Multiple sequence alignment - TraesCS5A01G057100

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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 TraesCS5A01G057100 chr5A 100.000 2822 0 0 1 2822 54462929 54465750 0.000000e+00 5212.0
1 TraesCS5A01G057100 chr5A 97.303 482 13 0 1159 1640 54482301 54481820 0.000000e+00 819.0
2 TraesCS5A01G057100 chr5A 81.622 370 57 9 1927 2285 169965580 169965949 2.130000e-76 296.0
3 TraesCS5A01G057100 chr5A 84.729 203 27 2 2503 2705 169966084 169966282 1.710000e-47 200.0
4 TraesCS5A01G057100 chr5D 92.397 1210 40 22 736 1913 64133893 64135082 0.000000e+00 1677.0
5 TraesCS5A01G057100 chr5D 87.887 743 42 25 5 731 64133135 64133845 0.000000e+00 830.0
6 TraesCS5A01G057100 chr5D 96.473 482 17 0 1159 1640 64144490 64144009 0.000000e+00 797.0
7 TraesCS5A01G057100 chr5B 91.269 1214 37 26 748 1913 66053948 66052756 0.000000e+00 1591.0
8 TraesCS5A01G057100 chr5B 95.851 482 20 0 1159 1640 66036894 66037375 0.000000e+00 780.0
9 TraesCS5A01G057100 chr5B 89.028 638 28 10 3 624 66054769 66054158 0.000000e+00 752.0
10 TraesCS5A01G057100 chr1D 80.333 661 97 21 1927 2564 296542413 296543063 1.180000e-128 470.0
11 TraesCS5A01G057100 chr3A 86.318 402 45 5 1928 2328 682005251 682005643 2.010000e-116 429.0
12 TraesCS5A01G057100 chr3A 80.380 316 51 8 1927 2231 607449224 607449539 2.190000e-56 230.0
13 TraesCS5A01G057100 chr1B 79.468 526 79 19 1927 2447 494314066 494313565 2.080000e-91 346.0
14 TraesCS5A01G057100 chr1B 85.938 64 9 0 2642 2705 494313436 494313373 5.040000e-08 69.4
15 TraesCS5A01G057100 chr2D 77.934 639 69 40 2197 2822 11246270 11245691 1.620000e-87 333.0
16 TraesCS5A01G057100 chr2D 83.582 201 33 0 1408 1608 49877508 49877708 3.710000e-44 189.0
17 TraesCS5A01G057100 chr3B 80.217 369 54 13 1935 2285 736355339 736355706 2.790000e-65 259.0
18 TraesCS5A01G057100 chr3B 81.095 201 34 3 2512 2712 736355741 736355937 1.050000e-34 158.0
19 TraesCS5A01G057100 chr2A 83.251 203 34 0 1406 1608 51583709 51583911 1.330000e-43 187.0
20 TraesCS5A01G057100 chr2B 82.587 201 35 0 1408 1608 77170461 77170661 8.030000e-41 178.0
21 TraesCS5A01G057100 chr1A 84.270 89 14 0 2536 2624 50519524 50519436 1.390000e-13 87.9


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 TraesCS5A01G057100 chr5A 54462929 54465750 2821 False 5212.0 5212 100.0000 1 2822 1 chr5A.!!$F1 2821
1 TraesCS5A01G057100 chr5A 169965580 169966282 702 False 248.0 296 83.1755 1927 2705 2 chr5A.!!$F2 778
2 TraesCS5A01G057100 chr5D 64133135 64135082 1947 False 1253.5 1677 90.1420 5 1913 2 chr5D.!!$F1 1908
3 TraesCS5A01G057100 chr5B 66052756 66054769 2013 True 1171.5 1591 90.1485 3 1913 2 chr5B.!!$R1 1910
4 TraesCS5A01G057100 chr1D 296542413 296543063 650 False 470.0 470 80.3330 1927 2564 1 chr1D.!!$F1 637
