Multiple sequence alignment - TraesCS1D01G096400

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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 TraesCS1D01G096400 chr1D 100.000 3196 0 0 1 3196 81724983 81728178 0.000000e+00 5903.0
1 TraesCS1D01G096400 chr1D 84.061 916 78 39 571 1441 467612503 467611611 0.000000e+00 821.0
2 TraesCS1D01G096400 chr1D 83.544 632 78 19 1771 2385 467610894 467610272 4.630000e-158 568.0
3 TraesCS1D01G096400 chr1D 83.333 240 37 2 143 380 5871021 5871259 5.370000e-53 219.0
4 TraesCS1D01G096400 chr1B 93.177 2008 104 18 570 2565 136311927 136313913 0.000000e+00 2918.0
5 TraesCS1D01G096400 chr1B 87.793 213 21 3 2988 3196 136316193 136316404 8.860000e-61 244.0
6 TraesCS1D01G096400 chr1B 96.117 103 3 1 2605 2706 136313910 136314012 1.970000e-37 167.0
7 TraesCS1D01G096400 chr1B 82.581 155 12 5 2868 3007 136314026 136314180 4.330000e-24 122.0
8 TraesCS1D01G096400 chr1A 95.593 885 20 7 581 1450 100104887 100104007 0.000000e+00 1400.0
9 TraesCS1D01G096400 chr1A 93.065 620 37 4 1 614 100105503 100104884 0.000000e+00 902.0
10 TraesCS1D01G096400 chr1A 86.253 742 60 14 1772 2490 100100432 100099710 0.000000e+00 767.0
11 TraesCS1D01G096400 chr1A 93.243 222 15 0 1220 1441 560371965 560372186 8.550000e-86 327.0
12 TraesCS1D01G096400 chr1A 80.465 430 44 25 725 1126 560371545 560371962 3.120000e-75 292.0
13 TraesCS1D01G096400 chr1A 86.758 219 25 1 1499 1717 100103859 100103645 1.150000e-59 241.0
14 TraesCS1D01G096400 chr7B 84.182 923 97 30 544 1446 578438138 578439031 0.000000e+00 850.0
15 TraesCS1D01G096400 chr7B 82.372 624 81 22 1768 2386 578439691 578440290 1.700000e-142 516.0
16 TraesCS1D01G096400 chr7B 88.670 203 16 5 2533 2733 61045791 61045594 1.150000e-59 241.0
17 TraesCS1D01G096400 chr7B 85.083 181 27 0 1513 1693 578439279 578439459 5.440000e-43 185.0
18 TraesCS1D01G096400 chr7A 83.819 927 101 32 543 1441 617386677 617385772 0.000000e+00 835.0
19 TraesCS1D01G096400 chr7A 82.026 612 79 20 1780 2386 617385205 617384620 2.860000e-135 492.0
20 TraesCS1D01G096400 chr7A 84.163 221 30 3 1491 1710 617385549 617385333 3.230000e-50 209.0
21 TraesCS1D01G096400 chr7A 87.209 172 17 3 2533 2703 107556333 107556166 1.170000e-44 191.0
22 TraesCS1D01G096400 chr7D 83.529 935 83 39 543 1446 535966640 535967534 0.000000e+00 808.0
23 TraesCS1D01G096400 chr7D 81.440 889 115 31 1513 2386 535967789 535968642 0.000000e+00 682.0
24 TraesCS1D01G096400 chr3D 85.772 246 31 4 136 379 376174105 376174348 1.140000e-64 257.0
25 TraesCS1D01G096400 chr3D 82.645 242 32 9 144 379 316825636 316825399 4.180000e-49 206.0
26 TraesCS1D01G096400 chr5B 85.294 238 32 3 144 379 21545491 21545727 3.190000e-60 243.0
27 TraesCS1D01G096400 chrUn 83.539 243 36 4 144 383 88837376 88837135 1.150000e-54 224.0
28 TraesCS1D01G096400 chrUn 83.539 243 36 4 144 383 88857266 88857025 1.150000e-54 224.0
29 TraesCS1D01G096400 chr4A 82.988 241 36 5 143 379 558224430 558224669 2.500000e-51 213.0
30 TraesCS1D01G096400 chr4A 78.818 203 41 2 1241 1442 75466027 75466228 5.560000e-28 135.0
31 TraesCS1D01G096400 chr4B 81.707 246 40 5 144 385 4956125 4955881 1.940000e-47 200.0
32 TraesCS1D01G096400 chr4D 78.365 208 42 3 1241 1446 394361889 394362095 7.190000e-27 132.0
33 TraesCS1D01G096400 chr2D 74.654 217 49 5 1207 1417 382128679 382128463 1.220000e-14 91.6
34 TraesCS1D01G096400 chr2B 74.194 217 50 5 1207 1417 452912548 452912332 5.680000e-13 86.1


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 TraesCS1D01G096400 chr1D 81724983 81728178 3195 False 5903.00 5903 100.00000 1 3196 1 chr1D.!!$F2 3195
1 TraesCS1D01G096400 chr1D 467610272 467612503 2231 True 694.50 821 83.80250 571 2385 2 chr1D.!!$R1 1814
2 TraesCS1D01G096400 chr1B 136311927 136316404 4477 False 862.75 2918 89.91700 570 3196 4 chr1B.!!$F1 2626
3 TraesCS1D01G096400 chr1A 100099710 100105503 5793 True 827.50 1400 90.41725 1 2490 4 chr1A.!!$R1 2489
4 TraesCS1D01G096400 chr1A 560371545 560372186 641 False 309.50 327 86.85400 725 1441 2 chr1A.!!$F1 716
5 TraesCS1D01G096400 chr7B 578438138 578440290 2152 False 517.00 850 83.87900 544 2386 3 chr7B.!!$F1 1842
6 TraesCS1D01G096400 chr7A 617384620 617386677 2057 True 512.00 835 83.33600 543 2386 3 chr7A.!!$R2 1843
7 TraesCS1D01G096400 chr7D 535966640 535968642 2002 False 745.00 808 82.48450 543 2386 2 chr7D.!!$F1 1843

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
868 949 1.03828 AAACTCTATCCTACCCCGCG 58.962 55.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2755 6350 0.03831 ACCTAGGCCAGAAACCAAGC 59.962 55.0 9.3 0.0 0.0 4.01 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
46 47 1.365293 CATAGGCCCATGATCCTCCA 58.635 55.000 5.02 0.00 34.02 3.86
