Multiple sequence alignment - TraesCS5B01G050700

Loading Multiple Alignment...

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 TraesCS5B01G050700 chr5B 100.000 2549 0 0 1 2549 55505597 55503049 0.000000e+00 4708
1 TraesCS5B01G050700 chr5D 91.577 2315 131 30 2 2289 52328557 52326280 0.000000e+00 3136
2 TraesCS5B01G050700 chr1A 86.659 922 85 20 890 1790 6335241 6336145 0.000000e+00 987
3 TraesCS5B01G050700 chr1A 85.820 945 95 20 869 1790 4503539 4502611 0.000000e+00 966
4 TraesCS5B01G050700 chr1A 85.820 945 95 20 869 1790 5499038 5499966 0.000000e+00 966
5 TraesCS5B01G050700 chr1A 88.043 828 66 16 982 1790 5500631 5501444 0.000000e+00 950
6 TraesCS5B01G050700 chr1D 83.728 971 96 34 866 1788 3968756 3969712 0.000000e+00 861
7 TraesCS5B01G050700 chr1D 80.942 446 49 24 1327 1750 3618233 3617802 1.140000e-83 320
8 TraesCS5B01G050700 chr1D 80.870 230 20 5 2032 2247 3970089 3970308 2.620000e-35 159
9 TraesCS5B01G050700 chr1D 86.813 91 10 2 1922 2011 3969921 3970010 1.610000e-17 100
10 TraesCS5B01G050700 chr1B 87.083 689 71 9 869 1547 5760364 5759684 0.000000e+00 763
11 TraesCS5B01G050700 chr1B 83.887 813 87 21 883 1659 6481552 6482356 0.000000e+00 736
12 TraesCS5B01G050700 chr1B 82.500 200 21 7 2075 2271 6482824 6483012 2.030000e-36 163
13 TraesCS5B01G050700 chr1B 81.773 203 23 7 2075 2274 5759063 5758872 9.440000e-35 158
14 TraesCS5B01G050700 chr3B 90.698 86 8 0 2463 2548 822112738 822112823 5.760000e-22 115


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 TraesCS5B01G050700 chr5B 55503049 55505597 2548 True 4708.000000 4708 100.000000 1 2549 1 chr5B.!!$R1 2548
1 TraesCS5B01G050700 chr5D 52326280 52328557 2277 True 3136.000000 3136 91.577000 2 2289 1 chr5D.!!$R1 2287
2 TraesCS5B01G050700 chr1A 6335241 6336145 904 False 987.000000 987 86.659000 890 1790 1 chr1A.!!$F1 900
3 TraesCS5B01G050700 chr1A 4502611 4503539 928 True 966.000000 966 85.820000 869 1790 1 chr1A.!!$R1 921
4 TraesCS5B01G050700 chr1A 5499038 5501444 2406 False 958.000000 966 86.931500 869 1790 2 chr1A.!!$F2 921
5 TraesCS5B01G050700 chr1D 3968756 3970308 1552 False 373.333333 861 83.803667 866 2247 3 chr1D.!!$F1 1381
6 TraesCS5B01G050700 chr1B 5758872 5760364 1492 True 460.500000 763 84.428000 869 2274 2 chr1B.!!$R1 1405
7 TraesCS5B01G050700 chr1B 6481552 6483012 1460 False 449.500000 736 83.193500 883 2271 2 chr1B.!!$F1 1388

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
475 476 0.181587 TCTGAAACAAGCGGGTTCCA 59.818 50.0 6.73 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2472 2857 0.034476 CTCTGTTGGCAGCTGACAGA 59.966 55.0 26.33 26.33 45.34 3.41 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
22 23 4.610333 GAGAACCCTCCCCAAAATAATGT 58.390 43.478 0.00 0.00 33.30 2.71
35 36 7.172703 CCCCAAAATAATGTTAGGACGTAGATC 59.827 40.741 0.00 0.00 0.00 2.75
40 41 8.571461 AATAATGTTAGGACGTAGATCGAAAC 57.429 34.615 0.00 0.00 42.86 2.78
58 59 1.512926 ACGTTGTGCATCTCTTGTCC 58.487 50.000 0.00 0.00 0.00 4.02
64 65 2.369860 TGTGCATCTCTTGTCCTCTGTT 59.630 45.455 0.00 0.00 0.00 3.16
107 108 4.301505 CAGGCTGGTGCGTGTTAT 57.698 55.556 6.61 0.00 46.36 1.89
108 109 1.796151 CAGGCTGGTGCGTGTTATG 59.204 57.895 6.61 0.00 46.36 1.90
109 110 0.673333 CAGGCTGGTGCGTGTTATGA 60.673 55.000 6.61 0.00 46.36 2.15
110 111 0.391661 AGGCTGGTGCGTGTTATGAG 60.392 55.000 0.00 0.00 40.82 2.90
111 112 0.673644 GGCTGGTGCGTGTTATGAGT 60.674 55.000 0.00 0.00 40.82 3.41
112 113 1.156736 GCTGGTGCGTGTTATGAGTT 58.843 50.000 0.00 0.00 0.00 3.01
113 114 1.128692 GCTGGTGCGTGTTATGAGTTC 59.871 52.381 0.00 0.00 0.00 3.01
114 115 2.688507 CTGGTGCGTGTTATGAGTTCT 58.311 47.619 0.00 0.00 0.00 3.01
115 116 2.668457 CTGGTGCGTGTTATGAGTTCTC 59.332 50.000 0.00 0.00 0.00 2.87
116 117 2.000447 GGTGCGTGTTATGAGTTCTCC 59.000 52.381 0.00 0.00 0.00 3.71
117 118 2.353803 GGTGCGTGTTATGAGTTCTCCT 60.354 50.000 0.00 0.00 0.00 3.69
118 119 2.924290 GTGCGTGTTATGAGTTCTCCTC 59.076 50.000 0.00 0.00 40.89 3.71
119 120 2.094182 TGCGTGTTATGAGTTCTCCTCC 60.094 50.000 0.00 0.00 39.65 4.30
124 125 2.068834 TATGAGTTCTCCTCCGTCCC 57.931 55.000 0.00 0.00 39.65 4.46
135 136 1.462627 TCCGTCCCTCCCCTGTTTT 60.463 57.895 0.00 0.00 0.00 2.43
140 141 2.614734 CGTCCCTCCCCTGTTTTTAGAC 60.615 54.545 0.00 0.00 0.00 2.59
141 142 1.990327 TCCCTCCCCTGTTTTTAGACC 59.010 52.381 0.00 0.00 0.00 3.85
142 143 1.005569 CCCTCCCCTGTTTTTAGACCC 59.994 57.143 0.00 0.00 0.00 4.46
143 144 1.005569 CCTCCCCTGTTTTTAGACCCC 59.994 57.143 0.00 0.00 0.00 4.95
144 145 1.005569 CTCCCCTGTTTTTAGACCCCC 59.994 57.143 0.00 0.00 0.00 5.40
218 219 1.132849 TCTGGTGTCCCTTCTCCTTCA 60.133 52.381 0.00 0.00 0.00 3.02
219 220 1.277557 CTGGTGTCCCTTCTCCTTCAG 59.722 57.143 0.00 0.00 0.00 3.02
225 226 1.152271 TCCCTTCTCCTTCAGTCCCTT 59.848 52.381 0.00 0.00 0.00 3.95
256 257 1.243902 CGGCAGATCTCTCTACCTCC 58.756 60.000 0.00 0.00 33.28 4.30
267 268 4.168871 TCTCTCTACCTCCTCCATCAATGA 59.831 45.833 0.00 0.00 0.00 2.57
295 296 1.331756 CTGCCATTAACATCTCCACGC 59.668 52.381 0.00 0.00 0.00 5.34
362 363 3.309138 CCAATTTGTCGCTGAGAGATCTG 59.691 47.826 0.00 0.00 0.00 2.90
371 372 2.008329 CTGAGAGATCTGTTTGCTGCC 58.992 52.381 0.00 0.00 0.00 4.85
372 373 1.627329 TGAGAGATCTGTTTGCTGCCT 59.373 47.619 0.00 0.00 0.00 4.75
