Multiple sequence alignment - TraesCS1B01G292700

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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 TraesCS1B01G292700 chr1B 100.000 3005 0 0 1 3005 510207308 510210312 0.000000e+00 5550
1 TraesCS1B01G292700 chr1B 84.085 1929 153 77 1134 3005 537493257 537491426 0.000000e+00 1720
2 TraesCS1B01G292700 chr1A 91.806 2929 115 29 120 3004 481215972 481218819 0.000000e+00 3964
3 TraesCS1B01G292700 chr1A 91.515 2475 121 29 578 3005 433525714 433528146 0.000000e+00 3325
4 TraesCS1B01G292700 chr1A 94.682 1937 76 7 150 2064 433736235 433738166 0.000000e+00 2981
5 TraesCS1B01G292700 chr1A 91.346 1768 100 18 627 2358 399893814 399892064 0.000000e+00 2368
6 TraesCS1B01G292700 chr1A 94.153 1488 62 5 894 2358 106533116 106534601 0.000000e+00 2242
7 TraesCS1B01G292700 chr1A 86.545 1925 146 54 1134 2972 496853449 496851552 0.000000e+00 2015
8 TraesCS1B01G292700 chr1A 97.117 763 21 1 132 894 106532317 106533078 0.000000e+00 1286
9 TraesCS1B01G292700 chr1A 98.058 515 10 0 121 635 399895045 399894531 0.000000e+00 896
10 TraesCS1B01G292700 chr1A 84.973 925 61 26 2117 3005 433738523 433739405 0.000000e+00 867
11 TraesCS1B01G292700 chr5D 92.619 1951 92 12 894 2820 88143258 88145180 0.000000e+00 2758
12 TraesCS1B01G292700 chr5D 96.658 778 21 3 121 894 88142444 88143220 0.000000e+00 1288
13 TraesCS1B01G292700 chr4B 95.219 1715 49 5 1292 3005 451335689 451334007 0.000000e+00 2682
14 TraesCS1B01G292700 chr4B 95.160 1715 49 6 1292 3005 451242309 451240628 0.000000e+00 2676
15 TraesCS1B01G292700 chr4B 95.044 1715 52 5 1292 3005 451311090 451309408 0.000000e+00 2665
16 TraesCS1B01G292700 chr4B 94.982 1714 53 10 1292 3005 451261759 451260079 0.000000e+00 2658
17 TraesCS1B01G292700 chr4B 77.725 211 29 16 2592 2795 451309857 451309658 2.450000e-21 113
18 TraesCS1B01G292700 chr1D 90.405 2001 91 36 1049 3005 83127372 83129315 0.000000e+00 2538
19 TraesCS1B01G292700 chr1D 92.896 1112 41 4 894 2002 82304308 82305384 0.000000e+00 1581
20 TraesCS1B01G292700 chr1D 84.029 1678 142 65 1376 3005 400411456 400409857 0.000000e+00 1498
21 TraesCS1B01G292700 chr1D 96.859 764 17 5 132 894 83126096 83126853 0.000000e+00 1271
22 TraesCS1B01G292700 chr1D 97.746 488 10 1 408 894 82303783 82304270 0.000000e+00 839
23 TraesCS1B01G292700 chr1D 96.296 459 16 1 133 591 400412565 400412108 0.000000e+00 752
24 TraesCS1B01G292700 chr6A 94.836 1162 51 1 894 2046 161156814 161155653 0.000000e+00 1805
25 TraesCS1B01G292700 chr6A 93.801 855 44 1 894 1739 161412053 161411199 0.000000e+00 1277
26 TraesCS1B01G292700 chr6A 96.475 766 24 3 121 886 161157622 161156860 0.000000e+00 1262
27 TraesCS1B01G292700 chr6A 96.569 612 20 1 287 897 161412699 161412088 0.000000e+00 1013
28 TraesCS1B01G292700 chr5B 96.000 125 2 1 17 138 419852956 419853080 1.830000e-47 200
29 TraesCS1B01G292700 chr5B 100.000 107 0 0 17 123 275239747 275239853 6.570000e-47 198
30 TraesCS1B01G292700 chr5B 98.214 56 1 0 894 949 99743235 99743290 6.860000e-17 99
31 TraesCS1B01G292700 chr3B 99.083 109 1 0 17 125 43724852 43724744 2.360000e-46 196
32 TraesCS1B01G292700 chr3B 97.368 114 2 1 17 129 689513962 689514075 3.060000e-45 193
33 TraesCS1B01G292700 chr3B 95.833 120 2 3 17 133 595692075 595691956 1.100000e-44 191
34 TraesCS1B01G292700 chr2B 95.200 125 4 2 17 140 69059991 69059868 2.360000e-46 196
35 TraesCS1B01G292700 chr2B 92.537 134 5 4 17 148 331010320 331010190 1.420000e-43 187