5 TraesCS5A01G057100 chr1B 494313373 494314066 693 True 207.7 346 82.7030 1927 2705 2 chr1B.!!$R1 778
6 TraesCS5A01G057100 chr2D 11245691 11246270 579 True 333.0 333 77.9340 2197 2822 1 chr2D.!!$R1 625
7 TraesCS5A01G057100 chr3B 736355339 736355937 598 False 208.5 259 80.6560 1935 2712 2 chr3B.!!$F1 777

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
257 260 0.036010 ATACTGTGCTCTGTGCCACC 60.036 55.0 8.38 0.00 42.00 4.61 F
1705 1856 0.249573 TTTCTTCGGTGGACGGACAC 60.250 55.0 3.45 3.45 44.45 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1861 0.252103 AGCTAACTTCCTCCCCGACA 60.252 55.0 0.0 0.0 0.00 4.35 R
2609 2843 0.318784 GTTGAGCGAGTTCGGACAGT 60.319 55.0 0.0 0.0 40.23 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
108 110 5.105834 AGTACGTACTAATCTTCGCATCC 57.894 43.478 26.36 0.00 34.13 3.51
110 112 2.691526 ACGTACTAATCTTCGCATCCCA 59.308 45.455 0.00 0.00 0.00 4.37
136 138 0.950836 TCACTGCCGGTTCAAACATG 59.049 50.000 1.90 0.00 0.00 3.21
140 142 2.552315 ACTGCCGGTTCAAACATGTTAG 59.448 45.455 12.39 4.62 0.00 2.34
168 170 0.947180 TAGCAAAAGTGTCGCCGTCC 60.947 55.000 0.00 0.00 0.00 4.79
184 186 0.880278 GTCCAGAGAAACACGCAGCA 60.880 55.000 0.00 0.00 0.00 4.41
185 187 0.880278 TCCAGAGAAACACGCAGCAC 60.880 55.000 0.00 0.00 0.00 4.40
186 188 0.882042 CCAGAGAAACACGCAGCACT 60.882 55.000 0.00 0.00 0.00 4.40
187 189 1.605457 CCAGAGAAACACGCAGCACTA 60.605 52.381 0.00 0.00 0.00 2.74
188 190 1.457303 CAGAGAAACACGCAGCACTAC 59.543 52.381 0.00 0.00 0.00 2.73
189 191 1.068588 AGAGAAACACGCAGCACTACA 59.931 47.619 0.00 0.00 0.00 2.74
190 192 1.864711 GAGAAACACGCAGCACTACAA 59.135 47.619 0.00 0.00 0.00 2.41
191 193 2.480419 GAGAAACACGCAGCACTACAAT 59.520 45.455 0.00 0.00 0.00 2.71
192 194 2.878406 AGAAACACGCAGCACTACAATT 59.122 40.909 0.00 0.00 0.00 2.32
193 195 2.969443 AACACGCAGCACTACAATTC 57.031 45.000 0.00 0.00 0.00 2.17
194 196 2.169832 ACACGCAGCACTACAATTCT 57.830 45.000 0.00 0.00 0.00 2.40
241 244 4.503991 CCCAGACAGGCCTCAGAATAATAC 60.504 50.000 0.00 0.00 35.39 1.89
242 245 4.346418 CCAGACAGGCCTCAGAATAATACT 59.654 45.833 0.00 0.00 0.00 2.12
243 246 5.295950 CAGACAGGCCTCAGAATAATACTG 58.704 45.833 0.00 0.00 36.80 2.74
257 260 0.036010 ATACTGTGCTCTGTGCCACC 60.036 55.000 8.38 0.00 42.00 4.61
260 263 3.349006 GTGCTCTGTGCCACCGTG 61.349 66.667 0.00 0.00 42.00 4.94
285 288 6.138088 CCGATACAATATGCATGTGAACTTG 58.862 40.000 10.16 0.00 32.27 3.16
297 300 0.249868 TGAACTTGGAGCTGGTCGTG 60.250 55.000 0.00 0.00 0.00 4.35
339 342 6.069440 TCTGAAATCTCTGGGAATTATGGTGT 60.069 38.462 0.00 0.00 0.00 4.16
417 430 3.060615 GGCCAGGAAGTGCAGCAG 61.061 66.667 0.00 0.00 0.00 4.24
624 644 2.674177 CGCCACCAGTTTACTACTCCAG 60.674 54.545 0.00 0.00 33.85 3.86
640 663 3.067461 ACTCCAGCATAGATCACGACTTC 59.933 47.826 0.00 0.00 0.00 3.01
