Multiple sequence alignment - TraesCS3A01G440200

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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 TraesCS3A01G440200 chr3A 100.000 3673 0 0 1 3673 683196984 683193312 0.000000e+00 6783.0
1 TraesCS3A01G440200 chr3A 97.382 191 4 1 1 191 574455889 574455700 1.270000e-84 324.0
2 TraesCS3A01G440200 chr3A 89.286 252 20 7 3015 3264 681463333 681463087 3.560000e-80 309.0
3 TraesCS3A01G440200 chr3A 96.951 164 3 2 1 163 19986927 19987089 1.300000e-69 274.0
4 TraesCS3A01G440200 chr3A 89.041 73 8 0 3554 3626 683251787 683251715 1.400000e-14 91.6
5 TraesCS3A01G440200 chr3D 92.983 3292 153 36 408 3673 546340753 546337514 0.000000e+00 4728.0
6 TraesCS3A01G440200 chr3D 96.087 230 9 0 947 1176 546342280 546342051 3.460000e-100 375.0
7 TraesCS3A01G440200 chr3D 89.020 255 23 4 3011 3264 544820651 544820401 9.900000e-81 311.0
8 TraesCS3A01G440200 chr3B 91.645 2322 122 30 189 2469 723455233 723452943 0.000000e+00 3147.0
9 TraesCS3A01G440200 chr3B 89.046 283 20 5 3265 3544 723452335 723452061 1.260000e-89 340.0
10 TraesCS3A01G440200 chr3B 92.276 246 8 8 2468 2706 723452861 723452620 4.540000e-89 339.0
11 TraesCS3A01G440200 chr3B 96.933 163 4 1 1 163 798650797 798650958 4.670000e-69 272.0
12 TraesCS3A01G440200 chr3B 95.706 163 6 1 1 163 684106909 684107070 1.010000e-65 261.0
13 TraesCS3A01G440200 chr6D 89.098 266 24 5 3001 3264 374123982 374123720 3.540000e-85 326.0
14 TraesCS3A01G440200 chr1D 88.760 258 25 4 3008 3264 100461846 100462100 2.750000e-81 313.0
15 TraesCS3A01G440200 chr1D 88.672 256 26 3 3008 3262 348665151 348664898 3.560000e-80 309.0
16 TraesCS3A01G440200 chr7D 88.760 258 23 6 3008 3264 552186338 552186590 9.900000e-81 311.0
17 TraesCS3A01G440200 chr5A 88.672 256 25 4 3008 3262 535518505 535518757 3.560000e-80 309.0
18 TraesCS3A01G440200 chr5A 96.933 163 4 1 1 163 454272944 454272783 4.670000e-69 272.0
19 TraesCS3A01G440200 chr1B 88.760 258 22 6 3008 3264 518263768 518264019 3.560000e-80 309.0
20 TraesCS3A01G440200 chr1B 95.706 163 6 1 1 163 21812640 21812801 1.010000e-65 261.0
21 TraesCS3A01G440200 chr6A 96.591 176 4 2 1 176 474990731 474990904 1.290000e-74 291.0
22 TraesCS3A01G440200 chr1A 96.512 172 4 2 1 171 73350672 73350842 2.160000e-72 283.0
23 TraesCS3A01G440200 chr4D 95.181 166 7 1 1 166 434983103 434982939 1.010000e-65 261.0


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 TraesCS3A01G440200 chr3A 683193312 683196984 3672 True 6783.000000 6783 100.000 1 3673 1 chr3A.!!$R3 3672
