Multiple sequence alignment - TraesCS4B01G051400

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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 TraesCS4B01G051400 chr4B 100.000 4619 0 0 1 4619 40066223 40061605 0.000000e+00 8530.0
1 TraesCS4B01G051400 chr4A 94.946 2948 113 16 808 3748 575798389 575801307 0.000000e+00 4586.0
2 TraesCS4B01G051400 chr4A 76.887 848 173 19 1365 2196 647092069 647091229 4.210000e-125 459.0
3 TraesCS4B01G051400 chr4A 87.805 82 2 6 46 122 575798314 575798392 6.370000e-14 89.8
4 TraesCS4B01G051400 chr4D 89.583 1584 112 21 859 2437 27385149 27383614 0.000000e+00 1962.0
5 TraesCS4B01G051400 chr4D 90.650 1016 69 8 2806 3809 27383071 27382070 0.000000e+00 1327.0
6 TraesCS4B01G051400 chr4D 96.405 306 10 1 364 668 477012271 477011966 1.920000e-138 503.0
7 TraesCS4B01G051400 chr4D 84.954 432 31 17 3999 4415 27381404 27380992 1.550000e-109 407.0
8 TraesCS4B01G051400 chr4D 97.143 210 5 1 116 324 477012714 477012505 2.040000e-93 353.0
9 TraesCS4B01G051400 chr4D 94.175 206 10 2 4416 4619 27380953 27380748 3.470000e-81 313.0
10 TraesCS4B01G051400 chr4D 79.500 400 38 15 2436 2809 27383532 27383151 1.280000e-60 244.0
11 TraesCS4B01G051400 chr4D 96.000 100 4 0 7 106 27385440 27385341 3.700000e-36 163.0
12 TraesCS4B01G051400 chr1B 98.857 700 4 3 117 813 295103157 295102459 0.000000e+00 1245.0
13 TraesCS4B01G051400 chrUn 99.271 686 4 1 120 804 40598723 40599408 0.000000e+00 1238.0
14 TraesCS4B01G051400 chr7B 97.691 693 15 1 119 811 591564810 591564119 0.000000e+00 1190.0
15 TraesCS4B01G051400 chr3A 97.085 446 9 2 364 808 383712614 383713056 0.000000e+00 749.0
16 TraesCS4B01G051400 chr3B 95.270 444 16 3 366 808 27052591 27053030 0.000000e+00 699.0
17 TraesCS4B01G051400 chr3B 97.959 245 5 0 121 365 27052056 27052300 4.270000e-115 425.0
18 TraesCS4B01G051400 chr2A 93.231 458 20 6 364 812 645956598 645956143 0.000000e+00 664.0
19 TraesCS4B01G051400 chr2A 78.347 859 154 24 1364 2196 611935603 611936455 1.140000e-145 527.0
20 TraesCS4B01G051400 chr2A 94.175 206 12 0 158 363 645957071 645956866 9.650000e-82 315.0
21 TraesCS4B01G051400 chr6B 90.719 431 34 5 376 805 494094939 494095364 1.860000e-158 569.0
22 TraesCS4B01G051400 chr6B 93.171 205 11 1 120 321 494094153 494094357 9.720000e-77 298.0
23 TraesCS4B01G051400 chr2D 78.885 843 151 20 1364 2183 470205643 470206481 3.140000e-151 545.0
24 TraesCS4B01G051400 chr2B 78.597 841 155 21 1364 2183 548946084 548946920 2.450000e-147 532.0
25 TraesCS4B01G051400 chr7D 78.323 835 157 20 1365 2181 40454168 40453340 6.850000e-143 518.0
26 TraesCS4B01G051400 chr7A 78.058 834 161 19 1365 2181 40365531 40364703 1.480000e-139 507.0
27 TraesCS4B01G051400 chr7A 92.308 52 2 2 314 365 185591563 185591612 6.410000e-09 73.1
28 TraesCS4B01G051400 chr3D 98.400 250 4 0 116 365 8969732 8969981 1.530000e-119 440.0
29 TraesCS4B01G051400 chr3D 98.942 189 1 1 364 551 29699879 29700067 2.060000e-88 337.0
30 TraesCS4B01G051400 chr3D 99.355 155 1 0 656 810 29700063 29700217 9.780000e-72 281.0
31 TraesCS4B01G051400 chr3D 97.516 161 4 0 515 675 8970284 8970444 4.550000e-70 276.0
32 TraesCS4B01G051400 chr5D 98.000 250 5 0 116 365 366007618 366007867 7.100000e-118 435.0
33 TraesCS4B01G051400 chr6A 79.085 153 27 5 663 813 602130430 602130281 2.940000e-17 100.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G051400 chr4B 40061605 40066223 4618 True 8530.0 8530 100.000000 1 4619 1 chr4B.!!$R1 4618
1 TraesCS4B01G051400 chr4A 575798314 575801307 2993 False 2337.9 4586 91.375500 46 3748 2 chr4A.!!$F1 3702
2 TraesCS4B01G051400 chr4A 647091229 647092069 840 True 459.0 459 76.887000 1365 2196 1 chr4A.!!$R1 831
3 TraesCS4B01G051400 chr4D 27380748 27385440 4692 True 736.0 1962 89.143667 7 4619 6 chr4D.!!$R1 4612
4 TraesCS4B01G051400 chr4D 477011966 477012714 748 True 428.0 503 96.774000 116 668 2 chr4D.!!$R2 552
5 TraesCS4B01G051400 chr1B 295102459 295103157 698 True 1245.0 1245 98.857000 117 813 1 chr1B.!!$R1 696
6 TraesCS4B01G051400 chrUn 40598723 40599408 685 False 1238.0 1238 99.271000 120 804 1 chrUn.!!$F1 684
7 TraesCS4B01G051400 chr7B 591564119 591564810 691 True 1190.0 1190 97.691000 119 811 1 chr7B.!!$R1 692
8 TraesCS4B01G051400 chr3B 27052056 27053030 974 False 562.0 699 96.614500 121 808 2 chr3B.!!$F1 687
9 TraesCS4B01G051400 chr2A 611935603 611936455 852 False 527.0 527 78.347000 1364 2196 1 chr2A.!!$F1 832
10 TraesCS4B01G051400 chr2A 645956143 645957071 928 True 489.5 664 93.703000 158 812 2 chr2A.!!$R1 654
11 TraesCS4B01G051400 chr6B 494094153 494095364 1211 False 433.5 569 91.945000 120 805 2 chr6B.!!$F1 685
12 TraesCS4B01G051400 chr2D 470205643 470206481 838 False 545.0 545 78.885000 1364 2183 1 chr2D.!!$F1 819
