Multiple sequence alignment - TraesCS1B01G446900

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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 TraesCS1B01G446900 chr1B 100.000 2640 0 0 1 2640 666827797 666825158 0.000000e+00 4876
1 TraesCS1B01G446900 chr1A 89.184 1091 54 27 654 1706 574938993 574937929 0.000000e+00 1303
2 TraesCS1B01G446900 chr1A 91.033 368 24 7 1 362 574940056 574939692 3.050000e-134 488
3 TraesCS1B01G446900 chr1A 92.254 142 9 1 2499 2640 574936959 574936820 1.600000e-47 200
4 TraesCS1B01G446900 chr1A 85.217 115 10 5 2167 2280 574937385 574937277 7.720000e-21 111
5 TraesCS1B01G446900 chr1A 81.890 127 16 5 393 517 544729589 544729468 1.670000e-17 100
6 TraesCS1B01G446900 chr1A 79.762 168 10 8 1859 2002 574937860 574937693 1.670000e-17 100
7 TraesCS1B01G446900 chr1D 88.683 972 51 20 1702 2640 478819173 478818228 0.000000e+00 1131
8 TraesCS1B01G446900 chr1D 92.384 604 22 11 1107 1706 478820067 478819484 0.000000e+00 839
9 TraesCS1B01G446900 chr1D 83.333 462 43 20 654 1105 478820555 478820118 1.900000e-106 396
10 TraesCS1B01G446900 chr1D 84.341 364 31 14 2 358 478821617 478821273 1.510000e-87 333
11 TraesCS1B01G446900 chr1D 83.721 129 14 4 393 518 449586865 449586741 5.970000e-22 115
12 TraesCS1B01G446900 chr7A 75.850 294 45 18 233 517 466201178 466200902 2.760000e-25 126


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 TraesCS1B01G446900 chr1B 666825158 666827797 2639 True 4876.00 4876 100.00000 1 2640 1 chr1B.!!$R1 2639
1 TraesCS1B01G446900 chr1A 574936820 574940056 3236 True 440.40 1303 87.49000 1 2640 5 chr1A.!!$R2 2639
2 TraesCS1B01G446900 chr1D 478818228 478821617 3389 True 674.75 1131 87.18525 2 2640 4 chr1D.!!$R2 2638

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
921 1410 0.107459 GCCACCTTCCATCACTCTCC 60.107 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 2666 0.037605 CACTCCCCCGTTACAGTGTC 60.038 60.0 0.0 0.0 33.03 3.67 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
44 45 2.851263 TTACACACACCCTGATCCAC 57.149 50.000 0.00 0.00 0.00 4.02
51 52 1.004745 ACACCCTGATCCACCATCAAC 59.995 52.381 0.00 0.00 41.25 3.18
65 66 4.326766 CAACGTTGCGTGGCCCAG 62.327 66.667 16.51 0.00 39.99 4.45
123 124 2.676471 GCAATTGCGGTCCCAGGT 60.676 61.111 15.87 0.00 0.00 4.00
124 125 2.700773 GCAATTGCGGTCCCAGGTC 61.701 63.158 15.87 0.00 0.00 3.85
125 126 2.046285 CAATTGCGGTCCCAGGTCC 61.046 63.158 0.00 0.00 0.00 4.46
