Multiple sequence alignment - TraesCS4A01G415400

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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 TraesCS4A01G415400 chr4A 100.000 2870 0 0 1 2870 685382598 685379729 0.000000e+00 5301
1 TraesCS4A01G415400 chr4A 84.158 303 46 2 1137 1438 685372125 685372426 2.800000e-75 292
2 TraesCS4A01G415400 chr4A 84.586 266 37 4 1156 1419 64956723 64956986 7.890000e-66 261
3 TraesCS4A01G415400 chr4A 80.682 264 38 12 1154 1412 544047785 544047530 2.920000e-45 193
4 TraesCS4A01G415400 chr4D 91.643 2860 133 43 29 2870 479000296 478997525 0.000000e+00 3860
5 TraesCS4A01G415400 chr4D 84.488 303 45 2 1137 1438 478992302 478992603 6.010000e-77 298
6 TraesCS4A01G415400 chr4D 80.755 265 36 14 1154 1412 52763827 52764082 2.920000e-45 193
7 TraesCS4A01G415400 chr4B 90.801 2870 157 40 25 2870 605694187 605691401 0.000000e+00 3738
8 TraesCS4A01G415400 chr4B 82.838 303 50 2 1137 1438 605682888 605683189 1.310000e-68 270
9 TraesCS4A01G415400 chr4B 80.682 264 38 12 1154 1412 77651297 77651552 2.920000e-45 193


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 TraesCS4A01G415400 chr4A 685379729 685382598 2869 True 5301 5301 100.000 1 2870 1 chr4A.!!$R2 2869
1 TraesCS4A01G415400 chr4D 478997525 479000296 2771 True 3860 3860 91.643 29 2870 1 chr4D.!!$R1 2841
2 TraesCS4A01G415400 chr4B 605691401 605694187 2786 True 3738 3738 90.801 25 2870 1 chr4B.!!$R1 2845

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
804 808 0.251297 TTGGGATTGGCAGAGTGGTG 60.251 55.0 0.00 0.00 0.0 4.17 F
1093 1109 0.028770 GGAGAGAGACAGCACGATCG 59.971 60.0 14.88 14.88 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 1830 1.153823 CCTCGCAGTCTTGGTACCG 60.154 63.158 7.57 0.0 0.00 4.02 R
2562 2591 1.223187 CTGCAGCATCATCGCATGTA 58.777 50.000 0.00 0.0 34.63 2.29 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
24 25 7.186021 CGTTTGACCATTTTTCTACTAGTGT 57.814 36.000 5.39 0.00 0.00 3.55
25 26 7.069569 CGTTTGACCATTTTTCTACTAGTGTG 58.930 38.462 5.39 0.00 0.00 3.82
26 27 6.554334 TTGACCATTTTTCTACTAGTGTGC 57.446 37.500 5.39 0.00 0.00 4.57
27 28 5.616270 TGACCATTTTTCTACTAGTGTGCA 58.384 37.500 5.39 0.00 0.00 4.57
41 42 7.572523 ACTAGTGTGCATGCATGTAATTTAT 57.427 32.000 25.64 10.66 0.00 1.40
42 43 7.420002 ACTAGTGTGCATGCATGTAATTTATG 58.580 34.615 25.64 13.96 0.00 1.90
43 44 6.453926 AGTGTGCATGCATGTAATTTATGA 57.546 33.333 25.64 0.00 0.00 2.15
44 45 7.046292 AGTGTGCATGCATGTAATTTATGAT 57.954 32.000 25.64 2.23 0.00 2.45
45 46 8.168790 AGTGTGCATGCATGTAATTTATGATA 57.831 30.769 25.64 0.00 0.00 2.15
