Multiple sequence alignment - TraesCS6B01G099500

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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 TraesCS6B01G099500 chr6B 100.000 4585 0 0 1 4585 77390475 77395059 0.000000e+00 8468.0
1 TraesCS6B01G099500 chr6B 95.221 272 13 0 1 272 28468520 28468249 9.110000e-117 431.0
2 TraesCS6B01G099500 chr6B 87.821 312 21 6 283 578 617081286 617081596 2.620000e-92 350.0
3 TraesCS6B01G099500 chr6B 74.222 450 103 12 1848 2287 77763910 77763464 4.710000e-40 176.0
4 TraesCS6B01G099500 chr6B 77.273 286 61 4 1848 2131 82157552 82157835 1.020000e-36 165.0
5 TraesCS6B01G099500 chr6B 85.714 70 8 2 4062 4131 18150296 18150363 6.360000e-09 73.1
6 TraesCS6B01G099500 chrUn 93.255 2476 132 17 1448 3895 104476337 104478805 0.000000e+00 3615.0
7 TraesCS6B01G099500 chrUn 89.165 563 45 4 898 1452 104461205 104461759 0.000000e+00 688.0
8 TraesCS6B01G099500 chrUn 87.793 598 57 11 3991 4585 104479791 104480375 0.000000e+00 686.0
9 TraesCS6B01G099500 chrUn 75.794 913 147 43 2749 3626 102514571 102513698 1.200000e-105 394.0
10 TraesCS6B01G099500 chrUn 77.628 371 81 2 1853 2222 26704359 26703990 1.660000e-54 224.0
11 TraesCS6B01G099500 chrUn 76.738 374 81 6 1849 2219 27073949 27074319 2.160000e-48 204.0
12 TraesCS6B01G099500 chrUn 74.347 421 99 8 1875 2287 112649817 112650236 2.190000e-38 171.0
13 TraesCS6B01G099500 chrUn 84.615 117 15 1 702 815 104460937 104461053 3.750000e-21 113.0
14 TraesCS6B01G099500 chrUn 87.805 82 8 2 4062 4143 71218790 71218711 1.360000e-15 95.3
15 TraesCS6B01G099500 chr3B 98.837 688 8 0 1 688 225181579 225180892 0.000000e+00 1227.0
16 TraesCS6B01G099500 chr3B 95.588 272 12 0 1 272 751913221 751913492 1.960000e-118 436.0
17 TraesCS6B01G099500 chr3B 82.812 64 11 0 636 699 744555011 744554948 1.780000e-04 58.4
18 TraesCS6B01G099500 chr4B 97.059 272 8 0 1 272 95103010 95102739 4.180000e-125 459.0
19 TraesCS6B01G099500 chr4B 83.562 73 10 2 617 688 22266322 22266393 2.960000e-07 67.6
20 TraesCS6B01G099500 chr2B 97.059 272 8 0 1 272 547915291 547915562 4.180000e-125 459.0
21 TraesCS6B01G099500 chr7B 95.956 272 11 0 1 272 720637772 720637501 4.210000e-120 442.0
22 TraesCS6B01G099500 chr7B 95.588 272 11 1 1 272 561135915 561135645 7.040000e-118 435.0
23 TraesCS6B01G099500 chr7B 100.000 30 0 0 1703 1732 744130599 744130628 6.410000e-04 56.5
24 TraesCS6B01G099500 chr5A 95.956 272 11 0 1 272 453346280 453346009 4.210000e-120 442.0
25 TraesCS6B01G099500 chr5A 84.507 71 7 4 620 688 338222388 338222320 2.960000e-07 67.6
26 TraesCS6B01G099500 chr7A 95.221 272 13 0 1 272 97240979 97241250 9.110000e-117 431.0
27 TraesCS6B01G099500 chr7A 100.000 30 0 0 1703 1732 735995653 735995624 6.410000e-04 56.5
28 TraesCS6B01G099500 chr4D 87.766 376 33 5 278 643 274148048 274148420 1.180000e-115 427.0
29 TraesCS6B01G099500 chr6A 75.225 444 105 5 1847 2287 34030065 34030506 6.010000e-49 206.0
30 TraesCS6B01G099500 chr6A 77.860 271 60 0 1847 2117 45065377 45065107 7.890000e-38 169.0
31 TraesCS6B01G099500 chr6A 75.254 295 52 14 1843 2128 41828258 41827976 2.240000e-23 121.0
32 TraesCS6B01G099500 chr6D 75.592 422 92 8 1873 2287 28657428 28657011 1.010000e-46 198.0
33 TraesCS6B01G099500 chr6D 84.000 100 15 1 3812 3910 27550870 27550771 1.360000e-15 95.3
34 TraesCS6B01G099500 chr3A 79.577 142 21 6 735 872 645615765 645615628 1.360000e-15 95.3
35 TraesCS6B01G099500 chr3A 79.577 142 21 6 735 872 719622467 719622330 1.360000e-15 95.3
36 TraesCS6B01G099500 chr4A 82.143 112 17 3 764 873 715367009 715367119 4.880000e-15 93.5
37 TraesCS6B01G099500 chr2A 83.544 79 10 3 617 694 508089287 508089363 2.290000e-08 71.3
38 TraesCS6B01G099500 chr1B 87.037 54 5 2 636 688 634149195 634149143 4.950000e-05 60.2
39 TraesCS6B01G099500 chr1A 83.871 62 8 2 636 696 140372214 140372274 1.780000e-04 58.4
40 TraesCS6B01G099500 chr7D 100.000 30 0 0 659 688 135393127 135393156 6.410000e-04 56.5
41 TraesCS6B01G099500 chr7D 100.000 30 0 0 659 688 607565178 607565149 6.410000e-04 56.5
42 TraesCS6B01G099500 chr7D 100.000 30 0 0 1703 1732 632086840 632086869 6.410000e-04 56.5


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 TraesCS6B01G099500 chr6B 77390475 77395059 4584 False 8468.0 8468 100.000 1 4585 1 chr6B.!!$F2 4584
1 TraesCS6B01G099500 chrUn 104476337 104480375 4038 False 2150.5 3615 90.524 1448 4585 2 chrUn.!!$F4 3137
2 TraesCS6B01G099500 chrUn 104460937 104461759 822 False 400.5 688 86.890 702 1452 2 chrUn.!!$F3 750
3 TraesCS6B01G099500 chrUn 102513698 102514571 873 True 394.0 394 75.794 2749 3626 1 chrUn.!!$R3 877
4 TraesCS6B01G099500 chr3B 225180892 225181579 687 True 1227.0 1227 98.837 1 688 1 chr3B.!!$R1 687

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