127 128 2.764637 AATTGCGGTCCCAGGTCCAC 62.765 60.000 0.88 0.00 0.00 4.02
130 131 2.038329 CGGTCCCAGGTCCACCTA 59.962 66.667 0.00 0.00 46.65 3.08
131 132 1.611261 CGGTCCCAGGTCCACCTAA 60.611 63.158 0.00 0.00 46.65 2.69
132 133 1.196104 CGGTCCCAGGTCCACCTAAA 61.196 60.000 0.00 0.00 46.65 1.85
158 163 6.884280 ACATTCCTATTAGCAATTGCCTAC 57.116 37.500 26.45 0.00 43.38 3.18
212 217 2.986306 GCTTGTTGCCGCTCATGCT 61.986 57.895 14.59 0.00 36.97 3.79
217 222 4.765449 TGCCGCTCATGCTTCGCT 62.765 61.111 0.00 0.00 36.97 4.93
387 456 9.932207 TCTTTGTCAGTTTTAATCGGTATCTTA 57.068 29.630 0.00 0.00 0.00 2.10
391 460 9.362539 TGTCAGTTTTAATCGGTATCTTAGTTC 57.637 33.333 0.00 0.00 0.00 3.01
405 474 9.953697 GGTATCTTAGTTCTAACACATGTCTAG 57.046 37.037 0.00 0.00 0.00 2.43
420 489 6.481976 CACATGTCTAGTTTTGGTGAGTACAA 59.518 38.462 0.00 0.00 0.00 2.41
453 522 0.586319 AGCGGACACGTGAAACATTG 59.414 50.000 25.01 5.50 43.45 2.82
461 532 5.338559 GGACACGTGAAACATTGTTTTATCG 59.661 40.000 25.01 19.09 33.25 2.92
529 998 8.243289 AGATGTTTTTGAAAAGCGGAAATATG 57.757 30.769 0.26 0.00 0.00 1.78
534 1003 9.497030 GTTTTTGAAAAGCGGAAATATGTTTTT 57.503 25.926 0.00 0.00 32.31 1.94
544 1013 7.120579 AGCGGAAATATGTTTTTCATAGTCACA 59.879 33.333 0.00 0.00 41.55 3.58
645 1115 8.736751 TTCATGTTTCTAAAGTTTATTTCCGC 57.263 30.769 0.00 0.00 0.00 5.54
646 1116 7.877003 TCATGTTTCTAAAGTTTATTTCCGCA 58.123 30.769 0.00 0.00 0.00 5.69
647 1117 8.353684 TCATGTTTCTAAAGTTTATTTCCGCAA 58.646 29.630 0.00 0.00 0.00 4.85
648 1118 8.973378 CATGTTTCTAAAGTTTATTTCCGCAAA 58.027 29.630 0.00 0.00 0.00 3.68
649 1119 8.928270 TGTTTCTAAAGTTTATTTCCGCAAAA 57.072 26.923 0.00 0.00 0.00 2.44
650 1120 9.367444 TGTTTCTAAAGTTTATTTCCGCAAAAA 57.633 25.926 0.00 0.00 0.00 1.94
776 1246 1.973515 AGATCAGCAGGACAAGTCACA 59.026 47.619 2.29 0.00 0.00 3.58
777 1247 2.072298 GATCAGCAGGACAAGTCACAC 58.928 52.381 2.29 0.00 0.00 3.82
823 1311 1.004320 CCAATGGTCCCGTCACGAA 60.004 57.895 0.00 0.00 0.00 3.85
828 1316 0.244450 TGGTCCCGTCACGAACATAC 59.756 55.000 0.00 0.00 0.00 2.39
830 1318 1.745087 GGTCCCGTCACGAACATACTA 59.255 52.381 0.00 0.00 0.00 1.82
872 1360 4.028490 TTGGCCCAATCCTCGCGT 62.028 61.111 5.77 0.00 0.00 6.01
921 1410 0.107459 GCCACCTTCCATCACTCTCC 60.107 60.000 0.00 0.00 0.00 3.71
947 1436 4.278513 CCCCAACCTTCCACCGCA 62.279 66.667 0.00 0.00 0.00 5.69
985 1474 4.838152 CCATCGCCACCTCACCCG 62.838 72.222 0.00 0.00 0.00 5.28
1084 1586 2.366916 ACTCAGAGTTCCAGACCAACAG 59.633 50.000 0.00 0.00 0.00 3.16
