Multiple sequence alignment - TraesCS3B01G324100

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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 TraesCS3B01G324100 chr3B 100.000 3233 0 0 1 3233 525013150 525016382 0.000000e+00 5971.0
1 TraesCS3B01G324100 chr3D 92.408 1923 76 32 241 2108 398957009 398958916 0.000000e+00 2678.0
2 TraesCS3B01G324100 chr3D 92.153 1096 80 4 2138 3231 471417239 471418330 0.000000e+00 1543.0
3 TraesCS3B01G324100 chr3A 91.997 1187 54 14 968 2120 517996274 517997453 0.000000e+00 1628.0
4 TraesCS3B01G324100 chr3A 89.328 759 40 18 73 810 517995010 517995748 0.000000e+00 915.0
5 TraesCS3B01G324100 chr3A 98.990 99 1 0 817 915 517995793 517995891 9.220000e-41 178.0
6 TraesCS3B01G324100 chr5B 92.280 1101 78 2 2138 3231 678421259 678420159 0.000000e+00 1555.0
7 TraesCS3B01G324100 chr5B 100.000 29 0 0 478 506 257760809 257760837 2.000000e-03 54.7
8 TraesCS3B01G324100 chr2B 85.205 1095 158 4 2138 3229 139402981 139404074 0.000000e+00 1122.0
9 TraesCS3B01G324100 chr2B 78.899 218 42 3 2590 2805 160201588 160201803 9.350000e-31 145.0
10 TraesCS3B01G324100 chr4A 84.440 1099 143 13 2138 3231 490587289 490588364 0.000000e+00 1057.0
11 TraesCS3B01G324100 chr2D 82.296 723 117 10 2515 3233 617248010 617247295 1.650000e-172 616.0
12 TraesCS3B01G324100 chr5D 81.185 675 112 13 2138 2805 484125598 484124932 2.210000e-146 529.0
13 TraesCS3B01G324100 chr6A 80.344 407 79 1 2137 2542 449939169 449938763 1.130000e-79 307.0
14 TraesCS3B01G324100 chr1D 78.599 257 50 4 2594 2846 276752686 276752431 7.180000e-37 165.0
15 TraesCS3B01G324100 chr1D 87.395 119 15 0 2239 2357 190429000 190428882 1.560000e-28 137.0
16 TraesCS3B01G324100 chr6D 78.099 242 48 4 2569 2805 56834941 56835182 7.230000e-32 148.0
17 TraesCS3B01G324100 chrUn 77.922 231 37 10 2579 2804 8148374 8148153 7.280000e-27 132.0


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 TraesCS3B01G324100 chr3B 525013150 525016382 3232 False 5971 5971 100.000000 1 3233 1 chr3B.!!$F1 3232
1 TraesCS3B01G324100 chr3D 398957009 398958916 1907 False 2678 2678 92.408000 241 2108 1 chr3D.!!$F1 1867
2 TraesCS3B01G324100 chr3D 471417239 471418330 1091 False 1543 1543 92.153000 2138 3231 1 chr3D.!!$F2 1093
3 TraesCS3B01G324100 chr3A 517995010 517997453 2443 False 907 1628 93.438333 73 2120 3 chr3A.!!$F1 2047
4 TraesCS3B01G324100 chr5B 678420159 678421259 1100 True 1555 1555 92.280000 2138 3231 1 chr5B.!!$R1 1093
