Multiple sequence alignment - TraesCS7D01G325100

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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 TraesCS7D01G325100 chr7D 100.000 5762 0 0 1 5762 415439165 415433404 0.000000e+00 10641.0
1 TraesCS7D01G325100 chr7D 100.000 1446 0 0 6180 7625 415432986 415431541 0.000000e+00 2671.0
2 TraesCS7D01G325100 chr7D 82.639 144 18 6 478 619 141225477 141225615 3.740000e-23 121.0
3 TraesCS7D01G325100 chr7D 77.928 222 26 18 3814 4020 351782952 351783165 4.830000e-22 117.0
4 TraesCS7D01G325100 chr7B 96.223 2992 77 13 2798 5762 429193200 429190218 0.000000e+00 4867.0
5 TraesCS7D01G325100 chr7B 95.255 1686 61 8 1110 2786 429195085 429193410 0.000000e+00 2652.0
6 TraesCS7D01G325100 chr7B 96.319 1467 28 10 6180 7625 429189893 429188432 0.000000e+00 2386.0
7 TraesCS7D01G325100 chr7B 84.740 865 122 8 1660 2514 153750645 153749781 0.000000e+00 857.0
8 TraesCS7D01G325100 chr7B 88.049 728 70 10 1 720 429196597 429195879 0.000000e+00 846.0
9 TraesCS7D01G325100 chr7B 90.598 351 24 8 809 1154 429195295 429194949 2.510000e-124 457.0
10 TraesCS7D01G325100 chr7B 82.332 283 30 10 2513 2786 153749678 153749407 2.140000e-55 228.0
11 TraesCS7D01G325100 chr7A 96.738 1686 44 6 1110 2786 477236754 477235071 0.000000e+00 2798.0
12 TraesCS7D01G325100 chr7A 96.161 1563 49 7 3841 5397 477233274 477231717 0.000000e+00 2543.0
13 TraesCS7D01G325100 chr7A 95.913 1468 36 8 6180 7625 477224239 477222774 0.000000e+00 2357.0
14 TraesCS7D01G325100 chr7A 95.775 1065 36 2 2798 3853 477234749 477233685 0.000000e+00 1709.0
15 TraesCS7D01G325100 chr7A 94.300 807 25 7 1 807 477238248 477237463 0.000000e+00 1216.0
16 TraesCS7D01G325100 chr7A 90.823 316 15 5 851 1154 477236922 477236609 1.980000e-110 411.0
17 TraesCS7D01G325100 chr7A 98.068 207 4 0 5394 5600 477224599 477224393 2.020000e-95 361.0
18 TraesCS7D01G325100 chr7A 98.936 94 1 0 5669 5762 477224388 477224295 1.320000e-37 169.0
19 TraesCS7D01G325100 chr6D 91.376 603 35 9 1841 2441 417647027 417646440 0.000000e+00 809.0
20 TraesCS7D01G325100 chr6D 87.379 103 10 1 4556 4658 96747799 96747898 1.740000e-21 115.0
21 TraesCS7D01G325100 chr6B 89.244 344 22 4 1858 2200 626378298 626377969 4.260000e-112 416.0
22 TraesCS7D01G325100 chr2A 90.674 193 13 1 3820 4012 640274387 640274200 1.270000e-62 252.0
23 TraesCS7D01G325100 chr2A 91.346 104 8 1 4547 4650 535152440 535152542 2.870000e-29 141.0
24 TraesCS7D01G325100 chr2A 80.874 183 20 13 3839 4011 420213135 420213312 6.210000e-26 130.0
25 TraesCS7D01G325100 chr4A 89.617 183 16 3 3831 4011 75927221 75927040 5.950000e-56 230.0
26 TraesCS7D01G325100 chr4A 78.774 212 27 15 3814 4012 176802288 176802494 8.030000e-25 126.0
