Multiple sequence alignment - TraesCS4A01G200000

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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 TraesCS4A01G200000 chr4A 100.000 3899 0 0 1 3899 488109321 488113219 0.000000e+00 7201.0
1 TraesCS4A01G200000 chr4A 86.207 174 20 4 3506 3678 618084990 618085160 6.650000e-43 185.0
2 TraesCS4A01G200000 chr4A 93.000 100 4 2 3084 3183 537597910 537598006 4.060000e-30 143.0
3 TraesCS4A01G200000 chr4D 94.259 2961 127 21 1 2948 93712967 93710037 0.000000e+00 4486.0
4 TraesCS4A01G200000 chr4D 92.135 178 13 1 3722 3899 93705249 93705073 2.330000e-62 250.0
5 TraesCS4A01G200000 chr4B 94.858 2178 69 13 902 3050 132168176 132166013 0.000000e+00 3362.0
6 TraesCS4A01G200000 chr4B 95.089 224 10 1 3677 3899 132165569 132165346 6.200000e-93 351.0
7 TraesCS4A01G200000 chr4B 92.079 101 8 0 3095 3195 427022073 427022173 4.060000e-30 143.0
8 TraesCS4A01G200000 chr4B 89.899 99 6 4 3184 3281 132166014 132165919 1.470000e-24 124.0
9 TraesCS4A01G200000 chr5A 81.547 1306 191 38 1428 2705 440735060 440733777 0.000000e+00 1031.0
10 TraesCS4A01G200000 chr5A 89.474 152 12 4 3532 3680 401740663 401740813 5.140000e-44 189.0
11 TraesCS4A01G200000 chr5B 80.982 1304 198 35 1428 2703 398626590 398625309 0.000000e+00 989.0
12 TraesCS4A01G200000 chr5D 80.908 1168 180 32 1562 2703 339654074 339652924 0.000000e+00 881.0
13 TraesCS4A01G200000 chr6B 90.625 160 10 4 3533 3689 420652057 420652214 1.420000e-49 207.0
14 TraesCS4A01G200000 chr1B 94.074 135 8 0 3552 3686 571434299 571434433 5.110000e-49 206.0
15 TraesCS4A01G200000 chr1A 94.656 131 5 2 3552 3681 380966225 380966096 6.610000e-48 202.0
16 TraesCS4A01G200000 chr1A 89.474 152 12 4 3532 3680 296529542 296529392 5.140000e-44 189.0
17 TraesCS4A01G200000 chr1D 89.032 155 10 7 3532 3680 57695426 57695579 6.650000e-43 185.0
18 TraesCS4A01G200000 chr1D 93.750 96 6 0 3094 3189 10750544 10750639 1.130000e-30 145.0
19 TraesCS4A01G200000 chr1D 92.079 101 7 1 3083 3182 159982718 159982818 1.460000e-29 141.0
20 TraesCS4A01G200000 chr6D 88.816 152 13 4 3532 3680 299316026 299316176 2.390000e-42 183.0
21 TraesCS4A01G200000 chr6D 88.816 152 13 4 3532 3680 371697879 371698029 2.390000e-42 183.0
22 TraesCS4A01G200000 chr2A 98.837 86 1 0 3097 3182 685469226 685469141 1.880000e-33 154.0
23 TraesCS4A01G200000 chr2A 93.750 96 6 0 3095 3190 500032944 500032849 1.130000e-30 145.0
24 TraesCS4A01G200000 chr7D 93.069 101 5 2 3092 3190 4902193 4902293 3.140000e-31 147.0
25 TraesCS4A01G200000 chr3A 89.286 112 9 3 3095 3204 120809536 120809646 1.890000e-28 137.0
26 TraesCS4A01G200000 chr7B 88.596 114 10 3 3089 3200 388716518 388716406 6.800000e-28 135.0
27 TraesCS4A01G200000 chr6A 100.000 28 0 0 3241 3268 432533315 432533288 7.000000e-03 52.8


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 TraesCS4A01G200000 chr4A 488109321 488113219 3898 False 7201 7201 100.000 1 3899 1 chr4A.!!$F1 3898
1 TraesCS4A01G200000 chr4D 93710037 93712967 2930 True 4486 4486 94.259 1 2948 1 chr4D.!!$R2 2947
2 TraesCS4A01G200000 chr4B 132165346 132168176 2830 True 1279 3362 93.282 902 3899 3 chr4B.!!$R1 2997
3 TraesCS4A01G200000 chr5A 440733777 440735060 1283 True 1031 1031 81.547 1428 2705 1 chr5A.!!$R1 1277
4 TraesCS4A01G200000 chr5B 398625309 398626590 1281 True 989 989 80.982 1428 2703 1 chr5B.!!$R1 1275
5 TraesCS4A01G200000 chr5D 339652924 339654074 1150 True 881 881 80.908 1562 2703 1 chr5D.!!$R1 1141

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
773 779 0.106769 TGTGGTGGCACTTGACATGT 60.107 50.000 18.45 0.0 34.33 3.21 F
776 782 1.141858 TGGTGGCACTTGACATGTACA 59.858 47.619 18.45 0.0 34.33 2.90 F
859 865 1.264020 CAAACACACATGTCCACCGAG 59.736 52.381 0.00 0.0 38.45 4.63 F
2239 2247 1.566018 GACGCCGTGGTTCAAGAAGG 61.566 60.000 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 2267 2.359230 GCTGGCGGCTCAAGACTT 60.359 61.111 11.99 0.0 38.06 3.01 R
2798 2825 4.396166 ACCAGACTAACATAAACATGCTGC 59.604 41.667 0.00 0.0 0.00 5.25 R
2799 2826 5.643348 TGACCAGACTAACATAAACATGCTG 59.357 40.000 0.00 0.0 0.00 4.41 R
3547 3694 0.410663 TGGGACGGAGGGAGTAAAGA 59.589 55.000 0.00 0.0 0.00 2.52 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
