Multiple sequence alignment - TraesCS6A01G126200

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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 TraesCS6A01G126200 chr6A 100.000 4151 0 0 1 4151 99787917 99783767 0.000000e+00 7666.0
1 TraesCS6A01G126200 chr6A 79.319 1939 378 17 1061 2989 98242378 98240453 0.000000e+00 1338.0
2 TraesCS6A01G126200 chr6A 77.397 2159 442 40 894 3029 98316056 98313921 0.000000e+00 1242.0
3 TraesCS6A01G126200 chr6A 76.981 1994 428 23 1053 3029 98249930 98247951 0.000000e+00 1110.0
4 TraesCS6A01G126200 chr6D 92.863 3461 198 29 479 3918 82965151 82961719 0.000000e+00 4977.0
5 TraesCS6A01G126200 chr6D 79.360 1938 377 18 1061 2988 81750104 81748180 0.000000e+00 1341.0
6 TraesCS6A01G126200 chr6D 77.690 2156 440 33 894 3029 81926270 81924136 0.000000e+00 1279.0
7 TraesCS6A01G126200 chr6D 83.673 1176 179 5 1065 2238 81920692 81919528 0.000000e+00 1096.0
8 TraesCS6A01G126200 chr6D 73.394 1977 458 48 1062 3013 83057891 83055958 0.000000e+00 675.0
9 TraesCS6A01G126200 chr6D 73.020 1957 477 35 1059 2998 83046836 83044914 3.500000e-180 641.0
10 TraesCS6A01G126200 chr6D 96.169 261 7 1 228 485 82970116 82969856 1.380000e-114 424.0
11 TraesCS6A01G126200 chr6B 91.268 3367 225 35 802 4145 157780026 157776706 0.000000e+00 4525.0
12 TraesCS6A01G126200 chr6B 94.861 1907 90 4 251 2155 157910738 157912638 0.000000e+00 2972.0
13 TraesCS6A01G126200 chr6B 93.093 1332 75 6 2136 3453 157930704 157932032 0.000000e+00 1934.0
14 TraesCS6A01G126200 chr6B 79.257 1938 381 17 1061 2989 156418364 156416439 0.000000e+00 1332.0
15 TraesCS6A01G126200 chr6B 77.226 2156 450 34 894 3029 156654925 156652791 0.000000e+00 1223.0
16 TraesCS6A01G126200 chr6B 77.151 2162 436 47 894 3026 157489395 157487263 0.000000e+00 1203.0
17 TraesCS6A01G126200 chr6B 74.568 1911 433 34 1330 3226 159390760 159392631 0.000000e+00 787.0
18 TraesCS6A01G126200 chr6B 93.494 538 16 10 228 762 157780538 157780017 0.000000e+00 782.0
19 TraesCS6A01G126200 chr6B 82.911 158 10 7 3440 3597 157932046 157932186 4.360000e-25 126.0
20 TraesCS6A01G126200 chr5D 88.337 3001 295 32 477 3460 372060831 372057869 0.000000e+00 3552.0
21 TraesCS6A01G126200 chr3B 94.037 218 12 1 1 217 546191361 546191144 3.090000e-86 329.0
22 TraesCS6A01G126200 chr2B 94.037 218 8 2 1 217 441888924 441889137 4.000000e-85 326.0
23 TraesCS6A01G126200 chr2B 94.037 218 8 2 1 217 522211481 522211694 4.000000e-85 326.0
24 TraesCS6A01G126200 chr1D 95.477 199 8 1 1 198 56509861 56509663 2.410000e-82 316.0
25 TraesCS6A01G126200 chr1D 98.148 54 0 1 428 481 303314744 303314692 4.420000e-15 93.5
26 TraesCS6A01G126200 chr1A 92.262 168 12 1 50 217 61712881 61713047 1.930000e-58 237.0
27 TraesCS6A01G126200 chr1A 96.296 54 1 1 428 481 380947125 380947073 2.060000e-13 87.9
28 TraesCS6A01G126200 chr5A 91.124 169 14 1 50 217 690403058 690403226 1.160000e-55 228.0
29 TraesCS6A01G126200 chr5A 96.000 50 2 0 437 486 605241820 605241771 9.560000e-12 82.4