373 374 2.039480 TGAGAGATCTGTTTGCTGCCTT 59.961 45.455 0.00 0.00 0.00 4.35
395 396 6.934645 CCTTCTTATCCTTGTGTTGTGAAGTA 59.065 38.462 0.00 0.00 0.00 2.24
436 437 1.208614 GCAGTCAGCTTGCTTTCCG 59.791 57.895 1.51 0.00 41.15 4.30
437 438 1.230635 GCAGTCAGCTTGCTTTCCGA 61.231 55.000 1.51 0.00 41.15 4.55
446 447 5.415701 TCAGCTTGCTTTCCGATTTTTAGAT 59.584 36.000 0.00 0.00 0.00 1.98
475 476 0.181587 TCTGAAACAAGCGGGTTCCA 59.818 50.000 6.73 0.00 0.00 3.53
512 513 1.847798 AATAGCGGCCACCAGGTGAA 61.848 55.000 22.37 0.00 35.23 3.18
529 530 4.105486 GGTGAACTGCTGTTTCTTGAAAC 58.895 43.478 16.62 16.62 36.39 2.78
598 599 8.695456 TGCTTATCTATGTCTGTAACATCTGAA 58.305 33.333 0.00 0.00 45.78 3.02
628 629 8.262715 TGAGAATAAAATGTTGATCGTGCTAA 57.737 30.769 0.00 0.00 0.00 3.09
655 656 5.125417 GCTGACATTTTAACTGGGAAGCATA 59.875 40.000 0.00 0.00 0.00 3.14
657 658 5.417580 TGACATTTTAACTGGGAAGCATACC 59.582 40.000 0.00 0.00 0.00 2.73
658 659 5.329399 ACATTTTAACTGGGAAGCATACCA 58.671 37.500 0.00 0.00 35.05 3.25
676 677 1.979855 CACATTTGTGGGTGTCCTCA 58.020 50.000 2.69 0.00 42.10 3.86
706 707 2.977914 TGTAGAATTCTGTGCAGAGCC 58.022 47.619 18.47 0.00 38.88 4.70
712 713 4.467795 AGAATTCTGTGCAGAGCCTACTTA 59.532 41.667 7.30 0.00 38.88 2.24
713 714 5.130145 AGAATTCTGTGCAGAGCCTACTTAT 59.870 40.000 7.30 0.00 38.88 1.73
714 715 4.826274 TTCTGTGCAGAGCCTACTTATT 57.174 40.909 5.87 0.00 38.88 1.40
715 716 4.392921 TCTGTGCAGAGCCTACTTATTC 57.607 45.455 5.87 0.00 32.82 1.75
750 751 2.979813 CGCAACACTTTAACAGGAATGC 59.020 45.455 0.00 0.00 0.00 3.56
760 761 3.626028 AACAGGAATGCACGAAACTTC 57.374 42.857 0.00 0.00 0.00 3.01
789 790 4.460263 TCTAACTGGAAAGCATTGTGTGT 58.540 39.130 0.00 0.00 0.00 3.72
823 824 4.157656 TGTTTGCTCATACTGTTATTGCCC 59.842 41.667 0.00 0.00 0.00 5.36
826 827 2.745152 GCTCATACTGTTATTGCCCCGT 60.745 50.000 0.00 0.00 0.00 5.28
874 876 5.424121 AACACTGTACTGAAAGCATTCAC 57.576 39.130 6.77 0.00 40.59 3.18
880 882 5.961272 TGTACTGAAAGCATTCACGATAGA 58.039 37.500 0.00 0.00 40.59 1.98
925 927 5.522456 TGACATGCATGAGACTTTTGTTTC 58.478 37.500 32.75 14.99 34.50 2.78
962 970 6.670695 AACACTTGCTTTTTAATCCCTGAT 57.329 33.333 0.00 0.00 0.00 2.90
974 982 3.806625 ATCCCTGATTTTTGATTGCCG 57.193 42.857 0.00 0.00 0.00 5.69
1047 1055 0.392193 CCAGCTTGATCGACCAGCTT 60.392 55.000 11.24 0.00 33.09 3.74
1048 1056 1.446907 CAGCTTGATCGACCAGCTTT 58.553 50.000 11.24 0.00 33.09 3.51
1127 1138 0.739112 GAGCAACAAGAGGAGCCTCG 60.739 60.000 10.69 0.83 46.90 4.63
1334 1345 4.819761 GCAGGAGGCGACGATGCA 62.820 66.667 10.04 0.00 37.69 3.96
1371 1382 3.123620 GCCAAGGAGCTGCACGAG 61.124 66.667 8.35 0.00 0.00 4.18
1413 1424 3.168528 AACCCCTCACCGTGCACT 61.169 61.111 16.19 0.00 0.00 4.40
1445 1456 2.048597 CTGCGCCGAGTGTTACCA 60.049 61.111 4.18 0.00 0.00 3.25
1500 1511 0.173481 CGGTCAAGAGATTCGAGGCA 59.827 55.000 0.00 0.00 0.00 4.75
1506 1517 0.249238 AGAGATTCGAGGCATGCGTC 60.249 55.000 26.58 26.58 0.00 5.19
1507 1518 0.528466 GAGATTCGAGGCATGCGTCA 60.528 55.000 32.67 19.23 0.00 4.35
1609 1712 4.881273 TGGTTTGTCGGGATGATTGAATAG 59.119 41.667 0.00 0.00 0.00 1.73
1666 1777 9.520515 ACCATCAGTTGTAGATTAAAATTCTGT 57.479 29.630 0.00 0.00 0.00 3.41
1667 1778 9.994432 CCATCAGTTGTAGATTAAAATTCTGTC 57.006 33.333 0.00 0.00 0.00 3.51
1795 1916 4.154556 TGGTTCGAATTAATGTTTCCCGAC 59.845 41.667 0.00 0.00 0.00 4.79
1833 1954 0.829333 TGGCTGCTTTTCCTTGCAAA 59.171 45.000 0.00 0.00 38.81 3.68
1835 1956 1.202568 GGCTGCTTTTCCTTGCAAAGT 60.203 47.619 0.00 0.00 44.25 2.66
1837 1958 2.388121 CTGCTTTTCCTTGCAAAGTCG 58.612 47.619 0.00 0.00 44.25 4.18
1849 1970 2.031245 TGCAAAGTCGTGGCATGTTTAG 60.031 45.455 6.60 0.00 31.58 1.85
1850 1971 2.668279 GCAAAGTCGTGGCATGTTTAGG 60.668 50.000 6.60 0.00 0.00 2.69
1852 1973 3.688694 AAGTCGTGGCATGTTTAGGTA 57.311 42.857 6.60 0.00 0.00 3.08
1860 1981 6.655848 TCGTGGCATGTTTAGGTAAAATAACT 59.344 34.615 6.60 0.00 0.00 2.24
1868 1989 6.707161 TGTTTAGGTAAAATAACTGTGCTCGT 59.293 34.615 0.00 0.00 0.00 4.18
1924 2160 5.887598 AGGTTGATTTAGCTTCATATGCACA 59.112 36.000 0.00 0.00 0.00 4.57
1973 2210 3.084039 TGGCAAAATCCATGTCTGAGTC 58.916 45.455 0.00 0.00 0.00 3.36
1991 2250 8.922676 GTCTGAGTCGTTCATAAAGAAAATGTA 58.077 33.333 0.00 0.00 38.13 2.29
2133 2462 3.069300 ACCAGATCAAGATCAGACCATCG 59.931 47.826 12.21 0.00 40.22 3.84
2147 2476 1.373497 CATCGCGGCCTAGGATGTC 60.373 63.158 14.75 0.00 34.33 3.06
2161 2490 2.036992 AGGATGTCGATTCAGAGATGCC 59.963 50.000 0.00 0.00 33.75 4.40
2171 2500 1.378646 AGAGATGCCCGACTCGACA 60.379 57.895 0.00 0.00 38.08 4.35
2208 2551 1.000607 CCGACACTTCTCGACCAAGAA 60.001 52.381 6.40 0.00 35.58 2.52
2289 2638 1.668826 ACAATCAAGGACCAGGCCTA 58.331 50.000 3.98 0.00 37.26 3.93
2294 2643 2.050144 TCAAGGACCAGGCCTATCATC 58.950 52.381 3.98 0.00 37.26 2.92
2295 2644 1.072965 CAAGGACCAGGCCTATCATCC 59.927 57.143 3.98 10.39 37.26 3.51
2298 2647 1.072965 GGACCAGGCCTATCATCCAAG 59.927 57.143 3.98 0.00 0.00 3.61
2300 2649 2.439507 GACCAGGCCTATCATCCAAGAA 59.560 50.000 3.98 0.00 0.00 2.52
2303 2652 4.078980 ACCAGGCCTATCATCCAAGAAAAT 60.079 41.667 3.98 0.00 0.00 1.82
2305 2654 4.522022 CAGGCCTATCATCCAAGAAAATCC 59.478 45.833 3.98 0.00 0.00 3.01
2306 2655 4.168675 AGGCCTATCATCCAAGAAAATCCA 59.831 41.667 1.29 0.00 0.00 3.41
