Multiple sequence alignment - TraesCS5A01G171700

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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 TraesCS5A01G171700 chr5A 100.000 2676 0 0 1 2676 364971584 364968909 0.000000e+00 4942.0
1 TraesCS5A01G171700 chr5A 84.855 482 53 14 704 1184 364979005 364978543 4.030000e-128 468.0
2 TraesCS5A01G171700 chr5A 83.426 537 36 29 1420 1919 364978336 364977816 1.460000e-122 449.0
3 TraesCS5A01G171700 chr5A 75.920 652 80 38 1060 1675 364962123 364961513 2.040000e-66 263.0
4 TraesCS5A01G171700 chr5A 94.375 160 9 0 1275 1434 364978544 364978385 2.060000e-61 246.0
5 TraesCS5A01G171700 chr5B 88.987 1580 87 37 544 2062 313312107 313310554 0.000000e+00 1873.0
6 TraesCS5A01G171700 chr5B 89.407 472 38 8 722 1184 313350638 313350170 3.840000e-163 584.0
7 TraesCS5A01G171700 chr5B 86.339 549 55 12 6 537 313343705 313343160 4.970000e-162 580.0
8 TraesCS5A01G171700 chr5B 83.579 542 35 26 1425 1919 313349913 313349379 2.430000e-125 459.0
9 TraesCS5A01G171700 chr5B 94.444 162 9 0 1273 1434 313350173 313350012 1.590000e-62 250.0
10 TraesCS5A01G171700 chr5B 95.522 67 3 0 598 664 313350731 313350665 1.010000e-19 108.0
11 TraesCS5A01G171700 chr5D 87.585 1627 92 42 364 1919 276547643 276546056 0.000000e+00 1784.0
12 TraesCS5A01G171700 chr5D 88.367 490 46 8 704 1184 276554192 276553705 1.790000e-161 579.0
13 TraesCS5A01G171700 chr5D 80.946 761 117 22 1936 2676 276546070 276545318 6.420000e-161 577.0
14 TraesCS5A01G171700 chr5D 81.919 542 32 27 1420 1917 276553498 276552979 5.370000e-107 398.0
15 TraesCS5A01G171700 chr5D 95.679 162 7 0 1273 1434 276553708 276553547 7.350000e-66 261.0
16 TraesCS5A01G171700 chr5D 87.805 164 14 5 204 362 276547995 276547833 1.260000e-43 187.0
17 TraesCS5A01G171700 chr3A 83.544 79 8 5 14 88 746091820 746091897 4.780000e-08 69.4
18 TraesCS5A01G171700 chr2A 97.143 35 1 0 2336 2370 52262005 52262039 2.880000e-05 60.2


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 TraesCS5A01G171700 chr5A 364968909 364971584 2675 True 4942.000000 4942 100.000000 1 2676 1 chr5A.!!$R2 2675
1 TraesCS5A01G171700 chr5A 364977816 364979005 1189 True 387.666667 468 87.552000 704 1919 3 chr5A.!!$R3 1215
2 TraesCS5A01G171700 chr5A 364961513 364962123 610 True 263.000000 263 75.920000 1060 1675 1 chr5A.!!$R1 615
3 TraesCS5A01G171700 chr5B 313310554 313312107 1553 True 1873.000000 1873 88.987000 544 2062 1 chr5B.!!$R1 1518
4 TraesCS5A01G171700 chr5B 313343160 313343705 545 True 580.000000 580 86.339000 6 537 1 chr5B.!!$R2 531
5 TraesCS5A01G171700 chr5B 313349379 313350731 1352 True 350.250000 584 90.738000 598 1919 4 chr5B.!!$R3 1321
6 TraesCS5A01G171700 chr5D 276545318 276547995 2677 True 849.333333 1784 85.445333 204 2676 3 chr5D.!!$R1 2472
7 TraesCS5A01G171700 chr5D 276552979 276554192 1213 True 412.666667 579 88.655000 704 1917 3 chr5D.!!$R2 1213

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
578 773 0.817013 AGAGAGAGCTAGCTGTGTGC 59.183 55.0 24.99 10.78 43.29 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 2651 0.526739 AACCAACCTCGCGTTTTTGC 60.527 50.0 5.77 0.0 29.93 3.68 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
