Multiple sequence alignment - TraesCS1D01G221800

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 TraesCS1D01G221800 chr1D 100.000 3860 0 0 1 3860 309583165 309587024 0.000000e+00 7129.0
1 TraesCS1D01G221800 chr1A 93.484 1765 66 19 530 2265 389128942 389130686 0.000000e+00 2577.0
2 TraesCS1D01G221800 chr1A 95.212 898 34 3 2430 3321 389130967 389131861 0.000000e+00 1411.0
3 TraesCS1D01G221800 chr1A 93.110 508 35 0 3353 3860 389132362 389132869 0.000000e+00 745.0
4 TraesCS1D01G221800 chr1B 92.965 1720 73 18 1 1693 419401389 419403087 0.000000e+00 2462.0
5 TraesCS1D01G221800 chr1B 97.028 673 16 1 2430 3098 419404094 419404766 0.000000e+00 1129.0
6 TraesCS1D01G221800 chr1B 96.010 401 14 1 1696 2094 419403210 419403610 0.000000e+00 651.0
7 TraesCS1D01G221800 chr1B 87.319 552 51 11 3085 3624 419411663 419412207 7.090000e-172 614.0
8 TraesCS1D01G221800 chr1B 92.353 170 12 1 2087 2255 419403633 419403802 1.390000e-59 241.0
9 TraesCS1D01G221800 chr1B 96.970 33 1 0 2219 2251 61077771 61077739 5.390000e-04 56.5
10 TraesCS1D01G221800 chr3A 85.988 521 69 4 1 519 174277247 174277765 4.360000e-154 555.0
11 TraesCS1D01G221800 chr2D 85.171 526 73 5 1 524 451028688 451029210 5.680000e-148 534.0
12 TraesCS1D01G221800 chr7D 84.486 535 79 4 1 532 41996306 41996839 3.420000e-145 525.0
13 TraesCS1D01G221800 chr5D 84.877 529 68 5 1 522 172256546 172257069 1.230000e-144 523.0
14 TraesCS1D01G221800 chr5D 85.259 502 66 6 3 501 447553210 447553706 9.570000e-141 510.0
15 TraesCS1D01G221800 chr5D 84.280 528 71 7 1 522 9289547 9289026 4.450000e-139 505.0
16 TraesCS1D01G221800 chr5B 84.261 521 80 2 6 525 489470382 489469863 1.240000e-139 507.0
17 TraesCS1D01G221800 chr3B 84.023 532 78 6 1 529 21188065 21187538 4.450000e-139 505.0
18 TraesCS1D01G221800 chr3B 83.681 527 78 8 1 524 420217848 420217327 1.250000e-134 490.0


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 TraesCS1D01G221800 chr1D 309583165 309587024 3859 False 7129.000000 7129 100.000000 1 3860 1 chr1D.!!$F1 3859
1 TraesCS1D01G221800 chr1A 389128942 389132869 3927 False 1577.666667 2577 93.935333 530 3860 3 chr1A.!!$F1 3330
2 TraesCS1D01G221800 chr1B 419401389 419404766 3377 False 1120.750000 2462 94.589000 1 3098 4 chr1B.!!$F2 3097
3 TraesCS1D01G221800 chr1B 419411663 419412207 544 False 614.000000 614 87.319000 3085 3624 1 chr1B.!!$F1 539
4 TraesCS1D01G221800 chr3A 174277247 174277765 518 False 555.000000 555 85.988000 1 519 1 chr3A.!!$F1 518
5 TraesCS1D01G221800 chr2D 451028688 451029210 522 False 534.000000 534 85.171000 1 524 1 chr2D.!!$F1 523
6 TraesCS1D01G221800 chr7D 41996306 41996839 533 False 525.000000 525 84.486000 1 532 1 chr7D.!!$F1 531
7 TraesCS1D01G221800 chr5D 172256546 172257069 523 False 523.000000 523 84.877000 1 522 1 chr5D.!!$F1 521
8 TraesCS1D01G221800 chr5D 9289026 9289547 521 True 505.000000 505 84.280000 1 522 1 chr5D.!!$R1 521
9 TraesCS1D01G221800 chr5B 489469863 489470382 519 True 507.000000 507 84.261000 6 525 1 chr5B.!!$R1 519