13 TraesCS4B01G051400 chr2B 548946084 548946920 836 False 532.0 532 78.597000 1364 2183 1 chr2B.!!$F1 819
14 TraesCS4B01G051400 chr7D 40453340 40454168 828 True 518.0 518 78.323000 1365 2181 1 chr7D.!!$R1 816
15 TraesCS4B01G051400 chr7A 40364703 40365531 828 True 507.0 507 78.058000 1365 2181 1 chr7A.!!$R1 816
16 TraesCS4B01G051400 chr3D 8969732 8970444 712 False 358.0 440 97.958000 116 675 2 chr3D.!!$F1 559

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
896 1788 1.068264 GCCCTTCGCTTTTTCTTGGAG 60.068 52.381 0.0 0.0 0.0 3.86 F
2228 3179 1.135141 CCACCCATTTTGTACATGCCG 60.135 52.381 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 3282 1.386533 ACACAAGCTCTGGCATATGC 58.613 50.0 19.79 19.79 41.70 3.14 R
4010 5640 0.036022 AGGAGAAGGCTGCAAGTGAC 59.964 55.0 0.50 0.00 34.49 3.67 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
23 24 5.262455 AGAAGTTGGGGAATTAGCTTTCT 57.738 39.130 0.00 0.00 0.00 2.52
28 29 2.170607 TGGGGAATTAGCTTTCTCGAGG 59.829 50.000 13.56 0.00 0.00 4.63
34 35 5.163844 GGAATTAGCTTTCTCGAGGTGAAAC 60.164 44.000 13.56 1.38 31.21 2.78
820 1601 8.161425 ACCAAAGACAGCCTTAGATTTAGTTAA 58.839 33.333 0.00 0.00 34.00 2.01
827 1608 8.383947 ACAGCCTTAGATTTAGTTAAGGTTTCT 58.616 33.333 10.88 0.00 45.01 2.52
869 1761 9.261035 AGGAGTAGTCAAAATTCAGATCTCTAA 57.739 33.333 0.00 0.00 0.00 2.10
883 1775 1.825474 TCTCTAACTGAAGGCCCTTCG 59.175 52.381 18.35 14.78 42.78 3.79
896 1788 1.068264 GCCCTTCGCTTTTTCTTGGAG 60.068 52.381 0.00 0.00 0.00 3.86
903 1795 5.446143 TCGCTTTTTCTTGGAGCAAATTA 57.554 34.783 0.00 0.00 36.22 1.40
952 1844 3.684788 ACGATTTCGATTCTTTGGTCTGG 59.315 43.478 7.01 0.00 43.02 3.86
962 1854 6.565999 CGATTCTTTGGTCTGGTTTAACTGAC 60.566 42.308 11.13 11.13 38.24 3.51
981 1873 4.733850 TGACTATTTGACGCAGAGTGTAG 58.266 43.478 0.00 0.00 0.00 2.74
982 1874 4.457949 TGACTATTTGACGCAGAGTGTAGA 59.542 41.667 0.00 0.00 0.00 2.59
988 1880 5.638596 TTGACGCAGAGTGTAGAAATCTA 57.361 39.130 0.00 0.00 0.00 1.98
1096 1988 4.252073 CTCTGTCAAGGAGGAGAATGTTG 58.748 47.826 0.00 0.00 0.00 3.33
1097 1989 3.903714 TCTGTCAAGGAGGAGAATGTTGA 59.096 43.478 0.00 0.00 0.00 3.18
1098 1990 4.533707 TCTGTCAAGGAGGAGAATGTTGAT 59.466 41.667 0.00 0.00 30.27 2.57
1099 1991 4.582869 TGTCAAGGAGGAGAATGTTGATG 58.417 43.478 0.00 0.00 30.27 3.07
1100 1992 4.286808 TGTCAAGGAGGAGAATGTTGATGA 59.713 41.667 0.00 0.00 30.27 2.92
1101 1993 5.045359 TGTCAAGGAGGAGAATGTTGATGAT 60.045 40.000 0.00 0.00 30.27 2.45
1102 1994 5.526846 GTCAAGGAGGAGAATGTTGATGATC 59.473 44.000 0.00 0.00 30.27 2.92
1103 1995 5.427806 TCAAGGAGGAGAATGTTGATGATCT 59.572 40.000 0.00 0.00 0.00 2.75
1104 1996 5.972327 AGGAGGAGAATGTTGATGATCTT 57.028 39.130 0.00 0.00 0.00 2.40
1105 1997 6.324601 AGGAGGAGAATGTTGATGATCTTT 57.675 37.500 0.00 0.00 0.00 2.52
1106 1998 6.355747 AGGAGGAGAATGTTGATGATCTTTC 58.644 40.000 0.00 0.00 0.00 2.62
1107 1999 5.236047 GGAGGAGAATGTTGATGATCTTTCG 59.764 44.000 0.00 0.00 0.00 3.46
1223 2139 1.275061 TGTAGAGGAGGAGGAGGAGGA 60.275 57.143 0.00 0.00 0.00 3.71
1224 2140 1.423921 GTAGAGGAGGAGGAGGAGGAG 59.576 61.905 0.00 0.00 0.00 3.69
1624 2540 1.303309 GATCATTGCCCCTGTTCTCG 58.697 55.000 0.00 0.00 0.00 4.04
1917 2840 2.226330 TGTTTTTGATGAGGTGACGGG 58.774 47.619 0.00 0.00 0.00 5.28
2228 3179 1.135141 CCACCCATTTTGTACATGCCG 60.135 52.381 0.00 0.00 0.00 5.69
2253 3204 6.503041 ACATGACCATAGCCTCCATATACTA 58.497 40.000 0.00 0.00 0.00 1.82
2331 3282 3.555917 CTTTCAGAAAGCTTGCTCTGG 57.444 47.619 22.21 6.19 39.67 3.86
2368 3319 2.488153 GTGTTGGCTCGGCTAATTTTCT 59.512 45.455 0.00 0.00 30.69 2.52
2373 3324 2.945668 GGCTCGGCTAATTTTCTCATGT 59.054 45.455 0.00 0.00 0.00 3.21
2505 3546 5.892160 TTCTCGTGTAGCTGTATACAACT 57.108 39.130 13.11 13.11 37.41 3.16
2738 3797 8.882736 TCTTGTTATACATGTCATGTTTGCTAG 58.117 33.333 23.05 16.33 41.63 3.42
2744 3803 6.579666 ACATGTCATGTTTGCTAGAATGTT 57.420 33.333 12.87 0.00 41.63 2.71
2750 3809 8.791675 TGTCATGTTTGCTAGAATGTTTATCAA 58.208 29.630 0.00 0.00 0.00 2.57
2764 3823 6.576662 TGTTTATCAAGGCGAATTTTGGTA 57.423 33.333 0.00 0.00 0.00 3.25
2766 3825 6.207810 TGTTTATCAAGGCGAATTTTGGTACT 59.792 34.615 0.00 0.00 0.00 2.73
2774 3833 4.561213 GGCGAATTTTGGTACTTTACATGC 59.439 41.667 0.00 0.00 0.00 4.06
2775 3834 4.561213 GCGAATTTTGGTACTTTACATGCC 59.439 41.667 0.00 0.00 0.00 4.40
2776 3835 5.704888 CGAATTTTGGTACTTTACATGCCA 58.295 37.500 0.00 0.00 0.00 4.92
2777 3836 5.571357 CGAATTTTGGTACTTTACATGCCAC 59.429 40.000 0.00 0.00 30.79 5.01
2780 3839 5.699097 TTTGGTACTTTACATGCCACTTC 57.301 39.130 0.00 0.00 30.79 3.01
2800 3859 7.545265 CCACTTCTTTTGTTTTGAAGATGTTGA 59.455 33.333 8.65 0.00 37.85 3.18
2926 4068 3.436243 AGAGGTGAGGGACTACAAGAAG 58.564 50.000 0.00 0.00 41.55 2.85
