Multiple sequence alignment - TraesCS3B01G473500

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 TraesCS3B01G473500 chr3B 100.000 3296 0 0 727 4022 722584424 722581129 0.000000e+00 6087
1 TraesCS3B01G473500 chr3B 91.854 2271 159 14 1770 4022 532747365 532745103 0.000000e+00 3145
2 TraesCS3B01G473500 chr3B 91.640 2189 141 24 1856 4009 13988721 13986540 0.000000e+00 2990
3 TraesCS3B01G473500 chr3B 91.107 2204 151 28 1856 4022 657695264 657693069 0.000000e+00 2942
4 TraesCS3B01G473500 chr3B 88.635 1839 148 37 1157 2966 692068509 692070315 0.000000e+00 2182
5 TraesCS3B01G473500 chr3B 100.000 431 0 0 1 431 722585150 722584720 0.000000e+00 797
6 TraesCS3B01G473500 chr5B 92.183 3198 172 34 853 4022 550237942 550241089 0.000000e+00 4449
7 TraesCS3B01G473500 chr5B 90.789 152 12 1 280 431 550237750 550237899 6.820000e-48 202
8 TraesCS3B01G473500 chr6B 93.090 2909 170 18 779 3666 187843939 187846837 0.000000e+00 4229
9 TraesCS3B01G473500 chr6B 92.810 2295 150 12 1735 4022 626667323 626669609 0.000000e+00 3310
10 TraesCS3B01G473500 chr6B 91.240 1564 84 17 753 2274 157236558 157235006 0.000000e+00 2080
11 TraesCS3B01G473500 chr6B 90.944 784 42 18 749 1506 594958633 594959413 0.000000e+00 1027
12 TraesCS3B01G473500 chr6B 92.715 151 9 1 281 431 157236740 157236592 2.430000e-52 217
13 TraesCS3B01G473500 chr4A 92.695 2861 167 23 1172 4022 660870276 660867448 0.000000e+00 4087
14 TraesCS3B01G473500 chr4A 93.404 1986 115 10 2043 4022 661731812 661733787 0.000000e+00 2928
15 TraesCS3B01G473500 chr4A 92.030 1079 59 8 750 1802 661730489 661731566 0.000000e+00 1491
16 TraesCS3B01G473500 chr4B 91.002 2845 199 28 1212 4022 212139919 212137098 0.000000e+00 3783
17 TraesCS3B01G473500 chr4B 92.167 2617 171 13 1218 3811 548297990 548295385 0.000000e+00 3666
18 TraesCS3B01G473500 chr4B 92.732 2449 145 17 1595 4022 212110389 212107953 0.000000e+00 3506
19 TraesCS3B01G473500 chr4B 91.247 2205 147 26 1856 4022 553948312 553946116 0.000000e+00 2961
20 TraesCS3B01G473500 chr4B 87.609 460 40 8 779 1222 548375114 548374656 5.960000e-143 518
21 TraesCS3B01G473500 chr3A 87.576 2648 249 52 1413 4022 450957039 450959644 0.000000e+00 2994
22 TraesCS3B01G473500 chr3A 90.506 158 15 0 4 161 358908202 358908359 4.070000e-50 209
23 TraesCS3B01G473500 chr7B 92.098 1101 58 16 727 1805 693458838 693459931 0.000000e+00 1524
24 TraesCS3B01G473500 chr7B 92.081 1086 55 13 750 1805 698988008 698989092 0.000000e+00 1500
25 TraesCS3B01G473500 chr7B 90.645 1101 69 11 727 1805 698516315 698517403 0.000000e+00 1432
26 TraesCS3B01G473500 chr7B 91.139 158 12 2 275 431 698987829 698987985 3.150000e-51 213
27 TraesCS3B01G473500 chr7B 93.056 144 9 1 288 431 693458679 693458821 4.070000e-50 209
28 TraesCS3B01G473500 chr7B 91.667 144 11 1 288 431 698516155 698516297 8.820000e-47 198
29 TraesCS3B01G473500 chr1B 88.267 750 56 14 995 1718 89962744 89963487 0.000000e+00 869
30 TraesCS3B01G473500 chr1B 95.570 158 7 0 4 161 409832496 409832339 1.860000e-63 254
31 TraesCS3B01G473500 chr5A 92.053 151 12 0 11 161 437245363 437245513 3.150000e-51 213
32 TraesCS3B01G473500 chr5D 89.103 156 14 3 750 903 526623826 526623980 1.480000e-44 191
33 TraesCS3B01G473500 chrUn 87.919 149 16 2 281 429 109030782 109030928 1.490000e-39 174
34 TraesCS3B01G473500 chr3D 91.870 123 6 4 41 161 61702341 61702461 6.910000e-38 169
35 TraesCS3B01G473500 chr3D 84.416 154 21 2 276 429 263228883 263229033 9.010000e-32 148
36 TraesCS3B01G473500 chr2B 87.234 141 14 4 766 903 95265074 95264935 1.500000e-34 158
37 TraesCS3B01G473500 chr1D 85.333 150 18 4 280 429 61374174 61374319 6.960000e-33 152
38 TraesCS3B01G473500 chr6D 83.436 163 24 3 268 429 318090020 318090180 9.010000e-32 148


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 TraesCS3B01G473500 chr3B 722581129 722585150 4021 True 3442.0 6087 100.0000 1 4022 2 chr3B.!!$R4 4021
1 TraesCS3B01G473500 chr3B 532745103 532747365 2262 True 3145.0 3145 91.8540 1770 4022 1 chr3B.!!$R2 2252
2 TraesCS3B01G473500 chr3B 13986540 13988721 2181 True 2990.0 2990 91.6400 1856 4009 1 chr3B.!!$R1 2153
3 TraesCS3B01G473500 chr3B 657693069 657695264 2195 True 2942.0 2942 91.1070 1856 4022 1 chr3B.!!$R3 2166
4 TraesCS3B01G473500 chr3B 692068509 692070315 1806 False 2182.0 2182 88.6350 1157 2966 1 chr3B.!!$F1 1809
5 TraesCS3B01G473500 chr5B 550237750 550241089 3339 False 2325.5 4449 91.4860 280 4022 2 chr5B.!!$F1 3742
6 TraesCS3B01G473500 chr6B 187843939 187846837 2898 False 4229.0 4229 93.0900 779 3666 1 chr6B.!!$F1 2887
7 TraesCS3B01G473500 chr6B 626667323 626669609 2286 False 3310.0 3310 92.8100 1735 4022 1 chr6B.!!$F3 2287
8 TraesCS3B01G473500 chr6B 157235006 157236740 1734 True 1148.5 2080 91.9775 281 2274 2 chr6B.!!$R1 1993
9 TraesCS3B01G473500 chr6B 594958633 594959413 780 False 1027.0 1027 90.9440 749 1506 1 chr6B.!!$F2 757
10 TraesCS3B01G473500 chr4A 660867448 660870276 2828 True 4087.0 4087 92.6950 1172 4022 1 chr4A.!!$R1 2850
11 TraesCS3B01G473500 chr4A 661730489 661733787 3298 False 2209.5 2928 92.7170 750 4022 2 chr4A.!!$F1 3272
12 TraesCS3B01G473500 chr4B 212137098 212139919 2821 True 3783.0 3783 91.0020 1212 4022 1 chr4B.!!$R2 2810
13 TraesCS3B01G473500 chr4B 548295385 548297990 2605 True 3666.0 3666 92.1670 1218 3811 1 chr4B.!!$R3 2593
14 TraesCS3B01G473500 chr4B 212107953 212110389 2436 True 3506.0 3506 92.7320 1595 4022 1 chr4B.!!$R1 2427
