Multiple sequence alignment - TraesCS1B01G030000

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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 TraesCS1B01G030000 chr1B 100.000 4215 0 0 1 4215 14843978 14848192 0.000000e+00 7784
1 TraesCS1B01G030000 chr1B 93.680 269 15 2 3943 4211 15424087 15423821 6.560000e-108 401
2 TraesCS1B01G030000 chr1B 86.716 271 24 5 851 1117 14263917 14264179 1.480000e-74 291
3 TraesCS1B01G030000 chr1B 92.000 150 10 2 3778 3927 15424222 15424075 4.270000e-50 209
4 TraesCS1B01G030000 chr1B 78.400 250 25 13 1013 1244 14513693 14513931 7.350000e-28 135
5 TraesCS1B01G030000 chr1D 89.036 3767 294 71 1 3693 9871706 9875427 0.000000e+00 4558
6 TraesCS1B01G030000 chr1D 89.043 721 47 14 3497 4213 9879484 9880176 0.000000e+00 865
7 TraesCS1B01G030000 chr1D 88.430 484 42 9 3744 4215 9877864 9878345 4.730000e-159 571
8 TraesCS1B01G030000 chr1D 89.349 338 12 9 3374 3690 9877442 9877776 1.830000e-108 403
9 TraesCS1B01G030000 chr1D 95.628 183 8 0 3692 3874 9875509 9875691 1.150000e-75 294
10 TraesCS1B01G030000 chr1A 89.284 3434 252 60 851 4215 11662616 11666002 0.000000e+00 4196
11 TraesCS1B01G030000 chr1A 90.517 232 17 3 3739 3967 12136139 12135910 6.850000e-78 302
12 TraesCS1B01G030000 chr1A 92.778 180 7 6 3794 3967 12138554 12138375 5.410000e-64 255
13 TraesCS1B01G030000 chr2D 88.722 133 12 3 3744 3874 617902961 617902830 4.360000e-35 159
14 TraesCS1B01G030000 chr3B 84.314 153 20 4 3734 3885 16445053 16445202 3.400000e-31 147


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 TraesCS1B01G030000 chr1B 14843978 14848192 4214 False 7784.0 7784 100.0000 1 4215 1 chr1B.!!$F3 4214
1 TraesCS1B01G030000 chr1D 9871706 9880176 8470 False 1338.2 4558 90.2972 1 4215 5 chr1D.!!$F1 4214
2 TraesCS1B01G030000 chr1A 11662616 11666002 3386 False 4196.0 4196 89.2840 851 4215 1 chr1A.!!$F1 3364
3 TraesCS1B01G030000 chr1A 12135910 12138554 2644 True 278.5 302 91.6475 3739 3967 2 chr1A.!!$R1 228

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
393 411 0.179119 GCCATGGCTTGTGCTGAATC 60.179 55.0 29.98 0.0 39.59 2.52 F
708 744 0.505231 TTCTCGCACGTTTACGCAAG 59.495 50.0 1.60 0.0 44.43 4.01 F
1524 1567 0.688487 CCACGGAGGGGAAAACTACA 59.312 55.0 0.00 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1237 0.095245 GCACATTGACATCGTCCACG 59.905 55.0 0.00 0.0 41.45 4.94 R
1947 2041 0.103937 GAGATGCCTGACCTTCCTCG 59.896 60.0 0.00 0.0 0.00 4.63 R
3297 3410 0.176680 CCAGTCTGACCAGGAATCGG 59.823 60.0 10.46 0.0 0.00 4.18 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
75 76 2.267642 CCGAATCGGGCCTGTTCA 59.732 61.111 14.91 0.00 44.15 3.18
136 145 2.409651 CGAGCGGGAGTAGAGTGC 59.590 66.667 0.00 0.00 0.00 4.40
143 152 1.435515 GGAGTAGAGTGCTCTGCCG 59.564 63.158 11.63 0.00 42.26 5.69
203 212 2.466186 GGTGGAGTTGGGGTTGGGA 61.466 63.158 0.00 0.00 0.00 4.37
209 218 1.612146 GTTGGGGTTGGGATTGGGG 60.612 63.158 0.00 0.00 0.00 4.96
243 258 4.559063 CGGCCCCAGCAGATCCAG 62.559 72.222 0.00 0.00 42.56 3.86
244 259 3.092511 GGCCCCAGCAGATCCAGA 61.093 66.667 0.00 0.00 42.56 3.86
250 265 0.249784 CCAGCAGATCCAGACATCCG 60.250 60.000 0.00 0.00 0.00 4.18
253 268 0.531532 GCAGATCCAGACATCCGGTG 60.532 60.000 0.00 1.37 0.00 4.94
254 269 0.531532 CAGATCCAGACATCCGGTGC 60.532 60.000 0.00 0.00 0.00 5.01
255 270 1.592669 GATCCAGACATCCGGTGCG 60.593 63.158 0.00 0.00 0.00 5.34
299 314 2.626840 CTTCCTTCTTCCAGCTGCTAC 58.373 52.381 8.66 0.00 0.00 3.58
315 330 2.092049 TGCTACAGCTAGCCAGGTACTA 60.092 50.000 12.13 0.00 44.45 1.82
316 331 2.293955 GCTACAGCTAGCCAGGTACTAC 59.706 54.545 12.13 0.00 39.79 2.73
317 332 1.777941 ACAGCTAGCCAGGTACTACC 58.222 55.000 12.13 0.00 36.02 3.18
319 334 1.409427 CAGCTAGCCAGGTACTACCAC 59.591 57.143 12.13 0.00 41.95 4.16
320 335 0.751452 GCTAGCCAGGTACTACCACC 59.249 60.000 2.29 0.00 41.95 4.61
321 336 1.411041 CTAGCCAGGTACTACCACCC 58.589 60.000 8.01 0.00 41.95 4.61
322 337 1.013197 TAGCCAGGTACTACCACCCT 58.987 55.000 8.01 3.06 41.95 4.34
343 358 4.528596 CCTTCTTCTTCTCTGTTACTCCCA 59.471 45.833 0.00 0.00 0.00 4.37
