Multiple sequence alignment - TraesCS7A01G422200

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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 TraesCS7A01G422200 chr7A 100.000 5127 0 0 1 5127 612771630 612766504 0.000000e+00 9468.0
1 TraesCS7A01G422200 chr7D 89.040 4352 217 93 2 4262 532628405 532624223 0.000000e+00 5155.0
2 TraesCS7A01G422200 chr7D 88.797 482 45 4 4228 4708 532622521 532622048 2.660000e-162 582.0
3 TraesCS7A01G422200 chr7D 91.791 268 6 8 4864 5127 532621032 532620777 4.880000e-95 359.0
4 TraesCS7A01G422200 chr7B 86.530 2836 165 89 155 2890 573109894 573107176 0.000000e+00 2920.0
5 TraesCS7A01G422200 chr7B 92.450 755 28 4 3305 4055 573106528 573105799 0.000000e+00 1051.0
6 TraesCS7A01G422200 chr7B 87.938 257 29 2 2883 3137 573107041 573106785 8.340000e-78 302.0
7 TraesCS7A01G422200 chr7B 87.347 245 24 6 4091 4334 573105795 573105557 1.820000e-69 274.0
8 TraesCS7A01G422200 chr7B 93.750 128 4 3 16 141 573110002 573109877 6.780000e-44 189.0
9 TraesCS7A01G422200 chr7B 88.387 155 4 4 4981 5127 573027009 573026861 1.900000e-39 174.0
10 TraesCS7A01G422200 chr7B 89.474 133 7 5 4863 4989 573102435 573102304 1.480000e-35 161.0
11 TraesCS7A01G422200 chr6D 80.128 156 23 6 4541 4695 10482202 10482054 5.430000e-20 110.0
12 TraesCS7A01G422200 chr4A 96.875 32 1 0 4900 4931 80159658 80159627 3.000000e-03 54.7


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 TraesCS7A01G422200 chr7A 612766504 612771630 5126 True 9468.000000 9468 100.0000 1 5127 1 chr7A.!!$R1 5126
1 TraesCS7A01G422200 chr7D 532620777 532628405 7628 True 2032.000000 5155 89.8760 2 5127 3 chr7D.!!$R1 5125
2 TraesCS7A01G422200 chr7B 573102304 573110002 7698 True 816.166667 2920 89.5815 16 4989 6 chr7B.!!$R2 4973

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
463 504 0.105039 CTGGAGCCGGAGTGTAATCC 59.895 60.0 5.05 0.27 35.88 3.01 F
465 506 0.105039 GGAGCCGGAGTGTAATCCAG 59.895 60.0 5.05 0.00 39.53 3.86 F
507 551 0.391793 CTCCCGTTGCTTCCTTCTCC 60.392 60.0 0.00 0.00 0.00 3.71 F
2233 2350 0.467290 TTTTTGGACTGAAGGCGCCT 60.467 50.0 27.08 27.08 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 2522 0.452987 CCGATCAGTTGTGCCATTGG 59.547 55.000 0.0 0.0 0.0 3.16 R
2456 2581 0.685785 CCCTAGCAGAGACCAGCAGA 60.686 60.000 0.0 0.0 0.0 4.26 R
2542 2668 7.836685 TGATGCCCTGTTTTCCTTAATAATGTA 59.163 33.333 0.0 0.0 0.0 2.29 R
4130 4546 0.034186 TGCGAATCAAATGCTCCCCT 60.034 50.000 0.0 0.0 0.0 4.79 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
60 61 2.742372 GTGGTGCGCAGGTAGGTG 60.742 66.667 12.22 0.00 0.00 4.00
117 123 2.203280 CTGCGTCCCAACCAACCA 60.203 61.111 0.00 0.00 0.00 3.67
118 124 1.826054 CTGCGTCCCAACCAACCAA 60.826 57.895 0.00 0.00 0.00 3.67
119 125 2.070654 CTGCGTCCCAACCAACCAAC 62.071 60.000 0.00 0.00 0.00 3.77
120 126 3.027292 CGTCCCAACCAACCAACG 58.973 61.111 0.00 0.00 0.00 4.10
121 127 2.548295 CGTCCCAACCAACCAACGG 61.548 63.158 0.00 0.00 0.00 4.44
122 128 2.196229 TCCCAACCAACCAACGGG 59.804 61.111 0.00 0.00 41.29 5.28
123 129 2.915137 CCCAACCAACCAACGGGG 60.915 66.667 0.00 0.00 44.81 5.73
124 130 2.196229 CCAACCAACCAACGGGGA 59.804 61.111 2.06 0.00 41.15 4.81
125 131 2.197605 CCAACCAACCAACGGGGAC 61.198 63.158 2.06 0.00 41.15 4.46
137 143 3.685435 GGGGACGGACGACTGTTA 58.315 61.111 0.00 0.00 35.56 2.41
138 144 1.509923 GGGGACGGACGACTGTTAG 59.490 63.158 0.00 0.00 35.56 2.34
139 145 1.246737 GGGGACGGACGACTGTTAGT 61.247 60.000 0.00 0.00 35.56 2.24
140 146 0.600057 GGGACGGACGACTGTTAGTT 59.400 55.000 0.00 0.00 35.56 2.24
141 147 1.000171 GGGACGGACGACTGTTAGTTT 60.000 52.381 0.00 0.00 35.56 2.66
142 148 2.546584 GGGACGGACGACTGTTAGTTTT 60.547 50.000 0.00 0.00 35.56 2.43
143 149 3.126073 GGACGGACGACTGTTAGTTTTT 58.874 45.455 0.00 0.00 35.56 1.94
178 184 4.702131 ACGGACGACTGTTAGTTAGGTTAT 59.298 41.667 0.00 0.00 30.63 1.89
179 185 5.183904 ACGGACGACTGTTAGTTAGGTTATT 59.816 40.000 0.00 0.00 30.63 1.40
180 186 6.374333 ACGGACGACTGTTAGTTAGGTTATTA 59.626 38.462 0.00 0.00 30.63 0.98
181 187 7.067494 ACGGACGACTGTTAGTTAGGTTATTAT 59.933 37.037 0.00 0.00 30.63 1.28
182 188 7.589221 CGGACGACTGTTAGTTAGGTTATTATC 59.411 40.741 0.00 0.00 0.00 1.75
183 189 8.408601 GGACGACTGTTAGTTAGGTTATTATCA 58.591 37.037 0.00 0.00 0.00 2.15
184 190 9.962783 GACGACTGTTAGTTAGGTTATTATCAT 57.037 33.333 0.00 0.00 0.00 2.45
248 271 4.615834 CGTCTCGCTCGCTAGGGC 62.616 72.222 1.02 0.00 41.46 5.19
278 311 1.853963 CCCTACTGGTAGAGTGCTGT 58.146 55.000 9.11 0.00 35.96 4.40
279 312 3.014304 CCCTACTGGTAGAGTGCTGTA 57.986 52.381 9.11 0.00 35.96 2.74
292 325 0.735978 TGCTGTATCGGACAACTGCG 60.736 55.000 14.91 0.00 41.75 5.18
328 361 1.063006 CGCATCCGCTGGTTTCATG 59.937 57.895 0.00 0.00 35.30 3.07
350 390 1.000274 GCGGTTGGTTTGATTGCTTCT 60.000 47.619 0.00 0.00 0.00 2.85