337 338 0.389817 CCTCATCAACGACGAAGCCA 60.390 55.0 0.0 0.0 0.00 4.75 F
1637 1742 0.039346 GAGGCTCGGTCGGCTTATAC 60.039 60.0 0.0 0.0 40.21 1.47 F
1817 1922 0.250770 GTGGAGGGTGGTGTCCTTTC 60.251 60.0 0.0 0.0 34.21 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2292 2397 0.027455 CTTGACACGAAACGCTGCAA 59.973 50.0 0.00 0.0 0.00 4.08 R
2676 2792 2.630098 TCTGGCACTCCATATACAGCTC 59.370 50.0 0.00 0.0 42.51 4.09 R
3660 3809 2.415625 GCTCTCTTGCAATTGCCTTGAG 60.416 50.0 26.94 26.0 41.18 3.02 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
64 65 1.351017 CTAGTTGGGGAAGGAGCAACA 59.649 52.381 0.00 0.00 0.00 3.33
337 338 0.389817 CCTCATCAACGACGAAGCCA 60.390 55.000 0.00 0.00 0.00 4.75
407 408 0.400594 AGAAGGGGGAAACAAGACGG 59.599 55.000 0.00 0.00 0.00 4.79
410 411 1.971695 GGGGGAAACAAGACGGCAG 60.972 63.158 0.00 0.00 0.00 4.85
582 583 3.357079 CCCTGCGCAGTGGTTGTC 61.357 66.667 33.75 0.00 0.00 3.18
688 689 3.488553 CGGCCGCTTTTTAGATTTTAGGG 60.489 47.826 14.67 0.00 0.00 3.53
689 690 3.697542 GGCCGCTTTTTAGATTTTAGGGA 59.302 43.478 0.00 0.00 0.00 4.20
690 691 4.158949 GGCCGCTTTTTAGATTTTAGGGAA 59.841 41.667 0.00 0.00 0.00 3.97
691 692 5.163447 GGCCGCTTTTTAGATTTTAGGGAAT 60.163 40.000 0.00 0.00 0.00 3.01
692 693 6.040054 GGCCGCTTTTTAGATTTTAGGGAATA 59.960 38.462 0.00 0.00 0.00 1.75
693 694 7.417003 GGCCGCTTTTTAGATTTTAGGGAATAA 60.417 37.037 0.00 0.00 0.00 1.40
694 695 7.648112 GCCGCTTTTTAGATTTTAGGGAATAAG 59.352 37.037 0.00 0.00 0.00 1.73
695 696 8.899771 CCGCTTTTTAGATTTTAGGGAATAAGA 58.100 33.333 0.00 0.00 0.00 2.10
742 746 4.048241 GGTCGAAAAACCCAATGAAACA 57.952 40.909 0.00 0.00 32.82 2.83
749 753 1.154488 CCCAATGAAACACGCGACG 60.154 57.895 15.93 5.81 0.00 5.12
756 760 1.006571 AAACACGCGACGGATGACT 60.007 52.632 15.93 0.00 0.00 3.41
769 773 1.050767 GATGACTATCCGTTACGCGC 58.949 55.000 5.73 0.00 39.71 6.86
781 785 2.696409 TTACGCGCGGTTGAGGACAA 62.696 55.000 35.22 10.00 0.00 3.18
782 786 3.777925 CGCGCGGTTGAGGACAAG 61.778 66.667 24.84 0.00 36.64 3.16
806 810 2.699954 AGCACAGAGATTGTTAACGGG 58.300 47.619 0.26 0.00 38.16 5.28
809 813 2.666508 CACAGAGATTGTTAACGGGTCG 59.333 50.000 0.26 0.00 38.16 4.79
815 819 1.459455 TTGTTAACGGGTCGGACGGA 61.459 55.000 1.43 0.00 35.23 4.69
816 820 1.444383 GTTAACGGGTCGGACGGAC 60.444 63.158 4.63 4.63 45.31 4.79
825 829 1.574134 GTCGGACGGACAGAAAAACA 58.426 50.000 8.19 0.00 45.36 2.83
828 832 1.003223 CGGACGGACAGAAAAACAACC 60.003 52.381 0.00 0.00 0.00 3.77
835 839 3.130340 GGACAGAAAAACAACCTGAAGCA 59.870 43.478 0.00 0.00 0.00 3.91
849 853 7.821846 ACAACCTGAAGCAAATTTAAAAACAGA 59.178 29.630 0.00 0.00 0.00 3.41
850 854 7.770801 ACCTGAAGCAAATTTAAAAACAGAC 57.229 32.000 0.00 0.00 0.00 3.51
851 855 6.475402 ACCTGAAGCAAATTTAAAAACAGACG 59.525 34.615 0.00 0.00 0.00 4.18
852 856 6.475402 CCTGAAGCAAATTTAAAAACAGACGT 59.525 34.615 0.00 0.00 0.00 4.34
869 873 9.931210 AAACAGACGTCTGAAAAATAGTAAAAG 57.069 29.630 43.55 17.83 46.59 2.27
872 962 8.761497 CAGACGTCTGAAAAATAGTAAAAGTGA 58.239 33.333 36.73 0.00 46.59 3.41
887 977 7.244192 AGTAAAAGTGATTAATTTCTCAGCGC 58.756 34.615 0.00 0.00 0.00 5.92
888 978 5.627499 AAAGTGATTAATTTCTCAGCGCA 57.373 34.783 11.47 0.00 0.00 6.09
889 979 4.606457 AGTGATTAATTTCTCAGCGCAC 57.394 40.909 11.47 0.00 0.00 5.34
890 980 4.002982 AGTGATTAATTTCTCAGCGCACA 58.997 39.130 11.47 0.00 0.00 4.57
891 981 4.637534 AGTGATTAATTTCTCAGCGCACAT 59.362 37.500 11.47 0.00 0.00 3.21
894 984 1.442769 AATTTCTCAGCGCACATCGT 58.557 45.000 11.47 0.00 41.07 3.73
896 986 1.291184 TTTCTCAGCGCACATCGTGG 61.291 55.000 11.47 0.00 41.07 4.94
906 996 1.238439 CACATCGTGGGCTTTGAAGT 58.762 50.000 0.00 0.00 0.00 3.01
920 1010 4.815269 CTTTGAAGTCCAGACTAGACCAG 58.185 47.826 0.00 0.00 41.58 4.00
954 1052 1.294659 CCTCTTCGACTTGCACTGCC 61.295 60.000 0.00 0.00 0.00 4.85
955 1053 1.621301 CTCTTCGACTTGCACTGCCG 61.621 60.000 0.00 0.00 0.00 5.69
959 1057 1.369209 CGACTTGCACTGCCGTTTG 60.369 57.895 0.00 0.00 0.00 2.93
972 1070 3.056328 GTTTGCTCCGCTCCACCC 61.056 66.667 0.00 0.00 0.00 4.61
984 1082 4.424711 CCACCCCCACCACATCCG 62.425 72.222 0.00 0.00 0.00 4.18
986 1084 2.856988 ACCCCCACCACATCCGTT 60.857 61.111 0.00 0.00 0.00 4.44
987 1085 2.045340 CCCCCACCACATCCGTTC 60.045 66.667 0.00 0.00 0.00 3.95
988 1086 2.045340 CCCCACCACATCCGTTCC 60.045 66.667 0.00 0.00 0.00 3.62
989 1087 2.435938 CCCACCACATCCGTTCCG 60.436 66.667 0.00 0.00 0.00 4.30
1011 1109 2.583593 GTCGAGATGACGGCCAGC 60.584 66.667 2.24 0.00 37.96 4.85
1073 1171 0.452184 GACGATGACTTGCTCTCCGA 59.548 55.000 0.00 0.00 0.00 4.55
1074 1172 0.453793 ACGATGACTTGCTCTCCGAG 59.546 55.000 0.00 0.00 0.00 4.63
1092 1190 4.565850 ATCCTCCTCCGCCTCCCC 62.566 72.222 0.00 0.00 0.00 4.81
1135 1233 0.677731 CGCCTCCCTCATCTGCAAAA 60.678 55.000 0.00 0.00 0.00 2.44