74 75 2.094752 GCAAAAAGCACCACATACGGAT 60.095 45.455 0.00 0.00 44.79 4.18
90 91 7.067494 CACATACGGATCCATCATGTATCTCTA 59.933 40.741 17.82 0.00 31.65 2.43
141 142 8.356657 AGCTACTTGACAGATAAGATACATGAC 58.643 37.037 0.00 0.00 0.00 3.06
151 152 8.952278 CAGATAAGATACATGACCTACTACCTC 58.048 40.741 0.00 0.00 0.00 3.85
171 172 6.424032 ACCTCCATCCTGGTTTATTAGTTTC 58.576 40.000 0.00 0.00 39.03 2.78
172 173 6.217693 ACCTCCATCCTGGTTTATTAGTTTCT 59.782 38.462 0.00 0.00 39.03 2.52
189 190 9.606631 ATTAGTTTCTTTTGTATGTTTTGCCAA 57.393 25.926 0.00 0.00 0.00 4.52
379 382 7.397192 ACTTATAAACCAGAACGGAGGTAGTAA 59.603 37.037 0.00 0.00 37.07 2.24
423 426 4.403734 AGGCTTCGGAGAAAAATAAACCA 58.596 39.130 0.00 0.00 45.90 3.67
489 492 6.310711 CCTCCGATTCAAAAGTTGTACTAGAC 59.689 42.308 0.00 0.00 0.00 2.59
512 515 6.046593 ACCTGCGACAATTAATTTAGATCGA 58.953 36.000 18.16 0.00 0.00 3.59
516 519 7.841486 TGCGACAATTAATTTAGATCGAAGAG 58.159 34.615 18.16 0.60 43.63 2.85
539 542 7.727186 AGAGAGTAACATATATTTACCCGGACA 59.273 37.037 0.73 0.00 30.88 4.02
561 564 2.033049 GGCAGAAGCATAGCTGTGATTG 59.967 50.000 19.08 7.35 44.61 2.67
773 834 7.309920 GTGAACAAGTTTGAAAAGTAGTCCAA 58.690 34.615 0.00 0.00 0.00 3.53
790 851 2.373169 TCCAAGGAGCTCAACTGATTGT 59.627 45.455 17.19 0.00 37.11 2.71
824 889 1.144093 AGTTGTCGATTGGGGTTGGAA 59.856 47.619 0.00 0.00 0.00 3.53
825 890 1.268625 GTTGTCGATTGGGGTTGGAAC 59.731 52.381 0.00 0.00 0.00 3.62
868 949 1.038280 AAACTCTATCCTACCCCGCG 58.962 55.000 0.00 0.00 0.00 6.46
976 1088 2.494059 CCGTTTCCTCACAGTGTTCAT 58.506 47.619 0.00 0.00 0.00 2.57
1627 1989 0.179040 TCGACGGCCTCAAAAACCTT 60.179 50.000 0.00 0.00 0.00 3.50
2009 5554 3.764466 CGCGGCTTCCTCCAGTCT 61.764 66.667 0.00 0.00 0.00 3.24
2198 5745 0.162933 GCGCGTTCGTCAATTGAGAA 59.837 50.000 8.80 11.60 38.14 2.87
2202 5749 3.546271 CGCGTTCGTCAATTGAGAATAGA 59.454 43.478 8.80 1.18 0.00 1.98
2205 5752 5.340803 CGTTCGTCAATTGAGAATAGAGGA 58.659 41.667 8.80 0.00 0.00 3.71
2206 5753 5.980116 CGTTCGTCAATTGAGAATAGAGGAT 59.020 40.000 8.80 0.00 0.00 3.24
2210 5761 5.312079 GTCAATTGAGAATAGAGGATGGGG 58.688 45.833 8.80 0.00 0.00 4.96
2304 5881 5.933617 TGAATTCATCTCCTATTGTCCAGG 58.066 41.667 3.38 0.00 34.20 4.45
2405 5991 6.139013 GCAAAAAGTCATTTCAATGTTTTCGC 59.861 34.615 0.00 0.00 37.65 4.70
2412 5998 6.198966 GTCATTTCAATGTTTTCGCTCAAACT 59.801 34.615 8.56 0.00 37.51 2.66
2417 6003 1.403679 TGTTTTCGCTCAAACTGTGGG 59.596 47.619 8.56 0.00 37.51 4.61
2418 6004 1.028905 TTTTCGCTCAAACTGTGGGG 58.971 50.000 0.00 0.00 0.00 4.96
2433 6019 3.486383 TGTGGGGAAGTGTTTGATTCTC 58.514 45.455 0.00 0.00 0.00 2.87
2462 6056 2.916702 ATATGATGTGAAGCTCGGCA 57.083 45.000 0.00 0.00 0.00 5.69
2477 6071 2.665185 GCAACCAAGTCGAGCCGT 60.665 61.111 0.00 0.00 0.00 5.68
2495 6089 1.268539 CGTGTGGTTTGTTTGCTCTCC 60.269 52.381 0.00 0.00 0.00 3.71
2508 6102 6.119536 TGTTTGCTCTCCTTTTTCTGACTTA 58.880 36.000 0.00 0.00 0.00 2.24
2528 6122 5.478332 ACTTAGCTCCCAATTTCCTTTTGAG 59.522 40.000 0.00 0.00 0.00 3.02
2530 6124 4.482990 AGCTCCCAATTTCCTTTTGAGAA 58.517 39.130 0.00 0.00 0.00 2.87
2542 6136 6.683974 TCCTTTTGAGAAGAACAACAAGAG 57.316 37.500 0.00 0.00 0.00 2.85
2560 6154 4.672587 AGAGCTCTGCCGTTTCATTATA 57.327 40.909 17.42 0.00 0.00 0.98
2561 6155 4.626042 AGAGCTCTGCCGTTTCATTATAG 58.374 43.478 17.42 0.00 0.00 1.31
2562 6156 4.342378 AGAGCTCTGCCGTTTCATTATAGA 59.658 41.667 17.42 0.00 0.00 1.98
2563 6157 5.023533 AGCTCTGCCGTTTCATTATAGAA 57.976 39.130 0.00 0.00 0.00 2.10
2564 6158 5.428253 AGCTCTGCCGTTTCATTATAGAAA 58.572 37.500 0.00 0.00 35.28 2.52
2565 6159 5.525378 AGCTCTGCCGTTTCATTATAGAAAG 59.475 40.000 0.00 0.00 38.11 2.62
2566 6160 5.277538 GCTCTGCCGTTTCATTATAGAAAGG 60.278 44.000 0.00 0.00 40.92 3.11
2601 6195 7.589958 TTTTTACAGCCCACTAATCAGAAAA 57.410 32.000 0.00 0.00 0.00 2.29
2602 6196 6.817765 TTTACAGCCCACTAATCAGAAAAG 57.182 37.500 0.00 0.00 0.00 2.27
2603 6197 3.084786 ACAGCCCACTAATCAGAAAAGC 58.915 45.455 0.00 0.00 0.00 3.51
2623 6217 1.267832 CGAAAACAACAGACCACACCG 60.268 52.381 0.00 0.00 0.00 4.94
2624 6218 1.064952 GAAAACAACAGACCACACCGG 59.935 52.381 0.00 0.00 42.50 5.28
2687 6282 6.437477 CCTATACATCCATTCTAGCAGTACCA 59.563 42.308 0.00 0.00 0.00 3.25
2706 6301 5.300411 ACCACTCATAGCATCATTCATCA 57.700 39.130 0.00 0.00 0.00 3.07
2707 6302 5.306394 ACCACTCATAGCATCATTCATCAG 58.694 41.667 0.00 0.00 0.00 2.90
2708 6303 5.071384 ACCACTCATAGCATCATTCATCAGA 59.929 40.000 0.00 0.00 0.00 3.27
2709 6304 5.639931 CCACTCATAGCATCATTCATCAGAG 59.360 44.000 0.00 0.00 0.00 3.35
2710 6305 6.224584 CACTCATAGCATCATTCATCAGAGT 58.775 40.000 0.00 0.00 33.32 3.24
2711 6306 6.146347 CACTCATAGCATCATTCATCAGAGTG 59.854 42.308 0.00 0.00 41.90 3.51
2712 6307 6.041751 ACTCATAGCATCATTCATCAGAGTGA 59.958 38.462 0.00 0.00 43.46 3.41
2714 6309 8.130671 TCATAGCATCATTCATCAGAGTGATA 57.869 34.615 3.64 0.00 45.92 2.15
