Multiple sequence alignment - TraesCS7D01G211700

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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 TraesCS7D01G211700 chr7D 100.000 3323 0 0 1 3323 169822996 169826318 0.000000e+00 6137
1 TraesCS7D01G211700 chr7D 98.851 522 4 2 2803 3323 89273740 89273220 0.000000e+00 929
2 TraesCS7D01G211700 chr7D 98.876 89 1 0 372 460 177106856 177106944 3.430000e-35 159
3 TraesCS7D01G211700 chr7D 95.833 96 3 1 369 463 485090970 485090875 1.600000e-33 154
4 TraesCS7D01G211700 chr7B 94.393 1516 57 5 459 1971 135527861 135529351 0.000000e+00 2303
5 TraesCS7D01G211700 chr7B 88.771 757 50 21 1969 2712 135529425 135530159 0.000000e+00 894
6 TraesCS7D01G211700 chr7B 96.517 201 6 1 24 224 135527393 135527592 6.870000e-87 331
7 TraesCS7D01G211700 chr7B 96.774 155 5 0 223 377 135527708 135527862 3.290000e-65 259
8 TraesCS7D01G211700 chr7A 94.615 1467 68 6 929 2393 172417838 172419295 0.000000e+00 2261
9 TraesCS7D01G211700 chr7A 84.390 410 38 15 2400 2809 172420519 172420902 2.420000e-101 379
10 TraesCS7D01G211700 chr7A 92.424 264 14 2 638 897 435003837 435004098 4.050000e-99 372
11 TraesCS7D01G211700 chr7A 91.209 273 18 2 638 906 535468572 535468302 1.880000e-97 366
12 TraesCS7D01G211700 chr7A 91.266 229 17 3 4 231 172417143 172417369 3.220000e-80 309
13 TraesCS7D01G211700 chr7A 95.604 182 7 1 459 640 172417600 172417780 1.170000e-74 291
14 TraesCS7D01G211700 chr7A 83.226 155 5 6 223 377 172417468 172417601 4.500000e-24 122
15 TraesCS7D01G211700 chr3D 99.417 515 3 0 2809 3323 297461382 297460868 0.000000e+00 935
16 TraesCS7D01G211700 chr3D 99.222 514 4 0 2810 3323 288119004 288118491 0.000000e+00 928
17 TraesCS7D01G211700 chr3D 99.223 515 3 1 2810 3323 491627754 491628268 0.000000e+00 928
18 TraesCS7D01G211700 chr6D 99.417 515 2 1 2810 3323 290842897 290842383 0.000000e+00 933
19 TraesCS7D01G211700 chr6D 92.424 264 14 2 638 897 24007135 24007396 4.050000e-99 372
20 TraesCS7D01G211700 chr6D 100.000 86 0 0 375 460 17316712 17316627 3.430000e-35 159
21 TraesCS7D01G211700 chr6D 95.789 95 4 0 366 460 168293745 168293839 1.600000e-33 154
22 TraesCS7D01G211700 chr6D 94.059 101 5 1 370 470 146072817 146072916 5.740000e-33 152
23 TraesCS7D01G211700 chr6D 85.926 135 12 7 373 504 145788549 145788419 1.610000e-28 137
24 TraesCS7D01G211700 chr4D 99.223 515 3 1 2810 3323 488033677 488033163 0.000000e+00 928
25 TraesCS7D01G211700 chr4D 95.876 97 4 0 372 468 453135400 453135304 1.230000e-34 158
26 TraesCS7D01G211700 chr1D 99.223 515 3 1 2810 3323 460321192 460320678 0.000000e+00 928
27 TraesCS7D01G211700 chr1D 99.223 515 3 1 2810 3323 488830891 488830377 0.000000e+00 928
28 TraesCS7D01G211700 chr1D 93.208 265 11 3 638 897 258094371 258094109 1.870000e-102 383
29 TraesCS7D01G211700 chr2D 98.292 527 5 3 2799 3323 593915921 593915397 0.000000e+00 920
30 TraesCS7D01G211700 chr2D 92.776 263 13 2 638 896 395940195 395940455 3.130000e-100 375
31 TraesCS7D01G211700 chr2D 92.424 264 14 4 637 896 535240293 535240032 4.050000e-99 372
