Multiple sequence alignment - TraesCS5B01G448900

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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 TraesCS5B01G448900 chr5B 100.000 6363 0 0 1 6363 621268403 621262041 0.000000e+00 11751.0
1 TraesCS5B01G448900 chr5A 93.616 5843 268 47 6 5806 624219015 624213236 0.000000e+00 8626.0
2 TraesCS5B01G448900 chr5A 77.500 520 50 38 5871 6363 624213124 624212645 3.810000e-62 250.0
3 TraesCS5B01G448900 chr5D 94.021 2241 85 20 1433 3640 499875802 499873578 0.000000e+00 3350.0
4 TraesCS5B01G448900 chr5D 94.453 1262 49 12 3683 4939 499873577 499872332 0.000000e+00 1923.0
5 TraesCS5B01G448900 chr5D 91.925 1226 59 14 162 1378 499877013 499875819 0.000000e+00 1679.0
6 TraesCS5B01G448900 chr5D 91.620 895 46 16 4917 5806 499872322 499871452 0.000000e+00 1210.0
7 TraesCS5B01G448900 chr5D 77.369 517 65 31 5871 6363 499871335 499870847 6.330000e-65 259.0
8 TraesCS5B01G448900 chr5D 90.551 127 12 0 6 132 499877135 499877009 1.100000e-37 169.0
9 TraesCS5B01G448900 chr7D 84.524 84 12 1 3009 3091 382475289 382475372 1.470000e-11 82.4
10 TraesCS5B01G448900 chr3B 84.524 84 12 1 3009 3091 113686379 113686462 1.470000e-11 82.4
11 TraesCS5B01G448900 chr2B 84.524 84 12 1 3009 3091 416749855 416749772 1.470000e-11 82.4
12 TraesCS5B01G448900 chr1A 84.706 85 9 4 3014 3096 376514832 376514914 1.470000e-11 82.4
13 TraesCS5B01G448900 chr1D 83.133 83 14 0 3014 3096 301641885 301641967 6.840000e-10 76.8
14 TraesCS5B01G448900 chr1B 83.133 83 14 0 3014 3096 407309007 407309089 6.840000e-10 76.8
15 TraesCS5B01G448900 chr7B 79.798 99 18 2 3090 3187 602894589 602894686 3.180000e-08 71.3


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 TraesCS5B01G448900 chr5B 621262041 621268403 6362 True 11751.000000 11751 100.000000 1 6363 1 chr5B.!!$R1 6362
1 TraesCS5B01G448900 chr5A 624212645 624219015 6370 True 4438.000000 8626 85.558000 6 6363 2 chr5A.!!$R1 6357
2 TraesCS5B01G448900 chr5D 499870847 499877135 6288 True 1431.666667 3350 89.989833 6 6363 6 chr5D.!!$R1 6357

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
305 307 0.179936 CTCTGCATCTTCCCACTCCC 59.820 60.000 0.00 0.00 0.00 4.30 F
306 308 1.225704 CTGCATCTTCCCACTCCCC 59.774 63.158 0.00 0.00 0.00 4.81 F
330 332 1.275856 CACATCCCCAACCACCAAATG 59.724 52.381 0.00 0.00 0.00 2.32 F
1574 1603 1.571955 AGGGTGCATGGGAAATTTCC 58.428 50.000 26.41 26.41 46.82 3.13 F
2267 2316 1.201965 GCTGAGTTGCTTGCACGATAC 60.202 52.381 0.00 0.00 0.00 2.24 F
2767 2817 1.480498 GGTGGAGGAAATGGTGGTGTT 60.480 52.381 0.00 0.00 0.00 3.32 F
3113 3165 1.632589 AAAAGTTGGCCCTCATCCAC 58.367 50.000 0.00 0.00 32.45 4.02 F
3470 3535 2.224523 GGTGACACCCAAGAAGATGTCA 60.225 50.000 14.16 1.91 46.92 3.58 F
5203 5306 0.674895 CAAGGAGAAAGAGCACCGGG 60.675 60.000 6.32 0.00 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1396 1422 0.040067 GAAACTGCGTTTGGCTCCTG 60.040 55.000 10.61 0.0 44.05 3.86 R
1565 1594 1.135112 GCACATCCACCGGAAATTTCC 60.135 52.381 24.90 24.9 44.05 3.13 R
1663 1695 2.158623 TCACATGGAAAAGCTGGTGACT 60.159 45.455 0.00 0.0 30.99 3.41 R
2419 2469 0.179032 TTTCCGCAGCCTCTTTCACA 60.179 50.000 0.00 0.0 0.00 3.58 R
3866 3931 1.193874 GGCAACGGTTGTCTTAGTTCG 59.806 52.381 20.92 0.0 31.13 3.95 R
3957 4022 3.340928 TGATCATCTTGTCTTGGCACAG 58.659 45.455 0.00 0.0 42.39 3.66 R
4626 4695 3.726557 TTTGCTCTGATGACCAAGGAT 57.273 42.857 0.00 0.0 0.00 3.24 R
5223 5326 1.451504 CTGGTGTTCACTGCCTCCA 59.548 57.895 2.98 0.0 0.00 3.86 R
6253 6451 0.103937 CAGCGAGAGGGATGAACTCC 59.896 60.000 0.00 0.0 44.11 3.85 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
34 35 7.595130 TCTCACGAAATTGATCGATATGGTTAG 59.405 37.037 6.54 0.00 45.48 2.34
37 38 9.353999 CACGAAATTGATCGATATGGTTAGATA 57.646 33.333 6.54 0.00 45.48 1.98
124 126 6.498538 TCAAATACAAGGGTTCCATATTGGT 58.501 36.000 0.00 0.00 39.03 3.67
136 138 4.430007 TCCATATTGGTCGAAAAGTCTCG 58.570 43.478 0.00 0.00 39.03 4.04
144 146 3.284323 TCGAAAAGTCTCGAGGAACTG 57.716 47.619 13.56 0.00 42.69 3.16
149 151 3.601443 AAGTCTCGAGGAACTGAATGG 57.399 47.619 13.56 0.00 41.55 3.16
153 155 3.929610 GTCTCGAGGAACTGAATGGAAAG 59.070 47.826 13.56 0.00 41.55 2.62
176 178 8.476985 AAAGAATTTCTAAAAGCCATGAACGGC 61.477 37.037 0.00 0.00 44.18 5.68
195 197 3.553511 CGGCTGCTTAGATACTTGTTGAG 59.446 47.826 0.00 0.00 0.00 3.02
203 205 3.177228 AGATACTTGTTGAGACCCTGCT 58.823 45.455 0.00 0.00 0.00 4.24
223 225 0.816018 TTTTCACCTTCTTCGCCGCA 60.816 50.000 0.00 0.00 0.00 5.69
