Multiple sequence alignment - TraesCS2A01G277200

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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 TraesCS2A01G277200 chr2A 100.000 2663 0 0 1 2663 458669073 458671735 0.000000e+00 4918.0
1 TraesCS2A01G277200 chr2A 80.172 348 64 3 5 351 775599345 775599002 3.400000e-64 255.0
2 TraesCS2A01G277200 chr2D 92.041 2136 104 29 1 2106 345520563 345518464 0.000000e+00 2942.0
3 TraesCS2A01G277200 chr2D 93.114 334 20 3 2207 2538 345517202 345516870 1.110000e-133 486.0
4 TraesCS2A01G277200 chr2D 80.466 343 61 4 13 355 525973793 525973457 9.460000e-65 257.0
5 TraesCS2A01G277200 chr2D 94.853 136 5 2 2529 2663 345516493 345516359 7.470000e-51 211.0
6 TraesCS2A01G277200 chr2B 90.721 1832 97 30 247 2041 411002317 411000522 0.000000e+00 2374.0
7 TraesCS2A01G277200 chr2B 93.750 240 11 2 2207 2446 410999256 410999021 9.070000e-95 357.0
8 TraesCS2A01G277200 chr2B 80.682 352 61 6 5 355 691788211 691787866 1.570000e-67 267.0
9 TraesCS2A01G277200 chr2B 92.029 138 11 0 2526 2663 410997228 410997091 7.520000e-46 195.0
10 TraesCS2A01G277200 chr2B 91.228 57 3 2 2127 2182 4635302 4635357 2.840000e-10 76.8
11 TraesCS2A01G277200 chr2B 88.889 54 6 0 2083 2136 411000526 411000473 1.710000e-07 67.6
12 TraesCS2A01G277200 chr6B 78.175 559 101 10 26 569 92748809 92748257 1.180000e-88 337.0
13 TraesCS2A01G277200 chr6B 79.545 176 31 3 179 354 92479457 92479287 1.290000e-23 121.0
14 TraesCS2A01G277200 chr3D 80.303 396 71 7 105 496 585992436 585992044 2.590000e-75 292.0
15 TraesCS2A01G277200 chr3D 81.017 295 38 9 290 569 474644176 474643885 4.460000e-53 219.0
16 TraesCS2A01G277200 chr5B 81.375 349 59 5 8 355 400422896 400422553 2.020000e-71 279.0
17 TraesCS2A01G277200 chr5B 94.231 52 2 1 2134 2185 509185791 509185741 7.900000e-11 78.7
18 TraesCS2A01G277200 chr5D 81.215 181 29 3 5 185 343116658 343116833 9.940000e-30 141.0
19 TraesCS2A01G277200 chr5D 97.917 48 0 1 2134 2181 380846927 380846973 6.110000e-12 82.4
20 TraesCS2A01G277200 chr1D 96.296 54 1 1 2132 2185 447257725 447257673 1.310000e-13 87.9
21 TraesCS2A01G277200 chr1D 86.667 75 10 0 313 387 493991180 493991106 1.700000e-12 84.2
22 TraesCS2A01G277200 chr1D 94.231 52 2 1 2134 2185 3654371 3654321 7.900000e-11 78.7
23 TraesCS2A01G277200 chr7D 94.231 52 2 1 2134 2185 182833554 182833504 7.900000e-11 78.7
