Multiple sequence alignment - TraesCS3B01G100900

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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 TraesCS3B01G100900 chr3B 100.000 3152 0 0 1 3152 67688621 67691772 0.000000e+00 5821.0
1 TraesCS3B01G100900 chr3B 87.857 280 22 5 2339 2610 68195552 68195827 5.070000e-83 318.0
2 TraesCS3B01G100900 chr3B 87.143 280 25 4 2339 2610 68206497 68206773 1.100000e-79 307.0
3 TraesCS3B01G100900 chr3B 79.458 443 70 13 861 1294 68253239 68253669 8.550000e-76 294.0
4 TraesCS3B01G100900 chr3B 86.420 162 21 1 2865 3026 529407950 529407790 3.230000e-40 176.0
5 TraesCS3B01G100900 chr3B 91.549 71 4 2 1403 1471 583376905 583376835 2.590000e-16 97.1
6 TraesCS3B01G100900 chr3A 92.559 3158 204 17 1 3150 80789196 80792330 0.000000e+00 4501.0
7 TraesCS3B01G100900 chr5D 89.271 494 45 8 2339 2831 498463185 498462699 2.080000e-171 612.0
8 TraesCS3B01G100900 chr5D 86.624 157 20 1 2871 3026 475153113 475152957 4.180000e-39 172.0
9 TraesCS3B01G100900 chr5D 85.276 163 23 1 2865 3026 319325105 319324943 1.940000e-37 167.0
10 TraesCS3B01G100900 chr5D 92.647 68 4 1 1399 1465 559461760 559461693 2.590000e-16 97.1
11 TraesCS3B01G100900 chr4D 86.698 421 42 6 2356 2764 378486618 378487036 3.710000e-124 455.0
12 TraesCS3B01G100900 chr4D 94.262 122 7 0 3023 3144 378487094 378487215 1.490000e-43 187.0
13 TraesCS3B01G100900 chr7A 88.768 276 20 6 2339 2606 28023183 28022911 8.430000e-86 327.0
14 TraesCS3B01G100900 chr7D 88.406 276 21 4 2339 2606 27806509 27806237 3.920000e-84 322.0
15 TraesCS3B01G100900 chr7D 93.939 66 4 0 269 334 501110608 501110673 2.000000e-17 100.0
16 TraesCS3B01G100900 chr7D 95.238 63 2 1 1404 1465 556285891 556285953 7.190000e-17 99.0
17 TraesCS3B01G100900 chr3D 79.318 440 66 16 861 1294 43512994 43513414 5.150000e-73 285.0
18 TraesCS3B01G100900 chr3D 78.924 446 66 16 861 1294 43509111 43509540 8.610000e-71 278.0
19 TraesCS3B01G100900 chr3D 85.799 169 23 1 2865 3033 421374432 421374599 8.980000e-41 178.0
20 TraesCS3B01G100900 chr3D 91.304 69 5 1 268 336 133123742 133123809 3.350000e-15 93.5
21 TraesCS3B01G100900 chr1D 87.654 162 20 0 2865 3026 324412228 324412389 4.150000e-44 189.0
22 TraesCS3B01G100900 chr1D 83.893 149 21 3 2445 2592 308271621 308271475 4.240000e-29 139.0
23 TraesCS3B01G100900 chr2A 80.851 235 39 4 2332 2563 747153992 747154223 2.500000e-41 180.0