242 244 3.610242 CGCATTACATATCTTCGGCTCTC 59.390 47.826 0.00 0.00 0.00 3.20
253 255 1.046204 TCGGCTCTCATGCATCTGAT 58.954 50.000 0.00 0.00 34.04 2.90
302 304 0.617413 CCACTCTGCATCTTCCCACT 59.383 55.000 0.00 0.00 0.00 4.00
303 305 1.406614 CCACTCTGCATCTTCCCACTC 60.407 57.143 0.00 0.00 0.00 3.51
304 306 0.908198 ACTCTGCATCTTCCCACTCC 59.092 55.000 0.00 0.00 0.00 3.85
305 307 0.179936 CTCTGCATCTTCCCACTCCC 59.820 60.000 0.00 0.00 0.00 4.30
306 308 1.225704 CTGCATCTTCCCACTCCCC 59.774 63.158 0.00 0.00 0.00 4.81
307 309 2.190578 GCATCTTCCCACTCCCCG 59.809 66.667 0.00 0.00 0.00 5.73
308 310 2.367202 GCATCTTCCCACTCCCCGA 61.367 63.158 0.00 0.00 0.00 5.14
309 311 1.522569 CATCTTCCCACTCCCCGAC 59.477 63.158 0.00 0.00 0.00 4.79
310 312 1.689582 ATCTTCCCACTCCCCGACC 60.690 63.158 0.00 0.00 0.00 4.79
311 313 2.471084 ATCTTCCCACTCCCCGACCA 62.471 60.000 0.00 0.00 0.00 4.02
312 314 2.926242 TTCCCACTCCCCGACCAC 60.926 66.667 0.00 0.00 0.00 4.16
313 315 3.777818 TTCCCACTCCCCGACCACA 62.778 63.158 0.00 0.00 0.00 4.17
330 332 1.275856 CACATCCCCAACCACCAAATG 59.724 52.381 0.00 0.00 0.00 2.32
347 349 4.221342 CAAATGTATTTGGCCATCGATCG 58.779 43.478 6.09 9.36 42.51 3.69
390 392 3.755378 AGTCGTCGACCTAAGCTAAAGAA 59.245 43.478 21.40 0.00 32.18 2.52
398 400 3.197983 ACCTAAGCTAAAGAAGGCGTCAT 59.802 43.478 2.69 0.00 31.98 3.06
481 486 2.343758 GGTCACTCGAGCCAAGCA 59.656 61.111 13.61 0.00 33.34 3.91
560 566 3.353836 CAGTTGGCGTGAACCGGG 61.354 66.667 6.32 0.00 36.94 5.73
574 581 2.745308 CCGGGTGATGATCCCTGCA 61.745 63.158 0.00 0.00 42.56 4.41
731 742 2.203294 AACGAAGCACCCACCCAC 60.203 61.111 0.00 0.00 0.00 4.61
732 743 3.785122 AACGAAGCACCCACCCACC 62.785 63.158 0.00 0.00 0.00 4.61
734 745 4.678743 GAAGCACCCACCCACCCC 62.679 72.222 0.00 0.00 0.00 4.95
1082 1103 2.045926 CACCAAAGGGGCGGAGAG 60.046 66.667 0.00 0.00 42.05 3.20
1235 1257 2.541762 CCGCTAGATCTGTTTTAGCTGC 59.458 50.000 5.18 0.00 38.08 5.25
1261 1283 2.215907 TTCATGCGTGTTTTTGGTGG 57.784 45.000 5.68 0.00 0.00 4.61
1331 1353 3.181468 CCTAGGGTTTCGTATTGGAGGAC 60.181 52.174 0.00 0.00 0.00 3.85
1350 1376 3.609853 GACACAGATTCAACATAGCCCA 58.390 45.455 0.00 0.00 0.00 5.36
1396 1422 4.082733 GGTTGTAGGACAAGGAATGCTTTC 60.083 45.833 3.77 3.77 39.00 2.62
1406 1432 1.895131 GGAATGCTTTCAGGAGCCAAA 59.105 47.619 13.72 0.00 42.01 3.28
1480 1506 5.196695 AGCTTTGAGAACTTCTTGTTTCCT 58.803 37.500 0.00 0.00 39.30 3.36
1565 1594 3.824133 TGAATCATTCTAGGGTGCATGG 58.176 45.455 0.00 0.00 0.00 3.66
1574 1603 1.571955 AGGGTGCATGGGAAATTTCC 58.428 50.000 26.41 26.41 46.82 3.13
1838 1872 1.340017 GGGCATCAGCTACAACTTCCA 60.340 52.381 0.00 0.00 41.70 3.53
1891 1926 8.814038 ATCTTGTTTCTTATTAGATGCTTGGT 57.186 30.769 0.00 0.00 0.00 3.67
1912 1947 9.128107 CTTGGTCACATATTTTTGTTATCACAC 57.872 33.333 0.00 0.00 30.32 3.82
1925 1960 9.883142 TTTTGTTATCACACATCTTTTCCTTTT 57.117 25.926 0.00 0.00 30.32 2.27
1926 1961 9.883142 TTTGTTATCACACATCTTTTCCTTTTT 57.117 25.926 0.00 0.00 30.32 1.94
2021 2058 8.156820 TCAATTTGAAGAGTTATGAGAAGTGGA 58.843 33.333 0.00 0.00 0.00 4.02
2038 2075 8.443953 AGAAGTGGAATTGAGTATCTTTATGC 57.556 34.615 0.00 0.00 34.92 3.14
2056 2093 9.982651 TCTTTATGCAGTTACATACCTAAGATC 57.017 33.333 0.00 0.00 32.32 2.75
2059 2096 6.161855 TGCAGTTACATACCTAAGATCTGG 57.838 41.667 0.00 0.00 0.00 3.86
2165 2213 6.378661 TGGCTATCATAATGCTCAGGTTAT 57.621 37.500 0.00 0.00 0.00 1.89
2267 2316 1.201965 GCTGAGTTGCTTGCACGATAC 60.202 52.381 0.00 0.00 0.00 2.24
2289 2338 5.730550 ACTTGCACCGAATAGTTTATGAGA 58.269 37.500 0.00 0.00 0.00 3.27
2370 2420 8.158025 TCCCTCTCATTACAATTCCTAGAAAA 57.842 34.615 0.00 0.00 0.00 2.29
2720 2770 3.659786 CGTACTGTTCCTCAACCATTCA 58.340 45.455 0.00 0.00 0.00 2.57
2767 2817 1.480498 GGTGGAGGAAATGGTGGTGTT 60.480 52.381 0.00 0.00 0.00 3.32
2930 2982 9.220767 AGTCTTGATTTTATTAGACCACAGTTC 57.779 33.333 0.00 0.00 38.17 3.01
3113 3165 1.632589 AAAAGTTGGCCCTCATCCAC 58.367 50.000 0.00 0.00 32.45 4.02
3131 3183 8.642935 TCATCCACACAAAGACCAATATTTTA 57.357 30.769 0.00 0.00 0.00 1.52
3470 3535 2.224523 GGTGACACCCAAGAAGATGTCA 60.225 50.000 14.16 1.91 46.92 3.58
3568 3633 4.378563 CGGTCTACACTCTACACTGTTCTG 60.379 50.000 0.00 0.00 0.00 3.02
3578 3643 7.600375 CACTCTACACTGTTCTGTCATTATGTT 59.400 37.037 0.00 0.00 0.00 2.71
3661 3726 6.803807 GCTGAAAGATGACTGGAAAATTACAC 59.196 38.462 0.00 0.00 34.07 2.90
3669 3734 6.353323 TGACTGGAAAATTACACTGTTCTGA 58.647 36.000 0.00 0.00 0.00 3.27
