Multiple sequence alignment - TraesCS5D01G297300

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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 TraesCS5D01G297300 chr5D 100.000 2613 0 0 1 2613 394164375 394161763 0.000000e+00 4826
1 TraesCS5D01G297300 chr5D 90.784 510 34 3 2116 2613 421912345 421912853 0.000000e+00 669
2 TraesCS5D01G297300 chr5D 86.400 125 13 2 1349 1469 394280610 394280486 1.630000e-27 134
3 TraesCS5D01G297300 chr5B 85.981 1284 93 41 405 1646 474048617 474047379 0.000000e+00 1293
4 TraesCS5D01G297300 chr5B 89.354 263 11 11 148 404 474049055 474048804 5.430000e-82 315
5 TraesCS5D01G297300 chr5B 84.507 213 11 7 1925 2116 474047111 474046900 9.540000e-45 191
6 TraesCS5D01G297300 chr5B 83.854 192 17 8 1643 1824 474047352 474047165 1.240000e-38 171
7 TraesCS5D01G297300 chr5A 87.273 935 55 34 1 892 496136351 496135438 0.000000e+00 1009
8 TraesCS5D01G297300 chr5A 88.331 797 46 26 930 1697 496135350 496134572 0.000000e+00 913
9 TraesCS5D01G297300 chr5A 88.078 411 40 5 2201 2611 413408632 413408231 1.820000e-131 479
10 TraesCS5D01G297300 chr7D 93.976 498 25 2 2116 2613 320286022 320285530 0.000000e+00 749
11 TraesCS5D01G297300 chr7D 91.650 503 37 1 2116 2613 342898656 342899158 0.000000e+00 691
12 TraesCS5D01G297300 chr7D 78.212 358 44 29 1078 1428 489299590 489299920 5.700000e-47 198
13 TraesCS5D01G297300 chr7D 76.364 385 53 27 1078 1455 484068735 484069088 3.460000e-39 172
14 TraesCS5D01G297300 chr1D 93.151 511 23 1 2115 2613 250741387 250740877 0.000000e+00 739
15 TraesCS5D01G297300 chr1D 89.412 255 21 2 2115 2369 204480145 204480393 1.510000e-82 316
16 TraesCS5D01G297300 chr6D 93.137 510 23 4 2116 2613 47269891 47270400 0.000000e+00 737
17 TraesCS5D01G297300 chrUn 92.549 510 25 2 2116 2613 115109769 115110277 0.000000e+00 719
18 TraesCS5D01G297300 chr3D 92.353 510 27 1 2116 2613 63764099 63763590 0.000000e+00 715
19 TraesCS5D01G297300 chr3D 92.157 510 28 4 2116 2613 161914303 161914812 0.000000e+00 710
20 TraesCS5D01G297300 chr3D 90.613 522 25 1 2116 2613 22360999 22361520 0.000000e+00 671
21 TraesCS5D01G297300 chr3D 90.204 490 28 2 2136 2613 479617279 479616798 2.860000e-174 621
22 TraesCS5D01G297300 chr4D 91.423 513 32 4 2113 2613 406229367 406229879 0.000000e+00 693
23 TraesCS5D01G297300 chr4D 76.676 373 44 29 1087 1428 437818854 437818494 1.610000e-37 167
24 TraesCS5D01G297300 chr4B 91.020 490 30 4 2116 2605 169600092 169600567 0.000000e+00 649
25 TraesCS5D01G297300 chr4B 76.567 367 44 27 1088 1424 540726444 540726090 2.080000e-36 163
26 TraesCS5D01G297300 chr7A 77.690 381 49 29 1083 1454 551540226 551540579 1.590000e-47 200
27 TraesCS5D01G297300 chr7B 77.225 382 51 29 1083 1455 509732855 509733209 9.540000e-45 191
28 TraesCS5D01G297300 chr4A 77.309 379 42 30 1088 1435 30286895 30287260 1.600000e-42 183


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 TraesCS5D01G297300 chr5D 394161763 394164375 2612 True 4826.0 4826 100.000 1 2613 1 chr5D.!!$R1 2612
1 TraesCS5D01G297300 chr5D 421912345 421912853 508 False 669.0 669 90.784 2116 2613 1 chr5D.!!$F1 497
2 TraesCS5D01G297300 chr5B 474046900 474049055 2155 True 492.5 1293 85.924 148 2116 4 chr5B.!!$R1 1968
3 TraesCS5D01G297300 chr5A 496134572 496136351 1779 True 961.0 1009 87.802 1 1697 2 chr5A.!!$R2 1696
4 TraesCS5D01G297300 chr7D 342898656 342899158 502 False 691.0 691 91.650 2116 2613 1 chr7D.!!$F1 497
5 TraesCS5D01G297300 chr1D 250740877 250741387 510 True 739.0 739 93.151 2115 2613 1 chr1D.!!$R1 498
6 TraesCS5D01G297300 chr6D 47269891 47270400 509 False 737.0 737 93.137 2116 2613 1 chr6D.!!$F1 497
7 TraesCS5D01G297300 chrUn 115109769 115110277 508 False 719.0 719 92.549 2116 2613 1 chrUn.!!$F1 497
8 TraesCS5D01G297300 chr3D 63763590 63764099 509 True 715.0 715 92.353 2116 2613 1 chr3D.!!$R1 497
9 TraesCS5D01G297300 chr3D 161914303 161914812 509 False 710.0 710 92.157 2116 2613 1 chr3D.!!$F2 497
10 TraesCS5D01G297300 chr3D 22360999 22361520 521 False 671.0 671 90.613 2116 2613 1 chr3D.!!$F1 497
11 TraesCS5D01G297300 chr4D 406229367 406229879 512 False 693.0 693 91.423 2113 2613 1 chr4D.!!$F1 500

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
58 59 0.038526 GAAGTCCGAACTCCGAAGCA 60.039 55.0 0.0 0.0 41.76 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 2236 0.108019 GAAGGAAACCTCACCCACGT 59.892 55.0 0.0 0.0 30.89 4.49 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.721718 GGCATTTCTTCGGTCTGTCG 59.278 55.000 0.00 0.00 0.00 4.35
34 35 2.589798 TTTCTTCGGTCTGTCGTTGT 57.410 45.000 0.00 0.00 0.00 3.32
39 40 4.046462 TCTTCGGTCTGTCGTTGTTAAAG 58.954 43.478 0.00 0.00 0.00 1.85