2715 6310 8.759782 TCATAGCATCATTCATCAGAGTGATAT 58.240 33.333 3.64 0.19 45.92 1.63
2716 6311 9.036671 CATAGCATCATTCATCAGAGTGATATC 57.963 37.037 3.64 0.00 45.92 1.63
2717 6312 7.005709 AGCATCATTCATCAGAGTGATATCA 57.994 36.000 0.00 0.00 45.92 2.15
2718 6313 7.625469 AGCATCATTCATCAGAGTGATATCAT 58.375 34.615 9.02 0.00 45.92 2.45
2719 6314 7.766738 AGCATCATTCATCAGAGTGATATCATC 59.233 37.037 9.02 7.72 45.92 2.92
2720 6315 7.766738 GCATCATTCATCAGAGTGATATCATCT 59.233 37.037 9.02 9.78 45.92 2.90
2721 6316 9.308318 CATCATTCATCAGAGTGATATCATCTC 57.692 37.037 19.42 19.42 45.92 2.75
2722 6317 8.653036 TCATTCATCAGAGTGATATCATCTCT 57.347 34.615 22.02 22.02 35.82 3.10
2723 6318 9.750783 TCATTCATCAGAGTGATATCATCTCTA 57.249 33.333 24.81 17.74 35.82 2.43
2730 6325 8.965819 TCAGAGTGATATCATCTCTAATTAGCC 58.034 37.037 24.81 5.61 34.76 3.93
2731 6326 8.196771 CAGAGTGATATCATCTCTAATTAGCCC 58.803 40.741 24.81 5.26 34.76 5.19
2732 6327 7.344352 AGAGTGATATCATCTCTAATTAGCCCC 59.656 40.741 24.40 4.18 34.76 5.80
2733 6328 6.385467 AGTGATATCATCTCTAATTAGCCCCC 59.615 42.308 9.02 0.00 31.86 5.40
2734 6329 6.156949 GTGATATCATCTCTAATTAGCCCCCA 59.843 42.308 9.02 0.00 0.00 4.96
2735 6330 6.735229 TGATATCATCTCTAATTAGCCCCCAA 59.265 38.462 7.67 0.00 0.00 4.12
2736 6331 7.407033 TGATATCATCTCTAATTAGCCCCCAAT 59.593 37.037 7.67 0.63 0.00 3.16
2737 6332 5.246981 TCATCTCTAATTAGCCCCCAATG 57.753 43.478 7.67 5.30 0.00 2.82
2738 6333 4.665009 TCATCTCTAATTAGCCCCCAATGT 59.335 41.667 7.67 0.00 0.00 2.71
2739 6334 5.134339 TCATCTCTAATTAGCCCCCAATGTT 59.866 40.000 7.67 0.00 0.00 2.71
2740 6335 6.331572 TCATCTCTAATTAGCCCCCAATGTTA 59.668 38.462 7.67 0.00 0.00 2.41
2741 6336 5.937111 TCTCTAATTAGCCCCCAATGTTAC 58.063 41.667 7.67 0.00 0.00 2.50
2742 6337 5.430417 TCTCTAATTAGCCCCCAATGTTACA 59.570 40.000 7.67 0.00 0.00 2.41
2743 6338 6.069323 TCTCTAATTAGCCCCCAATGTTACAA 60.069 38.462 7.67 0.00 0.00 2.41
2744 6339 6.678547 TCTAATTAGCCCCCAATGTTACAAT 58.321 36.000 7.67 0.00 0.00 2.71
2745 6340 5.612725 AATTAGCCCCCAATGTTACAATG 57.387 39.130 0.00 0.00 0.00 2.82
2746 6341 1.864669 AGCCCCCAATGTTACAATGG 58.135 50.000 12.23 12.23 34.45 3.16
2750 6345 2.671130 CCCAATGTTACAATGGGTGC 57.329 50.000 26.04 0.00 46.46 5.01
2751 6346 1.135141 CCCAATGTTACAATGGGTGCG 60.135 52.381 26.04 4.89 46.46 5.34
2752 6347 1.543802 CCAATGTTACAATGGGTGCGT 59.456 47.619 11.41 0.00 31.30 5.24
2753 6348 2.750166 CCAATGTTACAATGGGTGCGTA 59.250 45.455 11.41 0.00 31.30 4.42
2754 6349 3.191581 CCAATGTTACAATGGGTGCGTAA 59.808 43.478 11.41 0.00 31.30 3.18
2755 6350 4.411327 CAATGTTACAATGGGTGCGTAAG 58.589 43.478 0.00 0.00 43.44 2.34
2769 6364 0.521735 CGTAAGCTTGGTTTCTGGCC 59.478 55.000 9.86 0.00 0.00 5.36
2770 6365 1.882352 CGTAAGCTTGGTTTCTGGCCT 60.882 52.381 9.86 0.00 0.00 5.19
2771 6366 2.614481 CGTAAGCTTGGTTTCTGGCCTA 60.614 50.000 9.86 0.00 0.00 3.93
2772 6367 2.206576 AAGCTTGGTTTCTGGCCTAG 57.793 50.000 3.32 0.00 33.14 3.02
2773 6368 0.329596 AGCTTGGTTTCTGGCCTAGG 59.670 55.000 3.67 3.67 31.17 3.02
2774 6369 0.038310 GCTTGGTTTCTGGCCTAGGT 59.962 55.000 11.31 0.00 31.17 3.08
2775 6370 1.950954 GCTTGGTTTCTGGCCTAGGTC 60.951 57.143 6.37 6.37 31.17 3.85
2776 6371 0.696501 TTGGTTTCTGGCCTAGGTCC 59.303 55.000 11.80 12.88 0.00 4.46
2777 6372 0.178873 TGGTTTCTGGCCTAGGTCCT 60.179 55.000 11.80 0.00 0.00 3.85
2778 6373 0.992695 GGTTTCTGGCCTAGGTCCTT 59.007 55.000 11.80 0.00 0.00 3.36
2779 6374 1.065345 GGTTTCTGGCCTAGGTCCTTC 60.065 57.143 11.80 0.00 0.00 3.46
2780 6375 1.909986 GTTTCTGGCCTAGGTCCTTCT 59.090 52.381 11.80 0.00 0.00 2.85
2781 6376 2.306219 GTTTCTGGCCTAGGTCCTTCTT 59.694 50.000 11.80 0.00 0.00 2.52
2782 6377 2.344093 TCTGGCCTAGGTCCTTCTTT 57.656 50.000 11.80 0.00 0.00 2.52
2783 6378 2.188817 TCTGGCCTAGGTCCTTCTTTC 58.811 52.381 11.80 0.00 0.00 2.62
2784 6379 0.902531 TGGCCTAGGTCCTTCTTTCG 59.097 55.000 11.80 0.00 0.00 3.46
2785 6380 0.903236 GGCCTAGGTCCTTCTTTCGT 59.097 55.000 11.31 0.00 0.00 3.85
2786 6381 1.278413 GGCCTAGGTCCTTCTTTCGTT 59.722 52.381 11.31 0.00 0.00 3.85
2787 6382 2.290134 GGCCTAGGTCCTTCTTTCGTTT 60.290 50.000 11.31 0.00 0.00 3.60
2788 6383 3.055602 GGCCTAGGTCCTTCTTTCGTTTA 60.056 47.826 11.31 0.00 0.00 2.01
2789 6384 4.564199 GGCCTAGGTCCTTCTTTCGTTTAA 60.564 45.833 11.31 0.00 0.00 1.52
2790 6385 4.391216 GCCTAGGTCCTTCTTTCGTTTAAC 59.609 45.833 11.31 0.00 0.00 2.01
2791 6386 4.934001 CCTAGGTCCTTCTTTCGTTTAACC 59.066 45.833 0.00 0.00 0.00 2.85
2792 6387 4.701651 AGGTCCTTCTTTCGTTTAACCT 57.298 40.909 0.00 0.00 0.00 3.50
2793 6388 5.045012 AGGTCCTTCTTTCGTTTAACCTT 57.955 39.130 0.00 0.00 32.01 3.50
2794 6389 5.443283 AGGTCCTTCTTTCGTTTAACCTTT 58.557 37.500 0.00 0.00 32.01 3.11
2795 6390 5.889853 AGGTCCTTCTTTCGTTTAACCTTTT 59.110 36.000 0.00 0.00 32.01 2.27
