Multiple sequence alignment - TraesCS3D01G102600

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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 TraesCS3D01G102600 chr3D 100.000 2288 0 0 1 2288 55163840 55166127 0.000000e+00 4226.0
1 TraesCS3D01G102600 chr3D 84.404 218 21 6 1857 2064 55158000 55158214 3.850000e-48 202.0
2 TraesCS3D01G102600 chr7D 90.369 1734 136 14 1 1719 463975822 463974105 0.000000e+00 2248.0
3 TraesCS3D01G102600 chr7D 91.304 92 8 0 1719 1810 577930012 577930103 2.390000e-25 126.0
4 TraesCS3D01G102600 chr4B 90.382 1726 135 15 9 1719 551730120 551731829 0.000000e+00 2239.0
5 TraesCS3D01G102600 chr4B 90.138 1734 140 15 1 1719 551784720 551786437 0.000000e+00 2226.0
6 TraesCS3D01G102600 chr1A 90.282 1739 125 19 1 1719 504841500 504839786 0.000000e+00 2235.0
7 TraesCS3D01G102600 chr7B 90.017 1733 136 18 1 1719 150842119 150843828 0.000000e+00 2207.0
8 TraesCS3D01G102600 chr7B 84.173 417 43 12 1828 2231 641739851 641739445 1.280000e-102 383.0
9 TraesCS3D01G102600 chr7B 84.211 228 26 3 2013 2236 641372499 641372720 1.780000e-51 213.0
10 TraesCS3D01G102600 chr7B 100.000 36 0 0 1719 1754 641740593 641740558 1.470000e-07 67.6
11 TraesCS3D01G102600 chr5B 89.653 1730 155 14 1 1721 641300595 641298881 0.000000e+00 2182.0
12 TraesCS3D01G102600 chr6B 89.145 1732 150 23 1 1717 189103569 189105277 0.000000e+00 2122.0
13 TraesCS3D01G102600 chr2B 88.543 1737 163 17 1 1721 459481016 459479300 0.000000e+00 2073.0
14 TraesCS3D01G102600 chr4D 88.205 1738 157 30 1 1719 116524549 116522841 0.000000e+00 2030.0
15 TraesCS3D01G102600 chr7A 86.000 100 9 3 1848 1945 669867545 669867449 4.020000e-18 102.0


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 TraesCS3D01G102600 chr3D 55163840 55166127 2287 False 4226.0 4226 100.0000 1 2288 1 chr3D.!!$F2 2287
1 TraesCS3D01G102600 chr7D 463974105 463975822 1717 True 2248.0 2248 90.3690 1 1719 1 chr7D.!!$R1 1718
2 TraesCS3D01G102600 chr4B 551730120 551731829 1709 False 2239.0 2239 90.3820 9 1719 1 chr4B.!!$F1 1710
3 TraesCS3D01G102600 chr4B 551784720 551786437 1717 False 2226.0 2226 90.1380 1 1719 1 chr4B.!!$F2 1718
4 TraesCS3D01G102600 chr1A 504839786 504841500 1714 True 2235.0 2235 90.2820 1 1719 1 chr1A.!!$R1 1718
5 TraesCS3D01G102600 chr7B 150842119 150843828 1709 False 2207.0 2207 90.0170 1 1719 1 chr7B.!!$F1 1718
6 TraesCS3D01G102600 chr7B 641739445 641740593 1148 True 225.3 383 92.0865 1719 2231 2 chr7B.!!$R1 512
7 TraesCS3D01G102600 chr5B 641298881 641300595 1714 True 2182.0 2182 89.6530 1 1721 1 chr5B.!!$R1 1720
8 TraesCS3D01G102600 chr6B 189103569 189105277 1708 False 2122.0 2122 89.1450 1 1717 1 chr6B.!!$F1 1716
9 TraesCS3D01G102600 chr2B 459479300 459481016 1716 True 2073.0 2073 88.5430 1 1721 1 chr2B.!!$R1 1720
10 TraesCS3D01G102600 chr4D 116522841 116524549 1708 True 2030.0 2030 88.2050 1 1719 1 chr4D.!!$R1 1718

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
444 448 0.037326 GTTCGAGCACACCTCCATGA 60.037 55.0 0.0 0.0 37.27 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2804 0.03496 TGGCCTTATTGTAGCGCCAA 60.035 50.0 2.29 1.82 46.28 4.52 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
100 101 0.678684 TCGATCTGCCAGGTACGACA 60.679 55.000 0.00 0.00 0.00 4.35