36 TraesCS1B01G292700 chr6B 100.000 104 0 0 17 120 160667158 160667261 3.060000e-45 193
37 TraesCS1B01G292700 chr4A 95.122 123 1 5 17 135 420020480 420020359 3.950000e-44 189


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 TraesCS1B01G292700 chr1B 510207308 510210312 3004 False 5550.0 5550 100.0000 1 3005 1 chr1B.!!$F1 3004
1 TraesCS1B01G292700 chr1B 537491426 537493257 1831 True 1720.0 1720 84.0850 1134 3005 1 chr1B.!!$R1 1871
2 TraesCS1B01G292700 chr1A 481215972 481218819 2847 False 3964.0 3964 91.8060 120 3004 1 chr1A.!!$F2 2884
3 TraesCS1B01G292700 chr1A 433525714 433528146 2432 False 3325.0 3325 91.5150 578 3005 1 chr1A.!!$F1 2427
4 TraesCS1B01G292700 chr1A 496851552 496853449 1897 True 2015.0 2015 86.5450 1134 2972 1 chr1A.!!$R1 1838
5 TraesCS1B01G292700 chr1A 433736235 433739405 3170 False 1924.0 2981 89.8275 150 3005 2 chr1A.!!$F4 2855
6 TraesCS1B01G292700 chr1A 106532317 106534601 2284 False 1764.0 2242 95.6350 132 2358 2 chr1A.!!$F3 2226
7 TraesCS1B01G292700 chr1A 399892064 399895045 2981 True 1632.0 2368 94.7020 121 2358 2 chr1A.!!$R2 2237
8 TraesCS1B01G292700 chr5D 88142444 88145180 2736 False 2023.0 2758 94.6385 121 2820 2 chr5D.!!$F1 2699
9 TraesCS1B01G292700 chr4B 451334007 451335689 1682 True 2682.0 2682 95.2190 1292 3005 1 chr4B.!!$R3 1713
10 TraesCS1B01G292700 chr4B 451240628 451242309 1681 True 2676.0 2676 95.1600 1292 3005 1 chr4B.!!$R1 1713
11 TraesCS1B01G292700 chr4B 451260079 451261759 1680 True 2658.0 2658 94.9820 1292 3005 1 chr4B.!!$R2 1713
12 TraesCS1B01G292700 chr4B 451309408 451311090 1682 True 1389.0 2665 86.3845 1292 3005 2 chr4B.!!$R4 1713
13 TraesCS1B01G292700 chr1D 83126096 83129315 3219 False 1904.5 2538 93.6320 132 3005 2 chr1D.!!$F2 2873
14 TraesCS1B01G292700 chr1D 82303783 82305384 1601 False 1210.0 1581 95.3210 408 2002 2 chr1D.!!$F1 1594
15 TraesCS1B01G292700 chr1D 400409857 400412565 2708 True 1125.0 1498 90.1625 133 3005 2 chr1D.!!$R1 2872
16 TraesCS1B01G292700 chr6A 161155653 161157622 1969 True 1533.5 1805 95.6555 121 2046 2 chr6A.!!$R1 1925
17 TraesCS1B01G292700 chr6A 161411199 161412699 1500 True 1145.0 1277 95.1850 287 1739 2 chr6A.!!$R2 1452

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
45 46 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.0 0.00 0.0 37.28 3.67 F
46 47 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.0 0.00 0.0 34.81 2.73 F
1046 1859 0.585357 GGCGAGCTACATCTTGCATG 59.415 55.0 5.49 0.0 43.62 4.06 F
1246 2386 0.975040 GAGGCAGGGAAGAGAGCTGA 60.975 60.0 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1057 2196 0.037232 GAACACGAGCCTAGGTTGCT 60.037 55.0 11.31 0.4 43.03 3.91 R
1886 3512 0.108424 GCCACCACTAGCTCTGTCAG 60.108 60.0 0.00 0.0 0.00 3.51 R
1906 3542 0.321210 TGCATACCACCAGGAACACG 60.321 55.0 0.00 0.0 38.69 4.49 R
2920 5153 4.812626 ACGTATTCAAAGAAAGTTCACGGT 59.187 37.5 0.00 0.0 0.00 4.83 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
20 21 3.259207 GGATCGCATTGATGTGCTTAC 57.741 47.619 0.00 0.00 42.88 2.34
21 22 2.613595 GGATCGCATTGATGTGCTTACA 59.386 45.455 0.00 0.00 42.88 2.41
22 23 3.303593 GGATCGCATTGATGTGCTTACAG 60.304 47.826 0.00 0.00 42.88 2.74
23 24 2.971307 TCGCATTGATGTGCTTACAGA 58.029 42.857 0.00 0.00 42.88 3.41
24 25 3.333804 TCGCATTGATGTGCTTACAGAA 58.666 40.909 0.00 0.00 42.88 3.02
25 26 3.750652 TCGCATTGATGTGCTTACAGAAA 59.249 39.130 0.00 0.00 42.88 2.52
26 27 4.395854 TCGCATTGATGTGCTTACAGAAAT 59.604 37.500 0.00 0.00 42.88 2.17
