Multiple sequence alignment - TraesCS2B01G601500

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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 TraesCS2B01G601500 chr2B 100.000 3798 0 0 1 3798 784280490 784276693 0.000000e+00 7014.0
1 TraesCS2B01G601500 chr2B 92.867 715 49 2 1 714 689307279 689306566 0.000000e+00 1037.0
2 TraesCS2B01G601500 chr2B 81.238 517 81 10 1086 1597 784725851 784726356 1.640000e-108 403.0
3 TraesCS2B01G601500 chrUn 91.041 2065 110 31 722 2767 31029752 31031760 0.000000e+00 2719.0
4 TraesCS2B01G601500 chrUn 93.529 340 16 5 3459 3798 31088240 31088573 5.660000e-138 501.0
5 TraesCS2B01G601500 chrUn 97.235 217 6 0 3010 3226 31087309 31087525 5.990000e-98 368.0
6 TraesCS2B01G601500 chrUn 88.382 241 17 6 3222 3460 31087951 31088182 2.890000e-71 279.0
7 TraesCS2B01G601500 chr2D 93.017 1604 75 14 926 2528 648359305 648357738 0.000000e+00 2307.0
8 TraesCS2B01G601500 chr2D 88.095 588 46 13 3222 3798 648355996 648355422 0.000000e+00 676.0
9 TraesCS2B01G601500 chr2D 82.582 488 68 10 1086 1569 648702618 648703092 7.590000e-112 414.0
10 TraesCS2B01G601500 chr2D 91.964 224 11 4 722 943 648359537 648359319 1.330000e-79 307.0
11 TraesCS2B01G601500 chr2D 98.261 115 2 0 3010 3124 648356563 648356449 6.430000e-48 202.0
12 TraesCS2B01G601500 chr2D 76.000 375 73 13 1117 1483 648511837 648512202 1.080000e-40 178.0
13 TraesCS2B01G601500 chr2D 77.061 279 20 23 2554 2789 648357738 648357461 1.850000e-23 121.0
14 TraesCS2B01G601500 chr2D 88.889 54 6 0 630 683 57203094 57203147 2.450000e-07 67.6
15 TraesCS2B01G601500 chr2D 100.000 28 0 0 3199 3226 648356449 648356422 7.000000e-03 52.8
16 TraesCS2B01G601500 chr5A 93.689 713 43 2 1 712 34488918 34488207 0.000000e+00 1066.0
17 TraesCS2B01G601500 chr5A 92.779 637 45 1 1 637 447645839 447645204 0.000000e+00 920.0
18 TraesCS2B01G601500 chr5A 91.327 196 17 0 442 637 447638480 447638285 6.250000e-68 268.0
19 TraesCS2B01G601500 chr6B 93.427 715 45 2 1 714 118686837 118687550 0.000000e+00 1059.0


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 TraesCS2B01G601500 chr2B 784276693 784280490 3797 True 7014.000000 7014 100.000000 1 3798 1 chr2B.!!$R2 3797
1 TraesCS2B01G601500 chr2B 689306566 689307279 713 True 1037.000000 1037 92.867000 1 714 1 chr2B.!!$R1 713
2 TraesCS2B01G601500 chr2B 784725851 784726356 505 False 403.000000 403 81.238000 1086 1597 1 chr2B.!!$F1 511
3 TraesCS2B01G601500 chrUn 31029752 31031760 2008 False 2719.000000 2719 91.041000 722 2767 1 chrUn.!!$F1 2045
4 TraesCS2B01G601500 chrUn 31087309 31088573 1264 False 382.666667 501 93.048667 3010 3798 3 chrUn.!!$F2 788
5 TraesCS2B01G601500 chr2D 648355422 648359537 4115 True 610.966667 2307 91.399667 722 3798 6 chr2D.!!$R1 3076
6 TraesCS2B01G601500 chr5A 34488207 34488918 711 True 1066.000000 1066 93.689000 1 712 1 chr5A.!!$R1 711
7 TraesCS2B01G601500 chr5A 447645204 447645839 635 True 920.000000 920 92.779000 1 637 1 chr5A.!!$R3 636
8 TraesCS2B01G601500 chr6B 118686837 118687550 713 False 1059.000000 1059 93.427000 1 714 1 chr6B.!!$F1 713

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
624 625 0.457851 TGCCTCAAAACCCAAACACG 59.542 50.0 0.0 0.0 0.00 4.49 F
1356 1397 0.250234 CGCTTCATCAACCTCCAGGA 59.750 55.0 0.0 0.0 38.94 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2049 0.249120 TAGTGGGGTGCACTTCGATG 59.751 55.0 17.98 0.0 34.38 3.84 R
2917 3074 0.109597 GTTGGCGACCAAATCTGCTG 60.110 55.0 12.01 0.0 45.73 4.41 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
30 31 1.306825 ATGTCCTCCTCAGCCAGCT 60.307 57.895 0.00 0.00 0.00 4.24
47 48 1.136305 AGCTAGCGTGCCTCGAATTTA 59.864 47.619 9.55 0.00 42.86 1.40
79 80 4.221041 GCAAGGTCCTCTAGTTTGTACTCT 59.779 45.833 0.00 0.00 35.78 3.24
110 111 7.147620 TGGTATTCTGTATCAATAAGAACCGGT 60.148 37.037 0.00 0.00 33.01 5.28
113 114 4.049186 CTGTATCAATAAGAACCGGTCGG 58.951 47.826 8.04 7.97 42.03 4.79
131 132 4.235360 GTCGGTGATCGGATTTATCGAAT 58.765 43.478 11.43 0.00 40.15 3.34
185 186 2.033372 TCCGCCCATCGAATGTTACTA 58.967 47.619 0.00 0.00 41.67 1.82
229 230 0.744414 ATGTTTCCTCGTCGCCATGG 60.744 55.000 7.63 7.63 0.00 3.66
233 234 2.202932 CCTCGTCGCCATGGGAAG 60.203 66.667 15.13 11.38 0.00 3.46
243 244 0.816825 CCATGGGAAGATGTCGCCAG 60.817 60.000 2.85 0.00 38.42 4.85
248 249 1.471676 GGGAAGATGTCGCCAGTGTAG 60.472 57.143 0.00 0.00 33.06 2.74
302 303 1.952990 TCGTTGAAAGCTTGCATGGAA 59.047 42.857 8.28 0.00 0.00 3.53
413 414 9.155975 GACATAGCATGTAATTCCCTTATGTAG 57.844 37.037 0.00 0.00 45.03 2.74
449 450 1.376037 CCGTTCTCCACTTGGCTCC 60.376 63.158 0.00 0.00 34.44 4.70
458 459 1.284785 CCACTTGGCTCCCCATAAAGA 59.715 52.381 0.00 0.00 41.78 2.52
461 462 0.629058 TTGGCTCCCCATAAAGACCC 59.371 55.000 0.00 0.00 41.78 4.46
475 476 3.894547 GACCCGTGAACCGCCATGT 62.895 63.158 0.00 0.00 34.38 3.21
491 492 2.287547 CCATGTGTTGTTGGAACCTTCG 60.288 50.000 0.00 0.00 34.81 3.79
516 517 6.918892 TTATTCGGATGTCAATGTAGTTGG 57.081 37.500 0.00 0.00 38.39 3.77
525 526 7.438459 GGATGTCAATGTAGTTGGTATGTACTC 59.562 40.741 0.00 0.00 38.39 2.59