15 TraesCS3B01G473500 chr4B 553946116 553948312 2196 True 2961.0 2961 91.2470 1856 4022 1 chr4B.!!$R5 2166
16 TraesCS3B01G473500 chr3A 450957039 450959644 2605 False 2994.0 2994 87.5760 1413 4022 1 chr3A.!!$F2 2609
17 TraesCS3B01G473500 chr7B 693458679 693459931 1252 False 866.5 1524 92.5770 288 1805 2 chr7B.!!$F1 1517
18 TraesCS3B01G473500 chr7B 698987829 698989092 1263 False 856.5 1500 91.6100 275 1805 2 chr7B.!!$F3 1530
19 TraesCS3B01G473500 chr7B 698516155 698517403 1248 False 815.0 1432 91.1560 288 1805 2 chr7B.!!$F2 1517
20 TraesCS3B01G473500 chr1B 89962744 89963487 743 False 869.0 869 88.2670 995 1718 1 chr1B.!!$F1 723

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
37 38 0.035725 CTCCACTTGGCTGCTCATGA 60.036 55.0 0.00 0.0 34.44 3.07 F
385 387 0.041684 AGAAAAGGAAGGGGGCATGG 59.958 55.0 0.00 0.0 0.00 3.66 F
1155 1202 0.463295 CGCCCTCATGAGTGCATCTT 60.463 55.0 26.52 0.0 30.99 2.40 F
2616 2877 0.764271 TGGCAGGACAGTCATCAACA 59.236 50.0 2.17 0.0 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1871 3.069729 GCTAGAATAGATGTCCCCGTTGT 59.930 47.826 0.0 0.0 42.77 3.32 R
2297 2538 1.742831 GGAGTTGCACGCCATTATGAA 59.257 47.619 0.0 0.0 38.02 2.57 R
2726 2987 1.002576 CTTGCACAGCATCGTCAACAA 60.003 47.619 0.0 0.0 38.76 2.83 R
3695 3968 1.003003 TGAACGGCACCATCATCTCAA 59.997 47.619 0.0 0.0 0.00 3.02 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 3.060615 CTGCTTGGTCCAGCTGGC 61.061 66.667 28.91 21.69 40.79 4.85
19 20 3.564345 CTGCTTGGTCCAGCTGGCT 62.564 63.158 28.91 0.00 40.79 4.75
20 21 2.749441 GCTTGGTCCAGCTGGCTC 60.749 66.667 28.91 21.47 36.79 4.70
21 22 2.045536 CTTGGTCCAGCTGGCTCC 60.046 66.667 28.91 28.60 34.44 4.70
22 23 2.853542 TTGGTCCAGCTGGCTCCA 60.854 61.111 31.66 31.66 37.22 3.86
23 24 3.196207 TTGGTCCAGCTGGCTCCAC 62.196 63.158 33.73 24.79 38.13 4.02
24 25 3.325753 GGTCCAGCTGGCTCCACT 61.326 66.667 28.91 0.00 34.44 4.00
25 26 2.753029 GTCCAGCTGGCTCCACTT 59.247 61.111 28.91 0.00 34.44 3.16
26 27 1.673665 GTCCAGCTGGCTCCACTTG 60.674 63.158 28.91 0.67 34.44 3.16
27 28 2.360852 CCAGCTGGCTCCACTTGG 60.361 66.667 22.33 0.00 0.00 3.61
28 29 3.060615 CAGCTGGCTCCACTTGGC 61.061 66.667 5.57 0.00 34.44 4.52
29 30 3.255397 AGCTGGCTCCACTTGGCT 61.255 61.111 0.00 0.00 34.44 4.75
30 31 3.060615 GCTGGCTCCACTTGGCTG 61.061 66.667 0.00 0.00 34.44 4.85
31 32 3.060615 CTGGCTCCACTTGGCTGC 61.061 66.667 0.00 0.00 35.00 5.25
32 33 3.564345 CTGGCTCCACTTGGCTGCT 62.564 63.158 0.00 0.00 35.68 4.24
33 34 2.749441 GGCTCCACTTGGCTGCTC 60.749 66.667 0.00 0.00 35.68 4.26
34 35 2.033141 GCTCCACTTGGCTGCTCA 59.967 61.111 0.00 0.00 33.71 4.26
35 36 1.378250 GCTCCACTTGGCTGCTCAT 60.378 57.895 0.00 0.00 33.71 2.90
36 37 1.654954 GCTCCACTTGGCTGCTCATG 61.655 60.000 0.00 1.37 33.71 3.07
37 38 0.035725 CTCCACTTGGCTGCTCATGA 60.036 55.000 0.00 0.00 34.44 3.07
38 39 0.622136 TCCACTTGGCTGCTCATGAT 59.378 50.000 0.00 0.00 34.44 2.45
39 40 1.005097 TCCACTTGGCTGCTCATGATT 59.995 47.619 0.00 0.00 34.44 2.57
40 41 1.134367 CCACTTGGCTGCTCATGATTG 59.866 52.381 0.00 0.00 0.00 2.67
41 42 1.134367 CACTTGGCTGCTCATGATTGG 59.866 52.381 0.00 0.00 0.00 3.16
42 43 0.102481 CTTGGCTGCTCATGATTGGC 59.898 55.000 0.00 2.65 0.00 4.52
43 44 0.323999 TTGGCTGCTCATGATTGGCT 60.324 50.000 0.00 0.00 0.00 4.75
44 45 0.750546 TGGCTGCTCATGATTGGCTC 60.751 55.000 0.00 0.00 0.00 4.70
45 46 0.750546 GGCTGCTCATGATTGGCTCA 60.751 55.000 0.00 0.00 38.53 4.26
46 47 0.663688 GCTGCTCATGATTGGCTCAG 59.336 55.000 0.00 0.00 37.28 3.35
47 48 1.309950 CTGCTCATGATTGGCTCAGG 58.690 55.000 0.00 0.00 37.28 3.86
48 49 0.913924 TGCTCATGATTGGCTCAGGA 59.086 50.000 0.00 0.00 42.12 3.86
49 50 1.307097 GCTCATGATTGGCTCAGGAC 58.693 55.000 0.00 0.00 39.64 3.85
50 51 1.964552 CTCATGATTGGCTCAGGACC 58.035 55.000 0.00 0.00 39.64 4.46
51 52 1.211212 CTCATGATTGGCTCAGGACCA 59.789 52.381 0.00 0.00 39.64 4.02
57 58 1.619654 TTGGCTCAGGACCAAATGTG 58.380 50.000 0.00 0.00 44.11 3.21
58 59 0.895100 TGGCTCAGGACCAAATGTGC 60.895 55.000 0.00 0.00 33.12 4.57
59 60 0.895100 GGCTCAGGACCAAATGTGCA 60.895 55.000 8.11 0.00 37.86 4.57
60 61 0.242017 GCTCAGGACCAAATGTGCAC 59.758 55.000 10.75 10.75 37.86 4.57
61 62 0.883833 CTCAGGACCAAATGTGCACC 59.116 55.000 15.69 0.00 37.86 5.01
62 63 0.478072 TCAGGACCAAATGTGCACCT 59.522 50.000 15.69 0.23 37.86 4.00
63 64 1.133513 TCAGGACCAAATGTGCACCTT 60.134 47.619 15.69 8.15 37.86 3.50
64 65 1.000060 CAGGACCAAATGTGCACCTTG 60.000 52.381 15.69 16.88 37.86 3.61
65 66 1.133513 AGGACCAAATGTGCACCTTGA 60.134 47.619 23.42 3.88 37.86 3.02
66 67 1.270550 GGACCAAATGTGCACCTTGAG 59.729 52.381 23.42 17.16 34.99 3.02
67 68 2.229792 GACCAAATGTGCACCTTGAGA 58.770 47.619 23.42 2.81 0.00 3.27
68 69 2.622942 GACCAAATGTGCACCTTGAGAA 59.377 45.455 23.42 2.11 0.00 2.87
69 70 2.362077 ACCAAATGTGCACCTTGAGAAC 59.638 45.455 23.42 0.00 0.00 3.01
70 71 2.361757 CCAAATGTGCACCTTGAGAACA 59.638 45.455 23.42 0.78 0.00 3.18
71 72 3.181477 CCAAATGTGCACCTTGAGAACAA 60.181 43.478 23.42 0.02 34.65 2.83
78 79 6.271284 GTGCACCTTGAGAACAAGTTGGAG 62.271 50.000 5.22 0.00 44.15 3.86
82 83 2.930826 TGAGAACAAGTTGGAGGACC 57.069 50.000 7.96 0.00 0.00 4.46
83 84 2.123589 TGAGAACAAGTTGGAGGACCA 58.876 47.619 7.96 0.00 45.34 4.02
84 85 4.927357 CTTGAGAACAAGTTGGAGGACCAA 60.927 45.833 7.96 0.00 46.27 3.67
85 86 6.381815 CTTGAGAACAAGTTGGAGGACCAAA 61.382 44.000 7.96 0.00 45.95 3.28
98 99 6.991938 TGGAGGACCAAATAATTCACTTTTG 58.008 36.000 0.00 0.00 43.91 2.44
99 100 5.869344 GGAGGACCAAATAATTCACTTTTGC 59.131 40.000 0.00 0.00 35.97 3.68