10 TraesCS1D01G221800 chr3B 21187538 21188065 527 True 505.000000 505 84.023000 1 529 1 chr3B.!!$R1 528
11 TraesCS1D01G221800 chr3B 420217327 420217848 521 True 490.000000 490 83.681000 1 524 1 chr3B.!!$R2 523

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
871 902 0.249955 TCATCATTCGCAGTGGAGCA 59.750 50.0 0.0 0.0 0.0 4.26 F
1508 1558 0.036388 TCGGTTCTCATGCTTGACCC 60.036 55.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2499 0.618981 AAAAGAGGATGACCCCCGTC 59.381 55.0 0.0 0.0 39.66 4.79 R
3270 3699 1.027357 AGCAAATCATTAGCCAGCCG 58.973 50.0 0.0 0.0 0.00 5.52 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
50 52 3.889044 TCGCAGCGGACGGATCTC 61.889 66.667 16.42 0.00 0.00 2.75
275 290 1.207329 GTGACTAGGGTTTGCTCCGAT 59.793 52.381 0.00 0.00 0.00 4.18
302 317 3.581332 GGATGGGGACGAATATAAGTGGA 59.419 47.826 0.00 0.00 0.00 4.02
314 329 2.741878 TAAGTGGAGTCGGGTGGGCT 62.742 60.000 0.00 0.00 0.00 5.19
426 444 1.247567 CATTTGAGGCCCGTTTGAGT 58.752 50.000 0.00 0.00 0.00 3.41
497 517 1.227176 GGACGTATGAGGCGGGTTC 60.227 63.158 0.00 0.00 0.00 3.62
871 902 0.249955 TCATCATTCGCAGTGGAGCA 59.750 50.000 0.00 0.00 0.00 4.26
1467 1517 4.612412 GGCAACCCGGTCACGTCA 62.612 66.667 0.00 0.00 38.78 4.35
1508 1558 0.036388 TCGGTTCTCATGCTTGACCC 60.036 55.000 0.00 0.00 0.00 4.46
1608 1659 6.073003 GCTTAGAGAACACACTTGCAAATAGT 60.073 38.462 0.00 0.00 0.00 2.12
1611 1662 6.525629 AGAGAACACACTTGCAAATAGTAGT 58.474 36.000 0.00 0.00 0.00 2.73
1612 1663 7.667557 AGAGAACACACTTGCAAATAGTAGTA 58.332 34.615 0.00 0.00 0.00 1.82
1613 1664 7.599245 AGAGAACACACTTGCAAATAGTAGTAC 59.401 37.037 0.00 0.00 0.00 2.73
1702 1884 3.205815 TTTTTGCAGGCACAGAGGT 57.794 47.368 0.00 0.00 0.00 3.85
1771 1955 3.118629 GCTAGCTAGGCCATGTATATGCA 60.119 47.826 22.10 0.00 32.79 3.96
1776 1960 4.095483 GCTAGGCCATGTATATGCATGAAC 59.905 45.833 28.94 21.31 46.65 3.18
1980 2168 7.220599 ACACATCAAAAATCTCAAAAACGTG 57.779 32.000 0.00 0.00 0.00 4.49
2088 2276 8.840321 CAATGTGGATAAACTAAACCCTATCAG 58.160 37.037 0.00 0.00 0.00 2.90
2173 2392 1.135257 CCAGTGCAAACGAAAACACCA 60.135 47.619 0.00 0.00 33.46 4.17
2199 2419 4.434713 AATTTGGACCGTGCTACAAATC 57.565 40.909 0.00 0.00 41.24 2.17
2200 2420 2.552599 TTGGACCGTGCTACAAATCA 57.447 45.000 0.00 0.00 0.00 2.57
2213 2433 7.185453 GTGCTACAAATCAGATGTCAGATTTC 58.815 38.462 9.55 2.13 39.17 2.17
2223 2443 7.397221 TCAGATGTCAGATTTCTAAACATGGT 58.603 34.615 10.73 0.00 34.01 3.55
2243 2463 9.001542 ACATGGTAAATCAAATGTTTTTCATGG 57.998 29.630 21.01 12.47 36.81 3.66
2250 2470 8.804688 AATCAAATGTTTTTCATGGCAAATTG 57.195 26.923 0.00 0.00 36.81 2.32
2282 2502 1.865340 CATCATGTGATGCAGAGGACG 59.135 52.381 9.81 0.00 44.44 4.79
2283 2503 0.176449 TCATGTGATGCAGAGGACGG 59.824 55.000 0.00 0.00 0.00 4.79
2284 2504 0.812811 CATGTGATGCAGAGGACGGG 60.813 60.000 0.00 0.00 0.00 5.28
2285 2505 1.976132 ATGTGATGCAGAGGACGGGG 61.976 60.000 0.00 0.00 0.00 5.73
