Multiple sequence alignment - TraesCS2B01G211800

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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 TraesCS2B01G211800 chr2B 100.000 3088 0 0 1 3088 195454768 195457855 0.000000e+00 5703.0
1 TraesCS2B01G211800 chr2B 81.533 1083 137 41 1501 2535 195005690 195004623 0.000000e+00 833.0
2 TraesCS2B01G211800 chr2B 83.353 847 89 28 1323 2149 194995877 194995063 0.000000e+00 736.0
3 TraesCS2B01G211800 chr2B 95.545 404 17 1 2621 3024 149530642 149530240 0.000000e+00 645.0
4 TraesCS2B01G211800 chr2B 83.688 423 55 11 1562 1980 194950640 194950228 1.340000e-103 387.0
5 TraesCS2B01G211800 chr2B 81.182 457 51 18 803 1243 195170370 195169933 4.930000e-88 335.0
6 TraesCS2B01G211800 chr2B 100.000 65 0 0 3024 3088 776255447 776255511 1.500000e-23 121.0
7 TraesCS2B01G211800 chr2D 91.033 2565 132 30 470 2996 136753682 136756186 0.000000e+00 3373.0
8 TraesCS2B01G211800 chr2D 77.778 1170 143 61 1287 2403 136521214 136520109 2.040000e-171 612.0
9 TraesCS2B01G211800 chr2D 89.202 426 37 6 1 417 136744632 136745057 9.810000e-145 523.0
10 TraesCS2B01G211800 chr2D 83.146 445 53 21 2418 2848 136477626 136477190 1.340000e-103 387.0
11 TraesCS2B01G211800 chr2D 88.333 60 7 0 954 1013 136515475 136515416 4.270000e-09 73.1
12 TraesCS2B01G211800 chr2A 89.783 2535 141 39 470 2944 164769059 164766583 0.000000e+00 3138.0
13 TraesCS2B01G211800 chr2A 80.445 1754 200 73 1323 2990 165009184 165010880 0.000000e+00 1206.0
14 TraesCS2B01G211800 chr2A 78.010 764 95 44 1683 2398 165004158 165004896 2.220000e-111 412.0
15 TraesCS2B01G211800 chr2A 82.900 462 42 23 2417 2848 165114318 165114772 6.250000e-102 381.0
16 TraesCS2B01G211800 chr2A 89.048 210 18 5 40 245 164770868 164770660 3.950000e-64 255.0
17 TraesCS2B01G211800 chr4D 89.139 976 57 14 2021 2994 111556221 111557149 0.000000e+00 1170.0
18 TraesCS2B01G211800 chr7D 88.730 976 60 15 2021 2994 216469090 216470017 0.000000e+00 1147.0
19 TraesCS2B01G211800 chr7D 96.923 65 2 0 3024 3088 51268840 51268904 3.260000e-20 110.0
20 TraesCS2B01G211800 chr6A 88.320 976 65 14 2021 2994 4623605 4624533 0.000000e+00 1125.0
21 TraesCS2B01G211800 chr7A 88.217 976 66 19 2021 2994 697133778 697134706 0.000000e+00 1120.0
22 TraesCS2B01G211800 chr7A 92.667 150 11 0 1763 1912 652985761 652985612 1.860000e-52 217.0
23 TraesCS2B01G211800 chr7A 91.358 81 6 1 2118 2197 652985612 652985532 3.260000e-20 110.0
24 TraesCS2B01G211800 chr3D 88.136 826 49 18 2171 2994 131227857 131228635 0.000000e+00 937.0
25 TraesCS2B01G211800 chr3D 90.132 152 10 2 2021 2172 131227629 131227775 3.140000e-45 193.0
26 TraesCS2B01G211800 chr7B 95.802 405 15 2 2621 3024 6647919 6647516 0.000000e+00 652.0
27 TraesCS2B01G211800 chr7B 95.109 184 8 1 2382 2564 6648107 6647924 3.900000e-74 289.0
28 TraesCS2B01G211800 chr1B 100.000 65 0 0 3024 3088 307140828 307140892 1.500000e-23 121.0
