Multiple sequence alignment - TraesCS5A01G136300

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 TraesCS5A01G136300 chr5A 100.000 2411 0 0 1 2411 307496116 307498526 0.000000e+00 4453
1 TraesCS5A01G136300 chr2D 93.587 2339 126 14 1 2330 260388082 260385759 0.000000e+00 3467
2 TraesCS5A01G136300 chr2D 92.894 2350 140 14 1 2329 167550649 167548306 0.000000e+00 3389
3 TraesCS5A01G136300 chr2D 91.820 2335 173 11 1 2326 471597554 471595229 0.000000e+00 3238
4 TraesCS5A01G136300 chr5D 92.756 2333 144 11 1 2324 249656390 249654074 0.000000e+00 3349
5 TraesCS5A01G136300 chr5D 93.258 89 4 2 2324 2411 313953429 313953342 1.950000e-26 130
6 TraesCS5A01G136300 chr5D 93.258 89 4 2 2324 2411 421059317 421059230 1.950000e-26 130
7 TraesCS5A01G136300 chr5D 93.258 89 4 2 2324 2411 490805234 490805147 1.950000e-26 130
8 TraesCS5A01G136300 chr4D 93.017 2277 140 10 49 2319 65499330 65497067 0.000000e+00 3306
9 TraesCS5A01G136300 chr4D 93.182 88 5 1 2324 2411 34578949 34578863 7.000000e-26 128
10 TraesCS5A01G136300 chr7D 92.324 2345 149 17 1 2323 188532559 188534894 0.000000e+00 3304
11 TraesCS5A01G136300 chr7D 88.844 986 77 10 1346 2323 244716650 244717610 0.000000e+00 1181
12 TraesCS5A01G136300 chr7D 93.258 89 4 2 2324 2411 410764190 410764277 1.950000e-26 130
13 TraesCS5A01G136300 chr7D 93.333 90 2 4 2324 2411 546314937 546315024 1.950000e-26 130
14 TraesCS5A01G136300 chr3D 92.212 2337 152 19 1 2323 397849383 397851703 0.000000e+00 3280
15 TraesCS5A01G136300 chr3D 91.900 2358 157 17 1 2333 415199873 415197525 0.000000e+00 3265
16 TraesCS5A01G136300 chr3D 93.333 90 2 4 2324 2411 373627171 373627258 1.950000e-26 130
17 TraesCS5A01G136300 chr2A 91.727 2333 151 23 1 2324 652910313 652912612 0.000000e+00 3201
18 TraesCS5A01G136300 chr2B 89.544 1712 135 16 630 2324 56505338 56507022 0.000000e+00 2130
19 TraesCS5A01G136300 chr6B 94.382 89 3 2 2324 2411 7518660 7518573 4.180000e-28 135
20 TraesCS5A01G136300 chr6B 93.258 89 4 2 2324 2411 168310423 168310510 1.950000e-26 130
21 TraesCS5A01G136300 chr6D 93.258 89 4 2 2324 2411 171618700 171618613 1.950000e-26 130
22 TraesCS5A01G136300 chr6D 92.135 89 5 2 2324 2411 181319126 181319213 9.050000e-25 124


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 TraesCS5A01G136300 chr5A 307496116 307498526 2410 False 4453 4453 100.000 1 2411 1 chr5A.!!$F1 2410
