Multiple sequence alignment - TraesCS6A01G111800

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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 TraesCS6A01G111800 chr6A 100.000 4533 0 0 1 4533 80874813 80879345 0.000000e+00 8371.0
1 TraesCS6A01G111800 chr6A 99.465 187 1 0 4071 4257 392939571 392939385 1.560000e-89 340.0
2 TraesCS6A01G111800 chr6A 83.399 253 30 7 4255 4502 87759485 87759730 1.640000e-54 224.0
3 TraesCS6A01G111800 chr6B 94.889 3483 126 26 622 4075 137380252 137383711 0.000000e+00 5398.0
4 TraesCS6A01G111800 chr6B 91.148 305 19 1 1 297 137372624 137372928 1.520000e-109 407.0
5 TraesCS6A01G111800 chr6B 84.585 253 27 6 4255 4502 144964216 144964461 1.630000e-59 241.0
6 TraesCS6A01G111800 chr6B 84.314 255 22 8 4255 4504 137383699 137383940 2.730000e-57 233.0
7 TraesCS6A01G111800 chr6B 92.638 163 9 3 379 539 137378937 137379098 9.810000e-57 231.0
8 TraesCS6A01G111800 chr6B 100.000 85 0 0 293 377 137378768 137378852 1.690000e-34 158.0
9 TraesCS6A01G111800 chr6B 77.928 222 27 14 4276 4492 122296234 122296030 7.970000e-23 119.0
10 TraesCS6A01G111800 chr6D 94.749 3447 133 28 658 4075 63725781 63729208 0.000000e+00 5319.0
11 TraesCS6A01G111800 chr6D 86.070 402 46 4 11 402 63725164 63725565 1.510000e-114 424.0
12 TraesCS6A01G111800 chr6D 87.451 255 20 7 4255 4504 63729196 63729443 2.670000e-72 283.0
13 TraesCS6A01G111800 chr6D 84.252 254 27 7 4255 4502 69946029 69946275 7.580000e-58 235.0
14 TraesCS6A01G111800 chr6D 87.255 204 15 6 347 539 63725566 63725769 5.900000e-54 222.0
15 TraesCS6A01G111800 chr5D 93.312 2557 143 10 1056 3591 344546335 344543786 0.000000e+00 3749.0
16 TraesCS6A01G111800 chr5D 92.537 67 5 0 996 1062 344546417 344546351 3.730000e-16 97.1
17 TraesCS6A01G111800 chr5D 92.188 64 5 0 4255 4318 23824870 23824933 1.740000e-14 91.6
18 TraesCS6A01G111800 chr5B 93.109 2554 149 11 1056 3588 407215398 407217945 0.000000e+00 3716.0
19 TraesCS6A01G111800 chr5B 99.468 188 1 0 4071 4258 107732568 107732755 4.340000e-90 342.0
20 TraesCS6A01G111800 chr5B 92.308 78 6 0 996 1073 407215316 407215393 1.330000e-20 111.0
21 TraesCS6A01G111800 chr5B 92.593 54 4 0 1150 1203 311207773 311207720 1.350000e-10 78.7
22 TraesCS6A01G111800 chr5A 92.609 2557 159 9 1056 3588 447535248 447537798 0.000000e+00 3648.0
23 TraesCS6A01G111800 chr5A 97.959 196 4 0 4067 4262 227709971 227709776 1.560000e-89 340.0
24 TraesCS6A01G111800 chr5A 99.462 186 1 0 4071 4256 326040876 326040691 5.620000e-89 339.0
25 TraesCS6A01G111800 chr1A 88.125 480 25 13 3495 3973 278128856 278129304 3.990000e-150 542.0
26 TraesCS6A01G111800 chr1A 100.000 183 0 0 4071 4253 333878908 333878726 5.620000e-89 339.0
27 TraesCS6A01G111800 chr2B 98.942 189 2 0 4070 4258 367730703 367730891 5.620000e-89 339.0
28 TraesCS6A01G111800 chr2B 84.706 170 17 5 951 1111 324624090 324623921 1.310000e-35 161.0
29 TraesCS6A01G111800 chr4B 98.930 187 2 0 4071 4257 351874803 351874617 7.270000e-88 335.0
30 TraesCS6A01G111800 chr1B 97.462 197 2 3 4058 4253 288394435 288394629 2.610000e-87 333.0
31 TraesCS6A01G111800 chr2A 96.020 201 7 1 4061 4260 119305871 119305671 4.370000e-85 326.0
32 TraesCS6A01G111800 chr2A 90.066 151 12 2 3826 3973 5609562 5609712 4.630000e-45 193.0
33 TraesCS6A01G111800 chr2A 95.455 88 4 0 3495 3582 5609372 5609459 1.700000e-29 141.0
34 TraesCS6A01G111800 chr2A 94.286 70 4 0 1150 1219 704626368 704626299 1.720000e-19 108.0
35 TraesCS6A01G111800 chr2A 88.571 70 8 0 1150 1219 769384828 769384759 8.080000e-13 86.1
36 TraesCS6A01G111800 chr3A 91.045 67 6 0 4255 4321 723439286 723439220 1.740000e-14 91.6
37 TraesCS6A01G111800 chr1D 89.855 69 7 0 1151 1219 4079963 4079895 6.250000e-14 89.8


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 TraesCS6A01G111800 chr6A 80874813 80879345 4532 False 8371.00 8371 100.00000 1 4533 1 chr6A.!!$F1 4532
1 TraesCS6A01G111800 chr6B 137378768 137383940 5172 False 1505.00 5398 92.96025 293 4504 4 chr6B.!!$F3 4211
2 TraesCS6A01G111800 chr6D 63725164 63729443 4279 False 1562.00 5319 88.88125 11 4504 4 chr6D.!!$F2 4493
3 TraesCS6A01G111800 chr5D 344543786 344546417 2631 True 1923.05 3749 92.92450 996 3591 2 chr5D.!!$R1 2595
4 TraesCS6A01G111800 chr5B 407215316 407217945 2629 False 1913.50 3716 92.70850 996 3588 2 chr5B.!!$F2 2592
