Multiple sequence alignment - TraesCS5A01G154400

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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 TraesCS5A01G154400 chr5A 100.000 2973 0 0 1 2973 331887639 331884667 0 5491
1 TraesCS5A01G154400 chr1A 95.934 2976 86 19 1 2973 155143715 155140772 0 4793


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 TraesCS5A01G154400 chr5A 331884667 331887639 2972 True 5491 5491 100.000 1 2973 1 chr5A.!!$R1 2972
1 TraesCS5A01G154400 chr1A 155140772 155143715 2943 True 4793 4793 95.934 1 2973 1 chr1A.!!$R1 2972

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
475 476 0.249868 GGCCCCACTTTTTGCTTGAC 60.25 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2150 0.243907 AACCGACATCGTCAGACCTG 59.756 55.0 0.0 0.0 37.74 4.0 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
19 20 1.073199 CCAAGGTTCGAGCCAAGGT 59.927 57.895 21.22 0.00 0.00 3.50
78 79 2.491621 CGAGATCGTCAGGCAGCA 59.508 61.111 0.00 0.00 34.11 4.41
122 123 3.444805 GAGGCCGCGACTGTCTCT 61.445 66.667 8.23 0.00 0.00 3.10
124 125 2.507324 GGCCGCGACTGTCTCTTC 60.507 66.667 8.23 0.00 0.00 2.87
191 192 0.532573 ACGGGTGTGATGAGCTACTG 59.467 55.000 0.00 0.00 0.00 2.74
200 201 2.275318 GATGAGCTACTGTCAAGCACC 58.725 52.381 5.45 0.00 42.62 5.01
286 287 1.005748 TTGCGAGTCACTGAGCCTG 60.006 57.895 0.00 0.00 0.00 4.85
358 359 8.717821 GTCAGTGTATGCTTCAAGTTTATGTTA 58.282 33.333 0.00 0.00 0.00 2.41
422 423 2.654749 TGGACACGCTAATCAGTCTG 57.345 50.000 0.00 0.00 0.00 3.51
430 431 0.531532 CTAATCAGTCTGGCCAGCGG 60.532 60.000 28.91 21.81 0.00 5.52
475 476 0.249868 GGCCCCACTTTTTGCTTGAC 60.250 55.000 0.00 0.00 0.00 3.18
570 571 1.805428 GCACACAACCACCATCACCC 61.805 60.000 0.00 0.00 0.00 4.61
572 573 0.260230 ACACAACCACCATCACCCAA 59.740 50.000 0.00 0.00 0.00 4.12
589 590 2.222953 CCCAACAGTAAATAGAACGCGC 60.223 50.000 5.73 0.00 0.00 6.86
593 594 0.921347 AGTAAATAGAACGCGCGCTG 59.079 50.000 32.58 23.88 0.00 5.18
641 642 2.042831 CCCCTGCTTTTCTGCCTCG 61.043 63.158 0.00 0.00 0.00 4.63
699 701 1.226323 CAGCGCTGAAGCTTGCATC 60.226 57.895 33.66 0.00 46.80 3.91
776 778 1.063183 AAGCAAGAAGAGGAGGCAGT 58.937 50.000 0.00 0.00 0.00 4.40
777 779 0.324285 AGCAAGAAGAGGAGGCAGTG 59.676 55.000 0.00 0.00 0.00 3.66
815 817 1.490910 AGGAGGCAGGTATGTAAAGGC 59.509 52.381 0.00 0.00 0.00 4.35
