Multiple sequence alignment - TraesCS3A01G064100

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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 TraesCS3A01G064100 chr3A 100.000 3185 0 0 1 3185 38197335 38200519 0.000000e+00 5882.0
1 TraesCS3A01G064100 chr3A 75.163 765 161 22 919 1661 37832455 37833212 1.830000e-87 333.0
2 TraesCS3A01G064100 chr3A 92.683 41 3 0 2387 2427 37676131 37676171 3.430000e-05 60.2
3 TraesCS3A01G064100 chr3D 92.801 2917 160 22 310 3185 28233283 28236190 0.000000e+00 4178.0
4 TraesCS3A01G064100 chr3D 75.687 983 198 24 681 1654 27913095 27914045 1.350000e-123 453.0
5 TraesCS3A01G064100 chr3D 76.913 797 161 17 912 1691 27560441 27561231 6.310000e-117 431.0
6 TraesCS3A01G064100 chr3D 73.917 1016 212 38 683 1670 27940420 27939430 3.020000e-95 359.0
7 TraesCS3A01G064100 chr3D 97.423 194 5 0 73 266 28233115 28233308 6.590000e-87 331.0
8 TraesCS3A01G064100 chr3D 83.146 178 22 7 2444 2617 401268823 401268650 4.250000e-34 156.0
9 TraesCS3A01G064100 chr3B 92.166 2221 149 17 73 2284 47256049 47258253 0.000000e+00 3114.0
10 TraesCS3A01G064100 chr3B 77.778 657 128 14 1026 1670 46787940 46787290 3.850000e-104 388.0
11 TraesCS3A01G064100 chr3B 73.606 1004 222 24 688 1668 46592546 46591563 2.350000e-91 346.0
12 TraesCS3A01G064100 chr3B 83.173 208 29 5 1464 1670 46038833 46039035 5.430000e-43 185.0
13 TraesCS3A01G064100 chr3B 81.959 194 24 9 2429 2617 542111707 542111894 1.530000e-33 154.0
14 TraesCS3A01G064100 chr3B 92.188 64 5 0 1698 1761 46041418 46041481 1.220000e-14 91.6
15 TraesCS3A01G064100 chr3B 84.043 94 13 2 917 1009 28368452 28368360 4.380000e-14 89.8
16 TraesCS3A01G064100 chr3B 83.721 86 9 5 2418 2498 436405084 436404999 3.410000e-10 76.8
17 TraesCS3A01G064100 chr7B 82.990 194 20 11 2431 2617 167537908 167537721 2.540000e-36 163.0
18 TraesCS3A01G064100 chr7B 76.871 147 30 4 850 994 744048670 744048814 2.630000e-11 80.5
19 TraesCS3A01G064100 chr7B 70.956 272 79 0 777 1048 746423877 746423606 7.370000e-07 65.8
20 TraesCS3A01G064100 chr7B 100.000 28 0 0 1118 1145 745672449 745672422 6.000000e-03 52.8
21 TraesCS3A01G064100 chr7B 94.118 34 2 0 1118 1151 749162210 749162177 6.000000e-03 52.8
22 TraesCS3A01G064100 chr4B 81.959 194 22 11 2431 2617 47892597 47892410 5.500000e-33 152.0
23 TraesCS3A01G064100 chr6D 81.250 192 26 9 2431 2617 276869270 276869084 2.560000e-31 147.0
24 TraesCS3A01G064100 chr1B 85.926 135 17 2 2127 2260 510792833 510792966 3.310000e-30 143.0
25 TraesCS3A01G064100 chr1D 83.803 142 20 3 2120 2260 381006910 381007049 7.170000e-27 132.0