3704 3769 7.095270 TCTTACGTTTTCTGGAAGATCTTACC 58.905 38.462 15.31 14.45 46.36 2.85
3773 3838 4.734398 TTGTGAACTGAAAACATTGCCT 57.266 36.364 0.00 0.00 0.00 4.75
3786 3851 4.989279 ACATTGCCTACATGATGTTTCC 57.011 40.909 2.29 0.00 28.88 3.13
3988 4053 8.781196 CCAAGACAAGATGATCATAACCATTAG 58.219 37.037 8.54 0.00 0.00 1.73
3989 4054 9.334947 CAAGACAAGATGATCATAACCATTAGT 57.665 33.333 8.54 0.00 0.00 2.24
4138 4203 9.695526 AAAAAGGTAAGAACGTACTTTTGTTTT 57.304 25.926 8.17 0.00 34.56 2.43
4174 4239 7.141363 ACATTTGAGTTATTTGTGCTCTGTTC 58.859 34.615 0.00 0.00 0.00 3.18
4213 4278 4.434713 AATGTCTTGATTTAACACGGGC 57.565 40.909 0.00 0.00 0.00 6.13
4245 4310 8.774890 TGTTCTGTACTACACTTAAACAAACA 57.225 30.769 0.00 0.00 0.00 2.83
4626 4695 5.068067 AGCGGCTTTAAAACAACTAAGGAAA 59.932 36.000 0.00 0.00 0.00 3.13
4695 4764 1.378250 CCCTCCAAAGGCTGAGCTG 60.378 63.158 3.72 0.00 41.85 4.24
4709 4778 3.625313 GCTGAGCTGAAGAAGGTAATTCC 59.375 47.826 0.00 0.00 38.84 3.01
4710 4779 4.195416 CTGAGCTGAAGAAGGTAATTCCC 58.805 47.826 0.00 0.00 38.84 3.97
4754 4823 7.463469 AAAAATTGTACTTGCAGTTGCTTAC 57.537 32.000 5.62 5.22 42.66 2.34
4755 4824 6.391227 AAATTGTACTTGCAGTTGCTTACT 57.609 33.333 5.62 0.00 42.66 2.24
4756 4825 6.391227 AATTGTACTTGCAGTTGCTTACTT 57.609 33.333 5.62 0.00 42.66 2.24
4757 4826 4.811555 TGTACTTGCAGTTGCTTACTTG 57.188 40.909 5.62 0.00 42.66 3.16
4758 4827 2.781945 ACTTGCAGTTGCTTACTTGC 57.218 45.000 5.62 0.00 42.66 4.01
4759 4828 2.301346 ACTTGCAGTTGCTTACTTGCT 58.699 42.857 5.62 0.00 42.66 3.91
4761 4830 3.882888 ACTTGCAGTTGCTTACTTGCTTA 59.117 39.130 5.62 4.26 42.66 3.09
4763 4832 5.705441 ACTTGCAGTTGCTTACTTGCTTATA 59.295 36.000 5.62 0.00 42.66 0.98
4764 4833 5.545658 TGCAGTTGCTTACTTGCTTATAC 57.454 39.130 5.62 0.00 42.66 1.47
4765 4834 5.000591 TGCAGTTGCTTACTTGCTTATACA 58.999 37.500 5.62 0.00 42.66 2.29
4766 4835 5.647658 TGCAGTTGCTTACTTGCTTATACAT 59.352 36.000 5.62 0.00 42.66 2.29
4767 4836 5.967674 GCAGTTGCTTACTTGCTTATACATG 59.032 40.000 0.00 0.00 33.85 3.21
4768 4837 6.183360 GCAGTTGCTTACTTGCTTATACATGA 60.183 38.462 0.00 0.00 33.85 3.07
4769 4838 7.626240 GCAGTTGCTTACTTGCTTATACATGAA 60.626 37.037 0.00 0.00 33.85 2.57
4770 4839 8.236586 CAGTTGCTTACTTGCTTATACATGAAA 58.763 33.333 0.00 0.00 33.85 2.69
4844 4913 6.764379 TGTATATATCACCGAAATGAGCCAA 58.236 36.000 0.00 0.00 30.46 4.52
4845 4914 7.394016 TGTATATATCACCGAAATGAGCCAAT 58.606 34.615 0.00 0.00 30.46 3.16
4858 4928 8.081633 CGAAATGAGCCAATGCCTTATAATTAA 58.918 33.333 0.00 0.00 38.69 1.40
5131 5234 4.759693 TGCTCAGTCACGGATTTACATTTT 59.240 37.500 0.00 0.00 0.00 1.82
5203 5306 0.674895 CAAGGAGAAAGAGCACCGGG 60.675 60.000 6.32 0.00 0.00 5.73
5206 5309 1.627297 GGAGAAAGAGCACCGGGGAT 61.627 60.000 8.67 0.00 0.00 3.85
5245 5348 4.374702 GCAGTGAACACCAGCGCG 62.375 66.667 0.00 0.00 0.00 6.86
5281 5384 0.548031 ATCGTCACAGCATGGGGAAT 59.452 50.000 0.00 0.00 42.44 3.01
5347 5450 3.435186 GCCAAAGCCAGAGCCGTC 61.435 66.667 0.00 0.00 41.25 4.79
5496 5599 5.434182 TGATTCATGTAAGGTGGATGTCA 57.566 39.130 0.00 0.00 0.00 3.58
5520 5623 1.611977 AGTCACTCGGTCGTTTGATGA 59.388 47.619 0.00 0.00 0.00 2.92
5521 5624 2.231478 AGTCACTCGGTCGTTTGATGAT 59.769 45.455 0.00 0.00 0.00 2.45
5522 5625 2.345641 GTCACTCGGTCGTTTGATGATG 59.654 50.000 0.00 0.00 0.00 3.07
5536 5639 0.249120 ATGATGCCCTCGACGAACAA 59.751 50.000 0.00 0.00 0.00 2.83
5554 5657 5.397534 CGAACAAATTTGAGAGCTGAACTTG 59.602 40.000 24.64 0.00 0.00 3.16
5669 5772 6.585702 TGTGCTCATGTTTGTATTATTGTTGC 59.414 34.615 0.00 0.00 0.00 4.17
5683 5786 3.451141 TTGTTGCCATGGTTTGAGTTC 57.549 42.857 14.67 0.00 0.00 3.01
5710 5814 2.133281 TTGTCGGAGTATCTTCGGGA 57.867 50.000 0.00 0.00 32.62 5.14
5722 5827 3.350909 TTCGGGATCAGACGTGGCG 62.351 63.158 0.00 0.00 0.00 5.69
5733 5838 1.202417 AGACGTGGCGACCATGATAAG 60.202 52.381 20.38 4.78 42.73 1.73
5736 5841 0.180406 GTGGCGACCATGATAAGGGT 59.820 55.000 0.00 0.00 40.96 4.34
5745 5850 1.063717 CATGATAAGGGTTGGGCCAGT 60.064 52.381 6.23 0.00 39.65 4.00
5747 5852 1.005450 TGATAAGGGTTGGGCCAGTTC 59.995 52.381 6.23 1.34 39.65 3.01
5757 5862 3.116096 TGGGCCAGTTCTACATCTAGT 57.884 47.619 0.00 0.00 0.00 2.57
5759 5864 4.816126 TGGGCCAGTTCTACATCTAGTAT 58.184 43.478 0.00 0.00 30.93 2.12
5760 5865 5.960704 TGGGCCAGTTCTACATCTAGTATA 58.039 41.667 0.00 0.00 30.93 1.47
5762 5867 6.842280 TGGGCCAGTTCTACATCTAGTATAAA 59.158 38.462 0.00 0.00 30.93 1.40
5763 5868 7.512746 TGGGCCAGTTCTACATCTAGTATAAAT 59.487 37.037 0.00 0.00 30.93 1.40
