Multiple sequence alignment - TraesCS7B01G104100

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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 TraesCS7B01G104100 chr7B 100.000 5674 0 0 1 5674 119581883 119587556 0.000000e+00 10479.0
1 TraesCS7B01G104100 chr7B 87.037 108 13 1 2 108 336815355 336815248 2.780000e-23 121.0
2 TraesCS7B01G104100 chr7B 75.000 304 52 11 1 291 453120643 453120351 9.990000e-23 119.0
3 TraesCS7B01G104100 chr7B 81.061 132 21 4 115 244 725967070 725966941 1.010000e-17 102.0
4 TraesCS7B01G104100 chr7B 83.529 85 8 2 5458 5536 119321493 119321577 2.190000e-09 75.0
5 TraesCS7B01G104100 chr7D 95.275 2053 76 12 2873 4907 157102153 157104202 0.000000e+00 3234.0
6 TraesCS7B01G104100 chr7D 90.401 1573 112 20 619 2169 157099497 157101052 0.000000e+00 2032.0
7 TraesCS7B01G104100 chr7D 89.588 970 56 21 1735 2687 158993396 158994337 0.000000e+00 1190.0
8 TraesCS7B01G104100 chr7D 95.646 712 25 5 2165 2873 157101273 157101981 0.000000e+00 1138.0
9 TraesCS7B01G104100 chr7D 86.334 1061 99 16 400 1421 156916098 156917151 0.000000e+00 1114.0
10 TraesCS7B01G104100 chr7D 88.058 829 81 12 823 1643 158970280 158971098 0.000000e+00 966.0
11 TraesCS7B01G104100 chr7D 83.005 559 37 26 5153 5674 159006612 159007149 2.410000e-123 453.0
12 TraesCS7B01G104100 chr7D 81.923 520 75 14 1 517 158962113 158962616 6.800000e-114 422.0
13 TraesCS7B01G104100 chr7D 89.286 280 20 6 557 827 158964012 158964290 5.440000e-90 342.0
14 TraesCS7B01G104100 chr7D 95.312 192 6 3 2683 2873 158994448 158994637 9.240000e-78 302.0
15 TraesCS7B01G104100 chr7D 78.289 152 32 1 161 311 519274613 519274462 4.680000e-16 97.1
16 TraesCS7B01G104100 chr7D 76.699 206 22 11 1 193 436494633 436494441 2.180000e-14 91.6
17 TraesCS7B01G104100 chr7A 94.336 2048 83 11 2873 4909 159697893 159695868 0.000000e+00 3109.0
18 TraesCS7B01G104100 chr7A 89.028 1841 166 13 1 1819 159700946 159699120 0.000000e+00 2248.0
19 TraesCS7B01G104100 chr7A 91.842 711 48 8 2168 2873 159698770 159698065 0.000000e+00 983.0
20 TraesCS7B01G104100 chr7A 90.805 348 8 5 1847 2178 159699128 159698789 1.450000e-120 444.0
21 TraesCS7B01G104100 chr7A 79.106 761 61 48 4980 5674 159695612 159694884 8.730000e-118 435.0
22 TraesCS7B01G104100 chr7A 77.660 188 26 10 42 217 25139662 25139845 3.620000e-17 100.0
23 TraesCS7B01G104100 chr6A 77.160 324 39 12 1 311 9458847 9459148 7.610000e-34 156.0
24 TraesCS7B01G104100 chr2D 76.603 312 48 10 1 311 301359616 301359903 1.270000e-31 148.0
25 TraesCS7B01G104100 chr2D 78.235 170 34 3 143 311 499410352 499410519 7.770000e-19 106.0
26 TraesCS7B01G104100 chr1B 79.812 213 25 9 14 211 582109495 582109704 7.670000e-29 139.0
27 TraesCS7B01G104100 chr1B 80.412 97 12 7 382 474 672120715 672120808 3.670000e-07 67.6
28 TraesCS7B01G104100 chr6D 83.562 146 23 1 170 314 291219066 291218921 9.920000e-28 135.0
29 TraesCS7B01G104100 chr5A 79.227 207 34 6 1 205 437408546 437408347 9.920000e-28 135.0
30 TraesCS7B01G104100 chr5A 88.889 81 4 2 2130 2205 594959630 594959710 1.680000e-15 95.3
31 TraesCS7B01G104100 chr5D 76.103 272 55 7 47 314 367611895 367611630 3.570000e-27 134.0
32 TraesCS7B01G104100 chr5D 92.537 67 3 1 2127 2191 230024144 230024078 1.680000e-15 95.3
33 TraesCS7B01G104100 chr5D 83.838 99 16 0 14 112 391893803 391893705 1.680000e-15 95.3
34 TraesCS7B01G104100 chr5D 75.463 216 28 15 3 205 397075872 397076075 1.310000e-11 82.4
35 TraesCS7B01G104100 chr1A 79.787 188 23 8 44 219 403665137 403665321 7.720000e-24 122.0
36 TraesCS7B01G104100 chr1A 80.392 153 20 8 44 195 16928765 16928908 2.160000e-19 108.0
37 TraesCS7B01G104100 chr1A 83.784 111 11 4 1 110 496118120 496118016 1.300000e-16 99.0
38 TraesCS7B01G104100 chr1A 82.407 108 19 0 1067 1174 463231454 463231561 1.680000e-15 95.3
39 TraesCS7B01G104100 chr1A 90.278 72 4 2 2130 2200 540409138 540409069 2.180000e-14 91.6
40 TraesCS7B01G104100 chr2A 82.576 132 20 2 115 243 676338168 676338299 4.650000e-21 113.0
41 TraesCS7B01G104100 chr2A 93.846 65 4 0 2129 2193 475557155 475557219 1.300000e-16 99.0
42 TraesCS7B01G104100 chr4D 79.747 158 26 5 158 314 507977097 507977249 6.010000e-20 110.0
43 TraesCS7B01G104100 chr3A 74.653 288 52 13 44 314 70806120 70805837 2.160000e-19 108.0
44 TraesCS7B01G104100 chr3A 89.873 79 6 2 35 112 681331495 681331572 3.620000e-17 100.0
45 TraesCS7B01G104100 chr5B 92.958 71 3 2 2130 2200 453877994 453877926 1.010000e-17 102.0
46 TraesCS7B01G104100 chr3D 77.059 170 37 2 143 311 535502785 535502617 4.680000e-16 97.1
47 TraesCS7B01G104100 chr3D 90.411 73 5 2 2127 2198 567408805 567408734 1.680000e-15 95.3
48 TraesCS7B01G104100 chr4B 79.630 108 20 2 1063 1169 109049280 109049174 6.100000e-10 76.8


