Multiple sequence alignment - TraesCS3D01G298300

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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 TraesCS3D01G298300 chr3D 100.000 2884 0 0 1 2884 412357681 412354798 0.000000e+00 5326.0
1 TraesCS3D01G298300 chr3D 82.836 134 22 1 2464 2597 198092949 198092817 5.050000e-23 119.0
2 TraesCS3D01G298300 chr3A 89.791 1773 108 30 816 2552 537745369 537747104 0.000000e+00 2204.0
3 TraesCS3D01G298300 chr3A 90.354 508 27 10 1 504 537744268 537744757 0.000000e+00 647.0
4 TraesCS3D01G298300 chr3A 92.718 206 12 1 2682 2884 537752168 537752373 7.810000e-76 294.0
5 TraesCS3D01G298300 chr3A 91.176 102 8 1 2582 2683 523731341 523731441 1.390000e-28 137.0
6 TraesCS3D01G298300 chr3A 91.089 101 6 3 2594 2693 726444568 726444470 1.800000e-27 134.0
7 TraesCS3D01G298300 chr3A 94.545 55 3 0 733 787 537745314 537745368 5.120000e-13 86.1
8 TraesCS3D01G298300 chr3B 90.084 595 39 6 1552 2145 539404360 539403785 0.000000e+00 754.0
9 TraesCS3D01G298300 chr3B 88.866 494 25 12 1013 1493 539406581 539406105 5.360000e-162 580.0
10 TraesCS3D01G298300 chr3B 92.337 261 16 2 931 1187 539407035 539406775 4.540000e-98 368.0
11 TraesCS3D01G298300 chr3B 94.156 154 6 1 1039 1189 539406750 539406597 6.210000e-57 231.0
12 TraesCS3D01G298300 chr3B 93.913 115 7 0 125 239 539408447 539408333 1.060000e-39 174.0
13 TraesCS3D01G298300 chr3B 88.028 142 16 1 2181 2321 539403708 539403567 1.780000e-37 167.0
14 TraesCS3D01G298300 chr3B 90.476 105 8 2 2582 2686 452727432 452727330 1.390000e-28 137.0
15 TraesCS3D01G298300 chr3B 82.857 140 22 2 2462 2601 344658448 344658585 1.090000e-24 124.0
16 TraesCS3D01G298300 chr3B 93.333 45 3 0 310 354 539408305 539408261 1.850000e-07 67.6
17 TraesCS3D01G298300 chr7A 85.417 144 19 2 2682 2823 730554328 730554185 6.440000e-32 148.0
18 TraesCS3D01G298300 chr7A 82.482 137 20 2 2465 2601 502760160 502760028 1.820000e-22 117.0
19 TraesCS3D01G298300 chr7A 92.857 42 3 0 2339 2380 509759761 509759802 8.630000e-06 62.1
20 TraesCS3D01G298300 chr4B 85.417 144 18 3 2459 2601 95881283 95881142 2.320000e-31 147.0
21 TraesCS3D01G298300 chr4B 81.250 144 26 1 2682 2824 616313935 616313792 6.530000e-22 115.0
22 TraesCS3D01G298300 chr2B 94.681 94 4 1 2598 2691 31741716 31741624 8.330000e-31 145.0
23 TraesCS3D01G298300 chr2B 96.552 87 3 0 2598 2684 201234349 201234263 8.330000e-31 145.0
24 TraesCS3D01G298300 chr2B 78.862 123 17 8 1 123 559428334 559428221 1.110000e-09 75.0
25 TraesCS3D01G298300 chr1D 89.076 119 9 3 2590 2707 265533234 265533119 8.330000e-31 145.0
26 TraesCS3D01G298300 chr6B 85.106 141 19 2 2683 2821 620273282 620273142 3.000000e-30 143.0
27 TraesCS3D01G298300 chr6B 92.708 96 7 0 2592 2687 702668835 702668740 3.870000e-29 139.0
28 TraesCS3D01G298300 chr1A 87.705 122 15 0 1 122 428194665 428194544 3.000000e-30 143.0
29 TraesCS3D01G298300 chr4A 85.106 141 18 3 2461 2601 476176493 476176356 1.080000e-29 141.0
30 TraesCS3D01G298300 chr4A 83.803 142 21 1 2682 2821 669831411 669831270 1.800000e-27 134.0
31 TraesCS3D01G298300 chr7D 87.826 115 9 5 2574 2684 405908523 405908636 2.330000e-26 130.0
32 TraesCS3D01G298300 chr5A 85.075 134 11 9 2577 2707 338846076 338845949 8.390000e-26 128.0
33 TraesCS3D01G298300 chr5A 82.301 113 13 6 2682 2792 368551811 368551704 1.100000e-14 91.6
34 TraesCS3D01G298300 chr2A 83.571 140 17 5 2462 2601 75287287 75287154 3.020000e-25 126.0
35 TraesCS3D01G298300 chr2A 83.898 118 11 6 2695 2804 755253688 755253571 3.930000e-19 106.0
36 TraesCS3D01G298300 chrUn 86.364 110 11 4 2470 2578 25017030 25016924 1.820000e-22 117.0
37 TraesCS3D01G298300 chr7B 81.884 138 23 2 2464 2601 698925705 698925570 6.530000e-22 115.0
38 TraesCS3D01G298300 chr6A 82.171 129 13 3 1 123 24032388 24032512 5.080000e-18 102.0
39 TraesCS3D01G298300 chr6D 87.302 63 7 1 2342 2404 110214382 110214321 1.430000e-08 71.3
40 TraesCS3D01G298300 chr6D 84.211 57 7 2 2736 2792 100041537 100041483 1.000000e-03 54.7
41 TraesCS3D01G298300 chr5B 93.478 46 3 0 2735 2780 679140830 679140875 5.160000e-08 69.4


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 TraesCS3D01G298300 chr3D 412354798 412357681 2883 True 5326.000000 5326 100.000000 1 2884 1 chr3D.!!$R2 2883
1 TraesCS3D01G298300 chr3A 537744268 537747104 2836 False 979.033333 2204 91.563333 1 2552 3 chr3A.!!$F3 2551
2 TraesCS3D01G298300 chr3B 539403567 539408447 4880 True 334.514286 754 91.531000 125 2321 7 chr3B.!!$R2 2196

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
838 1859 0.038435 TCGGTTTATCGTGGACGCAA 60.038 50.0 0.0 0.0 39.6 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 5612 0.107456 ATGGCCAGCCTAATGTCTCG 59.893 55.0 13.05 0.0 36.94 4.04 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
93 95 8.682936 AATTTGATGTTCATATAGAGGGTGAC 57.317 34.615 0.00 0.00 0.00 3.67
123 125 2.494870 GAGCTCCTGTGCATTTTCCATT 59.505 45.455 0.87 0.00 34.99 3.16
222 224 0.324368 TGGACGGCTGATACTGGTCT 60.324 55.000 0.00 0.00 0.00 3.85
298 301 5.653346 TGTACCCTCCGTCCCATAATATAA 58.347 41.667 0.00 0.00 0.00 0.98
303 306 5.269991 CCTCCGTCCCATAATATAAGAGGA 58.730 45.833 0.00 0.00 40.69 3.71