68 69 6.613153 AGAAGTATAATGTGGGATAGGCTC 57.387 41.667 0.00 0.00 0.00 4.70
72 73 5.719085 AGTATAATGTGGGATAGGCTCAGAG 59.281 44.000 0.00 0.00 0.00 3.35
117 118 9.895138 TGGTTTAAACTAATTATGTCTCTACCC 57.105 33.333 17.50 0.00 0.00 3.69
118 119 9.334947 GGTTTAAACTAATTATGTCTCTACCCC 57.665 37.037 17.50 0.00 0.00 4.95
122 123 6.980416 ACTAATTATGTCTCTACCCCTCAC 57.020 41.667 0.00 0.00 0.00 3.51
128 129 2.025226 TGTCTCTACCCCTCACGATCTT 60.025 50.000 0.00 0.00 0.00 2.40
130 131 3.024547 TCTCTACCCCTCACGATCTTTG 58.975 50.000 0.00 0.00 0.00 2.77
155 156 8.092068 TGACTAAATTTGAAGTCTCGGTTGATA 58.908 33.333 17.77 0.00 42.17 2.15
157 158 6.743575 AAATTTGAAGTCTCGGTTGATAGG 57.256 37.500 0.00 0.00 0.00 2.57
166 167 5.661759 AGTCTCGGTTGATAGGGTCTTAAAT 59.338 40.000 0.00 0.00 0.00 1.40
167 168 6.156429 AGTCTCGGTTGATAGGGTCTTAAATT 59.844 38.462 0.00 0.00 0.00 1.82
168 169 6.479331 GTCTCGGTTGATAGGGTCTTAAATTC 59.521 42.308 0.00 0.00 0.00 2.17
275 276 9.160496 GACAATACATTTTGACAATCTCTCTCT 57.840 33.333 0.00 0.00 0.00 3.10
304 305 6.770746 AGGCTTATTTAGACTTAGACGTCA 57.229 37.500 19.50 0.48 40.22 4.35
325 327 8.124823 ACGTCAGATCGATTTAAAGTCGTATTA 58.875 33.333 0.00 2.71 39.91 0.98
402 595 8.857216 CATGCTTCAGATAACTCATTCAAAAAC 58.143 33.333 0.00 0.00 0.00 2.43
410 603 8.290325 AGATAACTCATTCAAAAACCGAAACTC 58.710 33.333 0.00 0.00 0.00 3.01
419 612 8.758633 TTCAAAAACCGAAACTCATAAAAACA 57.241 26.923 0.00 0.00 0.00 2.83
467 662 6.464222 TCTTTCGATGAGGTTAACTGTCAAT 58.536 36.000 13.07 4.97 0.00 2.57
521 716 5.468072 AGCAAGTTATCTTTGTGTCTGTCTG 59.532 40.000 0.00 0.00 0.00 3.51
561 756 3.659850 CGAGAGCGAGAGAGAGAGA 57.340 57.895 0.00 0.00 40.82 3.10
563 758 1.067060 CGAGAGCGAGAGAGAGAGAGA 59.933 57.143 0.00 0.00 40.82 3.10
565 760 2.362397 GAGAGCGAGAGAGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
567 762 1.202580 AGCGAGAGAGAGAGAGAGAGC 60.203 57.143 0.00 0.00 0.00 4.09
578 773 0.817013 AGAGAGAGCTAGCTGTGTGC 59.183 55.000 24.99 10.78 43.29 4.57
816 1016 1.580845 CCTTCGTTGCTGCTTCCCTG 61.581 60.000 0.00 0.00 0.00 4.45
872 1077 3.118956 AGGACGTCTTCTTGCTCATAAGG 60.119 47.826 16.46 0.00 0.00 2.69
925 1130 4.490799 GCACAAAAGCAAAACAACTCTTCG 60.491 41.667 0.00 0.00 0.00 3.79
928 1133 4.965119 AAAGCAAAACAACTCTTCGAGT 57.035 36.364 0.00 0.00 45.64 4.18
929 1134 6.128117 ACAAAAGCAAAACAACTCTTCGAGTA 60.128 34.615 0.00 0.00 42.59 2.59
930 1135 5.659048 AAGCAAAACAACTCTTCGAGTAG 57.341 39.130 0.00 0.00 42.59 2.57
931 1136 3.495001 AGCAAAACAACTCTTCGAGTAGC 59.505 43.478 0.00 0.00 42.59 3.58
982 1211 3.608316 AGCTTGGAGATTCTGTGAGAC 57.392 47.619 0.00 0.00 0.00 3.36
1013 1242 6.094881 GCAAGTTGCAAGATGGTTAAGGTATA 59.905 38.462 22.90 0.00 44.26 1.47
1038 1267 3.129287 CAGTTTGCTTGTCTTGTTCCAGT 59.871 43.478 0.00 0.00 0.00 4.00
1039 1268 3.378427 AGTTTGCTTGTCTTGTTCCAGTC 59.622 43.478 0.00 0.00 0.00 3.51
1042 1271 1.876156 GCTTGTCTTGTTCCAGTCCAG 59.124 52.381 0.00 0.00 0.00 3.86
1044 1273 1.801242 TGTCTTGTTCCAGTCCAGGA 58.199 50.000 0.00 0.00 35.41 3.86
1065 1294 1.403679 CTGGTGTTCCGTTTGCTCAAA 59.596 47.619 0.00 0.00 36.30 2.69