539 540 3.476295 TGTACTCGTGATGACGTTACC 57.524 47.619 4.24 0.00 46.20 2.85
566 567 7.815549 CCCAACTTATTGTACCAAAACATAACC 59.184 37.037 0.00 0.00 33.60 2.85
622 623 2.158842 CCATTGCCTCAAAACCCAAACA 60.159 45.455 0.00 0.00 0.00 2.83
624 625 0.457851 TGCCTCAAAACCCAAACACG 59.542 50.000 0.00 0.00 0.00 4.49
625 626 0.874175 GCCTCAAAACCCAAACACGC 60.874 55.000 0.00 0.00 0.00 5.34
627 628 0.744281 CTCAAAACCCAAACACGCCT 59.256 50.000 0.00 0.00 0.00 5.52
664 665 5.278660 CCTTAGCTTTGTTCAGATGTGCTTT 60.279 40.000 0.00 0.00 0.00 3.51
719 720 4.396357 TTGGATCCCCAAGAGCTAAAAA 57.604 40.909 9.90 0.00 46.94 1.94
752 753 9.880157 TCGCTTTAGTTTACTAATACTGGAATT 57.120 29.630 3.37 0.00 38.16 2.17
774 775 6.539649 TTTCTCAATCACTGTAAAGTTCGG 57.460 37.500 0.00 0.00 0.00 4.30
865 866 4.692371 GCAGTCGCTTAAAAGGTTTTTG 57.308 40.909 0.00 0.00 34.30 2.44
866 867 4.109766 GCAGTCGCTTAAAAGGTTTTTGT 58.890 39.130 0.00 0.00 34.30 2.83
872 879 9.373603 AGTCGCTTAAAAGGTTTTTGTTTTATT 57.626 25.926 0.00 0.00 30.27 1.40
930 937 8.574251 TTCAAGGCTCATGCTACTTTAATAAA 57.426 30.769 0.00 0.00 39.59 1.40
934 941 6.543831 AGGCTCATGCTACTTTAATAAACAGG 59.456 38.462 0.00 0.00 39.59 4.00
972 1013 2.037049 TGGCCCCGACGGTTACTA 59.963 61.111 13.94 0.00 0.00 1.82
973 1014 2.012902 CTGGCCCCGACGGTTACTAG 62.013 65.000 13.94 5.14 0.00 2.57
974 1015 2.105729 GCCCCGACGGTTACTAGC 59.894 66.667 13.94 1.98 0.00 3.42
975 1016 2.810403 CCCCGACGGTTACTAGCC 59.190 66.667 13.94 0.00 0.00 3.93
1313 1354 4.517703 GCGACGACTCGAGGGACG 62.518 72.222 18.41 19.34 43.06 4.79
1356 1397 0.250234 CGCTTCATCAACCTCCAGGA 59.750 55.000 0.00 0.00 38.94 3.86
1363 1404 3.003763 AACCTCCAGGACGGCCTC 61.004 66.667 7.01 0.00 44.80 4.70
1384 1425 2.202756 GACGTGCGTCATCCTCCC 60.203 66.667 18.32 0.00 44.02 4.30
1388 1429 3.770040 TGCGTCATCCTCCCCGTG 61.770 66.667 0.00 0.00 0.00 4.94
1582 1626 1.227205 CAGGAGGAGCACGCATCTC 60.227 63.158 0.00 0.00 0.00 2.75
1706 1750 0.320073 TAGTTTGCTTCCGGTGGACG 60.320 55.000 0.00 0.00 43.80 4.79
1707 1751 1.890510 GTTTGCTTCCGGTGGACGT 60.891 57.895 0.00 0.00 42.24 4.34
1708 1752 1.890041 TTTGCTTCCGGTGGACGTG 60.890 57.895 0.00 0.00 42.24 4.49
1709 1753 3.818121 TTGCTTCCGGTGGACGTGG 62.818 63.158 0.00 0.00 42.24 4.94
1710 1754 3.998672 GCTTCCGGTGGACGTGGA 61.999 66.667 0.00 0.00 42.24 4.02
1711 1755 2.048503 CTTCCGGTGGACGTGGAC 60.049 66.667 0.00 0.00 42.24 4.02
1732 1776 0.677098 ACAAGCAGCAGCAGGATCAG 60.677 55.000 3.17 0.00 45.49 2.90
1733 1777 1.749638 AAGCAGCAGCAGGATCAGC 60.750 57.895 3.17 0.00 45.49 4.26
1734 1778 2.437895 GCAGCAGCAGGATCAGCA 60.438 61.111 11.35 0.00 41.58 4.41
1750 1794 3.472263 GCAATCCGCGTTTCAAGTT 57.528 47.368 4.92 0.00 0.00 2.66
1809 1853 4.577246 CTGCGCCTACTCCTCGGC 62.577 72.222 4.18 0.00 42.86 5.54
1848 1892 1.070786 GTTGGACTGCTCCGGTCAA 59.929 57.895 0.00 0.00 41.15 3.18
1964 2008 3.321497 CATCAGATCTACGCCCTTAAGC 58.679 50.000 0.00 0.00 0.00 3.09
1981 2025 0.742281 AGCTAAGCATGGACACGCTG 60.742 55.000 0.00 0.00 38.82 5.18
1984 2028 1.298157 TAAGCATGGACACGCTGCAC 61.298 55.000 0.00 0.00 38.82 4.57
2005 2049 1.742750 GCCACTTTGACCGAGATACCC 60.743 57.143 0.00 0.00 0.00 3.69
2020 2064 1.906105 TACCCATCGAAGTGCACCCC 61.906 60.000 14.63 4.48 0.00 4.95
2032 2076 2.124736 CACCCCACTATGCCACGG 60.125 66.667 0.00 0.00 0.00 4.94
2056 2100 1.449601 AATCCCATGCACCGTCGAC 60.450 57.895 5.18 5.18 0.00 4.20
2081 2125 3.596214 AGGCTGTCGTTTGTTACCATAG 58.404 45.455 0.00 0.00 0.00 2.23
2129 2173 2.549754 ACCAAGCAAGAACAAGATGACG 59.450 45.455 0.00 0.00 0.00 4.35
2131 2175 3.003689 CCAAGCAAGAACAAGATGACGTT 59.996 43.478 0.00 0.00 0.00 3.99
2136 2180 4.702392 CAAGAACAAGATGACGTTGTAGC 58.298 43.478 0.00 0.00 37.13 3.58
2137 2181 3.990092 AGAACAAGATGACGTTGTAGCA 58.010 40.909 0.00 0.00 37.13 3.49
2138 2182 3.990469 AGAACAAGATGACGTTGTAGCAG 59.010 43.478 0.00 0.00 37.13 4.24
2139 2183 2.069273 ACAAGATGACGTTGTAGCAGC 58.931 47.619 0.00 0.00 36.35 5.25
2146 2190 1.461127 GACGTTGTAGCAGCCAAAGAG 59.539 52.381 4.74 0.00 0.00 2.85
2175 2219 3.431055 TGACAACGCCTGGCAAAG 58.569 55.556 20.29 9.52 41.45 2.77
2180 2224 1.968540 AACGCCTGGCAAAGCTCTC 60.969 57.895 20.29 0.00 0.00 3.20
2232 2276 2.333014 CTCGGTCTTCTTTGCAGAGAC 58.667 52.381 6.42 9.34 31.45 3.36
2263 2307 1.132640 GCTCGTCGAACAACATGGC 59.867 57.895 0.00 0.00 0.00 4.40
2278 2322 2.737830 GGCGGTGCCCTCTCTATC 59.262 66.667 0.00 0.00 44.06 2.08
2304 2348 2.301583 ACCTCAAGAGCAAGGAGAAGTC 59.698 50.000 0.00 0.00 36.46 3.01
2332 2376 3.188460 TGCATCTAAAGGACGAAACAAGC 59.812 43.478 0.00 0.00 0.00 4.01
2338 2382 0.946221 AGGACGAAACAAGCGAGCAG 60.946 55.000 0.00 0.00 0.00 4.24
2362 2406 4.309950 AGGGGCACGTGTCGGTTC 62.310 66.667 18.38 5.41 0.00 3.62
2462 2506 3.558746 GGTGCTCTATGAGATGGATTGGG 60.559 52.174 0.00 0.00 0.00 4.12
2463 2507 3.326006 GTGCTCTATGAGATGGATTGGGA 59.674 47.826 0.00 0.00 0.00 4.37
2464 2508 3.326006 TGCTCTATGAGATGGATTGGGAC 59.674 47.826 0.00 0.00 0.00 4.46
2480 2524 1.795177 GACGTCTTTCCGTCGACCG 60.795 63.158 10.58 8.26 46.47 4.79
2481 2525 2.175184 GACGTCTTTCCGTCGACCGA 62.175 60.000 10.58 6.20 46.47 4.69
