Multiple sequence alignment - TraesCS5D01G533500

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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 TraesCS5D01G533500 chr5D 100.000 3329 0 0 1 3329 547927357 547924029 0.000000e+00 6148.0
1 TraesCS5D01G533500 chr5D 82.784 1911 236 56 815 2684 547841428 547839570 0.000000e+00 1620.0
2 TraesCS5D01G533500 chr5D 90.819 806 66 8 1787 2587 547892134 547891332 0.000000e+00 1072.0
3 TraesCS5D01G533500 chr5D 89.130 782 78 6 1835 2612 547883295 547882517 0.000000e+00 966.0
4 TraesCS5D01G533500 chr5D 84.540 718 59 23 1061 1768 547884085 547883410 0.000000e+00 664.0
5 TraesCS5D01G533500 chr5D 86.842 342 32 7 1427 1768 547892510 547892182 1.460000e-98 370.0
6 TraesCS5D01G533500 chr5D 85.319 361 37 8 1041 1389 547892870 547892514 3.160000e-95 359.0
7 TraesCS5D01G533500 chr5D 97.436 39 1 0 977 1015 547892913 547892875 2.140000e-07 67.6
8 TraesCS5D01G533500 chr5B 90.318 2675 158 55 366 2979 691943665 691941031 0.000000e+00 3411.0
9 TraesCS5D01G533500 chr5B 85.862 1839 153 46 875 2675 691825490 691823721 0.000000e+00 1857.0
10 TraesCS5D01G533500 chr5B 83.969 1179 140 36 1406 2558 691798154 691796999 0.000000e+00 1085.0
11 TraesCS5D01G533500 chr5B 81.371 875 90 39 906 1768 691773892 691773079 0.000000e+00 645.0
12 TraesCS5D01G533500 chr5B 84.507 568 53 17 841 1388 691798693 691798141 2.270000e-146 529.0
13 TraesCS5D01G533500 chr5B 91.262 206 18 0 3124 3329 691822901 691822696 7.030000e-72 281.0
14 TraesCS5D01G533500 chr5B 90.698 129 12 0 2722 2850 691823545 691823417 4.420000e-39 172.0
15 TraesCS5D01G533500 chr5B 92.537 67 2 1 3009 3072 691823065 691822999 3.540000e-15 93.5
16 TraesCS5D01G533500 chr5B 93.617 47 0 1 3029 3072 691941032 691940986 2.140000e-07 67.6
17 TraesCS5D01G533500 chr4A 90.862 2331 131 41 367 2656 618530488 618528199 0.000000e+00 3049.0
18 TraesCS5D01G533500 chr4A 88.619 1274 120 19 1427 2685 618464189 618462926 0.000000e+00 1526.0
19 TraesCS5D01G533500 chr4A 83.474 1301 168 32 1371 2643 618412650 618411369 0.000000e+00 1168.0
20 TraesCS5D01G533500 chr4A 87.186 757 94 1 1835 2588 618418226 618417470 0.000000e+00 857.0
21 TraesCS5D01G533500 chr4A 81.946 925 79 48 882 1768 618419215 618418341 0.000000e+00 702.0
22 TraesCS5D01G533500 chr4A 82.099 648 76 18 2704 3329 618528200 618527571 4.920000e-143 518.0
23 TraesCS5D01G533500 chr4A 84.450 373 43 12 1 364 618531012 618530646 1.470000e-93 353.0
24 TraesCS5D01G533500 chr4A 80.457 481 68 19 2857 3329 618462746 618462284 8.840000e-91 344.0
25 TraesCS5D01G533500 chr4A 84.553 369 33 12 1041 1389 618464557 618464193 8.840000e-91 344.0