27 TraesCS7D01G325100 chr4A 75.135 185 40 6 138 318 36102828 36102646 1.760000e-11 82.4
28 TraesCS7D01G325100 chr3B 76.898 303 64 6 44 344 130309834 130309536 4.730000e-37 167.0
29 TraesCS7D01G325100 chr3B 84.167 120 15 4 4540 4656 74281849 74281967 6.250000e-21 113.0
30 TraesCS7D01G325100 chr3B 86.869 99 12 1 4561 4658 64003196 64003098 8.090000e-20 110.0
31 TraesCS7D01G325100 chr4D 90.090 111 11 0 4549 4659 500440024 500440134 2.220000e-30 145.0
32 TraesCS7D01G325100 chr4D 79.147 211 27 14 3814 4012 448533840 448534045 6.210000e-26 130.0
33 TraesCS7D01G325100 chr4D 87.255 102 10 2 4557 4657 379505557 379505458 6.250000e-21 113.0
34 TraesCS7D01G325100 chr5A 89.189 111 12 0 4549 4659 681286286 681286396 1.030000e-28 139.0
35 TraesCS7D01G325100 chr2D 78.774 212 26 16 3814 4012 480203313 480203518 2.890000e-24 124.0
36 TraesCS7D01G325100 chr1D 82.734 139 15 7 478 615 49434431 49434301 1.740000e-21 115.0
37 TraesCS7D01G325100 chr4B 75.862 174 28 8 140 308 534329187 534329023 8.200000e-10 76.8


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 TraesCS7D01G325100 chr7D 415431541 415439165 7624 True 6656.000000 10641 100.0000 1 7625 2 chr7D.!!$R1 7624
1 TraesCS7D01G325100 chr7B 429188432 429196597 8165 True 2241.600000 4867 93.2888 1 7625 5 chr7B.!!$R2 7624
2 TraesCS7D01G325100 chr7B 153749407 153750645 1238 True 542.500000 857 83.5360 1660 2786 2 chr7B.!!$R1 1126
3 TraesCS7D01G325100 chr7A 477231717 477238248 6531 True 1735.400000 2798 94.7594 1 5397 5 chr7A.!!$R2 5396
4 TraesCS7D01G325100 chr7A 477222774 477224599 1825 True 962.333333 2357 97.6390 5394 7625 3 chr7A.!!$R1 2231
5 TraesCS7D01G325100 chr6D 417646440 417647027 587 True 809.000000 809 91.3760 1841 2441 1 chr6D.!!$R1 600

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
588 596 0.310543 CGCTAGCCTTTGCACACAAA 59.689 50.0 9.66 0.0 43.45 2.83 F
1081 1917 0.106918 TCCGGCAACCATAATCCACC 60.107 55.0 0.00 0.0 0.00 4.61 F
1503 2339 0.107017 CCTTCATCACCGAGCCCAAT 60.107 55.0 0.00 0.0 0.00 3.16 F
2700 3667 0.813184 GGTCACTGGATGCAATGGTG 59.187 55.0 0.00 0.0 0.00 4.17 F
3931 5649 0.526662 CGTTGGACTCGCTACCTCTT 59.473 55.0 0.00 0.0 0.00 2.85 F
5104 6838 0.037877 AATCTCAAGCCACAGCAGCT 59.962 50.0 0.00 0.0 44.19 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 2624 0.537188 GATCCGGGAACAAGAGCTCA 59.463 55.0 17.77 0.0 0.00 4.26 R
2788 3761 0.387239 GCAGCCGAAAACATGGTGTC 60.387 55.0 0.00 0.0 0.00 3.67 R
3153 4444 0.033504 CAGGTTGTACCAGTCGCTGT 59.966 55.0 0.00 0.0 41.95 4.40 R
4659 6389 0.321564 TTCCAACATCTCCACCTGCG 60.322 55.0 0.00 0.0 0.00 5.18 R
5125 6859 0.595588 CGGAGGATGATCTGAGGTCG 59.404 60.0 0.00 0.0 0.00 4.79 R
7013 8762 1.527433 GCCTGTTCTCCAAGTTGGCC 61.527 60.0 17.68 0.0 37.47 5.36 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