26 TraesCS3A01G064100 chr1D 83.333 90 8 7 2427 2512 377405011 377404925 3.410000e-10 76.8
27 TraesCS3A01G064100 chr2D 78.472 144 25 6 2431 2570 439619683 439619824 4.380000e-14 89.8
28 TraesCS3A01G064100 chrUn 100.000 28 0 0 1118 1145 474629564 474629591 6.000000e-03 52.8
29 TraesCS3A01G064100 chr7A 94.118 34 2 0 1118 1151 736261351 736261318 6.000000e-03 52.8


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 TraesCS3A01G064100 chr3A 38197335 38200519 3184 False 5882.0 5882 100.000 1 3185 1 chr3A.!!$F3 3184
1 TraesCS3A01G064100 chr3A 37832455 37833212 757 False 333.0 333 75.163 919 1661 1 chr3A.!!$F2 742
2 TraesCS3A01G064100 chr3D 28233115 28236190 3075 False 2254.5 4178 95.112 73 3185 2 chr3D.!!$F3 3112
3 TraesCS3A01G064100 chr3D 27913095 27914045 950 False 453.0 453 75.687 681 1654 1 chr3D.!!$F2 973
4 TraesCS3A01G064100 chr3D 27560441 27561231 790 False 431.0 431 76.913 912 1691 1 chr3D.!!$F1 779
5 TraesCS3A01G064100 chr3D 27939430 27940420 990 True 359.0 359 73.917 683 1670 1 chr3D.!!$R1 987
6 TraesCS3A01G064100 chr3B 47256049 47258253 2204 False 3114.0 3114 92.166 73 2284 1 chr3B.!!$F1 2211
7 TraesCS3A01G064100 chr3B 46787290 46787940 650 True 388.0 388 77.778 1026 1670 1 chr3B.!!$R3 644
8 TraesCS3A01G064100 chr3B 46591563 46592546 983 True 346.0 346 73.606 688 1668 1 chr3B.!!$R2 980

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
204 205 0.241481 GAAATTGCAACCCGCCGTTA 59.759 50.0 0.0 0.0 41.33 3.18 F
1066 1152 0.184933 GGCTGGTGTATGGGGCAATA 59.815 55.0 0.0 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1251 0.312416 TCCAAATCCCGCAAACGTTG 59.688 50.0 0.0 0.0 37.7 4.10 R
2721 2877 0.325933 CCATCACTCCTTCACAGCCA 59.674 55.0 0.0 0.0 0.0 4.75 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 4.719369 GCAACAGGCAGCAGCAGC 62.719 66.667 2.65 0.00 44.61 5.25
28 29 4.340246 CAGCAGCAGCCTCCACCA 62.340 66.667 0.00 0.00 43.56 4.17
29 30 4.031129 AGCAGCAGCCTCCACCAG 62.031 66.667 0.00 0.00 43.56 4.00
37 38 4.351054 CCTCCACCAGGCCACCAC 62.351 72.222 5.01 0.00 34.56 4.16
38 39 3.252284 CTCCACCAGGCCACCACT 61.252 66.667 5.01 0.00 33.74 4.00
39 40 3.249189 TCCACCAGGCCACCACTC 61.249 66.667 5.01 0.00 33.74 3.51
40 41 4.351054 CCACCAGGCCACCACTCC 62.351 72.222 5.01 0.00 0.00 3.85
41 42 4.351054 CACCAGGCCACCACTCCC 62.351 72.222 5.01 0.00 0.00 4.30
47 48 4.035102 GCCACCACTCCCCCAGTC 62.035 72.222 0.00 0.00 30.26 3.51
48 49 3.330720 CCACCACTCCCCCAGTCC 61.331 72.222 0.00 0.00 30.26 3.85
49 50 3.706373 CACCACTCCCCCAGTCCG 61.706 72.222 0.00 0.00 30.26 4.79
50 51 4.250170 ACCACTCCCCCAGTCCGT 62.250 66.667 0.00 0.00 30.26 4.69