1 TraesCS3A01G440200 chr3D 546337514 546342280 4766 True 2551.500000 4728 94.535 408 3673 2 chr3D.!!$R2 3265
2 TraesCS3A01G440200 chr3B 723452061 723455233 3172 True 1275.333333 3147 90.989 189 3544 3 chr3B.!!$R1 3355

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
96 97 0.106217 GAGAGAGTCAGGGAGAGGGG 60.106 65.0 0.00 0.0 0.0 4.79 F
177 178 0.377203 CCGGGATGCGCTAGTTTTTC 59.623 55.0 9.73 0.0 0.0 2.29 F
858 2010 0.865769 GACGCGCTTCTTTCCTTTCA 59.134 50.0 5.73 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 2625 1.226802 CTCCTGCACGTCATCCTCG 60.227 63.158 0.00 0.0 0.00 4.63 R
2175 3327 0.611062 CCCAGTCGGTAGTGTCCTCA 60.611 60.000 0.00 0.0 0.00 3.86 R
2747 4017 1.258720 CACATGTGTCATATGCGACCG 59.741 52.381 18.03 0.0 34.88 4.79 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
44 45 3.741476 GGCTCCGCACAGGCTTTG 61.741 66.667 0.00 0.00 40.77 2.77
45 46 4.410743 GCTCCGCACAGGCTTTGC 62.411 66.667 15.51 15.51 40.77 3.68
80 81 4.161976 CGACGCGCGAGGAAGAGA 62.162 66.667 39.36 0.00 44.57 3.10
82 83 2.746671 ACGCGCGAGGAAGAGAGA 60.747 61.111 39.36 0.00 0.00 3.10
84 85 2.756025 CGCGCGAGGAAGAGAGAGT 61.756 63.158 28.94 0.00 0.00 3.24
86 87 1.649390 GCGCGAGGAAGAGAGAGTCA 61.649 60.000 12.10 0.00 0.00 3.41
87 88 0.376852 CGCGAGGAAGAGAGAGTCAG 59.623 60.000 0.00 0.00 0.00 3.51
88 89 0.738389 GCGAGGAAGAGAGAGTCAGG 59.262 60.000 0.00 0.00 0.00 3.86
89 90 1.388547 CGAGGAAGAGAGAGTCAGGG 58.611 60.000 0.00 0.00 0.00 4.45
90 91 1.065053 CGAGGAAGAGAGAGTCAGGGA 60.065 57.143 0.00 0.00 0.00 4.20
91 92 2.654863 GAGGAAGAGAGAGTCAGGGAG 58.345 57.143 0.00 0.00 0.00 4.30
92 93 2.241176 GAGGAAGAGAGAGTCAGGGAGA 59.759 54.545 0.00 0.00 0.00 3.71
94 95 2.654863 GAAGAGAGAGTCAGGGAGAGG 58.345 57.143 0.00 0.00 0.00 3.69
96 97 0.106217 GAGAGAGTCAGGGAGAGGGG 60.106 65.000 0.00 0.00 0.00 4.79
98 99 1.547755 AGAGTCAGGGAGAGGGGGA 60.548 63.158 0.00 0.00 0.00 4.81
100 101 2.041405 GTCAGGGAGAGGGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
102 103 4.101077 CAGGGAGAGGGGGAGGCT 62.101 72.222 0.00 0.00 0.00 4.58
103 104 4.101077 AGGGAGAGGGGGAGGCTG 62.101 72.222 0.00 0.00 0.00 4.85
173 174 4.547367 GGCCGGGATGCGCTAGTT 62.547 66.667 9.73 0.00 0.00 2.24
174 175 2.513897 GCCGGGATGCGCTAGTTT 60.514 61.111 9.73 0.00 0.00 2.66
175 176 2.112815 GCCGGGATGCGCTAGTTTT 61.113 57.895 9.73 0.00 0.00 2.43
176 177 1.654023 GCCGGGATGCGCTAGTTTTT 61.654 55.000 9.73 0.00 0.00 1.94
177 178 0.377203 CCGGGATGCGCTAGTTTTTC 59.623 55.000 9.73 0.00 0.00 2.29
178 179 1.369625 CGGGATGCGCTAGTTTTTCT 58.630 50.000 9.73 0.00 0.00 2.52