24 TraesCS3B01G100900 chr5A 85.802 162 23 0 2865 3026 605231143 605231304 4.180000e-39 172.0
25 TraesCS3B01G100900 chr5A 89.333 75 3 4 1400 1469 546897856 546897782 4.330000e-14 89.8
26 TraesCS3B01G100900 chr5A 88.158 76 6 3 1403 1477 369128184 369128111 1.560000e-13 87.9
27 TraesCS3B01G100900 chr6D 85.030 167 23 2 2865 3031 128093068 128092904 5.410000e-38 169.0
28 TraesCS3B01G100900 chr6D 89.189 74 6 2 276 349 310403275 310403204 1.200000e-14 91.6
29 TraesCS3B01G100900 chr1B 84.940 166 24 1 2865 3030 521219377 521219541 1.940000e-37 167.0
30 TraesCS3B01G100900 chr2D 93.939 66 2 2 271 336 555510384 555510321 7.190000e-17 99.0
31 TraesCS3B01G100900 chr2D 89.474 76 5 3 1403 1477 260976091 260976018 3.350000e-15 93.5
32 TraesCS3B01G100900 chr2B 93.846 65 2 2 1403 1465 373997326 373997390 2.590000e-16 97.1
33 TraesCS3B01G100900 chr2B 93.846 65 3 1 271 335 477406458 477406395 2.590000e-16 97.1
34 TraesCS3B01G100900 chr7B 92.537 67 4 1 276 341 31563281 31563215 9.310000e-16 95.3
35 TraesCS3B01G100900 chr6B 90.141 71 4 3 1398 1465 16434838 16434908 4.330000e-14 89.8
36 TraesCS3B01G100900 chr5B 87.179 78 7 2 270 347 89914 89988 5.600000e-13 86.1
37 TraesCS3B01G100900 chr5B 82.653 98 13 4 276 371 532347793 532347698 2.010000e-12 84.2
38 TraesCS3B01G100900 chr1A 90.769 65 4 2 2338 2401 575502900 575502837 5.600000e-13 86.1


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 TraesCS3B01G100900 chr3B 67688621 67691772 3151 False 5821.0 5821 100.000 1 3152 1 chr3B.!!$F1 3151
1 TraesCS3B01G100900 chr3A 80789196 80792330 3134 False 4501.0 4501 92.559 1 3150 1 chr3A.!!$F1 3149
2 TraesCS3B01G100900 chr4D 378486618 378487215 597 False 321.0 455 90.480 2356 3144 2 chr4D.!!$F1 788
3 TraesCS3B01G100900 chr3D 43509111 43513414 4303 False 281.5 285 79.121 861 1294 2 chr3D.!!$F3 433

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
48 49 0.032912 TCATGCCACAGATGCCCAAT 60.033 50.0 0.0 0.0 0.0 3.16 F
592 593 0.663153 AGCTGTTTTTGGCGAGTGAC 59.337 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1661 1.195115 CCTCCTTGCTGGCTGTACTA 58.805 55.0 0.0 0.0 35.26 1.82 R
2164 3103 0.179034 GCCACAATGGGTGCCAAAAA 60.179 50.0 0.0 0.0 46.50 1.94 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
38 39 0.035534 ATTGTAGCGGTCATGCCACA 60.036 50.000 0.00 0.00 34.69 4.17
