Multiple sequence alignment - TraesCS1D01G029200

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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 TraesCS1D01G029200 chr1D 100.000 5890 0 0 1 5890 11493275 11499164 0.000000e+00 10877.0
1 TraesCS1D01G029200 chr1D 88.772 2556 249 26 2598 5131 11178478 11181017 0.000000e+00 3096.0
2 TraesCS1D01G029200 chr1D 88.782 2487 256 15 2603 5070 11289723 11292205 0.000000e+00 3025.0
3 TraesCS1D01G029200 chr1D 87.495 2391 254 29 2595 4952 11455647 11458025 0.000000e+00 2717.0
4 TraesCS1D01G029200 chr1D 92.292 960 62 2 916 1863 11176953 11177912 0.000000e+00 1352.0
5 TraesCS1D01G029200 chr1A 91.961 3284 241 10 2611 5890 22614382 22611118 0.000000e+00 4580.0
6 TraesCS1D01G029200 chr1A 89.273 2433 247 13 2602 5028 13571225 13573649 0.000000e+00 3035.0
7 TraesCS1D01G029200 chr1A 90.240 2295 204 11 2603 4890 13415677 13417958 0.000000e+00 2979.0
8 TraesCS1D01G029200 chr1A 88.857 2423 253 13 2602 5020 13349001 13351410 0.000000e+00 2963.0
9 TraesCS1D01G029200 chr1A 90.413 2201 205 5 2598 4794 12589105 12586907 0.000000e+00 2891.0
10 TraesCS1D01G029200 chr1A 87.239 2296 269 20 2598 4890 13454715 13456989 0.000000e+00 2595.0
11 TraesCS1D01G029200 chr1A 90.521 960 79 3 916 1863 13453183 13454142 0.000000e+00 1258.0
12 TraesCS1D01G029200 chr1A 85.443 158 22 1 86 243 13345950 13346106 4.720000e-36 163.0
13 TraesCS1D01G029200 chr1A 88.550 131 15 0 113 243 22617366 22617236 6.110000e-35 159.0
14 TraesCS1D01G029200 chr1A 80.000 230 32 12 1873 2099 13315112 13315330 2.200000e-34 158.0
15 TraesCS1D01G029200 chr1A 75.542 323 56 16 4818 5131 12586837 12586529 2.860000e-28 137.0
16 TraesCS1D01G029200 chr1A 95.833 48 2 0 86 133 12597148 12597101 1.760000e-10 78.7
17 TraesCS1D01G029200 chr1B 88.581 2347 238 15 2607 4944 16891890 16894215 0.000000e+00 2822.0
18 TraesCS1D01G029200 chr1B 88.214 2223 252 6 2668 4883 17341988 17344207 0.000000e+00 2645.0
19 TraesCS1D01G029200 chr1B 93.099 855 58 1 1010 1864 16839563 16840416 0.000000e+00 1251.0
20 TraesCS1D01G029200 chr1B 92.614 853 63 0 1010 1862 17339072 17339924 0.000000e+00 1227.0
21 TraesCS1D01G029200 chr1B 93.124 829 57 0 1010 1838 16518256 16519084 0.000000e+00 1216.0
22 TraesCS1D01G029200 chr1B 86.456 886 96 13 999 1869 16856398 16857274 0.000000e+00 950.0
23 TraesCS1D01G029200 chr1B 87.893 413 43 6 2137 2543 16891457 16891868 4.130000e-131 479.0
24 TraesCS1D01G029200 chr1B 88.793 116 13 0 5775 5890 16634545 16634660 6.150000e-30 143.0
25 TraesCS1D01G029200 chr1B 86.486 74 6 3 515 584 16876143 16876216 1.760000e-10 78.7
26 TraesCS1D01G029200 chr1B 80.000 110 12 8 5636 5738 16524075 16524181 8.190000e-09 73.1
27 TraesCS1D01G029200 chrUn 92.614 853 63 0 1010 1862 317005226 317004374 0.000000e+00 1227.0
28 TraesCS1D01G029200 chrUn 92.614 853 63 0 1010 1862 317985026 317984174 0.000000e+00 1227.0
29 TraesCS1D01G029200 chrUn 92.614 853 63 0 1010 1862 346217273 346218125 0.000000e+00 1227.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G029200 chr1D 11493275 11499164 5889 False 10877.0 10877 100.0000 1 5890 1 chr1D.!!$F3 5889
1 TraesCS1D01G029200 chr1D 11289723 11292205 2482 False 3025.0 3025 88.7820 2603 5070 1 chr1D.!!$F1 2467
2 TraesCS1D01G029200 chr1D 11455647 11458025 2378 False 2717.0 2717 87.4950 2595 4952 1 chr1D.!!$F2 2357
3 TraesCS1D01G029200 chr1D 11176953 11181017 4064 False 2224.0 3096 90.5320 916 5131 2 chr1D.!!$F4 4215
4 TraesCS1D01G029200 chr1A 13571225 13573649 2424 False 3035.0 3035 89.2730 2602 5028 1 chr1A.!!$F3 2426
5 TraesCS1D01G029200 chr1A 13415677 13417958 2281 False 2979.0 2979 90.2400 2603 4890 1 chr1A.!!$F2 2287
6 TraesCS1D01G029200 chr1A 22611118 22617366 6248 True 2369.5 4580 90.2555 113 5890 2 chr1A.!!$R3 5777
7 TraesCS1D01G029200 chr1A 13453183 13456989 3806 False 1926.5 2595 88.8800 916 4890 2 chr1A.!!$F5 3974
8 TraesCS1D01G029200 chr1A 13345950 13351410 5460 False 1563.0 2963 87.1500 86 5020 2 chr1A.!!$F4 4934
9 TraesCS1D01G029200 chr1A 12586529 12589105 2576 True 1514.0 2891 82.9775 2598 5131 2 chr1A.!!$R2 2533
10 TraesCS1D01G029200 chr1B 17339072 17344207 5135 False 1936.0 2645 90.4140 1010 4883 2 chr1B.!!$F8 3873
11 TraesCS1D01G029200 chr1B 16891457 16894215 2758 False 1650.5 2822 88.2370 2137 4944 2 chr1B.!!$F7 2807
12 TraesCS1D01G029200 chr1B 16839563 16840416 853 False 1251.0 1251 93.0990 1010 1864 1 chr1B.!!$F4 854
13 TraesCS1D01G029200 chr1B 16518256 16519084 828 False 1216.0 1216 93.1240 1010 1838 1 chr1B.!!$F1 828
14 TraesCS1D01G029200 chr1B 16856398 16857274 876 False 950.0 950 86.4560 999 1869 1 chr1B.!!$F5 870
15 TraesCS1D01G029200 chrUn 317004374 317005226 852 True 1227.0 1227 92.6140 1010 1862 1 chrUn.!!$R1 852
16 TraesCS1D01G029200 chrUn 317984174 317985026 852 True 1227.0 1227 92.6140 1010 1862 1 chrUn.!!$R2 852
17 TraesCS1D01G029200 chrUn 346217273 346218125 852 False 1227.0 1227 92.6140 1010 1862 1 chrUn.!!$F1 852