45 46 4.210746 GGTCTGTCGTTGTTAAAGAAGTCC 59.789 45.833 0.00 0.00 0.00 3.85
49 50 4.268405 TGTCGTTGTTAAAGAAGTCCGAAC 59.732 41.667 0.00 0.00 0.00 3.95
50 51 4.505556 GTCGTTGTTAAAGAAGTCCGAACT 59.494 41.667 0.00 0.00 37.32 3.01
51 52 4.741676 TCGTTGTTAAAGAAGTCCGAACTC 59.258 41.667 0.00 0.00 33.48 3.01
52 53 4.084693 CGTTGTTAAAGAAGTCCGAACTCC 60.085 45.833 0.00 0.00 33.48 3.85
53 54 3.645884 TGTTAAAGAAGTCCGAACTCCG 58.354 45.455 0.00 0.00 33.48 4.63
54 55 3.318839 TGTTAAAGAAGTCCGAACTCCGA 59.681 43.478 0.00 0.00 41.76 4.55
55 56 4.202141 TGTTAAAGAAGTCCGAACTCCGAA 60.202 41.667 0.00 0.00 41.76 4.30
56 57 2.726832 AAGAAGTCCGAACTCCGAAG 57.273 50.000 0.00 0.00 41.76 3.79
57 58 0.244178 AGAAGTCCGAACTCCGAAGC 59.756 55.000 0.00 0.00 41.76 3.86
58 59 0.038526 GAAGTCCGAACTCCGAAGCA 60.039 55.000 0.00 0.00 41.76 3.91
59 60 0.391597 AAGTCCGAACTCCGAAGCAA 59.608 50.000 0.00 0.00 41.76 3.91
60 61 0.319641 AGTCCGAACTCCGAAGCAAC 60.320 55.000 0.00 0.00 41.76 4.17
61 62 0.599204 GTCCGAACTCCGAAGCAACA 60.599 55.000 0.00 0.00 41.76 3.33
65 66 2.607187 CGAACTCCGAAGCAACATAGT 58.393 47.619 0.00 0.00 41.76 2.12
76 77 1.618343 GCAACATAGTTGCCCAAACCT 59.382 47.619 20.85 0.00 39.85 3.50
98 99 4.235939 TGCAATTTTCGCTAGAGCAAAA 57.764 36.364 1.89 8.00 42.21 2.44
99 100 4.229096 TGCAATTTTCGCTAGAGCAAAAG 58.771 39.130 1.89 0.00 42.21 2.27
101 102 2.989422 TTTTCGCTAGAGCAAAAGCC 57.011 45.000 1.89 0.00 42.21 4.35
102 103 1.165270 TTTCGCTAGAGCAAAAGCCC 58.835 50.000 1.89 0.00 42.21 5.19
103 104 0.324943 TTCGCTAGAGCAAAAGCCCT 59.675 50.000 1.89 0.00 42.21 5.19
104 105 1.191535 TCGCTAGAGCAAAAGCCCTA 58.808 50.000 1.89 0.00 42.21 3.53
105 106 1.137086 TCGCTAGAGCAAAAGCCCTAG 59.863 52.381 1.89 2.16 42.21 3.02
106 107 1.134670 CGCTAGAGCAAAAGCCCTAGT 60.135 52.381 7.66 0.00 42.21 2.57
107 108 2.100916 CGCTAGAGCAAAAGCCCTAGTA 59.899 50.000 7.66 0.00 42.21 1.82
117 118 5.526479 GCAAAAGCCCTAGTACTACAATACC 59.474 44.000 0.00 0.00 0.00 2.73
125 129 7.708322 GCCCTAGTACTACAATACCTTTTGTAC 59.292 40.741 0.00 0.00 40.25 2.90
131 135 9.095065 GTACTACAATACCTTTTGTACTCCATG 57.905 37.037 0.00 0.00 40.25 3.66
133 137 6.817765 ACAATACCTTTTGTACTCCATGTG 57.182 37.500 0.00 0.00 38.04 3.21
145 149 2.490903 ACTCCATGTGCATTTTGAGAGC 59.509 45.455 11.65 0.00 0.00 4.09
161 168 5.046910 TGAGAGCAAAATTTCCATCGTTC 57.953 39.130 0.00 0.00 0.00 3.95
196 203 3.577667 TCCAACGTTTACGATAGGTGTG 58.422 45.455 9.53 0.00 43.02 3.82
197 204 3.005684 TCCAACGTTTACGATAGGTGTGT 59.994 43.478 9.53 0.00 43.02 3.72
212 219 7.277760 CGATAGGTGTGTTCACTCATTTGAATA 59.722 37.037 4.59 0.00 43.41 1.75
213 220 6.560253 AGGTGTGTTCACTCATTTGAATAC 57.440 37.500 5.96 5.96 43.96 1.89
214 221 6.299141 AGGTGTGTTCACTCATTTGAATACT 58.701 36.000 12.17 0.00 44.01 2.12
215 222 7.450074 AGGTGTGTTCACTCATTTGAATACTA 58.550 34.615 12.17 0.05 44.01 1.82
216 223 7.604164 AGGTGTGTTCACTCATTTGAATACTAG 59.396 37.037 12.17 0.00 44.01 2.57
217 224 7.387948 GGTGTGTTCACTCATTTGAATACTAGT 59.612 37.037 12.17 0.00 44.01 2.57
218 225 9.419297 GTGTGTTCACTCATTTGAATACTAGTA 57.581 33.333 4.77 4.77 44.01 1.82
258 265 0.526524 CGAGATTCCGAGCCACACTC 60.527 60.000 0.00 0.00 42.47 3.51
283 290 3.452474 GACACGAGAGCAGAAGCAATAT 58.548 45.455 0.00 0.00 45.49 1.28
355 369 1.226717 GCGACACCTCGGAGTCATC 60.227 63.158 12.80 1.90 40.53 2.92
498 703 3.906649 GCGACGACATGCAGCGAG 61.907 66.667 12.47 7.53 0.00 5.03
503 713 2.202743 GACATGCAGCGAGGCGTA 60.203 61.111 0.00 0.00 36.28 4.42
545 755 4.476410 GCGCAGTAAAAGCCCGCC 62.476 66.667 0.30 0.00 38.84 6.13
678 900 1.992834 TCCGGCCTTCCATACTGCA 60.993 57.895 0.00 0.00 0.00 4.41
681 904 1.453928 GGCCTTCCATACTGCACCC 60.454 63.158 0.00 0.00 0.00 4.61
683 906 1.227383 CCTTCCATACTGCACCCCC 59.773 63.158 0.00 0.00 0.00 5.40
705 938 4.615834 CTCTACCGCTCGCTCGCC 62.616 72.222 0.00 0.00 0.00 5.54
840 1076 3.306502 CCCCCGCTTCTCGCTATAAATAA 60.307 47.826 0.00 0.00 36.73 1.40
841 1077 3.678548 CCCCGCTTCTCGCTATAAATAAC 59.321 47.826 0.00 0.00 36.73 1.89
842 1078 4.557205 CCCGCTTCTCGCTATAAATAACT 58.443 43.478 0.00 0.00 36.73 2.24
843 1079 5.336213 CCCCGCTTCTCGCTATAAATAACTA 60.336 44.000 0.00 0.00 36.73 2.24
844 1080 5.572126 CCCGCTTCTCGCTATAAATAACTAC 59.428 44.000 0.00 0.00 36.73 2.73
845 1081 6.147581 CCGCTTCTCGCTATAAATAACTACA 58.852 40.000 0.00 0.00 36.73 2.74
846 1082 6.087820 CCGCTTCTCGCTATAAATAACTACAC 59.912 42.308 0.00 0.00 36.73 2.90
847 1083 6.183359 CGCTTCTCGCTATAAATAACTACACG 60.183 42.308 0.00 0.00 36.13 4.49
848 1084 6.398726 GCTTCTCGCTATAAATAACTACACGC 60.399 42.308 0.00 0.00 35.14 5.34
849 1085 6.063640 TCTCGCTATAAATAACTACACGCA 57.936 37.500 0.00 0.00 0.00 5.24
850 1086 5.911280 TCTCGCTATAAATAACTACACGCAC 59.089 40.000 0.00 0.00 0.00 5.34
851 1087 5.580661 TCGCTATAAATAACTACACGCACA 58.419 37.500 0.00 0.00 0.00 4.57
