Multiple sequence alignment - TraesCS7B01G123300

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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 TraesCS7B01G123300 chr7B 100.000 2762 0 0 1 2762 144658855 144661616 0.000000e+00 5101
1 TraesCS7B01G123300 chr7A 91.467 2215 142 34 1 2187 182613415 182615610 0.000000e+00 3000
2 TraesCS7B01G123300 chr7A 87.854 601 34 16 2183 2762 182615637 182616219 0.000000e+00 669
3 TraesCS7B01G123300 chr7D 90.278 2119 154 34 1 2099 178606327 178608413 0.000000e+00 2724
4 TraesCS7B01G123300 chr7D 89.983 599 39 7 2183 2762 178608553 178609149 0.000000e+00 754
5 TraesCS7B01G123300 chr7D 91.892 74 5 1 2114 2187 178608456 178608528 4.870000e-18 102


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 TraesCS7B01G123300 chr7B 144658855 144661616 2761 False 5101.000000 5101 100.000000 1 2762 1 chr7B.!!$F1 2761
1 TraesCS7B01G123300 chr7A 182613415 182616219 2804 False 1834.500000 3000 89.660500 1 2762 2 chr7A.!!$F1 2761
2 TraesCS7B01G123300 chr7D 178606327 178609149 2822 False 1193.333333 2724 90.717667 1 2762 3 chr7D.!!$F1 2761

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
260 262 0.257328 TGGTGTTCTCCCAAGCACAA 59.743 50.000 0.00 0.00 30.26 3.33 F
1113 1121 1.592131 GAGGCGAGAGATGCTGCAG 60.592 63.158 10.11 10.11 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1357 1371 0.033366 ACCGCAAGTTGGATTTTGCC 59.967 50.0 4.75 0.00 45.17 4.52 R
2432 2525 0.666374 TGTGAGAAGTCTTCGCGTGA 59.334 50.0 5.77 2.87 31.63 4.35 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
128 130 1.665599 GAAAAAGTCGGCCCGTCGA 60.666 57.895 1.63 0.00 36.76 4.20
217 219 1.261619 CAGACTCACACTTTTCGGTGC 59.738 52.381 0.00 0.00 40.52 5.01
248 250 2.301870 TGACTAGGTGGACATGGTGTTC 59.698 50.000 0.00 0.00 0.00 3.18
256 258 1.168714 GACATGGTGTTCTCCCAAGC 58.831 55.000 0.00 0.00 35.14 4.01
260 262 0.257328 TGGTGTTCTCCCAAGCACAA 59.743 50.000 0.00 0.00 30.26 3.33
264 266 3.763897 GGTGTTCTCCCAAGCACAATTAT 59.236 43.478 0.00 0.00 30.26 1.28
265 267 4.947388 GGTGTTCTCCCAAGCACAATTATA 59.053 41.667 0.00 0.00 30.26 0.98
334 336 8.020819 GGAGATTAGAGTTCTCATCTTACATCG 58.979 40.741 7.15 0.00 41.16 3.84
338 340 4.160439 AGAGTTCTCATCTTACATCGCCAA 59.840 41.667 2.64 0.00 0.00 4.52
339 341 5.028549 AGTTCTCATCTTACATCGCCAAT 57.971 39.130 0.00 0.00 0.00 3.16
340 342 4.813161 AGTTCTCATCTTACATCGCCAATG 59.187 41.667 0.00 0.00 41.48 2.82