2930 4072 4.284746 AGGTGAGGGACTACAAGAAGAAAG 59.715 45.833 0.00 0.00 41.55 2.62
2965 4107 4.178956 AGGGTCCTTGTTTCAAAGCTTA 57.821 40.909 0.00 0.00 0.00 3.09
3082 4224 3.139077 GACCACACGAAAAGAGATGGTT 58.861 45.455 0.00 0.00 40.51 3.67
3110 4252 1.073125 TGTTGGCCGGAATTCTCAAGA 59.927 47.619 5.05 2.06 0.00 3.02
3192 4334 0.253327 GACTGGGGCTGGAAGGTAAG 59.747 60.000 0.00 0.00 0.00 2.34
3194 4336 0.253327 CTGGGGCTGGAAGGTAAGAC 59.747 60.000 0.00 0.00 0.00 3.01
3195 4337 1.221021 GGGGCTGGAAGGTAAGACG 59.779 63.158 0.00 0.00 0.00 4.18
3223 4365 0.376152 GCCACGAACAGATGATGCAG 59.624 55.000 0.00 0.00 0.00 4.41
3284 4426 1.303074 CTTTGAGGCCAGCTGAGCA 60.303 57.895 17.39 4.44 0.00 4.26
3432 4574 0.314935 CACTTGTTGCGCTCCCAATT 59.685 50.000 9.73 0.07 0.00 2.32
3542 4695 5.496556 TCGATGGAGTTGAACCATGTAAAT 58.503 37.500 0.00 0.00 46.48 1.40
3750 4904 2.854805 GCAAAAACTCGCAGTTCTGTCC 60.855 50.000 1.78 0.00 37.47 4.02
3754 4908 2.049156 TCGCAGTTCTGTCCGCTG 60.049 61.111 1.78 0.00 0.00 5.18
3758 4912 2.031516 CAGTTCTGTCCGCTGCAGG 61.032 63.158 17.12 5.50 34.89 4.85
3772 4926 2.754552 GCTGCAGGTGTAATTTCCATCA 59.245 45.455 17.12 0.00 0.00 3.07
3784 4938 5.633655 AATTTCCATCAGAGCTCAGAGAT 57.366 39.130 17.77 12.99 0.00 2.75
3787 4941 1.413077 CCATCAGAGCTCAGAGATGCA 59.587 52.381 25.93 0.00 37.21 3.96
3795 4949 1.202268 GCTCAGAGATGCACAAATGGC 60.202 52.381 0.00 0.00 0.00 4.40
3802 4956 4.282703 AGAGATGCACAAATGGCTTTTTCT 59.717 37.500 0.00 0.00 0.00 2.52
3810 5031 7.598493 TGCACAAATGGCTTTTTCTAAGAATAC 59.402 33.333 0.00 0.00 0.00 1.89
3818 5039 6.183360 GGCTTTTTCTAAGAATACAGCAGGAG 60.183 42.308 0.00 0.00 0.00 3.69
3826 5047 4.718961 AGAATACAGCAGGAGTTTGTTGT 58.281 39.130 1.41 1.41 43.54 3.32
3828 5049 2.418368 ACAGCAGGAGTTTGTTGTCA 57.582 45.000 0.00 0.00 37.92 3.58
3831 5052 2.289002 CAGCAGGAGTTTGTTGTCAGTC 59.711 50.000 0.00 0.00 0.00 3.51
3839 5060 2.737376 GTTGTCAGTCGTCCCGGC 60.737 66.667 0.00 0.00 0.00 6.13
3844 5065 4.760047 CAGTCGTCCCGGCCAAGG 62.760 72.222 2.24 2.18 28.67 3.61
3863 5084 1.593196 GAAGCACTACACCAGCACAA 58.407 50.000 0.00 0.00 0.00 3.33
3865 5086 2.051334 AGCACTACACCAGCACAAAA 57.949 45.000 0.00 0.00 0.00 2.44
3866 5087 2.374184 AGCACTACACCAGCACAAAAA 58.626 42.857 0.00 0.00 0.00 1.94
3868 5089 3.052036 GCACTACACCAGCACAAAAATG 58.948 45.455 0.00 0.00 0.00 2.32
3869 5090 3.490761 GCACTACACCAGCACAAAAATGT 60.491 43.478 0.00 0.00 0.00 2.71
3870 5091 4.261405 GCACTACACCAGCACAAAAATGTA 60.261 41.667 0.00 0.00 0.00 2.29
3871 5092 5.451908 CACTACACCAGCACAAAAATGTAG 58.548 41.667 7.49 7.49 43.26 2.74
3872 5093 5.130350 ACTACACCAGCACAAAAATGTAGT 58.870 37.500 8.64 8.64 44.82 2.73
3873 5094 6.203915 CACTACACCAGCACAAAAATGTAGTA 59.796 38.462 12.97 0.00 46.76 1.82
3876 5192 6.292923 ACACCAGCACAAAAATGTAGTACTA 58.707 36.000 0.00 0.00 0.00 1.82
3878 5194 5.411669 ACCAGCACAAAAATGTAGTACTAGC 59.588 40.000 1.87 0.00 0.00 3.42
3885 5201 6.312918 ACAAAAATGTAGTACTAGCGTCATGG 59.687 38.462 1.87 0.00 0.00 3.66
3888 5204 1.600957 GTAGTACTAGCGTCATGGCGA 59.399 52.381 26.38 1.60 38.18 5.54
3895 5211 2.740826 CGTCATGGCGAACCCGTT 60.741 61.111 16.21 0.00 38.24 4.44
3896 5212 2.867472 GTCATGGCGAACCCGTTG 59.133 61.111 0.00 0.00 38.24 4.10
3899 5215 1.081509 CATGGCGAACCCGTTGTTG 60.082 57.895 0.00 0.00 37.29 3.33
3900 5216 2.265182 ATGGCGAACCCGTTGTTGG 61.265 57.895 0.00 0.00 37.29 3.77
3903 5219 2.637025 CGAACCCGTTGTTGGCTG 59.363 61.111 0.00 0.00 37.29 4.85
3904 5220 1.890041 CGAACCCGTTGTTGGCTGA 60.890 57.895 0.00 0.00 37.29 4.26
3905 5221 1.440938 CGAACCCGTTGTTGGCTGAA 61.441 55.000 0.00 0.00 37.29 3.02
3906 5222 0.030235 GAACCCGTTGTTGGCTGAAC 59.970 55.000 0.00 0.00 37.29 3.18
3907 5223 1.388837 AACCCGTTGTTGGCTGAACC 61.389 55.000 0.00 0.00 35.31 3.62
3908 5224 2.637025 CCGTTGTTGGCTGAACCG 59.363 61.111 0.00 0.00 43.94 4.44
3909 5225 2.184167 CCGTTGTTGGCTGAACCGT 61.184 57.895 0.00 0.00 43.94 4.83
3910 5226 0.881159 CCGTTGTTGGCTGAACCGTA 60.881 55.000 0.00 0.00 43.94 4.02
3911 5227 0.511221 CGTTGTTGGCTGAACCGTAG 59.489 55.000 0.00 0.00 43.94 3.51
3912 5228 1.589803 GTTGTTGGCTGAACCGTAGT 58.410 50.000 0.00 0.00 43.94 2.73
3913 5229 1.529865 GTTGTTGGCTGAACCGTAGTC 59.470 52.381 0.00 0.00 43.94 2.59
3914 5230 1.045407 TGTTGGCTGAACCGTAGTCT 58.955 50.000 0.00 0.00 43.94 3.24
3915 5231 2.241160 TGTTGGCTGAACCGTAGTCTA 58.759 47.619 0.00 0.00 43.94 2.59
3916 5232 2.629137 TGTTGGCTGAACCGTAGTCTAA 59.371 45.455 0.00 0.00 43.94 2.10
3917 5233 3.069872 TGTTGGCTGAACCGTAGTCTAAA 59.930 43.478 0.00 0.00 43.94 1.85
3918 5234 4.251268 GTTGGCTGAACCGTAGTCTAAAT 58.749 43.478 0.00 0.00 43.94 1.40
3919 5235 4.546829 TGGCTGAACCGTAGTCTAAATT 57.453 40.909 0.00 0.00 43.94 1.82
3920 5236 4.250464 TGGCTGAACCGTAGTCTAAATTG 58.750 43.478 0.00 0.00 43.94 2.32