100 101 6.418057 AGGACCAAATAATTCACTTTTGCA 57.582 33.333 0.00 0.00 0.00 4.08
101 102 6.825610 AGGACCAAATAATTCACTTTTGCAA 58.174 32.000 0.00 0.00 0.00 4.08
102 103 6.930722 AGGACCAAATAATTCACTTTTGCAAG 59.069 34.615 0.00 0.00 35.92 4.01
103 104 6.705825 GGACCAAATAATTCACTTTTGCAAGT 59.294 34.615 0.00 0.00 44.72 3.16
104 105 7.226523 GGACCAAATAATTCACTTTTGCAAGTT 59.773 33.333 0.00 0.00 40.66 2.66
105 106 8.504812 ACCAAATAATTCACTTTTGCAAGTTT 57.495 26.923 0.00 0.00 40.66 2.66
106 107 8.397148 ACCAAATAATTCACTTTTGCAAGTTTG 58.603 29.630 0.00 0.00 40.66 2.93
107 108 8.610896 CCAAATAATTCACTTTTGCAAGTTTGA 58.389 29.630 0.00 0.40 40.66 2.69
108 109 9.640974 CAAATAATTCACTTTTGCAAGTTTGAG 57.359 29.630 0.00 0.00 40.66 3.02
109 110 7.951530 ATAATTCACTTTTGCAAGTTTGAGG 57.048 32.000 0.00 0.00 40.66 3.86
110 111 5.596836 ATTCACTTTTGCAAGTTTGAGGA 57.403 34.783 0.00 0.00 40.66 3.71
111 112 4.370364 TCACTTTTGCAAGTTTGAGGAC 57.630 40.909 0.00 0.00 40.66 3.85
112 113 3.130340 TCACTTTTGCAAGTTTGAGGACC 59.870 43.478 0.00 0.00 40.66 4.46
113 114 3.096092 ACTTTTGCAAGTTTGAGGACCA 58.904 40.909 0.00 0.00 40.66 4.02
114 115 3.513515 ACTTTTGCAAGTTTGAGGACCAA 59.486 39.130 0.00 0.00 40.66 3.67
115 116 4.020662 ACTTTTGCAAGTTTGAGGACCAAA 60.021 37.500 0.00 0.00 40.66 3.28
116 117 4.543590 TTTGCAAGTTTGAGGACCAAAA 57.456 36.364 0.00 0.00 45.40 2.44
117 118 3.518634 TGCAAGTTTGAGGACCAAAAC 57.481 42.857 12.62 12.62 45.40 2.43
118 119 2.828520 TGCAAGTTTGAGGACCAAAACA 59.171 40.909 19.38 2.16 45.40 2.83
119 120 3.450457 TGCAAGTTTGAGGACCAAAACAT 59.550 39.130 19.38 9.22 45.40 2.71
120 121 4.051237 GCAAGTTTGAGGACCAAAACATC 58.949 43.478 19.38 8.42 45.40 3.06
121 122 4.441356 GCAAGTTTGAGGACCAAAACATCA 60.441 41.667 19.38 1.01 45.40 3.07
122 123 4.918810 AGTTTGAGGACCAAAACATCAC 57.081 40.909 19.38 4.97 45.40 3.06
123 124 4.277476 AGTTTGAGGACCAAAACATCACA 58.723 39.130 19.38 0.00 45.40 3.58
124 125 4.895297 AGTTTGAGGACCAAAACATCACAT 59.105 37.500 19.38 1.68 45.40 3.21
125 126 4.852134 TTGAGGACCAAAACATCACATG 57.148 40.909 0.00 0.00 0.00 3.21
126 127 2.557924 TGAGGACCAAAACATCACATGC 59.442 45.455 0.00 0.00 0.00 4.06
127 128 2.557924 GAGGACCAAAACATCACATGCA 59.442 45.455 0.00 0.00 0.00 3.96
128 129 2.964464 AGGACCAAAACATCACATGCAA 59.036 40.909 0.00 0.00 0.00 4.08
129 130 3.006110 AGGACCAAAACATCACATGCAAG 59.994 43.478 0.00 0.00 0.00 4.01
130 131 3.005684 GGACCAAAACATCACATGCAAGA 59.994 43.478 0.00 0.00 0.00 3.02
131 132 3.981211 ACCAAAACATCACATGCAAGAC 58.019 40.909 0.00 0.00 0.00 3.01
132 133 3.384146 ACCAAAACATCACATGCAAGACA 59.616 39.130 0.00 0.00 0.00 3.41
133 134 4.141981 ACCAAAACATCACATGCAAGACAA 60.142 37.500 0.00 0.00 0.00 3.18
134 135 4.446385 CCAAAACATCACATGCAAGACAAG 59.554 41.667 0.00 0.00 0.00 3.16
135 136 4.924305 AAACATCACATGCAAGACAAGT 57.076 36.364 0.00 0.00 0.00 3.16
136 137 4.924305 AACATCACATGCAAGACAAGTT 57.076 36.364 0.00 0.00 0.00 2.66
137 138 4.494350 ACATCACATGCAAGACAAGTTC 57.506 40.909 0.00 0.00 0.00 3.01
138 139 3.254166 ACATCACATGCAAGACAAGTTCC 59.746 43.478 0.00 0.00 0.00 3.62
139 140 2.929641 TCACATGCAAGACAAGTTCCA 58.070 42.857 0.00 0.00 0.00 3.53
140 141 2.880268 TCACATGCAAGACAAGTTCCAG 59.120 45.455 0.00 0.00 0.00 3.86
141 142 2.030540 CACATGCAAGACAAGTTCCAGG 60.031 50.000 0.00 0.00 0.00 4.45
142 143 2.158623 ACATGCAAGACAAGTTCCAGGA 60.159 45.455 0.00 0.00 0.00 3.86
143 144 1.967319 TGCAAGACAAGTTCCAGGAC 58.033 50.000 0.00 0.00 0.00 3.85
144 145 1.239347 GCAAGACAAGTTCCAGGACC 58.761 55.000 0.00 0.00 0.00 4.46
145 146 1.202818 GCAAGACAAGTTCCAGGACCT 60.203 52.381 0.00 0.00 0.00 3.85
146 147 2.498167 CAAGACAAGTTCCAGGACCTG 58.502 52.381 15.15 15.15 0.00 4.00
147 148 0.398318 AGACAAGTTCCAGGACCTGC 59.602 55.000 16.72 2.57 0.00 4.85
148 149 0.606673 GACAAGTTCCAGGACCTGCC 60.607 60.000 16.72 5.99 0.00 4.85
149 150 1.672356 CAAGTTCCAGGACCTGCCG 60.672 63.158 16.72 3.58 43.43 5.69
150 151 2.147387 AAGTTCCAGGACCTGCCGT 61.147 57.895 16.72 1.57 43.43 5.68
151 152 2.358737 GTTCCAGGACCTGCCGTG 60.359 66.667 16.72 2.41 43.43 4.94
152 153 4.329545 TTCCAGGACCTGCCGTGC 62.330 66.667 16.72 0.00 43.43 5.34
154 155 3.390521 CCAGGACCTGCCGTGCTA 61.391 66.667 16.72 0.00 42.04 3.49
155 156 2.735772 CCAGGACCTGCCGTGCTAT 61.736 63.158 16.72 0.00 42.04 2.97
156 157 1.221840 CAGGACCTGCCGTGCTATT 59.778 57.895 8.99 0.00 42.04 1.73
157 158 0.464036 CAGGACCTGCCGTGCTATTA 59.536 55.000 8.99 0.00 42.04 0.98
158 159 0.464452 AGGACCTGCCGTGCTATTAC 59.536 55.000 0.00 0.00 42.15 1.89
159 160 0.532196 GGACCTGCCGTGCTATTACC 60.532 60.000 0.00 0.00 0.00 2.85
160 161 0.464452 GACCTGCCGTGCTATTACCT 59.536 55.000 0.00 0.00 0.00 3.08
161 162 0.909623 ACCTGCCGTGCTATTACCTT 59.090 50.000 0.00 0.00 0.00 3.50
162 163 1.280998 ACCTGCCGTGCTATTACCTTT 59.719 47.619 0.00 0.00 0.00 3.11
163 164 2.290705 ACCTGCCGTGCTATTACCTTTT 60.291 45.455 0.00 0.00 0.00 2.27
164 165 2.354821 CCTGCCGTGCTATTACCTTTTC 59.645 50.000 0.00 0.00 0.00 2.29
165 166 2.354821 CTGCCGTGCTATTACCTTTTCC 59.645 50.000 0.00 0.00 0.00 3.13
166 167 2.290387 TGCCGTGCTATTACCTTTTCCA 60.290 45.455 0.00 0.00 0.00 3.53
167 168 2.949644 GCCGTGCTATTACCTTTTCCAT 59.050 45.455 0.00 0.00 0.00 3.41
168 169 3.380320 GCCGTGCTATTACCTTTTCCATT 59.620 43.478 0.00 0.00 0.00 3.16
169 170 4.142249 GCCGTGCTATTACCTTTTCCATTT 60.142 41.667 0.00 0.00 0.00 2.32
170 171 5.623596 GCCGTGCTATTACCTTTTCCATTTT 60.624 40.000 0.00 0.00 0.00 1.82
171 172 6.394809 CCGTGCTATTACCTTTTCCATTTTT 58.605 36.000 0.00 0.00 0.00 1.94