641 664 3.023832 TCCAGCATAGATCACGACTTCA 58.976 45.455 0.00 0.00 0.00 3.02
642 665 3.447229 TCCAGCATAGATCACGACTTCAA 59.553 43.478 0.00 0.00 0.00 2.69
644 667 4.428209 CAGCATAGATCACGACTTCAACT 58.572 43.478 0.00 0.00 0.00 3.16
647 670 5.590663 AGCATAGATCACGACTTCAACTAGA 59.409 40.000 0.00 0.00 0.00 2.43
648 671 5.683743 GCATAGATCACGACTTCAACTAGAC 59.316 44.000 0.00 0.00 0.00 2.59
741 807 1.500108 CAAGCATTTTGCCTTTGCGA 58.500 45.000 0.00 0.00 46.52 5.10
745 849 2.738314 AGCATTTTGCCTTTGCGATTTC 59.262 40.909 0.00 0.00 46.52 2.17
771 882 6.400096 AAGAATCCATCTTCCTCCTTTTCT 57.600 37.500 0.00 0.00 45.42 2.52
840 952 1.953138 CGCTGATCTGCATCGACCC 60.953 63.158 22.44 0.00 38.32 4.46
943 1068 2.331132 GCAGCCACACAGCTTCTCC 61.331 63.158 0.00 0.00 42.61 3.71
948 1073 1.079543 CACACAGCTTCTCCCTCCG 60.080 63.158 0.00 0.00 0.00 4.63
976 1101 0.460311 ATCTCCGACATGACCGTTCC 59.540 55.000 0.00 0.00 0.00 3.62
1011 1137 3.517901 CCATCCGCCTCCTATATAAACCA 59.482 47.826 0.00 0.00 0.00 3.67
1033 1159 2.038952 CCACCTCACAATCCTCTGAACA 59.961 50.000 0.00 0.00 0.00 3.18
1073 1199 3.054508 CCTTCAGCTTCATTCCTTCTCCT 60.055 47.826 0.00 0.00 0.00 3.69
1096 1222 2.150719 ACCCACCCACATCGACCAA 61.151 57.895 0.00 0.00 0.00 3.67
1102 1228 2.123589 ACCCACATCGACCAATCCATA 58.876 47.619 0.00 0.00 0.00 2.74
1104 1230 2.146342 CCACATCGACCAATCCATAGC 58.854 52.381 0.00 0.00 0.00 2.97
1642 1789 0.727970 CAGCAGCAGCATTGAGAGTC 59.272 55.000 3.17 0.00 45.49 3.36
1652 1799 2.100584 GCATTGAGAGTCTGTCCGAGAT 59.899 50.000 0.00 0.00 31.63 2.75
1653 1800 3.316588 GCATTGAGAGTCTGTCCGAGATA 59.683 47.826 0.00 0.00 31.63 1.98
1654 1801 4.556501 GCATTGAGAGTCTGTCCGAGATAG 60.557 50.000 0.00 0.00 31.63 2.08
1655 1802 4.489306 TTGAGAGTCTGTCCGAGATAGA 57.511 45.455 0.00 0.00 31.63 1.98
1656 1803 4.698201 TGAGAGTCTGTCCGAGATAGAT 57.302 45.455 0.00 0.00 32.81 1.98
1657 1804 5.810080 TGAGAGTCTGTCCGAGATAGATA 57.190 43.478 0.00 0.00 32.81 1.98
1658 1805 6.367374 TGAGAGTCTGTCCGAGATAGATAT 57.633 41.667 0.00 0.00 32.81 1.63
1659 1806 7.483580 TGAGAGTCTGTCCGAGATAGATATA 57.516 40.000 0.00 0.00 32.81 0.86
1663 1810 9.209048 AGAGTCTGTCCGAGATAGATATATAGT 57.791 37.037 0.00 0.00 32.81 2.12
1664 1811 9.472361 GAGTCTGTCCGAGATAGATATATAGTC 57.528 40.741 4.25 0.00 32.81 2.59
1665 1812 8.426489 AGTCTGTCCGAGATAGATATATAGTCC 58.574 40.741 4.25 0.00 32.81 3.85
1704 1855 0.682852 ATTTCTTCGGTGGACGGACA 59.317 50.000 0.00 0.00 44.45 4.02
1705 1856 0.249573 TTTCTTCGGTGGACGGACAC 60.250 55.000 3.45 3.45 44.45 3.67
1707 1858 1.183030 TCTTCGGTGGACGGACACAT 61.183 55.000 12.74 0.00 43.08 3.21
1708 1859 0.736325 CTTCGGTGGACGGACACATC 60.736 60.000 12.74 0.00 43.08 3.06
1709 1860 1.183030 TTCGGTGGACGGACACATCT 61.183 55.000 12.74 0.00 43.08 2.90