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 TraesCS7B01G104100 chr7B 119581883 119587556 5673 False 10479.000000 10479 100.0000 1 5674 1 chr7B.!!$F2 5673
1 TraesCS7B01G104100 chr7D 157099497 157104202 4705 False 2134.666667 3234 93.7740 619 4907 3 chr7D.!!$F4 4288
2 TraesCS7B01G104100 chr7D 156916098 156917151 1053 False 1114.000000 1114 86.3340 400 1421 1 chr7D.!!$F1 1021
3 TraesCS7B01G104100 chr7D 158970280 158971098 818 False 966.000000 966 88.0580 823 1643 1 chr7D.!!$F2 820
4 TraesCS7B01G104100 chr7D 158993396 158994637 1241 False 746.000000 1190 92.4500 1735 2873 2 chr7D.!!$F6 1138
5 TraesCS7B01G104100 chr7D 159006612 159007149 537 False 453.000000 453 83.0050 5153 5674 1 chr7D.!!$F3 521
6 TraesCS7B01G104100 chr7D 158962113 158964290 2177 False 382.000000 422 85.6045 1 827 2 chr7D.!!$F5 826
7 TraesCS7B01G104100 chr7A 159694884 159700946 6062 True 1443.800000 3109 89.0234 1 5674 5 chr7A.!!$R1 5673

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
552 810 0.391661 TTGGAGATGCCTTGACGAGC 60.392 55.0 0.00 0.00 37.63 5.03 F
1430 2839 0.032813 AATGTGGGCATTCTCCTGGG 60.033 55.0 0.00 0.00 41.08 4.45 F
1719 3128 0.460635 CTGCTCCTCTGCTTGAGAGC 60.461 60.0 11.01 11.01 46.36 4.09 F
2787 4556 0.604578 CTTTGCCAGTCCAACATGGG 59.395 55.0 0.00 0.00 38.32 4.00 F
3872 5814 0.250038 CATGCCATACCTGGAGTCCG 60.250 60.0 4.30 0.00 46.37 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 3259 0.257039 AGCAAAGGAGCCACCATAGG 59.743 55.000 0.47 0.0 42.04 2.57 R
2787 4556 2.850828 ATTTGCTCAGAGCCCTGCCC 62.851 60.000 20.16 0.0 41.51 5.36 R
2972 4913 3.933332 AGCTTTGGTACGTCTTATTGAGC 59.067 43.478 0.00 0.0 0.00 4.26 R
4315 6270 0.546598 GTGGTATTGGGACAGAGGGG 59.453 60.000 0.00 0.0 42.39 4.79 R
5309 7506 0.037017 TGTTCACCCATGTTACCCCG 59.963 55.000 0.00 0.0 0.00 5.73 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
36 37 4.791069 GGGTGGCGGAGGGGAGTA 62.791 72.222 0.00 0.00 0.00 2.59
42 43 0.759436 GGCGGAGGGGAGTAGAATGA 60.759 60.000 0.00 0.00 0.00 2.57
62 63 2.310779 AGTGGAGTGAAGTGGCTAGA 57.689 50.000 0.00 0.00 0.00 2.43
89 90 2.124109 AGCGAGCGGATGAGGAGA 60.124 61.111 0.00 0.00 0.00 3.71
105 106 4.283467 TGAGGAGAAATATATGTGGGGTCG 59.717 45.833 0.00 0.00 0.00 4.79
107 108 3.307480 GGAGAAATATATGTGGGGTCGGG 60.307 52.174 0.00 0.00 0.00 5.14
112 113 2.555021 ATATGTGGGGTCGGGTGGGA 62.555 60.000 0.00 0.00 0.00 4.37
113 114 2.555021 TATGTGGGGTCGGGTGGGAT 62.555 60.000 0.00 0.00 0.00 3.85
131 132 4.446413 GGGTCCGACGTGGCGATT 62.446 66.667 0.00 0.00 37.80 3.34
166 167 6.799827 CCCCCATATACTTCCCATATTTGAA 58.200 40.000 0.00 0.00 0.00 2.69
188 189 1.705997 GGATATGAGGGGTGCCGGTT 61.706 60.000 1.90 0.00 0.00 4.44
191 192 1.692173 TATGAGGGGTGCCGGTTAGC 61.692 60.000 1.90 1.96 0.00 3.09
205 206 2.706890 GGTTAGCCCGAACATTTGAGA 58.293 47.619 0.00 0.00 0.00 3.27
244 245 5.523916 CCGTCTGGATCGAATTTTTATGACT 59.476 40.000 0.00 0.00 37.49 3.41
245 246 6.414079 CGTCTGGATCGAATTTTTATGACTG 58.586 40.000 0.00 0.00 0.00 3.51
246 247 6.255670 CGTCTGGATCGAATTTTTATGACTGA 59.744 38.462 0.00 0.00 0.00 3.41
247 248 7.042456 CGTCTGGATCGAATTTTTATGACTGAT 60.042 37.037 0.00 0.00 0.00 2.90
248 249 8.279103 GTCTGGATCGAATTTTTATGACTGATC 58.721 37.037 0.00 0.00 0.00 2.92
249 250 7.986889 TCTGGATCGAATTTTTATGACTGATCA 59.013 33.333 0.00 0.00 39.83 2.92
250 251 8.146479 TGGATCGAATTTTTATGACTGATCAG 57.854 34.615 21.37 21.37 38.57 2.90
251 252 7.770433 TGGATCGAATTTTTATGACTGATCAGT 59.230 33.333 28.23 28.23 45.84 3.41
252 253 8.066595 GGATCGAATTTTTATGACTGATCAGTG 58.933 37.037 32.50 13.34 42.66 3.66
253 254 7.307493 TCGAATTTTTATGACTGATCAGTGG 57.693 36.000 32.50 5.95 42.66 4.00
254 255 5.967674 CGAATTTTTATGACTGATCAGTGGC 59.032 40.000 32.50 19.08 42.66 5.01
257 258 1.775385 TATGACTGATCAGTGGCCGA 58.225 50.000 32.50 11.21 42.66 5.54
273 285 2.280797 GAGCTGTTCGCCCACACA 60.281 61.111 0.00 0.00 40.39 3.72
316 329 3.891977 CCTACTGTAGATGCTCTAAGGCA 59.108 47.826 16.22 0.00 46.63 4.75
351 364 4.201647 GCAATTTCTTCAAATGCATCACCG 60.202 41.667 0.00 0.00 32.18 4.94
376 389 6.253727 GGATTCGCAATATAGGAACTCATACG 59.746 42.308 0.00 0.00 41.75 3.06
381 394 6.622549 GCAATATAGGAACTCATACGTAGCT 58.377 40.000 0.08 0.00 41.75 3.32
438 451 7.253420 CGCTTCATGTAGACAATTAAAACATGC 60.253 37.037 3.14 5.80 44.43 4.06
547 805 7.479352 TTTATTTCAATTGGAGATGCCTTGA 57.521 32.000 5.42 0.00 37.63 3.02
548 806 4.789012 TTTCAATTGGAGATGCCTTGAC 57.211 40.909 5.42 0.00 32.38 3.18
549 807 2.358957 TCAATTGGAGATGCCTTGACG 58.641 47.619 5.42 0.00 37.63 4.35
550 808 2.027285 TCAATTGGAGATGCCTTGACGA 60.027 45.455 5.42 0.00 37.63 4.20
551 809 2.322355 ATTGGAGATGCCTTGACGAG 57.678 50.000 0.00 0.00 37.63 4.18
552 810 0.391661 TTGGAGATGCCTTGACGAGC 60.392 55.000 0.00 0.00 37.63 5.03
553 811 1.522580 GGAGATGCCTTGACGAGCC 60.523 63.158 0.00 0.00 0.00 4.70
554 812 1.219124 GAGATGCCTTGACGAGCCA 59.781 57.895 0.00 0.00 0.00 4.75