5 TraesCS3B01G324100 chr2B 139402981 139404074 1093 False 1122 1122 85.205000 2138 3229 1 chr2B.!!$F1 1091
6 TraesCS3B01G324100 chr4A 490587289 490588364 1075 False 1057 1057 84.440000 2138 3231 1 chr4A.!!$F1 1093
7 TraesCS3B01G324100 chr2D 617247295 617248010 715 True 616 616 82.296000 2515 3233 1 chr2D.!!$R1 718
8 TraesCS3B01G324100 chr5D 484124932 484125598 666 True 529 529 81.185000 2138 2805 1 chr5D.!!$R1 667

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
152 157 0.033228 AGACACTCACACTGCTCAGC 59.967 55.000 0.0 0.0 0.00 4.26 F
184 190 0.036306 ACAACCAAGAACCCTAGCCG 59.964 55.000 0.0 0.0 0.00 5.52 F
185 191 0.036306 CAACCAAGAACCCTAGCCGT 59.964 55.000 0.0 0.0 0.00 5.68 F
188 194 0.179081 CCAAGAACCCTAGCCGTAGC 60.179 60.000 0.0 0.0 40.32 3.58 F
606 632 1.302431 CGTTGTCCCACATGCCAGA 60.302 57.895 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1085 1509 0.957395 CTTCATGCGCCTGGTCTTGT 60.957 55.000 12.90 0.0 0.00 3.16 R
1287 1729 1.338674 TGCGGGTGACAAAGTATCTGG 60.339 52.381 0.00 0.0 0.00 3.86 R
2074 2524 1.896220 CTTGCAAGCTACTCCCAACA 58.104 50.000 14.65 0.0 0.00 3.33 R
2130 2580 7.894708 TGTCCTCTATCAATGAAAAATTTGCA 58.105 30.769 0.00 0.0 0.00 4.08 R
2531 2992 0.179148 TGATCATGTCGGTTCGGACG 60.179 55.000 0.00 0.0 39.83 4.79 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
29 30 2.327081 CGTGCTAGTACGTGACTTGT 57.673 50.000 23.20 0.00 39.81 3.16
30 31 3.460362 CGTGCTAGTACGTGACTTGTA 57.540 47.619 23.20 0.00 39.81 2.41
31 32 3.813800 CGTGCTAGTACGTGACTTGTAA 58.186 45.455 23.20 0.00 39.81 2.41
32 33 3.601211 CGTGCTAGTACGTGACTTGTAAC 59.399 47.826 23.20 2.51 39.81 2.50
33 34 4.539870 GTGCTAGTACGTGACTTGTAACA 58.460 43.478 0.00 0.00 39.81 2.41
34 35 4.380974 GTGCTAGTACGTGACTTGTAACAC 59.619 45.833 0.00 0.00 39.81 3.32
35 36 4.276678 TGCTAGTACGTGACTTGTAACACT 59.723 41.667 0.00 0.00 39.81 3.55
36 37 5.218139 GCTAGTACGTGACTTGTAACACTT 58.782 41.667 0.00 0.00 39.81 3.16
37 38 6.017192 TGCTAGTACGTGACTTGTAACACTTA 60.017 38.462 0.00 0.00 39.81 2.24
38 39 7.025963 GCTAGTACGTGACTTGTAACACTTAT 58.974 38.462 0.00 0.00 39.81 1.73
39 40 7.217825 GCTAGTACGTGACTTGTAACACTTATC 59.782 40.741 0.00 0.00 39.81 1.75
40 41 6.973843 AGTACGTGACTTGTAACACTTATCA 58.026 36.000 0.00 0.00 33.13 2.15
41 42 7.600065 AGTACGTGACTTGTAACACTTATCAT 58.400 34.615 0.00 0.00 33.13 2.45
42 43 6.706055 ACGTGACTTGTAACACTTATCATG 57.294 37.500 0.00 0.00 35.23 3.07
43 44 6.220930 ACGTGACTTGTAACACTTATCATGT 58.779 36.000 0.00 0.00 35.23 3.21
44 45 6.365247 ACGTGACTTGTAACACTTATCATGTC 59.635 38.462 0.00 0.00 36.33 3.06