5 TraesCS6A01G111800 chr5A 447535248 447537798 2550 False 3648.00 3648 92.60900 1056 3588 1 chr5A.!!$F1 2532

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
473 575 0.313043 AACACTACACCGGTCGAGTG 59.687 55.000 30.77 30.77 43.97 3.51 F
890 2114 1.146566 GTCTACCTCCCGATTCCCCTA 59.853 57.143 0.00 0.00 0.00 3.53 F
1743 3034 1.452145 GCTCGGCTCTACAGGAGGAG 61.452 65.000 0.00 0.00 42.08 3.69 F
1857 3148 1.214062 CCTCTCACTGCGGTGTCTC 59.786 63.158 24.61 0.00 43.41 3.36 F
1952 3243 1.228552 GTGGTGGAATGGCTGGTGT 60.229 57.895 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 3083 0.464373 CCAGGTGTTGGGATCGGATG 60.464 60.000 0.0 0.0 43.75 3.51 R
1852 3143 0.880278 GCAAGCCAGACAACGAGACA 60.880 55.000 0.0 0.0 0.00 3.41 R
2637 3928 0.977627 AGCCACGATCACCATCTCCA 60.978 55.000 0.0 0.0 0.00 3.86 R
3304 4598 2.229784 CAGCCATGAACCTGTTTCCTTC 59.770 50.000 0.0 0.0 32.58 3.46 R
3773 5069 4.256110 TGAGAACATACTGGCACTCAATG 58.744 43.478 0.0 0.0 32.66 2.82 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
90 93 6.610830 ACAATTATGGAGGAAATTATGGTGCA 59.389 34.615 0.00 0.00 0.00 4.57
91 94 7.125507 ACAATTATGGAGGAAATTATGGTGCAA 59.874 33.333 0.00 0.00 0.00 4.08
97 100 5.241728 GGAGGAAATTATGGTGCAACTATCC 59.758 44.000 2.04 1.71 37.44 2.59
107 110 7.807977 ATGGTGCAACTATCCTATTTTAGTG 57.192 36.000 2.04 0.00 28.92 2.74
112 115 5.559035 GCAACTATCCTATTTTAGTGCAGCG 60.559 44.000 0.00 0.00 0.00 5.18
114 117 3.560636 ATCCTATTTTAGTGCAGCGGT 57.439 42.857 0.00 0.00 0.00 5.68
176 185 2.978156 TCATCTTTTCTTGCCCCACT 57.022 45.000 0.00 0.00 0.00 4.00
182 191 3.772025 TCTTTTCTTGCCCCACTTTTTGA 59.228 39.130 0.00 0.00 0.00 2.69
184 193 5.600484 TCTTTTCTTGCCCCACTTTTTGATA 59.400 36.000 0.00 0.00 0.00 2.15
188 197 1.431243 TGCCCCACTTTTTGATACCCT 59.569 47.619 0.00 0.00 0.00 4.34
191 200 4.264623 TGCCCCACTTTTTGATACCCTAAT 60.265 41.667 0.00 0.00 0.00 1.73
195 204 7.327975 CCCCACTTTTTGATACCCTAATTTTC 58.672 38.462 0.00 0.00 0.00 2.29
215 224 5.560966 TTCACTCACTTTTTGGTGTTCTC 57.439 39.130 0.00 0.00 38.28 2.87
216 225 4.584874 TCACTCACTTTTTGGTGTTCTCA 58.415 39.130 0.00 0.00 38.28 3.27
219 228 6.152661 TCACTCACTTTTTGGTGTTCTCAAAT 59.847 34.615 0.00 0.00 38.28 2.32
222 231 7.339466 ACTCACTTTTTGGTGTTCTCAAATAGT 59.661 33.333 0.00 0.00 42.60 2.12
241 250 2.880890 AGTGTTGTTGTTGGAGATGCTC 59.119 45.455 0.00 0.00 0.00 4.26
245 254 5.008613 GTGTTGTTGTTGGAGATGCTCTAAA 59.991 40.000 0.00 0.00 33.06 1.85
277 286 6.672593 ACATCTATGTGGTTTATGGGAATGT 58.327 36.000 0.00 0.00 40.03 2.71
278 287 7.125391 ACATCTATGTGGTTTATGGGAATGTT 58.875 34.615 0.00 0.00 40.03 2.71
279 288 7.619302 ACATCTATGTGGTTTATGGGAATGTTT 59.381 33.333 0.00 0.00 40.03 2.83
280 289 7.403312 TCTATGTGGTTTATGGGAATGTTTG 57.597 36.000 0.00 0.00 0.00 2.93
282 291 4.227197 TGTGGTTTATGGGAATGTTTGGT 58.773 39.130 0.00 0.00 0.00 3.67
283 292 4.656112 TGTGGTTTATGGGAATGTTTGGTT 59.344 37.500 0.00 0.00 0.00 3.67
284 293 5.839063 TGTGGTTTATGGGAATGTTTGGTTA 59.161 36.000 0.00 0.00 0.00 2.85
285 294 6.160684 GTGGTTTATGGGAATGTTTGGTTAC 58.839 40.000 0.00 0.00 0.00 2.50
287 296 5.404096 GTTTATGGGAATGTTTGGTTACCG 58.596 41.667 0.00 0.00 31.83 4.02
288 297 2.953284 TGGGAATGTTTGGTTACCGA 57.047 45.000 0.00 0.00 31.83 4.69
289 298 2.506444 TGGGAATGTTTGGTTACCGAC 58.494 47.619 0.00 0.00 31.83 4.79
290 299 2.158652 TGGGAATGTTTGGTTACCGACA 60.159 45.455 11.73 11.73 31.83 4.35
291 300 2.227149 GGGAATGTTTGGTTACCGACAC 59.773 50.000 11.61 5.16 0.00 3.67
473 575 0.313043 AACACTACACCGGTCGAGTG 59.687 55.000 30.77 30.77 43.97 3.51
623 729 3.990369 GGGGGTTTAGGGCTTTTTATCT 58.010 45.455 0.00 0.00 0.00 1.98
625 731 4.404715 GGGGGTTTAGGGCTTTTTATCTTC 59.595 45.833 0.00 0.00 0.00 2.87
628 734 6.127423 GGGGTTTAGGGCTTTTTATCTTCTTC 60.127 42.308 0.00 0.00 0.00 2.87
671 1876 1.314730 GTTTTGAAGGGCGGACAGAA 58.685 50.000 0.00 0.00 0.00 3.02
706 1918 4.856801 CGGCCCACGGGATGAAGG 62.857 72.222 6.21 0.00 39.42 3.46
791 2010 2.765807 CACCGATGCCTCCCTCCT 60.766 66.667 0.00 0.00 0.00 3.69
809 2028 4.777366 CCTCCTTCTCTTCTCCTTTCTTCT 59.223 45.833 0.00 0.00 0.00 2.85
890 2114 1.146566 GTCTACCTCCCGATTCCCCTA 59.853 57.143 0.00 0.00 0.00 3.53
902 2130 3.537874 CCCCTACCTTCTCGGCCG 61.538 72.222 22.12 22.12 35.61 6.13
903 2131 3.537874 CCCTACCTTCTCGGCCGG 61.538 72.222 27.83 16.54 35.61 6.13