5764 5869 8.376270 GGGCCAGTTCTACATCTAGTATAAATT 58.624 37.037 4.39 0.00 30.93 1.82
5765 5870 9.780186 GGCCAGTTCTACATCTAGTATAAATTT 57.220 33.333 0.00 0.00 30.93 1.82
5808 5970 0.335019 GCCACCCCAGGGAAATACTT 59.665 55.000 7.25 0.00 38.96 2.24
5828 5990 9.793259 AATACTTCCTCTGTCTCAAAATGTAAA 57.207 29.630 0.00 0.00 0.00 2.01
5830 5992 8.697507 ACTTCCTCTGTCTCAAAATGTAAAAT 57.302 30.769 0.00 0.00 0.00 1.82
5843 6005 9.469807 TCAAAATGTAAAATATGTGTTGACACC 57.530 29.630 11.42 0.00 45.88 4.16
5844 6006 8.423973 CAAAATGTAAAATATGTGTTGACACCG 58.576 33.333 11.42 0.00 45.88 4.94
5845 6007 6.811253 ATGTAAAATATGTGTTGACACCGT 57.189 33.333 11.42 3.66 45.88 4.83
5846 6008 5.991568 TGTAAAATATGTGTTGACACCGTG 58.008 37.500 11.42 0.00 45.88 4.94
5847 6009 5.758784 TGTAAAATATGTGTTGACACCGTGA 59.241 36.000 5.28 0.00 45.88 4.35
5848 6010 4.742438 AAATATGTGTTGACACCGTGAC 57.258 40.909 5.28 0.00 45.88 3.67
5850 6012 0.878523 ATGTGTTGACACCGTGACCG 60.879 55.000 5.28 0.00 45.88 4.79
5851 6013 1.519898 GTGTTGACACCGTGACCGT 60.520 57.895 5.28 0.00 40.85 4.83
5852 6014 1.519676 TGTTGACACCGTGACCGTG 60.520 57.895 5.28 2.56 0.00 4.94
5854 6016 1.227031 TTGACACCGTGACCGTGTC 60.227 57.895 23.84 23.84 41.37 3.67
5855 6017 1.946475 TTGACACCGTGACCGTGTCA 61.946 55.000 27.54 27.54 44.95 3.58
5857 6019 0.806884 GACACCGTGACCGTGTCAAA 60.807 55.000 25.04 0.00 44.49 2.69
5858 6020 0.391395 ACACCGTGACCGTGTCAAAA 60.391 50.000 5.28 0.00 44.49 2.44
5881 6043 2.564504 ACGTCTTAACAGGGGGAGTAAC 59.435 50.000 0.00 0.00 0.00 2.50
5885 6047 5.047092 CGTCTTAACAGGGGGAGTAACTTTA 60.047 44.000 0.00 0.00 0.00 1.85
5887 6049 6.877855 GTCTTAACAGGGGGAGTAACTTTAAG 59.122 42.308 0.00 0.00 0.00 1.85
5900 6062 8.068380 GGAGTAACTTTAAGCGCCATATTAAAG 58.932 37.037 25.82 25.82 46.88 1.85
5911 6073 5.360591 CGCCATATTAAAGGTGAGAGAAGT 58.639 41.667 0.00 0.00 37.61 3.01
5920 6082 5.690464 AAGGTGAGAGAAGTAGCATTCAT 57.310 39.130 0.00 0.00 0.00 2.57
5921 6083 5.690464 AGGTGAGAGAAGTAGCATTCATT 57.310 39.130 0.00 0.00 0.00 2.57
5922 6084 5.669477 AGGTGAGAGAAGTAGCATTCATTC 58.331 41.667 0.00 0.00 0.00 2.67
5923 6085 5.188555 AGGTGAGAGAAGTAGCATTCATTCA 59.811 40.000 0.00 0.00 0.00 2.57
5924 6086 5.293079 GGTGAGAGAAGTAGCATTCATTCAC 59.707 44.000 16.22 16.22 40.42 3.18
5925 6087 6.105333 GTGAGAGAAGTAGCATTCATTCACT 58.895 40.000 16.73 6.47 39.34 3.41
5926 6088 6.255453 GTGAGAGAAGTAGCATTCATTCACTC 59.745 42.308 16.73 12.45 39.34 3.51
5927 6089 5.669477 AGAGAAGTAGCATTCATTCACTCC 58.331 41.667 0.00 0.00 0.00 3.85
5928 6090 4.775236 AGAAGTAGCATTCATTCACTCCC 58.225 43.478 0.00 0.00 0.00 4.30
5933 6095 6.904626 AGTAGCATTCATTCACTCCCTTTAT 58.095 36.000 0.00 0.00 0.00 1.40
5966 6135 5.123820 TCATTAGGAAAAGAACGGAGCATTG 59.876 40.000 0.00 0.00 0.00 2.82
5984 6153 4.321230 GCATTGTTACTCCAACTTGAAGGG 60.321 45.833 0.00 0.00 38.05 3.95
5998 6167 7.611855 CCAACTTGAAGGGTCTCAATTATTAGT 59.388 37.037 0.00 0.00 34.86 2.24
6001 6170 7.988028 ACTTGAAGGGTCTCAATTATTAGTAGC 59.012 37.037 0.00 0.00 34.86 3.58
6002 6171 6.827727 TGAAGGGTCTCAATTATTAGTAGCC 58.172 40.000 0.00 0.00 0.00 3.93
6003 6172 6.615726 TGAAGGGTCTCAATTATTAGTAGCCT 59.384 38.462 0.00 0.00 34.99 4.58
6004 6173 7.127339 TGAAGGGTCTCAATTATTAGTAGCCTT 59.873 37.037 12.64 12.64 43.82 4.35
6005 6174 8.562949 AAGGGTCTCAATTATTAGTAGCCTTA 57.437 34.615 11.68 0.00 40.50 2.69
6006 6175 8.743636 AGGGTCTCAATTATTAGTAGCCTTAT 57.256 34.615 0.00 0.00 29.44 1.73
6007 6176 9.172060 AGGGTCTCAATTATTAGTAGCCTTATT 57.828 33.333 0.00 0.00 29.44 1.40
6031 6200 6.566197 AGCAGATAAAACTGACTTTTCCAG 57.434 37.500 0.00 0.00 39.94 3.86
6052 6221 0.328258 CTCCATTTCCTGACCCGGTT 59.672 55.000 0.00 0.00 0.00 4.44
6066 6238 4.402793 TGACCCGGTTTCAGAAATGAAAAA 59.597 37.500 0.00 0.00 39.20 1.94
6067 6239 4.944048 ACCCGGTTTCAGAAATGAAAAAG 58.056 39.130 0.00 3.21 39.20 2.27
6072 6244 7.065204 CCCGGTTTCAGAAATGAAAAAGAAAAA 59.935 33.333 0.00 0.00 39.20 1.94
6073 6245 8.611757 CCGGTTTCAGAAATGAAAAAGAAAAAT 58.388 29.630 5.07 0.00 39.20 1.82
6096 6268 3.881089 ACTACGTGGAAGGAAAAGGTTTG 59.119 43.478 5.70 0.00 0.00 2.93
6127 6299 7.238486 ACACAGTGGGCATATTTAAATTGAA 57.762 32.000 5.91 0.00 0.00 2.69
6128 6300 7.322664 ACACAGTGGGCATATTTAAATTGAAG 58.677 34.615 5.91 0.00 0.00 3.02
6130 6302 8.034215 CACAGTGGGCATATTTAAATTGAAGAA 58.966 33.333 5.91 0.00 0.00 2.52
6131 6303 8.034804 ACAGTGGGCATATTTAAATTGAAGAAC 58.965 33.333 5.91 0.11 0.00 3.01
6132 6304 7.492344 CAGTGGGCATATTTAAATTGAAGAACC 59.508 37.037 5.91 1.78 0.00 3.62