668 2061 3.672295 CTCTGTGCCCTCCGCTTCC 62.672 68.421 0.00 0.00 38.78 3.46
1131 2532 4.338539 GAGACGGTGCGGACGTGT 62.339 66.667 8.98 6.30 45.68 4.49
1185 2588 1.002624 CACACCCACCCTACGCATT 60.003 57.895 0.00 0.00 0.00 3.56
1196 2599 1.691976 CCTACGCATTATCCAGGGTGA 59.308 52.381 0.00 0.00 32.82 4.02
1197 2600 2.289072 CCTACGCATTATCCAGGGTGAG 60.289 54.545 0.00 0.00 32.82 3.51
1198 2601 0.469917 ACGCATTATCCAGGGTGAGG 59.530 55.000 0.00 0.00 0.00 3.86
1199 2602 0.250467 CGCATTATCCAGGGTGAGGG 60.250 60.000 0.00 0.00 0.00 4.30
1200 2603 0.846693 GCATTATCCAGGGTGAGGGT 59.153 55.000 0.00 0.00 0.00 4.34
1201 2604 1.215423 GCATTATCCAGGGTGAGGGTT 59.785 52.381 0.00 0.00 0.00 4.11
1202 2605 2.936202 CATTATCCAGGGTGAGGGTTG 58.064 52.381 0.00 0.00 0.00 3.77
1217 2620 2.303022 AGGGTTGTGTGATGTACTGGAG 59.697 50.000 0.00 0.00 0.00 3.86
1220 2623 3.244078 GGTTGTGTGATGTACTGGAGTGA 60.244 47.826 0.00 0.00 0.00 3.41
1222 2625 3.230976 TGTGTGATGTACTGGAGTGACT 58.769 45.455 0.00 0.00 0.00 3.41
1224 2627 5.016831 TGTGTGATGTACTGGAGTGACTAT 58.983 41.667 0.00 0.00 0.00 2.12
1226 2629 4.142160 TGTGATGTACTGGAGTGACTATGC 60.142 45.833 0.00 0.00 0.00 3.14
1258 2661 4.458642 ACTTCGTGAACTACCTTCTACTCC 59.541 45.833 0.00 0.00 0.00 3.85
1288 2691 2.285834 CGCTTGCCGTTAGATGAATGTC 60.286 50.000 0.00 0.00 0.00 3.06
1305 2708 5.640783 TGAATGTCAGATCAGTTACAGCAAG 59.359 40.000 0.00 0.00 0.00 4.01
1308 2711 2.302733 TCAGATCAGTTACAGCAAGCCA 59.697 45.455 0.00 0.00 0.00 4.75
1313 2716 2.153645 CAGTTACAGCAAGCCATGTGA 58.846 47.619 0.00 0.00 0.00 3.58
1346 2755 0.537188 AATGAGATGCTCCGGTTCGT 59.463 50.000 0.00 0.00 0.00 3.85
1401 2810 2.550855 CCAAGCTCAGGTGCTCAAAGTA 60.551 50.000 0.00 0.00 43.24 2.24
1422 2831 1.817881 CATCGGCAATGTGGGCATT 59.182 52.632 0.00 0.00 45.42 3.56
1423 2832 0.249155 CATCGGCAATGTGGGCATTC 60.249 55.000 0.00 0.00 42.91 2.67
1424 2833 0.396139 ATCGGCAATGTGGGCATTCT 60.396 50.000 0.00 0.00 42.91 2.40
1425 2834 1.031571 TCGGCAATGTGGGCATTCTC 61.032 55.000 0.00 0.00 42.91 2.87
1429 2838 1.108776 CAATGTGGGCATTCTCCTGG 58.891 55.000 0.00 0.00 42.91 4.45
1430 2839 0.032813 AATGTGGGCATTCTCCTGGG 60.033 55.000 0.00 0.00 41.08 4.45
1435 2844 2.742116 GGCATTCTCCTGGGGCGTA 61.742 63.158 0.00 0.00 0.00 4.42
1451 2860 1.071605 CGTAGCAACTTGGCTCTCAC 58.928 55.000 0.00 0.00 44.54 3.51
1457 2866 0.597637 AACTTGGCTCTCACGTCACG 60.598 55.000 0.00 0.00 0.00 4.35
1490 2899 1.279271 GGTGGAGCTTACAGGTGTGAT 59.721 52.381 0.00 0.00 0.00 3.06
1492 2901 3.412386 GTGGAGCTTACAGGTGTGATTT 58.588 45.455 0.00 0.00 0.00 2.17
1496 2905 4.083271 GGAGCTTACAGGTGTGATTTTGTC 60.083 45.833 0.00 0.00 0.00 3.18
1497 2906 4.718961 AGCTTACAGGTGTGATTTTGTCT 58.281 39.130 0.00 0.00 0.00 3.41
1498 2907 4.516698 AGCTTACAGGTGTGATTTTGTCTG 59.483 41.667 0.00 0.00 0.00 3.51
1499 2908 4.320494 GCTTACAGGTGTGATTTTGTCTGG 60.320 45.833 0.00 0.00 0.00 3.86
1501 2910 4.104383 ACAGGTGTGATTTTGTCTGGAT 57.896 40.909 0.00 0.00 0.00 3.41
1575 2984 5.090139 TCTTCAAGAATTTATGGCCCCAAA 58.910 37.500 0.00 0.00 0.00 3.28
1591 3000 4.032310 CCCCAAAATCTCATCCCAATCAA 58.968 43.478 0.00 0.00 0.00 2.57
1593 3002 5.840149 CCCCAAAATCTCATCCCAATCAATA 59.160 40.000 0.00 0.00 0.00 1.90
1608 3017 8.141909 TCCCAATCAATAAGACGTCTAAGTATG 58.858 37.037 20.39 13.45 0.00 2.39
1620 3029 7.067615 AGACGTCTAAGTATGACTCAATGTGAT 59.932 37.037 18.46 0.00 0.00 3.06
1638 3047 4.949238 TGTGATTTCAATGTGGATACTGGG 59.051 41.667 0.00 0.00 37.61 4.45
1653 3062 2.665185 GGGTCCCGCATGCGTATC 60.665 66.667 35.55 23.89 37.81 2.24
1673 3082 1.000283 CTCTGCCCCATGTCTCGTATC 60.000 57.143 0.00 0.00 0.00 2.24
1694 3103 4.905429 TCCTTGCAACTAGCTGATGTTTA 58.095 39.130 0.00 0.00 45.94 2.01
1719 3128 0.460635 CTGCTCCTCTGCTTGAGAGC 60.461 60.000 11.01 11.01 46.36 4.09
1760 3169 3.270027 CATTTATCAGGCTTGGTCACGA 58.730 45.455 0.00 0.00 0.00 4.35
1816 3225 4.467438 GGGATTGTGATGAATGTTTTCCCT 59.533 41.667 0.00 0.00 37.80 4.20
1817 3226 5.656416 GGGATTGTGATGAATGTTTTCCCTA 59.344 40.000 0.00 0.00 37.80 3.53
1818 3227 6.324770 GGGATTGTGATGAATGTTTTCCCTAT 59.675 38.462 0.00 0.00 37.80 2.57
1819 3228 7.505585 GGGATTGTGATGAATGTTTTCCCTATA 59.494 37.037 0.00 0.00 37.80 1.31
1820 3229 8.912988 GGATTGTGATGAATGTTTTCCCTATAA 58.087 33.333 0.00 0.00 0.00 0.98
1829 3238 9.919416 TGAATGTTTTCCCTATAATTCTGATCA 57.081 29.630 0.00 0.00 0.00 2.92
1836 3245 9.838339 TTTCCCTATAATTCTGATCACTCTTTC 57.162 33.333 0.00 0.00 0.00 2.62
1859 3268 7.739995 TCTATGATATCTTTCCCTATGGTGG 57.260 40.000 3.98 0.00 0.00 4.61
1875 3284 3.352648 TGGTGGCTCCTTTGCTAATTAC 58.647 45.455 7.19 0.00 37.07 1.89
2090 3499 8.981647 CATTTTCAAAATCTCCTTACAGTTTGG 58.018 33.333 0.00 0.00 0.00 3.28
2174 3822 6.715344 TTGTCGCTGGTTTAGTACAATTAG 57.285 37.500 0.00 0.00 32.84 1.73
2273 3921 5.105106 TGCTTTCCATTCAACTAGATCGGTA 60.105 40.000 0.00 0.00 0.00 4.02