346 348 6.321717 TCATCTTACATCGCCAATGTTTTTC 58.678 36.000 4.84 0.00 46.73 2.29
347 349 5.957842 TCTTACATCGCCAATGTTTTTCT 57.042 34.783 4.84 0.00 46.73 2.52
355 357 3.064545 CGCCAATGTTTTTCTTTTTGCCA 59.935 39.130 0.00 0.00 0.00 4.92
373 375 3.505680 TGCCAAAGTACATGTCCAATGAC 59.494 43.478 0.00 0.00 42.12 3.06
410 412 6.038050 GGAGAGAATGAATGCTTTTGGTAGAG 59.962 42.308 0.00 0.00 0.00 2.43
528 533 7.807977 TCAGATCAAACTTTTTAGCTCAAGT 57.192 32.000 0.00 0.00 34.58 3.16
531 536 8.993121 CAGATCAAACTTTTTAGCTCAAGTCTA 58.007 33.333 6.38 0.00 31.79 2.59
550 555 7.487822 AGTCTAATGGATATGTGGAGTATGG 57.512 40.000 0.00 0.00 0.00 2.74
580 585 2.375173 ACTTTAGGCGTTAGGTTCCG 57.625 50.000 0.00 0.00 0.00 4.30
584 589 4.478371 GGCGTTAGGTTCCGGGGG 62.478 72.222 0.00 0.00 0.00 5.40
596 601 3.702048 CGGGGGTGCCGAGAAGAA 61.702 66.667 0.00 0.00 0.00 2.52
598 603 1.682451 CGGGGGTGCCGAGAAGAATA 61.682 60.000 0.00 0.00 0.00 1.75
666 671 8.869109 TGAACAATCCAAAACAATAAGATTCCT 58.131 29.630 0.00 0.00 0.00 3.36
746 751 7.834881 TCATCCTTCTTATACACGATAACCT 57.165 36.000 0.00 0.00 0.00 3.50
769 774 6.239430 CCTGATAGAGGCTTTCAACAGCTATA 60.239 42.308 0.00 0.00 39.97 1.31
774 780 5.986135 AGAGGCTTTCAACAGCTATATTACG 59.014 40.000 0.00 0.00 39.97 3.18
785 791 9.318041 CAACAGCTATATTACGCATATTTGTTC 57.682 33.333 0.00 0.00 30.74 3.18
830 836 7.633193 ATCTATATATCACGAGGTCCAAGAC 57.367 40.000 0.00 0.00 0.00 3.01
906 914 5.813672 TGCGTGGTTTAATAGTTATGTCCTC 59.186 40.000 0.00 0.00 0.00 3.71
940 948 8.955061 AGTTTTCTGAATGTAATCATTTGACG 57.045 30.769 0.00 0.00 43.33 4.35
947 955 7.742151 TGAATGTAATCATTTGACGACTGAAG 58.258 34.615 0.00 0.00 43.33 3.02
988 996 4.483476 AAAGGCGTCTTTATGTTGTGAC 57.517 40.909 14.51 0.00 41.06 3.67
1113 1121 1.592131 GAGGCGAGAGATGCTGCAG 60.592 63.158 10.11 10.11 0.00 4.41
1172 1180 2.353406 GGCTGCATCAGTTCTTTGCAAT 60.353 45.455 0.00 0.00 44.99 3.56
1173 1181 3.119388 GGCTGCATCAGTTCTTTGCAATA 60.119 43.478 0.00 0.00 44.99 1.90
1174 1182 4.487948 GCTGCATCAGTTCTTTGCAATAA 58.512 39.130 0.00 0.00 44.99 1.40
1175 1183 4.925054 GCTGCATCAGTTCTTTGCAATAAA 59.075 37.500 0.00 0.00 44.99 1.40
1177 1185 6.753279 GCTGCATCAGTTCTTTGCAATAAATA 59.247 34.615 0.00 0.00 44.99 1.40
1178 1186 7.043590 GCTGCATCAGTTCTTTGCAATAAATAG 60.044 37.037 0.00 0.00 44.99 1.73
1179 1187 8.054152 TGCATCAGTTCTTTGCAATAAATAGA 57.946 30.769 0.00 0.00 42.95 1.98
1225 1239 5.286082 GCACTTTACACGCCAAATTTCATAG 59.714 40.000 0.00 0.00 0.00 2.23