1078 1307 1.044725 GCTCAAATTTGTGCGTCGTG 58.955 50.000 24.54 6.28 37.83 4.35
1090 1320 1.052287 GCGTCGTGCTGAATTTTTGG 58.948 50.000 0.00 0.00 41.73 3.28
1091 1321 1.334599 GCGTCGTGCTGAATTTTTGGA 60.335 47.619 0.00 0.00 41.73 3.53
1270 1519 3.012518 AGGAGGTGCTCAATTCAATTCG 58.987 45.455 0.00 0.00 31.08 3.34
1271 1520 3.009723 GGAGGTGCTCAATTCAATTCGA 58.990 45.455 0.00 0.00 31.08 3.71
1384 1633 2.022240 GCCTAGGCTACGCAGAGCTT 62.022 60.000 27.17 2.07 42.43 3.74
1520 1901 1.228154 GTCGGTTCCAAAGGTGGCT 60.228 57.895 0.00 0.00 45.54 4.75
1657 2038 2.573009 TCAGCATCAAGAACAGGATCCA 59.427 45.455 15.82 0.00 0.00 3.41
1682 2082 4.391216 GCTGCAGCATTATGTAGATGTAGG 59.609 45.833 33.36 0.00 41.59 3.18
1701 2114 9.310449 GATGTAGGTGTTAATTAGGGAGAGATA 57.690 37.037 0.00 0.00 0.00 1.98
1715 2128 1.004277 GAGATAATGCGTCGGCGAGG 61.004 60.000 23.88 23.88 44.10 4.63
1716 2129 1.007734 GATAATGCGTCGGCGAGGA 60.008 57.895 31.06 17.03 44.10 3.71
1717 2130 1.004277 GATAATGCGTCGGCGAGGAG 61.004 60.000 31.06 16.93 44.10 3.69
1766 2196 1.598701 GCATGACCCAGAAGTTGGCC 61.599 60.000 0.00 0.00 46.32 5.36
1837 2276 6.566197 GTACAGTACAGTACAGTACAGGTT 57.434 41.667 28.63 11.78 45.42 3.50
1917 2356 7.039011 GGAATGAATAAAAGGAAACTCAGGGTT 60.039 37.037 0.00 0.00 42.68 4.11
1919 2358 7.669089 TGAATAAAAGGAAACTCAGGGTTTT 57.331 32.000 0.00 0.00 46.77 2.43
1990 2432 8.511321 ACAAGATGCAAAATTACTCAAATACGA 58.489 29.630 0.00 0.00 0.00 3.43
1994 2436 5.083389 GCAAAATTACTCAAATACGACGCA 58.917 37.500 0.00 0.00 0.00 5.24
2000 2442 3.585862 ACTCAAATACGACGCAAGATGT 58.414 40.909 0.00 0.00 43.62 3.06
2045 2489 5.376625 ACTGACTAAAAGCATCTCCAACAA 58.623 37.500 0.00 0.00 0.00 2.83
2055 2499 3.209410 CATCTCCAACAACAGCCCTATC 58.791 50.000 0.00 0.00 0.00 2.08
2076 2520 5.181690 TCTTTGGGAATCTGTCGTTTTTG 57.818 39.130 0.00 0.00 0.00 2.44
2077 2521 4.884744 TCTTTGGGAATCTGTCGTTTTTGA 59.115 37.500 0.00 0.00 0.00 2.69
2079 2523 5.584253 TTGGGAATCTGTCGTTTTTGAAA 57.416 34.783 0.00 0.00 0.00 2.69
2086 2530 4.643953 TCTGTCGTTTTTGAAACACGAAG 58.356 39.130 19.13 17.07 44.10 3.79
2087 2531 3.749404 TGTCGTTTTTGAAACACGAAGG 58.251 40.909 19.13 0.00 44.10 3.46
2095 2539 3.768468 TGAAACACGAAGGGTCAAAAC 57.232 42.857 0.00 0.00 0.00 2.43
2105 2550 0.895559 GGGTCAAAACAGGCCTCCAG 60.896 60.000 0.00 0.00 0.00 3.86
2108 2553 0.538057 TCAAAACAGGCCTCCAGCAG 60.538 55.000 0.00 0.00 46.50 4.24
2111 2556 3.564345 AACAGGCCTCCAGCAGCTG 62.564 63.158 16.23 16.23 46.50 4.24
2116 2561 2.044252 CCTCCAGCAGCTGCCAAT 60.044 61.111 34.39 14.59 43.38 3.16
2117 2562 2.119655 CCTCCAGCAGCTGCCAATC 61.120 63.158 34.39 7.70 43.38 2.67
2118 2563 1.077644 CTCCAGCAGCTGCCAATCT 60.078 57.895 34.39 13.75 43.38 2.40
2122 2567 2.029623 CCAGCAGCTGCCAATCTTAAT 58.970 47.619 34.39 10.47 43.38 1.40
2123 2568 2.429610 CCAGCAGCTGCCAATCTTAATT 59.570 45.455 34.39 9.65 43.38 1.40
2124 2569 3.118884 CCAGCAGCTGCCAATCTTAATTT 60.119 43.478 34.39 9.07 43.38 1.82
2125 2570 4.110482 CAGCAGCTGCCAATCTTAATTTC 58.890 43.478 34.39 2.39 43.38 2.17
2126 2571 4.021916 AGCAGCTGCCAATCTTAATTTCT 58.978 39.130 34.39 8.36 43.38 2.52
2151 2603 3.442273 TGTAAGAAAAATTAGGCAGCCCG 59.558 43.478 8.22 0.00 35.76 6.13
