Multiple sequence alignment - TraesCS5B01G340400

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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 TraesCS5B01G340400 chr5B 100.000 9379 0 0 1 9379 524594863 524604241 0.000000e+00 17320
1 TraesCS5B01G340400 chr2B 96.350 7287 211 28 1 7256 155684388 155677126 0.000000e+00 11932
2 TraesCS5B01G340400 chr2B 95.419 5174 221 16 1 5169 379153188 379158350 0.000000e+00 8227
3 TraesCS5B01G340400 chr2B 95.192 5179 212 17 1 5171 179061817 179066966 0.000000e+00 8150
4 TraesCS5B01G340400 chr2B 94.667 5175 254 19 1 5169 75313234 75308076 0.000000e+00 8008
5 TraesCS5B01G340400 chr2B 93.586 5176 266 36 1 5169 259487841 259482725 0.000000e+00 7659
6 TraesCS5B01G340400 chr2B 95.451 2682 104 9 1 2679 535997791 536000457 0.000000e+00 4261
7 TraesCS5B01G340400 chr2B 97.044 2131 55 6 7254 9379 155677097 155674970 0.000000e+00 3579
8 TraesCS5B01G340400 chr2B 95.795 2069 75 11 5191 7256 179067101 179069160 0.000000e+00 3328
9 TraesCS5B01G340400 chr2B 95.303 2065 89 7 5193 7256 261021175 261023232 0.000000e+00 3269
10 TraesCS5B01G340400 chr2B 95.388 2060 86 8 5197 7256 701267949 701265899 0.000000e+00 3269
11 TraesCS5B01G340400 chr2B 94.961 2064 92 11 5193 7256 209872953 209870902 0.000000e+00 3225
12 TraesCS5B01G340400 chr2B 95.864 1475 42 6 7251 8722 179069186 179070644 0.000000e+00 2368
13 TraesCS5B01G340400 chr2B 94.101 1424 51 9 7255 8646 261023262 261024684 0.000000e+00 2134
14 TraesCS5B01G340400 chr2B 93.693 1427 52 11 7255 8646 209870872 209869449 0.000000e+00 2102
15 TraesCS5B01G340400 chr2B 93.407 1001 36 17 7250 8221 701265874 701264875 0.000000e+00 1456
16 TraesCS5B01G340400 chr2B 95.723 678 26 3 8703 9379 179070659 179071334 0.000000e+00 1088
17 TraesCS5B01G340400 chr2B 94.985 678 28 6 8703 9379 701264276 701263604 0.000000e+00 1059
18 TraesCS5B01G340400 chr2B 94.822 676 27 8 8703 9377 261024892 261025560 0.000000e+00 1048
19 TraesCS5B01G340400 chr2B 94.395 678 33 5 8703 9379 379162902 379163575 0.000000e+00 1037
20 TraesCS5B01G340400 chr6B 96.022 5179 185 17 1 5169 247390115 247395282 0.000000e+00 8403
21 TraesCS5B01G340400 chr6B 95.381 5174 222 16 1 5169 378835897 378841058 0.000000e+00 8215
22 TraesCS5B01G340400 chr6B 96.818 1477 38 7 7251 8722 247397484 247398956 0.000000e+00 2459
23 TraesCS5B01G340400 chr6B 92.737 1432 62 10 7254 8652 379090736 379089314 0.000000e+00 2030
24 TraesCS5B01G340400 chr6B 92.673 1433 60 5 7251 8652 378843252 378844670 0.000000e+00 2023
25 TraesCS5B01G340400 chr6B 96.018 678 24 3 8703 9379 247398971 247399646 0.000000e+00 1099
26 TraesCS5B01G340400 chr6B 95.280 678 26 6 8703 9379 378844872 378845544 0.000000e+00 1070
27 TraesCS5B01G340400 chr6B 95.775 71 1 2 8652 8722 379089196 379089128 7.700000e-21 113
