Multiple sequence alignment - TraesCS3B01G397200

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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 TraesCS3B01G397200 chr3B 100.000 5017 0 0 1 5017 627711400 627716416 0.000000e+00 9265.0
1 TraesCS3B01G397200 chr3D 90.750 4335 212 76 1 4259 472113135 472117356 0.000000e+00 5609.0
2 TraesCS3B01G397200 chr3D 90.339 590 37 12 4264 4843 472118026 472118605 0.000000e+00 756.0
3 TraesCS3B01G397200 chr3D 93.976 83 5 0 4845 4927 472118702 472118620 5.270000e-25 126.0
4 TraesCS3B01G397200 chr3D 95.238 63 3 0 4955 5017 472119536 472119598 3.200000e-17 100.0
5 TraesCS3B01G397200 chr3A 89.501 2486 119 56 2032 4454 614678367 614680773 0.000000e+00 3014.0
6 TraesCS3B01G397200 chr3A 89.410 2068 116 42 18 2040 614676332 614678341 0.000000e+00 2510.0
7 TraesCS3B01G397200 chr3A 91.830 306 13 6 4453 4755 614680943 614681239 2.790000e-112 416.0
8 TraesCS3B01G397200 chr3A 76.923 156 30 5 2907 3059 614691258 614691410 3.220000e-12 84.2
9 TraesCS3B01G397200 chr1B 75.875 257 53 7 3528 3778 39588283 39588030 6.820000e-24 122.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G397200 chr3B 627711400 627716416 5016 False 9265 9265 100.000 1 5017 1 chr3B.!!$F1 5016
1 TraesCS3B01G397200 chr3D 472113135 472119598 6463 False 2155 5609 92.109 1 5017 3 chr3D.!!$F1 5016
2 TraesCS3B01G397200 chr3A 614676332 614681239 4907 False 1980 3014 90.247 18 4755 3 chr3A.!!$F2 4737

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
599 616 0.314935 CGGCACTGCAAATCAAACCT 59.685 50.0 2.82 0.00 0.00 3.50 F
1489 1568 0.608856 TGTAATGCTGCCACCAGGTG 60.609 55.0 13.35 13.35 39.54 4.00 F
1962 2056 0.037975 CACCGCCGTTAACTGTAGGT 60.038 55.0 3.71 8.47 0.00 3.08 F
2186 2312 0.249911 AAGACAACTGAGGTCGGCAC 60.250 55.0 0.00 0.00 40.20 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1831 0.106167 AGGCTAGATGACAGCGGGTA 60.106 55.0 0.00 0.00 40.05 3.69 R
2992 3138 0.037697 TGTAGTTGGCCGTGTAGCAG 60.038 55.0 0.00 0.00 0.00 4.24 R
3226 3372 0.236711 TCGTCGAGTCCGAGTTGTTC 59.763 55.0 0.00 0.00 46.52 3.18 R
4043 4197 0.376152 CTTGCACGCAGGATCATGAC 59.624 55.0 12.39 1.59 0.00 3.06 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
39 46 2.242043 CAGCCCAACAGGAGATTTTGT 58.758 47.619 0.00 0.00 38.24 2.83
41 48 3.070015 CAGCCCAACAGGAGATTTTGTTT 59.930 43.478 0.00 0.00 38.24 2.83
46 53 4.739716 CCAACAGGAGATTTTGTTTGTTCG 59.260 41.667 0.00 0.00 35.46 3.95
53 60 5.451381 GGAGATTTTGTTTGTTCGGAAAGGT 60.451 40.000 0.00 0.00 0.00 3.50
92 99 1.613437 CCTCCATTTTTGTCCGCTGTT 59.387 47.619 0.00 0.00 0.00 3.16
106 113 0.580104 GCTGTTGACGTGTTAAGCGT 59.420 50.000 0.00 4.90 45.86 5.07
112 119 1.468127 TGACGTGTTAAGCGTATCCGA 59.532 47.619 0.00 0.00 43.04 4.55
147 154 2.574006 TGCAAGTGCTCTCTGGATTT 57.426 45.000 4.69 0.00 42.66 2.17
148 155 3.701205 TGCAAGTGCTCTCTGGATTTA 57.299 42.857 4.69 0.00 42.66 1.40
171 179 0.471022 ATTTGGGACCAAACCGCCTT 60.471 50.000 17.99 0.00 46.80 4.35
210 218 3.190535 AGTGTCGGACCAAATTATTGTGC 59.809 43.478 5.55 0.00 34.60 4.57
212 220 3.057876 TGTCGGACCAAATTATTGTGCAC 60.058 43.478 10.75 10.75 34.60 4.57
230 238 4.266029 GTGCACATGACAACAACTTCAAAG 59.734 41.667 13.17 0.00 0.00 2.77
276 284 1.664965 GTGCGGATGGGATACTCGC 60.665 63.158 0.00 0.00 45.60 5.03
316 324 3.374678 CCTCAGCTTTGAGAGATGCTTTC 59.625 47.826 4.59 0.00 41.55 2.62
323 331 5.633830 TTTGAGAGATGCTTTCATTGACC 57.366 39.130 0.00 0.00 31.96 4.02
328 336 4.219288 AGAGATGCTTTCATTGACCCAAAC 59.781 41.667 0.00 0.00 31.96 2.93
513 525 2.559330 GGCATTTTTCGCCGACGT 59.441 55.556 0.00 0.00 40.35 4.34
532 544 3.545574 TCGCCATATGCCAGCCGA 61.546 61.111 0.00 0.00 36.24 5.54
597 614 2.132740 TTCGGCACTGCAAATCAAAC 57.867 45.000 2.82 0.00 0.00 2.93
599 616 0.314935 CGGCACTGCAAATCAAACCT 59.685 50.000 2.82 0.00 0.00 3.50
609 626 4.520874 TGCAAATCAAACCTATCCACGAAA 59.479 37.500 0.00 0.00 0.00 3.46
610 627 4.857037 GCAAATCAAACCTATCCACGAAAC 59.143 41.667 0.00 0.00 0.00 2.78
621 638 6.157211 CCTATCCACGAAACGAGCTAATTAT 58.843 40.000 0.00 0.00 0.00 1.28
639 656 5.661056 ATTATTCAGAGGACTGTCGACAA 57.339 39.130 20.49 1.01 43.81 3.18
759 776 1.683790 CCAGAAGCTTTACGTCGCGG 61.684 60.000 6.13 0.00 0.00 6.46
891 913 5.701290 CCTATCGTGTTTCTTGGAAGACTTT 59.299 40.000 0.00 0.00 34.13 2.66
896 918 4.096382 GTGTTTCTTGGAAGACTTTGAGCA 59.904 41.667 0.00 0.00 34.13 4.26
912 934 2.263153 GCAATACAAGTTGCCCGGT 58.737 52.632 1.81 0.00 46.69 5.28
985 1016 1.000145 GAATCGTCTTCAACCTCGGC 59.000 55.000 0.00 0.00 0.00 5.54