350 365 3.572642 TCTCTGTTACTCCCACACTTCA 58.427 45.455 0.00 0.00 0.00 3.02
385 403 3.866379 TTCCTGCGCCATGGCTTGT 62.866 57.895 33.07 0.00 39.32 3.16
390 408 3.057548 CGCCATGGCTTGTGCTGA 61.058 61.111 33.07 0.00 39.59 4.26
391 409 2.628696 CGCCATGGCTTGTGCTGAA 61.629 57.895 33.07 0.00 39.59 3.02
393 411 0.179119 GCCATGGCTTGTGCTGAATC 60.179 55.000 29.98 0.00 39.59 2.52
439 475 4.744795 ATGGTACTCTAGTTCTTGCAGG 57.255 45.455 0.00 0.00 0.00 4.85
452 488 7.158099 AGTTCTTGCAGGGTTTGATTATTAC 57.842 36.000 0.00 0.00 0.00 1.89
456 492 6.719370 TCTTGCAGGGTTTGATTATTACAAGT 59.281 34.615 0.00 0.00 34.06 3.16
457 493 6.266168 TGCAGGGTTTGATTATTACAAGTG 57.734 37.500 0.00 0.00 0.00 3.16
460 496 7.178274 TGCAGGGTTTGATTATTACAAGTGAAT 59.822 33.333 0.00 0.00 0.00 2.57
510 546 3.181496 GCTGCAGGGTTACTAGCAATTTC 60.181 47.826 17.12 0.00 34.44 2.17
574 610 7.481275 CAAACCTGTTTGCTAAAATGTGAAT 57.519 32.000 9.59 0.00 42.66 2.57
587 623 4.909678 TGAATTGGTCACCGGCAA 57.090 50.000 0.00 0.00 0.00 4.52
671 707 3.565307 ACTTTTGGAAGGCACTGAATCA 58.435 40.909 0.00 0.00 40.86 2.57
708 744 0.505231 TTCTCGCACGTTTACGCAAG 59.495 50.000 1.60 0.00 44.43 4.01
710 746 2.153219 CTCGCACGTTTACGCAAGCA 62.153 55.000 1.60 0.00 44.43 3.91
715 751 1.996898 CACGTTTACGCAAGCAGGATA 59.003 47.619 1.60 0.00 44.43 2.59
719 755 1.635844 TTACGCAAGCAGGATACACG 58.364 50.000 0.00 0.00 45.62 4.49
763 799 2.606725 CGAGCAAGTCTTGGCTGAATAG 59.393 50.000 14.40 0.00 41.22 1.73
832 868 3.810941 TCCGCGTGTCTTTTCTACATTTT 59.189 39.130 4.92 0.00 0.00 1.82
843 879 9.959749 GTCTTTTCTACATTTTGGTTATGACAA 57.040 29.630 0.00 0.00 0.00 3.18
879 915 4.394610 GGTTTTGTTTGCTGGAATTGTTGT 59.605 37.500 0.00 0.00 0.00 3.32
887 923 2.554344 GCTGGAATTGTTGTAGGGGTCA 60.554 50.000 0.00 0.00 0.00 4.02
917 956 5.393866 AGAAAGGAAACCAAGGAAGCATTA 58.606 37.500 0.00 0.00 0.00 1.90
920 959 3.826729 AGGAAACCAAGGAAGCATTACAC 59.173 43.478 0.00 0.00 0.00 2.90
930 969 3.826466 GAAGCATTACACAACAGGCTTC 58.174 45.455 8.22 8.22 46.80 3.86
934 973 4.082571 AGCATTACACAACAGGCTTCATTC 60.083 41.667 0.00 0.00 0.00 2.67
939 978 1.425066 ACAACAGGCTTCATTCTGGGA 59.575 47.619 0.00 0.00 35.47 4.37
988 1031 8.798859 ACATTTAGAGCATAACATCAGACTTT 57.201 30.769 0.00 0.00 0.00 2.66
1032 1075 0.693049 AACCCAGGGATGTGTCAGAC 59.307 55.000 14.54 0.00 0.00 3.51
1035 1078 0.826715 CCAGGGATGTGTCAGACGAT 59.173 55.000 0.00 0.00 0.00 3.73
1164 1207 2.224079 CCACATGTCGGTCAAGTTTGAG 59.776 50.000 0.00 0.00 37.98 3.02
1173 1216 3.306364 CGGTCAAGTTTGAGGATCTCTGT 60.306 47.826 0.00 0.00 37.98 3.41
1194 1237 1.598701 GCTTCATGGTGGAGGGCAAC 61.599 60.000 0.00 0.00 0.00 4.17
1381 1424 5.465390 TCAGTGCTCACAAATACAGTTACAC 59.535 40.000 2.63 0.00 0.00 2.90
1410 1453 2.204291 ATCAGGAAGGGGGTGCCA 60.204 61.111 0.00 0.00 0.00 4.92
1524 1567 0.688487 CCACGGAGGGGAAAACTACA 59.312 55.000 0.00 0.00 0.00 2.74
1644 1689 9.630098 ATGCCTTGATAAAATTATTAATGAGCG 57.370 29.630 0.00 0.00 0.00 5.03
1656 1701 1.825090 AATGAGCGACATCCTGCAAA 58.175 45.000 0.00 0.00 38.38 3.68
1719 1764 6.899089 TCTATATGCTTCATTGGTTTGAGGA 58.101 36.000 0.00 0.00 0.00 3.71
1740 1785 4.082354 GGATGTTTGAAGCAGCATTCTTCT 60.082 41.667 0.00 0.00 39.19 2.85
1741 1786 5.124457 GGATGTTTGAAGCAGCATTCTTCTA 59.876 40.000 0.00 4.25 39.19 2.10
1742 1787 6.183360 GGATGTTTGAAGCAGCATTCTTCTAT 60.183 38.462 0.00 4.33 39.19 1.98
1775 1824 3.558674 GCTGCAAGAGCCCTTCTTA 57.441 52.632 0.00 0.00 44.34 2.10
1785 1878 6.543831 GCAAGAGCCCTTCTTATTTTGATCTA 59.456 38.462 0.00 0.00 44.34 1.98
1822 1916 3.262420 ACTGTCGTATCCAGATTGTTGC 58.738 45.455 0.00 0.00 34.04 4.17
1823 1917 2.267426 TGTCGTATCCAGATTGTTGCG 58.733 47.619 0.00 0.00 0.00 4.85
1844 1938 3.677121 CGCTCACTTATCAGCACATATCC 59.323 47.826 0.00 0.00 35.15 2.59
1871 1965 7.178074 GCTTTATGTACACTAATTCGGTGAAC 58.822 38.462 15.44 0.00 38.01 3.18
1885 1979 3.872771 TCGGTGAACCTGTGAAGTAAAAC 59.127 43.478 0.00 0.00 0.00 2.43
1947 2041 1.598701 GCCATCCCTGGTTGAACAGC 61.599 60.000 0.00 0.00 45.10 4.40
2076 2170 9.461312 TCAAATGTAATTTAACTCACCTAGCAT 57.539 29.630 0.00 0.00 46.64 3.79
