Multiple sequence alignment - TraesCS6A01G033900

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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 TraesCS6A01G033900 chr6A 100.000 3830 0 0 1 3830 16467521 16471350 0.000000e+00 7073.0
1 TraesCS6A01G033900 chr6A 96.078 51 2 0 3644 3694 16471084 16471134 2.450000e-12 84.2
2 TraesCS6A01G033900 chr6A 96.078 51 2 0 3564 3614 16471164 16471214 2.450000e-12 84.2
3 TraesCS6A01G033900 chr6D 95.254 2128 68 11 901 3024 16233899 16235997 0.000000e+00 3339.0
4 TraesCS6A01G033900 chr6D 91.234 1483 108 8 1387 2847 16247804 16246322 0.000000e+00 1999.0
5 TraesCS6A01G033900 chr6D 85.968 620 37 18 1 581 16233009 16233617 5.440000e-173 617.0
6 TraesCS6A01G033900 chr6D 84.599 474 37 12 3171 3643 16236007 16236445 4.540000e-119 438.0
7 TraesCS6A01G033900 chr6D 90.583 223 11 3 589 803 16233597 16233817 1.740000e-73 287.0
8 TraesCS6A01G033900 chr6D 87.793 213 20 5 3057 3268 16246321 16246114 1.060000e-60 244.0
9 TraesCS6A01G033900 chr6D 94.891 137 5 2 3695 3830 16236433 16236568 3.000000e-51 213.0
10 TraesCS6A01G033900 chr6D 88.435 147 17 0 1024 1170 16253100 16252954 1.090000e-40 178.0
11 TraesCS6A01G033900 chr6D 96.774 62 2 0 802 863 16233843 16233904 1.880000e-18 104.0
12 TraesCS6A01G033900 chr6B 93.086 998 53 5 912 1900 27967040 27968030 0.000000e+00 1447.0
13 TraesCS6A01G033900 chr6B 87.631 574 40 8 2018 2586 27968047 27968594 4.170000e-179 638.0
14 TraesCS6A01G033900 chr6B 91.331 323 24 3 2603 2922 27989079 27989400 4.540000e-119 438.0
15 TraesCS6A01G033900 chr6B 81.726 591 40 27 1 543 27966193 27966763 7.600000e-117 431.0
16 TraesCS6A01G033900 chr6B 86.405 331 29 11 3054 3375 27989399 27989722 7.870000e-92 348.0
17 TraesCS6A01G033900 chr6B 92.908 141 6 3 596 735 27966751 27966888 6.490000e-48 202.0
18 TraesCS6A01G033900 chr6B 93.939 66 4 0 63 128 27953780 27953845 2.430000e-17 100.0
19 TraesCS6A01G033900 chr5D 76.111 1193 241 31 1261 2422 36178432 36179611 5.510000e-163 584.0
20 TraesCS6A01G033900 chr5B 75.689 1197 239 37 1261 2422 27134655 27135834 5.590000e-153 551.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G033900 chr6A 16467521 16471350 3829 False 2413.8 7073 97.385333 1 3830 3 chr6A.!!$F1 3829
1 TraesCS6A01G033900 chr6D 16246114 16247804 1690 True 1121.5 1999 89.513500 1387 3268 2 chr6D.!!$R2 1881
2 TraesCS6A01G033900 chr6D 16233009 16236568 3559 False 833.0 3339 91.344833 1 3830 6 chr6D.!!$F1 3829
3 TraesCS6A01G033900 chr6B 27966193 27968594 2401 False 679.5 1447 88.837750 1 2586 4 chr6B.!!$F2 2585
4 TraesCS6A01G033900 chr6B 27989079 27989722 643 False 393.0 438 88.868000 2603 3375 2 chr6B.!!$F3 772
5 TraesCS6A01G033900 chr5D 36178432 36179611 1179 False 584.0 584 76.111000 1261 2422 1 chr5D.!!$F1 1161
6 TraesCS6A01G033900 chr5B 27134655 27135834 1179 False 551.0 551 75.689000 1261 2422 1 chr5B.!!$F1 1161

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
53 55 0.096976 GCACAATCACGATCCAACGG 59.903 55.0 0.0 0.0 37.61 4.44 F
868 953 0.106519 CCTGTGGGGAATAGGCAAGG 60.107 60.0 0.0 0.0 37.23 3.61 F
910 995 0.519077 CCTGAAACTGAAAGAGGCGC 59.481 55.0 0.0 0.0 37.43 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 1439 1.312815 GCAAGCTGTCCACAAAGACT 58.687 50.000 0.00 0.0 37.66 3.24 R
2787 2953 1.032657 CCGATGGGAGTCTGTCGAGT 61.033 60.000 11.89 0.0 36.25 4.18 R
2840 3006 2.409870 GGCTTCGCCCCTGTTGATG 61.410 63.158 0.00 0.0 44.06 3.07 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
18 19 2.104859 GCGACCCTAGAAAACCGCC 61.105 63.158 0.00 0.00 37.09 6.13
38 40 1.153647 CTTACATCGCTCCCGCACA 60.154 57.895 0.00 0.00 35.30 4.57
53 55 0.096976 GCACAATCACGATCCAACGG 59.903 55.000 0.00 0.00 37.61 4.44
74 86 2.093447 GTGGACGGAAATGATCTGGTCT 60.093 50.000 0.00 0.00 38.87 3.85
208 245 9.403583 ACTCCTCTTGTTTATTTTTGTAAGACA 57.596 29.630 0.00 0.00 0.00 3.41
247 286 8.871686 AACCAGAACATAAAACAGTTCAATTC 57.128 30.769 7.88 0.00 44.94 2.17
260 299 5.239525 ACAGTTCAATTCCAGCTGTCTTAAC 59.760 40.000 13.81 9.02 35.78 2.01
277 316 8.211116 TGTCTTAACCGATTTACAAAAGTGAA 57.789 30.769 0.00 0.00 0.00 3.18
280 319 8.842280 TCTTAACCGATTTACAAAAGTGAACAT 58.158 29.630 0.00 0.00 0.00 2.71
283 322 7.972832 ACCGATTTACAAAAGTGAACATAGA 57.027 32.000 0.00 0.00 0.00 1.98
311 350 9.593134 AGTATGTTTGATTGAGTCACTTAGATC 57.407 33.333 0.00 0.00 36.32 2.75
331 370 6.212235 AGATCTGCAATAACTAGATCACACG 58.788 40.000 13.89 0.00 45.79 4.49
