Multiple sequence alignment - TraesCS1B01G012800

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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 TraesCS1B01G012800 chr1B 100.000 6277 0 0 1 6277 6193320 6199596 0.000000e+00 11592.0
1 TraesCS1B01G012800 chr1B 85.430 2766 384 12 995 3743 6487746 6484983 0.000000e+00 2857.0
2 TraesCS1B01G012800 chr1B 83.690 2802 401 31 989 3743 629652711 629655503 0.000000e+00 2591.0
3 TraesCS1B01G012800 chr1B 84.454 2618 377 20 985 3588 29909044 29906443 0.000000e+00 2553.0
4 TraesCS1B01G012800 chr1B 83.041 2795 419 32 991 3743 5694912 5697693 0.000000e+00 2484.0
5 TraesCS1B01G012800 chr1B 82.738 2798 425 31 991 3743 6281137 6283921 0.000000e+00 2438.0
6 TraesCS1B01G012800 chr1B 86.483 2175 286 7 995 3165 5985933 5988103 0.000000e+00 2381.0
7 TraesCS1B01G012800 chr1B 85.418 2119 296 7 990 3106 5950026 5952133 0.000000e+00 2189.0
8 TraesCS1B01G012800 chr1B 95.779 1303 48 4 4481 5778 7420423 7421723 0.000000e+00 2095.0
9 TraesCS1B01G012800 chr1B 79.362 1410 230 29 3750 5111 5988823 5990219 0.000000e+00 935.0
10 TraesCS1B01G012800 chr1B 79.050 1389 258 27 3753 5124 7634578 7633206 0.000000e+00 922.0
11 TraesCS1B01G012800 chr1B 79.052 1413 230 36 3743 5111 6063283 6064673 0.000000e+00 909.0
12 TraesCS1B01G012800 chr1B 78.475 1403 248 33 3749 5124 29906314 29904939 0.000000e+00 869.0
13 TraesCS1B01G012800 chr1B 84.709 327 27 8 1 324 7258023 7257717 7.910000e-79 305.0
14 TraesCS1B01G012800 chr1B 89.908 218 9 3 5975 6187 7441559 7441768 1.040000e-67 268.0
15 TraesCS1B01G012800 chr1B 87.083 240 7 5 6043 6277 7082239 7082019 3.760000e-62 250.0
16 TraesCS1B01G012800 chr1B 74.504 706 98 47 215 867 5946186 5946862 1.360000e-56 231.0
17 TraesCS1B01G012800 chr1B 76.960 421 78 12 4704 5111 6483935 6483521 8.190000e-54 222.0
18 TraesCS1B01G012800 chr1B 85.714 210 25 5 120 327 5948835 5949041 3.810000e-52 217.0
19 TraesCS1B01G012800 chr1B 96.800 125 4 0 5863 5987 7440092 7440216 6.380000e-50 209.0
20 TraesCS1B01G012800 chr1B 74.630 540 87 27 4616 5117 6764618 6764091 6.420000e-45 193.0
21 TraesCS1B01G012800 chr1B 92.683 123 9 0 5756 5878 7439957 7440079 1.800000e-40 178.0
22 TraesCS1B01G012800 chr1B 96.703 91 2 1 6188 6277 7441803 7441893 3.920000e-32 150.0
23 TraesCS1B01G012800 chr1B 83.333 72 12 0 5331 5402 22720893 22720822 4.060000e-07 67.6
24 TraesCS1B01G012800 chr1B 100.000 28 0 0 921 948 6281071 6281098 1.100000e-02 52.8
25 TraesCS1B01G012800 chr1D 89.533 3124 292 22 771 3873 3175731 3178840 0.000000e+00 3925.0
26 TraesCS1B01G012800 chr1D 93.115 2629 133 17 3598 6184 3178712 3181334 0.000000e+00 3808.0
27 TraesCS1B01G012800 chr1D 84.877 3822 471 52 2 3743 5136256 5132462 0.000000e+00 3757.0
28 TraesCS1B01G012800 chr1D 79.011 1415 230 36 3743 5111 74951 73558 0.000000e+00 905.0
29 TraesCS1B01G012800 chr1D 78.037 1416 252 27 3743 5116 3972227 3970829 0.000000e+00 837.0
30 TraesCS1B01G012800 chr1D 79.583 960 166 16 3743 4688 4196183 4195240 0.000000e+00 660.0
31 TraesCS1B01G012800 chr1D 81.132 318 49 10 761 1072 3168083 3168395 1.750000e-60 244.0
32 TraesCS1B01G012800 chr1D 83.553 152 24 1 811 961 81144 80993 2.360000e-29 141.0
33 TraesCS1B01G012800 chr1D 75.969 258 22 21 486 706 5136517 5136263 5.180000e-16 97.1
34 TraesCS1B01G012800 chr1D 82.222 90 10 3 358 441 3167951 3168040 8.730000e-09 73.1
35 TraesCS1B01G012800 chr1D 92.857 42 2 1 909 949 77560 77519 6.800000e-05 60.2
36 TraesCS1B01G012800 chr1A 85.926 2771 369 15 991 3743 6341263 6338496 0.000000e+00 2937.0
37 TraesCS1B01G012800 chr1A 85.110 2767 393 13 991 3743 5505991 5503230 0.000000e+00 2809.0
38 TraesCS1B01G012800 chr1A 86.128 2177 295 6 991 3165 4497759 4499930 0.000000e+00 2340.0
39 TraesCS1B01G012800 chr1A 81.659 1374 228 17 3748 5112 6009852 6008494 0.000000e+00 1120.0
40 TraesCS1B01G012800 chr1A 79.357 1337 235 22 3757 5080 4552955 4554263 0.000000e+00 902.0
41 TraesCS1B01G012800 chr1A 78.762 1422 245 31 3743 5117 6338439 6337028 0.000000e+00 900.0
42 TraesCS1B01G012800 chr1A 77.252 1121 204 28 4026 5119 5647165 5646069 1.500000e-170 610.0
43 TraesCS1B01G012800 chr1A 86.250 80 11 0 5337 5416 6008386 6008307 3.120000e-13 87.9
44 TraesCS1B01G012800 chrUn 78.298 1410 244 38 3732 5116 9718847 9717475 0.000000e+00 852.0
45 TraesCS1B01G012800 chrUn 78.720 1297 222 33 3855 5124 117395583 117394314 0.000000e+00 817.0
46 TraesCS1B01G012800 chrUn 78.720 1297 222 33 3855 5124 336699161 336700430 0.000000e+00 817.0


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 TraesCS1B01G012800 chr1B 6193320 6199596 6276 False 11592.000000 11592 100.000000 1 6277 1 chr1B.!!$F3 6276
1 TraesCS1B01G012800 chr1B 629652711 629655503 2792 False 2591.000000 2591 83.690000 989 3743 1 chr1B.!!$F5 2754
2 TraesCS1B01G012800 chr1B 5694912 5697693 2781 False 2484.000000 2484 83.041000 991 3743 1 chr1B.!!$F1 2752
3 TraesCS1B01G012800 chr1B 7420423 7421723 1300 False 2095.000000 2095 95.779000 4481 5778 1 chr1B.!!$F4 1297
4 TraesCS1B01G012800 chr1B 29904939 29909044 4105 True 1711.000000 2553 81.464500 985 5124 2 chr1B.!!$R7 4139
5 TraesCS1B01G012800 chr1B 5985933 5990219 4286 False 1658.000000 2381 82.922500 995 5111 2 chr1B.!!$F7 4116