180 181 1.671328 GGGATGCGCTAGTTTTTCTCC 59.329 52.381 9.73 0.83 0.00 3.71
181 182 1.671328 GGATGCGCTAGTTTTTCTCCC 59.329 52.381 9.73 0.00 0.00 4.30
182 183 2.356135 GATGCGCTAGTTTTTCTCCCA 58.644 47.619 9.73 0.00 0.00 4.37
183 184 2.264005 TGCGCTAGTTTTTCTCCCAA 57.736 45.000 9.73 0.00 0.00 4.12
184 185 2.151202 TGCGCTAGTTTTTCTCCCAAG 58.849 47.619 9.73 0.00 0.00 3.61
185 186 2.224426 TGCGCTAGTTTTTCTCCCAAGA 60.224 45.455 9.73 0.00 0.00 3.02
186 187 3.010420 GCGCTAGTTTTTCTCCCAAGAT 58.990 45.455 0.00 0.00 0.00 2.40
187 188 3.064134 GCGCTAGTTTTTCTCCCAAGATC 59.936 47.826 0.00 0.00 0.00 2.75
221 222 1.171308 GCTCAAGCTGGAGATGCAAA 58.829 50.000 22.98 0.00 37.05 3.68
222 223 1.542915 GCTCAAGCTGGAGATGCAAAA 59.457 47.619 22.98 0.00 37.05 2.44
224 225 2.818432 CTCAAGCTGGAGATGCAAAACT 59.182 45.455 13.35 0.00 37.05 2.66
225 226 4.005650 CTCAAGCTGGAGATGCAAAACTA 58.994 43.478 13.35 0.00 37.05 2.24
226 227 4.592942 TCAAGCTGGAGATGCAAAACTAT 58.407 39.130 0.00 0.00 0.00 2.12
227 228 4.637534 TCAAGCTGGAGATGCAAAACTATC 59.362 41.667 0.00 0.00 0.00 2.08
232 233 5.803967 GCTGGAGATGCAAAACTATCTTTTG 59.196 40.000 0.00 1.88 41.09 2.44
233 234 6.349611 GCTGGAGATGCAAAACTATCTTTTGA 60.350 38.462 9.24 0.00 40.73 2.69
237 238 3.550561 TGCAAAACTATCTTTTGACGCG 58.449 40.909 3.53 3.53 40.73 6.01
280 287 3.414549 TTTTCTGGACGCAAAACTGTC 57.585 42.857 0.00 0.00 0.00 3.51
311 318 2.583520 GCAGACCCTCCTGAGCTG 59.416 66.667 0.00 0.00 36.29 4.24
333 340 2.185310 CTACTGGCCTGGTGGGTGAC 62.185 65.000 14.82 0.00 37.43 3.67
365 372 3.297134 TGGGCCTTAAGAAATGCTAGG 57.703 47.619 4.53 0.00 0.00 3.02
366 373 2.091885 TGGGCCTTAAGAAATGCTAGGG 60.092 50.000 4.53 0.00 0.00 3.53
368 375 3.215151 GGCCTTAAGAAATGCTAGGGTC 58.785 50.000 3.36 0.00 0.00 4.46
369 376 3.371595 GGCCTTAAGAAATGCTAGGGTCA 60.372 47.826 3.36 0.00 0.00 4.02
499 1619 2.132740 TGGCGTTTTAAAGCTGCTTG 57.867 45.000 16.73 3.15 33.77 4.01
506 1626 5.254842 CGTTTTAAAGCTGCTTGGTTTTTG 58.745 37.500 16.73 0.24 42.95 2.44
562 1683 1.758514 TAGCTGGGCCGAGAGAAGG 60.759 63.158 20.35 0.00 0.00 3.46
618 1739 2.186125 GGCTGTAGGCGGTGTACC 59.814 66.667 0.00 0.00 42.94 3.34
801 1949 4.974721 CCACCAAAGCACCGCCCT 62.975 66.667 0.00 0.00 0.00 5.19
802 1950 2.912025 CACCAAAGCACCGCCCTT 60.912 61.111 0.00 0.00 0.00 3.95
803 1951 2.597510 ACCAAAGCACCGCCCTTC 60.598 61.111 0.00 0.00 0.00 3.46
804 1952 3.373565 CCAAAGCACCGCCCTTCC 61.374 66.667 0.00 0.00 0.00 3.46
805 1953 2.282462 CAAAGCACCGCCCTTCCT 60.282 61.111 0.00 0.00 0.00 3.36