32 TraesCS7D01G211700 chr2D 96.739 92 3 0 369 460 124797315 124797406 1.600000e-33 154
33 TraesCS7D01G211700 chr5B 92.453 265 14 4 637 897 212799820 212800082 1.130000e-99 374
34 TraesCS7D01G211700 chr2B 92.424 264 14 2 637 896 723031947 723031686 4.050000e-99 372
35 TraesCS7D01G211700 chr5D 96.774 93 3 0 374 466 294640321 294640229 4.440000e-34 156


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 TraesCS7D01G211700 chr7D 169822996 169826318 3322 False 6137.00 6137 100.00000 1 3323 1 chr7D.!!$F1 3322
1 TraesCS7D01G211700 chr7D 89273220 89273740 520 True 929.00 929 98.85100 2803 3323 1 chr7D.!!$R1 520
2 TraesCS7D01G211700 chr7B 135527393 135530159 2766 False 946.75 2303 94.11375 24 2712 4 chr7B.!!$F1 2688
3 TraesCS7D01G211700 chr7A 172417143 172420902 3759 False 672.40 2261 89.82020 4 2809 5 chr7A.!!$F2 2805
4 TraesCS7D01G211700 chr3D 297460868 297461382 514 True 935.00 935 99.41700 2809 3323 1 chr3D.!!$R2 514
5 TraesCS7D01G211700 chr3D 288118491 288119004 513 True 928.00 928 99.22200 2810 3323 1 chr3D.!!$R1 513
6 TraesCS7D01G211700 chr3D 491627754 491628268 514 False 928.00 928 99.22300 2810 3323 1 chr3D.!!$F1 513
7 TraesCS7D01G211700 chr6D 290842383 290842897 514 True 933.00 933 99.41700 2810 3323 1 chr6D.!!$R3 513
8 TraesCS7D01G211700 chr4D 488033163 488033677 514 True 928.00 928 99.22300 2810 3323 1 chr4D.!!$R2 513
9 TraesCS7D01G211700 chr1D 460320678 460321192 514 True 928.00 928 99.22300 2810 3323 1 chr1D.!!$R2 513
10 TraesCS7D01G211700 chr1D 488830377 488830891 514 True 928.00 928 99.22300 2810 3323 1 chr1D.!!$R3 513
11 TraesCS7D01G211700 chr2D 593915397 593915921 524 True 920.00 920 98.29200 2799 3323 1 chr2D.!!$R2 524

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
394 514 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.0 0.00 0.00 0.00 2.71 F
395 515 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.0 0.00 0.00 0.00 1.90 F
1728 1876 0.028505 TGGATTACGCTCGTACTCGC 59.971 55.0 11.71 7.21 33.02 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1381 1528 0.244450 ATTGTGCGGGTGAAGCAATG 59.756 50.000 0.00 0.00 46.97 2.82 R
2106 2331 2.048222 ATCATCATACGGCGGCGG 60.048 61.111 35.05 17.87 0.00 6.13 R
2570 4016 0.249120 CCATCACCGTTAGAGCCACA 59.751 55.000 0.00 0.00 0.00 4.17 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
216 218 2.960819 ACGAAGTTGCTGGATACTGTC 58.039 47.619 0.00 0.00 37.78 3.51
217 219 2.563179 ACGAAGTTGCTGGATACTGTCT 59.437 45.455 0.00 0.00 37.78 3.41
218 220 3.182967 CGAAGTTGCTGGATACTGTCTC 58.817 50.000 0.00 0.00 37.92 3.36
219 221 2.949451 AGTTGCTGGATACTGTCTCG 57.051 50.000 0.00 0.00 37.92 4.04
220 222 2.171840 AGTTGCTGGATACTGTCTCGT 58.828 47.619 0.00 0.00 37.92 4.18
221 223 3.353557 AGTTGCTGGATACTGTCTCGTA 58.646 45.455 0.00 0.00 37.92 3.43
288 408 6.480981 AGCTTAGTTCGTAGTTAAGTGCAAAA 59.519 34.615 0.00 0.00 0.00 2.44
330 450 6.106648 TGCTTAGATATCATCAACCTCCTG 57.893 41.667 5.32 0.00 0.00 3.86
336 456 1.203441 TCATCAACCTCCTGCTGGCT 61.203 55.000 4.42 0.00 0.00 4.75
