Multiple sequence alignment - TraesCS3B01G207900

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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 TraesCS3B01G207900 chr3B 100.000 4640 0 0 1 4640 243766918 243771557 0.000000e+00 8569.0
1 TraesCS3B01G207900 chr3B 89.130 138 13 2 3464 3599 611485418 611485281 2.220000e-38 171.0
2 TraesCS3B01G207900 chr3A 97.655 3369 72 4 1273 4640 199147806 199144444 0.000000e+00 5777.0
3 TraesCS3B01G207900 chr3A 88.628 853 68 8 2 846 199150226 199149395 0.000000e+00 1011.0
4 TraesCS3B01G207900 chr3A 91.549 284 7 7 836 1107 199148493 199148215 4.380000e-100 375.0
5 TraesCS3B01G207900 chr3A 83.750 80 12 1 571 650 583702423 583702501 1.790000e-09 75.0
6 TraesCS3B01G207900 chr3A 73.864 176 42 4 469 642 10007908 10008081 3.000000e-07 67.6
7 TraesCS3B01G207900 chr3D 97.694 3209 61 4 1253 4457 168493287 168496486 0.000000e+00 5504.0
8 TraesCS3B01G207900 chr3D 92.540 1126 62 10 2 1109 168491859 168492980 0.000000e+00 1594.0
9 TraesCS3B01G207900 chr3D 94.709 189 9 1 4453 4640 168498234 168498422 4.540000e-75 292.0
10 TraesCS3B01G207900 chr1D 84.389 442 46 6 2495 2933 183748240 183747819 3.340000e-111 412.0
11 TraesCS3B01G207900 chr1D 89.855 138 12 2 3464 3599 183747803 183747666 4.770000e-40 176.0
12 TraesCS3B01G207900 chr1D 77.160 324 57 12 1 312 95570872 95571190 6.170000e-39 172.0
13 TraesCS3B01G207900 chr7A 86.590 261 27 4 646 898 617915758 617916018 9.830000e-72 281.0
14 TraesCS3B01G207900 chr7A 83.092 207 25 9 568 771 76549604 76549803 3.690000e-41 180.0
15 TraesCS3B01G207900 chr7A 86.842 114 9 2 683 790 76818974 76819087 6.300000e-24 122.0
16 TraesCS3B01G207900 chr4D 77.273 396 79 8 466 852 386829100 386829493 6.040000e-54 222.0
17 TraesCS3B01G207900 chr4D 78.571 196 36 6 3 192 6923900 6924095 1.750000e-24 124.0
18 TraesCS3B01G207900 chr7D 88.462 182 15 2 646 821 70154422 70154241 1.010000e-51 215.0
19 TraesCS3B01G207900 chr7D 88.816 152 11 2 646 791 70047895 70048046 1.030000e-41 182.0
20 TraesCS3B01G207900 chr7D 76.022 367 71 13 533 886 50733246 50732884 1.720000e-39 174.0
21 TraesCS3B01G207900 chr7D 94.286 35 2 0 3671 3705 374643569 374643603 2.000000e-03 54.7
22 TraesCS3B01G207900 chr5A 90.323 155 14 1 3401 3555 401376198 401376351 7.870000e-48 202.0
23 TraesCS3B01G207900 chr6A 91.216 148 12 1 3408 3555 87361648 87361502 2.830000e-47 200.0
24 TraesCS3B01G207900 chr5D 77.846 325 66 6 1 319 224865248 224865572 3.660000e-46 196.0
25 TraesCS3B01G207900 chr5D 87.248 149 17 2 1 147 408569089 408568941 7.980000e-38 169.0
26 TraesCS3B01G207900 chr5D 85.315 143 18 3 1 141 445066240 445066099 1.350000e-30 145.0
27 TraesCS3B01G207900 chr6B 76.655 287 56 10 41 319 27891586 27891869 1.040000e-31 148.0
28 TraesCS3B01G207900 chr5B 85.315 143 19 2 1 141 321980501 321980359 3.740000e-31 147.0
29 TraesCS3B01G207900 chr1A 85.470 117 17 0 3352 3468 171080758 171080874 6.300000e-24 122.0