844 846 2.421775 ACTCTCTGTATCACACTCGCAG 59.578 50.000 0.00 0.00 0.00 5.18
854 856 1.583404 CACACTCGCAGTTGCAAAAAC 59.417 47.619 0.00 0.00 42.21 2.43
864 866 6.148645 TCGCAGTTGCAAAAACTATTCATCTA 59.851 34.615 0.00 0.00 42.21 1.98
903 905 5.756950 TTGAAATGCTCGAGTTTAGTACG 57.243 39.130 15.13 0.00 0.00 3.67
948 950 9.699410 TTTGATTTACCAGATCCATCTTGTATT 57.301 29.630 2.26 0.00 35.69 1.89
966 968 8.721478 TCTTGTATTTTCTGTTCAATCTGTAGC 58.279 33.333 0.00 0.00 0.00 3.58
986 988 2.528743 CGCACCTCATCACATCGGC 61.529 63.158 0.00 0.00 0.00 5.54
990 992 1.323271 ACCTCATCACATCGGCGTCT 61.323 55.000 6.85 0.00 0.00 4.18
992 994 1.203928 CTCATCACATCGGCGTCTTC 58.796 55.000 6.85 0.00 0.00 2.87
1104 1106 5.233050 CGCAGTTACATCTAGGATTTCAGTG 59.767 44.000 0.00 0.00 0.00 3.66
1112 1114 3.758554 TCTAGGATTTCAGTGCAAAAGCC 59.241 43.478 8.30 8.30 41.42 4.35
1172 1174 5.649831 GGAAGTTGATAGCAGAGATTGGTTT 59.350 40.000 0.00 0.00 38.70 3.27
1327 1329 4.125703 TGATGTCAACAATGTTTTTGGGC 58.874 39.130 0.00 0.00 0.00 5.36
1333 1335 3.473923 ACAATGTTTTTGGGCTTCCAG 57.526 42.857 0.00 0.00 42.30 3.86
1354 1356 5.104109 CCAGTAGGTGGGAAAAGGATATCAA 60.104 44.000 4.83 0.00 43.63 2.57
1425 1427 2.027653 AGAAGAGCTTAGTGACAAGGGC 60.028 50.000 0.00 0.00 0.00 5.19
1433 1435 2.949177 AGTGACAAGGGCACACATAA 57.051 45.000 4.85 0.00 38.70 1.90
1437 1439 1.812571 GACAAGGGCACACATAACCTG 59.187 52.381 0.00 0.00 32.66 4.00
1445 1447 2.669391 GCACACATAACCTGAAAGCTGC 60.669 50.000 0.00 0.00 0.00 5.25
1456 1458 1.020437 GAAAGCTGCAGAGGCCATAC 58.980 55.000 20.43 0.00 40.13 2.39
1458 1460 1.500474 AAGCTGCAGAGGCCATACTA 58.500 50.000 20.43 0.00 40.13 1.82
1488 1490 0.395862 TCCAGGAAGACTCGCCTAGG 60.396 60.000 3.67 3.67 32.03 3.02
1489 1491 1.395826 CCAGGAAGACTCGCCTAGGG 61.396 65.000 11.72 0.44 32.03 3.53
1506 1508 2.119495 AGGGTCGCCATAGAGATGTTT 58.881 47.619 0.00 0.00 0.00 2.83
1521 1523 4.881920 AGATGTTTAAAATTGCCGCTGTT 58.118 34.783 0.00 0.00 0.00 3.16
1533 1535 9.958234 AAAATTGCCGCTGTTATTTTTATTTTT 57.042 22.222 0.00 0.00 28.64 1.94
1614 1616 5.822519 TGCACTGAACACAACTTTAGAGATT 59.177 36.000 0.00 0.00 0.00 2.40
1848 1851 7.604164 GTCCATGTTGATAAGAGAAGTTCTGAA 59.396 37.037 10.90 0.00 35.91 3.02
1907 1910 0.482446 AATTTGGACCTGGGTCAGCA 59.518 50.000 19.70 8.10 46.20 4.41
1996 1999 1.206072 GCGCTCAGTTGCAGTCAAG 59.794 57.895 0.00 0.00 31.93 3.02