28 TraesCS5B01G340400 chr6B 96.970 66 1 1 8652 8717 378844789 378844853 9.960000e-20 110
29 TraesCS5B01G340400 chr3B 95.979 5173 192 16 1 5169 236263127 236257967 0.000000e+00 8386
30 TraesCS5B01G340400 chr3B 95.574 5174 209 16 1 5169 252183219 252188377 0.000000e+00 8268
31 TraesCS5B01G340400 chr3B 94.015 5180 270 27 1 5169 129944634 129939484 0.000000e+00 7812
32 TraesCS5B01G340400 chr3B 96.081 2067 73 7 5191 7256 477785193 477787252 0.000000e+00 3362
33 TraesCS5B01G340400 chr3B 95.058 2064 95 7 5193 7256 252188522 252190578 0.000000e+00 3240
34 TraesCS5B01G340400 chr3B 96.735 1409 35 6 7251 8652 477787278 477788682 0.000000e+00 2337
35 TraesCS5B01G340400 chr3B 91.462 1265 93 10 7381 8638 572142693 572141437 0.000000e+00 1724
36 TraesCS5B01G340400 chr3B 96.018 678 20 7 8703 9379 477788884 477789555 0.000000e+00 1096
37 TraesCS5B01G340400 chr7B 95.732 5178 187 21 1 5171 207969081 207974231 0.000000e+00 8307
38 TraesCS5B01G340400 chr7B 95.085 4049 141 26 3256 7256 206193941 206189903 0.000000e+00 6322
39 TraesCS5B01G340400 chr7B 95.648 2068 82 7 5191 7256 207974366 207976427 0.000000e+00 3314
40 TraesCS5B01G340400 chr7B 97.156 1477 34 5 7251 8722 207976453 207977926 0.000000e+00 2488
41 TraesCS5B01G340400 chr7B 96.453 1297 34 5 7436 8722 206189759 206188465 0.000000e+00 2130
42 TraesCS5B01G340400 chr7B 96.465 679 21 3 8703 9379 207977941 207978618 0.000000e+00 1118
43 TraesCS5B01G340400 chr7B 95.775 71 3 0 8652 8722 33971914 33971984 2.140000e-21 115
44 TraesCS5B01G340400 chr6A 91.240 3105 208 32 2073 5169 158983621 158980573 0.000000e+00 4169
45 TraesCS5B01G340400 chr4B 89.926 3117 233 44 2073 5169 470130939 470133994 0.000000e+00 3941
46 TraesCS5B01G340400 chr4B 91.304 184 15 1 4986 5169 279976826 279977008 5.620000e-62 250
47 TraesCS5B01G340400 chr4B 95.775 71 2 1 8652 8722 494456732 494456801 7.700000e-21 113
48 TraesCS5B01G340400 chr4D 84.491 2792 327 59 2244 5014 168997425 168994719 0.000000e+00 2660
49 TraesCS5B01G340400 chr4D 87.597 903 89 11 4113 5014 148262354 148263234 0.000000e+00 1026
50 TraesCS5B01G340400 chr4D 96.104 77 3 0 5093 5169 274327505 274327581 9.890000e-25 126
51 TraesCS5B01G340400 chr4D 94.805 77 4 0 5093 5169 230592913 230592837 4.600000e-23 121
52 TraesCS5B01G340400 chr4D 94.805 77 4 0 5093 5169 310009270 310009346 4.600000e-23 121
53 TraesCS5B01G340400 chr4D 90.909 77 7 0 5093 5169 343825280 343825204 4.630000e-18 104
54 TraesCS5B01G340400 chr4D 80.132 151 18 11 5026 5169 144580369 144580224 1.670000e-17 102
55 TraesCS5B01G340400 chr1B 89.987 759 38 23 8652 9377 290980722 290981475 0.000000e+00 946
56 TraesCS5B01G340400 chr6D 95.139 144 5 2 5026 5169 256019667 256019808 9.480000e-55 226
