Multiple sequence alignment - TraesCS5A01G387300

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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 TraesCS5A01G387300 chr5A 100.000 2631 0 0 1 2631 584517880 584520510 0.000000e+00 4859
1 TraesCS5A01G387300 chr5A 88.764 89 10 0 2543 2631 43568439 43568351 2.770000e-20 110
2 TraesCS5A01G387300 chr5A 88.172 93 10 1 2539 2631 584592379 584592470 2.770000e-20 110
3 TraesCS5A01G387300 chr5D 92.072 1728 83 25 1 1681 464091119 464092839 0.000000e+00 2383
4 TraesCS5A01G387300 chr5D 85.581 860 91 17 1674 2522 464093525 464094362 0.000000e+00 870
5 TraesCS5A01G387300 chr5D 93.548 93 6 0 2539 2631 464094440 464094532 3.530000e-29 139
6 TraesCS5A01G387300 chr5D 90.323 93 9 0 2539 2631 464124590 464124682 3.560000e-24 122
7 TraesCS5A01G387300 chr5B 90.598 1755 84 31 1 1684 571186816 571188560 0.000000e+00 2252
8 TraesCS5A01G387300 chr5B 90.123 243 24 0 1812 2054 571189480 571189722 1.520000e-82 316
9 TraesCS5A01G387300 chr5B 92.537 134 9 1 1674 1806 571189185 571189318 9.610000e-45 191
10 TraesCS5A01G387300 chr5B 92.135 89 7 0 2539 2627 571211920 571212008 2.750000e-25 126
11 TraesCS5A01G387300 chr5B 90.323 93 9 0 2539 2631 57709144 57709052 3.560000e-24 122


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 TraesCS5A01G387300 chr5A 584517880 584520510 2630 False 4859.000000 4859 100.000000 1 2631 1 chr5A.!!$F1 2630
1 TraesCS5A01G387300 chr5D 464091119 464094532 3413 False 1130.666667 2383 90.400333 1 2631 3 chr5D.!!$F2 2630
2 TraesCS5A01G387300 chr5B 571186816 571189722 2906 False 919.666667 2252 91.086000 1 2054 3 chr5B.!!$F2 2053

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
990 1092 0.035881 CTTTCCTCTGCTCCTGCACA 59.964 55.0 0.0 0.0 45.31 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 3262 0.040958 CAGCCAACTCTGCGTTCAAC 60.041 55.0 0.0 0.0 32.27 3.18 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
513 531 5.268118 TGGAGTAGAAGACGACGTAGATA 57.732 43.478 0.00 0.00 0.00 1.98
615 678 4.209866 GCAGGGGCCGGGATGAAT 62.210 66.667 2.18 0.00 0.00 2.57
779 853 1.700029 CGATCGGGACAAACGAACG 59.300 57.895 7.38 3.39 46.64 3.95
878 960 0.685458 AATGCAAGCCCAGTGGATCC 60.685 55.000 11.95 4.20 0.00 3.36