1 TraesCS5A01G136300 chr2D 260385759 260388082 2323 True 3467 3467 93.587 1 2330 1 chr2D.!!$R2 2329
2 TraesCS5A01G136300 chr2D 167548306 167550649 2343 True 3389 3389 92.894 1 2329 1 chr2D.!!$R1 2328
3 TraesCS5A01G136300 chr2D 471595229 471597554 2325 True 3238 3238 91.820 1 2326 1 chr2D.!!$R3 2325
4 TraesCS5A01G136300 chr5D 249654074 249656390 2316 True 3349 3349 92.756 1 2324 1 chr5D.!!$R1 2323
5 TraesCS5A01G136300 chr4D 65497067 65499330 2263 True 3306 3306 93.017 49 2319 1 chr4D.!!$R2 2270
6 TraesCS5A01G136300 chr7D 188532559 188534894 2335 False 3304 3304 92.324 1 2323 1 chr7D.!!$F1 2322
7 TraesCS5A01G136300 chr7D 244716650 244717610 960 False 1181 1181 88.844 1346 2323 1 chr7D.!!$F2 977
8 TraesCS5A01G136300 chr3D 397849383 397851703 2320 False 3280 3280 92.212 1 2323 1 chr3D.!!$F2 2322
9 TraesCS5A01G136300 chr3D 415197525 415199873 2348 True 3265 3265 91.900 1 2333 1 chr3D.!!$R1 2332
10 TraesCS5A01G136300 chr2A 652910313 652912612 2299 False 3201 3201 91.727 1 2324 1 chr2A.!!$F1 2323
11 TraesCS5A01G136300 chr2B 56505338 56507022 1684 False 2130 2130 89.544 630 2324 1 chr2B.!!$F1 1694

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
68 83 0.321564 TGGTGCTCATTTGACCTCGG 60.322 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 1957 0.174617 CGCTGGTTCCTCTCTTCTCC 59.825 60.0 0.0 0.0 0.0 3.71 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
68 83 0.321564 TGGTGCTCATTTGACCTCGG 60.322 55.000 0.00 0.00 0.00 4.63
84 99 2.267961 GGTCGTGCCAACTAGGGG 59.732 66.667 0.00 0.00 38.09 4.79
124 140 9.444600 TGACCATAGACCAAGTTTAGTATTTTC 57.555 33.333 0.00 0.00 0.00 2.29
129 145 7.086685 AGACCAAGTTTAGTATTTTCCCTCA 57.913 36.000 0.00 0.00 0.00 3.86
132 148 8.349568 ACCAAGTTTAGTATTTTCCCTCATTC 57.650 34.615 0.00 0.00 0.00 2.67
282 300 2.127708 CACCTAACCCTAGCTCCCAAT 58.872 52.381 0.00 0.00 0.00 3.16
294 312 2.184020 CTCCCAATGTCAGCCGTCCA 62.184 60.000 0.00 0.00 0.00 4.02
312 330 0.603707 CAATCATACCCTCGCGCCAT 60.604 55.000 0.00 0.00 0.00 4.40
358 377 5.152306 TCTAGAAGGAATTAGGTGGGCTA 57.848 43.478 0.00 0.00 0.00 3.93
362 381 2.050918 AGGAATTAGGTGGGCTAGCTC 58.949 52.381 15.72 12.12 38.31 4.09
473 492 4.082523 GCTGCTCGCCCACCACTA 62.083 66.667 0.00 0.00 0.00 2.74
