Multiple sequence alignment - TraesCS2D01G377600

Loading Multiple Alignment...

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 TraesCS2D01G377600 chr2D 100.000 4246 0 0 1 4246 481987410 481991655 0.000000e+00 7841
1 TraesCS2D01G377600 chr2D 96.017 3791 98 27 490 4246 481960967 481964738 0.000000e+00 6115
2 TraesCS2D01G377600 chr2D 88.915 3004 247 41 542 3480 481688163 481691145 0.000000e+00 3624
3 TraesCS2D01G377600 chr2D 90.004 2541 219 17 970 3479 481656055 481658591 0.000000e+00 3253
4 TraesCS2D01G377600 chr2D 87.574 169 20 1 49 217 73402885 73403052 1.200000e-45 195
5 TraesCS2D01G377600 chr2D 89.855 138 12 2 211 347 481687854 481687990 4.360000e-40 176
6 TraesCS2D01G377600 chr2D 89.706 136 13 1 341 476 646915619 646915753 5.640000e-39 172
7 TraesCS2D01G377600 chr2D 88.971 136 14 1 341 476 646825111 646825245 2.630000e-37 167
8 TraesCS2D01G377600 chr2A 93.050 3813 189 38 490 4246 624457769 624461561 0.000000e+00 5504
9 TraesCS2D01G377600 chr2A 88.397 2982 238 50 560 3480 624393902 624396836 0.000000e+00 3491
10 TraesCS2D01G377600 chr2A 90.628 2486 200 18 1015 3480 624447180 624449652 0.000000e+00 3269
11 TraesCS2D01G377600 chr2A 88.582 2496 236 35 1015 3478 624359594 624362072 0.000000e+00 2985
12 TraesCS2D01G377600 chr2A 87.608 347 33 3 1 347 624457434 624457770 1.110000e-105 394
13 TraesCS2D01G377600 chr2A 80.845 355 42 18 3794 4134 624397157 624397499 5.450000e-64 255
14 TraesCS2D01G377600 chr2A 92.308 91 7 0 779 869 624446911 624447001 3.450000e-26 130
15 TraesCS2D01G377600 chr2B 93.758 3284 123 31 693 3950 565209751 565212978 0.000000e+00 4854
16 TraesCS2D01G377600 chr2B 90.995 2976 221 19 539 3480 565188530 565191492 0.000000e+00 3967
17 TraesCS2D01G377600 chr2B 88.117 2979 252 44 552 3483 565076034 565078957 0.000000e+00 3446
18 TraesCS2D01G377600 chr2B 93.667 300 19 0 3947 4246 565213011 565213310 2.330000e-122 449
19 TraesCS2D01G377600 chr2B 90.845 142 11 2 208 347 565188242 565188383 5.600000e-44 189
20 TraesCS2D01G377600 chr2B 91.270 126 11 0 355 480 767379859 767379734 5.640000e-39 172
21 TraesCS2D01G377600 chr2B 93.902 82 5 0 4012 4093 565080976 565081057 1.600000e-24 124
22 TraesCS2D01G377600 chr7A 89.286 168 17 1 49 216 732053482 732053316 4.300000e-50 209
23 TraesCS2D01G377600 chr1A 86.802 197 15 9 45 234 362059940 362060132 4.300000e-50 209
24 TraesCS2D01G377600 chr7B 86.932 176 20 3 44 217 663743581 663743407 1.200000e-45 195
25 TraesCS2D01G377600 chr6B 87.952 166 18 1 48 213 132353578 132353415 1.200000e-45 195
26 TraesCS2D01G377600 chr6B 90.909 132 12 0 346 477 42509025 42508894 1.210000e-40 178
27 TraesCS2D01G377600 chr1D 87.574 169 19 2 46 213 96949626 96949793 1.200000e-45 195
28 TraesCS2D01G377600 chr1D 85.052 194 18 9 45 234 289532109 289532295 2.020000e-43 187