1178 1216 8.768955 CATAGATAGAAGCTTTTCGCAATAAGT 58.231 33.333 0.00 0.00 42.61 2.24
1188 1226 5.779806 TTTCGCAATAAGTGAACTAGAGC 57.220 39.130 0.00 0.00 45.79 4.09
1267 1311 3.515502 TGCTTGACTTACAGTGGCTATCT 59.484 43.478 0.00 0.00 0.00 1.98
1284 1328 6.183360 TGGCTATCTAGAATTCAGAGTCAACC 60.183 42.308 8.44 6.73 0.00 3.77
1347 1424 9.702253 AGATAAAGTTGATAGTTCTGTAGGAGA 57.298 33.333 0.00 0.00 0.00 3.71
1348 1425 9.959749 GATAAAGTTGATAGTTCTGTAGGAGAG 57.040 37.037 0.00 0.00 30.18 3.20
1349 1426 7.784470 AAAGTTGATAGTTCTGTAGGAGAGT 57.216 36.000 0.00 0.00 30.18 3.24
1350 1427 7.784470 AAGTTGATAGTTCTGTAGGAGAGTT 57.216 36.000 0.00 0.00 30.18 3.01
1351 1428 7.164230 AGTTGATAGTTCTGTAGGAGAGTTG 57.836 40.000 0.00 0.00 30.18 3.16
1352 1429 6.948886 AGTTGATAGTTCTGTAGGAGAGTTGA 59.051 38.462 0.00 0.00 30.18 3.18
1353 1430 7.617723 AGTTGATAGTTCTGTAGGAGAGTTGAT 59.382 37.037 0.00 0.00 30.18 2.57
1354 1431 8.904834 GTTGATAGTTCTGTAGGAGAGTTGATA 58.095 37.037 0.00 0.00 30.18 2.15
1355 1432 8.684386 TGATAGTTCTGTAGGAGAGTTGATAG 57.316 38.462 0.00 0.00 30.18 2.08
1356 1433 8.275758 TGATAGTTCTGTAGGAGAGTTGATAGT 58.724 37.037 0.00 0.00 30.18 2.12
1357 1434 8.685838 ATAGTTCTGTAGGAGAGTTGATAGTC 57.314 38.462 0.00 0.00 30.18 2.59
1358 1435 6.486056 AGTTCTGTAGGAGAGTTGATAGTCA 58.514 40.000 0.00 0.00 30.18 3.41
1359 1436 7.122715 AGTTCTGTAGGAGAGTTGATAGTCAT 58.877 38.462 0.00 0.00 30.18 3.06
1360 1437 6.951062 TCTGTAGGAGAGTTGATAGTCATG 57.049 41.667 0.00 0.00 0.00 3.07
1361 1438 5.300539 TCTGTAGGAGAGTTGATAGTCATGC 59.699 44.000 0.00 0.00 0.00 4.06
1362 1439 4.956075 TGTAGGAGAGTTGATAGTCATGCA 59.044 41.667 0.00 0.00 0.00 3.96
1363 1440 4.669206 AGGAGAGTTGATAGTCATGCAG 57.331 45.455 0.00 0.00 0.00 4.41
1364 1441 3.387374 AGGAGAGTTGATAGTCATGCAGG 59.613 47.826 0.00 0.00 0.00 4.85
1365 1442 3.386078 GGAGAGTTGATAGTCATGCAGGA 59.614 47.826 0.00 0.00 0.00 3.86
1366 1443 4.367450 GAGAGTTGATAGTCATGCAGGAC 58.633 47.826 23.39 23.39 38.08 3.85
1409 1486 9.625747 TTCATGTATATGCCACAAAAATCTCTA 57.374 29.630 0.00 0.00 34.21 2.43
1412 1489 9.632638 ATGTATATGCCACAAAAATCTCTACTT 57.367 29.630 0.00 0.00 0.00 2.24
1421 1500 7.360101 CCACAAAAATCTCTACTTGTACTTCGG 60.360 40.741 0.00 0.00 31.00 4.30
1429 1508 3.655276 ACTTGTACTTCGGAATCGTGT 57.345 42.857 0.00 0.00 37.69 4.49
1458 1537 4.779475 CAAGCCCTTGTCTGACGT 57.221 55.556 2.98 0.00 35.92 4.34
1472 1551 2.693591 TCTGACGTCTTTGTTCCTCTGT 59.306 45.455 17.92 0.00 0.00 3.41
1489 1568 0.608856 TGTAATGCTGCCACCAGGTG 60.609 55.000 13.35 13.35 39.54 4.00
1504 1583 2.232941 CCAGGTGCAGAGCATGAAAATT 59.767 45.455 0.00 0.00 41.91 1.82
1534 1613 2.232399 TGCAACAGCACTGACATCATT 58.768 42.857 4.31 0.00 32.31 2.57
1713 1803 3.924686 TCTTCGAAAAACATAGAGCCGTC 59.075 43.478 0.00 0.00 0.00 4.79
1841 1935 4.380531 CTGACAGGCAGTTTAGTTTCTCA 58.619 43.478 0.00 0.00 39.85 3.27
1842 1936 4.380531 TGACAGGCAGTTTAGTTTCTCAG 58.619 43.478 0.00 0.00 0.00 3.35
1843 1937 4.100963 TGACAGGCAGTTTAGTTTCTCAGA 59.899 41.667 0.00 0.00 0.00 3.27
1927 2021 4.453480 AGGGAAGGTTCTGAAAATGACA 57.547 40.909 0.00 0.00 0.00 3.58
1962 2056 0.037975 CACCGCCGTTAACTGTAGGT 60.038 55.000 3.71 8.47 0.00 3.08
1973 2067 5.336531 CGTTAACTGTAGGTGACCTCATCTT 60.337 44.000 7.77 0.00 38.47 2.40
1992 2086 3.330192 ACACCCTCCAAGTGTGCA 58.670 55.556 0.00 0.00 46.43 4.57
2028 2122 3.213249 ACGACCAAGTCTCGTCATTAC 57.787 47.619 0.00 0.00 40.31 1.89
2029 2123 2.555325 ACGACCAAGTCTCGTCATTACA 59.445 45.455 0.00 0.00 40.31 2.41
2030 2124 3.172050 CGACCAAGTCTCGTCATTACAG 58.828 50.000 2.06 0.00 0.00 2.74
2035 2161 4.857588 CCAAGTCTCGTCATTACAGTACAC 59.142 45.833 0.00 0.00 0.00 2.90
2092 2218 2.853235 AACAGCTAAACTTACCGGCT 57.147 45.000 0.00 0.00 0.00 5.52
2095 2221 2.093816 ACAGCTAAACTTACCGGCTACC 60.094 50.000 0.00 0.00 0.00 3.18
2096 2222 1.483827 AGCTAAACTTACCGGCTACCC 59.516 52.381 0.00 0.00 0.00 3.69
2097 2223 1.207811 GCTAAACTTACCGGCTACCCA 59.792 52.381 0.00 0.00 0.00 4.51
2098 2224 2.158856 GCTAAACTTACCGGCTACCCAT 60.159 50.000 0.00 0.00 0.00 4.00
2099 2225 3.683564 GCTAAACTTACCGGCTACCCATT 60.684 47.826 0.00 0.00 0.00 3.16
2100 2226 2.704464 AACTTACCGGCTACCCATTC 57.296 50.000 0.00 0.00 0.00 2.67
2102 2228 1.910671 ACTTACCGGCTACCCATTCAA 59.089 47.619 0.00 0.00 0.00 2.69
2106 2232 1.005450 ACCGGCTACCCATTCAAACAT 59.995 47.619 0.00 0.00 0.00 2.71
2108 2234 3.117663 ACCGGCTACCCATTCAAACATAT 60.118 43.478 0.00 0.00 0.00 1.78
2111 2237 6.013206 ACCGGCTACCCATTCAAACATATATA 60.013 38.462 0.00 0.00 0.00 0.86
2112 2238 7.054124 CCGGCTACCCATTCAAACATATATAT 58.946 38.462 0.00 0.00 0.00 0.86