24 TraesCS2A01G277200 chr7D 88.710 62 3 4 2120 2181 528551785 528551728 3.680000e-09 73.1
25 TraesCS2A01G277200 chr7B 94.231 52 2 1 2134 2185 366055513 366055463 7.900000e-11 78.7
26 TraesCS2A01G277200 chr7A 92.593 54 2 2 2134 2187 109080873 109080822 2.840000e-10 76.8
27 TraesCS2A01G277200 chr4B 90.741 54 5 0 1036 1089 529676785 529676838 3.680000e-09 73.1
28 TraesCS2A01G277200 chr4D 87.097 62 8 0 1028 1089 431232077 431232138 1.320000e-08 71.3
29 TraesCS2A01G277200 chr4A 88.889 54 6 0 1036 1089 32653603 32653656 1.710000e-07 67.6


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 TraesCS2A01G277200 chr2A 458669073 458671735 2662 False 4918.0 4918 100.00000 1 2663 1 chr2A.!!$F1 2662
1 TraesCS2A01G277200 chr2D 345516359 345520563 4204 True 1213.0 2942 93.33600 1 2663 3 chr2D.!!$R2 2662
2 TraesCS2A01G277200 chr2B 410997091 411002317 5226 True 748.4 2374 91.34725 247 2663 4 chr2B.!!$R2 2416
3 TraesCS2A01G277200 chr6B 92748257 92748809 552 True 337.0 337 78.17500 26 569 1 chr6B.!!$R2 543

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
898 945 0.892755 TACTGGCCAGTTACCGAGTG 59.107 55.0 41.69 11.94 42.54 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 3963 0.033366 GCATTGTTTTCCCGCCACTT 59.967 50.0 0.0 0.0 0.0 3.16 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
62 63 2.805295 CGGGGCGCTGATATCTGTTTTA 60.805 50.000 7.64 0.00 0.00 1.52
74 75 1.002576 TCTGTTTTAGCGACGACGACA 60.003 47.619 12.29 5.06 42.66 4.35
81 82 2.769617 CGACGACGACAATGGCAC 59.230 61.111 0.00 0.00 42.66 5.01
85 86 2.024868 CGACGACAATGGCACCGAA 61.025 57.895 0.00 0.00 0.00 4.30
96 97 1.277842 TGGCACCGAAAAGAGCTATGA 59.722 47.619 0.00 0.00 0.00 2.15
119 120 2.518949 GCGTCGTTGACTTCGGTAATA 58.481 47.619 0.00 0.00 0.00 0.98
120 121 3.111098 GCGTCGTTGACTTCGGTAATAT 58.889 45.455 0.00 0.00 0.00 1.28
127 128 6.869913 TCGTTGACTTCGGTAATATGTTCTTT 59.130 34.615 0.00 0.00 0.00 2.52
137 138 2.172851 TATGTTCTTTCCGGCGTGTT 57.827 45.000 6.01 0.00 0.00 3.32
155 156 1.940613 GTTTGAGGTGCTCTTTCGTGT 59.059 47.619 0.00 0.00 0.00 4.49
284 286 1.098050 ATTTCCCATGTGAAGCTCGC 58.902 50.000 0.00 0.00 0.00 5.03
294 296 4.893424 TGTGAAGCTCGCTTTTAAAGTT 57.107 36.364 5.53 0.00 36.26 2.66
307 309 5.488645 TTTTAAAGTTGGAGTTGTCGGTC 57.511 39.130 0.00 0.00 0.00 4.79
402 405 2.281539 TGGACTCTACGGTGAAGTCA 57.718 50.000 19.70 8.72 0.00 3.41
454 457 2.559440 GATGATGCTTGTGACTCCTCC 58.441 52.381 0.00 0.00 0.00 4.30