194 202 0.549950 CAGCATCCACTTCTCCCCAT 59.450 55.000 0.00 0.00 0.00 4.00
363 371 3.432588 CCAGTCTCGTCGTCGCCT 61.433 66.667 0.00 0.00 36.96 5.52
453 461 4.036380 GCTCCAAGTTTTTCGAAGGAGAAA 59.964 41.667 25.12 10.12 44.12 2.52
492 500 5.844004 TGGCAAATTGGTAATACGTGTTTT 58.156 33.333 1.91 0.00 0.00 2.43
585 593 0.310854 AAACGCTAGCCTTTGCACAC 59.689 50.000 9.66 0.00 41.13 3.82
587 595 0.817634 ACGCTAGCCTTTGCACACAA 60.818 50.000 9.66 0.00 41.13 3.33
588 596 0.310543 CGCTAGCCTTTGCACACAAA 59.689 50.000 9.66 0.00 43.45 2.83
642 651 2.491693 CAACATGTGGTGGGATGGTTAC 59.508 50.000 0.00 0.00 0.00 2.50
645 654 1.057471 TGTGGTGGGATGGTTACGAA 58.943 50.000 0.00 0.00 0.00 3.85
662 671 4.909696 ACGAAGACAGTGATATCTCCAG 57.090 45.455 3.98 0.00 0.00 3.86
663 672 4.274147 ACGAAGACAGTGATATCTCCAGT 58.726 43.478 3.98 2.50 0.00 4.00
817 1653 3.057033 ACATACAACGCGTAGAAAGGACT 60.057 43.478 14.46 0.00 32.28 3.85
818 1654 2.061740 ACAACGCGTAGAAAGGACTC 57.938 50.000 14.46 0.00 0.00 3.36
824 1660 2.008329 GCGTAGAAAGGACTCTCTCGA 58.992 52.381 0.00 0.00 0.00 4.04
839 1675 1.207329 TCTCGATGTCTCCGTCTCAGA 59.793 52.381 0.00 0.00 0.00 3.27
842 1678 1.943340 CGATGTCTCCGTCTCAGATGA 59.057 52.381 0.00 0.00 0.00 2.92
849 1685 4.580995 GTCTCCGTCTCAGATGAGGATTTA 59.419 45.833 9.87 0.00 42.30 1.40
956 1792 1.089920 CGATCCAAGAGGCCAACAAG 58.910 55.000 5.01 0.00 33.74 3.16
985 1821 0.325671 TGCTCTCCTCCGGGAAGAAT 60.326 55.000 0.00 0.00 41.69 2.40
1069 1905 3.081409 GGCCTACTCCTCCGGCAA 61.081 66.667 0.00 0.00 45.53 4.52
1070 1906 2.187163 GCCTACTCCTCCGGCAAC 59.813 66.667 0.00 0.00 43.25 4.17
1071 1907 2.901042 CCTACTCCTCCGGCAACC 59.099 66.667 0.00 0.00 0.00 3.77
1072 1908 1.987855 CCTACTCCTCCGGCAACCA 60.988 63.158 0.00 0.00 0.00 3.67
1073 1909 1.338136 CCTACTCCTCCGGCAACCAT 61.338 60.000 0.00 0.00 0.00 3.55
1074 1910 1.410004 CTACTCCTCCGGCAACCATA 58.590 55.000 0.00 0.00 0.00 2.74
1075 1911 1.760613 CTACTCCTCCGGCAACCATAA 59.239 52.381 0.00 0.00 0.00 1.90
1076 1912 1.213296 ACTCCTCCGGCAACCATAAT 58.787 50.000 0.00 0.00 0.00 1.28
1077 1913 1.141053 ACTCCTCCGGCAACCATAATC 59.859 52.381 0.00 0.00 0.00 1.75
1078 1914 0.472471 TCCTCCGGCAACCATAATCC 59.528 55.000 0.00 0.00 0.00 3.01
1079 1915 0.182537 CCTCCGGCAACCATAATCCA 59.817 55.000 0.00 0.00 0.00 3.41
1080 1916 1.308998 CTCCGGCAACCATAATCCAC 58.691 55.000 0.00 0.00 0.00 4.02
1081 1917 0.106918 TCCGGCAACCATAATCCACC 60.107 55.000 0.00 0.00 0.00 4.61
1082 1918 1.444119 CCGGCAACCATAATCCACCG 61.444 60.000 0.00 0.00 38.88 4.94
1083 1919 0.462937 CGGCAACCATAATCCACCGA 60.463 55.000 0.00 0.00 41.61 4.69
1084 1920 1.021968 GGCAACCATAATCCACCGAC 58.978 55.000 0.00 0.00 0.00 4.79
1085 1921 1.021968 GCAACCATAATCCACCGACC 58.978 55.000 0.00 0.00 0.00 4.79
