Multiple sequence alignment - TraesCS6B01G005000

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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 TraesCS6B01G005000 chr6B 100.000 1548 0 0 1 1548 3869164 3870711 0.000000e+00 2859.0
1 TraesCS6B01G005000 chr6B 100.000 1392 0 0 1941 3332 3871104 3872495 0.000000e+00 2571.0
2 TraesCS6B01G005000 chr6B 86.546 996 117 12 2343 3332 4163299 4162315 0.000000e+00 1081.0
3 TraesCS6B01G005000 chr6B 88.722 399 35 5 972 1366 4175140 4174748 2.330000e-131 479.0
4 TraesCS6B01G005000 chr6B 80.863 695 60 32 1 671 4176306 4175661 2.330000e-131 479.0
5 TraesCS6B01G005000 chr6B 88.071 394 38 3 974 1364 4164220 4163833 3.030000e-125 459.0
6 TraesCS6B01G005000 chr6B 85.360 444 50 8 2344 2784 4173893 4173462 2.360000e-121 446.0
7 TraesCS6B01G005000 chr6B 88.123 261 24 6 1941 2201 4163768 4163515 1.500000e-78 303.0
8 TraesCS6B01G005000 chr6B 87.209 258 29 3 716 971 4175488 4175233 1.170000e-74 291.0
9 TraesCS6B01G005000 chr6B 81.180 356 67 0 1189 1544 4174854 4174499 1.510000e-73 287.0
10 TraesCS6B01G005000 chr6B 94.891 137 7 0 1976 2112 3870575 3870711 7.240000e-52 215.0
11 TraesCS6B01G005000 chr6B 94.891 137 7 0 1412 1548 3871139 3871275 7.240000e-52 215.0
12 TraesCS6B01G005000 chr6B 86.127 173 20 4 2037 2207 3871104 3871274 2.040000e-42 183.0
13 TraesCS6B01G005000 chr6B 88.060 134 6 5 1 134 4166041 4165918 2.070000e-32 150.0
14 TraesCS6B01G005000 chr6A 91.048 983 67 14 1 971 736568 735595 0.000000e+00 1308.0
15 TraesCS6B01G005000 chr6A 90.229 1003 75 14 2343 3332 687967 686975 0.000000e+00 1288.0
16 TraesCS6B01G005000 chr6A 91.552 580 46 1 972 1548 735502 734923 0.000000e+00 797.0
17 TraesCS6B01G005000 chr6A 88.793 580 44 3 972 1548 689168 688607 0.000000e+00 691.0
18 TraesCS6B01G005000 chr6A 81.895 707 79 27 187 870 690067 689387 4.860000e-153 551.0
19 TraesCS6B01G005000 chr6A 87.007 431 28 14 1941 2345 688425 687997 8.420000e-126 460.0
20 TraesCS6B01G005000 chr6A 88.352 352 36 4 2344 2690 734170 733819 5.140000e-113 418.0
21 TraesCS6B01G005000 chr6A 91.589 214 18 0 1944 2157 688326 688113 2.510000e-76 296.0
22 TraesCS6B01G005000 chr6A 89.593 221 23 0 1328 1548 688570 688350 7.040000e-72 281.0
23 TraesCS6B01G005000 chr6A 92.784 194 14 0 1976 2169 735059 734866 7.040000e-72 281.0
24 TraesCS6B01G005000 chr6A 88.511 235 21 6 1976 2207 688486 688255 2.530000e-71 279.0
25 TraesCS6B01G005000 chr6A 91.919 198 16 0 1980 2177 734503 734306 9.100000e-71 278.0
26 TraesCS6B01G005000 chr6A 95.364 151 7 0 1 151 690644 690494 1.190000e-59 241.0
27 TraesCS6B01G005000 chr6A 93.985 133 8 0 1941 2073 734998 734866 5.640000e-48 202.0
28 TraesCS6B01G005000 chr6A 93.600 125 8 0 1424 1548 688378 688254 1.580000e-43 187.0
29 TraesCS6B01G005000 chr6A 91.603 131 11 0 1418 1548 734501 734371 7.340000e-42 182.0
30 TraesCS6B01G005000 chr6A 79.468 263 44 7 1291 1548 688415 688158 9.500000e-41 178.0