2113 2239 7.556275 CCGGCTACCCATTCAAACATATATATT 59.444 37.037 0.00 0.00 0.00 1.28
2114 2240 8.956426 CGGCTACCCATTCAAACATATATATTT 58.044 33.333 0.00 0.00 0.00 1.40
2177 2303 1.768275 TCCTCTGGCAAAGACAACTGA 59.232 47.619 0.00 0.00 0.00 3.41
2186 2312 0.249911 AAGACAACTGAGGTCGGCAC 60.250 55.000 0.00 0.00 40.20 5.01
2192 2318 1.339097 ACTGAGGTCGGCACTAAGTT 58.661 50.000 0.00 0.00 0.00 2.66
2223 2349 1.078848 ACTTGACTCTGCCGCCATC 60.079 57.895 0.00 0.00 0.00 3.51
2230 2356 1.224075 CTCTGCCGCCATCTGTTATG 58.776 55.000 0.00 0.00 0.00 1.90
2250 2378 3.620488 TGATTTGTGGTGCTAGGGATTC 58.380 45.455 0.00 0.00 0.00 2.52
2251 2379 3.010027 TGATTTGTGGTGCTAGGGATTCA 59.990 43.478 0.00 0.00 0.00 2.57
2255 2383 4.046286 TGTGGTGCTAGGGATTCAAATT 57.954 40.909 0.00 0.00 0.00 1.82
2256 2384 4.415596 TGTGGTGCTAGGGATTCAAATTT 58.584 39.130 0.00 0.00 0.00 1.82
2257 2385 5.575157 TGTGGTGCTAGGGATTCAAATTTA 58.425 37.500 0.00 0.00 0.00 1.40
2258 2386 6.013379 TGTGGTGCTAGGGATTCAAATTTAA 58.987 36.000 0.00 0.00 0.00 1.52
2259 2387 6.071616 TGTGGTGCTAGGGATTCAAATTTAAC 60.072 38.462 0.00 0.00 0.00 2.01
2260 2388 6.152831 GTGGTGCTAGGGATTCAAATTTAACT 59.847 38.462 0.00 0.00 0.00 2.24
2261 2389 6.152661 TGGTGCTAGGGATTCAAATTTAACTG 59.847 38.462 0.00 0.00 0.00 3.16
2262 2390 6.377146 GGTGCTAGGGATTCAAATTTAACTGA 59.623 38.462 0.00 0.00 0.00 3.41
2263 2391 7.093945 GGTGCTAGGGATTCAAATTTAACTGAA 60.094 37.037 0.00 0.00 36.08 3.02
2264 2392 8.303876 GTGCTAGGGATTCAAATTTAACTGAAA 58.696 33.333 0.00 0.00 35.31 2.69
2265 2393 8.865090 TGCTAGGGATTCAAATTTAACTGAAAA 58.135 29.630 0.00 0.00 35.31 2.29
2266 2394 9.705290 GCTAGGGATTCAAATTTAACTGAAAAA 57.295 29.630 0.00 0.00 35.31 1.94
2550 2681 9.256477 GTCGTACTTGGTATAATCATCAATCAA 57.744 33.333 0.00 0.00 0.00 2.57
2557 2688 6.486320 TGGTATAATCATCAATCAACACGCAT 59.514 34.615 0.00 0.00 0.00 4.73
2577 2708 4.082571 GCATATACCATTCCTGTCCATTGC 60.083 45.833 0.00 0.00 0.00 3.56
2578 2709 3.959495 ATACCATTCCTGTCCATTGCT 57.041 42.857 0.00 0.00 0.00 3.91
2579 2710 2.134789 ACCATTCCTGTCCATTGCTC 57.865 50.000 0.00 0.00 0.00 4.26
2586 2717 3.562182 TCCTGTCCATTGCTCGATAGTA 58.438 45.455 0.00 0.00 37.40 1.82
2587 2718 4.152647 TCCTGTCCATTGCTCGATAGTAT 58.847 43.478 0.00 0.00 37.40 2.12
2588 2719 5.321927 TCCTGTCCATTGCTCGATAGTATA 58.678 41.667 0.00 0.00 37.40 1.47
2589 2720 5.952347 TCCTGTCCATTGCTCGATAGTATAT 59.048 40.000 0.00 0.00 37.40 0.86
2644 2782 1.780309 TCCTGGTTGTGGATGAGGTTT 59.220 47.619 0.00 0.00 0.00 3.27
2738 2876 4.052229 ACTCCGACGCCTTCACCG 62.052 66.667 0.00 0.00 0.00 4.94
2740 2878 3.569049 CTCCGACGCCTTCACCGTT 62.569 63.158 0.00 0.00 39.30 4.44
2782 2920 2.465860 ACCAGTGCGCAAGTATGTAA 57.534 45.000 14.00 0.00 41.68 2.41
2783 2921 2.073816 ACCAGTGCGCAAGTATGTAAC 58.926 47.619 14.00 0.00 41.68 2.50
2784 2922 1.060553 CCAGTGCGCAAGTATGTAACG 59.939 52.381 14.00 0.00 41.68 3.18
2791 2932 2.256174 GCAAGTATGTAACGCGTCAGA 58.744 47.619 14.44 0.52 0.00 3.27
2793 2934 2.169663 AGTATGTAACGCGTCAGACG 57.830 50.000 19.10 19.10 45.88 4.18
2860 3002 6.686630 TGTGTGACATCATTAATTTGGTTCC 58.313 36.000 0.00 0.00 0.00 3.62
3001 3147 2.809601 GTGGACGCCTGCTACACG 60.810 66.667 0.00 0.00 0.00 4.49
3226 3372 3.289834 GCCATGCCCACTATGCCG 61.290 66.667 0.00 0.00 0.00 5.69
3382 3528 2.665185 AACTGCTCCGTGAACGCC 60.665 61.111 0.00 0.00 38.18 5.68
3388 3534 4.287781 TCCGTGAACGCCTTCGCA 62.288 61.111 9.22 0.00 36.81 5.10
3556 3702 1.222113 GAGCCTGCCCTACAACTCC 59.778 63.158 0.00 0.00 0.00 3.85
3583 3729 1.078848 GATCGTGCTGCAGAACCCT 60.079 57.895 19.57 6.37 0.00 4.34
3589 3735 1.825622 GCTGCAGAACCCTATGGCC 60.826 63.158 20.43 0.00 33.59 5.36
3640 3786 1.597663 CACGGCTTCAACTTCTTCGTT 59.402 47.619 0.00 0.00 0.00 3.85
3778 3924 1.969589 CGCCAACAACCCAGGTACC 60.970 63.158 2.73 2.73 0.00 3.34
3779 3925 1.969589 GCCAACAACCCAGGTACCG 60.970 63.158 6.18 1.26 0.00 4.02
3781 3927 0.179012 CCAACAACCCAGGTACCGTT 60.179 55.000 6.18 1.74 0.00 4.44
3782 3928 1.072015 CCAACAACCCAGGTACCGTTA 59.928 52.381 6.18 0.00 0.00 3.18
3791 3937 3.215642 GGTACCGTTACCGTGCTTT 57.784 52.632 0.00 0.00 38.65 3.51
3792 3938 1.070821 GGTACCGTTACCGTGCTTTC 58.929 55.000 0.00 0.00 38.65 2.62
3793 3939 1.070821 GTACCGTTACCGTGCTTTCC 58.929 55.000 0.00 0.00 0.00 3.13
3794 3940 0.678395 TACCGTTACCGTGCTTTCCA 59.322 50.000 0.00 0.00 0.00 3.53
3795 3941 0.035739 ACCGTTACCGTGCTTTCCAT 59.964 50.000 0.00 0.00 0.00 3.41
3796 3942 1.275856 ACCGTTACCGTGCTTTCCATA 59.724 47.619 0.00 0.00 0.00 2.74
3797 3943 1.662122 CCGTTACCGTGCTTTCCATAC 59.338 52.381 0.00 0.00 0.00 2.39