882 964 0.393537 CAAGCCCAGTGGATCCTGTC 60.394 60.000 11.95 3.74 0.00 3.51
905 987 1.683441 CCGGTTTTAGTCTGGGCCT 59.317 57.895 4.53 0.00 0.00 5.19
906 988 0.037734 CCGGTTTTAGTCTGGGCCTT 59.962 55.000 4.53 0.00 0.00 4.35
990 1092 0.035881 CTTTCCTCTGCTCCTGCACA 59.964 55.000 0.00 0.00 45.31 4.57
1073 1175 4.104417 GCGAGCTGACGAGACGGT 62.104 66.667 0.00 0.00 35.09 4.83
1076 1178 3.268965 GAGCTGACGAGACGGTGCA 62.269 63.158 0.00 0.00 0.00 4.57
1150 1260 6.206243 GCACAAGCATCCAATTATATCTGTCT 59.794 38.462 0.00 0.00 41.58 3.41
1153 1263 7.994911 ACAAGCATCCAATTATATCTGTCTGAA 59.005 33.333 0.00 0.00 0.00 3.02
1174 1286 6.499172 TGAATACTGTAGAATTCTCTGAGCG 58.501 40.000 12.24 0.00 34.00 5.03
1183 1295 5.923204 AGAATTCTCTGAGCGATTATTGGT 58.077 37.500 0.88 0.00 0.00 3.67
1516 1637 4.814294 GGCGCCTCCGTGTACCTG 62.814 72.222 22.15 0.00 36.67 4.00
1586 1707 1.749638 ACCTACCTGCTCGAGACCG 60.750 63.158 18.75 3.94 37.07 4.79
1637 1758 2.036992 CCTCAGTCCATGTAGCAGGATC 59.963 54.545 0.00 0.00 36.11 3.36
1645 1766 3.006217 CCATGTAGCAGGATCTTCGATCA 59.994 47.826 6.23 0.00 0.00 2.92
1647 1768 4.736126 TGTAGCAGGATCTTCGATCAAA 57.264 40.909 6.23 0.00 0.00 2.69
1648 1769 5.084818 TGTAGCAGGATCTTCGATCAAAA 57.915 39.130 6.23 0.00 0.00 2.44
1649 1770 5.487433 TGTAGCAGGATCTTCGATCAAAAA 58.513 37.500 6.23 0.00 0.00 1.94
1710 2605 8.616076 CAGAAGTTAATGATTCTTAATCCGCTT 58.384 33.333 0.00 0.00 37.09 4.68
1739 2634 1.164041 CGTTTTGGCGTCTTCACCCT 61.164 55.000 0.00 0.00 0.00 4.34
1778 2674 1.537202 GCAACTCTACCCAAGCACAAG 59.463 52.381 0.00 0.00 0.00 3.16
1793 2689 6.350361 CCAAGCACAAGAATGAACCAATGATA 60.350 38.462 0.00 0.00 0.00 2.15
1806 2702 6.945435 TGAACCAATGATAAGCTTTCCAAGTA 59.055 34.615 3.20 0.00 0.00 2.24
1808 2704 7.961326 ACCAATGATAAGCTTTCCAAGTAAT 57.039 32.000 3.20 0.00 0.00 1.89
1809 2705 7.775120 ACCAATGATAAGCTTTCCAAGTAATG 58.225 34.615 3.20 0.43 0.00 1.90
1848 2900 6.119536 AGTTCAATGGTAGAACACACAAGAA 58.880 36.000 8.54 0.00 45.93 2.52
1850 2902 7.285401 AGTTCAATGGTAGAACACACAAGAAAT 59.715 33.333 8.54 0.00 45.93 2.17
1879 2931 5.089970 TGACAGGGAAATAGACATCACAG 57.910 43.478 0.00 0.00 0.00 3.66
1885 2937 5.958380 AGGGAAATAGACATCACAGTACAGA 59.042 40.000 0.00 0.00 0.00 3.41
1916 2968 5.178809 TGAAAATCATCAGCTGAGCATATCG 59.821 40.000 22.96 4.46 37.28 2.92