511 532 2.297597 CGTTGTTATTGGGCCCAAAAGA 59.702 45.455 40.00 27.44 39.55 2.52
545 566 0.606944 TTGGGCCGTAGAATTGCGTT 60.607 50.000 0.00 0.00 0.00 4.84
612 635 7.306515 GCTCTGTATTTTTGCATCGTTTGAAAA 60.307 33.333 0.00 0.00 30.51 2.29
615 638 7.394872 TGTATTTTTGCATCGTTTGAAAACAC 58.605 30.769 6.72 0.00 38.81 3.32
683 706 8.749026 TTATTTTTATCATGCAAAATGGCCAT 57.251 26.923 14.09 14.09 34.94 4.40
744 767 1.550130 ATGACCACGGATTCCCACGT 61.550 55.000 0.00 0.00 45.25 4.49
767 790 6.855914 CGTGTGCAATTAGCTTCTTTTTCTTA 59.144 34.615 0.00 0.00 45.94 2.10
813 836 1.518572 CGTGTACACTCCCGATGCC 60.519 63.158 23.01 0.00 0.00 4.40
819 842 3.319198 ACTCCCGATGCCGTGGTT 61.319 61.111 0.00 0.00 0.00 3.67
886 909 3.685756 GGCCAAATAACACGTAGCACTAA 59.314 43.478 0.00 0.00 0.00 2.24
889 912 5.172934 CCAAATAACACGTAGCACTAAGGA 58.827 41.667 0.00 0.00 0.00 3.36
941 964 2.568062 CTCATCCATCTCCCATCCTCTG 59.432 54.545 0.00 0.00 0.00 3.35
944 967 1.291939 TCCATCTCCCATCCTCTGTGA 59.708 52.381 0.00 0.00 0.00 3.58
1059 1082 1.681327 GTCGGAGTGGCTCTACCCA 60.681 63.158 0.00 0.00 37.83 4.51
1101 1124 0.516877 CACTACGTGTGTGGGCAATG 59.483 55.000 13.48 0.00 41.53 2.82
1149 1172 2.261671 GAGTTCTTCCTCGCGCCA 59.738 61.111 0.00 0.00 0.00 5.69
1164 1187 2.907179 GCCAGGCTACCACCACCTT 61.907 63.158 3.29 0.00 0.00 3.50
1188 1211 1.212935 CGGGGATCTCCAAGGATGTTT 59.787 52.381 13.38 0.00 37.91 2.83
1296 1319 1.326951 GGGTGTTTTGGTGTGGCTGT 61.327 55.000 0.00 0.00 0.00 4.40
1305 1328 1.133823 TGGTGTGGCTGTGAGTTCATT 60.134 47.619 0.00 0.00 0.00 2.57
1332 1355 1.341482 ACCACCCACAACATGTTCACA 60.341 47.619 8.48 0.00 0.00 3.58
1415 1441 1.918800 CCCCGGAGAAGTGAAGGGT 60.919 63.158 0.73 0.00 40.44 4.34
1436 1462 2.192443 CGGAGGAGGAGCGAGGTA 59.808 66.667 0.00 0.00 0.00 3.08
1454 1480 0.179702 TAGAGAAGGCGGCGTCTAGA 59.820 55.000 26.15 14.67 0.00 2.43
1529 1577 8.494433 AGTTGTAATACCATTGGACTATGTGAT 58.506 33.333 10.37 0.00 0.00 3.06
1656 1704 3.555966 GCTTGTTGGCCCTATCTACATT 58.444 45.455 0.00 0.00 0.00 2.71
1660 1708 6.940298 GCTTGTTGGCCCTATCTACATTTATA 59.060 38.462 0.00 0.00 0.00 0.98
1711 1760 4.285003 TGTTAGTAACCACCTAGTGCATGT 59.715 41.667 10.51 0.00 31.34 3.21
1743 1793 5.826208 ACGAACCCTTCTTTTCTTACACAAT 59.174 36.000 0.00 0.00 0.00 2.71
1762 1812 5.125257 CACAATCCACAAATATGTAGCCACA 59.875 40.000 0.00 0.00 37.82 4.17