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
397 830 0.109458 TACCACTCACGATCACACGC 60.109 55.000 0.00 0.0 36.70 5.34 F
563 1136 0.112606 ACTCCCAGAGACCTTGACGA 59.887 55.000 0.00 0.0 33.32 4.20 F
709 1357 0.886563 CTGACCCGGACGTAACTTCT 59.113 55.000 0.73 0.0 0.00 2.85 F
1178 1977 1.008424 CGCGTGACCAGCTCGATAT 60.008 57.895 0.00 0.0 35.64 1.63 F
1200 1999 1.768684 AAGTCAAGCTCTGGGCCGAA 61.769 55.000 0.00 0.0 43.05 4.30 F
2631 3702 1.992667 CGAGTTTGAGACGCATGCTTA 59.007 47.619 17.13 0.0 0.00 3.09 F
3087 5453 0.843309 TTTGACCAGTGGCCAGAAGA 59.157 50.000 5.11 0.0 0.00 2.87 F
4389 6761 0.311165 CCTTCGACGTCTCCGCATAT 59.689 55.000 14.70 0.0 37.70 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1999 1.298953 AGGAGAGCTCTCTGACCTCT 58.701 55.000 36.09 23.49 42.48 3.69 R
2446 3458 2.495155 TGTTGGATCAGTGACCATGG 57.505 50.000 11.19 11.19 36.02 3.66 R
2694 5058 3.299503 ACAAATCACAAAACTCAGGGCT 58.700 40.909 0.00 0.00 0.00 5.19 R
3072 5438 1.067295 TTCATCTTCTGGCCACTGGT 58.933 50.000 0.00 0.00 0.00 4.00 R
3074 5440 1.815003 GGTTTCATCTTCTGGCCACTG 59.185 52.381 0.00 0.00 0.00 3.66 R
4180 6551 0.038744 CACCCAGCATTCTCCCAAGT 59.961 55.000 0.00 0.00 0.00 3.16 R
4570 6942 0.537371 AAGGCCCAAGTCGAAACCAG 60.537 55.000 0.00 0.00 0.00 4.00 R
5645 8101 2.609459 CCAGCCATTCGATGTAACAGAC 59.391 50.000 0.00 0.00 0.00 3.51 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
54 55 3.820557 AGTGCTAAACTTGTGACCATGT 58.179 40.909 0.00 0.00 34.57 3.21
55 56 4.207165 AGTGCTAAACTTGTGACCATGTT 58.793 39.130 0.00 0.00 39.77 2.71
56 57 4.644685 AGTGCTAAACTTGTGACCATGTTT 59.355 37.500 10.32 10.32 45.51 2.83
57 58 5.127031 AGTGCTAAACTTGTGACCATGTTTT 59.873 36.000 10.63 0.00 42.83 2.43
58 59 5.810074 GTGCTAAACTTGTGACCATGTTTTT 59.190 36.000 10.63 0.00 42.83 1.94
59 60 6.975772 GTGCTAAACTTGTGACCATGTTTTTA 59.024 34.615 10.63 0.00 42.83 1.52
60 61 7.167468 GTGCTAAACTTGTGACCATGTTTTTAG 59.833 37.037 10.63 6.07 42.83 1.85
61 62 6.143919 GCTAAACTTGTGACCATGTTTTTAGC 59.856 38.462 10.63 10.57 42.83 3.09
62 63 4.584327 ACTTGTGACCATGTTTTTAGCC 57.416 40.909 0.00 0.00 0.00 3.93
63 64 4.215109 ACTTGTGACCATGTTTTTAGCCT 58.785 39.130 0.00 0.00 0.00 4.58
64 65 4.278419 ACTTGTGACCATGTTTTTAGCCTC 59.722 41.667 0.00 0.00 0.00 4.70
65 66 3.826524 TGTGACCATGTTTTTAGCCTCA 58.173 40.909 0.00 0.00 0.00 3.86
66 67 4.406456 TGTGACCATGTTTTTAGCCTCAT 58.594 39.130 0.00 0.00 0.00 2.90
67 68 4.218200 TGTGACCATGTTTTTAGCCTCATG 59.782 41.667 0.00 0.00 37.83 3.07
70 71 3.806625 CATGTTTTTAGCCTCATGGGG 57.193 47.619 7.48 7.48 35.47 4.96
72 73 2.524306 TGTTTTTAGCCTCATGGGGTG 58.476 47.619 14.66 0.00 46.46 4.61
73 74 2.109128 TGTTTTTAGCCTCATGGGGTGA 59.891 45.455 14.66 3.14 46.46 4.02
83 84 3.731547 TGGGGTGAGCTCCAGATG 58.268 61.111 12.15 0.00 41.16 2.90
84 85 1.229625 TGGGGTGAGCTCCAGATGT 60.230 57.895 12.15 0.00 41.16 3.06
92 93 0.690411 AGCTCCAGATGTGCTAGCCT 60.690 55.000 13.29 0.00 41.81 4.58
133 134 7.896811 TGATATGAGTATGTGGTATGAGGAAC 58.103 38.462 0.00 0.00 0.00 3.62
134 135 5.552870 ATGAGTATGTGGTATGAGGAACC 57.447 43.478 0.00 0.00 37.53 3.62
137 138 5.145564 GAGTATGTGGTATGAGGAACCCTA 58.854 45.833 0.00 0.00 36.06 3.53
147 148 6.990939 GGTATGAGGAACCCTAGTTGATTTAC 59.009 42.308 0.00 0.00 35.94 2.01
181 182 6.433093 TGAATCATGGCTGATATGAATCCAAG 59.567 38.462 0.00 0.00 41.34 3.61
185 186 5.378230 TGGCTGATATGAATCCAAGTTCT 57.622 39.130 0.00 0.00 0.00 3.01
215 216 8.304596 TGTTGTTACTTTGGTTGTGATTGTTTA 58.695 29.630 0.00 0.00 0.00 2.01
226 227 6.202570 GGTTGTGATTGTTTATTGCAACATGT 59.797 34.615 0.00 0.00 36.54 3.21
230 231 8.333908 TGTGATTGTTTATTGCAACATGTTTTC 58.666 29.630 8.77 4.50 36.54 2.29
231 232 8.333908 GTGATTGTTTATTGCAACATGTTTTCA 58.666 29.630 8.77 7.27 36.54 2.69
266 302 6.843069 AAAATTGTTGGTATGAACACAAGC 57.157 33.333 0.00 0.00 35.56 4.01
281 714 1.276421 ACAAGCGGTGCATCTTCTAGT 59.724 47.619 0.00 0.00 0.00 2.57
287 720 2.744202 CGGTGCATCTTCTAGTGCTTTT 59.256 45.455 0.00 0.00 41.78 2.27
288 721 3.425359 CGGTGCATCTTCTAGTGCTTTTG 60.425 47.826 0.00 0.00 41.78 2.44
289 722 3.503748 GGTGCATCTTCTAGTGCTTTTGT 59.496 43.478 4.86 0.00 41.78 2.83
290 723 4.470462 GTGCATCTTCTAGTGCTTTTGTG 58.530 43.478 4.86 0.00 41.78 3.33
303 736 2.797087 GCTTTTGTGATGATGATGCCGG 60.797 50.000 0.00 0.00 0.00 6.13
309 742 2.963928 GATGATGATGCCGGCCACCA 62.964 60.000 26.77 19.13 0.00 4.17
311 744 2.440796 ATGATGCCGGCCACCAAG 60.441 61.111 26.77 0.00 0.00 3.61
330 763 1.059369 CGATGCGCTTCTTTCCACG 59.941 57.895 19.63 3.13 0.00 4.94
333 766 4.103103 GCGCTTCTTTCCACGCCC 62.103 66.667 0.00 0.00 45.35 6.13
334 767 2.668212 CGCTTCTTTCCACGCCCA 60.668 61.111 0.00 0.00 0.00 5.36
335 768 2.954611 GCTTCTTTCCACGCCCAC 59.045 61.111 0.00 0.00 0.00 4.61
336 769 2.626780 GCTTCTTTCCACGCCCACC 61.627 63.158 0.00 0.00 0.00 4.61
337 770 1.971695 CTTCTTTCCACGCCCACCC 60.972 63.158 0.00 0.00 0.00 4.61
338 771 2.690653 CTTCTTTCCACGCCCACCCA 62.691 60.000 0.00 0.00 0.00 4.51