3923 5239 3.916761 TGAACCGTAGTCTAAATTGCGT 58.083 40.909 0.00 0.00 0.00 5.24
3925 5241 5.468592 TGAACCGTAGTCTAAATTGCGTAA 58.531 37.500 0.00 0.00 0.00 3.18
3926 5242 6.101332 TGAACCGTAGTCTAAATTGCGTAAT 58.899 36.000 0.00 0.00 0.00 1.89
3927 5243 7.257003 TGAACCGTAGTCTAAATTGCGTAATA 58.743 34.615 0.00 0.00 0.00 0.98
3928 5244 7.758980 TGAACCGTAGTCTAAATTGCGTAATAA 59.241 33.333 0.00 0.00 0.00 1.40
3931 5247 7.761249 ACCGTAGTCTAAATTGCGTAATAAGTT 59.239 33.333 0.00 0.00 0.00 2.66
3933 5249 9.615779 CGTAGTCTAAATTGCGTAATAAGTTTC 57.384 33.333 0.00 0.00 0.00 2.78
3935 5251 8.248117 AGTCTAAATTGCGTAATAAGTTTCGT 57.752 30.769 0.00 0.00 31.71 3.85
3936 5252 8.715088 AGTCTAAATTGCGTAATAAGTTTCGTT 58.285 29.630 0.00 0.00 31.71 3.85
3937 5253 9.956797 GTCTAAATTGCGTAATAAGTTTCGTTA 57.043 29.630 0.00 0.00 31.71 3.18
3944 5260 8.437443 TGCGTAATAAGTTTCGTTAAATTTGG 57.563 30.769 0.00 0.00 31.71 3.28
3945 5261 7.060864 TGCGTAATAAGTTTCGTTAAATTTGGC 59.939 33.333 0.00 0.00 31.71 4.52
3949 5265 8.663771 AATAAGTTTCGTTAAATTTGGCTACG 57.336 30.769 0.00 5.89 0.00 3.51
3951 5267 6.303021 AGTTTCGTTAAATTTGGCTACGAA 57.697 33.333 19.23 19.23 45.87 3.85
3953 5269 5.927954 TTCGTTAAATTTGGCTACGAAGT 57.072 34.783 19.23 0.00 43.65 3.01
3954 5270 5.927954 TCGTTAAATTTGGCTACGAAGTT 57.072 34.783 13.51 0.00 37.78 2.66
3955 5271 6.303021 TCGTTAAATTTGGCTACGAAGTTT 57.697 33.333 13.51 0.00 37.78 2.66
3958 5274 6.415573 CGTTAAATTTGGCTACGAAGTTTGTT 59.584 34.615 0.00 0.00 37.78 2.83
3959 5275 7.552187 GTTAAATTTGGCTACGAAGTTTGTTG 58.448 34.615 0.00 0.37 37.78 3.33
3960 5276 5.508200 AATTTGGCTACGAAGTTTGTTGA 57.492 34.783 8.67 0.00 37.78 3.18
3961 5277 3.955771 TTGGCTACGAAGTTTGTTGAC 57.044 42.857 8.67 6.26 37.78 3.18
3962 5278 3.188159 TGGCTACGAAGTTTGTTGACT 57.812 42.857 11.25 0.00 37.78 3.41
3963 5279 4.325028 TGGCTACGAAGTTTGTTGACTA 57.675 40.909 11.25 0.00 37.78 2.59
3964 5280 4.053295 TGGCTACGAAGTTTGTTGACTAC 58.947 43.478 11.25 0.00 37.78 2.73
3965 5281 3.120782 GGCTACGAAGTTTGTTGACTACG 59.879 47.826 8.67 0.00 37.78 3.51
3966 5282 3.120782 GCTACGAAGTTTGTTGACTACGG 59.879 47.826 8.67 0.00 37.78 4.02
3967 5283 3.169355 ACGAAGTTTGTTGACTACGGT 57.831 42.857 0.00 0.00 37.78 4.83
3971 5287 4.201744 CGAAGTTTGTTGACTACGGTTGTT 60.202 41.667 0.00 0.00 0.00 2.83
3972 5288 4.609691 AGTTTGTTGACTACGGTTGTTG 57.390 40.909 0.00 0.00 0.00 3.33
3973 5289 4.255301 AGTTTGTTGACTACGGTTGTTGA 58.745 39.130 0.00 0.00 0.00 3.18
3974 5290 4.879545 AGTTTGTTGACTACGGTTGTTGAT 59.120 37.500 0.00 0.00 0.00 2.57
3975 5291 5.355910 AGTTTGTTGACTACGGTTGTTGATT 59.644 36.000 0.00 0.00 0.00 2.57
3977 5293 4.443621 TGTTGACTACGGTTGTTGATTGA 58.556 39.130 0.00 0.00 0.00 2.57
3978 5294 5.060506 TGTTGACTACGGTTGTTGATTGAT 58.939 37.500 0.00 0.00 0.00 2.57
3979 5295 5.529430 TGTTGACTACGGTTGTTGATTGATT 59.471 36.000 0.00 0.00 0.00 2.57
3980 5296 5.605564 TGACTACGGTTGTTGATTGATTG 57.394 39.130 0.00 0.00 0.00 2.67
3981 5297 4.083537 TGACTACGGTTGTTGATTGATTGC 60.084 41.667 0.00 0.00 0.00 3.56
3989 5305 5.160641 GTTGTTGATTGATTGCACGGTTAT 58.839 37.500 0.00 0.00 0.00 1.89
3991 5307 3.419264 TGATTGATTGCACGGTTATGC 57.581 42.857 0.00 0.00 46.32 3.14
4010 5640 1.739371 GCAGTTTACTCGCTGGGTAGG 60.739 57.143 0.00 0.00 33.62 3.18
4014 5644 1.180029 TTACTCGCTGGGTAGGTCAC 58.820 55.000 0.00 0.00 0.00 3.67
4020 5650 0.674895 GCTGGGTAGGTCACTTGCAG 60.675 60.000 0.00 0.00 0.00 4.41
4035 5665 2.071778 TGCAGCCTTCTCCTTGTTTT 57.928 45.000 0.00 0.00 0.00 2.43
4039 5669 2.958355 CAGCCTTCTCCTTGTTTTCCAA 59.042 45.455 0.00 0.00 0.00 3.53
4047 5677 6.817765 TCTCCTTGTTTTCCAATGATGTAC 57.182 37.500 0.00 0.00 31.20 2.90
4053 5683 7.807907 CCTTGTTTTCCAATGATGTACTTGTAC 59.192 37.037 4.14 4.14 31.20 2.90
4057 5687 7.389803 TTTCCAATGATGTACTTGTACCATG 57.610 36.000 8.25 0.00 0.00 3.66
4063 5693 5.250200 TGATGTACTTGTACCATGGGTTTC 58.750 41.667 18.09 3.81 37.09 2.78
4065 5695 2.597578 ACTTGTACCATGGGTTTCCC 57.402 50.000 18.09 0.00 45.71 3.97
4090 5720 6.678663 CGAAAATCGACTGCATAAGTTTGTAG 59.321 38.462 0.00 0.00 43.74 2.74
4094 5724 8.718102 AATCGACTGCATAAGTTTGTAGTATT 57.282 30.769 8.11 4.73 41.76 1.89
4096 5726 7.317390 TCGACTGCATAAGTTTGTAGTATTCA 58.683 34.615 8.11 0.00 41.76 2.57
4097 5727 7.815549 TCGACTGCATAAGTTTGTAGTATTCAA 59.184 33.333 8.11 0.00 41.76 2.69
4098 5728 8.440059 CGACTGCATAAGTTTGTAGTATTCAAA 58.560 33.333 8.11 0.00 41.76 2.69
4099 5729 9.760660 GACTGCATAAGTTTGTAGTATTCAAAG 57.239 33.333 8.11 0.00 41.76 2.77
4101 5731 8.335532 TGCATAAGTTTGTAGTATTCAAAGCT 57.664 30.769 0.00 0.00 35.83 3.74
4112 5742 9.891828 TGTAGTATTCAAAGCTAAAACAACATG 57.108 29.630 0.00 0.00 0.00 3.21
4113 5743 9.893305 GTAGTATTCAAAGCTAAAACAACATGT 57.107 29.630 0.00 0.00 0.00 3.21