2325 3973 6.070021 TGGATGATCAAGTATATGGGGATGTC 60.070 42.308 0.00 0.00 0.00 3.06
2447 4099 5.952526 TCTTGAGTGATCTGTTACGTGTA 57.047 39.130 0.00 0.00 0.00 2.90
2494 4146 5.235186 GCACTGATCTCGTATTGTAATTGCT 59.765 40.000 0.00 0.00 0.00 3.91
2592 4245 4.201950 CCTTACACATAAGTCCAAGCATGC 60.202 45.833 10.51 10.51 36.77 4.06
2661 4314 1.323412 TGCCAACATTTAGCACCGTT 58.677 45.000 0.00 0.00 0.00 4.44
2682 4335 7.120138 ACCGTTTTACCAGGTTATATTGACTTG 59.880 37.037 0.00 0.00 33.96 3.16
2787 4556 0.604578 CTTTGCCAGTCCAACATGGG 59.395 55.000 0.00 0.00 38.32 4.00
2859 4628 9.219603 CTGTTATAAAGGACTCAGATGTCAAAA 57.780 33.333 0.00 0.00 38.61 2.44
2984 4925 4.902443 TCAGTCTAGGCTCAATAAGACG 57.098 45.455 0.00 4.91 42.51 4.18
2990 4931 4.951715 TCTAGGCTCAATAAGACGTACCAA 59.048 41.667 0.00 0.00 38.46 3.67
3073 5014 6.560253 ATTTTGATTGTTCTTACTGCTCGT 57.440 33.333 0.00 0.00 0.00 4.18
3178 5119 0.320421 TGTAGCGGCTGACTTTGGTC 60.320 55.000 13.86 0.00 42.42 4.02
3512 5453 9.246670 TCTGATCAAATTGACATCCAAGTTATT 57.753 29.630 0.00 0.00 40.61 1.40
3598 5539 6.870965 TCCGCTATTTGCATTTGTGTTTAAAT 59.129 30.769 0.00 0.00 43.06 1.40
3606 5547 9.612620 TTTGCATTTGTGTTTAAATTTTTCGTT 57.387 22.222 0.00 0.00 0.00 3.85
3665 5606 3.067106 TCGACTTGATTGTGGCTTTCTC 58.933 45.455 0.00 0.00 0.00 2.87
3672 5613 4.326826 TGATTGTGGCTTTCTCTGGTAAG 58.673 43.478 0.00 0.00 0.00 2.34
3872 5814 0.250038 CATGCCATACCTGGAGTCCG 60.250 60.000 4.30 0.00 46.37 4.79
3914 5856 2.930040 CCATCGGTAGTTAGCTGTTGTG 59.070 50.000 0.00 0.00 0.00 3.33
4009 5951 2.719426 AAAGTAGTTGTCCGTCTCCG 57.281 50.000 0.00 0.00 0.00 4.63
4100 6042 8.192743 AGATCATGCTAACAAGAGATGATACT 57.807 34.615 0.00 0.00 34.61 2.12
4105 6047 9.356433 CATGCTAACAAGAGATGATACTATCTG 57.644 37.037 0.00 0.00 37.53 2.90
4196 6145 7.676947 TGGTTAAAGGGGAGATTATCTATTCG 58.323 38.462 0.00 0.00 0.00 3.34
4199 6148 6.749036 AAAGGGGAGATTATCTATTCGTGT 57.251 37.500 0.00 0.00 0.00 4.49
4201 6150 7.469537 AAGGGGAGATTATCTATTCGTGTAG 57.530 40.000 0.00 0.00 0.00 2.74
4315 6270 3.656559 TCTCAGCCGGTTACAAGTTAAC 58.343 45.455 1.90 0.00 0.00 2.01
4328 6283 2.107552 CAAGTTAACCCCTCTGTCCCAA 59.892 50.000 0.88 0.00 0.00 4.12
4378 6333 5.047021 CCAAGGAGACACATAACTTCTCTCA 60.047 44.000 0.00 0.00 36.73 3.27
4382 6337 7.684529 AGGAGACACATAACTTCTCTCAAAAT 58.315 34.615 0.00 0.00 36.73 1.82
4398 6353 5.951747 TCTCAAAATGTTTAAGCTAGGGCAT 59.048 36.000 0.00 0.00 41.70 4.40
4403 6358 6.639632 AATGTTTAAGCTAGGGCATGTATG 57.360 37.500 0.00 0.00 41.70 2.39
4599 6555 3.207669 CAAGATCCAGCGCTGCCC 61.208 66.667 31.96 20.72 0.00 5.36
4606 6562 4.079850 CAGCGCTGCCCACTCTCT 62.080 66.667 26.68 0.00 0.00 3.10
4607 6563 4.079850 AGCGCTGCCCACTCTCTG 62.080 66.667 10.39 0.00 0.00 3.35
4644 6600 7.990886 TGTTCTGTTATGTTTCTACAGGTTTCT 59.009 33.333 0.00 0.00 39.71 2.52
4703 6663 0.174389 TCTGTCTCCTGATCGCTTGC 59.826 55.000 0.00 0.00 0.00 4.01
4819 6788 3.296854 ACGTCCATGTTAGCTCAGGATA 58.703 45.455 0.00 0.00 0.00 2.59
4836 6805 6.867662 CAGGATAACTATGCTGGGTAAAAG 57.132 41.667 9.69 0.00 45.07 2.27
4872 6841 0.478072 TGCATTTGGTGAGGGTGTCT 59.522 50.000 0.00 0.00 0.00 3.41
4874 6843 0.883833 CATTTGGTGAGGGTGTCTGC 59.116 55.000 0.00 0.00 0.00 4.26
4924 7094 2.817901 TGATGATGTGCTGATCTGACG 58.182 47.619 3.42 0.00 0.00 4.35
4926 7096 3.119029 TGATGATGTGCTGATCTGACGAA 60.119 43.478 3.42 0.00 0.00 3.85
4964 7134 1.284657 CACTCCTGTGCGCTATTCTG 58.715 55.000 9.73 0.00 37.38 3.02
4965 7135 0.898320 ACTCCTGTGCGCTATTCTGT 59.102 50.000 9.73 0.00 0.00 3.41
4966 7136 1.134965 ACTCCTGTGCGCTATTCTGTC 60.135 52.381 9.73 0.00 0.00 3.51
4967 7137 0.175760 TCCTGTGCGCTATTCTGTCC 59.824 55.000 9.73 0.00 0.00 4.02
4968 7138 1.148157 CCTGTGCGCTATTCTGTCCG 61.148 60.000 9.73 0.00 0.00 4.79
4969 7139 1.756375 CTGTGCGCTATTCTGTCCGC 61.756 60.000 9.73 0.00 45.99 5.54
4971 7141 3.330853 GCGCTATTCTGTCCGCGG 61.331 66.667 22.12 22.12 45.17 6.46
4972 7142 2.104331 CGCTATTCTGTCCGCGGT 59.896 61.111 27.15 7.03 41.72 5.68
4973 7143 1.518572 CGCTATTCTGTCCGCGGTT 60.519 57.895 27.15 6.86 41.72 4.44
4974 7144 0.248743 CGCTATTCTGTCCGCGGTTA 60.249 55.000 27.15 14.42 41.72 2.85
4975 7145 1.488527 GCTATTCTGTCCGCGGTTAG 58.511 55.000 27.15 23.08 0.00 2.34
4976 7146 1.868519 GCTATTCTGTCCGCGGTTAGG 60.869 57.143 27.15 13.85 0.00 2.69
4977 7147 0.748450 TATTCTGTCCGCGGTTAGGG 59.252 55.000 27.15 12.05 0.00 3.53
5010 7180 3.319405 GGTTCGGAATCTGCATCTAGAGA 59.681 47.826 0.00 0.00 0.00 3.10
5021 7191 2.049959 CATCTAGAGATGTCGCTTGCG 58.950 52.381 8.87 8.87 45.10 4.85
5040 7210 2.303175 CGGTTTCTTGAAAAGGGGTCA 58.697 47.619 0.00 0.00 46.24 4.02
5041 7211 2.890945 CGGTTTCTTGAAAAGGGGTCAT 59.109 45.455 0.00 0.00 46.24 3.06
5042 7212 4.076394 CGGTTTCTTGAAAAGGGGTCATA 58.924 43.478 0.00 0.00 46.24 2.15
5043 7213 4.705023 CGGTTTCTTGAAAAGGGGTCATAT 59.295 41.667 0.00 0.00 46.24 1.78