29 TraesCS2B01G211800 chr5B 100.000 62 0 0 3027 3088 64716553 64716492 7.000000e-22 115.0
30 TraesCS2B01G211800 chr5B 96.923 65 2 0 3024 3088 65526741 65526805 3.260000e-20 110.0
31 TraesCS2B01G211800 chr3B 98.462 65 1 0 3024 3088 43236117 43236181 7.000000e-22 115.0
32 TraesCS2B01G211800 chr6B 96.970 66 1 1 3023 3088 707913545 707913609 3.260000e-20 110.0
33 TraesCS2B01G211800 chr5D 93.333 75 3 2 3014 3088 526262981 526262909 3.260000e-20 110.0
34 TraesCS2B01G211800 chr4A 96.923 65 2 0 3024 3088 644663399 644663335 3.260000e-20 110.0


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 TraesCS2B01G211800 chr2B 195454768 195457855 3087 False 5703.0 5703 100.0000 1 3088 1 chr2B.!!$F1 3087
1 TraesCS2B01G211800 chr2B 195004623 195005690 1067 True 833.0 833 81.5330 1501 2535 1 chr2B.!!$R4 1034
2 TraesCS2B01G211800 chr2B 194995063 194995877 814 True 736.0 736 83.3530 1323 2149 1 chr2B.!!$R3 826
3 TraesCS2B01G211800 chr2D 136753682 136756186 2504 False 3373.0 3373 91.0330 470 2996 1 chr2D.!!$F2 2526
4 TraesCS2B01G211800 chr2D 136520109 136521214 1105 True 612.0 612 77.7780 1287 2403 1 chr2D.!!$R3 1116
5 TraesCS2B01G211800 chr2A 164766583 164770868 4285 True 1696.5 3138 89.4155 40 2944 2 chr2A.!!$R1 2904
6 TraesCS2B01G211800 chr2A 165009184 165010880 1696 False 1206.0 1206 80.4450 1323 2990 1 chr2A.!!$F2 1667
7 TraesCS2B01G211800 chr2A 165004158 165004896 738 False 412.0 412 78.0100 1683 2398 1 chr2A.!!$F1 715
8 TraesCS2B01G211800 chr4D 111556221 111557149 928 False 1170.0 1170 89.1390 2021 2994 1 chr4D.!!$F1 973
9 TraesCS2B01G211800 chr7D 216469090 216470017 927 False 1147.0 1147 88.7300 2021 2994 1 chr7D.!!$F2 973
10 TraesCS2B01G211800 chr6A 4623605 4624533 928 False 1125.0 1125 88.3200 2021 2994 1 chr6A.!!$F1 973
11 TraesCS2B01G211800 chr7A 697133778 697134706 928 False 1120.0 1120 88.2170 2021 2994 1 chr7A.!!$F1 973
12 TraesCS2B01G211800 chr3D 131227629 131228635 1006 False 565.0 937 89.1340 2021 2994 2 chr3D.!!$F1 973
13 TraesCS2B01G211800 chr7B 6647516 6648107 591 True 470.5 652 95.4555 2382 3024 2 chr7B.!!$R1 642

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
861 2299 0.321653 GATGCGGAGACCAAACCACT 60.322 55.0 0.0 0.0 0.00 4.00 F
1475 2957 0.318120 AAGCAAAACGCCCAATCCAG 59.682 50.0 0.0 0.0 44.04 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 3413 0.673985 CGATGATCAGGCCCGAGTTA 59.326 55.0 0.0 0.0 0.00 2.24 R
3050 4822 0.251354 TCACTCTTGATGCAGAGGCC 59.749 55.0 0.0 0.0 44.23 5.19 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
83 84 5.238650 ACTTGTTGGACTAAAGTGTACATGC 59.761 40.000 0.00 0.00 33.01 4.06
85 86 2.343101 TGGACTAAAGTGTACATGCGC 58.657 47.619 0.00 0.00 0.00 6.09
111 112 5.693104 ACAACATTGACTCACATTGCAATTC 59.307 36.000 9.83 5.12 34.44 2.17
124 125 7.500227 TCACATTGCAATTCCCTCTTTCTATAG 59.500 37.037 9.83 0.00 0.00 1.31
149 150 9.367444 AGGTAGTTTTGTCTAATTATGTTCTCG 57.633 33.333 0.00 0.00 0.00 4.04
