Multiple sequence alignment - TraesCS2B01G399300

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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 TraesCS2B01G399300 chr2B 100.000 5907 0 0 1 5907 567073476 567067570 0.000000e+00 10909.0
1 TraesCS2B01G399300 chr2B 97.015 134 4 0 1 134 617122754 617122621 5.960000e-55 226.0
2 TraesCS2B01G399300 chr2B 95.556 135 5 1 1 134 765979482 765979616 1.290000e-51 215.0
3 TraesCS2B01G399300 chr2B 94.815 135 6 1 1 134 651137165 651137031 6.000000e-50 209.0
4 TraesCS2B01G399300 chr2B 93.333 135 8 1 1 134 47557173 47557039 1.300000e-46 198.0
5 TraesCS2B01G399300 chr2D 97.078 4415 100 7 1 4394 482805963 482801557 0.000000e+00 7411.0
6 TraesCS2B01G399300 chr2D 97.340 639 10 4 4455 5086 482801364 482800726 0.000000e+00 1079.0
7 TraesCS2B01G399300 chr2D 94.815 135 6 1 1 134 558944994 558944860 6.000000e-50 209.0
8 TraesCS2B01G399300 chr2D 89.103 156 5 3 5083 5236 482800588 482800443 3.640000e-42 183.0
9 TraesCS2B01G399300 chr2A 96.477 4371 123 13 1 4361 625293797 625289448 0.000000e+00 7190.0
10 TraesCS2B01G399300 chr2A 92.308 1482 50 13 4436 5907 625289084 625287657 0.000000e+00 2047.0
11 TraesCS2B01G399300 chr2A 84.752 282 36 4 5268 5543 743537387 743537107 5.830000e-70 276.0
12 TraesCS2B01G399300 chr7A 93.245 3612 178 23 486 4083 307379547 307383106 0.000000e+00 5258.0
13 TraesCS2B01G399300 chr7A 92.876 772 43 4 4436 5204 307563144 307563906 0.000000e+00 1110.0
14 TraesCS2B01G399300 chr7A 92.593 324 20 2 4076 4396 307562679 307563001 4.170000e-126 462.0
15 TraesCS2B01G399300 chr7A 78.930 299 49 13 995 1284 206215391 206215684 2.170000e-44 191.0
16 TraesCS2B01G399300 chr7B 93.390 2254 130 8 1601 3844 263813333 263811089 0.000000e+00 3319.0
17 TraesCS2B01G399300 chr7B 92.832 851 52 6 756 1603 263946932 263946088 0.000000e+00 1225.0
18 TraesCS2B01G399300 chr7B 93.497 815 41 7 4436 5247 263671666 263670861 0.000000e+00 1201.0
19 TraesCS2B01G399300 chr7B 88.416 587 35 10 3840 4394 263685797 263685212 0.000000e+00 676.0
20 TraesCS2B01G399300 chr7B 88.353 249 24 3 516 760 264003980 264003733 1.610000e-75 294.0
21 TraesCS2B01G399300 chr7B 82.143 196 30 4 234 426 704635703 704635896 4.740000e-36 163.0
22 TraesCS2B01G399300 chr7D 94.327 1939 94 12 2377 4311 274067576 274069502 0.000000e+00 2957.0
23 TraesCS2B01G399300 chr7D 92.318 1432 89 10 487 1907 273855591 273857012 0.000000e+00 2015.0
24 TraesCS2B01G399300 chr7D 94.304 474 23 4 4610 5080 274255859 274256331 0.000000e+00 723.0
25 TraesCS2B01G399300 chr7D 94.624 465 25 0 1906 2370 274065373 274065837 0.000000e+00 721.0
