Multiple sequence alignment - TraesCS6A01G270900

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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 TraesCS6A01G270900 chr6A 100.000 6180 0 0 1 6180 497467512 497461333 0.000000e+00 11413
1 TraesCS6A01G270900 chr6D 91.556 4204 212 63 1601 5724 346555348 346559488 0.000000e+00 5664
2 TraesCS6A01G270900 chr6D 89.868 1589 69 34 8 1575 346553744 346555261 0.000000e+00 1958
3 TraesCS6A01G270900 chr6D 85.028 354 10 7 5775 6086 346559489 346559841 2.780000e-83 320
4 TraesCS6A01G270900 chr6B 91.212 3607 169 57 2587 6119 534923861 534920329 0.000000e+00 4769
5 TraesCS6A01G270900 chr6B 87.636 1197 66 34 397 1572 534925968 534924833 0.000000e+00 1315
6 TraesCS6A01G270900 chr6B 86.199 913 60 28 1601 2489 534924750 534923880 0.000000e+00 928
7 TraesCS6A01G270900 chr6B 91.057 369 19 8 8 375 534926591 534926236 2.590000e-133 486


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 TraesCS6A01G270900 chr6A 497461333 497467512 6179 True 11413.000000 11413 100.000000 1 6180 1 chr6A.!!$R1 6179
1 TraesCS6A01G270900 chr6D 346553744 346559841 6097 False 2647.333333 5664 88.817333 8 6086 3 chr6D.!!$F1 6078
2 TraesCS6A01G270900 chr6B 534920329 534926591 6262 True 1874.500000 4769 89.026000 8 6119 4 chr6B.!!$R1 6111

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
453 707 0.393132 TCCGTTGCGCCCATAAATCA 60.393 50.0 4.18 0.00 0.00 2.57 F
779 1045 0.886938 TTGAAATCTTCGGCCGTGCA 60.887 50.0 27.15 7.25 0.00 4.57 F
2049 2445 0.107508 AGCGTATGCCTGCAGAATGT 60.108 50.0 17.39 0.44 44.31 2.71 F
2293 2689 0.468226 TATGGGGTGTGGAGATTCGC 59.532 55.0 0.00 0.00 0.00 4.70 F
2319 2715 0.663153 GTTTTGCGTTGAGTGGAGCT 59.337 50.0 0.00 0.00 0.00 4.09 F
4125 4586 0.249398 ATTGGTACGTGGAGAGTGGC 59.751 55.0 0.00 0.00 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1396 1686 0.389391 ACCCGGAGTTATGCTGATCG 59.611 55.000 0.73 0.0 0.00 3.69 R
2702 3133 0.733223 GCGTCTGGGACTCTTTCGTC 60.733 60.000 0.00 0.0 0.00 4.20 R
3248 3705 1.002868 GCTCCTCCTGCTTGCTCAA 60.003 57.895 0.00 0.0 0.00 3.02 R
4068 4529 2.289882 TGAGTCCAGAACTTCCTGCATG 60.290 50.000 0.00 0.0 38.74 4.06 R
4228 4689 3.735746 GCCTGAAACACAATCCTTTTTCG 59.264 43.478 0.00 0.0 31.76 3.46 R
5445 5925 0.040336 CGACCTACGTCCCATCATCG 60.040 60.000 0.00 0.0 35.40 3.84 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
76 83 2.272471 CCGGGGAGGAGGAAAAGC 59.728 66.667 0.00 0.00 45.00 3.51
116 123 1.070134 GGGCCTTTTCAGTTTTCACCC 59.930 52.381 0.84 0.00 0.00 4.61
118 125 1.269569 GCCTTTTCAGTTTTCACCCCG 60.270 52.381 0.00 0.00 0.00 5.73
178 185 3.793144 CGCTTTCCGCCTCACAGC 61.793 66.667 0.00 0.00 34.21 4.40
179 186 2.669569 GCTTTCCGCCTCACAGCA 60.670 61.111 0.00 0.00 0.00 4.41
180 187 2.970974 GCTTTCCGCCTCACAGCAC 61.971 63.158 0.00 0.00 0.00 4.40
181 188 1.597854 CTTTCCGCCTCACAGCACA 60.598 57.895 0.00 0.00 0.00 4.57
182 189 1.572085 CTTTCCGCCTCACAGCACAG 61.572 60.000 0.00 0.00 0.00 3.66
242 250 2.481952 GCTCACAACAGAAAGCCTACTG 59.518 50.000 0.00 0.00 39.65 2.74
243 251 2.481952 CTCACAACAGAAAGCCTACTGC 59.518 50.000 0.00 0.00 37.61 4.40
263 271 1.448540 GTGCCCATGTCCTCGTGAG 60.449 63.158 0.00 0.00 32.78 3.51
269 277 3.023949 ATGTCCTCGTGAGCCCTGC 62.024 63.158 0.00 0.00 0.00 4.85
279 287 1.746991 GAGCCCTGCTTCTTTCCCG 60.747 63.158 0.00 0.00 39.88 5.14
281 289 2.041115 GCCCTGCTTCTTTCCCGAC 61.041 63.158 0.00 0.00 0.00 4.79
282 290 1.377333 CCCTGCTTCTTTCCCGACC 60.377 63.158 0.00 0.00 0.00 4.79
285 293 2.045242 GCTTCTTTCCCGACCCCC 60.045 66.667 0.00 0.00 0.00 5.40
429 683 3.851128 GTAGCACCGCCCTCCCTC 61.851 72.222 0.00 0.00 0.00 4.30
453 707 0.393132 TCCGTTGCGCCCATAAATCA 60.393 50.000 4.18 0.00 0.00 2.57
474 728 2.372690 CGTCCGGACAGCAAAGACG 61.373 63.158 32.80 13.57 43.52 4.18
522 782 4.555313 CGACGCCTCCGATTATTAGTAACA 60.555 45.833 0.00 0.00 38.29 2.41
558 818 2.823593 CGCCGTCAATGCATCCCA 60.824 61.111 0.00 0.00 0.00 4.37
566 826 1.968017 AATGCATCCCATAGCCGCG 60.968 57.895 0.00 0.00 32.67 6.46
591 851 1.686052 CTCGCTAGATTTGCTCCTCCT 59.314 52.381 0.00 0.00 0.00 3.69
592 852 1.683917 TCGCTAGATTTGCTCCTCCTC 59.316 52.381 0.00 0.00 0.00 3.71
593 853 1.270041 CGCTAGATTTGCTCCTCCTCC 60.270 57.143 0.00 0.00 0.00 4.30
594 854 2.046292 GCTAGATTTGCTCCTCCTCCT 58.954 52.381 0.00 0.00 0.00 3.69
595 855 2.037121 GCTAGATTTGCTCCTCCTCCTC 59.963 54.545 0.00 0.00 0.00 3.71
596 856 1.506025 AGATTTGCTCCTCCTCCTCC 58.494 55.000 0.00 0.00 0.00 4.30
637 897 2.280052 TTTTGCCTTTGCGCTGCC 60.280 55.556 9.73 0.00 41.78 4.85
653 913 1.866601 CTGCCGATGCGTCAATCATTA 59.133 47.619 6.75 0.00 41.78 1.90
654 914 1.597195 TGCCGATGCGTCAATCATTAC 59.403 47.619 6.75 0.00 41.78 1.89
655 915 1.069906 GCCGATGCGTCAATCATTACC 60.070 52.381 6.75 0.00 0.00 2.85
656 916 1.531149 CCGATGCGTCAATCATTACCC 59.469 52.381 6.75 0.00 0.00 3.69
657 917 2.483876 CGATGCGTCAATCATTACCCT 58.516 47.619 6.75 0.00 0.00 4.34
678 938 1.468054 GCATCTGAAAAGGCGCGATTT 60.468 47.619 12.10 7.17 0.00 2.17
679 939 2.867429 CATCTGAAAAGGCGCGATTTT 58.133 42.857 12.10 18.41 32.68 1.82