474 477 5.147330 TCCGCAGATGTCTTTCTTCTTTA 57.853 39.130 0.00 0.00 0.00 1.85
482 485 8.031864 CAGATGTCTTTCTTCTTTACAGCTCTA 58.968 37.037 0.00 0.00 34.81 2.43
487 490 8.994170 GTCTTTCTTCTTTACAGCTCTATGTTT 58.006 33.333 0.00 0.00 34.56 2.83
552 580 1.814394 GGTTTAGCCCGATTTTCCGTT 59.186 47.619 0.00 0.00 0.00 4.44
592 634 2.027837 ACCAATGAAAATGGCAAGCCTC 60.028 45.455 12.96 1.89 41.89 4.70
594 636 3.307199 CCAATGAAAATGGCAAGCCTCTT 60.307 43.478 12.96 3.30 36.94 2.85
595 637 4.081531 CCAATGAAAATGGCAAGCCTCTTA 60.082 41.667 12.96 0.00 36.94 2.10
604 646 4.973168 TGGCAAGCCTCTTATACCTTATG 58.027 43.478 12.96 0.00 36.94 1.90
607 649 6.100569 TGGCAAGCCTCTTATACCTTATGTAA 59.899 38.462 12.96 0.00 36.94 2.41
837 884 6.027749 GCCTGATATAAAACAAGTGTTTCCG 58.972 40.000 9.73 0.00 46.47 4.30
889 936 4.804597 TCATATACACTCTACTGGCCAGT 58.195 43.478 38.92 38.92 45.02 4.00
893 940 1.900486 ACACTCTACTGGCCAGTTACC 59.100 52.381 41.69 0.00 42.54 2.85
898 945 0.892755 TACTGGCCAGTTACCGAGTG 59.107 55.000 41.69 11.94 42.54 3.51
1017 1067 1.414061 CCATGCCGGGGAGAGAAGAT 61.414 60.000 2.18 0.00 0.00 2.40
1107 1157 2.354729 CATTCCGGGTCAGGCCAA 59.645 61.111 5.01 0.00 39.65 4.52
1188 1238 1.065701 CAGGTGGAATACTCCGACGAG 59.934 57.143 0.00 0.00 45.85 4.18
1264 1314 2.355193 GGCGAAGAGGAGGAGCTGT 61.355 63.158 0.00 0.00 0.00 4.40
1361 1411 3.188786 GGATGGCAGTCGTCGCAC 61.189 66.667 0.00 0.00 32.24 5.34
1542 1592 4.395583 AGTTCGTCCGGCGTCGTC 62.396 66.667 9.28 0.00 42.13 4.20
1568 1618 1.301677 GCAGCAGTGGTGGAAGCTAC 61.302 60.000 22.98 1.46 35.19 3.58
1569 1619 0.322975 CAGCAGTGGTGGAAGCTACT 59.677 55.000 14.66 0.00 35.19 2.57
1570 1620 0.322975 AGCAGTGGTGGAAGCTACTG 59.677 55.000 7.56 7.56 42.32 2.74
1571 1621 0.035458 GCAGTGGTGGAAGCTACTGT 59.965 55.000 12.43 0.00 41.84 3.55
1572 1622 1.275291 GCAGTGGTGGAAGCTACTGTA 59.725 52.381 12.43 0.00 41.84 2.74
1573 1623 2.093447 GCAGTGGTGGAAGCTACTGTAT 60.093 50.000 12.43 0.00 41.84 2.29
1574 1624 3.786635 CAGTGGTGGAAGCTACTGTATC 58.213 50.000 4.23 0.00 38.08 2.24
1583 1633 3.760580 AGCTACTGTATCAAGGATGGC 57.239 47.619 0.00 0.00 0.00 4.40
1675 1726 5.991606 GCTGCACCATAACTGATGAAGTATA 59.008 40.000 0.00 0.00 38.56 1.47
1682 1733 7.038659 CCATAACTGATGAAGTATAGCTAGCC 58.961 42.308 12.13 0.00 38.56 3.93
1724 1775 2.248280 TTGTCGGCCGCATGTATAAT 57.752 45.000 23.51 0.00 0.00 1.28