2033 2036 2.196742 TCAATCTCCAGGGTATGCCT 57.803 50.000 0.00 0.00 34.45 4.75
2081 2084 0.177141 TTTCCAAGACGATAGGGCCG 59.823 55.000 0.00 0.00 43.77 6.13
2140 2143 5.818336 TCGATGACCACTTTTCTTAACAACA 59.182 36.000 0.00 0.00 0.00 3.33
2141 2144 6.018262 TCGATGACCACTTTTCTTAACAACAG 60.018 38.462 0.00 0.00 0.00 3.16
2142 2145 5.828299 TGACCACTTTTCTTAACAACAGG 57.172 39.130 0.00 0.00 0.00 4.00
2143 2146 4.097286 TGACCACTTTTCTTAACAACAGGC 59.903 41.667 0.00 0.00 0.00 4.85
2144 2147 4.278310 ACCACTTTTCTTAACAACAGGCT 58.722 39.130 0.00 0.00 0.00 4.58
2145 2148 4.709886 ACCACTTTTCTTAACAACAGGCTT 59.290 37.500 0.00 0.00 0.00 4.35
2146 2149 5.186992 ACCACTTTTCTTAACAACAGGCTTT 59.813 36.000 0.00 0.00 0.00 3.51
2147 2150 5.748630 CCACTTTTCTTAACAACAGGCTTTC 59.251 40.000 0.00 0.00 0.00 2.62
2148 2151 6.329496 CACTTTTCTTAACAACAGGCTTTCA 58.671 36.000 0.00 0.00 0.00 2.69
2149 2152 6.473455 CACTTTTCTTAACAACAGGCTTTCAG 59.527 38.462 0.00 0.00 0.00 3.02
2150 2153 5.514274 TTTCTTAACAACAGGCTTTCAGG 57.486 39.130 0.00 0.00 0.00 3.86
2151 2154 4.164843 TCTTAACAACAGGCTTTCAGGT 57.835 40.909 0.00 0.00 0.00 4.00
2152 2155 4.134563 TCTTAACAACAGGCTTTCAGGTC 58.865 43.478 0.00 0.00 0.00 3.85
2153 2156 2.736670 AACAACAGGCTTTCAGGTCT 57.263 45.000 0.00 0.00 0.00 3.85
2154 2157 1.972872 ACAACAGGCTTTCAGGTCTG 58.027 50.000 0.00 0.00 43.72 3.51
2155 2158 1.490490 ACAACAGGCTTTCAGGTCTGA 59.510 47.619 3.06 0.00 40.98 3.27
2156 2159 1.876156 CAACAGGCTTTCAGGTCTGAC 59.124 52.381 0.00 0.00 40.98 3.51
2157 2160 0.034059 ACAGGCTTTCAGGTCTGACG 59.966 55.000 1.07 0.00 40.98 4.35
2158 2161 0.318441 CAGGCTTTCAGGTCTGACGA 59.682 55.000 1.07 0.00 40.98 4.20
2159 2162 1.066573 CAGGCTTTCAGGTCTGACGAT 60.067 52.381 1.07 0.00 40.98 3.73
2160 2163 1.066573 AGGCTTTCAGGTCTGACGATG 60.067 52.381 1.07 3.67 39.66 3.84
2161 2164 1.338200 GGCTTTCAGGTCTGACGATGT 60.338 52.381 1.07 0.00 39.66 3.06
2162 2165 1.996191 GCTTTCAGGTCTGACGATGTC 59.004 52.381 1.07 0.00 39.66 3.06
2173 2176 2.418976 CTGACGATGTCGGTTACTCTCA 59.581 50.000 7.38 0.00 44.95 3.27
2190 2193 5.670485 ACTCTCACATTTACATAATGCGGA 58.330 37.500 0.00 0.00 0.00 5.54
2245 2248 1.072173 CCACATGTTCAGGACACCAGA 59.928 52.381 0.00 0.00 42.04 3.86
2277 2280 1.463056 CAAGGTACAATTCAAGCGCGA 59.537 47.619 12.10 0.00 0.00 5.87
2291 2294 1.852067 GCGCGACACCCAACTCAAAT 61.852 55.000 12.10 0.00 0.00 2.32