48 49 9.247126 TGTGCATGCATGTAATTTATGATAAAC 57.753 29.630 25.64 4.45 0.00 2.01
49 50 9.247126 GTGCATGCATGTAATTTATGATAAACA 57.753 29.630 25.64 8.29 0.00 2.83
50 51 9.984190 TGCATGCATGTAATTTATGATAAACAT 57.016 25.926 26.79 0.00 42.39 2.71
154 155 3.003793 GTCAGTGGAAGGCAAAAGAGTTC 59.996 47.826 0.00 0.00 0.00 3.01
175 176 5.531122 TCGGACTCTTGGTTAGGATAATG 57.469 43.478 0.00 0.00 0.00 1.90
180 181 6.408662 GGACTCTTGGTTAGGATAATGAGCTT 60.409 42.308 0.00 0.00 0.00 3.74
202 203 5.282055 TCTTAACCCTACATGATGCAGAG 57.718 43.478 0.00 0.00 0.00 3.35
208 209 0.471191 TACATGATGCAGAGGCCAGG 59.529 55.000 5.01 0.00 40.13 4.45
262 263 1.529010 CTTTCCTGCAGGTGCCACA 60.529 57.895 31.58 9.23 41.18 4.17
281 282 2.205074 CATAGTTTAGAGCAGCCGGTG 58.795 52.381 1.90 0.89 0.00 4.94
332 333 7.015682 TCCTTTCCAAAACATATTTAAGTGGCA 59.984 33.333 0.00 0.00 0.00 4.92
333 334 7.823799 CCTTTCCAAAACATATTTAAGTGGCAT 59.176 33.333 0.00 0.00 0.00 4.40
334 335 9.868277 CTTTCCAAAACATATTTAAGTGGCATA 57.132 29.630 0.00 0.00 0.00 3.14
335 336 9.868277 TTTCCAAAACATATTTAAGTGGCATAG 57.132 29.630 0.00 0.00 0.00 2.23
405 406 1.266175 GACATACATGCCTGCTGATGC 59.734 52.381 0.00 0.00 40.20 3.91
406 407 0.596577 CATACATGCCTGCTGATGCC 59.403 55.000 0.00 0.00 38.71 4.40
420 421 4.826733 TGCTGATGCCCACGAATATAAATT 59.173 37.500 0.00 0.00 38.71 1.82
422 423 5.630680 GCTGATGCCCACGAATATAAATTTG 59.369 40.000 0.00 0.00 33.30 2.32
450 452 6.186957 ACACTTGTGCATATATTTTCCCTGA 58.813 36.000 0.10 0.00 0.00 3.86
495 497 7.230712 TCTGATCCCAAGGAAAAAGTTCTAAAC 59.769 37.037 0.00 0.00 34.34 2.01
510 512 9.588096 AAAGTTCTAAACTAATTTCCCATCACT 57.412 29.630 0.00 0.00 41.91 3.41
521 523 5.779241 TTTCCCATCACTTATTGTCTCCT 57.221 39.130 0.00 0.00 0.00 3.69
537 539 4.202367 TGTCTCCTGAGGAAAAGAAAGGAC 60.202 45.833 1.41 4.50 33.50 3.85
539 541 2.038557 TCCTGAGGAAAAGAAAGGACCG 59.961 50.000 0.00 0.00 32.07 4.79
582 584 1.001641 ACTTCTGGCCAGGTGATGC 60.002 57.895 32.23 0.00 0.00 3.91
627 629 1.408266 CCCCGGGTTTATCAACTGGAG 60.408 57.143 21.85 0.00 32.92 3.86
682 684 9.236691 CCCAACTAATCACAAAATAAATCATCG 57.763 33.333 0.00 0.00 0.00 3.84
691 693 1.229428 ATAAATCATCGCACGGGCAG 58.771 50.000 11.77 2.11 41.24 4.85
716 718 6.034683 GGCAGTCACGATAACAACTAAACTAG 59.965 42.308 0.00 0.00 0.00 2.57
748 750 7.360017 CGAGAGAAAGTTGTGTATAATTGCACA 60.360 37.037 7.82 7.82 45.20 4.57
753 755 2.360844 TGTGTATAATTGCACACCGGG 58.639 47.619 6.32 0.00 42.55 5.73
772 774 0.394352 GTGACCTAGCCCCATTGTGG 60.394 60.000 0.00 0.00 37.25 4.17
804 808 0.251297 TTGGGATTGGCAGAGTGGTG 60.251 55.000 0.00 0.00 0.00 4.17
805 809 1.380302 GGGATTGGCAGAGTGGTGT 59.620 57.895 0.00 0.00 0.00 4.16