26 TraesCS5D01G533500 chr4A 79.406 505 59 21 813 1300 618413134 618412658 6.930000e-82 315.0
27 TraesCS5D01G533500 chr4A 95.489 133 6 0 2722 2854 618462929 618462797 2.600000e-51 213.0


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 TraesCS5D01G533500 chr5D 547924029 547927357 3328 True 6148.000000 6148 100.000000 1 3329 1 chr5D.!!$R2 3328
1 TraesCS5D01G533500 chr5D 547839570 547841428 1858 True 1620.000000 1620 82.784000 815 2684 1 chr5D.!!$R1 1869
2 TraesCS5D01G533500 chr5D 547882517 547884085 1568 True 815.000000 966 86.835000 1061 2612 2 chr5D.!!$R3 1551
3 TraesCS5D01G533500 chr5D 547891332 547892913 1581 True 467.150000 1072 90.104000 977 2587 4 chr5D.!!$R4 1610
4 TraesCS5D01G533500 chr5B 691940986 691943665 2679 True 1739.300000 3411 91.967500 366 3072 2 chr5B.!!$R4 2706
5 TraesCS5D01G533500 chr5B 691796999 691798693 1694 True 807.000000 1085 84.238000 841 2558 2 chr5B.!!$R2 1717
6 TraesCS5D01G533500 chr5B 691773079 691773892 813 True 645.000000 645 81.371000 906 1768 1 chr5B.!!$R1 862
7 TraesCS5D01G533500 chr5B 691822696 691825490 2794 True 600.875000 1857 90.089750 875 3329 4 chr5B.!!$R3 2454
8 TraesCS5D01G533500 chr4A 618527571 618531012 3441 True 1306.666667 3049 85.803667 1 3329 3 chr4A.!!$R4 3328
9 TraesCS5D01G533500 chr4A 618417470 618419215 1745 True 779.500000 857 84.566000 882 2588 2 chr4A.!!$R2 1706
10 TraesCS5D01G533500 chr4A 618411369 618413134 1765 True 741.500000 1168 81.440000 813 2643 2 chr4A.!!$R1 1830
11 TraesCS5D01G533500 chr4A 618462284 618464557 2273 True 606.750000 1526 87.279500 1041 3329 4 chr4A.!!$R3 2288

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
136 138 0.530744 GCGACACTGGTAGGACATGA 59.469 55.000 0.0 0.0 0.0 3.07 F
1412 1651 0.392327 GCTCTGTTCCCTTCTGCCTC 60.392 60.000 0.0 0.0 0.0 4.70 F
2028 2409 2.124570 CTCCACCAGCCAATCCCG 60.125 66.667 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1956 0.744414 CCGCCGTCATCCACTGATTT 60.744 55.000 0.00 0.0 35.97 2.17 R
2229 2610 0.992072 CACGCGAGTTCATGACGAAT 59.008 50.000 15.93 0.0 46.40 3.34 R
2883 3679 1.066303 GCCGTCAGTAGTCCAGAGATG 59.934 57.143 0.00 0.0 0.00 2.90 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 4.223477 AGTGAATAATGCAACCCAATGCTT 59.777 37.500 0.00 0.00 46.54 3.91
40 41 6.070881 AGTGAATAATGCAACCCAATGCTTTA 60.071 34.615 9.19 9.19 46.54 1.85
45 46 5.674052 ATGCAACCCAATGCTTTATAACA 57.326 34.783 0.00 0.00 46.54 2.41
49 50 6.105333 GCAACCCAATGCTTTATAACATGAA 58.895 36.000 0.00 0.00 43.06 2.57
50 51 6.762661 GCAACCCAATGCTTTATAACATGAAT 59.237 34.615 0.00 0.00 43.06 2.57
81 82 3.322828 GCTCATGGGGTTTGCAATATGAT 59.677 43.478 0.00 0.00 0.00 2.45
83 84 3.896888 TCATGGGGTTTGCAATATGATCC 59.103 43.478 0.00 0.00 0.00 3.36