1086 1922 1.680555 GCAACCATAATCCACCGACCA 60.681 52.381 0.00 0.00 0.00 4.02
1087 1923 2.014128 CAACCATAATCCACCGACCAC 58.986 52.381 0.00 0.00 0.00 4.16
1088 1924 0.544697 ACCATAATCCACCGACCACC 59.455 55.000 0.00 0.00 0.00 4.61
1089 1925 0.531974 CCATAATCCACCGACCACCG 60.532 60.000 0.00 0.00 38.18 4.94
1090 1926 0.177141 CATAATCCACCGACCACCGT 59.823 55.000 0.00 0.00 36.31 4.83
1091 1927 0.906775 ATAATCCACCGACCACCGTT 59.093 50.000 0.00 0.00 36.31 4.44
1092 1928 0.247185 TAATCCACCGACCACCGTTC 59.753 55.000 0.00 0.00 36.31 3.95
1093 1929 2.459202 AATCCACCGACCACCGTTCC 62.459 60.000 0.00 0.00 36.31 3.62
1094 1930 3.931247 CCACCGACCACCGTTCCA 61.931 66.667 0.00 0.00 36.31 3.53
1095 1931 2.357034 CACCGACCACCGTTCCAG 60.357 66.667 0.00 0.00 36.31 3.86
1096 1932 2.522436 ACCGACCACCGTTCCAGA 60.522 61.111 0.00 0.00 36.31 3.86
1097 1933 2.048503 CCGACCACCGTTCCAGAC 60.049 66.667 0.00 0.00 36.31 3.51
1098 1934 2.732016 CGACCACCGTTCCAGACA 59.268 61.111 0.00 0.00 0.00 3.41
1099 1935 1.663702 CGACCACCGTTCCAGACAC 60.664 63.158 0.00 0.00 0.00 3.67
1100 1936 1.663702 GACCACCGTTCCAGACACG 60.664 63.158 0.00 0.00 37.39 4.49
1101 1937 3.041940 CCACCGTTCCAGACACGC 61.042 66.667 0.00 0.00 36.27 5.34
1102 1938 2.029073 CACCGTTCCAGACACGCT 59.971 61.111 0.00 0.00 36.27 5.07
1103 1939 2.029073 ACCGTTCCAGACACGCTG 59.971 61.111 0.00 0.00 44.49 5.18
1104 1940 2.029073 CCGTTCCAGACACGCTGT 59.971 61.111 0.00 0.00 43.33 4.40
1112 1948 4.504132 GACACGCTGTCAGGATCC 57.496 61.111 2.48 2.48 46.22 3.36
1113 1949 1.591703 GACACGCTGTCAGGATCCA 59.408 57.895 15.82 0.00 46.22 3.41
1114 1950 0.459237 GACACGCTGTCAGGATCCAG 60.459 60.000 15.82 6.08 46.22 3.86
1117 1953 2.202987 GCTGTCAGGATCCAGCCG 60.203 66.667 15.82 0.00 46.55 5.52
1118 1954 2.202987 CTGTCAGGATCCAGCCGC 60.203 66.667 15.82 0.56 0.00 6.53
1119 1955 3.746949 CTGTCAGGATCCAGCCGCC 62.747 68.421 15.82 0.00 0.00 6.13
1120 1956 4.899239 GTCAGGATCCAGCCGCCG 62.899 72.222 15.82 0.00 0.00 6.46
1137 1973 4.516195 GCTCCTTCCTCGGCCGTC 62.516 72.222 27.15 0.48 0.00 4.79
1138 1974 4.194720 CTCCTTCCTCGGCCGTCG 62.195 72.222 27.15 17.27 40.90 5.12
1296 2132 4.787280 CCACCGGCCCTCTCCTCT 62.787 72.222 0.00 0.00 0.00 3.69
1503 2339 0.107017 CCTTCATCACCGAGCCCAAT 60.107 55.000 0.00 0.00 0.00 3.16
1785 2624 4.320456 CAGCGTGCCTGGACCACT 62.320 66.667 0.00 0.00 37.93 4.00
1923 2765 5.231991 GGGTATTTTATTTTGCGATGTGCTG 59.768 40.000 0.00 0.00 46.63 4.41
2075 2918 6.321435 TGTGTCGAGTTGGAAGATCTATATGT 59.679 38.462 0.00 0.00 0.00 2.29
2522 3481 7.977904 TGTGTGCTGAACAAATATCTGAATAG 58.022 34.615 0.00 0.00 41.57 1.73
2700 3667 0.813184 GGTCACTGGATGCAATGGTG 59.187 55.000 0.00 0.00 0.00 4.17
2708 3675 4.201657 CTGGATGCAATGGTGATCTGTAA 58.798 43.478 0.00 0.00 0.00 2.41