352 392 2.034558 CGGTTGGTTTGATTGCTTCTGT 59.965 45.455 0.00 0.00 0.00 3.41
353 393 3.383761 GGTTGGTTTGATTGCTTCTGTG 58.616 45.455 0.00 0.00 0.00 3.66
354 394 3.181476 GGTTGGTTTGATTGCTTCTGTGT 60.181 43.478 0.00 0.00 0.00 3.72
373 413 0.598158 TTGTTTTCTCCGTCCGTCCG 60.598 55.000 0.00 0.00 0.00 4.79
374 414 1.006922 GTTTTCTCCGTCCGTCCGT 60.007 57.895 0.00 0.00 0.00 4.69
376 416 2.146073 TTTTCTCCGTCCGTCCGTCC 62.146 60.000 0.00 0.00 0.00 4.79
386 426 3.673484 GTCCGTCCGTCCGTCCAA 61.673 66.667 0.00 0.00 0.00 3.53
387 427 3.673484 TCCGTCCGTCCGTCCAAC 61.673 66.667 0.00 0.00 0.00 3.77
388 428 3.980989 CCGTCCGTCCGTCCAACA 61.981 66.667 0.00 0.00 0.00 3.33
389 429 2.430244 CGTCCGTCCGTCCAACAG 60.430 66.667 0.00 0.00 0.00 3.16
390 430 2.737376 GTCCGTCCGTCCAACAGC 60.737 66.667 0.00 0.00 0.00 4.40
391 431 2.915659 TCCGTCCGTCCAACAGCT 60.916 61.111 0.00 0.00 0.00 4.24
392 432 2.432628 CCGTCCGTCCAACAGCTC 60.433 66.667 0.00 0.00 0.00 4.09
393 433 2.805353 CGTCCGTCCAACAGCTCG 60.805 66.667 0.00 0.00 0.00 5.03
416 456 2.224159 TCCCCAGTGCCCTGTTCTC 61.224 63.158 0.00 0.00 36.95 2.87
462 503 0.530870 GCTGGAGCCGGAGTGTAATC 60.531 60.000 5.05 0.00 34.31 1.75
463 504 0.105039 CTGGAGCCGGAGTGTAATCC 59.895 60.000 5.05 0.27 35.88 3.01
464 505 0.616395 TGGAGCCGGAGTGTAATCCA 60.616 55.000 5.05 3.22 39.53 3.41
465 506 0.105039 GGAGCCGGAGTGTAATCCAG 59.895 60.000 5.05 0.00 39.53 3.86
466 507 0.530870 GAGCCGGAGTGTAATCCAGC 60.531 60.000 5.05 0.00 42.18 4.85
467 508 1.220749 GCCGGAGTGTAATCCAGCA 59.779 57.895 5.05 0.00 41.59 4.41
485 526 1.537202 GCACCAGCAGAGGTTTTGTAG 59.463 52.381 0.00 0.00 40.77 2.74
501 545 3.659089 TAGCGCTCCCGTTGCTTCC 62.659 63.158 16.34 0.00 40.06 3.46
503 547 2.358737 CGCTCCCGTTGCTTCCTT 60.359 61.111 0.00 0.00 0.00 3.36
507 551 0.391793 CTCCCGTTGCTTCCTTCTCC 60.392 60.000 0.00 0.00 0.00 3.71
508 552 1.741770 CCCGTTGCTTCCTTCTCCG 60.742 63.158 0.00 0.00 0.00 4.63
604 649 1.009829 GCGTGTGGGCTCTTGATTAG 58.990 55.000 0.00 0.00 0.00 1.73
605 650 1.676014 GCGTGTGGGCTCTTGATTAGT 60.676 52.381 0.00 0.00 0.00 2.24
606 651 2.418197 GCGTGTGGGCTCTTGATTAGTA 60.418 50.000 0.00 0.00 0.00 1.82
607 652 3.741388 GCGTGTGGGCTCTTGATTAGTAT 60.741 47.826 0.00 0.00 0.00 2.12
608 653 4.051922 CGTGTGGGCTCTTGATTAGTATC 58.948 47.826 0.00 0.00 0.00 2.24
617 662 7.440856 GGGCTCTTGATTAGTATCTCTTTCTTG 59.559 40.741 0.00 0.00 0.00 3.02
690 735 2.125753 GTGACGCTCTGCTCCCTG 60.126 66.667 0.00 0.00 0.00 4.45
694 761 4.093291 CGCTCTGCTCCCTGCCTT 62.093 66.667 0.00 0.00 42.00 4.35
702 769 1.221293 CTCCCTGCCTTCTCTGCTG 59.779 63.158 0.00 0.00 0.00 4.41
710 777 1.221293 CTTCTCTGCTGCCCTCCTG 59.779 63.158 0.00 0.00 0.00 3.86
711 778 2.872931 CTTCTCTGCTGCCCTCCTGC 62.873 65.000 0.00 0.00 38.72 4.85
712 779 3.400928 CTCTGCTGCCCTCCTGCT 61.401 66.667 0.00 0.00 38.99 4.24
714 781 4.486503 CTGCTGCCCTCCTGCTCC 62.487 72.222 0.00 0.00 38.99 4.70
726 793 3.798954 CTGCTCCGGCCCTCGATTC 62.799 68.421 0.00 0.00 42.43 2.52
729 796 2.363795 TCCGGCCCTCGATTCAGT 60.364 61.111 0.00 0.00 42.43 3.41
766 837 3.385749 GATCGCCTTTCGCCCCAGA 62.386 63.158 0.00 0.00 38.27 3.86
783 854 4.082026 CCCCAGAATCGCATTTCTTTTCTT 60.082 41.667 0.00 0.00 33.69 2.52
924 1022 2.039879 TGGACTTTACCCTTTCCTCTGC 59.960 50.000 0.00 0.00 0.00 4.26
925 1023 2.306219 GGACTTTACCCTTTCCTCTGCT 59.694 50.000 0.00 0.00 0.00 4.24
926 1024 3.339141 GACTTTACCCTTTCCTCTGCTG 58.661 50.000 0.00 0.00 0.00 4.41
927 1025 2.040412 ACTTTACCCTTTCCTCTGCTGG 59.960 50.000 0.00 0.00 0.00 4.85
928 1026 0.991920 TTACCCTTTCCTCTGCTGGG 59.008 55.000 0.00 0.00 43.26 4.45
929 1027 1.464198 ACCCTTTCCTCTGCTGGGT 60.464 57.895 0.00 0.00 45.47 4.51
930 1028 1.001641 CCCTTTCCTCTGCTGGGTG 60.002 63.158 0.00 0.00 33.49 4.61
931 1029 1.676967 CCTTTCCTCTGCTGGGTGC 60.677 63.158 0.00 0.00 43.25 5.01
958 1056 0.535553 GGTTTTGAGCCGGGTACACA 60.536 55.000 5.91 0.00 0.00 3.72
959 1057 0.589708 GTTTTGAGCCGGGTACACAC 59.410 55.000 5.91 0.00 0.00 3.82
1042 1140 1.062525 GCATCCACGCACCGATTTC 59.937 57.895 0.00 0.00 0.00 2.17
1066 1165 1.445095 CTCCCTCCTCCTGCGATTG 59.555 63.158 0.00 0.00 0.00 2.67
1082 1181 1.876156 GATTGCGGGTCCAGATTGATC 59.124 52.381 0.00 0.00 0.00 2.92
1101 1200 4.894896 ATCCCCGGCCGGATTTGC 62.895 66.667 45.44 0.00 39.80 3.68
1118 1217 1.517257 GCTCCGTCACATCACTCGG 60.517 63.158 0.00 0.00 43.65 4.63
1255 1360 3.499737 GACATGGTCAAGGCGGCG 61.500 66.667 0.51 0.51 32.09 6.46
1357 1462 4.877619 TCCTCCGCGCTCTCCGAT 62.878 66.667 5.56 0.00 40.02 4.18
1696 1810 1.080093 CAGCGCCTTCACCGAGTTA 60.080 57.895 2.29 0.00 0.00 2.24
1906 2023 1.006832 CCTCTTCCATTAACCGCGTG 58.993 55.000 4.92 0.00 0.00 5.34
1963 2080 4.148825 ATGGTGCTCGGACTCGGC 62.149 66.667 0.00 0.00 36.95 5.54
2095 2212 2.665089 ATCGATGGAACCACCGCCA 61.665 57.895 2.32 0.00 42.61 5.69
