Multiple sequence alignment - TraesCS6D01G103100

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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 TraesCS6D01G103100 chr6D 100.000 4585 0 0 1 4585 66629835 66625251 0.000000e+00 8468.0
1 TraesCS6D01G103100 chr6D 98.912 4596 33 5 1 4585 66264847 66260258 0.000000e+00 8194.0
2 TraesCS6D01G103100 chr6D 91.585 713 39 9 1313 2017 455534435 455535134 0.000000e+00 965.0
3 TraesCS6D01G103100 chr6D 89.076 238 16 3 1 238 66129002 66128775 2.090000e-73 287.0
4 TraesCS6D01G103100 chr6D 99.020 102 1 0 317 418 66264418 66264317 2.820000e-42 183.0
5 TraesCS6D01G103100 chr6D 98.990 99 1 0 320 418 66629414 66629316 1.310000e-40 178.0
6 TraesCS6D01G103100 chr6D 89.744 78 5 3 582 658 425063686 425063611 3.780000e-16 97.1
7 TraesCS6D01G103100 chr6D 100.000 32 0 0 99 130 66128942 66128911 4.950000e-05 60.2
8 TraesCS6D01G103100 chr1D 98.950 1904 18 1 2682 4585 470455536 470457437 0.000000e+00 3404.0
9 TraesCS6D01G103100 chr1D 97.483 1788 33 3 419 2198 470453755 470455538 0.000000e+00 3042.0
10 TraesCS6D01G103100 chr1D 93.612 454 24 3 1112 1563 189880286 189879836 0.000000e+00 673.0
11 TraesCS6D01G103100 chr1D 92.289 402 30 1 1450 1850 4551032 4550631 1.850000e-158 569.0
12 TraesCS6D01G103100 chr1D 89.726 146 14 1 966 1111 189881427 189881283 7.830000e-43 185.0
13 TraesCS6D01G103100 chr1D 93.220 118 8 0 301 418 470453739 470453856 1.700000e-39 174.0
14 TraesCS6D01G103100 chr1D 92.157 102 4 1 876 977 189881581 189881484 1.720000e-29 141.0
15 TraesCS6D01G103100 chr4A 94.420 2079 88 13 2518 4585 687394460 687396521 0.000000e+00 3171.0
16 TraesCS6D01G103100 chr4A 92.490 506 36 2 2047 2552 687393960 687394463 0.000000e+00 723.0
17 TraesCS6D01G103100 chr4A 80.359 779 78 27 2604 3349 579863132 579862396 5.260000e-144 521.0
18 TraesCS6D01G103100 chr7A 94.778 1781 54 17 419 2198 63315841 63314099 0.000000e+00 2737.0
19 TraesCS6D01G103100 chr7A 98.029 1573 25 3 2682 4252 63314101 63312533 0.000000e+00 2728.0
20 TraesCS6D01G103100 chr5B 92.919 1511 84 12 3084 4585 425669238 425670734 0.000000e+00 2176.0
21 TraesCS6D01G103100 chr5B 95.917 1347 41 8 2124 3469 649866000 649867333 0.000000e+00 2170.0
22 TraesCS6D01G103100 chr5B 95.990 1222 43 5 3366 4585 649867294 649868511 0.000000e+00 1980.0
23 TraesCS6D01G103100 chr5B 91.074 1210 83 11 3391 4585 626287226 626288425 0.000000e+00 1613.0
24 TraesCS6D01G103100 chr5B 94.200 569 25 5 718 1285 391868538 391869099 0.000000e+00 861.0
25 TraesCS6D01G103100 chr5B 89.336 422 28 9 2047 2464 399275242 399275650 8.800000e-142 514.0
26 TraesCS6D01G103100 chr5B 85.614 285 36 3 2184 2464 399227044 399227327 1.250000e-75 294.0