2482 2526 1.795177 CGTCTTTCCGTCGACCGAC 60.795 63.158 10.58 12.09 41.40 4.79
2483 2527 1.443363 GTCTTTCCGTCGACCGACC 60.443 63.158 15.74 0.43 41.76 4.79
2484 2528 2.126189 CTTTCCGTCGACCGACCC 60.126 66.667 15.74 0.00 41.76 4.46
2485 2529 2.598394 TTTCCGTCGACCGACCCT 60.598 61.111 15.74 0.00 41.76 4.34
2486 2530 2.151049 CTTTCCGTCGACCGACCCTT 62.151 60.000 15.74 0.00 41.76 3.95
2487 2531 2.424705 TTTCCGTCGACCGACCCTTG 62.425 60.000 15.74 3.12 41.76 3.61
2488 2532 3.677648 CCGTCGACCGACCCTTGT 61.678 66.667 15.74 0.00 41.76 3.16
2489 2533 2.126580 CGTCGACCGACCCTTGTC 60.127 66.667 15.74 0.00 41.76 3.18
2490 2534 2.623915 CGTCGACCGACCCTTGTCT 61.624 63.158 15.74 0.00 41.76 3.41
2491 2535 1.212229 GTCGACCGACCCTTGTCTC 59.788 63.158 11.13 0.00 39.47 3.36
2492 2536 1.074423 TCGACCGACCCTTGTCTCT 59.926 57.895 0.00 0.00 39.47 3.10
2493 2537 0.959372 TCGACCGACCCTTGTCTCTC 60.959 60.000 0.00 0.00 39.47 3.20
2502 2546 2.025321 ACCCTTGTCTCTCTCTCTCCTC 60.025 54.545 0.00 0.00 0.00 3.71
2529 2573 5.241949 GTGAGAGGTGAGAAACAAGAGTAGA 59.758 44.000 0.00 0.00 0.00 2.59
2530 2574 5.833667 TGAGAGGTGAGAAACAAGAGTAGAA 59.166 40.000 0.00 0.00 0.00 2.10
2534 2578 7.180051 AGAGGTGAGAAACAAGAGTAGAATGAT 59.820 37.037 0.00 0.00 0.00 2.45
2600 2644 7.440255 GTGGTAACTTGTTAGCTAGTTTCAGAA 59.560 37.037 19.12 0.00 40.24 3.02
2603 2647 8.989980 GTAACTTGTTAGCTAGTTTCAGAATGT 58.010 33.333 11.18 0.00 40.24 2.71
2607 2654 8.896320 TTGTTAGCTAGTTTCAGAATGTGTTA 57.104 30.769 0.00 0.00 37.40 2.41
2613 2660 8.299570 AGCTAGTTTCAGAATGTGTTATTTTGG 58.700 33.333 0.00 0.00 37.40 3.28
2648 2699 9.255304 GTTTGCAGATTATTTTGGTTTTAGTCA 57.745 29.630 0.00 0.00 0.00 3.41
2673 2750 1.812571 CTGTGGGTAGTGGTCATTTGC 59.187 52.381 0.00 0.00 0.00 3.68
2681 2758 4.270325 GGTAGTGGTCATTTGCTATCGTTC 59.730 45.833 0.00 0.00 0.00 3.95
2696 2773 2.841215 TCGTTCTTGGGTTTGTGGTAG 58.159 47.619 0.00 0.00 0.00 3.18
2713 2791 6.849502 TGTGGTAGTAGATCAAGAAACTACG 58.150 40.000 0.00 0.00 43.31 3.51
2715 2793 7.607607 TGTGGTAGTAGATCAAGAAACTACGTA 59.392 37.037 0.00 0.00 43.31 3.57
2716 2794 7.907563 GTGGTAGTAGATCAAGAAACTACGTAC 59.092 40.741 0.00 0.00 43.31 3.67
2732 2819 4.280436 ACGTACATTGATTCCTTGGACA 57.720 40.909 0.00 0.00 0.00 4.02
2755 2842 3.417069 TGGACGTGATGGTGAAATTCT 57.583 42.857 0.00 0.00 0.00 2.40
2761 2848 6.238211 GGACGTGATGGTGAAATTCTTATCAG 60.238 42.308 0.00 5.72 0.00 2.90
2767 2854 9.300681 TGATGGTGAAATTCTTATCAGTTCTTT 57.699 29.630 0.00 0.00 0.00 2.52
2768 2855 9.565213 GATGGTGAAATTCTTATCAGTTCTTTG 57.435 33.333 0.00 0.00 0.00 2.77
2784 2871 8.567948 TCAGTTCTTTGGTTAAGCTCAATAAAG 58.432 33.333 6.19 7.08 33.66 1.85
2799 2956 9.896645 AGCTCAATAAAGAATAGATGTCTTCAA 57.103 29.630 0.00 0.00 34.19 2.69
2807 2964 6.757237 AGAATAGATGTCTTCAATCGCTGAT 58.243 36.000 0.00 0.00 32.78 2.90
2808 2965 7.215789 AGAATAGATGTCTTCAATCGCTGATT 58.784 34.615 0.00 0.00 32.78 2.57
2810 2967 9.149225 GAATAGATGTCTTCAATCGCTGATTAT 57.851 33.333 3.96 0.00 32.78 1.28
2811 2968 6.782298 AGATGTCTTCAATCGCTGATTATG 57.218 37.500 3.96 0.00 32.78 1.90
2812 2969 5.699915 AGATGTCTTCAATCGCTGATTATGG 59.300 40.000 3.96 0.00 32.78 2.74
2815 2972 4.811024 GTCTTCAATCGCTGATTATGGTCA 59.189 41.667 3.96 0.00 32.78 4.02
2841 2998 7.907214 ATCTTTATGTAGAATTATGGTCGCC 57.093 36.000 0.00 0.00 0.00 5.54
2842 2999 6.822442 TCTTTATGTAGAATTATGGTCGCCA 58.178 36.000 1.01 1.01 38.19 5.69
2843 3000 7.276658 TCTTTATGTAGAATTATGGTCGCCAA 58.723 34.615 2.68 0.00 36.95 4.52
2844 3001 6.854496 TTATGTAGAATTATGGTCGCCAAC 57.146 37.500 2.68 0.00 36.95 3.77
2854 3011 3.010088 GTCGCCAACCATTTAACGC 57.990 52.632 0.00 0.00 0.00 4.84
2855 3012 0.791610 GTCGCCAACCATTTAACGCG 60.792 55.000 3.53 3.53 40.88 6.01
2857 3014 1.153920 GCCAACCATTTAACGCGGG 60.154 57.895 12.47 2.56 0.00 6.13
2858 3015 1.868987 GCCAACCATTTAACGCGGGT 61.869 55.000 12.47 3.35 34.43 5.28
2859 3016 1.451067 CCAACCATTTAACGCGGGTA 58.549 50.000 12.47 0.00 32.21 3.69
2860 3017 1.399089 CCAACCATTTAACGCGGGTAG 59.601 52.381 12.47 0.00 32.21 3.18
2861 3018 1.399089 CAACCATTTAACGCGGGTAGG 59.601 52.381 12.47 7.06 32.21 3.18
2863 3020 1.278699 ACCATTTAACGCGGGTAGGAA 59.721 47.619 12.47 1.55 0.00 3.36
2888 3045 8.934023 AAAAAGTTACCCTCATTGTCATAAGA 57.066 30.769 0.00 0.00 0.00 2.10
2889 3046 9.533831 AAAAAGTTACCCTCATTGTCATAAGAT 57.466 29.630 0.00 0.00 0.00 2.40
2891 3048 9.614792 AAAGTTACCCTCATTGTCATAAGATAC 57.385 33.333 0.00 0.00 0.00 2.24
2892 3049 8.319057 AGTTACCCTCATTGTCATAAGATACA 57.681 34.615 0.00 0.00 0.00 2.29
2893 3050 8.424918 AGTTACCCTCATTGTCATAAGATACAG 58.575 37.037 0.00 0.00 0.00 2.74
2894 3051 8.421784 GTTACCCTCATTGTCATAAGATACAGA 58.578 37.037 0.00 0.00 0.00 3.41
2895 3052 7.623999 ACCCTCATTGTCATAAGATACAGAT 57.376 36.000 0.00 0.00 0.00 2.90
2897 3054 8.811017 ACCCTCATTGTCATAAGATACAGATAG 58.189 37.037 0.00 0.00 0.00 2.08
2898 3055 7.763528 CCCTCATTGTCATAAGATACAGATAGC 59.236 40.741 0.00 0.00 0.00 2.97
2899 3056 8.309656 CCTCATTGTCATAAGATACAGATAGCA 58.690 37.037 0.00 0.00 0.00 3.49
2900 3057 9.702494 CTCATTGTCATAAGATACAGATAGCAA 57.298 33.333 0.00 0.00 0.00 3.91