2286 2506 3.083349 TGATGCAGAGGACGGGGG 61.083 66.667 0.00 0.00 0.00 5.40
2287 2507 3.083997 GATGCAGAGGACGGGGGT 61.084 66.667 0.00 0.00 0.00 4.95
2288 2508 3.083997 ATGCAGAGGACGGGGGTC 61.084 66.667 0.00 0.00 0.00 4.46
2289 2509 3.924013 ATGCAGAGGACGGGGGTCA 62.924 63.158 0.00 0.00 0.00 4.02
2290 2510 3.083997 GCAGAGGACGGGGGTCAT 61.084 66.667 0.00 0.00 0.00 3.06
2291 2511 3.095347 GCAGAGGACGGGGGTCATC 62.095 68.421 1.00 1.00 34.73 2.92
2292 2512 2.041819 AGAGGACGGGGGTCATCC 60.042 66.667 5.39 0.00 35.04 3.51
2293 2513 2.041819 GAGGACGGGGGTCATCCT 60.042 66.667 0.00 0.00 45.84 3.24
2294 2514 2.041819 AGGACGGGGGTCATCCTC 60.042 66.667 0.00 0.00 38.55 3.71
2295 2515 2.041819 GGACGGGGGTCATCCTCT 60.042 66.667 0.00 0.00 33.94 3.69
2296 2516 1.689582 GGACGGGGGTCATCCTCTT 60.690 63.158 0.00 0.00 33.94 2.85
2297 2517 1.272554 GGACGGGGGTCATCCTCTTT 61.273 60.000 0.00 0.00 33.94 2.52
2298 2518 0.618981 GACGGGGGTCATCCTCTTTT 59.381 55.000 0.00 0.00 33.94 2.27
2299 2519 1.004394 GACGGGGGTCATCCTCTTTTT 59.996 52.381 0.00 0.00 33.94 1.94
2328 2548 5.824904 AAAATACACATCATGAGCCTGTC 57.175 39.130 0.09 0.00 0.00 3.51
2329 2549 4.492494 AATACACATCATGAGCCTGTCA 57.508 40.909 0.09 0.00 40.38 3.58
2330 2550 2.865119 ACACATCATGAGCCTGTCAA 57.135 45.000 0.09 0.00 39.19 3.18
2331 2551 3.361281 ACACATCATGAGCCTGTCAAT 57.639 42.857 0.09 0.00 39.19 2.57
2332 2552 3.693807 ACACATCATGAGCCTGTCAATT 58.306 40.909 0.09 0.00 39.19 2.32
2333 2553 3.693085 ACACATCATGAGCCTGTCAATTC 59.307 43.478 0.09 0.00 39.19 2.17
2334 2554 3.066342 CACATCATGAGCCTGTCAATTCC 59.934 47.826 0.09 0.00 39.19 3.01
2335 2555 3.284617 CATCATGAGCCTGTCAATTCCA 58.715 45.455 0.09 0.00 39.19 3.53
2336 2556 3.657398 TCATGAGCCTGTCAATTCCAT 57.343 42.857 0.00 0.00 39.19 3.41
2337 2557 3.972133 TCATGAGCCTGTCAATTCCATT 58.028 40.909 0.00 0.00 39.19 3.16
2338 2558 4.346730 TCATGAGCCTGTCAATTCCATTT 58.653 39.130 0.00 0.00 39.19 2.32
2339 2559 5.508567 TCATGAGCCTGTCAATTCCATTTA 58.491 37.500 0.00 0.00 39.19 1.40
2340 2560 5.591472 TCATGAGCCTGTCAATTCCATTTAG 59.409 40.000 0.00 0.00 39.19 1.85
2341 2561 3.696051 TGAGCCTGTCAATTCCATTTAGC 59.304 43.478 0.00 0.00 29.64 3.09
2349 2569 6.164876 TGTCAATTCCATTTAGCAAACATGG 58.835 36.000 0.00 0.00 39.17 3.66
2359 2579 2.250031 AGCAAACATGGCAAATCCTGA 58.750 42.857 0.00 0.00 35.26 3.86
2361 2581 2.598589 CAAACATGGCAAATCCTGACG 58.401 47.619 0.00 0.00 34.74 4.35
2363 2583 1.909700 ACATGGCAAATCCTGACGTT 58.090 45.000 0.00 0.00 34.74 3.99
2397 2617 2.754552 GCCAGGATTTGTCATGCTTGTA 59.245 45.455 0.00 0.00 0.00 2.41
2398 2618 3.193267 GCCAGGATTTGTCATGCTTGTAA 59.807 43.478 0.00 0.00 0.00 2.41
2399 2619 4.142093 GCCAGGATTTGTCATGCTTGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
2400 2620 5.345702 CCAGGATTTGTCATGCTTGTAATG 58.654 41.667 0.00 0.00 0.00 1.90
2401 2621 4.802039 CAGGATTTGTCATGCTTGTAATGC 59.198 41.667 0.00 4.47 37.54 3.56
2402 2622 4.114794 GGATTTGTCATGCTTGTAATGCC 58.885 43.478 0.00 0.00 35.91 4.40