26 TraesCS2B01G399300 chr7D 93.301 209 9 3 5046 5251 274258791 274258997 2.670000e-78 303.0
27 TraesCS2B01G399300 chr7D 83.612 299 41 7 5482 5780 192444485 192444195 2.100000e-69 274.0
28 TraesCS2B01G399300 chr7D 90.052 191 7 6 4436 4625 274255664 274255843 2.750000e-58 237.0
29 TraesCS2B01G399300 chr7D 82.320 181 11 7 323 486 619049175 619048999 2.870000e-28 137.0
30 TraesCS2B01G399300 chr7D 87.097 93 1 2 4307 4396 274255513 274255597 1.750000e-15 95.3
31 TraesCS2B01G399300 chr6D 87.762 286 21 7 208 488 18006820 18006544 7.380000e-84 322.0
32 TraesCS2B01G399300 chr6D 83.529 255 32 4 240 486 199573598 199573850 4.600000e-56 230.0
33 TraesCS2B01G399300 chr6D 96.386 83 3 0 259 341 282064373 282064291 2.870000e-28 137.0
34 TraesCS2B01G399300 chrUn 85.971 278 30 5 5271 5543 31769834 31769561 7.490000e-74 289.0
35 TraesCS2B01G399300 chrUn 84.892 278 32 6 5271 5543 31788930 31788658 7.540000e-69 272.0
36 TraesCS2B01G399300 chrUn 82.677 254 36 5 236 484 111931885 111932135 9.970000e-53 219.0
37 TraesCS2B01G399300 chr6B 85.662 272 30 6 5276 5539 516542200 516541930 1.620000e-70 278.0
38 TraesCS2B01G399300 chr6B 80.658 243 24 12 265 487 34073512 34073751 3.660000e-37 167.0
39 TraesCS2B01G399300 chr6B 78.884 251 38 8 236 484 48298634 48298871 7.930000e-34 156.0
40 TraesCS2B01G399300 chr6B 79.565 230 28 10 259 484 364743392 364743606 4.770000e-31 147.0
41 TraesCS2B01G399300 chr5B 85.401 274 31 6 5276 5542 123215251 123215522 5.830000e-70 276.0
42 TraesCS2B01G399300 chr5B 83.942 274 35 6 5276 5542 123432782 123433053 2.730000e-63 254.0
43 TraesCS2B01G399300 chr1A 84.752 282 36 4 5268 5543 137693055 137692775 5.830000e-70 276.0
44 TraesCS2B01G399300 chr4A 78.311 438 62 25 995 1409 196773486 196773059 9.830000e-63 252.0
45 TraesCS2B01G399300 chr3B 84.766 256 34 2 5272 5522 682119457 682119202 9.830000e-63 252.0
46 TraesCS2B01G399300 chr1D 97.761 134 3 0 1 134 421492725 421492858 1.280000e-56 231.0
47 TraesCS2B01G399300 chr3D 97.037 135 3 1 1 134 577440422 577440556 5.960000e-55 226.0
48 TraesCS2B01G399300 chr6A 78.930 299 50 12 995 1284 36009528 36009822 2.170000e-44 191.0
49 TraesCS2B01G399300 chr5D 78.930 299 49 13 995 1284 84790676 84790383 2.170000e-44 191.0
50 TraesCS2B01G399300 chr4B 79.221 231 27 16 259 482 339145277 339145493 2.220000e-29 141.0
51 TraesCS2B01G399300 chr1B 90.769 65 6 0 420 484 524303387 524303323 2.930000e-13 87.9
52 TraesCS2B01G399300 chr4D 79.339 121 20 4 5598 5718 503111364 503111249 4.910000e-11 80.5


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 TraesCS2B01G399300 chr2B 567067570 567073476 5906 True 10909.000 10909 100.0000 1 5907 1 chr2B.!!$R2 5906
