Multiple sequence alignment - TraesCS6A01G138000

Loading Multiple Alignment...

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 TraesCS6A01G138000 chr6A 100.000 3519 0 0 1 3519 109134643 109138161 0.000000e+00 6499.0
1 TraesCS6A01G138000 chr6A 100.000 29 0 0 3843 3871 109138485 109138513 2.000000e-03 54.7
2 TraesCS6A01G138000 chr6B 92.506 2829 102 55 726 3519 173391419 173394172 0.000000e+00 3949.0
3 TraesCS6A01G138000 chr6B 91.682 553 23 10 3 553 173390807 173391338 0.000000e+00 745.0
4 TraesCS6A01G138000 chr6B 75.067 373 75 17 2469 2832 42004962 42004599 1.440000e-34 158.0
5 TraesCS6A01G138000 chr6D 93.234 1951 79 22 5 1947 90921654 90923559 0.000000e+00 2822.0
6 TraesCS6A01G138000 chr6D 95.088 1588 55 13 1927 3505 90923569 90925142 0.000000e+00 2479.0
7 TraesCS6A01G138000 chr6D 75.335 373 74 17 2469 2832 25804292 25803929 3.090000e-36 163.0
8 TraesCS6A01G138000 chr7A 74.735 566 113 26 2309 2859 670946630 670946080 3.890000e-55 226.0
9 TraesCS6A01G138000 chr7A 84.184 196 31 0 1322 1517 516997902 516997707 1.420000e-44 191.0
10 TraesCS6A01G138000 chr7A 83.838 198 32 0 1320 1517 517414495 517414298 5.110000e-44 189.0
11 TraesCS6A01G138000 chr7A 74.219 512 102 25 2309 2808 516997596 516997103 1.840000e-43 187.0
12 TraesCS6A01G138000 chr7A 74.046 524 100 28 2299 2808 517414206 517413705 8.540000e-42 182.0
13 TraesCS6A01G138000 chr7A 81.333 75 14 0 2782 2856 497778459 497778533 1.160000e-05 62.1
14 TraesCS6A01G138000 chr7D 84.848 198 30 0 1320 1517 478327891 478328088 2.360000e-47 200.0
15 TraesCS6A01G138000 chr7D 74.280 521 104 26 2299 2808 478328199 478328700 3.950000e-45 193.0
16 TraesCS6A01G138000 chr7D 82.828 198 34 0 1320 1517 478572286 478572089 1.110000e-40 178.0
17 TraesCS6A01G138000 chr7D 84.211 114 16 2 1118 1230 478333382 478333494 4.090000e-20 110.0
18 TraesCS6A01G138000 chr7D 81.890 127 19 4 1103 1227 478370371 478370495 1.900000e-18 104.0
19 TraesCS6A01G138000 chr7B 73.805 565 120 25 2309 2859 643295732 643295182 8.480000e-47 198.0
20 TraesCS6A01G138000 chr7B 83.838 198 32 0 1320 1517 503472874 503473071 5.110000e-44 189.0
21 TraesCS6A01G138000 chr7B 82.828 198 34 0 1320 1517 504244323 504244126 1.110000e-40 178.0
22 TraesCS6A01G138000 chr7B 74.092 413 90 15 1118 1517 503496278 503496686 1.860000e-33 154.0
23 TraesCS6A01G138000 chr7B 84.762 105 16 0 1126 1230 504244555 504244451 5.290000e-19 106.0
24 TraesCS6A01G138000 chr3A 84.000 200 32 0 1318 1517 113922267 113922068 3.950000e-45 193.0
25 TraesCS6A01G138000 chr3A 84.956 113 14 3 1123 1234 113922437 113922327 1.140000e-20 111.0
26 TraesCS6A01G138000 chr3B 81.169 154 24 5 1083 1234 146707048 146706898 6.790000e-23 119.0
