Multiple sequence alignment - TraesCS1A01G421100

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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 TraesCS1A01G421100 chr1A 100.000 2323 0 0 1 2323 577507845 577510167 0.000000e+00 4290.0
1 TraesCS1A01G421100 chr1D 89.356 1616 112 27 69 1666 480971274 480972847 0.000000e+00 1977.0
2 TraesCS1A01G421100 chr1D 88.676 521 28 12 1670 2174 480976442 480976947 7.100000e-170 606.0
3 TraesCS1A01G421100 chr1D 87.212 391 34 9 939 1322 480555420 480555039 4.590000e-117 431.0
4 TraesCS1A01G421100 chr1D 74.561 342 69 11 108 443 262033956 262033627 1.450000e-27 134.0
5 TraesCS1A01G421100 chr1D 100.000 30 0 0 839 868 480555522 480555493 3.220000e-04 56.5
6 TraesCS1A01G421100 chr1B 90.291 1030 59 15 390 1405 669191240 669192242 0.000000e+00 1310.0
7 TraesCS1A01G421100 chr1B 90.398 729 40 11 1040 1756 669336541 669335831 0.000000e+00 931.0
8 TraesCS1A01G421100 chr1B 87.868 577 39 17 1600 2154 669192239 669192806 0.000000e+00 649.0
9 TraesCS1A01G421100 chr1B 91.239 331 25 3 69 398 669339879 669339552 4.550000e-122 448.0
10 TraesCS1A01G421100 chr1B 90.671 343 17 6 521 858 669337082 669336750 2.120000e-120 442.0
11 TraesCS1A01G421100 chr1B 86.014 143 13 6 2033 2173 669335337 669335200 1.860000e-31 147.0
12 TraesCS1A01G421100 chr1B 91.250 80 3 2 1 76 669339972 669339893 3.160000e-19 106.0
13 TraesCS1A01G421100 chr1B 97.727 44 1 0 1997 2040 669335666 669335623 2.480000e-10 76.8
14 TraesCS1A01G421100 chr4A 82.995 394 54 7 69 451 170706512 170706121 6.150000e-91 344.0
15 TraesCS1A01G421100 chr4A 78.947 361 60 11 91 443 620584685 620585037 4.990000e-57 231.0
16 TraesCS1A01G421100 chr4A 86.029 136 18 1 2180 2315 551349012 551349146 6.690000e-31 145.0
17 TraesCS1A01G421100 chr4A 92.727 55 4 0 2261 2315 551348886 551348832 1.910000e-11 80.5
18 TraesCS1A01G421100 chr5A 79.494 395 67 8 69 454 666161266 666160877 3.800000e-68 268.0
19 TraesCS1A01G421100 chr3A 97.333 150 3 1 2174 2323 61531161 61531013 1.070000e-63 254.0
20 TraesCS1A01G421100 chr4B 91.837 147 10 2 2175 2321 587764357 587764501 1.090000e-48 204.0
21 TraesCS1A01G421100 chr4B 87.931 116 12 1 488 603 223542178 223542291 4.030000e-28 135.0
22 TraesCS1A01G421100 chr3B 91.275 149 12 1 2175 2323 828522195 828522048 3.910000e-48 202.0
23 TraesCS1A01G421100 chr3B 89.677 155 15 1 2170 2323 747738781 747738935 1.820000e-46 196.0
24 TraesCS1A01G421100 chr3B 89.655 116 10 1 488 603 201556355 201556468 1.860000e-31 147.0
25 TraesCS1A01G421100 chr2A 92.086 139 10 1 2185 2323 676176584 676176721 6.550000e-46 195.0
26 TraesCS1A01G421100 chr6D 86.861 137 18 0 2175 2311 336197935 336197799 1.110000e-33 154.0
27 TraesCS1A01G421100 chr5B 89.655 116 10 1 488 603 413611875 413611762 1.860000e-31 147.0
28 TraesCS1A01G421100 chrUn 88.235 119 9 4 488 603 443329123 443329239 1.120000e-28 137.0
29 TraesCS1A01G421100 chr7B 88.235 119 9 5 488 603 125522259 125522143 1.120000e-28 137.0
30 TraesCS1A01G421100 chr7B 88.034 117 10 4 489 603 105209921 105209807 4.030000e-28 135.0
31 TraesCS1A01G421100 chr4D 86.765 68 7 2 78 144 421352490 421352424 8.900000e-10 75.0


