Multiple sequence alignment - TraesCS5B01G504500

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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 TraesCS5B01G504500 chr5B 100.000 2408 0 0 1 2408 670688987 670691394 0 4447
1 TraesCS5B01G504500 chr5A 89.120 1443 149 7 1 1437 708964121 708962681 0 1788
2 TraesCS5B01G504500 chr5A 87.914 1448 163 9 1 1438 659381860 659383305 0 1694
3 TraesCS5B01G504500 chr3B 88.835 1442 153 7 1 1436 791881189 791882628 0 1764
4 TraesCS5B01G504500 chr3B 88.089 1444 164 7 1 1438 61903575 61902134 0 1707
5 TraesCS5B01G504500 chr6B 88.789 1445 153 8 1 1438 224858286 224859728 0 1762
6 TraesCS5B01G504500 chr1B 88.313 1446 157 11 1 1438 25166072 25164631 0 1724
7 TraesCS5B01G504500 chr1B 88.174 1446 158 12 1 1438 25205472 25204032 0 1711
8 TraesCS5B01G504500 chr1B 88.089 1444 164 7 1 1438 25128973 25127532 0 1707
9 TraesCS5B01G504500 chr1A 87.862 1450 161 9 1 1438 560302623 560301177 0 1688
10 TraesCS5B01G504500 chr5D 85.569 984 92 20 1437 2408 531407575 531408520 0 985
11 TraesCS5B01G504500 chr4A 86.801 841 88 12 1549 2380 641006823 641005997 0 917


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 TraesCS5B01G504500 chr5B 670688987 670691394 2407 False 4447 4447 100.000 1 2408 1 chr5B.!!$F1 2407
1 TraesCS5B01G504500 chr5A 708962681 708964121 1440 True 1788 1788 89.120 1 1437 1 chr5A.!!$R1 1436
2 TraesCS5B01G504500 chr5A 659381860 659383305 1445 False 1694 1694 87.914 1 1438 1 chr5A.!!$F1 1437
3 TraesCS5B01G504500 chr3B 791881189 791882628 1439 False 1764 1764 88.835 1 1436 1 chr3B.!!$F1 1435
4 TraesCS5B01G504500 chr3B 61902134 61903575 1441 True 1707 1707 88.089 1 1438 1 chr3B.!!$R1 1437
5 TraesCS5B01G504500 chr6B 224858286 224859728 1442 False 1762 1762 88.789 1 1438 1 chr6B.!!$F1 1437
6 TraesCS5B01G504500 chr1B 25164631 25166072 1441 True 1724 1724 88.313 1 1438 1 chr1B.!!$R2 1437
7 TraesCS5B01G504500 chr1B 25204032 25205472 1440 True 1711 1711 88.174 1 1438 1 chr1B.!!$R3 1437
8 TraesCS5B01G504500 chr1B 25127532 25128973 1441 True 1707 1707 88.089 1 1438 1 chr1B.!!$R1 1437
9 TraesCS5B01G504500 chr1A 560301177 560302623 1446 True 1688 1688 87.862 1 1438 1 chr1A.!!$R1 1437
10 TraesCS5B01G504500 chr5D 531407575 531408520 945 False 985 985 85.569 1437 2408 1 chr5D.!!$F1 971
11 TraesCS5B01G504500 chr4A 641005997 641006823 826 True 917 917 86.801 1549 2380 1 chr4A.!!$R1 831

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
365 368 0.036022 GAAGCACTTCCACAGGCTCT 59.964 55.0 0.0 0.0 35.11 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 2254 0.106419 TCCAAATATCCGTTGGGCCC 60.106 55.0 17.59 17.59 44.82 5.8 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
33 35 3.744660 TCTTGAACTCTTGAAGAAGGGC 58.255 45.455 0.00 0.00 32.12 5.19
34 36 3.392616 TCTTGAACTCTTGAAGAAGGGCT 59.607 43.478 0.00 0.00 32.12 5.19
37 39 2.575805 ACTCTTGAAGAAGGGCTTGG 57.424 50.000 0.00 0.00 36.83 3.61
48 50 1.742308 AGGGCTTGGTTTGGAGAGTA 58.258 50.000 0.00 0.00 0.00 2.59
