Multiple sequence alignment - TraesCS1D01G199700

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 TraesCS1D01G199700 chr1D 100.000 5244 0 0 1 5244 282294496 282289253 0.000000e+00 9684.0
1 TraesCS1D01G199700 chr1D 85.069 288 30 7 216 496 462262257 462262538 1.110000e-71 281.0
2 TraesCS1D01G199700 chr1D 81.707 164 26 3 1 162 228836681 228836842 3.290000e-27 134.0
3 TraesCS1D01G199700 chr1B 95.458 2576 78 16 563 3126 383804310 383801762 0.000000e+00 4072.0
4 TraesCS1D01G199700 chr1B 94.784 1572 66 11 3305 4863 383801776 383800208 0.000000e+00 2435.0
5 TraesCS1D01G199700 chr1B 88.566 516 45 7 12 525 383834985 383834482 9.650000e-172 614.0
6 TraesCS1D01G199700 chr1B 95.455 198 9 0 3119 3316 288396615 288396812 3.050000e-82 316.0
7 TraesCS1D01G199700 chr1B 94.118 204 8 2 3118 3319 255505595 255505394 1.830000e-79 307.0
8 TraesCS1D01G199700 chr1B 94.554 202 4 1 5050 5244 383800122 383799921 6.600000e-79 305.0
9 TraesCS1D01G199700 chr1B 87.273 55 7 0 4 58 99142828 99142774 4.380000e-06 63.9
10 TraesCS1D01G199700 chr1B 100.000 29 0 0 4831 4859 304179240 304179268 3.000000e-03 54.7
11 TraesCS1D01G199700 chr1A 93.323 2591 108 26 82 2654 354308671 354306128 0.000000e+00 3766.0
12 TraesCS1D01G199700 chr1A 95.750 1106 37 8 3729 4824 354304564 354303459 0.000000e+00 1773.0
13 TraesCS1D01G199700 chr1A 98.812 589 4 2 2539 3125 354306135 354305548 0.000000e+00 1046.0
14 TraesCS1D01G199700 chr1A 96.094 256 6 4 3305 3558 354305561 354305308 1.050000e-111 414.0
15 TraesCS1D01G199700 chr1A 92.248 129 8 2 5025 5151 354303279 354303151 1.160000e-41 182.0
16 TraesCS1D01G199700 chr1A 98.889 90 1 0 5155 5244 354302847 354302758 1.510000e-35 161.0
17 TraesCS1D01G199700 chr4A 87.368 285 33 2 218 502 96723518 96723237 1.820000e-84 324.0
18 TraesCS1D01G199700 chr6B 97.354 189 5 0 3127 3315 289689640 289689452 6.550000e-84 322.0
19 TraesCS1D01G199700 chr6B 93.810 210 8 4 3119 3325 708673065 708672858 1.420000e-80 311.0
20 TraesCS1D01G199700 chr7B 95.939 197 8 0 3120 3316 168758387 168758191 2.360000e-83 320.0
21 TraesCS1D01G199700 chr7B 94.089 203 12 0 3118 3320 127649407 127649205 5.100000e-80 309.0
22 TraesCS1D01G199700 chr7B 78.235 170 29 6 1 167 622810477 622810641 9.290000e-18 102.0
23 TraesCS1D01G199700 chr2B 96.842 190 6 0 3124 3313 40440824 40441013 8.470000e-83 318.0
24 TraesCS1D01G199700 chr2B 83.704 135 20 2 1 135 780816579 780816447 5.510000e-25 126.0
25 TraesCS1D01G199700 chr3D 97.814 183 4 0 3127 3309 189822307 189822489 3.050000e-82 316.0
26 TraesCS1D01G199700 chr3D 88.060 268 25 4 231 498 606736455 606736195 1.420000e-80 311.0
27 TraesCS1D01G199700 chr3D 83.849 291 41 5 217 507 419124389 419124673 6.690000e-69 272.0
28 TraesCS1D01G199700 chr3D 96.970 33 1 0 4827 4859 591662323 591662291 7.340000e-04 56.5
29 TraesCS1D01G199700 chr4B 94.175 206 11 1 3113 3318 482665961 482665757 3.940000e-81 313.0
30 TraesCS1D01G199700 chr4B 81.974 233 25 14 3623 3850 82417389 82417609 1.160000e-41 182.0
31 TraesCS1D01G199700 chr6D 85.714 280 36 3 219 498 315969101 315969376 5.140000e-75 292.0
32 TraesCS1D01G199700 chr7D 86.111 252 30 3 250 500 25130959 25130712 3.110000e-67 267.0
33 TraesCS1D01G199700 chr3B 83.392 283 36 5 221 498 163716656 163716932 8.720000e-63 252.0
34 TraesCS1D01G199700 chr5D 82.500 240 26 12 3650 3881 240849675 240849444 4.140000e-46 196.0
35 TraesCS1D01G199700 chr5D 75.688 218 50 3 5 221 8179953 8179738 7.180000e-19 106.0
36 TraesCS1D01G199700 chr5D 83.495 103 15 2 21 122 334261680 334261579 1.550000e-15 95.3
37 TraesCS1D01G199700 chr5D 100.000 28 0 0 4832 4859 480842375 480842348 9.000000e-03 52.8
38 TraesCS1D01G199700 chr5B 81.780 236 30 10 3650 3879 262822996 262823224 8.970000e-43 185.0
39 TraesCS1D01G199700 chr2A 80.645 124 24 0 3 126 655320416 655320539 4.320000e-16 97.1
40 TraesCS1D01G199700 chr2A 93.182 44 3 0 14 57 197922397 197922354 1.220000e-06 65.8
41 TraesCS1D01G199700 chr2A 100.000 29 0 0 4831 4859 777041151 777041123 3.000000e-03 54.7
42 TraesCS1D01G199700 chr7A 97.059 34 0 1 4826 4859 172205565 172205533 7.340000e-04 56.5


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 TraesCS1D01G199700 chr1D 282289253 282294496 5243 True 9684.000000 9684 100.000000 1 5244 1 chr1D.!!$R1 5243
1 TraesCS1D01G199700 chr1B 383799921 383804310 4389 True 2270.666667 4072 94.932000 563 5244 3 chr1B.!!$R4 4681
2 TraesCS1D01G199700 chr1B 383834482 383834985 503 True 614.000000 614 88.566000 12 525 1 chr1B.!!$R3 513
3 TraesCS1D01G199700 chr1A 354302758 354308671 5913 True 1223.666667 3766 95.852667 82 5244 6 chr1A.!!$R1 5162

