Multiple sequence alignment - TraesCS5B01G273700

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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 TraesCS5B01G273700 chr5B 100.000 4614 0 0 1 4614 458902573 458907186 0.000000e+00 8521.0
1 TraesCS5B01G273700 chr5B 83.784 407 50 11 384 787 378992074 378992467 5.640000e-99 372.0
2 TraesCS5B01G273700 chr5B 99.468 188 1 0 4427 4614 26449140 26448953 4.420000e-90 342.0
3 TraesCS5B01G273700 chr5D 95.545 1751 57 7 825 2575 382493578 382495307 0.000000e+00 2782.0
4 TraesCS5B01G273700 chr5D 93.849 1512 52 11 2617 4122 382495309 382496785 0.000000e+00 2239.0
5 TraesCS5B01G273700 chr5D 87.633 752 75 11 1 743 382492844 382493586 0.000000e+00 857.0
6 TraesCS5B01G273700 chr5D 94.434 557 30 1 1787 2343 383084865 383085420 0.000000e+00 856.0
7 TraesCS5B01G273700 chr5D 83.075 839 98 22 2476 3295 382943321 382942508 0.000000e+00 723.0
8 TraesCS5B01G273700 chr5D 89.677 465 21 11 2471 2935 383085417 383085854 6.700000e-158 568.0
9 TraesCS5B01G273700 chr5D 82.619 420 54 13 1787 2200 382943772 382943366 2.040000e-93 353.0
10 TraesCS5B01G273700 chr5D 75.916 764 136 29 1043 1779 382946274 382945532 9.500000e-92 348.0
11 TraesCS5B01G273700 chr5D 93.443 61 4 0 4119 4179 382496840 382496900 1.770000e-14 91.6
12 TraesCS5B01G273700 chr5A 89.627 1957 134 29 1 1949 482906828 482908723 0.000000e+00 2425.0
13 TraesCS5B01G273700 chr5A 95.346 1418 52 6 2471 3883 482920154 482921562 0.000000e+00 2241.0
14 TraesCS5B01G273700 chr5A 95.000 400 20 0 1944 2343 482919758 482920157 3.030000e-176 628.0
15 TraesCS5B01G273700 chr5A 91.133 203 15 1 3923 4122 482921545 482921747 5.880000e-69 272.0
16 TraesCS5B01G273700 chr7A 99.474 190 0 1 4426 4614 2015435 2015246 1.230000e-90 344.0
17 TraesCS5B01G273700 chr7A 99.471 189 1 0 4426 4614 45189397 45189585 1.230000e-90 344.0
18 TraesCS5B01G273700 chr7A 99.474 190 0 1 4426 4614 552450766 552450955 1.230000e-90 344.0
19 TraesCS5B01G273700 chr7A 99.474 190 0 1 4426 4614 552452736 552452925 1.230000e-90 344.0
20 TraesCS5B01G273700 chr7A 82.812 128 22 0 2345 2472 48163107 48162980 1.050000e-21 115.0
21 TraesCS5B01G273700 chr7A 81.890 127 23 0 2346 2472 6627357 6627231 1.760000e-19 108.0
22 TraesCS5B01G273700 chr6A 99.474 190 0 1 4426 4614 560642924 560643113 1.230000e-90 344.0
23 TraesCS5B01G273700 chr4A 99.471 189 1 0 4426 4614 658634749 658634561 1.230000e-90 344.0
24 TraesCS5B01G273700 chr4A 98.446 193 3 0 4422 4614 658636033 658636225 1.590000e-89 340.0
25 TraesCS5B01G273700 chr2B 98.469 196 1 2 4420 4614 416058656 416058850 1.230000e-90 344.0
26 TraesCS5B01G273700 chr7D 93.382 136 9 0 2339 2474 577750711 577750846 7.830000e-48 202.0
27 TraesCS5B01G273700 chr3A 92.701 137 9 1 2339 2474 724539867 724540003 3.640000e-46 196.0
28 TraesCS5B01G273700 chr3A 92.701 137 9 1 2339 2474 724540122 724540258 3.640000e-46 196.0
29 TraesCS5B01G273700 chr2A 92.647 136 10 0 2339 2474 750366033 750366168 3.640000e-46 196.0
30 TraesCS5B01G273700 chr2A 91.791 134 10 1 2339 2472 514859204 514859072 7.880000e-43 185.0
31 TraesCS5B01G273700 chr2D 83.871 124 20 0 2349 2472 76635209 76635332 8.110000e-23 119.0
32 TraesCS5B01G273700 chr3D 85.135 74 10 1 37 110 431721064 431720992 1.780000e-09 75.0


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 TraesCS5B01G273700 chr5B 458902573 458907186 4613 False 8521.000000 8521 100.000000 1 4614 1 chr5B.!!$F2 4613
1 TraesCS5B01G273700 chr5D 382492844 382496900 4056 False 1492.400000 2782 92.617500 1 4179 4 chr5D.!!$F1 4178
2 TraesCS5B01G273700 chr5D 383084865 383085854 989 False 712.000000 856 92.055500 1787 2935 2 chr5D.!!$F2 1148
3 TraesCS5B01G273700 chr5D 382942508 382946274 3766 True 474.666667 723 80.536667 1043 3295 3 chr5D.!!$R1 2252
4 TraesCS5B01G273700 chr5A 482906828 482908723 1895 False 2425.000000 2425 89.627000 1 1949 1 chr5A.!!$F1 1948
5 TraesCS5B01G273700 chr5A 482919758 482921747 1989 False 1047.000000 2241 93.826333 1944 4122 3 chr5A.!!$F2 2178
6 TraesCS5B01G273700 chr7A 552450766 552452925 2159 False 344.000000 344 99.474000 4426 4614 2 chr7A.!!$F2 188

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
890 909 0.107703 TGATCCTTTAGCGTGCCCAG 60.108 55.000 0.0 0.0 0.00 4.45 F
891 910 0.178068 GATCCTTTAGCGTGCCCAGA 59.822 55.000 0.0 0.0 0.00 3.86 F
937 956 0.394565 CTGAAGGAGCCGAATAGGGG 59.605 60.000 0.0 0.0 41.48 4.79 F
975 994 1.686110 ACTGAAGAGGTAGCGGGGG 60.686 63.158 0.0 0.0 0.00 5.40 F
2416 4219 2.226437 GCTGCTGTTCAAATCGAAGGAA 59.774 45.455 0.0 0.0 33.09 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 3726 0.324943 AAACTGCCGTGCCTGACTAT 59.675 50.000 0.0 0.0 0.00 2.12 R
2861 4673 1.150827 TGCAGTGCAATGAGACGAAG 58.849 50.000 20.0 0.0 34.76 3.79 R
2980 4802 4.878397 GCAGAGGCACATACAATTTAGACT 59.122 41.667 0.0 0.0 40.72 3.24 R
2989 4811 0.983467 TTCCAGCAGAGGCACATACA 59.017 50.000 0.0 0.0 44.61 2.29 R
4179 6074 0.036875 ACAGAAGCAGCCCTTGGTAC 59.963 55.000 0.0 0.0 36.24 3.34 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