1792 1852 3.264104 GCATGCAGCCACAACATATTTT 58.736 40.909 14.21 0.00 37.23 1.82
1822 1882 4.864704 ATTTGTCGTAGCAAAATGGGTT 57.135 36.364 6.64 0.00 41.03 4.11
1889 1951 5.163364 ACGATGCTCTAAATTGAGGAGACAT 60.163 40.000 0.00 8.44 37.80 3.06
1895 1957 5.491070 TCTAAATTGAGGAGACATGTGTGG 58.509 41.667 1.15 0.00 0.00 4.17
2004 2088 0.673333 ACGCATCAACGCATGAAGGA 60.673 50.000 0.00 0.00 42.54 3.36
2017 2101 3.792053 GAAGGATCGGTCGGCGCAT 62.792 63.158 10.83 0.00 0.00 4.73
2018 2102 3.792053 AAGGATCGGTCGGCGCATC 62.792 63.158 10.83 1.55 0.00 3.91
2072 2170 1.399440 CATGCATAGCACGCTTCTGTT 59.601 47.619 0.00 0.00 43.04 3.16
2108 2209 3.950397 AGACATTTAATGCAAGGGACGA 58.050 40.909 4.68 0.00 0.00 4.20
2122 2223 0.604511 GGACGACCCAACGAAACCAT 60.605 55.000 0.00 0.00 37.03 3.55
2307 2410 1.077429 GCTAAGGAACCAGGGGCAG 60.077 63.158 0.00 0.00 0.00 4.85
2350 2453 8.604640 TTTTAAATATTCCAAAACGGGGAAAC 57.395 30.769 0.00 0.00 46.76 2.78
2351 2454 5.810080 AAATATTCCAAAACGGGGAAACA 57.190 34.783 0.00 0.00 46.76 2.83
2352 2455 5.400066 AATATTCCAAAACGGGGAAACAG 57.600 39.130 0.00 0.00 46.76 3.16
2353 2456 2.146920 TTCCAAAACGGGGAAACAGT 57.853 45.000 0.00 0.00 41.30 3.55
2354 2457 1.394618 TCCAAAACGGGGAAACAGTG 58.605 50.000 0.00 0.00 34.36 3.66
2355 2458 0.249280 CCAAAACGGGGAAACAGTGC 60.249 55.000 0.00 0.00 0.00 4.40
2356 2459 0.744281 CAAAACGGGGAAACAGTGCT 59.256 50.000 0.00 0.00 0.00 4.40
2357 2460 1.950909 CAAAACGGGGAAACAGTGCTA 59.049 47.619 0.00 0.00 0.00 3.49
2358 2461 2.556622 CAAAACGGGGAAACAGTGCTAT 59.443 45.455 0.00 0.00 0.00 2.97
2359 2462 2.579410 AACGGGGAAACAGTGCTATT 57.421 45.000 0.00 0.00 0.00 1.73
2360 2463 3.706600 AACGGGGAAACAGTGCTATTA 57.293 42.857 0.00 0.00 0.00 0.98
2361 2464 3.261981 ACGGGGAAACAGTGCTATTAG 57.738 47.619 0.00 0.00 0.00 1.73
2362 2465 2.835764 ACGGGGAAACAGTGCTATTAGA 59.164 45.455 0.00 0.00 0.00 2.10
2363 2466 3.262405 ACGGGGAAACAGTGCTATTAGAA 59.738 43.478 0.00 0.00 0.00 2.10
2364 2467 3.621715 CGGGGAAACAGTGCTATTAGAAC 59.378 47.826 0.00 0.00 0.00 3.01
2365 2468 4.623171 CGGGGAAACAGTGCTATTAGAACT 60.623 45.833 0.00 0.00 33.25 3.01
2373 2476 6.801539 CAGTGCTATTAGAACTGTTTTGGA 57.198 37.500 19.92 0.00 45.05 3.53
2374 2477 6.835914 CAGTGCTATTAGAACTGTTTTGGAG 58.164 40.000 19.92 0.00 45.05 3.86