2793 3766 9.553064 AATCATGATAGACTTTCTTATGACACC 57.447 33.333 9.04 0.00 29.49 4.16
2794 3767 8.078060 TCATGATAGACTTTCTTATGACACCA 57.922 34.615 0.00 0.00 0.00 4.17
2795 3768 8.708378 TCATGATAGACTTTCTTATGACACCAT 58.292 33.333 0.00 0.00 36.81 3.55
2796 3769 8.771766 CATGATAGACTTTCTTATGACACCATG 58.228 37.037 0.00 0.00 34.31 3.66
2851 4134 3.601443 ATCTGTTGTCAGCTGTCTACC 57.399 47.619 18.90 5.84 41.10 3.18
2945 4236 5.945784 CCTGAATCTAATGGTTTTCACCTCA 59.054 40.000 0.00 0.00 44.61 3.86
3068 4359 6.521527 ACTATATCCATTTTGCCCTCTCTT 57.478 37.500 0.00 0.00 0.00 2.85
3070 4361 2.978156 TCCATTTTGCCCTCTCTTGT 57.022 45.000 0.00 0.00 0.00 3.16
3153 4444 6.938030 ACAGTAATATTTCCCAACAGAAACGA 59.062 34.615 0.00 0.00 38.51 3.85
3316 4608 2.488204 TGATTCAAATGAGGCGACCA 57.512 45.000 0.00 0.00 0.00 4.02
3575 4867 1.258445 CGTGGGCAGTACCTCCTTCT 61.258 60.000 0.00 0.00 39.10 2.85
3788 5080 2.029380 TGACCACTAGTTGACACCATCG 60.029 50.000 0.08 0.00 0.00 3.84
3803 5095 7.778083 TGACACCATCGTAATACTACATTTCT 58.222 34.615 0.00 0.00 0.00 2.52
3874 5590 2.554806 TTCGCACCATAGTACTCGTG 57.445 50.000 0.00 5.98 0.00 4.35
3909 5627 2.203422 CGGTGGGTTTCCTGGCAA 60.203 61.111 0.00 0.00 0.00 4.52
3931 5649 0.526662 CGTTGGACTCGCTACCTCTT 59.473 55.000 0.00 0.00 0.00 2.85
4087 5806 5.407387 CCATTTCCACATTGAGAAGCAAAAG 59.593 40.000 0.00 0.00 40.48 2.27
4093 5812 5.987347 CCACATTGAGAAGCAAAAGTTGAAT 59.013 36.000 0.00 0.00 40.48 2.57
4128 5847 5.175090 GCCTTAGCTAATGTTTGACCATC 57.825 43.478 6.64 0.00 35.50 3.51
4492 6214 9.196552 CACATGATATAGACGAAGAATTTAGCA 57.803 33.333 0.00 0.00 0.00 3.49
4569 6299 9.338622 CTTTCATTAAGTTATATTCCCTCCGTT 57.661 33.333 0.00 0.00 0.00 4.44
4628 6358 8.842280 TGAACTAAAATGAACTAAAACCACGAT 58.158 29.630 0.00 0.00 0.00 3.73
4659 6389 6.636454 TTGGGATGGAGGGAATATATACAC 57.364 41.667 0.00 0.00 0.00 2.90
4660 6390 4.714802 TGGGATGGAGGGAATATATACACG 59.285 45.833 0.00 0.00 0.00 4.49
4681 6415 2.029918 GCAGGTGGAGATGTTGGAAAAC 60.030 50.000 0.00 0.00 0.00 2.43
4739 6473 1.137697 GGATTCCGACATAGGGGGTT 58.862 55.000 0.00 0.00 0.00 4.11
4820 6554 7.066525 TGGAATAAAAGAGAAACAACGTTGAGT 59.933 33.333 33.66 20.18 0.00 3.41
5076 6810 4.184079 GAGCAATTGATCCAAGCACTTT 57.816 40.909 12.75 0.00 0.00 2.66
5104 6838 0.037877 AATCTCAAGCCACAGCAGCT 59.962 50.000 0.00 0.00 44.19 4.24
5125 6859 0.624254 AATTCTTCCTCCGTTCCCCC 59.376 55.000 0.00 0.00 0.00 5.40
5309 7043 8.381387 GTTGTAGCGATAAAAAGGAAAGACTAG 58.619 37.037 0.00 0.00 0.00 2.57
5428 7162 0.109913 CCCTCCGGGTTTATTAGCCC 59.890 60.000 0.00 0.00 41.58 5.19
5597 7332 4.082125 AGTTAGGTTCAGGCTTTGGATTG 58.918 43.478 0.00 0.00 0.00 2.67
5600 7335 2.108952 AGGTTCAGGCTTTGGATTGACT 59.891 45.455 0.00 0.00 0.00 3.41
5631 7366 1.270252 CCATGCAAGGTGGGTTTTCAC 60.270 52.381 0.00 0.00 36.95 3.18
