Multiple sequence alignment - TraesCS1D01G045300

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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 TraesCS1D01G045300 chr1D 100.000 4181 0 0 1 4181 24622637 24618457 0.000000e+00 7721.0
1 TraesCS1D01G045300 chr1D 97.143 35 1 0 1838 1872 487895305 487895271 4.510000e-05 60.2
2 TraesCS1D01G045300 chrUn 93.027 3313 144 31 1 3255 117148686 117151969 0.000000e+00 4758.0
3 TraesCS1D01G045300 chrUn 86.713 143 4 2 3252 3388 117152229 117152362 1.210000e-30 145.0
4 TraesCS1D01G045300 chr5A 97.004 801 16 1 3386 4178 601197427 601198227 0.000000e+00 1339.0
5 TraesCS1D01G045300 chr5D 82.627 236 21 12 3419 3653 29900617 29900401 1.530000e-44 191.0
6 TraesCS1D01G045300 chr1B 85.714 133 16 2 3494 3624 18114012 18114143 2.030000e-28 137.0
7 TraesCS1D01G045300 chr6B 85.714 63 5 4 1813 1873 149480525 149480465 3.490000e-06 63.9
8 TraesCS1D01G045300 chr6A 93.023 43 2 1 1832 1873 91892818 91892776 1.260000e-05 62.1
9 TraesCS1D01G045300 chr4A 97.143 35 1 0 1838 1872 729079874 729079840 4.510000e-05 60.2


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 TraesCS1D01G045300 chr1D 24618457 24622637 4180 True 7721.0 7721 100.000 1 4181 1 chr1D.!!$R1 4180
1 TraesCS1D01G045300 chrUn 117148686 117152362 3676 False 2451.5 4758 89.870 1 3388 2 chrUn.!!$F1 3387
2 TraesCS1D01G045300 chr5A 601197427 601198227 800 False 1339.0 1339 97.004 3386 4178 1 chr5A.!!$F1 792

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
108 109 0.732538 GTTTGATTGCCGGGCTTTCG 60.733 55.0 21.46 0.0 0.00 3.46 F
989 1020 0.833287 ATTGCTATGGTCGGCACTCT 59.167 50.0 0.00 0.0 38.23 3.24 F
2523 2580 0.321653 AGCTGACCAAACTAAGGGCG 60.322 55.0 0.00 0.0 36.77 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1276 0.312416 TCGTTTGTTTGGGGAATGCG 59.688 50.0 0.00 0.0 0.00 4.73 R
2889 2946 0.250124 CACAACTCTGGCGTTGGGTA 60.250 55.0 8.33 0.0 46.47 3.69 R
3632 3958 0.033228 GGCGGAGAGGATGATCTGTG 59.967 60.0 0.00 0.0 0.00 3.66 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 4.003648 GGAGGTGTACAACAAGATCCAAG 58.996 47.826 14.58 0.00 30.76 3.61
108 109 0.732538 GTTTGATTGCCGGGCTTTCG 60.733 55.000 21.46 0.00 0.00 3.46
113 114 3.894547 TTGCCGGGCTTTCGTCTCC 62.895 63.158 21.46 0.00 0.00 3.71
146 147 4.287067 ACTCCTGACATCAAGAGGCTTTTA 59.713 41.667 11.31 0.00 38.43 1.52
215 216 1.203441 TGTGGGATCTGGAGCAGCTT 61.203 55.000 0.00 0.00 0.00 3.74
310 316 8.868522 TCTAATTCTGTCTCAAATGGTTTCAT 57.131 30.769 0.00 0.00 34.56 2.57
344 350 3.503363 GGCAATCAATATTGATCGAGCCA 59.497 43.478 35.48 14.54 46.60 4.75
351 361 5.698089 TCAATATTGATCGAGCCAGAACATC 59.302 40.000 14.23 0.00 31.01 3.06
358 368 2.565391 TCGAGCCAGAACATCCTTACAA 59.435 45.455 0.00 0.00 0.00 2.41
362 372 5.106157 CGAGCCAGAACATCCTTACAATTTT 60.106 40.000 0.00 0.00 0.00 1.82
386 396 2.862541 TCCATCCCATAAATTCTGCCG 58.137 47.619 0.00 0.00 0.00 5.69
387 397 2.174639 TCCATCCCATAAATTCTGCCGT 59.825 45.455 0.00 0.00 0.00 5.68
431 443 4.814234 TGATGCACCGTATTAATCTGGAAC 59.186 41.667 11.72 5.02 0.00 3.62
453 465 8.272866 GGAACGTATTTTCCAAATCTTGTTTTG 58.727 33.333 0.00 0.00 44.14 2.44
496 508 8.379457 AGTTCTGACTCTAATTTTGTTGGTAC 57.621 34.615 0.00 0.00 0.00 3.34
497 509 7.990886 AGTTCTGACTCTAATTTTGTTGGTACA 59.009 33.333 0.00 0.00 0.00 2.90