45 46 6.183360 CGTGACTTGTAACACTTATCATGTCC 60.183 42.308 0.00 0.00 35.54 4.02
46 47 6.649141 GTGACTTGTAACACTTATCATGTCCA 59.351 38.462 0.00 0.00 35.54 4.02
47 48 7.172532 GTGACTTGTAACACTTATCATGTCCAA 59.827 37.037 0.00 0.00 35.54 3.53
48 49 7.717436 TGACTTGTAACACTTATCATGTCCAAA 59.283 33.333 0.00 0.00 35.54 3.28
49 50 8.099364 ACTTGTAACACTTATCATGTCCAAAG 57.901 34.615 0.00 0.00 0.00 2.77
50 51 7.174946 ACTTGTAACACTTATCATGTCCAAAGG 59.825 37.037 0.00 0.00 0.00 3.11
51 52 6.539173 TGTAACACTTATCATGTCCAAAGGT 58.461 36.000 0.00 0.00 0.00 3.50
52 53 7.681679 TGTAACACTTATCATGTCCAAAGGTA 58.318 34.615 0.00 0.00 0.00 3.08
53 54 8.158132 TGTAACACTTATCATGTCCAAAGGTAA 58.842 33.333 0.00 0.00 0.00 2.85
54 55 9.174166 GTAACACTTATCATGTCCAAAGGTAAT 57.826 33.333 0.00 0.00 0.00 1.89
55 56 8.650143 AACACTTATCATGTCCAAAGGTAATT 57.350 30.769 0.00 0.00 0.00 1.40
56 57 9.747898 AACACTTATCATGTCCAAAGGTAATTA 57.252 29.630 0.00 0.00 0.00 1.40
57 58 9.920946 ACACTTATCATGTCCAAAGGTAATTAT 57.079 29.630 0.00 0.00 0.00 1.28
62 63 8.995027 ATCATGTCCAAAGGTAATTATAGCAA 57.005 30.769 0.00 0.00 31.82 3.91
63 64 8.815565 TCATGTCCAAAGGTAATTATAGCAAA 57.184 30.769 0.00 0.00 31.82 3.68
64 65 9.249053 TCATGTCCAAAGGTAATTATAGCAAAA 57.751 29.630 0.00 0.00 31.82 2.44
65 66 9.301153 CATGTCCAAAGGTAATTATAGCAAAAC 57.699 33.333 0.00 0.00 31.82 2.43
66 67 8.410673 TGTCCAAAGGTAATTATAGCAAAACA 57.589 30.769 0.00 0.00 31.82 2.83
67 68 8.519526 TGTCCAAAGGTAATTATAGCAAAACAG 58.480 33.333 0.00 0.00 31.82 3.16
68 69 7.973944 GTCCAAAGGTAATTATAGCAAAACAGG 59.026 37.037 0.00 0.00 31.82 4.00
69 70 7.891183 TCCAAAGGTAATTATAGCAAAACAGGA 59.109 33.333 0.00 0.00 31.82 3.86
70 71 8.695456 CCAAAGGTAATTATAGCAAAACAGGAT 58.305 33.333 0.00 0.00 31.82 3.24
76 77 9.338622 GTAATTATAGCAAAACAGGATACAGGT 57.661 33.333 0.00 0.00 41.41 4.00
84 85 3.925090 GGATACAGGTCCGGCCGG 61.925 72.222 39.13 39.13 43.70 6.13
97 102 1.555741 CGGCCGGACGTCGTTAAAAA 61.556 55.000 25.18 0.00 37.11 1.94
108 113 1.731613 GTTAAAAAGGCGGTGGCGC 60.732 57.895 0.00 0.00 41.24 6.53
152 157 0.033228 AGACACTCACACTGCTCAGC 59.967 55.000 0.00 0.00 0.00 4.26
171 177 1.883638 GCTCAGAGGATGCAACAACCA 60.884 52.381 0.00 0.00 0.00 3.67
178 184 1.000843 GGATGCAACAACCAAGAACCC 59.999 52.381 0.00 0.00 0.00 4.11
182 188 1.269723 GCAACAACCAAGAACCCTAGC 59.730 52.381 0.00 0.00 0.00 3.42
183 189 1.886542 CAACAACCAAGAACCCTAGCC 59.113 52.381 0.00 0.00 0.00 3.93
184 190 0.036306 ACAACCAAGAACCCTAGCCG 59.964 55.000 0.00 0.00 0.00 5.52
