Multiple sequence alignment - TraesCS5B01G528300

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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 TraesCS5B01G528300 chr5B 100.000 4319 0 0 1 4319 687163174 687167492 0.000000e+00 7976
1 TraesCS5B01G528300 chr5B 81.760 1102 185 13 2161 3260 570935982 570937069 0.000000e+00 907
2 TraesCS5B01G528300 chr5D 93.284 3484 153 21 1 3441 544699330 544695885 0.000000e+00 5062
3 TraesCS5B01G528300 chr5D 93.370 724 30 6 3603 4319 544695886 544695174 0.000000e+00 1055
4 TraesCS5B01G528300 chr5D 95.238 168 8 0 3440 3607 42949724 42949557 2.560000e-67 267
5 TraesCS5B01G528300 chr1A 92.750 2745 135 35 722 3441 569449857 569452562 0.000000e+00 3908
6 TraesCS5B01G528300 chr1A 91.440 736 37 12 3603 4319 569452561 569453289 0.000000e+00 987
7 TraesCS5B01G528300 chr1A 89.413 699 42 15 12 704 569448094 569448766 0.000000e+00 852
8 TraesCS5B01G528300 chr1A 86.306 314 38 3 423 735 569449499 569449808 1.920000e-88 337
9 TraesCS5B01G528300 chr1A 92.537 201 12 1 504 704 569449291 569449488 7.070000e-73 285
10 TraesCS5B01G528300 chr1A 79.630 378 63 8 425 801 569447493 569447857 4.280000e-65 259
11 TraesCS5B01G528300 chrUn 83.238 1050 165 8 2162 3207 238784738 238785780 0.000000e+00 953
12 TraesCS5B01G528300 chrUn 83.238 1050 165 8 2162 3207 240351536 240350494 0.000000e+00 953
13 TraesCS5B01G528300 chrUn 82.459 1049 177 7 2161 3207 296501503 296500460 0.000000e+00 911
14 TraesCS5B01G528300 chrUn 80.019 1051 192 14 2148 3192 222089970 222088932 0.000000e+00 761
15 TraesCS5B01G528300 chr2B 83.143 1050 168 5 2161 3210 752829809 752828769 0.000000e+00 950
16 TraesCS5B01G528300 chr3D 82.659 1038 177 3 2162 3199 4967399 4966365 0.000000e+00 917
17 TraesCS5B01G528300 chr3D 81.879 1043 173 11 2158 3192 28331731 28332765 0.000000e+00 865
18 TraesCS5B01G528300 chr3D 92.432 185 11 3 3425 3607 550509612 550509429 1.190000e-65 261
19 TraesCS5B01G528300 chr3B 82.229 1041 178 7 2161 3199 13966269 13967304 0.000000e+00 891
20 TraesCS5B01G528300 chr1B 80.875 1051 188 10 2154 3198 10068903 10067860 0.000000e+00 815
21 TraesCS5B01G528300 chr1D 80.342 1053 195 9 2154 3199 7210748 7211795 0.000000e+00 787
22 TraesCS5B01G528300 chr1D 93.407 182 12 0 3429 3610 9218383 9218202 1.980000e-68 270
23 TraesCS5B01G528300 chr1D 95.238 168 8 0 3437 3604 220154301 220154134 2.560000e-67 267
24 TraesCS5B01G528300 chr7A 96.386 166 6 0 3440 3605 709731066 709731231 1.530000e-69 274
25 TraesCS5B01G528300 chr6D 95.376 173 7 1 3438 3609 104041328 104041156 1.530000e-69 274
26 TraesCS5B01G528300 chr2D 95.322 171 8 0 3439 3609 609886790 609886960 5.500000e-69 272
27 TraesCS5B01G528300 chr4D 94.767 172 9 0 3438 3609 93336682 93336853 7.120000e-68 268
28 TraesCS5B01G528300 chr4D 87.363 182 19 2 51 231 26252956 26252778 5.660000e-49 206
29 TraesCS5B01G528300 chr6A 92.308 182 12 2 3438 3617 115317415 115317234 1.540000e-64 257
30 TraesCS5B01G528300 chr4B 86.559 186 20 3 48 231 38792495 38792313 2.630000e-47 200
31 TraesCS5B01G528300 chr4B 93.333 75 5 0 1448 1522 38791947 38791873 1.270000e-20 111
32 TraesCS5B01G528300 chr4A 93.333 75 5 0 1448 1522 577046889 577046963 1.270000e-20 111


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 TraesCS5B01G528300 chr5B 687163174 687167492 4318 False 7976.000000 7976 100.000000 1 4319 1 chr5B.!!$F2 4318
1 TraesCS5B01G528300 chr5B 570935982 570937069 1087 False 907.000000 907 81.760000 2161 3260 1 chr5B.!!$F1 1099
2 TraesCS5B01G528300 chr5D 544695174 544699330 4156 True 3058.500000 5062 93.327000 1 4319 2 chr5D.!!$R2 4318
3 TraesCS5B01G528300 chr1A 569447493 569453289 5796 False 1104.666667 3908 88.679333 12 4319 6 chr1A.!!$F1 4307
4 TraesCS5B01G528300 chrUn 238784738 238785780 1042 False 953.000000 953 83.238000 2162 3207 1 chrUn.!!$F1 1045
5 TraesCS5B01G528300 chrUn 240350494 240351536 1042 True 953.000000 953 83.238000 2162 3207 1 chrUn.!!$R2 1045
6 TraesCS5B01G528300 chrUn 296500460 296501503 1043 True 911.000000 911 82.459000 2161 3207 1 chrUn.!!$R3 1046
7 TraesCS5B01G528300 chrUn 222088932 222089970 1038 True 761.000000 761 80.019000 2148 3192 1 chrUn.!!$R1 1044
8 TraesCS5B01G528300 chr2B 752828769 752829809 1040 True 950.000000 950 83.143000 2161 3210 1 chr2B.!!$R1 1049
9 TraesCS5B01G528300 chr3D 4966365 4967399 1034 True 917.000000 917 82.659000 2162 3199 1 chr3D.!!$R1 1037
10 TraesCS5B01G528300 chr3D 28331731 28332765 1034 False 865.000000 865 81.879000 2158 3192 1 chr3D.!!$F1 1034
11 TraesCS5B01G528300 chr3B 13966269 13967304 1035 False 891.000000 891 82.229000 2161 3199 1 chr3B.!!$F1 1038
12 TraesCS5B01G528300 chr1B 10067860 10068903 1043 True 815.000000 815 80.875000 2154 3198 1 chr1B.!!$R1 1044