1141 1239 0.172803 CCTCATCTGCAAAAGCTGGC 59.827 55.000 0.00 0.00 0.00 4.85
1253 1351 5.356470 AGGCGTTATCTATATCCTTCGTACC 59.644 44.000 0.00 0.00 0.00 3.34
1260 1358 5.247084 TCTATATCCTTCGTACCAGCTCTC 58.753 45.833 0.00 0.00 0.00 3.20
1285 1383 2.508439 CCAATCGTGTCCCCGTCG 60.508 66.667 0.00 0.00 0.00 5.12
1296 1394 4.587189 CCCGTCGGGCGATTCTCC 62.587 72.222 19.48 0.00 44.77 3.71
1303 1401 1.078143 GGGCGATTCTCCTTGCAGT 60.078 57.895 0.00 0.00 0.00 4.40
1310 1408 2.049156 CTCCTTGCAGTGCGACGA 60.049 61.111 11.20 7.24 0.00 4.20
1313 1411 3.030308 CTTGCAGTGCGACGACGT 61.030 61.111 11.20 0.00 41.98 4.34
1368 1466 1.680735 CTCGTCCTCATCTTCCTCCTG 59.319 57.143 0.00 0.00 0.00 3.86
1386 1484 0.179020 TGAAGCACAACCAGGTCCTG 60.179 55.000 12.40 12.40 0.00 3.86
1441 1539 1.671379 GCCGTTCCTCCGAGCTTTT 60.671 57.895 0.00 0.00 0.00 2.27
1453 1551 0.307760 GAGCTTTTGTGTGGTGACGG 59.692 55.000 0.00 0.00 0.00 4.79
1460 1558 3.299977 TGTGGTGACGGGGAGACG 61.300 66.667 0.00 0.00 40.31 4.18
1463 1561 3.756727 GGTGACGGGGAGACGGAC 61.757 72.222 0.00 0.00 38.39 4.79
1533 1638 6.291377 AGTGGTATTGATAGGCACATACAAG 58.709 40.000 0.00 0.00 0.00 3.16
1543 1648 3.758554 AGGCACATACAAGGAACAACATC 59.241 43.478 0.00 0.00 0.00 3.06
1548 1653 2.631160 ACAAGGAACAACATCCACGA 57.369 45.000 0.00 0.00 42.27 4.35
1555 1660 1.078709 ACAACATCCACGAGCAATCG 58.921 50.000 0.00 0.00 39.31 3.34
1569 1674 1.268743 GCAATCGCCTGCATTTACTCC 60.269 52.381 3.94 0.00 42.17 3.85
1595 1700 1.075482 CGGGCATATGGGGCAATCT 59.925 57.895 4.56 0.00 34.52 2.40
1596 1701 0.327924 CGGGCATATGGGGCAATCTA 59.672 55.000 4.56 0.00 34.52 1.98
1616 1721 2.447443 ACTCTCGACACTGCTTCCATA 58.553 47.619 0.00 0.00 0.00 2.74
1624 1729 0.461961 ACTGCTTCCATACGAGGCTC 59.538 55.000 3.87 3.87 43.82 4.70
1637 1742 0.039346 GAGGCTCGGTCGGCTTATAC 60.039 60.000 0.00 0.00 40.21 1.47
1656 1761 2.048603 GGGCATGGCTTGTGTCCTC 61.049 63.158 19.78 0.00 38.32 3.71
1662 1767 1.966451 GGCTTGTGTCCTCGTTGGG 60.966 63.158 0.00 0.00 36.20 4.12
1689 1794 5.337788 TGCCTTTATTGGGTTCTTATTGGT 58.662 37.500 0.00 0.00 0.00 3.67
1710 1815 2.560981 TGAGAGTCCACGCATACTTGAA 59.439 45.455 0.00 0.00 0.00 2.69
1739 1844 4.844349 TGGATAGGCAGAGCTTAACTTT 57.156 40.909 0.00 0.00 0.00 2.66
1759 1864 5.104360 ACTTTGATACATATGCCAGTGGACT 60.104 40.000 15.20 0.59 0.00 3.85
1765 1870 2.665649 TATGCCAGTGGACTTGTACG 57.334 50.000 15.20 0.00 0.00 3.67
1766 1871 0.673644 ATGCCAGTGGACTTGTACGC 60.674 55.000 15.20 0.00 0.00 4.42
1817 1922 0.250770 GTGGAGGGTGGTGTCCTTTC 60.251 60.000 0.00 0.00 34.21 2.62
1829 1934 4.827284 TGGTGTCCTTTCTTTCCTCATTTC 59.173 41.667 0.00 0.00 0.00 2.17
1830 1935 4.218635 GGTGTCCTTTCTTTCCTCATTTCC 59.781 45.833 0.00 0.00 0.00 3.13
1831 1936 5.073428 GTGTCCTTTCTTTCCTCATTTCCT 58.927 41.667 0.00 0.00 0.00 3.36
1940 2045 3.487372 ACAAGCTACTTTCCCTCAAACC 58.513 45.455 0.00 0.00 0.00 3.27
1947 2052 4.664688 ACTTTCCCTCAAACCAGATGAT 57.335 40.909 0.00 0.00 0.00 2.45
1976 2081 3.636764 CCCCAACTGATAATAGGGTTTGC 59.363 47.826 0.00 0.00 37.84 3.68
1978 2083 3.315191 CCAACTGATAATAGGGTTTGCCG 59.685 47.826 0.00 0.00 34.97 5.69
1988 2093 1.564348 AGGGTTTGCCGAGGACAATAT 59.436 47.619 0.00 0.00 34.97 1.28
1991 2096 2.479560 GGTTTGCCGAGGACAATATTGC 60.480 50.000 15.48 8.16 0.00 3.56
2003 2108 4.156008 GGACAATATTGCGTTCTTCCTGTT 59.844 41.667 15.48 0.00 0.00 3.16
2031 2136 1.811266 CGGCGTCTTCATGGTCCAG 60.811 63.158 0.00 0.00 0.00 3.86
2053 2158 5.049198 CAGCTTAAGTCATTGCAGTTCAAGA 60.049 40.000 4.02 0.00 38.22 3.02
2068 2173 6.162777 CAGTTCAAGAAACTTTCCAAAACCA 58.837 36.000 0.00 0.00 46.26 3.67
2071 2176 6.353404 TCAAGAAACTTTCCAAAACCAACT 57.647 33.333 0.00 0.00 0.00 3.16
2163 2268 3.668596 ACAGAAACAAGTCGGTTTTCG 57.331 42.857 0.00 0.00 40.85 3.46
2164 2269 3.264104 ACAGAAACAAGTCGGTTTTCGA 58.736 40.909 0.00 0.00 46.77 3.71
2199 2304 1.742761 ATGCTGTTCACATCCTTCCG 58.257 50.000 0.00 0.00 0.00 4.30
2292 2397 7.503566 ACATATAGCAATATTGTTCTGCACCTT 59.496 33.333 16.61 0.00 38.58 3.50
2294 2399 4.813027 AGCAATATTGTTCTGCACCTTTG 58.187 39.130 16.61 0.00 38.58 2.77
2320 2434 1.761244 TTCGTGTCAAGTGCGTGCTG 61.761 55.000 0.00 0.00 0.00 4.41
2324 2438 2.180204 GTCAAGTGCGTGCTGGTGT 61.180 57.895 0.00 0.00 0.00 4.16
2424 2538 2.674852 CTGAGACGATGGGTTGTCATTG 59.325 50.000 0.00 0.00 40.61 2.82
2432 2546 4.093408 CGATGGGTTGTCATTGTTCTACTG 59.907 45.833 0.00 0.00 0.00 2.74
2458 2572 5.184864 ACTGTGGTCTCTTTGATAGACTGAG 59.815 44.000 0.00 0.00 42.48 3.35
2502 2616 7.549134 AGCGATGTTGTTTCTAATATTCTCACA 59.451 33.333 0.00 0.00 0.00 3.58
2563 2678 4.459685 TCAAGTCTAGCCAACTGTCTCTAC 59.540 45.833 0.00 0.00 0.00 2.59
2676 2792 7.984422 TTCCCTACATATTCACATATGCAAG 57.016 36.000 1.58 0.00 44.48 4.01