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
52 53 0.037605 GACACGAGAAATCCACCGGT 60.038 55.0 0.00 0.0 0.0 5.28 F
908 931 0.242017 GCCGCATTGCTCTTTGTTCT 59.758 50.0 7.12 0.0 0.0 3.01 F
1185 1210 1.014804 ATCTCCTCCTGTCCTCCACT 58.985 55.0 0.00 0.0 0.0 4.00 F
3171 3317 0.873743 AATTGTGCGTTTTGCCACCG 60.874 50.0 0.00 0.0 45.6 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 1534 0.035458 CCCTGGTCTCACGAAGCTTT 59.965 55.0 0.00 0.0 0.00 3.51 R
1773 1807 3.523547 CAGCTTGAATGACTCTGAGAGG 58.476 50.0 14.83 0.0 33.35 3.69 R
3181 3327 0.521291 GCATGCGCTTTGGTCAGTAA 59.479 50.0 9.73 0.0 34.30 2.24 R
4998 5742 0.305313 GCGAACGGTTAAAGTGTGCA 59.695 50.0 0.00 0.0 0.00 4.57 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
33 34 9.307121 ACATGAGTTATAGTTTCAAAGATCTCG 57.693 33.333 0.00 0.00 0.00 4.04
36 37 8.520351 TGAGTTATAGTTTCAAAGATCTCGACA 58.480 33.333 0.00 0.00 0.00 4.35
51 52 1.076533 CGACACGAGAAATCCACCGG 61.077 60.000 0.00 0.00 0.00 5.28
52 53 0.037605 GACACGAGAAATCCACCGGT 60.038 55.000 0.00 0.00 0.00 5.28
58 59 2.095919 CGAGAAATCCACCGGTGAAAAC 60.096 50.000 36.07 20.57 0.00 2.43
64 65 1.065345 TCCACCGGTGAAAACAGTTCA 60.065 47.619 36.07 0.00 0.00 3.18
152 153 1.270839 ACTCATGTTGCGCTAAGTGGT 60.271 47.619 9.73 1.62 0.00 4.16
178 179 0.388907 GCAATGCGCCATTTGTCAGT 60.389 50.000 4.18 0.00 31.05 3.41
187 189 1.176527 CATTTGTCAGTGCCGGGAAT 58.823 50.000 2.18 0.00 0.00 3.01
240 242 7.657761 CCCTTAAGAGCATGGTTAATAGTACAG 59.342 40.741 3.36 0.00 0.00 2.74
356 360 1.956869 TGAGACATGACCCACCTCAT 58.043 50.000 0.00 0.00 0.00 2.90
416 420 5.051641 CGACTGTTAATCAATAGTCCGCTTC 60.052 44.000 0.25 0.00 45.31 3.86
481 485 6.006275 AGCTTACAATCCACCTATGTCATT 57.994 37.500 0.00 0.00 0.00 2.57
535 539 5.344884 ACCAAACAAACGGACACTTAAATG 58.655 37.500 0.00 0.00 0.00 2.32
652 664 0.795085 CTGAGCAATATAGGCTGCGC 59.205 55.000 0.00 0.00 42.78 6.09
838 853 3.821033 AGTCCAATTTCCCTTCTCGTTTG 59.179 43.478 0.00 0.00 0.00 2.93
903 926 2.401766 CCTCGCCGCATTGCTCTTT 61.402 57.895 7.12 0.00 0.00 2.52
904 927 1.226211 CTCGCCGCATTGCTCTTTG 60.226 57.895 7.12 0.00 0.00 2.77
905 928 1.915614 CTCGCCGCATTGCTCTTTGT 61.916 55.000 7.12 0.00 0.00 2.83
906 929 1.081242 CGCCGCATTGCTCTTTGTT 60.081 52.632 7.12 0.00 0.00 2.83
907 930 1.067199 CGCCGCATTGCTCTTTGTTC 61.067 55.000 7.12 0.00 0.00 3.18
908 931 0.242017 GCCGCATTGCTCTTTGTTCT 59.758 50.000 7.12 0.00 0.00 3.01
909 932 1.468520 GCCGCATTGCTCTTTGTTCTA 59.531 47.619 7.12 0.00 0.00 2.10
943 966 4.332543 TTGTCGCCCTCCCCCTCT 62.333 66.667 0.00 0.00 0.00 3.69
984 1009 2.363683 CTTCTTCAGATTCAGGCCCAC 58.636 52.381 0.00 0.00 0.00 4.61
991 1016 3.943137 ATTCAGGCCCACCCCTCGA 62.943 63.158 0.00 0.00 36.11 4.04
1170 1195 2.090663 ACCTACCCCCTTCCACTATCTC 60.091 54.545 0.00 0.00 0.00 2.75
1175 1200 1.221781 CCCCTTCCACTATCTCCTCCT 59.778 57.143 0.00 0.00 0.00 3.69
1176 1201 2.324541 CCCTTCCACTATCTCCTCCTG 58.675 57.143 0.00 0.00 0.00 3.86
1178 1203 2.962421 CCTTCCACTATCTCCTCCTGTC 59.038 54.545 0.00 0.00 0.00 3.51
1180 1205 2.218673 TCCACTATCTCCTCCTGTCCT 58.781 52.381 0.00 0.00 0.00 3.85
1181 1206 2.175931 TCCACTATCTCCTCCTGTCCTC 59.824 54.545 0.00 0.00 0.00 3.71
1182 1207 2.593026 CACTATCTCCTCCTGTCCTCC 58.407 57.143 0.00 0.00 0.00 4.30
1183 1208 2.091610 CACTATCTCCTCCTGTCCTCCA 60.092 54.545 0.00 0.00 0.00 3.86
1184 1209 2.091555 ACTATCTCCTCCTGTCCTCCAC 60.092 54.545 0.00 0.00 0.00 4.02
1185 1210 1.014804 ATCTCCTCCTGTCCTCCACT 58.985 55.000 0.00 0.00 0.00 4.00
1218 1243 7.941053 TCTCTCTAGAACCTAGAACCTAGAT 57.059 40.000 12.27 0.00 37.54 1.98
1219 1244 7.741785 TCTCTCTAGAACCTAGAACCTAGATG 58.258 42.308 12.27 9.82 37.54 2.90
1248 1280 1.440145 GCTCCAGATGCGCCCTTAAC 61.440 60.000 4.18 0.00 0.00 2.01
1282 1315 1.818363 CATGCGCCTCACATGCTCT 60.818 57.895 4.18 0.00 38.58 4.09
1322 1356 6.529220 GCTATTATGGTCTGATTTGGTCTCT 58.471 40.000 0.00 0.00 0.00 3.10
1404 1438 5.933187 TCATCTCCGATTTCGAAACAAAA 57.067 34.783 13.81 0.00 43.02 2.44
1434 1468 3.041940 AAACTCGCCCAGTTCGCG 61.042 61.111 0.00 0.00 45.32 5.87
1442 1476 1.227263 CCCAGTTCGCGGTCATAGG 60.227 63.158 6.13 0.95 0.00 2.57
1443 1477 1.227263 CCAGTTCGCGGTCATAGGG 60.227 63.158 6.13 0.00 0.00 3.53
1500 1534 2.767644 TCCTCGAGGGGATAATCACA 57.232 50.000 30.80 4.74 35.41 3.58
1509 1543 3.054361 AGGGGATAATCACAAAGCTTCGT 60.054 43.478 0.00 0.00 0.00 3.85
1512 1546 4.034510 GGGATAATCACAAAGCTTCGTGAG 59.965 45.833 23.53 7.69 44.83 3.51
1659 1693 1.134007 GGCATGACTGATGTGGATCCA 60.134 52.381 11.44 11.44 34.14 3.41
1662 1696 3.613030 CATGACTGATGTGGATCCAACA 58.387 45.455 18.20 16.96 0.00 3.33