2307 2656 4.279420 GGCCTATCATCCAAGAAAATCCAC 59.721 45.833 0.00 0.00 0.00 4.02
2309 2658 5.360714 GCCTATCATCCAAGAAAATCCACAA 59.639 40.000 0.00 0.00 0.00 3.33
2310 2659 6.681368 GCCTATCATCCAAGAAAATCCACAAC 60.681 42.308 0.00 0.00 0.00 3.32
2314 2663 2.962421 TCCAAGAAAATCCACAACACCC 59.038 45.455 0.00 0.00 0.00 4.61
2315 2664 2.697751 CCAAGAAAATCCACAACACCCA 59.302 45.455 0.00 0.00 0.00 4.51
2316 2665 3.133721 CCAAGAAAATCCACAACACCCAA 59.866 43.478 0.00 0.00 0.00 4.12
2317 2666 4.370917 CAAGAAAATCCACAACACCCAAG 58.629 43.478 0.00 0.00 0.00 3.61
2318 2667 2.365293 AGAAAATCCACAACACCCAAGC 59.635 45.455 0.00 0.00 0.00 4.01
2319 2668 2.086610 AAATCCACAACACCCAAGCT 57.913 45.000 0.00 0.00 0.00 3.74
2320 2669 1.331214 AATCCACAACACCCAAGCTG 58.669 50.000 0.00 0.00 0.00 4.24
2321 2670 1.181098 ATCCACAACACCCAAGCTGC 61.181 55.000 0.00 0.00 0.00 5.25
2322 2671 2.126596 CCACAACACCCAAGCTGCA 61.127 57.895 1.02 0.00 0.00 4.41
2323 2672 1.361271 CACAACACCCAAGCTGCAG 59.639 57.895 10.11 10.11 0.00 4.41
2324 2673 1.102809 CACAACACCCAAGCTGCAGA 61.103 55.000 20.43 0.00 0.00 4.26
2325 2674 0.820891 ACAACACCCAAGCTGCAGAG 60.821 55.000 20.43 6.06 0.00 3.35
2327 2676 0.820891 AACACCCAAGCTGCAGAGTG 60.821 55.000 20.43 17.11 0.00 3.51
2329 2678 2.033757 CCCAAGCTGCAGAGTGCT 59.966 61.111 20.43 4.84 45.31 4.40
2331 2680 2.333417 CCAAGCTGCAGAGTGCTGG 61.333 63.158 20.43 11.41 45.31 4.85
2333 2682 0.887836 CAAGCTGCAGAGTGCTGGAA 60.888 55.000 20.43 0.00 45.31 3.53
2334 2683 0.179009 AAGCTGCAGAGTGCTGGAAA 60.179 50.000 20.43 0.00 45.31 3.13
2335 2684 0.605860 AGCTGCAGAGTGCTGGAAAG 60.606 55.000 20.43 0.00 45.31 2.62
2336 2685 0.888285 GCTGCAGAGTGCTGGAAAGT 60.888 55.000 20.43 0.00 45.31 2.66
2338 2687 1.952296 CTGCAGAGTGCTGGAAAGTTT 59.048 47.619 8.42 0.00 45.31 2.66
2340 2689 2.225467 GCAGAGTGCTGGAAAGTTTCT 58.775 47.619 15.05 0.00 42.53 2.52
2341 2690 2.225255 GCAGAGTGCTGGAAAGTTTCTC 59.775 50.000 15.05 6.39 42.53 2.87
2342 2691 3.470709 CAGAGTGCTGGAAAGTTTCTCA 58.529 45.455 15.05 10.29 38.51 3.27
2343 2692 3.497640 CAGAGTGCTGGAAAGTTTCTCAG 59.502 47.826 20.83 20.83 38.51 3.35
2344 2693 3.389329 AGAGTGCTGGAAAGTTTCTCAGA 59.611 43.478 25.70 14.59 32.90 3.27
2346 2695 3.118261 AGTGCTGGAAAGTTTCTCAGACA 60.118 43.478 25.70 21.00 32.90 3.41
2347 2696 3.627577 GTGCTGGAAAGTTTCTCAGACAA 59.372 43.478 25.70 14.18 32.90 3.18
2348 2697 3.879295 TGCTGGAAAGTTTCTCAGACAAG 59.121 43.478 25.70 11.57 32.90 3.16
2349 2698 3.879892 GCTGGAAAGTTTCTCAGACAAGT 59.120 43.478 25.70 0.00 32.90 3.16
2350 2699 4.336713 GCTGGAAAGTTTCTCAGACAAGTT 59.663 41.667 25.70 0.00 32.90 2.66
2351 2700 5.527582 GCTGGAAAGTTTCTCAGACAAGTTA 59.472 40.000 25.70 0.00 32.90 2.24
2352 2701 6.205658 GCTGGAAAGTTTCTCAGACAAGTTAT 59.794 38.462 25.70 0.00 32.90 1.89
2353 2702 7.387948 GCTGGAAAGTTTCTCAGACAAGTTATA 59.612 37.037 25.70 0.00 32.90 0.98
2354 2703 8.833231 TGGAAAGTTTCTCAGACAAGTTATAG 57.167 34.615 15.05 0.00 0.00 1.31
2355 2704 7.387948 TGGAAAGTTTCTCAGACAAGTTATAGC 59.612 37.037 15.05 0.00 0.00 2.97
2356 2705 7.148390 GGAAAGTTTCTCAGACAAGTTATAGCC 60.148 40.741 15.05 0.00 0.00 3.93
2357 2706 6.360370 AGTTTCTCAGACAAGTTATAGCCA 57.640 37.500 0.00 0.00 0.00 4.75
2358 2707 6.402222 AGTTTCTCAGACAAGTTATAGCCAG 58.598 40.000 0.00 0.00 0.00 4.85
2359 2708 4.392921 TCTCAGACAAGTTATAGCCAGC 57.607 45.455 0.00 0.00 0.00 4.85
2360 2709 3.769300 TCTCAGACAAGTTATAGCCAGCA 59.231 43.478 0.00 0.00 0.00 4.41
2361 2710 3.861840 TCAGACAAGTTATAGCCAGCAC 58.138 45.455 0.00 0.00 0.00 4.40
2362 2711 3.515502 TCAGACAAGTTATAGCCAGCACT 59.484 43.478 0.00 0.00 0.00 4.40
2363 2712 3.620374 CAGACAAGTTATAGCCAGCACTG 59.380 47.826 0.00 0.00 0.00 3.66
2364 2713 2.352960 GACAAGTTATAGCCAGCACTGC 59.647 50.000 0.00 0.00 0.00 4.40
2365 2714 1.672881 CAAGTTATAGCCAGCACTGCC 59.327 52.381 0.00 0.00 0.00 4.85
2366 2715 0.911769 AGTTATAGCCAGCACTGCCA 59.088 50.000 0.00 0.00 0.00 4.92
2367 2716 1.017387 GTTATAGCCAGCACTGCCAC 58.983 55.000 0.00 0.00 0.00 5.01
2368 2717 0.617935 TTATAGCCAGCACTGCCACA 59.382 50.000 0.00 0.00 0.00 4.17
2369 2718 0.178767 TATAGCCAGCACTGCCACAG 59.821 55.000 0.00 0.00 37.52 3.66
2371 2720 1.191489 TAGCCAGCACTGCCACAGTA 61.191 55.000 0.00 0.00 43.43 2.74
2372 2721 1.377725 GCCAGCACTGCCACAGTAT 60.378 57.895 0.00 0.00 43.43 2.12
2374 2723 0.745845 CCAGCACTGCCACAGTATCC 60.746 60.000 0.00 0.00 43.43 2.59
2375 2724 0.745845 CAGCACTGCCACAGTATCCC 60.746 60.000 0.00 0.00 43.43 3.85
2376 2725 1.200760 AGCACTGCCACAGTATCCCA 61.201 55.000 0.00 0.00 43.43 4.37
2377 2726 0.745845 GCACTGCCACAGTATCCCAG 60.746 60.000 0.00 0.00 43.43 4.45
2379 2728 1.200760 ACTGCCACAGTATCCCAGCA 61.201 55.000 0.00 0.00 43.46 4.41
2380 2729 0.463295 CTGCCACAGTATCCCAGCAG 60.463 60.000 0.00 0.00 41.43 4.24
2381 2730 0.909133 TGCCACAGTATCCCAGCAGA 60.909 55.000 0.00 0.00 0.00 4.26
2382 2731 0.471617 GCCACAGTATCCCAGCAGAT 59.528 55.000 0.00 0.00 0.00 2.90
2383 2732 1.694150 GCCACAGTATCCCAGCAGATA 59.306 52.381 0.00 0.00 0.00 1.98
2388 2773 3.181450 ACAGTATCCCAGCAGATAAAGCC 60.181 47.826 0.00 0.00 30.66 4.35
2390 2775 2.355010 ATCCCAGCAGATAAAGCCAC 57.645 50.000 0.00 0.00 0.00 5.01
2391 2776 0.991146 TCCCAGCAGATAAAGCCACA 59.009 50.000 0.00 0.00 0.00 4.17