86 87 3.642377 TGGGGTTTGCAATATGATCCATG 59.358 43.478 0.00 0.00 0.00 3.66
136 138 0.530744 GCGACACTGGTAGGACATGA 59.469 55.000 0.00 0.00 0.00 3.07
138 140 1.467543 CGACACTGGTAGGACATGACG 60.468 57.143 0.00 0.00 0.00 4.35
168 170 2.988549 GCGACAACAGCGTCAGACG 61.989 63.158 19.10 19.10 45.88 4.18
171 173 1.597700 GACAACAGCGTCAGACGTCG 61.598 60.000 23.62 16.75 44.73 5.12
216 218 2.273179 CGTCGTCAGAGGGGGTTCA 61.273 63.158 0.00 0.00 0.00 3.18
217 219 1.292541 GTCGTCAGAGGGGGTTCAC 59.707 63.158 0.00 0.00 0.00 3.18
228 230 1.276622 GGGGTTCACTGAGGCTAGAA 58.723 55.000 0.00 0.00 0.00 2.10
238 240 2.357637 CTGAGGCTAGAAGAGGAAGACG 59.642 54.545 0.00 0.00 0.00 4.18
241 243 1.406180 GGCTAGAAGAGGAAGACGGTC 59.594 57.143 0.00 0.00 0.00 4.79
281 283 1.143073 ACGGCCCTTAGATTTCCATCC 59.857 52.381 0.00 0.00 0.00 3.51
284 286 2.495084 GCCCTTAGATTTCCATCCGAC 58.505 52.381 0.00 0.00 0.00 4.79
292 294 1.473497 TTTCCATCCGACGGTCCACA 61.473 55.000 14.79 0.00 0.00 4.17
294 296 2.654289 CATCCGACGGTCCACACA 59.346 61.111 14.79 0.00 0.00 3.72
306 308 1.461127 GTCCACACAGATTTGACGAGC 59.539 52.381 0.00 0.00 0.00 5.03
310 312 2.802247 CACACAGATTTGACGAGCTCAA 59.198 45.455 15.40 0.00 37.08 3.02
321 323 9.128107 GATTTGACGAGCTCAATTTTTATTTCA 57.872 29.630 15.40 0.00 38.74 2.69
323 325 8.864069 TTGACGAGCTCAATTTTTATTTCAAA 57.136 26.923 15.40 0.00 33.65 2.69
324 326 8.506140 TGACGAGCTCAATTTTTATTTCAAAG 57.494 30.769 15.40 0.00 0.00 2.77
325 327 8.134895 TGACGAGCTCAATTTTTATTTCAAAGT 58.865 29.630 15.40 0.00 0.00 2.66
326 328 8.507470 ACGAGCTCAATTTTTATTTCAAAGTC 57.493 30.769 15.40 0.00 0.00 3.01
327 329 7.595130 ACGAGCTCAATTTTTATTTCAAAGTCC 59.405 33.333 15.40 0.00 0.00 3.85
328 330 7.594758 CGAGCTCAATTTTTATTTCAAAGTCCA 59.405 33.333 15.40 0.00 0.00 4.02
330 332 9.428097 AGCTCAATTTTTATTTCAAAGTCCATC 57.572 29.630 0.00 0.00 0.00 3.51
332 334 9.709495 CTCAATTTTTATTTCAAAGTCCATCCA 57.291 29.630 0.00 0.00 0.00 3.41
346 356 5.497474 AGTCCATCCACTGTTTAATGGTAC 58.503 41.667 10.82 8.69 39.73 3.34
349 359 4.258543 CATCCACTGTTTAATGGTACGGT 58.741 43.478 0.00 0.00 37.27 4.83
350 360 5.421277 CATCCACTGTTTAATGGTACGGTA 58.579 41.667 0.00 0.00 37.27 4.02
351 361 5.480642 TCCACTGTTTAATGGTACGGTAA 57.519 39.130 0.00 0.00 37.27 2.85
352 362 5.862845 TCCACTGTTTAATGGTACGGTAAA 58.137 37.500 0.00 0.00 37.27 2.01
364 374 5.055812 TGGTACGGTAAAGTCGTTTTGAAT 58.944 37.500 0.00 0.00 41.38 2.57
371 536 7.115378 ACGGTAAAGTCGTTTTGAATGTAGTAG 59.885 37.037 0.00 0.00 37.61 2.57
373 538 9.410556 GGTAAAGTCGTTTTGAATGTAGTAGTA 57.589 33.333 0.00 0.00 0.00 1.82
424 589 0.606604 GGAACTCTGGCCACGACTTA 59.393 55.000 0.00 0.00 0.00 2.24
443 608 7.608761 ACGACTTAGAAAATAAGCCCACAATTA 59.391 33.333 0.00 0.00 0.00 1.40