27 28 4.497966 CGCATTGATGTGCTTACAGAAATG 59.502 41.667 10.86 10.86 42.88 2.32
28 29 5.404946 GCATTGATGTGCTTACAGAAATGT 58.595 37.500 14.18 0.00 41.82 2.71
29 30 6.554419 GCATTGATGTGCTTACAGAAATGTA 58.446 36.000 14.18 0.00 41.82 2.29
30 31 6.690098 GCATTGATGTGCTTACAGAAATGTAG 59.310 38.462 14.18 0.00 41.82 2.74
31 32 6.741992 TTGATGTGCTTACAGAAATGTAGG 57.258 37.500 0.00 0.00 0.00 3.18
32 33 5.185454 TGATGTGCTTACAGAAATGTAGGG 58.815 41.667 0.59 0.00 0.00 3.53
33 34 4.901197 TGTGCTTACAGAAATGTAGGGA 57.099 40.909 0.59 0.00 0.00 4.20
34 35 5.235850 TGTGCTTACAGAAATGTAGGGAA 57.764 39.130 0.59 0.00 0.00 3.97
35 36 5.626142 TGTGCTTACAGAAATGTAGGGAAA 58.374 37.500 0.59 0.00 0.00 3.13
36 37 5.705441 TGTGCTTACAGAAATGTAGGGAAAG 59.295 40.000 0.59 0.00 0.00 2.62
37 38 5.123979 GTGCTTACAGAAATGTAGGGAAAGG 59.876 44.000 0.59 0.00 0.00 3.11
38 39 4.096532 GCTTACAGAAATGTAGGGAAAGGC 59.903 45.833 0.59 0.00 0.00 4.35
39 40 5.501156 CTTACAGAAATGTAGGGAAAGGCT 58.499 41.667 0.00 0.00 0.00 4.58
40 41 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
41 42 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
42 43 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
43 44 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
44 45 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
45 46 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
46 47 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
47 48 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
48 49 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
49 50 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
50 51 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
51 52 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
52 53 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
53 54 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
54 55 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
55 56 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
56 57 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
57 58 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
58 59 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
59 60 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
60 61 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
61 62 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
62 63 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
67 68 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
68 69 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
69 70 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
70 71 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
71 72 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
72 73 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
73 74 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
74 75 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
75 76 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
81 82 4.735599 GGACCCTTCCCCGACCCT 62.736 72.222 0.00 0.00 35.57 4.34
82 83 3.400054 GACCCTTCCCCGACCCTG 61.400 72.222 0.00 0.00 0.00 4.45
108 109 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
109 110 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
110 111 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
111 112 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
112 113 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
113 114 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