3798 3944 2.339418 CGTTACCGTGCTTTCCATACA 58.661 47.619 0.00 0.00 0.00 2.29
3799 3945 2.933906 CGTTACCGTGCTTTCCATACAT 59.066 45.455 0.00 0.00 0.00 2.29
3800 3946 4.114073 CGTTACCGTGCTTTCCATACATA 58.886 43.478 0.00 0.00 0.00 2.29
3801 3947 4.026310 CGTTACCGTGCTTTCCATACATAC 60.026 45.833 0.00 0.00 0.00 2.39
3802 3948 2.546778 ACCGTGCTTTCCATACATACG 58.453 47.619 0.00 0.00 0.00 3.06
3803 3949 2.093869 ACCGTGCTTTCCATACATACGT 60.094 45.455 0.00 0.00 0.00 3.57
3804 3950 2.933906 CCGTGCTTTCCATACATACGTT 59.066 45.455 0.00 0.00 0.00 3.99
3805 3951 3.372822 CCGTGCTTTCCATACATACGTTT 59.627 43.478 0.00 0.00 0.00 3.60
3806 3952 4.493545 CCGTGCTTTCCATACATACGTTTC 60.494 45.833 0.00 0.00 0.00 2.78
3807 3953 4.328983 CGTGCTTTCCATACATACGTTTCT 59.671 41.667 0.00 0.00 0.00 2.52
3808 3954 5.500290 CGTGCTTTCCATACATACGTTTCTC 60.500 44.000 0.00 0.00 0.00 2.87
3809 3955 4.873827 TGCTTTCCATACATACGTTTCTCC 59.126 41.667 0.00 0.00 0.00 3.71
3856 4006 7.451877 TGGGCCTTGATTTTAACAGTGTTAATA 59.548 33.333 25.14 21.19 0.00 0.98
3874 4024 8.998377 GTGTTAATAATTTGATGTTTGGGCTTT 58.002 29.630 0.00 0.00 0.00 3.51
3875 4025 8.997323 TGTTAATAATTTGATGTTTGGGCTTTG 58.003 29.630 0.00 0.00 0.00 2.77
3876 4026 9.213799 GTTAATAATTTGATGTTTGGGCTTTGA 57.786 29.630 0.00 0.00 0.00 2.69
3877 4027 7.671495 AATAATTTGATGTTTGGGCTTTGAC 57.329 32.000 0.00 0.00 0.00 3.18
3878 4028 2.791383 TTGATGTTTGGGCTTTGACG 57.209 45.000 0.00 0.00 0.00 4.35
3879 4029 0.313672 TGATGTTTGGGCTTTGACGC 59.686 50.000 0.00 0.00 0.00 5.19
3880 4030 0.729140 GATGTTTGGGCTTTGACGCG 60.729 55.000 3.53 3.53 0.00 6.01
3881 4031 1.452145 ATGTTTGGGCTTTGACGCGT 61.452 50.000 13.85 13.85 0.00 6.01
3986 4136 4.479993 GCCGACTCCATGCTGCCT 62.480 66.667 0.00 0.00 0.00 4.75
4043 4197 0.165944 AAGTTTCCAGCGCGATTTCG 59.834 50.000 12.10 0.00 43.27 3.46
4052 4206 0.111089 GCGCGATTTCGTCATGATCC 60.111 55.000 12.10 0.00 42.22 3.36
4062 4216 0.376152 GTCATGATCCTGCGTGCAAG 59.624 55.000 0.00 0.00 0.00 4.01
4071 4225 1.806542 CCTGCGTGCAAGTTTACAGAT 59.193 47.619 0.59 0.00 0.00 2.90
4259 4425 3.195825 CAGAGGTTCATTTCCTACCGAGT 59.804 47.826 0.00 0.00 37.04 4.18
4260 4426 4.401519 CAGAGGTTCATTTCCTACCGAGTA 59.598 45.833 0.00 0.00 37.04 2.59
4261 4427 4.401837 AGAGGTTCATTTCCTACCGAGTAC 59.598 45.833 0.00 0.00 37.04 2.73
4265 5096 5.126061 GGTTCATTTCCTACCGAGTACTGTA 59.874 44.000 0.00 0.00 0.00 2.74
4274 5105 1.002684 CCGAGTACTGTACTGATCGGC 60.003 57.143 24.66 11.34 39.59 5.54
4308 5139 4.124970 ACGTTCTCTTCCTTTGGTGTAAC 58.875 43.478 0.00 0.00 0.00 2.50
4323 5154 5.294356 TGGTGTAACTATATGCCAACGATC 58.706 41.667 0.00 0.00 36.74 3.69
4356 5187 2.203800 TCGTATCATTCTGACGGTGC 57.796 50.000 0.00 0.00 37.20 5.01
4368 5199 6.459670 TTCTGACGGTGCATAAAGATACTA 57.540 37.500 0.00 0.00 0.00 1.82
4369 5200 6.073327 TCTGACGGTGCATAAAGATACTAG 57.927 41.667 0.00 0.00 0.00 2.57
4374 5205 6.501781 ACGGTGCATAAAGATACTAGTACAC 58.498 40.000 4.31 6.15 0.00 2.90
4385 5216 9.627395 AAAGATACTAGTACACGATTGCATATC 57.373 33.333 4.31 0.00 0.00 1.63
4408 5240 1.276138 ACTGATTGGAGTGCATGACGA 59.724 47.619 0.00 0.00 0.00 4.20
4442 5275 8.599876 TTGAATTTCAATACGTTGATTGATCG 57.400 30.769 13.14 0.00 43.56 3.69
4444 5277 6.918892 ATTTCAATACGTTGATTGATCGGA 57.081 33.333 13.14 0.00 43.56 4.55
4445 5278 5.966636 TTCAATACGTTGATTGATCGGAG 57.033 39.130 13.14 0.00 43.56 4.63
4446 5279 5.257082 TCAATACGTTGATTGATCGGAGA 57.743 39.130 9.22 0.00 40.18 3.71
4513 5518 1.002134 TGCTTGGCTTACCTGGAGC 60.002 57.895 0.00 0.00 39.41 4.70
4514 5519 1.301293 GCTTGGCTTACCTGGAGCT 59.699 57.895 0.00 0.00 40.01 4.09
4515 5520 1.028868 GCTTGGCTTACCTGGAGCTG 61.029 60.000 0.00 0.00 40.01 4.24
4516 5521 0.393537 CTTGGCTTACCTGGAGCTGG 60.394 60.000 0.00 0.00 40.01 4.85
4517 5522 0.840288 TTGGCTTACCTGGAGCTGGA 60.840 55.000 0.00 0.00 40.01 3.86
4518 5523 1.267574 TGGCTTACCTGGAGCTGGAG 61.268 60.000 0.00 0.00 40.01 3.86
4540 5545 1.453148 GCAACAACTTGAAATGCGAGC 59.547 47.619 0.00 0.00 0.00 5.03
4595 5600 4.704833 TGCTGCCGACTTGCCTCC 62.705 66.667 0.00 0.00 0.00 4.30
4609 5614 1.133823 TGCCTCCTGTTTCTTTCTGCA 60.134 47.619 0.00 0.00 0.00 4.41
4741 5749 8.851960 TCAATACGATGTTGACAGAATACTAC 57.148 34.615 0.00 0.00 31.07 2.73
4750 5758 9.684448 ATGTTGACAGAATACTACGAGAATATG 57.316 33.333 0.00 0.00 0.00 1.78
4755 5763 9.609950 GACAGAATACTACGAGAATATGTAACC 57.390 37.037 0.00 0.00 0.00 2.85
4761 5769 4.978083 ACGAGAATATGTAACCGAGTGT 57.022 40.909 0.00 0.00 0.00 3.55
4789 5797 7.148255 CGGTCTCATTTTGTGAATTATTCAGGA 60.148 37.037 8.00 0.00 41.01 3.86