196 197 9.944663 TTTACACTTAAAATTCATGTCTGTGAC 57.055 29.630 0.00 0.00 0.00 3.67
197 198 7.566760 ACACTTAAAATTCATGTCTGTGACA 57.433 32.000 2.77 2.77 46.90 3.58
232 233 8.899427 TCCATTTAGTGCAAATTTTGAATTCA 57.101 26.923 13.26 3.38 34.49 2.57
233 234 8.772705 TCCATTTAGTGCAAATTTTGAATTCAC 58.227 29.630 7.89 10.55 34.49 3.18
234 235 8.016801 CCATTTAGTGCAAATTTTGAATTCACC 58.983 33.333 7.89 0.00 34.49 4.02
235 236 8.776470 CATTTAGTGCAAATTTTGAATTCACCT 58.224 29.630 7.89 0.00 34.49 4.00
236 237 7.945033 TTAGTGCAAATTTTGAATTCACCTC 57.055 32.000 7.89 0.00 0.00 3.85
237 238 5.916318 AGTGCAAATTTTGAATTCACCTCA 58.084 33.333 7.89 0.00 0.00 3.86
238 239 6.527423 AGTGCAAATTTTGAATTCACCTCAT 58.473 32.000 7.89 0.00 0.00 2.90
239 240 6.993902 AGTGCAAATTTTGAATTCACCTCATT 59.006 30.769 7.89 1.56 0.00 2.57
240 241 7.499895 AGTGCAAATTTTGAATTCACCTCATTT 59.500 29.630 7.89 7.43 0.00 2.32
241 242 8.130469 GTGCAAATTTTGAATTCACCTCATTTT 58.870 29.630 7.89 0.57 0.00 1.82
242 243 9.334947 TGCAAATTTTGAATTCACCTCATTTTA 57.665 25.926 7.89 0.63 0.00 1.52
250 251 9.619316 TTGAATTCACCTCATTTTATGTTTACG 57.381 29.630 7.89 0.00 0.00 3.18
251 252 8.240682 TGAATTCACCTCATTTTATGTTTACGG 58.759 33.333 3.38 0.00 0.00 4.02
252 253 6.503589 TTCACCTCATTTTATGTTTACGGG 57.496 37.500 0.00 0.00 0.00 5.28
253 254 5.806818 TCACCTCATTTTATGTTTACGGGA 58.193 37.500 0.00 0.00 0.00 5.14
254 255 5.644636 TCACCTCATTTTATGTTTACGGGAC 59.355 40.000 0.00 0.00 0.00 4.46
255 256 5.646360 CACCTCATTTTATGTTTACGGGACT 59.354 40.000 0.00 0.00 0.00 3.85
256 257 6.819649 CACCTCATTTTATGTTTACGGGACTA 59.180 38.462 0.00 0.00 0.00 2.59
257 258 7.011109 CACCTCATTTTATGTTTACGGGACTAG 59.989 40.741 0.00 0.00 0.00 2.57
258 259 6.018180 CCTCATTTTATGTTTACGGGACTAGC 60.018 42.308 0.00 0.00 0.00 3.42
259 260 5.818857 TCATTTTATGTTTACGGGACTAGCC 59.181 40.000 0.00 0.00 0.00 3.93
260 261 4.822685 TTTATGTTTACGGGACTAGCCA 57.177 40.909 5.70 0.00 38.95 4.75
261 262 2.685850 ATGTTTACGGGACTAGCCAC 57.314 50.000 5.70 0.00 38.95 5.01
262 263 0.244450 TGTTTACGGGACTAGCCACG 59.756 55.000 0.00 0.00 38.95 4.94
263 264 0.244721 GTTTACGGGACTAGCCACGT 59.755 55.000 12.05 12.05 43.11 4.49
264 265 0.244450 TTTACGGGACTAGCCACGTG 59.756 55.000 17.21 9.08 41.53 4.49
265 266 0.608856 TTACGGGACTAGCCACGTGA 60.609 55.000 17.21 5.23 41.53 4.35
266 267 1.028330 TACGGGACTAGCCACGTGAG 61.028 60.000 17.21 9.33 41.53 3.51
267 268 2.184579 GGGACTAGCCACGTGAGC 59.815 66.667 19.30 18.44 38.95 4.26
268 269 2.202623 GGACTAGCCACGTGAGCG 60.203 66.667 19.30 9.40 44.93 5.03
269 270 2.202623 GACTAGCCACGTGAGCGG 60.203 66.667 19.30 17.36 43.45 5.52
270 271 2.989824 ACTAGCCACGTGAGCGGT 60.990 61.111 19.30 17.93 43.45 5.68
271 272 2.261671 CTAGCCACGTGAGCGGTT 59.738 61.111 19.30 0.00 43.45 4.44
272 273 1.374252 CTAGCCACGTGAGCGGTTT 60.374 57.895 19.30 5.51 43.45 3.27
273 274 0.949105 CTAGCCACGTGAGCGGTTTT 60.949 55.000 19.30 5.15 43.45 2.43
274 275 0.533308 TAGCCACGTGAGCGGTTTTT 60.533 50.000 19.30 4.46 43.45 1.94
275 276 0.533308 AGCCACGTGAGCGGTTTTTA 60.533 50.000 19.30 0.00 43.45 1.52
276 277 0.519961 GCCACGTGAGCGGTTTTTAT 59.480 50.000 19.30 0.00 43.45 1.40
277 278 1.068816 GCCACGTGAGCGGTTTTTATT 60.069 47.619 19.30 0.00 43.45 1.40
278 279 2.606065 GCCACGTGAGCGGTTTTTATTT 60.606 45.455 19.30 0.00 43.45 1.40
283 284 4.022676 ACGTGAGCGGTTTTTATTTTGGAT 60.023 37.500 0.00 0.00 43.45 3.41
380 382 1.339727 CGGTACAGAAAAGGAAGGGGG 60.340 57.143 0.00 0.00 0.00 5.40
385 387 0.041684 AGAAAAGGAAGGGGGCATGG 59.958 55.000 0.00 0.00 0.00 3.66
743 745 3.143338 GCTGTCCCTAGCTAGCCC 58.857 66.667 15.74 5.51 40.52 5.19
744 746 2.512355 GCTGTCCCTAGCTAGCCCC 61.512 68.421 15.74 5.16 40.52 5.80
745 747 1.839296 CTGTCCCTAGCTAGCCCCC 60.839 68.421 15.74 3.42 0.00 5.40
746 748 2.285868 GTCCCTAGCTAGCCCCCA 59.714 66.667 15.74 0.00 0.00 4.96
747 749 2.141448 GTCCCTAGCTAGCCCCCAC 61.141 68.421 15.74 3.04 0.00 4.61
751 753 4.475444 TAGCTAGCCCCCACGCCT 62.475 66.667 12.13 0.00 0.00 5.52
839 854 1.342374 GCCAGAAAGGGGATCCAACAT 60.342 52.381 15.23 0.00 38.09 2.71
851 867 1.208706 TCCAACATAATCGCCCCAGA 58.791 50.000 0.00 0.00 0.00 3.86
916 932 9.549078 AAGAGTAAAAGAAACTACTTCAAGAGG 57.451 33.333 0.00 0.00 36.40 3.69
1057 1081 2.378547 TGCATCTGTAAACCCCCTTCTT 59.621 45.455 0.00 0.00 0.00 2.52
1155 1202 0.463295 CGCCCTCATGAGTGCATCTT 60.463 55.000 26.52 0.00 30.99 2.40
1196 1244 8.833231 TTGAGATCAAGTTTAGTAGAAACTGG 57.167 34.615 3.59 1.25 40.10 4.00
1228 1286 3.857157 AAACTGGAGGTGTTCAGCTAA 57.143 42.857 4.48 0.00 34.57 3.09
1509 1586 5.296780 CCTGCTTTCTGAGTGAACACTTTAA 59.703 40.000 8.87 2.12 42.66 1.52
1786 1878 1.176527 AATGCATCCTGAACAACGGG 58.823 50.000 0.00 0.00 45.93 5.28
1865 2045 8.103305 AGAACTTTTGTCCATAGCTAATGAAGA 58.897 33.333 0.00 0.00 37.86 2.87
1912 2106 4.449068 CGCATATAATCTTCTCCCACACAC 59.551 45.833 0.00 0.00 0.00 3.82
1929 2123 3.266772 ACACACATATTCTGGTCCCACAT 59.733 43.478 0.00 0.00 0.00 3.21
2020 2233 7.862512 ATCTGTCATCCAATTCTTCTTTCTC 57.137 36.000 0.00 0.00 0.00 2.87
2297 2538 9.463443 GTCATGTAACTTTTGCAACTAAGATTT 57.537 29.630 16.01 5.29 0.00 2.17
2307 2550 8.477984 TTTGCAACTAAGATTTTCATAATGGC 57.522 30.769 0.00 0.00 0.00 4.40
2316 2559 3.485947 TTTCATAATGGCGTGCAACTC 57.514 42.857 0.00 0.00 31.75 3.01
2390 2639 7.041508 ACAACTGATGACATCACTTTCTTCTTC 60.042 37.037 14.24 0.00 35.06 2.87
2616 2877 0.764271 TGGCAGGACAGTCATCAACA 59.236 50.000 2.17 0.00 0.00 3.33
