Multiple sequence alignment - TraesCS7D01G203300

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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 TraesCS7D01G203300 chr7D 100.000 4631 0 0 1 4631 161483527 161478897 0.000000e+00 8552.0
1 TraesCS7D01G203300 chr7D 93.878 98 4 2 3203 3298 185552878 185552781 3.730000e-31 147.0
2 TraesCS7D01G203300 chr7D 91.262 103 8 1 3209 3310 231420157 231420055 6.250000e-29 139.0
3 TraesCS7D01G203300 chr7D 88.000 50 4 1 3792 3841 187081900 187081947 1.800000e-04 58.4
4 TraesCS7D01G203300 chr7B 97.005 2771 69 6 915 3682 123784477 123781718 0.000000e+00 4645.0
5 TraesCS7D01G203300 chr7B 98.535 751 10 1 3666 4416 123781656 123780907 0.000000e+00 1325.0
6 TraesCS7D01G203300 chr7B 89.555 517 33 16 380 881 123784988 123784478 1.820000e-178 636.0
7 TraesCS7D01G203300 chr7B 90.730 356 20 8 1 353 123785404 123785059 3.260000e-126 462.0
8 TraesCS7D01G203300 chr7B 97.340 188 4 1 4415 4601 123780803 123780616 7.480000e-83 318.0
9 TraesCS7D01G203300 chr7B 86.885 122 8 5 2431 2548 680907465 680907582 3.760000e-26 130.0
10 TraesCS7D01G203300 chr7B 100.000 28 0 0 2263 2290 627309872 627309899 8.000000e-03 52.8
11 TraesCS7D01G203300 chr7A 94.065 1112 38 6 893 1992 162774450 162773355 0.000000e+00 1663.0
12 TraesCS7D01G203300 chr7A 90.631 555 43 5 3293 3839 162772432 162771879 0.000000e+00 728.0
13 TraesCS7D01G203300 chr7A 97.051 373 10 1 380 752 162775708 162775337 1.090000e-175 627.0
14 TraesCS7D01G203300 chr7A 89.017 346 22 7 15 353 162776115 162775779 9.270000e-112 414.0
15 TraesCS7D01G203300 chr7A 84.028 432 56 7 2533 2960 162773054 162772632 2.010000e-108 403.0
16 TraesCS7D01G203300 chr7A 91.608 286 21 2 1981 2265 162773336 162773053 4.340000e-105 392.0
17 TraesCS7D01G203300 chr7A 93.793 145 9 0 2290 2434 634932984 634933128 7.800000e-53 219.0
18 TraesCS7D01G203300 chr7A 91.724 145 10 2 3067 3210 162772573 162772430 2.830000e-47 200.0
19 TraesCS7D01G203300 chr7A 92.453 106 5 1 2429 2534 498590283 498590385 1.040000e-31 148.0
20 TraesCS7D01G203300 chr7A 92.079 101 6 2 3200 3298 136806095 136806195 1.740000e-29 141.0
21 TraesCS7D01G203300 chr7A 90.909 66 1 1 770 835 162775285 162775225 2.970000e-12 84.2
22 TraesCS7D01G203300 chr5A 80.699 601 76 21 1602 2182 11945637 11946217 9.210000e-117 431.0
23 TraesCS7D01G203300 chr5A 100.000 30 0 0 3810 3839 427829074 427829103 6.470000e-04 56.5