4803 5811 8.980481 AATTATTCAGGACTCATTCGGTTTAT 57.020 30.769 0.00 0.00 0.00 1.40
4805 5813 9.712305 ATTATTCAGGACTCATTCGGTTTATAG 57.288 33.333 0.00 0.00 0.00 1.31
4843 5851 6.728411 ACGGAATAGGGAAAGTAAGGAAATT 58.272 36.000 0.00 0.00 0.00 1.82
4844 5852 6.602009 ACGGAATAGGGAAAGTAAGGAAATTG 59.398 38.462 0.00 0.00 0.00 2.32
4845 5853 6.602009 CGGAATAGGGAAAGTAAGGAAATTGT 59.398 38.462 0.00 0.00 0.00 2.71
4846 5854 7.415206 CGGAATAGGGAAAGTAAGGAAATTGTG 60.415 40.741 0.00 0.00 0.00 3.33
4848 5856 7.939784 ATAGGGAAAGTAAGGAAATTGTGTC 57.060 36.000 0.00 0.00 0.00 3.67
4850 5858 4.830600 GGGAAAGTAAGGAAATTGTGTCCA 59.169 41.667 0.00 0.00 37.65 4.02
4851 5859 5.480422 GGGAAAGTAAGGAAATTGTGTCCAT 59.520 40.000 0.00 0.00 37.65 3.41
4852 5860 6.661805 GGGAAAGTAAGGAAATTGTGTCCATA 59.338 38.462 0.00 0.00 37.65 2.74
4853 5861 7.342026 GGGAAAGTAAGGAAATTGTGTCCATAT 59.658 37.037 0.00 0.00 37.65 1.78
4855 5863 9.573133 GAAAGTAAGGAAATTGTGTCCATATTG 57.427 33.333 0.00 0.00 37.65 1.90
4856 5864 8.877864 AAGTAAGGAAATTGTGTCCATATTGA 57.122 30.769 0.00 0.00 37.65 2.57
4857 5865 8.281212 AGTAAGGAAATTGTGTCCATATTGAC 57.719 34.615 0.00 0.00 37.65 3.18
4858 5866 7.888021 AGTAAGGAAATTGTGTCCATATTGACA 59.112 33.333 5.55 5.55 42.75 3.58
4860 5868 7.722949 AGGAAATTGTGTCCATATTGACATT 57.277 32.000 12.36 3.51 46.20 2.71
4861 5869 8.821686 AGGAAATTGTGTCCATATTGACATTA 57.178 30.769 12.36 5.00 46.20 1.90
4862 5870 9.425248 AGGAAATTGTGTCCATATTGACATTAT 57.575 29.630 12.36 6.85 46.20 1.28
4867 5875 7.806409 TGTGTCCATATTGACATTATTCCTG 57.194 36.000 12.36 0.00 46.20 3.86
4868 5876 7.345691 TGTGTCCATATTGACATTATTCCTGT 58.654 34.615 12.36 0.00 46.20 4.00
4869 5877 7.282901 TGTGTCCATATTGACATTATTCCTGTG 59.717 37.037 12.36 0.00 46.20 3.66
4872 5880 9.071276 GTCCATATTGACATTATTCCTGTGAAT 57.929 33.333 2.13 0.00 38.63 2.57
4874 5882 9.903682 CCATATTGACATTATTCCTGTGAATTC 57.096 33.333 0.00 0.00 41.44 2.17
4875 5883 9.903682 CATATTGACATTATTCCTGTGAATTCC 57.096 33.333 2.27 0.00 41.44 3.01
4876 5884 9.872684 ATATTGACATTATTCCTGTGAATTCCT 57.127 29.630 2.27 0.00 41.44 3.36
4912 5922 9.807921 TTAGACCTCATGAAAAATTCCTAAAGT 57.192 29.630 0.00 0.00 0.00 2.66
4913 5923 8.712228 AGACCTCATGAAAAATTCCTAAAGTT 57.288 30.769 0.00 0.00 0.00 2.66
4914 5924 9.147732 AGACCTCATGAAAAATTCCTAAAGTTT 57.852 29.630 0.00 0.00 34.35 2.66
4978 6805 8.618702 ATCTTTTCGCATAGATCTTGATTCAT 57.381 30.769 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.323178 AATCTCCTGTTGGGCTGCAG 60.323 55.000 10.11 10.11 34.39 4.41
25 32 4.642885 TCCGAACAAACAAAATCTCCTGTT 59.357 37.500 0.00 0.00 37.36 3.16
31 38 5.592104 ACCTTTCCGAACAAACAAAATCT 57.408 34.783 0.00 0.00 0.00 2.40
39 46 6.016943 CCACAAGTTATACCTTTCCGAACAAA 60.017 38.462 0.00 0.00 0.00 2.83
41 48 4.998672 CCACAAGTTATACCTTTCCGAACA 59.001 41.667 0.00 0.00 0.00 3.18
46 53 3.692690 TGCCCACAAGTTATACCTTTCC 58.307 45.455 0.00 0.00 0.00 3.13
53 60 5.371176 TGGAGGATTATGCCCACAAGTTATA 59.629 40.000 0.00 0.00 0.00 0.98
106 113 4.922471 TTGATACACATTCCGTCGGATA 57.078 40.909 16.23 4.26 0.00 2.59
112 119 4.009675 ACTTGCATTGATACACATTCCGT 58.990 39.130 0.00 0.00 0.00 4.69
123 130 2.026542 TCCAGAGAGCACTTGCATTGAT 60.027 45.455 3.62 0.00 45.16 2.57
147 154 1.888826 CGGTTTGGTCCCAAATGGCTA 60.889 52.381 14.19 0.00 45.90 3.93
148 155 1.184970 CGGTTTGGTCCCAAATGGCT 61.185 55.000 14.19 0.00 45.90 4.75
171 179 5.509670 CCGACACTCAATTATCTATGCCAGA 60.510 44.000 0.00 0.00 37.79 3.86
210 218 3.798337 GGCTTTGAAGTTGTTGTCATGTG 59.202 43.478 0.00 0.00 0.00 3.21
212 220 3.068590 AGGGCTTTGAAGTTGTTGTCATG 59.931 43.478 0.00 0.00 0.00 3.07
242 250 1.023513 GCACCTGAACTAGCAGCCTG 61.024 60.000 0.00 0.00 34.56 4.85
276 284 1.131883 AGGTGTAGTAGCGTACAAGCG 59.868 52.381 0.00 0.00 43.00 4.68
323 331 0.745845 CCTGCTGATCCCTCGTTTGG 60.746 60.000 0.00 0.00 0.00 3.28
328 336 2.060383 TGTCCCTGCTGATCCCTCG 61.060 63.158 0.00 0.00 0.00 4.63
389 397 6.773638 ACATAGCTAAATAACTGGATGGGAG 58.226 40.000 0.00 0.00 0.00 4.30
455 464 5.502079 TCAGGAGTTTTACTTTTGGACACA 58.498 37.500 0.00 0.00 0.00 3.72
532 544 2.093973 AGCACCGTCGAATCATCTTTCT 60.094 45.455 0.00 0.00 0.00 2.52
597 614 3.431922 TTAGCTCGTTTCGTGGATAGG 57.568 47.619 0.00 0.00 0.00 2.57
599 616 7.204604 TGAATAATTAGCTCGTTTCGTGGATA 58.795 34.615 0.00 0.00 0.00 2.59
609 626 5.361285 ACAGTCCTCTGAATAATTAGCTCGT 59.639 40.000 0.00 0.00 43.76 4.18
610 627 5.837437 ACAGTCCTCTGAATAATTAGCTCG 58.163 41.667 0.00 0.00 43.76 5.03
621 638 1.000163 GCTTGTCGACAGTCCTCTGAA 60.000 52.381 19.11 0.00 43.76 3.02