640 808 1.745653 AGCCGCATAGAAAAAGAAGGC 59.254 47.619 0.00 0.00 43.29 4.35
689 857 2.202932 CTCAATCCCGGCGGTCAG 60.203 66.667 26.32 10.02 0.00 3.51
726 894 1.069924 GCATCTGATCTCGATCGCCG 61.070 60.000 11.09 3.94 40.63 6.46
741 909 1.729276 GCCGTTTATTTACCCCGCC 59.271 57.895 0.00 0.00 0.00 6.13
742 910 1.727511 GCCGTTTATTTACCCCGCCC 61.728 60.000 0.00 0.00 0.00 6.13
765 937 1.820906 CGCACCCACCATCATCCAG 60.821 63.158 0.00 0.00 0.00 3.86
954 1145 1.267574 TGTGCCTAGCCCTCTTCCTG 61.268 60.000 0.00 0.00 0.00 3.86
961 1155 3.181456 CCTAGCCCTCTTCCTGATTCTTG 60.181 52.174 0.00 0.00 0.00 3.02
1017 1211 3.712187 GATCATGTCTTCGTCTTCCTCC 58.288 50.000 0.00 0.00 0.00 4.30
1018 1212 2.808919 TCATGTCTTCGTCTTCCTCCT 58.191 47.619 0.00 0.00 0.00 3.69
1019 1213 2.755655 TCATGTCTTCGTCTTCCTCCTC 59.244 50.000 0.00 0.00 0.00 3.71
1230 1467 2.266554 CGTCTGTCTCTTCTTGATGCC 58.733 52.381 0.00 0.00 0.00 4.40
1412 1651 0.392327 GCTCTGTTCCCTTCTGCCTC 60.392 60.000 0.00 0.00 0.00 4.70
1458 1737 2.796593 GTGTTTGCTGAAATGCTGTTCC 59.203 45.455 0.00 0.00 0.00 3.62
1590 1891 5.922053 TCTTCAGAGATACCACCATTCATG 58.078 41.667 0.00 0.00 0.00 3.07
1593 1894 4.080413 TCAGAGATACCACCATTCATGCAA 60.080 41.667 0.00 0.00 0.00 4.08
1638 1944 4.458989 TGGGAACTAACATTGCATCTGAAC 59.541 41.667 3.97 0.00 0.00 3.18
1639 1945 4.458989 GGGAACTAACATTGCATCTGAACA 59.541 41.667 3.97 0.00 0.00 3.18
1790 2170 4.652421 ACCCTACGAAGCCAACTATATGAA 59.348 41.667 0.00 0.00 0.00 2.57
2028 2409 2.124570 CTCCACCAGCCAATCCCG 60.125 66.667 0.00 0.00 0.00 5.14
2226 2607 4.275508 CCAGTGGTGCAGCAGGGT 62.276 66.667 20.85 3.99 0.00 4.34
2229 2610 4.269523 GTGGTGCAGCAGGGTCCA 62.270 66.667 20.85 1.60 0.00 4.02
2331 2712 1.078143 GTGGAGCTCGGCCTGATTT 60.078 57.895 7.83 0.00 0.00 2.17
2344 2725 2.749621 GCCTGATTTTCATCGGTGTCTT 59.250 45.455 0.00 0.00 34.26 3.01
2643 3030 1.341080 AGTGGGGGCAAAGAACATTG 58.659 50.000 0.00 0.00 0.00 2.82
2712 3099 4.024048 GGTGAACATAAATATGAGCCACCG 60.024 45.833 18.07 0.00 39.00 4.94
2819 3335 7.052248 AGTGATCAAATTGTAGATGCAGATGA 58.948 34.615 0.00 0.00 0.00 2.92
2854 3415 3.365832 GTCATGTGTCACAAAACTGCTG 58.634 45.455 10.28 1.90 0.00 4.41
2875 3671 5.390145 GCTGAAATTTAATTGTTGCTGCCAG 60.390 40.000 0.00 0.00 0.00 4.85
2883 3679 8.477984 TTTAATTGTTGCTGCCAGATTTTATC 57.522 30.769 0.00 0.00 0.00 1.75
2899 3695 8.637099 CAGATTTTATCATCTCTGGACTACTGA 58.363 37.037 0.00 0.00 30.50 3.41
2901 3697 6.378710 TTTATCATCTCTGGACTACTGACG 57.621 41.667 0.00 0.00 0.00 4.35
2911 3707 4.018490 TGGACTACTGACGGCTTACATTA 58.982 43.478 0.00 0.00 0.00 1.90
2912 3708 4.463539 TGGACTACTGACGGCTTACATTAA 59.536 41.667 0.00 0.00 0.00 1.40