1710 1861 1.183030 TCGGTGGACGGACACATCTT 61.183 55.000 12.74 0.00 43.08 2.40
1711 1862 1.014044 CGGTGGACGGACACATCTTG 61.014 60.000 12.74 0.00 43.08 3.02
1712 1863 0.034896 GGTGGACGGACACATCTTGT 59.965 55.000 12.74 0.00 43.08 3.16
1719 1870 3.442996 GACACATCTTGTCGGGGAG 57.557 57.895 0.00 0.00 45.33 4.30
1720 1871 0.108138 GACACATCTTGTCGGGGAGG 60.108 60.000 0.00 0.00 45.33 4.30
1747 1909 1.534595 GCTAAGCTAGCCATGCATGTC 59.465 52.381 24.58 13.23 45.95 3.06
1801 1963 8.696374 TGATTGGTTACAACTGTTATTGGAAAA 58.304 29.630 0.00 0.00 39.87 2.29
1880 2052 2.433838 CGCCAGTGGTGCAGAGAG 60.434 66.667 10.38 0.00 0.00 3.20
1913 2085 5.359194 TTCTCCAGTGATTATCCAACTCC 57.641 43.478 0.00 0.00 0.00 3.85
1914 2086 3.711704 TCTCCAGTGATTATCCAACTCCC 59.288 47.826 0.00 0.00 0.00 4.30
1915 2087 2.777692 TCCAGTGATTATCCAACTCCCC 59.222 50.000 0.00 0.00 0.00 4.81
1916 2088 2.509548 CCAGTGATTATCCAACTCCCCA 59.490 50.000 0.00 0.00 0.00 4.96
1917 2089 3.545703 CAGTGATTATCCAACTCCCCAC 58.454 50.000 0.00 0.00 0.00 4.61
1918 2090 2.509964 AGTGATTATCCAACTCCCCACC 59.490 50.000 0.00 0.00 0.00 4.61
1919 2091 2.509964 GTGATTATCCAACTCCCCACCT 59.490 50.000 0.00 0.00 0.00 4.00
1920 2092 3.053619 GTGATTATCCAACTCCCCACCTT 60.054 47.826 0.00 0.00 0.00 3.50
1921 2093 3.596046 TGATTATCCAACTCCCCACCTTT 59.404 43.478 0.00 0.00 0.00 3.11
1922 2094 3.449746 TTATCCAACTCCCCACCTTTG 57.550 47.619 0.00 0.00 0.00 2.77
1923 2095 0.251787 ATCCAACTCCCCACCTTTGC 60.252 55.000 0.00 0.00 0.00 3.68
1924 2096 1.908299 CCAACTCCCCACCTTTGCC 60.908 63.158 0.00 0.00 0.00 4.52
1925 2097 2.115266 AACTCCCCACCTTTGCCG 59.885 61.111 0.00 0.00 0.00 5.69
1937 2109 0.671251 CTTTGCCGTGCCCTTGTTTA 59.329 50.000 0.00 0.00 0.00 2.01
1943 2115 1.067915 CCGTGCCCTTGTTTACATTGG 60.068 52.381 0.00 0.00 0.00 3.16
1980 2152 5.514279 CCACATCTTTGACAGAAACTTGAC 58.486 41.667 0.00 0.00 34.16 3.18
1989 2161 3.214328 ACAGAAACTTGACGATTTGCCT 58.786 40.909 0.00 0.00 0.00 4.75
2046 2218 0.692419 CCCTGCCCTACTCAGTCCAT 60.692 60.000 0.00 0.00 0.00 3.41
2050 2222 0.691078 GCCCTACTCAGTCCATCCCA 60.691 60.000 0.00 0.00 0.00 4.37
2053 2225 1.137086 CCTACTCAGTCCATCCCAACG 59.863 57.143 0.00 0.00 0.00 4.10
2055 2227 1.221840 CTCAGTCCATCCCAACGGG 59.778 63.158 0.00 0.00 46.11 5.28
2067 2239 1.191535 CCAACGGGGTACATCTCTCA 58.808 55.000 0.00 0.00 0.00 3.27
2068 2240 1.134788 CCAACGGGGTACATCTCTCAC 60.135 57.143 0.00 0.00 0.00 3.51
2069 2241 1.134788 CAACGGGGTACATCTCTCACC 60.135 57.143 0.00 0.00 0.00 4.02
2070 2242 1.035932 ACGGGGTACATCTCTCACCG 61.036 60.000 3.51 3.51 44.86 4.94
2071 2243 0.750546 CGGGGTACATCTCTCACCGA 60.751 60.000 0.00 0.00 42.19 4.69
2072 2244 1.033574 GGGGTACATCTCTCACCGAG 58.966 60.000 0.00 0.00 41.30 4.63
2073 2245 0.386113 GGGTACATCTCTCACCGAGC 59.614 60.000 0.00 0.00 39.70 5.03