834 838 9.750783 AGTATTAGTGTACCTACAGAAAAGAGA 57.249 33.333 0.00 0.00 36.78 3.10
836 840 8.880991 ATTAGTGTACCTACAGAAAAGAGAGA 57.119 34.615 0.00 0.00 36.78 3.10
837 841 8.701908 TTAGTGTACCTACAGAAAAGAGAGAA 57.298 34.615 0.00 0.00 36.78 2.87
838 842 7.598759 AGTGTACCTACAGAAAAGAGAGAAA 57.401 36.000 0.00 0.00 36.78 2.52
839 843 8.019656 AGTGTACCTACAGAAAAGAGAGAAAA 57.980 34.615 0.00 0.00 36.78 2.29
844 848 5.649831 CCTACAGAAAAGAGAGAAAATGGGG 59.350 44.000 0.00 0.00 0.00 4.96
861 865 2.124695 GGGGCAGAACTTAGCGGG 60.125 66.667 0.00 0.00 0.00 6.13
862 866 2.824489 GGGCAGAACTTAGCGGGC 60.824 66.667 0.00 0.00 0.00 6.13
863 867 2.824489 GGCAGAACTTAGCGGGCC 60.824 66.667 0.00 0.00 0.00 5.80
864 868 3.195698 GCAGAACTTAGCGGGCCG 61.196 66.667 24.35 24.35 0.00 6.13
865 869 2.511600 CAGAACTTAGCGGGCCGG 60.512 66.667 29.48 13.56 0.00 6.13
971 976 1.402787 CTAATCCCCAACCATGCACC 58.597 55.000 0.00 0.00 0.00 5.01
972 977 1.006813 TAATCCCCAACCATGCACCT 58.993 50.000 0.00 0.00 0.00 4.00
974 979 2.228841 ATCCCCAACCATGCACCTCC 62.229 60.000 0.00 0.00 0.00 4.30
978 983 1.687612 CAACCATGCACCTCCTCCT 59.312 57.895 0.00 0.00 0.00 3.69
981 986 2.503061 CATGCACCTCCTCCTCCG 59.497 66.667 0.00 0.00 0.00 4.63
982 987 3.474570 ATGCACCTCCTCCTCCGC 61.475 66.667 0.00 0.00 0.00 5.54
1049 1065 2.967946 ATCCTCAGCAGCAGCAGCA 61.968 57.895 12.92 0.00 45.49 4.41
1050 1066 2.878089 ATCCTCAGCAGCAGCAGCAG 62.878 60.000 12.92 3.97 45.49 4.24
1068 1084 4.758251 CCAGCGATCGCCACCACA 62.758 66.667 34.89 0.00 43.17 4.17
1069 1085 3.190849 CAGCGATCGCCACCACAG 61.191 66.667 34.89 13.29 43.17 3.66
1085 1101 1.247419 ACAGCACCGGAGAGAGACAG 61.247 60.000 9.46 0.00 0.00 3.51
1089 1105 2.336478 ACCGGAGAGAGACAGCACG 61.336 63.158 9.46 0.00 0.00 5.34
1093 1109 0.028770 GGAGAGAGACAGCACGATCG 59.971 60.000 14.88 14.88 0.00 3.69
1095 1111 1.064946 GAGAGACAGCACGATCGGG 59.935 63.158 20.98 17.95 0.00 5.14
1125 1145 2.721971 ATCCAGCGATCATCACCGGC 62.722 60.000 0.00 0.00 0.00 6.13
1177 1197 4.700365 GCGGGGCGTGCAAGTTTC 62.700 66.667 0.59 0.00 0.00 2.78
1542 1562 2.421739 GCGGATCAGTACGGGCAT 59.578 61.111 0.00 0.00 30.33 4.40
1545 1565 1.830145 GGATCAGTACGGGCATGGT 59.170 57.895 0.00 0.00 0.00 3.55
1549 1569 4.467084 AGTACGGGCATGGTGGCG 62.467 66.667 0.00 0.00 44.78 5.69
1569 1589 1.070786 CTACCAGTGGCACAACGGT 59.929 57.895 23.88 23.88 44.16 4.83
1570 1590 0.949105 CTACCAGTGGCACAACGGTC 60.949 60.000 24.04 0.00 44.16 4.79
1571 1591 1.404479 TACCAGTGGCACAACGGTCT 61.404 55.000 24.04 8.75 44.16 3.85
1575 1595 3.542676 TGGCACAACGGTCTCGGT 61.543 61.111 0.00 0.00 41.39 4.69