362 401 8.617809 TCGTATTGTTTAATCAAGGGATTTAGC 58.382 33.333 5.29 0.00 40.87 3.09
369 408 7.630242 TTAATCAAGGGATTTAGCAGAACTG 57.370 36.000 0.00 0.00 40.87 3.16
460 504 2.027100 AGAGAGGATTTTCGGGAACACC 60.027 50.000 0.00 0.00 0.00 4.16
526 576 1.337728 ACAGCCCAAAATAAAAGCGCC 60.338 47.619 2.29 0.00 0.00 6.53
705 763 3.207669 CATTCCTGCTCCTGCGCC 61.208 66.667 4.18 0.00 43.34 6.53
765 823 4.959596 GCCGCCGCCTCAGATCTC 62.960 72.222 0.00 0.00 0.00 2.75
831 916 5.221244 GCTTCCAACCCTATTTGCGATTATT 60.221 40.000 0.00 0.00 0.00 1.40
850 935 2.568623 TCCTCCTCTGTTTTGCTTCC 57.431 50.000 0.00 0.00 0.00 3.46
868 953 0.106519 CCTGTGGGGAATAGGCAAGG 60.107 60.000 0.00 0.00 37.23 3.61
872 957 2.291540 TGTGGGGAATAGGCAAGGAAAG 60.292 50.000 0.00 0.00 0.00 2.62
873 958 2.000048 TGGGGAATAGGCAAGGAAAGT 59.000 47.619 0.00 0.00 0.00 2.66
890 975 8.598075 CAAGGAAAGTTGCTAATTTTATGATGC 58.402 33.333 0.00 0.00 0.00 3.91
891 976 7.267857 AGGAAAGTTGCTAATTTTATGATGCC 58.732 34.615 0.00 0.00 0.00 4.40
892 977 6.479990 GGAAAGTTGCTAATTTTATGATGCCC 59.520 38.462 0.00 0.00 0.00 5.36
893 978 6.796785 AAGTTGCTAATTTTATGATGCCCT 57.203 33.333 0.00 0.00 0.00 5.19
894 979 6.152932 AGTTGCTAATTTTATGATGCCCTG 57.847 37.500 0.00 0.00 0.00 4.45
895 980 5.893255 AGTTGCTAATTTTATGATGCCCTGA 59.107 36.000 0.00 0.00 0.00 3.86
896 981 6.380846 AGTTGCTAATTTTATGATGCCCTGAA 59.619 34.615 0.00 0.00 0.00 3.02
897 982 6.788598 TGCTAATTTTATGATGCCCTGAAA 57.211 33.333 0.00 0.00 0.00 2.69
898 983 6.572519 TGCTAATTTTATGATGCCCTGAAAC 58.427 36.000 0.00 0.00 0.00 2.78
899 984 6.380846 TGCTAATTTTATGATGCCCTGAAACT 59.619 34.615 0.00 0.00 0.00 2.66
900 985 6.698766 GCTAATTTTATGATGCCCTGAAACTG 59.301 38.462 0.00 0.00 0.00 3.16
901 986 6.855763 AATTTTATGATGCCCTGAAACTGA 57.144 33.333 0.00 0.00 0.00 3.41
902 987 6.855763 ATTTTATGATGCCCTGAAACTGAA 57.144 33.333 0.00 0.00 0.00 3.02
903 988 6.662865 TTTTATGATGCCCTGAAACTGAAA 57.337 33.333 0.00 0.00 0.00 2.69
904 989 5.902613 TTATGATGCCCTGAAACTGAAAG 57.097 39.130 0.00 0.00 42.29 2.62
905 990 3.507162 TGATGCCCTGAAACTGAAAGA 57.493 42.857 0.00 0.00 37.43 2.52
906 991 3.415212 TGATGCCCTGAAACTGAAAGAG 58.585 45.455 0.00 0.00 37.43 2.85
907 992 2.276732 TGCCCTGAAACTGAAAGAGG 57.723 50.000 0.00 0.00 37.43 3.69
908 993 0.884514 GCCCTGAAACTGAAAGAGGC 59.115 55.000 0.00 0.00 37.43 4.70
909 994 1.160137 CCCTGAAACTGAAAGAGGCG 58.840 55.000 0.00 0.00 37.43 5.52
910 995 0.519077 CCTGAAACTGAAAGAGGCGC 59.481 55.000 0.00 0.00 37.43 6.53
944 1029 6.423905 AGTTTACACATGCTACTGTACTTGTG 59.576 38.462 20.98 20.98 43.68 3.33
973 1058 6.883217 ACTGAACTTTCATAACTCATGCTCAT 59.117 34.615 0.00 0.00 36.46 2.90
1044 1136 4.012374 CAATGGGCAACTATCTGACAAGT 58.988 43.478 0.00 0.00 36.35 3.16
1088 1180 2.422597 TGTCCATGTTAAACCAGCGAG 58.577 47.619 0.00 0.00 0.00 5.03
1089 1181 1.737793 GTCCATGTTAAACCAGCGAGG 59.262 52.381 0.00 0.00 45.67 4.63
1153 1245 2.611225 CCTTCCAGAGGTAGCATGTC 57.389 55.000 0.00 0.00 40.95 3.06
1170 1262 2.229792 TGTCAAGATTGCACACCCTTC 58.770 47.619 0.00 0.00 0.00 3.46
1182 1274 5.782047 TGCACACCCTTCATTTTGATTTAG 58.218 37.500 0.00 0.00 0.00 1.85
1251 1345 4.454678 TGATTCACTGAGCTGAAGTGTTT 58.545 39.130 20.28 12.11 44.42 2.83
1292 1386 8.092521 AGGATGTCTTATGCTCAATTTTATCG 57.907 34.615 0.00 0.00 0.00 2.92
1345 1439 2.048222 CTTGGCGAGCGAGTGGAA 60.048 61.111 0.00 0.00 0.00 3.53
1508 1614 9.691362 GAGGTTAAATTTATGTTTGAGAGCAAA 57.309 29.630 0.00 0.00 41.47 3.68
1895 2010 5.642063 GCACTTGCACTACTTGAAGGTTATA 59.358 40.000 0.00 0.00 41.59 0.98
1947 2062 2.856222 CTGCAAGTCTCTCCACCTTTT 58.144 47.619 0.00 0.00 0.00 2.27
1988 2103 3.379865 TATTGCCCTCCGTCACGCC 62.380 63.158 0.00 0.00 0.00 5.68
2108 2223 5.172934 ACGCTGGATGTTTTAATTCTACGA 58.827 37.500 0.00 0.00 0.00 3.43
2448 2591 8.320295 CGTTACATGCATTTTGAATGGTATTTC 58.680 33.333 0.00 0.00 37.73 2.17
2675 2841 0.706433 ATTGTGGAGAATGCCCCTGT 59.294 50.000 0.00 0.00 0.00 4.00
2749 2915 5.441718 TCCAGATGAAGTAAAGCCAGAAT 57.558 39.130 0.00 0.00 0.00 2.40
2787 2953 4.759793 TGATATGGTTAGAGGCCCTCTA 57.240 45.455 16.71 16.71 41.50 2.43
2815 2981 1.299648 CTCCCATCGGGTGCAAAGA 59.700 57.895 0.00 0.00 44.74 2.52
2884 3050 0.466189 CACCTGCTGGTTTCTGGTGT 60.466 55.000 13.36 0.00 46.05 4.16
2891 3057 0.546122 TGGTTTCTGGTGTGCAGAGT 59.454 50.000 0.00 0.00 0.00 3.24
2921 3087 2.893489 GCTAGGGGCAGAATTAATTGGG 59.107 50.000 5.17 0.00 41.35 4.12
2935 3101 2.816499 ATTGGGGTGCCTAGGGGGAA 62.816 60.000 11.72 0.00 37.23 3.97
2942 3108 0.326238 TGCCTAGGGGGAACGATTCT 60.326 55.000 11.72 0.00 37.23 2.40