13 TraesCS5B01G528300 chr1D 7210748 7211795 1047 False 787.000000 787 80.342000 2154 3199 1 chr1D.!!$F1 1045

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
259 852 0.249398 ACGCTGGGTATGGACAGAAC 59.751 55.0 0.0 0.0 36.86 3.01 F
1105 2804 0.686789 CCAGGGGCGTCATCATCATA 59.313 55.0 0.0 0.0 0.00 2.15 F
2646 4355 0.041535 AGATTGCCTTGGGGATTGCA 59.958 50.0 0.0 0.0 33.58 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1358 3057 0.107848 GCCACCACCGTAATACAGCT 60.108 55.0 0.0 0.00 0.00 4.24 R
3055 4776 0.512952 CCAACGAGACAAAGCTTCCG 59.487 55.0 0.0 1.61 0.00 4.30 R
3764 5497 1.446907 CTTGCCCTGCAACTCTAGTG 58.553 55.0 0.0 0.00 43.99 2.74 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
33 624 7.324616 GCGATTATTGATGAAATTAACAGAGCC 59.675 37.037 0.00 0.00 0.00 4.70
37 628 6.899393 TTGATGAAATTAACAGAGCCACTT 57.101 33.333 0.00 0.00 0.00 3.16
50 641 1.103398 GCCACTTGTGTTGAGCTGGT 61.103 55.000 0.00 0.00 0.00 4.00
63 654 2.436646 CTGGTAGCCTTGTGCCCG 60.437 66.667 0.00 0.00 42.71 6.13
67 658 2.284331 TAGCCTTGTGCCCGAGGA 60.284 61.111 6.66 0.00 44.19 3.71
68 659 2.359169 TAGCCTTGTGCCCGAGGAG 61.359 63.158 6.66 0.00 44.19 3.69
73 666 1.373570 CTTGTGCCCGAGGAGAATTC 58.626 55.000 0.00 0.00 0.00 2.17
84 677 4.256920 CGAGGAGAATTCTGGTTGTGAAT 58.743 43.478 14.00 0.00 35.88 2.57
94 687 0.895100 GGTTGTGAATGCAGCCTCCA 60.895 55.000 0.00 0.00 36.89 3.86
121 714 5.162075 GTGTTATAGTGGTCTGAGTGTGAC 58.838 45.833 0.00 0.00 0.00 3.67
242 835 3.003171 TGTCATGTTCAAATGGTCACACG 59.997 43.478 0.00 0.00 0.00 4.49
259 852 0.249398 ACGCTGGGTATGGACAGAAC 59.751 55.000 0.00 0.00 36.86 3.01
282 875 1.742831 GCATCTATCGTGGCACCAAAA 59.257 47.619 12.86 0.00 0.00 2.44
292 885 3.059051 CGTGGCACCAAAATTCCAAATTG 60.059 43.478 12.86 0.00 0.00 2.32
336 932 6.942576 ACTTACTCATCTTGGTTTGCTGTAAT 59.057 34.615 0.00 0.00 0.00 1.89
428 1024 1.741770 CAGCCTCCTGCCGTGTTAC 60.742 63.158 0.00 0.00 42.71 2.50
487 1083 1.051812 CCCGTCCCATCTTATCTGCT 58.948 55.000 0.00 0.00 0.00 4.24
520 1116 5.654650 TGCGGAAATAAATAACTGATTGGGT 59.345 36.000 0.00 0.00 0.00 4.51
624 1220 9.578576 TCAAAAGATAAATCTATCATCCCCAAG 57.421 33.333 0.00 0.00 37.05 3.61
644 2248 6.047870 CCAAGAAAACACAAATCCATGTTCA 58.952 36.000 0.00 0.00 38.08 3.18
655 2259 4.877378 ATCCATGTTCAGCACAATTTGT 57.123 36.364 0.00 0.00 39.50 2.83
663 2267 2.896044 TCAGCACAATTTGTATTGGCCA 59.104 40.909 0.00 0.00 44.42 5.36
674 2278 4.214986 TGTATTGGCCATTCTTCGAAGA 57.785 40.909 23.74 23.74 0.00 2.87
735 2401 3.691118 TGTGGCAGAATAAGTGCATCTTC 59.309 43.478 5.04 0.00 43.12 2.87
804 2471 6.971184 CCTTATGAGATGACAGCACAAATTTC 59.029 38.462 0.00 0.00 0.00 2.17
915 2614 3.173965 AGTGACTGCCACCTGTTATACT 58.826 45.455 0.00 0.00 46.87 2.12
944 2643 8.932791 TGTTTCTTTTTCTATCATAAGGACGAC 58.067 33.333 0.00 0.00 0.00 4.34
968 2667 4.806247 AGAATCGTAGCATTACAAGAGTGC 59.194 41.667 0.00 0.00 39.10 4.40
1097 2796 1.758440 GCTGATATCCAGGGGCGTCA 61.758 60.000 0.00 0.00 43.13 4.35
1102 2801 0.976641 TATCCAGGGGCGTCATCATC 59.023 55.000 0.00 0.00 0.00 2.92
1103 2802 1.056125 ATCCAGGGGCGTCATCATCA 61.056 55.000 0.00 0.00 0.00 3.07
1104 2803 1.056125 TCCAGGGGCGTCATCATCAT 61.056 55.000 0.00 0.00 0.00 2.45
1105 2804 0.686789 CCAGGGGCGTCATCATCATA 59.313 55.000 0.00 0.00 0.00 2.15
1246 2945 1.331756 CCATTACGATCAACAGCTGGC 59.668 52.381 19.93 0.75 0.00 4.85
1302 3001 1.347707 TCCTTCTTGGTTGTCGATGCT 59.652 47.619 0.00 0.00 37.07 3.79
1304 3003 2.932614 CCTTCTTGGTTGTCGATGCTAG 59.067 50.000 0.00 0.00 0.00 3.42
1337 3036 2.752358 CAGCTGCCCTGTTCCTCA 59.248 61.111 0.00 0.00 36.79 3.86
1338 3037 1.073722 CAGCTGCCCTGTTCCTCAA 59.926 57.895 0.00 0.00 36.79 3.02
1349 3048 1.758592 TTCCTCAACGGAACCAGGG 59.241 57.895 0.00 0.00 46.80 4.45
1351 3050 2.351276 CTCAACGGAACCAGGGGG 59.649 66.667 0.00 0.00 41.29 5.40
1358 3057 2.235761 GGAACCAGGGGGCTTACCA 61.236 63.158 0.00 0.00 42.91 3.25
1359 3058 1.303282 GAACCAGGGGGCTTACCAG 59.697 63.158 0.00 0.00 42.91 4.00
1360 3059 2.838748 GAACCAGGGGGCTTACCAGC 62.839 65.000 0.00 0.00 46.52 4.85
1362 3061 2.273449 CAGGGGGCTTACCAGCTG 59.727 66.667 6.78 6.78 46.44 4.24
1363 3062 2.204151 AGGGGGCTTACCAGCTGT 60.204 61.111 13.81 3.45 46.44 4.40
1364 3063 1.082206 AGGGGGCTTACCAGCTGTA 59.918 57.895 13.81 2.40 46.44 2.74
1365 3064 0.327576 AGGGGGCTTACCAGCTGTAT 60.328 55.000 13.81 2.69 46.44 2.29
1366 3065 0.551396 GGGGGCTTACCAGCTGTATT 59.449 55.000 13.81 0.00 46.44 1.89
1367 3066 1.772453 GGGGGCTTACCAGCTGTATTA 59.228 52.381 13.81 0.00 46.44 0.98
1368 3067 2.486727 GGGGGCTTACCAGCTGTATTAC 60.487 54.545 13.81 0.00 46.44 1.89
1370 3069 2.480845 GGCTTACCAGCTGTATTACGG 58.519 52.381 13.81 0.00 46.44 4.02
1372 3071 2.864343 GCTTACCAGCTGTATTACGGTG 59.136 50.000 13.81 7.45 43.51 4.94
1373 3072 3.454375 CTTACCAGCTGTATTACGGTGG 58.546 50.000 23.17 23.17 34.21 4.61