1652 1672 2.509336 CGGGCACGACTCCATCAC 60.509 66.667 0.00 0.00 44.60 3.06
1764 1784 4.208686 GGCTTCGAGACGGCGGAT 62.209 66.667 13.24 0.00 0.00 4.18
1779 1799 1.209275 CGGATCAGTCGTCATTCGGC 61.209 60.000 0.00 0.00 45.26 5.54
1810 1830 4.773117 GGTGGAGGTCGTCGTCGC 62.773 72.222 0.00 0.00 36.96 5.19
1961 1981 4.951715 CCTGAATCCTGATCATGTTTTGGA 59.048 41.667 0.00 0.00 0.00 3.53
2016 2036 3.965209 TTTTAAAGTCTGCGTCGATCG 57.035 42.857 9.36 9.36 43.12 3.69
2043 2063 3.801698 TCAATCATGCTCAGGTTCTAGC 58.198 45.455 0.00 0.00 39.25 3.42
2044 2064 3.453717 TCAATCATGCTCAGGTTCTAGCT 59.546 43.478 0.00 0.00 39.53 3.32
2045 2065 4.651045 TCAATCATGCTCAGGTTCTAGCTA 59.349 41.667 0.00 0.00 39.53 3.32
2046 2066 4.870123 ATCATGCTCAGGTTCTAGCTAG 57.130 45.455 15.01 15.01 39.53 3.42
2165 2190 5.230726 GCAAAAATGCTTCTTGGTATGATCG 59.769 40.000 0.00 0.00 0.00 3.69
2166 2191 6.324819 CAAAAATGCTTCTTGGTATGATCGT 58.675 36.000 0.00 0.00 0.00 3.73
2207 2232 8.117813 TGGTTTGGAAATAAGTTATCTTGTCC 57.882 34.615 0.00 2.60 35.36 4.02
2230 2255 6.656270 TCCGAGTTCTGTTCTGTATAGTTGTA 59.344 38.462 0.00 0.00 0.00 2.41
2243 2269 9.404848 TCTGTATAGTTGTAACTGCAGTAGTAT 57.595 33.333 22.01 17.96 39.18 2.12
2273 2299 2.349590 TGATTCGACTTGTCATGCCAG 58.650 47.619 1.59 0.00 0.00 4.85
2298 2324 9.499479 AGAAATATGTATGTATTGCCAAGAGAG 57.501 33.333 0.00 0.00 0.00 3.20
2299 2325 9.494271 GAAATATGTATGTATTGCCAAGAGAGA 57.506 33.333 0.00 0.00 0.00 3.10
2308 2334 2.915349 TGCCAAGAGAGATGATCAAGC 58.085 47.619 0.00 0.00 0.00 4.01
2379 2405 1.675483 GATTCAATGGCCGCACATGTA 59.325 47.619 0.00 0.00 0.00 2.29
2384 2410 1.382522 ATGGCCGCACATGTAGAAAG 58.617 50.000 0.00 0.00 0.00 2.62
2439 2465 2.935676 GCTCCTCCAACTCTTTTACGGG 60.936 54.545 0.00 0.00 0.00 5.28
2448 2474 5.338137 CCAACTCTTTTACGGGACCTATCTT 60.338 44.000 0.00 0.00 0.00 2.40
2449 2475 6.127253 CCAACTCTTTTACGGGACCTATCTTA 60.127 42.308 0.00 0.00 0.00 2.10
2454 2480 7.723324 TCTTTTACGGGACCTATCTTATCTTG 58.277 38.462 0.00 0.00 0.00 3.02
2458 2484 5.703310 ACGGGACCTATCTTATCTTGTACT 58.297 41.667 0.00 0.00 0.00 2.73
2479 2505 9.209048 TGTACTGCCTTTCTAAAGATTCCTATA 57.791 33.333 4.01 0.00 38.28 1.31
2524 2553 9.790344 AGTACGTGTTGGTATAATCTAGTATCT 57.210 33.333 0.00 0.00 0.00 1.98
2585 2614 2.818130 TGCGATGATGCTGCAGTATA 57.182 45.000 17.85 6.83 34.03 1.47
2604 2633 8.887717 GCAGTATACAATCCTTAATCATGATCC 58.112 37.037 9.06 0.00 0.00 3.36
2613 2642 5.869344 TCCTTAATCATGATCCGCTTAATCG 59.131 40.000 9.06 0.00 0.00 3.34
2618 2647 1.847818 TGATCCGCTTAATCGTTCGG 58.152 50.000 0.00 0.00 42.96 4.30
2619 2648 1.135527 TGATCCGCTTAATCGTTCGGT 59.864 47.619 0.00 0.00 42.28 4.69
