Multiple sequence alignment - TraesCS4D01G025500

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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 TraesCS4D01G025500 chr4D 100.000 3710 0 0 1 3710 10994093 10990384 0.000000e+00 6852.0
1 TraesCS4D01G025500 chr4A 93.259 1706 84 15 2014 3710 591878841 591877158 0.000000e+00 2484.0
2 TraesCS4D01G025500 chr4A 81.107 1138 109 57 859 1934 591880100 591879007 0.000000e+00 813.0
3 TraesCS4D01G025500 chr4A 77.778 414 54 15 326 711 591880617 591880214 1.730000e-53 220.0
4 TraesCS4D01G025500 chr4B 94.960 1369 48 8 2360 3710 20747516 20746151 0.000000e+00 2126.0
5 TraesCS4D01G025500 chr4B 77.836 1534 138 108 491 1934 20749480 20748059 0.000000e+00 763.0
6 TraesCS4D01G025500 chr4B 92.837 349 24 1 2013 2361 20747892 20747545 4.280000e-139 505.0
7 TraesCS4D01G025500 chr4B 81.152 191 20 11 1749 1939 557976088 557975914 5.000000e-29 139.0
8 TraesCS4D01G025500 chr3D 92.271 634 26 6 1 634 511280941 511281551 0.000000e+00 878.0
9 TraesCS4D01G025500 chr5D 78.317 309 43 17 1 298 532245327 532245622 1.060000e-40 178.0
10 TraesCS4D01G025500 chr6A 82.632 190 15 10 1750 1939 540091423 540091594 6.420000e-33 152.0
11 TraesCS4D01G025500 chr6A 77.000 300 37 12 1934 2232 540122971 540123239 3.860000e-30 143.0
12 TraesCS4D01G025500 chr6A 81.122 196 19 10 1741 1936 540122757 540122934 1.390000e-29 141.0
13 TraesCS4D01G025500 chr6A 76.667 300 38 12 1934 2232 540091628 540091896 1.800000e-28 137.0
14 TraesCS4D01G025500 chr6A 93.333 60 4 0 2173 2232 564511510 564511569 5.100000e-14 89.8
15 TraesCS4D01G025500 chr7A 76.412 301 46 15 1 297 6860822 6860543 5.000000e-29 139.0
16 TraesCS4D01G025500 chr1B 81.152 191 20 12 1749 1939 319902980 319902806 5.000000e-29 139.0
17 TraesCS4D01G025500 chr1B 80.928 194 20 11 1749 1939 480422795 480422616 1.800000e-28 137.0
18 TraesCS4D01G025500 chr1B 87.719 114 12 2 2120 2232 319902616 319902504 8.360000e-27 132.0
19 TraesCS4D01G025500 chr1B 87.379 103 11 2 2131 2232 480422415 480422314 2.340000e-22 117.0
20 TraesCS4D01G025500 chr1D 87.719 114 12 2 2120 2232 420510884 420510996 8.360000e-27 132.0
21 TraesCS4D01G025500 chr6D 86.726 113 15 0 2120 2232 305134179 305134067 3.890000e-25 126.0
22 TraesCS4D01G025500 chr6D 83.721 129 11 4 1811 1939 305134487 305134369 3.030000e-21 113.0
23 TraesCS4D01G025500 chr7D 78.140 215 31 11 1 212 398816866 398816665 5.030000e-24 122.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G025500 chr4D 10990384 10994093 3709 True 6852.000000 6852 100.000000 1 3710 1 chr4D.!!$R1 3709
1 TraesCS4D01G025500 chr4A 591877158 591880617 3459 True 1172.333333 2484 84.048000 326 3710 3 chr4A.!!$R1 3384
2 TraesCS4D01G025500 chr4B 20746151 20749480 3329 True 1131.333333 2126 88.544333 491 3710 3 chr4B.!!$R2 3219
3 TraesCS4D01G025500 chr3D 511280941 511281551 610 False 878.000000 878 92.271000 1 634 1 chr3D.!!$F1 633

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
915 1003 0.103208 CCTTGTCCTTCTCGATCGGG 59.897 60.0 16.41 13.07 0.00 5.14 F
1454 1625 0.030101 CCACACGATTTGCAAACCGT 59.970 50.0 25.69 25.69 36.07 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2314 0.321996 AAAGTGGGCCGAGACTTCTC 59.678 55.000 12.42 0.0 39.55 2.87 R
3312 3683 3.403038 TCAAGTTGGTAAAGCAGAGAGC 58.597 45.455 2.34 0.0 46.19 4.09 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
110 111 8.969260 AAAAAGAAAAGAGATGCTCCAAAAAT 57.031 26.923 0.00 0.00 0.00 1.82
117 118 6.786967 AGAGATGCTCCAAAAATGCTATTT 57.213 33.333 0.00 0.00 0.00 1.40
150 151 5.814705 TGGTTTTGTTTTATTTCTGCCACAG 59.185 36.000 0.00 0.00 0.00 3.66
161 162 3.050275 GCCACAGCCTCCACGAAC 61.050 66.667 0.00 0.00 0.00 3.95
195 196 3.719924 TGAAAACTTGCCAGCATTGAAG 58.280 40.909 0.00 0.00 0.00 3.02
281 282 2.450609 TTTTACTGTCCACTCGAGCC 57.549 50.000 13.61 0.00 0.00 4.70
296 297 0.389687 GAGCCCATATGAGCTCGAGC 60.390 60.000 30.01 30.01 45.44 5.03
311 312 1.067250 GAGCTAGCTGAGAAGGGCG 59.933 63.158 24.99 0.00 0.00 6.13
324 325 1.232621 AAGGGCGCTTTCGTTGTACC 61.233 55.000 10.73 0.00 38.14 3.34
413 415 9.844257 AGATTCAGAGTAAATCCAGGATAAAAG 57.156 33.333 1.02 0.00 34.34 2.27
416 418 6.069673 TCAGAGTAAATCCAGGATAAAAGCCA 60.070 38.462 1.02 0.00 0.00 4.75
434 437 1.134946 CCACCTGGATTTCATTTCGGC 59.865 52.381 0.00 0.00 37.39 5.54
467 470 2.126888 GCACCGCACGTGGAAATG 60.127 61.111 18.88 7.83 43.24 2.32
501 505 2.143925 GGAGGACGGTTAGCAATATGC 58.856 52.381 0.00 0.00 45.46 3.14
665 698 2.395690 GCGCACGCATGACACTAC 59.604 61.111 10.65 0.00 41.49 2.73
675 710 6.199154 GCACGCATGACACTACATATATATCC 59.801 42.308 0.00 0.00 0.00 2.59
680 715 5.265989 TGACACTACATATATATCCCGCCA 58.734 41.667 0.00 0.00 0.00 5.69