384 504 9.543783 CATGTTTACTTAAATACTACTCCCTCC 57.456 37.037 0.00 0.00 0.00 4.30
385 505 7.775120 TGTTTACTTAAATACTACTCCCTCCG 58.225 38.462 0.00 0.00 0.00 4.63
386 506 7.397192 TGTTTACTTAAATACTACTCCCTCCGT 59.603 37.037 0.00 0.00 0.00 4.69
387 507 7.573968 TTACTTAAATACTACTCCCTCCGTC 57.426 40.000 0.00 0.00 0.00 4.79
388 508 4.892345 ACTTAAATACTACTCCCTCCGTCC 59.108 45.833 0.00 0.00 0.00 4.79
389 509 2.378378 AATACTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
390 510 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
391 511 0.257039 TACTACTCCCTCCGTCCCAC 59.743 60.000 0.00 0.00 0.00 4.61
392 512 1.000019 CTACTCCCTCCGTCCCACA 60.000 63.158 0.00 0.00 0.00 4.17
393 513 0.613853 CTACTCCCTCCGTCCCACAA 60.614 60.000 0.00 0.00 0.00 3.33
394 514 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
395 515 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
396 516 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
397 517 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
398 518 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
399 519 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
400 520 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
401 521 3.006967 CCCTCCGTCCCACAATATAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
402 522 3.555168 CCTCCGTCCCACAATATAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
403 523 2.035449 TCCGTCCCACAATATAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
404 524 2.223971 CCGTCCCACAATATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
405 525 3.454375 CGTCCCACAATATAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
406 526 3.869246 CGTCCCACAATATAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
407 527 4.331717 CGTCCCACAATATAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
408 528 5.163794 CGTCCCACAATATAAGAGCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
409 529 6.027749 GTCCCACAATATAAGAGCGTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
410 530 5.941058 TCCCACAATATAAGAGCGTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
411 531 6.027749 CCCACAATATAAGAGCGTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
412 532 6.348950 CCCACAATATAAGAGCGTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
413 533 6.523201 CCACAATATAAGAGCGTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
414 534 7.298122 CACAATATAAGAGCGTTTTTGACACT 58.702 34.615 0.00 0.00 0.00 3.55
415 535 8.440059 CACAATATAAGAGCGTTTTTGACACTA 58.560 33.333 0.00 0.00 0.00 2.74
416 536 8.995220 ACAATATAAGAGCGTTTTTGACACTAA 58.005 29.630 0.00 0.00 0.00 2.24
417 537 9.988350 CAATATAAGAGCGTTTTTGACACTAAT 57.012 29.630 0.00 0.00 0.00 1.73
418 538 9.988350 AATATAAGAGCGTTTTTGACACTAATG 57.012 29.630 0.00 0.00 0.00 1.90
419 539 5.751243 AAGAGCGTTTTTGACACTAATGT 57.249 34.783 0.00 0.00 43.71 2.71
420 540 6.854496 AAGAGCGTTTTTGACACTAATGTA 57.146 33.333 0.00 0.00 39.95 2.29
421 541 6.467723 AGAGCGTTTTTGACACTAATGTAG 57.532 37.500 0.00 0.00 39.95 2.74