31 TraesCS6B01G005000 chr6D 88.832 582 54 4 972 1548 4202930 4203505 0.000000e+00 704.0
32 TraesCS6B01G005000 chr6D 90.955 398 26 4 973 1366 2166973 2167364 8.190000e-146 527.0
33 TraesCS6B01G005000 chr6D 86.907 443 55 3 2344 2784 2167986 2168427 8.300000e-136 494.0
34 TraesCS6B01G005000 chr6D 86.907 443 55 3 2344 2784 4204242 4204683 8.300000e-136 494.0
35 TraesCS6B01G005000 chr6D 93.493 292 15 1 1 292 4201480 4201767 6.600000e-117 431.0
36 TraesCS6B01G005000 chr6D 93.151 292 18 2 1 292 2165541 2165830 8.540000e-116 427.0
37 TraesCS6B01G005000 chr6D 88.000 200 20 3 1970 2166 4203361 4203559 2.000000e-57 233.0
38 TraesCS6B01G005000 chr6D 82.609 161 27 1 1190 1350 2167260 2167419 1.250000e-29 141.0
39 TraesCS6B01G005000 chr7D 74.208 221 32 19 3112 3315 60277392 60277604 5.960000e-08 69.4
40 TraesCS6B01G005000 chr4A 100.000 28 0 0 3288 3315 668695586 668695559 6.000000e-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 TraesCS6B01G005000 chr6B 3869164 3872495 3331 False 1208.600000 2859 95.181800 1 3332 5 chr6B.!!$F1 3331
1 TraesCS6B01G005000 chr6B 4162315 4166041 3726 True 498.250000 1081 87.700000 1 3332 4 chr6B.!!$R1 3331
2 TraesCS6B01G005000 chr6B 4173462 4176306 2844 True 396.400000 479 84.666800 1 2784 5 chr6B.!!$R2 2783
3 TraesCS6B01G005000 chr6A 733819 736568 2749 True 495.142857 1308 91.606143 1 2690 7 chr6A.!!$R2 2689
4 TraesCS6B01G005000 chr6A 686975 690644 3669 True 445.200000 1288 88.604900 1 3332 10 chr6A.!!$R1 3331
5 TraesCS6B01G005000 chr6D 4201480 4204683 3203 False 465.500000 704 89.308000 1 2784 4 chr6D.!!$F2 2783
6 TraesCS6B01G005000 chr6D 2165541 2168427 2886 False 397.250000 527 88.405500 1 2784 4 chr6D.!!$F1 2783

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
119 120 1.010419 ACCGCGTACTTAAAGGTGCG 61.010 55.0 4.92 8.35 45.34 5.34 F
1036 3097 0.033991 CCCCTCGTCCTCTCTTCTCA 60.034 60.0 0.00 0.00 0.00 3.27 F
1978 4790 0.609131 AGACCCAAAACCATCGCCAG 60.609 55.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1039 3100 0.321564 AGCATAAACAGCAGCGGTGA 60.322 50.0 20.69 0.0 34.87 4.02 R
2162 4998 0.035439 AGGTTGCGGTCCAGGTAATG 60.035 55.0 0.00 0.0 0.00 1.90 R
3276 6199 0.038744 AAGACTTCCTGGGTGCCATG 59.961 55.0 0.00 0.0 30.82 3.66 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
54 55 3.185797 GTGAAAGTTACAGCTACAACCGG 59.814 47.826 0.00 0.00 0.00 5.28
119 120 1.010419 ACCGCGTACTTAAAGGTGCG 61.010 55.000 4.92 8.35 45.34 5.34
330 1123 5.109903 ACTCATTTGCACTAGATTCCGTAC 58.890 41.667 0.00 0.00 0.00 3.67
376 1174 5.704053 ACCTCAAGTTTAAAATCCGACGATT 59.296 36.000 0.00 0.00 40.58 3.34
377 1175 7.255346 AACCTCAAGTTTAAAATCCGACGATTT 60.255 33.333 0.00 0.00 42.09 2.17
378 1176 7.388500 ACCTCAAGTTTAAAATCCGACGATTTA 59.612 33.333 0.00 0.00 45.92 1.40
379 1177 8.395633 CCTCAAGTTTAAAATCCGACGATTTAT 58.604 33.333 0.00 0.00 45.92 1.40