4114 5744 8.801715 AGTATTCAAAGCTAAAACAACATGTG 57.198 30.769 0.00 0.00 0.00 3.21
4115 5745 8.413229 AGTATTCAAAGCTAAAACAACATGTGT 58.587 29.630 0.00 0.00 44.64 3.72
4116 5746 6.884096 TTCAAAGCTAAAACAACATGTGTG 57.116 33.333 0.00 2.71 40.60 3.82
4117 5747 6.201226 TCAAAGCTAAAACAACATGTGTGA 57.799 33.333 0.00 0.00 40.60 3.58
4118 5748 6.033341 TCAAAGCTAAAACAACATGTGTGAC 58.967 36.000 0.00 0.00 40.60 3.67
4119 5749 5.574891 AAGCTAAAACAACATGTGTGACA 57.425 34.783 0.00 0.00 40.60 3.58
4120 5750 4.920376 AGCTAAAACAACATGTGTGACAC 58.080 39.130 9.14 9.14 40.60 3.67
4143 5773 5.473504 ACAACAAAGCTTACCTTATGAGTGG 59.526 40.000 0.00 0.00 32.20 4.00
4146 5776 3.802948 AGCTTACCTTATGAGTGGTCG 57.197 47.619 0.00 0.00 37.74 4.79
4147 5777 3.362706 AGCTTACCTTATGAGTGGTCGA 58.637 45.455 0.00 0.00 37.74 4.20
4148 5778 3.767673 AGCTTACCTTATGAGTGGTCGAA 59.232 43.478 0.00 0.00 37.74 3.71
4150 5780 4.142227 GCTTACCTTATGAGTGGTCGAAGA 60.142 45.833 0.00 0.00 37.74 2.87
4170 5800 3.066760 AGAAGGCGACTGGTTTTTCTTTG 59.933 43.478 0.00 0.00 42.68 2.77
4175 5805 3.489229 GCGACTGGTTTTTCTTTGAGCTT 60.489 43.478 0.00 0.00 0.00 3.74
4195 5825 0.533032 GAGTCAGTAGGTGGAGGTGC 59.467 60.000 0.00 0.00 0.00 5.01
4209 5848 2.289945 GGAGGTGCATCACTCTGTTCTT 60.290 50.000 0.00 0.00 34.40 2.52
4244 5885 5.977725 TGTAGTTTCAGAGAAAGAACACTCG 59.022 40.000 0.00 0.00 38.08 4.18
4261 5902 2.439156 GGCATCTCCCTGTGGCAC 60.439 66.667 11.55 11.55 40.30 5.01
4265 5906 1.918293 ATCTCCCTGTGGCACCGAA 60.918 57.895 16.26 0.00 0.00 4.30
4266 5907 1.903877 ATCTCCCTGTGGCACCGAAG 61.904 60.000 16.26 9.74 0.00 3.79
4267 5908 2.525629 TCCCTGTGGCACCGAAGA 60.526 61.111 16.26 6.42 0.00 2.87
4274 5915 1.012486 GTGGCACCGAAGAAGTACCG 61.012 60.000 6.29 0.00 0.00 4.02
4317 5958 1.063942 TCATCTCCCGTAGAGGCTGAA 60.064 52.381 0.00 0.00 43.44 3.02
4348 5989 5.353123 TCACTTGGAAATAGTTGTAATCGCC 59.647 40.000 0.00 0.00 0.00 5.54
4432 6115 8.477419 TTTCAGATAGAAATTGTGGACCTTTT 57.523 30.769 0.00 0.00 41.17 2.27
4447 6130 1.067635 CCTTTTCCCACAATGGCTTCG 60.068 52.381 0.00 0.00 35.79 3.79
4492 6175 0.746063 TGCAAACTTTGGTGCCTCAG 59.254 50.000 3.69 0.00 40.14 3.35
4539 6222 3.548745 TGGAGCATGATCTTGTACCTG 57.451 47.619 11.34 0.00 0.00 4.00
4578 6261 9.935682 CATAATTTACAATCGCTTCTACATGTT 57.064 29.630 2.30 0.00 0.00 2.71
4586 6271 9.128107 ACAATCGCTTCTACATGTTTATTTTTG 57.872 29.630 2.30 2.48 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.095036 CGAGAAAGCTAATTCCCCAACTTC 59.905 45.833 0.00 0.00 0.00 3.01
3 4 4.010349 CGAGAAAGCTAATTCCCCAACTT 58.990 43.478 0.00 0.00 0.00 2.66
5 6 3.606687 TCGAGAAAGCTAATTCCCCAAC 58.393 45.455 0.00 0.00 0.00 3.77
23 24 5.424252 AGGGAAATACATAGTTTCACCTCGA 59.576 40.000 0.00 0.00 39.28 4.04
28 29 6.817140 AGTCGAAGGGAAATACATAGTTTCAC 59.183 38.462 0.00 0.00 38.86 3.18
91 92 5.050769 GCGAACATACAGACATACCAATCAG 60.051 44.000 0.00 0.00 0.00 2.90
820 1601 3.701040 ACAACACAGAAATGCAGAAACCT 59.299 39.130 0.00 0.00 0.00 3.50
827 1608 4.085357 ACTCCTACAACACAGAAATGCA 57.915 40.909 0.00 0.00 0.00 3.96
834 1615 7.441157 TGAATTTTGACTACTCCTACAACACAG 59.559 37.037 0.00 0.00 0.00 3.66
869 1761 0.178990 AAAAGCGAAGGGCCTTCAGT 60.179 50.000 37.75 24.98 45.17 3.41
907 1799 3.380004 TGGAGAACTTCAACGTGCAAAAT 59.620 39.130 0.00 0.00 0.00 1.82
908 1800 2.750166 TGGAGAACTTCAACGTGCAAAA 59.250 40.909 0.00 0.00 0.00 2.44
909 1801 2.360844 TGGAGAACTTCAACGTGCAAA 58.639 42.857 0.00 0.00 0.00 3.68
910 1802 2.031258 TGGAGAACTTCAACGTGCAA 57.969 45.000 0.00 0.00 0.00 4.08
911 1803 1.668751 GTTGGAGAACTTCAACGTGCA 59.331 47.619 9.75 0.00 34.75 4.57
912 1804 2.384899 GTTGGAGAACTTCAACGTGC 57.615 50.000 9.75 0.00 34.75 5.34
916 1808 4.210537 TCGAAATCGTTGGAGAACTTCAAC 59.789 41.667 14.03 14.03 40.80 3.18
917 1809 4.373527 TCGAAATCGTTGGAGAACTTCAA 58.626 39.130 2.41 0.00 40.80 2.69
918 1810 3.985008 TCGAAATCGTTGGAGAACTTCA 58.015 40.909 2.41 0.00 40.80 3.02
919 1811 5.348997 AGAATCGAAATCGTTGGAGAACTTC 59.651 40.000 2.41 0.00 40.80 3.01
952 1844 6.145696 ACTCTGCGTCAAATAGTCAGTTAAAC 59.854 38.462 0.00 0.00 0.00 2.01
962 1854 6.754209 AGATTTCTACACTCTGCGTCAAATAG 59.246 38.462 0.00 0.00 0.00 1.73
981 1873 4.582240 CCCATTCTTGGCTTCCTAGATTTC 59.418 45.833 0.00 0.00 42.15 2.17
982 1874 4.540715 CCCATTCTTGGCTTCCTAGATTT 58.459 43.478 0.00 0.00 42.15 2.17
988 1880 1.063417 CATCCCCATTCTTGGCTTCCT 60.063 52.381 0.00 0.00 42.15 3.36
1096 1988 4.333649 TGAACTTGCATCCGAAAGATCATC 59.666 41.667 0.00 0.00 32.31 2.92
1097 1989 4.264253 TGAACTTGCATCCGAAAGATCAT 58.736 39.130 0.00 0.00 32.31 2.45
1098 1990 3.673902 TGAACTTGCATCCGAAAGATCA 58.326 40.909 0.00 0.00 34.14 2.92
1099 1991 4.889832 ATGAACTTGCATCCGAAAGATC 57.110 40.909 0.00 0.00 30.59 2.75