29 TraesCS2D01G377600 chr1D 85.052 194 18 9 45 234 289597325 289597511 2.020000e-43 187
30 TraesCS2D01G377600 chr6A 90.370 135 13 0 346 480 204007918 204007784 1.210000e-40 178
31 TraesCS2D01G377600 chr5A 91.339 127 11 0 346 472 662750005 662749879 1.570000e-39 174
32 TraesCS2D01G377600 chr5D 90.152 132 13 0 346 477 190342073 190342204 5.640000e-39 172
33 TraesCS2D01G377600 chr3A 90.698 129 10 2 341 469 589891319 589891445 2.030000e-38 171
34 TraesCS2D01G377600 chr3B 88.112 143 15 2 336 477 666446184 666446325 7.300000e-38 169


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 TraesCS2D01G377600 chr2D 481987410 481991655 4245 False 7841.0 7841 100.0000 1 4246 1 chr2D.!!$F4 4245
1 TraesCS2D01G377600 chr2D 481960967 481964738 3771 False 6115.0 6115 96.0170 490 4246 1 chr2D.!!$F3 3756
2 TraesCS2D01G377600 chr2D 481656055 481658591 2536 False 3253.0 3253 90.0040 970 3479 1 chr2D.!!$F2 2509
3 TraesCS2D01G377600 chr2D 481687854 481691145 3291 False 1900.0 3624 89.3850 211 3480 2 chr2D.!!$F7 3269
4 TraesCS2D01G377600 chr2A 624359594 624362072 2478 False 2985.0 2985 88.5820 1015 3478 1 chr2A.!!$F1 2463
5 TraesCS2D01G377600 chr2A 624457434 624461561 4127 False 2949.0 5504 90.3290 1 4246 2 chr2A.!!$F4 4245
6 TraesCS2D01G377600 chr2A 624393902 624397499 3597 False 1873.0 3491 84.6210 560 4134 2 chr2A.!!$F2 3574
7 TraesCS2D01G377600 chr2A 624446911 624449652 2741 False 1699.5 3269 91.4680 779 3480 2 chr2A.!!$F3 2701
8 TraesCS2D01G377600 chr2B 565209751 565213310 3559 False 2651.5 4854 93.7125 693 4246 2 chr2B.!!$F3 3553
9 TraesCS2D01G377600 chr2B 565188242 565191492 3250 False 2078.0 3967 90.9200 208 3480 2 chr2B.!!$F2 3272
10 TraesCS2D01G377600 chr2B 565076034 565081057 5023 False 1785.0 3446 91.0095 552 4093 2 chr2B.!!$F1 3541

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
488 491 0.317479 AAAGTGTCGAACGGAGGGAG 59.683 55.0 0.00 0.0 0.00 4.30 F
1016 1263 0.317160 TCAATGGAGTGCGAGAACGT 59.683 50.0 0.00 0.0 41.98 3.99 F
1020 1279 0.317160 TGGAGTGCGAGAACGTCAAT 59.683 50.0 0.00 0.0 41.98 2.57 F
2123 2424 0.541063 TCGGTGAGCTTGACCCACTA 60.541 55.0 9.65 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 1651 0.601841 TGGAACTTCTTCGGCGGTTC 60.602 55.000 7.21 12.08 37.79 3.62 R
2348 2649 1.403249 GCAAACATGAGCTTGCCGATT 60.403 47.619 16.13 0.00 40.15 3.34 R
2738 3039 2.806434 TGGCCATTGTTATCAGTGCTT 58.194 42.857 0.00 0.00 31.31 3.91 R
3940 4374 0.108992 ATCAGTGCATGCGCCAAAAG 60.109 50.000 26.95 12.37 37.32 2.27 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
26 27 8.684386 TTTGATCAACCTCTAAACACACATTA 57.316 30.769 7.89 0.00 0.00 1.90
57 58 7.362802 ACTGAAAACATATACTACTCCCTCC 57.637 40.000 0.00 0.00 0.00 4.30