1 TraesCS2B01G399300 chr2D 482800443 482805963 5520 True 2891.000 7411 94.5070 1 5236 3 chr2D.!!$R2 5235
2 TraesCS2B01G399300 chr2A 625287657 625293797 6140 True 4618.500 7190 94.3925 1 5907 2 chr2A.!!$R2 5906
3 TraesCS2B01G399300 chr7A 307379547 307383106 3559 False 5258.000 5258 93.2450 486 4083 1 chr7A.!!$F2 3597
4 TraesCS2B01G399300 chr7A 307562679 307563906 1227 False 786.000 1110 92.7345 4076 5204 2 chr7A.!!$F3 1128
5 TraesCS2B01G399300 chr7B 263811089 263813333 2244 True 3319.000 3319 93.3900 1601 3844 1 chr7B.!!$R3 2243
6 TraesCS2B01G399300 chr7B 263946088 263946932 844 True 1225.000 1225 92.8320 756 1603 1 chr7B.!!$R4 847
7 TraesCS2B01G399300 chr7B 263670861 263671666 805 True 1201.000 1201 93.4970 4436 5247 1 chr7B.!!$R1 811
8 TraesCS2B01G399300 chr7B 263685212 263685797 585 True 676.000 676 88.4160 3840 4394 1 chr7B.!!$R2 554
9 TraesCS2B01G399300 chr7D 273855591 273857012 1421 False 2015.000 2015 92.3180 487 1907 1 chr7D.!!$F1 1420
10 TraesCS2B01G399300 chr7D 274065373 274069502 4129 False 1839.000 2957 94.4755 1906 4311 2 chr7D.!!$F2 2405
11 TraesCS2B01G399300 chr7D 274255513 274258997 3484 False 339.575 723 91.1885 4307 5251 4 chr7D.!!$F3 944

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
847 874 0.103572 TATCCACCCGCTACTTTCGC 59.896 55.000 0.00 0.0 0.00 4.70 F
1376 1414 0.531532 CCTTCTGCTGCTCGGTATGG 60.532 60.000 0.00 0.0 0.00 2.74 F
2327 2366 0.603975 AGAACAGGCTTTGGAGACGC 60.604 55.000 0.00 0.0 35.43 5.19 F
4247 6035 1.065701 GGTGTCTCTATCACGCGATGT 59.934 52.381 15.93 0.0 36.76 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2327 2366 0.529378 GGCTTCACAAAGGGAGCATG 59.471 55.000 0.00 0.00 32.79 4.06 R
2675 4447 0.742505 GCACATGGACATGGATGTGG 59.257 55.000 24.55 13.55 46.40 4.17 R
4302 6118 1.664649 CTCCAACGCGAACAGCTCA 60.665 57.895 15.93 0.00 45.59 4.26 R
5105 9893 0.026285 GACGCACAACACAGTGACAC 59.974 55.000 7.81 0.00 42.05 3.67 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
79 80 4.712051 TGTATTTGCCTCTGGATGCTAT 57.288 40.909 0.27 0.00 0.00 2.97
119 120 6.324770 AGAGGAAAAATTGATGGTTCTGTGTT 59.675 34.615 0.00 0.00 0.00 3.32
145 146 5.725110 TCTTTCATACTCGTACTCGTACC 57.275 43.478 1.92 0.00 38.33 3.34
160 161 4.830046 ACTCGTACCTGAGATAATGATGCT 59.170 41.667 4.95 0.00 39.35 3.79
205 206 9.694520 GATGCATTTATGATATTCGTATGTCAC 57.305 33.333 0.00 0.00 35.13 3.67
339 340 4.079212 ACAACCATATAGTCCAAGGGCATT 60.079 41.667 0.00 0.00 0.00 3.56
345 346 6.296662 CCATATAGTCCAAGGGCATTACAGAT 60.297 42.308 0.00 0.00 0.00 2.90