2621 2650 0.244450 TCCGCTTAATCGTTCGGTGT 59.756 50.000 0.00 0.00 42.28 4.16
2645 2674 9.143155 TGTAATTATGCTTAGACTGTGATCCTA 57.857 33.333 0.00 0.00 0.00 2.94
2716 2747 3.481559 TTCTGAGGTTCTCTGGGAGAT 57.518 47.619 0.00 0.00 38.56 2.75
2728 2759 6.813293 TCTCTGGGAGATTATTTGATGTGA 57.187 37.500 0.00 0.00 33.35 3.58
2815 2848 5.290493 AGAACATAACTGTGAGGTTGTGA 57.710 39.130 0.00 0.00 39.53 3.58
2820 2853 5.239306 ACATAACTGTGAGGTTGTGACATTG 59.761 40.000 10.16 0.00 39.53 2.82
2857 2890 9.745880 AATATACTTGAATAACGTACAGGACTG 57.254 33.333 0.00 0.00 0.00 3.51
2858 2891 4.817517 ACTTGAATAACGTACAGGACTGG 58.182 43.478 4.14 0.00 34.19 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.069569 CACACTAGTAGAAAAATGGTCAAACG 58.930 38.462 3.59 0.00 0.00 3.60
2 3 6.544197 TGCACACTAGTAGAAAAATGGTCAAA 59.456 34.615 3.59 0.00 0.00 2.69
4 5 5.616270 TGCACACTAGTAGAAAAATGGTCA 58.384 37.500 3.59 0.00 0.00 4.02
5 6 6.546395 CATGCACACTAGTAGAAAAATGGTC 58.454 40.000 3.59 0.00 0.00 4.02
6 7 5.106157 GCATGCACACTAGTAGAAAAATGGT 60.106 40.000 14.21 0.00 0.00 3.55
7 8 5.106197 TGCATGCACACTAGTAGAAAAATGG 60.106 40.000 18.46 0.00 0.00 3.16
8 9 5.941733 TGCATGCACACTAGTAGAAAAATG 58.058 37.500 18.46 2.82 0.00 2.32
9 10 6.151648 ACATGCATGCACACTAGTAGAAAAAT 59.848 34.615 25.37 0.00 0.00 1.82
10 11 5.473162 ACATGCATGCACACTAGTAGAAAAA 59.527 36.000 25.37 0.00 0.00 1.94
11 12 5.003160 ACATGCATGCACACTAGTAGAAAA 58.997 37.500 25.37 0.00 0.00 2.29
12 13 4.578871 ACATGCATGCACACTAGTAGAAA 58.421 39.130 25.37 0.00 0.00 2.52
13 14 4.206477 ACATGCATGCACACTAGTAGAA 57.794 40.909 25.37 0.00 0.00 2.10
14 15 3.893326 ACATGCATGCACACTAGTAGA 57.107 42.857 25.37 0.00 0.00 2.59
15 16 6.609237 AATTACATGCATGCACACTAGTAG 57.391 37.500 25.37 7.97 0.00 2.57
16 17 8.558700 CATAAATTACATGCATGCACACTAGTA 58.441 33.333 25.37 16.91 0.00 1.82
17 18 5.902613 AAATTACATGCATGCACACTAGT 57.097 34.783 25.37 17.90 0.00 2.57
18 19 7.641760 TCATAAATTACATGCATGCACACTAG 58.358 34.615 25.37 12.97 0.00 2.57
19 20 7.565323 TCATAAATTACATGCATGCACACTA 57.435 32.000 25.37 9.60 0.00 2.74
20 21 6.453926 TCATAAATTACATGCATGCACACT 57.546 33.333 25.37 10.69 0.00 3.55
21 22 8.800231 TTATCATAAATTACATGCATGCACAC 57.200 30.769 25.37 0.00 0.00 3.82
22 23 9.247126 GTTTATCATAAATTACATGCATGCACA 57.753 29.630 25.37 8.58 0.00 4.57
23 24 9.247126 TGTTTATCATAAATTACATGCATGCAC 57.753 29.630 25.37 3.81 0.00 4.57
24 25 9.984190 ATGTTTATCATAAATTACATGCATGCA 57.016 25.926 26.53 25.04 34.67 3.96
43 44 9.112658 AGGTGGTGCTAACCTATATATGTTTAT 57.887 33.333 8.45 0.00 46.44 1.40
44 45 8.500667 AGGTGGTGCTAACCTATATATGTTTA 57.499 34.615 8.45 0.00 46.44 2.01
