Multiple sequence alignment - TraesCS4B01G275200

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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 TraesCS4B01G275200 chr4B 100.000 2615 0 0 1 2615 553339870 553337256 0.000000e+00 4830
1 TraesCS4B01G275200 chr4D 95.625 1417 45 7 645 2047 443742715 443741302 0.000000e+00 2257
2 TraesCS4B01G275200 chr4D 89.783 646 55 7 1 643 443743651 443743014 0.000000e+00 817
3 TraesCS4B01G275200 chr4D 84.698 281 19 13 2341 2613 443740948 443740684 2.580000e-65 259
4 TraesCS4B01G275200 chr4D 91.358 81 6 1 2216 2296 443741295 443741216 2.750000e-20 110
5 TraesCS4B01G275200 chr4A 93.167 1361 51 13 653 1990 24105750 24107091 0.000000e+00 1960
6 TraesCS4B01G275200 chr4A 90.415 313 28 2 1 312 24105158 24105469 6.740000e-111 411
7 TraesCS4B01G275200 chr4A 81.618 408 23 10 2220 2615 24107143 24107510 9.160000e-75 291
8 TraesCS4B01G275200 chr2B 86.503 163 19 3 2048 2210 639927633 639927474 2.670000e-40 176
9 TraesCS4B01G275200 chr2D 86.335 161 18 4 2050 2210 560153887 560154043 3.460000e-39 172
10 TraesCS4B01G275200 chr2D 84.393 173 21 6 2050 2222 478820898 478820732 5.790000e-37 165
11 TraesCS4B01G275200 chr5D 85.542 166 21 3 2053 2217 35290103 35289940 1.240000e-38 171
12 TraesCS4B01G275200 chr3D 85.976 164 17 6 2048 2210 87925998 87926156 1.240000e-38 171
13 TraesCS4B01G275200 chr3D 85.207 169 20 4 2049 2217 200383817 200383980 4.480000e-38 169
14 TraesCS4B01G275200 chr3D 83.333 180 24 5 2050 2228 526050789 526050615 7.490000e-36 161
15 TraesCS4B01G275200 chr6B 85.207 169 19 6 2050 2217 132353577 132353414 4.480000e-38 169
16 TraesCS4B01G275200 chr6B 85.542 166 16 5 2048 2210 583445981 583446141 1.610000e-37 167


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 TraesCS4B01G275200 chr4B 553337256 553339870 2614 True 4830.000000 4830 100.000 1 2615 1 chr4B.!!$R1 2614
1 TraesCS4B01G275200 chr4D 443740684 443743651 2967 True 860.750000 2257 90.366 1 2613 4 chr4D.!!$R1 2612
2 TraesCS4B01G275200 chr4A 24105158 24107510 2352 False 887.333333 1960 88.400 1 2615 3 chr4A.!!$F1 2614

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
821 1304 0.929734 TAGGTGAGCCCCTCCTACCT 60.93 60.0 8.67 8.67 39.31 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2541 0.035739 AAACGGTCACGGCATAACCT 59.964 50.0 0.0 0.0 46.48 3.5 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
56 57 5.957798 TGATTGCTTCTTCATAAAAGGCAG 58.042 37.500 0.00 0.00 0.00 4.85
58 59 5.376854 TTGCTTCTTCATAAAAGGCAGAC 57.623 39.130 0.00 0.00 0.00 3.51
59 60 4.397420 TGCTTCTTCATAAAAGGCAGACA 58.603 39.130 0.00 0.00 0.00 3.41
76 78 3.760151 CAGACAAAAGATCCATGCTCCAA 59.240 43.478 0.00 0.00 0.00 3.53
104 106 9.578439 GGAAAAACTTCTTCATTCCTGATTATG 57.422 33.333 0.00 0.00 37.23 1.90