62 64 2.427812 GGAGAGTAGGGAACGGAAGAAG 59.572 54.545 0.00 0.00 0.00 2.85
69 71 3.624777 AGGGAACGGAAGAAGTATACGA 58.375 45.455 0.00 0.00 0.00 3.43
72 74 4.349501 GGAACGGAAGAAGTATACGAGTG 58.650 47.826 0.00 0.00 0.00 3.51
78 80 1.404391 AGAAGTATACGAGTGTGGCGG 59.596 52.381 0.00 0.00 0.00 6.13
83 85 1.945354 ATACGAGTGTGGCGGGACAG 61.945 60.000 0.00 0.00 0.00 3.51
84 86 3.680786 CGAGTGTGGCGGGACAGA 61.681 66.667 0.00 0.00 0.00 3.41
90 92 1.227674 GTGGCGGGACAGATGGATC 60.228 63.158 0.00 0.00 0.00 3.36
114 116 3.391626 CCAGACCCTTCTCCTATAAACCC 59.608 52.174 0.00 0.00 0.00 4.11
144 146 0.693049 AAGGGAGGTGCAGAATTCGT 59.307 50.000 0.00 0.00 0.00 3.85
151 153 1.136057 GGTGCAGAATTCGTTTCGTCC 60.136 52.381 0.00 0.00 39.46 4.79
163 165 2.031157 CGTTTCGTCCCAGATTTGCTTT 60.031 45.455 0.00 0.00 0.00 3.51
170 173 4.082571 CGTCCCAGATTTGCTTTTGAGAAT 60.083 41.667 0.00 0.00 0.00 2.40
189 192 0.541764 TGGTTCATGGAAGGTTGGCC 60.542 55.000 0.00 0.00 0.00 5.36
192 195 0.899717 TTCATGGAAGGTTGGCCTGC 60.900 55.000 3.32 0.00 46.33 4.85
215 218 3.806941 GGGATACTTCATGCCTGCA 57.193 52.632 0.00 0.00 41.83 4.41
231 234 3.877559 CCTGCAGATGTTGTGGAGATTA 58.122 45.455 17.39 0.00 35.49 1.75
236 239 5.587443 TGCAGATGTTGTGGAGATTATGAAG 59.413 40.000 0.00 0.00 0.00 3.02
244 247 4.971282 TGTGGAGATTATGAAGATCAGGGT 59.029 41.667 0.00 0.00 0.00 4.34
274 277 5.407407 AGACAAGAGAATGATACGTTGGT 57.593 39.130 0.00 0.00 0.00 3.67
295 298 2.524148 GGGCCCTGGCAAGTTTGT 60.524 61.111 17.04 0.00 44.11 2.83
308 311 3.242936 GCAAGTTTGTCGCCTTTTCAGTA 60.243 43.478 0.00 0.00 0.00 2.74
356 359 2.550180 GGAAACTCACAGAAGCACTTCC 59.450 50.000 6.77 0.00 40.33 3.46
359 362 1.486310 ACTCACAGAAGCACTTCCACA 59.514 47.619 6.77 0.00 40.33 4.17
365 368 0.036022 GAAGCACTTCCACAGGCTCT 59.964 55.000 0.00 0.00 35.11 4.09
368 371 0.610687 GCACTTCCACAGGCTCTAGT 59.389 55.000 0.00 0.00 0.00 2.57
402 405 1.949257 CGTTGGGACTGCTGGAAAC 59.051 57.895 0.00 0.00 0.00 2.78
435 438 2.982488 ACTGATGTTCCTCCCTCAGTTT 59.018 45.455 0.00 0.00 44.39 2.66
470 473 0.533032 GGGTCGCTACAAGCTCTCTT 59.467 55.000 0.00 0.00 39.60 2.85
496 499 7.692539 TCCTACATGGAGCAACAAGCATATAAT 60.693 37.037 0.00 0.00 41.01 1.28
532 535 3.132646 AGTGATTTGTGCCATGTGTGTTT 59.867 39.130 0.00 0.00 0.00 2.83
581 586 1.959226 GTCGCTGCACCCTTTCGAA 60.959 57.895 0.00 0.00 0.00 3.71
595 600 4.081087 CCCTTTCGAAAGTTCTCTGGGATA 60.081 45.833 30.51 0.00 34.34 2.59
597 602 3.777465 TCGAAAGTTCTCTGGGATACG 57.223 47.619 0.00 0.00 37.60 3.06
603 608 1.048601 TTCTCTGGGATACGATGGCC 58.951 55.000 0.00 0.00 37.60 5.36
608 613 1.668151 GGGATACGATGGCCGAAGC 60.668 63.158 0.00 0.00 41.76 3.86
619 624 0.678048 GGCCGAAGCATGGACTCTTT 60.678 55.000 0.00 0.00 42.56 2.52
656 661 1.403780 GCAGAATACGGGTGTCGAGTT 60.404 52.381 0.00 0.00 42.43 3.01
658 663 1.203994 AGAATACGGGTGTCGAGTTGG 59.796 52.381 0.00 0.00 42.43 3.77
666 671 1.153269 TGTCGAGTTGGTGCTGCAA 60.153 52.632 2.77 0.00 0.00 4.08
668 673 1.146041 TCGAGTTGGTGCTGCAAGT 59.854 52.632 2.77 0.00 35.30 3.16