2901 3058 9.702494 TCATTGTCATAAGATACAGATAGCAAG 57.298 33.333 0.00 0.00 0.00 4.01
2902 3059 9.702494 CATTGTCATAAGATACAGATAGCAAGA 57.298 33.333 0.00 0.00 0.00 3.02
2910 3067 8.618702 AAGATACAGATAGCAAGATTTCATGG 57.381 34.615 0.00 0.00 0.00 3.66
2911 3068 7.743749 AGATACAGATAGCAAGATTTCATGGT 58.256 34.615 0.00 0.00 0.00 3.55
2913 3070 9.149225 GATACAGATAGCAAGATTTCATGGTAG 57.851 37.037 0.00 0.00 32.28 3.18
2914 3071 7.129457 ACAGATAGCAAGATTTCATGGTAGA 57.871 36.000 0.00 0.00 32.28 2.59
2917 3074 8.719648 CAGATAGCAAGATTTCATGGTAGAATC 58.280 37.037 0.00 0.00 32.28 2.52
2920 3077 5.298777 AGCAAGATTTCATGGTAGAATCAGC 59.701 40.000 0.00 7.00 0.00 4.26
2922 3079 6.726230 CAAGATTTCATGGTAGAATCAGCAG 58.274 40.000 0.00 0.00 0.00 4.24
2923 3080 6.244552 AGATTTCATGGTAGAATCAGCAGA 57.755 37.500 0.00 0.00 0.00 4.26
2924 3081 6.839454 AGATTTCATGGTAGAATCAGCAGAT 58.161 36.000 0.00 0.00 35.53 2.90
2926 3083 7.778853 AGATTTCATGGTAGAATCAGCAGATTT 59.221 33.333 5.75 0.00 44.30 2.17
2928 3085 5.128205 TCATGGTAGAATCAGCAGATTTGG 58.872 41.667 5.75 0.00 44.30 3.28
2929 3086 4.574674 TGGTAGAATCAGCAGATTTGGT 57.425 40.909 5.75 0.00 44.30 3.67
2931 3088 3.557595 GGTAGAATCAGCAGATTTGGTCG 59.442 47.826 5.75 0.00 44.30 4.79
2932 3089 2.012673 AGAATCAGCAGATTTGGTCGC 58.987 47.619 5.75 0.00 44.30 5.19
2934 3091 0.035152 ATCAGCAGATTTGGTCGCCA 60.035 50.000 0.00 0.00 31.36 5.69
2935 3092 0.250684 TCAGCAGATTTGGTCGCCAA 60.251 50.000 7.15 7.15 42.29 4.52
2937 3094 1.212751 GCAGATTTGGTCGCCAACC 59.787 57.895 10.30 0.00 43.82 3.77
2948 3105 2.874849 GTCGCCAACCATTTAACATGG 58.125 47.619 12.43 12.43 44.54 3.66
2958 3115 5.920193 CCATTTAACATGGTCAGGTTCAT 57.080 39.130 4.23 0.00 36.63 2.57
2959 3116 5.653507 CCATTTAACATGGTCAGGTTCATG 58.346 41.667 4.23 8.39 44.42 3.07
2961 3118 2.592102 AACATGGTCAGGTTCATGCT 57.408 45.000 0.00 0.00 43.12 3.79
2962 3119 2.119801 ACATGGTCAGGTTCATGCTC 57.880 50.000 0.00 0.00 43.12 4.26
2963 3120 1.340405 ACATGGTCAGGTTCATGCTCC 60.340 52.381 0.00 0.00 43.12 4.70
2965 3122 1.951209 TGGTCAGGTTCATGCTCCTA 58.049 50.000 7.92 0.00 32.26 2.94
2967 3124 2.642311 TGGTCAGGTTCATGCTCCTAAA 59.358 45.455 7.92 0.00 32.26 1.85
2968 3125 3.073798 TGGTCAGGTTCATGCTCCTAAAA 59.926 43.478 7.92 0.00 32.26 1.52
2971 3128 5.885912 GGTCAGGTTCATGCTCCTAAAAATA 59.114 40.000 7.92 0.00 32.26 1.40
2974 3131 8.470002 GTCAGGTTCATGCTCCTAAAAATATTT 58.530 33.333 7.92 0.00 32.26 1.40
2975 3132 8.469200 TCAGGTTCATGCTCCTAAAAATATTTG 58.531 33.333 0.39 0.00 32.26 2.32
2977 3134 9.205513 AGGTTCATGCTCCTAAAAATATTTGAT 57.794 29.630 0.39 0.00 31.66 2.57
2978 3135 9.252962 GGTTCATGCTCCTAAAAATATTTGATG 57.747 33.333 0.39 0.00 0.00 3.07
2979 3136 9.807649 GTTCATGCTCCTAAAAATATTTGATGT 57.192 29.630 0.39 0.00 0.00 3.06
2985 3142 8.811378 GCTCCTAAAAATATTTGATGTTCTTGC 58.189 33.333 0.39 0.00 0.00 4.01
2986 3143 9.305925 CTCCTAAAAATATTTGATGTTCTTGCC 57.694 33.333 0.39 0.00 0.00 4.52
2987 3144 8.811017 TCCTAAAAATATTTGATGTTCTTGCCA 58.189 29.630 0.39 0.00 0.00 4.92
2988 3145 9.434420 CCTAAAAATATTTGATGTTCTTGCCAA 57.566 29.630 0.39 0.00 0.00 4.52
2990 3147 8.907222 AAAAATATTTGATGTTCTTGCCAAGT 57.093 26.923 4.04 0.00 0.00 3.16
2991 3148 8.907222 AAAATATTTGATGTTCTTGCCAAGTT 57.093 26.923 4.04 0.00 0.00 2.66
2993 3150 8.538409 AATATTTGATGTTCTTGCCAAGTTTC 57.462 30.769 4.04 0.00 0.00 2.78
2996 3153 4.873817 TGATGTTCTTGCCAAGTTTCATG 58.126 39.130 4.04 0.00 0.00 3.07
2997 3154 3.096489 TGTTCTTGCCAAGTTTCATGC 57.904 42.857 4.04 0.00 0.00 4.06
2998 3155 2.694628 TGTTCTTGCCAAGTTTCATGCT 59.305 40.909 4.04 0.00 0.00 3.79
2999 3156 3.243501 TGTTCTTGCCAAGTTTCATGCTC 60.244 43.478 4.04 0.00 0.00 4.26
3000 3157 1.888512 TCTTGCCAAGTTTCATGCTCC 59.111 47.619 4.04 0.00 0.00 4.70
3001 3158 1.891150 CTTGCCAAGTTTCATGCTCCT 59.109 47.619 0.00 0.00 0.00 3.69
3002 3159 2.877097 TGCCAAGTTTCATGCTCCTA 57.123 45.000 0.00 0.00 0.00 2.94
3004 3161 3.495331 TGCCAAGTTTCATGCTCCTAAA 58.505 40.909 0.00 0.00 0.00 1.85
3005 3162 3.894427 TGCCAAGTTTCATGCTCCTAAAA 59.106 39.130 0.00 0.00 0.00 1.52
3007 3164 5.011943 TGCCAAGTTTCATGCTCCTAAAAAT 59.988 36.000 0.00 0.00 0.00 1.82
3104 3869 3.426695 CGATAGCAGCAACTCCCAAAAAG 60.427 47.826 0.00 0.00 0.00 2.27
3163 3928 9.855361 CTAGTGTATTAATTTGCTCTTCATTCG 57.145 33.333 0.00 0.00 0.00 3.34
3187 3952 4.877378 TTTGGAGATCTTGCTGCATTTT 57.123 36.364 1.84 0.00 36.10 1.82
3191 3956 5.255687 TGGAGATCTTGCTGCATTTTTCTA 58.744 37.500 1.84 0.00 30.90 2.10
3243 4438 3.940209 TGCTTCCTTGGTTATGCTTTG 57.060 42.857 0.00 0.00 0.00 2.77
3270 4465 1.228510 CAGGGGAGAATGGGCTTCC 59.771 63.158 0.00 0.00 34.11 3.46
3273 4468 1.691219 GGGAGAATGGGCTTCCACA 59.309 57.895 0.00 0.00 44.44 4.17
3332 4527 4.380867 CCACCTGAAGCAATAACACAATCC 60.381 45.833 0.00 0.00 0.00 3.01
3333 4528 4.218200 CACCTGAAGCAATAACACAATCCA 59.782 41.667 0.00 0.00 0.00 3.41
3337 4532 5.953183 TGAAGCAATAACACAATCCATGTC 58.047 37.500 0.00 0.00 41.46 3.06
3401 4598 1.979855 TGGCAGTATGTGTTGCACTT 58.020 45.000 0.00 0.00 42.02 3.16
3405 4602 2.549754 GCAGTATGTGTTGCACTTCACT 59.450 45.455 14.15 0.00 40.02 3.41