357 358 5.183904 GGGCATTACAGATTTTTCACTGACT 59.816 40.000 0.00 0.00 37.54 3.41
401 402 6.524101 AAACAGGCACTTTGAAAAGAACTA 57.476 33.333 9.71 0.00 39.31 2.24
455 472 8.741603 AGCTTATTTTTACGGGAGCTTATTTA 57.258 30.769 0.00 0.00 37.17 1.40
507 524 3.991999 GCAGGCAGCAGTCATTGA 58.008 55.556 0.00 0.00 44.79 2.57
514 531 0.671472 CAGCAGTCATTGAGGACGCA 60.671 55.000 12.35 0.00 42.62 5.24
637 663 4.033776 CTCCCTTCCCTTGGCGCA 62.034 66.667 10.83 0.00 0.00 6.09
740 766 0.198696 TTCCCCTTTCCCTCCCTCTT 59.801 55.000 0.00 0.00 0.00 2.85
800 827 2.082140 TGCTATCTTCGCCTCCCTTA 57.918 50.000 0.00 0.00 0.00 2.69
847 874 0.103572 TATCCACCCGCTACTTTCGC 59.896 55.000 0.00 0.00 0.00 4.70
931 962 4.884164 GTCTTATGAGGAGGGTTTGATTGG 59.116 45.833 0.00 0.00 0.00 3.16
987 1022 1.767759 ATAGCAGTGGGGCATTTCAC 58.232 50.000 0.00 0.00 35.83 3.18
1112 1150 4.083590 GCACCTCTACAAGCTCTTTGAAAG 60.084 45.833 0.00 0.00 39.21 2.62
1223 1261 3.542097 CGTCATGTACAAATGCTACGCTG 60.542 47.826 0.00 0.00 0.00 5.18
1376 1414 0.531532 CCTTCTGCTGCTCGGTATGG 60.532 60.000 0.00 0.00 0.00 2.74
1417 1455 3.588842 TGAAACCTCCCTCATCAACAGAT 59.411 43.478 0.00 0.00 0.00 2.90
1947 1986 2.107031 CAAGGGATATGCTGACATGGGA 59.893 50.000 0.00 0.00 37.04 4.37
2195 2234 6.026947 AGGATAAATGTCTACGCTCATACC 57.973 41.667 0.00 0.00 0.00 2.73
2327 2366 0.603975 AGAACAGGCTTTGGAGACGC 60.604 55.000 0.00 0.00 35.43 5.19
2440 4212 6.919721 TCAAAATTGGGTAGTTGCTTATCAC 58.080 36.000 0.00 0.00 0.00 3.06
2501 4273 2.380084 TGCTGACATAACGAAGGGAC 57.620 50.000 0.00 0.00 0.00 4.46
2687 4459 5.822519 TGCTTATTAGAACCACATCCATGTC 59.177 40.000 0.00 0.00 39.39 3.06
2825 4597 6.026947 TCTACTGTAAAGCTTGTCCTCTTC 57.973 41.667 0.00 0.00 0.00 2.87
2919 4692 1.885887 GAGTAAATGTGGCTGTGGCAA 59.114 47.619 0.00 0.00 40.46 4.52
3003 4776 6.699575 AATCATTTGTAGGTTATCACAGCC 57.300 37.500 0.00 0.00 0.00 4.85
3004 4777 5.172687 TCATTTGTAGGTTATCACAGCCA 57.827 39.130 0.00 0.00 0.00 4.75
3218 4998 2.904697 TGTAGCATGGAGATGAGCTG 57.095 50.000 0.00 0.00 37.94 4.24
3350 5131 7.093421 GGGAGGTACTAACAAGTTCTGAACTAT 60.093 40.741 22.30 14.15 41.55 2.12
3352 5133 9.786105 GAGGTACTAACAAGTTCTGAACTATAC 57.214 37.037 22.30 15.86 41.55 1.47
3707 5490 7.852971 ACTGATTTTTGGCAATTGATATTGG 57.147 32.000 10.34 0.00 41.21 3.16
3929 5717 3.719268 ACCTGCACAATATGAGGTTCA 57.281 42.857 0.00 0.00 36.17 3.18
3947 5735 4.438744 GGTTCACATGCATACTAGCCAAAC 60.439 45.833 0.00 0.00 0.00 2.93
3998 5786 1.448013 GCTTCAGTACACCCGCCTC 60.448 63.158 0.00 0.00 0.00 4.70
4083 5871 3.447229 TGCGTCACTTGATCTCATCCTTA 59.553 43.478 0.00 0.00 0.00 2.69