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 TraesCS1A01G421100 chr1A 577507845 577510167 2322 False 4290.000000 4290 100.0000 1 2323 1 chr1A.!!$F1 2322
1 TraesCS1A01G421100 chr1D 480971274 480976947 5673 False 1291.500000 1977 89.0160 69 2174 2 chr1D.!!$F1 2105
2 TraesCS1A01G421100 chr1B 669191240 669192806 1566 False 979.500000 1310 89.0795 390 2154 2 chr1B.!!$F1 1764
3 TraesCS1A01G421100 chr1B 669335200 669339972 4772 True 358.466667 931 91.2165 1 2173 6 chr1B.!!$R1 2172

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
213 242 0.24912 CGGTGTGTGCCTTAGATCCA 59.751 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 8486 0.042731 TCTTGCCCTAGCCTGGTAGT 59.957 55.0 0.0 0.0 38.69 2.73 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
43 48 2.903855 GGGCCTCGACGACGGATA 60.904 66.667 14.93 0.00 40.21 2.59
54 59 3.364964 CGACGACGGATATGTGATGATGA 60.365 47.826 0.00 0.00 35.72 2.92
58 63 4.299155 GACGGATATGTGATGATGAACGT 58.701 43.478 0.00 0.00 0.00 3.99
106 133 2.754472 CTGACAAGGTTGATGTGTCGA 58.246 47.619 0.00 0.00 43.73 4.20
128 155 5.619220 GATACCTGCTCTGAAGATGGATTT 58.381 41.667 0.00 0.00 0.00 2.17
141 168 3.517901 AGATGGATTTGTGGAAGACGGTA 59.482 43.478 0.00 0.00 0.00 4.02
152 179 3.142838 GACGGTAGCGGTGGCCTA 61.143 66.667 19.72 0.00 41.24 3.93
201 228 3.475494 TGCACTGGACCGGTGTGT 61.475 61.111 29.89 4.60 42.21 3.72
202 229 2.972505 GCACTGGACCGGTGTGTG 60.973 66.667 29.89 18.63 42.21 3.82
213 242 0.249120 CGGTGTGTGCCTTAGATCCA 59.751 55.000 0.00 0.00 0.00 3.41
262 291 3.325870 GTTTTAGATGTTGGGCTTTGGC 58.674 45.455 0.00 0.00 37.82 4.52
317 346 4.563580 GCACTCCTTCATCAAGTTGGTAGA 60.564 45.833 2.34 0.00 0.00 2.59
427 2838 1.679977 GCCCTGATGCAAAGGCTGA 60.680 57.895 12.35 0.00 42.34 4.26
488 2908 9.344772 TGGTAAGTTGACAAATACAGTACATTT 57.655 29.630 12.12 0.00 0.00 2.32
518 2938 1.737838 TTCCGCATTAACAGAGCAGG 58.262 50.000 0.00 0.00 0.00 4.85
526 2946 4.876107 GCATTAACAGAGCAGGCTAGTAAA 59.124 41.667 0.00 0.00 0.00 2.01
572 2992 3.912248 TGGGATAAGAGAGTGTCTACCC 58.088 50.000 15.52 15.52 40.69 3.69
582 3002 0.963962 GTGTCTACCCTGTCAACGGA 59.036 55.000 0.00 0.00 0.00 4.69
685 3107 0.894835 CATAACCACCAACCAAGCCC 59.105 55.000 0.00 0.00 0.00 5.19
691 3113 1.077265 ACCAACCAAGCCCATCCAG 59.923 57.895 0.00 0.00 0.00 3.86
745 3167 2.050077 GGCCAGAACACAAAGCGC 60.050 61.111 0.00 0.00 0.00 5.92
820 3242 2.475200 CGAGATCGTCACTGCACATA 57.525 50.000 0.00 0.00 34.11 2.29
1022 3500 5.290885 CCAAACCAAACAGAAGCAAAAGTAC 59.709 40.000 0.00 0.00 0.00 2.73
1124 3602 1.226859 TAAGAAGATGACGGCGGCG 60.227 57.895 31.06 31.06 0.00 6.46
1263 3741 1.609210 TGGGTGCTCGAGTCCATCA 60.609 57.895 22.99 13.83 0.00 3.07
1333 3813 5.122711 GGCTGTAAAATAAACCGAGCTGTAA 59.877 40.000 0.00 0.00 0.00 2.41
1446 3928 9.236006 ACAAATTCAGCAATTAATCTACTCTGT 57.764 29.630 0.00 0.00 31.51 3.41
1487 3969 8.405531 TGTGTTATTGGCTATTTTAGATCAAGC 58.594 33.333 0.00 0.00 0.00 4.01
1488 3970 8.624776 GTGTTATTGGCTATTTTAGATCAAGCT 58.375 33.333 0.00 0.00 33.67 3.74
1512 3999 9.454859 GCTATTTTCCTTTCTATATAGGCATGT 57.545 33.333 9.89 0.00 0.00 3.21
1563 4051 9.533253 TCATTCCGATGTATACATATATGCTTG 57.467 33.333 18.28 10.29 36.57 4.01