24 TraesCS7D01G203300 chr5A 100.000 28 0 0 2263 2290 227926529 227926502 8.000000e-03 52.8
25 TraesCS7D01G203300 chr2A 80.399 602 76 23 1602 2182 4023832 4024412 1.990000e-113 420.0
26 TraesCS7D01G203300 chr2A 93.878 98 5 1 3208 3304 498099530 498099433 3.730000e-31 147.0
27 TraesCS7D01G203300 chr5B 93.793 145 8 1 2292 2435 706457974 706458118 2.810000e-52 217.0
28 TraesCS7D01G203300 chr5B 94.286 35 2 0 3807 3841 18357311 18357277 2.000000e-03 54.7
29 TraesCS7D01G203300 chr5B 96.875 32 0 1 2260 2290 184199897 184199928 8.000000e-03 52.8
30 TraesCS7D01G203300 chr2D 94.286 140 8 0 2293 2432 630719577 630719438 1.010000e-51 215.0
31 TraesCS7D01G203300 chr2D 93.878 98 4 2 3211 3306 15682984 15682887 3.730000e-31 147.0
32 TraesCS7D01G203300 chr2D 100.000 30 0 0 3812 3841 607510265 607510236 6.470000e-04 56.5
33 TraesCS7D01G203300 chr2D 94.286 35 1 1 2257 2290 189840689 189840723 8.000000e-03 52.8
34 TraesCS7D01G203300 chr6A 91.667 144 12 0 2291 2434 119757556 119757699 2.830000e-47 200.0
35 TraesCS7D01G203300 chr6A 100.000 30 0 0 3812 3841 346567131 346567102 6.470000e-04 56.5
36 TraesCS7D01G203300 chr6D 91.608 143 12 0 2290 2432 162248644 162248786 1.020000e-46 198.0
37 TraesCS7D01G203300 chr6D 92.157 102 4 4 3211 3309 387886074 387885974 1.740000e-29 141.0
38 TraesCS7D01G203300 chr6D 90.476 105 5 3 2431 2535 327006505 327006604 2.910000e-27 134.0
39 TraesCS7D01G203300 chr6D 96.970 33 1 0 3809 3841 340997479 340997447 6.470000e-04 56.5
40 TraesCS7D01G203300 chr6D 100.000 29 0 0 3813 3841 191651500 191651472 2.000000e-03 54.7
41 TraesCS7D01G203300 chr6D 100.000 29 0 0 3813 3841 369072900 369072928 2.000000e-03 54.7
42 TraesCS7D01G203300 chr6D 100.000 29 0 0 3813 3841 437965452 437965424 2.000000e-03 54.7
43 TraesCS7D01G203300 chr6D 100.000 28 0 0 3814 3841 17316711 17316684 8.000000e-03 52.8
44 TraesCS7D01G203300 chr4B 94.488 127 7 0 2305 2431 663452960 663452834 3.660000e-46 196.0
45 TraesCS7D01G203300 chr4B 95.098 102 2 3 3203 3302 643774340 643774240 1.720000e-34 158.0
46 TraesCS7D01G203300 chr4B 87.273 55 5 2 3814 3866 457413355 457413409 1.390000e-05 62.1
47 TraesCS7D01G203300 chr4B 100.000 30 0 0 2261 2290 428410658 428410687 6.470000e-04 56.5
48 TraesCS7D01G203300 chr3D 89.630 135 14 0 2293 2427 308761934 308762068 6.160000e-39 172.0