1816 1850 7.013846 AGCTGGTAAGTTTTGCAGTTAACAATA 59.986 33.333 8.61 0.00 37.51 1.90
2035 2069 7.341445 TGTAAGTATTGCTTGTCCTTTTGTT 57.659 32.000 0.00 0.00 38.05 2.83
2191 2225 5.596772 TCCACATACTTGATCGTCCTGATTA 59.403 40.000 0.00 0.00 37.47 1.75
2263 2299 5.535030 GGATTTTGAAGTACCCACTGAAACT 59.465 40.000 0.00 0.00 34.36 2.66
2395 2431 5.523369 AGCTATGCAAAAGTTTGACAGAAC 58.477 37.500 7.96 0.00 40.55 3.01
3025 3169 3.141398 CAGACTAAGCTTTCAACCAGCA 58.859 45.455 3.20 0.00 39.99 4.41
3126 3272 7.083858 TGTTCATAGAAGCTTGTGTATTTTGC 58.916 34.615 2.10 0.00 0.00 3.68
3127 3273 6.816134 TCATAGAAGCTTGTGTATTTTGCA 57.184 33.333 2.10 0.00 0.00 4.08
3128 3274 7.395190 TCATAGAAGCTTGTGTATTTTGCAT 57.605 32.000 2.10 0.00 0.00 3.96
3129 3275 8.504812 TCATAGAAGCTTGTGTATTTTGCATA 57.495 30.769 2.10 0.00 0.00 3.14
3130 3276 8.615211 TCATAGAAGCTTGTGTATTTTGCATAG 58.385 33.333 2.10 0.00 0.00 2.23
3131 3277 6.824305 AGAAGCTTGTGTATTTTGCATAGT 57.176 33.333 2.10 0.00 0.00 2.12
3132 3278 7.219484 AGAAGCTTGTGTATTTTGCATAGTT 57.781 32.000 2.10 0.00 0.00 2.24
3133 3279 7.308435 AGAAGCTTGTGTATTTTGCATAGTTC 58.692 34.615 2.10 0.00 0.00 3.01
3134 3280 6.573664 AGCTTGTGTATTTTGCATAGTTCA 57.426 33.333 0.00 0.00 0.00 3.18
3135 3281 6.980593 AGCTTGTGTATTTTGCATAGTTCAA 58.019 32.000 0.00 0.00 0.00 2.69
3136 3282 7.432869 AGCTTGTGTATTTTGCATAGTTCAAA 58.567 30.769 0.00 0.00 0.00 2.69
3137 3283 7.925483 AGCTTGTGTATTTTGCATAGTTCAAAA 59.075 29.630 3.79 3.79 44.40 2.44
3138 3284 8.547069 GCTTGTGTATTTTGCATAGTTCAAAAA 58.453 29.630 5.21 0.00 43.77 1.94
3160 3306 2.173964 GCTTTAGGCGTTAATTGTGCG 58.826 47.619 0.00 0.00 0.00 5.34
3161 3307 2.413634 GCTTTAGGCGTTAATTGTGCGT 60.414 45.455 0.00 0.00 0.00 5.24
3162 3308 3.817238 CTTTAGGCGTTAATTGTGCGTT 58.183 40.909 0.00 0.00 0.00 4.84
3163 3309 3.900388 TTAGGCGTTAATTGTGCGTTT 57.100 38.095 0.00 0.00 0.00 3.60
3164 3310 2.785713 AGGCGTTAATTGTGCGTTTT 57.214 40.000 0.00 0.00 0.00 2.43
3165 3311 2.389998 AGGCGTTAATTGTGCGTTTTG 58.610 42.857 0.00 0.00 0.00 2.44
3166 3312 1.136748 GGCGTTAATTGTGCGTTTTGC 60.137 47.619 0.00 0.00 46.70 3.68
3167 3313 1.136748 GCGTTAATTGTGCGTTTTGCC 60.137 47.619 0.00 0.00 45.60 4.52
3168 3314 2.120232 CGTTAATTGTGCGTTTTGCCA 58.880 42.857 0.00 0.00 45.60 4.92
3169 3315 2.097637 CGTTAATTGTGCGTTTTGCCAC 60.098 45.455 0.00 0.00 45.60 5.01
3170 3316 2.141535 TAATTGTGCGTTTTGCCACC 57.858 45.000 0.00 0.00 45.60 4.61
3171 3317 0.873743 AATTGTGCGTTTTGCCACCG 60.874 50.000 0.00 0.00 45.60 4.94
3172 3318 4.560856 TGTGCGTTTTGCCACCGC 62.561 61.111 0.00 0.00 45.60 5.68
3175 3321 4.279043 GCGTTTTGCCACCGCCTT 62.279 61.111 0.00 0.00 41.50 4.35
3176 3322 2.354539 CGTTTTGCCACCGCCTTG 60.355 61.111 0.00 0.00 0.00 3.61
3177 3323 2.661537 GTTTTGCCACCGCCTTGC 60.662 61.111 0.00 0.00 0.00 4.01
3189 3335 1.502190 GCCTTGCGCTTTACTGACC 59.498 57.895 9.73 0.00 0.00 4.02
3190 3336 1.234615 GCCTTGCGCTTTACTGACCA 61.235 55.000 9.73 0.00 0.00 4.02
3191 3337 1.234821 CCTTGCGCTTTACTGACCAA 58.765 50.000 9.73 0.00 0.00 3.67
3192 3338 1.606668 CCTTGCGCTTTACTGACCAAA 59.393 47.619 9.73 0.00 0.00 3.28
3193 3339 2.350772 CCTTGCGCTTTACTGACCAAAG 60.351 50.000 9.73 0.00 36.32 2.77
3196 3342 3.384702 GCTTTACTGACCAAAGCGC 57.615 52.632 0.00 0.00 45.88 5.92
3197 3343 0.591170 GCTTTACTGACCAAAGCGCA 59.409 50.000 11.47 0.00 45.88 6.09
3198 3344 1.200020 GCTTTACTGACCAAAGCGCAT 59.800 47.619 11.47 0.00 45.88 4.73
3199 3345 2.855180 CTTTACTGACCAAAGCGCATG 58.145 47.619 11.47 8.38 0.00 4.06
3200 3346 0.521291 TTACTGACCAAAGCGCATGC 59.479 50.000 11.47 7.91 43.24 4.06
3214 3360 2.693797 GCATGCTTATGCGCAGTTAT 57.306 45.000 18.32 0.10 44.10 1.89
3215 3361 2.313234 GCATGCTTATGCGCAGTTATG 58.687 47.619 18.32 15.92 44.10 1.90
3247 3393 3.878086 CATAGTTATGCGCAATCCGTT 57.122 42.857 17.11 0.00 39.71 4.44
3248 3394 4.209452 CATAGTTATGCGCAATCCGTTT 57.791 40.909 17.11 0.00 39.71 3.60
3249 3395 4.597079 CATAGTTATGCGCAATCCGTTTT 58.403 39.130 17.11 0.00 39.71 2.43
3250 3396 2.862512 AGTTATGCGCAATCCGTTTTG 58.137 42.857 17.11 0.00 39.71 2.44
3251 3397 1.320259 GTTATGCGCAATCCGTTTTGC 59.680 47.619 17.11 8.96 46.70 3.68
3256 3402 2.140923 GCAATCCGTTTTGCCAACG 58.859 52.632 10.53 10.53 44.94 4.10
3257 3403 1.885814 GCAATCCGTTTTGCCAACGC 61.886 55.000 11.75 0.00 44.94 4.84
3258 3404 1.006688 AATCCGTTTTGCCAACGCC 60.007 52.632 11.75 0.00 41.85 5.68
3259 3405 1.460273 AATCCGTTTTGCCAACGCCT 61.460 50.000 11.75 0.35 41.85 5.52
3260 3406 0.606944 ATCCGTTTTGCCAACGCCTA 60.607 50.000 11.75 1.98 41.85 3.93
3261 3407 1.209127 CCGTTTTGCCAACGCCTAG 59.791 57.895 11.75 0.00 41.85 3.02