4247 6035 1.065701 GGTGTCTCTATCACGCGATGT 59.934 52.381 15.93 0.00 36.76 3.06
4361 6180 7.390996 AGGTGAATATGTATGTAGGAGTACGAG 59.609 40.741 0.00 0.00 30.95 4.18
4416 6319 6.000219 CCATCATCGATTCAATTAAGGGAGT 59.000 40.000 0.00 0.00 0.00 3.85
4417 6320 6.488006 CCATCATCGATTCAATTAAGGGAGTT 59.512 38.462 0.00 0.00 0.00 3.01
4419 6322 6.414732 TCATCGATTCAATTAAGGGAGTTGT 58.585 36.000 0.00 0.00 0.00 3.32
4420 6323 7.561251 TCATCGATTCAATTAAGGGAGTTGTA 58.439 34.615 0.00 0.00 0.00 2.41
4434 6535 3.067833 GAGTTGTAGTGAAGCAGGAACC 58.932 50.000 0.00 0.00 0.00 3.62
4546 6655 2.488153 GCGGCCTTATTTCATATGGGTC 59.512 50.000 0.00 0.00 32.30 4.46
4556 6665 1.134521 TCATATGGGTCGGCAACACTC 60.135 52.381 2.13 0.00 30.14 3.51
4838 6984 1.143183 GTGACTGGACGTGGTGTGT 59.857 57.895 0.00 0.00 0.00 3.72
4996 7142 8.432013 TGTTGCCTTATGATGATTGTAGATAGT 58.568 33.333 0.00 0.00 0.00 2.12
5105 9893 8.462143 AACTTAATTAGTATGTGTCGTCAGTG 57.538 34.615 0.00 0.00 35.54 3.66
5284 10073 7.548196 TTTTCTTTTGAACTAGATGACACGT 57.452 32.000 0.00 0.00 38.30 4.49
5285 10074 7.548196 TTTCTTTTGAACTAGATGACACGTT 57.452 32.000 0.00 0.00 38.30 3.99
5286 10075 6.525121 TCTTTTGAACTAGATGACACGTTG 57.475 37.500 0.00 0.00 0.00 4.10
5287 10076 4.725556 TTTGAACTAGATGACACGTTGC 57.274 40.909 0.00 0.00 0.00 4.17
5288 10077 2.324860 TGAACTAGATGACACGTTGCG 58.675 47.619 0.00 0.00 0.00 4.85
5289 10078 1.059264 GAACTAGATGACACGTTGCGC 59.941 52.381 0.00 0.00 0.00 6.09
5290 10079 0.736325 ACTAGATGACACGTTGCGCC 60.736 55.000 4.18 0.00 0.00 6.53
5291 10080 1.742900 CTAGATGACACGTTGCGCCG 61.743 60.000 4.18 4.34 0.00 6.46
5292 10081 2.202703 TAGATGACACGTTGCGCCGA 62.203 55.000 13.02 0.00 0.00 5.54
5328 10117 1.541588 GAGCGGACCAAGCTTTCAAAT 59.458 47.619 0.00 0.00 46.13 2.32
5354 10143 6.509418 TGCAAGTTGGAATATTTAGACACC 57.491 37.500 4.75 0.00 0.00 4.16
5357 10146 6.456988 GCAAGTTGGAATATTTAGACACCGAG 60.457 42.308 4.75 0.00 0.00 4.63
5365 10154 8.784043 GGAATATTTAGACACCGAGCATAAAAT 58.216 33.333 0.00 0.00 0.00 1.82
5492 10285 3.054728 TGGTAAGCAAAGCTACATAGGCA 60.055 43.478 0.00 0.00 38.25 4.75
5527 10320 7.611855 TCATATAGATAGCTTTGGTCATCGAGA 59.388 37.037 0.00 0.00 0.00 4.04
5533 10326 4.384056 AGCTTTGGTCATCGAGATTATGG 58.616 43.478 0.00 0.00 0.00 2.74
5540 10333 5.596772 TGGTCATCGAGATTATGGTAACTCA 59.403 40.000 0.00 0.00 37.61 3.41
5541 10334 6.153067 GGTCATCGAGATTATGGTAACTCAG 58.847 44.000 0.00 0.00 37.61 3.35
5542 10335 6.016192 GGTCATCGAGATTATGGTAACTCAGA 60.016 42.308 0.00 0.00 37.61 3.27
5571 10364 2.092103 AGGAAGGCCAAGTAACAACACA 60.092 45.455 5.01 0.00 36.29 3.72
5604 10397 6.428465 TGTGGATTATAAACGCTGAAAACAGA 59.572 34.615 0.00 0.00 0.00 3.41