2623 2884 3.509967 AGGACAGTCATCAACACGTGATA 59.490 43.478 25.01 7.15 45.69 2.15
2699 2960 1.620822 GTGGCAAATGTTCCTGGTCT 58.379 50.000 0.00 0.00 0.00 3.85
2726 2987 0.117340 ACTGAGCTAGGAGTTGGGGT 59.883 55.000 0.00 0.00 0.00 4.95
2735 2996 0.179040 GGAGTTGGGGTTGTTGACGA 60.179 55.000 0.00 0.00 0.00 4.20
2843 3104 7.446931 TCAAATTGCTAAGGATCACTACAACAA 59.553 33.333 0.00 0.00 0.00 2.83
2897 3158 0.542232 AACACCTCTAGGCGGACACT 60.542 55.000 6.07 0.00 39.32 3.55
2979 3240 1.417288 ATGATGGAGGAGCTGAGGCC 61.417 60.000 0.00 0.00 39.73 5.19
3004 3265 0.753262 CTGTCCTGGACCCTATTCCG 59.247 60.000 23.42 0.00 38.69 4.30
3014 3275 3.372241 GGACCCTATTCCGGATCCAAAAA 60.372 47.826 13.41 2.62 0.00 1.94
3071 3332 3.584406 TCCAATCTTTGCTGAAGAGGAGA 59.416 43.478 8.64 3.44 46.99 3.71
3100 3361 8.419442 AGTCCTAGTAAGAAAAAGAAGAAACGA 58.581 33.333 0.00 0.00 0.00 3.85
3262 3523 1.379916 CCACCAAGGCATCTCACCA 59.620 57.895 0.00 0.00 0.00 4.17
3410 3679 5.301551 TGCAACTGGAATGTCTTAATTGTGT 59.698 36.000 0.00 0.00 0.00 3.72
3428 3697 2.542595 GTGTAACTGGTGTCCAACTTCG 59.457 50.000 0.00 0.00 30.80 3.79
3549 3821 0.838122 AAGGTGCAGCTAGGTGTCCT 60.838 55.000 20.51 24.47 37.71 3.85
3601 3873 2.567169 TGTCCTATTACTGTGCAGCTGT 59.433 45.455 16.64 0.00 0.00 4.40
3662 3935 7.067615 TGTTTTCTTTTTGTAGTATGCAGGACA 59.932 33.333 4.50 0.00 27.68 4.02
3695 3968 3.914426 AATGGCAGAGTTCTACGGATT 57.086 42.857 0.00 0.00 0.00 3.01
3915 4188 1.229428 CTCGAAAAGCTTGTGAGGCA 58.771 50.000 0.00 0.00 0.00 4.75
3917 4190 0.239347 CGAAAAGCTTGTGAGGCAGG 59.761 55.000 0.00 0.00 0.00 4.85
3919 4192 1.538950 GAAAAGCTTGTGAGGCAGGAG 59.461 52.381 0.00 0.00 0.00 3.69
3920 4193 0.475906 AAAGCTTGTGAGGCAGGAGT 59.524 50.000 0.00 0.00 0.00 3.85
3923 4196 0.321671 GCTTGTGAGGCAGGAGTACA 59.678 55.000 0.00 0.00 0.00 2.90
3924 4197 1.065854 GCTTGTGAGGCAGGAGTACAT 60.066 52.381 0.00 0.00 0.00 2.29
3928 4201 3.374764 TGTGAGGCAGGAGTACATATGT 58.625 45.455 13.93 13.93 0.00 2.29
3958 4231 3.135225 CGTTTGACACCACCTACATGAA 58.865 45.455 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.360852 CCAGCTGGACCAAGCAGG 60.361 66.667 29.88 13.30 46.08 4.85
1 2 3.060615 GCCAGCTGGACCAAGCAG 61.061 66.667 37.21 6.70 46.08 4.24
2 3 3.557903 GAGCCAGCTGGACCAAGCA 62.558 63.158 37.21 0.00 46.08 3.91
3 4 2.749441 GAGCCAGCTGGACCAAGC 60.749 66.667 37.21 19.26 43.88 4.01
4 5 2.045536 GGAGCCAGCTGGACCAAG 60.046 66.667 37.21 9.14 37.39 3.61
5 6 2.853542 TGGAGCCAGCTGGACCAA 60.854 61.111 34.40 23.46 39.11 3.67
6 7 3.640407 GTGGAGCCAGCTGGACCA 61.640 66.667 37.21 34.96 39.51 4.02
7 8 2.900106 AAGTGGAGCCAGCTGGACC 61.900 63.158 37.21 33.00 37.39 4.46
8 9 1.673665 CAAGTGGAGCCAGCTGGAC 60.674 63.158 37.21 26.34 37.39 4.02
9 10 2.752358 CAAGTGGAGCCAGCTGGA 59.248 61.111 37.21 12.97 37.39 3.86
10 11 2.360852 CCAAGTGGAGCCAGCTGG 60.361 66.667 29.34 29.34 37.39 4.85
11 12 3.060615 GCCAAGTGGAGCCAGCTG 61.061 66.667 6.78 6.78 37.39 4.24
12 13 3.255397 AGCCAAGTGGAGCCAGCT 61.255 61.111 0.18 0.00 37.39 4.24
13 14 3.060615 CAGCCAAGTGGAGCCAGC 61.061 66.667 0.18 0.00 37.39 4.85
14 15 3.060615 GCAGCCAAGTGGAGCCAG 61.061 66.667 0.18 0.00 37.39 4.85
15 16 3.557903 GAGCAGCCAAGTGGAGCCA 62.558 63.158 0.18 0.00 38.15 4.75
16 17 2.749441 GAGCAGCCAAGTGGAGCC 60.749 66.667 0.18 0.00 38.15 4.70
17 18 1.378250 ATGAGCAGCCAAGTGGAGC 60.378 57.895 0.18 4.32 37.82 4.70
18 19 0.035725 TCATGAGCAGCCAAGTGGAG 60.036 55.000 0.18 0.00 37.39 3.86
19 20 0.622136 ATCATGAGCAGCCAAGTGGA 59.378 50.000 0.09 0.00 37.39 4.02
20 21 1.134367 CAATCATGAGCAGCCAAGTGG 59.866 52.381 0.09 0.00 38.53 4.00
21 22 1.134367 CCAATCATGAGCAGCCAAGTG 59.866 52.381 0.09 0.00 0.00 3.16
22 23 1.471119 CCAATCATGAGCAGCCAAGT 58.529 50.000 0.09 0.00 0.00 3.16
23 24 0.102481 GCCAATCATGAGCAGCCAAG 59.898 55.000 0.09 0.00 0.00 3.61
24 25 0.323999 AGCCAATCATGAGCAGCCAA 60.324 50.000 0.09 0.00 0.00 4.52
25 26 0.750546 GAGCCAATCATGAGCAGCCA 60.751 55.000 0.09 0.00 0.00 4.75
26 27 0.750546 TGAGCCAATCATGAGCAGCC 60.751 55.000 0.09 0.00 31.12 4.85
27 28 0.663688 CTGAGCCAATCATGAGCAGC 59.336 55.000 0.09 3.47 37.28 5.25
28 29 1.134189 TCCTGAGCCAATCATGAGCAG 60.134 52.381 0.09 2.07 37.28 4.24
29 30 0.913924 TCCTGAGCCAATCATGAGCA 59.086 50.000 0.09 0.00 37.28 4.26
30 31 1.307097 GTCCTGAGCCAATCATGAGC 58.693 55.000 0.09 0.00 37.28 4.26
31 32 1.211212 TGGTCCTGAGCCAATCATGAG 59.789 52.381 0.09 0.00 37.28 2.90
32 33 1.288188 TGGTCCTGAGCCAATCATGA 58.712 50.000 0.00 0.00 37.28 3.07
33 34 2.133281 TTGGTCCTGAGCCAATCATG 57.867 50.000 0.00 0.00 40.69 3.07
34 35 2.905415 TTTGGTCCTGAGCCAATCAT 57.095 45.000 0.00 0.00 44.44 2.45
35 36 2.225091 ACATTTGGTCCTGAGCCAATCA 60.225 45.455 0.00 0.00 44.44 2.57
36 37 2.165030 CACATTTGGTCCTGAGCCAATC 59.835 50.000 0.00 0.00 44.44 2.67
37 38 2.173519 CACATTTGGTCCTGAGCCAAT 58.826 47.619 0.00 0.00 44.44 3.16
38 39 1.619654 CACATTTGGTCCTGAGCCAA 58.380 50.000 0.00 0.00 43.51 4.52
39 40 0.895100 GCACATTTGGTCCTGAGCCA 60.895 55.000 0.00 0.00 0.00 4.75
40 41 0.895100 TGCACATTTGGTCCTGAGCC 60.895 55.000 0.00 0.00 0.00 4.70
41 42 0.242017 GTGCACATTTGGTCCTGAGC 59.758 55.000 13.17 0.00 0.00 4.26
42 43 0.883833 GGTGCACATTTGGTCCTGAG 59.116 55.000 20.43 0.00 0.00 3.35
43 44 0.478072 AGGTGCACATTTGGTCCTGA 59.522 50.000 20.43 0.00 0.00 3.86
44 45 1.000060 CAAGGTGCACATTTGGTCCTG 60.000 52.381 20.43 0.37 0.00 3.86
45 46 1.133513 TCAAGGTGCACATTTGGTCCT 60.134 47.619 24.38 7.75 0.00 3.85
46 47 1.270550 CTCAAGGTGCACATTTGGTCC 59.729 52.381 24.38 5.69 0.00 4.46