308 311 8.120538 TCCGTCCCATAATATAAGAGGAAGTAT 58.879 37.037 0.00 0.00 0.00 2.12
350 353 3.824443 ACCACGCCTTTAAAATGTAAGCT 59.176 39.130 0.00 0.00 0.00 3.74
388 710 1.909302 TCTTCTCCAACCTAGCTTGGG 59.091 52.381 18.75 11.16 41.15 4.12
403 725 2.883888 GCTTGGGTTGCCATCTTCCTTA 60.884 50.000 0.00 0.00 0.00 2.69
404 726 3.430453 CTTGGGTTGCCATCTTCCTTAA 58.570 45.455 0.00 0.00 0.00 1.85
492 1139 1.673920 CAACCCACAACGCAACTACTT 59.326 47.619 0.00 0.00 0.00 2.24
521 1380 1.406205 GGTAGAGAAGCAAGTGGAGCC 60.406 57.143 0.00 0.00 0.00 4.70
608 1469 5.475273 AGCTCATGTGTCGATGTATTTTG 57.525 39.130 0.00 0.00 0.00 2.44
617 1478 7.815641 TGTGTCGATGTATTTTGTCATGAAAT 58.184 30.769 0.00 0.00 0.00 2.17
637 1658 8.774890 TGAAATTTTGCAAACATGCAGTATAT 57.225 26.923 12.39 0.00 46.21 0.86
794 1815 4.379143 CGCGGACGAGACGTGTCA 62.379 66.667 13.65 0.00 41.37 3.58
795 1816 2.178521 GCGGACGAGACGTGTCAT 59.821 61.111 13.65 0.00 41.37 3.06
796 1817 1.426621 GCGGACGAGACGTGTCATA 59.573 57.895 13.65 0.00 41.37 2.15
797 1818 0.589229 GCGGACGAGACGTGTCATAG 60.589 60.000 13.65 0.00 41.37 2.23
798 1819 1.004595 CGGACGAGACGTGTCATAGA 58.995 55.000 13.65 0.00 41.37 1.98
799 1820 1.395954 CGGACGAGACGTGTCATAGAA 59.604 52.381 13.65 0.00 41.37 2.10
800 1821 2.159612 CGGACGAGACGTGTCATAGAAA 60.160 50.000 13.65 0.00 41.37 2.52
801 1822 3.169733 GGACGAGACGTGTCATAGAAAC 58.830 50.000 13.65 0.00 41.37 2.78
803 1824 1.578023 CGAGACGTGTCATAGAAACGC 59.422 52.381 13.65 3.46 45.97 4.84
804 1825 1.918609 GAGACGTGTCATAGAAACGCC 59.081 52.381 8.00 0.00 45.97 5.68
805 1826 1.271379 AGACGTGTCATAGAAACGCCA 59.729 47.619 9.46 0.00 45.97 5.69
806 1827 2.063266 GACGTGTCATAGAAACGCCAA 58.937 47.619 9.46 0.00 45.97 4.52
807 1828 1.796459 ACGTGTCATAGAAACGCCAAC 59.204 47.619 9.46 0.00 45.97 3.77
808 1829 3.736475 ACGTGTCATAGAAACGCCAACG 61.736 50.000 9.46 0.00 45.97 4.10
809 1830 2.063266 GTGTCATAGAAACGCCAACGA 58.937 47.619 0.00 0.00 43.93 3.85
810 1831 2.671396 GTGTCATAGAAACGCCAACGAT 59.329 45.455 0.00 0.00 43.93 3.73
811 1832 3.124636 GTGTCATAGAAACGCCAACGATT 59.875 43.478 0.00 0.00 43.93 3.34
812 1833 3.749088 TGTCATAGAAACGCCAACGATTT 59.251 39.130 0.00 0.00 43.93 2.17
813 1834 4.214545 TGTCATAGAAACGCCAACGATTTT 59.785 37.500 0.00 0.00 43.93 1.82
814 1835 5.151389 GTCATAGAAACGCCAACGATTTTT 58.849 37.500 0.00 0.00 43.93 1.94
815 1836 5.283012 GTCATAGAAACGCCAACGATTTTTC 59.717 40.000 0.00 0.00 43.93 2.29
816 1837 3.007979 AGAAACGCCAACGATTTTTCC 57.992 42.857 0.00 0.00 43.93 3.13
817 1838 1.711824 GAAACGCCAACGATTTTTCCG 59.288 47.619 0.00 0.00 43.93 4.30
818 1839 0.662077 AACGCCAACGATTTTTCCGC 60.662 50.000 0.00 0.00 43.93 5.54
819 1840 1.209127 CGCCAACGATTTTTCCGCT 59.791 52.632 0.00 0.00 43.93 5.52
820 1841 0.793104 CGCCAACGATTTTTCCGCTC 60.793 55.000 0.00 0.00 43.93 5.03
837 1858 0.457166 CTCGGTTTATCGTGGACGCA 60.457 55.000 0.00 0.00 39.60 5.24
838 1859 0.038435 TCGGTTTATCGTGGACGCAA 60.038 50.000 0.00 0.00 39.60 4.85
853 1874 3.120385 CAAGAGCATCGCGTGGCA 61.120 61.111 22.44 0.00 42.67 4.92
893 1915 4.072088 CCTCGCGCGTGTTTCCAC 62.072 66.667 30.98 0.00 38.27 4.02
903 1925 1.267334 CGTGTTTCCACCGCATAATCG 60.267 52.381 0.00 0.00 38.41 3.34
904 1926 0.730265 TGTTTCCACCGCATAATCGC 59.270 50.000 0.00 0.00 0.00 4.58
913 1935 3.806257 GCATAATCGCGACAAGTGG 57.194 52.632 12.93 0.00 0.00 4.00
914 1936 1.286501 GCATAATCGCGACAAGTGGA 58.713 50.000 12.93 0.00 0.00 4.02
915 1937 1.004927 GCATAATCGCGACAAGTGGAC 60.005 52.381 12.93 0.00 0.00 4.02
916 1938 1.255342 CATAATCGCGACAAGTGGACG 59.745 52.381 12.93 0.00 0.00 4.79
917 1939 0.241749 TAATCGCGACAAGTGGACGT 59.758 50.000 12.93 0.00 0.00 4.34
918 1940 1.282248 AATCGCGACAAGTGGACGTG 61.282 55.000 12.93 0.00 38.58 4.49
919 1941 2.416244 ATCGCGACAAGTGGACGTGT 62.416 55.000 12.93 0.00 41.09 4.49
920 1942 2.645510 CGCGACAAGTGGACGTGTC 61.646 63.158 13.82 13.82 46.81 3.67
950 1972 2.673523 GCCCAGTCTGGTGCAGAT 59.326 61.111 21.07 0.00 42.73 2.90
982 2005 4.973360 CGTTGCAAACCGGCGGTG 62.973 66.667 34.87 22.43 46.28 4.94
1089 2288 1.447489 CAAGAGAGCTCCTGCCGTG 60.447 63.158 10.93 2.56 40.80 4.94
1183 2580 1.154073 GTCGTCGGTGCTGTAGGTC 60.154 63.158 0.00 0.00 0.00 3.85
1184 2581 2.202440 CGTCGGTGCTGTAGGTCG 60.202 66.667 0.00 0.00 0.00 4.79
1185 2582 2.181021 GTCGGTGCTGTAGGTCGG 59.819 66.667 0.00 0.00 0.00 4.79
1186 2583 2.282674 TCGGTGCTGTAGGTCGGT 60.283 61.111 0.00 0.00 0.00 4.69
1187 2584 2.126071 CGGTGCTGTAGGTCGGTG 60.126 66.667 0.00 0.00 0.00 4.94
1218 2615 2.719046 CGTCAACGCTTGATTTGTTTCC 59.281 45.455 4.21 0.00 42.47 3.13
1228 2642 1.202348 GATTTGTTTCCCGCCTTCCTG 59.798 52.381 0.00 0.00 0.00 3.86
1229 2643 0.106419 TTTGTTTCCCGCCTTCCTGT 60.106 50.000 0.00 0.00 0.00 4.00
1233 2647 1.423794 TTTCCCGCCTTCCTGTCCTT 61.424 55.000 0.00 0.00 0.00 3.36
1255 2669 2.434702 CCCTCCGGCTAACTCTTGTATT 59.565 50.000 0.00 0.00 0.00 1.89
1374 2788 0.600057 GGCTCTGTTTCTTGCCCTTG 59.400 55.000 0.00 0.00 39.49 3.61
1376 2790 2.504367 GCTCTGTTTCTTGCCCTTGTA 58.496 47.619 0.00 0.00 0.00 2.41
1381 2795 4.041567 TCTGTTTCTTGCCCTTGTATGAGA 59.958 41.667 0.00 0.00 0.00 3.27
