Multiple sequence alignment - TraesCS3B01G468100

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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 TraesCS3B01G468100 chr3B 100.000 5315 0 0 1 5315 712568475 712563161 0.000000e+00 9816
1 TraesCS3B01G468100 chr3B 92.391 92 5 2 2688 2778 48667301 48667391 4.320000e-26 130
2 TraesCS3B01G468100 chr3A 93.520 2716 130 23 1 2700 673443708 673441023 0.000000e+00 3999
3 TraesCS3B01G468100 chr3A 96.759 2067 57 5 2777 4836 673441038 673438975 0.000000e+00 3437
4 TraesCS3B01G468100 chr3A 85.990 414 22 11 4835 5214 673438871 673438460 1.380000e-110 411
5 TraesCS3B01G468100 chr3A 98.734 79 1 0 2700 2778 527824798 527824720 2.000000e-29 141
6 TraesCS3B01G468100 chr3A 96.429 84 3 0 2700 2783 698350700 698350617 7.180000e-29 139
7 TraesCS3B01G468100 chr3A 92.391 92 5 2 2688 2778 301131272 301131362 4.320000e-26 130
8 TraesCS3B01G468100 chr3D 92.879 1671 70 15 1 1654 537913302 537911664 0.000000e+00 2381
9 TraesCS3B01G468100 chr3D 88.858 1813 147 30 2777 4554 537910691 537908899 0.000000e+00 2178
10 TraesCS3B01G468100 chr3D 92.829 1018 48 9 1684 2700 537911669 537910676 0.000000e+00 1452
11 TraesCS3B01G468100 chr3D 91.599 369 25 6 4855 5220 537908138 537907773 6.140000e-139 505
12 TraesCS3B01G468100 chr3D 90.347 259 14 4 4586 4836 537908516 537908261 3.970000e-86 329
13 TraesCS3B01G468100 chr3D 95.918 98 3 1 5218 5315 537907655 537907559 1.980000e-34 158
14 TraesCS3B01G468100 chr6B 98.734 79 1 0 2700 2778 227274613 227274691 2.000000e-29 141
15 TraesCS3B01G468100 chr6B 93.407 91 5 1 2700 2790 287471851 287471940 3.340000e-27 134
16 TraesCS3B01G468100 chr4D 98.734 79 1 0 2700 2778 313574280 313574202 2.000000e-29 141
17 TraesCS3B01G468100 chr4A 97.500 80 2 0 2700 2779 58113512 58113433 2.580000e-28 137
18 TraesCS3B01G468100 chrUn 92.391 92 5 2 2700 2789 340618267 340618176 4.320000e-26 130


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 TraesCS3B01G468100 chr3B 712563161 712568475 5314 True 9816.000000 9816 100.000000 1 5315 1 chr3B.!!$R1 5314
1 TraesCS3B01G468100 chr3A 673438460 673443708 5248 True 2615.666667 3999 92.089667 1 5214 3 chr3A.!!$R3 5213
2 TraesCS3B01G468100 chr3D 537907559 537913302 5743 True 1167.166667 2381 92.071667 1 5315 6 chr3D.!!$R1 5314

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
352 364 0.961019 TGGCTTTTCATGGTCAGTGC 59.039 50.0 0.0 0.0 0.0 4.40 F
2095 2128 0.037590 TTGCTCCCACCATGTACCAC 59.962 55.0 0.0 0.0 0.0 4.16 F
2749 2785 0.187361 TAGCCTGCCCCAACTTGTTT 59.813 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2304 0.253610 ACCACGGTGTTTTGACCTGA 59.746 50.000 7.45 0.0 33.35 3.86 R
2959 2995 1.227438 CCGTGTCAAAGGTGTCGGT 60.227 57.895 0.00 0.0 33.51 4.69 R
4331 4379 0.315251 CACTTCCGCTCACAGACAGA 59.685 55.000 0.00 0.0 0.00 3.41 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
135 139 2.952978 AGACGTTTTTGTAATGTGGGCA 59.047 40.909 0.00 0.00 0.00 5.36
136 140 3.572255 AGACGTTTTTGTAATGTGGGCAT 59.428 39.130 0.00 0.00 36.80 4.40
137 141 3.908213 ACGTTTTTGTAATGTGGGCATC 58.092 40.909 0.00 0.00 33.50 3.91
163 167 5.098893 TCGCCAAAATATTTGTCCATTTCG 58.901 37.500 0.39 0.00 0.00 3.46
287 299 7.094205 GGGTATCTGGTTGCCATATAAATCAAG 60.094 40.741 0.00 0.00 30.82 3.02
335 347 5.170748 GTTCCAAACTAGATGCCATTTTGG 58.829 41.667 10.93 10.93 45.11 3.28
348 360 4.005487 CCATTTTGGCTTTTCATGGTCA 57.995 40.909 0.00 0.00 31.33 4.02
349 361 3.998341 CCATTTTGGCTTTTCATGGTCAG 59.002 43.478 0.00 0.00 31.33 3.51
350 362 4.503643 CCATTTTGGCTTTTCATGGTCAGT 60.504 41.667 0.00 0.00 31.33 3.41
352 364 0.961019 TGGCTTTTCATGGTCAGTGC 59.039 50.000 0.00 0.00 0.00 4.40
354 366 2.224744 TGGCTTTTCATGGTCAGTGCTA 60.225 45.455 0.00 0.00 0.00 3.49
509 531 7.969536 TTCAAAGATAGAGAAGTTTGACTGG 57.030 36.000 0.00 0.00 38.35 4.00
639 669 6.721704 ACAGAACTAGACAGATATGATGCA 57.278 37.500 0.00 0.00 0.00 3.96
680 710 5.550403 TGGTTTTACCTCTCCTTATTGTCCT 59.450 40.000 0.00 0.00 39.58 3.85
685 715 5.793030 ACCTCTCCTTATTGTCCTATTCG 57.207 43.478 0.00 0.00 0.00 3.34
742 772 4.721776 TGCCCTACACTCCTTCATAGAATT 59.278 41.667 0.00 0.00 0.00 2.17