2392 2777 1.065199 TCCCAGCAGATAAAGCCACAG 60.065 52.381 0.00 0.00 0.00 3.66
2393 2778 1.340405 CCCAGCAGATAAAGCCACAGT 60.340 52.381 0.00 0.00 0.00 3.55
2394 2779 2.440409 CCAGCAGATAAAGCCACAGTT 58.560 47.619 0.00 0.00 0.00 3.16
2401 2786 5.403466 GCAGATAAAGCCACAGTTGAAAAAG 59.597 40.000 0.00 0.00 0.00 2.27
2402 2787 6.507023 CAGATAAAGCCACAGTTGAAAAAGT 58.493 36.000 0.00 0.00 0.00 2.66
2404 2789 8.299570 CAGATAAAGCCACAGTTGAAAAAGTAT 58.700 33.333 0.00 0.00 0.00 2.12
2409 2794 5.827797 AGCCACAGTTGAAAAAGTATCTTGA 59.172 36.000 0.00 0.00 0.00 3.02
2414 2799 9.013490 CACAGTTGAAAAAGTATCTTGAACAAG 57.987 33.333 8.09 8.09 39.71 3.16
2415 2800 8.739972 ACAGTTGAAAAAGTATCTTGAACAAGT 58.260 29.630 13.15 5.12 39.38 3.16
2423 2808 9.529325 AAAAGTATCTTGAACAAGTTAAAAGGC 57.471 29.630 13.15 0.36 39.38 4.35
2424 2809 7.215719 AGTATCTTGAACAAGTTAAAAGGCC 57.784 36.000 13.15 0.00 39.38 5.19
2426 2811 5.514274 TCTTGAACAAGTTAAAAGGCCAG 57.486 39.130 5.01 0.00 39.38 4.85
2427 2812 4.953579 TCTTGAACAAGTTAAAAGGCCAGT 59.046 37.500 5.01 0.00 39.38 4.00
2428 2813 4.647424 TGAACAAGTTAAAAGGCCAGTG 57.353 40.909 5.01 0.00 0.00 3.66
2429 2814 4.020543 TGAACAAGTTAAAAGGCCAGTGT 58.979 39.130 5.01 0.00 0.00 3.55
2430 2815 4.097286 TGAACAAGTTAAAAGGCCAGTGTC 59.903 41.667 5.01 0.00 0.00 3.67
2432 2817 4.278310 ACAAGTTAAAAGGCCAGTGTCTT 58.722 39.130 5.01 0.00 38.29 3.01
2433 2818 4.338400 ACAAGTTAAAAGGCCAGTGTCTTC 59.662 41.667 5.01 0.00 34.67 2.87
2435 2820 4.390264 AGTTAAAAGGCCAGTGTCTTCTC 58.610 43.478 5.01 0.00 34.67 2.87
2436 2821 4.134563 GTTAAAAGGCCAGTGTCTTCTCA 58.865 43.478 5.01 0.00 34.67 3.27
2437 2822 3.515602 AAAAGGCCAGTGTCTTCTCAT 57.484 42.857 5.01 0.00 34.67 2.90
2438 2823 2.777832 AAGGCCAGTGTCTTCTCATC 57.222 50.000 5.01 0.00 27.45 2.92
2441 2826 1.277557 GGCCAGTGTCTTCTCATCAGT 59.722 52.381 0.00 0.00 0.00 3.41
2442 2827 2.289945 GGCCAGTGTCTTCTCATCAGTT 60.290 50.000 0.00 0.00 0.00 3.16
2443 2828 3.055819 GGCCAGTGTCTTCTCATCAGTTA 60.056 47.826 0.00 0.00 0.00 2.24
2444 2829 4.563580 GGCCAGTGTCTTCTCATCAGTTAA 60.564 45.833 0.00 0.00 0.00 2.01
2445 2830 4.390297 GCCAGTGTCTTCTCATCAGTTAAC 59.610 45.833 0.00 0.00 0.00 2.01
2446 2831 4.932200 CCAGTGTCTTCTCATCAGTTAACC 59.068 45.833 0.88 0.00 0.00 2.85
2447 2832 5.511373 CCAGTGTCTTCTCATCAGTTAACCA 60.511 44.000 0.88 0.00 0.00 3.67
2448 2833 5.991606 CAGTGTCTTCTCATCAGTTAACCAA 59.008 40.000 0.88 0.00 0.00 3.67
2449 2834 6.483307 CAGTGTCTTCTCATCAGTTAACCAAA 59.517 38.462 0.88 0.00 0.00 3.28
2450 2835 6.483640 AGTGTCTTCTCATCAGTTAACCAAAC 59.516 38.462 0.88 0.00 38.46 2.93
2451 2836 6.260050 GTGTCTTCTCATCAGTTAACCAAACA 59.740 38.462 0.88 0.00 40.83 2.83
2452 2837 6.826231 TGTCTTCTCATCAGTTAACCAAACAA 59.174 34.615 0.88 0.00 40.83 2.83
2453 2838 7.338196 TGTCTTCTCATCAGTTAACCAAACAAA 59.662 33.333 0.88 0.00 40.83 2.83
2454 2839 8.352942 GTCTTCTCATCAGTTAACCAAACAAAT 58.647 33.333 0.88 0.00 40.83 2.32
2455 2840 8.567948 TCTTCTCATCAGTTAACCAAACAAATC 58.432 33.333 0.88 0.00 40.83 2.17
2456 2841 7.815840 TCTCATCAGTTAACCAAACAAATCA 57.184 32.000 0.88 0.00 40.83 2.57
2457 2842 8.231692 TCTCATCAGTTAACCAAACAAATCAA 57.768 30.769 0.88 0.00 40.83 2.57
2458 2843 8.690884 TCTCATCAGTTAACCAAACAAATCAAA 58.309 29.630 0.88 0.00 40.83 2.69
2459 2844 9.311916 CTCATCAGTTAACCAAACAAATCAAAA 57.688 29.630 0.88 0.00 40.83 2.44
2460 2845 9.658799 TCATCAGTTAACCAAACAAATCAAAAA 57.341 25.926 0.88 0.00 40.83 1.94
2461 2846 9.701355 CATCAGTTAACCAAACAAATCAAAAAC 57.299 29.630 0.88 0.00 40.83 2.43
2462 2847 8.833231 TCAGTTAACCAAACAAATCAAAAACA 57.167 26.923 0.88 0.00 40.83 2.83
2463 2848 8.930760 TCAGTTAACCAAACAAATCAAAAACAG 58.069 29.630 0.88 0.00 40.83 3.16
2464 2849 8.930760 CAGTTAACCAAACAAATCAAAAACAGA 58.069 29.630 0.88 0.00 40.83 3.41
2465 2850 9.150348 AGTTAACCAAACAAATCAAAAACAGAG 57.850 29.630 0.88 0.00 40.83 3.35
2466 2851 6.983474 AACCAAACAAATCAAAAACAGAGG 57.017 33.333 0.00 0.00 0.00 3.69
2467 2852 4.875536 ACCAAACAAATCAAAAACAGAGGC 59.124 37.500 0.00 0.00 0.00 4.70
2468 2853 5.118286 CCAAACAAATCAAAAACAGAGGCT 58.882 37.500 0.00 0.00 0.00 4.58
2469 2854 6.127196 ACCAAACAAATCAAAAACAGAGGCTA 60.127 34.615 0.00 0.00 0.00 3.93
2470 2855 6.760770 CCAAACAAATCAAAAACAGAGGCTAA 59.239 34.615 0.00 0.00 0.00 3.09
2471 2856 7.279758 CCAAACAAATCAAAAACAGAGGCTAAA 59.720 33.333 0.00 0.00 0.00 1.85
2472 2857 8.829612 CAAACAAATCAAAAACAGAGGCTAAAT 58.170 29.630 0.00 0.00 0.00 1.40
2473 2858 8.593492 AACAAATCAAAAACAGAGGCTAAATC 57.407 30.769 0.00 0.00 0.00 2.17
2474 2859 7.955918 ACAAATCAAAAACAGAGGCTAAATCT 58.044 30.769 0.00 0.00 0.00 2.40
2481 2866 3.540314 CAGAGGCTAAATCTGTCAGCT 57.460 47.619 0.00 0.00 39.48 4.24
2482 2867 3.196463 CAGAGGCTAAATCTGTCAGCTG 58.804 50.000 7.63 7.63 39.48 4.24
2483 2868 1.939255 GAGGCTAAATCTGTCAGCTGC 59.061 52.381 9.47 4.92 35.60 5.25
2484 2869 1.020437 GGCTAAATCTGTCAGCTGCC 58.980 55.000 9.47 0.00 35.60 4.85
2485 2870 1.679944 GGCTAAATCTGTCAGCTGCCA 60.680 52.381 9.47 2.00 38.99 4.92
2486 2871 2.086869 GCTAAATCTGTCAGCTGCCAA 58.913 47.619 9.47 0.00 32.46 4.52
2487 2872 2.159462 GCTAAATCTGTCAGCTGCCAAC 60.159 50.000 9.47 2.53 32.46 3.77
2488 2873 1.985473 AAATCTGTCAGCTGCCAACA 58.015 45.000 9.47 7.74 0.00 3.33
2499 2884 3.327600 TGCCAACAGAGGACACATG 57.672 52.632 0.00 0.00 0.00 3.21