2375 2478 6.428159 CAGTGCTATTAGAACTGTTTTGGAGT 59.572 38.462 19.92 0.00 45.05 3.85
2376 2479 6.651225 AGTGCTATTAGAACTGTTTTGGAGTC 59.349 38.462 3.35 0.00 31.34 3.36
2377 2480 6.426937 GTGCTATTAGAACTGTTTTGGAGTCA 59.573 38.462 0.00 0.00 0.00 3.41
2378 2481 6.650807 TGCTATTAGAACTGTTTTGGAGTCAG 59.349 38.462 0.00 0.00 35.60 3.51
2379 2482 6.651225 GCTATTAGAACTGTTTTGGAGTCAGT 59.349 38.462 0.00 0.00 43.04 3.41
2387 2490 7.549615 ACTGTTTTGGAGTCAGTTTACTTAC 57.450 36.000 0.00 0.00 39.00 2.34
2388 2491 6.541278 ACTGTTTTGGAGTCAGTTTACTTACC 59.459 38.462 0.00 0.00 39.00 2.85
2389 2492 5.524646 TGTTTTGGAGTCAGTTTACTTACCG 59.475 40.000 0.00 0.00 0.00 4.02
2390 2493 4.942761 TTGGAGTCAGTTTACTTACCGT 57.057 40.909 0.00 0.00 0.00 4.83
2391 2494 6.403866 TTTGGAGTCAGTTTACTTACCGTA 57.596 37.500 0.00 0.00 0.00 4.02
2392 2495 5.376854 TGGAGTCAGTTTACTTACCGTAC 57.623 43.478 0.00 0.00 0.00 3.67
2393 2496 4.083324 TGGAGTCAGTTTACTTACCGTACG 60.083 45.833 8.69 8.69 0.00 3.67
2394 2497 4.154195 GGAGTCAGTTTACTTACCGTACGA 59.846 45.833 18.76 0.00 0.00 3.43
2395 2498 5.035784 AGTCAGTTTACTTACCGTACGAC 57.964 43.478 18.76 3.94 0.00 4.34
2396 2499 4.515191 AGTCAGTTTACTTACCGTACGACA 59.485 41.667 18.76 0.00 0.00 4.35
2397 2500 5.182001 AGTCAGTTTACTTACCGTACGACAT 59.818 40.000 18.76 4.27 0.00 3.06
2398 2501 6.371548 AGTCAGTTTACTTACCGTACGACATA 59.628 38.462 18.76 3.20 0.00 2.29
2399 2502 6.466097 GTCAGTTTACTTACCGTACGACATAC 59.534 42.308 18.76 3.07 0.00 2.39
2400 2503 5.739161 CAGTTTACTTACCGTACGACATACC 59.261 44.000 18.76 0.00 0.00 2.73
2401 2504 5.648092 AGTTTACTTACCGTACGACATACCT 59.352 40.000 18.76 0.00 0.00 3.08
2402 2505 6.821665 AGTTTACTTACCGTACGACATACCTA 59.178 38.462 18.76 0.00 0.00 3.08
2403 2506 7.499232 AGTTTACTTACCGTACGACATACCTAT 59.501 37.037 18.76 0.00 0.00 2.57
2404 2507 7.801716 TTACTTACCGTACGACATACCTATT 57.198 36.000 18.76 0.00 0.00 1.73
2405 2508 6.305693 ACTTACCGTACGACATACCTATTC 57.694 41.667 18.76 0.00 0.00 1.75
2406 2509 3.885484 ACCGTACGACATACCTATTCG 57.115 47.619 18.76 0.00 38.73 3.34
2407 2510 2.031682 ACCGTACGACATACCTATTCGC 60.032 50.000 18.76 0.00 36.18 4.70
2408 2511 2.225019 CCGTACGACATACCTATTCGCT 59.775 50.000 18.76 0.00 36.18 4.93
2409 2512 3.304257 CCGTACGACATACCTATTCGCTT 60.304 47.826 18.76 0.00 36.18 4.68