37 38 3.668141 TGCATGTTGTAGGATGGGATT 57.332 42.857 0.00 0.00 0.00 3.01
63 64 2.432972 GCGGCACAAGCAAATGGG 60.433 61.111 0.00 0.00 44.61 4.00
95 96 7.388500 CCAACAACAAGAATATTTGCCTTTCAT 59.612 33.333 0.00 0.00 0.00 2.57
106 107 4.524316 TTGCCTTTCATCATTGTTGGAG 57.476 40.909 0.00 0.00 0.00 3.86
121 122 3.149196 GTTGGAGCCTGATCAAGAACAA 58.851 45.455 0.00 0.00 0.00 2.83
145 146 3.005472 ACGAAGTGAAAGACGAGGAATGA 59.995 43.478 0.00 0.00 42.51 2.57
156 157 1.202734 CGAGGAATGATGAGGCACCAT 60.203 52.381 0.00 0.00 0.00 3.55
161 162 2.715749 ATGATGAGGCACCATCGAAA 57.284 45.000 12.90 0.17 44.37 3.46
210 211 0.895530 ACGGAGGTTGACGATGACAT 59.104 50.000 0.00 0.00 0.00 3.06
256 257 1.671379 GGGTCAAGCAAGGGACGAC 60.671 63.158 0.00 0.00 34.87 4.34
270 271 2.385803 GGACGACCTGATAGGAGGAAA 58.614 52.381 1.13 0.00 37.67 3.13
339 340 6.836007 TGAGAGAGAAGGTTGATAAGCTGATA 59.164 38.462 0.00 0.00 39.57 2.15
358 359 8.103305 AGCTGATAGTAAAGAAGAAATTGGTGA 58.897 33.333 0.00 0.00 0.00 4.02
361 362 7.876068 TGATAGTAAAGAAGAAATTGGTGACGT 59.124 33.333 0.00 0.00 0.00 4.34
403 404 1.689273 ACTTGACGGAGAAGAAGCACT 59.311 47.619 0.00 0.00 0.00 4.40
414 415 7.660208 ACGGAGAAGAAGCACTAAGAAAAATTA 59.340 33.333 0.00 0.00 0.00 1.40
432 433 1.835494 TAGGAAGGTGGTGAGAGACG 58.165 55.000 0.00 0.00 0.00 4.18
436 437 0.314302 AAGGTGGTGAGAGACGAACG 59.686 55.000 0.00 0.00 0.00 3.95
437 438 0.536687 AGGTGGTGAGAGACGAACGA 60.537 55.000 0.14 0.00 0.00 3.85
438 439 0.386985 GGTGGTGAGAGACGAACGAC 60.387 60.000 0.14 0.00 0.00 4.34
439 440 0.309922 GTGGTGAGAGACGAACGACA 59.690 55.000 0.14 0.00 0.00 4.35
440 441 1.026584 TGGTGAGAGACGAACGACAA 58.973 50.000 0.14 0.00 0.00 3.18
441 442 1.611977 TGGTGAGAGACGAACGACAAT 59.388 47.619 0.14 0.00 0.00 2.71
458 459 3.861840 ACAATGAGATGTGTAAGGACGG 58.138 45.455 0.00 0.00 30.82 4.79
476 477 2.281345 CATGGAGGAGCATCGGCC 60.281 66.667 0.00 0.00 42.56 6.13
485 486 0.681733 GAGCATCGGCCTCTATTGGA 59.318 55.000 0.00 0.00 42.56 3.53
487 488 0.681733 GCATCGGCCTCTATTGGAGA 59.318 55.000 0.00 0.00 44.45 3.71
495 496 2.168728 GCCTCTATTGGAGAAGAACCGT 59.831 50.000 0.00 0.00 44.45 4.83
507 508 0.472471 AGAACCGTTTGAGGCAAGGA 59.528 50.000 0.00 0.00 33.69 3.36
511 512 0.527565 CCGTTTGAGGCAAGGAATGG 59.472 55.000 0.00 0.00 0.00 3.16
515 516 1.909700 TTGAGGCAAGGAATGGTGTC 58.090 50.000 0.00 0.00 0.00 3.67
518 519 2.700773 GGCAAGGAATGGTGTCCGC 61.701 63.158 0.00 0.00 43.03 5.54
528 529 1.177895 TGGTGTCCGCGGTTAGTGTA 61.178 55.000 27.15 0.00 0.00 2.90
543 544 7.464178 GCGGTTAGTGTATGAAGTTGAATAGTG 60.464 40.741 0.00 0.00 0.00 2.74
580 583 2.412421 AACACTCGAACGTCTGGTAC 57.588 50.000 0.00 0.00 0.00 3.34
600 603 2.230864 CGAGGCAAATCGAACGTTTTC 58.769 47.619 0.46 0.00 45.56 2.29
642 645 4.520492 GTGAGGATGACAATTTCAGTTGGT 59.480 41.667 0.00 0.00 37.77 3.67
654 657 4.829064 TTCAGTTGGTAAGCATGACAAC 57.171 40.909 0.00 3.38 42.51 3.32
660 663 2.805671 TGGTAAGCATGACAACTTCGTG 59.194 45.455 0.00 0.00 43.36 4.35
661 664 3.064207 GGTAAGCATGACAACTTCGTGA 58.936 45.455 0.00 0.00 43.20 4.35
711 716 4.811555 TGTGTGTCAACTAACTTGCATC 57.188 40.909 0.00 0.00 0.00 3.91
712 717 3.563808 TGTGTGTCAACTAACTTGCATCC 59.436 43.478 0.00 0.00 0.00 3.51
713 718 3.815401 GTGTGTCAACTAACTTGCATCCT 59.185 43.478 0.00 0.00 0.00 3.24
714 719 4.065088 TGTGTCAACTAACTTGCATCCTC 58.935 43.478 0.00 0.00 0.00 3.71
715 720 3.123621 GTGTCAACTAACTTGCATCCTCG 59.876 47.826 0.00 0.00 0.00 4.63
724 730 2.238646 ACTTGCATCCTCGGGTCAATAA 59.761 45.455 0.00 0.00 0.00 1.40
733 739 5.502079 TCCTCGGGTCAATAAAATTGCTAA 58.498 37.500 0.00 0.00 0.00 3.09
751 757 5.333513 TGCTAACGAAAACGTTCAATTTGT 58.666 33.333 11.07 0.00 32.89 2.83
758 764 5.331458 CGAAAACGTTCAATTTGTCATGTGG 60.331 40.000 0.00 0.00 32.89 4.17
760 766 3.963665 ACGTTCAATTTGTCATGTGGTG 58.036 40.909 0.00 0.00 0.00 4.17
762 768 3.059166 GTTCAATTTGTCATGTGGTGGC 58.941 45.455 0.00 0.00 0.00 5.01
765 771 1.999648 ATTTGTCATGTGGTGGCACT 58.000 45.000 18.45 0.00 43.36 4.40
772 778 1.068125 CATGTGGTGGCACTTGACATG 60.068 52.381 27.39 27.39 38.35 3.21
773 779 0.106769 TGTGGTGGCACTTGACATGT 60.107 50.000 18.45 0.00 34.33 3.21
775 781 1.535462 GTGGTGGCACTTGACATGTAC 59.465 52.381 18.45 0.00 34.33 2.90