6 TraesCS1B01G012800 chr1B 6483521 6487746 4225 True 1539.500000 2857 81.195000 995 5111 2 chr1B.!!$R6 4116
7 TraesCS1B01G012800 chr1B 6281071 6283921 2850 False 1245.400000 2438 91.369000 921 3743 2 chr1B.!!$F8 2822
8 TraesCS1B01G012800 chr1B 7633206 7634578 1372 True 922.000000 922 79.050000 3753 5124 1 chr1B.!!$R4 1371
9 TraesCS1B01G012800 chr1B 6063283 6064673 1390 False 909.000000 909 79.052000 3743 5111 1 chr1B.!!$F2 1368
10 TraesCS1B01G012800 chr1B 5946186 5952133 5947 False 879.000000 2189 81.878667 120 3106 3 chr1B.!!$F6 2986
11 TraesCS1B01G012800 chr1B 7439957 7441893 1936 False 201.250000 268 94.023500 5756 6277 4 chr1B.!!$F9 521
12 TraesCS1B01G012800 chr1D 3175731 3181334 5603 False 3866.500000 3925 91.324000 771 6184 2 chr1D.!!$F2 5413
13 TraesCS1B01G012800 chr1D 5132462 5136517 4055 True 1927.050000 3757 80.423000 2 3743 2 chr1D.!!$R4 3741
14 TraesCS1B01G012800 chr1D 3970829 3972227 1398 True 837.000000 837 78.037000 3743 5116 1 chr1D.!!$R1 1373
15 TraesCS1B01G012800 chr1D 4195240 4196183 943 True 660.000000 660 79.583000 3743 4688 1 chr1D.!!$R2 945
16 TraesCS1B01G012800 chr1D 73558 81144 7586 True 368.733333 905 85.140333 811 5111 3 chr1D.!!$R3 4300
17 TraesCS1B01G012800 chr1A 5503230 5505991 2761 True 2809.000000 2809 85.110000 991 3743 1 chr1A.!!$R1 2752
18 TraesCS1B01G012800 chr1A 4497759 4499930 2171 False 2340.000000 2340 86.128000 991 3165 1 chr1A.!!$F1 2174
19 TraesCS1B01G012800 chr1A 6337028 6341263 4235 True 1918.500000 2937 82.344000 991 5117 2 chr1A.!!$R4 4126
20 TraesCS1B01G012800 chr1A 4552955 4554263 1308 False 902.000000 902 79.357000 3757 5080 1 chr1A.!!$F2 1323
21 TraesCS1B01G012800 chr1A 5646069 5647165 1096 True 610.000000 610 77.252000 4026 5119 1 chr1A.!!$R2 1093
22 TraesCS1B01G012800 chr1A 6008307 6009852 1545 True 603.950000 1120 83.954500 3748 5416 2 chr1A.!!$R3 1668
23 TraesCS1B01G012800 chrUn 9717475 9718847 1372 True 852.000000 852 78.298000 3732 5116 1 chrUn.!!$R1 1384
24 TraesCS1B01G012800 chrUn 117394314 117395583 1269 True 817.000000 817 78.720000 3855 5124 1 chrUn.!!$R2 1269
25 TraesCS1B01G012800 chrUn 336699161 336700430 1269 False 817.000000 817 78.720000 3855 5124 1 chrUn.!!$F1 1269

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
86 87 0.105593 ATATGTCTGCCAGTGCCTCG 59.894 55.000 0.00 0.0 36.33 4.63 F
1003 4074 0.032815 TCGTGTGAGCGTTCCAATGA 59.967 50.000 0.00 0.0 0.00 2.57 F
1984 8232 0.040942 TATGGGTGCAAACAGGGCAT 59.959 50.000 0.00 0.0 44.11 4.40 F
2118 8366 1.344114 GTGGAGAGATGCTCTGGATCC 59.656 57.143 4.20 4.2 41.35 3.36 F
2994 9266 2.045045 TTGAAGAGCATGCCCCCG 60.045 61.111 15.66 0.0 0.00 5.73 F
3644 10111 1.064906 CCAGAGATGGGATGTTGCTGT 60.065 52.381 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 4131 0.113776 TCCAGTAGGGAGTTGGACGT 59.886 55.000 0.00 0.0 42.15 4.34 R
2063 8311 0.179124 CTCGACTAGTTCAGCAGGCC 60.179 60.000 0.00 0.0 0.00 5.19 R
3541 10005 0.838608 TAACCTCCACCACACGGTTT 59.161 50.000 0.00 0.0 46.31 3.27 R
3624 10091 1.064906 ACAGCAACATCCCATCTCTGG 60.065 52.381 0.00 0.0 42.73 3.86 R
4927 11899 2.125147 TGACCTGTATGCCTGCGC 60.125 61.111 0.00 0.0 0.00 6.09 R
5453 12468 1.624813 TCCGAGGTTTACCCACGAAAT 59.375 47.619 14.56 0.0 38.12 2.17 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
30 31 9.726438 ACTGACATATAATATTTTCCTACCTGC 57.274 33.333 0.00 0.00 0.00 4.85
31 32 9.725019 CTGACATATAATATTTTCCTACCTGCA 57.275 33.333 0.00 0.00 0.00 4.41
37 38 3.806949 ATTTTCCTACCTGCAAGTGGA 57.193 42.857 0.00 1.80 0.00 4.02
39 40 2.787473 TTCCTACCTGCAAGTGGATG 57.213 50.000 0.00 0.00 0.00 3.51
40 41 1.656587 TCCTACCTGCAAGTGGATGT 58.343 50.000 0.00 0.00 0.00 3.06
41 42 1.985159 TCCTACCTGCAAGTGGATGTT 59.015 47.619 0.00 0.00 0.00 2.71
43 44 3.157087 CCTACCTGCAAGTGGATGTTTT 58.843 45.455 0.00 0.00 0.00 2.43
44 45 3.057315 CCTACCTGCAAGTGGATGTTTTG 60.057 47.826 0.00 0.00 0.00 2.44
45 46 2.387757 ACCTGCAAGTGGATGTTTTGT 58.612 42.857 0.00 0.00 0.00 2.83
46 47 3.561143 ACCTGCAAGTGGATGTTTTGTA 58.439 40.909 0.00 0.00 0.00 2.41
47 48 3.957497 ACCTGCAAGTGGATGTTTTGTAA 59.043 39.130 0.00 0.00 0.00 2.41
48 49 4.202111 ACCTGCAAGTGGATGTTTTGTAAC 60.202 41.667 0.00 0.00 34.75 2.50
49 50 4.037923 CCTGCAAGTGGATGTTTTGTAACT 59.962 41.667 0.00 0.00 35.24 2.24
50 51 4.930963 TGCAAGTGGATGTTTTGTAACTG 58.069 39.130 0.00 0.00 35.24 3.16
52 53 5.126222 TGCAAGTGGATGTTTTGTAACTGAA 59.874 36.000 0.00 0.00 35.24 3.02
53 54 5.687285 GCAAGTGGATGTTTTGTAACTGAAG 59.313 40.000 0.00 0.00 35.24 3.02
55 56 6.377327 AGTGGATGTTTTGTAACTGAAGTG 57.623 37.500 0.00 0.00 35.24 3.16
56 57 4.976116 GTGGATGTTTTGTAACTGAAGTGC 59.024 41.667 0.00 0.00 35.24 4.40
58 59 4.976116 GGATGTTTTGTAACTGAAGTGCAC 59.024 41.667 9.40 9.40 35.24 4.57
62 63 5.804473 TGTTTTGTAACTGAAGTGCACATTG 59.196 36.000 21.04 8.52 35.24 2.82
64 65 4.811555 TGTAACTGAAGTGCACATTGTC 57.188 40.909 21.04 10.92 0.00 3.18
65 66 3.563808 TGTAACTGAAGTGCACATTGTCC 59.436 43.478 21.04 7.16 0.00 4.02
66 67 1.609208 ACTGAAGTGCACATTGTCCC 58.391 50.000 21.04 0.00 0.00 4.46
67 68 1.133823 ACTGAAGTGCACATTGTCCCA 60.134 47.619 21.04 0.00 0.00 4.37