696 701 1.146637 CTCTGCCAGATATTGAGCGC 58.853 55.000 0.00 0.00 0.00 5.92
713 718 1.780806 CGCTCGATGCTTCTCATGAT 58.219 50.000 0.00 0.00 40.11 2.45
714 719 1.456165 CGCTCGATGCTTCTCATGATG 59.544 52.381 0.00 0.00 40.11 3.07
715 720 1.194997 GCTCGATGCTTCTCATGATGC 59.805 52.381 0.00 2.11 41.84 3.91
717 722 3.860002 GCTCGATGCTTCTCATGATGCTA 60.860 47.826 13.90 4.53 41.96 3.49
730 735 2.044806 GATGCTATGGAGGGCGTGGT 62.045 60.000 0.00 0.00 0.00 4.16
738 743 1.386525 GGAGGGCGTGGTACATACGA 61.387 60.000 21.36 0.00 44.52 3.43
744 749 3.128349 GGCGTGGTACATACGAAATGAT 58.872 45.455 21.36 0.00 44.52 2.45
770 775 4.134563 GTCCATAATAAATCACCGCCACT 58.865 43.478 0.00 0.00 0.00 4.00
805 810 3.119101 TCGAAGGTTCTTGATGAGCTACC 60.119 47.826 0.00 0.00 32.84 3.18
812 817 5.163301 GGTTCTTGATGAGCTACCTGGATTA 60.163 44.000 0.00 0.00 31.11 1.75
822 827 6.558775 TGAGCTACCTGGATTATCTAATTGGT 59.441 38.462 0.00 0.00 32.78 3.67
824 829 8.506196 AGCTACCTGGATTATCTAATTGGTAA 57.494 34.615 0.00 0.00 32.04 2.85
839 844 9.627123 TCTAATTGGTAATAAAACTGATCTGGG 57.373 33.333 4.49 0.00 0.00 4.45
862 867 2.747799 GCTGATCCTAGCAAAGGGAAGG 60.748 54.545 5.38 0.00 46.55 3.46
870 875 2.105766 AGCAAAGGGAAGGCAATCATC 58.894 47.619 0.00 0.00 0.00 2.92
877 882 5.070823 AGGGAAGGCAATCATCACATATT 57.929 39.130 0.00 0.00 0.00 1.28
889 894 3.819564 TCACATATTCTCCAGTTCGGG 57.180 47.619 0.00 0.00 34.36 5.14
898 903 2.741985 CAGTTCGGGCACATGCGA 60.742 61.111 0.00 0.00 43.26 5.10
899 904 2.434884 AGTTCGGGCACATGCGAG 60.435 61.111 0.00 0.00 43.26 5.03
900 905 2.742372 GTTCGGGCACATGCGAGT 60.742 61.111 0.00 0.00 43.26 4.18
913 918 1.029681 TGCGAGTATGGTCGTAGCAT 58.970 50.000 0.00 5.21 42.17 3.79
915 920 2.817844 TGCGAGTATGGTCGTAGCATAT 59.182 45.455 9.06 1.83 40.22 1.78
926 931 3.319972 GTCGTAGCATATCCCAAGTGGTA 59.680 47.826 0.00 0.00 34.77 3.25
932 937 3.329386 CATATCCCAAGTGGTATGCTCG 58.671 50.000 0.00 0.00 34.77 5.03
952 957 2.283298 GTAAGCCCGGTTAGGTTAAGC 58.717 52.381 0.00 0.00 38.74 3.09
987 998 5.221682 TGGTTCATTTGCTGTTGATGGATTT 60.222 36.000 0.00 0.00 0.00 2.17
989 1000 5.471556 TCATTTGCTGTTGATGGATTTGT 57.528 34.783 0.00 0.00 0.00 2.83
1022 1033 2.696707 TGGTGTTAAGAGACGACAAGGT 59.303 45.455 0.00 0.00 0.00 3.50
1025 1036 4.022503 GGTGTTAAGAGACGACAAGGTAGT 60.023 45.833 0.00 0.00 0.00 2.73
1044 1059 7.496747 AGGTAGTTATCATCTTCTCTTCTTGC 58.503 38.462 0.00 0.00 0.00 4.01
1056 1071 4.256920 TCTCTTCTTGCAGGCAGTTATTC 58.743 43.478 0.00 0.00 0.00 1.75
1062 1077 3.423539 TGCAGGCAGTTATTCTCTTGT 57.576 42.857 0.00 0.00 0.00 3.16
1074 1089 0.247460 TCTCTTGTCGGGATGCACTG 59.753 55.000 0.00 0.00 0.00 3.66
1089 1104 2.424601 TGCACTGGAAGCTGAATTATGC 59.575 45.455 0.00 0.00 37.60 3.14
1149 1164 2.949451 AGTTACCAGTGCAGATCGAG 57.051 50.000 0.00 0.00 0.00 4.04
1203 1218 2.626840 GCTTCAGAGGTTGACAGATCC 58.373 52.381 0.00 0.00 34.94 3.36
1206 1221 2.248248 TCAGAGGTTGACAGATCCGTT 58.752 47.619 0.00 0.00 0.00 4.44
1209 1224 3.927142 CAGAGGTTGACAGATCCGTTTAC 59.073 47.826 0.00 0.00 0.00 2.01