882 913 1.588139 GAAGGCATTGCGCATCTGC 60.588 57.895 27.98 27.98 45.17 4.26
1151 1182 0.962356 GTCCACATCCACAGGCCAAG 60.962 60.000 5.01 0.00 0.00 3.61
1323 1356 1.009829 CGTATTGGGAGCTTCAGTGC 58.990 55.000 0.00 0.00 0.00 4.40
1331 1364 0.888285 GAGCTTCAGTGCCAGCAAGT 60.888 55.000 14.51 0.00 38.61 3.16
1355 1388 8.807118 AGTAAGTTGACAGAAGATCATGTTAGA 58.193 33.333 0.00 0.00 0.00 2.10
1357 1390 7.473735 AGTTGACAGAAGATCATGTTAGAGA 57.526 36.000 0.00 0.00 0.00 3.10
1375 1408 3.953612 AGAGAGCACAGGATAAGTGAGAG 59.046 47.826 0.00 0.00 39.30 3.20
1380 1413 4.284490 AGCACAGGATAAGTGAGAGAAACA 59.716 41.667 0.00 0.00 39.30 2.83
1385 1418 7.224362 CACAGGATAAGTGAGAGAAACATGATC 59.776 40.741 0.00 0.00 39.30 2.92
1398 1431 7.973388 AGAGAAACATGATCGAGAAGAACTTAG 59.027 37.037 0.00 0.00 0.00 2.18
1403 1436 6.378564 ACATGATCGAGAAGAACTTAGAGGAA 59.621 38.462 0.00 0.00 0.00 3.36
1412 1445 4.260170 AGAACTTAGAGGAATGCTTGCAG 58.740 43.478 0.87 0.00 0.00 4.41
1452 1485 5.545658 TGAAACTGAAATGATTAGTCCGC 57.454 39.130 0.00 0.00 0.00 5.54
1453 1486 5.000591 TGAAACTGAAATGATTAGTCCGCA 58.999 37.500 0.00 0.00 0.00 5.69
1457 1490 3.198068 TGAAATGATTAGTCCGCAGCTC 58.802 45.455 0.00 0.00 0.00 4.09
1480 1513 8.397906 GCTCTGTTCTTTTGTATACAATGCATA 58.602 33.333 18.69 0.98 35.55 3.14
1530 1563 8.347004 TGATATTGTGCATTTCTTTTAGGTCA 57.653 30.769 0.00 0.00 0.00 4.02
1622 1655 2.004733 GTTACCACACTCGTTATGGGC 58.995 52.381 0.00 0.00 37.86 5.36
1666 1699 5.514500 ACTTACATATGTTTCCTGGGTGT 57.486 39.130 14.77 0.00 0.00 4.16
1667 1700 5.497474 ACTTACATATGTTTCCTGGGTGTC 58.503 41.667 14.77 0.00 0.00 3.67
1691 1724 1.095228 GCAGCCTGGCGCAGTATTAA 61.095 55.000 23.79 0.00 41.38 1.40
1692 1725 1.378531 CAGCCTGGCGCAGTATTAAA 58.621 50.000 13.96 0.00 41.38 1.52
1700 1733 3.021355 GCGCAGTATTAAATATCGCCG 57.979 47.619 0.30 0.00 35.71 6.46
1707 1740 6.347079 GCAGTATTAAATATCGCCGCAACTTA 60.347 38.462 0.00 0.00 0.00 2.24
1714 1747 1.003851 TCGCCGCAACTTACTAATGC 58.996 50.000 0.00 0.00 36.74 3.56
1824 1857 8.777413 GCTTGTGCAATATTCTGTATCTTCATA 58.223 33.333 0.00 0.00 39.41 2.15
1841 1874 4.963276 TCATAAGGGAATTCTTGTTGCG 57.037 40.909 5.23 0.00 0.00 4.85
1885 1918 6.366877 CCTTAATCAACCTTGCATGTTCTTTG 59.633 38.462 0.00 0.00 0.00 2.77
1888 1921 2.364970 CAACCTTGCATGTTCTTTGGGA 59.635 45.455 0.00 0.00 0.00 4.37
1890 1923 1.547372 CCTTGCATGTTCTTTGGGAGG 59.453 52.381 0.00 0.00 0.00 4.30
1908 1941 6.303839 TGGGAGGTTATATTTTAGACCATGC 58.696 40.000 0.00 0.00 34.60 4.06
1913 1946 8.034313 AGGTTATATTTTAGACCATGCAGAGA 57.966 34.615 0.00 0.00 34.60 3.10
1950 1983 9.035607 CAATGCATTAAGATAGTAAACGAGTCT 57.964 33.333 12.53 0.00 0.00 3.24
1955 1988 9.569167 CATTAAGATAGTAAACGAGTCTGAACA 57.431 33.333 0.00 0.00 0.00 3.18
1976 2009 1.593265 CCAAGAATGGCCAAGCACC 59.407 57.895 10.96 0.00 40.58 5.01
2014 2047 7.037438 ACGACTAAAGAAACAGAAACTGTACA 58.963 34.615 4.84 0.00 44.62 2.90
2015 2048 7.546667 ACGACTAAAGAAACAGAAACTGTACAA 59.453 33.333 4.84 0.00 44.62 2.41
2016 2049 8.548721 CGACTAAAGAAACAGAAACTGTACAAT 58.451 33.333 4.84 0.00 44.62 2.71
2017 2050 9.651718 GACTAAAGAAACAGAAACTGTACAATG 57.348 33.333 4.84 0.00 44.62 2.82
2018 2051 8.129211 ACTAAAGAAACAGAAACTGTACAATGC 58.871 33.333 4.84 0.00 44.62 3.56
2019 2052 6.699575 AAGAAACAGAAACTGTACAATGCT 57.300 33.333 4.84 0.00 44.62 3.79
2020 2053 6.064846 AGAAACAGAAACTGTACAATGCTG 57.935 37.500 12.68 12.68 44.62 4.41
2021 2054 5.590259 AGAAACAGAAACTGTACAATGCTGT 59.410 36.000 13.74 13.74 44.62 4.40
2022 2055 6.765989 AGAAACAGAAACTGTACAATGCTGTA 59.234 34.615 17.97 0.00 44.62 2.74
2074 2107 1.308998 CCAAAACTCGCAACAGACCT 58.691 50.000 0.00 0.00 0.00 3.85
2095 2128 0.037590 TTGCTCCCACCATGTACCAC 59.962 55.000 0.00 0.00 0.00 4.16
2101 2134 1.547675 CCCACCATGTACCACAGCTTT 60.548 52.381 0.00 0.00 0.00 3.51
2194 2227 2.087646 GTCCTTCCAGATGAACCAAGC 58.912 52.381 0.00 0.00 0.00 4.01
2195 2228 1.988107 TCCTTCCAGATGAACCAAGCT 59.012 47.619 0.00 0.00 0.00 3.74
2207 2240 6.948309 AGATGAACCAAGCTACCAAAATAGTT 59.052 34.615 0.00 0.00 0.00 2.24
2251 2284 1.962807 CATTTTGGTGAAGGCCTGACA 59.037 47.619 5.69 7.53 0.00 3.58