858 1097 0.673644 AACTACACGCACATCCAGCC 60.674 55.000 0.00 0.00 0.00 4.85
863 1102 4.790962 CGCACATCCAGCCAGCCT 62.791 66.667 0.00 0.00 0.00 4.58
892 1131 1.213926 ACCATTGGAGGAGCTTCCATC 59.786 52.381 10.37 0.00 46.22 3.51
896 1166 1.694169 GGAGGAGCTTCCATCCCCA 60.694 63.158 0.00 0.00 39.61 4.96
897 1167 1.529309 GAGGAGCTTCCATCCCCAC 59.471 63.158 5.21 0.00 39.61 4.61
900 1170 1.566298 GGAGCTTCCATCCCCACACT 61.566 60.000 0.00 0.00 36.28 3.55
926 1196 2.599578 CACCCCAGCTTGCTTGCT 60.600 61.111 0.00 0.00 45.18 3.91
932 1202 3.363351 AGCTTGCTTGCTGGCTTC 58.637 55.556 3.36 0.00 42.33 3.86
945 1235 3.261580 GCTGGCTTCTCTTCTTCTTCTC 58.738 50.000 0.00 0.00 0.00 2.87
946 1236 3.055891 GCTGGCTTCTCTTCTTCTTCTCT 60.056 47.826 0.00 0.00 0.00 3.10
947 1237 4.159506 GCTGGCTTCTCTTCTTCTTCTCTA 59.840 45.833 0.00 0.00 0.00 2.43
948 1238 5.679638 GCTGGCTTCTCTTCTTCTTCTCTAG 60.680 48.000 0.00 0.00 0.00 2.43
951 1241 5.450550 GGCTTCTCTTCTTCTTCTCTAGCTC 60.451 48.000 0.00 0.00 0.00 4.09
960 1250 6.964464 TCTTCTTCTCTAGCTCCTTCTCTAA 58.036 40.000 0.00 0.00 0.00 2.10
964 1254 5.043737 TCTCTAGCTCCTTCTCTAACTCC 57.956 47.826 0.00 0.00 0.00 3.85
974 1264 4.381505 CCTTCTCTAACTCCTTCTGTCTGC 60.382 50.000 0.00 0.00 0.00 4.26
975 1265 3.093057 TCTCTAACTCCTTCTGTCTGCC 58.907 50.000 0.00 0.00 0.00 4.85
976 1266 2.167487 CTCTAACTCCTTCTGTCTGCCC 59.833 54.545 0.00 0.00 0.00 5.36
977 1267 2.183679 CTAACTCCTTCTGTCTGCCCT 58.816 52.381 0.00 0.00 0.00 5.19
978 1268 0.689623 AACTCCTTCTGTCTGCCCTG 59.310 55.000 0.00 0.00 0.00 4.45
1069 1359 1.001378 GTGTGGTGTTCATCCTTGTGC 60.001 52.381 0.00 0.00 0.00 4.57
1079 1369 1.204704 CATCCTTGTGCTCGGTCTGTA 59.795 52.381 0.00 0.00 0.00 2.74
1159 1450 4.849329 CCACTACGACGAGCCGGC 62.849 72.222 21.89 21.89 0.00 6.13
1262 1559 3.673484 GCGCCCAAGAAGCAGCAA 61.673 61.111 0.00 0.00 32.54 3.91
1461 1767 1.686800 AAGGTACGTACGGCCCCAT 60.687 57.895 21.06 6.14 0.00 4.00
1487 1793 6.992063 AAGAATGTGTAATTACTGCTGGAG 57.008 37.500 16.33 0.00 0.00 3.86
1526 1833 7.513371 TTTTGTCGTAATGGTTGGAACTTAT 57.487 32.000 0.00 0.00 0.00 1.73
1537 1844 6.542821 TGGTTGGAACTTATTGACTGATCTT 58.457 36.000 0.00 0.00 0.00 2.40
1538 1845 7.004086 TGGTTGGAACTTATTGACTGATCTTT 58.996 34.615 0.00 0.00 0.00 2.52
1539 1846 7.505585 TGGTTGGAACTTATTGACTGATCTTTT 59.494 33.333 0.00 0.00 0.00 2.27
1540 1847 8.023706 GGTTGGAACTTATTGACTGATCTTTTC 58.976 37.037 0.00 0.00 0.00 2.29
1541 1848 7.364522 TGGAACTTATTGACTGATCTTTTCG 57.635 36.000 0.00 0.00 0.00 3.46
1627 1937 4.649705 TGAGCCGAACCCCTCCCA 62.650 66.667 0.00 0.00 0.00 4.37
1631 1941 4.506255 CCGAACCCCTCCCATGCC 62.506 72.222 0.00 0.00 0.00 4.40
1632 1942 3.411517 CGAACCCCTCCCATGCCT 61.412 66.667 0.00 0.00 0.00 4.75
1633 1943 2.276740 GAACCCCTCCCATGCCTG 59.723 66.667 0.00 0.00 0.00 4.85
1637 1947 4.064768 CCCTCCCATGCCTGCCAA 62.065 66.667 0.00 0.00 0.00 4.52
1638 1948 2.757099 CCTCCCATGCCTGCCAAC 60.757 66.667 0.00 0.00 0.00 3.77
1639 1949 3.136123 CTCCCATGCCTGCCAACG 61.136 66.667 0.00 0.00 0.00 4.10
1642 1952 4.738998 CCATGCCTGCCAACGGGA 62.739 66.667 0.00 0.00 46.41 5.14
1644 1954 2.361610 ATGCCTGCCAACGGGAAG 60.362 61.111 0.00 0.00 46.41 3.46
1676 2018 4.580167 TGCGTGTTTATACCGGAGTAGTAT 59.420 41.667 9.46 0.00 34.79 2.12
1678 2020 5.979517 GCGTGTTTATACCGGAGTAGTATTT 59.020 40.000 9.46 0.00 32.71 1.40
1679 2021 7.138736 GCGTGTTTATACCGGAGTAGTATTTA 58.861 38.462 9.46 0.00 32.71 1.40
1680 2022 7.113544 GCGTGTTTATACCGGAGTAGTATTTAC 59.886 40.741 9.46 0.00 32.71 2.01
1702 2053 9.921637 TTTACATTTTCACTTTCTCTTGTTGTT 57.078 25.926 0.00 0.00 0.00 2.83
1703 2054 7.816945 ACATTTTCACTTTCTCTTGTTGTTG 57.183 32.000 0.00 0.00 0.00 3.33
1704 2055 6.813152 ACATTTTCACTTTCTCTTGTTGTTGG 59.187 34.615 0.00 0.00 0.00 3.77
1705 2056 4.981806 TTCACTTTCTCTTGTTGTTGGG 57.018 40.909 0.00 0.00 0.00 4.12
1706 2057 3.963129 TCACTTTCTCTTGTTGTTGGGT 58.037 40.909 0.00 0.00 0.00 4.51
1707 2058 5.105567 TCACTTTCTCTTGTTGTTGGGTA 57.894 39.130 0.00 0.00 0.00 3.69
1708 2059 5.123227 TCACTTTCTCTTGTTGTTGGGTAG 58.877 41.667 0.00 0.00 0.00 3.18
1709 2060 4.881850 CACTTTCTCTTGTTGTTGGGTAGT 59.118 41.667 0.00 0.00 0.00 2.73
1710 2061 5.357032 CACTTTCTCTTGTTGTTGGGTAGTT 59.643 40.000 0.00 0.00 0.00 2.24
1711 2062 5.589050 ACTTTCTCTTGTTGTTGGGTAGTTC 59.411 40.000 0.00 0.00 0.00 3.01
1715 2066 4.957296 TCTTGTTGTTGGGTAGTTCTCTC 58.043 43.478 0.00 0.00 0.00 3.20
1725 2076 2.353579 GGTAGTTCTCTCTCTCTGCGAC 59.646 54.545 0.00 0.00 0.00 5.19
1733 2084 1.797933 CTCTCTGCGACGTTCGTGG 60.798 63.158 1.74 2.57 42.81 4.94
1736 2087 2.354188 CTGCGACGTTCGTGGTGA 60.354 61.111 1.74 0.00 42.81 4.02
1737 2088 1.733041 CTGCGACGTTCGTGGTGAT 60.733 57.895 1.74 0.00 42.81 3.06