2158 2252 4.511527 TGAAGACAGAGGAAGATGCATTC 58.488 43.478 0.00 0.00 0.00 2.67
2257 2351 7.180322 TGAGCAGAGAGTATTCAAAGATCTT 57.820 36.000 0.88 0.88 0.00 2.40
2327 2426 6.825213 TGCTATCATTTCTCACTTACAATGCT 59.175 34.615 0.00 0.00 0.00 3.79
2328 2427 7.986889 TGCTATCATTTCTCACTTACAATGCTA 59.013 33.333 0.00 0.00 0.00 3.49
2331 2430 7.558161 TCATTTCTCACTTACAATGCTATGG 57.442 36.000 0.00 0.00 0.00 2.74
2339 2438 6.658816 TCACTTACAATGCTATGGTTGTGAAT 59.341 34.615 1.34 0.00 38.84 2.57
2346 2445 9.970395 ACAATGCTATGGTTGTGAATTATATTG 57.030 29.630 0.00 0.00 37.19 1.90
2348 2447 6.980593 TGCTATGGTTGTGAATTATATTGGC 58.019 36.000 0.00 0.00 0.00 4.52
2393 2492 1.407979 GCTCATCTTGAAGCAATGGGG 59.592 52.381 0.00 0.00 0.00 4.96
2453 2552 2.892852 CCTCTTCTCCAAAACATTGCCA 59.107 45.455 0.00 0.00 0.00 4.92
2456 2555 3.511146 TCTTCTCCAAAACATTGCCATCC 59.489 43.478 0.00 0.00 0.00 3.51
2465 2564 1.559682 ACATTGCCATCCGAGGTTAGT 59.440 47.619 0.00 0.00 0.00 2.24
2468 2567 1.271856 TGCCATCCGAGGTTAGTCAA 58.728 50.000 0.00 0.00 0.00 3.18
2469 2568 1.207089 TGCCATCCGAGGTTAGTCAAG 59.793 52.381 0.00 0.00 0.00 3.02
2480 2586 6.214399 CGAGGTTAGTCAAGAGTTTACTTGT 58.786 40.000 0.00 0.00 44.96 3.16
2520 2626 7.323420 TCTTTCGTCAATGATCTGTACAGAAT 58.677 34.615 28.43 16.07 41.36 2.40
2542 2648 8.641541 AGAATTCACTGTAAAACCATTTCACAT 58.358 29.630 8.44 0.00 0.00 3.21
2578 2685 0.106149 GTGAACAGACAACCCTCCGT 59.894 55.000 0.00 0.00 0.00 4.69
2590 2697 1.375908 CCTCCGTGTGTGGGATGTG 60.376 63.158 0.00 0.00 31.99 3.21
2591 2698 1.371183 CTCCGTGTGTGGGATGTGT 59.629 57.895 0.00 0.00 31.99 3.72
2629 2736 0.321653 AGGTCTTGTTCCATGTCGCC 60.322 55.000 0.00 0.00 0.00 5.54
2650 2757 3.578688 CCTAGCAATTTTCAAGGTGTGC 58.421 45.455 0.00 0.00 0.00 4.57
2654 2761 2.796593 GCAATTTTCAAGGTGTGCACTC 59.203 45.455 19.41 14.79 32.29 3.51
2657 2764 1.679139 TTTCAAGGTGTGCACTCAGG 58.321 50.000 19.41 7.77 0.00 3.86
2693 2800 4.187694 GCATGTTTTCCCAAAGTGTTTGA 58.812 39.130 0.87 0.00 43.26 2.69
2694 2801 4.633565 GCATGTTTTCCCAAAGTGTTTGAA 59.366 37.500 0.87 0.00 43.26 2.69
2703 2810 6.369629 TCCCAAAGTGTTTGAATTCCTTCTA 58.630 36.000 2.27 0.00 43.26 2.10
2716 2823 5.904362 ATTCCTTCTACTTGTTTGGCATC 57.096 39.130 0.00 0.00 0.00 3.91
2832 2939 3.639099 CAGACAACTGCCCATCACT 57.361 52.632 0.00 0.00 37.33 3.41
2837 2944 5.371526 CAGACAACTGCCCATCACTTATAT 58.628 41.667 0.00 0.00 37.33 0.86
2843 2950 2.981784 TGCCCATCACTTATATGAGCCT 59.018 45.455 0.00 0.00 30.46 4.58
2869 2976 4.873827 TGAACTGCTCACGGTAAATATTCC 59.126 41.667 0.00 0.00 32.87 3.01
2870 2977 4.481368 ACTGCTCACGGTAAATATTCCA 57.519 40.909 0.00 0.00 31.99 3.53
2871 2978 5.036117 ACTGCTCACGGTAAATATTCCAT 57.964 39.130 0.00 0.00 31.99 3.41
2879 2986 7.757526 TCACGGTAAATATTCCATCTTTTGTG 58.242 34.615 0.00 0.00 0.00 3.33
2882 2989 5.977129 GGTAAATATTCCATCTTTTGTGCCG 59.023 40.000 0.00 0.00 0.00 5.69
2891 2998 2.333926 TCTTTTGTGCCGACAGATACG 58.666 47.619 0.00 0.00 32.26 3.06
2903 3010 3.373130 CGACAGATACGGTGAAGTAGTCA 59.627 47.826 0.00 0.00 0.00 3.41
2931 3038 8.464404 GGATGATGCACAATGTTATAAGCATAT 58.536 33.333 7.90 3.80 42.18 1.78
2933 3040 8.168790 TGATGCACAATGTTATAAGCATATGT 57.831 30.769 7.90 7.98 42.18 2.29
2936 3043 8.675705 TGCACAATGTTATAAGCATATGTAGT 57.324 30.769 4.29 0.00 0.00 2.73
2940 3047 9.066892 ACAATGTTATAAGCATATGTAGTTGGG 57.933 33.333 4.29 0.00 0.00 4.12
2945 3052 4.844349 AAGCATATGTAGTTGGGACACT 57.156 40.909 4.29 0.00 39.29 3.55
2953 3060 9.046296 CATATGTAGTTGGGACACTAAGAAATC 57.954 37.037 0.00 0.00 39.29 2.17
2955 3062 7.016153 TGTAGTTGGGACACTAAGAAATCAT 57.984 36.000 0.00 0.00 39.29 2.45
2991 3099 8.698973 AAGTCAGCAGTATTTAGAGCTATCTA 57.301 34.615 0.00 0.00 36.96 1.98
2993 3101 8.956426 AGTCAGCAGTATTTAGAGCTATCTATC 58.044 37.037 0.00 0.00 37.86 2.08
2997 3105 9.308000 AGCAGTATTTAGAGCTATCTATCTGTT 57.692 33.333 0.00 0.00 37.86 3.16
3025 3133 6.010294 ATCAAGTAGATATTGCATGCTTGC 57.990 37.500 20.33 17.19 41.54 4.01
3027 3135 6.294010 ATCAAGTAGATATTGCATGCTTGCAG 60.294 38.462 24.21 11.06 46.93 4.41