127 129 4.261825 GCTTGTGTTTTATGTGGCCTACAA 60.262 41.667 3.32 1.25 43.77 2.41
130 132 4.890581 TGTGTTTTATGTGGCCTACAAGTT 59.109 37.500 3.32 0.00 43.77 2.66
141 143 5.705905 GTGGCCTACAAGTTCTTGAAACTAT 59.294 40.000 17.75 0.00 0.00 2.12
144 146 5.938125 GCCTACAAGTTCTTGAAACTATGGA 59.062 40.000 17.75 0.00 0.00 3.41
171 173 4.020307 ACCTTTTCCTACATTGCCCATTTG 60.020 41.667 0.00 0.00 0.00 2.32
207 209 5.295152 GGACTTATTTATGTCCTACACGGG 58.705 45.833 12.93 0.00 46.65 5.28
257 259 5.833131 TGAGATCAACAACTTAAAAGCCCTT 59.167 36.000 0.00 0.00 0.00 3.95
312 314 3.584848 CCTAGCTTCTTGGGCTATATGGT 59.415 47.826 0.00 0.00 40.79 3.55
316 318 3.565902 GCTTCTTGGGCTATATGGTTCAC 59.434 47.826 0.00 0.00 0.00 3.18
328 436 2.859165 TGGTTCACCAGGAATGACTC 57.141 50.000 0.00 0.00 42.01 3.36
367 551 3.702045 TCCCCCAAACCTATATTTTTGCG 59.298 43.478 2.10 0.00 32.34 4.85
412 598 3.739519 GCACTGGATTACCTACAGAGCAG 60.740 52.174 8.12 0.00 44.55 4.24
428 614 2.103941 GAGCAGCTACTATGGAGGCTTT 59.896 50.000 0.00 0.00 32.30 3.51
470 656 7.675403 GCATTCAAATAATTGACATGGCAGTTG 60.675 37.037 18.90 11.09 45.01 3.16
504 690 8.734218 TTGTTGTACAGAACATTTTGTACCTA 57.266 30.769 17.88 7.65 45.64 3.08
521 707 9.720769 TTTGTACCTATTTTTGTTTGAAAACCA 57.279 25.926 3.59 0.00 38.11 3.67
535 721 8.879759 TGTTTGAAAACCAATAAAAATACGCAA 58.120 25.926 3.59 0.00 38.11 4.85
538 724 8.066668 TGAAAACCAATAAAAATACGCAACAG 57.933 30.769 0.00 0.00 0.00 3.16
543 729 5.732647 CCAATAAAAATACGCAACAGAGTCG 59.267 40.000 0.00 0.00 0.00 4.18
549 735 2.553268 GCAACAGAGTCGTGCAGC 59.447 61.111 10.48 0.00 0.00 5.25
567 753 4.220602 TGCAGCTTCCCTTAAGAAAAATCC 59.779 41.667 3.36 0.00 37.38 3.01
581 767 4.944317 AGAAAAATCCAATCCTCCTCGAAC 59.056 41.667 0.00 0.00 0.00 3.95
586 772 4.093472 TCCAATCCTCCTCGAACAAAAA 57.907 40.909 0.00 0.00 0.00 1.94
614 800 5.703130 GGCAATCTAATCTATGAACCTGGAC 59.297 44.000 0.00 0.00 0.00 4.02
629 815 7.712797 TGAACCTGGACAATCTTTTAGTTTTC 58.287 34.615 0.00 0.00 0.00 2.29
632 818 8.990163 ACCTGGACAATCTTTTAGTTTTCTTA 57.010 30.769 0.00 0.00 0.00 2.10
758 1241 4.021368 CCCTTCTCTTCTCGGACAAACTAA 60.021 45.833 0.00 0.00 0.00 2.24
762 1245 6.829229 TCTCTTCTCGGACAAACTAATGTA 57.171 37.500 0.00 0.00 32.57 2.29
821 1304 0.929734 TAGGTGAGCCCCTCCTACCT 60.930 60.000 8.67 8.67 39.31 3.08
1500 1998 1.521234 GCTGCTGCTCTGCTACCTC 60.521 63.158 8.53 0.00 36.79 3.85
1503 2001 3.074999 GCTGCTCTGCTACCTCGCT 62.075 63.158 0.00 0.00 0.00 4.93
1783 2287 2.834574 TTGTTCGTGTGCAATTTCGT 57.165 40.000 0.00 0.00 0.00 3.85
1896 2407 1.068610 TCTACAATTGCACCGCTTTGC 60.069 47.619 5.05 0.00 43.31 3.68
1936 2447 1.846124 TCTTTTCGGCCACCTCCCT 60.846 57.895 2.24 0.00 0.00 4.20
1970 2481 5.239525 ACTGTGTCCTTTATCTTTCTGTTGC 59.760 40.000 0.00 0.00 0.00 4.17