48 49 0.032912 TCATGCCACAGATGCCCAAT 60.033 50.000 0.00 0.00 0.00 3.16
71 72 2.557924 GGATGCCTTGTCATTGTCAACA 59.442 45.455 0.00 0.00 0.00 3.33
90 91 8.031864 TGTCAACACACTCAATTTATTTGTTGT 58.968 29.630 10.42 4.38 41.85 3.32
91 92 8.531530 GTCAACACACTCAATTTATTTGTTGTC 58.468 33.333 10.42 3.09 41.85 3.18
102 103 8.977505 CAATTTATTTGTTGTCGTCAAGGAATT 58.022 29.630 0.00 0.00 33.97 2.17
125 126 5.660460 TCTTGCGATAGACAAGCTGATTAA 58.340 37.500 0.00 0.00 44.37 1.40
137 138 3.356290 AGCTGATTAACATGTTGGGTCC 58.644 45.455 21.42 6.38 0.00 4.46
144 145 1.149101 ACATGTTGGGTCCAGGTCTT 58.851 50.000 0.00 0.00 0.00 3.01
170 171 8.836413 TCATTTCGTCTTGTTTCTTTATGTTCT 58.164 29.630 0.00 0.00 0.00 3.01
173 174 9.498307 TTTCGTCTTGTTTCTTTATGTTCTTTC 57.502 29.630 0.00 0.00 0.00 2.62
179 180 7.639113 TGTTTCTTTATGTTCTTTCCACAGT 57.361 32.000 0.00 0.00 0.00 3.55
216 217 3.568853 TGAGGTACTATCTTTAGCCGCTC 59.431 47.826 0.00 0.00 41.55 5.03
227 228 1.905637 TAGCCGCTCGAAGGATGATA 58.094 50.000 10.46 0.00 0.00 2.15
288 289 2.443887 AAAATATGGCCGCATGCATC 57.556 45.000 19.57 8.10 43.89 3.91
291 292 0.885879 ATATGGCCGCATGCATCTTG 59.114 50.000 19.57 0.00 43.89 3.02
328 329 4.797912 GGGGTCATCCTCCTTTTCTAAT 57.202 45.455 0.00 0.00 35.33 1.73
423 424 5.193663 TGGCAAAAACATTGATTTCGAGA 57.806 34.783 0.00 0.00 0.00 4.04
452 453 7.660112 TCGTAAAGTACTTAGTCCAATGAACA 58.340 34.615 8.92 0.00 0.00 3.18
453 454 8.308931 TCGTAAAGTACTTAGTCCAATGAACAT 58.691 33.333 8.92 0.00 0.00 2.71
466 467 7.492669 AGTCCAATGAACATGAAGTATAGAACG 59.507 37.037 0.00 0.00 0.00 3.95
500 501 1.079503 GATGAACACAACCTCCGAGC 58.920 55.000 0.00 0.00 0.00 5.03
507 508 2.038557 ACACAACCTCCGAGCACTATTT 59.961 45.455 0.00 0.00 0.00 1.40
517 518 4.163458 TCCGAGCACTATTTGTATTTCCCT 59.837 41.667 0.00 0.00 0.00 4.20
565 566 5.725362 AGAGATTTCCTAAAGGAGTTGTCG 58.275 41.667 0.00 0.00 46.36 4.35
568 569 6.712276 AGATTTCCTAAAGGAGTTGTCGATT 58.288 36.000 0.00 0.00 46.36 3.34
592 593 0.663153 AGCTGTTTTTGGCGAGTGAC 59.337 50.000 0.00 0.00 0.00 3.67
597 598 2.948979 TGTTTTTGGCGAGTGACTCAAT 59.051 40.909 13.67 0.00 0.00 2.57
605 606 2.283617 GCGAGTGACTCAATATGCACTG 59.716 50.000 13.67 0.00 41.30 3.66
625 626 6.749118 GCACTGGAAACAATAAATTCTAGCAG 59.251 38.462 0.00 0.00 42.06 4.24
744 745 6.168164 ACTTGCACAAAAACAACAAATCTG 57.832 33.333 0.00 0.00 0.00 2.90
754 755 9.862585 CAAAAACAACAAATCTGTAATTTAGGC 57.137 29.630 0.00 0.00 33.45 3.93