2796 6391 6.379133 AGGTCCTTCTTTCGTTTAACCTTTTT 59.621 34.615 0.00 0.00 32.01 1.94
2797 6392 6.694411 GGTCCTTCTTTCGTTTAACCTTTTTC 59.306 38.462 0.00 0.00 0.00 2.29
2798 6393 6.694411 GTCCTTCTTTCGTTTAACCTTTTTCC 59.306 38.462 0.00 0.00 0.00 3.13
2799 6394 6.377712 TCCTTCTTTCGTTTAACCTTTTTCCA 59.622 34.615 0.00 0.00 0.00 3.53
2800 6395 7.068962 TCCTTCTTTCGTTTAACCTTTTTCCAT 59.931 33.333 0.00 0.00 0.00 3.41
2801 6396 7.169140 CCTTCTTTCGTTTAACCTTTTTCCATG 59.831 37.037 0.00 0.00 0.00 3.66
2802 6397 5.980715 TCTTTCGTTTAACCTTTTTCCATGC 59.019 36.000 0.00 0.00 0.00 4.06
2803 6398 5.523438 TTCGTTTAACCTTTTTCCATGCT 57.477 34.783 0.00 0.00 0.00 3.79
2804 6399 5.523438 TCGTTTAACCTTTTTCCATGCTT 57.477 34.783 0.00 0.00 0.00 3.91
2805 6400 5.525199 TCGTTTAACCTTTTTCCATGCTTC 58.475 37.500 0.00 0.00 0.00 3.86
2806 6401 5.300792 TCGTTTAACCTTTTTCCATGCTTCT 59.699 36.000 0.00 0.00 0.00 2.85
2807 6402 5.629435 CGTTTAACCTTTTTCCATGCTTCTC 59.371 40.000 0.00 0.00 0.00 2.87
2808 6403 5.722021 TTAACCTTTTTCCATGCTTCTCC 57.278 39.130 0.00 0.00 0.00 3.71
2809 6404 2.529632 ACCTTTTTCCATGCTTCTCCC 58.470 47.619 0.00 0.00 0.00 4.30
2810 6405 2.110721 ACCTTTTTCCATGCTTCTCCCT 59.889 45.455 0.00 0.00 0.00 4.20
2811 6406 3.168292 CCTTTTTCCATGCTTCTCCCTT 58.832 45.455 0.00 0.00 0.00 3.95
2812 6407 3.580022 CCTTTTTCCATGCTTCTCCCTTT 59.420 43.478 0.00 0.00 0.00 3.11
2813 6408 4.322273 CCTTTTTCCATGCTTCTCCCTTTC 60.322 45.833 0.00 0.00 0.00 2.62
2814 6409 2.514458 TTCCATGCTTCTCCCTTTCC 57.486 50.000 0.00 0.00 0.00 3.13
2815 6410 1.673767 TCCATGCTTCTCCCTTTCCT 58.326 50.000 0.00 0.00 0.00 3.36
2816 6411 1.995542 TCCATGCTTCTCCCTTTCCTT 59.004 47.619 0.00 0.00 0.00 3.36
2817 6412 2.025887 TCCATGCTTCTCCCTTTCCTTC 60.026 50.000 0.00 0.00 0.00 3.46
2818 6413 2.025510 CCATGCTTCTCCCTTTCCTTCT 60.026 50.000 0.00 0.00 0.00 2.85
2819 6414 3.563043 CCATGCTTCTCCCTTTCCTTCTT 60.563 47.826 0.00 0.00 0.00 2.52
2820 6415 3.884037 TGCTTCTCCCTTTCCTTCTTT 57.116 42.857 0.00 0.00 0.00 2.52
2821 6416 4.184649 TGCTTCTCCCTTTCCTTCTTTT 57.815 40.909 0.00 0.00 0.00 2.27
2822 6417 4.145052 TGCTTCTCCCTTTCCTTCTTTTC 58.855 43.478 0.00 0.00 0.00 2.29
2823 6418 3.508012 GCTTCTCCCTTTCCTTCTTTTCC 59.492 47.826 0.00 0.00 0.00 3.13
2824 6419 3.808834 TCTCCCTTTCCTTCTTTTCCC 57.191 47.619 0.00 0.00 0.00 3.97
2825 6420 2.039879 TCTCCCTTTCCTTCTTTTCCCG 59.960 50.000 0.00 0.00 0.00 5.14
2826 6421 1.778484 TCCCTTTCCTTCTTTTCCCGT 59.222 47.619 0.00 0.00 0.00 5.28
2827 6422 2.176148 TCCCTTTCCTTCTTTTCCCGTT 59.824 45.455 0.00 0.00 0.00 4.44
2828 6423 2.557056 CCCTTTCCTTCTTTTCCCGTTC 59.443 50.000 0.00 0.00 0.00 3.95
2829 6424 3.487372 CCTTTCCTTCTTTTCCCGTTCT 58.513 45.455 0.00 0.00 0.00 3.01
2830 6425 3.889538 CCTTTCCTTCTTTTCCCGTTCTT 59.110 43.478 0.00 0.00 0.00 2.52
2831 6426 4.341235 CCTTTCCTTCTTTTCCCGTTCTTT 59.659 41.667 0.00 0.00 0.00 2.52
2832 6427 5.533528 CCTTTCCTTCTTTTCCCGTTCTTTA 59.466 40.000 0.00 0.00 0.00 1.85
2833 6428 6.294010 CCTTTCCTTCTTTTCCCGTTCTTTAG 60.294 42.308 0.00 0.00 0.00 1.85
2834 6429 4.648651 TCCTTCTTTTCCCGTTCTTTAGG 58.351 43.478 0.00 0.00 0.00 2.69
2835 6430 3.190744 CCTTCTTTTCCCGTTCTTTAGGC 59.809 47.826 0.00 0.00 0.00 3.93
2836 6431 3.782656 TCTTTTCCCGTTCTTTAGGCT 57.217 42.857 0.00 0.00 0.00 4.58
2837 6432 3.408634 TCTTTTCCCGTTCTTTAGGCTG 58.591 45.455 0.00 0.00 0.00 4.85
2838 6433 1.530323 TTTCCCGTTCTTTAGGCTGC 58.470 50.000 0.00 0.00 0.00 5.25
2839 6434 0.690762 TTCCCGTTCTTTAGGCTGCT 59.309 50.000 0.00 0.00 0.00 4.24
2840 6435 0.690762 TCCCGTTCTTTAGGCTGCTT 59.309 50.000 0.00 0.00 0.00 3.91
2841 6436 1.903860 TCCCGTTCTTTAGGCTGCTTA 59.096 47.619 0.00 0.00 0.00 3.09
2842 6437 2.504175 TCCCGTTCTTTAGGCTGCTTAT 59.496 45.455 0.00 0.00 0.00 1.73
2843 6438 2.614057 CCCGTTCTTTAGGCTGCTTATG 59.386 50.000 0.00 0.00 0.00 1.90
2844 6439 2.614057 CCGTTCTTTAGGCTGCTTATGG 59.386 50.000 0.00 0.00 0.00 2.74
2845 6440 2.032178 CGTTCTTTAGGCTGCTTATGGC 59.968 50.000 0.00 0.00 42.22 4.40
2851 6446 1.142531 GGCTGCTTATGGCCTTTGC 59.857 57.895 3.32 6.83 44.48 3.68
2852 6447 1.606885 GGCTGCTTATGGCCTTTGCA 61.607 55.000 3.32 11.17 44.48 4.08
2853 6448 0.459063 GCTGCTTATGGCCTTTGCAC 60.459 55.000 3.32 4.23 40.92 4.57
2854 6449 0.174162 CTGCTTATGGCCTTTGCACC 59.826 55.000 3.32 0.00 40.92 5.01
2855 6450 0.541530 TGCTTATGGCCTTTGCACCA 60.542 50.000 3.32 0.00 40.92 4.17
2857 6452 1.472026 GCTTATGGCCTTTGCACCATG 60.472 52.381 15.06 2.74 46.20 3.66
2858 6453 1.137479 CTTATGGCCTTTGCACCATGG 59.863 52.381 11.19 11.19 46.20 3.66
2859 6454 0.040942 TATGGCCTTTGCACCATGGT 59.959 50.000 13.00 13.00 46.20 3.55
2860 6455 1.546589 ATGGCCTTTGCACCATGGTG 61.547 55.000 36.07 36.07 45.03 4.17
2907 6502 0.323629 CCTTTGGTCTTCGGGCTACA 59.676 55.000 0.00 0.00 0.00 2.74