27 TraesCS6A01G138000 chr3D 80.392 153 25 5 1084 1234 95840333 95840184 1.140000e-20 111.0
28 TraesCS6A01G138000 chr1A 100.000 28 0 0 3844 3871 554911340 554911313 7.000000e-03 52.8


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 TraesCS6A01G138000 chr6A 109134643 109138513 3870 False 3276.85 6499 100.000 1 3871 2 chr6A.!!$F1 3870
1 TraesCS6A01G138000 chr6B 173390807 173394172 3365 False 2347.00 3949 92.094 3 3519 2 chr6B.!!$F1 3516
2 TraesCS6A01G138000 chr6D 90921654 90925142 3488 False 2650.50 2822 94.161 5 3505 2 chr6D.!!$F1 3500
3 TraesCS6A01G138000 chr7A 670946080 670946630 550 True 226.00 226 74.735 2309 2859 1 chr7A.!!$R1 550

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
221 222 0.319728 CGGATGGGTGCTGATAGGAG 59.680 60.0 0.0 0.0 0.0 3.69 F
1545 1549 0.248907 TCGCTCGCTACTTACCATGC 60.249 55.0 0.0 0.0 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2079 0.033504 ATCGAGACAGTGCCGTGTTT 59.966 50.0 0.0 0.0 0.0 2.83 R
2874 2935 0.600057 GGGAGTTCGTTCGTGGTACT 59.400 55.0 0.0 0.0 0.0 2.73 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
194 195 3.000623 CGTGTCTCGATACAAGCTACGTA 59.999 47.826 5.07 0.00 42.86 3.57
195 196 4.270102 GTGTCTCGATACAAGCTACGTAC 58.730 47.826 5.07 0.00 0.00 3.67
196 197 3.000623 TGTCTCGATACAAGCTACGTACG 59.999 47.826 15.01 15.01 0.00 3.67
197 198 3.000724 GTCTCGATACAAGCTACGTACGT 59.999 47.826 25.98 25.98 0.00 3.57
209 210 2.510691 GTACGTGGTGCGGATGGG 60.511 66.667 0.00 0.00 46.52 4.00
210 211 2.998480 TACGTGGTGCGGATGGGT 60.998 61.111 0.00 0.00 46.52 4.51
211 212 3.303761 TACGTGGTGCGGATGGGTG 62.304 63.158 0.00 0.00 46.52 4.61
213 214 4.722700 GTGGTGCGGATGGGTGCT 62.723 66.667 0.00 0.00 0.00 4.40
214 215 4.720902 TGGTGCGGATGGGTGCTG 62.721 66.667 0.00 0.00 0.00 4.41
215 216 4.408821 GGTGCGGATGGGTGCTGA 62.409 66.667 0.00 0.00 0.00 4.26
216 217 2.124570 GTGCGGATGGGTGCTGAT 60.125 61.111 0.00 0.00 0.00 2.90
217 218 1.146041 GTGCGGATGGGTGCTGATA 59.854 57.895 0.00 0.00 0.00 2.15
218 219 0.882042 GTGCGGATGGGTGCTGATAG 60.882 60.000 0.00 0.00 0.00 2.08
219 220 1.302033 GCGGATGGGTGCTGATAGG 60.302 63.158 0.00 0.00 0.00 2.57
220 221 1.758440 GCGGATGGGTGCTGATAGGA 61.758 60.000 0.00 0.00 0.00 2.94
221 222 0.319728 CGGATGGGTGCTGATAGGAG 59.680 60.000 0.00 0.00 0.00 3.69
296 297 4.493547 CAAGAAAAAGTTGACAACAGCCA 58.506 39.130 20.08 0.00 0.00 4.75
299 300 1.459450 AAAGTTGACAACAGCCACGT 58.541 45.000 20.08 0.00 0.00 4.49
367 368 1.218316 CAGTGACCTCGTTAGCCCC 59.782 63.158 0.00 0.00 0.00 5.80
474 475 1.666872 CACTTCCACCGTCCGGAAC 60.667 63.158 5.23 0.00 37.62 3.62
497 498 9.653067 GAACGAATCTAGATATATACATCCGTG 57.347 37.037 5.46 0.00 0.00 4.94
520 521 0.800012 GCGTCAACTAATTTCGGGCA 59.200 50.000 0.00 0.00 0.00 5.36