1990 2501 2.741878 GCGGCATCTGAAGGCTAGTTTA 60.742 50.000 4.94 0.00 31.41 2.01
2025 2538 1.374631 GCGCACAGGTCATGTCAGA 60.375 57.895 0.30 0.00 41.41 3.27
2028 2541 1.873486 CGCACAGGTCATGTCAGACAA 60.873 52.381 7.50 0.00 41.41 3.18
2044 2557 4.609995 AAGGTTATGCCGTGACCG 57.390 55.556 0.00 0.00 41.23 4.79
2047 2560 0.035739 AGGTTATGCCGTGACCGTTT 59.964 50.000 0.00 0.00 41.23 3.60
2048 2561 1.275856 AGGTTATGCCGTGACCGTTTA 59.724 47.619 0.00 0.00 41.23 2.01
2050 2563 3.132646 AGGTTATGCCGTGACCGTTTATA 59.867 43.478 0.00 0.00 41.23 0.98
2051 2564 3.245990 GGTTATGCCGTGACCGTTTATAC 59.754 47.826 0.00 0.00 0.00 1.47
2052 2565 2.973694 ATGCCGTGACCGTTTATACT 57.026 45.000 0.00 0.00 0.00 2.12
2053 2566 2.282701 TGCCGTGACCGTTTATACTC 57.717 50.000 0.00 0.00 0.00 2.59
2054 2567 1.135024 TGCCGTGACCGTTTATACTCC 60.135 52.381 0.00 0.00 0.00 3.85
2055 2568 1.803998 GCCGTGACCGTTTATACTCCC 60.804 57.143 0.00 0.00 0.00 4.30
2056 2569 1.753073 CCGTGACCGTTTATACTCCCT 59.247 52.381 0.00 0.00 0.00 4.20
2057 2570 2.223665 CCGTGACCGTTTATACTCCCTC 60.224 54.545 0.00 0.00 0.00 4.30
2058 2571 2.540361 CGTGACCGTTTATACTCCCTCG 60.540 54.545 0.00 0.00 0.00 4.63
2059 2572 2.026641 TGACCGTTTATACTCCCTCGG 58.973 52.381 0.00 0.00 42.94 4.63
2060 2573 2.149973 ACCGTTTATACTCCCTCGGT 57.850 50.000 0.00 0.00 44.87 4.69
2061 2574 2.027385 ACCGTTTATACTCCCTCGGTC 58.973 52.381 0.00 0.00 46.33 4.79
2062 2575 2.305009 CCGTTTATACTCCCTCGGTCT 58.695 52.381 0.00 0.00 34.38 3.85
2063 2576 2.292845 CCGTTTATACTCCCTCGGTCTC 59.707 54.545 0.00 0.00 34.38 3.36
2064 2577 3.212685 CGTTTATACTCCCTCGGTCTCT 58.787 50.000 0.00 0.00 0.00 3.10
2065 2578 4.384056 CGTTTATACTCCCTCGGTCTCTA 58.616 47.826 0.00 0.00 0.00 2.43
2066 2579 4.818546 CGTTTATACTCCCTCGGTCTCTAA 59.181 45.833 0.00 0.00 0.00 2.10
2067 2580 5.297776 CGTTTATACTCCCTCGGTCTCTAAA 59.702 44.000 0.00 0.00 0.00 1.85
2068 2581 6.016443 CGTTTATACTCCCTCGGTCTCTAAAT 60.016 42.308 0.00 0.00 0.00 1.40
2069 2582 7.173907 CGTTTATACTCCCTCGGTCTCTAAATA 59.826 40.741 0.00 0.00 0.00 1.40
2070 2583 9.022884 GTTTATACTCCCTCGGTCTCTAAATAT 57.977 37.037 0.00 0.00 0.00 1.28
2073 2586 8.810990 ATACTCCCTCGGTCTCTAAATATAAG 57.189 38.462 0.00 0.00 0.00 1.73
2074 2587 6.612741 ACTCCCTCGGTCTCTAAATATAAGT 58.387 40.000 0.00 0.00 0.00 2.24
2075 2588 6.716173 ACTCCCTCGGTCTCTAAATATAAGTC 59.284 42.308 0.00 0.00 0.00 3.01
2076 2589 6.850234 TCCCTCGGTCTCTAAATATAAGTCT 58.150 40.000 0.00 0.00 0.00 3.24
2077 2590 7.296098 TCCCTCGGTCTCTAAATATAAGTCTT 58.704 38.462 0.00 0.00 0.00 3.01
2078 2591 7.783596 TCCCTCGGTCTCTAAATATAAGTCTTT 59.216 37.037 0.00 0.00 0.00 2.52
2079 2592 8.422566 CCCTCGGTCTCTAAATATAAGTCTTTT 58.577 37.037 0.00 0.00 0.00 2.27
2080 2593 9.819267 CCTCGGTCTCTAAATATAAGTCTTTTT 57.181 33.333 0.00 0.00 0.00 1.94