5044 7214 5.883673 CGGTTTCTTGAAAAGGGGTCATATA 59.116 40.000 0.00 0.00 46.24 0.86
5045 7215 6.546034 CGGTTTCTTGAAAAGGGGTCATATAT 59.454 38.462 0.00 0.00 46.24 0.86
5046 7216 7.717875 CGGTTTCTTGAAAAGGGGTCATATATA 59.282 37.037 0.00 0.00 46.24 0.86
5075 7245 0.039527 GCCAACCAAAGTAAGGTGCG 60.040 55.000 0.00 0.00 39.86 5.34
5076 7246 0.039527 CCAACCAAAGTAAGGTGCGC 60.040 55.000 0.00 0.00 39.86 6.09
5077 7247 0.665835 CAACCAAAGTAAGGTGCGCA 59.334 50.000 5.66 5.66 39.86 6.09
5079 7249 0.464735 ACCAAAGTAAGGTGCGCACA 60.465 50.000 38.60 18.86 38.13 4.57
5080 7250 0.881118 CCAAAGTAAGGTGCGCACAT 59.119 50.000 38.60 32.11 0.00 3.21
5082 7252 2.486203 CCAAAGTAAGGTGCGCACATAA 59.514 45.455 38.60 21.58 0.00 1.90
5084 7254 3.824414 AAGTAAGGTGCGCACATAAAC 57.176 42.857 38.60 30.81 0.00 2.01
5085 7255 2.773487 AGTAAGGTGCGCACATAAACA 58.227 42.857 38.60 17.33 0.00 2.83
5086 7256 3.142951 AGTAAGGTGCGCACATAAACAA 58.857 40.909 38.60 15.21 0.00 2.83
5087 7257 3.756434 AGTAAGGTGCGCACATAAACAAT 59.244 39.130 38.60 20.27 0.00 2.71
5088 7258 3.658757 AAGGTGCGCACATAAACAATT 57.341 38.095 38.60 15.13 0.00 2.32
5089 7259 3.658757 AGGTGCGCACATAAACAATTT 57.341 38.095 38.60 10.09 0.00 1.82
5090 7260 3.574614 AGGTGCGCACATAAACAATTTC 58.425 40.909 38.60 18.43 0.00 2.17
5095 7265 4.858140 TGCGCACATAAACAATTTCTCATG 59.142 37.500 5.66 0.00 0.00 3.07
5103 7273 4.436242 AACAATTTCTCATGCAGCAGAG 57.564 40.909 0.00 8.27 0.00 3.35
5115 7285 2.224597 TGCAGCAGAGAGTTTGAATCCA 60.225 45.455 0.00 0.00 0.00 3.41
5116 7286 3.015327 GCAGCAGAGAGTTTGAATCCAT 58.985 45.455 0.00 0.00 0.00 3.41
5140 7310 5.964958 TCAAATCTTGAAACCATCAGGTC 57.035 39.130 0.00 0.00 39.56 3.85
5141 7311 5.634118 TCAAATCTTGAAACCATCAGGTCT 58.366 37.500 0.00 0.00 39.56 3.85
5241 7429 4.441634 GCTACATCACAGTATTCCGTTCCT 60.442 45.833 0.00 0.00 0.00 3.36
5279 7468 0.251653 TGGCTACCGTCACTCTCCTT 60.252 55.000 0.00 0.00 0.00 3.36
5289 7486 2.685380 CTCTCCTTCCCCCAGCGT 60.685 66.667 0.00 0.00 0.00 5.07
5309 7506 2.480555 CCACAAATCGCACGAGCC 59.519 61.111 0.00 0.00 37.52 4.70
5332 7536 3.244981 GGGGTAACATGGGTGAACAGTAA 60.245 47.826 0.00 0.00 39.74 2.24
5421 7653 2.126228 GCGTGATCGTCCCGTTGA 60.126 61.111 0.00 0.00 39.49 3.18
5460 7696 1.008194 GAACGGGGAAAACGGCAAC 60.008 57.895 0.00 0.00 35.23 4.17
5489 7725 0.106918 GGTGGTCCAGTCCAAACACA 60.107 55.000 0.00 0.00 39.34 3.72
5490 7726 1.478654 GGTGGTCCAGTCCAAACACAT 60.479 52.381 0.00 0.00 39.34 3.21
5491 7727 2.306847 GTGGTCCAGTCCAAACACATT 58.693 47.619 0.00 0.00 39.34 2.71
5549 7793 1.774217 AGGTCAAGTCCTTGGGGCA 60.774 57.895 7.16 0.00 40.78 5.36
5554 7802 1.146774 TCAAGTCCTTGGGGCATTTGA 59.853 47.619 7.16 0.00 40.78 2.69
5567 7815 1.136141 GCATTTGACAGTCTGCGTGAG 60.136 52.381 1.31 0.00 0.00 3.51
5581 7829 2.217353 CGTGAGCGTGACAAAGAATG 57.783 50.000 0.00 0.00 0.00 2.67
5582 7830 1.792367 CGTGAGCGTGACAAAGAATGA 59.208 47.619 0.00 0.00 0.00 2.57
5583 7831 2.410262 CGTGAGCGTGACAAAGAATGAC 60.410 50.000 0.00 0.00 0.00 3.06
5584 7832 2.543848 GTGAGCGTGACAAAGAATGACA 59.456 45.455 0.00 0.00 0.00 3.58
5585 7833 2.802247 TGAGCGTGACAAAGAATGACAG 59.198 45.455 0.00 0.00 34.40 3.51
5586 7834 2.146342 AGCGTGACAAAGAATGACAGG 58.854 47.619 0.00 0.00 40.77 4.00
5587 7835 1.197721 GCGTGACAAAGAATGACAGGG 59.802 52.381 0.00 0.00 39.09 4.45
5588 7836 2.766313 CGTGACAAAGAATGACAGGGA 58.234 47.619 0.00 0.00 36.43 4.20
5589 7837 2.738846 CGTGACAAAGAATGACAGGGAG 59.261 50.000 0.00 0.00 36.43 4.30
5590 7838 3.744660 GTGACAAAGAATGACAGGGAGT 58.255 45.455 0.00 0.00 34.40 3.85
5591 7839 3.499918 GTGACAAAGAATGACAGGGAGTG 59.500 47.826 0.00 0.00 34.40 3.51
5592 7840 2.485814 GACAAAGAATGACAGGGAGTGC 59.514 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.660938 GCCACCCAAGCTCCCGTT 62.661 66.667 0.00 0.00 0.00 4.44
36 37 3.808618 GCCACTTCACTCCACTTCATTCT 60.809 47.826 0.00 0.00 0.00 2.40
42 43 2.564947 CTCTAGCCACTTCACTCCACTT 59.435 50.000 0.00 0.00 0.00 3.16
62 63 2.357517 CGCTCGCTGGACCAAACT 60.358 61.111 0.00 0.00 0.00 2.66
89 90 2.107552 CCACCCGACCCCACATATATTT 59.892 50.000 0.00 0.00 0.00 1.40
105 106 3.793888 GTCGGACCCATCCCACCC 61.794 72.222 0.00 0.00 42.83 4.61
107 108 3.387947 ACGTCGGACCCATCCCAC 61.388 66.667 1.91 0.00 42.83 4.61
153 154 7.233632 CCTCATATCCAGTTCAAATATGGGAA 58.766 38.462 3.59 0.00 36.40 3.97
154 155 6.240263 CCCTCATATCCAGTTCAAATATGGGA 60.240 42.308 3.59 0.00 36.40 4.37
166 167 1.410850 CGGCACCCCTCATATCCAGT 61.411 60.000 0.00 0.00 0.00 4.00
188 189 2.483013 CGGATCTCAAATGTTCGGGCTA 60.483 50.000 0.00 0.00 0.00 3.93
191 192 2.024176 ACGGATCTCAAATGTTCGGG 57.976 50.000 0.00 0.00 0.00 5.14
195 196 4.142687 CGCCTTAAACGGATCTCAAATGTT 60.143 41.667 0.00 0.00 0.00 2.71
205 206 2.512974 CGGGCGCCTTAAACGGAT 60.513 61.111 28.56 0.00 0.00 4.18