185 191 0.036306 CAACCAAGAACCCTAGCCGT 59.964 55.000 0.00 0.00 0.00 5.68
186 192 1.276989 CAACCAAGAACCCTAGCCGTA 59.723 52.381 0.00 0.00 0.00 4.02
187 193 1.192428 ACCAAGAACCCTAGCCGTAG 58.808 55.000 0.00 0.00 0.00 3.51
188 194 0.179081 CCAAGAACCCTAGCCGTAGC 60.179 60.000 0.00 0.00 40.32 3.58
224 236 2.974692 TTTGCAGCGCAGGAAAGGGA 62.975 55.000 15.19 0.00 40.61 4.20
298 310 1.511887 CACCCTTTTCGCGCAATCG 60.512 57.895 8.75 0.00 39.07 3.34
353 365 1.752310 CCGCTGCTCTCTCCTCTCA 60.752 63.158 0.00 0.00 0.00 3.27
427 439 3.210223 TTTGCGTCGTGGCCTCGTA 62.210 57.895 25.10 10.66 0.00 3.43
445 459 2.753247 GTAGAATGGGGTCTCAGGAGT 58.247 52.381 0.00 0.00 0.00 3.85
453 467 1.446272 GTCTCAGGAGTTTCGCCCG 60.446 63.158 0.00 0.00 0.00 6.13
454 468 2.125512 CTCAGGAGTTTCGCCCGG 60.126 66.667 0.00 0.00 0.00 5.73
455 469 2.602267 TCAGGAGTTTCGCCCGGA 60.602 61.111 0.73 0.00 0.00 5.14
456 470 2.434359 CAGGAGTTTCGCCCGGAC 60.434 66.667 0.73 0.00 0.00 4.79
523 545 1.406887 CGATCGGTGATTCCCTTTGGT 60.407 52.381 7.38 0.00 0.00 3.67
597 619 2.753701 CCATGTCCCGTTGTCCCA 59.246 61.111 0.00 0.00 0.00 4.37
606 632 1.302431 CGTTGTCCCACATGCCAGA 60.302 57.895 0.00 0.00 0.00 3.86
765 802 4.167268 CACTACTGTAGCTTTCGAAGTCC 58.833 47.826 14.55 0.00 0.00 3.85
796 833 2.330286 CGCCAAACGTGATGTACTACA 58.670 47.619 0.00 0.00 36.87 2.74
810 847 7.120285 GTGATGTACTACAACTACAGTGGAGTA 59.880 40.741 8.88 0.00 0.00 2.59
905 980 4.171005 GACGGCTTATTAAAACTTTGGCC 58.829 43.478 0.00 0.00 35.53 5.36
1005 1411 3.620226 CGGACTCTTCTCTCCTCACACTA 60.620 52.174 0.00 0.00 0.00 2.74
1022 1441 4.991056 CACACTACAAGCTCACATAACACT 59.009 41.667 0.00 0.00 0.00 3.55
1295 1737 2.765807 AGCAGCCCGCCAGATACT 60.766 61.111 0.00 0.00 44.04 2.12
1307 1749 1.338674 CCAGATACTTTGTCACCCGCA 60.339 52.381 0.00 0.00 0.00 5.69
1311 1753 3.726517 CTTTGTCACCCGCAGCCG 61.727 66.667 0.00 0.00 0.00 5.52
1412 1860 4.189188 CGCCACTACTCCGTCGGG 62.189 72.222 12.29 4.77 0.00 5.14
1748 2196 3.243873 GCAACTCGATGGTGGAGATGATA 60.244 47.826 3.65 0.00 36.69 2.15
1962 2410 1.424403 TCGTCCATGTAACAAGTGCG 58.576 50.000 0.00 0.00 0.00 5.34
1980 2428 2.290641 TGCGGGTGGTTCATAATTGACT 60.291 45.455 0.00 0.00 0.00 3.41
1981 2429 2.097466 GCGGGTGGTTCATAATTGACTG 59.903 50.000 0.00 0.00 0.00 3.51
2041 2490 4.456253 CGCGCTGTCCGTACTCGT 62.456 66.667 5.56 0.00 39.71 4.18
2052 2502 5.824429 TGTCCGTACTCGTATTATCCAAAG 58.176 41.667 0.00 0.00 35.01 2.77
2154 2604 8.937634 ATGCAAATTTTTCATTGATAGAGGAC 57.062 30.769 0.00 0.00 0.00 3.85