51 52 2.928396 CCACTCCCCCAGTCCGTT 60.928 66.667 0.00 0.00 30.26 4.44
52 53 2.663196 CACTCCCCCAGTCCGTTC 59.337 66.667 0.00 0.00 30.26 3.95
53 54 1.913762 CACTCCCCCAGTCCGTTCT 60.914 63.158 0.00 0.00 30.26 3.01
54 55 1.609794 ACTCCCCCAGTCCGTTCTC 60.610 63.158 0.00 0.00 0.00 2.87
55 56 2.678934 TCCCCCAGTCCGTTCTCG 60.679 66.667 0.00 0.00 0.00 4.04
56 57 4.452733 CCCCCAGTCCGTTCTCGC 62.453 72.222 0.00 0.00 35.54 5.03
57 58 4.452733 CCCCAGTCCGTTCTCGCC 62.453 72.222 0.00 0.00 35.54 5.54
58 59 4.796231 CCCAGTCCGTTCTCGCCG 62.796 72.222 0.00 0.00 35.54 6.46
59 60 4.796231 CCAGTCCGTTCTCGCCGG 62.796 72.222 0.00 0.00 46.83 6.13
60 61 4.796231 CAGTCCGTTCTCGCCGGG 62.796 72.222 2.18 0.00 45.51 5.73
62 63 4.493747 GTCCGTTCTCGCCGGGAG 62.494 72.222 2.18 8.70 45.51 4.30
64 65 3.136123 CCGTTCTCGCCGGGAGTA 61.136 66.667 16.53 7.33 43.60 2.59
65 66 2.408022 CGTTCTCGCCGGGAGTAG 59.592 66.667 16.53 8.09 43.60 2.57
66 67 2.104530 GTTCTCGCCGGGAGTAGC 59.895 66.667 16.53 7.31 43.60 3.58
67 68 2.361992 TTCTCGCCGGGAGTAGCA 60.362 61.111 16.53 0.00 43.60 3.49
68 69 2.415608 TTCTCGCCGGGAGTAGCAG 61.416 63.158 16.53 0.00 43.60 4.24
69 70 3.141488 CTCGCCGGGAGTAGCAGT 61.141 66.667 2.18 0.00 38.02 4.40
70 71 3.417275 CTCGCCGGGAGTAGCAGTG 62.417 68.421 2.18 0.00 38.02 3.66
112 113 0.808755 AAATCCAAATGGCGGACGAC 59.191 50.000 0.00 0.00 34.69 4.34
204 205 0.241481 GAAATTGCAACCCGCCGTTA 59.759 50.000 0.00 0.00 41.33 3.18
297 367 2.367512 GCCCCTCCACCCTCAGAT 60.368 66.667 0.00 0.00 0.00 2.90
298 368 2.447714 GCCCCTCCACCCTCAGATC 61.448 68.421 0.00 0.00 0.00 2.75
299 369 1.768077 CCCCTCCACCCTCAGATCC 60.768 68.421 0.00 0.00 0.00 3.36
300 370 1.003442 CCCTCCACCCTCAGATCCA 59.997 63.158 0.00 0.00 0.00 3.41
301 371 1.341156 CCCTCCACCCTCAGATCCAC 61.341 65.000 0.00 0.00 0.00 4.02
302 372 1.680522 CCTCCACCCTCAGATCCACG 61.681 65.000 0.00 0.00 0.00 4.94
303 373 1.680522 CTCCACCCTCAGATCCACGG 61.681 65.000 0.00 0.00 0.00 4.94
304 374 1.990060 CCACCCTCAGATCCACGGT 60.990 63.158 0.00 0.00 0.00 4.83
305 375 0.686441 CCACCCTCAGATCCACGGTA 60.686 60.000 0.00 0.00 0.00 4.02
306 376 1.191535 CACCCTCAGATCCACGGTAA 58.808 55.000 0.00 0.00 0.00 2.85
307 377 1.762957 CACCCTCAGATCCACGGTAAT 59.237 52.381 0.00 0.00 0.00 1.89
308 378 1.762957 ACCCTCAGATCCACGGTAATG 59.237 52.381 0.00 0.00 0.00 1.90
309 379 2.039418 CCCTCAGATCCACGGTAATGA 58.961 52.381 0.00 0.00 0.00 2.57
310 380 2.036475 CCCTCAGATCCACGGTAATGAG 59.964 54.545 0.00 0.00 35.14 2.90
311 381 2.036475 CCTCAGATCCACGGTAATGAGG 59.964 54.545 14.45 14.45 45.56 3.86
312 382 2.959030 CTCAGATCCACGGTAATGAGGA 59.041 50.000 0.00 0.00 32.44 3.71
