Multiple sequence alignment - TraesCS5D01G161000

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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 TraesCS5D01G161000 chr5D 100.000 3802 0 0 1 3802 251066090 251062289 0.000000e+00 7022.0
1 TraesCS5D01G161000 chr5D 97.561 41 0 1 1426 1466 233046244 233046283 6.810000e-08 69.4
2 TraesCS5D01G161000 chr5B 91.594 2855 178 23 984 3802 283625004 283622176 0.000000e+00 3886.0
3 TraesCS5D01G161000 chr5B 94.995 919 45 1 1 918 283625910 283624992 0.000000e+00 1441.0
4 TraesCS5D01G161000 chr5A 94.010 2504 128 13 981 3484 334265966 334263485 0.000000e+00 3773.0
5 TraesCS5D01G161000 chr5A 94.794 922 43 3 7 927 334266868 334265951 0.000000e+00 1432.0
6 TraesCS5D01G161000 chr5A 96.238 319 12 0 3484 3802 334263266 334262948 1.210000e-144 523.0
7 TraesCS5D01G161000 chr6B 89.051 137 15 0 1943 2079 539727679 539727543 1.820000e-38 171.0
8 TraesCS5D01G161000 chr6B 84.906 159 24 0 1921 2079 564993598 564993440 1.090000e-35 161.0
9 TraesCS5D01G161000 chr6D 84.906 159 24 0 1921 2079 378379440 378379282 1.090000e-35 161.0
10 TraesCS5D01G161000 chr6A 84.906 159 24 0 1921 2079 520355710 520355552 1.090000e-35 161.0
11 TraesCS5D01G161000 chr7D 84.810 158 24 0 1921 2078 174992614 174992771 3.930000e-35 159.0
12 TraesCS5D01G161000 chr7D 95.652 46 1 1 1422 1466 296736160 296736205 5.270000e-09 73.1
13 TraesCS5D01G161000 chr7B 84.810 158 24 0 1921 2078 140652907 140653064 3.930000e-35 159.0
14 TraesCS5D01G161000 chr7A 84.810 158 24 0 1921 2078 177136164 177136321 3.930000e-35 159.0
15 TraesCS5D01G161000 chr2A 79.429 175 35 1 1894 2067 778914972 778915146 5.160000e-24 122.0
16 TraesCS5D01G161000 chr2B 79.191 173 35 1 1896 2067 777549285 777549113 6.670000e-23 119.0
17 TraesCS5D01G161000 chr2B 79.213 178 30 5 1894 2067 777521735 777521561 2.400000e-22 117.0
18 TraesCS5D01G161000 chr2B 79.630 162 31 2 1907 2067 777658735 777658575 8.630000e-22 115.0
19 TraesCS5D01G161000 chr2D 78.756 193 28 11 1883 2067 634658625 634658438 2.400000e-22 117.0
20 TraesCS5D01G161000 chr4D 97.619 42 0 1 1425 1466 207363109 207363069 1.890000e-08 71.3
21 TraesCS5D01G161000 chrUn 100.000 37 0 0 1430 1466 180666723 180666687 6.810000e-08 69.4
22 TraesCS5D01G161000 chrUn 100.000 37 0 0 1430 1466 216511442 216511406 6.810000e-08 69.4
23 TraesCS5D01G161000 chrUn 100.000 37 0 0 1430 1466 286271941 286271977 6.810000e-08 69.4
24 TraesCS5D01G161000 chrUn 100.000 37 0 0 1430 1466 354078096 354078132 6.810000e-08 69.4


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 TraesCS5D01G161000 chr5D 251062289 251066090 3801 True 7022.000000 7022 100.0000 1 3802 1 chr5D.!!$R1 3801
1 TraesCS5D01G161000 chr5B 283622176 283625910 3734 True 2663.500000 3886 93.2945 1 3802 2 chr5B.!!$R1 3801
2 TraesCS5D01G161000 chr5A 334262948 334266868 3920 True 1909.333333 3773 95.0140 7 3802 3 chr5A.!!$R1 3795

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
194 196 0.032952 ACCGTGTTTTCTAGCTGCGA 59.967 50.0 0.00 0.0 0.00 5.10 F
278 280 1.195115 GGATGAGACCTGGTGTGCTA 58.805 55.0 2.82 0.0 0.00 3.49 F
1651 1665 0.108329 TGGGCGCTTAGAGTTGTAGC 60.108 55.0 7.64 0.0 0.00 3.58 F
2174 2188 0.109597 GCACAGGGATGAACTTTGCG 60.110 55.0 0.00 0.0 32.75 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1078 1092 2.029623 TGGCTAGATCTACAACGGGTC 58.970 52.381 0.0 0.0 0.00 4.46 R
2231 2245 0.039618 ATGATGACCCAAAGGCGGTT 59.960 50.000 0.0 0.0 36.11 4.44 R
2633 2647 0.036164 TCACATTGTTCCCAGTCCCG 59.964 55.000 0.0 0.0 0.00 5.14 R
3715 3950 4.202357 TGCTTTAAGAGTGTGTGAGATGGT 60.202 41.667 0.0 0.0 0.00 3.55 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