521 522 1.198178 GCGTCAACTAATTTCGGGCAA 59.802 47.619 0.00 0.00 0.00 4.52
536 539 1.583054 GGCAAAGGGAGCAGTATACG 58.417 55.000 0.00 0.00 0.00 3.06
545 548 3.887716 GGGAGCAGTATACGGAAGAGTTA 59.112 47.826 7.24 0.00 0.00 2.24
637 640 8.433421 TCATTTTCTAGGTACGATCATTTTCC 57.567 34.615 0.00 0.00 0.00 3.13
661 664 4.729856 GCGCCCGTAAGACCGTGT 62.730 66.667 0.00 0.00 43.02 4.49
662 665 2.807895 CGCCCGTAAGACCGTGTG 60.808 66.667 0.00 0.00 43.02 3.82
666 669 1.068127 GCCCGTAAGACCGTGTGATAT 59.932 52.381 0.00 0.00 43.02 1.63
667 670 2.294233 GCCCGTAAGACCGTGTGATATA 59.706 50.000 0.00 0.00 43.02 0.86
668 671 3.243501 GCCCGTAAGACCGTGTGATATAA 60.244 47.826 0.00 0.00 43.02 0.98
671 674 5.508489 CCCGTAAGACCGTGTGATATAATGT 60.508 44.000 0.00 0.00 43.02 2.71
672 675 6.294120 CCCGTAAGACCGTGTGATATAATGTA 60.294 42.308 0.00 0.00 43.02 2.29
673 676 6.800408 CCGTAAGACCGTGTGATATAATGTAG 59.200 42.308 0.00 0.00 43.02 2.74
674 677 6.800408 CGTAAGACCGTGTGATATAATGTAGG 59.200 42.308 0.00 0.00 43.02 3.18
675 678 6.971726 AAGACCGTGTGATATAATGTAGGA 57.028 37.500 0.00 0.00 0.00 2.94
692 695 8.896722 AATGTAGGAGTACTAGGGTATAATGG 57.103 38.462 0.00 0.00 30.77 3.16
795 799 1.300931 CCCGCCCGTGATCAGTATG 60.301 63.158 0.00 0.00 37.54 2.39
813 817 5.414454 CAGTATGGTTCATTTTTCCTTCGGA 59.586 40.000 0.00 0.00 0.00 4.55
912 916 2.882777 CGCTGCCACTGCTACTCG 60.883 66.667 0.00 0.00 38.71 4.18
913 917 2.262915 GCTGCCACTGCTACTCGT 59.737 61.111 0.00 0.00 38.71 4.18
965 969 4.810184 GGAGGGCCGGGGGAACTA 62.810 72.222 2.18 0.00 0.00 2.24
975 979 3.118847 GCCGGGGGAACTAATACTATAGC 60.119 52.174 2.18 0.00 0.00 2.97
1149 1153 1.745489 GTCCATTGTGAGGTCGGGC 60.745 63.158 0.00 0.00 0.00 6.13
1238 1242 3.517699 CGTCAACGTACGTCGCCG 61.518 66.667 23.05 18.57 44.19 6.46
1260 1264 4.561734 CGAAAGTTCCTTCCTGCTACTCTT 60.562 45.833 0.00 0.00 0.00 2.85
1261 1265 4.545208 AAGTTCCTTCCTGCTACTCTTC 57.455 45.455 0.00 0.00 0.00 2.87
1294 1298 0.806868 ACGCTGCAAATGGTCTCATG 59.193 50.000 0.00 0.00 33.18 3.07
1297 1301 1.133790 GCTGCAAATGGTCTCATGTCC 59.866 52.381 0.00 0.00 33.18 4.02
1356 1360 4.056125 TGCTGCTGGACGACTCGG 62.056 66.667 2.98 0.00 0.00 4.63
1529 1533 5.566623 GTTAACCTGGTAATTTAAGCTCGC 58.433 41.667 0.00 0.00 0.00 5.03
1533 1537 1.931172 TGGTAATTTAAGCTCGCTCGC 59.069 47.619 0.00 0.00 0.00 5.03
1544 1548 1.759994 CTCGCTCGCTACTTACCATG 58.240 55.000 0.00 0.00 0.00 3.66
1545 1549 0.248907 TCGCTCGCTACTTACCATGC 60.249 55.000 0.00 0.00 0.00 4.06
1546 1550 0.527600 CGCTCGCTACTTACCATGCA 60.528 55.000 0.00 0.00 0.00 3.96
1547 1551 0.931005 GCTCGCTACTTACCATGCAC 59.069 55.000 0.00 0.00 0.00 4.57
1654 1664 7.827236 TCGCCTTATTATTTCAGAGAGGAAAAA 59.173 33.333 0.00 0.00 39.94 1.94
1657 1667 8.125448 CCTTATTATTTCAGAGAGGAAAAAGCG 58.875 37.037 0.00 0.00 39.94 4.68