776 782 1.141858 TGGTGGCACTTGACATGTACA 59.858 47.619 18.45 0.00 34.33 2.90
777 783 2.224744 TGGTGGCACTTGACATGTACAT 60.225 45.455 18.45 1.41 34.33 2.29
778 784 3.008485 TGGTGGCACTTGACATGTACATA 59.992 43.478 18.45 0.00 34.33 2.29
779 785 4.199310 GGTGGCACTTGACATGTACATAT 58.801 43.478 18.45 0.00 34.33 1.78
782 788 6.486657 GGTGGCACTTGACATGTACATATTAT 59.513 38.462 18.45 0.00 34.33 1.28
786 792 8.840321 GGCACTTGACATGTACATATTATTTCT 58.160 33.333 8.32 0.00 0.00 2.52
850 856 5.123661 TGGAGTGTATATGCAAACACACATG 59.876 40.000 23.88 0.00 46.71 3.21
859 865 1.264020 CAAACACACATGTCCACCGAG 59.736 52.381 0.00 0.00 38.45 4.63
867 873 1.726791 CATGTCCACCGAGTTTCGAAG 59.273 52.381 0.00 0.00 43.74 3.79
873 879 2.480845 CACCGAGTTTCGAAGGTTTCT 58.519 47.619 4.17 0.00 43.74 2.52
875 881 3.059800 CACCGAGTTTCGAAGGTTTCTTC 60.060 47.826 4.17 0.00 43.74 2.87
881 887 5.891451 AGTTTCGAAGGTTTCTTCTTTTGG 58.109 37.500 0.00 0.00 45.36 3.28
900 906 2.813779 GCAGAAACGTGCCAGAATAG 57.186 50.000 0.00 0.00 37.49 1.73
1162 1170 2.094757 AACACCACGCTCACCGATCA 62.095 55.000 0.00 0.00 41.02 2.92
1184 1192 2.026301 GATCGCCTCCCGTTCTCG 59.974 66.667 0.00 0.00 38.35 4.04
1191 1199 1.982938 CTCCCGTTCTCGTCCCCTT 60.983 63.158 0.00 0.00 35.01 3.95
1192 1200 1.946475 CTCCCGTTCTCGTCCCCTTC 61.946 65.000 0.00 0.00 35.01 3.46
1193 1201 2.577593 CCGTTCTCGTCCCCTTCC 59.422 66.667 0.00 0.00 35.01 3.46
1812 1820 2.125512 GCCGTCGACTTCTGCCAT 60.126 61.111 14.70 0.00 0.00 4.40
2239 2247 1.566018 GACGCCGTGGTTCAAGAAGG 61.566 60.000 0.00 0.00 0.00 3.46
2259 2267 2.366301 TCCATCGCCAAGCCCCTA 60.366 61.111 0.00 0.00 0.00 3.53
2661 2687 1.813786 GAGTACCTCTCGTTCTGCTGT 59.186 52.381 0.00 0.00 33.25 4.40
2919 2957 8.040132 TGTTATCTGAATATCATGTGTGTGTCA 58.960 33.333 0.00 0.00 0.00 3.58
2928 2966 0.455410 TGTGTGTGTCAAAGCTTGCC 59.545 50.000 0.00 0.00 0.00 4.52
2973 3011 4.083537 GCGATTGTTTGACAGTGTGGATTA 60.084 41.667 0.00 0.00 0.00 1.75
2978 3016 7.809546 TTGTTTGACAGTGTGGATTAACATA 57.190 32.000 0.00 0.00 31.49 2.29
3028 3090 5.064707 GTGACTGTGTCAGTGTATTGTGTTT 59.935 40.000 7.14 0.00 45.44 2.83
3029 3091 5.645929 TGACTGTGTCAGTGTATTGTGTTTT 59.354 36.000 7.14 0.00 45.44 2.43
3071 3133 9.270640 AGAAAGCACTTCTCATATATAAGCAAG 57.729 33.333 0.00 0.00 40.61 4.01
3073 3135 5.936956 AGCACTTCTCATATATAAGCAAGGC 59.063 40.000 0.00 0.00 0.00 4.35
3074 3136 5.702670 GCACTTCTCATATATAAGCAAGGCA 59.297 40.000 0.00 0.00 0.00 4.75
3075 3137 6.373774 GCACTTCTCATATATAAGCAAGGCAT 59.626 38.462 0.00 0.00 0.00 4.40
3076 3138 7.413877 GCACTTCTCATATATAAGCAAGGCATC 60.414 40.741 0.00 0.00 0.00 3.91
3077 3139 7.823310 CACTTCTCATATATAAGCAAGGCATCT 59.177 37.037 0.00 0.00 0.00 2.90
3078 3140 9.040259 ACTTCTCATATATAAGCAAGGCATCTA 57.960 33.333 0.00 0.00 0.00 1.98
3087 3149 9.799106 ATATAAGCAAGGCATCTATAACAAACT 57.201 29.630 0.00 0.00 0.00 2.66
3089 3151 7.938140 AAGCAAGGCATCTATAACAAACTAA 57.062 32.000 0.00 0.00 0.00 2.24
3090 3152 7.321745 AGCAAGGCATCTATAACAAACTAAC 57.678 36.000 0.00 0.00 0.00 2.34
3091 3153 6.884295 AGCAAGGCATCTATAACAAACTAACA 59.116 34.615 0.00 0.00 0.00 2.41
3092 3154 7.393234 AGCAAGGCATCTATAACAAACTAACAA 59.607 33.333 0.00 0.00 0.00 2.83
3093 3155 8.190784 GCAAGGCATCTATAACAAACTAACAAT 58.809 33.333 0.00 0.00 0.00 2.71
3107 3169 9.220906 ACAAACTAACAATATATACTCCCTCCA 57.779 33.333 0.00 0.00 0.00 3.86
3124 3186 8.817876 ACTCCCTCCATAAACTAATATAAGAGC 58.182 37.037 0.00 0.00 0.00 4.09
3125 3187 8.736097 TCCCTCCATAAACTAATATAAGAGCA 57.264 34.615 0.00 0.00 0.00 4.26
3126 3188 9.338968 TCCCTCCATAAACTAATATAAGAGCAT 57.661 33.333 0.00 0.00 0.00 3.79
3127 3189 9.965902 CCCTCCATAAACTAATATAAGAGCATT 57.034 33.333 0.00 0.00 0.00 3.56
3178 3240 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
3179 3241 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
3180 3242 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
3196 3258 9.693739 ACAGAGGGAGTAGAATATATACATCTG 57.306 37.037 9.22 0.00 33.13 2.90
3197 3259 8.629158 CAGAGGGAGTAGAATATATACATCTGC 58.371 40.741 9.22 8.15 0.00 4.26
3198 3260 8.565239 AGAGGGAGTAGAATATATACATCTGCT 58.435 37.037 14.12 14.12 38.59 4.24
3199 3261 9.854668 GAGGGAGTAGAATATATACATCTGCTA 57.145 37.037 14.18 0.00 36.47 3.49