1382 2796 4.326826 TGTTTCTTGCCCTTGTATGAGAG 58.673 43.478 0.00 0.00 0.00 3.20
1384 2798 2.191400 TCTTGCCCTTGTATGAGAGCT 58.809 47.619 0.00 0.00 0.00 4.09
1385 2799 2.169352 TCTTGCCCTTGTATGAGAGCTC 59.831 50.000 5.27 5.27 0.00 4.09
1386 2800 0.833287 TGCCCTTGTATGAGAGCTCC 59.167 55.000 10.93 2.40 0.00 4.70
1443 2869 1.639722 AAAATTACCGCCCTTTGCCT 58.360 45.000 0.00 0.00 36.24 4.75
1484 2910 0.036388 CTAACCAGCCGCTCAGGAAA 60.036 55.000 3.80 0.00 45.00 3.13
1496 2927 6.651225 AGCCGCTCAGGAAATATTAATAGTTC 59.349 38.462 21.76 21.76 45.00 3.01
1528 2959 3.192001 TGTAGCAGTATTCTTCGAACGGT 59.808 43.478 0.00 0.00 0.00 4.83
1541 2972 0.824759 GAACGGTCAGGCCTATGAGT 59.175 55.000 3.98 0.26 34.25 3.41
1569 4681 3.196469 CACCGGATCCACAGCTGATATAT 59.804 47.826 23.35 8.00 0.00 0.86
1570 4682 4.402474 CACCGGATCCACAGCTGATATATA 59.598 45.833 23.35 0.00 0.00 0.86
1571 4683 5.069648 CACCGGATCCACAGCTGATATATAT 59.930 44.000 23.35 4.64 0.00 0.86
1572 4684 6.265422 CACCGGATCCACAGCTGATATATATA 59.735 42.308 23.35 0.00 0.00 0.86
1573 4685 7.013220 ACCGGATCCACAGCTGATATATATAT 58.987 38.462 23.35 4.86 0.00 0.86
1574 4686 7.510685 ACCGGATCCACAGCTGATATATATATT 59.489 37.037 23.35 0.00 0.00 1.28
1575 4687 9.025041 CCGGATCCACAGCTGATATATATATTA 57.975 37.037 23.35 2.16 0.00 0.98
1626 4738 7.141363 GCTACACTTTGCTTTATAATGGATGG 58.859 38.462 1.00 0.00 0.00 3.51
1627 4739 5.906073 ACACTTTGCTTTATAATGGATGGC 58.094 37.500 1.00 0.00 0.00 4.40
1697 4809 0.250234 TGGCCTCGTGATGAAGGAAG 59.750 55.000 3.32 0.00 0.00 3.46
1700 4812 2.420687 GGCCTCGTGATGAAGGAAGATT 60.421 50.000 0.00 0.00 0.00 2.40
1702 4814 3.064545 GCCTCGTGATGAAGGAAGATTTG 59.935 47.826 0.00 0.00 0.00 2.32
1754 4867 3.593096 TCTATGCTTCAGTTCACTGCAG 58.407 45.455 13.48 13.48 43.46 4.41
1768 4881 2.214181 CTGCAGTTCTCCCGTAGCGT 62.214 60.000 5.25 0.00 0.00 5.07
1772 4885 0.608582 AGTTCTCCCGTAGCGTGAGT 60.609 55.000 1.53 0.00 33.45 3.41
1787 4900 6.237313 AGCGTGAGTAGATTTTTGTTTACC 57.763 37.500 0.00 0.00 0.00 2.85
1791 4904 7.645402 CGTGAGTAGATTTTTGTTTACCCTTT 58.355 34.615 0.00 0.00 0.00 3.11
1795 4908 7.948357 AGTAGATTTTTGTTTACCCTTTGGTC 58.052 34.615 0.00 0.00 43.06 4.02
1803 4916 0.320374 TACCCTTTGGTCTGCAGACG 59.680 55.000 34.28 23.64 43.06 4.18
1880 4993 4.040461 TCGTGGAGAAGATTCTTCAAAGGT 59.960 41.667 24.51 6.95 44.08 3.50
1915 5028 2.760092 TCACATGTCACCTCGATCATCA 59.240 45.455 0.00 0.00 0.00 3.07
1929 5042 8.158132 ACCTCGATCATCACTAGATAGAACTAA 58.842 37.037 0.00 0.00 31.88 2.24
1986 5100 6.198216 ACAATGTGTTTAATTGCGTTTCAGTC 59.802 34.615 0.00 0.00 38.36 3.51
2085 5199 5.329399 ACTAGAAATGGGCAAACACCAATA 58.671 37.500 0.00 0.00 42.17 1.90
2127 5241 2.410939 TGCTGCTATTCGAGATCATGC 58.589 47.619 0.00 0.00 0.00 4.06
2128 5242 2.036862 TGCTGCTATTCGAGATCATGCT 59.963 45.455 0.00 0.00 0.00 3.79
2301 5459 3.631686 CGGGATTTGAGCATGGTAAATCA 59.368 43.478 24.64 9.74 40.70 2.57
2314 5472 8.303876 AGCATGGTAAATCAAACGTTTTCTATT 58.696 29.630 11.66 8.77 0.00 1.73
2315 5473 8.372521 GCATGGTAAATCAAACGTTTTCTATTG 58.627 33.333 11.66 0.00 0.00 1.90
2362 5520 0.317160 AACTTGTCATCCTCGCGTCA 59.683 50.000 5.77 0.00 0.00 4.35
2363 5521 0.532573 ACTTGTCATCCTCGCGTCAT 59.467 50.000 5.77 0.00 0.00 3.06
2376 5534 4.963953 CCTCGCGTCATTAAAATTGTCATC 59.036 41.667 5.77 0.00 0.00 2.92
2380 5538 6.304445 TCGCGTCATTAAAATTGTCATCAAAC 59.696 34.615 5.77 0.00 37.11 2.93
2407 5565 3.096092 TGATTTGCTATGGTCAAACCCC 58.904 45.455 1.92 0.00 37.50 4.95
2430 5588 5.741982 CCGAACGTTTGGGATTTATCATTTC 59.258 40.000 24.79 0.00 0.00 2.17
2432 5590 6.404293 CGAACGTTTGGGATTTATCATTTCCT 60.404 38.462 7.72 0.00 0.00 3.36
2433 5591 6.850752 ACGTTTGGGATTTATCATTTCCTT 57.149 33.333 0.00 0.00 0.00 3.36
2459 5617 2.006888 TGCGGGATTCATTTTCGAGAC 58.993 47.619 0.00 0.00 0.00 3.36
2466 5624 5.278022 GGGATTCATTTTCGAGACATTAGGC 60.278 44.000 0.00 0.00 0.00 3.93
2499 5657 4.836175 TGATGGTATCTTAGCCGGTATCAA 59.164 41.667 1.90 0.00 0.00 2.57
2501 5659 3.006537 TGGTATCTTAGCCGGTATCAAGC 59.993 47.826 1.90 0.00 0.00 4.01
2507 5665 1.141019 GCCGGTATCAAGCACTCGA 59.859 57.895 1.90 0.00 0.00 4.04
2508 5666 0.872021 GCCGGTATCAAGCACTCGAG 60.872 60.000 11.84 11.84 0.00 4.04
2510 5668 1.534175 CCGGTATCAAGCACTCGAGAC 60.534 57.143 21.68 10.86 0.00 3.36
2520 5678 1.721926 GCACTCGAGACTAGCAAACAC 59.278 52.381 21.68 0.00 0.00 3.32
2521 5679 2.862530 GCACTCGAGACTAGCAAACACA 60.863 50.000 21.68 0.00 0.00 3.72
2523 5681 2.288273 ACTCGAGACTAGCAAACACACC 60.288 50.000 21.68 0.00 0.00 4.16
2543 5702 3.823873 ACCGATGTGGCAGACAATTAAAA 59.176 39.130 0.00 0.00 43.94 1.52
2569 5728 8.927675 AAGAGAGAGAGAGAGTTAAAGTAACA 57.072 34.615 1.33 0.00 41.07 2.41
2570 5729 9.528489 AAGAGAGAGAGAGAGTTAAAGTAACAT 57.472 33.333 1.33 0.00 41.07 2.71
2573 5732 9.403583 AGAGAGAGAGAGTTAAAGTAACATAGG 57.596 37.037 1.33 0.00 41.07 2.57
2574 5733 9.181061 GAGAGAGAGAGTTAAAGTAACATAGGT 57.819 37.037 1.33 0.00 41.07 3.08
2627 5786 9.670442 TCCCTCCATAAACTAATATAAGAGTGT 57.330 33.333 0.00 0.00 0.00 3.55
2656 5815 9.733219 AGATCACTACTTTAGTTATCTAAACGC 57.267 33.333 7.85 0.00 43.99 4.84
2657 5816 9.733219 GATCACTACTTTAGTTATCTAAACGCT 57.267 33.333 2.47 0.00 40.05 5.07
2658 5817 9.733219 ATCACTACTTTAGTTATCTAAACGCTC 57.267 33.333 2.47 0.00 40.05 5.03