2135 2252 3.239587 AGAAGACTAAGAAGAAGGCGC 57.760 47.619 0.00 0.00 0.00 6.53
2233 2350 0.467290 TTTTTGGACTGAAGGCGCCT 60.467 50.000 27.08 27.08 0.00 5.52
2338 2455 1.190643 TACCTGATGCGTCATCCACA 58.809 50.000 9.53 0.00 39.87 4.17
2356 2473 2.267174 CAGATGGGCTGGTAAGGATG 57.733 55.000 0.00 0.00 41.07 3.51
2358 2475 2.092212 CAGATGGGCTGGTAAGGATGTT 60.092 50.000 0.00 0.00 41.07 2.71
2368 2485 6.127980 GGCTGGTAAGGATGTTTAGTTTCTTC 60.128 42.308 0.00 0.00 0.00 2.87
2588 2715 6.694411 GCATCACATCCAAGTGTTTAATCATC 59.306 38.462 0.00 0.00 40.37 2.92
2593 2720 7.067859 CACATCCAAGTGTTTAATCATCTGGAT 59.932 37.037 18.09 18.09 39.74 3.41
2710 2862 9.634021 TGTTTTATATGCAATACTACCCATTGA 57.366 29.630 0.00 0.00 35.77 2.57
2729 2881 8.885722 CCCATTGAAACTCAAAATTCCAATATG 58.114 33.333 0.00 0.00 40.12 1.78
2775 2927 6.097554 TCTCCTTGAGTCATAATCTTCAGGAC 59.902 42.308 2.42 0.00 0.00 3.85
2785 2937 7.066766 GTCATAATCTTCAGGACATGCTTCTTT 59.933 37.037 0.00 0.00 0.00 2.52
2873 3025 7.243487 ACGAATACATGTTTGCATCAGTTTAG 58.757 34.615 2.30 0.00 31.99 1.85
2918 3213 8.880750 GCTTTATAACAACTCTAGGTTAACTGG 58.119 37.037 5.42 0.00 36.23 4.00
2925 3220 6.126565 ACAACTCTAGGTTAACTGGACCTTTT 60.127 38.462 5.42 0.00 45.06 2.27
2957 3252 4.682787 TGGCTTATCTCAACTGTATCACG 58.317 43.478 0.00 0.00 0.00 4.35
2960 3255 5.232414 GGCTTATCTCAACTGTATCACGTTC 59.768 44.000 0.00 0.00 0.00 3.95
3166 3500 9.995003 TTAGATGATTTTGTACAGCCAATTTTT 57.005 25.926 0.00 0.00 0.00 1.94
3247 3581 5.240183 AGCCATAAACTACATTAGCATGCTG 59.760 40.000 30.42 16.89 33.05 4.41
3277 3642 5.270893 TGTGAGCTATAAGCCAATAACGA 57.729 39.130 0.00 0.00 43.77 3.85
3390 3777 1.596477 GCTATCAGGGAAGGCAGCG 60.596 63.158 0.00 0.00 0.00 5.18
3407 3794 3.426695 GCAGCGTACAGAAATTGAAGCAT 60.427 43.478 0.00 0.00 0.00 3.79
3562 3949 2.031163 GCTCACAGTCGCAACCCT 59.969 61.111 0.00 0.00 0.00 4.34
3597 3988 1.481363 GCCCTCCCAAGTAGTGTAGTC 59.519 57.143 0.00 0.00 0.00 2.59
3601 3992 3.193691 CCTCCCAAGTAGTGTAGTCTGTG 59.806 52.174 0.00 0.00 0.00 3.66
3602 3993 4.079970 CTCCCAAGTAGTGTAGTCTGTGA 58.920 47.826 0.00 0.00 0.00 3.58
3614 4005 7.752695 AGTGTAGTCTGTGAAAGTTTGAAAAG 58.247 34.615 0.00 0.00 0.00 2.27
3620 4011 5.418840 TCTGTGAAAGTTTGAAAAGGAGCTT 59.581 36.000 0.00 0.00 0.00 3.74
3621 4012 5.650543 TGTGAAAGTTTGAAAAGGAGCTTC 58.349 37.500 0.00 0.00 0.00 3.86
3640 4031 2.544721 TCTGAAGGTCCTCATGCTCTT 58.455 47.619 0.00 0.00 0.00 2.85
3836 4236 5.133941 TGTGATCATGTAGAGAGGGTAGAC 58.866 45.833 0.00 0.00 0.00 2.59
3863 4263 3.244215 CCTGTAGAGTGGCTTCTTTGTCA 60.244 47.826 0.00 0.00 0.00 3.58
3864 4264 3.993081 CTGTAGAGTGGCTTCTTTGTCAG 59.007 47.826 0.00 0.00 0.00 3.51
3865 4265 2.557920 AGAGTGGCTTCTTTGTCAGG 57.442 50.000 0.00 0.00 0.00 3.86
3866 4266 1.072965 AGAGTGGCTTCTTTGTCAGGG 59.927 52.381 0.00 0.00 0.00 4.45
3867 4267 0.111253 AGTGGCTTCTTTGTCAGGGG 59.889 55.000 0.00 0.00 0.00 4.79
3868 4268 0.110486 GTGGCTTCTTTGTCAGGGGA 59.890 55.000 0.00 0.00 0.00 4.81
3869 4269 1.075601 TGGCTTCTTTGTCAGGGGAT 58.924 50.000 0.00 0.00 0.00 3.85
3870 4270 2.026262 GTGGCTTCTTTGTCAGGGGATA 60.026 50.000 0.00 0.00 0.00 2.59
3871 4271 2.239654 TGGCTTCTTTGTCAGGGGATAG 59.760 50.000 0.00 0.00 0.00 2.08
3872 4272 2.293170 GCTTCTTTGTCAGGGGATAGC 58.707 52.381 0.00 0.00 0.00 2.97
3873 4273 2.092699 GCTTCTTTGTCAGGGGATAGCT 60.093 50.000 0.00 0.00 0.00 3.32
3874 4274 3.539604 CTTCTTTGTCAGGGGATAGCTG 58.460 50.000 0.00 0.00 0.00 4.24
3875 4275 1.839994 TCTTTGTCAGGGGATAGCTGG 59.160 52.381 0.00 0.00 0.00 4.85
3876 4276 0.255890 TTTGTCAGGGGATAGCTGGC 59.744 55.000 0.00 0.00 0.00 4.85
3877 4277 0.621571 TTGTCAGGGGATAGCTGGCT 60.622 55.000 0.00 0.00 0.00 4.75
3878 4278 0.621571 TGTCAGGGGATAGCTGGCTT 60.622 55.000 0.00 0.00 0.00 4.35
3879 4279 0.107643 GTCAGGGGATAGCTGGCTTC 59.892 60.000 0.00 0.00 0.00 3.86
3880 4280 0.030705 TCAGGGGATAGCTGGCTTCT 60.031 55.000 0.00 0.00 0.00 2.85
3881 4281 0.842635 CAGGGGATAGCTGGCTTCTT 59.157 55.000 0.00 0.00 0.00 2.52
3882 4282 1.213926 CAGGGGATAGCTGGCTTCTTT 59.786 52.381 0.00 0.00 0.00 2.52
3883 4283 1.213926 AGGGGATAGCTGGCTTCTTTG 59.786 52.381 0.00 0.00 0.00 2.77
3884 4284 1.064389 GGGGATAGCTGGCTTCTTTGT 60.064 52.381 0.00 0.00 0.00 2.83
3885 4285 2.293170 GGGATAGCTGGCTTCTTTGTC 58.707 52.381 0.00 0.00 0.00 3.18
4013 4429 3.565902 AGTGCTTCTGTTACTTTGCTTCC 59.434 43.478 0.00 0.00 0.00 3.46
4030 4446 2.961526 TCCGTCTTATGCTCTGAACC 57.038 50.000 0.00 0.00 0.00 3.62
4042 4458 2.238395 GCTCTGAACCCTCTGAAGGAAT 59.762 50.000 0.00 0.00 46.67 3.01
4102 4518 8.268738 GCACAGCTCTAAATTTTTGTACAAAAG 58.731 33.333 27.55 18.61 40.83 2.27
4122 4538 7.964011 ACAAAAGTGAATCTGCAAAATTTGTTG 59.036 29.630 7.60 2.37 35.60 3.33
4125 4541 5.055812 GTGAATCTGCAAAATTTGTTGGGA 58.944 37.500 7.60 1.92 0.00 4.37