2403 2623 4.381825 GGATTTGTCATGCTTGTAATGCCA 60.382 41.667 0.00 0.00 35.91 4.92
2404 2624 3.853831 TTGTCATGCTTGTAATGCCAG 57.146 42.857 0.00 0.00 35.91 4.85
2411 2673 3.164268 TGCTTGTAATGCCAGGATTTGT 58.836 40.909 0.00 0.00 35.91 2.83
2419 2681 1.546923 TGCCAGGATTTGTCATGCTTG 59.453 47.619 0.00 0.00 0.00 4.01
2420 2682 1.738030 GCCAGGATTTGTCATGCTTGC 60.738 52.381 0.00 0.00 0.00 4.01
2421 2683 1.822990 CCAGGATTTGTCATGCTTGCT 59.177 47.619 0.00 0.00 0.00 3.91
2422 2684 2.159282 CCAGGATTTGTCATGCTTGCTC 60.159 50.000 0.00 0.00 0.00 4.26
2423 2685 2.490509 CAGGATTTGTCATGCTTGCTCA 59.509 45.455 0.00 0.00 0.00 4.26
2425 2687 3.575256 AGGATTTGTCATGCTTGCTCAAA 59.425 39.130 17.57 17.57 34.01 2.69
2426 2688 3.924686 GGATTTGTCATGCTTGCTCAAAG 59.075 43.478 18.94 0.00 39.07 2.77
2427 2689 3.374220 TTTGTCATGCTTGCTCAAAGG 57.626 42.857 13.99 0.00 36.30 3.11
2428 2690 2.275134 TGTCATGCTTGCTCAAAGGA 57.725 45.000 0.00 0.00 40.91 3.36
2475 2886 6.371809 TCACGTATTAATTTTCAGATGCCC 57.628 37.500 0.00 0.00 0.00 5.36
2975 3396 1.374343 CTGCCATGCATGAGTCGCTT 61.374 55.000 28.31 0.00 38.13 4.68
3166 3594 3.868757 TGTGACCATCTACTTTCTCCG 57.131 47.619 0.00 0.00 0.00 4.63
3184 3612 6.795144 TCTCCGTCCCAAAATAAGTGTATA 57.205 37.500 0.00 0.00 0.00 1.47
3185 3613 7.369551 TCTCCGTCCCAAAATAAGTGTATAT 57.630 36.000 0.00 0.00 0.00 0.86
3217 3645 7.972832 AACATAACTTATTTTGTGACGGAGA 57.027 32.000 0.00 0.00 31.29 3.71
3234 3663 2.229302 GGAGAGAGTATATGCCACCGTC 59.771 54.545 0.00 0.00 0.00 4.79
3249 3678 3.071602 CCACCGTCTCCCTGATTTCATAT 59.928 47.826 0.00 0.00 0.00 1.78
3252 3681 6.467677 CACCGTCTCCCTGATTTCATATTAT 58.532 40.000 0.00 0.00 0.00 1.28
3270 3699 5.941948 ATTATGGCTGCCTAATTTACGAC 57.058 39.130 21.03 0.00 0.00 4.34
3274 3703 1.935933 CTGCCTAATTTACGACGGCT 58.064 50.000 0.00 0.00 41.25 5.52
3292 3721 3.676873 CGGCTGGCTAATGATTTGCTTTT 60.677 43.478 11.08 0.00 0.00 2.27
3342 3773 7.352739 TCTTCTTAAAGCTCGTCACATTTTTC 58.647 34.615 0.00 0.00 32.18 2.29
3343 3774 5.997385 TCTTAAAGCTCGTCACATTTTTCC 58.003 37.500 0.00 0.00 0.00 3.13
3345 3776 1.534729 AGCTCGTCACATTTTTCCCC 58.465 50.000 0.00 0.00 0.00 4.81
3354 4252 3.951037 TCACATTTTTCCCCCATATGACG 59.049 43.478 3.65 0.00 0.00 4.35
3368 4266 1.821216 ATGACGCGAAAATGGGACTT 58.179 45.000 15.93 0.00 0.00 3.01
3373 4271 1.665735 CGCGAAAATGGGACTTGGTTG 60.666 52.381 0.00 0.00 0.00 3.77
3376 4274 2.029110 CGAAAATGGGACTTGGTTGCAT 60.029 45.455 0.00 0.00 0.00 3.96
3385 4283 3.430098 GGACTTGGTTGCATTGTCAAACA 60.430 43.478 7.25 7.25 41.44 2.83
3396 4294 5.632764 TGCATTGTCAAACAATAATGGAACG 59.367 36.000 5.08 0.00 46.22 3.95
3414 4312 7.681939 TGGAACGAAAAGATAGCAAAATAGT 57.318 32.000 0.00 0.00 0.00 2.12
3624 4524 7.507733 AGATCATACTCCATGCAAGAAAATC 57.492 36.000 0.00 0.00 34.35 2.17
3627 4527 5.525012 TCATACTCCATGCAAGAAAATCTCG 59.475 40.000 0.00 0.00 34.35 4.04
3658 4558 3.513119 TCCAAAATCATTTCCATCGGCAA 59.487 39.130 0.00 0.00 0.00 4.52
3672 4572 4.431809 CATCGGCAATTTCCAAAAGCATA 58.568 39.130 0.00 0.00 0.00 3.14