47 48 2.229792 TCTCAAGGTGCACATTTGGTC 58.770 47.619 24.38 6.26 0.00 4.02
48 49 2.362077 GTTCTCAAGGTGCACATTTGGT 59.638 45.455 24.38 0.97 0.00 3.67
49 50 2.361757 TGTTCTCAAGGTGCACATTTGG 59.638 45.455 24.38 16.33 0.00 3.28
50 51 3.713858 TGTTCTCAAGGTGCACATTTG 57.286 42.857 20.43 20.77 0.00 2.32
51 52 4.311816 CTTGTTCTCAAGGTGCACATTT 57.688 40.909 20.43 9.63 45.02 2.32
52 53 3.996150 CTTGTTCTCAAGGTGCACATT 57.004 42.857 20.43 16.17 45.02 2.71
60 61 6.508041 TGGTCCTCCAACTTGTTCTCAAGG 62.508 50.000 11.69 0.00 45.06 3.61
61 62 3.433598 TGGTCCTCCAACTTGTTCTCAAG 60.434 47.826 6.44 6.44 45.59 3.02
62 63 2.507886 TGGTCCTCCAACTTGTTCTCAA 59.492 45.455 0.00 0.00 41.25 3.02
63 64 2.123589 TGGTCCTCCAACTTGTTCTCA 58.876 47.619 0.00 0.00 41.25 3.27
64 65 2.930826 TGGTCCTCCAACTTGTTCTC 57.069 50.000 0.00 0.00 41.25 2.87
74 75 6.518200 GCAAAAGTGAATTATTTGGTCCTCCA 60.518 38.462 0.00 0.00 42.66 3.86
75 76 5.869344 GCAAAAGTGAATTATTTGGTCCTCC 59.131 40.000 0.00 0.00 35.21 4.30
76 77 6.454795 TGCAAAAGTGAATTATTTGGTCCTC 58.545 36.000 0.00 0.00 35.21 3.71
77 78 6.418057 TGCAAAAGTGAATTATTTGGTCCT 57.582 33.333 0.00 0.00 35.21 3.85
78 79 6.705825 ACTTGCAAAAGTGAATTATTTGGTCC 59.294 34.615 0.00 0.00 35.21 4.46
79 80 7.713764 ACTTGCAAAAGTGAATTATTTGGTC 57.286 32.000 0.00 0.00 35.21 4.02
80 81 8.397148 CAAACTTGCAAAAGTGAATTATTTGGT 58.603 29.630 0.00 0.00 35.21 3.67
81 82 8.610896 TCAAACTTGCAAAAGTGAATTATTTGG 58.389 29.630 0.00 0.00 35.21 3.28
82 83 9.640974 CTCAAACTTGCAAAAGTGAATTATTTG 57.359 29.630 0.00 0.00 37.17 2.32
83 84 8.829612 CCTCAAACTTGCAAAAGTGAATTATTT 58.170 29.630 0.00 0.00 32.47 1.40
84 85 8.203485 TCCTCAAACTTGCAAAAGTGAATTATT 58.797 29.630 0.00 0.00 32.47 1.40
85 86 7.653311 GTCCTCAAACTTGCAAAAGTGAATTAT 59.347 33.333 0.00 0.00 32.47 1.28
86 87 6.978080 GTCCTCAAACTTGCAAAAGTGAATTA 59.022 34.615 0.00 0.00 32.47 1.40
87 88 5.812127 GTCCTCAAACTTGCAAAAGTGAATT 59.188 36.000 0.00 0.00 32.47 2.17
88 89 5.351458 GTCCTCAAACTTGCAAAAGTGAAT 58.649 37.500 0.00 0.00 32.47 2.57
89 90 4.381505 GGTCCTCAAACTTGCAAAAGTGAA 60.382 41.667 0.00 0.00 32.47 3.18
90 91 3.130340 GGTCCTCAAACTTGCAAAAGTGA 59.870 43.478 0.00 3.11 32.47 3.41
91 92 3.119173 TGGTCCTCAAACTTGCAAAAGTG 60.119 43.478 0.00 0.00 32.47 3.16
92 93 3.096092 TGGTCCTCAAACTTGCAAAAGT 58.904 40.909 0.00 0.00 33.76 2.66
93 94 3.799281 TGGTCCTCAAACTTGCAAAAG 57.201 42.857 0.00 0.00 0.00 2.27
94 95 4.543590 TTTGGTCCTCAAACTTGCAAAA 57.456 36.364 0.00 0.00 40.14 2.44
95 96 4.249661 GTTTTGGTCCTCAAACTTGCAAA 58.750 39.130 0.00 0.00 44.20 3.68
96 97 3.259374 TGTTTTGGTCCTCAAACTTGCAA 59.741 39.130 14.70 0.00 44.20 4.08
97 98 2.828520 TGTTTTGGTCCTCAAACTTGCA 59.171 40.909 14.70 0.00 44.20 4.08
98 99 3.518634 TGTTTTGGTCCTCAAACTTGC 57.481 42.857 14.70 0.00 44.20 4.01
99 100 5.043248 GTGATGTTTTGGTCCTCAAACTTG 58.957 41.667 14.70 0.00 44.20 3.16
100 101 4.709397 TGTGATGTTTTGGTCCTCAAACTT 59.291 37.500 14.70 10.31 44.20 2.66
101 102 4.277476 TGTGATGTTTTGGTCCTCAAACT 58.723 39.130 14.70 4.79 44.20 2.66
102 103 4.647424 TGTGATGTTTTGGTCCTCAAAC 57.353 40.909 9.28 9.28 44.20 2.93
103 104 4.501229 GCATGTGATGTTTTGGTCCTCAAA 60.501 41.667 0.00 0.00 42.98 2.69
104 105 3.005684 GCATGTGATGTTTTGGTCCTCAA 59.994 43.478 0.00 0.00 0.00 3.02
105 106 2.557924 GCATGTGATGTTTTGGTCCTCA 59.442 45.455 0.00 0.00 0.00 3.86
106 107 2.557924 TGCATGTGATGTTTTGGTCCTC 59.442 45.455 0.00 0.00 0.00 3.71
107 108 2.596346 TGCATGTGATGTTTTGGTCCT 58.404 42.857 0.00 0.00 0.00 3.85
108 109 3.005684 TCTTGCATGTGATGTTTTGGTCC 59.994 43.478 0.00 0.00 0.00 4.46
109 110 3.983344 GTCTTGCATGTGATGTTTTGGTC 59.017 43.478 0.00 0.00 0.00 4.02
110 111 3.384146 TGTCTTGCATGTGATGTTTTGGT 59.616 39.130 0.00 0.00 0.00 3.67
111 112 3.979948 TGTCTTGCATGTGATGTTTTGG 58.020 40.909 0.00 0.00 0.00 3.28
112 113 5.045215 ACTTGTCTTGCATGTGATGTTTTG 58.955 37.500 0.00 0.00 34.66 2.44
113 114 5.266733 ACTTGTCTTGCATGTGATGTTTT 57.733 34.783 0.00 0.00 34.66 2.43
114 115 4.924305 ACTTGTCTTGCATGTGATGTTT 57.076 36.364 0.00 0.00 34.66 2.83
115 116 4.261741 GGAACTTGTCTTGCATGTGATGTT 60.262 41.667 0.00 2.97 35.90 2.71
116 117 3.254166 GGAACTTGTCTTGCATGTGATGT 59.746 43.478 0.00 0.00 35.90 3.06
117 118 3.253921 TGGAACTTGTCTTGCATGTGATG 59.746 43.478 0.00 0.00 35.90 3.07
118 119 3.489355 TGGAACTTGTCTTGCATGTGAT 58.511 40.909 0.00 0.00 35.90 3.06
119 120 2.880268 CTGGAACTTGTCTTGCATGTGA 59.120 45.455 0.00 0.00 35.90 3.58
120 121 2.030540 CCTGGAACTTGTCTTGCATGTG 60.031 50.000 0.00 0.00 35.90 3.21
121 122 2.158623 TCCTGGAACTTGTCTTGCATGT 60.159 45.455 0.00 0.00 37.10 3.21
122 123 2.227388 GTCCTGGAACTTGTCTTGCATG 59.773 50.000 0.00 0.00 0.00 4.06
123 124 2.508526 GTCCTGGAACTTGTCTTGCAT 58.491 47.619 0.00 0.00 0.00 3.96
124 125 1.476833 GGTCCTGGAACTTGTCTTGCA 60.477 52.381 3.98 0.00 0.00 4.08
125 126 1.202818 AGGTCCTGGAACTTGTCTTGC 60.203 52.381 8.88 0.00 0.00 4.01
126 127 2.498167 CAGGTCCTGGAACTTGTCTTG 58.502 52.381 12.63 0.00 0.00 3.02
127 128 1.202818 GCAGGTCCTGGAACTTGTCTT 60.203 52.381 20.72 0.00 31.21 3.01
128 129 0.398318 GCAGGTCCTGGAACTTGTCT 59.602 55.000 20.72 0.00 31.21 3.41
129 130 0.606673 GGCAGGTCCTGGAACTTGTC 60.607 60.000 20.72 5.78 31.21 3.18
130 131 1.456287 GGCAGGTCCTGGAACTTGT 59.544 57.895 20.72 0.00 31.21 3.16
131 132 1.672356 CGGCAGGTCCTGGAACTTG 60.672 63.158 20.72 9.05 31.21 3.16
132 133 2.147387 ACGGCAGGTCCTGGAACTT 61.147 57.895 20.72 0.00 31.21 2.66
133 134 2.526873 ACGGCAGGTCCTGGAACT 60.527 61.111 20.72 8.88 31.21 3.01