49 TraesCS7D01G203300 chr3D 90.909 110 6 4 3189 3295 303788434 303788542 1.340000e-30 145.0
50 TraesCS7D01G203300 chr4A 91.262 103 5 2 2431 2533 477033305 477033207 2.250000e-28 137.0
51 TraesCS7D01G203300 chr3A 90.090 111 4 3 2431 2537 686191318 686191211 2.250000e-28 137.0
52 TraesCS7D01G203300 chrUn 90.476 105 5 3 2431 2535 476757008 476757107 2.910000e-27 134.0
53 TraesCS7D01G203300 chr5D 88.496 113 8 3 2436 2547 113384628 113384736 1.050000e-26 132.0
54 TraesCS7D01G203300 chr1A 84.496 129 14 4 2431 2557 16442904 16443028 6.290000e-24 122.0
55 TraesCS7D01G203300 chr1A 100.000 29 0 0 2262 2290 352174201 352174173 2.000000e-03 54.7
56 TraesCS7D01G203300 chr1A 100.000 29 0 0 3813 3841 526751910 526751938 2.000000e-03 54.7
57 TraesCS7D01G203300 chr4D 97.059 34 0 1 2257 2290 338384547 338384515 6.470000e-04 56.5
58 TraesCS7D01G203300 chr4D 100.000 29 0 0 3813 3841 90993551 90993523 2.000000e-03 54.7
59 TraesCS7D01G203300 chr4D 94.444 36 0 1 3806 3841 372361600 372361567 2.000000e-03 54.7
60 TraesCS7D01G203300 chr1D 94.595 37 1 1 3813 3849 322928430 322928395 6.470000e-04 56.5
61 TraesCS7D01G203300 chr1D 96.970 33 0 1 3809 3841 416034192 416034161 2.000000e-03 54.7
62 TraesCS7D01G203300 chr1D 100.000 28 0 0 3814 3841 346679597 346679624 8.000000e-03 52.8
63 TraesCS7D01G203300 chr2B 92.308 39 1 2 3804 3841 1273443 1273480 2.000000e-03 54.7
64 TraesCS7D01G203300 chr3B 100.000 28 0 0 2263 2290 817612300 817612327 8.000000e-03 52.8


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 TraesCS7D01G203300 chr7D 161478897 161483527 4630 True 8552.0 8552 100.000000 1 4631 1 chr7D.!!$R1 4630
1 TraesCS7D01G203300 chr7B 123780616 123785404 4788 True 1477.2 4645 94.633000 1 4601 5 chr7B.!!$R1 4600
2 TraesCS7D01G203300 chr7A 162771879 162776115 4236 True 563.9 1663 91.129125 15 3839 8 chr7A.!!$R1 3824
3 TraesCS7D01G203300 chr5A 11945637 11946217 580 False 431.0 431 80.699000 1602 2182 1 chr5A.!!$F1 580
4 TraesCS7D01G203300 chr2A 4023832 4024412 580 False 420.0 420 80.399000 1602 2182 1 chr2A.!!$F1 580

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
961 1797 0.322098 CCGGCTCATTACCACCACAA 60.322 55.0 0.00 0.0 0.00 3.33 F
1424 2266 1.086634 GCATCCTGAAGCGTGAGGAC 61.087 60.0 10.41 0.0 41.27 3.85 F
2321 3226 0.893270 CGGCAATCCACCAACTTCCA 60.893 55.0 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 3207 0.893270 TGGAAGTTGGTGGATTGCCG 60.893 55.000 0.00 0.0 36.79 5.69 R