686 721 7.987458 CACTACATATATATCCCGCCATTTCTT 59.013 37.037 0.00 0.00 0.00 2.52
709 764 3.043998 GCTAGCTAGCTAGGCTCCA 57.956 57.895 39.60 15.91 45.62 3.86
710 765 0.601057 GCTAGCTAGCTAGGCTCCAC 59.399 60.000 39.60 24.67 45.62 4.02
711 766 1.253100 CTAGCTAGCTAGGCTCCACC 58.747 60.000 34.95 3.65 41.58 4.61
712 767 0.178958 TAGCTAGCTAGGCTCCACCC 60.179 60.000 20.67 2.91 40.44 4.61
713 768 1.458588 GCTAGCTAGGCTCCACCCT 60.459 63.158 22.10 0.00 40.44 4.34
714 769 1.468506 GCTAGCTAGGCTCCACCCTC 61.469 65.000 22.10 0.00 40.44 4.30
715 770 0.830023 CTAGCTAGGCTCCACCCTCC 60.830 65.000 13.32 0.00 40.44 4.30
716 771 1.590339 TAGCTAGGCTCCACCCTCCA 61.590 60.000 0.00 0.00 40.44 3.86
717 772 2.736826 GCTAGGCTCCACCCTCCAC 61.737 68.421 0.00 0.00 40.58 4.02
718 773 2.363795 TAGGCTCCACCCTCCACG 60.364 66.667 0.00 0.00 40.58 4.94
719 774 3.976490 TAGGCTCCACCCTCCACGG 62.976 68.421 0.00 0.00 40.58 4.94
722 777 4.087892 CTCCACCCTCCACGGCAG 62.088 72.222 0.00 0.00 0.00 4.85
729 784 4.056125 CTCCACGGCAGCGACTGA 62.056 66.667 10.46 0.00 32.44 3.41
730 785 3.978723 CTCCACGGCAGCGACTGAG 62.979 68.421 10.46 6.24 32.44 3.35
731 786 4.056125 CCACGGCAGCGACTGAGA 62.056 66.667 10.46 0.00 32.44 3.27
732 787 2.807045 CACGGCAGCGACTGAGAC 60.807 66.667 10.46 0.51 32.44 3.36
733 788 2.986413 ACGGCAGCGACTGAGACT 60.986 61.111 10.46 0.00 32.44 3.24
758 813 4.492160 CACGCCGCCGAAGAGCTA 62.492 66.667 0.00 0.00 38.29 3.32
759 814 3.755628 ACGCCGCCGAAGAGCTAA 61.756 61.111 0.00 0.00 38.29 3.09
760 815 2.956964 CGCCGCCGAAGAGCTAAG 60.957 66.667 0.00 0.00 36.29 2.18
761 816 3.265636 GCCGCCGAAGAGCTAAGC 61.266 66.667 0.00 0.00 0.00 3.09
762 817 2.586357 CCGCCGAAGAGCTAAGCC 60.586 66.667 0.00 0.00 0.00 4.35
763 818 2.956964 CGCCGAAGAGCTAAGCCG 60.957 66.667 0.00 0.00 0.00 5.52
764 819 2.586357 GCCGAAGAGCTAAGCCGG 60.586 66.667 0.00 0.00 42.74 6.13
765 820 2.893398 CCGAAGAGCTAAGCCGGT 59.107 61.111 1.90 0.00 35.83 5.28
766 821 1.227002 CCGAAGAGCTAAGCCGGTC 60.227 63.158 1.90 0.00 35.83 4.79
767 822 1.586564 CGAAGAGCTAAGCCGGTCG 60.587 63.158 1.90 0.00 36.57 4.79
768 823 1.807886 GAAGAGCTAAGCCGGTCGA 59.192 57.895 1.90 0.00 36.57 4.20
769 824 0.248702 GAAGAGCTAAGCCGGTCGAG 60.249 60.000 1.90 0.00 36.57 4.04
770 825 0.680280 AAGAGCTAAGCCGGTCGAGA 60.680 55.000 1.90 0.00 36.57 4.04
771 826 1.098712 AGAGCTAAGCCGGTCGAGAG 61.099 60.000 1.90 0.00 36.57 3.20
772 827 1.378124 GAGCTAAGCCGGTCGAGAGT 61.378 60.000 1.90 0.00 0.00 3.24
773 828 1.064458 GCTAAGCCGGTCGAGAGTC 59.936 63.158 1.90 0.00 0.00 3.36
774 829 1.352404 CTAAGCCGGTCGAGAGTCG 59.648 63.158 1.90 0.00 42.10 4.18
782 837 2.271497 TCGAGAGTCGAGACCCCC 59.729 66.667 0.00 0.00 44.82 5.40
797 852 2.612251 CCCCCTCTCTCCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
810 865 1.305201 CCTCCTCACTAGTCTCTCGC 58.695 60.000 0.00 0.00 0.00 5.03
811 866 1.134220 CCTCCTCACTAGTCTCTCGCT 60.134 57.143 0.00 0.00 0.00 4.93
812 867 2.210116 CTCCTCACTAGTCTCTCGCTC 58.790 57.143 0.00 0.00 0.00 5.03
816 871 1.136500 TCACTAGTCTCTCGCTCGCTA 59.864 52.381 0.00 0.00 0.00 4.26
817 872 1.259507 CACTAGTCTCTCGCTCGCTAC 59.740 57.143 0.00 0.00 0.00 3.58
910 998 5.865552 CGTTTAAATACCTTGTCCTTCTCGA 59.134 40.000 0.00 0.00 0.00 4.04
911 999 6.534079 CGTTTAAATACCTTGTCCTTCTCGAT 59.466 38.462 0.00 0.00 0.00 3.59
913 1001 3.992260 ATACCTTGTCCTTCTCGATCG 57.008 47.619 9.36 9.36 0.00 3.69
914 1002 0.818296 ACCTTGTCCTTCTCGATCGG 59.182 55.000 16.41 6.26 0.00 4.18
915 1003 0.103208 CCTTGTCCTTCTCGATCGGG 59.897 60.000 16.41 13.07 0.00 5.14
916 1004 0.103208 CTTGTCCTTCTCGATCGGGG 59.897 60.000 16.43 12.32 0.00 5.73
919 1007 0.465824 GTCCTTCTCGATCGGGGAGA 60.466 60.000 25.47 12.84 38.71 3.71
920 1008 0.179015 TCCTTCTCGATCGGGGAGAG 60.179 60.000 25.47 14.47 41.26 3.20
921 1009 0.179015 CCTTCTCGATCGGGGAGAGA 60.179 60.000 25.47 12.06 41.26 3.10
922 1010 1.234821 CTTCTCGATCGGGGAGAGAG 58.765 60.000 19.20 4.28 41.26 3.20
923 1011 0.837940 TTCTCGATCGGGGAGAGAGA 59.162 55.000 16.43 5.71 41.26 3.10
924 1012 0.394938 TCTCGATCGGGGAGAGAGAG 59.605 60.000 16.43 1.49 35.70 3.20
925 1013 0.394938 CTCGATCGGGGAGAGAGAGA 59.605 60.000 16.41 0.00 38.06 3.10
926 1014 0.394938 TCGATCGGGGAGAGAGAGAG 59.605 60.000 16.41 0.00 0.00 3.20
927 1015 0.394938 CGATCGGGGAGAGAGAGAGA 59.605 60.000 7.38 0.00 0.00 3.10
928 1016 1.608025 CGATCGGGGAGAGAGAGAGAG 60.608 61.905 7.38 0.00 0.00 3.20
929 1017 1.697432 GATCGGGGAGAGAGAGAGAGA 59.303 57.143 0.00 0.00 0.00 3.10
930 1018 1.128200 TCGGGGAGAGAGAGAGAGAG 58.872 60.000 0.00 0.00 0.00 3.20
931 1019 1.128200 CGGGGAGAGAGAGAGAGAGA 58.872 60.000 0.00 0.00 0.00 3.10
955 1043 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
975 1063 2.951229 GGAACCAACCAGGAAGAAGA 57.049 50.000 0.00 0.00 41.22 2.87