2917 3713 4.442706 ACTGACGGCTTACATTAATCCTG 58.557 43.478 0.00 0.00 0.00 3.86
2970 3767 6.003326 TGGTTGATTGAAATTGAGAGTGCTA 58.997 36.000 0.00 0.00 0.00 3.49
2972 3769 7.177216 TGGTTGATTGAAATTGAGAGTGCTATT 59.823 33.333 0.00 0.00 0.00 1.73
2973 3770 8.677300 GGTTGATTGAAATTGAGAGTGCTATTA 58.323 33.333 0.00 0.00 0.00 0.98
2975 3772 9.453572 TTGATTGAAATTGAGAGTGCTATTAGT 57.546 29.630 0.00 0.00 0.00 2.24
2976 3773 8.886719 TGATTGAAATTGAGAGTGCTATTAGTG 58.113 33.333 0.00 0.00 0.00 2.74
2977 3774 8.798859 ATTGAAATTGAGAGTGCTATTAGTGT 57.201 30.769 0.00 0.00 0.00 3.55
2978 3775 7.601073 TGAAATTGAGAGTGCTATTAGTGTG 57.399 36.000 0.00 0.00 0.00 3.82
2979 3776 7.161404 TGAAATTGAGAGTGCTATTAGTGTGT 58.839 34.615 0.00 0.00 0.00 3.72
2980 3777 8.311109 TGAAATTGAGAGTGCTATTAGTGTGTA 58.689 33.333 0.00 0.00 0.00 2.90
2981 3778 9.319143 GAAATTGAGAGTGCTATTAGTGTGTAT 57.681 33.333 0.00 0.00 0.00 2.29
2982 3779 8.879342 AATTGAGAGTGCTATTAGTGTGTATC 57.121 34.615 0.00 0.00 0.00 2.24
2983 3780 7.404671 TTGAGAGTGCTATTAGTGTGTATCA 57.595 36.000 0.00 0.00 0.00 2.15
2984 3781 7.588497 TGAGAGTGCTATTAGTGTGTATCAT 57.412 36.000 0.00 0.00 0.00 2.45
2985 3782 8.011844 TGAGAGTGCTATTAGTGTGTATCATT 57.988 34.615 0.00 0.00 0.00 2.57
2986 3783 7.922811 TGAGAGTGCTATTAGTGTGTATCATTG 59.077 37.037 0.00 0.00 0.00 2.82
2987 3784 7.786030 AGAGTGCTATTAGTGTGTATCATTGT 58.214 34.615 0.00 0.00 0.00 2.71
2988 3785 8.260818 AGAGTGCTATTAGTGTGTATCATTGTT 58.739 33.333 0.00 0.00 0.00 2.83
2989 3786 8.792830 AGTGCTATTAGTGTGTATCATTGTTT 57.207 30.769 0.00 0.00 0.00 2.83
2990 3787 8.668353 AGTGCTATTAGTGTGTATCATTGTTTG 58.332 33.333 0.00 0.00 0.00 2.93
2991 3788 8.664798 GTGCTATTAGTGTGTATCATTGTTTGA 58.335 33.333 0.00 0.00 39.12 2.69
2992 3789 9.394767 TGCTATTAGTGTGTATCATTGTTTGAT 57.605 29.630 0.00 0.00 46.86 2.57
3075 3897 0.040514 TAGTGTTGTGTGCGCATTGC 60.041 50.000 15.91 7.68 46.70 3.56
3145 3992 0.321387 CTTCAAGGCTGAGCTGCTGA 60.321 55.000 7.01 0.00 31.69 4.26
3185 4032 7.739498 TTTTGTCTGTTGGTTTAGAGGATAC 57.261 36.000 0.00 0.00 0.00 2.24
3195 4042 7.185318 TGGTTTAGAGGATACGTATTTTCCA 57.815 36.000 9.92 7.56 46.39 3.53
3226 4073 5.003804 TGTCCTAAAAGGCTGACAGATTTC 58.996 41.667 6.65 0.00 34.61 2.17
3241 4088 7.279615 TGACAGATTTCCTAGTCAAAGTTGAA 58.720 34.615 0.00 0.00 39.21 2.69
3267 4114 3.434167 GCTCTTGGCCATCTTAATGAGGA 60.434 47.826 6.09 0.00 34.61 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.466798 GGGTTGCATTATTCACTATGTTTAACT 58.533 33.333 0.00 0.00 0.00 2.24
22 23 6.047511 TGTTATAAAGCATTGGGTTGCATT 57.952 33.333 0.00 0.00 45.23 3.56
26 27 7.980662 TGATTCATGTTATAAAGCATTGGGTTG 59.019 33.333 0.00 0.00 34.38 3.77
29 30 8.528917 CATGATTCATGTTATAAAGCATTGGG 57.471 34.615 16.93 0.00 37.12 4.12