761 762 8.409358 ACAAATCTGTAATTTAGGCAGTTCTT 57.591 30.769 0.00 0.00 32.54 2.52
794 796 9.453572 AAGGTATATGCAATATGTGTATTCCTG 57.546 33.333 0.00 0.00 40.40 3.86
795 797 8.049117 AGGTATATGCAATATGTGTATTCCTGG 58.951 37.037 0.00 0.00 40.40 4.45
898 901 9.823647 ACATTCAAGACAAATATATTCGAGAGT 57.176 29.630 0.00 0.00 0.00 3.24
952 957 9.793259 TCTACAGAATAAATGTGTTCCTTTCTT 57.207 29.630 0.00 0.00 32.02 2.52
979 985 6.252995 TCTTAAACAATAGATGGGTGCCTTT 58.747 36.000 0.00 0.00 0.00 3.11
994 1000 7.122715 TGGGTGCCTTTTTGTACTATATCATT 58.877 34.615 0.00 0.00 0.00 2.57
1030 1036 6.692849 TTCATGTCCTCTGCATATCCTATT 57.307 37.500 0.00 0.00 0.00 1.73
1032 1038 5.188555 TCATGTCCTCTGCATATCCTATTCC 59.811 44.000 0.00 0.00 0.00 3.01
1041 1047 5.056480 TGCATATCCTATTCCTTCACAACG 58.944 41.667 0.00 0.00 0.00 4.10
1046 1052 3.751175 TCCTATTCCTTCACAACGCAAAG 59.249 43.478 0.00 0.00 0.00 2.77
1065 1071 2.957474 AGCATACAAACCCCAAAGTGT 58.043 42.857 0.00 0.00 0.00 3.55
1298 1304 8.383175 TCCATCAGTTTAGGAGTTTTTGTCTAT 58.617 33.333 0.00 0.00 0.00 1.98
1341 1466 7.168219 TCCTGTTATACACAAAAAGAGATGCT 58.832 34.615 0.00 0.00 33.87 3.79
1411 1537 3.508012 CCCAGAAGTGATATACTCCTCCG 59.492 52.174 0.00 0.00 39.18 4.63
1414 1540 4.216687 CAGAAGTGATATACTCCTCCGTCC 59.783 50.000 0.00 0.00 39.18 4.79
1434 1560 5.163488 CGTCCCATAATGTAGGTAGTGTCAA 60.163 44.000 0.00 0.00 0.00 3.18
1512 1640 1.051812 ACAGGAGAAGTGGACACCAG 58.948 55.000 0.00 0.00 32.34 4.00
1513 1641 1.051812 CAGGAGAAGTGGACACCAGT 58.948 55.000 0.00 0.00 39.10 4.00
1533 1661 2.803030 ATCAGAACAAGCAGCATCCT 57.197 45.000 0.00 0.00 0.00 3.24
1567 1695 0.521735 GGAGGGTTTTGCAAGCTACG 59.478 55.000 0.00 0.00 0.00 3.51
1585 1713 4.096081 GCTACGTATGTACCTCAGACAACT 59.904 45.833 0.00 0.00 38.06 3.16
1586 1714 5.295292 GCTACGTATGTACCTCAGACAACTA 59.705 44.000 0.00 0.00 38.06 2.24
1684 1812 1.937899 GCAATTTGCAATGATCCAGCC 59.062 47.619 16.35 0.00 44.26 4.85
1741 1869 0.318275 GCGGCGGTTGTGATGAAAAA 60.318 50.000 9.78 0.00 0.00 1.94
1777 1905 3.939740 AGGCTGCTAATGAAAGATGGA 57.060 42.857 0.00 0.00 0.00 3.41
1803 2196 8.780846 TGGCAGTTTTTCTATATCGAGTTAAA 57.219 30.769 0.00 0.00 0.00 1.52
1825 2218 1.846007 ACAAAGGTTGCCTTGTGTCA 58.154 45.000 0.71 0.00 43.92 3.58
1827 2220 2.362077 ACAAAGGTTGCCTTGTGTCATC 59.638 45.455 0.71 0.00 43.92 2.92
1840 2233 6.318648 GCCTTGTGTCATCTGGATATTGTAAA 59.681 38.462 0.00 0.00 0.00 2.01