57 TraesCS5B01G340400 chr6D 94.118 119 5 2 5026 5144 249248945 249249061 7.480000e-41 180
58 TraesCS5B01G340400 chr3D 94.958 119 4 2 5026 5144 254420792 254420676 1.610000e-42 185
59 TraesCS5B01G340400 chr3D 94.872 117 4 2 5026 5142 353284192 353284306 2.080000e-41 182
60 TraesCS5B01G340400 chr1D 94.118 119 5 2 5026 5144 296771499 296771615 7.480000e-41 180
61 TraesCS5B01G340400 chr1D 93.277 119 6 2 5026 5144 88010125 88010009 3.480000e-39 174
62 TraesCS5B01G340400 chr1D 91.597 119 7 3 5026 5144 78751883 78751768 2.710000e-35 161
63 TraesCS5B01G340400 chr1D 97.403 77 2 0 5093 5169 371718999 371719075 2.130000e-26 132
64 TraesCS5B01G340400 chr1D 93.506 77 5 0 5093 5169 266079792 266079716 2.140000e-21 115
65 TraesCS5B01G340400 chr1A 94.118 119 5 2 5026 5144 303523059 303523175 7.480000e-41 180
66 TraesCS5B01G340400 chr5D 93.277 119 6 2 5026 5144 108667146 108667030 3.480000e-39 174
67 TraesCS5B01G340400 chr5D 92.437 119 7 2 5026 5144 56001505 56001389 1.620000e-37 169


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 TraesCS5B01G340400 chr5B 524594863 524604241 9378 False 17320.000000 17320 100.000000 1 9379 1 chr5B.!!$F1 9378
1 TraesCS5B01G340400 chr2B 379153188 379158350 5162 False 8227.000000 8227 95.419000 1 5169 1 chr2B.!!$F1 5168
2 TraesCS5B01G340400 chr2B 75308076 75313234 5158 True 8008.000000 8008 94.667000 1 5169 1 chr2B.!!$R1 5168
3 TraesCS5B01G340400 chr2B 155674970 155684388 9418 True 7755.500000 11932 96.697000 1 9379 2 chr2B.!!$R3 9378
4 TraesCS5B01G340400 chr2B 259482725 259487841 5116 True 7659.000000 7659 93.586000 1 5169 1 chr2B.!!$R2 5168
5 TraesCS5B01G340400 chr2B 535997791 536000457 2666 False 4261.000000 4261 95.451000 1 2679 1 chr2B.!!$F3 2678
6 TraesCS5B01G340400 chr2B 179061817 179071334 9517 False 3733.500000 8150 95.643500 1 9379 4 chr2B.!!$F4 9378
7 TraesCS5B01G340400 chr2B 209869449 209872953 3504 True 2663.500000 3225 94.327000 5193 8646 2 chr2B.!!$R4 3453
8 TraesCS5B01G340400 chr2B 261021175 261025560 4385 False 2150.333333 3269 94.742000 5193 9377 3 chr2B.!!$F5 4184
9 TraesCS5B01G340400 chr2B 701263604 701267949 4345 True 1928.000000 3269 94.593333 5197 9379 3 chr2B.!!$R5 4182
10 TraesCS5B01G340400 chr2B 379162902 379163575 673 False 1037.000000 1037 94.395000 8703 9379 1 chr2B.!!$F2 676
11 TraesCS5B01G340400 chr6B 247390115 247399646 9531 False 3987.000000 8403 96.286000 1 9379 3 chr6B.!!$F1 9378
12 TraesCS5B01G340400 chr6B 378835897 378845544 9647 False 2854.500000 8215 95.076000 1 9379 4 chr6B.!!$F2 9378
13 TraesCS5B01G340400 chr6B 379089128 379090736 1608 True 1071.500000 2030 94.256000 7254 8722 2 chr6B.!!$R1 1468
14 TraesCS5B01G340400 chr3B 236257967 236263127 5160 True 8386.000000 8386 95.979000 1 5169 1 chr3B.!!$R2 5168