6307 8042 2.364002 GGCAGAGTTTTTAGCCCAAACA 59.636 45.455 0.00 0.00 41.25 2.83
6835 8583 5.549228 TGGAGCAGGAGGTCATTTATATGAT 59.451 40.000 0.00 0.00 42.49 2.45
6914 8662 3.510531 TGGCACAGTAATGGTTTGGTA 57.489 42.857 0.00 0.00 0.00 3.25
6916 8664 4.411927 TGGCACAGTAATGGTTTGGTATT 58.588 39.130 0.00 0.00 0.00 1.89
7026 8775 2.429930 CCACGGCCAACTTGGAGA 59.570 61.111 12.37 0.00 40.96 3.71
7332 9081 1.081242 CTGTGCGGTGTTGATTGGC 60.081 57.895 0.00 0.00 0.00 4.52
7441 9193 5.186021 TCTCCTCTTCCTAGTTGTCACAATC 59.814 44.000 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 120 1.474330 TCTCCAGCGCACTTCATCTA 58.526 50.000 11.47 0.00 0.00 1.98
194 202 5.963214 TCTTGATGATCATGAGGAGGAAA 57.037 39.130 14.30 0.00 0.00 3.13
363 371 2.270923 CACATCAATCTTCTTCGGCGA 58.729 47.619 4.99 4.99 0.00 5.54
453 461 5.612725 TTTGCCATGGAAAAAGAAGAAGT 57.387 34.783 16.10 0.00 0.00 3.01
466 474 4.142271 ACACGTATTACCAATTTGCCATGG 60.142 41.667 7.63 7.63 42.60 3.66
625 634 1.281419 TCGTAACCATCCCACCACAT 58.719 50.000 0.00 0.00 0.00 3.21
642 651 4.261405 GGACTGGAGATATCACTGTCTTCG 60.261 50.000 23.60 5.38 0.00 3.79
645 654 3.957497 GTGGACTGGAGATATCACTGTCT 59.043 47.826 23.60 0.43 0.00 3.41
662 671 2.558359 CCTGATTTGAACCTTGGTGGAC 59.442 50.000 0.00 0.00 39.71 4.02
663 672 2.490718 CCCTGATTTGAACCTTGGTGGA 60.491 50.000 0.00 0.00 39.71 4.02
818 1654 1.597195 CTGAGACGGAGACATCGAGAG 59.403 57.143 0.00 0.00 0.00 3.20
824 1660 2.092158 TCCTCATCTGAGACGGAGACAT 60.092 50.000 12.91 0.00 44.74 3.06
876 1712 1.275657 CGTCAAACTTGCTTCGCGT 59.724 52.632 5.77 0.00 0.00 6.01
1066 1902 1.021968 GGTCGGTGGATTATGGTTGC 58.978 55.000 0.00 0.00 0.00 4.17
1067 1903 2.014128 GTGGTCGGTGGATTATGGTTG 58.986 52.381 0.00 0.00 0.00 3.77
1068 1904 1.064979 GGTGGTCGGTGGATTATGGTT 60.065 52.381 0.00 0.00 0.00 3.67
1069 1905 0.544697 GGTGGTCGGTGGATTATGGT 59.455 55.000 0.00 0.00 0.00 3.55
1070 1906 0.531974 CGGTGGTCGGTGGATTATGG 60.532 60.000 0.00 0.00 34.75 2.74
1071 1907 0.177141 ACGGTGGTCGGTGGATTATG 59.823 55.000 0.00 0.00 44.45 1.90
1072 1908 0.906775 AACGGTGGTCGGTGGATTAT 59.093 50.000 0.00 0.00 44.45 1.28
1073 1909 0.247185 GAACGGTGGTCGGTGGATTA 59.753 55.000 0.00 0.00 39.92 1.75
1074 1910 1.004200 GAACGGTGGTCGGTGGATT 60.004 57.895 0.00 0.00 39.92 3.01
1075 1911 2.660802 GAACGGTGGTCGGTGGAT 59.339 61.111 0.00 0.00 39.92 3.41
1076 1912 3.618750 GGAACGGTGGTCGGTGGA 61.619 66.667 0.00 0.00 39.92 4.02
1077 1913 3.876589 CTGGAACGGTGGTCGGTGG 62.877 68.421 0.00 0.00 39.92 4.61
1078 1914 2.357034 CTGGAACGGTGGTCGGTG 60.357 66.667 0.00 0.00 39.92 4.94
1079 1915 2.522436 TCTGGAACGGTGGTCGGT 60.522 61.111 0.00 0.00 44.24 4.69
1080 1916 2.048503 GTCTGGAACGGTGGTCGG 60.049 66.667 0.00 0.00 44.45 4.79
1081 1917 1.663702 GTGTCTGGAACGGTGGTCG 60.664 63.158 0.00 0.00 45.88 4.79
