Multiple sequence alignment - TraesCS4B01G120700

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G120700 chr4B 100.000 3590 0 0 1 3590 142429961 142433550 0.000000e+00 6630.0
1 TraesCS4B01G120700 chr4A 96.007 1653 65 1 922 2574 476346734 476345083 0.000000e+00 2686.0
2 TraesCS4B01G120700 chr4A 88.189 508 24 19 2991 3475 476344404 476343910 1.120000e-159 573.0
3 TraesCS4B01G120700 chr4A 91.254 343 14 5 2576 2903 476345027 476344686 1.520000e-123 453.0
4 TraesCS4B01G120700 chr4D 95.384 1668 53 12 909 2574 100199436 100201081 0.000000e+00 2632.0
5 TraesCS4B01G120700 chr4D 88.218 348 18 6 2576 2903 100201136 100201480 9.340000e-106 394.0
6 TraesCS4B01G120700 chr4D 81.720 372 47 10 3145 3511 100202789 100203144 1.260000e-74 291.0
7 TraesCS4B01G120700 chr4D 97.333 75 2 0 3080 3154 100201708 100201782 1.050000e-25 128.0
8 TraesCS4B01G120700 chr5B 94.150 906 37 3 6 900 390716905 390716005 0.000000e+00 1365.0
9 TraesCS4B01G120700 chr5B 93.617 47 1 2 3473 3517 337468027 337467981 6.430000e-08 69.4
10 TraesCS4B01G120700 chr3A 93.894 868 42 3 41 897 314612443 314613310 0.000000e+00 1299.0
11 TraesCS4B01G120700 chr3A 91.398 93 5 3 3500 3590 337118842 337118933 1.350000e-24 124.0
12 TraesCS4B01G120700 chr3A 95.238 42 1 1 3470 3511 102108177 102108217 8.320000e-07 65.8
13 TraesCS4B01G120700 chr3A 87.500 56 5 2 3457 3511 436662165 436662111 2.990000e-06 63.9
14 TraesCS4B01G120700 chr2A 93.277 833 42 3 77 896 729420369 729419538 0.000000e+00 1216.0
15 TraesCS4B01G120700 chr2A 97.561 41 1 0 3471 3511 185729102 185729142 1.790000e-08 71.3
16 TraesCS4B01G120700 chr3D 91.941 819 47 3 91 897 94841800 94842611 0.000000e+00 1129.0
17 TraesCS4B01G120700 chr3D 93.666 521 19 3 387 897 72269166 72269682 0.000000e+00 767.0
18 TraesCS4B01G120700 chr3D 95.562 338 15 0 6 343 72268826 72269163 3.150000e-150 542.0
19 TraesCS4B01G120700 chr3D 96.296 81 3 0 3510 3590 457861078 457861158 2.250000e-27 134.0
20 TraesCS4B01G120700 chr3D 95.556 45 0 2 3468 3511 436459803 436459760 1.790000e-08 71.3
21 TraesCS4B01G120700 chr1A 89.699 864 71 7 43 894 525908310 525907453 0.000000e+00 1086.0
22 TraesCS4B01G120700 chr6A 92.331 652 39 2 247 887 504492590 504491939 0.000000e+00 917.0
23 TraesCS4B01G120700 chr6A 93.839 211 10 1 41 251 504617987 504617780 7.480000e-82 315.0
24 TraesCS4B01G120700 chr6A 90.741 54 1 3 3459 3511 520842714 520842764 6.430000e-08 69.4
25 TraesCS4B01G120700 chr1D 96.296 81 2 1 3511 3590 343523006 343523086 8.090000e-27 132.0
26 TraesCS4B01G120700 chr1D 96.296 81 2 1 3511 3590 343795550 343795470 8.090000e-27 132.0
27 TraesCS4B01G120700 chr1D 92.391 92 4 2 3500 3590 336628467 336628378 1.050000e-25 128.0
28 TraesCS4B01G120700 chr7D 95.181 83 3 1 3509 3590 21265953 21265871 2.910000e-26 130.0
29 TraesCS4B01G120700 chr7D 91.304 92 4 2 3500 3590 233356689 233356601 4.870000e-24 122.0
30 TraesCS4B01G120700 chr7B 94.118 85 3 2 3507 3590 615182600 615182517 1.050000e-25 128.0
31 TraesCS4B01G120700 chr6B 92.308 91 6 1 3501 3590 426136859 426136949 1.050000e-25 128.0
32 TraesCS4B01G120700 chr6B 84.848 66 10 0 1494 1559 643436255 643436190 2.310000e-07 67.6
33 TraesCS4B01G120700 chr1B 90.385 52 3 2 3460 3511 61526013 61525964 2.310000e-07 67.6
34 TraesCS4B01G120700 chr3B 85.246 61 7 2 3469 3529 730168890 730168832 1.080000e-05 62.1
35 TraesCS4B01G120700 chr2B 85.246 61 7 2 3472 3532 28905573 28905515 1.080000e-05 62.1


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 TraesCS4B01G120700 chr4B 142429961 142433550 3589 False 6630.000000 6630 100.000000 1 3590 1 chr4B.!!$F1 3589
1 TraesCS4B01G120700 chr4A 476343910 476346734 2824 True 1237.333333 2686 91.816667 922 3475 3 chr4A.!!$R1 2553
2 TraesCS4B01G120700 chr4D 100199436 100203144 3708 False 861.250000 2632 90.663750 909 3511 4 chr4D.!!$F1 2602
3 TraesCS4B01G120700 chr5B 390716005 390716905 900 True 1365.000000 1365 94.150000 6 900 1 chr5B.!!$R2 894
4 TraesCS4B01G120700 chr3A 314612443 314613310 867 False 1299.000000 1299 93.894000 41 897 1 chr3A.!!$F2 856
5 TraesCS4B01G120700 chr2A 729419538 729420369 831 True 1216.000000 1216 93.277000 77 896 1 chr2A.!!$R1 819
6 TraesCS4B01G120700 chr3D 94841800 94842611 811 False 1129.000000 1129 91.941000 91 897 1 chr3D.!!$F1 806
7 TraesCS4B01G120700 chr3D 72268826 72269682 856 False 654.500000 767 94.614000 6 897 2 chr3D.!!$F3 891
8 TraesCS4B01G120700 chr1A 525907453 525908310 857 True 1086.000000 1086 89.699000 43 894 1 chr1A.!!$R1 851
9 TraesCS4B01G120700 chr6A 504491939 504492590 651 True 917.000000 917 92.331000 247 887 1 chr6A.!!$R1 640