2410 2513 4.285292 CGTACGACATACCTATTCGCTTT 58.715 43.478 10.44 0.00 36.18 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 83 0.250597 AAACCCCTAGTTGGCACGAC 60.251 55.000 0.00 0.00 39.19 4.34
77 92 6.014584 GGTCATTTTCATGAAAAACCCCTAGT 60.015 38.462 31.39 14.04 41.30 2.57
84 99 8.087750 TGGTCTATGGTCATTTTCATGAAAAAC 58.912 33.333 31.39 25.40 41.30 2.43
193 211 3.436704 CGAAGGCTTTGACTGAGCATAAA 59.563 43.478 8.93 0.00 41.89 1.40
263 281 2.127708 CATTGGGAGCTAGGGTTAGGT 58.872 52.381 0.00 0.00 40.20 3.08
282 300 1.134521 GGTATGATTGGACGGCTGACA 60.135 52.381 0.00 0.00 0.00 3.58
294 312 0.603707 CATGGCGCGAGGGTATGATT 60.604 55.000 12.10 0.00 0.00 2.57
312 330 0.247460 CAGATCTGAGGGTTGTCGCA 59.753 55.000 18.34 0.00 0.00 5.10
358 377 4.079850 CAGAGCCTGCACGGAGCT 62.080 66.667 6.40 0.00 45.94 4.09
612 635 1.877637 TGCTACGCAATGTCAAGTGT 58.122 45.000 1.27 1.27 34.76 3.55
636 659 5.720371 AATTTGGCCCTTAAAAATTTGGC 57.280 34.783 0.00 7.74 41.42 4.52
767 790 7.497579 GTGGGAAACAGTGGTTTGAAAAATAAT 59.502 33.333 0.00 0.00 46.84 1.28
770 793 5.182487 GTGGGAAACAGTGGTTTGAAAAAT 58.818 37.500 0.00 0.00 46.84 1.82
813 836 1.551145 CCGTTTTCAAACCAACCACG 58.449 50.000 0.00 0.00 35.51 4.94
819 842 4.015084 TGAAGTAACCCGTTTTCAAACCA 58.985 39.130 0.00 0.00 35.51 3.67
886 909 3.181439 GCAGAGGGTGGCTTAAATATCCT 60.181 47.826 0.00 0.00 0.00 3.24
941 964 0.807496 GCAAGAAGGGCAGATGTCAC 59.193 55.000 0.00 0.00 0.00 3.67
944 967 0.990374 AGAGCAAGAAGGGCAGATGT 59.010 50.000 0.00 0.00 0.00 3.06
1048 1071 3.009115 GCCAGGTGGGTAGAGCCA 61.009 66.667 0.00 0.00 39.65 4.75
1059 1082 1.006571 CTCAACGTACACGCCAGGT 60.007 57.895 0.85 0.00 44.43 4.00
1147 1170 1.299976 GAAGGTGGTGGTAGCCTGG 59.700 63.158 0.00 0.00 32.16 4.45
1149 1172 2.291043 CGGAAGGTGGTGGTAGCCT 61.291 63.158 0.00 0.00 0.00 4.58
1164 1187 3.154473 CTTGGAGATCCCCGCGGA 61.154 66.667 30.73 8.21 44.33 5.54
1188 1211 0.895530 GGATGACCTCCTCGACACAA 59.104 55.000 0.00 0.00 41.29 3.33
1208 1231 2.596338 CAACCACCACCCCGTTCC 60.596 66.667 0.00 0.00 0.00 3.62
1209 1232 3.292159 GCAACCACCACCCCGTTC 61.292 66.667 0.00 0.00 0.00 3.95
1305 1328 0.323816 TGTTGTGGGTGGTGAAAGCA 60.324 50.000 0.00 0.00 45.41 3.91
1332 1355 2.572104 GGGGAAGATGTTGGTGTACTCT 59.428 50.000 0.00 0.00 0.00 3.24
1436 1462 1.077644 TCTAGACGCCGCCTTCTCT 60.078 57.895 0.00 0.00 0.00 3.10