498 510 8.784043 GTTCTGACTCTAATTTTGTTGGTACAT 58.216 33.333 0.00 0.00 39.30 2.29
499 511 8.918202 TCTGACTCTAATTTTGTTGGTACATT 57.082 30.769 0.00 0.00 39.30 2.71
578 601 3.758755 TCATCATGTATCTCACTGCCC 57.241 47.619 0.00 0.00 0.00 5.36
598 621 4.263331 GCCCTATTTCTGATATTTCCCCGA 60.263 45.833 0.00 0.00 0.00 5.14
609 632 1.060729 TTTCCCCGAACATCACCTCA 58.939 50.000 0.00 0.00 0.00 3.86
610 633 1.285280 TTCCCCGAACATCACCTCAT 58.715 50.000 0.00 0.00 0.00 2.90
643 666 3.347216 CTTGACCCCTTCACCACTAATG 58.653 50.000 0.00 0.00 32.26 1.90
672 695 6.500041 AGCTCATTTAAACGTTGCTTTAACA 58.500 32.000 0.00 0.00 39.30 2.41
673 696 6.975772 AGCTCATTTAAACGTTGCTTTAACAA 59.024 30.769 0.00 0.00 39.30 2.83
744 767 2.874701 CCTGCAGATTATGGTGTACAGC 59.125 50.000 17.39 18.10 0.00 4.40
835 858 2.226330 TGTACATGTGGCACTTTGGTC 58.774 47.619 19.83 12.96 0.00 4.02
841 868 1.528076 TGGCACTTTGGTCGCATGT 60.528 52.632 0.00 0.00 0.00 3.21
847 874 1.081892 CTTTGGTCGCATGTGGAGAG 58.918 55.000 6.39 0.00 0.00 3.20
861 888 6.519043 GCATGTGGAGAGAAGCCTATATGTTA 60.519 42.308 0.00 0.00 0.00 2.41
862 889 7.619050 CATGTGGAGAGAAGCCTATATGTTAT 58.381 38.462 0.00 0.00 0.00 1.89
863 890 7.618019 TGTGGAGAGAAGCCTATATGTTATT 57.382 36.000 0.00 0.00 0.00 1.40
864 891 7.671302 TGTGGAGAGAAGCCTATATGTTATTC 58.329 38.462 0.00 0.00 0.00 1.75
865 892 7.290014 TGTGGAGAGAAGCCTATATGTTATTCA 59.710 37.037 0.00 0.00 0.00 2.57
866 893 7.816995 GTGGAGAGAAGCCTATATGTTATTCAG 59.183 40.741 0.00 0.00 0.00 3.02
867 894 7.730332 TGGAGAGAAGCCTATATGTTATTCAGA 59.270 37.037 0.00 0.00 0.00 3.27
868 895 8.032451 GGAGAGAAGCCTATATGTTATTCAGAC 58.968 40.741 0.00 0.00 0.00 3.51
869 896 7.902087 AGAGAAGCCTATATGTTATTCAGACC 58.098 38.462 0.00 0.00 0.00 3.85
870 897 7.510685 AGAGAAGCCTATATGTTATTCAGACCA 59.489 37.037 0.00 0.00 0.00 4.02
871 898 7.445945 AGAAGCCTATATGTTATTCAGACCAC 58.554 38.462 0.00 0.00 0.00 4.16
879 906 8.723942 ATATGTTATTCAGACCACTTCAGAAC 57.276 34.615 0.00 0.00 32.94 3.01
883 910 2.838736 TCAGACCACTTCAGAACAAGC 58.161 47.619 0.00 0.00 0.00 4.01
902 929 6.392354 ACAAGCAATGTTCATGTGATTAAGG 58.608 36.000 0.00 0.00 40.06 2.69
903 930 6.015180 ACAAGCAATGTTCATGTGATTAAGGT 60.015 34.615 0.00 0.00 40.06 3.50
905 932 7.088589 AGCAATGTTCATGTGATTAAGGTAC 57.911 36.000 0.00 0.00 0.00 3.34
917 948 7.544622 TGTGATTAAGGTACTCTCACATGTAC 58.455 38.462 0.00 0.00 42.84 2.90
919 950 6.376299 TGATTAAGGTACTCTCACATGTACGT 59.624 38.462 0.00 0.00 38.49 3.57
926 957 7.441760 AGGTACTCTCACATGTACGTAGATTAG 59.558 40.741 1.83 1.87 39.70 1.73
929 960 7.695820 ACTCTCACATGTACGTAGATTAGAAC 58.304 38.462 1.83 0.00 0.00 3.01
949 980 7.526142 AGAACTTAGTATCAACACAGAGACA 57.474 36.000 0.00 0.00 32.35 3.41
955 986 9.254133 CTTAGTATCAACACAGAGACATTATGG 57.746 37.037 0.00 0.00 32.35 2.74
979 1010 5.473504 GGTGTAGTTCCCATTATTGCTATGG 59.526 44.000 0.00 0.00 41.83 2.74
983 1014 3.417069 TCCCATTATTGCTATGGTCGG 57.583 47.619 0.00 0.00 40.80 4.79
984 1015 1.812571 CCCATTATTGCTATGGTCGGC 59.187 52.381 0.00 0.00 40.80 5.54
989 1020 0.833287 ATTGCTATGGTCGGCACTCT 59.167 50.000 0.00 0.00 38.23 3.24
997 1028 2.244695 TGGTCGGCACTCTCTCTTTTA 58.755 47.619 0.00 0.00 0.00 1.52
1010 1041 8.821894 CACTCTCTCTTTTACACAATATAAGGC 58.178 37.037 0.00 0.00 0.00 4.35
1011 1042 8.540388 ACTCTCTCTTTTACACAATATAAGGCA 58.460 33.333 0.00 0.00 0.00 4.75