652 669 1.077169 GGGTCTGATGGGGAGGTTTTT 59.923 52.381 0.00 0.00 0.00 1.94
759 776 2.869897 TCCCATTTAAATTTGCGCGAC 58.130 42.857 12.10 0.88 0.00 5.19
766 783 5.280985 GCCCCCTCTTTTCCCATTTAAATTT 60.281 40.000 0.00 0.00 0.00 1.82
772 789 0.491371 TGCCCCCTCTTTTCCCATTT 59.509 50.000 0.00 0.00 0.00 2.32
896 918 1.613255 CCTGACCGGGCAACTTGTATT 60.613 52.381 13.37 0.00 0.00 1.89
909 931 0.391130 TTCTTTGGCGATCCTGACCG 60.391 55.000 0.00 0.00 0.00 4.79
912 934 3.634397 ATCTTTCTTTGGCGATCCTGA 57.366 42.857 0.00 0.00 0.00 3.86
985 1016 1.745141 CGCCATGGAAGAAGAGGAAGG 60.745 57.143 18.40 0.00 0.00 3.46
1074 1108 5.762825 AGAGAAGTACTGTGAACGTGTAA 57.237 39.130 0.00 0.00 0.00 2.41
1080 1114 7.435305 AGAAGGTAAAGAGAAGTACTGTGAAC 58.565 38.462 0.00 0.00 0.00 3.18
1178 1216 1.343142 TGGCGAAGTTGCTCTAGTTCA 59.657 47.619 0.00 0.00 34.52 3.18
1188 1226 1.001048 CATATGGGCATGGCGAAGTTG 60.001 52.381 13.76 5.26 0.00 3.16
1347 1424 3.517100 ACTGTCCTGCATGACTATCAACT 59.483 43.478 20.71 0.00 36.21 3.16
1348 1425 3.866651 ACTGTCCTGCATGACTATCAAC 58.133 45.455 20.71 0.00 36.21 3.18
1349 1426 4.223700 AGAACTGTCCTGCATGACTATCAA 59.776 41.667 20.71 1.93 36.21 2.57
1350 1427 3.771479 AGAACTGTCCTGCATGACTATCA 59.229 43.478 20.71 2.33 36.21 2.15
1351 1428 4.399004 AGAACTGTCCTGCATGACTATC 57.601 45.455 20.71 15.48 36.21 2.08
1352 1429 6.015010 GGTATAGAACTGTCCTGCATGACTAT 60.015 42.308 20.71 12.75 36.21 2.12
1353 1430 5.302059 GGTATAGAACTGTCCTGCATGACTA 59.698 44.000 20.71 7.01 36.21 2.59
1354 1431 4.100189 GGTATAGAACTGTCCTGCATGACT 59.900 45.833 20.71 3.16 36.21 3.41
1355 1432 4.100189 AGGTATAGAACTGTCCTGCATGAC 59.900 45.833 14.52 14.52 35.77 3.06
1356 1433 4.290093 AGGTATAGAACTGTCCTGCATGA 58.710 43.478 0.00 0.00 0.00 3.07
1357 1434 4.679373 AGGTATAGAACTGTCCTGCATG 57.321 45.455 0.00 0.00 0.00 4.06
1358 1435 7.380423 AAATAGGTATAGAACTGTCCTGCAT 57.620 36.000 0.00 0.00 0.00 3.96
1359 1436 6.808321 AAATAGGTATAGAACTGTCCTGCA 57.192 37.500 0.00 0.00 0.00 4.41
1360 1437 7.769044 TGAAAAATAGGTATAGAACTGTCCTGC 59.231 37.037 0.00 0.00 0.00 4.85
1361 1438 9.838339 ATGAAAAATAGGTATAGAACTGTCCTG 57.162 33.333 0.00 0.00 0.00 3.86
1362 1439 9.838339 CATGAAAAATAGGTATAGAACTGTCCT 57.162 33.333 0.00 0.00 0.00 3.85
1363 1440 9.614792 ACATGAAAAATAGGTATAGAACTGTCC 57.385 33.333 0.00 0.00 0.00 4.02
1397 1474 7.439381 TCCGAAGTACAAGTAGAGATTTTTGT 58.561 34.615 0.00 0.00 37.51 2.83
1404 1481 4.940046 ACGATTCCGAAGTACAAGTAGAGA 59.060 41.667 0.00 0.00 39.50 3.10
1405 1482 5.029014 CACGATTCCGAAGTACAAGTAGAG 58.971 45.833 0.00 0.00 39.50 2.43
1409 1486 3.655276 ACACGATTCCGAAGTACAAGT 57.345 42.857 0.00 0.00 39.50 3.16
1412 1489 5.355071 ACTGTATACACGATTCCGAAGTACA 59.645 40.000 0.08 0.00 39.50 2.90
1421 1500 5.686397 GCTTGTAGGACTGTATACACGATTC 59.314 44.000 0.08 0.00 31.83 2.52
1458 1537 3.753272 GCAGCATTACAGAGGAACAAAGA 59.247 43.478 0.00 0.00 0.00 2.52
1472 1551 1.678635 GCACCTGGTGGCAGCATTA 60.679 57.895 27.02 0.00 37.54 1.90
1489 1568 3.861689 GCTGGTTAATTTTCATGCTCTGC 59.138 43.478 0.00 0.00 0.00 4.26
1585 1664 0.891904 TCACATCGACGACCACCTCA 60.892 55.000 0.00 0.00 0.00 3.86
1651 1730 4.103469 TGAAAGTTTTCTGTAGCTGGGGTA 59.897 41.667 0.00 0.00 38.02 3.69
1741 1831 0.106167 AGGCTAGATGACAGCGGGTA 60.106 55.000 0.00 0.00 40.05 3.69
1782 1876 2.619177 GTCCTGCGAACTAGCTAGATGA 59.381 50.000 27.45 5.86 38.13 2.92
1843 1937 9.810545 GCTAAGATAGTCAGACAAACTAATCTT 57.189 33.333 2.66 9.15 34.77 2.40
1927 2021 1.988406 GTGCCTCGGAAGGTAGGGT 60.988 63.158 0.00 0.00 45.34 4.34
1953 2047 5.542635 TGTTAAGATGAGGTCACCTACAGTT 59.457 40.000 0.00 0.00 31.76 3.16
1962 2056 2.838202 GGAGGGTGTTAAGATGAGGTCA 59.162 50.000 0.00 0.00 0.00 4.02
2177 2303 1.692519 ACTGAAACTTAGTGCCGACCT 59.307 47.619 0.00 0.00 0.00 3.85
2186 2312 1.798813 GTGCCGACCACTGAAACTTAG 59.201 52.381 0.00 0.00 41.35 2.18
2223 2349 4.336433 CCCTAGCACCACAAATCATAACAG 59.664 45.833 0.00 0.00 0.00 3.16
2230 2356 3.620488 TGAATCCCTAGCACCACAAATC 58.380 45.455 0.00 0.00 0.00 2.17
2263 2391 4.929211 GCCGCCAAAGATCAGTTAATTTTT 59.071 37.500 0.00 0.00 0.00 1.94
2264 2392 4.021544 TGCCGCCAAAGATCAGTTAATTTT 60.022 37.500 0.00 0.00 0.00 1.82
2265 2393 3.509575 TGCCGCCAAAGATCAGTTAATTT 59.490 39.130 0.00 0.00 0.00 1.82
2266 2394 3.088532 TGCCGCCAAAGATCAGTTAATT 58.911 40.909 0.00 0.00 0.00 1.40
2267 2395 2.684881 CTGCCGCCAAAGATCAGTTAAT 59.315 45.455 0.00 0.00 0.00 1.40
2298 2426 1.548357 ATGGCGTCAGCTTCTGGAGT 61.548 55.000 0.00 0.00 44.37 3.85
2301 2429 2.110967 CCATGGCGTCAGCTTCTGG 61.111 63.158 0.00 0.00 44.37 3.86