15 TraesCS5B01G340400 chr3B 129939484 129944634 5150 True 7812.000000 7812 94.015000 1 5169 1 chr3B.!!$R1 5168
16 TraesCS5B01G340400 chr3B 252183219 252190578 7359 False 5754.000000 8268 95.316000 1 7256 2 chr3B.!!$F1 7255
17 TraesCS5B01G340400 chr3B 477785193 477789555 4362 False 2265.000000 3362 96.278000 5191 9379 3 chr3B.!!$F2 4188
18 TraesCS5B01G340400 chr3B 572141437 572142693 1256 True 1724.000000 1724 91.462000 7381 8638 1 chr3B.!!$R3 1257
19 TraesCS5B01G340400 chr7B 206188465 206193941 5476 True 4226.000000 6322 95.769000 3256 8722 2 chr7B.!!$R1 5466
20 TraesCS5B01G340400 chr7B 207969081 207978618 9537 False 3806.750000 8307 96.250250 1 9379 4 chr7B.!!$F2 9378
21 TraesCS5B01G340400 chr6A 158980573 158983621 3048 True 4169.000000 4169 91.240000 2073 5169 1 chr6A.!!$R1 3096
22 TraesCS5B01G340400 chr4B 470130939 470133994 3055 False 3941.000000 3941 89.926000 2073 5169 1 chr4B.!!$F2 3096
23 TraesCS5B01G340400 chr4D 168994719 168997425 2706 True 2660.000000 2660 84.491000 2244 5014 1 chr4D.!!$R2 2770
24 TraesCS5B01G340400 chr4D 148262354 148263234 880 False 1026.000000 1026 87.597000 4113 5014 1 chr4D.!!$F1 901
25 TraesCS5B01G340400 chr1B 290980722 290981475 753 False 946.000000 946 89.987000 8652 9377 1 chr1B.!!$F1 725

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
534 538 0.109504 GCGACAGAGACGAAAGAGCT 60.110 55.000 0.00 0.00 0.00 4.09 F
578 582 1.134037 ACCACCCGCAAAAACTGTCTA 60.134 47.619 0.00 0.00 0.00 2.59 F
2071 2132 0.478072 TGATTTGTGCCCACTGGAGT 59.522 50.000 0.00 0.00 0.00 3.85 F
2820 2895 0.320374 GACCTCCATCAACACCGACA 59.680 55.000 0.00 0.00 0.00 4.35 F
3495 3589 0.175073 GCAGGGTTCGTAGGATCGTT 59.825 55.000 0.00 0.00 0.00 3.85 F
5359 5638 0.248907 GCCGTGTATAAGCGCTCAGA 60.249 55.000 12.06 0.00 0.00 3.27 F
5480 5759 0.108138 GAACGACCCACTGCATAGCT 60.108 55.000 0.00 0.00 0.00 3.32 F
6933 7234 0.324943 CTCCCAAATCCCACAGTCGT 59.675 55.000 0.00 0.00 0.00 4.34 F
7738 8130 2.164827 TGAATCAAGCAGCGCATGAATT 59.835 40.909 11.47 0.96 39.63 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1822 1.807165 CGCCTCCGACACTGTCATG 60.807 63.158 9.84 0.19 36.29 3.07 R
2714 2789 5.656859 AGTGAGACTATGTGTGGTGCTAATA 59.343 40.000 0.00 0.00 0.00 0.98 R
2906 2981 1.595109 CCACTTGCACGTCTCTGCA 60.595 57.895 0.00 0.00 45.59 4.41 R
4501 4641 1.148310 CGGCGTGTTGATCTTGTTCT 58.852 50.000 0.00 0.00 0.00 3.01 R
5401 5680 1.070289 GGGCTCCGGACCTGTTTATAG 59.930 57.143 18.67 0.03 37.73 1.31 R
7100 7401 0.532862 CTTGTCTGGTTCGCTGGTGT 60.533 55.000 0.00 0.00 0.00 4.16 R
7905 8303 6.942532 TTTACAAGTGATAATCCATGAGGC 57.057 37.500 0.00 0.00 33.74 4.70 R
8196 8602 1.139058 GTAGAATGGGTGGATGACGCT 59.861 52.381 0.00 0.00 38.35 5.07 R