2500 2885 0.473755 TGCCAACAGAGGACACATGT 59.526 50.000 0.00 0.00 0.00 3.21
2501 2886 1.160137 GCCAACAGAGGACACATGTC 58.840 55.000 0.00 3.27 44.04 3.06
2502 2887 1.432514 CCAACAGAGGACACATGTCG 58.567 55.000 0.00 0.00 45.65 4.35
2503 2888 0.792640 CAACAGAGGACACATGTCGC 59.207 55.000 0.00 1.30 45.65 5.19
2504 2889 0.320771 AACAGAGGACACATGTCGCC 60.321 55.000 0.00 0.00 45.65 5.54
2505 2890 1.807165 CAGAGGACACATGTCGCCG 60.807 63.158 0.00 0.00 45.65 6.46
2506 2891 2.261671 GAGGACACATGTCGCCGT 59.738 61.111 0.00 0.00 45.65 5.68
2507 2892 1.374252 GAGGACACATGTCGCCGTT 60.374 57.895 0.00 0.00 45.65 4.44
2508 2893 0.108992 GAGGACACATGTCGCCGTTA 60.109 55.000 0.00 0.00 45.65 3.18
2509 2894 0.108804 AGGACACATGTCGCCGTTAG 60.109 55.000 0.00 0.00 45.65 2.34
2510 2895 1.693083 GGACACATGTCGCCGTTAGC 61.693 60.000 0.00 0.00 45.65 3.09
2530 2915 3.933740 CGCAAGCGACTAAATTTTGTG 57.066 42.857 9.11 4.39 42.83 3.33
2531 2916 3.550561 CGCAAGCGACTAAATTTTGTGA 58.449 40.909 9.11 0.00 42.83 3.58
2532 2917 4.158384 CGCAAGCGACTAAATTTTGTGAT 58.842 39.130 9.11 0.00 42.83 3.06
2533 2918 5.320723 CGCAAGCGACTAAATTTTGTGATA 58.679 37.500 9.11 0.00 42.83 2.15
2534 2919 5.225129 CGCAAGCGACTAAATTTTGTGATAC 59.775 40.000 9.11 0.00 42.83 2.24
2535 2920 6.083630 GCAAGCGACTAAATTTTGTGATACA 58.916 36.000 10.05 0.00 0.00 2.29
2536 2921 6.747280 GCAAGCGACTAAATTTTGTGATACAT 59.253 34.615 10.05 0.00 0.00 2.29
2537 2922 7.273381 GCAAGCGACTAAATTTTGTGATACATT 59.727 33.333 10.05 0.00 0.00 2.71
2538 2923 8.788813 CAAGCGACTAAATTTTGTGATACATTC 58.211 33.333 10.05 0.00 0.00 2.67
2539 2924 8.268850 AGCGACTAAATTTTGTGATACATTCT 57.731 30.769 10.05 0.00 0.00 2.40
2540 2925 8.730680 AGCGACTAAATTTTGTGATACATTCTT 58.269 29.630 10.05 0.00 0.00 2.52
2541 2926 9.982291 GCGACTAAATTTTGTGATACATTCTTA 57.018 29.630 10.05 0.00 0.00 2.10
2547 2932 7.660030 ATTTTGTGATACATTCTTAAGGGGG 57.340 36.000 1.85 0.00 0.00 5.40
2548 2933 4.164843 TGTGATACATTCTTAAGGGGGC 57.835 45.455 1.85 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.610333 ACATTATTTTGGGGAGGGTTCTC 58.390 43.478 0.00 0.00 39.25 2.87
35 36 2.032894 ACAAGAGATGCACAACGTTTCG 60.033 45.455 0.00 0.00 0.00 3.46
40 41 1.728971 GAGGACAAGAGATGCACAACG 59.271 52.381 0.00 0.00 0.00 4.10
64 65 2.395336 AGAGATAGCAGATCTGGCCA 57.605 50.000 23.89 4.71 0.00 5.36
76 77 2.892852 CCAGCCTGAGGAGAAGAGATAG 59.107 54.545 0.65 0.00 0.00 2.08
108 109 1.038681 GGAGGGACGGAGGAGAACTC 61.039 65.000 0.00 0.00 45.84 3.01
109 110 1.000612 GGAGGGACGGAGGAGAACT 59.999 63.158 0.00 0.00 0.00 3.01
110 111 2.059190 GGGAGGGACGGAGGAGAAC 61.059 68.421 0.00 0.00 0.00 3.01
111 112 2.363361 GGGAGGGACGGAGGAGAA 59.637 66.667 0.00 0.00 0.00 2.87
112 113 3.752167 GGGGAGGGACGGAGGAGA 61.752 72.222 0.00 0.00 0.00 3.71
113 114 3.756783 AGGGGAGGGACGGAGGAG 61.757 72.222 0.00 0.00 0.00 3.69
114 115 4.075793 CAGGGGAGGGACGGAGGA 62.076 72.222 0.00 0.00 0.00 3.71
115 116 3.925914 AACAGGGGAGGGACGGAGG 62.926 68.421 0.00 0.00 0.00 4.30
116 117 1.489560 AAAACAGGGGAGGGACGGAG 61.490 60.000 0.00 0.00 0.00 4.63
117 118 1.063654 AAAAACAGGGGAGGGACGGA 61.064 55.000 0.00 0.00 0.00 4.69
118 119 0.694196 TAAAAACAGGGGAGGGACGG 59.306 55.000 0.00 0.00 0.00 4.79
119 120 1.626825 TCTAAAAACAGGGGAGGGACG 59.373 52.381 0.00 0.00 0.00 4.79
124 125 1.005569 GGGGGTCTAAAAACAGGGGAG 59.994 57.143 0.00 0.00 0.00 4.30
141 142 1.382971 CATTGATTGGGGGTGGGGG 60.383 63.158 0.00 0.00 0.00 5.40
142 143 0.687427 GACATTGATTGGGGGTGGGG 60.687 60.000 0.00 0.00 0.00 4.96
143 144 0.040942 TGACATTGATTGGGGGTGGG 59.959 55.000 0.00 0.00 0.00 4.61
144 145 1.272648 ACTGACATTGATTGGGGGTGG 60.273 52.381 0.00 0.00 0.00 4.61
145 146 1.820519 CACTGACATTGATTGGGGGTG 59.179 52.381 0.00 0.00 0.00 4.61
146 147 1.892329 GCACTGACATTGATTGGGGGT 60.892 52.381 0.00 0.00 0.00 4.95
147 148 0.819582 GCACTGACATTGATTGGGGG 59.180 55.000 0.00 0.00 0.00 5.40
148 149 1.548081 TGCACTGACATTGATTGGGG 58.452 50.000 0.00 0.00 0.00 4.96
171 172 0.178921 AGCAGTGGAGAAGAGGGACA 60.179 55.000 0.00 0.00 0.00 4.02
174 175 0.676151 GCAAGCAGTGGAGAAGAGGG 60.676 60.000 0.00 0.00 0.00 4.30
204 205 0.906066 GGGACTGAAGGAGAAGGGAC 59.094 60.000 0.00 0.00 0.00 4.46
218 219 2.021457 CGTGGAAACAAACAAGGGACT 58.979 47.619 0.00 0.00 46.06 3.85
219 220 1.066454 CCGTGGAAACAAACAAGGGAC 59.934 52.381 0.00 0.00 46.06 4.46
225 226 1.606668 GATCTGCCGTGGAAACAAACA 59.393 47.619 0.00 0.00 46.06 2.83
267 268 4.275810 AGATGTTAATGGCAGCTCAATGT 58.724 39.130 0.00 0.00 0.00 2.71
295 296 5.641209 AGAAAGATCTGGATGAGTTTTCACG 59.359 40.000 0.00 0.00 35.34 4.35
362 363 3.507622 ACAAGGATAAGAAGGCAGCAAAC 59.492 43.478 0.00 0.00 0.00 2.93
371 372 6.867662 ACTTCACAACACAAGGATAAGAAG 57.132 37.500 0.00 0.00 36.82 2.85
372 373 7.276658 TGTACTTCACAACACAAGGATAAGAA 58.723 34.615 0.00 0.00 32.95 2.52
373 374 6.822442 TGTACTTCACAACACAAGGATAAGA 58.178 36.000 0.00 0.00 32.95 2.10
436 437 6.294473 TCAGAGGCTGATGGATCTAAAAATC 58.706 40.000 0.00 0.00 35.39 2.17
437 438 6.257994 TCAGAGGCTGATGGATCTAAAAAT 57.742 37.500 0.00 0.00 35.39 1.82
446 447 2.877300 GCTTGTTTCAGAGGCTGATGGA 60.877 50.000 0.00 0.00 40.39 3.41
475 476 5.008019 CGCTATTACAGAAGCAAATGATGGT 59.992 40.000 0.00 0.00 42.88 3.55