45 46 7.388638 AGGTGGTGCTAACCTATATATGTTT 57.611 36.000 8.45 0.00 46.44 2.83
48 49 6.381420 AGCTAGGTGGTGCTAACCTATATATG 59.619 42.308 11.57 3.74 46.65 1.78
49 50 6.503944 AGCTAGGTGGTGCTAACCTATATAT 58.496 40.000 11.57 0.00 46.65 0.86
50 51 5.900437 AGCTAGGTGGTGCTAACCTATATA 58.100 41.667 11.57 0.00 46.65 0.86
51 52 4.753186 AGCTAGGTGGTGCTAACCTATAT 58.247 43.478 11.57 3.54 46.65 0.86
52 53 4.194678 AGCTAGGTGGTGCTAACCTATA 57.805 45.455 11.57 0.00 46.65 1.31
154 155 5.531122 TCATTATCCTAACCAAGAGTCCG 57.469 43.478 0.00 0.00 0.00 4.79
175 176 4.513318 GCATCATGTAGGGTTAAGAAGCTC 59.487 45.833 0.00 0.00 0.00 4.09
180 181 4.101585 CCTCTGCATCATGTAGGGTTAAGA 59.898 45.833 1.50 0.00 27.67 2.10
208 209 2.032681 AACTTCTGCGACCCTGCC 59.967 61.111 0.00 0.00 0.00 4.85
262 263 1.473434 GCACCGGCTGCTCTAAACTAT 60.473 52.381 18.16 0.00 43.33 2.12
281 282 2.752903 CCCAACATGTACCCTAAACTGC 59.247 50.000 0.00 0.00 0.00 4.40
285 286 1.997040 AGCCCCAACATGTACCCTAAA 59.003 47.619 0.00 0.00 0.00 1.85
332 333 9.959693 AGTGGGCTAATATACCAATCTATCTAT 57.040 33.333 0.00 0.00 35.77 1.98
333 334 9.201989 CAGTGGGCTAATATACCAATCTATCTA 57.798 37.037 0.00 0.00 35.77 1.98
334 335 7.365117 GCAGTGGGCTAATATACCAATCTATCT 60.365 40.741 0.00 0.00 40.25 1.98
335 336 6.763610 GCAGTGGGCTAATATACCAATCTATC 59.236 42.308 0.00 0.00 40.25 2.08
405 406 7.648142 AGTGTATGCAAATTTATATTCGTGGG 58.352 34.615 0.00 0.00 0.00 4.61
406 407 8.957028 CAAGTGTATGCAAATTTATATTCGTGG 58.043 33.333 0.00 0.00 0.00 4.94
422 423 6.863126 GGGAAAATATATGCACAAGTGTATGC 59.137 38.462 13.03 0.00 42.40 3.14
495 497 7.995488 AGGAGACAATAAGTGATGGGAAATTAG 59.005 37.037 0.00 0.00 0.00 1.73
510 512 6.942576 CCTTTCTTTTCCTCAGGAGACAATAA 59.057 38.462 0.00 0.00 31.21 1.40
521 523 2.051692 TCCGGTCCTTTCTTTTCCTCA 58.948 47.619 0.00 0.00 0.00 3.86
537 539 4.212213 TGTCGTTTGTGTTATTTTCCGG 57.788 40.909 0.00 0.00 0.00 5.14
539 541 4.855531 AGCTGTCGTTTGTGTTATTTTCC 58.144 39.130 0.00 0.00 0.00 3.13
691 693 4.689345 AGTTTAGTTGTTATCGTGACTGCC 59.311 41.667 0.00 0.00 0.00 4.85
716 718 4.859629 ACACAACTTTCTCTCGTGTTTC 57.140 40.909 0.00 0.00 37.53 2.78
753 755 0.394352 CCACAATGGGGCTAGGTCAC 60.394 60.000 0.00 0.00 32.67 3.67
772 774 3.507622 CCAATCCCAAGAGAAGGACAAAC 59.492 47.826 0.00 0.00 34.20 2.93
844 848 2.124695 CCCGCTAAGTTCTGCCCC 60.125 66.667 0.00 0.00 0.00 5.80
852 856 3.148279 CTCTCCGGCCCGCTAAGT 61.148 66.667 0.00 0.00 0.00 2.24
883 887 3.243201 GCCTCCATTATTTTGAGCTTCCG 60.243 47.826 0.00 0.00 0.00 4.30
945 949 1.455773 GTTGGGGATTAGGGCCAGC 60.456 63.158 6.18 0.00 0.00 4.85
946 950 1.230212 GGTTGGGGATTAGGGCCAG 59.770 63.158 6.18 0.00 0.00 4.85