9003 9570 3.714280 TGGTATAATCCTAGCACTTGCCA 59.286 43.478 0.00 0.00 43.38 4.92 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
47 48 5.129485 ACTCATGGATAAGTACAACCTCCAG 59.871 44.000 10.81 5.43 39.25 3.86
428 432 4.638304 ACAAAACACGCTGACCTACTATT 58.362 39.130 0.00 0.00 0.00 1.73
451 455 2.307496 TTGACACCCAGATGGCAAAT 57.693 45.000 0.00 0.00 44.76 2.32
534 538 0.109504 GCGACAGAGACGAAAGAGCT 60.110 55.000 0.00 0.00 0.00 4.09
578 582 1.134037 ACCACCCGCAAAAACTGTCTA 60.134 47.619 0.00 0.00 0.00 2.59
829 838 2.404566 TAAGGCTGCCAGCGTTCCAA 62.405 55.000 26.09 8.34 44.97 3.53
843 852 6.128007 CCAGCGTTCCAAAGAAATACATACTT 60.128 38.462 0.00 0.00 32.58 2.24
1410 1464 2.282816 CCACCACGCCCCATCAAA 60.283 61.111 0.00 0.00 0.00 2.69
1768 1822 4.670221 GCCAATCAGACGAAGACAATGAAC 60.670 45.833 0.00 0.00 0.00 3.18
1905 1959 8.982723 AGACTGAACAATACATAGTGGTTATCT 58.017 33.333 0.00 0.00 0.00 1.98
2013 2071 7.658575 ACCAAGACTTATTTAGCTTTAACGTCA 59.341 33.333 0.00 0.00 0.00 4.35
2071 2132 0.478072 TGATTTGTGCCCACTGGAGT 59.522 50.000 0.00 0.00 0.00 3.85
2136 2197 4.056050 GACACAAAACGATACTGTGACCT 58.944 43.478 12.80 0.00 42.48 3.85
2156 2217 8.933807 GTGACCTAGTAACTCAGGAAAAATAAC 58.066 37.037 0.00 0.00 35.76 1.89
2739 2814 2.634940 AGCACCACACATAGTCTCACTT 59.365 45.455 0.00 0.00 0.00 3.16
2777 2852 5.708697 TCAATTGCACTTCAATCATCAGTCT 59.291 36.000 0.00 0.00 44.23 3.24
2820 2895 0.320374 GACCTCCATCAACACCGACA 59.680 55.000 0.00 0.00 0.00 4.35
2906 2981 4.400251 CAGTAAAATGCCATCATCACCACT 59.600 41.667 0.00 0.00 31.27 4.00
3138 3229 2.406002 AAATCCCCGTCCACGCACTT 62.406 55.000 0.00 0.00 38.18 3.16
3196 3289 1.080569 CAAACCACCATTGCCGCTC 60.081 57.895 0.00 0.00 0.00 5.03
3341 3435 3.209410 ACCTCGTCGATATTAACGTCCT 58.791 45.455 0.00 0.00 39.78 3.85
3440 3534 2.396157 GCGTACCAGAAAAGGCCGG 61.396 63.158 0.00 0.00 0.00 6.13
3495 3589 0.175073 GCAGGGTTCGTAGGATCGTT 59.825 55.000 0.00 0.00 0.00 3.85
3722 3820 6.633668 CTAGATGTACTAGTGTGTTTGTGC 57.366 41.667 5.39 0.00 42.44 4.57
4389 4529 1.070758 CGGTATGGAGATCAACCCCAG 59.929 57.143 0.00 0.00 32.90 4.45
4420 4560 0.957395 ACATTCAGCGCAAGTGGAGG 60.957 55.000 11.47 0.00 41.68 4.30
4501 4641 4.220382 CACCCATTCTACAAAGGCATGAAA 59.780 41.667 0.00 0.00 0.00 2.69
4648 4788 5.010719 ACATCATAGACGGTTCGGAATATGT 59.989 40.000 0.00 0.00 0.00 2.29
4676 4816 2.681097 GCGGGAGGCTGAAAACTTCTAT 60.681 50.000 0.00 0.00 39.11 1.98
5015 5165 0.306533 ATCACACAACGTTGTTCCGC 59.693 50.000 30.49 0.00 39.91 5.54
5110 5262 3.639538 CCGTAAGCGCTACTATGAATGT 58.360 45.455 12.05 0.00 36.67 2.71
5222 5501 1.419381 AAAAATGACCGCCCAAGGTT 58.581 45.000 0.00 0.00 46.09 3.50
5359 5638 0.248907 GCCGTGTATAAGCGCTCAGA 60.249 55.000 12.06 0.00 0.00 3.27
5468 5747 3.173240 GAGAGCACGCGAACGACC 61.173 66.667 15.93 0.00 43.93 4.79