1580 4068 3.244875 TGCTTGAATTGTTGGAGCCTCTA 60.245 43.478 0.00 0.00 32.53 2.43
1676 7753 7.890515 AGGACATGAGAGTATGTACATACATG 58.109 38.462 35.73 30.82 45.77 3.21
1708 7785 3.431415 AGGTTGCTTTCTTATTCCACCC 58.569 45.455 0.00 0.00 0.00 4.61
1723 7803 1.000396 ACCCAGGAGCTTCAATGGC 60.000 57.895 0.00 0.00 0.00 4.40
1854 7939 8.548721 CCTTGTGACTATATTTTGGAATCGTAC 58.451 37.037 0.00 0.00 0.00 3.67
1870 7955 6.292381 GGAATCGTACATACACTCATTGCTTC 60.292 42.308 0.00 0.00 0.00 3.86
1910 7995 1.686325 GCTCCATGTAGCCCCGAAGA 61.686 60.000 0.00 0.00 36.45 2.87
1936 8021 6.846283 CGAAATTTCTTATTCGTGAGCATACC 59.154 38.462 15.92 0.00 42.47 2.73
2001 8086 6.851318 TCATGATTTCCCTGCTCCATATAAA 58.149 36.000 0.00 0.00 0.00 1.40
2100 8493 8.771920 TTTACTCACATGTCATTTACTACCAG 57.228 34.615 0.00 0.00 0.00 4.00
2101 8494 5.734720 ACTCACATGTCATTTACTACCAGG 58.265 41.667 0.00 0.00 0.00 4.45
2102 8495 4.513442 TCACATGTCATTTACTACCAGGC 58.487 43.478 0.00 0.00 0.00 4.85
2104 8497 5.423931 TCACATGTCATTTACTACCAGGCTA 59.576 40.000 0.00 0.00 0.00 3.93
2108 8501 2.704065 TCATTTACTACCAGGCTAGGGC 59.296 50.000 7.70 0.00 37.82 5.19
2110 8503 2.257391 TTACTACCAGGCTAGGGCAA 57.743 50.000 7.70 0.00 40.87 4.52
2111 8504 1.789523 TACTACCAGGCTAGGGCAAG 58.210 55.000 7.70 1.33 40.87 4.01
2113 8506 1.204146 CTACCAGGCTAGGGCAAGAA 58.796 55.000 7.70 0.00 40.87 2.52
2122 8515 1.852157 TAGGGCAAGAAGGTGGCAGG 61.852 60.000 0.00 0.00 45.56 4.85
2125 8518 2.633509 GCAAGAAGGTGGCAGGCAG 61.634 63.158 0.00 0.00 0.00 4.85
2138 8531 1.745653 GCAGGCAGGGTCTATGAAAAC 59.254 52.381 0.00 0.00 0.00 2.43
2177 8570 8.917414 ATTTCTATATAGAGCACCTTATGGGA 57.083 34.615 12.16 0.00 34.69 4.37
2178 8571 7.962995 TTCTATATAGAGCACCTTATGGGAG 57.037 40.000 12.16 0.00 34.69 4.30
2186 8579 3.627395 CACCTTATGGGAGCAACTACA 57.373 47.619 0.00 0.00 38.76 2.74
2187 8580 3.950397 CACCTTATGGGAGCAACTACAA 58.050 45.455 0.00 0.00 38.76 2.41
2188 8581 4.526970 CACCTTATGGGAGCAACTACAAT 58.473 43.478 0.00 0.00 38.76 2.71
2189 8582 5.680619 CACCTTATGGGAGCAACTACAATA 58.319 41.667 0.00 0.00 38.76 1.90
2190 8583 5.760253 CACCTTATGGGAGCAACTACAATAG 59.240 44.000 0.00 0.00 38.76 1.73
2191 8584 5.665812 ACCTTATGGGAGCAACTACAATAGA 59.334 40.000 0.00 0.00 38.76 1.98
2192 8585 6.157994 ACCTTATGGGAGCAACTACAATAGAA 59.842 38.462 0.00 0.00 38.76 2.10
2193 8586 7.054124 CCTTATGGGAGCAACTACAATAGAAA 58.946 38.462 0.00 0.00 37.23 2.52
2194 8587 7.556275 CCTTATGGGAGCAACTACAATAGAAAA 59.444 37.037 0.00 0.00 37.23 2.29
2195 8588 6.759497 ATGGGAGCAACTACAATAGAAAAC 57.241 37.500 0.00 0.00 0.00 2.43
2196 8589 5.626142 TGGGAGCAACTACAATAGAAAACA 58.374 37.500 0.00 0.00 0.00 2.83
2197 8590 5.705441 TGGGAGCAACTACAATAGAAAACAG 59.295 40.000 0.00 0.00 0.00 3.16
2198 8591 5.123979 GGGAGCAACTACAATAGAAAACAGG 59.876 44.000 0.00 0.00 0.00 4.00
2199 8592 5.392057 GGAGCAACTACAATAGAAAACAGGC 60.392 44.000 0.00 0.00 0.00 4.85
2200 8593 5.316987 AGCAACTACAATAGAAAACAGGCT 58.683 37.500 0.00 0.00 0.00 4.58
2201 8594 5.770162 AGCAACTACAATAGAAAACAGGCTT 59.230 36.000 0.00 0.00 0.00 4.35
2202 8595 5.858581 GCAACTACAATAGAAAACAGGCTTG 59.141 40.000 0.00 0.00 0.00 4.01
2203 8596 6.515035 GCAACTACAATAGAAAACAGGCTTGT 60.515 38.462 0.00 0.00 39.87 3.16