244 245 1.830587 AACAGCTCGGCCACTGATCA 61.831 55.000 20.89 0.00 37.35 2.92
245 246 1.078848 AACAGCTCGGCCACTGATC 60.079 57.895 20.89 0.00 37.35 2.92
246 247 1.078848 GAACAGCTCGGCCACTGAT 60.079 57.895 20.89 11.34 37.35 2.90
247 248 2.343758 GAACAGCTCGGCCACTGA 59.656 61.111 20.89 1.64 37.35 3.41
248 249 3.114616 CGAACAGCTCGGCCACTG 61.115 66.667 14.24 14.24 44.20 3.66
265 277 2.568090 CGCCTCAAATGTGTGGGC 59.432 61.111 6.13 8.91 38.60 5.36
273 285 2.282783 GCCCCAAACCGCCTCAAAT 61.283 57.895 0.00 0.00 0.00 2.32
316 329 2.601905 AGAAATTGCTCAAACCCTGCT 58.398 42.857 0.00 0.00 0.00 4.24
321 334 5.236911 TGCATTTGAAGAAATTGCTCAAACC 59.763 36.000 11.13 7.79 33.87 3.27
351 364 6.253727 CGTATGAGTTCCTATATTGCGAATCC 59.746 42.308 0.00 0.00 0.00 3.01
376 389 3.247006 TCGGGTCATTCTGAAAGCTAC 57.753 47.619 0.00 0.00 0.00 3.58
381 394 2.837591 TCTCCATCGGGTCATTCTGAAA 59.162 45.455 0.00 0.00 34.93 2.69
396 409 4.780815 TGAAGCGTCCATAAAATCTCCAT 58.219 39.130 0.00 0.00 0.00 3.41
547 805 0.886490 CTTGTCAAGGCTTGGCTCGT 60.886 55.000 29.80 0.00 35.94 4.18
548 806 1.871772 CTTGTCAAGGCTTGGCTCG 59.128 57.895 29.80 17.73 35.94 5.03
549 807 1.583477 GCTTGTCAAGGCTTGGCTC 59.417 57.895 29.80 18.64 35.94 4.70
550 808 3.769201 GCTTGTCAAGGCTTGGCT 58.231 55.556 29.80 0.00 35.94 4.75
644 2034 1.254284 CGGAGGGCACAGAGAGTTCT 61.254 60.000 0.00 0.00 0.00 3.01
678 2076 2.269241 GAGGGGGAAGGAAGTGCG 59.731 66.667 0.00 0.00 0.00 5.34
885 2285 0.466189 CCTAACGCCATGGGAGCAAT 60.466 55.000 15.13 0.00 0.00 3.56
1185 2588 1.285280 CACAACCCTCACCCTGGATA 58.715 55.000 0.00 0.00 0.00 2.59
1196 2599 2.303022 CTCCAGTACATCACACAACCCT 59.697 50.000 0.00 0.00 0.00 4.34
1197 2600 2.038557 ACTCCAGTACATCACACAACCC 59.961 50.000 0.00 0.00 0.00 4.11
1198 2601 3.067106 CACTCCAGTACATCACACAACC 58.933 50.000 0.00 0.00 0.00 3.77
1199 2602 3.741344 GTCACTCCAGTACATCACACAAC 59.259 47.826 0.00 0.00 0.00 3.32
1200 2603 3.641436 AGTCACTCCAGTACATCACACAA 59.359 43.478 0.00 0.00 0.00 3.33
1201 2604 3.230976 AGTCACTCCAGTACATCACACA 58.769 45.455 0.00 0.00 0.00 3.72
1202 2605 3.944055 AGTCACTCCAGTACATCACAC 57.056 47.619 0.00 0.00 0.00 3.82
1217 2620 5.459107 ACGAAGTTATTCATCGCATAGTCAC 59.541 40.000 0.00 0.00 37.78 3.67
1220 2623 5.588240 TCACGAAGTTATTCATCGCATAGT 58.412 37.500 0.00 0.00 41.61 2.12
1222 2625 6.040247 AGTTCACGAAGTTATTCATCGCATA 58.960 36.000 0.00 0.00 41.61 3.14
1224 2627 4.242475 AGTTCACGAAGTTATTCATCGCA 58.758 39.130 0.00 0.00 41.61 5.10
1226 2629 6.034591 AGGTAGTTCACGAAGTTATTCATCG 58.965 40.000 0.00 0.00 41.61 3.84
1275 2678 8.932945 TGTAACTGATCTGACATTCATCTAAC 57.067 34.615 6.60 0.00 0.00 2.34
1288 2691 2.703416 TGGCTTGCTGTAACTGATCTG 58.297 47.619 0.00 0.00 0.00 2.90
1305 2708 1.003839 TTCCTCACGGTCACATGGC 60.004 57.895 0.00 0.00 0.00 4.40
1308 2711 1.338107 TGAGTTCCTCACGGTCACAT 58.662 50.000 0.00 0.00 35.39 3.21
1313 2716 2.248248 TCTCATTGAGTTCCTCACGGT 58.752 47.619 13.23 0.00 40.46 4.83
1324 2733 2.208431 GAACCGGAGCATCTCATTGAG 58.792 52.381 9.46 7.38 33.73 3.02
1325 2734 1.471501 CGAACCGGAGCATCTCATTGA 60.472 52.381 9.46 0.00 33.73 2.57
1328 2737 0.537188 AACGAACCGGAGCATCTCAT 59.463 50.000 9.46 0.00 33.73 2.90
1335 2744 2.542595 CCACATATTAACGAACCGGAGC 59.457 50.000 9.46 0.00 0.00 4.70
1336 2745 4.049546 TCCACATATTAACGAACCGGAG 57.950 45.455 9.46 0.76 0.00 4.63
1346 2755 4.513442 GGCATAGCGGATCCACATATTAA 58.487 43.478 13.41 0.00 0.00 1.40
1422 2831 2.284331 TTGCTACGCCCCAGGAGA 60.284 61.111 0.00 0.00 0.00 3.71
1423 2832 2.125106 GTTGCTACGCCCCAGGAG 60.125 66.667 0.00 0.00 0.00 3.69
1424 2833 2.221299 AAGTTGCTACGCCCCAGGA 61.221 57.895 0.00 0.00 0.00 3.86
1425 2834 2.040544 CAAGTTGCTACGCCCCAGG 61.041 63.158 0.00 0.00 0.00 4.45
1429 2838 2.359975 AGCCAAGTTGCTACGCCC 60.360 61.111 0.00 0.00 40.56 6.13
1430 2839 1.362406 GAGAGCCAAGTTGCTACGCC 61.362 60.000 0.00 0.00 42.95 5.68
1435 2844 0.601311 GACGTGAGAGCCAAGTTGCT 60.601 55.000 0.00 0.00 46.37 3.91
1440 2849 1.734477 CCGTGACGTGAGAGCCAAG 60.734 63.158 3.64 0.00 0.00 3.61
1442 2851 2.023414 AAACCGTGACGTGAGAGCCA 62.023 55.000 3.64 0.00 0.00 4.75
1444 2853 0.318784 AGAAACCGTGACGTGAGAGC 60.319 55.000 3.64 0.00 0.00 4.09
1451 2860 0.388649 CCTCCTGAGAAACCGTGACG 60.389 60.000 0.00 0.00 0.00 4.35
1457 2866 0.615850 CTCCACCCTCCTGAGAAACC 59.384 60.000 0.00 0.00 0.00 3.27
1490 2899 9.261035 AGAAGTCTAGAGAATATCCAGACAAAA 57.739 33.333 6.27 0.00 45.86 2.44
1492 2901 8.055790 TGAGAAGTCTAGAGAATATCCAGACAA 58.944 37.037 6.27 0.00 45.86 3.18
1496 2905 7.231317 AGCTTGAGAAGTCTAGAGAATATCCAG 59.769 40.741 0.00 0.00 0.00 3.86
1497 2906 7.014134 CAGCTTGAGAAGTCTAGAGAATATCCA 59.986 40.741 0.00 0.00 0.00 3.41
1498 2907 7.370383 CAGCTTGAGAAGTCTAGAGAATATCC 58.630 42.308 0.00 0.00 0.00 2.59
1499 2908 6.863126 GCAGCTTGAGAAGTCTAGAGAATATC 59.137 42.308 0.00 0.00 0.00 1.63