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
465 466 0.299895 CACGAACATCATGCTCGCTC 59.700 55.0 10.39 0.0 39.34 5.03 F
1785 1805 0.613260 TCGGTGGCTATGTGAAGCTT 59.387 50.0 0.00 0.0 42.37 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 1990 0.426025 CGCGTACATATCAACGAGCG 59.574 55.0 9.89 2.33 41.55 5.03 R
3538 4864 0.256464 TGGCAGGCACATCATCATCA 59.744 50.0 0.00 0.00 0.00 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
242 243 1.608717 GCCATGGTCGAGTCTCCACT 61.609 60.000 14.67 0.00 36.50 4.00
270 271 1.134560 GCTCCTCGACGGTCTATTTGT 59.865 52.381 6.57 0.00 0.00 2.83
279 280 3.039011 ACGGTCTATTTGTAGCCTGGAT 58.961 45.455 0.00 0.00 0.00 3.41
338 339 4.692475 GGGCGGCAGGTGTACGTT 62.692 66.667 12.47 0.00 0.00 3.99
465 466 0.299895 CACGAACATCATGCTCGCTC 59.700 55.000 10.39 0.00 39.34 5.03
551 555 3.861341 GCAGCATGGTGGAGTAGAA 57.139 52.632 25.24 0.00 35.86 2.10
552 556 1.661341 GCAGCATGGTGGAGTAGAAG 58.339 55.000 25.24 0.00 35.86 2.85
553 557 1.208052 GCAGCATGGTGGAGTAGAAGA 59.792 52.381 25.24 0.00 35.86 2.87
566 570 4.039730 GGAGTAGAAGAAGGCATGCATCTA 59.960 45.833 21.36 14.58 0.00 1.98
640 645 2.498248 GCTCGAGATGGCAGCAGA 59.502 61.111 18.75 2.93 33.06 4.26
679 684 1.419387 ACTGCAGCTTGAGAAACTCCT 59.581 47.619 15.27 0.00 0.00 3.69
739 745 7.624549 AGTTCACAAGAGAATAAGGCTGAATA 58.375 34.615 0.00 0.00 0.00 1.75
897 917 7.771361 TCGCTAATATTCCTTATCCAAACAACA 59.229 33.333 0.00 0.00 0.00 3.33
900 920 6.693315 ATATTCCTTATCCAAACAACACCG 57.307 37.500 0.00 0.00 0.00 4.94
901 921 2.785562 TCCTTATCCAAACAACACCGG 58.214 47.619 0.00 0.00 0.00 5.28
902 922 1.201414 CCTTATCCAAACAACACCGGC 59.799 52.381 0.00 0.00 0.00 6.13
903 923 0.875728 TTATCCAAACAACACCGGCG 59.124 50.000 0.00 0.00 0.00 6.46
904 924 1.579084 TATCCAAACAACACCGGCGC 61.579 55.000 0.00 0.00 0.00 6.53
905 925 4.639171 CCAAACAACACCGGCGCC 62.639 66.667 19.07 19.07 0.00 6.53
906 926 3.893763 CAAACAACACCGGCGCCA 61.894 61.111 28.98 0.00 0.00 5.69
907 927 3.591835 AAACAACACCGGCGCCAG 61.592 61.111 28.98 19.42 0.00 4.85
911 931 4.344865 AACACCGGCGCCAGGATT 62.345 61.111 33.94 25.31 0.00 3.01
912 932 2.961893 AACACCGGCGCCAGGATTA 61.962 57.895 33.94 0.00 0.00 1.75
913 933 2.588877 CACCGGCGCCAGGATTAG 60.589 66.667 33.94 20.11 0.00 1.73
916 936 1.153249 CCGGCGCCAGGATTAGAAA 60.153 57.895 28.98 0.00 0.00 2.52
928 948 4.940046 CAGGATTAGAAACTGACATGCACT 59.060 41.667 0.00 0.00 34.21 4.40
948 968 2.593956 GGACGAACTTCTGGGCCCT 61.594 63.158 25.70 0.00 0.00 5.19
950 970 2.125512 CGAACTTCTGGGCCCTCG 60.126 66.667 25.70 19.02 0.00 4.63
968 988 1.003928 TCGTGTCAGCTACTAGTCCCA 59.996 52.381 0.00 0.00 0.00 4.37
1003 1023 1.885871 GTTGGACCTGGCTTCATGC 59.114 57.895 0.00 0.00 41.94 4.06
1143 1163 2.678934 CACCCGTCCTTCCTCCGA 60.679 66.667 0.00 0.00 0.00 4.55
1328 1348 3.083349 CATCCCCACTCCGCTCCA 61.083 66.667 0.00 0.00 0.00 3.86
1408 1428 2.203126 CATCCTCTGCGGCCTTCC 60.203 66.667 0.00 0.00 0.00 3.46
1608 1628 1.449423 CGATGTGGCGGGTGATTCA 60.449 57.895 0.00 0.00 0.00 2.57
1620 1640 2.161855 GGTGATTCACATGGTGCAGAA 58.838 47.619 18.09 0.00 35.86 3.02
1638 1658 4.310769 CAGAACGATTGTCTCAGGAAACT 58.689 43.478 0.00 0.00 46.44 2.66
1785 1805 0.613260 TCGGTGGCTATGTGAAGCTT 59.387 50.000 0.00 0.00 42.37 3.74
1798 1818 3.263261 GTGAAGCTTAGGAGGTACAAGC 58.737 50.000 0.00 6.74 43.97 4.01
1832 1852 2.082231 CTTCCAAGTGATGCAGGACAG 58.918 52.381 0.00 0.00 0.00 3.51
1863 1883 1.200716 CCGACCGAGCTAACACTTGTA 59.799 52.381 0.00 0.00 0.00 2.41
1953 1973 1.214589 CAAGGGCATTGCAGCTGAC 59.785 57.895 20.43 9.67 34.17 3.51
1968 1988 3.938963 CAGCTGACGGTTATGTTGGTAAT 59.061 43.478 8.42 0.00 0.00 1.89
1970 1990 3.486875 GCTGACGGTTATGTTGGTAATGC 60.487 47.826 0.00 0.00 0.00 3.56
2131 2151 8.267620 TCTGAAGCTATTTGATTCGATGAAAA 57.732 30.769 0.00 0.00 43.42 2.29
2132 2152 8.177663 TCTGAAGCTATTTGATTCGATGAAAAC 58.822 33.333 0.00 0.00 43.42 2.43
2292 2312 1.332195 TAGACATGCTCTGCCGCTAT 58.668 50.000 7.74 0.00 0.00 2.97
2481 2501 7.477144 TGTCATCACGATATCCAATGTTTAC 57.523 36.000 0.00 0.00 0.00 2.01
2531 2551 4.586421 TGAGCATCTGAGAACGAGGATAAT 59.414 41.667 0.00 0.00 34.92 1.28
2532 2552 5.069648 TGAGCATCTGAGAACGAGGATAATT 59.930 40.000 0.00 0.00 34.92 1.40
2556 2576 2.542907 CGGTGTTTGGAAGCACGCT 61.543 57.895 0.96 0.00 40.51 5.07
2574 2594 1.003116 GCTGCACACAGTCAAGTTGAG 60.003 52.381 5.62 0.00 46.30 3.02
2595 2669 5.360999 TGAGGATTCGTCAATCTGAGTACAT 59.639 40.000 6.59 0.00 38.85 2.29
2668 2747 8.492673 TGGTACTATTTCTGAATGTTGTGATC 57.507 34.615 0.00 0.00 0.00 2.92