5605 10398 7.041030 TGTGGATTATAAACGCTGAAAACAGAA 60.041 33.333 0.00 0.00 0.00 3.02
5662 10455 4.055360 TCGCCATGAACATATAGGTTTCG 58.945 43.478 3.99 4.39 0.00 3.46
5681 10474 6.353302 GTTTCGTGAGTACAAAAGAAGCTAC 58.647 40.000 0.00 0.00 0.00 3.58
5682 10475 5.449107 TCGTGAGTACAAAAGAAGCTACT 57.551 39.130 0.00 0.00 0.00 2.57
5683 10476 5.220381 TCGTGAGTACAAAAGAAGCTACTG 58.780 41.667 0.00 0.00 0.00 2.74
5684 10477 4.982916 CGTGAGTACAAAAGAAGCTACTGT 59.017 41.667 0.00 0.00 0.00 3.55
5685 10478 6.016860 TCGTGAGTACAAAAGAAGCTACTGTA 60.017 38.462 0.00 0.00 0.00 2.74
5696 10489 6.240549 AGAAGCTACTGTATTATGCTTGGT 57.759 37.500 14.39 2.44 42.95 3.67
5700 10493 9.706691 GAAGCTACTGTATTATGCTTGGTATTA 57.293 33.333 14.39 0.00 42.95 0.98
5707 10500 8.746052 TGTATTATGCTTGGTATTACAAAGCT 57.254 30.769 27.92 18.84 0.00 3.74
5731 10524 6.704512 ATTTATTCATCGGTGCACAAAAAC 57.295 33.333 20.43 0.00 0.00 2.43
5786 10579 3.007940 GGCTCCATACATATGTAGTGGCA 59.992 47.826 24.83 17.67 33.32 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.686438 ACTACTGTGCATGAAAACATGAATA 57.314 32.000 13.30 1.59 34.66 1.75
64 65 2.440627 ACAATGATAGCATCCAGAGGCA 59.559 45.455 7.09 0.00 41.13 4.75
119 120 7.383572 GGTACGAGTACGAGTATGAAAGATCTA 59.616 40.741 0.00 0.00 42.66 1.98
145 146 8.443937 CACATCATACAAGCATCATTATCTCAG 58.556 37.037 0.00 0.00 0.00 3.35
160 161 8.857694 ATGCATCATTATCTCACATCATACAA 57.142 30.769 0.00 0.00 0.00 2.41
232 233 5.167845 ACTTCAAAACACCACAACATGTTC 58.832 37.500 8.48 0.00 38.08 3.18
238 239 3.750639 TCGACTTCAAAACACCACAAC 57.249 42.857 0.00 0.00 0.00 3.32
339 340 9.990360 TGTTGTATAGTCAGTGAAAAATCTGTA 57.010 29.630 0.00 0.00 33.89 2.74
401 402 9.320295 AGATAAGCTCCAGATAATAAGCTAGTT 57.680 33.333 0.00 0.00 44.03 2.24
440 457 3.196039 TGCTGTGTAAATAAGCTCCCGTA 59.804 43.478 0.00 0.00 37.82 4.02
455 472 4.214971 CAGTTCTTTTGAGCTATGCTGTGT 59.785 41.667 0.00 0.00 39.88 3.72
514 531 2.519780 GGGAGACGAGGAGGCGAT 60.520 66.667 0.00 0.00 34.83 4.58
637 663 1.276138 TCGATTGTCACAGACCTGCAT 59.724 47.619 0.00 0.00 0.00 3.96
740 766 0.036105 CATACAGCCAGCAGTGTGGA 60.036 55.000 13.85 0.00 40.44 4.02
800 827 2.597455 CACTGGAAACCCCAATCTTGT 58.403 47.619 0.00 0.00 46.07 3.16
847 874 3.462021 CCTAGGAGAAAAGAGGAATGCG 58.538 50.000 1.05 0.00 0.00 4.73
931 962 7.646314 AGAAGATGTGTATTTGCATTATCAGC 58.354 34.615 0.00 0.00 0.00 4.26
987 1022 3.638627 GGGAAATCATGGCCTTCCTTTAG 59.361 47.826 17.62 0.00 38.94 1.85
1376 1414 6.204359 GTTTCATTATCACTGACATCCATGC 58.796 40.000 0.00 0.00 0.00 4.06
1417 1455 4.272489 GGATTTTCACTGACATCCATGGA 58.728 43.478 18.88 18.88 36.04 3.41