806 1954 1.903404 CAAAGCACCGCCCTTCCTT 60.903 57.895 0.00 0.00 0.00 3.36
810 1958 4.426313 CACCGCCCTTCCTTCCCC 62.426 72.222 0.00 0.00 0.00 4.81
856 2008 0.868406 CAGACGCGCTTCTTTCCTTT 59.132 50.000 14.53 0.00 0.00 3.11
858 2010 0.865769 GACGCGCTTCTTTCCTTTCA 59.134 50.000 5.73 0.00 0.00 2.69
860 2012 1.197721 ACGCGCTTCTTTCCTTTCATG 59.802 47.619 5.73 0.00 0.00 3.07
910 2062 7.281549 GGATTTGTCTTCGCTTTATTAGGGTTA 59.718 37.037 0.00 0.00 37.99 2.85
912 2064 5.667466 TGTCTTCGCTTTATTAGGGTTAGG 58.333 41.667 0.00 0.00 37.99 2.69
917 2069 3.433173 CGCTTTATTAGGGTTAGGCACCT 60.433 47.826 0.00 0.00 46.38 4.00
921 2073 1.580059 TTAGGGTTAGGCACCTCCTG 58.420 55.000 5.82 0.00 46.98 3.86
923 2075 2.301738 GGGTTAGGCACCTCCTGCT 61.302 63.158 0.00 0.00 46.98 4.24
930 2082 4.767255 CACCTCCTGCTCCGGTGC 62.767 72.222 21.41 21.41 41.39 5.01
932 2084 4.154347 CCTCCTGCTCCGGTGCTC 62.154 72.222 27.24 2.17 0.00 4.26
958 2110 3.443045 CCATCACCGCCACAAGCC 61.443 66.667 0.00 0.00 38.78 4.35
959 2111 3.803082 CATCACCGCCACAAGCCG 61.803 66.667 0.00 0.00 38.78 5.52
960 2112 4.329545 ATCACCGCCACAAGCCGT 62.330 61.111 0.00 0.00 38.78 5.68
961 2113 4.980805 TCACCGCCACAAGCCGTC 62.981 66.667 0.00 0.00 38.78 4.79
1095 2247 2.820037 GTGAAGCGCTACTGGCCC 60.820 66.667 12.05 0.00 37.74 5.80
1326 2478 1.938657 CTGAGATCGTGTCCACCGCT 61.939 60.000 0.00 0.00 0.00 5.52
1347 2499 3.706373 GAGGAGCGGGACAGGCAA 61.706 66.667 0.00 0.00 0.00 4.52
1473 2625 3.535962 CAGGAGGAGGAGCCGCTC 61.536 72.222 12.27 12.27 43.43 5.03
1744 2896 1.211818 GCTCAACGAGGATGCTAGCG 61.212 60.000 10.77 0.00 0.00 4.26
1791 2943 2.869897 CAGAACGAAGCTGAGGAGTAC 58.130 52.381 0.00 0.00 35.39 2.73
1806 2958 4.282496 AGGAGTACGAGTCATGGAAGAAT 58.718 43.478 0.00 0.00 0.00 2.40
1852 3004 1.282157 ACAGGGAGGAAAGGTATGCAC 59.718 52.381 0.00 0.00 0.00 4.57
1932 3084 2.357257 GGAATGGGAGAAGAAGAACCCC 60.357 54.545 0.00 0.00 41.44 4.95
2175 3327 6.959639 ACAAAGTGGACACATCTTGTTAAT 57.040 33.333 5.14 0.00 39.17 1.40
2247 3399 9.023967 GCATTACTGCTTTATACCTGAAAAATG 57.976 33.333 0.00 0.00 45.32 2.32
2251 3403 8.177119 ACTGCTTTATACCTGAAAAATGTTCA 57.823 30.769 0.00 0.00 0.00 3.18
2252 3404 8.299570 ACTGCTTTATACCTGAAAAATGTTCAG 58.700 33.333 6.19 6.19 44.05 3.02
2328 3480 2.684943 TCCACTACTTGGTCCAGACAA 58.315 47.619 0.00 0.00 46.97 3.18
2329 3481 3.248024 TCCACTACTTGGTCCAGACAAT 58.752 45.455 0.00 0.00 46.97 2.71
2349 3505 9.469097 AGACAATATACTAGCCTACATAGAAGG 57.531 37.037 0.00 0.00 37.17 3.46
2394 3550 5.105513 GCAGAATACTAATAGCCCCTCTCTC 60.106 48.000 0.00 0.00 0.00 3.20