422 542 5.989777 AGAGCGTTTTTGACACTAATGTAGT 59.010 36.000 0.00 0.00 39.95 2.73
450 570 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
451 571 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
452 572 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
453 573 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
454 574 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
455 575 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
456 576 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
457 577 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
458 578 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
459 579 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
511 631 5.516339 GGTGCACATCAATATGCTGTTAAAC 59.484 40.000 20.43 0.00 42.55 2.01
677 797 7.948278 ATTTACTCCGCATATTAGAGTTGAC 57.052 36.000 4.78 0.00 41.09 3.18
682 802 5.592054 TCCGCATATTAGAGTTGACTGAAG 58.408 41.667 0.00 0.00 0.00 3.02
767 887 9.546428 CTATATGATGTGTGGAAGTACATTCAA 57.454 33.333 0.00 0.00 39.91 2.69
850 970 9.934190 ATTTTGTCAAAATTTACAATGCTTGAC 57.066 25.926 16.26 7.61 41.80 3.18
851 971 8.715191 TTTGTCAAAATTTACAATGCTTGACT 57.285 26.923 17.33 0.00 41.91 3.41
852 972 8.715191 TTGTCAAAATTTACAATGCTTGACTT 57.285 26.923 17.33 0.00 41.91 3.01
853 973 8.715191 TGTCAAAATTTACAATGCTTGACTTT 57.285 26.923 17.33 0.20 41.91 2.66
854 974 8.602328 TGTCAAAATTTACAATGCTTGACTTTG 58.398 29.630 17.33 0.00 41.91 2.77
855 975 8.816144 GTCAAAATTTACAATGCTTGACTTTGA 58.184 29.630 12.93 0.00 39.54 2.69
856 976 8.816144 TCAAAATTTACAATGCTTGACTTTGAC 58.184 29.630 0.00 0.00 36.99 3.18
896 1016 6.536582 GGAGTAAATAAAAACGGAGGGAGTAC 59.463 42.308 0.00 0.00 0.00 2.73
1071 1218 5.471456 ACAGTCCATGTTGTTCAGAGAAATC 59.529 40.000 0.00 0.00 39.96 2.17
1131 1278 2.046313 CATTATGCGCGCAATTTCTCC 58.954 47.619 39.68 2.07 0.00 3.71
1242 1389 6.379417 AGAAGGGTTTTTCTGGATTCATGATC 59.621 38.462 0.00 0.00 36.12 2.92
1381 1528 4.448210 TCATCCTTACAAAAGTATCGGCC 58.552 43.478 0.00 0.00 0.00 6.13
1440 1587 0.764890 CACTCTGGAGGGGAAACACA 59.235 55.000 2.58 0.00 34.58 3.72
1484 1631 1.410882 GACTCAGGTCCTGCATCCTAC 59.589 57.143 14.64 0.00 36.53 3.18
1492 1639 1.138859 TCCTGCATCCTACACATTCCG 59.861 52.381 0.00 0.00 0.00 4.30
1499 1646 1.483415 TCCTACACATTCCGCCCTTAC 59.517 52.381 0.00 0.00 0.00 2.34
1596 1744 1.981256 TTGCCTTCAAGGACCACTTC 58.019 50.000 7.98 0.00 37.67 3.01
1632 1780 4.336280 ACTTTAGAAAGGACAAGGATGGC 58.664 43.478 6.94 0.00 40.31 4.40
1728 1876 0.028505 TGGATTACGCTCGTACTCGC 59.971 55.000 11.71 7.21 33.02 5.03
1941 2089 3.808728 TCTTGTTGGTTCTCTTGAGGTG 58.191 45.455 0.00 0.00 0.00 4.00
1972 2123 8.303876 ACCATACCATTGTTTCTGTAAATTCAC 58.696 33.333 0.00 0.00 0.00 3.18
1976 2201 8.918202 ACCATTGTTTCTGTAAATTCACTCTA 57.082 30.769 0.00 0.00 0.00 2.43
1977 2202 8.784043 ACCATTGTTTCTGTAAATTCACTCTAC 58.216 33.333 0.00 0.00 0.00 2.59
2064 2289 2.521465 TTGCTTGGCTGGGGTGTG 60.521 61.111 0.00 0.00 0.00 3.82
2076 2301 2.031919 GGTGTGACGATGGGTGCA 59.968 61.111 0.00 0.00 0.00 4.57
