Multiple sequence alignment - TraesCS5B01G305700

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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 TraesCS5B01G305700 chr5B 100.000 4801 0 0 1 4801 489612114 489616914 0.000000e+00 8866
1 TraesCS5B01G305700 chr5B 97.403 77 1 1 2924 3000 489617179 489617104 3.900000e-26 130
2 TraesCS5B01G305700 chr5D 92.537 2050 108 23 1 2033 408300156 408302177 0.000000e+00 2896
3 TraesCS5B01G305700 chr5D 91.825 1737 99 22 2781 4498 408302908 408304620 0.000000e+00 2381
4 TraesCS5B01G305700 chr5D 94.747 514 24 2 2027 2540 408302301 408302811 0.000000e+00 797
5 TraesCS5B01G305700 chr5D 91.694 301 23 2 4502 4801 408304837 408305136 2.670000e-112 416
6 TraesCS5B01G305700 chr5A 92.961 1932 96 18 2889 4801 514095076 514096986 0.000000e+00 2778
7 TraesCS5B01G305700 chr5A 91.605 1084 61 15 961 2033 514093168 514094232 0.000000e+00 1471
8 TraesCS5B01G305700 chr5A 88.571 980 69 15 1 973 514091957 514092900 0.000000e+00 1149
9 TraesCS5B01G305700 chr5A 93.499 523 29 3 2025 2545 514094349 514094868 0.000000e+00 773
10 TraesCS5B01G305700 chr5A 87.669 519 61 2 2028 2546 548605269 548605784 6.880000e-168 601
11 TraesCS5B01G305700 chr5A 81.913 481 65 10 2742 3217 548606250 548606713 2.100000e-103 387
12 TraesCS5B01G305700 chr5A 86.290 124 10 4 1 123 514040608 514040725 1.400000e-25 128
13 TraesCS5B01G305700 chr3B 79.396 364 52 17 860 1202 341297037 341296676 8.030000e-58 235
14 TraesCS5B01G305700 chr3B 92.913 127 7 2 2539 2663 658489676 658489550 2.950000e-42 183
15 TraesCS5B01G305700 chr2A 79.121 364 51 15 860 1202 296494544 296494903 1.340000e-55 228
16 TraesCS5B01G305700 chr4A 78.846 364 52 18 860 1202 525579058 525578699 6.250000e-54 222
17 TraesCS5B01G305700 chr6A 78.512 363 55 16 860 1202 462412398 462412039 2.910000e-52 217
18 TraesCS5B01G305700 chr1A 93.893 131 3 4 2538 2665 498452794 498452666 4.900000e-45 193
19 TraesCS5B01G305700 chr4D 93.701 127 6 2 2548 2672 494876029 494875903 6.340000e-44 189
20 TraesCS5B01G305700 chr2D 92.481 133 8 2 2536 2666 109700337 109700469 6.340000e-44 189
21 TraesCS5B01G305700 chr1B 92.593 135 3 7 2548 2677 611680540 611680408 2.280000e-43 187
22 TraesCS5B01G305700 chr7D 94.262 122 5 2 2546 2665 543628165 543628044 8.210000e-43 185
23 TraesCS5B01G305700 chr1D 94.958 119 4 2 2548 2664 344594232 344594114 8.210000e-43 185
24 TraesCS5B01G305700 chr3A 92.969 128 6 3 2539 2663 24029946 24030073 2.950000e-42 183
25 TraesCS5B01G305700 chr4B 93.496 123 6 2 2548 2668 564869585 564869463 1.060000e-41 182


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 TraesCS5B01G305700 chr5B 489612114 489616914 4800 False 8866.00 8866 100.00000 1 4801 1 chr5B.!!$F1 4800
1 TraesCS5B01G305700 chr5D 408300156 408305136 4980 False 1622.50 2896 92.70075 1 4801 4 chr5D.!!$F1 4800
2 TraesCS5B01G305700 chr5A 514091957 514096986 5029 False 1542.75 2778 91.65900 1 4801 4 chr5A.!!$F2 4800
3 TraesCS5B01G305700 chr5A 548605269 548606713 1444 False 494.00 601 84.79100 2028 3217 2 chr5A.!!$F3 1189

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
562 574 0.179062 CCAGCTTCCAGGATTCTCCG 60.179 60.0 0.0 0.0 42.75 4.63 F
1972 2285 0.545309 AGCAGGCAGTGGAGGAAGTA 60.545 55.0 0.0 0.0 0.00 2.24 F
2653 3098 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 2622 0.175760 GGCTTGCGTCTGTATCCAGA 59.824 55.000 0.0 0.0 45.44 3.86 R
3797 4634 1.063764 GTCATCGACTCACCGTCCTAC 59.936 57.143 0.0 0.0 39.56 3.18 R
4500 5355 0.178846 TGGGGATTTGGGAGGAGTGA 60.179 55.000 0.0 0.0 0.00 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
57 59 5.810074 ACAACATCTTGTTAAACCTGCAAAC 59.190 36.000 0.00 0.00 38.77 2.93
60 62 6.402222 ACATCTTGTTAAACCTGCAAACAAA 58.598 32.000 13.13 6.66 41.22 2.83
115 117 9.807649 AGCATTTCATAAATTAAACCATCACTC 57.192 29.630 0.00 0.00 0.00 3.51
124 126 3.490759 CCATCACTCGTGTGGCGC 61.491 66.667 16.88 0.00 43.94 6.53
128 130 0.955428 ATCACTCGTGTGGCGCAAAT 60.955 50.000 16.88 0.08 43.94 2.32
145 147 4.872691 CGCAAATTAAACATAAATGGCCCA 59.127 37.500 0.00 0.00 0.00 5.36
156 158 5.598417 ACATAAATGGCCCATTAGAAAGTCC 59.402 40.000 9.91 0.00 32.43 3.85
212 214 9.415544 CAAAGAGAAAATACAAAATCTGAAGGG 57.584 33.333 0.00 0.00 0.00 3.95
241 243 6.267496 AGGTCAAAGTTATATGTGTTTGGC 57.733 37.500 0.00 0.00 34.46 4.52
266 268 7.500559 GCCATCTAGTCCAGAGTAAAATCATTT 59.499 37.037 0.00 0.00 36.48 2.32
443 454 0.463833 CCCTATTCCGCTGACAACCC 60.464 60.000 0.00 0.00 0.00 4.11
445 456 0.463833 CTATTCCGCTGACAACCCCC 60.464 60.000 0.00 0.00 0.00 5.40
446 457 1.202099 TATTCCGCTGACAACCCCCA 61.202 55.000 0.00 0.00 0.00 4.96
450 461 4.678743 GCTGACAACCCCCACCCC 62.679 72.222 0.00 0.00 0.00 4.95
451 462 3.979497 CTGACAACCCCCACCCCC 61.979 72.222 0.00 0.00 0.00 5.40
520 531 2.190578 GCCGGGGATTGAGACCAG 59.809 66.667 2.18 0.00 0.00 4.00
562 574 0.179062 CCAGCTTCCAGGATTCTCCG 60.179 60.000 0.00 0.00 42.75 4.63
643 655 1.341581 GGACGGGGATGGGATTTTTCA 60.342 52.381 0.00 0.00 0.00 2.69