2396 3552 7.406916 CAGAATACTAATAGCCCCTCTCTCTA 58.593 42.308 0.00 0.00 0.00 2.43
2399 3555 5.673130 ACTAATAGCCCCTCTCTCTAGTT 57.327 43.478 0.00 0.00 0.00 2.24
2498 3743 1.707989 TGGTAAAGGGCAGTCATTCCA 59.292 47.619 0.00 0.00 0.00 3.53
2545 3791 7.545615 GGCCCTTACTTATTTCTTGTTGAATTG 59.454 37.037 0.00 0.00 34.24 2.32
2657 3903 5.220710 AGAAGATGAAGGATTGGGATACG 57.779 43.478 0.00 0.00 37.60 3.06
2747 4017 8.976986 ATGCAGATGTTTTTCTTCTTTATGTC 57.023 30.769 0.00 0.00 0.00 3.06
2812 4082 5.095691 TGCTGTGAAAATTCTTCGTCTTC 57.904 39.130 0.00 0.00 0.00 2.87
2928 4199 7.761249 ACTTCTATGCTATTTGTTGGAAAATGC 59.239 33.333 0.00 0.00 32.16 3.56
2942 4213 0.541863 AAATGCTGTCGTCCCCTAGG 59.458 55.000 0.06 0.06 0.00 3.02
3014 4285 2.420058 AGCCTTAATTTGTCCCTCCG 57.580 50.000 0.00 0.00 0.00 4.63
3019 4290 1.961133 TAATTTGTCCCTCCGGTCCT 58.039 50.000 0.00 0.00 0.00 3.85
3020 4291 1.073098 AATTTGTCCCTCCGGTCCTT 58.927 50.000 0.00 0.00 0.00 3.36
3021 4292 1.073098 ATTTGTCCCTCCGGTCCTTT 58.927 50.000 0.00 0.00 0.00 3.11
3052 4324 5.123820 TGCATATAAGTTTGCCTGAAGTCAC 59.876 40.000 0.00 0.00 38.08 3.67
3256 4528 0.532115 TACGCGGAGTTAAAGGGACC 59.468 55.000 12.47 0.00 0.00 4.46
3420 4694 6.040209 TGCTGCCTCATTTCATTTAATTGT 57.960 33.333 0.00 0.00 0.00 2.71
3516 4791 8.822652 ACCAATCTCAGTTCAAAATTCAAATC 57.177 30.769 0.00 0.00 0.00 2.17
3559 4834 3.846430 CCGACTACCCCGAAGCCC 61.846 72.222 0.00 0.00 0.00 5.19
3560 4835 4.203076 CGACTACCCCGAAGCCCG 62.203 72.222 0.00 0.00 38.18 6.13
3581 4856 1.194781 GCAGACCCTCCTGAACTGGA 61.195 60.000 0.00 0.00 36.29 3.86
3618 4894 3.559384 GGTGAACTAAAGCCTTGGTAGCT 60.559 47.826 0.00 0.00 44.19 3.32
3633 4909 3.695060 TGGTAGCTTCTCTCGAACCTTAG 59.305 47.826 0.00 0.00 0.00 2.18
3636 4912 2.425668 AGCTTCTCTCGAACCTTAGAGC 59.574 50.000 0.00 0.00 39.30 4.09
3641 4917 2.093106 TCTCGAACCTTAGAGCTGTCC 58.907 52.381 0.00 0.00 34.66 4.02
3645 4921 3.323979 TCGAACCTTAGAGCTGTCCTTTT 59.676 43.478 0.00 0.00 0.00 2.27
3646 4922 4.525487 TCGAACCTTAGAGCTGTCCTTTTA 59.475 41.667 0.00 0.00 0.00 1.52
3649 4927 6.204108 CGAACCTTAGAGCTGTCCTTTTAAAA 59.796 38.462 0.00 0.00 0.00 1.52
3651 4929 8.478775 AACCTTAGAGCTGTCCTTTTAAAAAT 57.521 30.769 1.66 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 4.161976 TCTCTTCCTCGCGCGTCG 62.162 66.667 30.98 21.07 40.15 5.12
64 65 2.277628 CTCTCTTCCTCGCGCGTC 60.278 66.667 30.98 0.00 0.00 5.19
65 66 2.746671 TCTCTCTTCCTCGCGCGT 60.747 61.111 30.98 0.00 0.00 6.01
66 67 2.024022 CTCTCTCTTCCTCGCGCG 59.976 66.667 26.76 26.76 0.00 6.86