1374 3073 1.272807 ACCAGCTGTATTACGGTGGT 58.727 50.000 24.03 24.03 35.51 4.16
1375 3074 1.066430 ACCAGCTGTATTACGGTGGTG 60.066 52.381 26.59 17.30 37.43 4.17
1376 3075 1.651987 CAGCTGTATTACGGTGGTGG 58.348 55.000 5.25 0.00 0.00 4.61
1377 3076 0.107848 AGCTGTATTACGGTGGTGGC 60.108 55.000 4.63 0.00 0.00 5.01
1378 3077 0.107848 GCTGTATTACGGTGGTGGCT 60.108 55.000 4.63 0.00 0.00 4.75
1379 3078 1.677820 GCTGTATTACGGTGGTGGCTT 60.678 52.381 4.63 0.00 0.00 4.35
1380 3079 2.706890 CTGTATTACGGTGGTGGCTTT 58.293 47.619 0.00 0.00 0.00 3.51
1381 3080 3.078837 CTGTATTACGGTGGTGGCTTTT 58.921 45.455 0.00 0.00 0.00 2.27
1382 3081 3.488363 TGTATTACGGTGGTGGCTTTTT 58.512 40.909 0.00 0.00 0.00 1.94
1383 3082 3.253677 TGTATTACGGTGGTGGCTTTTTG 59.746 43.478 0.00 0.00 0.00 2.44
1388 3087 0.673985 GGTGGTGGCTTTTTGAGGTC 59.326 55.000 0.00 0.00 0.00 3.85
1403 3102 0.543174 AGGTCAGAAGGCTCGGAGTT 60.543 55.000 6.90 0.00 0.00 3.01
1404 3103 1.183549 GGTCAGAAGGCTCGGAGTTA 58.816 55.000 6.90 0.00 0.00 2.24
1408 3107 1.936547 CAGAAGGCTCGGAGTTAATGC 59.063 52.381 6.90 0.00 0.00 3.56
1409 3108 1.834263 AGAAGGCTCGGAGTTAATGCT 59.166 47.619 6.90 0.00 0.00 3.79
1424 3123 2.361737 GCTTGAACTGGCCCCTCC 60.362 66.667 0.00 0.00 0.00 4.30
1426 3125 2.121506 TTGAACTGGCCCCTCCCT 60.122 61.111 0.00 0.00 0.00 4.20
1427 3126 2.203549 CTTGAACTGGCCCCTCCCTC 62.204 65.000 0.00 0.00 0.00 4.30
1428 3127 2.285743 GAACTGGCCCCTCCCTCT 60.286 66.667 0.00 0.00 0.00 3.69
1432 3131 1.925455 CTGGCCCCTCCCTCTTCAA 60.925 63.158 0.00 0.00 0.00 2.69
1435 3134 0.396278 GGCCCCTCCCTCTTCAATTG 60.396 60.000 0.00 0.00 0.00 2.32
1436 3135 1.039785 GCCCCTCCCTCTTCAATTGC 61.040 60.000 0.00 0.00 0.00 3.56
1440 3139 1.470098 CCTCCCTCTTCAATTGCGTTG 59.530 52.381 0.00 0.00 39.25 4.10
1463 3162 0.238289 ACCTTTGTGAATTGCTCGCG 59.762 50.000 0.00 0.00 37.37 5.87
1464 3163 0.238289 CCTTTGTGAATTGCTCGCGT 59.762 50.000 5.77 0.00 37.37 6.01
1481 3180 2.000447 GCGTGAGGTCAGGAACAATAC 59.000 52.381 3.88 0.00 33.92 1.89
1484 3183 3.193691 CGTGAGGTCAGGAACAATACTCT 59.806 47.826 0.00 0.00 33.92 3.24
1490 3189 5.889289 AGGTCAGGAACAATACTCTCTACTC 59.111 44.000 0.00 0.00 0.00 2.59
1494 3193 5.419155 CAGGAACAATACTCTCTACTCACCA 59.581 44.000 0.00 0.00 0.00 4.17
1505 3204 0.472044 TACTCACCAGTTGCTTGCCA 59.528 50.000 0.00 0.00 33.62 4.92
1506 3205 0.178981 ACTCACCAGTTGCTTGCCAT 60.179 50.000 0.00 0.00 0.00 4.40
1590 3289 0.181350 CTTCCTGTGGATACCTGGGC 59.819 60.000 0.00 0.00 0.00 5.36
1591 3290 1.279025 TTCCTGTGGATACCTGGGCC 61.279 60.000 0.00 0.00 0.00 5.80
1592 3291 1.694169 CCTGTGGATACCTGGGCCT 60.694 63.158 4.53 0.00 0.00 5.19
1593 3292 1.528824 CTGTGGATACCTGGGCCTG 59.471 63.158 4.53 3.68 0.00 4.85
1594 3293 1.987807 CTGTGGATACCTGGGCCTGG 61.988 65.000 26.31 26.31 0.00 4.45
1595 3294 3.096495 TGGATACCTGGGCCTGGC 61.096 66.667 27.65 11.05 0.00 4.85
1603 3302 2.036098 TGGGCCTGGCTGTGATTG 59.964 61.111 19.68 0.00 0.00 2.67
1606 3305 1.598701 GGGCCTGGCTGTGATTGTTC 61.599 60.000 19.68 0.00 0.00 3.18
1642 3341 8.834465 AGAGATCGCCATATTATGCAAATTATC 58.166 33.333 0.00 0.00 0.00 1.75
1696 3395 3.364964 CGCAGTTAGTTTTCCGCAAGATT 60.365 43.478 0.00 0.00 43.02 2.40
1723 3422 5.880054 ATGTACTACATGTGGCTTTGAAC 57.120 39.130 9.11 0.00 37.45 3.18
1724 3423 4.709250 TGTACTACATGTGGCTTTGAACA 58.291 39.130 9.11 1.72 0.00 3.18
1797 3497 0.392706 TTCTCTCACGCACCACACAT 59.607 50.000 0.00 0.00 0.00 3.21
1803 3503 1.302752 ACGCACCACACATGCTCAT 60.303 52.632 0.00 0.00 41.10 2.90
1868 3568 2.108075 TCCTTTCTGAACCTTGGCATGA 59.892 45.455 0.00 0.00 0.00 3.07
1871 3571 2.425143 TCTGAACCTTGGCATGATCC 57.575 50.000 0.00 0.00 0.00 3.36
1893 3593 3.342719 TGCAGCGAATTAATCAGTGGAA 58.657 40.909 0.00 0.00 0.00 3.53
1907 3607 7.487822 AATCAGTGGAATGAAGTCTAGAAGA 57.512 36.000 0.00 0.00 31.76 2.87
1910 3610 8.001881 TCAGTGGAATGAAGTCTAGAAGATAC 57.998 38.462 0.00 0.00 0.00 2.24
1931 3631 3.702045 ACACGTGGGAAAAGATTTTGGAA 59.298 39.130 21.57 0.00 0.00 3.53
1958 3658 2.411160 GCTAACTCGTTTGTTTCCTCGC 60.411 50.000 0.00 0.00 0.00 5.03
1962 3662 3.395639 ACTCGTTTGTTTCCTCGCATAA 58.604 40.909 0.00 0.00 0.00 1.90
2043 3743 2.086869 CTGGTACCTCACAGCCATTTG 58.913 52.381 14.36 0.00 0.00 2.32
2086 3786 9.014297 AGTCCCTTTATTTATCTGTTTGTTCTG 57.986 33.333 0.00 0.00 0.00 3.02
2159 3859 9.840427 TTACTAAAGACTGCATAAATTTGCTTC 57.160 29.630 0.00 0.00 43.18 3.86
2457 4160 6.381801 CAACTGCAACGGAGAAGATTTTATT 58.618 36.000 0.00 0.00 0.00 1.40
2646 4355 0.041535 AGATTGCCTTGGGGATTGCA 59.958 50.000 0.00 0.00 33.58 4.08
2874 4583 1.705186 AGCTTTGGTGTGGTATCCAGT 59.295 47.619 0.00 0.00 32.34 4.00
3020 4729 0.106519 AGGCAACAAGAAGTGGCTGT 60.107 50.000 0.00 0.00 46.90 4.40
3055 4776 0.390340 TGAGATGCACGAGTTGGAGC 60.390 55.000 0.00 0.00 30.71 4.70
3102 4823 3.459145 CTGCATCCAGATGAAGTCTCAG 58.541 50.000 11.81 4.43 41.77 3.35