3673 4573 4.527509 TCGGCAATTTCCAAAAGCATAA 57.472 36.364 0.00 0.00 0.00 1.90
3682 4582 9.868389 CAATTTCCAAAAGCATAAGTTTTCTTC 57.132 29.630 0.00 0.00 40.91 2.87
3714 4614 2.774234 TCATCATTTCTGACCCCCTCTC 59.226 50.000 0.00 0.00 33.22 3.20
3730 4630 4.387437 CCCCTCTCTAACTTCTCCAGATCT 60.387 50.000 0.00 0.00 0.00 2.75
3741 4641 2.063979 CCAGATCTACCCGCCACCA 61.064 63.158 0.00 0.00 0.00 4.17
3763 4663 1.536662 ACAGAGTTCGCCCCCTTCT 60.537 57.895 0.00 0.00 0.00 2.85
3765 4665 1.079438 AGAGTTCGCCCCCTTCTCT 59.921 57.895 0.00 0.00 0.00 3.10
3773 4673 1.835693 CCCCCTTCTCTCTCCATGC 59.164 63.158 0.00 0.00 0.00 4.06
3778 4678 1.072015 CCTTCTCTCTCCATGCCCATC 59.928 57.143 0.00 0.00 0.00 3.51
3784 4684 2.281002 TCCATGCCCATCATCGCG 60.281 61.111 0.00 0.00 31.79 5.87
3788 4688 1.893808 ATGCCCATCATCGCGAACC 60.894 57.895 15.24 0.00 0.00 3.62
3839 4739 2.173519 CCTTGCTCCAACACCATTCAT 58.826 47.619 0.00 0.00 0.00 2.57
3854 4754 5.977725 CACCATTCATTCATCTTCAGATTGC 59.022 40.000 0.00 0.00 31.21 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 103 3.171535 TTGGAGGGGGCAATGGCAA 62.172 57.895 9.51 0.00 43.71 4.52
199 208 1.600916 GCTCACCTCCAGCGGTTTT 60.601 57.895 0.00 0.00 34.29 2.43
275 290 0.757561 TATTCGTCCCCATCCGCTCA 60.758 55.000 0.00 0.00 0.00 4.26
302 317 1.995626 AATGCTAGCCCACCCGACT 60.996 57.895 13.29 0.00 0.00 4.18
314 329 4.169696 CGGACCCGGCCAATGCTA 62.170 66.667 2.24 0.00 37.74 3.49
353 368 2.383521 ATATGGGGCAGATATGGGGT 57.616 50.000 0.00 0.00 0.00 4.95
426 444 2.312722 TTTTTGACCCAGACGAACGA 57.687 45.000 0.14 0.00 0.00 3.85
497 517 0.820074 ATCTACAGCCGGACCTCTCG 60.820 60.000 5.05 0.00 0.00 4.04
536 556 3.485463 TGGTCTTGTTGTAAGGGTGAG 57.515 47.619 0.00 0.00 0.00 3.51
871 902 4.221262 TGCTAATTTGCTTCCATCAGCTTT 59.779 37.500 12.99 0.00 40.79 3.51
968 1009 1.671742 CTCCACACACTAAGCCGGT 59.328 57.895 1.90 0.00 0.00 5.28
1074 1124 4.106925 CCTGCAGCACCTCTCCCC 62.107 72.222 8.66 0.00 0.00 4.81
1315 1365 2.281070 CTGCAGTTGCTCGGTGGT 60.281 61.111 5.25 0.00 42.66 4.16
1404 1454 1.803943 GACGACATCTCGGCTCAGT 59.196 57.895 0.00 0.00 45.37 3.41
1467 1517 2.434884 CTCACGATTGTGGCGCCT 60.435 61.111 29.70 6.86 46.42 5.52
1611 1662 8.939929 ACGCTACGCAGAAATATAGTAATAGTA 58.060 33.333 0.00 0.00 0.00 1.82
1612 1663 7.749570 CACGCTACGCAGAAATATAGTAATAGT 59.250 37.037 0.00 0.00 0.00 2.12
1613 1664 7.253354 GCACGCTACGCAGAAATATAGTAATAG 60.253 40.741 0.00 0.00 0.00 1.73
1688 1747 0.895530 GTACTACCTCTGTGCCTGCA 59.104 55.000 0.00 0.00 0.00 4.41
1689 1748 1.187087 AGTACTACCTCTGTGCCTGC 58.813 55.000 0.00 0.00 0.00 4.85
1690 1749 5.599999 AATTAGTACTACCTCTGTGCCTG 57.400 43.478 0.91 0.00 0.00 4.85
1691 1750 6.321690 CACTAATTAGTACTACCTCTGTGCCT 59.678 42.308 17.62 0.00 34.13 4.75
1692 1751 6.461231 CCACTAATTAGTACTACCTCTGTGCC 60.461 46.154 17.62 0.00 34.13 5.01
1693 1752 6.096564 ACCACTAATTAGTACTACCTCTGTGC 59.903 42.308 17.62 0.00 34.13 4.57
1694 1753 7.466996 CGACCACTAATTAGTACTACCTCTGTG 60.467 44.444 17.62 8.31 34.13 3.66