2909 6504 1.002087 CTTTGGTCTTCGGGCTACAGT 59.998 52.381 0.00 0.00 0.00 3.55
2911 6506 1.255667 TGGTCTTCGGGCTACAGTCC 61.256 60.000 0.00 0.00 36.18 3.85
2919 6514 1.886886 GGGCTACAGTCCGTTTTGAA 58.113 50.000 0.00 0.00 0.00 2.69
2954 6553 7.844009 AGCATGATGTACCTTTCATTTCAAAT 58.156 30.769 0.00 0.00 30.24 2.32
3039 8681 5.030295 GGAATCTGATAACACAATGTTGCG 58.970 41.667 4.46 0.00 41.30 4.85
3045 8687 4.513318 TGATAACACAATGTTGCGACTCAA 59.487 37.500 5.50 0.00 41.30 3.02
3054 8696 0.034198 TTGCGACTCAAACGGGATCA 59.966 50.000 0.00 0.00 0.00 2.92
3055 8697 0.389817 TGCGACTCAAACGGGATCAG 60.390 55.000 0.00 0.00 0.00 2.90
3087 8729 6.817765 TTATTGTTTAGTCTCCTTGCCTTG 57.182 37.500 0.00 0.00 0.00 3.61
3088 8730 3.857157 TGTTTAGTCTCCTTGCCTTGT 57.143 42.857 0.00 0.00 0.00 3.16
3097 8739 4.393371 GTCTCCTTGCCTTGTCTCATTTAC 59.607 45.833 0.00 0.00 0.00 2.01
3108 8750 3.254060 GTCTCATTTACGAGCTCAGCAA 58.746 45.455 15.40 2.62 32.75 3.91
3109 8751 3.868077 GTCTCATTTACGAGCTCAGCAAT 59.132 43.478 15.40 5.03 32.75 3.56
3145 8788 6.449635 TCAAGCAGAGTTTGTGTTAAACAT 57.550 33.333 5.46 0.00 38.99 2.71
3187 8833 5.901884 CGAAGTGTAGATTTTTCACACACAC 59.098 40.000 6.83 0.00 43.96 3.82
3188 8834 6.456315 CGAAGTGTAGATTTTTCACACACACA 60.456 38.462 6.83 0.00 43.96 3.72
3192 8838 8.085296 AGTGTAGATTTTTCACACACACAAAAA 58.915 29.630 6.83 0.00 43.96 1.94
3193 8839 8.372521 GTGTAGATTTTTCACACACACAAAAAG 58.627 33.333 0.00 0.00 41.71 2.27
3195 8841 9.134734 GTAGATTTTTCACACACACAAAAAGAA 57.865 29.630 0.00 0.00 33.64 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.657398 TTGCAACATCTGGAGGATCAT 57.343 42.857 0.00 0.00 36.25 2.45
74 75 9.607333 AGGTTATCTTTAGAGATACATGATGGA 57.393 33.333 0.00 0.00 42.97 3.41
107 108 9.507329 TCTTATCTGTCAAGTAGCTTCAAAATT 57.493 29.630 0.00 0.00 0.00 1.82
342 345 9.152595 GTTCTGGTTTATAAGTCTCCTTTGTAG 57.847 37.037 0.00 0.00 31.89 2.74
351 354 4.776308 ACCTCCGTTCTGGTTTATAAGTCT 59.224 41.667 0.00 0.00 39.52 3.24
366 369 8.241497 TCATATGTGTATTTACTACCTCCGTT 57.759 34.615 1.90 0.00 0.00 4.44
379 382 8.609483 AGCCTATTCCTGAATCATATGTGTATT 58.391 33.333 1.90 0.00 32.50 1.89
398 401 6.661805 TGGTTTATTTTTCTCCGAAGCCTATT 59.338 34.615 0.00 0.00 0.00 1.73
440 443 4.895961 AGTAGCTAGTTTGGACTTTGGAC 58.104 43.478 0.00 0.00 37.33 4.02
489 492 6.525121 TCGATCTAAATTAATTGTCGCAGG 57.475 37.500 0.39 0.00 0.00 4.85
512 515 8.583296 GTCCGGGTAAATATATGTTACTCTCTT 58.417 37.037 0.00 0.00 30.96 2.85
516 519 7.095270 CCTGTCCGGGTAAATATATGTTACTC 58.905 42.308 0.00 10.26 32.96 2.59
539 542 0.907486 TCACAGCTATGCTTCTGCCT 59.093 50.000 0.00 0.00 36.40 4.75
773 834 2.290577 GGGAACAATCAGTTGAGCTCCT 60.291 50.000 12.15 0.00 41.51 3.69
790 851 2.806745 CGACAACTTGCAGAAGAGGGAA 60.807 50.000 0.00 0.00 32.98 3.97
824 889 1.348696 TGGATGGATAGATGCATGCGT 59.651 47.619 13.43 13.43 46.91 5.24
825 890 2.103537 TGGATGGATAGATGCATGCG 57.896 50.000 14.09 0.00 46.91 4.73
976 1088 2.833943 TGCTAAGAGGCTGATGAAGTGA 59.166 45.455 0.00 0.00 0.00 3.41
1101 1247 2.675423 TAGTCCACGCGCAGGTCT 60.675 61.111 18.55 18.55 0.00 3.85
1108 1257 0.247576 CAGTCGTAGTAGTCCACGCG 60.248 60.000 3.53 3.53 38.05 6.01
1627 1989 4.510340 GTGGCGTTTCTGAACTTCTCTTTA 59.490 41.667 0.00 0.00 33.51 1.85
2162 5709 2.815647 CAGCGCTTCCGGACTTCC 60.816 66.667 7.50 0.00 34.32 3.46
2198 5745 0.471971 CGTGGTCCCCCATCCTCTAT 60.472 60.000 0.00 0.00 44.35 1.98
2202 5749 3.009115 CACGTGGTCCCCCATCCT 61.009 66.667 7.95 0.00 44.35 3.24
2210 5761 0.386476 TGTATATCCGCACGTGGTCC 59.614 55.000 18.88 0.00 0.00 4.46
2293 5866 8.786898 CACATACCAATTATTCCTGGACAATAG 58.213 37.037 0.00 0.00 36.49 1.73
2304 5881 7.151999 TGGTTGACACACATACCAATTATTC 57.848 36.000 0.00 0.00 37.03 1.75
2405 5991 2.348411 ACACTTCCCCACAGTTTGAG 57.652 50.000 0.00 0.00 0.00 3.02
2412 5998 3.117701 TGAGAATCAAACACTTCCCCACA 60.118 43.478 0.00 0.00 45.97 4.17
2433 6019 4.494690 GCTTCACATCATATTCGTGTGGTG 60.495 45.833 10.38 0.00 42.55 4.17
2462 6056 1.594293 CACACGGCTCGACTTGGTT 60.594 57.895 1.50 0.00 0.00 3.67
2477 6071 2.435372 AGGAGAGCAAACAAACCACA 57.565 45.000 0.00 0.00 0.00 4.17
2495 6089 6.581171 AATTGGGAGCTAAGTCAGAAAAAG 57.419 37.500 0.00 0.00 0.00 2.27
2508 6102 4.118168 TCTCAAAAGGAAATTGGGAGCT 57.882 40.909 0.00 0.00 32.46 4.09
2528 6122 2.225255 GGCAGAGCTCTTGTTGTTCTTC 59.775 50.000 15.27 0.00 0.00 2.87
2530 6124 1.875576 CGGCAGAGCTCTTGTTGTTCT 60.876 52.381 15.27 0.00 0.00 3.01
2542 6136 5.277538 CCTTTCTATAATGAAACGGCAGAGC 60.278 44.000 0.00 0.00 33.11 4.09
2577 6171 7.589958 TTTTCTGATTAGTGGGCTGTAAAAA 57.410 32.000 0.00 0.00 0.00 1.94
2578 6172 6.294508 GCTTTTCTGATTAGTGGGCTGTAAAA 60.295 38.462 0.00 0.00 0.00 1.52
2579 6173 5.183140 GCTTTTCTGATTAGTGGGCTGTAAA 59.817 40.000 0.00 0.00 0.00 2.01
2580 6174 4.700213 GCTTTTCTGATTAGTGGGCTGTAA 59.300 41.667 0.00 0.00 0.00 2.41