4130 4546 6.166984 TCTGCAAAATTTGTTGGGACATTA 57.833 33.333 7.60 0.00 39.30 1.90
4173 4589 7.201767 GCAAGATTCCTAAAGCATGTGAATAGT 60.202 37.037 0.00 0.00 0.00 2.12
4175 4591 9.553064 AAGATTCCTAAAGCATGTGAATAGTAG 57.447 33.333 0.00 0.00 0.00 2.57
4176 4592 8.709308 AGATTCCTAAAGCATGTGAATAGTAGT 58.291 33.333 0.00 0.00 0.00 2.73
4177 4593 9.982651 GATTCCTAAAGCATGTGAATAGTAGTA 57.017 33.333 0.00 0.00 0.00 1.82
4225 4641 5.777223 TGTCATCTATGAATCCTAGGTCTGG 59.223 44.000 9.08 0.00 38.75 3.86
4226 4642 5.186797 GTCATCTATGAATCCTAGGTCTGGG 59.813 48.000 9.08 0.00 38.75 4.45
4236 4652 2.092914 CCTAGGTCTGGGAAACATCACC 60.093 54.545 0.00 0.00 33.85 4.02
4314 6466 6.385443 TCCTAGGATTGGAGAACATCATAGT 58.615 40.000 7.62 0.00 0.00 2.12
4334 6486 9.066892 TCATAGTAAAAACAAAGCAAGATGTCT 57.933 29.630 0.00 0.00 0.00 3.41
4335 6487 9.683069 CATAGTAAAAACAAAGCAAGATGTCTT 57.317 29.630 0.00 0.00 36.45 3.01
4375 6527 4.462508 TCTTCTCCAAGATAGTGCACAG 57.537 45.455 21.04 4.84 33.38 3.66
4377 6529 1.833630 TCTCCAAGATAGTGCACAGGG 59.166 52.381 21.04 10.50 0.00 4.45
4401 6553 5.914033 GGGACCCTAAGAAATATTTTTGCC 58.086 41.667 2.09 0.00 0.00 4.52
4433 6585 9.513906 TTTCTATTGTGTGAATCAAATGGTCTA 57.486 29.630 0.00 0.00 0.00 2.59
4435 6587 8.321353 TCTATTGTGTGAATCAAATGGTCTACT 58.679 33.333 0.00 0.00 0.00 2.57
4439 6591 7.676004 TGTGTGAATCAAATGGTCTACTAAGA 58.324 34.615 0.00 0.00 0.00 2.10
4485 6637 8.524870 AATTTCTGTGAAATTCCTTTGAATCG 57.475 30.769 11.18 0.00 40.34 3.34
4539 6691 9.539825 GTGTCATCAGAATCTTTAGTCACATAT 57.460 33.333 0.00 0.00 0.00 1.78
4565 9380 7.977818 TGTATCTATAGTGCCATCAAATTCCT 58.022 34.615 0.00 0.00 0.00 3.36
4574 9389 8.773033 AGTGCCATCAAATTCCTAATCTAAAT 57.227 30.769 0.00 0.00 0.00 1.40
4633 9448 7.721286 AATCATGTTGTAGCTAATCTGTAGC 57.279 36.000 0.00 0.00 40.67 3.58
4643 9458 1.359848 AATCTGTAGCTCAAACGGCG 58.640 50.000 4.80 4.80 34.52 6.46
4675 9490 8.574196 AATTAAGATTTTTATCAATTCCCGCG 57.426 30.769 0.00 0.00 0.00 6.46
4692 9507 1.400142 CGCGGTGCCAAATCTATTGAA 59.600 47.619 0.00 0.00 0.00 2.69
4737 10432 1.697432 AGAGGGGAAACACACGATTGA 59.303 47.619 0.00 0.00 34.58 2.57
4741 10436 3.506067 AGGGGAAACACACGATTGAAATC 59.494 43.478 0.00 0.00 34.58 2.17
4742 10437 3.254657 GGGGAAACACACGATTGAAATCA 59.745 43.478 4.06 0.00 35.11 2.57
4743 10438 4.082245 GGGGAAACACACGATTGAAATCAT 60.082 41.667 4.06 0.00 35.11 2.45
4745 10440 6.027749 GGGAAACACACGATTGAAATCATAC 58.972 40.000 4.06 0.00 35.11 2.39
4746 10441 6.027749 GGAAACACACGATTGAAATCATACC 58.972 40.000 4.06 0.00 35.11 2.73
4747 10442 4.857871 ACACACGATTGAAATCATACCG 57.142 40.909 4.06 0.00 35.11 4.02
4749 10444 5.412640 ACACACGATTGAAATCATACCGTA 58.587 37.500 4.06 0.00 35.11 4.02
4750 10445 5.518847 ACACACGATTGAAATCATACCGTAG 59.481 40.000 4.06 0.00 35.11 3.51
4751 10446 5.746721 CACACGATTGAAATCATACCGTAGA 59.253 40.000 4.06 0.00 35.11 2.59
4754 10477 7.494625 ACACGATTGAAATCATACCGTAGAAAT 59.505 33.333 4.06 0.00 35.11 2.17
4757 10480 9.158364 CGATTGAAATCATACCGTAGAAATTTG 57.842 33.333 0.00 0.00 35.11 2.32
4767 10490 5.134661 ACCGTAGAAATTTGGGTCAAAGAA 58.865 37.500 0.00 0.00 36.76 2.52
4768 10491 5.595133 ACCGTAGAAATTTGGGTCAAAGAAA 59.405 36.000 0.00 0.00 36.76 2.52
4769 10492 6.097129 ACCGTAGAAATTTGGGTCAAAGAAAA 59.903 34.615 0.00 0.00 36.76 2.29
4788 10511 7.429636 AGAAAATTTCATGCCACATGAAAAG 57.570 32.000 29.19 0.00 46.84 2.27
4791 10514 7.429636 AAATTTCATGCCACATGAAAAGAAG 57.570 32.000 29.19 0.00 46.84 2.85
4819 10542 9.739276 ATTTTATTTTTGAGGGGAAAAGGATTC 57.261 29.630 0.00 0.00 30.36 2.52
4820 10543 5.762179 ATTTTTGAGGGGAAAAGGATTCC 57.238 39.130 0.00 0.00 37.86 3.01
4821 10544 4.485653 TTTTGAGGGGAAAAGGATTCCT 57.514 40.909 0.00 0.00 38.61 3.36
4822 10545 5.608798 TTTTGAGGGGAAAAGGATTCCTA 57.391 39.130 5.43 0.00 38.61 2.94
4823 10546 5.813965 TTTGAGGGGAAAAGGATTCCTAT 57.186 39.130 5.43 0.00 38.61 2.57
4824 10547 5.813965 TTGAGGGGAAAAGGATTCCTATT 57.186 39.130 5.43 0.23 38.61 1.73
4825 10548 5.388599 TGAGGGGAAAAGGATTCCTATTC 57.611 43.478 5.43 0.00 38.61 1.75
4826 10549 4.168088 TGAGGGGAAAAGGATTCCTATTCC 59.832 45.833 5.43 6.43 38.61 3.01
4827 10550 4.393725 AGGGGAAAAGGATTCCTATTCCT 58.606 43.478 5.43 6.44 45.70 3.36
4828 10551 5.558379 AGGGGAAAAGGATTCCTATTCCTA 58.442 41.667 5.43 0.00 42.90 2.94
4829 10552 6.168488 AGGGGAAAAGGATTCCTATTCCTAT 58.832 40.000 5.43 0.00 42.90 2.57
4830 10553 6.629930 AGGGGAAAAGGATTCCTATTCCTATT 59.370 38.462 5.43 0.00 42.90 1.73
4831 10554 6.948886 GGGGAAAAGGATTCCTATTCCTATTC 59.051 42.308 5.43 3.04 42.90 1.75
4855 10578 7.735917 TCCTATTCCTATGAATCAAACGACAT 58.264 34.615 0.00 0.00 41.44 3.06
4861 10584 7.431249 TCCTATGAATCAAACGACATACTACC 58.569 38.462 0.00 0.00 0.00 3.18
4906 10669 4.918588 TCCCAAACTCCTGTAGAATTTCC 58.081 43.478 0.00 0.00 0.00 3.13