982 1114 3.196685 CCAACCAGGAAGAAGAGTAGAGG 59.803 52.174 0.00 0.00 41.22 3.69
998 1130 2.261729 AGAGGGAGAGAGGGACAAAAC 58.738 52.381 0.00 0.00 0.00 2.43
1006 1138 0.603065 GAGGGACAAAACCATGGCAC 59.397 55.000 13.04 0.00 29.05 5.01
1010 1142 0.675633 GACAAAACCATGGCACTGCT 59.324 50.000 13.04 0.00 0.00 4.24
1011 1143 0.390124 ACAAAACCATGGCACTGCTG 59.610 50.000 13.04 3.52 0.00 4.41
1012 1144 0.675083 CAAAACCATGGCACTGCTGA 59.325 50.000 13.04 0.00 0.00 4.26
1013 1145 1.068895 CAAAACCATGGCACTGCTGAA 59.931 47.619 13.04 0.00 0.00 3.02
1014 1146 0.963962 AAACCATGGCACTGCTGAAG 59.036 50.000 13.04 0.00 0.00 3.02
1015 1147 1.530013 AACCATGGCACTGCTGAAGC 61.530 55.000 13.04 0.00 42.50 3.86
1042 1177 1.676746 CATTGGCTGCAGCAGTATCT 58.323 50.000 37.63 14.43 44.36 1.98
1048 1189 1.015109 CTGCAGCAGTATCTTGGCAG 58.985 55.000 14.90 0.00 42.14 4.85
1056 1197 0.179034 GTATCTTGGCAGGAGCAGGG 60.179 60.000 5.31 0.00 44.61 4.45
1059 1200 2.853542 TTGGCAGGAGCAGGGTCA 60.854 61.111 0.56 0.00 44.61 4.02
1118 1259 1.739562 CTGTCTTCCTCCTGCACGC 60.740 63.158 0.00 0.00 0.00 5.34
1162 1306 1.435105 CATCTCCTCTCGCGCAAGA 59.565 57.895 8.75 1.82 43.02 3.02
1168 1312 3.573772 CTCTCGCGCAAGACCACCA 62.574 63.158 8.75 0.00 43.02 4.17
1169 1313 3.414700 CTCGCGCAAGACCACCAC 61.415 66.667 8.75 0.00 43.02 4.16
1175 1319 4.308458 CAAGACCACCACCGGCGA 62.308 66.667 9.30 0.00 0.00 5.54
1322 1478 2.202892 CGCCCGAGTTCCTAAGCC 60.203 66.667 0.00 0.00 0.00 4.35
1325 1481 1.823976 CCCGAGTTCCTAAGCCTCC 59.176 63.158 0.00 0.00 0.00 4.30
1328 1484 1.069358 CCGAGTTCCTAAGCCTCCATC 59.931 57.143 0.00 0.00 0.00 3.51
1329 1485 2.035632 CGAGTTCCTAAGCCTCCATCT 58.964 52.381 0.00 0.00 0.00 2.90
1333 1489 4.107820 AGTTCCTAAGCCTCCATCTTCTT 58.892 43.478 0.00 0.00 0.00 2.52
1335 1491 4.494091 TCCTAAGCCTCCATCTTCTTTG 57.506 45.455 0.00 0.00 0.00 2.77
1336 1492 2.948315 CCTAAGCCTCCATCTTCTTTGC 59.052 50.000 0.00 0.00 0.00 3.68
1339 1495 1.039785 GCCTCCATCTTCTTTGCCCC 61.040 60.000 0.00 0.00 0.00 5.80
1340 1496 0.627986 CCTCCATCTTCTTTGCCCCT 59.372 55.000 0.00 0.00 0.00 4.79
1341 1497 1.684248 CCTCCATCTTCTTTGCCCCTG 60.684 57.143 0.00 0.00 0.00 4.45
1342 1498 0.332632 TCCATCTTCTTTGCCCCTGG 59.667 55.000 0.00 0.00 0.00 4.45
1366 1536 1.943340 GTCTTTCCGGATCTTCATGCC 59.057 52.381 4.15 0.00 0.00 4.40
1370 1540 1.072159 CCGGATCTTCATGCCCTCC 59.928 63.158 0.00 0.00 0.00 4.30
1371 1541 1.072159 CGGATCTTCATGCCCTCCC 59.928 63.158 0.00 0.00 0.00 4.30
1373 1543 1.064824 GGATCTTCATGCCCTCCCCT 61.065 60.000 0.00 0.00 0.00 4.79
1374 1544 0.849417 GATCTTCATGCCCTCCCCTT 59.151 55.000 0.00 0.00 0.00 3.95
1375 1545 0.849417 ATCTTCATGCCCTCCCCTTC 59.151 55.000 0.00 0.00 0.00 3.46
1383 1554 3.551407 CCTCCCCTTCCCGCTAGC 61.551 72.222 4.06 4.06 0.00 3.42
1397 1568 1.871676 CGCTAGCGTCAGATAGGTGTA 59.128 52.381 28.66 0.00 36.89 2.90
1400 1571 2.060050 AGCGTCAGATAGGTGTAGCT 57.940 50.000 0.00 0.00 0.00 3.32
1411 1582 1.131638 GGTGTAGCTGGATGGATGGA 58.868 55.000 0.00 0.00 0.00 3.41
1420 1591 3.752665 CTGGATGGATGGATTTCCTCTG 58.247 50.000 0.00 0.00 36.68 3.35
1422 1593 3.117776 TGGATGGATGGATTTCCTCTGTG 60.118 47.826 0.00 0.00 36.68 3.66
1445 1616 3.354678 GCACCTGCCACACGATTT 58.645 55.556 0.00 0.00 34.31 2.17
1446 1617 1.081242 GCACCTGCCACACGATTTG 60.081 57.895 0.00 0.00 34.31 2.32
1447 1618 1.081242 CACCTGCCACACGATTTGC 60.081 57.895 0.00 0.00 0.00 3.68
1448 1619 1.528076 ACCTGCCACACGATTTGCA 60.528 52.632 0.00 0.00 0.00 4.08
1449 1620 1.106351 ACCTGCCACACGATTTGCAA 61.106 50.000 0.00 0.00 32.58 4.08
1451 1622 1.130955 CTGCCACACGATTTGCAAAC 58.869 50.000 15.41 7.79 32.58 2.93
1453 1624 1.274798 GCCACACGATTTGCAAACCG 61.275 55.000 24.19 24.19 0.00 4.44
1454 1625 0.030101 CCACACGATTTGCAAACCGT 59.970 50.000 25.69 25.69 36.07 4.83
1455 1626 1.535015 CCACACGATTTGCAAACCGTT 60.535 47.619 28.54 16.77 33.91 4.44
1456 1627 2.189342 CACACGATTTGCAAACCGTTT 58.811 42.857 28.54 20.27 33.91 3.60
1457 1628 2.035009 CACACGATTTGCAAACCGTTTG 60.035 45.455 28.54 27.06 43.44 2.93
1458 1629 2.159366 ACACGATTTGCAAACCGTTTGA 60.159 40.909 28.54 7.19 43.26 2.69
1459 1630 2.467305 CACGATTTGCAAACCGTTTGAG 59.533 45.455 28.54 13.89 43.26 3.02
1460 1631 1.451651 CGATTTGCAAACCGTTTGAGC 59.548 47.619 24.99 12.70 43.26 4.26
1461 1632 2.742774 GATTTGCAAACCGTTTGAGCT 58.257 42.857 24.99 8.03 43.26 4.09
1462 1633 2.202295 TTTGCAAACCGTTTGAGCTC 57.798 45.000 24.99 6.82 43.26 4.09
1463 1634 1.388547 TTGCAAACCGTTTGAGCTCT 58.611 45.000 24.99 0.00 43.26 4.09
1467 1638 3.186909 GCAAACCGTTTGAGCTCTTTTT 58.813 40.909 24.99 2.57 43.26 1.94
1469 1640 4.801516 GCAAACCGTTTGAGCTCTTTTTAA 59.198 37.500 24.99 0.00 43.26 1.52
1471 1642 6.183360 GCAAACCGTTTGAGCTCTTTTTAAAA 60.183 34.615 24.99 2.80 43.26 1.52