194 196 0.032952 ACCGTGTTTTCTAGCTGCGA 59.967 50.000 0.00 0.00 0.00 5.10
278 280 1.195115 GGATGAGACCTGGTGTGCTA 58.805 55.000 2.82 0.00 0.00 3.49
294 296 4.452455 GTGTGCTATTCATACCCATGCTAC 59.548 45.833 0.00 0.00 31.46 3.58
346 348 2.126057 TCCATGCATGTCATAGACCCA 58.874 47.619 24.58 0.00 33.19 4.51
527 529 4.679372 GCATTAGGCTCGTCTTTCTCTCTT 60.679 45.833 0.00 0.00 40.25 2.85
611 613 1.968493 TCACCTCTAGCCGTTTTGTCT 59.032 47.619 0.00 0.00 0.00 3.41
624 626 3.698250 TTGTCTTCCAGGGACAACG 57.302 52.632 7.09 0.00 45.14 4.10
760 762 6.028146 TCTGCGGTAGTGTTTAAACATCTA 57.972 37.500 23.11 20.35 41.59 1.98
863 865 1.630369 CCCTTCATTCACCTGGTGAGA 59.370 52.381 26.94 19.73 43.69 3.27
905 907 7.558444 TCTCTATCACTTACTCTTTCTCCCTTC 59.442 40.741 0.00 0.00 0.00 3.46
907 909 6.943899 ATCACTTACTCTTTCTCCCTTCTT 57.056 37.500 0.00 0.00 0.00 2.52
909 911 6.078664 TCACTTACTCTTTCTCCCTTCTTCT 58.921 40.000 0.00 0.00 0.00 2.85
910 912 6.555360 TCACTTACTCTTTCTCCCTTCTTCTT 59.445 38.462 0.00 0.00 0.00 2.52
911 913 6.871492 CACTTACTCTTTCTCCCTTCTTCTTC 59.129 42.308 0.00 0.00 0.00 2.87
912 914 6.785466 ACTTACTCTTTCTCCCTTCTTCTTCT 59.215 38.462 0.00 0.00 0.00 2.85
913 915 7.291416 ACTTACTCTTTCTCCCTTCTTCTTCTT 59.709 37.037 0.00 0.00 0.00 2.52
914 916 6.109156 ACTCTTTCTCCCTTCTTCTTCTTC 57.891 41.667 0.00 0.00 0.00 2.87
915 917 5.843969 ACTCTTTCTCCCTTCTTCTTCTTCT 59.156 40.000 0.00 0.00 0.00 2.85
916 918 6.328934 ACTCTTTCTCCCTTCTTCTTCTTCTT 59.671 38.462 0.00 0.00 0.00 2.52
917 919 6.764379 TCTTTCTCCCTTCTTCTTCTTCTTC 58.236 40.000 0.00 0.00 0.00 2.87
918 920 6.556874 TCTTTCTCCCTTCTTCTTCTTCTTCT 59.443 38.462 0.00 0.00 0.00 2.85
919 921 6.755542 TTCTCCCTTCTTCTTCTTCTTCTT 57.244 37.500 0.00 0.00 0.00 2.52
920 922 6.353404 TCTCCCTTCTTCTTCTTCTTCTTC 57.647 41.667 0.00 0.00 0.00 2.87
921 923 6.081356 TCTCCCTTCTTCTTCTTCTTCTTCT 58.919 40.000 0.00 0.00 0.00 2.85
922 924 6.556874 TCTCCCTTCTTCTTCTTCTTCTTCTT 59.443 38.462 0.00 0.00 0.00 2.52
923 925 6.764379 TCCCTTCTTCTTCTTCTTCTTCTTC 58.236 40.000 0.00 0.00 0.00 2.87
924 926 6.556874 TCCCTTCTTCTTCTTCTTCTTCTTCT 59.443 38.462 0.00 0.00 0.00 2.85
925 927 7.071824 TCCCTTCTTCTTCTTCTTCTTCTTCTT 59.928 37.037 0.00 0.00 0.00 2.52
926 928 7.387673 CCCTTCTTCTTCTTCTTCTTCTTCTTC 59.612 40.741 0.00 0.00 0.00 2.87
927 929 8.150296 CCTTCTTCTTCTTCTTCTTCTTCTTCT 58.850 37.037 0.00 0.00 0.00 2.85
928 930 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
929 931 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
930 932 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
931 933 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
932 934 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
933 935 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
934 936 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
935 937 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
936 938 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
937 939 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
938 940 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
939 941 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
940 942 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
941 943 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
942 944 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
943 945 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
944 946 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
945 947 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
946 948 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
947 949 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