1843 2236 8.722480 TTGTGTCATCTGGATATTGTAAAGAG 57.278 34.615 0.00 0.00 0.00 2.85
2017 2808 4.400529 TGTTCTTTTTGCCCCTTCTTTC 57.599 40.909 0.00 0.00 0.00 2.62
2059 2994 3.373748 CCTTTTGTCCCAACAAGTTTTGC 59.626 43.478 0.00 0.00 45.72 3.68
2062 2997 1.403679 TGTCCCAACAAGTTTTGCTCG 59.596 47.619 0.00 0.00 30.70 5.03
2090 3025 1.390565 GCATGAGCTTTGCCTCATCT 58.609 50.000 10.61 0.00 46.75 2.90
2138 3077 4.694037 AGACAAACTTATAACCGGAAGTGC 59.306 41.667 9.46 0.00 36.05 4.40
2141 3080 5.640783 ACAAACTTATAACCGGAAGTGCTAC 59.359 40.000 9.46 0.00 36.05 3.58
2145 3084 5.067544 ACTTATAACCGGAAGTGCTACTCTC 59.932 44.000 9.46 0.00 34.61 3.20
2164 3103 9.945904 CTACTCTCCCAAGATTAAACTTTAACT 57.054 33.333 0.00 0.00 0.00 2.24
2179 3906 5.122519 ACTTTAACTTTTTGGCACCCATTG 58.877 37.500 0.00 0.00 31.53 2.82
2187 3914 3.136750 GCACCCATTGTGGCACAA 58.863 55.556 32.77 32.77 45.55 3.33
2188 3915 1.445095 GCACCCATTGTGGCACAAA 59.555 52.632 34.01 19.02 45.55 2.83
2189 3916 0.600782 GCACCCATTGTGGCACAAAG 60.601 55.000 34.01 29.00 45.55 2.77
2190 3917 0.600782 CACCCATTGTGGCACAAAGC 60.601 55.000 34.01 0.45 44.16 3.51
2202 3929 1.179152 CACAAAGCATGGCCTCATCA 58.821 50.000 3.32 0.00 0.00 3.07
2211 3938 6.585695 AGCATGGCCTCATCATTAATTAAG 57.414 37.500 3.32 0.00 0.00 1.85
2230 3957 2.393646 AGCTTAAAAGGTTTGGTGGCA 58.606 42.857 0.00 0.00 31.69 4.92
2269 3996 6.397272 TGGAGGATGCATACAATTTTCAAAC 58.603 36.000 12.53 0.00 0.00 2.93
2275 4002 9.328845 GGATGCATACAATTTTCAAACCATAAT 57.671 29.630 3.28 0.00 0.00 1.28
2579 4830 9.707957 AATTTATATGTGGAGTAAAATGGACCA 57.292 29.630 0.00 0.00 0.00 4.02
2662 4925 8.612486 TGGTGGATTTAACCTATTACTACTCA 57.388 34.615 0.00 0.00 38.60 3.41
2710 4973 7.840931 AGGATTCGAGGAAAGCATTAAAATTT 58.159 30.769 0.00 0.00 0.00 1.82
2873 5140 6.641169 ATTCACATTCTCTATACTCGCTCA 57.359 37.500 0.00 0.00 0.00 4.26
2884 5151 6.069331 TCTATACTCGCTCAGTCCCTAAATT 58.931 40.000 0.00 0.00 36.43 1.82
2888 5155 5.801380 ACTCGCTCAGTCCCTAAATTTAAA 58.199 37.500 0.00 0.00 0.00 1.52
2994 5261 9.404848 CGTATGTAGTCCATATTAGAATCCCTA 57.595 37.037 0.00 0.00 38.29 3.53
3015 5282 9.444600 TCCCTACAAAGACTTATATTTGTGAAC 57.555 33.333 12.27 0.00 46.90 3.18
3016 5283 9.226606 CCCTACAAAGACTTATATTTGTGAACA 57.773 33.333 12.27 0.00 46.90 3.18
3026 5293 8.258708 ACTTATATTTGTGAACAGAGGGAGTAC 58.741 37.037 0.00 0.00 0.00 2.73