3213 4934 4.087892 CACGCCCCTGTAGCTGCT 62.088 66.667 7.57 7.57 0.00 4.24
3215 4936 4.845580 CGCCCCTGTAGCTGCTGG 62.846 72.222 18.95 18.95 0.00 4.85
3261 4982 1.961793 CTACTCTGTCGGAGGAGGAG 58.038 60.000 12.70 8.60 46.65 3.69
3264 4985 0.184933 CTCTGTCGGAGGAGGAGGAT 59.815 60.000 0.11 0.00 38.35 3.24
3355 5086 5.209818 TCACGGTTCAGTGAGATTTACTT 57.790 39.130 2.03 0.00 45.18 2.24
3364 5095 9.997482 GTTCAGTGAGATTTACTTGTTTTTACA 57.003 29.630 0.00 0.00 0.00 2.41
3413 5145 8.507249 GGTATGTACTATGATTGAAATCTTGCC 58.493 37.037 4.76 0.00 36.39 4.52
3440 5172 2.290008 ACGTGGATGTGCCTGACAAATA 60.290 45.455 0.00 0.00 38.36 1.40
3441 5173 2.095853 CGTGGATGTGCCTGACAAATAC 59.904 50.000 0.00 0.00 38.36 1.89
3442 5174 3.347216 GTGGATGTGCCTGACAAATACT 58.653 45.455 0.00 0.00 38.36 2.12
3443 5175 3.375299 GTGGATGTGCCTGACAAATACTC 59.625 47.826 0.00 0.00 38.36 2.59
3444 5176 2.945668 GGATGTGCCTGACAAATACTCC 59.054 50.000 0.00 0.00 38.36 3.85
3445 5177 2.489938 TGTGCCTGACAAATACTCCC 57.510 50.000 0.00 0.00 0.00 4.30
3446 5178 1.985159 TGTGCCTGACAAATACTCCCT 59.015 47.619 0.00 0.00 0.00 4.20
3447 5179 2.027192 TGTGCCTGACAAATACTCCCTC 60.027 50.000 0.00 0.00 0.00 4.30
3448 5180 1.559682 TGCCTGACAAATACTCCCTCC 59.440 52.381 0.00 0.00 0.00 4.30
3449 5181 1.473434 GCCTGACAAATACTCCCTCCG 60.473 57.143 0.00 0.00 0.00 4.63
3450 5182 1.831736 CCTGACAAATACTCCCTCCGT 59.168 52.381 0.00 0.00 0.00 4.69
3451 5183 2.236395 CCTGACAAATACTCCCTCCGTT 59.764 50.000 0.00 0.00 0.00 4.44
3452 5184 3.522553 CTGACAAATACTCCCTCCGTTC 58.477 50.000 0.00 0.00 0.00 3.95
3453 5185 2.235402 TGACAAATACTCCCTCCGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
3454 5186 1.558294 ACAAATACTCCCTCCGTTCCC 59.442 52.381 0.00 0.00 0.00 3.97
3455 5187 1.557832 CAAATACTCCCTCCGTTCCCA 59.442 52.381 0.00 0.00 0.00 4.37
3456 5188 1.961133 AATACTCCCTCCGTTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
3457 5189 1.961133 ATACTCCCTCCGTTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3458 5190 1.961133 TACTCCCTCCGTTCCCAAAT 58.039 50.000 0.00 0.00 0.00 2.32
3459 5191 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3460 5192 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3461 5193 3.660959 ACTCCCTCCGTTCCCAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
3462 5194 4.042174 ACTCCCTCCGTTCCCAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
3463 5195 4.102681 ACTCCCTCCGTTCCCAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
3464 5196 4.042174 TCCCTCCGTTCCCAAATATAAGT 58.958 43.478 0.00 0.00 0.00 2.24
3465 5197 4.102054 TCCCTCCGTTCCCAAATATAAGTC 59.898 45.833 0.00 0.00 0.00 3.01
3466 5198 4.102681 CCCTCCGTTCCCAAATATAAGTCT 59.897 45.833 0.00 0.00 0.00 3.24
3467 5199 5.397559 CCCTCCGTTCCCAAATATAAGTCTT 60.398 44.000 0.00 0.00 0.00 3.01
3468 5200 6.120220 CCTCCGTTCCCAAATATAAGTCTTT 58.880 40.000 0.00 0.00 0.00 2.52
3469 5201 6.260271 CCTCCGTTCCCAAATATAAGTCTTTC 59.740 42.308 0.00 0.00 0.00 2.62
3470 5202 6.954232 TCCGTTCCCAAATATAAGTCTTTCT 58.046 36.000 0.00 0.00 0.00 2.52
3471 5203 8.081517 TCCGTTCCCAAATATAAGTCTTTCTA 57.918 34.615 0.00 0.00 0.00 2.10
3472 5204 8.202137 TCCGTTCCCAAATATAAGTCTTTCTAG 58.798 37.037 0.00 0.00 0.00 2.43
3473 5205 8.202137 CCGTTCCCAAATATAAGTCTTTCTAGA 58.798 37.037 0.00 0.00 0.00 2.43
3474 5206 9.250624 CGTTCCCAAATATAAGTCTTTCTAGAG 57.749 37.037 0.00 0.00 0.00 2.43
3487 5219 8.600449 AGTCTTTCTAGAGATTTCAACAAGTG 57.400 34.615 0.00 0.00 0.00 3.16
3488 5220 8.424918 AGTCTTTCTAGAGATTTCAACAAGTGA 58.575 33.333 0.00 0.00 0.00 3.41
3489 5221 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3490 5222 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
3491 5223 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
3492 5224 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
3493 5225 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
3494 5226 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
3497 5229 9.376075 AGAGATTTCAACAAGTGACTACATATG 57.624 33.333 0.00 0.00 35.39 1.78
3498 5230 8.498054 AGATTTCAACAAGTGACTACATATGG 57.502 34.615 7.80 0.00 35.39 2.74
3499 5231 8.321353 AGATTTCAACAAGTGACTACATATGGA 58.679 33.333 7.80 0.00 35.39 3.41
3500 5232 7.905604 TTTCAACAAGTGACTACATATGGAG 57.094 36.000 13.77 13.77 35.39 3.86
3501 5233 5.419542 TCAACAAGTGACTACATATGGAGC 58.580 41.667 15.30 8.47 0.00 4.70
3502 5234 5.046663 TCAACAAGTGACTACATATGGAGCA 60.047 40.000 15.30 10.95 0.00 4.26
3503 5235 5.420725 ACAAGTGACTACATATGGAGCAA 57.579 39.130 15.30 0.16 0.00 3.91
3504 5236 5.804639 ACAAGTGACTACATATGGAGCAAA 58.195 37.500 15.30 0.00 0.00 3.68
3505 5237 6.237901 ACAAGTGACTACATATGGAGCAAAA 58.762 36.000 15.30 0.00 0.00 2.44
3506 5238 6.886459 ACAAGTGACTACATATGGAGCAAAAT 59.114 34.615 15.30 0.00 0.00 1.82