2948 3114 1.913419 AGGGGGAACGATTCTTTGCTA 59.087 47.619 0.00 0.00 0.00 3.49
2952 3118 3.369576 GGGGAACGATTCTTTGCTAGACT 60.370 47.826 0.00 0.00 30.90 3.24
2957 3123 2.932614 CGATTCTTTGCTAGACTGGTGG 59.067 50.000 0.00 0.00 30.90 4.61
2968 3134 1.490490 AGACTGGTGGAGTTCTTGCAA 59.510 47.619 0.00 0.00 33.83 4.08
2982 3148 2.050691 CTTGCAAAATCGTTTCGGTGG 58.949 47.619 0.00 0.00 0.00 4.61
2985 3151 1.198178 GCAAAATCGTTTCGGTGGCTA 59.802 47.619 0.00 0.00 0.00 3.93
2986 3152 2.727916 GCAAAATCGTTTCGGTGGCTAG 60.728 50.000 0.00 0.00 0.00 3.42
2989 3155 2.588856 ATCGTTTCGGTGGCTAGGGC 62.589 60.000 0.00 0.00 37.82 5.19
2990 3156 2.818274 GTTTCGGTGGCTAGGGCG 60.818 66.667 0.00 0.00 39.81 6.13
2991 3157 2.998480 TTTCGGTGGCTAGGGCGA 60.998 61.111 0.00 0.00 39.81 5.54
2993 3159 1.906105 TTTCGGTGGCTAGGGCGAAT 61.906 55.000 0.00 0.00 39.81 3.34
3003 3171 0.748005 TAGGGCGAATGGCTTCTTGC 60.748 55.000 0.00 0.00 42.94 4.01
3031 3199 3.435186 GAGCTCCAAACCAGCGCC 61.435 66.667 2.29 0.00 42.14 6.53
3032 3200 3.909086 GAGCTCCAAACCAGCGCCT 62.909 63.158 2.29 0.00 42.14 5.52
3033 3201 3.435186 GCTCCAAACCAGCGCCTC 61.435 66.667 2.29 0.00 0.00 4.70
3034 3202 2.032528 CTCCAAACCAGCGCCTCA 59.967 61.111 2.29 0.00 0.00 3.86
3035 3203 2.281484 TCCAAACCAGCGCCTCAC 60.281 61.111 2.29 0.00 0.00 3.51
3037 3205 3.726517 CAAACCAGCGCCTCACGG 61.727 66.667 2.29 0.00 43.93 4.94
3044 3212 2.431260 GCGCCTCACGGTTCGTTA 60.431 61.111 0.00 0.00 43.93 3.18
3045 3213 2.723719 GCGCCTCACGGTTCGTTAC 61.724 63.158 0.00 0.00 43.93 2.50
3046 3214 1.080974 CGCCTCACGGTTCGTTACT 60.081 57.895 0.00 0.00 38.32 2.24
3047 3215 0.665369 CGCCTCACGGTTCGTTACTT 60.665 55.000 0.00 0.00 38.32 2.24
3048 3216 0.788391 GCCTCACGGTTCGTTACTTG 59.212 55.000 0.00 0.00 38.32 3.16
3049 3217 0.788391 CCTCACGGTTCGTTACTTGC 59.212 55.000 0.00 0.00 38.32 4.01
3050 3218 1.604693 CCTCACGGTTCGTTACTTGCT 60.605 52.381 0.00 0.00 38.32 3.91
3051 3219 1.719780 CTCACGGTTCGTTACTTGCTC 59.280 52.381 0.00 0.00 38.32 4.26
3052 3220 0.788391 CACGGTTCGTTACTTGCTCC 59.212 55.000 0.00 0.00 38.32 4.70
3062 3230 1.600023 TACTTGCTCCGGTGTTTTGG 58.400 50.000 0.00 0.00 0.00 3.28
3068 3236 0.323629 CTCCGGTGTTTTGGGAGCTA 59.676 55.000 0.00 0.00 40.76 3.32
3080 3252 1.770658 TGGGAGCTATGGAAGGACATG 59.229 52.381 0.00 0.00 32.39 3.21
3099 3271 2.952714 GTCTTCAACCAGGCAGCAT 58.047 52.632 0.00 0.00 0.00 3.79
3102 3274 0.957395 CTTCAACCAGGCAGCATCGT 60.957 55.000 0.00 0.00 0.00 3.73
3109 3281 2.268920 GGCAGCATCGTCCTTGGA 59.731 61.111 0.00 0.00 0.00 3.53
3144 3316 1.153823 CGTGTTCTTCGGAGCGGAT 60.154 57.895 0.00 0.00 0.00 4.18
3193 3365 2.932622 GCCTTCTTTCAGTCATCGAGCA 60.933 50.000 0.00 0.00 0.00 4.26
3211 3383 4.441495 CGAGCAGGTGGATGTTGTTAGATA 60.441 45.833 0.00 0.00 0.00 1.98
3212 3384 5.028549 AGCAGGTGGATGTTGTTAGATAG 57.971 43.478 0.00 0.00 0.00 2.08
3214 3386 4.141711 GCAGGTGGATGTTGTTAGATAGGA 60.142 45.833 0.00 0.00 0.00 2.94
3215 3387 5.629133 GCAGGTGGATGTTGTTAGATAGGAA 60.629 44.000 0.00 0.00 0.00 3.36
3219 3391 7.402071 AGGTGGATGTTGTTAGATAGGAAGTTA 59.598 37.037 0.00 0.00 0.00 2.24
3242 3415 9.091784 GTTATATATGATGATGTAGGTGCACTG 57.908 37.037 17.98 0.00 0.00 3.66
3283 3459 5.295787 GCATGATAACGTTTGTATTGGAGGA 59.704 40.000 5.91 0.00 0.00 3.71
3284 3460 6.017109 GCATGATAACGTTTGTATTGGAGGAT 60.017 38.462 5.91 0.00 0.00 3.24
3287 3463 7.757526 TGATAACGTTTGTATTGGAGGATTTG 58.242 34.615 5.91 0.00 0.00 2.32
3306 3482 1.210722 TGTGTCCCTGTGCTGTACAAA 59.789 47.619 0.00 0.00 39.20 2.83
3346 3522 7.038154 TGTCCTTTTGTACATCTTTTCAAGG 57.962 36.000 0.00 0.97 0.00 3.61
3367 3543 3.497584 GGGTTTGAATTGGCAATTTGGGA 60.498 43.478 25.02 10.25 0.00 4.37
3398 3574 2.291465 CCAAGTGTGTGTGAGTGATTGG 59.709 50.000 0.00 0.00 0.00 3.16
3403 3579 2.159028 TGTGTGTGAGTGATTGGAACGA 60.159 45.455 0.00 0.00 0.00 3.85
3448 3624 2.131776 AAAAGTTGTGTTCGGGGACA 57.868 45.000 0.00 0.00 0.00 4.02
3499 3676 6.815089 TGTATTCCAAACAAGCATTTTGTCT 58.185 32.000 0.00 0.00 32.92 3.41
3538 3715 0.771755 GGGAAGAACCAACTCCAGGT 59.228 55.000 0.00 0.00 42.34 4.00
3539 3716 1.271434 GGGAAGAACCAACTCCAGGTC 60.271 57.143 0.00 0.00 38.76 3.85
3540 3717 1.271434 GGAAGAACCAACTCCAGGTCC 60.271 57.143 0.00 0.00 38.76 4.46
3541 3718 1.420138 GAAGAACCAACTCCAGGTCCA 59.580 52.381 0.00 0.00 38.76 4.02
3542 3719 1.059913 AGAACCAACTCCAGGTCCAG 58.940 55.000 0.00 0.00 38.76 3.86
3543 3720 0.036875 GAACCAACTCCAGGTCCAGG 59.963 60.000 0.00 0.00 38.76 4.45