58 59 6.326843 ACTGAAAACATATACTACTCCCTCCC 59.673 42.308 0.00 0.00 0.00 4.30
61 62 6.997942 AAACATATACTACTCCCTCCCTTC 57.002 41.667 0.00 0.00 0.00 3.46
75 76 6.699688 TCCCTCCCTTCCTAAATATAAGTCA 58.300 40.000 0.00 0.00 0.00 3.41
79 80 9.868160 CCTCCCTTCCTAAATATAAGTCATTTT 57.132 33.333 0.00 0.00 0.00 1.82
102 103 9.515226 TTTTAAAGATTTCACTGTAGGCTACAT 57.485 29.630 26.39 11.64 38.15 2.29
107 108 3.286329 TCACTGTAGGCTACATACGGA 57.714 47.619 26.39 17.62 38.15 4.69
109 110 2.950309 CACTGTAGGCTACATACGGAGT 59.050 50.000 26.39 16.81 38.15 3.85
173 174 5.674525 TCTGAATGCAGTCTTTATAGTGGG 58.325 41.667 16.05 0.00 42.84 4.61
176 177 7.290014 TCTGAATGCAGTCTTTATAGTGGGATA 59.710 37.037 16.05 0.00 42.84 2.59
205 206 8.959705 AAAAGGACTTATATTTAGGAACGGAG 57.040 34.615 0.00 0.00 0.00 4.63
289 291 1.376166 TCCATACCAACGTTGCCCG 60.376 57.895 22.93 11.84 44.03 6.13
312 314 4.130286 AGCAAAGTTAGATTCCTCGGAG 57.870 45.455 0.00 0.00 0.00 4.63
332 335 6.486657 TCGGAGACAAGATTGAAGAAACAAAT 59.513 34.615 0.00 0.00 33.44 2.32
345 348 7.380536 TGAAGAAACAAATAGCATTGCATCTT 58.619 30.769 11.91 12.98 39.35 2.40
346 349 8.522003 TGAAGAAACAAATAGCATTGCATCTTA 58.478 29.630 11.91 0.00 38.02 2.10
347 350 8.693542 AAGAAACAAATAGCATTGCATCTTAC 57.306 30.769 11.91 0.00 37.05 2.34
348 351 8.059798 AGAAACAAATAGCATTGCATCTTACT 57.940 30.769 11.91 0.00 33.52 2.24
349 352 8.186821 AGAAACAAATAGCATTGCATCTTACTC 58.813 33.333 11.91 0.00 33.52 2.59
350 353 7.636150 AACAAATAGCATTGCATCTTACTCT 57.364 32.000 11.91 0.00 33.52 3.24
351 354 7.256756 ACAAATAGCATTGCATCTTACTCTC 57.743 36.000 11.91 0.00 33.52 3.20
352 355 7.052873 ACAAATAGCATTGCATCTTACTCTCT 58.947 34.615 11.91 0.00 33.52 3.10
353 356 7.555554 ACAAATAGCATTGCATCTTACTCTCTT 59.444 33.333 11.91 0.00 33.52 2.85
354 357 7.727331 AATAGCATTGCATCTTACTCTCTTC 57.273 36.000 11.91 0.00 0.00 2.87
355 358 4.118410 AGCATTGCATCTTACTCTCTTCG 58.882 43.478 11.91 0.00 0.00 3.79
356 359 3.868077 GCATTGCATCTTACTCTCTTCGT 59.132 43.478 3.15 0.00 0.00 3.85
357 360 4.331168 GCATTGCATCTTACTCTCTTCGTT 59.669 41.667 3.15 0.00 0.00 3.85
358 361 5.501574 GCATTGCATCTTACTCTCTTCGTTC 60.502 44.000 3.15 0.00 0.00 3.95
359 362 4.111375 TGCATCTTACTCTCTTCGTTCC 57.889 45.455 0.00 0.00 0.00 3.62
360 363 3.764434 TGCATCTTACTCTCTTCGTTCCT 59.236 43.478 0.00 0.00 0.00 3.36
361 364 4.948004 TGCATCTTACTCTCTTCGTTCCTA 59.052 41.667 0.00 0.00 0.00 2.94
362 365 5.417894 TGCATCTTACTCTCTTCGTTCCTAA 59.582 40.000 0.00 0.00 0.00 2.69
363 366 6.071560 TGCATCTTACTCTCTTCGTTCCTAAA 60.072 38.462 0.00 0.00 0.00 1.85
364 367 6.981559 GCATCTTACTCTCTTCGTTCCTAAAT 59.018 38.462 0.00 0.00 0.00 1.40
365 368 8.136165 GCATCTTACTCTCTTCGTTCCTAAATA 58.864 37.037 0.00 0.00 0.00 1.40
372 375 9.411189 ACTCTCTTCGTTCCTAAATATAAGTCT 57.589 33.333 0.00 0.00 0.00 3.24