6133 6305 6.761242 GTGGGCATATTTAAATTGAAGAACCC 59.239 38.462 5.91 8.61 0.00 4.11
6134 6306 6.441924 TGGGCATATTTAAATTGAAGAACCCA 59.558 34.615 5.91 10.82 38.73 4.51
6135 6307 6.986231 GGGCATATTTAAATTGAAGAACCCAG 59.014 38.462 5.91 0.00 0.00 4.45
6137 6309 8.257306 GGCATATTTAAATTGAAGAACCCAGAA 58.743 33.333 5.91 0.00 0.00 3.02
6138 6310 9.651913 GCATATTTAAATTGAAGAACCCAGAAA 57.348 29.630 5.91 0.00 0.00 2.52
6153 6334 2.555227 CCAGAAAGCCACCCTGTTATGT 60.555 50.000 0.00 0.00 0.00 2.29
6157 6338 4.039124 AGAAAGCCACCCTGTTATGTTTTG 59.961 41.667 0.00 0.00 0.00 2.44
6159 6340 2.627699 AGCCACCCTGTTATGTTTTGTG 59.372 45.455 0.00 0.00 0.00 3.33
6180 6361 7.439157 TGTGTCGAAAAGAAAAGATCATCAT 57.561 32.000 0.00 0.00 0.00 2.45
6181 6362 7.521529 TGTGTCGAAAAGAAAAGATCATCATC 58.478 34.615 0.00 0.00 0.00 2.92
6182 6363 7.173047 TGTGTCGAAAAGAAAAGATCATCATCA 59.827 33.333 0.00 0.00 0.00 3.07
6183 6364 7.691463 GTGTCGAAAAGAAAAGATCATCATCAG 59.309 37.037 0.00 0.00 0.00 2.90
6184 6365 6.686253 GTCGAAAAGAAAAGATCATCATCAGC 59.314 38.462 0.00 0.00 0.00 4.26
6185 6366 6.372381 TCGAAAAGAAAAGATCATCATCAGCA 59.628 34.615 0.00 0.00 0.00 4.41
6186 6367 7.025365 CGAAAAGAAAAGATCATCATCAGCAA 58.975 34.615 0.00 0.00 0.00 3.91
6187 6368 7.701078 CGAAAAGAAAAGATCATCATCAGCAAT 59.299 33.333 0.00 0.00 0.00 3.56
6198 6379 4.632538 TCATCAGCAATTCAGCATTCAG 57.367 40.909 0.00 0.00 36.85 3.02
6244 6442 3.755112 TCTCGTGTACATTTCCAACCA 57.245 42.857 0.00 0.00 0.00 3.67
6245 6443 4.074627 TCTCGTGTACATTTCCAACCAA 57.925 40.909 0.00 0.00 0.00 3.67
6246 6444 4.647611 TCTCGTGTACATTTCCAACCAAT 58.352 39.130 0.00 0.00 0.00 3.16
6248 6446 4.647611 TCGTGTACATTTCCAACCAATCT 58.352 39.130 0.00 0.00 0.00 2.40
6249 6447 4.454161 TCGTGTACATTTCCAACCAATCTG 59.546 41.667 0.00 0.00 0.00 2.90
6253 6451 2.819608 ACATTTCCAACCAATCTGGACG 59.180 45.455 0.00 0.00 42.76 4.79
6294 6509 4.462483 TGTCCCTTTGACTGGAATTATTGC 59.538 41.667 0.00 0.00 44.75 3.56
6295 6510 4.706962 GTCCCTTTGACTGGAATTATTGCT 59.293 41.667 0.00 0.00 41.03 3.91
6296 6511 5.885912 GTCCCTTTGACTGGAATTATTGCTA 59.114 40.000 0.00 0.00 41.03 3.49
6297 6512 6.038714 GTCCCTTTGACTGGAATTATTGCTAG 59.961 42.308 0.00 0.00 41.03 3.42
6298 6513 5.888161 CCCTTTGACTGGAATTATTGCTAGT 59.112 40.000 0.00 0.36 0.00 2.57
6299 6514 7.054124 CCCTTTGACTGGAATTATTGCTAGTA 58.946 38.462 0.00 0.00 0.00 1.82
6300 6515 7.721399 CCCTTTGACTGGAATTATTGCTAGTAT 59.279 37.037 0.00 0.00 0.00 2.12
6301 6516 9.125026 CCTTTGACTGGAATTATTGCTAGTATT 57.875 33.333 0.00 0.00 0.00 1.89
6302 6517 9.941664 CTTTGACTGGAATTATTGCTAGTATTG 57.058 33.333 0.00 0.00 0.00 1.90
6303 6518 8.450578 TTGACTGGAATTATTGCTAGTATTGG 57.549 34.615 0.00 0.00 0.00 3.16
6339 6556 5.874093 TCTCTCTCAGCCTTCAATTCTTTT 58.126 37.500 0.00 0.00 0.00 2.27
6340 6557 5.936956 TCTCTCTCAGCCTTCAATTCTTTTC 59.063 40.000 0.00 0.00 0.00 2.29
6360 6577 4.735662 TCTTGTTTATTGGACGGTTTCG 57.264 40.909 0.00 0.00 43.02 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.461407 CGATCAATTTCGTGAGATCAGACAT 59.539 40.000 0.00 0.00 41.60 3.06
1 2 4.800471 CGATCAATTTCGTGAGATCAGACA 59.200 41.667 0.00 0.00 41.60 3.41
2 3 5.037385 TCGATCAATTTCGTGAGATCAGAC 58.963 41.667 0.00 0.00 41.60 3.51
3 4 5.248870 TCGATCAATTTCGTGAGATCAGA 57.751 39.130 0.00 0.00 41.60 3.27
4 5 7.201418 CCATATCGATCAATTTCGTGAGATCAG 60.201 40.741 0.00 0.00 41.60 2.90
12 13 9.355215 GTATCTAACCATATCGATCAATTTCGT 57.645 33.333 0.00 0.00 40.03 3.85
34 35 2.543777 TTATCCTTGCAGGCGGTATC 57.456 50.000 0.00 0.00 34.61 2.24
37 38 2.024414 GATTTTATCCTTGCAGGCGGT 58.976 47.619 0.00 0.00 34.61 5.68
124 126 2.882761 TCAGTTCCTCGAGACTTTTCGA 59.117 45.455 15.71 1.13 46.41 3.71
136 138 7.459795 AGAAATTCTTTCCATTCAGTTCCTC 57.540 36.000 0.00 0.00 40.54 3.71
144 146 8.876790 CATGGCTTTTAGAAATTCTTTCCATTC 58.123 33.333 0.00 0.00 40.54 2.67
149 151 7.062255 CCGTTCATGGCTTTTAGAAATTCTTTC 59.938 37.037 0.00 0.00 39.96 2.62
176 178 5.105146 AGGGTCTCAACAAGTATCTAAGCAG 60.105 44.000 0.00 0.00 0.00 4.24
195 197 2.587522 AGAAGGTGAAAAAGCAGGGTC 58.412 47.619 0.00 0.00 0.00 4.46
203 205 0.309612 GCGGCGAAGAAGGTGAAAAA 59.690 50.000 12.98 0.00 0.00 1.94
223 225 5.174395 GCATGAGAGCCGAAGATATGTAAT 58.826 41.667 0.00 0.00 0.00 1.89
242 244 3.075148 GGTGGAGATGATCAGATGCATG 58.925 50.000 2.46 0.00 0.00 4.06
253 255 4.081142 ACATGACAATAACGGTGGAGATGA 60.081 41.667 0.00 0.00 0.00 2.92
302 304 3.874370 TTGGGGATGTGGTCGGGGA 62.874 63.158 0.00 0.00 0.00 4.81