1824 2175 1.196012 TGTATGATGTGGCGTGGGTA 58.804 50.000 0.00 0.00 0.00 3.69
1825 2176 1.555533 TGTATGATGTGGCGTGGGTAA 59.444 47.619 0.00 0.00 0.00 2.85
1826 2177 1.937899 GTATGATGTGGCGTGGGTAAC 59.062 52.381 0.00 0.00 0.00 2.50
1827 2178 0.326595 ATGATGTGGCGTGGGTAACA 59.673 50.000 0.00 0.00 39.74 2.41
1828 2179 0.604243 TGATGTGGCGTGGGTAACAC 60.604 55.000 0.00 0.00 46.78 3.32
1838 2189 2.629051 GTGGGTAACACTGGCTATGAC 58.371 52.381 0.00 0.00 46.72 3.06
1839 2190 1.557832 TGGGTAACACTGGCTATGACC 59.442 52.381 0.00 0.00 39.74 4.02
1840 2191 1.557832 GGGTAACACTGGCTATGACCA 59.442 52.381 0.00 0.00 36.72 4.02
1841 2192 2.172717 GGGTAACACTGGCTATGACCAT 59.827 50.000 0.00 0.00 37.44 3.55
1842 2193 3.371595 GGGTAACACTGGCTATGACCATT 60.372 47.826 0.00 0.00 37.44 3.16
1843 2194 4.270008 GGTAACACTGGCTATGACCATTT 58.730 43.478 0.00 0.00 39.54 2.32
1844 2195 4.335594 GGTAACACTGGCTATGACCATTTC 59.664 45.833 0.00 0.00 39.54 2.17
1845 2196 2.632377 ACACTGGCTATGACCATTTCG 58.368 47.619 0.00 0.00 39.54 3.46
1846 2197 2.236146 ACACTGGCTATGACCATTTCGA 59.764 45.455 0.00 0.00 39.54 3.71
1847 2198 2.868583 CACTGGCTATGACCATTTCGAG 59.131 50.000 0.00 0.00 39.54 4.04
1848 2199 1.869767 CTGGCTATGACCATTTCGAGC 59.130 52.381 0.00 0.00 39.54 5.03
1849 2200 1.486310 TGGCTATGACCATTTCGAGCT 59.514 47.619 0.00 0.00 36.48 4.09
1850 2201 2.092968 TGGCTATGACCATTTCGAGCTT 60.093 45.455 0.00 0.00 36.48 3.74
1851 2202 2.545946 GGCTATGACCATTTCGAGCTTC 59.454 50.000 0.00 0.00 36.48 3.86
1852 2203 3.462021 GCTATGACCATTTCGAGCTTCT 58.538 45.455 0.00 0.00 34.40 2.85
1853 2204 4.501571 GGCTATGACCATTTCGAGCTTCTA 60.502 45.833 0.00 0.00 36.48 2.10
1854 2205 4.446051 GCTATGACCATTTCGAGCTTCTAC 59.554 45.833 0.00 0.00 34.40 2.59
1855 2206 4.744795 ATGACCATTTCGAGCTTCTACT 57.255 40.909 0.00 0.00 0.00 2.57
1856 2207 4.111375 TGACCATTTCGAGCTTCTACTC 57.889 45.455 0.00 0.00 0.00 2.59
1857 2208 3.764434 TGACCATTTCGAGCTTCTACTCT 59.236 43.478 0.00 0.00 34.35 3.24
1858 2209 4.142359 TGACCATTTCGAGCTTCTACTCTC 60.142 45.833 0.00 0.00 34.35 3.20
1859 2210 4.020543 ACCATTTCGAGCTTCTACTCTCT 58.979 43.478 0.00 0.00 34.35 3.10
1860 2211 4.097286 ACCATTTCGAGCTTCTACTCTCTC 59.903 45.833 0.00 0.00 34.35 3.20
1861 2212 4.338118 CCATTTCGAGCTTCTACTCTCTCT 59.662 45.833 0.00 0.00 34.35 3.10
1862 2213 5.505654 CCATTTCGAGCTTCTACTCTCTCTC 60.506 48.000 0.00 0.00 34.35 3.20
1863 2214 4.481368 TTCGAGCTTCTACTCTCTCTCT 57.519 45.455 0.00 0.00 34.35 3.10
1864 2215 4.054780 TCGAGCTTCTACTCTCTCTCTC 57.945 50.000 0.00 0.00 34.35 3.20
1865 2216 3.704566 TCGAGCTTCTACTCTCTCTCTCT 59.295 47.826 0.00 0.00 34.35 3.10
1866 2217 4.051922 CGAGCTTCTACTCTCTCTCTCTC 58.948 52.174 0.00 0.00 34.35 3.20
1867 2218 4.202161 CGAGCTTCTACTCTCTCTCTCTCT 60.202 50.000 0.00 0.00 34.35 3.10
1868 2219 5.283457 AGCTTCTACTCTCTCTCTCTCTC 57.717 47.826 0.00 0.00 0.00 3.20
1869 2220 4.965532 AGCTTCTACTCTCTCTCTCTCTCT 59.034 45.833 0.00 0.00 0.00 3.10
1870 2221 5.069781 AGCTTCTACTCTCTCTCTCTCTCTC 59.930 48.000 0.00 0.00 0.00 3.20
1871 2222 5.069781 GCTTCTACTCTCTCTCTCTCTCTCT 59.930 48.000 0.00 0.00 0.00 3.10
1872 2223 6.716934 TTCTACTCTCTCTCTCTCTCTCTC 57.283 45.833 0.00 0.00 0.00 3.20
1873 2224 6.019656 TCTACTCTCTCTCTCTCTCTCTCT 57.980 45.833 0.00 0.00 0.00 3.10
1874 2225 6.065374 TCTACTCTCTCTCTCTCTCTCTCTC 58.935 48.000 0.00 0.00 0.00 3.20
1875 2226 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
1876 2227 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
1877 2228 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1878 2229 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1879 2230 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1880 2231 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1881 2232 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1882 2233 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
1883 2234 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
1884 2235 5.766590 TCTCTCTCTCTCTCTCTCTCTGTA 58.233 45.833 0.00 0.00 0.00 2.74
1885 2236 6.194967 TCTCTCTCTCTCTCTCTCTCTGTAA 58.805 44.000 0.00 0.00 0.00 2.41
1886 2237 6.096987 TCTCTCTCTCTCTCTCTCTCTGTAAC 59.903 46.154 0.00 0.00 0.00 2.50
1887 2238 5.006153 TCTCTCTCTCTCTCTCTGTAACG 57.994 47.826 0.00 0.00 0.00 3.18
1888 2239 4.464951 TCTCTCTCTCTCTCTCTGTAACGT 59.535 45.833 0.00 0.00 0.00 3.99
1889 2240 4.500127 TCTCTCTCTCTCTCTGTAACGTG 58.500 47.826 0.00 0.00 0.00 4.49
1890 2241 3.601435 TCTCTCTCTCTCTGTAACGTGG 58.399 50.000 0.00 0.00 0.00 4.94
1891 2242 2.680841 CTCTCTCTCTCTGTAACGTGGG 59.319 54.545 0.00 0.00 0.00 4.61
1892 2243 2.040012 TCTCTCTCTCTGTAACGTGGGT 59.960 50.000 0.00 0.00 0.00 4.51
1893 2244 2.160205 TCTCTCTCTGTAACGTGGGTG 58.840 52.381 0.00 0.00 0.00 4.61