1697 1879 6.893583 TCGACCACTAATTAGTACTACCTCT 58.106 40.000 17.62 0.00 34.13 3.69
1702 1884 9.618890 AGTGTAATCGACCACTAATTAGTACTA 57.381 33.333 17.62 0.00 40.03 1.82
1771 1955 8.682936 AGATAAGACAAGACAAAACTGTTCAT 57.317 30.769 0.00 0.00 0.00 2.57
1776 1960 7.872993 TGGTAGAGATAAGACAAGACAAAACTG 59.127 37.037 0.00 0.00 0.00 3.16
1980 2168 4.020128 AGGGTGGAAAAGTCAGTGATAGAC 60.020 45.833 0.00 0.00 36.26 2.59
2094 2282 7.667043 TCGACAATTAGAATGTAAAGCTTGT 57.333 32.000 0.00 0.00 0.00 3.16
2173 2392 4.391155 TGTAGCACGGTCCAAATTAAACT 58.609 39.130 0.00 0.00 0.00 2.66
2199 2419 7.621428 ACCATGTTTAGAAATCTGACATCTG 57.379 36.000 9.79 7.91 34.24 2.90
2200 2420 9.739276 TTTACCATGTTTAGAAATCTGACATCT 57.261 29.630 9.79 0.49 34.24 2.90
2232 2452 2.032204 GCGCAATTTGCCATGAAAAACA 60.032 40.909 15.45 0.00 41.12 2.83
2243 2463 1.736249 GCTCACGATGCGCAATTTGC 61.736 55.000 17.11 11.42 40.69 3.68
2250 2470 1.082951 CATGATGCTCACGATGCGC 60.083 57.895 0.00 0.00 0.00 6.09
2265 2485 0.812811 CCCGTCCTCTGCATCACATG 60.813 60.000 0.00 0.00 0.00 3.21
2266 2486 1.524002 CCCGTCCTCTGCATCACAT 59.476 57.895 0.00 0.00 0.00 3.21
2267 2487 2.659063 CCCCGTCCTCTGCATCACA 61.659 63.158 0.00 0.00 0.00 3.58
2268 2488 2.187946 CCCCGTCCTCTGCATCAC 59.812 66.667 0.00 0.00 0.00 3.06
2269 2489 3.083349 CCCCCGTCCTCTGCATCA 61.083 66.667 0.00 0.00 0.00 3.07
2270 2490 3.083997 ACCCCCGTCCTCTGCATC 61.084 66.667 0.00 0.00 0.00 3.91
2271 2491 3.083997 GACCCCCGTCCTCTGCAT 61.084 66.667 0.00 0.00 32.40 3.96
2272 2492 3.924013 ATGACCCCCGTCCTCTGCA 62.924 63.158 0.00 0.00 38.32 4.41
2274 2494 2.435693 GGATGACCCCCGTCCTCTG 61.436 68.421 0.00 0.00 45.58 3.35
2279 2499 0.618981 AAAAGAGGATGACCCCCGTC 59.381 55.000 0.00 0.00 39.66 4.79
2280 2500 1.073098 AAAAAGAGGATGACCCCCGT 58.927 50.000 0.00 0.00 36.73 5.28
2281 2501 3.978876 AAAAAGAGGATGACCCCCG 57.021 52.632 0.00 0.00 36.73 5.73
2305 2525 5.711506 TGACAGGCTCATGATGTGTATTTTT 59.288 36.000 5.18 0.00 0.00 1.94
2306 2526 5.255687 TGACAGGCTCATGATGTGTATTTT 58.744 37.500 5.18 0.00 0.00 1.82
2307 2527 4.847198 TGACAGGCTCATGATGTGTATTT 58.153 39.130 5.18 0.00 0.00 1.40
2308 2528 4.492494 TGACAGGCTCATGATGTGTATT 57.508 40.909 5.18 0.00 0.00 1.89
2309 2529 4.492494 TTGACAGGCTCATGATGTGTAT 57.508 40.909 5.18 0.00 0.00 2.29
2310 2530 3.979101 TTGACAGGCTCATGATGTGTA 57.021 42.857 5.18 0.00 0.00 2.90
2311 2531 2.865119 TTGACAGGCTCATGATGTGT 57.135 45.000 5.18 4.98 0.00 3.72
2312 2532 3.066342 GGAATTGACAGGCTCATGATGTG 59.934 47.826 5.18 1.85 0.00 3.21
2313 2533 3.285484 GGAATTGACAGGCTCATGATGT 58.715 45.455 0.00 0.00 0.00 3.06
2314 2534 3.284617 TGGAATTGACAGGCTCATGATG 58.715 45.455 0.00 0.00 0.00 3.07
2315 2535 3.657398 TGGAATTGACAGGCTCATGAT 57.343 42.857 0.00 0.00 0.00 2.45
2316 2536 3.657398 ATGGAATTGACAGGCTCATGA 57.343 42.857 0.00 0.00 0.00 3.07
2317 2537 4.730949 AAATGGAATTGACAGGCTCATG 57.269 40.909 0.00 0.00 36.10 3.07
2318 2538 4.340381 GCTAAATGGAATTGACAGGCTCAT 59.660 41.667 0.00 0.00 36.10 2.90