904 2132 4.222847 CCTACCTTCTCGGCCGGC 62.223 72.222 27.83 21.18 35.61 6.13
905 2133 4.222847 CTACCTTCTCGGCCGGCC 62.223 72.222 36.69 36.69 35.61 6.13
929 2157 3.357079 CTTGGACTGCCGCACCAC 61.357 66.667 2.24 0.00 36.79 4.16
991 2237 2.125106 GAACCCTAGCGCCCACTG 60.125 66.667 2.29 0.00 0.00 3.66
1015 2261 2.573869 CGATGGACGAGCACCAGT 59.426 61.111 0.00 0.00 45.77 4.00
1285 2552 3.119709 CTGCTCGACTCGCTCTCCC 62.120 68.421 0.00 0.00 0.00 4.30
1728 3019 2.511145 GCTCAGGCCTTCTGCTCG 60.511 66.667 0.00 0.00 43.06 5.03
1743 3034 1.452145 GCTCGGCTCTACAGGAGGAG 61.452 65.000 0.00 0.00 42.08 3.69
1852 3143 2.167900 GGTAATTACCTCTCACTGCGGT 59.832 50.000 24.79 0.00 43.10 5.68
1857 3148 1.214062 CCTCTCACTGCGGTGTCTC 59.786 63.158 24.61 0.00 43.41 3.36
1863 3154 1.299926 ACTGCGGTGTCTCGTTGTC 60.300 57.895 0.00 0.00 0.00 3.18
1952 3243 1.228552 GTGGTGGAATGGCTGGTGT 60.229 57.895 0.00 0.00 0.00 4.16
1974 3265 4.409218 CATGGGCACGCACAGCAC 62.409 66.667 0.00 0.00 35.50 4.40
2088 3379 4.956075 GGTGAATTGGAGGATGTATTTGGT 59.044 41.667 0.00 0.00 0.00 3.67
2852 4143 4.352595 TCCATTCTACAAGGAAGGGACAAA 59.647 41.667 6.52 0.00 46.70 2.83
3126 4417 9.588774 CTTTTTGCTTTGTTTGACATCATATTG 57.411 29.630 0.00 0.00 0.00 1.90
3172 4463 4.213482 GGTGGTTTGAACGGATATATGAGC 59.787 45.833 0.00 0.00 0.00 4.26
3216 4509 5.195940 TGCAGAAATAGCTAGCCATCTTTT 58.804 37.500 12.13 4.47 0.00 2.27
3234 4528 6.486253 TCTTTTCCTCAAAATCTCATCACG 57.514 37.500 0.00 0.00 30.91 4.35
3291 4585 3.876309 TTGCAGGGGAAAGAGTAAACT 57.124 42.857 0.00 0.00 0.00 2.66
3304 4598 8.743099 GGAAAGAGTAAACTGAAAACAAAATCG 58.257 33.333 0.00 0.00 0.00 3.34
3567 4861 5.590259 TGCTTCTAATGTGGAAGAAATAGGC 59.410 40.000 5.63 0.00 41.71 3.93
3685 4979 9.131791 AGTTCACTTTTGTTGGAGTATATTTGT 57.868 29.630 0.00 0.00 0.00 2.83
3743 5037 7.750903 GGTAACAGTGAAATATCTTTGACTTGC 59.249 37.037 0.00 0.00 36.79 4.01
3748 5044 7.063426 CAGTGAAATATCTTTGACTTGCGACTA 59.937 37.037 0.00 0.00 36.79 2.59
3749 5045 7.766278 AGTGAAATATCTTTGACTTGCGACTAT 59.234 33.333 0.00 0.00 35.61 2.12
3758 5054 4.371786 TGACTTGCGACTATGGATTGATC 58.628 43.478 0.00 0.00 0.00 2.92
3833 5129 9.974980 TGGTACTTCCAACAAATAATTTCTTTC 57.025 29.630 0.00 0.00 44.12 2.62
3875 5171 3.737559 TTGGTACCCAGATCATGCTTT 57.262 42.857 10.07 0.00 33.81 3.51
3880 5176 4.384208 GGTACCCAGATCATGCTTTACACT 60.384 45.833 0.00 0.00 0.00 3.55
3893 5189 5.479306 TGCTTTACACTGACCTCATTCTAC 58.521 41.667 0.00 0.00 0.00 2.59
3905 5201 8.262601 TGACCTCATTCTACCATATGTATTGT 57.737 34.615 1.24 0.00 0.00 2.71
3968 5267 4.702831 TGTTCACTCACTGCATTCTACAA 58.297 39.130 0.00 0.00 0.00 2.41
3980 5279 5.649557 TGCATTCTACAATTGTGTATTGGC 58.350 37.500 21.42 16.26 46.49 4.52
3989 5288 6.237901 ACAATTGTGTATTGGCAACTCTCTA 58.762 36.000 11.07 0.00 46.49 2.43
4071 5373 7.168219 TCTATAAGGTGTTTTGCTCATGAACT 58.832 34.615 0.00 0.00 0.00 3.01
4072 5374 8.318412 TCTATAAGGTGTTTTGCTCATGAACTA 58.682 33.333 0.00 0.00 0.00 2.24
4073 5375 7.944729 ATAAGGTGTTTTGCTCATGAACTAT 57.055 32.000 0.00 0.00 0.00 2.12
4074 5376 5.633830 AGGTGTTTTGCTCATGAACTATG 57.366 39.130 0.00 0.00 38.17 2.23
4075 5377 5.072741 AGGTGTTTTGCTCATGAACTATGT 58.927 37.500 0.00 0.00 38.01 2.29
4076 5378 5.536161 AGGTGTTTTGCTCATGAACTATGTT 59.464 36.000 0.00 0.00 38.01 2.71
4077 5379 6.040842 AGGTGTTTTGCTCATGAACTATGTTT 59.959 34.615 0.00 0.00 38.01 2.83
4078 5380 6.701400 GGTGTTTTGCTCATGAACTATGTTTT 59.299 34.615 0.00 0.00 38.01 2.43
4079 5381 7.224557 GGTGTTTTGCTCATGAACTATGTTTTT 59.775 33.333 0.00 0.00 38.01 1.94
4081 5383 9.809096 TGTTTTGCTCATGAACTATGTTTTTAA 57.191 25.926 0.00 0.00 38.01 1.52
4083 5385 9.474920 TTTTGCTCATGAACTATGTTTTTAAGG 57.525 29.630 0.00 0.00 38.01 2.69
4084 5386 6.620678 TGCTCATGAACTATGTTTTTAAGGC 58.379 36.000 0.00 0.00 38.01 4.35
4085 5387 5.739161 GCTCATGAACTATGTTTTTAAGGCG 59.261 40.000 0.00 0.00 38.01 5.52
4086 5388 6.403200 GCTCATGAACTATGTTTTTAAGGCGA 60.403 38.462 0.00 0.00 38.01 5.54
4087 5389 6.837992 TCATGAACTATGTTTTTAAGGCGAC 58.162 36.000 0.00 0.00 38.01 5.19
4088 5390 5.272167 TGAACTATGTTTTTAAGGCGACG 57.728 39.130 0.00 0.00 0.00 5.12
4089 5391 3.734776 ACTATGTTTTTAAGGCGACGC 57.265 42.857 12.43 12.43 0.00 5.19
4101 5403 2.491152 CGACGCCTTACCGCCTTA 59.509 61.111 0.00 0.00 0.00 2.69
4102 5404 1.588139 CGACGCCTTACCGCCTTAG 60.588 63.158 0.00 0.00 0.00 2.18
4103 5405 1.227176 GACGCCTTACCGCCTTAGG 60.227 63.158 0.00 0.00 37.30 2.69