948 950 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
949 951 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
950 952 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
951 953 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
952 954 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
953 955 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
954 956 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
955 957 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
956 958 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
957 959 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
958 960 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
959 961 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
960 962 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
961 963 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
962 964 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
963 965 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
964 966 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
965 967 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
966 968 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
967 969 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
968 970 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
969 971 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
970 972 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
971 973 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
972 974 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
973 975 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
974 976 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
975 977 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
976 978 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
977 979 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
978 980 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
979 981 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
1015 1017 1.606606 GTGCATGCGACTTTTGCTAC 58.393 50.000 14.09 0.00 37.28 3.58
1025 1027 4.811557 GCGACTTTTGCTACATAATCTCCT 59.188 41.667 0.00 0.00 0.00 3.69
1029 1031 5.587844 ACTTTTGCTACATAATCTCCTGCAG 59.412 40.000 6.78 6.78 0.00 4.41
1078 1092 5.401079 GCTAGCTAGCGATCTTCACTTTAAG 59.599 44.000 28.89 0.00 39.82 1.85
1095 1109 6.973474 CACTTTAAGACCCGTTGTAGATCTAG 59.027 42.308 1.64 0.00 0.00 2.43
1156 1170 5.123820 GTGTTCCTGTGTACATGCATGTATT 59.876 40.000 35.33 16.84 44.25 1.89
1291 1305 2.437002 GGCGGCCGTATGTTTCCA 60.437 61.111 28.70 0.00 0.00 3.53
1295 1309 1.533129 GCGGCCGTATGTTTCCATTTC 60.533 52.381 28.70 0.00 32.29 2.17
1399 1413 6.015519 TGCATGCCAGATTTACTAGTTTTGTT 60.016 34.615 16.68 0.00 0.00 2.83
1490 1504 5.875224 TCCATGTTGGATTCACTACTTTGA 58.125 37.500 0.00 0.00 42.67 2.69
1605 1619 1.044611 GAGAGTATGGGGAGAGGCAC 58.955 60.000 0.00 0.00 0.00 5.01
1651 1665 0.108329 TGGGCGCTTAGAGTTGTAGC 60.108 55.000 7.64 0.00 0.00 3.58
1653 1667 1.407979 GGGCGCTTAGAGTTGTAGCTA 59.592 52.381 7.64 0.00 32.80 3.32
1724 1738 6.845302 TGCACTTATCATGACATTTTGAGTC 58.155 36.000 0.00 0.00 36.55 3.36
1847 1861 1.133823 TCAAACTCCAAGAGCAAGGCA 60.134 47.619 0.00 0.00 32.04 4.75
2133 2147 3.307906 CCTCACCGGAACCCACGA 61.308 66.667 9.46 0.00 33.16 4.35
2139 2153 2.430244 CGGAACCCACGACTGTCG 60.430 66.667 26.94 26.94 46.93 4.35
2174 2188 0.109597 GCACAGGGATGAACTTTGCG 60.110 55.000 0.00 0.00 32.75 4.85
2200 2214 1.203994 CCTCCCGACGTTTATGTCTGT 59.796 52.381 0.00 0.00 36.71 3.41
2231 2245 1.072266 TTCCAAGCAGCCTTTCCCTA 58.928 50.000 0.00 0.00 0.00 3.53
2249 2263 0.693622 TAACCGCCTTTGGGTCATCA 59.306 50.000 0.00 0.00 36.57 3.07