3549 3726 0.192566 ACTCCAGGTCCAGGGTACAA 59.807 55.000 0.00 0.00 0.00 2.41
3575 3752 0.951558 TCAAGGAAGCAAAGAACCGC 59.048 50.000 0.00 0.00 0.00 5.68
3576 3753 0.667993 CAAGGAAGCAAAGAACCGCA 59.332 50.000 0.00 0.00 0.00 5.69
3577 3754 1.066908 CAAGGAAGCAAAGAACCGCAA 59.933 47.619 0.00 0.00 0.00 4.85
3578 3755 0.668535 AGGAAGCAAAGAACCGCAAC 59.331 50.000 0.00 0.00 0.00 4.17
3579 3756 0.668535 GGAAGCAAAGAACCGCAACT 59.331 50.000 0.00 0.00 0.00 3.16
3580 3757 1.600413 GGAAGCAAAGAACCGCAACTG 60.600 52.381 0.00 0.00 0.00 3.16
3581 3758 1.333619 GAAGCAAAGAACCGCAACTGA 59.666 47.619 0.00 0.00 0.00 3.41
3582 3759 1.388547 AGCAAAGAACCGCAACTGAA 58.611 45.000 0.00 0.00 0.00 3.02
3583 3760 1.334869 AGCAAAGAACCGCAACTGAAG 59.665 47.619 0.00 0.00 0.00 3.02
3584 3761 1.758783 CAAAGAACCGCAACTGAAGC 58.241 50.000 0.00 0.00 0.00 3.86
3585 3762 0.668535 AAAGAACCGCAACTGAAGCC 59.331 50.000 0.00 0.00 0.00 4.35
3586 3763 0.179018 AAGAACCGCAACTGAAGCCT 60.179 50.000 0.00 0.00 0.00 4.58
3587 3764 0.886490 AGAACCGCAACTGAAGCCTG 60.886 55.000 0.00 0.00 0.00 4.85
3588 3765 0.884704 GAACCGCAACTGAAGCCTGA 60.885 55.000 0.00 0.00 0.00 3.86
3589 3766 1.166531 AACCGCAACTGAAGCCTGAC 61.167 55.000 0.00 0.00 0.00 3.51
3590 3767 2.328099 CCGCAACTGAAGCCTGACC 61.328 63.158 0.00 0.00 0.00 4.02
3591 3768 2.671177 CGCAACTGAAGCCTGACCG 61.671 63.158 0.00 0.00 0.00 4.79
3603 3780 0.460987 CCTGACCGACAAGGATCAGC 60.461 60.000 0.00 0.00 45.00 4.26
3632 3809 9.698617 GTTTTGACTAACAAGCTTATATAACCG 57.301 33.333 0.00 0.00 39.77 4.44
3633 3810 9.656040 TTTTGACTAACAAGCTTATATAACCGA 57.344 29.630 0.00 0.00 39.77 4.69
3634 3811 9.656040 TTTGACTAACAAGCTTATATAACCGAA 57.344 29.630 0.00 0.00 39.77 4.30
3635 3812 9.656040 TTGACTAACAAGCTTATATAACCGAAA 57.344 29.630 0.00 0.00 34.20 3.46
3636 3813 9.656040 TGACTAACAAGCTTATATAACCGAAAA 57.344 29.630 0.00 0.00 0.00 2.29
3658 3835 3.619233 TCTTTAGCAAAGAACCGCAAC 57.381 42.857 8.34 0.00 44.10 4.17
3659 3836 3.211045 TCTTTAGCAAAGAACCGCAACT 58.789 40.909 8.34 0.00 44.10 3.16
3660 3837 3.003275 TCTTTAGCAAAGAACCGCAACTG 59.997 43.478 8.34 0.00 44.10 3.16
3661 3838 2.248280 TAGCAAAGAACCGCAACTGA 57.752 45.000 0.00 0.00 0.00 3.41
3662 3839 1.388547 AGCAAAGAACCGCAACTGAA 58.611 45.000 0.00 0.00 0.00 3.02
3663 3840 1.334869 AGCAAAGAACCGCAACTGAAG 59.665 47.619 0.00 0.00 0.00 3.02
3664 3841 1.758783 CAAAGAACCGCAACTGAAGC 58.241 50.000 0.00 0.00 0.00 3.86
3665 3842 0.668535 AAAGAACCGCAACTGAAGCC 59.331 50.000 0.00 0.00 0.00 4.35
3666 3843 0.179018 AAGAACCGCAACTGAAGCCT 60.179 50.000 0.00 0.00 0.00 4.58
3667 3844 0.886490 AGAACCGCAACTGAAGCCTG 60.886 55.000 0.00 0.00 0.00 4.85
3668 3845 0.884704 GAACCGCAACTGAAGCCTGA 60.885 55.000 0.00 0.00 0.00 3.86
3669 3846 1.166531 AACCGCAACTGAAGCCTGAC 61.167 55.000 0.00 0.00 0.00 3.51
3670 3847 2.328099 CCGCAACTGAAGCCTGACC 61.328 63.158 0.00 0.00 0.00 4.02
3671 3848 2.671177 CGCAACTGAAGCCTGACCG 61.671 63.158 0.00 0.00 0.00 4.79
3672 3849 1.301716 GCAACTGAAGCCTGACCGA 60.302 57.895 0.00 0.00 0.00 4.69
3673 3850 1.569479 GCAACTGAAGCCTGACCGAC 61.569 60.000 0.00 0.00 0.00 4.79
3674 3851 0.249868 CAACTGAAGCCTGACCGACA 60.250 55.000 0.00 0.00 0.00 4.35
3675 3852 0.468226 AACTGAAGCCTGACCGACAA 59.532 50.000 0.00 0.00 0.00 3.18
3676 3853 0.468226 ACTGAAGCCTGACCGACAAA 59.532 50.000 0.00 0.00 0.00 2.83
3677 3854 1.151668 CTGAAGCCTGACCGACAAAG 58.848 55.000 0.00 0.00 0.00 2.77
3678 3855 0.756294 TGAAGCCTGACCGACAAAGA 59.244 50.000 0.00 0.00 0.00 2.52
3679 3856 1.347707 TGAAGCCTGACCGACAAAGAT 59.652 47.619 0.00 0.00 0.00 2.40
3680 3857 2.003301 GAAGCCTGACCGACAAAGATC 58.997 52.381 0.00 0.00 0.00 2.75
3681 3858 0.976641 AGCCTGACCGACAAAGATCA 59.023 50.000 0.00 0.00 0.00 2.92
3682 3859 1.066573 AGCCTGACCGACAAAGATCAG 60.067 52.381 0.00 0.00 38.65 2.90
3684 3861 2.751166 CTGACCGACAAAGATCAGGT 57.249 50.000 0.00 0.00 35.87 4.00
3685 3862 2.341257 CTGACCGACAAAGATCAGGTG 58.659 52.381 0.00 0.00 35.87 4.00
3686 3863 1.001974 TGACCGACAAAGATCAGGTGG 59.998 52.381 0.00 0.00 35.00 4.61
3687 3864 1.002087 GACCGACAAAGATCAGGTGGT 59.998 52.381 0.00 1.10 35.00 4.16
3688 3865 1.420138 ACCGACAAAGATCAGGTGGTT 59.580 47.619 0.00 0.00 33.37 3.67
3689 3866 2.158667 ACCGACAAAGATCAGGTGGTTT 60.159 45.455 0.00 0.00 33.37 3.27
3690 3867 2.884639 CCGACAAAGATCAGGTGGTTTT 59.115 45.455 0.00 0.00 0.00 2.43
3691 3868 3.304659 CCGACAAAGATCAGGTGGTTTTG 60.305 47.826 0.00 0.00 35.47 2.44
3692 3869 3.563808 CGACAAAGATCAGGTGGTTTTGA 59.436 43.478 7.97 0.00 33.98 2.69