3266 3328 1.577328 AAATGCTCCCGCGTGAACAG 61.577 55.000 4.92 0.00 39.65 3.16
3281 3343 5.416083 CGTGAACAGTCCCATGAATAGTAA 58.584 41.667 0.00 0.00 0.00 2.24
3282 3344 5.872617 CGTGAACAGTCCCATGAATAGTAAA 59.127 40.000 0.00 0.00 0.00 2.01
3283 3345 6.370442 CGTGAACAGTCCCATGAATAGTAAAA 59.630 38.462 0.00 0.00 0.00 1.52
3319 3462 6.421377 AAAACCAATGACTTCTTTGTTTGC 57.579 33.333 4.65 0.00 31.42 3.68
3457 3604 5.825593 TTTTCCCAGAACACTAGAGATGT 57.174 39.130 0.00 0.00 0.00 3.06
3506 3653 7.869937 GTGTGTATATGCAGACAGTTCATCTAT 59.130 37.037 14.87 0.00 33.49 1.98
3507 3654 8.084684 TGTGTATATGCAGACAGTTCATCTATC 58.915 37.037 0.00 0.00 0.00 2.08
3509 3656 8.864087 TGTATATGCAGACAGTTCATCTATCTT 58.136 33.333 0.00 0.00 25.78 2.40
3510 3657 9.703892 GTATATGCAGACAGTTCATCTATCTTT 57.296 33.333 0.00 0.00 25.78 2.52
3516 3663 8.721478 GCAGACAGTTCATCTATCTTTTTGTTA 58.279 33.333 0.00 0.00 25.78 2.41
3559 3706 9.939802 TGTCTTTTTACTATTCTTTACTCCCTC 57.060 33.333 0.00 0.00 0.00 4.30
3560 3707 9.381033 GTCTTTTTACTATTCTTTACTCCCTCC 57.619 37.037 0.00 0.00 0.00 4.30
3561 3708 8.255905 TCTTTTTACTATTCTTTACTCCCTCCG 58.744 37.037 0.00 0.00 0.00 4.63
3562 3709 7.486407 TTTTACTATTCTTTACTCCCTCCGT 57.514 36.000 0.00 0.00 0.00 4.69
3563 3710 6.705863 TTACTATTCTTTACTCCCTCCGTC 57.294 41.667 0.00 0.00 0.00 4.79
3564 3711 3.959449 ACTATTCTTTACTCCCTCCGTCC 59.041 47.826 0.00 0.00 0.00 4.79
3565 3712 1.565067 TTCTTTACTCCCTCCGTCCC 58.435 55.000 0.00 0.00 0.00 4.46
3566 3713 0.410663 TCTTTACTCCCTCCGTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
3567 3714 1.203212 TCTTTACTCCCTCCGTCCCAA 60.203 52.381 0.00 0.00 0.00 4.12
3568 3715 1.626825 CTTTACTCCCTCCGTCCCAAA 59.373 52.381 0.00 0.00 0.00 3.28
3569 3716 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
3570 3717 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3571 3718 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3572 3719 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3573 3720 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3574 3721 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3575 3722 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3576 3723 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3577 3724 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3578 3725 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3579 3726 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3580 3727 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3581 3728 5.566469 TCCGTCCCAAAATTCTTGTCTTAT 58.434 37.500 0.00 0.00 0.00 1.73
3582 3729 6.713276 TCCGTCCCAAAATTCTTGTCTTATA 58.287 36.000 0.00 0.00 0.00 0.98
3583 3730 7.343357 TCCGTCCCAAAATTCTTGTCTTATAT 58.657 34.615 0.00 0.00 0.00 0.86
3584 3731 7.832187 TCCGTCCCAAAATTCTTGTCTTATATT 59.168 33.333 0.00 0.00 0.00 1.28
3585 3732 8.129211 CCGTCCCAAAATTCTTGTCTTATATTC 58.871 37.037 0.00 0.00 0.00 1.75
3586 3733 8.893727 CGTCCCAAAATTCTTGTCTTATATTCT 58.106 33.333 0.00 0.00 0.00 2.40
3632 3779 6.963049 ACTAAAACGTGACTTCATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
3633 3780 4.921470 AAAACGTGACTTCATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
3634 3781 3.587797 AACGTGACTTCATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
3635 3782 4.707030 AACGTGACTTCATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
3636 3783 4.913335 ACGTGACTTCATACATCCGTAT 57.087 40.909 0.00 0.00 38.96 3.06
3637 3784 5.258456 ACGTGACTTCATACATCCGTATT 57.742 39.130 0.00 0.00 36.11 1.89
3638 3785 5.657474 ACGTGACTTCATACATCCGTATTT 58.343 37.500 0.00 0.00 36.11 1.40
3639 3786 6.798482 ACGTGACTTCATACATCCGTATTTA 58.202 36.000 0.00 0.00 36.11 1.40
3640 3787 6.916387 ACGTGACTTCATACATCCGTATTTAG 59.084 38.462 0.00 0.00 36.11 1.85
3641 3788 7.136772 CGTGACTTCATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 36.11 2.10
3642 3789 7.113124 CGTGACTTCATACATCCGTATTTAGAC 59.887 40.741 0.00 0.00 36.11 2.59
3643 3790 7.919091 GTGACTTCATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 36.11 3.41
3644 3791 8.471609 TGACTTCATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 36.11 3.18
3645 3792 9.309516 GACTTCATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 36.11 2.83