1683 1693 2.892425 GGCACTCGATCGCCTTGG 60.892 66.667 11.09 0.00 45.29 3.61
1694 1704 2.506957 CGCCTTGGCCAAAAGGGTT 61.507 57.895 22.51 0.00 45.91 4.11
1766 1776 4.794648 GCACATGTGGGCGGGCTA 62.795 66.667 26.55 0.00 33.30 3.93
1767 1777 2.514592 CACATGTGGGCGGGCTAG 60.515 66.667 18.51 0.00 0.00 3.42
1768 1778 4.489771 ACATGTGGGCGGGCTAGC 62.490 66.667 6.04 6.04 0.00 3.42
1838 1848 4.401022 TGTTGGCAACTTGATCTTCTGAT 58.599 39.130 28.71 0.00 34.21 2.90
1839 1849 4.216902 TGTTGGCAACTTGATCTTCTGATG 59.783 41.667 28.71 0.00 32.29 3.07
1840 1850 4.025040 TGGCAACTTGATCTTCTGATGT 57.975 40.909 0.00 0.00 32.29 3.06
1841 1851 3.754850 TGGCAACTTGATCTTCTGATGTG 59.245 43.478 0.00 0.00 32.29 3.21
1842 1852 3.128242 GGCAACTTGATCTTCTGATGTGG 59.872 47.826 0.00 0.00 32.19 4.17
1898 1908 5.065218 GGTACAGATGTGGACATTTCATCAC 59.935 44.000 7.63 0.00 39.65 3.06
1906 1916 3.067106 GGACATTTCATCACACTGACGT 58.933 45.455 0.00 0.00 0.00 4.34
1980 2021 1.579084 GAGAGACTGAGACCACGCGT 61.579 60.000 5.58 5.58 0.00 6.01
2037 2078 1.006571 CACCACGACGTACTTGGCT 60.007 57.895 0.00 0.00 40.94 4.75
2038 2079 0.241749 CACCACGACGTACTTGGCTA 59.758 55.000 0.00 0.00 40.94 3.93
2043 2084 2.154389 CACGACGTACTTGGCTAAACAC 59.846 50.000 0.00 0.00 0.00 3.32
2044 2085 1.384409 CGACGTACTTGGCTAAACACG 59.616 52.381 12.40 12.40 35.62 4.49
2045 2086 1.723003 GACGTACTTGGCTAAACACGG 59.277 52.381 16.57 3.58 33.90 4.94
2046 2087 0.441145 CGTACTTGGCTAAACACGGC 59.559 55.000 7.66 0.00 0.00 5.68
2047 2088 1.515081 GTACTTGGCTAAACACGGCA 58.485 50.000 0.00 0.00 34.94 5.69
2048 2089 1.196127 GTACTTGGCTAAACACGGCAC 59.804 52.381 0.00 0.00 36.62 5.01
2074 2115 6.752351 TGTCTCGATCTAGCTAAACAAACATC 59.248 38.462 0.00 0.00 0.00 3.06
2094 2135 5.812642 ACATCGCTCGAAAGTCTGAAATAAT 59.187 36.000 0.00 0.00 0.00 1.28
2096 2137 6.094739 TCGCTCGAAAGTCTGAAATAATTG 57.905 37.500 0.00 0.00 0.00 2.32
2097 2138 5.867174 TCGCTCGAAAGTCTGAAATAATTGA 59.133 36.000 0.00 0.00 0.00 2.57
2099 2140 7.015289 CGCTCGAAAGTCTGAAATAATTGAAA 58.985 34.615 0.00 0.00 0.00 2.69
2181 2236 3.391049 AGTTCACCGTCTTTTGAGCTAC 58.609 45.455 0.00 0.00 32.14 3.58
2262 2323 2.883574 TCCGTACTTGCTTGATTACCG 58.116 47.619 0.00 0.00 0.00 4.02
2277 2338 1.021202 TACCGCATGTGCCTATTTGC 58.979 50.000 0.00 0.00 37.91 3.68
2873 2934 1.313091 GCCGGAAGCCCAACTAAAGG 61.313 60.000 5.05 0.00 34.35 3.11
2874 2935 0.326927 CCGGAAGCCCAACTAAAGGA 59.673 55.000 0.00 0.00 0.00 3.36
2876 2937 1.003233 CGGAAGCCCAACTAAAGGAGT 59.997 52.381 0.00 0.00 41.56 3.85
2879 2940 3.607741 GAAGCCCAACTAAAGGAGTACC 58.392 50.000 0.00 0.00 37.44 3.34
2893 2955 0.600057 AGTACCACGAACGAACTCCC 59.400 55.000 0.14 0.00 0.00 4.30
2939 3001 3.475566 TTGCCAGCTAGTAGCATTAGG 57.524 47.619 23.77 18.61 45.56 2.69
