Multiple sequence alignment - TraesCS3D01G164700

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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 TraesCS3D01G164700 chr3D 100.000 3954 0 0 1 3954 136400357 136404310 0.000000e+00 7302
1 TraesCS3D01G164700 chr3A 95.050 2404 68 12 887 3276 154030549 154032915 0.000000e+00 3733
2 TraesCS3D01G164700 chr3A 92.097 620 31 7 3342 3953 154032939 154033548 0.000000e+00 857
3 TraesCS3D01G164700 chr3A 82.759 464 27 20 444 880 154029941 154030378 8.070000e-97 364
4 TraesCS3D01G164700 chr3A 94.706 170 8 1 197 365 154029633 154029802 3.030000e-66 263
5 TraesCS3D01G164700 chr3A 96.104 154 6 0 1 154 154029341 154029494 6.560000e-63 252
6 TraesCS3D01G164700 chr3B 95.270 1353 42 17 650 1997 194757497 194758832 0.000000e+00 2124
7 TraesCS3D01G164700 chr3B 92.338 1279 43 14 2032 3294 194758826 194760065 0.000000e+00 1768
8 TraesCS3D01G164700 chr3B 93.312 613 32 6 3342 3952 194760070 194760675 0.000000e+00 896
9 TraesCS3D01G164700 chr3B 89.946 368 22 7 9 365 194756735 194757098 1.000000e-125 460
10 TraesCS3D01G164700 chr3B 89.604 202 14 4 452 648 194757244 194757443 2.360000e-62 250
11 TraesCS3D01G164700 chr1A 83.641 434 56 6 2422 2840 186213063 186213496 1.030000e-105 394
12 TraesCS3D01G164700 chr1A 81.794 379 58 8 2435 2806 387029190 387028816 1.380000e-79 307
13 TraesCS3D01G164700 chr1A 79.198 399 79 4 1541 1937 186212226 186212622 1.400000e-69 274
14 TraesCS3D01G164700 chr1D 82.949 434 59 5 2422 2840 127504596 127505029 1.040000e-100 377
15 TraesCS3D01G164700 chr1D 81.266 379 60 8 2435 2806 307832764 307832390 2.990000e-76 296
16 TraesCS3D01G164700 chr1D 79.699 399 77 4 1541 1937 127503755 127504151 6.470000e-73 285
17 TraesCS3D01G164700 chr1B 82.719 434 60 5 2422 2840 246454723 246455156 4.830000e-99 372
18 TraesCS3D01G164700 chr1B 81.530 379 59 8 2435 2806 416822559 416822185 6.420000e-78 302
19 TraesCS3D01G164700 chr2D 77.023 383 82 6 2448 2827 498228147 498228526 8.610000e-52 215


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 TraesCS3D01G164700 chr3D 136400357 136404310 3953 False 7302.0 7302 100.0000 1 3954 1 chr3D.!!$F1 3953
1 TraesCS3D01G164700 chr3A 154029341 154033548 4207 False 1093.8 3733 92.1432 1 3953 5 chr3A.!!$F1 3952
2 TraesCS3D01G164700 chr3B 194756735 194760675 3940 False 1099.6 2124 92.0940 9 3952 5 chr3B.!!$F1 3943
3 TraesCS3D01G164700 chr1A 186212226 186213496 1270 False 334.0 394 81.4195 1541 2840 2 chr1A.!!$F1 1299
4 TraesCS3D01G164700 chr1D 127503755 127505029 1274 False 331.0 377 81.3240 1541 2840 2 chr1D.!!$F1 1299

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
382 547 1.090728 GTTCTCAGCTAGGCCTTTGC 58.909 55.0 12.58 16.85 0.00 3.68 F
1305 1751 0.460987 CACACTCGCAGATCCCTTCC 60.461 60.0 0.00 0.00 33.89 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1927 0.244994 ACTGTCAGCGCTACCTTGAG 59.755 55.0 10.99 2.94 0.0 3.02 R