303 305 3.334891 TTGGGGATGTGGTCGGGG 61.335 66.667 0.00 0.00 0.00 5.73
304 306 2.045340 GTTGGGGATGTGGTCGGG 60.045 66.667 0.00 0.00 0.00 5.14
305 307 2.045340 GGTTGGGGATGTGGTCGG 60.045 66.667 0.00 0.00 0.00 4.79
306 308 1.674322 GTGGTTGGGGATGTGGTCG 60.674 63.158 0.00 0.00 0.00 4.79
307 309 1.304134 GGTGGTTGGGGATGTGGTC 60.304 63.158 0.00 0.00 0.00 4.02
308 310 1.660019 TTGGTGGTTGGGGATGTGGT 61.660 55.000 0.00 0.00 0.00 4.16
309 311 0.470833 TTTGGTGGTTGGGGATGTGG 60.471 55.000 0.00 0.00 0.00 4.17
310 312 1.275856 CATTTGGTGGTTGGGGATGTG 59.724 52.381 0.00 0.00 0.00 3.21
311 313 1.132881 ACATTTGGTGGTTGGGGATGT 60.133 47.619 0.00 0.00 0.00 3.06
312 314 1.643310 ACATTTGGTGGTTGGGGATG 58.357 50.000 0.00 0.00 0.00 3.51
313 315 3.774842 ATACATTTGGTGGTTGGGGAT 57.225 42.857 0.00 0.00 0.00 3.85
427 429 3.171528 GGTACCATGACCTATACCTCCC 58.828 54.545 7.15 0.00 36.47 4.30
428 430 3.853207 TGGTACCATGACCTATACCTCC 58.147 50.000 11.60 0.00 40.46 4.30
458 463 0.038892 TGGCTCGAGTGACCGTTAAC 60.039 55.000 15.13 0.00 0.00 2.01
465 470 2.029844 GGTGCTTGGCTCGAGTGAC 61.030 63.158 15.13 5.65 0.00 3.67
488 494 1.003233 GTGTGTCAAGAGGAGGGGC 60.003 63.158 0.00 0.00 0.00 5.80
560 566 1.098050 GGTGTTGCAGGGATCATCAC 58.902 55.000 0.00 0.00 34.88 3.06
574 581 2.360350 CTGGCTGGCGATGGTGTT 60.360 61.111 0.00 0.00 0.00 3.32
844 862 2.125106 CACCAACCCCGCTAGCTC 60.125 66.667 13.93 0.00 0.00 4.09
876 894 3.471806 GGTCGCCTTCCCCCTCTC 61.472 72.222 0.00 0.00 0.00 3.20
1082 1103 3.941483 ACTGTAAGACTGCCATTACATGC 59.059 43.478 0.00 0.00 40.19 4.06
1261 1283 7.506114 ACCAAGAAAAAGAATCCCCTAAAAAC 58.494 34.615 0.00 0.00 0.00 2.43
1331 1353 3.346315 TGTGGGCTATGTTGAATCTGTG 58.654 45.455 0.00 0.00 0.00 3.66
1350 1376 2.870411 GAGTTCAGTGTAAGGCGTTTGT 59.130 45.455 0.00 0.00 0.00 2.83
1378 1404 3.587061 TCCTGAAAGCATTCCTTGTCCTA 59.413 43.478 0.00 0.00 34.49 2.94
1396 1422 0.040067 GAAACTGCGTTTGGCTCCTG 60.040 55.000 10.61 0.00 44.05 3.86
1423 1449 2.621668 GCTGGGCTCCTAACCAAAATCT 60.622 50.000 0.00 0.00 36.09 2.40
1425 1451 1.359130 AGCTGGGCTCCTAACCAAAAT 59.641 47.619 0.00 0.00 36.09 1.82
1531 1560 5.124645 AGAATGATTCAAGCTTGCTAGAGG 58.875 41.667 21.99 0.00 0.00 3.69
1565 1594 1.135112 GCACATCCACCGGAAATTTCC 60.135 52.381 24.90 24.90 44.05 3.13
1574 1603 4.457496 AGGAGCGCACATCCACCG 62.457 66.667 11.47 0.00 39.47 4.94
1663 1695 2.158623 TCACATGGAAAAGCTGGTGACT 60.159 45.455 0.00 0.00 30.99 3.41
1765 1799 2.369860 ACTGCATATCGACCATCCACAT 59.630 45.455 0.00 0.00 0.00 3.21
1771 1805 4.282957 AGATCTCAACTGCATATCGACCAT 59.717 41.667 0.00 0.00 0.00 3.55
1772 1806 3.638627 AGATCTCAACTGCATATCGACCA 59.361 43.478 0.00 0.00 0.00 4.02
1838 1872 3.320541 TCCATTTTTCCTTGACAACGCAT 59.679 39.130 0.00 0.00 0.00 4.73
1930 1965 9.734620 CAGTTTATGTCTTGATGTTCTCAAAAA 57.265 29.630 0.00 0.00 43.20 1.94
1943 1978 3.853831 TGCATGCCAGTTTATGTCTTG 57.146 42.857 16.68 0.00 0.00 3.02
1972 2009 6.478016 TGAACATCTGAATCGAATTGCTCTAG 59.522 38.462 0.00 0.00 0.00 2.43
2038 2075 5.070446 TGGCCAGATCTTAGGTATGTAACTG 59.930 44.000 0.00 0.00 0.00 3.16
2056 2093 3.256631 AGCACTTCTGTAAATTTGGCCAG 59.743 43.478 5.11 4.67 0.00 4.85
2059 2096 4.773323 AGAGCACTTCTGTAAATTTGGC 57.227 40.909 0.00 0.00 33.93 4.52
2165 2213 7.775093 AGTGTATTCAAGCAAATGATAGGCTTA 59.225 33.333 0.00 0.00 45.42 3.09
2267 2316 6.851222 ATCTCATAAACTATTCGGTGCAAG 57.149 37.500 0.00 0.00 0.00 4.01
2419 2469 0.179032 TTTCCGCAGCCTCTTTCACA 60.179 50.000 0.00 0.00 0.00 3.58
2720 2770 4.600062 ACCCTTCTTTGAGTTGAAAGTGT 58.400 39.130 0.00 0.00 34.95 3.55
2930 2982 6.871492 ACGTTAGGGCCAAAAATCAAATTAAG 59.129 34.615 6.18 0.00 0.00 1.85
3145 3197 7.827701 TGTGACCAAAGTGTACAATACAAAAA 58.172 30.769 0.00 0.00 40.93 1.94
3146 3198 7.392494 TGTGACCAAAGTGTACAATACAAAA 57.608 32.000 0.00 0.00 40.93 2.44
3147 3199 7.392494 TTGTGACCAAAGTGTACAATACAAA 57.608 32.000 0.00 0.00 40.93 2.83
3262 3327 6.899114 AGAAATTTAAGATGTTCCACGACAC 58.101 36.000 0.00 0.00 31.30 3.67
3470 3535 3.237268 TGAAATGTAAGGCCAGGTTGT 57.763 42.857 5.01 0.00 0.00 3.32
3661 3726 7.186804 ACGTAAGAAACAAATTGTCAGAACAG 58.813 34.615 0.00 0.00 43.62 3.16
3669 3734 7.540299 TCCAGAAAACGTAAGAAACAAATTGT 58.460 30.769 0.00 0.00 43.62 2.71
3704 3769 4.487948 CTTGTGGGTTCATAGCACAAATG 58.512 43.478 0.00 0.00 35.68 2.32
3773 3838 3.104512 ACGAGGAGGGAAACATCATGTA 58.895 45.455 0.00 0.00 44.67 2.29
3786 3851 2.737252 GTTTCAAACTGCTACGAGGAGG 59.263 50.000 0.00 0.00 38.06 4.30
3866 3931 1.193874 GGCAACGGTTGTCTTAGTTCG 59.806 52.381 20.92 0.00 31.13 3.95