3262 3408 1.231958 CCGTTTTGCCAACGCCTAGA 61.232 55.000 11.75 0.00 41.85 2.43
3263 3409 0.165944 CGTTTTGCCAACGCCTAGAG 59.834 55.000 5.44 0.00 36.82 2.43
3264 3410 0.109735 GTTTTGCCAACGCCTAGAGC 60.110 55.000 0.00 0.00 38.52 4.09
3373 3519 7.487822 TTTTATGTTATGGCTTGGGAATCAA 57.512 32.000 0.00 0.00 0.00 2.57
3505 3655 7.462571 ACTGTTTAGGGGCTATTAAAAACTG 57.537 36.000 0.00 0.00 34.18 3.16
3563 3713 5.636543 GTGAGGTATATACAAATGCCCGTAC 59.363 44.000 14.70 0.00 32.42 3.67
3605 3755 7.063544 GTCTACTGTTTGTATTGTCTGTCCATC 59.936 40.741 0.00 0.00 0.00 3.51
3609 3759 3.245518 TGTATTGTCTGTCCATCGTGG 57.754 47.619 0.00 0.00 39.43 4.94
3653 3880 1.687493 GCTGGGTGCTACTCCCTCT 60.687 63.158 6.31 0.00 44.84 3.69
3654 3881 1.965754 GCTGGGTGCTACTCCCTCTG 61.966 65.000 6.31 0.00 44.84 3.35
3668 3895 2.576191 TCCCTCTGTCTGGTTTATTGGG 59.424 50.000 0.00 0.00 0.00 4.12
3670 3897 2.369394 CTCTGTCTGGTTTATTGGGCC 58.631 52.381 0.00 0.00 0.00 5.80
3671 3898 1.005450 TCTGTCTGGTTTATTGGGCCC 59.995 52.381 17.59 17.59 0.00 5.80
3712 4272 3.157087 ACTTTGGCCATCTGTAAACCTG 58.843 45.455 6.09 0.00 0.00 4.00
3772 4498 8.868522 ATTGTTGGATTTGTATTTGAGAGAGA 57.131 30.769 0.00 0.00 0.00 3.10
3885 4615 1.134098 CCCGGACGGAGGTAGTACTTA 60.134 57.143 13.13 0.00 37.50 2.24
3942 4672 5.593679 TCAGTTCCAGTAGTAGTAATGCC 57.406 43.478 0.00 0.00 0.00 4.40
4090 4820 7.730084 TCATAGAAGGAATCATCGATGAAGTT 58.270 34.615 30.41 21.24 40.69 2.66
4180 4910 3.066190 CGCCTGGACTCGTGGGTA 61.066 66.667 0.00 0.00 0.00 3.69
4247 4977 2.125673 TCGTGGCGGCTTAGCTTC 60.126 61.111 11.43 0.00 37.29 3.86
4254 4984 3.502572 GGCTTAGCTTCTTGGCCG 58.497 61.111 3.59 0.00 33.30 6.13
4458 5188 2.202810 GCAGAGGGCGTCACTAGC 60.203 66.667 10.15 4.31 0.00 3.42
4500 5231 2.107950 TCTGTAATCCAGCGGTTTGG 57.892 50.000 0.00 0.00 41.25 3.28
4617 5350 0.364515 GCTGCGTACGGTTTCTAACG 59.635 55.000 18.39 0.00 38.34 3.18
4620 5353 2.252747 TGCGTACGGTTTCTAACGATG 58.747 47.619 18.39 0.00 37.53 3.84
4746 5479 2.855570 GCATGCATCAATTTCGATCGCA 60.856 45.455 14.21 0.00 35.44 5.10
4799 5533 9.666626 CATACTCTATCTACTTGTAAAACCTCG 57.333 37.037 0.00 0.00 0.00 4.63
4803 5537 7.983307 TCTATCTACTTGTAAAACCTCGAGAC 58.017 38.462 15.71 3.91 0.00 3.36
4804 5538 5.039480 TCTACTTGTAAAACCTCGAGACG 57.961 43.478 15.71 0.00 0.00 4.18
4812 5546 2.080286 AACCTCGAGACGAAACCATG 57.920 50.000 15.71 0.00 34.74 3.66
4819 5553 2.411547 CGAGACGAAACCATGCAACTTC 60.412 50.000 0.00 0.00 0.00 3.01
4824 5558 2.095768 CGAAACCATGCAACTTCGACAT 60.096 45.455 14.13 0.00 42.44 3.06
4847 5583 8.079809 ACATATAGTAACAACAACAACAAAGCC 58.920 33.333 0.00 0.00 0.00 4.35
4863 5599 5.660460 ACAAAGCCTTTAGTTTCAACTTGG 58.340 37.500 0.00 0.47 40.37 3.61
4864 5600 5.186992 ACAAAGCCTTTAGTTTCAACTTGGT 59.813 36.000 0.00 0.00 40.37 3.67
4865 5601 5.932619 AAGCCTTTAGTTTCAACTTGGTT 57.067 34.783 0.00 0.00 40.37 3.67
4866 5602 7.093684 ACAAAGCCTTTAGTTTCAACTTGGTTA 60.094 33.333 0.00 0.00 40.37 2.85
4867 5603 6.635030 AGCCTTTAGTTTCAACTTGGTTAG 57.365 37.500 0.00 0.00 40.37 2.34
4868 5604 6.362248 AGCCTTTAGTTTCAACTTGGTTAGA 58.638 36.000 0.00 0.00 40.37 2.10
4870 5606 6.294010 GCCTTTAGTTTCAACTTGGTTAGAGG 60.294 42.308 0.00 0.00 40.37 3.69
4872 5608 7.255139 CCTTTAGTTTCAACTTGGTTAGAGGTG 60.255 40.741 0.00 0.00 40.37 4.00
4873 5609 3.883489 AGTTTCAACTTGGTTAGAGGTGC 59.117 43.478 0.00 0.00 35.21 5.01
4886 5630 5.301555 GTTAGAGGTGCCCATAAGATCTTC 58.698 45.833 12.24 0.00 0.00 2.87
4887 5631 3.387962 AGAGGTGCCCATAAGATCTTCA 58.612 45.455 12.24 0.00 0.00 3.02
4888 5632 3.135530 AGAGGTGCCCATAAGATCTTCAC 59.864 47.826 12.24 12.89 0.00 3.18
4889 5633 2.158900 AGGTGCCCATAAGATCTTCACG 60.159 50.000 12.24 1.46 0.00 4.35
4890 5634 1.599542 GTGCCCATAAGATCTTCACGC 59.400 52.381 12.24 10.12 0.00 5.34
4891 5635 1.209261 TGCCCATAAGATCTTCACGCA 59.791 47.619 12.24 12.55 0.00 5.24
4894 5638 2.213499 CCATAAGATCTTCACGCACCC 58.787 52.381 12.24 0.00 0.00 4.61
4895 5639 2.213499 CATAAGATCTTCACGCACCCC 58.787 52.381 12.24 0.00 0.00 4.95
4897 5641 0.036010 AAGATCTTCACGCACCCCTG 60.036 55.000 0.88 0.00 0.00 4.45
4899 5643 0.535335 GATCTTCACGCACCCCTGTA 59.465 55.000 0.00 0.00 0.00 2.74
4900 5644 1.139058 GATCTTCACGCACCCCTGTAT 59.861 52.381 0.00 0.00 0.00 2.29
4903 5647 2.102420 TCTTCACGCACCCCTGTATATG 59.898 50.000 0.00 0.00 0.00 1.78
4904 5648 0.105964 TCACGCACCCCTGTATATGC 59.894 55.000 0.00 0.00 34.66 3.14
4913 5657 4.348168 CACCCCTGTATATGCCTAGTCTTT 59.652 45.833 0.00 0.00 0.00 2.52
4914 5658 4.975794 ACCCCTGTATATGCCTAGTCTTTT 59.024 41.667 0.00 0.00 0.00 2.27
4917 5661 5.765182 CCCTGTATATGCCTAGTCTTTTTGG 59.235 44.000 0.00 0.00 0.00 3.28