2296 2299 1.737793 GACACCCAACTCAAATAGGCG 59.262 52.381 0.00 0.00 0.00 5.52
2478 2482 0.836606 TTCTGCAGTTCTCACACCCA 59.163 50.000 14.67 0.00 0.00 4.51
2508 2512 6.690194 ATTTATCTGAGAGAACACAATGCC 57.310 37.500 0.00 0.00 0.00 4.40
2555 2559 2.432456 GCAGGCATCACACGACGA 60.432 61.111 0.00 0.00 0.00 4.20
2602 2606 4.706842 ATGATTAGTTTAGCCGATGGGT 57.293 40.909 0.00 0.00 37.19 4.51
2672 2676 3.065786 CGAGACATTGCAATTGCTGGTAT 59.934 43.478 29.37 20.71 42.66 2.73
2673 2677 4.439153 CGAGACATTGCAATTGCTGGTATT 60.439 41.667 29.37 15.75 42.66 1.89
2674 2678 4.751060 AGACATTGCAATTGCTGGTATTG 58.249 39.130 29.37 17.42 42.66 1.90
2675 2679 4.463539 AGACATTGCAATTGCTGGTATTGA 59.536 37.500 29.37 5.34 42.66 2.57
2676 2680 4.497300 ACATTGCAATTGCTGGTATTGAC 58.503 39.130 29.37 0.00 42.66 3.18
2685 2689 1.838077 GCTGGTATTGACCCCTGTACT 59.162 52.381 0.00 0.00 46.32 2.73
2693 2697 2.318908 TGACCCCTGTACTGTTACGTT 58.681 47.619 0.00 0.00 0.00 3.99
2709 2713 7.274033 ACTGTTACGTTGTTTTTAGCCTTTTTC 59.726 33.333 0.00 0.00 0.00 2.29
2745 2749 6.238703 CCGTGTTAACCAGTTAGCCTTTTTAA 60.239 38.462 2.48 0.00 0.00 1.52
2824 2828 6.643388 TGATCATATAGGTGCATCACATACC 58.357 40.000 0.00 0.00 33.54 2.73
2828 2832 2.190398 AGGTGCATCACATACCCCTA 57.810 50.000 0.00 0.00 35.86 3.53
2901 2905 2.577700 TGCGGATGGTAAGTGTTTTGT 58.422 42.857 0.00 0.00 0.00 2.83
2902 2906 2.952978 TGCGGATGGTAAGTGTTTTGTT 59.047 40.909 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.986970 CGTAGCATGTCCAGCCATA 57.013 52.632 0.00 0.00 0.00 2.74
78 79 0.882042 CTGTGCTTGTTCAGTCCGCT 60.882 55.000 0.00 0.00 0.00 5.52
88 89 4.290622 CCCCTGGCCTGTGCTTGT 62.291 66.667 3.32 0.00 37.74 3.16
118 119 2.169978 CACCATGAGGCAGATGAAGAGA 59.830 50.000 0.00 0.00 39.06 3.10
122 123 2.506644 TGATCACCATGAGGCAGATGAA 59.493 45.455 0.00 0.00 39.06 2.57
124 125 2.617308 GTTGATCACCATGAGGCAGATG 59.383 50.000 0.00 0.00 39.06 2.90
191 192 1.207329 AGAACGGATAGGGTGCTTGAC 59.793 52.381 0.00 0.00 0.00 3.18
200 201 5.936686 TGTCTACGATTAGAACGGATAGG 57.063 43.478 0.00 0.00 36.03 2.57
286 287 5.180271 TGACCCATTAACGACCTAATCAAC 58.820 41.667 0.00 0.00 0.00 3.18
390 391 1.224075 GTGTCCATCCGATGATGCAG 58.776 55.000 10.12 0.00 45.86 4.41
422 423 0.316841 TCAACATTTTTCCGCTGGCC 59.683 50.000 0.00 0.00 0.00 5.36
430 431 8.539770 TCTCTCTGACTATGTCAACATTTTTC 57.460 34.615 0.20 0.00 42.26 2.29