2672 2751 7.478322 ACTATTTCTGAATGTTGTGATCATGC 58.522 34.615 0.00 0.00 0.00 4.06
2691 2770 2.684374 TGCGCATATCTTCAATTGCAGT 59.316 40.909 5.66 0.00 34.80 4.40
2815 2908 7.406104 AGAGGACCTTGTTATTAAGCTGAAAT 58.594 34.615 0.00 0.00 0.00 2.17
2816 2909 7.337942 AGAGGACCTTGTTATTAAGCTGAAATG 59.662 37.037 0.00 0.00 0.00 2.32
2818 2911 5.965922 ACCTTGTTATTAAGCTGAAATGGC 58.034 37.500 5.10 0.00 0.00 4.40
2821 2914 3.704061 TGTTATTAAGCTGAAATGGCCCC 59.296 43.478 0.00 0.00 0.00 5.80
2890 2983 4.081642 TGCTGGAGCTACTTAATCGAGTTT 60.082 41.667 0.00 0.00 42.66 2.66
2903 2996 5.560966 AATCGAGTTTGCAAATATTCCGT 57.439 34.783 16.21 2.10 0.00 4.69
2904 2997 6.671614 AATCGAGTTTGCAAATATTCCGTA 57.328 33.333 16.21 5.92 0.00 4.02
2905 2998 6.671614 ATCGAGTTTGCAAATATTCCGTAA 57.328 33.333 16.21 1.32 0.00 3.18
2906 2999 5.860641 TCGAGTTTGCAAATATTCCGTAAC 58.139 37.500 16.21 0.00 0.00 2.50
2907 3000 4.721977 CGAGTTTGCAAATATTCCGTAACG 59.278 41.667 16.21 5.78 0.00 3.18
2925 3018 3.678056 ACGGAGTTATTGCAGTTCTGA 57.322 42.857 3.84 0.00 37.78 3.27
2927 3020 3.997021 ACGGAGTTATTGCAGTTCTGAAG 59.003 43.478 3.84 0.00 37.78 3.02
2928 3021 4.245660 CGGAGTTATTGCAGTTCTGAAGA 58.754 43.478 3.84 0.00 0.00 2.87
2929 3022 4.690748 CGGAGTTATTGCAGTTCTGAAGAA 59.309 41.667 3.84 0.00 0.00 2.52
2937 3030 1.860078 GTTCTGAAGAACGGTGCCG 59.140 57.895 9.29 9.29 43.97 5.69
2939 3032 2.725203 TTCTGAAGAACGGTGCCGGG 62.725 60.000 15.44 0.00 44.69 5.73
2948 3041 4.195334 GGTGCCGGGCCTGATGAT 62.195 66.667 17.97 0.00 0.00 2.45
2949 3042 2.903855 GTGCCGGGCCTGATGATG 60.904 66.667 17.97 0.00 0.00 3.07
2952 3045 1.754234 GCCGGGCCTGATGATGTTT 60.754 57.895 15.09 0.00 0.00 2.83
2953 3046 1.322538 GCCGGGCCTGATGATGTTTT 61.323 55.000 15.09 0.00 0.00 2.43
2954 3047 0.457035 CCGGGCCTGATGATGTTTTG 59.543 55.000 15.09 0.00 0.00 2.44
2955 3048 0.457035 CGGGCCTGATGATGTTTTGG 59.543 55.000 5.28 0.00 0.00 3.28
2957 3050 2.733956 GGGCCTGATGATGTTTTGGTA 58.266 47.619 0.84 0.00 0.00 3.25
2958 3051 2.689983 GGGCCTGATGATGTTTTGGTAG 59.310 50.000 0.84 0.00 0.00 3.18
2959 3052 2.099756 GGCCTGATGATGTTTTGGTAGC 59.900 50.000 0.00 0.00 0.00 3.58
2961 3054 3.193267 GCCTGATGATGTTTTGGTAGCAA 59.807 43.478 2.54 2.54 0.00 3.91
2962 3055 4.737054 CCTGATGATGTTTTGGTAGCAAC 58.263 43.478 6.90 0.00 0.00 4.17
2964 3057 3.190327 TGATGATGTTTTGGTAGCAACGG 59.810 43.478 6.90 0.00 0.00 4.44
2965 3058 2.852449 TGATGTTTTGGTAGCAACGGA 58.148 42.857 6.90 0.00 0.00 4.69
2966 3059 3.215151 TGATGTTTTGGTAGCAACGGAA 58.785 40.909 6.90 0.00 0.00 4.30
2967 3060 3.632604 TGATGTTTTGGTAGCAACGGAAA 59.367 39.130 6.90 0.00 0.00 3.13
2969 3062 4.451629 TGTTTTGGTAGCAACGGAAAAA 57.548 36.364 6.90 0.00 0.00 1.94
2970 3063 4.174762 TGTTTTGGTAGCAACGGAAAAAC 58.825 39.130 6.90 8.57 36.09 2.43
2971 3064 3.439895 TTTGGTAGCAACGGAAAAACC 57.560 42.857 6.90 0.00 0.00 3.27
2974 3067 1.001048 GGTAGCAACGGAAAAACCCAC 60.001 52.381 0.00 0.00 34.64 4.61
2977 3070 0.458260 GCAACGGAAAAACCCACTGT 59.542 50.000 0.00 0.00 34.64 3.55
2978 3071 1.535226 GCAACGGAAAAACCCACTGTC 60.535 52.381 0.00 0.00 34.64 3.51
2980 3073 1.675552 ACGGAAAAACCCACTGTCAG 58.324 50.000 0.00 0.00 34.64 3.51
2981 3074 0.951558 CGGAAAAACCCACTGTCAGG 59.048 55.000 4.53 0.00 34.64 3.86
2982 3075 0.673985 GGAAAAACCCACTGTCAGGC 59.326 55.000 4.53 0.00 0.00 4.85
2983 3076 1.398692 GAAAAACCCACTGTCAGGCA 58.601 50.000 4.53 0.00 0.00 4.75
2984 3077 1.963515 GAAAAACCCACTGTCAGGCAT 59.036 47.619 4.53 0.00 0.00 4.40
2985 3078 2.969821 AAAACCCACTGTCAGGCATA 57.030 45.000 4.53 0.00 0.00 3.14
2986 3079 2.200373 AAACCCACTGTCAGGCATAC 57.800 50.000 4.53 0.00 0.00 2.39
2988 3081 2.247699 ACCCACTGTCAGGCATACTA 57.752 50.000 4.53 0.00 0.00 1.82
2989 3082 2.111384 ACCCACTGTCAGGCATACTAG 58.889 52.381 4.53 0.00 0.00 2.57
3007 3294 8.032952 CATACTAGAATGCTGTTTGTTCAGAA 57.967 34.615 0.00 0.00 37.61 3.02
3077 3364 3.074687 TGGGCTAACCTAAACCAATCACA 59.925 43.478 0.00 0.00 41.11 3.58
3210 4513 6.237808 CCTCATCAAAACCACGAAAACAAAAG 60.238 38.462 0.00 0.00 0.00 2.27
3223 4526 6.583427 ACGAAAACAAAAGGACAACAAACTAC 59.417 34.615 0.00 0.00 0.00 2.73
3224 4527 6.804783 CGAAAACAAAAGGACAACAAACTACT 59.195 34.615 0.00 0.00 0.00 2.57
3225 4528 7.964011 CGAAAACAAAAGGACAACAAACTACTA 59.036 33.333 0.00 0.00 0.00 1.82
3241 4544 9.284968 ACAAACTACTAATAAACAATCAGCAGT 57.715 29.630 0.00 0.00 0.00 4.40
3253 4561 2.507407 TCAGCAGTTAAATCCACCCC 57.493 50.000 0.00 0.00 0.00 4.95
3254 4562 1.094785 CAGCAGTTAAATCCACCCCG 58.905 55.000 0.00 0.00 0.00 5.73
3279 4587 0.235926 GAAACAACACGGCAGAGAGC 59.764 55.000 0.00 0.00 44.65 4.09