680 940 3.244976 CATCTGAAAAGGCGCGATTTTT 58.755 40.909 12.10 15.51 30.22 1.94
681 941 2.928694 TCTGAAAAGGCGCGATTTTTC 58.071 42.857 27.37 27.37 41.42 2.29
682 942 1.643810 CTGAAAAGGCGCGATTTTTCG 59.356 47.619 27.72 22.02 43.05 3.46
683 943 1.002251 TGAAAAGGCGCGATTTTTCGT 60.002 42.857 27.72 9.99 43.05 3.85
684 944 2.048498 GAAAAGGCGCGATTTTTCGTT 58.952 42.857 23.29 6.92 34.68 3.85
685 945 1.681825 AAAGGCGCGATTTTTCGTTC 58.318 45.000 12.10 0.00 35.26 3.95
690 950 1.235695 CGCGATTTTTCGTTCGTTCC 58.764 50.000 0.00 0.00 37.66 3.62
762 1028 2.386935 GGGAGGGGTGAGGGGATTG 61.387 68.421 0.00 0.00 0.00 2.67
769 1035 2.023984 GGGGTGAGGGGATTGAAATCTT 60.024 50.000 3.21 0.00 35.73 2.40
779 1045 0.886938 TTGAAATCTTCGGCCGTGCA 60.887 50.000 27.15 7.25 0.00 4.57
780 1046 1.298157 TGAAATCTTCGGCCGTGCAG 61.298 55.000 27.15 19.12 0.00 4.41
781 1047 1.982073 GAAATCTTCGGCCGTGCAGG 61.982 60.000 27.15 6.57 44.97 4.85
891 1158 1.006832 CGGCAGCGCATTTACTAGTT 58.993 50.000 11.47 0.00 0.00 2.24
911 1178 8.695456 ACTAGTTGTTTTGAGATTGGTTTTCAT 58.305 29.630 0.00 0.00 0.00 2.57
946 1213 2.579201 CCCGTTGCGATGTCTCCT 59.421 61.111 0.00 0.00 0.00 3.69
962 1229 3.777556 CTGGGTTTCAGGTTGGGC 58.222 61.111 0.00 0.00 39.76 5.36
963 1230 1.153756 CTGGGTTTCAGGTTGGGCT 59.846 57.895 0.00 0.00 39.76 5.19
967 1234 1.971695 GTTTCAGGTTGGGCTCCCG 60.972 63.158 0.00 0.00 39.42 5.14
994 1261 3.009115 CTTGCCGGGGAGGAGGAA 61.009 66.667 2.18 0.00 45.00 3.36
995 1262 3.009115 TTGCCGGGGAGGAGGAAG 61.009 66.667 2.18 0.00 45.00 3.46
1080 1347 2.347731 GACCAAGAGCCGGAAAGTAAG 58.652 52.381 5.05 0.00 0.00 2.34
1081 1348 1.087501 CCAAGAGCCGGAAAGTAAGC 58.912 55.000 5.05 0.00 0.00 3.09
1082 1349 1.610624 CCAAGAGCCGGAAAGTAAGCA 60.611 52.381 5.05 0.00 0.00 3.91
1083 1350 2.359900 CAAGAGCCGGAAAGTAAGCAT 58.640 47.619 5.05 0.00 0.00 3.79
1084 1351 3.531538 CAAGAGCCGGAAAGTAAGCATA 58.468 45.455 5.05 0.00 0.00 3.14
1085 1352 3.906720 AGAGCCGGAAAGTAAGCATAA 57.093 42.857 5.05 0.00 0.00 1.90
1086 1353 3.532542 AGAGCCGGAAAGTAAGCATAAC 58.467 45.455 5.05 0.00 0.00 1.89
1087 1354 3.055385 AGAGCCGGAAAGTAAGCATAACA 60.055 43.478 5.05 0.00 0.00 2.41
1088 1355 3.681593 AGCCGGAAAGTAAGCATAACAA 58.318 40.909 5.05 0.00 0.00 2.83
1100 1376 2.026822 AGCATAACAAGACAGACCCCTG 60.027 50.000 0.00 0.00 45.76 4.45
1174 1455 5.072055 TGATCTGTTCATGTGGTGTTCATT 58.928 37.500 0.00 0.00 0.00 2.57
1210 1492 8.706492 ATGTTCGTATCTTCGTTACCATTTTA 57.294 30.769 0.00 0.00 0.00 1.52
1245 1527 3.755378 CACGAGTTGGTAGTGGTACTAGT 59.245 47.826 0.00 0.00 30.12 2.57
1246 1528 4.937620 CACGAGTTGGTAGTGGTACTAGTA 59.062 45.833 0.00 0.00 30.12 1.82
1247 1529 5.064452 CACGAGTTGGTAGTGGTACTAGTAG 59.936 48.000 1.87 0.00 30.12 2.57
1258 1540 8.328517 GTAGTGGTACTAGTAGCTGTTAGCTGA 61.329 44.444 27.42 6.32 40.83 4.26
1272 1554 2.182842 GCTGATGGATGCCCGTGTC 61.183 63.158 0.00 0.00 34.29 3.67
1336 1618 2.640316 ATCTGGCCCGAAATTAGGAC 57.360 50.000 0.00 0.00 0.00 3.85
1344 1634 4.277672 GGCCCGAAATTAGGACCTTTTATC 59.722 45.833 0.00 0.00 0.00 1.75
1396 1686 3.851128 GCCGGGCCTGGTAGAGAC 61.851 72.222 31.62 10.30 0.00 3.36
1400 1690 1.797211 CGGGCCTGGTAGAGACGATC 61.797 65.000 2.57 0.00 0.00 3.69
1470 1760 2.282462 CCAGCCCCCACTGTTCAC 60.282 66.667 0.00 0.00 35.83 3.18
1542 1832 4.662961 CTGCTGTGCGACGTGGGA 62.663 66.667 0.00 0.00 0.00 4.37
1575 1865 1.906824 ACCGGCCACGAAAGAGAGA 60.907 57.895 0.00 0.00 44.60 3.10
1576 1866 1.153745 CCGGCCACGAAAGAGAGAG 60.154 63.158 2.24 0.00 44.60 3.20
1577 1867 1.595993 CCGGCCACGAAAGAGAGAGA 61.596 60.000 2.24 0.00 44.60 3.10
1591 1881 0.247736 GAGAGACACGGCAACTGGAT 59.752 55.000 0.00 0.00 0.00 3.41
1592 1882 1.476891 GAGAGACACGGCAACTGGATA 59.523 52.381 0.00 0.00 0.00 2.59
1593 1883 1.899814 AGAGACACGGCAACTGGATAA 59.100 47.619 0.00 0.00 0.00 1.75
1594 1884 2.501723 AGAGACACGGCAACTGGATAAT 59.498 45.455 0.00 0.00 0.00 1.28
1596 1886 1.593006 GACACGGCAACTGGATAATCG 59.407 52.381 0.00 0.00 0.00 3.34
1597 1887 0.304705 CACGGCAACTGGATAATCGC 59.695 55.000 0.00 0.00 0.00 4.58
1598 1888 0.814010 ACGGCAACTGGATAATCGCC 60.814 55.000 0.00 0.00 36.16 5.54
1599 1889 1.941812 GGCAACTGGATAATCGCCG 59.058 57.895 0.00 0.00 0.00 6.46
1622 1978 3.297620 CCCTGGCAACACAGCACC 61.298 66.667 0.00 0.00 46.17 5.01
1629 1985 1.596752 CAACACAGCACCGGCACTA 60.597 57.895 0.00 0.00 44.61 2.74
1673 2029 2.563427 GCCGACTTTTGCCTCTGC 59.437 61.111 0.00 0.00 38.26 4.26
1690 2049 1.523938 GCCTACCCATCAACGGCTC 60.524 63.158 0.00 0.00 37.76 4.70
1710 2069 1.000145 GCTTCGAACCCGTGAAGATC 59.000 55.000 6.18 0.00 43.34 2.75
1735 2100 0.690762 TCTCCGGCTACTTTTTGGCT 59.309 50.000 0.00 0.00 0.00 4.75
1756 2121 0.804989 CTTTCTGGTGCCATCCGTTC 59.195 55.000 0.00 0.00 0.00 3.95
1811 2176 7.281774 CCCGTAGAGTTGTTTATACAGTAGAGA 59.718 40.741 0.00 0.00 35.28 3.10
1812 2177 8.336806 CCGTAGAGTTGTTTATACAGTAGAGAG 58.663 40.741 0.00 0.00 35.28 3.20
1813 2178 8.336806 CGTAGAGTTGTTTATACAGTAGAGAGG 58.663 40.741 0.00 0.00 35.28 3.69
1814 2179 7.648039 AGAGTTGTTTATACAGTAGAGAGGG 57.352 40.000 0.00 0.00 35.28 4.30
1815 2180 6.608002 AGAGTTGTTTATACAGTAGAGAGGGG 59.392 42.308 0.00 0.00 35.28 4.79
