Multiple sequence alignment - TraesCS1D01G367400

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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 TraesCS1D01G367400 chr1D 100.000 3537 0 0 1 3537 447258058 447261594 0.000000e+00 6532.0
1 TraesCS1D01G367400 chr1D 86.353 447 56 5 2841 3285 447366553 447366996 1.910000e-132 483.0
2 TraesCS1D01G367400 chr1D 84.419 353 45 4 1801 2149 447282799 447283145 4.370000e-89 339.0
3 TraesCS1D01G367400 chr1D 82.609 207 32 2 2025 2227 447317189 447317395 2.810000e-41 180.0
4 TraesCS1D01G367400 chr1D 86.000 150 20 1 2841 2990 447377882 447378030 3.650000e-35 159.0
5 TraesCS1D01G367400 chr1D 88.350 103 9 1 1207 1306 447368510 447368612 1.720000e-23 121.0
6 TraesCS1D01G367400 chr1D 100.000 35 0 0 3415 3449 447444801 447444835 8.200000e-07 65.8
7 TraesCS1D01G367400 chr1A 90.313 2044 141 21 1518 3537 543068133 543070143 0.000000e+00 2625.0
8 TraesCS1D01G367400 chr1A 92.556 806 38 10 725 1510 543067228 543068031 0.000000e+00 1136.0
9 TraesCS1D01G367400 chr1A 92.297 714 24 9 36 728 543066235 543066938 0.000000e+00 985.0
10 TraesCS1D01G367400 chr1A 85.388 438 58 6 2841 3276 543188492 543188925 1.940000e-122 449.0
11 TraesCS1D01G367400 chr1A 84.101 434 53 5 1720 2149 543187031 543187452 4.250000e-109 405.0
12 TraesCS1D01G367400 chr1A 83.815 346 47 3 1801 2142 543170391 543170731 1.580000e-83 320.0
13 TraesCS1D01G367400 chr1A 86.000 150 20 1 2841 2990 543193341 543193489 3.650000e-35 159.0
14 TraesCS1D01G367400 chr1A 89.109 101 8 1 1207 1304 543190438 543190538 4.790000e-24 122.0
15 TraesCS1D01G367400 chr1B 91.460 1534 71 27 1 1510 612892176 612893673 0.000000e+00 2052.0
16 TraesCS1D01G367400 chr1B 87.044 1536 135 26 1517 3041 612893773 612895255 0.000000e+00 1676.0
17 TraesCS1D01G367400 chr1B 91.068 515 39 3 3024 3537 612895276 612895784 0.000000e+00 689.0
18 TraesCS1D01G367400 chr1B 81.173 324 45 5 1908 2227 612901340 612901651 2.730000e-61 246.0
19 TraesCS1D01G367400 chr1B 91.964 112 5 4 1541 1651 612900510 612900618 1.700000e-33 154.0
20 TraesCS1D01G367400 chr7A 83.113 302 35 7 1812 2112 41059412 41059126 9.740000e-66 261.0
21 TraesCS1D01G367400 chr7B 80.000 325 39 10 1789 2112 65343350 65343649 2.140000e-52 217.0
22 TraesCS1D01G367400 chr4D 89.062 64 7 0 1206 1269 419158900 419158837 2.930000e-11 80.5
23 TraesCS1D01G367400 chr4B 89.062 64 7 0 1206 1269 516956820 516956757 2.930000e-11 80.5