3406 4603 3.003689 GCAGTATGTGTTGCACTTCACTT 59.996 43.478 14.15 11.23 40.02 3.16
3411 4608 4.782019 TGTGTTGCACTTCACTTTTTCT 57.218 36.364 14.15 0.00 35.11 2.52
3445 4642 3.834813 TGAATCTTCACAGTGCTCCTAGT 59.165 43.478 0.00 0.00 31.01 2.57
3446 4643 5.016831 TGAATCTTCACAGTGCTCCTAGTA 58.983 41.667 0.00 0.00 31.01 1.82
3447 4644 5.126222 TGAATCTTCACAGTGCTCCTAGTAG 59.874 44.000 0.00 0.00 31.01 2.57
3529 4785 8.587952 AAAAAGATTGTTTGCCTACATGTTAC 57.412 30.769 2.30 0.00 0.00 2.50
3531 4787 7.466746 AAGATTGTTTGCCTACATGTTACAT 57.533 32.000 2.30 0.00 0.00 2.29
3553 4809 1.568504 ACTTACGAGGGCTGGAATGA 58.431 50.000 0.00 0.00 0.00 2.57
3720 4976 2.851798 CTCTGGCCAAGAGCAGAAC 58.148 57.895 7.01 0.00 45.93 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.685785 CTAGCTGGCTGAGGAGGACA 60.686 60.000 5.25 0.00 0.00 4.02
30 31 1.132834 TCGTAAATTCGAGGCACGCTA 59.867 47.619 0.00 0.00 42.26 4.26
69 70 5.578727 CAGAATACCAGCTCAGAGTACAAAC 59.421 44.000 0.00 0.00 0.00 2.93
71 72 4.772624 ACAGAATACCAGCTCAGAGTACAA 59.227 41.667 0.00 0.00 0.00 2.41
79 80 8.250143 TCTTATTGATACAGAATACCAGCTCA 57.750 34.615 0.00 0.00 0.00 4.26
110 111 3.994204 TTCGATAAATCCGATCACCGA 57.006 42.857 0.00 0.00 41.76 4.69
113 114 5.926542 TGAGGAATTCGATAAATCCGATCAC 59.073 40.000 0.00 0.00 35.84 3.06
131 132 0.677288 ACGGTGTGTCGAATGAGGAA 59.323 50.000 0.00 0.00 0.00 3.36
185 186 0.811915 AGCGTCTAGATCGTGCAACT 59.188 50.000 13.65 0.00 31.75 3.16
229 230 1.927895 CTACACTGGCGACATCTTCC 58.072 55.000 0.00 0.00 41.51 3.46
233 234 0.391130 TTGGCTACACTGGCGACATC 60.391 55.000 0.00 0.00 41.51 3.06
243 244 0.389948 CTGGACGACCTTGGCTACAC 60.390 60.000 5.33 0.00 37.04 2.90
302 303 3.302344 GTTGCATGGCCCCAACGT 61.302 61.111 13.16 0.00 32.96 3.99
360 361 1.755380 GCCGTGGTTACTATCTGGAGT 59.245 52.381 0.00 0.00 0.00 3.85
367 368 2.764010 TCAGACATGCCGTGGTTACTAT 59.236 45.455 0.00 0.00 0.00 2.12
413 414 1.069500 CGGAAACATTTGACGTGGGAC 60.069 52.381 0.00 0.00 0.00 4.46
449 450 1.746470 GGTTCACGGGTCTTTATGGG 58.254 55.000 0.00 0.00 0.00 4.00
458 459 3.948719 ACATGGCGGTTCACGGGT 61.949 61.111 0.00 0.00 44.51 5.28
475 476 5.504337 CGAATAAACGAAGGTTCCAACAACA 60.504 40.000 0.00 0.00 34.62 3.33
491 492 7.148306 ACCAACTACATTGACATCCGAATAAAC 60.148 37.037 0.00 0.00 41.23 2.01
566 567 2.417379 CGATGGTAGAAGTGGTGGTCTG 60.417 54.545 0.00 0.00 0.00 3.51
624 625 0.964700 AAGGCAGAAAAGCTCAAGGC 59.035 50.000 0.00 0.00 42.19 4.35
625 626 2.163211 GCTAAGGCAGAAAAGCTCAAGG 59.837 50.000 0.00 0.00 38.54 3.61
627 628 3.146104 AGCTAAGGCAGAAAAGCTCAA 57.854 42.857 0.00 0.00 41.35 3.02
676 677 0.249398 GCGGGTAAGACCAGATGTGT 59.751 55.000 0.00 0.00 41.02 3.72
685 686 0.179054 GATCCAAGGGCGGGTAAGAC 60.179 60.000 0.00 0.00 0.00 3.01
716 717 7.981102 AGTAAACTAAAGCGAGGAGATTTTT 57.019 32.000 0.00 0.00 39.43 1.94
717 718 9.668497 ATTAGTAAACTAAAGCGAGGAGATTTT 57.332 29.630 6.66 0.00 41.27 1.82
719 720 9.747293 GTATTAGTAAACTAAAGCGAGGAGATT 57.253 33.333 6.66 0.00 41.27 2.40
720 721 9.134055 AGTATTAGTAAACTAAAGCGAGGAGAT 57.866 33.333 6.66 0.00 41.27 2.75
752 753 5.465390 CACCGAACTTTACAGTGATTGAGAA 59.535 40.000 0.00 0.00 31.60 2.87
844 845 4.109766 ACAAAAACCTTTTAAGCGACTGC 58.890 39.130 0.00 0.00 43.24 4.40
845 846 6.641176 AAACAAAAACCTTTTAAGCGACTG 57.359 33.333 0.00 0.00 0.00 3.51
853 854 8.255905 TCCGTGGAATAAAACAAAAACCTTTTA 58.744 29.630 0.00 0.00 0.00 1.52
863 864 5.915758 CGTCAAAATCCGTGGAATAAAACAA 59.084 36.000 0.00 0.00 0.00 2.83
864 865 5.238868 TCGTCAAAATCCGTGGAATAAAACA 59.761 36.000 0.00 0.00 0.00 2.83
865 866 5.691815 TCGTCAAAATCCGTGGAATAAAAC 58.308 37.500 0.00 0.00 0.00 2.43
866 867 5.943706 TCGTCAAAATCCGTGGAATAAAA 57.056 34.783 0.00 0.00 0.00 1.52
872 879 2.080693 CCAATCGTCAAAATCCGTGGA 58.919 47.619 0.00 0.00 0.00 4.02
947 984 2.573340 GTCGGGGCCAGCAATTTG 59.427 61.111 4.39 0.00 0.00 2.32
1199 1240 3.839432 GAGGAAGGCCCGGTCGAG 61.839 72.222 0.00 0.00 40.87 4.04
1339 1380 1.406069 CCGTCCTGGAGGTTGATGAAG 60.406 57.143 14.71 0.00 42.00 3.02
1384 1425 0.797249 CGAACGAGTAGAAGGCACGG 60.797 60.000 0.00 0.00 0.00 4.94
1388 1429 1.615502 GTGACGAACGAGTAGAAGGC 58.384 55.000 0.14 0.00 0.00 4.35
1518 1562 4.344865 GGAGCTTGTTGGGCCCGA 62.345 66.667 19.37 14.11 0.00 5.14
1706 1750 2.912624 GCTGCTGCTTGTGGTCCAC 61.913 63.158 15.64 15.64 36.03 4.02
1707 1751 2.595463 GCTGCTGCTTGTGGTCCA 60.595 61.111 8.53 0.00 36.03 4.02
1708 1752 2.595463 TGCTGCTGCTTGTGGTCC 60.595 61.111 17.00 0.00 40.48 4.46
1709 1753 2.623915 CCTGCTGCTGCTTGTGGTC 61.624 63.158 17.00 0.00 40.48 4.02
1710 1754 2.421923 ATCCTGCTGCTGCTTGTGGT 62.422 55.000 17.00 0.00 40.48 4.16
1711 1755 1.654954 GATCCTGCTGCTGCTTGTGG 61.655 60.000 17.00 12.70 40.48 4.17
1732 1776 1.766069 AAACTTGAAACGCGGATTGC 58.234 45.000 12.47 0.00 41.47 3.56
1733 1777 5.627367 TCAATAAAACTTGAAACGCGGATTG 59.373 36.000 12.47 0.00 32.35 2.67
1734 1778 5.764131 TCAATAAAACTTGAAACGCGGATT 58.236 33.333 12.47 4.81 32.35 3.01
1740 1784 8.901748 CCTTGTACATCAATAAAACTTGAAACG 58.098 33.333 0.00 0.00 38.55 3.60