3028 3136 9.591788 ATCAAGTAGATATTGCATGCTTGCAGC 62.592 40.741 24.21 15.83 46.93 5.25
3050 3158 5.375417 CAATTGATTGCCACACACTAGAA 57.625 39.130 0.00 0.00 0.00 2.10
3056 3164 4.558226 TTGCCACACACTAGAATCTGAT 57.442 40.909 0.00 0.00 0.00 2.90
3062 3170 6.763135 GCCACACACTAGAATCTGATTTATCA 59.237 38.462 4.11 0.00 35.16 2.15
3069 3180 9.007901 CACTAGAATCTGATTTATCATTTCCCC 57.992 37.037 4.11 0.00 36.02 4.81
3070 3181 8.166726 ACTAGAATCTGATTTATCATTTCCCCC 58.833 37.037 4.11 0.00 36.02 5.40
3074 3185 8.628368 AATCTGATTTATCATTTCCCCCTTTT 57.372 30.769 0.00 0.00 36.02 2.27
3121 3232 1.680735 GGCTCCATGACAACAAACACA 59.319 47.619 0.00 0.00 0.00 3.72
3272 3385 3.632145 GCCCTGAGTGTTTTGAAGAAAGA 59.368 43.478 0.00 0.00 0.00 2.52
3276 3389 5.237344 CCTGAGTGTTTTGAAGAAAGACGAT 59.763 40.000 0.00 0.00 0.00 3.73
3283 3396 6.074516 TGTTTTGAAGAAAGACGATACGACAG 60.075 38.462 0.00 0.00 0.00 3.51
3296 3409 0.108585 ACGACAGGGTGAGTTTGCAT 59.891 50.000 0.00 0.00 0.00 3.96
3297 3410 0.798776 CGACAGGGTGAGTTTGCATC 59.201 55.000 0.00 0.00 0.00 3.91
3299 3412 0.606401 ACAGGGTGAGTTTGCATCCG 60.606 55.000 0.00 0.00 43.97 4.18
3357 3470 2.182030 GCTCGAGGTCCACCGAAG 59.818 66.667 15.58 4.26 42.08 3.79
3360 3473 0.961358 CTCGAGGTCCACCGAAGACT 60.961 60.000 3.91 0.00 42.08 3.24
3363 3476 0.898789 GAGGTCCACCGAAGACTGGA 60.899 60.000 0.00 0.00 42.08 3.86
3514 3647 2.605818 CCGATGGCATTTGCTTGATTTG 59.394 45.455 0.00 0.00 41.70 2.32
3555 3688 7.367285 TGTATGTGTGAAATGGAGCTAAAAAC 58.633 34.615 0.00 0.00 0.00 2.43
3601 3736 5.976458 ACTTGATTTTGCTTCTGGTTGAAA 58.024 33.333 0.00 0.00 33.79 2.69
3649 3784 3.118038 ACAGTTGAGAAAGCCAGGTTGTA 60.118 43.478 0.00 0.00 0.00 2.41
3681 3816 6.038356 CCAAATTCTCAGTGTTTATGGCATC 58.962 40.000 1.65 0.00 0.00 3.91
3687 3822 5.587443 TCTCAGTGTTTATGGCATCTGATTG 59.413 40.000 14.06 6.28 32.73 2.67
3688 3823 5.499313 TCAGTGTTTATGGCATCTGATTGA 58.501 37.500 1.65 0.00 0.00 2.57
3689 3824 5.355071 TCAGTGTTTATGGCATCTGATTGAC 59.645 40.000 1.65 0.00 0.00 3.18
3691 3826 4.641989 GTGTTTATGGCATCTGATTGACCT 59.358 41.667 1.65 0.00 0.00 3.85
3692 3827 5.822519 GTGTTTATGGCATCTGATTGACCTA 59.177 40.000 1.65 0.00 0.00 3.08
3693 3828 6.017605 GTGTTTATGGCATCTGATTGACCTAG 60.018 42.308 1.65 0.00 0.00 3.02
3694 3829 6.126796 TGTTTATGGCATCTGATTGACCTAGA 60.127 38.462 1.65 0.00 0.00 2.43
3695 3830 6.499106 TTATGGCATCTGATTGACCTAGAA 57.501 37.500 1.65 0.00 0.00 2.10
3696 3831 4.842531 TGGCATCTGATTGACCTAGAAA 57.157 40.909 0.00 0.00 0.00 2.52
3697 3832 5.178096 TGGCATCTGATTGACCTAGAAAA 57.822 39.130 0.00 0.00 0.00 2.29
3699 3834 5.189180 GGCATCTGATTGACCTAGAAAACT 58.811 41.667 0.00 0.00 0.00 2.66
3700 3835 5.065731 GGCATCTGATTGACCTAGAAAACTG 59.934 44.000 0.00 0.00 0.00 3.16
3701 3836 5.877012 GCATCTGATTGACCTAGAAAACTGA 59.123 40.000 0.00 0.00 0.00 3.41
3703 3838 5.482908 TCTGATTGACCTAGAAAACTGAGC 58.517 41.667 0.00 0.00 0.00 4.26
3704 3839 5.247110 TCTGATTGACCTAGAAAACTGAGCT 59.753 40.000 0.00 0.00 0.00 4.09
3705 3840 6.437477 TCTGATTGACCTAGAAAACTGAGCTA 59.563 38.462 0.00 0.00 0.00 3.32
3721 3856 5.724328 CTGAGCTACAGGATTGTGTTTAGA 58.276 41.667 5.54 0.00 42.39 2.10
3722 3857 6.109156 TGAGCTACAGGATTGTGTTTAGAA 57.891 37.500 0.00 0.00 38.23 2.10
3723 3858 6.166279 TGAGCTACAGGATTGTGTTTAGAAG 58.834 40.000 0.00 0.00 38.23 2.85
3724 3859 4.938226 AGCTACAGGATTGTGTTTAGAAGC 59.062 41.667 0.00 0.00 38.23 3.86
3725 3860 4.095036 GCTACAGGATTGTGTTTAGAAGCC 59.905 45.833 0.00 0.00 38.23 4.35
3727 3862 3.074412 CAGGATTGTGTTTAGAAGCCGT 58.926 45.455 0.00 0.00 40.30 5.68
3728 3863 4.250464 CAGGATTGTGTTTAGAAGCCGTA 58.750 43.478 0.00 0.00 40.30 4.02
3729 3864 4.876107 CAGGATTGTGTTTAGAAGCCGTAT 59.124 41.667 0.00 0.00 40.30 3.06
3737 3872 5.515626 GTGTTTAGAAGCCGTATCTAGTGTG 59.484 44.000 0.00 0.00 31.41 3.82
3738 3873 2.873133 AGAAGCCGTATCTAGTGTGC 57.127 50.000 0.00 0.00 0.00 4.57
3739 3874 1.065701 AGAAGCCGTATCTAGTGTGCG 59.934 52.381 0.00 0.00 0.00 5.34
3740 3875 0.815734 AAGCCGTATCTAGTGTGCGT 59.184 50.000 7.34 0.00 0.00 5.24