1512 1555 5.309020 AGCATCTATCACATAGTCCAATGGT 59.691 40.000 0.00 0.00 34.47 3.55
1519 1567 5.355596 GCCCATAGCATCTATCACATAGTC 58.644 45.833 0.00 0.00 42.97 2.59
1605 1653 4.857037 CACGATCACATAGTTGAAACTCGA 59.143 41.667 0.00 0.00 40.37 4.04
1607 1655 4.627467 AGCACGATCACATAGTTGAAACTC 59.373 41.667 0.00 0.00 40.37 3.01
1660 1708 6.183360 GCGAGCTCTCTAAGAAAACAATCAAT 60.183 38.462 12.85 0.00 0.00 2.57
1711 1760 1.053424 AGAAGGGTTCGTTGTGGCTA 58.947 50.000 0.00 0.00 34.02 3.93
1743 1793 5.063204 GCTATGTGGCTACATATTTGTGGA 58.937 41.667 21.52 0.94 45.90 4.02
1762 1812 0.471191 TGGCTGCATGCACTAGCTAT 59.529 50.000 24.35 0.00 45.15 2.97
1822 1882 2.885113 CGATCCACTCGCACCTGA 59.115 61.111 0.00 0.00 41.14 3.86
1889 1951 1.971357 GTTCCTCTCTTCTCCCACACA 59.029 52.381 0.00 0.00 0.00 3.72
1895 1957 0.174617 CGCTGGTTCCTCTCTTCTCC 59.825 60.000 0.00 0.00 0.00 3.71
1993 2058 1.226974 CGACCGATCCTTCATGCGT 60.227 57.895 0.00 0.00 0.00 5.24
2018 2102 2.617225 CTGCATGCGTCGATGTCG 59.383 61.111 14.09 0.00 41.45 4.35
2019 2103 3.009140 CCTGCATGCGTCGATGTC 58.991 61.111 14.09 0.00 0.00 3.06
2084 2182 5.527214 TCGTCCCTTGCATTAAATGTCTATG 59.473 40.000 0.00 0.00 0.00 2.23
2085 2183 5.527582 GTCGTCCCTTGCATTAAATGTCTAT 59.472 40.000 0.00 0.00 0.00 1.98
2089 2189 2.752903 GGTCGTCCCTTGCATTAAATGT 59.247 45.455 0.00 0.00 0.00 2.71
2108 2209 1.906333 GGCCATGGTTTCGTTGGGT 60.906 57.895 14.67 0.00 0.00 4.51
2122 2223 1.303236 CTGTTCGACCATTGGGCCA 60.303 57.895 0.00 0.00 37.90 5.36
2230 2333 4.608514 TCCCCACTCCCTTGCCCA 62.609 66.667 0.00 0.00 0.00 5.36
2329 2432 5.305902 ACTGTTTCCCCGTTTTGGAATATTT 59.694 36.000 0.00 0.00 41.36 1.40
2332 2435 3.570550 CACTGTTTCCCCGTTTTGGAATA 59.429 43.478 0.00 0.00 41.36 1.75
2333 2436 2.364002 CACTGTTTCCCCGTTTTGGAAT 59.636 45.455 0.00 0.00 41.36 3.01
2334 2437 1.751924 CACTGTTTCCCCGTTTTGGAA 59.248 47.619 0.00 0.00 42.00 3.53
2335 2438 1.394618 CACTGTTTCCCCGTTTTGGA 58.605 50.000 0.00 0.00 42.00 3.53
2336 2439 0.249280 GCACTGTTTCCCCGTTTTGG 60.249 55.000 0.00 0.00 37.55 3.28
2337 2440 0.744281 AGCACTGTTTCCCCGTTTTG 59.256 50.000 0.00 0.00 0.00 2.44
2338 2441 2.351706 TAGCACTGTTTCCCCGTTTT 57.648 45.000 0.00 0.00 0.00 2.43
2339 2442 2.579410 ATAGCACTGTTTCCCCGTTT 57.421 45.000 0.00 0.00 0.00 3.60
2340 2443 2.579410 AATAGCACTGTTTCCCCGTT 57.421 45.000 0.00 0.00 0.00 4.44