1233 1247 7.524065 ACACGCCAAATTTCATAGTAGTAAAC 58.476 34.615 0.00 0.00 0.00 2.01
1236 1250 9.439500 ACGCCAAATTTCATAGTAGTAAACTTA 57.561 29.630 0.00 0.00 39.80 2.24
1246 1260 9.158233 TCATAGTAGTAAACTTACATTGTTGCC 57.842 33.333 0.00 0.00 39.80 4.52
1254 1268 9.632807 GTAAACTTACATTGTTGCCAATTATGA 57.367 29.630 8.24 0.00 39.28 2.15
1357 1371 0.905357 AGCAGCTAGTACTTGGGGTG 59.095 55.000 0.00 9.09 0.00 4.61
1377 1391 2.715737 GCAAAATCCAACTTGCGGTA 57.284 45.000 0.00 0.00 38.66 4.02
1396 1411 6.439375 TGCGGTAAGGTCTATATACCATGAAT 59.561 38.462 9.75 0.00 42.40 2.57
1397 1412 6.979238 GCGGTAAGGTCTATATACCATGAATC 59.021 42.308 9.75 0.00 42.40 2.52
1401 1416 9.319143 GTAAGGTCTATATACCATGAATCATGC 57.681 37.037 17.27 0.96 42.40 4.06
1410 1425 3.704566 ACCATGAATCATGCAAATCAGCT 59.295 39.130 17.27 0.00 40.20 4.24
1433 1448 7.391833 AGCTGGATTTTACCTACTTTTCTTCAG 59.608 37.037 0.00 0.00 0.00 3.02
1434 1449 7.448748 TGGATTTTACCTACTTTTCTTCAGC 57.551 36.000 0.00 0.00 0.00 4.26
1439 1454 3.149981 ACCTACTTTTCTTCAGCTTGCC 58.850 45.455 0.00 0.00 0.00 4.52
1442 1457 4.219288 CCTACTTTTCTTCAGCTTGCCAAT 59.781 41.667 0.00 0.00 0.00 3.16
1449 1466 9.837525 CTTTTCTTCAGCTTGCCAATATATATC 57.162 33.333 0.00 0.00 0.00 1.63
1488 1505 3.214328 GCACAGGAAGTTGAAGAAAGGA 58.786 45.455 0.00 0.00 0.00 3.36
1566 1583 3.995199 TGTCTGTGATGACAAGGAAGTC 58.005 45.455 0.00 0.00 43.08 3.01
1593 1610 1.506718 GACGACTGCTGATCCGACA 59.493 57.895 0.00 0.00 0.00 4.35
1670 1687 2.221169 GCCATCATCTACGCCAAATCA 58.779 47.619 0.00 0.00 0.00 2.57
1672 1689 3.205338 CCATCATCTACGCCAAATCACA 58.795 45.455 0.00 0.00 0.00 3.58
1770 1787 2.681848 CCTGTCATCCTGATTGCTGTTC 59.318 50.000 0.00 0.00 0.00 3.18
1810 1827 2.549064 ATGCTGTATGCGCCATCTTA 57.451 45.000 4.18 0.00 46.63 2.10
1979 1997 9.906660 TTATTTTGTAATGAAGCCTTGTACTTG 57.093 29.630 0.00 0.00 0.00 3.16
1984 2002 4.708726 ATGAAGCCTTGTACTTGATTGC 57.291 40.909 0.00 0.00 0.00 3.56
2000 2018 1.825090 TTGCAGTGGTTATGGAGCTG 58.175 50.000 0.00 0.00 0.00 4.24
2040 2058 2.933906 GCAATTGGAAACATGCAGATGG 59.066 45.455 7.72 0.00 40.54 3.51
2042 2060 4.571919 CAATTGGAAACATGCAGATGGTT 58.428 39.130 0.00 0.00 42.53 3.67
2083 2101 9.129209 GTCTTAAGACTTCATAAACATTTTGCC 57.871 33.333 25.30 0.00 41.65 4.52
2099 2117 2.212812 TGCCCAACATGCATAACTGA 57.787 45.000 0.00 0.00 32.85 3.41
2100 2118 2.737544 TGCCCAACATGCATAACTGAT 58.262 42.857 0.00 0.00 32.85 2.90