30 TraesCS6A01G126200 chr4B 94.326 141 3 3 78 217 586318857 586318993 1.170000e-50 211.0
31 TraesCS6A01G126200 chr4B 87.037 162 20 1 56 217 475279013 475278853 9.170000e-42 182.0
32 TraesCS6A01G126200 chr4B 97.895 95 2 0 1 95 586318403 586318497 9.230000e-37 165.0
33 TraesCS6A01G126200 chr7D 83.854 192 20 9 29 217 133324075 133323892 5.520000e-39 172.0
34 TraesCS6A01G126200 chr1B 96.296 54 1 1 428 481 410794015 410793963 2.060000e-13 87.9
35 TraesCS6A01G126200 chr3D 96.000 50 2 0 434 483 175543172 175543123 9.560000e-12 82.4
36 TraesCS6A01G126200 chr2A 88.525 61 7 0 431 491 541196569 541196509 1.600000e-09 75.0


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 TraesCS6A01G126200 chr6A 99783767 99787917 4150 True 7666.0 7666 100.0000 1 4151 1 chr6A.!!$R4 4150
1 TraesCS6A01G126200 chr6A 98240453 98242378 1925 True 1338.0 1338 79.3190 1061 2989 1 chr6A.!!$R1 1928
2 TraesCS6A01G126200 chr6A 98313921 98316056 2135 True 1242.0 1242 77.3970 894 3029 1 chr6A.!!$R3 2135
3 TraesCS6A01G126200 chr6A 98247951 98249930 1979 True 1110.0 1110 76.9810 1053 3029 1 chr6A.!!$R2 1976
4 TraesCS6A01G126200 chr6D 82961719 82965151 3432 True 4977.0 4977 92.8630 479 3918 1 chr6D.!!$R2 3439
5 TraesCS6A01G126200 chr6D 81748180 81750104 1924 True 1341.0 1341 79.3600 1061 2988 1 chr6D.!!$R1 1927
6 TraesCS6A01G126200 chr6D 81919528 81926270 6742 True 1187.5 1279 80.6815 894 3029 2 chr6D.!!$R6 2135
7 TraesCS6A01G126200 chr6D 83055958 83057891 1933 True 675.0 675 73.3940 1062 3013 1 chr6D.!!$R5 1951
8 TraesCS6A01G126200 chr6D 83044914 83046836 1922 True 641.0 641 73.0200 1059 2998 1 chr6D.!!$R4 1939
9 TraesCS6A01G126200 chr6B 157910738 157912638 1900 False 2972.0 2972 94.8610 251 2155 1 chr6B.!!$F1 1904
10 TraesCS6A01G126200 chr6B 157776706 157780538 3832 True 2653.5 4525 92.3810 228 4145 2 chr6B.!!$R4 3917
11 TraesCS6A01G126200 chr6B 156416439 156418364 1925 True 1332.0 1332 79.2570 1061 2989 1 chr6B.!!$R1 1928
12 TraesCS6A01G126200 chr6B 156652791 156654925 2134 True 1223.0 1223 77.2260 894 3029 1 chr6B.!!$R2 2135
13 TraesCS6A01G126200 chr6B 157487263 157489395 2132 True 1203.0 1203 77.1510 894 3026 1 chr6B.!!$R3 2132
14 TraesCS6A01G126200 chr6B 157930704 157932186 1482 False 1030.0 1934 88.0020 2136 3597 2 chr6B.!!$F3 1461
15 TraesCS6A01G126200 chr6B 159390760 159392631 1871 False 787.0 787 74.5680 1330 3226 1 chr6B.!!$F2 1896
16 TraesCS6A01G126200 chr5D 372057869 372060831 2962 True 3552.0 3552 88.3370 477 3460 1 chr5D.!!$R1 2983

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
211 212 0.179468 AGCAACGCGTGGGGTATTAT 59.821 50.000 14.98 0.0 0.00 1.28 F
212 213 0.584876 GCAACGCGTGGGGTATTATC 59.415 55.000 14.98 0.0 0.00 1.75 F
213 214 1.808891 GCAACGCGTGGGGTATTATCT 60.809 52.381 14.98 0.0 0.00 1.98 F
1301 1339 1.969862 CGTCCCTCGGTAACCTTGT 59.030 57.895 0.00 0.0 35.71 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 1331 1.616159 GCAGAAGGCCAACAAGGTTA 58.384 50.000 5.01 0.0 40.61 2.85 R
1836 1877 6.828785 TGAAATTATTCCTTCCAAGGTCTAGC 59.171 38.462 5.24 0.0 46.54 3.42 R