33 34 3.548818 CGACATGTCGCATAGATGACTGA 60.549 47.826 32.93 0.00 46.50 3.41
34 35 4.554292 GACATGTCGCATAGATGACTGAT 58.446 43.478 10.69 0.00 36.10 2.90
64 65 2.252535 TGTCTCATGTCTCCCCATCA 57.747 50.000 0.00 0.00 0.00 3.07
85 86 1.150536 GGGTGTTGCTGGAACTCCA 59.849 57.895 26.80 0.00 46.18 3.86
626 643 7.119699 TGTTTTTAAGCATATGTCTCACTCCAG 59.880 37.037 4.29 0.00 0.00 3.86
646 663 0.984995 GGTCTTTCCCCAGCTACACT 59.015 55.000 0.00 0.00 0.00 3.55
667 684 7.268586 ACACTAGATAACTTGTAAGCATGAGG 58.731 38.462 0.00 0.00 31.64 3.86
812 831 7.504924 AGAATAAACAGTCAACGAAATGGAA 57.495 32.000 0.00 0.00 0.00 3.53
823 842 1.885887 CGAAATGGAAGGAAACAGCCA 59.114 47.619 0.00 0.00 39.63 4.75
878 897 3.947834 CGAATAAAGCCCACTTGATCCTT 59.052 43.478 0.00 0.00 35.85 3.36
884 903 1.679032 GCCCACTTGATCCTTTAGCGT 60.679 52.381 0.00 0.00 0.00 5.07
886 905 1.398390 CCACTTGATCCTTTAGCGTGC 59.602 52.381 0.00 0.00 0.00 5.34
887 906 1.398390 CACTTGATCCTTTAGCGTGCC 59.602 52.381 0.00 0.00 0.00 5.01
888 907 1.017387 CTTGATCCTTTAGCGTGCCC 58.983 55.000 0.00 0.00 0.00 5.36
890 909 0.107703 TGATCCTTTAGCGTGCCCAG 60.108 55.000 0.00 0.00 0.00 4.45
891 910 0.178068 GATCCTTTAGCGTGCCCAGA 59.822 55.000 0.00 0.00 0.00 3.86
892 911 0.839946 ATCCTTTAGCGTGCCCAGAT 59.160 50.000 0.00 0.00 0.00 2.90
894 913 0.734889 CCTTTAGCGTGCCCAGATTG 59.265 55.000 0.00 0.00 0.00 2.67
895 914 1.678728 CCTTTAGCGTGCCCAGATTGA 60.679 52.381 0.00 0.00 0.00 2.57
937 956 0.394565 CTGAAGGAGCCGAATAGGGG 59.605 60.000 0.00 0.00 41.48 4.79
975 994 1.686110 ACTGAAGAGGTAGCGGGGG 60.686 63.158 0.00 0.00 0.00 5.40
1080 1099 2.435059 GCTCAGAGGACAACGGCC 60.435 66.667 0.00 0.00 0.00 6.13
1235 1269 5.021458 AGTGGTAAGATCTTCTTTCGGGTA 58.979 41.667 12.24 0.00 37.89 3.69
1236 1270 5.127356 AGTGGTAAGATCTTCTTTCGGGTAG 59.873 44.000 12.24 0.00 37.89 3.18
1237 1271 4.142004 TGGTAAGATCTTCTTTCGGGTAGC 60.142 45.833 12.24 1.28 37.89 3.58
1334 1369 2.369257 CTGATATGGAGGTGCCGCGT 62.369 60.000 4.92 0.00 40.66 6.01
1540 1581 6.094742 TGTTCATTGTTTTGACTTGCTGTCTA 59.905 34.615 10.73 2.23 45.54 2.59
1686 1727 5.984695 TCTACAAGCTCAGTGTTGTATCT 57.015 39.130 5.55 0.00 38.23 1.98
1815 3613 8.472413 CCATATTATTGGACATTCATTGGATCC 58.528 37.037 4.20 4.20 39.25 3.36
2125 3928 6.006275 AGTTTGTCAGGCTGATATACCAAT 57.994 37.500 23.79 9.31 0.00 3.16
2246 4049 9.665719 AAATGCGATTTTTAGGGAAACATTATT 57.334 25.926 0.00 0.00 0.00 1.40
2416 4219 2.226437 GCTGCTGTTCAAATCGAAGGAA 59.774 45.455 0.00 0.00 33.09 3.36
2426 4229 6.155475 TCAAATCGAAGGAATTGTGGTTTT 57.845 33.333 0.00 0.00 35.13 2.43
2427 4230 6.578023 TCAAATCGAAGGAATTGTGGTTTTT 58.422 32.000 0.00 0.00 35.13 1.94
2590 4402 4.348168 TCTTGAGAGAAGTGTTAAGGGCTT 59.652 41.667 0.00 0.00 0.00 4.35
2598 4410 5.889289 AGAAGTGTTAAGGGCTTTGTTTGTA 59.111 36.000 0.00 0.00 0.00 2.41
2861 4673 5.043248 GGCATGATGTATTGTTAAACTGCC 58.957 41.667 0.00 0.00 38.70 4.85
2865 4677 6.176975 TGATGTATTGTTAAACTGCCTTCG 57.823 37.500 0.00 0.00 0.00 3.79
3158 4982 5.576384 GCACTCTTTCTGTTCTATCTGTCAG 59.424 44.000 0.00 0.00 0.00 3.51
3219 5045 8.525316 TGTTTGTAATCCGATTTCAGTAGTCTA 58.475 33.333 0.00 0.00 0.00 2.59
3243 5069 6.787085 CCAAGTCTTGGTTAAACTCTGTAG 57.213 41.667 21.76 0.00 45.93 2.74
3244 5070 5.701290 CCAAGTCTTGGTTAAACTCTGTAGG 59.299 44.000 21.76 0.00 45.93 3.18
3312 5142 8.992835 TGTATCTGCTGTATCAATATGATGTC 57.007 34.615 3.17 0.00 37.70 3.06
3395 5225 5.045872 GCATTTCTTTTGGATATGGCTCAC 58.954 41.667 0.00 0.00 35.10 3.51
3403 5233 4.077300 TGGATATGGCTCACTCAATCAC 57.923 45.455 0.00 0.00 0.00 3.06
3415 5245 7.170658 GGCTCACTCAATCACTAACTGAATATC 59.829 40.741 0.00 0.00 30.60 1.63
3454 5284 1.957877 CCGGTTCTCCTCCTCTACATC 59.042 57.143 0.00 0.00 0.00 3.06
3490 5320 0.877071 ATGTTGCTGGCGTGAAGAAG 59.123 50.000 0.00 0.00 0.00 2.85
3607 5437 2.625314 CTCTCCCTATGACGATTCTGCA 59.375 50.000 0.00 0.00 0.00 4.41
3637 5467 1.339438 TGAGGCTCAGGTTCTTGATGC 60.339 52.381 14.43 0.00 0.00 3.91
3638 5468 0.990374 AGGCTCAGGTTCTTGATGCT 59.010 50.000 0.00 0.00 0.00 3.79
3691 5521 3.068590 GGTATTTTCTGGATGGGCATGTG 59.931 47.826 0.00 0.00 0.00 3.21
3797 5627 2.033372 TGTTCGGGCGTAGAATATGGA 58.967 47.619 0.00 0.00 0.00 3.41
3798 5628 2.035449 TGTTCGGGCGTAGAATATGGAG 59.965 50.000 0.00 0.00 0.00 3.86
3799 5629 0.601558 TCGGGCGTAGAATATGGAGC 59.398 55.000 0.00 0.00 0.00 4.70
3800 5630 0.389948 CGGGCGTAGAATATGGAGCC 60.390 60.000 0.00 0.00 43.47 4.70
3801 5631 3.534721 GGCGTAGAATATGGAGCCC 57.465 57.895 0.00 0.00 38.72 5.19
3802 5632 0.036294 GGCGTAGAATATGGAGCCCC 60.036 60.000 0.00 0.00 38.72 5.80
3821 5651 0.039618 CAGGCCCCCAGTGTGTAATT 59.960 55.000 0.00 0.00 0.00 1.40
3826 5656 2.100749 GCCCCCAGTGTGTAATTTATGC 59.899 50.000 0.00 0.00 0.00 3.14
3854 5684 3.238108 AGTTCTCATCTGTACAAGCCG 57.762 47.619 0.00 0.00 0.00 5.52
3868 5698 2.963101 ACAAGCCGCCATATGTCTAGTA 59.037 45.455 1.24 0.00 0.00 1.82
3869 5699 3.578716 ACAAGCCGCCATATGTCTAGTAT 59.421 43.478 1.24 0.00 0.00 2.12
3870 5700 4.177026 CAAGCCGCCATATGTCTAGTATC 58.823 47.826 1.24 0.00 0.00 2.24