3142 3659 0.689055 TCTGCATCTCACAACTGGCT 59.311 50.0 0.00 0.00 0.0 4.75 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
122 127 4.286320 CTCTTCCCCCGGCGATCG 62.286 72.222 11.69 11.69 38.88 3.69
158 289 4.103785 AGCCTGTTCCAATGTGCTAGATAT 59.896 41.667 0.00 0.00 0.00 1.63
163 294 7.548427 CCTGTTCCAATGTGCTAGATATATCAG 59.452 40.741 15.08 10.67 0.00 2.90
166 297 9.929180 GTTCCAATGTGCTAGATATATCAGTAA 57.071 33.333 15.08 0.00 0.00 2.24
230 361 1.522258 GCAAAATGCAAGGTGTGAACG 59.478 47.619 0.00 0.00 44.26 3.95
273 405 5.613142 GCGCTTCAATTTGATTGGTTTTGAG 60.613 40.000 0.00 0.00 40.61 3.02
316 448 3.208594 GGTGCTTGCATACATGATCAGA 58.791 45.455 0.00 0.00 0.00 3.27
367 532 6.292919 GCGTTGTTATGTTCAGAGAAAGTTCT 60.293 38.462 0.00 0.00 41.00 3.01
378 543 2.545810 AGAAAGTTCTCAGCTAGGCCT 58.454 47.619 11.78 11.78 29.94 5.19
379 544 2.909662 AGAAAGTTCTCAGCTAGGCCTT 59.090 45.455 12.58 0.00 29.94 4.35
381 546 2.777832 AGTTCTCAGCTAGGCCTTTG 57.222 50.000 12.58 8.01 0.00 2.77
382 547 1.090728 GTTCTCAGCTAGGCCTTTGC 58.909 55.000 12.58 16.85 0.00 3.68
385 550 2.402564 TCTCAGCTAGGCCTTTGCTAT 58.597 47.619 25.90 8.93 37.74 2.97
392 569 3.563390 GCTAGGCCTTTGCTATTTCAGAG 59.437 47.826 12.58 0.00 37.74 3.35
421 598 9.541724 CGGATCACGGATTTTATAATTGTATTG 57.458 33.333 0.00 0.00 39.42 1.90
608 836 8.523915 AAAATGGCATATGTGATAGTTTGAGA 57.476 30.769 0.00 0.00 0.00 3.27
615 843 7.466455 GCATATGTGATAGTTTGAGAACTGTGG 60.466 40.741 4.29 0.00 45.46 4.17
618 846 5.057149 GTGATAGTTTGAGAACTGTGGTGT 58.943 41.667 2.25 0.00 45.46 4.16
619 847 6.183360 TGTGATAGTTTGAGAACTGTGGTGTA 60.183 38.462 2.25 0.00 45.46 2.90
625 853 7.903145 AGTTTGAGAACTGTGGTGTATATACA 58.097 34.615 11.62 11.62 44.27 2.29
749 1028 8.709646 ACTATTTTAGACATTGTCGACTGAAAC 58.290 33.333 17.92 5.88 37.67 2.78
750 1029 6.912203 TTTTAGACATTGTCGACTGAAACA 57.088 33.333 17.92 0.00 37.67 2.83
752 1031 7.490962 TTTAGACATTGTCGACTGAAACAAT 57.509 32.000 17.92 4.57 44.72 2.71
837 1119 5.232463 AGCAATGGTTATGACAGCAAAAAG 58.768 37.500 0.00 0.00 0.00 2.27
838 1120 4.990426 GCAATGGTTATGACAGCAAAAAGT 59.010 37.500 0.00 0.00 0.00 2.66
840 1122 6.346838 GCAATGGTTATGACAGCAAAAAGTTC 60.347 38.462 0.00 0.00 0.00 3.01
841 1123 6.655078 ATGGTTATGACAGCAAAAAGTTCT 57.345 33.333 0.00 0.00 0.00 3.01
843 1125 6.503524 TGGTTATGACAGCAAAAAGTTCTTC 58.496 36.000 0.00 0.00 0.00 2.87
844 1126 6.096141 TGGTTATGACAGCAAAAAGTTCTTCA 59.904 34.615 0.00 0.00 0.00 3.02
845 1127 6.638468 GGTTATGACAGCAAAAAGTTCTTCAG 59.362 38.462 0.00 0.00 0.00 3.02
846 1128 5.841957 ATGACAGCAAAAAGTTCTTCAGT 57.158 34.783 0.00 0.00 0.00 3.41
883 1165 3.633986 CCTGGGAAGTTGATTAATGCCTC 59.366 47.826 0.00 0.00 0.00 4.70
884 1166 4.530875 CTGGGAAGTTGATTAATGCCTCT 58.469 43.478 0.00 0.00 0.00 3.69
904 1350 6.072618 GCCTCTTATCATGATCATTGTGAAGG 60.073 42.308 12.53 9.91 0.00 3.46
1305 1751 0.460987 CACACTCGCAGATCCCTTCC 60.461 60.000 0.00 0.00 33.89 3.46
1356 1802 1.028905 TTGCTGACAAAGGAAACCCG 58.971 50.000 0.00 0.00 32.57 5.28