556 557 2.465860 AGCATGTGCAAAGTACGGTA 57.534 45.000 7.83 0.00 45.16 4.02
557 558 1.604604 AAGCATGTGCAAAGTACGGT 58.395 45.000 7.83 0.00 45.16 4.83
558 559 3.623060 AGATAAGCATGTGCAAAGTACGG 59.377 43.478 7.83 0.00 45.16 4.02
559 560 4.864916 AGATAAGCATGTGCAAAGTACG 57.135 40.909 7.83 0.00 45.16 3.67
560 561 7.225538 AGACATAGATAAGCATGTGCAAAGTAC 59.774 37.037 7.83 0.00 45.16 2.73
598 599 7.752239 CACGATCAACATTTTATTCTCAAGCTT 59.248 33.333 0.00 0.00 0.00 3.74
628 629 5.567423 GCTTCCCAGTTAAAATGTCAGCAAT 60.567 40.000 0.00 0.00 0.00 3.56
657 658 1.979855 TGAGGACACCCACAAATGTG 58.020 50.000 6.57 6.57 45.23 3.21
658 659 2.376518 AGATGAGGACACCCACAAATGT 59.623 45.455 0.00 0.00 36.63 2.71
676 677 9.107177 CTGCACAGAATTCTACATTAAGAAGAT 57.893 33.333 7.86 0.00 38.81 2.40
706 707 8.817100 TGCGTAACAGAATGAATGAATAAGTAG 58.183 33.333 0.00 0.00 39.69 2.57
712 713 6.072508 AGTGTTGCGTAACAGAATGAATGAAT 60.073 34.615 19.76 0.00 46.75 2.57
713 714 5.238432 AGTGTTGCGTAACAGAATGAATGAA 59.762 36.000 19.76 0.00 46.75 2.57
714 715 4.754618 AGTGTTGCGTAACAGAATGAATGA 59.245 37.500 19.76 0.00 46.75 2.57
715 716 5.034554 AGTGTTGCGTAACAGAATGAATG 57.965 39.130 19.76 0.00 46.75 2.67
750 751 6.636850 CCAGTTAGAATTTTGGAAGTTTCGTG 59.363 38.462 0.00 0.00 32.34 4.35
760 761 6.930722 ACAATGCTTTCCAGTTAGAATTTTGG 59.069 34.615 0.00 0.00 0.00 3.28
789 790 9.013229 ACAGTATGAGCAAACAAATTCAGAATA 57.987 29.630 0.00 0.00 39.69 1.75
823 824 9.663904 CCACATGTTAAATAGAATGAATTACGG 57.336 33.333 0.00 0.00 0.00 4.02
874 876 9.130661 AGTAGAATGAATATCTGGGATCTATCG 57.869 37.037 0.00 0.00 0.00 2.92
880 882 8.717717 TGTCAAAGTAGAATGAATATCTGGGAT 58.282 33.333 0.00 0.00 0.00 3.85
925 927 6.017400 AGCAAGTGTTATGGATGTTCAAAG 57.983 37.500 0.00 0.00 0.00 2.77
962 970 2.593346 AACAGCACGGCAATCAAAAA 57.407 40.000 0.00 0.00 0.00 1.94
974 982 3.316308 AGACAACAATCCTGAAACAGCAC 59.684 43.478 0.00 0.00 0.00 4.40
1047 1055 1.867812 CTTCTCGTCATCGCGCGAA 60.868 57.895 38.07 19.64 36.65 4.70
1048 1056 2.277310 CTTCTCGTCATCGCGCGA 60.277 61.111 36.65 36.65 36.96 5.87
1127 1138 0.251787 AAGTTCCCTGCCATTGTCCC 60.252 55.000 0.00 0.00 0.00 4.46
1334 1345 2.122768 CCCTCTTGGTAAGCTCCTCAT 58.877 52.381 0.00 0.00 0.00 2.90
1371 1382 0.037447 AGGGCAGCTTGAACTCCTTC 59.963 55.000 0.00 0.00 0.00 3.46
1440 1451 2.027192 GTCCTGGATGTTGCTCTGGTAA 60.027 50.000 0.00 0.00 0.00 2.85
1445 1456 1.903877 CGGGTCCTGGATGTTGCTCT 61.904 60.000 0.00 0.00 0.00 4.09
1491 1502 2.176273 GCTGACGCATGCCTCGAAT 61.176 57.895 13.15 0.00 35.78 3.34
1527 1538 4.051167 TGAGCAGCCCCCATGGTG 62.051 66.667 11.73 3.08 36.04 4.17
1528 1539 3.736224 CTGAGCAGCCCCCATGGT 61.736 66.667 11.73 0.00 36.04 3.55
1529 1540 3.736224 ACTGAGCAGCCCCCATGG 61.736 66.667 4.14 4.14 37.09 3.66
1530 1541 2.439701 CACTGAGCAGCCCCCATG 60.440 66.667 0.00 0.00 0.00 3.66
1557 1625 0.240411 GTACGACACCTCGCTCACTT 59.760 55.000 0.00 0.00 44.33 3.16
1580 1648 3.491342 TCATCCCGACAAACCAAAATCA 58.509 40.909 0.00 0.00 0.00 2.57
1609 1712 2.091541 TCACCGAAAATCCATTCAGGC 58.908 47.619 0.00 0.00 37.29 4.85
1666 1777 1.303236 CACCGGTGCAATCCCTTGA 60.303 57.895 24.02 0.00 34.04 3.02
1667 1778 3.277133 CACCGGTGCAATCCCTTG 58.723 61.111 24.02 0.00 35.36 3.61
1795 1916 7.387948 AGCAGCCATTTTACCTAAATATACTCG 59.612 37.037 0.00 0.00 34.69 4.18
1833 1954 3.688694 TTACCTAAACATGCCACGACT 57.311 42.857 0.00 0.00 0.00 4.18
1835 1956 6.655848 AGTTATTTTACCTAAACATGCCACGA 59.344 34.615 0.00 0.00 0.00 4.35
1837 1958 7.540745 CACAGTTATTTTACCTAAACATGCCAC 59.459 37.037 0.00 0.00 0.00 5.01
1849 1970 6.203647 ACAAAACGAGCACAGTTATTTTACC 58.796 36.000 0.00 0.00 0.00 2.85
1850 1971 7.673810 AACAAAACGAGCACAGTTATTTTAC 57.326 32.000 0.00 0.00 0.00 2.01
1852 1973 6.035542 CCAAACAAAACGAGCACAGTTATTTT 59.964 34.615 0.00 0.00 0.00 1.82
1860 1981 1.464734 TCCCAAACAAAACGAGCACA 58.535 45.000 0.00 0.00 0.00 4.57
1868 1989 7.713073 GGTTATTCAAACTCATCCCAAACAAAA 59.287 33.333 0.00 0.00 0.00 2.44
1924 2160 0.173481 CAAAGCAGCAGCAGCATCAT 59.827 50.000 12.92 0.00 45.49 2.45
2041 2370 1.269448 CATGTACCCCAGTGTTGTTGC 59.731 52.381 0.00 0.00 0.00 4.17
2133 2462 0.667792 GAATCGACATCCTAGGCCGC 60.668 60.000 2.96 0.00 0.00 6.53
2147 2476 0.387202 AGTCGGGCATCTCTGAATCG 59.613 55.000 0.00 0.00 0.00 3.34
2161 2490 1.505353 GTGTAGGGTGTCGAGTCGG 59.495 63.158 13.54 0.00 0.00 4.79
2289 2638 5.047092 GGTGTTGTGGATTTTCTTGGATGAT 60.047 40.000 0.00 0.00 0.00 2.45
2294 2643 2.697751 TGGGTGTTGTGGATTTTCTTGG 59.302 45.455 0.00 0.00 0.00 3.61
2295 2644 4.370917 CTTGGGTGTTGTGGATTTTCTTG 58.629 43.478 0.00 0.00 0.00 3.02
2298 2647 2.365293 AGCTTGGGTGTTGTGGATTTTC 59.635 45.455 0.00 0.00 0.00 2.29
2300 2649 1.688197 CAGCTTGGGTGTTGTGGATTT 59.312 47.619 0.00 0.00 0.00 2.17
2303 2652 1.827789 GCAGCTTGGGTGTTGTGGA 60.828 57.895 0.00 0.00 33.19 4.02
2305 2654 1.102809 TCTGCAGCTTGGGTGTTGTG 61.103 55.000 9.47 0.00 33.19 3.33
2306 2655 0.820891 CTCTGCAGCTTGGGTGTTGT 60.821 55.000 9.47 0.00 33.19 3.32
2307 2656 0.820891 ACTCTGCAGCTTGGGTGTTG 60.821 55.000 9.47 0.00 33.19 3.33
2309 2658 1.228063 CACTCTGCAGCTTGGGTGT 60.228 57.895 9.47 0.00 33.19 4.16
2310 2659 2.623915 GCACTCTGCAGCTTGGGTG 61.624 63.158 9.47 12.83 44.26 4.61
2320 2669 2.225255 GAGAAACTTTCCAGCACTCTGC 59.775 50.000 0.00 0.00 45.46 4.26