2155 2607 3.576550 AGAAAAATTAGGCAGCCCGAAAA 59.423 39.130 8.22 0.00 35.76 2.29
2171 2623 1.873591 GAAAAAGAGGCTTCTCGTGCA 59.126 47.619 0.00 0.00 42.18 4.57
2177 2629 0.607489 AGGCTTCTCGTGCAGCAAAT 60.607 50.000 11.06 0.00 37.81 2.32
2180 2632 1.717645 GCTTCTCGTGCAGCAAATTTG 59.282 47.619 14.03 14.03 35.95 2.32
2181 2633 2.322161 CTTCTCGTGCAGCAAATTTGG 58.678 47.619 19.47 5.27 0.00 3.28
2189 2641 1.815021 GCAGCAAATTTGGGGCACTTT 60.815 47.619 19.47 0.00 0.00 2.66
2192 2644 1.237533 CAAATTTGGGGCACTTTGGC 58.762 50.000 10.49 0.00 42.88 4.52
2193 2645 0.842635 AAATTTGGGGCACTTTGGCA 59.157 45.000 1.86 0.00 45.76 4.92
2195 2647 1.482748 ATTTGGGGCACTTTGGCAGG 61.483 55.000 1.86 0.00 45.76 4.85
2204 2656 4.212913 TTTGGCAGGCGCGCAAAA 62.213 55.556 34.42 20.11 39.92 2.44
2206 2658 4.940593 TGGCAGGCGCGCAAAAAC 62.941 61.111 34.42 18.44 39.92 2.43
2216 2668 3.916439 GCAAAAACGCGAGGTTGG 58.084 55.556 15.93 1.78 42.68 3.77
2219 2671 1.915952 CAAAAACGCGAGGTTGGTTT 58.084 45.000 15.93 0.00 42.68 3.27
2220 2672 1.849829 CAAAAACGCGAGGTTGGTTTC 59.150 47.619 15.93 0.00 42.68 2.78
2227 2679 2.281276 AGGTTGGTTTCGGACGCC 60.281 61.111 0.00 0.00 0.00 5.68
2230 2682 2.975799 TTGGTTTCGGACGCCTGC 60.976 61.111 0.00 0.00 0.00 4.85
2246 2698 1.078497 TGCATGCGATCGGAAACCT 60.078 52.632 14.89 0.00 0.00 3.50
2248 2700 0.451783 GCATGCGATCGGAAACCTTT 59.548 50.000 14.89 0.00 0.00 3.11
2249 2701 1.668751 GCATGCGATCGGAAACCTTTA 59.331 47.619 14.89 0.00 0.00 1.85
2250 2702 2.096819 GCATGCGATCGGAAACCTTTAA 59.903 45.455 14.89 0.00 0.00 1.52
2254 2706 4.258543 TGCGATCGGAAACCTTTAAATCT 58.741 39.130 18.30 0.00 0.00 2.40
2258 2710 4.028993 TCGGAAACCTTTAAATCTGCCT 57.971 40.909 0.00 0.00 0.00 4.75
2261 2713 3.368427 GGAAACCTTTAAATCTGCCTGCC 60.368 47.826 0.00 0.00 0.00 4.85
2262 2714 1.852633 ACCTTTAAATCTGCCTGCCC 58.147 50.000 0.00 0.00 0.00 5.36
2285 2737 3.204827 CTGCTGCGTACCATGGCC 61.205 66.667 13.04 0.00 0.00 5.36
2293 2745 3.161450 TACCATGGCCGGCTCCTC 61.161 66.667 28.56 10.32 0.00 3.71
2316 2768 2.915659 CTGCCGCCGACCCCTATA 60.916 66.667 0.00 0.00 0.00 1.31
2317 2769 2.915659 TGCCGCCGACCCCTATAG 60.916 66.667 0.00 0.00 0.00 1.31
2318 2770 3.692406 GCCGCCGACCCCTATAGG 61.692 72.222 12.27 12.27 0.00 2.57
2381 2833 1.203523 AGTTTTGCCTTGTTTCGTGCA 59.796 42.857 0.00 0.00 0.00 4.57
2382 2834 1.996191 GTTTTGCCTTGTTTCGTGCAA 59.004 42.857 0.00 0.00 41.57 4.08
2420 2876 5.063880 GCCCTATTATAGGTCTGTTGTTGG 58.936 45.833 16.25 0.00 44.73 3.77
2422 2878 6.525629 CCCTATTATAGGTCTGTTGTTGGAG 58.474 44.000 16.25 0.00 44.73 3.86
2424 2880 7.016661 CCCTATTATAGGTCTGTTGTTGGAGAT 59.983 40.741 16.25 0.00 44.73 2.75
2451 2907 1.543358 TGCTCGTGCATAAAAATGGCA 59.457 42.857 8.30 0.00 45.31 4.92
2452 2908 2.029560 TGCTCGTGCATAAAAATGGCAA 60.030 40.909 8.30 0.00 45.31 4.52
2456 2912 5.390779 GCTCGTGCATAAAAATGGCAATTTT 60.391 36.000 16.68 16.68 41.88 1.82
2473 2929 5.852755 GCAATTTTTGTGCCTTAAATCTTGC 59.147 36.000 0.00 0.00 35.91 4.01
2474 2930 6.293571 GCAATTTTTGTGCCTTAAATCTTGCT 60.294 34.615 0.00 0.00 34.91 3.91
2476 2932 5.528043 TTTTGTGCCTTAAATCTTGCTCA 57.472 34.783 0.00 0.00 0.00 4.26