648 660 2.840038 GGGGATGGGATTTTTCAAGCTT 59.160 45.455 0.00 0.00 0.00 3.74
651 663 4.223700 GGGATGGGATTTTTCAAGCTTTCT 59.776 41.667 0.00 0.00 0.00 2.52
652 664 5.280164 GGGATGGGATTTTTCAAGCTTTCTT 60.280 40.000 0.00 0.00 0.00 2.52
653 665 5.871524 GGATGGGATTTTTCAAGCTTTCTTC 59.128 40.000 0.00 0.00 0.00 2.87
654 666 4.870363 TGGGATTTTTCAAGCTTTCTTCG 58.130 39.130 0.00 0.00 0.00 3.79
655 667 4.237724 GGGATTTTTCAAGCTTTCTTCGG 58.762 43.478 0.00 0.00 0.00 4.30
656 668 4.237724 GGATTTTTCAAGCTTTCTTCGGG 58.762 43.478 0.00 0.00 0.00 5.14
657 669 2.793278 TTTTCAAGCTTTCTTCGGGC 57.207 45.000 0.00 0.00 0.00 6.13
815 827 1.884235 CTTCGTTAGGATCATGGGGC 58.116 55.000 0.00 0.00 0.00 5.80
820 832 0.916086 TTAGGATCATGGGGCGTTGT 59.084 50.000 0.00 0.00 0.00 3.32
895 907 3.539604 CCTGGTCTTTGCTATCTGAAGG 58.460 50.000 0.00 0.00 0.00 3.46
896 908 3.054802 CCTGGTCTTTGCTATCTGAAGGT 60.055 47.826 0.00 0.00 0.00 3.50
905 917 8.489489 TCTTTGCTATCTGAAGGTCTGATATTT 58.511 33.333 5.60 0.00 36.93 1.40
906 918 9.118300 CTTTGCTATCTGAAGGTCTGATATTTT 57.882 33.333 5.60 0.00 36.93 1.82
910 922 8.555361 GCTATCTGAAGGTCTGATATTTTTCAC 58.445 37.037 5.60 0.00 36.93 3.18
957 978 4.378459 GGTCTACCAGATTTTGCAAGAACG 60.378 45.833 0.00 0.00 35.64 3.95
973 994 3.583806 AGAACGAGATCTTGCAGTTCTG 58.416 45.455 23.56 0.00 46.47 3.02
974 995 1.719600 ACGAGATCTTGCAGTTCTGC 58.280 50.000 16.65 16.65 0.00 4.26
975 996 1.001293 ACGAGATCTTGCAGTTCTGCA 59.999 47.619 21.30 21.30 43.81 4.41
976 997 2.277969 CGAGATCTTGCAGTTCTGCAT 58.722 47.619 24.74 12.71 44.94 3.96
977 998 3.118992 ACGAGATCTTGCAGTTCTGCATA 60.119 43.478 24.74 17.29 44.94 3.14
978 999 3.244814 CGAGATCTTGCAGTTCTGCATAC 59.755 47.826 24.74 16.37 44.94 2.39
979 1000 4.440880 GAGATCTTGCAGTTCTGCATACT 58.559 43.478 24.74 19.72 44.94 2.12
980 1001 4.841422 AGATCTTGCAGTTCTGCATACTT 58.159 39.130 24.74 12.32 44.94 2.24
981 1002 5.251764 AGATCTTGCAGTTCTGCATACTTT 58.748 37.500 24.74 10.79 44.94 2.66
985 1284 3.743521 TGCAGTTCTGCATACTTTCTGT 58.256 40.909 21.30 0.00 40.23 3.41
1197 1496 2.124151 GCCGGCAATGTCTCCCAT 60.124 61.111 24.80 0.00 34.36 4.00
1371 1670 2.044946 GGGCTCAAGGCGACCAAT 60.045 61.111 0.00 0.00 42.94 3.16
1398 1697 3.050275 GCCTTCCATATCGCGGCC 61.050 66.667 6.13 0.00 34.75 6.13
1447 1746 6.997655 TCTTCTCTGCTTCTTTCAGTTCATA 58.002 36.000 0.00 0.00 33.48 2.15
1494 1801 3.418047 TGGTCACGATGAACTCTGTCTA 58.582 45.455 0.00 0.00 34.53 2.59
1504 1811 6.471841 CGATGAACTCTGTCTATCAAGTCAAG 59.528 42.308 0.00 0.00 0.00 3.02
1508 1815 6.463995 ACTCTGTCTATCAAGTCAAGGATC 57.536 41.667 0.00 0.00 0.00 3.36
1589 1897 3.871463 GCTGATCAGTGGAACCATTCACT 60.871 47.826 23.38 0.00 44.12 3.41
1599 1907 4.518970 TGGAACCATTCACTTTAGCTTGTC 59.481 41.667 0.00 0.00 0.00 3.18
1617 1925 6.314896 AGCTTGTCTATAGTTGCACATTTCTC 59.685 38.462 0.00 0.00 0.00 2.87
1653 1961 6.481954 AATGACTTGTATTCGGTTGACTTC 57.518 37.500 0.00 0.00 0.00 3.01
1663 1971 2.050691 CGGTTGACTTCGGCAAAATTG 58.949 47.619 0.00 0.00 0.00 2.32
1817 2125 3.009363 TCCACATTCCAGCTCATCTTTCA 59.991 43.478 0.00 0.00 0.00 2.69
1853 2161 1.956477 GACAGGCAAAACTGACCATGT 59.044 47.619 0.00 0.00 40.97 3.21
1865 2178 6.959639 AACTGACCATGTATTCACAGTTTT 57.040 33.333 0.00 0.00 43.02 2.43
1867 2180 7.672983 ACTGACCATGTATTCACAGTTTTAG 57.327 36.000 0.00 0.00 38.30 1.85
1920 2233 2.355197 TCATGTATCCAAACCAGTGCG 58.645 47.619 0.00 0.00 0.00 5.34
1959 2272 5.702349 AGCAAGATAATGAAATAGCAGGC 57.298 39.130 0.00 0.00 0.00 4.85
1960 2273 5.135383 AGCAAGATAATGAAATAGCAGGCA 58.865 37.500 0.00 0.00 0.00 4.75
1961 2274 5.241064 AGCAAGATAATGAAATAGCAGGCAG 59.759 40.000 0.00 0.00 0.00 4.85
1963 2276 6.436261 CAAGATAATGAAATAGCAGGCAGTG 58.564 40.000 0.00 0.00 0.00 3.66
1965 2278 3.370840 AATGAAATAGCAGGCAGTGGA 57.629 42.857 0.00 0.00 0.00 4.02
1966 2279 2.408271 TGAAATAGCAGGCAGTGGAG 57.592 50.000 0.00 0.00 0.00 3.86
1967 2280 1.065199 TGAAATAGCAGGCAGTGGAGG 60.065 52.381 0.00 0.00 0.00 4.30
1969 2282 1.289160 AATAGCAGGCAGTGGAGGAA 58.711 50.000 0.00 0.00 0.00 3.36
1970 2283 0.835941 ATAGCAGGCAGTGGAGGAAG 59.164 55.000 0.00 0.00 0.00 3.46
1972 2285 0.545309 AGCAGGCAGTGGAGGAAGTA 60.545 55.000 0.00 0.00 0.00 2.24
1975 2288 2.911484 CAGGCAGTGGAGGAAGTAATC 58.089 52.381 0.00 0.00 0.00 1.75
1976 2289 2.503356 CAGGCAGTGGAGGAAGTAATCT 59.497 50.000 0.00 0.00 0.00 2.40
1977 2290 2.503356 AGGCAGTGGAGGAAGTAATCTG 59.497 50.000 0.00 0.00 0.00 2.90
1978 2291 2.237392 GGCAGTGGAGGAAGTAATCTGT 59.763 50.000 0.00 0.00 0.00 3.41
1979 2292 3.307762 GGCAGTGGAGGAAGTAATCTGTT 60.308 47.826 0.00 0.00 0.00 3.16
1980 2293 3.935828 GCAGTGGAGGAAGTAATCTGTTC 59.064 47.826 0.00 0.00 0.00 3.18
1981 2294 4.563580 GCAGTGGAGGAAGTAATCTGTTCA 60.564 45.833 0.00 0.00 0.00 3.18
1982 2295 5.738909 CAGTGGAGGAAGTAATCTGTTCAT 58.261 41.667 0.00 0.00 0.00 2.57
1983 2296 6.630413 GCAGTGGAGGAAGTAATCTGTTCATA 60.630 42.308 0.00 0.00 0.00 2.15
1984 2297 7.504403 CAGTGGAGGAAGTAATCTGTTCATAT 58.496 38.462 0.00 0.00 0.00 1.78
