Multiple sequence alignment - TraesCS5B01G171300

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 TraesCS5B01G171300 chr5B 100.000 2462 0 0 1 2462 315915242 315912781 0.000000e+00 4547.0
1 TraesCS5B01G171300 chr5B 94.613 2339 118 3 72 2410 478553146 478550816 0.000000e+00 3615.0
2 TraesCS5B01G171300 chr5B 94.271 2339 126 6 72 2409 184289570 184291901 0.000000e+00 3570.0
3 TraesCS5B01G171300 chr5B 91.398 93 5 3 1 91 616681332 616681241 9.240000e-25 124.0
4 TraesCS5B01G171300 chr7D 94.530 2340 116 8 72 2410 550636511 550638839 0.000000e+00 3602.0
5 TraesCS5B01G171300 chr7D 90.426 94 7 2 1 94 514362774 514362865 3.320000e-24 122.0
6 TraesCS5B01G171300 chr5D 94.319 2341 119 5 72 2412 350368906 350366580 0.000000e+00 3574.0
7 TraesCS5B01G171300 chr5D 94.055 2338 128 4 72 2409 41770739 41768413 0.000000e+00 3537.0
8 TraesCS5B01G171300 chr5D 96.296 54 2 0 2409 2462 26276308 26276255 3.370000e-14 89.8
9 TraesCS5B01G171300 chr3B 94.188 2340 110 11 72 2404 522780045 522782365 0.000000e+00 3544.0
10 TraesCS5B01G171300 chr3B 96.364 55 2 0 2408 2462 395042101 395042155 9.380000e-15 91.6
11 TraesCS5B01G171300 chr7B 93.987 2345 134 4 72 2412 584020885 584023226 0.000000e+00 3542.0
12 TraesCS5B01G171300 chr1B 94.002 2334 135 5 72 2404 535919227 535916898 0.000000e+00 3530.0
13 TraesCS5B01G171300 chr1B 98.077 52 1 0 2411 2462 667310969 667310918 9.380000e-15 91.6
14 TraesCS5B01G171300 chr1B 96.226 53 2 0 2410 2462 447184021 447184073 1.210000e-13 87.9
15 TraesCS5B01G171300 chr2B 93.803 2340 138 6 72 2411 485170492 485172824 0.000000e+00 3511.0
16 TraesCS5B01G171300 chr6B 94.253 87 3 2 1 87 226521758 226521842 5.520000e-27 132.0
17 TraesCS5B01G171300 chr3A 93.258 89 6 0 1 89 667863321 667863409 5.520000e-27 132.0
18 TraesCS5B01G171300 chr6D 94.118 85 5 0 1 85 472218102 472218186 1.990000e-26 130.0
19 TraesCS5B01G171300 chr5A 95.000 80 4 0 1 80 328180663 328180742 2.570000e-25 126.0
20 TraesCS5B01G171300 chr5A 91.398 93 4 4 1 93 562266219 562266307 9.240000e-25 124.0
21 TraesCS5B01G171300 chr4B 89.216 102 9 2 1 101 246476660 246476560 2.570000e-25 126.0
22 TraesCS5B01G171300 chr4B 96.364 55 2 0 2408 2462 135780112 135780058 9.380000e-15 91.6
23 TraesCS5B01G171300 chr1A 95.000 80 4 0 1 80 456580367 456580446 2.570000e-25 126.0
24 TraesCS5B01G171300 chr6A 98.077 52 1 0 2411 2462 480579131 480579182 9.380000e-15 91.6