3048 5315 0.317160 TATCCTAGCCATTCACCGCG 59.683 55.000 0.00 0.00 0.00 6.46
3119 5587 4.196971 CTCATGTGATGGAAGATGCAGAA 58.803 43.478 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.147958 GACCGCTACAATTCAACACCA 58.852 47.619 0.00 0.00 0.00 4.17
38 39 1.453633 AGGCATCCTATTGGGCATCT 58.546 50.000 0.00 0.00 34.39 2.90
48 49 3.998913 TGACAATGACAAGGCATCCTA 57.001 42.857 0.00 0.00 31.13 2.94
71 72 7.022055 TGACGACAACAAATAAATTGAGTGT 57.978 32.000 0.00 0.00 41.85 3.55
113 114 4.151883 ACCCAACATGTTAATCAGCTTGT 58.848 39.130 11.53 0.00 0.00 3.16
125 126 1.073923 GAAGACCTGGACCCAACATGT 59.926 52.381 0.00 0.00 0.00 3.21
137 138 5.237344 AGAAACAAGACGAAATGAAGACCTG 59.763 40.000 0.00 0.00 0.00 4.00
144 145 8.836413 AGAACATAAAGAAACAAGACGAAATGA 58.164 29.630 0.00 0.00 0.00 2.57
189 190 5.692204 CGGCTAAAGATAGTACCTCACATTG 59.308 44.000 0.00 0.00 0.00 2.82
192 193 3.067742 GCGGCTAAAGATAGTACCTCACA 59.932 47.826 0.00 0.00 0.00 3.58
291 292 3.830192 CCCGGCCTCTGCATTTGC 61.830 66.667 0.00 0.00 40.13 3.68
429 430 9.431887 TCATGTTCATTGGACTAAGTACTTTAC 57.568 33.333 14.49 5.72 0.00 2.01
441 442 7.254455 CCGTTCTATACTTCATGTTCATTGGAC 60.254 40.741 0.00 0.00 0.00 4.02
452 453 4.341520 GTGTCCTCCCGTTCTATACTTCAT 59.658 45.833 0.00 0.00 0.00 2.57
453 454 3.698040 GTGTCCTCCCGTTCTATACTTCA 59.302 47.826 0.00 0.00 0.00 3.02
466 467 2.755103 GTTCATCCAATTGTGTCCTCCC 59.245 50.000 4.43 0.00 0.00 4.30
556 557 1.079503 GCTGGACAATCGACAACTCC 58.920 55.000 0.00 0.00 0.00 3.85
565 566 2.407090 GCCAAAAACAGCTGGACAATC 58.593 47.619 19.93 0.00 34.35 2.67
568 569 0.749818 TCGCCAAAAACAGCTGGACA 60.750 50.000 19.93 0.00 34.35 4.02
592 593 9.590451 AATTTATTGTTTCCAGTGCATATTGAG 57.410 29.630 0.00 0.00 0.00 3.02
597 598 8.405531 GCTAGAATTTATTGTTTCCAGTGCATA 58.594 33.333 0.00 0.00 0.00 3.14
605 606 9.860898 AATGTTCTGCTAGAATTTATTGTTTCC 57.139 29.630 0.00 0.00 36.50 3.13
794 796 8.870075 ATTTACCCTCATCTAATTAGAATGCC 57.130 34.615 18.79 0.00 35.69 4.40
891 894 6.262193 TGTGTGTCATTAATACACTCTCGA 57.738 37.500 16.91 0.00 46.81 4.04
950 955 7.545615 GGCACCCATCTATTGTTTAAGAAAAAG 59.454 37.037 0.00 0.00 0.00 2.27
952 957 6.723977 AGGCACCCATCTATTGTTTAAGAAAA 59.276 34.615 0.00 0.00 0.00 2.29
953 958 6.252995 AGGCACCCATCTATTGTTTAAGAAA 58.747 36.000 0.00 0.00 0.00 2.52
954 959 5.826643 AGGCACCCATCTATTGTTTAAGAA 58.173 37.500 0.00 0.00 0.00 2.52