1918 2970 4.532314 ATCATCAGCTGAGCATATCGAA 57.468 40.909 22.96 0.00 37.28 3.71
1967 3019 6.627395 TCAACACCTATTTTGTTCATCGTT 57.373 33.333 0.00 0.00 34.91 3.85
1990 3042 9.313323 CGTTACATGTTACAATTCAACTGTTAG 57.687 33.333 14.76 0.00 0.00 2.34
2034 3086 3.728076 ATGCTATAGTACACACCACCG 57.272 47.619 0.84 0.00 0.00 4.94
2039 3091 0.757512 TAGTACACACCACCGCCAAA 59.242 50.000 0.00 0.00 0.00 3.28
2061 3113 4.871933 AAAAGCAGGTGAAAACCTATGG 57.128 40.909 0.00 0.00 38.22 2.74
2069 3121 2.945668 GTGAAAACCTATGGCCTAGCAG 59.054 50.000 3.32 0.00 0.00 4.24
2071 3123 3.265737 TGAAAACCTATGGCCTAGCAGAA 59.734 43.478 3.32 0.00 0.00 3.02
2072 3124 3.283259 AAACCTATGGCCTAGCAGAAC 57.717 47.619 3.32 0.00 0.00 3.01
2073 3125 2.182516 ACCTATGGCCTAGCAGAACT 57.817 50.000 3.32 0.00 0.00 3.01
2074 3126 2.043227 ACCTATGGCCTAGCAGAACTC 58.957 52.381 3.32 0.00 0.00 3.01
2075 3127 2.042464 CCTATGGCCTAGCAGAACTCA 58.958 52.381 3.32 0.00 0.00 3.41
2076 3128 2.636893 CCTATGGCCTAGCAGAACTCAT 59.363 50.000 3.32 0.00 0.00 2.90
2077 3129 3.072184 CCTATGGCCTAGCAGAACTCATT 59.928 47.826 3.32 0.00 0.00 2.57
2078 3130 3.659183 ATGGCCTAGCAGAACTCATTT 57.341 42.857 3.32 0.00 0.00 2.32
2086 3138 1.888512 GCAGAACTCATTTGCCCTCAA 59.111 47.619 0.00 0.00 31.79 3.02
2093 3145 4.948847 ACTCATTTGCCCTCAAGAAAAAC 58.051 39.130 0.00 0.00 33.12 2.43
2097 3149 5.759273 TCATTTGCCCTCAAGAAAAACAATG 59.241 36.000 0.00 0.00 33.12 2.82
2099 3151 2.224257 TGCCCTCAAGAAAAACAATGCC 60.224 45.455 0.00 0.00 0.00 4.40
2101 3153 3.656559 CCCTCAAGAAAAACAATGCCTG 58.343 45.455 0.00 0.00 0.00 4.85
2102 3154 3.062042 CCTCAAGAAAAACAATGCCTGC 58.938 45.455 0.00 0.00 0.00 4.85
2109 3161 4.039488 AGAAAAACAATGCCTGCATCTTCA 59.961 37.500 4.89 0.00 35.31 3.02
2117 3169 1.531423 CCTGCATCTTCAGTGTTGCT 58.469 50.000 0.00 0.00 36.10 3.91
2128 3180 2.338577 AGTGTTGCTGATATCCAGGC 57.661 50.000 0.00 3.11 43.13 4.85
2130 3182 1.945394 GTGTTGCTGATATCCAGGCAG 59.055 52.381 12.52 0.00 43.13 4.85
2139 3191 3.887110 TGATATCCAGGCAGCTGAAAATG 59.113 43.478 20.43 9.31 0.00 2.32
2146 3198 1.603678 GGCAGCTGAAAATGTGGTGTG 60.604 52.381 20.43 0.00 0.00 3.82
2173 3225 2.225019 CGCATCAGATAAATGTCCAGGC 59.775 50.000 0.00 0.00 0.00 4.85
2191 3243 1.539065 GGCCTGGTGTATGATGACGAG 60.539 57.143 0.00 0.00 0.00 4.18