1086 1588 1.071385 CAGAGTTCCAGACCAACAGCT 59.929 52.381 0.00 0.00 0.00 4.24
1415 1966 1.043673 CCCCAACTACGAGGAGGAGG 61.044 65.000 0.00 0.00 34.15 4.30
1416 1967 0.033405 CCCAACTACGAGGAGGAGGA 60.033 60.000 0.00 0.00 34.15 3.71
1417 1968 1.394618 CCAACTACGAGGAGGAGGAG 58.605 60.000 0.00 0.00 34.15 3.69
1423 1974 1.308326 CGAGGAGGAGGAGGAAGGT 59.692 63.158 0.00 0.00 0.00 3.50
1428 1979 3.412408 GGAGGAGGAAGGTGGGGC 61.412 72.222 0.00 0.00 0.00 5.80
1541 2104 2.203640 AGGAGCACGACCACCAGA 60.204 61.111 0.00 0.00 0.00 3.86
1592 2155 2.469886 TGTCGTGTTGATCTTCGTTTCG 59.530 45.455 0.00 0.00 0.00 3.46
1597 2164 2.475111 TGTTGATCTTCGTTTCGTCTGC 59.525 45.455 0.00 0.00 0.00 4.26
1606 2173 1.300931 TTTCGTCTGCGCTCTGCTT 60.301 52.632 9.73 0.00 46.63 3.91
1607 2174 0.038618 TTTCGTCTGCGCTCTGCTTA 60.039 50.000 9.73 0.00 46.63 3.09
1608 2175 0.732880 TTCGTCTGCGCTCTGCTTAC 60.733 55.000 9.73 0.00 46.63 2.34
1609 2176 2.161486 CGTCTGCGCTCTGCTTACC 61.161 63.158 9.73 0.00 46.63 2.85
1610 2177 1.079819 GTCTGCGCTCTGCTTACCA 60.080 57.895 9.73 0.00 46.63 3.25
1611 2178 0.670546 GTCTGCGCTCTGCTTACCAA 60.671 55.000 9.73 0.00 46.63 3.67
1682 2250 5.105146 AGTGGATCAGTTAACCTCTGTCATC 60.105 44.000 0.88 0.00 34.86 2.92
1712 2595 4.699257 CCCTCTGGTTTCTTCTGATTCTTG 59.301 45.833 0.00 0.00 0.00 3.02
1732 2615 2.034939 TGCTCCACTGATTTTGTGCTTG 59.965 45.455 0.00 0.00 34.38 4.01
1747 2630 3.274288 GTGCTTGGATGTCTTAAGGAGG 58.726 50.000 1.85 0.00 0.00 4.30
1752 2635 4.620086 TGGATGTCTTAAGGAGGGAGTA 57.380 45.455 1.85 0.00 0.00 2.59
1783 2666 2.399611 GATTTCAAGCGGCCGTCG 59.600 61.111 28.70 15.55 42.76 5.12
1784 2667 2.047655 ATTTCAAGCGGCCGTCGA 60.048 55.556 28.70 17.75 42.43 4.20
1785 2668 2.292802 GATTTCAAGCGGCCGTCGAC 62.293 60.000 28.70 10.05 42.43 4.20
1792 2675 2.256158 CGGCCGTCGACACTGTAA 59.744 61.111 19.50 0.00 42.43 2.41
1793 2676 2.084681 CGGCCGTCGACACTGTAAC 61.085 63.158 19.50 0.00 42.43 2.50
1794 2677 2.084681 GGCCGTCGACACTGTAACG 61.085 63.158 17.16 8.82 35.01 3.18
1798 2681 1.080298 GTCGACACTGTAACGGGGG 60.080 63.158 11.55 0.00 0.00 5.40
1800 2683 1.214589 CGACACTGTAACGGGGGAG 59.785 63.158 0.00 0.00 0.00 4.30
1801 2684 1.530013 CGACACTGTAACGGGGGAGT 61.530 60.000 0.00 0.00 0.00 3.85
1804 2687 2.267961 CTGTAACGGGGGAGTGGC 59.732 66.667 0.00 0.00 0.00 5.01
1805 2688 2.203877 TGTAACGGGGGAGTGGCT 60.204 61.111 0.00 0.00 0.00 4.75
1806 2689 2.240162 CTGTAACGGGGGAGTGGCTC 62.240 65.000 0.00 0.00 0.00 4.70