4951 10714 3.624777 TGAATCCCCTGCTCTGAAATTC 58.375 45.455 0.00 0.00 0.00 2.17
4994 10761 2.453497 ATCACCAACCCCCACCCA 60.453 61.111 0.00 0.00 0.00 4.51
4995 10762 2.547595 ATCACCAACCCCCACCCAG 61.548 63.158 0.00 0.00 0.00 4.45
4996 10763 4.994756 CACCAACCCCCACCCAGC 62.995 72.222 0.00 0.00 0.00 4.85
5099 10869 1.153647 CACAGCCGCCAAGACGATA 60.154 57.895 0.00 0.00 34.06 2.92
5102 10872 1.756950 AGCCGCCAAGACGATAGGA 60.757 57.895 0.00 0.00 43.77 2.94
5104 10874 1.300233 CCGCCAAGACGATAGGAGC 60.300 63.158 0.00 0.00 43.77 4.70
5122 10892 2.985139 GAGCAGCAGCACAAAAGATTTC 59.015 45.455 3.17 0.00 45.49 2.17
5123 10893 2.363038 AGCAGCAGCACAAAAGATTTCA 59.637 40.909 3.17 0.00 45.49 2.69
5124 10894 3.006537 AGCAGCAGCACAAAAGATTTCAT 59.993 39.130 3.17 0.00 45.49 2.57
5126 10896 4.143179 GCAGCAGCACAAAAGATTTCATTC 60.143 41.667 0.00 0.00 41.58 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 123 3.677648 CAGTCGTCCGTCCCCGTT 61.678 66.667 0.00 0.00 0.00 4.44
118 124 4.962836 ACAGTCGTCCGTCCCCGT 62.963 66.667 0.00 0.00 0.00 5.28
119 125 2.262471 CTAACAGTCGTCCGTCCCCG 62.262 65.000 0.00 0.00 0.00 5.73
120 126 1.246737 ACTAACAGTCGTCCGTCCCC 61.247 60.000 0.00 0.00 0.00 4.81
121 127 0.600057 AACTAACAGTCGTCCGTCCC 59.400 55.000 0.00 0.00 0.00 4.46
122 128 2.428888 AAACTAACAGTCGTCCGTCC 57.571 50.000 0.00 0.00 0.00 4.79
145 151 3.784338 ACAGTCGTCCGTTACTCAAAAA 58.216 40.909 0.00 0.00 0.00 1.94
146 152 3.441496 ACAGTCGTCCGTTACTCAAAA 57.559 42.857 0.00 0.00 0.00 2.44
147 153 3.441496 AACAGTCGTCCGTTACTCAAA 57.559 42.857 0.00 0.00 0.00 2.69
148 154 3.565482 ACTAACAGTCGTCCGTTACTCAA 59.435 43.478 0.00 0.00 0.00 3.02
149 155 3.141398 ACTAACAGTCGTCCGTTACTCA 58.859 45.455 0.00 0.00 0.00 3.41
150 156 3.820777 ACTAACAGTCGTCCGTTACTC 57.179 47.619 0.00 0.00 0.00 2.59
151 157 4.154918 CCTAACTAACAGTCGTCCGTTACT 59.845 45.833 0.00 0.00 0.00 2.24
152 158 4.083271 ACCTAACTAACAGTCGTCCGTTAC 60.083 45.833 0.00 0.00 0.00 2.50
153 159 4.072131 ACCTAACTAACAGTCGTCCGTTA 58.928 43.478 0.00 0.00 0.00 3.18
178 184 9.292195 ACGAAAAGAAAAGGAGGTTAATGATAA 57.708 29.630 0.00 0.00 0.00 1.75
179 185 8.857694 ACGAAAAGAAAAGGAGGTTAATGATA 57.142 30.769 0.00 0.00 0.00 2.15
180 186 7.761038 ACGAAAAGAAAAGGAGGTTAATGAT 57.239 32.000 0.00 0.00 0.00 2.45
181 187 7.576861 AACGAAAAGAAAAGGAGGTTAATGA 57.423 32.000 0.00 0.00 0.00 2.57
182 188 8.135529 AGAAACGAAAAGAAAAGGAGGTTAATG 58.864 33.333 0.00 0.00 0.00 1.90
183 189 8.234136 AGAAACGAAAAGAAAAGGAGGTTAAT 57.766 30.769 0.00 0.00 0.00 1.40
184 190 7.634671 AGAAACGAAAAGAAAAGGAGGTTAA 57.365 32.000 0.00 0.00 0.00 2.01
185 191 7.555195 AGAAGAAACGAAAAGAAAAGGAGGTTA 59.445 33.333 0.00 0.00 0.00 2.85
186 192 6.377429 AGAAGAAACGAAAAGAAAAGGAGGTT 59.623 34.615 0.00 0.00 0.00 3.50
191 211 7.379797 GGAATCAGAAGAAACGAAAAGAAAAGG 59.620 37.037 0.00 0.00 0.00 3.11
203 223 3.365220 CGAGACACGGAATCAGAAGAAAC 59.635 47.826 0.00 0.00 38.46 2.78
248 271 3.387947 AGTAGGGTCGCCGTTGGG 61.388 66.667 0.00 0.00 0.00 4.12
270 303 2.263077 CAGTTGTCCGATACAGCACTC 58.737 52.381 7.29 0.00 41.47 3.51
271 304 1.673033 GCAGTTGTCCGATACAGCACT 60.673 52.381 7.29 0.16 41.47 4.40
272 305 0.721718 GCAGTTGTCCGATACAGCAC 59.278 55.000 7.29 0.00 41.47 4.40
273 306 0.735978 CGCAGTTGTCCGATACAGCA 60.736 55.000 7.29 0.00 41.47 4.41
274 307 1.421410 CCGCAGTTGTCCGATACAGC 61.421 60.000 0.00 0.00 39.87 4.40
275 308 1.421410 GCCGCAGTTGTCCGATACAG 61.421 60.000 0.00 0.00 39.87 2.74
276 309 1.447140 GCCGCAGTTGTCCGATACA 60.447 57.895 0.00 0.00 35.88 2.29
277 310 2.171725 GGCCGCAGTTGTCCGATAC 61.172 63.158 0.00 0.00 0.00 2.24
278 311 2.185867 GGCCGCAGTTGTCCGATA 59.814 61.111 0.00 0.00 0.00 2.92
328 361 0.598065 AGCAATCAAACCAACCGCTC 59.402 50.000 0.00 0.00 0.00 5.03
350 390 1.292061 CGGACGGAGAAAACAACACA 58.708 50.000 0.00 0.00 0.00 3.72
352 392 1.574134 GACGGACGGAGAAAACAACA 58.426 50.000 0.00 0.00 0.00 3.33
353 393 0.863799 GGACGGACGGAGAAAACAAC 59.136 55.000 0.00 0.00 0.00 3.32
354 394 0.598158 CGGACGGACGGAGAAAACAA 60.598 55.000 0.00 0.00 0.00 2.83
373 413 2.737376 GCTGTTGGACGGACGGAC 60.737 66.667 0.00 0.00 0.00 4.79
374 414 2.915659 AGCTGTTGGACGGACGGA 60.916 61.111 0.00 0.00 0.00 4.69
376 416 2.805353 CGAGCTGTTGGACGGACG 60.805 66.667 0.00 0.00 0.00 4.79
377 417 3.112709 GCGAGCTGTTGGACGGAC 61.113 66.667 0.00 0.00 0.00 4.79
378 418 2.942796 ATGCGAGCTGTTGGACGGA 61.943 57.895 0.00 0.00 0.00 4.69
381 421 1.639298 GGACATGCGAGCTGTTGGAC 61.639 60.000 0.00 0.00 0.00 4.02
382 422 1.375908 GGACATGCGAGCTGTTGGA 60.376 57.895 0.00 0.00 0.00 3.53
383 423 2.401766 GGGACATGCGAGCTGTTGG 61.402 63.158 0.00 0.00 0.00 3.77
384 424 2.401766 GGGGACATGCGAGCTGTTG 61.402 63.158 0.00 0.00 0.00 3.33
385 425 2.045926 GGGGACATGCGAGCTGTT 60.046 61.111 0.00 0.00 0.00 3.16