2477 2933 5.726980 TTTGTGCCTTAAATCTTGCTCAT 57.273 34.783 0.00 0.00 0.00 2.90
2490 2949 3.814842 TCTTGCTCATCATGTTTTCGTGT 59.185 39.130 0.00 0.00 37.97 4.49
2520 2979 1.963515 GGGTTGTTGTTGGAGATGCTT 59.036 47.619 0.00 0.00 0.00 3.91
2530 2989 5.869579 TGTTGGAGATGCTTTAAAGTCTCT 58.130 37.500 24.21 20.67 37.74 3.10
2537 2996 7.606073 GGAGATGCTTTAAAGTCTCTCTTTTCT 59.394 37.037 28.69 15.36 42.95 2.52
2539 2998 8.374743 AGATGCTTTAAAGTCTCTCTTTTCTCT 58.625 33.333 16.38 1.29 42.95 3.10
2549 3008 7.688343 AGTCTCTCTTTTCTCTCCATCAAAAT 58.312 34.615 0.00 0.00 0.00 1.82
2552 3011 8.327271 TCTCTCTTTTCTCTCCATCAAAATCAT 58.673 33.333 0.00 0.00 0.00 2.45
2553 3012 8.277490 TCTCTTTTCTCTCCATCAAAATCATG 57.723 34.615 0.00 0.00 0.00 3.07
2554 3013 6.860080 TCTTTTCTCTCCATCAAAATCATGC 58.140 36.000 0.00 0.00 0.00 4.06
2555 3014 5.587388 TTTCTCTCCATCAAAATCATGCC 57.413 39.130 0.00 0.00 0.00 4.40
2557 3016 4.204799 TCTCTCCATCAAAATCATGCCAG 58.795 43.478 0.00 0.00 0.00 4.85
2562 3021 6.834969 TCTCCATCAAAATCATGCCAGAATTA 59.165 34.615 0.00 0.00 0.00 1.40
2577 3036 6.538742 TGCCAGAATTACTGCACTAATCTAAC 59.461 38.462 0.00 0.00 44.52 2.34
2578 3037 6.763610 GCCAGAATTACTGCACTAATCTAACT 59.236 38.462 0.00 0.00 44.52 2.24
2579 3038 7.926555 GCCAGAATTACTGCACTAATCTAACTA 59.073 37.037 0.00 0.00 44.52 2.24
2622 3081 6.883756 TGCAAGGTTTTCTTTCTTTCCATTTT 59.116 30.769 0.00 0.00 32.41 1.82
2644 3103 6.767524 TTCAGTTGGACAAAAATGTAGTGT 57.232 33.333 0.00 0.00 0.00 3.55
2649 3108 6.377146 AGTTGGACAAAAATGTAGTGTGAAGT 59.623 34.615 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.147320 ACCCCATATGAGAGTCAAATCAATACA 60.147 37.037 3.65 0.00 0.00 2.29
50 51 5.655394 ACTCTGAGCCTATCCCACATTATA 58.345 41.667 4.19 0.00 0.00 0.98
68 69 6.183360 CCAATAATGACTTGGCTTGTACTCTG 60.183 42.308 0.00 0.00 36.98 3.35
72 73 5.897377 ACCAATAATGACTTGGCTTGTAC 57.103 39.130 2.07 0.00 45.83 2.90
105 106 3.394940 AGATCGTGAGGGGTAGAGACATA 59.605 47.826 0.00 0.00 0.00 2.29
106 107 2.175931 AGATCGTGAGGGGTAGAGACAT 59.824 50.000 0.00 0.00 0.00 3.06
117 118 7.364522 TCAAATTTAGTCAAAGATCGTGAGG 57.635 36.000 2.70 0.00 0.00 3.86
118 119 8.499162 ACTTCAAATTTAGTCAAAGATCGTGAG 58.501 33.333 2.70 0.00 0.00 3.51
122 123 7.895259 CGAGACTTCAAATTTAGTCAAAGATCG 59.105 37.037 18.78 15.04 42.51 3.69
128 129 6.764085 TCAACCGAGACTTCAAATTTAGTCAA 59.236 34.615 18.78 0.00 42.51 3.18
130 131 6.780706 TCAACCGAGACTTCAAATTTAGTC 57.219 37.500 11.60 11.60 40.82 2.59
218 219 9.884636 TGTCTTCATTAGATCCGAATTTTAAGA 57.115 29.630 0.00 0.00 34.79 2.10
221 222 8.559536 GCATGTCTTCATTAGATCCGAATTTTA 58.440 33.333 0.00 0.00 34.79 1.52
232 233 7.330262 TGTATTGTCTGCATGTCTTCATTAGA 58.670 34.615 0.00 0.00 31.15 2.10
233 234 7.543947 TGTATTGTCTGCATGTCTTCATTAG 57.456 36.000 0.00 0.00 31.15 1.73
235 236 7.400599 AATGTATTGTCTGCATGTCTTCATT 57.599 32.000 0.00 0.00 29.77 2.57
275 276 8.784994 CGTCTAAGTCTAAATAAGCCTAGATGA 58.215 37.037 0.00 0.00 0.00 2.92
325 327 5.552870 AAGACCCTCTCAACGCAATATAT 57.447 39.130 0.00 0.00 0.00 0.86
330 335 3.478857 TTAAAGACCCTCTCAACGCAA 57.521 42.857 0.00 0.00 0.00 4.85