380 1178 9.422196 CTCAAGTTTAAAATCCGACGATTTATC 57.578 33.333 0.00 0.00 45.92 1.75
406 1205 3.495434 ACAACAAAACATCCTACGGGA 57.505 42.857 0.00 0.00 46.81 5.14
460 1259 7.102346 TCTTGCACCTCAAATTTTTCTCAAAA 58.898 30.769 0.00 0.00 36.30 2.44
529 1352 7.782049 TCATATGTAGTCTACACAAAGGGAAG 58.218 38.462 14.95 0.00 42.23 3.46
548 2059 8.209917 AGGGAAGAAACGACAAATACATAATC 57.790 34.615 0.00 0.00 0.00 1.75
587 2098 6.678568 TCTATTGAATTTGGGCTGGAAAAA 57.321 33.333 0.00 0.00 0.00 1.94
743 2392 2.456577 TGCTCACAGCCATCTACTACA 58.543 47.619 0.00 0.00 41.51 2.74
871 2521 3.614092 TCTATCCGGACGAACACTACTT 58.386 45.455 6.12 0.00 0.00 2.24
971 2937 3.704061 TCCAAAAGGCAAAGCTAACAAGT 59.296 39.130 0.00 0.00 0.00 3.16
972 2938 3.803778 CCAAAAGGCAAAGCTAACAAGTG 59.196 43.478 0.00 0.00 0.00 3.16
976 2942 2.430332 AGGCAAAGCTAACAAGTGCAAA 59.570 40.909 0.00 0.00 36.93 3.68
1036 3097 0.033991 CCCCTCGTCCTCTCTTCTCA 60.034 60.000 0.00 0.00 0.00 3.27
1039 3100 3.499563 CCCCTCGTCCTCTCTTCTCATAT 60.500 52.174 0.00 0.00 0.00 1.78
1051 3112 1.114627 TCTCATATCACCGCTGCTGT 58.885 50.000 0.00 0.00 0.00 4.40
1142 3203 1.203050 CCCACAGGTGAACCCAAATCT 60.203 52.381 0.00 0.00 36.42 2.40
1204 3265 2.291540 CCATTACCAGACCCACAACCAT 60.292 50.000 0.00 0.00 0.00 3.55
1206 3267 3.603965 TTACCAGACCCACAACCATTT 57.396 42.857 0.00 0.00 0.00 2.32
1399 3717 1.571936 ACCCACAACCTAACCCAAACT 59.428 47.619 0.00 0.00 0.00 2.66
1416 3734 2.758327 TCGCGGCCACTACCAGAT 60.758 61.111 6.13 0.00 0.00 2.90
1440 3758 2.570284 GCCAAACCCAAACCCTCGG 61.570 63.158 0.00 0.00 0.00 4.63
1477 3795 3.028850 CAGCCTGATCCAAATCCACAAT 58.971 45.455 0.00 0.00 0.00 2.71
1479 3797 3.053095 AGCCTGATCCAAATCCACAATCT 60.053 43.478 0.00 0.00 0.00 2.40
1507 3959 1.044611 CCCAAACCCGAAACCATTGT 58.955 50.000 0.00 0.00 0.00 2.71
1960 4412 2.436417 CACAACCATTACCAGACCCAG 58.564 52.381 0.00 0.00 0.00 4.45
1973 4425 1.075536 AGACCCAGACCCAAAACCATC 59.924 52.381 0.00 0.00 0.00 3.51
1977 4429 0.893270 CAGACCCAAAACCATCGCCA 60.893 55.000 0.00 0.00 0.00 5.69
1978 4790 0.609131 AGACCCAAAACCATCGCCAG 60.609 55.000 0.00 0.00 0.00 4.85
2034 4870 0.749454 GACCGCAGCCTGATCCAAAT 60.749 55.000 0.00 0.00 0.00 2.32
2040 4876 1.747355 CAGCCTGATCCAAATCCACAC 59.253 52.381 0.00 0.00 0.00 3.82
2074 4910 0.824182 AAACCCGAAACCATTGCCGA 60.824 50.000 0.00 0.00 0.00 5.54
2115 4951 0.911769 CTCAGCCATTACCAGGACCA 59.088 55.000 0.00 0.00 0.00 4.02
2122 4958 2.574369 CCATTACCAGGACCACAACCTA 59.426 50.000 0.00 0.00 35.84 3.08
2156 4992 1.076513 ACCATTACCAGACCCAAACCC 59.923 52.381 0.00 0.00 0.00 4.11
2157 4993 1.459450 CATTACCAGACCCAAACCCG 58.541 55.000 0.00 0.00 0.00 5.28
2158 4994 1.003812 CATTACCAGACCCAAACCCGA 59.996 52.381 0.00 0.00 0.00 5.14
2159 4995 1.138568 TTACCAGACCCAAACCCGAA 58.861 50.000 0.00 0.00 0.00 4.30
2160 4996 0.688487 TACCAGACCCAAACCCGAAG 59.312 55.000 0.00 0.00 0.00 3.79