139 140 3.332493 CTGGCATGTGCACCGCTTC 62.332 63.158 22.95 11.44 44.36 3.86
236 240 1.971357 CGGTCATTAGGAGCCCAGTAT 59.029 52.381 0.00 0.00 40.99 2.12
302 306 4.360643 GCCTGATTCATGGCCCAA 57.639 55.556 0.00 0.00 43.11 4.12
389 393 2.413142 GGCCTTCATGAGCACTGCC 61.413 63.158 8.97 7.96 0.00 4.85
398 402 2.299993 TGAGCACTGCCTTAGATTCG 57.700 50.000 0.00 0.00 0.00 3.34
444 448 0.037326 GTTCGAGCACACCTCCATGA 60.037 55.000 0.00 0.00 37.27 3.07
463 467 2.143122 GATGTTCTCGAACTTGGTGCA 58.857 47.619 10.75 0.00 41.67 4.57
536 541 2.349755 GGGTTGGCGTTGGAGCTA 59.650 61.111 0.00 0.00 37.29 3.32
585 598 3.823873 GGTTGACAGTGAGAGAAGAGAGA 59.176 47.826 0.00 0.00 0.00 3.10
588 601 3.073798 TGACAGTGAGAGAAGAGAGAGGT 59.926 47.826 0.00 0.00 0.00 3.85
632 646 4.850386 GGGTGAGTAAATATAGGGGGATGT 59.150 45.833 0.00 0.00 0.00 3.06
660 676 2.233431 GGAGAAGAGTGACAGTCATGCT 59.767 50.000 6.51 4.45 0.00 3.79
674 690 6.918043 CAGTCATGCTGTTTTAACTTTAGC 57.082 37.500 8.46 0.00 40.27 3.09
675 691 5.858581 CAGTCATGCTGTTTTAACTTTAGCC 59.141 40.000 8.46 0.00 40.27 3.93
676 692 5.534654 AGTCATGCTGTTTTAACTTTAGCCA 59.465 36.000 0.00 0.00 33.60 4.75
677 693 6.209391 AGTCATGCTGTTTTAACTTTAGCCAT 59.791 34.615 0.00 0.00 33.60 4.40
678 694 6.308766 GTCATGCTGTTTTAACTTTAGCCATG 59.691 38.462 0.00 0.00 33.60 3.66
679 695 6.208402 TCATGCTGTTTTAACTTTAGCCATGA 59.792 34.615 0.00 0.00 33.66 3.07
680 696 6.398234 TGCTGTTTTAACTTTAGCCATGAA 57.602 33.333 0.00 0.00 33.60 2.57
681 697 6.212955 TGCTGTTTTAACTTTAGCCATGAAC 58.787 36.000 0.00 0.00 33.60 3.18
714 730 3.077484 AGCCATGAACTATGTGCTGTT 57.923 42.857 0.00 0.00 39.92 3.16
719 735 4.978186 CATGAACTATGTGCTGTTCTTGG 58.022 43.478 11.41 0.00 41.00 3.61
742 758 3.688235 TCCATGAATTGTGTGCAGATCA 58.312 40.909 0.00 0.00 0.00 2.92
786 802 4.115199 GTGCTCCCGGCCCTTGAT 62.115 66.667 0.00 0.00 40.92 2.57
898 914 2.765807 ACGAGGGCATGGAGGAGG 60.766 66.667 0.00 0.00 0.00 4.30
1026 1045 2.301346 CTGGACTTCACCAAGCACTTT 58.699 47.619 0.00 0.00 39.59 2.66
1074 1094 0.249911 GGAACAACACCGACTGCTCT 60.250 55.000 0.00 0.00 0.00 4.09
1089 1109 0.670854 GCTCTTGGAAGGTGACGGTC 60.671 60.000 0.00 0.00 0.00 4.79
1200 1220 2.878429 CTCCTCACTCCCGACACG 59.122 66.667 0.00 0.00 0.00 4.49
1237 1258 0.525455 CGACGACGATGGCATTGAGA 60.525 55.000 21.46 0.00 42.66 3.27
1268 1289 2.809601 CGGGAAGCACGACGAAGG 60.810 66.667 0.00 0.00 0.00 3.46
1295 1316 4.176752 CAAGGAGTAGGGCCGGGC 62.177 72.222 22.00 22.00 0.00 6.13
1309 1330 1.971695 CGGGCCACCTCTTTCCAAC 60.972 63.158 4.39 0.00 33.28 3.77
1313 1334 1.543871 GGCCACCTCTTTCCAACGTAA 60.544 52.381 0.00 0.00 0.00 3.18
1331 1352 5.035443 ACGTAATATCGAGTCTGCTTTGAC 58.965 41.667 0.00 0.00 37.23 3.18
1381 1420 7.842982 TGTTATGAAGTGTGGTACTGCTTATA 58.157 34.615 0.00 0.00 40.26 0.98
1383 1422 8.979574 GTTATGAAGTGTGGTACTGCTTATATC 58.020 37.037 0.00 0.00 40.26 1.63
1384 1423 6.791867 TGAAGTGTGGTACTGCTTATATCT 57.208 37.500 0.00 0.00 40.26 1.98
1385 1424 6.573434 TGAAGTGTGGTACTGCTTATATCTG 58.427 40.000 0.00 0.00 40.26 2.90
1387 1426 6.791867 AGTGTGGTACTGCTTATATCTGAA 57.208 37.500 0.00 0.00 38.49 3.02
1388 1427 7.366847 AGTGTGGTACTGCTTATATCTGAAT 57.633 36.000 0.00 0.00 38.49 2.57
1392 1431 7.495606 TGTGGTACTGCTTATATCTGAATTGTG 59.504 37.037 0.00 0.00 0.00 3.33