2220 2672 1.269998 GAAGGCGCGAGTATGATACCT 59.730 52.381 12.10 0.00 0.00 3.08
2226 2678 2.030717 CGCGAGTATGATACCTGAAGCT 60.031 50.000 0.00 0.00 0.00 3.74
2229 2681 5.620205 CGCGAGTATGATACCTGAAGCTAAT 60.620 44.000 0.00 0.00 0.00 1.73
2368 2828 4.760047 ACGAGGCACCACATCCGC 62.760 66.667 0.00 0.00 0.00 5.54
2387 2847 2.745884 CGATCGCAGCCCCAAACA 60.746 61.111 0.26 0.00 0.00 2.83
2407 2867 2.161808 CACGACAGGATCAACGTACTCT 59.838 50.000 0.00 0.00 37.22 3.24
2429 2889 1.035923 CCTAGAGCGCCAAGAGATCA 58.964 55.000 2.29 0.00 0.00 2.92
2471 2931 2.114411 GGGCCAAGGACGGAAACA 59.886 61.111 4.39 0.00 0.00 2.83
2483 2943 1.291877 CGGAAACAGTGGGAGAAGCG 61.292 60.000 0.00 0.00 0.00 4.68
2531 2992 1.963338 GCCTACGCCATGAGATGCC 60.963 63.158 0.00 0.00 0.00 4.40
2560 3023 6.564686 CGAACCGACATGATCATTTCCATAAG 60.565 42.308 14.71 2.38 0.00 1.73
2706 3170 2.492012 GGCACAGATAGAAGCCATGAG 58.508 52.381 0.00 0.00 46.26 2.90
2837 3302 4.442375 TTGAGATCAGAAGACGAGGAAC 57.558 45.455 0.00 0.00 0.00 3.62
2882 3347 1.683707 ACATGGAGGAGAGCTGCGA 60.684 57.895 0.00 0.00 0.00 5.10
2897 3362 2.938823 GCGAACACGCGAGCTTTGA 61.939 57.895 15.93 0.00 42.84 2.69
3122 3608 4.362476 GTGCGGGCAAGCCAAAGG 62.362 66.667 13.87 0.08 37.98 3.11
3204 3690 1.634702 CGAAGAAGCCGGAGAGAAAG 58.365 55.000 5.05 0.00 0.00 2.62
3221 3707 4.070552 GACGGCCTTCGGAGCACT 62.071 66.667 0.00 0.00 44.45 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.253999 CGTACTAGCACGTTCCGAAC 58.746 55.000 7.36 0.76 37.16 3.95
3 4 3.681705 CGTACTAGCACGTTCCGAA 57.318 52.632 7.36 0.00 37.16 4.30
11 12 4.380974 GTGTTACAAGTCACGTACTAGCAC 59.619 45.833 0.00 0.00 37.50 4.40
12 13 4.276678 AGTGTTACAAGTCACGTACTAGCA 59.723 41.667 0.00 0.00 37.50 3.49
13 14 4.791974 AGTGTTACAAGTCACGTACTAGC 58.208 43.478 0.00 0.00 37.50 3.42
14 15 8.232513 TGATAAGTGTTACAAGTCACGTACTAG 58.767 37.037 0.00 0.00 37.50 2.57
15 16 8.098220 TGATAAGTGTTACAAGTCACGTACTA 57.902 34.615 0.00 0.00 37.50 1.82
16 17 6.973843 TGATAAGTGTTACAAGTCACGTACT 58.026 36.000 0.00 0.00 41.49 2.73
17 18 7.327761 ACATGATAAGTGTTACAAGTCACGTAC 59.672 37.037 0.00 0.00 39.25 3.67
18 19 7.372714 ACATGATAAGTGTTACAAGTCACGTA 58.627 34.615 0.00 0.00 39.25 3.57
19 20 6.220930 ACATGATAAGTGTTACAAGTCACGT 58.779 36.000 0.00 0.00 39.25 4.49
20 21 6.183360 GGACATGATAAGTGTTACAAGTCACG 60.183 42.308 0.00 0.00 39.25 4.35
21 22 6.649141 TGGACATGATAAGTGTTACAAGTCAC 59.351 38.462 0.00 0.00 34.24 3.67
22 23 6.764379 TGGACATGATAAGTGTTACAAGTCA 58.236 36.000 0.00 0.00 34.24 3.41