1733 1784 3.515630 CCGCATGTATAATCAGATCGCT 58.484 45.455 0.00 0.00 0.00 4.93
1734 1785 3.549471 CCGCATGTATAATCAGATCGCTC 59.451 47.826 0.00 0.00 0.00 5.03
1735 1786 3.239254 CGCATGTATAATCAGATCGCTCG 59.761 47.826 0.00 0.00 0.00 5.03
1736 1787 4.415735 GCATGTATAATCAGATCGCTCGA 58.584 43.478 0.00 0.00 0.00 4.04
1751 1802 1.339610 GCTCGATCATAGCCTCACAGT 59.660 52.381 5.88 0.00 33.73 3.55
1804 1857 1.320555 CGAAGCAAATCGTCCGTAGTG 59.679 52.381 0.00 0.00 38.01 2.74
1837 1890 4.152402 ACCAACAGTTTTGATCGATCTTCG 59.848 41.667 25.02 10.67 42.10 3.79
1926 1998 4.528987 ACTTAGGCCTTCTTAGCTATAGCC 59.471 45.833 21.17 3.39 43.38 3.93
1927 1999 3.268034 AGGCCTTCTTAGCTATAGCCT 57.732 47.619 21.17 13.68 44.25 4.58
1931 2003 6.399639 GGCCTTCTTAGCTATAGCCTATAG 57.600 45.833 21.17 13.43 43.38 1.31
2004 2076 9.975218 AAAATCCTAAGACTAATGTAATGGTGT 57.025 29.630 0.00 0.00 0.00 4.16
2067 2139 2.526077 GTCAGCATCGTCGACAATGTA 58.474 47.619 17.34 1.79 0.00 2.29
2068 2140 2.531912 GTCAGCATCGTCGACAATGTAG 59.468 50.000 17.34 10.43 0.00 2.74
2074 2146 4.548916 GCATCGTCGACAATGTAGAACATG 60.549 45.833 17.34 4.96 37.97 3.21
2078 2150 4.030641 CGTCGACAATGTAGAACATGTCTG 59.969 45.833 17.16 5.43 37.97 3.51
2114 2217 9.125026 AGAAAACGCCAATATCTTATCTTGAAT 57.875 29.630 0.00 0.00 0.00 2.57
2123 2226 9.650539 CAATATCTTATCTTGAATCCATCTCGT 57.349 33.333 0.00 0.00 0.00 4.18
2126 2229 7.353414 TCTTATCTTGAATCCATCTCGTCTT 57.647 36.000 0.00 0.00 0.00 3.01
2130 2233 5.661458 TCTTGAATCCATCTCGTCTTTACC 58.339 41.667 0.00 0.00 0.00 2.85
2131 2234 5.186992 TCTTGAATCCATCTCGTCTTTACCA 59.813 40.000 0.00 0.00 0.00 3.25
2132 2235 5.614324 TGAATCCATCTCGTCTTTACCAT 57.386 39.130 0.00 0.00 0.00 3.55
2133 2236 5.989477 TGAATCCATCTCGTCTTTACCATT 58.011 37.500 0.00 0.00 0.00 3.16
2134 2237 7.119709 TGAATCCATCTCGTCTTTACCATTA 57.880 36.000 0.00 0.00 0.00 1.90
2135 2238 6.984474 TGAATCCATCTCGTCTTTACCATTAC 59.016 38.462 0.00 0.00 0.00 1.89
2136 2239 6.732896 ATCCATCTCGTCTTTACCATTACT 57.267 37.500 0.00 0.00 0.00 2.24
2137 2240 6.145338 TCCATCTCGTCTTTACCATTACTC 57.855 41.667 0.00 0.00 0.00 2.59
2138 2241 5.068723 TCCATCTCGTCTTTACCATTACTCC 59.931 44.000 0.00 0.00 0.00 3.85
2139 2242 4.996788 TCTCGTCTTTACCATTACTCCC 57.003 45.455 0.00 0.00 0.00 4.30
2140 2243 4.607239 TCTCGTCTTTACCATTACTCCCT 58.393 43.478 0.00 0.00 0.00 4.20
2141 2244 5.021458 TCTCGTCTTTACCATTACTCCCTT 58.979 41.667 0.00 0.00 0.00 3.95