119 120 2.917227 CACCGGGCTGCCCTTTTT 60.917 61.111 33.39 13.23 42.67 1.94
127 128 2.501316 GGGCTGCCCTTTTTATTGATGT 59.499 45.455 30.42 0.00 41.34 3.06
129 130 3.055891 GGCTGCCCTTTTTATTGATGTGT 60.056 43.478 7.66 0.00 0.00 3.72
130 131 3.928375 GCTGCCCTTTTTATTGATGTGTG 59.072 43.478 0.00 0.00 0.00 3.82
172 176 7.938715 TCCAGTCTTCTACTAACGAAATATCC 58.061 38.462 0.00 0.00 35.76 2.59
608 617 4.082571 GCTCATAAACTTGGCTGATGTTGT 60.083 41.667 0.00 0.00 0.00 3.32
734 1469 6.588719 ATTGCCAAGCTCTTGTATGTTTAA 57.411 33.333 8.60 0.00 38.85 1.52
886 1622 3.165071 ACCAGGGAAGCCTTAACAAATG 58.835 45.455 0.00 0.00 0.00 2.32
1046 1859 0.585357 GGCGAGCTACATCTTGCATG 59.415 55.000 5.49 0.00 43.62 4.06
1057 2196 4.314961 ACATCTTGCATGTACAAACGAGA 58.685 39.130 16.62 16.62 0.00 4.04
1060 2199 2.162319 TGCATGTACAAACGAGAGCA 57.838 45.000 0.00 0.00 0.00 4.26
1224 2364 2.123854 ATCGGGGCTAGCGAGTCA 60.124 61.111 9.00 0.00 0.00 3.41
1246 2386 0.975040 GAGGCAGGGAAGAGAGCTGA 60.975 60.000 0.00 0.00 0.00 4.26
1248 2388 1.548357 GGCAGGGAAGAGAGCTGACA 61.548 60.000 0.00 0.00 0.00 3.58
1488 3091 5.112129 AGACCGTTGGCTAATATCCTTTT 57.888 39.130 0.00 0.00 0.00 2.27
1687 3290 1.002624 CAAGGGAAGCAGCCGGTTA 60.003 57.895 1.90 0.00 31.57 2.85
1764 3373 4.025396 CCTCTATATGTTGCTTTGCTCACG 60.025 45.833 0.00 0.00 0.00 4.35
1833 3442 9.598517 ACATTTCAGTTACAAATTCAACATGTT 57.401 25.926 4.92 4.92 0.00 2.71
1872 3498 1.099689 TTAGCATGGCGGGCTTTTAC 58.900 50.000 8.03 0.00 42.62 2.01
1886 3512 4.497507 GGGCTTTTACCACGCAATATTCTC 60.498 45.833 0.00 0.00 0.00 2.87
1906 3542 1.219393 GACAGAGCTAGTGGTGGCC 59.781 63.158 0.00 0.00 0.00 5.36
2316 4330 7.448748 ACGGCTTTCATGTTAGTAGATTTTT 57.551 32.000 0.00 0.00 0.00 1.94
2532 4559 5.852827 TGAACCTTTTCCAATGGTTGAATC 58.147 37.500 10.62 0.00 45.67 2.52
2587 4652 4.618489 GTGAGCGATTTTGGAATTTGTGAG 59.382 41.667 0.00 0.00 0.00 3.51
2602 4667 8.797438 GGAATTTGTGAGGAGTTTTTAGAATCT 58.203 33.333 0.00 0.00 0.00 2.40
2610 4675 7.939039 TGAGGAGTTTTTAGAATCTGTGAACAT 59.061 33.333 0.00 0.00 0.00 2.71
2624 4711 9.767228 AATCTGTGAACATTTTTGAATTCATCA 57.233 25.926 9.40 5.28 33.85 3.07
2626 4713 9.198837 TCTGTGAACATTTTTGAATTCATCATG 57.801 29.630 9.40 13.34 38.03 3.07
2673 4802 9.696917 ACATTTTTGGAATTCATACTTGTCTTC 57.303 29.630 7.93 0.00 0.00 2.87
2699 4867 8.686418 CAATATGAAAACATTTTTCGAACACGA 58.314 29.630 0.00 0.00 0.00 4.35
2700 4868 8.964420 ATATGAAAACATTTTTCGAACACGAT 57.036 26.923 0.00 0.00 35.96 3.73
2703 4871 8.789881 TGAAAACATTTTTCGAACACGATAAT 57.210 26.923 0.00 0.00 35.96 1.28
2820 4999 6.814076 ACGCGAACATTTAACAATTTTTCA 57.186 29.167 15.93 0.00 0.00 2.69
2889 5120 8.456904 AATATGTGATCATTTTATGAATGCGC 57.543 30.769 0.00 0.00 43.50 6.09
2907 5138 2.092055 GCGCGAACATTTTTGGAATTCC 59.908 45.455 18.17 18.17 0.00 3.01
2981 5217 3.000041 GGCAACATTTTTCGAATTCCCC 59.000 45.455 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.004854 ACATTTCTGTAAGCACATCAATGCGA 62.005 38.462 0.00 0.00 41.51 5.10
4 5 5.900934 ACATTTCTGTAAGCACATCAATGCG 60.901 40.000 7.72 0.00 41.51 4.73
5 6 5.404946 ACATTTCTGTAAGCACATCAATGC 58.595 37.500 7.72 0.00 37.42 3.56
6 7 7.191551 CCTACATTTCTGTAAGCACATCAATG 58.808 38.462 0.00 0.00 37.41 2.82
7 8 6.319658 CCCTACATTTCTGTAAGCACATCAAT 59.680 38.462 0.00 0.00 37.41 2.57
8 9 5.647658 CCCTACATTTCTGTAAGCACATCAA 59.352 40.000 0.00 0.00 37.41 2.57
9 10 5.045942 TCCCTACATTTCTGTAAGCACATCA 60.046 40.000 0.00 0.00 37.41 3.07
10 11 5.428253 TCCCTACATTTCTGTAAGCACATC 58.572 41.667 0.00 0.00 37.41 3.06