134 135 2.358737 CACGGCAGGTCCTGGAAC 60.359 66.667 20.72 2.72 31.21 3.62
135 136 4.329545 GCACGGCAGGTCCTGGAA 62.330 66.667 20.72 0.00 31.21 3.53
136 137 3.897681 TAGCACGGCAGGTCCTGGA 62.898 63.158 20.72 0.00 31.21 3.86
137 138 2.257409 AATAGCACGGCAGGTCCTGG 62.257 60.000 20.72 7.28 31.21 4.45
138 139 0.464036 TAATAGCACGGCAGGTCCTG 59.536 55.000 15.15 15.15 34.12 3.86
139 140 0.464452 GTAATAGCACGGCAGGTCCT 59.536 55.000 0.00 0.00 0.00 3.85
140 141 0.532196 GGTAATAGCACGGCAGGTCC 60.532 60.000 0.00 0.00 0.00 4.46
141 142 0.464452 AGGTAATAGCACGGCAGGTC 59.536 55.000 0.00 0.00 0.00 3.85
142 143 0.909623 AAGGTAATAGCACGGCAGGT 59.090 50.000 0.00 0.00 0.00 4.00
143 144 2.038387 AAAGGTAATAGCACGGCAGG 57.962 50.000 0.00 0.00 0.00 4.85
144 145 2.354821 GGAAAAGGTAATAGCACGGCAG 59.645 50.000 0.00 0.00 0.00 4.85
145 146 2.290387 TGGAAAAGGTAATAGCACGGCA 60.290 45.455 0.00 0.00 0.00 5.69
146 147 2.361789 TGGAAAAGGTAATAGCACGGC 58.638 47.619 0.00 0.00 0.00 5.68
147 148 5.576447 AAATGGAAAAGGTAATAGCACGG 57.424 39.130 0.00 0.00 0.00 4.94
170 171 9.944663 GTCACAGACATGAATTTTAAGTGTAAA 57.055 29.630 0.00 0.00 32.09 2.01
171 172 9.114952 TGTCACAGACATGAATTTTAAGTGTAA 57.885 29.630 0.00 0.00 37.67 2.41
172 173 8.669946 TGTCACAGACATGAATTTTAAGTGTA 57.330 30.769 0.00 0.00 37.67 2.90
173 174 7.566760 TGTCACAGACATGAATTTTAAGTGT 57.433 32.000 0.00 0.00 37.67 3.55
206 207 9.504708 TGAATTCAAAATTTGCACTAAATGGAT 57.495 25.926 5.45 0.00 38.93 3.41
207 208 8.772705 GTGAATTCAAAATTTGCACTAAATGGA 58.227 29.630 10.35 0.00 38.93 3.41
208 209 8.016801 GGTGAATTCAAAATTTGCACTAAATGG 58.983 33.333 10.35 0.00 38.93 3.16
209 210 8.776470 AGGTGAATTCAAAATTTGCACTAAATG 58.224 29.630 10.35 0.00 38.93 2.32
210 211 8.907222 AGGTGAATTCAAAATTTGCACTAAAT 57.093 26.923 10.35 0.63 40.67 1.40
211 212 7.984050 TGAGGTGAATTCAAAATTTGCACTAAA 59.016 29.630 10.35 0.00 0.00 1.85
212 213 7.495901 TGAGGTGAATTCAAAATTTGCACTAA 58.504 30.769 10.35 0.00 0.00 2.24
213 214 7.048629 TGAGGTGAATTCAAAATTTGCACTA 57.951 32.000 10.35 1.01 0.00 2.74
214 215 5.916318 TGAGGTGAATTCAAAATTTGCACT 58.084 33.333 10.35 0.00 0.00 4.40
215 216 6.790285 ATGAGGTGAATTCAAAATTTGCAC 57.210 33.333 10.35 3.55 0.00 4.57
216 217 7.804843 AAATGAGGTGAATTCAAAATTTGCA 57.195 28.000 10.35 2.66 0.00 4.08
224 225 9.619316 CGTAAACATAAAATGAGGTGAATTCAA 57.381 29.630 10.35 0.00 0.00 2.69
225 226 8.240682 CCGTAAACATAAAATGAGGTGAATTCA 58.759 33.333 3.38 3.38 0.00 2.57
226 227 7.700656 CCCGTAAACATAAAATGAGGTGAATTC 59.299 37.037 0.00 0.00 0.00 2.17
227 228 7.394923 TCCCGTAAACATAAAATGAGGTGAATT 59.605 33.333 0.00 0.00 0.00 2.17
228 229 6.887545 TCCCGTAAACATAAAATGAGGTGAAT 59.112 34.615 0.00 0.00 0.00 2.57
229 230 6.149807 GTCCCGTAAACATAAAATGAGGTGAA 59.850 38.462 0.00 0.00 0.00 3.18
230 231 5.644636 GTCCCGTAAACATAAAATGAGGTGA 59.355 40.000 0.00 0.00 0.00 4.02
231 232 5.646360 AGTCCCGTAAACATAAAATGAGGTG 59.354 40.000 0.00 0.00 0.00 4.00
232 233 5.812286 AGTCCCGTAAACATAAAATGAGGT 58.188 37.500 0.00 0.00 0.00 3.85
233 234 6.018180 GCTAGTCCCGTAAACATAAAATGAGG 60.018 42.308 0.00 0.00 0.00 3.86
234 235 6.018180 GGCTAGTCCCGTAAACATAAAATGAG 60.018 42.308 0.00 0.00 0.00 2.90
235 236 5.818857 GGCTAGTCCCGTAAACATAAAATGA 59.181 40.000 0.00 0.00 0.00 2.57
236 237 5.587043 TGGCTAGTCCCGTAAACATAAAATG 59.413 40.000 0.00 0.00 0.00 2.32
237 238 5.587443 GTGGCTAGTCCCGTAAACATAAAAT 59.413 40.000 0.00 0.00 0.00 1.82
238 239 4.937015 GTGGCTAGTCCCGTAAACATAAAA 59.063 41.667 0.00 0.00 0.00 1.52
239 240 4.506758 GTGGCTAGTCCCGTAAACATAAA 58.493 43.478 0.00 0.00 0.00 1.40
240 241 3.429272 CGTGGCTAGTCCCGTAAACATAA 60.429 47.826 0.00 0.00 0.00 1.90
241 242 2.099592 CGTGGCTAGTCCCGTAAACATA 59.900 50.000 0.00 0.00 0.00 2.29
242 243 1.134907 CGTGGCTAGTCCCGTAAACAT 60.135 52.381 0.00 0.00 0.00 2.71
243 244 0.244450 CGTGGCTAGTCCCGTAAACA 59.756 55.000 0.00 0.00 0.00 2.83
244 245 0.244721 ACGTGGCTAGTCCCGTAAAC 59.755 55.000 2.10 0.00 39.06 2.01
245 246 0.244450 CACGTGGCTAGTCCCGTAAA 59.756 55.000 4.11 0.00 38.90 2.01
246 247 0.608856 TCACGTGGCTAGTCCCGTAA 60.609 55.000 17.00 0.00 38.90 3.18
247 248 1.002257 TCACGTGGCTAGTCCCGTA 60.002 57.895 17.00 0.00 38.90 4.02
248 249 2.282674 TCACGTGGCTAGTCCCGT 60.283 61.111 17.00 0.00 40.65 5.28
249 250 2.490217 CTCACGTGGCTAGTCCCG 59.510 66.667 17.00 0.00 35.52 5.14
250 251 2.184579 GCTCACGTGGCTAGTCCC 59.815 66.667 17.00 0.00 0.00 4.46
251 252 2.202623 CGCTCACGTGGCTAGTCC 60.203 66.667 17.00 0.00 33.53 3.85
252 253 2.202623 CCGCTCACGTGGCTAGTC 60.203 66.667 17.00 1.88 37.70 2.59
253 254 2.095978 AAACCGCTCACGTGGCTAGT 62.096 55.000 17.00 14.08 44.86 2.57
254 255 0.949105 AAAACCGCTCACGTGGCTAG 60.949 55.000 17.00 13.50 44.86 3.42
255 256 0.533308 AAAAACCGCTCACGTGGCTA 60.533 50.000 17.00 0.00 44.86 3.93
256 257 0.533308 TAAAAACCGCTCACGTGGCT 60.533 50.000 17.00 3.87 44.86 4.75
257 258 0.519961 ATAAAAACCGCTCACGTGGC 59.480 50.000 17.00 16.53 44.86 5.01
258 259 2.981400 AATAAAAACCGCTCACGTGG 57.019 45.000 17.00 7.71 46.44 4.94
259 260 3.423867 CCAAAATAAAAACCGCTCACGTG 59.576 43.478 9.94 9.94 37.70 4.49
260 261 3.315749 TCCAAAATAAAAACCGCTCACGT 59.684 39.130 0.00 0.00 37.70 4.49
261 262 3.891324 TCCAAAATAAAAACCGCTCACG 58.109 40.909 0.00 0.00 39.67 4.35
262 263 4.091365 GCATCCAAAATAAAAACCGCTCAC 59.909 41.667 0.00 0.00 0.00 3.51
263 264 4.241681 GCATCCAAAATAAAAACCGCTCA 58.758 39.130 0.00 0.00 0.00 4.26
264 265 3.303229 CGCATCCAAAATAAAAACCGCTC 59.697 43.478 0.00 0.00 0.00 5.03
265 266 3.249917 CGCATCCAAAATAAAAACCGCT 58.750 40.909 0.00 0.00 0.00 5.52