1501 2910 5.068460 GGCAGCTTGAGAAGTCTAGAGAATA 59.932 44.000 0.00 0.00 0.00 1.75
1575 2984 6.595682 ACGTCTTATTGATTGGGATGAGATT 58.404 36.000 0.00 0.00 0.00 2.40
1591 3000 8.904834 ACATTGAGTCATACTTAGACGTCTTAT 58.095 33.333 25.44 12.79 40.84 1.73
1593 3002 7.030165 CACATTGAGTCATACTTAGACGTCTT 58.970 38.462 25.44 8.59 40.84 3.01
1608 3017 6.258230 TCCACATTGAAATCACATTGAGTC 57.742 37.500 0.00 0.00 0.00 3.36
1620 3029 3.308832 GGGACCCAGTATCCACATTGAAA 60.309 47.826 5.33 0.00 38.06 2.69
1638 3047 0.941463 CAGAGATACGCATGCGGGAC 60.941 60.000 39.95 28.60 44.69 4.46
1653 3062 1.000283 GATACGAGACATGGGGCAGAG 60.000 57.143 0.00 0.00 0.00 3.35
1673 3082 5.449588 CCATAAACATCAGCTAGTTGCAAGG 60.450 44.000 0.00 0.00 45.94 3.61
1694 3103 0.913451 AAGCAGAGGAGCAGTCCCAT 60.913 55.000 0.00 0.00 45.26 4.00
1728 3137 5.203528 AGCCTGATAAATGCTGTTACCAAT 58.796 37.500 0.00 0.00 33.23 3.16
1760 3169 4.440826 TGTGTACAGGTACCAAAACCAT 57.559 40.909 15.94 0.00 42.40 3.55
1836 3245 6.157645 AGCCACCATAGGGAAAGATATCATAG 59.842 42.308 0.00 0.00 38.05 2.23
1841 3250 3.589288 GGAGCCACCATAGGGAAAGATAT 59.411 47.826 0.00 0.00 38.79 1.63
1843 3252 1.777272 GGAGCCACCATAGGGAAAGAT 59.223 52.381 0.00 0.00 38.79 2.40
1844 3253 1.213296 GGAGCCACCATAGGGAAAGA 58.787 55.000 0.00 0.00 38.79 2.52
1846 3255 1.681229 AAGGAGCCACCATAGGGAAA 58.319 50.000 0.00 0.00 42.04 3.13
1847 3256 1.284785 CAAAGGAGCCACCATAGGGAA 59.715 52.381 0.00 0.00 42.04 3.97
1849 3258 0.753111 GCAAAGGAGCCACCATAGGG 60.753 60.000 0.00 0.00 42.04 3.53
1850 3259 0.257039 AGCAAAGGAGCCACCATAGG 59.743 55.000 0.47 0.00 42.04 2.57
1859 3268 3.063588 GTCACGGTAATTAGCAAAGGAGC 59.936 47.826 14.62 0.00 0.00 4.70
1875 3284 1.073964 CAGAGTCATTGCTGTCACGG 58.926 55.000 0.00 0.00 0.00 4.94
2174 3822 3.498334 AGTTACTCCCTCCGATCCATAC 58.502 50.000 0.00 0.00 0.00 2.39
2325 3973 4.973396 AGCACATGTCAATTGATTACACG 58.027 39.130 12.12 0.71 0.00 4.49
2420 4072 4.564372 CGTAACAGATCACTCAAGATGTGG 59.436 45.833 0.00 0.00 41.95 4.17
2447 4099 6.156256 TGCTATAATCACTGTAACCAGGAACT 59.844 38.462 0.00 0.00 43.36 3.01
2541 4193 9.440773 CTTCTTGCTGGATATAATAACTATGCA 57.559 33.333 0.00 0.00 0.00 3.96
2575 4228 4.494091 AGTAGCATGCTTGGACTTATGT 57.506 40.909 28.02 0.00 0.00 2.29
2682 4335 5.729176 GCCAAAAACATTGGTTTGCAAGTAC 60.729 40.000 0.00 0.00 46.20 2.73
2787 4556 2.850828 ATTTGCTCAGAGCCCTGCCC 62.851 60.000 20.16 0.00 41.51 5.36
2929 4870 8.899427 AGAAGACAGATAACACATCATATTGG 57.101 34.615 0.00 0.00 0.00 3.16
2966 4907 4.337555 TGGTACGTCTTATTGAGCCTAGAC 59.662 45.833 0.00 0.00 34.96 2.59
2972 4913 3.933332 AGCTTTGGTACGTCTTATTGAGC 59.067 43.478 0.00 0.00 0.00 4.26
2984 4925 5.488341 TGAAATGACTAGGAGCTTTGGTAC 58.512 41.667 0.00 0.00 0.00 3.34
3178 5119 5.758296 TGCACTGAAGAAAGTTAACTAGTGG 59.242 40.000 24.83 13.35 35.92 4.00
3243 5184 8.326765 ACCATACTTGGACAACATATACCTTA 57.673 34.615 0.00 0.00 46.92 2.69
3364 5305 4.141914 ACTGTACTGCTGGGTTATAGCTTC 60.142 45.833 0.00 0.00 41.66 3.86
3512 5453 4.299586 TCCAGAAACATATGCCTGTTGA 57.700 40.909 1.58 0.04 39.25 3.18
3598 5539 9.967346 TTTGTGATGGTAATTATCAACGAAAAA 57.033 25.926 1.78 0.50 36.41 1.94
3603 5544 9.702726 CTTACTTTGTGATGGTAATTATCAACG 57.297 33.333 1.78 0.00 36.41 4.10
3665 5606 5.934625 ACATAAGAGTGCAGTTTCTTACCAG 59.065 40.000 14.19 10.94 38.37 4.00
3672 5613 7.861630 TCAAAGTAACATAAGAGTGCAGTTTC 58.138 34.615 0.00 0.00 0.00 2.78
3872 5814 4.133796 GCCAAGGACCGCCAATGC 62.134 66.667 0.00 0.00 36.29 3.56
4003 5945 3.889520 ACAAGATTTCCTACCGGAGAC 57.110 47.619 9.46 0.00 41.25 3.36
4009 5951 6.295719 TCCACTAGAACAAGATTTCCTACC 57.704 41.667 0.00 0.00 0.00 3.18
4196 6145 4.046938 TCATGCTAAGCTGCTACTACAC 57.953 45.455 0.90 0.00 0.00 2.90
4199 6148 2.036475 GGCTCATGCTAAGCTGCTACTA 59.964 50.000 0.90 0.00 39.75 1.82
4201 6150 1.224965 GGCTCATGCTAAGCTGCTAC 58.775 55.000 0.90 0.00 39.75 3.58
4315 6270 0.546598 GTGGTATTGGGACAGAGGGG 59.453 60.000 0.00 0.00 42.39 4.79
4328 6283 3.756434 GTGTGCATGGTTAGTTGTGGTAT 59.244 43.478 0.00 0.00 0.00 2.73
4378 6333 7.341769 TCATACATGCCCTAGCTTAAACATTTT 59.658 33.333 0.00 0.00 40.80 1.82
4382 6337 5.366482 TCATACATGCCCTAGCTTAAACA 57.634 39.130 0.00 0.00 40.80 2.83
4398 6353 9.448438 AGTGTAGCTATTGAATTGTTTCATACA 57.552 29.630 0.00 0.00 41.38 2.29
4403 6358 9.846248 ATCAAAGTGTAGCTATTGAATTGTTTC 57.154 29.630 10.66 0.00 35.62 2.78
4579 6535 2.478890 GCAGCGCTGGATCTTGCAT 61.479 57.895 36.47 0.00 0.00 3.96
4599 6555 5.873712 AGAACACAATAAGCATCAGAGAGTG 59.126 40.000 0.00 0.00 0.00 3.51
4606 6562 7.686438 ACATAACAGAACACAATAAGCATCA 57.314 32.000 0.00 0.00 0.00 3.07
4607 6563 8.970691 AAACATAACAGAACACAATAAGCATC 57.029 30.769 0.00 0.00 0.00 3.91
4644 6600 2.094494 GGATCTCAGTCTGCTCGAAACA 60.094 50.000 0.00 0.00 0.00 2.83
4819 6788 4.042934 AGACCACTTTTACCCAGCATAGTT 59.957 41.667 0.00 0.00 0.00 2.24