408 411 8.840833 TTCAATAAGTGACTACATACAAAGCA 57.159 30.769 0.00 0.00 35.39 3.91
409 412 8.840833 TCAATAAGTGACTACATACAAAGCAA 57.159 30.769 0.00 0.00 0.00 3.91
410 413 9.278978 TCAATAAGTGACTACATACAAAGCAAA 57.721 29.630 0.00 0.00 0.00 3.68
411 414 9.891828 CAATAAGTGACTACATACAAAGCAAAA 57.108 29.630 0.00 0.00 0.00 2.44
414 417 7.744087 AGTGACTACATACAAAGCAAAATGA 57.256 32.000 0.00 0.00 0.00 2.57
415 418 7.810658 AGTGACTACATACAAAGCAAAATGAG 58.189 34.615 0.00 0.00 0.00 2.90
416 419 7.445402 AGTGACTACATACAAAGCAAAATGAGT 59.555 33.333 0.00 0.00 0.00 3.41
417 420 7.535258 GTGACTACATACAAAGCAAAATGAGTG 59.465 37.037 0.00 0.00 0.00 3.51
418 421 7.443879 TGACTACATACAAAGCAAAATGAGTGA 59.556 33.333 0.00 0.00 0.00 3.41
419 422 8.165239 ACTACATACAAAGCAAAATGAGTGAA 57.835 30.769 0.00 0.00 0.00 3.18
420 423 8.796475 ACTACATACAAAGCAAAATGAGTGAAT 58.204 29.630 0.00 0.00 0.00 2.57
421 424 9.282247 CTACATACAAAGCAAAATGAGTGAATC 57.718 33.333 0.00 0.00 0.00 2.52
422 425 7.889469 ACATACAAAGCAAAATGAGTGAATCT 58.111 30.769 0.00 0.00 0.00 2.40
423 426 9.013229 ACATACAAAGCAAAATGAGTGAATCTA 57.987 29.630 0.00 0.00 0.00 1.98
458 461 9.692749 AATATGTCTACATACTTCCATACGTTG 57.307 33.333 4.98 0.00 41.15 4.10
459 462 6.519679 TGTCTACATACTTCCATACGTTGT 57.480 37.500 0.00 0.00 0.00 3.32
460 463 7.628769 TGTCTACATACTTCCATACGTTGTA 57.371 36.000 0.00 0.00 0.00 2.41
461 464 7.700505 TGTCTACATACTTCCATACGTTGTAG 58.299 38.462 10.56 10.56 37.48 2.74
462 465 7.337689 TGTCTACATACTTCCATACGTTGTAGT 59.662 37.037 14.53 10.67 37.44 2.73
463 466 7.854916 GTCTACATACTTCCATACGTTGTAGTC 59.145 40.741 14.53 8.25 37.44 2.59
464 467 5.899299 ACATACTTCCATACGTTGTAGTCC 58.101 41.667 0.00 0.00 0.00 3.85
465 468 5.419788 ACATACTTCCATACGTTGTAGTCCA 59.580 40.000 0.00 0.00 0.00 4.02
466 469 6.097839 ACATACTTCCATACGTTGTAGTCCAT 59.902 38.462 0.00 0.00 0.00 3.41
467 470 5.416271 ACTTCCATACGTTGTAGTCCATT 57.584 39.130 0.00 0.00 0.00 3.16
468 471 5.801380 ACTTCCATACGTTGTAGTCCATTT 58.199 37.500 0.00 0.00 0.00 2.32
469 472 6.938507 ACTTCCATACGTTGTAGTCCATTTA 58.061 36.000 0.00 0.00 0.00 1.40
470 473 7.388437 ACTTCCATACGTTGTAGTCCATTTAA 58.612 34.615 0.00 0.00 0.00 1.52
471 474 7.879160 ACTTCCATACGTTGTAGTCCATTTAAA 59.121 33.333 0.00 0.00 0.00 1.52
472 475 7.837202 TCCATACGTTGTAGTCCATTTAAAG 57.163 36.000 0.00 0.00 0.00 1.85
473 476 7.388437 TCCATACGTTGTAGTCCATTTAAAGT 58.612 34.615 0.00 0.00 0.00 2.66
474 477 7.332430 TCCATACGTTGTAGTCCATTTAAAGTG 59.668 37.037 0.00 0.00 0.00 3.16
475 478 7.118680 CCATACGTTGTAGTCCATTTAAAGTGT 59.881 37.037 0.00 0.00 0.00 3.55
476 479 6.535274 ACGTTGTAGTCCATTTAAAGTGTC 57.465 37.500 0.00 0.00 0.00 3.67
477 480 5.176223 ACGTTGTAGTCCATTTAAAGTGTCG 59.824 40.000 0.00 0.00 0.00 4.35
478 481 5.403166 CGTTGTAGTCCATTTAAAGTGTCGA 59.597 40.000 0.00 0.00 0.00 4.20