3288 4596 4.170723 GCAGAGAGCGCGTTTACT 57.829 55.556 8.43 2.22 0.00 2.24
3289 4597 1.992188 GCAGAGAGCGCGTTTACTC 59.008 57.895 8.43 11.44 0.00 2.59
3290 4598 0.456995 GCAGAGAGCGCGTTTACTCT 60.457 55.000 12.88 12.88 45.85 3.24
3337 4659 3.130693 TCCAACAAACCTTGGTTAAACCG 59.869 43.478 5.38 0.00 42.58 4.44
3338 4660 3.119065 CCAACAAACCTTGGTTAAACCGT 60.119 43.478 5.38 0.00 42.58 4.83
3339 4661 3.786516 ACAAACCTTGGTTAAACCGTG 57.213 42.857 5.38 2.21 42.58 4.94
3340 4662 2.427812 ACAAACCTTGGTTAAACCGTGG 59.572 45.455 5.38 0.00 42.58 4.94
3341 4663 2.427812 CAAACCTTGGTTAAACCGTGGT 59.572 45.455 5.38 0.00 44.50 4.16
3342 4664 2.440517 ACCTTGGTTAAACCGTGGTT 57.559 45.000 0.00 0.00 41.49 3.67
3343 4665 2.300433 ACCTTGGTTAAACCGTGGTTC 58.700 47.619 4.46 0.00 41.49 3.62
3344 4666 1.264826 CCTTGGTTAAACCGTGGTTCG 59.735 52.381 4.46 0.00 42.58 3.95
3345 4667 1.941975 CTTGGTTAAACCGTGGTTCGT 59.058 47.619 4.46 0.00 42.58 3.85
3346 4668 1.297664 TGGTTAAACCGTGGTTCGTG 58.702 50.000 4.46 0.00 42.58 4.35
3353 4675 1.445582 CCGTGGTTCGTGAGGCTAC 60.446 63.158 0.00 0.00 37.94 3.58
3359 4681 2.230508 TGGTTCGTGAGGCTACTTACAG 59.769 50.000 0.00 0.00 33.11 2.74
3363 4685 3.418995 TCGTGAGGCTACTTACAGAGTT 58.581 45.455 0.00 0.00 39.86 3.01
3384 4706 4.847990 TTTGGTATTATGACCCCTCGTT 57.152 40.909 0.00 0.00 38.89 3.85
3395 4717 1.002087 ACCCCTCGTTGACACTTCATC 59.998 52.381 0.00 0.00 0.00 2.92
3411 4733 6.127591 ACACTTCATCTCTACTTGTATCGCTT 60.128 38.462 0.00 0.00 0.00 4.68
3412 4734 6.198029 CACTTCATCTCTACTTGTATCGCTTG 59.802 42.308 0.00 0.00 0.00 4.01
3420 4742 2.806244 ACTTGTATCGCTTGTGGTGTTC 59.194 45.455 0.00 0.00 0.00 3.18
3436 4762 3.454375 GTGTTCTTGTGTTCTTCTCGGA 58.546 45.455 0.00 0.00 0.00 4.55
3448 4774 6.017852 GTGTTCTTCTCGGAGTCAATTTCTTT 60.018 38.462 4.69 0.00 0.00 2.52
3481 4807 6.449956 TCTTTGTTACCCATATACTCCCTCT 58.550 40.000 0.00 0.00 0.00 3.69
3485 4811 3.261818 ACCCATATACTCCCTCTGTCC 57.738 52.381 0.00 0.00 0.00 4.02
3486 4812 2.158143 ACCCATATACTCCCTCTGTCCC 60.158 54.545 0.00 0.00 0.00 4.46
3489 4815 4.264850 CCCATATACTCCCTCTGTCCCATA 60.265 50.000 0.00 0.00 0.00 2.74
3490 4816 5.342017 CCATATACTCCCTCTGTCCCATAA 58.658 45.833 0.00 0.00 0.00 1.90
3496 4822 8.846423 ATACTCCCTCTGTCCCATAATATAAG 57.154 38.462 0.00 0.00 0.00 1.73
3498 4824 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
3532 4858 9.967346 TGACATCTCTACTCTTATAAAAATCGG 57.033 33.333 0.00 0.00 0.00 4.18
3533 4859 9.413048 GACATCTCTACTCTTATAAAAATCGGG 57.587 37.037 0.00 0.00 0.00 5.14
3534 4860 8.925338 ACATCTCTACTCTTATAAAAATCGGGT 58.075 33.333 0.00 0.00 0.00 5.28
3535 4861 9.765795 CATCTCTACTCTTATAAAAATCGGGTT 57.234 33.333 0.00 0.00 0.00 4.11
3536 4862 9.765795 ATCTCTACTCTTATAAAAATCGGGTTG 57.234 33.333 0.00 0.00 0.00 3.77
3537 4863 8.202137 TCTCTACTCTTATAAAAATCGGGTTGG 58.798 37.037 0.00 0.00 0.00 3.77
3538 4864 7.854337 TCTACTCTTATAAAAATCGGGTTGGT 58.146 34.615 0.00 0.00 0.00 3.67
3539 4865 6.753107 ACTCTTATAAAAATCGGGTTGGTG 57.247 37.500 0.00 0.00 0.00 4.17
3540 4866 6.478129 ACTCTTATAAAAATCGGGTTGGTGA 58.522 36.000 0.00 0.00 0.00 4.02
3541 4867 7.116736 ACTCTTATAAAAATCGGGTTGGTGAT 58.883 34.615 0.00 0.00 0.00 3.06
3542 4868 7.067008 ACTCTTATAAAAATCGGGTTGGTGATG 59.933 37.037 0.00 0.00 0.00 3.07
3543 4869 7.113437 TCTTATAAAAATCGGGTTGGTGATGA 58.887 34.615 0.00 0.00 0.00 2.92
3544 4870 7.777910 TCTTATAAAAATCGGGTTGGTGATGAT 59.222 33.333 0.00 0.00 0.00 2.45
3545 4871 4.454728 AAAAATCGGGTTGGTGATGATG 57.545 40.909 0.00 0.00 0.00 3.07
3546 4872 3.364460 AAATCGGGTTGGTGATGATGA 57.636 42.857 0.00 0.00 0.00 2.92
3547 4873 3.582998 AATCGGGTTGGTGATGATGAT 57.417 42.857 0.00 0.00 0.00 2.45
3548 4874 2.330440 TCGGGTTGGTGATGATGATG 57.670 50.000 0.00 0.00 0.00 3.07
3549 4875 1.559219 TCGGGTTGGTGATGATGATGT 59.441 47.619 0.00 0.00 0.00 3.06
3550 4876 1.672363 CGGGTTGGTGATGATGATGTG 59.328 52.381 0.00 0.00 0.00 3.21
3551 4877 1.406539 GGGTTGGTGATGATGATGTGC 59.593 52.381 0.00 0.00 0.00 4.57
3552 4878 1.406539 GGTTGGTGATGATGATGTGCC 59.593 52.381 0.00 0.00 0.00 5.01
3553 4879 2.372264 GTTGGTGATGATGATGTGCCT 58.628 47.619 0.00 0.00 0.00 4.75
3554 4880 2.047002 TGGTGATGATGATGTGCCTG 57.953 50.000 0.00 0.00 0.00 4.85
3555 4881 0.666913 GGTGATGATGATGTGCCTGC 59.333 55.000 0.00 0.00 0.00 4.85
3556 4882 0.666913 GTGATGATGATGTGCCTGCC 59.333 55.000 0.00 0.00 0.00 4.85
3557 4883 0.256464 TGATGATGATGTGCCTGCCA 59.744 50.000 0.00 0.00 0.00 4.92
3558 4884 1.133606 TGATGATGATGTGCCTGCCAT 60.134 47.619 0.00 0.00 0.00 4.40
3559 4885 1.540267 GATGATGATGTGCCTGCCATC 59.460 52.381 11.37 11.37 39.32 3.51