2457 2585 3.958860 GGGCGGATGATGAGGGGG 61.959 72.222 0.00 0.00 0.00 5.40
2550 2681 3.494398 GGACAGGAATGGTATATGCGTGT 60.494 47.826 0.00 0.00 0.00 4.49
2557 2688 4.503123 CGAGCAATGGACAGGAATGGTATA 60.503 45.833 0.00 0.00 0.00 1.47
2577 2708 8.087136 CCATCCATCCATCAATATACTATCGAG 58.913 40.741 0.00 0.00 0.00 4.04
2578 2709 7.015584 CCCATCCATCCATCAATATACTATCGA 59.984 40.741 0.00 0.00 0.00 3.59
2579 2710 7.157347 CCCATCCATCCATCAATATACTATCG 58.843 42.308 0.00 0.00 0.00 2.92
2586 2717 3.530564 CCTCCCCATCCATCCATCAATAT 59.469 47.826 0.00 0.00 0.00 1.28
2587 2718 2.921612 CCTCCCCATCCATCCATCAATA 59.078 50.000 0.00 0.00 0.00 1.90
2588 2719 1.714787 CCTCCCCATCCATCCATCAAT 59.285 52.381 0.00 0.00 0.00 2.57
2589 2720 1.151760 CCTCCCCATCCATCCATCAA 58.848 55.000 0.00 0.00 0.00 2.57
2644 2782 3.625897 CACCACTCGCCTGTCCCA 61.626 66.667 0.00 0.00 0.00 4.37
2782 2920 1.006571 AATTCACCGTCTGACGCGT 60.007 52.632 23.87 13.85 40.91 6.01
2783 2921 0.732880 AGAATTCACCGTCTGACGCG 60.733 55.000 23.87 18.45 40.91 6.01
2784 2922 0.716108 CAGAATTCACCGTCTGACGC 59.284 55.000 23.87 8.94 43.32 5.19
2786 2924 4.557205 AGTTACAGAATTCACCGTCTGAC 58.443 43.478 8.44 0.00 43.32 3.51
2791 2932 4.202326 ACCTGAAGTTACAGAATTCACCGT 60.202 41.667 8.44 4.43 39.94 4.83
2793 2934 5.305585 TCACCTGAAGTTACAGAATTCACC 58.694 41.667 8.44 0.00 39.94 4.02
2846 2988 7.516785 CGTCTCATCTACGGAACCAAATTAATG 60.517 40.741 0.00 0.00 36.71 1.90
2850 2992 4.181578 CGTCTCATCTACGGAACCAAATT 58.818 43.478 0.00 0.00 36.71 1.82
2860 3002 1.811428 CCGTGAACGTCTCATCTACG 58.189 55.000 1.75 0.00 45.64 3.51
2992 3138 0.037697 TGTAGTTGGCCGTGTAGCAG 60.038 55.000 0.00 0.00 0.00 4.24
3001 3147 1.670083 GTCCGTGGTGTAGTTGGCC 60.670 63.158 0.00 0.00 0.00 5.36
3226 3372 0.236711 TCGTCGAGTCCGAGTTGTTC 59.763 55.000 0.00 0.00 46.52 3.18
3566 3712 0.833287 ATAGGGTTCTGCAGCACGAT 59.167 50.000 9.47 2.97 0.00 3.73
3583 3729 2.042741 TCCGACGGGAAGGCCATA 60.043 61.111 15.25 0.00 40.15 2.74
3589 3735 3.068691 TGGCTCTCCGACGGGAAG 61.069 66.667 15.25 12.65 43.27 3.46
3677 3823 2.347490 CAGGTTGTAGGCGCTGGT 59.653 61.111 7.64 0.00 0.00 4.00
3779 3925 4.026310 CGTATGTATGGAAAGCACGGTAAC 60.026 45.833 0.00 0.00 0.00 2.50
3781 3927 3.130869 ACGTATGTATGGAAAGCACGGTA 59.869 43.478 0.00 0.00 32.52 4.02
3782 3928 2.093869 ACGTATGTATGGAAAGCACGGT 60.094 45.455 0.00 0.00 32.52 4.83
3787 3933 4.272748 GGGAGAAACGTATGTATGGAAAGC 59.727 45.833 0.00 0.00 0.00 3.51
3789 3935 5.687166 AGGGAGAAACGTATGTATGGAAA 57.313 39.130 0.00 0.00 0.00 3.13
3791 3937 6.989155 AATAGGGAGAAACGTATGTATGGA 57.011 37.500 0.00 0.00 0.00 3.41
3792 3938 6.365247 CGAAATAGGGAGAAACGTATGTATGG 59.635 42.308 0.00 0.00 0.00 2.74
3793 3939 6.365247 CCGAAATAGGGAGAAACGTATGTATG 59.635 42.308 0.00 0.00 0.00 2.39
3794 3940 6.453092 CCGAAATAGGGAGAAACGTATGTAT 58.547 40.000 0.00 0.00 0.00 2.29
3795 3941 5.737063 GCCGAAATAGGGAGAAACGTATGTA 60.737 44.000 0.00 0.00 0.00 2.29
3796 3942 4.690122 CCGAAATAGGGAGAAACGTATGT 58.310 43.478 0.00 0.00 0.00 2.29
3797 3943 3.493503 GCCGAAATAGGGAGAAACGTATG 59.506 47.826 0.00 0.00 0.00 2.39
3798 3944 3.493873 GGCCGAAATAGGGAGAAACGTAT 60.494 47.826 0.00 0.00 0.00 3.06
3799 3945 2.159057 GGCCGAAATAGGGAGAAACGTA 60.159 50.000 0.00 0.00 0.00 3.57
3800 3946 1.406477 GGCCGAAATAGGGAGAAACGT 60.406 52.381 0.00 0.00 0.00 3.99
3801 3947 1.296727 GGCCGAAATAGGGAGAAACG 58.703 55.000 0.00 0.00 0.00 3.60
3802 3948 1.064979 TGGGCCGAAATAGGGAGAAAC 60.065 52.381 0.00 0.00 0.00 2.78
3803 3949 1.291109 TGGGCCGAAATAGGGAGAAA 58.709 50.000 0.00 0.00 0.00 2.52
3804 3950 1.291109 TTGGGCCGAAATAGGGAGAA 58.709 50.000 0.00 0.00 0.00 2.87
3805 3951 1.064979 GTTTGGGCCGAAATAGGGAGA 60.065 52.381 16.49 0.00 0.00 3.71
3806 3952 1.064685 AGTTTGGGCCGAAATAGGGAG 60.065 52.381 16.49 0.00 0.00 4.30
3807 3953 0.996583 AGTTTGGGCCGAAATAGGGA 59.003 50.000 16.49 0.00 0.00 4.20
3808 3954 2.721425 TAGTTTGGGCCGAAATAGGG 57.279 50.000 16.49 0.00 0.00 3.53
3809 3955 4.700213 CCATATAGTTTGGGCCGAAATAGG 59.300 45.833 16.49 10.68 0.00 2.57
3856 4006 4.057432 CGTCAAAGCCCAAACATCAAATT 58.943 39.130 0.00 0.00 0.00 1.82
3862 4012 1.285641 CGCGTCAAAGCCCAAACAT 59.714 52.632 0.00 0.00 0.00 2.71
3874 4024 1.736282 CACATGCCTACACGCGTCA 60.736 57.895 9.86 3.90 0.00 4.35
3875 4025 2.452813 CCACATGCCTACACGCGTC 61.453 63.158 9.86 0.00 0.00 5.19
3876 4026 2.434185 CCACATGCCTACACGCGT 60.434 61.111 5.58 5.58 0.00 6.01
3877 4027 1.966493 GAACCACATGCCTACACGCG 61.966 60.000 3.53 3.53 0.00 6.01
3878 4028 0.673644 AGAACCACATGCCTACACGC 60.674 55.000 0.00 0.00 0.00 5.34