2142 2245 5.126707 TCTCGTCTTTACCATTACTCCCTTC 59.873 44.000 0.00 0.00 0.00 3.46
2143 2246 4.161001 TCGTCTTTACCATTACTCCCTTCC 59.839 45.833 0.00 0.00 0.00 3.46
2144 2247 4.439968 GTCTTTACCATTACTCCCTTCCG 58.560 47.826 0.00 0.00 0.00 4.30
2145 2248 4.081254 GTCTTTACCATTACTCCCTTCCGT 60.081 45.833 0.00 0.00 0.00 4.69
2146 2249 4.533311 TCTTTACCATTACTCCCTTCCGTT 59.467 41.667 0.00 0.00 0.00 4.44
2147 2250 4.914177 TTACCATTACTCCCTTCCGTTT 57.086 40.909 0.00 0.00 0.00 3.60
2148 2251 3.345508 ACCATTACTCCCTTCCGTTTC 57.654 47.619 0.00 0.00 0.00 2.78
2149 2252 2.640826 ACCATTACTCCCTTCCGTTTCA 59.359 45.455 0.00 0.00 0.00 2.69
2150 2253 3.073356 ACCATTACTCCCTTCCGTTTCAA 59.927 43.478 0.00 0.00 0.00 2.69
2151 2254 4.076394 CCATTACTCCCTTCCGTTTCAAA 58.924 43.478 0.00 0.00 0.00 2.69
2152 2255 4.521256 CCATTACTCCCTTCCGTTTCAAAA 59.479 41.667 0.00 0.00 0.00 2.44
2153 2256 5.185056 CCATTACTCCCTTCCGTTTCAAAAT 59.815 40.000 0.00 0.00 0.00 1.82
2154 2257 6.376018 CCATTACTCCCTTCCGTTTCAAAATA 59.624 38.462 0.00 0.00 0.00 1.40
2155 2258 7.094118 CCATTACTCCCTTCCGTTTCAAAATAA 60.094 37.037 0.00 0.00 0.00 1.40
2156 2259 7.820578 TTACTCCCTTCCGTTTCAAAATAAA 57.179 32.000 0.00 0.00 0.00 1.40
2157 2260 6.911250 ACTCCCTTCCGTTTCAAAATAAAT 57.089 33.333 0.00 0.00 0.00 1.40
2158 2261 6.687604 ACTCCCTTCCGTTTCAAAATAAATG 58.312 36.000 0.00 0.00 0.00 2.32
2159 2262 6.492087 ACTCCCTTCCGTTTCAAAATAAATGA 59.508 34.615 0.00 0.00 0.00 2.57
2160 2263 6.683715 TCCCTTCCGTTTCAAAATAAATGAC 58.316 36.000 0.00 0.00 0.00 3.06
2161 2264 6.492087 TCCCTTCCGTTTCAAAATAAATGACT 59.508 34.615 0.00 0.00 0.00 3.41
2162 2265 6.806739 CCCTTCCGTTTCAAAATAAATGACTC 59.193 38.462 0.00 0.00 0.00 3.36
2163 2266 7.367285 CCTTCCGTTTCAAAATAAATGACTCA 58.633 34.615 0.00 0.00 0.00 3.41
2164 2267 7.865385 CCTTCCGTTTCAAAATAAATGACTCAA 59.135 33.333 0.00 0.00 0.00 3.02
2165 2268 8.568732 TTCCGTTTCAAAATAAATGACTCAAC 57.431 30.769 0.00 0.00 0.00 3.18
2166 2269 7.936584 TCCGTTTCAAAATAAATGACTCAACT 58.063 30.769 0.00 0.00 0.00 3.16
2167 2270 8.410141 TCCGTTTCAAAATAAATGACTCAACTT 58.590 29.630 0.00 0.00 0.00 2.66
2168 2271 9.030301 CCGTTTCAAAATAAATGACTCAACTTT 57.970 29.630 0.00 0.00 0.00 2.66
2245 3852 3.053077 AGGGCCTGCATAAATGGTACTA 58.947 45.455 4.50 0.00 0.00 1.82
2301 3908 1.810755 GGCGTTCCGATTTTTCTCCTT 59.189 47.619 0.00 0.00 0.00 3.36
2313 3920 6.310467 CGATTTTTCTCCTTCACGTAGATTCA 59.690 38.462 0.00 0.00 0.00 2.57