45 46 3.383505 CCCATGAGCACAACATGATTCAT 59.616 43.478 0.00 0.00 45.22 2.57
49 50 1.006281 ACCCCATGAGCACAACATGAT 59.994 47.619 0.00 0.00 45.22 2.45
50 51 0.405198 ACCCCATGAGCACAACATGA 59.595 50.000 0.00 0.00 45.22 3.07
64 65 3.395054 TGGATCATATTGCAAACCCCA 57.605 42.857 1.71 2.79 0.00 4.96
86 87 3.677121 TGACAACAAAACATGTGTGCAAC 59.323 39.130 0.00 0.00 42.99 4.17
124 126 1.663379 CTCGCCGTCATGTCCTACCA 61.663 60.000 0.00 0.00 0.00 3.25
150 152 2.846918 GTCTGACGCTGTTGTCGC 59.153 61.111 0.00 0.00 41.87 5.19
161 163 2.126424 GCTCCACCGACGTCTGAC 60.126 66.667 14.31 0.00 0.00 3.51
168 170 4.767255 CCTGCCAGCTCCACCGAC 62.767 72.222 0.00 0.00 0.00 4.79
193 195 3.062466 CCCTCTGACGACGCTGGA 61.062 66.667 0.00 0.00 0.00 3.86
194 196 4.135153 CCCCTCTGACGACGCTGG 62.135 72.222 0.00 0.00 0.00 4.85
198 200 2.273179 TGAACCCCCTCTGACGACG 61.273 63.158 0.00 0.00 0.00 5.12
199 201 1.186267 AGTGAACCCCCTCTGACGAC 61.186 60.000 0.00 0.00 0.00 4.34
200 202 1.155390 AGTGAACCCCCTCTGACGA 59.845 57.895 0.00 0.00 0.00 4.20
204 206 1.986413 CCTCAGTGAACCCCCTCTG 59.014 63.158 0.00 0.00 0.00 3.35
216 218 3.361786 GTCTTCCTCTTCTAGCCTCAGT 58.638 50.000 0.00 0.00 0.00 3.41
217 219 2.357637 CGTCTTCCTCTTCTAGCCTCAG 59.642 54.545 0.00 0.00 0.00 3.35
228 230 1.378778 CTCCGGACCGTCTTCCTCT 60.379 63.158 13.94 0.00 32.88 3.69
238 240 1.758906 CCTCCTTCTCCTCCGGACC 60.759 68.421 0.00 0.00 0.00 4.46
241 243 3.157949 GCCCTCCTTCTCCTCCGG 61.158 72.222 0.00 0.00 0.00 5.14
269 271 1.684983 GGACCGTCGGATGGAAATCTA 59.315 52.381 22.75 0.00 0.00 1.98
281 283 0.790207 CAAATCTGTGTGGACCGTCG 59.210 55.000 0.00 0.00 0.00 5.12
284 286 0.790207 CGTCAAATCTGTGTGGACCG 59.210 55.000 0.00 0.00 0.00 4.79
306 308 9.709495 TGGATGGACTTTGAAATAAAAATTGAG 57.291 29.630 0.00 0.00 0.00 3.02
310 312 8.650490 ACAGTGGATGGACTTTGAAATAAAAAT 58.350 29.630 0.00 0.00 0.00 1.82
321 323 5.393866 ACCATTAAACAGTGGATGGACTTT 58.606 37.500 18.21 2.13 41.20 2.66
323 325 4.657814 ACCATTAAACAGTGGATGGACT 57.342 40.909 18.21 1.35 41.20 3.85
324 326 4.331717 CGTACCATTAAACAGTGGATGGAC 59.668 45.833 18.21 12.57 41.20 4.02
325 327 4.509616 CGTACCATTAAACAGTGGATGGA 58.490 43.478 18.21 5.31 41.20 3.41
326 328 3.625764 CCGTACCATTAAACAGTGGATGG 59.374 47.826 12.67 12.67 43.65 3.51
327 329 4.258543 ACCGTACCATTAAACAGTGGATG 58.741 43.478 0.00 0.00 38.86 3.51
328 330 4.563140 ACCGTACCATTAAACAGTGGAT 57.437 40.909 0.00 0.00 38.86 3.41
330 332 5.702209 ACTTTACCGTACCATTAAACAGTGG 59.298 40.000 0.00 0.00 41.35 4.00
332 334 5.634859 CGACTTTACCGTACCATTAAACAGT 59.365 40.000 0.00 0.00 0.00 3.55
346 356 6.219302 ACTACATTCAAAACGACTTTACCG 57.781 37.500 0.00 0.00 0.00 4.02