11 12 5.435686 TCCCTACATTTCTGTAAGCACAT 57.564 39.130 0.00 0.00 37.41 3.21
12 13 4.901197 TCCCTACATTTCTGTAAGCACA 57.099 40.909 0.00 0.00 37.41 4.57
13 14 5.123979 CCTTTCCCTACATTTCTGTAAGCAC 59.876 44.000 0.00 0.00 37.41 4.40
14 15 5.253330 CCTTTCCCTACATTTCTGTAAGCA 58.747 41.667 0.00 0.00 37.41 3.91
15 16 4.096532 GCCTTTCCCTACATTTCTGTAAGC 59.903 45.833 0.00 0.00 37.41 3.09
16 17 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
17 18 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
18 19 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
19 20 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
20 21 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
21 22 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
22 23 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
23 24 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
24 25 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
25 26 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
26 27 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
27 28 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
28 29 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
29 30 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
30 31 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
31 32 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
32 33 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
33 34 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
34 35 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
35 36 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
36 37 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
37 38 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
38 39 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
39 40 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
40 41 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
41 42 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
51 52 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
52 53 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
53 54 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
54 55 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
55 56 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
56 57 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
57 58 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
58 59 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
64 65 4.735599 AGGGTCGGGGAAGGGTCC 62.736 72.222 0.00 0.00 44.10 4.46
65 66 3.400054 CAGGGTCGGGGAAGGGTC 61.400 72.222 0.00 0.00 0.00 4.46
80 81 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
83 84 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
84 85 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
85 86 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
86 87 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
92 93 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
93 94 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
94 95 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
95 96 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
96 97 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
106 107 2.501316 ACATCAATAAAAAGGGCAGCCC 59.499 45.455 24.90 24.90 45.90 5.19
107 108 3.055891 ACACATCAATAAAAAGGGCAGCC 60.056 43.478 1.26 1.26 0.00 4.85
108 109 3.928375 CACACATCAATAAAAAGGGCAGC 59.072 43.478 0.00 0.00 0.00 5.25