339 772 2.969300 TTCTTTCCACGCCCACCCAC 62.969 60.000 0.00 0.00 0.00 4.61
340 773 4.589675 TTTCCACGCCCACCCACC 62.590 66.667 0.00 0.00 0.00 4.61
360 793 3.892162 CCCACCCACCCACCGAAA 61.892 66.667 0.00 0.00 0.00 3.46
361 794 2.282180 CCACCCACCCACCGAAAG 60.282 66.667 0.00 0.00 0.00 2.62
362 795 2.983592 CACCCACCCACCGAAAGC 60.984 66.667 0.00 0.00 0.00 3.51
363 796 3.494254 ACCCACCCACCGAAAGCA 61.494 61.111 0.00 0.00 0.00 3.91
366 799 1.595093 CCCACCCACCGAAAGCATTC 61.595 60.000 0.00 0.00 0.00 2.67
377 810 3.507622 CCGAAAGCATTCCCTTTCTTCTT 59.492 43.478 11.46 0.00 45.30 2.52
379 812 5.183140 CCGAAAGCATTCCCTTTCTTCTTTA 59.817 40.000 11.46 0.00 45.30 1.85
380 813 6.086871 CGAAAGCATTCCCTTTCTTCTTTAC 58.913 40.000 11.46 0.00 45.30 2.01
381 814 5.984695 AAGCATTCCCTTTCTTCTTTACC 57.015 39.130 0.00 0.00 0.00 2.85
382 815 4.998051 AGCATTCCCTTTCTTCTTTACCA 58.002 39.130 0.00 0.00 0.00 3.25
383 816 4.767409 AGCATTCCCTTTCTTCTTTACCAC 59.233 41.667 0.00 0.00 0.00 4.16
384 817 4.767409 GCATTCCCTTTCTTCTTTACCACT 59.233 41.667 0.00 0.00 0.00 4.00
385 818 5.106118 GCATTCCCTTTCTTCTTTACCACTC 60.106 44.000 0.00 0.00 0.00 3.51
386 819 5.640158 TTCCCTTTCTTCTTTACCACTCA 57.360 39.130 0.00 0.00 0.00 3.41
387 820 4.969484 TCCCTTTCTTCTTTACCACTCAC 58.031 43.478 0.00 0.00 0.00 3.51
388 821 3.746492 CCCTTTCTTCTTTACCACTCACG 59.254 47.826 0.00 0.00 0.00 4.35
389 822 4.502604 CCCTTTCTTCTTTACCACTCACGA 60.503 45.833 0.00 0.00 0.00 4.35
390 823 5.238583 CCTTTCTTCTTTACCACTCACGAT 58.761 41.667 0.00 0.00 0.00 3.73
391 824 5.348997 CCTTTCTTCTTTACCACTCACGATC 59.651 44.000 0.00 0.00 0.00 3.69
392 825 5.462530 TTCTTCTTTACCACTCACGATCA 57.537 39.130 0.00 0.00 0.00 2.92
393 826 4.806330 TCTTCTTTACCACTCACGATCAC 58.194 43.478 0.00 0.00 0.00 3.06
394 827 4.279922 TCTTCTTTACCACTCACGATCACA 59.720 41.667 0.00 0.00 0.00 3.58
395 828 3.909430 TCTTTACCACTCACGATCACAC 58.091 45.455 0.00 0.00 0.00 3.82
396 829 2.341318 TTACCACTCACGATCACACG 57.659 50.000 0.00 0.00 39.31 4.49
397 830 0.109458 TACCACTCACGATCACACGC 60.109 55.000 0.00 0.00 36.70 5.34
403 836 0.666274 TCACGATCACACGCACCTTC 60.666 55.000 0.00 0.00 36.70 3.46
422 855 1.077787 TCCCACATCCAACGCATCC 60.078 57.895 0.00 0.00 0.00 3.51
432 865 1.003355 AACGCATCCACCACTGAGG 60.003 57.895 0.00 0.00 45.67 3.86
456 1013 4.285517 TGTTGCTCTCTTCCTCTCATTCTT 59.714 41.667 0.00 0.00 0.00 2.52
478 1035 1.648568 TCTCCTCCTCTCCTCCATTGT 59.351 52.381 0.00 0.00 0.00 2.71
482 1039 2.465813 CTCCTCTCCTCCATTGTGTCT 58.534 52.381 0.00 0.00 0.00 3.41
486 1043 1.819288 TCTCCTCCATTGTGTCTCGTC 59.181 52.381 0.00 0.00 0.00 4.20
492 1049 0.667487 CATTGTGTCTCGTCGCCTGT 60.667 55.000 0.00 0.00 0.00 4.00
497 1054 2.159476 TGTGTCTCGTCGCCTGTAATAC 60.159 50.000 0.00 0.00 0.00 1.89
500 1057 3.878699 TGTCTCGTCGCCTGTAATACATA 59.121 43.478 0.00 0.00 0.00 2.29
530 1102 0.683973 CAACCTCCACTGAGTGCTCT 59.316 55.000 7.16 0.00 36.86 4.09
540 1112 3.007920 AGTGCTCTCCCCTGCCAG 61.008 66.667 0.00 0.00 0.00 4.85
547 1119 3.005539 TCCCCTGCCAGCTCACTC 61.006 66.667 0.00 0.00 0.00 3.51
550 1122 3.324930 CCTGCCAGCTCACTCCCA 61.325 66.667 0.00 0.00 0.00 4.37
563 1136 0.112606 ACTCCCAGAGACCTTGACGA 59.887 55.000 0.00 0.00 33.32 4.20
611 1230 4.277515 ACTGATTACTTCTGCTGCTTGA 57.722 40.909 0.00 0.00 0.00 3.02
621 1240 3.359950 TCTGCTGCTTGAGAGTCTGATA 58.640 45.455 0.00 0.00 0.00 2.15
641 1260 7.121168 TCTGATAGATTTGTGTTGGTTGAATCC 59.879 37.037 0.00 0.00 0.00 3.01
642 1261 6.718912 TGATAGATTTGTGTTGGTTGAATCCA 59.281 34.615 0.00 0.00 35.49 3.41
647 1269 1.886542 GTGTTGGTTGAATCCAGGGTC 59.113 52.381 0.00 0.00 38.80 4.46
661 1283 2.489971 CAGGGTCGCAGTGAAAAACTA 58.510 47.619 0.00 0.00 36.83 2.24
666 1288 3.933332 GGTCGCAGTGAAAAACTAGCTAT 59.067 43.478 0.00 0.00 36.83 2.97
709 1357 0.886563 CTGACCCGGACGTAACTTCT 59.113 55.000 0.73 0.00 0.00 2.85
735 1383 2.224606 CCTTTCTTGCTGTTCTGCTCA 58.775 47.619 3.65 0.00 0.00 4.26
759 1433 4.262164 CCTTGTTAATCTGCTGGTTTGCTT 60.262 41.667 0.00 0.00 0.00 3.91
760 1434 5.048083 CCTTGTTAATCTGCTGGTTTGCTTA 60.048 40.000 0.00 0.00 0.00 3.09
761 1435 5.371115 TGTTAATCTGCTGGTTTGCTTAC 57.629 39.130 0.00 0.00 0.00 2.34
762 1436 5.070001 TGTTAATCTGCTGGTTTGCTTACT 58.930 37.500 0.00 0.00 0.00 2.24
763 1437 6.234920 TGTTAATCTGCTGGTTTGCTTACTA 58.765 36.000 0.00 0.00 0.00 1.82
764 1438 6.148811 TGTTAATCTGCTGGTTTGCTTACTAC 59.851 38.462 0.00 0.00 0.00 2.73
765 1439 3.762407 TCTGCTGGTTTGCTTACTACA 57.238 42.857 0.00 0.00 0.00 2.74
766 1440 3.664107 TCTGCTGGTTTGCTTACTACAG 58.336 45.455 0.00 0.00 0.00 2.74
767 1441 3.071023 TCTGCTGGTTTGCTTACTACAGT 59.929 43.478 0.00 0.00 0.00 3.55
795 1469 9.660180 GATTATAGTTTCTTCTTCTTCCACACT 57.340 33.333 0.00 0.00 0.00 3.55
817 1507 2.046507 GCAGTGAGCCTCTGGTGG 60.047 66.667 0.00 0.00 37.23 4.61
878 1584 2.348998 CCCCGCTCTGTTCTGCTT 59.651 61.111 0.00 0.00 0.00 3.91
924 1639 5.302823 AGAATCTTGCTAAGTTTTGGCTTGT 59.697 36.000 0.00 0.00 38.08 3.16
954 1669 4.639310 AGTTCTAGAGCTTGGATTGCATTG 59.361 41.667 2.81 0.00 0.00 2.82