1060 1091 3.062763 CGTTGCAAGTCAAGTGAGATCT 58.937 45.455 0.00 0.00 34.91 2.75
1078 1109 9.705290 GTGAGATCTTCCCTATTTATCTTTCTC 57.295 37.037 0.00 0.00 0.00 2.87
1081 1112 9.897040 AGATCTTCCCTATTTATCTTTCTCTCT 57.103 33.333 0.00 0.00 0.00 3.10
1084 1115 9.369672 TCTTCCCTATTTATCTTTCTCTCTACC 57.630 37.037 0.00 0.00 0.00 3.18
1100 1131 7.492524 TCTCTCTACCAAGCATTTATGTACAG 58.507 38.462 0.33 0.00 0.00 2.74
1123 1154 7.888546 ACAGCTACCCAAACAAACTATTCTAAT 59.111 33.333 0.00 0.00 0.00 1.73
1124 1155 8.398665 CAGCTACCCAAACAAACTATTCTAATC 58.601 37.037 0.00 0.00 0.00 1.75
1126 1157 8.903820 GCTACCCAAACAAACTATTCTAATCAT 58.096 33.333 0.00 0.00 0.00 2.45
1129 1160 9.308000 ACCCAAACAAACTATTCTAATCATCAA 57.692 29.630 0.00 0.00 0.00 2.57
1130 1161 9.573133 CCCAAACAAACTATTCTAATCATCAAC 57.427 33.333 0.00 0.00 0.00 3.18
1162 1219 4.680975 GCTTTCTCAATCTAACTACCGCCT 60.681 45.833 0.00 0.00 0.00 5.52
1169 1226 5.526111 TCAATCTAACTACCGCCTTAATTGC 59.474 40.000 0.00 0.00 0.00 3.56
1171 1228 4.439057 TCTAACTACCGCCTTAATTGCTG 58.561 43.478 0.00 0.00 0.00 4.41
1175 1232 0.893270 ACCGCCTTAATTGCTGTGCA 60.893 50.000 0.00 0.00 36.47 4.57
1178 1235 2.294233 CCGCCTTAATTGCTGTGCATAT 59.706 45.455 0.00 0.00 38.76 1.78
1182 1239 5.535333 GCCTTAATTGCTGTGCATATTGAT 58.465 37.500 0.00 0.00 38.76 2.57
1223 1280 4.321718 CATGGAATGGAGATCTAACGCAT 58.678 43.478 0.00 0.00 41.79 4.73
1226 1283 3.748568 GGAATGGAGATCTAACGCATTCC 59.251 47.826 18.39 18.39 37.06 3.01
1236 1293 2.232756 AACGCATTCCCCAAACAAAC 57.767 45.000 0.00 0.00 0.00 2.93
1255 1312 5.703592 ACAAACGAATGCAGGTACTTGATTA 59.296 36.000 9.51 0.00 34.60 1.75
1258 1315 6.363577 ACGAATGCAGGTACTTGATTATTG 57.636 37.500 9.51 0.00 34.60 1.90
1279 1336 5.300411 TGTTGATGATATCTGGAGCACAT 57.700 39.130 3.98 0.00 0.00 3.21
1389 1446 1.066929 ACGTCATGCTGTGCTGACATA 60.067 47.619 16.13 0.00 41.46 2.29
1512 1569 2.945668 GCGGGAAGTAGCAGATGAAATT 59.054 45.455 0.00 0.00 0.00 1.82
1526 1583 7.929785 AGCAGATGAAATTTTGAAGAAATGTGT 59.070 29.630 0.00 0.00 0.00 3.72
1530 1587 8.735692 ATGAAATTTTGAAGAAATGTGTTGGT 57.264 26.923 0.00 0.00 0.00 3.67
1557 1614 5.573502 GCCATTGGCCATAATCAGTATAGGA 60.574 44.000 17.28 0.00 44.06 2.94
1588 1645 1.939934 CCAGCAAAAGTCGAACAGTCA 59.060 47.619 0.00 0.00 0.00 3.41
1599 1656 2.429250 TCGAACAGTCAAAGTCTGGTCA 59.571 45.455 10.76 0.00 46.33 4.02
1630 1687 2.748605 AGTCTGTTTCTTCTGCAGTCG 58.251 47.619 14.67 6.14 0.00 4.18
1671 1728 7.092137 TGACCAAATGAAGAGAATATTGCTG 57.908 36.000 0.00 0.00 0.00 4.41
1755 1812 3.194968 CGGAGGGTTACTACATTGACAGT 59.805 47.826 0.00 0.00 0.00 3.55
1794 1851 2.936202 TGGATGGCTGAAGGCTTAATC 58.064 47.619 0.00 0.00 41.69 1.75
2022 2079 0.661552 CATGGAAGATTCGCTGGCTG 59.338 55.000 0.00 0.00 0.00 4.85
2044 2101 2.634940 TCCCTCCACTTGAACTCTTCTG 59.365 50.000 0.00 0.00 0.00 3.02
2091 2148 1.645034 CATCGCATCTTCGGTCACTT 58.355 50.000 0.00 0.00 0.00 3.16
2181 2238 3.391049 AGGCGTTGTGAAGTCTAAGAAC 58.609 45.455 0.00 0.00 0.00 3.01
2188 2245 5.592104 TGTGAAGTCTAAGAACTGTCACA 57.408 39.130 13.21 13.21 40.64 3.58
2292 2349 1.202348 GAGCTTCCGGAACAAATTGGG 59.798 52.381 14.35 1.70 0.00 4.12
2301 2358 3.588955 GGAACAAATTGGGAATCTGCAC 58.411 45.455 0.00 0.00 0.00 4.57
2310 2367 3.321039 TGGGAATCTGCACCATCTAGAT 58.679 45.455 0.00 0.00 32.80 1.98