188 190 2.183679 ACCTCCTGGTCTCTGAATGAC 58.816 52.381 0.00 0.00 44.78 3.06
190 192 2.168106 CCTCCTGGTCTCTGAATGACTG 59.832 54.545 0.00 0.00 35.04 3.51
197 199 2.095461 TCTCTGAATGACTGTCCTCGG 58.905 52.381 5.17 7.32 0.00 4.63
204 206 3.771577 ATGACTGTCCTCGGTTTTTCT 57.228 42.857 5.17 0.00 32.75 2.52
205 207 3.553828 TGACTGTCCTCGGTTTTTCTT 57.446 42.857 5.17 0.00 32.75 2.52
235 239 9.939802 TTTAAACAGAGGGAAGTATTCTAAGAC 57.060 33.333 0.00 0.00 46.56 3.01
239 243 6.098982 ACAGAGGGAAGTATTCTAAGACCATG 59.901 42.308 0.00 0.00 46.56 3.66
245 249 8.211629 GGGAAGTATTCTAAGACCATGTACAAT 58.788 37.037 0.00 0.00 46.56 2.71
246 250 9.046296 GGAAGTATTCTAAGACCATGTACAATG 57.954 37.037 0.00 0.00 46.56 2.82
249 253 8.213679 AGTATTCTAAGACCATGTACAATGCAT 58.786 33.333 0.00 0.00 0.00 3.96
250 254 6.682423 TTCTAAGACCATGTACAATGCATG 57.318 37.500 0.00 0.00 42.29 4.06
267 1677 7.443575 ACAATGCATGTATTTGGAGAGATACTC 59.556 37.037 6.26 0.00 41.63 2.59
280 1690 9.886132 TTGGAGAGATACTCAGTAAAATAAACC 57.114 33.333 0.00 0.00 46.54 3.27
281 1691 9.268282 TGGAGAGATACTCAGTAAAATAAACCT 57.732 33.333 0.00 0.00 46.54 3.50
319 1730 7.043590 GCATGATGCTTATTTCAATCACAGAAC 60.044 37.037 10.72 0.00 40.96 3.01
321 1732 5.643379 TGCTTATTTCAATCACAGAACCC 57.357 39.130 0.00 0.00 0.00 4.11
326 1737 7.336931 GCTTATTTCAATCACAGAACCCTCTAA 59.663 37.037 0.00 0.00 0.00 2.10
327 1738 9.231297 CTTATTTCAATCACAGAACCCTCTAAA 57.769 33.333 0.00 0.00 0.00 1.85
374 1785 9.657419 AAAATAGGTTCATTTTTCTAGGCAATG 57.343 29.630 0.00 0.00 35.12 2.82
376 1787 5.086621 AGGTTCATTTTTCTAGGCAATGGT 58.913 37.500 8.64 0.00 0.00 3.55
389 1800 3.449737 AGGCAATGGTATGTACGTGTAGT 59.550 43.478 0.00 0.00 0.00 2.73
400 1811 0.682209 ACGTGTAGTACCTGCGGGAT 60.682 55.000 21.41 6.24 36.25 3.85
407 1818 2.063979 TACCTGCGGGATGGGTCAG 61.064 63.158 21.41 0.00 34.86 3.51
408 1819 2.815684 TACCTGCGGGATGGGTCAGT 62.816 60.000 21.41 0.00 34.86 3.41
409 1820 2.063979 CCTGCGGGATGGGTCAGTA 61.064 63.158 5.28 0.00 33.58 2.74
412 1823 0.916086 TGCGGGATGGGTCAGTATTT 59.084 50.000 0.00 0.00 0.00 1.40
413 1824 1.283613 TGCGGGATGGGTCAGTATTTT 59.716 47.619 0.00 0.00 0.00 1.82
414 1825 2.291282 TGCGGGATGGGTCAGTATTTTT 60.291 45.455 0.00 0.00 0.00 1.94
434 1845 1.600023 TTTTTGTGTCCAGCGGTAGG 58.400 50.000 0.00 0.00 0.00 3.18
435 1846 0.887387 TTTTGTGTCCAGCGGTAGGC 60.887 55.000 0.00 0.00 44.05 3.93
566 1982 8.854979 TTCAAACTAATTCAAATCAGTGTGTG 57.145 30.769 0.00 0.00 29.90 3.82
686 2121 5.119694 AGCAGAGAAAAGAAACGAGAAAGT 58.880 37.500 0.00 0.00 0.00 2.66
734 2169 7.968405 TCCAAGAAACGAGAAAAGAAAAGAAAG 59.032 33.333 0.00 0.00 0.00 2.62
735 2170 7.968405 CCAAGAAACGAGAAAAGAAAAGAAAGA 59.032 33.333 0.00 0.00 0.00 2.52
736 2171 9.341899 CAAGAAACGAGAAAAGAAAAGAAAGAA 57.658 29.630 0.00 0.00 0.00 2.52
777 2212 7.254852 AGTACGATCTCTGAAACTGAAATCTC 58.745 38.462 0.00 0.00 0.00 2.75
795 2233 4.679373 TCTCAGAAAGCACTGTCTTCTT 57.321 40.909 0.00 0.00 38.79 2.52