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 TraesCS1D01G367400 chr1D 447258058 447261594 3536 False 6532.000000 6532 100.000000 1 3537 1 chr1D.!!$F1 3536
1 TraesCS1D01G367400 chr1D 447366553 447368612 2059 False 302.000000 483 87.351500 1207 3285 2 chr1D.!!$F6 2078
2 TraesCS1D01G367400 chr1A 543066235 543070143 3908 False 1582.000000 2625 91.722000 36 3537 3 chr1A.!!$F2 3501
3 TraesCS1D01G367400 chr1A 543187031 543193489 6458 False 283.750000 449 86.149500 1207 3276 4 chr1A.!!$F3 2069
4 TraesCS1D01G367400 chr1B 612892176 612895784 3608 False 1472.333333 2052 89.857333 1 3537 3 chr1B.!!$F1 3536

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
216 219 0.179065 CAGATCAGAATCCAGCGCCA 60.179 55.0 2.29 0.0 31.78 5.69 F
914 1234 0.240678 CACCATAACGCAGCAAGCAA 59.759 50.0 0.00 0.0 46.13 3.91 F
1891 2339 0.039617 CAGAGATGGCTCGACGATCC 60.040 60.0 10.80 10.8 45.98 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 2165 0.179936 CAGACCTGCCTCAATCCCTC 59.820 60.0 0.0 0.0 0.0 4.30 R
2441 3079 0.812549 TGCGACCGAGTGTATTGCTA 59.187 50.0 0.0 0.0 0.0 3.49 R
3452 7174 1.277326 GCATCTATCAACGACGTGCA 58.723 50.0 0.0 0.0 0.0 4.57 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 46 3.189287 AGAACGGTGCAAGCTTAATTGAG 59.811 43.478 0.00 0.00 31.55 3.02
190 193 0.739813 GGCCGTCCCATATACGATGC 60.740 60.000 0.00 0.00 42.90 3.91
216 219 0.179065 CAGATCAGAATCCAGCGCCA 60.179 55.000 2.29 0.00 31.78 5.69
418 435 5.070047 ACCAAAAGTGTGCTAGTACAGTACT 59.930 40.000 19.95 17.51 40.30 2.73
483 503 0.313672 TTTCAGTGGTGAAATGCGCC 59.686 50.000 4.18 0.00 45.82 6.53
529 553 3.382546 ACAAAGGAGGCATGCATGATTAC 59.617 43.478 30.64 16.91 0.00 1.89
598 622 1.152610 ATGATGGTCCATGCCAGGC 60.153 57.895 9.76 3.66 42.47 4.85
751 1068 0.242825 TACAGGCTTTCGTCAGACGG 59.757 55.000 22.66 8.16 42.81 4.79
913 1233 1.585267 CCACCATAACGCAGCAAGCA 61.585 55.000 0.00 0.00 46.13 3.91
914 1234 0.240678 CACCATAACGCAGCAAGCAA 59.759 50.000 0.00 0.00 46.13 3.91
1213 1547 4.994471 TGCACTGGCGCAGGTGAG 62.994 66.667 27.77 11.03 45.35 3.51
1345 1679 0.321122 ACGCTTCCTCTGCTTCTTGG 60.321 55.000 0.00 0.00 0.00 3.61
1363 1697 1.606885 GGAGAGTGCTCTGCTCTGCT 61.607 60.000 12.51 0.00 44.55 4.24
1369 1703 0.395686 TGCTCTGCTCTGCTTGTCTT 59.604 50.000 0.00 0.00 0.00 3.01
1370 1704 0.797542 GCTCTGCTCTGCTTGTCTTG 59.202 55.000 0.00 0.00 0.00 3.02