30 TraesCS3B01G207900 chr1A 100.000 28 0 0 3678 3705 410465736 410465763 8.000000e-03 52.8
31 TraesCS3B01G207900 chr2D 81.319 91 13 4 766 854 567805161 567805073 2.320000e-08 71.3


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 TraesCS3B01G207900 chr3B 243766918 243771557 4639 False 8569.000000 8569 100.000000 1 4640 1 chr3B.!!$F1 4639
1 TraesCS3B01G207900 chr3A 199144444 199150226 5782 True 2387.666667 5777 92.610667 2 4640 3 chr3A.!!$R1 4638
2 TraesCS3B01G207900 chr3D 168491859 168498422 6563 False 2463.333333 5504 94.981000 2 4640 3 chr3D.!!$F1 4638
3 TraesCS3B01G207900 chr1D 183747666 183748240 574 True 294.000000 412 87.122000 2495 3599 2 chr1D.!!$R1 1104

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
521 546 1.006086 CCAATAGCACGCAATCACGA 58.994 50.0 0.0 0.0 36.7 4.35 F
1120 2086 0.037697 GCACACACCCGTCACTATCA 60.038 55.0 0.0 0.0 0.0 2.15 F
1239 2205 0.179134 CCGATGTTGTCCTCTCCGTC 60.179 60.0 0.0 0.0 0.0 4.79 F
1937 3146 0.613012 ATGGAAGTGGAAAGGGCTGC 60.613 55.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 2749 1.035932 GCCAGAGCACCAATCAGCAT 61.036 55.000 0.0 0.0 39.53 3.79 R
3021 4233 1.533753 CCTGCCAGCCTTCCCAAAA 60.534 57.895 0.0 0.0 0.00 2.44 R
3405 4617 3.490439 TTGAAACATGCAGAGTCAGGA 57.510 42.857 0.0 0.0 0.00 3.86 R
3804 5018 0.034476 CTCTCCAGACAGCAGCACAA 59.966 55.000 0.0 0.0 0.00 3.33 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
84 85 1.299976 CAAGGGGAAGAAGGGACGG 59.700 63.158 0.00 0.00 0.00 4.79
108 109 2.504175 TGGAAGGAAATAAGACCGGGAG 59.496 50.000 6.32 0.00 0.00 4.30
162 164 1.180456 TGTTCGAACTCCCGCTACCA 61.180 55.000 27.32 1.78 0.00 3.25
201 207 9.442047 ACATTGTCTCTAATTTGTAGGAGAAAG 57.558 33.333 0.00 0.00 36.72 2.62
209 215 3.837213 TTGTAGGAGAAAGTACGTCCG 57.163 47.619 0.00 0.00 35.33 4.79
267 273 2.292267 CTTTTGCAGTCTGGACAGTGT 58.708 47.619 0.00 0.00 0.00 3.55
305 311 1.344114 ACGGTTTAAGGGTCAGCGTTA 59.656 47.619 0.00 0.00 41.60 3.18
433 458 3.005367 TCGCCAAAGGAAATCAAAAGTCC 59.995 43.478 0.00 0.00 0.00 3.85
435 460 4.702831 GCCAAAGGAAATCAAAAGTCCAA 58.297 39.130 0.00 0.00 33.57 3.53
457 482 3.103911 GTCGACCGCGTTGGAGTG 61.104 66.667 3.51 0.00 42.00 3.51
515 540 3.130819 CGGCCCAATAGCACGCAA 61.131 61.111 0.00 0.00 0.00 4.85
521 546 1.006086 CCAATAGCACGCAATCACGA 58.994 50.000 0.00 0.00 36.70 4.35
613 638 4.666253 GCTTGGAGGCTGGGCACA 62.666 66.667 0.00 0.00 0.00 4.57
630 655 4.002506 ACGAGCCGGCATGACACA 62.003 61.111 31.54 0.00 0.00 3.72
731 759 1.341209 GCCCAAATACAGCCCATAAGC 59.659 52.381 0.00 0.00 0.00 3.09
896 1843 2.203337 TGATTAGCATGGGCCGGC 60.203 61.111 21.18 21.18 42.56 6.13
988 1954 1.574263 ACCCTGCTCTCCTAGGTTTC 58.426 55.000 9.08 0.00 31.99 2.78
1116 2082 4.602259 CCGCACACACCCGTCACT 62.602 66.667 0.00 0.00 0.00 3.41
1117 2083 2.337170 CGCACACACCCGTCACTA 59.663 61.111 0.00 0.00 0.00 2.74
1118 2084 1.080093 CGCACACACCCGTCACTAT 60.080 57.895 0.00 0.00 0.00 2.12