2316 2373 6.370994 GGAATCTGCACCATCTAGATGTATTG 59.629 42.308 27.03 21.20 37.11 1.90
2397 2454 3.565307 AGTGTGCCTTTTTCTGGATGAA 58.435 40.909 0.00 0.00 0.00 2.57
2406 2463 7.233348 TGCCTTTTTCTGGATGAAATCTTTACT 59.767 33.333 0.00 0.00 44.71 2.24
2491 2548 5.643348 TGTAATGCATCTGTAAGGTCTGTTG 59.357 40.000 0.00 0.00 0.00 3.33
2502 2559 2.035442 GTCTGTTGAAGGGCTCGGC 61.035 63.158 0.00 0.00 0.00 5.54
2523 2580 0.321653 AGCTGACCAAACTAAGGGCG 60.322 55.000 0.00 0.00 36.77 6.13
2545 2602 6.638468 GGCGCTGAAGATTAAATGGATTTTAG 59.362 38.462 7.64 0.00 31.57 1.85
2607 2664 1.211703 TGTGCCTCAACTCTGTCCAAA 59.788 47.619 0.00 0.00 0.00 3.28
2616 2673 1.134521 ACTCTGTCCAAACTCGTTGCA 60.135 47.619 0.00 0.00 35.74 4.08
2670 2727 8.473219 GGGATCAAAAGCTCTGATTTCTTAAAT 58.527 33.333 11.47 0.00 33.63 1.40
2673 2730 8.955061 TCAAAAGCTCTGATTTCTTAAATTCG 57.045 30.769 0.00 0.00 0.00 3.34
2695 2752 1.371558 GTGTTTCCGAGTGGCTCCT 59.628 57.895 0.00 0.00 34.14 3.69
2755 2812 3.326836 GAAATTTTGATTTCCCCGCCA 57.673 42.857 0.00 0.00 35.18 5.69
2781 2838 3.556862 AGCCAGATCAGATCCCTCATA 57.443 47.619 6.80 0.00 0.00 2.15
2826 2883 5.464722 CAGATATGTTCGTGAAATGGGAGAG 59.535 44.000 0.00 0.00 0.00 3.20
2846 2903 2.700897 AGGAAGGTGTCAATATCCTCGG 59.299 50.000 0.00 0.00 35.65 4.63
2877 2934 4.197750 CCATGCTGCTCTCTCTTACAATT 58.802 43.478 0.00 0.00 0.00 2.32
2878 2935 4.272991 CCATGCTGCTCTCTCTTACAATTC 59.727 45.833 0.00 0.00 0.00 2.17
2881 2938 3.309410 GCTGCTCTCTCTTACAATTCTGC 59.691 47.826 0.00 0.00 0.00 4.26
2889 2946 6.323482 TCTCTCTTACAATTCTGCTGCTCTAT 59.677 38.462 0.00 0.00 0.00 1.98
2968 3025 2.249413 CTTCCATGGCGAGACCTGCT 62.249 60.000 6.96 0.00 40.22 4.24
3063 3120 1.225704 CCCTGGATTGCTCCACCTC 59.774 63.158 0.00 0.00 46.95 3.85
3150 3207 1.943340 GAAATCAGAAGCGTCCATCCC 59.057 52.381 0.00 0.00 0.00 3.85
3189 3246 0.693049 GGAGGGTCTGAAGAGGCAAA 59.307 55.000 0.00 0.00 0.00 3.68
3190 3247 1.283321 GGAGGGTCTGAAGAGGCAAAT 59.717 52.381 0.00 0.00 0.00 2.32
3191 3248 2.291217 GGAGGGTCTGAAGAGGCAAATT 60.291 50.000 0.00 0.00 0.00 1.82
3192 3249 3.013219 GAGGGTCTGAAGAGGCAAATTC 58.987 50.000 0.00 0.00 0.00 2.17
3193 3250 1.740025 GGGTCTGAAGAGGCAAATTCG 59.260 52.381 0.00 0.00 0.00 3.34
3194 3251 1.131315 GGTCTGAAGAGGCAAATTCGC 59.869 52.381 0.00 0.00 0.00 4.70
3195 3252 1.806542 GTCTGAAGAGGCAAATTCGCA 59.193 47.619 0.00 0.00 0.00 5.10
3196 3253 2.226437 GTCTGAAGAGGCAAATTCGCAA 59.774 45.455 0.00 0.00 0.00 4.85
3223 3280 1.745141 GCAGCTAACCTGTGGAGGATG 60.745 57.143 0.00 0.00 42.93 3.51
3274 3594 6.590234 TGAGAGTTAAGTCATTCAGCAGTA 57.410 37.500 12.77 0.00 0.00 2.74
3322 3642 3.964875 CACGGGTGCCAACAGTGC 61.965 66.667 0.00 0.00 32.38 4.40
3342 3662 3.014623 GCCCACACTCTTATTGTAACCC 58.985 50.000 0.00 0.00 0.00 4.11
3343 3663 3.617284 CCCACACTCTTATTGTAACCCC 58.383 50.000 0.00 0.00 0.00 4.95
3440 3766 1.183549 AGTGGACGGAGCTAAATCGT 58.816 50.000 4.03 4.03 39.99 3.73
3475 3801 6.429791 TGTTGTACATTCGGGATTACATTG 57.570 37.500 0.00 0.00 0.00 2.82
3602 3928 9.935241 CATAGATATTTTGTGCTATGTACTCCT 57.065 33.333 0.00 0.00 36.86 3.69
3627 3953 2.065993 TCAGCTAGTGCGAAACAGAC 57.934 50.000 0.00 0.00 45.42 3.51
3632 3958 0.320421 TAGTGCGAAACAGACAGGCC 60.320 55.000 0.00 0.00 0.00 5.19
3843 4177 2.608988 CACCCCAGCCTCCTGACT 60.609 66.667 0.00 0.00 41.77 3.41