4918 5662 6.357367 CCTGTATATGCCTAGTCTTTTTGGT 58.643 40.000 0.00 0.00 0.00 3.67
4919 5663 6.260936 CCTGTATATGCCTAGTCTTTTTGGTG 59.739 42.308 0.00 0.00 0.00 4.17
4920 5664 6.953101 TGTATATGCCTAGTCTTTTTGGTGA 58.047 36.000 0.00 0.00 0.00 4.02
4921 5665 7.573710 TGTATATGCCTAGTCTTTTTGGTGAT 58.426 34.615 0.00 0.00 0.00 3.06
4922 5666 8.710239 TGTATATGCCTAGTCTTTTTGGTGATA 58.290 33.333 0.00 0.00 0.00 2.15
4923 5667 9.726438 GTATATGCCTAGTCTTTTTGGTGATAT 57.274 33.333 0.00 0.00 0.00 1.63
4925 5669 7.961326 ATGCCTAGTCTTTTTGGTGATATTT 57.039 32.000 0.00 0.00 0.00 1.40
4926 5670 7.391148 TGCCTAGTCTTTTTGGTGATATTTC 57.609 36.000 0.00 0.00 0.00 2.17
4927 5671 6.945435 TGCCTAGTCTTTTTGGTGATATTTCA 59.055 34.615 0.00 0.00 0.00 2.69
4928 5672 7.121168 TGCCTAGTCTTTTTGGTGATATTTCAG 59.879 37.037 0.00 0.00 30.85 3.02
4929 5673 7.121315 GCCTAGTCTTTTTGGTGATATTTCAGT 59.879 37.037 0.00 0.00 30.85 3.41
4930 5674 8.669243 CCTAGTCTTTTTGGTGATATTTCAGTC 58.331 37.037 0.00 0.00 30.85 3.51
4931 5675 7.454260 AGTCTTTTTGGTGATATTTCAGTCC 57.546 36.000 0.00 0.00 30.85 3.85
4932 5676 7.234355 AGTCTTTTTGGTGATATTTCAGTCCT 58.766 34.615 0.00 0.00 30.85 3.85
4933 5677 7.725844 AGTCTTTTTGGTGATATTTCAGTCCTT 59.274 33.333 0.00 0.00 30.85 3.36
4934 5678 8.360390 GTCTTTTTGGTGATATTTCAGTCCTTT 58.640 33.333 0.00 0.00 30.85 3.11
4935 5679 9.581289 TCTTTTTGGTGATATTTCAGTCCTTTA 57.419 29.630 0.00 0.00 30.85 1.85
4972 5716 6.801862 CGGACTCTTTCATGTTAAATTTGGTC 59.198 38.462 0.00 0.00 0.00 4.02
4973 5717 7.308589 CGGACTCTTTCATGTTAAATTTGGTCT 60.309 37.037 0.00 0.00 0.00 3.85
4986 5730 6.911250 AAATTTGGTCTATCCCGAACTTTT 57.089 33.333 0.00 0.00 30.59 2.27
5014 5758 7.551262 TGATATTATCTGCACACTTTAACCGTT 59.449 33.333 5.33 0.00 0.00 4.44
5017 5761 0.305313 TGCACACTTTAACCGTTCGC 59.695 50.000 0.00 0.00 0.00 4.70
5022 5766 2.414138 ACACTTTAACCGTTCGCTATGC 59.586 45.455 0.00 0.00 0.00 3.14
5037 5801 3.495193 GCTATGCACATTGAATATGCCG 58.505 45.455 5.92 0.00 38.63 5.69
5041 5805 4.031418 TGCACATTGAATATGCCGAAAG 57.969 40.909 5.92 0.00 38.63 2.62
5082 5847 8.730680 TGGATAAGCTTCTTTGACAGATTTAAC 58.269 33.333 0.00 0.00 0.00 2.01
5153 6219 7.645340 CCAGACAGTCAAAAGAAAATGTTACTG 59.355 37.037 2.66 0.00 39.14 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.307121 CGAGATCTTTGAAACTATAACTCATGT 57.693 33.333 0.00 0.00 0.00 3.21
8 9 9.521503 TCGAGATCTTTGAAACTATAACTCATG 57.478 33.333 0.00 0.00 0.00 3.07
9 10 9.522804 GTCGAGATCTTTGAAACTATAACTCAT 57.477 33.333 0.00 0.00 0.00 2.90
10 11 8.520351 TGTCGAGATCTTTGAAACTATAACTCA 58.480 33.333 0.00 0.00 0.00 3.41
14 15 7.532571 TCGTGTCGAGATCTTTGAAACTATAA 58.467 34.615 14.06 0.15 0.00 0.98
17 18 5.366829 TCGTGTCGAGATCTTTGAAACTA 57.633 39.130 14.06 4.34 0.00 2.24
33 34 0.037605 ACCGGTGGATTTCTCGTGTC 60.038 55.000 6.12 0.00 0.00 3.67
36 37 0.682852 TTCACCGGTGGATTTCTCGT 59.317 50.000 33.40 0.00 0.00 4.18
51 52 5.163561 TGTCCAAATCCTGAACTGTTTTCAC 60.164 40.000 0.00 0.00 0.00 3.18
52 53 4.952957 TGTCCAAATCCTGAACTGTTTTCA 59.047 37.500 0.00 0.00 0.00 2.69
58 59 3.192001 CCATGTGTCCAAATCCTGAACTG 59.808 47.826 0.00 0.00 0.00 3.16
64 65 3.524095 TGAACCATGTGTCCAAATCCT 57.476 42.857 0.00 0.00 0.00 3.24
126 127 2.405892 AGCGCAACATGAGTGTTTTC 57.594 45.000 11.47 0.00 46.07 2.29
127 128 3.315191 ACTTAGCGCAACATGAGTGTTTT 59.685 39.130 11.47 0.00 46.07 2.43
128 129 2.878406 ACTTAGCGCAACATGAGTGTTT 59.122 40.909 11.47 0.00 46.07 2.83
131 132 1.129251 CCACTTAGCGCAACATGAGTG 59.871 52.381 11.47 11.19 35.48 3.51
132 133 1.270839 ACCACTTAGCGCAACATGAGT 60.271 47.619 11.47 0.00 0.00 3.41
135 136 0.454957 GCACCACTTAGCGCAACATG 60.455 55.000 11.47 2.02 0.00 3.21
178 179 2.705658 AGTCATTCTCATATTCCCGGCA 59.294 45.455 0.00 0.00 0.00 5.69
187 189 5.774690 ACCCTTTGCAAAAGTCATTCTCATA 59.225 36.000 13.84 0.00 0.00 2.15
340 344 2.503356 AGAGAATGAGGTGGGTCATGTC 59.497 50.000 0.00 0.00 37.24 3.06
356 360 3.173151 TCCTAGGCATGTTGTGAGAGAA 58.827 45.455 2.96 0.00 0.00 2.87
394 398 5.116882 GGAAGCGGACTATTGATTAACAGT 58.883 41.667 0.00 0.00 0.00 3.55
416 420 2.107366 GAGTTGGAGGAGAGAGAAGGG 58.893 57.143 0.00 0.00 0.00 3.95
458 462 5.636903 ATGACATAGGTGGATTGTAAGCT 57.363 39.130 0.00 0.00 0.00 3.74
466 470 5.393068 ACAATGGAATGACATAGGTGGAT 57.607 39.130 0.00 0.00 0.00 3.41
481 485 6.436218 TGACTAGTTAGAGCAAGTACAATGGA 59.564 38.462 0.00 0.00 0.00 3.41
591 603 4.223125 AAGCAGCCCAGCCCAACA 62.223 61.111 0.00 0.00 34.23 3.33
629 641 2.424557 CAGCCTATATTGCTCAGCCAG 58.575 52.381 0.00 0.00 36.81 4.85
630 642 1.544093 GCAGCCTATATTGCTCAGCCA 60.544 52.381 0.00 0.00 36.81 4.75