3560 4886 0.549469 TGATGATGTGCCTGCCATCT 59.451 50.000 16.28 6.98 39.54 2.90
3561 4887 1.064240 TGATGATGTGCCTGCCATCTT 60.064 47.619 16.28 12.20 39.54 2.40
3562 4888 1.337071 GATGATGTGCCTGCCATCTTG 59.663 52.381 16.28 0.00 39.54 3.02
3563 4889 1.317431 TGATGTGCCTGCCATCTTGC 61.317 55.000 16.28 0.00 39.54 4.01
3564 4890 1.304630 ATGTGCCTGCCATCTTGCA 60.305 52.632 0.00 0.00 39.37 4.08
3565 4891 0.901114 ATGTGCCTGCCATCTTGCAA 60.901 50.000 0.00 0.00 41.51 4.08
3566 4892 0.901114 TGTGCCTGCCATCTTGCAAT 60.901 50.000 0.00 0.00 41.51 3.56
3567 4893 1.105457 GTGCCTGCCATCTTGCAATA 58.895 50.000 0.00 0.00 41.51 1.90
3568 4894 1.684983 GTGCCTGCCATCTTGCAATAT 59.315 47.619 0.00 0.00 41.51 1.28
3569 4895 2.886523 GTGCCTGCCATCTTGCAATATA 59.113 45.455 0.00 0.00 41.51 0.86
3570 4896 3.057736 GTGCCTGCCATCTTGCAATATAG 60.058 47.826 0.00 0.00 41.51 1.31
3571 4897 3.181441 TGCCTGCCATCTTGCAATATAGA 60.181 43.478 0.00 0.00 41.51 1.98
3572 4898 3.190118 GCCTGCCATCTTGCAATATAGAC 59.810 47.826 0.00 0.00 41.51 2.59
3573 4899 3.755378 CCTGCCATCTTGCAATATAGACC 59.245 47.826 0.00 0.00 41.51 3.85
3574 4900 3.402110 TGCCATCTTGCAATATAGACCG 58.598 45.455 0.00 0.00 38.56 4.79
3575 4901 3.181455 TGCCATCTTGCAATATAGACCGT 60.181 43.478 0.00 0.00 38.56 4.83
3576 4902 3.433615 GCCATCTTGCAATATAGACCGTC 59.566 47.826 0.00 0.00 0.00 4.79
3577 4903 3.997021 CCATCTTGCAATATAGACCGTCC 59.003 47.826 0.00 0.00 0.00 4.79
3578 4904 3.364889 TCTTGCAATATAGACCGTCCG 57.635 47.619 0.00 0.00 0.00 4.79
3579 4905 2.953648 TCTTGCAATATAGACCGTCCGA 59.046 45.455 0.00 0.00 0.00 4.55
3580 4906 3.572682 TCTTGCAATATAGACCGTCCGAT 59.427 43.478 0.00 0.00 0.00 4.18
3581 4907 3.570926 TGCAATATAGACCGTCCGATC 57.429 47.619 0.00 0.00 0.00 3.69
3582 4908 3.154710 TGCAATATAGACCGTCCGATCT 58.845 45.455 0.00 0.00 0.00 2.75
3583 4909 4.329392 TGCAATATAGACCGTCCGATCTA 58.671 43.478 0.00 0.00 32.11 1.98
3584 4910 4.948004 TGCAATATAGACCGTCCGATCTAT 59.052 41.667 8.53 8.53 40.47 1.98
3585 4911 6.117488 TGCAATATAGACCGTCCGATCTATA 58.883 40.000 12.02 12.02 42.05 1.31
3586 4912 6.771267 TGCAATATAGACCGTCCGATCTATAT 59.229 38.462 14.93 14.93 46.24 0.86
3587 4913 7.041303 TGCAATATAGACCGTCCGATCTATATC 60.041 40.741 19.07 11.25 44.71 1.63
3588 4914 7.173562 GCAATATAGACCGTCCGATCTATATCT 59.826 40.741 19.07 10.15 44.71 1.98
3589 4915 8.499967 CAATATAGACCGTCCGATCTATATCTG 58.500 40.741 19.07 15.61 44.71 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.135939 CGTGCGGACAGACGACATA 59.864 57.895 8.11 0.00 37.81 2.29
279 280 3.483808 TGCAAACAGAGTGGATGTACA 57.516 42.857 0.00 0.00 0.00 2.90
328 329 1.544691 AGAAGCATCGAACGTACACCT 59.455 47.619 0.00 0.00 0.00 4.00
338 339 3.067106 GGAACAACTGAAGAAGCATCGA 58.933 45.455 0.00 0.00 0.00 3.59
465 466 2.108514 CACTGGTACGCAGGGCATG 61.109 63.158 13.68 0.00 0.00 4.06
551 555 2.860009 CCACATAGATGCATGCCTTCT 58.140 47.619 16.68 18.85 33.09 2.85
552 556 1.268899 GCCACATAGATGCATGCCTTC 59.731 52.381 16.68 12.33 0.00 3.46
553 557 1.325355 GCCACATAGATGCATGCCTT 58.675 50.000 16.68 1.92 0.00 4.35
579 583 2.292569 TCGACTTCTCTTTGCGTACAGT 59.707 45.455 0.00 0.00 0.00 3.55
640 645 5.769662 TGCAGTTCCTGATATTTGACACTTT 59.230 36.000 0.00 0.00 32.44 2.66
679 684 1.271856 TACCCAGATTGAGCACCGAA 58.728 50.000 0.00 0.00 0.00 4.30
739 745 5.505654 CGTCTTGTTTCCTGCTTGTACAATT 60.506 40.000 9.13 0.00 0.00 2.32
897 917 1.906105 TTTCTAATCCTGGCGCCGGT 61.906 55.000 32.63 17.91 0.00 5.28
900 920 1.017387 CAGTTTCTAATCCTGGCGCC 58.983 55.000 22.73 22.73 0.00 6.53
901 921 1.666189 GTCAGTTTCTAATCCTGGCGC 59.334 52.381 0.00 0.00 0.00 6.53
902 922 2.972625 TGTCAGTTTCTAATCCTGGCG 58.027 47.619 0.00 0.00 33.58 5.69
903 923 3.065925 GCATGTCAGTTTCTAATCCTGGC 59.934 47.826 0.00 0.00 0.00 4.85
904 924 4.095483 GTGCATGTCAGTTTCTAATCCTGG 59.905 45.833 0.00 0.00 0.00 4.45
905 925 4.940046 AGTGCATGTCAGTTTCTAATCCTG 59.060 41.667 0.00 0.00 0.00 3.86
906 926 5.171339 AGTGCATGTCAGTTTCTAATCCT 57.829 39.130 0.00 0.00 0.00 3.24
907 927 4.033358 CGAGTGCATGTCAGTTTCTAATCC 59.967 45.833 0.00 0.00 0.00 3.01
908 928 4.033358 CCGAGTGCATGTCAGTTTCTAATC 59.967 45.833 0.00 0.00 0.00 1.75
909 929 3.935203 CCGAGTGCATGTCAGTTTCTAAT 59.065 43.478 0.00 0.00 0.00 1.73
910 930 3.006430 TCCGAGTGCATGTCAGTTTCTAA 59.994 43.478 0.00 0.00 0.00 2.10
911 931 2.560981 TCCGAGTGCATGTCAGTTTCTA 59.439 45.455 0.00 0.00 0.00 2.10
912 932 1.344438 TCCGAGTGCATGTCAGTTTCT 59.656 47.619 0.00 0.00 0.00 2.52
913 933 1.461127 GTCCGAGTGCATGTCAGTTTC 59.539 52.381 0.00 0.00 0.00 2.78
916 936 1.080501 CGTCCGAGTGCATGTCAGT 60.081 57.895 0.00 0.00 0.00 3.41