69 70 3.244875 ACTGAAGTGCACATTGTCCCATA 60.245 43.478 21.04 0.00 0.00 2.74
71 72 3.695556 TGAAGTGCACATTGTCCCATATG 59.304 43.478 21.04 0.00 0.00 1.78
72 73 3.370840 AGTGCACATTGTCCCATATGT 57.629 42.857 21.04 0.00 35.45 2.29
73 74 3.282021 AGTGCACATTGTCCCATATGTC 58.718 45.455 21.04 0.00 32.88 3.06
75 76 3.065786 GTGCACATTGTCCCATATGTCTG 59.934 47.826 13.17 0.00 32.88 3.51
77 78 2.620115 CACATTGTCCCATATGTCTGCC 59.380 50.000 1.24 0.00 32.88 4.85
78 79 2.241941 ACATTGTCCCATATGTCTGCCA 59.758 45.455 1.24 0.00 29.23 4.92
79 80 2.715749 TTGTCCCATATGTCTGCCAG 57.284 50.000 1.24 0.00 0.00 4.85
80 81 1.583556 TGTCCCATATGTCTGCCAGT 58.416 50.000 1.24 0.00 0.00 4.00
81 82 1.210234 TGTCCCATATGTCTGCCAGTG 59.790 52.381 1.24 0.00 0.00 3.66
82 83 0.181114 TCCCATATGTCTGCCAGTGC 59.819 55.000 1.24 0.00 38.26 4.40
85 86 1.590932 CATATGTCTGCCAGTGCCTC 58.409 55.000 0.00 0.00 36.33 4.70
86 87 0.105593 ATATGTCTGCCAGTGCCTCG 59.894 55.000 0.00 0.00 36.33 4.63
89 90 3.241530 TCTGCCAGTGCCTCGGTT 61.242 61.111 0.00 0.00 36.33 4.44
91 92 1.003839 CTGCCAGTGCCTCGGTTTA 60.004 57.895 0.00 0.00 36.33 2.01
92 93 1.003839 TGCCAGTGCCTCGGTTTAG 60.004 57.895 0.00 0.00 36.33 1.85
93 94 2.399356 GCCAGTGCCTCGGTTTAGC 61.399 63.158 0.00 0.00 0.00 3.09
94 95 1.296715 CCAGTGCCTCGGTTTAGCT 59.703 57.895 0.00 0.00 0.00 3.32
95 96 0.535335 CCAGTGCCTCGGTTTAGCTA 59.465 55.000 0.00 0.00 0.00 3.32
97 98 2.420129 CCAGTGCCTCGGTTTAGCTATT 60.420 50.000 0.00 0.00 0.00 1.73
99 100 3.063997 CAGTGCCTCGGTTTAGCTATTTG 59.936 47.826 0.00 0.00 0.00 2.32
101 102 3.063588 GTGCCTCGGTTTAGCTATTTGAC 59.936 47.826 0.00 0.00 0.00 3.18
102 103 3.055385 TGCCTCGGTTTAGCTATTTGACT 60.055 43.478 0.00 0.00 0.00 3.41
104 105 5.114081 GCCTCGGTTTAGCTATTTGACTAA 58.886 41.667 0.00 0.00 0.00 2.24
105 106 5.758784 GCCTCGGTTTAGCTATTTGACTAAT 59.241 40.000 0.00 0.00 0.00 1.73
106 107 6.260271 GCCTCGGTTTAGCTATTTGACTAATT 59.740 38.462 0.00 0.00 0.00 1.40
107 108 7.440255 GCCTCGGTTTAGCTATTTGACTAATTA 59.560 37.037 0.00 0.00 0.00 1.40
108 109 9.321562 CCTCGGTTTAGCTATTTGACTAATTAA 57.678 33.333 0.00 0.00 0.00 1.40
116 117 8.348285 AGCTATTTGACTAATTAAAACCTGCA 57.652 30.769 0.00 0.00 0.00 4.41
117 118 8.244113 AGCTATTTGACTAATTAAAACCTGCAC 58.756 33.333 0.00 0.00 0.00 4.57
119 120 5.365403 TTGACTAATTAAAACCTGCACCG 57.635 39.130 0.00 0.00 0.00 4.94
120 121 4.391155 TGACTAATTAAAACCTGCACCGT 58.609 39.130 0.00 0.00 0.00 4.83
121 122 4.822896 TGACTAATTAAAACCTGCACCGTT 59.177 37.500 0.00 0.00 0.00 4.44
122 123 5.996513 TGACTAATTAAAACCTGCACCGTTA 59.003 36.000 0.00 0.00 0.00 3.18
123 124 6.485984 TGACTAATTAAAACCTGCACCGTTAA 59.514 34.615 0.00 0.00 0.00 2.01
124 125 7.175293 TGACTAATTAAAACCTGCACCGTTAAT 59.825 33.333 0.00 0.00 0.00 1.40
126 127 8.024865 ACTAATTAAAACCTGCACCGTTAATTC 58.975 33.333 12.46 0.00 36.37 2.17
128 129 4.657436 AAAACCTGCACCGTTAATTCAA 57.343 36.364 0.00 0.00 0.00 2.69
129 130 4.657436 AAACCTGCACCGTTAATTCAAA 57.343 36.364 0.00 0.00 0.00 2.69
130 131 3.636282 ACCTGCACCGTTAATTCAAAC 57.364 42.857 0.00 0.00 0.00 2.93
131 132 2.295070 ACCTGCACCGTTAATTCAAACC 59.705 45.455 0.00 0.00 0.00 3.27
132 133 2.294791 CCTGCACCGTTAATTCAAACCA 59.705 45.455 0.00 0.00 0.00 3.67
133 134 3.305110 CTGCACCGTTAATTCAAACCAC 58.695 45.455 0.00 0.00 0.00 4.16
135 136 2.295070 GCACCGTTAATTCAAACCACCT 59.705 45.455 0.00 0.00 0.00 4.00
136 137 3.243602 GCACCGTTAATTCAAACCACCTT 60.244 43.478 0.00 0.00 0.00 3.50
138 139 3.955551 ACCGTTAATTCAAACCACCTTGT 59.044 39.130 0.00 0.00 0.00 3.16
140 141 5.008911 ACCGTTAATTCAAACCACCTTGTAC 59.991 40.000 0.00 0.00 0.00 2.90
141 142 5.008811 CCGTTAATTCAAACCACCTTGTACA 59.991 40.000 0.00 0.00 0.00 2.90
144 1846 7.325097 CGTTAATTCAAACCACCTTGTACATTC 59.675 37.037 0.00 0.00 0.00 2.67
150 1852 2.108250 ACCACCTTGTACATTCTTGGCT 59.892 45.455 0.00 0.00 0.00 4.75
154 1856 3.327757 ACCTTGTACATTCTTGGCTCTGA 59.672 43.478 0.00 0.00 0.00 3.27
161 1863 2.698855 TTCTTGGCTCTGAGTATGGC 57.301 50.000 6.53 0.00 0.00 4.40
164 1866 1.209019 CTTGGCTCTGAGTATGGCTGT 59.791 52.381 6.53 0.00 0.00 4.40
179 1881 2.037901 GGCTGTCTGATCTCATGAGGA 58.962 52.381 22.42 8.97 0.00 3.71
191 1893 5.946942 TCTCATGAGGACTATTGCTTTCT 57.053 39.130 22.42 0.00 0.00 2.52
243 1976 4.009675 CAGGGCTATTGCTAACTGTTTCA 58.990 43.478 0.00 0.00 39.59 2.69
250 1983 8.026607 GGCTATTGCTAACTGTTTCAATGTTTA 58.973 33.333 20.89 8.42 39.59 2.01
362 2181 4.295051 GAGATAATTCTCTGTCAGCCGAC 58.705 47.826 0.00 0.00 44.29 4.79
397 2217 5.836347 TGAGATCAATCCTGTACTCAATCG 58.164 41.667 0.00 0.00 35.07 3.34
403 2223 7.770801 TCAATCCTGTACTCAATCGTAATTG 57.229 36.000 0.00 0.00 43.10 2.32
470 2296 7.227314 GGTGATAAGTATGTGATGCATTGAAGA 59.773 37.037 0.00 0.00 38.94 2.87
502 2328 4.016444 TCCAAGAACACCATTATTCTGGC 58.984 43.478 0.00 0.00 40.15 4.85
547 2373 9.973450 CTTGAGATAAGTATATGCTGTAGTTGT 57.027 33.333 0.00 0.00 0.00 3.32
580 2416 5.916661 TGTCTAGTCAGTGGAGGTAATTC 57.083 43.478 0.00 0.00 0.00 2.17
633 2472 4.792521 TGGGAAAATTCGTACCATTTGG 57.207 40.909 0.00 0.00 42.17 3.28
634 2473 3.511934 TGGGAAAATTCGTACCATTTGGG 59.488 43.478 0.96 0.00 44.81 4.12
681 2603 2.423538 GGATGCACTGACACAAATACCC 59.576 50.000 0.00 0.00 0.00 3.69
790 3139 6.775629 GTCCTATTATACATCAGCCCCAAAAA 59.224 38.462 0.00 0.00 0.00 1.94