27 TraesCS6D01G103100 chr2B 91.218 1207 80 12 3394 4585 776826382 776825187 0.000000e+00 1618.0
28 TraesCS6D01G103100 chr2B 87.952 166 14 2 419 579 249190859 249191023 1.680000e-44 191.0
29 TraesCS6D01G103100 chr2B 91.892 111 9 0 302 412 249190844 249190954 6.140000e-34 156.0
30 TraesCS6D01G103100 chr3B 90.721 1207 86 12 3394 4585 798182490 798181295 0.000000e+00 1585.0
31 TraesCS6D01G103100 chr3B 94.129 1005 38 4 660 1649 568344002 568345000 0.000000e+00 1509.0
32 TraesCS6D01G103100 chr3B 90.303 165 11 1 419 578 591494059 591494223 1.290000e-50 211.0
33 TraesCS6D01G103100 chr3B 89.157 166 12 2 419 579 10678725 10678889 7.780000e-48 202.0
34 TraesCS6D01G103100 chr3B 93.966 116 7 0 303 418 591494045 591494160 4.710000e-40 176.0
35 TraesCS6D01G103100 chr3B 91.379 116 10 0 303 418 813800284 813800169 4.750000e-35 159.0
36 TraesCS6D01G103100 chr4D 91.819 709 38 9 1316 2017 95124513 95123818 0.000000e+00 970.0
37 TraesCS6D01G103100 chr4D 82.505 463 62 11 2886 3337 22022750 22023204 5.560000e-104 388.0
38 TraesCS6D01G103100 chr4D 81.585 429 46 10 2464 2860 22022331 22022758 1.590000e-84 324.0
39 TraesCS6D01G103100 chr4D 94.872 39 2 0 1 39 261081199 261081237 1.380000e-05 62.1
40 TraesCS6D01G103100 chr3D 92.718 563 28 8 1456 2017 533430974 533430424 0.000000e+00 800.0
41 TraesCS6D01G103100 chr3D 89.855 69 5 2 584 650 327745406 327745474 2.270000e-13 87.9
42 TraesCS6D01G103100 chr2D 90.569 615 33 13 1408 2017 520581213 520580619 0.000000e+00 791.0
43 TraesCS6D01G103100 chr2D 95.070 142 7 0 419 560 542307006 542306865 1.660000e-54 224.0
44 TraesCS6D01G103100 chr2D 89.759 166 12 1 419 579 38529895 38529730 1.670000e-49 207.0
45 TraesCS6D01G103100 chr2D 88.304 171 14 4 1357 1524 2279360 2279193 2.800000e-47 200.0
46 TraesCS6D01G103100 chr2D 95.726 117 5 0 302 418 542307021 542306905 6.060000e-44 189.0
47 TraesCS6D01G103100 chr2D 94.017 117 7 0 302 418 38529910 38529794 1.310000e-40 178.0
48 TraesCS6D01G103100 chr2D 81.553 206 22 8 582 775 573799331 573799130 6.140000e-34 156.0
49 TraesCS6D01G103100 chr2D 83.851 161 14 4 582 732 92837959 92838117 4.780000e-30 143.0
50 TraesCS6D01G103100 chr2D 96.970 33 1 0 4 36 532480702 532480734 6.410000e-04 56.5
51 TraesCS6D01G103100 chr4B 81.808 929 115 24 2464 3349 34027674 34028591 0.000000e+00 730.0
52 TraesCS6D01G103100 chr4B 89.157 166 13 1 419 579 180199628 180199793 7.780000e-48 202.0
53 TraesCS6D01G103100 chr5D 92.891 422 25 3 2047 2464 340099639 340100059 3.920000e-170 608.0
54 TraesCS6D01G103100 chr5D 82.569 436 57 11 2047 2464 340066851 340067285 2.610000e-97 366.0
55 TraesCS6D01G103100 chr7B 93.985 399 19 5 727 1122 44937724 44937328 2.360000e-167 599.0
56 TraesCS6D01G103100 chr1B 87.400 500 53 8 1357 1850 40201803 40202298 2.390000e-157 566.0