2062 2105 7.230510 TCTGCCATTAAAGTTGTTGTACAGAAT 59.769 33.333 0.00 0.0 0.00 2.40 R
3230 4293 1.691976 TCGAACCTTCTGGAAGCTTGA 59.308 47.619 2.10 0.0 37.11 3.02 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
21 22 4.201208 CTAAGAATACCGCAGCAATGTG 57.799 45.455 0.00 0.00 0.00 3.21
22 23 0.734889 AGAATACCGCAGCAATGTGC 59.265 50.000 0.00 0.00 45.46 4.57
48 49 6.113411 GTGCACCACCATATCCTATATAACC 58.887 44.000 5.22 0.00 0.00 2.85
49 50 5.788014 TGCACCACCATATCCTATATAACCA 59.212 40.000 0.00 0.00 0.00 3.67
50 51 6.273495 TGCACCACCATATCCTATATAACCAA 59.727 38.462 0.00 0.00 0.00 3.67
51 52 7.172342 GCACCACCATATCCTATATAACCAAA 58.828 38.462 0.00 0.00 0.00 3.28
52 53 7.668052 GCACCACCATATCCTATATAACCAAAA 59.332 37.037 0.00 0.00 0.00 2.44
53 54 9.581289 CACCACCATATCCTATATAACCAAAAA 57.419 33.333 0.00 0.00 0.00 1.94
54 55 9.807921 ACCACCATATCCTATATAACCAAAAAG 57.192 33.333 0.00 0.00 0.00 2.27
166 167 9.850628 TCATGTTTCAAAGAATCAAATCTCATC 57.149 29.630 0.00 0.00 0.00 2.92
167 168 9.634163 CATGTTTCAAAGAATCAAATCTCATCA 57.366 29.630 0.00 0.00 0.00 3.07
194 195 3.874392 ATTGTAACCAATTCCTGCAGC 57.126 42.857 8.66 0.00 38.10 5.25
195 196 2.284754 TGTAACCAATTCCTGCAGCA 57.715 45.000 8.66 0.00 0.00 4.41
196 197 2.591923 TGTAACCAATTCCTGCAGCAA 58.408 42.857 8.66 0.00 0.00 3.91
197 198 2.295909 TGTAACCAATTCCTGCAGCAAC 59.704 45.455 8.66 0.00 0.00 4.17
198 199 0.314935 AACCAATTCCTGCAGCAACG 59.685 50.000 8.66 0.00 0.00 4.10
199 200 1.444895 CCAATTCCTGCAGCAACGC 60.445 57.895 8.66 0.00 0.00 4.84
200 201 1.798725 CAATTCCTGCAGCAACGCG 60.799 57.895 8.66 3.53 33.35 6.01
201 202 2.260869 AATTCCTGCAGCAACGCGT 61.261 52.632 5.58 5.58 33.35 6.01
202 203 2.462255 AATTCCTGCAGCAACGCGTG 62.462 55.000 14.98 8.57 33.35 5.34
208 209 2.435938 CAGCAACGCGTGGGGTAT 60.436 61.111 14.98 0.00 0.00 2.73
209 210 2.038269 CAGCAACGCGTGGGGTATT 61.038 57.895 14.98 0.00 0.00 1.89
210 211 0.741574 CAGCAACGCGTGGGGTATTA 60.742 55.000 14.98 0.00 0.00 0.98
211 212 0.179468 AGCAACGCGTGGGGTATTAT 59.821 50.000 14.98 0.00 0.00 1.28
212 213 0.584876 GCAACGCGTGGGGTATTATC 59.415 55.000 14.98 0.00 0.00 1.75
213 214 1.808891 GCAACGCGTGGGGTATTATCT 60.809 52.381 14.98 0.00 0.00 1.98
214 215 2.546373 GCAACGCGTGGGGTATTATCTA 60.546 50.000 14.98 0.00 0.00 1.98
215 216 3.314553 CAACGCGTGGGGTATTATCTAG 58.685 50.000 14.98 0.00 0.00 2.43
216 217 2.590821 ACGCGTGGGGTATTATCTAGT 58.409 47.619 12.93 0.00 0.00 2.57
217 218 2.555757 ACGCGTGGGGTATTATCTAGTC 59.444 50.000 12.93 0.00 0.00 2.59
218 219 2.818432 CGCGTGGGGTATTATCTAGTCT 59.182 50.000 0.00 0.00 0.00 3.24
219 220 4.005650 CGCGTGGGGTATTATCTAGTCTA 58.994 47.826 0.00 0.00 0.00 2.59
220 221 4.142730 CGCGTGGGGTATTATCTAGTCTAC 60.143 50.000 0.00 0.00 0.00 2.59
221 222 4.763793 GCGTGGGGTATTATCTAGTCTACA 59.236 45.833 0.00 0.00 0.00 2.74
222 223 5.242393 GCGTGGGGTATTATCTAGTCTACAA 59.758 44.000 0.00 0.00 0.00 2.41
223 224 6.071503 GCGTGGGGTATTATCTAGTCTACAAT 60.072 42.308 0.00 0.00 0.00 2.71