1410 1454 3.329386 TGTGCTAGTTGATGCTCTGTTC 58.671 45.455 0.00 0.00 0.00 3.18
1421 1465 5.173664 TGATGCTCTGTTCATACTCTGTTG 58.826 41.667 0.00 0.00 0.00 3.33
1547 1591 2.158385 TGCCTTGGGTTTGTCCACTAAT 60.158 45.455 0.00 0.00 36.38 1.73
1548 1592 2.492088 GCCTTGGGTTTGTCCACTAATC 59.508 50.000 0.00 0.00 36.38 1.75
1550 1594 4.010349 CCTTGGGTTTGTCCACTAATCTC 58.990 47.826 0.00 0.00 36.38 2.75
1680 1724 4.223032 CAGGTTAGGTGGAGAAGTGTATGT 59.777 45.833 0.00 0.00 0.00 2.29
1754 1798 6.416514 GGCTAATAAACGACGTCATAAAAGG 58.583 40.000 17.16 0.00 0.00 3.11
1766 2363 4.260375 CGTCATAAAAGGGAGCTTCATTCG 60.260 45.833 0.00 0.00 0.00 3.34
1768 2365 5.123979 GTCATAAAAGGGAGCTTCATTCGTT 59.876 40.000 0.00 0.00 0.00 3.85
1770 2367 2.568623 AAGGGAGCTTCATTCGTTGT 57.431 45.000 0.00 0.00 0.00 3.32
1771 2368 3.695830 AAGGGAGCTTCATTCGTTGTA 57.304 42.857 0.00 0.00 0.00 2.41
1772 2369 3.252974 AGGGAGCTTCATTCGTTGTAG 57.747 47.619 0.00 0.00 0.00 2.74
1774 2371 2.673368 GGGAGCTTCATTCGTTGTAGTG 59.327 50.000 0.00 0.00 0.00 2.74
1776 2373 3.585862 GAGCTTCATTCGTTGTAGTGGA 58.414 45.455 0.00 0.00 0.00 4.02
1780 2473 6.170506 AGCTTCATTCGTTGTAGTGGAATAA 58.829 36.000 0.00 0.00 0.00 1.40
1791 2484 5.846203 TGTAGTGGAATAAATACTACGGCC 58.154 41.667 0.00 0.00 46.01 6.13
1798 2491 0.749049 AAATACTACGGCCGGACCTC 59.251 55.000 31.76 0.00 35.61 3.85
1807 2500 2.269241 CCGGACCTCTGGCTTTCC 59.731 66.667 0.00 0.00 35.28 3.13
1808 2501 2.125512 CGGACCTCTGGCTTTCCG 60.126 66.667 0.00 0.00 44.65 4.30
1809 2502 2.269241 GGACCTCTGGCTTTCCGG 59.731 66.667 0.00 0.00 40.23 5.14
1819 2512 1.077716 GCTTTCCGGCCATACTGGT 60.078 57.895 2.24 0.00 46.11 4.00
1820 2513 1.376609 GCTTTCCGGCCATACTGGTG 61.377 60.000 2.24 0.00 46.11 4.17
1821 2514 0.748005 CTTTCCGGCCATACTGGTGG 60.748 60.000 2.24 0.00 46.11 4.61
1846 2539 1.168407 CGGTCATGCATGTGGGATCC 61.168 60.000 25.43 16.54 0.00 3.36
1857 2550 2.199208 TGTGGGATCCATCACATGAGT 58.801 47.619 17.09 0.00 43.03 3.41
1861 2560 1.602311 GATCCATCACATGAGTGCCC 58.398 55.000 0.00 0.00 45.49 5.36
1877 2576 4.293648 CCTGCCGGTCGTGTCACA 62.294 66.667 1.90 0.00 0.00 3.58
1878 2577 2.734723 CTGCCGGTCGTGTCACAG 60.735 66.667 1.90 0.00 0.00 3.66
1881 2580 2.049433 CCGGTCGTGTCACAGTCC 60.049 66.667 3.42 2.95 0.00 3.85
1978 2677 2.959030 CGGTGGATCAGATTACTCTCCA 59.041 50.000 0.00 0.00 34.55 3.86
1980 2679 4.329462 GTGGATCAGATTACTCTCCACC 57.671 50.000 8.50 0.87 43.25 4.61
1981 2680 3.706594 GTGGATCAGATTACTCTCCACCA 59.293 47.826 8.50 2.96 43.25 4.17
1982 2681 3.706594 TGGATCAGATTACTCTCCACCAC 59.293 47.826 0.00 0.00 33.04 4.16
1983 2682 3.070302 GGATCAGATTACTCTCCACCACC 59.930 52.174 0.00 0.00 0.00 4.61
2000 2699 2.051345 CCAACGGCAGTGCGTTTC 60.051 61.111 18.39 1.39 0.00 2.78
2011 2712 0.782384 GTGCGTTTCGTCACTACAGG 59.218 55.000 8.51 0.00 33.64 4.00
2017 2718 4.440103 GCGTTTCGTCACTACAGGTATATG 59.560 45.833 0.00 0.00 0.00 1.78
2046 2747 5.407995 TGAAATTTGGATGCCGAAATGTTTC 59.592 36.000 0.00 0.00 30.23 2.78
2054 2755 5.394115 GGATGCCGAAATGTTTCCTTTATGT 60.394 40.000 0.25 0.00 33.68 2.29
2064 2765 8.814038 AATGTTTCCTTTATGTAGATTGCTCT 57.186 30.769 0.00 0.00 35.39 4.09
2067 2768 9.330063 TGTTTCCTTTATGTAGATTGCTCTATG 57.670 33.333 0.00 0.00 36.40 2.23