652 664 1.878656 GAGGGGTGGAGACGTGTCAG 61.879 65.000 15.28 0.00 0.00 3.51
703 718 1.675219 GTACGGGTGGAAGAAGCCA 59.325 57.895 0.00 0.00 37.59 4.75
805 820 2.311688 AATTGGACTAGGCGAGGCGG 62.312 60.000 0.00 0.00 31.49 6.13
806 821 0.462047 AAATTGGACTAGGCGAGGCG 60.462 55.000 0.00 0.00 31.49 5.52
807 822 1.300481 GAAATTGGACTAGGCGAGGC 58.700 55.000 0.00 0.00 0.00 4.70
808 823 1.475213 GGGAAATTGGACTAGGCGAGG 60.475 57.143 0.00 0.00 0.00 4.63
809 824 1.486726 AGGGAAATTGGACTAGGCGAG 59.513 52.381 0.00 0.00 0.00 5.03
810 825 1.580059 AGGGAAATTGGACTAGGCGA 58.420 50.000 0.00 0.00 0.00 5.54
811 826 2.092914 AGAAGGGAAATTGGACTAGGCG 60.093 50.000 0.00 0.00 0.00 5.52
812 827 3.546724 GAGAAGGGAAATTGGACTAGGC 58.453 50.000 0.00 0.00 0.00 3.93
813 828 3.197983 ACGAGAAGGGAAATTGGACTAGG 59.802 47.826 0.00 0.00 0.00 3.02
903 926 3.369052 CCACCGCCAACTAGAATAGAACA 60.369 47.826 0.00 0.00 42.77 3.18
904 927 3.195661 CCACCGCCAACTAGAATAGAAC 58.804 50.000 0.00 0.00 42.77 3.01
905 928 2.835764 ACCACCGCCAACTAGAATAGAA 59.164 45.455 0.00 0.00 42.77 2.10
906 929 2.463752 ACCACCGCCAACTAGAATAGA 58.536 47.619 0.00 0.00 42.77 1.98
907 930 2.936498 CAACCACCGCCAACTAGAATAG 59.064 50.000 0.00 0.00 46.50 1.73
908 931 2.303600 ACAACCACCGCCAACTAGAATA 59.696 45.455 0.00 0.00 0.00 1.75
909 932 1.073284 ACAACCACCGCCAACTAGAAT 59.927 47.619 0.00 0.00 0.00 2.40
943 966 2.866351 CCTTTTCCGTTAGGGTTTGGA 58.134 47.619 0.00 0.00 38.33 3.53
984 1009 3.138798 ATGGACGACGTCGAGGGG 61.139 66.667 41.52 15.30 43.02 4.79
1170 1195 1.268283 GGGAAGTGGAGGACAGGAGG 61.268 65.000 0.00 0.00 0.00 4.30
1196 1221 7.454553 ACATCTAGGTTCTAGGTTCTAGAGA 57.545 40.000 16.18 0.64 40.69 3.10
1218 1243 1.415289 CATCTGGAGCCTGCATCTACA 59.585 52.381 1.64 1.64 0.00 2.74
1219 1244 1.877258 GCATCTGGAGCCTGCATCTAC 60.877 57.143 0.00 0.00 35.96 2.59
1243 1275 1.806542 AGTTGTCGCATGCCAGTTAAG 59.193 47.619 13.15 0.00 0.00 1.85
1248 1280 0.098200 CATGAGTTGTCGCATGCCAG 59.902 55.000 13.15 0.00 42.71 4.85
1304 1337 3.133003 CCGTAGAGACCAAATCAGACCAT 59.867 47.826 0.00 0.00 0.00 3.55
1322 1356 4.674101 GCAGAATAAACAGCAATTGCCGTA 60.674 41.667 26.45 13.54 43.38 4.02
1380 1414 5.933187 TTGTTTCGAAATCGGAGATGAAA 57.067 34.783 14.69 0.00 45.12 2.69
1404 1438 3.578688 GGCGAGTTTGAGCAAATTGATT 58.421 40.909 0.00 0.00 32.36 2.57
1434 1468 2.660258 ATTGGCGCGACCCTATGACC 62.660 60.000 10.82 0.00 37.83 4.02
1442 1476 3.041940 CGGGATATTGGCGCGACC 61.042 66.667 10.82 11.50 43.28 4.79
1443 1477 2.028484 TCGGGATATTGGCGCGAC 59.972 61.111 12.10 8.22 44.10 5.19
1500 1534 0.035458 CCCTGGTCTCACGAAGCTTT 59.965 55.000 0.00 0.00 0.00 3.51
1509 1543 3.385384 CGCAGCTCCCTGGTCTCA 61.385 66.667 0.00 0.00 39.54 3.27
1512 1546 3.453070 GATCCGCAGCTCCCTGGTC 62.453 68.421 0.00 0.00 39.54 4.02
1659 1693 0.969894 AGAAGCTAGCGTGGACTGTT 59.030 50.000 8.23 0.00 0.00 3.16
1662 1696 1.746220 CAGTAGAAGCTAGCGTGGACT 59.254 52.381 8.23 8.00 0.00 3.85
1773 1807 3.523547 CAGCTTGAATGACTCTGAGAGG 58.476 50.000 14.83 0.00 33.35 3.69
1816 1850 7.338703 ACATTCTTCTGCTGTACAATCAATGAT 59.661 33.333 0.00 0.00 0.00 2.45
1821 1855 5.308014 ACACATTCTTCTGCTGTACAATCA 58.692 37.500 0.00 0.00 0.00 2.57
2035 2069 5.270083 CACGAACAAGCAACACTTAATTCA 58.730 37.500 0.00 0.00 36.04 2.57
2116 2150 5.474578 AGTGGAATAGATGACATACGCAT 57.525 39.130 0.00 0.00 0.00 4.73
2208 2242 7.601073 TGATACTTGCAGTGTAGAATTCAAG 57.399 36.000 8.44 3.16 37.51 3.02
2395 2431 9.559958 CTTTGTATACAAAAGGCTTCATAACTG 57.440 33.333 26.60 10.20 44.24 3.16
2506 2542 6.130569 AGTACACCCAAATTACTTGTCCAAA 58.869 36.000 0.00 0.00 32.65 3.28
3112 3258 7.636259 TTTGAACTATGCAAAATACACAAGC 57.364 32.000 0.00 0.00 32.75 4.01
3135 3281 5.176774 GCACAATTAACGCCTAAAGCTTTTT 59.823 36.000 18.47 7.65 40.39 1.94
3136 3282 4.684242 GCACAATTAACGCCTAAAGCTTTT 59.316 37.500 18.47 0.00 40.39 2.27
3137 3283 4.234574 GCACAATTAACGCCTAAAGCTTT 58.765 39.130 17.30 17.30 40.39 3.51
3138 3284 3.669557 CGCACAATTAACGCCTAAAGCTT 60.670 43.478 0.00 0.00 40.39 3.74
3139 3285 2.159572 CGCACAATTAACGCCTAAAGCT 60.160 45.455 0.00 0.00 40.39 3.74
3140 3286 2.173964 CGCACAATTAACGCCTAAAGC 58.826 47.619 0.00 0.00 38.52 3.51
3141 3287 3.465122 ACGCACAATTAACGCCTAAAG 57.535 42.857 0.00 0.00 0.00 1.85
3142 3288 3.900388 AACGCACAATTAACGCCTAAA 57.100 38.095 0.00 0.00 0.00 1.85
3143 3289 3.900388 AAACGCACAATTAACGCCTAA 57.100 38.095 0.00 0.00 0.00 2.69
3144 3290 3.556513 CAAAACGCACAATTAACGCCTA 58.443 40.909 0.00 0.00 0.00 3.93
3145 3291 2.389998 CAAAACGCACAATTAACGCCT 58.610 42.857 0.00 0.00 0.00 5.52
3146 3292 1.136748 GCAAAACGCACAATTAACGCC 60.137 47.619 0.00 0.00 41.79 5.68