3947 4281 1.889170 GGAGGTGCCTTTTCCTTCAAG 59.111 52.381 0.00 0.00 33.83 3.02
4056 4390 0.968405 TCTTTCTTGCCACCATTGCC 59.032 50.000 0.00 0.00 0.00 4.52
4098 4432 2.635427 ACTTTGGTCTCTTCCTCCAGAC 59.365 50.000 0.00 0.00 38.71 3.51
4126 4460 7.849804 TTATCTCATTAACAACCTCTTCTGC 57.150 36.000 0.00 0.00 0.00 4.26
4178 4512 1.106285 CTTCCAGCCCCAATACTTGC 58.894 55.000 0.00 0.00 0.00 4.01
4179 4513 0.324275 TTCCAGCCCCAATACTTGCC 60.324 55.000 0.00 0.00 0.00 4.52
4180 4514 1.000233 CCAGCCCCAATACTTGCCA 60.000 57.895 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 0.388520 GCCCGGCAATCAAACTGTTC 60.389 55.000 3.91 0.00 0.00 3.18
113 114 0.596577 TGTCAGGAGTCCGAGAAACG 59.403 55.000 2.76 0.00 42.18 3.60
122 123 1.830477 AGCCTCTTGATGTCAGGAGTC 59.170 52.381 17.47 7.94 45.32 3.36
128 129 6.707440 TGTTTTAAAAGCCTCTTGATGTCA 57.293 33.333 0.00 0.00 0.00 3.58
146 147 9.300681 TCATTGACTTGAAAGAGGATATGTTTT 57.699 29.630 0.00 0.00 0.00 2.43
215 216 4.353777 AGTGTTCCCTGAGCTTGAGTATA 58.646 43.478 0.00 0.00 0.00 1.47
283 289 9.300681 TGAAACCATTTGAGACAGAATTAGAAT 57.699 29.630 0.00 0.00 0.00 2.40
293 299 6.897706 TCATTCATGAAACCATTTGAGACA 57.102 33.333 13.09 0.00 33.08 3.41
294 300 9.294030 GTTATCATTCATGAAACCATTTGAGAC 57.706 33.333 13.09 9.39 40.69 3.36
304 310 7.259882 TGATTGCCTGTTATCATTCATGAAAC 58.740 34.615 13.09 6.25 40.69 2.78
310 316 9.134055 TCAATATTGATTGCCTGTTATCATTCA 57.866 29.630 14.23 0.00 42.01 2.57
362 372 5.395103 CGGCAGAATTTATGGGATGGAAAAA 60.395 40.000 0.00 0.00 0.00 1.94
365 375 3.221771 CGGCAGAATTTATGGGATGGAA 58.778 45.455 0.00 0.00 0.00 3.53
366 376 2.174639 ACGGCAGAATTTATGGGATGGA 59.825 45.455 0.00 0.00 0.00 3.41
384 394 1.733389 GCAAGAATGATGTTGCCACGG 60.733 52.381 0.00 0.00 46.95 4.94
453 465 9.880064 GTCAGAACTAAAAATTAACTCAGAACC 57.120 33.333 0.00 0.00 0.00 3.62
514 526 9.396022 TCTCTCCATTTAAATAAGCTCGAATTT 57.604 29.630 0.00 0.00 0.00 1.82
515 527 8.964476 TCTCTCCATTTAAATAAGCTCGAATT 57.036 30.769 0.00 0.00 0.00 2.17
516 528 8.207545 ACTCTCTCCATTTAAATAAGCTCGAAT 58.792 33.333 0.00 0.00 0.00 3.34
561 573 5.604231 AGAAATAGGGCAGTGAGATACATGA 59.396 40.000 0.00 0.00 0.00 3.07
564 576 4.962362 TCAGAAATAGGGCAGTGAGATACA 59.038 41.667 0.00 0.00 0.00 2.29
565 577 5.537300 TCAGAAATAGGGCAGTGAGATAC 57.463 43.478 0.00 0.00 0.00 2.24
567 579 6.949117 ATATCAGAAATAGGGCAGTGAGAT 57.051 37.500 0.00 0.00 0.00 2.75
568 580 6.753913 AATATCAGAAATAGGGCAGTGAGA 57.246 37.500 0.00 0.00 0.00 3.27
569 581 6.429385 GGAAATATCAGAAATAGGGCAGTGAG 59.571 42.308 0.00 0.00 0.00 3.51
578 601 7.661437 TGATGTTCGGGGAAATATCAGAAATAG 59.339 37.037 0.00 0.00 29.99 1.73
598 621 4.445448 GGAAGAGGCATATGAGGTGATGTT 60.445 45.833 6.97 0.00 0.00 2.71
609 632 1.777272 GGGTCAAGGGAAGAGGCATAT 59.223 52.381 0.00 0.00 0.00 1.78
610 633 1.213296 GGGTCAAGGGAAGAGGCATA 58.787 55.000 0.00 0.00 0.00 3.14
643 666 3.598246 GCAACGTTTAAATGAGCTTCGAC 59.402 43.478 14.33 0.00 0.00 4.20
744 767 5.238583 AGAGTACTTCCATTCTTTGTTCCG 58.761 41.667 0.00 0.00 0.00 4.30
782 805 5.185828 TGAACAAGCTAGACTATGCTTCAGA 59.814 40.000 13.15 1.15 46.29 3.27
784 807 5.405935 TGAACAAGCTAGACTATGCTTCA 57.594 39.130 13.15 8.45 46.29 3.02
809 832 3.325293 AGTGCCACATGTACAGAAGAG 57.675 47.619 0.00 0.00 31.00 2.85
835 858 0.461548 TAGGCTTCTCTCCACATGCG 59.538 55.000 0.00 0.00 0.00 4.73