2581 6175 4.261801 GCTTTTCTGATTAGTGGGCTGTA 58.738 43.478 0.00 0.00 0.00 2.74
2582 6176 3.084786 GCTTTTCTGATTAGTGGGCTGT 58.915 45.455 0.00 0.00 0.00 4.40
2583 6177 2.096496 CGCTTTTCTGATTAGTGGGCTG 59.904 50.000 0.00 0.00 0.00 4.85
2584 6178 2.027192 TCGCTTTTCTGATTAGTGGGCT 60.027 45.455 0.00 0.00 0.00 5.19
2585 6179 2.356135 TCGCTTTTCTGATTAGTGGGC 58.644 47.619 0.00 0.00 0.00 5.36
2586 6180 5.154222 GTTTTCGCTTTTCTGATTAGTGGG 58.846 41.667 0.00 0.00 0.00 4.61
2587 6181 5.757886 TGTTTTCGCTTTTCTGATTAGTGG 58.242 37.500 0.00 0.00 0.00 4.00
2588 6182 6.690957 TGTTGTTTTCGCTTTTCTGATTAGTG 59.309 34.615 0.00 0.00 0.00 2.74
2589 6183 6.791303 TGTTGTTTTCGCTTTTCTGATTAGT 58.209 32.000 0.00 0.00 0.00 2.24
2590 6184 7.112148 GTCTGTTGTTTTCGCTTTTCTGATTAG 59.888 37.037 0.00 0.00 0.00 1.73
2591 6185 6.910433 GTCTGTTGTTTTCGCTTTTCTGATTA 59.090 34.615 0.00 0.00 0.00 1.75
2592 6186 5.743872 GTCTGTTGTTTTCGCTTTTCTGATT 59.256 36.000 0.00 0.00 0.00 2.57
2593 6187 5.273944 GTCTGTTGTTTTCGCTTTTCTGAT 58.726 37.500 0.00 0.00 0.00 2.90
2594 6188 4.438200 GGTCTGTTGTTTTCGCTTTTCTGA 60.438 41.667 0.00 0.00 0.00 3.27
2595 6189 3.791353 GGTCTGTTGTTTTCGCTTTTCTG 59.209 43.478 0.00 0.00 0.00 3.02
2596 6190 3.442273 TGGTCTGTTGTTTTCGCTTTTCT 59.558 39.130 0.00 0.00 0.00 2.52
2597 6191 3.546271 GTGGTCTGTTGTTTTCGCTTTTC 59.454 43.478 0.00 0.00 0.00 2.29
2598 6192 3.057174 TGTGGTCTGTTGTTTTCGCTTTT 60.057 39.130 0.00 0.00 0.00 2.27
2599 6193 2.490115 TGTGGTCTGTTGTTTTCGCTTT 59.510 40.909 0.00 0.00 0.00 3.51
2600 6194 2.088423 TGTGGTCTGTTGTTTTCGCTT 58.912 42.857 0.00 0.00 0.00 4.68
2601 6195 1.400494 GTGTGGTCTGTTGTTTTCGCT 59.600 47.619 0.00 0.00 0.00 4.93
2602 6196 1.533129 GGTGTGGTCTGTTGTTTTCGC 60.533 52.381 0.00 0.00 0.00 4.70
2603 6197 1.267832 CGGTGTGGTCTGTTGTTTTCG 60.268 52.381 0.00 0.00 0.00 3.46
2687 6282 6.041751 TCACTCTGATGAATGATGCTATGAGT 59.958 38.462 0.00 0.00 0.00 3.41
2706 6301 7.344352 GGGGCTAATTAGAGATGATATCACTCT 59.656 40.741 26.67 26.67 42.51 3.24
2707 6302 7.418483 GGGGGCTAATTAGAGATGATATCACTC 60.418 44.444 16.85 19.42 32.43 3.51
2708 6303 6.385467 GGGGGCTAATTAGAGATGATATCACT 59.615 42.308 16.85 7.50 34.55 3.41
2709 6304 6.156949 TGGGGGCTAATTAGAGATGATATCAC 59.843 42.308 16.85 2.47 0.00 3.06
2710 6305 6.271537 TGGGGGCTAATTAGAGATGATATCA 58.728 40.000 16.85 8.10 0.00 2.15
2711 6306 6.814954 TGGGGGCTAATTAGAGATGATATC 57.185 41.667 16.85 0.00 0.00 1.63
2712 6307 7.185304 ACATTGGGGGCTAATTAGAGATGATAT 59.815 37.037 16.85 0.00 0.00 1.63
2713 6308 6.505344 ACATTGGGGGCTAATTAGAGATGATA 59.495 38.462 16.85 0.00 0.00 2.15
2714 6309 5.314306 ACATTGGGGGCTAATTAGAGATGAT 59.686 40.000 16.85 0.11 0.00 2.45
2715 6310 4.665009 ACATTGGGGGCTAATTAGAGATGA 59.335 41.667 16.85 0.00 0.00 2.92
2716 6311 4.990526 ACATTGGGGGCTAATTAGAGATG 58.009 43.478 16.85 11.11 0.00 2.90
2717 6312 5.669798 AACATTGGGGGCTAATTAGAGAT 57.330 39.130 16.85 0.00 0.00 2.75
2718 6313 5.430417 TGTAACATTGGGGGCTAATTAGAGA 59.570 40.000 16.85 0.00 0.00 3.10
2719 6314 5.690865 TGTAACATTGGGGGCTAATTAGAG 58.309 41.667 16.85 0.00 0.00 2.43
2720 6315 5.718801 TGTAACATTGGGGGCTAATTAGA 57.281 39.130 16.85 0.00 0.00 2.10
2721 6316 6.239289 CCATTGTAACATTGGGGGCTAATTAG 60.239 42.308 8.20 8.20 32.98 1.73
2722 6317 5.600484 CCATTGTAACATTGGGGGCTAATTA 59.400 40.000 0.00 0.00 32.98 1.40
2723 6318 4.408596 CCATTGTAACATTGGGGGCTAATT 59.591 41.667 0.00 0.00 32.98 1.40
2724 6319 3.966665 CCATTGTAACATTGGGGGCTAAT 59.033 43.478 0.00 0.00 32.98 1.73
2725 6320 3.370104 CCATTGTAACATTGGGGGCTAA 58.630 45.455 0.00 0.00 32.98 3.09
2726 6321 2.358721 CCCATTGTAACATTGGGGGCTA 60.359 50.000 14.62 0.00 45.83 3.93
2727 6322 1.622173 CCCATTGTAACATTGGGGGCT 60.622 52.381 14.62 0.00 45.83 5.19
2728 6323 0.829990 CCCATTGTAACATTGGGGGC 59.170 55.000 14.62 0.00 45.83 5.80
2732 6327 1.543802 ACGCACCCATTGTAACATTGG 59.456 47.619 0.00 0.00 35.42 3.16
2733 6328 4.411327 CTTACGCACCCATTGTAACATTG 58.589 43.478 0.00 0.00 0.00 2.82
2734 6329 3.119637 GCTTACGCACCCATTGTAACATT 60.120 43.478 0.00 0.00 35.78 2.71
2735 6330 2.422127 GCTTACGCACCCATTGTAACAT 59.578 45.455 0.00 0.00 35.78 2.71
2736 6331 1.807742 GCTTACGCACCCATTGTAACA 59.192 47.619 0.00 0.00 35.78 2.41
2737 6332 2.081462 AGCTTACGCACCCATTGTAAC 58.919 47.619 0.00 0.00 39.10 2.50
2738 6333 2.483014 AGCTTACGCACCCATTGTAA 57.517 45.000 0.00 0.00 39.10 2.41
2739 6334 2.080693 CAAGCTTACGCACCCATTGTA 58.919 47.619 0.00 0.00 39.10 2.41
2740 6335 0.881118 CAAGCTTACGCACCCATTGT 59.119 50.000 0.00 0.00 39.10 2.71
2741 6336 0.171007 CCAAGCTTACGCACCCATTG 59.829 55.000 0.00 0.00 39.10 2.82
2742 6337 0.251165 ACCAAGCTTACGCACCCATT 60.251 50.000 0.00 0.00 39.10 3.16
2743 6338 0.251165 AACCAAGCTTACGCACCCAT 60.251 50.000 0.00 0.00 39.10 4.00
2744 6339 0.466555 AAACCAAGCTTACGCACCCA 60.467 50.000 0.00 0.00 39.10 4.51