2297 2311 4.415332 CCTGGTGGGACGACGTCG 62.415 72.222 34.58 34.58 46.33 5.12
2321 2335 0.333993 TAGACGTGCTAAGAGGGGGT 59.666 55.000 0.00 0.00 0.00 4.95
2443 2457 1.895131 GGTGTCATTTGGCATTCCAGT 59.105 47.619 0.00 0.00 44.53 4.00
2516 2530 4.484236 CCGCAACTGCTTCAATATTTCAA 58.516 39.130 0.00 0.00 39.32 2.69
2521 2535 3.448660 ACTGCTTCAATATTTCAAGGGGC 59.551 43.478 6.19 0.00 0.00 5.80
2526 2540 4.871871 TCAATATTTCAAGGGGCCACTA 57.128 40.909 8.71 0.00 0.00 2.74
2608 2622 2.080336 AATGGTGGAGGTGGTGGTGG 62.080 60.000 0.00 0.00 0.00 4.61
2665 2679 1.135603 CAATGTGACGATGGGCAACAG 60.136 52.381 0.00 0.00 39.74 3.16
2759 2773 3.524789 ACTGGATCAACAATGGAGGATCA 59.475 43.478 11.24 0.00 38.27 2.92
2841 2855 4.467438 GGAAATGGAGGTCATTGAATTGGT 59.533 41.667 0.00 0.00 44.68 3.67
2873 2887 7.225397 GGTCAATCGTTTTCTTACTAGTTTCG 58.775 38.462 0.00 0.00 0.00 3.46
2883 2897 1.711206 ACTAGTTTCGGCGCTTCTTC 58.289 50.000 7.64 0.00 0.00 2.87
2884 2898 1.272769 ACTAGTTTCGGCGCTTCTTCT 59.727 47.619 7.64 3.78 0.00 2.85
2885 2899 2.288886 ACTAGTTTCGGCGCTTCTTCTT 60.289 45.455 7.64 0.00 0.00 2.52
2886 2900 1.149148 AGTTTCGGCGCTTCTTCTTC 58.851 50.000 7.64 0.00 0.00 2.87
2929 2945 5.389859 TCGCTCCATCATTTTCATGTTTT 57.610 34.783 0.00 0.00 0.00 2.43
3123 3139 3.149005 TGGTTTACCCACTGATCCAAC 57.851 47.619 0.00 0.00 38.72 3.77
3443 3459 5.578727 ACTCTTGTCAATCGAGCTAATTCAC 59.421 40.000 0.00 0.00 0.00 3.18
3492 3727 8.155620 AGATGATAATGATAGGCCACATTAGT 57.844 34.615 23.68 16.56 40.60 2.24
3508 3743 6.304922 CCACATTAGTACGCGTGATCTATTAC 59.695 42.308 24.59 9.43 0.00 1.89
3544 3779 5.506686 AGAAAACTTGAAAGGTTGCTCTC 57.493 39.130 0.00 0.00 36.94 3.20
3569 3804 4.607239 AGCATTTCCATCATCAAGGTTCT 58.393 39.130 0.00 0.00 0.00 3.01
3700 3935 7.420800 GGTAACAGAGATTGGCTCATAAATTG 58.579 38.462 0.00 0.00 46.45 2.32
3742 3977 6.942532 TCTCACACACTCTTAAAGCAAAAT 57.057 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.884961 TCTTGGGCTAGAACTCTATCCTT 58.115 43.478 6.59 0.00 35.60 3.36
194 196 6.931790 ATATCTGGCTATCTTGTCAGTGAT 57.068 37.500 0.00 0.00 40.28 3.06
278 280 4.598807 TCATGAGGTAGCATGGGTATGAAT 59.401 41.667 0.00 0.00 44.44 2.57
294 296 1.620323 TCACACACCTGTCTCATGAGG 59.380 52.381 22.42 9.96 35.26 3.86
346 348 1.620819 GGATGGACGGATGCACTCTAT 59.379 52.381 0.00 0.00 0.00 1.98
420 422 0.106335 CAACAGCAAAACATGGGGCA 59.894 50.000 0.00 0.00 0.00 5.36
611 613 3.961414 GGCCCGTTGTCCCTGGAA 61.961 66.667 0.00 0.00 0.00 3.53
624 626 1.746991 GCTGTAGAGCTGTTGGCCC 60.747 63.158 4.27 0.00 42.52 5.80
863 865 8.991275 AGTGATAGAGATCAAAGGAAGAAGAAT 58.009 33.333 0.00 0.00 43.77 2.40
905 907 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
907 909 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
909 911 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
910 912 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
911 913 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
912 914 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
913 915 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
914 916 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
915 917 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
916 918 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
917 919 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
918 920 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
919 921 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
920 922 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
921 923 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
922 924 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