57 TraesCS6D01G103100 chr1B 76.634 719 89 30 2521 3206 190284716 190285388 1.590000e-84 324.0
58 TraesCS6D01G103100 chr1B 94.444 36 2 0 4 39 454925047 454925012 6.410000e-04 56.5
59 TraesCS6D01G103100 chr5A 92.424 396 27 3 1450 1843 605316196 605315802 3.100000e-156 562.0
60 TraesCS6D01G103100 chr5A 89.665 358 32 3 2111 2464 441194750 441195106 7.000000e-123 451.0
61 TraesCS6D01G103100 chr5A 87.368 285 31 3 2184 2464 441183162 441183445 5.720000e-84 322.0
62 TraesCS6D01G103100 chr6A 90.361 166 11 1 419 579 584423299 584423464 3.590000e-51 213.0
63 TraesCS6D01G103100 chr6B 90.411 73 7 0 1857 1929 56225851 56225779 3.780000e-16 97.1
64 TraesCS6D01G103100 chr3A 86.420 81 10 1 584 664 441868972 441869051 2.270000e-13 87.9
65 TraesCS6D01G103100 chr3A 92.308 39 3 0 1 39 184626382 184626344 6.410000e-04 56.5


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 TraesCS6D01G103100 chr6D 66625251 66629835 4584 True 4323.000000 8468 99.495000 1 4585 2 chr6D.!!$R4 4584
1 TraesCS6D01G103100 chr6D 66260258 66264847 4589 True 4188.500000 8194 98.966000 1 4585 2 chr6D.!!$R3 4584
2 TraesCS6D01G103100 chr6D 455534435 455535134 699 False 965.000000 965 91.585000 1313 2017 1 chr6D.!!$F1 704
3 TraesCS6D01G103100 chr1D 470453739 470457437 3698 False 2206.666667 3404 96.551000 301 4585 3 chr1D.!!$F1 4284
4 TraesCS6D01G103100 chr1D 189879836 189881581 1745 True 333.000000 673 91.831667 876 1563 3 chr1D.!!$R2 687
5 TraesCS6D01G103100 chr4A 687393960 687396521 2561 False 1947.000000 3171 93.455000 2047 4585 2 chr4A.!!$F1 2538
6 TraesCS6D01G103100 chr4A 579862396 579863132 736 True 521.000000 521 80.359000 2604 3349 1 chr4A.!!$R1 745
7 TraesCS6D01G103100 chr7A 63312533 63315841 3308 True 2732.500000 2737 96.403500 419 4252 2 chr7A.!!$R1 3833
8 TraesCS6D01G103100 chr5B 425669238 425670734 1496 False 2176.000000 2176 92.919000 3084 4585 1 chr5B.!!$F4 1501
9 TraesCS6D01G103100 chr5B 649866000 649868511 2511 False 2075.000000 2170 95.953500 2124 4585 2 chr5B.!!$F6 2461
10 TraesCS6D01G103100 chr5B 626287226 626288425 1199 False 1613.000000 1613 91.074000 3391 4585 1 chr5B.!!$F5 1194
11 TraesCS6D01G103100 chr5B 391868538 391869099 561 False 861.000000 861 94.200000 718 1285 1 chr5B.!!$F1 567
12 TraesCS6D01G103100 chr2B 776825187 776826382 1195 True 1618.000000 1618 91.218000 3394 4585 1 chr2B.!!$R1 1191
13 TraesCS6D01G103100 chr3B 798181295 798182490 1195 True 1585.000000 1585 90.721000 3394 4585 1 chr3B.!!$R1 1191
14 TraesCS6D01G103100 chr3B 568344002 568345000 998 False 1509.000000 1509 94.129000 660 1649 1 chr3B.!!$F2 989
15 TraesCS6D01G103100 chr4D 95123818 95124513 695 True 970.000000 970 91.819000 1316 2017 1 chr4D.!!$R1 701