2271 2304 1.985473 TGCAATGCAGAAGACCAAGT 58.015 45.000 2.72 0.00 33.32 3.16
2292 2325 1.871039 CAGGTCAAAACACCGTGGTAG 59.129 52.381 3.03 0.00 41.90 3.18
2293 2326 1.764134 AGGTCAAAACACCGTGGTAGA 59.236 47.619 3.03 0.00 41.90 2.59
2294 2327 2.370849 AGGTCAAAACACCGTGGTAGAT 59.629 45.455 3.03 0.00 41.90 1.98
2295 2328 2.740447 GGTCAAAACACCGTGGTAGATC 59.260 50.000 3.03 0.00 0.00 2.75
2296 2329 2.740447 GTCAAAACACCGTGGTAGATCC 59.260 50.000 3.03 0.00 0.00 3.36
2297 2330 1.730064 CAAAACACCGTGGTAGATCCG 59.270 52.381 3.03 0.00 39.52 4.18
2298 2331 0.971386 AAACACCGTGGTAGATCCGT 59.029 50.000 3.03 0.00 39.52 4.69
2299 2332 1.838112 AACACCGTGGTAGATCCGTA 58.162 50.000 3.03 0.00 39.52 4.02
2304 2337 2.228059 CCGTGGTAGATCCGTAGATGT 58.772 52.381 0.00 0.00 39.52 3.06
2311 2344 4.321082 GGTAGATCCGTAGATGTTACTGCC 60.321 50.000 0.00 0.00 30.90 4.85
2407 2440 5.300792 CCTTTTGGTACCACTTCAAGCTTTA 59.699 40.000 16.04 0.00 34.07 1.85
2409 2442 6.777213 TTTGGTACCACTTCAAGCTTTAAA 57.223 33.333 16.04 0.00 0.00 1.52
2438 2471 2.430465 CTTGCCGGCATATATTCTGCT 58.570 47.619 33.25 0.00 39.60 4.24
2479 2513 6.743575 ATAAGTGCAGTTCCAGTAATCAAC 57.256 37.500 10.78 0.00 0.00 3.18
2484 2518 3.758554 GCAGTTCCAGTAATCAACCACAT 59.241 43.478 0.00 0.00 0.00 3.21
2561 2595 4.944317 TCCATTGTTTTATCACGTGGCATA 59.056 37.500 17.00 4.16 0.00 3.14
2562 2596 5.592282 TCCATTGTTTTATCACGTGGCATAT 59.408 36.000 17.00 4.06 0.00 1.78
2643 2678 5.964958 TTTCCTGCCAGAGTAAAAGATTG 57.035 39.130 0.00 0.00 0.00 2.67
2696 2732 5.902613 ATTGTTACCCTGACATGACAATG 57.097 39.130 0.00 0.00 36.63 2.82
2706 2742 3.624326 ACATGACAATGTTGTTGGTCG 57.376 42.857 0.00 0.00 44.94 4.79
2707 2743 2.287547 ACATGACAATGTTGTTGGTCGC 60.288 45.455 0.00 0.00 44.94 5.19
2708 2744 0.306228 TGACAATGTTGTTGGTCGCG 59.694 50.000 0.00 0.00 42.43 5.87
2709 2745 0.584396 GACAATGTTGTTGGTCGCGA 59.416 50.000 3.71 3.71 42.43 5.87
2710 2746 0.586319 ACAATGTTGTTGGTCGCGAG 59.414 50.000 10.24 0.00 38.47 5.03
2711 2747 0.865111 CAATGTTGTTGGTCGCGAGA 59.135 50.000 10.24 0.00 38.16 4.04
2712 2748 1.464608 CAATGTTGTTGGTCGCGAGAT 59.535 47.619 10.24 0.00 45.19 2.75
2713 2749 1.359848 ATGTTGTTGGTCGCGAGATC 58.640 50.000 10.24 2.63 45.19 2.75
2714 2750 0.317160 TGTTGTTGGTCGCGAGATCT 59.683 50.000 10.24 0.00 43.23 2.75
2715 2751 1.270094 TGTTGTTGGTCGCGAGATCTT 60.270 47.619 10.24 0.00 43.23 2.40
2716 2752 2.029739 TGTTGTTGGTCGCGAGATCTTA 60.030 45.455 10.24 0.00 43.23 2.10
2717 2753 3.187700 GTTGTTGGTCGCGAGATCTTAT 58.812 45.455 10.24 0.00 43.23 1.73
2718 2754 2.809446 TGTTGGTCGCGAGATCTTATG 58.191 47.619 10.24 0.00 43.23 1.90
2719 2755 2.128035 GTTGGTCGCGAGATCTTATGG 58.872 52.381 10.24 0.00 43.23 2.74
2720 2756 0.673985 TGGTCGCGAGATCTTATGGG 59.326 55.000 10.24 0.00 43.23 4.00
2721 2757 0.674534 GGTCGCGAGATCTTATGGGT 59.325 55.000 10.24 0.00 45.19 4.51
2722 2758 1.068741 GGTCGCGAGATCTTATGGGTT 59.931 52.381 10.24 0.00 45.19 4.11
2723 2759 2.483188 GGTCGCGAGATCTTATGGGTTT 60.483 50.000 10.24 0.00 45.19 3.27
2724 2760 2.795470 GTCGCGAGATCTTATGGGTTTC 59.205 50.000 10.24 0.00 45.19 2.78
2725 2761 2.429250 TCGCGAGATCTTATGGGTTTCA 59.571 45.455 3.71 0.00 33.31 2.69
2726 2762 2.540101 CGCGAGATCTTATGGGTTTCAC 59.460 50.000 0.00 0.00 0.00 3.18
2727 2763 2.872858 GCGAGATCTTATGGGTTTCACC 59.127 50.000 0.00 0.00 37.60 4.02
2728 2764 3.432326 GCGAGATCTTATGGGTTTCACCT 60.432 47.826 0.00 0.00 38.64 4.00
2729 2765 4.372656 CGAGATCTTATGGGTTTCACCTC 58.627 47.826 0.00 0.00 38.64 3.85
2730 2766 4.100189 CGAGATCTTATGGGTTTCACCTCT 59.900 45.833 0.00 0.00 38.64 3.69
2731 2767 5.302059 CGAGATCTTATGGGTTTCACCTCTA 59.698 44.000 0.00 0.00 38.64 2.43
2732 2768 6.515862 CGAGATCTTATGGGTTTCACCTCTAG 60.516 46.154 0.00 0.00 38.64 2.43
2733 2769 4.755266 TCTTATGGGTTTCACCTCTAGC 57.245 45.455 0.00 0.00 38.64 3.42
2734 2770 3.454812 TCTTATGGGTTTCACCTCTAGCC 59.545 47.826 0.00 0.00 38.64 3.93
2735 2771 1.972588 ATGGGTTTCACCTCTAGCCT 58.027 50.000 0.00 0.00 38.64 4.58
2736 2772 0.984230 TGGGTTTCACCTCTAGCCTG 59.016 55.000 0.00 0.00 38.64 4.85
2737 2773 0.393132 GGGTTTCACCTCTAGCCTGC 60.393 60.000 0.00 0.00 38.64 4.85
2738 2774 0.393132 GGTTTCACCTCTAGCCTGCC 60.393 60.000 0.00 0.00 34.73 4.85