3646 3793 9.832445 ACTTCATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 36.11 2.32
3670 3817 9.810545 AATTTAAGACAAAAATTTTGAGACGGA 57.189 25.926 23.39 7.01 33.78 4.69
3671 3818 8.850454 TTTAAGACAAAAATTTTGAGACGGAG 57.150 30.769 23.39 0.00 0.00 4.63
3672 3819 5.438761 AGACAAAAATTTTGAGACGGAGG 57.561 39.130 23.39 0.00 0.00 4.30
3673 3820 4.278419 AGACAAAAATTTTGAGACGGAGGG 59.722 41.667 23.39 0.00 0.00 4.30
3674 3821 4.211920 ACAAAAATTTTGAGACGGAGGGA 58.788 39.130 23.39 0.00 0.00 4.20
3675 3822 4.278419 ACAAAAATTTTGAGACGGAGGGAG 59.722 41.667 23.39 0.00 0.00 4.30
3676 3823 3.790089 AAATTTTGAGACGGAGGGAGT 57.210 42.857 0.00 0.00 0.00 3.85
3677 3824 4.903045 AAATTTTGAGACGGAGGGAGTA 57.097 40.909 0.00 0.00 0.00 2.59
3678 3825 5.437191 AAATTTTGAGACGGAGGGAGTAT 57.563 39.130 0.00 0.00 0.00 2.12
3679 3826 5.437191 AATTTTGAGACGGAGGGAGTATT 57.563 39.130 0.00 0.00 0.00 1.89
3702 3849 1.017177 TTACGGTTCATCGCAGGTGC 61.017 55.000 0.00 0.00 37.78 5.01
3727 3874 2.296190 TGAGCTCGCAAGTAGAAGAACA 59.704 45.455 9.64 0.00 39.48 3.18
3732 3879 4.024809 GCTCGCAAGTAGAAGAACACTTTT 60.025 41.667 0.00 0.00 32.72 2.27
3742 3889 9.236006 AGTAGAAGAACACTTTTGCATGAATAT 57.764 29.630 0.00 0.00 0.00 1.28
3743 3890 9.282247 GTAGAAGAACACTTTTGCATGAATATG 57.718 33.333 0.00 0.00 37.36 1.78
3839 3986 7.466746 ACCAAAGCAACATGACATATTTACT 57.533 32.000 0.00 0.00 0.00 2.24
3867 4014 2.292794 AAATTCGCTCGCTAGCCCGA 62.293 55.000 9.66 12.08 46.68 5.14
3878 4025 1.410882 GCTAGCCCGAATCTTCTGTCT 59.589 52.381 2.29 0.00 0.00 3.41
3885 4032 3.369471 CCCGAATCTTCTGTCTGGCTAAA 60.369 47.826 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.700539 TCCCATCCTACAACATGCAAATG 59.299 43.478 0.00 0.00 0.00 2.32
52 53 0.680618 TGGACTTGCCCATTTGCTTG 59.319 50.000 0.00 0.00 34.97 4.01
63 64 6.346838 GCAAATATTCTTGTTGTTGGACTTGC 60.347 38.462 0.00 0.00 0.00 4.01
95 96 3.009363 TCTTGATCAGGCTCCAACAATGA 59.991 43.478 0.00 0.00 0.00 2.57
106 107 2.143122 TCGTGTTGTTCTTGATCAGGC 58.857 47.619 0.00 0.00 0.00 4.85
121 122 1.679680 TCCTCGTCTTTCACTTCGTGT 59.320 47.619 0.00 0.00 34.79 4.49
131 132 2.237143 TGCCTCATCATTCCTCGTCTTT 59.763 45.455 0.00 0.00 0.00 2.52
138 139 1.202734 CGATGGTGCCTCATCATTCCT 60.203 52.381 14.16 0.00 42.58 3.36
161 162 2.043992 GGTACTTGGCCCTTTGGTTTT 58.956 47.619 0.00 0.00 0.00 2.43
166 167 0.036306 ACGAGGTACTTGGCCCTTTG 59.964 55.000 0.00 0.00 46.15 2.77
169 170 3.709567 GACGAGGTACTTGGCCCT 58.290 61.111 0.00 0.00 43.79 5.19
210 211 2.366167 CTCCTGGGCCTCCTCTCA 59.634 66.667 4.53 0.00 0.00 3.27
256 257 0.767998 GCCCCTTTCCTCCTATCAGG 59.232 60.000 0.00 0.00 36.46 3.86
270 271 2.366167 AGCATCTCCTTCGCCCCT 60.366 61.111 0.00 0.00 0.00 4.79
304 305 3.640967 ACCTTCTCTCTCATGTATGGAGC 59.359 47.826 0.00 0.00 32.38 4.70
339 340 6.053005 TCACGTCACCAATTTCTTCTTTACT 58.947 36.000 0.00 0.00 0.00 2.24
361 362 2.869801 CCAACTTGTCTTGCGTTACTCA 59.130 45.455 0.00 0.00 0.00 3.41
403 404 7.751646 TCTCACCACCTTCCTAATTTTTCTTA 58.248 34.615 0.00 0.00 0.00 2.10
414 415 0.112606 TCGTCTCTCACCACCTTCCT 59.887 55.000 0.00 0.00 0.00 3.36
432 433 5.062308 GTCCTTACACATCTCATTGTCGTTC 59.938 44.000 0.00 0.00 0.00 3.95
436 437 3.865745 CCGTCCTTACACATCTCATTGTC 59.134 47.826 0.00 0.00 0.00 3.18
437 438 3.861840 CCGTCCTTACACATCTCATTGT 58.138 45.455 0.00 0.00 0.00 2.71
438 439 2.609459 GCCGTCCTTACACATCTCATTG 59.391 50.000 0.00 0.00 0.00 2.82
439 440 2.236146 TGCCGTCCTTACACATCTCATT 59.764 45.455 0.00 0.00 0.00 2.57
440 441 1.831106 TGCCGTCCTTACACATCTCAT 59.169 47.619 0.00 0.00 0.00 2.90
441 442 1.262417 TGCCGTCCTTACACATCTCA 58.738 50.000 0.00 0.00 0.00 3.27
458 459 2.976903 GCCGATGCTCCTCCATGC 60.977 66.667 0.00 0.00 33.53 4.06
476 477 5.479306 TCAAACGGTTCTTCTCCAATAGAG 58.521 41.667 0.00 0.00 44.75 2.43
485 486 2.222027 CTTGCCTCAAACGGTTCTTCT 58.778 47.619 0.00 0.00 0.00 2.85
487 488 1.133915 TCCTTGCCTCAAACGGTTCTT 60.134 47.619 0.00 0.00 0.00 2.52
495 496 2.238521 GACACCATTCCTTGCCTCAAA 58.761 47.619 0.00 0.00 0.00 2.69
507 508 0.672401 CACTAACCGCGGACACCATT 60.672 55.000 35.90 17.37 0.00 3.16
511 512 1.135315 TCATACACTAACCGCGGACAC 60.135 52.381 35.90 0.00 0.00 3.67
515 516 2.288961 ACTTCATACACTAACCGCGG 57.711 50.000 26.86 26.86 0.00 6.46
518 519 7.544566 ACACTATTCAACTTCATACACTAACCG 59.455 37.037 0.00 0.00 0.00 4.44