3742 3877 2.019249 AGCCGTATCTAGTGTGCGTTA 58.981 47.619 7.34 0.00 0.00 3.18
3749 3969 6.183360 CCGTATCTAGTGTGCGTTATTTTTGT 60.183 38.462 7.34 0.00 0.00 2.83
3775 3995 6.315642 TGTTAATCACCAAACGTTGAAGTACA 59.684 34.615 0.00 0.00 0.00 2.90
3792 4012 5.808042 AGTACAATAGCATTGCAACTCTG 57.192 39.130 11.91 0.00 0.00 3.35
3874 6398 3.553922 GGATCGAAACCTGGCTCTGATAG 60.554 52.174 0.00 0.00 0.00 2.08
3930 6458 7.322664 TCAGTTCAATATGATTGGGCTTTTTC 58.677 34.615 0.00 0.00 0.00 2.29
3983 6511 2.258286 GTTGCGTTCATGGCCCAC 59.742 61.111 0.00 0.00 0.00 4.61
4072 8460 9.830975 ATTTACATTTTATGCATCCCCTAAAAC 57.169 29.630 0.19 0.00 29.82 2.43
4073 8461 6.865834 ACATTTTATGCATCCCCTAAAACA 57.134 33.333 0.19 0.00 29.82 2.83
4074 8462 7.251321 ACATTTTATGCATCCCCTAAAACAA 57.749 32.000 0.19 0.00 29.82 2.83
4075 8463 7.860584 ACATTTTATGCATCCCCTAAAACAAT 58.139 30.769 0.19 0.00 29.82 2.71
4076 8464 8.328014 ACATTTTATGCATCCCCTAAAACAATT 58.672 29.630 0.19 0.00 29.82 2.32
4077 8465 9.829507 CATTTTATGCATCCCCTAAAACAATTA 57.170 29.630 0.19 0.00 29.82 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 249 0.531532 CACCGGATGTCTGGATCTGC 60.532 60.000 9.46 0.00 45.36 4.26
299 314 1.409427 GTGGTAGTACCTGGCTAGCTG 59.591 57.143 20.07 7.95 39.58 4.24
315 330 2.695585 ACAGAGAAGAAGAAGGGTGGT 58.304 47.619 0.00 0.00 0.00 4.16
316 331 3.778954 AACAGAGAAGAAGAAGGGTGG 57.221 47.619 0.00 0.00 0.00 4.61
317 332 5.474825 GAGTAACAGAGAAGAAGAAGGGTG 58.525 45.833 0.00 0.00 0.00 4.61
319 334 4.081365 GGGAGTAACAGAGAAGAAGAAGGG 60.081 50.000 0.00 0.00 0.00 3.95
320 335 4.528596 TGGGAGTAACAGAGAAGAAGAAGG 59.471 45.833 0.00 0.00 0.00 3.46
321 336 5.011125 TGTGGGAGTAACAGAGAAGAAGAAG 59.989 44.000 0.00 0.00 0.00 2.85
322 337 4.899457 TGTGGGAGTAACAGAGAAGAAGAA 59.101 41.667 0.00 0.00 0.00 2.52
357 372 1.583709 GCGCAGGAAAAGCATACGC 60.584 57.895 0.30 0.00 37.93 4.42
385 403 1.002430 AGACGAGCTTTGGATTCAGCA 59.998 47.619 0.00 0.00 38.61 4.41
390 408 5.361285 ACATAGTAGAGACGAGCTTTGGATT 59.639 40.000 0.00 0.00 0.00 3.01
391 409 4.890581 ACATAGTAGAGACGAGCTTTGGAT 59.109 41.667 0.00 0.00 0.00 3.41
393 411 4.640789 ACATAGTAGAGACGAGCTTTGG 57.359 45.455 0.00 0.00 0.00 3.28
482 518 1.645710 AGTAACCCTGCAGCACTAGT 58.354 50.000 8.66 0.00 0.00 2.57
510 546 2.099141 TCGCTCTTGAAGAATGGGTG 57.901 50.000 0.00 0.00 0.00 4.61
554 590 5.990996 ACCAATTCACATTTTAGCAAACAGG 59.009 36.000 0.00 0.00 0.00 4.00
574 610 1.626686 ATCAAATTGCCGGTGACCAA 58.373 45.000 1.90 0.00 0.00 3.67
612 648 5.626543 CACAATTCTTTGTCGATTGAACAGG 59.373 40.000 0.00 0.00 44.24 4.00
620 656 7.819415 TGAAGAGTATCACAATTCTTTGTCGAT 59.181 33.333 0.00 0.00 44.24 3.59
622 658 7.116948 ACTGAAGAGTATCACAATTCTTTGTCG 59.883 37.037 0.00 0.00 44.24 4.35
635 671 7.878127 CCTTCCAAAAGTTACTGAAGAGTATCA 59.122 37.037 10.51 0.00 37.82 2.15
671 707 4.908687 TTGCTCGCACACGCCACT 62.909 61.111 0.00 0.00 39.84 4.00
708 744 1.207329 AGGTCCTTTCGTGTATCCTGC 59.793 52.381 0.00 0.00 0.00 4.85
710 746 2.236395 CCAAGGTCCTTTCGTGTATCCT 59.764 50.000 0.00 0.00 0.00 3.24
715 751 0.250338 GCTCCAAGGTCCTTTCGTGT 60.250 55.000 0.00 0.00 0.00 4.49
719 755 0.608640 TCTCGCTCCAAGGTCCTTTC 59.391 55.000 0.00 0.00 0.00 2.62
763 799 5.279156 GCACAAATCCCATCCAAATCTATCC 60.279 44.000 0.00 0.00 0.00 2.59
797 833 0.108992 ACGCGGAAATGTAAGCTCGA 60.109 50.000 12.47 0.00 0.00 4.04
798 834 0.025001 CACGCGGAAATGTAAGCTCG 59.975 55.000 12.47 0.00 0.00 5.03
799 835 1.060698 GACACGCGGAAATGTAAGCTC 59.939 52.381 12.47 0.00 0.00 4.09
801 837 1.076332 AGACACGCGGAAATGTAAGC 58.924 50.000 12.47 0.00 0.00 3.09
802 838 3.806316 AAAGACACGCGGAAATGTAAG 57.194 42.857 12.47 0.00 0.00 2.34
832 868 6.878923 CCAGAGTTGATTAGTTGTCATAACCA 59.121 38.462 0.00 0.00 0.00 3.67
843 879 6.096846 AGCAAACAAAACCAGAGTTGATTAGT 59.903 34.615 0.00 0.00 35.97 2.24
879 915 1.275291 CTTTCTCGCTGTTGACCCCTA 59.725 52.381 0.00 0.00 0.00 3.53
887 923 2.341846 TGGTTTCCTTTCTCGCTGTT 57.658 45.000 0.00 0.00 0.00 3.16
917 956 2.233271 CCAGAATGAAGCCTGTTGTGT 58.767 47.619 0.00 0.00 39.69 3.72
920 959 2.089980 CTCCCAGAATGAAGCCTGTTG 58.910 52.381 0.00 0.00 39.69 3.33