2068 2769 9.331282 GTTTCCTTTATGTAGATTGCTCTATGT 57.669 33.333 0.00 0.00 36.40 2.29
2069 2770 9.547753 TTTCCTTTATGTAGATTGCTCTATGTC 57.452 33.333 0.00 0.00 36.40 3.06
2070 2771 8.484214 TCCTTTATGTAGATTGCTCTATGTCT 57.516 34.615 0.00 0.00 36.40 3.41
2071 2772 8.363390 TCCTTTATGTAGATTGCTCTATGTCTG 58.637 37.037 0.00 0.00 36.40 3.51
2080 2781 5.483685 TTGCTCTATGTCTGTAACAAGGT 57.516 39.130 0.00 0.00 42.37 3.50
2084 2785 7.041721 TGCTCTATGTCTGTAACAAGGTAATG 58.958 38.462 0.00 0.00 42.37 1.90
2089 2790 5.804639 TGTCTGTAACAAGGTAATGCAGAT 58.195 37.500 0.00 0.00 34.03 2.90
2099 2800 7.895759 ACAAGGTAATGCAGATTTGTAAACAT 58.104 30.769 0.00 0.00 0.00 2.71
2103 2804 9.189156 AGGTAATGCAGATTTGTAAACATACAT 57.811 29.630 0.00 0.00 0.00 2.29
2106 2807 8.706492 AATGCAGATTTGTAAACATACATTGG 57.294 30.769 0.00 0.00 0.00 3.16
2107 2808 6.098679 TGCAGATTTGTAAACATACATTGGC 58.901 36.000 0.00 0.00 0.00 4.52
2108 2809 5.229887 GCAGATTTGTAAACATACATTGGCG 59.770 40.000 0.00 0.00 0.00 5.69
2109 2810 5.229887 CAGATTTGTAAACATACATTGGCGC 59.770 40.000 0.00 0.00 0.00 6.53
2110 2811 4.775058 TTTGTAAACATACATTGGCGCT 57.225 36.364 7.64 0.00 0.00 5.92
2111 2812 5.881777 TTTGTAAACATACATTGGCGCTA 57.118 34.783 7.64 0.00 0.00 4.26
2112 2813 4.868450 TGTAAACATACATTGGCGCTAC 57.132 40.909 7.64 0.00 0.00 3.58
2113 2814 4.254492 TGTAAACATACATTGGCGCTACA 58.746 39.130 7.64 0.00 0.00 2.74
2114 2815 4.695928 TGTAAACATACATTGGCGCTACAA 59.304 37.500 7.64 4.10 34.41 2.41
2121 2826 1.001378 CATTGGCGCTACAATAAGGCC 60.001 52.381 7.64 0.00 38.94 5.19
2127 2832 1.014352 GCTACAATAAGGCCACACGG 58.986 55.000 5.01 0.00 0.00 4.94
2129 2834 0.985760 TACAATAAGGCCACACGGGT 59.014 50.000 5.01 0.00 39.65 5.28
2133 2838 1.910580 ATAAGGCCACACGGGTCCTG 61.911 60.000 5.01 0.00 44.85 3.86
2149 2854 3.368323 GGTCCTGCACATTAACAAATGGG 60.368 47.826 3.41 0.00 36.66 4.00
2157 2862 3.006752 ACATTAACAAATGGGTGCACCTG 59.993 43.478 33.91 25.71 41.11 4.00
2162 2867 0.482446 AAATGGGTGCACCTGGAGAA 59.518 50.000 33.91 13.98 41.11 2.87
2172 2877 4.081642 GTGCACCTGGAGAAGTGAATAGTA 60.082 45.833 5.22 0.00 36.01 1.82
2209 2914 7.084486 ACGTTTCCTTCTTTAGAAAATGCATC 58.916 34.615 0.00 0.00 33.98 3.91
2226 2931 8.830201 AAATGCATCTAATTGTACTTTTTGCA 57.170 26.923 0.00 0.00 41.25 4.08
2231 2936 7.331687 GCATCTAATTGTACTTTTTGCACCAAT 59.668 33.333 0.00 0.00 0.00 3.16
2232 2937 9.853555 CATCTAATTGTACTTTTTGCACCAATA 57.146 29.630 0.00 0.00 0.00 1.90
2262 2967 5.871396 ATTGTGTATGTAGAATCGGGTCT 57.129 39.130 0.00 0.00 0.00 3.85
2263 2968 4.913335 TGTGTATGTAGAATCGGGTCTC 57.087 45.455 0.00 0.00 0.00 3.36
2264 2969 3.635373 TGTGTATGTAGAATCGGGTCTCC 59.365 47.826 0.00 0.00 0.00 3.71
2265 2970 3.635373 GTGTATGTAGAATCGGGTCTCCA 59.365 47.826 0.00 0.00 0.00 3.86
2266 2971 3.889538 TGTATGTAGAATCGGGTCTCCAG 59.110 47.826 0.00 0.00 0.00 3.86
2267 2972 1.112113 TGTAGAATCGGGTCTCCAGC 58.888 55.000 0.00 0.00 0.00 4.85
2268 2973 1.342076 TGTAGAATCGGGTCTCCAGCT 60.342 52.381 0.00 0.00 0.00 4.24
2269 2974 1.338655 GTAGAATCGGGTCTCCAGCTC 59.661 57.143 0.00 0.00 0.00 4.09
2270 2975 1.045911 AGAATCGGGTCTCCAGCTCC 61.046 60.000 0.00 0.00 0.00 4.70
2271 2976 1.002274 AATCGGGTCTCCAGCTCCT 59.998 57.895 0.00 0.00 0.00 3.69
2272 2977 0.261991 AATCGGGTCTCCAGCTCCTA 59.738 55.000 0.00 0.00 0.00 2.94