2659 5818 8.954350 TCACTACTTTAGTTATCTAAACGCTCT 58.046 33.333 2.47 0.00 40.05 4.09
2660 5819 9.570488 CACTACTTTAGTTATCTAAACGCTCTT 57.430 33.333 2.47 0.00 40.05 2.85
2674 5833 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2675 5834 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2676 5835 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2677 5836 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2678 5837 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2679 5838 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2680 5839 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2681 5840 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
2682 5841 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
2685 5844 9.592196 TTATATTAGTTTACGGAGGGAGTATGT 57.408 33.333 0.00 0.00 0.00 2.29
2686 5845 6.803366 ATTAGTTTACGGAGGGAGTATGTT 57.197 37.500 0.00 0.00 0.00 2.71
2687 5846 7.902920 ATTAGTTTACGGAGGGAGTATGTTA 57.097 36.000 0.00 0.00 0.00 2.41
2688 5847 5.588958 AGTTTACGGAGGGAGTATGTTAC 57.411 43.478 0.00 0.00 0.00 2.50
2689 5848 5.267587 AGTTTACGGAGGGAGTATGTTACT 58.732 41.667 0.00 0.00 42.86 2.24
2690 5849 6.426587 AGTTTACGGAGGGAGTATGTTACTA 58.573 40.000 0.00 0.00 39.59 1.82
2691 5850 7.065504 AGTTTACGGAGGGAGTATGTTACTAT 58.934 38.462 0.00 0.00 39.59 2.12
2692 5851 8.220559 AGTTTACGGAGGGAGTATGTTACTATA 58.779 37.037 0.00 0.00 39.59 1.31
2693 5852 7.986085 TTACGGAGGGAGTATGTTACTATAC 57.014 40.000 0.00 0.00 39.59 1.47
2694 5853 4.999950 ACGGAGGGAGTATGTTACTATACG 59.000 45.833 0.00 0.00 39.59 3.06
2695 5854 4.999950 CGGAGGGAGTATGTTACTATACGT 59.000 45.833 0.00 0.00 39.59 3.57
2696 5855 5.121454 CGGAGGGAGTATGTTACTATACGTC 59.879 48.000 0.00 0.00 39.59 4.34
2697 5856 6.000219 GGAGGGAGTATGTTACTATACGTCA 59.000 44.000 0.00 0.00 39.59 4.35
2698 5857 6.658391 GGAGGGAGTATGTTACTATACGTCAT 59.342 42.308 0.00 0.00 39.59 3.06
2699 5858 7.361885 GGAGGGAGTATGTTACTATACGTCATG 60.362 44.444 0.00 0.00 39.59 3.07
2700 5859 6.072064 AGGGAGTATGTTACTATACGTCATGC 60.072 42.308 0.00 0.00 39.59 4.06
2701 5860 6.294342 GGGAGTATGTTACTATACGTCATGCA 60.294 42.308 0.00 0.00 39.59 3.96
2702 5861 7.313646 GGAGTATGTTACTATACGTCATGCAT 58.686 38.462 0.00 0.00 39.59 3.96
2703 5862 7.273598 GGAGTATGTTACTATACGTCATGCATG 59.726 40.741 21.07 21.07 39.59 4.06
2704 5863 7.658261 AGTATGTTACTATACGTCATGCATGT 58.342 34.615 25.43 9.95 38.32 3.21
2705 5864 8.141909 AGTATGTTACTATACGTCATGCATGTT 58.858 33.333 25.43 13.78 38.32 2.71
2706 5865 9.401873 GTATGTTACTATACGTCATGCATGTTA 57.598 33.333 25.43 15.37 0.00 2.41
2707 5866 8.880878 ATGTTACTATACGTCATGCATGTTAA 57.119 30.769 25.43 10.79 0.00 2.01
2708 5867 8.880878 TGTTACTATACGTCATGCATGTTAAT 57.119 30.769 25.43 16.36 0.00 1.40
2709 5868 9.968870 TGTTACTATACGTCATGCATGTTAATA 57.031 29.630 25.43 16.57 0.00 0.98
2716 5875 9.758651 ATACGTCATGCATGTTAATAAGTAAGA 57.241 29.630 25.43 0.00 0.00 2.10
2717 5876 8.662781 ACGTCATGCATGTTAATAAGTAAGAT 57.337 30.769 25.43 0.00 0.00 2.40
2718 5877 8.765219 ACGTCATGCATGTTAATAAGTAAGATC 58.235 33.333 25.43 0.00 0.00 2.75
2719 5878 8.764287 CGTCATGCATGTTAATAAGTAAGATCA 58.236 33.333 25.43 0.00 0.00 2.92
2788 5947 8.366359 TCATACACTGGTATCATATGTATGCT 57.634 34.615 23.56 2.67 43.57 3.79
2789 5948 9.474313 TCATACACTGGTATCATATGTATGCTA 57.526 33.333 23.56 12.79 43.57 3.49
2790 5949 9.521503 CATACACTGGTATCATATGTATGCTAC 57.478 37.037 19.73 5.78 41.11 3.58
2791 5950 7.782897 ACACTGGTATCATATGTATGCTACT 57.217 36.000 1.90 0.00 36.23 2.57
2792 5951 8.879427 ACACTGGTATCATATGTATGCTACTA 57.121 34.615 1.90 6.84 36.23 1.82
2793 5952 8.961634 ACACTGGTATCATATGTATGCTACTAG 58.038 37.037 18.05 18.05 43.46 2.57
2806 5965 9.643735 ATGTATGCTACTAGTATATAACTCCCC 57.356 37.037 2.33 0.00 39.80 4.81
2807 5966 8.617491 TGTATGCTACTAGTATATAACTCCCCA 58.383 37.037 2.33 0.00 39.80 4.96
2808 5967 7.957992 ATGCTACTAGTATATAACTCCCCAC 57.042 40.000 2.33 0.00 39.80 4.61
2809 5968 7.100068 TGCTACTAGTATATAACTCCCCACT 57.900 40.000 2.33 0.00 39.80 4.00
2810 5969 8.223378 TGCTACTAGTATATAACTCCCCACTA 57.777 38.462 2.33 0.00 39.80 2.74
2811 5970 8.843773 TGCTACTAGTATATAACTCCCCACTAT 58.156 37.037 2.33 0.00 39.80 2.12
2812 5971 9.122779 GCTACTAGTATATAACTCCCCACTATG 57.877 40.741 2.33 0.00 39.80 2.23
2815 5974 8.902881 ACTAGTATATAACTCCCCACTATGAGT 58.097 37.037 0.00 0.00 43.47 3.41
2818 5977 7.835181 AGTATATAACTCCCCACTATGAGTAGC 59.165 40.741 0.00 0.00 40.84 3.58
2819 5978 2.089600 ACTCCCCACTATGAGTAGCC 57.910 55.000 0.00 0.00 39.96 3.93
2820 5979 1.576272 ACTCCCCACTATGAGTAGCCT 59.424 52.381 0.00 0.00 39.96 4.58
2821 5980 2.022918 ACTCCCCACTATGAGTAGCCTT 60.023 50.000 0.00 0.00 39.96 4.35
2822 5981 3.206866 ACTCCCCACTATGAGTAGCCTTA 59.793 47.826 0.00 0.00 39.96 2.69
2823 5982 3.573695 TCCCCACTATGAGTAGCCTTAC 58.426 50.000 0.00 0.00 0.00 2.34
2824 5983 3.206866 TCCCCACTATGAGTAGCCTTACT 59.793 47.826 0.00 0.00 42.79 2.24
2825 5984 3.322254 CCCCACTATGAGTAGCCTTACTG 59.678 52.174 0.00 0.00 40.21 2.74
2826 5985 4.215908 CCCACTATGAGTAGCCTTACTGA 58.784 47.826 0.00 0.00 40.21 3.41
2827 5986 4.835615 CCCACTATGAGTAGCCTTACTGAT 59.164 45.833 0.00 0.00 40.21 2.90