1082 1918 1.663702 CGTGTCTGGAACGGTGGTC 60.664 63.158 0.00 0.00 37.39 4.02
1083 1919 2.420043 CGTGTCTGGAACGGTGGT 59.580 61.111 0.00 0.00 37.39 4.16
1084 1920 3.041940 GCGTGTCTGGAACGGTGG 61.042 66.667 0.00 0.00 41.31 4.61
1096 1932 1.593787 CTGGATCCTGACAGCGTGT 59.406 57.895 14.23 0.00 0.00 4.49
1097 1933 4.509756 CTGGATCCTGACAGCGTG 57.490 61.111 14.23 0.00 0.00 5.34
1101 1937 2.202987 GCGGCTGGATCCTGACAG 60.203 66.667 23.06 16.24 37.76 3.51
1102 1938 3.785859 GGCGGCTGGATCCTGACA 61.786 66.667 23.06 0.00 0.00 3.58
1103 1939 4.899239 CGGCGGCTGGATCCTGAC 62.899 72.222 21.91 18.29 0.00 3.51
1120 1956 4.516195 GACGGCCGAGGAAGGAGC 62.516 72.222 35.90 5.10 0.00 4.70
1121 1957 4.194720 CGACGGCCGAGGAAGGAG 62.195 72.222 35.90 9.24 41.76 3.69
1148 1984 0.537371 GGGGATTATGGTTGCCGGAG 60.537 60.000 5.05 0.00 0.00 4.63
1149 1985 1.282653 TGGGGATTATGGTTGCCGGA 61.283 55.000 5.05 0.00 0.00 5.14
1150 1986 0.396417 TTGGGGATTATGGTTGCCGG 60.396 55.000 0.00 0.00 0.00 6.13
1151 1987 1.032014 CTTGGGGATTATGGTTGCCG 58.968 55.000 0.00 0.00 0.00 5.69
1152 1988 2.031870 GACTTGGGGATTATGGTTGCC 58.968 52.381 0.00 0.00 0.00 4.52
1503 2339 1.226859 CTCCGCCGAGCAAACGATA 60.227 57.895 0.00 0.00 35.09 2.92
1711 2550 0.538057 TCCCTTGTGAAAGCTGCCAG 60.538 55.000 0.00 0.00 0.00 4.85
1785 2624 0.537188 GATCCGGGAACAAGAGCTCA 59.463 55.000 17.77 0.00 0.00 4.26
1923 2765 3.126343 ACCACGTTTTCACAAGTTCAGAC 59.874 43.478 0.00 0.00 0.00 3.51
2075 2918 6.211587 CATCAGGAATGCTGGTTTTGATAA 57.788 37.500 1.05 0.00 0.00 1.75
2314 3161 4.342665 TGGGTAACATGTTTTCAGGGTTTC 59.657 41.667 17.78 0.00 35.77 2.78
2682 3649 1.825090 TCACCATTGCATCCAGTGAC 58.175 50.000 5.55 0.00 32.75 3.67
2700 3667 6.261158 GGAAAACAGCCTAATCCTTACAGATC 59.739 42.308 0.00 0.00 0.00 2.75
2708 3675 4.043435 AGTGAAGGAAAACAGCCTAATCCT 59.957 41.667 0.00 0.00 42.22 3.24
2786 3759 1.541147 CAGCCGAAAACATGGTGTCAT 59.459 47.619 0.94 0.00 0.00 3.06
2787 3760 0.950836 CAGCCGAAAACATGGTGTCA 59.049 50.000 0.94 0.00 0.00 3.58
2788 3761 0.387239 GCAGCCGAAAACATGGTGTC 60.387 55.000 0.00 0.00 0.00 3.67
2791 3764 0.749649 TTTGCAGCCGAAAACATGGT 59.250 45.000 0.00 0.00 0.00 3.55
2792 3765 1.139163 GTTTGCAGCCGAAAACATGG 58.861 50.000 0.00 0.00 36.50 3.66
2793 3766 1.139163 GGTTTGCAGCCGAAAACATG 58.861 50.000 5.88 0.00 37.89 3.21
2794 3767 0.749649 TGGTTTGCAGCCGAAAACAT 59.250 45.000 5.88 0.00 37.89 2.71
2795 3768 0.532573 TTGGTTTGCAGCCGAAAACA 59.467 45.000 5.88 1.19 37.89 2.83
2796 3769 1.208259 CTTGGTTTGCAGCCGAAAAC 58.792 50.000 0.00 0.00 35.89 2.43
2851 4134 1.068333 CCACAACTCAGGGCGAAATTG 60.068 52.381 0.00 0.00 0.00 2.32
2945 4236 5.453057 CCTGAGCTAGATCTAATGCACAGTT 60.453 44.000 25.61 7.71 40.63 3.16
2998 4289 4.676924 GCATATACCTGAAGCGAAAAATGC 59.323 41.667 0.00 0.00 0.00 3.56