2356 3963 9.474313 AGCCTTTCACCATATATTAAACAGAAA 57.526 29.630 0.00 0.00 0.00 2.52
2400 4007 4.872691 AGTAATCAAAAGATCAGCGTGGAG 59.127 41.667 0.00 0.00 0.00 3.86
2441 4048 1.470112 GCGGTGAGCTAAAGTCTCTCC 60.470 57.143 0.00 10.15 44.04 3.71
2485 5506 2.436173 GAGGGGTCTCTAAACATGGAGG 59.564 54.545 0.00 0.00 37.07 4.30
2487 5508 1.559682 GGGTCTCTAAACATGGAGGCA 59.440 52.381 0.00 0.00 36.07 4.75
2561 5968 4.739137 GCACTAACAGGTTCCATGCAAAAA 60.739 41.667 0.00 0.00 0.00 1.94
2569 5976 5.814705 CAGGTTCCATGCAAAAACAAAACTA 59.185 36.000 10.26 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.248487 GTCGTCGTCGCTAAAACAGAT 58.752 47.619 0.00 0.00 36.96 2.90
62 63 2.809601 GCCATTGTCGTCGTCGCT 60.810 61.111 0.00 0.00 36.96 4.93
74 75 2.489938 TAGCTCTTTTCGGTGCCATT 57.510 45.000 0.00 0.00 0.00 3.16
81 82 1.453524 CGCGATCATAGCTCTTTTCGG 59.546 52.381 0.00 0.00 0.00 4.30
85 86 1.065701 ACGACGCGATCATAGCTCTTT 59.934 47.619 15.93 0.00 0.00 2.52
96 97 1.800315 CCGAAGTCAACGACGCGAT 60.800 57.895 15.93 0.00 37.39 4.58
119 120 1.001815 CAAACACGCCGGAAAGAACAT 60.002 47.619 5.05 0.00 0.00 2.71
120 121 0.378962 CAAACACGCCGGAAAGAACA 59.621 50.000 5.05 0.00 0.00 3.18
127 128 2.280524 CACCTCAAACACGCCGGA 60.281 61.111 5.05 0.00 0.00 5.14
137 138 1.134521 ACACACGAAAGAGCACCTCAA 60.135 47.619 0.00 0.00 32.06 3.02
187 188 1.003355 CCACCTGAACACGCTCCAT 60.003 57.895 0.00 0.00 0.00 3.41
284 286 5.494632 ACCGACAACTCCAACTTTAAAAG 57.505 39.130 0.00 0.00 0.00 2.27
294 296 2.649034 GAGCGACCGACAACTCCA 59.351 61.111 0.00 0.00 0.00 3.86
402 405 1.004440 GCCCTGAACAAGCGACTCT 60.004 57.895 0.00 0.00 0.00 3.24
454 457 5.669848 GCTGTAAAGAAGAAAGACATCTGCG 60.670 44.000 0.00 0.00 29.57 5.18
474 477 3.441572 GCCAACATGAAACATAGAGCTGT 59.558 43.478 0.00 0.00 0.00 4.40
482 485 0.602562 CACCGGCCAACATGAAACAT 59.397 50.000 0.00 0.00 0.00 2.71
487 490 2.045708 GCATCACCGGCCAACATGA 61.046 57.895 0.00 0.00 0.00 3.07
511 538 3.568007 CCAATACAATCCAACCCATACGG 59.432 47.826 0.00 0.00 37.81 4.02
552 580 8.740906 TCATTGGTTAAATTGCTCCGTTAATTA 58.259 29.630 0.00 0.00 0.00 1.40
570 611 2.372837 AGGCTTGCCATTTTCATTGGTT 59.627 40.909 14.54 0.00 36.57 3.67
617 659 3.785122 AAGCCGACCCACACAACCC 62.785 63.158 0.00 0.00 0.00 4.11
622 664 1.966451 CTTCCAAGCCGACCCACAC 60.966 63.158 0.00 0.00 0.00 3.82
675 717 2.765807 CTGGGGGACATCTCGGCT 60.766 66.667 0.00 0.00 0.00 5.52