879 3848 2.093658 TCGCTCCCAGAAAGTCAATACC 60.094 50.000 0.00 0.00 0.00 2.73
919 3889 4.071423 TCATTACTAGCAAAGCAAGCACA 58.929 39.130 0.00 0.00 0.00 4.57
961 3938 1.808945 CTCCATTCCACACTGTGCTTC 59.191 52.381 7.90 0.00 31.34 3.86
975 3952 1.673920 GTGCTTCGTGTTTCCCTTTGA 59.326 47.619 0.00 0.00 0.00 2.69
1003 4074 0.032815 TCGTGTGAGCGTTCCAATGA 59.967 50.000 0.00 0.00 0.00 2.57
1060 4131 5.814481 TGGTATCCATGTTGATGAACAAGA 58.186 37.500 0.73 2.77 45.23 3.02
1074 4145 2.005370 ACAAGACGTCCAACTCCCTA 57.995 50.000 13.01 0.00 0.00 3.53
1137 4208 3.058639 ACAAGATTCTCAAACGCAAGCTC 60.059 43.478 0.00 0.00 45.62 4.09
1173 4244 2.158959 CATGACCGACGCCGAGAAC 61.159 63.158 0.00 0.00 38.22 3.01
1299 4765 0.889186 GCCGTGAAGCCAGGAAGAAA 60.889 55.000 0.00 0.00 0.00 2.52
1353 5123 9.668497 GTAATAAAACTCTTCCCTACTCACAAT 57.332 33.333 0.00 0.00 0.00 2.71
1452 7673 4.599041 TGCATGCCTTTAGGTTCAAGTAT 58.401 39.130 16.68 0.00 37.57 2.12
1461 7709 5.471556 TTAGGTTCAAGTATCGACCACAA 57.528 39.130 0.00 0.00 34.60 3.33
1671 7919 7.307989 GCGCAACTCATATACAATGAACCTAAT 60.308 37.037 0.30 0.00 0.00 1.73
1677 7925 9.559732 CTCATATACAATGAACCTAATGTCCAA 57.440 33.333 0.00 0.00 0.00 3.53
1694 7942 1.794116 CCAAAAGCATTTCCAGTTGCG 59.206 47.619 0.00 0.00 43.61 4.85
1717 7965 3.332919 CTTTGGGTCTGTGTCTCTGATG 58.667 50.000 0.00 0.00 0.00 3.07
1765 8013 4.591072 AGAGTATAGTTGAAGCATCTCCCC 59.409 45.833 0.00 0.00 0.00 4.81
1776 8024 2.099405 GCATCTCCCCGGAAAAATGAA 58.901 47.619 0.73 0.00 0.00 2.57
1779 8027 3.067684 TCTCCCCGGAAAAATGAAGAC 57.932 47.619 0.73 0.00 0.00 3.01
1797 8045 0.463116 ACACGGACAAACCACCACTC 60.463 55.000 0.00 0.00 38.90 3.51
1800 8048 0.531090 CGGACAAACCACCACTCGAA 60.531 55.000 0.00 0.00 38.90 3.71
1819 8067 5.827666 TCGAAAGACTTCAAAAATTGGTCC 58.172 37.500 0.00 0.00 33.31 4.46
1821 8069 5.588240 GAAAGACTTCAAAAATTGGTCCGT 58.412 37.500 0.00 0.00 0.00 4.69
1834 8082 0.757935 GGTCCGTGGGCAGAGGTATA 60.758 60.000 0.00 0.00 0.00 1.47
1837 8085 1.133294 TCCGTGGGCAGAGGTATATCA 60.133 52.381 0.00 0.00 0.00 2.15
1984 8232 0.040942 TATGGGTGCAAACAGGGCAT 59.959 50.000 0.00 0.00 44.11 4.40
2063 8311 8.321650 AGAGCATTCAGTTTAGAGAAAGAAAG 57.678 34.615 0.00 0.00 0.00 2.62
2101 8349 3.558829 CGAGATGGTTGATGAGATTGTGG 59.441 47.826 0.00 0.00 0.00 4.17
2118 8366 1.344114 GTGGAGAGATGCTCTGGATCC 59.656 57.143 4.20 4.20 41.35 3.36
2146 8400 2.662596 CAACGGCACTGGGCTCTA 59.337 61.111 0.21 0.00 44.01 2.43
2192 8446 6.936900 GTGAAAGAATGGAAGGCTATAGCATA 59.063 38.462 25.53 4.89 44.36 3.14
2227 8481 2.106338 TGCACTGAGGAAACTGGAATCA 59.894 45.455 0.00 0.00 44.43 2.57
2403 8657 5.302823 AGGAAGTCTTGAAACCATTGGAAAG 59.697 40.000 10.37 7.62 0.00 2.62
2483 8752 2.614481 GCGACAGGGAGTATTGTTCCAA 60.614 50.000 0.00 0.00 36.40 3.53
2573 8842 4.226761 GTTGCAATTAAGGAACCAAGTCG 58.773 43.478 0.59 0.00 34.24 4.18
2588 8857 2.724977 AGTCGAATCGAGTTGCTTCA 57.275 45.000 5.25 0.00 35.97 3.02
2654 8923 9.927081 AGAAGGTATTTTGAATGATTCTATGGT 57.073 29.630 6.73 0.00 0.00 3.55
2682 8951 2.742348 TCCCTTGCTATCCGAACACTA 58.258 47.619 0.00 0.00 0.00 2.74
2994 9266 2.045045 TTGAAGAGCATGCCCCCG 60.045 61.111 15.66 0.00 0.00 5.73
3253 9599 3.931907 ATTTCGAACCTCATGATGGGA 57.068 42.857 7.95 0.00 0.00 4.37
3361 9708 9.636965 GTGAAAGATTGCAATTTTTGTTTAGAC 57.363 29.630 27.13 14.17 0.00 2.59
3365 9712 5.382573 TTGCAATTTTTGTTTAGACGTGC 57.617 34.783 0.00 0.00 0.00 5.34
3514 9864 6.494893 TTAAGTATTGTGGAATGCTGACAC 57.505 37.500 0.00 0.00 34.98 3.67
3515 9865 4.019792 AGTATTGTGGAATGCTGACACA 57.980 40.909 0.00 0.00 42.77 3.72
3600 10067 3.196254 CGTTTCCTGCCCTAAAGGTACTA 59.804 47.826 0.00 0.00 38.49 1.82
3601 10068 4.679905 CGTTTCCTGCCCTAAAGGTACTAG 60.680 50.000 0.00 0.00 38.49 2.57
3604 10071 4.892198 TCCTGCCCTAAAGGTACTAGAAT 58.108 43.478 0.00 0.00 38.49 2.40
3607 10074 5.367945 TGCCCTAAAGGTACTAGAATTGG 57.632 43.478 0.00 0.00 38.49 3.16
3610 10077 6.056236 GCCCTAAAGGTACTAGAATTGGAAG 58.944 44.000 0.00 0.00 38.49 3.46
3616 10083 7.554959 AAGGTACTAGAATTGGAAGACTTGA 57.445 36.000 0.00 0.00 38.49 3.02
3624 10091 5.704978 AGAATTGGAAGACTTGAAGAGCTTC 59.295 40.000 17.66 17.66 37.58 3.86
3629 10096 3.959535 AGACTTGAAGAGCTTCCAGAG 57.040 47.619 15.67 9.81 38.77 3.35
3630 10097 3.505386 AGACTTGAAGAGCTTCCAGAGA 58.495 45.455 15.67 0.00 38.77 3.10
3638 10105 1.767681 GAGCTTCCAGAGATGGGATGT 59.232 52.381 0.00 0.00 33.63 3.06
3639 10106 2.172293 GAGCTTCCAGAGATGGGATGTT 59.828 50.000 0.00 0.00 33.63 2.71
3641 10108 2.295885 CTTCCAGAGATGGGATGTTGC 58.704 52.381 0.00 0.00 33.63 4.17
3642 10109 1.588239 TCCAGAGATGGGATGTTGCT 58.412 50.000 0.00 0.00 0.00 3.91
3643 10110 1.211212 TCCAGAGATGGGATGTTGCTG 59.789 52.381 0.00 0.00 0.00 4.41
3644 10111 1.064906 CCAGAGATGGGATGTTGCTGT 60.065 52.381 0.00 0.00 0.00 4.40
3645 10112 2.619849 CCAGAGATGGGATGTTGCTGTT 60.620 50.000 0.00 0.00 0.00 3.16
3648 10115 3.084039 GAGATGGGATGTTGCTGTTGAA 58.916 45.455 0.00 0.00 0.00 2.69
3649 10116 3.087031 AGATGGGATGTTGCTGTTGAAG 58.913 45.455 0.00 0.00 0.00 3.02
3650 10117 1.619654 TGGGATGTTGCTGTTGAAGG 58.380 50.000 0.00 0.00 0.00 3.46
3651 10118 1.144708 TGGGATGTTGCTGTTGAAGGA 59.855 47.619 0.00 0.00 0.00 3.36