1389 1835 1.594833 ACGCCTCGTTAATCCTGCA 59.405 52.632 0.00 0.00 36.35 4.41
1427 1873 1.761784 ACCAACAAAAGCAGCATCCAA 59.238 42.857 0.00 0.00 0.00 3.53
1481 1927 2.872858 GTGATTCCGCTCTAACCATTCC 59.127 50.000 0.00 0.00 0.00 3.01
1653 2099 1.887707 GAAGCGCCTTGGATACGGG 60.888 63.158 2.29 0.00 42.51 5.28
1689 2135 2.227036 CCTTGTGGAGCTCAGGGGT 61.227 63.158 17.19 0.00 34.57 4.95
1960 2406 5.059161 TGGTTCACTTCAGAGTTCAGATTG 58.941 41.667 0.00 0.00 32.54 2.67
1998 2444 5.425630 ACCTTGTTATTGGTACTCGATTCC 58.574 41.667 0.00 0.00 34.36 3.01
2022 2468 0.516877 CGGTGTTTGTGCGATGACAT 59.483 50.000 0.00 0.00 0.00 3.06
2023 2469 1.725611 CGGTGTTTGTGCGATGACATG 60.726 52.381 0.00 0.00 0.00 3.21
2030 2476 7.283633 GTGTTTGTGCGATGACATGTATATAG 58.716 38.462 0.00 0.00 0.00 1.31
2101 2551 0.035630 ATGCCTCTGAGGTGTTGCTC 60.036 55.000 23.92 6.90 37.80 4.26
2107 2557 0.038251 CTGAGGTGTTGCTCGCACTA 60.038 55.000 0.00 0.00 37.07 2.74
2722 3229 2.066393 CCCCCAGAAGAGGATCGCA 61.066 63.158 0.00 0.00 42.67 5.10
2880 3387 4.269523 AGAGCGTGGCCTTGGCAA 62.270 61.111 14.04 0.00 40.46 4.52
3110 3627 2.418628 TCATTTGCTAACGGCTGCTAAC 59.581 45.455 0.00 0.00 42.39 2.34
3125 3642 5.412904 GGCTGCTAACTGAACTATCAAGTTT 59.587 40.000 0.00 0.00 46.09 2.66
3126 3643 6.072452 GGCTGCTAACTGAACTATCAAGTTTT 60.072 38.462 0.00 0.00 46.09 2.43
3127 3644 6.798959 GCTGCTAACTGAACTATCAAGTTTTG 59.201 38.462 0.00 0.00 46.09 2.44
3128 3645 7.520614 GCTGCTAACTGAACTATCAAGTTTTGT 60.521 37.037 0.00 0.00 46.09 2.83
3129 3646 8.896320 TGCTAACTGAACTATCAAGTTTTGTA 57.104 30.769 0.00 0.00 46.09 2.41
3130 3647 8.770828 TGCTAACTGAACTATCAAGTTTTGTAC 58.229 33.333 0.00 0.00 46.09 2.90
3131 3648 8.228464 GCTAACTGAACTATCAAGTTTTGTACC 58.772 37.037 0.00 0.00 46.09 3.34
3132 3649 9.490379 CTAACTGAACTATCAAGTTTTGTACCT 57.510 33.333 0.00 0.00 46.09 3.08
3133 3650 7.964604 ACTGAACTATCAAGTTTTGTACCTC 57.035 36.000 0.00 0.00 46.09 3.85
3134 3651 7.736893 ACTGAACTATCAAGTTTTGTACCTCT 58.263 34.615 0.00 0.00 46.09 3.69
3135 3652 7.657761 ACTGAACTATCAAGTTTTGTACCTCTG 59.342 37.037 0.00 0.00 46.09 3.35
3136 3653 6.426937 TGAACTATCAAGTTTTGTACCTCTGC 59.573 38.462 0.00 0.00 46.09 4.26
3137 3654 6.115448 ACTATCAAGTTTTGTACCTCTGCT 57.885 37.500 0.00 0.00 29.00 4.24
3138 3655 6.166982 ACTATCAAGTTTTGTACCTCTGCTC 58.833 40.000 0.00 0.00 29.00 4.26
3139 3656 3.390135 TCAAGTTTTGTACCTCTGCTCG 58.610 45.455 0.00 0.00 0.00 5.03
3140 3657 3.131396 CAAGTTTTGTACCTCTGCTCGT 58.869 45.455 0.00 0.00 0.00 4.18
3141 3658 4.038282 TCAAGTTTTGTACCTCTGCTCGTA 59.962 41.667 0.00 0.00 0.00 3.43
3142 3659 4.595762 AGTTTTGTACCTCTGCTCGTAA 57.404 40.909 0.00 0.00 0.00 3.18
3143 3660 4.557205 AGTTTTGTACCTCTGCTCGTAAG 58.443 43.478 0.00 0.00 0.00 2.34
3255 3772 2.487934 AGACTGTGCACATGACTGAAC 58.512 47.619 22.00 8.16 0.00 3.18
3256 3773 1.532868 GACTGTGCACATGACTGAACC 59.467 52.381 22.00 0.21 0.00 3.62
3258 3775 1.534163 CTGTGCACATGACTGAACCTG 59.466 52.381 22.00 0.00 0.00 4.00