4104 5406 2.108362 CGCCTTACCGCCTTAGGG 59.892 66.667 0.00 0.00 35.02 3.53
4105 5407 2.428925 CGCCTTACCGCCTTAGGGA 61.429 63.158 0.00 0.00 35.02 4.20
4106 5408 1.446366 GCCTTACCGCCTTAGGGAG 59.554 63.158 0.00 0.00 35.02 4.30
4152 5454 4.467084 CTAGGCGGGCGCTTTGGA 62.467 66.667 7.64 0.00 41.60 3.53
4153 5455 4.770874 TAGGCGGGCGCTTTGGAC 62.771 66.667 7.64 0.00 41.60 4.02
4161 5463 3.195698 CGCTTTGGACGCCTAGGC 61.196 66.667 24.75 24.75 37.85 3.93
4179 5481 3.274067 GCCCAAAGCGGTCGATTT 58.726 55.556 0.55 0.55 33.72 2.17
4180 5482 1.584495 GCCCAAAGCGGTCGATTTT 59.416 52.632 3.79 0.00 30.80 1.82
4181 5483 0.456142 GCCCAAAGCGGTCGATTTTC 60.456 55.000 3.79 0.00 30.80 2.29
4182 5484 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.00 30.80 3.13
4183 5485 0.878416 CCAAAGCGGTCGATTTTCCA 59.122 50.000 3.79 0.00 30.80 3.53
4184 5486 1.268352 CCAAAGCGGTCGATTTTCCAA 59.732 47.619 3.79 0.00 30.80 3.53
4185 5487 2.287909 CCAAAGCGGTCGATTTTCCAAA 60.288 45.455 3.79 0.00 30.80 3.28
4186 5488 2.979813 CAAAGCGGTCGATTTTCCAAAG 59.020 45.455 3.79 0.00 30.80 2.77
4187 5489 0.521735 AGCGGTCGATTTTCCAAAGC 59.478 50.000 0.00 0.00 0.00 3.51
4188 5490 0.793104 GCGGTCGATTTTCCAAAGCG 60.793 55.000 0.54 0.54 0.00 4.68
4189 5491 0.179200 CGGTCGATTTTCCAAAGCGG 60.179 55.000 7.00 0.00 0.00 5.52
4190 5492 1.161843 GGTCGATTTTCCAAAGCGGA 58.838 50.000 7.00 0.00 44.40 5.54
4197 5499 3.009115 TCCAAAGCGGAGGGGGAG 61.009 66.667 0.00 0.00 39.64 4.30
4198 5500 4.803908 CCAAAGCGGAGGGGGAGC 62.804 72.222 0.00 0.00 36.56 4.70
4205 5507 3.717294 GGAGGGGGAGCGCTTTGA 61.717 66.667 13.26 0.00 0.00 2.69
4206 5508 2.436824 GAGGGGGAGCGCTTTGAC 60.437 66.667 13.26 2.82 0.00 3.18
4207 5509 4.394712 AGGGGGAGCGCTTTGACG 62.395 66.667 13.26 0.00 0.00 4.35
4243 5545 3.459063 GTCGCCTTAGGGACGCCT 61.459 66.667 0.00 0.00 44.82 5.52
4244 5546 2.682494 TCGCCTTAGGGACGCCTT 60.682 61.111 0.00 0.00 34.09 4.35
4245 5547 2.267961 CGCCTTAGGGACGCCTTT 59.732 61.111 0.00 0.00 33.58 3.11
4246 5548 0.971959 TCGCCTTAGGGACGCCTTTA 60.972 55.000 0.00 0.00 34.09 1.85
4247 5549 0.108041 CGCCTTAGGGACGCCTTTAA 60.108 55.000 0.00 0.00 33.58 1.52
4248 5550 1.676615 CGCCTTAGGGACGCCTTTAAA 60.677 52.381 0.00 0.00 33.58 1.52
4249 5551 2.439409 GCCTTAGGGACGCCTTTAAAA 58.561 47.619 0.00 0.00 33.58 1.52
4250 5552 2.163010 GCCTTAGGGACGCCTTTAAAAC 59.837 50.000 0.00 0.00 33.58 2.43
4251 5553 3.414269 CCTTAGGGACGCCTTTAAAACA 58.586 45.455 0.00 0.00 33.58 2.83
4252 5554 4.014406 CCTTAGGGACGCCTTTAAAACAT 58.986 43.478 0.00 0.00 33.58 2.71
4253 5555 4.095932 CCTTAGGGACGCCTTTAAAACATC 59.904 45.833 0.00 0.00 33.58 3.06
4254 5556 2.081462 AGGGACGCCTTTAAAACATCG 58.919 47.619 0.00 0.00 0.00 3.84
4255 5557 1.466866 GGGACGCCTTTAAAACATCGC 60.467 52.381 0.00 0.00 0.00 4.58
4256 5558 1.467342 GGACGCCTTTAAAACATCGCT 59.533 47.619 0.00 0.00 0.00 4.93
4257 5559 2.475685 GGACGCCTTTAAAACATCGCTC 60.476 50.000 0.00 0.00 0.00 5.03
4258 5560 2.147958 ACGCCTTTAAAACATCGCTCA 58.852 42.857 0.00 0.00 0.00 4.26
4259 5561 2.747446 ACGCCTTTAAAACATCGCTCAT 59.253 40.909 0.00 0.00 0.00 2.90
4260 5562 3.100817 CGCCTTTAAAACATCGCTCATG 58.899 45.455 0.00 0.00 38.64 3.07
4261 5563 3.181511 CGCCTTTAAAACATCGCTCATGA 60.182 43.478 0.00 0.00 36.21 3.07
4262 5564 4.671508 CGCCTTTAAAACATCGCTCATGAA 60.672 41.667 0.00 0.00 36.21 2.57
4263 5565 4.558860 GCCTTTAAAACATCGCTCATGAAC 59.441 41.667 0.00 0.00 36.21 3.18
4264 5566 5.698832 CCTTTAAAACATCGCTCATGAACA 58.301 37.500 0.00 0.00 36.21 3.18
4265 5567 6.324819 CCTTTAAAACATCGCTCATGAACAT 58.675 36.000 0.00 0.00 36.21 2.71
4266 5568 6.808212 CCTTTAAAACATCGCTCATGAACATT 59.192 34.615 0.00 0.00 36.21 2.71
4267 5569 7.201376 CCTTTAAAACATCGCTCATGAACATTG 60.201 37.037 0.00 0.00 36.21 2.82
4268 5570 5.375417 AAAACATCGCTCATGAACATTGA 57.625 34.783 0.00 0.00 36.21 2.57
4269 5571 4.346734 AACATCGCTCATGAACATTGAC 57.653 40.909 0.00 0.00 36.21 3.18
4270 5572 3.603532 ACATCGCTCATGAACATTGACT 58.396 40.909 0.00 0.00 36.21 3.41
4271 5573 3.373130 ACATCGCTCATGAACATTGACTG 59.627 43.478 0.00 0.00 36.21 3.51
4272 5574 1.733912 TCGCTCATGAACATTGACTGC 59.266 47.619 0.00 0.00 0.00 4.40
4273 5575 1.528400 CGCTCATGAACATTGACTGCG 60.528 52.381 5.92 5.92 35.22 5.18
4274 5576 1.202110 GCTCATGAACATTGACTGCGG 60.202 52.381 0.00 0.00 0.00 5.69