3871 5701 3.702792 AGCCGCCATATGTCTAGTATCT 58.297 45.455 1.24 0.00 0.00 1.98
3872 5702 4.856509 AGCCGCCATATGTCTAGTATCTA 58.143 43.478 1.24 0.00 0.00 1.98
3873 5703 5.262009 AGCCGCCATATGTCTAGTATCTAA 58.738 41.667 1.24 0.00 0.00 2.10
3874 5704 5.125739 AGCCGCCATATGTCTAGTATCTAAC 59.874 44.000 1.24 0.00 0.00 2.34
3875 5705 5.125739 GCCGCCATATGTCTAGTATCTAACT 59.874 44.000 1.24 0.00 42.62 2.24
3876 5706 6.350277 GCCGCCATATGTCTAGTATCTAACTT 60.350 42.308 1.24 0.00 39.80 2.66
3877 5707 7.148120 GCCGCCATATGTCTAGTATCTAACTTA 60.148 40.741 1.24 0.00 39.80 2.24
3975 5805 6.837048 TGCCCCTTTTTCCTATAAATCTTACC 59.163 38.462 0.00 0.00 0.00 2.85
3996 5826 6.737254 ACCGAAATTCTGTAGTGGTTATTG 57.263 37.500 0.00 0.00 0.00 1.90
4160 6055 1.064017 TCACTGGCAAACCCTGAAGTT 60.064 47.619 0.00 0.00 36.47 2.66
4161 6056 1.067516 CACTGGCAAACCCTGAAGTTG 59.932 52.381 0.00 0.00 36.47 3.16
4179 6074 5.536554 AGTTGAGAAAGATGCATGTTACG 57.463 39.130 9.82 0.00 0.00 3.18
4180 6075 4.997395 AGTTGAGAAAGATGCATGTTACGT 59.003 37.500 9.82 0.00 0.00 3.57
4181 6076 6.163476 AGTTGAGAAAGATGCATGTTACGTA 58.837 36.000 9.82 0.00 0.00 3.57
4182 6077 6.090898 AGTTGAGAAAGATGCATGTTACGTAC 59.909 38.462 9.82 5.32 0.00 3.67
4183 6078 4.868171 TGAGAAAGATGCATGTTACGTACC 59.132 41.667 9.82 0.00 0.00 3.34
4184 6079 4.827692 AGAAAGATGCATGTTACGTACCA 58.172 39.130 9.82 0.00 0.00 3.25
4185 6080 5.242434 AGAAAGATGCATGTTACGTACCAA 58.758 37.500 9.82 0.00 0.00 3.67
4186 6081 5.351465 AGAAAGATGCATGTTACGTACCAAG 59.649 40.000 9.82 0.00 0.00 3.61
4187 6082 3.531538 AGATGCATGTTACGTACCAAGG 58.468 45.455 2.46 0.00 0.00 3.61
4188 6083 2.102070 TGCATGTTACGTACCAAGGG 57.898 50.000 0.00 0.00 0.00 3.95
4189 6084 0.730840 GCATGTTACGTACCAAGGGC 59.269 55.000 0.00 0.00 0.00 5.19
4190 6085 1.677820 GCATGTTACGTACCAAGGGCT 60.678 52.381 0.00 0.00 0.00 5.19
4191 6086 2.006888 CATGTTACGTACCAAGGGCTG 58.993 52.381 0.00 0.00 0.00 4.85
4192 6087 0.320946 TGTTACGTACCAAGGGCTGC 60.321 55.000 0.00 0.00 0.00 5.25
4193 6088 0.036671 GTTACGTACCAAGGGCTGCT 60.037 55.000 0.00 0.00 0.00 4.24
4194 6089 0.688487 TTACGTACCAAGGGCTGCTT 59.312 50.000 0.00 0.00 0.00 3.91
4195 6090 0.248289 TACGTACCAAGGGCTGCTTC 59.752 55.000 0.00 0.00 0.00 3.86
4196 6091 1.296715 CGTACCAAGGGCTGCTTCT 59.703 57.895 0.00 0.00 0.00 2.85
4197 6092 1.021390 CGTACCAAGGGCTGCTTCTG 61.021 60.000 0.00 0.00 0.00 3.02
4198 6093 0.036875 GTACCAAGGGCTGCTTCTGT 59.963 55.000 0.00 0.00 0.00 3.41
4199 6094 0.324943 TACCAAGGGCTGCTTCTGTC 59.675 55.000 0.00 0.00 0.00 3.51
4200 6095 2.037136 CCAAGGGCTGCTTCTGTCG 61.037 63.158 0.00 0.00 0.00 4.35
4201 6096 1.302033 CAAGGGCTGCTTCTGTCGT 60.302 57.895 0.00 0.00 0.00 4.34
4202 6097 1.004440 AAGGGCTGCTTCTGTCGTC 60.004 57.895 0.00 0.00 0.00 4.20
4203 6098 2.435059 GGGCTGCTTCTGTCGTCC 60.435 66.667 0.00 0.00 0.00 4.79
4204 6099 2.811317 GGCTGCTTCTGTCGTCCG 60.811 66.667 0.00 0.00 0.00 4.79
4205 6100 2.049063 GCTGCTTCTGTCGTCCGT 60.049 61.111 0.00 0.00 0.00 4.69
4206 6101 1.664965 GCTGCTTCTGTCGTCCGTT 60.665 57.895 0.00 0.00 0.00 4.44
4207 6102 1.891060 GCTGCTTCTGTCGTCCGTTG 61.891 60.000 0.00 0.00 0.00 4.10
4208 6103 0.597637 CTGCTTCTGTCGTCCGTTGT 60.598 55.000 0.00 0.00 0.00 3.32
4209 6104 0.596600 TGCTTCTGTCGTCCGTTGTC 60.597 55.000 0.00 0.00 0.00 3.18
4210 6105 0.596600 GCTTCTGTCGTCCGTTGTCA 60.597 55.000 0.00 0.00 0.00 3.58
4211 6106 1.129326 CTTCTGTCGTCCGTTGTCAC 58.871 55.000 0.00 0.00 0.00 3.67
4212 6107 0.742505 TTCTGTCGTCCGTTGTCACT 59.257 50.000 0.00 0.00 0.00 3.41
4213 6108 0.742505 TCTGTCGTCCGTTGTCACTT 59.257 50.000 0.00 0.00 0.00 3.16
4214 6109 1.135527 TCTGTCGTCCGTTGTCACTTT 59.864 47.619 0.00 0.00 0.00 2.66
4215 6110 1.931172 CTGTCGTCCGTTGTCACTTTT 59.069 47.619 0.00 0.00 0.00 2.27
4216 6111 3.117794 CTGTCGTCCGTTGTCACTTTTA 58.882 45.455 0.00 0.00 0.00 1.52
4217 6112 2.859538 TGTCGTCCGTTGTCACTTTTAC 59.140 45.455 0.00 0.00 0.00 2.01
4218 6113 2.859538 GTCGTCCGTTGTCACTTTTACA 59.140 45.455 0.00 0.00 0.00 2.41
4219 6114 3.306703 GTCGTCCGTTGTCACTTTTACAA 59.693 43.478 0.00 0.00 34.56 2.41
4220 6115 3.931468 TCGTCCGTTGTCACTTTTACAAA 59.069 39.130 0.00 0.00 38.50 2.83
4221 6116 4.391216 TCGTCCGTTGTCACTTTTACAAAA 59.609 37.500 0.00 0.00 38.50 2.44
4222 6117 5.087397 CGTCCGTTGTCACTTTTACAAAAA 58.913 37.500 0.00 0.00 38.50 1.94
4223 6118 5.226360 CGTCCGTTGTCACTTTTACAAAAAG 59.774 40.000 9.92 9.92 38.50 2.27
4224 6119 6.088173 GTCCGTTGTCACTTTTACAAAAAGT 58.912 36.000 11.08 11.08 40.80 2.66
4225 6120 7.242783 GTCCGTTGTCACTTTTACAAAAAGTA 58.757 34.615 15.32 0.96 38.32 2.24
4226 6121 7.216881 GTCCGTTGTCACTTTTACAAAAAGTAC 59.783 37.037 15.32 13.74 38.32 2.73
4227 6122 6.469915 CCGTTGTCACTTTTACAAAAAGTACC 59.530 38.462 15.32 10.36 38.32 3.34
4228 6123 7.022384 CGTTGTCACTTTTACAAAAAGTACCA 58.978 34.615 15.32 12.27 38.32 3.25
4229 6124 7.537991 CGTTGTCACTTTTACAAAAAGTACCAA 59.462 33.333 15.32 16.08 38.32 3.67
4230 6125 8.641155 GTTGTCACTTTTACAAAAAGTACCAAC 58.359 33.333 24.49 24.49 39.69 3.77
4231 6126 7.314393 TGTCACTTTTACAAAAAGTACCAACC 58.686 34.615 15.32 3.96 38.32 3.77