1119 2085 1.076533 CGCACACACCCGTCACTATC 61.077 60.000 0.00 0.00 0.00 2.08
1120 2086 0.037697 GCACACACCCGTCACTATCA 60.038 55.000 0.00 0.00 0.00 2.15
1121 2087 1.996292 CACACACCCGTCACTATCAG 58.004 55.000 0.00 0.00 0.00 2.90
1122 2088 0.246635 ACACACCCGTCACTATCAGC 59.753 55.000 0.00 0.00 0.00 4.26
1123 2089 0.802222 CACACCCGTCACTATCAGCG 60.802 60.000 0.00 0.00 0.00 5.18
1124 2090 1.878522 CACCCGTCACTATCAGCGC 60.879 63.158 0.00 0.00 0.00 5.92
1125 2091 2.279517 CCCGTCACTATCAGCGCC 60.280 66.667 2.29 0.00 0.00 6.53
1126 2092 2.655364 CCGTCACTATCAGCGCCG 60.655 66.667 2.29 0.00 0.00 6.46
1127 2093 2.407616 CGTCACTATCAGCGCCGA 59.592 61.111 2.29 0.00 0.00 5.54
1128 2094 1.655654 CGTCACTATCAGCGCCGAG 60.656 63.158 2.29 0.00 0.00 4.63
1141 2107 4.214327 CCGAGCTCCTCCGCCTTC 62.214 72.222 8.47 0.00 0.00 3.46
1142 2108 3.144193 CGAGCTCCTCCGCCTTCT 61.144 66.667 8.47 0.00 0.00 2.85
1143 2109 2.811799 GAGCTCCTCCGCCTTCTC 59.188 66.667 0.87 0.00 0.00 2.87
1144 2110 1.756561 GAGCTCCTCCGCCTTCTCT 60.757 63.158 0.87 0.00 0.00 3.10
1145 2111 1.734388 GAGCTCCTCCGCCTTCTCTC 61.734 65.000 0.87 0.00 0.00 3.20
1146 2112 2.791868 GCTCCTCCGCCTTCTCTCC 61.792 68.421 0.00 0.00 0.00 3.71
1147 2113 2.440430 TCCTCCGCCTTCTCTCCG 60.440 66.667 0.00 0.00 0.00 4.63
1148 2114 4.214327 CCTCCGCCTTCTCTCCGC 62.214 72.222 0.00 0.00 0.00 5.54
1149 2115 4.214327 CTCCGCCTTCTCTCCGCC 62.214 72.222 0.00 0.00 0.00 6.13
1169 2135 4.308458 CCCCGCTTGGACACACGA 62.308 66.667 0.00 0.00 35.39 4.35
1170 2136 3.041940 CCCGCTTGGACACACGAC 61.042 66.667 0.00 0.00 35.39 4.34
1171 2137 3.041940 CCGCTTGGACACACGACC 61.042 66.667 0.00 0.00 33.02 4.79
1172 2138 2.029073 CGCTTGGACACACGACCT 59.971 61.111 0.00 0.00 0.00 3.85
1173 2139 2.310233 CGCTTGGACACACGACCTG 61.310 63.158 0.00 0.00 0.00 4.00
1174 2140 1.961277 GCTTGGACACACGACCTGG 60.961 63.158 0.00 0.00 0.00 4.45
1175 2141 1.961277 CTTGGACACACGACCTGGC 60.961 63.158 0.00 0.00 0.00 4.85
1176 2142 2.383245 CTTGGACACACGACCTGGCT 62.383 60.000 0.00 0.00 0.00 4.75
1177 2143 2.048127 GGACACACGACCTGGCTC 60.048 66.667 0.00 0.00 0.00 4.70
1178 2144 2.430921 GACACACGACCTGGCTCG 60.431 66.667 14.31 14.31 39.68 5.03
1179 2145 2.910479 ACACACGACCTGGCTCGA 60.910 61.111 20.23 0.00 37.11 4.04
1180 2146 2.126307 CACACGACCTGGCTCGAG 60.126 66.667 20.23 8.45 37.11 4.04
1181 2147 4.057428 ACACGACCTGGCTCGAGC 62.057 66.667 29.38 29.38 37.11 5.03
1191 2157 3.894947 GCTCGAGCCGTCTCCTCC 61.895 72.222 27.22 0.00 35.94 4.30
1192 2158 2.438614 CTCGAGCCGTCTCCTCCA 60.439 66.667 0.00 0.00 35.94 3.86
1193 2159 2.750637 TCGAGCCGTCTCCTCCAC 60.751 66.667 0.00 0.00 35.94 4.02
1194 2160 3.827898 CGAGCCGTCTCCTCCACC 61.828 72.222 0.00 0.00 35.94 4.61
1195 2161 3.462678 GAGCCGTCTCCTCCACCC 61.463 72.222 0.00 0.00 33.19 4.61
1196 2162 3.966930 GAGCCGTCTCCTCCACCCT 62.967 68.421 0.00 0.00 33.19 4.34