2112 2158 7.279536 ACATGCATAACTGATCAAGTAGAAGTG 59.720 37.037 0.00 0.00 38.56 3.16
2143 2189 9.467258 CCAATCAATTAGTAGCATAATTGTTGG 57.533 33.333 24.54 24.54 46.34 3.77
2225 2301 6.270927 AGCTGACATACACATGATTACCCTAT 59.729 38.462 0.00 0.00 35.96 2.57
2228 2304 9.342308 CTGACATACACATGATTACCCTATTTT 57.658 33.333 0.00 0.00 35.96 1.82
2305 2397 0.956633 AGTGTGAGCAACAGCAATGG 59.043 50.000 0.00 0.00 40.26 3.16
2332 2425 5.014202 AGCAGGTAAAAACACCGGATAATT 58.986 37.500 9.46 0.00 43.84 1.40
2338 2431 4.428615 AAAACACCGGATAATTCCAACG 57.571 40.909 9.46 0.00 42.74 4.10
2351 2444 0.821711 TCCAACGAAACAAGGCCCTG 60.822 55.000 0.00 0.00 0.00 4.45
2418 2511 6.002062 GCATAAGCTGTTACAAAACTGAGT 57.998 37.500 0.00 0.00 36.85 3.41
2432 2525 7.491682 ACAAAACTGAGTTTAATTCTGCACAT 58.508 30.769 11.43 0.00 34.43 3.21
2434 2527 6.882610 AACTGAGTTTAATTCTGCACATCA 57.117 33.333 0.00 0.00 0.00 3.07
2436 2529 5.106948 ACTGAGTTTAATTCTGCACATCACG 60.107 40.000 0.00 0.00 0.00 4.35
2443 2536 1.008875 TCTGCACATCACGCGAAGAC 61.009 55.000 15.93 0.00 0.00 3.01
2473 2569 6.358030 CACAAAGATTAGCGACTTCAAAACTG 59.642 38.462 0.00 0.00 0.00 3.16
2478 2574 0.310854 GCGACTTCAAAACTGGTGGG 59.689 55.000 0.00 0.00 0.00 4.61
2518 2614 6.241207 ACATCCAATTCGTTCACTACAAAG 57.759 37.500 0.00 0.00 0.00 2.77
2575 2671 3.177487 CGACTCATCTGTCAGACACATG 58.823 50.000 11.59 11.59 36.82 3.21
2752 2851 2.685388 TGTAGTCTGCCTCTCAATCTCG 59.315 50.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.335583 CGCCTTTGAAAGTTCCAATCATACA 60.336 40.000 4.02 0.00 0.00 2.29
72 73 0.908198 AAGCTCTGAACCCCTAGCAG 59.092 55.000 0.00 0.00 37.44 4.24
128 130 0.177604 CTTCCTCGATTGCAGCTCCT 59.822 55.000 0.00 0.00 0.00 3.69
217 219 8.307483 CCATGTCCACCTAGTCAGTATAATTAG 58.693 40.741 0.00 0.00 0.00 1.73
248 250 7.581213 TTAACCATATAATTGTGCTTGGGAG 57.419 36.000 0.00 0.00 0.00 4.30
283 285 9.010029 CCTTTTAAGCAAGAACCTGATAACTAA 57.990 33.333 0.00 0.00 0.00 2.24
287 289 7.458397 TCTCCTTTTAAGCAAGAACCTGATAA 58.542 34.615 0.00 0.00 0.00 1.75
334 336 4.629251 TGGCAAAAAGAAAAACATTGGC 57.371 36.364 0.00 0.00 44.14 4.52
338 340 7.913674 TGTACTTTGGCAAAAAGAAAAACAT 57.086 28.000 14.43 0.00 0.00 2.71
339 341 7.389053 ACATGTACTTTGGCAAAAAGAAAAACA 59.611 29.630 14.43 10.17 0.00 2.83
340 342 7.747888 ACATGTACTTTGGCAAAAAGAAAAAC 58.252 30.769 14.43 5.34 0.00 2.43
346 348 4.942852 TGGACATGTACTTTGGCAAAAAG 58.057 39.130 14.43 5.73 0.00 2.27