2409 3314 2.427453 GGCTCTGTTCGGAATCACTCTA 59.573 50.000 0.00 0.0 0.00 2.43 R
4310 5302 1.351350 AGTTTCTTAGTGCACTCCCCC 59.649 52.381 25.56 7.8 0.00 5.40 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
61 63 5.534207 AGCAACAATTGTGAGGAATTCAA 57.466 34.783 12.82 0.00 37.61 2.69
130 132 2.094286 AGCGACAACTTCATCAGAGAGG 60.094 50.000 0.00 0.00 0.00 3.69
154 156 1.280886 CCGAGCTATCATGCAGACGC 61.281 60.000 0.00 0.00 39.24 5.19
205 207 6.255215 CAACAAACGCTCTTAAGACAAAAGA 58.745 36.000 0.00 0.00 0.00 2.52
209 211 6.679327 AACGCTCTTAAGACAAAAGAACTT 57.321 33.333 0.00 0.00 32.77 2.66
210 212 6.049263 ACGCTCTTAAGACAAAAGAACTTG 57.951 37.500 0.00 0.00 32.77 3.16
211 213 5.815740 ACGCTCTTAAGACAAAAGAACTTGA 59.184 36.000 0.00 0.00 32.77 3.02
212 214 6.130058 CGCTCTTAAGACAAAAGAACTTGAC 58.870 40.000 0.00 0.00 32.77 3.18
214 216 7.128976 GCTCTTAAGACAAAAGAACTTGACAG 58.871 38.462 0.00 0.00 32.77 3.51
215 217 7.011482 GCTCTTAAGACAAAAGAACTTGACAGA 59.989 37.037 0.00 0.00 32.77 3.41
216 218 8.786826 TCTTAAGACAAAAGAACTTGACAGAA 57.213 30.769 0.00 0.00 30.15 3.02
218 220 5.491635 AGACAAAAGAACTTGACAGAAGC 57.508 39.130 0.00 0.00 0.00 3.86
233 236 5.182950 TGACAGAAGCAGAACAAGTTCAAAA 59.817 36.000 14.69 0.00 41.84 2.44
347 356 7.066284 GCCCTAATAATATACTTGGTGCATCAG 59.934 40.741 0.00 0.00 0.00 2.90
355 415 2.289694 ACTTGGTGCATCAGTGGAGTAC 60.290 50.000 0.00 0.00 0.00 2.73
372 432 5.221481 TGGAGTACACGTTATTGAACTGGAA 60.221 40.000 0.00 0.00 33.01 3.53
373 433 5.347907 GGAGTACACGTTATTGAACTGGAAG 59.652 44.000 0.00 0.00 42.29 3.46
374 434 5.235516 AGTACACGTTATTGAACTGGAAGG 58.764 41.667 0.00 0.00 39.30 3.46
375 435 4.081322 ACACGTTATTGAACTGGAAGGT 57.919 40.909 0.00 0.00 39.30 3.50
376 436 3.813166 ACACGTTATTGAACTGGAAGGTG 59.187 43.478 0.00 0.00 41.25 4.00
377 437 3.188460 CACGTTATTGAACTGGAAGGTGG 59.812 47.826 0.00 0.00 39.30 4.61
378 438 2.161609 CGTTATTGAACTGGAAGGTGGC 59.838 50.000 0.00 0.00 39.30 5.01
382 442 2.380064 TGAACTGGAAGGTGGCAAAT 57.620 45.000 0.00 0.00 39.30 2.32
441 501 1.176527 CGCCATTGGATTCCAACAGT 58.823 50.000 20.21 2.13 46.95 3.55
468 528 1.668101 CGTAGCCCTCTCTCCGCTTT 61.668 60.000 0.00 0.00 34.03 3.51
737 802 2.121538 CCCTGCTCGGACGATCAGA 61.122 63.158 22.53 0.00 39.82 3.27
740 805 1.404181 CCTGCTCGGACGATCAGAAAA 60.404 52.381 22.53 0.00 39.82 2.29