352 362 9.245962 GCATATACTACTACATTCAAAACGACT 57.754 33.333 0.00 0.00 0.00 4.18
364 374 6.412214 TCTGATAGCCGCATATACTACTACA 58.588 40.000 0.00 0.00 0.00 2.74
371 536 5.805486 TCGAATTTCTGATAGCCGCATATAC 59.195 40.000 0.00 0.00 0.00 1.47
373 538 4.820897 TCGAATTTCTGATAGCCGCATAT 58.179 39.130 0.00 0.00 0.00 1.78
449 614 6.764085 CCACTCCCGTTTTCCTTTTTAAAAAT 59.236 34.615 13.55 0.00 0.00 1.82
450 615 6.107343 CCACTCCCGTTTTCCTTTTTAAAAA 58.893 36.000 12.62 12.62 0.00 1.94
451 616 5.187381 ACCACTCCCGTTTTCCTTTTTAAAA 59.813 36.000 0.00 0.00 0.00 1.52
452 617 4.710865 ACCACTCCCGTTTTCCTTTTTAAA 59.289 37.500 0.00 0.00 0.00 1.52
453 618 4.279982 ACCACTCCCGTTTTCCTTTTTAA 58.720 39.130 0.00 0.00 0.00 1.52
454 619 3.900971 ACCACTCCCGTTTTCCTTTTTA 58.099 40.909 0.00 0.00 0.00 1.52
459 627 0.179001 CCAACCACTCCCGTTTTCCT 60.179 55.000 0.00 0.00 0.00 3.36
548 716 4.796231 ATGGCCGACGACGTGCTC 62.796 66.667 4.58 0.00 36.50 4.26
640 808 1.798725 CGCGTGGCTGCTTTCATTG 60.799 57.895 0.00 0.00 0.00 2.82
661 829 2.529744 GGATTGAGGGGATCGGGGG 61.530 68.421 0.00 0.00 0.00 5.40
662 830 2.529744 GGGATTGAGGGGATCGGGG 61.530 68.421 0.00 0.00 0.00 5.73
663 831 2.883828 CGGGATTGAGGGGATCGGG 61.884 68.421 0.00 0.00 0.00 5.14
664 832 2.743718 CGGGATTGAGGGGATCGG 59.256 66.667 0.00 0.00 0.00 4.18
665 833 2.743718 CCGGGATTGAGGGGATCG 59.256 66.667 0.00 0.00 0.00 3.69
666 834 2.432123 GCCGGGATTGAGGGGATC 59.568 66.667 2.18 0.00 0.00 3.36
667 835 3.560251 CGCCGGGATTGAGGGGAT 61.560 66.667 2.18 0.00 42.30 3.85
726 894 1.105457 GGTGGGCGGGGTAAATAAAC 58.895 55.000 0.00 0.00 0.00 2.01
741 909 3.976701 GATGGTGGGTGCGAGGTGG 62.977 68.421 0.00 0.00 0.00 4.61
742 910 2.436646 GATGGTGGGTGCGAGGTG 60.437 66.667 0.00 0.00 0.00 4.00
751 919 1.454479 GGTGCTGGATGATGGTGGG 60.454 63.158 0.00 0.00 0.00 4.61
879 1062 1.273606 CTGGAGCTCGTCTTTCTGGAA 59.726 52.381 7.83 0.00 0.00 3.53
954 1145 2.604614 GGCGGTCACAACAACAAGAATC 60.605 50.000 0.00 0.00 0.00 2.52
961 1155 1.433837 AAGACGGCGGTCACAACAAC 61.434 55.000 24.31 0.00 45.92 3.32
1143 1337 1.570979 GATTGAGAGGGGGATTGGGTT 59.429 52.381 0.00 0.00 0.00 4.11
1150 1346 3.154473 CGGCGATTGAGAGGGGGA 61.154 66.667 0.00 0.00 0.00 4.81
1154 1353 1.594862 GAATTCACGGCGATTGAGAGG 59.405 52.381 16.62 0.00 0.00 3.69
1412 1651 1.337703 CGGGCAATATCAACATGGTGG 59.662 52.381 11.68 0.00 0.00 4.61
1458 1737 1.291877 CGGCAGAAACCCAGAAGACG 61.292 60.000 0.00 0.00 0.00 4.18
1590 1891 6.633856 AGTCAAAATAGAATGGGTCAATTGC 58.366 36.000 0.00 0.00 0.00 3.56
1593 1894 6.155049 CCCAAGTCAAAATAGAATGGGTCAAT 59.845 38.462 0.00 0.00 39.95 2.57
1638 1944 6.875726 TCATCCACTGATTTTAGAACAGAGTG 59.124 38.462 0.00 0.00 35.85 3.51
1639 1945 6.876257 GTCATCCACTGATTTTAGAACAGAGT 59.124 38.462 0.00 0.00 35.97 3.24