3652 10119 1.815003 GGGATGTTGCTGTTGAAGGAG 59.185 52.381 0.00 0.00 0.00 3.69
3653 10120 1.815003 GGATGTTGCTGTTGAAGGAGG 59.185 52.381 0.00 0.00 0.00 4.30
3655 10122 1.967319 TGTTGCTGTTGAAGGAGGAC 58.033 50.000 0.00 0.00 0.00 3.85
3656 10123 1.490490 TGTTGCTGTTGAAGGAGGACT 59.510 47.619 0.00 0.00 0.00 3.85
3657 10124 1.876156 GTTGCTGTTGAAGGAGGACTG 59.124 52.381 0.00 0.00 0.00 3.51
3658 10125 1.423584 TGCTGTTGAAGGAGGACTGA 58.576 50.000 0.00 0.00 0.00 3.41
3659 10126 1.980765 TGCTGTTGAAGGAGGACTGAT 59.019 47.619 0.00 0.00 0.00 2.90
3660 10127 2.027745 TGCTGTTGAAGGAGGACTGATC 60.028 50.000 0.00 0.00 0.00 2.92
3667 10140 6.183361 TGTTGAAGGAGGACTGATCTTGTTTA 60.183 38.462 0.00 0.00 0.00 2.01
3671 10144 5.087323 AGGAGGACTGATCTTGTTTACTCA 58.913 41.667 0.00 0.00 0.00 3.41
3694 10167 6.992123 TCAGCTTGAGAAACTGTCAATTAAGA 59.008 34.615 0.00 0.00 33.49 2.10
3702 10175 4.098914 ACTGTCAATTAAGAACTGCCCA 57.901 40.909 0.00 0.00 0.00 5.36
3708 10181 5.183140 GTCAATTAAGAACTGCCCAAAGCTA 59.817 40.000 0.00 0.00 44.23 3.32
3711 10184 5.643379 TTAAGAACTGCCCAAAGCTAATG 57.357 39.130 0.00 0.00 44.23 1.90
3712 10185 2.450476 AGAACTGCCCAAAGCTAATGG 58.550 47.619 10.79 10.79 44.23 3.16
3721 10194 4.038042 GCCCAAAGCTAATGGATTTACCTC 59.962 45.833 17.80 0.00 40.56 3.85
3722 10195 4.275936 CCCAAAGCTAATGGATTTACCTCG 59.724 45.833 17.80 0.00 40.56 4.63
3761 10435 7.444183 TCAAGAACTCGAATTGAAATACTTGGT 59.556 33.333 0.00 0.00 34.04 3.67
3821 10501 5.783111 ACAAATATTGTTTCCACTTCTGGC 58.217 37.500 0.00 0.00 42.22 4.85
4021 10902 3.547468 GTGCATTTCAATTGTACCGATGC 59.453 43.478 18.21 18.21 38.97 3.91
4439 11362 3.807538 GCAGCAGGGCATGTCACG 61.808 66.667 0.00 0.00 0.00 4.35
4591 11514 2.482142 GCGGTTCTAGATCTTCCACCAG 60.482 54.545 0.00 3.09 0.00 4.00
4869 11841 4.316823 TCGGGAGAGCACCCCACT 62.317 66.667 8.50 0.00 46.62 4.00
4927 11899 1.072173 TGGCATCCCTACCGAATGATG 59.928 52.381 0.00 0.00 38.08 3.07
5269 12267 4.074526 GCAGAGGCAGGCTCGTCA 62.075 66.667 17.90 0.00 40.72 4.35
5295 12293 9.138596 ACAGTTGAAGGTTATTTAGCCTTTTTA 57.861 29.630 7.10 0.00 45.31 1.52
5353 12364 8.175925 TGGTTTGTTCTGATATCATTTGTGAA 57.824 30.769 5.72 3.13 0.00 3.18
5364 12375 8.720562 TGATATCATTTGTGAAATATACAGCGG 58.279 33.333 0.00 0.00 0.00 5.52
5407 12422 3.323979 TGGAAGGAAATACCGAGGATAGC 59.676 47.826 0.00 0.00 44.74 2.97
5668 12685 7.792032 TCTTCCTCAGATATTTGTAATTCGGT 58.208 34.615 0.00 0.00 0.00 4.69
5683 12700 6.540914 TGTAATTCGGTTCTAATTCATGTCCC 59.459 38.462 0.00 0.00 0.00 4.46
5684 12701 4.837093 TTCGGTTCTAATTCATGTCCCT 57.163 40.909 0.00 0.00 0.00 4.20
5822 12839 7.610865 TGAGAAACCTTTTCAACTGTGATTTT 58.389 30.769 1.72 0.00 32.48 1.82
5901 12946 4.199310 GTGGAGCCTGCTGAACAATATTA 58.801 43.478 0.00 0.00 0.00 0.98
6008 14408 6.220930 TGTACTGTAGTCACTTTCCATTGAC 58.779 40.000 0.00 0.00 42.17 3.18
6019 14419 4.653341 ACTTTCCATTGACAATTGTTGGGA 59.347 37.500 22.00 14.40 34.12 4.37
6047 14447 3.318384 TAGGGCGACTGCTTGGCA 61.318 61.111 0.00 0.00 42.25 4.92
6091 14491 6.051717 ACGATCTGATCTGGATTAGGTTTTG 58.948 40.000 15.16 0.00 0.00 2.44
6127 14542 3.025619 GCATGGTCGCCATACTGC 58.974 61.111 10.44 8.59 43.15 4.40
6128 14543 1.524621 GCATGGTCGCCATACTGCT 60.525 57.895 10.44 0.00 43.15 4.24
6129 14544 0.249868 GCATGGTCGCCATACTGCTA 60.250 55.000 10.44 0.00 43.15 3.49
6130 14545 1.609061 GCATGGTCGCCATACTGCTAT 60.609 52.381 10.44 0.00 43.15 2.97
6131 14546 2.353704 GCATGGTCGCCATACTGCTATA 60.354 50.000 10.44 0.00 43.15 1.31
6154 14569 3.812053 GGCCAGTGTTCTATCTGCATAAG 59.188 47.826 0.00 0.00 0.00 1.73
6205 14654 4.093998 CAGAGTACAAATAAGCAGCACAGG 59.906 45.833 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.520515 CCACTTGCAGGTAGGAAAATATTATAT 57.479 33.333 0.00 0.00 0.00 0.86
12 13 7.582719 TCCACTTGCAGGTAGGAAAATATTAT 58.417 34.615 14.69 0.00 0.00 1.28
15 16 5.450818 TCCACTTGCAGGTAGGAAAATAT 57.549 39.130 14.69 0.00 0.00 1.28
17 18 3.806949 TCCACTTGCAGGTAGGAAAAT 57.193 42.857 14.69 0.00 0.00 1.82
18 19 3.181434 ACATCCACTTGCAGGTAGGAAAA 60.181 43.478 18.90 3.19 31.17 2.29
20 21 1.985159 ACATCCACTTGCAGGTAGGAA 59.015 47.619 18.90 7.64 31.17 3.36
21 22 1.656587 ACATCCACTTGCAGGTAGGA 58.343 50.000 17.84 17.84 0.00 2.94
23 24 3.569701 ACAAAACATCCACTTGCAGGTAG 59.430 43.478 0.00 0.00 0.00 3.18
24 25 3.561143 ACAAAACATCCACTTGCAGGTA 58.439 40.909 0.00 0.00 0.00 3.08
25 26 2.387757 ACAAAACATCCACTTGCAGGT 58.612 42.857 0.00 0.00 0.00 4.00
26 27 4.037923 AGTTACAAAACATCCACTTGCAGG 59.962 41.667 0.00 0.00 38.12 4.85
27 28 4.977963 CAGTTACAAAACATCCACTTGCAG 59.022 41.667 0.00 0.00 38.12 4.41
29 30 5.181690 TCAGTTACAAAACATCCACTTGC 57.818 39.130 0.00 0.00 38.12 4.01
30 31 6.692681 CACTTCAGTTACAAAACATCCACTTG 59.307 38.462 0.00 0.00 38.12 3.16
31 32 6.680378 GCACTTCAGTTACAAAACATCCACTT 60.680 38.462 0.00 0.00 38.12 3.16
33 34 4.976116 GCACTTCAGTTACAAAACATCCAC 59.024 41.667 0.00 0.00 38.12 4.02
35 36 4.976116 GTGCACTTCAGTTACAAAACATCC 59.024 41.667 10.32 0.00 38.12 3.51
37 38 5.574891 TGTGCACTTCAGTTACAAAACAT 57.425 34.783 19.41 0.00 38.12 2.71
39 40 5.804979 ACAATGTGCACTTCAGTTACAAAAC 59.195 36.000 19.41 0.00 35.72 2.43
40 41 5.960113 ACAATGTGCACTTCAGTTACAAAA 58.040 33.333 19.41 0.00 0.00 2.44