1829 2723 2.208431 GCTAACAGCCAGAGCATACAG 58.792 52.381 0.00 0.00 43.56 2.74
1838 2732 2.102252 CCAGAGCATACAGGGAACTCTC 59.898 54.545 0.00 0.00 40.21 3.20
1839 2733 2.762887 CAGAGCATACAGGGAACTCTCA 59.237 50.000 0.00 0.00 40.21 3.27
1848 2743 3.007398 ACAGGGAACTCTCAATGTCTGAC 59.993 47.826 0.00 0.00 40.21 3.51
1898 2800 9.831737 CAAACCTCTCATCTAACAATTAAACAG 57.168 33.333 0.00 0.00 0.00 3.16
2002 2930 3.044305 GGCACACACGGTCAGAGC 61.044 66.667 0.00 0.00 0.00 4.09
2003 2931 2.280119 GCACACACGGTCAGAGCA 60.280 61.111 0.00 0.00 0.00 4.26
2004 2932 2.313172 GCACACACGGTCAGAGCAG 61.313 63.158 0.00 0.00 0.00 4.24
2005 2933 1.363807 CACACACGGTCAGAGCAGA 59.636 57.895 0.00 0.00 0.00 4.26
2006 2934 0.665670 CACACACGGTCAGAGCAGAG 60.666 60.000 0.00 0.00 0.00 3.35
2007 2935 1.109920 ACACACGGTCAGAGCAGAGT 61.110 55.000 0.00 0.00 0.00 3.24
2008 2936 0.032678 CACACGGTCAGAGCAGAGTT 59.967 55.000 0.00 0.00 0.00 3.01
2009 2937 0.315568 ACACGGTCAGAGCAGAGTTC 59.684 55.000 0.00 0.00 0.00 3.01
2010 2938 0.600557 CACGGTCAGAGCAGAGTTCT 59.399 55.000 0.00 0.00 0.00 3.01
2020 2948 5.069648 TCAGAGCAGAGTTCTTTCTCTTCAA 59.930 40.000 7.56 0.00 42.10 2.69
2021 2949 5.757320 CAGAGCAGAGTTCTTTCTCTTCAAA 59.243 40.000 7.56 0.00 42.10 2.69
2136 3186 1.846973 GGGGGCTGGGGAGAAATAG 59.153 63.158 0.00 0.00 0.00 1.73
2155 3205 3.483255 AGGAGTCTTTAGGGCTTCTCT 57.517 47.619 0.00 0.00 0.00 3.10
2156 3206 3.797312 AGGAGTCTTTAGGGCTTCTCTT 58.203 45.455 0.00 0.00 0.00 2.85
2157 3207 3.772572 AGGAGTCTTTAGGGCTTCTCTTC 59.227 47.826 0.00 0.00 0.00 2.87
2158 3208 3.772572 GGAGTCTTTAGGGCTTCTCTTCT 59.227 47.826 0.00 0.00 0.00 2.85
2163 3262 4.785376 TCTTTAGGGCTTCTCTTCTCCAAT 59.215 41.667 0.00 0.00 0.00 3.16
2197 3296 5.063880 CCCTGCCAAGATATTAAGTGGTAC 58.936 45.833 0.00 0.00 33.43 3.34
2229 3328 9.206870 CACTTTATTTATTGCCAAAACAGATGT 57.793 29.630 0.00 0.00 0.00 3.06
2231 3330 9.421806 CTTTATTTATTGCCAAAACAGATGTCA 57.578 29.630 0.00 0.00 0.00 3.58
2238 3337 8.674263 ATTGCCAAAACAGATGTCAAAAATTA 57.326 26.923 0.00 0.00 0.00 1.40
2239 3338 8.674263 TTGCCAAAACAGATGTCAAAAATTAT 57.326 26.923 0.00 0.00 0.00 1.28
2240 3339 9.770097 TTGCCAAAACAGATGTCAAAAATTATA 57.230 25.926 0.00 0.00 0.00 0.98
2241 3340 9.941325 TGCCAAAACAGATGTCAAAAATTATAT 57.059 25.926 0.00 0.00 0.00 0.86
2311 3410 6.633500 TTTCCATTGGTGTACTTTTCAGAG 57.367 37.500 1.86 0.00 0.00 3.35
2315 3414 5.997746 CCATTGGTGTACTTTTCAGAGAAGA 59.002 40.000 7.70 0.00 0.00 2.87