4836 6805 1.668751 TGCAAACGAACTTGAGACCAC 59.331 47.619 0.00 0.00 0.00 4.16
4924 7094 1.276145 AAGCACGAACTCGCGACTTC 61.276 55.000 3.71 11.73 44.43 3.01
4926 7096 2.016704 CAAGCACGAACTCGCGACT 61.017 57.895 3.71 0.00 44.43 4.18
4928 7098 3.403057 GCAAGCACGAACTCGCGA 61.403 61.111 9.26 9.26 44.43 5.87
4964 7134 2.496341 GTACCCCTAACCGCGGAC 59.504 66.667 35.90 13.51 0.00 4.79
4965 7135 2.759560 GGTACCCCTAACCGCGGA 60.760 66.667 35.90 9.83 0.00 5.54
4987 7157 3.300388 TCTAGATGCAGATTCCGAACCT 58.700 45.455 0.00 0.00 0.00 3.50
5010 7180 0.238289 CAAGAAACCGCAAGCGACAT 59.762 50.000 16.97 0.61 42.83 3.06
5017 7187 1.410882 CCCCTTTTCAAGAAACCGCAA 59.589 47.619 0.00 0.00 0.00 4.85
5018 7188 1.036707 CCCCTTTTCAAGAAACCGCA 58.963 50.000 0.00 0.00 0.00 5.69
5019 7189 1.000607 GACCCCTTTTCAAGAAACCGC 60.001 52.381 0.00 0.00 0.00 5.68
5020 7190 2.303175 TGACCCCTTTTCAAGAAACCG 58.697 47.619 0.00 0.00 0.00 4.44
5021 7191 7.898014 ATATATGACCCCTTTTCAAGAAACC 57.102 36.000 0.00 0.00 0.00 3.27
5062 7232 3.822594 TTATGTGCGCACCTTACTTTG 57.177 42.857 35.72 0.00 0.00 2.77
5072 7242 4.495911 TGAGAAATTGTTTATGTGCGCA 57.504 36.364 5.66 5.66 0.00 6.09
5075 7245 5.220340 GCTGCATGAGAAATTGTTTATGTGC 60.220 40.000 0.00 0.00 0.00 4.57
5076 7246 5.865013 TGCTGCATGAGAAATTGTTTATGTG 59.135 36.000 0.00 0.00 0.00 3.21
5077 7247 6.028146 TGCTGCATGAGAAATTGTTTATGT 57.972 33.333 0.00 0.00 0.00 2.29
5079 7249 6.376299 TCTCTGCTGCATGAGAAATTGTTTAT 59.624 34.615 21.38 0.00 36.52 1.40
5080 7250 5.706833 TCTCTGCTGCATGAGAAATTGTTTA 59.293 36.000 21.38 4.35 36.52 2.01
5082 7252 4.077108 TCTCTGCTGCATGAGAAATTGTT 58.923 39.130 21.38 0.00 36.52 2.83
5084 7254 3.690139 ACTCTCTGCTGCATGAGAAATTG 59.310 43.478 27.65 18.90 38.64 2.32
5085 7255 3.952931 ACTCTCTGCTGCATGAGAAATT 58.047 40.909 27.65 15.25 38.64 1.82
5086 7256 3.630892 ACTCTCTGCTGCATGAGAAAT 57.369 42.857 27.65 17.69 38.64 2.17
5087 7257 3.413846 AACTCTCTGCTGCATGAGAAA 57.586 42.857 27.65 12.15 38.64 2.52
5088 7258 3.072211 CAAACTCTCTGCTGCATGAGAA 58.928 45.455 27.65 14.92 38.64 2.87
5089 7259 2.301009 TCAAACTCTCTGCTGCATGAGA 59.699 45.455 27.65 24.70 37.69 3.27
5090 7260 2.696506 TCAAACTCTCTGCTGCATGAG 58.303 47.619 22.57 22.57 0.00 2.90
5095 7265 2.430465 TGGATTCAAACTCTCTGCTGC 58.570 47.619 0.00 0.00 0.00 5.25
5116 7286 6.729690 ACCTGATGGTTTCAAGATTTGAAA 57.270 33.333 11.71 11.71 46.05 2.69
5132 7302 3.608506 CGTCACGTCTTTTAGACCTGATG 59.391 47.826 10.30 10.73 42.12 3.07
5137 7307 0.706729 CGCGTCACGTCTTTTAGACC 59.293 55.000 0.00 0.00 42.12 3.85
5138 7308 1.678360 TCGCGTCACGTCTTTTAGAC 58.322 50.000 5.77 0.00 44.19 2.59
5139 7309 2.247637 CATCGCGTCACGTCTTTTAGA 58.752 47.619 5.77 0.00 44.19 2.10
5140 7310 1.266404 GCATCGCGTCACGTCTTTTAG 60.266 52.381 5.77 0.00 44.19 1.85
5141 7311 0.711670 GCATCGCGTCACGTCTTTTA 59.288 50.000 5.77 0.00 44.19 1.52
5241 7429 0.249953 ACGTGATACCAACGGCAACA 60.250 50.000 0.00 0.00 0.00 3.33
5289 7486 2.281139 TCGTGCGATTTGTGGCCA 60.281 55.556 0.00 0.00 0.00 5.36
5309 7506 0.037017 TGTTCACCCATGTTACCCCG 59.963 55.000 0.00 0.00 0.00 5.73
5332 7536 3.000819 TGATCCCTCGCCAACGGT 61.001 61.111 0.00 0.00 40.63 4.83
5421 7653 2.049433 CACTCTCCGACCGCGTTT 60.049 61.111 4.92 0.00 35.23 3.60
5460 7696 0.464373 CTGGACCACCATGAATCCCG 60.464 60.000 0.00 0.00 45.87 5.14
5549 7793 1.151668 GCTCACGCAGACTGTCAAAT 58.848 50.000 10.88 0.00 35.78 2.32
5554 7802 2.355126 CACGCTCACGCAGACTGT 60.355 61.111 3.99 0.00 45.53 3.55
5567 7815 1.197721 CCCTGTCATTCTTTGTCACGC 59.802 52.381 0.00 0.00 0.00 5.34
5568 7816 2.738846 CTCCCTGTCATTCTTTGTCACG 59.261 50.000 0.00 0.00 0.00 4.35
5569 7817 3.499918 CACTCCCTGTCATTCTTTGTCAC 59.500 47.826 0.00 0.00 0.00 3.67
5570 7818 3.743521 CACTCCCTGTCATTCTTTGTCA 58.256 45.455 0.00 0.00 0.00 3.58
5571 7819 2.485814 GCACTCCCTGTCATTCTTTGTC 59.514 50.000 0.00 0.00 0.00 3.18
5573 7821 2.507484 TGCACTCCCTGTCATTCTTTG 58.493 47.619 0.00 0.00 0.00 2.77
5574 7822 2.957402 TGCACTCCCTGTCATTCTTT 57.043 45.000 0.00 0.00 0.00 2.52
5576 7824 1.681166 GCATGCACTCCCTGTCATTCT 60.681 52.381 14.21 0.00 0.00 2.40
5577 7825 0.737219 GCATGCACTCCCTGTCATTC 59.263 55.000 14.21 0.00 0.00 2.67
5578 7826 1.028330 CGCATGCACTCCCTGTCATT 61.028 55.000 19.57 0.00 0.00 2.57
5579 7827 1.450848 CGCATGCACTCCCTGTCAT 60.451 57.895 19.57 0.00 0.00 3.06
5580 7828 2.046988 CGCATGCACTCCCTGTCA 60.047 61.111 19.57 0.00 0.00 3.58
5581 7829 2.046892 ACGCATGCACTCCCTGTC 60.047 61.111 19.57 0.00 0.00 3.51
5582 7830 2.359107 CACGCATGCACTCCCTGT 60.359 61.111 19.57 2.04 0.00 4.00
5583 7831 2.359107 ACACGCATGCACTCCCTG 60.359 61.111 19.57 1.32 0.00 4.45
5584 7832 2.046892 GACACGCATGCACTCCCT 60.047 61.111 19.57 0.00 0.00 4.20
5585 7833 3.490759 CGACACGCATGCACTCCC 61.491 66.667 19.57 1.29 0.00 4.30


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

AutoCloner maintained by Alex Coulton.