1985 2298 8.642432 CAGTGGAGGAAGTAATCTGTTCATATA 58.358 37.037 0.00 0.00 0.00 0.86
1986 2299 9.386122 AGTGGAGGAAGTAATCTGTTCATATAT 57.614 33.333 0.00 0.00 0.00 0.86
1987 2300 9.646427 GTGGAGGAAGTAATCTGTTCATATATC 57.354 37.037 0.00 0.00 0.00 1.63
1988 2301 9.607333 TGGAGGAAGTAATCTGTTCATATATCT 57.393 33.333 0.00 0.00 0.00 1.98
2090 2535 1.339291 GAGCTATTGCAGGCATTTCCC 59.661 52.381 1.12 0.00 42.74 3.97
2120 2565 2.115348 TGACGACGAGTTCTGTGAAC 57.885 50.000 0.00 2.54 0.00 3.18
2177 2622 6.350445 GCCACATTGGTATTGTCAATCTTCTT 60.350 38.462 0.07 0.00 40.46 2.52
2333 2778 1.079543 CAGGAAGGGACAGACAGCG 60.080 63.158 0.00 0.00 0.00 5.18
2432 2877 2.844348 GGAGGATAACAAGGGGAACAGA 59.156 50.000 0.00 0.00 0.00 3.41
2476 2921 1.967779 GGGCAACACCATTGTAGGTTT 59.032 47.619 0.00 0.00 40.77 3.27
2553 2998 9.925268 CGTGTTAATAATTTGTTGTATACTCCC 57.075 33.333 4.17 0.00 0.00 4.30
2557 3002 9.550406 TTAATAATTTGTTGTATACTCCCTCCG 57.450 33.333 4.17 0.00 0.00 4.63
2558 3003 5.431179 AATTTGTTGTATACTCCCTCCGT 57.569 39.130 4.17 0.00 0.00 4.69
2559 3004 4.460948 TTTGTTGTATACTCCCTCCGTC 57.539 45.455 4.17 0.00 0.00 4.79
2560 3005 2.381911 TGTTGTATACTCCCTCCGTCC 58.618 52.381 4.17 0.00 0.00 4.79
2561 3006 1.336125 GTTGTATACTCCCTCCGTCCG 59.664 57.143 4.17 0.00 0.00 4.79
2562 3007 0.839277 TGTATACTCCCTCCGTCCGA 59.161 55.000 4.17 0.00 0.00 4.55
2563 3008 1.212688 TGTATACTCCCTCCGTCCGAA 59.787 52.381 4.17 0.00 0.00 4.30
2564 3009 2.301346 GTATACTCCCTCCGTCCGAAA 58.699 52.381 0.00 0.00 0.00 3.46
2565 3010 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2566 3011 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
2585 3030 5.473066 AAAAACTGTCCCTCAAATGGATG 57.527 39.130 0.00 0.00 33.65 3.51
2586 3031 3.814504 AACTGTCCCTCAAATGGATGT 57.185 42.857 0.00 0.00 33.65 3.06
2587 3032 4.927267 AACTGTCCCTCAAATGGATGTA 57.073 40.909 0.00 0.00 33.65 2.29
2588 3033 5.456921 AACTGTCCCTCAAATGGATGTAT 57.543 39.130 0.00 0.00 33.65 2.29
2589 3034 5.041191 ACTGTCCCTCAAATGGATGTATC 57.959 43.478 0.00 0.00 33.65 2.24
2590 3035 4.723789 ACTGTCCCTCAAATGGATGTATCT 59.276 41.667 0.00 0.00 33.65 1.98
2591 3036 5.905331 ACTGTCCCTCAAATGGATGTATCTA 59.095 40.000 0.00 0.00 33.65 1.98
2592 3037 6.174720 TGTCCCTCAAATGGATGTATCTAC 57.825 41.667 0.00 0.00 33.65 2.59
2593 3038 5.071788 TGTCCCTCAAATGGATGTATCTACC 59.928 44.000 0.00 0.00 33.65 3.18
2594 3039 5.071788 GTCCCTCAAATGGATGTATCTACCA 59.928 44.000 0.00 0.00 38.09 3.25
2595 3040 5.071788 TCCCTCAAATGGATGTATCTACCAC 59.928 44.000 0.00 0.00 36.49 4.16
2596 3041 5.163205 CCCTCAAATGGATGTATCTACCACA 60.163 44.000 0.00 0.00 36.49 4.17
2597 3042 6.356556 CCTCAAATGGATGTATCTACCACAA 58.643 40.000 0.00 0.00 36.49 3.33
2598 3043 6.828273 CCTCAAATGGATGTATCTACCACAAA 59.172 38.462 0.00 0.00 36.49 2.83
2599 3044 7.012704 CCTCAAATGGATGTATCTACCACAAAG 59.987 40.741 0.00 0.00 36.49 2.77
2600 3045 7.402054 TCAAATGGATGTATCTACCACAAAGT 58.598 34.615 0.00 0.00 36.49 2.66
2601 3046 7.888021 TCAAATGGATGTATCTACCACAAAGTT 59.112 33.333 0.00 0.00 36.49 2.66
2602 3047 9.173021 CAAATGGATGTATCTACCACAAAGTTA 57.827 33.333 0.00 0.00 36.49 2.24
2603 3048 8.964476 AATGGATGTATCTACCACAAAGTTAG 57.036 34.615 0.00 0.00 36.49 2.34
2604 3049 7.490657 TGGATGTATCTACCACAAAGTTAGT 57.509 36.000 0.00 0.00 0.00 2.24
2605 3050 7.327975 TGGATGTATCTACCACAAAGTTAGTG 58.672 38.462 0.00 0.00 36.76 2.74
2606 3051 6.258068 GGATGTATCTACCACAAAGTTAGTGC 59.742 42.308 0.00 0.00 35.69 4.40
2607 3052 6.354794 TGTATCTACCACAAAGTTAGTGCT 57.645 37.500 0.00 0.00 35.69 4.40
2608 3053 7.470935 TGTATCTACCACAAAGTTAGTGCTA 57.529 36.000 0.00 0.00 35.69 3.49
2609 3054 7.544622 TGTATCTACCACAAAGTTAGTGCTAG 58.455 38.462 0.00 0.00 35.69 3.42
2610 3055 6.852420 ATCTACCACAAAGTTAGTGCTAGA 57.148 37.500 0.00 0.00 38.09 2.43
2611 3056 6.659745 TCTACCACAAAGTTAGTGCTAGAA 57.340 37.500 0.00 0.00 33.51 2.10
2612 3057 6.453092 TCTACCACAAAGTTAGTGCTAGAAC 58.547 40.000 0.00 0.00 33.51 3.01
2613 3058 5.031066 ACCACAAAGTTAGTGCTAGAACA 57.969 39.130 3.00 0.00 35.69 3.18
2614 3059 5.621193 ACCACAAAGTTAGTGCTAGAACAT 58.379 37.500 3.00 0.00 35.69 2.71
2615 3060 5.701290 ACCACAAAGTTAGTGCTAGAACATC 59.299 40.000 3.00 0.00 35.69 3.06
2616 3061 5.122396 CCACAAAGTTAGTGCTAGAACATCC 59.878 44.000 3.00 0.00 35.69 3.51
2617 3062 5.700832 CACAAAGTTAGTGCTAGAACATCCA 59.299 40.000 3.00 0.00 0.00 3.41
2618 3063 6.372659 CACAAAGTTAGTGCTAGAACATCCAT 59.627 38.462 3.00 0.00 0.00 3.41
2619 3064 6.942576 ACAAAGTTAGTGCTAGAACATCCATT 59.057 34.615 3.00 0.00 0.00 3.16
2620 3065 7.448469 ACAAAGTTAGTGCTAGAACATCCATTT 59.552 33.333 3.00 0.00 0.00 2.32
2621 3066 6.992063 AGTTAGTGCTAGAACATCCATTTG 57.008 37.500 3.00 0.00 0.00 2.32
2622 3067 6.711277 AGTTAGTGCTAGAACATCCATTTGA 58.289 36.000 3.00 0.00 0.00 2.69
2623 3068 6.820656 AGTTAGTGCTAGAACATCCATTTGAG 59.179 38.462 3.00 0.00 0.00 3.02
2624 3069 5.426689 AGTGCTAGAACATCCATTTGAGA 57.573 39.130 3.00 0.00 0.00 3.27