2316 3415 6.656693 CCATTGGTGTACTTTTCAGAGAAGAT 59.343 38.462 7.70 0.00 0.00 2.40
2318 3417 9.219603 CATTGGTGTACTTTTCAGAGAAGATAA 57.780 33.333 7.70 0.00 0.00 1.75
2320 3419 7.963532 TGGTGTACTTTTCAGAGAAGATAAGT 58.036 34.615 7.70 0.00 40.94 2.24
2321 3420 8.088981 TGGTGTACTTTTCAGAGAAGATAAGTC 58.911 37.037 7.70 0.00 39.44 3.01
2322 3421 8.088981 GGTGTACTTTTCAGAGAAGATAAGTCA 58.911 37.037 7.70 0.00 39.44 3.41
2323 3422 9.477484 GTGTACTTTTCAGAGAAGATAAGTCAA 57.523 33.333 7.70 0.00 39.44 3.18
2324 3423 9.698309 TGTACTTTTCAGAGAAGATAAGTCAAG 57.302 33.333 7.70 0.00 39.44 3.02
2325 3424 9.915629 GTACTTTTCAGAGAAGATAAGTCAAGA 57.084 33.333 7.70 0.00 39.44 3.02
2327 3426 8.093927 ACTTTTCAGAGAAGATAAGTCAAGAGG 58.906 37.037 7.70 0.00 35.73 3.69
2328 3427 6.537453 TTCAGAGAAGATAAGTCAAGAGGG 57.463 41.667 0.00 0.00 0.00 4.30
2329 3428 4.404073 TCAGAGAAGATAAGTCAAGAGGGC 59.596 45.833 0.00 0.00 0.00 5.19
2371 3470 2.910688 AGAGACGGCTTCTGAAAACA 57.089 45.000 0.00 0.00 33.22 2.83
2490 3590 4.518211 AGTTTGAGATTCAGCAAGGAACTG 59.482 41.667 0.00 0.00 40.86 3.16
2532 3820 8.821894 GTTTTCTTTAGCTACTGATGATACCTG 58.178 37.037 0.00 0.00 0.00 4.00
2582 3870 2.234908 AGATGTGTAGGAAGAGTGGTGC 59.765 50.000 0.00 0.00 0.00 5.01
2583 3871 1.717032 TGTGTAGGAAGAGTGGTGCT 58.283 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.126888 GCCACGCAACGTTGATGG 60.127 61.111 32.25 32.25 38.32 3.51
65 66 4.469657 TCATATGTGATTTTAGGTGGGCC 58.530 43.478 1.90 0.00 0.00 5.80
120 121 7.707467 ATAGGAATGTAATTTAGGTGGACCT 57.293 36.000 3.29 3.29 43.42 3.85
122 123 9.000486 GCTAATAGGAATGTAATTTAGGTGGAC 58.000 37.037 0.00 0.00 36.07 4.02
123 124 8.719596 TGCTAATAGGAATGTAATTTAGGTGGA 58.280 33.333 0.00 0.00 36.07 4.02
124 125 8.918202 TGCTAATAGGAATGTAATTTAGGTGG 57.082 34.615 0.00 0.00 36.07 4.61
130 131 8.927411 AGGCAATTGCTAATAGGAATGTAATTT 58.073 29.630 28.42 0.00 36.36 1.82
131 132 8.482852 AGGCAATTGCTAATAGGAATGTAATT 57.517 30.769 28.42 0.00 36.36 1.40
132 133 9.014297 GTAGGCAATTGCTAATAGGAATGTAAT 57.986 33.333 28.42 0.00 36.36 1.89
158 163 2.419198 CCCCGATTCTCTCGCCTG 59.581 66.667 0.00 0.00 46.25 4.85
212 217 0.388134 GTGAGCGAACCTACAGCGAA 60.388 55.000 0.00 0.00 35.78 4.70
217 222 2.085320 GAGAGAGTGAGCGAACCTACA 58.915 52.381 0.00 0.00 0.00 2.74
387 456 7.226720 CACCAAAACTAGACATGTGTTAGAACT 59.773 37.037 16.84 4.10 0.00 3.01
391 460 6.706270 ACTCACCAAAACTAGACATGTGTTAG 59.294 38.462 1.15 7.75 0.00 2.34
420 489 4.608890 CGTGTCCGCTAAAAACGTACATTT 60.609 41.667 0.00 0.00 31.97 2.32