25 TraesCS5B01G171300 chr3D 98.077 52 1 0 2411 2462 307828917 307828866 9.380000e-15 91.6
26 TraesCS5B01G171300 chr2D 94.444 54 3 0 2409 2462 79334349 79334402 1.570000e-12 84.2
27 TraesCS5B01G171300 chr4D 94.231 52 3 0 2411 2462 127155072 127155021 2.030000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G171300 chr5B 315912781 315915242 2461 True 4547 4547 100.000 1 2462 1 chr5B.!!$R1 2461
1 TraesCS5B01G171300 chr5B 478550816 478553146 2330 True 3615 3615 94.613 72 2410 1 chr5B.!!$R2 2338
2 TraesCS5B01G171300 chr5B 184289570 184291901 2331 False 3570 3570 94.271 72 2409 1 chr5B.!!$F1 2337
3 TraesCS5B01G171300 chr7D 550636511 550638839 2328 False 3602 3602 94.530 72 2410 1 chr7D.!!$F2 2338
4 TraesCS5B01G171300 chr5D 350366580 350368906 2326 True 3574 3574 94.319 72 2412 1 chr5D.!!$R3 2340
5 TraesCS5B01G171300 chr5D 41768413 41770739 2326 True 3537 3537 94.055 72 2409 1 chr5D.!!$R2 2337
6 TraesCS5B01G171300 chr3B 522780045 522782365 2320 False 3544 3544 94.188 72 2404 1 chr3B.!!$F2 2332
7 TraesCS5B01G171300 chr7B 584020885 584023226 2341 False 3542 3542 93.987 72 2412 1 chr7B.!!$F1 2340
8 TraesCS5B01G171300 chr1B 535916898 535919227 2329 True 3530 3530 94.002 72 2404 1 chr1B.!!$R1 2332
9 TraesCS5B01G171300 chr2B 485170492 485172824 2332 False 3511 3511 93.803 72 2411 1 chr2B.!!$F1 2339

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
30 31 1.018910 TGCATCACCATGATCTTGCG 58.981 50.0 3.07 0.3 34.28 4.85 F
1128 1140 1.002069 TCCTTGATGGCCCTGACAAT 58.998 50.0 0.00 0.0 35.26 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 1380 0.106769 TGGCCTTGTTGTCAAGCAGA 60.107 50.0 3.32 0.0 46.74 4.26 R
2378 2397 0.454196 GGTTGCCGTTGTGAACAGTT 59.546 50.0 0.00 0.0 0.00 3.16 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
19 20 1.939974 TCTCGTTGCTATGCATCACC 58.060 50.000 0.19 0.00 38.76 4.02
20 21 1.206849 TCTCGTTGCTATGCATCACCA 59.793 47.619 0.19 0.00 38.76 4.17
21 22 2.158914 TCTCGTTGCTATGCATCACCAT 60.159 45.455 0.19 0.00 38.76 3.55
22 23 1.941975 TCGTTGCTATGCATCACCATG 59.058 47.619 0.19 0.00 38.76 3.66
23 24 1.941975 CGTTGCTATGCATCACCATGA 59.058 47.619 0.19 0.00 38.76 3.07
24 25 2.551032 CGTTGCTATGCATCACCATGAT 59.449 45.455 0.19 0.00 38.76 2.45
25 26 3.364664 CGTTGCTATGCATCACCATGATC 60.365 47.826 0.19 0.00 38.76 2.92
26 27 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75
27 28 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
28 29 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