67 68 1.063488 GACTCTCTCTTCCTCGCGC 59.937 63.158 0.00 0.00 0.00 6.86
68 69 0.376852 CTGACTCTCTCTTCCTCGCG 59.623 60.000 0.00 0.00 0.00 5.87
70 71 1.065053 TCCCTGACTCTCTCTTCCTCG 60.065 57.143 0.00 0.00 0.00 4.63
72 73 2.242196 CTCTCCCTGACTCTCTCTTCCT 59.758 54.545 0.00 0.00 0.00 3.36
73 74 2.654863 CTCTCCCTGACTCTCTCTTCC 58.345 57.143 0.00 0.00 0.00 3.46
76 77 0.926293 CCCTCTCCCTGACTCTCTCT 59.074 60.000 0.00 0.00 0.00 3.10
77 78 0.106217 CCCCTCTCCCTGACTCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
78 79 1.589399 CCCCCTCTCCCTGACTCTCT 61.589 65.000 0.00 0.00 0.00 3.10
79 80 1.075600 CCCCCTCTCCCTGACTCTC 60.076 68.421 0.00 0.00 0.00 3.20
80 81 1.547755 TCCCCCTCTCCCTGACTCT 60.548 63.158 0.00 0.00 0.00 3.24
82 83 2.641746 CCTCCCCCTCTCCCTGACT 61.642 68.421 0.00 0.00 0.00 3.41
84 85 4.095400 GCCTCCCCCTCTCCCTGA 62.095 72.222 0.00 0.00 0.00 3.86
86 87 4.101077 CAGCCTCCCCCTCTCCCT 62.101 72.222 0.00 0.00 0.00 4.20
156 157 4.547367 AACTAGCGCATCCCGGCC 62.547 66.667 11.47 0.00 37.44 6.13
157 158 1.654023 AAAAACTAGCGCATCCCGGC 61.654 55.000 11.47 0.00 37.44 6.13
158 159 0.377203 GAAAAACTAGCGCATCCCGG 59.623 55.000 11.47 0.00 37.44 5.73
160 161 1.671328 GGAGAAAAACTAGCGCATCCC 59.329 52.381 11.47 0.00 0.00 3.85
161 162 1.671328 GGGAGAAAAACTAGCGCATCC 59.329 52.381 11.47 2.23 0.00 3.51
164 165 2.151202 CTTGGGAGAAAAACTAGCGCA 58.849 47.619 11.47 0.00 0.00 6.09
165 166 2.423577 TCTTGGGAGAAAAACTAGCGC 58.576 47.619 0.00 0.00 0.00 5.92
166 167 4.331168 CAGATCTTGGGAGAAAAACTAGCG 59.669 45.833 0.00 0.00 35.07 4.26
168 169 6.372937 GGAACAGATCTTGGGAGAAAAACTAG 59.627 42.308 0.00 0.00 35.07 2.57
169 170 6.044404 AGGAACAGATCTTGGGAGAAAAACTA 59.956 38.462 0.00 0.00 35.07 2.24
170 171 5.073428 GGAACAGATCTTGGGAGAAAAACT 58.927 41.667 0.00 0.00 35.07 2.66
172 173 5.073691 AGAGGAACAGATCTTGGGAGAAAAA 59.926 40.000 0.00 0.00 35.07 1.94
173 174 4.599241 AGAGGAACAGATCTTGGGAGAAAA 59.401 41.667 0.00 0.00 35.07 2.29
174 175 4.171234 AGAGGAACAGATCTTGGGAGAAA 58.829 43.478 0.00 0.00 35.07 2.52
175 176 3.796111 AGAGGAACAGATCTTGGGAGAA 58.204 45.455 0.00 0.00 35.07 2.87
176 177 3.481559 AGAGGAACAGATCTTGGGAGA 57.518 47.619 0.00 0.00 36.09 3.71
177 178 4.566426 AAAGAGGAACAGATCTTGGGAG 57.434 45.455 0.00 0.00 35.95 4.30
178 179 4.104738 ACAAAAGAGGAACAGATCTTGGGA 59.895 41.667 0.00 0.00 35.95 4.37
180 181 4.320788 GCACAAAAGAGGAACAGATCTTGG 60.321 45.833 0.00 0.00 35.95 3.61
181 182 4.518211 AGCACAAAAGAGGAACAGATCTTG 59.482 41.667 0.00 0.00 35.95 3.02
182 183 4.723309 AGCACAAAAGAGGAACAGATCTT 58.277 39.130 0.00 0.00 37.36 2.40