475 476 4.626042 GTCCAGCAAGTAGATATCACCAG 58.374 47.826 5.32 0.00 0.00 4.00
570 571 2.678705 CGCGCGTTCTATTTACTGTTG 58.321 47.619 24.19 0.00 0.00 3.33
572 573 0.643820 GCGCGCGTTCTATTTACTGT 59.356 50.000 32.35 0.00 0.00 3.55
589 590 1.646189 GCTCCCTTCTAGTTTCAGCG 58.354 55.000 0.00 0.00 0.00 5.18
593 594 2.007547 GCACCGCTCCCTTCTAGTTTC 61.008 57.143 0.00 0.00 0.00 2.78
699 701 3.736483 GCTGGTGCCATGGATACG 58.264 61.111 18.40 3.21 42.51 3.06
744 746 3.238108 TCTTGCTTGAATCCTCGACTC 57.762 47.619 0.00 0.00 0.00 3.36
776 778 3.072915 TCCTGTTCTTGCTTGAATCCTCA 59.927 43.478 0.00 0.00 0.00 3.86
777 779 3.679389 TCCTGTTCTTGCTTGAATCCTC 58.321 45.455 0.00 0.00 0.00 3.71
815 817 6.169094 AGTGTGATACAGAGAGTTGGATTTG 58.831 40.000 0.00 0.00 0.00 2.32
844 846 9.443283 CTGCTATAGATGAATAGTTTTTGCAAC 57.557 33.333 3.21 0.00 32.89 4.17
854 856 7.782168 TGGATCCCTACTGCTATAGATGAATAG 59.218 40.741 9.90 0.00 33.37 1.73
864 866 5.912149 TTTCAATGGATCCCTACTGCTAT 57.088 39.130 9.90 0.00 0.00 2.97
948 950 2.411748 CGCGCTACAGATTGAACAGAAA 59.588 45.455 5.56 0.00 0.00 2.52
966 968 2.863853 CGATGTGATGAGGTGCGCG 61.864 63.158 0.00 0.00 0.00 6.86
990 992 2.749839 CTTTCCATGCCGGCCGAA 60.750 61.111 30.73 19.62 33.14 4.30
1082 1084 6.108687 TGCACTGAAATCCTAGATGTAACTG 58.891 40.000 0.00 0.00 0.00 3.16
1104 1106 1.994916 ATATGTTGCACGGCTTTTGC 58.005 45.000 0.00 0.00 46.64 3.68
1112 1114 2.632377 ACTGGGAGAATATGTTGCACG 58.368 47.619 0.00 0.00 0.00 5.34
1172 1174 3.731136 GTGACAGCACGCCTTCAA 58.269 55.556 0.00 0.00 34.94 2.69
1327 1329 2.642807 TCCTTTTCCCACCTACTGGAAG 59.357 50.000 0.00 0.00 43.95 3.46
1333 1335 5.751586 TGTTGATATCCTTTTCCCACCTAC 58.248 41.667 0.00 0.00 0.00 3.18
1425 1427 2.553602 TGCAGCTTTCAGGTTATGTGTG 59.446 45.455 0.00 0.00 0.00 3.82
1433 1435 1.303155 GCCTCTGCAGCTTTCAGGT 60.303 57.895 17.20 0.00 37.47 4.00
1437 1439 1.020437 GTATGGCCTCTGCAGCTTTC 58.980 55.000 9.47 0.00 40.13 2.62
1445 1447 5.674525 TGTCTTTCAATAGTATGGCCTCTG 58.325 41.667 3.32 0.00 0.00 3.35
1456 1458 6.648192 AGTCTTCCTGGATGTCTTTCAATAG 58.352 40.000 9.18 0.00 0.00 1.73
1458 1460 5.495640 GAGTCTTCCTGGATGTCTTTCAAT 58.504 41.667 9.91 0.00 0.00 2.57
1488 1490 6.619801 ATTTTAAACATCTCTATGGCGACC 57.380 37.500 0.00 0.00 37.43 4.79
1489 1491 6.414987 GCAATTTTAAACATCTCTATGGCGAC 59.585 38.462 0.00 0.00 37.43 5.19