1894 2245 2.160205 CTCTCTCTGTAACGTGGGTGA 58.840 52.381 0.00 0.00 0.00 4.02
1895 2246 2.160205 TCTCTCTGTAACGTGGGTGAG 58.840 52.381 0.00 0.00 0.00 3.51
1896 2247 1.202582 CTCTCTGTAACGTGGGTGAGG 59.797 57.143 0.00 0.00 0.00 3.86
1897 2248 0.966920 CTCTGTAACGTGGGTGAGGT 59.033 55.000 0.00 0.00 0.00 3.85
1898 2249 1.343465 CTCTGTAACGTGGGTGAGGTT 59.657 52.381 0.00 0.00 36.61 3.50
1899 2250 1.764134 TCTGTAACGTGGGTGAGGTTT 59.236 47.619 0.00 0.00 34.50 3.27
1900 2251 2.140717 CTGTAACGTGGGTGAGGTTTC 58.859 52.381 0.00 0.00 34.50 2.78
1901 2252 1.202675 TGTAACGTGGGTGAGGTTTCC 60.203 52.381 0.00 0.00 34.50 3.13
1907 2258 1.143073 GTGGGTGAGGTTTCCTTCTGT 59.857 52.381 0.00 0.00 31.76 3.41
1908 2259 1.142870 TGGGTGAGGTTTCCTTCTGTG 59.857 52.381 0.00 0.00 31.76 3.66
1936 2313 0.247460 CTCTGTGTTCATCAGCCCGA 59.753 55.000 0.00 0.00 33.48 5.14
1941 2318 0.391661 TGTTCATCAGCCCGAGAAGC 60.392 55.000 0.00 0.00 0.00 3.86
1948 2325 0.957395 CAGCCCGAGAAGCACAATGT 60.957 55.000 0.00 0.00 0.00 2.71
1949 2326 0.250901 AGCCCGAGAAGCACAATGTT 60.251 50.000 0.00 0.00 0.00 2.71
1954 2331 3.252215 CCCGAGAAGCACAATGTTTACAA 59.748 43.478 0.00 0.00 0.00 2.41
1955 2332 4.261405 CCCGAGAAGCACAATGTTTACAAA 60.261 41.667 0.00 0.00 0.00 2.83
2001 2385 2.071688 AACGAGCTCTCACATCACAC 57.928 50.000 12.85 0.00 0.00 3.82
2019 2411 0.671781 ACTGCATTGCACGAGAGGAC 60.672 55.000 7.38 0.00 33.79 3.85
2028 2420 3.733960 CGAGAGGACACGGCGACA 61.734 66.667 16.62 0.00 0.00 4.35
2036 2428 3.124921 CACGGCGACATTGGGTCC 61.125 66.667 16.62 0.00 43.95 4.46
2111 2509 0.829182 CAATAGGCAATGGGGGCTCC 60.829 60.000 0.00 0.00 43.38 4.70
2155 2553 7.562454 TTAACCTATGGACGAAATCAAATCC 57.438 36.000 0.00 0.00 0.00 3.01
2157 2555 3.498397 CCTATGGACGAAATCAAATCCCG 59.502 47.826 0.00 0.00 0.00 5.14
2171 2569 1.285280 ATCCCGGAATGAACTGTCCA 58.715 50.000 0.73 0.00 33.10 4.02
2201 2599 0.249953 TCACGCGGCTGACCTTTTTA 60.250 50.000 12.47 0.00 0.00 1.52
2209 2607 2.812011 GGCTGACCTTTTTATGTGACGT 59.188 45.455 0.00 0.00 0.00 4.34
2339 2761 0.175302 CCTGAGAGCTAGGCAGTGTG 59.825 60.000 8.57 0.00 0.00 3.82
2530 2952 2.165845 GTGTAACGCCTATCTGTGAGGT 59.834 50.000 0.00 0.00 36.37 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.455877 AGACCGAAGAAATGCCTTTTAGTG 59.544 41.667 0.00 0.00 0.00 2.74
30 31 4.084693 CGGAGTTCGGACTTCTTTAACAAC 60.085 45.833 0.00 0.00 35.88 3.32
34 35 4.553323 CTTCGGAGTTCGGACTTCTTTAA 58.447 43.478 0.00 0.00 35.88 1.52
39 40 0.038526 TGCTTCGGAGTTCGGACTTC 60.039 55.000 0.00 0.00 35.88 3.01
45 46 2.607187 ACTATGTTGCTTCGGAGTTCG 58.393 47.619 0.00 0.00 40.90 3.95
49 50 1.398390 GGCAACTATGTTGCTTCGGAG 59.602 52.381 27.12 0.00 44.36 4.63
50 51 1.448985 GGCAACTATGTTGCTTCGGA 58.551 50.000 27.12 0.00 44.36 4.55
51 52 0.451783 GGGCAACTATGTTGCTTCGG 59.548 55.000 27.12 0.00 44.36 4.30
52 53 1.164411 TGGGCAACTATGTTGCTTCG 58.836 50.000 27.12 0.00 44.36 3.79
53 54 3.317150 GTTTGGGCAACTATGTTGCTTC 58.683 45.455 27.12 20.99 44.36 3.86
54 55 2.037121 GGTTTGGGCAACTATGTTGCTT 59.963 45.455 27.12 0.00 44.36 3.91
55 56 1.618343 GGTTTGGGCAACTATGTTGCT 59.382 47.619 27.12 0.00 44.36 3.91
56 57 1.618343 AGGTTTGGGCAACTATGTTGC 59.382 47.619 22.50 22.50 44.22 4.17
57 58 3.652274 CAAGGTTTGGGCAACTATGTTG 58.348 45.455 6.12 6.12 35.46 3.33
58 59 2.037121 GCAAGGTTTGGGCAACTATGTT 59.963 45.455 0.00 0.00 35.46 2.71
59 60 1.618343 GCAAGGTTTGGGCAACTATGT 59.382 47.619 0.00 0.00 35.46 2.29
60 61 1.617850 TGCAAGGTTTGGGCAACTATG 59.382 47.619 0.00 0.00 35.46 2.23
61 62 2.008242 TGCAAGGTTTGGGCAACTAT 57.992 45.000 0.00 0.00 35.46 2.12
76 77 3.913548 TTGCTCTAGCGAAAATTGCAA 57.086 38.095 0.00 0.00 45.83 4.08
98 99 6.442885 ACAAAAGGTATTGTAGTACTAGGGCT 59.557 38.462 1.87 0.00 41.56 5.19
99 100 6.647229 ACAAAAGGTATTGTAGTACTAGGGC 58.353 40.000 1.87 0.00 41.56 5.19
103 104 9.532494 TGGAGTACAAAAGGTATTGTAGTACTA 57.468 33.333 14.88 0.00 44.85 1.82
104 105 8.426569 TGGAGTACAAAAGGTATTGTAGTACT 57.573 34.615 14.88 0.00 44.85 2.73
105 106 9.095065 CATGGAGTACAAAAGGTATTGTAGTAC 57.905 37.037 9.35 9.35 45.09 2.73
106 107 8.818860 ACATGGAGTACAAAAGGTATTGTAGTA 58.181 33.333 7.34 0.00 45.09 1.82
107 108 7.606456 CACATGGAGTACAAAAGGTATTGTAGT 59.394 37.037 7.13 7.13 46.78 2.73
117 118 6.215121 TCAAAATGCACATGGAGTACAAAAG 58.785 36.000 0.00 0.00 0.00 2.27
125 129 2.490509 TGCTCTCAAAATGCACATGGAG 59.509 45.455 0.00 0.00 0.00 3.86
145 149 8.289618 TCTTAACTCTGAACGATGGAAATTTTG 58.710 33.333 0.00 0.00 0.00 2.44
161 168 3.589988 ACGTTGGATGCTCTTAACTCTG 58.410 45.455 0.00 0.00 0.00 3.35
212 219 6.042638 TGTGTTACTCGAGGTAGTACTAGT 57.957 41.667 18.41 0.00 31.73 2.57
213 220 6.974932 TTGTGTTACTCGAGGTAGTACTAG 57.025 41.667 18.41 0.00 31.73 2.57