183 184 4.202398 TGAGCACAAAAGAGGAACAGATCT 60.202 41.667 0.00 0.00 0.00 2.75
184 185 4.067896 TGAGCACAAAAGAGGAACAGATC 58.932 43.478 0.00 0.00 0.00 2.75
185 186 4.090761 TGAGCACAAAAGAGGAACAGAT 57.909 40.909 0.00 0.00 0.00 2.90
186 187 3.558931 TGAGCACAAAAGAGGAACAGA 57.441 42.857 0.00 0.00 0.00 3.41
187 188 3.549625 GCTTGAGCACAAAAGAGGAACAG 60.550 47.826 0.00 0.00 41.59 3.16
221 222 4.024893 CCATATGCGCGTCAAAAGATAGTT 60.025 41.667 4.79 0.00 0.00 2.24
222 223 3.494626 CCATATGCGCGTCAAAAGATAGT 59.505 43.478 4.79 0.00 0.00 2.12
224 225 2.223144 GCCATATGCGCGTCAAAAGATA 59.777 45.455 4.79 0.00 0.00 1.98
225 226 1.002468 GCCATATGCGCGTCAAAAGAT 60.002 47.619 4.79 0.00 0.00 2.40
226 227 0.376852 GCCATATGCGCGTCAAAAGA 59.623 50.000 4.79 0.00 0.00 2.52
227 228 0.098552 TGCCATATGCGCGTCAAAAG 59.901 50.000 4.79 0.75 45.60 2.27
232 233 1.518102 CATTTTTGCCATATGCGCGTC 59.482 47.619 4.79 0.00 45.60 5.19
233 234 1.135141 ACATTTTTGCCATATGCGCGT 60.135 42.857 8.43 7.55 45.60 6.01
264 271 3.108144 CAAAAGACAGTTTTGCGTCCAG 58.892 45.455 0.00 0.00 33.38 3.86
266 273 3.105937 GTCAAAAGACAGTTTTGCGTCC 58.894 45.455 5.52 0.00 38.79 4.79
280 287 3.737172 CTGCCCGGGCGTCAAAAG 61.737 66.667 39.00 26.02 45.51 2.27
311 318 2.670148 CCCACCAGGCCAGTAGTCC 61.670 68.421 5.01 0.00 0.00 3.85
333 340 0.842635 AAGGCCCAAGAGATGCTAGG 59.157 55.000 0.00 0.00 0.00 3.02
434 1554 3.690475 ATCTGACTGATGTTCACTGCA 57.310 42.857 0.00 0.00 33.43 4.41
499 1619 7.045416 ACACTTTTGAATTCCCTACAAAAACC 58.955 34.615 2.27 0.00 40.98 3.27
533 1654 1.940613 GGCCCAGCTACTTTACAATCG 59.059 52.381 0.00 0.00 0.00 3.34
596 1717 3.760035 ACCGCCTACAGCCAGACG 61.760 66.667 0.00 0.00 38.78 4.18
801 1949 2.459710 GGAGGGGAGGGGAAGGAA 59.540 66.667 0.00 0.00 0.00 3.36
802 1950 3.707189 GGGAGGGGAGGGGAAGGA 61.707 72.222 0.00 0.00 0.00 3.36
803 1951 4.845307 GGGGAGGGGAGGGGAAGG 62.845 77.778 0.00 0.00 0.00 3.46
804 1952 3.711782 AGGGGAGGGGAGGGGAAG 61.712 72.222 0.00 0.00 0.00 3.46
805 1953 3.707189 GAGGGGAGGGGAGGGGAA 61.707 72.222 0.00 0.00 0.00 3.97
860 2012 0.033109 AGGCTAGGGTTTGATTGCCC 60.033 55.000 0.00 0.00 45.16 5.36
1119 2271 2.362503 ATGTCGTCCTCGGCCTCA 60.363 61.111 0.00 0.00 41.33 3.86
1173 2325 2.543067 CTTCCTCGGCCTTGGGGAAG 62.543 65.000 20.98 20.98 45.49 3.46
1308 2460 1.977009 AGCGGTGGACACGATCTCA 60.977 57.895 0.00 0.00 0.00 3.27
1326 2478 2.363018 CTGTCCCGCTCCTCCTCA 60.363 66.667 0.00 0.00 0.00 3.86
1347 2499 3.615811 TCCTCCACCTGGGCCTCT 61.616 66.667 4.53 0.00 36.21 3.69