2739 2775 0.393132 GTTTCACCTCTAGCCTGCCC 60.393 60.000 0.00 0.00 0.00 5.36
2740 2776 1.562672 TTTCACCTCTAGCCTGCCCC 61.563 60.000 0.00 0.00 0.00 5.80
2741 2777 2.688666 CACCTCTAGCCTGCCCCA 60.689 66.667 0.00 0.00 0.00 4.96
2742 2778 2.124996 ACCTCTAGCCTGCCCCAA 59.875 61.111 0.00 0.00 0.00 4.12
2743 2779 2.301738 ACCTCTAGCCTGCCCCAAC 61.302 63.158 0.00 0.00 0.00 3.77
2744 2780 1.997874 CCTCTAGCCTGCCCCAACT 60.998 63.158 0.00 0.00 0.00 3.16
2745 2781 1.566298 CCTCTAGCCTGCCCCAACTT 61.566 60.000 0.00 0.00 0.00 2.66
2746 2782 0.393537 CTCTAGCCTGCCCCAACTTG 60.394 60.000 0.00 0.00 0.00 3.16
2747 2783 1.133809 TCTAGCCTGCCCCAACTTGT 61.134 55.000 0.00 0.00 0.00 3.16
2748 2784 0.251341 CTAGCCTGCCCCAACTTGTT 60.251 55.000 0.00 0.00 0.00 2.83
2749 2785 0.187361 TAGCCTGCCCCAACTTGTTT 59.813 50.000 0.00 0.00 0.00 2.83
2750 2786 1.069596 GCCTGCCCCAACTTGTTTG 59.930 57.895 0.00 0.00 34.63 2.93
2761 2797 3.123050 CAACTTGTTTGGCACTAAAGGC 58.877 45.455 0.00 0.00 0.00 4.35
2762 2798 2.666317 ACTTGTTTGGCACTAAAGGCT 58.334 42.857 0.00 0.00 34.73 4.58
2763 2799 3.031013 ACTTGTTTGGCACTAAAGGCTT 58.969 40.909 0.00 0.00 34.73 4.35
2764 2800 3.450817 ACTTGTTTGGCACTAAAGGCTTT 59.549 39.130 17.76 17.76 34.73 3.51
2765 2801 3.451141 TGTTTGGCACTAAAGGCTTTG 57.549 42.857 22.32 13.97 34.73 2.77
2766 2802 2.763448 TGTTTGGCACTAAAGGCTTTGT 59.237 40.909 22.32 14.58 34.73 2.83
2767 2803 3.196685 TGTTTGGCACTAAAGGCTTTGTT 59.803 39.130 22.32 6.06 34.73 2.83
2768 2804 3.451141 TTGGCACTAAAGGCTTTGTTG 57.549 42.857 22.32 18.03 34.73 3.33
2769 2805 2.383855 TGGCACTAAAGGCTTTGTTGT 58.616 42.857 22.32 14.44 34.73 3.32
2770 2806 2.763448 TGGCACTAAAGGCTTTGTTGTT 59.237 40.909 22.32 0.00 34.73 2.83
2771 2807 3.123050 GGCACTAAAGGCTTTGTTGTTG 58.877 45.455 22.32 11.95 0.00 3.33
2772 2808 3.430236 GGCACTAAAGGCTTTGTTGTTGT 60.430 43.478 22.32 8.35 0.00 3.32
2773 2809 4.180817 GCACTAAAGGCTTTGTTGTTGTT 58.819 39.130 22.32 0.00 0.00 2.83
2774 2810 4.032786 GCACTAAAGGCTTTGTTGTTGTTG 59.967 41.667 22.32 8.24 0.00 3.33
2775 2811 5.167845 CACTAAAGGCTTTGTTGTTGTTGT 58.832 37.500 22.32 0.00 0.00 3.32
2776 2812 5.637387 CACTAAAGGCTTTGTTGTTGTTGTT 59.363 36.000 22.32 0.00 0.00 2.83
2777 2813 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
2778 2814 3.951775 AGGCTTTGTTGTTGTTGTTGA 57.048 38.095 0.00 0.00 0.00 3.18
2779 2815 3.584834 AGGCTTTGTTGTTGTTGTTGAC 58.415 40.909 0.00 0.00 0.00 3.18
2780 2816 3.006323 AGGCTTTGTTGTTGTTGTTGACA 59.994 39.130 0.00 0.00 36.19 3.58
2781 2817 3.932089 GGCTTTGTTGTTGTTGTTGACAT 59.068 39.130 0.00 0.00 38.26 3.06
2782 2818 4.201705 GGCTTTGTTGTTGTTGTTGACATG 60.202 41.667 0.00 0.00 38.26 3.21
2783 2819 4.624882 GCTTTGTTGTTGTTGTTGACATGA 59.375 37.500 0.00 0.00 38.26 3.07
2784 2820 5.444481 GCTTTGTTGTTGTTGTTGACATGAC 60.444 40.000 0.00 0.00 38.26 3.06
2785 2821 4.773323 TGTTGTTGTTGTTGACATGACA 57.227 36.364 0.00 0.00 38.26 3.58
2786 2822 5.126396 TGTTGTTGTTGTTGACATGACAA 57.874 34.783 6.51 6.51 36.90 3.18
2787 2823 5.718146 TGTTGTTGTTGTTGACATGACAAT 58.282 33.333 13.54 0.00 39.71 2.71
2788 2824 5.575995 TGTTGTTGTTGTTGACATGACAATG 59.424 36.000 13.54 0.00 39.71 2.82
2877 2913 3.642848 ACACAGACAGGAAAATTGGCATT 59.357 39.130 0.00 0.00 0.00 3.56
2959 2995 1.686587 TCTTCAACTCTCGAAGCACCA 59.313 47.619 0.00 0.00 39.80 4.17
2979 3015 0.531090 CCGACACCTTTGACACGGAA 60.531 55.000 0.00 0.00 38.60 4.30
3843 3891 2.371841 TGCTGCTTCTAAAGGACTCCAA 59.628 45.455 0.00 0.00 0.00 3.53
3865 3913 8.183536 TCCAATTCATATTCTTGATGAACAACG 58.816 33.333 0.40 0.00 44.03 4.10
3873 3921 9.773328 ATATTCTTGATGAACAACGTACATTTG 57.227 29.630 0.00 3.23 37.52 2.32
4220 4268 2.086094 TGTTAGTCGAGCGTACCATGA 58.914 47.619 0.00 0.00 0.00 3.07
4231 4279 1.464608 CGTACCATGAACACTTGGCAG 59.535 52.381 0.00 0.00 36.41 4.85
4272 4320 4.178545 ACAAAATGCGAGGGAATTTGAG 57.821 40.909 4.95 0.00 31.52 3.02
4299 4347 6.294508 CGGAGTGGAAAACCAAAATTAGTGAT 60.295 38.462 0.00 0.00 0.00 3.06
4331 4379 9.077885 TGAAGGATGAAGTAGCAGTTTAATTTT 57.922 29.630 0.00 0.00 0.00 1.82
4417 4465 2.336088 CTGCCCCTTGTGTTTGCG 59.664 61.111 0.00 0.00 0.00 4.85