479 482 6.074195 CGTTGTAGTCCATTTAAAGTGTCGAA 60.074 38.462 0.00 0.00 0.00 3.71
480 483 6.774354 TGTAGTCCATTTAAAGTGTCGAAC 57.226 37.500 0.00 0.00 0.00 3.95
481 484 4.985044 AGTCCATTTAAAGTGTCGAACG 57.015 40.909 0.00 0.00 0.00 3.95
482 485 3.744426 AGTCCATTTAAAGTGTCGAACGG 59.256 43.478 0.00 0.00 0.00 4.44
483 486 3.742369 GTCCATTTAAAGTGTCGAACGGA 59.258 43.478 0.00 0.00 0.00 4.69
484 487 3.991773 TCCATTTAAAGTGTCGAACGGAG 59.008 43.478 0.00 0.00 0.00 4.63
485 488 3.124636 CCATTTAAAGTGTCGAACGGAGG 59.875 47.826 0.00 0.00 0.00 4.30
486 489 2.443887 TTAAAGTGTCGAACGGAGGG 57.556 50.000 0.00 0.00 0.00 4.30
487 490 1.619654 TAAAGTGTCGAACGGAGGGA 58.380 50.000 0.00 0.00 0.00 4.20
488 491 0.317479 AAAGTGTCGAACGGAGGGAG 59.683 55.000 0.00 0.00 0.00 4.30
596 733 4.368808 CGCGCACCAACCAGTTCG 62.369 66.667 8.75 0.00 0.00 3.95
638 780 4.093952 CGGCTGCCACAAAGCGAG 62.094 66.667 20.29 0.00 41.78 5.03
730 884 4.373116 TCAACCTCGCCGTCCAGC 62.373 66.667 0.00 0.00 0.00 4.85
760 923 1.194781 CCCACTGCCTCACACCTACT 61.195 60.000 0.00 0.00 0.00 2.57
773 937 2.843113 ACACCTACTCCTACTACTCGGT 59.157 50.000 0.00 0.00 0.00 4.69
903 1093 4.038522 AGGACACAGATCAATCCAGATACG 59.961 45.833 0.00 0.00 33.33 3.06
975 1222 5.760253 GGAATCCAGATACACATACACTTGG 59.240 44.000 0.00 0.00 0.00 3.61
1016 1263 0.317160 TCAATGGAGTGCGAGAACGT 59.683 50.000 0.00 0.00 41.98 3.99
1020 1279 0.317160 TGGAGTGCGAGAACGTCAAT 59.683 50.000 0.00 0.00 41.98 2.57
1523 1824 1.823169 TTAACGCTGGAGCCTTCGGT 61.823 55.000 0.00 0.00 37.91 4.69
1532 1833 4.078516 GCCTTCGGTACCGGCACT 62.079 66.667 32.80 0.00 43.25 4.40
2123 2424 0.541063 TCGGTGAGCTTGACCCACTA 60.541 55.000 9.65 0.00 0.00 2.74
2144 2445 6.317140 CACTAATGAAGCCAAAGCAAGATAGA 59.683 38.462 0.00 0.00 43.56 1.98
2348 2649 2.602267 AGGCTTGCCATTGCTGCA 60.602 55.556 14.54 0.00 38.66 4.41
2800 3101 2.224018 GCGAGAAGGATCTTCTGCTCAT 60.224 50.000 14.05 0.00 38.98 2.90
3469 3801 6.149973 ACAGTGTGTGATAAGTTTCCATGATG 59.850 38.462 0.00 0.00 0.00 3.07
3600 4014 5.112220 TCTTGCATCTAGTTTTTGCAGTG 57.888 39.130 10.56 0.00 46.10 3.66
3678 4104 9.924650 CTGTATTATTCACCTATTGTACTACCC 57.075 37.037 0.00 0.00 0.00 3.69
3936 4370 6.517605 TGTGGCGCATATTTGTATTCTACTA 58.482 36.000 10.83 0.00 0.00 1.82
3939 4373 6.866770 TGGCGCATATTTGTATTCTACTACTC 59.133 38.462 10.83 0.00 0.00 2.59
3940 4374 6.310711 GGCGCATATTTGTATTCTACTACTCC 59.689 42.308 10.83 0.00 0.00 3.85
3941 4375 7.091443 GCGCATATTTGTATTCTACTACTCCT 58.909 38.462 0.30 0.00 0.00 3.69
3950 4384 1.897133 TCTACTACTCCTTTTGGCGCA 59.103 47.619 10.83 0.00 40.12 6.09
3959 5866 0.108992 CTTTTGGCGCATGCACTGAT 60.109 50.000 19.57 0.00 45.35 2.90
4004 5911 6.375174 ACGTATGTATAATGTATGTCCGGCTA 59.625 38.462 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.851387 TTCAGTTGTCTGTAATGTGTGTTTA 57.149 32.000 0.00 0.00 41.91 2.01