2232 2457 3.512516 GCTGGCGCCAACATCCTC 61.513 66.667 32.09 9.52 0.00 3.71
2256 2481 3.964875 GTTGCGGGTGCTGGTGTG 61.965 66.667 0.00 0.00 43.34 3.82
2316 2541 1.153229 GAAGTATGGGTCCGGTGGC 60.153 63.158 0.00 0.00 0.00 5.01
2393 2618 7.172019 GCTTTTGAATAAAATCTGCCATATGGG 59.828 37.037 23.30 7.76 35.39 4.00
2396 2621 5.539574 TGAATAAAATCTGCCATATGGGGTG 59.460 40.000 23.30 0.00 37.04 4.61
2399 2624 1.225373 ATCTGCCATATGGGGTGTGT 58.775 50.000 23.30 0.00 37.04 3.72
2401 2626 2.417652 TCTGCCATATGGGGTGTGTAT 58.582 47.619 23.30 0.00 37.04 2.29
2402 2627 2.371841 TCTGCCATATGGGGTGTGTATC 59.628 50.000 23.30 3.71 37.04 2.24
2403 2628 2.373169 CTGCCATATGGGGTGTGTATCT 59.627 50.000 23.30 0.00 37.04 1.98
2407 2632 4.136796 CCATATGGGGTGTGTATCTTGTG 58.863 47.826 14.52 0.00 0.00 3.33
2429 3874 0.179234 TGATCCTATTTCGGCGCCAA 59.821 50.000 28.98 15.18 0.00 4.52
2528 3974 5.811399 TCAACTGATCAAACGAACAAACT 57.189 34.783 0.00 0.00 0.00 2.66
2529 3975 5.568482 TCAACTGATCAAACGAACAAACTG 58.432 37.500 0.00 0.00 0.00 3.16
2531 3977 5.811399 ACTGATCAAACGAACAAACTGAA 57.189 34.783 0.00 0.00 0.00 3.02
2557 4003 4.564769 GCAGAGTATGAGACTAGTTTGCAC 59.435 45.833 0.00 0.00 39.06 4.57
2558 4004 5.623368 GCAGAGTATGAGACTAGTTTGCACT 60.623 44.000 0.00 0.00 39.06 4.40
2559 4005 6.393990 CAGAGTATGAGACTAGTTTGCACTT 58.606 40.000 0.00 0.00 39.06 3.16
2561 4007 6.870965 AGAGTATGAGACTAGTTTGCACTTTG 59.129 38.462 0.00 0.00 39.06 2.77
2562 4008 4.756084 ATGAGACTAGTTTGCACTTTGC 57.244 40.909 0.00 0.00 45.29 3.68
2563 4009 6.964131 AGTATGAGACTAGTTTGCACTTTGCA 60.964 38.462 0.00 0.00 44.43 4.08
2616 4063 8.066612 TGGAGGAATGAATGAAACCTATTTTC 57.933 34.615 0.00 0.00 43.63 2.29
2631 4078 7.145932 ACCTATTTTCGAAGATTTGGTTCAG 57.854 36.000 15.48 3.82 35.04 3.02
2661 4108 6.125029 ACAAAGCCAGTAAGCTATTGATCAT 58.875 36.000 0.00 0.00 44.11 2.45
2663 4110 5.822132 AGCCAGTAAGCTATTGATCATCT 57.178 39.130 0.00 0.00 42.70 2.90
2664 4111 6.185114 AGCCAGTAAGCTATTGATCATCTT 57.815 37.500 0.00 1.06 42.70 2.40
2698 4145 5.244626 ACCAAATCCAATTCCAGTTCTTCAG 59.755 40.000 0.00 0.00 0.00 3.02
2726 4173 4.404073 GGTATCAGTCATCTGTTCTCCACT 59.596 45.833 0.00 0.00 41.91 4.00
2728 4175 4.263018 TCAGTCATCTGTTCTCCACTTG 57.737 45.455 0.00 0.00 41.91 3.16
2759 4206 3.304928 GGGCATCTGTTTCTGTTGTTCAG 60.305 47.826 0.00 0.00 44.85 3.02
2780 4227 4.025480 CAGTTAACTGTACCGGTCAAACAC 60.025 45.833 24.70 3.28 39.09 3.32
2786 4233 3.199677 TGTACCGGTCAAACACTTTCAG 58.800 45.455 12.40 0.00 0.00 3.02
2985 4434 4.719369 AGGCTCGACGGCGTTGAC 62.719 66.667 25.30 20.11 44.22 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.070009 GGTGGTAACTTTGTAAGTCCCAG 58.930 47.826 9.76 0.00 41.91 4.45
208 210 2.022195 TGCCCACTACGAGACAGTATC 58.978 52.381 0.00 0.00 0.00 2.24
213 215 1.228769 ACCTGCCCACTACGAGACA 60.229 57.895 0.00 0.00 0.00 3.41
214 216 0.966370 AGACCTGCCCACTACGAGAC 60.966 60.000 0.00 0.00 0.00 3.36
215 217 0.680280 GAGACCTGCCCACTACGAGA 60.680 60.000 0.00 0.00 0.00 4.04
216 218 0.965866 TGAGACCTGCCCACTACGAG 60.966 60.000 0.00 0.00 0.00 4.18