798 897 3.062466 GCAAACCTCCTTCCGGCC 61.062 66.667 0.00 0.00 0.00 6.13
799 898 2.361230 CAAACCTCCTTCCGGCCC 60.361 66.667 0.00 0.00 0.00 5.80
800 899 4.029809 AAACCTCCTTCCGGCCCG 62.030 66.667 0.00 0.00 0.00 6.13
883 1719 4.717629 CGCCTCACGCCGTGAAGA 62.718 66.667 21.56 0.00 42.26 2.87
885 1721 2.962569 CCTCACGCCGTGAAGAGA 59.037 61.111 21.56 0.00 42.26 3.10
886 1722 1.444553 CCTCACGCCGTGAAGAGAC 60.445 63.158 21.56 0.00 42.26 3.36
887 1723 1.797933 CTCACGCCGTGAAGAGACG 60.798 63.158 21.56 4.41 42.26 4.18
889 1725 2.050351 ACGCCGTGAAGAGACGTG 60.050 61.111 0.00 0.00 37.66 4.49
890 1726 3.470567 CGCCGTGAAGAGACGTGC 61.471 66.667 0.00 0.00 37.66 5.34
891 1727 2.049063 GCCGTGAAGAGACGTGCT 60.049 61.111 0.00 0.00 37.66 4.40
961 1797 0.322098 CCGGCTCATTACCACCACAA 60.322 55.000 0.00 0.00 0.00 3.33
967 1803 4.142469 GGCTCATTACCACCACAACATAAC 60.142 45.833 0.00 0.00 0.00 1.89
974 1810 1.464608 CACCACAACATAACTCGCCAG 59.535 52.381 0.00 0.00 0.00 4.85
1303 2139 1.745115 TGCTCGCCGAAATTCCCTG 60.745 57.895 0.00 0.00 0.00 4.45
1400 2242 2.360852 GACCTCGAGACCGTCCCA 60.361 66.667 15.71 0.00 37.05 4.37
1424 2266 1.086634 GCATCCTGAAGCGTGAGGAC 61.087 60.000 10.41 0.00 41.27 3.85
1512 2354 3.452264 ACAGTAGCTAGGAACATGCATCA 59.548 43.478 0.00 0.00 0.00 3.07
1550 2392 8.737175 TCAGTCTTGATACTTAATGAGTAACGT 58.263 33.333 0.00 0.00 43.76 3.99
1579 2421 5.857268 TCTGTTGTCAATTCTCATCAGTCA 58.143 37.500 12.91 0.00 34.76 3.41
1660 2502 1.163420 AATCGTTCAACGTGCTGGCA 61.163 50.000 10.31 0.00 43.14 4.92
1701 2543 6.605119 AGGTAATTCATATGTTTCCTCCCTG 58.395 40.000 1.90 0.00 0.00 4.45
1823 2688 4.948341 AATGACAACCCCTGTTTTTACC 57.052 40.909 0.00 0.00 38.84 2.85
2263 3168 4.474226 GACTTTTGTCGAGCAACAATCT 57.526 40.909 0.00 0.00 38.83 2.40
2302 3207 6.128254 GGAATTACTTGTCTTAGTGCCTGTTC 60.128 42.308 0.00 0.00 0.00 3.18
2321 3226 0.893270 CGGCAATCCACCAACTTCCA 60.893 55.000 0.00 0.00 0.00 3.53
2409 3314 2.048127 GAGCGGAGTTGCGGAGTT 60.048 61.111 0.00 0.00 40.67 3.01
2418 3323 3.368531 GGAGTTGCGGAGTTAGAGTGATT 60.369 47.826 0.00 0.00 0.00 2.57
2504 3409 7.589958 ACATCCGTATCTAGACAAATCTTCT 57.410 36.000 0.00 0.00 36.29 2.85
2597 3504 4.588899 TCTCCCATGTGTGTCCATTAAAG 58.411 43.478 0.00 0.00 0.00 1.85
2987 3894 7.489435 TCAGTGCTCTGTAAAGAAATAAGATCG 59.511 37.037 15.01 0.00 41.91 3.69
3225 4133 4.834406 ATCTATTACTCCCTCTGTCCCA 57.166 45.455 0.00 0.00 0.00 4.37