4283 5585 1.200716 CATTGACTGCGGCAACTGATT 59.799 47.619 3.44 0.00 0.00 2.57
4295 5597 4.143030 CGGCAACTGATTTCAGACTTACTG 60.143 45.833 14.29 0.00 46.59 2.74
4356 5658 4.700692 GTCTCCCAGGACAATTTAGTTTCC 59.299 45.833 0.00 0.00 36.35 3.13
4357 5659 4.601857 TCTCCCAGGACAATTTAGTTTCCT 59.398 41.667 0.00 0.00 39.17 3.36
4359 5661 3.689649 CCCAGGACAATTTAGTTTCCTCG 59.310 47.826 0.00 0.00 36.26 4.63
4376 5678 9.521841 AGTTTCCTCGTATGATATATCTCTTCA 57.478 33.333 13.79 0.00 0.00 3.02
4431 5733 3.370103 GCCTGGTGGTGCTACTTTGTATA 60.370 47.826 0.00 0.00 35.27 1.47
4437 5739 5.250982 GTGGTGCTACTTTGTATAAGGGTT 58.749 41.667 0.00 0.00 0.00 4.11
4463 5765 8.649973 GCACTTACTGCTGTTTCTAGTTATAT 57.350 34.615 0.09 0.00 43.33 0.86
4464 5766 8.543774 GCACTTACTGCTGTTTCTAGTTATATG 58.456 37.037 0.09 0.00 43.33 1.78
4465 5767 9.803315 CACTTACTGCTGTTTCTAGTTATATGA 57.197 33.333 0.09 0.00 0.00 2.15
4493 5796 4.154195 CCAATAGATACCCTGTAATTGCGC 59.846 45.833 0.00 0.00 0.00 6.09
4504 5807 3.936453 CTGTAATTGCGCCCTAAACTGTA 59.064 43.478 4.18 0.00 0.00 2.74
4505 5808 3.936453 TGTAATTGCGCCCTAAACTGTAG 59.064 43.478 4.18 0.00 0.00 2.74
4506 5809 2.781681 ATTGCGCCCTAAACTGTAGT 57.218 45.000 4.18 0.00 0.00 2.73
4507 5810 1.803334 TTGCGCCCTAAACTGTAGTG 58.197 50.000 4.18 0.00 0.00 2.74
4508 5811 0.672401 TGCGCCCTAAACTGTAGTGC 60.672 55.000 4.18 0.00 0.00 4.40
4509 5812 1.366854 GCGCCCTAAACTGTAGTGCC 61.367 60.000 0.00 0.00 0.00 5.01
4510 5813 0.249398 CGCCCTAAACTGTAGTGCCT 59.751 55.000 0.00 0.00 0.00 4.75
4511 5814 1.739371 CGCCCTAAACTGTAGTGCCTC 60.739 57.143 0.00 0.00 0.00 4.70
4512 5815 1.739371 GCCCTAAACTGTAGTGCCTCG 60.739 57.143 0.00 0.00 0.00 4.63
4513 5816 1.822990 CCCTAAACTGTAGTGCCTCGA 59.177 52.381 0.00 0.00 0.00 4.04
4514 5817 2.232941 CCCTAAACTGTAGTGCCTCGAA 59.767 50.000 0.00 0.00 0.00 3.71
4515 5818 3.251571 CCTAAACTGTAGTGCCTCGAAC 58.748 50.000 0.00 0.00 0.00 3.95
4516 5819 3.056749 CCTAAACTGTAGTGCCTCGAACT 60.057 47.826 0.00 0.00 0.00 3.01
4517 5820 3.470645 AAACTGTAGTGCCTCGAACTT 57.529 42.857 0.00 0.00 0.00 2.66
4518 5821 4.595762 AAACTGTAGTGCCTCGAACTTA 57.404 40.909 0.00 0.00 0.00 2.24
4519 5822 3.851976 ACTGTAGTGCCTCGAACTTAG 57.148 47.619 0.00 0.00 0.00 2.18
4520 5823 3.418995 ACTGTAGTGCCTCGAACTTAGA 58.581 45.455 0.00 0.00 0.00 2.10
4521 5824 3.440872 ACTGTAGTGCCTCGAACTTAGAG 59.559 47.826 0.00 0.00 35.60 2.43
4522 5825 3.682696 TGTAGTGCCTCGAACTTAGAGA 58.317 45.455 0.71 0.00 37.93 3.10
4523 5826 4.077108 TGTAGTGCCTCGAACTTAGAGAA 58.923 43.478 0.71 0.00 37.93 2.87
4524 5827 4.521639 TGTAGTGCCTCGAACTTAGAGAAA 59.478 41.667 0.71 0.00 37.93 2.52
4525 5828 4.602340 AGTGCCTCGAACTTAGAGAAAA 57.398 40.909 0.71 0.00 37.93 2.29
4526 5829 4.561105 AGTGCCTCGAACTTAGAGAAAAG 58.439 43.478 0.71 0.00 37.93 2.27
4527 5830 4.281182 AGTGCCTCGAACTTAGAGAAAAGA 59.719 41.667 0.71 0.00 37.93 2.52
4528 5831 4.989168 GTGCCTCGAACTTAGAGAAAAGAA 59.011 41.667 0.71 0.00 37.93 2.52
4529 5832 5.465724 GTGCCTCGAACTTAGAGAAAAGAAA 59.534 40.000 0.71 0.00 37.93 2.52
4530 5833 5.696724 TGCCTCGAACTTAGAGAAAAGAAAG 59.303 40.000 0.71 0.00 37.93 2.62
4531 5834 5.697178 GCCTCGAACTTAGAGAAAAGAAAGT 59.303 40.000 0.71 0.00 37.93 2.66
4532 5835 6.346999 GCCTCGAACTTAGAGAAAAGAAAGTG 60.347 42.308 0.71 0.00 37.93 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 6.610830 TGCACCATAATTTCCTCCATAATTGT 59.389 34.615 0.00 0.00 0.00 2.71
90 93 5.057149 CCGCTGCACTAAAATAGGATAGTT 58.943 41.667 0.00 0.00 30.09 2.24
91 94 4.101119 ACCGCTGCACTAAAATAGGATAGT 59.899 41.667 0.00 0.00 32.69 2.12
97 100 4.025647 GCTCTAACCGCTGCACTAAAATAG 60.026 45.833 0.00 0.00 0.00 1.73
106 109 0.321564 ACATTGCTCTAACCGCTGCA 60.322 50.000 0.00 0.00 0.00 4.41
107 110 0.804989 AACATTGCTCTAACCGCTGC 59.195 50.000 0.00 0.00 0.00 5.25
157 160 2.978156 AGTGGGGCAAGAAAAGATGA 57.022 45.000 0.00 0.00 0.00 2.92
176 185 9.362151 AGTGAGTGAAAATTAGGGTATCAAAAA 57.638 29.630 0.00 0.00 0.00 1.94
182 191 8.585018 CCAAAAAGTGAGTGAAAATTAGGGTAT 58.415 33.333 0.00 0.00 0.00 2.73
184 193 6.382859 ACCAAAAAGTGAGTGAAAATTAGGGT 59.617 34.615 0.00 0.00 0.00 4.34
188 197 8.527810 AGAACACCAAAAAGTGAGTGAAAATTA 58.472 29.630 0.00 0.00 40.34 1.40
191 200 6.015856 TGAGAACACCAAAAAGTGAGTGAAAA 60.016 34.615 0.00 0.00 40.34 2.29
195 204 4.963276 TGAGAACACCAAAAAGTGAGTG 57.037 40.909 0.00 0.00 40.34 3.51