2161 4997 1.971695 CCAGACCCAAACCCGAAGC 60.972 63.158 0.00 0.00 0.00 3.86
2162 4998 1.971695 CAGACCCAAACCCGAAGCC 60.972 63.158 0.00 0.00 0.00 4.35
2163 4999 2.114411 GACCCAAACCCGAAGCCA 59.886 61.111 0.00 0.00 0.00 4.75
2164 5000 1.304134 GACCCAAACCCGAAGCCAT 60.304 57.895 0.00 0.00 0.00 4.40
2165 5001 0.898326 GACCCAAACCCGAAGCCATT 60.898 55.000 0.00 0.00 0.00 3.16
2166 5002 0.406361 ACCCAAACCCGAAGCCATTA 59.594 50.000 0.00 0.00 0.00 1.90
2167 5003 0.815095 CCCAAACCCGAAGCCATTAC 59.185 55.000 0.00 0.00 0.00 1.89
2168 5004 0.815095 CCAAACCCGAAGCCATTACC 59.185 55.000 0.00 0.00 0.00 2.85
2169 5005 1.615919 CCAAACCCGAAGCCATTACCT 60.616 52.381 0.00 0.00 0.00 3.08
2170 5006 1.472480 CAAACCCGAAGCCATTACCTG 59.528 52.381 0.00 0.00 0.00 4.00
2180 5016 2.477880 CATTACCTGGACCGCAACC 58.522 57.895 0.00 0.00 0.00 3.77
2181 5017 0.035439 CATTACCTGGACCGCAACCT 60.035 55.000 0.00 0.00 0.00 3.50
2182 5018 0.035439 ATTACCTGGACCGCAACCTG 60.035 55.000 0.00 0.00 0.00 4.00
2183 5019 1.122632 TTACCTGGACCGCAACCTGA 61.123 55.000 0.00 0.00 0.00 3.86
2184 5020 0.907704 TACCTGGACCGCAACCTGAT 60.908 55.000 0.00 0.00 0.00 2.90
2185 5021 1.450312 CCTGGACCGCAACCTGATC 60.450 63.158 0.00 0.00 0.00 2.92
2186 5022 1.450312 CTGGACCGCAACCTGATCC 60.450 63.158 0.00 0.00 0.00 3.36
2187 5023 2.184020 CTGGACCGCAACCTGATCCA 62.184 60.000 0.00 0.00 37.11 3.41
2188 5024 1.002624 GGACCGCAACCTGATCCAA 60.003 57.895 0.00 0.00 0.00 3.53
2189 5025 0.608035 GGACCGCAACCTGATCCAAA 60.608 55.000 0.00 0.00 0.00 3.28
2190 5026 0.521735 GACCGCAACCTGATCCAAAC 59.478 55.000 0.00 0.00 0.00 2.93
2191 5027 0.893727 ACCGCAACCTGATCCAAACC 60.894 55.000 0.00 0.00 0.00 3.27
2192 5028 1.595093 CCGCAACCTGATCCAAACCC 61.595 60.000 0.00 0.00 0.00 4.11
2193 5029 0.893270 CGCAACCTGATCCAAACCCA 60.893 55.000 0.00 0.00 0.00 4.51
2194 5030 0.890683 GCAACCTGATCCAAACCCAG 59.109 55.000 0.00 0.00 0.00 4.45
2195 5031 1.547675 GCAACCTGATCCAAACCCAGA 60.548 52.381 0.00 0.00 0.00 3.86
2196 5032 2.875296 CAACCTGATCCAAACCCAGAA 58.125 47.619 0.00 0.00 0.00 3.02
2197 5033 2.558359 CAACCTGATCCAAACCCAGAAC 59.442 50.000 0.00 0.00 0.00 3.01
2198 5034 1.075536 ACCTGATCCAAACCCAGAACC 59.924 52.381 0.00 0.00 0.00 3.62
2199 5035 1.075374 CCTGATCCAAACCCAGAACCA 59.925 52.381 0.00 0.00 0.00 3.67
2200 5036 2.291800 CCTGATCCAAACCCAGAACCAT 60.292 50.000 0.00 0.00 0.00 3.55
2201 5037 3.434309 CTGATCCAAACCCAGAACCATT 58.566 45.455 0.00 0.00 0.00 3.16
2202 5038 4.569653 CCTGATCCAAACCCAGAACCATTA 60.570 45.833 0.00 0.00 0.00 1.90
2203 5039 4.340617 TGATCCAAACCCAGAACCATTAC 58.659 43.478 0.00 0.00 0.00 1.89
2204 5040 3.163616 TCCAAACCCAGAACCATTACC 57.836 47.619 0.00 0.00 0.00 2.85
2205 5041 2.447429 TCCAAACCCAGAACCATTACCA 59.553 45.455 0.00 0.00 0.00 3.25
2206 5042 2.825532 CCAAACCCAGAACCATTACCAG 59.174 50.000 0.00 0.00 0.00 4.00
2207 5043 3.499563 CCAAACCCAGAACCATTACCAGA 60.500 47.826 0.00 0.00 0.00 3.86