3693 3870 4.554723 CGACAAAGATCAGGTGGTTTTGAC 60.555 45.833 7.97 2.39 33.98 3.18
3694 3871 3.636764 ACAAAGATCAGGTGGTTTTGACC 59.363 43.478 7.97 0.00 33.98 4.02
3695 3872 2.586648 AGATCAGGTGGTTTTGACCC 57.413 50.000 0.00 0.00 33.51 4.46
3696 3873 1.165270 GATCAGGTGGTTTTGACCCG 58.835 55.000 0.00 0.00 33.51 5.28
3732 3909 5.303259 TGCAGGCAAGTATATACATCCAA 57.697 39.130 15.18 1.38 0.00 3.53
3751 3928 9.927081 ACATCCAAAATTAAGACCTGATAATCT 57.073 29.630 0.00 0.00 0.00 2.40
3789 3966 9.533253 CAAAATTTCTGAAGAACCAACAACTAT 57.467 29.630 0.00 0.00 33.13 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 55 2.093447 AGACCAGATCATTTCCGTCCAC 60.093 50.000 0.00 0.00 0.00 4.02
68 80 5.696724 ACGACTTTTCTAAATGTCAGACCAG 59.303 40.000 16.85 6.38 40.87 4.00
74 86 6.277605 TCTGACACGACTTTTCTAAATGTCA 58.722 36.000 16.85 12.48 41.85 3.58
223 262 7.069331 TGGAATTGAACTGTTTTATGTTCTGGT 59.931 33.333 0.00 0.00 41.99 4.00
224 263 7.432869 TGGAATTGAACTGTTTTATGTTCTGG 58.567 34.615 0.00 0.00 41.99 3.86
247 286 4.250464 TGTAAATCGGTTAAGACAGCTGG 58.750 43.478 19.93 0.00 0.00 4.85
260 299 8.251750 TCTCTATGTTCACTTTTGTAAATCGG 57.748 34.615 0.00 0.00 0.00 4.18
277 316 8.753133 TGACTCAATCAAACATACTCTCTATGT 58.247 33.333 0.00 0.00 34.41 2.29
280 319 8.354711 AGTGACTCAATCAAACATACTCTCTA 57.645 34.615 0.00 0.00 39.72 2.43
283 322 8.807118 TCTAAGTGACTCAATCAAACATACTCT 58.193 33.333 0.00 0.00 39.72 3.24
311 350 6.647212 TTTCGTGTGATCTAGTTATTGCAG 57.353 37.500 0.00 0.00 0.00 4.41
421 465 8.824756 TCCTCTCTCTGCTTTAAAGTTCTATA 57.175 34.615 16.38 0.00 0.00 1.31
423 467 7.726033 ATCCTCTCTCTGCTTTAAAGTTCTA 57.274 36.000 16.38 1.15 0.00 2.10
424 468 6.619329 ATCCTCTCTCTGCTTTAAAGTTCT 57.381 37.500 16.38 0.00 0.00 3.01
526 576 5.783111 ACAAAGAAAAGGATTGATTTCCCG 58.217 37.500 0.00 0.00 36.44 5.14
593 643 6.419484 ACGGAGGAAAAAGGATTGATTTTT 57.581 33.333 0.00 0.00 41.32 1.94
594 644 6.223120 CAACGGAGGAAAAAGGATTGATTTT 58.777 36.000 0.00 0.00 0.00 1.82
595 645 5.783111 CAACGGAGGAAAAAGGATTGATTT 58.217 37.500 0.00 0.00 0.00 2.17
596 646 4.321974 GCAACGGAGGAAAAAGGATTGATT 60.322 41.667 0.00 0.00 0.00 2.57
597 647 3.193479 GCAACGGAGGAAAAAGGATTGAT 59.807 43.478 0.00 0.00 0.00 2.57
705 763 3.596459 TTCTGGGGAGGGAAGGGGG 62.596 68.421 0.00 0.00 0.00 5.40
711 769 1.279025 CCGGAATTTCTGGGGAGGGA 61.279 60.000 15.47 0.00 39.28 4.20
712 770 1.227383 CCGGAATTTCTGGGGAGGG 59.773 63.158 15.47 0.00 39.28 4.30
765 823 4.500837 CGTCGGAATAATTGACTGACTGAG 59.499 45.833 13.96 0.00 37.66 3.35
831 916 2.057922 AGGAAGCAAAACAGAGGAGGA 58.942 47.619 0.00 0.00 0.00 3.71
850 935 0.918983 TCCTTGCCTATTCCCCACAG 59.081 55.000 0.00 0.00 0.00 3.66
863 948 8.598075 CATCATAAAATTAGCAACTTTCCTTGC 58.402 33.333 0.00 0.00 45.93 4.01
868 953 7.223387 CAGGGCATCATAAAATTAGCAACTTTC 59.777 37.037 0.00 0.00 0.00 2.62
872 957 6.147864 TCAGGGCATCATAAAATTAGCAAC 57.852 37.500 0.00 0.00 0.00 4.17
873 958 6.788598 TTCAGGGCATCATAAAATTAGCAA 57.211 33.333 0.00 0.00 0.00 3.91
876 961 7.999679 TCAGTTTCAGGGCATCATAAAATTAG 58.000 34.615 0.00 0.00 0.00 1.73
877 962 7.953005 TCAGTTTCAGGGCATCATAAAATTA 57.047 32.000 0.00 0.00 0.00 1.40
878 963 6.855763 TCAGTTTCAGGGCATCATAAAATT 57.144 33.333 0.00 0.00 0.00 1.82
879 964 6.855763 TTCAGTTTCAGGGCATCATAAAAT 57.144 33.333 0.00 0.00 0.00 1.82
880 965 6.493115 TCTTTCAGTTTCAGGGCATCATAAAA 59.507 34.615 0.00 0.00 0.00 1.52
881 966 6.009589 TCTTTCAGTTTCAGGGCATCATAAA 58.990 36.000 0.00 0.00 0.00 1.40
882 967 5.569355 TCTTTCAGTTTCAGGGCATCATAA 58.431 37.500 0.00 0.00 0.00 1.90
883 968 5.178096 TCTTTCAGTTTCAGGGCATCATA 57.822 39.130 0.00 0.00 0.00 2.15
884 969 4.015084 CTCTTTCAGTTTCAGGGCATCAT 58.985 43.478 0.00 0.00 0.00 2.45
885 970 3.415212 CTCTTTCAGTTTCAGGGCATCA 58.585 45.455 0.00 0.00 0.00 3.07
886 971 2.751806 CCTCTTTCAGTTTCAGGGCATC 59.248 50.000 0.00 0.00 0.00 3.91
887 972 2.800250 CCTCTTTCAGTTTCAGGGCAT 58.200 47.619 0.00 0.00 0.00 4.40
888 973 1.819305 GCCTCTTTCAGTTTCAGGGCA 60.819 52.381 0.00 0.00 38.35 5.36
889 974 0.884514 GCCTCTTTCAGTTTCAGGGC 59.115 55.000 0.00 0.00 0.00 5.19
890 975 1.160137 CGCCTCTTTCAGTTTCAGGG 58.840 55.000 0.00 0.00 0.00 4.45
891 976 0.519077 GCGCCTCTTTCAGTTTCAGG 59.481 55.000 0.00 0.00 0.00 3.86
892 977 0.519077 GGCGCCTCTTTCAGTTTCAG 59.481 55.000 22.15 0.00 0.00 3.02
893 978 1.227999 CGGCGCCTCTTTCAGTTTCA 61.228 55.000 26.68 0.00 0.00 2.69
894 979 0.949105 TCGGCGCCTCTTTCAGTTTC 60.949 55.000 26.68 0.00 0.00 2.78
895 980 0.534203 TTCGGCGCCTCTTTCAGTTT 60.534 50.000 26.68 0.00 0.00 2.66