1503 1674 4.524316 TTCAAAGCCATGGAGTTTCATG 57.476 40.909 18.40 3.66 42.92 3.07
1508 1682 3.878778 AGCCATGGAGTTTCATGAGTAC 58.121 45.455 18.40 0.00 45.30 2.73
1513 1687 5.104941 CCATGGAGTTTCATGAGTACTACCA 60.105 44.000 5.56 20.36 45.30 3.25
1544 1718 3.055328 TCATCAGGAAATATGGCCTCCA 58.945 45.455 3.32 0.00 38.19 3.86
1551 1725 3.381590 GGAAATATGGCCTCCAGTTTGAC 59.618 47.826 3.32 0.00 36.75 3.18
1554 1728 1.843368 ATGGCCTCCAGTTTGACATG 58.157 50.000 3.32 0.00 36.75 3.21
1557 1731 1.963515 GGCCTCCAGTTTGACATGTTT 59.036 47.619 0.00 0.00 0.00 2.83
1561 1735 3.891366 CCTCCAGTTTGACATGTTTTCCT 59.109 43.478 0.00 0.00 0.00 3.36
1562 1736 4.022849 CCTCCAGTTTGACATGTTTTCCTC 60.023 45.833 0.00 0.00 0.00 3.71
1563 1737 4.531854 TCCAGTTTGACATGTTTTCCTCA 58.468 39.130 0.00 0.00 0.00 3.86
1564 1738 5.139727 TCCAGTTTGACATGTTTTCCTCAT 58.860 37.500 0.00 0.00 0.00 2.90
1565 1739 5.009911 TCCAGTTTGACATGTTTTCCTCATG 59.990 40.000 0.00 4.66 45.41 3.07
1617 1809 0.609957 CAATGGCAGTGCTGGGAAGA 60.610 55.000 16.11 0.00 0.00 2.87
1620 1812 0.991146 TGGCAGTGCTGGGAAGAATA 59.009 50.000 16.11 0.00 0.00 1.75
1695 1887 4.600576 TGCGCCGTGCTCTTCACA 62.601 61.111 4.18 0.00 45.92 3.58
1817 2019 5.925509 GGGCAGATTTACAATGACCTAGTA 58.074 41.667 0.00 0.00 39.20 1.82
1819 2021 5.758784 GGCAGATTTACAATGACCTAGTACC 59.241 44.000 0.00 0.00 0.00 3.34
1870 2076 6.539649 GCATAATGCATCTAACCGTTTCTA 57.460 37.500 0.00 0.00 44.26 2.10
1873 2079 5.813080 AATGCATCTAACCGTTTCTAACC 57.187 39.130 0.00 0.00 0.00 2.85
1875 2081 3.998341 TGCATCTAACCGTTTCTAACCAC 59.002 43.478 0.00 0.00 0.00 4.16
1876 2082 3.998341 GCATCTAACCGTTTCTAACCACA 59.002 43.478 0.00 0.00 0.00 4.17
1877 2083 4.634443 GCATCTAACCGTTTCTAACCACAT 59.366 41.667 0.00 0.00 0.00 3.21
1878 2084 5.813672 GCATCTAACCGTTTCTAACCACATA 59.186 40.000 0.00 0.00 0.00 2.29
1879 2085 6.018994 GCATCTAACCGTTTCTAACCACATAG 60.019 42.308 0.00 0.00 0.00 2.23
1880 2086 6.594788 TCTAACCGTTTCTAACCACATAGT 57.405 37.500 0.00 0.00 0.00 2.12
1884 2090 5.910614 ACCGTTTCTAACCACATAGTATCC 58.089 41.667 0.00 0.00 0.00 2.59
1886 2092 6.155737 ACCGTTTCTAACCACATAGTATCCTT 59.844 38.462 0.00 0.00 0.00 3.36
1887 2093 6.700520 CCGTTTCTAACCACATAGTATCCTTC 59.299 42.308 0.00 0.00 0.00 3.46
1888 2094 7.417570 CCGTTTCTAACCACATAGTATCCTTCT 60.418 40.741 0.00 0.00 0.00 2.85
1889 2095 7.648510 CGTTTCTAACCACATAGTATCCTTCTC 59.351 40.741 0.00 0.00 0.00 2.87
1890 2096 7.598759 TTCTAACCACATAGTATCCTTCTCC 57.401 40.000 0.00 0.00 0.00 3.71
1891 2097 6.075984 TCTAACCACATAGTATCCTTCTCCC 58.924 44.000 0.00 0.00 0.00 4.30
1892 2098 4.280789 ACCACATAGTATCCTTCTCCCA 57.719 45.455 0.00 0.00 0.00 4.37
1893 2099 4.832492 ACCACATAGTATCCTTCTCCCAT 58.168 43.478 0.00 0.00 0.00 4.00
1894 2100 5.977533 ACCACATAGTATCCTTCTCCCATA 58.022 41.667 0.00 0.00 0.00 2.74
1895 2101 6.575411 ACCACATAGTATCCTTCTCCCATAT 58.425 40.000 0.00 0.00 0.00 1.78
1896 2102 7.719424 ACCACATAGTATCCTTCTCCCATATA 58.281 38.462 0.00 0.00 0.00 0.86
1897 2103 8.355256 ACCACATAGTATCCTTCTCCCATATAT 58.645 37.037 0.00 0.00 0.00 0.86
1943 2247 5.293569 CCGTAACTACAGAATTTCCATCCAC 59.706 44.000 0.00 0.00 0.00 4.02
1956 2260 2.239402 TCCATCCACAAGCTGATAAGCA 59.761 45.455 4.45 0.00 37.25 3.91
1962 2266 1.815003 ACAAGCTGATAAGCAGTTGGC 59.185 47.619 4.45 0.00 46.62 4.52
1973 2277 0.109132 GCAGTTGGCATAGTTGGTGC 60.109 55.000 0.00 0.00 43.97 5.01
1979 2283 2.266070 GCATAGTTGGTGCCAAGCA 58.734 52.632 3.57 0.00 36.52 3.91
1980 2284 0.819582 GCATAGTTGGTGCCAAGCAT 59.180 50.000 3.57 0.00 41.91 3.79
1981 2285 2.023673 GCATAGTTGGTGCCAAGCATA 58.976 47.619 3.57 0.00 41.91 3.14
1982 2286 2.624838 GCATAGTTGGTGCCAAGCATAT 59.375 45.455 3.57 1.49 41.91 1.78
1983 2287 3.551454 GCATAGTTGGTGCCAAGCATATG 60.551 47.826 17.59 17.59 41.91 1.78
1993 2297 4.396166 GTGCCAAGCATATGTAGAACACTT 59.604 41.667 4.29 0.00 41.91 3.16
1998 2302 7.246311 CCAAGCATATGTAGAACACTTTGAAG 58.754 38.462 4.29 0.00 0.00 3.02
2003 2307 8.289618 GCATATGTAGAACACTTTGAAGTTTGA 58.710 33.333 4.29 0.00 37.08 2.69
2006 2310 6.848451 TGTAGAACACTTTGAAGTTTGAACC 58.152 36.000 0.00 0.00 37.08 3.62
2007 2311 4.981794 AGAACACTTTGAAGTTTGAACCG 58.018 39.130 0.00 0.00 37.08 4.44
2008 2312 4.698304 AGAACACTTTGAAGTTTGAACCGA 59.302 37.500 0.00 0.00 37.08 4.69
2009 2313 4.616181 ACACTTTGAAGTTTGAACCGAG 57.384 40.909 0.00 0.00 37.08 4.63
2010 2314 3.377172 ACACTTTGAAGTTTGAACCGAGG 59.623 43.478 0.00 0.00 37.08 4.63
2011 2315 3.625764 CACTTTGAAGTTTGAACCGAGGA 59.374 43.478 0.00 0.00 37.08 3.71
2028 2332 1.545706 GGAGAAGTCTCGGCCCACTT 61.546 60.000 8.75 8.75 43.76 3.16
2030 2334 1.549170 GAGAAGTCTCGGCCCACTTTA 59.451 52.381 10.05 0.00 32.83 1.85
2037 2341 3.065371 GTCTCGGCCCACTTTAATTGATG 59.935 47.826 0.00 0.00 0.00 3.07