923 925 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
924 926 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
925 927 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
926 928 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
927 929 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
928 930 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
929 931 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
930 932 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
931 933 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
932 934 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
933 935 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
934 936 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
935 937 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
936 938 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
937 939 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
938 940 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
939 941 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
940 942 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
941 943 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
942 944 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
943 945 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
944 946 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
945 947 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
946 948 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
947 949 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
948 950 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
949 951 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
950 952 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
951 953 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
952 954 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
953 955 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
954 956 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
955 957 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
956 958 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
957 959 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
958 960 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
959 961 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
960 962 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
961 963 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
962 964 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
963 965 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
964 966 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
965 967 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
966 968 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
967 969 8.147704 GGAAGAAGAAGAAGAAGAAGAAGAAGA 58.852 37.037 0.00 0.00 0.00 2.87
968 970 8.150296 AGGAAGAAGAAGAAGAAGAAGAAGAAG 58.850 37.037 0.00 0.00 0.00 2.85
969 971 8.028652 AGGAAGAAGAAGAAGAAGAAGAAGAA 57.971 34.615 0.00 0.00 0.00 2.52
970 972 7.523052 CGAGGAAGAAGAAGAAGAAGAAGAAGA 60.523 40.741 0.00 0.00 0.00 2.87
971 973 6.586082 CGAGGAAGAAGAAGAAGAAGAAGAAG 59.414 42.308 0.00 0.00 0.00 2.85
972 974 6.041069 ACGAGGAAGAAGAAGAAGAAGAAGAA 59.959 38.462 0.00 0.00 0.00 2.52
973 975 5.536916 ACGAGGAAGAAGAAGAAGAAGAAGA 59.463 40.000 0.00 0.00 0.00 2.87
974 976 5.633182 CACGAGGAAGAAGAAGAAGAAGAAG 59.367 44.000 0.00 0.00 0.00 2.85
975 977 5.533482 CACGAGGAAGAAGAAGAAGAAGAA 58.467 41.667 0.00 0.00 0.00 2.52
976 978 4.559704 GCACGAGGAAGAAGAAGAAGAAGA 60.560 45.833 0.00 0.00 0.00 2.87
977 979 3.677596 GCACGAGGAAGAAGAAGAAGAAG 59.322 47.826 0.00 0.00 0.00 2.85