841 868 7.730332 TCTGAATAACATATAGGCTTCTCTCCA 59.270 37.037 0.00 0.00 0.00 3.86
847 874 7.445945 AGTGGTCTGAATAACATATAGGCTTC 58.554 38.462 0.00 0.00 0.00 3.86
861 888 3.817647 GCTTGTTCTGAAGTGGTCTGAAT 59.182 43.478 0.00 0.00 43.57 2.57
862 889 3.206150 GCTTGTTCTGAAGTGGTCTGAA 58.794 45.455 0.00 0.00 40.69 3.02
863 890 2.170397 TGCTTGTTCTGAAGTGGTCTGA 59.830 45.455 0.00 0.00 32.77 3.27
864 891 2.564771 TGCTTGTTCTGAAGTGGTCTG 58.435 47.619 0.00 0.00 0.00 3.51
865 892 3.281727 TTGCTTGTTCTGAAGTGGTCT 57.718 42.857 0.00 0.00 0.00 3.85
866 893 3.316308 ACATTGCTTGTTCTGAAGTGGTC 59.684 43.478 0.00 0.00 33.74 4.02
867 894 3.290710 ACATTGCTTGTTCTGAAGTGGT 58.709 40.909 0.00 0.00 33.74 4.16
868 895 3.996150 ACATTGCTTGTTCTGAAGTGG 57.004 42.857 0.00 0.00 33.74 4.00
879 906 6.392354 ACCTTAATCACATGAACATTGCTTG 58.608 36.000 0.00 0.00 0.00 4.01
883 910 8.498054 AGAGTACCTTAATCACATGAACATTG 57.502 34.615 0.00 0.00 0.00 2.82
897 924 7.105588 TCTACGTACATGTGAGAGTACCTTAA 58.894 38.462 9.11 0.00 37.83 1.85
901 928 6.374565 AATCTACGTACATGTGAGAGTACC 57.625 41.667 9.11 0.00 37.83 3.34
902 929 8.362860 TCTAATCTACGTACATGTGAGAGTAC 57.637 38.462 9.11 0.00 37.75 2.73
903 930 8.824781 GTTCTAATCTACGTACATGTGAGAGTA 58.175 37.037 9.11 8.40 0.00 2.59
905 932 7.921787 AGTTCTAATCTACGTACATGTGAGAG 58.078 38.462 9.11 0.59 0.00 3.20
906 933 7.860918 AGTTCTAATCTACGTACATGTGAGA 57.139 36.000 9.11 6.34 0.00 3.27
917 948 9.999009 TGTGTTGATACTAAGTTCTAATCTACG 57.001 33.333 0.00 0.00 0.00 3.51
926 957 8.764524 AATGTCTCTGTGTTGATACTAAGTTC 57.235 34.615 0.00 0.00 0.00 3.01
929 960 9.254133 CCATAATGTCTCTGTGTTGATACTAAG 57.746 37.037 0.00 0.00 0.00 2.18
955 986 5.473504 CCATAGCAATAATGGGAACTACACC 59.526 44.000 0.00 0.00 40.27 4.16
979 1010 2.987821 GTGTAAAAGAGAGAGTGCCGAC 59.012 50.000 0.00 0.00 0.00 4.79
983 1014 8.821894 CCTTATATTGTGTAAAAGAGAGAGTGC 58.178 37.037 0.00 0.00 0.00 4.40
984 1015 8.821894 GCCTTATATTGTGTAAAAGAGAGAGTG 58.178 37.037 0.00 0.00 0.00 3.51
1010 1041 6.914757 GCTGGCTTAAGCTCAAAGTTTATATG 59.085 38.462 25.88 8.27 40.20 1.78
1011 1042 7.032377 GCTGGCTTAAGCTCAAAGTTTATAT 57.968 36.000 25.88 0.00 40.20 0.86
1025 1056 0.730494 GCAACGCAAGCTGGCTTAAG 60.730 55.000 12.26 0.00 45.62 1.85
1027 1058 1.451337 TTGCAACGCAAGCTGGCTTA 61.451 50.000 12.26 0.00 43.99 3.09
1040 1071 4.083590 GGAAGATCTCACTTGACTTGCAAC 60.084 45.833 0.00 0.00 31.96 4.17
1060 1091 9.502035 TTGGTAGAGAGAAAGATAAATAGGGAA 57.498 33.333 0.00 0.00 0.00 3.97
1078 1109 6.051717 AGCTGTACATAAATGCTTGGTAGAG 58.948 40.000 0.00 0.00 0.00 2.43
1081 1112 6.053005 GGTAGCTGTACATAAATGCTTGGTA 58.947 40.000 11.31 0.00 35.47 3.25
1084 1115 4.881273 TGGGTAGCTGTACATAAATGCTTG 59.119 41.667 11.31 0.00 35.47 4.01
1100 1131 8.276252 TGATTAGAATAGTTTGTTTGGGTAGC 57.724 34.615 0.00 0.00 0.00 3.58
1123 1154 6.524734 TGAGAAAGCTTCTAACTGTTGATGA 58.475 36.000 0.00 0.00 40.87 2.92
1124 1155 6.791887 TGAGAAAGCTTCTAACTGTTGATG 57.208 37.500 0.00 3.10 40.87 3.07
1126 1157 7.220030 AGATTGAGAAAGCTTCTAACTGTTGA 58.780 34.615 0.00 0.00 40.87 3.18
1127 1158 7.432350 AGATTGAGAAAGCTTCTAACTGTTG 57.568 36.000 0.00 0.00 40.87 3.33
1129 1160 8.541133 GTTAGATTGAGAAAGCTTCTAACTGT 57.459 34.615 18.56 0.00 42.49 3.55
1133 1164 7.974501 CGGTAGTTAGATTGAGAAAGCTTCTAA 59.025 37.037 0.00 0.00 40.87 2.10