1214 1229 3.928727 TGACAGATCCGTTTACTCGTT 57.071 42.857 0.00 0.00 0.00 3.85
1225 1240 4.492570 CCGTTTACTCGTTCATCATCAAGC 60.493 45.833 0.00 0.00 0.00 4.01
1227 1242 5.220472 CGTTTACTCGTTCATCATCAAGCAT 60.220 40.000 0.00 0.00 0.00 3.79
1322 1337 5.012328 AGCTTAGCTAAGTTTGCTCGTAT 57.988 39.130 29.42 2.51 41.46 3.06
1324 1339 6.570692 AGCTTAGCTAAGTTTGCTCGTATTA 58.429 36.000 29.42 0.00 41.46 0.98
1356 1371 4.278419 ACCATGACTTTGTTAGGTTCTTGC 59.722 41.667 0.00 0.00 0.00 4.01
1366 1381 0.178891 AGGTTCTTGCCCTCCTGAGA 60.179 55.000 0.00 0.00 0.00 3.27
1377 1392 2.289945 CCCTCCTGAGACTTTGGAACTG 60.290 54.545 0.00 0.00 0.00 3.16
1379 1394 2.370189 CTCCTGAGACTTTGGAACTGGT 59.630 50.000 0.00 0.00 0.00 4.00
1399 1414 5.380900 TGGTTGTGATTGATTGTAAGGACA 58.619 37.500 0.00 0.00 0.00 4.02
1402 1417 7.667635 TGGTTGTGATTGATTGTAAGGACATTA 59.332 33.333 0.00 0.00 34.86 1.90
1404 1419 7.864108 TGTGATTGATTGTAAGGACATTAGG 57.136 36.000 0.00 0.00 34.86 2.69
1405 1420 7.402054 TGTGATTGATTGTAAGGACATTAGGT 58.598 34.615 0.00 0.00 34.86 3.08
1458 1475 2.430610 TTGCTGTGGTTGGGTTGGC 61.431 57.895 0.00 0.00 0.00 4.52
1460 1477 2.430610 GCTGTGGTTGGGTTGGCAA 61.431 57.895 0.00 0.00 0.00 4.52
1479 1496 3.677601 CAAATGATGCAGTCACGACATC 58.322 45.455 6.23 6.23 40.28 3.06
1528 1546 3.485394 TCTAGGCAAAGTTGTGCATCAA 58.515 40.909 10.72 0.00 46.81 2.57
1535 1553 4.984161 GCAAAGTTGTGCATCAATAGTTGT 59.016 37.500 0.00 0.00 44.29 3.32
1536 1554 5.117592 GCAAAGTTGTGCATCAATAGTTGTC 59.882 40.000 0.00 0.00 44.29 3.18
1539 1557 5.065914 AGTTGTGCATCAATAGTTGTCAGT 58.934 37.500 0.00 0.00 38.38 3.41
1611 1629 2.863704 GCCAGATTGTGCACCTTGTTTC 60.864 50.000 15.69 2.26 0.00 2.78
1613 1631 1.001378 AGATTGTGCACCTTGTTTCGC 60.001 47.619 15.69 0.00 0.00 4.70
1737 1756 6.086241 CCGTATTCGAACAATGTTCACAAAAG 59.914 38.462 23.72 11.41 39.71 2.27
1747 1766 7.719483 ACAATGTTCACAAAAGAGTTCATGAT 58.281 30.769 0.00 0.00 0.00 2.45
1935 1955 1.742411 CGGAGTGTGTCAACCAGTGTT 60.742 52.381 0.00 0.00 34.14 3.32
2000 2036 5.070446 ACAAGTGGTCGTGATATCATACCAT 59.930 40.000 30.39 20.12 42.63 3.55
2044 2080 3.181461 GGCACCTTATGAGAGCACTGTAT 60.181 47.826 0.00 0.00 0.00 2.29
2065 2101 2.203538 ACCTGGCTGCTTGGTTGG 60.204 61.111 10.37 2.56 0.00 3.77
2068 2104 1.073722 CTGGCTGCTTGGTTGGAGA 59.926 57.895 0.00 0.00 0.00 3.71
2083 2119 6.942976 TGGTTGGAGAAACGAGAAGTTATAT 58.057 36.000 0.00 0.00 43.37 0.86
2084 2120 8.070034 TGGTTGGAGAAACGAGAAGTTATATA 57.930 34.615 0.00 0.00 43.37 0.86
2148 2184 1.039856 AAAACAGGCGGACAAGCAAT 58.960 45.000 0.00 0.00 39.27 3.56
2155 2191 2.324330 CGGACAAGCAATGCACGGA 61.324 57.895 8.35 0.00 0.00 4.69
2165 2201 2.223340 GCAATGCACGGATCGAGAATTT 60.223 45.455 0.00 0.00 0.00 1.82
2181 2217 4.589908 AGAATTTGAGGTGGGTGATGTAC 58.410 43.478 0.00 0.00 0.00 2.90
2218 2254 2.991250 ACCGTTCATCCAATCTTCAGG 58.009 47.619 0.00 0.00 0.00 3.86
2225 2261 1.145900 TCCAATCTTCAGGGGCCCAA 61.146 55.000 27.72 10.61 0.00 4.12
2234 2270 0.106217 CAGGGGCCCAACGGATATTT 60.106 55.000 27.72 0.00 0.00 1.40