928 948 2.654877 GCCCAGAAGTTCGTCCGA 59.345 61.111 0.00 0.00 0.00 4.55
948 968 1.003928 TGGGACTAGTAGCTGACACGA 59.996 52.381 0.00 0.00 0.00 4.35
950 970 2.417515 GCTTGGGACTAGTAGCTGACAC 60.418 54.545 7.92 0.00 0.00 3.67
984 1004 1.926511 GCATGAAGCCAGGTCCAACG 61.927 60.000 0.00 0.00 37.23 4.10
986 1006 1.675310 CGCATGAAGCCAGGTCCAA 60.675 57.895 0.00 0.00 41.38 3.53
1132 1152 2.754658 GACGGCTCGGAGGAAGGA 60.755 66.667 7.20 0.00 0.00 3.36
1143 1163 4.049817 AGTCGGGAGAGGACGGCT 62.050 66.667 0.00 0.00 40.64 5.52
1211 1231 0.753848 GAAGAGGGACGGGGAGAGAG 60.754 65.000 0.00 0.00 0.00 3.20
1392 1412 3.483869 GGGAAGGCCGCAGAGGAT 61.484 66.667 0.00 0.00 45.00 3.24
1400 1420 2.044946 CCTTGAAGGGGAAGGCCG 60.045 66.667 2.50 0.00 33.84 6.13
1438 1458 1.153086 CGCAGCCCAGCTTTAGGAT 60.153 57.895 0.00 0.00 36.40 3.24
1608 1628 1.806542 GACAATCGTTCTGCACCATGT 59.193 47.619 0.00 0.00 0.00 3.21
1620 1640 3.320673 GGAGTTTCCTGAGACAATCGT 57.679 47.619 0.00 0.00 32.53 3.73
1638 1658 4.523943 CACCATGAAATGTTCCTTTCAGGA 59.476 41.667 11.47 0.00 45.17 3.86
1644 1664 3.255642 CGTTCCACCATGAAATGTTCCTT 59.744 43.478 0.00 0.00 44.81 3.36
1785 1805 3.609853 CAATGCTTGCTTGTACCTCCTA 58.390 45.455 0.00 0.00 0.00 2.94
1811 1831 1.271543 TGTCCTGCATCACTTGGAAGG 60.272 52.381 0.00 0.00 0.00 3.46
1820 1840 1.687014 ATGCCACTGTCCTGCATCA 59.313 52.632 3.82 0.00 41.68 3.07
1863 1883 1.843368 CACATGCCCCAAGAACAGAT 58.157 50.000 0.00 0.00 0.00 2.90
1953 1973 1.668751 AGCGCATTACCAACATAACCG 59.331 47.619 11.47 0.00 0.00 4.44
1968 1988 1.472990 CGTACATATCAACGAGCGCA 58.527 50.000 11.47 0.00 41.55 6.09
1970 1990 0.426025 CGCGTACATATCAACGAGCG 59.574 55.000 9.89 2.33 41.55 5.03
2115 2135 5.416952 AGGCTCAGTTTTCATCGAATCAAAT 59.583 36.000 0.00 0.00 0.00 2.32
2131 2151 1.904537 TGTGACATGATCAGGCTCAGT 59.095 47.619 7.40 0.00 38.28 3.41
2132 2152 2.685850 TGTGACATGATCAGGCTCAG 57.314 50.000 7.40 0.00 38.28 3.35
2441 2461 2.383245 GACATCCCCATCATCGGCGT 62.383 60.000 6.85 0.00 0.00 5.68
2481 2501 1.094073 CCCATCTCCTTGCTTCTGCG 61.094 60.000 0.00 0.00 43.34 5.18
2531 2551 1.133407 GCTTCCAAACACCGTGTTCAA 59.867 47.619 17.11 9.57 40.14 2.69
2532 2552 0.736053 GCTTCCAAACACCGTGTTCA 59.264 50.000 17.11 2.35 40.14 3.18
2556 2576 1.209261 TCCTCAACTTGACTGTGTGCA 59.791 47.619 0.00 0.00 0.00 4.57
2574 2594 4.985409 GGATGTACTCAGATTGACGAATCC 59.015 45.833 0.00 0.00 39.14 3.01
2595 2669 1.909459 TATTGAAGCTGCGGCCTGGA 61.909 55.000 15.55 0.00 39.73 3.86
2660 2739 4.024641 TGAAGATATGCGCATGATCACAAC 60.025 41.667 32.48 18.98 0.00 3.32
2668 2747 3.634283 TGCAATTGAAGATATGCGCATG 58.366 40.909 32.48 14.34 41.61 4.06
2672 2751 5.334319 TCAAACTGCAATTGAAGATATGCG 58.666 37.500 20.85 2.60 41.61 4.73
2691 2770 6.899393 AGAAGCCTACAAAATCACATCAAA 57.101 33.333 0.00 0.00 0.00 2.69
2739 2831 5.105310 AGCATGGTTACTAACTTGACGATCT 60.105 40.000 0.00 0.00 0.00 2.75
2740 2832 5.005779 CAGCATGGTTACTAACTTGACGATC 59.994 44.000 0.00 0.00 0.00 3.69
2815 2908 0.699399 TCCATCTTAAAACGGGGCCA 59.301 50.000 4.39 0.00 0.00 5.36
2816 2909 1.389555 CTCCATCTTAAAACGGGGCC 58.610 55.000 0.00 0.00 0.00 5.80
2818 2911 1.743394 GTGCTCCATCTTAAAACGGGG 59.257 52.381 0.00 0.00 0.00 5.73
2821 2914 3.334691 TCCAGTGCTCCATCTTAAAACG 58.665 45.455 0.00 0.00 0.00 3.60
2903 2996 5.142061 TCAGAACTGCAATAACTCCGTTA 57.858 39.130 0.00 0.00 32.36 3.18
2904 2997 4.002906 TCAGAACTGCAATAACTCCGTT 57.997 40.909 0.00 0.00 0.00 4.44
2905 2998 3.678056 TCAGAACTGCAATAACTCCGT 57.322 42.857 0.00 0.00 0.00 4.69
2906 2999 4.245660 TCTTCAGAACTGCAATAACTCCG 58.754 43.478 0.00 0.00 0.00 4.63
2920 3013 1.301401 CCGGCACCGTTCTTCAGAA 60.301 57.895 8.49 0.00 37.81 3.02
2921 3014 2.342279 CCGGCACCGTTCTTCAGA 59.658 61.111 8.49 0.00 37.81 3.27
2922 3015 2.742372 CCCGGCACCGTTCTTCAG 60.742 66.667 8.49 0.00 37.81 3.02
2931 3024 4.195334 ATCATCAGGCCCGGCACC 62.195 66.667 12.58 0.00 0.00 5.01
2932 3025 2.903855 CATCATCAGGCCCGGCAC 60.904 66.667 12.58 0.31 0.00 5.01
2936 3029 0.457035 CCAAAACATCATCAGGCCCG 59.543 55.000 0.00 0.00 0.00 6.13
2937 3030 1.560505 ACCAAAACATCATCAGGCCC 58.439 50.000 0.00 0.00 0.00 5.80
2939 3032 2.754552 TGCTACCAAAACATCATCAGGC 59.245 45.455 0.00 0.00 0.00 4.85
2940 3033 4.672542 CGTTGCTACCAAAACATCATCAGG 60.673 45.833 0.00 0.00 31.68 3.86
2941 3034 4.406069 CGTTGCTACCAAAACATCATCAG 58.594 43.478 0.00 0.00 31.68 2.90
2943 3036 3.438781 TCCGTTGCTACCAAAACATCATC 59.561 43.478 0.00 0.00 31.68 2.92
2945 3038 2.852449 TCCGTTGCTACCAAAACATCA 58.148 42.857 0.00 0.00 31.68 3.07
2946 3039 3.907894 TTCCGTTGCTACCAAAACATC 57.092 42.857 0.00 0.00 31.68 3.06