375 568 6.688637 TTGAATGAGTTATCTGAAGCATGG 57.311 37.500 0.00 0.00 0.00 3.66
386 579 7.936584 TGAGTTTCGGTTTTTGAATGAGTTAT 58.063 30.769 0.00 0.00 0.00 1.89
387 580 7.323049 TGAGTTTCGGTTTTTGAATGAGTTA 57.677 32.000 0.00 0.00 0.00 2.24
391 584 9.587772 TTTTTATGAGTTTCGGTTTTTGAATGA 57.412 25.926 0.00 0.00 0.00 2.57
402 595 4.215399 TCTGCCTGTTTTTATGAGTTTCGG 59.785 41.667 0.00 0.00 0.00 4.30
410 603 9.599322 GAAATATATCGTCTGCCTGTTTTTATG 57.401 33.333 0.00 0.00 0.00 1.90
419 612 5.057149 GGTGTTGAAATATATCGTCTGCCT 58.943 41.667 0.00 0.00 0.00 4.75
521 716 3.873952 GCTCTCTCTCTCTCTCTTCAGAC 59.126 52.174 0.00 0.00 0.00 3.51
555 750 2.239654 ACACAGCTAGCTCTCTCTCTCT 59.760 50.000 16.15 0.00 0.00 3.10
559 754 0.817013 GCACACAGCTAGCTCTCTCT 59.183 55.000 16.15 0.00 41.15 3.10
578 773 1.321474 TTGCTCTTGCTCCAAACCAG 58.679 50.000 0.00 0.00 40.48 4.00
580 775 2.680577 CATTTGCTCTTGCTCCAAACC 58.319 47.619 0.00 0.00 40.48 3.27
581 776 2.064014 GCATTTGCTCTTGCTCCAAAC 58.936 47.619 0.00 0.00 40.48 2.93
816 1016 0.325203 AGGCAGAGAGAAGAGGGACC 60.325 60.000 0.00 0.00 0.00 4.46
872 1077 3.512516 GCAACAGATGAGCCGCCC 61.513 66.667 0.00 0.00 0.00 6.13
1013 1242 4.402155 TGGAACAAGACAAGCAAACTGAAT 59.598 37.500 0.00 0.00 31.92 2.57
1042 1271 0.818040 AGCAAACGGAACACCAGTCC 60.818 55.000 0.00 0.00 0.00 3.85
1044 1273 0.107410 TGAGCAAACGGAACACCAGT 60.107 50.000 0.00 0.00 0.00 4.00
1047 1276 2.793278 ATTTGAGCAAACGGAACACC 57.207 45.000 0.00 0.00 32.51 4.16
1054 1283 1.851666 ACGCACAAATTTGAGCAAACG 59.148 42.857 30.95 20.57 43.56 3.60
1065 1294 0.874390 ATTCAGCACGACGCACAAAT 59.126 45.000 0.00 0.00 46.13 2.32
1078 1307 7.131498 TGCAACAAATATCCAAAAATTCAGC 57.869 32.000 0.00 0.00 0.00 4.26
1090 1320 7.355332 ACAATCTTTTGCTGCAACAAATATC 57.645 32.000 15.72 0.00 39.18 1.63
1091 1321 6.369615 GGACAATCTTTTGCTGCAACAAATAT 59.630 34.615 15.72 9.86 39.18 1.28
1291 1540 3.533068 TGATGATCTTTTCCCCCTCCATT 59.467 43.478 0.00 0.00 0.00 3.16
1384 1633 3.733960 CCGGACGACACGCTGAGA 61.734 66.667 0.00 0.00 0.00 3.27
1657 2038 3.181447 ACATCTACATAATGCTGCAGCCT 60.181 43.478 34.64 23.69 41.18 4.58
1682 2082 6.929606 ACGCATTATCTCTCCCTAATTAACAC 59.070 38.462 0.00 0.00 0.00 3.32
1715 2128 3.699134 CTAAACCCCGGCCCTGCTC 62.699 68.421 0.00 0.00 0.00 4.26
1716 2129 3.728373 CTAAACCCCGGCCCTGCT 61.728 66.667 0.00 0.00 0.00 4.24
1717 2130 4.815108 CCTAAACCCCGGCCCTGC 62.815 72.222 0.00 0.00 0.00 4.85
1749 2178 1.002134 CGGCCAACTTCTGGGTCAT 60.002 57.895 2.24 0.00 46.54 3.06
1766 2196 1.021202 AACATCGCTCTCCTCTCTCG 58.979 55.000 0.00 0.00 0.00 4.04
1824 2263 3.480505 ACCAACCAACCTGTACTGTAC 57.519 47.619 10.98 10.98 0.00 2.90
1825 2264 3.433882 CCAACCAACCAACCTGTACTGTA 60.434 47.826 0.00 0.00 0.00 2.74
1826 2265 2.650322 CAACCAACCAACCTGTACTGT 58.350 47.619 0.00 0.00 0.00 3.55
1827 2266 1.953686 CCAACCAACCAACCTGTACTG 59.046 52.381 0.00 0.00 0.00 2.74
1828 2267 1.847737 TCCAACCAACCAACCTGTACT 59.152 47.619 0.00 0.00 0.00 2.73
1829 2268 2.351706 TCCAACCAACCAACCTGTAC 57.648 50.000 0.00 0.00 0.00 2.90
1830 2269 2.443632 TGATCCAACCAACCAACCTGTA 59.556 45.455 0.00 0.00 0.00 2.74
1831 2270 1.216678 TGATCCAACCAACCAACCTGT 59.783 47.619 0.00 0.00 0.00 4.00