2208 5044 4.344104 CAAACCCAGAACCATTACCAGAT 58.656 43.478 0.00 0.00 0.00 2.90
2238 5074 3.329889 CCACTGCCAGGCCCACTA 61.330 66.667 9.64 0.00 0.00 2.74
2241 5077 3.011517 CTGCCAGGCCCACTACCT 61.012 66.667 9.64 0.00 38.35 3.08
2247 5083 2.609610 GGCCCACTACCTGACCCA 60.610 66.667 0.00 0.00 0.00 4.51
2272 5108 2.166664 GCACAACCAAAACCACCACTTA 59.833 45.455 0.00 0.00 0.00 2.24
2352 5256 7.063544 GCATGAGATGTTCGGGTACTTATATTC 59.936 40.741 0.00 0.00 0.00 1.75
2380 5284 7.094720 CGGTTGGATTAAATAAGTGGTGTGTTA 60.095 37.037 0.00 0.00 0.00 2.41
2409 5314 2.371306 CACCATCAAGTCATGCCATGA 58.629 47.619 2.53 2.53 36.84 3.07
2416 5321 7.772292 ACCATCAAGTCATGCCATGATATATAC 59.228 37.037 11.14 0.00 42.04 1.47
2487 5392 8.296713 TGTGATTGTTCTTATTTACTTTCCTGC 58.703 33.333 0.00 0.00 0.00 4.85
2577 5486 8.801715 TTTCTACTGTGTACCGTTAGTTTTAG 57.198 34.615 0.00 0.00 0.00 1.85
2650 5561 4.651503 TGTGCCAATAAGAAAGGTGGAAAA 59.348 37.500 0.00 0.00 32.54 2.29
2651 5562 5.129485 TGTGCCAATAAGAAAGGTGGAAAAA 59.871 36.000 0.00 0.00 32.54 1.94
2673 5585 6.926630 AATTTTACAGGGTAAATCTTGGCA 57.073 33.333 2.73 0.00 0.00 4.92
2790 5705 5.242393 CCAGGATTCTAATTTGGGCATACAG 59.758 44.000 0.00 0.00 0.00 2.74
2807 5722 3.708563 ACAGTTGCCACATGTTACAAC 57.291 42.857 23.88 23.88 42.08 3.32
2901 5817 5.925969 CCACAAACTACTTTTTGGGCTTATG 59.074 40.000 1.04 0.00 38.38 1.90
2922 5838 3.181458 TGTCGCCCAAAAGAAGAACTACT 60.181 43.478 0.00 0.00 0.00 2.57
3103 6019 3.181449 CCCTCATCCTCTCTTCTCGTAGA 60.181 52.174 0.00 0.00 0.00 2.59
3226 6149 3.646611 TCGAACAATCACTACCACGAA 57.353 42.857 0.00 0.00 0.00 3.85
3237 6160 0.892358 TACCACGAACAGGACGAGCT 60.892 55.000 0.00 0.00 34.70 4.09
3261 6184 1.065928 CATCGCTCACCTACCGGAC 59.934 63.158 9.46 0.00 0.00 4.79
3264 6187 1.749638 CGCTCACCTACCGGACTCT 60.750 63.158 9.46 0.00 0.00 3.24
3265 6188 0.463295 CGCTCACCTACCGGACTCTA 60.463 60.000 9.46 0.00 0.00 2.43
3276 6199 1.104577 CGGACTCTAGCCTGACCTCC 61.105 65.000 0.00 0.00 0.00 4.30
3280 6203 1.047002 CTCTAGCCTGACCTCCATGG 58.953 60.000 4.97 4.97 42.93 3.66
3286 6209 2.531428 TGACCTCCATGGCACCCA 60.531 61.111 6.96 0.00 40.22 4.51
3329 6252 4.164221 CCCCTAAGGCTCTTGTAATCTTCA 59.836 45.833 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.374053 ACATTTCATACACCAATCACGATCAA 59.626 34.615 0.00 0.00 0.00 2.57
119 120 3.944087 AGCTTTCCTATTGGACAGTGAC 58.056 45.455 10.46 0.00 43.06 3.67
176 509 2.229784 CCAAGAAGCCTAGCAACAAAGG 59.770 50.000 0.00 0.00 35.86 3.11
182 515 3.719268 TGAATCCAAGAAGCCTAGCAA 57.281 42.857 0.00 0.00 0.00 3.91
252 656 8.846943 TTCTATGACTCAAACAACACATACAT 57.153 30.769 0.00 0.00 0.00 2.29
330 1123 6.824704 AGGTTTGCATGGATGGATTTATTTTG 59.175 34.615 0.00 0.00 0.00 2.44
376 1174 8.995220 GTAGGATGTTTTGTTGTACACAGATAA 58.005 33.333 0.00 0.00 36.48 1.75
377 1175 7.329962 CGTAGGATGTTTTGTTGTACACAGATA 59.670 37.037 0.00 0.00 36.48 1.98