386 426 3.320879 CTGGGGACATGCGAGCTGT 62.321 63.158 0.00 0.00 41.51 4.40
387 427 2.513204 CTGGGGACATGCGAGCTG 60.513 66.667 0.00 0.00 41.51 4.24
388 428 3.005539 ACTGGGGACATGCGAGCT 61.006 61.111 0.00 0.00 41.51 4.09
389 429 2.821366 CACTGGGGACATGCGAGC 60.821 66.667 0.00 0.00 41.51 5.03
390 430 2.821366 GCACTGGGGACATGCGAG 60.821 66.667 0.00 0.00 41.51 5.03
391 431 4.408821 GGCACTGGGGACATGCGA 62.409 66.667 0.00 0.00 42.22 5.10
393 433 4.052518 AGGGCACTGGGGACATGC 62.053 66.667 0.00 0.00 41.51 4.06
416 456 1.440893 CAGCTCCAGGGAGTGATCG 59.559 63.158 16.31 0.00 43.70 3.69
440 481 4.154347 CACTCCGGCTCCAGCTCC 62.154 72.222 0.00 0.00 41.70 4.70
441 482 1.605058 TTACACTCCGGCTCCAGCTC 61.605 60.000 0.00 0.00 41.70 4.09
442 483 0.978146 ATTACACTCCGGCTCCAGCT 60.978 55.000 0.00 0.00 41.70 4.24
443 484 0.530870 GATTACACTCCGGCTCCAGC 60.531 60.000 0.00 0.00 41.14 4.85
444 485 0.105039 GGATTACACTCCGGCTCCAG 59.895 60.000 0.00 0.00 0.00 3.86
445 486 0.616395 TGGATTACACTCCGGCTCCA 60.616 55.000 0.00 0.00 38.21 3.86
446 487 0.105039 CTGGATTACACTCCGGCTCC 59.895 60.000 0.00 0.00 38.21 4.70
447 488 3.669354 CTGGATTACACTCCGGCTC 57.331 57.895 0.00 0.00 38.21 4.70
450 491 0.462047 GGTGCTGGATTACACTCCGG 60.462 60.000 0.00 0.00 43.50 5.14
451 492 0.249120 TGGTGCTGGATTACACTCCG 59.751 55.000 0.00 0.00 38.21 4.63
462 503 0.825010 AAAACCTCTGCTGGTGCTGG 60.825 55.000 0.00 0.00 40.73 4.85
463 504 0.313043 CAAAACCTCTGCTGGTGCTG 59.687 55.000 0.00 0.00 40.73 4.41
464 505 0.106519 ACAAAACCTCTGCTGGTGCT 60.107 50.000 0.00 0.00 40.73 4.40
465 506 1.537202 CTACAAAACCTCTGCTGGTGC 59.463 52.381 0.00 0.00 40.73 5.01
466 507 1.537202 GCTACAAAACCTCTGCTGGTG 59.463 52.381 0.00 0.00 40.73 4.17
467 508 1.878102 CGCTACAAAACCTCTGCTGGT 60.878 52.381 0.00 0.00 43.11 4.00
501 545 2.890847 ATCGGTCGCAAGCGGAGAAG 62.891 60.000 14.98 2.75 46.13 2.85
503 547 3.411418 GATCGGTCGCAAGCGGAGA 62.411 63.158 14.98 11.49 46.13 3.71
508 552 1.880340 CAGGAGATCGGTCGCAAGC 60.880 63.158 0.79 0.00 37.18 4.01
586 631 2.386661 ACTAATCAAGAGCCCACACG 57.613 50.000 0.00 0.00 0.00 4.49
587 632 5.069781 AGAGATACTAATCAAGAGCCCACAC 59.930 44.000 0.00 0.00 34.28 3.82
588 633 5.211973 AGAGATACTAATCAAGAGCCCACA 58.788 41.667 0.00 0.00 34.28 4.17
589 634 5.799827 AGAGATACTAATCAAGAGCCCAC 57.200 43.478 0.00 0.00 34.28 4.61
590 635 6.613271 AGAAAGAGATACTAATCAAGAGCCCA 59.387 38.462 0.00 0.00 34.28 5.36
591 636 7.061566 AGAAAGAGATACTAATCAAGAGCCC 57.938 40.000 0.00 0.00 34.28 5.19
690 735 2.124778 GAGGGCAGCAGAGAAGGC 60.125 66.667 0.00 0.00 0.00 4.35
694 761 3.397439 GCAGGAGGGCAGCAGAGA 61.397 66.667 0.00 0.00 0.00 3.10
710 777 3.798954 CTGAATCGAGGGCCGGAGC 62.799 68.421 5.05 0.00 39.14 4.70
711 778 1.961180 AACTGAATCGAGGGCCGGAG 61.961 60.000 5.05 0.00 39.14 4.63
712 779 1.956629 GAACTGAATCGAGGGCCGGA 61.957 60.000 5.05 0.00 39.14 5.14
714 781 0.807667 CTGAACTGAATCGAGGGCCG 60.808 60.000 0.00 0.00 40.25 6.13
726 793 2.743928 GGCCACCGAGCTGAACTG 60.744 66.667 0.00 0.00 0.00 3.16
729 796 4.704833 GCAGGCCACCGAGCTGAA 62.705 66.667 5.01 0.00 0.00 3.02
945 1043 2.181021 CTCGTGTGTACCCGGCTC 59.819 66.667 0.00 0.00 0.00 4.70
950 1048 2.126189 GACGCCTCGTGTGTACCC 60.126 66.667 0.00 0.00 41.37 3.69
1042 1140 3.039526 AGGAGGAGGGAGGAGGGG 61.040 72.222 0.00 0.00 0.00 4.79
1066 1165 0.034059 ATCGATCAATCTGGACCCGC 59.966 55.000 0.00 0.00 0.00 6.13
1082 1181 4.250305 AAATCCGGCCGGGGATCG 62.250 66.667 42.36 17.73 46.08 3.69
1101 1200 1.139734 CCCGAGTGATGTGACGGAG 59.860 63.158 0.00 0.00 46.94 4.63
1357 1462 1.984570 CGAGGAGGAGTTGGAGGCA 60.985 63.158 0.00 0.00 0.00 4.75
1750 1867 1.544825 CCTCAAAGTCGAGCTCCCCA 61.545 60.000 8.47 0.00 0.00 4.96
1835 1952 2.029666 GATGCCGTCGATCCCCTG 59.970 66.667 0.00 0.00 0.00 4.45
1906 2023 2.433231 CTATGCCGGAGCTGGAGAGC 62.433 65.000 5.05 0.00 46.64 4.09
2008 2125 0.802222 ACCATTCGCTGTCATCGTCG 60.802 55.000 0.00 0.00 0.00 5.12
2095 2212 2.011122 TCTTCTTCTTCTCCACCGGT 57.989 50.000 0.00 0.00 0.00 5.28
2135 2252 2.169789 CAGCGGCGATGTCCTTCAG 61.170 63.158 18.23 0.00 0.00 3.02
2338 2455 1.898863 ACATCCTTACCAGCCCATCT 58.101 50.000 0.00 0.00 0.00 2.90
2368 2485 9.740239 CATGAACAGGAATACCAAAATTATCTG 57.260 33.333 0.00 0.00 38.94 2.90
2397 2522 0.452987 CCGATCAGTTGTGCCATTGG 59.547 55.000 0.00 0.00 0.00 3.16
2409 2534 0.933097 CAGGCATTTCGACCGATCAG 59.067 55.000 0.00 0.00 0.00 2.90
2416 2541 1.154150 GCAGTGCAGGCATTTCGAC 60.154 57.895 11.09 0.00 0.00 4.20
2456 2581 0.685785 CCCTAGCAGAGACCAGCAGA 60.686 60.000 0.00 0.00 0.00 4.26
2542 2668 7.836685 TGATGCCCTGTTTTCCTTAATAATGTA 59.163 33.333 0.00 0.00 0.00 2.29
2588 2715 5.104776 TCCTTCTTCCATCTACACAATCCAG 60.105 44.000 0.00 0.00 0.00 3.86
2593 2720 6.361433 TGTTTTCCTTCTTCCATCTACACAA 58.639 36.000 0.00 0.00 0.00 3.33