23 24 7.667043 TTGGACATGATAAGTGTTACAAGTC 57.333 36.000 0.00 0.00 32.61 3.01
24 25 7.174946 CCTTTGGACATGATAAGTGTTACAAGT 59.825 37.037 0.00 0.00 32.41 3.16
25 26 7.174946 ACCTTTGGACATGATAAGTGTTACAAG 59.825 37.037 0.00 0.00 32.41 3.16
26 27 7.001674 ACCTTTGGACATGATAAGTGTTACAA 58.998 34.615 0.00 0.00 0.00 2.41
27 28 6.539173 ACCTTTGGACATGATAAGTGTTACA 58.461 36.000 0.00 0.00 0.00 2.41
28 29 8.556213 TTACCTTTGGACATGATAAGTGTTAC 57.444 34.615 0.00 0.00 0.00 2.50
29 30 9.747898 AATTACCTTTGGACATGATAAGTGTTA 57.252 29.630 0.00 0.00 0.00 2.41
30 31 8.650143 AATTACCTTTGGACATGATAAGTGTT 57.350 30.769 0.00 0.00 0.00 3.32
31 32 9.920946 ATAATTACCTTTGGACATGATAAGTGT 57.079 29.630 0.00 1.26 0.00 3.55
37 38 8.995027 TTGCTATAATTACCTTTGGACATGAT 57.005 30.769 0.00 0.00 0.00 2.45
38 39 8.815565 TTTGCTATAATTACCTTTGGACATGA 57.184 30.769 0.00 0.00 0.00 3.07
39 40 9.301153 GTTTTGCTATAATTACCTTTGGACATG 57.699 33.333 0.00 0.00 0.00 3.21
40 41 9.030452 TGTTTTGCTATAATTACCTTTGGACAT 57.970 29.630 0.00 0.00 0.00 3.06
41 42 8.410673 TGTTTTGCTATAATTACCTTTGGACA 57.589 30.769 0.00 0.00 0.00 4.02
42 43 7.973944 CCTGTTTTGCTATAATTACCTTTGGAC 59.026 37.037 0.00 0.00 0.00 4.02
43 44 7.891183 TCCTGTTTTGCTATAATTACCTTTGGA 59.109 33.333 0.00 0.00 0.00 3.53
44 45 8.062065 TCCTGTTTTGCTATAATTACCTTTGG 57.938 34.615 0.00 0.00 0.00 3.28
47 48 9.914834 TGTATCCTGTTTTGCTATAATTACCTT 57.085 29.630 0.00 0.00 0.00 3.50
48 49 9.561069 CTGTATCCTGTTTTGCTATAATTACCT 57.439 33.333 0.00 0.00 0.00 3.08
49 50 8.784043 CCTGTATCCTGTTTTGCTATAATTACC 58.216 37.037 0.00 0.00 0.00 2.85
50 51 9.338622 ACCTGTATCCTGTTTTGCTATAATTAC 57.661 33.333 0.00 0.00 0.00 1.89
51 52 9.555727 GACCTGTATCCTGTTTTGCTATAATTA 57.444 33.333 0.00 0.00 0.00 1.40
52 53 7.502561 GGACCTGTATCCTGTTTTGCTATAATT 59.497 37.037 0.00 0.00 35.68 1.40
53 54 6.998673 GGACCTGTATCCTGTTTTGCTATAAT 59.001 38.462 0.00 0.00 35.68 1.28
54 55 6.354130 GGACCTGTATCCTGTTTTGCTATAA 58.646 40.000 0.00 0.00 35.68 0.98
55 56 5.452776 CGGACCTGTATCCTGTTTTGCTATA 60.453 44.000 0.00 0.00 36.52 1.31
56 57 4.683400 CGGACCTGTATCCTGTTTTGCTAT 60.683 45.833 0.00 0.00 36.52 2.97
57 58 3.369052 CGGACCTGTATCCTGTTTTGCTA 60.369 47.826 0.00 0.00 36.52 3.49
58 59 2.615493 CGGACCTGTATCCTGTTTTGCT 60.615 50.000 0.00 0.00 36.52 3.91
59 60 1.737793 CGGACCTGTATCCTGTTTTGC 59.262 52.381 0.00 0.00 36.52 3.68
60 61 2.356135 CCGGACCTGTATCCTGTTTTG 58.644 52.381 0.00 0.00 36.52 2.44
61 62 1.339727 GCCGGACCTGTATCCTGTTTT 60.340 52.381 5.05 0.00 36.52 2.43