3260 3777 2.103941 TGTGCACATGACTGAACCTGTA 59.896 45.455 17.42 0.00 0.00 2.74
3261 3778 3.138304 GTGCACATGACTGAACCTGTAA 58.862 45.455 13.17 0.00 0.00 2.41
3262 3779 3.753272 GTGCACATGACTGAACCTGTAAT 59.247 43.478 13.17 0.00 0.00 1.89
3275 3809 8.576442 ACTGAACCTGTAATATCCTTGTTTTTG 58.424 33.333 0.00 0.00 0.00 2.44
3289 3823 9.830975 ATCCTTGTTTTTGTTTTGCTATTTACT 57.169 25.926 0.00 0.00 0.00 2.24
3290 3824 9.660180 TCCTTGTTTTTGTTTTGCTATTTACTT 57.340 25.926 0.00 0.00 0.00 2.24
3304 3838 9.801873 TTGCTATTTACTTTTGATTAATCAGGC 57.198 29.630 17.28 10.44 38.19 4.85
3305 3839 9.189156 TGCTATTTACTTTTGATTAATCAGGCT 57.811 29.630 17.28 5.49 38.19 4.58
3306 3840 9.455847 GCTATTTACTTTTGATTAATCAGGCTG 57.544 33.333 17.28 8.58 38.19 4.85
3310 3844 9.691362 TTTACTTTTGATTAATCAGGCTGAAAC 57.309 29.630 22.84 11.29 38.19 2.78
3311 3845 7.288810 ACTTTTGATTAATCAGGCTGAAACA 57.711 32.000 22.84 13.61 38.19 2.83
3312 3846 7.899973 ACTTTTGATTAATCAGGCTGAAACAT 58.100 30.769 22.84 12.92 38.19 2.71
3313 3847 7.816031 ACTTTTGATTAATCAGGCTGAAACATG 59.184 33.333 22.84 11.65 38.19 3.21
3314 3848 7.465353 TTTGATTAATCAGGCTGAAACATGA 57.535 32.000 22.84 4.81 38.19 3.07
3315 3849 7.465353 TTGATTAATCAGGCTGAAACATGAA 57.535 32.000 22.84 10.62 38.19 2.57
3316 3850 7.465353 TGATTAATCAGGCTGAAACATGAAA 57.535 32.000 22.84 8.36 32.11 2.69
3317 3851 7.315142 TGATTAATCAGGCTGAAACATGAAAC 58.685 34.615 22.84 3.89 32.11 2.78
3318 3852 6.647334 TTAATCAGGCTGAAACATGAAACA 57.353 33.333 22.84 0.00 0.00 2.83
3319 3853 5.733620 AATCAGGCTGAAACATGAAACAT 57.266 34.783 22.84 0.00 0.00 2.71
3320 3854 6.839124 AATCAGGCTGAAACATGAAACATA 57.161 33.333 22.84 0.00 0.00 2.29
3321 3855 6.839124 ATCAGGCTGAAACATGAAACATAA 57.161 33.333 22.84 0.00 0.00 1.90
3322 3856 6.647334 TCAGGCTGAAACATGAAACATAAA 57.353 33.333 16.28 0.00 0.00 1.40
3323 3857 7.048629 TCAGGCTGAAACATGAAACATAAAA 57.951 32.000 16.28 0.00 0.00 1.52
3324 3858 7.669427 TCAGGCTGAAACATGAAACATAAAAT 58.331 30.769 16.28 0.00 0.00 1.82
3325 3859 8.801299 TCAGGCTGAAACATGAAACATAAAATA 58.199 29.630 16.28 0.00 0.00 1.40
3326 3860 9.421806 CAGGCTGAAACATGAAACATAAAATAA 57.578 29.630 9.42 0.00 0.00 1.40
3327 3861 9.995003 AGGCTGAAACATGAAACATAAAATAAA 57.005 25.926 0.00 0.00 0.00 1.40
3340 3874 8.447787 AACATAAAATAAACATCGAGTTGTGC 57.552 30.769 0.00 0.00 41.19 4.57
3358 3892 0.242017 GCTGGTCATCAAAGTGGCAC 59.758 55.000 10.29 10.29 0.00 5.01
3359 3893 1.608055 CTGGTCATCAAAGTGGCACA 58.392 50.000 21.41 0.00 0.00 4.57
3360 3894 2.165167 CTGGTCATCAAAGTGGCACAT 58.835 47.619 21.41 4.57 44.52 3.21
3361 3895 1.887854 TGGTCATCAAAGTGGCACATG 59.112 47.619 21.41 17.71 44.52 3.21
3380 3915 5.798434 CACATGCATGTTCTATTCACACTTG 59.202 40.000 29.48 9.49 39.39 3.16
3404 3939 1.238439 GGCAACTGAAGCTAAGTGCA 58.762 50.000 17.50 0.00 45.94 4.57
3408 3944 1.517242 ACTGAAGCTAAGTGCAGCAC 58.483 50.000 18.55 18.55 44.35 4.40
3484 4020 2.426522 TCATCTTCCAGAAACGGCAAG 58.573 47.619 0.00 0.00 0.00 4.01