970 1010 5.412594 TGTCCAAAAGTCTGATGTTATGCTC 59.587 40.000 0.00 0.00 0.00 4.26
974 1014 8.641498 ATTCTTGTCCAAAAGTCTGATGTTAT 57.359 30.769 0.00 0.00 0.00 1.89
975 1015 9.739276 ATATTCTTGTCCAAAAGTCTGATGTTA 57.261 29.630 0.00 0.00 0.00 2.41
976 1016 6.966534 ATTCTTGTCCAAAAGTCTGATGTT 57.033 33.333 0.00 0.00 0.00 2.71
988 1031 5.656416 GGATCCCAAACATATTCTTGTCCAA 59.344 40.000 0.00 0.00 0.00 3.53
1032 1075 2.205074 CTCCTCGGGTTGAAATCATCG 58.795 52.381 0.00 0.00 0.00 3.84
1035 1078 1.555075 CTCCTCCTCGGGTTGAAATCA 59.445 52.381 0.00 0.00 0.00 2.57
1164 1207 1.211457 ACCATGAAGCCACAGAGATCC 59.789 52.381 0.00 0.00 0.00 3.36
1173 1216 3.089838 CCCTCCACCATGAAGCCA 58.910 61.111 0.00 0.00 0.00 4.75
1194 1237 0.095245 GCACATTGACATCGTCCACG 59.905 55.000 0.00 0.00 41.45 4.94
1381 1424 1.413445 CTTCCTGATCAGCCTCCTCAG 59.587 57.143 17.76 1.09 36.89 3.35
1410 1453 4.269523 TTTGGCCTCAGCGCTGGT 62.270 61.111 35.36 0.00 41.24 4.00
1425 1468 0.690762 ACACCGACAGCCATACCTTT 59.309 50.000 0.00 0.00 0.00 3.11
1644 1689 2.229543 TGATGCTTGTTTGCAGGATGTC 59.770 45.455 0.00 0.00 46.71 3.06
1656 1701 7.916927 ATGGATGAAGCCATCTGATGCTTGT 62.917 44.000 22.83 15.02 45.36 3.16
1696 1741 7.230108 ACATCCTCAAACCAATGAAGCATATAG 59.770 37.037 0.00 0.00 0.00 1.31
1697 1742 7.062322 ACATCCTCAAACCAATGAAGCATATA 58.938 34.615 0.00 0.00 0.00 0.86
1719 1764 6.770746 ATAGAAGAATGCTGCTTCAAACAT 57.229 33.333 13.52 0.00 43.19 2.71
1740 1785 8.504812 TCTTGCAGCAACAAGTATGAATAATA 57.495 30.769 2.83 0.00 45.86 0.98
1741 1786 7.395190 TCTTGCAGCAACAAGTATGAATAAT 57.605 32.000 2.83 0.00 45.86 1.28
1742 1787 6.816134 TCTTGCAGCAACAAGTATGAATAA 57.184 33.333 2.83 0.00 45.86 1.40
1806 1899 1.258982 GAGCGCAACAATCTGGATACG 59.741 52.381 11.47 0.00 42.51 3.06
1807 1900 2.030946 GTGAGCGCAACAATCTGGATAC 59.969 50.000 11.47 0.00 0.00 2.24
1811 1904 0.877071 AAGTGAGCGCAACAATCTGG 59.123 50.000 11.47 0.00 0.00 3.86
1822 1916 3.677121 GGATATGTGCTGATAAGTGAGCG 59.323 47.826 0.00 0.00 37.40 5.03
1823 1917 3.677121 CGGATATGTGCTGATAAGTGAGC 59.323 47.826 0.00 0.00 34.91 4.26
1844 1938 4.807304 ACCGAATTAGTGTACATAAAGCCG 59.193 41.667 0.00 4.77 0.00 5.52
1871 1965 5.695851 AGCATTCAGTTTTACTTCACAGG 57.304 39.130 0.00 0.00 0.00 4.00
1885 1979 3.444742 TCCTGTAATGGCAAAGCATTCAG 59.555 43.478 0.00 0.00 0.00 3.02
1947 2041 0.103937 GAGATGCCTGACCTTCCTCG 59.896 60.000 0.00 0.00 0.00 4.63
2064 2158 3.957497 CTGTTAGGAGATGCTAGGTGAGT 59.043 47.826 0.00 0.00 0.00 3.41
2076 2170 6.069206 ACCCTGTAGTACATACTGTTAGGAGA 60.069 42.308 2.82 0.00 37.10 3.71
2158 2252 0.176680 AGAGTACGGCAAGCATCCAG 59.823 55.000 0.00 0.00 0.00 3.86
2167 2261 3.134574 ACATTTTCCAAGAGTACGGCA 57.865 42.857 0.00 0.00 0.00 5.69
2307 2403 7.112122 ACCATAGCATTGTAAGTGAGAAATGA 58.888 34.615 0.00 0.00 32.86 2.57
2308 2404 7.325660 ACCATAGCATTGTAAGTGAGAAATG 57.674 36.000 0.00 0.00 33.98 2.32
2321 2417 9.414295 CCAATATAATTCACAACCATAGCATTG 57.586 33.333 0.00 0.00 0.00 2.82
2328 2427 7.986889 GGAAAAGCCAATATAATTCACAACCAT 59.013 33.333 0.00 0.00 36.34 3.55
2346 2445 3.161866 TCCTGTACCATTTGGAAAAGCC 58.838 45.455 3.01 0.00 38.94 4.35
2348 2447 5.047092 AGCAATCCTGTACCATTTGGAAAAG 60.047 40.000 3.01 0.00 38.94 2.27
2393 2492 4.777140 GGCAACAAGTGAAACATCAAAC 57.223 40.909 0.00 0.00 41.43 2.93
2426 2525 3.360867 TGTTTTGGAGAAGAGGCACAAA 58.639 40.909 0.00 0.00 0.00 2.83
2429 2528 3.858503 GCAATGTTTTGGAGAAGAGGCAC 60.859 47.826 0.00 0.00 33.22 5.01
2432 2531 2.892852 TGGCAATGTTTTGGAGAAGAGG 59.107 45.455 0.00 0.00 33.22 3.69
2453 2552 5.715753 AGTAAACTCTTGACTAACCTCGGAT 59.284 40.000 0.00 0.00 0.00 4.18
2456 2555 6.214399 ACAAGTAAACTCTTGACTAACCTCG 58.786 40.000 12.38 0.00 45.11 4.63
2488 2594 8.954950 ACAGATCATTGACGAAAGAGATAAAT 57.045 30.769 0.00 0.00 0.00 1.40
2496 2602 6.951256 TTCTGTACAGATCATTGACGAAAG 57.049 37.500 25.68 0.00 37.29 2.62
2499 2605 6.531594 GTGAATTCTGTACAGATCATTGACGA 59.468 38.462 25.68 8.41 37.29 4.20
2500 2606 6.533012 AGTGAATTCTGTACAGATCATTGACG 59.467 38.462 25.68 0.00 37.29 4.35