453 522 8.568732 TTGAAAATGTCCAAAGTCGATAAAAC 57.431 30.769 0.00 0.00 0.00 2.43
461 532 9.643693 ATCATGTATTTGAAAATGTCCAAAGTC 57.356 29.630 0.00 0.00 35.97 3.01
776 1246 2.048503 GTGCCGCCTACAGAACGT 60.049 61.111 0.00 0.00 0.00 3.99
777 1247 0.179121 TATGTGCCGCCTACAGAACG 60.179 55.000 0.00 0.00 0.00 3.95
814 1302 1.844357 CGCTTAGTATGTTCGTGACGG 59.156 52.381 4.70 0.00 0.00 4.79
823 1311 0.459585 CCACGCCACGCTTAGTATGT 60.460 55.000 0.00 0.00 0.00 2.29
852 1340 3.508840 CGAGGATTGGGCCAACGC 61.509 66.667 23.59 16.50 0.00 4.84
853 1341 3.508840 GCGAGGATTGGGCCAACG 61.509 66.667 23.59 20.99 34.72 4.10
854 1342 3.508840 CGCGAGGATTGGGCCAAC 61.509 66.667 23.59 15.15 0.00 3.77
855 1343 3.969250 GACGCGAGGATTGGGCCAA 62.969 63.158 23.33 23.33 35.50 4.52
856 1344 4.467084 GACGCGAGGATTGGGCCA 62.467 66.667 15.93 0.00 35.50 5.36
859 1347 4.143333 ACGGACGCGAGGATTGGG 62.143 66.667 15.93 0.00 38.61 4.12
863 1351 2.321263 TAGAGGACGGACGCGAGGAT 62.321 60.000 15.93 0.00 0.00 3.24
872 1360 0.818445 GGCGACATCTAGAGGACGGA 60.818 60.000 25.48 0.00 31.78 4.69
921 1410 0.615850 GAAGGTTGGGGAGGAGTCTG 59.384 60.000 0.00 0.00 0.00 3.51
947 1436 1.003812 AGGAGTCTAGAGAGTGCGTGT 59.996 52.381 0.00 0.00 40.25 4.49
998 1487 2.430367 GGCGGGGCTTATGTAGGG 59.570 66.667 0.00 0.00 0.00 3.53
1036 1525 1.139498 TGTGGGTGGGATGTGATGGT 61.139 55.000 0.00 0.00 0.00 3.55
1084 1586 1.318576 GAGCTCTCCTCTCCTGTAGC 58.681 60.000 6.43 0.00 37.60 3.58
1086 1588 1.636003 TGTGAGCTCTCCTCTCCTGTA 59.364 52.381 16.19 0.00 41.35 2.74
1415 1966 4.785453 CTGCGCCCCACCTTCCTC 62.785 72.222 4.18 0.00 0.00 3.71
1440 1991 4.388499 CCACCTCCCCGACAACCG 62.388 72.222 0.00 0.00 38.18 4.44
1443 1994 2.606519 CCTCCACCTCCCCGACAA 60.607 66.667 0.00 0.00 0.00 3.18
1444 1995 3.899545 GACCTCCACCTCCCCGACA 62.900 68.421 0.00 0.00 0.00 4.35
1528 2091 0.389948 CCTACTTCTGGTGGTCGTGC 60.390 60.000 0.00 0.00 0.00 5.34
1541 2104 1.134965 GCACACGATCAGCTCCTACTT 60.135 52.381 0.00 0.00 0.00 2.24
1592 2155 0.670546 TTGGTAAGCAGAGCGCAGAC 60.671 55.000 11.47 0.00 46.13 3.51
1597 2164 2.309528 TGGTATTGGTAAGCAGAGCG 57.690 50.000 0.00 0.00 0.00 5.03
1606 2173 3.961849 ACACACATGCATGGTATTGGTA 58.038 40.909 29.41 0.00 0.00 3.25
1607 2174 2.806434 ACACACATGCATGGTATTGGT 58.194 42.857 29.41 15.35 0.00 3.67
1608 2175 4.157472 TGTTACACACATGCATGGTATTGG 59.843 41.667 29.41 14.77 0.00 3.16
1609 2176 5.307926 TGTTACACACATGCATGGTATTG 57.692 39.130 29.41 20.28 0.00 1.90