1832 2271 1.888512 CTGATCCAACCAACCAACCTG 59.111 52.381 0.00 0.00 0.00 4.00
1833 2272 1.823250 GCTGATCCAACCAACCAACCT 60.823 52.381 0.00 0.00 0.00 3.50
1834 2273 0.603065 GCTGATCCAACCAACCAACC 59.397 55.000 0.00 0.00 0.00 3.77
1835 2274 1.327303 TGCTGATCCAACCAACCAAC 58.673 50.000 0.00 0.00 0.00 3.77
1836 2275 2.079170 TTGCTGATCCAACCAACCAA 57.921 45.000 0.00 0.00 0.00 3.67
1837 2276 1.894466 CATTGCTGATCCAACCAACCA 59.106 47.619 0.00 0.00 0.00 3.67
1984 2426 6.656314 TTTTGATACATCTTGCGTCGTATT 57.344 33.333 0.00 0.00 0.00 1.89
1985 2427 6.478673 TGATTTTGATACATCTTGCGTCGTAT 59.521 34.615 0.00 0.00 0.00 3.06
1990 2432 6.489675 GTCATGATTTTGATACATCTTGCGT 58.510 36.000 0.00 0.00 0.00 5.24
1994 2436 5.009010 GCCCGTCATGATTTTGATACATCTT 59.991 40.000 0.00 0.00 0.00 2.40
2000 2442 6.038161 CAGTTAAGCCCGTCATGATTTTGATA 59.962 38.462 0.00 0.00 0.00 2.15
2045 2489 3.117738 CAGATTCCCAAAGATAGGGCTGT 60.118 47.826 0.00 0.00 46.36 4.40
2055 2499 5.181690 TCAAAAACGACAGATTCCCAAAG 57.818 39.130 0.00 0.00 0.00 2.77
2062 2506 5.224562 TCGTGTTTCAAAAACGACAGATT 57.775 34.783 11.66 0.00 41.08 2.40
2063 2507 4.868450 TCGTGTTTCAAAAACGACAGAT 57.132 36.364 11.66 0.00 41.08 2.90
2066 2510 3.426426 CCCTTCGTGTTTCAAAAACGACA 60.426 43.478 15.28 6.34 45.20 4.35
2076 2520 3.488553 CCTGTTTTGACCCTTCGTGTTTC 60.489 47.826 0.00 0.00 0.00 2.78
2077 2521 2.425668 CCTGTTTTGACCCTTCGTGTTT 59.574 45.455 0.00 0.00 0.00 2.83
2079 2523 1.675552 CCTGTTTTGACCCTTCGTGT 58.324 50.000 0.00 0.00 0.00 4.49
2086 2530 0.895559 CTGGAGGCCTGTTTTGACCC 60.896 60.000 12.00 2.07 0.00 4.46
2087 2531 1.527433 GCTGGAGGCCTGTTTTGACC 61.527 60.000 12.00 3.01 34.27 4.02
2105 2550 4.382345 AGAAATTAAGATTGGCAGCTGC 57.618 40.909 30.88 30.88 41.14 5.25
2108 2553 8.532977 TTACAAAAGAAATTAAGATTGGCAGC 57.467 30.769 0.00 0.00 0.00 5.25
2124 2569 7.151976 GGCTGCCTAATTTTTCTTACAAAAGA 58.848 34.615 12.43 0.00 40.03 2.52
2125 2570 6.368791 GGGCTGCCTAATTTTTCTTACAAAAG 59.631 38.462 19.68 0.00 0.00 2.27
2126 2571 6.227522 GGGCTGCCTAATTTTTCTTACAAAA 58.772 36.000 19.68 0.00 0.00 2.44
2142 2594 1.303643 CCTCTTTTTCGGGCTGCCT 60.304 57.895 19.68 0.00 0.00 4.75
2151 2603 1.873591 TGCACGAGAAGCCTCTTTTTC 59.126 47.619 0.00 0.00 37.28 2.29
2155 2607 1.375268 GCTGCACGAGAAGCCTCTT 60.375 57.895 0.52 0.00 40.87 2.85
2163 2615 0.597568 CCCAAATTTGCTGCACGAGA 59.402 50.000 12.92 0.00 0.00 4.04
2171 2623 1.202794 CCAAAGTGCCCCAAATTTGCT 60.203 47.619 12.92 1.14 32.54 3.91
2177 2629 2.139484 CCTGCCAAAGTGCCCCAAA 61.139 57.895 0.00 0.00 0.00 3.28
2189 2641 4.940593 GTTTTTGCGCGCCTGCCA 62.941 61.111 30.77 6.23 38.08 4.92
2199 2651 0.526739 AACCAACCTCGCGTTTTTGC 60.527 50.000 5.77 0.00 29.93 3.68
2204 2656 2.248835 CCGAAACCAACCTCGCGTT 61.249 57.895 5.77 0.00 33.70 4.84
2206 2658 2.356553 TCCGAAACCAACCTCGCG 60.357 61.111 0.00 0.00 33.70 5.87
2208 2660 2.664436 GCGTCCGAAACCAACCTCG 61.664 63.158 0.00 0.00 34.83 4.63
2213 2665 2.975799 GCAGGCGTCCGAAACCAA 60.976 61.111 0.00 0.00 0.00 3.67
2216 2668 2.480555 CATGCAGGCGTCCGAAAC 59.519 61.111 0.00 0.00 0.00 2.78
2227 2679 1.091771 AGGTTTCCGATCGCATGCAG 61.092 55.000 19.57 10.78 0.00 4.41