2273 2978 0.468400 ATCGGGTCTCCAGCTCCTAC 60.468 60.000 0.00 0.00 0.00 3.18
2274 2979 1.076632 CGGGTCTCCAGCTCCTACT 60.077 63.158 0.00 0.00 0.00 2.57
2275 2980 1.104577 CGGGTCTCCAGCTCCTACTC 61.105 65.000 0.00 0.00 0.00 2.59
2276 2981 1.104577 GGGTCTCCAGCTCCTACTCG 61.105 65.000 0.00 0.00 0.00 4.18
2277 2982 0.394625 GGTCTCCAGCTCCTACTCGT 60.395 60.000 0.00 0.00 0.00 4.18
2278 2983 1.018910 GTCTCCAGCTCCTACTCGTC 58.981 60.000 0.00 0.00 0.00 4.20
2279 2984 0.618981 TCTCCAGCTCCTACTCGTCA 59.381 55.000 0.00 0.00 0.00 4.35
2280 2985 1.004394 TCTCCAGCTCCTACTCGTCAA 59.996 52.381 0.00 0.00 0.00 3.18
2281 2986 1.819288 CTCCAGCTCCTACTCGTCAAA 59.181 52.381 0.00 0.00 0.00 2.69
2282 2987 1.544691 TCCAGCTCCTACTCGTCAAAC 59.455 52.381 0.00 0.00 0.00 2.93
2283 2988 1.404315 CCAGCTCCTACTCGTCAAACC 60.404 57.143 0.00 0.00 0.00 3.27
2284 2989 0.526662 AGCTCCTACTCGTCAAACCG 59.473 55.000 0.00 0.00 0.00 4.44
2285 2990 0.243095 GCTCCTACTCGTCAAACCGT 59.757 55.000 0.00 0.00 0.00 4.83
2286 2991 1.731750 GCTCCTACTCGTCAAACCGTC 60.732 57.143 0.00 0.00 0.00 4.79
2287 2992 0.883833 TCCTACTCGTCAAACCGTCC 59.116 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 0.603975 AGGAAGAAGAAGCGGTGCAC 60.604 55.000 8.80 8.80 0.00 4.57
236 240 3.118408 AGAAGTGGTGCAAGTACAAGACA 60.118 43.478 0.00 0.00 0.00 3.41
302 306 2.183478 TGGCAGTTGACATCATTCGT 57.817 45.000 0.00 0.00 0.00 3.85
389 393 3.243877 CGGACATGCAGAACGAATCTAAG 59.756 47.826 0.00 0.00 36.32 2.18
398 402 3.909662 ATGCCGGACATGCAGAAC 58.090 55.556 5.05 0.00 42.92 3.01
444 448 2.146342 CTGCACCAAGTTCGAGAACAT 58.854 47.619 17.00 3.44 43.47 2.71
463 467 3.626924 GGTGGTCGGCTGGTGACT 61.627 66.667 0.00 0.00 36.58 3.41
536 541 2.815945 CCCCATCGCCATGAGCTCT 61.816 63.158 16.19 0.00 40.39 4.09
585 598 1.982958 CCACCACTACTTACCCAACCT 59.017 52.381 0.00 0.00 0.00 3.50
588 601 0.694196 GCCCACCACTACTTACCCAA 59.306 55.000 0.00 0.00 0.00 4.12
632 646 3.589735 ACTGTCACTCTTCTCCTCCTCTA 59.410 47.826 0.00 0.00 0.00 2.43
660 676 6.040391 AGCAGTTCATGGCTAAAGTTAAAACA 59.960 34.615 0.00 0.00 38.90 2.83
670 686 3.701205 TGAAGAGCAGTTCATGGCTAA 57.299 42.857 0.00 0.00 41.22 3.09
671 687 3.701205 TTGAAGAGCAGTTCATGGCTA 57.299 42.857 1.95 0.00 41.22 3.93
673 689 3.863142 AATTGAAGAGCAGTTCATGGC 57.137 42.857 1.95 0.00 36.34 4.40
674 690 4.201990 GGCTAATTGAAGAGCAGTTCATGG 60.202 45.833 4.54 0.00 40.64 3.66
675 691 4.397103 TGGCTAATTGAAGAGCAGTTCATG 59.603 41.667 4.54 0.00 40.64 3.07
676 692 4.592942 TGGCTAATTGAAGAGCAGTTCAT 58.407 39.130 4.54 0.00 40.64 2.57
677 693 4.019792 TGGCTAATTGAAGAGCAGTTCA 57.980 40.909 4.54 0.00 40.64 3.18
678 694 4.637534 TCATGGCTAATTGAAGAGCAGTTC 59.362 41.667 4.54 0.00 40.64 3.01
679 695 4.592942 TCATGGCTAATTGAAGAGCAGTT 58.407 39.130 4.54 0.00 40.64 3.16
680 696 4.226427 TCATGGCTAATTGAAGAGCAGT 57.774 40.909 4.54 0.00 40.64 4.40
681 697 4.639310 AGTTCATGGCTAATTGAAGAGCAG 59.361 41.667 4.54 0.00 40.64 4.24
714 730 2.821378 CACACAATTCATGGAGCCAAGA 59.179 45.455 0.00 0.00 0.00 3.02
719 735 1.814394 TCTGCACACAATTCATGGAGC 59.186 47.619 0.00 0.00 32.32 4.70
742 758 1.133853 GCCCATCTCATTGCTCTCCTT 60.134 52.381 0.00 0.00 0.00 3.36
1074 1094 0.534203 GCTTGACCGTCACCTTCCAA 60.534 55.000 0.00 0.00 0.00 3.53
1089 1109 1.651240 CCCTGCCGTTCATCAGCTTG 61.651 60.000 0.00 0.00 0.00 4.01