2108 2621 9.400638 GAGATTTCAATAAGAGACTACATACGG 57.599 37.037 0.00 0.00 0.00 4.02
2109 2622 9.132923 AGATTTCAATAAGAGACTACATACGGA 57.867 33.333 0.00 0.00 0.00 4.69
2110 2623 9.400638 GATTTCAATAAGAGACTACATACGGAG 57.599 37.037 0.00 0.00 0.00 4.63
2111 2624 6.315091 TCAATAAGAGACTACATACGGAGC 57.685 41.667 0.00 0.00 0.00 4.70
2112 2625 5.826208 TCAATAAGAGACTACATACGGAGCA 59.174 40.000 0.00 0.00 0.00 4.26
2113 2626 6.320418 TCAATAAGAGACTACATACGGAGCAA 59.680 38.462 0.00 0.00 0.00 3.91
2114 2627 4.373348 AAGAGACTACATACGGAGCAAC 57.627 45.455 0.00 0.00 0.00 4.17
2115 2628 3.353557 AGAGACTACATACGGAGCAACA 58.646 45.455 0.00 0.00 0.00 3.33
2116 2629 3.954904 AGAGACTACATACGGAGCAACAT 59.045 43.478 0.00 0.00 0.00 2.71
2117 2630 5.131067 AGAGACTACATACGGAGCAACATA 58.869 41.667 0.00 0.00 0.00 2.29
2118 2631 5.593095 AGAGACTACATACGGAGCAACATAA 59.407 40.000 0.00 0.00 0.00 1.90
2119 2632 5.833082 AGACTACATACGGAGCAACATAAG 58.167 41.667 0.00 0.00 0.00 1.73
2120 2633 5.360144 AGACTACATACGGAGCAACATAAGT 59.640 40.000 0.00 0.00 0.00 2.24
2121 2634 5.348986 ACTACATACGGAGCAACATAAGTG 58.651 41.667 0.00 0.00 0.00 3.16
2122 2635 4.465632 ACATACGGAGCAACATAAGTGA 57.534 40.909 0.00 0.00 0.00 3.41
2123 2636 4.827692 ACATACGGAGCAACATAAGTGAA 58.172 39.130 0.00 0.00 0.00 3.18
2124 2637 5.428253 ACATACGGAGCAACATAAGTGAAT 58.572 37.500 0.00 0.00 0.00 2.57
2125 2638 5.523916 ACATACGGAGCAACATAAGTGAATC 59.476 40.000 0.00 0.00 0.00 2.52
2126 2639 4.207891 ACGGAGCAACATAAGTGAATCT 57.792 40.909 0.00 0.00 0.00 2.40
2127 2640 5.339008 ACGGAGCAACATAAGTGAATCTA 57.661 39.130 0.00 0.00 0.00 1.98
2128 2641 5.109903 ACGGAGCAACATAAGTGAATCTAC 58.890 41.667 0.00 0.00 0.00 2.59
2129 2642 5.109210 CGGAGCAACATAAGTGAATCTACA 58.891 41.667 0.00 0.00 0.00 2.74
2130 2643 5.005779 CGGAGCAACATAAGTGAATCTACAC 59.994 44.000 0.00 0.00 40.60 2.90
2209 2722 9.392259 AGAAAAACTTATATTTAGGAACGGAGG 57.608 33.333 0.00 0.00 0.00 4.30
2210 2723 9.170734 GAAAAACTTATATTTAGGAACGGAGGT 57.829 33.333 0.00 0.00 0.00 3.85
2296 2816 1.422950 ATCGCCATTTGCAATTGCGC 61.423 50.000 24.58 19.30 45.83 6.09
2297 2817 2.786584 GCCATTTGCAATTGCGCC 59.213 55.556 24.58 6.07 45.83 6.53
2298 2818 2.033755 GCCATTTGCAATTGCGCCA 61.034 52.632 24.58 11.79 45.83 5.69
2321 2841 2.046864 CCTTGAGACGGGCGAGAGA 61.047 63.158 0.00 0.00 0.00 3.10
2323 2843 1.002502 TTGAGACGGGCGAGAGAGA 60.003 57.895 0.00 0.00 0.00 3.10
2422 3165 1.335415 CCTCACTCTGTCACTCACACG 60.335 57.143 0.00 0.00 0.00 4.49
2423 3166 0.668535 TCACTCTGTCACTCACACGG 59.331 55.000 0.00 0.00 0.00 4.94
2424 3167 0.319040 CACTCTGTCACTCACACGGG 60.319 60.000 0.00 0.00 0.00 5.28
2425 3168 1.373497 CTCTGTCACTCACACGGGC 60.373 63.158 0.00 0.00 0.00 6.13
2426 3169 2.087462 CTCTGTCACTCACACGGGCA 62.087 60.000 0.00 0.00 0.00 5.36