2723 2839 3.264897 GCATAGCTGCGGTGTCGG 61.265 66.667 0.00 0.00 38.92 4.79
2724 2840 2.586079 CATAGCTGCGGTGTCGGG 60.586 66.667 0.00 0.00 36.79 5.14
2789 2905 9.125026 AGACAACTTGAACTAGAATGAACAAAT 57.875 29.630 0.00 0.00 0.00 2.32
3083 3207 4.898829 TTGTCATGTTCACTTCTGTTGG 57.101 40.909 0.00 0.00 0.00 3.77
3096 3223 7.284074 TCACTTCTGTTGGTAGGAATTGTTAA 58.716 34.615 0.00 0.00 0.00 2.01
3102 3229 7.390440 TCTGTTGGTAGGAATTGTTAACATGAG 59.610 37.037 9.56 0.00 0.00 2.90
3198 3325 8.160521 TCTGATTAGCTAATAGTCTGAGTGTC 57.839 38.462 18.87 3.89 0.00 3.67
3301 3432 8.880750 GTGTGGTTTTGTCTATCTATTCCTAAC 58.119 37.037 0.00 0.00 0.00 2.34
3306 3437 7.766219 TTTGTCTATCTATTCCTAACGTTGC 57.234 36.000 11.99 0.00 0.00 4.17
3311 3442 3.766151 TCTATTCCTAACGTTGCACGAG 58.234 45.455 11.99 0.00 46.05 4.18
3317 3448 0.386476 TAACGTTGCACGAGACCTGT 59.614 50.000 11.99 0.00 46.05 4.00
3372 3504 5.726980 AGCTGAATATTTTGGAGCAACAA 57.273 34.783 10.50 0.00 31.80 2.83
3374 3506 5.477984 AGCTGAATATTTTGGAGCAACAAGA 59.522 36.000 10.50 0.00 31.80 3.02
3383 3515 4.431416 TGGAGCAACAAGAAGAAACCTA 57.569 40.909 0.00 0.00 0.00 3.08
3414 3555 7.976175 GTCCATTTCTCAATGAAACCCTAATTC 59.024 37.037 0.00 0.00 46.08 2.17
3453 3594 3.837146 TCCCTCTGATGCCTTCTCATATC 59.163 47.826 0.00 0.00 0.00 1.63
3608 3753 0.037232 ACGCTGACCAGGTAAGCTTC 60.037 55.000 24.72 0.00 37.86 3.86
3620 3765 2.354199 GGTAAGCTTCTCTTCTGCATGC 59.646 50.000 11.82 11.82 36.25 4.06
3631 3776 5.474532 TCTCTTCTGCATGCAAGTTTATTGT 59.525 36.000 22.88 0.00 0.00 2.71
3660 3809 8.593492 ATTGCTTTCCTTTTTACTGTCATTTC 57.407 30.769 0.00 0.00 0.00 2.17
3680 3829 3.079578 TCTCAAGGCAATTGCAAGAGAG 58.920 45.455 29.25 26.57 44.36 3.20
3750 3899 0.104120 CACCCATCATGCTTGCATGG 59.896 55.000 28.25 17.95 37.42 3.66
3759 3908 2.048023 GCTTGCATGGTAGGCTGCA 61.048 57.895 4.64 0.00 46.08 4.41
3780 3929 4.514816 GCATCTTGGATCTTTTCTCTAGGC 59.485 45.833 0.00 0.00 0.00 3.93
3802 3951 3.386402 CCTTGAGTCCTCATTCCTACCTC 59.614 52.174 0.00 0.00 39.64 3.85
3820 3969 2.355920 CCTCTGCAGCTTTCCATTCTCT 60.356 50.000 9.47 0.00 0.00 3.10
3860 4009 6.325286 CCCAGCTACCTTCTCTTCTATTTACT 59.675 42.308 0.00 0.00 0.00 2.24
3872 4021 8.908903 TCTCTTCTATTTACTGATGTTCTCTCC 58.091 37.037 0.00 0.00 0.00 3.71
3873 4022 8.012957 TCTTCTATTTACTGATGTTCTCTCCC 57.987 38.462 0.00 0.00 0.00 4.30
3895 4044 2.932614 CCCTACTGAATGTGCTCTTTCG 59.067 50.000 9.12 7.09 32.59 3.46
3896 4045 2.349886 CCTACTGAATGTGCTCTTTCGC 59.650 50.000 9.12 0.00 32.59 4.70
3897 4046 1.882912 ACTGAATGTGCTCTTTCGCA 58.117 45.000 9.12 0.00 37.62 5.10
3898 4047 2.430465 ACTGAATGTGCTCTTTCGCAT 58.570 42.857 9.12 0.00 42.62 4.73
3899 4048 2.161012 ACTGAATGTGCTCTTTCGCATG 59.839 45.455 9.12 0.00 42.62 4.06
3900 4049 1.135603 TGAATGTGCTCTTTCGCATGC 60.136 47.619 7.91 7.91 42.62 4.06
3901 4050 0.171903 AATGTGCTCTTTCGCATGCC 59.828 50.000 13.15 0.00 42.62 4.40
3902 4051 1.660560 ATGTGCTCTTTCGCATGCCC 61.661 55.000 13.15 0.00 42.62 5.36
3903 4052 2.042831 GTGCTCTTTCGCATGCCCT 61.043 57.895 13.15 0.00 42.62 5.19
3905 4054 2.817423 GCTCTTTCGCATGCCCTCG 61.817 63.158 13.15 0.00 0.00 4.63
3906 4055 2.817423 CTCTTTCGCATGCCCTCGC 61.817 63.158 13.15 0.00 0.00 5.03
3929 4776 6.292381 CGCTTCTGTTATATTGTCTAGTTGCC 60.292 42.308 0.00 0.00 0.00 4.52
3942 4789 4.214332 GTCTAGTTGCCAGTTTTCTTCCTG 59.786 45.833 0.00 0.00 0.00 3.86
3962 4809 4.443598 CCTGCTTAGTATTCCTCCAGTTCC 60.444 50.000 0.00 0.00 0.00 3.62
3978 4825 4.333926 CCAGTTCCTTCTAATAGTGCAAGC 59.666 45.833 0.00 0.00 0.00 4.01
3979 4826 4.937620 CAGTTCCTTCTAATAGTGCAAGCA 59.062 41.667 0.00 0.00 0.00 3.91
3980 4827 5.587844 CAGTTCCTTCTAATAGTGCAAGCAT 59.412 40.000 0.00 0.00 0.00 3.79
3997 4844 5.658468 CAAGCATACTTCTCAGATGACTGA 58.342 41.667 0.00 0.00 41.45 3.41
4050 5091 0.107214 TAGCAAAATAGCGCCAGCCT 60.107 50.000 2.29 0.00 46.67 4.58
4060 5101 2.442413 AGCGCCAGCCTTTAAAATACA 58.558 42.857 2.29 0.00 46.67 2.29
4074 5115 9.169468 CCTTTAAAATACATTATTAGCGTGCTG 57.831 33.333 4.25 0.00 0.00 4.41
4080 5121 3.245284 ACATTATTAGCGTGCTGTTAGCG 59.755 43.478 4.25 0.00 46.26 4.26
4086 5127 1.009389 GCGTGCTGTTAGCGAGACTT 61.009 55.000 0.00 0.00 46.26 3.01
4106 5147 9.974750 GAGACTTTGTACACAGATTTATTTAGC 57.025 33.333 15.81 0.00 0.00 3.09
4171 5212 2.701243 GGACCCTTCCCCATTCCCC 61.701 68.421 0.00 0.00 35.57 4.81
4177 5218 2.426268 CCCTTCCCCATTCCCCTATTTG 60.426 54.545 0.00 0.00 0.00 2.32
4200 5241 2.229784 GGATTTGTTTGTCCCTGCTCAG 59.770 50.000 0.00 0.00 0.00 3.35
4209 5252 1.138661 GTCCCTGCTCAGAGAGGAATG 59.861 57.143 14.42 2.58 27.87 2.67
4263 5306 6.485171 ACAGAAATAATCCCTTTACTGTGCT 58.515 36.000 0.00 0.00 36.29 4.40
4266 5309 6.316390 AGAAATAATCCCTTTACTGTGCTTCG 59.684 38.462 0.00 0.00 0.00 3.79
4277 5321 3.214328 ACTGTGCTTCGTGGAATTTTCT 58.786 40.909 0.00 0.00 0.00 2.52