3879 4029 1.732259 GAAGAACCACATGCCTACACG 59.268 52.381 0.00 0.00 0.00 4.49
3880 4030 2.084546 GGAAGAACCACATGCCTACAC 58.915 52.381 0.00 0.00 38.79 2.90
3881 4031 1.702401 TGGAAGAACCACATGCCTACA 59.298 47.619 0.00 0.00 44.64 2.74
3998 4148 1.415289 CTCTAGCACATGGGCAGATCA 59.585 52.381 24.51 0.00 35.83 2.92
4025 4175 0.949105 ACGAAATCGCGCTGGAAACT 60.949 50.000 5.56 0.00 44.43 2.66
4027 4177 0.946700 TGACGAAATCGCGCTGGAAA 60.947 50.000 5.56 0.00 44.43 3.13
4028 4178 0.739462 ATGACGAAATCGCGCTGGAA 60.739 50.000 5.56 0.00 44.43 3.53
4029 4179 1.153647 ATGACGAAATCGCGCTGGA 60.154 52.632 5.56 0.00 44.43 3.86
4030 4180 1.011904 CATGACGAAATCGCGCTGG 60.012 57.895 5.56 0.00 44.43 4.85
4031 4181 0.578683 ATCATGACGAAATCGCGCTG 59.421 50.000 5.56 0.00 44.43 5.18
4032 4182 0.855349 GATCATGACGAAATCGCGCT 59.145 50.000 5.56 0.00 44.43 5.92
4043 4197 0.376152 CTTGCACGCAGGATCATGAC 59.624 55.000 12.39 1.59 0.00 3.06
4052 4206 3.542712 AATCTGTAAACTTGCACGCAG 57.457 42.857 0.00 0.00 0.00 5.18
4106 4260 2.890109 CGTATACGCTCCGTCGCCT 61.890 63.158 13.08 0.00 41.54 5.52
4116 4275 2.522638 GCCCTGCACACGTATACGC 61.523 63.158 24.64 9.22 44.43 4.42
4117 4276 1.881252 GGCCCTGCACACGTATACG 60.881 63.158 23.24 23.24 46.33 3.06
4227 4392 7.834803 AGGAAATGAACCTCTGAAATTGAATC 58.165 34.615 0.00 0.00 31.43 2.52
4259 4425 0.099968 GCACGCCGATCAGTACAGTA 59.900 55.000 0.00 0.00 0.00 2.74
4260 4426 1.153823 GCACGCCGATCAGTACAGT 60.154 57.895 0.00 0.00 0.00 3.55
4261 4427 0.528466 ATGCACGCCGATCAGTACAG 60.528 55.000 0.00 0.00 0.00 2.74
4265 5096 3.197790 GCATGCACGCCGATCAGT 61.198 61.111 14.21 0.00 0.00 3.41
4274 5105 0.247419 GAGAACGTCATGCATGCACG 60.247 55.000 31.66 31.66 37.35 5.34
4308 5139 4.982295 TGAAGTTCGATCGTTGGCATATAG 59.018 41.667 15.94 0.00 0.00 1.31
4344 5175 5.918608 AGTATCTTTATGCACCGTCAGAAT 58.081 37.500 0.00 0.00 0.00 2.40
4356 5187 8.797266 TGCAATCGTGTACTAGTATCTTTATG 57.203 34.615 5.75 3.98 0.00 1.90
4374 5205 4.923281 TCCAATCAGTACGATATGCAATCG 59.077 41.667 21.64 21.64 46.02 3.34
4385 5216 2.604914 GTCATGCACTCCAATCAGTACG 59.395 50.000 0.00 0.00 0.00 3.67
4408 5240 6.866480 ACGTATTGAAATTCAAAGATGCCAT 58.134 32.000 12.75 0.00 40.12 4.40
4440 5273 2.744741 CAGCTCGCTAGATATTCTCCGA 59.255 50.000 0.00 0.00 32.26 4.55
4442 5275 3.085533 TCCAGCTCGCTAGATATTCTCC 58.914 50.000 0.00 0.00 0.00 3.71
4444 5277 4.339748 TCATCCAGCTCGCTAGATATTCT 58.660 43.478 0.00 0.00 0.00 2.40
4445 5278 4.397730 TCTCATCCAGCTCGCTAGATATTC 59.602 45.833 0.00 0.00 0.00 1.75
4446 5279 4.339748 TCTCATCCAGCTCGCTAGATATT 58.660 43.478 0.00 0.00 0.00 1.28
4513 5518 1.691196 TTCAAGTTGTTGCCCTCCAG 58.309 50.000 2.11 0.00 33.23 3.86
4514 5519 2.151502 TTTCAAGTTGTTGCCCTCCA 57.848 45.000 2.11 0.00 33.23 3.86
4515 5520 2.867647 GCATTTCAAGTTGTTGCCCTCC 60.868 50.000 13.58 0.00 33.23 4.30
4516 5521 2.407090 GCATTTCAAGTTGTTGCCCTC 58.593 47.619 13.58 0.00 33.23 4.30
4517 5522 1.269726 CGCATTTCAAGTTGTTGCCCT 60.270 47.619 16.73 0.00 33.23 5.19
4518 5523 1.139163 CGCATTTCAAGTTGTTGCCC 58.861 50.000 16.73 1.11 33.23 5.36
4540 5545 1.341531 ACTTTGTCCTCTGGTGACGAG 59.658 52.381 0.00 0.00 35.46 4.18
4741 5749 4.288531 GGACACTCGGTTACATATTCTCG 58.711 47.826 0.00 0.00 0.00 4.04
4755 5763 1.726791 CAAAATGAGACCGGACACTCG 59.273 52.381 9.46 0.00 36.11 4.18
4761 5769 6.657117 TGAATAATTCACAAAATGAGACCGGA 59.343 34.615 9.46 0.00 38.99 5.14
4765 5773 8.734386 AGTCCTGAATAATTCACAAAATGAGAC 58.266 33.333 0.00 0.00 38.99 3.36
4796 5804 8.284693 CCGTTGATTTAAATACCCTATAAACCG 58.715 37.037 0.00 0.00 0.00 4.44
4803 5811 8.158789 CCCTATTCCGTTGATTTAAATACCCTA 58.841 37.037 0.00 0.00 0.00 3.53
4805 5813 6.999871 TCCCTATTCCGTTGATTTAAATACCC 59.000 38.462 0.00 0.00 0.00 3.69
4820 5828 6.602009 ACAATTTCCTTACTTTCCCTATTCCG 59.398 38.462 0.00 0.00 0.00 4.30
4827 5835 4.830600 TGGACACAATTTCCTTACTTTCCC 59.169 41.667 0.00 0.00 33.84 3.97
4846 5854 8.450578 TTCACAGGAATAATGTCAATATGGAC 57.549 34.615 2.99 2.99 38.29 4.02
4848 5856 9.903682 GAATTCACAGGAATAATGTCAATATGG 57.096 33.333 0.00 0.00 42.87 2.74
4850 5858 9.872684 AGGAATTCACAGGAATAATGTCAATAT 57.127 29.630 7.93 0.00 42.87 1.28
4852 5860 9.699410 TTAGGAATTCACAGGAATAATGTCAAT 57.301 29.630 7.93 0.00 42.87 2.57
4853 5861 9.699410 ATTAGGAATTCACAGGAATAATGTCAA 57.301 29.630 7.93 0.00 42.87 3.18
4887 5897 9.807921 AACTTTAGGAATTTTTCATGAGGTCTA 57.192 29.630 0.00 0.00 0.00 2.59
4947 6369 9.464714 TCAAGATCTATGCGAAAAGATAACTAC 57.535 33.333 0.00 0.00 32.60 2.73
4978 6805 7.756272 GCAACTGATCACACAATTTCATCATTA 59.244 33.333 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.