2625 3070 5.809001 AGTGCTAGAACATCCATTTGAGAA 58.191 37.500 3.00 0.00 0.00 2.87
2626 3071 6.240894 AGTGCTAGAACATCCATTTGAGAAA 58.759 36.000 3.00 0.00 0.00 2.52
2627 3072 6.150140 AGTGCTAGAACATCCATTTGAGAAAC 59.850 38.462 3.00 0.00 0.00 2.78
2628 3073 6.003326 TGCTAGAACATCCATTTGAGAAACA 58.997 36.000 0.00 0.00 0.00 2.83
2629 3074 6.489700 TGCTAGAACATCCATTTGAGAAACAA 59.510 34.615 0.00 0.00 36.65 2.83
2630 3075 7.025963 GCTAGAACATCCATTTGAGAAACAAG 58.974 38.462 0.00 0.00 39.77 3.16
2631 3076 5.776744 AGAACATCCATTTGAGAAACAAGC 58.223 37.500 0.00 0.00 39.77 4.01
2632 3077 5.537674 AGAACATCCATTTGAGAAACAAGCT 59.462 36.000 0.00 0.00 39.77 3.74
2633 3078 5.796424 ACATCCATTTGAGAAACAAGCTT 57.204 34.783 0.00 0.00 39.77 3.74
2634 3079 5.535333 ACATCCATTTGAGAAACAAGCTTG 58.465 37.500 24.84 24.84 39.77 4.01
2635 3080 4.589216 TCCATTTGAGAAACAAGCTTGG 57.411 40.909 29.18 12.28 39.77 3.61
2636 3081 3.321682 TCCATTTGAGAAACAAGCTTGGG 59.678 43.478 29.18 16.37 39.77 4.12
2637 3082 3.321682 CCATTTGAGAAACAAGCTTGGGA 59.678 43.478 29.18 7.03 39.77 4.37
2638 3083 4.301628 CATTTGAGAAACAAGCTTGGGAC 58.698 43.478 29.18 18.46 39.77 4.46
2639 3084 2.727123 TGAGAAACAAGCTTGGGACA 57.273 45.000 29.18 17.71 0.00 4.02
2640 3085 3.360867 TTGAGAAACAAGCTTGGGACAA 58.639 40.909 29.18 21.59 37.48 3.18
2641 3086 3.381272 TTGAGAAACAAGCTTGGGACAAG 59.619 43.478 29.18 3.71 37.48 3.16
2642 3087 6.232513 TTGAGAAACAAGCTTGGGACAAGC 62.233 45.833 29.18 22.54 43.31 4.01
2651 3096 3.811031 TGGGACAAGCTTTTTCGGA 57.189 47.368 0.00 0.00 31.92 4.55
2652 3097 1.314730 TGGGACAAGCTTTTTCGGAC 58.685 50.000 0.00 0.00 31.92 4.79
2653 3098 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
2654 3099 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
2655 3100 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
2656 3101 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
2657 3102 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
2658 3103 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
2659 3104 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
2660 3105 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
2661 3106 0.320697 CTTTTTCGGACGGAGGGAGT 59.679 55.000 0.00 0.00 0.00 3.85
2662 3107 1.547372 CTTTTTCGGACGGAGGGAGTA 59.453 52.381 0.00 0.00 0.00 2.59
2663 3108 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
2664 3109 1.856629 TTTCGGACGGAGGGAGTATT 58.143 50.000 0.00 0.00 0.00 1.89
2665 3110 2.734755 TTCGGACGGAGGGAGTATTA 57.265 50.000 0.00 0.00 0.00 0.98
2666 3111 2.965671 TCGGACGGAGGGAGTATTAT 57.034 50.000 0.00 0.00 0.00 1.28
2680 3125 7.872138 AGGGAGTATTATTTTCTTGTCCATCA 58.128 34.615 0.00 0.00 0.00 3.07
2697 3144 6.257849 TGTCCATCATAAGTTCATTTACGAGC 59.742 38.462 0.00 0.00 0.00 5.03
2704 3151 8.255206 TCATAAGTTCATTTACGAGCTTCCTTA 58.745 33.333 0.00 0.00 37.57 2.69
2715 3162 4.040095 ACGAGCTTCCTTACTTAAACCAGT 59.960 41.667 0.00 0.00 0.00 4.00
2735 3182 5.549347 CAGTAATGCTGGATGCTCTAGAAT 58.451 41.667 0.00 0.00 41.42 2.40
2737 3184 6.812656 CAGTAATGCTGGATGCTCTAGAATAG 59.187 42.308 0.00 0.00 41.42 1.73
2791 3625 8.410141 TGTACAAAAATAGTGGAAAGGTTTCTG 58.590 33.333 0.00 0.00 37.35 3.02
2803 3637 7.660208 GTGGAAAGGTTTCTGTTCATAGACTTA 59.340 37.037 2.60 0.00 37.35 2.24
2834 3668 7.566760 TCATGAAGTTCTAAGCAGTTTCAAA 57.433 32.000 4.17 0.00 0.00 2.69
2851 3685 7.435192 CAGTTTCAAACAGAATTTTAGTGGACC 59.565 37.037 2.41 0.00 35.83 4.46
2862 3696 8.376270 AGAATTTTAGTGGACCTAGGTATATGC 58.624 37.037 16.29 1.03 0.00 3.14
2907 3744 5.098211 GCTTCATAACTTGCATCCTTTGAC 58.902 41.667 0.00 0.00 0.00 3.18
3119 3956 3.303406 CAAGCAGCTTAAGCAAACAGTC 58.697 45.455 28.39 9.29 45.16 3.51
3410 4247 9.561270 GCTTTTATAATCTTCTTGGTCTTTGAC 57.439 33.333 0.00 0.00 0.00 3.18
3414 4251 5.574970 AATCTTCTTGGTCTTTGACTCCT 57.425 39.130 0.00 0.00 32.47 3.69
3428 4265 5.505181 TTGACTCCTTGGCTCTCTTTATT 57.495 39.130 0.00 0.00 0.00 1.40
3434 4271 3.311048 CCTTGGCTCTCTTTATTTCGCTC 59.689 47.826 0.00 0.00 0.00 5.03
3437 4274 1.259244 GCTCTCTTTATTTCGCTCGCC 59.741 52.381 0.00 0.00 0.00 5.54
3440 4277 0.996462 TCTTTATTTCGCTCGCCGTG 59.004 50.000 0.00 0.00 38.35 4.94
3557 4394 3.671716 CATATCAGCAGCCTTCATAGCA 58.328 45.455 0.00 0.00 0.00 3.49
3613 4450 2.672996 GGCTTGGTGCACGATGGT 60.673 61.111 11.45 0.00 45.15 3.55
3728 4565 1.142748 GTCCTCCATGAGCCAGTCG 59.857 63.158 0.00 0.00 0.00 4.18
3797 4634 1.280982 ACAAGACGATGTATGCGCTG 58.719 50.000 9.73 0.00 0.00 5.18
3805 4642 0.032130 ATGTATGCGCTGTAGGACGG 59.968 55.000 9.73 0.00 0.00 4.79
3808 4645 1.033202 TATGCGCTGTAGGACGGTGA 61.033 55.000 9.73 0.00 37.15 4.02
3827 4664 4.408378 TCGATGACCGACACCTCA 57.592 55.556 0.00 0.00 43.23 3.86
3831 4668 0.108186 GATGACCGACACCTCATGCA 60.108 55.000 0.00 0.00 0.00 3.96
3832 4669 0.324614 ATGACCGACACCTCATGCAA 59.675 50.000 0.00 0.00 0.00 4.08
3858 4695 4.610333 AGTCATGTATATATCGGAGCCCA 58.390 43.478 0.00 0.00 0.00 5.36
3872 4709 4.757355 CCCATTTGCCCGAGCCCA 62.757 66.667 0.00 0.00 38.69 5.36