5480 5759 0.108138 GAACGACCCACTGCATAGCT 60.108 55.000 0.00 0.00 0.00 3.32
6102 6389 9.869844 CTGACAAGTTCAACTACTAAAATTCAG 57.130 33.333 0.00 0.00 32.21 3.02
6223 6514 7.747690 TCTCAAACACCCAACCTAAGTTATAA 58.252 34.615 0.00 0.00 33.27 0.98
6342 6633 7.305361 CCGTGCATTGTATGAAATTACAATTCG 60.305 37.037 7.02 10.85 45.85 3.34
6762 7061 4.096003 CAGAACGGCGACCCCCAT 62.096 66.667 16.62 0.00 0.00 4.00
6854 7154 0.820226 TGTCTTCCATCTCTGCCTCG 59.180 55.000 0.00 0.00 0.00 4.63
6922 7223 4.835056 CCCAAAAACTTCTCTCTCCCAAAT 59.165 41.667 0.00 0.00 0.00 2.32
6933 7234 0.324943 CTCCCAAATCCCACAGTCGT 59.675 55.000 0.00 0.00 0.00 4.34
6976 7277 2.247267 GTTCCGCCAAACGTCACG 59.753 61.111 0.00 0.00 41.42 4.35
7363 7696 8.421784 ACGATTATAGTCATCTGTTTGTACCAT 58.578 33.333 0.00 0.00 0.00 3.55
7480 7814 6.422333 TGGATTGTTTCACCAGATTAGCATA 58.578 36.000 0.00 0.00 0.00 3.14
7738 8130 2.164827 TGAATCAAGCAGCGCATGAATT 59.835 40.909 11.47 0.96 39.63 2.17
7905 8303 8.504815 GCATGGCTCATAATATATAAGCATCTG 58.495 37.037 5.87 2.07 34.65 2.90
8292 8701 1.639298 GCCAGACAACCTCATCACGC 61.639 60.000 0.00 0.00 0.00 5.34
8294 8703 1.676916 CCAGACAACCTCATCACGCAT 60.677 52.381 0.00 0.00 0.00 4.73
8339 8748 4.690748 ACGTACAAGTCATGGAAGACAATG 59.309 41.667 0.00 0.00 40.98 2.82
9128 9695 8.697507 AGGAGAAAAATCACAAGAAACATAGT 57.302 30.769 0.00 0.00 0.00 2.12
9144 9711 7.498570 AGAAACATAGTAGGAAGACGTACTAGG 59.501 40.741 15.16 15.16 46.10 3.02
9168 9736 8.421002 AGGCTCAAACAACACAAAAGTAAATAT 58.579 29.630 0.00 0.00 0.00 1.28
9169 9737 9.685828 GGCTCAAACAACACAAAAGTAAATATA 57.314 29.630 0.00 0.00 0.00 0.86
9332 9900 5.137551 ACCAGTGCTTTAACTTGTACCATT 58.862 37.500 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
534 538 1.616865 AGCGCACTAGGTACTTTGTGA 59.383 47.619 20.56 0.00 41.67 3.58
578 582 3.633609 ATGCGTGCTGAGCCCACAT 62.634 57.895 0.23 0.00 32.85 3.21
843 852 1.483415 GGGCGTTTGGTGTATCTCCTA 59.517 52.381 0.00 0.00 0.00 2.94
1194 1203 1.516161 GCTCTTGAGTGTGCACATGA 58.484 50.000 24.69 14.48 0.00 3.07
1381 1417 1.822615 GTGGTGGCTTTTTGGCTGT 59.177 52.632 0.00 0.00 42.34 4.40
1410 1464 3.370231 GGGCCAAATTCCACGCGT 61.370 61.111 5.58 5.58 0.00 6.01
1768 1822 1.807165 CGCCTCCGACACTGTCATG 60.807 63.158 9.84 0.19 36.29 3.07
2714 2789 5.656859 AGTGAGACTATGTGTGGTGCTAATA 59.343 40.000 0.00 0.00 0.00 0.98
2739 2814 5.239744 AGTGCAATTGAACGTACCAAATACA 59.760 36.000 10.34 3.99 32.79 2.29
2777 2852 3.977134 ACTCCTCTACTGTCGTACTCA 57.023 47.619 0.00 0.00 0.00 3.41
2820 2895 1.523711 CCCACTTGCACGTGTCAGT 60.524 57.895 20.52 15.86 33.07 3.41
2906 2981 1.595109 CCACTTGCACGTCTCTGCA 60.595 57.895 0.00 0.00 45.59 4.41
3054 3142 3.931247 CGTGGGGGTCACCGTTCA 61.931 66.667 0.00 0.00 43.23 3.18
3138 3229 4.766891 GTGGAAGAGAATGGGATTTTGTGA 59.233 41.667 0.00 0.00 0.00 3.58