2193 3245 1.136891 CCTGGTGTATGATGACGAGCA 59.863 52.381 0.00 0.00 0.00 4.26
2210 3262 6.479990 TGACGAGCAAATGATTGGTATTCTAG 59.520 38.462 0.00 0.00 46.70 2.43
2211 3263 6.349300 ACGAGCAAATGATTGGTATTCTAGT 58.651 36.000 0.00 0.00 46.70 2.57
2216 3268 8.462016 AGCAAATGATTGGTATTCTAGTTGAAC 58.538 33.333 0.00 0.00 45.01 3.18
2261 3313 9.655769 CAGAAATGAACGATTCCACAATAATAG 57.344 33.333 0.00 0.00 0.00 1.73
2268 3320 7.931578 ACGATTCCACAATAATAGTTGGAAA 57.068 32.000 6.03 0.00 38.67 3.13
2277 3329 7.593273 CACAATAATAGTTGGAAAACGCTGAAA 59.407 33.333 0.00 0.00 33.40 2.69
2326 3378 4.821589 GCACGAGGGCCTCCTTCG 62.822 72.222 27.36 18.88 45.05 3.79
2327 3379 3.068691 CACGAGGGCCTCCTTCGA 61.069 66.667 27.36 0.00 45.05 3.71
2330 3382 1.265454 ACGAGGGCCTCCTTCGATTT 61.265 55.000 27.36 0.00 45.05 2.17
2355 3407 7.328737 TGTAGGATTTCTAAAACTGAGTAGGC 58.671 38.462 0.00 0.00 0.00 3.93
2356 3408 6.628644 AGGATTTCTAAAACTGAGTAGGCT 57.371 37.500 0.00 0.00 0.00 4.58
2367 3419 6.803154 AACTGAGTAGGCTAAACACATTTC 57.197 37.500 0.00 0.00 0.00 2.17
2396 3448 6.403866 TGGCAAACAAATCAGTGATAACTT 57.596 33.333 5.94 0.00 0.00 2.66
2399 3451 7.768120 TGGCAAACAAATCAGTGATAACTTTTT 59.232 29.630 5.94 0.00 0.00 1.94
2434 3486 9.770097 ATTGTGATAATGACTTCCACATACTAG 57.230 33.333 0.00 0.00 37.55 2.57
2445 3501 4.298626 TCCACATACTAGAAAGCTCCCAT 58.701 43.478 0.00 0.00 0.00 4.00
2456 3512 5.574188 AGAAAGCTCCCATCAGTTAACAAT 58.426 37.500 8.61 0.00 0.00 2.71
2461 3517 4.035208 GCTCCCATCAGTTAACAATAACCG 59.965 45.833 8.61 0.00 41.98 4.44
2468 3524 8.388103 CCATCAGTTAACAATAACCGTAAAGAG 58.612 37.037 8.61 0.00 41.98 2.85
2472 3528 6.592994 AGTTAACAATAACCGTAAAGAGAGCC 59.407 38.462 8.61 0.00 41.98 4.70
2481 3537 4.202284 ACCGTAAAGAGAGCCTGTTAAACA 60.202 41.667 0.00 0.00 0.00 2.83
2497 3553 2.292103 AACAAAGCAAAGCTCGCAAA 57.708 40.000 10.42 0.00 38.25 3.68
2507 3563 2.191128 AGCTCGCAAAGGAAGACAAT 57.809 45.000 0.00 0.00 0.00 2.71
2508 3564 2.508526 AGCTCGCAAAGGAAGACAATT 58.491 42.857 0.00 0.00 0.00 2.32
2535 3591 9.745880 TTTTACTCTTATTTCTAGCAGATACGG 57.254 33.333 0.00 0.00 0.00 4.02
2536 3592 8.687292 TTACTCTTATTTCTAGCAGATACGGA 57.313 34.615 0.00 0.00 0.00 4.69
2538 3594 6.773685 ACTCTTATTTCTAGCAGATACGGACT 59.226 38.462 0.00 0.00 0.00 3.85