19 20 6.751514 TGTTTTCAGTTGTCTGTAATGTGT 57.248 33.333 0.00 0.00 41.91 3.72
26 27 9.640963 GAGTAGTATATGTTTTCAGTTGTCTGT 57.359 33.333 0.00 0.00 41.91 3.41
75 76 9.515226 TGTAGCCTACAGTGAAATCTTTAAAAT 57.485 29.630 0.00 0.00 34.06 1.82
79 80 7.919091 CGTATGTAGCCTACAGTGAAATCTTTA 59.081 37.037 10.78 0.00 42.77 1.85
81 82 6.273825 CGTATGTAGCCTACAGTGAAATCTT 58.726 40.000 10.78 0.00 42.77 2.40
83 84 4.982916 CCGTATGTAGCCTACAGTGAAATC 59.017 45.833 10.78 0.00 42.77 2.17
88 89 2.950309 ACTCCGTATGTAGCCTACAGTG 59.050 50.000 10.78 2.67 42.77 3.66
92 93 8.355913 ACTTATTTTACTCCGTATGTAGCCTAC 58.644 37.037 0.00 0.00 0.00 3.18
137 138 8.303156 AGACTGCATTCAGATGTATATAGACAC 58.697 37.037 1.52 0.00 42.95 3.67
138 139 8.414629 AGACTGCATTCAGATGTATATAGACA 57.585 34.615 2.07 2.07 42.95 3.41
148 149 6.204301 CCCACTATAAAGACTGCATTCAGATG 59.796 42.308 6.84 0.00 42.95 2.90
152 153 5.692115 TCCCACTATAAAGACTGCATTCA 57.308 39.130 6.84 0.00 0.00 2.57
187 188 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
202 203 1.072806 TGCATGCATCATACTCCCTCC 59.927 52.381 18.46 0.00 0.00 4.30
205 206 0.870393 CGTGCATGCATCATACTCCC 59.130 55.000 25.64 6.36 0.00 4.30
261 263 3.197766 ACGTTGGTATGGACTGATGACAT 59.802 43.478 0.00 0.00 0.00 3.06
289 291 5.007385 TCCGAGGAATCTAACTTTGCTAC 57.993 43.478 0.00 0.00 0.00 3.58
312 314 8.976986 ATGCTATTTGTTTCTTCAATCTTGTC 57.023 30.769 0.00 0.00 0.00 3.18
332 335 5.163509 ACGAAGAGAGTAAGATGCAATGCTA 60.164 40.000 6.82 0.00 0.00 3.49
346 349 9.411189 AGACTTATATTTAGGAACGAAGAGAGT 57.589 33.333 0.00 0.00 0.00 3.24
382 385 9.278978 TGCTTTGTATGTAGTCACTTATTGAAA 57.721 29.630 0.00 0.00 35.39 2.69
383 386 8.840833 TGCTTTGTATGTAGTCACTTATTGAA 57.159 30.769 0.00 0.00 35.39 2.69
384 387 8.840833 TTGCTTTGTATGTAGTCACTTATTGA 57.159 30.769 0.00 0.00 0.00 2.57
385 388 9.891828 TTTTGCTTTGTATGTAGTCACTTATTG 57.108 29.630 0.00 0.00 0.00 1.90
388 391 9.278978 TCATTTTGCTTTGTATGTAGTCACTTA 57.721 29.630 0.00 0.00 0.00 2.24
389 392 8.165239 TCATTTTGCTTTGTATGTAGTCACTT 57.835 30.769 0.00 0.00 0.00 3.16
390 393 7.445402 ACTCATTTTGCTTTGTATGTAGTCACT 59.555 33.333 0.00 0.00 0.00 3.41
391 394 7.535258 CACTCATTTTGCTTTGTATGTAGTCAC 59.465 37.037 0.00 0.00 0.00 3.67
392 395 7.443879 TCACTCATTTTGCTTTGTATGTAGTCA 59.556 33.333 0.00 0.00 0.00 3.41
393 396 7.806690 TCACTCATTTTGCTTTGTATGTAGTC 58.193 34.615 0.00 0.00 0.00 2.59
394 397 7.744087 TCACTCATTTTGCTTTGTATGTAGT 57.256 32.000 0.00 0.00 0.00 2.73
395 398 9.282247 GATTCACTCATTTTGCTTTGTATGTAG 57.718 33.333 0.00 0.00 0.00 2.74
396 399 9.013229 AGATTCACTCATTTTGCTTTGTATGTA 57.987 29.630 0.00 0.00 0.00 2.29
397 400 7.889469 AGATTCACTCATTTTGCTTTGTATGT 58.111 30.769 0.00 0.00 0.00 2.29