1750 1794 7.226918 TCGTTGTTGTCCTTGTACATCAATAAA 59.773 33.333 0.00 0.00 39.77 1.40
1818 1862 4.572571 TCCAACCACCACCACCGC 62.573 66.667 0.00 0.00 0.00 5.68
1848 1892 1.686110 CGGGAAGCCAGGTAGGACT 60.686 63.158 0.00 0.00 41.22 3.85
1922 1966 4.880759 TGGTTTTGGTAATGCATGAACAG 58.119 39.130 1.05 0.00 0.00 3.16
1981 2025 2.954753 CTCGGTCAAAGTGGCGTGC 61.955 63.158 0.00 0.00 0.00 5.34
1984 2028 1.278238 GTATCTCGGTCAAAGTGGCG 58.722 55.000 0.00 0.00 0.00 5.69
2005 2049 0.249120 TAGTGGGGTGCACTTCGATG 59.751 55.000 17.98 0.00 34.38 3.84
2023 2067 4.497984 ATTGGCGGCCGTGGCATA 62.498 61.111 28.70 8.98 44.53 3.14
2032 2076 4.211502 GTGCATGGGATTGGCGGC 62.212 66.667 0.00 0.00 0.00 6.53
2056 2100 1.193874 GTAACAAACGACAGCCTTCCG 59.806 52.381 0.00 0.00 0.00 4.30
2081 2125 1.226717 CTGCTACGCCGTCTTCTCC 60.227 63.158 0.00 0.00 0.00 3.71
2104 2148 3.228188 TCTTGTTCTTGCTTGGTCCAT 57.772 42.857 0.00 0.00 0.00 3.41
2129 2173 3.815401 TCTTTCTCTTTGGCTGCTACAAC 59.185 43.478 0.00 0.00 0.00 3.32
2131 2175 3.769739 TCTTTCTCTTTGGCTGCTACA 57.230 42.857 0.00 0.00 0.00 2.74
2136 2180 5.240183 TCATCTTGTTCTTTCTCTTTGGCTG 59.760 40.000 0.00 0.00 0.00 4.85
2137 2181 5.240403 GTCATCTTGTTCTTTCTCTTTGGCT 59.760 40.000 0.00 0.00 0.00 4.75
2138 2182 5.009010 TGTCATCTTGTTCTTTCTCTTTGGC 59.991 40.000 0.00 0.00 0.00 4.52
2139 2183 6.624352 TGTCATCTTGTTCTTTCTCTTTGG 57.376 37.500 0.00 0.00 0.00 3.28
2146 2190 3.251004 AGGCGTTGTCATCTTGTTCTTTC 59.749 43.478 0.00 0.00 0.00 2.62
2180 2224 4.463879 CCCCAGGCTCGTCAGCTG 62.464 72.222 7.63 7.63 46.03 4.24
2190 2234 1.115930 TATTCTCTCGCTCCCCAGGC 61.116 60.000 0.00 0.00 0.00 4.85
2218 2262 2.038295 ACCTCTGGTCTCTGCAAAGAAG 59.962 50.000 0.00 0.00 0.00 2.85
2232 2276 1.294659 GACGAGCAAAGCACCTCTGG 61.295 60.000 0.00 0.00 0.00 3.86
2278 2322 0.734253 CCTTGCTCTTGAGGTCGACG 60.734 60.000 9.92 0.00 0.00 5.12
2304 2348 0.861837 GTCCTTTAGATGCATCGGCG 59.138 55.000 20.67 0.00 45.35 6.46
2332 2376 2.587194 CCCCTCGAATGCTGCTCG 60.587 66.667 0.00 2.78 37.66 5.03
2338 2382 3.499737 CACGTGCCCCTCGAATGC 61.500 66.667 0.82 0.00 0.00 3.56
2339 2383 2.047274 ACACGTGCCCCTCGAATG 60.047 61.111 17.22 0.00 0.00 2.67
2340 2384 2.264794 GACACGTGCCCCTCGAAT 59.735 61.111 17.22 0.00 0.00 3.34
2341 2385 4.351938 CGACACGTGCCCCTCGAA 62.352 66.667 17.22 0.00 0.00 3.71
2344 2388 4.309950 AACCGACACGTGCCCCTC 62.310 66.667 17.22 4.49 0.00 4.30
2362 2406 1.064803 CTACTGCTGCACGACTCTAGG 59.935 57.143 0.00 0.00 0.00 3.02
2392 2436 2.562738 TCTGTATCCATGGCTGTATCCG 59.437 50.000 6.96 0.00 0.00 4.18
2419 2463 1.315257 GGGGTGCTTGTAGGCATGTG 61.315 60.000 0.00 0.00 44.34 3.21
2425 2469 3.327404 ACCGGGGGTGCTTGTAGG 61.327 66.667 6.32 0.00 32.98 3.18
2446 2490 3.576118 AGACGTCCCAATCCATCTCATAG 59.424 47.826 13.01 0.00 0.00 2.23
2449 2493 1.866015 AGACGTCCCAATCCATCTCA 58.134 50.000 13.01 0.00 0.00 3.27
2464 2508 1.795177 GTCGGTCGACGGAAAGACG 60.795 63.158 25.13 13.73 44.45 4.18
2480 2524 2.025321 AGGAGAGAGAGAGACAAGGGTC 60.025 54.545 0.00 0.00 44.66 4.46
2481 2525 2.000048 AGGAGAGAGAGAGACAAGGGT 59.000 52.381 0.00 0.00 0.00 4.34
2482 2526 2.025416 TGAGGAGAGAGAGAGACAAGGG 60.025 54.545 0.00 0.00 0.00 3.95
2483 2527 3.282021 CTGAGGAGAGAGAGAGACAAGG 58.718 54.545 0.00 0.00 0.00 3.61
2484 2528 3.282021 CCTGAGGAGAGAGAGAGACAAG 58.718 54.545 0.00 0.00 0.00 3.16
2485 2529 2.647299 ACCTGAGGAGAGAGAGAGACAA 59.353 50.000 4.99 0.00 0.00 3.18
2486 2530 2.026356 CACCTGAGGAGAGAGAGAGACA 60.026 54.545 4.99 0.00 0.00 3.41
2487 2531 2.238646 TCACCTGAGGAGAGAGAGAGAC 59.761 54.545 4.99 0.00 0.00 3.36
2488 2532 2.505407 CTCACCTGAGGAGAGAGAGAGA 59.495 54.545 19.55 0.00 41.78 3.10
2489 2533 2.505407 TCTCACCTGAGGAGAGAGAGAG 59.495 54.545 22.28 9.32 42.71 3.20
2490 2534 2.556766 TCTCACCTGAGGAGAGAGAGA 58.443 52.381 22.28 14.13 42.71 3.10
2502 2546 3.070159 TCTTGTTTCTCACCTCTCACCTG 59.930 47.826 0.00 0.00 0.00 4.00
2540 2584 7.412853 TCCTACATGGTTTTTAAAATAGCCC 57.587 36.000 0.55 1.17 37.07 5.19
2558 2602 9.661563 CAAGTTACCACTTAAATGTATCCTACA 57.338 33.333 0.00 0.00 41.69 2.74
2600 2644 9.474920 CAAACACATACTTCCAAAATAACACAT 57.525 29.630 0.00 0.00 0.00 3.21
2603 2647 7.492524 TGCAAACACATACTTCCAAAATAACA 58.507 30.769 0.00 0.00 0.00 2.41
2607 2654 6.403866 TCTGCAAACACATACTTCCAAAAT 57.596 33.333 0.00 0.00 0.00 1.82
2613 2660 8.863049 CCAAAATAATCTGCAAACACATACTTC 58.137 33.333 0.00 0.00 0.00 3.01
2673 2750 3.408634 ACCACAAACCCAAGAACGATAG 58.591 45.455 0.00 0.00 46.19 2.08
2681 2758 5.160607 TGATCTACTACCACAAACCCAAG 57.839 43.478 0.00 0.00 0.00 3.61
2696 2773 8.906636 TCAATGTACGTAGTTTCTTGATCTAC 57.093 34.615 0.00 0.00 37.78 2.59
2713 2791 5.106157 CCAACTGTCCAAGGAATCAATGTAC 60.106 44.000 0.00 0.00 0.00 2.90
2715 2793 3.828451 CCAACTGTCCAAGGAATCAATGT 59.172 43.478 0.00 0.00 0.00 2.71
2716 2794 4.081406 TCCAACTGTCCAAGGAATCAATG 58.919 43.478 0.00 0.00 0.00 2.82
2732 2819 2.631160 TTTCACCATCACGTCCAACT 57.369 45.000 0.00 0.00 0.00 3.16
2755 2842 8.635765 ATTGAGCTTAACCAAAGAACTGATAA 57.364 30.769 0.00 0.00 37.38 1.75
2761 2848 9.914131 ATTCTTTATTGAGCTTAACCAAAGAAC 57.086 29.630 27.31 0.68 40.98 3.01