29 30 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
30 31 1.018910 TGCATCACCATGATCTTGCG 58.981 50.000 3.07 0.30 34.28 4.85
31 32 1.019673 GCATCACCATGATCTTGCGT 58.980 50.000 3.07 0.87 34.28 5.24
32 33 1.268386 GCATCACCATGATCTTGCGTG 60.268 52.381 17.02 17.02 34.28 5.34
33 34 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
34 35 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
35 36 1.159285 CACCATGATCTTGCGTGTGT 58.841 50.000 15.81 3.20 0.00 3.72
36 37 1.135888 CACCATGATCTTGCGTGTGTG 60.136 52.381 15.81 9.68 0.00 3.82
37 38 1.159285 CCATGATCTTGCGTGTGTGT 58.841 50.000 3.07 0.00 0.00 3.72
38 39 2.289382 ACCATGATCTTGCGTGTGTGTA 60.289 45.455 3.07 0.00 0.00 2.90
39 40 2.349580 CCATGATCTTGCGTGTGTGTAG 59.650 50.000 3.07 0.00 0.00 2.74
40 41 2.078849 TGATCTTGCGTGTGTGTAGG 57.921 50.000 0.00 0.00 0.00 3.18
41 42 1.616374 TGATCTTGCGTGTGTGTAGGA 59.384 47.619 0.00 0.00 0.00 2.94
42 43 2.036604 TGATCTTGCGTGTGTGTAGGAA 59.963 45.455 0.00 0.00 0.00 3.36
43 44 2.831685 TCTTGCGTGTGTGTAGGAAT 57.168 45.000 0.00 0.00 0.00 3.01
44 45 3.120321 TCTTGCGTGTGTGTAGGAATT 57.880 42.857 0.00 0.00 0.00 2.17
45 46 3.472652 TCTTGCGTGTGTGTAGGAATTT 58.527 40.909 0.00 0.00 0.00 1.82
46 47 3.880490 TCTTGCGTGTGTGTAGGAATTTT 59.120 39.130 0.00 0.00 0.00 1.82
47 48 4.336993 TCTTGCGTGTGTGTAGGAATTTTT 59.663 37.500 0.00 0.00 0.00 1.94
78 79 7.504924 TTACTATGTTTCCCAACAGTTGAAG 57.495 36.000 15.36 5.94 46.25 3.02
117 118 9.617523 TTGAATCATGCTTAGATCTGTGATTTA 57.382 29.630 5.18 7.50 36.68 1.40
140 141 3.091545 AGCTATTGGTGGTCCATTTGTG 58.908 45.455 0.00 0.00 43.91 3.33
182 183 8.427902 AGATGTATGTTCCTGCTCATAGATTA 57.572 34.615 0.00 0.00 33.02 1.75
187 188 4.832823 TGTTCCTGCTCATAGATTATCCGA 59.167 41.667 0.00 0.00 0.00 4.55
272 274 6.121590 TGTATGCTTCTGCTTTCATGGATTA 58.878 36.000 0.00 0.00 40.48 1.75
329 331 3.452755 TGCTACGATTGTAGGACATGG 57.547 47.619 19.70 0.00 46.72 3.66
344 346 1.303561 ATGGCCACACAGACGCAAT 60.304 52.632 8.16 0.00 0.00 3.56
367 369 1.822990 CTTAGTCAGGCCCTTGTCGTA 59.177 52.381 0.00 0.00 0.00 3.43
596 607 1.225376 GCCGTTCATGTCCACGTTCA 61.225 55.000 11.87 0.00 34.47 3.18
846 858 1.599606 CTGGAGGCAGAGCACTACGT 61.600 60.000 0.00 0.00 0.00 3.57
902 914 4.766891 CCTTTTCATACTGTCCACCATTGT 59.233 41.667 0.00 0.00 0.00 2.71
997 1009 2.979678 ACACCCATCCAGAACTACAACT 59.020 45.455 0.00 0.00 0.00 3.16
1005 1017 5.939764 TCCAGAACTACAACTAGATGCAT 57.060 39.130 0.00 0.00 0.00 3.96