2539 3595 7.285858 ACTCTTATTTCTAGCAGATACGGACTT 59.714 37.037 0.00 0.00 0.00 3.01
2540 3596 7.426410 TCTTATTTCTAGCAGATACGGACTTG 58.574 38.462 0.00 0.00 0.00 3.16
2541 3597 5.854010 ATTTCTAGCAGATACGGACTTGA 57.146 39.130 0.00 0.00 0.00 3.02
2551 3668 4.880120 AGATACGGACTTGAACGAGATACA 59.120 41.667 0.00 0.00 0.00 2.29
2553 3670 2.163815 ACGGACTTGAACGAGATACAGG 59.836 50.000 0.00 0.00 0.00 4.00
2561 3678 3.258372 TGAACGAGATACAGGCTTGAACT 59.742 43.478 1.40 0.00 0.00 3.01
2577 3694 1.160329 AACTTCACCGTGCTCTGTGC 61.160 55.000 5.56 0.00 43.25 4.57
2587 3704 2.046023 CTCTGTGCGGATTGCCCA 60.046 61.111 0.00 0.00 45.60 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
480 498 1.399714 TCTACTCCATGTACGGGCAG 58.600 55.000 0.00 0.00 0.00 4.85
482 500 2.029623 TCTTCTACTCCATGTACGGGC 58.970 52.381 0.00 0.00 0.00 6.13
483 501 2.033049 CGTCTTCTACTCCATGTACGGG 59.967 54.545 0.00 0.00 0.00 5.28
486 504 3.373439 ACGTCGTCTTCTACTCCATGTAC 59.627 47.826 0.00 0.00 0.00 2.90
600 663 2.696125 ACATTCATCCCGGCCCCT 60.696 61.111 0.00 0.00 0.00 4.79
724 797 1.106944 TGTCGTGTCAGAGTGAGCCA 61.107 55.000 0.00 0.00 0.00 4.75
767 841 3.343421 AGCGGCGTTCGTTTGTCC 61.343 61.111 9.37 0.00 41.72 4.02
769 843 4.307908 GCAGCGGCGTTCGTTTGT 62.308 61.111 9.37 0.00 41.72 2.83
830 909 3.899981 CTGCTGCAAGGGCCGTACA 62.900 63.158 3.02 0.00 40.13 2.90
841 920 2.079088 TTTGGATCCCACCTGCTGCA 62.079 55.000 9.90 0.88 30.78 4.41
878 960 0.036306 ACTAAAACCGGGCCTGACAG 59.964 55.000 15.09 4.77 0.00 3.51
882 964 0.676782 CCAGACTAAAACCGGGCCTG 60.677 60.000 6.32 3.88 0.00 4.85
925 1007 4.819769 TCACGTGGGTAGGTTGTTTATAC 58.180 43.478 17.00 0.00 0.00 1.47
1150 1260 6.318900 TCGCTCAGAGAATTCTACAGTATTCA 59.681 38.462 8.25 0.00 35.23 2.57
1153 1263 6.892658 ATCGCTCAGAGAATTCTACAGTAT 57.107 37.500 8.25 1.12 30.73 2.12
1174 1286 4.943705 TCCAAGAACTGCAGACCAATAATC 59.056 41.667 23.35 5.23 0.00 1.75
1183 1295 1.070758 GTCACCTCCAAGAACTGCAGA 59.929 52.381 23.35 0.00 0.00 4.26
1333 1445 3.959991 GAAGCACACGGGCTCCTCC 62.960 68.421 0.00 0.00 45.07 4.30
1429 1541 4.241999 GGTGGCGCGTGATGATGC 62.242 66.667 8.43 0.00 0.00 3.91
1586 1707 1.364171 CGAGGATCATGTCGGGGAC 59.636 63.158 0.00 0.00 33.17 4.46
1647 1768 6.745794 TCCCTTCCAAAGATGACAAATTTT 57.254 33.333 0.00 0.00 0.00 1.82