796 2234 4.626042 TCTCAGAAAGCACTGTCTTCTTC 58.374 43.478 0.00 0.00 38.79 2.87
797 2235 4.343526 TCTCAGAAAGCACTGTCTTCTTCT 59.656 41.667 0.00 0.00 38.79 2.85
798 2236 4.375272 TCAGAAAGCACTGTCTTCTTCTG 58.625 43.478 10.14 10.14 38.79 3.02
799 2237 3.059051 CAGAAAGCACTGTCTTCTTCTGC 60.059 47.826 0.00 0.00 29.51 4.26
800 2238 2.926778 AAGCACTGTCTTCTTCTGCT 57.073 45.000 0.00 0.00 39.92 4.24
801 2239 2.166821 AGCACTGTCTTCTTCTGCTG 57.833 50.000 0.00 0.00 36.83 4.41
802 2240 0.516439 GCACTGTCTTCTTCTGCTGC 59.484 55.000 0.00 0.00 0.00 5.25
803 2241 1.155042 CACTGTCTTCTTCTGCTGCC 58.845 55.000 0.00 0.00 0.00 4.85
804 2242 1.055040 ACTGTCTTCTTCTGCTGCCT 58.945 50.000 0.00 0.00 0.00 4.75
805 2243 2.028658 CACTGTCTTCTTCTGCTGCCTA 60.029 50.000 0.00 0.00 0.00 3.93
861 2299 0.321653 GATGCGGAGACCAAACCACT 60.322 55.000 0.00 0.00 0.00 4.00
893 2339 2.314852 TCCTCCTCATCCTCACCTGTAA 59.685 50.000 0.00 0.00 0.00 2.41
1040 2486 6.014584 CCCCTTAATTAGTTGCTTTCCTGTTT 60.015 38.462 0.00 0.00 0.00 2.83
1048 2494 4.464597 AGTTGCTTTCCTGTTTGTTGGTAA 59.535 37.500 0.00 0.00 0.00 2.85
1058 2504 5.330455 TGTTTGTTGGTAATTTGCTGTGA 57.670 34.783 0.00 0.00 0.00 3.58
1059 2505 5.347342 TGTTTGTTGGTAATTTGCTGTGAG 58.653 37.500 0.00 0.00 0.00 3.51
1064 2510 7.987750 TGTTGGTAATTTGCTGTGAGTATTA 57.012 32.000 0.00 0.00 0.00 0.98
1208 2654 2.092968 TGGCTCTGGATAGCGTTTCAAT 60.093 45.455 0.00 0.00 43.74 2.57
1220 2666 7.148306 GGATAGCGTTTCAATTAGTTTTCCTGA 60.148 37.037 0.00 0.00 0.00 3.86
1234 2680 6.725246 AGTTTTCCTGACGTTATTTGTTCAG 58.275 36.000 0.00 0.00 0.00 3.02
1458 2940 1.404583 GCATGCCAGGGTAAGCAAAAG 60.405 52.381 6.36 0.00 43.36 2.27
1459 2941 0.897621 ATGCCAGGGTAAGCAAAAGC 59.102 50.000 0.00 0.00 43.36 3.51
1460 2942 0.468958 TGCCAGGGTAAGCAAAAGCA 60.469 50.000 0.00 0.00 35.69 3.91
1461 2943 0.678950 GCCAGGGTAAGCAAAAGCAA 59.321 50.000 0.00 0.00 0.00 3.91
1462 2944 1.069978 GCCAGGGTAAGCAAAAGCAAA 59.930 47.619 0.00 0.00 0.00 3.68
1463 2945 2.484594 GCCAGGGTAAGCAAAAGCAAAA 60.485 45.455 0.00 0.00 0.00 2.44
1475 2957 0.318120 AAGCAAAACGCCCAATCCAG 59.682 50.000 0.00 0.00 44.04 3.86
1483 2965 0.394216 CGCCCAATCCAGTTCCATCA 60.394 55.000 0.00 0.00 0.00 3.07
1486 2969 2.101917 GCCCAATCCAGTTCCATCATTG 59.898 50.000 0.00 0.00 0.00 2.82
1538 3027 4.272261 CGATTCGATCTCTCTCAGTCTTCA 59.728 45.833 0.00 0.00 0.00 3.02
1577 3071 3.064324 GTGCAGCCGCCCAAGATT 61.064 61.111 0.00 0.00 37.32 2.40
1947 3462 3.414700 GTGTTGTGAGCCTCGCCG 61.415 66.667 2.25 0.00 0.00 6.46
1964 3479 1.938016 GCCGTGACCGTCTACAACATT 60.938 52.381 0.00 0.00 0.00 2.71
2009 3535 5.003804 TGCTGTTTTCCTTTGATCTCCTAC 58.996 41.667 0.00 0.00 0.00 3.18
2103 3697 2.831333 CTTAGCTGCGGATGATTGAGT 58.169 47.619 0.00 0.00 0.00 3.41
2128 3722 0.250513 GGAACCTCAAGAGTGGCGAT 59.749 55.000 0.00 0.00 31.50 4.58
2263 3949 7.187824 ACTATCTGAACTCAGCAAGGATTTA 57.812 36.000 1.61 0.00 43.46 1.40