2041 2345 3.443681 CGGCCCACTTTAATTGATGTCTT 59.556 43.478 0.00 0.00 0.00 3.01
2042 2346 4.082245 CGGCCCACTTTAATTGATGTCTTT 60.082 41.667 0.00 0.00 0.00 2.52
2061 2366 6.427853 TGTCTTTAAGTCATCAACAGACCATG 59.572 38.462 0.00 0.00 36.68 3.66
2217 2522 1.914634 ACATGTTCGTCGCTCAGATC 58.085 50.000 0.00 0.00 0.00 2.75
2250 2555 1.745489 CGGTGTGCTAGCCCTTTCC 60.745 63.158 13.29 6.84 0.00 3.13
2280 2585 2.203408 GGATGGCTAGCAAGGGGC 60.203 66.667 18.24 0.00 45.30 5.80
2399 2734 7.324935 TGAACTCTTATTTATACGTGGCTTCA 58.675 34.615 0.00 0.00 0.00 3.02
2431 2766 4.030977 GCTACGAAATGCAGCAAAGAAATG 59.969 41.667 0.00 0.00 35.35 2.32
2460 2795 7.631717 AAGCTCACCTCTTTTTATGATAACC 57.368 36.000 0.00 0.00 0.00 2.85
2526 2861 7.485810 AGTTTCACCATTTACAACTTTGGTAC 58.514 34.615 0.00 0.00 40.44 3.34
2529 2864 3.058777 ACCATTTACAACTTTGGTACGCG 60.059 43.478 3.53 3.53 40.62 6.01
2532 2867 1.421382 TACAACTTTGGTACGCGCTC 58.579 50.000 5.73 0.00 0.00 5.03
2621 2956 4.997395 TGTCCTGAAACTACAGCAGAATTC 59.003 41.667 0.00 0.00 36.67 2.17
2718 3054 3.374745 CTGCAAGTTTTGATTCAAGCGT 58.625 40.909 0.00 0.00 0.00 5.07
2723 3059 2.100584 AGTTTTGATTCAAGCGTTGGCA 59.899 40.909 0.00 0.00 43.41 4.92
3113 3455 0.039798 GTTGCATGCACACTGACAGG 60.040 55.000 22.58 0.00 0.00 4.00
3308 3679 5.874810 TGTTGCACTAATCATCCTGAACTAC 59.125 40.000 0.00 0.00 0.00 2.73
3309 3680 5.939764 TGCACTAATCATCCTGAACTACT 57.060 39.130 0.00 0.00 0.00 2.57
3310 3681 7.093509 TGTTGCACTAATCATCCTGAACTACTA 60.094 37.037 0.00 0.00 0.00 1.82
3311 3682 7.418337 TGCACTAATCATCCTGAACTACTAA 57.582 36.000 0.00 0.00 0.00 2.24
3312 3683 7.492524 TGCACTAATCATCCTGAACTACTAAG 58.507 38.462 0.00 0.00 0.00 2.18
3313 3684 6.422400 GCACTAATCATCCTGAACTACTAAGC 59.578 42.308 0.00 0.00 0.00 3.09
3314 3685 7.685641 GCACTAATCATCCTGAACTACTAAGCT 60.686 40.741 0.00 0.00 0.00 3.74
3315 3686 7.865385 CACTAATCATCCTGAACTACTAAGCTC 59.135 40.741 0.00 0.00 0.00 4.09
3316 3687 7.782644 ACTAATCATCCTGAACTACTAAGCTCT 59.217 37.037 0.00 0.00 0.00 4.09
3317 3688 6.648879 ATCATCCTGAACTACTAAGCTCTC 57.351 41.667 0.00 0.00 0.00 3.20
3318 3689 5.761205 TCATCCTGAACTACTAAGCTCTCT 58.239 41.667 0.00 0.00 0.00 3.10
3319 3690 5.592282 TCATCCTGAACTACTAAGCTCTCTG 59.408 44.000 0.00 0.00 0.00 3.35
3320 3691 3.697045 TCCTGAACTACTAAGCTCTCTGC 59.303 47.826 0.00 0.00 43.29 4.26
3333 3704 3.403038 GCTCTCTGCTTTACCAACTTGA 58.597 45.455 0.00 0.00 38.95 3.02
3337 3708 6.515696 GCTCTCTGCTTTACCAACTTGAAAAT 60.516 38.462 0.00 0.00 38.95 1.82
3352 3723 9.897744 CAACTTGAAAATTTAGCTAATCAGACA 57.102 29.630 7.08 3.39 0.00 3.41
3357 3728 8.742777 TGAAAATTTAGCTAATCAGACAATGCT 58.257 29.630 7.08 0.00 34.92 3.79
3368 3739 5.065704 TCAGACAATGCTAGTCTCAAGAC 57.934 43.478 1.79 1.79 44.11 3.01
3386 3758 9.605275 TCTCAAGACAAAATATCCAGTTATCTG 57.395 33.333 0.00 0.00 41.01 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.005662 TGTCATTTTACGATGAAATTTTGCAG 57.994 30.769 0.00 0.00 37.75 4.41
85 86 8.833493 CATTTTTGGAGCATCTCTTTTCTTTTT 58.167 29.630 0.00 0.00 33.73 1.94
86 87 7.041576 GCATTTTTGGAGCATCTCTTTTCTTTT 60.042 33.333 0.00 0.00 33.73 2.27
87 88 6.426025 GCATTTTTGGAGCATCTCTTTTCTTT 59.574 34.615 0.00 0.00 33.73 2.52
88 89 5.930569 GCATTTTTGGAGCATCTCTTTTCTT 59.069 36.000 0.00 0.00 33.73 2.52
89 90 5.245526 AGCATTTTTGGAGCATCTCTTTTCT 59.754 36.000 0.00 0.00 33.73 2.52
90 91 5.476614 AGCATTTTTGGAGCATCTCTTTTC 58.523 37.500 0.00 0.00 33.73 2.29
91 92 5.479124 AGCATTTTTGGAGCATCTCTTTT 57.521 34.783 0.00 0.00 33.73 2.27
92 93 6.786967 ATAGCATTTTTGGAGCATCTCTTT 57.213 33.333 0.00 0.00 33.73 2.52
93 94 6.786967 AATAGCATTTTTGGAGCATCTCTT 57.213 33.333 0.00 0.00 33.73 2.85
96 97 8.297470 TCTAAAATAGCATTTTTGGAGCATCT 57.703 30.769 10.66 0.00 33.01 2.90
110 111 9.606631 AAACAAAACCAACATTCTAAAATAGCA 57.393 25.926 0.00 0.00 0.00 3.49
142 143 3.535629 TTCGTGGAGGCTGTGGCAG 62.536 63.158 0.00 0.00 40.87 4.85
150 151 1.060122 CGAAATAACGTTCGTGGAGGC 59.940 52.381 2.82 0.00 44.20 4.70
161 162 4.258471 GCAAGTTTTCATCGCGAAATAACG 60.258 41.667 15.24 5.93 43.12 3.18
171 172 2.642139 ATGCTGGCAAGTTTTCATCG 57.358 45.000 0.00 0.00 0.00 3.84
251 252 7.307989 CGAGTGGACAGTAAAATCAGAAAACAT 60.308 37.037 0.00 0.00 0.00 2.71
271 272 0.320247 GCTCATATGGGCTCGAGTGG 60.320 60.000 20.72 0.00 0.00 4.00
296 297 0.107945 AAAGCGCCCTTCTCAGCTAG 60.108 55.000 2.29 0.00 39.25 3.42
297 298 0.108138 GAAAGCGCCCTTCTCAGCTA 60.108 55.000 2.29 0.00 39.25 3.32
298 299 1.376553 GAAAGCGCCCTTCTCAGCT 60.377 57.895 2.29 0.00 42.35 4.24
299 300 2.744768 CGAAAGCGCCCTTCTCAGC 61.745 63.158 2.29 0.00 0.00 4.26
300 301 0.951040 AACGAAAGCGCCCTTCTCAG 60.951 55.000 2.29 0.00 42.48 3.35
311 312 5.638234 AGAGAAATACTGGTACAACGAAAGC 59.362 40.000 0.00 0.00 38.70 3.51