971 976 1.528309 GAGAGGAGCGGAGGAGGAG 60.528 68.421 0.00 0.00 0.00 3.69
972 977 2.598467 GAGAGGAGCGGAGGAGGA 59.402 66.667 0.00 0.00 0.00 3.71
974 979 0.183971 TAAGGAGAGGAGCGGAGGAG 59.816 60.000 0.00 0.00 0.00 3.69
978 983 2.240279 GCTTATAAGGAGAGGAGCGGA 58.760 52.381 14.28 0.00 0.00 5.54
981 986 4.322567 CCATTGCTTATAAGGAGAGGAGC 58.677 47.826 16.74 2.22 0.00 4.70
982 987 4.322567 GCCATTGCTTATAAGGAGAGGAG 58.677 47.826 22.50 8.34 33.53 3.69
1051 1067 4.758251 TGTGGTGGCGATCGCTGG 62.758 66.667 36.25 0.00 41.60 4.85
1052 1068 3.190849 CTGTGGTGGCGATCGCTG 61.191 66.667 36.25 15.48 41.60 5.18
1055 1071 3.490759 GTGCTGTGGTGGCGATCG 61.491 66.667 11.69 11.69 0.00 3.69
1056 1072 3.127533 GGTGCTGTGGTGGCGATC 61.128 66.667 0.00 0.00 0.00 3.69
1061 1077 3.596066 CTCTCCGGTGCTGTGGTGG 62.596 68.421 0.00 0.00 0.00 4.61
1068 1084 2.347322 GCTGTCTCTCTCCGGTGCT 61.347 63.158 0.00 0.00 0.00 4.40
1069 1085 2.183046 GCTGTCTCTCTCCGGTGC 59.817 66.667 0.00 0.00 0.00 5.01
1093 1109 3.432051 CTGGATCGCTCGGTGACCC 62.432 68.421 0.00 0.00 0.00 4.46
1095 1111 2.583593 GCTGGATCGCTCGGTGAC 60.584 66.667 0.00 0.00 0.00 3.67
1125 1145 1.431488 CCGTCATGCTCATCAACCGG 61.431 60.000 0.00 0.00 0.00 5.28
1164 1184 2.427410 CGCAGAAACTTGCACGCC 60.427 61.111 0.00 0.00 44.28 5.68
1242 1262 4.776322 TGGATGGCGGCGAAGTGG 62.776 66.667 12.98 0.00 0.00 4.00
1542 1562 4.015406 CACTGGTAGGCGCCACCA 62.015 66.667 33.94 33.94 43.82 4.17
1550 1570 1.671054 CCGTTGTGCCACTGGTAGG 60.671 63.158 0.00 0.00 0.00 3.18
1551 1571 0.949105 GACCGTTGTGCCACTGGTAG 60.949 60.000 6.91 0.00 31.86 3.18
1557 1577 3.041940 CCGAGACCGTTGTGCCAC 61.042 66.667 0.00 0.00 0.00 5.01
1677 1697 3.548214 CGTGGTACATCATGTAGTCCGAG 60.548 52.174 0.00 0.00 44.52 4.63
1756 1776 1.945354 AATGACGACTGATCCGCCGT 61.945 55.000 0.00 0.00 38.01 5.68
1764 1784 1.443702 CGTGCCGAATGACGACTGA 60.444 57.895 0.00 0.00 45.77 3.41
1773 1793 3.082579 GCTCTCCTCCGTGCCGAAT 62.083 63.158 0.00 0.00 0.00 3.34
1779 1799 4.135153 CACCCGCTCTCCTCCGTG 62.135 72.222 0.00 0.00 0.00 4.94
1810 1830 1.153823 CCTCGCAGTCTTGGTACCG 60.154 63.158 7.57 0.00 0.00 4.02
1851 1871 3.687572 TCTTACGAGCGCTTAAGGTAG 57.312 47.619 22.51 12.06 0.00 3.18
1860 1880 1.266466 GTAGTGGTTCTTACGAGCGC 58.734 55.000 0.00 0.00 0.00 5.92
1961 1981 3.933861 ACCCAACTCAAACTCTCAAGT 57.066 42.857 0.00 0.00 37.32 3.16
2016 2036 3.661944 ACCTGAGCATGATTGATCGATC 58.338 45.455 18.72 18.72 41.23 3.69
2187 2212 6.942976 ACTCGGACAAGATAACTTATTTCCA 58.057 36.000 7.54 0.00 34.70 3.53
2207 2232 8.021973 AGTTACAACTATACAGAACAGAACTCG 58.978 37.037 0.00 0.00 37.52 4.18