2345 4044 9.533831 AACTATTTCTGTAGGGAATGTTTCATT 57.466 29.630 0.00 0.00 0.00 2.57
2438 4142 5.105756 GGTGGATCCTTGGTTCTTGTTAATG 60.106 44.000 14.23 0.00 0.00 1.90
2500 4205 9.273016 GATCCTGATCGGTTCTTCAATATTTAA 57.727 33.333 0.00 0.00 0.00 1.52
2683 4390 9.368674 CTACCATGAAATAATCTAGATGCAGAG 57.631 37.037 5.86 0.00 0.00 3.35
2722 4429 5.889853 CAGATCTTGATGAAAAGAATGGGGA 59.110 40.000 0.00 0.00 39.54 4.81
2790 4529 3.005897 TGTGAGACAACAGTTAGGAGCTC 59.994 47.826 4.71 4.71 0.00 4.09
2878 4636 3.973973 TCAGGGGGTAGTAATCAGATTGG 59.026 47.826 5.85 0.00 0.00 3.16
3061 4833 4.247380 CTCCCCGGCCTCTGCATC 62.247 72.222 0.00 0.00 40.13 3.91
3063 4835 4.113815 CCCCGGCCTCTGCATCAA 62.114 66.667 0.00 0.00 40.13 2.57
3064 4836 2.515523 CCCGGCCTCTGCATCAAG 60.516 66.667 0.00 0.00 40.13 3.02
3065 4837 2.586245 CCGGCCTCTGCATCAAGA 59.414 61.111 0.00 0.00 40.13 3.02
3066 4838 1.523258 CCGGCCTCTGCATCAAGAG 60.523 63.158 0.00 0.00 42.90 2.85
3067 4839 1.220206 CGGCCTCTGCATCAAGAGT 59.780 57.895 0.00 0.00 41.89 3.24
3068 4840 1.088340 CGGCCTCTGCATCAAGAGTG 61.088 60.000 0.00 0.00 41.89 3.51
3069 4841 0.251354 GGCCTCTGCATCAAGAGTGA 59.749 55.000 0.00 0.00 41.89 3.41
3070 4842 1.134159 GGCCTCTGCATCAAGAGTGAT 60.134 52.381 0.00 0.00 45.80 3.06
3079 4851 1.939974 TCAAGAGTGATGCATACGGC 58.060 50.000 0.00 0.00 45.13 5.68
3080 4852 0.940126 CAAGAGTGATGCATACGGCC 59.060 55.000 0.00 0.00 43.89 6.13
3081 4853 0.541392 AAGAGTGATGCATACGGCCA 59.459 50.000 2.24 0.00 43.89 5.36
3082 4854 0.761187 AGAGTGATGCATACGGCCAT 59.239 50.000 2.24 0.00 43.89 4.40
3083 4855 1.151668 GAGTGATGCATACGGCCATC 58.848 55.000 2.24 0.00 43.89 3.51
3084 4856 0.761187 AGTGATGCATACGGCCATCT 59.239 50.000 2.24 0.00 43.89 2.90
3085 4857 1.141657 AGTGATGCATACGGCCATCTT 59.858 47.619 2.24 0.00 43.89 2.40
3086 4858 2.368548 AGTGATGCATACGGCCATCTTA 59.631 45.455 2.24 0.00 43.89 2.10
3087 4859 3.008375 AGTGATGCATACGGCCATCTTAT 59.992 43.478 2.24 0.00 43.89 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.775629 TGGCTACACATACTTTCTTCCTTTTT 59.224 34.615 0.00 0.00 0.00 1.94
19 20 6.206829 GTGGCTACACATACTTTCTTCCTTTT 59.793 38.462 0.00 0.00 46.90 2.27
20 21 5.705905 GTGGCTACACATACTTTCTTCCTTT 59.294 40.000 0.00 0.00 46.90 3.11
21 22 5.246307 GTGGCTACACATACTTTCTTCCTT 58.754 41.667 0.00 0.00 46.90 3.36
22 23 4.833390 GTGGCTACACATACTTTCTTCCT 58.167 43.478 0.00 0.00 46.90 3.36
35 36 9.641770 AGTACTAAACTGATCGTGTGGCTACAC 62.642 44.444 22.31 22.31 44.40 2.90
36 37 2.831685 AAACTGATCGTGTGGCTACA 57.168 45.000 0.00 0.00 0.00 2.74
37 38 3.846360 ACTAAACTGATCGTGTGGCTAC 58.154 45.455 0.00 0.00 0.00 3.58
38 39 4.703575 AGTACTAAACTGATCGTGTGGCTA 59.296 41.667 0.00 0.00 36.93 3.93
46 47 6.157211 AGTCCAACAAGTACTAAACTGATCG 58.843 40.000 0.00 0.00 38.88 3.69
52 53 8.429493 ACACTTTAGTCCAACAAGTACTAAAC 57.571 34.615 0.00 0.00 39.53 2.01
83 84 2.753989 TGTGAGTCAATGTTGTTGCG 57.246 45.000 0.00 0.00 0.00 4.85