2243 2279 4.397420 CCCAACGGATATTTGGATCATCA 58.603 43.478 6.27 0.00 45.69 3.07
2247 2283 3.066380 CGGATATTTGGATCATCACGCA 58.934 45.455 0.00 0.00 0.00 5.24
2254 2290 1.516386 GATCATCACGCACGTCGGT 60.516 57.895 11.13 0.00 43.86 4.69
2262 2298 2.858158 GCACGTCGGTAAAGTGGC 59.142 61.111 0.00 0.00 37.77 5.01
2265 2301 1.662446 ACGTCGGTAAAGTGGCGTG 60.662 57.895 0.00 0.00 0.00 5.34
2318 2354 1.183030 TTCGGTGGTCCACGTCTCAT 61.183 55.000 15.93 0.00 34.83 2.90
2319 2355 0.322726 TCGGTGGTCCACGTCTCATA 60.323 55.000 15.93 0.00 34.83 2.15
2320 2356 0.744874 CGGTGGTCCACGTCTCATAT 59.255 55.000 15.93 0.00 34.83 1.78
2321 2357 1.951602 CGGTGGTCCACGTCTCATATA 59.048 52.381 15.93 0.00 34.83 0.86
2322 2358 2.031069 CGGTGGTCCACGTCTCATATAG 60.031 54.545 15.93 0.00 34.83 1.31
2323 2359 2.957006 GGTGGTCCACGTCTCATATAGT 59.043 50.000 15.93 0.00 34.83 2.12
2324 2360 3.004524 GGTGGTCCACGTCTCATATAGTC 59.995 52.174 15.93 0.00 34.83 2.59
2325 2361 3.630769 GTGGTCCACGTCTCATATAGTCA 59.369 47.826 6.18 0.00 0.00 3.41
2326 2362 4.278669 GTGGTCCACGTCTCATATAGTCAT 59.721 45.833 6.18 0.00 0.00 3.06
2338 2374 8.405531 GTCTCATATAGTCATATCTCAAGAGGC 58.594 40.741 0.00 0.00 0.00 4.70
2357 2393 1.419922 CGATTGGCGTTGAGGTTCG 59.580 57.895 0.00 0.00 34.64 3.95
2370 2406 0.473117 AGGTTCGGGTGGAGAAGGAA 60.473 55.000 0.00 0.00 0.00 3.36
2395 2431 5.207110 ACCTCCAGATAACAAGATCATCG 57.793 43.478 0.00 0.00 0.00 3.84
2396 2432 4.039730 ACCTCCAGATAACAAGATCATCGG 59.960 45.833 0.00 0.00 0.00 4.18
2400 2436 5.245977 TCCAGATAACAAGATCATCGGCATA 59.754 40.000 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.042684 AGCCCTTCTTCAAGAGTTCAAGAT 59.957 41.667 0.00 0.00 0.00 2.40
33 35 3.676093 GTTCCCTACTCTCCAAACCAAG 58.324 50.000 0.00 0.00 0.00 3.61
34 36 2.038033 CGTTCCCTACTCTCCAAACCAA 59.962 50.000 0.00 0.00 0.00 3.67
37 39 1.897802 TCCGTTCCCTACTCTCCAAAC 59.102 52.381 0.00 0.00 0.00 2.93
48 50 3.624777 TCGTATACTTCTTCCGTTCCCT 58.375 45.455 0.56 0.00 0.00 4.20
62 64 0.248784 GTCCCGCCACACTCGTATAC 60.249 60.000 0.00 0.00 0.00 1.47
69 71 2.665000 CATCTGTCCCGCCACACT 59.335 61.111 0.00 0.00 0.00 3.55
72 74 1.227674 GATCCATCTGTCCCGCCAC 60.228 63.158 0.00 0.00 0.00 5.01
78 80 0.761802 GTCTGGGGATCCATCTGTCC 59.238 60.000 15.23 4.70 43.11 4.02
83 85 0.767998 GAAGGGTCTGGGGATCCATC 59.232 60.000 15.23 5.71 44.96 3.51
84 86 0.348370 AGAAGGGTCTGGGGATCCAT 59.652 55.000 15.23 0.00 44.96 3.41
90 92 3.346146 TTATAGGAGAAGGGTCTGGGG 57.654 52.381 0.00 0.00 32.80 4.96
144 146 3.634448 TCAAAAGCAAATCTGGGACGAAA 59.366 39.130 0.00 0.00 0.00 3.46
151 153 5.143376 ACCATTCTCAAAAGCAAATCTGG 57.857 39.130 0.00 0.00 0.00 3.86
163 165 4.387026 ACCTTCCATGAACCATTCTCAA 57.613 40.909 0.00 0.00 0.00 3.02
170 173 0.541764 GGCCAACCTTCCATGAACCA 60.542 55.000 0.00 0.00 0.00 3.67
189 192 3.397482 GCATGAAGTATCCCTGTAGCAG 58.603 50.000 0.00 0.00 0.00 4.24
192 195 3.805108 GCAGGCATGAAGTATCCCTGTAG 60.805 52.174 0.62 0.00 43.80 2.74
199 202 3.474600 ACATCTGCAGGCATGAAGTATC 58.525 45.455 19.28 0.00 33.25 2.24