3486 4022 1.593196 TCTTCCAGAAACGGCAAGTG 58.407 50.000 0.00 0.00 0.00 3.16
3491 4027 1.197721 CCAGAAACGGCAAGTGCTAAG 59.802 52.381 2.85 0.00 41.70 2.18
3511 4047 6.292381 GCTAAGCTACAACCAATTCATCTACG 60.292 42.308 0.00 0.00 0.00 3.51
3532 4068 2.900546 GGTCATACCATCACCCCTAGAG 59.099 54.545 0.00 0.00 38.42 2.43
3535 4071 5.145564 GTCATACCATCACCCCTAGAGTTA 58.854 45.833 0.00 0.00 0.00 2.24
3547 4083 5.845065 ACCCCTAGAGTTATTCCATACCTTC 59.155 44.000 0.00 0.00 0.00 3.46
3583 4119 5.894393 TGATTTACACACCCTTTTTCTTCCA 59.106 36.000 0.00 0.00 0.00 3.53
3586 4122 2.430694 ACACACCCTTTTTCTTCCAAGC 59.569 45.455 0.00 0.00 0.00 4.01
3681 4223 0.388649 CGTGTCTCCCTTCAGTTCCG 60.389 60.000 0.00 0.00 0.00 4.30
3770 4312 1.904287 AACCGGCAAAGCACTTATCA 58.096 45.000 0.00 0.00 0.00 2.15
3903 4445 0.109597 GGTCTCAAAATGCTGCACCG 60.110 55.000 3.57 0.00 0.00 4.94
3953 4495 2.288334 TGGCATGAAGAACAATGCACAC 60.288 45.455 9.59 0.00 41.44 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 129 1.538876 AACAGGCTAGCAGGGGTGA 60.539 57.895 18.24 0.00 0.00 4.02
158 289 7.718272 CGGTTTAATCCGGAATTTACTGATA 57.282 36.000 9.01 0.00 45.88 2.15
193 324 5.991328 TTTTGCAACGCATTGGAATTAAA 57.009 30.435 0.00 0.00 44.52 1.52
194 325 5.616424 GCATTTTGCAACGCATTGGAATTAA 60.616 36.000 0.00 0.00 44.52 1.40
229 360 1.069022 CCAAACCAAGCAGACATGTCG 60.069 52.381 19.85 15.27 34.09 4.35
230 361 1.336240 GCCAAACCAAGCAGACATGTC 60.336 52.381 18.47 18.47 0.00 3.06
273 405 3.541516 CGAACAATCGCGAAGGAACATAC 60.542 47.826 15.24 0.00 42.96 2.39
316 448 1.800586 CAAACTAGCATGTGAGCGTGT 59.199 47.619 0.00 0.00 40.15 4.49
367 532 3.054434 TGAAATAGCAAAGGCCTAGCTGA 60.054 43.478 32.08 20.38 42.56 4.26
378 543 5.351465 GTGATCCGTTCTCTGAAATAGCAAA 59.649 40.000 0.00 0.00 0.00 3.68
379 544 4.870426 GTGATCCGTTCTCTGAAATAGCAA 59.130 41.667 0.00 0.00 0.00 3.91
381 546 3.487574 CGTGATCCGTTCTCTGAAATAGC 59.512 47.826 0.00 0.00 0.00 2.97
382 547 4.045104 CCGTGATCCGTTCTCTGAAATAG 58.955 47.826 0.00 0.00 33.66 1.73
385 550 1.890489 TCCGTGATCCGTTCTCTGAAA 59.110 47.619 0.00 0.00 33.66 2.69
392 569 7.636326 ACAATTATAAAATCCGTGATCCGTTC 58.364 34.615 0.00 0.00 33.66 3.95
415 592 6.233905 ACAGGCATACAGATGTACAATACA 57.766 37.500 0.00 0.00 43.80 2.29
421 598 2.100916 ACGGACAGGCATACAGATGTAC 59.899 50.000 0.00 0.00 35.30 2.90
427 604 0.246360 TGTCACGGACAGGCATACAG 59.754 55.000 3.02 0.00 37.67 2.74
496 724 4.754372 ACATGCACATACAGACAAGTTG 57.246 40.909 0.00 0.00 0.00 3.16
497 725 5.049198 CAGAACATGCACATACAGACAAGTT 60.049 40.000 0.00 0.00 0.00 2.66
526 754 9.027129 CCATGAATATGCAAGAAGTGTAATTTG 57.973 33.333 0.00 0.00 32.79 2.32
724 1003 8.708742 TGTTTCAGTCGACAATGTCTAAAATAG 58.291 33.333 19.50 0.00 0.00 1.73
725 1004 8.596271 TGTTTCAGTCGACAATGTCTAAAATA 57.404 30.769 19.50 0.96 0.00 1.40
727 1006 6.912203 TGTTTCAGTCGACAATGTCTAAAA 57.088 33.333 19.50 2.21 0.00 1.52
783 1063 8.506196 TGTATTCCTGGTTATATAGCCTTCTT 57.494 34.615 15.76 1.80 0.00 2.52