16 TraesCS6D01G103100 chr4D 22022331 22023204 873 False 356.000000 388 82.045000 2464 3337 2 chr4D.!!$F2 873
17 TraesCS6D01G103100 chr3D 533430424 533430974 550 True 800.000000 800 92.718000 1456 2017 1 chr3D.!!$R1 561
18 TraesCS6D01G103100 chr2D 520580619 520581213 594 True 791.000000 791 90.569000 1408 2017 1 chr2D.!!$R2 609
19 TraesCS6D01G103100 chr4B 34027674 34028591 917 False 730.000000 730 81.808000 2464 3349 1 chr4B.!!$F1 885
20 TraesCS6D01G103100 chr1B 190284716 190285388 672 False 324.000000 324 76.634000 2521 3206 1 chr1B.!!$F2 685

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
672 786 0.468214 TCAGCTCCCGTAGATCCCTG 60.468 60.0 0.00 0.0 0.00 4.45 F
1909 3129 0.975040 TTTGGTGCTTTGGTGTGCCT 60.975 50.0 0.00 0.0 35.27 4.75 F
2219 3445 1.668101 GAGGACAGCTCGGTGGTAGG 61.668 65.0 0.93 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2219 3445 4.487412 CACCCTCGTACGTCGCCC 62.487 72.222 16.05 0.0 39.67 6.13 R
2836 4138 2.052690 TAGCGGTGCTCTGGACTCC 61.053 63.158 0.00 0.0 40.44 3.85 R
3619 5014 8.608185 AGCCATTTATTTCAGGATAAAAAGGA 57.392 30.769 12.47 0.0 35.70 3.36 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
205 207 3.040147 AGAGAGACTCGGATCGATCTC 57.960 52.381 23.96 13.62 38.80 2.75
282 294 1.760480 GCCCCGGGGTTGCATAATT 60.760 57.895 39.80 0.00 37.65 1.40
318 330 3.356290 GGTGCATCCCATTGTTAGAGTT 58.644 45.455 0.00 0.00 0.00 3.01
319 331 3.763897 GGTGCATCCCATTGTTAGAGTTT 59.236 43.478 0.00 0.00 0.00 2.66
320 332 4.380867 GGTGCATCCCATTGTTAGAGTTTG 60.381 45.833 0.00 0.00 0.00 2.93
321 333 4.458989 GTGCATCCCATTGTTAGAGTTTGA 59.541 41.667 0.00 0.00 0.00 2.69
322 334 5.048083 GTGCATCCCATTGTTAGAGTTTGAA 60.048 40.000 0.00 0.00 0.00 2.69
323 335 5.048083 TGCATCCCATTGTTAGAGTTTGAAC 60.048 40.000 0.00 0.00 0.00 3.18
324 336 5.622233 GCATCCCATTGTTAGAGTTTGAACC 60.622 44.000 0.00 0.00 0.00 3.62
325 337 5.055265 TCCCATTGTTAGAGTTTGAACCA 57.945 39.130 0.00 0.00 0.00 3.67
326 338 5.450453 TCCCATTGTTAGAGTTTGAACCAA 58.550 37.500 0.00 0.00 0.00 3.67
327 339 5.894393 TCCCATTGTTAGAGTTTGAACCAAA 59.106 36.000 0.00 0.00 0.00 3.28
328 340 6.381420 TCCCATTGTTAGAGTTTGAACCAAAA 59.619 34.615 0.00 0.00 35.03 2.44
329 341 7.070571 TCCCATTGTTAGAGTTTGAACCAAAAT 59.929 33.333 0.00 0.00 35.03 1.82
330 342 7.171337 CCCATTGTTAGAGTTTGAACCAAAATG 59.829 37.037 0.00 0.00 35.03 2.32
331 343 7.925483 CCATTGTTAGAGTTTGAACCAAAATGA 59.075 33.333 0.00 0.00 35.03 2.57
332 344 9.311916 CATTGTTAGAGTTTGAACCAAAATGAA 57.688 29.630 0.00 0.00 35.03 2.57
333 345 8.925161 TTGTTAGAGTTTGAACCAAAATGAAG 57.075 30.769 0.00 0.00 35.03 3.02
334 346 6.978080 TGTTAGAGTTTGAACCAAAATGAAGC 59.022 34.615 0.00 0.00 35.03 3.86