224 225 7.121759 GCGTGGGGTATTATCTAGTCTACAATA 59.878 40.741 0.00 0.00 0.00 1.90
225 226 9.017509 CGTGGGGTATTATCTAGTCTACAATAA 57.982 37.037 0.00 0.00 0.00 1.40
244 245 6.558775 ACAATAATAGTGGAGGCAGGAGAATA 59.441 38.462 0.00 0.00 0.00 1.75
288 290 9.095065 ACGTAAACATCAGACAATAATAGTTCC 57.905 33.333 0.00 0.00 0.00 3.62
446 448 8.002459 TCCCATGTACTACTATCATAGTGTCAA 58.998 37.037 7.66 0.00 39.81 3.18
505 507 3.752412 TGCTCATCAAATCTTTCGCAG 57.248 42.857 0.00 0.00 0.00 5.18
623 630 8.847444 CAAAGGATGCATTAAGAAGTGATAAC 57.153 34.615 0.00 0.00 0.00 1.89
670 677 2.538512 AGTGAAGGTGGTAACGGAAC 57.461 50.000 0.00 0.00 42.51 3.62
809 821 2.029020 TGCCATTAGAGTATAGCAGGCG 60.029 50.000 0.00 0.00 43.59 5.52
1107 1137 3.817084 CCATCAGTTCTTGCACAGAGAAA 59.183 43.478 0.92 0.00 35.11 2.52
1301 1339 1.969862 CGTCCCTCGGTAACCTTGT 59.030 57.895 0.00 0.00 35.71 3.16
1648 1689 4.214545 TCTGTTACAACCAATTTACAGGCG 59.785 41.667 0.00 0.00 35.06 5.52
1836 1877 2.015736 AGCTCAGCAATCTGGTTACG 57.984 50.000 0.00 0.00 40.69 3.18
2062 2105 5.208890 TGCCTAGGCTGAAAACTCTAGATA 58.791 41.667 33.07 5.21 42.51 1.98
2602 2654 0.838987 AGCCCGTTTAGACCCAAGGA 60.839 55.000 0.00 0.00 0.00 3.36
2855 2914 1.634973 TCTCATTGGTGCAATCCCAGA 59.365 47.619 0.00 0.00 31.05 3.86
3037 3097 2.926901 TTCAACACGTCCACCCACCG 62.927 60.000 0.00 0.00 0.00 4.94
3129 3194 4.344102 GGGGTGTTGTATGATCAGCTAGTA 59.656 45.833 0.09 0.00 0.00 1.82
3230 4293 3.129287 GGTTCAGCAAAATGTCCATCGAT 59.871 43.478 0.00 0.00 0.00 3.59
3299 6319 2.350522 AGTGTGAAGCGTGATTCCATC 58.649 47.619 0.00 0.00 0.00 3.51
3320 6340 6.739112 CATCTCGTGGAGATTCACAAGTATA 58.261 40.000 5.42 0.00 45.86 1.47
3449 7599 8.831715 ACTGAAACTTCAATTTTTCACAGTTT 57.168 26.923 0.00 0.00 36.92 2.66
3587 7742 6.358030 CACAAAATCTTCTTAGAACAAGCACG 59.642 38.462 0.00 0.00 33.20 5.34
3628 7783 1.083806 TTGGTAAGCAGCGCATCTCG 61.084 55.000 11.47 0.00 42.12 4.04
3629 7784 1.226974 GGTAAGCAGCGCATCTCGA 60.227 57.895 11.47 0.00 41.67 4.04
3661 7816 0.030235 GTCCGTGGCAGGTGTTTTTC 59.970 55.000 6.43 0.00 0.00 2.29
3665 7820 1.535860 CGTGGCAGGTGTTTTTCTTGG 60.536 52.381 0.00 0.00 0.00 3.61
3666 7821 1.754226 GTGGCAGGTGTTTTTCTTGGA 59.246 47.619 0.00 0.00 0.00 3.53
3668 7823 2.306847 GGCAGGTGTTTTTCTTGGAGA 58.693 47.619 0.00 0.00 0.00 3.71
3669 7824 2.893489 GGCAGGTGTTTTTCTTGGAGAT 59.107 45.455 0.00 0.00 0.00 2.75
3682 7837 1.065928 GGAGATGTACCTCCGCACG 59.934 63.158 2.81 0.00 42.80 5.34
3844 8016 3.492383 CGAGCTGATTTACTACATGCCTG 59.508 47.826 0.00 0.00 0.00 4.85
3848 8020 2.509548 TGATTTACTACATGCCTGGCCT 59.490 45.455 17.53 2.69 0.00 5.19
3929 8101 2.599578 CAAGCTGCTTGGGTGCCT 60.600 61.111 29.91 0.00 37.77 4.75
3930 8102 2.282745 AAGCTGCTTGGGTGCCTC 60.283 61.111 15.16 0.00 0.00 4.70
3931 8103 2.838467 AAGCTGCTTGGGTGCCTCT 61.838 57.895 15.16 0.00 0.00 3.69
3932 8104 2.282745 GCTGCTTGGGTGCCTCTT 60.283 61.111 0.00 0.00 0.00 2.85
3933 8105 2.338785 GCTGCTTGGGTGCCTCTTC 61.339 63.158 0.00 0.00 0.00 2.87
3934 8106 1.377994 CTGCTTGGGTGCCTCTTCT 59.622 57.895 0.00 0.00 0.00 2.85