214 221 6.540189 GGATTGTGTTACTCGAGGTAGTACTA 59.460 42.308 18.41 0.00 31.73 1.82
215 222 5.356470 GGATTGTGTTACTCGAGGTAGTACT 59.644 44.000 18.41 0.00 31.73 2.73
216 223 5.576895 GGATTGTGTTACTCGAGGTAGTAC 58.423 45.833 18.41 9.44 31.73 2.73
217 224 4.333649 CGGATTGTGTTACTCGAGGTAGTA 59.666 45.833 18.41 0.00 0.00 1.82
218 225 3.128242 CGGATTGTGTTACTCGAGGTAGT 59.872 47.826 18.41 0.00 0.00 2.73
267 274 7.644986 ACGTATTAATATTGCTTCTGCTCTC 57.355 36.000 0.00 0.00 40.48 3.20
283 290 5.289193 CCGCAAGCTTTGTACTACGTATTAA 59.711 40.000 0.00 0.00 0.00 1.40
495 700 0.989890 CGTTCCTTTTCTACGCCTCG 59.010 55.000 0.00 0.00 0.00 4.63
496 701 1.356938 CCGTTCCTTTTCTACGCCTC 58.643 55.000 0.00 0.00 34.16 4.70
497 702 0.672711 GCCGTTCCTTTTCTACGCCT 60.673 55.000 0.00 0.00 34.16 5.52
498 703 1.792301 GCCGTTCCTTTTCTACGCC 59.208 57.895 0.00 0.00 34.16 5.68
503 713 2.671963 GGGCGCCGTTCCTTTTCT 60.672 61.111 22.54 0.00 0.00 2.52
545 755 4.323477 TGGTCCCTCGTTTGGCGG 62.323 66.667 0.00 0.00 41.72 6.13
577 787 2.433318 GCAGAGCGGTGTCTGTCC 60.433 66.667 0.00 0.00 45.07 4.02
681 904 1.894756 CGAGCGGTAGAGAGAGGGG 60.895 68.421 0.00 0.00 0.00 4.79
683 906 1.503818 GAGCGAGCGGTAGAGAGAGG 61.504 65.000 0.00 0.00 0.00 3.69
705 938 1.574428 CGGCGAGGTTTGACAAAGG 59.426 57.895 0.00 0.00 0.00 3.11
824 1060 6.635641 TGCGTGTAGTTATTTATAGCGAGAAG 59.364 38.462 0.00 0.00 0.00 2.85
840 1076 1.079127 GGCTGGATGTGCGTGTAGT 60.079 57.895 0.00 0.00 0.00 2.73
841 1077 1.079197 TGGCTGGATGTGCGTGTAG 60.079 57.895 0.00 0.00 0.00 2.74
842 1078 1.079197 CTGGCTGGATGTGCGTGTA 60.079 57.895 0.00 0.00 0.00 2.90
843 1079 2.359107 CTGGCTGGATGTGCGTGT 60.359 61.111 0.00 0.00 0.00 4.49
844 1080 3.807538 GCTGGCTGGATGTGCGTG 61.808 66.667 0.00 0.00 0.00 5.34
846 1082 4.790962 AGGCTGGCTGGATGTGCG 62.791 66.667 1.67 0.00 0.00 5.34
847 1083 3.138798 CAGGCTGGCTGGATGTGC 61.139 66.667 22.32 0.00 0.00 4.57
848 1084 3.138798 GCAGGCTGGCTGGATGTG 61.139 66.667 29.23 7.39 0.00 3.21
849 1085 4.437587 GGCAGGCTGGCTGGATGT 62.438 66.667 31.42 0.00 40.14 3.06
850 1086 4.435970 TGGCAGGCTGGCTGGATG 62.436 66.667 36.29 8.48 44.10 3.51
851 1087 4.124943 CTGGCAGGCTGGCTGGAT 62.125 66.667 36.29 0.00 44.10 3.41
858 1097 4.980702 TGGTTGGCTGGCAGGCTG 62.981 66.667 36.29 10.94 41.96 4.85
872 1111 2.791253 TGGAAGCTCCTCCAATGGT 58.209 52.632 4.57 0.00 42.69 3.55
885 1124 0.035056 GGTCAGTGTGGGGATGGAAG 60.035 60.000 0.00 0.00 0.00 3.46
909 1179 2.599578 AGCAAGCAAGCTGGGGTG 60.600 61.111 1.81 0.00 44.66 4.61
926 1196 4.159506 GCTAGAGAAGAAGAAGAGAAGCCA 59.840 45.833 0.00 0.00 0.00 4.75
927 1197 4.402474 AGCTAGAGAAGAAGAAGAGAAGCC 59.598 45.833 0.00 0.00 0.00 4.35
928 1198 5.450550 GGAGCTAGAGAAGAAGAAGAGAAGC 60.451 48.000 0.00 0.00 0.00 3.86
929 1199 5.888161 AGGAGCTAGAGAAGAAGAAGAGAAG 59.112 44.000 0.00 0.00 0.00 2.85
930 1200 5.826643 AGGAGCTAGAGAAGAAGAAGAGAA 58.173 41.667 0.00 0.00 0.00 2.87
932 1202 5.888161 AGAAGGAGCTAGAGAAGAAGAAGAG 59.112 44.000 0.00 0.00 0.00 2.85
945 1235 5.299279 CAGAAGGAGTTAGAGAAGGAGCTAG 59.701 48.000 0.00 0.00 0.00 3.42
946 1236 5.197451 CAGAAGGAGTTAGAGAAGGAGCTA 58.803 45.833 0.00 0.00 0.00 3.32
947 1237 4.023291 CAGAAGGAGTTAGAGAAGGAGCT 58.977 47.826 0.00 0.00 0.00 4.09
948 1238 3.767131 ACAGAAGGAGTTAGAGAAGGAGC 59.233 47.826 0.00 0.00 0.00 4.70
951 1241 4.381505 GCAGACAGAAGGAGTTAGAGAAGG 60.382 50.000 0.00 0.00 0.00 3.46
960 1250 1.835927 GCAGGGCAGACAGAAGGAGT 61.836 60.000 0.00 0.00 0.00 3.85
964 1254 2.045536 GGGCAGGGCAGACAGAAG 60.046 66.667 0.00 0.00 0.00 2.85
992 1282 0.390860 CCTTACCTCCATCTGGCTCG 59.609 60.000 0.00 0.00 34.44 5.03
1069 1359 2.271800 GCAAGACCAATACAGACCGAG 58.728 52.381 0.00 0.00 0.00 4.63
1441 1738 2.510012 GGGCCGTACGTACCTTGC 60.510 66.667 19.67 18.02 0.00 4.01
1442 1739 1.963464 ATGGGGCCGTACGTACCTTG 61.963 60.000 19.67 9.75 0.00 3.61
1461 1767 8.856153 TCCAGCAGTAATTACACATTCTTTTA 57.144 30.769 17.65 0.00 0.00 1.52
1487 1793 4.741185 ACGACAAAAATTAAAGAAACCCGC 59.259 37.500 0.00 0.00 0.00 6.13
1526 1833 6.429791 TCAAACAACGAAAAGATCAGTCAA 57.570 33.333 0.00 0.00 0.00 3.18
1537 1844 1.066303 AGCCGCATTCAAACAACGAAA 59.934 42.857 0.00 0.00 0.00 3.46
1538 1845 0.665835 AGCCGCATTCAAACAACGAA 59.334 45.000 0.00 0.00 0.00 3.85
1539 1846 0.665835 AAGCCGCATTCAAACAACGA 59.334 45.000 0.00 0.00 0.00 3.85
1540 1847 0.777631 CAAGCCGCATTCAAACAACG 59.222 50.000 0.00 0.00 0.00 4.10
1541 1848 1.522258 CACAAGCCGCATTCAAACAAC 59.478 47.619 0.00 0.00 0.00 3.32
1614 1921 4.506255 GGCATGGGAGGGGTTCGG 62.506 72.222 0.00 0.00 0.00 4.30
1616 1923 2.276740 CAGGCATGGGAGGGGTTC 59.723 66.667 0.00 0.00 0.00 3.62
1621 1931 2.757099 GTTGGCAGGCATGGGAGG 60.757 66.667 0.00 0.00 0.00 4.30
1627 1937 2.361610 CTTCCCGTTGGCAGGCAT 60.362 61.111 0.00 0.00 0.00 4.40