1100 1992 5.471456 GGATATGAACTTGCATCCGAAAGAT 59.529 40.000 0.00 0.00 34.66 2.40
1101 1993 4.816385 GGATATGAACTTGCATCCGAAAGA 59.184 41.667 0.00 0.00 0.00 2.52
1102 1994 4.576053 TGGATATGAACTTGCATCCGAAAG 59.424 41.667 0.00 0.00 39.92 2.62
1103 1995 4.522114 TGGATATGAACTTGCATCCGAAA 58.478 39.130 0.00 0.00 39.92 3.46
1104 1996 4.149511 TGGATATGAACTTGCATCCGAA 57.850 40.909 0.00 0.00 39.92 4.30
1105 1997 3.836365 TGGATATGAACTTGCATCCGA 57.164 42.857 0.00 0.00 39.92 4.55
1106 1998 4.153655 CAGATGGATATGAACTTGCATCCG 59.846 45.833 0.00 0.00 40.40 4.18
1107 1999 5.068636 ACAGATGGATATGAACTTGCATCC 58.931 41.667 0.00 0.00 40.40 3.51
1223 2139 2.304831 GCTTCTCTCCCCTTGGCCT 61.305 63.158 3.32 0.00 0.00 5.19
1224 2140 2.273776 GCTTCTCTCCCCTTGGCC 59.726 66.667 0.00 0.00 0.00 5.36
1624 2540 3.118261 TCATCCACCCAGTTTGATAGAGC 60.118 47.826 0.00 0.00 0.00 4.09
1917 2840 5.652452 ACAATGATTTAGGGTACTTGCTTCC 59.348 40.000 0.00 0.00 0.00 3.46
2228 3179 4.833478 ATATGGAGGCTATGGTCATGTC 57.167 45.455 0.00 0.00 0.00 3.06
2233 3184 7.561722 TGATTCTAGTATATGGAGGCTATGGTC 59.438 40.741 0.00 0.00 0.00 4.02
2234 3185 7.343316 GTGATTCTAGTATATGGAGGCTATGGT 59.657 40.741 0.00 0.00 0.00 3.55
2253 3204 6.294473 ACACATGAAGTTGAGAAGTGATTCT 58.706 36.000 0.00 0.00 0.00 2.40
2331 3282 1.386533 ACACAAGCTCTGGCATATGC 58.613 50.000 19.79 19.79 41.70 3.14
2738 3797 6.589907 ACCAAAATTCGCCTTGATAAACATTC 59.410 34.615 0.00 0.00 0.00 2.67
2744 3803 6.827586 AAGTACCAAAATTCGCCTTGATAA 57.172 33.333 0.00 0.00 0.00 1.75
2750 3809 5.621329 GCATGTAAAGTACCAAAATTCGCCT 60.621 40.000 0.00 0.00 0.00 5.52
2764 3823 5.852282 ACAAAAGAAGTGGCATGTAAAGT 57.148 34.783 0.00 0.00 0.00 2.66
2766 3825 7.099764 TCAAAACAAAAGAAGTGGCATGTAAA 58.900 30.769 0.00 0.00 0.00 2.01
2774 3833 7.545265 TCAACATCTTCAAAACAAAAGAAGTGG 59.455 33.333 0.00 0.00 39.69 4.00
2775 3834 8.464770 TCAACATCTTCAAAACAAAAGAAGTG 57.535 30.769 0.00 0.00 39.69 3.16
2776 3835 9.487790 TTTCAACATCTTCAAAACAAAAGAAGT 57.512 25.926 0.00 0.00 39.69 3.01
2777 3836 9.962759 CTTTCAACATCTTCAAAACAAAAGAAG 57.037 29.630 0.00 0.00 39.98 2.85
2836 3978 2.936202 AGCAGAGGCACAGAAAAAGAA 58.064 42.857 0.00 0.00 44.61 2.52
2838 3980 2.288030 CCAAGCAGAGGCACAGAAAAAG 60.288 50.000 0.00 0.00 44.61 2.27
2926 4068 6.940867 AGGACCCTTTTGTTGACTATACTTTC 59.059 38.462 0.00 0.00 0.00 2.62
2930 4072 6.002082 ACAAGGACCCTTTTGTTGACTATAC 58.998 40.000 0.00 0.00 34.00 1.47
2942 4084 3.374764 AGCTTTGAAACAAGGACCCTTT 58.625 40.909 0.00 0.00 33.42 3.11
3082 4224 1.701031 TTCCGGCCAACAGACCTCAA 61.701 55.000 2.24 0.00 0.00 3.02
3110 4252 2.033757 CAACCTCTGCTGCTGCCT 59.966 61.111 13.47 0.00 38.71 4.75
3284 4426 2.360350 CCTTCGGCACCTGCACAT 60.360 61.111 0.00 0.00 44.36 3.21
3384 4526 0.315251 GGCGATCATCACGGATCAGA 59.685 55.000 0.00 0.00 43.07 3.27
3432 4574 0.615331 GCCAGTCCTTCCTCATGTCA 59.385 55.000 0.00 0.00 0.00 3.58
3617 4770 0.784250 CAACGGAAATCGACAACGCG 60.784 55.000 3.53 3.53 42.43 6.01
3733 4887 1.222115 GCGGACAGAACTGCGAGTTT 61.222 55.000 1.46 0.00 38.80 2.66
3750 4904 1.164411 TGGAAATTACACCTGCAGCG 58.836 50.000 8.66 3.76 0.00 5.18
3754 4908 3.065925 GCTCTGATGGAAATTACACCTGC 59.934 47.826 0.00 0.00 0.00 4.85
3758 4912 5.423015 TCTGAGCTCTGATGGAAATTACAC 58.577 41.667 18.39 0.00 0.00 2.90
3772 4926 3.271729 CATTTGTGCATCTCTGAGCTCT 58.728 45.455 16.19 0.00 0.00 4.09
3784 4938 5.528043 TCTTAGAAAAAGCCATTTGTGCA 57.472 34.783 0.00 0.00 0.00 4.57
3787 4941 7.814587 GCTGTATTCTTAGAAAAAGCCATTTGT 59.185 33.333 12.79 0.00 0.00 2.83
3795 4949 7.913674 ACTCCTGCTGTATTCTTAGAAAAAG 57.086 36.000 0.00 0.00 0.00 2.27
3802 4956 6.296026 ACAACAAACTCCTGCTGTATTCTTA 58.704 36.000 0.00 0.00 0.00 2.10
3810 5031 2.289002 GACTGACAACAAACTCCTGCTG 59.711 50.000 0.00 0.00 0.00 4.41
3839 5060 1.813513 CTGGTGTAGTGCTTCCTTGG 58.186 55.000 0.00 0.00 0.00 3.61
3844 5065 1.593196 TTGTGCTGGTGTAGTGCTTC 58.407 50.000 0.00 0.00 0.00 3.86
3863 5084 4.809426 GCCATGACGCTAGTACTACATTTT 59.191 41.667 0.00 0.00 0.00 1.82
3865 5086 3.550233 CGCCATGACGCTAGTACTACATT 60.550 47.826 0.00 0.00 0.00 2.71
3866 5087 2.031069 CGCCATGACGCTAGTACTACAT 60.031 50.000 0.00 0.00 0.00 2.29
3868 5089 1.600957 TCGCCATGACGCTAGTACTAC 59.399 52.381 0.00 0.00 0.00 2.73
3869 5090 1.957668 TCGCCATGACGCTAGTACTA 58.042 50.000 1.89 1.89 0.00 1.82
3870 5091 1.100510 TTCGCCATGACGCTAGTACT 58.899 50.000 0.00 0.00 0.00 2.73
3871 5092 1.197910 GTTCGCCATGACGCTAGTAC 58.802 55.000 0.00 0.00 0.00 2.73
3872 5093 0.101759 GGTTCGCCATGACGCTAGTA 59.898 55.000 0.00 0.00 37.19 1.82
3873 5094 1.153628 GGTTCGCCATGACGCTAGT 60.154 57.895 0.00 0.00 37.19 2.57
3878 5194 2.740826 AACGGGTTCGCCATGACG 60.741 61.111 0.00 0.00 40.63 4.35
3885 5201 3.284449 AGCCAACAACGGGTTCGC 61.284 61.111 4.17 4.17 43.03 4.70