4282 5326 2.412847 GCTTCGTGGAATTTTCTGGTCG 60.413 50.000 0.00 0.00 0.00 4.79
4309 5353 1.064003 ACTGGGTGCCACATTGTCTA 58.936 50.000 0.00 0.00 0.00 2.59
4310 5354 1.423541 ACTGGGTGCCACATTGTCTAA 59.576 47.619 0.00 0.00 0.00 2.10
4314 5358 3.521531 TGGGTGCCACATTGTCTAAGATA 59.478 43.478 0.00 0.00 0.00 1.98
4330 5374 9.398170 TGTCTAAGATATATTTTACGCGGTTAC 57.602 33.333 12.47 0.00 0.00 2.50
4332 5376 8.503196 TCTAAGATATATTTTACGCGGTTACGA 58.497 33.333 12.47 0.00 44.60 3.43
4339 5383 5.871531 TTTTACGCGGTTACGAATCTATC 57.128 39.130 12.47 0.00 44.60 2.08
4353 5397 4.083217 CGAATCTATCAAGTACTCCCTCCG 60.083 50.000 0.00 0.00 0.00 4.63
4357 5401 0.702902 TCAAGTACTCCCTCCGTCCT 59.297 55.000 0.00 0.00 0.00 3.85
4366 5410 8.347557 AGTACTCCCTCCGTCCTATAATATAT 57.652 38.462 0.00 0.00 0.00 0.86
4417 5461 7.787517 ATATTATGGGGCAAAGGGAGTATAT 57.212 36.000 0.00 0.00 0.00 0.86
4418 5462 8.885900 ATATTATGGGGCAAAGGGAGTATATA 57.114 34.615 0.00 0.00 0.00 0.86
4423 5467 7.597850 TGGGGCAAAGGGAGTATATATAATT 57.402 36.000 0.00 0.00 0.00 1.40
4425 5469 7.240828 TGGGGCAAAGGGAGTATATATAATTGA 59.759 37.037 0.00 0.00 0.00 2.57
4426 5470 8.282256 GGGGCAAAGGGAGTATATATAATTGAT 58.718 37.037 0.00 0.00 0.00 2.57
4473 5517 6.713450 TGGCTTCGACTTTCCTTTAGTTATTT 59.287 34.615 0.00 0.00 0.00 1.40
4476 5520 7.443259 TTCGACTTTCCTTTAGTTATTTGGG 57.557 36.000 0.00 0.00 0.00 4.12
4479 5523 6.072119 CGACTTTCCTTTAGTTATTTGGGCTT 60.072 38.462 0.00 0.00 0.00 4.35
4480 5524 7.120138 CGACTTTCCTTTAGTTATTTGGGCTTA 59.880 37.037 0.00 0.00 0.00 3.09
4481 5525 8.895141 ACTTTCCTTTAGTTATTTGGGCTTAT 57.105 30.769 0.00 0.00 0.00 1.73
4490 5534 6.784031 AGTTATTTGGGCTTATAGCTATGCT 58.216 36.000 16.77 0.00 41.99 3.79
4525 5569 5.643777 GCCGCTCACATGGTATTCTTATAAT 59.356 40.000 0.00 0.00 0.00 1.28
4555 5599 7.741027 ATGCTGAGTAATACATTCTGGATTG 57.259 36.000 0.00 0.00 32.21 2.67
4563 5607 6.748333 AATACATTCTGGATTGTGTCACAG 57.252 37.500 5.67 0.00 27.73 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 2.027745 AGCATCATCGACAACCTGTCTT 60.028 45.455 5.34 0.00 44.85 3.01
407 408 1.569479 AACCGAAGAAGAAGCGCTGC 61.569 55.000 12.58 9.98 0.00 5.25
410 411 1.636570 GGGAACCGAAGAAGAAGCGC 61.637 60.000 0.00 0.00 40.86 5.92
582 583 2.615493 CCCACCAGTACTTTGCTACCTG 60.615 54.545 0.00 0.00 0.00 4.00
691 692 9.801873 CATGGTCTTCTTTTTGAAACTTTCTTA 57.198 29.630 3.22 0.00 33.79 2.10
692 693 8.531146 TCATGGTCTTCTTTTTGAAACTTTCTT 58.469 29.630 3.22 0.00 33.79 2.52
693 694 7.976175 GTCATGGTCTTCTTTTTGAAACTTTCT 59.024 33.333 3.22 0.00 33.79 2.52
694 695 7.044052 CGTCATGGTCTTCTTTTTGAAACTTTC 60.044 37.037 0.00 0.00 33.79 2.62
695 696 6.751888 CGTCATGGTCTTCTTTTTGAAACTTT 59.248 34.615 0.00 0.00 33.79 2.66
696 697 6.265577 CGTCATGGTCTTCTTTTTGAAACTT 58.734 36.000 0.00 0.00 33.79 2.66
697 698 5.221048 CCGTCATGGTCTTCTTTTTGAAACT 60.221 40.000 0.00 0.00 33.79 2.66
698 699 4.976116 CCGTCATGGTCTTCTTTTTGAAAC 59.024 41.667 0.00 0.00 33.79 2.78
699 700 4.037446 CCCGTCATGGTCTTCTTTTTGAAA 59.963 41.667 0.00 0.00 32.62 2.69
700 701 3.568007 CCCGTCATGGTCTTCTTTTTGAA 59.432 43.478 0.00 0.00 35.15 2.69
742 746 1.653115 GGATAGTCATCCGTCGCGT 59.347 57.895 5.77 0.00 41.50 6.01
749 753 1.682982 CGCGTAACGGATAGTCATCC 58.317 55.000 0.00 0.00 46.51 3.51
764 768 4.595538 TTGTCCTCAACCGCGCGT 62.596 61.111 29.95 14.24 0.00 6.01
769 773 1.901650 GCTTCGCTTGTCCTCAACCG 61.902 60.000 0.00 0.00 34.97 4.44
781 785 2.175878 AACAATCTCTGTGCTTCGCT 57.824 45.000 0.00 0.00 38.67 4.93
782 786 3.722082 CGTTAACAATCTCTGTGCTTCGC 60.722 47.826 6.39 0.00 38.67 4.70
784 788 3.125316 CCCGTTAACAATCTCTGTGCTTC 59.875 47.826 6.39 0.00 38.67 3.86
786 790 2.038557 ACCCGTTAACAATCTCTGTGCT 59.961 45.455 6.39 0.00 38.67 4.40
789 793 2.353406 CCGACCCGTTAACAATCTCTGT 60.353 50.000 6.39 0.00 41.27 3.41
798 802 1.444383 GTCCGTCCGACCCGTTAAC 60.444 63.158 0.00 0.00 35.23 2.01
799 803 1.865788 CTGTCCGTCCGACCCGTTAA 61.866 60.000 0.00 0.00 41.18 2.01
801 805 3.677648 CTGTCCGTCCGACCCGTT 61.678 66.667 0.00 0.00 41.18 4.44
806 810 1.574134 TGTTTTTCTGTCCGTCCGAC 58.426 50.000 0.00 0.00 42.33 4.79
809 813 2.032924 CAGGTTGTTTTTCTGTCCGTCC 59.967 50.000 0.00 0.00 0.00 4.79
815 819 4.799564 TTGCTTCAGGTTGTTTTTCTGT 57.200 36.364 0.00 0.00 0.00 3.41
816 820 6.667007 AATTTGCTTCAGGTTGTTTTTCTG 57.333 33.333 0.00 0.00 0.00 3.02
817 821 8.785329 TTAAATTTGCTTCAGGTTGTTTTTCT 57.215 26.923 0.00 0.00 0.00 2.52
818 822 9.833182 TTTTAAATTTGCTTCAGGTTGTTTTTC 57.167 25.926 0.00 0.00 0.00 2.29
820 824 9.619316 GTTTTTAAATTTGCTTCAGGTTGTTTT 57.381 25.926 0.00 0.00 0.00 2.43
821 825 8.787852 TGTTTTTAAATTTGCTTCAGGTTGTTT 58.212 25.926 0.00 0.00 0.00 2.83
822 826 8.329203 TGTTTTTAAATTTGCTTCAGGTTGTT 57.671 26.923 0.00 0.00 0.00 2.83