2319 2539 3.696051 GCTAAATGGAATTGACAGGCTCA 59.304 43.478 0.00 0.00 36.10 4.26
2320 2540 3.696051 TGCTAAATGGAATTGACAGGCTC 59.304 43.478 0.00 0.00 36.10 4.70
2321 2541 3.700538 TGCTAAATGGAATTGACAGGCT 58.299 40.909 0.00 0.00 36.10 4.58
2322 2542 4.454728 TTGCTAAATGGAATTGACAGGC 57.545 40.909 0.00 0.00 36.10 4.85
2323 2543 5.782047 TGTTTGCTAAATGGAATTGACAGG 58.218 37.500 0.00 0.00 36.10 4.00
2324 2544 6.311935 CCATGTTTGCTAAATGGAATTGACAG 59.688 38.462 12.97 0.00 43.00 3.51
2325 2545 6.164876 CCATGTTTGCTAAATGGAATTGACA 58.835 36.000 12.97 0.00 43.00 3.58
2326 2546 5.063817 GCCATGTTTGCTAAATGGAATTGAC 59.936 40.000 18.64 4.26 43.00 3.18
2327 2547 5.177326 GCCATGTTTGCTAAATGGAATTGA 58.823 37.500 18.64 0.00 43.00 2.57
2328 2548 4.936411 TGCCATGTTTGCTAAATGGAATTG 59.064 37.500 18.64 1.84 43.00 2.32
2329 2549 5.163281 TGCCATGTTTGCTAAATGGAATT 57.837 34.783 18.64 0.00 43.00 2.17
2330 2550 4.822685 TGCCATGTTTGCTAAATGGAAT 57.177 36.364 18.64 0.00 43.00 3.01
2331 2551 4.613925 TTGCCATGTTTGCTAAATGGAA 57.386 36.364 18.64 10.50 43.00 3.53
2332 2552 4.613925 TTTGCCATGTTTGCTAAATGGA 57.386 36.364 18.64 7.56 43.00 3.41
2333 2553 4.333372 GGATTTGCCATGTTTGCTAAATGG 59.667 41.667 13.55 13.55 43.18 3.16
2334 2554 5.064198 CAGGATTTGCCATGTTTGCTAAATG 59.936 40.000 0.00 0.00 40.02 2.32
2335 2555 5.046448 TCAGGATTTGCCATGTTTGCTAAAT 60.046 36.000 0.00 0.00 40.02 1.40
2336 2556 4.282957 TCAGGATTTGCCATGTTTGCTAAA 59.717 37.500 0.00 0.00 40.02 1.85
2337 2557 3.831333 TCAGGATTTGCCATGTTTGCTAA 59.169 39.130 0.00 0.00 40.02 3.09
2338 2558 3.193267 GTCAGGATTTGCCATGTTTGCTA 59.807 43.478 0.00 0.00 40.02 3.49
2339 2559 2.028748 GTCAGGATTTGCCATGTTTGCT 60.029 45.455 0.00 0.00 40.02 3.91
2340 2560 2.340337 GTCAGGATTTGCCATGTTTGC 58.660 47.619 0.00 0.00 40.02 3.68
2341 2561 2.030007 ACGTCAGGATTTGCCATGTTTG 60.030 45.455 0.00 0.00 40.02 2.93
2384 2604 2.492881 CCTGGCATTACAAGCATGACAA 59.507 45.455 0.00 0.00 39.26 3.18
2387 2607 2.804986 TCCTGGCATTACAAGCATGA 57.195 45.000 0.00 0.00 0.00 3.07
2400 2620 1.738030 GCAAGCATGACAAATCCTGGC 60.738 52.381 0.00 0.00 0.00 4.85
2401 2621 1.822990 AGCAAGCATGACAAATCCTGG 59.177 47.619 0.00 0.00 0.00 4.45
2402 2622 2.490509 TGAGCAAGCATGACAAATCCTG 59.509 45.455 0.00 0.00 0.00 3.86
2403 2623 2.799017 TGAGCAAGCATGACAAATCCT 58.201 42.857 0.00 0.00 0.00 3.24
2404 2624 3.581024 TTGAGCAAGCATGACAAATCC 57.419 42.857 0.00 0.00 0.00 3.01
2411 2673 4.525487 AGAAATTCCTTTGAGCAAGCATGA 59.475 37.500 0.00 0.00 0.00 3.07
2419 2681 5.278218 GGCTATGCTAGAAATTCCTTTGAGC 60.278 44.000 0.00 0.00 33.47 4.26
2420 2682 6.060788 AGGCTATGCTAGAAATTCCTTTGAG 58.939 40.000 0.00 0.00 0.00 3.02
2421 2683 6.006275 AGGCTATGCTAGAAATTCCTTTGA 57.994 37.500 0.00 0.00 0.00 2.69
2422 2684 5.824624 TGAGGCTATGCTAGAAATTCCTTTG 59.175 40.000 0.00 0.00 0.00 2.77
2423 2685 6.006275 TGAGGCTATGCTAGAAATTCCTTT 57.994 37.500 0.00 0.00 0.00 3.11
2425 2687 5.839517 ATGAGGCTATGCTAGAAATTCCT 57.160 39.130 0.00 0.00 0.00 3.36
2426 2688 6.706295 AGTATGAGGCTATGCTAGAAATTCC 58.294 40.000 0.00 0.00 0.00 3.01