347 349 5.344743 TTGGACATGTACTTTGGCAAAAA 57.655 34.783 14.43 2.33 0.00 1.94
373 375 4.645535 TCATTCTCTCCCTTTTGTGACTG 58.354 43.478 0.00 0.00 0.00 3.51
376 378 4.460382 GCATTCATTCTCTCCCTTTTGTGA 59.540 41.667 0.00 0.00 0.00 3.58
410 412 4.201861 GCACTATGCCTTTTCTCTACAAGC 60.202 45.833 0.00 0.00 37.42 4.01
528 533 6.669591 CCTCCATACTCCACATATCCATTAGA 59.330 42.308 0.00 0.00 0.00 2.10
531 536 5.415065 TCCTCCATACTCCACATATCCATT 58.585 41.667 0.00 0.00 0.00 3.16
533 538 4.485653 TCCTCCATACTCCACATATCCA 57.514 45.455 0.00 0.00 0.00 3.41
534 539 4.383552 GCATCCTCCATACTCCACATATCC 60.384 50.000 0.00 0.00 0.00 2.59
580 585 0.106894 CTATTCTTCTCGGCACCCCC 59.893 60.000 0.00 0.00 0.00 5.40
584 589 1.841450 CGTCCTATTCTTCTCGGCAC 58.159 55.000 0.00 0.00 0.00 5.01
590 595 3.961408 ACTGGTATGCGTCCTATTCTTCT 59.039 43.478 0.00 0.00 0.00 2.85
592 597 3.961408 AGACTGGTATGCGTCCTATTCTT 59.039 43.478 0.00 0.00 0.00 2.52
596 601 2.887783 CAGAGACTGGTATGCGTCCTAT 59.112 50.000 0.00 0.00 0.00 2.57
598 603 1.107114 CAGAGACTGGTATGCGTCCT 58.893 55.000 0.00 0.00 0.00 3.85
704 709 6.991064 AGGATGAAGCTATATATCTCCCTCA 58.009 40.000 0.00 0.00 0.00 3.86
705 710 7.784550 AGAAGGATGAAGCTATATATCTCCCTC 59.215 40.741 0.00 0.00 0.00 4.30
706 711 7.661126 AGAAGGATGAAGCTATATATCTCCCT 58.339 38.462 0.00 0.00 0.00 4.20
746 751 3.988976 AGCTGTTGAAAGCCTCTATCA 57.011 42.857 0.00 0.00 44.68 2.15
769 774 7.074507 TGGTTTACGAACAAATATGCGTAAT 57.925 32.000 0.00 0.00 45.09 1.89
774 780 7.219344 GGTGTAATGGTTTACGAACAAATATGC 59.781 37.037 0.00 0.00 40.55 3.14
882 890 5.736813 AGGACATAACTATTAAACCACGCA 58.263 37.500 0.00 0.00 0.00 5.24
884 892 7.837202 TTGAGGACATAACTATTAAACCACG 57.163 36.000 0.00 0.00 0.00 4.94
940 948 7.195839 ACTAAATCTTTGTTGCTCTTCAGTC 57.804 36.000 0.00 0.00 0.00 3.51
947 955 7.148967 CGCCTTTTAACTAAATCTTTGTTGCTC 60.149 37.037 0.00 0.00 0.00 4.26
988 996 1.441738 TGCCACATGTGTCAGATTCG 58.558 50.000 23.79 7.52 0.00 3.34
1113 1121 2.095718 GCGACAGTGGTCCAGAAATTTC 60.096 50.000 10.33 10.33 41.13 2.17
1185 1193 9.524106 GTGTAAAGTGCAGTAGGTTTTTAATTT 57.476 29.630 0.00 0.00 0.00 1.82
1186 1194 7.858879 CGTGTAAAGTGCAGTAGGTTTTTAATT 59.141 33.333 0.00 0.00 0.00 1.40
1187 1195 7.357303 CGTGTAAAGTGCAGTAGGTTTTTAAT 58.643 34.615 0.00 0.00 0.00 1.40
1189 1197 5.277442 GCGTGTAAAGTGCAGTAGGTTTTTA 60.277 40.000 0.00 0.00 0.00 1.52
1190 1198 4.496840 GCGTGTAAAGTGCAGTAGGTTTTT 60.497 41.667 0.00 0.00 0.00 1.94