4232 6127 6.753279 GTCACTTTTACAAAAAGTACCAACCC 59.247 38.462 15.32 0.00 38.32 4.11
4233 6128 5.744819 CACTTTTACAAAAAGTACCAACCCG 59.255 40.000 15.32 0.66 38.32 5.28
4234 6129 5.418524 ACTTTTACAAAAAGTACCAACCCGT 59.581 36.000 14.41 0.00 38.58 5.28
4235 6130 4.897025 TTACAAAAAGTACCAACCCGTG 57.103 40.909 0.00 0.00 30.91 4.94
4236 6131 9.446507 ACTTTTACAAAAAGTACCAACCCGTGG 62.447 40.741 14.41 0.00 41.85 4.94
4248 6143 5.744666 CCAACCCGTGGTATAATGTTAAG 57.255 43.478 0.00 0.00 43.20 1.85
4249 6144 5.187687 CCAACCCGTGGTATAATGTTAAGT 58.812 41.667 0.00 0.00 43.20 2.24
4250 6145 5.065474 CCAACCCGTGGTATAATGTTAAGTG 59.935 44.000 0.00 0.00 43.20 3.16
4251 6146 5.680594 ACCCGTGGTATAATGTTAAGTGA 57.319 39.130 0.00 0.00 32.11 3.41
4252 6147 5.667466 ACCCGTGGTATAATGTTAAGTGAG 58.333 41.667 0.00 0.00 32.11 3.51
4253 6148 5.422970 ACCCGTGGTATAATGTTAAGTGAGA 59.577 40.000 0.00 0.00 32.11 3.27
4254 6149 6.070653 ACCCGTGGTATAATGTTAAGTGAGAA 60.071 38.462 0.00 0.00 32.11 2.87
4255 6150 6.819649 CCCGTGGTATAATGTTAAGTGAGAAA 59.180 38.462 0.00 0.00 0.00 2.52
4256 6151 7.334921 CCCGTGGTATAATGTTAAGTGAGAAAA 59.665 37.037 0.00 0.00 0.00 2.29
4257 6152 8.723311 CCGTGGTATAATGTTAAGTGAGAAAAA 58.277 33.333 0.00 0.00 0.00 1.94
4258 6153 9.537848 CGTGGTATAATGTTAAGTGAGAAAAAC 57.462 33.333 0.00 0.00 0.00 2.43
4259 6154 9.836076 GTGGTATAATGTTAAGTGAGAAAAACC 57.164 33.333 0.00 0.00 0.00 3.27
4260 6155 8.723311 TGGTATAATGTTAAGTGAGAAAAACCG 58.277 33.333 0.00 0.00 0.00 4.44
4261 6156 8.179615 GGTATAATGTTAAGTGAGAAAAACCGG 58.820 37.037 0.00 0.00 0.00 5.28
4262 6157 7.754851 ATAATGTTAAGTGAGAAAAACCGGT 57.245 32.000 0.00 0.00 0.00 5.28
4263 6158 6.459670 AATGTTAAGTGAGAAAAACCGGTT 57.540 33.333 15.86 15.86 0.00 4.44
4264 6159 5.488645 TGTTAAGTGAGAAAAACCGGTTC 57.511 39.130 22.53 8.71 0.00 3.62
4265 6160 4.942483 TGTTAAGTGAGAAAAACCGGTTCA 59.058 37.500 22.53 11.45 0.00 3.18
4266 6161 5.591067 TGTTAAGTGAGAAAAACCGGTTCAT 59.409 36.000 22.53 12.71 0.00 2.57
4267 6162 6.095720 TGTTAAGTGAGAAAAACCGGTTCATT 59.904 34.615 22.53 18.60 0.00 2.57
4268 6163 5.592104 AAGTGAGAAAAACCGGTTCATTT 57.408 34.783 22.53 18.33 0.00 2.32
4269 6164 5.592104 AGTGAGAAAAACCGGTTCATTTT 57.408 34.783 22.53 17.55 0.00 1.82
4270 6165 5.588240 AGTGAGAAAAACCGGTTCATTTTC 58.412 37.500 25.47 25.47 41.24 2.29
4271 6166 4.743151 GTGAGAAAAACCGGTTCATTTTCC 59.257 41.667 27.59 21.62 41.64 3.13
4272 6167 3.972403 AGAAAAACCGGTTCATTTTCCG 58.028 40.909 27.59 0.00 41.64 4.30
4273 6168 3.382227 AGAAAAACCGGTTCATTTTCCGT 59.618 39.130 27.59 15.12 44.51 4.69
4274 6169 3.804786 AAAACCGGTTCATTTTCCGTT 57.195 38.095 22.53 4.65 44.51 4.44
4275 6170 3.804786 AAACCGGTTCATTTTCCGTTT 57.195 38.095 22.53 0.00 44.51 3.60
4276 6171 3.804786 AACCGGTTCATTTTCCGTTTT 57.195 38.095 15.86 0.00 44.51 2.43
4277 6172 3.804786 ACCGGTTCATTTTCCGTTTTT 57.195 38.095 0.00 0.00 44.51 1.94
4312 6207 9.841295 AACTGTACTTTTAGTTAATCAACCTGA 57.159 29.630 0.00 0.00 35.50 3.86
4313 6208 9.490379 ACTGTACTTTTAGTTAATCAACCTGAG 57.510 33.333 0.00 0.00 35.05 3.35
4314 6209 8.842358 TGTACTTTTAGTTAATCAACCTGAGG 57.158 34.615 0.00 0.00 35.05 3.86
4315 6210 8.434392 TGTACTTTTAGTTAATCAACCTGAGGT 58.566 33.333 0.00 0.00 37.65 3.85
4316 6211 7.981102 ACTTTTAGTTAATCAACCTGAGGTC 57.019 36.000 3.76 0.00 33.12 3.85
4317 6212 6.940867 ACTTTTAGTTAATCAACCTGAGGTCC 59.059 38.462 3.76 0.00 33.12 4.46
4318 6213 6.697641 TTTAGTTAATCAACCTGAGGTCCT 57.302 37.500 3.76 0.00 33.12 3.85
4319 6214 7.801893 TTTAGTTAATCAACCTGAGGTCCTA 57.198 36.000 3.76 0.00 33.12 2.94
4320 6215 7.989947 TTAGTTAATCAACCTGAGGTCCTAT 57.010 36.000 3.76 0.00 33.12 2.57
4321 6216 6.893020 AGTTAATCAACCTGAGGTCCTATT 57.107 37.500 3.76 7.87 33.12 1.73
4322 6217 7.272144 AGTTAATCAACCTGAGGTCCTATTT 57.728 36.000 3.76 0.00 33.12 1.40
4323 6218 7.699878 AGTTAATCAACCTGAGGTCCTATTTT 58.300 34.615 3.76 0.00 33.12 1.82
4324 6219 8.832735 AGTTAATCAACCTGAGGTCCTATTTTA 58.167 33.333 3.76 0.00 33.12 1.52
4325 6220 9.457436 GTTAATCAACCTGAGGTCCTATTTTAA 57.543 33.333 3.76 1.81 33.12 1.52
4326 6221 9.681062 TTAATCAACCTGAGGTCCTATTTTAAG 57.319 33.333 3.76 0.00 33.12 1.85
4327 6222 6.697641 TCAACCTGAGGTCCTATTTTAAGT 57.302 37.500 3.76 0.00 33.12 2.24
4328 6223 7.086685 TCAACCTGAGGTCCTATTTTAAGTT 57.913 36.000 3.76 0.00 33.12 2.66
4329 6224 7.523415 TCAACCTGAGGTCCTATTTTAAGTTT 58.477 34.615 3.76 0.00 33.12 2.66
4330 6225 8.662255 TCAACCTGAGGTCCTATTTTAAGTTTA 58.338 33.333 3.76 0.00 33.12 2.01
4331 6226 9.292195 CAACCTGAGGTCCTATTTTAAGTTTAA 57.708 33.333 3.76 0.00 33.12 1.52
4332 6227 9.871175 AACCTGAGGTCCTATTTTAAGTTTAAA 57.129 29.630 3.76 0.00 33.12 1.52
4333 6228 9.871175 ACCTGAGGTCCTATTTTAAGTTTAAAA 57.129 29.630 0.00 11.05 44.07 1.52
4363 6258 1.917872 TTTGGAAAACCCCCTGATCG 58.082 50.000 0.00 0.00 0.00 3.69
4364 6259 0.774908 TTGGAAAACCCCCTGATCGT 59.225 50.000 0.00 0.00 0.00 3.73
4365 6260 0.774908 TGGAAAACCCCCTGATCGTT 59.225 50.000 0.00 0.00 0.00 3.85
4366 6261 1.146152 TGGAAAACCCCCTGATCGTTT 59.854 47.619 0.00 0.00 0.00 3.60