2205 8598 6.970484 ACTACAATAGAAAACAGGCTTGTTG 58.030 36.000 15.63 3.99 46.54 3.33
2206 8599 5.852282 ACAATAGAAAACAGGCTTGTTGT 57.148 34.783 15.63 9.89 46.54 3.32
2207 8600 6.952773 ACAATAGAAAACAGGCTTGTTGTA 57.047 33.333 15.63 7.90 46.54 2.41
2208 8601 6.735130 ACAATAGAAAACAGGCTTGTTGTAC 58.265 36.000 15.63 9.50 46.54 2.90
2209 8602 6.320164 ACAATAGAAAACAGGCTTGTTGTACA 59.680 34.615 15.63 1.23 46.54 2.90
2210 8603 6.952773 ATAGAAAACAGGCTTGTTGTACAA 57.047 33.333 15.63 3.59 46.54 2.41
2211 8604 5.652994 AGAAAACAGGCTTGTTGTACAAA 57.347 34.783 15.63 0.00 46.54 2.83
2212 8605 6.031751 AGAAAACAGGCTTGTTGTACAAAA 57.968 33.333 15.63 0.99 46.54 2.44
2213 8606 6.459923 AGAAAACAGGCTTGTTGTACAAAAA 58.540 32.000 15.63 10.65 46.54 1.94
2214 8607 7.102993 AGAAAACAGGCTTGTTGTACAAAAAT 58.897 30.769 15.63 0.00 46.54 1.82
2215 8608 8.254508 AGAAAACAGGCTTGTTGTACAAAAATA 58.745 29.630 15.63 0.00 46.54 1.40
2216 8609 8.419076 AAAACAGGCTTGTTGTACAAAAATAG 57.581 30.769 15.63 2.59 46.54 1.73
2217 8610 6.952773 ACAGGCTTGTTGTACAAAAATAGA 57.047 33.333 11.62 0.00 37.69 1.98
2218 8611 7.341445 ACAGGCTTGTTGTACAAAAATAGAA 57.659 32.000 11.62 0.00 37.69 2.10
2219 8612 7.777095 ACAGGCTTGTTGTACAAAAATAGAAA 58.223 30.769 11.62 0.00 37.69 2.52
2220 8613 8.254508 ACAGGCTTGTTGTACAAAAATAGAAAA 58.745 29.630 11.62 0.00 37.69 2.29
2221 8614 9.092876 CAGGCTTGTTGTACAAAAATAGAAAAA 57.907 29.630 11.62 0.00 37.69 1.94
2238 8631 1.425412 AAAATCGTTCTGGACCGTCG 58.575 50.000 0.00 0.00 0.00 5.12
2239 8632 0.389426 AAATCGTTCTGGACCGTCGG 60.389 55.000 10.48 10.48 0.00 4.79
2240 8633 1.246056 AATCGTTCTGGACCGTCGGA 61.246 55.000 20.51 0.00 0.00 4.55
2241 8634 1.035932 ATCGTTCTGGACCGTCGGAT 61.036 55.000 20.51 1.57 0.00 4.18
2242 8635 1.226603 CGTTCTGGACCGTCGGATC 60.227 63.158 20.51 11.57 0.00 3.36
2243 8636 1.141234 GTTCTGGACCGTCGGATCC 59.859 63.158 20.51 20.14 35.37 3.36
2244 8637 1.304630 TTCTGGACCGTCGGATCCA 60.305 57.895 24.79 24.79 42.88 3.41
2245 8638 0.901114 TTCTGGACCGTCGGATCCAA 60.901 55.000 25.71 17.74 44.42 3.53
2246 8639 0.901114 TCTGGACCGTCGGATCCAAA 60.901 55.000 25.71 16.61 44.42 3.28
2247 8640 0.036765 CTGGACCGTCGGATCCAAAA 60.037 55.000 25.71 11.61 44.42 2.44
2248 8641 0.616371 TGGACCGTCGGATCCAAAAT 59.384 50.000 24.48 0.28 42.14 1.82
2249 8642 1.014352 GGACCGTCGGATCCAAAATG 58.986 55.000 20.51 1.84 34.87 2.32
2250 8643 1.014352 GACCGTCGGATCCAAAATGG 58.986 55.000 20.51 13.24 39.43 3.16
2268 8661 2.347500 TGGATGGCCCATATTCTAGCA 58.653 47.619 0.00 0.00 40.82 3.49
2269 8662 2.306805 TGGATGGCCCATATTCTAGCAG 59.693 50.000 0.00 0.00 40.82 4.24
2270 8663 2.573462 GGATGGCCCATATTCTAGCAGA 59.427 50.000 0.00 0.00 34.14 4.26
2271 8664 3.370315 GGATGGCCCATATTCTAGCAGAG 60.370 52.174 0.00 0.00 34.14 3.35
2272 8665 2.976440 TGGCCCATATTCTAGCAGAGA 58.024 47.619 0.00 0.00 0.00 3.10
2273 8666 2.634940 TGGCCCATATTCTAGCAGAGAC 59.365 50.000 0.00 0.00 32.31 3.36
2274 8667 2.634940 GGCCCATATTCTAGCAGAGACA 59.365 50.000 0.00 0.00 32.31 3.41
2275 8668 3.262915 GGCCCATATTCTAGCAGAGACAT 59.737 47.826 0.00 0.00 32.31 3.06
2276 8669 4.502962 GCCCATATTCTAGCAGAGACATC 58.497 47.826 0.00 0.00 32.31 3.06
2277 8670 4.622695 GCCCATATTCTAGCAGAGACATCC 60.623 50.000 0.00 0.00 32.31 3.51