1828 2193 2.284995 AGGGGAGTGGAGTGGAGC 60.285 66.667 0.00 0.00 0.00 4.70
1929 2321 2.332514 GCACGCTGCTGCTTTTGA 59.667 55.556 14.03 0.00 40.96 2.69
1930 2322 1.728426 GCACGCTGCTGCTTTTGAG 60.728 57.895 14.03 0.00 40.96 3.02
1931 2323 1.944035 CACGCTGCTGCTTTTGAGA 59.056 52.632 14.03 0.00 36.97 3.27
1932 2324 0.385223 CACGCTGCTGCTTTTGAGAC 60.385 55.000 14.03 0.00 36.97 3.36
2047 2443 0.877649 CGAGCGTATGCCTGCAGAAT 60.878 55.000 17.39 11.13 44.31 2.40
2048 2444 0.585357 GAGCGTATGCCTGCAGAATG 59.415 55.000 17.39 0.00 44.31 2.67
2049 2445 0.107508 AGCGTATGCCTGCAGAATGT 60.108 50.000 17.39 0.44 44.31 2.71
2079 2475 2.670414 GCACCTCGTGAGAATCTTTCTG 59.330 50.000 0.00 0.00 40.87 3.02
2116 2512 1.134670 GTAGGTCACTGGATGGAGTGC 60.135 57.143 0.00 0.00 42.74 4.40
2134 2530 5.006746 GGAGTGCCGATAATTAGTTTCTGTG 59.993 44.000 0.00 0.00 0.00 3.66
2136 2532 5.351465 AGTGCCGATAATTAGTTTCTGTGTG 59.649 40.000 0.00 0.00 0.00 3.82
2179 2575 7.496591 ACAATGAGTTTTTGCATGATGTTCTTT 59.503 29.630 0.00 0.00 0.00 2.52
2220 2616 5.122239 TGATCTTTGAATAAGGACGTTGCTG 59.878 40.000 0.00 0.00 0.00 4.41
2235 2631 3.669023 CGTTGCTGCTTTCTCAGGATTTC 60.669 47.826 0.00 0.00 34.41 2.17
2245 2641 9.295825 TGCTTTCTCAGGATTTCTATTGTAAAA 57.704 29.630 0.00 0.00 0.00 1.52
2269 2665 8.732746 AATTGTAACTTTTATAGACGATGGCT 57.267 30.769 0.00 0.00 0.00 4.75
2275 2671 8.556213 AACTTTTATAGACGATGGCTGTTTTA 57.444 30.769 0.00 0.00 0.00 1.52
2291 2687 4.340617 TGTTTTATGGGGTGTGGAGATTC 58.659 43.478 0.00 0.00 0.00 2.52
2293 2689 0.468226 TATGGGGTGTGGAGATTCGC 59.532 55.000 0.00 0.00 0.00 4.70
2297 2693 1.026718 GGGTGTGGAGATTCGCTTGG 61.027 60.000 0.00 0.00 0.00 3.61
2304 2700 2.955660 TGGAGATTCGCTTGGTTGTTTT 59.044 40.909 0.00 0.00 0.00 2.43
2307 2703 1.451651 GATTCGCTTGGTTGTTTTGCG 59.548 47.619 0.00 0.00 46.71 4.85
2319 2715 0.663153 GTTTTGCGTTGAGTGGAGCT 59.337 50.000 0.00 0.00 0.00 4.09
2372 2798 9.657728 ACTATAGCTAATAGGTAGTTTGGACTT 57.342 33.333 0.00 0.00 41.78 3.01
2421 2847 7.169982 ACAACTATGTAGTCTATACCGTCGTAC 59.830 40.741 0.00 0.00 38.24 3.67
2516 2946 2.938956 AAGCATGTGGGATAGCCTAC 57.061 50.000 6.57 6.57 45.25 3.18
2524 2954 5.717078 TGTGGGATAGCCTACTTATAACG 57.283 43.478 15.03 0.00 45.26 3.18
2525 2955 5.142639 TGTGGGATAGCCTACTTATAACGT 58.857 41.667 15.03 0.00 45.26 3.99
2527 2957 4.456911 TGGGATAGCCTACTTATAACGTCG 59.543 45.833 0.00 0.00 0.00 5.12
2543 2973 3.986277 ACGTCGTTCTAAGTTTGTCCAT 58.014 40.909 0.00 0.00 0.00 3.41
2627 3057 6.014647 GGTTAACCAGGGGTTCTCTTTAAAT 58.985 40.000 20.12 0.00 43.05 1.40
2690 3120 2.838386 AGCGCTCATATGCACTTTTG 57.162 45.000 2.64 0.00 0.00 2.44
2702 3133 4.829064 TGCACTTTTGTAAGCTTAGTGG 57.171 40.909 21.88 8.91 37.33 4.00
2793 3226 7.493320 GGACGTACATTGGTCAATTCATAGTTA 59.507 37.037 0.00 0.00 34.87 2.24
2798 3231 7.633789 ACATTGGTCAATTCATAGTTACTCCT 58.366 34.615 0.00 0.00 0.00 3.69
2834 3285 0.877071 AACCACGATGAGCTGCAAAG 59.123 50.000 1.02 0.00 0.00 2.77
2838 3289 1.733912 CACGATGAGCTGCAAAGCTTA 59.266 47.619 0.00 0.00 46.36 3.09
2845 3296 5.766150 TGAGCTGCAAAGCTTACTTAAAA 57.234 34.783 0.00 0.00 46.36 1.52
2850 3301 8.917415 AGCTGCAAAGCTTACTTAAAATATTC 57.083 30.769 0.00 0.00 43.52 1.75
2852 3303 7.222805 GCTGCAAAGCTTACTTAAAATATTCCC 59.777 37.037 0.00 0.00 34.05 3.97
2869 3320 9.821240 AAATATTCCCAATAAGGTGCATATGTA 57.179 29.630 4.29 0.00 34.66 2.29
2870 3321 9.995594 AATATTCCCAATAAGGTGCATATGTAT 57.004 29.630 4.29 0.00 34.66 2.29
2873 3324 5.012239 CCCAATAAGGTGCATATGTATGCT 58.988 41.667 21.63 7.80 45.92 3.79
2889 3340 4.395854 TGTATGCTTGCATAAGTTCAGTGG 59.604 41.667 15.73 0.00 36.27 4.00
2890 3341 2.862541 TGCTTGCATAAGTTCAGTGGT 58.137 42.857 0.00 0.00 36.27 4.16
2896 3347 3.820467 TGCATAAGTTCAGTGGTCCAAAG 59.180 43.478 0.00 0.00 0.00 2.77
2897 3348 4.072131 GCATAAGTTCAGTGGTCCAAAGA 58.928 43.478 0.00 0.00 0.00 2.52
2940 3397 6.114221 TCCTATTTTAATCCGTTCTTTGCG 57.886 37.500 0.00 0.00 0.00 4.85
2949 3406 4.866508 TCCGTTCTTTGCGATATCCTAT 57.133 40.909 0.00 0.00 0.00 2.57
2953 3410 4.090642 CGTTCTTTGCGATATCCTATGCTC 59.909 45.833 0.00 0.00 0.00 4.26
2965 3422 2.149578 CCTATGCTCAGGTGCTATTGC 58.850 52.381 0.00 0.00 40.20 3.56
2997 3454 4.388485 TCTGACTAAGCATTTTCAGTGCA 58.612 39.130 0.69 0.00 44.87 4.57
3006 3463 5.191426 AGCATTTTCAGTGCATATGTCTCT 58.809 37.500 4.29 0.77 44.87 3.10
3100 3557 2.681848 CCTCGAGAGCTGCATTTTCAAT 59.318 45.455 15.71 0.00 0.00 2.57
3248 3705 1.925255 TCTCTTCCCAATGCCTTCCAT 59.075 47.619 0.00 0.00 35.06 3.41
3289 3746 6.258727 AGCATTCACTTTATGAGTTGGATACG 59.741 38.462 0.00 0.00 38.99 3.06
3361 3818 2.544685 ACGTTGAGTGCTGCTGATATC 58.455 47.619 0.00 0.00 0.00 1.63
3433 3890 0.957888 GAGGTGCCAGAGGAGTTTGC 60.958 60.000 0.00 0.00 0.00 3.68
3495 3953 6.852420 AGGTATACTGAACTTCACAAGCTA 57.148 37.500 2.25 0.00 0.00 3.32
3514 3972 7.556635 ACAAGCTACCCAATTTAGTATTCCTTC 59.443 37.037 0.00 0.00 0.00 3.46
3521 3980 8.373220 ACCCAATTTAGTATTCCTTCTATACCG 58.627 37.037 0.00 0.00 0.00 4.02
3830 4289 2.434359 CCGAAGGCCCGTTCAGAC 60.434 66.667 0.00 0.00 46.14 3.51
3892 4351 5.299028 CCATGCTAATTGTATGTTGCCACTA 59.701 40.000 0.00 0.00 37.11 2.74
