4.853924 AAATTCACTCATTTTGCTCCGT 57.146 36.364 0.00 0.00 0.00 4.69
4800 4970 5.957842 AAATTCACTCATTTTGCTCCGTA 57.042 34.783 0.00 0.00 0.00 4.02
4801 4971 6.515272 AAATTCACTCATTTTGCTCCGTAT 57.485 33.333 0.00 0.00 0.00 3.06
4802 4972 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4803 4973 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4804 4974 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
4805 4975 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
4806 4976 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
4807 4977 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
4808 4978 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
4809 4979 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
4810 4980 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
4811 4981 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
4812 4982 5.801531 TTTGCTCCGTATGTAGTCCATAT 57.198 39.130 0.00 0.00 38.29 1.78
4813 4983 5.801531 TTGCTCCGTATGTAGTCCATATT 57.198 39.130 0.00 0.00 38.29 1.28
4814 4984 6.904463 TTGCTCCGTATGTAGTCCATATTA 57.096 37.500 0.00 0.00 38.29 0.98
4815 4985 6.510879 TGCTCCGTATGTAGTCCATATTAG 57.489 41.667 0.00 0.00 38.29 1.73
4816 4986 6.243148 TGCTCCGTATGTAGTCCATATTAGA 58.757 40.000 0.00 0.00 38.29 2.10
4817 4987 6.717997 TGCTCCGTATGTAGTCCATATTAGAA 59.282 38.462 0.00 0.00 38.29 2.10
4818 4988 7.396339 TGCTCCGTATGTAGTCCATATTAGAAT 59.604 37.037 0.00 0.00 38.29 2.40
4819 4989 7.916450 GCTCCGTATGTAGTCCATATTAGAATC 59.084 40.741 0.00 0.00 38.29 2.52
4820 4990 9.179909 CTCCGTATGTAGTCCATATTAGAATCT 57.820 37.037 0.00 0.00 38.29 2.40
4821 4991 9.175312 TCCGTATGTAGTCCATATTAGAATCTC 57.825 37.037 0.00 0.00 38.29 2.75
4822 4992 9.179909 CCGTATGTAGTCCATATTAGAATCTCT 57.820 37.037 0.00 0.00 38.29 3.10
4849 5019 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
4850 5020 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
4851 5021 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
4852 5022 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
4891 5062 8.027189 GTGTAATTTCTTGGAAAGTTATGTCCC 58.973 37.037 0.00 0.00 46.34 4.46
4916 5087 7.096477 CCGTGAAAAGAAAATCTAAAAGTGCTG 60.096 37.037 0.00 0.00 0.00 4.41
4986 5157 9.883142 AAGTTAATCATTTTTGTCCAGTGAAAA 57.117 25.926 0.00 0.00 0.00 2.29
5015 5198 9.965902 ATATCTAATTCTGTTGGTTCTGAGTTT 57.034 29.630 0.00 0.00 0.00 2.66
5020 5203 2.936498 CTGTTGGTTCTGAGTTTCGTGT 59.064 45.455 0.00 0.00 0.00 4.49
5037 5220 2.417719 GTGTTTCTGCCCTCTACACAG 58.582 52.381 0.00 0.00 39.05 3.66
5075 5258 2.717639 AGCCTAGTTATGCAGGTTGG 57.282 50.000 0.00 0.00 34.18 3.77
5123 5313 5.970612 CACGTGAGATTCAACATTTTCACAA 59.029 36.000 10.90 0.00 35.80 3.33