41 42 5.449862 GGACAATGTGCACTTCAGTTACAAA 60.450 40.000 19.41 0.00 0.00 2.83
43 44 3.563808 GGACAATGTGCACTTCAGTTACA 59.436 43.478 19.41 0.00 0.00 2.41
44 45 3.058224 GGGACAATGTGCACTTCAGTTAC 60.058 47.826 19.41 10.59 0.00 2.50
45 46 3.146066 GGGACAATGTGCACTTCAGTTA 58.854 45.455 19.41 0.00 0.00 2.24
46 47 1.956477 GGGACAATGTGCACTTCAGTT 59.044 47.619 19.41 2.52 0.00 3.16
47 48 1.133823 TGGGACAATGTGCACTTCAGT 60.134 47.619 19.41 13.63 31.92 3.41
48 49 1.608055 TGGGACAATGTGCACTTCAG 58.392 50.000 19.41 10.55 31.92 3.02
49 50 3.817187 TGGGACAATGTGCACTTCA 57.183 47.368 19.41 2.69 31.92 3.02
62 63 1.959042 CACTGGCAGACATATGGGAC 58.041 55.000 23.66 0.00 0.00 4.46
64 65 0.820891 GGCACTGGCAGACATATGGG 60.821 60.000 23.66 0.00 43.71 4.00
65 66 0.182061 AGGCACTGGCAGACATATGG 59.818 55.000 23.66 2.49 43.71 2.74
66 67 1.590932 GAGGCACTGGCAGACATATG 58.409 55.000 23.66 9.72 41.55 1.78
67 68 0.105593 CGAGGCACTGGCAGACATAT 59.894 55.000 23.66 2.42 41.55 1.78
69 70 2.267006 CGAGGCACTGGCAGACAT 59.733 61.111 23.66 10.49 41.55 3.06
71 72 3.537206 AACCGAGGCACTGGCAGAC 62.537 63.158 23.66 12.58 41.55 3.51
72 73 1.476845 TAAACCGAGGCACTGGCAGA 61.477 55.000 23.66 0.00 41.55 4.26
73 74 1.003839 TAAACCGAGGCACTGGCAG 60.004 57.895 14.16 14.16 41.55 4.85
75 76 2.399356 GCTAAACCGAGGCACTGGC 61.399 63.158 0.00 0.00 41.55 4.85
77 78 2.604046 ATAGCTAAACCGAGGCACTG 57.396 50.000 0.00 0.00 41.55 3.66
79 80 3.063588 GTCAAATAGCTAAACCGAGGCAC 59.936 47.826 0.00 0.00 0.00 5.01
80 81 3.055385 AGTCAAATAGCTAAACCGAGGCA 60.055 43.478 0.00 0.00 0.00 4.75
81 82 3.532542 AGTCAAATAGCTAAACCGAGGC 58.467 45.455 0.00 0.00 0.00 4.70
82 83 7.787725 AATTAGTCAAATAGCTAAACCGAGG 57.212 36.000 0.00 0.00 31.91 4.63
91 92 8.244113 GTGCAGGTTTTAATTAGTCAAATAGCT 58.756 33.333 0.00 0.00 0.00 3.32
92 93 7.488150 GGTGCAGGTTTTAATTAGTCAAATAGC 59.512 37.037 0.00 0.00 0.00 2.97
93 94 7.696453 CGGTGCAGGTTTTAATTAGTCAAATAG 59.304 37.037 0.00 0.00 0.00 1.73
94 95 7.175293 ACGGTGCAGGTTTTAATTAGTCAAATA 59.825 33.333 0.00 0.00 0.00 1.40
95 96 6.015772 ACGGTGCAGGTTTTAATTAGTCAAAT 60.016 34.615 0.00 0.00 0.00 2.32
97 98 4.822896 ACGGTGCAGGTTTTAATTAGTCAA 59.177 37.500 0.00 0.00 0.00 3.18
99 100 5.366829 AACGGTGCAGGTTTTAATTAGTC 57.633 39.130 0.00 0.00 0.00 2.59
101 102 8.024285 TGAATTAACGGTGCAGGTTTTAATTAG 58.976 33.333 8.24 0.00 34.18 1.73
102 103 7.883217 TGAATTAACGGTGCAGGTTTTAATTA 58.117 30.769 8.24 0.00 34.18 1.40
104 105 6.334102 TGAATTAACGGTGCAGGTTTTAAT 57.666 33.333 8.24 3.28 0.00 1.40
105 106 5.769484 TGAATTAACGGTGCAGGTTTTAA 57.231 34.783 8.24 1.17 0.00 1.52
106 107 5.769484 TTGAATTAACGGTGCAGGTTTTA 57.231 34.783 8.24 0.00 0.00 1.52
107 108 4.657436 TTGAATTAACGGTGCAGGTTTT 57.343 36.364 8.24 0.00 0.00 2.43
108 109 4.364860 GTTTGAATTAACGGTGCAGGTTT 58.635 39.130 8.24 0.00 0.00 3.27
109 110 3.243602 GGTTTGAATTAACGGTGCAGGTT 60.244 43.478 8.05 8.05 0.00 3.50
110 111 2.295070 GGTTTGAATTAACGGTGCAGGT 59.705 45.455 0.00 0.00 0.00 4.00
111 112 2.294791 TGGTTTGAATTAACGGTGCAGG 59.705 45.455 0.00 0.00 0.00 4.85
112 113 3.305110 GTGGTTTGAATTAACGGTGCAG 58.695 45.455 0.00 0.00 0.00 4.41
114 115 2.295070 AGGTGGTTTGAATTAACGGTGC 59.705 45.455 0.00 0.00 0.00 5.01
115 116 4.202070 ACAAGGTGGTTTGAATTAACGGTG 60.202 41.667 0.00 0.00 0.00 4.94
116 117 3.955551 ACAAGGTGGTTTGAATTAACGGT 59.044 39.130 0.00 0.00 0.00 4.83
117 118 4.577834 ACAAGGTGGTTTGAATTAACGG 57.422 40.909 0.00 0.00 0.00 4.44
119 120 8.357402 AGAATGTACAAGGTGGTTTGAATTAAC 58.643 33.333 0.00 0.00 0.00 2.01
120 121 8.472007 AGAATGTACAAGGTGGTTTGAATTAA 57.528 30.769 0.00 0.00 0.00 1.40
121 122 8.356657 CAAGAATGTACAAGGTGGTTTGAATTA 58.643 33.333 0.00 0.00 0.00 1.40
122 123 6.976934 AGAATGTACAAGGTGGTTTGAATT 57.023 33.333 0.00 0.00 0.00 2.17
123 124 6.239289 CCAAGAATGTACAAGGTGGTTTGAAT 60.239 38.462 0.00 0.00 0.00 2.57
124 125 5.068460 CCAAGAATGTACAAGGTGGTTTGAA 59.932 40.000 0.00 0.00 0.00 2.69
126 127 4.795962 GCCAAGAATGTACAAGGTGGTTTG 60.796 45.833 15.55 7.78 0.00 2.93
128 129 2.890945 GCCAAGAATGTACAAGGTGGTT 59.109 45.455 15.55 0.00 0.00 3.67
129 130 2.108250 AGCCAAGAATGTACAAGGTGGT 59.892 45.455 15.55 1.36 0.00 4.16
130 131 2.749621 GAGCCAAGAATGTACAAGGTGG 59.250 50.000 0.00 6.75 0.00 4.61
131 132 3.438087 CAGAGCCAAGAATGTACAAGGTG 59.562 47.826 0.00 0.00 0.00 4.00
132 133 3.327757 TCAGAGCCAAGAATGTACAAGGT 59.672 43.478 0.00 0.00 0.00 3.50
133 134 3.937706 CTCAGAGCCAAGAATGTACAAGG 59.062 47.826 0.00 0.00 0.00 3.61
135 136 4.623932 ACTCAGAGCCAAGAATGTACAA 57.376 40.909 0.00 0.00 0.00 2.41
136 137 5.395657 CCATACTCAGAGCCAAGAATGTACA 60.396 44.000 0.00 0.00 0.00 2.90
138 139 4.443457 GCCATACTCAGAGCCAAGAATGTA 60.443 45.833 0.00 0.00 0.00 2.29
140 141 2.877168 GCCATACTCAGAGCCAAGAATG 59.123 50.000 0.00 0.00 0.00 2.67
141 142 2.776536 AGCCATACTCAGAGCCAAGAAT 59.223 45.455 0.00 0.00 0.00 2.40
144 1846 1.209019 ACAGCCATACTCAGAGCCAAG 59.791 52.381 0.00 0.00 0.00 3.61
150 1852 3.888323 GAGATCAGACAGCCATACTCAGA 59.112 47.826 0.00 0.00 0.00 3.27
154 1856 4.221530 TCATGAGATCAGACAGCCATACT 58.778 43.478 0.00 0.00 0.00 2.12
161 1863 6.448852 CAATAGTCCTCATGAGATCAGACAG 58.551 44.000 24.62 4.68 0.00 3.51
164 1866 5.146298 AGCAATAGTCCTCATGAGATCAGA 58.854 41.667 24.62 9.72 0.00 3.27