215 224 5.630680 GCATCTCCAACAACAACACTATTTG 59.369 40.000 0.00 0.00 0.00 2.32
216 225 5.536161 AGCATCTCCAACAACAACACTATTT 59.464 36.000 0.00 0.00 0.00 1.40
219 228 4.065088 GAGCATCTCCAACAACAACACTA 58.935 43.478 0.00 0.00 0.00 2.74
253 262 6.672593 ACATTCCCATAAACCACATAGATGT 58.327 36.000 0.00 0.00 42.84 3.06
259 268 4.843516 ACCAAACATTCCCATAAACCACAT 59.156 37.500 0.00 0.00 0.00 3.21
271 280 3.058501 CAGTGTCGGTAACCAAACATTCC 60.059 47.826 0.00 0.00 0.00 3.01
272 281 3.562557 ACAGTGTCGGTAACCAAACATTC 59.437 43.478 0.00 0.00 0.00 2.67
275 284 2.695127 ACAGTGTCGGTAACCAAACA 57.305 45.000 0.00 0.00 0.00 2.83
276 285 4.359971 AAAACAGTGTCGGTAACCAAAC 57.640 40.909 0.00 0.00 0.00 2.93
277 286 4.458295 TCAAAAACAGTGTCGGTAACCAAA 59.542 37.500 0.00 0.00 0.00 3.28
278 287 4.008330 TCAAAAACAGTGTCGGTAACCAA 58.992 39.130 0.00 0.00 0.00 3.67
279 288 3.607741 TCAAAAACAGTGTCGGTAACCA 58.392 40.909 0.00 0.00 0.00 3.67
280 289 3.547413 GCTCAAAAACAGTGTCGGTAACC 60.547 47.826 0.00 0.00 0.00 2.85
282 291 2.614983 GGCTCAAAAACAGTGTCGGTAA 59.385 45.455 0.00 0.00 0.00 2.85
283 292 2.215196 GGCTCAAAAACAGTGTCGGTA 58.785 47.619 0.00 0.00 0.00 4.02
284 293 1.021968 GGCTCAAAAACAGTGTCGGT 58.978 50.000 0.00 0.00 0.00 4.69
285 294 1.021202 TGGCTCAAAAACAGTGTCGG 58.979 50.000 0.00 0.00 0.00 4.79
287 296 4.515191 TGTAGATGGCTCAAAAACAGTGTC 59.485 41.667 0.00 0.00 0.00 3.67
288 297 4.460263 TGTAGATGGCTCAAAAACAGTGT 58.540 39.130 0.00 0.00 0.00 3.55
289 298 5.413833 AGATGTAGATGGCTCAAAAACAGTG 59.586 40.000 0.00 0.00 0.00 3.66
290 299 5.564550 AGATGTAGATGGCTCAAAAACAGT 58.435 37.500 0.00 0.00 0.00 3.55
291 300 7.255035 CCATAGATGTAGATGGCTCAAAAACAG 60.255 40.741 0.00 0.00 36.45 3.16
508 610 4.691685 TCAAAATAGACTCGGCGCTAAAAA 59.308 37.500 7.64 0.00 0.00 1.94
509 611 4.247258 TCAAAATAGACTCGGCGCTAAAA 58.753 39.130 7.64 0.00 0.00 1.52
510 612 3.852286 TCAAAATAGACTCGGCGCTAAA 58.148 40.909 7.64 0.00 0.00 1.85
511 613 3.513680 TCAAAATAGACTCGGCGCTAA 57.486 42.857 7.64 0.00 0.00 3.09
512 614 3.728076 ATCAAAATAGACTCGGCGCTA 57.272 42.857 7.64 0.00 0.00 4.26
513 615 2.604046 ATCAAAATAGACTCGGCGCT 57.396 45.000 7.64 0.00 0.00 5.92
514 616 3.675467 AAATCAAAATAGACTCGGCGC 57.325 42.857 0.00 0.00 0.00 6.53
606 712 9.982651 AAAAGAAGAAGATAAAAAGCCCTAAAC 57.017 29.630 0.00 0.00 0.00 2.01
671 1876 0.383590 CGTCGATCTGGATGCTCTGT 59.616 55.000 0.00 0.00 0.00 3.41
699 1904 1.227002 GCCCGTCGTCTCCTTCATC 60.227 63.158 0.00 0.00 0.00 2.92
701 1906 3.379445 GGCCCGTCGTCTCCTTCA 61.379 66.667 0.00 0.00 0.00 3.02
702 1907 3.066233 GAGGCCCGTCGTCTCCTTC 62.066 68.421 0.00 0.00 0.00 3.46
728 1940 1.142048 TATCATGGGCTGGGGATGGG 61.142 60.000 0.00 0.00 0.00 4.00
730 1942 0.330604 CCTATCATGGGCTGGGGATG 59.669 60.000 0.00 0.00 0.00 3.51
731 1943 0.196888 TCCTATCATGGGCTGGGGAT 59.803 55.000 0.00 0.00 0.00 3.85
786 1998 4.777366 AGAAGAAAGGAGAAGAGAAGGAGG 59.223 45.833 0.00 0.00 0.00 4.30
791 2010 5.608860 AGGGAAAGAAGAAAGGAGAAGAGAA 59.391 40.000 0.00 0.00 0.00 2.87
1015 2261 1.756950 CCTTGACGAGATCCCCGGA 60.757 63.158 0.73 0.00 0.00 5.14
1123 2390 4.717629 CGCGTGCTCGTCTGGGAA 62.718 66.667 10.18 0.00 39.49 3.97
1743 3034 5.537188 AGCAGCTTATAGTAATCAGACAGC 58.463 41.667 0.00 0.00 0.00 4.40
1792 3083 0.464373 CCAGGTGTTGGGATCGGATG 60.464 60.000 0.00 0.00 43.75 3.51
1852 3143 0.880278 GCAAGCCAGACAACGAGACA 60.880 55.000 0.00 0.00 0.00 3.41
1857 3148 1.864862 CTCAGCAAGCCAGACAACG 59.135 57.895 0.00 0.00 0.00 4.10
1952 3243 2.438254 GTGCGTGCCCATGGATCA 60.438 61.111 15.22 8.02 0.00 2.92
2031 3322 2.922335 GCTTCGGACCATTTCAAACAGC 60.922 50.000 0.00 0.00 0.00 4.40
2088 3379 2.886523 CTGCCCAACAATGAAGAACTCA 59.113 45.455 0.00 0.00 38.81 3.41
2340 3631 1.281867 TCTACCACCAATGCCTCCAAG 59.718 52.381 0.00 0.00 0.00 3.61
2443 3734 2.033801 CCTGCCCAAGAAGCAAATATCG 59.966 50.000 0.00 0.00 40.35 2.92
2637 3928 0.977627 AGCCACGATCACCATCTCCA 60.978 55.000 0.00 0.00 0.00 3.86
2768 4059 3.584406 TCCAGTCAGAGAATGGTCAACAT 59.416 43.478 12.53 0.00 46.34 2.71
2852 4143 2.664402 AACAAACTGAGCCCTGATGT 57.336 45.000 0.00 0.00 0.00 3.06
3076 4367 2.358258 TCTCAAAATTCCCAGGGACCT 58.642 47.619 8.12 0.00 0.00 3.85
3126 4417 4.487412 GCATGGCTGCGGAACTGC 62.487 66.667 0.00 0.00 38.92 4.40
3172 4463 7.280876 TCTGCAATAATCTAACCTTAGTTGCAG 59.719 37.037 25.03 25.03 43.07 4.41
3216 4509 4.808414 AGACGTGATGAGATTTTGAGGA 57.192 40.909 0.00 0.00 0.00 3.71