1128 1140 1.002069 TCCTTGATGGCCCTGACAAT 58.998 50.000 0.00 0.00 35.26 2.71
1227 1245 4.660168 AGGAGATCAATGTCTTTTGCAGT 58.340 39.130 0.00 0.00 0.00 4.40
1407 1425 2.676471 GGGTTCGTTGCCATGGCT 60.676 61.111 35.53 0.00 42.51 4.75
1582 1600 6.377146 GGGCTCAAAAACTATTTGATGGTCTA 59.623 38.462 4.28 0.00 37.72 2.59
1619 1637 5.137429 AGGTGGTATATACTAACCCCTCACT 59.863 44.000 23.55 10.13 33.62 3.41
1724 1742 2.976589 TGCTATGCCGTATGATCATGG 58.023 47.619 18.72 12.67 0.00 3.66
1917 1935 2.167487 TGCACAAGTGGCATCGTATAGA 59.833 45.455 2.00 0.00 36.11 1.98
2047 2065 3.142174 GTCAAAGTGGAAGCTGCTAAGT 58.858 45.455 0.90 0.00 0.00 2.24
2048 2066 4.202315 TGTCAAAGTGGAAGCTGCTAAGTA 60.202 41.667 0.90 0.00 0.00 2.24
2054 2072 3.133003 GTGGAAGCTGCTAAGTAGGATCA 59.867 47.826 0.90 0.00 0.00 2.92
2230 2249 1.419922 CGTGTTCATGTGCCGCTAC 59.580 57.895 0.00 0.00 0.00 3.58
2250 2269 4.679412 CCAATGCAGGCAACCAAC 57.321 55.556 0.00 0.00 37.17 3.77
2259 2278 1.204467 CAGGCAACCAACACAAAGTGT 59.796 47.619 0.00 0.00 44.03 3.55
2301 2320 0.108138 GGACACTAGACGCAGGCAAT 60.108 55.000 0.00 0.00 0.00 3.56
2378 2397 1.482182 AGAAGTGTATGCGATGCAGGA 59.518 47.619 0.00 0.00 43.65 3.86
2404 2423 0.109086 CACAACGGCAACCAAACACA 60.109 50.000 0.00 0.00 0.00 3.72
2412 2431 2.303175 GCAACCAAACACACCCTAAGA 58.697 47.619 0.00 0.00 0.00 2.10
2413 2432 2.293399 GCAACCAAACACACCCTAAGAG 59.707 50.000 0.00 0.00 0.00 2.85
2414 2433 2.271944 ACCAAACACACCCTAAGAGC 57.728 50.000 0.00 0.00 0.00 4.09
2415 2434 1.493022 ACCAAACACACCCTAAGAGCA 59.507 47.619 0.00 0.00 0.00 4.26
2416 2435 2.108250 ACCAAACACACCCTAAGAGCAT 59.892 45.455 0.00 0.00 0.00 3.79
2417 2436 2.489329 CCAAACACACCCTAAGAGCATG 59.511 50.000 0.00 0.00 0.00 4.06
2418 2437 3.149196 CAAACACACCCTAAGAGCATGT 58.851 45.455 0.00 0.00 0.00 3.21
2419 2438 2.770164 ACACACCCTAAGAGCATGTC 57.230 50.000 0.00 0.00 0.00 3.06
2420 2439 2.260822 ACACACCCTAAGAGCATGTCT 58.739 47.619 0.00 0.00 36.94 3.41
2421 2440 3.441101 ACACACCCTAAGAGCATGTCTA 58.559 45.455 0.00 0.00 32.65 2.59
2422 2441 3.449018 ACACACCCTAAGAGCATGTCTAG 59.551 47.826 0.00 0.00 32.65 2.43
2423 2442 3.449018 CACACCCTAAGAGCATGTCTAGT 59.551 47.826 0.00 0.00 32.65 2.57
2424 2443 4.645136 CACACCCTAAGAGCATGTCTAGTA 59.355 45.833 0.00 0.00 32.65 1.82
2425 2444 4.890581 ACACCCTAAGAGCATGTCTAGTAG 59.109 45.833 0.00 0.00 32.65 2.57
2426 2445 5.133941 CACCCTAAGAGCATGTCTAGTAGA 58.866 45.833 0.00 0.00 32.65 2.59