85 86 4.361420 TGCAATGTGAGTCAATGTTGTTG 58.639 39.130 0.00 0.00 30.32 3.33
111 112 8.080363 AGACAAAACTACCTATAGAAAGAGGG 57.920 38.462 0.00 0.00 38.51 4.30
124 125 8.601476 CCGAGAACATAATTAGACAAAACTACC 58.399 37.037 0.00 0.00 0.00 3.18
143 144 6.033966 ACAAACTCAAATTTTCACCGAGAAC 58.966 36.000 8.91 0.00 35.56 3.01
145 146 5.828299 ACAAACTCAAATTTTCACCGAGA 57.172 34.783 8.91 0.00 0.00 4.04
146 147 5.912955 GGTACAAACTCAAATTTTCACCGAG 59.087 40.000 0.00 0.00 0.00 4.63
147 148 5.591067 AGGTACAAACTCAAATTTTCACCGA 59.409 36.000 0.00 0.00 31.99 4.69
148 149 5.827666 AGGTACAAACTCAAATTTTCACCG 58.172 37.500 0.00 0.00 31.99 4.94
149 150 6.040504 AGGAGGTACAAACTCAAATTTTCACC 59.959 38.462 0.00 0.00 36.70 4.02
214 218 5.590818 TGGTCTTAGAATACTTCCCTCTGT 58.409 41.667 0.00 0.00 0.00 3.41
220 224 9.046296 CATTGTACATGGTCTTAGAATACTTCC 57.954 37.037 0.00 0.00 0.00 3.46
221 225 8.552034 GCATTGTACATGGTCTTAGAATACTTC 58.448 37.037 0.00 0.00 0.00 3.01
239 243 6.925610 TCTCTCCAAATACATGCATTGTAC 57.074 37.500 0.00 0.00 43.46 2.90
245 249 6.098838 ACTGAGTATCTCTCCAAATACATGCA 59.901 38.462 0.00 0.00 42.12 3.96
246 250 6.520272 ACTGAGTATCTCTCCAAATACATGC 58.480 40.000 0.00 0.00 42.12 4.06
333 1744 7.719193 TGAACCTATTTTTCTTCATCACTGTCA 59.281 33.333 0.00 0.00 0.00 3.58
363 1774 4.160814 ACACGTACATACCATTGCCTAGAA 59.839 41.667 0.00 0.00 0.00 2.10
364 1775 3.702548 ACACGTACATACCATTGCCTAGA 59.297 43.478 0.00 0.00 0.00 2.43
365 1776 4.054780 ACACGTACATACCATTGCCTAG 57.945 45.455 0.00 0.00 0.00 3.02
366 1777 4.646040 ACTACACGTACATACCATTGCCTA 59.354 41.667 0.00 0.00 0.00 3.93
367 1778 3.449737 ACTACACGTACATACCATTGCCT 59.550 43.478 0.00 0.00 0.00 4.75
394 1805 2.052782 AAAATACTGACCCATCCCGC 57.947 50.000 0.00 0.00 0.00 6.13
415 1826 1.600023 CCTACCGCTGGACACAAAAA 58.400 50.000 1.50 0.00 0.00 1.94
416 1827 0.887387 GCCTACCGCTGGACACAAAA 60.887 55.000 1.50 0.00 0.00 2.44
417 1828 1.302192 GCCTACCGCTGGACACAAA 60.302 57.895 1.50 0.00 0.00 2.83
418 1829 2.345991 GCCTACCGCTGGACACAA 59.654 61.111 1.50 0.00 0.00 3.33
447 1858 1.620822 ACCGCTGGATGCTTCTTTTT 58.379 45.000 1.50 0.00 40.11 1.94
448 1859 2.359900 CTACCGCTGGATGCTTCTTTT 58.640 47.619 1.50 0.00 40.11 2.27
449 1860 1.407437 CCTACCGCTGGATGCTTCTTT 60.407 52.381 1.50 0.00 40.11 2.52
450 1861 0.179000 CCTACCGCTGGATGCTTCTT 59.821 55.000 1.50 0.00 40.11 2.52
451 1862 1.826024 CCTACCGCTGGATGCTTCT 59.174 57.895 1.50 0.00 40.11 2.85
452 1863 1.889573 GCCTACCGCTGGATGCTTC 60.890 63.158 1.50 0.00 40.11 3.86
453 1864 2.190578 GCCTACCGCTGGATGCTT 59.809 61.111 1.50 0.00 40.11 3.91
454 1865 3.866582 GGCCTACCGCTGGATGCT 61.867 66.667 0.00 0.00 40.11 3.79
455 1866 2.893682 AAAGGCCTACCGCTGGATGC 62.894 60.000 5.16 0.00 42.76 3.91
456 1867 1.097547 CAAAGGCCTACCGCTGGATG 61.098 60.000 5.16 0.00 42.76 3.51
457 1868 1.224592 CAAAGGCCTACCGCTGGAT 59.775 57.895 5.16 0.00 42.76 3.41
458 1869 2.668632 CAAAGGCCTACCGCTGGA 59.331 61.111 5.16 0.00 42.76 3.86