378 1176 6.147164 CGTAGGATGTTTTGTTGTACACAGAT 59.853 38.462 0.00 0.00 36.48 2.90
379 1177 5.464057 CGTAGGATGTTTTGTTGTACACAGA 59.536 40.000 0.00 0.00 36.48 3.41
380 1178 5.675970 CGTAGGATGTTTTGTTGTACACAG 58.324 41.667 0.00 0.00 36.48 3.66
426 1225 7.951530 AATTTGAGGTGCAAGAATAAAGTTG 57.048 32.000 0.00 0.00 37.87 3.16
571 2082 6.430616 CACACAATATTTTTCCAGCCCAAATT 59.569 34.615 0.00 0.00 0.00 1.82
587 2098 7.992608 TGATGATTTGTAGGCTACACACAATAT 59.007 33.333 26.21 15.26 38.63 1.28
763 2412 7.591426 GTGAACAACCTGATCACTTTCAATAAC 59.409 37.037 9.14 0.00 43.88 1.89
871 2521 8.846211 CAACAAAAAGTTATCTAGGGAAGTTGA 58.154 33.333 0.00 0.00 38.74 3.18
971 2937 3.608241 GCTTGTGTTGCTACGTATTTGCA 60.608 43.478 4.05 4.05 34.69 4.08
972 2938 2.908626 GCTTGTGTTGCTACGTATTTGC 59.091 45.455 0.00 0.00 0.00 3.68
976 2942 3.617263 GCTAAGCTTGTGTTGCTACGTAT 59.383 43.478 9.86 0.00 40.22 3.06
1036 3097 2.549754 GCATAAACAGCAGCGGTGATAT 59.450 45.455 20.69 0.00 34.87 1.63
1039 3100 0.321564 AGCATAAACAGCAGCGGTGA 60.322 50.000 20.69 0.00 34.87 4.02
1068 3129 2.345760 CCCCGCAGCAAGAGCAAAT 61.346 57.895 0.00 0.00 45.49 2.32
1142 3203 2.173782 TGTTTTCCTGGCAGTGGTTCTA 59.826 45.455 14.43 0.00 0.00 2.10
1204 3265 0.761323 TCTGGTCGTGGTCCTGGAAA 60.761 55.000 0.00 0.00 0.00 3.13
1206 3267 1.906824 GTCTGGTCGTGGTCCTGGA 60.907 63.158 0.00 0.00 0.00 3.86
1386 3447 1.004200 CCGCGAGTTTGGGTTAGGT 60.004 57.895 8.23 0.00 0.00 3.08
1389 3707 2.358984 GGCCGCGAGTTTGGGTTA 60.359 61.111 8.23 0.00 0.00 2.85
1399 3717 2.758327 ATCTGGTAGTGGCCGCGA 60.758 61.111 8.23 1.77 0.00 5.87
1416 3734 2.128507 GTTTGGGTTTGGCCGTGGA 61.129 57.895 0.00 0.00 38.44 4.02
1440 3758 1.819632 CTGCGGTCCTGGTAATGGC 60.820 63.158 0.00 0.00 0.00 4.40
1477 3795 1.072648 CGGGTTTGGGTCTGGTAAAGA 59.927 52.381 0.00 0.00 0.00 2.52
1479 3797 1.138568 TCGGGTTTGGGTCTGGTAAA 58.861 50.000 0.00 0.00 0.00 2.01
1507 3959 1.527380 GGTTTGGCTGTGGGTTCGA 60.527 57.895 0.00 0.00 0.00 3.71
1960 4412 0.608035 TCTGGCGATGGTTTTGGGTC 60.608 55.000 0.00 0.00 0.00 4.46
1973 4425 4.641645 TTGGCTGTGGGTCTGGCG 62.642 66.667 0.00 0.00 41.93 5.69
1977 4429 1.943730 TTGGGTTTGGCTGTGGGTCT 61.944 55.000 0.00 0.00 0.00 3.85
1978 4790 1.045911 TTTGGGTTTGGCTGTGGGTC 61.046 55.000 0.00 0.00 0.00 4.46
2034 4870 0.988832 GGTCTGGTAATGGGTGTGGA 59.011 55.000 0.00 0.00 0.00 4.02
2040 4876 1.618616 GGGTTTGGGTCTGGTAATGGG 60.619 57.143 0.00 0.00 0.00 4.00
2074 4910 0.618968 TTTGGGTTTGGCTGTGGGTT 60.619 50.000 0.00 0.00 0.00 4.11
2115 4951 3.603965 TGTGGGTTTGGATTAGGTTGT 57.396 42.857 0.00 0.00 0.00 3.32
2122 4958 3.580895 GGTAATGGTTGTGGGTTTGGATT 59.419 43.478 0.00 0.00 0.00 3.01
2162 4998 0.035439 AGGTTGCGGTCCAGGTAATG 60.035 55.000 0.00 0.00 0.00 1.90
2163 4999 0.035439 CAGGTTGCGGTCCAGGTAAT 60.035 55.000 0.00 0.00 0.00 1.89
2164 5000 1.122632 TCAGGTTGCGGTCCAGGTAA 61.123 55.000 0.00 0.00 0.00 2.85
2165 5001 0.907704 ATCAGGTTGCGGTCCAGGTA 60.908 55.000 0.00 0.00 0.00 3.08