202 205 1.816835 CAACATCTGCAGGCATGAAGT 59.183 47.619 19.28 0.00 33.25 3.01
206 209 0.172578 CCACAACATCTGCAGGCATG 59.827 55.000 15.13 13.63 0.00 4.06
212 215 5.101648 TCATAATCTCCACAACATCTGCA 57.898 39.130 0.00 0.00 0.00 4.41
215 218 7.799081 TGATCTTCATAATCTCCACAACATCT 58.201 34.615 0.00 0.00 0.00 2.90
231 234 0.179000 GGCGACACCCTGATCTTCAT 59.821 55.000 0.00 0.00 0.00 2.57
236 239 0.741221 GTCTTGGCGACACCCTGATC 60.741 60.000 0.00 0.00 42.67 2.92
261 264 1.953311 GCCCCACACCAACGTATCATT 60.953 52.381 0.00 0.00 0.00 2.57
295 298 2.870435 GCACTCCTTACTGAAAAGGCGA 60.870 50.000 9.42 0.00 44.89 5.54
308 311 0.038526 CGAACTGGTACGCACTCCTT 60.039 55.000 0.00 0.00 0.00 3.36
329 332 9.225513 GAAGTGCTTCTGTGAGTTTCCTCAAAA 62.226 40.741 4.80 0.00 41.42 2.44
339 342 1.486310 TGTGGAAGTGCTTCTGTGAGT 59.514 47.619 11.18 0.00 39.45 3.41
356 359 1.402984 GGACGTGAACTAGAGCCTGTG 60.403 57.143 0.00 0.00 0.00 3.66
359 362 1.178276 CTGGACGTGAACTAGAGCCT 58.822 55.000 0.00 0.00 0.00 4.58
365 368 0.535335 GCCCATCTGGACGTGAACTA 59.465 55.000 0.00 0.00 37.39 2.24
368 371 2.107041 AACGCCCATCTGGACGTGAA 62.107 55.000 11.37 0.00 43.10 3.18
402 405 6.090483 AGGAACATCAGTCGACCATATAAG 57.910 41.667 13.01 0.00 0.00 1.73
470 473 1.350684 TGCTTGTTGCTCCATGTAGGA 59.649 47.619 0.00 0.00 45.91 2.94
482 485 8.345565 GTTTCCAGTCCTATTATATGCTTGTTG 58.654 37.037 0.00 0.00 0.00 3.33
496 499 6.464222 CACAAATCACTAGTTTCCAGTCCTA 58.536 40.000 0.00 0.00 0.00 2.94
500 503 3.821033 GGCACAAATCACTAGTTTCCAGT 59.179 43.478 0.00 0.00 0.00 4.00
581 586 2.103263 GCCATCGTATCCCAGAGAACTT 59.897 50.000 0.00 0.00 0.00 2.66
595 600 2.514592 CCATGCTTCGGCCATCGT 60.515 61.111 2.24 0.00 40.91 3.73
597 602 1.153086 AGTCCATGCTTCGGCCATC 60.153 57.895 2.24 0.00 40.91 3.51
603 608 4.691860 ATTTGAAAGAGTCCATGCTTCG 57.308 40.909 0.00 0.00 0.00 3.79
645 650 1.961277 CAGCACCAACTCGACACCC 60.961 63.158 0.00 0.00 0.00 4.61
666 671 1.696336 TCTGGCAGAGAAGCAAGAACT 59.304 47.619 14.43 0.00 41.49 3.01
668 673 4.767578 ATATCTGGCAGAGAAGCAAGAA 57.232 40.909 23.24 0.00 46.97 2.52
676 681 1.269988 GCGCTCAATATCTGGCAGAGA 60.270 52.381 23.24 19.32 34.25 3.10
696 701 2.756829 AGCATCATGAGAAGCATCGAG 58.243 47.619 16.74 0.00 40.78 4.04
713 718 1.382009 TACCACGCCCTCCATAGCA 60.382 57.895 0.00 0.00 0.00 3.49
714 719 1.069258 GTACCACGCCCTCCATAGC 59.931 63.158 0.00 0.00 0.00 2.97
715 720 1.048601 ATGTACCACGCCCTCCATAG 58.951 55.000 0.00 0.00 0.00 2.23
717 722 0.756903 GTATGTACCACGCCCTCCAT 59.243 55.000 0.00 0.00 0.00 3.41
744 749 6.205853 GTGGCGGTGATTTATTATGGACAATA 59.794 38.462 0.00 0.00 0.00 1.90
770 775 0.826715 CCTTCGAGAAGCCTCCATGA 59.173 55.000 7.30 0.00 37.11 3.07
822 827 6.061022 TCAGCACCCAGATCAGTTTTATTA 57.939 37.500 0.00 0.00 0.00 0.98
824 829 4.574674 TCAGCACCCAGATCAGTTTTAT 57.425 40.909 0.00 0.00 0.00 1.40
862 867 6.565435 CGAACTGGAGAATATGTGATGATTGC 60.565 42.308 0.00 0.00 0.00 3.56
870 875 2.213499 GCCCGAACTGGAGAATATGTG 58.787 52.381 0.00 0.00 42.00 3.21