313 383 2.959030 TCAGATCCACGGTAATGAGGAG 59.041 50.000 0.00 0.00 31.96 3.69
314 384 2.036475 CAGATCCACGGTAATGAGGAGG 59.964 54.545 0.00 0.00 31.96 4.30
315 385 1.344763 GATCCACGGTAATGAGGAGGG 59.655 57.143 0.00 0.00 31.96 4.30
316 386 1.146263 CCACGGTAATGAGGAGGGC 59.854 63.158 0.00 0.00 0.00 5.19
317 387 1.227263 CACGGTAATGAGGAGGGCG 60.227 63.158 0.00 0.00 0.00 6.13
318 388 2.280186 CGGTAATGAGGAGGGCGC 60.280 66.667 0.00 0.00 0.00 6.53
319 389 2.111251 GGTAATGAGGAGGGCGCC 59.889 66.667 21.18 21.18 0.00 6.53
320 390 2.280186 GTAATGAGGAGGGCGCCG 60.280 66.667 22.54 0.00 0.00 6.46
321 391 3.546543 TAATGAGGAGGGCGCCGG 61.547 66.667 22.54 0.00 0.00 6.13
575 649 3.764466 CCTCCGCGGCTTCTCTGT 61.764 66.667 23.51 0.00 0.00 3.41
663 737 2.464865 CTCCTTAATCGTCGCTCCTTG 58.535 52.381 0.00 0.00 0.00 3.61
738 812 2.790791 CCCTCCTCAGCGCTTCGAT 61.791 63.158 7.50 0.00 0.00 3.59
1066 1152 0.184933 GGCTGGTGTATGGGGCAATA 59.815 55.000 0.00 0.00 0.00 1.90
1073 1159 4.106179 TGGTGTATGGGGCAATATCATCTT 59.894 41.667 0.00 0.00 0.00 2.40
1078 1164 4.458256 TGGGGCAATATCATCTTCACAT 57.542 40.909 0.00 0.00 0.00 3.21
1080 1166 6.143551 TGGGGCAATATCATCTTCACATAT 57.856 37.500 0.00 0.00 0.00 1.78
1113 1199 0.836606 TTGCTGATGCTAATCCCGGA 59.163 50.000 0.73 0.00 40.48 5.14
1153 1239 5.645497 GTCCTTTACTGGTCGTCTAAGTCTA 59.355 44.000 0.00 0.00 0.00 2.59
1165 1251 2.037251 TCTAAGTCTATTGATGCCGGCC 59.963 50.000 26.77 10.34 0.00 6.13
1168 1254 0.663153 GTCTATTGATGCCGGCCAAC 59.337 55.000 26.77 15.63 0.00 3.77
1174 1260 4.356442 ATGCCGGCCAACGTTTGC 62.356 61.111 26.77 15.57 42.24 3.68
1190 1279 0.817634 TTGCGGGATTTGGATAGGCG 60.818 55.000 0.00 0.00 0.00 5.52
1253 1342 1.993653 CTGTGATCAAGGGGCCTCA 59.006 57.895 4.79 0.00 0.00 3.86
1254 1343 0.549950 CTGTGATCAAGGGGCCTCAT 59.450 55.000 4.79 0.00 0.00 2.90
1285 1374 6.186957 AGTAACTCACTCAGACATCAGATCT 58.813 40.000 0.00 0.00 28.33 2.75
1349 1438 2.355197 TGGTAGATTCACAATGTGGCG 58.645 47.619 13.95 0.00 33.87 5.69
1439 1528 0.908198 GGGCTCTCTCATCACCTTGT 59.092 55.000 0.00 0.00 0.00 3.16
1637 1756 4.125703 GGTGATTGCTCATCCTTAGTCTG 58.874 47.826 0.00 0.00 32.98 3.51
1650 1769 6.921486 TCCTTAGTCTGTGTATTGTGGTAA 57.079 37.500 0.00 0.00 0.00 2.85
1736 1859 3.496870 GGTCACTTGTTGAAGATCCCTGT 60.497 47.826 0.00 0.00 35.39 4.00
1747 1870 0.798776 GATCCCTGTTGCAAGTGACG 59.201 55.000 0.00 0.00 0.00 4.35
1817 1940 7.520451 TTGTCTCTAACAAGCTAGTGTAGAA 57.480 36.000 0.00 0.00 42.95 2.10
1821 1944 8.865001 GTCTCTAACAAGCTAGTGTAGAATTTG 58.135 37.037 0.00 0.00 0.00 2.32
1842 1965 7.768807 TTTGTTAGTTTGGGTGTGCTATTAT 57.231 32.000 0.00 0.00 0.00 1.28