1191 1199 3.002965 GCGTGTAAAGTGCAGTAGGTTTT 59.997 43.478 0.00 0.00 0.00 2.43
1192 1200 2.546789 GCGTGTAAAGTGCAGTAGGTTT 59.453 45.455 0.00 0.00 0.00 3.27
1193 1201 2.140717 GCGTGTAAAGTGCAGTAGGTT 58.859 47.619 0.00 0.00 0.00 3.50
1194 1202 1.607251 GGCGTGTAAAGTGCAGTAGGT 60.607 52.381 0.00 0.00 0.00 3.08
1196 1204 1.790755 TGGCGTGTAAAGTGCAGTAG 58.209 50.000 0.00 0.00 0.00 2.57
1198 1206 1.384525 TTTGGCGTGTAAAGTGCAGT 58.615 45.000 0.00 0.00 0.00 4.40
1199 1207 2.704725 ATTTGGCGTGTAAAGTGCAG 57.295 45.000 0.00 0.00 0.00 4.41
1203 1211 6.569179 ACTATGAAATTTGGCGTGTAAAGT 57.431 33.333 0.00 0.00 0.00 2.66
1204 1212 7.748847 ACTACTATGAAATTTGGCGTGTAAAG 58.251 34.615 0.00 0.00 0.00 1.85
1205 1213 7.675962 ACTACTATGAAATTTGGCGTGTAAA 57.324 32.000 0.00 0.00 0.00 2.01
1207 1215 8.658609 GTTTACTACTATGAAATTTGGCGTGTA 58.341 33.333 0.00 0.00 0.00 2.90
1208 1216 7.389607 AGTTTACTACTATGAAATTTGGCGTGT 59.610 33.333 0.00 0.00 34.56 4.49
1241 1255 5.971202 CGTTAACCTGATCATAATTGGCAAC 59.029 40.000 0.00 1.48 0.00 4.17
1246 1260 6.822073 TCGACGTTAACCTGATCATAATTG 57.178 37.500 0.00 0.00 0.00 2.32
1254 1268 3.587797 ACACATCGACGTTAACCTGAT 57.412 42.857 0.00 0.00 0.00 2.90
1300 1314 0.245266 TAAGTTCAGCGACCGCATCA 59.755 50.000 16.97 0.00 44.88 3.07
1357 1371 0.033366 ACCGCAAGTTGGATTTTGCC 59.967 50.000 4.75 0.00 45.17 4.52
1377 1391 7.921304 TGCATGATTCATGGTATATAGACCTT 58.079 34.615 24.29 8.51 41.64 3.50
1410 1425 7.231467 AGCTGAAGAAAAGTAGGTAAAATCCA 58.769 34.615 0.00 0.00 0.00 3.41
1417 1432 4.202419 TGGCAAGCTGAAGAAAAGTAGGTA 60.202 41.667 0.00 0.00 0.00 3.08
1419 1434 3.149196 TGGCAAGCTGAAGAAAAGTAGG 58.851 45.455 0.00 0.00 0.00 3.18
1423 1438 9.837525 GATATATATTGGCAAGCTGAAGAAAAG 57.162 33.333 5.96 0.00 0.00 2.27
1449 1466 5.512788 CCTGTGCGCATTCAAAATTAAGTAG 59.487 40.000 15.91 0.00 0.00 2.57
1466 1483 2.031682 CCTTTCTTCAACTTCCTGTGCG 60.032 50.000 0.00 0.00 0.00 5.34
1467 1484 3.214328 TCCTTTCTTCAACTTCCTGTGC 58.786 45.455 0.00 0.00 0.00 4.57
1488 1505 5.804639 TGTATCTGTCCTGCTATTGTGTTT 58.195 37.500 0.00 0.00 0.00 2.83
1593 1610 1.482365 GGGGAAGGTGAAAATGGTGGT 60.482 52.381 0.00 0.00 0.00 4.16
1670 1687 4.760530 TCAACTGCCTCTATGCTATTGT 57.239 40.909 0.00 0.00 32.28 2.71
1672 1689 4.649692 CCATCAACTGCCTCTATGCTATT 58.350 43.478 0.00 0.00 0.00 1.73
1743 1760 2.777536 TCAGGATGACAGGCACCTT 58.222 52.632 0.00 0.00 42.56 3.50
1770 1787 1.202687 TCCAGCTGTGAAAGTGACTGG 60.203 52.381 13.81 0.00 44.87 4.00