1200 1220 2.863137 GTCGAAGATGATGACCTTGAGC 59.137 50.000 0.00 0.00 40.67 4.26
1237 1258 2.073816 CTTCCCGCACTTGTTAACGAT 58.926 47.619 0.26 0.00 0.00 3.73
1295 1316 4.506654 CGATATTACGTTGGAAAGAGGTGG 59.493 45.833 0.00 0.00 0.00 4.61
1302 1323 4.802039 GCAGACTCGATATTACGTTGGAAA 59.198 41.667 0.00 0.00 34.70 3.13
1309 1330 5.034797 TGTCAAAGCAGACTCGATATTACG 58.965 41.667 5.72 0.00 39.27 3.18
1313 1334 5.016051 ACATGTCAAAGCAGACTCGATAT 57.984 39.130 0.00 0.00 39.27 1.63
1331 1352 6.806249 AGTTCAACGCATAAACCATAAACATG 59.194 34.615 0.00 0.00 0.00 3.21
1381 1420 5.191426 AGCATCAACTAGCACAATTCAGAT 58.809 37.500 0.00 0.00 0.00 2.90
1383 1422 4.634883 AGAGCATCAACTAGCACAATTCAG 59.365 41.667 0.00 0.00 37.82 3.02
1384 1423 4.393990 CAGAGCATCAACTAGCACAATTCA 59.606 41.667 0.00 0.00 37.82 2.57
1385 1424 4.394300 ACAGAGCATCAACTAGCACAATTC 59.606 41.667 0.00 0.00 37.82 2.17
1387 1426 3.947868 ACAGAGCATCAACTAGCACAAT 58.052 40.909 0.00 0.00 37.82 2.71
1388 1427 3.407424 ACAGAGCATCAACTAGCACAA 57.593 42.857 0.00 0.00 37.82 3.33
1392 1431 5.355596 AGTATGAACAGAGCATCAACTAGC 58.644 41.667 0.00 0.00 37.82 3.42
1410 1454 6.314648 ACACATCATAAGCACAACAGAGTATG 59.685 38.462 0.00 0.00 0.00 2.39
1421 1465 4.260907 CCATGTAGCACACATCATAAGCAC 60.261 45.833 1.26 0.00 44.99 4.40
1468 1512 2.644798 ACCTCTTTGGCTAGTTGGTGAT 59.355 45.455 0.00 0.00 40.22 3.06
1547 1591 0.467290 GGTGTTTGGTTGCCTGGAGA 60.467 55.000 0.00 0.00 0.00 3.71
1548 1592 0.754957 TGGTGTTTGGTTGCCTGGAG 60.755 55.000 0.00 0.00 0.00 3.86
1550 1594 1.741525 CTGGTGTTTGGTTGCCTGG 59.258 57.895 0.00 0.00 0.00 4.45
1680 1724 0.249155 GCGCTACAGTACCCGCATTA 60.249 55.000 13.41 0.00 45.21 1.90
1754 1798 2.673368 CCACTACAACGAATGAAGCTCC 59.327 50.000 0.00 0.00 0.00 4.70
1766 2363 6.201615 GGCCGTAGTATTTATTCCACTACAAC 59.798 42.308 10.67 3.09 43.06 3.32
1768 2365 5.507817 CGGCCGTAGTATTTATTCCACTACA 60.508 44.000 19.50 0.00 43.06 2.74
1770 2367 4.022068 CCGGCCGTAGTATTTATTCCACTA 60.022 45.833 26.12 0.00 0.00 2.74
1771 2368 3.243975 CCGGCCGTAGTATTTATTCCACT 60.244 47.826 26.12 0.00 0.00 4.00
1772 2369 3.062042 CCGGCCGTAGTATTTATTCCAC 58.938 50.000 26.12 0.00 0.00 4.02
1774 2371 3.320626 GTCCGGCCGTAGTATTTATTCC 58.679 50.000 26.12 0.00 0.00 3.01
1776 2373 2.967887 AGGTCCGGCCGTAGTATTTATT 59.032 45.455 26.12 0.00 43.70 1.40
1780 2473 0.106318 AGAGGTCCGGCCGTAGTATT 60.106 55.000 26.12 3.92 43.70 1.89
1791 2484 2.125512 CGGAAAGCCAGAGGTCCG 60.126 66.667 0.00 0.00 46.23 4.79
1811 2504 2.749865 CCGCGTTGCCACCAGTATG 61.750 63.158 4.92 0.00 0.00 2.39
1812 2505 2.435938 CCGCGTTGCCACCAGTAT 60.436 61.111 4.92 0.00 0.00 2.12
1813 2506 3.869473 GACCGCGTTGCCACCAGTA 62.869 63.158 4.92 0.00 0.00 2.74
1816 2509 4.634703 ATGACCGCGTTGCCACCA 62.635 61.111 4.92 0.00 0.00 4.17
1817 2510 4.101790 CATGACCGCGTTGCCACC 62.102 66.667 4.92 0.00 0.00 4.61
1818 2511 4.759096 GCATGACCGCGTTGCCAC 62.759 66.667 4.92 0.00 0.00 5.01
1820 2513 3.814268 ATGCATGACCGCGTTGCC 61.814 61.111 4.92 0.00 35.51 4.52
1821 2514 2.577644 CATGCATGACCGCGTTGC 60.578 61.111 22.59 9.43 36.91 4.17
1822 2515 1.512522 CACATGCATGACCGCGTTG 60.513 57.895 32.75 14.69 33.35 4.10
1823 2516 2.689785 CCACATGCATGACCGCGTT 61.690 57.895 32.75 5.74 33.35 4.84