3873 4710 2.679642 CCATTTGCCCGAGCCCAA 60.680 61.111 0.00 0.00 38.69 4.12
3874 4711 2.059786 CCATTTGCCCGAGCCCAAT 61.060 57.895 0.00 0.00 38.69 3.16
3875 4712 1.616091 CCATTTGCCCGAGCCCAATT 61.616 55.000 0.00 0.00 38.69 2.32
3876 4713 0.179103 CATTTGCCCGAGCCCAATTC 60.179 55.000 0.00 0.00 38.69 2.17
3887 4724 1.322538 GCCCAATTCCACGGCATTCT 61.323 55.000 0.00 0.00 42.52 2.40
3906 4743 1.531578 CTGCGGATTCGACTCGAGATA 59.468 52.381 21.68 0.19 37.14 1.98
4021 4858 1.771255 GGATGCAGTTCCTGGGTAGAT 59.229 52.381 0.00 0.00 32.68 1.98
4123 4963 5.661312 TCTTATGCTTACTACCACTGTGGAT 59.339 40.000 32.30 18.39 40.96 3.41
4146 4986 7.201741 GGATGATGATGATGATGACAATCCATC 60.202 40.741 0.00 0.00 42.38 3.51
4157 4997 9.763837 ATGATGACAATCCATCCAATTATGTAT 57.236 29.630 0.00 0.00 41.60 2.29
4160 5000 8.862325 TGACAATCCATCCAATTATGTATACC 57.138 34.615 0.00 0.00 0.00 2.73
4161 5001 8.443979 TGACAATCCATCCAATTATGTATACCA 58.556 33.333 0.00 0.00 0.00 3.25
4162 5002 9.295825 GACAATCCATCCAATTATGTATACCAA 57.704 33.333 0.00 0.00 0.00 3.67
4163 5003 9.300681 ACAATCCATCCAATTATGTATACCAAG 57.699 33.333 0.00 0.00 0.00 3.61
4164 5004 9.300681 CAATCCATCCAATTATGTATACCAAGT 57.699 33.333 0.00 0.00 0.00 3.16
4195 5036 8.904099 ACCAGTATAGTAGAATAAATTGCCAC 57.096 34.615 0.00 0.00 0.00 5.01
4212 5053 3.957497 TGCCACTTTGTCAAACCTATGTT 59.043 39.130 0.00 0.00 35.82 2.71
4247 5088 5.190677 TCATCTTGATCTTGTGCATCATGT 58.809 37.500 0.00 0.00 30.26 3.21
4260 5101 4.157289 GTGCATCATGTGTCAAAAGGAGAT 59.843 41.667 0.00 0.00 0.00 2.75
4293 5134 5.630121 TCATATGGTTATGGTCATTGGGAC 58.370 41.667 2.13 0.00 46.20 4.46
4296 5137 2.024414 GGTTATGGTCATTGGGACTGC 58.976 52.381 0.00 0.00 46.16 4.40
4297 5138 2.357154 GGTTATGGTCATTGGGACTGCT 60.357 50.000 0.00 0.00 46.16 4.24
4298 5139 2.684881 GTTATGGTCATTGGGACTGCTG 59.315 50.000 0.00 0.00 46.16 4.41
4299 5140 0.994247 ATGGTCATTGGGACTGCTGA 59.006 50.000 0.00 0.00 46.16 4.26
4300 5141 0.770499 TGGTCATTGGGACTGCTGAA 59.230 50.000 0.00 0.00 46.16 3.02
4301 5142 1.168714 GGTCATTGGGACTGCTGAAC 58.831 55.000 0.00 0.00 46.16 3.18
4302 5143 1.545428 GGTCATTGGGACTGCTGAACA 60.545 52.381 0.00 0.00 46.16 3.18
4303 5144 2.229792 GTCATTGGGACTGCTGAACAA 58.770 47.619 0.00 0.04 43.46 2.83
4305 5146 5.455754 GTCATTGGGACTGCTGAACAAGC 62.456 52.174 0.00 0.00 44.02 4.01
4360 5209 4.590647 TCATCACTTCTCTGGACTTTGACT 59.409 41.667 0.00 0.00 0.00 3.41
4399 5248 4.016113 AGAACAAGTTTTGCGACTGTTC 57.984 40.909 5.34 5.34 37.62 3.18
4447 5302 1.135859 GTGATTGAGCAGCTTTCACCG 60.136 52.381 17.27 0.00 32.47 4.94
4459 5314 2.030805 GCTTTCACCGTCAAATTCTGCT 60.031 45.455 0.00 0.00 0.00 4.24
4466 5321 6.378582 TCACCGTCAAATTCTGCTTTTTATC 58.621 36.000 0.00 0.00 0.00 1.75
4498 5353 0.603975 AGCCGTCAAAACTCTCAGGC 60.604 55.000 0.00 0.00 43.07 4.85
4500 5355 1.813513 CCGTCAAAACTCTCAGGCAT 58.186 50.000 0.00 0.00 0.00 4.40
4543 5611 7.332678 CCAGAATTCCAAGACAAAATTTCATCC 59.667 37.037 0.65 0.00 0.00 3.51
4563 5631 1.144936 GAAGCCAGGGTCTCCATCG 59.855 63.158 0.00 0.00 34.83 3.84
4577 5645 1.215423 TCCATCGACCTCTGAGATCCA 59.785 52.381 6.17 0.00 0.00 3.41
4578 5646 2.158400 TCCATCGACCTCTGAGATCCAT 60.158 50.000 6.17 0.00 0.00 3.41
4706 5774 1.608046 TGGAATTTTGCCCCGGTCC 60.608 57.895 0.00 0.00 0.00 4.46
4711 5779 4.589675 TTTGCCCCGGTCCACACC 62.590 66.667 0.00 0.00 39.69 4.16
4716 5784 2.366435 CCCGGTCCACACCCCTAT 60.366 66.667 0.00 0.00 40.01 2.57
4721 5789 0.255033 GGTCCACACCCCTATTGTCC 59.745 60.000 0.00 0.00 36.54 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.423061 ACAAGATGTTGTTATTTCTTAATTGCC 57.577 29.630 1.68 0.00 45.00 4.52
124 126 9.829507 TCTAATGGGCCATTTATGTTTAATTTG 57.170 29.630 34.78 9.79 35.54 2.32
128 130 9.041354 ACTTTCTAATGGGCCATTTATGTTTAA 57.959 29.630 34.78 14.74 35.54 1.52
145 147 6.439058 AGCTACTGTCTCTTGGACTTTCTAAT 59.561 38.462 0.00 0.00 44.74 1.73
241 243 8.970859 AAATGATTTTACTCTGGACTAGATGG 57.029 34.615 0.00 0.00 34.21 3.51
298 300 3.758554 AGGGAATATTTGTGTCACTGTGC 59.241 43.478 2.12 0.00 0.00 4.57
520 531 1.493311 CACCAGACTTTTCTCGCGC 59.507 57.895 0.00 0.00 0.00 6.86
562 574 0.957888 GGAGCAAAGGACTCACTGGC 60.958 60.000 0.00 0.00 35.79 4.85
626 638 1.136891 GCTTGAAAAATCCCATCCCCG 59.863 52.381 0.00 0.00 0.00 5.73
643 655 3.056328 GCGGCCCGAAGAAAGCTT 61.056 61.111 7.68 0.00 36.96 3.74
657 669 2.436646 AATCAACGGAGCAGGCGG 60.437 61.111 0.00 0.00 0.00 6.13
661 673 1.396301 GCTGAAGAATCAACGGAGCAG 59.604 52.381 0.00 0.00 34.49 4.24
812 824 3.049912 GTCAAGAAAATCAACAACGCCC 58.950 45.455 0.00 0.00 0.00 6.13
815 827 4.275936 AGGGAGTCAAGAAAATCAACAACG 59.724 41.667 0.00 0.00 0.00 4.10
820 832 4.074970 GCAGAGGGAGTCAAGAAAATCAA 58.925 43.478 0.00 0.00 0.00 2.57
895 907 9.132521 CACTTGAATTGGTGAAAAATATCAGAC 57.867 33.333 0.00 0.00 35.69 3.51
896 908 8.859090 ACACTTGAATTGGTGAAAAATATCAGA 58.141 29.630 9.00 0.00 37.22 3.27
905 917 4.582656 CCAGGTACACTTGAATTGGTGAAA 59.417 41.667 9.00 0.00 37.22 2.69