2767 2854 9.905713 ACATCTATTCTTTATTGAGCTTAACCA 57.094 29.630 0.00 0.00 0.00 3.67
2773 2860 9.896645 TTGAAGACATCTATTCTTTATTGAGCT 57.103 29.630 0.00 0.00 33.30 4.09
2784 2871 7.418840 AATCAGCGATTGAAGACATCTATTC 57.581 36.000 3.51 0.00 39.77 1.75
2792 2949 4.811024 TGACCATAATCAGCGATTGAAGAC 59.189 41.667 12.17 4.21 39.77 3.01
2799 2956 9.322773 CATAAAGATATGACCATAATCAGCGAT 57.677 33.333 0.00 0.00 41.25 4.58
2801 2958 8.484641 ACATAAAGATATGACCATAATCAGCG 57.515 34.615 3.03 0.00 41.25 5.18
2815 2972 9.601217 GGCGACCATAATTCTACATAAAGATAT 57.399 33.333 0.00 0.00 0.00 1.63
2838 2995 1.513160 CCGCGTTAAATGGTTGGCG 60.513 57.895 4.92 0.00 42.92 5.69
2839 2996 1.153920 CCCGCGTTAAATGGTTGGC 60.154 57.895 4.92 0.00 0.00 4.52
2840 2997 1.399089 CTACCCGCGTTAAATGGTTGG 59.601 52.381 4.92 0.00 32.27 3.77
2841 2998 1.399089 CCTACCCGCGTTAAATGGTTG 59.601 52.381 4.92 4.89 32.27 3.77
2842 2999 1.278699 TCCTACCCGCGTTAAATGGTT 59.721 47.619 4.92 0.00 32.27 3.67
2843 3000 0.903942 TCCTACCCGCGTTAAATGGT 59.096 50.000 4.92 6.53 34.85 3.55
2844 3001 2.027003 TTCCTACCCGCGTTAAATGG 57.973 50.000 4.92 0.00 0.00 3.16
2863 3020 8.934023 TCTTATGACAATGAGGGTAACTTTTT 57.066 30.769 0.00 0.00 0.00 1.94
2867 3024 8.319057 TGTATCTTATGACAATGAGGGTAACT 57.681 34.615 0.00 0.00 0.00 2.24
2868 3025 8.421784 TCTGTATCTTATGACAATGAGGGTAAC 58.578 37.037 0.00 0.00 0.00 2.50
2870 3027 8.727100 ATCTGTATCTTATGACAATGAGGGTA 57.273 34.615 0.00 0.00 0.00 3.69
2871 3028 7.623999 ATCTGTATCTTATGACAATGAGGGT 57.376 36.000 0.00 0.00 0.00 4.34
2872 3029 7.763528 GCTATCTGTATCTTATGACAATGAGGG 59.236 40.741 0.00 0.00 0.00 4.30
2874 3031 9.702494 TTGCTATCTGTATCTTATGACAATGAG 57.298 33.333 0.00 0.00 0.00 2.90
2875 3032 9.702494 CTTGCTATCTGTATCTTATGACAATGA 57.298 33.333 0.00 0.00 0.00 2.57
2876 3033 9.702494 TCTTGCTATCTGTATCTTATGACAATG 57.298 33.333 0.00 0.00 0.00 2.82
2884 3041 9.716531 CCATGAAATCTTGCTATCTGTATCTTA 57.283 33.333 0.00 0.00 0.00 2.10
2885 3042 8.216423 ACCATGAAATCTTGCTATCTGTATCTT 58.784 33.333 0.00 0.00 0.00 2.40
2886 3043 7.743749 ACCATGAAATCTTGCTATCTGTATCT 58.256 34.615 0.00 0.00 0.00 1.98
2887 3044 7.976135 ACCATGAAATCTTGCTATCTGTATC 57.024 36.000 0.00 0.00 0.00 2.24
2888 3045 8.874156 TCTACCATGAAATCTTGCTATCTGTAT 58.126 33.333 0.00 0.00 0.00 2.29
2889 3046 8.250143 TCTACCATGAAATCTTGCTATCTGTA 57.750 34.615 0.00 0.00 0.00 2.74
2890 3047 7.129457 TCTACCATGAAATCTTGCTATCTGT 57.871 36.000 0.00 0.00 0.00 3.41
2891 3048 8.618702 ATTCTACCATGAAATCTTGCTATCTG 57.381 34.615 0.00 0.00 0.00 2.90
2892 3049 8.435187 TGATTCTACCATGAAATCTTGCTATCT 58.565 33.333 0.00 0.00 0.00 1.98
2893 3050 8.613060 TGATTCTACCATGAAATCTTGCTATC 57.387 34.615 0.00 0.00 0.00 2.08
2894 3051 7.174599 GCTGATTCTACCATGAAATCTTGCTAT 59.825 37.037 0.00 0.00 0.00 2.97
2895 3052 6.484643 GCTGATTCTACCATGAAATCTTGCTA 59.515 38.462 0.00 0.00 0.00 3.49
2897 3054 5.066893 TGCTGATTCTACCATGAAATCTTGC 59.933 40.000 0.00 7.64 0.00 4.01
2898 3055 6.541278 TCTGCTGATTCTACCATGAAATCTTG 59.459 38.462 0.00 0.00 0.00 3.02
2899 3056 6.656902 TCTGCTGATTCTACCATGAAATCTT 58.343 36.000 0.00 0.00 0.00 2.40
2900 3057 6.244552 TCTGCTGATTCTACCATGAAATCT 57.755 37.500 0.00 0.00 0.00 2.40
2901 3058 7.507733 AATCTGCTGATTCTACCATGAAATC 57.492 36.000 12.62 0.00 38.42 2.17
2902 3059 7.201884 CCAAATCTGCTGATTCTACCATGAAAT 60.202 37.037 17.89 0.00 41.62 2.17
2904 3061 5.591472 CCAAATCTGCTGATTCTACCATGAA 59.409 40.000 17.89 0.00 41.62 2.57
2905 3062 5.128205 CCAAATCTGCTGATTCTACCATGA 58.872 41.667 17.89 0.00 41.62 3.07
2907 3064 5.121380 ACCAAATCTGCTGATTCTACCAT 57.879 39.130 17.89 0.25 41.62 3.55
2908 3065 4.517285 GACCAAATCTGCTGATTCTACCA 58.483 43.478 17.89 0.00 41.62 3.25
2909 3066 3.557595 CGACCAAATCTGCTGATTCTACC 59.442 47.826 17.89 8.39 41.62 3.18
2910 3067 3.001736 GCGACCAAATCTGCTGATTCTAC 59.998 47.826 17.89 9.81 41.62 2.59
2911 3068 3.198068 GCGACCAAATCTGCTGATTCTA 58.802 45.455 17.89 0.00 41.62 2.10
2913 3070 1.064654 GGCGACCAAATCTGCTGATTC 59.935 52.381 17.89 6.18 41.62 2.52
2914 3071 1.098050 GGCGACCAAATCTGCTGATT 58.902 50.000 12.62 12.62 44.08 2.57
2917 3074 0.109597 GTTGGCGACCAAATCTGCTG 60.110 55.000 12.01 0.00 45.73 4.41
2928 3085 2.874849 CCATGTTAAATGGTTGGCGAC 58.125 47.619 0.00 0.00 34.56 5.19
2937 3094 5.104374 GCATGAACCTGACCATGTTAAATG 58.896 41.667 0.00 0.00 41.49 2.32
2938 3095 5.018809 AGCATGAACCTGACCATGTTAAAT 58.981 37.500 0.00 0.00 41.49 1.40
2939 3096 4.406456 AGCATGAACCTGACCATGTTAAA 58.594 39.130 0.00 0.00 41.49 1.52
2940 3097 4.009675 GAGCATGAACCTGACCATGTTAA 58.990 43.478 0.00 0.00 41.49 2.01
2941 3098 3.609853 GAGCATGAACCTGACCATGTTA 58.390 45.455 0.00 0.00 41.49 2.41
2942 3099 2.440409 GAGCATGAACCTGACCATGTT 58.560 47.619 0.00 0.00 41.49 2.71
2943 3100 1.340405 GGAGCATGAACCTGACCATGT 60.340 52.381 0.00 0.00 41.49 3.21
2944 3101 1.064906 AGGAGCATGAACCTGACCATG 60.065 52.381 9.75 0.00 42.13 3.66
2945 3102 1.293062 AGGAGCATGAACCTGACCAT 58.707 50.000 9.75 0.00 34.99 3.55
2948 3105 5.904362 ATTTTTAGGAGCATGAACCTGAC 57.096 39.130 17.53 0.00 37.68 3.51