4439 4507 8.028540 TGCGCCTGTATAATTAAAGACATATG 57.971 34.615 4.18 0.00 0.00 1.78
4454 4522 6.747414 AGACATATGTTTGCTATGGAGGTA 57.253 37.500 10.30 0.00 32.06 3.08
4571 4639 6.388619 AATGCCGTCTCCCCTATATATTTT 57.611 37.500 0.00 0.00 0.00 1.82
4616 5035 7.476540 AGTAAATGCATCGAGGTATGGTATA 57.523 36.000 0.34 0.00 0.00 1.47
4637 5056 8.068380 GGTATATTCATTCGTCCTTTACTTTGC 58.932 37.037 0.00 0.00 0.00 3.68
4793 5220 4.384056 CTCCTGAACAAGAATGTGACAGT 58.616 43.478 0.00 0.00 40.46 3.55
4979 5515 6.689241 CACGTAACTCATTGTTTTTACAGCAA 59.311 34.615 0.00 0.00 39.89 3.91
4982 5542 4.606961 ACTCATTGTTTTTACAGCAACGG 58.393 39.130 0.00 0.00 0.00 4.44
4988 5548 3.057876 TGTTTTTACAGCAACGGCATAGG 60.058 43.478 0.00 0.00 44.61 2.57
5022 5582 3.454812 ACCCGATTCTTGCTAGGTATGTT 59.545 43.478 0.00 0.00 0.00 2.71
5025 5585 4.508124 CCGATTCTTGCTAGGTATGTTGTC 59.492 45.833 0.00 0.00 0.00 3.18
5090 5650 5.847304 TGCTATGAGATGCTAGAATTCGTT 58.153 37.500 0.00 0.00 0.00 3.85
5104 5664 5.591099 AGAATTCGTTTTGCAACAAGACAT 58.409 33.333 0.00 0.00 32.54 3.06
5121 5681 1.619827 ACATGCCAATTGACCAACCAG 59.380 47.619 7.12 0.00 0.00 4.00
5129 5689 5.713025 CCAATTGACCAACCAGTAATCTTG 58.287 41.667 7.12 0.00 0.00 3.02
5165 5729 7.546250 TCTAGTGTCATCTCTTCCTTCTTTT 57.454 36.000 0.00 0.00 0.00 2.27
5167 5731 9.090103 TCTAGTGTCATCTCTTCCTTCTTTTAA 57.910 33.333 0.00 0.00 0.00 1.52
5168 5732 9.364989 CTAGTGTCATCTCTTCCTTCTTTTAAG 57.635 37.037 0.00 0.00 0.00 1.85
5182 5749 5.365403 TCTTTTAAGTATTGGTTGTGCGG 57.635 39.130 0.00 0.00 0.00 5.69
5220 5788 2.437281 AGGCAGATGATACCTGACCAAG 59.563 50.000 0.00 0.00 40.50 3.61
5222 5790 3.201290 GCAGATGATACCTGACCAAGTG 58.799 50.000 0.00 0.00 33.65 3.16
5224 5792 4.623886 GCAGATGATACCTGACCAAGTGAA 60.624 45.833 0.00 0.00 33.65 3.18
5225 5793 5.491070 CAGATGATACCTGACCAAGTGAAA 58.509 41.667 0.00 0.00 33.65 2.69
5226 5794 5.352569 CAGATGATACCTGACCAAGTGAAAC 59.647 44.000 0.00 0.00 33.65 2.78
5228 5796 3.392947 TGATACCTGACCAAGTGAAACCA 59.607 43.478 0.00 0.00 37.80 3.67
5229 5797 2.348411 ACCTGACCAAGTGAAACCAG 57.652 50.000 0.00 0.00 37.80 4.00
5253 5940 9.918379 CAGAAATCCTGCCCTTCATTAGGACTT 62.918 44.444 0.00 0.00 41.76 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 139 4.709397 TGGACAAATATTTTGGCGAAGGAT 59.291 37.500 0.00 0.00 0.00 3.24
136 140 4.082845 TGGACAAATATTTTGGCGAAGGA 58.917 39.130 0.00 0.00 0.00 3.36
137 141 4.448537 TGGACAAATATTTTGGCGAAGG 57.551 40.909 0.00 0.00 0.00 3.46
163 167 3.644966 TGAATCACACCTTATGGTCCC 57.355 47.619 0.00 0.00 46.60 4.46
335 347 4.708726 ATTAGCACTGACCATGAAAAGC 57.291 40.909 0.00 0.00 0.00 3.51
336 348 8.299570 AGTAAAATTAGCACTGACCATGAAAAG 58.700 33.333 0.00 0.00 0.00 2.27
341 353 6.500684 ACAGTAAAATTAGCACTGACCATG 57.499 37.500 16.60 0.00 41.80 3.66
342 354 7.883311 ACTAACAGTAAAATTAGCACTGACCAT 59.117 33.333 16.60 6.42 41.80 3.55
344 356 7.668525 ACTAACAGTAAAATTAGCACTGACC 57.331 36.000 16.60 0.00 41.80 4.02
509 531 5.841957 AAATGGATGATGCTTTAGGTGTC 57.158 39.130 0.00 0.00 0.00 3.67
639 669 5.796424 AAACCAAAGTTCTGATGCTCAAT 57.204 34.783 0.00 0.00 34.19 2.57
742 772 9.412460 ACAGCATATTCTCATTTTGAAGGAATA 57.588 29.630 0.00 0.00 32.06 1.75
882 913 3.249799 TGTTCTGTGGTTTATTGTCTGCG 59.750 43.478 0.00 0.00 0.00 5.18
1081 1112 2.476320 GCAAAGCCCATCGGAGAGC 61.476 63.158 0.00 0.00 43.63 4.09
1151 1182 7.997773 AAAAGAGAATTCTTACTTGGGGTAC 57.002 36.000 9.87 0.00 42.80 3.34
1323 1356 4.380531 TCTTCTGTCAACTTACTTGCTGG 58.619 43.478 0.00 0.00 0.00 4.85
1331 1364 9.025041 TCTCTAACATGATCTTCTGTCAACTTA 57.975 33.333 0.00 0.00 0.00 2.24
1355 1388 3.974719 TCTCTCACTTATCCTGTGCTCT 58.025 45.455 0.00 0.00 35.58 4.09
1357 1390 4.284490 TGTTTCTCTCACTTATCCTGTGCT 59.716 41.667 0.00 0.00 35.58 4.40
1375 1408 7.221838 CCTCTAAGTTCTTCTCGATCATGTTTC 59.778 40.741 0.00 0.00 0.00 2.78
1380 1413 7.432869 CATTCCTCTAAGTTCTTCTCGATCAT 58.567 38.462 0.00 0.00 0.00 2.45
1385 1418 5.004922 AGCATTCCTCTAAGTTCTTCTCG 57.995 43.478 0.00 0.00 0.00 4.04
1398 1431 5.180868 CCTTATACATCTGCAAGCATTCCTC 59.819 44.000 0.00 0.00 0.00 3.71
1403 1436 5.039920 TCACCTTATACATCTGCAAGCAT 57.960 39.130 0.00 0.00 0.00 3.79