2828 5987 5.305644 CCCACTATGAGTAGCCTTACTGATT 59.694 44.000 0.00 0.00 40.21 2.57
2829 5988 6.183361 CCCACTATGAGTAGCCTTACTGATTT 60.183 42.308 0.00 0.00 40.21 2.17
2830 5989 7.015292 CCCACTATGAGTAGCCTTACTGATTTA 59.985 40.741 0.00 0.00 40.21 1.40
2831 5990 8.421784 CCACTATGAGTAGCCTTACTGATTTAA 58.578 37.037 0.00 0.00 40.21 1.52
2832 5991 9.817809 CACTATGAGTAGCCTTACTGATTTAAA 57.182 33.333 0.00 0.00 40.21 1.52
2834 5993 7.793927 ATGAGTAGCCTTACTGATTTAAAGC 57.206 36.000 0.00 0.00 40.21 3.51
2835 5994 6.707290 TGAGTAGCCTTACTGATTTAAAGCA 58.293 36.000 5.94 5.94 40.21 3.91
2836 5995 6.594159 TGAGTAGCCTTACTGATTTAAAGCAC 59.406 38.462 1.13 0.00 40.21 4.40
2837 5996 6.712276 AGTAGCCTTACTGATTTAAAGCACT 58.288 36.000 1.13 0.00 38.69 4.40
2838 5997 7.848128 AGTAGCCTTACTGATTTAAAGCACTA 58.152 34.615 1.13 0.00 38.69 2.74
2839 5998 7.982354 AGTAGCCTTACTGATTTAAAGCACTAG 59.018 37.037 1.13 0.54 38.69 2.57
2840 5999 5.586643 AGCCTTACTGATTTAAAGCACTAGC 59.413 40.000 1.13 2.08 42.56 3.42
2841 6000 5.354234 GCCTTACTGATTTAAAGCACTAGCA 59.646 40.000 1.13 0.00 45.49 3.49
2842 6001 6.675728 GCCTTACTGATTTAAAGCACTAGCAC 60.676 42.308 1.13 0.00 45.49 4.40
2843 6002 6.371548 CCTTACTGATTTAAAGCACTAGCACA 59.628 38.462 1.13 0.00 45.49 4.57
2844 6003 5.613358 ACTGATTTAAAGCACTAGCACAC 57.387 39.130 1.13 0.00 45.49 3.82
2845 6004 4.152402 ACTGATTTAAAGCACTAGCACACG 59.848 41.667 1.13 0.00 45.49 4.49
2846 6005 4.062293 TGATTTAAAGCACTAGCACACGT 58.938 39.130 1.13 0.00 45.49 4.49
2847 6006 3.870723 TTTAAAGCACTAGCACACGTG 57.129 42.857 15.48 15.48 45.49 4.49
2848 6007 2.519377 TAAAGCACTAGCACACGTGT 57.481 45.000 17.22 17.22 45.49 4.49
2849 6008 2.519377 AAAGCACTAGCACACGTGTA 57.481 45.000 22.90 5.00 45.49 2.90
2850 6009 2.743636 AAGCACTAGCACACGTGTAT 57.256 45.000 22.90 15.53 45.49 2.29
2851 6010 2.279582 AGCACTAGCACACGTGTATC 57.720 50.000 22.90 15.93 45.49 2.24
2852 6011 1.819288 AGCACTAGCACACGTGTATCT 59.181 47.619 22.90 21.92 45.49 1.98
2853 6012 3.014623 AGCACTAGCACACGTGTATCTA 58.985 45.455 22.90 21.87 45.49 1.98
2854 6013 3.632604 AGCACTAGCACACGTGTATCTAT 59.367 43.478 22.90 11.92 45.49 1.98
2855 6014 3.975670 GCACTAGCACACGTGTATCTATC 59.024 47.826 22.90 12.61 41.58 2.08
2856 6015 4.261238 GCACTAGCACACGTGTATCTATCT 60.261 45.833 22.90 13.15 41.58 1.98
2857 6016 5.049612 GCACTAGCACACGTGTATCTATCTA 60.050 44.000 22.90 13.54 41.58 1.98
2858 6017 6.364261 CACTAGCACACGTGTATCTATCTAC 58.636 44.000 22.90 2.63 0.00 2.59
2859 6018 4.469625 AGCACACGTGTATCTATCTACG 57.530 45.455 22.90 5.90 41.86 3.51
2861 6020 5.052481 AGCACACGTGTATCTATCTACGTA 58.948 41.667 22.90 0.00 46.62 3.57
2862 6021 5.525012 AGCACACGTGTATCTATCTACGTAA 59.475 40.000 22.90 0.00 46.62 3.18
2863 6022 6.204301 AGCACACGTGTATCTATCTACGTAAT 59.796 38.462 22.90 0.00 46.62 1.89
2864 6023 7.386025 AGCACACGTGTATCTATCTACGTAATA 59.614 37.037 22.90 0.00 46.62 0.98
2865 6024 8.011673 GCACACGTGTATCTATCTACGTAATAA 58.988 37.037 22.90 0.00 46.62 1.40
2866 6025 9.868389 CACACGTGTATCTATCTACGTAATAAA 57.132 33.333 22.90 0.00 46.62 1.40
2883 6042 8.196103 ACGTAATAAAAGGAGAGATTCTACACC 58.804 37.037 0.00 0.00 26.62 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.081476 GGAATCTTGGGATTTCAAACCTGG 60.081 45.833 0.00 0.00 41.68 4.45
68 70 7.442364 CGTCACCCTCTATATGAACATCAAATT 59.558 37.037 0.00 0.00 0.00 1.82
76 78 3.381949 GTGCGTCACCCTCTATATGAAC 58.618 50.000 0.00 0.00 0.00 3.18
160 162 5.548056 CCACCATATAGGGTTCAGGAATACT 59.452 44.000 6.28 0.00 43.89 2.12
260 263 5.251700 GGAGGGTACATATGGATTGGAGATT 59.748 44.000 7.80 0.00 0.00 2.40
261 264 4.785376 GGAGGGTACATATGGATTGGAGAT 59.215 45.833 7.80 0.00 0.00 2.75
308 311 7.009357 GCGTGGTATTGAAACTAACAAAAACAA 59.991 33.333 0.00 0.00 0.00 2.83
350 353 7.108847 GGAGAAGATTTGGAGAGATTTGAAGA 58.891 38.462 0.00 0.00 0.00 2.87
388 710 7.011857 CAGAATAGACTTAAGGAAGATGGCAAC 59.988 40.741 7.53 0.00 36.45 4.17
403 725 3.327757 TGTGGACAAGGCAGAATAGACTT 59.672 43.478 0.00 0.00 37.32 3.01
404 726 2.906389 TGTGGACAAGGCAGAATAGACT 59.094 45.455 0.00 0.00 0.00 3.24
492 1139 1.183549 GCTTCTCTACCTTGTCCGGA 58.816 55.000 0.00 0.00 0.00 5.14
673 1694 9.540431 AATCAAAACAAATGTTTCAAAGTTTCG 57.460 25.926 11.61 0.00 46.47 3.46
718 1739 2.675519 GTGCTCGAGCTCCATTGAG 58.324 57.895 35.27 9.94 42.66 3.02
725 1746 1.493311 CGTTTTGGTGCTCGAGCTC 59.507 57.895 35.27 31.07 42.66 4.09
727 1748 2.127232 GCGTTTTGGTGCTCGAGC 60.127 61.111 30.42 30.42 42.50 5.03
728 1749 0.238289 AATGCGTTTTGGTGCTCGAG 59.762 50.000 8.45 8.45 0.00 4.04
729 1750 0.665835 AAATGCGTTTTGGTGCTCGA 59.334 45.000 0.00 0.00 0.00 4.04
730 1751 1.052287 GAAATGCGTTTTGGTGCTCG 58.948 50.000 5.17 0.00 0.00 5.03
731 1752 2.053627 CAGAAATGCGTTTTGGTGCTC 58.946 47.619 5.17 0.00 0.00 4.26
787 1808 1.796459 GTTGGCGTTTCTATGACACGT 59.204 47.619 7.83 0.00 37.92 4.49
790 1811 2.442212 TCGTTGGCGTTTCTATGACA 57.558 45.000 0.00 0.00 39.49 3.58
791 1812 4.336532 AAATCGTTGGCGTTTCTATGAC 57.663 40.909 0.00 0.00 39.49 3.06
793 1814 4.557301 GGAAAAATCGTTGGCGTTTCTATG 59.443 41.667 0.00 0.00 39.49 2.23
794 1815 4.670735 CGGAAAAATCGTTGGCGTTTCTAT 60.671 41.667 0.00 0.00 39.49 1.98