5129 5319 6.211515 AGATTCAACATTTTCACAACAGCTC 58.788 36.000 0.00 0.00 0.00 4.09
5131 5321 3.625313 TCAACATTTTCACAACAGCTCGA 59.375 39.130 0.00 0.00 0.00 4.04
5149 5339 4.728882 GCTCGACATGCTTATGAAACAAGG 60.729 45.833 0.00 0.00 0.00 3.61
5155 5345 5.068987 ACATGCTTATGAAACAAGGTTGTGT 59.931 36.000 0.00 0.00 41.31 3.72
5184 5374 6.038825 ACAACAAGGTTAACGATGAAATGTGA 59.961 34.615 14.11 0.00 0.00 3.58
5186 5376 4.946784 AGGTTAACGATGAAATGTGAGC 57.053 40.909 0.00 0.00 0.00 4.26
5212 5402 4.092529 CCTGTTGAGTCAGTCGATCATTTG 59.907 45.833 0.00 0.00 34.02 2.32
5221 5411 5.578336 GTCAGTCGATCATTTGAACTGATCA 59.422 40.000 20.65 8.98 46.08 2.92
5222 5412 5.578336 TCAGTCGATCATTTGAACTGATCAC 59.422 40.000 20.65 17.10 46.08 3.06
5223 5413 5.579904 CAGTCGATCATTTGAACTGATCACT 59.420 40.000 20.65 18.47 46.08 3.41
5258 5448 3.198872 GTTTCTCCCTACTGCTATGTGC 58.801 50.000 0.00 0.00 43.25 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 3.248363 TGTGAGTTCGTTTCTCAATGCTG 59.752 43.478 8.05 0.00 42.42 4.41
159 164 5.009110 TGGTTTCTATGTTTCGCAATGTGAA 59.991 36.000 4.98 4.98 0.00 3.18
276 282 9.482627 GTTGAAATGGTTAATATGTTTGGAACA 57.517 29.630 0.00 0.00 46.94 3.18
363 369 0.976073 TGCCTGTAGGACTGTAGGGC 60.976 60.000 1.17 0.00 37.39 5.19
379 385 7.011669 TGGTTTTTCTAGTATATAAAGCGTGCC 59.988 37.037 0.00 0.00 0.00 5.01
388 394 7.774134 TCGTGCACTGGTTTTTCTAGTATATA 58.226 34.615 16.19 0.00 35.70 0.86
391 397 4.890088 TCGTGCACTGGTTTTTCTAGTAT 58.110 39.130 16.19 0.00 35.70 2.12
519 539 6.707440 TTGTAAGTCACCAATTGAACACAT 57.293 33.333 7.12 0.00 35.39 3.21
524 544 4.320861 CGCCATTGTAAGTCACCAATTGAA 60.321 41.667 7.12 0.00 35.39 2.69
829 852 4.760047 TCTTCCCGCCTGCTTCGC 62.760 66.667 0.00 0.00 0.00 4.70
830 853 2.510238 CTCTTCCCGCCTGCTTCG 60.510 66.667 0.00 0.00 0.00 3.79
831 854 2.124942 CCTCTTCCCGCCTGCTTC 60.125 66.667 0.00 0.00 0.00 3.86
832 855 4.416738 GCCTCTTCCCGCCTGCTT 62.417 66.667 0.00 0.00 0.00 3.91
842 865 2.104530 GTACGCCTCCGCCTCTTC 59.895 66.667 0.00 0.00 38.22 2.87
843 866 3.823330 CGTACGCCTCCGCCTCTT 61.823 66.667 0.52 0.00 38.22 2.85
853 876 3.807538 TGTCTCTCGCCGTACGCC 61.808 66.667 10.49 0.00 43.23 5.68
877 902 4.823157 TCTATTCTATCTCGCGCTAGTCT 58.177 43.478 8.95 0.81 0.00 3.24
896 921 1.134310 TCACGTGGTCCTATCGCTCTA 60.134 52.381 17.00 0.00 0.00 2.43
897 922 0.393944 TCACGTGGTCCTATCGCTCT 60.394 55.000 17.00 0.00 0.00 4.09
898 923 0.029567 CTCACGTGGTCCTATCGCTC 59.970 60.000 17.00 0.00 0.00 5.03
899 924 2.005960 GCTCACGTGGTCCTATCGCT 62.006 60.000 17.00 0.00 0.00 4.93
900 925 1.589196 GCTCACGTGGTCCTATCGC 60.589 63.158 17.00 2.40 0.00 4.58
901 926 1.298413 CGCTCACGTGGTCCTATCG 60.298 63.158 17.00 0.00 33.53 2.92
902 927 1.065928 CCGCTCACGTGGTCCTATC 59.934 63.158 17.00 0.00 37.70 2.08