728 770 4.742201 CGTGGGAGGAGTGCACGG 62.742 72.222 12.01 0.00 35.87 4.94
889 936 1.225855 CTTGTTGCAGCACTCGGTAA 58.774 50.000 1.37 0.00 0.00 2.85
893 940 2.127496 CGCTTGTTGCAGCACTCG 60.127 61.111 1.37 5.99 43.06 4.18
898 945 0.658536 GTTCACTCGCTTGTTGCAGC 60.659 55.000 0.00 0.00 43.06 5.25
1188 1238 3.169908 GACCATAGAATCCTCCTCCTCC 58.830 54.545 0.00 0.00 0.00 4.30
1264 1314 0.880278 GTCTGACCTCGCACTTGCAA 60.880 55.000 0.00 0.00 42.21 4.08
1506 1556 2.571757 GCGGTGTCGTGGAGATCA 59.428 61.111 0.00 0.00 38.89 2.92
1551 1601 0.322975 CAGTAGCTTCCACCACTGCT 59.677 55.000 0.00 0.00 39.30 4.24
1568 1618 3.144506 GTCCATGCCATCCTTGATACAG 58.855 50.000 0.00 0.00 0.00 2.74
1569 1619 2.158623 GGTCCATGCCATCCTTGATACA 60.159 50.000 0.00 0.00 0.00 2.29
1570 1620 2.107204 AGGTCCATGCCATCCTTGATAC 59.893 50.000 0.00 0.00 0.00 2.24
1571 1621 2.107031 CAGGTCCATGCCATCCTTGATA 59.893 50.000 0.00 0.00 0.00 2.15
1572 1622 1.133575 CAGGTCCATGCCATCCTTGAT 60.134 52.381 0.00 0.00 0.00 2.57
1573 1623 0.256752 CAGGTCCATGCCATCCTTGA 59.743 55.000 0.00 0.00 0.00 3.02
1574 1624 1.389609 GCAGGTCCATGCCATCCTTG 61.390 60.000 0.00 0.00 40.43 3.61
1583 1633 2.707849 GCTTGGCTGCAGGTCCATG 61.708 63.158 17.12 17.04 31.54 3.66
1675 1726 0.614979 TTCTCGTTCCCTGGCTAGCT 60.615 55.000 15.72 0.00 0.00 3.32
1682 1733 0.036875 AAGGCCTTTCTCGTTCCCTG 59.963 55.000 13.78 0.00 0.00 4.45
1733 1784 3.023832 TGAACTGTGAGGCTATGATCGA 58.976 45.455 0.00 0.00 0.00 3.59
1734 1785 3.119291 GTGAACTGTGAGGCTATGATCG 58.881 50.000 0.00 0.00 0.00 3.69
1735 1786 3.133721 AGGTGAACTGTGAGGCTATGATC 59.866 47.826 0.00 0.00 0.00 2.92
1736 1787 3.110705 AGGTGAACTGTGAGGCTATGAT 58.889 45.455 0.00 0.00 0.00 2.45
1751 1802 5.417580 ACTTGAAACAAACAAGCTAGGTGAA 59.582 36.000 0.00 0.00 45.66 3.18
1804 1857 4.398044 TCAAAACTGTTGGTTCTTGTCTCC 59.602 41.667 0.00 0.00 37.12 3.71
1837 1890 7.827729 ACCTGGTAATGAAAATTAGGAGTACAC 59.172 37.037 0.00 0.00 0.00 2.90
1934 2006 0.928451 GTTTCGTTGGAAGCACGTGC 60.928 55.000 32.79 32.79 38.81 5.34
2067 2139 0.035630 GCTGGCTCCAGACATGTTCT 60.036 55.000 19.45 0.00 46.30 3.01
2068 2140 2.475666 GCTGGCTCCAGACATGTTC 58.524 57.895 19.45 0.00 46.30 3.18
2078 2150 2.982744 GCGTTTTCTGGCTGGCTCC 61.983 63.158 2.00 0.00 0.00 4.70
2114 2217 5.068723 GGAGTAATGGTAAAGACGAGATGGA 59.931 44.000 0.00 0.00 0.00 3.41
2123 2226 4.098894 ACGGAAGGGAGTAATGGTAAAGA 58.901 43.478 0.00 0.00 0.00 2.52