1533 1535 2.378038 GAAGGACATAGCAAATGCCCA 58.622 47.619 0.94 0.00 43.38 5.36
1614 1616 8.420222 ACAAATTCACACCAATCAAATTGACTA 58.580 29.630 0.00 0.00 42.83 2.59
1693 1695 4.268644 CACAAGATGTATAGTTGAGTGCCG 59.731 45.833 0.00 0.00 0.00 5.69
1781 1784 7.383687 ACAGAATGCATGTCATTTTCAGAATT 58.616 30.769 0.00 0.00 44.95 2.17
1782 1785 6.931838 ACAGAATGCATGTCATTTTCAGAAT 58.068 32.000 0.00 0.00 44.95 2.40
1789 1792 3.752747 TCACGACAGAATGCATGTCATTT 59.247 39.130 16.84 0.00 45.96 2.32
1794 1797 4.991056 GGTATATCACGACAGAATGCATGT 59.009 41.667 0.00 0.00 42.53 3.21
1848 1851 6.608808 CCTGATGAGGGGTGATAAGAAAAATT 59.391 38.462 0.00 0.00 35.40 1.82
1907 1910 0.889306 CGAAGGGTCTCGAGGAGTTT 59.111 55.000 13.56 2.78 41.44 2.66
2063 2066 1.820581 CGGCCCTATCGTCTTGGAA 59.179 57.895 0.00 0.00 0.00 3.53
2071 2074 1.592669 CAACTGAGCGGCCCTATCG 60.593 63.158 0.00 0.00 0.00 2.92
2079 2082 1.597663 ACTCGAAAAACAACTGAGCGG 59.402 47.619 0.00 0.00 0.00 5.52
2081 2084 3.944422 TGACTCGAAAAACAACTGAGC 57.056 42.857 0.00 0.00 0.00 4.26
2140 2143 1.066573 CATCGTCAGACCTGAAAGCCT 60.067 52.381 0.70 0.00 41.85 4.58
2141 2144 1.338200 ACATCGTCAGACCTGAAAGCC 60.338 52.381 0.70 0.00 41.85 4.35
2142 2145 1.996191 GACATCGTCAGACCTGAAAGC 59.004 52.381 0.70 0.00 41.85 3.51
2143 2146 2.254459 CGACATCGTCAGACCTGAAAG 58.746 52.381 0.70 0.00 41.85 2.62
2144 2147 1.067846 CCGACATCGTCAGACCTGAAA 60.068 52.381 0.70 0.00 41.85 2.69
2145 2148 0.526211 CCGACATCGTCAGACCTGAA 59.474 55.000 0.70 0.00 41.85 3.02
2146 2149 0.608308 ACCGACATCGTCAGACCTGA 60.608 55.000 0.00 0.00 37.74 3.86
2147 2150 0.243907 AACCGACATCGTCAGACCTG 59.756 55.000 0.00 0.00 37.74 4.00
2148 2151 1.471684 GTAACCGACATCGTCAGACCT 59.528 52.381 0.00 0.00 37.74 3.85
2149 2152 1.471684 AGTAACCGACATCGTCAGACC 59.528 52.381 0.00 0.00 37.74 3.85
2150 2153 2.419324 AGAGTAACCGACATCGTCAGAC 59.581 50.000 0.00 0.00 37.74 3.51
2151 2154 2.676839 GAGAGTAACCGACATCGTCAGA 59.323 50.000 0.00 0.00 37.74 3.27
2152 2155 2.418976 TGAGAGTAACCGACATCGTCAG 59.581 50.000 0.00 0.00 37.74 3.51
2153 2156 2.161012 GTGAGAGTAACCGACATCGTCA 59.839 50.000 0.00 0.00 37.74 4.35
2154 2157 2.161012 TGTGAGAGTAACCGACATCGTC 59.839 50.000 0.00 0.00 37.74 4.20
2155 2158 2.156917 TGTGAGAGTAACCGACATCGT 58.843 47.619 0.00 0.00 37.74 3.73
2156 2159 2.913777 TGTGAGAGTAACCGACATCG 57.086 50.000 0.00 0.00 39.44 3.84