3935 8107 0.251077 CTGCTTGGGTGCCTCTTCTT 60.251 55.000 0.00 0.00 0.00 2.52
3936 8108 0.185901 TGCTTGGGTGCCTCTTCTTT 59.814 50.000 0.00 0.00 0.00 2.52
3937 8109 1.332195 GCTTGGGTGCCTCTTCTTTT 58.668 50.000 0.00 0.00 0.00 2.27
3938 8110 1.688735 GCTTGGGTGCCTCTTCTTTTT 59.311 47.619 0.00 0.00 0.00 1.94
3962 8134 4.601084 TCTTGAGCAAGCTACTAGTACCT 58.399 43.478 0.00 0.00 38.28 3.08
3963 8135 5.752650 TCTTGAGCAAGCTACTAGTACCTA 58.247 41.667 0.00 0.00 38.28 3.08
3964 8136 5.589452 TCTTGAGCAAGCTACTAGTACCTAC 59.411 44.000 0.00 0.00 38.28 3.18
3965 8137 4.205587 TGAGCAAGCTACTAGTACCTACC 58.794 47.826 0.00 0.00 0.00 3.18
3966 8138 4.079901 TGAGCAAGCTACTAGTACCTACCT 60.080 45.833 0.00 0.00 0.00 3.08
3968 8140 3.318557 GCAAGCTACTAGTACCTACCTGG 59.681 52.174 0.00 0.00 42.93 4.45
3976 8148 3.555117 AGTACCTACCTGGGTTTCAGA 57.445 47.619 0.00 0.00 46.18 3.27
3979 8151 1.978580 ACCTACCTGGGTTTCAGAGTG 59.021 52.381 0.00 0.00 46.18 3.51
3980 8152 1.978580 CCTACCTGGGTTTCAGAGTGT 59.021 52.381 0.00 0.00 46.18 3.55
3981 8153 2.372172 CCTACCTGGGTTTCAGAGTGTT 59.628 50.000 0.00 0.00 46.18 3.32
3982 8154 3.581332 CCTACCTGGGTTTCAGAGTGTTA 59.419 47.826 0.00 0.00 46.18 2.41
3983 8155 3.771577 ACCTGGGTTTCAGAGTGTTAG 57.228 47.619 0.00 0.00 46.18 2.34
3984 8156 2.372172 ACCTGGGTTTCAGAGTGTTAGG 59.628 50.000 0.00 0.00 46.18 2.69
3985 8157 2.372172 CCTGGGTTTCAGAGTGTTAGGT 59.628 50.000 0.00 0.00 46.18 3.08
3986 8158 3.557264 CCTGGGTTTCAGAGTGTTAGGTC 60.557 52.174 0.00 0.00 46.18 3.85
3988 8160 2.067013 GGTTTCAGAGTGTTAGGTCGC 58.933 52.381 0.00 0.00 0.00 5.19
3989 8161 1.719780 GTTTCAGAGTGTTAGGTCGCG 59.280 52.381 0.00 0.00 0.00 5.87
3992 8164 0.803117 CAGAGTGTTAGGTCGCGAGA 59.197 55.000 10.24 0.00 38.16 4.04
4068 8261 3.876274 TTCTCCTGGCTATCGCATATC 57.124 47.619 0.00 0.00 38.10 1.63
4069 8262 2.807676 TCTCCTGGCTATCGCATATCA 58.192 47.619 0.00 0.00 38.10 2.15
4077 8270 0.975887 TATCGCATATCAGCCAGCCA 59.024 50.000 0.00 0.00 0.00 4.75
4102 8295 1.452801 GGTTTCAGGGACCGGTTCA 59.547 57.895 16.62 0.00 0.00 3.18
4103 8296 0.605589 GGTTTCAGGGACCGGTTCAG 60.606 60.000 16.62 6.73 0.00 3.02
4104 8297 1.072505 TTTCAGGGACCGGTTCAGC 59.927 57.895 16.62 0.00 0.00 4.26
4105 8298 2.406002 TTTCAGGGACCGGTTCAGCC 62.406 60.000 16.62 8.52 0.00 4.85
4121 8314 4.382788 CCGTTCGGGCCTGTTTTA 57.617 55.556 12.43 0.00 0.00 1.52
4134 8327 2.411547 CCTGTTTTAGAAGCTTCGCGTG 60.412 50.000 20.43 8.43 0.00 5.34
4135 8328 1.529438 TGTTTTAGAAGCTTCGCGTGG 59.471 47.619 20.43 0.78 0.00 4.94
4137 8330 2.728690 TTTAGAAGCTTCGCGTGGTA 57.271 45.000 20.43 3.86 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.546815 GCACATTGCTGCGGTATTCTTAG 60.547 47.826 0.00 0.00 40.96 2.18
2 3 1.133025 GCACATTGCTGCGGTATTCTT 59.867 47.619 0.00 0.00 40.96 2.52
3 4 0.734889 GCACATTGCTGCGGTATTCT 59.265 50.000 0.00 0.00 40.96 2.40
4 5 3.240684 GCACATTGCTGCGGTATTC 57.759 52.632 0.00 0.00 40.96 1.75
11 12 4.345962 TGCACCGCACATTGCTGC 62.346 61.111 5.65 5.65 42.61 5.25
24 25 6.113411 GGTTATATAGGATATGGTGGTGCAC 58.887 44.000 8.80 8.80 0.00 4.57