1197 2163 3.462678 GCCGTCTCCTCCACCCTC 61.463 72.222 0.00 0.00 0.00 4.30
1198 2164 2.360980 CCGTCTCCTCCACCCTCT 59.639 66.667 0.00 0.00 0.00 3.69
1199 2165 1.755008 CCGTCTCCTCCACCCTCTC 60.755 68.421 0.00 0.00 0.00 3.20
1200 2166 1.755008 CGTCTCCTCCACCCTCTCC 60.755 68.421 0.00 0.00 0.00 3.71
1201 2167 1.755008 GTCTCCTCCACCCTCTCCG 60.755 68.421 0.00 0.00 0.00 4.63
1202 2168 3.151022 CTCCTCCACCCTCTCCGC 61.151 72.222 0.00 0.00 0.00 5.54
1203 2169 4.779733 TCCTCCACCCTCTCCGCC 62.780 72.222 0.00 0.00 0.00 6.13
1224 2190 4.516326 CCTTCCCCCTCCCCCGAT 62.516 72.222 0.00 0.00 0.00 4.18
1225 2191 3.171388 CTTCCCCCTCCCCCGATG 61.171 72.222 0.00 0.00 0.00 3.84
1226 2192 4.033251 TTCCCCCTCCCCCGATGT 62.033 66.667 0.00 0.00 0.00 3.06
1227 2193 3.589627 TTCCCCCTCCCCCGATGTT 62.590 63.158 0.00 0.00 0.00 2.71
1228 2194 3.809013 CCCCCTCCCCCGATGTTG 61.809 72.222 0.00 0.00 0.00 3.33
1229 2195 3.015145 CCCCTCCCCCGATGTTGT 61.015 66.667 0.00 0.00 0.00 3.32
1230 2196 2.590092 CCCTCCCCCGATGTTGTC 59.410 66.667 0.00 0.00 0.00 3.18
1231 2197 2.590092 CCTCCCCCGATGTTGTCC 59.410 66.667 0.00 0.00 0.00 4.02
1232 2198 1.995626 CCTCCCCCGATGTTGTCCT 60.996 63.158 0.00 0.00 0.00 3.85
1233 2199 1.522569 CTCCCCCGATGTTGTCCTC 59.477 63.158 0.00 0.00 0.00 3.71
1234 2200 0.978146 CTCCCCCGATGTTGTCCTCT 60.978 60.000 0.00 0.00 0.00 3.69
1235 2201 0.976073 TCCCCCGATGTTGTCCTCTC 60.976 60.000 0.00 0.00 0.00 3.20
1236 2202 1.522569 CCCCGATGTTGTCCTCTCC 59.477 63.158 0.00 0.00 0.00 3.71
1237 2203 1.141881 CCCGATGTTGTCCTCTCCG 59.858 63.158 0.00 0.00 0.00 4.63
1238 2204 1.605058 CCCGATGTTGTCCTCTCCGT 61.605 60.000 0.00 0.00 0.00 4.69
1239 2205 0.179134 CCGATGTTGTCCTCTCCGTC 60.179 60.000 0.00 0.00 0.00 4.79
1240 2206 0.179134 CGATGTTGTCCTCTCCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
1241 2207 1.187087 GATGTTGTCCTCTCCGTCCT 58.813 55.000 0.00 0.00 0.00 3.85
1242 2208 1.135333 GATGTTGTCCTCTCCGTCCTC 59.865 57.143 0.00 0.00 0.00 3.71
1243 2209 0.898789 TGTTGTCCTCTCCGTCCTCC 60.899 60.000 0.00 0.00 0.00 4.30
1244 2210 1.677966 TTGTCCTCTCCGTCCTCCG 60.678 63.158 0.00 0.00 0.00 4.63
1245 2211 3.519930 GTCCTCTCCGTCCTCCGC 61.520 72.222 0.00 0.00 34.38 5.54
1246 2212 3.729489 TCCTCTCCGTCCTCCGCT 61.729 66.667 0.00 0.00 34.38 5.52
1247 2213 3.213402 CCTCTCCGTCCTCCGCTC 61.213 72.222 0.00 0.00 34.38 5.03
1248 2214 3.213402 CTCTCCGTCCTCCGCTCC 61.213 72.222 0.00 0.00 34.38 4.70
1249 2215 4.816984 TCTCCGTCCTCCGCTCCC 62.817 72.222 0.00 0.00 34.38 4.30
1250 2216 4.824515 CTCCGTCCTCCGCTCCCT 62.825 72.222 0.00 0.00 34.38 4.20
1251 2217 3.414193 TCCGTCCTCCGCTCCCTA 61.414 66.667 0.00 0.00 34.38 3.53
1456 2665 0.989602 TCTAGTCTCCACCCTCGTCA 59.010 55.000 0.00 0.00 0.00 4.35
1540 2749 1.372499 GCGTTCTCTGCGTACACCA 60.372 57.895 0.00 0.00 0.00 4.17
1937 3146 0.613012 ATGGAAGTGGAAAGGGCTGC 60.613 55.000 0.00 0.00 0.00 5.25
2679 3889 5.501156 AGTTATGGGTTTCTTCCTGATGTC 58.499 41.667 0.00 0.00 0.00 3.06