1412 1445 7.280876 TCAGTTTCAGCATTCACCTTATACATC 59.719 37.037 0.00 0.00 0.00 3.06
1452 1485 6.744537 GCATTGTATACAAAAGAACAGAGCTG 59.255 38.462 21.57 11.66 39.55 4.24
1453 1486 6.430925 TGCATTGTATACAAAAGAACAGAGCT 59.569 34.615 21.57 0.00 39.55 4.09
1493 1526 4.141937 TGCACAATATCAGTGTCCTACTCC 60.142 45.833 9.26 0.00 37.60 3.85
1501 1534 8.246180 CCTAAAAGAAATGCACAATATCAGTGT 58.754 33.333 9.26 0.00 39.17 3.55
1530 1563 9.453572 TTTGTCAATTATGAGTATCTCTGCTTT 57.546 29.630 0.00 0.00 35.88 3.51
1691 1724 4.084013 GCATTAGTAAGTTGCGGCGATATT 60.084 41.667 12.98 1.27 0.00 1.28
1692 1725 3.432252 GCATTAGTAAGTTGCGGCGATAT 59.568 43.478 12.98 0.00 0.00 1.63
1714 1747 3.077484 ACCCAGAGGTCACATGAAATG 57.923 47.619 0.00 0.00 46.45 2.32
1824 1857 1.541588 GCTCGCAACAAGAATTCCCTT 59.458 47.619 0.65 0.00 0.00 3.95
1835 1868 1.005037 CCAGTACCTGCTCGCAACA 60.005 57.895 0.00 0.00 0.00 3.33
1841 1874 2.237392 AGGATTTGTCCAGTACCTGCTC 59.763 50.000 0.00 0.00 0.00 4.26
1853 1886 6.024552 TGCAAGGTTGATTAAGGATTTGTC 57.975 37.500 0.00 0.00 0.00 3.18
1885 1918 6.303839 TGCATGGTCTAAAATATAACCTCCC 58.696 40.000 0.00 0.00 32.82 4.30
1888 1921 8.034313 TCTCTGCATGGTCTAAAATATAACCT 57.966 34.615 0.00 0.00 32.82 3.50
1890 1923 9.937175 GTTTCTCTGCATGGTCTAAAATATAAC 57.063 33.333 0.00 0.00 0.00 1.89
1950 1983 2.392662 TGGCCATTCTTGGTTTGTTCA 58.607 42.857 0.00 0.00 45.57 3.18
1955 1988 1.070601 GTGCTTGGCCATTCTTGGTTT 59.929 47.619 6.09 0.00 45.57 3.27
1976 2009 5.404946 TCTTTAGTCGTATCGTTCCTTTGG 58.595 41.667 0.00 0.00 0.00 3.28
2074 2107 1.145945 TGGTACATGGTGGGAGCAAAA 59.854 47.619 0.00 0.00 0.00 2.44
2095 2128 5.879223 AGAGACAAGGATGAATACAAAGCTG 59.121 40.000 0.00 0.00 0.00 4.24
2101 2134 4.705023 TCGACAGAGACAAGGATGAATACA 59.295 41.667 0.00 0.00 0.00 2.29
2194 2227 4.919168 TCGACACGACAACTATTTTGGTAG 59.081 41.667 0.00 0.00 0.00 3.18
2195 2228 4.869215 TCGACACGACAACTATTTTGGTA 58.131 39.130 0.00 0.00 0.00 3.25
2207 2240 2.915659 AGGGGCTTCGACACGACA 60.916 61.111 0.00 0.00 34.89 4.35
2251 2284 2.490903 GACTTGGTCTTCTGCATTGCAT 59.509 45.455 12.53 0.00 38.13 3.96
2271 2304 0.253610 ACCACGGTGTTTTGACCTGA 59.746 50.000 7.45 0.00 33.35 3.86
2292 2325 3.553096 CCTGGCAGTAACATCTACGGATC 60.553 52.174 14.43 0.00 0.00 3.36
2293 2326 2.365617 CCTGGCAGTAACATCTACGGAT 59.634 50.000 14.43 0.00 0.00 4.18
2294 2327 1.754803 CCTGGCAGTAACATCTACGGA 59.245 52.381 14.43 0.00 0.00 4.69
2295 2328 1.480954 ACCTGGCAGTAACATCTACGG 59.519 52.381 14.43 0.00 0.00 4.02
2296 2329 2.540515 CACCTGGCAGTAACATCTACG 58.459 52.381 14.43 0.00 0.00 3.51
2297 2330 2.420129 CCCACCTGGCAGTAACATCTAC 60.420 54.545 14.43 0.00 0.00 2.59
2298 2331 1.837439 CCCACCTGGCAGTAACATCTA 59.163 52.381 14.43 0.00 0.00 1.98
2299 2332 0.620556 CCCACCTGGCAGTAACATCT 59.379 55.000 14.43 0.00 0.00 2.90
2304 2337 0.770557 AACCTCCCACCTGGCAGTAA 60.771 55.000 14.43 0.00 0.00 2.24
2311 2344 1.697432 TGTGTTCTAACCTCCCACCTG 59.303 52.381 0.00 0.00 0.00 4.00
2347 2380 8.955061 AATTTGTTTTGTCGATTGTCATAGAG 57.045 30.769 0.00 0.00 0.00 2.43
2409 2442 6.664428 ATATATGCCGGCAAGGTAATTTTT 57.336 33.333 36.33 15.64 43.70 1.94
2413 2446 4.943705 CAGAATATATGCCGGCAAGGTAAT 59.056 41.667 36.33 22.33 43.70 1.89
2416 2449 2.783135 CAGAATATATGCCGGCAAGGT 58.217 47.619 36.33 23.69 43.70 3.50
2502 2536 6.042777 TGCTCGTGTCTCCTTTTATATCAAG 58.957 40.000 0.00 0.00 0.00 3.02
2582 2616 4.360951 TGTTCCCTTACAACCGAGAAAT 57.639 40.909 0.00 0.00 0.00 2.17
2696 2732 1.429463 AAGATCTCGCGACCAACAAC 58.571 50.000 3.71 0.00 0.00 3.32
2697 2733 3.186909 CATAAGATCTCGCGACCAACAA 58.813 45.455 3.71 0.00 0.00 2.83
2698 2734 2.481276 CCATAAGATCTCGCGACCAACA 60.481 50.000 3.71 0.00 0.00 3.33
2699 2735 2.128035 CCATAAGATCTCGCGACCAAC 58.872 52.381 3.71 0.00 0.00 3.77
2700 2736 1.068588 CCCATAAGATCTCGCGACCAA 59.931 52.381 3.71 0.00 0.00 3.67
2701 2737 0.673985 CCCATAAGATCTCGCGACCA 59.326 55.000 3.71 0.00 0.00 4.02
2702 2738 0.674534 ACCCATAAGATCTCGCGACC 59.325 55.000 3.71 0.00 0.00 4.79
2703 2739 2.510768 AACCCATAAGATCTCGCGAC 57.489 50.000 3.71 0.00 0.00 5.19
2704 2740 2.429250 TGAAACCCATAAGATCTCGCGA 59.571 45.455 9.26 9.26 0.00 5.87
2705 2741 2.540101 GTGAAACCCATAAGATCTCGCG 59.460 50.000 0.00 0.00 0.00 5.87