823 827 7.821846 TCTGTTTTTAAATTTGCTTCAGGTTGT 59.178 29.630 0.00 0.00 0.00 3.32
824 828 8.116136 GTCTGTTTTTAAATTTGCTTCAGGTTG 58.884 33.333 0.00 0.00 0.00 3.77
825 829 7.010091 CGTCTGTTTTTAAATTTGCTTCAGGTT 59.990 33.333 0.00 0.00 0.00 3.50
828 832 7.432252 AGACGTCTGTTTTTAAATTTGCTTCAG 59.568 33.333 19.30 3.88 0.00 3.02
866 870 5.048782 TGTGCGCTGAGAAATTAATCACTTT 60.049 36.000 9.73 0.00 0.00 2.66
867 871 4.455533 TGTGCGCTGAGAAATTAATCACTT 59.544 37.500 9.73 0.00 0.00 3.16
869 873 4.340894 TGTGCGCTGAGAAATTAATCAC 57.659 40.909 9.73 0.00 0.00 3.06
872 962 3.623060 ACGATGTGCGCTGAGAAATTAAT 59.377 39.130 9.73 0.00 46.04 1.40
880 970 3.190849 CCCACGATGTGCGCTGAG 61.191 66.667 9.73 0.00 46.04 3.35
886 976 0.109597 CTTCAAAGCCCACGATGTGC 60.110 55.000 0.00 0.00 31.34 4.57
887 977 1.197721 GACTTCAAAGCCCACGATGTG 59.802 52.381 0.00 0.00 0.00 3.21
888 978 1.523758 GACTTCAAAGCCCACGATGT 58.476 50.000 0.00 0.00 0.00 3.06
889 979 0.804989 GGACTTCAAAGCCCACGATG 59.195 55.000 0.00 0.00 0.00 3.84
890 980 0.400213 TGGACTTCAAAGCCCACGAT 59.600 50.000 0.00 0.00 33.32 3.73
891 981 0.250295 CTGGACTTCAAAGCCCACGA 60.250 55.000 0.00 0.00 33.32 4.35
894 984 1.140312 AGTCTGGACTTCAAAGCCCA 58.860 50.000 0.00 0.00 38.83 5.36
896 986 3.591023 GTCTAGTCTGGACTTCAAAGCC 58.409 50.000 9.01 0.00 42.54 4.35
906 996 3.643237 CCCAATACTGGTCTAGTCTGGA 58.357 50.000 15.32 0.00 41.68 3.86
910 1000 1.416772 GGGCCCAATACTGGTCTAGTC 59.583 57.143 19.95 0.00 41.72 2.59
920 1010 3.094498 AGGTCGGGGGCCCAATAC 61.094 66.667 26.86 18.17 35.37 1.89
984 1082 0.809385 TCATCTCGACCTCACGGAAC 59.191 55.000 0.00 0.00 0.00 3.62
986 1084 1.366854 CGTCATCTCGACCTCACGGA 61.367 60.000 0.00 0.00 42.07 4.69
987 1085 1.062685 CGTCATCTCGACCTCACGG 59.937 63.158 0.00 0.00 42.07 4.94
988 1086 1.062685 CCGTCATCTCGACCTCACG 59.937 63.158 0.00 0.00 42.07 4.35
989 1087 1.226717 GCCGTCATCTCGACCTCAC 60.227 63.158 0.00 0.00 42.07 3.51
1048 1146 0.109086 AGCAAGTCATCGTCGTCCAG 60.109 55.000 0.00 0.00 0.00 3.86
1049 1147 0.109272 GAGCAAGTCATCGTCGTCCA 60.109 55.000 0.00 0.00 0.00 4.02
1051 1149 1.540407 GAGAGCAAGTCATCGTCGTC 58.460 55.000 0.00 0.00 0.00 4.20
1052 1150 0.171455 GGAGAGCAAGTCATCGTCGT 59.829 55.000 0.00 0.00 0.00 4.34
1053 1151 0.863538 CGGAGAGCAAGTCATCGTCG 60.864 60.000 0.00 0.00 0.00 5.12
1073 1171 2.200092 GGAGGCGGAGGAGGATCT 59.800 66.667 0.00 0.00 33.73 2.75
1074 1172 2.920384 GGGAGGCGGAGGAGGATC 60.920 72.222 0.00 0.00 0.00 3.36
1092 1190 4.101077 AGGGAGGAGGGCTGAGGG 62.101 72.222 0.00 0.00 0.00 4.30
1199 1297 3.090532 AACCGAGGATGGGAGGGC 61.091 66.667 0.00 0.00 35.02 5.19
1202 1300 0.466124 GAAGGAACCGAGGATGGGAG 59.534 60.000 0.00 0.00 35.02 4.30
1230 1328 5.124457 TGGTACGAAGGATATAGATAACGCC 59.876 44.000 0.00 0.00 0.00 5.68
1232 1330 6.093771 AGCTGGTACGAAGGATATAGATAACG 59.906 42.308 0.00 0.00 0.00 3.18
1238 1336 4.093703 CGAGAGCTGGTACGAAGGATATAG 59.906 50.000 0.00 0.00 0.00 1.31
1285 1383 1.078143 ACTGCAAGGAGAATCGCCC 60.078 57.895 0.00 0.00 39.30 6.13
1296 1394 2.988549 GACGTCGTCGCACTGCAAG 61.989 63.158 10.05 0.00 41.18 4.01
1322 1420 2.947532 CGGCAGTTGAGGAGGCTGA 61.948 63.158 0.00 0.00 34.60 4.26
1368 1466 0.890996 CCAGGACCTGGTTGTGCTTC 60.891 60.000 29.93 0.00 45.82 3.86
1441 1539 2.123208 TCTCCCCGTCACCACACA 60.123 61.111 0.00 0.00 0.00 3.72
1491 1589 1.318576 CTTGGAAGTGGTGGTTGTCC 58.681 55.000 0.00 0.00 0.00 4.02
1533 1638 1.234821 TTGCTCGTGGATGTTGTTCC 58.765 50.000 0.00 0.00 36.24 3.62
1543 1648 3.869272 GCAGGCGATTGCTCGTGG 61.869 66.667 4.59 0.00 46.71 4.94
1548 1653 1.672881 GAGTAAATGCAGGCGATTGCT 59.327 47.619 4.59 0.53 44.38 3.91
1555 1660 0.178068 TCCGAGGAGTAAATGCAGGC 59.822 55.000 0.00 0.00 0.00 4.85
1569 1674 1.290324 CCATATGCCCGTCTCCGAG 59.710 63.158 0.00 0.00 35.63 4.63
1578 1683 1.355720 AGTAGATTGCCCCATATGCCC 59.644 52.381 0.00 0.00 0.00 5.36
1595 1700 1.905637 TGGAAGCAGTGTCGAGAGTA 58.094 50.000 0.00 0.00 0.00 2.59
1596 1701 1.261480 ATGGAAGCAGTGTCGAGAGT 58.739 50.000 0.00 0.00 0.00 3.24
1624 1729 2.355481 GCCCGTATAAGCCGACCG 60.355 66.667 0.00 0.00 0.00 4.79
1637 1742 3.443045 GGACACAAGCCATGCCCG 61.443 66.667 0.00 0.00 0.00 6.13
1656 1761 3.520569 CCAATAAAGGCAATTCCCAACG 58.479 45.455 0.00 0.00 34.51 4.10
1662 1767 7.495606 CCAATAAGAACCCAATAAAGGCAATTC 59.504 37.037 0.00 0.00 0.00 2.17
1689 1794 2.167662 TCAAGTATGCGTGGACTCTCA 58.832 47.619 0.00 0.00 0.00 3.27
1710 1815 4.801164 AGCTCTGCCTATCCAAATCAAAT 58.199 39.130 0.00 0.00 0.00 2.32
1739 1844 4.164030 ACAAGTCCACTGGCATATGTATCA 59.836 41.667 4.29 0.48 0.00 2.15
1759 1864 1.466950 GCAAGCATTAGTGGCGTACAA 59.533 47.619 0.00 0.00 36.08 2.41
1765 1870 2.167075 AGAAATGGCAAGCATTAGTGGC 59.833 45.455 0.00 0.00 40.55 5.01
1766 1871 3.444742 TGAGAAATGGCAAGCATTAGTGG 59.555 43.478 0.00 0.00 0.00 4.00