2074 2246 1.103803 GGTACATCTCTCACCGAGCA 58.896 55.000 0.00 0.00 39.70 4.26
2075 2247 1.202313 GGTACATCTCTCACCGAGCAC 60.202 57.143 0.00 0.00 39.70 4.40
2165 2362 1.971695 CTCACCCAGCCCGGAAAAC 60.972 63.158 0.73 0.00 36.56 2.43
2186 2383 4.021925 GGCCTCTCCAAGCACGGT 62.022 66.667 0.00 0.00 34.01 4.83
2307 2513 3.744719 CAGAAGCCGGACGGACGA 61.745 66.667 15.99 0.00 37.50 4.20
2364 2570 3.208383 TGGGCGTGCTTGTGTGTG 61.208 61.111 0.00 0.00 0.00 3.82
2365 2571 4.629115 GGGCGTGCTTGTGTGTGC 62.629 66.667 0.00 0.00 0.00 4.57
2439 2672 2.606961 CGTGCATGACGTGTGCCTT 61.607 57.895 17.08 0.00 43.50 4.35
2543 2777 0.875059 TGTTGTGTTTGTGTGCGTGA 59.125 45.000 0.00 0.00 0.00 4.35
2609 2843 1.830587 ATGCACAGAGAAGGACGCCA 61.831 55.000 0.00 0.00 0.00 5.69
2626 2860 1.285950 CACTGTCCGAACTCGCTCA 59.714 57.895 0.00 0.00 38.18 4.26
2627 2861 0.318699 CACTGTCCGAACTCGCTCAA 60.319 55.000 0.00 0.00 38.18 3.02
2634 2868 1.372997 GAACTCGCTCAACTCGCCA 60.373 57.895 0.00 0.00 0.00 5.69
2712 2946 3.490759 CGCCACATCCAGCACGAC 61.491 66.667 0.00 0.00 0.00 4.34
2713 2947 2.046892 GCCACATCCAGCACGACT 60.047 61.111 0.00 0.00 0.00 4.18
2715 2949 1.807165 CCACATCCAGCACGACTCG 60.807 63.158 0.00 0.00 0.00 4.18
2716 2950 1.080501 CACATCCAGCACGACTCGT 60.081 57.895 0.00 0.00 42.36 4.18
2762 3007 2.525248 ATGCACGCGCGTCTATTGG 61.525 57.895 35.61 21.96 42.97 3.16
2767 3012 2.860628 CGCGCGTCTATTGGTGCTC 61.861 63.158 24.19 0.00 37.52 4.26
2772 3017 1.421410 CGTCTATTGGTGCTCGTGGC 61.421 60.000 0.00 0.00 42.22 5.01
2774 3019 2.125310 TATTGGTGCTCGTGGCGG 60.125 61.111 0.00 0.00 45.43 6.13
2802 3047 4.386951 CCACGCCGTCATGGGTGA 62.387 66.667 8.36 0.00 39.77 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.499004 TGCTTCCACTTTTACTACTCCAT 57.501 39.130 0.00 0.00 0.00 3.41
1 2 4.967084 TGCTTCCACTTTTACTACTCCA 57.033 40.909 0.00 0.00 0.00 3.86
46 48 1.805428 ATGAACCGCAAACCACCAGC 61.805 55.000 0.00 0.00 0.00 4.85
49 51 1.209127 CGATGAACCGCAAACCACC 59.791 57.895 0.00 0.00 0.00 4.61
60 62 1.138047 CCTACGCGGTGTCGATGAAC 61.138 60.000 12.47 0.00 39.00 3.18
83 85 3.940852 TGCGAAGATTAGTACGTACTCCA 59.059 43.478 30.53 19.08 37.73 3.86
84 86 4.542662 TGCGAAGATTAGTACGTACTCC 57.457 45.455 30.53 19.91 37.73 3.85
85 87 5.145759 GGATGCGAAGATTAGTACGTACTC 58.854 45.833 30.53 17.24 37.73 2.59
86 88 4.023365 GGGATGCGAAGATTAGTACGTACT 60.023 45.833 29.62 29.62 40.24 2.73
87 89 4.225208 GGGATGCGAAGATTAGTACGTAC 58.775 47.826 18.10 18.10 0.00 3.67
88 90 3.884693 TGGGATGCGAAGATTAGTACGTA 59.115 43.478 0.00 0.00 0.00 3.57
108 110 1.669115 CCGGCAGTGACAAGACTGG 60.669 63.158 0.00 0.00 43.17 4.00
110 112 0.249911 GAACCGGCAGTGACAAGACT 60.250 55.000 0.00 0.00 0.00 3.24
136 138 1.421382 TTTGCTACGCGACACCTAAC 58.579 50.000 15.93 0.00 0.00 2.34
140 142 0.110823 CACTTTTGCTACGCGACACC 60.111 55.000 15.93 0.00 0.00 4.16