2729 2881 8.110908 AGGAGATACACTATAGACCAGAATACC 58.889 40.741 6.78 0.22 0.00 2.73
2775 2927 0.529378 GGCTCACCCAAAGAAGCATG 59.471 55.000 0.00 0.00 0.00 4.06
2785 2937 0.776810 TGAAAATCCAGGCTCACCCA 59.223 50.000 0.00 0.00 36.11 4.51
2849 3001 7.243487 ACTAAACTGATGCAAACATGTATTCG 58.757 34.615 0.00 0.00 36.35 3.34
2873 3025 5.864628 AAGCTCATTTTTCTCGTCCTAAC 57.135 39.130 0.00 0.00 0.00 2.34
2918 3213 5.904362 AAGCCATCACTCATTAAAAGGTC 57.096 39.130 0.00 0.00 0.00 3.85
2925 3220 6.988580 CAGTTGAGATAAGCCATCACTCATTA 59.011 38.462 0.00 0.00 37.43 1.90
2957 3252 6.335777 TGCCTTAAGGTATCTAGTTTCGAAC 58.664 40.000 22.55 0.89 37.57 3.95
2960 3255 5.177696 GCATGCCTTAAGGTATCTAGTTTCG 59.822 44.000 21.01 9.49 38.51 3.46
3082 3378 3.142028 TCTTCAGGGGGAAAAGGTCAAAT 59.858 43.478 0.00 0.00 34.44 2.32
3247 3581 4.640201 TGGCTTATAGCTCACATGGTTTTC 59.360 41.667 0.00 0.00 41.99 2.29
3390 3777 7.076842 TCTGCTTATGCTTCAATTTCTGTAC 57.923 36.000 1.96 0.00 40.48 2.90
3407 3794 1.609061 GGAGTGCACTGCTTCTGCTTA 60.609 52.381 28.95 0.00 40.48 3.09
3522 3909 5.686159 TTTTGGCATTGCGAAAATTCAAT 57.314 30.435 22.53 0.00 40.23 2.57
3523 3910 4.554330 GCTTTTGGCATTGCGAAAATTCAA 60.554 37.500 25.25 10.21 43.02 2.69
3562 3949 1.967494 GGGCCCAAAACTCGCGTTA 60.967 57.895 19.95 0.00 31.86 3.18
3597 3988 5.254339 AGCTCCTTTTCAAACTTTCACAG 57.746 39.130 0.00 0.00 0.00 3.66
3601 3992 6.136541 TCAGAAGCTCCTTTTCAAACTTTC 57.863 37.500 0.00 0.00 0.00 2.62
3602 3993 6.406288 CCTTCAGAAGCTCCTTTTCAAACTTT 60.406 38.462 4.41 0.00 0.00 2.66
3614 4005 1.270907 TGAGGACCTTCAGAAGCTCC 58.729 55.000 14.72 14.72 34.12 4.70
3620 4011 2.244486 AGAGCATGAGGACCTTCAGA 57.756 50.000 0.00 0.00 0.00 3.27
3621 4012 2.500910 AGAAGAGCATGAGGACCTTCAG 59.499 50.000 0.00 0.00 36.59 3.02
3629 4020 3.683802 AGAACCAAAGAAGAGCATGAGG 58.316 45.455 0.00 0.00 0.00 3.86
3640 4031 0.850100 TCCCCTGCAAGAACCAAAGA 59.150 50.000 0.00 0.00 34.07 2.52
3863 4263 1.213926 CAAAGAAGCCAGCTATCCCCT 59.786 52.381 0.00 0.00 0.00 4.79
3864 4264 1.064389 ACAAAGAAGCCAGCTATCCCC 60.064 52.381 0.00 0.00 0.00 4.81
3865 4265 2.293170 GACAAAGAAGCCAGCTATCCC 58.707 52.381 0.00 0.00 0.00 3.85
3866 4266 2.941720 CTGACAAAGAAGCCAGCTATCC 59.058 50.000 0.00 0.00 0.00 2.59
3867 4267 2.941720 CCTGACAAAGAAGCCAGCTATC 59.058 50.000 0.00 0.00 0.00 2.08
3868 4268 2.356535 CCCTGACAAAGAAGCCAGCTAT 60.357 50.000 0.00 0.00 0.00 2.97
3869 4269 1.003580 CCCTGACAAAGAAGCCAGCTA 59.996 52.381 0.00 0.00 0.00 3.32
3870 4270 0.251077 CCCTGACAAAGAAGCCAGCT 60.251 55.000 0.00 0.00 0.00 4.24
3871 4271 1.246737 CCCCTGACAAAGAAGCCAGC 61.247 60.000 0.00 0.00 0.00 4.85
3872 4272 0.401738 TCCCCTGACAAAGAAGCCAG 59.598 55.000 0.00 0.00 0.00 4.85
3873 4273 1.075601 ATCCCCTGACAAAGAAGCCA 58.924 50.000 0.00 0.00 0.00 4.75
3874 4274 2.924421 CTATCCCCTGACAAAGAAGCC 58.076 52.381 0.00 0.00 0.00 4.35
3875 4275 2.092699 AGCTATCCCCTGACAAAGAAGC 60.093 50.000 0.00 0.00 0.00 3.86
3876 4276 3.539604 CAGCTATCCCCTGACAAAGAAG 58.460 50.000 0.00 0.00 32.03 2.85
3877 4277 2.356125 GCAGCTATCCCCTGACAAAGAA 60.356 50.000 0.00 0.00 32.03 2.52
3878 4278 1.210478 GCAGCTATCCCCTGACAAAGA 59.790 52.381 0.00 0.00 32.03 2.52
3879 4279 1.211457 AGCAGCTATCCCCTGACAAAG 59.789 52.381 0.00 0.00 32.03 2.77
3880 4280 1.065199 CAGCAGCTATCCCCTGACAAA 60.065 52.381 0.00 0.00 32.03 2.83
3881 4281 0.543277 CAGCAGCTATCCCCTGACAA 59.457 55.000 0.00 0.00 32.03 3.18
3882 4282 1.340399 CCAGCAGCTATCCCCTGACA 61.340 60.000 0.00 0.00 32.03 3.58
3883 4283 1.341156 ACCAGCAGCTATCCCCTGAC 61.341 60.000 0.00 0.00 32.03 3.51
3884 4284 0.621571 AACCAGCAGCTATCCCCTGA 60.622 55.000 0.00 0.00 32.03 3.86
3885 4285 1.071385 CTAACCAGCAGCTATCCCCTG 59.929 57.143 0.00 0.00 0.00 4.45
3955 4371 3.932710 CAGCACTGTACCATTGTTACGAT 59.067 43.478 0.00 0.00 0.00 3.73
4013 4429 2.428890 AGAGGGTTCAGAGCATAAGACG 59.571 50.000 0.00 0.00 0.00 4.18
4030 4446 1.089920 CGGTGCAATTCCTTCAGAGG 58.910 55.000 0.00 0.00 45.02 3.69
4058 4474 0.244721 GCCAGAACATTTGGGAGCAC 59.755 55.000 0.00 0.00 36.19 4.40
4059 4475 0.178967 TGCCAGAACATTTGGGAGCA 60.179 50.000 0.00 0.00 36.19 4.26
4060 4476 0.244721 GTGCCAGAACATTTGGGAGC 59.755 55.000 0.00 0.00 36.67 4.70
4061 4477 1.542915 CTGTGCCAGAACATTTGGGAG 59.457 52.381 0.00 0.00 36.67 4.30
4074 4490 4.935352 ACAAAAATTTAGAGCTGTGCCA 57.065 36.364 0.00 0.00 0.00 4.92
4089 4505 8.539770 TTTGCAGATTCACTTTTGTACAAAAA 57.460 26.923 28.52 17.52 39.49 1.94
4102 4518 5.050159 GTCCCAACAAATTTTGCAGATTCAC 60.050 40.000 9.04 0.00 0.00 3.18
4122 4538 2.091885 TCAAATGCTCCCCTAATGTCCC 60.092 50.000 0.00 0.00 0.00 4.46
4125 4541 3.885297 CGAATCAAATGCTCCCCTAATGT 59.115 43.478 0.00 0.00 0.00 2.71
4130 4546 0.034186 TGCGAATCAAATGCTCCCCT 60.034 50.000 0.00 0.00 0.00 4.79
4207 4623 5.366768 TGTTTCCCAGACCTAGGATTCATAG 59.633 44.000 17.98 0.00 30.55 2.23