904 929 3.755628 GCCGCTCACGTGGTCCTA 61.756 66.667 17.00 0.00 42.91 2.94
933 962 0.811281 AAAAGTGCGCTATGGGCTTC 59.189 50.000 9.73 2.26 42.10 3.86
937 966 1.024579 ACGGAAAAGTGCGCTATGGG 61.025 55.000 9.73 0.00 43.33 4.00
945 974 1.396815 CGAAACGAGACGGAAAAGTGC 60.397 52.381 0.00 0.00 0.00 4.40
948 977 3.529085 GAAACGAAACGAGACGGAAAAG 58.471 45.455 0.00 0.00 0.00 2.27
954 983 1.058404 GAGGGAAACGAAACGAGACG 58.942 55.000 0.00 0.00 0.00 4.18
956 985 1.271656 GAGGAGGGAAACGAAACGAGA 59.728 52.381 0.00 0.00 0.00 4.04
958 987 0.038892 CGAGGAGGGAAACGAAACGA 60.039 55.000 0.00 0.00 0.00 3.85
959 988 1.623973 GCGAGGAGGGAAACGAAACG 61.624 60.000 0.00 0.00 0.00 3.60
960 989 1.623973 CGCGAGGAGGGAAACGAAAC 61.624 60.000 0.00 0.00 34.27 2.78
961 990 1.373748 CGCGAGGAGGGAAACGAAA 60.374 57.895 0.00 0.00 34.27 3.46
962 991 2.260434 CGCGAGGAGGGAAACGAA 59.740 61.111 0.00 0.00 34.27 3.85
1278 1312 2.490685 GAGGAGAAGACCGCGACC 59.509 66.667 8.23 0.00 34.73 4.79
1725 1759 2.029964 GTCGCGAAGTTGGGGTCA 59.970 61.111 12.06 0.00 0.00 4.02
1785 1819 2.203907 AGCTGCACCCCTGAGAGT 60.204 61.111 1.02 0.00 0.00 3.24
1791 1825 3.958860 GTGTGGAGCTGCACCCCT 61.959 66.667 32.10 0.00 0.00 4.79
1795 1829 2.670934 CAGGGTGTGGAGCTGCAC 60.671 66.667 29.44 29.44 35.07 4.57
1872 1906 1.735198 CAAGCACTGGCATTTGGCG 60.735 57.895 0.00 0.00 46.16 5.69
1906 1940 1.851021 CGCGGCATCAGGTCAAACAA 61.851 55.000 0.00 0.00 0.00 2.83
1923 1957 0.392060 AGGTTACCAAATCGTCCCGC 60.392 55.000 3.51 0.00 0.00 6.13
2215 2249 4.333649 CACATCGATGGTCTTTGTAGCATT 59.666 41.667 28.09 0.00 37.69 3.56
2250 2284 6.479972 AGAACATAACCCGAGATCATTGTA 57.520 37.500 0.00 0.00 0.00 2.41
2310 2344 0.690762 TGCCCACTTCCAAGAGGTAC 59.309 55.000 2.58 0.00 35.31 3.34
2605 2639 6.072728 CCTTCCATACTCATTTGACGAAACAA 60.073 38.462 0.00 0.00 0.00 2.83
2724 2758 5.473273 TCTGCTCTTATGGGACCCTTTATA 58.527 41.667 13.00 0.00 0.00 0.98
2893 2927 5.585047 GGCATAATAAACTCACCGACTCTTT 59.415 40.000 0.00 0.00 0.00 2.52
3339 3373 6.234177 ACCAGGTATCTTCTGAACTTTCTTG 58.766 40.000 0.00 0.00 34.36 3.02
3486 3520 1.218316 GTCTGGCCTGGGAACGTAG 59.782 63.158 10.07 0.00 0.00 3.51
3577 3611 5.581874 GGGTTTGAACTATGAAAATGCATGG 59.418 40.000 0.00 0.00 33.50 3.66
3681 3715 0.179048 TGGATCAGCAATACAGCGGG 60.179 55.000 0.00 0.00 40.15 6.13
3684 3718 2.854963 TGGATGGATCAGCAATACAGC 58.145 47.619 0.00 0.00 33.54 4.40
3714 3748 3.265221 TCCTGATTCCTGCTGTCTCATTT 59.735 43.478 0.00 0.00 0.00 2.32
3715 3749 2.842496 TCCTGATTCCTGCTGTCTCATT 59.158 45.455 0.00 0.00 0.00 2.57
3724 3758 5.011533 ACAGTATACTGATCCTGATTCCTGC 59.988 44.000 34.16 0.00 46.59 4.85
3831 3878 8.897752 GGTGCATGTTCTAGAAGAAGAAAATAT 58.102 33.333 5.12 0.00 37.24 1.28