25 26 5.788014 TGGTTATATAGGATATGGTGGTGCA 59.212 40.000 0.00 0.00 0.00 4.57
26 27 6.308015 TGGTTATATAGGATATGGTGGTGC 57.692 41.667 0.00 0.00 0.00 5.01
27 28 9.581289 TTTTTGGTTATATAGGATATGGTGGTG 57.419 33.333 0.00 0.00 0.00 4.17
28 29 9.807921 CTTTTTGGTTATATAGGATATGGTGGT 57.192 33.333 0.00 0.00 0.00 4.16
140 141 9.850628 GATGAGATTTGATTCTTTGAAACATGA 57.149 29.630 0.00 0.00 0.00 3.07
141 142 9.634163 TGATGAGATTTGATTCTTTGAAACATG 57.366 29.630 0.00 0.00 0.00 3.21
168 169 8.792633 GCTGCAGGAATTGGTTACAATATATTA 58.207 33.333 17.12 0.00 46.25 0.98
169 170 7.287466 TGCTGCAGGAATTGGTTACAATATATT 59.713 33.333 17.12 0.00 46.25 1.28
170 171 6.777091 TGCTGCAGGAATTGGTTACAATATAT 59.223 34.615 17.12 0.00 46.25 0.86
171 172 6.125719 TGCTGCAGGAATTGGTTACAATATA 58.874 36.000 17.12 0.00 46.25 0.86
172 173 4.955450 TGCTGCAGGAATTGGTTACAATAT 59.045 37.500 17.12 0.00 46.25 1.28
173 174 4.339748 TGCTGCAGGAATTGGTTACAATA 58.660 39.130 17.12 0.00 46.25 1.90
175 176 2.591923 TGCTGCAGGAATTGGTTACAA 58.408 42.857 17.12 0.00 41.59 2.41
176 177 2.284754 TGCTGCAGGAATTGGTTACA 57.715 45.000 17.12 0.00 0.00 2.41
177 178 2.668279 CGTTGCTGCAGGAATTGGTTAC 60.668 50.000 24.13 8.86 0.00 2.50
178 179 1.539388 CGTTGCTGCAGGAATTGGTTA 59.461 47.619 24.13 0.00 0.00 2.85
179 180 0.314935 CGTTGCTGCAGGAATTGGTT 59.685 50.000 24.13 0.00 0.00 3.67
180 181 1.959085 CGTTGCTGCAGGAATTGGT 59.041 52.632 24.13 0.00 0.00 3.67
181 182 1.444895 GCGTTGCTGCAGGAATTGG 60.445 57.895 24.13 16.36 34.15 3.16
182 183 1.798725 CGCGTTGCTGCAGGAATTG 60.799 57.895 24.13 19.26 34.15 2.32
183 184 2.260869 ACGCGTTGCTGCAGGAATT 61.261 52.632 24.13 6.25 34.15 2.17
184 185 2.669569 ACGCGTTGCTGCAGGAAT 60.670 55.556 24.13 4.84 34.15 3.01
185 186 3.648982 CACGCGTTGCTGCAGGAA 61.649 61.111 17.55 17.55 34.15 3.36
191 192 0.741574 TAATACCCCACGCGTTGCTG 60.742 55.000 10.22 2.41 0.00 4.41
192 193 0.179468 ATAATACCCCACGCGTTGCT 59.821 50.000 10.22 0.00 0.00 3.91
193 194 0.584876 GATAATACCCCACGCGTTGC 59.415 55.000 10.22 0.00 0.00 4.17
194 195 2.234300 AGATAATACCCCACGCGTTG 57.766 50.000 10.22 6.05 0.00 4.10
195 196 2.961062 ACTAGATAATACCCCACGCGTT 59.039 45.455 10.22 0.00 0.00 4.84
196 197 2.555757 GACTAGATAATACCCCACGCGT 59.444 50.000 5.58 5.58 0.00 6.01
197 198 2.818432 AGACTAGATAATACCCCACGCG 59.182 50.000 3.53 3.53 0.00 6.01
198 199 4.763793 TGTAGACTAGATAATACCCCACGC 59.236 45.833 0.00 0.00 0.00 5.34
199 200 6.889301 TTGTAGACTAGATAATACCCCACG 57.111 41.667 0.00 0.00 0.00 4.94
209 210 9.463902 GCCTCCACTATTATTGTAGACTAGATA 57.536 37.037 0.00 0.00 0.00 1.98
210 211 7.950684 TGCCTCCACTATTATTGTAGACTAGAT 59.049 37.037 0.00 0.00 0.00 1.98
211 212 7.295340 TGCCTCCACTATTATTGTAGACTAGA 58.705 38.462 0.00 0.00 0.00 2.43
212 213 7.309499 CCTGCCTCCACTATTATTGTAGACTAG 60.309 44.444 0.00 0.00 0.00 2.57
213 214 6.493802 CCTGCCTCCACTATTATTGTAGACTA 59.506 42.308 0.00 0.00 0.00 2.59
214 215 5.305644 CCTGCCTCCACTATTATTGTAGACT 59.694 44.000 0.00 0.00 0.00 3.24
215 216 5.304614 TCCTGCCTCCACTATTATTGTAGAC 59.695 44.000 0.00 0.00 0.00 2.59