795 1075 7.502226 CCATTGCTAATTCTGTATTCCTGGTTA 59.498 37.037 0.00 0.00 0.00 2.85
796 1076 6.322201 CCATTGCTAATTCTGTATTCCTGGTT 59.678 38.462 0.00 0.00 0.00 3.67
797 1077 5.829924 CCATTGCTAATTCTGTATTCCTGGT 59.170 40.000 0.00 0.00 0.00 4.00
883 1165 7.563888 ACACCTTCACAATGATCATGATAAG 57.436 36.000 9.46 10.42 0.00 1.73
884 1166 7.394077 ACAACACCTTCACAATGATCATGATAA 59.606 33.333 9.46 0.46 0.00 1.75
904 1350 9.592720 GCATTATAATTCCAAACAAAACAACAC 57.407 29.630 0.00 0.00 0.00 3.32
1134 1580 1.753141 GCTGTGGATGGATTGGCAGAT 60.753 52.381 0.00 0.00 0.00 2.90
1305 1751 2.373540 TGGGACGTGGTTTCTTATCG 57.626 50.000 0.00 0.00 0.00 2.92
1356 1802 1.336755 AGGCGTTTTGTCATGTGGTTC 59.663 47.619 0.00 0.00 0.00 3.62
1427 1873 6.237901 TCTTGTGTATTACTGTTCATGCCTT 58.762 36.000 0.00 0.00 0.00 4.35
1481 1927 0.244994 ACTGTCAGCGCTACCTTGAG 59.755 55.000 10.99 2.94 0.00 3.02
1653 2099 2.514803 AGGTAAACACTGCCAATGTCC 58.485 47.619 0.00 0.00 30.62 4.02
1689 2135 3.081741 CGCGAAGAACGTGTCTGTA 57.918 52.632 0.00 0.00 45.77 2.74
1998 2444 1.837538 ATCGCACAAACACCGAACCG 61.838 55.000 0.00 0.00 34.42 4.44
2030 2476 7.204496 AGAGAATTATGATGAGCAATTGAGC 57.796 36.000 10.34 0.00 0.00 4.26
2107 2557 5.802060 TGCCTAGCATGTGGAGGTACTCT 62.802 52.174 10.26 0.00 44.85 3.24
2608 3100 1.669115 CTCCACCACGTTGCTCAGG 60.669 63.158 0.00 0.00 0.00 3.86
2722 3229 4.660938 GTGGCGCCCCTCTTGGTT 62.661 66.667 26.77 0.00 0.00 3.67
3110 3627 7.360438 GCAGAGGTACAAAACTTGATAGTTCAG 60.360 40.741 0.00 0.00 43.74 3.02
3136 3653 2.724977 TCTCACAACTGGCTTACGAG 57.275 50.000 0.00 0.00 0.00 4.18
3137 3654 2.930887 GCATCTCACAACTGGCTTACGA 60.931 50.000 0.00 0.00 0.00 3.43
3138 3655 1.394917 GCATCTCACAACTGGCTTACG 59.605 52.381 0.00 0.00 0.00 3.18
3139 3656 2.417933 CTGCATCTCACAACTGGCTTAC 59.582 50.000 0.00 0.00 0.00 2.34
3140 3657 2.302733 TCTGCATCTCACAACTGGCTTA 59.697 45.455 0.00 0.00 0.00 3.09
3141 3658 1.072806 TCTGCATCTCACAACTGGCTT 59.927 47.619 0.00 0.00 0.00 4.35
3142 3659 0.689055 TCTGCATCTCACAACTGGCT 59.311 50.000 0.00 0.00 0.00 4.75
3143 3660 0.801251 GTCTGCATCTCACAACTGGC 59.199 55.000 0.00 0.00 0.00 4.85
3144 3661 2.174363 TGTCTGCATCTCACAACTGG 57.826 50.000 0.00 0.00 0.00 4.00
3145 3662 4.001652 AGAATGTCTGCATCTCACAACTG 58.998 43.478 0.00 0.00 33.50 3.16
3146 3663 4.283363 AGAATGTCTGCATCTCACAACT 57.717 40.909 0.00 0.00 33.50 3.16
3147 3664 5.368256 AAAGAATGTCTGCATCTCACAAC 57.632 39.130 0.00 0.00 33.50 3.32
3186 3703 5.999044 AGCAGACATGTTTCCATCTAATCT 58.001 37.500 0.00 0.00 0.00 2.40
3187 3704 6.690194 AAGCAGACATGTTTCCATCTAATC 57.310 37.500 0.00 0.00 0.00 1.75
3188 3705 8.579850 TTTAAGCAGACATGTTTCCATCTAAT 57.420 30.769 0.00 0.00 31.67 1.73
3189 3706 7.994425 TTTAAGCAGACATGTTTCCATCTAA 57.006 32.000 0.00 0.00 31.67 2.10
3190 3707 8.049117 AGATTTAAGCAGACATGTTTCCATCTA 58.951 33.333 0.00 0.00 31.88 1.98
3191 3708 6.888632 AGATTTAAGCAGACATGTTTCCATCT 59.111 34.615 0.00 0.00 31.67 2.90