2427 2689 8.614469 AAAGTATGAGGCTATGCTAGAAATTC 57.386 34.615 0.00 0.00 0.00 2.17
2428 2690 8.213679 TGAAAGTATGAGGCTATGCTAGAAATT 58.786 33.333 0.00 0.00 0.00 1.82
2475 2886 4.034510 GTCAACATTTCTCTCCCGCAATAG 59.965 45.833 0.00 0.00 0.00 1.73
2492 2903 1.155424 GGCTTCCGTGAACGTCAACA 61.155 55.000 1.75 0.00 37.74 3.33
2896 3313 2.279318 GCTAGCCGCCGTTCTACC 60.279 66.667 2.29 0.00 0.00 3.18
2975 3396 4.858140 CGACGATCTACGAGATAAGCTAGA 59.142 45.833 0.00 0.00 45.77 2.43
3056 3477 6.598753 TCCTGCGCTCTAAATGTTAATTAC 57.401 37.500 9.73 0.00 0.00 1.89
3217 3645 2.240279 GGAGACGGTGGCATATACTCT 58.760 52.381 0.00 0.00 0.00 3.24
3234 3663 5.125097 GCAGCCATAATATGAAATCAGGGAG 59.875 44.000 1.10 0.00 0.00 4.30
3249 3678 3.805422 CGTCGTAAATTAGGCAGCCATAA 59.195 43.478 15.80 9.83 0.00 1.90
3252 3681 1.647346 CGTCGTAAATTAGGCAGCCA 58.353 50.000 15.80 0.00 0.00 4.75
3270 3699 1.027357 AGCAAATCATTAGCCAGCCG 58.973 50.000 0.00 0.00 0.00 5.52
3274 3703 4.081531 CCTCCAAAAGCAAATCATTAGCCA 60.082 41.667 0.00 0.00 0.00 4.75
3292 3721 7.790782 AATTGTTTCTTAAAATAGGCCTCCA 57.209 32.000 9.68 0.00 0.00 3.86
3331 3760 4.202010 CGTCATATGGGGGAAAAATGTGAC 60.202 45.833 2.13 0.00 38.40 3.67
3342 3773 1.266718 CATTTTCGCGTCATATGGGGG 59.733 52.381 5.77 4.32 0.00 5.40
3343 3774 1.266718 CCATTTTCGCGTCATATGGGG 59.733 52.381 5.77 0.00 33.66 4.96
3345 3776 2.032030 GTCCCATTTTCGCGTCATATGG 60.032 50.000 18.51 18.51 36.38 2.74
3354 4252 1.934849 GCAACCAAGTCCCATTTTCGC 60.935 52.381 0.00 0.00 0.00 4.70
3376 4274 8.191446 TCTTTTCGTTCCATTATTGTTTGACAA 58.809 29.630 0.00 0.00 42.95 3.18
3396 4294 8.379457 ACGGGATACTATTTTGCTATCTTTTC 57.621 34.615 0.00 0.00 0.00 2.29
3477 4375 4.868171 CGGTTTGTGCTGTTAGCTTAGATA 59.132 41.667 0.00 0.00 42.97 1.98
3624 4524 6.615264 AATGATTTTGGAGATGATCACGAG 57.385 37.500 0.00 0.00 31.94 4.18
3627 4527 7.104043 TGGAAATGATTTTGGAGATGATCAC 57.896 36.000 0.00 0.00 31.94 3.06
3658 4558 8.210265 TGGAAGAAAACTTATGCTTTTGGAAAT 58.790 29.630 0.00 0.00 0.00 2.17
3672 4572 8.912988 TGATGAAACAACTATGGAAGAAAACTT 58.087 29.630 0.00 0.00 0.00 2.66
3673 4573 8.463930 TGATGAAACAACTATGGAAGAAAACT 57.536 30.769 0.00 0.00 0.00 2.66
3682 4582 7.253422 GGTCAGAAATGATGAAACAACTATGG 58.747 38.462 0.00 0.00 0.00 2.74
3714 4614 3.004944 GCGGGTAGATCTGGAGAAGTTAG 59.995 52.174 5.18 0.00 0.00 2.34
3730 4630 2.524640 TGTGACTGGTGGCGGGTA 60.525 61.111 0.00 0.00 0.00 3.69
3741 4641 2.584391 GGGGGCGAACTCTGTGACT 61.584 63.158 0.00 0.00 0.00 3.41
3763 4663 0.683412 CGATGATGGGCATGGAGAGA 59.317 55.000 0.00 0.00 37.34 3.10
3765 4665 1.071987 GCGATGATGGGCATGGAGA 59.928 57.895 0.00 0.00 37.34 3.71
3773 4673 3.640000 GCGGTTCGCGATGATGGG 61.640 66.667 10.88 0.00 44.55 4.00
3784 4684 3.062466 GGGAGGCTTTGGCGGTTC 61.062 66.667 0.00 0.00 39.81 3.62
3788 4688 2.964978 CAAAGGGAGGCTTTGGCG 59.035 61.111 0.00 0.00 37.94 5.69


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

AutoCloner maintained by Alex Coulton.