459 1870 3.134127 GCAAAGGCCTACCGCTGG 61.134 66.667 5.16 0.00 42.76 4.85
460 1871 3.499737 CGCAAAGGCCTACCGCTG 61.500 66.667 5.16 0.00 42.76 5.18
461 1872 3.546714 AACGCAAAGGCCTACCGCT 62.547 57.895 5.16 0.00 42.76 5.52
462 1873 3.035576 GAACGCAAAGGCCTACCGC 62.036 63.158 5.16 8.46 42.76 5.68
463 1874 2.396157 GGAACGCAAAGGCCTACCG 61.396 63.158 5.16 12.09 42.76 4.02
464 1875 2.044555 GGGAACGCAAAGGCCTACC 61.045 63.158 5.16 1.10 36.38 3.18
465 1876 2.044555 GGGGAACGCAAAGGCCTAC 61.045 63.158 5.16 0.00 42.57 3.18
466 1877 2.228480 AGGGGAACGCAAAGGCCTA 61.228 57.895 5.16 0.00 46.88 3.93
467 1878 3.580319 AGGGGAACGCAAAGGCCT 61.580 61.111 0.00 0.00 46.88 5.19
468 1879 3.373565 CAGGGGAACGCAAAGGCC 61.374 66.667 0.00 0.00 46.88 5.19
507 1922 8.020819 CAGATGATAGAACGAAAGAGAGTATCC 58.979 40.741 0.00 0.00 33.66 2.59
529 1944 9.985730 TTGAATTAGTTTGAAAATTGAGCAGAT 57.014 25.926 0.00 0.00 0.00 2.90
566 1982 6.198216 TCACTTTAACGTACTACAACGAAACC 59.802 38.462 3.10 0.00 45.68 3.27
686 2121 3.519510 ACTGACTAGCTCCAAATGGCTAA 59.480 43.478 0.00 0.00 40.00 3.09
734 2169 1.136891 ACTTGCAGTTGCCACCTTTTC 59.863 47.619 1.06 0.00 41.18 2.29
735 2170 1.194218 ACTTGCAGTTGCCACCTTTT 58.806 45.000 1.06 0.00 41.18 2.27
736 2171 1.681264 GTACTTGCAGTTGCCACCTTT 59.319 47.619 1.06 0.00 41.18 3.11
777 2212 3.059051 GCAGAAGAAGACAGTGCTTTCTG 60.059 47.826 16.52 16.52 36.51 3.02
825 2263 2.745152 GCATCGGTAAGGCTGGTACAAT 60.745 50.000 0.00 0.00 38.70 2.71
861 2299 0.994247 TGAGGAGGAGGTACACGGTA 59.006 55.000 0.00 0.00 0.00 4.02
893 2339 1.541233 GGCGTCTGGTTATATGCAGCT 60.541 52.381 0.00 0.00 0.00 4.24
1040 2486 6.892658 AATACTCACAGCAAATTACCAACA 57.107 33.333 0.00 0.00 0.00 3.33
1069 2515 8.962884 AAAAATCTTAGGCACAAATTTTCACT 57.037 26.923 0.00 0.00 31.17 3.41
1182 2628 0.179000 CGCTATCCAGAGCCAAACCT 59.821 55.000 0.00 0.00 39.43 3.50
1183 2629 0.107654 ACGCTATCCAGAGCCAAACC 60.108 55.000 0.00 0.00 39.43 3.27
1184 2630 1.739067 AACGCTATCCAGAGCCAAAC 58.261 50.000 0.00 0.00 39.43 2.93
1208 2654 8.211116 TGAACAAATAACGTCAGGAAAACTAA 57.789 30.769 0.00 0.00 0.00 2.24
1220 2666 5.176958 GTGTGACTAGCTGAACAAATAACGT 59.823 40.000 0.00 0.00 0.00 3.99
1417 2878 1.925455 CCCCTCCTCCTTTGCTCCA 60.925 63.158 0.00 0.00 0.00 3.86
1458 2940 0.033366 AACTGGATTGGGCGTTTTGC 59.967 50.000 0.00 0.00 45.38 3.68
1459 2941 1.336795 GGAACTGGATTGGGCGTTTTG 60.337 52.381 0.00 0.00 0.00 2.44
1460 2942 0.966179 GGAACTGGATTGGGCGTTTT 59.034 50.000 0.00 0.00 0.00 2.43
1461 2943 0.178975 TGGAACTGGATTGGGCGTTT 60.179 50.000 0.00 0.00 0.00 3.60
1462 2944 0.039618 ATGGAACTGGATTGGGCGTT 59.960 50.000 0.00 0.00 0.00 4.84
1463 2945 0.394352 GATGGAACTGGATTGGGCGT 60.394 55.000 0.00 0.00 0.00 5.68
1483 2965 4.036518 AGGAGCTTACAGATGAGACCAAT 58.963 43.478 0.00 0.00 0.00 3.16
1486 2969 3.704061 AGAAGGAGCTTACAGATGAGACC 59.296 47.826 0.00 0.00 0.00 3.85
1538 3027 4.035909 ACGGAAACAAAGAAAAGCACGTAT 59.964 37.500 0.00 0.00 0.00 3.06