2745 6340 0.240145 GAAACCAAGCTTACGCACCC 59.760 55.000 0.00 0.00 39.10 4.61
2746 6341 1.069227 CAGAAACCAAGCTTACGCACC 60.069 52.381 0.00 0.00 39.10 5.01
2747 6342 1.069227 CCAGAAACCAAGCTTACGCAC 60.069 52.381 0.00 0.00 39.10 5.34
2748 6343 1.234821 CCAGAAACCAAGCTTACGCA 58.765 50.000 0.00 0.00 39.10 5.24
2749 6344 0.109735 GCCAGAAACCAAGCTTACGC 60.110 55.000 0.00 0.00 0.00 4.42
2750 6345 0.521735 GGCCAGAAACCAAGCTTACG 59.478 55.000 0.00 0.00 0.00 3.18
2751 6346 1.911057 AGGCCAGAAACCAAGCTTAC 58.089 50.000 5.01 0.00 0.00 2.34
2752 6347 2.026262 CCTAGGCCAGAAACCAAGCTTA 60.026 50.000 5.01 0.00 0.00 3.09
2753 6348 1.272147 CCTAGGCCAGAAACCAAGCTT 60.272 52.381 5.01 0.00 0.00 3.74
2754 6349 0.329596 CCTAGGCCAGAAACCAAGCT 59.670 55.000 5.01 0.00 0.00 3.74
2755 6350 0.038310 ACCTAGGCCAGAAACCAAGC 59.962 55.000 9.30 0.00 0.00 4.01
2756 6351 1.340114 GGACCTAGGCCAGAAACCAAG 60.340 57.143 9.30 0.00 0.00 3.61
2757 6352 0.696501 GGACCTAGGCCAGAAACCAA 59.303 55.000 9.30 0.00 0.00 3.67
2758 6353 0.178873 AGGACCTAGGCCAGAAACCA 60.179 55.000 20.25 0.00 0.00 3.67
2759 6354 0.992695 AAGGACCTAGGCCAGAAACC 59.007 55.000 20.25 2.48 0.00 3.27
2760 6355 1.909986 AGAAGGACCTAGGCCAGAAAC 59.090 52.381 20.25 9.23 0.00 2.78
2761 6356 2.344093 AGAAGGACCTAGGCCAGAAA 57.656 50.000 20.25 0.00 0.00 2.52
2762 6357 2.344093 AAGAAGGACCTAGGCCAGAA 57.656 50.000 20.25 0.00 0.00 3.02
2763 6358 2.188817 GAAAGAAGGACCTAGGCCAGA 58.811 52.381 20.25 0.00 0.00 3.86
2764 6359 1.134670 CGAAAGAAGGACCTAGGCCAG 60.135 57.143 20.25 0.00 0.00 4.85
2765 6360 0.902531 CGAAAGAAGGACCTAGGCCA 59.097 55.000 20.25 0.00 0.00 5.36
2766 6361 0.903236 ACGAAAGAAGGACCTAGGCC 59.097 55.000 9.30 11.45 0.00 5.19
2767 6362 2.764439 AACGAAAGAAGGACCTAGGC 57.236 50.000 9.30 1.17 0.00 3.93
2768 6363 4.934001 GGTTAAACGAAAGAAGGACCTAGG 59.066 45.833 7.41 7.41 0.00 3.02
2769 6364 5.791666 AGGTTAAACGAAAGAAGGACCTAG 58.208 41.667 0.00 0.00 34.86 3.02
2770 6365 5.813513 AGGTTAAACGAAAGAAGGACCTA 57.186 39.130 0.00 0.00 34.86 3.08
2771 6366 4.701651 AGGTTAAACGAAAGAAGGACCT 57.298 40.909 0.00 0.00 32.99 3.85
2772 6367 5.762825 AAAGGTTAAACGAAAGAAGGACC 57.237 39.130 0.00 0.00 0.00 4.46
2773 6368 6.694411 GGAAAAAGGTTAAACGAAAGAAGGAC 59.306 38.462 0.00 0.00 0.00 3.85
2774 6369 6.377712 TGGAAAAAGGTTAAACGAAAGAAGGA 59.622 34.615 0.00 0.00 0.00 3.36
2775 6370 6.566141 TGGAAAAAGGTTAAACGAAAGAAGG 58.434 36.000 0.00 0.00 0.00 3.46
2776 6371 7.306574 GCATGGAAAAAGGTTAAACGAAAGAAG 60.307 37.037 0.00 0.00 0.00 2.85
2777 6372 6.477360 GCATGGAAAAAGGTTAAACGAAAGAA 59.523 34.615 0.00 0.00 0.00 2.52
2778 6373 5.980715 GCATGGAAAAAGGTTAAACGAAAGA 59.019 36.000 0.00 0.00 0.00 2.52
2779 6374 5.983118 AGCATGGAAAAAGGTTAAACGAAAG 59.017 36.000 0.00 0.00 0.00 2.62
2780 6375 5.908341 AGCATGGAAAAAGGTTAAACGAAA 58.092 33.333 0.00 0.00 0.00 3.46
2781 6376 5.523438 AGCATGGAAAAAGGTTAAACGAA 57.477 34.783 0.00 0.00 0.00 3.85
2782 6377 5.300792 AGAAGCATGGAAAAAGGTTAAACGA 59.699 36.000 0.00 0.00 0.00 3.85
2783 6378 5.528870 AGAAGCATGGAAAAAGGTTAAACG 58.471 37.500 0.00 0.00 0.00 3.60
2784 6379 5.926542 GGAGAAGCATGGAAAAAGGTTAAAC 59.073 40.000 0.00 0.00 0.00 2.01
2785 6380 5.011635 GGGAGAAGCATGGAAAAAGGTTAAA 59.988 40.000 0.00 0.00 0.00 1.52
2786 6381 4.526650 GGGAGAAGCATGGAAAAAGGTTAA 59.473 41.667 0.00 0.00 0.00 2.01
2787 6382 4.086457 GGGAGAAGCATGGAAAAAGGTTA 58.914 43.478 0.00 0.00 0.00 2.85
2788 6383 2.899900 GGGAGAAGCATGGAAAAAGGTT 59.100 45.455 0.00 0.00 0.00 3.50
2789 6384 2.110721 AGGGAGAAGCATGGAAAAAGGT 59.889 45.455 0.00 0.00 0.00 3.50
2790 6385 2.812658 AGGGAGAAGCATGGAAAAAGG 58.187 47.619 0.00 0.00 0.00 3.11
2791 6386 4.322273 GGAAAGGGAGAAGCATGGAAAAAG 60.322 45.833 0.00 0.00 0.00 2.27
2792 6387 3.578282 GGAAAGGGAGAAGCATGGAAAAA 59.422 43.478 0.00 0.00 0.00 1.94
2793 6388 3.165071 GGAAAGGGAGAAGCATGGAAAA 58.835 45.455 0.00 0.00 0.00 2.29
2794 6389 2.379907 AGGAAAGGGAGAAGCATGGAAA 59.620 45.455 0.00 0.00 0.00 3.13
2795 6390 1.995542 AGGAAAGGGAGAAGCATGGAA 59.004 47.619 0.00 0.00 0.00 3.53
2796 6391 1.673767 AGGAAAGGGAGAAGCATGGA 58.326 50.000 0.00 0.00 0.00 3.41
2797 6392 2.025510 AGAAGGAAAGGGAGAAGCATGG 60.026 50.000 0.00 0.00 0.00 3.66
2798 6393 3.362870 AGAAGGAAAGGGAGAAGCATG 57.637 47.619 0.00 0.00 0.00 4.06
2799 6394 4.394797 AAAGAAGGAAAGGGAGAAGCAT 57.605 40.909 0.00 0.00 0.00 3.79
2800 6395 3.884037 AAAGAAGGAAAGGGAGAAGCA 57.116 42.857 0.00 0.00 0.00 3.91
2801 6396 3.508012 GGAAAAGAAGGAAAGGGAGAAGC 59.492 47.826 0.00 0.00 0.00 3.86
2802 6397 4.082845 GGGAAAAGAAGGAAAGGGAGAAG 58.917 47.826 0.00 0.00 0.00 2.85
2803 6398 3.497942 CGGGAAAAGAAGGAAAGGGAGAA 60.498 47.826 0.00 0.00 0.00 2.87
2804 6399 2.039879 CGGGAAAAGAAGGAAAGGGAGA 59.960 50.000 0.00 0.00 0.00 3.71
2805 6400 2.224793 ACGGGAAAAGAAGGAAAGGGAG 60.225 50.000 0.00 0.00 0.00 4.30