1769 1874 7.095774 GCATAAATGAGAAATGGCAAGCATTAG 60.096 37.037 0.00 0.00 0.00 1.73
1817 1922 4.240881 TCCCATGAGGAAATGAGGAAAG 57.759 45.455 0.00 0.00 43.78 2.62
1829 1934 1.396653 GGCATTGAAGTCCCATGAGG 58.603 55.000 0.00 0.00 0.00 3.86
1830 1935 1.341285 TGGGCATTGAAGTCCCATGAG 60.341 52.381 3.45 0.00 44.62 2.90
1831 1936 0.703488 TGGGCATTGAAGTCCCATGA 59.297 50.000 3.45 0.00 44.62 3.07
1940 2045 1.648302 TTGGGGCCCTCCATCATCTG 61.648 60.000 25.93 0.00 36.58 2.90
1947 2052 0.551377 TTATCAGTTGGGGCCCTCCA 60.551 55.000 25.93 9.63 37.22 3.86
1949 2054 2.040412 CCTATTATCAGTTGGGGCCCTC 59.960 54.545 25.93 16.78 0.00 4.30
1976 2081 2.550978 AGAACGCAATATTGTCCTCGG 58.449 47.619 16.61 3.06 0.00 4.63
1978 2083 4.034510 CAGGAAGAACGCAATATTGTCCTC 59.965 45.833 16.31 10.73 0.00 3.71
1988 2093 2.031258 TGTCAACAGGAAGAACGCAA 57.969 45.000 0.00 0.00 0.00 4.85
1991 2096 4.616181 ACTTTTGTCAACAGGAAGAACG 57.384 40.909 12.45 0.00 0.00 3.95
2031 2136 5.362556 TCTTGAACTGCAATGACTTAAGC 57.637 39.130 1.29 0.00 35.59 3.09
2053 2158 6.999950 ACAAGTAGTTGGTTTTGGAAAGTTT 58.000 32.000 14.69 0.00 38.07 2.66
2068 2173 7.667575 ATGGATGATAGTGAGACAAGTAGTT 57.332 36.000 0.00 0.00 0.00 2.24
2071 2176 6.546034 TCGAATGGATGATAGTGAGACAAGTA 59.454 38.462 0.00 0.00 0.00 2.24
2163 2268 2.744202 AGCATTTCGTCAACCACTCATC 59.256 45.455 0.00 0.00 0.00 2.92
2164 2269 2.485426 CAGCATTTCGTCAACCACTCAT 59.515 45.455 0.00 0.00 0.00 2.90
2166 2271 1.873591 ACAGCATTTCGTCAACCACTC 59.126 47.619 0.00 0.00 0.00 3.51
2171 2276 3.332761 TGTGAACAGCATTTCGTCAAC 57.667 42.857 0.00 0.00 0.00 3.18
2224 2329 8.261908 GCAACAAATGAAATAATTGATACGAGC 58.738 33.333 0.00 0.00 0.00 5.03
2292 2397 0.027455 CTTGACACGAAACGCTGCAA 59.973 50.000 0.00 0.00 0.00 4.08
2294 2399 0.654472 CACTTGACACGAAACGCTGC 60.654 55.000 0.00 0.00 0.00 5.25
2299 2404 0.923911 GCACGCACTTGACACGAAAC 60.924 55.000 0.00 0.00 0.00 2.78
2320 2434 8.391106 CAGCTCAGAACTATTACATAAAACACC 58.609 37.037 0.00 0.00 0.00 4.16
2324 2438 9.733556 TTTCCAGCTCAGAACTATTACATAAAA 57.266 29.630 0.00 0.00 0.00 1.52
2401 2515 1.691976 TGACAACCCATCGTCTCAGTT 59.308 47.619 0.00 0.00 33.18 3.16
2409 2523 4.093408 CAGTAGAACAATGACAACCCATCG 59.907 45.833 0.00 0.00 0.00 3.84
2424 2538 5.708877 AAGAGACCACAGTACAGTAGAAC 57.291 43.478 0.00 0.00 0.00 3.01
2432 2546 6.151312 TCAGTCTATCAAAGAGACCACAGTAC 59.849 42.308 0.00 0.00 43.72 2.73
2535 2650 2.731976 CAGTTGGCTAGACTTGAACGAC 59.268 50.000 0.00 0.00 0.00 4.34
2563 2678 6.460123 GCATGGACATTCCTACAATAAAGTGG 60.460 42.308 0.00 0.00 37.46 4.00
2676 2792 2.630098 TCTGGCACTCCATATACAGCTC 59.370 50.000 0.00 0.00 42.51 4.09
2890 3006 7.744087 AGCAAGTCATTGTTACTGATTTACA 57.256 32.000 0.00 0.00 38.76 2.41
2940 3056 7.511959 AAAGGTTTCTCTCCAAGTGATAAAC 57.488 36.000 0.00 0.00 32.98 2.01
3008 3132 8.945481 TTGACATGAAAATGTGAAATGAACTT 57.055 26.923 0.00 0.00 34.45 2.66
3070 3194 5.690865 ACAATTCCTACCAACAGAAGTGAA 58.309 37.500 6.45 0.00 37.70 3.18
3169 3296 9.415008 ACTCAGACTATTAGCTAATCAGAAGAA 57.585 33.333 22.09 2.61 0.00 2.52
3383 3515 4.387026 TTCATTGAGAAATGGACCAGGT 57.613 40.909 0.00 0.00 32.05 4.00
3414 3555 6.544931 TCAGAGGGATATTCAGCTGAATTTTG 59.455 38.462 39.03 26.74 41.64 2.44
3418 3559 5.803795 GCATCAGAGGGATATTCAGCTGAAT 60.804 44.000 36.84 36.84 45.77 2.57
3453 3594 6.599244 TGTCATTCCAATAGAAAGCCAACTAG 59.401 38.462 0.00 0.00 38.21 2.57
3592 3737 3.513515 AGAAGAGAAGCTTACCTGGTCAG 59.486 47.826 0.63 2.40 36.83 3.51
3608 3753 5.706916 ACAATAAACTTGCATGCAGAAGAG 58.293 37.500 23.03 18.66 0.00 2.85
3660 3809 2.415625 GCTCTCTTGCAATTGCCTTGAG 60.416 50.000 26.94 26.00 41.18 3.02
3680 3829 4.629200 AGATCAGAGAGAATTTTGACGTGC 59.371 41.667 0.00 0.00 0.00 5.34
3750 3899 2.926778 AGATCCAAGATGCAGCCTAC 57.073 50.000 0.00 0.00 0.00 3.18
3759 3908 4.974501 AGGCCTAGAGAAAAGATCCAAGAT 59.025 41.667 1.29 0.00 0.00 2.40
3780 3929 3.379452 AGGTAGGAATGAGGACTCAAGG 58.621 50.000 6.06 0.00 43.58 3.61
3802 3951 3.079578 TGAAGAGAATGGAAAGCTGCAG 58.920 45.455 10.11 10.11 0.00 4.41
3820 3969 2.025037 AGCTGGGTTAAGGCATGATGAA 60.025 45.455 0.00 0.00 0.00 2.57
3872 4021 1.207791 AGAGCACATTCAGTAGGGGG 58.792 55.000 0.00 0.00 0.00 5.40
3873 4022 3.274288 GAAAGAGCACATTCAGTAGGGG 58.726 50.000 0.00 0.00 0.00 4.79
3895 4044 0.744414 TAACAGAAGCGAGGGCATGC 60.744 55.000 9.90 9.90 43.41 4.06
3896 4045 1.959042 ATAACAGAAGCGAGGGCATG 58.041 50.000 0.00 0.00 43.41 4.06
3897 4046 4.067896 CAATATAACAGAAGCGAGGGCAT 58.932 43.478 0.00 0.00 43.41 4.40
3898 4047 3.118408 ACAATATAACAGAAGCGAGGGCA 60.118 43.478 0.00 0.00 43.41 5.36
3899 4048 3.467803 ACAATATAACAGAAGCGAGGGC 58.532 45.455 0.00 0.00 40.37 5.19
3900 4049 4.950050 AGACAATATAACAGAAGCGAGGG 58.050 43.478 0.00 0.00 0.00 4.30
3901 4050 6.740110 ACTAGACAATATAACAGAAGCGAGG 58.260 40.000 0.00 0.00 0.00 4.63