3833 3880 6.128172 CGGTGCATGTTCTAGAAGAAGAAAAT 60.128 38.462 5.12 0.00 37.24 1.82
3846 3894 0.168788 CGCATTTCGGTGCATGTTCT 59.831 50.000 0.00 0.00 45.30 3.01
3865 3913 7.544566 TCTTCGACTCCTAATACAAAATGACAC 59.455 37.037 0.00 0.00 0.00 3.67
3868 3916 8.311836 AGTTCTTCGACTCCTAATACAAAATGA 58.688 33.333 0.00 0.00 0.00 2.57
3873 3921 8.571461 TCTTAGTTCTTCGACTCCTAATACAA 57.429 34.615 0.00 0.00 0.00 2.41
3875 3923 7.914871 GGTTCTTAGTTCTTCGACTCCTAATAC 59.085 40.741 0.00 0.00 0.00 1.89
3877 3925 6.436532 TGGTTCTTAGTTCTTCGACTCCTAAT 59.563 38.462 0.00 0.00 0.00 1.73
3878 3926 5.771666 TGGTTCTTAGTTCTTCGACTCCTAA 59.228 40.000 0.00 0.00 0.00 2.69
3879 3927 5.319453 TGGTTCTTAGTTCTTCGACTCCTA 58.681 41.667 0.00 0.00 0.00 2.94
3935 3988 8.266392 CCATATTAAAATGGCTTTTTCTGCAA 57.734 30.769 13.60 4.59 40.07 4.08
3936 3989 7.846644 CCATATTAAAATGGCTTTTTCTGCA 57.153 32.000 13.60 0.00 40.07 4.41
3986 4125 6.974622 AGCAACATAGAAACAGAACAAAACAG 59.025 34.615 0.00 0.00 0.00 3.16
4024 4163 1.885887 CAGTCTTCCAAATCGCCCAAA 59.114 47.619 0.00 0.00 0.00 3.28
4046 4185 4.520492 AGACAAAAGAACTAACTGCATGGG 59.480 41.667 0.00 0.00 0.00 4.00
4155 4294 9.109246 TCCTTTATCACCATCAGAATATCAGAT 57.891 33.333 0.00 0.00 0.00 2.90
4185 4325 8.387354 TCTATGCAACATTTGTACAATAACGAG 58.613 33.333 9.56 0.03 0.00 4.18
4229 4370 3.063997 GGAAACATGGAATCGTACTGCAG 59.936 47.826 13.48 13.48 0.00 4.41
4287 4428 1.079503 GAGCGTTTAGGGTTCAGCTG 58.920 55.000 7.63 7.63 34.85 4.24
4331 4472 3.425162 ACAAACAAAACAAAAGGGGCA 57.575 38.095 0.00 0.00 0.00 5.36
4407 4548 7.606349 ACAAAAAGGAGAAAATGAGAATAGGC 58.394 34.615 0.00 0.00 0.00 3.93
4490 4660 3.012518 CCAAGATGGACCTGACACATTC 58.987 50.000 0.00 0.00 40.96 2.67
4491 4661 2.376518 ACCAAGATGGACCTGACACATT 59.623 45.455 2.85 0.00 40.96 2.71
4492 4662 1.988107 ACCAAGATGGACCTGACACAT 59.012 47.619 2.85 0.00 40.96 3.21
4493 4663 1.347707 GACCAAGATGGACCTGACACA 59.652 52.381 2.85 0.00 40.96 3.72
4494 4664 1.347707 TGACCAAGATGGACCTGACAC 59.652 52.381 2.85 0.00 40.96 3.67
4495 4665 1.728323 TGACCAAGATGGACCTGACA 58.272 50.000 2.85 0.00 40.96 3.58
4496 4666 2.026822 ACATGACCAAGATGGACCTGAC 60.027 50.000 0.00 0.00 40.96 3.51
4497 4667 2.269023 ACATGACCAAGATGGACCTGA 58.731 47.619 0.00 0.00 40.96 3.86
4498 4668 2.795231 ACATGACCAAGATGGACCTG 57.205 50.000 0.00 3.24 40.96 4.00
4499 4669 3.392616 GGATACATGACCAAGATGGACCT 59.607 47.826 0.00 0.00 40.96 3.85
4500 4670 3.496870 GGGATACATGACCAAGATGGACC 60.497 52.174 0.00 0.00 38.04 4.46
4501 4671 3.496870 GGGGATACATGACCAAGATGGAC 60.497 52.174 0.00 0.00 38.04 4.02
4502 4672 2.711009 GGGGATACATGACCAAGATGGA 59.289 50.000 0.00 0.00 38.04 3.41
4503 4673 2.713167 AGGGGATACATGACCAAGATGG 59.287 50.000 0.00 0.00 41.11 3.51