795 1816 3.364167 CGGAAAAATCGTTGGCGTTTCTA 60.364 43.478 0.00 0.00 39.49 2.10
796 1817 2.603652 CGGAAAAATCGTTGGCGTTTCT 60.604 45.455 0.00 0.00 39.49 2.52
797 1818 1.711824 CGGAAAAATCGTTGGCGTTTC 59.288 47.619 0.00 0.00 39.49 2.78
798 1819 1.761206 CGGAAAAATCGTTGGCGTTT 58.239 45.000 0.00 0.00 39.49 3.60
799 1820 0.662077 GCGGAAAAATCGTTGGCGTT 60.662 50.000 0.00 0.00 39.49 4.84
800 1821 1.081708 GCGGAAAAATCGTTGGCGT 60.082 52.632 0.00 0.00 39.49 5.68
801 1822 0.793104 GAGCGGAAAAATCGTTGGCG 60.793 55.000 0.00 0.00 39.92 5.69
802 1823 0.793104 CGAGCGGAAAAATCGTTGGC 60.793 55.000 0.00 0.00 0.00 4.52
803 1824 0.179200 CCGAGCGGAAAAATCGTTGG 60.179 55.000 2.00 0.00 37.50 3.77
804 1825 0.515564 ACCGAGCGGAAAAATCGTTG 59.484 50.000 16.83 0.00 38.96 4.10
805 1826 1.232119 AACCGAGCGGAAAAATCGTT 58.768 45.000 16.83 0.00 38.96 3.85
806 1827 1.232119 AAACCGAGCGGAAAAATCGT 58.768 45.000 16.83 0.00 38.96 3.73
807 1828 3.604392 GATAAACCGAGCGGAAAAATCG 58.396 45.455 16.83 0.00 38.96 3.34
808 1829 3.063045 ACGATAAACCGAGCGGAAAAATC 59.937 43.478 16.83 10.98 38.96 2.17
809 1830 3.004862 ACGATAAACCGAGCGGAAAAAT 58.995 40.909 16.83 3.48 38.96 1.82
810 1831 2.158058 CACGATAAACCGAGCGGAAAAA 59.842 45.455 16.83 0.00 38.96 1.94
811 1832 1.727880 CACGATAAACCGAGCGGAAAA 59.272 47.619 16.83 0.18 38.96 2.29
812 1833 1.352114 CACGATAAACCGAGCGGAAA 58.648 50.000 16.83 0.55 38.96 3.13
813 1834 0.458889 CCACGATAAACCGAGCGGAA 60.459 55.000 16.83 0.93 38.96 4.30
814 1835 1.140161 CCACGATAAACCGAGCGGA 59.860 57.895 16.83 0.00 38.96 5.54
815 1836 1.140161 TCCACGATAAACCGAGCGG 59.860 57.895 7.48 7.48 42.03 5.52
816 1837 1.469126 CGTCCACGATAAACCGAGCG 61.469 60.000 0.00 0.00 43.02 5.03
817 1838 1.749609 GCGTCCACGATAAACCGAGC 61.750 60.000 2.58 0.00 43.02 5.03
818 1839 0.457166 TGCGTCCACGATAAACCGAG 60.457 55.000 2.58 0.00 43.02 4.63
819 1840 0.038435 TTGCGTCCACGATAAACCGA 60.038 50.000 2.58 0.00 43.02 4.69
820 1841 0.368907 CTTGCGTCCACGATAAACCG 59.631 55.000 2.58 0.00 43.02 4.44
837 1858 2.358615 TTGCCACGCGATGCTCTT 60.359 55.556 15.93 0.00 0.00 2.85
838 1859 2.816958 CTTGCCACGCGATGCTCT 60.817 61.111 15.93 0.00 0.00 4.09
861 1883 4.423209 AGGGTGAGGGAGAGGGCC 62.423 72.222 0.00 0.00 0.00 5.80
903 1925 3.231501 GACACGTCCACTTGTCGC 58.768 61.111 1.02 0.00 35.83 5.19
934 1956 1.407437 GGTAATCTGCACCAGACTGGG 60.407 57.143 25.34 14.87 43.63 4.45
938 1960 0.462047 CCCGGTAATCTGCACCAGAC 60.462 60.000 0.00 0.00 43.63 3.51
939 1961 1.904771 CCCGGTAATCTGCACCAGA 59.095 57.895 0.00 0.00 44.99 3.86
942 1964 0.963355 TTTGCCCGGTAATCTGCACC 60.963 55.000 0.00 0.00 32.63 5.01
950 1972 1.071814 AACGCTCTTTGCCCGGTAA 59.928 52.632 0.00 0.00 38.78 2.85
966 1989 4.639171 CCACCGCCGGTTTGCAAC 62.639 66.667 5.76 0.00 31.02 4.17
1218 2615 2.269241 GGAAGGACAGGAAGGCGG 59.731 66.667 0.00 0.00 0.00 6.13
1255 2669 0.546122 AAGCCGGCAGATACCATCAA 59.454 50.000 31.54 0.00 0.00 2.57
1382 2796 1.510480 AACGAACAGCAAGCAGGAGC 61.510 55.000 0.00 0.00 42.56 4.70
1384 2798 1.165907 CCAACGAACAGCAAGCAGGA 61.166 55.000 0.00 0.00 0.00 3.86
1385 2799 1.283793 CCAACGAACAGCAAGCAGG 59.716 57.895 0.00 0.00 0.00 4.85
1386 2800 1.370900 GCCAACGAACAGCAAGCAG 60.371 57.895 0.00 0.00 0.00 4.24
1431 2857 1.474330 ATTTAGAAGGCAAAGGGCGG 58.526 50.000 0.00 0.00 46.16 6.13
1443 2869 4.286910 GCAGTGTTGCGTTGAATTTAGAA 58.713 39.130 0.00 0.00 41.13 2.10
1496 2927 5.978814 AGAATACTGCTACAACCCTAAGTG 58.021 41.667 0.00 0.00 0.00 3.16
1528 2959 1.050988 GCCCTGACTCATAGGCCTGA 61.051 60.000 17.99 4.75 39.60 3.86
1541 2972 3.399181 GTGGATCCGGTGCCCTGA 61.399 66.667 7.39 0.00 0.00 3.86
1569 4681 8.561769 TGACCAAGTTTGAAAGGGGATAATATA 58.438 33.333 0.00 0.00 0.00 0.86
1570 4682 7.418378 TGACCAAGTTTGAAAGGGGATAATAT 58.582 34.615 0.00 0.00 0.00 1.28
1571 4683 6.795590 TGACCAAGTTTGAAAGGGGATAATA 58.204 36.000 0.00 0.00 0.00 0.98
1572 4684 5.650283 TGACCAAGTTTGAAAGGGGATAAT 58.350 37.500 0.00 0.00 0.00 1.28
1573 4685 5.068215 TGACCAAGTTTGAAAGGGGATAA 57.932 39.130 0.00 0.00 0.00 1.75
1574 4686 4.733077 TGACCAAGTTTGAAAGGGGATA 57.267 40.909 0.00 0.00 0.00 2.59
1575 4687 3.611025 TGACCAAGTTTGAAAGGGGAT 57.389 42.857 0.00 0.00 0.00 3.85
1626 4738 6.970484 TGTTCAATCTAAACAAAGAGAAGGC 58.030 36.000 0.00 0.00 33.86 4.35
1687 4799 7.539712 TCGAACATACAAATCTTCCTTCATC 57.460 36.000 0.00 0.00 0.00 2.92
1697 4809 4.498009 CCCTTGGCATCGAACATACAAATC 60.498 45.833 0.00 0.00 0.00 2.17
1700 4812 2.290641 ACCCTTGGCATCGAACATACAA 60.291 45.455 0.00 0.00 0.00 2.41
1702 4814 1.670811 CACCCTTGGCATCGAACATAC 59.329 52.381 0.00 0.00 0.00 2.39
1768 4881 7.947282 CCAAAGGGTAAACAAAAATCTACTCA 58.053 34.615 0.00 0.00 0.00 3.41
1787 4900 0.588252 CAACGTCTGCAGACCAAAGG 59.412 55.000 35.07 24.60 41.86 3.11
1791 4904 0.529773 GTCACAACGTCTGCAGACCA 60.530 55.000 35.07 13.67 41.86 4.02
1803 4916 1.641677 GACAGCACACCGTCACAAC 59.358 57.895 0.00 0.00 32.24 3.32
1812 4925 1.002033 CAAAGAAGCAGGACAGCACAC 60.002 52.381 0.00 0.00 36.85 3.82
1880 4993 7.039574 AGGTGACATGTGATTGATGATTTTCAA 60.040 33.333 1.15 0.00 39.77 2.69
1915 5028 5.369110 TCTCCCGTCCTTAGTTCTATCTAGT 59.631 44.000 0.00 0.00 0.00 2.57
1929 5042 0.971447 GCCTTACAGTCTCCCGTCCT 60.971 60.000 0.00 0.00 0.00 3.85