4068 4529 2.937799 CCAATGGCATATGCAACCAAAC 59.062 45.455 28.07 10.16 44.36 2.93
4125 4586 0.249398 ATTGGTACGTGGAGAGTGGC 59.751 55.000 0.00 0.00 0.00 5.01
4224 4685 4.566488 CCTGAACAAGGGCTATCTCAGTTT 60.566 45.833 0.00 0.00 43.15 2.66
4228 4689 2.941720 CAAGGGCTATCTCAGTTTCAGC 59.058 50.000 0.00 0.00 0.00 4.26
4230 4691 1.137086 GGGCTATCTCAGTTTCAGCGA 59.863 52.381 0.00 0.00 32.97 4.93
4365 4826 4.846779 TCCAAAGGCAAGTACACAAATC 57.153 40.909 0.00 0.00 0.00 2.17
4418 4888 9.602568 TTTTACCGAGTTGTATAATAGATTGCA 57.397 29.630 0.00 0.00 0.00 4.08
4419 4889 9.772973 TTTACCGAGTTGTATAATAGATTGCAT 57.227 29.630 0.00 0.00 0.00 3.96
4424 4894 9.143631 CGAGTTGTATAATAGATTGCATGATCA 57.856 33.333 0.00 0.00 0.00 2.92
4471 4941 0.108207 CTGGCAGATCTAGCTTGGGG 59.892 60.000 9.42 0.00 0.00 4.96
4540 5010 7.727331 AGAAATCTTTGTTTCTCTGAGTCTG 57.273 36.000 4.32 0.00 43.09 3.51
4672 5142 2.485814 GTGGAAGTTCATGAAGGACAGC 59.514 50.000 8.80 0.00 0.00 4.40
4732 5202 0.753479 TCGAGACCCTCATCCAGCTC 60.753 60.000 0.00 0.00 0.00 4.09
4733 5203 0.754957 CGAGACCCTCATCCAGCTCT 60.755 60.000 0.00 0.00 0.00 4.09
4762 5232 2.893682 GATTCCCCAACCTGCCTCCG 62.894 65.000 0.00 0.00 0.00 4.63
4803 5273 5.895534 TGAAGGTCCAGTATAACGAGGTAAT 59.104 40.000 0.00 0.00 0.00 1.89
4838 5308 2.197324 ACAACATGCCGGTGGGTT 59.803 55.556 1.90 1.75 34.97 4.11
4843 5313 1.248101 ACATGCCGGTGGGTTAAAGC 61.248 55.000 1.90 0.00 34.97 3.51
4872 5342 4.613944 TGCTTGTGCATTTTTCTGAGAAG 58.386 39.130 0.00 0.00 45.31 2.85
4936 5406 1.404315 GCCTACTCGAGGGTTCTTGTG 60.404 57.143 18.41 0.00 46.81 3.33
5068 5538 4.155733 TACCTGGCGGGCATCACG 62.156 66.667 13.63 0.00 39.10 4.35
5195 5665 1.451927 TGATGTGAATGGGCGAGGC 60.452 57.895 0.00 0.00 0.00 4.70
5248 5718 2.217750 TGCGTACACAAGTTGCATCTT 58.782 42.857 1.81 4.13 34.36 2.40
5249 5719 3.394719 TGCGTACACAAGTTGCATCTTA 58.605 40.909 9.65 0.00 34.36 2.10
5251 5721 3.424433 GCGTACACAAGTTGCATCTTACC 60.424 47.826 9.65 0.00 0.00 2.85
5252 5722 3.994392 CGTACACAAGTTGCATCTTACCT 59.006 43.478 9.65 0.00 0.00 3.08
5253 5723 4.451096 CGTACACAAGTTGCATCTTACCTT 59.549 41.667 9.65 0.00 0.00 3.50
5254 5724 5.636121 CGTACACAAGTTGCATCTTACCTTA 59.364 40.000 9.65 0.00 0.00 2.69
5255 5725 5.941948 ACACAAGTTGCATCTTACCTTAC 57.058 39.130 9.65 0.00 0.00 2.34
5280 5750 9.681062 ACTACTACTAATGGTGCATTTGTAATT 57.319 29.630 0.00 0.00 39.81 1.40
5283 5753 8.802267 ACTACTAATGGTGCATTTGTAATTTGT 58.198 29.630 0.00 0.00 39.81 2.83
5344 5821 0.394762 GCTGATGGCAACCCAGATGA 60.395 55.000 15.87 0.00 46.24 2.92
5345 5822 1.753141 GCTGATGGCAACCCAGATGAT 60.753 52.381 15.87 0.00 46.24 2.45
5346 5823 1.954382 CTGATGGCAACCCAGATGATG 59.046 52.381 8.61 0.00 46.24 3.07
5401 5879 1.507141 CTTGGTCAGGTTCGTGTGCC 61.507 60.000 0.00 0.00 0.00 5.01
5439 5919 0.396556 TACCTGACGATGCCTGCCTA 60.397 55.000 0.00 0.00 0.00 3.93
5445 5925 0.179073 ACGATGCCTGCCTATGTGAC 60.179 55.000 0.00 0.00 0.00 3.67
5455 5935 1.344438 GCCTATGTGACGATGATGGGA 59.656 52.381 0.00 0.00 0.00 4.37
5456 5936 2.868044 GCCTATGTGACGATGATGGGAC 60.868 54.545 0.00 0.00 0.00 4.46
5458 5938 0.824109 ATGTGACGATGATGGGACGT 59.176 50.000 0.00 0.00 42.84 4.34
5461 5952 1.029681 TGACGATGATGGGACGTAGG 58.970 55.000 0.00 0.00 40.29 3.18
5538 6029 1.295423 CGTCTCCGGTTTGTGGGAT 59.705 57.895 0.00 0.00 0.00 3.85
5587 6078 1.662026 GCGGAATGGAACGTGTCAAAC 60.662 52.381 0.00 0.00 0.00 2.93
5619 6113 2.294512 GCTTGGAGTTGGAGTTTTCAGG 59.705 50.000 0.00 0.00 0.00 3.86
5683 6177 3.361977 GATTTGCCGTGCCGTGGT 61.362 61.111 0.00 0.00 0.00 4.16
5699 6193 0.892755 TGGTGACCGCGTAATTCTCT 59.107 50.000 4.92 0.00 0.00 3.10
5700 6194 1.135199 TGGTGACCGCGTAATTCTCTC 60.135 52.381 4.92 0.00 0.00 3.20
5701 6195 1.135199 GGTGACCGCGTAATTCTCTCA 60.135 52.381 4.92 0.00 0.00 3.27
5800 6294 5.050490 CCGTATATTTGACTGAAGAGTGGG 58.950 45.833 0.00 0.00 30.16 4.61
5826 6320 1.078759 GTGTGATGGGAGAACGCGAG 61.079 60.000 15.93 0.00 0.00 5.03
6019 6548 4.511454 CGGCTCCAGAATTATGATCGAAAA 59.489 41.667 0.54 0.00 0.00 2.29
6020 6549 5.333645 CGGCTCCAGAATTATGATCGAAAAG 60.334 44.000 0.54 0.00 0.00 2.27
6021 6550 5.529060 GGCTCCAGAATTATGATCGAAAAGT 59.471 40.000 0.54 0.00 0.00 2.66
6022 6551 6.038714 GGCTCCAGAATTATGATCGAAAAGTT 59.961 38.462 0.54 0.00 0.00 2.66
6049 6584 1.999051 CAGATTTCTTCGTCCGGCG 59.001 57.895 11.37 11.37 43.01 6.46
6108 6643 4.442706 GTTCCCACGACTGATGATATTGT 58.557 43.478 0.00 0.00 0.00 2.71
6109 6644 4.322080 TCCCACGACTGATGATATTGTC 57.678 45.455 0.00 0.00 0.00 3.18
6116 6651 6.133569 CGACTGATGATATTGTCGTGAATC 57.866 41.667 0.00 0.00 44.65 2.52
6117 6652 5.687285 CGACTGATGATATTGTCGTGAATCA 59.313 40.000 0.00 0.00 44.65 2.57
6118 6653 6.364435 CGACTGATGATATTGTCGTGAATCAT 59.636 38.462 0.00 0.00 44.65 2.45
6119 6654 7.095899 CGACTGATGATATTGTCGTGAATCATT 60.096 37.037 0.00 0.00 44.65 2.57
6120 6655 8.442632 ACTGATGATATTGTCGTGAATCATTT 57.557 30.769 0.00 0.00 38.77 2.32
6121 6656 8.896744 ACTGATGATATTGTCGTGAATCATTTT 58.103 29.630 0.00 0.00 38.77 1.82
6122 6657 9.726232 CTGATGATATTGTCGTGAATCATTTTT 57.274 29.630 0.00 0.00 38.77 1.94