432 435 9.692749 CAACGTATGGAAGTATGTAGACATATT 57.307 33.333 5.69 0.00 40.53 1.28
433 436 8.857098 ACAACGTATGGAAGTATGTAGACATAT 58.143 33.333 5.69 0.00 40.53 1.78
434 437 8.229253 ACAACGTATGGAAGTATGTAGACATA 57.771 34.615 0.00 0.00 37.76 2.29
435 438 7.108841 ACAACGTATGGAAGTATGTAGACAT 57.891 36.000 0.08 0.08 40.22 3.06
436 439 6.519679 ACAACGTATGGAAGTATGTAGACA 57.480 37.500 0.00 0.00 0.00 3.41
437 440 7.701445 ACTACAACGTATGGAAGTATGTAGAC 58.299 38.462 19.63 0.00 40.56 2.59
438 441 7.012704 GGACTACAACGTATGGAAGTATGTAGA 59.987 40.741 19.63 0.00 40.56 2.59
439 442 7.137426 GGACTACAACGTATGGAAGTATGTAG 58.863 42.308 13.83 13.83 42.61 2.74
440 443 6.602803 TGGACTACAACGTATGGAAGTATGTA 59.397 38.462 0.00 0.00 31.68 2.29
441 444 5.419788 TGGACTACAACGTATGGAAGTATGT 59.580 40.000 0.00 0.00 31.68 2.29
442 445 5.898174 TGGACTACAACGTATGGAAGTATG 58.102 41.667 0.00 0.00 31.68 2.39
443 446 6.726490 ATGGACTACAACGTATGGAAGTAT 57.274 37.500 0.00 0.00 31.68 2.12
444 447 6.534475 AATGGACTACAACGTATGGAAGTA 57.466 37.500 0.00 0.00 31.68 2.24
445 448 5.416271 AATGGACTACAACGTATGGAAGT 57.584 39.130 0.00 0.00 33.53 3.01
446 449 7.837202 TTAAATGGACTACAACGTATGGAAG 57.163 36.000 0.00 0.00 0.00 3.46
447 450 7.879160 ACTTTAAATGGACTACAACGTATGGAA 59.121 33.333 0.00 0.00 0.00 3.53
448 451 7.332430 CACTTTAAATGGACTACAACGTATGGA 59.668 37.037 0.00 0.00 0.00 3.41
449 452 7.118680 ACACTTTAAATGGACTACAACGTATGG 59.881 37.037 0.00 0.00 0.00 2.74
450 453 8.025243 ACACTTTAAATGGACTACAACGTATG 57.975 34.615 0.00 0.00 0.00 2.39
451 454 7.062605 CGACACTTTAAATGGACTACAACGTAT 59.937 37.037 0.00 0.00 0.00 3.06
452 455 6.363088 CGACACTTTAAATGGACTACAACGTA 59.637 38.462 0.00 0.00 0.00 3.57
453 456 5.176223 CGACACTTTAAATGGACTACAACGT 59.824 40.000 0.00 0.00 0.00 3.99
454 457 5.403166 TCGACACTTTAAATGGACTACAACG 59.597 40.000 0.00 0.00 0.00 4.10
455 458 6.774354 TCGACACTTTAAATGGACTACAAC 57.226 37.500 0.00 0.00 0.00 3.32
456 459 6.074195 CGTTCGACACTTTAAATGGACTACAA 60.074 38.462 0.00 0.00 0.00 2.41
457 460 5.403166 CGTTCGACACTTTAAATGGACTACA 59.597 40.000 0.00 0.00 0.00 2.74
458 461 5.164022 CCGTTCGACACTTTAAATGGACTAC 60.164 44.000 0.00 0.00 30.77 2.73
459 462 4.925054 CCGTTCGACACTTTAAATGGACTA 59.075 41.667 0.00 0.00 30.77 2.59
460 463 3.744426 CCGTTCGACACTTTAAATGGACT 59.256 43.478 0.00 0.00 30.77 3.85
461 464 3.742369 TCCGTTCGACACTTTAAATGGAC 59.258 43.478 0.00 0.00 33.05 4.02
462 465 3.991773 CTCCGTTCGACACTTTAAATGGA 59.008 43.478 0.00 0.00 35.88 3.41
463 466 3.124636 CCTCCGTTCGACACTTTAAATGG 59.875 47.826 0.00 0.00 0.00 3.16
464 467 3.124636 CCCTCCGTTCGACACTTTAAATG 59.875 47.826 0.00 0.00 0.00 2.32
465 468 3.007182 TCCCTCCGTTCGACACTTTAAAT 59.993 43.478 0.00 0.00 0.00 1.40
466 469 2.364970 TCCCTCCGTTCGACACTTTAAA 59.635 45.455 0.00 0.00 0.00 1.52