335 347 5.596836 AGAGTTTGAACCAAAATGAAGCA 57.403 34.783 0.00 0.00 35.03 3.91
336 348 5.976458 AGAGTTTGAACCAAAATGAAGCAA 58.024 33.333 0.00 0.00 35.03 3.91
337 349 6.585416 AGAGTTTGAACCAAAATGAAGCAAT 58.415 32.000 0.00 0.00 35.03 3.56
338 350 6.703165 AGAGTTTGAACCAAAATGAAGCAATC 59.297 34.615 0.00 0.00 35.03 2.67
339 351 6.585416 AGTTTGAACCAAAATGAAGCAATCT 58.415 32.000 0.00 0.00 35.03 2.40
340 352 6.703165 AGTTTGAACCAAAATGAAGCAATCTC 59.297 34.615 0.00 0.00 35.03 2.75
341 353 5.787953 TGAACCAAAATGAAGCAATCTCA 57.212 34.783 0.00 0.00 0.00 3.27
342 354 5.775686 TGAACCAAAATGAAGCAATCTCAG 58.224 37.500 0.00 0.00 0.00 3.35
343 355 4.796038 ACCAAAATGAAGCAATCTCAGG 57.204 40.909 0.00 0.00 0.00 3.86
344 356 3.056322 ACCAAAATGAAGCAATCTCAGGC 60.056 43.478 0.00 0.00 0.00 4.85
345 357 3.518590 CAAAATGAAGCAATCTCAGGCC 58.481 45.455 0.00 0.00 0.00 5.19
346 358 2.519771 AATGAAGCAATCTCAGGCCA 57.480 45.000 5.01 0.00 0.00 5.36
347 359 2.750141 ATGAAGCAATCTCAGGCCAT 57.250 45.000 5.01 0.00 0.00 4.40
348 360 1.758936 TGAAGCAATCTCAGGCCATG 58.241 50.000 5.01 0.00 0.00 3.66
349 361 1.005097 TGAAGCAATCTCAGGCCATGT 59.995 47.619 5.01 0.00 0.00 3.21
350 362 1.404391 GAAGCAATCTCAGGCCATGTG 59.596 52.381 5.01 1.55 0.00 3.21
351 363 1.035932 AGCAATCTCAGGCCATGTGC 61.036 55.000 5.01 5.60 40.16 4.57
369 381 4.933064 CCTCGCAGCCGTCCGATC 62.933 72.222 0.00 0.00 35.54 3.69
373 385 4.194720 GCAGCCGTCCGATCGTCT 62.195 66.667 15.09 0.06 0.00 4.18
374 386 2.490217 CAGCCGTCCGATCGTCTT 59.510 61.111 15.09 0.00 0.00 3.01
375 387 1.586564 CAGCCGTCCGATCGTCTTC 60.587 63.158 15.09 0.49 0.00 2.87
376 388 2.278661 GCCGTCCGATCGTCTTCC 60.279 66.667 15.09 0.00 0.00 3.46
377 389 2.412112 CCGTCCGATCGTCTTCCC 59.588 66.667 15.09 0.00 0.00 3.97
378 390 2.024305 CGTCCGATCGTCTTCCCG 59.976 66.667 15.09 2.92 0.00 5.14
379 391 2.412112 GTCCGATCGTCTTCCCGG 59.588 66.667 15.09 0.00 43.02 5.73
380 392 2.831742 TCCGATCGTCTTCCCGGG 60.832 66.667 16.85 16.85 42.03 5.73
381 393 4.587189 CCGATCGTCTTCCCGGGC 62.587 72.222 18.49 0.00 38.42 6.13
382 394 4.925576 CGATCGTCTTCCCGGGCG 62.926 72.222 18.49 14.45 0.00 6.13
400 412 4.570663 CGTCCTGGCCGTCGGATC 62.571 72.222 17.49 6.79 0.00 3.36
401 413 3.148279 GTCCTGGCCGTCGGATCT 61.148 66.667 17.49 0.00 0.00 2.75
402 414 2.833582 TCCTGGCCGTCGGATCTC 60.834 66.667 17.49 1.33 0.00 2.75
403 415 3.917760 CCTGGCCGTCGGATCTCC 61.918 72.222 17.49 7.12 0.00 3.71
413 425 4.356979 GGATCTCCGAGTGGACCA 57.643 61.111 0.00 0.00 40.17 4.02
414 426 2.591915 GGATCTCCGAGTGGACCAA 58.408 57.895 0.00 0.00 40.17 3.67
415 427 1.123928 GGATCTCCGAGTGGACCAAT 58.876 55.000 0.00 0.00 40.17 3.16
416 428 1.486726 GGATCTCCGAGTGGACCAATT 59.513 52.381 0.00 0.00 40.17 2.32
417 429 2.483889 GGATCTCCGAGTGGACCAATTC 60.484 54.545 0.00 0.00 40.17 2.17