324 325 4.822026 AGAACGTTCCCAGAGAAATACTG 58.178 43.478 24.22 0.00 35.85 2.74
413 415 1.134946 CCGAAATGAAATCCAGGTGGC 59.865 52.381 0.00 0.00 34.44 5.01
416 418 2.094675 CTGCCGAAATGAAATCCAGGT 58.905 47.619 0.00 0.00 0.00 4.00
662 691 7.442364 CCAAGAAATGGCGGGATATATATGTAG 59.558 40.741 0.00 0.00 43.80 2.74
665 698 6.624352 CCAAGAAATGGCGGGATATATATG 57.376 41.667 0.00 0.00 43.80 1.78
696 751 0.830023 GGAGGGTGGAGCCTAGCTAG 60.830 65.000 14.20 14.20 39.88 3.42
697 752 1.233369 GGAGGGTGGAGCCTAGCTA 59.767 63.158 0.00 0.00 39.88 3.32
701 756 2.363795 CGTGGAGGGTGGAGCCTA 60.364 66.667 0.00 0.00 37.43 3.93
705 760 4.087892 CTGCCGTGGAGGGTGGAG 62.088 72.222 0.00 0.00 41.48 3.86
712 767 3.978723 CTCAGTCGCTGCCGTGGAG 62.979 68.421 0.00 0.00 35.54 3.86
713 768 4.056125 CTCAGTCGCTGCCGTGGA 62.056 66.667 0.00 0.00 35.54 4.02
714 769 4.056125 TCTCAGTCGCTGCCGTGG 62.056 66.667 0.00 0.00 35.54 4.94
715 770 2.807045 GTCTCAGTCGCTGCCGTG 60.807 66.667 0.00 0.00 35.54 4.94
716 771 2.986413 AGTCTCAGTCGCTGCCGT 60.986 61.111 0.00 0.00 35.54 5.68
717 772 2.505777 CAGTCTCAGTCGCTGCCG 60.506 66.667 0.00 0.00 0.00 5.69
718 773 1.445238 GTCAGTCTCAGTCGCTGCC 60.445 63.158 0.00 0.00 0.00 4.85
719 774 0.455972 GAGTCAGTCTCAGTCGCTGC 60.456 60.000 2.45 0.00 42.34 5.25
720 775 1.164411 AGAGTCAGTCTCAGTCGCTG 58.836 55.000 0.00 1.02 44.98 5.18
721 776 3.642938 AGAGTCAGTCTCAGTCGCT 57.357 52.632 0.00 0.00 44.98 4.93
729 784 2.336478 CGGCGTGGAGAGTCAGTCT 61.336 63.158 0.00 0.00 38.71 3.24
730 785 2.179517 CGGCGTGGAGAGTCAGTC 59.820 66.667 0.00 0.00 0.00 3.51
731 786 4.057428 GCGGCGTGGAGAGTCAGT 62.057 66.667 9.37 0.00 0.00 3.41
732 787 4.803426 GGCGGCGTGGAGAGTCAG 62.803 72.222 9.37 0.00 0.00 3.51
758 813 2.359602 TCGACTCTCGACCGGCTT 60.360 61.111 0.00 0.00 44.82 4.35
759 814 2.820479 CTCGACTCTCGACCGGCT 60.820 66.667 0.00 0.00 44.82 5.52
760 815 2.818714 TCTCGACTCTCGACCGGC 60.819 66.667 0.00 0.00 44.82 6.13
761 816 2.462782 GGTCTCGACTCTCGACCGG 61.463 68.421 0.00 0.00 44.82 5.28
762 817 2.462782 GGGTCTCGACTCTCGACCG 61.463 68.421 12.98 0.00 44.82 4.79
763 818 2.114051 GGGGTCTCGACTCTCGACC 61.114 68.421 11.37 11.37 44.82 4.79
764 819 2.114051 GGGGGTCTCGACTCTCGAC 61.114 68.421 0.00 0.00 44.82 4.20
780 835 2.328589 TGAGGAGGGAGAGAGGGGG 61.329 68.421 0.00 0.00 0.00 5.40
781 836 1.075600 GTGAGGAGGGAGAGAGGGG 60.076 68.421 0.00 0.00 0.00 4.79
782 837 1.144913 CTAGTGAGGAGGGAGAGAGGG 59.855 61.905 0.00 0.00 0.00 4.30
783 838 1.850345 ACTAGTGAGGAGGGAGAGAGG 59.150 57.143 0.00 0.00 0.00 3.69
784 839 2.777692 AGACTAGTGAGGAGGGAGAGAG 59.222 54.545 0.00 0.00 0.00 3.20
785 840 2.775384 GAGACTAGTGAGGAGGGAGAGA 59.225 54.545 0.00 0.00 0.00 3.10
788 843 2.484770 CGAGAGACTAGTGAGGAGGGAG 60.485 59.091 0.00 0.00 0.00 4.30
791 846 1.134220 AGCGAGAGACTAGTGAGGAGG 60.134 57.143 0.00 0.00 0.00 4.30
793 848 1.471851 CGAGCGAGAGACTAGTGAGGA 60.472 57.143 0.00 0.00 0.00 3.71
796 851 0.108089 AGCGAGCGAGAGACTAGTGA 60.108 55.000 0.00 0.00 0.00 3.41
797 852 1.259507 GTAGCGAGCGAGAGACTAGTG 59.740 57.143 0.00 0.00 0.00 2.74
810 865 1.894756 CGAGGAGAGGGGTAGCGAG 60.895 68.421 0.00 0.00 0.00 5.03
811 866 2.192443 CGAGGAGAGGGGTAGCGA 59.808 66.667 0.00 0.00 0.00 4.93
812 867 3.597728 GCGAGGAGAGGGGTAGCG 61.598 72.222 0.00 0.00 0.00 4.26
910 998 1.699634 CTCTCTCTCTCTCTCCCCGAT 59.300 57.143 0.00 0.00 0.00 4.18
911 999 1.128200 CTCTCTCTCTCTCTCCCCGA 58.872 60.000 0.00 0.00 0.00 5.14
913 1001 2.370189 CTCTCTCTCTCTCTCTCTCCCC 59.630 59.091 0.00 0.00 0.00 4.81
914 1002 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
915 1003 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
916 1004 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
919 1007 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
920 1008 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
921 1009 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
922 1010 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
923 1011 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
924 1012 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
925 1013 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
926 1014 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
927 1015 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
928 1016 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
929 1017 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
930 1018 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
931 1019 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
955 1043 1.423921 TCTTCTTCCTGGTTGGTTCCC 59.576 52.381 0.00 0.00 37.07 3.97
975 1063 1.988539 TGTCCCTCTCTCCCTCTACT 58.011 55.000 0.00 0.00 0.00 2.57
982 1114 2.619074 CCATGGTTTTGTCCCTCTCTCC 60.619 54.545 2.57 0.00 0.00 3.71