2278 8671 4.081198 CCCATATTCTAGCAGAGACATCCC 60.081 50.000 0.00 0.00 32.31 3.85
2279 8672 4.529769 CCATATTCTAGCAGAGACATCCCA 59.470 45.833 0.00 0.00 32.31 4.37
2280 8673 5.337410 CCATATTCTAGCAGAGACATCCCAG 60.337 48.000 0.00 0.00 32.31 4.45
2281 8674 2.079170 TCTAGCAGAGACATCCCAGG 57.921 55.000 0.00 0.00 0.00 4.45
2282 8675 0.392336 CTAGCAGAGACATCCCAGGC 59.608 60.000 0.00 0.00 0.00 4.85
2283 8676 1.050988 TAGCAGAGACATCCCAGGCC 61.051 60.000 0.00 0.00 0.00 5.19
2284 8677 2.673200 GCAGAGACATCCCAGGCCA 61.673 63.158 5.01 0.00 0.00 5.36
2285 8678 1.222936 CAGAGACATCCCAGGCCAC 59.777 63.158 5.01 0.00 0.00 5.01
2286 8679 1.081833 AGAGACATCCCAGGCCACT 59.918 57.895 5.01 0.00 0.00 4.00
2287 8680 0.548682 AGAGACATCCCAGGCCACTT 60.549 55.000 5.01 0.00 0.00 3.16
2288 8681 1.204146 GAGACATCCCAGGCCACTTA 58.796 55.000 5.01 0.00 0.00 2.24
2289 8682 1.559682 GAGACATCCCAGGCCACTTAA 59.440 52.381 5.01 0.00 0.00 1.85
2290 8683 2.173569 GAGACATCCCAGGCCACTTAAT 59.826 50.000 5.01 0.00 0.00 1.40
2291 8684 2.092212 AGACATCCCAGGCCACTTAATG 60.092 50.000 5.01 4.52 0.00 1.90
2308 8701 8.702163 CACTTAATGGACATTTTATGGAAACC 57.298 34.615 2.53 0.00 32.50 3.27
2309 8702 7.763985 CACTTAATGGACATTTTATGGAAACCC 59.236 37.037 2.53 0.00 32.50 4.11
2310 8703 5.692115 AATGGACATTTTATGGAAACCCC 57.308 39.130 0.00 0.00 33.60 4.95
2311 8704 3.445987 TGGACATTTTATGGAAACCCCC 58.554 45.455 0.00 0.00 33.60 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.223377 TCATCACATATCCGTCGTCGAG 59.777 50.000 2.98 0.00 39.71 4.04
43 48 1.725641 ACGCACGTTCATCATCACAT 58.274 45.000 0.00 0.00 0.00 3.21
54 59 2.654877 CACCTCCCTACGCACGTT 59.345 61.111 0.00 0.00 0.00 3.99
89 116 3.260884 AGGTATCGACACATCAACCTTGT 59.739 43.478 0.00 0.00 33.59 3.16
106 133 5.104193 ACAAATCCATCTTCAGAGCAGGTAT 60.104 40.000 0.00 0.00 0.00 2.73
128 155 1.904865 ACCGCTACCGTCTTCCACA 60.905 57.895 0.00 0.00 0.00 4.17
141 168 3.402681 ACTGCATAGGCCACCGCT 61.403 61.111 5.01 0.00 40.13 5.52
178 205 2.126307 CGGTCCAGTGCACTCTCG 60.126 66.667 18.64 14.09 0.00 4.04
201 228 2.742856 CGCAATCACTGGATCTAAGGCA 60.743 50.000 0.00 0.00 31.88 4.75
202 229 1.869767 CGCAATCACTGGATCTAAGGC 59.130 52.381 0.00 0.00 31.88 4.35
213 242 0.537143 TCAACCAAGCCGCAATCACT 60.537 50.000 0.00 0.00 0.00 3.41
262 291 2.821366 GCCTGCCCAGATGTCACG 60.821 66.667 0.00 0.00 0.00 4.35
317 346 6.346477 TCTTGGCAATATCTATCGCTACTT 57.654 37.500 0.00 0.00 0.00 2.24
488 2908 9.834628 CTCTGTTAATGCGGAAATAAGTAAAAA 57.165 29.630 0.00 0.00 0.00 1.94
489 2909 7.966204 GCTCTGTTAATGCGGAAATAAGTAAAA 59.034 33.333 0.00 0.00 0.00 1.52
502 2922 1.863454 CTAGCCTGCTCTGTTAATGCG 59.137 52.381 0.00 0.00 0.00 4.73
552 2972 3.892588 CAGGGTAGACACTCTCTTATCCC 59.107 52.174 0.00 0.00 30.99 3.85
563 2983 0.963962 TCCGTTGACAGGGTAGACAC 59.036 55.000 0.00 0.00 0.00 3.67
564 2984 1.933021 ATCCGTTGACAGGGTAGACA 58.067 50.000 0.00 0.00 0.00 3.41
565 2985 2.361438 CCTATCCGTTGACAGGGTAGAC 59.639 54.545 4.25 0.00 43.46 2.59
566 2986 2.662866 CCTATCCGTTGACAGGGTAGA 58.337 52.381 4.25 0.00 43.46 2.59
567 2987 1.687123 CCCTATCCGTTGACAGGGTAG 59.313 57.143 0.00 0.00 42.50 3.18