1883 2031 5.163301 TGTGGGATAAATTCTAGGCAGTCTC 60.163 44.000 0.00 0.00 0.00 3.36
1884 2032 5.071115 GTGGGATAAATTCTAGGCAGTCTCT 59.929 44.000 0.00 0.00 0.00 3.10
1885 2033 5.667626 TGGGATAAATTCTAGGCAGTCTCTT 59.332 40.000 0.00 0.00 0.00 2.85
1916 2064 8.831000 TTCTTACAAGCGAAAACTTTCTTTAC 57.169 30.769 1.03 0.00 35.07 2.01
1953 2102 8.814038 ATATTACTGTTTCTGGATTGCTCTTT 57.186 30.769 0.00 0.00 0.00 2.52
2096 2245 4.761739 TGCCTCTTATGTCTTTTCCTTGTG 59.238 41.667 0.00 0.00 0.00 3.33
2135 2284 5.426689 TGACTTCTTATGCTTCTGGTCAT 57.573 39.130 0.00 0.00 0.00 3.06
2150 2299 1.212935 GGTCATAGCCATTCCTGGTGT 59.787 52.381 0.00 0.00 45.10 4.16
2217 2366 3.119424 TGGTTGCATGTCATAATGTGCTG 60.119 43.478 0.00 0.00 38.37 4.41
2313 2468 0.533755 ACTATTGCTCATCCGGCTGC 60.534 55.000 0.00 0.62 0.00 5.25
2344 2499 6.667661 TCATGGATGTTAATGATGGGTACAA 58.332 36.000 0.00 0.00 0.00 2.41
2398 2553 1.597195 TGACGTGCAGATGTTTCACAC 59.403 47.619 0.00 0.00 0.00 3.82
2451 2606 1.244816 GCTGGGTGTTTGGTTAGACC 58.755 55.000 0.00 0.00 39.22 3.85
2540 2696 6.016777 GGTCTCATGGAAAATTGATAAGCGAT 60.017 38.462 0.00 0.00 0.00 4.58
2546 2702 9.681692 CATGGAAAATTGATAAGCGATATTTCA 57.318 29.630 0.00 0.00 0.00 2.69
2601 2757 8.494016 AATAACCGAAGAAAACTGAGAATAGG 57.506 34.615 0.00 0.00 0.00 2.57
2713 2869 0.441533 CGCTGGATATTCTCGCATGC 59.558 55.000 7.91 7.91 0.00 4.06
2743 2899 1.002430 GCTGTGAAGGAGTGATGGTCA 59.998 52.381 0.00 0.00 0.00 4.02
2806 2963 3.326578 TGCGTGGTAGCCATGGGT 61.327 61.111 22.15 22.15 40.61 4.51
2807 2964 2.824041 GCGTGGTAGCCATGGGTG 60.824 66.667 26.70 10.25 40.61 4.61
2870 3027 4.530325 CCGCGCGGTAACATTGGC 62.530 66.667 39.71 0.00 0.00 4.52
2938 3095 0.034186 TGGGATTGCATGAGGTGGAC 60.034 55.000 0.00 0.00 0.00 4.02
2969 3126 2.058798 GGTGGTGATACGTGATATGCG 58.941 52.381 0.00 0.00 0.00 4.73
3025 3182 1.302832 GTGGGACTGCTCCTGTTGG 60.303 63.158 0.00 0.00 36.68 3.77
3047 3204 3.743396 GCTAGAAGCTTCGTATTGATGGG 59.257 47.826 20.43 4.36 38.45 4.00
3169 3335 0.094046 GCGAACCGAACATACAACCG 59.906 55.000 0.00 0.00 0.00 4.44
3176 3342 3.878699 ACCGAACATACAACCGAAGTTTT 59.121 39.130 0.00 0.00 32.45 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.052229 CTGCTGCTGCCTGTTGCC 62.052 66.667 13.47 0.00 40.16 4.52
3 4 4.719369 GCTGCTGCTGCCTGTTGC 62.719 66.667 19.30 6.07 38.71 4.17
4 5 4.052229 GGCTGCTGCTGCCTGTTG 62.052 66.667 34.54 3.41 43.62 3.33
11 12 4.340246 TGGTGGAGGCTGCTGCTG 62.340 66.667 15.64 0.77 39.59 4.41
12 13 4.031129 CTGGTGGAGGCTGCTGCT 62.031 66.667 15.64 1.41 39.59 4.24
20 21 4.351054 GTGGTGGCCTGGTGGAGG 62.351 72.222 3.32 0.00 46.13 4.30
21 22 3.252284 AGTGGTGGCCTGGTGGAG 61.252 66.667 3.32 0.00 34.57 3.86