1986 5100 2.755650 ACGACCAGTCTAACTTGCTTG 58.244 47.619 0.00 0.00 0.00 4.01
2127 5241 0.249238 GCGCACCATGAGGACTAGAG 60.249 60.000 0.30 0.00 38.69 2.43
2128 5242 0.970427 TGCGCACCATGAGGACTAGA 60.970 55.000 5.66 0.00 38.69 2.43
2301 5459 8.303876 AGTATGGAATTGCAATAGAAAACGTTT 58.696 29.630 13.39 7.96 0.00 3.60
2314 5472 4.847198 ACATGACTGAGTATGGAATTGCA 58.153 39.130 0.79 0.79 0.00 4.08
2315 5473 4.877823 TGACATGACTGAGTATGGAATTGC 59.122 41.667 0.00 0.00 0.00 3.56
2355 5513 5.538067 TGATGACAATTTTAATGACGCGA 57.462 34.783 15.93 0.00 0.00 5.87
2357 5515 7.219922 GTGTTTGATGACAATTTTAATGACGC 58.780 34.615 0.00 0.00 35.85 5.19
2380 5538 4.418013 TGACCATAGCAAATCAAACGTG 57.582 40.909 0.00 0.00 0.00 4.49
2387 5545 2.099098 CGGGGTTTGACCATAGCAAATC 59.901 50.000 0.00 0.00 41.02 2.17
2393 5551 1.338389 ACGTTCGGGGTTTGACCATAG 60.338 52.381 0.00 0.00 41.02 2.23
2407 5565 5.741982 GGAAATGATAAATCCCAAACGTTCG 59.258 40.000 0.00 0.00 0.00 3.95
2442 5600 5.278022 GCCTAATGTCTCGAAAATGAATCCC 60.278 44.000 0.00 0.00 0.00 3.85
2452 5610 0.178068 GGCCAGCCTAATGTCTCGAA 59.822 55.000 0.00 0.00 0.00 3.71
2454 5612 0.107456 ATGGCCAGCCTAATGTCTCG 59.893 55.000 13.05 0.00 36.94 4.04
2459 5617 2.936919 TCACTATGGCCAGCCTAATG 57.063 50.000 13.05 0.00 36.94 1.90
2499 5657 1.613925 TGTTTGCTAGTCTCGAGTGCT 59.386 47.619 13.13 13.96 0.00 4.40
2501 5659 2.726760 GTGTGTTTGCTAGTCTCGAGTG 59.273 50.000 13.13 2.96 0.00 3.51
2507 5665 2.037251 ACATCGGTGTGTTTGCTAGTCT 59.963 45.455 0.00 0.00 37.14 3.24
2508 5666 2.413837 ACATCGGTGTGTTTGCTAGTC 58.586 47.619 0.00 0.00 37.14 2.59
2520 5678 1.167851 AATTGTCTGCCACATCGGTG 58.832 50.000 0.00 0.00 44.85 4.94
2521 5679 2.779755 TAATTGTCTGCCACATCGGT 57.220 45.000 0.00 0.00 33.90 4.69
2543 5702 9.357161 TGTTACTTTAACTCTCTCTCTCTCTTT 57.643 33.333 0.00 0.00 39.38 2.52
2601 5760 9.670442 ACACTCTTATATTAGTTTATGGAGGGA 57.330 33.333 0.00 0.00 0.00 4.20
2631 5790 9.733219 AGCGTTTAGATAACTAAAGTAGTGATC 57.267 33.333 5.51 5.03 45.42 2.92
2632 5791 9.733219 GAGCGTTTAGATAACTAAAGTAGTGAT 57.267 33.333 5.51 0.00 45.42 3.06
2633 5792 8.954350 AGAGCGTTTAGATAACTAAAGTAGTGA 58.046 33.333 5.51 0.00 45.42 3.41
2634 5793 9.570488 AAGAGCGTTTAGATAACTAAAGTAGTG 57.430 33.333 5.51 0.00 45.42 2.74
2648 5807 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2649 5808 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2650 5809 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2651 5810 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2652 5811 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2653 5812 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2654 5813 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2655 5814 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2656 5815 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2659 5818 9.592196 ACATACTCCCTCCGTAAACTAATATAA 57.408 33.333 0.00 0.00 0.00 0.98
2660 5819 9.592196 AACATACTCCCTCCGTAAACTAATATA 57.408 33.333 0.00 0.00 0.00 0.86
2661 5820 8.488308 AACATACTCCCTCCGTAAACTAATAT 57.512 34.615 0.00 0.00 0.00 1.28
2662 5821 7.902920 AACATACTCCCTCCGTAAACTAATA 57.097 36.000 0.00 0.00 0.00 0.98
2663 5822 6.803366 AACATACTCCCTCCGTAAACTAAT 57.197 37.500 0.00 0.00 0.00 1.73
2664 5823 6.891908 AGTAACATACTCCCTCCGTAAACTAA 59.108 38.462 0.00 0.00 32.47 2.24
2665 5824 6.426587 AGTAACATACTCCCTCCGTAAACTA 58.573 40.000 0.00 0.00 32.47 2.24
2666 5825 5.267587 AGTAACATACTCCCTCCGTAAACT 58.732 41.667 0.00 0.00 32.47 2.66
2667 5826 5.588958 AGTAACATACTCCCTCCGTAAAC 57.411 43.478 0.00 0.00 32.47 2.01
2668 5827 7.173218 CGTATAGTAACATACTCCCTCCGTAAA 59.827 40.741 0.00 0.00 40.14 2.01
2669 5828 6.650807 CGTATAGTAACATACTCCCTCCGTAA 59.349 42.308 0.00 0.00 40.14 3.18
2670 5829 6.166279 CGTATAGTAACATACTCCCTCCGTA 58.834 44.000 0.00 0.00 40.14 4.02
2671 5830 4.999950 CGTATAGTAACATACTCCCTCCGT 59.000 45.833 0.00 0.00 40.14 4.69
2672 5831 4.999950 ACGTATAGTAACATACTCCCTCCG 59.000 45.833 0.00 0.00 40.14 4.63
2673 5832 6.000219 TGACGTATAGTAACATACTCCCTCC 59.000 44.000 0.00 0.00 40.14 4.30
2674 5833 7.528307 CATGACGTATAGTAACATACTCCCTC 58.472 42.308 0.00 0.00 40.14 4.30
2675 5834 6.072064 GCATGACGTATAGTAACATACTCCCT 60.072 42.308 0.00 0.00 40.14 4.20
2676 5835 6.091437 GCATGACGTATAGTAACATACTCCC 58.909 44.000 0.00 0.00 40.14 4.30
2677 5836 6.675026 TGCATGACGTATAGTAACATACTCC 58.325 40.000 0.00 0.00 40.14 3.85
2678 5837 7.808381 ACATGCATGACGTATAGTAACATACTC 59.192 37.037 32.75 0.00 40.14 2.59
2679 5838 7.658261 ACATGCATGACGTATAGTAACATACT 58.342 34.615 32.75 0.57 42.68 2.12
2680 5839 7.869016 ACATGCATGACGTATAGTAACATAC 57.131 36.000 32.75 0.00 0.00 2.39
2681 5840 9.968870 TTAACATGCATGACGTATAGTAACATA 57.031 29.630 32.75 1.73 0.00 2.29
2682 5841 8.880878 TTAACATGCATGACGTATAGTAACAT 57.119 30.769 32.75 2.07 0.00 2.71
2683 5842 8.880878 ATTAACATGCATGACGTATAGTAACA 57.119 30.769 32.75 5.80 0.00 2.41
2690 5849 9.758651 TCTTACTTATTAACATGCATGACGTAT 57.241 29.630 32.75 19.76 0.00 3.06
2691 5850 9.758651 ATCTTACTTATTAACATGCATGACGTA 57.241 29.630 32.75 17.53 0.00 3.57
2692 5851 8.662781 ATCTTACTTATTAACATGCATGACGT 57.337 30.769 32.75 18.51 0.00 4.34