2940 3002 1.070758 TGCCAGCTAGTAGCATTAGGC 59.929 52.381 27.23 27.23 45.56 3.93
2941 3003 1.609320 GCCAGCTAGTAGCATTAGGCC 60.609 57.143 25.25 14.27 45.56 5.19
3045 3118 4.767255 GGCGCTGTCAGGTGAGGG 62.767 72.222 7.64 0.00 0.00 4.30
3110 3185 4.293415 GTCAAGTTTTGATTGCTCACCAG 58.707 43.478 0.00 0.00 42.47 4.00
3168 3243 1.465689 CGTCGGCATTGCTTTGGTAAG 60.466 52.381 8.82 0.00 34.36 2.34
3169 3244 1.539827 GTCGGCATTGCTTTGGTAAGT 59.460 47.619 8.82 0.00 33.74 2.24
3197 3272 7.119846 GGGTGCATTCTTTATCTGTACCATATC 59.880 40.741 10.46 0.00 44.53 1.63
3277 3352 9.388506 TGATTGTTTTGCAAGGAAAGAAATTAA 57.611 25.926 0.00 0.00 40.86 1.40
3347 3422 0.896019 TGTACCAAACCCGGGCATTG 60.896 55.000 24.08 25.05 0.00 2.82
3354 3429 4.805768 CCCGGGCATTGCGGGTAA 62.806 66.667 8.08 0.00 38.10 2.85
3388 3464 3.769300 TCTCGATGGGATCTTCAACTGAA 59.231 43.478 0.00 0.00 0.00 3.02
3400 3476 6.525578 TCTTCAACTGAACATACGTCCTAT 57.474 37.500 0.00 0.00 0.00 2.57
3401 3477 6.330278 TCTTCAACTGAACATACGTCCTATG 58.670 40.000 0.00 0.00 38.65 2.23
3406 3482 6.282199 ACTGAACATACGTCCTATGAAACT 57.718 37.500 3.85 0.00 36.45 2.66
3407 3483 7.400599 ACTGAACATACGTCCTATGAAACTA 57.599 36.000 3.85 0.00 36.45 2.24
3452 3528 4.641645 TGCCAAGCCCGACCACAG 62.642 66.667 0.00 0.00 0.00 3.66
3490 3568 7.826690 TGAACAAATCTATTCTAAAACCCAGC 58.173 34.615 0.00 0.00 0.00 4.85
3492 3570 9.174166 GAACAAATCTATTCTAAAACCCAGCTA 57.826 33.333 0.00 0.00 0.00 3.32
3508 3586 5.059833 CCCAGCTAATCAAACTATCACTCC 58.940 45.833 0.00 0.00 0.00 3.85
3513 3591 7.496920 CAGCTAATCAAACTATCACTCCATCAA 59.503 37.037 0.00 0.00 0.00 2.57
3863 3941 4.640771 TTGTCAGGTGGCTCTTTCTTAT 57.359 40.909 0.00 0.00 0.00 1.73
3864 3942 4.640771 TGTCAGGTGGCTCTTTCTTATT 57.359 40.909 0.00 0.00 0.00 1.40
3865 3943 4.985538 TGTCAGGTGGCTCTTTCTTATTT 58.014 39.130 0.00 0.00 0.00 1.40
3866 3944 4.761739 TGTCAGGTGGCTCTTTCTTATTTG 59.238 41.667 0.00 0.00 0.00 2.32
3867 3945 5.003804 GTCAGGTGGCTCTTTCTTATTTGA 58.996 41.667 0.00 0.00 0.00 2.69
3868 3946 5.649831 GTCAGGTGGCTCTTTCTTATTTGAT 59.350 40.000 0.00 0.00 0.00 2.57
3869 3947 5.882557 TCAGGTGGCTCTTTCTTATTTGATC 59.117 40.000 0.00 0.00 0.00 2.92
3870 3948 5.649395 CAGGTGGCTCTTTCTTATTTGATCA 59.351 40.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.368571 GGCAGTGTGGCTTGAGGC 61.369 66.667 0.00 0.00 40.14 4.70
3 4 2.113774 TGGCAGTGTGGCTTGAGG 59.886 61.111 1.91 0.00 44.10 3.86
58 59 8.963725 TGATTGTATTGCATTCTTCTCTTCATT 58.036 29.630 0.00 0.00 0.00 2.57
59 60 8.404000 GTGATTGTATTGCATTCTTCTCTTCAT 58.596 33.333 0.00 0.00 0.00 2.57
194 195 4.697756 CACCCATCCGCACCACGT 62.698 66.667 0.00 0.00 41.42 4.49
196 197 4.722700 AGCACCCATCCGCACCAC 62.723 66.667 0.00 0.00 0.00 4.16
197 198 4.720902 CAGCACCCATCCGCACCA 62.721 66.667 0.00 0.00 0.00 4.17