3888 5204 1.388837 GGTTCAGCCAACAACGGGTT 61.389 55.000 0.00 0.00 41.47 4.11
3894 5210 1.414919 AGACTACGGTTCAGCCAACAA 59.585 47.619 0.00 0.00 36.61 2.83
3895 5211 1.045407 AGACTACGGTTCAGCCAACA 58.955 50.000 0.00 0.00 36.61 3.33
3896 5212 3.308438 TTAGACTACGGTTCAGCCAAC 57.692 47.619 0.00 0.00 36.97 3.77
3899 5215 3.063588 GCAATTTAGACTACGGTTCAGCC 59.936 47.826 0.00 0.00 0.00 4.85
3900 5216 3.241995 CGCAATTTAGACTACGGTTCAGC 60.242 47.826 0.00 0.00 0.00 4.26
3901 5217 3.924686 ACGCAATTTAGACTACGGTTCAG 59.075 43.478 0.00 0.00 0.00 3.02
3903 5219 6.579491 ATTACGCAATTTAGACTACGGTTC 57.421 37.500 0.00 0.00 0.00 3.62
3904 5220 7.761249 ACTTATTACGCAATTTAGACTACGGTT 59.239 33.333 0.00 0.00 0.00 4.44
3905 5221 7.260603 ACTTATTACGCAATTTAGACTACGGT 58.739 34.615 0.00 0.00 0.00 4.83
3906 5222 7.689953 ACTTATTACGCAATTTAGACTACGG 57.310 36.000 0.00 0.00 0.00 4.02
3907 5223 9.615779 GAAACTTATTACGCAATTTAGACTACG 57.384 33.333 0.00 0.00 0.00 3.51
3908 5224 9.615779 CGAAACTTATTACGCAATTTAGACTAC 57.384 33.333 0.00 0.00 0.00 2.73
3909 5225 9.357652 ACGAAACTTATTACGCAATTTAGACTA 57.642 29.630 0.00 0.00 0.00 2.59
3910 5226 8.248117 ACGAAACTTATTACGCAATTTAGACT 57.752 30.769 0.00 0.00 0.00 3.24
3911 5227 8.870242 AACGAAACTTATTACGCAATTTAGAC 57.130 30.769 0.00 0.00 0.00 2.59
3918 5234 8.903723 CCAAATTTAACGAAACTTATTACGCAA 58.096 29.630 0.00 0.00 0.00 4.85
3919 5235 7.060864 GCCAAATTTAACGAAACTTATTACGCA 59.939 33.333 0.00 0.00 0.00 5.24
3920 5236 7.271868 AGCCAAATTTAACGAAACTTATTACGC 59.728 33.333 0.00 0.00 0.00 4.42
3923 5239 9.757859 CGTAGCCAAATTTAACGAAACTTATTA 57.242 29.630 8.15 0.00 35.66 0.98
3925 5241 8.031848 TCGTAGCCAAATTTAACGAAACTTAT 57.968 30.769 12.15 0.00 39.40 1.73
3926 5242 7.418840 TCGTAGCCAAATTTAACGAAACTTA 57.581 32.000 12.15 0.00 39.40 2.24
3927 5243 6.303021 TCGTAGCCAAATTTAACGAAACTT 57.697 33.333 12.15 0.00 39.40 2.66
3928 5244 5.927954 TCGTAGCCAAATTTAACGAAACT 57.072 34.783 12.15 0.00 39.40 2.66
3931 5247 5.927954 ACTTCGTAGCCAAATTTAACGAA 57.072 34.783 19.73 19.73 46.67 3.85
3933 5249 5.910723 ACAAACTTCGTAGCCAAATTTAACG 59.089 36.000 0.00 0.00 34.99 3.18
3935 5251 7.432838 GTCAACAAACTTCGTAGCCAAATTTAA 59.567 33.333 0.00 0.00 0.00 1.52
3936 5252 6.913673 GTCAACAAACTTCGTAGCCAAATTTA 59.086 34.615 0.00 0.00 0.00 1.40
3937 5253 5.746721 GTCAACAAACTTCGTAGCCAAATTT 59.253 36.000 0.00 0.00 0.00 1.82
3939 5255 4.578928 AGTCAACAAACTTCGTAGCCAAAT 59.421 37.500 0.00 0.00 0.00 2.32
3940 5256 3.942748 AGTCAACAAACTTCGTAGCCAAA 59.057 39.130 0.00 0.00 0.00 3.28
3941 5257 3.537580 AGTCAACAAACTTCGTAGCCAA 58.462 40.909 0.00 0.00 0.00 4.52
3942 5258 3.188159 AGTCAACAAACTTCGTAGCCA 57.812 42.857 0.00 0.00 0.00 4.75
3943 5259 3.120782 CGTAGTCAACAAACTTCGTAGCC 59.879 47.826 0.00 0.00 35.93 3.93
3944 5260 3.120782 CCGTAGTCAACAAACTTCGTAGC 59.879 47.826 3.13 0.00 38.07 3.58
3945 5261 4.293415 ACCGTAGTCAACAAACTTCGTAG 58.707 43.478 3.13 0.00 38.07 3.51
3948 5264 3.307782 ACAACCGTAGTCAACAAACTTCG 59.692 43.478 0.00 0.00 39.06 3.79
3949 5265 4.870221 ACAACCGTAGTCAACAAACTTC 57.130 40.909 0.00 0.00 0.00 3.01
3951 5267 4.255301 TCAACAACCGTAGTCAACAAACT 58.745 39.130 0.00 0.00 0.00 2.66
3952 5268 4.603231 TCAACAACCGTAGTCAACAAAC 57.397 40.909 0.00 0.00 0.00 2.93
3953 5269 5.354513 TCAATCAACAACCGTAGTCAACAAA 59.645 36.000 0.00 0.00 0.00 2.83
3954 5270 4.876679 TCAATCAACAACCGTAGTCAACAA 59.123 37.500 0.00 0.00 0.00 2.83
3955 5271 4.443621 TCAATCAACAACCGTAGTCAACA 58.556 39.130 0.00 0.00 0.00 3.33
3958 5274 4.083537 GCAATCAATCAACAACCGTAGTCA 60.084 41.667 0.00 0.00 0.00 3.41
3959 5275 4.083537 TGCAATCAATCAACAACCGTAGTC 60.084 41.667 0.00 0.00 0.00 2.59
3960 5276 3.818210 TGCAATCAATCAACAACCGTAGT 59.182 39.130 0.00 0.00 0.00 2.73
3961 5277 4.158384 GTGCAATCAATCAACAACCGTAG 58.842 43.478 0.00 0.00 0.00 3.51
3962 5278 3.364465 CGTGCAATCAATCAACAACCGTA 60.364 43.478 0.00 0.00 0.00 4.02
3963 5279 2.604373 CGTGCAATCAATCAACAACCGT 60.604 45.455 0.00 0.00 0.00 4.83
3964 5280 1.978097 CGTGCAATCAATCAACAACCG 59.022 47.619 0.00 0.00 0.00 4.44
3965 5281 2.288152 ACCGTGCAATCAATCAACAACC 60.288 45.455 0.00 0.00 0.00 3.77
3966 5282 3.011949 ACCGTGCAATCAATCAACAAC 57.988 42.857 0.00 0.00 0.00 3.32
3967 5283 3.724508 AACCGTGCAATCAATCAACAA 57.275 38.095 0.00 0.00 0.00 2.83
3971 5287 3.419264 GCATAACCGTGCAATCAATCA 57.581 42.857 0.00 0.00 44.43 2.57
3980 5296 2.222729 CGAGTAAACTGCATAACCGTGC 60.223 50.000 0.00 0.00 45.25 5.34
3981 5297 2.222729 GCGAGTAAACTGCATAACCGTG 60.223 50.000 0.00 0.00 0.00 4.94
3989 5305 0.970640 TACCCAGCGAGTAAACTGCA 59.029 50.000 0.00 0.00 32.37 4.41
3991 5307 1.549170 ACCTACCCAGCGAGTAAACTG 59.451 52.381 0.00 0.00 0.00 3.16
3992 5308 1.823610 GACCTACCCAGCGAGTAAACT 59.176 52.381 0.00 0.00 0.00 2.66