568 2988 1.288633 TCCCTATCCGTTGACAGGGTA 59.711 52.381 5.86 0.00 46.73 3.69
569 2989 0.042131 TCCCTATCCGTTGACAGGGT 59.958 55.000 5.86 0.00 46.73 4.34
572 2992 2.656002 TCTCTCCCTATCCGTTGACAG 58.344 52.381 0.00 0.00 0.00 3.51
582 3002 4.534103 AGACAGCTTTTGTTCTCTCCCTAT 59.466 41.667 0.00 0.00 41.05 2.57
587 3007 5.276240 GCTTAGACAGCTTTTGTTCTCTC 57.724 43.478 0.00 0.00 46.27 3.20
685 3107 1.303888 AGTTGGTGGCTGCTGGATG 60.304 57.895 0.00 0.00 0.00 3.51
745 3167 1.134788 GGTGGACCGGAGACAAGTATG 60.135 57.143 9.46 0.00 0.00 2.39
780 3202 0.681243 GGAGGGTGGCTTTGACATCC 60.681 60.000 0.00 0.00 43.53 3.51
833 3259 0.178767 CTTCGTGGGAGGATCATGCA 59.821 55.000 0.23 0.00 36.25 3.96
975 3430 2.584492 GCAAAATGCCAGTATGTCCC 57.416 50.000 0.00 0.00 37.42 4.46
1022 3500 2.015587 GCTCTGGGATTTCAGCTCTTG 58.984 52.381 0.00 0.00 34.91 3.02
1091 3569 1.683943 TCTTACGTATCCACTCCCGG 58.316 55.000 0.00 0.00 0.00 5.73
1263 3741 3.532155 GAGCCTGGCGAGGACGAT 61.532 66.667 20.35 0.05 42.93 3.73
1318 3796 7.081976 GTCAAACAAATTACAGCTCGGTTTAT 58.918 34.615 0.00 0.00 0.00 1.40
1446 3928 7.469456 GCCAATAACACAACTTTTGTAGGAAGA 60.469 37.037 0.00 0.00 43.23 2.87
1483 3965 9.507329 TGCCTATATAGAAAGGAAAATAGCTTG 57.493 33.333 11.53 0.00 34.58 4.01
1485 3967 9.678260 CATGCCTATATAGAAAGGAAAATAGCT 57.322 33.333 11.53 0.00 34.58 3.32
1486 3968 9.454859 ACATGCCTATATAGAAAGGAAAATAGC 57.545 33.333 11.53 2.30 34.58 2.97
1522 4009 7.941238 ACATCGGAATGAGGAAAATATGAGAAT 59.059 33.333 0.00 0.00 36.67 2.40
1525 4012 8.783833 ATACATCGGAATGAGGAAAATATGAG 57.216 34.615 0.00 0.00 36.67 2.90
1535 4022 8.363390 AGCATATATGTATACATCGGAATGAGG 58.637 37.037 21.49 5.75 37.76 3.86
1557 4045 2.494870 GAGGCTCCAACAATTCAAGCAT 59.505 45.455 2.15 0.00 34.65 3.79
1558 4046 1.888512 GAGGCTCCAACAATTCAAGCA 59.111 47.619 2.15 0.00 34.65 3.91
1563 4051 5.009410 CCAATCATAGAGGCTCCAACAATTC 59.991 44.000 11.71 0.00 0.00 2.17
1580 4068 6.041979 ACTTTTTCCAGCAAACTACCAATCAT 59.958 34.615 0.00 0.00 0.00 2.45
1708 7785 1.807886 GCAGCCATTGAAGCTCCTG 59.192 57.895 0.00 0.00 38.95 3.86
1723 7803 4.989168 GGTCTTATGTATAAGAACCCGCAG 59.011 45.833 15.59 0.00 46.43 5.18
1840 7925 8.397906 CAATGAGTGTATGTACGATTCCAAAAT 58.602 33.333 0.00 0.00 0.00 1.82
2001 8086 1.573026 TACGCACGACACACAACAAT 58.427 45.000 0.00 0.00 0.00 2.71
2081 8474 4.517285 AGCCTGGTAGTAAATGACATGTG 58.483 43.478 1.15 0.00 0.00 3.21
2082 8475 4.844349 AGCCTGGTAGTAAATGACATGT 57.156 40.909 0.00 0.00 0.00 3.21
2088 8481 2.438021 TGCCCTAGCCTGGTAGTAAATG 59.562 50.000 0.00 0.00 38.69 2.32
2089 8482 2.771688 TGCCCTAGCCTGGTAGTAAAT 58.228 47.619 0.00 0.00 38.69 1.40
2090 8483 2.257391 TGCCCTAGCCTGGTAGTAAA 57.743 50.000 0.00 0.00 38.69 2.01
2091 8484 2.116238 CTTGCCCTAGCCTGGTAGTAA 58.884 52.381 0.00 0.00 38.69 2.24
2092 8485 1.289830 TCTTGCCCTAGCCTGGTAGTA 59.710 52.381 0.00 0.00 38.69 1.82
2093 8486 0.042731 TCTTGCCCTAGCCTGGTAGT 59.957 55.000 0.00 0.00 38.69 2.73
2094 8487 1.139853 CTTCTTGCCCTAGCCTGGTAG 59.860 57.143 0.00 0.00 38.69 3.18
2097 8490 1.225704 CCTTCTTGCCCTAGCCTGG 59.774 63.158 0.00 0.00 38.69 4.45
2098 8491 0.393537 CACCTTCTTGCCCTAGCCTG 60.394 60.000 0.00 0.00 38.69 4.85
2099 8492 1.566298 CCACCTTCTTGCCCTAGCCT 61.566 60.000 0.00 0.00 38.69 4.58