109 110 5.138125 ACACACATCAATAAAAAGGGCAG 57.862 39.130 0.00 0.00 0.00 4.85
110 111 5.295950 CAACACACATCAATAAAAAGGGCA 58.704 37.500 0.00 0.00 0.00 5.36
111 112 4.690280 CCAACACACATCAATAAAAAGGGC 59.310 41.667 0.00 0.00 0.00 5.19
112 113 5.852827 ACCAACACACATCAATAAAAAGGG 58.147 37.500 0.00 0.00 0.00 3.95
113 114 6.760770 ACAACCAACACACATCAATAAAAAGG 59.239 34.615 0.00 0.00 0.00 3.11
114 115 7.769272 ACAACCAACACACATCAATAAAAAG 57.231 32.000 0.00 0.00 0.00 2.27
115 116 8.687242 TCTACAACCAACACACATCAATAAAAA 58.313 29.630 0.00 0.00 0.00 1.94
116 117 8.132362 GTCTACAACCAACACACATCAATAAAA 58.868 33.333 0.00 0.00 0.00 1.52
117 118 7.283354 TGTCTACAACCAACACACATCAATAAA 59.717 33.333 0.00 0.00 0.00 1.40
118 119 6.768381 TGTCTACAACCAACACACATCAATAA 59.232 34.615 0.00 0.00 0.00 1.40
119 120 6.203915 GTGTCTACAACCAACACACATCAATA 59.796 38.462 0.00 0.00 42.21 1.90
734 1469 7.519032 TGATTTTTCTTTAAAGTCCACCGAT 57.481 32.000 14.74 2.42 32.98 4.18
767 1502 1.765314 TGGCCAGATCTAGCTTCTTCC 59.235 52.381 12.98 0.00 0.00 3.46
886 1622 5.056592 AAGAGAGGTTCTTGGAGAGAGTCC 61.057 50.000 0.00 0.00 44.46 3.85
1046 1859 3.251571 CCTAGGTTGCTCTCGTTTGTAC 58.748 50.000 0.00 0.00 0.00 2.90
1057 2196 0.037232 GAACACGAGCCTAGGTTGCT 60.037 55.000 11.31 0.40 43.03 3.91
1060 2199 0.243095 GTCGAACACGAGCCTAGGTT 59.757 55.000 11.31 3.54 36.72 3.50
1193 2333 3.054065 AGCCCCGATCTGATTTCTTCTTT 60.054 43.478 0.00 0.00 0.00 2.52
1224 2364 0.545646 GCTCTCTTCCCTGCCTCATT 59.454 55.000 0.00 0.00 0.00 2.57
1246 2386 2.614446 CGTCGACGAGTGGACCTGT 61.614 63.158 33.35 0.00 43.02 4.00
1248 2388 2.031616 TCGTCGACGAGTGGACCT 59.968 61.111 34.97 0.00 44.22 3.85
1419 3010 1.063616 CGCTTGTTGATGAGCTCATGG 59.936 52.381 33.33 15.59 36.57 3.66
1420 3011 2.004733 TCGCTTGTTGATGAGCTCATG 58.995 47.619 33.33 18.23 36.57 3.07
1421 3012 2.391616 TCGCTTGTTGATGAGCTCAT 57.608 45.000 29.09 29.09 39.70 2.90
1488 3091 3.443145 ACCATCCCACGGTATGAAAAA 57.557 42.857 0.00 0.00 34.02 1.94
1764 3373 8.078596 GGATGCAACTTCAAGATAATATGAACC 58.921 37.037 0.00 0.00 32.46 3.62
1833 3442 2.251818 ACTCAGCAGCTTCCTCAACTA 58.748 47.619 0.00 0.00 0.00 2.24
1872 3498 3.785486 TCTGTCAGAGAATATTGCGTGG 58.215 45.455 0.00 0.00 0.00 4.94
1886 3512 0.108424 GCCACCACTAGCTCTGTCAG 60.108 60.000 0.00 0.00 0.00 3.51
1906 3542 0.321210 TGCATACCACCAGGAACACG 60.321 55.000 0.00 0.00 38.69 4.49
2285 4299 8.418662 TCTACTAACATGAAAGCCGTATACAAT 58.581 33.333 0.00 0.00 0.00 2.71
2500 4522 7.131565 CCATTGGAAAAGGTTCAAAATTTTCG 58.868 34.615 0.00 0.00 41.61 3.46
2587 4652 9.750125 AAAATGTTCACAGATTCTAAAAACTCC 57.250 29.630 0.00 0.00 0.00 3.85
2602 4667 9.543783 TTCATGATGAATTCAAAAATGTTCACA 57.456 25.926 13.09 0.00 38.03 3.58
2673 4802 8.686418 TCGTGTTCGAAAAATGTTTTCATATTG 58.314 29.630 0.00 0.00 43.34 1.90
2730 4898 7.561237 AATTCCAAAAATGTTATCGTGTTCG 57.439 32.000 0.00 0.00 38.55 3.95
2731 4899 8.760569 ACAAATTCCAAAAATGTTATCGTGTTC 58.239 29.630 0.00 0.00 0.00 3.18
2732 4900 8.547069 CACAAATTCCAAAAATGTTATCGTGTT 58.453 29.630 0.00 0.00 0.00 3.32
2734 4902 8.291888 TCACAAATTCCAAAAATGTTATCGTG 57.708 30.769 0.00 0.00 0.00 4.35
2796 4975 7.223058 TGAAAAATTGTTAAATGTTCGCGTT 57.777 28.000 5.77 0.00 0.00 4.84
2820 4999 8.482128 TCAAAACAAGTTCATGGGTTCTAAAAT 58.518 29.630 0.00 0.00 0.00 1.82
2918 5151 6.479660 ACGTATTCAAAGAAAGTTCACGGTTA 59.520 34.615 0.00 0.00 0.00 2.85
2920 5153 4.812626 ACGTATTCAAAGAAAGTTCACGGT 59.187 37.500 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.