906 918 4.141287 CCAGGTACACTTGAATTGGTGAA 58.859 43.478 9.00 0.00 37.22 3.18
910 922 4.256920 CTCTCCAGGTACACTTGAATTGG 58.743 47.826 0.00 0.00 0.00 3.16
973 994 5.392380 CCAAATCCAGTGACAGAAAGTATGC 60.392 44.000 0.00 0.00 0.00 3.14
974 995 5.124457 CCCAAATCCAGTGACAGAAAGTATG 59.876 44.000 0.00 0.00 0.00 2.39
975 996 5.256474 CCCAAATCCAGTGACAGAAAGTAT 58.744 41.667 0.00 0.00 0.00 2.12
976 997 4.506625 CCCCAAATCCAGTGACAGAAAGTA 60.507 45.833 0.00 0.00 0.00 2.24
977 998 3.490348 CCCAAATCCAGTGACAGAAAGT 58.510 45.455 0.00 0.00 0.00 2.66
978 999 2.821969 CCCCAAATCCAGTGACAGAAAG 59.178 50.000 0.00 0.00 0.00 2.62
979 1000 2.445145 TCCCCAAATCCAGTGACAGAAA 59.555 45.455 0.00 0.00 0.00 2.52
980 1001 2.061848 TCCCCAAATCCAGTGACAGAA 58.938 47.619 0.00 0.00 0.00 3.02
981 1002 1.741028 TCCCCAAATCCAGTGACAGA 58.259 50.000 0.00 0.00 0.00 3.41
985 1284 1.565759 CTCCATCCCCAAATCCAGTGA 59.434 52.381 0.00 0.00 0.00 3.41
1032 1331 0.903942 AGCTCTTGAGCTTCTCCAGG 59.096 55.000 18.29 0.00 43.52 4.45
1197 1496 1.667154 CGGCGAAGATCCTCTGGACA 61.667 60.000 0.00 0.00 32.98 4.02
1281 1580 4.424566 TTCTCGGCGGCCACGTAC 62.425 66.667 20.71 0.00 43.45 3.67
1371 1670 3.367395 CGATATGGAAGGCATCGAAGCTA 60.367 47.826 12.92 0.00 43.20 3.32
1398 1697 0.542702 AACCCAGATGGCCCTGTTTG 60.543 55.000 0.00 0.00 37.83 2.93
1447 1746 3.439857 AACAATACACCACCATCAGCT 57.560 42.857 0.00 0.00 0.00 4.24
1494 1801 7.883833 CCATAATCATCAGATCCTTGACTTGAT 59.116 37.037 0.00 0.00 31.46 2.57
1504 1811 7.572523 TCAAACAACCATAATCATCAGATCC 57.427 36.000 0.00 0.00 31.90 3.36
1508 1815 7.161773 AGGTTCAAACAACCATAATCATCAG 57.838 36.000 6.30 0.00 42.69 2.90
1589 1897 7.921786 AATGTGCAACTATAGACAAGCTAAA 57.078 32.000 6.78 0.00 38.04 1.85
1599 1907 7.840342 AAGACAGAGAAATGTGCAACTATAG 57.160 36.000 0.00 0.00 38.04 1.31
1663 1971 5.216566 TGCAATCACAACGAATTACTAGC 57.783 39.130 0.00 0.00 0.00 3.42
1817 2125 2.224113 CCTGTCAAACCAAGCAAAGCAT 60.224 45.455 0.00 0.00 0.00 3.79
1865 2178 6.037062 GCAACAGCAACACATCATACATACTA 59.963 38.462 0.00 0.00 0.00 1.82
1866 2179 5.163723 GCAACAGCAACACATCATACATACT 60.164 40.000 0.00 0.00 0.00 2.12
1867 2180 5.030295 GCAACAGCAACACATCATACATAC 58.970 41.667 0.00 0.00 0.00 2.39
1953 2266 0.545309 TACTTCCTCCACTGCCTGCT 60.545 55.000 0.00 0.00 0.00 4.24
1954 2267 0.324943 TTACTTCCTCCACTGCCTGC 59.675 55.000 0.00 0.00 0.00 4.85
1955 2268 2.503356 AGATTACTTCCTCCACTGCCTG 59.497 50.000 0.00 0.00 0.00 4.85
1956 2269 2.503356 CAGATTACTTCCTCCACTGCCT 59.497 50.000 0.00 0.00 0.00 4.75
1957 2270 2.237392 ACAGATTACTTCCTCCACTGCC 59.763 50.000 0.00 0.00 0.00 4.85
1958 2271 3.618690 ACAGATTACTTCCTCCACTGC 57.381 47.619 0.00 0.00 0.00 4.40
1959 2272 5.152623 TGAACAGATTACTTCCTCCACTG 57.847 43.478 0.00 0.00 0.00 3.66
1960 2273 7.682787 ATATGAACAGATTACTTCCTCCACT 57.317 36.000 0.00 0.00 0.00 4.00
1961 2274 9.646427 GATATATGAACAGATTACTTCCTCCAC 57.354 37.037 0.00 0.00 0.00 4.02
2090 2535 0.315625 TCGTCGTCATAGCTAACGCG 60.316 55.000 19.44 19.44 42.32 6.01
2120 2565 1.626654 CGGTGTCTAAAGCTGTGGCG 61.627 60.000 0.00 0.00 44.37 5.69
2177 2622 0.175760 GGCTTGCGTCTGTATCCAGA 59.824 55.000 0.00 0.00 45.44 3.86
2333 2778 0.389426 CTTTGGAAGCCATGTGCAGC 60.389 55.000 8.58 0.00 44.83 5.25
2390 2835 6.312141 TCCAAATGGATTACTGAGACATCA 57.688 37.500 0.00 0.00 39.78 3.07
2546 2991 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
2548 2993 2.444281 TTTTTCGGACGGAGGGAGT 58.556 52.632 0.00 0.00 0.00 3.85
2563 3008 4.901250 ACATCCATTTGAGGGACAGTTTTT 59.099 37.500 0.00 0.00 37.23 1.94
2564 3009 4.482990 ACATCCATTTGAGGGACAGTTTT 58.517 39.130 0.00 0.00 37.23 2.43
2565 3010 4.118168 ACATCCATTTGAGGGACAGTTT 57.882 40.909 0.00 0.00 37.23 2.66
2566 3011 3.814504 ACATCCATTTGAGGGACAGTT 57.185 42.857 0.00 0.00 37.23 3.16
2567 3012 4.723789 AGATACATCCATTTGAGGGACAGT 59.276 41.667 0.00 0.00 37.23 3.55
2568 3013 5.301835 AGATACATCCATTTGAGGGACAG 57.698 43.478 0.00 0.00 37.23 3.51
2569 3014 5.071788 GGTAGATACATCCATTTGAGGGACA 59.928 44.000 0.00 0.00 37.23 4.02
2570 3015 5.071788 TGGTAGATACATCCATTTGAGGGAC 59.928 44.000 0.00 0.00 37.23 4.46
2571 3016 5.071788 GTGGTAGATACATCCATTTGAGGGA 59.928 44.000 0.00 0.00 39.14 4.20
2572 3017 5.163205 TGTGGTAGATACATCCATTTGAGGG 60.163 44.000 0.00 0.00 33.68 4.30
2573 3018 5.928976 TGTGGTAGATACATCCATTTGAGG 58.071 41.667 0.00 0.00 33.68 3.86
2574 3019 7.554118 ACTTTGTGGTAGATACATCCATTTGAG 59.446 37.037 0.00 0.00 33.68 3.02
2575 3020 7.402054 ACTTTGTGGTAGATACATCCATTTGA 58.598 34.615 0.00 0.00 33.68 2.69
2576 3021 7.630242 ACTTTGTGGTAGATACATCCATTTG 57.370 36.000 0.00 0.00 33.68 2.32
2577 3022 9.396022 CTAACTTTGTGGTAGATACATCCATTT 57.604 33.333 0.00 0.00 38.19 2.32
2578 3023 8.548877 ACTAACTTTGTGGTAGATACATCCATT 58.451 33.333 0.00 0.00 38.19 3.16
2579 3024 7.987458 CACTAACTTTGTGGTAGATACATCCAT 59.013 37.037 0.00 0.00 38.19 3.41
2580 3025 7.327975 CACTAACTTTGTGGTAGATACATCCA 58.672 38.462 0.00 0.00 38.19 3.41