896 981 0.534203 TTTCGGCGCCTCTTTCAGTT 60.534 50.000 26.68 0.00 0.00 3.16
897 982 0.321653 ATTTCGGCGCCTCTTTCAGT 60.322 50.000 26.68 0.00 0.00 3.41
898 983 0.804989 AATTTCGGCGCCTCTTTCAG 59.195 50.000 26.68 6.92 0.00 3.02
899 984 0.521291 CAATTTCGGCGCCTCTTTCA 59.479 50.000 26.68 2.17 0.00 2.69
900 985 0.802494 TCAATTTCGGCGCCTCTTTC 59.198 50.000 26.68 0.00 0.00 2.62
901 986 0.804989 CTCAATTTCGGCGCCTCTTT 59.195 50.000 26.68 9.89 0.00 2.52
902 987 0.321653 ACTCAATTTCGGCGCCTCTT 60.322 50.000 26.68 9.33 0.00 2.85
903 988 0.321653 AACTCAATTTCGGCGCCTCT 60.322 50.000 26.68 2.62 0.00 3.69
904 989 0.521735 AAACTCAATTTCGGCGCCTC 59.478 50.000 26.68 0.00 0.00 4.70
905 990 1.467342 GTAAACTCAATTTCGGCGCCT 59.533 47.619 26.68 1.35 0.00 5.52
906 991 1.198178 TGTAAACTCAATTTCGGCGCC 59.802 47.619 19.07 19.07 0.00 6.53
907 992 2.239201 GTGTAAACTCAATTTCGGCGC 58.761 47.619 0.00 0.00 0.00 6.53
908 993 3.529634 TGTGTAAACTCAATTTCGGCG 57.470 42.857 0.00 0.00 0.00 6.46
909 994 3.608073 GCATGTGTAAACTCAATTTCGGC 59.392 43.478 0.00 0.00 0.00 5.54
910 995 5.046910 AGCATGTGTAAACTCAATTTCGG 57.953 39.130 0.00 0.00 0.00 4.30
944 1029 6.798959 GCATGAGTTATGAAAGTTCAGTCAAC 59.201 38.462 0.00 4.43 41.08 3.18
973 1058 7.099764 GTGACATCAGAGAAACAAGAGGATAA 58.900 38.462 0.00 0.00 0.00 1.75
1044 1136 2.696775 TCCTCTGGTTTGGTTCCTGTA 58.303 47.619 0.00 0.00 0.00 2.74
1116 1208 7.228706 TCTGGAAGGTCTTGAAGTTTAATGTTC 59.771 37.037 0.00 0.00 0.00 3.18
1153 1245 3.947910 AATGAAGGGTGTGCAATCTTG 57.052 42.857 0.00 0.00 0.00 3.02
1251 1345 5.186797 AGACATCCTTCAACAACACCAAAAA 59.813 36.000 0.00 0.00 0.00 1.94
1292 1386 1.683385 ACCTCTTTTGCAGGCAGTTTC 59.317 47.619 0.00 0.00 33.84 2.78
1345 1439 1.312815 GCAAGCTGTCCACAAAGACT 58.687 50.000 0.00 0.00 37.66 3.24
1508 1614 5.171476 CAATTGTCGAGGTGATGAACTAGT 58.829 41.667 0.00 0.00 0.00 2.57
1895 2010 9.427821 AACTCTATCTTGGTTATCTCACAGTAT 57.572 33.333 0.00 0.00 0.00 2.12
1947 2062 6.474140 AGGTATGTATGTTCCATCGTACAA 57.526 37.500 0.00 0.00 41.23 2.41
2139 2256 4.911390 AGTTGCACAAGCTAACTCCTTAT 58.089 39.130 0.00 0.00 42.74 1.73
2146 2263 4.913924 CAGAAATGAGTTGCACAAGCTAAC 59.086 41.667 0.00 0.00 42.74 2.34
2448 2591 4.672413 GCAGAGAGAAACAATGTTTGAACG 59.328 41.667 16.78 1.26 0.00 3.95
2589 2755 5.506483 CGAGACACGGATATTCTTCAGATGT 60.506 44.000 0.00 0.00 38.46 3.06
2675 2841 2.969262 TCCACAGTCACAACCTGTATCA 59.031 45.455 0.00 0.00 41.10 2.15
2749 2915 5.179929 CCATATCAAGCGCATCACTATTGAA 59.820 40.000 11.47 0.92 34.61 2.69
2787 2953 1.032657 CCGATGGGAGTCTGTCGAGT 61.033 60.000 11.89 0.00 36.25 4.18
2840 3006 2.409870 GGCTTCGCCCCTGTTGATG 61.410 63.158 0.00 0.00 44.06 3.07
2921 3087 1.632965 AATCGTTCCCCCTAGGCACC 61.633 60.000 2.05 0.00 34.51 5.01
2935 3101 3.589988 CACCAGTCTAGCAAAGAATCGT 58.410 45.455 0.00 0.00 35.47 3.73
2942 3108 2.972713 AGAACTCCACCAGTCTAGCAAA 59.027 45.455 0.00 0.00 32.30 3.68
2948 3114 1.131638 TGCAAGAACTCCACCAGTCT 58.868 50.000 0.00 0.00 32.30 3.24
2952 3118 2.293122 CGATTTTGCAAGAACTCCACCA 59.707 45.455 0.00 0.00 0.00 4.17
2957 3123 3.664025 CCGAAACGATTTTGCAAGAACTC 59.336 43.478 0.00 0.00 0.00 3.01
2968 3134 1.677820 CCCTAGCCACCGAAACGATTT 60.678 52.381 0.00 0.00 0.00 2.17
2982 3148 0.464554 AAGAAGCCATTCGCCCTAGC 60.465 55.000 0.00 0.00 40.58 3.42
2985 3151 2.048603 GCAAGAAGCCATTCGCCCT 61.049 57.895 0.00 0.00 40.58 5.19
2986 3152 2.491621 GCAAGAAGCCATTCGCCC 59.508 61.111 0.00 0.00 40.58 6.13
3031 3199 1.719780 GAGCAAGTAACGAACCGTGAG 59.280 52.381 0.00 0.00 39.99 3.51
3032 3200 1.603678 GGAGCAAGTAACGAACCGTGA 60.604 52.381 0.00 0.00 39.99 4.35
3033 3201 0.788391 GGAGCAAGTAACGAACCGTG 59.212 55.000 0.00 0.00 39.99 4.94
3034 3202 0.665369 CGGAGCAAGTAACGAACCGT 60.665 55.000 0.00 0.00 43.97 4.83
3035 3203 1.349259 CCGGAGCAAGTAACGAACCG 61.349 60.000 0.00 0.00 38.83 4.44
3036 3204 0.320160 ACCGGAGCAAGTAACGAACC 60.320 55.000 9.46 0.00 0.00 3.62
3037 3205 0.788391 CACCGGAGCAAGTAACGAAC 59.212 55.000 9.46 0.00 0.00 3.95
3038 3206 0.390124 ACACCGGAGCAAGTAACGAA 59.610 50.000 9.46 0.00 0.00 3.85
3039 3207 0.390124 AACACCGGAGCAAGTAACGA 59.610 50.000 9.46 0.00 0.00 3.85
3040 3208 1.223187 AAACACCGGAGCAAGTAACG 58.777 50.000 9.46 0.00 0.00 3.18
3041 3209 2.287368 CCAAAACACCGGAGCAAGTAAC 60.287 50.000 9.46 0.00 0.00 2.50
3042 3210 1.950909 CCAAAACACCGGAGCAAGTAA 59.049 47.619 9.46 0.00 0.00 2.24
3043 3211 1.600023 CCAAAACACCGGAGCAAGTA 58.400 50.000 9.46 0.00 0.00 2.24