2157 2160 6.097356 TGTAAATGTGAGAGTAACCGACATC 58.903 40.000 0.00 0.00 0.00 3.06
2158 2161 6.032956 TGTAAATGTGAGAGTAACCGACAT 57.967 37.500 0.00 0.00 0.00 3.06
2159 2162 5.456548 TGTAAATGTGAGAGTAACCGACA 57.543 39.130 0.00 0.00 0.00 4.35
2160 2163 8.540492 CATTATGTAAATGTGAGAGTAACCGAC 58.460 37.037 0.00 0.00 0.00 4.79
2161 2164 7.223971 GCATTATGTAAATGTGAGAGTAACCGA 59.776 37.037 0.00 0.00 0.00 4.69
2162 2165 7.345192 GCATTATGTAAATGTGAGAGTAACCG 58.655 38.462 0.00 0.00 0.00 4.44
2173 2176 5.385198 AGGGATTCCGCATTATGTAAATGT 58.615 37.500 0.00 0.00 38.33 2.71
2216 2219 2.289882 CCTGAACATGTGGCTCTTCTGA 60.290 50.000 0.00 0.00 0.00 3.27
2245 2248 8.121305 TGAATTGTACCTTGTAGCATTTGATT 57.879 30.769 0.00 0.00 0.00 2.57
2277 2280 1.613255 CCGCCTATTTGAGTTGGGTGT 60.613 52.381 0.00 0.00 0.00 4.16
2291 2294 3.154473 CTAGCTGTGCCCCGCCTA 61.154 66.667 0.00 0.00 0.00 3.93
2296 2299 1.077429 CCTTTCCTAGCTGTGCCCC 60.077 63.158 0.00 0.00 0.00 5.80
2321 2324 2.032030 ACGAAGATGGTTTGCAAAGTCG 60.032 45.455 13.26 15.68 0.00 4.18
2478 2482 7.615403 TGTGTTCTCTCAGATAAATTGCTACT 58.385 34.615 0.00 0.00 0.00 2.57
2508 2512 2.869646 ATGTTGCGCATGACACGG 59.130 55.556 16.65 0.00 36.26 4.94
2548 2552 1.148310 AAAGCAACCATCTCGTCGTG 58.852 50.000 0.00 0.00 0.00 4.35
2549 2553 1.531149 CAAAAGCAACCATCTCGTCGT 59.469 47.619 0.00 0.00 0.00 4.34
2555 2559 2.309613 TGTCTGCAAAAGCAACCATCT 58.690 42.857 0.00 0.00 0.00 2.90
2602 2606 5.296531 GGGTGTTGAAGTTACTCGGTAAAAA 59.703 40.000 0.00 0.00 29.42 1.94
2672 2676 2.318908 ACGTAACAGTACAGGGGTCAA 58.681 47.619 0.00 0.00 0.00 3.18
2673 2677 1.999648 ACGTAACAGTACAGGGGTCA 58.000 50.000 0.00 0.00 0.00 4.02
2674 2678 2.036346 ACAACGTAACAGTACAGGGGTC 59.964 50.000 0.00 0.00 0.00 4.46
2675 2679 2.041701 ACAACGTAACAGTACAGGGGT 58.958 47.619 0.00 0.00 0.00 4.95
2676 2680 2.825861 ACAACGTAACAGTACAGGGG 57.174 50.000 0.00 0.00 0.00 4.79
2685 2689 6.250951 CGAAAAAGGCTAAAAACAACGTAACA 59.749 34.615 0.00 0.00 0.00 2.41
2715 2719 4.696877 GGCTAACTGGTTAACACGGTTAAT 59.303 41.667 19.94 6.83 0.00 1.40
2772 2776 4.440802 GGCAACATGAAACTGGTTAACACA 60.441 41.667 8.10 2.45 0.00 3.72
2824 2828 3.490348 GATTGGTGGGACATTGATAGGG 58.510 50.000 0.00 0.00 44.52 3.53
2828 2832 1.284785 ACGGATTGGTGGGACATTGAT 59.715 47.619 0.00 0.00 44.52 2.57


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

AutoCloner maintained by Alex Coulton.