209 210 3.495806 CCAAATCTCCCTCCTATCAGCAC 60.496 52.174 0.00 0.00 0.00 4.40
210 211 2.707791 CCAAATCTCCCTCCTATCAGCA 59.292 50.000 0.00 0.00 0.00 4.41
211 212 2.551938 GCCAAATCTCCCTCCTATCAGC 60.552 54.545 0.00 0.00 0.00 4.26
212 213 2.707791 TGCCAAATCTCCCTCCTATCAG 59.292 50.000 0.00 0.00 0.00 2.90
213 214 2.775418 TGCCAAATCTCCCTCCTATCA 58.225 47.619 0.00 0.00 0.00 2.15
214 215 4.379302 AATGCCAAATCTCCCTCCTATC 57.621 45.455 0.00 0.00 0.00 2.08
215 216 4.448347 GGAAATGCCAAATCTCCCTCCTAT 60.448 45.833 0.00 0.00 36.34 2.57
216 217 3.117512 GGAAATGCCAAATCTCCCTCCTA 60.118 47.826 0.00 0.00 36.34 2.94
217 218 2.358615 GGAAATGCCAAATCTCCCTCCT 60.359 50.000 0.00 0.00 36.34 3.69
218 219 2.034878 GGAAATGCCAAATCTCCCTCC 58.965 52.381 0.00 0.00 36.34 4.30
219 220 3.023939 AGGAAATGCCAAATCTCCCTC 57.976 47.619 0.00 0.00 40.02 4.30
220 221 4.608170 TTAGGAAATGCCAAATCTCCCT 57.392 40.909 0.00 0.00 40.02 4.20
221 222 4.895297 TGATTAGGAAATGCCAAATCTCCC 59.105 41.667 0.00 0.00 40.02 4.30
367 368 1.272212 GGTAATGCAGGTGGTTGGTTG 59.728 52.381 0.00 0.00 0.00 3.77
474 475 8.827677 TCACACGGATGTATATATCTAGATTCG 58.172 37.037 11.25 4.86 36.72 3.34
483 484 4.457949 TGACGCTCACACGGATGTATATAT 59.542 41.667 0.00 0.00 36.72 0.86
484 485 3.816523 TGACGCTCACACGGATGTATATA 59.183 43.478 0.00 0.00 36.72 0.86
485 486 2.621526 TGACGCTCACACGGATGTATAT 59.378 45.455 0.00 0.00 36.72 0.86
486 487 2.018515 TGACGCTCACACGGATGTATA 58.981 47.619 0.00 0.00 36.72 1.47
497 498 2.093783 CCCGAAATTAGTTGACGCTCAC 59.906 50.000 0.00 0.00 0.00 3.51
520 521 3.371965 TCTTCCGTATACTGCTCCCTTT 58.628 45.455 0.56 0.00 0.00 3.11
521 522 2.959707 CTCTTCCGTATACTGCTCCCTT 59.040 50.000 0.56 0.00 0.00 3.95
536 539 5.483811 CTCCTTCCAAGAACTAACTCTTCC 58.516 45.833 0.00 0.00 33.25 3.46
545 548 2.777692 TGAACACCTCCTTCCAAGAACT 59.222 45.455 0.00 0.00 0.00 3.01
666 669 9.986157 CCATTATACCCTAGTACTCCTACATTA 57.014 37.037 0.00 0.00 0.00 1.90
667 670 8.685311 TCCATTATACCCTAGTACTCCTACATT 58.315 37.037 0.00 0.00 0.00 2.71
668 671 8.240881 TCCATTATACCCTAGTACTCCTACAT 57.759 38.462 0.00 0.00 0.00 2.29
671 674 7.124052 GCATCCATTATACCCTAGTACTCCTA 58.876 42.308 0.00 0.00 0.00 2.94
672 675 5.958987 GCATCCATTATACCCTAGTACTCCT 59.041 44.000 0.00 0.00 0.00 3.69
673 676 5.720041 TGCATCCATTATACCCTAGTACTCC 59.280 44.000 0.00 0.00 0.00 3.85
674 677 6.852420 TGCATCCATTATACCCTAGTACTC 57.148 41.667 0.00 0.00 0.00 2.59
675 678 6.959954 TCATGCATCCATTATACCCTAGTACT 59.040 38.462 0.00 0.00 0.00 2.73
692 695 1.664659 GCTGCGATCCTATCATGCATC 59.335 52.381 0.00 0.00 34.66 3.91
813 817 2.035626 CGGTTGTTGCCAGGGGAT 59.964 61.111 0.00 0.00 0.00 3.85
912 916 3.988517 CAGTTCCTTTACGACTTGGAGAC 59.011 47.826 0.00 0.00 0.00 3.36