3957 4022 3.340928 TGATCATCTTGTCTTGGCACAG 58.659 45.455 0.00 0.00 42.39 3.66
4174 4239 3.901222 ACATTTTTCCTTTACCAGGGTGG 59.099 43.478 0.06 0.00 44.12 4.61
4213 4278 8.827177 TTAAGTGTAGTACAGAACAAAGGATG 57.173 34.615 2.39 0.00 0.00 3.51
4245 4310 4.130118 CGCCTAGTAATGCTGGAAAATCT 58.870 43.478 0.00 0.00 0.00 2.40
4626 4695 3.726557 TTTGCTCTGATGACCAAGGAT 57.273 42.857 0.00 0.00 0.00 3.24
4709 4778 9.912634 ATTTTTATGCGGAAATACAAGATATGG 57.087 29.630 0.00 0.00 0.00 2.74
4780 4849 6.835488 AGCACCACATCCATTAAATGTAGATT 59.165 34.615 0.00 0.00 35.62 2.40
4953 5055 9.474313 ACAAATGGAAAGCCTTATAGATGTAAA 57.526 29.630 0.00 0.00 34.31 2.01
5046 5148 8.685838 TTGCCAGTAGTCAGTAAACTAAAATT 57.314 30.769 0.00 0.00 33.68 1.82
5047 5149 8.154856 TCTTGCCAGTAGTCAGTAAACTAAAAT 58.845 33.333 0.00 0.00 33.68 1.82
5131 5234 3.367910 GCACCTTCACAGAACAAAACCAA 60.368 43.478 0.00 0.00 0.00 3.67
5223 5326 1.451504 CTGGTGTTCACTGCCTCCA 59.548 57.895 2.98 0.00 0.00 3.86
5245 5348 4.783621 TGCGCCCTGTGAGATGCC 62.784 66.667 4.18 0.00 0.00 4.40
5281 5384 2.423577 GCTTTCTTGGCGTCTTTAGGA 58.576 47.619 0.00 0.00 0.00 2.94
5347 5450 1.522668 TCATTCAGCTCACGGGTTTG 58.477 50.000 0.00 0.00 0.00 2.93
5407 5510 2.477375 GGTTTGTACAGCGACATTCGAA 59.523 45.455 0.00 0.00 43.74 3.71
5496 5599 1.030457 AAACGACCGAGTGACTGACT 58.970 50.000 0.00 0.00 37.76 3.41
5520 5623 1.821216 AATTTGTTCGTCGAGGGCAT 58.179 45.000 5.12 0.00 0.00 4.40
5521 5624 1.265635 CAAATTTGTTCGTCGAGGGCA 59.734 47.619 10.15 2.46 0.00 5.36
5522 5625 1.533731 TCAAATTTGTTCGTCGAGGGC 59.466 47.619 17.47 0.00 0.00 5.19
5536 5639 4.098349 TGCAACAAGTTCAGCTCTCAAATT 59.902 37.500 0.00 0.00 0.00 1.82
5554 5657 4.440127 CCAGCGGGGCAATGCAAC 62.440 66.667 7.79 0.00 0.00 4.17
5669 5772 3.731652 TTTGCAGAACTCAAACCATGG 57.268 42.857 11.19 11.19 0.00 3.66
5683 5786 5.551760 AAGATACTCCGACAAATTTGCAG 57.448 39.130 18.12 11.66 0.00 4.41
5710 5814 1.153568 CATGGTCGCCACGTCTGAT 60.154 57.895 0.50 0.00 35.80 2.90
5722 5827 1.692411 GCCCAACCCTTATCATGGTC 58.308 55.000 0.00 0.00 32.40 4.02
5733 5838 0.331616 ATGTAGAACTGGCCCAACCC 59.668 55.000 0.00 0.00 37.83 4.11
5736 5841 3.450904 ACTAGATGTAGAACTGGCCCAA 58.549 45.455 3.49 0.00 0.00 4.12
5808 5970 9.739276 ACATATTTTACATTTTGAGACAGAGGA 57.261 29.630 0.00 0.00 0.00 3.71
5833 5995 1.519898 ACGGTCACGGTGTCAACAC 60.520 57.895 8.17 4.67 46.48 3.32
5836 5998 1.227031 GACACGGTCACGGTGTCAA 60.227 57.895 32.70 0.00 43.74 3.18
5838 6000 0.806884 TTTGACACGGTCACGGTGTC 60.807 55.000 31.64 31.64 42.60 3.67
5840 6002 0.727970 TTTTTGACACGGTCACGGTG 59.272 50.000 13.67 13.67 42.60 4.94
5857 6019 2.440627 ACTCCCCCTGTTAAGACGTTTT 59.559 45.455 0.00 0.00 0.00 2.43
5858 6020 2.052468 ACTCCCCCTGTTAAGACGTTT 58.948 47.619 0.00 0.00 0.00 3.60
5860 6022 2.564504 GTTACTCCCCCTGTTAAGACGT 59.435 50.000 0.00 0.00 0.00 4.34
5861 6023 2.830321 AGTTACTCCCCCTGTTAAGACG 59.170 50.000 0.00 0.00 0.00 4.18
5863 6025 6.521255 GCTTAAAGTTACTCCCCCTGTTAAGA 60.521 42.308 12.08 0.00 31.84 2.10
5864 6026 5.646793 GCTTAAAGTTACTCCCCCTGTTAAG 59.353 44.000 6.26 6.26 32.83 1.85
5865 6027 5.563592 GCTTAAAGTTACTCCCCCTGTTAA 58.436 41.667 0.00 0.00 0.00 2.01
5866 6028 4.322953 CGCTTAAAGTTACTCCCCCTGTTA 60.323 45.833 0.00 0.00 0.00 2.41
5867 6029 3.558533 CGCTTAAAGTTACTCCCCCTGTT 60.559 47.826 0.00 0.00 0.00 3.16
5869 6031 2.629051 CGCTTAAAGTTACTCCCCCTG 58.371 52.381 0.00 0.00 0.00 4.45
5870 6032 1.065636 GCGCTTAAAGTTACTCCCCCT 60.066 52.381 0.00 0.00 0.00 4.79
5875 6037 8.068380 CCTTTAATATGGCGCTTAAAGTTACTC 58.932 37.037 25.46 2.78 40.71 2.59
5881 6043 6.260050 TCTCACCTTTAATATGGCGCTTAAAG 59.740 38.462 22.88 22.88 41.42 1.85
5885 6047 4.130118 CTCTCACCTTTAATATGGCGCTT 58.870 43.478 7.64 0.00 0.00 4.68
5887 6049 3.728845 TCTCTCACCTTTAATATGGCGC 58.271 45.455 0.00 0.00 0.00 6.53
5900 6062 5.293079 GTGAATGAATGCTACTTCTCTCACC 59.707 44.000 12.55 0.00 34.66 4.02
5911 6073 8.593945 AAAATAAAGGGAGTGAATGAATGCTA 57.406 30.769 0.00 0.00 0.00 3.49
5920 6082 8.884124 ATGAATGAGAAAATAAAGGGAGTGAA 57.116 30.769 0.00 0.00 0.00 3.18
5921 6083 8.884124 AATGAATGAGAAAATAAAGGGAGTGA 57.116 30.769 0.00 0.00 0.00 3.41
5923 6085 9.413734 CCTAATGAATGAGAAAATAAAGGGAGT 57.586 33.333 0.00 0.00 0.00 3.85
5924 6086 9.632638 TCCTAATGAATGAGAAAATAAAGGGAG 57.367 33.333 0.00 0.00 0.00 4.30
5925 6087 9.989296 TTCCTAATGAATGAGAAAATAAAGGGA 57.011 29.630 0.00 0.00 0.00 4.20
5933 6095 8.296713 CCGTTCTTTTCCTAATGAATGAGAAAA 58.703 33.333 0.00 0.00 37.30 2.29