877 882 1.296392 CATGTGCCCGAACTGGAGA 59.704 57.895 0.00 0.00 42.00 3.71
889 894 0.806102 ACGACCATACTCGCATGTGC 60.806 55.000 0.00 0.00 37.15 4.57
898 903 3.774734 TGGGATATGCTACGACCATACT 58.225 45.455 0.00 0.00 0.00 2.12
899 904 4.021368 ACTTGGGATATGCTACGACCATAC 60.021 45.833 0.00 0.00 0.00 2.39
900 905 4.021456 CACTTGGGATATGCTACGACCATA 60.021 45.833 0.00 0.00 0.00 2.74
913 918 2.394632 ACGAGCATACCACTTGGGATA 58.605 47.619 0.00 0.00 36.33 2.59
915 920 1.855295 TACGAGCATACCACTTGGGA 58.145 50.000 0.00 0.00 41.15 4.37
932 937 2.093288 AGCTTAACCTAACCGGGCTTAC 60.093 50.000 6.32 0.00 36.97 2.34
942 947 5.247564 ACCATCAGTACACAGCTTAACCTAA 59.752 40.000 0.00 0.00 0.00 2.69
952 957 4.456911 AGCAAATGAACCATCAGTACACAG 59.543 41.667 0.00 0.00 39.39 3.66
987 998 0.251121 ACACCATTCCGGCATCAACA 60.251 50.000 0.00 0.00 39.03 3.33
989 1000 2.498644 TAACACCATTCCGGCATCAA 57.501 45.000 0.00 0.00 39.03 2.57
1022 1033 7.495901 CCTGCAAGAAGAGAAGATGATAACTA 58.504 38.462 0.00 0.00 34.07 2.24
1025 1036 5.121811 GCCTGCAAGAAGAGAAGATGATAA 58.878 41.667 0.00 0.00 34.07 1.75
1044 1059 2.932614 CCGACAAGAGAATAACTGCCTG 59.067 50.000 0.00 0.00 0.00 4.85
1056 1071 0.742281 CCAGTGCATCCCGACAAGAG 60.742 60.000 0.00 0.00 0.00 2.85
1062 1077 2.268920 GCTTCCAGTGCATCCCGA 59.731 61.111 0.00 0.00 0.00 5.14
1074 1089 2.658285 CATGCGCATAATTCAGCTTCC 58.342 47.619 24.84 0.00 0.00 3.46
1089 1104 2.620115 AGATAAACCTTCCATGCATGCG 59.380 45.455 21.69 14.24 0.00 4.73
1129 1144 2.826128 TCTCGATCTGCACTGGTAACTT 59.174 45.455 0.00 0.00 37.61 2.66
1203 1218 4.091365 TGCTTGATGATGAACGAGTAAACG 59.909 41.667 0.00 0.00 39.31 3.60
1206 1221 9.196552 CTAATATGCTTGATGATGAACGAGTAA 57.803 33.333 0.00 0.00 0.00 2.24
1209 1224 7.880059 TCTAATATGCTTGATGATGAACGAG 57.120 36.000 0.00 0.00 0.00 4.18
1240 1255 9.701098 AGTAATACAATTTTCACGTAGAGACAA 57.299 29.630 0.00 0.00 0.00 3.18
1311 1326 5.292834 GGTTCTACCCTTAATACGAGCAAAC 59.707 44.000 0.00 0.00 30.04 2.93
1322 1337 6.195600 ACAAAGTCATGGTTCTACCCTTAA 57.804 37.500 0.00 0.00 37.50 1.85
1324 1339 4.724279 ACAAAGTCATGGTTCTACCCTT 57.276 40.909 0.00 0.00 37.50 3.95
1354 1369 0.473694 TCCAAAGTCTCAGGAGGGCA 60.474 55.000 0.00 0.00 0.00 5.36
1356 1371 1.981495 AGTTCCAAAGTCTCAGGAGGG 59.019 52.381 0.00 0.00 32.11 4.30
1366 1381 4.277476 TCAATCACAACCAGTTCCAAAGT 58.723 39.130 0.00 0.00 0.00 2.66
1377 1392 5.957842 TGTCCTTACAATCAATCACAACC 57.042 39.130 0.00 0.00 30.91 3.77
1379 1394 7.888021 ACCTAATGTCCTTACAATCAATCACAA 59.112 33.333 0.00 0.00 39.58 3.33
1405 1420 9.974980 TGCGTGTAGAAATTATATTACTCATCA 57.025 29.630 0.00 0.00 0.00 3.07
1444 1460 0.467384 CATTTGCCAACCCAACCACA 59.533 50.000 0.00 0.00 0.00 4.17
1458 1475 3.677601 GATGTCGTGACTGCATCATTTG 58.322 45.455 10.04 0.00 40.28 2.32
1460 1477 1.929169 CGATGTCGTGACTGCATCATT 59.071 47.619 13.64 0.00 40.28 2.57
1472 1489 2.433145 CAGCAGCACCGATGTCGT 60.433 61.111 0.00 0.00 37.74 4.34
1475 1492 0.250234 ATACACAGCAGCACCGATGT 59.750 50.000 0.00 0.00 0.00 3.06
1476 1493 0.654160 CATACACAGCAGCACCGATG 59.346 55.000 0.00 0.00 0.00 3.84