62 63 0.252197 GCCGGACCTGTATCCTGTTT 59.748 55.000 5.05 0.00 36.52 2.83
63 64 1.623542 GGCCGGACCTGTATCCTGTT 61.624 60.000 5.05 0.00 36.52 3.16
64 65 2.064581 GGCCGGACCTGTATCCTGT 61.065 63.158 5.05 0.00 36.52 4.00
65 66 2.822399 GGCCGGACCTGTATCCTG 59.178 66.667 5.05 0.00 36.52 3.86
66 67 2.838225 CGGCCGGACCTGTATCCT 60.838 66.667 20.10 0.00 36.52 3.24
67 68 3.925090 CCGGCCGGACCTGTATCC 61.925 72.222 41.82 0.00 37.50 2.59
68 69 2.836360 TCCGGCCGGACCTGTATC 60.836 66.667 42.66 0.00 39.76 2.24
84 85 0.861185 ACCGCCTTTTTAACGACGTC 59.139 50.000 5.18 5.18 0.00 4.34
131 136 0.390492 TGAGCAGTGTGAGTGTCTGG 59.610 55.000 0.00 0.00 0.00 3.86
152 157 2.189594 TGGTTGTTGCATCCTCTGAG 57.810 50.000 0.00 0.00 0.00 3.35
171 177 1.335882 GGGCTACGGCTAGGGTTCTT 61.336 60.000 0.00 0.00 38.73 2.52
188 194 0.817013 AAATGTTGCATGCCTACGGG 59.183 50.000 16.68 0.00 0.00 5.28
246 258 2.863484 TGATTGGGTGGGGCCTGT 60.863 61.111 0.84 0.00 37.43 4.00
339 351 1.379176 CCCGTGAGAGGAGAGAGCA 60.379 63.158 0.00 0.00 0.00 4.26
349 361 1.004277 CCATTCCTTTTCCCCGTGAGA 59.996 52.381 0.00 0.00 0.00 3.27
353 365 2.525368 CTTTCCATTCCTTTTCCCCGT 58.475 47.619 0.00 0.00 0.00 5.28
427 439 2.350863 AACTCCTGAGACCCCATTCT 57.649 50.000 0.22 0.00 0.00 2.40
492 513 3.665226 CCGATCGAGGAGGCGAGG 61.665 72.222 18.66 0.00 44.26 4.63
523 545 3.118555 TGGGAACAGAAAGTGAGACGAAA 60.119 43.478 0.00 0.00 35.01 3.46
589 611 1.589716 GCTCTGGCATGTGGGACAAC 61.590 60.000 0.00 0.00 38.28 3.32
590 612 1.303561 GCTCTGGCATGTGGGACAA 60.304 57.895 0.00 0.00 38.28 3.18
597 619 1.153289 CGGCTTAGCTCTGGCATGT 60.153 57.895 3.59 0.00 41.70 3.21
606 632 0.107831 TCAACAACACCGGCTTAGCT 59.892 50.000 0.00 0.00 0.00 3.32
714 742 0.179215 GCGACATGCAAGCAGTACAC 60.179 55.000 0.00 0.00 45.45 2.90
784 821 6.072064 ACTCCACTGTAGTTGTAGTACATCAC 60.072 42.308 12.71 5.71 33.90 3.06
810 847 6.252869 CGTGATTGACGCTAATGTTTAGTACT 59.747 38.462 0.00 0.00 42.21 2.73
972 1377 3.224324 GAGTCCGGCGCTATGGGA 61.224 66.667 7.64 6.65 0.00 4.37
1005 1411 4.281941 TCTCTCAGTGTTATGTGAGCTTGT 59.718 41.667 0.00 0.00 40.13 3.16
1022 1441 4.033009 TCATGGCTATGGTTTCTCTCTCA 58.967 43.478 10.47 0.00 34.97 3.27
1085 1509 0.957395 CTTCATGCGCCTGGTCTTGT 60.957 55.000 12.90 0.00 0.00 3.16
1287 1729 1.338674 TGCGGGTGACAAAGTATCTGG 60.339 52.381 0.00 0.00 0.00 3.86
1307 1749 4.664677 GGCACGATATCGGCGGCT 62.665 66.667 27.58 4.69 44.95 5.52
1466 1914 3.923864 ACACACTGCGGCGAGGAA 61.924 61.111 12.98 0.00 0.00 3.36