955 960 5.450818 AGGCACCCATCTATTGTTTAAGA 57.549 39.130 0.00 0.00 0.00 2.10
994 1000 9.875691 GCAGAGGACATGAATATATACACATAA 57.124 33.333 0.00 0.00 0.00 1.90
1019 1025 4.083802 GCGTTGTGAAGGAATAGGATATGC 60.084 45.833 0.00 0.00 0.00 3.14
1030 1036 1.317613 ATGCTTTGCGTTGTGAAGGA 58.682 45.000 0.00 0.00 0.00 3.36
1032 1038 3.266541 TGTATGCTTTGCGTTGTGAAG 57.733 42.857 0.00 0.00 0.00 3.02
1041 1047 2.829741 TTGGGGTTTGTATGCTTTGC 57.170 45.000 0.00 0.00 0.00 3.68
1046 1052 2.890945 AGACACTTTGGGGTTTGTATGC 59.109 45.455 0.00 0.00 0.00 3.14
1298 1304 6.585695 ACAGGAGAAGTCGACTTAATTGTA 57.414 37.500 29.79 0.00 36.11 2.41
1341 1466 5.244755 TGTGCAAACTACATCATCTTGCTA 58.755 37.500 6.64 0.00 42.24 3.49
1411 1537 5.864418 TGACACTACCTACATTATGGGAC 57.136 43.478 0.00 0.00 31.84 4.46
1442 1568 6.392625 TCTCCCTTCGTCTCATAATGTAAG 57.607 41.667 0.00 0.00 0.00 2.34
1512 1640 3.539604 AGGATGCTGCTTGTTCTGATAC 58.460 45.455 0.00 0.00 0.00 2.24
1513 1641 3.920231 AGGATGCTGCTTGTTCTGATA 57.080 42.857 0.00 0.00 0.00 2.15
1533 1661 1.195115 CCTCCTTGCTGGCTGTACTA 58.805 55.000 0.00 0.00 35.26 1.82
1567 1695 9.517609 CTTGTTATAGTTGTCTGAGGTACATAC 57.482 37.037 0.00 0.00 0.00 2.39
1619 1747 8.225603 ACATACCAAGTTTTATCACCATCATC 57.774 34.615 0.00 0.00 0.00 2.92
1741 1869 5.209659 AGCAGCCTATACTACTTGTAGGTT 58.790 41.667 11.82 2.38 37.80 3.50
1746 1874 6.978674 TCATTAGCAGCCTATACTACTTGT 57.021 37.500 0.00 0.00 0.00 3.16
1777 1905 8.958119 TTAACTCGATATAGAAAAACTGCCAT 57.042 30.769 0.00 0.00 0.00 4.40
1803 2196 3.957497 TGACACAAGGCAACCTTTGTAAT 59.043 39.130 11.55 1.83 41.69 1.89
1813 2206 2.885135 ATCCAGATGACACAAGGCAA 57.115 45.000 0.00 0.00 0.00 4.52
1814 2207 4.201657 CAATATCCAGATGACACAAGGCA 58.798 43.478 0.00 0.00 0.00 4.75
1871 2319 7.166473 GCAGCAATTAACAATAGCTTGTCATAC 59.834 37.037 0.00 0.00 44.83 2.39
2017 2808 9.662545 CAAAAGGCTTTGTTATTGTTTTTATGG 57.337 29.630 14.19 0.00 37.69 2.74
2059 2994 1.424493 GCTCATGCCTCCGTTTCGAG 61.424 60.000 0.00 0.00 0.00 4.04
2062 2997 1.135575 CAAAGCTCATGCCTCCGTTTC 60.136 52.381 0.00 0.00 40.80 2.78
2090 3025 7.957992 TTGTAACAAAAACTTCCCTCCTTAA 57.042 32.000 0.00 0.00 0.00 1.85
2138 3077 9.945904 AGTTAAAGTTTAATCTTGGGAGAGTAG 57.054 33.333 11.12 0.00 34.32 2.57
2145 3084 8.556194 GCCAAAAAGTTAAAGTTTAATCTTGGG 58.444 33.333 24.18 20.87 0.00 4.12
2164 3103 0.179034 GCCACAATGGGTGCCAAAAA 60.179 50.000 0.00 0.00 46.50 1.94