4504 4674 3.137176 ACAGGGGATACATGACCAAGATG 59.863 47.826 0.00 0.00 39.74 2.90
4505 4675 3.397527 ACAGGGGATACATGACCAAGAT 58.602 45.455 0.00 0.00 39.74 2.40
4506 4676 2.845659 ACAGGGGATACATGACCAAGA 58.154 47.619 0.00 0.00 39.74 3.02
4507 4677 3.454447 TGTACAGGGGATACATGACCAAG 59.546 47.826 0.00 0.00 39.74 3.61
4508 4678 3.455849 TGTACAGGGGATACATGACCAA 58.544 45.455 0.00 0.00 39.74 3.67
4509 4679 3.123392 TGTACAGGGGATACATGACCA 57.877 47.619 0.00 0.00 39.74 4.02
4510 4680 4.223032 CCTATGTACAGGGGATACATGACC 59.777 50.000 10.36 0.00 42.06 4.02
4511 4681 4.322801 GCCTATGTACAGGGGATACATGAC 60.323 50.000 17.72 0.00 42.06 3.06
4512 4682 3.838317 GCCTATGTACAGGGGATACATGA 59.162 47.826 17.72 0.00 42.06 3.07
4513 4683 4.207891 GCCTATGTACAGGGGATACATG 57.792 50.000 17.72 0.00 42.06 3.21
4521 4691 2.029073 CCGCGCCTATGTACAGGG 59.971 66.667 0.00 11.89 36.10 4.45
4547 4717 7.968405 GCCGTCAAAGAATTATATGAACTTTGT 59.032 33.333 19.52 0.00 44.04 2.83
4570 4740 1.129998 CAGCATTGAGAGTTTGAGCCG 59.870 52.381 0.00 0.00 0.00 5.52
4573 4743 4.665281 CTGTCAGCATTGAGAGTTTGAG 57.335 45.455 0.00 0.00 39.28 3.02
4605 4775 2.543777 TGCAGAACTTACACAGTCCC 57.456 50.000 0.00 0.00 32.94 4.46
4641 4811 4.786609 GCTGTCCAAGTTCAAGACGAAAAG 60.787 45.833 0.00 0.00 34.69 2.27
4645 4815 1.138069 TGCTGTCCAAGTTCAAGACGA 59.862 47.619 0.00 0.00 33.09 4.20
4656 4826 7.537715 CACACAAATAGAATAATGCTGTCCAA 58.462 34.615 0.00 0.00 0.00 3.53
4680 4850 4.101585 CAGAGGGAGTAGAACATTATGGCA 59.898 45.833 0.00 0.00 0.00 4.92
4693 4863 9.364653 GACTTATATTTAGGAACAGAGGGAGTA 57.635 37.037 0.00 0.00 0.00 2.59
4694 4864 8.068733 AGACTTATATTTAGGAACAGAGGGAGT 58.931 37.037 0.00 0.00 0.00 3.85
4695 4865 8.485578 AGACTTATATTTAGGAACAGAGGGAG 57.514 38.462 0.00 0.00 0.00 4.30
4696 4866 8.855804 AAGACTTATATTTAGGAACAGAGGGA 57.144 34.615 0.00 0.00 0.00 4.20
4697 4867 9.907229 AAAAGACTTATATTTAGGAACAGAGGG 57.093 33.333 0.00 0.00 0.00 4.30
4725 4895 9.698309 CCGTATGTAGTTCATATTCAAATCTCT 57.302 33.333 0.00 0.00 40.54 3.10
4726 4896 9.692749 TCCGTATGTAGTTCATATTCAAATCTC 57.307 33.333 0.00 0.00 40.54 2.75
4729 4899 9.996554 TCATCCGTATGTAGTTCATATTCAAAT 57.003 29.630 0.00 0.00 40.54 2.32
4730 4900 9.825109 TTCATCCGTATGTAGTTCATATTCAAA 57.175 29.630 0.00 0.00 40.54 2.69
4731 4901 9.996554 ATTCATCCGTATGTAGTTCATATTCAA 57.003 29.630 0.00 0.00 40.54 2.69
4738 4908 8.448615 CGTCTATATTCATCCGTATGTAGTTCA 58.551 37.037 0.00 0.00 34.50 3.18
4739 4909 8.449397 ACGTCTATATTCATCCGTATGTAGTTC 58.551 37.037 0.00 0.00 34.50 3.01
4740 4910 8.332996 ACGTCTATATTCATCCGTATGTAGTT 57.667 34.615 0.00 0.00 34.50 2.24
4741 4911 7.918536 ACGTCTATATTCATCCGTATGTAGT 57.081 36.000 0.00 0.00 34.50 2.73