1376 1717 2.067766 GCTCTGCTTGTCTTGACTGAG 58.932 52.381 2.35 2.21 0.00 3.35
1384 1725 4.025313 GCTTGTCTTGACTGAGTGTTTCTC 60.025 45.833 0.00 0.00 43.03 2.87
1395 1736 2.996621 GAGTGTTTCTCCGTTCCATCTG 59.003 50.000 0.00 0.00 37.22 2.90
1399 1740 3.181459 TGTTTCTCCGTTCCATCTGTTGA 60.181 43.478 0.00 0.00 0.00 3.18
1498 1840 5.340803 ACGTAGCATTGTGTATGTCTAGTG 58.659 41.667 0.00 0.00 36.57 2.74
1510 1852 7.832685 TGTGTATGTCTAGTGTAACCAGAGTAT 59.167 37.037 0.00 0.00 37.80 2.12
1511 1853 9.334947 GTGTATGTCTAGTGTAACCAGAGTATA 57.665 37.037 0.00 0.00 37.80 1.47
1524 1960 9.420551 GTAACCAGAGTATAATAGAATTTCCCG 57.579 37.037 0.00 0.00 0.00 5.14
1527 1963 5.577164 CAGAGTATAATAGAATTTCCCGGCG 59.423 44.000 0.00 0.00 0.00 6.46
1538 1974 7.373778 AGAATTTCCCGGCGATAATAATAAC 57.626 36.000 9.30 0.09 0.00 1.89
1619 2065 4.079253 AGCCGTACACCTGAAAAATTCAT 58.921 39.130 0.00 0.00 39.30 2.57
1621 2067 4.621034 GCCGTACACCTGAAAAATTCATTG 59.379 41.667 0.00 0.00 39.30 2.82
1708 2154 2.884012 ACTCAAATGACGACCATGCAAA 59.116 40.909 0.00 0.00 35.24 3.68
1752 2198 5.045578 AGGCAGGTCTGATTTTGTATGTACT 60.046 40.000 1.65 0.00 0.00 2.73
1753 2199 5.294552 GGCAGGTCTGATTTTGTATGTACTC 59.705 44.000 1.65 0.00 0.00 2.59
1754 2200 5.005779 GCAGGTCTGATTTTGTATGTACTCG 59.994 44.000 1.65 0.00 0.00 4.18
1755 2201 6.100004 CAGGTCTGATTTTGTATGTACTCGT 58.900 40.000 0.00 0.00 0.00 4.18
1756 2202 7.255569 CAGGTCTGATTTTGTATGTACTCGTA 58.744 38.462 0.00 0.00 0.00 3.43
1757 2203 7.220300 CAGGTCTGATTTTGTATGTACTCGTAC 59.780 40.741 0.35 0.35 36.79 3.67
1795 2243 6.984474 TGTAGTCGTTTCTCTGAAAGTTTCAT 59.016 34.615 18.35 2.87 39.30 2.57
1799 2247 8.244113 AGTCGTTTCTCTGAAAGTTTCATTTTT 58.756 29.630 18.35 0.00 39.30 1.94
1861 2309 6.418101 AGTAAAGGTTGTATCTGACATGCAT 58.582 36.000 0.00 0.00 38.07 3.96
1891 2339 0.039617 CAGAGATGGCTCGACGATCC 60.040 60.000 10.80 10.80 45.98 3.36
1912 2360 0.835941 AGGCATTCATCGCTCTTCCT 59.164 50.000 0.00 0.00 0.00 3.36
1916 2364 2.483714 GCATTCATCGCTCTTCCTGGTA 60.484 50.000 0.00 0.00 0.00 3.25
1922 2370 0.537188 CGCTCTTCCTGGTACCACAT 59.463 55.000 11.60 0.00 0.00 3.21
1937 2385 4.207891 ACCACATGCTTAACGATCTTCT 57.792 40.909 0.00 0.00 0.00 2.85
1944 2392 8.060679 CACATGCTTAACGATCTTCTTAATCAG 58.939 37.037 0.00 0.00 0.00 2.90
1974 2428 2.784712 CGACCGATCGTGCTCATAC 58.215 57.895 15.09 0.00 43.66 2.39
1980 2434 2.032290 CCGATCGTGCTCATACGTTAGA 60.032 50.000 15.09 0.00 44.06 2.10