2581 3026 6.258068 GCACTAACTTTGTGGTAGATACATCC 59.742 42.308 5.65 0.00 38.19 3.51
2582 3027 7.042335 AGCACTAACTTTGTGGTAGATACATC 58.958 38.462 6.31 0.00 43.17 3.06
2583 3028 6.947464 AGCACTAACTTTGTGGTAGATACAT 58.053 36.000 6.31 0.00 43.17 2.29
2584 3029 6.354794 AGCACTAACTTTGTGGTAGATACA 57.645 37.500 6.31 0.00 43.17 2.29
2590 3035 6.164417 TGTTCTAGCACTAACTTTGTGGTA 57.836 37.500 12.61 12.61 43.17 3.25
2591 3036 5.031066 TGTTCTAGCACTAACTTTGTGGT 57.969 39.130 11.80 11.80 46.10 4.16
2592 3037 5.122396 GGATGTTCTAGCACTAACTTTGTGG 59.878 44.000 5.65 0.00 36.08 4.17
2593 3038 5.700832 TGGATGTTCTAGCACTAACTTTGTG 59.299 40.000 0.00 0.00 38.36 3.33
2594 3039 5.865085 TGGATGTTCTAGCACTAACTTTGT 58.135 37.500 0.00 0.00 0.00 2.83
2595 3040 6.992063 ATGGATGTTCTAGCACTAACTTTG 57.008 37.500 0.00 0.00 0.00 2.77
2596 3041 7.665559 TCAAATGGATGTTCTAGCACTAACTTT 59.334 33.333 0.00 0.00 0.00 2.66
2597 3042 7.168219 TCAAATGGATGTTCTAGCACTAACTT 58.832 34.615 0.00 0.00 0.00 2.66
2598 3043 6.711277 TCAAATGGATGTTCTAGCACTAACT 58.289 36.000 0.00 0.00 0.00 2.24
2599 3044 6.818644 TCTCAAATGGATGTTCTAGCACTAAC 59.181 38.462 0.00 0.00 0.00 2.34
2600 3045 6.946340 TCTCAAATGGATGTTCTAGCACTAA 58.054 36.000 0.00 0.00 0.00 2.24
2601 3046 6.544928 TCTCAAATGGATGTTCTAGCACTA 57.455 37.500 0.00 0.00 0.00 2.74
2602 3047 5.426689 TCTCAAATGGATGTTCTAGCACT 57.573 39.130 0.00 0.00 0.00 4.40
2603 3048 6.072508 TGTTTCTCAAATGGATGTTCTAGCAC 60.073 38.462 0.00 0.00 0.00 4.40
2604 3049 6.003326 TGTTTCTCAAATGGATGTTCTAGCA 58.997 36.000 0.00 0.00 0.00 3.49
2605 3050 6.500684 TGTTTCTCAAATGGATGTTCTAGC 57.499 37.500 0.00 0.00 0.00 3.42
2606 3051 7.025963 GCTTGTTTCTCAAATGGATGTTCTAG 58.974 38.462 0.00 0.00 35.48 2.43
2607 3052 6.716628 AGCTTGTTTCTCAAATGGATGTTCTA 59.283 34.615 0.00 0.00 35.48 2.10
2608 3053 5.537674 AGCTTGTTTCTCAAATGGATGTTCT 59.462 36.000 0.00 0.00 35.48 3.01
2609 3054 5.776744 AGCTTGTTTCTCAAATGGATGTTC 58.223 37.500 0.00 0.00 35.48 3.18
2610 3055 5.796424 AGCTTGTTTCTCAAATGGATGTT 57.204 34.783 0.00 0.00 35.48 2.71
2611 3056 5.510179 CCAAGCTTGTTTCTCAAATGGATGT 60.510 40.000 24.35 0.00 36.92 3.06
2612 3057 4.927425 CCAAGCTTGTTTCTCAAATGGATG 59.073 41.667 24.35 0.00 36.92 3.51
2613 3058 4.020839 CCCAAGCTTGTTTCTCAAATGGAT 60.021 41.667 24.35 0.00 36.92 3.41
2614 3059 3.321682 CCCAAGCTTGTTTCTCAAATGGA 59.678 43.478 24.35 0.00 36.92 3.41
2615 3060 3.321682 TCCCAAGCTTGTTTCTCAAATGG 59.678 43.478 24.35 14.01 35.48 3.16
2616 3061 4.202141 TGTCCCAAGCTTGTTTCTCAAATG 60.202 41.667 24.35 5.47 35.48 2.32
2617 3062 3.960102 TGTCCCAAGCTTGTTTCTCAAAT 59.040 39.130 24.35 0.00 35.48 2.32
2618 3063 3.360867 TGTCCCAAGCTTGTTTCTCAAA 58.639 40.909 24.35 0.00 35.48 2.69
2619 3064 3.011566 TGTCCCAAGCTTGTTTCTCAA 57.988 42.857 24.35 1.41 34.61 3.02
2620 3065 2.727123 TGTCCCAAGCTTGTTTCTCA 57.273 45.000 24.35 12.85 0.00 3.27
2621 3066 2.287849 GCTTGTCCCAAGCTTGTTTCTC 60.288 50.000 24.35 10.65 40.01 2.87
2622 3067 1.683385 GCTTGTCCCAAGCTTGTTTCT 59.317 47.619 24.35 0.00 40.01 2.52
2623 3068 2.140065 GCTTGTCCCAAGCTTGTTTC 57.860 50.000 24.35 13.85 40.01 2.78
2630 3075 1.602920 CCGAAAAAGCTTGTCCCAAGC 60.603 52.381 18.69 18.69 43.31 4.01
2631 3076 1.953686 TCCGAAAAAGCTTGTCCCAAG 59.046 47.619 0.00 0.00 0.00 3.61
2632 3077 1.679153 GTCCGAAAAAGCTTGTCCCAA 59.321 47.619 0.00 0.00 0.00 4.12
2633 3078 1.314730 GTCCGAAAAAGCTTGTCCCA 58.685 50.000 0.00 0.00 0.00 4.37
2634 3079 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
2635 3080 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
2636 3081 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
2637 3082 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
2638 3083 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
2639 3084 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
2640 3085 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
2641 3086 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
2642 3087 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
2643 3088 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
2644 3089 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2645 3090 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
2646 3091 2.734755 TAATACTCCCTCCGTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
2647 3092 2.965671 ATAATACTCCCTCCGTCCGA 57.034 50.000 0.00 0.00 0.00 4.55
2648 3093 4.038883 AGAAAATAATACTCCCTCCGTCCG 59.961 45.833 0.00 0.00 0.00 4.79
2649 3094 5.548181 AGAAAATAATACTCCCTCCGTCC 57.452 43.478 0.00 0.00 0.00 4.79
2650 3095 6.346896 ACAAGAAAATAATACTCCCTCCGTC 58.653 40.000 0.00 0.00 0.00 4.79
2651 3096 6.309389 ACAAGAAAATAATACTCCCTCCGT 57.691 37.500 0.00 0.00 0.00 4.69
2652 3097 5.758784 GGACAAGAAAATAATACTCCCTCCG 59.241 44.000 0.00 0.00 0.00 4.63
2653 3098 6.659824 TGGACAAGAAAATAATACTCCCTCC 58.340 40.000 0.00 0.00 0.00 4.30
2654 3099 7.993183 TGATGGACAAGAAAATAATACTCCCTC 59.007 37.037 0.00 0.00 0.00 4.30
2655 3100 7.872138 TGATGGACAAGAAAATAATACTCCCT 58.128 34.615 0.00 0.00 0.00 4.20