4218 4634 0.324943 CGGTGATGTTTCCCAGACCT 59.675 55.000 0.00 0.00 30.50 3.85
4225 4641 1.611491 TGCTTTTCCGGTGATGTTTCC 59.389 47.619 0.00 0.00 0.00 3.13
4226 4642 3.363341 TTGCTTTTCCGGTGATGTTTC 57.637 42.857 0.00 0.00 0.00 2.78
4236 4652 3.017265 ACATCTTGCTTTGCTTTTCCG 57.983 42.857 0.00 0.00 0.00 4.30
4334 6486 5.246981 AGAATTCCATCCACTCAACTCAA 57.753 39.130 0.65 0.00 0.00 3.02
4335 6487 4.916041 AGAATTCCATCCACTCAACTCA 57.084 40.909 0.65 0.00 0.00 3.41
4336 6488 5.809719 GAAGAATTCCATCCACTCAACTC 57.190 43.478 0.65 0.00 39.83 3.01
4377 6529 5.163343 GGCAAAAATATTTCTTAGGGTCCCC 60.163 44.000 3.51 0.00 0.00 4.81
4401 6553 9.865321 ATTTGATTCACACAATAGAAATCCTTG 57.135 29.630 0.00 0.00 0.00 3.61
4511 6663 6.166279 GTGACTAAAGATTCTGATGACACCA 58.834 40.000 0.00 0.00 0.00 4.17
4512 6664 6.166279 TGTGACTAAAGATTCTGATGACACC 58.834 40.000 0.00 0.00 0.00 4.16
4531 6683 9.307121 GATGGCACTATAGATACAATATGTGAC 57.693 37.037 6.78 0.00 33.29 3.67
4539 6691 8.439971 AGGAATTTGATGGCACTATAGATACAA 58.560 33.333 6.78 1.88 0.00 2.41
4548 9363 9.866655 ATTTAGATTAGGAATTTGATGGCACTA 57.133 29.630 0.00 0.00 0.00 2.74
4549 9364 8.773033 ATTTAGATTAGGAATTTGATGGCACT 57.227 30.769 0.00 0.00 0.00 4.40
4609 9424 7.721286 GCTACAGATTAGCTACAACATGATT 57.279 36.000 0.00 0.00 37.56 2.57
4621 9436 2.285488 GCCGTTTGAGCTACAGATTAGC 59.715 50.000 0.00 0.00 40.67 3.09
4624 9439 1.337823 ACGCCGTTTGAGCTACAGATT 60.338 47.619 0.00 0.00 0.00 2.40
4633 9448 1.241315 ATTTGGGGACGCCGTTTGAG 61.241 55.000 3.81 0.00 0.00 3.02
4635 9450 0.882474 TAATTTGGGGACGCCGTTTG 59.118 50.000 3.81 0.00 0.00 2.93
4639 9454 1.675552 ATCTTAATTTGGGGACGCCG 58.324 50.000 3.81 0.00 0.00 6.46
4640 9455 4.465632 AAAATCTTAATTTGGGGACGCC 57.534 40.909 0.53 0.53 35.27 5.68
4672 9487 1.013596 TCAATAGATTTGGCACCGCG 58.986 50.000 0.00 0.00 0.00 6.46
4675 9490 4.365723 CTGCATTCAATAGATTTGGCACC 58.634 43.478 0.00 0.00 0.00 5.01
4708 9523 3.230976 GTGTTTCCCCTCTTCCATGTTT 58.769 45.455 0.00 0.00 0.00 2.83
4709 9524 2.176798 TGTGTTTCCCCTCTTCCATGTT 59.823 45.455 0.00 0.00 0.00 2.71
4718 10413 2.178912 TCAATCGTGTGTTTCCCCTC 57.821 50.000 0.00 0.00 0.00 4.30
4737 10432 6.887545 TGACCCAAATTTCTACGGTATGATTT 59.112 34.615 0.00 0.00 0.00 2.17
4741 10436 6.373216 TCTTTGACCCAAATTTCTACGGTATG 59.627 38.462 0.00 0.00 32.70 2.39
4742 10437 6.478129 TCTTTGACCCAAATTTCTACGGTAT 58.522 36.000 0.00 0.00 32.70 2.73
4743 10438 5.867330 TCTTTGACCCAAATTTCTACGGTA 58.133 37.500 0.00 0.00 32.70 4.02
4745 10440 5.699097 TTCTTTGACCCAAATTTCTACGG 57.301 39.130 0.00 0.00 32.70 4.02
4746 10441 8.587952 AATTTTCTTTGACCCAAATTTCTACG 57.412 30.769 0.00 0.00 32.70 3.51
4749 10444 9.631257 ATGAAATTTTCTTTGACCCAAATTTCT 57.369 25.926 20.99 10.34 46.47 2.52
4750 10445 9.667989 CATGAAATTTTCTTTGACCCAAATTTC 57.332 29.630 16.64 16.64 46.49 2.17
4751 10446 8.136800 GCATGAAATTTTCTTTGACCCAAATTT 58.863 29.630 10.33 0.00 40.08 1.82
4754 10477 5.530543 GGCATGAAATTTTCTTTGACCCAAA 59.469 36.000 10.33 0.00 0.00 3.28
4757 10480 4.452114 GTGGCATGAAATTTTCTTTGACCC 59.548 41.667 10.33 6.55 0.00 4.46
4767 10490 6.428771 CCTTCTTTTCATGTGGCATGAAATTT 59.571 34.615 27.21 0.00 44.45 1.82
4768 10491 5.935789 CCTTCTTTTCATGTGGCATGAAATT 59.064 36.000 27.21 0.00 44.45 1.82
4769 10492 5.246656 TCCTTCTTTTCATGTGGCATGAAAT 59.753 36.000 27.21 0.00 44.45 2.17
4788 10511 9.219603 CTTTTCCCCTCAAAAATAAAATCCTTC 57.780 33.333 0.00 0.00 0.00 3.46
4791 10514 7.685481 TCCTTTTCCCCTCAAAAATAAAATCC 58.315 34.615 0.00 0.00 0.00 3.01
4825 10548 9.155975 CGTTTGATTCATAGGAATAGGAATAGG 57.844 37.037 1.96 0.00 43.69 2.57
4826 10549 9.929180 TCGTTTGATTCATAGGAATAGGAATAG 57.071 33.333 1.96 0.00 43.69 1.73
4827 10550 9.706691 GTCGTTTGATTCATAGGAATAGGAATA 57.293 33.333 1.96 0.00 43.69 1.75
4828 10551 8.210946 TGTCGTTTGATTCATAGGAATAGGAAT 58.789 33.333 1.96 0.00 43.69 3.01
4829 10552 7.561251 TGTCGTTTGATTCATAGGAATAGGAA 58.439 34.615 1.96 0.00 43.69 3.36
4830 10553 7.119709 TGTCGTTTGATTCATAGGAATAGGA 57.880 36.000 1.96 0.00 43.69 2.94
4831 10554 7.969536 ATGTCGTTTGATTCATAGGAATAGG 57.030 36.000 1.96 0.00 43.69 2.57
4861 10584 8.139989 GGGAGGATTTTGTGAGATTTTCATATG 58.860 37.037 0.00 0.00 38.29 1.78
4951 10714 1.788308 CAGCGACACCAAATTTTGCAG 59.212 47.619 3.50 1.23 0.00 4.41
4994 10761 1.453379 GTCATGGGCTGATGCTGCT 60.453 57.895 0.00 0.00 39.59 4.24
4995 10762 2.487532 GGTCATGGGCTGATGCTGC 61.488 63.158 0.00 0.00 39.59 5.25
4996 10763 0.818445 GAGGTCATGGGCTGATGCTG 60.818 60.000 0.00 0.00 39.59 4.41
5099 10869 0.179009 TCTTTTGTGCTGCTGCTCCT 60.179 50.000 17.00 0.00 40.48 3.69
5102 10872 2.363038 TGAAATCTTTTGTGCTGCTGCT 59.637 40.909 17.00 0.00 40.48 4.24
5104 10874 5.511088 GAATGAAATCTTTTGTGCTGCTG 57.489 39.130 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.