22 23 3.249189 GAGTGGTGGCCTGGTGGA 61.249 66.667 3.32 0.00 34.57 4.02
23 24 4.351054 GGAGTGGTGGCCTGGTGG 62.351 72.222 3.32 0.00 0.00 4.61
24 25 4.351054 GGGAGTGGTGGCCTGGTG 62.351 72.222 3.32 0.00 0.00 4.17
30 31 4.035102 GACTGGGGGAGTGGTGGC 62.035 72.222 0.00 0.00 33.83 5.01
31 32 3.330720 GGACTGGGGGAGTGGTGG 61.331 72.222 0.00 0.00 33.83 4.61
32 33 3.706373 CGGACTGGGGGAGTGGTG 61.706 72.222 0.00 0.00 33.83 4.17
33 34 3.786866 AACGGACTGGGGGAGTGGT 62.787 63.158 0.00 0.00 33.83 4.16
34 35 2.928396 AACGGACTGGGGGAGTGG 60.928 66.667 0.00 0.00 33.83 4.00
35 36 1.889530 GAGAACGGACTGGGGGAGTG 61.890 65.000 0.00 0.00 33.83 3.51
36 37 1.609794 GAGAACGGACTGGGGGAGT 60.610 63.158 0.00 0.00 37.76 3.85
37 38 2.711922 CGAGAACGGACTGGGGGAG 61.712 68.421 0.00 0.00 35.72 4.30
38 39 2.678934 CGAGAACGGACTGGGGGA 60.679 66.667 0.00 0.00 35.72 4.81
39 40 4.452733 GCGAGAACGGACTGGGGG 62.453 72.222 0.00 0.00 40.15 5.40
40 41 4.452733 GGCGAGAACGGACTGGGG 62.453 72.222 0.00 0.00 40.15 4.96
41 42 4.796231 CGGCGAGAACGGACTGGG 62.796 72.222 0.00 0.00 40.15 4.45
48 49 2.408022 CTACTCCCGGCGAGAACG 59.592 66.667 22.16 9.15 41.63 3.95
49 50 2.104530 GCTACTCCCGGCGAGAAC 59.895 66.667 22.16 10.02 41.63 3.01
50 51 2.361992 TGCTACTCCCGGCGAGAA 60.362 61.111 22.16 0.00 41.63 2.87
51 52 2.829003 CTGCTACTCCCGGCGAGA 60.829 66.667 22.16 0.00 41.63 4.04
52 53 3.141488 ACTGCTACTCCCGGCGAG 61.141 66.667 9.30 15.85 44.95 5.03
53 54 3.449227 CACTGCTACTCCCGGCGA 61.449 66.667 9.30 0.00 0.00 5.54
55 56 4.840005 GGCACTGCTACTCCCGGC 62.840 72.222 0.00 0.00 0.00 6.13
56 57 3.077556 AGGCACTGCTACTCCCGG 61.078 66.667 0.00 0.00 37.18 5.73
57 58 2.496817 GAGGCACTGCTACTCCCG 59.503 66.667 0.00 0.00 41.55 5.14
58 59 2.496817 CGAGGCACTGCTACTCCC 59.503 66.667 0.00 0.00 41.55 4.30
59 60 2.202810 GCGAGGCACTGCTACTCC 60.203 66.667 0.00 0.00 41.55 3.85
60 61 2.202810 GGCGAGGCACTGCTACTC 60.203 66.667 0.00 0.00 41.55 2.59
61 62 4.135153 CGGCGAGGCACTGCTACT 62.135 66.667 0.00 0.00 41.55 2.57
117 118 3.760035 GAGGGCAGTTCGCTCCGA 61.760 66.667 0.00 0.00 45.13 4.55
280 350 2.367512 ATCTGAGGGTGGAGGGGC 60.368 66.667 0.00 0.00 0.00 5.80
281 351 1.768077 GGATCTGAGGGTGGAGGGG 60.768 68.421 0.00 0.00 0.00 4.79
282 352 1.003442 TGGATCTGAGGGTGGAGGG 59.997 63.158 0.00 0.00 0.00 4.30
283 353 1.680522 CGTGGATCTGAGGGTGGAGG 61.681 65.000 0.00 0.00 0.00 4.30
284 354 1.680522 CCGTGGATCTGAGGGTGGAG 61.681 65.000 0.00 0.00 0.00 3.86
285 355 1.685765 CCGTGGATCTGAGGGTGGA 60.686 63.158 0.00 0.00 0.00 4.02
286 356 0.686441 TACCGTGGATCTGAGGGTGG 60.686 60.000 15.66 2.78 33.65 4.61