2179 3906 2.047939 GGCCATGCTTTGTGCCAC 60.048 61.111 0.00 0.00 39.87 5.01
2184 3911 2.154567 ATGATGAGGCCATGCTTTGT 57.845 45.000 5.01 0.00 32.09 2.83
2185 3912 4.659111 TTAATGATGAGGCCATGCTTTG 57.341 40.909 5.01 0.00 32.09 2.77
2186 3913 5.881923 AATTAATGATGAGGCCATGCTTT 57.118 34.783 5.01 0.00 32.09 3.51
2187 3914 6.517864 GCTTAATTAATGATGAGGCCATGCTT 60.518 38.462 5.01 0.00 32.09 3.91
2188 3915 5.047519 GCTTAATTAATGATGAGGCCATGCT 60.048 40.000 5.01 0.00 32.09 3.79
2189 3916 5.047519 AGCTTAATTAATGATGAGGCCATGC 60.048 40.000 5.01 0.00 32.09 4.06
2190 3917 6.585695 AGCTTAATTAATGATGAGGCCATG 57.414 37.500 5.01 0.00 32.09 3.66
2191 3918 8.710749 TTAAGCTTAATTAATGATGAGGCCAT 57.289 30.769 14.96 0.00 35.29 4.40
2192 3919 8.532186 TTTAAGCTTAATTAATGATGAGGCCA 57.468 30.769 19.27 0.00 0.00 5.36
2202 3929 9.719355 CCACCAAACCTTTTAAGCTTAATTAAT 57.281 29.630 19.27 4.05 0.00 1.40
2211 3938 2.364002 TCTGCCACCAAACCTTTTAAGC 59.636 45.455 0.00 0.00 0.00 3.09
2230 3957 1.683707 TCCATCACAGGAGCGCTCT 60.684 57.895 34.46 19.07 32.77 4.09
2563 4814 2.576191 CCCTCTGGTCCATTTTACTCCA 59.424 50.000 0.00 0.00 0.00 3.86
2662 4925 8.989131 TCCTTGTTATTTAGTGCTAGGAACTAT 58.011 33.333 0.00 0.00 41.70 2.12
2666 4929 7.494625 CGAATCCTTGTTATTTAGTGCTAGGAA 59.505 37.037 0.00 0.00 36.70 3.36
2710 4973 7.335673 TGCCTAAAATATTCGTGTCTTGAATGA 59.664 33.333 0.00 0.00 36.74 2.57
2819 5086 8.978539 ACACATACATGATAAATTAGTAGTGCG 58.021 33.333 0.00 0.00 0.00 5.34
2854 5121 4.517453 GGACTGAGCGAGTATAGAGAATGT 59.483 45.833 0.00 0.00 33.83 2.71
2869 5136 9.929180 AAAAAGATTTAAATTTAGGGACTGAGC 57.071 29.630 1.43 0.00 41.52 4.26
2943 5210 6.754675 GGAGCAAAGTAAGTGAATCTACTCTC 59.245 42.308 0.00 0.00 0.00 3.20
2960 5227 3.520290 TGGACTACATACGGAGCAAAG 57.480 47.619 0.00 0.00 0.00 2.77
2994 5261 9.003658 CCTCTGTTCACAAATATAAGTCTTTGT 57.996 33.333 0.00 0.00 44.23 2.83
3010 5277 6.308566 AGGATATAGTACTCCCTCTGTTCAC 58.691 44.000 0.00 0.00 31.49 3.18
3011 5278 6.532119 AGGATATAGTACTCCCTCTGTTCA 57.468 41.667 0.00 0.00 31.49 3.18
3015 5282 5.044772 TGGCTAGGATATAGTACTCCCTCTG 60.045 48.000 0.00 1.35 31.49 3.35
3016 5283 5.109479 TGGCTAGGATATAGTACTCCCTCT 58.891 45.833 0.00 0.00 31.49 3.69
3017 5284 5.453866 TGGCTAGGATATAGTACTCCCTC 57.546 47.826 0.00 0.00 31.49 4.30
3026 5293 3.735208 CGCGGTGAATGGCTAGGATATAG 60.735 52.174 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.