913 917 3.006537 CCAGTTCCTTTACGACTTGGAGA 59.993 47.826 0.00 0.00 0.00 3.71
975 979 1.212616 GCGAGCTTGGTATAGCAGTG 58.787 55.000 4.57 3.99 43.68 3.66
1012 1016 2.418910 CCACCGCTCTCCTCGACAT 61.419 63.158 0.00 0.00 0.00 3.06
1120 1124 1.817099 CAATGGACTCCAGGCTCGC 60.817 63.158 3.62 0.00 36.75 5.03
1149 1153 4.386951 TGGACGGCGGACACCATG 62.387 66.667 13.24 0.00 0.00 3.66
1179 1183 3.839353 GAGGATGGAGGCGCCCATG 62.839 68.421 26.15 0.00 46.34 3.66
1260 1264 2.239400 CAGCGTATGGATGGAGGTAGA 58.761 52.381 0.00 0.00 0.00 2.59
1261 1265 1.337260 GCAGCGTATGGATGGAGGTAG 60.337 57.143 0.00 0.00 31.06 3.18
1294 1298 2.481795 CGGCCATGGATTTGAAATGGAC 60.482 50.000 18.40 0.77 44.75 4.02
1297 1301 1.574134 GCGGCCATGGATTTGAAATG 58.426 50.000 18.40 0.00 0.00 2.32
1300 1304 3.062500 GCGCGGCCATGGATTTGAA 62.063 57.895 18.40 0.00 0.00 2.69
1529 1533 1.200483 CGTGCATGGTAAGTAGCGAG 58.800 55.000 0.00 0.00 0.00 5.03
1545 1549 2.400798 GGATGTCGTGCATGCGTG 59.599 61.111 14.09 7.99 38.06 5.34
1546 1550 2.819595 GGGATGTCGTGCATGCGT 60.820 61.111 14.09 0.00 45.44 5.24
1547 1551 3.576356 GGGGATGTCGTGCATGCG 61.576 66.667 14.09 0.00 45.44 4.73
1558 1562 6.208402 CAGATCTATATATCTCCACGGGGATG 59.792 46.154 6.99 1.01 43.91 3.51
1683 1693 3.576550 TGGAATAAGTGAACCCTTTTGGC 59.423 43.478 0.00 0.00 37.83 4.52
1694 1704 8.610248 TGTTAAAAAGACGATGGAATAAGTGA 57.390 30.769 0.00 0.00 0.00 3.41
1737 1747 1.998315 CACATGTGCTGACTAGTGCTC 59.002 52.381 13.94 0.00 0.00 4.26
1761 1771 2.202946 GTTCTGCGAGGCTAGCCC 60.203 66.667 30.42 19.75 36.58 5.19
1762 1772 2.202946 GGTTCTGCGAGGCTAGCC 60.203 66.667 27.19 27.19 0.00 3.93
1765 1775 4.143333 GCGGGTTCTGCGAGGCTA 62.143 66.667 0.00 0.00 0.00 3.93
1768 1778 1.079405 TAAAGCGGGTTCTGCGAGG 60.079 57.895 0.00 0.00 37.44 4.63
1770 1780 1.735198 CGTAAAGCGGGTTCTGCGA 60.735 57.895 0.00 0.00 37.44 5.10
1771 1781 2.776072 CGTAAAGCGGGTTCTGCG 59.224 61.111 0.00 0.00 37.44 5.18
1858 1868 8.857098 ACATCTGTACCATGTTCGTTACTATAT 58.143 33.333 2.40 0.00 29.75 0.86
1898 1908 5.063186 AGTGTAATCTCTACGTACGTCAGTG 59.937 44.000 26.53 18.94 0.00 3.66
1906 1916 8.496707 TGTATTCACAGTGTAATCTCTACGTA 57.503 34.615 0.00 0.00 0.00 3.57
1960 2001 1.302383 CGCGTGGTCTCAGTCTCTCT 61.302 60.000 0.00 0.00 0.00 3.10
2037 2078 0.669619 TCGAGACAGTGCCGTGTTTA 59.330 50.000 0.00 0.00 0.00 2.01
2038 2079 0.033504 ATCGAGACAGTGCCGTGTTT 59.966 50.000 0.00 0.00 0.00 2.83
2043 2084 0.317436 GCTAGATCGAGACAGTGCCG 60.317 60.000 7.06 0.00 0.00 5.69
2044 2085 1.028905 AGCTAGATCGAGACAGTGCC 58.971 55.000 7.06 0.00 0.00 5.01
2045 2086 3.972950 TTAGCTAGATCGAGACAGTGC 57.027 47.619 7.06 0.00 0.00 4.40
2046 2087 5.236655 TGTTTAGCTAGATCGAGACAGTG 57.763 43.478 7.06 0.00 0.00 3.66
2047 2088 5.899120 TTGTTTAGCTAGATCGAGACAGT 57.101 39.130 7.06 0.00 0.00 3.55