179 1881 9.525409 GCATCATTTTAATCAGAAAGCAATAGT 57.475 29.630 0.00 0.00 0.00 2.12
292 2025 3.391049 GTGGTTACACACTCCTCAGTTC 58.609 50.000 0.00 0.00 46.90 3.01
354 2173 3.006430 TCAGAACAAACATAGTCGGCTGA 59.994 43.478 0.00 0.00 0.00 4.26
362 2181 7.551974 ACAGGATTGATCTCAGAACAAACATAG 59.448 37.037 0.88 0.00 28.93 2.23
422 2248 5.766174 ACCGAAGCAAGTGGTTATTTTCTTA 59.234 36.000 0.00 0.00 35.69 2.10
470 2296 7.781324 AATGGTGTTCTTGGATTAGTTGAAT 57.219 32.000 0.00 0.00 0.00 2.57
547 2373 4.640647 CACTGACTAGACATACCTACTGCA 59.359 45.833 0.00 0.00 0.00 4.41
762 3111 5.221843 TGGGGCTGATGTATAATAGGACAAC 60.222 44.000 0.00 0.00 0.00 3.32
790 3139 0.538977 AACAGCTCAGCACTGGCATT 60.539 50.000 0.00 5.06 44.61 3.56
792 3141 1.598962 GAACAGCTCAGCACTGGCA 60.599 57.895 0.00 0.00 44.61 4.92
793 3142 1.168407 TTGAACAGCTCAGCACTGGC 61.168 55.000 0.00 0.73 39.55 4.85
879 3848 0.961753 GAAACTGGAAGCCAAGGTGG 59.038 55.000 0.00 0.00 41.55 4.61
919 3889 3.996921 AGAGAATGGTGTGAGCAAGAT 57.003 42.857 0.00 0.00 0.00 2.40
961 3938 1.335872 GGCACATCAAAGGGAAACACG 60.336 52.381 0.00 0.00 0.00 4.49
975 3952 1.638388 CGCTCACACGATTGGCACAT 61.638 55.000 0.00 0.00 33.77 3.21
1060 4131 0.113776 TCCAGTAGGGAGTTGGACGT 59.886 55.000 0.00 0.00 42.15 4.34
1137 4208 4.096003 ACGTCAAGGATGGCCGGG 62.096 66.667 2.18 0.00 39.96 5.73
1242 4425 7.134815 ACTTGAATTCGTCAAAGACTTCATTG 58.865 34.615 9.54 0.00 45.67 2.82
1299 4765 0.607489 CAAGCTTGCTGTAGTGCCCT 60.607 55.000 14.65 0.00 0.00 5.19
1353 5123 5.980698 TTTTGTAACGGAACACAATACGA 57.019 34.783 0.00 0.00 34.78 3.43
1577 7825 3.610786 CAAGATCTGCATTGCTAGCTG 57.389 47.619 17.23 8.00 0.00 4.24
1638 7886 6.918892 TTGTATATGAGTTGCGCTAATGTT 57.081 33.333 9.73 0.00 0.00 2.71
1671 7919 3.740764 GCAACTGGAAATGCTTTTGGACA 60.741 43.478 1.76 0.00 39.46 4.02
1674 7922 1.794116 CGCAACTGGAAATGCTTTTGG 59.206 47.619 1.76 0.00 40.39 3.28
1677 7925 0.319813 GCCGCAACTGGAAATGCTTT 60.320 50.000 0.00 0.00 40.39 3.51
1694 7942 0.398318 AGAGACACAGACCCAAAGCC 59.602 55.000 0.00 0.00 0.00 4.35
1717 7965 3.077359 CCAGGGAGTTCACATCAAAGAC 58.923 50.000 0.00 0.00 0.00 3.01
1765 8013 2.546368 TGTCCGTGTCTTCATTTTTCCG 59.454 45.455 0.00 0.00 0.00 4.30
1776 8024 0.463116 GTGGTGGTTTGTCCGTGTCT 60.463 55.000 0.00 0.00 39.52 3.41
1779 8027 1.495584 CGAGTGGTGGTTTGTCCGTG 61.496 60.000 0.00 0.00 39.52 4.94
1797 8045 4.675114 CGGACCAATTTTTGAAGTCTTTCG 59.325 41.667 0.00 0.00 36.04 3.46
1800 8048 4.202111 CCACGGACCAATTTTTGAAGTCTT 60.202 41.667 0.00 0.00 0.00 3.01
1819 8067 3.244215 ACAATGATATACCTCTGCCCACG 60.244 47.826 0.00 0.00 0.00 4.94
1821 8069 6.475504 CAATACAATGATATACCTCTGCCCA 58.524 40.000 0.00 0.00 0.00 5.36
1834 8082 6.008331 CCCAGACATCATCCAATACAATGAT 58.992 40.000 0.00 0.00 42.03 2.45
1837 8085 5.103982 TGTCCCAGACATCATCCAATACAAT 60.104 40.000 0.00 0.00 37.67 2.71
1984 8232 5.945784 CCTCCAAAACATTGAGATTGTAGGA 59.054 40.000 6.61 0.00 32.39 2.94
2063 8311 0.179124 CTCGACTAGTTCAGCAGGCC 60.179 60.000 0.00 0.00 0.00 5.19
2118 8366 1.971167 TGCCGTTGCAGCTAAAGGG 60.971 57.895 13.24 13.24 44.23 3.95
2227 8481 6.591935 TGTAGCTAAGCTTTAGTATTGGCAT 58.408 36.000 3.20 0.00 40.44 4.40
2381 8635 4.984785 GCTTTCCAATGGTTTCAAGACTTC 59.015 41.667 0.00 0.00 0.00 3.01
2382 8636 4.405358 TGCTTTCCAATGGTTTCAAGACTT 59.595 37.500 0.00 0.00 0.00 3.01
2403 8657 3.069158 AGGCCAGCTCATTGAAAATATGC 59.931 43.478 5.01 0.00 0.00 3.14
2499 8768 6.196079 GCAATATCATGCATCAGATCATGT 57.804 37.500 16.27 10.18 45.70 3.21
2536 8805 9.643693 CTTAATTGCAACAATACATTCCTTTCT 57.356 29.630 0.00 0.00 0.00 2.52
2548 8817 6.173427 ACTTGGTTCCTTAATTGCAACAAT 57.827 33.333 0.00 0.00 0.00 2.71
2573 8842 4.688021 AGTATCCTGAAGCAACTCGATTC 58.312 43.478 0.00 0.00 40.57 2.52
2582 8851 3.617284 TGTCGAGTAGTATCCTGAAGCA 58.383 45.455 0.00 0.00 0.00 3.91
2588 8857 9.886132 ACAAAAATAAATGTCGAGTAGTATCCT 57.114 29.630 0.00 0.00 0.00 3.24
2654 8923 3.454447 TCGGATAGCAAGGGATCTTTTCA 59.546 43.478 0.00 0.00 0.00 2.69
2994 9266 5.131067 AGGTTTGTGAGTTTTCCTAGTTCC 58.869 41.667 0.00 0.00 0.00 3.62
3361 9708 0.877071 AAAGTGAAGGATGCAGCACG 59.123 50.000 3.51 0.00 36.43 5.34
3365 9712 4.589216 TTTGGAAAAGTGAAGGATGCAG 57.411 40.909 0.00 0.00 0.00 4.41
3541 10005 0.838608 TAACCTCCACCACACGGTTT 59.161 50.000 0.00 0.00 46.31 3.27
3600 10067 5.240013 AGCTCTTCAAGTCTTCCAATTCT 57.760 39.130 0.00 0.00 0.00 2.40
3601 10068 5.106357 GGAAGCTCTTCAAGTCTTCCAATTC 60.106 44.000 24.11 7.47 46.57 2.17
3604 10071 3.744660 GGAAGCTCTTCAAGTCTTCCAA 58.255 45.455 24.11 0.00 46.57 3.53
3607 10074 4.021544 TCTCTGGAAGCTCTTCAAGTCTTC 60.022 45.833 12.39 11.36 40.63 2.87
3610 10077 3.951775 TCTCTGGAAGCTCTTCAAGTC 57.048 47.619 12.39 0.00 40.63 3.01
3616 10083 2.260639 TCCCATCTCTGGAAGCTCTT 57.739 50.000 0.00 0.00 46.37 2.85
3624 10091 1.064906 ACAGCAACATCCCATCTCTGG 60.065 52.381 0.00 0.00 42.73 3.86
3629 10096 2.165030 CCTTCAACAGCAACATCCCATC 59.835 50.000 0.00 0.00 0.00 3.51
3630 10097 2.173519 CCTTCAACAGCAACATCCCAT 58.826 47.619 0.00 0.00 0.00 4.00
3638 10105 1.768275 TCAGTCCTCCTTCAACAGCAA 59.232 47.619 0.00 0.00 0.00 3.91
3639 10106 1.423584 TCAGTCCTCCTTCAACAGCA 58.576 50.000 0.00 0.00 0.00 4.41