2947 3040 4.657436 TTTTCCGTTGCTACCAAAACAT 57.343 36.364 0.00 0.00 31.68 2.71
2948 3041 4.174762 GTTTTTCCGTTGCTACCAAAACA 58.825 39.130 16.28 1.35 31.68 2.83
2949 3042 3.552699 GGTTTTTCCGTTGCTACCAAAAC 59.447 43.478 14.36 14.36 31.68 2.43
2952 3045 1.682323 GGGTTTTTCCGTTGCTACCAA 59.318 47.619 0.00 0.00 37.00 3.67
2953 3046 1.320507 GGGTTTTTCCGTTGCTACCA 58.679 50.000 0.00 0.00 37.00 3.25
2954 3047 1.001048 GTGGGTTTTTCCGTTGCTACC 60.001 52.381 0.00 0.00 37.00 3.18
2955 3048 1.951602 AGTGGGTTTTTCCGTTGCTAC 59.048 47.619 0.00 0.00 37.00 3.58
2957 3050 0.744281 CAGTGGGTTTTTCCGTTGCT 59.256 50.000 0.00 0.00 37.00 3.91
2958 3051 0.458260 ACAGTGGGTTTTTCCGTTGC 59.542 50.000 0.00 0.00 37.00 4.17
2959 3052 1.746220 TGACAGTGGGTTTTTCCGTTG 59.254 47.619 0.00 0.00 37.00 4.10
2961 3054 1.675552 CTGACAGTGGGTTTTTCCGT 58.324 50.000 0.00 0.00 37.00 4.69
2962 3055 0.951558 CCTGACAGTGGGTTTTTCCG 59.048 55.000 0.93 0.00 37.00 4.30
2964 3057 1.398692 TGCCTGACAGTGGGTTTTTC 58.601 50.000 0.93 0.00 0.00 2.29
2965 3058 2.086610 ATGCCTGACAGTGGGTTTTT 57.913 45.000 0.93 0.00 0.00 1.94
2966 3059 2.108250 AGTATGCCTGACAGTGGGTTTT 59.892 45.455 0.93 0.00 0.00 2.43
2967 3060 1.705186 AGTATGCCTGACAGTGGGTTT 59.295 47.619 0.93 0.00 0.00 3.27
2969 3062 2.111384 CTAGTATGCCTGACAGTGGGT 58.889 52.381 0.93 0.00 0.00 4.51
2970 3063 2.388735 TCTAGTATGCCTGACAGTGGG 58.611 52.381 0.93 0.00 0.00 4.61
2971 3064 4.375272 CATTCTAGTATGCCTGACAGTGG 58.625 47.826 0.93 0.00 0.00 4.00
2982 3075 7.601073 TCTGAACAAACAGCATTCTAGTATG 57.399 36.000 5.04 5.04 37.75 2.39
2983 3076 8.798859 ATTCTGAACAAACAGCATTCTAGTAT 57.201 30.769 0.00 0.00 37.75 2.12
2984 3077 9.719355 TTATTCTGAACAAACAGCATTCTAGTA 57.281 29.630 0.00 0.00 37.75 1.82
2985 3078 8.621532 TTATTCTGAACAAACAGCATTCTAGT 57.378 30.769 0.00 0.00 37.75 2.57
2986 3079 9.552114 CTTTATTCTGAACAAACAGCATTCTAG 57.448 33.333 0.00 0.00 37.75 2.43
2988 3081 7.945134 ACTTTATTCTGAACAAACAGCATTCT 58.055 30.769 0.00 0.00 37.75 2.40
2989 3082 8.579682 AACTTTATTCTGAACAAACAGCATTC 57.420 30.769 0.00 0.00 37.75 2.67
3002 3289 8.774586 GCTTACAACTTCTGAACTTTATTCTGA 58.225 33.333 0.00 0.00 0.00 3.27
3077 3364 3.797865 GCTTCAACTTCAGCACAGCAAAT 60.798 43.478 0.00 0.00 35.95 2.32
3087 3374 1.856265 GCCACCGGCTTCAACTTCAG 61.856 60.000 0.00 0.00 46.69 3.02
3225 4528 8.034804 GGTGGATTTAACTGCTGATTGTTTATT 58.965 33.333 0.00 0.00 0.00 1.40
3241 4544 0.626916 CCTTCCCGGGGTGGATTTAA 59.373 55.000 23.50 3.37 42.00 1.52
3253 4561 1.946267 CCGTGTTGTTTCCTTCCCG 59.054 57.895 0.00 0.00 0.00 5.14
3254 4562 1.104577 TGCCGTGTTGTTTCCTTCCC 61.105 55.000 0.00 0.00 0.00 3.97
3279 4587 6.310197 AGTAGTACAAGTAAGAGTAAACGCG 58.690 40.000 3.53 3.53 0.00 6.01
3337 4659 2.029649 TGTAAGTAGCCTCACGAACCAC 60.030 50.000 0.00 0.00 0.00 4.16
3338 4660 2.230508 CTGTAAGTAGCCTCACGAACCA 59.769 50.000 0.00 0.00 0.00 3.67
3339 4661 2.490903 TCTGTAAGTAGCCTCACGAACC 59.509 50.000 0.00 0.00 33.76 3.62
3340 4662 3.190953 ACTCTGTAAGTAGCCTCACGAAC 59.809 47.826 0.00 0.00 36.07 3.95
3341 4663 3.418995 ACTCTGTAAGTAGCCTCACGAA 58.581 45.455 0.00 0.00 36.07 3.85
3342 4664 3.069079 ACTCTGTAAGTAGCCTCACGA 57.931 47.619 0.00 0.00 36.07 4.35
3343 4665 3.851976 AACTCTGTAAGTAGCCTCACG 57.148 47.619 0.00 0.00 37.17 4.35
3344 4666 4.691216 CCAAAACTCTGTAAGTAGCCTCAC 59.309 45.833 0.00 0.00 37.17 3.51
3345 4667 4.347000 ACCAAAACTCTGTAAGTAGCCTCA 59.653 41.667 0.00 0.00 37.17 3.86
3346 4668 4.895961 ACCAAAACTCTGTAAGTAGCCTC 58.104 43.478 0.00 0.00 37.17 4.70
3353 4675 7.282450 GGGGTCATAATACCAAAACTCTGTAAG 59.718 40.741 0.00 0.00 41.67 2.34
3359 4681 4.814771 CGAGGGGTCATAATACCAAAACTC 59.185 45.833 0.00 0.00 41.67 3.01
3363 4685 4.225492 TCAACGAGGGGTCATAATACCAAA 59.775 41.667 0.00 0.00 41.67 3.28
3384 4706 6.678164 GCGATACAAGTAGAGATGAAGTGTCA 60.678 42.308 0.00 0.00 38.41 3.58
3395 4717 3.859961 CACCACAAGCGATACAAGTAGAG 59.140 47.826 0.00 0.00 0.00 2.43
3411 4733 3.938963 GAGAAGAACACAAGAACACCACA 59.061 43.478 0.00 0.00 0.00 4.17
3412 4734 3.001330 CGAGAAGAACACAAGAACACCAC 59.999 47.826 0.00 0.00 0.00 4.16
3420 4742 3.371102 TGACTCCGAGAAGAACACAAG 57.629 47.619 1.33 0.00 0.00 3.16
3452 4778 9.856162 GGGAGTATATGGGTAACAAAGATTAAA 57.144 33.333 0.00 0.00 39.74 1.52
3455 4781 7.572861 AGAGGGAGTATATGGGTAACAAAGATT 59.427 37.037 0.00 0.00 39.74 2.40
3506 4832 9.967346 CCGATTTTTATAAGAGTAGAGATGTCA 57.033 33.333 0.00 0.00 0.00 3.58
3507 4833 9.413048 CCCGATTTTTATAAGAGTAGAGATGTC 57.587 37.037 0.00 0.00 0.00 3.06
3508 4834 8.925338 ACCCGATTTTTATAAGAGTAGAGATGT 58.075 33.333 0.00 0.00 0.00 3.06