2126 2229 4.286549 TGAAACGGAAGGGAGTAATGGTAA 59.713 41.667 0.00 0.00 0.00 2.85
2130 2233 5.699097 TTTTGAAACGGAAGGGAGTAATG 57.301 39.130 0.00 0.00 0.00 1.90
2131 2234 8.411991 TTTATTTTGAAACGGAAGGGAGTAAT 57.588 30.769 0.00 0.00 0.00 1.89
2132 2235 7.820578 TTTATTTTGAAACGGAAGGGAGTAA 57.179 32.000 0.00 0.00 0.00 2.24
2133 2236 7.666388 TCATTTATTTTGAAACGGAAGGGAGTA 59.334 33.333 0.00 0.00 0.00 2.59
2134 2237 6.492087 TCATTTATTTTGAAACGGAAGGGAGT 59.508 34.615 0.00 0.00 0.00 3.85
2135 2238 6.806739 GTCATTTATTTTGAAACGGAAGGGAG 59.193 38.462 0.00 0.00 0.00 4.30
2136 2239 6.492087 AGTCATTTATTTTGAAACGGAAGGGA 59.508 34.615 0.00 0.00 0.00 4.20
2137 2240 6.687604 AGTCATTTATTTTGAAACGGAAGGG 58.312 36.000 0.00 0.00 0.00 3.95
2138 2241 7.367285 TGAGTCATTTATTTTGAAACGGAAGG 58.633 34.615 0.00 0.00 0.00 3.46
2139 2242 8.690840 GTTGAGTCATTTATTTTGAAACGGAAG 58.309 33.333 0.00 0.00 0.00 3.46
2140 2243 8.410141 AGTTGAGTCATTTATTTTGAAACGGAA 58.590 29.630 0.00 0.00 0.00 4.30
2141 2244 7.936584 AGTTGAGTCATTTATTTTGAAACGGA 58.063 30.769 0.00 0.00 0.00 4.69
2142 2245 8.574196 AAGTTGAGTCATTTATTTTGAAACGG 57.426 30.769 0.00 0.00 0.00 4.44
2178 2281 9.064706 CGACCAGAGATTATAAGGTAGTTCTAA 57.935 37.037 0.00 0.00 31.57 2.10
2179 2282 7.174599 GCGACCAGAGATTATAAGGTAGTTCTA 59.825 40.741 0.00 0.00 31.57 2.10
2180 2283 6.016108 GCGACCAGAGATTATAAGGTAGTTCT 60.016 42.308 0.00 0.00 31.57 3.01
2181 2284 6.151004 GCGACCAGAGATTATAAGGTAGTTC 58.849 44.000 0.00 0.00 31.57 3.01
2182 2285 5.010820 GGCGACCAGAGATTATAAGGTAGTT 59.989 44.000 0.00 0.00 31.57 2.24
2245 3852 5.118729 ACAGAGGCTCTACAGTAGTACAT 57.881 43.478 18.26 0.00 0.00 2.29
2321 3928 2.832838 TGGTGAAAGGCTGGATCTCTA 58.167 47.619 0.00 0.00 0.00 2.43
2356 3963 0.033366 GCATTGTTTTCCCGCCACTT 59.967 50.000 0.00 0.00 0.00 3.16
2400 4007 3.702330 CCCCGTTTTTGTGTTTCTCTTC 58.298 45.455 0.00 0.00 0.00 2.87
2460 4067 3.379452 CATGTTTAGAGACCCCTCTCCT 58.621 50.000 0.00 0.00 46.38 3.69
2464 4071 2.436173 CCTCCATGTTTAGAGACCCCTC 59.564 54.545 0.00 0.00 39.72 4.30
2485 5506 4.283403 TTTGGCGCCTTGCTGTGC 62.283 61.111 29.70 0.00 45.43 4.57
2487 5508 3.982241 GCTTTGGCGCCTTGCTGT 61.982 61.111 29.70 0.00 45.43 4.40
2569 5976 7.225734 CCAAATTCGTCCAAAACCTGTTAATTT 59.774 33.333 0.00 0.00 0.00 1.82
2587 5995 1.724582 GGATCCACCGGCCAAATTCG 61.725 60.000 6.95 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.