1755 3261 2.876645 CTTCTCCGACAGCGCGAC 60.877 66.667 12.10 0.04 35.83 5.19
1799 3305 1.755179 CCATGATCCACTGGTTCACC 58.245 55.000 10.50 0.00 34.73 4.02
1896 3411 1.689273 GATGATCAGGCCCGAGTTACT 59.311 52.381 0.00 0.00 0.00 2.24
1898 3413 0.673985 CGATGATCAGGCCCGAGTTA 59.326 55.000 0.00 0.00 0.00 2.24
1899 3414 1.443407 CGATGATCAGGCCCGAGTT 59.557 57.895 0.00 0.00 0.00 3.01
1947 3462 1.990563 CCGAATGTTGTAGACGGTCAC 59.009 52.381 11.27 7.26 38.97 3.67
1964 3479 3.244422 ACAAGAACTGAATTACCTGCCGA 60.244 43.478 0.00 0.00 0.00 5.54
2009 3535 3.636300 TCCCTCAAACAATGAACAGGTTG 59.364 43.478 0.00 0.00 37.67 3.77
2128 3722 2.037772 GCAAGTCTGACCCTTCTTCAGA 59.962 50.000 3.76 0.00 45.84 3.27
2263 3949 2.502745 TCCTATCCCCCAAATGAAGCT 58.497 47.619 0.00 0.00 0.00 3.74
2345 4044 6.780031 TCAAATCCCCATCAACAAGTTCTTTA 59.220 34.615 0.00 0.00 0.00 1.85
2349 4048 5.665916 ATCAAATCCCCATCAACAAGTTC 57.334 39.130 0.00 0.00 0.00 3.01
2438 4142 1.813102 AGGAGAAGATCACATCCCCC 58.187 55.000 0.00 0.00 31.86 5.40
2500 4205 5.566230 GCAGCCAGTCTGAAATTTCTTTGAT 60.566 40.000 18.64 0.00 45.72 2.57
2575 4281 5.567138 AACCCAGAAACAAATCGATGATC 57.433 39.130 0.00 0.00 0.00 2.92
2683 4390 8.614346 CATCAAGATCTGAATTCTTCTTTCCTC 58.386 37.037 7.05 0.00 37.67 3.71
2722 4429 6.597672 TGACACACACTTTTGTACTTCTGATT 59.402 34.615 0.00 0.00 33.30 2.57
2790 4529 9.941664 CTACTGTTTTAGCATGATAAAATGGAG 57.058 33.333 26.47 22.75 37.08 3.86
2857 4613 3.973973 TCCAATCTGATTACTACCCCCTG 59.026 47.826 1.98 0.00 0.00 4.45
2890 4648 5.388654 ACCATGACATTTCTTCCTCTGTTT 58.611 37.500 0.00 0.00 0.00 2.83
3044 4816 4.247380 GATGCAGAGGCCGGGGAG 62.247 72.222 2.18 0.00 40.13 4.30
3046 4818 4.113815 TTGATGCAGAGGCCGGGG 62.114 66.667 2.18 0.00 40.13 5.73
3047 4819 2.515523 CTTGATGCAGAGGCCGGG 60.516 66.667 2.18 0.00 40.13 5.73
3048 4820 1.523258 CTCTTGATGCAGAGGCCGG 60.523 63.158 0.00 0.00 37.28 6.13
3049 4821 1.088340 CACTCTTGATGCAGAGGCCG 61.088 60.000 0.00 0.00 44.23 6.13
3050 4822 0.251354 TCACTCTTGATGCAGAGGCC 59.749 55.000 0.00 0.00 44.23 5.19
3051 4823 2.328819 ATCACTCTTGATGCAGAGGC 57.671 50.000 5.76 0.00 44.23 4.70
3059 4831 2.487934 GCCGTATGCATCACTCTTGAT 58.512 47.619 0.19 0.00 43.80 2.57
3060 4832 1.473257 GGCCGTATGCATCACTCTTGA 60.473 52.381 0.19 0.00 43.89 3.02
3061 4833 0.940126 GGCCGTATGCATCACTCTTG 59.060 55.000 0.19 0.00 43.89 3.02
3062 4834 0.541392 TGGCCGTATGCATCACTCTT 59.459 50.000 0.19 0.00 43.89 2.85
3063 4835 0.761187 ATGGCCGTATGCATCACTCT 59.239 50.000 0.19 0.00 43.89 3.24
3064 4836 1.151668 GATGGCCGTATGCATCACTC 58.848 55.000 0.19 0.00 43.89 3.51
3065 4837 0.761187 AGATGGCCGTATGCATCACT 59.239 50.000 0.19 0.00 43.89 3.41
3066 4838 1.597742 AAGATGGCCGTATGCATCAC 58.402 50.000 0.19 0.00 43.89 3.06
3067 4839 3.701205 ATAAGATGGCCGTATGCATCA 57.299 42.857 0.19 0.00 43.89 3.07


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

AutoCloner maintained by Alex Coulton.