2656 3101 8.697507 ATGATGGACAAGAAAATAATACTCCC 57.302 34.615 0.00 0.00 0.00 4.30
2680 3125 8.258708 AGTAAGGAAGCTCGTAAATGAACTTAT 58.741 33.333 0.00 0.00 0.00 1.73
2683 3128 6.038997 AGTAAGGAAGCTCGTAAATGAACT 57.961 37.500 0.00 0.00 0.00 3.01
2692 3137 4.040095 ACTGGTTTAAGTAAGGAAGCTCGT 59.960 41.667 0.00 0.00 0.00 4.18
2697 3144 7.752695 CAGCATTACTGGTTTAAGTAAGGAAG 58.247 38.462 11.65 1.40 43.67 3.46
2735 3182 7.176515 TGGACTGCAAATTGCTTAAGAATTCTA 59.823 33.333 19.34 0.00 45.31 2.10
2737 3184 6.089954 GTGGACTGCAAATTGCTTAAGAATTC 59.910 38.462 19.34 0.00 45.31 2.17
2744 3572 4.039004 ACATTGTGGACTGCAAATTGCTTA 59.961 37.500 19.34 0.00 45.31 3.09
2757 3585 7.209471 TCCACTATTTTTGTACATTGTGGAC 57.791 36.000 19.85 0.00 44.97 4.02
2763 3591 9.758651 GAAACCTTTCCACTATTTTTGTACATT 57.241 29.630 0.00 0.00 0.00 2.71
2803 3637 8.401490 ACTGCTTAGAACTTCATGATTTTCTT 57.599 30.769 19.26 8.39 30.89 2.52
2810 3644 7.066887 TGTTTGAAACTGCTTAGAACTTCATGA 59.933 33.333 9.69 0.00 0.00 3.07
2834 3668 7.750947 ATACCTAGGTCCACTAAAATTCTGT 57.249 36.000 20.32 0.00 0.00 3.41
2851 3685 9.155975 CTTAAATGGCTAAGTGCATATACCTAG 57.844 37.037 0.00 0.00 45.15 3.02
2862 3696 8.538409 AAGCAAAATTCTTAAATGGCTAAGTG 57.462 30.769 0.00 0.00 31.32 3.16
2907 3744 8.055279 ACCATCTGTAAGGAATTACACAAATG 57.945 34.615 0.00 0.00 34.12 2.32
3119 3956 2.130395 ACGTCATGCTTGATATCGCTG 58.870 47.619 5.49 0.00 33.56 5.18
3410 4247 3.311048 GCGAAATAAAGAGAGCCAAGGAG 59.689 47.826 0.00 0.00 0.00 3.69
3414 4251 2.930040 CGAGCGAAATAAAGAGAGCCAA 59.070 45.455 0.00 0.00 0.00 4.52
3434 4271 4.953868 TGGACAACGACCACGGCG 62.954 66.667 4.80 4.80 44.46 6.46
3437 4274 1.663702 GGTCTGGACAACGACCACG 60.664 63.158 3.72 0.00 46.98 4.94
3440 4277 4.284747 CAGAGAGGTCTGGACAACGACC 62.285 59.091 3.10 0.00 45.85 4.79
3455 4292 4.313282 TCTGCTCAACAACAATCAGAGAG 58.687 43.478 0.00 0.00 0.00 3.20
3458 4295 3.817084 CCTTCTGCTCAACAACAATCAGA 59.183 43.478 0.00 0.00 0.00 3.27
3497 4334 5.688621 CCACATCAACTTGTTCATCACAAAG 59.311 40.000 0.00 0.00 45.11 2.77
3613 4450 1.864565 CATAATCACGGTGCCGATCA 58.135 50.000 18.16 0.68 42.83 2.92
3728 4565 2.287069 CGAGTCGACTGATATGGACCAC 60.287 54.545 25.58 2.38 0.00 4.16
3797 4634 1.063764 GTCATCGACTCACCGTCCTAC 59.936 57.143 0.00 0.00 39.56 3.18
3827 4664 7.038048 CCGATATATACATGACTCTGTTGCAT 58.962 38.462 0.00 0.00 0.00 3.96
3831 4668 6.127591 GGCTCCGATATATACATGACTCTGTT 60.128 42.308 0.00 0.00 0.00 3.16
3832 4669 5.358442 GGCTCCGATATATACATGACTCTGT 59.642 44.000 0.00 0.00 0.00 3.41
3858 4695 1.329913 GGAATTGGGCTCGGGCAAAT 61.330 55.000 10.74 5.48 40.87 2.32
3887 4724 1.589803 TATCTCGAGTCGAATCCGCA 58.410 50.000 17.27 0.00 34.74 5.69
3906 4743 3.777522 GCCATGTTCCTAGGCCTAGATAT 59.222 47.826 36.80 20.39 42.58 1.63
4009 4846 2.576191 CTGGAACCAATCTACCCAGGAA 59.424 50.000 0.00 0.00 40.39 3.36
4021 4858 2.436109 GGCTCTGCCTGGAACCAA 59.564 61.111 0.00 0.00 46.69 3.67
4062 4899 6.479006 TGCTTCACAAGTACTACTACTCCTA 58.521 40.000 0.00 0.00 31.42 2.94
4063 4900 5.322754 TGCTTCACAAGTACTACTACTCCT 58.677 41.667 0.00 0.00 31.42 3.69
4123 4963 5.944007 GGATGGATTGTCATCATCATCATCA 59.056 40.000 7.08 0.00 43.82 3.07
4146 4986 8.626526 GGTTGGTAACTTGGTATACATAATTGG 58.373 37.037 5.01 0.00 37.61 3.16
4157 4997 8.115384 TCTACTATACTGGTTGGTAACTTGGTA 58.885 37.037 0.00 0.00 37.61 3.25
4158 4998 6.955851 TCTACTATACTGGTTGGTAACTTGGT 59.044 38.462 0.00 0.00 37.61 3.67
4159 4999 7.414222 TCTACTATACTGGTTGGTAACTTGG 57.586 40.000 0.00 0.00 37.61 3.61
4195 5036 6.016360 TCCATGACAACATAGGTTTGACAAAG 60.016 38.462 0.00 0.00 34.21 2.77
4212 5053 3.918294 TCAAGATGAGCATCCATGACA 57.082 42.857 6.84 0.00 38.58 3.58
4247 5088 5.164620 TGCATCACTATCTCCTTTTGACA 57.835 39.130 0.00 0.00 0.00 3.58
4260 5101 7.019656 ACCATAACCATATGATGCATCACTA 57.980 36.000 30.92 22.10 41.25 2.74
4310 5151 5.352569 TGTCATCGTTGGTTTTTGCATTTTT 59.647 32.000 0.00 0.00 0.00 1.94
4313 5154 3.801594 GTGTCATCGTTGGTTTTTGCATT 59.198 39.130 0.00 0.00 0.00 3.56
4360 5209 4.639755 TGTTCTTGCTTTCTCATGTCAACA 59.360 37.500 0.00 0.00 0.00 3.33
4423 5273 3.748048 GTGAAAGCTGCTCAATCACTGTA 59.252 43.478 24.17 1.48 37.87 2.74
4447 5302 7.298122 TCAGACGATAAAAAGCAGAATTTGAC 58.702 34.615 0.00 0.00 0.00 3.18
4492 5347 0.979709 TGGGAGGAGTGATGCCTGAG 60.980 60.000 0.00 0.00 35.44 3.35
4498 5353 1.133668 GGGGATTTGGGAGGAGTGATG 60.134 57.143 0.00 0.00 0.00 3.07
4500 5355 0.178846 TGGGGATTTGGGAGGAGTGA 60.179 55.000 0.00 0.00 0.00 3.41
4543 5611 0.179936 GATGGAGACCCTGGCTTCAG 59.820 60.000 0.00 0.00 38.21 3.02
4563 5631 2.302260 TCACGATGGATCTCAGAGGTC 58.698 52.381 1.46 1.46 0.00 3.85
4567 5635 1.268079 GCGATCACGATGGATCTCAGA 59.732 52.381 12.22 0.00 41.21 3.27
4577 5645 4.924924 GCTCTACGCGATCACGAT 57.075 55.556 15.93 0.00 42.66 3.73
4706 5774 2.393416 TGGGGACAATAGGGGTGTG 58.607 57.895 0.00 0.00 37.44 3.82


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

AutoCloner maintained by Alex Coulton.