1648 1769 6.745794 TTCCCTTCCAAAGATGACAAATTT 57.254 33.333 0.00 0.00 0.00 1.82
1649 1770 6.940430 ATTCCCTTCCAAAGATGACAAATT 57.060 33.333 0.00 0.00 0.00 1.82
1650 1771 6.350445 CGAATTCCCTTCCAAAGATGACAAAT 60.350 38.462 0.00 0.00 0.00 2.32
1710 2605 1.357334 GCCAAAACGGACTTCGCAA 59.643 52.632 0.00 0.00 43.89 4.85
1739 2634 8.043113 AGAGTTGCTGTTGACATTTATCTGATA 58.957 33.333 0.00 0.00 0.00 2.15
1778 2674 6.866480 TGGAAAGCTTATCATTGGTTCATTC 58.134 36.000 0.00 0.00 0.00 2.67
1823 2875 6.119536 TCTTGTGTGTTCTACCATTGAACTT 58.880 36.000 7.89 0.00 42.86 2.66
1848 2900 2.380064 TTTCCCTGTCAGGCACAATT 57.620 45.000 13.99 0.00 33.31 2.32
1850 2902 2.642311 TCTATTTCCCTGTCAGGCACAA 59.358 45.455 13.99 5.78 33.31 3.33
1879 2931 4.678509 TGATTTTCATGCCGTTCTGTAC 57.321 40.909 0.00 0.00 0.00 2.90
1885 2937 2.756760 AGCTGATGATTTTCATGCCGTT 59.243 40.909 0.00 0.00 37.20 4.44
1916 2968 4.336532 TTCGCGGAAGAAAATAGCTTTC 57.663 40.909 6.13 0.00 43.36 2.62
1918 2970 4.759516 TTTTCGCGGAAGAAAATAGCTT 57.240 36.364 6.13 0.00 42.91 3.74
1967 3019 9.332502 ACACTAACAGTTGAATTGTAACATGTA 57.667 29.630 0.00 0.00 0.00 2.29
1978 3030 8.073768 CACGGAAATAAACACTAACAGTTGAAT 58.926 33.333 0.00 0.00 0.00 2.57
1990 3042 2.550606 TGCCTCACACGGAAATAAACAC 59.449 45.455 0.00 0.00 0.00 3.32
2055 3107 2.042464 TGAGTTCTGCTAGGCCATAGG 58.958 52.381 5.01 0.00 31.55 2.57
2061 3113 1.403323 GGCAAATGAGTTCTGCTAGGC 59.597 52.381 0.00 0.00 36.32 3.93
2069 3121 4.853924 TTTCTTGAGGGCAAATGAGTTC 57.146 40.909 0.00 0.00 32.73 3.01
2071 3123 4.405358 TGTTTTTCTTGAGGGCAAATGAGT 59.595 37.500 0.00 0.00 32.73 3.41
2072 3124 4.947645 TGTTTTTCTTGAGGGCAAATGAG 58.052 39.130 0.00 0.00 32.73 2.90
2073 3125 5.350504 TTGTTTTTCTTGAGGGCAAATGA 57.649 34.783 0.00 0.00 32.73 2.57
2074 3126 5.561339 GCATTGTTTTTCTTGAGGGCAAATG 60.561 40.000 0.00 0.00 32.73 2.32
2075 3127 4.516321 GCATTGTTTTTCTTGAGGGCAAAT 59.484 37.500 0.00 0.00 32.73 2.32
2076 3128 3.876320 GCATTGTTTTTCTTGAGGGCAAA 59.124 39.130 0.00 0.00 32.73 3.68
2077 3129 3.465871 GCATTGTTTTTCTTGAGGGCAA 58.534 40.909 0.00 0.00 0.00 4.52
2078 3130 2.224257 GGCATTGTTTTTCTTGAGGGCA 60.224 45.455 0.00 0.00 0.00 5.36
2086 3138 4.039488 TGAAGATGCAGGCATTGTTTTTCT 59.961 37.500 8.34 0.00 36.70 2.52
2093 3145 1.816835 ACACTGAAGATGCAGGCATTG 59.183 47.619 8.34 4.20 40.20 2.82