6150 6685 4.386954 CGGGAAGATATGTCGTGAATCATG 59.613 45.833 0.00 0.00 0.00 3.07
6151 6686 5.541845 GGGAAGATATGTCGTGAATCATGA 58.458 41.667 0.22 0.22 0.00 3.07
6152 6687 6.169094 GGGAAGATATGTCGTGAATCATGAT 58.831 40.000 8.54 1.18 31.77 2.45
6153 6688 6.652481 GGGAAGATATGTCGTGAATCATGATT 59.348 38.462 20.85 20.85 31.77 2.57
6154 6689 7.360691 GGGAAGATATGTCGTGAATCATGATTG 60.361 40.741 25.37 11.38 31.77 2.67
6155 6690 7.360691 GGAAGATATGTCGTGAATCATGATTGG 60.361 40.741 25.37 13.74 31.77 3.16
6156 6691 3.976793 ATGTCGTGAATCATGATTGGC 57.023 42.857 25.37 13.08 31.77 4.52
6157 6692 2.989909 TGTCGTGAATCATGATTGGCT 58.010 42.857 25.37 0.88 31.77 4.75
6158 6693 3.346315 TGTCGTGAATCATGATTGGCTT 58.654 40.909 25.37 1.42 31.77 4.35
6159 6694 4.512484 TGTCGTGAATCATGATTGGCTTA 58.488 39.130 25.37 4.55 31.77 3.09
6160 6695 5.125356 TGTCGTGAATCATGATTGGCTTAT 58.875 37.500 25.37 0.00 31.77 1.73
6161 6696 5.007921 TGTCGTGAATCATGATTGGCTTATG 59.992 40.000 25.37 11.08 31.77 1.90
6162 6697 5.008019 GTCGTGAATCATGATTGGCTTATGT 59.992 40.000 25.37 0.00 31.77 2.29
6163 6698 6.202762 GTCGTGAATCATGATTGGCTTATGTA 59.797 38.462 25.37 0.00 31.77 2.29
6164 6699 6.202762 TCGTGAATCATGATTGGCTTATGTAC 59.797 38.462 25.37 7.48 0.00 2.90
6165 6700 6.203530 CGTGAATCATGATTGGCTTATGTACT 59.796 38.462 25.37 0.00 0.00 2.73
6166 6701 7.570140 CGTGAATCATGATTGGCTTATGTACTC 60.570 40.741 25.37 6.92 0.00 2.59
6167 6702 6.424812 TGAATCATGATTGGCTTATGTACTCG 59.575 38.462 25.37 0.00 0.00 4.18
6168 6703 4.058124 TCATGATTGGCTTATGTACTCGC 58.942 43.478 0.00 0.00 0.00 5.03
6169 6704 3.819564 TGATTGGCTTATGTACTCGCT 57.180 42.857 0.00 0.00 0.00 4.93
6170 6705 3.457234 TGATTGGCTTATGTACTCGCTG 58.543 45.455 0.00 0.00 0.00 5.18
6171 6706 1.651987 TTGGCTTATGTACTCGCTGC 58.348 50.000 0.00 0.00 0.00 5.25
6172 6707 0.824109 TGGCTTATGTACTCGCTGCT 59.176 50.000 0.00 0.00 0.00 4.24
6173 6708 1.207089 TGGCTTATGTACTCGCTGCTT 59.793 47.619 0.00 0.00 0.00 3.91
6174 6709 1.594862 GGCTTATGTACTCGCTGCTTG 59.405 52.381 0.00 0.00 0.00 4.01
6175 6710 2.271800 GCTTATGTACTCGCTGCTTGT 58.728 47.619 0.00 0.00 0.00 3.16
6176 6711 2.673368 GCTTATGTACTCGCTGCTTGTT 59.327 45.455 0.00 0.00 0.00 2.83
6177 6712 3.125316 GCTTATGTACTCGCTGCTTGTTT 59.875 43.478 0.00 0.00 0.00 2.83
6178 6713 4.378459 GCTTATGTACTCGCTGCTTGTTTT 60.378 41.667 0.00 0.00 0.00 2.43
6179 6714 5.163893 GCTTATGTACTCGCTGCTTGTTTTA 60.164 40.000 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.110518 GCCTCTCCCGAGAACTAGGG 61.111 65.000 12.72 12.72 45.64 3.53
2 3 1.110518 GGCCTCTCCCGAGAACTAGG 61.111 65.000 0.00 0.00 39.74 3.02
3 4 2.421220 GGCCTCTCCCGAGAACTAG 58.579 63.158 0.00 0.00 39.74 2.57
4 5 4.680487 GGCCTCTCCCGAGAACTA 57.320 61.111 0.00 0.00 39.74 2.24
13 14 3.775654 CCTGACCACGGCCTCTCC 61.776 72.222 0.00 0.00 0.00 3.71
24 25 2.202756 GGCGATGACGACCTGACC 60.203 66.667 0.00 0.00 42.35 4.02
76 83 2.966309 GAGGTTTGTTGGCTCGCGG 61.966 63.158 6.13 0.00 0.00 6.46
116 123 1.014564 GGCGAGGTGAAAAGAGACGG 61.015 60.000 0.00 0.00 0.00 4.79
118 125 0.673956 GGGGCGAGGTGAAAAGAGAC 60.674 60.000 0.00 0.00 0.00 3.36
149 156 0.391661 GGAAAGCGATGACCTGAGCA 60.392 55.000 0.00 0.00 0.00 4.26
150 157 1.424493 CGGAAAGCGATGACCTGAGC 61.424 60.000 0.00 0.00 0.00 4.26
245 253 1.448540 CTCACGAGGACATGGGCAC 60.449 63.158 0.00 0.00 0.00 5.01
246 254 2.981302 CTCACGAGGACATGGGCA 59.019 61.111 0.00 0.00 0.00 5.36
263 271 2.041115 GTCGGGAAAGAAGCAGGGC 61.041 63.158 0.00 0.00 0.00 5.19
269 277 1.602771 GAGGGGGTCGGGAAAGAAG 59.397 63.158 0.00 0.00 0.00 2.85
453 707 3.530910 CTTTGCTGTCCGGACGGGT 62.531 63.158 37.89 0.00 38.13 5.28
474 728 3.376859 TGATGGTGATAAATCCGTTGTGC 59.623 43.478 0.00 0.00 0.00 4.57
487 741 1.141881 GGCGTCGACTGATGGTGAT 59.858 57.895 14.70 0.00 0.00 3.06
489 743 1.517257 GAGGCGTCGACTGATGGTG 60.517 63.158 4.62 0.00 0.00 4.17
490 744 2.711922 GGAGGCGTCGACTGATGGT 61.712 63.158 4.62 0.00 0.00 3.55
491 745 2.105128 GGAGGCGTCGACTGATGG 59.895 66.667 4.62 0.00 0.00 3.51
566 826 1.797635 GAGCAAATCTAGCGAGGATGC 59.202 52.381 9.97 9.97 37.01 3.91
567 827 2.036992 AGGAGCAAATCTAGCGAGGATG 59.963 50.000 0.00 0.00 37.01 3.51
592 852 9.023967 CGAAAAATAAAGAATTGCTAATGGAGG 57.976 33.333 0.00 0.00 0.00 4.30
593 853 8.534778 GCGAAAAATAAAGAATTGCTAATGGAG 58.465 33.333 0.00 0.00 0.00 3.86
594 854 8.250332 AGCGAAAAATAAAGAATTGCTAATGGA 58.750 29.630 0.00 0.00 0.00 3.41
595 855 8.411318 AGCGAAAAATAAAGAATTGCTAATGG 57.589 30.769 0.00 0.00 0.00 3.16
637 897 2.221749 CAGGGTAATGATTGACGCATCG 59.778 50.000 0.00 0.00 0.00 3.84
653 913 0.962356 CGCCTTTTCAGATGCAGGGT 60.962 55.000 0.00 0.00 0.00 4.34
654 914 1.805254 CGCCTTTTCAGATGCAGGG 59.195 57.895 0.00 0.00 0.00 4.45
655 915 1.138247 GCGCCTTTTCAGATGCAGG 59.862 57.895 0.00 0.00 0.00 4.85
656 916 1.226211 CGCGCCTTTTCAGATGCAG 60.226 57.895 0.00 0.00 0.00 4.41
657 917 1.026182 ATCGCGCCTTTTCAGATGCA 61.026 50.000 0.00 0.00 0.00 3.96
678 938 1.518102 CGAACGAAGGAACGAACGAAA 59.482 47.619 0.14 0.00 37.45 3.46
679 939 1.122849 CGAACGAAGGAACGAACGAA 58.877 50.000 0.14 0.00 37.45 3.85
680 940 0.029300 ACGAACGAAGGAACGAACGA 59.971 50.000 0.14 0.00 38.05 3.85