965 1680 2.548904 GGATTGCATTGCAGCTCTCTAG 59.451 50.000 11.76 0.00 40.61 2.43
966 1681 2.034104 TTGCATTGCAGCTCTCTAGG 57.966 50.000 11.76 0.00 40.61 3.02
986 1701 5.200368 AGGTTCATCGATTTGCAGTTTTT 57.800 34.783 0.00 0.00 0.00 1.94
1176 1975 4.498520 CCGCGTGACCAGCTCGAT 62.499 66.667 4.92 0.00 35.64 3.59
1178 1977 1.008424 CGCGTGACCAGCTCGATAT 60.008 57.895 0.00 0.00 35.64 1.63
1200 1999 1.768684 AAGTCAAGCTCTGGGCCGAA 61.769 55.000 0.00 0.00 43.05 4.30
1841 2670 4.397417 AGAGAACAAAAGGTATGCATGAGC 59.603 41.667 10.16 3.45 42.57 4.26
1847 2676 3.482156 AAGGTATGCATGAGCTACAGG 57.518 47.619 10.16 0.00 42.74 4.00
1869 2821 9.787435 ACAGGAAAAAGTTACACTATTGTATGA 57.213 29.630 0.00 0.00 38.05 2.15
1954 2906 7.695055 TGTGTTTGATTCTTCCCTCCTTTATA 58.305 34.615 0.00 0.00 0.00 0.98
2021 2975 3.080300 ACTTATTGGCATCGGTCCAAA 57.920 42.857 7.75 0.00 45.63 3.28
2022 2976 3.631250 ACTTATTGGCATCGGTCCAAAT 58.369 40.909 7.75 0.00 45.63 2.32
2072 3036 8.956426 TCAGAGAAATGGGTGTAATAACAATTC 58.044 33.333 0.00 0.00 37.36 2.17
2102 3075 6.834168 ATATTACACACAAAGGAAAGTGGG 57.166 37.500 0.00 0.00 44.54 4.61
2104 3077 3.094484 ACACACAAAGGAAAGTGGGAA 57.906 42.857 1.38 0.00 41.62 3.97
2107 3080 4.141959 ACACACAAAGGAAAGTGGGAAATG 60.142 41.667 1.38 0.00 41.62 2.32
2118 3091 6.868339 GGAAAGTGGGAAATGAATGTTACAAG 59.132 38.462 0.00 0.00 0.00 3.16
2135 3108 8.934507 TGTTACAAGAATTTAAAAACCCACTG 57.065 30.769 0.00 0.00 0.00 3.66
2232 3235 5.168526 TGATTGACGACAAAACAAGAAGG 57.831 39.130 4.09 0.00 39.54 3.46
2291 3297 7.889873 TCCATGACTTTTTCTGGAAACTTAA 57.110 32.000 0.00 0.00 34.91 1.85
2302 3308 8.647143 TTTCTGGAAACTTAAATCAGCAAAAG 57.353 30.769 0.00 0.00 0.00 2.27
2332 3338 6.151985 ACGAAAGGATAATGCCACACAATTTA 59.848 34.615 0.00 0.00 0.00 1.40
2364 3375 5.987098 AGAGGTCATTAGCTGCCATATATG 58.013 41.667 5.68 5.68 32.30 1.78
2412 3424 5.545723 AGGGTCTTTCTGATATATCACCTGG 59.454 44.000 11.49 2.57 32.50 4.45
2467 3536 2.751259 CCATGGTCACTGATCCAACAAG 59.249 50.000 2.57 0.00 37.27 3.16
2470 3539 3.476552 TGGTCACTGATCCAACAAGTTC 58.523 45.455 0.00 0.00 0.00 3.01
2496 3565 7.881232 CCTAGTTGTGTTTTACTCCCTTGAATA 59.119 37.037 0.00 0.00 0.00 1.75
2543 3614 5.224821 TCATCTGATTGGAGGCTCATAAG 57.775 43.478 17.69 4.88 0.00 1.73
2544 3615 4.657504 TCATCTGATTGGAGGCTCATAAGT 59.342 41.667 17.69 0.00 0.00 2.24
2549 3620 6.327365 TCTGATTGGAGGCTCATAAGTCATAA 59.673 38.462 17.69 3.12 0.00 1.90
2555 3626 6.938596 TGGAGGCTCATAAGTCATAATTCATG 59.061 38.462 17.69 0.00 35.81 3.07
2556 3627 6.128063 GGAGGCTCATAAGTCATAATTCATGC 60.128 42.308 17.69 0.00 34.35 4.06
2558 3629 7.002879 AGGCTCATAAGTCATAATTCATGCTT 58.997 34.615 0.00 0.00 36.04 3.91
2559 3630 7.174599 AGGCTCATAAGTCATAATTCATGCTTC 59.825 37.037 0.00 0.00 34.72 3.86
2560 3631 7.040892 GGCTCATAAGTCATAATTCATGCTTCA 60.041 37.037 0.00 0.00 34.72 3.02
2561 3632 8.347771 GCTCATAAGTCATAATTCATGCTTCAA 58.652 33.333 0.00 0.00 34.72 2.69
2562 3633 9.880064 CTCATAAGTCATAATTCATGCTTCAAG 57.120 33.333 0.00 0.00 34.72 3.02
2563 3634 9.617523 TCATAAGTCATAATTCATGCTTCAAGA 57.382 29.630 0.00 0.00 34.72 3.02
2564 3635 9.880064 CATAAGTCATAATTCATGCTTCAAGAG 57.120 33.333 0.00 0.00 34.72 2.85
2565 3636 9.842775 ATAAGTCATAATTCATGCTTCAAGAGA 57.157 29.630 0.00 0.00 34.72 3.10
2566 3637 8.571461 AAGTCATAATTCATGCTTCAAGAGAA 57.429 30.769 0.00 0.00 34.35 2.87
2567 3638 8.749026 AGTCATAATTCATGCTTCAAGAGAAT 57.251 30.769 0.00 0.00 34.35 2.40
2568 3639 8.838365 AGTCATAATTCATGCTTCAAGAGAATC 58.162 33.333 0.00 0.00 34.35 2.52
2569 3640 8.618677 GTCATAATTCATGCTTCAAGAGAATCA 58.381 33.333 0.00 0.00 34.70 2.57
2570 3641 8.618677 TCATAATTCATGCTTCAAGAGAATCAC 58.381 33.333 0.00 0.00 33.19 3.06
2571 3642 6.829229 AATTCATGCTTCAAGAGAATCACA 57.171 33.333 0.00 0.00 37.82 3.58
2572 3643 7.406031 AATTCATGCTTCAAGAGAATCACAT 57.594 32.000 0.00 0.00 37.82 3.21
2573 3644 6.829229 TTCATGCTTCAAGAGAATCACATT 57.171 33.333 0.00 0.00 37.82 2.71
2574 3645 6.190954 TCATGCTTCAAGAGAATCACATTG 57.809 37.500 0.00 0.00 37.82 2.82
2575 3646 5.708697 TCATGCTTCAAGAGAATCACATTGT 59.291 36.000 0.00 0.00 37.82 2.71
2576 3647 6.880529 TCATGCTTCAAGAGAATCACATTGTA 59.119 34.615 0.00 0.00 37.82 2.41
2577 3648 6.732531 TGCTTCAAGAGAATCACATTGTAG 57.267 37.500 0.00 0.00 37.82 2.74
2578 3649 6.466812 TGCTTCAAGAGAATCACATTGTAGA 58.533 36.000 0.00 0.00 37.82 2.59
2579 3650 7.108194 TGCTTCAAGAGAATCACATTGTAGAT 58.892 34.615 0.00 0.00 37.82 1.98
2580 3651 7.609146 TGCTTCAAGAGAATCACATTGTAGATT 59.391 33.333 11.68 11.68 37.82 2.40
2581 3652 8.121708 GCTTCAAGAGAATCACATTGTAGATTC 58.878 37.037 21.61 21.61 46.54 2.52
2631 3702 1.992667 CGAGTTTGAGACGCATGCTTA 59.007 47.619 17.13 0.00 0.00 3.09
2700 5065 5.188434 CACCCATATGTTCATATAGCCCTG 58.812 45.833 1.24 0.00 0.00 4.45
2712 5077 6.662755 TCATATAGCCCTGAGTTTTGTGATT 58.337 36.000 0.00 0.00 0.00 2.57
3072 5438 7.227314 CCATCATTACTATTGCTAGTGCTTTGA 59.773 37.037 0.00 0.00 38.65 2.69
3074 5440 6.538742 TCATTACTATTGCTAGTGCTTTGACC 59.461 38.462 0.00 0.00 38.65 4.02