543 544 8.879759 TCGAGTGTTATCAGATTCCATAAAAAC 58.120 33.333 0.00 0.00 0.00 2.43
557 560 2.555325 ACCAGACGTTCGAGTGTTATCA 59.445 45.455 0.00 0.00 0.00 2.15
580 583 2.230864 GAAAACGTTCGATTTGCCTCG 58.769 47.619 0.00 0.00 39.99 4.63
600 603 6.695713 TCCTCACGACACTAAATTTATCATCG 59.304 38.462 17.05 17.05 0.00 3.84
601 604 8.491152 CATCCTCACGACACTAAATTTATCATC 58.509 37.037 0.00 0.00 0.00 2.92
602 605 8.204160 TCATCCTCACGACACTAAATTTATCAT 58.796 33.333 0.00 0.00 0.00 2.45
605 608 7.327975 TGTCATCCTCACGACACTAAATTTAT 58.672 34.615 0.00 0.00 37.23 1.40
609 612 4.801330 TGTCATCCTCACGACACTAAAT 57.199 40.909 0.00 0.00 37.23 1.40
612 615 4.801330 AATTGTCATCCTCACGACACTA 57.199 40.909 0.00 0.00 41.67 2.74
617 620 4.271696 ACTGAAATTGTCATCCTCACGA 57.728 40.909 0.00 0.00 35.07 4.35
619 622 4.520492 ACCAACTGAAATTGTCATCCTCAC 59.480 41.667 0.00 0.00 35.07 3.51
620 623 4.728772 ACCAACTGAAATTGTCATCCTCA 58.271 39.130 0.00 0.00 35.07 3.86
635 638 4.611355 CGAAGTTGTCATGCTTACCAACTG 60.611 45.833 13.44 3.34 44.88 3.16
642 645 4.994217 TGAATCACGAAGTTGTCATGCTTA 59.006 37.500 0.00 0.00 41.61 3.09
690 693 3.563808 GGATGCAAGTTAGTTGACACACA 59.436 43.478 3.69 0.00 38.60 3.72
694 697 3.325870 CGAGGATGCAAGTTAGTTGACA 58.674 45.455 3.69 2.08 38.60 3.58
708 713 4.339247 AGCAATTTTATTGACCCGAGGATG 59.661 41.667 3.70 0.00 0.00 3.51
709 714 4.536765 AGCAATTTTATTGACCCGAGGAT 58.463 39.130 3.70 0.00 0.00 3.24
710 715 3.963129 AGCAATTTTATTGACCCGAGGA 58.037 40.909 3.70 0.00 0.00 3.71
711 716 5.578776 GTTAGCAATTTTATTGACCCGAGG 58.421 41.667 3.70 0.00 0.00 4.63
712 717 5.064198 TCGTTAGCAATTTTATTGACCCGAG 59.936 40.000 3.70 0.00 0.00 4.63
713 718 4.936411 TCGTTAGCAATTTTATTGACCCGA 59.064 37.500 3.70 2.82 0.00 5.14
714 719 5.224562 TCGTTAGCAATTTTATTGACCCG 57.775 39.130 3.70 0.82 0.00 5.28
715 720 7.409980 CGTTTTCGTTAGCAATTTTATTGACCC 60.410 37.037 3.70 0.00 38.65 4.46
751 757 0.182299 TGTCAAGTGCCACCACATGA 59.818 50.000 0.00 0.00 44.62 3.07
758 764 5.818136 AATATGTACATGTCAAGTGCCAC 57.182 39.130 18.81 0.00 0.00 5.01
760 766 8.840321 AGAAATAATATGTACATGTCAAGTGCC 58.160 33.333 18.81 0.82 0.00 5.01
836 842 1.340889 GGTGGACATGTGTGTTTGCAT 59.659 47.619 1.15 0.00 39.09 3.96
837 843 0.743688 GGTGGACATGTGTGTTTGCA 59.256 50.000 1.15 0.00 39.09 4.08
850 856 0.033090 ACCTTCGAAACTCGGTGGAC 59.967 55.000 6.05 0.00 40.88 4.02
859 865 4.503007 GCCAAAAGAAGAAACCTTCGAAAC 59.497 41.667 0.00 0.00 43.58 2.78
873 879 2.202295 GCACGTTTCTGCCAAAAGAA 57.798 45.000 0.00 0.00 34.36 2.52
881 887 2.076863 ACTATTCTGGCACGTTTCTGC 58.923 47.619 0.00 0.00 36.33 4.26
893 899 6.975197 TGACGAAGAGCAATTCTACTATTCTG 59.025 38.462 0.00 0.00 34.14 3.02
894 900 7.101652 TGACGAAGAGCAATTCTACTATTCT 57.898 36.000 0.00 0.00 34.14 2.40
895 901 6.419413 CCTGACGAAGAGCAATTCTACTATTC 59.581 42.308 0.00 0.00 34.14 1.75
896 902 6.096987 TCCTGACGAAGAGCAATTCTACTATT 59.903 38.462 0.00 0.00 34.14 1.73
897 903 5.594725 TCCTGACGAAGAGCAATTCTACTAT 59.405 40.000 0.00 0.00 34.14 2.12
898 904 4.948004 TCCTGACGAAGAGCAATTCTACTA 59.052 41.667 0.00 0.00 34.14 1.82
899 905 3.764434 TCCTGACGAAGAGCAATTCTACT 59.236 43.478 0.00 0.00 34.14 2.57
900 906 4.111375 TCCTGACGAAGAGCAATTCTAC 57.889 45.455 0.00 0.00 34.14 2.59
1114 1122 3.585289 TGGTGCCCTGTGATTAGTTTAGA 59.415 43.478 0.00 0.00 0.00 2.10
1162 1170 2.351336 GAACGGGAGGCGATCGATGT 62.351 60.000 21.57 0.89 0.00 3.06
1237 1245 2.430921 GACGTCAGTGCCTGGTCG 60.431 66.667 11.55 13.80 36.23 4.79
1464 1472 3.900892 ACGCGGCCCATCTCGTAG 61.901 66.667 12.47 0.00 33.02 3.51
1986 1994 2.967397 CCGTCGTAGCCCTTGTCA 59.033 61.111 0.00 0.00 0.00 3.58
2189 2197 4.735132 CGACGGTGATGCGGGTGT 62.735 66.667 0.00 0.00 0.00 4.16
2259 2267 2.359230 GCTGGCGGCTCAAGACTT 60.359 61.111 11.99 0.00 38.06 3.01
2796 2823 5.124457 CCAGACTAACATAAACATGCTGCTT 59.876 40.000 0.00 0.00 0.00 3.91
2797 2824 4.637534 CCAGACTAACATAAACATGCTGCT 59.362 41.667 0.00 0.00 0.00 4.24
2798 2825 4.396166 ACCAGACTAACATAAACATGCTGC 59.604 41.667 0.00 0.00 0.00 5.25
2799 2826 5.643348 TGACCAGACTAACATAAACATGCTG 59.357 40.000 0.00 0.00 0.00 4.41
2907 2945 2.121786 GCAAGCTTTGACACACACATG 58.878 47.619 0.00 0.00 0.00 3.21
2914 2952 0.316204 ATGCAGGCAAGCTTTGACAC 59.684 50.000 0.00 0.00 42.71 3.67