3918 4910 2.416431 GCTCATCAAGGCATTTTCGCTT 60.416 45.455 0.00 0.00 0.00 4.68
3925 4917 4.947388 TCAAGGCATTTTCGCTTAGGTATT 59.053 37.500 0.00 0.00 0.00 1.89
4147 5139 3.527533 CATTTCTGGACATGGCAAATGG 58.472 45.455 12.81 0.00 32.91 3.16
4281 5273 2.104792 TCACAAAGCTAGCCTTGAGTGT 59.895 45.455 28.52 13.33 39.49 3.55
4286 5278 5.592688 ACAAAGCTAGCCTTGAGTGTAAAAA 59.407 36.000 28.52 0.00 33.01 1.94
4287 5279 5.690997 AAGCTAGCCTTGAGTGTAAAAAC 57.309 39.130 12.13 0.00 30.99 2.43
4310 5302 3.763360 TGTATGGGAAGTGGCTCATTTTG 59.237 43.478 0.00 0.00 30.16 2.44
4353 5345 5.468540 ACCTTAAGAATTGAAAACCCAGC 57.531 39.130 3.36 0.00 0.00 4.85
4392 5384 3.552132 TTGGTCACAAGCAAGTCAGTA 57.448 42.857 0.00 0.00 37.94 2.74
4597 5695 8.896320 TTATAAGACATTAACGTGTGGCATAT 57.104 30.769 4.75 5.03 31.16 1.78
4601 5699 4.771903 ACATTAACGTGTGGCATATGGTA 58.228 39.130 8.37 2.60 0.00 3.25
4602 5700 4.573201 ACATTAACGTGTGGCATATGGTAC 59.427 41.667 8.37 0.00 0.00 3.34
4603 5701 4.475051 TTAACGTGTGGCATATGGTACT 57.525 40.909 8.37 0.00 0.00 2.73
4604 5702 3.343941 AACGTGTGGCATATGGTACTT 57.656 42.857 8.37 0.00 0.00 2.24
4605 5703 2.627945 ACGTGTGGCATATGGTACTTG 58.372 47.619 8.37 0.00 0.00 3.16
4606 5704 2.027561 ACGTGTGGCATATGGTACTTGT 60.028 45.455 8.37 0.00 0.00 3.16
4607 5705 3.196039 ACGTGTGGCATATGGTACTTGTA 59.804 43.478 8.37 0.00 0.00 2.41
4608 5706 3.554324 CGTGTGGCATATGGTACTTGTAC 59.446 47.826 4.56 2.55 0.00 2.90
4609 5707 4.679639 CGTGTGGCATATGGTACTTGTACT 60.680 45.833 4.56 0.00 0.00 2.73
4610 5708 5.450826 CGTGTGGCATATGGTACTTGTACTA 60.451 44.000 4.56 5.30 0.00 1.82
4611 5709 5.751990 GTGTGGCATATGGTACTTGTACTAC 59.248 44.000 4.56 0.00 0.00 2.73
4612 5710 4.980434 GTGGCATATGGTACTTGTACTACG 59.020 45.833 4.56 0.00 0.00 3.51
4613 5711 4.888823 TGGCATATGGTACTTGTACTACGA 59.111 41.667 4.56 0.00 0.00 3.43
4614 5712 5.537295 TGGCATATGGTACTTGTACTACGAT 59.463 40.000 4.56 0.00 0.00 3.73
4615 5713 6.716173 TGGCATATGGTACTTGTACTACGATA 59.284 38.462 4.56 0.00 0.00 2.92
4616 5714 7.395206 TGGCATATGGTACTTGTACTACGATAT 59.605 37.037 4.56 0.00 30.05 1.63
4617 5715 8.248945 GGCATATGGTACTTGTACTACGATATT 58.751 37.037 4.56 0.00 28.44 1.28
4618 5716 9.635520 GCATATGGTACTTGTACTACGATATTT 57.364 33.333 4.56 0.00 28.44 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 7.275183 TCTTACTTGATATATTGCACAGCTGT 58.725 34.615 15.25 15.25 0.00 4.40
130 132 2.491298 TCTGCATGATAGCTCGGATCTC 59.509 50.000 0.00 0.00 34.99 2.75