4367 6262 1.544246 GGAAAACCCCCTGATCGTTTG 59.456 52.381 0.00 0.00 30.41 2.93
4368 6263 1.544246 GAAAACCCCCTGATCGTTTGG 59.456 52.381 0.00 0.00 30.41 3.28
4369 6264 0.481128 AAACCCCCTGATCGTTTGGT 59.519 50.000 0.00 0.00 0.00 3.67
4370 6265 0.481128 AACCCCCTGATCGTTTGGTT 59.519 50.000 4.28 4.28 0.00 3.67
4371 6266 1.364269 ACCCCCTGATCGTTTGGTTA 58.636 50.000 0.00 0.00 0.00 2.85
4372 6267 1.706305 ACCCCCTGATCGTTTGGTTAA 59.294 47.619 0.00 0.00 0.00 2.01
4373 6268 2.310647 ACCCCCTGATCGTTTGGTTAAT 59.689 45.455 0.00 0.00 0.00 1.40
4374 6269 2.949644 CCCCCTGATCGTTTGGTTAATC 59.050 50.000 0.00 0.00 0.00 1.75
4375 6270 3.616219 CCCCTGATCGTTTGGTTAATCA 58.384 45.455 0.00 0.00 0.00 2.57
4376 6271 4.013728 CCCCTGATCGTTTGGTTAATCAA 58.986 43.478 0.00 0.00 0.00 2.57
4377 6272 4.142469 CCCCTGATCGTTTGGTTAATCAAC 60.142 45.833 0.00 0.00 0.00 3.18
4386 6281 2.092374 GTTAATCAACCCGCCGTCC 58.908 57.895 0.00 0.00 0.00 4.79
4387 6282 0.674269 GTTAATCAACCCGCCGTCCA 60.674 55.000 0.00 0.00 0.00 4.02
4388 6283 0.253610 TTAATCAACCCGCCGTCCAT 59.746 50.000 0.00 0.00 0.00 3.41
4389 6284 0.179067 TAATCAACCCGCCGTCCATC 60.179 55.000 0.00 0.00 0.00 3.51
4390 6285 1.910580 AATCAACCCGCCGTCCATCT 61.911 55.000 0.00 0.00 0.00 2.90
4391 6286 1.046472 ATCAACCCGCCGTCCATCTA 61.046 55.000 0.00 0.00 0.00 1.98
4392 6287 1.046472 TCAACCCGCCGTCCATCTAT 61.046 55.000 0.00 0.00 0.00 1.98
4393 6288 0.179056 CAACCCGCCGTCCATCTATT 60.179 55.000 0.00 0.00 0.00 1.73
4394 6289 1.069513 CAACCCGCCGTCCATCTATTA 59.930 52.381 0.00 0.00 0.00 0.98
4395 6290 1.640917 ACCCGCCGTCCATCTATTAT 58.359 50.000 0.00 0.00 0.00 1.28
4396 6291 1.275291 ACCCGCCGTCCATCTATTATG 59.725 52.381 0.00 0.00 0.00 1.90
4397 6292 1.275291 CCCGCCGTCCATCTATTATGT 59.725 52.381 0.00 0.00 0.00 2.29
4398 6293 2.289444 CCCGCCGTCCATCTATTATGTT 60.289 50.000 0.00 0.00 0.00 2.71
4399 6294 3.399330 CCGCCGTCCATCTATTATGTTT 58.601 45.455 0.00 0.00 0.00 2.83
4400 6295 3.186409 CCGCCGTCCATCTATTATGTTTG 59.814 47.826 0.00 0.00 0.00 2.93
4401 6296 3.186409 CGCCGTCCATCTATTATGTTTGG 59.814 47.826 0.00 0.00 0.00 3.28
4402 6297 3.502211 GCCGTCCATCTATTATGTTTGGG 59.498 47.826 0.00 0.00 0.00 4.12
4403 6298 3.502211 CCGTCCATCTATTATGTTTGGGC 59.498 47.826 0.00 0.00 0.00 5.36
4404 6299 4.133820 CGTCCATCTATTATGTTTGGGCA 58.866 43.478 0.00 0.00 31.49 5.36
4405 6300 4.214119 CGTCCATCTATTATGTTTGGGCAG 59.786 45.833 0.00 0.00 31.49 4.85
4406 6301 5.376625 GTCCATCTATTATGTTTGGGCAGA 58.623 41.667 0.00 0.00 32.32 4.26
4407 6302 6.006449 GTCCATCTATTATGTTTGGGCAGAT 58.994 40.000 0.00 0.00 32.32 2.90
4408 6303 6.491403 GTCCATCTATTATGTTTGGGCAGATT 59.509 38.462 0.00 0.00 32.32 2.40
4409 6304 7.014615 GTCCATCTATTATGTTTGGGCAGATTT 59.985 37.037 0.00 0.00 32.32 2.17
4410 6305 8.224025 TCCATCTATTATGTTTGGGCAGATTTA 58.776 33.333 0.00 0.00 0.00 1.40
4411 6306 8.859090 CCATCTATTATGTTTGGGCAGATTTAA 58.141 33.333 0.00 0.00 0.00 1.52
4420 6315 9.791801 ATGTTTGGGCAGATTTAAATAACTTTT 57.208 25.926 0.00 0.00 0.00 2.27
4421 6316 9.620259 TGTTTGGGCAGATTTAAATAACTTTTT 57.380 25.926 0.00 0.00 0.00 1.94
4422 6317 9.877137 GTTTGGGCAGATTTAAATAACTTTTTG 57.123 29.630 0.00 0.00 0.00 2.44
4423 6318 9.838339 TTTGGGCAGATTTAAATAACTTTTTGA 57.162 25.926 0.00 0.00 0.00 2.69
4424 6319 9.838339 TTGGGCAGATTTAAATAACTTTTTGAA 57.162 25.926 0.00 0.00 0.00 2.69
4425 6320 9.838339 TGGGCAGATTTAAATAACTTTTTGAAA 57.162 25.926 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.769822 GGAGACATGAGACATTCAACCATTAT 59.230 38.462 0.00 0.00 39.77 1.28
34 35 6.115446 GGAGACATGAGACATTCAACCATTA 58.885 40.000 0.00 0.00 39.77 1.90
64 65 1.620822 GAGTTCCAGCAACACCCAAT 58.379 50.000 0.00 0.00 37.48 3.16
85 86 4.796110 AAGGGCAATGATACCATGTACT 57.204 40.909 0.00 0.00 32.36 2.73
441 452 8.829612 GTTTGTGGAATTGAAAAAGTTCATCAT 58.170 29.630 0.00 0.00 43.29 2.45
486 499 9.430623 TGGCCTGTTTCTTAAAATTAAAATAGC 57.569 29.630 3.32 0.00 0.00 2.97
494 507 8.574251 AAAACTTTGGCCTGTTTCTTAAAATT 57.426 26.923 17.62 0.00 35.63 1.82
574 590 7.394816 AGAAAACACTGCTACATGGTATAGTT 58.605 34.615 0.00 0.00 0.00 2.24
587 603 6.162777 TGCTTAAAAACAAGAAAACACTGCT 58.837 32.000 0.00 0.00 0.00 4.24
678 695 7.375106 TCAATGAAAACAGTTGTTGCAATTT 57.625 28.000 0.59 0.00 38.44 1.82
700 719 0.179086 TCAGCGACTGCACTGTTTCA 60.179 50.000 2.37 0.00 46.23 2.69
709 728 3.661936 CGTTAAACTTCTTCAGCGACTGC 60.662 47.826 2.45 0.00 43.24 4.40
760 779 2.766313 CGACTTGACTGTTTGGATGGA 58.234 47.619 0.00 0.00 0.00 3.41
812 831 2.096248 TCGTTTTGTTGGCTGTTTCCT 58.904 42.857 0.00 0.00 0.00 3.36
878 897 1.737838 CTTCAATCTGGGCACGCTAA 58.262 50.000 0.00 0.00 0.00 3.09
884 903 0.178938 TTTGGGCTTCAATCTGGGCA 60.179 50.000 0.00 0.00 34.98 5.36
886 905 2.833338 TCAATTTGGGCTTCAATCTGGG 59.167 45.455 0.00 0.00 34.98 4.45
887 906 4.221262 TCTTCAATTTGGGCTTCAATCTGG 59.779 41.667 0.00 0.00 34.98 3.86
888 907 5.395682 TCTTCAATTTGGGCTTCAATCTG 57.604 39.130 0.00 0.00 34.98 2.90
890 909 5.517770 CGAATCTTCAATTTGGGCTTCAATC 59.482 40.000 0.00 0.00 34.98 2.67
891 910 5.413499 CGAATCTTCAATTTGGGCTTCAAT 58.587 37.500 0.00 0.00 34.98 2.57