287 357 1.191535 TTACCGTGGATCTGAGGGTG 58.808 55.000 15.66 0.00 33.65 4.61
288 358 1.762957 CATTACCGTGGATCTGAGGGT 59.237 52.381 12.36 12.36 35.73 4.34
289 359 2.036475 CTCATTACCGTGGATCTGAGGG 59.964 54.545 0.00 0.00 0.00 4.30
290 360 2.036475 CCTCATTACCGTGGATCTGAGG 59.964 54.545 15.61 15.61 42.59 3.86
291 361 2.959030 TCCTCATTACCGTGGATCTGAG 59.041 50.000 0.00 1.62 0.00 3.35
292 362 2.959030 CTCCTCATTACCGTGGATCTGA 59.041 50.000 0.00 0.00 0.00 3.27
293 363 2.036475 CCTCCTCATTACCGTGGATCTG 59.964 54.545 0.00 0.00 0.00 2.90
294 364 2.320781 CCTCCTCATTACCGTGGATCT 58.679 52.381 0.00 0.00 0.00 2.75
295 365 1.344763 CCCTCCTCATTACCGTGGATC 59.655 57.143 0.00 0.00 0.00 3.36
296 366 1.424638 CCCTCCTCATTACCGTGGAT 58.575 55.000 0.00 0.00 0.00 3.41
297 367 1.335132 GCCCTCCTCATTACCGTGGA 61.335 60.000 0.00 0.00 0.00 4.02
298 368 1.146263 GCCCTCCTCATTACCGTGG 59.854 63.158 0.00 0.00 0.00 4.94
299 369 1.227263 CGCCCTCCTCATTACCGTG 60.227 63.158 0.00 0.00 0.00 4.94
300 370 3.090219 GCGCCCTCCTCATTACCGT 62.090 63.158 0.00 0.00 0.00 4.83
301 371 2.280186 GCGCCCTCCTCATTACCG 60.280 66.667 0.00 0.00 0.00 4.02
302 372 2.111251 GGCGCCCTCCTCATTACC 59.889 66.667 18.11 0.00 0.00 2.85
303 373 2.280186 CGGCGCCCTCCTCATTAC 60.280 66.667 23.46 0.00 0.00 1.89
304 374 3.546543 CCGGCGCCCTCCTCATTA 61.547 66.667 23.46 0.00 0.00 1.90
320 390 2.737376 GCAACGTCGGGTCACTCC 60.737 66.667 0.00 0.00 0.00 3.85
321 391 2.022129 CTGCAACGTCGGGTCACTC 61.022 63.158 0.00 0.00 0.00 3.51
322 392 2.029073 CTGCAACGTCGGGTCACT 59.971 61.111 0.00 0.00 0.00 3.41
323 393 3.712881 GCTGCAACGTCGGGTCAC 61.713 66.667 0.00 0.00 0.00 3.67
324 394 4.980805 GGCTGCAACGTCGGGTCA 62.981 66.667 0.50 0.00 0.00 4.02
332 402 4.520846 GAATCGCGGGCTGCAACG 62.521 66.667 19.92 10.92 46.97 4.10
333 403 4.179579 GGAATCGCGGGCTGCAAC 62.180 66.667 19.92 5.84 46.97 4.17
334 404 3.993614 ATGGAATCGCGGGCTGCAA 62.994 57.895 19.92 0.00 46.97 4.08
335 405 4.488136 ATGGAATCGCGGGCTGCA 62.488 61.111 19.92 6.00 46.97 4.41
663 737 2.551270 CACTTGTCACGGCGCTTC 59.449 61.111 6.90 0.00 0.00 3.86
738 812 3.964221 GACGCCGTGATGTCGCAGA 62.964 63.158 0.00 0.00 0.00 4.26
839 913 0.744771 GATGGGGGCGAAGACAACTC 60.745 60.000 0.00 0.00 37.00 3.01
971 1048 0.038166 GACCACCTTGAATGGGCTCA 59.962 55.000 0.00 0.00 42.62 4.26
1066 1152 5.791666 ACATCGAGCATATGTGAAGATGAT 58.208 37.500 24.92 14.30 36.24 2.45
1113 1199 7.228706 CAGTAAAGGACATTACCAACAAGAACT 59.771 37.037 0.00 0.00 36.62 3.01
1153 1239 1.531739 AAACGTTGGCCGGCATCAAT 61.532 50.000 30.85 7.43 42.24 2.57
1165 1251 0.312416 TCCAAATCCCGCAAACGTTG 59.688 50.000 0.00 0.00 37.70 4.10