3507 5239 6.932356 AGTGACTACATATGGAGCAAAATG 57.068 37.500 15.30 0.00 0.00 2.32
3508 5240 6.653020 AGTGACTACATATGGAGCAAAATGA 58.347 36.000 15.30 0.00 0.00 2.57
3509 5241 6.765036 AGTGACTACATATGGAGCAAAATGAG 59.235 38.462 15.30 0.00 0.00 2.90
3510 5242 6.540189 GTGACTACATATGGAGCAAAATGAGT 59.460 38.462 15.30 0.00 0.00 3.41
3511 5243 7.066284 GTGACTACATATGGAGCAAAATGAGTT 59.934 37.037 15.30 0.00 0.00 3.01
3512 5244 8.264347 TGACTACATATGGAGCAAAATGAGTTA 58.736 33.333 15.30 0.00 0.00 2.24
3513 5245 9.109393 GACTACATATGGAGCAAAATGAGTTAA 57.891 33.333 15.30 0.00 0.00 2.01
3514 5246 9.632638 ACTACATATGGAGCAAAATGAGTTAAT 57.367 29.630 15.30 0.00 0.00 1.40
3516 5248 8.757982 ACATATGGAGCAAAATGAGTTAATCT 57.242 30.769 7.80 0.00 0.00 2.40
3517 5249 9.851686 ACATATGGAGCAAAATGAGTTAATCTA 57.148 29.630 7.80 0.00 0.00 1.98
3519 5251 9.851686 ATATGGAGCAAAATGAGTTAATCTACA 57.148 29.630 0.00 0.00 0.00 2.74
3520 5252 7.377766 TGGAGCAAAATGAGTTAATCTACAC 57.622 36.000 0.00 0.00 0.00 2.90
3521 5253 7.168219 TGGAGCAAAATGAGTTAATCTACACT 58.832 34.615 0.00 0.00 0.00 3.55
3522 5254 7.334421 TGGAGCAAAATGAGTTAATCTACACTC 59.666 37.037 0.00 0.00 40.03 3.51
3523 5255 7.550906 GGAGCAAAATGAGTTAATCTACACTCT 59.449 37.037 1.31 0.00 40.24 3.24
3524 5256 9.587772 GAGCAAAATGAGTTAATCTACACTCTA 57.412 33.333 1.31 0.00 40.24 2.43
3525 5257 9.944376 AGCAAAATGAGTTAATCTACACTCTAA 57.056 29.630 1.31 0.00 40.24 2.10
3598 5330 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3599 5331 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3600 5332 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3601 5333 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
3602 5334 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
3643 5375 1.773856 TTTGGTGACCGCCTGATGGA 61.774 55.000 0.00 0.00 34.57 3.41
3660 5393 3.543680 TGGAGCGGATTAGGAAGAAAG 57.456 47.619 0.00 0.00 0.00 2.62
3744 5477 2.497273 CAACCCTTCCTTGCCCATTTAG 59.503 50.000 0.00 0.00 0.00 1.85
3754 5487 3.414759 TGCCCATTTAGAGAGTAGGGA 57.585 47.619 0.00 0.00 38.60 4.20
3764 5497 1.478916 GAGAGTAGGGAGGCACAAGAC 59.521 57.143 0.00 0.00 0.00 3.01
3881 5633 3.131326 GCATTGCTTTGATGCTGCA 57.869 47.368 4.13 4.13 44.92 4.41
3883 5635 1.327460 GCATTGCTTTGATGCTGCATG 59.673 47.619 21.53 6.59 44.92 4.06
3972 5725 2.168728 GAGGAAGTCGGGCTACTGAAAT 59.831 50.000 0.00 0.00 32.79 2.17
4021 5774 2.863137 TCGGTTCTGCATTTTGTTTTGC 59.137 40.909 0.00 0.00 39.33 3.68
4148 5904 3.768757 CAGAACCTCCTCTTGTGATCTCT 59.231 47.826 0.00 0.00 0.00 3.10
4200 5956 4.652679 TTCTCTACTGACCTACCAGTGA 57.347 45.455 6.79 2.58 46.00 3.41
4216 5973 1.887198 AGTGACCGACTTCATCTTCGT 59.113 47.619 0.00 0.00 33.23 3.85
4219 5976 2.159612 TGACCGACTTCATCTTCGTACG 60.160 50.000 9.53 9.53 33.23 3.67
4227 5984 3.482722 TCATCTTCGTACGAGGTGTTC 57.517 47.619 24.36 0.00 0.00 3.18
4281 6038 6.227298 TGAGATCCAGGATTCAAGAACTAC 57.773 41.667 2.53 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.219546 TCTGTTAATTTCATCAATAATCGCCA 57.780 30.769 0.00 0.00 0.00 5.69
10 11 9.193806 AGTGGCTCTGTTAATTTCATCAATAAT 57.806 29.630 0.00 0.00 0.00 1.28
13 14 7.039504 ACAAGTGGCTCTGTTAATTTCATCAAT 60.040 33.333 0.00 0.00 0.00 2.57
17 608 5.536161 ACACAAGTGGCTCTGTTAATTTCAT 59.464 36.000 5.08 0.00 34.19 2.57
33 624 1.532868 GCTACCAGCTCAACACAAGTG 59.467 52.381 0.00 0.00 38.45 3.16
37 628 0.764890 AAGGCTACCAGCTCAACACA 59.235 50.000 0.00 0.00 41.99 3.72
50 641 2.284331 TCCTCGGGCACAAGGCTA 60.284 61.111 0.00 0.00 44.01 3.93
63 654 4.142513 GCATTCACAACCAGAATTCTCCTC 60.143 45.833 4.57 0.00 33.64 3.71
67 658 3.057033 GCTGCATTCACAACCAGAATTCT 60.057 43.478 0.88 0.88 33.64 2.40
68 659 3.248266 GCTGCATTCACAACCAGAATTC 58.752 45.455 0.00 0.00 33.64 2.17
73 666 0.524862 GAGGCTGCATTCACAACCAG 59.475 55.000 0.50 0.00 0.00 4.00
94 687 2.427453 CTCAGACCACTATAACACGGCT 59.573 50.000 0.00 0.00 0.00 5.52
121 714 1.001293 TGGACTGCAGCAAGTCTACAG 59.999 52.381 15.27 0.00 44.98 2.74
232 825 0.107703 CATACCCAGCGTGTGACCAT 60.108 55.000 0.00 0.00 35.70 3.55
242 835 2.292267 CATGTTCTGTCCATACCCAGC 58.708 52.381 0.00 0.00 0.00 4.85
259 852 0.870393 GGTGCCACGATAGATGCATG 59.130 55.000 2.46 0.00 44.75 4.06
292 885 9.827411 GAGTAAGTCCAAGTTGTATTCAATTTC 57.173 33.333 1.45 0.00 35.92 2.17
336 932 2.619931 TCACCTTCATGTCCTTCTCCA 58.380 47.619 0.00 0.00 0.00 3.86
428 1024 2.763933 ACAATCACACTCAGACAGCTG 58.236 47.619 13.48 13.48 43.67 4.24
487 1083 4.513406 ATTTATTTCCGCAACCCCTCTA 57.487 40.909 0.00 0.00 0.00 2.43
520 1116 6.544928 TTCTCACATAGCAACTATTCCTCA 57.455 37.500 0.00 0.00 0.00 3.86
624 1220 5.049167 TGCTGAACATGGATTTGTGTTTTC 58.951 37.500 0.00 0.00 38.57 2.29
644 2248 4.223477 AGAATGGCCAATACAAATTGTGCT 59.777 37.500 10.96 0.00 40.84 4.40
655 2259 5.097742 TCTTCTTCGAAGAATGGCCAATA 57.902 39.130 34.19 14.26 45.90 1.90