2919 2957 2.380084 CAATCATGCAGGCAAGCTTT 57.620 45.000 0.00 0.00 34.99 3.51
2973 3011 6.431234 AGAATTGAGCGAAAACCTCTTATGTT 59.569 34.615 0.00 0.00 0.00 2.71
2978 3016 4.137543 ACAGAATTGAGCGAAAACCTCTT 58.862 39.130 0.00 0.00 0.00 2.85
3046 3108 8.502387 CCTTGCTTATATATGAGAAGTGCTTTC 58.498 37.037 8.63 0.00 35.97 2.62
3047 3109 7.040823 GCCTTGCTTATATATGAGAAGTGCTTT 60.041 37.037 8.63 0.00 0.00 3.51
3050 3112 5.702670 TGCCTTGCTTATATATGAGAAGTGC 59.297 40.000 8.63 12.44 0.00 4.40
3051 3113 7.823310 AGATGCCTTGCTTATATATGAGAAGTG 59.177 37.037 8.63 5.37 0.00 3.16
3061 3123 9.799106 AGTTTGTTATAGATGCCTTGCTTATAT 57.201 29.630 0.00 0.00 0.00 0.86
3063 3125 9.627123 TTAGTTTGTTATAGATGCCTTGCTTAT 57.373 29.630 0.00 0.00 0.00 1.73
3064 3126 8.889717 GTTAGTTTGTTATAGATGCCTTGCTTA 58.110 33.333 0.00 0.00 0.00 3.09
3067 3129 7.083875 TGTTAGTTTGTTATAGATGCCTTGC 57.916 36.000 0.00 0.00 0.00 4.01
3081 3143 9.220906 TGGAGGGAGTATATATTGTTAGTTTGT 57.779 33.333 0.00 0.00 0.00 2.83
3098 3160 8.817876 GCTCTTATATTAGTTTATGGAGGGAGT 58.182 37.037 0.00 0.00 0.00 3.85
3099 3161 8.816894 TGCTCTTATATTAGTTTATGGAGGGAG 58.183 37.037 0.00 0.00 0.00 4.30
3100 3162 8.736097 TGCTCTTATATTAGTTTATGGAGGGA 57.264 34.615 0.00 0.00 0.00 4.20
3101 3163 9.965902 AATGCTCTTATATTAGTTTATGGAGGG 57.034 33.333 0.00 0.00 0.00 4.30
3152 3214 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
3153 3215 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
3154 3216 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
3170 3232 9.693739 CAGATGTATATATTCTACTCCCTCTGT 57.306 37.037 0.00 0.00 0.00 3.41
3171 3233 8.629158 GCAGATGTATATATTCTACTCCCTCTG 58.371 40.741 0.00 0.00 0.00 3.35
3172 3234 8.565239 AGCAGATGTATATATTCTACTCCCTCT 58.435 37.037 0.00 0.00 0.00 3.69
3173 3235 8.760980 AGCAGATGTATATATTCTACTCCCTC 57.239 38.462 0.00 0.00 0.00 4.30
3257 3319 1.453155 ATTCATGGGACTGTTCACGC 58.547 50.000 0.00 0.00 0.00 5.34
3298 3438 4.081198 TGGCAAACAAAGAAGTCATTGGTT 60.081 37.500 1.79 0.00 35.18 3.67
3300 3440 4.057406 TGGCAAACAAAGAAGTCATTGG 57.943 40.909 1.79 0.00 0.00 3.16
3349 3492 9.883142 TTGTTTTTCTCCATGAAATTTTGTAGT 57.117 25.926 0.00 0.00 43.34 2.73
3364 3507 9.780413 CTAGAGCATTTAAGATTGTTTTTCTCC 57.220 33.333 0.00 0.00 0.00 3.71
3476 3623 7.555965 TGAACTGTCTGCATATACACACTTAT 58.444 34.615 0.00 0.00 0.00 1.73
3477 3624 6.930731 TGAACTGTCTGCATATACACACTTA 58.069 36.000 0.00 0.00 0.00 2.24
3487 3634 8.886719 CAAAAAGATAGATGAACTGTCTGCATA 58.113 33.333 0.00 0.00 44.30 3.14
3542 3689 3.959449 GGACGGAGGGAGTAAAGAATAGT 59.041 47.826 0.00 0.00 0.00 2.12
3543 3690 3.321396 GGGACGGAGGGAGTAAAGAATAG 59.679 52.174 0.00 0.00 0.00 1.73
3544 3691 3.303049 GGGACGGAGGGAGTAAAGAATA 58.697 50.000 0.00 0.00 0.00 1.75
3545 3692 2.117051 GGGACGGAGGGAGTAAAGAAT 58.883 52.381 0.00 0.00 0.00 2.40
3546 3693 1.203212 TGGGACGGAGGGAGTAAAGAA 60.203 52.381 0.00 0.00 0.00 2.52
3547 3694 0.410663 TGGGACGGAGGGAGTAAAGA 59.589 55.000 0.00 0.00 0.00 2.52
3548 3695 1.272807 TTGGGACGGAGGGAGTAAAG 58.727 55.000 0.00 0.00 0.00 1.85
3549 3696 1.732117 TTTGGGACGGAGGGAGTAAA 58.268 50.000 0.00 0.00 0.00 2.01
3552 3699 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
3553 3700 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
3555 3702 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3556 3703 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3557 3704 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3558 3705 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3559 3706 5.897377 ATAAGACAAGAATTTTGGGACGG 57.103 39.130 0.00 0.00 0.00 4.79
3560 3707 8.893727 AGAATATAAGACAAGAATTTTGGGACG 58.106 33.333 5.68 0.00 0.00 4.79
3606 3753 9.095065 GGATGTATGAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
3607 3754 7.434307 CGGATGTATGAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
3608 3755 6.748658 CGGATGTATGAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
3609 3756 5.575606 CGGATGTATGAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
3610 3757 5.575606 ACGGATGTATGAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
3611 3758 5.472148 ACGGATGTATGAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