2166 5002 2.185310 GATCAGGTTGCGGTCCAGGT 62.185 60.000 0.00 0.00 0.00 4.00
2167 5003 1.450312 GATCAGGTTGCGGTCCAGG 60.450 63.158 0.00 0.00 0.00 4.45
2168 5004 1.450312 GGATCAGGTTGCGGTCCAG 60.450 63.158 0.00 0.00 0.00 3.86
2169 5005 1.773856 TTGGATCAGGTTGCGGTCCA 61.774 55.000 0.00 0.00 37.20 4.02
2170 5006 0.608035 TTTGGATCAGGTTGCGGTCC 60.608 55.000 0.00 0.00 0.00 4.46
2171 5007 0.521735 GTTTGGATCAGGTTGCGGTC 59.478 55.000 0.00 0.00 0.00 4.79
2172 5008 0.893727 GGTTTGGATCAGGTTGCGGT 60.894 55.000 0.00 0.00 0.00 5.68
2173 5009 1.595093 GGGTTTGGATCAGGTTGCGG 61.595 60.000 0.00 0.00 0.00 5.69
2174 5010 0.893270 TGGGTTTGGATCAGGTTGCG 60.893 55.000 0.00 0.00 0.00 4.85
2175 5011 0.890683 CTGGGTTTGGATCAGGTTGC 59.109 55.000 0.00 0.00 0.00 4.17
2176 5012 2.558359 GTTCTGGGTTTGGATCAGGTTG 59.442 50.000 0.00 0.00 0.00 3.77
2177 5013 2.490902 GGTTCTGGGTTTGGATCAGGTT 60.491 50.000 0.00 0.00 0.00 3.50
2178 5014 1.075536 GGTTCTGGGTTTGGATCAGGT 59.924 52.381 0.00 0.00 0.00 4.00
2179 5015 1.075374 TGGTTCTGGGTTTGGATCAGG 59.925 52.381 0.00 0.00 0.00 3.86
2180 5016 2.584835 TGGTTCTGGGTTTGGATCAG 57.415 50.000 0.00 0.00 0.00 2.90
2181 5017 3.541242 AATGGTTCTGGGTTTGGATCA 57.459 42.857 0.00 0.00 0.00 2.92
2182 5018 3.699538 GGTAATGGTTCTGGGTTTGGATC 59.300 47.826 0.00 0.00 0.00 3.36
2183 5019 3.076785 TGGTAATGGTTCTGGGTTTGGAT 59.923 43.478 0.00 0.00 0.00 3.41
2184 5020 2.447429 TGGTAATGGTTCTGGGTTTGGA 59.553 45.455 0.00 0.00 0.00 3.53
2185 5021 2.825532 CTGGTAATGGTTCTGGGTTTGG 59.174 50.000 0.00 0.00 0.00 3.28
2186 5022 3.761897 TCTGGTAATGGTTCTGGGTTTG 58.238 45.455 0.00 0.00 0.00 2.93
2187 5023 4.569865 GGATCTGGTAATGGTTCTGGGTTT 60.570 45.833 0.00 0.00 0.00 3.27
2188 5024 3.053619 GGATCTGGTAATGGTTCTGGGTT 60.054 47.826 0.00 0.00 0.00 4.11
2189 5025 2.509964 GGATCTGGTAATGGTTCTGGGT 59.490 50.000 0.00 0.00 0.00 4.51
2190 5026 2.509548 TGGATCTGGTAATGGTTCTGGG 59.490 50.000 0.00 0.00 0.00 4.45
2191 5027 3.931907 TGGATCTGGTAATGGTTCTGG 57.068 47.619 0.00 0.00 0.00 3.86
2192 5028 5.300286 GGATTTGGATCTGGTAATGGTTCTG 59.700 44.000 0.00 0.00 32.66 3.02
2193 5029 5.044179 TGGATTTGGATCTGGTAATGGTTCT 60.044 40.000 0.00 0.00 32.66 3.01
2194 5030 5.067805 GTGGATTTGGATCTGGTAATGGTTC 59.932 44.000 0.00 0.00 32.66 3.62
2195 5031 4.956075 GTGGATTTGGATCTGGTAATGGTT 59.044 41.667 0.00 0.00 32.66 3.67
2196 5032 4.017591 TGTGGATTTGGATCTGGTAATGGT 60.018 41.667 0.00 0.00 32.66 3.55
2197 5033 4.535781 TGTGGATTTGGATCTGGTAATGG 58.464 43.478 0.00 0.00 32.66 3.16
2198 5034 5.163519 GGTTGTGGATTTGGATCTGGTAATG 60.164 44.000 0.00 0.00 32.66 1.90
2199 5035 4.956075 GGTTGTGGATTTGGATCTGGTAAT 59.044 41.667 0.00 0.00 32.66 1.89
2200 5036 4.202620 TGGTTGTGGATTTGGATCTGGTAA 60.203 41.667 0.00 0.00 32.66 2.85
2201 5037 3.332187 TGGTTGTGGATTTGGATCTGGTA 59.668 43.478 0.00 0.00 32.66 3.25
2202 5038 2.109834 TGGTTGTGGATTTGGATCTGGT 59.890 45.455 0.00 0.00 32.66 4.00