2321 2670 3.470709 TGAGAAACTTTCCAGCACTCTG 58.529 45.455 0.00 0.00 40.02 3.35
2322 2671 3.389329 TCTGAGAAACTTTCCAGCACTCT 59.611 43.478 12.01 0.00 31.90 3.24
2323 2672 3.496507 GTCTGAGAAACTTTCCAGCACTC 59.503 47.826 12.01 0.00 31.90 3.51
2324 2673 3.118261 TGTCTGAGAAACTTTCCAGCACT 60.118 43.478 12.01 0.00 31.90 4.40
2325 2674 3.206150 TGTCTGAGAAACTTTCCAGCAC 58.794 45.455 12.01 11.41 31.90 4.40
2327 2676 3.879892 ACTTGTCTGAGAAACTTTCCAGC 59.120 43.478 12.01 9.31 31.90 4.85
2329 2678 7.387948 GCTATAACTTGTCTGAGAAACTTTCCA 59.612 37.037 0.00 0.00 0.00 3.53
2331 2680 7.387948 TGGCTATAACTTGTCTGAGAAACTTTC 59.612 37.037 0.00 0.00 0.00 2.62
2333 2682 6.769512 TGGCTATAACTTGTCTGAGAAACTT 58.230 36.000 0.00 0.00 0.00 2.66
2334 2683 6.360370 TGGCTATAACTTGTCTGAGAAACT 57.640 37.500 0.00 0.00 0.00 2.66
2335 2684 5.064071 GCTGGCTATAACTTGTCTGAGAAAC 59.936 44.000 0.00 0.00 0.00 2.78
2336 2685 5.178797 GCTGGCTATAACTTGTCTGAGAAA 58.821 41.667 0.00 0.00 0.00 2.52
2338 2687 3.769300 TGCTGGCTATAACTTGTCTGAGA 59.231 43.478 0.00 0.00 0.00 3.27
2340 2689 3.515502 AGTGCTGGCTATAACTTGTCTGA 59.484 43.478 0.00 0.00 0.00 3.27
2341 2690 3.620374 CAGTGCTGGCTATAACTTGTCTG 59.380 47.826 0.00 0.00 0.00 3.51
2342 2691 3.866651 CAGTGCTGGCTATAACTTGTCT 58.133 45.455 0.00 0.00 0.00 3.41
2343 2692 2.352960 GCAGTGCTGGCTATAACTTGTC 59.647 50.000 8.18 0.00 0.00 3.18
2344 2693 2.359900 GCAGTGCTGGCTATAACTTGT 58.640 47.619 8.18 0.00 0.00 3.16
2355 2704 0.745845 GGATACTGTGGCAGTGCTGG 60.746 60.000 16.11 5.44 45.01 4.85
2356 2705 0.745845 GGGATACTGTGGCAGTGCTG 60.746 60.000 16.11 5.80 45.01 4.41
2357 2706 1.200760 TGGGATACTGTGGCAGTGCT 61.201 55.000 16.11 0.00 45.01 4.40
2358 2707 0.745845 CTGGGATACTGTGGCAGTGC 60.746 60.000 6.55 6.55 45.01 4.40
2359 2708 0.745845 GCTGGGATACTGTGGCAGTG 60.746 60.000 11.57 0.00 45.01 3.66
2361 2710 0.463295 CTGCTGGGATACTGTGGCAG 60.463 60.000 0.00 0.00 40.52 4.85
2362 2711 0.909133 TCTGCTGGGATACTGTGGCA 60.909 55.000 0.00 0.00 0.00 4.92
2363 2712 0.471617 ATCTGCTGGGATACTGTGGC 59.528 55.000 0.00 0.00 0.00 5.01
2364 2713 4.384056 CTTTATCTGCTGGGATACTGTGG 58.616 47.826 0.00 0.00 0.00 4.17
2365 2714 3.812053 GCTTTATCTGCTGGGATACTGTG 59.188 47.826 0.00 0.00 0.00 3.66
2366 2715 3.181450 GGCTTTATCTGCTGGGATACTGT 60.181 47.826 0.00 0.00 0.00 3.55
2367 2716 3.181451 TGGCTTTATCTGCTGGGATACTG 60.181 47.826 0.00 0.00 0.00 2.74
2368 2717 3.048600 TGGCTTTATCTGCTGGGATACT 58.951 45.455 0.00 0.00 0.00 2.12
2369 2718 3.142174 GTGGCTTTATCTGCTGGGATAC 58.858 50.000 0.00 0.00 0.00 2.24
2371 2720 1.565759 TGTGGCTTTATCTGCTGGGAT 59.434 47.619 0.00 0.00 0.00 3.85
2372 2721 0.991146 TGTGGCTTTATCTGCTGGGA 59.009 50.000 0.00 0.00 0.00 4.37
2374 2723 2.119801 ACTGTGGCTTTATCTGCTGG 57.880 50.000 0.00 0.00 0.00 4.85
2375 2724 3.076621 TCAACTGTGGCTTTATCTGCTG 58.923 45.455 0.00 0.00 0.00 4.41
2376 2725 3.423539 TCAACTGTGGCTTTATCTGCT 57.576 42.857 0.00 0.00 0.00 4.24
2377 2726 4.503741 TTTCAACTGTGGCTTTATCTGC 57.496 40.909 0.00 0.00 0.00 4.26
2379 2728 6.715347 ACTTTTTCAACTGTGGCTTTATCT 57.285 33.333 0.00 0.00 0.00 1.98
2380 2729 8.515414 AGATACTTTTTCAACTGTGGCTTTATC 58.485 33.333 0.00 0.00 0.00 1.75
2381 2730 8.409358 AGATACTTTTTCAACTGTGGCTTTAT 57.591 30.769 0.00 0.00 0.00 1.40
2382 2731 7.817418 AGATACTTTTTCAACTGTGGCTTTA 57.183 32.000 0.00 0.00 0.00 1.85
2383 2732 6.715347 AGATACTTTTTCAACTGTGGCTTT 57.285 33.333 0.00 0.00 0.00 3.51
2388 2773 8.909708 TTGTTCAAGATACTTTTTCAACTGTG 57.090 30.769 0.00 0.00 0.00 3.66
2390 2775 9.573133 AACTTGTTCAAGATACTTTTTCAACTG 57.427 29.630 17.75 0.00 0.00 3.16
2401 2786 6.977213 TGGCCTTTTAACTTGTTCAAGATAC 58.023 36.000 17.75 0.77 0.00 2.24
2402 2787 6.775629 ACTGGCCTTTTAACTTGTTCAAGATA 59.224 34.615 17.75 8.64 0.00 1.98
2404 2789 4.953579 ACTGGCCTTTTAACTTGTTCAAGA 59.046 37.500 17.75 0.00 0.00 3.02
2409 2794 4.278310 AGACACTGGCCTTTTAACTTGTT 58.722 39.130 3.32 0.00 0.00 2.83
2414 2799 4.134563 TGAGAAGACACTGGCCTTTTAAC 58.865 43.478 3.32 0.00 0.00 2.01
2415 2800 4.431416 TGAGAAGACACTGGCCTTTTAA 57.569 40.909 3.32 0.00 0.00 1.52
2419 2804 1.980765 TGATGAGAAGACACTGGCCTT 59.019 47.619 3.32 0.00 0.00 4.35
2420 2805 1.554160 CTGATGAGAAGACACTGGCCT 59.446 52.381 3.32 0.00 0.00 5.19
2421 2806 1.277557 ACTGATGAGAAGACACTGGCC 59.722 52.381 0.00 0.00 0.00 5.36
2423 2808 4.932200 GGTTAACTGATGAGAAGACACTGG 59.068 45.833 5.42 0.00 0.00 4.00
2424 2809 5.541845 TGGTTAACTGATGAGAAGACACTG 58.458 41.667 5.42 0.00 0.00 3.66
2426 2811 6.260050 TGTTTGGTTAACTGATGAGAAGACAC 59.740 38.462 5.42 0.00 37.64 3.67
2427 2812 6.353323 TGTTTGGTTAACTGATGAGAAGACA 58.647 36.000 5.42 0.00 37.64 3.41
2428 2813 6.861065 TGTTTGGTTAACTGATGAGAAGAC 57.139 37.500 5.42 0.00 37.64 3.01
2429 2814 7.873719 TTTGTTTGGTTAACTGATGAGAAGA 57.126 32.000 5.42 0.00 37.64 2.87
2430 2815 8.352201 TGATTTGTTTGGTTAACTGATGAGAAG 58.648 33.333 5.42 0.00 37.64 2.85
2432 2817 7.815840 TGATTTGTTTGGTTAACTGATGAGA 57.184 32.000 5.42 0.00 37.64 3.27
2433 2818 8.870160 TTTGATTTGTTTGGTTAACTGATGAG 57.130 30.769 5.42 0.00 37.64 2.90
2435 2820 9.701355 GTTTTTGATTTGTTTGGTTAACTGATG 57.299 29.630 5.42 0.00 37.64 3.07
2436 2821 9.442047 TGTTTTTGATTTGTTTGGTTAACTGAT 57.558 25.926 5.42 0.00 37.64 2.90
2437 2822 8.833231 TGTTTTTGATTTGTTTGGTTAACTGA 57.167 26.923 5.42 0.00 37.64 3.41