2002 2456 7.282332 AGAAGAGCTTGCTTACAATTTTCTT 57.718 32.000 0.00 0.00 34.76 2.52
2003 2457 7.720442 AGAAGAGCTTGCTTACAATTTTCTTT 58.280 30.769 0.00 0.00 33.45 2.52
2004 2458 8.200120 AGAAGAGCTTGCTTACAATTTTCTTTT 58.800 29.630 0.00 0.00 33.45 2.27
2005 2459 9.463443 GAAGAGCTTGCTTACAATTTTCTTTTA 57.537 29.630 0.00 0.00 33.45 1.52
2006 2460 9.987272 AAGAGCTTGCTTACAATTTTCTTTTAT 57.013 25.926 0.00 0.00 34.61 1.40
2062 2516 5.678583 CTGTTGGAGATGATAACATGGTCT 58.321 41.667 0.00 0.00 36.82 3.85
2066 2520 6.505048 TGGAGATGATAACATGGTCTCAAT 57.495 37.500 2.61 0.00 36.82 2.57
2068 2522 6.769341 TGGAGATGATAACATGGTCTCAATTG 59.231 38.462 2.61 0.00 36.82 2.32
2096 2550 3.759086 TCACAACAAACCTGTAAGCAACA 59.241 39.130 0.00 0.00 33.45 3.33
2097 2551 4.218635 TCACAACAAACCTGTAAGCAACAA 59.781 37.500 0.00 0.00 37.74 2.83
2115 2572 8.915057 AGCAACAAAGCATAACAGATAGATAT 57.085 30.769 0.00 0.00 36.85 1.63
2122 2580 7.860918 AGCATAACAGATAGATATTGCATGG 57.139 36.000 0.00 0.00 0.00 3.66
2142 2600 1.069973 GCAAATTGGCCGCAGTTTTTC 60.070 47.619 0.00 0.00 0.00 2.29
2150 2608 0.249699 CCGCAGTTTTTCCCCCAAAC 60.250 55.000 0.00 0.00 34.80 2.93
2151 2609 0.249699 CGCAGTTTTTCCCCCAAACC 60.250 55.000 0.00 0.00 35.10 3.27
2152 2610 0.107831 GCAGTTTTTCCCCCAAACCC 59.892 55.000 0.00 0.00 35.10 4.11
2153 2611 1.501582 CAGTTTTTCCCCCAAACCCA 58.498 50.000 0.00 0.00 35.10 4.51
2154 2612 1.840635 CAGTTTTTCCCCCAAACCCAA 59.159 47.619 0.00 0.00 35.10 4.12
2155 2613 2.239907 CAGTTTTTCCCCCAAACCCAAA 59.760 45.455 0.00 0.00 35.10 3.28
2161 2619 1.428139 TCCCCCAAACCCAAACGAATA 59.572 47.619 0.00 0.00 0.00 1.75
2170 2799 4.287766 ACCCAAACGAATAGAGCTTTCT 57.712 40.909 0.00 0.00 0.00 2.52
2183 2812 5.175090 AGAGCTTTCTGTTGCTAACAAAC 57.825 39.130 0.00 0.00 41.61 2.93
2258 2887 2.417243 GCTTGCACTGTTTGACAAAGGT 60.417 45.455 0.00 0.96 0.00 3.50
2280 2909 1.800655 CGAGAGAGGGCTTCATCAACG 60.801 57.143 0.00 1.55 0.00 4.10
2315 2944 0.679505 TACTTGTCTCAGCGCCAACT 59.320 50.000 2.29 0.00 0.00 3.16
2318 2947 2.358003 GTCTCAGCGCCAACTGCT 60.358 61.111 2.29 0.00 45.31 4.24
2398 3027 9.952030 TCTTTATATTCACACACTACATTTCCA 57.048 29.630 0.00 0.00 0.00 3.53
2441 3079 8.986991 ACATGTCCTTTTCTTCTCTATGTATCT 58.013 33.333 0.00 0.00 0.00 1.98
2510 3148 1.680735 AGATCTCAGAGCTTGGCTACG 59.319 52.381 0.00 0.00 39.88 3.51
2626 3264 2.969443 AAAGAAATTCAGCGTCACGG 57.031 45.000 0.00 0.00 0.00 4.94