2892 4104 2.213499 CATATCTCTCCAACGGTTGCC 58.787 52.381 15.31 0.00 0.00 4.52
3489 4701 5.406780 GGAGGCGTATCACATATTTGAAGAG 59.593 44.000 0.00 0.00 0.00 2.85
3633 4846 2.687297 TCCCAGCATGCTTCTAGATCT 58.313 47.619 19.98 0.00 31.97 2.75
3711 4924 2.289320 GCTGTGACTGAGTTGATCTGGT 60.289 50.000 0.00 0.00 0.00 4.00
3804 5018 3.857052 CTGAAATTGAATGCATGCCTGT 58.143 40.909 16.68 0.00 0.00 4.00
3816 5030 1.521450 ATGCCTGTTGTGCTGCTGTC 61.521 55.000 0.00 0.00 0.00 3.51
3947 5161 8.355169 CCTAATCATATGTTGGAACCAATCTTG 58.645 37.037 9.53 6.13 38.28 3.02
3971 5185 6.543465 TGTTATCAGGTAAGCTGATGATTTGG 59.457 38.462 0.00 0.00 41.16 3.28
3989 5203 0.391263 GGACCCTCCAAGTTAGCACG 60.391 60.000 0.00 0.00 36.28 5.34
3991 5205 0.320697 ACCCTCCAAGTTAGCACGTC 59.679 55.000 0.00 0.00 0.00 4.34
4010 5224 6.668323 CACGTCAACTTATTTTGGAACATCT 58.332 36.000 0.00 0.00 39.30 2.90
4038 5252 4.156455 ACCTTAGCCATATGAACCACAG 57.844 45.455 3.65 0.00 0.00 3.66
4052 5266 2.162681 ACCACAGTTAATGCAGAAGGC 58.837 47.619 0.00 0.00 45.13 4.35
4065 5279 5.880054 TGCAGAAGGCTTAGTTTGAATAC 57.120 39.130 0.00 0.00 45.15 1.89
4182 5399 2.609747 TGGTGTGCTCCTCTAGACTTT 58.390 47.619 0.00 0.00 0.00 2.66
4249 5466 1.581934 CTTCACTCGAAACAGGCACA 58.418 50.000 0.00 0.00 0.00 4.57
4407 5624 4.744795 TTTTGCCTCCTTGCTGTTTAAA 57.255 36.364 0.00 0.00 0.00 1.52
4417 5634 8.672815 CCTCCTTGCTGTTTAAATTTTCAAAAA 58.327 29.630 0.00 0.00 0.00 1.94
4418 5635 9.706846 CTCCTTGCTGTTTAAATTTTCAAAAAG 57.293 29.630 0.00 0.00 0.00 2.27
4478 7447 5.136828 TGGAATGTTGAAAGTTAGCCAGAA 58.863 37.500 0.00 0.00 0.00 3.02
4537 7506 8.887717 CATTGGTGTTTTTGTTGAAAATTCCTA 58.112 29.630 0.00 0.00 39.29 2.94
4604 7574 8.036575 TGAGGAATGGAATTGAAATTTCATCAC 58.963 33.333 21.10 14.04 42.40 3.06
4629 7599 9.353999 ACTGATGTTAAAAAGTTGAGTTTGTTC 57.646 29.630 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.229096 GTTGTTGTGTTATACGTCTCCGA 58.771 43.478 0.00 0.00 37.88 4.55
19 20 3.982701 TGTTGTTGTGTTATACGTCTCCG 59.017 43.478 0.00 0.00 40.83 4.63
84 85 3.532542 CCGGTCTTATTTCCTTCCACTC 58.467 50.000 0.00 0.00 0.00 3.51
98 99 1.571773 CCAATTCCCCTCCCGGTCTT 61.572 60.000 0.00 0.00 0.00 3.01
140 142 2.537792 TAGCGGGAGTTCGAACAGCG 62.538 60.000 28.78 10.48 42.69 5.18
146 148 2.345760 GGTGGTAGCGGGAGTTCGA 61.346 63.158 0.00 0.00 0.00 3.71
162 164 1.152567 CAATGTGTGTGGGGGTGGT 60.153 57.895 0.00 0.00 0.00 4.16
201 207 2.325857 CGATCGGTCCGGACGTAC 59.674 66.667 27.68 16.95 0.00 3.67
338 363 9.453325 GCCCAAAATGATGCAAAAATAATAATG 57.547 29.630 0.00 0.00 0.00 1.90
339 364 8.631797 GGCCCAAAATGATGCAAAAATAATAAT 58.368 29.630 0.00 0.00 0.00 1.28
340 365 7.833183 AGGCCCAAAATGATGCAAAAATAATAA 59.167 29.630 0.00 0.00 0.00 1.40
341 366 7.344913 AGGCCCAAAATGATGCAAAAATAATA 58.655 30.769 0.00 0.00 0.00 0.98
342 367 6.189133 AGGCCCAAAATGATGCAAAAATAAT 58.811 32.000 0.00 0.00 0.00 1.28
343 368 5.568392 AGGCCCAAAATGATGCAAAAATAA 58.432 33.333 0.00 0.00 0.00 1.40