3902 4051 7.306283 GCAACTAGACAATATAACAGAAGCGAG 60.306 40.741 0.00 0.00 0.00 5.03
3903 4052 6.475727 GCAACTAGACAATATAACAGAAGCGA 59.524 38.462 0.00 0.00 0.00 4.93
3905 4054 6.538742 TGGCAACTAGACAATATAACAGAAGC 59.461 38.462 0.00 0.00 26.55 3.86
3906 4055 7.766278 ACTGGCAACTAGACAATATAACAGAAG 59.234 37.037 0.00 0.00 32.28 2.85
3929 4776 6.881602 AGGAATACTAAGCAGGAAGAAAACTG 59.118 38.462 0.00 0.00 37.76 3.16
3942 4789 5.129650 AGAAGGAACTGGAGGAATACTAAGC 59.870 44.000 0.00 0.00 40.86 3.09
3962 4809 7.708322 TGAGAAGTATGCTTGCACTATTAGAAG 59.292 37.037 0.00 0.00 34.61 2.85
4018 5059 6.128172 CGCTATTTTGCTATAGCCTGCTATTT 60.128 38.462 21.84 0.00 46.60 1.40
4025 5066 2.224523 TGGCGCTATTTTGCTATAGCCT 60.225 45.455 21.84 6.83 46.60 4.58
4044 5085 8.349983 ACGCTAATAATGTATTTTAAAGGCTGG 58.650 33.333 0.00 0.00 0.00 4.85
4046 5087 7.860872 GCACGCTAATAATGTATTTTAAAGGCT 59.139 33.333 0.00 0.00 0.00 4.58
4060 5101 3.713288 TCGCTAACAGCACGCTAATAAT 58.287 40.909 0.00 0.00 42.58 1.28
4074 5115 4.543692 TCTGTGTACAAAGTCTCGCTAAC 58.456 43.478 12.86 0.00 0.00 2.34
4080 5121 9.974750 GCTAAATAAATCTGTGTACAAAGTCTC 57.025 33.333 12.86 0.00 0.00 3.36
4086 5127 7.815549 TGTCTCGCTAAATAAATCTGTGTACAA 59.184 33.333 0.00 0.00 0.00 2.41
4106 5147 8.376203 CACTATAGTGTTTTGAGAATTGTCTCG 58.624 37.037 22.48 0.00 45.24 4.04
4145 5186 4.404691 GGAAGGGTCCAAGCACTG 57.595 61.111 0.00 0.00 44.26 3.66
4171 5212 6.158598 CAGGGACAAACAAATCCACAAATAG 58.841 40.000 0.00 0.00 36.65 1.73
4177 5218 1.963515 AGCAGGGACAAACAAATCCAC 59.036 47.619 0.00 0.00 36.65 4.02
4200 5241 5.181748 ACTTAGCATGACAACATTCCTCTC 58.818 41.667 0.00 0.00 34.15 3.20
4237 5280 8.107095 AGCACAGTAAAGGGATTATTTCTGTTA 58.893 33.333 0.00 0.00 31.59 2.41
4238 5281 6.948309 AGCACAGTAAAGGGATTATTTCTGTT 59.052 34.615 0.00 0.00 31.59 3.16
4239 5282 6.485171 AGCACAGTAAAGGGATTATTTCTGT 58.515 36.000 0.00 0.00 32.87 3.41
4240 5283 7.396540 AAGCACAGTAAAGGGATTATTTCTG 57.603 36.000 0.00 0.00 0.00 3.02
4241 5284 6.316390 CGAAGCACAGTAAAGGGATTATTTCT 59.684 38.462 0.00 0.00 0.00 2.52
4242 5285 6.093633 ACGAAGCACAGTAAAGGGATTATTTC 59.906 38.462 0.00 0.00 0.00 2.17
4246 5289 4.250464 CACGAAGCACAGTAAAGGGATTA 58.750 43.478 0.00 0.00 0.00 1.75
4255 5298 4.213270 CAGAAAATTCCACGAAGCACAGTA 59.787 41.667 0.00 0.00 0.00 2.74
4263 5306 2.841215 ACGACCAGAAAATTCCACGAA 58.159 42.857 0.00 0.00 0.00 3.85
4266 5309 6.980051 ATAAGTACGACCAGAAAATTCCAC 57.020 37.500 0.00 0.00 0.00 4.02
4277 5321 2.428171 GCACCCAGTATAAGTACGACCA 59.572 50.000 0.00 0.00 35.92 4.02
4282 5326 3.899052 TGTGGCACCCAGTATAAGTAC 57.101 47.619 16.26 0.00 32.34 2.73
4309 5353 7.928908 TTCGTAACCGCGTAAAATATATCTT 57.071 32.000 4.92 0.00 0.00 2.40
4310 5354 8.025445 AGATTCGTAACCGCGTAAAATATATCT 58.975 33.333 4.92 1.60 0.00 1.98
4314 5358 7.809331 TGATAGATTCGTAACCGCGTAAAATAT 59.191 33.333 4.92 0.00 0.00 1.28
4322 5366 3.369385 ACTTGATAGATTCGTAACCGCG 58.631 45.455 0.00 0.00 0.00 6.46
4323 5367 5.517904 AGTACTTGATAGATTCGTAACCGC 58.482 41.667 0.00 0.00 0.00 5.68
4324 5368 6.141462 GGAGTACTTGATAGATTCGTAACCG 58.859 44.000 0.00 0.00 0.00 4.44
4330 5374 4.083217 CGGAGGGAGTACTTGATAGATTCG 60.083 50.000 0.00 0.00 0.00 3.34
4332 5376 4.805744 ACGGAGGGAGTACTTGATAGATT 58.194 43.478 0.00 0.00 0.00 2.40
4339 5383 2.431954 TAGGACGGAGGGAGTACTTG 57.568 55.000 0.00 0.00 34.13 3.16
4392 5436 8.885900 ATATACTCCCTTTGCCCCATAATATA 57.114 34.615 0.00 0.00 0.00 0.86
4417 5461 9.256477 CTCTAGCGTTGTTGGTTATCAATTATA 57.744 33.333 0.00 0.00 37.73 0.98
4418 5462 7.254795 GCTCTAGCGTTGTTGGTTATCAATTAT 60.255 37.037 0.00 0.00 37.73 1.28
4423 5467 3.259064 GCTCTAGCGTTGTTGGTTATCA 58.741 45.455 0.00 0.00 0.00 2.15
4425 5469 3.328382 TGCTCTAGCGTTGTTGGTTAT 57.672 42.857 0.00 0.00 45.83 1.89
4426 5470 2.823924 TGCTCTAGCGTTGTTGGTTA 57.176 45.000 0.00 0.00 45.83 2.85
4427 5471 2.185004 ATGCTCTAGCGTTGTTGGTT 57.815 45.000 0.00 0.00 45.83 3.67
4428 5472 3.935993 ATGCTCTAGCGTTGTTGGT 57.064 47.368 0.00 0.00 45.83 3.67
4460 5504 7.812306 AGCTATAAGCCCAAATAACTAAAGGA 58.188 34.615 0.00 0.00 43.77 3.36
4461 5505 9.740710 ATAGCTATAAGCCCAAATAACTAAAGG 57.259 33.333 3.84 0.00 43.77 3.11
4473 5517 3.244561 GGAACAGCATAGCTATAAGCCCA 60.245 47.826 5.77 0.00 43.77 5.36
4476 5520 4.380531 TGTGGAACAGCATAGCTATAAGC 58.619 43.478 5.77 6.93 45.67 3.09
4540 5584 6.240894 ACTGTGACACAATCCAGAATGTATT 58.759 36.000 10.02 0.00 32.72 1.89
4541 5585 5.809001 ACTGTGACACAATCCAGAATGTAT 58.191 37.500 10.02 0.00 32.72 2.29
4555 5599 2.031069 TGCTCTTCGAGTACTGTGACAC 60.031 50.000 0.00 0.00 31.39 3.67
4563 5607 2.094700 TGTGGACATGCTCTTCGAGTAC 60.095 50.000 0.00 0.00 31.39 2.73


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

AutoCloner maintained by Alex Coulton.