3087 5453 0.843309 TTTGACCAGTGGCCAGAAGA 59.157 50.000 5.11 0.00 0.00 2.87
3156 5522 7.159322 TCTGGACTAACAGAAGATAACAGTC 57.841 40.000 0.00 0.00 44.03 3.51
3275 5641 7.528481 TCGCGAGATTAATAGAGATAGACTC 57.472 40.000 3.71 0.00 39.69 3.36
3675 6044 4.843728 TCTGTCAAGGTTTGAAGTTCTGT 58.156 39.130 4.17 0.00 42.15 3.41
4121 6492 3.056250 AGTCTCTGTGCAACCTACATCAG 60.056 47.826 0.00 0.00 34.36 2.90
4158 6529 8.638685 AATTATTGATTGCAATTCCGAAGAAG 57.361 30.769 14.33 0.00 41.87 2.85
4180 6551 5.258841 AGCATCTTTTGAACTGATGGATCA 58.741 37.500 0.00 0.00 38.30 2.92
4389 6761 0.311165 CCTTCGACGTCTCCGCATAT 59.689 55.000 14.70 0.00 37.70 1.78
4452 6824 0.538118 TGGGTTCCGCTGTATGGTAC 59.462 55.000 0.00 0.00 0.00 3.34
4470 6842 4.873827 TGGTACACTTTGACTTGAACTGTC 59.126 41.667 0.00 0.00 35.21 3.51
4498 6870 5.574055 CAGCAACGCAGATAATGTTTGAATT 59.426 36.000 0.00 0.00 0.00 2.17
4528 6900 2.854522 CGAGGGCGGAATCAGTTTT 58.145 52.632 0.00 0.00 0.00 2.43
4570 6942 2.159282 TCGCGAAAGAGGATGGTAACTC 60.159 50.000 6.20 0.00 37.61 3.01
4589 6961 0.537371 CTGGTTTCGACTTGGGCCTT 60.537 55.000 4.53 0.00 0.00 4.35
4616 6988 3.764466 CTGCTCTCCCTTCGGCGT 61.764 66.667 6.85 0.00 0.00 5.68
4723 7095 2.383601 ATCCCAACCATCCCCCGAC 61.384 63.158 0.00 0.00 0.00 4.79
4745 7117 2.625314 TGAAATTGACATGTTCCCGCAA 59.375 40.909 0.00 0.00 0.00 4.85
5643 8099 0.445436 CTGAGAGCCATCGTTGTTGC 59.555 55.000 0.00 0.00 0.00 4.17
5644 8100 0.035317 TGAGAGCCATCGTTGTTGCT 59.965 50.000 0.00 0.00 36.62 3.91
5645 8101 0.445436 GAGAGCCATCGTTGTTGCTG 59.555 55.000 2.50 0.00 33.41 4.41
5646 8102 0.250467 AGAGCCATCGTTGTTGCTGT 60.250 50.000 2.50 0.00 33.41 4.40
5749 8207 7.809331 TCATGTTTGTAATGACTGAAATTCTGC 59.191 33.333 0.00 0.00 0.00 4.26
5789 8247 1.401530 TCGTAAACAACTGCGACTCG 58.598 50.000 0.00 0.00 0.00 4.18
5833 8291 7.394359 TCAGAAAATATTTACTTGCTCTGGCTT 59.606 33.333 18.52 0.00 39.59 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.516314 GTCACAAGTTTAGCACTTCTTTTTATT 57.484 29.630 0.00 0.00 44.60 1.40
24 25 8.135529 GGTCACAAGTTTAGCACTTCTTTTTAT 58.864 33.333 0.00 0.00 44.60 1.40
25 26 7.121463 TGGTCACAAGTTTAGCACTTCTTTTTA 59.879 33.333 0.00 0.00 44.60 1.52
26 27 6.071616 TGGTCACAAGTTTAGCACTTCTTTTT 60.072 34.615 0.00 0.00 44.60 1.94
27 28 5.417580 TGGTCACAAGTTTAGCACTTCTTTT 59.582 36.000 0.00 0.00 44.60 2.27
28 29 4.947388 TGGTCACAAGTTTAGCACTTCTTT 59.053 37.500 0.00 0.00 44.60 2.52
29 30 4.523083 TGGTCACAAGTTTAGCACTTCTT 58.477 39.130 0.00 0.00 44.60 2.52
30 31 4.150897 TGGTCACAAGTTTAGCACTTCT 57.849 40.909 0.00 0.00 44.60 2.85
31 32 4.275936 ACATGGTCACAAGTTTAGCACTTC 59.724 41.667 0.00 0.00 44.60 3.01
32 33 6.350949 AAAACATGGTCACAAGTTTAGCACTT 60.351 34.615 0.00 0.00 44.84 3.16
33 34 3.820557 ACATGGTCACAAGTTTAGCACT 58.179 40.909 0.00 0.00 37.30 4.40
34 35 4.568152 AACATGGTCACAAGTTTAGCAC 57.432 40.909 0.00 0.00 35.16 4.40
35 36 5.590530 AAAACATGGTCACAAGTTTAGCA 57.409 34.783 0.00 0.00 44.84 3.49
36 37 6.143919 GCTAAAAACATGGTCACAAGTTTAGC 59.856 38.462 15.78 15.78 44.84 3.09
37 38 6.640907 GGCTAAAAACATGGTCACAAGTTTAG 59.359 38.462 6.15 6.15 44.84 1.85
38 39 6.322712 AGGCTAAAAACATGGTCACAAGTTTA 59.677 34.615 0.00 0.00 44.84 2.01
39 40 5.128663 AGGCTAAAAACATGGTCACAAGTTT 59.871 36.000 0.00 0.00 46.80 2.66
40 41 4.649218 AGGCTAAAAACATGGTCACAAGTT 59.351 37.500 0.00 0.00 39.95 2.66
41 42 4.215109 AGGCTAAAAACATGGTCACAAGT 58.785 39.130 0.00 0.00 0.00 3.16
42 43 4.278170 TGAGGCTAAAAACATGGTCACAAG 59.722 41.667 0.00 0.00 0.00 3.16
43 44 4.211125 TGAGGCTAAAAACATGGTCACAA 58.789 39.130 0.00 0.00 0.00 3.33
44 45 3.826524 TGAGGCTAAAAACATGGTCACA 58.173 40.909 0.00 0.00 0.00 3.58
45 46 4.737054 CATGAGGCTAAAAACATGGTCAC 58.263 43.478 0.00 0.00 37.18 3.67
50 51 3.099141 ACCCCATGAGGCTAAAAACATG 58.901 45.455 6.23 6.23 39.51 3.21
51 52 3.099141 CACCCCATGAGGCTAAAAACAT 58.901 45.455 0.00 0.00 0.00 2.71
52 53 2.109128 TCACCCCATGAGGCTAAAAACA 59.891 45.455 0.00 0.00 31.91 2.83
53 54 2.802719 TCACCCCATGAGGCTAAAAAC 58.197 47.619 0.00 0.00 31.91 2.43
63 64 0.326904 ATCTGGAGCTCACCCCATGA 60.327 55.000 17.19 5.11 35.45 3.07
64 65 0.179026 CATCTGGAGCTCACCCCATG 60.179 60.000 17.19 6.06 0.00 3.66
65 66 0.622738 ACATCTGGAGCTCACCCCAT 60.623 55.000 17.19 0.00 0.00 4.00
66 67 1.229625 ACATCTGGAGCTCACCCCA 60.230 57.895 17.19 3.60 0.00 4.96
67 68 1.222936 CACATCTGGAGCTCACCCC 59.777 63.158 17.19 0.00 0.00 4.95
68 69 1.451028 GCACATCTGGAGCTCACCC 60.451 63.158 17.19 0.00 0.00 4.61
69 70 0.826715 TAGCACATCTGGAGCTCACC 59.173 55.000 17.19 0.00 39.68 4.02
70 71 1.805871 GCTAGCACATCTGGAGCTCAC 60.806 57.143 17.19 5.63 39.68 3.51
71 72 0.463204 GCTAGCACATCTGGAGCTCA 59.537 55.000 17.19 0.61 39.68 4.26
72 73 0.249826 GGCTAGCACATCTGGAGCTC 60.250 60.000 18.24 4.71 39.68 4.09
73 74 0.690411 AGGCTAGCACATCTGGAGCT 60.690 55.000 18.24 0.00 42.14 4.09
74 75 0.179936 AAGGCTAGCACATCTGGAGC 59.820 55.000 18.24 0.00 0.00 4.70
75 76 2.706339 AAAGGCTAGCACATCTGGAG 57.294 50.000 18.24 0.00 0.00 3.86