2693 5852 8.764287 TGATCTTACTTATTAACATGCATGACG 58.236 33.333 32.75 10.24 0.00 4.35
2762 5921 8.985922 AGCATACATATGATACCAGTGTATGAT 58.014 33.333 21.26 15.63 45.95 2.45
2763 5922 8.366359 AGCATACATATGATACCAGTGTATGA 57.634 34.615 21.26 1.88 45.95 2.15
2764 5923 9.521503 GTAGCATACATATGATACCAGTGTATG 57.478 37.037 16.01 16.01 45.12 2.39
2780 5939 9.643735 GGGGAGTTATATACTAGTAGCATACAT 57.356 37.037 8.85 0.00 40.01 2.29
2781 5940 8.617491 TGGGGAGTTATATACTAGTAGCATACA 58.383 37.037 8.85 0.48 40.01 2.29
2782 5941 8.901793 GTGGGGAGTTATATACTAGTAGCATAC 58.098 40.741 8.85 4.64 38.55 2.39
2783 5942 8.843773 AGTGGGGAGTTATATACTAGTAGCATA 58.156 37.037 8.85 5.92 37.17 3.14
2784 5943 7.710579 AGTGGGGAGTTATATACTAGTAGCAT 58.289 38.462 8.85 6.85 37.17 3.79
2785 5944 7.100068 AGTGGGGAGTTATATACTAGTAGCA 57.900 40.000 8.85 0.00 37.17 3.49
2786 5945 9.122779 CATAGTGGGGAGTTATATACTAGTAGC 57.877 40.741 8.85 0.00 37.17 3.58
2789 5948 8.902881 ACTCATAGTGGGGAGTTATATACTAGT 58.097 37.037 0.00 0.00 41.40 2.57
2792 5951 7.835181 GCTACTCATAGTGGGGAGTTATATACT 59.165 40.741 0.00 0.00 41.40 2.12
2793 5952 7.068470 GGCTACTCATAGTGGGGAGTTATATAC 59.932 44.444 0.00 0.00 41.40 1.47
2794 5953 7.036059 AGGCTACTCATAGTGGGGAGTTATATA 60.036 40.741 0.00 0.00 41.40 0.86
2795 5954 5.958987 GGCTACTCATAGTGGGGAGTTATAT 59.041 44.000 0.00 0.00 41.40 0.86
2796 5955 5.076039 AGGCTACTCATAGTGGGGAGTTATA 59.924 44.000 0.00 0.00 41.40 0.98
2797 5956 4.140663 AGGCTACTCATAGTGGGGAGTTAT 60.141 45.833 0.00 0.00 41.40 1.89
2798 5957 3.206866 AGGCTACTCATAGTGGGGAGTTA 59.793 47.826 0.00 0.00 41.40 2.24
2799 5958 2.022918 AGGCTACTCATAGTGGGGAGTT 60.023 50.000 0.00 0.00 41.40 3.01
2800 5959 1.576272 AGGCTACTCATAGTGGGGAGT 59.424 52.381 0.00 0.00 45.72 3.85
2801 5960 2.390225 AGGCTACTCATAGTGGGGAG 57.610 55.000 0.00 0.00 37.18 4.30
2802 5961 2.868964 AAGGCTACTCATAGTGGGGA 57.131 50.000 0.00 0.00 0.00 4.81
2803 5962 3.322254 CAGTAAGGCTACTCATAGTGGGG 59.678 52.174 0.00 0.00 36.14 4.96
2804 5963 4.215908 TCAGTAAGGCTACTCATAGTGGG 58.784 47.826 0.00 0.00 36.14 4.61
2805 5964 6.412362 AATCAGTAAGGCTACTCATAGTGG 57.588 41.667 0.00 0.00 36.14 4.00
2806 5965 9.817809 TTTAAATCAGTAAGGCTACTCATAGTG 57.182 33.333 0.00 0.00 36.14 2.74
2808 5967 8.983724 GCTTTAAATCAGTAAGGCTACTCATAG 58.016 37.037 0.00 0.00 36.14 2.23
2809 5968 8.482943 TGCTTTAAATCAGTAAGGCTACTCATA 58.517 33.333 0.00 0.00 36.14 2.15
2810 5969 7.281100 GTGCTTTAAATCAGTAAGGCTACTCAT 59.719 37.037 0.00 0.00 36.14 2.90
2811 5970 6.594159 GTGCTTTAAATCAGTAAGGCTACTCA 59.406 38.462 0.00 0.00 36.14 3.41
2812 5971 6.819146 AGTGCTTTAAATCAGTAAGGCTACTC 59.181 38.462 0.00 0.00 36.14 2.59
2813 5972 6.712276 AGTGCTTTAAATCAGTAAGGCTACT 58.288 36.000 0.00 0.00 39.04 2.57
2814 5973 6.986904 AGTGCTTTAAATCAGTAAGGCTAC 57.013 37.500 0.00 0.00 37.08 3.58
2815 5974 6.761714 GCTAGTGCTTTAAATCAGTAAGGCTA 59.238 38.462 7.73 0.00 37.08 3.93
2816 5975 5.586643 GCTAGTGCTTTAAATCAGTAAGGCT 59.413 40.000 7.73 0.00 37.08 4.58
2817 5976 5.354234 TGCTAGTGCTTTAAATCAGTAAGGC 59.646 40.000 7.73 8.71 40.48 4.35
2818 5977 6.371548 TGTGCTAGTGCTTTAAATCAGTAAGG 59.628 38.462 7.73 0.42 40.48 2.69
2819 5978 7.237173 GTGTGCTAGTGCTTTAAATCAGTAAG 58.763 38.462 7.73 4.49 40.48 2.34
2820 5979 6.128661 CGTGTGCTAGTGCTTTAAATCAGTAA 60.129 38.462 7.73 0.00 40.48 2.24
2821 5980 5.347635 CGTGTGCTAGTGCTTTAAATCAGTA 59.652 40.000 6.46 6.46 40.48 2.74
2822 5981 4.152402 CGTGTGCTAGTGCTTTAAATCAGT 59.848 41.667 4.87 4.87 40.48 3.41
2823 5982 4.152402 ACGTGTGCTAGTGCTTTAAATCAG 59.848 41.667 0.00 0.00 40.48 2.90
2824 5983 4.062293 ACGTGTGCTAGTGCTTTAAATCA 58.938 39.130 0.00 0.00 40.48 2.57
2825 5984 4.084013 ACACGTGTGCTAGTGCTTTAAATC 60.084 41.667 22.71 0.00 41.72 2.17
2826 5985 3.813166 ACACGTGTGCTAGTGCTTTAAAT 59.187 39.130 22.71 0.00 41.72 1.40
2827 5986 3.199677 ACACGTGTGCTAGTGCTTTAAA 58.800 40.909 22.71 0.00 41.72 1.52
2828 5987 2.828877 ACACGTGTGCTAGTGCTTTAA 58.171 42.857 22.71 0.00 41.72 1.52
2829 5988 2.519377 ACACGTGTGCTAGTGCTTTA 57.481 45.000 22.71 0.00 41.72 1.85
2830 5989 2.519377 TACACGTGTGCTAGTGCTTT 57.481 45.000 30.83 1.52 41.72 3.51
2831 5990 2.231478 AGATACACGTGTGCTAGTGCTT 59.769 45.455 30.83 2.09 41.72 3.91
2832 5991 1.819288 AGATACACGTGTGCTAGTGCT 59.181 47.619 30.83 13.34 41.72 4.40
2833 5992 2.279582 AGATACACGTGTGCTAGTGC 57.720 50.000 30.83 11.42 41.72 4.40
2834 5993 5.425577 AGATAGATACACGTGTGCTAGTG 57.574 43.478 30.83 0.00 43.46 2.74
2835 5994 5.177142 CGTAGATAGATACACGTGTGCTAGT 59.823 44.000 30.83 21.21 0.00 2.57
2836 5995 5.177142 ACGTAGATAGATACACGTGTGCTAG 59.823 44.000 30.83 18.73 45.14 3.42
2837 5996 5.052481 ACGTAGATAGATACACGTGTGCTA 58.948 41.667 30.83 27.55 45.14 3.49
2838 5997 3.875727 ACGTAGATAGATACACGTGTGCT 59.124 43.478 30.83 26.44 45.14 4.40
2839 5998 4.206698 ACGTAGATAGATACACGTGTGC 57.793 45.455 30.83 21.31 45.14 4.57
2840 5999 9.868389 TTTATTACGTAGATAGATACACGTGTG 57.132 33.333 30.83 12.28 46.19 3.82
2857 6016 8.196103 GGTGTAGAATCTCTCCTTTTATTACGT 58.804 37.037 0.00 0.00 0.00 3.57
2858 6017 8.576936 GGTGTAGAATCTCTCCTTTTATTACG 57.423 38.462 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.