3147 3293 1.136748 GGCAAAACGCACAATTAACGC 60.137 47.619 0.00 0.00 45.17 4.84
3148 3294 2.097637 GTGGCAAAACGCACAATTAACG 60.098 45.455 0.00 0.00 45.17 3.18
3149 3295 2.219903 GGTGGCAAAACGCACAATTAAC 59.780 45.455 0.00 0.00 45.17 2.01
3150 3296 2.474816 GGTGGCAAAACGCACAATTAA 58.525 42.857 0.00 0.00 45.17 1.40
3151 3297 1.600663 CGGTGGCAAAACGCACAATTA 60.601 47.619 0.00 0.00 45.17 1.40
3152 3298 0.873743 CGGTGGCAAAACGCACAATT 60.874 50.000 0.00 0.00 45.17 2.32
3153 3299 1.299773 CGGTGGCAAAACGCACAAT 60.300 52.632 0.00 0.00 45.17 2.71
3154 3300 2.103143 CGGTGGCAAAACGCACAA 59.897 55.556 0.00 0.00 45.17 3.33
3159 3305 2.354539 CAAGGCGGTGGCAAAACG 60.355 61.111 0.00 0.00 42.47 3.60
3160 3306 2.661537 GCAAGGCGGTGGCAAAAC 60.662 61.111 0.00 0.00 42.47 2.43
3171 3317 1.234615 TGGTCAGTAAAGCGCAAGGC 61.235 55.000 11.47 0.00 44.05 4.35
3172 3318 1.234821 TTGGTCAGTAAAGCGCAAGG 58.765 50.000 11.47 0.00 38.28 3.61
3173 3319 2.921126 CTTTGGTCAGTAAAGCGCAAG 58.079 47.619 11.47 0.00 43.44 4.01
3179 3325 2.855180 CATGCGCTTTGGTCAGTAAAG 58.145 47.619 9.73 0.00 38.00 1.85
3180 3326 1.068610 GCATGCGCTTTGGTCAGTAAA 60.069 47.619 9.73 0.00 34.30 2.01
3181 3327 0.521291 GCATGCGCTTTGGTCAGTAA 59.479 50.000 9.73 0.00 34.30 2.24
3182 3328 2.170738 GCATGCGCTTTGGTCAGTA 58.829 52.632 9.73 0.00 34.30 2.74
3183 3329 2.956987 GCATGCGCTTTGGTCAGT 59.043 55.556 9.73 0.00 34.30 3.41
3196 3342 2.313234 GCATAACTGCGCATAAGCATG 58.687 47.619 12.24 11.51 46.97 4.06
3197 3343 2.693797 GCATAACTGCGCATAAGCAT 57.306 45.000 12.24 0.00 46.97 3.79
3207 3353 6.017605 ACTATGCTTAATCTGTGCATAACTGC 60.018 38.462 8.02 0.00 45.28 4.40
3208 3354 7.488187 ACTATGCTTAATCTGTGCATAACTG 57.512 36.000 8.02 1.03 45.28 3.16
3209 3355 9.784531 ATAACTATGCTTAATCTGTGCATAACT 57.215 29.630 8.02 2.19 45.28 2.24
3210 3356 9.817365 CATAACTATGCTTAATCTGTGCATAAC 57.183 33.333 8.02 0.00 45.28 1.89
3227 3373 3.878086 AACGGATTGCGCATAACTATG 57.122 42.857 12.75 0.00 36.78 2.23
3228 3374 4.597079 CAAAACGGATTGCGCATAACTAT 58.403 39.130 12.75 0.00 0.00 2.12
3229 3375 3.729462 GCAAAACGGATTGCGCATAACTA 60.729 43.478 12.75 0.00 45.37 2.24
3230 3376 2.862512 CAAAACGGATTGCGCATAACT 58.137 42.857 12.75 0.00 0.00 2.24
3231 3377 1.320259 GCAAAACGGATTGCGCATAAC 59.680 47.619 12.75 5.62 45.37 1.89
3232 3378 1.623359 GCAAAACGGATTGCGCATAA 58.377 45.000 12.75 0.00 45.37 1.90
3233 3379 3.320884 GCAAAACGGATTGCGCATA 57.679 47.368 12.75 2.21 45.37 3.14
3234 3380 4.167483 GCAAAACGGATTGCGCAT 57.833 50.000 12.75 0.40 45.37 4.73
3239 3385 1.281566 GGCGTTGGCAAAACGGATTG 61.282 55.000 20.96 0.00 43.25 2.67
3240 3386 1.006688 GGCGTTGGCAAAACGGATT 60.007 52.632 20.96 0.00 43.25 3.01
3241 3387 0.606944 TAGGCGTTGGCAAAACGGAT 60.607 50.000 20.96 0.00 43.25 4.18
3242 3388 1.227883 TAGGCGTTGGCAAAACGGA 60.228 52.632 20.96 0.00 43.25 4.69
3243 3389 1.209127 CTAGGCGTTGGCAAAACGG 59.791 57.895 20.96 5.19 43.25 4.44
3244 3390 0.165944 CTCTAGGCGTTGGCAAAACG 59.834 55.000 16.88 16.88 45.56 3.60
3245 3391 0.109735 GCTCTAGGCGTTGGCAAAAC 60.110 55.000 0.00 0.00 42.47 2.43
3246 3392 2.253513 GCTCTAGGCGTTGGCAAAA 58.746 52.632 0.00 0.00 42.47 2.44
3247 3393 3.981308 GCTCTAGGCGTTGGCAAA 58.019 55.556 0.00 0.00 42.47 3.68
3302 3448 9.469097 AGGCATACAACAAAATACCATAGTTAA 57.531 29.630 0.00 0.00 0.00 2.01
3303 3449 9.116067 GAGGCATACAACAAAATACCATAGTTA 57.884 33.333 0.00 0.00 0.00 2.24
3304 3450 7.834181 AGAGGCATACAACAAAATACCATAGTT 59.166 33.333 0.00 0.00 0.00 2.24
3305 3451 7.346471 AGAGGCATACAACAAAATACCATAGT 58.654 34.615 0.00 0.00 0.00 2.12
3306 3452 7.807977 AGAGGCATACAACAAAATACCATAG 57.192 36.000 0.00 0.00 0.00 2.23
3307 3453 7.613801 ACAAGAGGCATACAACAAAATACCATA 59.386 33.333 0.00 0.00 0.00 2.74
3308 3454 6.437162 ACAAGAGGCATACAACAAAATACCAT 59.563 34.615 0.00 0.00 0.00 3.55
3309 3455 5.772672 ACAAGAGGCATACAACAAAATACCA 59.227 36.000 0.00 0.00 0.00 3.25
3310 3456 6.267496 ACAAGAGGCATACAACAAAATACC 57.733 37.500 0.00 0.00 0.00 2.73
3311 3457 8.587952 AAAACAAGAGGCATACAACAAAATAC 57.412 30.769 0.00 0.00 0.00 1.89
3313 3459 9.206870 CATAAAACAAGAGGCATACAACAAAAT 57.793 29.630 0.00 0.00 0.00 1.82
3314 3460 7.170658 GCATAAAACAAGAGGCATACAACAAAA 59.829 33.333 0.00 0.00 0.00 2.44
3315 3461 6.644592 GCATAAAACAAGAGGCATACAACAAA 59.355 34.615 0.00 0.00 0.00 2.83
3316 3462 6.015519 AGCATAAAACAAGAGGCATACAACAA 60.016 34.615 0.00 0.00 0.00 2.83
3317 3463 5.476599 AGCATAAAACAAGAGGCATACAACA 59.523 36.000 0.00 0.00 0.00 3.33
3318 3464 5.954335 AGCATAAAACAAGAGGCATACAAC 58.046 37.500 0.00 0.00 0.00 3.32
3373 3519 6.208599 CCACTGTCTAAATATGTGTTGGGTTT 59.791 38.462 0.00 0.00 0.00 3.27