538 652 1.609072 TCTAACCATCCGATCGAGCTG 59.391 52.381 18.66 10.37 0.00 4.24
672 786 0.468214 TCAGCTCCCGTAGATCCCTG 60.468 60.000 0.00 0.00 0.00 4.45
674 788 1.457831 GCTCCCGTAGATCCCTGGT 60.458 63.158 0.00 0.00 0.00 4.00
1909 3129 0.975040 TTTGGTGCTTTGGTGTGCCT 60.975 50.000 0.00 0.00 35.27 4.75
2219 3445 1.668101 GAGGACAGCTCGGTGGTAGG 61.668 65.000 0.93 0.00 0.00 3.18
2836 4138 6.256757 GTCTTCAATCTTGGTAGAAATCTCCG 59.743 42.308 0.00 0.00 33.20 4.63
3410 4739 8.791675 TCTTCAGTTTATTTGTACATTGATGCA 58.208 29.630 0.00 0.00 0.00 3.96
3619 5014 4.494484 TGATGATTTCGTCGATTCACACT 58.506 39.130 9.74 0.00 34.69 3.55
3620 5015 4.562789 TGATGATTTCGTCGATTCACACTC 59.437 41.667 9.74 5.96 34.69 3.51
4383 5794 4.335400 TGGGTTCAAATTTTTCTCCTGC 57.665 40.909 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.203326 GGCCTAGCCCCTATTAGGTCT 60.203 57.143 8.91 7.74 44.06 3.85
87 88 2.025887 CCCCTATTAGGTGCATCCATCC 60.026 54.545 8.91 0.00 39.02 3.51
318 330 6.159299 TGAGATTGCTTCATTTTGGTTCAA 57.841 33.333 0.00 0.00 0.00 2.69
319 331 5.279106 CCTGAGATTGCTTCATTTTGGTTCA 60.279 40.000 0.00 0.00 0.00 3.18
320 332 5.166398 CCTGAGATTGCTTCATTTTGGTTC 58.834 41.667 0.00 0.00 0.00 3.62
321 333 4.562143 GCCTGAGATTGCTTCATTTTGGTT 60.562 41.667 0.00 0.00 0.00 3.67
322 334 3.056322 GCCTGAGATTGCTTCATTTTGGT 60.056 43.478 0.00 0.00 0.00 3.67
323 335 3.518590 GCCTGAGATTGCTTCATTTTGG 58.481 45.455 0.00 0.00 0.00 3.28
324 336 3.056393 TGGCCTGAGATTGCTTCATTTTG 60.056 43.478 3.32 0.00 0.00 2.44
325 337 3.167485 TGGCCTGAGATTGCTTCATTTT 58.833 40.909 3.32 0.00 0.00 1.82
326 338 2.811410 TGGCCTGAGATTGCTTCATTT 58.189 42.857 3.32 0.00 0.00 2.32
327 339 2.519771 TGGCCTGAGATTGCTTCATT 57.480 45.000 3.32 0.00 0.00 2.57
328 340 2.307768 CATGGCCTGAGATTGCTTCAT 58.692 47.619 3.32 0.00 0.00 2.57
329 341 1.005097 ACATGGCCTGAGATTGCTTCA 59.995 47.619 3.32 0.00 0.00 3.02
330 342 1.404391 CACATGGCCTGAGATTGCTTC 59.596 52.381 3.32 0.00 0.00 3.86
331 343 1.471119 CACATGGCCTGAGATTGCTT 58.529 50.000 3.32 0.00 0.00 3.91
332 344 1.035932 GCACATGGCCTGAGATTGCT 61.036 55.000 3.32 0.00 36.11 3.91
333 345 1.436336 GCACATGGCCTGAGATTGC 59.564 57.895 3.32 2.24 36.11 3.56
352 364 4.933064 GATCGGACGGCTGCGAGG 62.933 72.222 0.00 0.00 44.15 4.63
359 371 2.278661 GGAAGACGATCGGACGGC 60.279 66.667 20.98 9.89 42.10 5.68
360 372 2.412112 GGGAAGACGATCGGACGG 59.588 66.667 20.98 0.00 37.61 4.79
361 373 2.024305 CGGGAAGACGATCGGACG 59.976 66.667 20.98 10.11 39.31 4.79
362 374 2.412112 CCGGGAAGACGATCGGAC 59.588 66.667 20.98 12.93 44.69 4.79
363 375 2.831742 CCCGGGAAGACGATCGGA 60.832 66.667 18.48 0.00 44.69 4.55
364 376 4.587189 GCCCGGGAAGACGATCGG 62.587 72.222 29.31 0.00 41.90 4.18