1610 2177 5.973899 TTGTTACACACATGCATGGTATT 57.026 34.783 29.41 13.86 34.43 1.89
1611 2178 5.973899 TTTGTTACACACATGCATGGTAT 57.026 34.783 29.41 16.25 34.43 2.73
1635 2202 9.599322 CACTTCCACGCTTGATTATTATTTATC 57.401 33.333 0.00 0.00 0.00 1.75
1637 2204 7.771361 TCCACTTCCACGCTTGATTATTATTTA 59.229 33.333 0.00 0.00 0.00 1.40
1682 2250 2.431954 AGAAACCAGAGGGATGCATG 57.568 50.000 2.46 0.00 38.05 4.06
1712 2595 2.608752 CCAAGCACAAAATCAGTGGAGC 60.609 50.000 0.00 0.00 37.46 4.70
1732 2615 4.262678 GCATACTCCCTCCTTAAGACATCC 60.263 50.000 3.36 0.00 0.00 3.51
1747 2630 3.746045 TCGGTTATGGAAGCATACTCC 57.254 47.619 0.00 0.00 32.32 3.85
1752 2635 4.202050 GCTTGAAATCGGTTATGGAAGCAT 60.202 41.667 0.00 0.00 35.68 3.79
1779 2662 1.443194 CCCCGTTACAGTGTCGACG 60.443 63.158 19.56 19.56 35.44 5.12
1781 2664 1.228521 TCCCCCGTTACAGTGTCGA 60.229 57.895 0.00 0.00 0.00 4.20
1783 2666 0.037605 CACTCCCCCGTTACAGTGTC 60.038 60.000 0.00 0.00 33.03 3.67
1784 2667 1.477685 CCACTCCCCCGTTACAGTGT 61.478 60.000 0.00 0.00 35.46 3.55
1785 2668 1.295423 CCACTCCCCCGTTACAGTG 59.705 63.158 0.00 0.00 36.75 3.66
1788 2671 2.203877 AGCCACTCCCCCGTTACA 60.204 61.111 0.00 0.00 0.00 2.41
1789 2672 2.582978 GAGCCACTCCCCCGTTAC 59.417 66.667 0.00 0.00 0.00 2.50
1798 2681 1.355066 GCTGTTAGCACGAGCCACTC 61.355 60.000 0.00 0.00 41.89 3.51
1800 2683 3.169198 GCTGTTAGCACGAGCCAC 58.831 61.111 0.00 0.00 41.89 5.01
1804 2687 1.080995 GCTCTGGCTGTTAGCACGAG 61.081 60.000 2.99 8.30 44.75 4.18
1805 2688 1.079819 GCTCTGGCTGTTAGCACGA 60.080 57.895 2.99 0.00 44.75 4.35
1806 2689 1.374631 TGCTCTGGCTGTTAGCACG 60.375 57.895 2.99 0.00 44.75 5.34
1811 2705 1.486310 CCCTGTATGCTCTGGCTGTTA 59.514 52.381 0.00 0.00 39.59 2.41
1829 2723 2.611518 CGTCAGACATTGAGAGTTCCC 58.388 52.381 0.41 0.00 36.21 3.97
1838 2732 2.598589 CAATTTGCCCGTCAGACATTG 58.401 47.619 0.41 0.00 0.00 2.82
1839 2733 1.067635 GCAATTTGCCCGTCAGACATT 60.068 47.619 10.34 0.00 37.42 2.71
1898 2800 5.343593 CACATCTAGACTTGTGTTTCGACTC 59.656 44.000 15.49 0.00 38.69 3.36
2002 2930 6.038050 AGTGCTTTTGAAGAGAAAGAACTCTG 59.962 38.462 4.74 0.00 45.56 3.35
2003 2931 6.118852 AGTGCTTTTGAAGAGAAAGAACTCT 58.881 36.000 4.74 0.00 45.56 3.24
2004 2932 6.370433 AGTGCTTTTGAAGAGAAAGAACTC 57.630 37.500 4.74 0.00 45.56 3.01
2006 2934 5.201181 CGAGTGCTTTTGAAGAGAAAGAAC 58.799 41.667 1.11 0.77 41.15 3.01
2007 2935 4.273480 CCGAGTGCTTTTGAAGAGAAAGAA 59.727 41.667 1.11 0.00 36.45 2.52
2008 2936 3.809832 CCGAGTGCTTTTGAAGAGAAAGA 59.190 43.478 1.11 0.00 36.45 2.52