2427 3170 1.665916 CTGTCACTCACACGGGCAG 60.666 63.158 0.00 0.00 0.00 4.85
2428 3171 3.044305 GTCACTCACACGGGCAGC 61.044 66.667 0.00 0.00 0.00 5.25
2429 3172 3.233980 TCACTCACACGGGCAGCT 61.234 61.111 0.00 0.00 0.00 4.24
2430 3173 2.740055 CACTCACACGGGCAGCTC 60.740 66.667 0.00 0.00 0.00 4.09
2431 3174 2.919856 ACTCACACGGGCAGCTCT 60.920 61.111 0.00 0.00 0.00 4.09
2432 3175 2.433838 CTCACACGGGCAGCTCTG 60.434 66.667 0.00 0.00 0.00 3.35
2470 3213 1.852895 CGCTGTACTGAACTATTCCGC 59.147 52.381 3.61 0.00 0.00 5.54
2516 3264 2.264005 AAACCAGTAACCATCACGCA 57.736 45.000 0.00 0.00 0.00 5.24
2532 3281 2.554032 CACGCACCAATCTTTTCCTCTT 59.446 45.455 0.00 0.00 0.00 2.85
2541 3290 5.121454 CCAATCTTTTCCTCTTGTTCGAGAG 59.879 44.000 9.45 9.45 42.26 3.20
2561 3314 2.976589 GGACCCGTCCGAAATTAAGAA 58.023 47.619 0.00 0.00 40.36 2.52
2564 3317 3.593096 ACCCGTCCGAAATTAAGAAGAC 58.407 45.455 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.852091 AGCAATCAGAAGAAAATATTGTCTTTC 57.148 29.630 19.71 13.42 34.23 2.62
50 51 2.494870 GCATGGATCTTTTGTCTGCCTT 59.505 45.455 0.00 0.00 0.00 4.35
56 57 3.426695 CGTTGGAGCATGGATCTTTTGTC 60.427 47.826 0.00 0.00 0.00 3.18
58 59 2.159338 CCGTTGGAGCATGGATCTTTTG 60.159 50.000 0.00 0.00 0.00 2.44
59 60 2.094675 CCGTTGGAGCATGGATCTTTT 58.905 47.619 0.00 0.00 0.00 2.27
76 78 5.130350 TCAGGAATGAAGAAGTTTTTCCGT 58.870 37.500 3.86 0.00 40.60 4.69
104 106 3.254657 TGTAGGCCACATAAAACACAAGC 59.745 43.478 5.01 0.00 30.04 4.01
127 129 6.784031 AGGTGATTCCATAGTTTCAAGAACT 58.216 36.000 0.00 0.00 39.02 3.01
130 132 7.176690 GGAAAAGGTGATTCCATAGTTTCAAGA 59.823 37.037 0.56 0.00 44.70 3.02
144 146 3.769300 GGGCAATGTAGGAAAAGGTGATT 59.231 43.478 0.00 0.00 0.00 2.57
171 173 7.602265 ACATAAATAAGTCCAACAACATTTGGC 59.398 33.333 0.00 0.00 45.12 4.52
204 206 1.447643 CCAGGAATGTAGGAGCCCG 59.552 63.158 0.00 0.00 0.00 6.13
207 209 0.475906 ATGCCCAGGAATGTAGGAGC 59.524 55.000 0.00 0.00 0.00 4.70
257 259 7.030300 CTCCAGAGAGAATGGAACACCAAGA 62.030 48.000 0.00 0.00 46.04 3.02
312 314 5.715439 AATATGGAGTCATTCCTGGTGAA 57.285 39.130 0.00 0.00 46.92 3.18
316 318 7.470563 GCCTTTAAAATATGGAGTCATTCCTGG 60.471 40.741 0.00 0.00 46.92 4.45
328 436 3.646162 GGGGGAAGGCCTTTAAAATATGG 59.354 47.826 21.54 0.00 0.00 2.74
412 598 2.875317 GCTTGAAAGCCTCCATAGTAGC 59.125 50.000 3.56 0.00 46.20 3.58
470 656 9.730420 AAATGTTCTGTACAACAAAACTATGAC 57.270 29.630 4.55 0.00 39.69 3.06
507 693 9.704098 GCGTATTTTTATTGGTTTTCAAACAAA 57.296 25.926 4.85 0.00 40.63 2.83
508 694 8.879759 TGCGTATTTTTATTGGTTTTCAAACAA 58.120 25.926 4.85 0.00 40.63 2.83
509 695 8.420374 TGCGTATTTTTATTGGTTTTCAAACA 57.580 26.923 4.85 0.00 40.63 2.83
510 696 9.149556 GTTGCGTATTTTTATTGGTTTTCAAAC 57.850 29.630 0.00 0.00 39.05 2.93
519 705 5.732647 CGACTCTGTTGCGTATTTTTATTGG 59.267 40.000 0.00 0.00 0.00 3.16