1824 2517 3.126879 CCACATGCATGACCGCGT 61.127 61.111 32.75 6.55 33.35 6.01
1825 2518 3.879682 CCCACATGCATGACCGCG 61.880 66.667 32.75 14.24 33.35 6.46
1826 2519 1.789078 GATCCCACATGCATGACCGC 61.789 60.000 32.75 12.50 0.00 5.68
1834 2527 3.500331 TGTGATGGATCCCACATGC 57.500 52.632 17.09 4.85 38.26 4.06
1846 2539 1.381928 GGCAGGGCACTCATGTGATG 61.382 60.000 0.94 0.00 46.55 3.07
1861 2560 2.734723 CTGTGACACGACCGGCAG 60.735 66.667 0.00 0.00 0.00 4.85
1875 2574 0.107456 CTTCTGTGGCACAGGACTGT 59.893 55.000 38.88 0.00 45.94 3.55
1877 2576 1.757306 CCTTCTGTGGCACAGGACT 59.243 57.895 38.88 0.00 45.94 3.85
1878 2577 4.386413 CCTTCTGTGGCACAGGAC 57.614 61.111 38.88 6.44 45.94 3.85
1935 2634 2.103042 GTGGTGCAGTGCCGATCTC 61.103 63.158 13.72 0.00 0.00 2.75
1960 2659 3.706594 GTGGTGGAGAGTAATCTGATCCA 59.293 47.826 0.00 0.00 35.24 3.41
1967 2666 2.677037 CGTTGGGTGGTGGAGAGTAATC 60.677 54.545 0.00 0.00 0.00 1.75
2000 2699 3.639538 GGTGCATATACCTGTAGTGACG 58.360 50.000 0.00 0.00 37.74 4.35
2011 2712 5.922544 GCATCCAAATTTCAGGTGCATATAC 59.077 40.000 15.09 0.00 34.36 1.47
2017 2718 1.736696 CGGCATCCAAATTTCAGGTGC 60.737 52.381 12.59 12.59 33.83 5.01
2046 2747 8.147058 ACAGACATAGAGCAATCTACATAAAGG 58.853 37.037 0.00 0.00 0.00 3.11
2054 2755 7.124298 ACCTTGTTACAGACATAGAGCAATCTA 59.876 37.037 0.00 0.00 38.26 1.98
2064 2765 6.941857 TCTGCATTACCTTGTTACAGACATA 58.058 36.000 0.00 0.00 38.26 2.29
2066 2767 5.222079 TCTGCATTACCTTGTTACAGACA 57.778 39.130 0.00 0.00 36.19 3.41
2067 2768 6.743575 AATCTGCATTACCTTGTTACAGAC 57.256 37.500 0.00 0.00 35.68 3.51
2068 2769 6.714810 ACAAATCTGCATTACCTTGTTACAGA 59.285 34.615 0.00 0.00 37.13 3.41
2069 2770 6.913170 ACAAATCTGCATTACCTTGTTACAG 58.087 36.000 0.00 0.00 0.00 2.74
2070 2771 6.892658 ACAAATCTGCATTACCTTGTTACA 57.107 33.333 0.00 0.00 0.00 2.41
2071 2772 9.124807 GTTTACAAATCTGCATTACCTTGTTAC 57.875 33.333 0.00 0.00 0.00 2.50
2080 2781 9.800433 CCAATGTATGTTTACAAATCTGCATTA 57.200 29.630 0.00 0.00 41.51 1.90
2084 2785 5.229887 CGCCAATGTATGTTTACAAATCTGC 59.770 40.000 0.00 0.00 41.51 4.26
2089 2790 4.775058 AGCGCCAATGTATGTTTACAAA 57.225 36.364 2.29 0.00 41.51 2.83
2099 2800 2.875933 GCCTTATTGTAGCGCCAATGTA 59.124 45.455 18.52 8.32 35.85 2.29
2103 2804 0.034960 TGGCCTTATTGTAGCGCCAA 60.035 50.000 2.29 1.82 46.28 4.52
2105 2806 0.746563 TGTGGCCTTATTGTAGCGCC 60.747 55.000 2.29 0.00 40.16 6.53
2106 2807 0.377203 GTGTGGCCTTATTGTAGCGC 59.623 55.000 3.32 0.00 0.00 5.92
2107 2808 0.650512 CGTGTGGCCTTATTGTAGCG 59.349 55.000 3.32 0.00 0.00 4.26
2108 2809 1.014352 CCGTGTGGCCTTATTGTAGC 58.986 55.000 3.32 0.00 0.00 3.58
2109 2810 1.065709 ACCCGTGTGGCCTTATTGTAG 60.066 52.381 3.32 0.00 37.83 2.74
2110 2811 0.985760 ACCCGTGTGGCCTTATTGTA 59.014 50.000 3.32 0.00 37.83 2.41
2111 2812 0.322187 GACCCGTGTGGCCTTATTGT 60.322 55.000 3.32 0.00 37.83 2.71
2112 2813 1.029947 GGACCCGTGTGGCCTTATTG 61.030 60.000 3.32 0.00 37.83 1.90
2113 2814 1.205460 AGGACCCGTGTGGCCTTATT 61.205 55.000 3.32 0.00 37.35 1.40
2114 2815 1.615424 AGGACCCGTGTGGCCTTAT 60.615 57.895 3.32 0.00 37.35 1.73
2121 2826 0.321210 TAATGTGCAGGACCCGTGTG 60.321 55.000 0.00 0.00 0.00 3.82
2127 2832 3.368323 CCCATTTGTTAATGTGCAGGACC 60.368 47.826 0.00 0.00 39.62 4.46
2129 2834 3.257873 CACCCATTTGTTAATGTGCAGGA 59.742 43.478 0.00 0.00 39.62 3.86