1134 1165 7.481642 CGGTAGTTAGATTGAGAAAGCTTCTA 58.518 38.462 0.00 0.00 40.87 2.10
1135 1166 6.334202 CGGTAGTTAGATTGAGAAAGCTTCT 58.666 40.000 0.00 0.00 44.21 2.85
1136 1167 5.005875 GCGGTAGTTAGATTGAGAAAGCTTC 59.994 44.000 0.00 0.00 0.00 3.86
1193 1250 8.800332 GTTAGATCTCCATTCCATGCAAAATAT 58.200 33.333 0.00 0.00 0.00 1.28
1219 1276 0.312416 TCGTTTGTTTGGGGAATGCG 59.688 50.000 0.00 0.00 0.00 4.73
1223 1280 1.757118 TGCATTCGTTTGTTTGGGGAA 59.243 42.857 0.00 0.00 0.00 3.97
1226 1283 1.068434 ACCTGCATTCGTTTGTTTGGG 59.932 47.619 0.00 0.00 0.00 4.12
1236 1293 6.363577 ACAATAATCAAGTACCTGCATTCG 57.636 37.500 0.00 0.00 0.00 3.34
1255 1312 5.687780 TGTGCTCCAGATATCATCAACAAT 58.312 37.500 5.32 0.00 0.00 2.71
1258 1315 4.388165 CGATGTGCTCCAGATATCATCAAC 59.612 45.833 5.32 0.00 33.59 3.18
1279 1336 0.821301 TTCACATGTTGCCAAGCCGA 60.821 50.000 0.00 0.00 0.00 5.54
1322 1379 6.816640 TGTAGCAATTATTCTACTTCGCTTGT 59.183 34.615 12.28 0.00 36.88 3.16
1326 1383 6.900299 GTGTTGTAGCAATTATTCTACTTCGC 59.100 38.462 12.28 9.35 36.88 4.70
1355 1412 3.747193 CATGACGTTGCCACATTCTTAC 58.253 45.455 0.00 0.00 0.00 2.34
1389 1446 2.610479 CGCTTCATACATATGCCCGTCT 60.610 50.000 1.58 0.00 33.76 4.18
1462 1519 0.804989 GGACAACATTCGCCTGAAGG 59.195 55.000 0.00 0.00 41.52 3.46
1500 1557 7.929785 ACACATTTCTTCAAAATTTCATCTGCT 59.070 29.630 0.00 0.00 0.00 4.24
1512 1569 4.633565 GGCAAACCAACACATTTCTTCAAA 59.366 37.500 0.00 0.00 35.26 2.69
1557 1614 5.472137 TCGACTTTTGCTGGCTAATAAACTT 59.528 36.000 0.00 0.00 0.00 2.66
1571 1628 4.016113 ACTTTGACTGTTCGACTTTTGC 57.984 40.909 0.00 0.00 0.00 3.68
1588 1645 5.826208 ACTTCCGTATTTTTGACCAGACTTT 59.174 36.000 0.00 0.00 0.00 2.66
1599 1656 7.639945 CAGAAGAAACAGACTTCCGTATTTTT 58.360 34.615 0.00 0.00 43.01 1.94
1671 1728 5.351740 GTGTGGAAGGTCAAGATAACTAAGC 59.648 44.000 0.00 0.00 0.00 3.09
1731 1788 2.762327 GTCAATGTAGTAACCCTCCGGA 59.238 50.000 2.93 2.93 0.00 5.14
1755 1812 8.587608 GCCATCCAATTCCATATCAAAAATCTA 58.412 33.333 0.00 0.00 0.00 1.98
1794 1851 3.386768 TCTTCTCTGTTTTCTCCACCG 57.613 47.619 0.00 0.00 0.00 4.94
1945 2002 0.610174 TCTTCCGCAGCTTGAGATGT 59.390 50.000 0.00 0.00 33.30 3.06
1946 2003 1.005340 GTCTTCCGCAGCTTGAGATG 58.995 55.000 0.00 0.00 34.00 2.90
1974 2031 8.142994 GGTATTTACCATCTATCAACACAGTG 57.857 38.462 0.00 0.00 45.73 3.66
2022 2079 2.635427 AGAAGAGTTCAAGTGGAGGGAC 59.365 50.000 0.00 0.00 0.00 4.46
2181 2238 4.834357 TCCAATGTGTTCAATGTGACAG 57.166 40.909 0.00 0.00 0.00 3.51
2188 2245 8.408043 TGATAGAAACTTCCAATGTGTTCAAT 57.592 30.769 0.00 0.00 0.00 2.57
2292 2349 6.370994 CCAATACATCTAGATGGTGCAGATTC 59.629 42.308 31.19 0.00 42.91 2.52
2301 2358 8.694540 CCTCTAAGATCCAATACATCTAGATGG 58.305 40.741 31.19 18.26 42.91 3.51
2397 2454 1.555075 TCAGGCAGCGGAGTAAAGATT 59.445 47.619 0.00 0.00 0.00 2.40
2406 2463 0.749091 CAATTCCATCAGGCAGCGGA 60.749 55.000 0.00 0.00 33.74 5.54
2502 2559 1.726853 CCCTTAGTTTGGTCAGCTCG 58.273 55.000 0.00 0.00 0.00 5.03
2523 2580 9.875691 AAACCTAAAATCCATTTAATCTTCAGC 57.124 29.630 0.00 0.00 33.20 4.26
2545 2602 4.766375 TCATCGAGAACCCTATCAAAACC 58.234 43.478 0.00 0.00 0.00 3.27
2592 2649 3.099267 ACGAGTTTGGACAGAGTTGAG 57.901 47.619 0.00 0.00 0.00 3.02
2607 2664 1.166531 GGAGGCTGTTTGCAACGAGT 61.167 55.000 0.00 0.00 45.15 4.18