169 171 2.202395 TTTGTTGGGAGCAGGCAGC 61.202 57.895 0.00 0.00 46.19 5.25
205 207 4.265073 ACTTGTTCTGCTTCTGTCAAGTT 58.735 39.130 0.00 0.00 41.31 2.66
209 211 3.872696 TGAACTTGTTCTGCTTCTGTCA 58.127 40.909 13.65 0.00 0.00 3.58
210 212 4.882671 TTGAACTTGTTCTGCTTCTGTC 57.117 40.909 13.65 0.00 0.00 3.51
211 213 5.643379 TTTTGAACTTGTTCTGCTTCTGT 57.357 34.783 13.65 0.00 0.00 3.41
212 214 6.753279 TGAATTTTGAACTTGTTCTGCTTCTG 59.247 34.615 13.65 0.00 0.00 3.02
214 216 7.524294 TTGAATTTTGAACTTGTTCTGCTTC 57.476 32.000 13.65 11.14 0.00 3.86
215 217 9.034544 GTATTGAATTTTGAACTTGTTCTGCTT 57.965 29.630 13.65 3.85 0.00 3.91
216 218 7.653311 GGTATTGAATTTTGAACTTGTTCTGCT 59.347 33.333 13.65 0.00 0.00 4.24
218 220 7.114811 CCGGTATTGAATTTTGAACTTGTTCTG 59.885 37.037 13.65 0.00 0.00 3.02
233 236 3.023119 TGCTGAAATGCCGGTATTGAAT 58.977 40.909 19.08 2.81 0.00 2.57
347 356 4.387862 CCAGTTCAATAACGTGTACTCCAC 59.612 45.833 0.00 0.00 40.73 4.02
355 415 3.188460 CCACCTTCCAGTTCAATAACGTG 59.812 47.826 0.00 0.00 40.73 4.49
364 424 2.238521 TGATTTGCCACCTTCCAGTTC 58.761 47.619 0.00 0.00 0.00 3.01
368 428 3.513515 GGTTAATGATTTGCCACCTTCCA 59.486 43.478 0.00 0.00 0.00 3.53
372 432 4.019174 CTCTGGTTAATGATTTGCCACCT 58.981 43.478 0.00 0.00 0.00 4.00
373 433 3.131046 CCTCTGGTTAATGATTTGCCACC 59.869 47.826 0.00 0.00 0.00 4.61
374 434 3.763897 ACCTCTGGTTAATGATTTGCCAC 59.236 43.478 0.00 0.00 27.29 5.01
375 435 4.046286 ACCTCTGGTTAATGATTTGCCA 57.954 40.909 1.55 1.55 27.29 4.92
376 436 5.405935 AAACCTCTGGTTAATGATTTGCC 57.594 39.130 2.15 0.00 46.20 4.52
377 437 6.071616 TGGTAAACCTCTGGTTAATGATTTGC 60.072 38.462 2.15 0.00 46.20 3.68
378 438 7.461182 TGGTAAACCTCTGGTTAATGATTTG 57.539 36.000 2.15 0.00 46.20 2.32
382 442 4.585879 GCTGGTAAACCTCTGGTTAATGA 58.414 43.478 2.15 0.00 46.20 2.57
437 497 2.604174 GGCTACGTGCGCAAACTGT 61.604 57.895 14.00 11.49 44.05 3.55
468 528 3.888460 TTGCTGAGTGGCAGGGCA 61.888 61.111 0.00 0.00 45.03 5.36
557 618 3.839432 GAACCCTCCTCCTCGCGG 61.839 72.222 6.13 0.00 0.00 6.46
656 717 3.388703 GAGGCAGCTGCTCCTCCTG 62.389 68.421 35.82 8.05 42.30 3.86
678 739 1.330655 GCCGGAGACATGGAGGAGAA 61.331 60.000 5.05 0.00 0.00 2.87
737 802 1.439679 CGCGCCTTTCCTCTACTTTT 58.560 50.000 0.00 0.00 0.00 2.27
740 805 2.893398 CCGCGCCTTTCCTCTACT 59.107 61.111 0.00 0.00 0.00 2.57
881 1717 3.274455 CTCGCCACAGCACGTCTCT 62.274 63.158 0.00 0.00 39.83 3.10