2427 2446 5.772672 CACCCTAAGAGCATGTCTAGTAGAT 59.227 44.000 2.51 0.00 32.65 1.98
2428 2447 6.007703 ACCCTAAGAGCATGTCTAGTAGATC 58.992 44.000 2.51 0.00 32.65 2.75
2429 2448 5.417580 CCCTAAGAGCATGTCTAGTAGATCC 59.582 48.000 2.51 0.00 32.65 3.36
2430 2449 5.417580 CCTAAGAGCATGTCTAGTAGATCCC 59.582 48.000 2.51 0.00 32.65 3.85
2431 2450 4.740154 AGAGCATGTCTAGTAGATCCCT 57.260 45.455 2.51 0.00 31.71 4.20
2432 2451 4.662278 AGAGCATGTCTAGTAGATCCCTC 58.338 47.826 2.51 7.39 31.71 4.30
2433 2452 4.105537 AGAGCATGTCTAGTAGATCCCTCA 59.894 45.833 2.51 0.00 31.71 3.86
2434 2453 4.809193 AGCATGTCTAGTAGATCCCTCAA 58.191 43.478 2.51 0.00 0.00 3.02
2435 2454 5.211973 AGCATGTCTAGTAGATCCCTCAAA 58.788 41.667 2.51 0.00 0.00 2.69
2436 2455 5.069781 AGCATGTCTAGTAGATCCCTCAAAC 59.930 44.000 2.51 0.00 0.00 2.93
2437 2456 5.740513 GCATGTCTAGTAGATCCCTCAAACC 60.741 48.000 2.51 0.00 0.00 3.27
2438 2457 4.287552 TGTCTAGTAGATCCCTCAAACCC 58.712 47.826 2.51 0.00 0.00 4.11
2439 2458 4.016479 TGTCTAGTAGATCCCTCAAACCCT 60.016 45.833 2.51 0.00 0.00 4.34
2440 2459 4.963628 GTCTAGTAGATCCCTCAAACCCTT 59.036 45.833 2.51 0.00 0.00 3.95
2441 2460 6.134754 GTCTAGTAGATCCCTCAAACCCTTA 58.865 44.000 2.51 0.00 0.00 2.69
2442 2461 6.610425 GTCTAGTAGATCCCTCAAACCCTTAA 59.390 42.308 2.51 0.00 0.00 1.85
2443 2462 7.125356 GTCTAGTAGATCCCTCAAACCCTTAAA 59.875 40.741 2.51 0.00 0.00 1.52
2444 2463 6.910259 AGTAGATCCCTCAAACCCTTAAAT 57.090 37.500 0.00 0.00 0.00 1.40
2445 2464 6.901300 AGTAGATCCCTCAAACCCTTAAATC 58.099 40.000 0.00 0.00 0.00 2.17
2446 2465 6.678857 AGTAGATCCCTCAAACCCTTAAATCT 59.321 38.462 0.00 0.00 0.00 2.40
2447 2466 7.849904 AGTAGATCCCTCAAACCCTTAAATCTA 59.150 37.037 0.00 0.00 0.00 1.98
2448 2467 7.525158 AGATCCCTCAAACCCTTAAATCTAA 57.475 36.000 0.00 0.00 0.00 2.10
2449 2468 7.939781 AGATCCCTCAAACCCTTAAATCTAAA 58.060 34.615 0.00 0.00 0.00 1.85
2450 2469 8.398743 AGATCCCTCAAACCCTTAAATCTAAAA 58.601 33.333 0.00 0.00 0.00 1.52
2451 2470 7.770366 TCCCTCAAACCCTTAAATCTAAAAC 57.230 36.000 0.00 0.00 0.00 2.43
2452 2471 7.532199 TCCCTCAAACCCTTAAATCTAAAACT 58.468 34.615 0.00 0.00 0.00 2.66
2453 2472 8.671409 TCCCTCAAACCCTTAAATCTAAAACTA 58.329 33.333 0.00 0.00 0.00 2.24
2454 2473 8.957466 CCCTCAAACCCTTAAATCTAAAACTAG 58.043 37.037 0.00 0.00 0.00 2.57
2455 2474 9.516546 CCTCAAACCCTTAAATCTAAAACTAGT 57.483 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.206849 TGGTGATGCATAGCAACGAGA 59.793 47.619 0.00 0.00 43.62 4.04