2203 5039 2.493278 GTGGTTGTGGATTTGGATCTGG 59.507 50.000 0.00 0.00 32.66 3.86
2204 5040 3.192001 CAGTGGTTGTGGATTTGGATCTG 59.808 47.826 0.00 0.00 32.66 2.90
2205 5041 3.424703 CAGTGGTTGTGGATTTGGATCT 58.575 45.455 0.00 0.00 32.66 2.75
2206 5042 2.094545 GCAGTGGTTGTGGATTTGGATC 60.095 50.000 0.00 0.00 0.00 3.36
2207 5043 1.895131 GCAGTGGTTGTGGATTTGGAT 59.105 47.619 0.00 0.00 0.00 3.41
2208 5044 1.327303 GCAGTGGTTGTGGATTTGGA 58.673 50.000 0.00 0.00 0.00 3.53
2238 5074 1.039856 GTTGTGCATTTGGGTCAGGT 58.960 50.000 0.00 0.00 0.00 4.00
2241 5077 1.489481 TTGGTTGTGCATTTGGGTCA 58.511 45.000 0.00 0.00 0.00 4.02
2247 5083 2.026822 TGGTGGTTTTGGTTGTGCATTT 60.027 40.909 0.00 0.00 0.00 2.32
2272 5108 3.297134 TCCTTTTTCTGCTTGTGTCCT 57.703 42.857 0.00 0.00 0.00 3.85
2352 5256 4.097286 CACCACTTATTTAATCCAACCGGG 59.903 45.833 6.32 0.00 38.37 5.73
2380 5284 2.647299 TGACTTGATGGTGGTGGGTTAT 59.353 45.455 0.00 0.00 0.00 1.89
2416 5321 7.386025 TGCCGTAATCTTGATTGATCTTGATAG 59.614 37.037 6.15 0.00 0.00 2.08
2418 5323 6.057533 TGCCGTAATCTTGATTGATCTTGAT 58.942 36.000 6.15 0.00 0.00 2.57
2483 5388 0.541863 AATCCTCCGTACAAGGCAGG 59.458 55.000 6.44 3.62 33.65 4.85
2487 5392 4.119862 CACATACAATCCTCCGTACAAGG 58.880 47.826 5.14 5.14 35.05 3.61
2650 5561 6.926630 TGCCAAGATTTACCCTGTAAAATT 57.073 33.333 3.77 0.67 0.00 1.82
2651 5562 8.602472 TTATGCCAAGATTTACCCTGTAAAAT 57.398 30.769 3.77 0.00 0.00 1.82
2687 5599 3.441222 TGCACCATGCTTTATTCACTCTG 59.559 43.478 2.02 0.00 45.31 3.35
2762 5677 2.961062 CCCAAATTAGAATCCTGGCCAG 59.039 50.000 26.87 26.87 0.00 4.85
2790 5705 5.629020 CACATAAGTTGTAACATGTGGCAAC 59.371 40.000 25.77 25.77 42.83 4.17
2799 5714 9.737427 CAACATTTTACCACATAAGTTGTAACA 57.263 29.630 0.00 0.00 36.10 2.41
2901 5817 3.400255 AGTAGTTCTTCTTTTGGGCGAC 58.600 45.455 0.00 0.00 0.00 5.19
2922 5838 9.188588 CCGAATAGTGCGTTATCTATAGAAAAA 57.811 33.333 6.52 1.74 0.00 1.94
2946 5862 0.758734 TGCATGGGGAGAATAGACCG 59.241 55.000 0.00 0.00 0.00 4.79
3021 5937 6.592798 TGGTAAAAGTTCGTACAGTTTGAG 57.407 37.500 0.00 0.00 0.00 3.02
3029 5945 5.967088 CCACAAACTTGGTAAAAGTTCGTAC 59.033 40.000 4.09 0.00 39.36 3.67
3033 5949 7.892778 TTTTCCACAAACTTGGTAAAAGTTC 57.107 32.000 4.09 0.00 39.36 3.01
3226 6149 1.539560 ATGACAGCAGCTCGTCCTGT 61.540 55.000 17.31 5.76 42.10 4.00
3237 6160 0.173481 GTAGGTGAGCGATGACAGCA 59.827 55.000 0.00 0.00 37.04 4.41
3261 6184 1.047002 CCATGGAGGTCAGGCTAGAG 58.953 60.000 5.56 0.00 0.00 2.43
3264 6187 3.647367 GCCATGGAGGTCAGGCTA 58.353 61.111 18.40 0.00 43.70 3.93
3276 6199 0.038744 AAGACTTCCTGGGTGCCATG 59.961 55.000 0.00 0.00 30.82 3.66
3280 6203 0.951040 CACGAAGACTTCCTGGGTGC 60.951 60.000 9.63 0.00 0.00 5.01
3286 6209 0.039074 CACGAGCACGAAGACTTCCT 60.039 55.000 11.40 1.06 42.66 3.36


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

AutoCloner maintained by Alex Coulton.