1639 1677 6.917533 AGTTTGATTTCCAGAGCATACAAAG 58.082 36.000 0.00 0.00 0.00 2.77
1774 1813 1.340088 ACAATTGCACAGCCATCCAA 58.660 45.000 5.05 0.00 0.00 3.53
1809 1848 9.288576 ACAGAAACTCATCACAAATTGAGAATA 57.711 29.630 0.00 0.00 41.53 1.75
1884 1923 4.037923 GCATGTTGTCCCCACCTATTTATG 59.962 45.833 0.00 0.00 0.00 1.90
2185 2224 1.400737 GTAGGGTCTGGTATGAGCGT 58.599 55.000 0.00 0.00 35.52 5.07
2195 2234 4.226168 AGAAAAATCAGGAGGTAGGGTCTG 59.774 45.833 0.00 0.00 0.00 3.51
2327 2366 0.529378 GGCTTCACAAAGGGAGCATG 59.471 55.000 0.00 0.00 32.79 4.06
2370 2409 0.746659 GGCAGCATTACCATTCCCAC 59.253 55.000 0.00 0.00 0.00 4.61
2440 4212 3.057245 GCTTAAAAAGTGCTTCCTGAGGG 60.057 47.826 0.00 0.00 0.00 4.30
2675 4447 0.742505 GCACATGGACATGGATGTGG 59.257 55.000 24.55 13.55 46.40 4.17
2687 4459 2.422479 CTCCAGTTGATCTTGCACATGG 59.578 50.000 0.00 0.00 0.00 3.66
2825 4597 6.369065 GGTGAGGGCTTCGTCTTATATATTTG 59.631 42.308 0.00 0.00 0.00 2.32
2919 4692 1.202639 TCACACGATTTCCACACTGCT 60.203 47.619 0.00 0.00 0.00 4.24
3003 4776 5.913137 TGGGAAGCCACAAAAGTATAATG 57.087 39.130 0.00 0.00 0.00 1.90
3004 4777 7.494922 AAATGGGAAGCCACAAAAGTATAAT 57.505 32.000 0.00 0.00 0.00 1.28
3218 4998 4.273480 CACCTGAATCACGGAATAATGGTC 59.727 45.833 5.89 0.00 0.00 4.02
3350 5131 6.877611 AGAATTTTTGGCTTTTCTCTCGTA 57.122 33.333 0.00 0.00 0.00 3.43
3352 5133 6.306596 GCTTAGAATTTTTGGCTTTTCTCTCG 59.693 38.462 0.00 0.00 31.29 4.04
3586 5369 7.350744 ACATGGCAAAGCATTATTATCAGAA 57.649 32.000 0.00 0.00 0.00 3.02
3929 5717 2.288666 CGGTTTGGCTAGTATGCATGT 58.711 47.619 10.16 0.00 34.04 3.21
3947 5735 9.624697 CAATTAATATTGTATGGGAATCAACGG 57.375 33.333 0.00 0.00 37.06 4.44
4083 5871 4.326504 TTCTCCCTTTTTCTCGTAACGT 57.673 40.909 0.00 0.00 0.00 3.99
4247 6035 2.609747 GCCCTACAGGTCATGATAGGA 58.390 52.381 18.04 0.16 35.97 2.94
4302 6118 1.664649 CTCCAACGCGAACAGCTCA 60.665 57.895 15.93 0.00 45.59 4.26
4361 6180 7.012515 TCCAGATCTAGTTCTCGTCATCTTAAC 59.987 40.741 0.00 0.00 0.00 2.01
4416 6319 3.788227 ATGGTTCCTGCTTCACTACAA 57.212 42.857 0.00 0.00 0.00 2.41
4417 6320 5.435686 AATATGGTTCCTGCTTCACTACA 57.564 39.130 0.00 0.00 0.00 2.74
4419 6322 9.778741 CTTAATAATATGGTTCCTGCTTCACTA 57.221 33.333 0.00 0.00 0.00 2.74
4420 6323 7.721399 CCTTAATAATATGGTTCCTGCTTCACT 59.279 37.037 0.00 0.00 0.00 3.41
4556 6665 6.876804 TCTACATGCACAATTCGATATTTCG 58.123 36.000 0.00 0.00 46.87 3.46
4658 6800 7.765360 TCAAAATCAATGCCATAATCCTGAAAC 59.235 33.333 0.00 0.00 0.00 2.78
5013 7159 2.159179 ACCCCAAAATATGACTGGCC 57.841 50.000 0.00 0.00 0.00 5.36
5105 9893 0.026285 GACGCACAACACAGTGACAC 59.974 55.000 7.81 0.00 42.05 3.67