1748 2196 3.490759 CCGATGCGCTTGCTCGTT 61.491 61.111 9.73 0.00 37.47 3.85
1962 2410 4.589908 ACTCAGTCAATTATGAACCACCC 58.410 43.478 0.00 0.00 37.30 4.61
1980 2428 4.116961 CTGTCAAAAAGTCACCGTACTCA 58.883 43.478 0.00 0.00 0.00 3.41
1981 2429 4.117685 ACTGTCAAAAAGTCACCGTACTC 58.882 43.478 0.00 0.00 0.00 2.59
2070 2520 3.027412 TGCAAGCTACTCCCAACAAAAA 58.973 40.909 0.00 0.00 0.00 1.94
2074 2524 1.896220 CTTGCAAGCTACTCCCAACA 58.104 50.000 14.65 0.00 0.00 3.33
2120 2570 9.201127 TCAATGAAAAATTTGCATATTCGTGAA 57.799 25.926 0.00 0.00 0.00 3.18
2121 2571 8.754230 TCAATGAAAAATTTGCATATTCGTGA 57.246 26.923 0.00 0.00 0.00 4.35
2129 2579 8.533657 TGTCCTCTATCAATGAAAAATTTGCAT 58.466 29.630 0.00 0.00 0.00 3.96
2130 2580 7.894708 TGTCCTCTATCAATGAAAAATTTGCA 58.105 30.769 0.00 0.00 0.00 4.08
2131 2581 8.761575 TTGTCCTCTATCAATGAAAAATTTGC 57.238 30.769 0.00 0.00 0.00 3.68
2220 2672 6.006275 AGCATCCCTCTTTTATTAGCTTCA 57.994 37.500 0.00 0.00 0.00 3.02
2226 2678 4.446311 GGGCTGAGCATCCCTCTTTTATTA 60.446 45.833 6.82 0.00 41.35 0.98
2229 2681 1.212935 GGGCTGAGCATCCCTCTTTTA 59.787 52.381 6.82 0.00 41.35 1.52
2368 2828 2.745884 TTTGGGGCTGCGATCGTG 60.746 61.111 17.81 11.16 0.00 4.35
2387 2847 2.419324 GAGAGTACGTTGATCCTGTCGT 59.581 50.000 0.00 0.00 39.74 4.34
2407 2867 0.323451 TCTCTTGGCGCTCTAGGTGA 60.323 55.000 7.64 4.08 0.00 4.02
2471 2931 3.077556 ATCGGCGCTTCTCCCACT 61.078 61.111 7.64 0.00 0.00 4.00
2483 2943 1.986378 GCTATGTACGTCATCATCGGC 59.014 52.381 0.00 1.45 37.91 5.54
2531 2992 0.179148 TGATCATGTCGGTTCGGACG 60.179 55.000 0.00 0.00 39.83 4.79
2560 3023 5.264448 CGTCCCCGATGTTGGATTTCAAC 62.264 52.174 0.50 0.50 45.26 3.18
2587 3050 3.395639 TCGAAGGCGTTGTCTTATTTGT 58.604 40.909 0.00 0.00 38.98 2.83
2706 3170 1.531578 GTCACCTTCTTGAAGGCGTTC 59.468 52.381 24.58 12.18 43.80 3.95
2837 3302 3.311871 GCAGCTCCAATCTACATGTTGAG 59.688 47.826 15.09 2.77 0.00 3.02
2882 3347 2.032799 TCATTTTCAAAGCTCGCGTGTT 59.967 40.909 5.77 0.00 0.00 3.32
2897 3362 2.948979 TGCCTCGTCAACTTGTCATTTT 59.051 40.909 0.00 0.00 0.00 1.82
3054 3539 4.697756 TTGGCCGCGTCCCTTCTG 62.698 66.667 2.60 0.00 0.00 3.02
3055 3540 4.699522 GTTGGCCGCGTCCCTTCT 62.700 66.667 2.60 0.00 0.00 2.85
3083 3568 3.842923 CTCATGCGGCTCCGTCCT 61.843 66.667 10.24 0.00 42.09 3.85
3128 3614 0.179018 AGTCCAAGACCTGCGCTTTT 60.179 50.000 9.73 0.00 32.18 2.27
3179 3665 0.108138 CTCCGGCTTCTTCGGTTCAT 60.108 55.000 0.00 0.00 46.82 2.57


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

AutoCloner maintained by Alex Coulton.