3509 4835 9.765795 AACCCGATTTTTATAAGAGTAGAGATG 57.234 33.333 0.00 0.00 0.00 2.90
3510 4836 9.765795 CAACCCGATTTTTATAAGAGTAGAGAT 57.234 33.333 0.00 0.00 0.00 2.75
3511 4837 8.202137 CCAACCCGATTTTTATAAGAGTAGAGA 58.798 37.037 0.00 0.00 0.00 3.10
3512 4838 7.985752 ACCAACCCGATTTTTATAAGAGTAGAG 59.014 37.037 0.00 0.00 0.00 2.43
3513 4839 7.767198 CACCAACCCGATTTTTATAAGAGTAGA 59.233 37.037 0.00 0.00 0.00 2.59
3514 4840 7.767198 TCACCAACCCGATTTTTATAAGAGTAG 59.233 37.037 0.00 0.00 0.00 2.57
3515 4841 7.622713 TCACCAACCCGATTTTTATAAGAGTA 58.377 34.615 0.00 0.00 0.00 2.59
3516 4842 6.478129 TCACCAACCCGATTTTTATAAGAGT 58.522 36.000 0.00 0.00 0.00 3.24
3517 4843 6.995511 TCACCAACCCGATTTTTATAAGAG 57.004 37.500 0.00 0.00 0.00 2.85
3518 4844 7.113437 TCATCACCAACCCGATTTTTATAAGA 58.887 34.615 0.00 0.00 0.00 2.10
3519 4845 7.328277 TCATCACCAACCCGATTTTTATAAG 57.672 36.000 0.00 0.00 0.00 1.73
3520 4846 7.558081 TCATCATCACCAACCCGATTTTTATAA 59.442 33.333 0.00 0.00 0.00 0.98
3521 4847 7.057264 TCATCATCACCAACCCGATTTTTATA 58.943 34.615 0.00 0.00 0.00 0.98
3522 4848 5.890985 TCATCATCACCAACCCGATTTTTAT 59.109 36.000 0.00 0.00 0.00 1.40
3523 4849 5.257262 TCATCATCACCAACCCGATTTTTA 58.743 37.500 0.00 0.00 0.00 1.52
3524 4850 4.085733 TCATCATCACCAACCCGATTTTT 58.914 39.130 0.00 0.00 0.00 1.94
3525 4851 3.696045 TCATCATCACCAACCCGATTTT 58.304 40.909 0.00 0.00 0.00 1.82
3526 4852 3.364460 TCATCATCACCAACCCGATTT 57.636 42.857 0.00 0.00 0.00 2.17
3527 4853 3.216800 CATCATCATCACCAACCCGATT 58.783 45.455 0.00 0.00 0.00 3.34
3528 4854 2.173356 ACATCATCATCACCAACCCGAT 59.827 45.455 0.00 0.00 0.00 4.18
3529 4855 1.559219 ACATCATCATCACCAACCCGA 59.441 47.619 0.00 0.00 0.00 5.14
3530 4856 1.672363 CACATCATCATCACCAACCCG 59.328 52.381 0.00 0.00 0.00 5.28
3531 4857 1.406539 GCACATCATCATCACCAACCC 59.593 52.381 0.00 0.00 0.00 4.11
3532 4858 1.406539 GGCACATCATCATCACCAACC 59.593 52.381 0.00 0.00 0.00 3.77
3533 4859 2.098607 CAGGCACATCATCATCACCAAC 59.901 50.000 0.00 0.00 0.00 3.77
3534 4860 2.371306 CAGGCACATCATCATCACCAA 58.629 47.619 0.00 0.00 0.00 3.67
3535 4861 2.020181 GCAGGCACATCATCATCACCA 61.020 52.381 0.00 0.00 0.00 4.17
3536 4862 0.666913 GCAGGCACATCATCATCACC 59.333 55.000 0.00 0.00 0.00 4.02
3537 4863 0.666913 GGCAGGCACATCATCATCAC 59.333 55.000 0.00 0.00 0.00 3.06
3538 4864 0.256464 TGGCAGGCACATCATCATCA 59.744 50.000 0.00 0.00 0.00 3.07
3539 4865 1.540267 GATGGCAGGCACATCATCATC 59.460 52.381 0.00 4.15 43.21 2.92
3540 4866 1.145119 AGATGGCAGGCACATCATCAT 59.855 47.619 18.41 2.29 45.49 2.45
3541 4867 0.549469 AGATGGCAGGCACATCATCA 59.451 50.000 18.41 0.00 45.49 3.07
3542 4868 1.337071 CAAGATGGCAGGCACATCATC 59.663 52.381 18.41 10.93 45.49 2.92
3543 4869 1.399714 CAAGATGGCAGGCACATCAT 58.600 50.000 18.41 8.97 45.49 2.45
3544 4870 1.317431 GCAAGATGGCAGGCACATCA 61.317 55.000 18.41 0.00 45.49 3.07
3545 4871 1.317431 TGCAAGATGGCAGGCACATC 61.317 55.000 0.00 6.90 43.87 3.06
3546 4872 0.901114 TTGCAAGATGGCAGGCACAT 60.901 50.000 0.00 0.00 45.88 3.21
3547 4873 0.901114 ATTGCAAGATGGCAGGCACA 60.901 50.000 4.94 0.00 45.88 4.57
3548 4874 1.105457 TATTGCAAGATGGCAGGCAC 58.895 50.000 4.94 0.00 45.88 5.01
3549 4875 2.076207 ATATTGCAAGATGGCAGGCA 57.924 45.000 5.61 0.00 45.88 4.75
3550 4876 3.190118 GTCTATATTGCAAGATGGCAGGC 59.810 47.826 16.68 4.08 45.88 4.85
3551 4877 3.755378 GGTCTATATTGCAAGATGGCAGG 59.245 47.826 16.68 2.45 45.88 4.85
3552 4878 3.434641 CGGTCTATATTGCAAGATGGCAG 59.565 47.826 16.68 6.42 45.88 4.85
3553 4879 3.181455 ACGGTCTATATTGCAAGATGGCA 60.181 43.478 16.68 1.69 43.19 4.92
3554 4880 3.403038 ACGGTCTATATTGCAAGATGGC 58.597 45.455 16.68 9.50 0.00 4.40
3555 4881 3.997021 GGACGGTCTATATTGCAAGATGG 59.003 47.826 16.68 13.71 0.00 3.51
3556 4882 3.675225 CGGACGGTCTATATTGCAAGATG 59.325 47.826 16.68 6.94 0.00 2.90
3557 4883 3.572682 TCGGACGGTCTATATTGCAAGAT 59.427 43.478 11.88 11.88 0.00 2.40
3558 4884 2.953648 TCGGACGGTCTATATTGCAAGA 59.046 45.455 4.94 0.00 0.00 3.02
3559 4885 3.364889 TCGGACGGTCTATATTGCAAG 57.635 47.619 4.94 0.00 0.00 4.01
3560 4886 3.572682 AGATCGGACGGTCTATATTGCAA 59.427 43.478 5.58 0.00 0.00 4.08
3561 4887 3.154710 AGATCGGACGGTCTATATTGCA 58.845 45.455 5.58 0.00 0.00 4.08
3562 4888 3.851976 AGATCGGACGGTCTATATTGC 57.148 47.619 5.58 0.00 0.00 3.56
3563 4889 8.499967 CAGATATAGATCGGACGGTCTATATTG 58.500 40.741 31.81 27.07 44.58 1.90
3564 4890 8.610248 CAGATATAGATCGGACGGTCTATATT 57.390 38.462 31.81 23.25 44.58 1.28


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

AutoCloner maintained by Alex Coulton.