3192 3709 7.093322 AGATTTAAGCAGACATGTTTCCATC 57.907 36.000 0.00 0.00 31.67 3.51
3193 3710 7.472334 AAGATTTAAGCAGACATGTTTCCAT 57.528 32.000 0.00 0.00 31.67 3.41
3194 3711 6.899393 AAGATTTAAGCAGACATGTTTCCA 57.101 33.333 0.00 0.00 31.67 3.53
3223 3740 1.069364 GCACAGTCTTCAGCTTTCAGC 60.069 52.381 0.00 0.00 42.84 4.26
3238 3755 1.534163 CAGGTTCAGTCATGTGCACAG 59.466 52.381 25.84 16.57 0.00 3.66
3255 3772 8.495148 GCAAAACAAAAACAAGGATATTACAGG 58.505 33.333 0.00 0.00 0.00 4.00
3256 3773 9.260002 AGCAAAACAAAAACAAGGATATTACAG 57.740 29.630 0.00 0.00 0.00 2.74
3284 3818 9.691362 GTTTCAGCCTGATTAATCAAAAGTAAA 57.309 29.630 18.47 13.02 36.18 2.01
3285 3819 8.855110 TGTTTCAGCCTGATTAATCAAAAGTAA 58.145 29.630 18.47 8.41 36.18 2.24
3286 3820 8.402798 TGTTTCAGCCTGATTAATCAAAAGTA 57.597 30.769 18.47 6.13 36.18 2.24
3287 3821 7.288810 TGTTTCAGCCTGATTAATCAAAAGT 57.711 32.000 18.47 2.11 36.18 2.66
3288 3822 8.030692 TCATGTTTCAGCCTGATTAATCAAAAG 58.969 33.333 18.47 11.43 36.18 2.27
3289 3823 7.894708 TCATGTTTCAGCCTGATTAATCAAAA 58.105 30.769 18.47 12.57 36.18 2.44
3290 3824 7.465353 TCATGTTTCAGCCTGATTAATCAAA 57.535 32.000 18.47 7.41 36.18 2.69
3291 3825 7.465353 TTCATGTTTCAGCCTGATTAATCAA 57.535 32.000 18.47 1.28 36.18 2.57
3292 3826 7.039853 TGTTTCATGTTTCAGCCTGATTAATCA 60.040 33.333 17.07 17.07 35.16 2.57
3293 3827 7.315142 TGTTTCATGTTTCAGCCTGATTAATC 58.685 34.615 8.60 8.60 0.00 1.75
3294 3828 7.230849 TGTTTCATGTTTCAGCCTGATTAAT 57.769 32.000 0.00 0.00 0.00 1.40
3295 3829 6.647334 TGTTTCATGTTTCAGCCTGATTAA 57.353 33.333 0.00 0.00 0.00 1.40
3296 3830 6.839124 ATGTTTCATGTTTCAGCCTGATTA 57.161 33.333 0.00 0.00 0.00 1.75
3297 3831 5.733620 ATGTTTCATGTTTCAGCCTGATT 57.266 34.783 0.00 0.00 0.00 2.57
3298 3832 6.839124 TTATGTTTCATGTTTCAGCCTGAT 57.161 33.333 0.00 0.00 0.00 2.90
3299 3833 6.647334 TTTATGTTTCATGTTTCAGCCTGA 57.353 33.333 0.00 0.00 0.00 3.86
3300 3834 7.894376 ATTTTATGTTTCATGTTTCAGCCTG 57.106 32.000 0.00 0.00 0.00 4.85
3301 3835 9.995003 TTTATTTTATGTTTCATGTTTCAGCCT 57.005 25.926 0.00 0.00 0.00 4.58
3314 3848 8.911662 GCACAACTCGATGTTTATTTTATGTTT 58.088 29.630 0.00 0.00 36.63 2.83
3315 3849 8.296713 AGCACAACTCGATGTTTATTTTATGTT 58.703 29.630 0.00 0.00 36.63 2.71
3316 3850 7.750458 CAGCACAACTCGATGTTTATTTTATGT 59.250 33.333 0.00 0.00 36.63 2.29
3317 3851 7.218773 CCAGCACAACTCGATGTTTATTTTATG 59.781 37.037 0.00 0.00 36.63 1.90
3318 3852 7.094377 ACCAGCACAACTCGATGTTTATTTTAT 60.094 33.333 0.00 0.00 36.63 1.40
3319 3853 6.205853 ACCAGCACAACTCGATGTTTATTTTA 59.794 34.615 0.00 0.00 36.63 1.52
3320 3854 5.009610 ACCAGCACAACTCGATGTTTATTTT 59.990 36.000 0.00 0.00 36.63 1.82
3321 3855 4.518970 ACCAGCACAACTCGATGTTTATTT 59.481 37.500 0.00 0.00 36.63 1.40
3322 3856 4.072131 ACCAGCACAACTCGATGTTTATT 58.928 39.130 0.00 0.00 36.63 1.40
3323 3857 3.674997 ACCAGCACAACTCGATGTTTAT 58.325 40.909 0.00 0.00 36.63 1.40
3324 3858 3.064207 GACCAGCACAACTCGATGTTTA 58.936 45.455 0.00 0.00 36.63 2.01