2510 2616 7.490962 TGGTTTTACAGTGAATTCTGTACAG 57.509 36.000 17.17 17.17 46.30 2.74
2520 2626 9.522804 GTAAATGTGAAATGGTTTTACAGTGAA 57.477 29.630 0.00 0.00 41.53 3.18
2556 2663 2.650322 GGAGGGTTGTCTGTTCACAAA 58.350 47.619 0.00 0.00 38.01 2.83
2578 2685 5.320277 TCATTGAATAACACATCCCACACA 58.680 37.500 0.00 0.00 0.00 3.72
2590 2697 6.151817 AGACCTTTGCTCCTTCATTGAATAAC 59.848 38.462 0.00 0.00 0.00 1.89
2591 2698 6.248433 AGACCTTTGCTCCTTCATTGAATAA 58.752 36.000 0.00 0.00 0.00 1.40
2629 2736 3.005684 TGCACACCTTGAAAATTGCTAGG 59.994 43.478 0.00 0.00 34.93 3.02
2657 2764 5.866092 GGAAAACATGCAAAGAGGAGATTTC 59.134 40.000 0.00 0.00 0.00 2.17
2671 2778 4.187694 TCAAACACTTTGGGAAAACATGC 58.812 39.130 0.00 0.00 40.98 4.06
2693 2800 5.774690 TGATGCCAAACAAGTAGAAGGAATT 59.225 36.000 0.00 0.00 0.00 2.17
2694 2801 5.183904 GTGATGCCAAACAAGTAGAAGGAAT 59.816 40.000 0.00 0.00 0.00 3.01
2703 2810 4.470334 AACAAAGTGATGCCAAACAAGT 57.530 36.364 0.00 0.00 0.00 3.16
2746 2853 7.082700 TCGTCTTCTCTCATCTGCATATATC 57.917 40.000 0.00 0.00 0.00 1.63
2751 2858 3.890756 AGATCGTCTTCTCTCATCTGCAT 59.109 43.478 0.00 0.00 0.00 3.96
2832 2939 5.557576 AGCAGTTCATCAGGCTCATATAA 57.442 39.130 0.00 0.00 28.71 0.98
2843 2950 3.394674 TTTACCGTGAGCAGTTCATCA 57.605 42.857 0.00 0.00 38.29 3.07
2869 2976 3.242091 CGTATCTGTCGGCACAAAAGATG 60.242 47.826 0.00 0.00 29.82 2.90
2870 2977 2.930040 CGTATCTGTCGGCACAAAAGAT 59.070 45.455 0.00 0.00 29.82 2.40
2871 2978 2.333926 CGTATCTGTCGGCACAAAAGA 58.666 47.619 0.00 0.00 29.82 2.52
2882 2989 4.959596 TGACTACTTCACCGTATCTGTC 57.040 45.455 0.00 0.00 0.00 3.51
2891 2998 3.873952 GCATCATCCTTGACTACTTCACC 59.126 47.826 0.00 0.00 33.85 4.02
2903 3010 6.321945 TGCTTATAACATTGTGCATCATCCTT 59.678 34.615 0.00 0.00 0.00 3.36
2931 3038 6.428083 TGATTTCTTAGTGTCCCAACTACA 57.572 37.500 0.00 0.00 32.39 2.74
2933 3040 8.375493 ACTATGATTTCTTAGTGTCCCAACTA 57.625 34.615 5.59 0.00 36.06 2.24
2936 3043 9.667107 CTTTACTATGATTTCTTAGTGTCCCAA 57.333 33.333 13.52 1.21 37.39 4.12
2964 3071 8.482128 AGATAGCTCTAAATACTGCTGACTTTT 58.518 33.333 0.00 0.00 37.02 2.27
3028 3136 5.375417 TTCTAGTGTGTGGCAATCAATTG 57.625 39.130 0.00 0.00 40.66 2.32
3029 3137 5.948162 AGATTCTAGTGTGTGGCAATCAATT 59.052 36.000 0.00 0.00 0.00 2.32
3033 3141 4.507710 TCAGATTCTAGTGTGTGGCAATC 58.492 43.478 0.00 0.00 0.00 2.67
3035 3143 4.558226 ATCAGATTCTAGTGTGTGGCAA 57.442 40.909 0.00 0.00 0.00 4.52
3037 3145 6.763135 TGATAAATCAGATTCTAGTGTGTGGC 59.237 38.462 0.00 0.00 32.11 5.01
3038 3146 8.899427 ATGATAAATCAGATTCTAGTGTGTGG 57.101 34.615 0.00 0.00 40.64 4.17
3047 3155 7.171822 AGGGGGAAATGATAAATCAGATTCT 57.828 36.000 15.33 0.00 40.64 2.40
3050 3158 8.628368 AAAAAGGGGGAAATGATAAATCAGAT 57.372 30.769 0.00 0.00 40.64 2.90
3074 3185 6.730175 TCTTATCAAACGCAAACTAGCAAAA 58.270 32.000 0.00 0.00 0.00 2.44
3078 3189 5.739161 CCAATCTTATCAAACGCAAACTAGC 59.261 40.000 0.00 0.00 0.00 3.42
3088 3199 5.357878 TGTCATGGAGCCAATCTTATCAAAC 59.642 40.000 0.00 0.00 0.00 2.93
3091 3202 4.776435 TGTCATGGAGCCAATCTTATCA 57.224 40.909 0.00 0.00 0.00 2.15
3115 3226 7.148656 CGTTTCCTTTCTTTTGTGATTGTGTTT 60.149 33.333 0.00 0.00 0.00 2.83
3121 3232 4.142049 TGCCGTTTCCTTTCTTTTGTGATT 60.142 37.500 0.00 0.00 0.00 2.57
3169 3280 0.534203 GCCGTCTGGTTCTTTGGTCA 60.534 55.000 0.00 0.00 37.67 4.02
3199 3310 1.808343 GCGCATCATGCATCCATCTTA 59.192 47.619 11.00 0.00 45.36 2.10
3256 3368 5.981315 TCGTATCGTCTTTCTTCAAAACACT 59.019 36.000 0.00 0.00 0.00 3.55
3272 3385 1.542492 AACTCACCCTGTCGTATCGT 58.458 50.000 0.00 0.00 0.00 3.73
3276 3389 0.753867 TGCAAACTCACCCTGTCGTA 59.246 50.000 0.00 0.00 0.00 3.43
3283 3396 1.401905 GAATCGGATGCAAACTCACCC 59.598 52.381 0.00 0.00 0.00 4.61
3296 3409 1.186200 CAGTCTGACCAGGAATCGGA 58.814 55.000 3.76 0.00 0.00 4.55
3297 3410 0.176680 CCAGTCTGACCAGGAATCGG 59.823 60.000 10.46 0.00 0.00 4.18
3299 3412 3.454082 AGAATCCAGTCTGACCAGGAATC 59.546 47.826 19.45 19.48 33.17 2.52
3353 3466 6.288294 TCCCATAATACATTTCCAGTCTTCG 58.712 40.000 0.00 0.00 0.00 3.79
3357 3470 7.682021 GCAACTTCCCATAATACATTTCCAGTC 60.682 40.741 0.00 0.00 0.00 3.51