5193 9982 8.579863 AGAAACTAAAATTGACATGGAAAGAGG 58.420 33.333 0.00 0.00 0.00 3.69
5311 10100 3.504863 CATGATTTGAAAGCTTGGTCCG 58.495 45.455 0.00 0.00 0.00 4.79
5328 10117 7.148086 GGTGTCTAAATATTCCAACTTGCATGA 60.148 37.037 6.60 0.00 0.00 3.07
5354 10143 7.325338 CCTTATGCTTCAATGATTTTATGCTCG 59.675 37.037 0.00 0.00 0.00 5.03
5357 10146 7.436118 TCCCTTATGCTTCAATGATTTTATGC 58.564 34.615 0.00 0.00 0.00 3.14
5429 10218 4.866508 TTAGCCTATGAACCTACCATCG 57.133 45.455 0.00 0.00 0.00 3.84
5492 10285 8.205512 CCAAAGCTATCTATATGATGCATCTCT 58.794 37.037 26.32 16.19 36.65 3.10
5527 10320 9.661954 TCCTTTATCTCTCTGAGTTACCATAAT 57.338 33.333 4.32 0.00 0.00 1.28
5533 10326 6.277605 GCCTTCCTTTATCTCTCTGAGTTAC 58.722 44.000 4.32 0.00 0.00 2.50
5540 10333 4.107820 ACTTGGCCTTCCTTTATCTCTCT 58.892 43.478 3.32 0.00 0.00 3.10
5541 10334 4.495690 ACTTGGCCTTCCTTTATCTCTC 57.504 45.455 3.32 0.00 0.00 3.20
5542 10335 5.250774 TGTTACTTGGCCTTCCTTTATCTCT 59.749 40.000 3.32 0.00 0.00 3.10
5571 10364 5.590259 AGCGTTTATAATCCACATTGCTTCT 59.410 36.000 0.00 0.00 0.00 2.85
5604 10397 5.452636 ATGCTTACATTTTGAACCAACGGTT 60.453 36.000 0.00 0.00 40.44 4.44
5605 10398 3.381908 TGCTTACATTTTGAACCAACGGT 59.618 39.130 0.00 0.00 37.65 4.83
5650 10443 8.697846 TCTTTTGTACTCACGAAACCTATATG 57.302 34.615 0.00 0.00 33.85 1.78
5658 10451 6.200286 CAGTAGCTTCTTTTGTACTCACGAAA 59.800 38.462 0.00 0.00 35.98 3.46
5662 10455 8.535690 AATACAGTAGCTTCTTTTGTACTCAC 57.464 34.615 0.00 0.00 0.00 3.51
5681 10474 8.840321 AGCTTTGTAATACCAAGCATAATACAG 58.160 33.333 24.75 0.00 0.00 2.74
5682 10475 8.746052 AGCTTTGTAATACCAAGCATAATACA 57.254 30.769 24.75 0.00 0.00 2.29
5700 10493 5.356751 TGCACCGATGAATAAATAGCTTTGT 59.643 36.000 0.00 0.00 0.00 2.83
5704 10497 4.450976 TGTGCACCGATGAATAAATAGCT 58.549 39.130 15.69 0.00 0.00 3.32
5705 10498 4.811555 TGTGCACCGATGAATAAATAGC 57.188 40.909 15.69 0.00 0.00 2.97
5707 10500 6.524933 CGTTTTTGTGCACCGATGAATAAATA 59.475 34.615 15.69 0.00 25.58 1.40
5709 10502 4.677378 CGTTTTTGTGCACCGATGAATAAA 59.323 37.500 15.69 2.32 0.00 1.40
5721 10514 1.332375 GTACCTCTGCGTTTTTGTGCA 59.668 47.619 0.00 0.00 39.13 4.57
5731 10524 0.741221 GGCCTTCAAGTACCTCTGCG 60.741 60.000 0.00 0.00 0.00 5.18
5795 10590 5.990996 CACATTATGTTGTTCCTTGCCTTTT 59.009 36.000 0.00 0.00 0.00 2.27
5796 10591 5.511202 CCACATTATGTTGTTCCTTGCCTTT 60.511 40.000 0.00 0.00 0.00 3.11
5855 10650 7.870826 TGGAGTAACAAACAAACAGATGTATG 58.129 34.615 0.00 0.00 32.02 2.39
5864 10659 4.109766 GTGGCTTGGAGTAACAAACAAAC 58.890 43.478 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.