3044 3212 1.106944 CCCAAAACACCGGAGCAAGT 61.107 55.000 9.46 0.00 0.00 3.16
3045 3213 0.821711 TCCCAAAACACCGGAGCAAG 60.822 55.000 9.46 0.00 0.00 4.01
3046 3214 0.821711 CTCCCAAAACACCGGAGCAA 60.822 55.000 9.46 0.00 37.00 3.91
3047 3215 1.228124 CTCCCAAAACACCGGAGCA 60.228 57.895 9.46 0.00 37.00 4.26
3048 3216 3.668386 CTCCCAAAACACCGGAGC 58.332 61.111 9.46 0.00 37.00 4.70
3049 3217 0.323629 TAGCTCCCAAAACACCGGAG 59.676 55.000 9.46 1.26 45.12 4.63
3050 3218 0.988832 ATAGCTCCCAAAACACCGGA 59.011 50.000 9.46 0.00 0.00 5.14
3051 3219 1.094785 CATAGCTCCCAAAACACCGG 58.905 55.000 0.00 0.00 0.00 5.28
3052 3220 1.094785 CCATAGCTCCCAAAACACCG 58.905 55.000 0.00 0.00 0.00 4.94
3062 3230 1.771255 ACCATGTCCTTCCATAGCTCC 59.229 52.381 0.00 0.00 0.00 4.70
3068 3236 3.690460 GTTGAAGACCATGTCCTTCCAT 58.310 45.455 16.77 0.00 32.18 3.41
3093 3265 0.809241 CTCTCCAAGGACGATGCTGC 60.809 60.000 0.00 0.00 0.00 5.25
3099 3271 0.034380 ACCGATCTCTCCAAGGACGA 60.034 55.000 0.00 0.00 0.00 4.20
3102 3274 0.335019 TGGACCGATCTCTCCAAGGA 59.665 55.000 5.89 0.00 33.39 3.36
3109 3281 0.395862 ACGACCATGGACCGATCTCT 60.396 55.000 28.29 10.51 0.00 3.10
3144 3316 0.179111 CGATACGAAGAAGCCCAGCA 60.179 55.000 0.00 0.00 0.00 4.41
3193 3365 5.726793 ACTTCCTATCTAACAACATCCACCT 59.273 40.000 0.00 0.00 0.00 4.00
3212 3384 9.319143 GCACCTACATCATCATATATAACTTCC 57.681 37.037 0.00 0.00 0.00 3.46
3214 3386 9.658799 GTGCACCTACATCATCATATATAACTT 57.341 33.333 5.22 0.00 0.00 2.66
3215 3387 9.040259 AGTGCACCTACATCATCATATATAACT 57.960 33.333 14.63 0.00 0.00 2.24
3219 3391 7.250032 ACAGTGCACCTACATCATCATATAT 57.750 36.000 14.63 0.00 0.00 0.86
3242 3415 5.666969 TCATGCTATATAAACGCACCAAC 57.333 39.130 0.00 0.00 36.37 3.77
3254 3430 9.719355 TCCAATACAAACGTTATCATGCTATAT 57.281 29.630 0.00 0.00 0.00 0.86
3283 3459 2.158682 TGTACAGCACAGGGACACAAAT 60.159 45.455 0.00 0.00 31.89 2.32
3284 3460 1.210722 TGTACAGCACAGGGACACAAA 59.789 47.619 0.00 0.00 31.89 2.83
3287 3463 1.961793 TTTGTACAGCACAGGGACAC 58.038 50.000 0.00 0.00 38.72 3.67
3316 3492 9.750125 GAAAAGATGTACAAAAGGACAAGATTT 57.250 29.630 0.00 0.00 0.00 2.17
3346 3522 3.749226 TCCCAAATTGCCAATTCAAACC 58.251 40.909 2.61 0.00 0.00 3.27
3367 3543 3.683822 CACACACACTTGGCAAATTTGTT 59.316 39.130 19.03 0.00 0.00 2.83
3398 3574 9.297586 TCACAACTGATGTATATTAACTCGTTC 57.702 33.333 0.00 0.00 41.46 3.95
3428 3604 2.448453 TGTCCCCGAACACAACTTTTT 58.552 42.857 0.00 0.00 0.00 1.94
3429 3605 2.131776 TGTCCCCGAACACAACTTTT 57.868 45.000 0.00 0.00 0.00 2.27
3431 3607 2.131776 TTTGTCCCCGAACACAACTT 57.868 45.000 0.00 0.00 32.19 2.66
3432 3608 2.358322 ATTTGTCCCCGAACACAACT 57.642 45.000 0.00 0.00 32.19 3.16
3441 3617 4.314740 TTTTCTCAACAATTTGTCCCCG 57.685 40.909 1.83 0.00 34.02 5.73
3488 3665 7.521871 AGAATTTCTTCTCAGACAAAATGCT 57.478 32.000 0.00 0.00 37.09 3.79
3575 3752 0.249868 TGTCGGTCAGGCTTCAGTTG 60.250 55.000 0.00 0.00 0.00 3.16
3576 3753 0.468226 TTGTCGGTCAGGCTTCAGTT 59.532 50.000 0.00 0.00 0.00 3.16
3577 3754 0.034059 CTTGTCGGTCAGGCTTCAGT 59.966 55.000 0.00 0.00 0.00 3.41
3578 3755 0.671781 CCTTGTCGGTCAGGCTTCAG 60.672 60.000 0.00 0.00 0.00 3.02
3579 3756 1.118965 TCCTTGTCGGTCAGGCTTCA 61.119 55.000 0.00 0.00 0.00 3.02
3580 3757 0.250513 ATCCTTGTCGGTCAGGCTTC 59.749 55.000 0.00 0.00 0.00 3.86
3581 3758 0.250513 GATCCTTGTCGGTCAGGCTT 59.749 55.000 0.00 0.00 0.00 4.35
3582 3759 0.904865 TGATCCTTGTCGGTCAGGCT 60.905 55.000 0.00 0.00 0.00 4.58
3583 3760 0.460987 CTGATCCTTGTCGGTCAGGC 60.461 60.000 0.00 0.00 37.32 4.85
3584 3761 0.460987 GCTGATCCTTGTCGGTCAGG 60.461 60.000 1.36 0.00 39.39 3.86
3585 3762 0.534412 AGCTGATCCTTGTCGGTCAG 59.466 55.000 0.00 0.00 40.70 3.51
3586 3763 0.247460 CAGCTGATCCTTGTCGGTCA 59.753 55.000 8.42 0.00 0.00 4.02
3587 3764 0.460987 CCAGCTGATCCTTGTCGGTC 60.461 60.000 17.39 0.00 0.00 4.79
3588 3765 1.194781 ACCAGCTGATCCTTGTCGGT 61.195 55.000 17.39 0.00 0.00 4.69
3589 3766 0.036010 AACCAGCTGATCCTTGTCGG 60.036 55.000 17.39 0.00 0.00 4.79
3590 3767 1.813513 AAACCAGCTGATCCTTGTCG 58.186 50.000 17.39 0.00 0.00 4.35
3591 3768 3.057946 GTCAAAACCAGCTGATCCTTGTC 60.058 47.826 17.39 7.20 0.00 3.18
3632 3809 5.689961 TGCGGTTCTTTGCTAAAGATTTTTC 59.310 36.000 10.72 3.56 46.15 2.29
3633 3810 5.596845 TGCGGTTCTTTGCTAAAGATTTTT 58.403 33.333 10.72 0.00 46.15 1.94
3634 3811 5.195001 TGCGGTTCTTTGCTAAAGATTTT 57.805 34.783 10.72 0.00 46.15 1.82
3635 3812 4.846779 TGCGGTTCTTTGCTAAAGATTT 57.153 36.364 10.72 0.00 46.15 2.17