365 377 4.925576 CGCCCGGGAAGACGATCG 62.926 72.222 29.31 14.88 35.47 3.69
383 395 4.570663 GATCCGACGGCCAGGACG 62.571 72.222 15.24 15.24 39.66 4.79
384 396 3.140225 GAGATCCGACGGCCAGGAC 62.140 68.421 9.66 8.10 39.66 3.85
385 397 2.833582 GAGATCCGACGGCCAGGA 60.834 66.667 9.66 13.18 41.30 3.86
386 398 3.917760 GGAGATCCGACGGCCAGG 61.918 72.222 9.66 2.49 0.00 4.45
396 408 1.123928 ATTGGTCCACTCGGAGATCC 58.876 55.000 12.86 8.47 43.99 3.36
397 409 2.799917 CGAATTGGTCCACTCGGAGATC 60.800 54.545 12.86 0.00 43.99 2.75
398 410 1.137086 CGAATTGGTCCACTCGGAGAT 59.863 52.381 12.86 0.00 43.99 2.75
399 411 0.530744 CGAATTGGTCCACTCGGAGA 59.469 55.000 12.86 0.00 43.99 3.71
400 412 0.246635 ACGAATTGGTCCACTCGGAG 59.753 55.000 21.09 2.83 43.99 4.63
401 413 0.245539 GACGAATTGGTCCACTCGGA 59.754 55.000 21.09 0.00 39.79 4.55
402 414 0.246635 AGACGAATTGGTCCACTCGG 59.753 55.000 21.09 8.24 37.66 4.63
403 415 1.067846 TCAGACGAATTGGTCCACTCG 60.068 52.381 16.02 17.29 37.66 4.18
404 416 2.737252 GTTCAGACGAATTGGTCCACTC 59.263 50.000 16.02 3.08 37.66 3.51
405 417 2.550208 GGTTCAGACGAATTGGTCCACT 60.550 50.000 16.02 0.00 37.66 4.00
406 418 1.804748 GGTTCAGACGAATTGGTCCAC 59.195 52.381 16.02 10.72 37.66 4.02
407 419 1.418264 TGGTTCAGACGAATTGGTCCA 59.582 47.619 16.02 5.54 37.66 4.02
408 420 2.178912 TGGTTCAGACGAATTGGTCC 57.821 50.000 16.02 3.00 37.66 4.46
409 421 4.561735 TTTTGGTTCAGACGAATTGGTC 57.438 40.909 12.27 12.27 37.19 4.02
410 422 4.582656 TCATTTTGGTTCAGACGAATTGGT 59.417 37.500 0.00 0.00 32.61 3.67
411 423 5.119931 TCATTTTGGTTCAGACGAATTGG 57.880 39.130 0.00 0.00 32.61 3.16
412 424 5.117592 GCTTCATTTTGGTTCAGACGAATTG 59.882 40.000 0.00 0.00 32.61 2.32
413 425 5.221224 TGCTTCATTTTGGTTCAGACGAATT 60.221 36.000 0.00 0.00 32.61 2.17
414 426 4.278170 TGCTTCATTTTGGTTCAGACGAAT 59.722 37.500 0.00 0.00 32.61 3.34
415 427 3.629855 TGCTTCATTTTGGTTCAGACGAA 59.370 39.130 0.00 0.00 0.00 3.85
416 428 3.210227 TGCTTCATTTTGGTTCAGACGA 58.790 40.909 0.00 0.00 0.00 4.20
417 429 3.624326 TGCTTCATTTTGGTTCAGACG 57.376 42.857 0.00 0.00 0.00 4.18
672 786 1.826487 GAGAGGAGAGGAGGCGACC 60.826 68.421 0.00 0.00 0.00 4.79
674 788 2.598467 GGAGAGGAGAGGAGGCGA 59.402 66.667 0.00 0.00 0.00 5.54
1909 3129 4.764050 TCCAACAACACCAGTCTAAAGA 57.236 40.909 0.00 0.00 0.00 2.52
2219 3445 4.487412 CACCCTCGTACGTCGCCC 62.487 72.222 16.05 0.00 39.67 6.13
2836 4138 2.052690 TAGCGGTGCTCTGGACTCC 61.053 63.158 0.00 0.00 40.44 3.85
3619 5014 8.608185 AGCCATTTATTTCAGGATAAAAAGGA 57.392 30.769 12.47 0.00 35.70 3.36
3620 5015 9.671279 AAAGCCATTTATTTCAGGATAAAAAGG 57.329 29.630 0.00 0.00 35.70 3.11
4383 5794 5.530519 TTCTATAGCTGCACGAAAACTTG 57.469 39.130 1.02 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.