2616 2673 3.151906 AGCGAGTGGAGGCTGTTT 58.848 55.556 0.00 0.00 38.27 2.83
2627 2684 1.301244 CCAGTGAAGTGCAGCGAGT 60.301 57.895 0.00 0.00 0.00 4.18
2628 2685 2.031516 CCCAGTGAAGTGCAGCGAG 61.032 63.158 0.00 0.00 0.00 5.03
2670 2727 0.531090 CACTCGGAAACACCCACGAA 60.531 55.000 0.00 0.00 34.70 3.85
2673 2730 2.258726 GCCACTCGGAAACACCCAC 61.259 63.158 0.00 0.00 34.64 4.61
2695 2752 1.929088 TCCGGAGAGGTGGAGGAGA 60.929 63.158 0.00 0.00 41.99 3.71
2755 2812 2.641815 GGGATCTGATCTGGCTTGGTAT 59.358 50.000 16.61 0.00 0.00 2.73
2781 2838 1.002502 GCTAAGGCGGGTGAGGTTT 60.003 57.895 0.00 0.00 0.00 3.27
2826 2883 2.807108 GCCGAGGATATTGACACCTTCC 60.807 54.545 0.00 0.00 33.89 3.46
2877 2934 1.409064 CGTTGGGTATAGAGCAGCAGA 59.591 52.381 0.00 0.00 0.00 4.26
2878 2935 1.858091 CGTTGGGTATAGAGCAGCAG 58.142 55.000 0.00 0.00 0.00 4.24
2881 2938 0.464036 TGGCGTTGGGTATAGAGCAG 59.536 55.000 0.00 0.00 0.00 4.24
2889 2946 0.250124 CACAACTCTGGCGTTGGGTA 60.250 55.000 8.33 0.00 46.47 3.69
2952 3009 2.110967 CAAGCAGGTCTCGCCATGG 61.111 63.158 7.63 7.63 40.61 3.66
2955 3012 1.078918 CATCAAGCAGGTCTCGCCA 60.079 57.895 0.00 0.00 40.61 5.69
2968 3025 1.538047 GCTCCTGGCTCAAACATCAA 58.462 50.000 0.00 0.00 38.06 2.57
3063 3120 1.738350 CTGACATGCTTGAGGCTTGAG 59.262 52.381 9.34 0.00 45.38 3.02
3193 3250 1.211190 GTTAGCTGCTGCACCTTGC 59.789 57.895 18.42 3.05 45.29 4.01
3194 3251 0.607489 AGGTTAGCTGCTGCACCTTG 60.607 55.000 22.93 0.00 41.15 3.61
3195 3252 0.607489 CAGGTTAGCTGCTGCACCTT 60.607 55.000 24.99 12.89 41.15 3.50
3196 3253 1.002868 CAGGTTAGCTGCTGCACCT 60.003 57.895 22.93 22.93 43.66 4.00
3223 3280 4.627467 CCAGCAAGTTCTGTACTACATGTC 59.373 45.833 0.00 0.00 35.54 3.06
3319 3639 3.439129 GGTTACAATAAGAGTGTGGGCAC 59.561 47.826 0.00 0.00 45.57 5.01
3320 3640 3.560453 GGGTTACAATAAGAGTGTGGGCA 60.560 47.826 0.00 0.00 0.00 5.36
3321 3641 3.014623 GGGTTACAATAAGAGTGTGGGC 58.985 50.000 0.00 0.00 0.00 5.36
3322 3642 3.009695 TGGGGTTACAATAAGAGTGTGGG 59.990 47.826 0.00 0.00 0.00 4.61
3323 3643 4.007659 GTGGGGTTACAATAAGAGTGTGG 58.992 47.826 0.00 0.00 0.00 4.17
3333 3653 3.845109 AAATCTGGGTGGGGTTACAAT 57.155 42.857 0.00 0.00 0.00 2.71
3342 3662 5.174037 TGTTAGGAAGTAAATCTGGGTGG 57.826 43.478 0.00 0.00 0.00 4.61
3343 3663 5.045869 TCCTGTTAGGAAGTAAATCTGGGTG 60.046 44.000 0.00 0.00 42.51 4.61
3412 3738 2.159085 AGCTCCGTCCACTAAGTAATGC 60.159 50.000 0.00 0.00 0.00 3.56
3440 3766 1.070914 TGTACAACATCTTGTGGCGGA 59.929 47.619 0.00 0.00 40.98 5.54
3475 3801 2.435805 TGGGGATGAGCTATGTTCAGAC 59.564 50.000 0.00 0.00 0.00 3.51
3602 3928 3.812609 TGTTTCGCACTAGCTGATTTGAA 59.187 39.130 0.00 0.00 39.10 2.69
3627 3953 1.070445 GAGAGGATGATCTGTGGCCTG 59.930 57.143 3.32 0.00 0.00 4.85
3632 3958 0.033228 GGCGGAGAGGATGATCTGTG 59.967 60.000 0.00 0.00 0.00 3.66
3734 4068 4.758165 CCTTTTCATGCAGAAATTTTGGCT 59.242 37.500 13.83 0.00 45.15 4.75
3906 4240 5.192927 TCCAAGTGGGAAAATATGTAGCTG 58.807 41.667 0.00 0.00 44.80 4.24
4006 4340 5.621193 TCAGGGAAGAAGGTAAAACAAGAG 58.379 41.667 0.00 0.00 0.00 2.85
4056 4390 7.715265 AAGTGAAGACAGTAGTGTTGTTATG 57.285 36.000 4.32 0.00 36.88 1.90
4098 4432 9.829507 AGAAGAGGTTGTTAATGAGATAATCTG 57.170 33.333 0.00 0.00 0.00 2.90
4126 4460 7.080724 GGAAAAACTGAAGAGTAAGCAATCTG 58.919 38.462 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.