892 911 4.321899 CCGAATCTTCAATTTGGGCTTCAA 60.322 41.667 0.00 0.00 0.00 2.69
894 913 3.193479 ACCGAATCTTCAATTTGGGCTTC 59.807 43.478 8.53 0.00 36.98 3.86
895 914 3.056607 CACCGAATCTTCAATTTGGGCTT 60.057 43.478 8.53 0.00 36.98 4.35
975 994 2.183046 GTGTCTCCTCTGCGCTCC 59.817 66.667 9.73 0.00 0.00 4.70
976 995 2.183046 GGTGTCTCCTCTGCGCTC 59.817 66.667 9.73 0.00 0.00 5.03
1235 1269 2.158475 TGAACAATGGAGTTTGGGAGCT 60.158 45.455 0.00 0.00 0.00 4.09
1236 1270 2.238521 TGAACAATGGAGTTTGGGAGC 58.761 47.619 0.00 0.00 0.00 4.70
1237 1271 4.379813 CGAATGAACAATGGAGTTTGGGAG 60.380 45.833 0.00 0.00 0.00 4.30
1334 1369 4.480115 TCCTGGTCTTCTTCTTACTGACA 58.520 43.478 0.00 0.00 0.00 3.58
1575 1616 3.009723 ACATCCAAGAAATGCACCTACG 58.990 45.455 0.00 0.00 0.00 3.51
1660 1701 4.372656 ACAACACTGAGCTTGTAGAAGAC 58.627 43.478 3.33 0.00 0.00 3.01
1686 1727 3.769300 TGTGGCTTCTATGTAGCTCTGAA 59.231 43.478 0.00 0.00 38.67 3.02
1815 3613 5.602978 AGTATGGTACCTACAATGAGAAGGG 59.397 44.000 14.36 0.00 34.52 3.95
1928 3726 0.324943 AAACTGCCGTGCCTGACTAT 59.675 50.000 0.00 0.00 0.00 2.12
2104 3907 7.136822 ACTATTGGTATATCAGCCTGACAAA 57.863 36.000 0.00 0.00 0.00 2.83
2111 3914 8.094548 TGATGTTGTACTATTGGTATATCAGCC 58.905 37.037 0.00 0.00 31.34 4.85
2246 4049 7.942341 CCCTTACACATATTATTTTCTAGGGCA 59.058 37.037 0.00 0.00 31.86 5.36
2861 4673 1.150827 TGCAGTGCAATGAGACGAAG 58.849 50.000 20.00 0.00 34.76 3.79
2980 4802 4.878397 GCAGAGGCACATACAATTTAGACT 59.122 41.667 0.00 0.00 40.72 3.24
2989 4811 0.983467 TTCCAGCAGAGGCACATACA 59.017 50.000 0.00 0.00 44.61 2.29
3131 4955 6.626302 ACAGATAGAACAGAAAGAGTGCTAC 58.374 40.000 0.00 0.00 30.13 3.58
3204 5030 6.197364 AGACTTGGTAGACTACTGAAATCG 57.803 41.667 12.31 0.00 0.00 3.34
3243 5069 2.189499 GGCTCGGGAATGCATGTCC 61.189 63.158 15.57 15.57 0.00 4.02
3244 5070 0.820891 ATGGCTCGGGAATGCATGTC 60.821 55.000 0.00 0.00 0.00 3.06
3310 5140 0.389166 CAGAGCCAACTCCACTCGAC 60.389 60.000 0.00 0.00 44.65 4.20
3312 5142 0.389166 GTCAGAGCCAACTCCACTCG 60.389 60.000 0.00 0.00 44.65 4.18
3367 5197 6.050432 GCCATATCCAAAAGAAATGCATGAA 58.950 36.000 0.00 0.00 0.00 2.57
3395 5225 9.087424 TGAAACGATATTCAGTTAGTGATTGAG 57.913 33.333 0.00 0.00 34.50 3.02
3415 5245 2.221749 CGGCATCCTATGTCATGAAACG 59.778 50.000 0.00 0.00 33.60 3.60
3454 5284 2.079158 ACATCGAACAGGAATGCACAG 58.921 47.619 0.00 0.00 0.00 3.66
3490 5320 1.106285 CCAAGCCTTGCCTTCCATAC 58.894 55.000 0.00 0.00 0.00 2.39
3607 5437 5.485708 AGAACCTGAGCCTCATAACTAGTTT 59.514 40.000 14.49 0.00 0.00 2.66
3638 5468 3.203716 GCAGTCTCATTCTCATGCATGA 58.796 45.455 27.10 27.10 33.92 3.07
3691 5521 5.523438 AATCTCTAGGAGTTTGATCCGAC 57.477 43.478 0.00 0.00 44.65 4.79
3801 5631 1.863155 ATTACACACTGGGGGCCTGG 61.863 60.000 0.84 0.00 0.00 4.45
3802 5632 0.039618 AATTACACACTGGGGGCCTG 59.960 55.000 0.84 0.00 0.00 4.85
3803 5633 0.783850 AAATTACACACTGGGGGCCT 59.216 50.000 0.84 0.00 0.00 5.19
3804 5634 2.517998 TAAATTACACACTGGGGGCC 57.482 50.000 0.00 0.00 0.00 5.80
3805 5635 2.100749 GCATAAATTACACACTGGGGGC 59.899 50.000 0.00 0.00 0.00 5.80
3806 5636 2.357637 CGCATAAATTACACACTGGGGG 59.642 50.000 0.00 0.00 0.00 5.40
3814 5644 7.561556 AGAACTTATACGCGCATAAATTACAC 58.438 34.615 12.58 0.00 0.00 2.90
3821 5651 5.629435 CAGATGAGAACTTATACGCGCATAA 59.371 40.000 5.73 9.11 0.00 1.90
3826 5656 5.507974 TGTACAGATGAGAACTTATACGCG 58.492 41.667 3.53 3.53 0.00 6.01
3936 5766 9.674068 GGAAAAAGGGGCAATTTTGTATATAAA 57.326 29.630 0.42 0.00 30.52 1.40
3940 5770 6.943899 AGGAAAAAGGGGCAATTTTGTATA 57.056 33.333 0.42 0.00 30.52 1.47
3948 5778 7.995052 AAGATTTATAGGAAAAAGGGGCAAT 57.005 32.000 0.00 0.00 0.00 3.56
3975 5805 8.246908 TGTACAATAACCACTACAGAATTTCG 57.753 34.615 0.00 0.00 0.00 3.46
4123 5960 0.960364 TGAACGATTGGGCCTTCTGC 60.960 55.000 4.53 0.00 40.16 4.26
4124 5961 0.804989 GTGAACGATTGGGCCTTCTG 59.195 55.000 4.53 1.72 0.00 3.02
4160 6055 4.868171 GGTACGTAACATGCATCTTTCTCA 59.132 41.667 5.55 0.00 0.00 3.27
4161 6056 4.868171 TGGTACGTAACATGCATCTTTCTC 59.132 41.667 9.81 0.00 0.00 2.87
4179 6074 0.036875 ACAGAAGCAGCCCTTGGTAC 59.963 55.000 0.00 0.00 36.24 3.34
4180 6075 0.324943 GACAGAAGCAGCCCTTGGTA 59.675 55.000 0.00 0.00 36.24 3.25
4181 6076 1.073897 GACAGAAGCAGCCCTTGGT 59.926 57.895 0.00 0.00 39.75 3.67
4182 6077 2.037136 CGACAGAAGCAGCCCTTGG 61.037 63.158 0.00 0.00 32.78 3.61
4183 6078 1.294659 GACGACAGAAGCAGCCCTTG 61.295 60.000 0.00 0.00 32.78 3.61
4184 6079 1.004440 GACGACAGAAGCAGCCCTT 60.004 57.895 0.00 0.00 36.19 3.95
4185 6080 2.659610 GACGACAGAAGCAGCCCT 59.340 61.111 0.00 0.00 0.00 5.19
4186 6081 2.435059 GGACGACAGAAGCAGCCC 60.435 66.667 0.00 0.00 0.00 5.19
4187 6082 2.811317 CGGACGACAGAAGCAGCC 60.811 66.667 0.00 0.00 0.00 4.85
4188 6083 1.664965 AACGGACGACAGAAGCAGC 60.665 57.895 0.00 0.00 0.00 5.25
4189 6084 0.597637 ACAACGGACGACAGAAGCAG 60.598 55.000 0.00 0.00 0.00 4.24
4190 6085 0.596600 GACAACGGACGACAGAAGCA 60.597 55.000 0.00 0.00 0.00 3.91
4191 6086 0.596600 TGACAACGGACGACAGAAGC 60.597 55.000 0.00 0.00 0.00 3.86