521 707 6.304126 CACGACTCTGTTGCGTATTTTTATT 58.696 36.000 0.00 0.00 36.37 1.40
535 721 1.005630 GGAAGCTGCACGACTCTGT 60.006 57.895 1.02 0.00 0.00 3.41
538 724 0.246635 TAAGGGAAGCTGCACGACTC 59.753 55.000 1.02 0.00 0.00 3.36
543 729 4.584327 TTTTTCTTAAGGGAAGCTGCAC 57.416 40.909 1.02 0.00 34.87 4.57
549 735 7.147828 GGAGGATTGGATTTTTCTTAAGGGAAG 60.148 40.741 1.85 0.00 36.38 3.46
586 772 7.286316 CCAGGTTCATAGATTAGATTGCCTTTT 59.714 37.037 0.00 0.00 0.00 2.27
588 774 6.101734 TCCAGGTTCATAGATTAGATTGCCTT 59.898 38.462 0.00 0.00 0.00 4.35
589 775 5.608437 TCCAGGTTCATAGATTAGATTGCCT 59.392 40.000 0.00 0.00 0.00 4.75
590 776 5.703130 GTCCAGGTTCATAGATTAGATTGCC 59.297 44.000 0.00 0.00 0.00 4.52
591 777 6.291377 TGTCCAGGTTCATAGATTAGATTGC 58.709 40.000 0.00 0.00 0.00 3.56
758 1241 1.065854 GCAGAGCTGACAAGGGTACAT 60.066 52.381 0.85 0.00 0.00 2.29
762 1245 1.072159 GTGCAGAGCTGACAAGGGT 59.928 57.895 0.85 0.00 0.00 4.34
821 1304 3.755628 GTGGCGCCTCGTCAGGTA 61.756 66.667 29.70 0.00 43.72 3.08
1503 2001 3.403057 GCGCGCTTGTCGTTGAGA 61.403 61.111 26.67 0.00 41.07 3.27
1527 2025 0.179137 TGAAGGCGCTGACGATGTAG 60.179 55.000 7.64 0.00 43.93 2.74
1531 2029 2.125512 GGTGAAGGCGCTGACGAT 60.126 61.111 7.64 0.00 43.93 3.73
1652 2153 1.282930 GGACGAACGTGTTGAGCTCC 61.283 60.000 12.15 0.00 0.00 4.70
1896 2407 5.971202 AGACAAACGCAATTACACAAAGAAG 59.029 36.000 0.00 0.00 0.00 2.85
1936 2447 3.281727 AAGGACACAGTGAAAAGAGCA 57.718 42.857 7.81 0.00 0.00 4.26
1970 2481 2.029838 AAACTAGCCTTCAGATGCCG 57.970 50.000 0.00 0.00 0.00 5.69
2016 2529 3.609853 GGCATAACCTTGTCTGACATGA 58.390 45.455 21.27 3.89 34.51 3.07
2025 2538 0.672401 CGGTCACGGCATAACCTTGT 60.672 55.000 0.00 0.00 38.80 3.16
2028 2541 0.035739 AAACGGTCACGGCATAACCT 59.964 50.000 0.00 0.00 46.48 3.50
2044 2557 6.705863 TTTAGAGACCGAGGGAGTATAAAC 57.294 41.667 0.00 0.00 0.00 2.01
2047 2560 9.902684 CTTATATTTAGAGACCGAGGGAGTATA 57.097 37.037 0.00 0.00 0.00 1.47
2048 2561 8.392479 ACTTATATTTAGAGACCGAGGGAGTAT 58.608 37.037 0.00 0.00 0.00 2.12
2050 2563 6.612741 ACTTATATTTAGAGACCGAGGGAGT 58.387 40.000 0.00 0.00 0.00 3.85
2051 2564 6.943718 AGACTTATATTTAGAGACCGAGGGAG 59.056 42.308 0.00 0.00 0.00 4.30
2052 2565 6.850234 AGACTTATATTTAGAGACCGAGGGA 58.150 40.000 0.00 0.00 0.00 4.20
2053 2566 7.527568 AAGACTTATATTTAGAGACCGAGGG 57.472 40.000 0.00 0.00 0.00 4.30
2054 2567 9.819267 AAAAAGACTTATATTTAGAGACCGAGG 57.181 33.333 0.00 0.00 0.00 4.63
2082 2595 9.400638 CCGTATGTAGTCTCTTATTGAAATCTC 57.599 37.037 0.00 0.00 0.00 2.75
2083 2596 9.132923 TCCGTATGTAGTCTCTTATTGAAATCT 57.867 33.333 0.00 0.00 0.00 2.40
2084 2597 9.400638 CTCCGTATGTAGTCTCTTATTGAAATC 57.599 37.037 0.00 0.00 0.00 2.17
2085 2598 7.868415 GCTCCGTATGTAGTCTCTTATTGAAAT 59.132 37.037 0.00 0.00 0.00 2.17