2685 3325 1.760029 TGCTGGTCGTTGCCATCTATA 59.240 47.619 0.00 0.00 37.96 1.31
2725 3366 9.988815 AATTGCATTACCAAGTATGTTTTGTTA 57.011 25.926 0.00 0.00 0.00 2.41
2800 3441 5.513094 GCAGCTGGGATATGTTATAGGTGAA 60.513 44.000 17.12 0.00 36.16 3.18
2803 3444 7.120285 CAGCTGGGATATGTTATAGGTGAATTG 59.880 40.741 5.57 0.00 36.16 2.32
2835 3476 3.361917 CGTTTTCTTCGCAATTTGCAAGG 60.362 43.478 20.56 3.58 45.36 3.61
2843 3484 3.055963 TCGCAATTTGCAAGGATTCCAAT 60.056 39.130 20.56 0.00 45.36 3.16
2991 3823 7.125811 TGTTTGTATAGCTTCTCTACAGGGATT 59.874 37.037 0.00 0.00 27.83 3.01
3002 3834 8.840200 TTCTCTACAGGGATTGTTCTATAGTT 57.160 34.615 0.00 0.00 41.29 2.24
3025 3897 9.300681 AGTTTTCCATAATTGAGAAGACATGAA 57.699 29.630 0.00 0.00 29.53 2.57
3097 3969 4.640771 TCTTAGTTGGCCATCTGAAAGT 57.359 40.909 23.99 6.02 33.76 2.66
3099 3971 4.761739 TCTTAGTTGGCCATCTGAAAGTTG 59.238 41.667 23.99 6.10 33.46 3.16
3192 4064 3.822940 AGTTTCGGACCCATTACAACAA 58.177 40.909 0.00 0.00 0.00 2.83
3241 4113 0.034574 TGCCACAACGAATAGGCCAT 60.035 50.000 5.01 0.00 46.45 4.40
3276 4150 2.571212 ACAATGAAAGCTGTCGTGGAA 58.429 42.857 7.56 0.00 0.00 3.53
3290 4164 6.622896 GCTGTCGTGGAATAGTTTAAAGCAAT 60.623 38.462 0.00 0.00 0.00 3.56
3341 4215 2.762745 TGACCTTCCTACGCTTTGTTC 58.237 47.619 0.00 0.00 0.00 3.18
3360 4234 4.873129 CGACCGCTGTATGCCGCT 62.873 66.667 0.00 0.00 38.78 5.52
3452 7174 2.964310 ATGCCCTTCAGCTCAGCGT 61.964 57.895 0.00 0.00 0.00 5.07
3477 7199 2.627945 GTCGTTGATAGATGCACCCAA 58.372 47.619 0.00 0.00 0.00 4.12
3502 7230 0.896940 TGGTTCCCGCGTTAGAGACT 60.897 55.000 4.92 0.00 0.00 3.24
3509 7237 0.450583 CGCGTTAGAGACTAGCCACA 59.549 55.000 0.00 0.00 0.00 4.17
3524 7252 1.672881 GCCACATTATGCTGAGACCAC 59.327 52.381 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 46 4.030195 GGTTCTCGCAACGATTTAAAATGC 59.970 41.667 0.00 0.62 34.61 3.56
190 193 3.557475 GCTGGATTCTGATCTGATGAGGG 60.557 52.174 4.28 0.00 32.66 4.30
216 219 6.266786 GGAATGGATGTTTATTTTACCCGGAT 59.733 38.462 0.73 0.00 0.00 4.18
347 356 1.545759 CTTAGCACTCGCGATCGAAA 58.454 50.000 21.57 4.33 44.98 3.46
418 435 2.740580 GCACCGGCAGTAATAACAGCTA 60.741 50.000 0.00 0.00 38.16 3.32
424 441 4.524869 CGGCACCGGCAGTAATAA 57.475 55.556 0.00 0.00 43.71 1.40
483 503 2.123854 AGGAGCATGCATGGGCTG 60.124 61.111 27.34 4.17 41.22 4.85
529 553 1.268896 GCCATGCAAATCTGGATCGTG 60.269 52.381 8.28 0.00 34.24 4.35