76 77 3.084039 CAAAAAGGCTAGCACATCTGGA 58.916 45.455 18.24 0.00 0.00 3.86
77 78 2.165030 CCAAAAAGGCTAGCACATCTGG 59.835 50.000 18.24 12.92 0.00 3.86
78 79 3.084039 TCCAAAAAGGCTAGCACATCTG 58.916 45.455 18.24 7.65 37.29 2.90
79 80 3.439857 TCCAAAAAGGCTAGCACATCT 57.560 42.857 18.24 0.57 37.29 2.90
80 81 4.158394 TCAATCCAAAAAGGCTAGCACATC 59.842 41.667 18.24 0.00 37.29 3.06
81 82 4.088634 TCAATCCAAAAAGGCTAGCACAT 58.911 39.130 18.24 0.00 37.29 3.21
82 83 3.495331 TCAATCCAAAAAGGCTAGCACA 58.505 40.909 18.24 0.00 37.29 4.57
83 84 4.427312 CATCAATCCAAAAAGGCTAGCAC 58.573 43.478 18.24 6.06 37.29 4.40
84 85 3.448301 CCATCAATCCAAAAAGGCTAGCA 59.552 43.478 18.24 0.00 37.29 3.49
92 93 6.608405 ACTCATATCAGCCATCAATCCAAAAA 59.392 34.615 0.00 0.00 0.00 1.94
133 134 9.542462 TTCAGATAATTCGTAAATCAACTAGGG 57.458 33.333 0.00 0.00 0.00 3.53
147 148 6.738832 ATCAGCCATGATTCAGATAATTCG 57.261 37.500 0.00 0.00 43.92 3.34
181 182 5.305139 ACCAAAGTAACAACACACAGAAC 57.695 39.130 0.00 0.00 0.00 3.01
185 186 4.519350 TCACAACCAAAGTAACAACACACA 59.481 37.500 0.00 0.00 0.00 3.72
243 244 5.461737 CGCTTGTGTTCATACCAACAATTTT 59.538 36.000 0.00 0.00 38.01 1.82
244 245 4.981674 CGCTTGTGTTCATACCAACAATTT 59.018 37.500 0.00 0.00 38.01 1.82
245 246 4.545610 CGCTTGTGTTCATACCAACAATT 58.454 39.130 0.00 0.00 38.01 2.32
261 297 1.276421 ACTAGAAGATGCACCGCTTGT 59.724 47.619 0.00 2.59 0.00 3.16
262 298 1.662629 CACTAGAAGATGCACCGCTTG 59.337 52.381 0.00 0.00 0.00 4.01
265 301 0.460987 AGCACTAGAAGATGCACCGC 60.461 55.000 0.00 0.00 44.59 5.68
266 302 2.015736 AAGCACTAGAAGATGCACCG 57.984 50.000 0.00 0.00 44.59 4.94
281 714 2.159352 CGGCATCATCATCACAAAAGCA 60.159 45.455 0.00 0.00 0.00 3.91
287 720 1.526686 GGCCGGCATCATCATCACA 60.527 57.895 30.85 0.00 0.00 3.58
288 721 1.526686 TGGCCGGCATCATCATCAC 60.527 57.895 30.85 6.94 0.00 3.06
289 722 1.526686 GTGGCCGGCATCATCATCA 60.527 57.895 30.85 11.59 0.00 3.07
290 723 2.263741 GGTGGCCGGCATCATCATC 61.264 63.158 30.85 13.37 0.00 2.92
317 750 2.668212 TGGGCGTGGAAAGAAGCG 60.668 61.111 0.00 0.00 0.00 4.68
318 751 2.626780 GGTGGGCGTGGAAAGAAGC 61.627 63.158 0.00 0.00 0.00 3.86
319 752 1.971695 GGGTGGGCGTGGAAAGAAG 60.972 63.158 0.00 0.00 0.00 2.85
320 753 2.114411 GGGTGGGCGTGGAAAGAA 59.886 61.111 0.00 0.00 0.00 2.52
321 754 3.172106 TGGGTGGGCGTGGAAAGA 61.172 61.111 0.00 0.00 0.00 2.52
322 755 2.983592 GTGGGTGGGCGTGGAAAG 60.984 66.667 0.00 0.00 0.00 2.62
323 756 4.589675 GGTGGGTGGGCGTGGAAA 62.590 66.667 0.00 0.00 0.00 3.13
343 776 3.860930 CTTTCGGTGGGTGGGTGGG 62.861 68.421 0.00 0.00 0.00 4.61
344 777 2.282180 CTTTCGGTGGGTGGGTGG 60.282 66.667 0.00 0.00 0.00 4.61
345 778 2.983592 GCTTTCGGTGGGTGGGTG 60.984 66.667 0.00 0.00 0.00 4.61
346 779 2.366153 AATGCTTTCGGTGGGTGGGT 62.366 55.000 0.00 0.00 0.00 4.51
347 780 1.595093 GAATGCTTTCGGTGGGTGGG 61.595 60.000 0.00 0.00 0.00 4.61
348 781 1.595093 GGAATGCTTTCGGTGGGTGG 61.595 60.000 6.28 0.00 32.28 4.61
349 782 1.595093 GGGAATGCTTTCGGTGGGTG 61.595 60.000 6.28 0.00 32.28 4.61
350 783 1.304134 GGGAATGCTTTCGGTGGGT 60.304 57.895 6.28 0.00 32.28 4.51
351 784 0.611896 AAGGGAATGCTTTCGGTGGG 60.612 55.000 6.28 0.00 32.28 4.61
352 785 1.202348 GAAAGGGAATGCTTTCGGTGG 59.798 52.381 6.28 0.00 32.28 4.61
353 786 2.162681 AGAAAGGGAATGCTTTCGGTG 58.837 47.619 6.28 0.00 42.48 4.94
354 787 2.586648 AGAAAGGGAATGCTTTCGGT 57.413 45.000 6.28 0.00 42.48 4.69
355 788 3.084786 AGAAGAAAGGGAATGCTTTCGG 58.915 45.455 6.28 0.00 42.48 4.30
356 789 4.773323 AAGAAGAAAGGGAATGCTTTCG 57.227 40.909 6.28 0.00 42.48 3.46
357 790 6.015434 TGGTAAAGAAGAAAGGGAATGCTTTC 60.015 38.462 3.77 3.77 39.20 2.62
358 791 5.838521 TGGTAAAGAAGAAAGGGAATGCTTT 59.161 36.000 0.00 0.00 0.00 3.51
359 792 5.243954 GTGGTAAAGAAGAAAGGGAATGCTT 59.756 40.000 0.00 0.00 0.00 3.91
360 793 4.767409 GTGGTAAAGAAGAAAGGGAATGCT 59.233 41.667 0.00 0.00 0.00 3.79
361 794 4.767409 AGTGGTAAAGAAGAAAGGGAATGC 59.233 41.667 0.00 0.00 0.00 3.56
362 795 6.003950 TGAGTGGTAAAGAAGAAAGGGAATG 58.996 40.000 0.00 0.00 0.00 2.67
363 796 6.004574 GTGAGTGGTAAAGAAGAAAGGGAAT 58.995 40.000 0.00 0.00 0.00 3.01
366 799 3.746492 CGTGAGTGGTAAAGAAGAAAGGG 59.254 47.826 0.00 0.00 0.00 3.95
377 810 1.667756 GCGTGTGATCGTGAGTGGTAA 60.668 52.381 0.00 0.00 0.00 2.85
379 812 1.372997 GCGTGTGATCGTGAGTGGT 60.373 57.895 0.00 0.00 0.00 4.16
380 813 1.372872 TGCGTGTGATCGTGAGTGG 60.373 57.895 0.00 0.00 0.00 4.00
381 814 1.617755 GGTGCGTGTGATCGTGAGTG 61.618 60.000 0.00 0.00 0.00 3.51
382 815 1.372997 GGTGCGTGTGATCGTGAGT 60.373 57.895 0.00 0.00 0.00 3.41
383 816 0.667487 AAGGTGCGTGTGATCGTGAG 60.667 55.000 0.00 0.00 0.00 3.51
384 817 0.666274 GAAGGTGCGTGTGATCGTGA 60.666 55.000 0.00 0.00 0.00 4.35
385 818 0.667487 AGAAGGTGCGTGTGATCGTG 60.667 55.000 0.00 0.00 0.00 4.35
386 819 0.388649 GAGAAGGTGCGTGTGATCGT 60.389 55.000 0.00 0.00 0.00 3.73
387 820 1.078759 GGAGAAGGTGCGTGTGATCG 61.079 60.000 0.00 0.00 0.00 3.69