1464 2616 3.219928 TCATCCTCGAGCGGCTCC 61.220 66.667 23.36 6.87 0.00 4.70
1473 2625 1.226802 CTCCTGCACGTCATCCTCG 60.227 63.158 0.00 0.00 0.00 4.63
1527 2679 2.124024 GCCATGCCCATCTGCTCA 60.124 61.111 0.00 0.00 0.00 4.26
1791 2943 3.111838 CTCACGATTCTTCCATGACTCG 58.888 50.000 0.00 0.00 42.30 4.18
1806 2958 1.730451 TAATCCGCGCCATCTCACGA 61.730 55.000 0.00 0.00 0.00 4.35
1852 3004 2.563179 TCTCTTCCTTCTCCTTCAACCG 59.437 50.000 0.00 0.00 0.00 4.44
2175 3327 0.611062 CCCAGTCGGTAGTGTCCTCA 60.611 60.000 0.00 0.00 0.00 3.86
2349 3505 3.669023 GCTGAAAAGCATACACAGAGTGC 60.669 47.826 0.00 0.00 39.10 4.40
2394 3550 4.514441 CAGGCATGCCAATAGAAGAACTAG 59.486 45.833 37.18 6.20 38.92 2.57
2396 3552 3.054139 TCAGGCATGCCAATAGAAGAACT 60.054 43.478 37.18 10.31 38.92 3.01
2399 3555 3.870538 ATCAGGCATGCCAATAGAAGA 57.129 42.857 37.18 21.42 38.92 2.87
2498 3743 6.122964 GGCCAGACTTCCTTGTTATAAGATT 58.877 40.000 0.00 0.00 0.00 2.40
2545 3791 1.376609 CCCGTTTGTAGCCCATCTGC 61.377 60.000 0.00 0.00 0.00 4.26
2657 3903 8.155923 GCAACAAACATTTAATCATCTCGTTTC 58.844 33.333 0.00 0.00 0.00 2.78
2747 4017 1.258720 CACATGTGTCATATGCGACCG 59.741 52.381 18.03 0.00 34.88 4.79
2796 4066 9.371333 GTAAAAGACTGAAGACGAAGAATTTTC 57.629 33.333 0.00 0.00 0.00 2.29
2928 4199 1.443407 CATGCCTAGGGGACGACAG 59.557 63.158 11.72 0.00 33.58 3.51
2942 4213 5.177511 TCAAGAGCACGTAAATATAGCATGC 59.822 40.000 10.51 10.51 0.00 4.06
3014 4285 8.507524 AACTTATATGCAGACTAAAAAGGACC 57.492 34.615 0.00 0.00 0.00 4.46
3019 4290 8.243426 CAGGCAAACTTATATGCAGACTAAAAA 58.757 33.333 0.00 0.00 44.32 1.94
3020 4291 7.609918 TCAGGCAAACTTATATGCAGACTAAAA 59.390 33.333 0.00 0.00 44.32 1.52
3021 4292 7.109501 TCAGGCAAACTTATATGCAGACTAAA 58.890 34.615 0.00 0.00 44.32 1.85
3256 4528 4.523083 TCTTCCATTTAAACATCCCTCCG 58.477 43.478 0.00 0.00 0.00 4.63
3380 4654 4.641989 GGCAGCAAATTCTGGAGAAATAGA 59.358 41.667 0.00 0.00 37.61 1.98
3397 4671 6.040209 ACAATTAAATGAAATGAGGCAGCA 57.960 33.333 0.00 0.00 0.00 4.41
3420 4694 3.360867 ACACAACAACCAAATGGACAGA 58.639 40.909 6.42 0.00 38.94 3.41
3488 4762 7.452880 TGAATTTTGAACTGAGATTGGTAGG 57.547 36.000 0.00 0.00 0.00 3.18
3561 4836 1.298014 CAGTTCAGGAGGGTCTGCC 59.702 63.158 0.00 0.00 34.91 4.85
3564 4839 0.489567 AGTCCAGTTCAGGAGGGTCT 59.510 55.000 0.00 0.00 38.64 3.85
3565 4840 0.610687 CAGTCCAGTTCAGGAGGGTC 59.389 60.000 0.00 0.00 38.64 4.46
3566 4841 1.484444 GCAGTCCAGTTCAGGAGGGT 61.484 60.000 0.00 0.00 38.64 4.34
3595 4870 2.287977 ACCAAGGCTTTAGTTCACCC 57.712 50.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.