3097 4388 1.466025 TTTTGAAGGGGCAGCTGCAG 61.466 55.000 37.63 10.11 44.36 4.41
3153 4444 0.033504 CAGGTTGTACCAGTCGCTGT 59.966 55.000 0.00 0.00 41.95 4.40
3316 4608 4.029520 ACCTGATGAGAAGTACATGAGCT 58.970 43.478 0.00 0.00 30.04 4.09
3575 4867 2.036098 CATGCTCTGCCCACCCAA 59.964 61.111 0.00 0.00 0.00 4.12
3874 5590 2.951745 CACTCGCTCGCCATCGAC 60.952 66.667 0.00 0.00 40.21 4.20
3931 5649 5.073691 AGAAACATTCAGGAGGAGAGGAAAA 59.926 40.000 0.00 0.00 0.00 2.29
4017 5736 5.671493 AGAAGGTGGTTATGCATGTAGTAC 58.329 41.667 10.16 2.09 0.00 2.73
4128 5847 3.084039 TGTCAGGCTTATTGCTTTGGAG 58.916 45.455 0.00 0.00 42.39 3.86
4373 6095 9.618890 AGTGTGTATGCTGAAACTGAAATATAT 57.381 29.630 0.00 0.00 0.00 0.86
4492 6214 8.051535 AGAATATGGTTCATGTGATTCAGAACT 58.948 33.333 13.70 2.58 40.05 3.01
4628 6358 6.606241 ATTCCCTCCATCCCAAAATAAGTA 57.394 37.500 0.00 0.00 0.00 2.24
4657 6387 1.300971 CCAACATCTCCACCTGCGTG 61.301 60.000 0.00 0.00 39.91 5.34
4659 6389 0.321564 TTCCAACATCTCCACCTGCG 60.322 55.000 0.00 0.00 0.00 5.18
4660 6390 1.909700 TTTCCAACATCTCCACCTGC 58.090 50.000 0.00 0.00 0.00 4.85
4739 6473 3.706055 GTGAGCCTTCACCAGTTCA 57.294 52.632 0.00 0.00 46.47 3.18
4820 6554 6.037281 TGCGTATTTTGAGTTATAATTCCGCA 59.963 34.615 18.52 18.52 37.71 5.69
5076 6810 3.149196 GTGGCTTGAGATTTGGTGAAGA 58.851 45.455 0.00 0.00 0.00 2.87
5104 6838 1.280998 GGGGAACGGAGGAAGAATTGA 59.719 52.381 0.00 0.00 0.00 2.57
5125 6859 0.595588 CGGAGGATGATCTGAGGTCG 59.404 60.000 0.00 0.00 0.00 4.79
5263 6997 5.163893 ACAACTAAAATGCGGTCACGATAAG 60.164 40.000 0.00 0.00 44.60 1.73
5274 7008 7.044966 CCTTTTTATCGCTACAACTAAAATGCG 60.045 37.037 0.00 0.00 43.95 4.73
5309 7043 7.332182 CACCTCAGAAGATAAGACAAGTTTACC 59.668 40.741 0.00 0.00 0.00 2.85
5387 7121 9.549984 GAGGGAGGAAGTATATTAGTATTTCCT 57.450 37.037 9.76 9.76 46.99 3.36
5625 7360 3.363627 ACCCAACCCTTTAACGTGAAAA 58.636 40.909 0.00 0.00 0.00 2.29
5631 7366 2.951269 GGGACCCAACCCTTTAACG 58.049 57.895 5.33 0.00 45.90 3.18
6307 8042 6.160576 ACATGCAACAAAGATAACAGGTTT 57.839 33.333 0.00 0.00 0.00 3.27
6481 8218 3.950397 TGGAAGCACAGGTACAATAAGG 58.050 45.455 0.00 0.00 0.00 2.69
6723 8463 3.957671 ATGCAGATGTATTGTGAAGCG 57.042 42.857 0.00 0.00 0.00 4.68
7013 8762 1.527433 GCCTGTTCTCCAAGTTGGCC 61.527 60.000 17.68 0.00 37.47 5.36
7026 8775 2.116125 GGCTTGTGAGGGCCTGTT 59.884 61.111 12.95 0.00 44.48 3.16
7332 9081 4.281182 AGGGAGCATTCTATACCAGTAACG 59.719 45.833 0.00 0.00 0.00 3.18
7441 9193 8.184304 AGTATGCTAGGAGTACTAATTGGAAG 57.816 38.462 0.00 0.00 0.00 3.46
7593 9351 9.472361 CATTTTAGGAAGGCATGAATCAAATAG 57.528 33.333 0.00 0.00 0.00 1.73
7602 9362 3.386932 AGGCATTTTAGGAAGGCATGA 57.613 42.857 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.