2230 2682 4.349663 TTTAAAGGTTTCCGATCGCATG 57.650 40.909 10.32 0.00 0.00 4.06
2235 2687 4.640647 AGGCAGATTTAAAGGTTTCCGATC 59.359 41.667 0.00 0.00 0.00 3.69
2236 2688 4.399303 CAGGCAGATTTAAAGGTTTCCGAT 59.601 41.667 0.00 0.00 0.00 4.18
2240 2692 3.368427 GGGCAGGCAGATTTAAAGGTTTC 60.368 47.826 0.00 0.00 0.00 2.78
2246 2698 1.319614 GGCGGGCAGGCAGATTTAAA 61.320 55.000 6.27 0.00 45.92 1.52
2248 2700 2.124320 GGCGGGCAGGCAGATTTA 60.124 61.111 6.27 0.00 45.92 1.40
2268 2720 3.204827 GGCCATGGTACGCAGCAG 61.205 66.667 14.67 0.00 35.19 4.24
2276 2728 3.161450 GAGGAGCCGGCCATGGTA 61.161 66.667 26.15 0.00 0.00 3.25
2300 2752 2.915659 CTATAGGGGTCGGCGGCA 60.916 66.667 15.59 0.00 0.00 5.69
2363 2815 2.370281 TTGCACGAAACAAGGCAAAA 57.630 40.000 0.00 0.00 42.66 2.44
2405 2861 3.370953 GCCATCTCCAACAACAGACCTAT 60.371 47.826 0.00 0.00 0.00 2.57
2408 2864 1.168714 GCCATCTCCAACAACAGACC 58.831 55.000 0.00 0.00 0.00 3.85
2410 2866 1.421268 AGTGCCATCTCCAACAACAGA 59.579 47.619 0.00 0.00 0.00 3.41
2420 2876 2.084844 CACGAGCAAGTGCCATCTC 58.915 57.895 0.00 0.00 43.38 2.75
2451 2907 6.991531 TGAGCAAGATTTAAGGCACAAAAATT 59.008 30.769 0.00 0.00 0.00 1.82
2452 2908 6.523840 TGAGCAAGATTTAAGGCACAAAAAT 58.476 32.000 0.00 0.00 0.00 1.82
2456 2912 4.766373 TGATGAGCAAGATTTAAGGCACAA 59.234 37.500 0.00 0.00 31.06 3.33
2463 2919 7.538334 CACGAAAACATGATGAGCAAGATTTAA 59.462 33.333 0.00 0.00 0.00 1.52
2464 2920 7.022979 CACGAAAACATGATGAGCAAGATTTA 58.977 34.615 0.00 0.00 0.00 1.40
2469 2925 4.151258 ACACGAAAACATGATGAGCAAG 57.849 40.909 0.00 0.00 0.00 4.01
2472 2928 2.483877 TGGACACGAAAACATGATGAGC 59.516 45.455 0.00 0.00 0.00 4.26
2473 2929 4.747540 TTGGACACGAAAACATGATGAG 57.252 40.909 0.00 0.00 0.00 2.90
2474 2930 5.506686 TTTTGGACACGAAAACATGATGA 57.493 34.783 0.00 0.00 0.00 2.92
2476 2932 7.090173 CCTATTTTTGGACACGAAAACATGAT 58.910 34.615 0.00 0.00 41.47 2.45
2477 2933 6.442952 CCTATTTTTGGACACGAAAACATGA 58.557 36.000 0.00 0.00 41.47 3.07
2490 2949 4.962995 TCCAACAACAACCCTATTTTTGGA 59.037 37.500 1.44 1.44 39.11 3.53
2520 2979 8.195165 TGATGGAGAGAAAAGAGAGACTTTAA 57.805 34.615 0.00 0.00 46.55 1.52
2530 2989 6.127535 GGCATGATTTTGATGGAGAGAAAAGA 60.128 38.462 0.00 0.00 0.00 2.52
2537 2996 4.239428 TCTGGCATGATTTTGATGGAGA 57.761 40.909 0.00 0.00 0.00 3.71
2539 2998 5.943349 AATTCTGGCATGATTTTGATGGA 57.057 34.783 0.00 0.00 0.00 3.41
2549 3008 3.354948 AGTGCAGTAATTCTGGCATGA 57.645 42.857 0.00 0.00 43.78 3.07
2552 3011 5.102953 AGATTAGTGCAGTAATTCTGGCA 57.897 39.130 24.18 0.00 43.78 4.92
2553 3012 6.763610 AGTTAGATTAGTGCAGTAATTCTGGC 59.236 38.462 24.18 13.19 43.78 4.85
2554 3013 9.817809 TTAGTTAGATTAGTGCAGTAATTCTGG 57.182 33.333 24.18 0.00 43.78 3.86
2598 3057 6.925610 AAATGGAAAGAAAGAAAACCTTGC 57.074 33.333 0.00 0.00 34.79 4.01
2603 3062 8.390354 CCAACTGAAAATGGAAAGAAAGAAAAC 58.610 33.333 0.00 0.00 39.12 2.43
2604 3063 8.317679 TCCAACTGAAAATGGAAAGAAAGAAAA 58.682 29.630 0.00 0.00 42.61 2.29
2608 3067 6.572519 TGTCCAACTGAAAATGGAAAGAAAG 58.427 36.000 0.00 0.00 46.78 2.62
2622 3081 5.883115 TCACACTACATTTTTGTCCAACTGA 59.117 36.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.