168 170 1.457303 GTAGTGCTGCGTGTTTCTCTG 59.543 52.381 0.00 0.00 0.00 3.35
186 188 9.976511 CGGGAATAGAATTGTAGTAGAATTGTA 57.023 33.333 9.83 10.35 0.00 2.41
187 189 8.483758 ACGGGAATAGAATTGTAGTAGAATTGT 58.516 33.333 9.83 8.55 0.00 2.71
188 190 8.765219 CACGGGAATAGAATTGTAGTAGAATTG 58.235 37.037 9.83 0.00 0.00 2.32
189 191 8.483758 ACACGGGAATAGAATTGTAGTAGAATT 58.516 33.333 5.01 5.01 0.00 2.17
190 192 8.019656 ACACGGGAATAGAATTGTAGTAGAAT 57.980 34.615 0.00 0.00 0.00 2.40
191 193 7.414222 ACACGGGAATAGAATTGTAGTAGAA 57.586 36.000 0.00 0.00 0.00 2.10
192 194 7.414222 AACACGGGAATAGAATTGTAGTAGA 57.586 36.000 0.00 0.00 0.00 2.59
193 195 6.700520 GGAACACGGGAATAGAATTGTAGTAG 59.299 42.308 0.00 0.00 0.00 2.57
194 196 6.407299 GGGAACACGGGAATAGAATTGTAGTA 60.407 42.308 0.00 0.00 0.00 1.82
260 263 4.214119 AGTTCACATGCATATTGTATCGGC 59.786 41.667 0.00 0.00 0.00 5.54
285 288 1.669440 TGGTTACACGACCAGCTCC 59.331 57.895 0.00 0.00 44.53 4.70
297 300 4.537135 TCAGAATGTCTGGTCTGGTTAC 57.463 45.455 5.46 0.00 44.39 2.50
339 342 0.249363 TTGGCAAGTGTACGTACGCA 60.249 50.000 33.74 15.47 39.08 5.24
381 394 2.751816 GCCCAAACCAGTGTTCCTACTT 60.752 50.000 0.00 0.00 32.15 2.24
406 419 1.849976 GCACTGTCCTGCTGCACTTC 61.850 60.000 0.00 0.00 34.06 3.01
561 581 3.495377 TGACGTGGTTTTGTTAATCTCGG 59.505 43.478 0.00 0.00 0.00 4.63
624 644 5.683743 GTCTAGTTGAAGTCGTGATCTATGC 59.316 44.000 0.00 0.00 0.00 3.14
682 743 2.544685 CTCCTTTGCGGACTACATCTG 58.455 52.381 0.00 0.00 36.69 2.90
683 744 1.482593 CCTCCTTTGCGGACTACATCT 59.517 52.381 0.00 0.00 36.69 2.90
684 745 1.480954 TCCTCCTTTGCGGACTACATC 59.519 52.381 0.00 0.00 36.69 3.06
685 746 1.482593 CTCCTCCTTTGCGGACTACAT 59.517 52.381 0.00 0.00 36.69 2.29
686 747 0.895530 CTCCTCCTTTGCGGACTACA 59.104 55.000 0.00 0.00 36.69 2.74
687 748 0.896226 ACTCCTCCTTTGCGGACTAC 59.104 55.000 0.00 0.00 36.69 2.73
770 881 8.755018 CCAAAGTGCAAAATCTAAACAGTTTAG 58.245 33.333 22.56 22.56 43.09 1.85
771 882 7.708752 CCCAAAGTGCAAAATCTAAACAGTTTA 59.291 33.333 5.61 5.61 33.36 2.01
840 952 2.490903 CCAAGCCAAGTCAAAGGAGATG 59.509 50.000 0.00 0.00 0.00 2.90
948 1073 0.103208 ATGTCGGAGATCTGAACGCC 59.897 55.000 0.00 0.00 40.67 5.68
976 1101 1.153005 GGATGGGAAGCAGAGGCAG 60.153 63.158 0.00 0.00 44.61 4.85
1011 1137 2.030027 TCAGAGGATTGTGAGGTGGT 57.970 50.000 0.00 0.00 0.00 4.16
1033 1159 3.350219 AGGTGCGATTAACTTGGATGT 57.650 42.857 0.00 0.00 0.00 3.06
1073 1199 2.294839 CGATGTGGGTGGGTGGGTA 61.295 63.158 0.00 0.00 0.00 3.69
1096 1222 0.322975 GCACGGAGATGGCTATGGAT 59.677 55.000 0.00 0.00 0.00 3.41
1102 1228 2.437359 GCTTGCACGGAGATGGCT 60.437 61.111 0.00 0.00 0.00 4.75
1104 1230 1.769098 CGATGCTTGCACGGAGATGG 61.769 60.000 0.00 0.00 0.00 3.51
1642 1789 7.211573 ACGGACTATATATCTATCTCGGACAG 58.788 42.308 0.00 0.00 0.00 3.51