3641 10108 4.252073 CAAGATCAGTCCTCCTTCAACAG 58.748 47.826 0.00 0.00 0.00 3.16
3642 10109 3.648067 ACAAGATCAGTCCTCCTTCAACA 59.352 43.478 0.00 0.00 0.00 3.33
3643 10110 4.278975 ACAAGATCAGTCCTCCTTCAAC 57.721 45.455 0.00 0.00 0.00 3.18
3644 10111 4.982241 AACAAGATCAGTCCTCCTTCAA 57.018 40.909 0.00 0.00 0.00 2.69
3645 10112 4.982241 AAACAAGATCAGTCCTCCTTCA 57.018 40.909 0.00 0.00 0.00 3.02
3648 10115 5.087323 TGAGTAAACAAGATCAGTCCTCCT 58.913 41.667 0.00 0.00 0.00 3.69
3649 10116 5.407407 TGAGTAAACAAGATCAGTCCTCC 57.593 43.478 0.00 0.00 0.00 4.30
3650 10117 4.867608 GCTGAGTAAACAAGATCAGTCCTC 59.132 45.833 0.00 1.50 41.00 3.71
3651 10118 4.530161 AGCTGAGTAAACAAGATCAGTCCT 59.470 41.667 0.00 0.00 41.00 3.85
3652 10119 4.826556 AGCTGAGTAAACAAGATCAGTCC 58.173 43.478 0.00 0.00 41.00 3.85
3653 10120 5.928839 TCAAGCTGAGTAAACAAGATCAGTC 59.071 40.000 0.00 0.00 41.00 3.51
3655 10122 6.162079 TCTCAAGCTGAGTAAACAAGATCAG 58.838 40.000 11.37 0.00 44.58 2.90
3656 10123 6.101650 TCTCAAGCTGAGTAAACAAGATCA 57.898 37.500 11.37 0.00 44.58 2.92
3657 10124 7.172361 AGTTTCTCAAGCTGAGTAAACAAGATC 59.828 37.037 23.14 0.00 44.58 2.75
3658 10125 6.995091 AGTTTCTCAAGCTGAGTAAACAAGAT 59.005 34.615 23.14 12.61 44.58 2.40
3659 10126 6.258727 CAGTTTCTCAAGCTGAGTAAACAAGA 59.741 38.462 23.14 6.59 44.58 3.02
3660 10127 6.037610 ACAGTTTCTCAAGCTGAGTAAACAAG 59.962 38.462 23.14 19.92 44.58 3.16
3667 10140 3.827008 TGACAGTTTCTCAAGCTGAGT 57.173 42.857 7.06 0.00 44.58 3.41
3671 10144 7.500559 AGTTCTTAATTGACAGTTTCTCAAGCT 59.499 33.333 0.00 0.00 31.22 3.74
3684 10157 4.021981 AGCTTTGGGCAGTTCTTAATTGAC 60.022 41.667 0.00 0.00 44.79 3.18
3687 10160 6.351286 CCATTAGCTTTGGGCAGTTCTTAATT 60.351 38.462 7.37 0.00 44.79 1.40
3688 10161 5.127682 CCATTAGCTTTGGGCAGTTCTTAAT 59.872 40.000 7.37 0.00 44.79 1.40
3694 10167 2.603075 TCCATTAGCTTTGGGCAGTT 57.397 45.000 13.71 0.00 44.79 3.16
3708 10181 2.238646 TGGTGCTCGAGGTAAATCCATT 59.761 45.455 15.58 0.00 39.02 3.16
3711 10184 2.614057 CAATGGTGCTCGAGGTAAATCC 59.386 50.000 15.58 0.00 0.00 3.01
3712 10185 3.951979 CAATGGTGCTCGAGGTAAATC 57.048 47.619 15.58 0.00 0.00 2.17
3736 10209 7.535258 CACCAAGTATTTCAATTCGAGTTCTTG 59.465 37.037 9.28 9.28 0.00 3.02
3761 10435 2.421107 GCATCCCATCTCTGAAAGCTCA 60.421 50.000 0.00 0.00 0.00 4.26
3821 10501 5.210715 GGCATTTCTGAATTGATAGCTTCG 58.789 41.667 14.56 0.00 0.00 3.79
4021 10902 3.636300 TGGTTCCATTTCTCCTTGTTGTG 59.364 43.478 0.00 0.00 0.00 3.33
4109 10996 6.135454 AGATGTCCAAAATAATACCATGGCA 58.865 36.000 13.04 0.00 0.00 4.92
4117 11004 7.624360 ACGCTTCAAGATGTCCAAAATAATA 57.376 32.000 0.00 0.00 0.00 0.98
4299 11220 3.011821 ACTCAATAGACTCCAGACCAGGA 59.988 47.826 0.00 0.00 36.00 3.86
4347 11268 2.236146 AGATGCTGGGACGTTGAACATA 59.764 45.455 0.00 0.00 0.00 2.29
4439 11362 3.628032 GCAAGATAGCCCTTGAACTAACC 59.372 47.826 13.29 0.00 44.66 2.85
4869 11841 2.570415 TTACAAGGGATTCCAACGCA 57.430 45.000 4.80 0.00 34.83 5.24
4927 11899 2.125147 TGACCTGTATGCCTGCGC 60.125 61.111 0.00 0.00 0.00 6.09
5269 12267 7.597288 AAAAGGCTAAATAACCTTCAACTGT 57.403 32.000 0.00 0.00 45.62 3.55
5353 12364 5.583457 GGTTTAAGTGACACCGCTGTATATT 59.417 40.000 0.84 0.00 32.63 1.28
5362 12373 3.623960 TGTCTTTGGTTTAAGTGACACCG 59.376 43.478 0.84 0.00 32.52 4.94
5364 12375 5.298276 TCCATGTCTTTGGTTTAAGTGACAC 59.702 40.000 0.00 0.00 36.84 3.67
5407 12422 2.513204 CATGGCTCCGCTCACAGG 60.513 66.667 0.00 0.00 0.00 4.00
5452 12467 2.830923 TCCGAGGTTTACCCACGAAATA 59.169 45.455 14.56 0.00 38.12 1.40
5453 12468 1.624813 TCCGAGGTTTACCCACGAAAT 59.375 47.619 14.56 0.00 38.12 2.17
5597 12614 5.575957 CCAGATTGATTATAATCATGCCGC 58.424 41.667 25.05 14.13 44.27 6.53
5598 12615 5.356190 AGCCAGATTGATTATAATCATGCCG 59.644 40.000 25.05 15.33 44.27 5.69
5668 12685 6.126863 ACTGTTGAGGGACATGAATTAGAA 57.873 37.500 0.00 0.00 0.00 2.10
5683 12700 2.158755 ACTGAACCTGGGAACTGTTGAG 60.159 50.000 0.00 0.00 34.83 3.02
5684 12701 1.843851 ACTGAACCTGGGAACTGTTGA 59.156 47.619 0.00 0.00 0.00 3.18
5866 12911 1.221840 CTCCACCAACATCTCCCCG 59.778 63.158 0.00 0.00 0.00 5.73
5901 12946 6.950619 GGAGGCCTATTATCCAAGAAATTCAT 59.049 38.462 4.42 0.00 33.08 2.57
6008 14408 2.094675 CCTACAGGCTCCCAACAATTG 58.905 52.381 3.24 3.24 0.00 2.32
6019 14419 2.444140 CGCCCTACCCTACAGGCT 60.444 66.667 0.00 0.00 43.48 4.58
6047 14447 1.315981 TTCAGCCTGCTCGACTCGAT 61.316 55.000 0.62 0.00 34.61 3.59
6124 14539 4.526262 AGATAGAACACTGGCCTATAGCAG 59.474 45.833 3.32 5.98 46.50 4.24
6125 14540 4.281941 CAGATAGAACACTGGCCTATAGCA 59.718 45.833 3.32 0.00 46.50 3.49
6126 14541 4.815269 CAGATAGAACACTGGCCTATAGC 58.185 47.826 3.32 0.00 42.60 2.97
6127 14542 4.281941 TGCAGATAGAACACTGGCCTATAG 59.718 45.833 3.32 0.00 35.05 1.31
6128 14543 4.223144 TGCAGATAGAACACTGGCCTATA 58.777 43.478 3.32 0.00 35.05 1.31
6129 14544 3.041211 TGCAGATAGAACACTGGCCTAT 58.959 45.455 3.32 0.00 35.05 2.57
6130 14545 2.466846 TGCAGATAGAACACTGGCCTA 58.533 47.619 3.32 0.00 35.05 3.93
6131 14546 1.279496 TGCAGATAGAACACTGGCCT 58.721 50.000 3.32 0.00 35.05 5.19
6154 14569 3.726291 AGGTTTGTAATGTGGTGCAAC 57.274 42.857 0.00 0.00 0.00 4.17
6205 14654 5.636121 TGAAATGAAACATGAATTGCTGCTC 59.364 36.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.