217 219 1.076014 TGAGACCTGCCCACTACGA 59.924 57.895 0.00 0.00 0.00 3.43
218 220 1.215647 GTGAGACCTGCCCACTACG 59.784 63.158 0.00 0.00 0.00 3.51
219 221 1.215647 CGTGAGACCTGCCCACTAC 59.784 63.158 0.00 0.00 0.00 2.73
220 222 1.076014 TCGTGAGACCTGCCCACTA 59.924 57.895 0.00 0.00 33.31 2.74
221 223 2.203640 TCGTGAGACCTGCCCACT 60.204 61.111 0.00 0.00 33.31 4.00
288 408 9.593134 TCTAAGCAACAAATTGTTACACAAAAT 57.407 25.926 11.33 0.00 41.96 1.82
303 423 6.767902 GGAGGTTGATGATATCTAAGCAACAA 59.232 38.462 19.68 4.02 37.83 2.83
330 450 1.137404 CGCCAACATTACAGCCAGC 59.863 57.895 0.00 0.00 0.00 4.85
336 456 6.502136 TGAAAATACATCGCCAACATTACA 57.498 33.333 0.00 0.00 0.00 2.41
377 497 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
378 498 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
379 499 2.969950 TCTTATATTGTGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
380 500 3.555168 GCTCTTATATTGTGGGACGGAGG 60.555 52.174 0.00 0.00 0.00 4.30
381 501 3.654414 GCTCTTATATTGTGGGACGGAG 58.346 50.000 0.00 0.00 0.00 4.63
382 502 2.035449 CGCTCTTATATTGTGGGACGGA 59.965 50.000 0.00 0.00 0.00 4.69
383 503 2.223971 ACGCTCTTATATTGTGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79
384 504 3.093717 ACGCTCTTATATTGTGGGACG 57.906 47.619 0.00 0.00 0.00 4.79
385 505 5.813080 AAAACGCTCTTATATTGTGGGAC 57.187 39.130 0.00 0.00 0.00 4.46
386 506 5.941058 TCAAAAACGCTCTTATATTGTGGGA 59.059 36.000 0.00 0.00 0.00 4.37
387 507 6.027749 GTCAAAAACGCTCTTATATTGTGGG 58.972 40.000 0.00 0.00 0.00 4.61
388 508 6.523201 GTGTCAAAAACGCTCTTATATTGTGG 59.477 38.462 0.00 0.00 35.42 4.17
389 509 7.298122 AGTGTCAAAAACGCTCTTATATTGTG 58.702 34.615 0.00 0.00 45.69 3.33
390 510 7.435068 AGTGTCAAAAACGCTCTTATATTGT 57.565 32.000 0.00 0.00 45.69 2.71
391 511 9.988350 ATTAGTGTCAAAAACGCTCTTATATTG 57.012 29.630 0.00 0.00 45.69 1.90
392 512 9.988350 CATTAGTGTCAAAAACGCTCTTATATT 57.012 29.630 0.00 0.00 45.69 1.28
393 513 9.162764 ACATTAGTGTCAAAAACGCTCTTATAT 57.837 29.630 0.00 0.00 45.69 0.86
394 514 8.542497 ACATTAGTGTCAAAAACGCTCTTATA 57.458 30.769 0.00 0.00 45.69 0.98
395 515 7.435068 ACATTAGTGTCAAAAACGCTCTTAT 57.565 32.000 0.00 0.00 45.69 1.73
396 516 6.854496 ACATTAGTGTCAAAAACGCTCTTA 57.146 33.333 0.00 0.00 45.69 2.10
397 517 5.751243 ACATTAGTGTCAAAAACGCTCTT 57.249 34.783 0.00 0.00 45.69 2.85
398 518 5.989777 ACTACATTAGTGTCAAAAACGCTCT 59.010 36.000 0.00 0.00 45.69 4.09
399 519 6.071463 CACTACATTAGTGTCAAAAACGCTC 58.929 40.000 5.34 0.00 45.69 5.03
426 546 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
427 547 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
428 548 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
429 549 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
430 550 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
431 551 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
432 552 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
433 553 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