663 2267 6.202954 ACACGACAAATTCTTCTTCGAAGAAT 59.797 34.615 34.19 21.10 45.87 2.40
674 2278 7.504924 TCAAGGAAATACACGACAAATTCTT 57.495 32.000 0.00 0.00 0.00 2.52
725 2391 6.233434 TGACAATCTTTACAGAAGATGCACT 58.767 36.000 2.34 0.00 37.11 4.40
804 2471 2.953648 AGTTTCCGTAACACCCCAAAAG 59.046 45.455 1.24 0.00 39.30 2.27
944 2643 5.276584 GCACTCTTGTAATGCTACGATTCTG 60.277 44.000 0.00 0.00 36.40 3.02
968 2667 4.637483 TGTTCTGCCTTCTTTTCAAGTG 57.363 40.909 0.00 0.00 0.00 3.16
1097 2796 7.637511 AGAAAAAGGAGGACAAGTATGATGAT 58.362 34.615 0.00 0.00 0.00 2.45
1102 2801 5.617751 CGCAAGAAAAAGGAGGACAAGTATG 60.618 44.000 0.00 0.00 43.02 2.39
1103 2802 4.455877 CGCAAGAAAAAGGAGGACAAGTAT 59.544 41.667 0.00 0.00 43.02 2.12
1104 2803 3.813166 CGCAAGAAAAAGGAGGACAAGTA 59.187 43.478 0.00 0.00 43.02 2.24
1105 2804 2.618709 CGCAAGAAAAAGGAGGACAAGT 59.381 45.455 0.00 0.00 43.02 3.16
1302 3001 2.679059 GCTGCTGCTCAAGTCCAATCTA 60.679 50.000 8.53 0.00 36.03 1.98
1304 3003 0.450983 GCTGCTGCTCAAGTCCAATC 59.549 55.000 8.53 0.00 36.03 2.67
1337 3036 1.848895 TAAGCCCCCTGGTTCCGTT 60.849 57.895 0.00 0.00 35.89 4.44
1338 3037 2.204029 TAAGCCCCCTGGTTCCGT 60.204 61.111 0.00 0.00 35.89 4.69
1358 3057 0.107848 GCCACCACCGTAATACAGCT 60.108 55.000 0.00 0.00 0.00 4.24
1359 3058 0.107848 AGCCACCACCGTAATACAGC 60.108 55.000 0.00 0.00 0.00 4.40
1360 3059 2.396590 AAGCCACCACCGTAATACAG 57.603 50.000 0.00 0.00 0.00 2.74
1362 3061 3.502979 TCAAAAAGCCACCACCGTAATAC 59.497 43.478 0.00 0.00 0.00 1.89
1363 3062 3.752665 TCAAAAAGCCACCACCGTAATA 58.247 40.909 0.00 0.00 0.00 0.98
1364 3063 2.556622 CTCAAAAAGCCACCACCGTAAT 59.443 45.455 0.00 0.00 0.00 1.89
1365 3064 1.950909 CTCAAAAAGCCACCACCGTAA 59.049 47.619 0.00 0.00 0.00 3.18
1366 3065 1.600023 CTCAAAAAGCCACCACCGTA 58.400 50.000 0.00 0.00 0.00 4.02
1367 3066 1.106944 CCTCAAAAAGCCACCACCGT 61.107 55.000 0.00 0.00 0.00 4.83
1368 3067 1.106944 ACCTCAAAAAGCCACCACCG 61.107 55.000 0.00 0.00 0.00 4.94
1370 3069 1.338020 CTGACCTCAAAAAGCCACCAC 59.662 52.381 0.00 0.00 0.00 4.16
1372 3071 1.981256 TCTGACCTCAAAAAGCCACC 58.019 50.000 0.00 0.00 0.00 4.61
1373 3072 2.294512 CCTTCTGACCTCAAAAAGCCAC 59.705 50.000 0.00 0.00 0.00 5.01
1374 3073 2.586425 CCTTCTGACCTCAAAAAGCCA 58.414 47.619 0.00 0.00 0.00 4.75
1375 3074 1.270826 GCCTTCTGACCTCAAAAAGCC 59.729 52.381 0.00 0.00 0.00 4.35
1376 3075 2.227626 GAGCCTTCTGACCTCAAAAAGC 59.772 50.000 0.00 0.00 0.00 3.51
1377 3076 2.481952 CGAGCCTTCTGACCTCAAAAAG 59.518 50.000 0.00 0.00 0.00 2.27
1378 3077 2.494059 CGAGCCTTCTGACCTCAAAAA 58.506 47.619 0.00 0.00 0.00 1.94
1379 3078 1.270839 CCGAGCCTTCTGACCTCAAAA 60.271 52.381 0.00 0.00 0.00 2.44
1380 3079 0.321671 CCGAGCCTTCTGACCTCAAA 59.678 55.000 0.00 0.00 0.00 2.69
1381 3080 0.541998 TCCGAGCCTTCTGACCTCAA 60.542 55.000 0.00 0.00 0.00 3.02
1382 3081 0.967887 CTCCGAGCCTTCTGACCTCA 60.968 60.000 0.00 0.00 0.00 3.86
1383 3082 0.968393 ACTCCGAGCCTTCTGACCTC 60.968 60.000 0.00 0.00 0.00 3.85
1388 3087 1.936547 GCATTAACTCCGAGCCTTCTG 59.063 52.381 0.00 0.00 0.00 3.02
1403 3102 0.704076 AGGGGCCAGTTCAAGCATTA 59.296 50.000 4.39 0.00 0.00 1.90
1404 3103 0.613012 GAGGGGCCAGTTCAAGCATT 60.613 55.000 4.39 0.00 0.00 3.56
1408 3107 2.203549 GAGGGAGGGGCCAGTTCAAG 62.204 65.000 4.39 0.00 38.95 3.02
1409 3108 2.121506 AGGGAGGGGCCAGTTCAA 60.122 61.111 4.39 0.00 38.95 2.69
1424 3123 0.883833 AGCCAACGCAATTGAAGAGG 59.116 50.000 10.34 10.51 41.23 3.69
1426 3125 1.810151 GGTAGCCAACGCAATTGAAGA 59.190 47.619 10.34 0.00 41.23 2.87
1427 3126 1.812571 AGGTAGCCAACGCAATTGAAG 59.187 47.619 10.34 4.66 41.23 3.02
1428 3127 1.904287 AGGTAGCCAACGCAATTGAA 58.096 45.000 10.34 0.00 41.23 2.69
1432 3131 1.269448 CACAAAGGTAGCCAACGCAAT 59.731 47.619 0.00 0.00 37.52 3.56
1435 3134 0.948678 TTCACAAAGGTAGCCAACGC 59.051 50.000 0.00 0.00 0.00 4.84
1436 3135 3.564511 CAATTCACAAAGGTAGCCAACG 58.435 45.455 0.00 0.00 0.00 4.10
1440 3139 2.159517 CGAGCAATTCACAAAGGTAGCC 60.160 50.000 0.00 0.00 0.00 3.93
1463 3162 4.464597 AGAGAGTATTGTTCCTGACCTCAC 59.535 45.833 0.00 0.00 0.00 3.51
1464 3163 4.678256 AGAGAGTATTGTTCCTGACCTCA 58.322 43.478 0.00 0.00 0.00 3.86
1481 3180 3.583806 CAAGCAACTGGTGAGTAGAGAG 58.416 50.000 0.00 0.00 0.00 3.20
1484 3183 1.270839 GGCAAGCAACTGGTGAGTAGA 60.271 52.381 0.00 0.00 0.00 2.59
1490 3189 0.171903 GCTATGGCAAGCAACTGGTG 59.828 55.000 14.15 0.00 42.30 4.17
1590 3289 1.171308 CCAGAACAATCACAGCCAGG 58.829 55.000 0.00 0.00 0.00 4.45
1591 3290 2.189594 TCCAGAACAATCACAGCCAG 57.810 50.000 0.00 0.00 0.00 4.85
1592 3291 2.507484 CTTCCAGAACAATCACAGCCA 58.493 47.619 0.00 0.00 0.00 4.75
1593 3292 1.815003 CCTTCCAGAACAATCACAGCC 59.185 52.381 0.00 0.00 0.00 4.85
1594 3293 1.200948 GCCTTCCAGAACAATCACAGC 59.799 52.381 0.00 0.00 0.00 4.40
1595 3294 1.466167 CGCCTTCCAGAACAATCACAG 59.534 52.381 0.00 0.00 0.00 3.66