887 1204 1.969064 GCGTTATGGTGGTGTGGCA 60.969 57.895 0.00 0.00 0.00 4.92
893 1210 1.586154 GCTTGCTGCGTTATGGTGGT 61.586 55.000 0.00 0.00 0.00 4.16
923 1243 2.022129 CGTCGTGTCTGGCCTTGTC 61.022 63.158 3.32 0.00 0.00 3.18
924 1244 2.029073 CGTCGTGTCTGGCCTTGT 59.971 61.111 3.32 0.00 0.00 3.16
926 1246 2.338984 GTCGTCGTGTCTGGCCTT 59.661 61.111 3.32 0.00 0.00 4.35
1103 1434 1.437986 GATTCGCCTACCAGCTCGT 59.562 57.895 0.00 0.00 0.00 4.18
1147 1478 4.058817 AGCTTAACTTGACAAGAAGACGG 58.941 43.478 21.95 7.52 0.00 4.79
1253 1587 4.899239 GCGACGAGGCCCATGAGG 62.899 72.222 0.00 0.00 39.47 3.86
1322 1656 0.514691 GAAGCAGAGGAAGCGTTGTG 59.485 55.000 0.00 0.00 37.01 3.33
1345 1679 0.247185 AAGCAGAGCAGAGCACTCTC 59.753 55.000 0.00 0.00 42.62 3.20
1363 1697 4.442706 GGAGAAACACTCAGTCAAGACAA 58.557 43.478 2.72 0.00 46.54 3.18
1376 1717 2.767505 ACAGATGGAACGGAGAAACAC 58.232 47.619 0.00 0.00 0.00 3.32
1384 1725 1.442769 CCTGTCAACAGATGGAACGG 58.557 55.000 11.70 0.00 46.59 4.44
1498 1840 9.420551 CGGGAAATTCTATTATACTCTGGTTAC 57.579 37.037 0.00 0.00 0.00 2.50
1511 1853 9.675464 TTATTATTATCGCCGGGAAATTCTATT 57.325 29.630 2.18 0.00 0.00 1.73
1513 1855 8.095792 TGTTATTATTATCGCCGGGAAATTCTA 58.904 33.333 2.18 0.00 0.00 2.10
1515 1857 7.136289 TGTTATTATTATCGCCGGGAAATTC 57.864 36.000 2.18 0.00 0.00 2.17
1524 1960 8.776680 ATTGTCGTTTTGTTATTATTATCGCC 57.223 30.769 0.00 0.00 0.00 5.54
1538 1974 8.547069 ACCAAATTCACATAAATTGTCGTTTTG 58.453 29.630 0.00 0.00 36.00 2.44
1619 2065 2.575735 TGAGATAACCTCATGTGGCCAA 59.424 45.455 7.24 0.00 46.38 4.52
1690 2136 4.143073 CCAAATTTGCATGGTCGTCATTTG 60.143 41.667 12.92 0.00 32.92 2.32
1719 2165 0.179936 CAGACCTGCCTCAATCCCTC 59.820 60.000 0.00 0.00 0.00 4.30
1721 2167 0.842635 ATCAGACCTGCCTCAATCCC 59.157 55.000 0.00 0.00 0.00 3.85
1722 2168 2.725221 AATCAGACCTGCCTCAATCC 57.275 50.000 0.00 0.00 0.00 3.01
1729 2175 5.186198 AGTACATACAAAATCAGACCTGCC 58.814 41.667 0.00 0.00 0.00 4.85
1752 2198 9.571810 ACGACTACAAAATATAATGTTGTACGA 57.428 29.630 14.72 0.00 36.03 3.43
1768 2216 7.332430 TGAAACTTTCAGAGAAACGACTACAAA 59.668 33.333 0.00 0.00 34.08 2.83
1769 2217 6.814644 TGAAACTTTCAGAGAAACGACTACAA 59.185 34.615 0.00 0.00 34.08 2.41
1770 2218 6.334989 TGAAACTTTCAGAGAAACGACTACA 58.665 36.000 0.00 0.00 34.08 2.74
1772 2220 8.433421 AAATGAAACTTTCAGAGAAACGACTA 57.567 30.769 9.97 0.00 43.98 2.59