1 2 1.655484 TGGTGATGCATAGCAACGAG 58.345 50.000 0.00 0.00 43.62 4.18
2 3 1.941975 CATGGTGATGCATAGCAACGA 59.058 47.619 0.00 0.00 43.62 3.85
3 4 1.941975 TCATGGTGATGCATAGCAACG 59.058 47.619 0.00 1.35 43.62 4.10
4 5 3.819337 AGATCATGGTGATGCATAGCAAC 59.181 43.478 0.00 0.00 43.62 4.17
5 6 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
6 7 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
7 8 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
8 9 3.120304 CGCAAGATCATGGTGATGCATAG 60.120 47.826 0.00 0.00 37.20 2.23
9 10 2.809696 CGCAAGATCATGGTGATGCATA 59.190 45.455 0.00 0.00 37.20 3.14
10 11 1.607148 CGCAAGATCATGGTGATGCAT 59.393 47.619 0.00 0.00 37.20 3.96
11 12 1.018910 CGCAAGATCATGGTGATGCA 58.981 50.000 11.83 0.00 37.20 3.96
12 13 1.019673 ACGCAAGATCATGGTGATGC 58.980 50.000 0.00 3.06 37.20 3.91
13 14 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
14 15 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
15 16 1.270785 ACACACGCAAGATCATGGTGA 60.271 47.619 19.56 0.00 43.62 4.02
16 17 1.135888 CACACACGCAAGATCATGGTG 60.136 52.381 14.17 14.17 43.62 4.17
17 18 1.159285 CACACACGCAAGATCATGGT 58.841 50.000 0.00 0.00 43.62 3.55
18 19 1.159285 ACACACACGCAAGATCATGG 58.841 50.000 0.00 0.00 43.62 3.66
19 20 2.349580 CCTACACACACGCAAGATCATG 59.650 50.000 0.00 0.00 43.62 3.07
20 21 2.233676 TCCTACACACACGCAAGATCAT 59.766 45.455 0.00 0.00 43.62 2.45
21 22 1.616374 TCCTACACACACGCAAGATCA 59.384 47.619 0.00 0.00 43.62 2.92
22 23 2.363788 TCCTACACACACGCAAGATC 57.636 50.000 0.00 0.00 43.62 2.75
23 24 2.831685 TTCCTACACACACGCAAGAT 57.168 45.000 0.00 0.00 43.62 2.40
24 25 2.831685 ATTCCTACACACACGCAAGA 57.168 45.000 0.00 0.00 43.62 3.02
26 27 4.640789 AAAAATTCCTACACACACGCAA 57.359 36.364 0.00 0.00 0.00 4.85
46 47 9.757227 CTGTTGGGAAACATAGTAATTTCAAAA 57.243 29.630 10.71 4.03 36.69 2.44
47 48 8.919145 ACTGTTGGGAAACATAGTAATTTCAAA 58.081 29.630 10.71 4.28 36.69 2.69
48 49 8.472007 ACTGTTGGGAAACATAGTAATTTCAA 57.528 30.769 10.71 0.00 36.69 2.69
49 50 8.356657 CAACTGTTGGGAAACATAGTAATTTCA 58.643 33.333 12.66 0.00 36.69 2.69
50 51 8.573035 TCAACTGTTGGGAAACATAGTAATTTC 58.427 33.333 19.55 2.90 34.65 2.17
51 52 8.472007 TCAACTGTTGGGAAACATAGTAATTT 57.528 30.769 19.55 0.00 31.47 1.82
52 53 8.472007 TTCAACTGTTGGGAAACATAGTAATT 57.528 30.769 19.55 0.00 31.47 1.40
53 54 7.309194 GCTTCAACTGTTGGGAAACATAGTAAT 60.309 37.037 19.55 0.00 31.47 1.89