434 554 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
435 555 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
436 556 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
437 557 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
438 558 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
439 559 4.154942 GTTACTCCCTCCGTCCCATAATA 58.845 47.826 0.00 0.00 0.00 0.98
440 560 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
441 561 2.292389 TGTTACTCCCTCCGTCCCATAA 60.292 50.000 0.00 0.00 0.00 1.90
442 562 1.288633 TGTTACTCCCTCCGTCCCATA 59.711 52.381 0.00 0.00 0.00 2.74
443 563 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
444 564 0.042131 ATGTTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
445 565 1.201424 AATGTTACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
446 566 3.345508 AAAATGTTACTCCCTCCGTCC 57.654 47.619 0.00 0.00 0.00 4.79
447 567 6.997239 AATAAAAATGTTACTCCCTCCGTC 57.003 37.500 0.00 0.00 0.00 4.79
448 568 7.231925 ACAAAATAAAAATGTTACTCCCTCCGT 59.768 33.333 0.00 0.00 0.00 4.69
449 569 7.599171 ACAAAATAAAAATGTTACTCCCTCCG 58.401 34.615 0.00 0.00 0.00 4.63
450 570 9.772973 AAACAAAATAAAAATGTTACTCCCTCC 57.227 29.630 0.00 0.00 36.33 4.30
511 631 4.184629 GCAGTAGGGAGAACAACTACATG 58.815 47.826 0.00 0.00 39.54 3.21
851 971 4.265893 TCCGCATATTAGCTTTGGTCAAA 58.734 39.130 0.00 0.00 0.00 2.69
852 972 3.876914 CTCCGCATATTAGCTTTGGTCAA 59.123 43.478 0.00 0.00 0.00 3.18
853 973 3.118408 ACTCCGCATATTAGCTTTGGTCA 60.118 43.478 0.00 0.00 0.00 4.02
854 974 3.467803 ACTCCGCATATTAGCTTTGGTC 58.532 45.455 0.00 0.00 0.00 4.02
855 975 3.560636 ACTCCGCATATTAGCTTTGGT 57.439 42.857 0.00 0.00 0.00 3.67
856 976 6.560253 ATTTACTCCGCATATTAGCTTTGG 57.440 37.500 0.00 0.00 0.00 3.28
1131 1278 3.924073 TCGTCTGATGGTATTTTGTCACG 59.076 43.478 0.00 0.00 0.00 4.35
1215 1362 4.407365 TGAATCCAGAAAAACCCTTCTCC 58.593 43.478 0.00 0.00 33.25 3.71
1242 1389 5.648092 AGAAACTCCACCCATTAGAAAATCG 59.352 40.000 0.00 0.00 0.00 3.34
1381 1528 0.244450 ATTGTGCGGGTGAAGCAATG 59.756 50.000 0.00 0.00 46.97 2.82
1440 1587 4.196971 GGAAGTAACGGATAACATTGGCT 58.803 43.478 0.00 0.00 0.00 4.75
1484 1631 3.934457 AAAAAGTAAGGGCGGAATGTG 57.066 42.857 0.00 0.00 0.00 3.21
1512 1660 9.557338 CACTTTCATGAAAAGAAAAATGCAAAA 57.443 25.926 20.82 0.00 46.18 2.44
1513 1661 8.182881 CCACTTTCATGAAAAGAAAAATGCAAA 58.817 29.630 20.82 0.00 46.18 3.68
1514 1662 7.551974 TCCACTTTCATGAAAAGAAAAATGCAA 59.448 29.630 20.82 0.00 46.18 4.08
1515 1663 7.011295 GTCCACTTTCATGAAAAGAAAAATGCA 59.989 33.333 20.82 0.00 46.18 3.96
1596 1744 4.145876 TCTAAAGTTGAACATGCGCTTG 57.854 40.909 20.60 20.60 0.00 4.01
1680 1828 3.063997 ACACAAACAACAGAGAAGAAGCG 59.936 43.478 0.00 0.00 0.00 4.68
1779 1927 2.095212 GCGATAGACATCTACGATGCCA 60.095 50.000 12.19 0.00 39.76 4.92
1809 1957 4.111016 CGGACACCGTCGCTAGCA 62.111 66.667 16.45 0.00 42.73 3.49
1887 2035 2.165030 GAGGGAGTCGTACATTCCGAAA 59.835 50.000 0.00 0.00 35.89 3.46
1941 2089 8.556213 TTACAGAAACAATGGTATGGTTACTC 57.444 34.615 0.00 0.00 28.22 2.59