3505 3655 4.747540 GGATTTGCAATCAAAACCCAAC 57.252 40.909 0.00 0.00 44.59 3.77
3576 3726 6.973843 ACAGACAATACAAACAGTAGACGTA 58.026 36.000 0.00 0.00 35.85 3.57
3609 3759 4.943705 TCTGAAACAGATGGGAAGTAATGC 59.056 41.667 0.00 0.00 35.39 3.56
3653 3880 0.040499 GGGGCCCAATAAACCAGACA 59.960 55.000 26.86 0.00 0.00 3.41
3654 3881 0.686441 GGGGGCCCAATAAACCAGAC 60.686 60.000 26.86 0.00 35.81 3.51
3677 3904 4.349342 TGGCCAAAGTTTGACCCAAAATAT 59.651 37.500 17.24 0.00 35.03 1.28
3885 4615 7.056635 TCTGGAAAGAAACTGAAACAGATCTT 58.943 34.615 5.76 10.83 40.14 2.40
3903 4633 5.509501 GGAACTGATGCACAAAATCTGGAAA 60.510 40.000 0.00 0.00 0.00 3.13
4090 4820 1.601903 GAAACATGAACCGTGCTGTCA 59.398 47.619 0.00 0.00 0.00 3.58
4180 4910 1.586154 GCGTGGTATGCACTTTGCCT 61.586 55.000 0.00 0.00 44.23 4.75
4198 4928 1.364626 CTGCCTCGATGGACAACAGC 61.365 60.000 5.24 0.00 38.35 4.40
4247 4977 4.439305 TTCAGAATCATTTTCGGCCAAG 57.561 40.909 2.24 0.00 0.00 3.61
4254 4984 7.550712 ACCAAAGCCTATTCAGAATCATTTTC 58.449 34.615 0.00 0.00 0.00 2.29
4799 5533 2.411547 CGAAGTTGCATGGTTTCGTCTC 60.412 50.000 11.74 0.00 38.03 3.36
4803 5537 1.262950 TGTCGAAGTTGCATGGTTTCG 59.737 47.619 13.05 13.05 42.61 3.46
4804 5538 3.559238 ATGTCGAAGTTGCATGGTTTC 57.441 42.857 0.00 0.00 0.00 2.78
4812 5546 7.285783 TGTTGTTACTATATGTCGAAGTTGC 57.714 36.000 0.00 0.00 0.00 4.17
4819 5553 9.313323 CTTTGTTGTTGTTGTTACTATATGTCG 57.687 33.333 0.00 0.00 0.00 4.35
4824 5558 7.811117 AGGCTTTGTTGTTGTTGTTACTATA 57.189 32.000 0.00 0.00 0.00 1.31
4847 5583 7.639945 CACCTCTAACCAAGTTGAAACTAAAG 58.360 38.462 3.87 0.00 38.57 1.85
4870 5606 1.599542 GCGTGAAGATCTTATGGGCAC 59.400 52.381 8.25 10.67 0.00 5.01
4872 5608 1.599542 GTGCGTGAAGATCTTATGGGC 59.400 52.381 8.25 10.19 0.00 5.36
4873 5609 2.213499 GGTGCGTGAAGATCTTATGGG 58.787 52.381 8.25 0.00 0.00 4.00
4886 5630 0.884704 GGCATATACAGGGGTGCGTG 60.885 60.000 0.00 0.00 38.43 5.34
4887 5631 1.054406 AGGCATATACAGGGGTGCGT 61.054 55.000 0.00 0.00 38.43 5.24
4888 5632 0.973632 TAGGCATATACAGGGGTGCG 59.026 55.000 0.00 0.00 38.43 5.34
4889 5633 1.978580 ACTAGGCATATACAGGGGTGC 59.021 52.381 0.00 0.00 36.88 5.01
4890 5634 3.511477 AGACTAGGCATATACAGGGGTG 58.489 50.000 0.00 0.00 0.00 4.61
4891 5635 3.925261 AGACTAGGCATATACAGGGGT 57.075 47.619 0.00 0.00 0.00 4.95
4894 5638 6.260936 CACCAAAAAGACTAGGCATATACAGG 59.739 42.308 0.00 0.00 0.00 4.00
4895 5639 7.047891 TCACCAAAAAGACTAGGCATATACAG 58.952 38.462 0.00 0.00 0.00 2.74
4897 5641 9.726438 ATATCACCAAAAAGACTAGGCATATAC 57.274 33.333 0.00 0.00 0.00 1.47
4899 5643 9.646522 AAATATCACCAAAAAGACTAGGCATAT 57.353 29.630 0.00 0.00 0.00 1.78
4900 5644 9.120538 GAAATATCACCAAAAAGACTAGGCATA 57.879 33.333 0.00 0.00 0.00 3.14
4903 5647 7.121315 ACTGAAATATCACCAAAAAGACTAGGC 59.879 37.037 0.00 0.00 0.00 3.93
4904 5648 8.567285 ACTGAAATATCACCAAAAAGACTAGG 57.433 34.615 0.00 0.00 0.00 3.02
4943 5687 9.672086 CAAATTTAACATGAAAGAGTCCGTAAA 57.328 29.630 0.00 0.00 0.00 2.01
4944 5688 8.293867 CCAAATTTAACATGAAAGAGTCCGTAA 58.706 33.333 0.00 0.00 0.00 3.18
4945 5689 7.446013 ACCAAATTTAACATGAAAGAGTCCGTA 59.554 33.333 0.00 0.00 0.00 4.02
4946 5690 6.264518 ACCAAATTTAACATGAAAGAGTCCGT 59.735 34.615 0.00 0.00 0.00 4.69
4947 5691 6.677913 ACCAAATTTAACATGAAAGAGTCCG 58.322 36.000 0.00 0.00 0.00 4.79
4948 5692 7.886338 AGACCAAATTTAACATGAAAGAGTCC 58.114 34.615 0.00 0.00 0.00 3.85
4952 5696 8.966868 GGGATAGACCAAATTTAACATGAAAGA 58.033 33.333 0.00 0.00 41.20 2.52
4953 5697 7.915397 CGGGATAGACCAAATTTAACATGAAAG 59.085 37.037 0.00 0.00 41.20 2.62
4954 5698 7.612244 TCGGGATAGACCAAATTTAACATGAAA 59.388 33.333 0.00 0.00 41.20 2.69
4962 5706 8.411991 AAAAAGTTCGGGATAGACCAAATTTA 57.588 30.769 0.00 0.00 41.20 1.40
4986 5730 8.394877 CGGTTAAAGTGTGCAGATAATATCAAA 58.605 33.333 2.84 0.00 0.00 2.69
4997 5741 1.659211 GCGAACGGTTAAAGTGTGCAG 60.659 52.381 0.00 0.00 0.00 4.41
4998 5742 0.305313 GCGAACGGTTAAAGTGTGCA 59.695 50.000 0.00 0.00 0.00 4.57
5003 5747 2.414138 GTGCATAGCGAACGGTTAAAGT 59.586 45.455 3.96 0.00 0.00 2.66
5004 5748 2.413796 TGTGCATAGCGAACGGTTAAAG 59.586 45.455 3.96 0.00 0.00 1.85
5009 5753 0.726827 CAATGTGCATAGCGAACGGT 59.273 50.000 4.11 4.11 0.00 4.83
5011 5755 2.804421 TTCAATGTGCATAGCGAACG 57.196 45.000 0.00 0.00 0.00 3.95
5014 5758 4.408993 GCATATTCAATGTGCATAGCGA 57.591 40.909 13.85 0.00 45.37 4.93
5045 5809 4.872691 AGAAGCTTATCCAACATCGTTGAG 59.127 41.667 0.00 0.00 0.00 3.02
5095 5860 6.156748 ACATTGATGGATCATTTCACATGG 57.843 37.500 0.00 0.00 36.56 3.66
5153 6219 3.194116 TCCCAAATACGAGTACTGGACAC 59.806 47.826 12.28 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.