2133 2838 2.736192 GTGCACCCATTTGTTAATGTGC 59.264 45.455 5.22 5.54 41.00 4.57
2149 2854 2.191128 ATTCACTTCTCCAGGTGCAC 57.809 50.000 8.80 8.80 33.91 4.57
2157 2862 8.738645 ATTTTGTGGATACTATTCACTTCTCC 57.261 34.615 8.66 0.00 37.61 3.71
2162 2867 9.444600 AACGTAATTTTGTGGATACTATTCACT 57.555 29.630 8.66 0.00 37.61 3.41
2172 2877 6.894339 AGAAGGAAACGTAATTTTGTGGAT 57.106 33.333 0.00 0.00 0.00 3.41
2185 2890 7.308435 AGATGCATTTTCTAAAGAAGGAAACG 58.692 34.615 0.00 0.00 35.43 3.60
2236 2941 9.256228 AGACCCGATTCTACATACACAATATAT 57.744 33.333 0.00 0.00 0.00 0.86
2237 2942 8.645814 AGACCCGATTCTACATACACAATATA 57.354 34.615 0.00 0.00 0.00 0.86
2238 2943 7.309867 GGAGACCCGATTCTACATACACAATAT 60.310 40.741 0.00 0.00 0.00 1.28
2239 2944 6.015688 GGAGACCCGATTCTACATACACAATA 60.016 42.308 0.00 0.00 0.00 1.90
2240 2945 5.221461 GGAGACCCGATTCTACATACACAAT 60.221 44.000 0.00 0.00 0.00 2.71
2241 2946 4.098960 GGAGACCCGATTCTACATACACAA 59.901 45.833 0.00 0.00 0.00 3.33
2242 2947 3.635373 GGAGACCCGATTCTACATACACA 59.365 47.826 0.00 0.00 0.00 3.72
2243 2948 3.635373 TGGAGACCCGATTCTACATACAC 59.365 47.826 0.00 0.00 30.92 2.90
2244 2949 3.889538 CTGGAGACCCGATTCTACATACA 59.110 47.826 0.00 0.00 35.80 2.29
2245 2950 3.305471 GCTGGAGACCCGATTCTACATAC 60.305 52.174 0.00 0.00 35.80 2.39
2246 2951 2.891580 GCTGGAGACCCGATTCTACATA 59.108 50.000 0.00 0.00 35.80 2.29
2247 2952 1.689273 GCTGGAGACCCGATTCTACAT 59.311 52.381 0.00 0.00 35.80 2.29
2248 2953 1.112113 GCTGGAGACCCGATTCTACA 58.888 55.000 0.00 0.00 33.74 2.74
2249 2954 1.338655 GAGCTGGAGACCCGATTCTAC 59.661 57.143 0.00 0.00 34.29 2.59
2250 2955 1.693627 GAGCTGGAGACCCGATTCTA 58.306 55.000 0.00 0.00 34.29 2.10
2251 2956 1.045911 GGAGCTGGAGACCCGATTCT 61.046 60.000 0.00 0.00 34.29 2.40
2252 2957 1.045911 AGGAGCTGGAGACCCGATTC 61.046 60.000 0.00 0.00 34.29 2.52
2253 2958 0.261991 TAGGAGCTGGAGACCCGATT 59.738 55.000 0.00 0.00 34.29 3.34
2254 2959 0.468400 GTAGGAGCTGGAGACCCGAT 60.468 60.000 0.00 0.00 34.29 4.18
2255 2960 1.076923 GTAGGAGCTGGAGACCCGA 60.077 63.158 0.00 0.00 34.29 5.14
2256 2961 1.076632 AGTAGGAGCTGGAGACCCG 60.077 63.158 0.00 0.00 34.29 5.28
2257 2962 1.104577 CGAGTAGGAGCTGGAGACCC 61.105 65.000 0.00 0.00 0.00 4.46
2258 2963 0.394625 ACGAGTAGGAGCTGGAGACC 60.395 60.000 0.00 0.00 0.00 3.85
2259 2964 1.018910 GACGAGTAGGAGCTGGAGAC 58.981 60.000 0.00 0.00 0.00 3.36
2260 2965 0.618981 TGACGAGTAGGAGCTGGAGA 59.381 55.000 0.00 0.00 0.00 3.71
2261 2966 1.464734 TTGACGAGTAGGAGCTGGAG 58.535 55.000 0.00 0.00 0.00 3.86
2262 2967 1.544691 GTTTGACGAGTAGGAGCTGGA 59.455 52.381 0.00 0.00 0.00 3.86
2263 2968 1.404315 GGTTTGACGAGTAGGAGCTGG 60.404 57.143 0.00 0.00 0.00 4.85
2264 2969 1.732732 CGGTTTGACGAGTAGGAGCTG 60.733 57.143 0.00 0.00 35.47 4.24
2265 2970 0.526662 CGGTTTGACGAGTAGGAGCT 59.473 55.000 0.00 0.00 35.47 4.09
2266 2971 0.243095 ACGGTTTGACGAGTAGGAGC 59.757 55.000 0.00 0.00 37.61 4.70
2267 2972 1.135460 GGACGGTTTGACGAGTAGGAG 60.135 57.143 0.00 0.00 37.61 3.69
2268 2973 0.883833 GGACGGTTTGACGAGTAGGA 59.116 55.000 0.00 0.00 37.61 2.94
2269 2974 3.413522 GGACGGTTTGACGAGTAGG 57.586 57.895 0.00 0.00 37.61 3.18


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

AutoCloner maintained by Alex Coulton.