1773 2221 6.927294 AATGAAACTTTCAGAGAAACGACT 57.073 33.333 9.97 0.00 43.98 4.18
1808 2256 6.352222 CCCACACTCTCACCTAATATCTGTTT 60.352 42.308 0.00 0.00 0.00 2.83
1861 2309 0.914644 CCATCTCTGCTTTCCTCCCA 59.085 55.000 0.00 0.00 0.00 4.37
1891 2339 0.857935 GAAGAGCGATGAATGCCTCG 59.142 55.000 0.00 0.00 37.92 4.63
1894 2342 0.942962 CAGGAAGAGCGATGAATGCC 59.057 55.000 0.00 0.00 0.00 4.40
1912 2360 3.196901 AGATCGTTAAGCATGTGGTACCA 59.803 43.478 11.60 11.60 0.00 3.25
1916 2364 4.207891 AGAAGATCGTTAAGCATGTGGT 57.792 40.909 0.00 0.00 0.00 4.16
1922 2370 7.548097 AGACTGATTAAGAAGATCGTTAAGCA 58.452 34.615 12.55 12.55 34.35 3.91
1937 2385 6.487668 TCGGTCGATAATGGTAGACTGATTAA 59.512 38.462 2.26 0.00 42.15 1.40
1974 2428 5.786401 ATTGTAAGCAAGCTCTTCTAACG 57.214 39.130 0.00 0.00 38.10 3.18
1980 2434 9.987272 ATAAAAGAAAATTGTAAGCAAGCTCTT 57.013 25.926 0.00 0.00 38.10 2.85
2062 2516 5.130145 AGGTTTGTTGTGAATTCCCAATTGA 59.870 36.000 7.12 0.00 0.00 2.57
2066 2520 3.772025 ACAGGTTTGTTGTGAATTCCCAA 59.228 39.130 2.27 0.34 32.28 4.12
2068 2522 5.523438 TTACAGGTTTGTTGTGAATTCCC 57.477 39.130 2.27 0.00 38.76 3.97
2096 2550 8.737175 CCATGCAATATCTATCTGTTATGCTTT 58.263 33.333 0.00 0.00 0.00 3.51
2097 2551 7.148120 GCCATGCAATATCTATCTGTTATGCTT 60.148 37.037 0.00 0.00 0.00 3.91
2122 2580 0.943673 AAAAACTGCGGCCAATTTGC 59.056 45.000 2.24 0.00 0.00 3.68
2142 2600 1.822371 CTATTCGTTTGGGTTTGGGGG 59.178 52.381 0.00 0.00 0.00 5.40
2150 2608 4.003648 ACAGAAAGCTCTATTCGTTTGGG 58.996 43.478 0.00 0.00 32.04 4.12
2151 2609 5.385617 CAACAGAAAGCTCTATTCGTTTGG 58.614 41.667 0.00 0.00 32.04 3.28
2152 2610 4.848299 GCAACAGAAAGCTCTATTCGTTTG 59.152 41.667 0.00 0.00 31.78 2.93
2153 2611 4.757149 AGCAACAGAAAGCTCTATTCGTTT 59.243 37.500 0.00 0.00 36.00 3.60
2154 2612 4.319177 AGCAACAGAAAGCTCTATTCGTT 58.681 39.130 0.00 0.00 36.00 3.85
2155 2613 3.931578 AGCAACAGAAAGCTCTATTCGT 58.068 40.909 0.00 0.00 36.00 3.85
2161 2619 4.640201 TGTTTGTTAGCAACAGAAAGCTCT 59.360 37.500 0.00 0.00 43.27 4.09
2170 2799 6.641169 TTGGTATGATGTTTGTTAGCAACA 57.359 33.333 0.00 0.00 40.21 3.33
2183 2812 6.071952 GCAACCCAACCTATATTGGTATGATG 60.072 42.308 9.36 4.27 46.72 3.07
2258 2887 0.972471 TGATGAAGCCCTCTCTCGCA 60.972 55.000 0.00 0.00 0.00 5.10
2280 2909 4.307432 ACAAGTATGTGTGTACAGTCTGC 58.693 43.478 0.00 0.00 40.79 4.26
2315 2944 1.171549 TTGTCAGCAATTCCGCAGCA 61.172 50.000 0.00 0.00 0.00 4.41