2720 2756 0.393132 GGGCAGGCTAGAGGTGAAAC 60.393 60.000 0.00 0.00 0.00 2.78
2721 2757 1.562672 GGGGCAGGCTAGAGGTGAAA 61.563 60.000 0.00 0.00 0.00 2.69
2722 2758 1.995626 GGGGCAGGCTAGAGGTGAA 60.996 63.158 0.00 0.00 0.00 3.18
2723 2759 2.365635 GGGGCAGGCTAGAGGTGA 60.366 66.667 0.00 0.00 0.00 4.02
2724 2760 2.300967 TTGGGGCAGGCTAGAGGTG 61.301 63.158 0.00 0.00 0.00 4.00
2725 2761 2.124996 TTGGGGCAGGCTAGAGGT 59.875 61.111 0.00 0.00 0.00 3.85
2726 2762 1.566298 AAGTTGGGGCAGGCTAGAGG 61.566 60.000 0.00 0.00 0.00 3.69
2727 2763 0.393537 CAAGTTGGGGCAGGCTAGAG 60.394 60.000 0.00 0.00 0.00 2.43
2728 2764 1.133809 ACAAGTTGGGGCAGGCTAGA 61.134 55.000 7.96 0.00 0.00 2.43
2729 2765 0.251341 AACAAGTTGGGGCAGGCTAG 60.251 55.000 7.96 0.00 0.00 3.42
2730 2766 0.187361 AAACAAGTTGGGGCAGGCTA 59.813 50.000 7.96 0.00 0.00 3.93
2731 2767 1.075301 AAACAAGTTGGGGCAGGCT 60.075 52.632 7.96 0.00 0.00 4.58
2732 2768 1.069596 CAAACAAGTTGGGGCAGGC 59.930 57.895 7.96 0.00 33.18 4.85
2740 2776 3.123050 GCCTTTAGTGCCAAACAAGTTG 58.877 45.455 0.00 0.00 36.94 3.16
2741 2777 3.031013 AGCCTTTAGTGCCAAACAAGTT 58.969 40.909 0.00 0.00 0.00 2.66
2742 2778 2.666317 AGCCTTTAGTGCCAAACAAGT 58.334 42.857 0.00 0.00 0.00 3.16
2743 2779 3.733443 AAGCCTTTAGTGCCAAACAAG 57.267 42.857 0.00 0.00 0.00 3.16
2744 2780 3.196685 ACAAAGCCTTTAGTGCCAAACAA 59.803 39.130 0.00 0.00 0.00 2.83
2745 2781 2.763448 ACAAAGCCTTTAGTGCCAAACA 59.237 40.909 0.00 0.00 0.00 2.83
2746 2782 3.452755 ACAAAGCCTTTAGTGCCAAAC 57.547 42.857 0.00 0.00 0.00 2.93
2747 2783 3.196685 ACAACAAAGCCTTTAGTGCCAAA 59.803 39.130 0.00 0.00 0.00 3.28
2748 2784 2.763448 ACAACAAAGCCTTTAGTGCCAA 59.237 40.909 0.00 0.00 0.00 4.52
2749 2785 2.383855 ACAACAAAGCCTTTAGTGCCA 58.616 42.857 0.00 0.00 0.00 4.92
2750 2786 3.123050 CAACAACAAAGCCTTTAGTGCC 58.877 45.455 0.00 0.00 0.00 5.01
2751 2787 3.780902 ACAACAACAAAGCCTTTAGTGC 58.219 40.909 0.00 0.00 0.00 4.40
2752 2788 5.167845 ACAACAACAACAAAGCCTTTAGTG 58.832 37.500 0.00 0.00 0.00 2.74
2753 2789 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
2754 2790 5.866633 TCAACAACAACAACAAAGCCTTTAG 59.133 36.000 0.00 0.00 0.00 1.85
2755 2791 5.635700 GTCAACAACAACAACAAAGCCTTTA 59.364 36.000 0.00 0.00 0.00 1.85
2756 2792 4.450757 GTCAACAACAACAACAAAGCCTTT 59.549 37.500 0.00 0.00 0.00 3.11
2757 2793 3.993736 GTCAACAACAACAACAAAGCCTT 59.006 39.130 0.00 0.00 0.00 4.35
2758 2794 3.006323 TGTCAACAACAACAACAAAGCCT 59.994 39.130 0.00 0.00 34.03 4.58
2759 2795 3.321497 TGTCAACAACAACAACAAAGCC 58.679 40.909 0.00 0.00 34.03 4.35
2760 2796 4.624882 TCATGTCAACAACAACAACAAAGC 59.375 37.500 0.00 0.00 42.37 3.51
2761 2797 5.632764 TGTCATGTCAACAACAACAACAAAG 59.367 36.000 0.00 0.00 42.37 2.77
2762 2798 5.532557 TGTCATGTCAACAACAACAACAAA 58.467 33.333 0.00 0.00 42.37 2.83
2763 2799 5.126396 TGTCATGTCAACAACAACAACAA 57.874 34.783 0.00 0.00 42.37 2.83
2764 2800 4.773323 TGTCATGTCAACAACAACAACA 57.227 36.364 0.00 0.00 42.37 3.33
2765 2801 5.576384 ACATTGTCATGTCAACAACAACAAC 59.424 36.000 7.55 0.00 39.69 3.32
2766 2802 5.718146 ACATTGTCATGTCAACAACAACAA 58.282 33.333 7.55 0.69 39.69 2.83
2767 2803 5.321959 ACATTGTCATGTCAACAACAACA 57.678 34.783 7.55 0.00 39.69 3.33
2768 2804 5.500610 GCAACATTGTCATGTCAACAACAAC 60.501 40.000 7.55 0.00 43.34 3.32
2769 2805 4.565962 GCAACATTGTCATGTCAACAACAA 59.434 37.500 7.55 2.84 43.34 2.83
2770 2806 4.111198 GCAACATTGTCATGTCAACAACA 58.889 39.130 7.55 0.00 43.34 3.33
2771 2807 4.362279 AGCAACATTGTCATGTCAACAAC 58.638 39.130 7.55 0.00 43.34 3.32
2772 2808 4.652421 AGCAACATTGTCATGTCAACAA 57.348 36.364 7.55 4.30 43.34 2.83
2773 2809 4.320421 GCTAGCAACATTGTCATGTCAACA 60.320 41.667 10.63 0.00 43.34 3.33
2774 2810 4.083110 AGCTAGCAACATTGTCATGTCAAC 60.083 41.667 18.83 0.00 43.34 3.18
2775 2811 4.074259 AGCTAGCAACATTGTCATGTCAA 58.926 39.130 18.83 7.83 43.34 3.18
2776 2812 3.678289 AGCTAGCAACATTGTCATGTCA 58.322 40.909 18.83 0.00 43.34 3.58
2777 2813 4.394300 AGAAGCTAGCAACATTGTCATGTC 59.606 41.667 18.83 0.00 43.34 3.06
2778 2814 4.155462 CAGAAGCTAGCAACATTGTCATGT 59.845 41.667 18.83 0.00 46.34 3.21