467 470 1.962807 TCCCTCCGTTCGACACTTTAA 59.037 47.619 0.00 0.00 0.00 1.52
468 471 1.542915 CTCCCTCCGTTCGACACTTTA 59.457 52.381 0.00 0.00 0.00 1.85
469 472 0.317479 CTCCCTCCGTTCGACACTTT 59.683 55.000 0.00 0.00 0.00 2.66
470 473 0.826672 ACTCCCTCCGTTCGACACTT 60.827 55.000 0.00 0.00 0.00 3.16
471 474 0.037303 TACTCCCTCCGTTCGACACT 59.963 55.000 0.00 0.00 0.00 3.55
472 475 0.450983 CTACTCCCTCCGTTCGACAC 59.549 60.000 0.00 0.00 0.00 3.67
473 476 0.325933 TCTACTCCCTCCGTTCGACA 59.674 55.000 0.00 0.00 0.00 4.35
474 477 1.677942 ATCTACTCCCTCCGTTCGAC 58.322 55.000 0.00 0.00 0.00 4.20
475 478 3.118112 AGTTATCTACTCCCTCCGTTCGA 60.118 47.826 0.00 0.00 28.23 3.71
476 479 3.212685 AGTTATCTACTCCCTCCGTTCG 58.787 50.000 0.00 0.00 28.23 3.95
477 480 4.834357 GAGTTATCTACTCCCTCCGTTC 57.166 50.000 0.00 0.00 46.30 3.95
578 715 4.683334 GAACTGGTTGGTGCGCGC 62.683 66.667 27.26 27.26 0.00 6.86
596 733 2.970324 TCGACGTGGGCAAAGCAC 60.970 61.111 0.00 0.00 0.00 4.40
730 884 0.321653 GGCAGTGGGTTGGTGTAGAG 60.322 60.000 0.00 0.00 0.00 2.43
760 923 1.660560 GGCGCAACCGAGTAGTAGGA 61.661 60.000 10.83 0.00 36.29 2.94
903 1093 1.815421 CTCGGCAGGTGGTGTATGC 60.815 63.158 0.00 0.00 39.25 3.14
951 1148 5.760253 CCAAGTGTATGTGTATCTGGATTCC 59.240 44.000 0.00 0.00 0.00 3.01
975 1222 7.285783 TGAAATATGCACAGACGTACTAAAC 57.714 36.000 0.00 0.00 0.00 2.01
1016 1263 1.466856 GCACAAGCCATCTCCATTGA 58.533 50.000 0.00 0.00 33.58 2.57
1020 1279 1.672030 CACGCACAAGCCATCTCCA 60.672 57.895 0.00 0.00 37.52 3.86
1056 1315 3.636231 CCCCAGTTGAGCGGGTCA 61.636 66.667 5.66 5.66 41.30 4.02
1392 1651 0.601841 TGGAACTTCTTCGGCGGTTC 60.602 55.000 7.21 12.08 37.79 3.62
1478 1779 1.134753 CTGAACAGGCAAGCAACACAA 59.865 47.619 0.00 0.00 0.00 3.33
2123 2424 7.523380 GCATATCTATCTTGCTTTGGCTTCATT 60.523 37.037 0.00 0.00 39.59 2.57
2348 2649 1.403249 GCAAACATGAGCTTGCCGATT 60.403 47.619 16.13 0.00 40.15 3.34
2738 3039 2.806434 TGGCCATTGTTATCAGTGCTT 58.194 42.857 0.00 0.00 31.31 3.91
3600 4014 5.048643 TGAACTTAGTGAGCAGAGTACTGAC 60.049 44.000 0.00 0.00 46.03 3.51
3678 4104 8.208718 TCGAAAAATTGTATGAAGAGGTATGG 57.791 34.615 0.00 0.00 0.00 2.74
3717 4143 3.197766 TCATGTGACATTCCCTCCTGTAC 59.802 47.826 0.00 0.00 0.00 2.90
3879 4309 6.145696 GCAACCTTACAATCTCCATATACGTC 59.854 42.308 0.00 0.00 0.00 4.34
3936 4370 1.902918 TGCATGCGCCAAAAGGAGT 60.903 52.632 14.09 0.00 37.32 3.85
3939 4373 1.735198 CAGTGCATGCGCCAAAAGG 60.735 57.895 26.95 6.90 37.32 3.11
3940 4374 0.108992 ATCAGTGCATGCGCCAAAAG 60.109 50.000 26.95 12.37 37.32 2.27
3941 4375 0.317799 AATCAGTGCATGCGCCAAAA 59.682 45.000 26.95 10.89 37.32 2.44
3959 5866 1.600107 GGCAGGATACGGTGGACAA 59.400 57.895 0.00 0.00 46.39 3.18


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

AutoCloner maintained by Alex Coulton.