2950 3107 8.469200 TCAAATATTTTTAGGAGCATGAACCTG 58.531 33.333 17.53 2.58 37.68 4.00
2951 3108 8.593945 TCAAATATTTTTAGGAGCATGAACCT 57.406 30.769 13.98 13.98 39.95 3.50
2952 3109 9.252962 CATCAAATATTTTTAGGAGCATGAACC 57.747 33.333 0.00 0.00 0.00 3.62
2953 3110 9.807649 ACATCAAATATTTTTAGGAGCATGAAC 57.192 29.630 0.00 0.00 0.00 3.18
2958 3115 9.859427 CAAGAACATCAAATATTTTTAGGAGCA 57.141 29.630 0.00 0.00 0.00 4.26
2959 3116 8.811378 GCAAGAACATCAAATATTTTTAGGAGC 58.189 33.333 0.00 0.00 0.00 4.70
2961 3118 8.811017 TGGCAAGAACATCAAATATTTTTAGGA 58.189 29.630 0.00 0.00 0.00 2.94
2962 3119 9.434420 TTGGCAAGAACATCAAATATTTTTAGG 57.566 29.630 0.00 0.00 0.00 2.69
2965 3122 8.907222 ACTTGGCAAGAACATCAAATATTTTT 57.093 26.923 32.50 1.68 0.00 1.94
2967 3124 8.907222 AAACTTGGCAAGAACATCAAATATTT 57.093 26.923 32.50 14.79 0.00 1.40
2968 3125 8.149647 TGAAACTTGGCAAGAACATCAAATATT 58.850 29.630 32.50 9.62 0.00 1.28
2971 3128 5.916318 TGAAACTTGGCAAGAACATCAAAT 58.084 33.333 32.50 4.78 0.00 2.32
2974 3131 4.796946 GCATGAAACTTGGCAAGAACATCA 60.797 41.667 32.50 25.68 0.00 3.07
2975 3132 3.676646 GCATGAAACTTGGCAAGAACATC 59.323 43.478 32.50 21.76 0.00 3.06
2977 3134 2.694628 AGCATGAAACTTGGCAAGAACA 59.305 40.909 32.50 25.09 0.00 3.18
2978 3135 3.311966 GAGCATGAAACTTGGCAAGAAC 58.688 45.455 32.50 21.02 0.00 3.01
2979 3136 2.297033 GGAGCATGAAACTTGGCAAGAA 59.703 45.455 32.50 15.22 0.00 2.52
2981 3138 1.891150 AGGAGCATGAAACTTGGCAAG 59.109 47.619 25.06 25.06 0.00 4.01
2985 3142 9.305925 GAATATTTTTAGGAGCATGAAACTTGG 57.694 33.333 0.00 0.00 0.00 3.61
2986 3143 9.305925 GGAATATTTTTAGGAGCATGAAACTTG 57.694 33.333 0.00 0.00 0.00 3.16
2987 3144 9.034800 TGGAATATTTTTAGGAGCATGAAACTT 57.965 29.630 0.00 0.00 0.00 2.66
2988 3145 8.593945 TGGAATATTTTTAGGAGCATGAAACT 57.406 30.769 0.00 0.00 0.00 2.66
2989 3146 9.822185 AATGGAATATTTTTAGGAGCATGAAAC 57.178 29.630 0.00 0.00 0.00 2.78
2990 3147 9.820725 CAATGGAATATTTTTAGGAGCATGAAA 57.179 29.630 0.00 0.00 0.00 2.69
2991 3148 8.980596 ACAATGGAATATTTTTAGGAGCATGAA 58.019 29.630 0.00 0.00 0.00 2.57
2993 3150 7.869429 GGACAATGGAATATTTTTAGGAGCATG 59.131 37.037 0.00 0.00 0.00 4.06
2996 3153 6.039382 ACGGACAATGGAATATTTTTAGGAGC 59.961 38.462 0.00 0.00 0.00 4.70
2997 3154 7.067008 ACACGGACAATGGAATATTTTTAGGAG 59.933 37.037 0.00 0.00 0.00 3.69
2998 3155 6.887545 ACACGGACAATGGAATATTTTTAGGA 59.112 34.615 0.00 0.00 0.00 2.94
2999 3156 7.095695 ACACGGACAATGGAATATTTTTAGG 57.904 36.000 0.00 0.00 0.00 2.69
3000 3157 9.663904 CATACACGGACAATGGAATATTTTTAG 57.336 33.333 0.00 0.00 0.00 1.85
3001 3158 8.625651 CCATACACGGACAATGGAATATTTTTA 58.374 33.333 3.09 0.00 42.36 1.52
3002 3159 7.488322 CCATACACGGACAATGGAATATTTTT 58.512 34.615 3.09 0.00 42.36 1.94
3004 3161 5.009610 GCCATACACGGACAATGGAATATTT 59.990 40.000 11.20 0.00 42.36 1.40
3005 3162 4.518970 GCCATACACGGACAATGGAATATT 59.481 41.667 11.20 0.00 42.36 1.28
3007 3164 3.118223 TGCCATACACGGACAATGGAATA 60.118 43.478 11.20 0.00 42.36 1.75
3104 3869 3.423571 CCATACGTACGTCTTGAGTGAC 58.576 50.000 26.53 0.00 0.00 3.67
3163 3928 1.542915 TGCAGCAAGATCTCCAAAAGC 59.457 47.619 0.00 0.00 0.00 3.51
3187 3952 2.967201 TCAACAAGGGAGGACGTTAGAA 59.033 45.455 0.00 0.00 0.00 2.10
3191 3956 3.370527 CCATATCAACAAGGGAGGACGTT 60.371 47.826 0.00 0.00 0.00 3.99
3243 4438 1.753073 CATTCTCCCCTGCCAATCAAC 59.247 52.381 0.00 0.00 0.00 3.18
3288 4483 1.451067 CTTCTTCTGAAGGCAGGCAG 58.549 55.000 16.83 0.00 44.33 4.85
3289 4484 3.639099 CTTCTTCTGAAGGCAGGCA 57.361 52.632 16.83 0.00 44.33 4.75
3332 4527 2.233271 ACCACAGGCTTTTCTGACATG 58.767 47.619 0.00 0.00 38.11 3.21
3333 4528 2.624838 CAACCACAGGCTTTTCTGACAT 59.375 45.455 0.00 0.00 38.11 3.06
3337 4532 2.166254 ACAACAACCACAGGCTTTTCTG 59.834 45.455 0.00 0.00 40.40 3.02
3387 4584 6.265577 AGAAAAAGTGAAGTGCAACACATAC 58.734 36.000 17.73 1.98 41.43 2.39
3411 4608 8.583296 CACTGTGAAGATTCATATCATCTAGGA 58.417 37.037 0.32 0.00 39.73 2.94
3445 4642 9.098355 CTCAAACCAACGAATTCTTATCATCTA 57.902 33.333 3.52 0.00 0.00 1.98
3446 4643 7.824289 TCTCAAACCAACGAATTCTTATCATCT 59.176 33.333 3.52 0.00 0.00 2.90
3447 4644 7.974675 TCTCAAACCAACGAATTCTTATCATC 58.025 34.615 3.52 0.00 0.00 2.92
3526 4782 4.467082 TCCAGCCCTCGTAAGTTTATGTAA 59.533 41.667 0.00 0.00 39.48 2.41
3529 4785 3.536956 TCCAGCCCTCGTAAGTTTATG 57.463 47.619 0.00 0.00 39.48 1.90
3531 4787 3.516300 TCATTCCAGCCCTCGTAAGTTTA 59.484 43.478 0.00 0.00 39.48 2.01
3553 4809 2.629137 TGCCTTGTTCATTCAGCATTGT 59.371 40.909 0.00 0.00 0.00 2.71
3604 4860 7.619982 GCAGTTTCAAGTTTTCAACTGAGTTTG 60.620 37.037 17.24 0.00 46.08 2.93
3620 4876 5.512788 CAGTTTGTTGTACTGCAGTTTCAAG 59.487 40.000 27.06 13.00 36.88 3.02
3623 4879 4.981794 ACAGTTTGTTGTACTGCAGTTTC 58.018 39.130 27.06 18.44 45.38 2.78
3717 4973 8.885302 AGAGTTTACAGTTTGTTTTTACGTTC 57.115 30.769 0.00 0.00 0.00 3.95
3720 4976 8.601476 AGAGAGAGTTTACAGTTTGTTTTTACG 58.399 33.333 0.00 0.00 0.00 3.18
3753 5009 8.398665 GTTCAAGTATCAGTTCAGTTCTGTTTT 58.601 33.333 0.00 0.00 34.86 2.43


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

AutoCloner maintained by Alex Coulton.