388 821 0.741221 GGGAGAAGGTGCGTGTGATC 60.741 60.000 0.00 0.00 0.00 2.92
389 822 1.296715 GGGAGAAGGTGCGTGTGAT 59.703 57.895 0.00 0.00 0.00 3.06
390 823 2.137528 TGGGAGAAGGTGCGTGTGA 61.138 57.895 0.00 0.00 0.00 3.58
391 824 1.961277 GTGGGAGAAGGTGCGTGTG 60.961 63.158 0.00 0.00 0.00 3.82
392 825 1.768684 ATGTGGGAGAAGGTGCGTGT 61.769 55.000 0.00 0.00 0.00 4.49
393 826 1.003355 ATGTGGGAGAAGGTGCGTG 60.003 57.895 0.00 0.00 0.00 5.34
394 827 1.296715 GATGTGGGAGAAGGTGCGT 59.703 57.895 0.00 0.00 0.00 5.24
395 828 1.450312 GGATGTGGGAGAAGGTGCG 60.450 63.158 0.00 0.00 0.00 5.34
396 829 0.038166 TTGGATGTGGGAGAAGGTGC 59.962 55.000 0.00 0.00 0.00 5.01
397 830 1.826385 GTTGGATGTGGGAGAAGGTG 58.174 55.000 0.00 0.00 0.00 4.00
403 836 1.097547 GGATGCGTTGGATGTGGGAG 61.098 60.000 0.00 0.00 0.00 4.30
432 865 3.608316 ATGAGAGGAAGAGAGCAACAC 57.392 47.619 0.00 0.00 0.00 3.32
433 866 3.837146 AGAATGAGAGGAAGAGAGCAACA 59.163 43.478 0.00 0.00 0.00 3.33
434 867 4.470334 AGAATGAGAGGAAGAGAGCAAC 57.530 45.455 0.00 0.00 0.00 4.17
435 868 6.610830 AGATAAGAATGAGAGGAAGAGAGCAA 59.389 38.462 0.00 0.00 0.00 3.91
441 998 6.074648 GGAGGAGATAAGAATGAGAGGAAGA 58.925 44.000 0.00 0.00 0.00 2.87
456 1013 3.469006 ACAATGGAGGAGAGGAGGAGATA 59.531 47.826 0.00 0.00 0.00 1.98
478 1035 2.086094 TGTATTACAGGCGACGAGACA 58.914 47.619 0.00 0.00 0.00 3.41
482 1039 4.320714 GGATGTATGTATTACAGGCGACGA 60.321 45.833 0.00 0.00 43.87 4.20
486 1043 2.666508 GCGGATGTATGTATTACAGGCG 59.333 50.000 2.53 0.00 43.87 5.52
492 1049 5.012664 AGGTTGGATGCGGATGTATGTATTA 59.987 40.000 0.00 0.00 0.00 0.98
497 1054 2.146342 GAGGTTGGATGCGGATGTATG 58.854 52.381 0.00 0.00 0.00 2.39
500 1057 1.224592 GGAGGTTGGATGCGGATGT 59.775 57.895 0.00 0.00 0.00 3.06
530 1102 3.005539 GAGTGAGCTGGCAGGGGA 61.006 66.667 17.64 0.00 0.00 4.81
540 1112 0.248843 CAAGGTCTCTGGGAGTGAGC 59.751 60.000 0.00 0.00 36.72 4.26
547 1119 1.592223 GGTCGTCAAGGTCTCTGGG 59.408 63.158 0.00 0.00 0.00 4.45
550 1122 2.963371 GCGGTCGTCAAGGTCTCT 59.037 61.111 0.00 0.00 0.00 3.10
611 1230 6.365970 ACCAACACAAATCTATCAGACTCT 57.634 37.500 0.00 0.00 0.00 3.24
621 1240 4.281688 CCTGGATTCAACCAACACAAATCT 59.718 41.667 0.00 0.00 39.59 2.40
641 1260 1.308998 AGTTTTTCACTGCGACCCTG 58.691 50.000 0.00 0.00 32.83 4.45
642 1261 2.767505 CTAGTTTTTCACTGCGACCCT 58.232 47.619 0.00 0.00 35.97 4.34
647 1269 5.348724 TCTTGATAGCTAGTTTTTCACTGCG 59.651 40.000 0.00 0.00 35.97 5.18
661 1283 4.163839 AGCTCTGAATGGTTCTTGATAGCT 59.836 41.667 0.00 0.00 0.00 3.32
666 1288 3.557898 GGTCAGCTCTGAATGGTTCTTGA 60.558 47.826 0.54 0.00 41.85 3.02
696 1333 2.228343 AGGTGAGAAGAAGTTACGTCCG 59.772 50.000 0.00 0.00 0.00 4.79
700 1337 5.333416 GCAAGAAAGGTGAGAAGAAGTTACG 60.333 44.000 0.00 0.00 0.00 3.18
709 1357 3.879295 CAGAACAGCAAGAAAGGTGAGAA 59.121 43.478 0.00 0.00 40.11 2.87
735 1383 3.005791 GCAAACCAGCAGATTAACAAGGT 59.994 43.478 0.00 0.00 0.00 3.50
776 1450 3.565902 CCCAGTGTGGAAGAAGAAGAAAC 59.434 47.826 0.00 0.00 40.96 2.78
795 1469 2.121385 AGAGGCTCACTGCTCCCA 59.879 61.111 18.26 0.00 42.39 4.37
858 1564 4.020617 CAGAACAGAGCGGGGGCA 62.021 66.667 0.00 0.00 0.00 5.36
868 1574 0.662619 TTCACGGCAAAGCAGAACAG 59.337 50.000 0.00 0.00 0.00 3.16
878 1584 1.732917 CTTTGGTGCTTCACGGCAA 59.267 52.632 0.00 0.00 44.18 4.52
907 1622 5.358442 TGAGTTTACAAGCCAAAACTTAGCA 59.642 36.000 2.34 0.00 43.97 3.49
924 1639 6.859112 ATCCAAGCTCTAGAACTGAGTTTA 57.141 37.500 0.00 0.00 34.16 2.01
954 1669 1.678627 TCGATGAACCTAGAGAGCTGC 59.321 52.381 0.00 0.00 0.00 5.25
965 1680 4.981674 TGAAAAACTGCAAATCGATGAACC 59.018 37.500 0.00 0.00 0.00 3.62
966 1681 5.387752 GCTGAAAAACTGCAAATCGATGAAC 60.388 40.000 0.00 0.00 41.89 3.18
986 1701 1.211212 CCTCCATGACCAATCAGCTGA 59.789 52.381 20.79 20.79 38.57 4.26
1072 1871 1.710103 TTCTTGACGCGCTTGTGCAA 61.710 50.000 5.73 0.34 39.64 4.08
1101 1900 3.197333 TCTCAAGCTCCATGGAGAGAAAG 59.803 47.826 40.29 28.80 44.53 2.62
1164 1963 1.482182 ACTTGCATATCGAGCTGGTCA 59.518 47.619 7.70 0.00 0.00 4.02
1176 1975 1.679944 GCCCAGAGCTTGACTTGCATA 60.680 52.381 0.00 0.00 38.99 3.14
1178 1977 1.601759 GCCCAGAGCTTGACTTGCA 60.602 57.895 0.00 0.00 38.99 4.08
1200 1999 1.298953 AGGAGAGCTCTCTGACCTCT 58.701 55.000 36.09 23.49 42.48 3.69
1281 2080 1.300697 GCCGGAGTTGTCGTGAGTT 60.301 57.895 5.05 0.00 0.00 3.01
1282 2081 2.338984 GCCGGAGTTGTCGTGAGT 59.661 61.111 5.05 0.00 0.00 3.41
1809 2638 7.554476 GCATACCTTTTGTTCTCTAGGAATTCT 59.446 37.037 5.23 0.00 36.24 2.40
1930 2882 8.575649 TTATAAAGGAGGGAAGAATCAAACAC 57.424 34.615 0.00 0.00 0.00 3.32
1985 2939 6.324819 CCAATAAGTTTCAGCCAGTGTAATG 58.675 40.000 0.00 0.00 0.00 1.90
1992 2946 3.488047 CGATGCCAATAAGTTTCAGCCAG 60.488 47.826 0.00 0.00 0.00 4.85
2082 3046 4.237976 TCCCACTTTCCTTTGTGTGTAA 57.762 40.909 0.00 0.00 32.76 2.41
2088 3052 5.366477 ACATTCATTTCCCACTTTCCTTTGT 59.634 36.000 0.00 0.00 0.00 2.83
2089 3053 5.857268 ACATTCATTTCCCACTTTCCTTTG 58.143 37.500 0.00 0.00 0.00 2.77
2129 3102 3.817709 ATGTGTTTCAAAACCAGTGGG 57.182 42.857 15.21 0.00 38.11 4.61