4760 4930 9.924650 AGTGAATTTACACTCTAAAATACGTCT 57.075 29.630 2.93 0.00 46.36 4.18
4774 4944 5.569059 CGGAGCAAAATGAGTGAATTTACAC 59.431 40.000 2.93 0.00 40.60 2.90
4775 4945 5.240623 ACGGAGCAAAATGAGTGAATTTACA 59.759 36.000 2.93 0.00 0.00 2.41
4776 4946 5.699839 ACGGAGCAAAATGAGTGAATTTAC 58.300 37.500 0.00 0.00 0.00 2.01
4777 4947 5.957842 ACGGAGCAAAATGAGTGAATTTA 57.042 34.783 0.00 0.00 0.00 1.40
4778 4948 4.853924 ACGGAGCAAAATGAGTGAATTT 57.146 36.364 0.00 0.00 0.00 1.82
4779 4949 5.415701 ACATACGGAGCAAAATGAGTGAATT 59.584 36.000 0.00 0.00 0.00 2.17
4780 4950 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4781 4951 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
4782 4952 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4783 4953 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
4784 4954 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
4785 4955 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
4786 4956 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
4787 4957 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
4788 4958 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
4789 4959 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
4790 4960 5.801531 ATATGGACTACATACGGAGCAAA 57.198 39.130 0.00 0.00 44.41 3.68
4791 4961 5.801531 AATATGGACTACATACGGAGCAA 57.198 39.130 0.00 0.00 44.41 3.91
4792 4962 6.243148 TCTAATATGGACTACATACGGAGCA 58.757 40.000 0.00 0.00 44.41 4.26
4793 4963 6.754702 TCTAATATGGACTACATACGGAGC 57.245 41.667 0.00 0.00 44.41 4.70
4794 4964 9.179909 AGATTCTAATATGGACTACATACGGAG 57.820 37.037 0.00 0.00 44.41 4.63
4795 4965 9.175312 GAGATTCTAATATGGACTACATACGGA 57.825 37.037 0.00 0.00 44.41 4.69
4796 4966 9.179909 AGAGATTCTAATATGGACTACATACGG 57.820 37.037 0.00 0.00 44.41 4.02
4823 4993 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
4824 4994 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
4825 4995 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
4826 4996 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4827 4997 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4828 4998 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4829 4999 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4830 5000 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4831 5001 7.529555 TCTACTCCCTCCGTTCCTAAATATAA 58.470 38.462 0.00 0.00 0.00 0.98
4832 5002 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
4833 5003 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
4834 5004 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
4835 5005 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
4836 5006 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