3271 4565 3.137544 TCAGTTTACTCTTTCCCCTGCAA 59.862 43.478 0.00 0.00 0.00 4.08
3291 4585 6.039616 CCTGTTTCCTTCGATTTTGTTTTCA 58.960 36.000 0.00 0.00 0.00 2.69
3304 4598 2.229784 CAGCCATGAACCTGTTTCCTTC 59.770 50.000 0.00 0.00 32.58 3.46
3567 4861 6.153756 CCCCAACCAAAAAGTAAATCTAACG 58.846 40.000 0.00 0.00 0.00 3.18
3665 4959 8.730680 AGCACTACAAATATACTCCAACAAAAG 58.269 33.333 0.00 0.00 0.00 2.27
3670 4964 6.113411 ACCAGCACTACAAATATACTCCAAC 58.887 40.000 0.00 0.00 0.00 3.77
3685 4979 4.551702 TGAGAAGCAAATACCAGCACTA 57.448 40.909 0.00 0.00 0.00 2.74
3724 5018 6.170675 AGTCGCAAGTCAAAGATATTTCAC 57.829 37.500 0.00 0.00 39.48 3.18
3748 5044 8.862085 TGCACAATACATAAATGATCAATCCAT 58.138 29.630 0.00 0.00 0.00 3.41
3749 5045 8.235359 TGCACAATACATAAATGATCAATCCA 57.765 30.769 0.00 0.00 0.00 3.41
3773 5069 4.256110 TGAGAACATACTGGCACTCAATG 58.744 43.478 0.00 0.00 32.66 2.82
3786 5082 9.865321 GTACCAAGTGTAGTATTTGAGAACATA 57.135 33.333 0.00 0.00 0.00 2.29
3875 5171 6.839134 ACATATGGTAGAATGAGGTCAGTGTA 59.161 38.462 7.80 0.00 0.00 2.90
3880 5176 8.150296 CACAATACATATGGTAGAATGAGGTCA 58.850 37.037 7.80 0.00 34.92 4.02
3938 5236 9.182214 AGAATGCAGTGAGTGAACATTATATTT 57.818 29.630 0.00 0.00 31.40 1.40
3968 5267 5.186198 GGTAGAGAGTTGCCAATACACAAT 58.814 41.667 0.00 0.00 0.00 2.71
3980 5279 9.751542 ATAAAGAAATATGACGGTAGAGAGTTG 57.248 33.333 0.00 0.00 0.00 3.16
3989 5288 7.042051 CGTGGATTCATAAAGAAATATGACGGT 60.042 37.037 0.00 0.00 40.92 4.83
4050 5352 6.714810 ACATAGTTCATGAGCAAAACACCTTA 59.285 34.615 12.41 0.00 38.10 2.69
4064 5366 5.732647 CGTCGCCTTAAAAACATAGTTCATG 59.267 40.000 0.00 0.00 40.78 3.07
4089 5391 1.408453 CCCTCCCTAAGGCGGTAAGG 61.408 65.000 0.00 0.00 44.71 2.69
4090 5392 1.408453 CCCCTCCCTAAGGCGGTAAG 61.408 65.000 0.00 0.00 44.71 2.34
4091 5393 1.383525 CCCCTCCCTAAGGCGGTAA 60.384 63.158 0.00 0.00 44.71 2.85
4092 5394 2.284493 CCCCTCCCTAAGGCGGTA 59.716 66.667 0.00 0.00 44.71 4.02
4093 5395 4.817909 CCCCCTCCCTAAGGCGGT 62.818 72.222 0.00 0.00 44.71 5.68
4135 5437 4.467084 TCCAAAGCGCCCGCCTAG 62.467 66.667 2.29 0.00 43.17 3.02
4136 5438 4.770874 GTCCAAAGCGCCCGCCTA 62.771 66.667 2.29 0.00 43.17 3.93
4144 5446 3.195698 GCCTAGGCGTCCAAAGCG 61.196 66.667 20.16 0.00 35.00 4.68
4162 5464 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.000 0.00 0.00 45.45 5.36
4163 5465 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.000 0.00 0.00 44.64 4.12
4164 5466 0.878416 TGGAAAATCGACCGCTTTGG 59.122 50.000 0.00 0.00 46.41 3.28
4165 5467 2.697431 TTGGAAAATCGACCGCTTTG 57.303 45.000 0.00 0.00 0.00 2.77
4166 5468 2.607038 GCTTTGGAAAATCGACCGCTTT 60.607 45.455 0.00 0.00 0.00 3.51
4167 5469 1.068541 GCTTTGGAAAATCGACCGCTT 60.069 47.619 0.00 0.00 0.00 4.68
4168 5470 0.521735 GCTTTGGAAAATCGACCGCT 59.478 50.000 0.00 0.00 0.00 5.52
4169 5471 0.793104 CGCTTTGGAAAATCGACCGC 60.793 55.000 0.00 0.00 0.00 5.68
4170 5472 0.179200 CCGCTTTGGAAAATCGACCG 60.179 55.000 0.00 0.00 42.00 4.79
4171 5473 1.161843 TCCGCTTTGGAAAATCGACC 58.838 50.000 0.00 0.00 46.38 4.79
4181 5483 4.803908 GCTCCCCCTCCGCTTTGG 62.804 72.222 0.00 0.00 40.09 3.28
4188 5490 3.717294 TCAAAGCGCTCCCCCTCC 61.717 66.667 12.06 0.00 0.00 4.30
4189 5491 2.436824 GTCAAAGCGCTCCCCCTC 60.437 66.667 12.06 0.00 0.00 4.30
4190 5492 4.394712 CGTCAAAGCGCTCCCCCT 62.395 66.667 12.06 0.00 0.00 4.79
4226 5528 2.517484 AAAGGCGTCCCTAAGGCGAC 62.517 60.000 0.00 0.00 41.90 5.19
4227 5529 0.971959 TAAAGGCGTCCCTAAGGCGA 60.972 55.000 0.00 0.00 41.90 5.54
4228 5530 0.108041 TTAAAGGCGTCCCTAAGGCG 60.108 55.000 0.00 0.00 41.90 5.52
4229 5531 2.118313 TTTAAAGGCGTCCCTAAGGC 57.882 50.000 0.00 0.00 41.90 4.35
4230 5532 3.414269 TGTTTTAAAGGCGTCCCTAAGG 58.586 45.455 0.00 0.00 41.90 2.69
4231 5533 4.201783 CGATGTTTTAAAGGCGTCCCTAAG 60.202 45.833 7.86 0.00 41.90 2.18
4232 5534 3.685756 CGATGTTTTAAAGGCGTCCCTAA 59.314 43.478 7.86 0.00 41.90 2.69
4233 5535 3.264104 CGATGTTTTAAAGGCGTCCCTA 58.736 45.455 7.86 0.00 41.90 3.53
4234 5536 2.081462 CGATGTTTTAAAGGCGTCCCT 58.919 47.619 7.86 0.00 45.77 4.20
4235 5537 1.466866 GCGATGTTTTAAAGGCGTCCC 60.467 52.381 0.00 0.00 0.00 4.46
4236 5538 1.467342 AGCGATGTTTTAAAGGCGTCC 59.533 47.619 0.00 0.00 0.00 4.79
4237 5539 2.158841 TGAGCGATGTTTTAAAGGCGTC 59.841 45.455 0.00 0.00 0.00 5.19