1603 3302 1.535015 CGATCTCTCGCCTTCCAGAAC 60.535 57.143 0.00 0.00 38.20 3.01
1674 3373 1.529438 TCTTGCGGAAAACTAACTGCG 59.471 47.619 0.00 0.00 40.76 5.18
1702 3401 4.709250 TGTTCAAAGCCACATGTAGTACA 58.291 39.130 5.24 5.24 0.00 2.90
1703 3402 5.449304 GTTGTTCAAAGCCACATGTAGTAC 58.551 41.667 0.00 0.00 0.00 2.73
1704 3403 4.517453 GGTTGTTCAAAGCCACATGTAGTA 59.483 41.667 0.00 0.00 0.00 1.82
1706 3405 3.305335 GGGTTGTTCAAAGCCACATGTAG 60.305 47.826 0.00 0.00 37.71 2.74
1707 3406 2.625790 GGGTTGTTCAAAGCCACATGTA 59.374 45.455 0.00 0.00 37.71 2.29
1708 3407 1.412343 GGGTTGTTCAAAGCCACATGT 59.588 47.619 0.00 0.00 37.71 3.21
1709 3408 1.688197 AGGGTTGTTCAAAGCCACATG 59.312 47.619 8.84 0.00 40.12 3.21
1710 3409 2.086610 AGGGTTGTTCAAAGCCACAT 57.913 45.000 8.84 0.00 40.12 3.21
1711 3410 1.480137 CAAGGGTTGTTCAAAGCCACA 59.520 47.619 8.84 0.00 40.12 4.17
1713 3412 0.463620 GCAAGGGTTGTTCAAAGCCA 59.536 50.000 8.84 0.00 40.12 4.75
1714 3413 0.249868 GGCAAGGGTTGTTCAAAGCC 60.250 55.000 0.00 0.00 38.05 4.35
1715 3414 0.597377 CGGCAAGGGTTGTTCAAAGC 60.597 55.000 0.00 0.00 0.00 3.51
1716 3415 0.744281 ACGGCAAGGGTTGTTCAAAG 59.256 50.000 0.00 0.00 0.00 2.77
1717 3416 1.134965 CAACGGCAAGGGTTGTTCAAA 60.135 47.619 0.00 0.00 39.83 2.69
1718 3417 0.457851 CAACGGCAAGGGTTGTTCAA 59.542 50.000 0.00 0.00 39.83 2.69
1719 3418 2.010582 GCAACGGCAAGGGTTGTTCA 62.011 55.000 6.54 0.00 45.01 3.18
1720 3419 1.299850 GCAACGGCAAGGGTTGTTC 60.300 57.895 6.54 0.00 45.01 3.18
1721 3420 1.734388 GAGCAACGGCAAGGGTTGTT 61.734 55.000 6.54 0.52 45.01 2.83
1722 3421 2.123897 AGCAACGGCAAGGGTTGT 60.124 55.556 6.54 0.00 45.01 3.32
1723 3422 2.133742 CTGAGCAACGGCAAGGGTTG 62.134 60.000 0.54 0.54 45.76 3.77
1724 3423 1.898574 CTGAGCAACGGCAAGGGTT 60.899 57.895 0.00 0.00 44.61 4.11
1797 3497 4.466015 TGATGTAGACCAAGTGTATGAGCA 59.534 41.667 0.00 0.00 0.00 4.26
1803 3503 8.758829 ACAATTAGATGATGTAGACCAAGTGTA 58.241 33.333 0.00 0.00 0.00 2.90
1868 3568 3.562973 CACTGATTAATTCGCTGCAGGAT 59.437 43.478 17.12 0.02 0.00 3.24
1871 3571 2.938451 TCCACTGATTAATTCGCTGCAG 59.062 45.455 10.11 10.11 0.00 4.41
1893 3593 5.067936 CCCACGTGTATCTTCTAGACTTCAT 59.932 44.000 15.65 0.00 0.00 2.57
1907 3607 5.074115 TCCAAAATCTTTTCCCACGTGTAT 58.926 37.500 15.65 0.00 0.00 2.29
1910 3610 4.048504 GTTCCAAAATCTTTTCCCACGTG 58.951 43.478 9.08 9.08 0.00 4.49
1931 3631 5.124936 AGGAAACAAACGAGTTAGCAAAAGT 59.875 36.000 0.00 0.00 0.00 2.66
2030 3730 8.246180 AGTTAATCAATAACAAATGGCTGTGAG 58.754 33.333 1.68 0.00 45.29 3.51
2568 4271 8.023050 ACGAAAAGATGTATTTGTCAAGAGAG 57.977 34.615 0.00 0.00 0.00 3.20
2874 4583 5.584649 CCCGAAGCTGTAAACATCAGATTTA 59.415 40.000 0.00 0.00 40.76 1.40
3017 4726 3.974222 TCTGCCGCAGATATCACAG 57.026 52.632 19.36 4.71 35.39 3.66
3055 4776 0.512952 CCAACGAGACAAAGCTTCCG 59.487 55.000 0.00 1.61 0.00 4.30
3213 4934 1.340248 GAGAAGACGTGGTGAGAACCA 59.660 52.381 0.00 0.00 37.46 3.67
3215 4936 2.293677 TCAGAGAAGACGTGGTGAGAAC 59.706 50.000 0.00 0.00 0.00 3.01
3261 4982 3.487544 GCGTAGAAGCACCATCAAAATCC 60.488 47.826 0.00 0.00 37.05 3.01
3264 4985 2.499197 TGCGTAGAAGCACCATCAAAA 58.501 42.857 0.00 0.00 42.92 2.44
3355 5086 5.802956 GCACTGCTACAAAAGTGTAAAAACA 59.197 36.000 4.87 0.00 44.59 2.83
3364 5095 0.944386 CACGGCACTGCTACAAAAGT 59.056 50.000 0.00 0.00 0.00 2.66
3440 5172 1.961133 TATTTGGGAACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3441 5173 4.102681 ACTTATATTTGGGAACGGAGGGAG 59.897 45.833 0.00 0.00 0.00 4.30
3442 5174 4.042174 ACTTATATTTGGGAACGGAGGGA 58.958 43.478 0.00 0.00 0.00 4.20
3443 5175 4.102681 AGACTTATATTTGGGAACGGAGGG 59.897 45.833 0.00 0.00 0.00 4.30
3444 5176 5.291905 AGACTTATATTTGGGAACGGAGG 57.708 43.478 0.00 0.00 0.00 4.30
3445 5177 7.048512 AGAAAGACTTATATTTGGGAACGGAG 58.951 38.462 0.00 0.00 0.00 4.63
3446 5178 6.954232 AGAAAGACTTATATTTGGGAACGGA 58.046 36.000 0.00 0.00 0.00 4.69
3447 5179 8.202137 TCTAGAAAGACTTATATTTGGGAACGG 58.798 37.037 0.00 0.00 0.00 4.44
3448 5180 9.250624 CTCTAGAAAGACTTATATTTGGGAACG 57.749 37.037 0.00 0.00 0.00 3.95
3461 5193 9.050601 CACTTGTTGAAATCTCTAGAAAGACTT 57.949 33.333 0.00 0.00 0.00 3.01
3462 5194 8.424918 TCACTTGTTGAAATCTCTAGAAAGACT 58.575 33.333 0.00 0.00 0.00 3.24
3463 5195 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3464 5196 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3465 5197 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3466 5198 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
3467 5199 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
3468 5200 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
3469 5201 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
3471 5203 9.376075 CATATGTAGTCACTTGTTGAAATCTCT 57.624 33.333 0.00 0.00 35.39 3.10
3472 5204 8.607459 CCATATGTAGTCACTTGTTGAAATCTC 58.393 37.037 1.24 0.00 35.39 2.75