266 267 2.990514 ACGCATCCAAAATAAAAACCGC 59.009 40.909 0.00 0.00 0.00 5.68
267 268 4.481463 AGACGCATCCAAAATAAAAACCG 58.519 39.130 0.00 0.00 0.00 4.44
268 269 6.526674 CACTAGACGCATCCAAAATAAAAACC 59.473 38.462 0.00 0.00 0.00 3.27
269 270 6.526674 CCACTAGACGCATCCAAAATAAAAAC 59.473 38.462 0.00 0.00 0.00 2.43
270 271 6.349777 CCCACTAGACGCATCCAAAATAAAAA 60.350 38.462 0.00 0.00 0.00 1.94
271 272 5.124776 CCCACTAGACGCATCCAAAATAAAA 59.875 40.000 0.00 0.00 0.00 1.52
272 273 4.638421 CCCACTAGACGCATCCAAAATAAA 59.362 41.667 0.00 0.00 0.00 1.40
273 274 4.196193 CCCACTAGACGCATCCAAAATAA 58.804 43.478 0.00 0.00 0.00 1.40
274 275 3.804036 CCCACTAGACGCATCCAAAATA 58.196 45.455 0.00 0.00 0.00 1.40
275 276 2.643551 CCCACTAGACGCATCCAAAAT 58.356 47.619 0.00 0.00 0.00 1.82
276 277 1.948611 GCCCACTAGACGCATCCAAAA 60.949 52.381 0.00 0.00 0.00 2.44
277 278 0.392461 GCCCACTAGACGCATCCAAA 60.392 55.000 0.00 0.00 0.00 3.28
278 279 1.220749 GCCCACTAGACGCATCCAA 59.779 57.895 0.00 0.00 0.00 3.53
356 358 0.680618 TTCCTTTTCTGTACCGCGGA 59.319 50.000 35.90 13.31 0.00 5.54
380 382 2.442087 GGTAAGGTGGCCCCATGC 60.442 66.667 12.24 4.37 40.16 4.06
385 387 4.832608 CGCTCGGTAAGGTGGCCC 62.833 72.222 0.00 0.00 0.00 5.80
726 728 2.512355 GGGGCTAGCTAGGGACAGC 61.512 68.421 22.10 9.14 42.12 4.40
727 729 1.839296 GGGGGCTAGCTAGGGACAG 60.839 68.421 22.10 0.00 0.00 3.51
728 730 2.285868 GGGGGCTAGCTAGGGACA 59.714 66.667 22.10 0.00 0.00 4.02
729 731 2.141448 GTGGGGGCTAGCTAGGGAC 61.141 68.421 22.10 5.63 0.00 4.46
730 732 2.285868 GTGGGGGCTAGCTAGGGA 59.714 66.667 22.10 0.00 0.00 4.20
731 733 3.234730 CGTGGGGGCTAGCTAGGG 61.235 72.222 22.10 0.00 0.00 3.53
732 734 3.930012 GCGTGGGGGCTAGCTAGG 61.930 72.222 22.10 4.82 0.00 3.02
733 735 3.930012 GGCGTGGGGGCTAGCTAG 61.930 72.222 16.84 16.84 38.40 3.42
839 854 0.326238 AGAAGGGTCTGGGGCGATTA 60.326 55.000 0.00 0.00 30.83 1.75
851 867 0.494095 ACAGGAGGAGGAAGAAGGGT 59.506 55.000 0.00 0.00 0.00 4.34
897 913 6.655425 GGTATGCCTCTTGAAGTAGTTTCTTT 59.345 38.462 0.00 0.00 36.71 2.52
916 932 1.474498 CCCCTTCTACCGTTGGTATGC 60.474 57.143 0.00 0.00 37.56 3.14
1057 1081 5.571791 TGGATTTGCTGATAGATCCATGA 57.428 39.130 0.00 0.00 42.21 3.07
1141 1188 3.690475 AGTGTGAAGATGCACTCATGA 57.310 42.857 0.00 0.00 41.58 3.07
1155 1202 6.295249 TGATCTCAAACCATGTTTAGTGTGA 58.705 36.000 0.00 0.00 0.00 3.58
1196 1244 5.531287 ACACCTCCAGTTTAGAAAACATGTC 59.469 40.000 0.00 0.00 0.00 3.06
1228 1286 4.762251 GCCAGAAAATCTGTCTTAGTTGGT 59.238 41.667 6.62 0.00 42.80 3.67
1549 1628 5.195001 TGTTTAGTTGGCCAGAAAACATC 57.805 39.130 26.05 11.08 35.69 3.06
1610 1695 6.798427 TCAGTTGCCTAGAATAGATGTCTT 57.202 37.500 0.00 0.00 42.77 3.01
1778 1870 4.443034 GCTAGAATAGATGTCCCCGTTGTT 60.443 45.833 0.00 0.00 42.77 2.83
1779 1871 3.069729 GCTAGAATAGATGTCCCCGTTGT 59.930 47.826 0.00 0.00 42.77 3.32
1784 1876 4.706842 TTTGGCTAGAATAGATGTCCCC 57.293 45.455 0.00 0.00 42.77 4.81
1786 1878 5.437060 TGGTTTTGGCTAGAATAGATGTCC 58.563 41.667 0.00 0.00 42.77 4.02
1815 1995 4.812091 TGTGTTTTTGCTGTCGTACTACAT 59.188 37.500 0.06 0.00 0.00 2.29
1865 2045 7.966204 GCGTGACTATTTTAATATGGTTTGTGT 59.034 33.333 0.00 0.00 0.00 3.72
1902 2096 3.535561 GACCAGAATATGTGTGTGGGAG 58.464 50.000 0.00 0.00 32.13 4.30
1912 2106 5.413833 GCAATAGATGTGGGACCAGAATATG 59.586 44.000 0.00 0.00 0.00 1.78
2297 2538 1.742831 GGAGTTGCACGCCATTATGAA 59.257 47.619 0.00 0.00 38.02 2.57
2307 2550 5.416947 ACTTAGTAAATAGGGAGTTGCACG 58.583 41.667 0.00 0.00 0.00 5.34
2390 2639 5.181245 CCACACACTCCCTACACATAAAAAG 59.819 44.000 0.00 0.00 0.00 2.27
2616 2877 3.228453 CACCACTATAGGGGTATCACGT 58.772 50.000 26.44 0.00 35.09 4.49
2699 2960 2.312140 ACTCCTAGCTCAGTCCTGGTTA 59.688 50.000 0.00 0.00 0.00 2.85
2726 2987 1.002576 CTTGCACAGCATCGTCAACAA 60.003 47.619 0.00 0.00 38.76 2.83
2735 2996 2.434428 CTTCTTCTCCTTGCACAGCAT 58.566 47.619 0.00 0.00 38.76 3.79
2843 3104 2.822215 CCCATCTGTAGGGCGTAGT 58.178 57.895 0.00 0.00 39.96 2.73
2874 3135 2.029623 GTCCGCCTAGAGGTGTTCATA 58.970 52.381 8.29 0.00 43.97 2.15
2979 3240 2.301738 GGGTCCAGGACAGGAAGGG 61.302 68.421 21.75 0.00 39.92 3.95
2982 3243 2.478292 GAATAGGGTCCAGGACAGGAA 58.522 52.381 21.75 3.87 39.92 3.36
3004 3265 5.841810 TCACTGTCAACAATTTTTGGATCC 58.158 37.500 4.20 4.20 34.12 3.36
3014 3275 5.184479 CCATTTCCTCATCACTGTCAACAAT 59.816 40.000 0.00 0.00 0.00 2.71
3100 3361 5.527582 AGTCTGCTTTATTGTCTCGTGTTTT 59.472 36.000 0.00 0.00 0.00 2.43
3394 3663 7.871853 ACACCAGTTACACAATTAAGACATTC 58.128 34.615 0.00 0.00 0.00 2.67
3410 3679 1.139256 TGCGAAGTTGGACACCAGTTA 59.861 47.619 0.00 0.00 33.81 2.24
3428 3697 7.934457 ACCAAAGTGATATAGAAACATCATGC 58.066 34.615 0.00 0.00 33.92 4.06
3516 3788 5.580691 AGCTGCACCTTTTTAAAAACACTTC 59.419 36.000 9.31 0.11 0.00 3.01
3549 3821 5.336690 GGCACAGAAGATAATTGCAGGAAAA 60.337 40.000 0.00 0.00 34.76 2.29
3662 3935 8.272889 AGAACTCTGCCATTATATGCATCATAT 58.727 33.333 0.19 0.00 39.86 1.78
3695 3968 1.003003 TGAACGGCACCATCATCTCAA 59.997 47.619 0.00 0.00 0.00 3.02
3908 4181 4.408182 AACATATGTACTCCTGCCTCAC 57.592 45.455 9.21 0.00 0.00 3.51
3911 4184 3.054434 TGCAAACATATGTACTCCTGCCT 60.054 43.478 9.21 0.00 0.00 4.75
3924 4197 5.412904 TGGTGTCAAACGATATGCAAACATA 59.587 36.000 0.00 0.00 42.85 2.29
3928 4201 3.057876 GGTGGTGTCAAACGATATGCAAA 60.058 43.478 0.00 0.00 0.00 3.68
3958 4231 4.201773 CGAACGGCATATTGTACATGTTGT 60.202 41.667 2.30 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.