1644 1954 1.644786 ATAAACACGCAGCTTCCCGC 61.645 55.000 0.00 0.00 39.57 6.13
1650 1992 0.533491 TCCGGTATAAACACGCAGCT 59.467 50.000 0.00 0.00 0.00 4.24
1676 2018 9.921637 AACAACAAGAGAAAGTGAAAATGTAAA 57.078 25.926 0.00 0.00 0.00 2.01
1678 2020 7.973388 CCAACAACAAGAGAAAGTGAAAATGTA 59.027 33.333 0.00 0.00 0.00 2.29
1679 2021 6.813152 CCAACAACAAGAGAAAGTGAAAATGT 59.187 34.615 0.00 0.00 0.00 2.71
1680 2022 6.256321 CCCAACAACAAGAGAAAGTGAAAATG 59.744 38.462 0.00 0.00 0.00 2.32
1701 2052 3.093057 GCAGAGAGAGAGAACTACCCAA 58.907 50.000 0.00 0.00 0.00 4.12
1702 2053 2.729194 GCAGAGAGAGAGAACTACCCA 58.271 52.381 0.00 0.00 0.00 4.51
1703 2054 1.673920 CGCAGAGAGAGAGAACTACCC 59.326 57.143 0.00 0.00 0.00 3.69
1704 2055 2.353579 GTCGCAGAGAGAGAGAACTACC 59.646 54.545 0.00 0.00 36.95 3.18
1705 2056 2.029970 CGTCGCAGAGAGAGAGAACTAC 59.970 54.545 0.00 0.00 36.95 2.73
1706 2057 2.272678 CGTCGCAGAGAGAGAGAACTA 58.727 52.381 0.00 0.00 36.95 2.24
1707 2058 1.083489 CGTCGCAGAGAGAGAGAACT 58.917 55.000 0.00 0.00 36.95 3.01
1708 2059 0.800012 ACGTCGCAGAGAGAGAGAAC 59.200 55.000 0.00 0.00 36.95 3.01
1709 2060 1.465387 GAACGTCGCAGAGAGAGAGAA 59.535 52.381 0.00 0.00 36.95 2.87
1710 2061 1.080298 GAACGTCGCAGAGAGAGAGA 58.920 55.000 0.00 0.00 36.95 3.10
1711 2062 0.247497 CGAACGTCGCAGAGAGAGAG 60.247 60.000 0.00 0.00 36.95 3.20
1715 2066 1.797933 CCACGAACGTCGCAGAGAG 60.798 63.158 7.21 0.00 45.12 3.20
1725 2076 1.350193 CCAAGAGATCACCACGAACG 58.650 55.000 0.00 0.00 0.00 3.95
1733 2084 0.807496 GCCACAAGCCAAGAGATCAC 59.193 55.000 0.00 0.00 34.35 3.06
1736 2087 1.074405 TCTTGCCACAAGCCAAGAGAT 59.926 47.619 2.41 0.00 42.71 2.75
1737 2088 0.473755 TCTTGCCACAAGCCAAGAGA 59.526 50.000 2.41 0.00 42.71 3.10
1808 2159 0.326595 TGTTACCCACGCCACATCAT 59.673 50.000 0.00 0.00 0.00 2.45
1810 2161 2.168054 GTGTTACCCACGCCACATC 58.832 57.895 0.00 0.00 33.61 3.06
1824 2175 3.009723 CGAAATGGTCATAGCCAGTGTT 58.990 45.455 0.00 0.00 42.47 3.32
1825 2176 2.236146 TCGAAATGGTCATAGCCAGTGT 59.764 45.455 0.00 0.00 42.47 3.55
1826 2177 2.868583 CTCGAAATGGTCATAGCCAGTG 59.131 50.000 0.00 0.00 42.47 3.66
1827 2178 2.743183 GCTCGAAATGGTCATAGCCAGT 60.743 50.000 0.00 0.00 42.47 4.00
1828 2179 1.869767 GCTCGAAATGGTCATAGCCAG 59.130 52.381 0.00 0.00 42.47 4.85
1829 2180 1.486310 AGCTCGAAATGGTCATAGCCA 59.514 47.619 0.00 0.00 43.48 4.75
1830 2181 2.246719 AGCTCGAAATGGTCATAGCC 57.753 50.000 0.00 0.00 36.14 3.93
1831 2182 3.462021 AGAAGCTCGAAATGGTCATAGC 58.538 45.455 0.00 0.00 35.87 2.97
1832 2183 5.837437 AGTAGAAGCTCGAAATGGTCATAG 58.163 41.667 0.00 0.00 0.00 2.23
1833 2184 5.594725 AGAGTAGAAGCTCGAAATGGTCATA 59.405 40.000 0.00 0.00 40.26 2.15
1834 2185 4.404073 AGAGTAGAAGCTCGAAATGGTCAT 59.596 41.667 0.00 0.00 40.26 3.06
1835 2186 3.764434 AGAGTAGAAGCTCGAAATGGTCA 59.236 43.478 0.00 0.00 40.26 4.02
1836 2187 4.097286 AGAGAGTAGAAGCTCGAAATGGTC 59.903 45.833 0.00 0.00 40.26 4.02
1837 2188 4.020543 AGAGAGTAGAAGCTCGAAATGGT 58.979 43.478 0.00 0.00 40.26 3.55
1838 2189 4.338118 AGAGAGAGTAGAAGCTCGAAATGG 59.662 45.833 0.00 0.00 40.26 3.16
1839 2190 5.296780 AGAGAGAGAGTAGAAGCTCGAAATG 59.703 44.000 0.00 0.00 40.26 2.32
1840 2191 5.437060 AGAGAGAGAGTAGAAGCTCGAAAT 58.563 41.667 0.00 0.00 40.26 2.17
1841 2192 4.839121 AGAGAGAGAGTAGAAGCTCGAAA 58.161 43.478 0.00 0.00 40.26 3.46
1842 2193 4.161565 AGAGAGAGAGAGTAGAAGCTCGAA 59.838 45.833 0.00 0.00 40.26 3.71
1843 2194 3.704566 AGAGAGAGAGAGTAGAAGCTCGA 59.295 47.826 0.00 0.00 40.26 4.04
1844 2195 4.051922 GAGAGAGAGAGAGTAGAAGCTCG 58.948 52.174 0.00 0.00 40.26 5.03
1845 2196 5.069781 AGAGAGAGAGAGAGAGTAGAAGCTC 59.930 48.000 0.00 0.00 35.82 4.09
1846 2197 4.965532 AGAGAGAGAGAGAGAGTAGAAGCT 59.034 45.833 0.00 0.00 0.00 3.74
1847 2198 5.069781 AGAGAGAGAGAGAGAGAGTAGAAGC 59.930 48.000 0.00 0.00 0.00 3.86
1848 2199 6.549364 AGAGAGAGAGAGAGAGAGAGTAGAAG 59.451 46.154 0.00 0.00 0.00 2.85
1849 2200 6.436027 AGAGAGAGAGAGAGAGAGAGTAGAA 58.564 44.000 0.00 0.00 0.00 2.10
1850 2201 6.019656 AGAGAGAGAGAGAGAGAGAGTAGA 57.980 45.833 0.00 0.00 0.00 2.59
1851 2202 6.068010 AGAGAGAGAGAGAGAGAGAGAGTAG 58.932 48.000 0.00 0.00 0.00 2.57
1852 2203 6.019656 AGAGAGAGAGAGAGAGAGAGAGTA 57.980 45.833 0.00 0.00 0.00 2.59
1853 2204 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
1854 2205 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1855 2206 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1856 2207 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1857 2208 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1858 2209 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
1859 2210 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
1860 2211 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