2086 2599 7.147966 TGCTCCGTATGTAGTCTCTTATTGAAA 60.148 37.037 0.00 0.00 0.00 2.69
2087 2600 6.320418 TGCTCCGTATGTAGTCTCTTATTGAA 59.680 38.462 0.00 0.00 0.00 2.69
2088 2601 5.826208 TGCTCCGTATGTAGTCTCTTATTGA 59.174 40.000 0.00 0.00 0.00 2.57
2089 2602 6.073327 TGCTCCGTATGTAGTCTCTTATTG 57.927 41.667 0.00 0.00 0.00 1.90
2090 2603 6.096423 TGTTGCTCCGTATGTAGTCTCTTATT 59.904 38.462 0.00 0.00 0.00 1.40
2091 2604 5.593095 TGTTGCTCCGTATGTAGTCTCTTAT 59.407 40.000 0.00 0.00 0.00 1.73
2092 2605 4.945543 TGTTGCTCCGTATGTAGTCTCTTA 59.054 41.667 0.00 0.00 0.00 2.10
2093 2606 3.762288 TGTTGCTCCGTATGTAGTCTCTT 59.238 43.478 0.00 0.00 0.00 2.85
2094 2607 3.353557 TGTTGCTCCGTATGTAGTCTCT 58.646 45.455 0.00 0.00 0.00 3.10
2095 2608 3.777465 TGTTGCTCCGTATGTAGTCTC 57.223 47.619 0.00 0.00 0.00 3.36
2096 2609 5.360144 ACTTATGTTGCTCCGTATGTAGTCT 59.640 40.000 0.00 0.00 0.00 3.24
2097 2610 5.459107 CACTTATGTTGCTCCGTATGTAGTC 59.541 44.000 0.00 0.00 0.00 2.59
2098 2611 5.126545 TCACTTATGTTGCTCCGTATGTAGT 59.873 40.000 0.00 0.00 0.00 2.73
2099 2612 5.588240 TCACTTATGTTGCTCCGTATGTAG 58.412 41.667 0.00 0.00 0.00 2.74
2100 2613 5.585820 TCACTTATGTTGCTCCGTATGTA 57.414 39.130 0.00 0.00 0.00 2.29
2101 2614 4.465632 TCACTTATGTTGCTCCGTATGT 57.534 40.909 0.00 0.00 0.00 2.29
2102 2615 5.755375 AGATTCACTTATGTTGCTCCGTATG 59.245 40.000 0.00 0.00 0.00 2.39
2103 2616 5.918608 AGATTCACTTATGTTGCTCCGTAT 58.081 37.500 0.00 0.00 0.00 3.06
2104 2617 5.339008 AGATTCACTTATGTTGCTCCGTA 57.661 39.130 0.00 0.00 0.00 4.02
2105 2618 4.207891 AGATTCACTTATGTTGCTCCGT 57.792 40.909 0.00 0.00 0.00 4.69
2106 2619 5.005779 GTGTAGATTCACTTATGTTGCTCCG 59.994 44.000 0.00 0.00 35.68 4.63
2107 2620 6.109359 AGTGTAGATTCACTTATGTTGCTCC 58.891 40.000 0.00 0.00 44.92 4.70
2108 2621 7.038659 AGAGTGTAGATTCACTTATGTTGCTC 58.961 38.462 0.98 0.00 46.81 4.26
2109 2622 6.940739 AGAGTGTAGATTCACTTATGTTGCT 58.059 36.000 0.98 0.00 46.81 3.91
2110 2623 8.596380 GTTAGAGTGTAGATTCACTTATGTTGC 58.404 37.037 0.98 0.00 46.81 4.17
2111 2624 9.639601 TGTTAGAGTGTAGATTCACTTATGTTG 57.360 33.333 0.98 0.00 46.81 3.33
2183 2696 9.392259 CCTCCGTTCCTAAATATAAGTTTTTCT 57.608 33.333 0.00 0.00 0.00 2.52
2184 2697 9.170734 ACCTCCGTTCCTAAATATAAGTTTTTC 57.829 33.333 0.00 0.00 0.00 2.29
2194 2707 9.592196 ACAGTATATTACCTCCGTTCCTAAATA 57.408 33.333 0.00 0.00 0.00 1.40
2195 2708 8.488308 ACAGTATATTACCTCCGTTCCTAAAT 57.512 34.615 0.00 0.00 0.00 1.40
2196 2709 7.902920 ACAGTATATTACCTCCGTTCCTAAA 57.097 36.000 0.00 0.00 0.00 1.85
2197 2710 8.220559 ACTACAGTATATTACCTCCGTTCCTAA 58.779 37.037 0.00 0.00 0.00 2.69
2198 2711 7.749666 ACTACAGTATATTACCTCCGTTCCTA 58.250 38.462 0.00 0.00 0.00 2.94
2199 2712 6.608922 ACTACAGTATATTACCTCCGTTCCT 58.391 40.000 0.00 0.00 0.00 3.36