54 55 6.016610 GCTTCAACTGTTGGGAAACATAGTAA 60.017 38.462 19.55 2.35 31.47 2.24
55 56 5.472137 GCTTCAACTGTTGGGAAACATAGTA 59.528 40.000 19.55 0.00 31.47 1.82
56 57 4.278419 GCTTCAACTGTTGGGAAACATAGT 59.722 41.667 19.55 0.00 31.47 2.12
57 58 4.520492 AGCTTCAACTGTTGGGAAACATAG 59.480 41.667 19.55 6.59 31.47 2.23
58 59 4.469657 AGCTTCAACTGTTGGGAAACATA 58.530 39.130 19.55 0.00 31.47 2.29
59 60 3.299503 AGCTTCAACTGTTGGGAAACAT 58.700 40.909 19.55 0.00 31.47 2.71
60 61 2.733956 AGCTTCAACTGTTGGGAAACA 58.266 42.857 19.55 0.00 0.00 2.83
61 62 3.119137 ACAAGCTTCAACTGTTGGGAAAC 60.119 43.478 19.55 4.31 0.00 2.78
62 63 3.096092 ACAAGCTTCAACTGTTGGGAAA 58.904 40.909 19.55 6.80 0.00 3.13
63 64 2.426738 CACAAGCTTCAACTGTTGGGAA 59.573 45.455 19.55 7.48 0.00 3.97
64 65 2.023673 CACAAGCTTCAACTGTTGGGA 58.976 47.619 19.55 8.65 0.00 4.37
65 66 1.536709 GCACAAGCTTCAACTGTTGGG 60.537 52.381 19.55 13.61 37.91 4.12
66 67 1.843992 GCACAAGCTTCAACTGTTGG 58.156 50.000 19.55 6.56 37.91 3.77
78 79 3.082698 TGATTCAACACAAGCACAAGC 57.917 42.857 0.00 0.00 42.56 4.01
140 141 4.870363 ACATCTACAACAAACAACATGCC 58.130 39.130 0.00 0.00 0.00 4.40
182 183 5.605534 GCTATCATACCAAGCATATCGGAT 58.394 41.667 0.00 0.00 36.26 4.18
187 188 6.225981 TCATCGCTATCATACCAAGCATAT 57.774 37.500 0.00 0.00 35.98 1.78
272 274 3.466836 CATAGCACACAACATACCGGAT 58.533 45.455 9.46 0.00 0.00 4.18
329 331 1.656652 AGATATTGCGTCTGTGTGGC 58.343 50.000 0.00 0.00 0.00 5.01
344 346 2.693591 CGACAAGGGCCTGACTAAGATA 59.306 50.000 6.92 0.00 0.00 1.98
367 369 1.338200 GGAGCAAACTGACTGTCGGAT 60.338 52.381 22.76 8.66 0.00 4.18
376 378 2.548057 GACAAACGATGGAGCAAACTGA 59.452 45.455 0.00 0.00 0.00 3.41
596 607 2.486982 GCTCACACATCTTGTTCAGCAT 59.513 45.455 0.00 0.00 39.80 3.79
739 751 3.072476 TCCATCGACTTTTCCACTTCCTT 59.928 43.478 0.00 0.00 0.00 3.36
846 858 3.709880 CTAACCGCGACATGGCCGA 62.710 63.158 8.23 0.00 0.00 5.54
902 914 6.071784 TGTTGTTAGTTGCGATTAGGAGTAGA 60.072 38.462 0.00 0.00 0.00 2.59
1128 1140 1.228552 GAAGGGCTTTGCAGTGGGA 60.229 57.895 0.00 0.00 0.00 4.37
1362 1380 0.106769 TGGCCTTGTTGTCAAGCAGA 60.107 50.000 3.32 0.00 46.74 4.26
1381 1399 1.388837 GCAACGAACCCAACACCCTT 61.389 55.000 0.00 0.00 0.00 3.95
1407 1425 3.233980 AGCACCCTGTGAGCGTCA 61.234 61.111 0.00 0.00 35.23 4.35
1515 1533 2.598637 CGTCATCGTCATCATCGTTGTT 59.401 45.455 0.00 0.00 32.27 2.83
1518 1536 2.451132 GTCGTCATCGTCATCATCGTT 58.549 47.619 0.00 0.00 38.33 3.85