1652 1799 4.160439 ACGGACGGACGGACTATATATCTA 59.840 45.833 6.00 0.00 38.39 1.98
1653 1800 3.055530 ACGGACGGACGGACTATATATCT 60.056 47.826 6.00 0.00 38.39 1.98
1654 1801 3.265791 ACGGACGGACGGACTATATATC 58.734 50.000 6.00 0.00 38.39 1.63
1655 1802 3.265791 GACGGACGGACGGACTATATAT 58.734 50.000 6.00 0.00 38.39 0.86
1656 1803 2.612972 GGACGGACGGACGGACTATATA 60.613 54.545 6.00 0.00 38.39 0.86
1657 1804 1.517242 GACGGACGGACGGACTATAT 58.483 55.000 6.00 0.00 38.39 0.86
1658 1805 0.532862 GGACGGACGGACGGACTATA 60.533 60.000 6.00 0.00 38.39 1.31
1659 1806 1.821332 GGACGGACGGACGGACTAT 60.821 63.158 6.00 0.00 38.39 2.12
1704 1855 0.905357 CTTCCTCCCCGACAAGATGT 59.095 55.000 0.00 0.00 0.00 3.06
1705 1856 0.905357 ACTTCCTCCCCGACAAGATG 59.095 55.000 0.00 0.00 0.00 2.90
1707 1858 2.176889 CTAACTTCCTCCCCGACAAGA 58.823 52.381 0.00 0.00 0.00 3.02
1708 1859 1.405661 GCTAACTTCCTCCCCGACAAG 60.406 57.143 0.00 0.00 0.00 3.16
1709 1860 0.611714 GCTAACTTCCTCCCCGACAA 59.388 55.000 0.00 0.00 0.00 3.18
1710 1861 0.252103 AGCTAACTTCCTCCCCGACA 60.252 55.000 0.00 0.00 0.00 4.35
1711 1862 1.772836 TAGCTAACTTCCTCCCCGAC 58.227 55.000 0.00 0.00 0.00 4.79
1712 1863 2.385803 CTTAGCTAACTTCCTCCCCGA 58.614 52.381 0.86 0.00 0.00 5.14
1713 1864 1.202545 GCTTAGCTAACTTCCTCCCCG 60.203 57.143 0.86 0.00 0.00 5.73
1714 1865 2.120312 AGCTTAGCTAACTTCCTCCCC 58.880 52.381 4.30 0.00 36.99 4.81
1715 1866 4.594123 CTAGCTTAGCTAACTTCCTCCC 57.406 50.000 15.23 0.00 40.82 4.30
1747 1909 7.284716 TCAAGAATTCAAGATCCATTCATCCAG 59.715 37.037 8.44 0.00 30.51 3.86
1824 1988 5.644636 TCACCACGTTCAGTTAGTTTCTTTT 59.355 36.000 0.00 0.00 0.00 2.27
1869 2041 8.635765 AGAAAATTATTTAACTCTCTGCACCA 57.364 30.769 0.00 0.00 0.00 4.17
1914 2086 4.974721 AGGGCACGGCAAAGGTGG 62.975 66.667 0.00 0.00 35.94 4.61
1915 2087 2.912025 AAGGGCACGGCAAAGGTG 60.912 61.111 0.00 0.00 38.42 4.00
1916 2088 2.912025 CAAGGGCACGGCAAAGGT 60.912 61.111 0.00 0.00 0.00 3.50
1917 2089 2.026945 AAACAAGGGCACGGCAAAGG 62.027 55.000 0.00 0.00 0.00 3.11
1918 2090 0.671251 TAAACAAGGGCACGGCAAAG 59.329 50.000 0.00 0.00 0.00 2.77
1919 2091 0.386113 GTAAACAAGGGCACGGCAAA 59.614 50.000 0.00 0.00 0.00 3.68
1920 2092 0.752009 TGTAAACAAGGGCACGGCAA 60.752 50.000 0.00 0.00 0.00 4.52
1921 2093 0.538516 ATGTAAACAAGGGCACGGCA 60.539 50.000 0.00 0.00 0.00 5.69
1922 2094 0.601057 AATGTAAACAAGGGCACGGC 59.399 50.000 0.00 0.00 0.00 5.68
1923 2095 1.067915 CCAATGTAAACAAGGGCACGG 60.068 52.381 0.00 0.00 0.00 4.94
1924 2096 1.668628 GCCAATGTAAACAAGGGCACG 60.669 52.381 18.24 0.00 43.95 5.34
1925 2097 1.342819 TGCCAATGTAAACAAGGGCAC 59.657 47.619 20.63 0.00 46.83 5.01
1943 2115 4.119442 AGATGTGGCAAAAGATCAATGC 57.881 40.909 8.41 8.41 39.33 3.56
1962 2134 6.486248 CAAATCGTCAAGTTTCTGTCAAAGA 58.514 36.000 0.00 0.00 0.00 2.52