1810 1827 9.660180 TTTTAATCACAAACTTTTTGCTACCTT 57.340 25.926 0.00 0.00 0.00 3.50
1867 1885 8.821686 TTATCTCATTTGTACACCATGGATTT 57.178 30.769 21.47 4.11 0.00 2.17
1868 1886 9.425248 AATTATCTCATTTGTACACCATGGATT 57.575 29.630 21.47 6.94 0.00 3.01
1979 1997 2.357009 CAGCTCCATAACCACTGCAATC 59.643 50.000 0.00 0.00 0.00 2.67
1984 2002 1.674441 CATGCAGCTCCATAACCACTG 59.326 52.381 0.00 0.00 0.00 3.66
2033 2051 2.357009 CAGGTGCATCTAAACCATCTGC 59.643 50.000 0.00 0.00 39.05 4.26
2040 2058 3.059352 AGACCACAGGTGCATCTAAAC 57.941 47.619 0.00 0.00 35.25 2.01
2042 2060 4.530553 TCTTAAGACCACAGGTGCATCTAA 59.469 41.667 0.00 0.00 35.25 2.10
2083 2101 5.571784 ACTTGATCAGTTATGCATGTTGG 57.428 39.130 10.16 0.00 27.32 3.77
2099 2117 5.189736 TGATTGGCTACCACTTCTACTTGAT 59.810 40.000 0.00 0.00 30.78 2.57
2100 2118 4.530553 TGATTGGCTACCACTTCTACTTGA 59.469 41.667 0.00 0.00 30.78 3.02
2112 2158 7.979444 TTATGCTACTAATTGATTGGCTACC 57.021 36.000 0.00 0.00 0.00 3.18
2187 2263 1.021390 GTCAGCTTGCACTACGGCAT 61.021 55.000 0.00 0.00 44.48 4.40
2228 2304 8.621532 AGTCTTGCTGAAATACTGTTTGATTA 57.378 30.769 0.00 0.00 0.00 1.75
2238 2314 3.994392 TCCGACAAGTCTTGCTGAAATAC 59.006 43.478 12.66 0.00 0.00 1.89
2281 2373 1.202675 TGCTGTTGCTCACACTGATGA 60.203 47.619 0.00 0.00 40.48 2.92
2305 2397 1.601914 CGGTGTTTTTACCTGCTTGGC 60.602 52.381 0.00 0.00 38.62 4.52
2332 2425 0.821711 CAGGGCCTTGTTTCGTTGGA 60.822 55.000 1.32 0.00 0.00 3.53
2338 2431 1.886542 CACCTTACAGGGCCTTGTTTC 59.113 52.381 27.05 0.00 40.58 2.78
2351 2444 2.742589 GTCAGCAACTAAGGCACCTTAC 59.257 50.000 5.00 0.00 37.47 2.34
2405 2498 8.462811 TGTGCAGAATTAAACTCAGTTTTGTAA 58.537 29.630 8.41 0.00 37.01 2.41
2418 2511 2.739379 TCGCGTGATGTGCAGAATTAAA 59.261 40.909 5.77 0.00 0.00 1.52
2432 2525 0.666374 TGTGAGAAGTCTTCGCGTGA 59.334 50.000 5.77 2.87 31.63 4.35
2434 2527 2.128035 CTTTGTGAGAAGTCTTCGCGT 58.872 47.619 5.77 0.00 31.63 6.01
2436 2529 4.999751 AATCTTTGTGAGAAGTCTTCGC 57.000 40.909 9.21 9.21 38.06 4.70
2443 2536 5.635280 TGAAGTCGCTAATCTTTGTGAGAAG 59.365 40.000 0.00 0.00 38.06 2.85
2473 2569 7.189079 TGTTTCAAATTTATATTCCCCCACC 57.811 36.000 0.00 0.00 0.00 4.61
2518 2614 4.214119 TGTGTCTGTCAAGCTATTTTCTGC 59.786 41.667 0.00 0.00 0.00 4.26
2575 2671 1.200020 AGTTGTAGGCTTTTCGCATGC 59.800 47.619 7.91 7.91 41.67 4.06


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

AutoCloner maintained by Alex Coulton.