882 1718 2.807045 CTCGCCACAGCACGTCTC 60.807 66.667 0.00 0.00 39.83 3.36
883 1719 4.363990 CCTCGCCACAGCACGTCT 62.364 66.667 0.00 0.00 39.83 4.18
961 1797 1.811266 CTGCGCTGGCGAGTTATGT 60.811 57.895 19.31 0.00 44.10 2.29
1303 2139 3.682292 AATGGAGCGTTCCTCGGGC 62.682 63.158 19.73 0.00 44.36 6.13
1337 2174 1.413118 AAGCAAGTCCCAAAACCCTG 58.587 50.000 0.00 0.00 0.00 4.45
1400 2242 4.131376 CGCTTCAGGATGCGGAAT 57.869 55.556 18.38 0.00 46.78 3.01
1424 2266 3.486043 CCACTTGTCTGATCTCGTACTCG 60.486 52.174 0.00 0.00 38.55 4.18
1512 2354 2.048127 GACTGACCGCGCTTCCTT 60.048 61.111 5.56 0.00 0.00 3.36
1550 2392 5.551305 TGAGAATTGACAACAGAAGAGGA 57.449 39.130 0.00 0.00 0.00 3.71
1701 2543 1.024271 TTCCTTTCACAGCACAGCAC 58.976 50.000 0.00 0.00 0.00 4.40
1739 2602 6.155049 ACCATCATAAATTTCCCTTCAGTTGG 59.845 38.462 0.00 0.00 0.00 3.77
1823 2688 1.448013 GCGAACTTCCTCCTTCCGG 60.448 63.158 0.00 0.00 0.00 5.14
2302 3207 0.893270 TGGAAGTTGGTGGATTGCCG 60.893 55.000 0.00 0.00 36.79 5.69
2308 3213 3.647636 TGGATTTTTGGAAGTTGGTGGA 58.352 40.909 0.00 0.00 0.00 4.02
2321 3226 3.019564 CTCCGCAGATCCTTGGATTTTT 58.980 45.455 3.43 0.00 0.00 1.94
2409 3314 2.427453 GGCTCTGTTCGGAATCACTCTA 59.573 50.000 0.00 0.00 0.00 2.43
2418 3323 3.260884 ACAAATCTAAGGCTCTGTTCGGA 59.739 43.478 0.00 0.00 0.00 4.55
2463 3368 9.760077 ATACGGATGTATCTAACACTAAAAAGG 57.240 33.333 0.00 0.00 42.09 3.11
2502 3407 5.246656 TCCGTCCCAAATTACTTGTCTTAGA 59.753 40.000 0.00 0.00 32.65 2.10
2503 3408 5.484715 TCCGTCCCAAATTACTTGTCTTAG 58.515 41.667 0.00 0.00 32.65 2.18
2504 3409 5.484715 CTCCGTCCCAAATTACTTGTCTTA 58.515 41.667 0.00 0.00 32.65 2.10
2597 3504 2.457366 ATGAGGACAGGACGTGAAAC 57.543 50.000 0.00 0.00 0.00 2.78
4176 5168 5.483937 TCACCCATAAATCTGTACTGTGAGT 59.516 40.000 0.00 0.00 0.00 3.41
4281 5273 4.993028 AGCCACTTCCCATACAGTTTTTA 58.007 39.130 0.00 0.00 0.00 1.52
4286 5278 1.656587 TGAGCCACTTCCCATACAGT 58.343 50.000 0.00 0.00 0.00 3.55
4287 5279 3.287867 AATGAGCCACTTCCCATACAG 57.712 47.619 0.00 0.00 0.00 2.74
4310 5302 1.351350 AGTTTCTTAGTGCACTCCCCC 59.649 52.381 25.56 7.80 0.00 5.40
4392 5384 2.820197 GGTCGGAGAAAGAATTTGGCTT 59.180 45.455 0.00 0.00 39.27 4.35
4540 5638 7.584122 AGAAAGAATTGCTGATGCTCATAAT 57.416 32.000 0.00 0.00 40.48 1.28


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

AutoCloner maintained by Alex Coulton.