3473 5205 8.321353 TCCATATGTAGTCACTTGTTGAAATCT 58.679 33.333 1.24 0.00 35.39 2.40
3474 5206 8.492673 TCCATATGTAGTCACTTGTTGAAATC 57.507 34.615 1.24 0.00 35.39 2.17
3475 5207 7.066284 GCTCCATATGTAGTCACTTGTTGAAAT 59.934 37.037 1.24 0.00 35.39 2.17
3476 5208 6.371548 GCTCCATATGTAGTCACTTGTTGAAA 59.628 38.462 1.24 0.00 35.39 2.69
3477 5209 5.874810 GCTCCATATGTAGTCACTTGTTGAA 59.125 40.000 1.24 0.00 35.39 2.69
3478 5210 5.046663 TGCTCCATATGTAGTCACTTGTTGA 60.047 40.000 1.24 0.00 0.00 3.18
3479 5211 5.178061 TGCTCCATATGTAGTCACTTGTTG 58.822 41.667 1.24 0.00 0.00 3.33
3480 5212 5.420725 TGCTCCATATGTAGTCACTTGTT 57.579 39.130 1.24 0.00 0.00 2.83
3481 5213 5.420725 TTGCTCCATATGTAGTCACTTGT 57.579 39.130 1.24 0.00 0.00 3.16
3482 5214 6.741992 TTTTGCTCCATATGTAGTCACTTG 57.258 37.500 1.24 0.00 0.00 3.16
3483 5215 7.112122 TCATTTTGCTCCATATGTAGTCACTT 58.888 34.615 1.24 0.00 0.00 3.16
3484 5216 6.653020 TCATTTTGCTCCATATGTAGTCACT 58.347 36.000 1.24 0.00 0.00 3.41
3485 5217 6.540189 ACTCATTTTGCTCCATATGTAGTCAC 59.460 38.462 1.24 0.00 0.00 3.67
3486 5218 6.653020 ACTCATTTTGCTCCATATGTAGTCA 58.347 36.000 1.24 0.00 0.00 3.41
3487 5219 7.559590 AACTCATTTTGCTCCATATGTAGTC 57.440 36.000 1.24 0.00 0.00 2.59
3488 5220 9.632638 ATTAACTCATTTTGCTCCATATGTAGT 57.367 29.630 1.24 0.00 0.00 2.73
3490 5222 9.851686 AGATTAACTCATTTTGCTCCATATGTA 57.148 29.630 1.24 0.00 0.00 2.29
3491 5223 8.757982 AGATTAACTCATTTTGCTCCATATGT 57.242 30.769 1.24 0.00 0.00 2.29
3493 5225 9.851686 TGTAGATTAACTCATTTTGCTCCATAT 57.148 29.630 0.00 0.00 0.00 1.78
3494 5226 9.109393 GTGTAGATTAACTCATTTTGCTCCATA 57.891 33.333 0.00 0.00 0.00 2.74
3495 5227 7.831193 AGTGTAGATTAACTCATTTTGCTCCAT 59.169 33.333 0.00 0.00 0.00 3.41
3496 5228 7.168219 AGTGTAGATTAACTCATTTTGCTCCA 58.832 34.615 0.00 0.00 0.00 3.86
3497 5229 7.550906 AGAGTGTAGATTAACTCATTTTGCTCC 59.449 37.037 5.68 0.00 44.34 4.70
3498 5230 8.485976 AGAGTGTAGATTAACTCATTTTGCTC 57.514 34.615 5.68 0.00 44.34 4.26
3499 5231 9.944376 TTAGAGTGTAGATTAACTCATTTTGCT 57.056 29.630 5.68 0.00 44.34 3.91
3572 5304 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3573 5305 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
3574 5306 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3575 5307 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3576 5308 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3577 5309 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3578 5310 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3579 5311 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3581 5313 9.417561 CATATACTCCCTCCGTTCCTAAATATA 57.582 37.037 0.00 0.00 0.00 0.86
3582 5314 7.899709 ACATATACTCCCTCCGTTCCTAAATAT 59.100 37.037 0.00 0.00 0.00 1.28
3583 5315 7.243824 ACATATACTCCCTCCGTTCCTAAATA 58.756 38.462 0.00 0.00 0.00 1.40
3584 5316 6.082707 ACATATACTCCCTCCGTTCCTAAAT 58.917 40.000 0.00 0.00 0.00 1.40
3585 5317 5.461327 ACATATACTCCCTCCGTTCCTAAA 58.539 41.667 0.00 0.00 0.00 1.85
3586 5318 5.070823 ACATATACTCCCTCCGTTCCTAA 57.929 43.478 0.00 0.00 0.00 2.69
3587 5319 4.105217 TGACATATACTCCCTCCGTTCCTA 59.895 45.833 0.00 0.00 0.00 2.94
3588 5320 3.117246 TGACATATACTCCCTCCGTTCCT 60.117 47.826 0.00 0.00 0.00 3.36
3589 5321 3.228453 TGACATATACTCCCTCCGTTCC 58.772 50.000 0.00 0.00 0.00 3.62
3590 5322 4.142790 TCTGACATATACTCCCTCCGTTC 58.857 47.826 0.00 0.00 0.00 3.95
3591 5323 4.180377 TCTGACATATACTCCCTCCGTT 57.820 45.455 0.00 0.00 0.00 4.44
3592 5324 3.878237 TCTGACATATACTCCCTCCGT 57.122 47.619 0.00 0.00 0.00 4.69
3593 5325 6.831353 AGATTATCTGACATATACTCCCTCCG 59.169 42.308 0.00 0.00 0.00 4.63
3643 5375 4.031611 AGTACCTTTCTTCCTAATCCGCT 58.968 43.478 0.00 0.00 0.00 5.52
3682 5415 8.646004 TGAAATTTCTCCAACATTGTTTCCATA 58.354 29.630 18.64 0.00 0.00 2.74
3744 5477 1.478916 GTCTTGTGCCTCCCTACTCTC 59.521 57.143 0.00 0.00 0.00 3.20
3754 5487 2.548920 GCAACTCTAGTGTCTTGTGCCT 60.549 50.000 7.72 0.00 0.00 4.75
3764 5497 1.446907 CTTGCCCTGCAACTCTAGTG 58.553 55.000 0.00 0.00 43.99 2.74
3881 5633 4.472833 AGGAAGATTGTACTGCTCCTTCAT 59.527 41.667 0.00 0.00 33.63 2.57
3883 5635 4.479786 AGGAAGATTGTACTGCTCCTTC 57.520 45.455 0.00 0.00 0.00 3.46
3972 5725 5.121925 CACGAGAAACACTGCTACTACTCTA 59.878 44.000 0.00 0.00 0.00 2.43
4048 5801 6.634805 TGCACCTTTAACATTTTGTTTCTCA 58.365 32.000 0.00 0.00 41.45 3.27
4109 5862 3.095912 TCTGCAGGCCTTGTACTACTA 57.904 47.619 15.13 0.00 0.00 1.82
4200 5956 2.079158 TCGTACGAAGATGAAGTCGGT 58.921 47.619 17.11 0.00 41.56 4.69
4227 5984 9.072981 TGCACCTTTAAGATGCATCTGATGATG 62.073 40.741 29.34 21.72 40.50 3.07
4281 6038 6.212955 CCATATTTTGGGTGCTTTTATACGG 58.787 40.000 0.00 0.00 42.33 4.02


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

AutoCloner maintained by Alex Coulton.