2009 2937 3.058639 CCCGAGTGCTTTTGAAGAGAAAG 60.059 47.826 0.00 0.00 37.21 2.62
2010 2938 2.878406 CCCGAGTGCTTTTGAAGAGAAA 59.122 45.455 0.00 0.00 0.00 2.52
2020 2948 4.080863 AGTCTGAATTATCCCGAGTGCTTT 60.081 41.667 0.00 0.00 0.00 3.51
2021 2949 3.452627 AGTCTGAATTATCCCGAGTGCTT 59.547 43.478 0.00 0.00 0.00 3.91
2123 3167 5.071115 CCTAAAGACTCCTATTTCTCCCCAG 59.929 48.000 0.00 0.00 0.00 4.45
2132 3182 5.534070 AGAGAAGCCCTAAAGACTCCTATT 58.466 41.667 0.00 0.00 0.00 1.73
2136 3186 3.772572 AGAAGAGAAGCCCTAAAGACTCC 59.227 47.826 0.00 0.00 0.00 3.85
2155 3205 3.025978 GGGATCACATTGCATTGGAGAA 58.974 45.455 12.87 0.00 0.00 2.87
2156 3206 2.242965 AGGGATCACATTGCATTGGAGA 59.757 45.455 12.87 10.18 0.00 3.71
2157 3207 2.361119 CAGGGATCACATTGCATTGGAG 59.639 50.000 12.87 5.46 0.00 3.86
2158 3208 2.380941 CAGGGATCACATTGCATTGGA 58.619 47.619 12.87 7.65 0.00 3.53
2163 3262 0.251698 TTGGCAGGGATCACATTGCA 60.252 50.000 10.97 0.00 38.27 4.08
2197 3296 9.862585 GTTTTGGCAATAAATAAAGTGAACTTG 57.137 29.630 0.00 0.00 36.12 3.16
2298 3397 9.698309 CTTGACTTATCTTCTCTGAAAAGTACA 57.302 33.333 0.00 0.00 0.00 2.90
2311 3410 3.202097 GCAGCCCTCTTGACTTATCTTC 58.798 50.000 0.00 0.00 0.00 2.87
2315 3414 0.179000 CCGCAGCCCTCTTGACTTAT 59.821 55.000 0.00 0.00 0.00 1.73
2316 3415 1.192146 ACCGCAGCCCTCTTGACTTA 61.192 55.000 0.00 0.00 0.00 2.24
2318 3417 2.056906 AAACCGCAGCCCTCTTGACT 62.057 55.000 0.00 0.00 0.00 3.41
2320 3419 1.302511 GAAACCGCAGCCCTCTTGA 60.303 57.895 0.00 0.00 0.00 3.02
2321 3420 1.302832 AGAAACCGCAGCCCTCTTG 60.303 57.895 0.00 0.00 0.00 3.02
2322 3421 1.302832 CAGAAACCGCAGCCCTCTT 60.303 57.895 0.00 0.00 0.00 2.85
2323 3422 1.192146 TACAGAAACCGCAGCCCTCT 61.192 55.000 0.00 0.00 0.00 3.69
2324 3423 1.019805 GTACAGAAACCGCAGCCCTC 61.020 60.000 0.00 0.00 0.00 4.30
2325 3424 1.003718 GTACAGAAACCGCAGCCCT 60.004 57.895 0.00 0.00 0.00 5.19
2326 3425 0.605589 AAGTACAGAAACCGCAGCCC 60.606 55.000 0.00 0.00 0.00 5.19
2327 3426 0.796927 GAAGTACAGAAACCGCAGCC 59.203 55.000 0.00 0.00 0.00 4.85
2328 3427 1.508632 TGAAGTACAGAAACCGCAGC 58.491 50.000 0.00 0.00 0.00 5.25
2490 3590 3.823304 AGAAAACAGTTGGATCTCCTTGC 59.177 43.478 0.00 0.00 36.82 4.01
2582 3870 2.224606 TGTTTTTCCAGCAGCAGAGAG 58.775 47.619 0.00 0.00 0.00 3.20
2583 3871 2.158769 TCTGTTTTTCCAGCAGCAGAGA 60.159 45.455 0.00 0.00 32.32 3.10


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

AutoCloner maintained by Alex Coulton.