1861 2212 4.614475 ACAGAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
1862 2213 6.276847 GTTACAGAGAGAGAGAGAGAGAGAG 58.723 48.000 0.00 0.00 0.00 3.20
1863 2214 5.163550 CGTTACAGAGAGAGAGAGAGAGAGA 60.164 48.000 0.00 0.00 0.00 3.10
1864 2215 5.043903 CGTTACAGAGAGAGAGAGAGAGAG 58.956 50.000 0.00 0.00 0.00 3.20
1865 2216 4.464951 ACGTTACAGAGAGAGAGAGAGAGA 59.535 45.833 0.00 0.00 0.00 3.10
1866 2217 4.566759 CACGTTACAGAGAGAGAGAGAGAG 59.433 50.000 0.00 0.00 0.00 3.20
1867 2218 4.500127 CACGTTACAGAGAGAGAGAGAGA 58.500 47.826 0.00 0.00 0.00 3.10
1868 2219 3.621268 CCACGTTACAGAGAGAGAGAGAG 59.379 52.174 0.00 0.00 0.00 3.20
1869 2220 3.601435 CCACGTTACAGAGAGAGAGAGA 58.399 50.000 0.00 0.00 0.00 3.10
1870 2221 2.680841 CCCACGTTACAGAGAGAGAGAG 59.319 54.545 0.00 0.00 0.00 3.20
1871 2222 2.040012 ACCCACGTTACAGAGAGAGAGA 59.960 50.000 0.00 0.00 0.00 3.10
1872 2223 2.162608 CACCCACGTTACAGAGAGAGAG 59.837 54.545 0.00 0.00 0.00 3.20
1873 2224 2.160205 CACCCACGTTACAGAGAGAGA 58.840 52.381 0.00 0.00 0.00 3.10
1874 2225 2.160205 TCACCCACGTTACAGAGAGAG 58.840 52.381 0.00 0.00 0.00 3.20
1875 2226 2.160205 CTCACCCACGTTACAGAGAGA 58.840 52.381 0.00 0.00 0.00 3.10
1876 2227 1.202582 CCTCACCCACGTTACAGAGAG 59.797 57.143 6.45 0.00 0.00 3.20
1877 2228 1.254026 CCTCACCCACGTTACAGAGA 58.746 55.000 6.45 0.00 0.00 3.10
1878 2229 0.966920 ACCTCACCCACGTTACAGAG 59.033 55.000 0.00 0.00 0.00 3.35
1879 2230 1.416243 AACCTCACCCACGTTACAGA 58.584 50.000 0.00 0.00 0.00 3.41
1880 2231 2.140717 GAAACCTCACCCACGTTACAG 58.859 52.381 0.00 0.00 0.00 2.74
1881 2232 1.202675 GGAAACCTCACCCACGTTACA 60.203 52.381 0.00 0.00 0.00 2.41
1882 2233 1.071228 AGGAAACCTCACCCACGTTAC 59.929 52.381 0.00 0.00 0.00 2.50
1883 2234 1.426751 AGGAAACCTCACCCACGTTA 58.573 50.000 0.00 0.00 0.00 3.18
1884 2235 0.549469 AAGGAAACCTCACCCACGTT 59.451 50.000 0.00 0.00 30.89 3.99
1885 2236 0.108019 GAAGGAAACCTCACCCACGT 59.892 55.000 0.00 0.00 30.89 4.49
1886 2237 0.396811 AGAAGGAAACCTCACCCACG 59.603 55.000 0.00 0.00 30.89 4.94
1887 2238 1.143073 ACAGAAGGAAACCTCACCCAC 59.857 52.381 0.00 0.00 30.89 4.61
1888 2239 1.142870 CACAGAAGGAAACCTCACCCA 59.857 52.381 0.00 0.00 30.89 4.51
1889 2240 1.143073 ACACAGAAGGAAACCTCACCC 59.857 52.381 0.00 0.00 30.89 4.61
1890 2241 2.222027 CACACAGAAGGAAACCTCACC 58.778 52.381 0.00 0.00 30.89 4.02
1891 2242 1.604278 GCACACAGAAGGAAACCTCAC 59.396 52.381 0.00 0.00 30.89 3.51
1892 2243 1.211703 TGCACACAGAAGGAAACCTCA 59.788 47.619 0.00 0.00 30.89 3.86
1893 2244 1.967319 TGCACACAGAAGGAAACCTC 58.033 50.000 0.00 0.00 30.89 3.85
1894 2245 2.024414 GTTGCACACAGAAGGAAACCT 58.976 47.619 0.00 0.00 33.87 3.50
1895 2246 1.748493 TGTTGCACACAGAAGGAAACC 59.252 47.619 0.00 0.00 0.00 3.27
1896 2247 3.316308 AGATGTTGCACACAGAAGGAAAC 59.684 43.478 7.58 0.00 39.40 2.78
1897 2248 3.554934 AGATGTTGCACACAGAAGGAAA 58.445 40.909 7.58 0.00 39.40 3.13
1898 2249 3.141398 GAGATGTTGCACACAGAAGGAA 58.859 45.455 7.58 0.00 39.40 3.36
1899 2250 2.369860 AGAGATGTTGCACACAGAAGGA 59.630 45.455 7.58 0.00 39.40 3.36
1900 2251 2.483106 CAGAGATGTTGCACACAGAAGG 59.517 50.000 7.58 0.00 39.40 3.46
1901 2252 3.059120 CACAGAGATGTTGCACACAGAAG 60.059 47.826 7.58 0.71 39.40 2.85
1907 2258 2.916640 TGAACACAGAGATGTTGCACA 58.083 42.857 0.00 0.00 42.89 4.57
1908 2259 3.499537 TGATGAACACAGAGATGTTGCAC 59.500 43.478 0.00 0.00 42.89 4.57
1921 2272 1.363744 CTTCTCGGGCTGATGAACAC 58.636 55.000 0.00 0.00 0.00 3.32
1922 2273 0.391661 GCTTCTCGGGCTGATGAACA 60.392 55.000 0.00 0.00 0.00 3.18
1936 2313 7.715657 TCAGAATTTGTAAACATTGTGCTTCT 58.284 30.769 0.00 0.00 0.00 2.85
1941 2318 9.467258 ACTTGATCAGAATTTGTAAACATTGTG 57.533 29.630 0.00 0.00 0.00 3.33
1954 2331 9.034544 GTTTGCAACTTAAACTTGATCAGAATT 57.965 29.630 0.00 0.00 35.65 2.17
1955 2332 8.196771 TGTTTGCAACTTAAACTTGATCAGAAT 58.803 29.630 0.00 0.00 38.50 2.40
2001 2385 0.671472 TGTCCTCTCGTGCAATGCAG 60.671 55.000 8.73 3.06 40.08 4.41
2019 2411 3.124921 GGACCCAATGTCGCCGTG 61.125 66.667 0.00 0.00 45.46 4.94
2028 2420 4.759205 GCCAAGCCCGGACCCAAT 62.759 66.667 0.73 0.00 0.00 3.16
2039 2431 2.555547 GGGATGCATACGGCCAAGC 61.556 63.158 2.24 0.44 43.89 4.01
2047 2439 2.030562 CGACCCCGGGATGCATAC 59.969 66.667 26.32 0.00 0.00 2.39
2155 2553 2.401583 TCATGGACAGTTCATTCCGG 57.598 50.000 0.00 0.00 34.24 5.14
2157 2555 7.396540 AATAGTTTCATGGACAGTTCATTCC 57.603 36.000 0.00 0.00 0.00 3.01
2278 2676 2.384653 TTTCGGATCACACGGGTGCA 62.385 55.000 14.50 2.22 44.87 4.57
2351 2773 0.682852 ACCACTAGTGCAACGCCTAA 59.317 50.000 17.86 0.00 45.86 2.69
2514 2936 1.066858 CAACACCTCACAGATAGGCGT 60.067 52.381 0.00 0.00 37.67 5.68


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

AutoCloner maintained by Alex Coulton.