2438 2823 8.930760 TCTGTTTTTGATTTGTTTGGTTAACTG 58.069 29.630 5.42 0.00 37.64 3.16
2441 2826 7.065204 GCCTCTGTTTTTGATTTGTTTGGTTAA 59.935 33.333 0.00 0.00 0.00 2.01
2442 2827 6.536941 GCCTCTGTTTTTGATTTGTTTGGTTA 59.463 34.615 0.00 0.00 0.00 2.85
2443 2828 5.353956 GCCTCTGTTTTTGATTTGTTTGGTT 59.646 36.000 0.00 0.00 0.00 3.67
2444 2829 4.875536 GCCTCTGTTTTTGATTTGTTTGGT 59.124 37.500 0.00 0.00 0.00 3.67
2445 2830 5.118286 AGCCTCTGTTTTTGATTTGTTTGG 58.882 37.500 0.00 0.00 0.00 3.28
2446 2831 7.769272 TTAGCCTCTGTTTTTGATTTGTTTG 57.231 32.000 0.00 0.00 0.00 2.93
2447 2832 8.962884 ATTTAGCCTCTGTTTTTGATTTGTTT 57.037 26.923 0.00 0.00 0.00 2.83
2448 2833 8.424133 AGATTTAGCCTCTGTTTTTGATTTGTT 58.576 29.630 0.00 0.00 0.00 2.83
2449 2834 7.869429 CAGATTTAGCCTCTGTTTTTGATTTGT 59.131 33.333 0.00 0.00 36.26 2.83
2450 2835 8.236084 CAGATTTAGCCTCTGTTTTTGATTTG 57.764 34.615 0.00 0.00 36.26 2.32
2461 2846 3.196463 CAGCTGACAGATTTAGCCTCTG 58.804 50.000 8.42 0.00 44.60 3.35
2462 2847 2.419851 GCAGCTGACAGATTTAGCCTCT 60.420 50.000 20.43 0.00 38.18 3.69
2463 2848 1.939255 GCAGCTGACAGATTTAGCCTC 59.061 52.381 20.43 0.00 38.18 4.70
2464 2849 1.407989 GGCAGCTGACAGATTTAGCCT 60.408 52.381 20.43 0.00 38.18 4.58
2465 2850 1.020437 GGCAGCTGACAGATTTAGCC 58.980 55.000 20.43 5.67 38.18 3.93
2466 2851 1.742761 TGGCAGCTGACAGATTTAGC 58.257 50.000 21.20 0.00 37.71 3.09
2467 2852 3.076621 TGTTGGCAGCTGACAGATTTAG 58.923 45.455 23.97 0.00 32.66 1.85
2468 2853 3.076621 CTGTTGGCAGCTGACAGATTTA 58.923 45.455 23.97 4.18 42.54 1.40
2469 2854 1.884579 CTGTTGGCAGCTGACAGATTT 59.115 47.619 23.97 0.00 42.54 2.17
2470 2855 1.072806 TCTGTTGGCAGCTGACAGATT 59.927 47.619 25.08 0.00 43.38 2.40
2471 2856 0.689055 TCTGTTGGCAGCTGACAGAT 59.311 50.000 25.08 0.00 43.38 2.90
2472 2857 0.034476 CTCTGTTGGCAGCTGACAGA 59.966 55.000 26.33 26.33 45.34 3.41
2473 2858 0.954449 CCTCTGTTGGCAGCTGACAG 60.954 60.000 23.97 22.82 42.29 3.51
2474 2859 1.071987 CCTCTGTTGGCAGCTGACA 59.928 57.895 21.20 21.20 42.29 3.58
2475 2860 0.952984 GTCCTCTGTTGGCAGCTGAC 60.953 60.000 20.43 17.52 42.29 3.51
2476 2861 1.372683 GTCCTCTGTTGGCAGCTGA 59.627 57.895 20.43 10.26 42.29 4.26
2477 2862 1.071987 TGTCCTCTGTTGGCAGCTG 59.928 57.895 10.11 10.11 42.29 4.24
2478 2863 1.072159 GTGTCCTCTGTTGGCAGCT 59.928 57.895 2.28 0.00 42.29 4.24
2479 2864 0.607489 ATGTGTCCTCTGTTGGCAGC 60.607 55.000 0.00 0.00 42.29 5.25
2480 2865 1.162698 CATGTGTCCTCTGTTGGCAG 58.837 55.000 0.00 0.00 43.87 4.85
2481 2866 0.473755 ACATGTGTCCTCTGTTGGCA 59.526 50.000 0.00 0.00 0.00 4.92
2482 2867 1.160137 GACATGTGTCCTCTGTTGGC 58.840 55.000 1.15 0.00 39.07 4.52
2483 2868 1.432514 CGACATGTGTCCTCTGTTGG 58.567 55.000 1.15 0.00 41.86 3.77
2484 2869 0.792640 GCGACATGTGTCCTCTGTTG 59.207 55.000 1.15 0.00 41.86 3.33
2485 2870 0.320771 GGCGACATGTGTCCTCTGTT 60.321 55.000 1.15 0.00 41.86 3.16
2486 2871 1.293498 GGCGACATGTGTCCTCTGT 59.707 57.895 1.15 0.00 41.86 3.41
2487 2872 1.807165 CGGCGACATGTGTCCTCTG 60.807 63.158 1.15 1.94 41.86 3.35
2488 2873 1.816863 AACGGCGACATGTGTCCTCT 61.817 55.000 16.62 0.00 41.86 3.69
2489 2874 0.108992 TAACGGCGACATGTGTCCTC 60.109 55.000 16.62 0.48 41.86 3.71
2490 2875 0.108804 CTAACGGCGACATGTGTCCT 60.109 55.000 16.62 0.00 41.86 3.85
2491 2876 1.693083 GCTAACGGCGACATGTGTCC 61.693 60.000 16.62 2.64 41.86 4.02
2492 2877 1.708027 GCTAACGGCGACATGTGTC 59.292 57.895 16.62 3.07 41.47 3.67
2493 2878 3.870606 GCTAACGGCGACATGTGT 58.129 55.556 16.62 0.00 0.00 3.72
2502 2887 4.500568 GTCGCTTGCGCTAACGGC 62.501 66.667 14.18 9.15 40.57 5.68
2503 2888 1.074319 TTAGTCGCTTGCGCTAACGG 61.074 55.000 14.18 0.00 40.57 4.44
2504 2889 0.711670 TTTAGTCGCTTGCGCTAACG 59.288 50.000 21.53 8.94 44.07 3.18
2505 2890 3.385079 AATTTAGTCGCTTGCGCTAAC 57.615 42.857 21.53 12.12 0.00 2.34
2506 2891 4.155449 CAAAATTTAGTCGCTTGCGCTAA 58.845 39.130 19.47 19.47 0.00 3.09
2507 2892 3.187637 ACAAAATTTAGTCGCTTGCGCTA 59.812 39.130 9.73 11.62 0.00 4.26
2508 2893 2.031157 ACAAAATTTAGTCGCTTGCGCT 60.031 40.909 9.73 12.55 0.00 5.92
2509 2894 2.088969 CACAAAATTTAGTCGCTTGCGC 59.911 45.455 10.38 0.00 0.00 6.09
2510 2895 3.550561 TCACAAAATTTAGTCGCTTGCG 58.449 40.909 8.87 8.87 0.00 4.85
2511 2896 6.083630 TGTATCACAAAATTTAGTCGCTTGC 58.916 36.000 0.00 0.00 0.00 4.01
2512 2897 8.673626 AATGTATCACAAAATTTAGTCGCTTG 57.326 30.769 0.00 0.00 0.00 4.01
2513 2898 8.730680 AGAATGTATCACAAAATTTAGTCGCTT 58.269 29.630 0.00 0.00 0.00 4.68
2514 2899 8.268850 AGAATGTATCACAAAATTTAGTCGCT 57.731 30.769 0.00 0.00 0.00 4.93
2515 2900 8.895932 AAGAATGTATCACAAAATTTAGTCGC 57.104 30.769 0.00 0.00 0.00 5.19
2521 2906 8.539544 CCCCCTTAAGAATGTATCACAAAATTT 58.460 33.333 3.36 0.00 0.00 1.82
2522 2907 7.364673 GCCCCCTTAAGAATGTATCACAAAATT 60.365 37.037 3.36 0.00 0.00 1.82
2523 2908 6.098266 GCCCCCTTAAGAATGTATCACAAAAT 59.902 38.462 3.36 0.00 0.00 1.82
2524 2909 5.420739 GCCCCCTTAAGAATGTATCACAAAA 59.579 40.000 3.36 0.00 0.00 2.44
2525 2910 4.953579 GCCCCCTTAAGAATGTATCACAAA 59.046 41.667 3.36 0.00 0.00 2.83
2526 2911 4.532834 GCCCCCTTAAGAATGTATCACAA 58.467 43.478 3.36 0.00 0.00 3.33
2527 2912 4.164843 GCCCCCTTAAGAATGTATCACA 57.835 45.455 3.36 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.