3325 3859 1.873591 GACCAGCACAACTCGATGTTT 59.126 47.619 0.00 0.00 36.63 2.83
3326 3860 1.202639 TGACCAGCACAACTCGATGTT 60.203 47.619 0.00 0.00 39.92 2.71
3327 3861 0.392706 TGACCAGCACAACTCGATGT 59.607 50.000 0.00 0.00 0.00 3.06
3328 3862 1.662629 GATGACCAGCACAACTCGATG 59.337 52.381 0.00 0.00 0.00 3.84
3329 3863 1.276138 TGATGACCAGCACAACTCGAT 59.724 47.619 0.00 0.00 0.00 3.59
3330 3864 0.678950 TGATGACCAGCACAACTCGA 59.321 50.000 0.00 0.00 0.00 4.04
3331 3865 1.511850 TTGATGACCAGCACAACTCG 58.488 50.000 0.00 0.00 0.00 4.18
3332 3866 2.880890 ACTTTGATGACCAGCACAACTC 59.119 45.455 0.00 0.00 0.00 3.01
3333 3867 2.620115 CACTTTGATGACCAGCACAACT 59.380 45.455 0.00 0.00 0.00 3.16
3334 3868 2.287788 CCACTTTGATGACCAGCACAAC 60.288 50.000 0.00 0.00 0.00 3.32
3335 3869 1.955778 CCACTTTGATGACCAGCACAA 59.044 47.619 0.00 0.00 0.00 3.33
3336 3870 1.608055 CCACTTTGATGACCAGCACA 58.392 50.000 0.00 0.00 0.00 4.57
3337 3871 0.242017 GCCACTTTGATGACCAGCAC 59.758 55.000 0.00 0.00 0.00 4.40
3338 3872 0.178995 TGCCACTTTGATGACCAGCA 60.179 50.000 0.00 0.00 0.00 4.41
3339 3873 0.242017 GTGCCACTTTGATGACCAGC 59.758 55.000 0.00 0.00 0.00 4.85
3340 3874 1.608055 TGTGCCACTTTGATGACCAG 58.392 50.000 0.00 0.00 0.00 4.00
3358 3892 4.796830 GCAAGTGTGAATAGAACATGCATG 59.203 41.667 25.09 25.09 34.92 4.06
3359 3893 4.460034 TGCAAGTGTGAATAGAACATGCAT 59.540 37.500 0.00 0.00 38.16 3.96
3360 3894 3.819902 TGCAAGTGTGAATAGAACATGCA 59.180 39.130 1.27 1.27 39.80 3.96
3361 3895 4.154737 TCTGCAAGTGTGAATAGAACATGC 59.845 41.667 0.00 0.00 35.22 4.06
3380 3915 1.736681 CTTAGCTTCAGTTGCCTCTGC 59.263 52.381 0.00 0.00 35.63 4.26
3389 3924 1.517242 GTGCTGCACTTAGCTTCAGT 58.483 50.000 24.68 0.00 45.94 3.41
3390 3925 0.441533 CGTGCTGCACTTAGCTTCAG 59.558 55.000 28.04 7.58 45.94 3.02
3391 3926 1.568612 GCGTGCTGCACTTAGCTTCA 61.569 55.000 28.04 0.00 45.94 3.02
3392 3927 1.133458 GCGTGCTGCACTTAGCTTC 59.867 57.895 28.04 1.94 45.94 3.86
3402 3937 4.047059 ATGCTTGGTGCGTGCTGC 62.047 61.111 0.00 0.00 46.63 5.25
3408 3944 3.119673 TGGTTTTATACATGCTTGGTGCG 60.120 43.478 4.44 0.00 46.63 5.34
3438 3974 2.294233 TCGCCACGTTATATGTCTACCC 59.706 50.000 0.00 0.00 0.00 3.69
3484 4020 5.355350 AGATGAATTGGTTGTAGCTTAGCAC 59.645 40.000 7.07 3.45 0.00 4.40
3486 4022 6.292381 CGTAGATGAATTGGTTGTAGCTTAGC 60.292 42.308 0.00 0.00 0.00 3.09
3491 4027 4.189231 ACCGTAGATGAATTGGTTGTAGC 58.811 43.478 0.00 0.00 0.00 3.58
3511 4047 2.900546 CTCTAGGGGTGATGGTATGACC 59.099 54.545 0.00 0.00 39.22 4.02
3532 4068 3.875134 CCACACGGAAGGTATGGAATAAC 59.125 47.826 0.00 0.00 36.52 1.89
3535 4071 2.193127 TCCACACGGAAGGTATGGAAT 58.807 47.619 0.00 0.00 38.83 3.01
3547 4083 4.078363 GTGTAAATCACAATCCACACGG 57.922 45.455 0.00 0.00 45.51 4.94
3656 4198 3.959991 GAAGGGAGACACGCCAGCC 62.960 68.421 0.00 0.00 0.00 4.85
3903 4445 4.079253 TCATTCTTACAAGCCTTTCACCC 58.921 43.478 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.