3636 3813 4.278419 AGTTGCGGTTCTTTGCTAAAGATT 59.722 37.500 10.72 0.00 46.15 2.40
3637 3814 3.821033 AGTTGCGGTTCTTTGCTAAAGAT 59.179 39.130 10.72 0.00 46.15 2.40
3638 3815 3.003275 CAGTTGCGGTTCTTTGCTAAAGA 59.997 43.478 7.09 7.09 45.30 2.52
3639 3816 3.003275 TCAGTTGCGGTTCTTTGCTAAAG 59.997 43.478 0.00 0.00 39.88 1.85
3640 3817 2.946329 TCAGTTGCGGTTCTTTGCTAAA 59.054 40.909 0.00 0.00 0.00 1.85
3641 3818 2.566913 TCAGTTGCGGTTCTTTGCTAA 58.433 42.857 0.00 0.00 0.00 3.09
3642 3819 2.248280 TCAGTTGCGGTTCTTTGCTA 57.752 45.000 0.00 0.00 0.00 3.49
3643 3820 1.334869 CTTCAGTTGCGGTTCTTTGCT 59.665 47.619 0.00 0.00 0.00 3.91
3644 3821 1.758783 CTTCAGTTGCGGTTCTTTGC 58.241 50.000 0.00 0.00 0.00 3.68
3645 3822 1.600413 GGCTTCAGTTGCGGTTCTTTG 60.600 52.381 0.00 0.00 0.00 2.77
3646 3823 0.668535 GGCTTCAGTTGCGGTTCTTT 59.331 50.000 0.00 0.00 0.00 2.52
3647 3824 0.179018 AGGCTTCAGTTGCGGTTCTT 60.179 50.000 0.00 0.00 0.00 2.52
3648 3825 0.886490 CAGGCTTCAGTTGCGGTTCT 60.886 55.000 0.00 0.00 0.00 3.01
3649 3826 0.884704 TCAGGCTTCAGTTGCGGTTC 60.885 55.000 0.00 0.00 0.00 3.62
3650 3827 1.148273 TCAGGCTTCAGTTGCGGTT 59.852 52.632 0.00 0.00 0.00 4.44
3651 3828 1.598130 GTCAGGCTTCAGTTGCGGT 60.598 57.895 0.00 0.00 0.00 5.68
3652 3829 2.328099 GGTCAGGCTTCAGTTGCGG 61.328 63.158 0.00 0.00 0.00 5.69
3653 3830 2.671177 CGGTCAGGCTTCAGTTGCG 61.671 63.158 0.00 0.00 0.00 4.85
3654 3831 1.301716 TCGGTCAGGCTTCAGTTGC 60.302 57.895 0.00 0.00 0.00 4.17
3655 3832 0.249868 TGTCGGTCAGGCTTCAGTTG 60.250 55.000 0.00 0.00 0.00 3.16
3656 3833 0.468226 TTGTCGGTCAGGCTTCAGTT 59.532 50.000 0.00 0.00 0.00 3.16
3657 3834 0.468226 TTTGTCGGTCAGGCTTCAGT 59.532 50.000 0.00 0.00 0.00 3.41
3658 3835 1.151668 CTTTGTCGGTCAGGCTTCAG 58.848 55.000 0.00 0.00 0.00 3.02
3659 3836 0.756294 TCTTTGTCGGTCAGGCTTCA 59.244 50.000 0.00 0.00 0.00 3.02
3660 3837 2.003301 GATCTTTGTCGGTCAGGCTTC 58.997 52.381 0.00 0.00 0.00 3.86
3661 3838 1.347707 TGATCTTTGTCGGTCAGGCTT 59.652 47.619 0.00 0.00 0.00 4.35
3662 3839 0.976641 TGATCTTTGTCGGTCAGGCT 59.023 50.000 0.00 0.00 0.00 4.58
3663 3840 1.363744 CTGATCTTTGTCGGTCAGGC 58.636 55.000 0.00 0.00 35.58 4.85
3665 3842 2.341257 CACCTGATCTTTGTCGGTCAG 58.659 52.381 0.00 0.00 38.20 3.51
3666 3843 1.001974 CCACCTGATCTTTGTCGGTCA 59.998 52.381 0.00 0.00 0.00 4.02
3667 3844 1.002087 ACCACCTGATCTTTGTCGGTC 59.998 52.381 0.00 0.00 0.00 4.79
3668 3845 1.056660 ACCACCTGATCTTTGTCGGT 58.943 50.000 0.00 0.00 0.00 4.69
3669 3846 2.185004 AACCACCTGATCTTTGTCGG 57.815 50.000 0.00 0.00 0.00 4.79
3670 3847 3.563808 TCAAAACCACCTGATCTTTGTCG 59.436 43.478 0.00 0.00 0.00 4.35
3671 3848 4.261614 GGTCAAAACCACCTGATCTTTGTC 60.262 45.833 0.00 0.00 45.68 3.18
3672 3849 3.636764 GGTCAAAACCACCTGATCTTTGT 59.363 43.478 0.00 0.00 45.68 2.83
3673 3850 4.243007 GGTCAAAACCACCTGATCTTTG 57.757 45.455 0.00 0.00 45.68 2.77
3674 3851 7.909739 TTCGGGTCAAAACCACCTGATCTTT 62.910 44.000 1.20 0.00 46.68 2.52
3675 3852 6.515683 TTCGGGTCAAAACCACCTGATCTT 62.516 45.833 1.20 0.00 46.68 2.40
3676 3853 5.087281 TTCGGGTCAAAACCACCTGATCT 62.087 47.826 1.20 0.00 46.68 2.75
3677 3854 2.812613 TTCGGGTCAAAACCACCTGATC 60.813 50.000 1.20 0.00 46.68 2.92
3678 3855 1.144093 TTCGGGTCAAAACCACCTGAT 59.856 47.619 1.20 0.00 46.68 2.90
3685 3862 5.503357 GCAAAAGATTTTTCGGGTCAAAACC 60.503 40.000 0.00 0.00 45.65 3.27
3686 3863 5.293324 AGCAAAAGATTTTTCGGGTCAAAAC 59.707 36.000 0.00 0.00 0.00 2.43
3687 3864 5.293079 CAGCAAAAGATTTTTCGGGTCAAAA 59.707 36.000 0.00 0.00 0.00 2.44
3688 3865 4.808364 CAGCAAAAGATTTTTCGGGTCAAA 59.192 37.500 0.00 0.00 0.00 2.69
3689 3866 4.367450 CAGCAAAAGATTTTTCGGGTCAA 58.633 39.130 0.00 0.00 0.00 3.18
3690 3867 3.798548 GCAGCAAAAGATTTTTCGGGTCA 60.799 43.478 0.00 0.00 0.00 4.02
3691 3868 2.731451 GCAGCAAAAGATTTTTCGGGTC 59.269 45.455 0.00 0.00 0.00 4.46
3692 3869 2.102252 TGCAGCAAAAGATTTTTCGGGT 59.898 40.909 0.00 0.00 0.00 5.28
3693 3870 2.733026 CTGCAGCAAAAGATTTTTCGGG 59.267 45.455 0.00 0.00 0.00 5.14
3694 3871 2.733026 CCTGCAGCAAAAGATTTTTCGG 59.267 45.455 8.66 0.00 0.00 4.30
3695 3872 2.156310 GCCTGCAGCAAAAGATTTTTCG 59.844 45.455 8.66 0.00 42.97 3.46
3696 3873 3.800929 GCCTGCAGCAAAAGATTTTTC 57.199 42.857 8.66 0.00 42.97 2.29
3750 3927 6.544622 TCAGAAATTTTGTGCAAGCAAAAAG 58.455 32.000 16.36 7.29 46.91 2.27
3751 3928 6.492007 TCAGAAATTTTGTGCAAGCAAAAA 57.508 29.167 16.36 6.30 46.91 1.94
3789 3966 7.549134 GGTGATCAAAACTGTGAGATATGTGTA 59.451 37.037 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.