2130 3103 7.784633 AAAATATGTGTTTCAAAACCAGTGG 57.215 32.000 7.91 7.91 38.11 4.00
2135 3108 9.332502 ACCCTTTAAAATATGTGTTTCAAAACC 57.667 29.630 3.33 0.00 38.11 3.27
2141 3140 6.459923 TGCCACCCTTTAAAATATGTGTTTC 58.540 36.000 0.00 0.00 0.00 2.78
2207 3210 6.197096 CCTTCTTGTTTTGTCGTCAATCAAAG 59.803 38.462 11.77 8.79 35.47 2.77
2217 3220 9.543018 GAGATAATTTACCTTCTTGTTTTGTCG 57.457 33.333 0.00 0.00 0.00 4.35
2268 3271 9.196552 GATTTAAGTTTCCAGAAAAAGTCATGG 57.803 33.333 0.00 0.00 31.33 3.66
2273 3276 7.781056 TGCTGATTTAAGTTTCCAGAAAAAGT 58.219 30.769 0.00 0.00 31.33 2.66
2291 3297 6.173339 TCCTTTCGTCTATCTTTTGCTGATT 58.827 36.000 0.00 0.00 0.00 2.57
2302 3308 5.177696 GTGTGGCATTATCCTTTCGTCTATC 59.822 44.000 0.00 0.00 0.00 2.08
2332 3338 4.081198 CAGCTAATGACCTCTTGGAGACTT 60.081 45.833 0.00 0.00 37.04 3.01
2412 3424 8.082242 ACAATTAACTACAGAAGTTCAAATGGC 58.918 33.333 5.50 0.00 45.64 4.40
2446 3458 2.495155 TGTTGGATCAGTGACCATGG 57.505 50.000 11.19 11.19 36.02 3.66
2447 3459 3.415212 ACTTGTTGGATCAGTGACCATG 58.585 45.455 13.14 8.23 36.02 3.66
2467 3536 5.618236 AGGGAGTAAAACACAACTAGGAAC 58.382 41.667 0.00 0.00 0.00 3.62
2470 3539 5.617252 TCAAGGGAGTAAAACACAACTAGG 58.383 41.667 0.00 0.00 0.00 3.02
2512 3581 6.489361 AGCCTCCAATCAGATGATAAACAATC 59.511 38.462 0.00 0.00 33.73 2.67
2513 3582 6.371278 AGCCTCCAATCAGATGATAAACAAT 58.629 36.000 0.00 0.00 33.73 2.71
2519 3588 6.499699 ACTTATGAGCCTCCAATCAGATGATA 59.500 38.462 0.00 0.00 33.73 2.15
2543 3614 8.618677 TGATTCTCTTGAAGCATGAATTATGAC 58.381 33.333 0.00 0.28 42.72 3.06
2544 3615 8.741603 TGATTCTCTTGAAGCATGAATTATGA 57.258 30.769 0.00 0.00 42.72 2.15
2555 3626 6.974932 TCTACAATGTGATTCTCTTGAAGC 57.025 37.500 0.00 0.00 38.90 3.86
2592 3663 9.831737 CAAACTCGACAATATGATTCTCTTTTT 57.168 29.630 0.00 0.00 0.00 1.94
2593 3664 9.219603 TCAAACTCGACAATATGATTCTCTTTT 57.780 29.630 0.00 0.00 0.00 2.27
2594 3665 8.777865 TCAAACTCGACAATATGATTCTCTTT 57.222 30.769 0.00 0.00 0.00 2.52
2595 3666 8.253810 TCTCAAACTCGACAATATGATTCTCTT 58.746 33.333 0.00 0.00 0.00 2.85
2596 3667 7.704472 GTCTCAAACTCGACAATATGATTCTCT 59.296 37.037 0.00 0.00 0.00 3.10
2686 5050 5.880332 TCACAAAACTCAGGGCTATATGAAC 59.120 40.000 0.00 0.00 0.00 3.18
2694 5058 3.299503 ACAAATCACAAAACTCAGGGCT 58.700 40.909 0.00 0.00 0.00 5.19
2712 5077 9.006839 CAGAGTATCCGTGTAAGGTATATACAA 57.993 37.037 14.70 0.00 33.09 2.41
2729 5094 9.523168 AGATACCTACATTAGTTCAGAGTATCC 57.477 37.037 0.00 0.00 36.03 2.59
2768 5133 7.315142 CCCACAATTTTTCATCCCATATATCG 58.685 38.462 0.00 0.00 0.00 2.92
3072 5438 1.067295 TTCATCTTCTGGCCACTGGT 58.933 50.000 0.00 0.00 0.00 4.00
3074 5440 1.815003 GGTTTCATCTTCTGGCCACTG 59.185 52.381 0.00 0.00 0.00 3.66
3087 5453 2.564062 CCCACTCATGCTTTGGTTTCAT 59.436 45.455 6.39 0.00 0.00 2.57
3156 5522 7.985184 AGATAGTATTCTACGCATCTCCTCTAG 59.015 40.741 0.00 0.00 33.14 2.43
3252 5618 7.297229 TGAGTCTATCTCTATTAATCTCGCG 57.703 40.000 0.00 0.00 43.13 5.87
3275 5641 0.819259 CGGCCACCCACTTCCATATG 60.819 60.000 2.24 0.00 0.00 1.78
3675 6044 4.461431 ACAGTCCGACATATCAAGTACACA 59.539 41.667 0.40 0.00 0.00 3.72
4121 6492 9.935682 TTGCAATCAATAATTAGACTTTCGATC 57.064 29.630 0.00 0.00 0.00 3.69
4158 6529 5.125097 AGTGATCCATCAGTTCAAAAGATGC 59.875 40.000 0.00 0.00 37.15 3.91
4180 6551 0.038744 CACCCAGCATTCTCCCAAGT 59.961 55.000 0.00 0.00 0.00 3.16
4389 6761 1.454847 GTGTTTGGTGGGTGCTCCA 60.455 57.895 7.20 0.85 44.79 3.86
4452 6824 4.507756 TGATCGACAGTTCAAGTCAAAGTG 59.492 41.667 0.00 0.00 35.77 3.16
4466 6838 2.065765 ATCTGCGTTGCTGATCGACAG 61.066 52.381 5.48 9.73 42.03 3.51
4470 6842 2.541346 ACATTATCTGCGTTGCTGATCG 59.459 45.455 13.37 7.47 43.98 3.69
4498 6870 4.033776 CCCTCGGCAAAGCTCCCA 62.034 66.667 0.00 0.00 0.00 4.37
4550 6922 2.159226 AGAGTTACCATCCTCTTTCGCG 60.159 50.000 0.00 0.00 34.40 5.87
4570 6942 0.537371 AAGGCCCAAGTCGAAACCAG 60.537 55.000 0.00 0.00 0.00 4.00
4616 6988 0.695924 ACATCCAAATCCGGACACCA 59.304 50.000 6.12 0.00 38.07 4.17
4626 6998 4.210331 GCTCCACCAGAATACATCCAAAT 58.790 43.478 0.00 0.00 0.00 2.32
4723 7095 2.228582 TGCGGGAACATGTCAATTTCAG 59.771 45.455 0.00 0.00 0.00 3.02
4745 7117 2.761208 AGCGTCAGTACCTTCTGCTATT 59.239 45.455 0.00 0.00 35.63 1.73
5350 7806 3.314080 TGCAACTTTACCAACTACACAGC 59.686 43.478 0.00 0.00 0.00 4.40
5598 8054 5.233476 CGAAACAGAGCAACTTACTACAACA 59.767 40.000 0.00 0.00 0.00 3.33
5643 8099 3.308053 CAGCCATTCGATGTAACAGACAG 59.692 47.826 0.00 0.00 42.79 3.51
5644 8100 3.261580 CAGCCATTCGATGTAACAGACA 58.738 45.455 0.00 0.00 43.97 3.41
5645 8101 2.609459 CCAGCCATTCGATGTAACAGAC 59.391 50.000 0.00 0.00 0.00 3.51
5646 8102 2.905075 CCAGCCATTCGATGTAACAGA 58.095 47.619 0.00 0.00 0.00 3.41
5789 8247 6.877611 TTCTGAAGTAAGGAATCCAACAAC 57.122 37.500 0.61 0.00 0.00 3.32
5833 8291 4.877823 CCACAAAACATGCAGAGCTCTATA 59.122 41.667 17.75 8.82 0.00 1.31


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

AutoCloner maintained by Alex Coulton.