2097 3149 0.109412 GCAACACTGAAGATGCAGGC 60.109 55.000 0.00 0.00 40.20 4.85
2109 3161 1.561076 TGCCTGGATATCAGCAACACT 59.439 47.619 10.78 0.00 42.05 3.55
2117 3169 3.650281 TTTTCAGCTGCCTGGATATCA 57.350 42.857 9.47 0.00 39.61 2.15
2122 3174 1.250328 CACATTTTCAGCTGCCTGGA 58.750 50.000 9.47 0.00 39.61 3.86
2123 3175 0.245539 CCACATTTTCAGCTGCCTGG 59.754 55.000 9.47 2.99 39.61 4.45
2127 3179 1.067516 ACACACCACATTTTCAGCTGC 59.932 47.619 9.47 0.00 0.00 5.25
2128 3180 3.441496 AACACACCACATTTTCAGCTG 57.559 42.857 7.63 7.63 0.00 4.24
2130 3182 4.048504 GGTTAACACACCACATTTTCAGC 58.951 43.478 8.10 0.00 36.73 4.26
2131 3183 4.286910 CGGTTAACACACCACATTTTCAG 58.713 43.478 8.10 0.00 36.49 3.02
2132 3184 3.489398 GCGGTTAACACACCACATTTTCA 60.489 43.478 8.10 0.00 36.49 2.69
2133 3185 3.047093 GCGGTTAACACACCACATTTTC 58.953 45.455 8.10 0.00 36.49 2.29
2139 3191 1.196808 CTGATGCGGTTAACACACCAC 59.803 52.381 8.10 2.25 36.49 4.16
2146 3198 5.295787 TGGACATTTATCTGATGCGGTTAAC 59.704 40.000 0.00 0.00 0.00 2.01
2173 3225 1.136891 TGCTCGTCATCATACACCAGG 59.863 52.381 0.00 0.00 0.00 4.45
2177 3229 5.663795 ATCATTTGCTCGTCATCATACAC 57.336 39.130 0.00 0.00 0.00 2.90
2179 3231 5.008019 ACCAATCATTTGCTCGTCATCATAC 59.992 40.000 0.00 0.00 0.00 2.39
2191 3243 7.429340 CGTTCAACTAGAATACCAATCATTTGC 59.571 37.037 0.00 0.00 38.76 3.68
2193 3245 7.120579 TGCGTTCAACTAGAATACCAATCATTT 59.879 33.333 0.00 0.00 38.76 2.32
2210 3262 0.040958 CAGCCAACTCTGCGTTCAAC 60.041 55.000 0.00 0.00 32.27 3.18
2211 3263 0.463654 ACAGCCAACTCTGCGTTCAA 60.464 50.000 0.00 0.00 37.59 2.69
2216 3268 0.514691 GAAGAACAGCCAACTCTGCG 59.485 55.000 0.00 0.00 37.59 5.18
2261 3313 5.315118 CTGAATTTTCAGCGTTTTCCAAC 57.685 39.130 7.34 0.00 46.97 3.77
2284 3336 6.333416 GCTTCATTCTCTATGTGTACTGACA 58.667 40.000 0.00 0.00 35.64 3.58
2286 3338 5.582550 CGCTTCATTCTCTATGTGTACTGA 58.417 41.667 0.00 0.00 35.64 3.41
2289 3341 4.026475 GTGCGCTTCATTCTCTATGTGTAC 60.026 45.833 9.73 0.00 35.64 2.90
2330 3382 7.180408 AGCCTACTCAGTTTTAGAAATCCTACA 59.820 37.037 0.00 0.00 0.00 2.74
2410 3462 8.533569 TCTAGTATGTGGAAGTCATTATCACA 57.466 34.615 0.00 0.00 41.64 3.58
2411 3463 9.817809 TTTCTAGTATGTGGAAGTCATTATCAC 57.182 33.333 0.00 0.00 0.00 3.06