2100 8493 1.077429 CCACCTTCTTGCCCTAGCC 60.077 63.158 0.00 0.00 38.69 3.93
2101 8494 1.750780 GCCACCTTCTTGCCCTAGC 60.751 63.158 0.00 0.00 40.48 3.42
2102 8495 0.393537 CTGCCACCTTCTTGCCCTAG 60.394 60.000 0.00 0.00 0.00 3.02
2104 8497 2.437897 CTGCCACCTTCTTGCCCT 59.562 61.111 0.00 0.00 0.00 5.19
2108 8501 1.975407 CCTGCCTGCCACCTTCTTG 60.975 63.158 0.00 0.00 0.00 3.02
2110 8503 3.655211 CCCTGCCTGCCACCTTCT 61.655 66.667 0.00 0.00 0.00 2.85
2111 8504 3.927481 GACCCTGCCTGCCACCTTC 62.927 68.421 0.00 0.00 0.00 3.46
2113 8506 2.847292 ATAGACCCTGCCTGCCACCT 62.847 60.000 0.00 0.00 0.00 4.00
2122 8515 3.190874 CTCGAGTTTTCATAGACCCTGC 58.809 50.000 3.62 0.00 0.00 4.85
2125 8518 2.742204 GCCCTCGAGTTTTCATAGACCC 60.742 54.545 12.31 0.00 0.00 4.46
2174 8567 5.123979 CCTGTTTTCTATTGTAGTTGCTCCC 59.876 44.000 0.00 0.00 0.00 4.30
2175 8568 5.392057 GCCTGTTTTCTATTGTAGTTGCTCC 60.392 44.000 0.00 0.00 0.00 4.70
2176 8569 5.412904 AGCCTGTTTTCTATTGTAGTTGCTC 59.587 40.000 0.00 0.00 0.00 4.26
2177 8570 5.316987 AGCCTGTTTTCTATTGTAGTTGCT 58.683 37.500 0.00 0.00 0.00 3.91
2178 8571 5.629079 AGCCTGTTTTCTATTGTAGTTGC 57.371 39.130 0.00 0.00 0.00 4.17
2179 8572 6.970484 ACAAGCCTGTTTTCTATTGTAGTTG 58.030 36.000 0.00 0.00 28.57 3.16
2180 8573 7.068226 ACAACAAGCCTGTTTTCTATTGTAGTT 59.932 33.333 0.00 0.00 43.45 2.24
2181 8574 6.546034 ACAACAAGCCTGTTTTCTATTGTAGT 59.454 34.615 0.00 0.00 43.45 2.73
2182 8575 6.970484 ACAACAAGCCTGTTTTCTATTGTAG 58.030 36.000 0.00 0.00 43.45 2.74
2183 8576 6.952773 ACAACAAGCCTGTTTTCTATTGTA 57.047 33.333 0.00 0.00 43.45 2.41
2184 8577 5.852282 ACAACAAGCCTGTTTTCTATTGT 57.148 34.783 0.00 0.00 43.45 2.71
2185 8578 6.734137 TGTACAACAAGCCTGTTTTCTATTG 58.266 36.000 0.00 0.00 43.45 1.90
2186 8579 6.952773 TGTACAACAAGCCTGTTTTCTATT 57.047 33.333 0.00 0.00 43.45 1.73
2187 8580 6.952773 TTGTACAACAAGCCTGTTTTCTAT 57.047 33.333 3.59 0.00 43.45 1.98
2188 8581 6.761099 TTTGTACAACAAGCCTGTTTTCTA 57.239 33.333 8.07 0.00 43.45 2.10
2189 8582 5.652994 TTTGTACAACAAGCCTGTTTTCT 57.347 34.783 8.07 0.00 43.45 2.52
2190 8583 6.713792 TTTTTGTACAACAAGCCTGTTTTC 57.286 33.333 8.07 0.00 43.45 2.29
2191 8584 8.254508 TCTATTTTTGTACAACAAGCCTGTTTT 58.745 29.630 8.07 0.00 43.45 2.43
2192 8585 7.777095 TCTATTTTTGTACAACAAGCCTGTTT 58.223 30.769 8.07 0.00 43.45 2.83
2194 8587 6.952773 TCTATTTTTGTACAACAAGCCTGT 57.047 33.333 8.07 0.00 39.53 4.00
2195 8588 8.641499 TTTTCTATTTTTGTACAACAAGCCTG 57.359 30.769 8.07 0.96 39.53 4.85
2218 8611 1.796459 CGACGGTCCAGAACGATTTTT 59.204 47.619 12.81 0.00 45.97 1.94
2219 8612 1.425412 CGACGGTCCAGAACGATTTT 58.575 50.000 12.81 0.00 45.97 1.82
2220 8613 0.389426 CCGACGGTCCAGAACGATTT 60.389 55.000 12.81 0.00 45.97 2.17
2221 8614 1.214589 CCGACGGTCCAGAACGATT 59.785 57.895 12.81 0.00 45.97 3.34
2222 8615 1.035932 ATCCGACGGTCCAGAACGAT 61.036 55.000 14.79 0.00 45.97 3.73
2223 8616 1.651240 GATCCGACGGTCCAGAACGA 61.651 60.000 14.79 0.00 45.97 3.85
2225 8618 1.141234 GGATCCGACGGTCCAGAAC 59.859 63.158 22.78 1.81 34.57 3.01
2226 8619 0.901114 TTGGATCCGACGGTCCAGAA 60.901 55.000 26.40 16.72 44.74 3.02
2227 8620 0.901114 TTTGGATCCGACGGTCCAGA 60.901 55.000 26.40 22.50 44.74 3.86