4238 5540 2.147958 TGAGCGATGTTTTAAAGGCGT 58.852 42.857 0.00 0.00 0.00 5.68
4239 5541 2.892373 TGAGCGATGTTTTAAAGGCG 57.108 45.000 0.00 0.00 0.00 5.52
4240 5542 4.355543 TCATGAGCGATGTTTTAAAGGC 57.644 40.909 0.00 0.00 33.29 4.35
4241 5543 5.698832 TGTTCATGAGCGATGTTTTAAAGG 58.301 37.500 5.02 0.00 33.29 3.11
4242 5544 7.538334 TCAATGTTCATGAGCGATGTTTTAAAG 59.462 33.333 5.02 0.00 33.29 1.85
4243 5545 7.325821 GTCAATGTTCATGAGCGATGTTTTAAA 59.674 33.333 5.02 0.00 33.29 1.52
4244 5546 6.801377 GTCAATGTTCATGAGCGATGTTTTAA 59.199 34.615 5.02 0.00 33.29 1.52
4245 5547 6.149308 AGTCAATGTTCATGAGCGATGTTTTA 59.851 34.615 5.02 0.00 33.29 1.52
4246 5548 5.048504 AGTCAATGTTCATGAGCGATGTTTT 60.049 36.000 5.02 0.00 33.29 2.43
4247 5549 4.456911 AGTCAATGTTCATGAGCGATGTTT 59.543 37.500 5.02 0.00 33.29 2.83
4248 5550 4.005650 AGTCAATGTTCATGAGCGATGTT 58.994 39.130 5.02 0.00 33.29 2.71
4249 5551 3.373130 CAGTCAATGTTCATGAGCGATGT 59.627 43.478 5.02 0.00 33.29 3.06
4250 5552 3.787805 GCAGTCAATGTTCATGAGCGATG 60.788 47.826 5.02 6.57 0.00 3.84
4251 5553 2.353889 GCAGTCAATGTTCATGAGCGAT 59.646 45.455 5.02 0.00 0.00 4.58
4252 5554 1.733912 GCAGTCAATGTTCATGAGCGA 59.266 47.619 5.02 0.00 0.00 4.93
4253 5555 1.528400 CGCAGTCAATGTTCATGAGCG 60.528 52.381 5.02 5.51 35.91 5.03
4254 5556 1.202110 CCGCAGTCAATGTTCATGAGC 60.202 52.381 2.05 2.05 0.00 4.26
4255 5557 1.202110 GCCGCAGTCAATGTTCATGAG 60.202 52.381 0.00 0.00 0.00 2.90
4256 5558 0.804364 GCCGCAGTCAATGTTCATGA 59.196 50.000 0.00 0.00 0.00 3.07
4257 5559 0.522626 TGCCGCAGTCAATGTTCATG 59.477 50.000 0.00 0.00 0.00 3.07
4258 5560 1.068333 GTTGCCGCAGTCAATGTTCAT 60.068 47.619 0.00 0.00 0.00 2.57
4259 5561 0.310543 GTTGCCGCAGTCAATGTTCA 59.689 50.000 0.00 0.00 0.00 3.18
4260 5562 0.593128 AGTTGCCGCAGTCAATGTTC 59.407 50.000 0.00 0.00 0.00 3.18
4261 5563 0.311790 CAGTTGCCGCAGTCAATGTT 59.688 50.000 0.00 0.00 0.00 2.71
4262 5564 0.534877 TCAGTTGCCGCAGTCAATGT 60.535 50.000 0.00 0.00 0.00 2.71
4263 5565 0.806868 ATCAGTTGCCGCAGTCAATG 59.193 50.000 0.00 0.00 0.00 2.82
4264 5566 1.538047 AATCAGTTGCCGCAGTCAAT 58.462 45.000 0.00 0.00 0.00 2.57
4265 5567 1.266718 GAAATCAGTTGCCGCAGTCAA 59.733 47.619 0.00 0.00 0.00 3.18
4266 5568 0.874390 GAAATCAGTTGCCGCAGTCA 59.126 50.000 0.00 0.00 0.00 3.41
4267 5569 0.874390 TGAAATCAGTTGCCGCAGTC 59.126 50.000 0.00 0.00 0.00 3.51
4268 5570 0.877071 CTGAAATCAGTTGCCGCAGT 59.123 50.000 2.18 0.00 39.09 4.40
4269 5571 1.135859 GTCTGAAATCAGTTGCCGCAG 60.136 52.381 10.06 0.00 44.12 5.18
4270 5572 0.874390 GTCTGAAATCAGTTGCCGCA 59.126 50.000 10.06 0.00 44.12 5.69
4271 5573 1.160137 AGTCTGAAATCAGTTGCCGC 58.840 50.000 10.06 0.00 44.12 6.53
4272 5574 3.997021 AGTAAGTCTGAAATCAGTTGCCG 59.003 43.478 10.06 0.00 44.12 5.69
4273 5575 4.757149 ACAGTAAGTCTGAAATCAGTTGCC 59.243 41.667 10.06 0.00 46.27 4.52
4274 5576 5.921429 GACAGTAAGTCTGAAATCAGTTGC 58.079 41.667 10.06 2.76 46.27 4.17
4328 5630 2.507110 ATTGTCCTGGGAGACGCACG 62.507 60.000 0.00 0.00 39.77 5.34
4387 5689 4.513442 CACCAGCTAGCTGTACCAAATAA 58.487 43.478 36.14 0.00 42.15 1.40
4391 5693 0.036388 GCACCAGCTAGCTGTACCAA 60.036 55.000 36.14 0.00 42.15 3.67
4394 5696 0.460987 CAGGCACCAGCTAGCTGTAC 60.461 60.000 36.14 25.85 42.15 2.90
4396 5698 2.667418 CAGGCACCAGCTAGCTGT 59.333 61.111 36.14 24.09 42.15 4.40
4397 5699 2.124819 CCAGGCACCAGCTAGCTG 60.125 66.667 33.58 33.58 43.26 4.24
4398 5700 2.608988 ACCAGGCACCAGCTAGCT 60.609 61.111 12.68 12.68 41.70 3.32
4399 5701 2.437359 CACCAGGCACCAGCTAGC 60.437 66.667 6.62 6.62 41.70 3.42
4400 5702 2.270205 CCACCAGGCACCAGCTAG 59.730 66.667 0.00 0.00 41.70 3.42
4401 5703 2.529136 ACCACCAGGCACCAGCTA 60.529 61.111 0.00 0.00 41.70 3.32
4465 5767 9.297037 GCAATTACAGGGTATCTATTGGTTAAT 57.703 33.333 0.00 0.00 0.00 1.40
4473 5775 3.307480 GGGCGCAATTACAGGGTATCTAT 60.307 47.826 10.83 0.00 0.00 1.98
4488 5791 1.803334 CACTACAGTTTAGGGCGCAA 58.197 50.000 10.83 0.00 0.00 4.85
4493 5796 1.822990 TCGAGGCACTACAGTTTAGGG 59.177 52.381 0.00 0.00 41.55 3.53
4505 5808 4.557205 TCTTTTCTCTAAGTTCGAGGCAC 58.443 43.478 4.70 0.00 0.00 5.01
4506 5809 4.866508 TCTTTTCTCTAAGTTCGAGGCA 57.133 40.909 4.70 0.00 0.00 4.75
4507 5810 5.697178 ACTTTCTTTTCTCTAAGTTCGAGGC 59.303 40.000 4.70 0.00 0.00 4.70
4508 5811 7.111353 CACTTTCTTTTCTCTAAGTTCGAGG 57.889 40.000 4.70 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.