2779 2815 4.155462 ACAGAAGCTAGCAACATTGTCATG 59.845 41.667 18.83 5.35 36.34 3.07
2780 2816 4.155462 CACAGAAGCTAGCAACATTGTCAT 59.845 41.667 18.83 0.00 0.00 3.06
2781 2817 3.499537 CACAGAAGCTAGCAACATTGTCA 59.500 43.478 18.83 0.00 0.00 3.58
2782 2818 3.748048 TCACAGAAGCTAGCAACATTGTC 59.252 43.478 18.83 2.38 0.00 3.18
2783 2819 3.743521 TCACAGAAGCTAGCAACATTGT 58.256 40.909 18.83 10.60 0.00 2.71
2784 2820 4.634883 AGATCACAGAAGCTAGCAACATTG 59.365 41.667 18.83 9.97 0.00 2.82
2785 2821 4.634883 CAGATCACAGAAGCTAGCAACATT 59.365 41.667 18.83 1.39 0.00 2.71
2786 2822 4.190001 CAGATCACAGAAGCTAGCAACAT 58.810 43.478 18.83 0.00 0.00 2.71
2787 2823 3.007290 ACAGATCACAGAAGCTAGCAACA 59.993 43.478 18.83 0.00 0.00 3.33
2788 2824 3.594134 ACAGATCACAGAAGCTAGCAAC 58.406 45.455 18.83 10.23 0.00 4.17
2877 2913 1.777878 TGGCAACCTACCAAAGAAGGA 59.222 47.619 0.00 0.00 36.66 3.36
2959 2995 1.227438 CCGTGTCAAAGGTGTCGGT 60.227 57.895 0.00 0.00 33.51 4.69
2979 3015 2.566746 AGGGAAGGGTCATCAAGATGT 58.433 47.619 9.66 0.00 39.72 3.06
3036 3072 8.757982 ACTTGAGACCAATTATAGCATTGAAT 57.242 30.769 0.00 0.00 36.39 2.57
3042 3078 7.828717 TCAAATGACTTGAGACCAATTATAGCA 59.171 33.333 0.00 0.00 39.20 3.49
3698 3746 8.078596 TGTCAGTGTAATCATGAGATAGAATCG 58.921 37.037 0.09 0.00 33.08 3.34
3843 3891 9.161629 TGTACGTTGTTCATCAAGAATATGAAT 57.838 29.630 0.00 0.00 43.29 2.57
3873 3921 7.332926 TCTGATTGCTTGACTTCTTGAAGTATC 59.667 37.037 14.99 13.02 32.22 2.24
4027 4075 2.714250 TCCTTGCCTTTTTACTGGGAGA 59.286 45.455 0.00 0.00 0.00 3.71
4084 4132 2.551459 CAAAACTCTGCAAGGGAGTCAG 59.449 50.000 7.48 0.00 35.24 3.51
4220 4268 1.131638 TCTCTGACCTGCCAAGTGTT 58.868 50.000 0.00 0.00 0.00 3.32
4299 4347 5.827797 ACTGCTACTTCATCCTTCAAACAAA 59.172 36.000 0.00 0.00 0.00 2.83
4331 4379 0.315251 CACTTCCGCTCACAGACAGA 59.685 55.000 0.00 0.00 0.00 3.41
4571 4639 6.520021 ACTAATGGATGATTGGATGGAAGA 57.480 37.500 0.00 0.00 0.00 2.87
4616 5035 6.879458 AGTAGCAAAGTAAAGGACGAATGAAT 59.121 34.615 0.00 0.00 0.00 2.57
4652 5071 4.386652 GGCAGCAAAGTTATGTTCATTGTG 59.613 41.667 0.00 0.00 0.00 3.33
4663 5082 1.541147 GCACATGAGGCAGCAAAGTTA 59.459 47.619 0.00 0.00 0.00 2.24
4793 5220 4.083324 GCTTGTTCATCTCCATCGTTTTCA 60.083 41.667 0.00 0.00 0.00 2.69
4852 5387 0.606604 GCCCCACTCAGAAAGTACGA 59.393 55.000 0.00 0.00 36.07 3.43
4853 5388 0.320374 TGCCCCACTCAGAAAGTACG 59.680 55.000 0.00 0.00 36.07 3.67
4926 5462 2.622436 GAAGCTAGTACCTTGCCTGTG 58.378 52.381 0.00 0.00 33.03 3.66
4979 5515 3.688694 TGACTGTAAAACCTATGCCGT 57.311 42.857 0.00 0.00 0.00 5.68
4982 5542 3.126343 CGGGTTGACTGTAAAACCTATGC 59.874 47.826 18.90 6.75 44.43 3.14
4988 5548 5.449304 CAAGAATCGGGTTGACTGTAAAAC 58.551 41.667 0.00 0.00 0.00 2.43
5022 5582 6.859112 AGTAAAAGCTGATAGAAGAGGACA 57.141 37.500 0.00 0.00 0.00 4.02
5025 5585 9.877178 TTTCTTAGTAAAAGCTGATAGAAGAGG 57.123 33.333 0.00 0.00 0.00 3.69
5090 5650 2.975732 TTGGCATGTCTTGTTGCAAA 57.024 40.000 0.00 0.00 40.66 3.68
5104 5664 2.666272 TACTGGTTGGTCAATTGGCA 57.334 45.000 12.93 0.00 0.00 4.92
5161 5725 4.915085 CACCGCACAACCAATACTTAAAAG 59.085 41.667 0.00 0.00 0.00 2.27
5165 5729 1.807742 GCACCGCACAACCAATACTTA 59.192 47.619 0.00 0.00 0.00 2.24
5167 5731 0.536233 TGCACCGCACAACCAATACT 60.536 50.000 0.00 0.00 31.71 2.12
5168 5732 0.525761 ATGCACCGCACAACCAATAC 59.474 50.000 0.00 0.00 43.04 1.89
5182 5749 1.919918 CCTCGAGTCTTCAGATGCAC 58.080 55.000 12.31 0.00 0.00 4.57
5220 5788 1.546029 GGGCAGGATTTCTGGTTTCAC 59.454 52.381 0.00 0.00 43.54 3.18
5222 5790 2.222227 AGGGCAGGATTTCTGGTTTC 57.778 50.000 0.00 0.00 43.54 2.78
5224 5792 1.428912 TGAAGGGCAGGATTTCTGGTT 59.571 47.619 0.00 0.00 43.54 3.67
5225 5793 1.075601 TGAAGGGCAGGATTTCTGGT 58.924 50.000 0.00 0.00 43.54 4.00
5226 5794 2.449137 ATGAAGGGCAGGATTTCTGG 57.551 50.000 0.00 0.00 43.54 3.86
5228 5796 3.788142 TCCTAATGAAGGGCAGGATTTCT 59.212 43.478 0.00 0.00 46.55 2.52
5229 5797 4.170468 TCCTAATGAAGGGCAGGATTTC 57.830 45.455 0.00 0.00 46.55 2.17
5253 5940 3.844211 AGCCATAGTAGGACAAAGTGGAA 59.156 43.478 0.00 0.00 0.00 3.53
5254 5941 3.197766 CAGCCATAGTAGGACAAAGTGGA 59.802 47.826 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.