1168 1254 1.333619 CCTATCCAAATCCCGCAAACG 59.666 52.381 0.00 0.00 39.67 3.60
1174 1260 1.227823 TGCGCCTATCCAAATCCCG 60.228 57.895 4.18 0.00 0.00 5.14
1190 1279 5.912396 TCAAACTCAATTATGTCGTTTGTGC 59.088 36.000 17.21 0.00 42.56 4.57
1285 1374 1.988107 AGAACCATCCTCTGCCTTGAA 59.012 47.619 0.00 0.00 0.00 2.69
1340 1429 1.402968 CAATCTTCCTCCGCCACATTG 59.597 52.381 0.00 0.00 0.00 2.82
1349 1438 4.337555 CACCATGACAATCAATCTTCCTCC 59.662 45.833 0.00 0.00 0.00 4.30
1439 1528 3.886123 TCTATCCATCTCGGCGATATCA 58.114 45.455 11.27 0.00 33.14 2.15
1678 1801 9.401058 CTATTTCAGAAGTTATTCCATCAACCT 57.599 33.333 0.00 0.00 35.94 3.50
1736 1859 2.882927 AGTGTACTCGTCACTTGCAA 57.117 45.000 0.00 0.00 42.50 4.08
1803 1926 9.599322 CAAACTAACAAATTCTACACTAGCTTG 57.401 33.333 0.00 0.00 0.00 4.01
1810 1933 6.915843 CACACCCAAACTAACAAATTCTACAC 59.084 38.462 0.00 0.00 0.00 2.90
1817 1940 6.664428 AATAGCACACCCAAACTAACAAAT 57.336 33.333 0.00 0.00 0.00 2.32
1821 1944 7.625828 AAGATAATAGCACACCCAAACTAAC 57.374 36.000 0.00 0.00 0.00 2.34
1842 1965 3.054434 CCCACATATCCAGGTGACAAAGA 60.054 47.826 0.00 0.00 38.76 2.52
1916 2064 8.969267 CAGAAACAGTAATATTTAGCTACCTCG 58.031 37.037 0.00 0.00 0.00 4.63
1953 2102 8.388484 ACAAAGCCACATAATTTTTAAATGCA 57.612 26.923 0.00 0.00 0.00 3.96
2096 2245 6.786207 AGAAGTCAAGCGATTAATAAAAGCC 58.214 36.000 0.00 0.00 0.00 4.35
2135 2284 1.202639 CGCATACACCAGGAATGGCTA 60.203 52.381 0.00 0.00 0.00 3.93
2150 2299 3.198409 ACATTTCAGCTCCATCGCATA 57.802 42.857 0.00 0.00 0.00 3.14
2217 2366 4.339814 TGTTGTTACCTGTTGAACCATTCC 59.660 41.667 0.00 0.00 0.00 3.01
2313 2468 6.461927 CCATCATTAACATCCATGAAACCCTG 60.462 42.308 0.00 0.00 33.13 4.45
2398 2553 0.449786 TCAACAGCAACACAACACCG 59.550 50.000 0.00 0.00 0.00 4.94
2540 2696 4.634004 CCAAACTATCGGTGCACTGAAATA 59.366 41.667 31.03 18.77 34.49 1.40
2546 2702 2.423577 GAACCAAACTATCGGTGCACT 58.576 47.619 17.98 0.00 35.08 4.40
2601 2757 2.987232 ACGGATTTCTTGCTCCCTAAC 58.013 47.619 0.00 0.00 0.00 2.34
2721 2877 0.325933 CCATCACTCCTTCACAGCCA 59.674 55.000 0.00 0.00 0.00 4.75
2761 2918 1.747745 GACAACGTACATGGCCCCC 60.748 63.158 0.00 0.00 0.00 5.40
2791 2948 2.824041 GCACCCATGGCTACCACG 60.824 66.667 6.09 0.00 35.80 4.94
2851 3008 3.794242 CAATGTTACCGCGCGGCA 61.794 61.111 46.22 35.44 39.32 5.69
2914 3071 1.389609 CCTCATGCAATCCCAGTGGC 61.390 60.000 2.61 0.00 0.00 5.01
2938 3095 3.381136 CACCACCGCCCCCATTTG 61.381 66.667 0.00 0.00 0.00 2.32
3025 3182 3.743396 CCCATCAATACGAAGCTTCTAGC 59.257 47.826 23.50 0.00 42.84 3.42
3047 3204 4.702131 CCCATCATAACTAAGCCCAATAGC 59.298 45.833 0.00 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.