344 369 5.176741 AGGCCCAAAATGATGCAAAAATA 57.823 34.783 0.00 0.00 0.00 1.40
345 370 4.036941 AGGCCCAAAATGATGCAAAAAT 57.963 36.364 0.00 0.00 0.00 1.82
416 441 4.990426 CGCATTGGACTTTTGATTTCCTTT 59.010 37.500 0.00 0.00 0.00 3.11
457 482 3.492102 TTGGCCAGCTATATCTCCAAC 57.508 47.619 5.11 0.00 0.00 3.77
515 540 4.082523 CCTGGGCCGTGTCGTGAT 62.083 66.667 0.00 0.00 0.00 3.06
537 562 2.332654 CGTTTAGCCTGGGTGGTGC 61.333 63.158 9.02 0.00 38.35 5.01
587 612 2.677875 CCTCCAAGCCCAAGCACC 60.678 66.667 0.00 0.00 43.56 5.01
613 638 3.529341 TTGTGTCATGCCGGCTCGT 62.529 57.895 29.70 11.11 0.00 4.18
616 641 2.672996 GGTTGTGTCATGCCGGCT 60.673 61.111 29.70 10.60 0.00 5.52
624 649 9.627395 CAAAATAATAATAAACGGGTTGTGTCA 57.373 29.630 0.00 0.00 0.00 3.58
731 759 1.798813 GCAGTCTGTTTACAGTTCGGG 59.201 52.381 9.53 4.77 44.12 5.14
896 1843 3.058160 CAGAGCTGGCCAAACGGG 61.058 66.667 7.01 0.00 40.85 5.28
988 1954 0.179129 GCCGCCATGAAAATCCACTG 60.179 55.000 0.00 0.00 0.00 3.66
1111 2077 1.946650 GCTCGGCGCTGATAGTGAC 60.947 63.158 21.31 1.64 35.14 3.67
1112 2078 2.413351 GCTCGGCGCTGATAGTGA 59.587 61.111 21.31 0.00 35.14 3.41
1124 2090 4.214327 GAAGGCGGAGGAGCTCGG 62.214 72.222 7.83 0.00 37.29 4.63
1125 2091 3.132481 GAGAAGGCGGAGGAGCTCG 62.132 68.421 7.83 0.00 37.29 5.03
1126 2092 1.734388 GAGAGAAGGCGGAGGAGCTC 61.734 65.000 4.71 4.71 37.29 4.09
1127 2093 1.756561 GAGAGAAGGCGGAGGAGCT 60.757 63.158 0.00 0.00 37.29 4.09
1128 2094 2.791868 GGAGAGAAGGCGGAGGAGC 61.792 68.421 0.00 0.00 0.00 4.70
1129 2095 2.485795 CGGAGAGAAGGCGGAGGAG 61.486 68.421 0.00 0.00 0.00 3.69
1130 2096 2.440430 CGGAGAGAAGGCGGAGGA 60.440 66.667 0.00 0.00 0.00 3.71
1131 2097 4.214327 GCGGAGAGAAGGCGGAGG 62.214 72.222 0.00 0.00 0.00 4.30
1132 2098 4.214327 GGCGGAGAGAAGGCGGAG 62.214 72.222 0.00 0.00 0.00 4.63
1152 2118 4.308458 TCGTGTGTCCAAGCGGGG 62.308 66.667 0.00 0.00 37.22 5.73
1153 2119 3.041940 GTCGTGTGTCCAAGCGGG 61.042 66.667 0.00 0.00 38.37 6.13
1154 2120 3.041940 GGTCGTGTGTCCAAGCGG 61.042 66.667 0.00 0.00 0.00 5.52
1155 2121 2.029073 AGGTCGTGTGTCCAAGCG 59.971 61.111 0.00 0.00 0.00 4.68
1156 2122 1.961277 CCAGGTCGTGTGTCCAAGC 60.961 63.158 0.00 0.00 0.00 4.01
1157 2123 1.961277 GCCAGGTCGTGTGTCCAAG 60.961 63.158 0.00 0.00 0.00 3.61
1158 2124 2.110213 GCCAGGTCGTGTGTCCAA 59.890 61.111 0.00 0.00 0.00 3.53
1159 2125 2.842462 AGCCAGGTCGTGTGTCCA 60.842 61.111 0.00 0.00 0.00 4.02
1160 2126 2.048127 GAGCCAGGTCGTGTGTCC 60.048 66.667 0.00 0.00 0.00 4.02
1161 2127 2.430921 CGAGCCAGGTCGTGTGTC 60.431 66.667 10.91 0.00 35.14 3.67
1162 2128 2.910479 TCGAGCCAGGTCGTGTGT 60.910 61.111 17.67 0.00 40.93 3.72
1163 2129 2.126307 CTCGAGCCAGGTCGTGTG 60.126 66.667 17.67 7.09 40.93 3.82
1164 2130 4.057428 GCTCGAGCCAGGTCGTGT 62.057 66.667 27.22 0.00 40.93 4.49
1174 2140 3.894947 GGAGGAGACGGCTCGAGC 61.895 72.222 29.38 29.38 42.25 5.03
1175 2141 2.438614 TGGAGGAGACGGCTCGAG 60.439 66.667 13.25 8.45 42.25 4.04