2318 2947 1.603456 TCTTTGTCAGCAATTCCGCA 58.397 45.000 0.00 0.00 34.18 5.69
2397 3026 7.656948 AGGACATGTAAACACATTTGGAAAATG 59.343 33.333 0.00 10.41 0.00 2.32
2398 3027 7.734942 AGGACATGTAAACACATTTGGAAAAT 58.265 30.769 0.00 0.00 0.00 1.82
2399 3028 7.118496 AGGACATGTAAACACATTTGGAAAA 57.882 32.000 0.00 0.00 0.00 2.29
2400 3029 6.723298 AGGACATGTAAACACATTTGGAAA 57.277 33.333 0.00 0.00 0.00 3.13
2401 3030 6.723298 AAGGACATGTAAACACATTTGGAA 57.277 33.333 0.00 0.00 0.00 3.53
2402 3031 6.723298 AAAGGACATGTAAACACATTTGGA 57.277 33.333 0.00 0.00 0.00 3.53
2403 3032 7.209475 AGAAAAGGACATGTAAACACATTTGG 58.791 34.615 0.00 0.00 0.00 3.28
2441 3079 0.812549 TGCGACCGAGTGTATTGCTA 59.187 50.000 0.00 0.00 0.00 3.49
2604 3242 3.303725 CCGTGACGCTGAATTTCTTTTGA 60.304 43.478 0.00 0.00 0.00 2.69
2618 3256 2.203800 TCATATCTCAACCGTGACGC 57.796 50.000 0.00 0.00 0.00 5.19
2725 3366 3.678056 TTCACCGTAGACAGCAAGAAT 57.322 42.857 0.00 0.00 0.00 2.40
2800 3441 5.684184 GCGAAGAAAACGAAAAAGGTACAAT 59.316 36.000 0.00 0.00 0.00 2.71
2803 3444 4.590226 TGCGAAGAAAACGAAAAAGGTAC 58.410 39.130 0.00 0.00 0.00 3.34
2923 3755 7.558444 GGGTGTAAAAATATGACCACTATGGAA 59.442 37.037 0.84 0.00 40.96 3.53
2984 3816 9.627123 TTATGGAAAACTATAGAACAATCCCTG 57.373 33.333 6.78 0.00 0.00 4.45
3002 3834 8.868522 AGTTCATGTCTTCTCAATTATGGAAA 57.131 30.769 0.00 0.00 0.00 3.13
3043 3915 5.527582 GTGGAATTCACTCGTTATATTGGCT 59.472 40.000 7.93 0.00 42.86 4.75
3044 3916 5.748592 GTGGAATTCACTCGTTATATTGGC 58.251 41.667 7.93 0.00 42.86 4.52
3099 3971 9.235537 GGTAGAATTCTCGTAAAGTGAGATAAC 57.764 37.037 12.24 0.00 41.80 1.89
3192 4064 3.079578 CTGCCAACATGTGATCTTGAGT 58.920 45.455 0.00 0.00 0.00 3.41
3241 4113 2.040947 TCATTGTATTGTGGGGCACTCA 59.959 45.455 0.00 0.00 35.11 3.41
3276 4150 4.777366 AGTGCCCCAATTGCTTTAAACTAT 59.223 37.500 0.00 0.00 0.00 2.12
3290 4164 1.371183 CTCGACAAGAGTGCCCCAA 59.629 57.895 0.00 0.00 41.99 4.12
3360 4234 3.785486 CGCAGATGATGGTGTAGAAGAA 58.215 45.455 0.00 0.00 0.00 2.52
3452 7174 1.277326 GCATCTATCAACGACGTGCA 58.723 50.000 0.00 0.00 0.00 4.57
3460 7182 1.331756 CGCTTGGGTGCATCTATCAAC 59.668 52.381 0.00 0.00 0.00 3.18
3502 7230 2.771372 TGGTCTCAGCATAATGTGGCTA 59.229 45.455 0.00 0.00 38.56 3.93
3509 7237 4.256920 GTTGAGTGTGGTCTCAGCATAAT 58.743 43.478 5.86 0.00 43.85 1.28


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

AutoCloner maintained by Alex Coulton.