681 941 0.158096 CACGAACGAAGGAACGAACG 59.842 55.000 0.14 0.00 39.31 3.95
682 942 0.505655 CCACGAACGAAGGAACGAAC 59.494 55.000 0.14 0.00 37.03 3.95
683 943 1.216941 GCCACGAACGAAGGAACGAA 61.217 55.000 12.50 0.00 37.03 3.85
684 944 1.662446 GCCACGAACGAAGGAACGA 60.662 57.895 12.50 0.00 37.03 3.85
685 945 2.664436 GGCCACGAACGAAGGAACG 61.664 63.158 0.00 0.00 39.31 3.95
690 950 3.411351 CCACGGCCACGAACGAAG 61.411 66.667 2.24 0.00 44.60 3.79
762 1028 1.425428 CTGCACGGCCGAAGATTTC 59.575 57.895 35.90 12.14 0.00 2.17
801 1067 2.509336 CGGCGAACGGCAAGAGAT 60.509 61.111 19.40 0.00 46.16 2.75
824 1090 4.335584 GATCGGAGGCGAGGCGAG 62.336 72.222 0.00 0.00 0.00 5.03
891 1158 6.568869 ACGAATGAAAACCAATCTCAAAACA 58.431 32.000 0.00 0.00 0.00 2.83
925 1192 4.166011 GACATCGCAACGGGCAGC 62.166 66.667 2.26 0.00 45.17 5.25
946 1213 1.152830 GAGCCCAACCTGAAACCCA 59.847 57.895 0.00 0.00 0.00 4.51
967 1234 3.869272 CCGGCAAGCACGATCAGC 61.869 66.667 0.00 0.00 0.00 4.26
993 1260 3.431486 GCGTCTTCATCCTCATCTTCCTT 60.431 47.826 0.00 0.00 0.00 3.36
994 1261 2.102252 GCGTCTTCATCCTCATCTTCCT 59.898 50.000 0.00 0.00 0.00 3.36
995 1262 2.102252 AGCGTCTTCATCCTCATCTTCC 59.898 50.000 0.00 0.00 0.00 3.46
996 1263 3.122297 CAGCGTCTTCATCCTCATCTTC 58.878 50.000 0.00 0.00 0.00 2.87
1080 1347 2.359900 CAGGGGTCTGTCTTGTTATGC 58.640 52.381 0.00 0.00 36.30 3.14
1174 1455 6.474427 CGAAGATACGAACATAAACTGCCTTA 59.526 38.462 0.00 0.00 35.09 2.69
1210 1492 3.525537 CAACTCGTGCACTTGAGGATAT 58.474 45.455 21.18 6.35 36.53 1.63
1247 1529 0.950116 GGCATCCATCAGCTAACAGC 59.050 55.000 0.00 0.00 42.84 4.40
1258 1540 2.124570 GCAGACACGGGCATCCAT 60.125 61.111 0.00 0.00 0.00 3.41
1336 1618 4.321974 GGTGAAAGGGTTGCAGATAAAAGG 60.322 45.833 0.00 0.00 0.00 3.11
1344 1634 0.825010 AGCAGGTGAAAGGGTTGCAG 60.825 55.000 0.00 0.00 37.24 4.41
1396 1686 0.389391 ACCCGGAGTTATGCTGATCG 59.611 55.000 0.73 0.00 0.00 3.69
1400 1690 0.828022 TACCACCCGGAGTTATGCTG 59.172 55.000 0.73 0.00 35.59 4.41
1458 1748 3.229156 TACGCGGTGAACAGTGGGG 62.229 63.158 12.47 0.00 0.00 4.96
1459 1749 2.025418 GTACGCGGTGAACAGTGGG 61.025 63.158 12.47 0.00 0.00 4.61
1497 1787 2.898738 CATCGCCAGCCTCTGACT 59.101 61.111 0.00 0.00 32.44 3.41
1498 1788 2.894387 GCATCGCCAGCCTCTGAC 60.894 66.667 0.00 0.00 32.44 3.51
1542 1832 1.409661 GCCGGTGATCCCCATTTACTT 60.410 52.381 1.90 0.00 0.00 2.24
1575 1865 2.738643 CGATTATCCAGTTGCCGTGTCT 60.739 50.000 0.00 0.00 0.00 3.41
1576 1866 1.593006 CGATTATCCAGTTGCCGTGTC 59.407 52.381 0.00 0.00 0.00 3.67
1577 1867 1.651987 CGATTATCCAGTTGCCGTGT 58.348 50.000 0.00 0.00 0.00 4.49
1591 1881 1.682451 CCAGGGGAAGTCGGCGATTA 61.682 60.000 14.79 0.00 0.00 1.75
1592 1882 2.584608 CAGGGGAAGTCGGCGATT 59.415 61.111 14.79 5.78 0.00 3.34
1593 1883 3.470888 CCAGGGGAAGTCGGCGAT 61.471 66.667 14.79 0.00 0.00 4.58
1596 1886 4.344865 TTGCCAGGGGAAGTCGGC 62.345 66.667 0.00 0.00 45.11 5.54
1597 1887 2.359975 GTTGCCAGGGGAAGTCGG 60.360 66.667 0.00 0.00 0.00 4.79
1598 1888 1.966451 GTGTTGCCAGGGGAAGTCG 60.966 63.158 0.00 0.00 0.00 4.18
1599 1889 0.890996 CTGTGTTGCCAGGGGAAGTC 60.891 60.000 0.00 0.00 0.00 3.01
1622 1978 3.243301 ACCATACTGTAATCGTAGTGCCG 60.243 47.826 0.00 0.00 0.00 5.69
1629 1985 3.620427 TGGCAACCATACTGTAATCGT 57.380 42.857 0.00 0.00 0.00 3.73
1673 2029 1.227263 CGAGCCGTTGATGGGTAGG 60.227 63.158 0.00 0.00 40.53 3.18
1690 2049 0.736325 ATCTTCACGGGTTCGAAGCG 60.736 55.000 20.14 16.99 38.80 4.68
1710 2069 4.083271 CCAAAAAGTAGCCGGAGAAAAGAG 60.083 45.833 5.05 0.00 0.00 2.85
1735 2100 1.299648 CGGATGGCACCAGAAAGGA 59.700 57.895 0.00 0.00 41.22 3.36
1756 2121 2.861935 AGAAATATACAAACGGACGCGG 59.138 45.455 12.47 0.00 0.00 6.46
1811 2176 2.284995 GCTCCACTCCACTCCCCT 60.285 66.667 0.00 0.00 0.00 4.79
1812 2177 3.775654 CGCTCCACTCCACTCCCC 61.776 72.222 0.00 0.00 0.00 4.81
1813 2178 3.775654 CCGCTCCACTCCACTCCC 61.776 72.222 0.00 0.00 0.00 4.30
1814 2179 2.680352 TCCGCTCCACTCCACTCC 60.680 66.667 0.00 0.00 0.00 3.85
1815 2180 2.888863 CTCCGCTCCACTCCACTC 59.111 66.667 0.00 0.00 0.00 3.51
1928 2320 3.691744 CTGCCCTGCGTCTCGTCTC 62.692 68.421 0.00 0.00 0.00 3.36
1929 2321 3.753434 CTGCCCTGCGTCTCGTCT 61.753 66.667 0.00 0.00 0.00 4.18
1930 2322 4.803426 CCTGCCCTGCGTCTCGTC 62.803 72.222 0.00 0.00 0.00 4.20
1932 2324 3.417275 CTACCTGCCCTGCGTCTCG 62.417 68.421 0.00 0.00 0.00 4.04
1989 2385 1.485032 GGTTATCCTGCCGTTACGCG 61.485 60.000 3.53 3.53 40.95 6.01
2018 2414 4.830765 TACGCTCGCCCCACATGC 62.831 66.667 0.00 0.00 0.00 4.06
2033 2429 2.086869 ACACACATTCTGCAGGCATAC 58.913 47.619 15.13 0.00 0.00 2.39
2116 2512 6.978343 TTCCACACAGAAACTAATTATCGG 57.022 37.500 0.00 0.00 0.00 4.18
2134 2530 0.885196 TTTGTAGCCCGCATTTCCAC 59.115 50.000 0.00 0.00 0.00 4.02
2136 2532 0.885196 TGTTTGTAGCCCGCATTTCC 59.115 50.000 0.00 0.00 0.00 3.13
2192 2588 8.181573 GCAACGTCCTTATTCAAAGATCAAATA 58.818 33.333 0.00 0.00 0.00 1.40
2193 2589 7.029563 GCAACGTCCTTATTCAAAGATCAAAT 58.970 34.615 0.00 0.00 0.00 2.32
2245 2641 7.769044 ACAGCCATCGTCTATAAAAGTTACAAT 59.231 33.333 0.00 0.00 0.00 2.71
2255 2651 5.995282 CCCATAAAACAGCCATCGTCTATAA 59.005 40.000 0.00 0.00 0.00 0.98