3196 3289 3.492482 GGTTTGTGTTCAGTGGAAATGGG 60.492 47.826 0.00 0.00 34.13 4.00
3330 3424 3.181493 GCTTCTCACCGAGGACGTTAATA 60.181 47.826 0.00 0.00 37.88 0.98
3341 3435 2.036571 TACTCGCGCTTCTCACCGA 61.037 57.895 5.56 0.00 0.00 4.69
3495 3589 1.890041 GTAGTGCACACCAACGCCA 60.890 57.895 21.04 0.00 0.00 5.69
3615 3711 3.026694 GCAGGGCAAATGAGTAGGATTT 58.973 45.455 0.00 0.00 0.00 2.17
3765 3865 9.754382 ATTGCATCAGGTTCATAAATACATTTC 57.246 29.630 0.00 0.00 0.00 2.17
4389 4529 2.778659 GCTGAATGTCGATGAACTTGC 58.221 47.619 0.00 0.00 0.00 4.01
4420 4560 4.070009 ACTCTTTTTCGGTGTATGGAACC 58.930 43.478 0.00 0.00 0.00 3.62
4501 4641 1.148310 CGGCGTGTTGATCTTGTTCT 58.852 50.000 0.00 0.00 0.00 3.01
4676 4816 3.804329 GGGCAATAGGGGCGGTCA 61.804 66.667 0.00 0.00 0.00 4.02
5015 5165 4.485024 AGTGTACTGAGTTGTACTGACG 57.515 45.455 0.00 0.00 42.22 4.35
5110 5262 9.091784 CGTGTAGACTAAGTTGTACTGATAGTA 57.908 37.037 0.00 0.00 25.75 1.82
5205 5484 1.615919 CCTAACCTTGGGCGGTCATTT 60.616 52.381 0.00 0.00 35.89 2.32
5236 5515 6.631016 TCGAGTTCAAGTATCTAGCATTGTT 58.369 36.000 0.00 0.00 0.00 2.83
5306 5585 1.943730 TTGACCTGTGGGCCCTTGTT 61.944 55.000 25.70 2.83 35.63 2.83
5309 5588 1.774217 TCTTGACCTGTGGGCCCTT 60.774 57.895 25.70 1.13 35.63 3.95
5359 5638 4.767928 AGTCGAACTCCTCTGAACACTTAT 59.232 41.667 0.00 0.00 0.00 1.73
5401 5680 1.070289 GGGCTCCGGACCTGTTTATAG 59.930 57.143 18.67 0.03 37.73 1.31
5480 5759 3.209812 AGATAGCTCGTCCGCGCA 61.210 61.111 8.75 0.00 38.14 6.09
6342 6633 8.280497 CACTTATGTTTTAGTACTGTGTGAACC 58.720 37.037 5.39 0.00 0.00 3.62
6434 6725 5.640732 AGTTGTTGCTCAAAAGTTGTACTG 58.359 37.500 0.00 0.00 37.81 2.74
6639 6932 3.327757 TGCCCTGATTAGTCTTGTCAAGT 59.672 43.478 12.30 0.00 0.00 3.16
6762 7061 1.466025 GGACGTGGGTGTAGTGGTCA 61.466 60.000 0.00 0.00 0.00 4.02
6854 7154 1.000274 GGCAATGGTGGTTCTGTGAAC 60.000 52.381 2.16 2.16 0.00 3.18
6933 7234 4.838152 GCCATCGCCTTGCTCCGA 62.838 66.667 0.00 0.00 37.91 4.55
6959 7260 1.562575 ATCGTGACGTTTGGCGGAAC 61.563 55.000 4.40 0.00 46.52 3.62
7100 7401 0.532862 CTTGTCTGGTTCGCTGGTGT 60.533 55.000 0.00 0.00 0.00 4.16
7905 8303 6.942532 TTTACAAGTGATAATCCATGAGGC 57.057 37.500 0.00 0.00 33.74 4.70
8090 8496 4.145052 GGTTGATTTCCAAACCAGACTCT 58.855 43.478 0.00 0.00 36.47 3.24
8196 8602 1.139058 GTAGAATGGGTGGATGACGCT 59.861 52.381 0.00 0.00 38.35 5.07
8339 8748 2.489329 CCAACCTGTCATGATGTTGTCC 59.511 50.000 22.99 3.49 37.08 4.02
9003 9570 3.714280 TGGTATAATCCTAGCACTTGCCA 59.286 43.478 0.00 0.00 43.38 4.92
9128 9695 3.920231 TGAGCCTAGTACGTCTTCCTA 57.080 47.619 0.00 0.00 0.00 2.94
9332 9900 8.821147 TTATCGAACTTTAGCAGTTGAACTTA 57.179 30.769 0.00 0.00 46.53 2.24


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

AutoCloner maintained by Alex Coulton.