216 217 5.464069 TCCTGCCTCCACTATTATTGTAGA 58.536 41.667 0.00 0.00 0.00 2.59
217 218 5.540337 TCTCCTGCCTCCACTATTATTGTAG 59.460 44.000 0.00 0.00 0.00 2.74
218 219 5.464069 TCTCCTGCCTCCACTATTATTGTA 58.536 41.667 0.00 0.00 0.00 2.41
219 220 4.298626 TCTCCTGCCTCCACTATTATTGT 58.701 43.478 0.00 0.00 0.00 2.71
220 221 4.963318 TCTCCTGCCTCCACTATTATTG 57.037 45.455 0.00 0.00 0.00 1.90
221 222 7.633018 TTATTCTCCTGCCTCCACTATTATT 57.367 36.000 0.00 0.00 0.00 1.40
222 223 7.633018 TTTATTCTCCTGCCTCCACTATTAT 57.367 36.000 0.00 0.00 0.00 1.28
223 224 7.446106 TTTTATTCTCCTGCCTCCACTATTA 57.554 36.000 0.00 0.00 0.00 0.98
224 225 5.975988 TTTATTCTCCTGCCTCCACTATT 57.024 39.130 0.00 0.00 0.00 1.73
225 226 5.975988 TTTTATTCTCCTGCCTCCACTAT 57.024 39.130 0.00 0.00 0.00 2.12
226 227 5.772393 TTTTTATTCTCCTGCCTCCACTA 57.228 39.130 0.00 0.00 0.00 2.74
505 507 0.746659 AACAACAGTTGCTGAAGGCC 59.253 50.000 13.56 0.00 40.92 5.19
670 677 6.142139 TCGCAATTAAACTTGAACAGACATG 58.858 36.000 0.00 0.00 0.00 3.21
678 687 6.851609 ACAGCATATCGCAATTAAACTTGAA 58.148 32.000 0.00 0.00 46.13 2.69
825 837 5.412640 TCTTAGTTCACACTGACGTTTCAA 58.587 37.500 0.00 0.00 34.06 2.69
1293 1331 1.616159 GCAGAAGGCCAACAAGGTTA 58.384 50.000 5.01 0.00 40.61 2.85
1836 1877 6.828785 TGAAATTATTCCTTCCAAGGTCTAGC 59.171 38.462 5.24 0.00 46.54 3.42
2062 2105 7.230510 TCTGCCATTAAAGTTGTTGTACAGAAT 59.769 33.333 0.00 0.00 0.00 2.40
2324 2370 6.628185 AGATTCTCAAAACCATCAATGAAGC 58.372 36.000 0.00 0.00 0.00 3.86
2434 2480 4.122776 CCGGTGAGTTGATTTCCTGATAG 58.877 47.826 0.00 0.00 0.00 2.08
2543 2589 4.304110 CAACATTTGCATATCCATCAGGC 58.696 43.478 0.00 0.00 33.74 4.85
2602 2654 6.041751 CCCCTATAAACTGGTAGTTCGAAGAT 59.958 42.308 0.00 0.00 37.47 2.40
2855 2914 4.217118 GGAAGTTCAGTCTGTTCAATGCAT 59.783 41.667 5.01 0.00 0.00 3.96
3037 3097 3.059166 CAGTTTGTTTGGTTGCCATAGC 58.941 45.455 0.00 0.00 40.48 2.97
3154 3219 9.814899 GAGATATACTGATATGGAAACTGGATG 57.185 37.037 0.00 0.00 0.00 3.51
3230 4293 1.691976 TCGAACCTTCTGGAAGCTTGA 59.308 47.619 2.10 0.00 37.11 3.02
3272 5957 5.232414 GGAATCACGCTTCACACTAGAATAC 59.768 44.000 0.00 0.00 0.00 1.89
3320 6340 7.701539 TCAGCCAACAATCTTACATTGTTAT 57.298 32.000 11.39 0.85 46.73 1.89
3449 7599 4.455533 ACTGATTTCGCATGAAGCAAAGTA 59.544 37.500 0.00 0.00 46.13 2.24
3558 7713 8.292448 GCTTGTTCTAAGAAGATTTTGTGATGA 58.708 33.333 3.95 0.00 31.45 2.92
3600 7755 1.069227 GCTGCTTACCAAACCTGTTCG 60.069 52.381 0.00 0.00 0.00 3.95
3636 7791 3.047877 CCTGCCACGGACGGTTTC 61.048 66.667 0.00 0.00 0.00 2.78
3665 7820 1.065928 CCGTGCGGAGGTACATCTC 59.934 63.158 7.56 0.00 37.50 2.75
3666 7821 3.077519 GCCGTGCGGAGGTACATCT 62.078 63.158 15.45 0.00 37.50 2.90
3699 7854 2.764128 ATGCCGTCGGGAGGACAT 60.764 61.111 14.38 4.40 46.42 3.06
3771 7926 4.090057 GCTCCGCAGTTCCGCAAC 62.090 66.667 0.00 0.00 0.00 4.17
3827 7996 2.509548 AGGCCAGGCATGTAGTAAATCA 59.490 45.455 15.19 0.00 0.00 2.57
3936 8108 6.649557 GGTACTAGTAGCTTGCTCAAGAAAAA 59.350 38.462 22.03 0.00 40.79 1.94