3360 3473 5.362430 GGCAACTTCCCATAATACATTTCCA 59.638 40.000 0.00 0.00 0.00 3.53
3363 3476 6.865834 TTGGCAACTTCCCATAATACATTT 57.134 33.333 0.00 0.00 37.61 2.32
3514 3647 4.331717 CACATACAACAAATCGGGACTACC 59.668 45.833 0.00 0.00 0.00 3.18
3585 3719 5.108517 GTCACAATTTCAACCAGAAGCAAA 58.891 37.500 0.00 0.00 37.57 3.68
3601 3736 4.773674 ACCACATCAAATCCATGTCACAAT 59.226 37.500 0.00 0.00 31.83 2.71
3649 3784 4.536765 ACACTGAGAATTTGGACACCTTT 58.463 39.130 0.00 0.00 0.00 3.11
3681 3816 5.486526 AGCTCAGTTTTCTAGGTCAATCAG 58.513 41.667 0.00 0.00 0.00 2.90
3687 3822 4.463186 TCCTGTAGCTCAGTTTTCTAGGTC 59.537 45.833 10.86 0.00 42.19 3.85
3688 3823 4.417437 TCCTGTAGCTCAGTTTTCTAGGT 58.583 43.478 10.86 0.00 42.19 3.08
3689 3824 5.606348 ATCCTGTAGCTCAGTTTTCTAGG 57.394 43.478 10.86 0.00 42.19 3.02
3691 3826 6.166279 CACAATCCTGTAGCTCAGTTTTCTA 58.834 40.000 10.86 0.00 42.19 2.10
3692 3827 4.999950 CACAATCCTGTAGCTCAGTTTTCT 59.000 41.667 10.86 0.00 42.19 2.52
3693 3828 4.757149 ACACAATCCTGTAGCTCAGTTTTC 59.243 41.667 10.86 0.00 42.19 2.29
3694 3829 4.718961 ACACAATCCTGTAGCTCAGTTTT 58.281 39.130 10.86 3.56 42.19 2.43
3695 3830 4.357918 ACACAATCCTGTAGCTCAGTTT 57.642 40.909 10.86 3.83 42.19 2.66
3696 3831 4.357918 AACACAATCCTGTAGCTCAGTT 57.642 40.909 10.86 0.00 42.19 3.16
3697 3832 4.357918 AAACACAATCCTGTAGCTCAGT 57.642 40.909 10.86 0.00 42.19 3.41
3699 3834 5.738619 TCTAAACACAATCCTGTAGCTCA 57.261 39.130 0.00 0.00 33.22 4.26
3700 3835 5.064071 GCTTCTAAACACAATCCTGTAGCTC 59.936 44.000 0.00 0.00 33.22 4.09
3701 3836 4.938226 GCTTCTAAACACAATCCTGTAGCT 59.062 41.667 0.00 0.00 33.22 3.32
3703 3838 4.330074 CGGCTTCTAAACACAATCCTGTAG 59.670 45.833 0.00 0.00 33.22 2.74
3704 3839 4.250464 CGGCTTCTAAACACAATCCTGTA 58.750 43.478 0.00 0.00 33.22 2.74
3705 3840 3.074412 CGGCTTCTAAACACAATCCTGT 58.926 45.455 0.00 0.00 35.63 4.00
3708 3843 5.116882 AGATACGGCTTCTAAACACAATCC 58.883 41.667 0.00 0.00 0.00 3.01
3709 3844 6.979238 ACTAGATACGGCTTCTAAACACAATC 59.021 38.462 0.00 0.00 0.00 2.67
3712 3847 5.184479 ACACTAGATACGGCTTCTAAACACA 59.816 40.000 0.00 0.00 0.00 3.72
3713 3848 5.515626 CACACTAGATACGGCTTCTAAACAC 59.484 44.000 0.00 0.00 0.00 3.32
3714 3849 5.647589 CACACTAGATACGGCTTCTAAACA 58.352 41.667 0.00 0.00 0.00 2.83
3715 3850 4.503370 GCACACTAGATACGGCTTCTAAAC 59.497 45.833 0.00 0.00 0.00 2.01
3716 3851 4.679662 GCACACTAGATACGGCTTCTAAA 58.320 43.478 0.00 0.00 0.00 1.85
3717 3852 3.242969 CGCACACTAGATACGGCTTCTAA 60.243 47.826 0.00 0.00 0.00 2.10
3718 3853 2.289820 CGCACACTAGATACGGCTTCTA 59.710 50.000 0.00 0.00 0.00 2.10
3719 3854 1.065701 CGCACACTAGATACGGCTTCT 59.934 52.381 0.00 0.00 0.00 2.85
3721 3856 0.815734 ACGCACACTAGATACGGCTT 59.184 50.000 0.00 0.00 0.00 4.35
3722 3857 0.815734 AACGCACACTAGATACGGCT 59.184 50.000 0.00 0.00 0.00 5.52
3723 3858 2.480224 TAACGCACACTAGATACGGC 57.520 50.000 0.00 0.00 0.00 5.68
3724 3859 5.961395 AAAATAACGCACACTAGATACGG 57.039 39.130 0.00 0.00 0.00 4.02
3725 3860 6.758149 ACAAAAATAACGCACACTAGATACG 58.242 36.000 0.00 0.00 0.00 3.06
3727 3862 8.090250 ACAACAAAAATAACGCACACTAGATA 57.910 30.769 0.00 0.00 0.00 1.98
3728 3863 6.966021 ACAACAAAAATAACGCACACTAGAT 58.034 32.000 0.00 0.00 0.00 1.98
3729 3864 6.366315 ACAACAAAAATAACGCACACTAGA 57.634 33.333 0.00 0.00 0.00 2.43
3737 3872 7.396190 TGGTGATTAACAACAAAAATAACGC 57.604 32.000 0.00 0.00 43.76 4.84
3749 3969 6.197364 ACTTCAACGTTTGGTGATTAACAA 57.803 33.333 0.00 0.00 0.00 2.83
3775 3995 5.706916 CTTGTTCAGAGTTGCAATGCTATT 58.293 37.500 6.82 0.00 0.00 1.73
3792 4012 2.666619 CGCCACTCTGATTTGCTTGTTC 60.667 50.000 0.00 0.00 0.00 3.18
3847 4067 4.225497 CAGGTTTCGATCCTGGGC 57.775 61.111 21.96 0.00 46.03 5.36
3930 6458 2.423373 CCCAATCATACACCCCTGGAAG 60.423 54.545 0.00 0.00 0.00 3.46
3973 6501 1.980232 ACGTCGTAGTGGGCCATGA 60.980 57.895 10.70 2.73 0.00 3.07
3983 6511 0.099082 GAAGAGGAGGCACGTCGTAG 59.901 60.000 0.00 0.00 38.28 3.51
4086 8474 9.956640 AAATTCAGGTTTCCAAAATATATGCAA 57.043 25.926 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.