3612 3759 4.312443 ACGGATGTATGAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
3613 3760 3.921677 ACGGATGTATGAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
3614 3761 3.587797 ACGGATGTATGAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
3615 3762 4.913335 ATACGGATGTATGAAGTCACGT 57.087 40.909 0.00 0.00 39.81 4.49
3616 3763 7.113124 GTCTAAATACGGATGTATGAAGTCACG 59.887 40.741 0.00 0.00 40.42 4.35
3617 3764 7.919091 TGTCTAAATACGGATGTATGAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
3618 3765 8.002984 TGTCTAAATACGGATGTATGAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
3619 3766 8.867112 TTGTCTAAATACGGATGTATGAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
3620 3767 9.832445 ATTTGTCTAAATACGGATGTATGAAGT 57.168 29.630 0.00 0.00 40.42 3.01
3644 3791 9.810545 TCCGTCTCAAAATTTTTGTCTTAAATT 57.189 25.926 18.69 0.00 36.91 1.82
3645 3792 9.463443 CTCCGTCTCAAAATTTTTGTCTTAAAT 57.537 29.630 18.69 0.00 0.00 1.40
3646 3793 7.918562 CCTCCGTCTCAAAATTTTTGTCTTAAA 59.081 33.333 18.69 1.22 0.00 1.52
3647 3794 7.422399 CCTCCGTCTCAAAATTTTTGTCTTAA 58.578 34.615 18.69 1.84 0.00 1.85
3648 3795 6.016610 CCCTCCGTCTCAAAATTTTTGTCTTA 60.017 38.462 18.69 2.16 0.00 2.10
3649 3796 5.221244 CCCTCCGTCTCAAAATTTTTGTCTT 60.221 40.000 18.69 0.00 0.00 3.01
3650 3797 4.278419 CCCTCCGTCTCAAAATTTTTGTCT 59.722 41.667 18.69 0.00 0.00 3.41
3651 3798 4.277423 TCCCTCCGTCTCAAAATTTTTGTC 59.723 41.667 18.69 11.09 0.00 3.18
3652 3799 4.211920 TCCCTCCGTCTCAAAATTTTTGT 58.788 39.130 18.69 0.00 0.00 2.83
3653 3800 4.278419 ACTCCCTCCGTCTCAAAATTTTTG 59.722 41.667 14.41 14.41 0.00 2.44
3654 3801 4.470602 ACTCCCTCCGTCTCAAAATTTTT 58.529 39.130 0.00 0.00 0.00 1.94
3655 3802 4.100279 ACTCCCTCCGTCTCAAAATTTT 57.900 40.909 0.00 0.00 0.00 1.82
3656 3803 3.790089 ACTCCCTCCGTCTCAAAATTT 57.210 42.857 0.00 0.00 0.00 1.82
3657 3804 5.437191 AATACTCCCTCCGTCTCAAAATT 57.563 39.130 0.00 0.00 0.00 1.82
3658 3805 6.749036 ATAATACTCCCTCCGTCTCAAAAT 57.251 37.500 0.00 0.00 0.00 1.82
3659 3806 6.555463 AATAATACTCCCTCCGTCTCAAAA 57.445 37.500 0.00 0.00 0.00 2.44
3660 3807 6.555463 AAATAATACTCCCTCCGTCTCAAA 57.445 37.500 0.00 0.00 0.00 2.69
3661 3808 6.555463 AAAATAATACTCCCTCCGTCTCAA 57.445 37.500 0.00 0.00 0.00 3.02
3662 3809 6.238842 CGTAAAATAATACTCCCTCCGTCTCA 60.239 42.308 0.00 0.00 0.00 3.27
3663 3810 6.148264 CGTAAAATAATACTCCCTCCGTCTC 58.852 44.000 0.00 0.00 0.00 3.36
3664 3811 5.010415 CCGTAAAATAATACTCCCTCCGTCT 59.990 44.000 0.00 0.00 0.00 4.18
3665 3812 5.221322 ACCGTAAAATAATACTCCCTCCGTC 60.221 44.000 0.00 0.00 0.00 4.79
3666 3813 4.651045 ACCGTAAAATAATACTCCCTCCGT 59.349 41.667 0.00 0.00 0.00 4.69
3667 3814 5.205759 ACCGTAAAATAATACTCCCTCCG 57.794 43.478 0.00 0.00 0.00 4.63
3668 3815 6.585416 TGAACCGTAAAATAATACTCCCTCC 58.415 40.000 0.00 0.00 0.00 4.30
3669 3816 7.115947 CGATGAACCGTAAAATAATACTCCCTC 59.884 40.741 0.00 0.00 0.00 4.30
3670 3817 6.927381 CGATGAACCGTAAAATAATACTCCCT 59.073 38.462 0.00 0.00 0.00 4.20
3671 3818 6.347160 GCGATGAACCGTAAAATAATACTCCC 60.347 42.308 0.00 0.00 0.00 4.30
3672 3819 6.201425 TGCGATGAACCGTAAAATAATACTCC 59.799 38.462 0.00 0.00 0.00 3.85
3673 3820 7.169035 TGCGATGAACCGTAAAATAATACTC 57.831 36.000 0.00 0.00 0.00 2.59
3674 3821 6.202188 CCTGCGATGAACCGTAAAATAATACT 59.798 38.462 0.00 0.00 0.00 2.12
3675 3822 6.018507 ACCTGCGATGAACCGTAAAATAATAC 60.019 38.462 0.00 0.00 0.00 1.89
3676 3823 6.018588 CACCTGCGATGAACCGTAAAATAATA 60.019 38.462 0.00 0.00 0.00 0.98
3677 3824 4.879545 ACCTGCGATGAACCGTAAAATAAT 59.120 37.500 0.00 0.00 0.00 1.28
3678 3825 4.093703 CACCTGCGATGAACCGTAAAATAA 59.906 41.667 0.00 0.00 0.00 1.40
3679 3826 3.619483 CACCTGCGATGAACCGTAAAATA 59.381 43.478 0.00 0.00 0.00 1.40
3702 3849 3.928992 TCTTCTACTTGCGAGCTCAAATG 59.071 43.478 15.40 5.81 0.00 2.32
3742 3889 4.576216 TGCTTTGTAAAAGAATTCGGCA 57.424 36.364 3.95 0.00 0.00 5.69
3743 3890 5.612492 GCTTTGCTTTGTAAAAGAATTCGGC 60.612 40.000 3.95 0.00 35.79 5.54
3803 3950 8.363390 TCATGTTGCTTTGGTATTTGTGAAATA 58.637 29.630 0.00 0.00 32.38 1.40
3839 3986 1.732077 GCGAGCGAATTTGCATTCCAA 60.732 47.619 19.82 0.00 36.18 3.53
3867 4014 7.530426 ACAAAATTTAGCCAGACAGAAGATT 57.470 32.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.