4192 6087 1.129326 GTGACAACGGACGACAGAAG 58.871 55.000 0.00 0.00 0.00 2.85
4193 6088 0.742505 AGTGACAACGGACGACAGAA 59.257 50.000 0.00 0.00 0.00 3.02
4194 6089 0.742505 AAGTGACAACGGACGACAGA 59.257 50.000 0.00 0.00 0.00 3.41
4195 6090 1.567504 AAAGTGACAACGGACGACAG 58.432 50.000 0.00 0.00 0.00 3.51
4196 6091 2.012937 AAAAGTGACAACGGACGACA 57.987 45.000 0.00 0.00 0.00 4.35
4197 6092 2.859538 TGTAAAAGTGACAACGGACGAC 59.140 45.455 0.00 0.00 0.00 4.34
4198 6093 3.162202 TGTAAAAGTGACAACGGACGA 57.838 42.857 0.00 0.00 0.00 4.20
4199 6094 3.929417 TTGTAAAAGTGACAACGGACG 57.071 42.857 0.00 0.00 31.92 4.79
4200 6095 6.088173 ACTTTTTGTAAAAGTGACAACGGAC 58.912 36.000 14.73 0.00 38.88 4.79
4201 6096 6.256912 ACTTTTTGTAAAAGTGACAACGGA 57.743 33.333 14.73 0.00 38.88 4.69
4202 6097 6.469915 GGTACTTTTTGTAAAAGTGACAACGG 59.530 38.462 21.56 0.00 40.38 4.44
4203 6098 7.022384 TGGTACTTTTTGTAAAAGTGACAACG 58.978 34.615 21.56 0.00 40.38 4.10
4204 6099 8.641155 GTTGGTACTTTTTGTAAAAGTGACAAC 58.359 33.333 27.19 27.19 42.91 3.32
4205 6100 7.813627 GGTTGGTACTTTTTGTAAAAGTGACAA 59.186 33.333 21.56 20.70 40.38 3.18
4206 6101 7.314393 GGTTGGTACTTTTTGTAAAAGTGACA 58.686 34.615 21.56 17.49 40.38 3.58
4207 6102 6.753279 GGGTTGGTACTTTTTGTAAAAGTGAC 59.247 38.462 21.56 15.78 40.38 3.67
4208 6103 6.404513 CGGGTTGGTACTTTTTGTAAAAGTGA 60.405 38.462 21.56 7.91 40.38 3.41
4209 6104 5.744819 CGGGTTGGTACTTTTTGTAAAAGTG 59.255 40.000 21.56 7.66 40.38 3.16
4210 6105 5.418524 ACGGGTTGGTACTTTTTGTAAAAGT 59.581 36.000 18.27 18.27 42.53 2.66
4211 6106 5.744819 CACGGGTTGGTACTTTTTGTAAAAG 59.255 40.000 9.67 9.67 32.25 2.27
4212 6107 5.393896 CCACGGGTTGGTACTTTTTGTAAAA 60.394 40.000 0.00 0.00 41.10 1.52
4213 6108 4.097589 CCACGGGTTGGTACTTTTTGTAAA 59.902 41.667 0.00 0.00 41.10 2.01
4214 6109 3.631227 CCACGGGTTGGTACTTTTTGTAA 59.369 43.478 0.00 0.00 41.10 2.41
4215 6110 3.212685 CCACGGGTTGGTACTTTTTGTA 58.787 45.455 0.00 0.00 41.10 2.41
4216 6111 2.025898 CCACGGGTTGGTACTTTTTGT 58.974 47.619 0.00 0.00 41.10 2.83
4217 6112 2.785713 CCACGGGTTGGTACTTTTTG 57.214 50.000 0.00 0.00 41.10 2.44
4227 6122 5.875910 TCACTTAACATTATACCACGGGTTG 59.124 40.000 0.72 0.00 37.09 3.77
4228 6123 6.052405 TCACTTAACATTATACCACGGGTT 57.948 37.500 0.72 0.00 37.09 4.11
4229 6124 5.422970 TCTCACTTAACATTATACCACGGGT 59.577 40.000 1.14 1.14 40.16 5.28
4230 6125 5.909477 TCTCACTTAACATTATACCACGGG 58.091 41.667 0.00 0.00 0.00 5.28
4231 6126 7.837202 TTTCTCACTTAACATTATACCACGG 57.163 36.000 0.00 0.00 0.00 4.94
4232 6127 9.537848 GTTTTTCTCACTTAACATTATACCACG 57.462 33.333 0.00 0.00 0.00 4.94
4233 6128 9.836076 GGTTTTTCTCACTTAACATTATACCAC 57.164 33.333 0.00 0.00 0.00 4.16
4234 6129 8.723311 CGGTTTTTCTCACTTAACATTATACCA 58.277 33.333 0.00 0.00 0.00 3.25
4235 6130 8.179615 CCGGTTTTTCTCACTTAACATTATACC 58.820 37.037 0.00 0.00 0.00 2.73
4236 6131 8.724229 ACCGGTTTTTCTCACTTAACATTATAC 58.276 33.333 0.00 0.00 0.00 1.47
4237 6132 8.851541 ACCGGTTTTTCTCACTTAACATTATA 57.148 30.769 0.00 0.00 0.00 0.98
4238 6133 7.754851 ACCGGTTTTTCTCACTTAACATTAT 57.245 32.000 0.00 0.00 0.00 1.28
4239 6134 7.282675 TGAACCGGTTTTTCTCACTTAACATTA 59.717 33.333 23.22 0.00 0.00 1.90
4240 6135 6.095720 TGAACCGGTTTTTCTCACTTAACATT 59.904 34.615 23.22 0.00 0.00 2.71
4241 6136 5.591067 TGAACCGGTTTTTCTCACTTAACAT 59.409 36.000 23.22 0.00 0.00 2.71
4242 6137 4.942483 TGAACCGGTTTTTCTCACTTAACA 59.058 37.500 23.22 6.85 0.00 2.41
4243 6138 5.488645 TGAACCGGTTTTTCTCACTTAAC 57.511 39.130 23.22 3.98 0.00 2.01
4244 6139 6.702716 AATGAACCGGTTTTTCTCACTTAA 57.297 33.333 23.22 0.00 0.00 1.85
4245 6140 6.702716 AAATGAACCGGTTTTTCTCACTTA 57.297 33.333 23.22 0.00 0.00 2.24
4246 6141 5.592104 AAATGAACCGGTTTTTCTCACTT 57.408 34.783 23.22 7.75 0.00 3.16
4247 6142 5.451381 GGAAAATGAACCGGTTTTTCTCACT 60.451 40.000 28.85 11.12 38.68 3.41
4248 6143 4.743151 GGAAAATGAACCGGTTTTTCTCAC 59.257 41.667 28.85 16.71 38.68 3.51
4249 6144 4.498345 CGGAAAATGAACCGGTTTTTCTCA 60.498 41.667 28.85 20.85 44.59 3.27
4250 6145 3.978855 CGGAAAATGAACCGGTTTTTCTC 59.021 43.478 28.85 21.50 44.59 2.87
4251 6146 3.972403 CGGAAAATGAACCGGTTTTTCT 58.028 40.909 28.85 13.79 44.59 2.52
4286 6181 9.841295 TCAGGTTGATTAACTAAAAGTACAGTT 57.159 29.630 0.00 0.00 38.50 3.16
4287 6182 9.490379 CTCAGGTTGATTAACTAAAAGTACAGT 57.510 33.333 0.00 0.00 36.99 3.55
4288 6183 8.936864 CCTCAGGTTGATTAACTAAAAGTACAG 58.063 37.037 0.00 0.00 36.99 2.74
4289 6184 8.434392 ACCTCAGGTTGATTAACTAAAAGTACA 58.566 33.333 0.00 0.00 36.99 2.90
4290 6185 8.843885 ACCTCAGGTTGATTAACTAAAAGTAC 57.156 34.615 0.00 0.00 36.99 2.73
4291 6186 8.098912 GGACCTCAGGTTGATTAACTAAAAGTA 58.901 37.037 0.00 0.00 35.25 2.24
4292 6187 6.940867 GGACCTCAGGTTGATTAACTAAAAGT 59.059 38.462 0.00 0.00 35.25 2.66
4293 6188 7.168905 AGGACCTCAGGTTGATTAACTAAAAG 58.831 38.462 0.00 0.00 35.25 2.27
4294 6189 7.086685 AGGACCTCAGGTTGATTAACTAAAA 57.913 36.000 0.00 0.00 35.25 1.52
4295 6190 6.697641 AGGACCTCAGGTTGATTAACTAAA 57.302 37.500 0.00 0.00 35.25 1.85
4296 6191 7.989947 ATAGGACCTCAGGTTGATTAACTAA 57.010 36.000 0.00 0.00 35.25 2.24