5966 6135 4.202326 TGAGACCCTTCAAGTTGGAGTAAC 60.202 45.833 10.36 1.27 39.65 2.50
5977 6146 7.127339 AGGCTACTAATAATTGAGACCCTTCAA 59.873 37.037 0.00 0.00 41.00 2.69
5998 6167 8.705594 AGTCAGTTTTATCTGCTAATAAGGCTA 58.294 33.333 0.00 0.00 35.63 3.93
6004 6173 9.733556 TGGAAAAGTCAGTTTTATCTGCTAATA 57.266 29.630 0.00 0.00 38.54 0.98
6005 6174 8.635765 TGGAAAAGTCAGTTTTATCTGCTAAT 57.364 30.769 0.00 0.00 38.54 1.73
6006 6175 7.174946 CCTGGAAAAGTCAGTTTTATCTGCTAA 59.825 37.037 0.00 0.00 38.54 3.09
6007 6176 6.655003 CCTGGAAAAGTCAGTTTTATCTGCTA 59.345 38.462 0.00 0.00 38.54 3.49
6008 6177 5.474876 CCTGGAAAAGTCAGTTTTATCTGCT 59.525 40.000 0.00 0.00 38.54 4.24
6009 6178 5.703876 CCTGGAAAAGTCAGTTTTATCTGC 58.296 41.667 0.00 0.00 38.54 4.26
6031 6200 1.452108 CGGGTCAGGAAATGGAGCC 60.452 63.158 0.00 0.00 45.80 4.70
6066 6238 7.174426 CCTTTTCCTTCCACGTAGTATTTTTCT 59.826 37.037 0.00 0.00 41.61 2.52
6067 6239 7.040892 ACCTTTTCCTTCCACGTAGTATTTTTC 60.041 37.037 0.00 0.00 41.61 2.29
6072 6244 5.494390 AACCTTTTCCTTCCACGTAGTAT 57.506 39.130 0.00 0.00 41.61 2.12
6073 6245 4.961438 AACCTTTTCCTTCCACGTAGTA 57.039 40.909 0.00 0.00 41.61 1.82
6075 6247 3.252458 CCAAACCTTTTCCTTCCACGTAG 59.748 47.826 0.00 0.00 0.00 3.51
6076 6248 3.117963 TCCAAACCTTTTCCTTCCACGTA 60.118 43.478 0.00 0.00 0.00 3.57
6077 6249 2.028876 CCAAACCTTTTCCTTCCACGT 58.971 47.619 0.00 0.00 0.00 4.49
6078 6250 2.303175 TCCAAACCTTTTCCTTCCACG 58.697 47.619 0.00 0.00 0.00 4.94
6079 6251 3.006859 CCATCCAAACCTTTTCCTTCCAC 59.993 47.826 0.00 0.00 0.00 4.02
6080 6252 3.238597 CCATCCAAACCTTTTCCTTCCA 58.761 45.455 0.00 0.00 0.00 3.53
6081 6253 2.567169 CCCATCCAAACCTTTTCCTTCC 59.433 50.000 0.00 0.00 0.00 3.46
6096 6268 2.044946 GCCCACTGTGTCCCATCC 60.045 66.667 7.08 0.00 0.00 3.51
6108 6280 6.761242 GGGTTCTTCAATTTAAATATGCCCAC 59.239 38.462 0.01 0.00 0.00 4.61
6111 6283 7.781056 TCTGGGTTCTTCAATTTAAATATGCC 58.219 34.615 0.01 0.00 0.00 4.40
6112 6284 9.651913 TTTCTGGGTTCTTCAATTTAAATATGC 57.348 29.630 0.01 0.00 0.00 3.14
6127 6299 1.068352 AGGGTGGCTTTCTGGGTTCT 61.068 55.000 0.00 0.00 0.00 3.01
6128 6300 0.895559 CAGGGTGGCTTTCTGGGTTC 60.896 60.000 0.00 0.00 0.00 3.62
6130 6302 1.655114 AACAGGGTGGCTTTCTGGGT 61.655 55.000 0.00 0.00 33.19 4.51
6131 6303 0.404040 TAACAGGGTGGCTTTCTGGG 59.596 55.000 0.00 0.00 33.19 4.45
6132 6304 2.094675 CATAACAGGGTGGCTTTCTGG 58.905 52.381 0.00 0.00 33.19 3.86
6133 6305 2.795329 ACATAACAGGGTGGCTTTCTG 58.205 47.619 0.00 0.00 34.91 3.02
6134 6306 3.525800 AACATAACAGGGTGGCTTTCT 57.474 42.857 0.00 0.00 0.00 2.52
6135 6307 4.202212 ACAAAACATAACAGGGTGGCTTTC 60.202 41.667 0.00 0.00 0.00 2.62
6137 6309 3.069443 CACAAAACATAACAGGGTGGCTT 59.931 43.478 0.00 0.00 0.00 4.35
6138 6310 2.627699 CACAAAACATAACAGGGTGGCT 59.372 45.455 0.00 0.00 0.00 4.75
6153 6334 8.187480 TGATGATCTTTTCTTTTCGACACAAAA 58.813 29.630 0.00 0.00 0.00 2.44
6157 6338 7.521529 TGATGATGATCTTTTCTTTTCGACAC 58.478 34.615 0.00 0.00 0.00 3.67
6159 6340 6.686253 GCTGATGATGATCTTTTCTTTTCGAC 59.314 38.462 0.00 0.00 0.00 4.20
6180 6361 2.933495 GCTGAATGCTGAATTGCTGA 57.067 45.000 0.00 0.00 38.95 4.26
6198 6379 1.074752 CAAGAAGAAGAGGCGACAGC 58.925 55.000 0.00 0.00 44.18 4.40
6253 6451 0.103937 CAGCGAGAGGGATGAACTCC 59.896 60.000 0.00 0.00 44.11 3.85
6257 6468 1.330655 GGGACAGCGAGAGGGATGAA 61.331 60.000 0.00 0.00 0.00 2.57
6294 6509 6.666417 AGATTTCTACGCGTACCAATACTAG 58.334 40.000 16.41 3.99 0.00 2.57
6295 6510 6.484643 AGAGATTTCTACGCGTACCAATACTA 59.515 38.462 16.41 0.00 0.00 1.82
6296 6511 5.298777 AGAGATTTCTACGCGTACCAATACT 59.701 40.000 16.41 14.29 0.00 2.12
6297 6512 5.517904 AGAGATTTCTACGCGTACCAATAC 58.482 41.667 16.41 12.60 0.00 1.89
6298 6513 5.530171 AGAGAGATTTCTACGCGTACCAATA 59.470 40.000 16.41 0.00 32.53 1.90
6299 6514 4.338682 AGAGAGATTTCTACGCGTACCAAT 59.661 41.667 16.41 15.53 32.53 3.16
6300 6515 3.693085 AGAGAGATTTCTACGCGTACCAA 59.307 43.478 16.41 11.21 32.53 3.67
6301 6516 3.276857 AGAGAGATTTCTACGCGTACCA 58.723 45.455 16.41 1.46 32.53 3.25
6302 6517 3.311871 TGAGAGAGATTTCTACGCGTACC 59.688 47.826 16.41 2.53 32.53 3.34
6303 6518 4.520078 CTGAGAGAGATTTCTACGCGTAC 58.480 47.826 16.41 5.20 32.53 3.67
6339 6556 4.024725 CACGAAACCGTCCAATAAACAAGA 60.025 41.667 0.00 0.00 38.35 3.02
6340 6557 4.215965 CACGAAACCGTCCAATAAACAAG 58.784 43.478 0.00 0.00 38.35 3.16


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

AutoCloner maintained by Alex Coulton.