2269 2665 4.340617 GAATCTCCACACCCCATAAAACA 58.659 43.478 0.00 0.00 0.00 2.83
2275 2671 1.224592 GCGAATCTCCACACCCCAT 59.775 57.895 0.00 0.00 0.00 4.00
2293 2689 2.598192 CACTCAACGCAAAACAACCAAG 59.402 45.455 0.00 0.00 0.00 3.61
2297 2693 2.450160 CTCCACTCAACGCAAAACAAC 58.550 47.619 0.00 0.00 0.00 3.32
2304 2700 1.388547 AAAAAGCTCCACTCAACGCA 58.611 45.000 0.00 0.00 0.00 5.24
2325 2721 5.109903 AGTATCATCACAGAAACGGCTTAC 58.890 41.667 0.00 0.00 0.00 2.34
2367 2793 6.987404 CCCAGACTTAGCTTAATCTAAAGTCC 59.013 42.308 16.14 3.41 32.91 3.85
2368 2794 7.557724 ACCCAGACTTAGCTTAATCTAAAGTC 58.442 38.462 13.16 13.16 32.80 3.01
2369 2795 7.180408 TGACCCAGACTTAGCTTAATCTAAAGT 59.820 37.037 0.00 0.00 0.00 2.66
2370 2796 7.492994 GTGACCCAGACTTAGCTTAATCTAAAG 59.507 40.741 0.00 0.00 0.00 1.85
2371 2797 7.038587 TGTGACCCAGACTTAGCTTAATCTAAA 60.039 37.037 0.00 0.00 0.00 1.85
2372 2798 6.439375 TGTGACCCAGACTTAGCTTAATCTAA 59.561 38.462 0.00 0.00 0.00 2.10
2373 2799 5.955959 TGTGACCCAGACTTAGCTTAATCTA 59.044 40.000 0.00 0.00 0.00 1.98
2421 2847 4.400845 CAAAAGAATCGTGTGCATCTCTG 58.599 43.478 0.00 0.00 0.00 3.35
2491 2917 3.282021 GCTATCCCACATGCTTTTCTGA 58.718 45.455 0.00 0.00 0.00 3.27
2516 2946 7.326789 TGGACAAACTTAGAACGACGTTATAAG 59.673 37.037 35.67 35.67 46.35 1.73
2524 2954 5.917541 TTCATGGACAAACTTAGAACGAC 57.082 39.130 0.00 0.00 0.00 4.34
2525 2955 6.480524 CATTCATGGACAAACTTAGAACGA 57.519 37.500 0.00 0.00 0.00 3.85
2553 2983 1.002366 CGCATTCTACAGTCAGGTGC 58.998 55.000 0.00 0.00 0.00 5.01
2627 3057 1.421268 AGCTGTTGATGTTCCAGGTGA 59.579 47.619 0.00 0.00 35.75 4.02
2690 3120 4.807443 ACTCTTTCGTCCACTAAGCTTAC 58.193 43.478 0.86 0.00 0.00 2.34
2702 3133 0.733223 GCGTCTGGGACTCTTTCGTC 60.733 60.000 0.00 0.00 0.00 4.20
2760 3191 4.895961 TGACCAATGTACGTCCATTGTTA 58.104 39.130 26.06 13.11 46.61 2.41
2764 3195 5.007034 TGAATTGACCAATGTACGTCCATT 58.993 37.500 0.00 0.00 35.45 3.16
2779 3212 7.907214 AACACAGGAGTAACTATGAATTGAC 57.093 36.000 0.00 0.00 0.00 3.18
2780 3213 7.936847 ACAAACACAGGAGTAACTATGAATTGA 59.063 33.333 0.00 0.00 0.00 2.57
2793 3226 3.366052 ACCAAGAACAAACACAGGAGT 57.634 42.857 0.00 0.00 0.00 3.85
2838 3289 8.602472 TGCACCTTATTGGGAATATTTTAAGT 57.398 30.769 0.00 0.00 41.11 2.24
2845 3296 9.412460 CATACATATGCACCTTATTGGGAATAT 57.588 33.333 1.58 0.00 41.11 1.28
2867 3318 4.396166 ACCACTGAACTTATGCAAGCATAC 59.604 41.667 13.89 4.21 38.48 2.39
2869 3320 3.424703 ACCACTGAACTTATGCAAGCAT 58.575 40.909 12.66 12.66 40.19 3.79
2870 3321 2.813754 GACCACTGAACTTATGCAAGCA 59.186 45.455 0.00 0.00 34.94 3.91
2873 3324 3.500448 TGGACCACTGAACTTATGCAA 57.500 42.857 0.00 0.00 0.00 4.08
2889 3340 5.183904 ACAACTGCTATTGGATTCTTTGGAC 59.816 40.000 5.65 0.00 33.63 4.02
2890 3341 5.324409 ACAACTGCTATTGGATTCTTTGGA 58.676 37.500 5.65 0.00 33.63 3.53
2940 3397 5.867903 ATAGCACCTGAGCATAGGATATC 57.132 43.478 12.65 0.00 40.42 1.63
2949 3406 2.108514 GCGCAATAGCACCTGAGCA 61.109 57.895 0.30 0.00 42.27 4.26
2953 3410 2.819595 ACGGCGCAATAGCACCTG 60.820 61.111 10.83 0.00 40.87 4.00
2965 3422 1.148157 CTTAGTCAGATGCCACGGCG 61.148 60.000 4.80 4.80 45.51 6.46
2981 3438 6.825213 AGAGACATATGCACTGAAAATGCTTA 59.175 34.615 1.58 0.00 43.77 3.09
3248 3705 1.002868 GCTCCTCCTGCTTGCTCAA 60.003 57.895 0.00 0.00 0.00 3.02
3289 3746 3.181491 GGAGTAGATGGATAGCATCGAGC 60.181 52.174 0.00 0.00 46.19 5.03
3328 3785 4.024893 GCACTCAACGTATATGTGATTGGG 60.025 45.833 12.79 0.00 0.00 4.12
3361 3818 5.091431 GCAAACTTCTCCTTCATGATTTCG 58.909 41.667 0.00 0.00 0.00 3.46
3433 3890 3.123620 GACAAGGCCAGAGCAGCG 61.124 66.667 5.01 0.00 42.56 5.18
3495 3953 8.373220 CGGTATAGAAGGAATACTAAATTGGGT 58.627 37.037 0.00 0.00 31.71 4.51
3514 3972 9.133627 CTCATTTTAGTGATGATGACGGTATAG 57.866 37.037 0.00 0.00 33.39 1.31
3521 3980 5.725110 ACGCTCATTTTAGTGATGATGAC 57.275 39.130 0.00 0.00 33.39 3.06
4068 4529 2.289882 TGAGTCCAGAACTTCCTGCATG 60.290 50.000 0.00 0.00 38.74 4.06
4142 4603 5.306678 TGTCTTTCACCATTATTTTTGCCCT 59.693 36.000 0.00 0.00 0.00 5.19
4212 4673 4.928661 TTTTCGCTGAAACTGAGATAGC 57.071 40.909 3.71 0.00 30.83 2.97
4224 4685 4.097135 TGAAACACAATCCTTTTTCGCTGA 59.903 37.500 0.00 0.00 31.76 4.26
4228 4689 3.735746 GCCTGAAACACAATCCTTTTTCG 59.264 43.478 0.00 0.00 31.76 3.46
4230 4691 6.478512 TTAGCCTGAAACACAATCCTTTTT 57.521 33.333 0.00 0.00 0.00 1.94
4365 4826 8.786937 ATGCAAGTAAAATGCGAGTAAATATG 57.213 30.769 0.00 0.00 46.76 1.78
4416 4886 9.569167 CCAATCAAGTATTCATTATGATCATGC 57.431 33.333 18.72 0.00 0.00 4.06
4424 4894 8.523915 TGCAAGTCCAATCAAGTATTCATTAT 57.476 30.769 0.00 0.00 0.00 1.28
4471 4941 3.478540 GGCATGGTACAGGTCTTCC 57.521 57.895 0.00 0.00 43.50 3.46
4540 5010 3.877801 CACGCTATGCTCGGTTTTC 57.122 52.632 0.00 0.00 0.00 2.29
4561 5031 1.829222 TCTAACCGGTTCATGGTCTCC 59.171 52.381 26.16 0.00 39.29 3.71
4672 5142 1.027255 TCTTCTCCAGCTCCGACGAG 61.027 60.000 0.00 0.00 39.33 4.18
4732 5202 3.084786 GTTGGGGAATCTGGACTTCAAG 58.915 50.000 0.00 0.00 0.00 3.02
4733 5203 2.225017 GGTTGGGGAATCTGGACTTCAA 60.225 50.000 0.00 0.00 0.00 2.69