2228 8621 0.036765 TTTTGGATCCGACGGTCCAG 60.037 55.000 26.40 0.84 44.74 3.86
2229 8622 0.616371 ATTTTGGATCCGACGGTCCA 59.384 50.000 25.11 25.11 42.55 4.02
2230 8623 1.014352 CATTTTGGATCCGACGGTCC 58.986 55.000 21.61 21.61 35.02 4.46
2231 8624 1.014352 CCATTTTGGATCCGACGGTC 58.986 55.000 14.79 10.57 40.96 4.79
2232 8625 0.616371 TCCATTTTGGATCCGACGGT 59.384 50.000 14.79 0.67 42.67 4.83
2233 8626 3.469564 TCCATTTTGGATCCGACGG 57.530 52.632 7.84 7.84 42.67 4.79
2249 8642 2.573462 TCTGCTAGAATATGGGCCATCC 59.427 50.000 25.07 13.52 0.00 3.51
2250 8643 3.517100 TCTCTGCTAGAATATGGGCCATC 59.483 47.826 25.07 10.29 0.00 3.51
2251 8644 3.262915 GTCTCTGCTAGAATATGGGCCAT 59.737 47.826 24.69 24.69 35.47 4.40
2252 8645 2.634940 GTCTCTGCTAGAATATGGGCCA 59.365 50.000 9.61 9.61 35.47 5.36
2253 8646 2.634940 TGTCTCTGCTAGAATATGGGCC 59.365 50.000 0.00 0.00 35.47 5.80
2254 8647 4.502962 GATGTCTCTGCTAGAATATGGGC 58.497 47.826 0.00 0.00 35.47 5.36
2255 8648 4.081198 GGGATGTCTCTGCTAGAATATGGG 60.081 50.000 0.00 0.00 35.47 4.00
2256 8649 4.529769 TGGGATGTCTCTGCTAGAATATGG 59.470 45.833 0.00 0.00 35.47 2.74
2257 8650 5.337410 CCTGGGATGTCTCTGCTAGAATATG 60.337 48.000 0.00 0.00 35.47 1.78
2258 8651 4.776837 CCTGGGATGTCTCTGCTAGAATAT 59.223 45.833 0.00 0.00 35.47 1.28
2259 8652 4.155709 CCTGGGATGTCTCTGCTAGAATA 58.844 47.826 0.00 0.00 35.47 1.75
2260 8653 2.971330 CCTGGGATGTCTCTGCTAGAAT 59.029 50.000 0.00 0.00 35.47 2.40
2261 8654 2.392662 CCTGGGATGTCTCTGCTAGAA 58.607 52.381 0.00 0.00 35.47 2.10
2262 8655 2.031624 GCCTGGGATGTCTCTGCTAGA 61.032 57.143 0.00 0.00 0.00 2.43
2263 8656 0.392336 GCCTGGGATGTCTCTGCTAG 59.608 60.000 0.00 0.00 0.00 3.42
2264 8657 1.050988 GGCCTGGGATGTCTCTGCTA 61.051 60.000 0.00 0.00 0.00 3.49
2265 8658 2.373707 GGCCTGGGATGTCTCTGCT 61.374 63.158 0.00 0.00 0.00 4.24
2266 8659 2.191641 GGCCTGGGATGTCTCTGC 59.808 66.667 0.00 0.00 0.00 4.26
2267 8660 1.222936 GTGGCCTGGGATGTCTCTG 59.777 63.158 3.32 0.00 0.00 3.35
2268 8661 0.548682 AAGTGGCCTGGGATGTCTCT 60.549 55.000 3.32 0.00 0.00 3.10
2269 8662 1.204146 TAAGTGGCCTGGGATGTCTC 58.796 55.000 3.32 0.00 0.00 3.36
2270 8663 1.668826 TTAAGTGGCCTGGGATGTCT 58.331 50.000 3.32 0.00 0.00 3.41
2271 8664 2.301346 CATTAAGTGGCCTGGGATGTC 58.699 52.381 3.32 0.00 0.00 3.06
2272 8665 1.063717 CCATTAAGTGGCCTGGGATGT 60.064 52.381 3.32 0.00 42.12 3.06
2273 8666 1.696063 CCATTAAGTGGCCTGGGATG 58.304 55.000 3.32 2.04 42.12 3.51
2283 8676 7.763985 GGGTTTCCATAAAATGTCCATTAAGTG 59.236 37.037 0.00 0.00 0.00 3.16
2284 8677 7.093068 GGGGTTTCCATAAAATGTCCATTAAGT 60.093 37.037 0.00 0.00 35.00 2.24
2285 8678 7.272244 GGGGTTTCCATAAAATGTCCATTAAG 58.728 38.462 0.00 0.00 35.00 1.85
2286 8679 6.157123 GGGGGTTTCCATAAAATGTCCATTAA 59.843 38.462 0.00 0.00 37.22 1.40
2287 8680 5.663556 GGGGGTTTCCATAAAATGTCCATTA 59.336 40.000 0.00 0.00 37.22 1.90
2288 8681 4.473196 GGGGGTTTCCATAAAATGTCCATT 59.527 41.667 0.00 0.00 37.22 3.16
2289 8682 4.037222 GGGGGTTTCCATAAAATGTCCAT 58.963 43.478 0.00 0.00 37.22 3.41
2290 8683 3.445987 GGGGGTTTCCATAAAATGTCCA 58.554 45.455 0.00 0.00 37.22 4.02


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

AutoCloner maintained by Alex Coulton.