2048 2089 6.093404 TGTTTGTTTAGCTAGATCGAGACAG 58.907 40.000 7.06 0.00 0.00 3.51
2074 2115 6.094739 TCAATTATTTCAGACTTTCGAGCG 57.905 37.500 0.00 0.00 0.00 5.03
2262 2323 1.473677 TGTGAGCAAATAGGCACATGC 59.526 47.619 0.00 0.00 36.77 4.06
2277 2338 3.483558 CACGTACGTCATCATCATGTGAG 59.516 47.826 19.94 0.00 40.92 3.51
2693 2754 1.679305 GAGCTCCTGGTCCGAGTGA 60.679 63.158 0.87 0.00 34.87 3.41
2873 2934 1.402062 GGGAGTTCGTTCGTGGTACTC 60.402 57.143 0.00 0.00 35.61 2.59
2874 2935 0.600057 GGGAGTTCGTTCGTGGTACT 59.400 55.000 0.00 0.00 0.00 2.73
2876 2937 1.865788 CGGGGAGTTCGTTCGTGGTA 61.866 60.000 0.00 0.00 0.00 3.25
2879 2940 1.443872 CTCGGGGAGTTCGTTCGTG 60.444 63.158 0.00 0.00 0.00 4.35
2893 2955 1.518572 CGAACCCCACGAATCTCGG 60.519 63.158 0.67 0.00 45.59 4.63
3045 3118 2.888111 GGTCCCGTACGTTCCTCC 59.112 66.667 15.21 5.59 0.00 4.30
3085 3158 4.214437 GTGAGCAATCAAAACTTGACGAG 58.786 43.478 0.00 0.00 43.48 4.18
3168 3243 3.270877 ACAGATAAAGAATGCACCCGAC 58.729 45.455 0.00 0.00 0.00 4.79
3169 3244 3.627395 ACAGATAAAGAATGCACCCGA 57.373 42.857 0.00 0.00 0.00 5.14
3225 3300 1.468520 GGAGCCACGTACGTACTTACA 59.531 52.381 22.34 0.00 0.00 2.41
3277 3352 8.680903 CATGAGCAAAGTGTCCTTTCTTATTAT 58.319 33.333 0.00 0.00 38.87 1.28
3278 3353 7.665559 ACATGAGCAAAGTGTCCTTTCTTATTA 59.334 33.333 0.00 0.00 38.87 0.98
3279 3354 6.491403 ACATGAGCAAAGTGTCCTTTCTTATT 59.509 34.615 0.00 0.00 38.87 1.40
3347 3422 2.754002 AGAGAACTGTACTCTTACCCGC 59.246 50.000 0.00 0.00 41.20 6.13
3388 3464 4.038883 GCCCTAGTTTCATAGGACGTATGT 59.961 45.833 13.39 0.00 44.50 2.29
3400 3476 1.339631 CCGGTCAATGCCCTAGTTTCA 60.340 52.381 0.00 0.00 0.00 2.69
3401 3477 1.379527 CCGGTCAATGCCCTAGTTTC 58.620 55.000 0.00 0.00 0.00 2.78
3406 3482 1.301623 CAACCCGGTCAATGCCCTA 59.698 57.895 0.00 0.00 0.00 3.53
3407 3483 2.035626 CAACCCGGTCAATGCCCT 59.964 61.111 0.00 0.00 0.00 5.19
3438 3514 2.743928 GCTCTGTGGTCGGGCTTG 60.744 66.667 0.00 0.00 0.00 4.01
3452 3528 4.397417 AGATTTGTTCATAGTGCTTGGCTC 59.603 41.667 0.00 0.00 0.00 4.70
3490 3568 8.954950 AGTTGATGGAGTGATAGTTTGATTAG 57.045 34.615 0.00 0.00 0.00 1.73
3492 3570 7.989741 CCTAGTTGATGGAGTGATAGTTTGATT 59.010 37.037 0.00 0.00 0.00 2.57
3842 3920 4.640771 ATAAGAAAGAGCCACCTGACAA 57.359 40.909 0.00 0.00 0.00 3.18
3843 3921 4.640771 AATAAGAAAGAGCCACCTGACA 57.359 40.909 0.00 0.00 0.00 3.58
3844 3922 5.003804 TCAAATAAGAAAGAGCCACCTGAC 58.996 41.667 0.00 0.00 0.00 3.51
3845 3923 5.241403 TCAAATAAGAAAGAGCCACCTGA 57.759 39.130 0.00 0.00 0.00 3.86
3846 3924 5.649395 TGATCAAATAAGAAAGAGCCACCTG 59.351 40.000 0.00 0.00 0.00 4.00
3847 3925 5.819991 TGATCAAATAAGAAAGAGCCACCT 58.180 37.500 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.