4777 5247 3.446161 CCTCGTTATACTGGACCTTCACA 59.554 47.826 0.00 0.00 0.00 3.58
4803 5273 6.641169 TGTTGTGCCATGACAAACTTATTA 57.359 33.333 1.82 0.00 37.58 0.98
4869 5339 2.087646 GCACCATCCAAGGAGTTCTTC 58.912 52.381 0.00 0.00 32.41 2.87
4872 5342 1.457346 CTGCACCATCCAAGGAGTTC 58.543 55.000 0.00 0.00 0.00 3.01
4909 5379 2.482333 CCTCGAGTAGGCCTCCACG 61.482 68.421 9.68 9.19 38.97 4.94
4936 5406 3.338275 TATGCTGAACGCCACCCCC 62.338 63.158 0.00 0.00 38.05 5.40
4954 5424 4.988716 TCCGCCACCCGAGACAGT 62.989 66.667 0.00 0.00 40.02 3.55
4960 5430 2.443952 ATGATCTCCGCCACCCGA 60.444 61.111 0.00 0.00 40.02 5.14
5021 5491 1.546961 GAGAGGTCGAACTTGAGGGA 58.453 55.000 3.47 0.00 0.00 4.20
5195 5665 1.438651 CATCACCCTGTACAACACCG 58.561 55.000 0.00 0.00 0.00 4.94
5248 5718 8.543293 AATGCACCATTAGTAGTAGTAAGGTA 57.457 34.615 13.87 5.59 31.77 3.08
5249 5719 7.433537 AATGCACCATTAGTAGTAGTAAGGT 57.566 36.000 8.24 9.59 31.77 3.50
5251 5721 8.718102 ACAAATGCACCATTAGTAGTAGTAAG 57.282 34.615 3.89 0.00 32.43 2.34
5254 5724 9.681062 AATTACAAATGCACCATTAGTAGTAGT 57.319 29.630 0.00 0.00 32.43 2.73
5280 5750 3.119531 GCCAATGCTGCTGTTACATACAA 60.120 43.478 0.00 0.00 33.15 2.41
5281 5751 2.423185 GCCAATGCTGCTGTTACATACA 59.577 45.455 0.00 0.00 32.75 2.29
5282 5752 2.223572 GGCCAATGCTGCTGTTACATAC 60.224 50.000 0.00 0.00 37.74 2.39
5283 5753 2.023673 GGCCAATGCTGCTGTTACATA 58.976 47.619 0.00 0.00 37.74 2.29
5284 5754 0.819582 GGCCAATGCTGCTGTTACAT 59.180 50.000 0.00 0.00 37.74 2.29
5344 5821 0.942410 CGTTGCAAAAGCAGCAGCAT 60.942 50.000 0.00 0.00 43.75 3.79
5345 5822 1.589461 CGTTGCAAAAGCAGCAGCA 60.589 52.632 0.00 0.00 43.75 4.41
5346 5823 2.305127 CCGTTGCAAAAGCAGCAGC 61.305 57.895 0.00 0.00 43.75 5.25
5367 5844 3.279434 GACCAAGACACAACAGGTTTCT 58.721 45.455 0.00 0.00 38.16 2.52
5401 5879 5.181245 CAGGTACAAATCTACAACCAACCAG 59.819 44.000 0.00 0.00 32.43 4.00
5439 5919 0.824109 ACGTCCCATCATCGTCACAT 59.176 50.000 0.00 0.00 32.26 3.21
5445 5925 0.040336 CGACCTACGTCCCATCATCG 60.040 60.000 0.00 0.00 35.40 3.84
5458 5938 1.226463 CACGCACGCATACGACCTA 60.226 57.895 0.00 0.00 43.93 3.08
5461 5952 1.066656 TACACACGCACGCATACGAC 61.067 55.000 0.00 0.00 43.93 4.34
5466 5957 0.598942 TCTTGTACACACGCACGCAT 60.599 50.000 0.00 0.00 0.00 4.73
5530 6021 1.002659 CCCACACGTCTAATCCCACAA 59.997 52.381 0.00 0.00 0.00 3.33
5531 6022 0.611200 CCCACACGTCTAATCCCACA 59.389 55.000 0.00 0.00 0.00 4.17
5538 6029 1.070105 GCCACACCCACACGTCTAA 59.930 57.895 0.00 0.00 0.00 2.10
5619 6113 1.068250 GGCGGTAGGATCAGTCTGC 59.932 63.158 0.00 0.34 0.00 4.26
5683 6177 2.425668 TCATGAGAGAATTACGCGGTCA 59.574 45.455 12.47 0.06 0.00 4.02
5699 6193 2.094442 TCGATTAACCACGTGCTCATGA 60.094 45.455 10.91 0.00 0.00 3.07
5700 6194 2.267426 TCGATTAACCACGTGCTCATG 58.733 47.619 10.91 0.00 0.00 3.07
5701 6195 2.665649 TCGATTAACCACGTGCTCAT 57.334 45.000 10.91 0.00 0.00 2.90
5800 6294 1.448540 CTCCCATCACACGCTCACC 60.449 63.158 0.00 0.00 0.00 4.02
5826 6320 1.319669 GAGCGTTTCGTCGTGGAATAC 59.680 52.381 0.00 0.00 0.00 1.89
5917 6446 4.767255 CAGCAGGTGGACCGAGGC 62.767 72.222 0.00 0.00 42.08 4.70
5989 6518 2.558554 AATTCTGGAGCCGACGGACG 62.559 60.000 20.50 0.00 42.18 4.79
6019 6548 4.083643 CGAAGAAATCTGCATGTCACAACT 60.084 41.667 0.00 0.00 0.00 3.16
6020 6549 4.153986 CGAAGAAATCTGCATGTCACAAC 58.846 43.478 0.00 0.00 0.00 3.32
6021 6550 3.814842 ACGAAGAAATCTGCATGTCACAA 59.185 39.130 0.00 0.00 0.00 3.33
6022 6551 3.402110 ACGAAGAAATCTGCATGTCACA 58.598 40.909 0.00 0.00 0.00 3.58
6121 6656 3.126171 CACGACATATCTTCCCGCAAAAA 59.874 43.478 0.00 0.00 0.00 1.94
6122 6657 2.675844 CACGACATATCTTCCCGCAAAA 59.324 45.455 0.00 0.00 0.00 2.44
6123 6658 2.093921 TCACGACATATCTTCCCGCAAA 60.094 45.455 0.00 0.00 0.00 3.68
6124 6659 1.478916 TCACGACATATCTTCCCGCAA 59.521 47.619 0.00 0.00 0.00 4.85
6125 6660 1.107945 TCACGACATATCTTCCCGCA 58.892 50.000 0.00 0.00 0.00 5.69
6126 6661 2.218953 TTCACGACATATCTTCCCGC 57.781 50.000 0.00 0.00 0.00 6.13
6127 6662 3.977427 TGATTCACGACATATCTTCCCG 58.023 45.455 0.00 0.00 0.00 5.14
6128 6663 5.541845 TCATGATTCACGACATATCTTCCC 58.458 41.667 0.00 0.00 0.00 3.97
6129 6664 7.360691 CCAATCATGATTCACGACATATCTTCC 60.361 40.741 18.16 0.00 0.00 3.46
6130 6665 7.516481 CCAATCATGATTCACGACATATCTTC 58.484 38.462 18.16 0.00 0.00 2.87
6131 6666 6.072838 GCCAATCATGATTCACGACATATCTT 60.073 38.462 18.16 0.00 0.00 2.40
6132 6667 5.410746 GCCAATCATGATTCACGACATATCT 59.589 40.000 18.16 0.00 0.00 1.98
6133 6668 5.410746 AGCCAATCATGATTCACGACATATC 59.589 40.000 18.16 0.00 0.00 1.63
6150 6685 2.221981 GCAGCGAGTACATAAGCCAATC 59.778 50.000 0.00 0.00 0.00 2.67
6151 6686 2.158900 AGCAGCGAGTACATAAGCCAAT 60.159 45.455 0.00 0.00 0.00 3.16
6152 6687 1.207089 AGCAGCGAGTACATAAGCCAA 59.793 47.619 0.00 0.00 0.00 4.52
6153 6688 0.824109 AGCAGCGAGTACATAAGCCA 59.176 50.000 0.00 0.00 0.00 4.75
6154 6689 1.594862 CAAGCAGCGAGTACATAAGCC 59.405 52.381 0.00 0.00 0.00 4.35
6155 6690 2.271800 ACAAGCAGCGAGTACATAAGC 58.728 47.619 0.00 0.00 0.00 3.09
6156 6691 4.928661 AAACAAGCAGCGAGTACATAAG 57.071 40.909 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.