998 1130 1.677966 AGCTTCAGCAGTGCCATGG 60.678 57.895 12.58 7.63 45.16 3.66
1010 1142 3.063704 CAATGCCGGGCAGCTTCA 61.064 61.111 27.62 1.81 43.65 3.02
1011 1143 3.830192 CCAATGCCGGGCAGCTTC 61.830 66.667 27.62 0.00 43.65 3.86
1038 1173 0.621571 ACCCTGCTCCTGCCAAGATA 60.622 55.000 0.00 0.00 38.71 1.98
1040 1175 2.530151 ACCCTGCTCCTGCCAAGA 60.530 61.111 0.00 0.00 38.71 3.02
1042 1177 2.853542 TGACCCTGCTCCTGCCAA 60.854 61.111 0.00 0.00 38.71 4.52
1048 1189 3.591254 GACACCGTGACCCTGCTCC 62.591 68.421 5.28 0.00 0.00 4.70
1056 1197 3.044305 GCTGCCAGACACCGTGAC 61.044 66.667 5.28 0.00 0.00 3.67
1095 1236 0.687354 GCAGGAGGAAGACAGGTGAA 59.313 55.000 0.00 0.00 0.00 3.18
1172 1316 4.492160 TCGTCCTCATGGCGTCGC 62.492 66.667 9.22 9.22 35.47 5.19
1175 1319 2.362503 TCCTCGTCCTCATGGCGT 60.363 61.111 0.00 0.00 35.47 5.68
1179 1323 2.069465 CTCGCCTCCTCGTCCTCATG 62.069 65.000 0.00 0.00 0.00 3.07
1180 1324 1.826054 CTCGCCTCCTCGTCCTCAT 60.826 63.158 0.00 0.00 0.00 2.90
1181 1325 2.438614 CTCGCCTCCTCGTCCTCA 60.439 66.667 0.00 0.00 0.00 3.86
1225 1381 4.166011 GACATTGGCCGCTGACGC 62.166 66.667 11.07 0.00 38.22 5.19
1228 1384 2.741985 CGTGACATTGGCCGCTGA 60.742 61.111 11.07 0.00 0.00 4.26
1229 1385 4.465512 GCGTGACATTGGCCGCTG 62.466 66.667 15.36 0.00 42.66 5.18
1307 1463 0.976073 TGGAGGCTTAGGAACTCGGG 60.976 60.000 0.00 0.00 41.75 5.14
1322 1478 1.684248 CCAGGGGCAAAGAAGATGGAG 60.684 57.143 0.00 0.00 0.00 3.86
1336 1492 4.426313 GGAAAGACCGGCCAGGGG 62.426 72.222 16.44 6.12 46.96 4.79
1348 1518 1.133976 AGGGCATGAAGATCCGGAAAG 60.134 52.381 9.01 0.00 0.00 2.62
1351 1521 1.410850 GGAGGGCATGAAGATCCGGA 61.411 60.000 6.61 6.61 0.00 5.14
1366 1536 3.551407 GCTAGCGGGAAGGGGAGG 61.551 72.222 0.00 0.00 0.00 4.30
1370 1540 3.432051 CTGACGCTAGCGGGAAGGG 62.432 68.421 37.66 18.48 44.69 3.95
1371 1541 1.739338 ATCTGACGCTAGCGGGAAGG 61.739 60.000 37.66 22.46 44.69 3.46
1373 1543 0.952280 CTATCTGACGCTAGCGGGAA 59.048 55.000 37.66 22.40 44.69 3.97
1374 1544 0.889638 CCTATCTGACGCTAGCGGGA 60.890 60.000 37.66 29.90 44.69 5.14
1375 1545 1.173444 ACCTATCTGACGCTAGCGGG 61.173 60.000 37.66 28.32 44.69 6.13
1379 1550 3.058570 CAGCTACACCTATCTGACGCTAG 60.059 52.174 0.00 0.00 0.00 3.42
1383 1554 2.298610 TCCAGCTACACCTATCTGACG 58.701 52.381 0.00 0.00 0.00 4.35
1397 1568 2.107901 GAGGAAATCCATCCATCCAGCT 59.892 50.000 1.67 0.00 42.27 4.24
1400 1571 3.117776 CACAGAGGAAATCCATCCATCCA 60.118 47.826 1.67 0.00 42.27 3.41
1411 1582 0.537143 TGCCGTTGCACAGAGGAAAT 60.537 50.000 0.00 0.00 44.23 2.17
1441 1612 2.726241 GAGCTCAAACGGTTTGCAAATC 59.274 45.455 24.97 14.35 40.43 2.17
1443 1614 1.748493 AGAGCTCAAACGGTTTGCAAA 59.252 42.857 24.97 8.05 40.43 3.68
1444 1615 1.388547 AGAGCTCAAACGGTTTGCAA 58.611 45.000 24.97 10.96 40.43 4.08
1445 1616 1.388547 AAGAGCTCAAACGGTTTGCA 58.611 45.000 24.97 14.57 40.43 4.08
1446 1617 2.492019 AAAGAGCTCAAACGGTTTGC 57.508 45.000 24.97 16.24 40.43 3.68
1447 1618 6.879188 TTTAAAAAGAGCTCAAACGGTTTG 57.121 33.333 24.07 24.07 41.96 2.93
1448 1619 6.869388 TGTTTTAAAAAGAGCTCAAACGGTTT 59.131 30.769 17.77 3.39 0.00 3.27
1449 1620 6.391537 TGTTTTAAAAAGAGCTCAAACGGTT 58.608 32.000 17.77 0.00 0.00 4.44
1451 1622 6.918022 AGATGTTTTAAAAAGAGCTCAAACGG 59.082 34.615 17.77 0.00 0.00 4.44
1469 1640 8.156165 TCCATGGCTTTGAAAATAAAGATGTTT 58.844 29.630 6.96 0.00 39.46 2.83
1471 1642 7.038799 ACTCCATGGCTTTGAAAATAAAGATGT 60.039 33.333 6.96 0.00 39.46 3.06
1483 1654 3.760151 CTCATGAAACTCCATGGCTTTGA 59.240 43.478 6.96 1.48 43.01 2.69
1493 1664 9.614792 ATTATTTGGTAGTACTCATGAAACTCC 57.385 33.333 12.43 13.16 0.00 3.85
1532 1706 3.737559 TGTCAAACTGGAGGCCATATT 57.262 42.857 5.01 0.00 30.82 1.28
1533 1707 3.053395 ACATGTCAAACTGGAGGCCATAT 60.053 43.478 5.01 0.00 30.82 1.78
1536 1710 0.478072 ACATGTCAAACTGGAGGCCA 59.522 50.000 5.01 0.00 0.00 5.36
1551 1725 9.642327 TCATGATTTTAACATGAGGAAAACATG 57.358 29.630 21.53 21.53 45.71 3.21
1562 1736 6.145534 GCCTGCATCATCATGATTTTAACATG 59.854 38.462 5.16 0.00 44.20 3.21
1563 1737 6.220930 GCCTGCATCATCATGATTTTAACAT 58.779 36.000 5.16 0.00 34.28 2.71
1564 1738 5.593968 GCCTGCATCATCATGATTTTAACA 58.406 37.500 5.16 0.52 34.28 2.41
1565 1739 4.678287 CGCCTGCATCATCATGATTTTAAC 59.322 41.667 5.16 0.00 34.28 2.01
1567 1741 3.304861 GCGCCTGCATCATCATGATTTTA 60.305 43.478 5.16 0.00 42.15 1.52
1568 1742 2.545113 GCGCCTGCATCATCATGATTTT 60.545 45.455 5.16 0.00 42.15 1.82
1590 1782 0.248289 GCACTGCCATTGCCAAGAAT 59.752 50.000 0.00 0.00 36.33 2.40
1695 1887 1.157276 AGGTGGTGAGTCTGGAGCT 59.843 57.895 0.00 0.00 0.00 4.09
1726 1918 6.894339 AAAATTGGTGTTGACTAGTAAGGG 57.106 37.500 0.00 0.00 0.00 3.95
1762 1962 4.450082 TGTTCGTAGCTGTGTGTGATAT 57.550 40.909 0.00 0.00 0.00 1.63