978 980 3.069586 TGCACGAGGAAGAAGAAGAAGAA 59.930 43.478 0.00 0.00 0.00 2.52
979 981 2.628178 TGCACGAGGAAGAAGAAGAAGA 59.372 45.455 0.00 0.00 0.00 2.87
1015 1017 4.172505 GAGCGATACTGCAGGAGATTATG 58.827 47.826 19.93 0.00 37.31 1.90
1078 1092 2.029623 TGGCTAGATCTACAACGGGTC 58.970 52.381 0.00 0.00 0.00 4.46
1183 1197 6.349611 CCAAACAAGGTAGGTCATGAATTCAG 60.350 42.308 14.54 6.44 0.00 3.02
1185 1199 5.476945 ACCAAACAAGGTAGGTCATGAATTC 59.523 40.000 0.00 0.00 40.98 2.17
1291 1305 5.598417 CCTGGAAATATCCCCTTTTCGAAAT 59.402 40.000 12.12 0.00 45.95 2.17
1295 1309 2.623416 GCCTGGAAATATCCCCTTTTCG 59.377 50.000 0.00 0.00 45.95 3.46
1422 1436 8.082852 TCCGATCCAATTTTTCGTAAATCAAAA 58.917 29.630 0.00 0.00 0.00 2.44
1432 1446 4.624882 TGCAAAATCCGATCCAATTTTTCG 59.375 37.500 9.04 3.18 33.86 3.46
1724 1738 6.596888 AGTGAGACATGTAGAATCATTGGTTG 59.403 38.462 0.00 0.00 0.00 3.77
1847 1861 4.414956 TCCCCCGCCATCTGACCT 62.415 66.667 0.00 0.00 0.00 3.85
1870 1884 3.968837 TTCTTCTCCGCCCCCGCTA 62.969 63.158 0.00 0.00 0.00 4.26
1876 1890 2.188207 GAGGCTTCTTCTCCGCCC 59.812 66.667 0.00 0.00 44.84 6.13
2120 2134 2.841044 ACAGTCGTGGGTTCCGGT 60.841 61.111 0.00 0.00 0.00 5.28
2121 2135 2.048503 GACAGTCGTGGGTTCCGG 60.049 66.667 0.00 0.00 0.00 5.14
2200 2214 3.243839 GCTGCTTGGAATCTCAAAACCAA 60.244 43.478 0.00 0.00 39.60 3.67
2231 2245 0.039618 ATGATGACCCAAAGGCGGTT 59.960 50.000 0.00 0.00 36.11 4.44
2297 2311 3.429135 CCCCTCTTAGCACGTCTAGAAAC 60.429 52.174 0.00 0.00 0.00 2.78
2312 2326 2.612115 CCTCCTGCACCCCCTCTT 60.612 66.667 0.00 0.00 0.00 2.85
2321 2335 0.034767 CATCAAGAAGCCCTCCTGCA 60.035 55.000 0.00 0.00 0.00 4.41
2381 2395 1.410004 CATTGCCTGATCCAATGGCT 58.590 50.000 12.74 0.00 46.23 4.75
2386 2400 2.030571 GCATCCCATTGCCTGATCCAA 61.031 52.381 0.00 0.00 36.60 3.53
2398 2412 1.228063 GGCGTCATCAGCATCCCAT 60.228 57.895 0.00 0.00 36.08 4.00
2425 2439 2.562298 GGAACTGGAATGCCAAATGACA 59.438 45.455 0.00 0.00 45.41 3.58
2516 2530 3.618855 TTCCTCGCTAGTGGCCCCT 62.619 63.158 0.00 0.00 37.74 4.79
2521 2535 1.339610 CATCTCCTTCCTCGCTAGTGG 59.660 57.143 2.90 0.00 0.00 4.00
2526 2540 1.388065 CCGTCATCTCCTTCCTCGCT 61.388 60.000 0.00 0.00 0.00 4.93
2608 2622 0.179073 ATGCACGCCTCCTGATACAC 60.179 55.000 0.00 0.00 0.00 2.90
2633 2647 0.036164 TCACATTGTTCCCAGTCCCG 59.964 55.000 0.00 0.00 0.00 5.14
2665 2679 5.964887 ATTGTTGTTGTTGTGTATGTTGC 57.035 34.783 0.00 0.00 0.00 4.17
2841 2855 3.815809 AGAAAACGATTGACCCACTTCA 58.184 40.909 0.00 0.00 0.00 3.02
2873 2887 4.467735 CAAGTAAAAGAAGAAGAAGCGCC 58.532 43.478 2.29 0.00 0.00 6.53
2883 2897 9.107367 CGAAATAAGTCAAGCAAGTAAAAGAAG 57.893 33.333 0.00 0.00 0.00 2.85
2884 2898 7.589954 GCGAAATAAGTCAAGCAAGTAAAAGAA 59.410 33.333 0.00 0.00 0.00 2.52
2885 2899 7.041372 AGCGAAATAAGTCAAGCAAGTAAAAGA 60.041 33.333 0.00 0.00 0.00 2.52
2886 2900 7.078228 AGCGAAATAAGTCAAGCAAGTAAAAG 58.922 34.615 0.00 0.00 0.00 2.27
2929 2945 5.941555 ACAAAACAATCCCCACTTAAACA 57.058 34.783 0.00 0.00 0.00 2.83
2986 3002 8.736742 CAAACAATACTTAATTAAGCATCGCAG 58.263 33.333 22.45 10.39 36.79 5.18
3050 3066 7.717568 TCTCTACAACATCACCTAGATAAAGC 58.282 38.462 0.00 0.00 34.43 3.51
3352 3368 9.992910 AGAAGAAAAATGCTTGAAAATTGTTTC 57.007 25.926 0.00 0.00 43.04 2.78
3490 3725 6.754702 ATATGGTAATAGATCACGCGTACT 57.245 37.500 13.44 14.42 0.00 2.73
3492 3727 7.823665 AGAAATATGGTAATAGATCACGCGTA 58.176 34.615 13.44 0.28 0.00 4.42
3544 3779 6.320672 AGAACCTTGATGATGGAAATGCTAAG 59.679 38.462 0.00 0.00 0.00 2.18
3700 3935 8.391106 GTGTGAGATGGTGAATATCTTGTTAAC 58.609 37.037 0.00 0.00 35.14 2.01
3715 3950 4.202357 TGCTTTAAGAGTGTGTGAGATGGT 60.202 41.667 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.