2806 6401 1.778484 ACGGGAAAAGAAGGAAAGGGA 59.222 47.619 0.00 0.00 0.00 4.20
2807 6402 2.287977 ACGGGAAAAGAAGGAAAGGG 57.712 50.000 0.00 0.00 0.00 3.95
2808 6403 3.487372 AGAACGGGAAAAGAAGGAAAGG 58.513 45.455 0.00 0.00 0.00 3.11
2809 6404 5.515797 AAAGAACGGGAAAAGAAGGAAAG 57.484 39.130 0.00 0.00 0.00 2.62
2810 6405 5.533528 CCTAAAGAACGGGAAAAGAAGGAAA 59.466 40.000 0.00 0.00 0.00 3.13
2811 6406 5.067954 CCTAAAGAACGGGAAAAGAAGGAA 58.932 41.667 0.00 0.00 0.00 3.36
2812 6407 4.648651 CCTAAAGAACGGGAAAAGAAGGA 58.351 43.478 0.00 0.00 0.00 3.36
2813 6408 3.190744 GCCTAAAGAACGGGAAAAGAAGG 59.809 47.826 0.00 0.00 0.00 3.46
2814 6409 4.072839 AGCCTAAAGAACGGGAAAAGAAG 58.927 43.478 0.00 0.00 0.00 2.85
2815 6410 3.818773 CAGCCTAAAGAACGGGAAAAGAA 59.181 43.478 0.00 0.00 0.00 2.52
2816 6411 3.408634 CAGCCTAAAGAACGGGAAAAGA 58.591 45.455 0.00 0.00 0.00 2.52
2817 6412 2.095212 GCAGCCTAAAGAACGGGAAAAG 60.095 50.000 0.00 0.00 0.00 2.27
2818 6413 1.883926 GCAGCCTAAAGAACGGGAAAA 59.116 47.619 0.00 0.00 0.00 2.29
2819 6414 1.073284 AGCAGCCTAAAGAACGGGAAA 59.927 47.619 0.00 0.00 0.00 3.13
2820 6415 0.690762 AGCAGCCTAAAGAACGGGAA 59.309 50.000 0.00 0.00 0.00 3.97
2821 6416 0.690762 AAGCAGCCTAAAGAACGGGA 59.309 50.000 0.00 0.00 0.00 5.14
2822 6417 2.396590 TAAGCAGCCTAAAGAACGGG 57.603 50.000 0.00 0.00 0.00 5.28
2823 6418 2.614057 CCATAAGCAGCCTAAAGAACGG 59.386 50.000 0.00 0.00 0.00 4.44
2824 6419 2.032178 GCCATAAGCAGCCTAAAGAACG 59.968 50.000 0.00 0.00 42.97 3.95
2825 6420 2.359214 GGCCATAAGCAGCCTAAAGAAC 59.641 50.000 0.00 0.00 46.14 3.01
2826 6421 2.654863 GGCCATAAGCAGCCTAAAGAA 58.345 47.619 0.00 0.00 46.14 2.52
2827 6422 2.348411 GGCCATAAGCAGCCTAAAGA 57.652 50.000 0.00 0.00 46.14 2.52
2834 6429 0.459063 GTGCAAAGGCCATAAGCAGC 60.459 55.000 5.01 0.00 46.50 5.25
2835 6430 0.174162 GGTGCAAAGGCCATAAGCAG 59.826 55.000 5.01 0.00 46.50 4.24
2836 6431 0.541530 TGGTGCAAAGGCCATAAGCA 60.542 50.000 5.01 6.82 46.50 3.91
2837 6432 0.826062 ATGGTGCAAAGGCCATAAGC 59.174 50.000 5.01 3.72 43.09 3.09
2838 6433 1.137479 CCATGGTGCAAAGGCCATAAG 59.863 52.381 5.01 0.00 43.05 1.73
2839 6434 1.193323 CCATGGTGCAAAGGCCATAA 58.807 50.000 5.01 0.00 43.05 1.90
2840 6435 0.040942 ACCATGGTGCAAAGGCCATA 59.959 50.000 18.99 0.00 43.05 2.74
2841 6436 1.229272 ACCATGGTGCAAAGGCCAT 60.229 52.632 18.99 0.79 45.55 4.40
2842 6437 2.200930 ACCATGGTGCAAAGGCCA 59.799 55.556 18.99 0.00 40.13 5.36
2843 6438 2.658422 CACCATGGTGCAAAGGCC 59.342 61.111 31.13 0.00 39.39 5.19
2852 6447 4.523083 ACTTTTATATCACGCACCATGGT 58.477 39.130 13.00 13.00 0.00 3.55
2853 6448 5.499139 AACTTTTATATCACGCACCATGG 57.501 39.130 11.19 11.19 0.00 3.66
2854 6449 6.550843 TGAAACTTTTATATCACGCACCATG 58.449 36.000 0.00 0.00 0.00 3.66
2855 6450 6.751514 TGAAACTTTTATATCACGCACCAT 57.248 33.333 0.00 0.00 0.00 3.55
2856 6451 6.150307 ACATGAAACTTTTATATCACGCACCA 59.850 34.615 0.00 0.00 0.00 4.17
2857 6452 6.551736 ACATGAAACTTTTATATCACGCACC 58.448 36.000 0.00 0.00 0.00 5.01
2858 6453 9.716507 ATTACATGAAACTTTTATATCACGCAC 57.283 29.630 0.00 0.00 0.00 5.34
2870 6465 7.791029 ACCAAAGGTCAATTACATGAAACTTT 58.209 30.769 0.00 0.00 38.37 2.66
2907 6502 8.958119 TGCTCTTATATATTTCAAAACGGACT 57.042 30.769 0.00 0.00 0.00 3.85
2909 6504 9.554395 TCATGCTCTTATATATTTCAAAACGGA 57.446 29.630 0.00 0.00 0.00 4.69
2961 6560 4.167892 TGATGTAGTGAAATTGGGGGCTAT 59.832 41.667 0.00 0.00 0.00 2.97
2962 6561 3.525609 TGATGTAGTGAAATTGGGGGCTA 59.474 43.478 0.00 0.00 0.00 3.93
2964 6563 2.733956 TGATGTAGTGAAATTGGGGGC 58.266 47.619 0.00 0.00 0.00 5.80
2965 6564 4.955450 TCATTGATGTAGTGAAATTGGGGG 59.045 41.667 0.00 0.00 0.00 5.40
3016 8658 5.030295 CGCAACATTGTGTTATCAGATTCC 58.970 41.667 0.00 0.00 38.77 3.01
3021 8663 4.152223 TGAGTCGCAACATTGTGTTATCAG 59.848 41.667 5.16 0.00 38.77 2.90
3027 8669 2.538737 CGTTTGAGTCGCAACATTGTGT 60.539 45.455 5.16 0.00 39.58 3.72
3031 8673 0.591170 CCCGTTTGAGTCGCAACATT 59.409 50.000 5.99 0.00 35.91 2.71
3032 8674 0.250124 TCCCGTTTGAGTCGCAACAT 60.250 50.000 5.99 0.00 35.91 2.71
3039 8681 3.821421 ATACCTGATCCCGTTTGAGTC 57.179 47.619 0.00 0.00 0.00 3.36
3072 8714 2.889512 TGAGACAAGGCAAGGAGACTA 58.110 47.619 0.00 0.00 42.68 2.59
3087 8729 2.881074 TGCTGAGCTCGTAAATGAGAC 58.119 47.619 9.64 0.00 38.28 3.36
3088 8730 3.592898 TTGCTGAGCTCGTAAATGAGA 57.407 42.857 9.64 0.00 38.28 3.27
3097 8739 1.648504 TGATGTGATTGCTGAGCTCG 58.351 50.000 9.64 5.21 0.00 5.03
3108 8750 5.886474 ACTCTGCTTGAAATGATGATGTGAT 59.114 36.000 0.00 0.00 0.00 3.06
3109 8751 5.250982 ACTCTGCTTGAAATGATGATGTGA 58.749 37.500 0.00 0.00 0.00 3.58
3145 8788 1.003003 TCGTGGAAGCATGGTTGATGA 59.997 47.619 16.18 9.21 33.31 2.92


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

AutoCloner maintained by Alex Coulton.