2200 2713 6.890979 ACTACAGTATATTACCTCCGTTCC 57.109 41.667 0.00 0.00 0.00 3.62
2203 2716 9.359653 ACATTTACTACAGTATATTACCTCCGT 57.640 33.333 0.00 0.00 0.00 4.69
2204 2717 9.622004 CACATTTACTACAGTATATTACCTCCG 57.378 37.037 0.00 0.00 0.00 4.63
2214 2727 9.751542 GAGCTGTATTCACATTTACTACAGTAT 57.248 33.333 0.00 0.62 40.74 2.12
2218 2731 7.611770 ACAGAGCTGTATTCACATTTACTACA 58.388 34.615 0.41 0.00 42.90 2.74
2296 2816 2.738521 CCGTCTCAAGGTGCGTGG 60.739 66.667 0.00 0.00 0.00 4.94
2297 2817 2.738521 CCCGTCTCAAGGTGCGTG 60.739 66.667 0.00 0.00 0.00 5.34
2298 2818 4.681978 GCCCGTCTCAAGGTGCGT 62.682 66.667 0.00 0.00 0.00 5.24
2321 2841 1.075151 GGATCCGAAGACCCCCTCT 60.075 63.158 0.00 0.00 0.00 3.69
2323 2843 1.383248 CTGGATCCGAAGACCCCCT 60.383 63.158 7.39 0.00 0.00 4.79
2402 3145 1.335415 CGTGTGAGTGACAGAGTGAGG 60.335 57.143 0.00 0.00 34.28 3.86
2425 3168 2.436292 GTGAGCAGGGCAGAGCTG 60.436 66.667 0.00 0.00 42.04 4.24
2426 3169 2.926779 TGTGAGCAGGGCAGAGCT 60.927 61.111 0.00 0.00 45.25 4.09
2427 3170 2.745492 GTGTGAGCAGGGCAGAGC 60.745 66.667 0.00 0.00 0.00 4.09
2428 3171 1.025113 CATGTGTGAGCAGGGCAGAG 61.025 60.000 0.00 0.00 0.00 3.35
2429 3172 1.002990 CATGTGTGAGCAGGGCAGA 60.003 57.895 0.00 0.00 0.00 4.26
2430 3173 2.044555 CCATGTGTGAGCAGGGCAG 61.045 63.158 0.00 0.00 33.41 4.85
2431 3174 2.034532 CCATGTGTGAGCAGGGCA 59.965 61.111 0.00 0.00 33.41 5.36
2433 3176 2.753043 GGCCATGTGTGAGCAGGG 60.753 66.667 0.00 0.00 42.62 4.45
2434 3177 3.129502 CGGCCATGTGTGAGCAGG 61.130 66.667 2.24 0.00 0.00 4.85
2435 3178 3.807538 GCGGCCATGTGTGAGCAG 61.808 66.667 2.24 0.00 0.00 4.24
2436 3179 4.334118 AGCGGCCATGTGTGAGCA 62.334 61.111 2.24 0.00 0.00 4.26
2437 3180 3.807538 CAGCGGCCATGTGTGAGC 61.808 66.667 2.24 0.00 0.00 4.26
2438 3181 1.079197 TACAGCGGCCATGTGTGAG 60.079 57.895 18.54 0.00 32.02 3.51
2439 3182 1.375396 GTACAGCGGCCATGTGTGA 60.375 57.895 18.54 0.00 32.02 3.58
2440 3183 1.375908 AGTACAGCGGCCATGTGTG 60.376 57.895 18.54 3.40 32.02 3.82
2470 3213 0.237761 GTCCACGATCTATCCGTCGG 59.762 60.000 4.39 4.39 41.87 4.79
2516 3264 4.714632 TCGAACAAGAGGAAAAGATTGGT 58.285 39.130 0.00 0.00 0.00 3.67
2532 3281 1.975407 GGACGGGTCCTCTCGAACA 60.975 63.158 10.60 0.00 46.16 3.18
2541 3290 2.678471 TCTTAATTTCGGACGGGTCC 57.322 50.000 7.82 7.82 46.18 4.46
2542 3291 3.615937 GTCTTCTTAATTTCGGACGGGTC 59.384 47.826 0.00 0.00 0.00 4.46
2561 3314 6.127338 TGACGGTCATTGATAAATCTCAGTCT 60.127 38.462 6.76 0.00 0.00 3.24
2564 3317 6.045318 AGTGACGGTCATTGATAAATCTCAG 58.955 40.000 14.78 0.00 0.00 3.35
2577 3330 0.684805 GGGGAGAGAGTGACGGTCAT 60.685 60.000 14.78 3.53 0.00 3.06
2578 3331 1.304217 GGGGAGAGAGTGACGGTCA 60.304 63.158 6.76 6.76 0.00 4.02


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

AutoCloner maintained by Alex Coulton.