1817 2019 6.950619 AGATTTTCTTTGAAGCTAATCAGGGT 59.049 34.615 14.40 0.00 32.63 4.34
1819 2021 9.947669 CATAGATTTTCTTTGAAGCTAATCAGG 57.052 33.333 14.40 0.00 32.63 3.86
1877 2083 9.937876 CCAACTATATATGGGAGAAGGATACTA 57.062 37.037 0.80 0.00 38.57 1.82
1878 2084 8.410623 ACCAACTATATATGGGAGAAGGATACT 58.589 37.037 7.20 0.00 46.10 2.12
1879 2085 8.611051 ACCAACTATATATGGGAGAAGGATAC 57.389 38.462 7.20 0.00 41.17 2.24
1918 2125 4.814771 GGATGGAAATTCTGTAGTTACGGG 59.185 45.833 0.00 0.00 33.41 5.28
1919 2126 5.293569 GTGGATGGAAATTCTGTAGTTACGG 59.706 44.000 0.00 0.00 0.00 4.02
1934 2141 3.282021 GCTTATCAGCTTGTGGATGGAA 58.718 45.455 0.00 0.00 43.51 3.53
1962 2266 3.633525 ACATATGCTTGGCACCAACTATG 59.366 43.478 1.58 14.50 43.04 2.23
1965 2269 2.220653 ACATATGCTTGGCACCAACT 57.779 45.000 1.58 0.00 43.04 3.16
1966 2270 3.278574 TCTACATATGCTTGGCACCAAC 58.721 45.455 1.58 0.00 43.04 3.77
1967 2271 3.643199 TCTACATATGCTTGGCACCAA 57.357 42.857 1.58 1.46 43.04 3.67
1968 2272 3.278574 GTTCTACATATGCTTGGCACCA 58.721 45.455 1.58 0.00 43.04 4.17
1970 2274 3.941483 AGTGTTCTACATATGCTTGGCAC 59.059 43.478 1.58 7.32 43.04 5.01
1971 2275 4.220693 AGTGTTCTACATATGCTTGGCA 57.779 40.909 1.58 0.00 44.86 4.92
1972 2276 5.123820 TCAAAGTGTTCTACATATGCTTGGC 59.876 40.000 1.58 0.00 0.00 4.52
1973 2277 6.741992 TCAAAGTGTTCTACATATGCTTGG 57.258 37.500 1.58 0.00 0.00 3.61
1974 2278 7.810658 ACTTCAAAGTGTTCTACATATGCTTG 58.189 34.615 1.58 0.00 37.98 4.01
1976 2280 7.986085 AACTTCAAAGTGTTCTACATATGCT 57.014 32.000 1.58 0.00 39.66 3.79
1977 2281 8.289618 TCAAACTTCAAAGTGTTCTACATATGC 58.710 33.333 1.58 0.00 39.66 3.14
1980 2284 8.617809 GGTTCAAACTTCAAAGTGTTCTACATA 58.382 33.333 0.00 0.00 39.66 2.29
1981 2285 7.480810 GGTTCAAACTTCAAAGTGTTCTACAT 58.519 34.615 0.00 0.00 39.66 2.29
1982 2286 6.402766 CGGTTCAAACTTCAAAGTGTTCTACA 60.403 38.462 0.00 0.00 39.66 2.74
1983 2287 5.963586 CGGTTCAAACTTCAAAGTGTTCTAC 59.036 40.000 0.00 0.00 39.66 2.59
1993 2297 3.830744 TCTCCTCGGTTCAAACTTCAA 57.169 42.857 0.00 0.00 0.00 2.69
1998 2302 3.318886 GAGACTTCTCCTCGGTTCAAAC 58.681 50.000 0.00 0.00 37.02 2.93
2007 2311 1.682684 TGGGCCGAGACTTCTCCTC 60.683 63.158 0.00 0.00 39.79 3.71
2008 2312 1.985116 GTGGGCCGAGACTTCTCCT 60.985 63.158 0.00 0.00 39.79 3.69
2009 2313 1.545706 AAGTGGGCCGAGACTTCTCC 61.546 60.000 7.45 0.00 39.79 3.71
2010 2314 0.321996 AAAGTGGGCCGAGACTTCTC 59.678 55.000 12.42 0.00 39.55 2.87
2011 2315 1.640917 TAAAGTGGGCCGAGACTTCT 58.359 50.000 12.42 7.13 31.02 2.85
2020 2324 5.405935 AAAGACATCAATTAAAGTGGGCC 57.594 39.130 0.00 0.00 0.00 5.80
2037 2341 6.650807 TCATGGTCTGTTGATGACTTAAAGAC 59.349 38.462 0.00 0.00 35.04 3.01
2041 2345 7.448161 ACAATTCATGGTCTGTTGATGACTTAA 59.552 33.333 0.00 0.00 35.04 1.85
2042 2346 6.942005 ACAATTCATGGTCTGTTGATGACTTA 59.058 34.615 0.00 0.00 35.04 2.24
2061 2366 9.426837 TGAAAATTTCAGGAATCATCACAATTC 57.573 29.630 4.03 0.00 34.08 2.17
2250 2555 2.824041 CATCCGGGCCCGAACAAG 60.824 66.667 45.44 27.72 42.83 3.16
2370 2705 7.919621 AGCCACGTATAAATAAGAGTTCAGTAC 59.080 37.037 0.00 0.00 0.00 2.73
2529 2864 4.811364 GCAGCCCCAGGGAAGAGC 62.811 72.222 7.25 0.69 37.50 4.09
2599 2934 5.241662 AGAATTCTGCTGTAGTTTCAGGAC 58.758 41.667 7.30 0.00 36.12 3.85
2621 2956 8.186821 GGGTCAATGTTTGATTCTCAATCTAAG 58.813 37.037 0.00 0.00 42.47 2.18
2718 3054 4.160814 CCATCAAGAATCAGGAAATGCCAA 59.839 41.667 0.00 0.00 40.02 4.52
2723 3059 7.729124 ATCAAACCATCAAGAATCAGGAAAT 57.271 32.000 0.00 0.00 0.00 2.17
2876 3215 6.020440 GCGTGAACCATGATCAATAACAATTG 60.020 38.462 3.24 3.24 0.00 2.32
3113 3455 4.509970 GGGTTTGCAAACTGTAATTTGTCC 59.490 41.667 34.39 21.81 40.92 4.02
3312 3683 3.403038 TCAAGTTGGTAAAGCAGAGAGC 58.597 45.455 2.34 0.00 46.19 4.09
3313 3684 6.377327 TTTTCAAGTTGGTAAAGCAGAGAG 57.623 37.500 2.34 0.00 0.00 3.20
3314 3685 6.959639 ATTTTCAAGTTGGTAAAGCAGAGA 57.040 33.333 2.34 0.00 0.00 3.10
3315 3686 9.185192 CTAAATTTTCAAGTTGGTAAAGCAGAG 57.815 33.333 2.34 0.00 0.00 3.35
3316 3687 7.651704 GCTAAATTTTCAAGTTGGTAAAGCAGA 59.348 33.333 2.34 0.00 0.00 4.26
3317 3688 7.653311 AGCTAAATTTTCAAGTTGGTAAAGCAG 59.347 33.333 2.34 4.81 0.00 4.24
3318 3689 7.496747 AGCTAAATTTTCAAGTTGGTAAAGCA 58.503 30.769 2.34 0.00 0.00 3.91
3319 3690 7.946655 AGCTAAATTTTCAAGTTGGTAAAGC 57.053 32.000 2.34 4.47 0.00 3.51
3324 3695 9.077885 TCTGATTAGCTAAATTTTCAAGTTGGT 57.922 29.630 10.85 0.00 0.00 3.67
3337 3708 7.786030 AGACTAGCATTGTCTGATTAGCTAAA 58.214 34.615 10.85 0.00 42.46 1.85
3352 3723 8.049117 TGGATATTTTGTCTTGAGACTAGCATT 58.951 33.333 12.00 0.00 44.99 3.56
3386 3758 4.682778 TGGCTGGGATGTATAGTAACAC 57.317 45.455 0.00 0.00 30.75 3.32
3439 3814 9.807921 AATTTTCAGAAGTCTATGGGAACTTAA 57.192 29.630 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.