4297 6192 7.989947 AATAGGACCTCAGGTTGATTAACTA 57.010 36.000 0.00 0.00 35.25 2.24
4298 6193 6.893020 AATAGGACCTCAGGTTGATTAACT 57.107 37.500 0.00 0.00 35.25 2.24
4299 6194 7.939784 AAAATAGGACCTCAGGTTGATTAAC 57.060 36.000 0.00 0.00 35.25 2.01
4300 6195 9.681062 CTTAAAATAGGACCTCAGGTTGATTAA 57.319 33.333 0.00 0.00 35.25 1.40
4301 6196 8.832735 ACTTAAAATAGGACCTCAGGTTGATTA 58.167 33.333 0.00 0.00 35.25 1.75
4302 6197 7.699878 ACTTAAAATAGGACCTCAGGTTGATT 58.300 34.615 0.00 0.00 35.25 2.57
4303 6198 7.272144 ACTTAAAATAGGACCTCAGGTTGAT 57.728 36.000 0.00 0.00 35.25 2.57
4304 6199 6.697641 ACTTAAAATAGGACCTCAGGTTGA 57.302 37.500 0.00 0.00 35.25 3.18
4305 6200 7.761038 AAACTTAAAATAGGACCTCAGGTTG 57.239 36.000 0.00 0.00 35.25 3.77
4306 6201 9.871175 TTTAAACTTAAAATAGGACCTCAGGTT 57.129 29.630 0.00 0.00 30.60 3.50
4307 6202 9.871175 TTTTAAACTTAAAATAGGACCTCAGGT 57.129 29.630 0.00 0.00 37.61 4.00
4342 6237 2.630580 CGATCAGGGGGTTTTCCAAAAA 59.369 45.455 0.00 0.00 42.91 1.94
4343 6238 2.243810 CGATCAGGGGGTTTTCCAAAA 58.756 47.619 0.00 0.00 42.91 2.44
4344 6239 1.146152 ACGATCAGGGGGTTTTCCAAA 59.854 47.619 0.00 0.00 42.91 3.28
4345 6240 0.774908 ACGATCAGGGGGTTTTCCAA 59.225 50.000 0.00 0.00 42.91 3.53
4346 6241 0.774908 AACGATCAGGGGGTTTTCCA 59.225 50.000 0.00 0.00 42.91 3.53
4347 6242 1.544246 CAAACGATCAGGGGGTTTTCC 59.456 52.381 0.00 0.00 39.75 3.13
4348 6243 1.544246 CCAAACGATCAGGGGGTTTTC 59.456 52.381 0.00 0.00 31.95 2.29
4349 6244 1.133294 ACCAAACGATCAGGGGGTTTT 60.133 47.619 0.00 0.00 31.95 2.43
4350 6245 0.481128 ACCAAACGATCAGGGGGTTT 59.519 50.000 0.00 0.00 34.42 3.27
4351 6246 0.481128 AACCAAACGATCAGGGGGTT 59.519 50.000 0.00 3.71 33.99 4.11
4352 6247 1.364269 TAACCAAACGATCAGGGGGT 58.636 50.000 0.00 0.00 0.00 4.95
4353 6248 2.500392 TTAACCAAACGATCAGGGGG 57.500 50.000 0.00 0.00 0.00 5.40
4354 6249 3.616219 TGATTAACCAAACGATCAGGGG 58.384 45.455 0.00 0.00 0.00 4.79
4355 6250 4.981794 GTTGATTAACCAAACGATCAGGG 58.018 43.478 0.00 0.00 30.92 4.45
4368 6263 0.674269 TGGACGGCGGGTTGATTAAC 60.674 55.000 13.24 0.00 36.04 2.01
4369 6264 0.253610 ATGGACGGCGGGTTGATTAA 59.746 50.000 13.24 0.00 0.00 1.40
4370 6265 0.179067 GATGGACGGCGGGTTGATTA 60.179 55.000 13.24 0.00 0.00 1.75
4371 6266 1.451387 GATGGACGGCGGGTTGATT 60.451 57.895 13.24 0.00 0.00 2.57
4372 6267 1.046472 TAGATGGACGGCGGGTTGAT 61.046 55.000 13.24 0.00 0.00 2.57
4373 6268 1.046472 ATAGATGGACGGCGGGTTGA 61.046 55.000 13.24 0.00 0.00 3.18
4374 6269 0.179056 AATAGATGGACGGCGGGTTG 60.179 55.000 13.24 0.00 0.00 3.77
4375 6270 1.416243 TAATAGATGGACGGCGGGTT 58.584 50.000 13.24 0.00 0.00 4.11
4376 6271 1.275291 CATAATAGATGGACGGCGGGT 59.725 52.381 13.24 0.00 0.00 5.28
4377 6272 1.275291 ACATAATAGATGGACGGCGGG 59.725 52.381 13.24 0.00 0.00 6.13
4378 6273 2.743636 ACATAATAGATGGACGGCGG 57.256 50.000 13.24 0.00 0.00 6.13
4379 6274 3.186409 CCAAACATAATAGATGGACGGCG 59.814 47.826 4.80 4.80 32.82 6.46
4380 6275 3.502211 CCCAAACATAATAGATGGACGGC 59.498 47.826 0.00 0.00 32.82 5.68
4381 6276 3.502211 GCCCAAACATAATAGATGGACGG 59.498 47.826 0.00 0.00 32.82 4.79
4382 6277 4.133820 TGCCCAAACATAATAGATGGACG 58.866 43.478 0.00 0.00 32.82 4.79
4383 6278 5.376625 TCTGCCCAAACATAATAGATGGAC 58.623 41.667 0.00 0.00 32.82 4.02
4384 6279 5.645056 TCTGCCCAAACATAATAGATGGA 57.355 39.130 0.00 0.00 32.82 3.41
4385 6280 6.906157 AATCTGCCCAAACATAATAGATGG 57.094 37.500 0.00 0.00 0.00 3.51
4394 6289 9.791801 AAAAGTTATTTAAATCTGCCCAAACAT 57.208 25.926 3.39 0.00 0.00 2.71
4395 6290 9.620259 AAAAAGTTATTTAAATCTGCCCAAACA 57.380 25.926 3.39 0.00 0.00 2.83
4396 6291 9.877137 CAAAAAGTTATTTAAATCTGCCCAAAC 57.123 29.630 3.39 2.08 0.00 2.93
4397 6292 9.838339 TCAAAAAGTTATTTAAATCTGCCCAAA 57.162 25.926 3.39 0.00 0.00 3.28
4398 6293 9.838339 TTCAAAAAGTTATTTAAATCTGCCCAA 57.162 25.926 3.39 0.00 0.00 4.12
4399 6294 9.838339 TTTCAAAAAGTTATTTAAATCTGCCCA 57.162 25.926 3.39 0.00 0.00 5.36
4417 6312 9.430623 GCCCTTTTGCTAGTTATATTTCAAAAA 57.569 29.630 0.00 0.00 34.39 1.94
4418 6313 8.038351 GGCCCTTTTGCTAGTTATATTTCAAAA 58.962 33.333 0.00 0.00 33.90 2.44
4419 6314 7.364320 GGGCCCTTTTGCTAGTTATATTTCAAA 60.364 37.037 17.04 0.00 0.00 2.69
4420 6315 6.097696 GGGCCCTTTTGCTAGTTATATTTCAA 59.902 38.462 17.04 0.00 0.00 2.69
4421 6316 5.596772 GGGCCCTTTTGCTAGTTATATTTCA 59.403 40.000 17.04 0.00 0.00 2.69
4422 6317 5.278315 CGGGCCCTTTTGCTAGTTATATTTC 60.278 44.000 22.43 0.00 0.00 2.17
4423 6318 4.583073 CGGGCCCTTTTGCTAGTTATATTT 59.417 41.667 22.43 0.00 0.00 1.40
4424 6319 4.142038 CGGGCCCTTTTGCTAGTTATATT 58.858 43.478 22.43 0.00 0.00 1.28
4425 6320 3.137728 ACGGGCCCTTTTGCTAGTTATAT 59.862 43.478 22.43 0.00 0.00 0.86
4426 6321 2.506644 ACGGGCCCTTTTGCTAGTTATA 59.493 45.455 22.43 0.00 0.00 0.98
4427 6322 1.283905 ACGGGCCCTTTTGCTAGTTAT 59.716 47.619 22.43 0.00 0.00 1.89
4428 6323 0.694196 ACGGGCCCTTTTGCTAGTTA 59.306 50.000 22.43 0.00 0.00 2.24
4429 6324 0.893727 CACGGGCCCTTTTGCTAGTT 60.894 55.000 22.43 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.