4837 5007 3.629087 CTTCTACTCCCTCCGTTCCTAA 58.371 50.000 0.00 0.00 0.00 2.69
4838 5008 2.686118 GCTTCTACTCCCTCCGTTCCTA 60.686 54.545 0.00 0.00 0.00 2.94
4839 5009 1.960953 GCTTCTACTCCCTCCGTTCCT 60.961 57.143 0.00 0.00 0.00 3.36
4840 5010 0.460722 GCTTCTACTCCCTCCGTTCC 59.539 60.000 0.00 0.00 0.00 3.62
4841 5011 1.476477 AGCTTCTACTCCCTCCGTTC 58.524 55.000 0.00 0.00 0.00 3.95
4842 5012 2.822707 TAGCTTCTACTCCCTCCGTT 57.177 50.000 0.00 0.00 0.00 4.44
4843 5013 2.959707 CAATAGCTTCTACTCCCTCCGT 59.040 50.000 0.00 0.00 0.00 4.69
4844 5014 2.297597 CCAATAGCTTCTACTCCCTCCG 59.702 54.545 0.00 0.00 0.00 4.63
4845 5015 3.070302 CACCAATAGCTTCTACTCCCTCC 59.930 52.174 0.00 0.00 0.00 4.30
4846 5016 3.707102 ACACCAATAGCTTCTACTCCCTC 59.293 47.826 0.00 0.00 0.00 4.30
4847 5017 3.725634 ACACCAATAGCTTCTACTCCCT 58.274 45.455 0.00 0.00 0.00 4.20
4848 5018 5.609533 TTACACCAATAGCTTCTACTCCC 57.390 43.478 0.00 0.00 0.00 4.30
4849 5019 7.988028 AGAAATTACACCAATAGCTTCTACTCC 59.012 37.037 0.00 0.00 0.00 3.85
4850 5020 8.950208 AGAAATTACACCAATAGCTTCTACTC 57.050 34.615 0.00 0.00 0.00 2.59
4851 5021 9.167311 CAAGAAATTACACCAATAGCTTCTACT 57.833 33.333 0.00 0.00 0.00 2.57
4852 5022 8.398665 CCAAGAAATTACACCAATAGCTTCTAC 58.601 37.037 0.00 0.00 0.00 2.59
4885 5055 7.519032 TTTAGATTTTCTTTTCACGGGACAT 57.481 32.000 0.00 0.00 0.00 3.06
4891 5062 7.432252 ACAGCACTTTTAGATTTTCTTTTCACG 59.568 33.333 0.00 0.00 0.00 4.35
4916 5087 5.153950 AGCTTAGATTTATCCATCCGGAC 57.846 43.478 6.12 0.00 46.79 4.79
4986 5157 9.829507 CTCAGAACCAACAGAATTAGATATTCT 57.170 33.333 0.00 0.00 38.78 2.40
4990 5161 9.436957 GAAACTCAGAACCAACAGAATTAGATA 57.563 33.333 0.00 0.00 0.00 1.98
5015 5198 1.000506 GTGTAGAGGGCAGAAACACGA 59.999 52.381 0.00 0.00 32.05 4.35
5020 5203 3.857157 AAACTGTGTAGAGGGCAGAAA 57.143 42.857 0.00 0.00 34.60 2.52
5051 5234 3.028850 ACCTGCATAACTAGGCTTACGA 58.971 45.455 0.00 0.00 37.61 3.43
5059 5242 2.292267 CCTGCCAACCTGCATAACTAG 58.708 52.381 0.00 0.00 41.16 2.57
5075 5258 1.544724 TATGGTTTTCACAGGCCTGC 58.455 50.000 33.06 14.88 0.00 4.85
5123 5313 2.967599 TCATAAGCATGTCGAGCTGT 57.032 45.000 0.00 0.00 42.53 4.40
5129 5319 4.685169 ACCTTGTTTCATAAGCATGTCG 57.315 40.909 0.00 0.00 33.57 4.35
5131 5321 5.068987 ACACAACCTTGTTTCATAAGCATGT 59.931 36.000 0.00 0.00 39.91 3.21
5155 5345 4.633175 TCATCGTTAACCTTGTTGTGCTA 58.367 39.130 0.00 0.00 0.00 3.49
5184 5374 0.315568 GACTGACTCAACAGGTCGCT 59.684 55.000 0.00 0.00 41.59 4.93
5186 5376 0.591659 TCGACTGACTCAACAGGTCG 59.408 55.000 10.73 10.73 41.59 4.79
5236 5426 3.369471 GCACATAGCAGTAGGGAGAAACA 60.369 47.826 0.00 0.00 44.79 2.83


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

AutoCloner maintained by Alex Coulton.