2243 2269 9.034544 CATGACAAGTCGAATCATATACAGAAA 57.965 33.333 0.00 0.00 31.83 2.52
2273 2299 9.494271 TCTCTCTTGGCAATACATACATATTTC 57.506 33.333 0.00 0.00 0.00 2.17
2298 2324 4.115516 TCTAGCTTGTTCGCTTGATCATC 58.884 43.478 0.00 0.00 41.30 2.92
2299 2325 4.128925 TCTAGCTTGTTCGCTTGATCAT 57.871 40.909 0.00 0.00 41.30 2.45
2308 2334 1.728971 CACTGCCTTCTAGCTTGTTCG 59.271 52.381 0.00 0.00 0.00 3.95
2408 2434 1.335496 GTTGGAGGAGCTAGCTAGTCG 59.665 57.143 19.38 0.00 0.00 4.18
2439 2465 6.658188 AGGCAGTACAAGATAAGATAGGTC 57.342 41.667 0.00 0.00 0.00 3.85
2448 2474 9.601217 GAATCTTTAGAAAGGCAGTACAAGATA 57.399 33.333 0.00 0.00 36.67 1.98
2449 2475 7.554476 GGAATCTTTAGAAAGGCAGTACAAGAT 59.446 37.037 0.00 0.00 36.67 2.40
2458 2484 8.275187 TCCATATAGGAATCTTTAGAAAGGCA 57.725 34.615 2.29 0.00 45.65 4.75
2479 2505 8.300286 CACGTACTACTTCAATATCAGATCCAT 58.700 37.037 0.00 0.00 0.00 3.41
2531 2560 8.492748 GCTAGCTATATATACTACTCTTGCGAG 58.507 40.741 7.70 0.00 43.10 5.03
2532 2561 8.205512 AGCTAGCTATATATACTACTCTTGCGA 58.794 37.037 17.69 0.00 0.00 5.10
2533 2562 8.373048 AGCTAGCTATATATACTACTCTTGCG 57.627 38.462 17.69 0.00 0.00 4.85
2545 2574 9.823647 ATCGCATGTAAAAAGCTAGCTATATAT 57.176 29.630 19.70 12.18 0.00 0.86
2546 2575 9.087424 CATCGCATGTAAAAAGCTAGCTATATA 57.913 33.333 19.70 10.43 0.00 0.86
2547 2576 7.819415 TCATCGCATGTAAAAAGCTAGCTATAT 59.181 33.333 19.70 9.42 0.00 0.86
2562 2591 1.223187 CTGCAGCATCATCGCATGTA 58.777 50.000 0.00 0.00 34.63 2.29
2585 2614 4.978099 AGCGGATCATGATTAAGGATTGT 58.022 39.130 10.14 0.00 0.00 2.71
2604 2633 4.509915 AATTACACCGAACGATTAAGCG 57.490 40.909 12.26 12.26 37.29 4.68
2613 2642 6.534079 ACAGTCTAAGCATAATTACACCGAAC 59.466 38.462 0.00 0.00 0.00 3.95
2618 2647 7.928706 AGGATCACAGTCTAAGCATAATTACAC 59.071 37.037 0.00 0.00 0.00 2.90
2619 2648 8.023021 AGGATCACAGTCTAAGCATAATTACA 57.977 34.615 0.00 0.00 0.00 2.41
2697 2728 3.481559 AATCTCCCAGAGAACCTCAGA 57.518 47.619 0.00 0.00 42.27 3.27
2698 2729 5.885449 AATAATCTCCCAGAGAACCTCAG 57.115 43.478 0.00 0.00 42.27 3.35
2699 2730 5.726308 TCAAATAATCTCCCAGAGAACCTCA 59.274 40.000 0.00 0.00 42.27 3.86
2700 2731 6.240549 TCAAATAATCTCCCAGAGAACCTC 57.759 41.667 0.00 0.00 42.27 3.85
2701 2732 6.159398 ACATCAAATAATCTCCCAGAGAACCT 59.841 38.462 0.00 0.00 42.27 3.50
2702 2733 6.261826 CACATCAAATAATCTCCCAGAGAACC 59.738 42.308 0.00 0.00 42.27 3.62
2706 2737 7.052873 AGTTCACATCAAATAATCTCCCAGAG 58.947 38.462 0.00 0.00 0.00 3.35
2710 2741 8.964476 TCTTAGTTCACATCAAATAATCTCCC 57.036 34.615 0.00 0.00 0.00 4.30
2831 2864 9.745880 CAGTCCTGTACGTTATTCAAGTATATT 57.254 33.333 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.