3937 8109 6.014499 AGGTACTAGTAGCTTGCTCAAGAAAA 60.014 38.462 25.40 0.00 40.62 2.29
3938 8110 5.480772 AGGTACTAGTAGCTTGCTCAAGAAA 59.519 40.000 25.40 0.00 40.62 2.52
3939 8111 5.017490 AGGTACTAGTAGCTTGCTCAAGAA 58.983 41.667 25.40 0.00 40.62 2.52
3940 8112 4.601084 AGGTACTAGTAGCTTGCTCAAGA 58.399 43.478 25.40 0.00 40.62 3.02
3941 8113 4.993029 AGGTACTAGTAGCTTGCTCAAG 57.007 45.455 25.40 5.31 40.62 3.02
3942 8114 4.643784 GGTAGGTACTAGTAGCTTGCTCAA 59.356 45.833 33.01 15.93 44.14 3.02
3943 8115 4.079901 AGGTAGGTACTAGTAGCTTGCTCA 60.080 45.833 33.01 16.57 44.14 4.26
3944 8116 4.276431 CAGGTAGGTACTAGTAGCTTGCTC 59.724 50.000 33.01 21.48 44.14 4.26
3945 8117 4.208746 CAGGTAGGTACTAGTAGCTTGCT 58.791 47.826 33.01 16.16 44.14 3.91
3946 8118 3.318557 CCAGGTAGGTACTAGTAGCTTGC 59.681 52.174 33.01 25.37 44.14 4.01
3947 8119 3.890147 CCCAGGTAGGTACTAGTAGCTTG 59.110 52.174 33.01 25.32 44.14 4.01
3953 8125 4.045079 TCTGAAACCCAGGTAGGTACTAGT 59.955 45.833 0.00 0.00 41.00 2.57
3954 8126 4.607239 TCTGAAACCCAGGTAGGTACTAG 58.393 47.826 0.00 0.00 41.00 2.57
3957 8129 3.056035 CACTCTGAAACCCAGGTAGGTAC 60.056 52.174 0.00 0.00 43.12 3.34
3959 8131 1.978580 CACTCTGAAACCCAGGTAGGT 59.021 52.381 0.00 0.00 43.12 3.08
3962 8134 3.581332 CCTAACACTCTGAAACCCAGGTA 59.419 47.826 0.00 0.00 43.12 3.08
3963 8135 2.372172 CCTAACACTCTGAAACCCAGGT 59.628 50.000 0.00 0.00 43.12 4.00
3964 8136 2.372172 ACCTAACACTCTGAAACCCAGG 59.628 50.000 0.00 0.00 43.12 4.45
3965 8137 3.665190 GACCTAACACTCTGAAACCCAG 58.335 50.000 0.00 0.00 44.27 4.45
3966 8138 2.036733 CGACCTAACACTCTGAAACCCA 59.963 50.000 0.00 0.00 0.00 4.51
3968 8140 2.067013 GCGACCTAACACTCTGAAACC 58.933 52.381 0.00 0.00 0.00 3.27
3976 8148 1.500844 CGTCTCGCGACCTAACACT 59.499 57.895 3.71 0.00 44.77 3.55
3979 8151 2.578981 GCCGTCTCGCGACCTAAC 60.579 66.667 3.71 0.00 44.77 2.34
3988 8160 0.029567 AAATAGCTCTCGCCGTCTCG 59.970 55.000 0.00 0.00 36.60 4.04
3989 8161 1.335496 AGAAATAGCTCTCGCCGTCTC 59.665 52.381 0.00 0.00 36.60 3.36
3992 8164 3.949031 GAGAAATAGCTCTCGCCGT 57.051 52.632 0.00 0.00 36.60 5.68
4014 8207 1.587613 GGAAGCTACTCTCGCGCTG 60.588 63.158 5.56 0.00 33.64 5.18
4017 8210 1.297745 GACGGAAGCTACTCTCGCG 60.298 63.158 0.00 0.00 0.00 5.87
4068 8261 2.142292 AACCCTTACCTGGCTGGCTG 62.142 60.000 10.71 1.43 40.22 4.85
4069 8262 1.435346 AAACCCTTACCTGGCTGGCT 61.435 55.000 10.71 0.78 40.22 4.75
4073 8266 0.698818 CCTGAAACCCTTACCTGGCT 59.301 55.000 0.00 0.00 0.00 4.75
4077 8270 1.369403 GGTCCCTGAAACCCTTACCT 58.631 55.000 0.00 0.00 0.00 3.08
4104 8297 0.320946 TCTAAAACAGGCCCGAACGG 60.321 55.000 0.00 6.25 0.00 4.44
4105 8298 1.463444 CTTCTAAAACAGGCCCGAACG 59.537 52.381 0.00 0.00 0.00 3.95
4106 8299 1.199327 GCTTCTAAAACAGGCCCGAAC 59.801 52.381 0.00 0.00 0.00 3.95
4107 8300 1.073284 AGCTTCTAAAACAGGCCCGAA 59.927 47.619 0.00 0.00 0.00 4.30
4108 8301 0.690762 AGCTTCTAAAACAGGCCCGA 59.309 50.000 0.00 0.00 0.00 5.14
4109 8302 1.468914 GAAGCTTCTAAAACAGGCCCG 59.531 52.381 19.44 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.