1648 1954 2.276201 CGCCGTCATCCACTGATTTTA 58.724 47.619 0.00 0.00 35.97 1.52
1649 1955 1.086696 CGCCGTCATCCACTGATTTT 58.913 50.000 0.00 0.00 35.97 1.82
1650 1956 0.744414 CCGCCGTCATCCACTGATTT 60.744 55.000 0.00 0.00 35.97 2.17
1651 1957 1.153369 CCGCCGTCATCCACTGATT 60.153 57.895 0.00 0.00 35.97 2.57
1790 2170 4.799678 CAGAGTTAGTGTCGAGTGATTGT 58.200 43.478 0.00 0.00 0.00 2.71
2226 2607 1.640428 GCGAGTTCATGACGAATGGA 58.360 50.000 8.26 0.00 36.86 3.41
2229 2610 0.992072 CACGCGAGTTCATGACGAAT 59.008 50.000 15.93 0.00 46.40 3.34
2322 2703 1.401905 GACACCGATGAAAATCAGGCC 59.598 52.381 0.00 0.00 0.00 5.19
2344 2725 2.399916 TGTTGATCATCATCACGGCA 57.600 45.000 2.22 0.00 38.86 5.69
2515 2901 4.974645 AAGTTCCTCCTCATTACACACA 57.025 40.909 0.00 0.00 0.00 3.72
2712 3099 5.066593 ACTGAGAAGATCAAACAAAGGGTC 58.933 41.667 0.00 0.00 37.52 4.46
2819 3335 5.473162 TGACACATGACGAATCCTTTGAAAT 59.527 36.000 0.00 0.00 0.00 2.17
2854 3415 6.973229 ATCTGGCAGCAACAATTAAATTTC 57.027 33.333 10.34 0.00 0.00 2.17
2875 3671 7.593273 CGTCAGTAGTCCAGAGATGATAAAATC 59.407 40.741 0.00 0.00 0.00 2.17
2883 3679 1.066303 GCCGTCAGTAGTCCAGAGATG 59.934 57.143 0.00 0.00 0.00 2.90
2901 3697 9.301153 CATTGTTTTACAGGATTAATGTAAGCC 57.699 33.333 0.00 0.00 42.40 4.35
2942 3739 7.814107 GCACTCTCAATTTCAATCAACCATAAA 59.186 33.333 0.00 0.00 0.00 1.40
2943 3740 7.177216 AGCACTCTCAATTTCAATCAACCATAA 59.823 33.333 0.00 0.00 0.00 1.90
2954 3751 7.161404 ACACACTAATAGCACTCTCAATTTCA 58.839 34.615 0.00 0.00 0.00 2.69
2961 3758 7.923344 ACAATGATACACACTAATAGCACTCTC 59.077 37.037 0.00 0.00 0.00 3.20
3020 3817 6.261603 CACTCTGCATTGCTATCAAATAAGGA 59.738 38.462 10.49 0.00 35.56 3.36
3022 3819 5.913514 GCACTCTGCATTGCTATCAAATAAG 59.086 40.000 10.49 0.00 44.26 1.73
3075 3897 8.618702 AATCATATAGCTCATCAAAACCTCTG 57.381 34.615 0.00 0.00 0.00 3.35
3121 3948 2.419851 GCAGCTCAGCCTTGAAGATAGT 60.420 50.000 0.00 0.00 31.69 2.12
3166 4013 7.414222 AATACGTATCCTCTAAACCAACAGA 57.586 36.000 8.86 0.00 0.00 3.41
3180 4027 7.758495 ACAGTCAATTTGGAAAATACGTATCC 58.242 34.615 8.86 7.65 0.00 2.59
3184 4031 5.768164 AGGACAGTCAATTTGGAAAATACGT 59.232 36.000 2.17 0.00 0.00 3.57
3185 4032 6.254281 AGGACAGTCAATTTGGAAAATACG 57.746 37.500 2.17 0.00 0.00 3.06
3195 4042 5.241728 GTCAGCCTTTTAGGACAGTCAATTT 59.758 40.000 2.17 0.00 37.67 1.82
3226 4073 6.566197 AGAGCAAATTCAACTTTGACTAGG 57.434 37.500 0.00 0.00 38.17 3.02
3241 4088 4.957954 TCATTAAGATGGCCAAGAGCAAAT 59.042 37.500 10.96 2.38 46.50 2.32
3301 4148 4.202461 ACTGGAGCAAAGACTTTACATCCA 60.202 41.667 19.24 19.24 34.55 3.41


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

AutoCloner maintained by Alex Coulton.