2064 2289 3.628646 AAGCCCTGCACCCATCGTC 62.629 63.158 0.00 0.00 0.00 4.20
2106 2331 2.048222 ATCATCATACGGCGGCGG 60.048 61.111 35.05 17.87 0.00 6.13
2130 2355 4.338012 TCTTATACTTCACGGACTCACCA 58.662 43.478 0.00 0.00 38.90 4.17
2316 2541 2.533266 ACAGCATCCATACTTAGCCG 57.467 50.000 0.00 0.00 0.00 5.52
2393 2618 4.130118 GGATCATCCACAAGATACACACC 58.870 47.826 0.00 0.00 36.28 4.16
2396 2621 7.116948 CGAAATAGGATCATCCACAAGATACAC 59.883 40.741 6.42 0.00 39.61 2.90
2399 2624 6.701340 CCGAAATAGGATCATCCACAAGATA 58.299 40.000 6.42 0.00 39.61 1.98
2401 2626 4.743651 GCCGAAATAGGATCATCCACAAGA 60.744 45.833 6.42 0.00 39.61 3.02
2402 2627 3.499918 GCCGAAATAGGATCATCCACAAG 59.500 47.826 6.42 0.00 39.61 3.16
2403 2628 3.476552 GCCGAAATAGGATCATCCACAA 58.523 45.455 6.42 0.00 39.61 3.33
2407 2632 1.079503 GCGCCGAAATAGGATCATCC 58.920 55.000 0.00 0.00 36.58 3.51
2528 3974 8.409371 CAAACTAGTCTCATACTCTGCTATTCA 58.591 37.037 0.00 0.00 39.80 2.57
2529 3975 7.381139 GCAAACTAGTCTCATACTCTGCTATTC 59.619 40.741 0.00 0.00 39.80 1.75
2531 3977 6.322456 TGCAAACTAGTCTCATACTCTGCTAT 59.678 38.462 0.00 0.00 39.80 2.97
2557 4003 0.530744 AGCCACATGATGCTGCAAAG 59.469 50.000 6.36 0.00 36.23 2.77
2558 4004 0.528924 GAGCCACATGATGCTGCAAA 59.471 50.000 16.42 0.00 38.11 3.68
2559 4005 0.323087 AGAGCCACATGATGCTGCAA 60.323 50.000 16.42 0.00 38.11 4.08
2561 4007 1.332997 GTTAGAGCCACATGATGCTGC 59.667 52.381 16.42 9.38 38.11 5.25
2562 4008 1.596260 CGTTAGAGCCACATGATGCTG 59.404 52.381 16.42 0.00 38.11 4.41
2563 4009 1.473965 CCGTTAGAGCCACATGATGCT 60.474 52.381 12.41 12.41 41.42 3.79
2565 4011 1.935873 CACCGTTAGAGCCACATGATG 59.064 52.381 0.00 0.00 0.00 3.07
2566 4012 1.831106 TCACCGTTAGAGCCACATGAT 59.169 47.619 0.00 0.00 0.00 2.45
2567 4013 1.262417 TCACCGTTAGAGCCACATGA 58.738 50.000 0.00 0.00 0.00 3.07
2568 4014 1.935873 CATCACCGTTAGAGCCACATG 59.064 52.381 0.00 0.00 0.00 3.21
2569 4015 1.134401 CCATCACCGTTAGAGCCACAT 60.134 52.381 0.00 0.00 0.00 3.21
2570 4016 0.249120 CCATCACCGTTAGAGCCACA 59.751 55.000 0.00 0.00 0.00 4.17
2571 4017 0.535335 TCCATCACCGTTAGAGCCAC 59.465 55.000 0.00 0.00 0.00 5.01
2616 4063 8.795786 TTTGTTATTTCTGAACCAAATCTTCG 57.204 30.769 0.00 0.00 0.00 3.79
2631 4078 8.458843 TCAATAGCTTACTGGCTTTGTTATTTC 58.541 33.333 0.00 0.00 42.97 2.17
2673 4120 6.310941 TGAAGAACTGGAATTGGATTTGGTA 58.689 36.000 0.00 0.00 0.00 3.25
2698 4145 6.926272 GGAGAACAGATGACTGATACCAATAC 59.074 42.308 0.00 0.00 46.03 1.89
2726 4173 0.249120 CAGATGCCCGGTACAGTCAA 59.751 55.000 0.00 0.00 0.00 3.18
2728 4175 0.249398 AACAGATGCCCGGTACAGTC 59.751 55.000 0.00 0.00 0.00 3.51
2759 4206 4.122046 AGTGTTTGACCGGTACAGTTAAC 58.878 43.478 7.34 9.66 0.00 2.01
2802 4249 8.040727 ACAGTTTTATTCAGCTTTCAAAAAGGT 58.959 29.630 0.00 0.00 0.00 3.50
2978 4427 4.627467 AGATATCTGTTTCAGTGTCAACGC 59.373 41.667 3.89 0.00 32.61 4.84
2985 4434 6.537566 CCGTTTCAAGATATCTGTTTCAGTG 58.462 40.000 5.86 0.00 32.61 3.66


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

AutoCloner maintained by Alex Coulton.