2424 3476 4.101585 TGATGGGAGCTTTCTAGTATGTGG 59.898 45.833 0.00 0.00 0.00 4.17
2431 3483 5.734720 TGTTAACTGATGGGAGCTTTCTAG 58.265 41.667 7.22 0.00 0.00 2.43
2434 3486 5.904362 ATTGTTAACTGATGGGAGCTTTC 57.096 39.130 7.22 0.00 0.00 2.62
2445 3501 7.330208 GCTCTCTTTACGGTTATTGTTAACTGA 59.670 37.037 7.22 0.00 44.29 3.41
2456 3512 5.726980 TTAACAGGCTCTCTTTACGGTTA 57.273 39.130 0.00 0.00 0.00 2.85
2461 3517 6.143496 GCTTTGTTTAACAGGCTCTCTTTAC 58.857 40.000 14.36 0.00 0.00 2.01
2468 3524 3.490896 GCTTTGCTTTGTTTAACAGGCTC 59.509 43.478 19.40 4.90 32.63 4.70
2472 3528 3.180387 GCGAGCTTTGCTTTGTTTAACAG 59.820 43.478 0.00 0.00 39.88 3.16
2481 3537 1.032014 TCCTTTGCGAGCTTTGCTTT 58.968 45.000 12.38 0.00 39.88 3.51
2522 3578 3.064958 CGTTCAAGTCCGTATCTGCTAGA 59.935 47.826 0.00 0.00 0.00 2.43
2524 3580 3.011818 TCGTTCAAGTCCGTATCTGCTA 58.988 45.455 0.00 0.00 0.00 3.49
2527 3583 3.759527 TCTCGTTCAAGTCCGTATCTG 57.240 47.619 0.00 0.00 0.00 2.90
2530 3586 4.036498 CCTGTATCTCGTTCAAGTCCGTAT 59.964 45.833 0.00 0.00 0.00 3.06
2531 3587 3.376234 CCTGTATCTCGTTCAAGTCCGTA 59.624 47.826 0.00 0.00 0.00 4.02
2532 3588 2.163815 CCTGTATCTCGTTCAAGTCCGT 59.836 50.000 0.00 0.00 0.00 4.69
2533 3589 2.798680 CCTGTATCTCGTTCAAGTCCG 58.201 52.381 0.00 0.00 0.00 4.79
2534 3590 2.166664 AGCCTGTATCTCGTTCAAGTCC 59.833 50.000 0.00 0.00 0.00 3.85
2535 3591 3.512033 AGCCTGTATCTCGTTCAAGTC 57.488 47.619 0.00 0.00 0.00 3.01
2536 3592 3.258372 TCAAGCCTGTATCTCGTTCAAGT 59.742 43.478 0.00 0.00 0.00 3.16
2538 3594 3.953712 TCAAGCCTGTATCTCGTTCAA 57.046 42.857 0.00 0.00 0.00 2.69
2539 3595 3.258372 AGTTCAAGCCTGTATCTCGTTCA 59.742 43.478 0.00 0.00 0.00 3.18
2540 3596 3.851098 AGTTCAAGCCTGTATCTCGTTC 58.149 45.455 0.00 0.00 0.00 3.95
2541 3597 3.963428 AGTTCAAGCCTGTATCTCGTT 57.037 42.857 0.00 0.00 0.00 3.85
2551 3668 1.166531 GCACGGTGAAGTTCAAGCCT 61.167 55.000 13.29 0.00 0.00 4.58
2553 3670 0.235926 GAGCACGGTGAAGTTCAAGC 59.764 55.000 13.29 9.59 0.00 4.01
2561 3678 2.661537 CGCACAGAGCACGGTGAA 60.662 61.111 17.61 0.00 46.13 3.18
2577 3694 0.662970 CAACGTGTTTGGGCAATCCG 60.663 55.000 0.00 0.00 38.76 4.18
2587 3704 0.753479 TGACATGGCCCAACGTGTTT 60.753 50.000 0.00 0.00 40.49 2.83


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

AutoCloner maintained by Alex Coulton.