3993 5309 1.547372 TGACCTACCCAGCGAGTAAAC 59.453 52.381 0.00 0.00 0.00 2.01
3995 5311 1.180029 GTGACCTACCCAGCGAGTAA 58.820 55.000 0.00 0.00 0.00 2.24
3996 5312 0.330604 AGTGACCTACCCAGCGAGTA 59.669 55.000 0.00 0.00 0.00 2.59
4010 5640 0.036022 AGGAGAAGGCTGCAAGTGAC 59.964 55.000 0.50 0.00 34.49 3.67
4014 5644 1.613836 AACAAGGAGAAGGCTGCAAG 58.386 50.000 0.50 0.00 34.49 4.01
4020 5650 3.573967 TCATTGGAAAACAAGGAGAAGGC 59.426 43.478 0.00 0.00 44.16 4.35
4039 5669 9.921056 GGGAAACCCATGGTACAAGTACATCAT 62.921 44.444 11.73 4.87 45.77 2.45
4063 5693 2.936498 ACTTATGCAGTCGATTTTCGGG 59.064 45.455 0.00 0.00 40.88 5.14
4065 5695 5.382303 ACAAACTTATGCAGTCGATTTTCG 58.618 37.500 0.00 0.00 42.10 3.46
4068 5698 8.718102 ATACTACAAACTTATGCAGTCGATTT 57.282 30.769 0.00 0.00 32.94 2.17
4070 5700 7.979537 TGAATACTACAAACTTATGCAGTCGAT 59.020 33.333 0.00 0.00 32.94 3.59
4072 5702 7.520119 TGAATACTACAAACTTATGCAGTCG 57.480 36.000 0.00 0.00 32.94 4.18
4075 5705 8.454106 AGCTTTGAATACTACAAACTTATGCAG 58.546 33.333 0.00 0.00 34.30 4.41
4090 5720 8.479280 CACACATGTTGTTTTAGCTTTGAATAC 58.521 33.333 0.00 0.00 35.67 1.89
4094 5724 6.033341 GTCACACATGTTGTTTTAGCTTTGA 58.967 36.000 0.00 0.00 35.67 2.69
4096 5726 5.804979 GTGTCACACATGTTGTTTTAGCTTT 59.195 36.000 2.00 0.00 35.67 3.51
4097 5727 5.105957 TGTGTCACACATGTTGTTTTAGCTT 60.106 36.000 6.50 0.00 39.62 3.74
4098 5728 4.397730 TGTGTCACACATGTTGTTTTAGCT 59.602 37.500 6.50 0.00 39.62 3.32
4099 5729 4.667262 TGTGTCACACATGTTGTTTTAGC 58.333 39.130 6.50 0.00 39.62 3.09
4101 5731 6.013842 TGTTGTGTCACACATGTTGTTTTA 57.986 33.333 12.49 0.00 44.16 1.52
4104 5734 4.511617 TTGTTGTGTCACACATGTTGTT 57.488 36.364 12.49 0.00 44.16 2.83
4105 5735 4.484236 CTTTGTTGTGTCACACATGTTGT 58.516 39.130 12.49 0.00 44.16 3.32
4106 5736 3.304026 GCTTTGTTGTGTCACACATGTTG 59.696 43.478 12.49 2.99 44.16 3.33
4107 5737 3.193267 AGCTTTGTTGTGTCACACATGTT 59.807 39.130 12.49 0.00 44.16 2.71
4108 5738 2.754552 AGCTTTGTTGTGTCACACATGT 59.245 40.909 12.49 0.00 44.16 3.21
4109 5739 3.425577 AGCTTTGTTGTGTCACACATG 57.574 42.857 12.49 1.57 44.16 3.21
4110 5740 4.202010 GGTAAGCTTTGTTGTGTCACACAT 60.202 41.667 12.49 0.00 44.16 3.21
4111 5741 3.127895 GGTAAGCTTTGTTGTGTCACACA 59.872 43.478 6.50 6.50 43.02 3.72
4112 5742 3.377172 AGGTAAGCTTTGTTGTGTCACAC 59.623 43.478 3.20 0.00 34.56 3.82
4113 5743 3.616219 AGGTAAGCTTTGTTGTGTCACA 58.384 40.909 3.20 0.18 0.00 3.58
4114 5744 4.632538 AAGGTAAGCTTTGTTGTGTCAC 57.367 40.909 3.20 0.00 0.00 3.67
4115 5745 6.058833 TCATAAGGTAAGCTTTGTTGTGTCA 58.941 36.000 3.20 0.00 0.00 3.58
4116 5746 6.204882 ACTCATAAGGTAAGCTTTGTTGTGTC 59.795 38.462 3.20 0.00 0.00 3.67
4117 5747 6.017109 CACTCATAAGGTAAGCTTTGTTGTGT 60.017 38.462 3.20 0.00 0.00 3.72
4118 5748 6.373779 CACTCATAAGGTAAGCTTTGTTGTG 58.626 40.000 3.20 5.01 0.00 3.33
4119 5749 5.473504 CCACTCATAAGGTAAGCTTTGTTGT 59.526 40.000 3.20 0.00 0.00 3.32
4120 5750 5.473504 ACCACTCATAAGGTAAGCTTTGTTG 59.526 40.000 3.20 0.00 36.07 3.33
4146 5776 2.879026 AGAAAAACCAGTCGCCTTCTTC 59.121 45.455 0.00 0.00 0.00 2.87
4147 5777 2.932261 AGAAAAACCAGTCGCCTTCTT 58.068 42.857 0.00 0.00 0.00 2.52
4148 5778 2.640316 AGAAAAACCAGTCGCCTTCT 57.360 45.000 0.00 0.00 0.00 2.85
4150 5780 3.020984 TCAAAGAAAAACCAGTCGCCTT 58.979 40.909 0.00 0.00 0.00 4.35
4170 5800 2.165437 CTCCACCTACTGACTCAAGCTC 59.835 54.545 0.00 0.00 0.00 4.09
4175 5805 1.924731 CACCTCCACCTACTGACTCA 58.075 55.000 0.00 0.00 0.00 3.41
4195 5825 6.554419 TCAACAAACAAAGAACAGAGTGATG 58.446 36.000 0.00 0.00 0.00 3.07
4209 5848 7.857734 TCTCTGAAACTACATCAACAAACAA 57.142 32.000 0.00 0.00 0.00 2.83
4244 5885 2.439156 GTGCCACAGGGAGATGCC 60.439 66.667 0.00 0.00 35.59 4.40
4261 5902 1.538512 TGTCAGTCGGTACTTCTTCGG 59.461 52.381 0.00 0.00 31.97 4.30
4265 5906 3.700038 CCCTTATGTCAGTCGGTACTTCT 59.300 47.826 0.00 0.00 31.97 2.85
4266 5907 3.446516 ACCCTTATGTCAGTCGGTACTTC 59.553 47.826 0.00 0.00 31.97 3.01
4267 5908 3.438183 ACCCTTATGTCAGTCGGTACTT 58.562 45.455 0.00 0.00 31.97 2.24
4317 5958 7.418337 ACAACTATTTCCAAGTGAAAAAGGT 57.582 32.000 0.00 0.00 45.67 3.50
4364 6005 0.966179 TGCACTGTCATACTCCACGT 59.034 50.000 0.00 0.00 0.00 4.49
4366 6007 4.256920 AGAAATGCACTGTCATACTCCAC 58.743 43.478 0.00 0.00 0.00 4.02
4393 6038 3.272439 TCTGAAATTGCTGCTTTCGTG 57.728 42.857 0.00 1.79 35.77 4.35
4427 6110 1.067635 CGAAGCCATTGTGGGAAAAGG 60.068 52.381 0.00 0.00 38.19 3.11
4447 6130 0.455005 GCATTCTTTGGAGAGCAGGC 59.545 55.000 0.00 0.00 32.44 4.85
4477 6160 2.558359 GCAATACTGAGGCACCAAAGTT 59.442 45.455 0.29 0.00 0.00 2.66
4492 6175 2.009774 AGATGTGAAGCACGGCAATAC 58.990 47.619 0.00 0.00 37.14 1.89
4566 6249 6.868339 AGCCACAAAAATAAACATGTAGAAGC 59.132 34.615 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.