1996 2168 2.771372 ACATTTTACAATGGGCCCATCC 59.229 45.455 37.44 3.21 43.82 3.51
2007 2179 3.070302 GGGGCAGTTTGGACATTTTACAA 59.930 43.478 0.00 0.00 0.00 2.41
2050 2222 1.192428 GGTGAGAGATGTACCCCGTT 58.808 55.000 0.00 0.00 0.00 4.44
2053 2225 3.202548 TCGGTGAGAGATGTACCCC 57.797 57.895 0.00 0.00 0.00 4.95
2070 2242 4.070552 AGGTCTTCCCGCGTGCTC 62.071 66.667 4.92 0.00 38.74 4.26
2071 2243 4.379243 CAGGTCTTCCCGCGTGCT 62.379 66.667 4.92 0.00 38.74 4.40
2072 2244 4.373116 TCAGGTCTTCCCGCGTGC 62.373 66.667 4.92 0.00 38.74 5.34
2073 2245 2.125912 CTCAGGTCTTCCCGCGTG 60.126 66.667 4.92 0.00 38.74 5.34
2074 2246 3.382832 CCTCAGGTCTTCCCGCGT 61.383 66.667 4.92 0.00 38.74 6.01
2075 2247 4.821589 GCCTCAGGTCTTCCCGCG 62.822 72.222 0.00 0.00 38.74 6.46
2157 2354 2.361230 GAGGCCCAGGTTTTCCGG 60.361 66.667 0.00 0.00 46.35 5.14
2165 2362 3.333219 TGCTTGGAGAGGCCCAGG 61.333 66.667 0.00 0.00 37.53 4.45
2328 2534 2.816360 CGCACACATCATCCGCTGG 61.816 63.158 0.00 0.00 0.00 4.85
2331 2537 2.400798 CACGCACACATCATCCGC 59.599 61.111 0.00 0.00 0.00 5.54
2334 2540 2.793946 GCCCACGCACACATCATC 59.206 61.111 0.00 0.00 34.03 2.92
2335 2541 3.126879 CGCCCACGCACACATCAT 61.127 61.111 0.00 0.00 34.03 2.45
2336 2542 4.617520 ACGCCCACGCACACATCA 62.618 61.111 0.00 0.00 45.53 3.07
2364 2570 1.280886 CTCACACAGAGCACTCACGC 61.281 60.000 0.00 0.00 37.59 5.34
2365 2571 2.806577 CTCACACAGAGCACTCACG 58.193 57.895 0.00 0.00 37.59 4.35
2426 2636 3.049674 CGCCAAGGCACACGTCAT 61.050 61.111 12.19 0.00 42.06 3.06
2427 2637 4.539083 ACGCCAAGGCACACGTCA 62.539 61.111 12.19 0.00 42.06 4.35
2447 2680 2.588877 AGGCACTCACACACACGC 60.589 61.111 0.00 0.00 0.00 5.34
2448 2681 2.885676 GCAGGCACTCACACACACG 61.886 63.158 0.00 0.00 34.60 4.49
2472 2706 0.036105 TAGAGCATGCACCCACACAG 60.036 55.000 21.98 0.00 0.00 3.66
2521 2755 1.201181 ACGCACACAAACACAACACAT 59.799 42.857 0.00 0.00 0.00 3.21
2526 2760 1.135831 CACTCACGCACACAAACACAA 60.136 47.619 0.00 0.00 0.00 3.33
2609 2843 0.318784 GTTGAGCGAGTTCGGACAGT 60.319 55.000 0.00 0.00 40.23 3.55
2618 2852 1.373497 CTTGGCGAGTTGAGCGAGT 60.373 57.895 0.00 0.00 35.00 4.18
2626 2860 3.612247 ATGGCGAGCTTGGCGAGTT 62.612 57.895 21.60 0.00 37.19 3.01
2627 2861 4.087892 ATGGCGAGCTTGGCGAGT 62.088 61.111 21.60 8.36 37.19 4.18
2634 2868 2.437359 GCTGTCCATGGCGAGCTT 60.437 61.111 21.55 0.00 0.00 3.74
2740 2974 3.751401 TAGACGCGCGTGCATCTCC 62.751 63.158 42.90 23.83 40.08 3.71
2741 2975 1.209275 AATAGACGCGCGTGCATCTC 61.209 55.000 42.90 24.64 40.08 2.75
2750 2995 2.860628 CGAGCACCAATAGACGCGC 61.861 63.158 5.73 0.00 0.00 6.86
2793 3038 1.376086 CTGCACTGGTCACCCATGA 59.624 57.895 0.00 0.00 40.90 3.07


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

AutoCloner maintained by Alex Coulton.