1477 1494 0.462581 CCATACACAGCAGCACCGAT 60.463 55.000 0.00 0.00 0.00 4.18
1479 1496 2.753966 GCCATACACAGCAGCACCG 61.754 63.158 0.00 0.00 0.00 4.94
1511 1529 4.178545 ACTATTGATGCACAACTTTGCC 57.821 40.909 0.00 0.00 42.25 4.52
1518 1536 5.062528 TCACTGACAACTATTGATGCACAA 58.937 37.500 0.00 0.00 42.95 3.33
1528 1546 3.804325 GCATGCGTATCACTGACAACTAT 59.196 43.478 0.00 0.00 0.00 2.12
1611 1629 6.496524 AAAAGAAATGAGAAAAACGAAGCG 57.503 33.333 0.00 0.00 0.00 4.68
1664 1682 6.037726 ACCTTTTGTTTTCGTTTTCGCTATT 58.962 32.000 0.00 0.00 43.73 1.73
1889 1909 0.865111 CGTCAGTTTGCGGATGACAA 59.135 50.000 9.39 0.00 42.76 3.18
1935 1955 2.093500 AGCAACGCAGATATGTCTCCAA 60.093 45.455 0.00 0.00 30.42 3.53
2020 2056 0.253044 GTGCTCTCATAAGGTGCCCA 59.747 55.000 0.00 0.00 0.00 5.36
2023 2059 2.393271 ACAGTGCTCTCATAAGGTGC 57.607 50.000 0.00 0.00 0.00 5.01
2044 2080 4.020617 CCAAGCAGCCAGGTCCGA 62.021 66.667 0.00 0.00 0.00 4.55
2065 2101 9.667989 GAGTTCCTATATAACTTCTCGTTTCTC 57.332 37.037 3.00 0.00 37.31 2.87
2068 2104 8.536340 AGGAGTTCCTATATAACTTCTCGTTT 57.464 34.615 0.00 0.00 46.48 3.60
2148 2184 2.270923 CTCAAATTCTCGATCCGTGCA 58.729 47.619 0.00 0.00 0.00 4.57
2155 2191 2.571653 TCACCCACCTCAAATTCTCGAT 59.428 45.455 0.00 0.00 0.00 3.59
2165 2201 2.832129 GAGAAGTACATCACCCACCTCA 59.168 50.000 0.31 0.00 0.00 3.86
2181 2217 1.732732 CGGTTGCAGTCGTAGGAGAAG 60.733 57.143 3.10 0.00 0.00 2.85
2218 2254 0.106419 TCCAAATATCCGTTGGGCCC 60.106 55.000 17.59 17.59 44.82 5.80
2225 2261 3.067106 GCGTGATGATCCAAATATCCGT 58.933 45.455 0.00 0.00 0.00 4.69
2234 2270 1.516169 CGACGTGCGTGATGATCCA 60.516 57.895 0.67 0.00 34.64 3.41
2243 2279 1.662446 CCACTTTACCGACGTGCGT 60.662 57.895 0.00 0.00 38.67 5.24
2247 2283 1.662446 CACGCCACTTTACCGACGT 60.662 57.895 0.00 0.00 0.00 4.34
2254 2290 1.234615 GGAGCTTGCACGCCACTTTA 61.235 55.000 12.13 0.00 0.00 1.85
2262 2298 1.294659 GAGGAGTTGGAGCTTGCACG 61.295 60.000 0.00 0.00 0.00 5.34
2265 2301 0.739112 CTCGAGGAGTTGGAGCTTGC 60.739 60.000 3.91 0.00 0.00 4.01
2318 2354 5.816682 TCGGCCTCTTGAGATATGACTATA 58.183 41.667 0.00 0.00 0.00 1.31
2319 2355 4.667573 TCGGCCTCTTGAGATATGACTAT 58.332 43.478 0.00 0.00 0.00 2.12
2320 2356 4.100279 TCGGCCTCTTGAGATATGACTA 57.900 45.455 0.00 0.00 0.00 2.59
2321 2357 2.950781 TCGGCCTCTTGAGATATGACT 58.049 47.619 0.00 0.00 0.00 3.41
2322 2358 3.951775 ATCGGCCTCTTGAGATATGAC 57.048 47.619 0.00 0.00 0.00 3.06
2323 2359 3.007290 CCAATCGGCCTCTTGAGATATGA 59.993 47.826 13.98 0.00 0.00 2.15
2324 2360 3.332919 CCAATCGGCCTCTTGAGATATG 58.667 50.000 13.98 4.36 0.00 1.78
2325 2361 3.692257 CCAATCGGCCTCTTGAGATAT 57.308 47.619 13.98 0.00 0.00 1.63
2338 2374 1.794222 GAACCTCAACGCCAATCGG 59.206 57.895 0.00 0.00 43.86 4.18
2347 2383 0.395312 TTCTCCACCCGAACCTCAAC 59.605 55.000 0.00 0.00 0.00 3.18
2357 2393 1.954035 AGGTAGTTCCTTCTCCACCC 58.046 55.000 0.00 0.00 45.67 4.61
2370 2406 6.015856 CGATGATCTTGTTATCTGGAGGTAGT 60.016 42.308 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.