1176 2142 2.750637 GTGGAGGAGACGGCTCGA 60.751 66.667 13.25 0.00 42.25 4.04
1177 2143 3.827898 GGTGGAGGAGACGGCTCG 61.828 72.222 13.25 0.00 42.25 5.03
1178 2144 3.462678 GGGTGGAGGAGACGGCTC 61.463 72.222 10.76 10.76 40.54 4.70
1179 2145 3.966930 GAGGGTGGAGGAGACGGCT 62.967 68.421 0.00 0.00 0.00 5.52
1180 2146 3.462678 GAGGGTGGAGGAGACGGC 61.463 72.222 0.00 0.00 0.00 5.68
1181 2147 1.755008 GAGAGGGTGGAGGAGACGG 60.755 68.421 0.00 0.00 0.00 4.79
1182 2148 1.755008 GGAGAGGGTGGAGGAGACG 60.755 68.421 0.00 0.00 0.00 4.18
1183 2149 1.755008 CGGAGAGGGTGGAGGAGAC 60.755 68.421 0.00 0.00 0.00 3.36
1184 2150 2.684104 CGGAGAGGGTGGAGGAGA 59.316 66.667 0.00 0.00 0.00 3.71
1185 2151 3.151022 GCGGAGAGGGTGGAGGAG 61.151 72.222 0.00 0.00 0.00 3.69
1186 2152 4.779733 GGCGGAGAGGGTGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
1207 2173 4.516326 ATCGGGGGAGGGGGAAGG 62.516 72.222 0.00 0.00 0.00 3.46
1208 2174 3.171388 CATCGGGGGAGGGGGAAG 61.171 72.222 0.00 0.00 0.00 3.46
1209 2175 3.589627 AACATCGGGGGAGGGGGAA 62.590 63.158 0.00 0.00 0.00 3.97
1210 2176 4.033251 AACATCGGGGGAGGGGGA 62.033 66.667 0.00 0.00 0.00 4.81
1211 2177 3.809013 CAACATCGGGGGAGGGGG 61.809 72.222 0.00 0.00 0.00 5.40
1212 2178 3.015145 ACAACATCGGGGGAGGGG 61.015 66.667 0.00 0.00 0.00 4.79
1213 2179 2.590092 GACAACATCGGGGGAGGG 59.410 66.667 0.00 0.00 0.00 4.30
1214 2180 1.972660 GAGGACAACATCGGGGGAGG 61.973 65.000 0.00 0.00 0.00 4.30
1215 2181 0.978146 AGAGGACAACATCGGGGGAG 60.978 60.000 0.00 0.00 31.71 4.30
1216 2182 0.976073 GAGAGGACAACATCGGGGGA 60.976 60.000 0.00 0.00 31.71 4.81
1217 2183 1.522569 GAGAGGACAACATCGGGGG 59.477 63.158 0.00 0.00 31.71 5.40
1218 2184 1.522569 GGAGAGGACAACATCGGGG 59.477 63.158 0.00 0.00 31.71 5.73
1219 2185 1.141881 CGGAGAGGACAACATCGGG 59.858 63.158 0.00 0.00 31.71 5.14
1220 2186 0.179134 GACGGAGAGGACAACATCGG 60.179 60.000 0.00 0.00 31.71 4.18
1221 2187 0.179134 GGACGGAGAGGACAACATCG 60.179 60.000 0.00 0.00 31.71 3.84
1222 2188 1.135333 GAGGACGGAGAGGACAACATC 59.865 57.143 0.00 0.00 0.00 3.06
1223 2189 1.187087 GAGGACGGAGAGGACAACAT 58.813 55.000 0.00 0.00 0.00 2.71
1224 2190 0.898789 GGAGGACGGAGAGGACAACA 60.899 60.000 0.00 0.00 0.00 3.33
1225 2191 1.891616 GGAGGACGGAGAGGACAAC 59.108 63.158 0.00 0.00 0.00 3.32
1226 2192 1.677966 CGGAGGACGGAGAGGACAA 60.678 63.158 0.00 0.00 39.42 3.18
1227 2193 2.045242 CGGAGGACGGAGAGGACA 60.045 66.667 0.00 0.00 39.42 4.02
1228 2194 3.519930 GCGGAGGACGGAGAGGAC 61.520 72.222 0.00 0.00 44.51 3.85
1229 2195 3.700831 GAGCGGAGGACGGAGAGGA 62.701 68.421 0.00 0.00 44.51 3.71
1230 2196 3.213402 GAGCGGAGGACGGAGAGG 61.213 72.222 0.00 0.00 44.51 3.69
1231 2197 3.213402 GGAGCGGAGGACGGAGAG 61.213 72.222 0.00 0.00 44.51 3.20
1232 2198 4.816984 GGGAGCGGAGGACGGAGA 62.817 72.222 0.00 0.00 44.51 3.71
1233 2199 3.417167 TAGGGAGCGGAGGACGGAG 62.417 68.421 0.00 0.00 44.51 4.63