1523 1541 1.733360 TGTACGTCGTCATCGTCATCA 59.267 47.619 0.00 0.00 41.72 3.07
1619 1637 0.396435 ACCGCAAGTTCACCATCAGA 59.604 50.000 0.00 0.00 0.00 3.27
1724 1742 4.570369 GGAGCAGAAGAGAAGTAAAGCATC 59.430 45.833 0.00 0.00 0.00 3.91
1917 1935 7.444487 GTCTTGAACCCTCTATAGTTGTTGTTT 59.556 37.037 0.00 0.00 0.00 2.83
2047 2065 3.114606 TCAGCCCAAACTGATGATCCTA 58.885 45.455 0.00 0.00 41.72 2.94
2048 2066 1.918262 TCAGCCCAAACTGATGATCCT 59.082 47.619 0.00 0.00 41.72 3.24
2054 2072 1.074405 TCAGCTTCAGCCCAAACTGAT 59.926 47.619 0.00 0.00 45.75 2.90
2301 2320 1.001487 CGCCATCTGCAAGTTGTTTGA 60.001 47.619 4.48 1.26 41.33 2.69
2322 2341 4.255833 TGAGCAAAAACAGGCCTTAATG 57.744 40.909 0.00 0.00 0.00 1.90
2327 2346 0.752658 GGTTGAGCAAAAACAGGCCT 59.247 50.000 0.00 0.00 0.00 5.19
2378 2397 0.454196 GGTTGCCGTTGTGAACAGTT 59.546 50.000 0.00 0.00 0.00 3.16
2404 2423 5.390087 TCTACTAGACATGCTCTTAGGGT 57.610 43.478 0.00 0.00 0.00 4.34
2412 2431 4.461450 TGAGGGATCTACTAGACATGCT 57.539 45.455 0.00 0.00 0.00 3.79
2413 2432 5.293560 GTTTGAGGGATCTACTAGACATGC 58.706 45.833 0.00 0.00 0.00 4.06
2414 2433 5.221541 GGGTTTGAGGGATCTACTAGACATG 60.222 48.000 0.00 0.00 0.00 3.21
2415 2434 4.902448 GGGTTTGAGGGATCTACTAGACAT 59.098 45.833 0.00 0.00 0.00 3.06
2416 2435 4.016479 AGGGTTTGAGGGATCTACTAGACA 60.016 45.833 0.00 0.00 0.00 3.41
2417 2436 4.548669 AGGGTTTGAGGGATCTACTAGAC 58.451 47.826 0.00 0.00 0.00 2.59
2418 2437 4.901785 AGGGTTTGAGGGATCTACTAGA 57.098 45.455 0.00 0.00 0.00 2.43
2419 2438 7.433537 TTTAAGGGTTTGAGGGATCTACTAG 57.566 40.000 0.00 0.00 0.00 2.57
2420 2439 7.849904 AGATTTAAGGGTTTGAGGGATCTACTA 59.150 37.037 0.00 0.00 0.00 1.82
2421 2440 6.678857 AGATTTAAGGGTTTGAGGGATCTACT 59.321 38.462 0.00 0.00 0.00 2.57
2422 2441 6.901300 AGATTTAAGGGTTTGAGGGATCTAC 58.099 40.000 0.00 0.00 0.00 2.59
2423 2442 8.632731 TTAGATTTAAGGGTTTGAGGGATCTA 57.367 34.615 0.00 0.00 0.00 1.98
2424 2443 7.525158 TTAGATTTAAGGGTTTGAGGGATCT 57.475 36.000 0.00 0.00 0.00 2.75
2425 2444 8.467598 GTTTTAGATTTAAGGGTTTGAGGGATC 58.532 37.037 0.00 0.00 0.00 3.36
2426 2445 8.177456 AGTTTTAGATTTAAGGGTTTGAGGGAT 58.823 33.333 0.00 0.00 0.00 3.85
2427 2446 7.532199 AGTTTTAGATTTAAGGGTTTGAGGGA 58.468 34.615 0.00 0.00 0.00 4.20
2428 2447 7.776618 AGTTTTAGATTTAAGGGTTTGAGGG 57.223 36.000 0.00 0.00 0.00 4.30
2429 2448 9.516546 ACTAGTTTTAGATTTAAGGGTTTGAGG 57.483 33.333 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.