1234 2200 3.414193 TAGGGAGCGGAGGACGGA 61.414 66.667 0.00 0.00 44.51 4.69
1235 2201 3.217743 GTAGGGAGCGGAGGACGG 61.218 72.222 0.00 0.00 44.51 4.79
1237 2203 0.683504 TTCTGTAGGGAGCGGAGGAC 60.684 60.000 0.00 0.00 0.00 3.85
1238 2204 0.683504 GTTCTGTAGGGAGCGGAGGA 60.684 60.000 0.00 0.00 0.00 3.71
1239 2205 0.970937 TGTTCTGTAGGGAGCGGAGG 60.971 60.000 0.00 0.00 0.00 4.30
1240 2206 0.173708 GTGTTCTGTAGGGAGCGGAG 59.826 60.000 0.00 0.00 0.00 4.63
1241 2207 1.255667 GGTGTTCTGTAGGGAGCGGA 61.256 60.000 0.00 0.00 0.00 5.54
1242 2208 1.218316 GGTGTTCTGTAGGGAGCGG 59.782 63.158 0.00 0.00 0.00 5.52
1243 2209 0.173708 GAGGTGTTCTGTAGGGAGCG 59.826 60.000 0.00 0.00 0.00 5.03
1244 2210 1.478916 GAGAGGTGTTCTGTAGGGAGC 59.521 57.143 0.00 0.00 35.87 4.70
1245 2211 3.020984 GAGAGAGGTGTTCTGTAGGGAG 58.979 54.545 0.00 0.00 35.87 4.30
1246 2212 2.618302 CGAGAGAGGTGTTCTGTAGGGA 60.618 54.545 0.00 0.00 35.87 4.20
1247 2213 1.746220 CGAGAGAGGTGTTCTGTAGGG 59.254 57.143 0.00 0.00 35.87 3.53
1248 2214 1.133407 GCGAGAGAGGTGTTCTGTAGG 59.867 57.143 0.00 0.00 35.87 3.18
1249 2215 1.133407 GGCGAGAGAGGTGTTCTGTAG 59.867 57.143 0.00 0.00 35.87 2.74
1250 2216 1.174783 GGCGAGAGAGGTGTTCTGTA 58.825 55.000 0.00 0.00 35.87 2.74
1251 2217 1.867919 CGGCGAGAGAGGTGTTCTGT 61.868 60.000 0.00 0.00 35.87 3.41
1540 2749 1.035932 GCCAGAGCACCAATCAGCAT 61.036 55.000 0.00 0.00 39.53 3.79
2679 3889 6.494893 TGAATCAAAATGGAGTAACTTCGG 57.505 37.500 0.00 0.00 0.00 4.30
2892 4104 7.767659 AGACCATCAATAATCGATCCATATGTG 59.232 37.037 0.00 0.00 0.00 3.21
3021 4233 1.533753 CCTGCCAGCCTTCCCAAAA 60.534 57.895 0.00 0.00 0.00 2.44
3405 4617 3.490439 TTGAAACATGCAGAGTCAGGA 57.510 42.857 0.00 0.00 0.00 3.86
3489 4701 2.950309 TCTACATGCCCTTAGACGAGTC 59.050 50.000 0.00 0.00 0.00 3.36
3659 4872 2.823196 TTCTGCAACAACAAGTGTCG 57.177 45.000 0.00 0.00 40.60 4.35
3711 4924 4.013728 ACCAAGAAGCACAAACTGTACAA 58.986 39.130 0.00 0.00 0.00 2.41
3804 5018 0.034476 CTCTCCAGACAGCAGCACAA 59.966 55.000 0.00 0.00 0.00 3.33
3971 5185 0.320697 ACGTGCTAACTTGGAGGGTC 59.679 55.000 0.00 0.00 0.00 4.46
4010 5224 7.284489 GTGGTTCATATGGCTAAGGTTTGATAA 59.716 37.037 2.13 0.00 0.00 1.75
4038 5252 6.254281 TCAAACTAAGCCTTCTGCATTAAC 57.746 37.500 0.00 0.00 44.83 2.01
4182 5399 5.667539 TTTTCAACAACACCAATGAAGGA 57.332 34.783 0.00 0.00 33.71 3.36
4238 5455 4.241590 TCATGTGATTTGTGCCTGTTTC 57.758 40.909 0.00 0.00 0.00 2.78
4305 5522 2.584835 TTGGTCAGCAAGCTACCAAT 57.415 45.000 21.44 0.00 45.85 3.16
4417 5634 9.566432 ACTGAAGATTGTCTCTAAATTCAAACT 57.434 29.630 0.00 0.00 32.41 2.66
4478 7447 8.556589 AGTCTAGAGGAGCATATCATACTATGT 58.443 37.037 0.00 0.00 32.69 2.29
4562 7532 2.684374 TCCTCAAATCATGTGATTGGCG 59.316 45.455 8.86 1.61 43.41 5.69
4604 7574 8.523464 CGAACAAACTCAACTTTTTAACATCAG 58.477 33.333 0.00 0.00 0.00 2.90
4617 7587 2.111756 CAGCAAGCGAACAAACTCAAC 58.888 47.619 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.