2341 2444 2.835764 TCTAATAGCACTGTTTCCCCGT 59.164 45.455 0.00 0.00 0.00 5.28
2342 2445 3.536956 TCTAATAGCACTGTTTCCCCG 57.463 47.619 0.00 0.00 0.00 5.73
2343 2446 4.636206 CAGTTCTAATAGCACTGTTTCCCC 59.364 45.833 11.11 0.00 35.27 4.81
2344 2447 5.803020 CAGTTCTAATAGCACTGTTTCCC 57.197 43.478 11.11 0.00 35.27 3.97
2350 2453 6.428159 ACTCCAAAACAGTTCTAATAGCACTG 59.572 38.462 16.45 16.45 43.56 3.66
2351 2454 6.534634 ACTCCAAAACAGTTCTAATAGCACT 58.465 36.000 0.00 0.00 0.00 4.40
2352 2455 6.426937 TGACTCCAAAACAGTTCTAATAGCAC 59.573 38.462 0.00 0.00 0.00 4.40
2353 2456 6.530120 TGACTCCAAAACAGTTCTAATAGCA 58.470 36.000 0.00 0.00 0.00 3.49
2354 2457 6.651225 ACTGACTCCAAAACAGTTCTAATAGC 59.349 38.462 0.00 0.00 41.21 2.97
2363 2466 6.541278 GGTAAGTAAACTGACTCCAAAACAGT 59.459 38.462 0.00 0.00 45.02 3.55
2364 2467 6.292703 CGGTAAGTAAACTGACTCCAAAACAG 60.293 42.308 0.00 0.00 37.62 3.16
2365 2468 5.524646 CGGTAAGTAAACTGACTCCAAAACA 59.475 40.000 0.00 0.00 0.00 2.83
2366 2469 5.525012 ACGGTAAGTAAACTGACTCCAAAAC 59.475 40.000 0.00 0.00 0.00 2.43
2367 2470 5.673514 ACGGTAAGTAAACTGACTCCAAAA 58.326 37.500 0.00 0.00 0.00 2.44
2368 2471 5.280654 ACGGTAAGTAAACTGACTCCAAA 57.719 39.130 0.00 0.00 0.00 3.28
2369 2472 4.942761 ACGGTAAGTAAACTGACTCCAA 57.057 40.909 0.00 0.00 0.00 3.53
2370 2473 4.083324 CGTACGGTAAGTAAACTGACTCCA 60.083 45.833 7.57 0.00 37.02 3.86
2371 2474 4.154195 TCGTACGGTAAGTAAACTGACTCC 59.846 45.833 16.52 0.00 37.02 3.85
2372 2475 5.082723 GTCGTACGGTAAGTAAACTGACTC 58.917 45.833 16.52 0.00 37.02 3.36
2373 2476 4.515191 TGTCGTACGGTAAGTAAACTGACT 59.485 41.667 16.52 0.00 37.02 3.41
2374 2477 4.783242 TGTCGTACGGTAAGTAAACTGAC 58.217 43.478 16.52 1.62 37.02 3.51
2375 2478 5.627499 ATGTCGTACGGTAAGTAAACTGA 57.373 39.130 16.52 0.00 37.02 3.41
2376 2479 5.739161 GGTATGTCGTACGGTAAGTAAACTG 59.261 44.000 16.52 0.00 37.02 3.16
2377 2480 5.648092 AGGTATGTCGTACGGTAAGTAAACT 59.352 40.000 16.52 0.23 37.02 2.66
2378 2481 5.880341 AGGTATGTCGTACGGTAAGTAAAC 58.120 41.667 16.52 3.92 37.02 2.01
2379 2482 7.801716 ATAGGTATGTCGTACGGTAAGTAAA 57.198 36.000 16.52 0.00 37.02 2.01
2380 2483 7.307160 CGAATAGGTATGTCGTACGGTAAGTAA 60.307 40.741 16.52 0.00 37.02 2.24
2381 2484 6.145534 CGAATAGGTATGTCGTACGGTAAGTA 59.854 42.308 16.52 0.00 33.94 2.24
2382 2485 5.050091 CGAATAGGTATGTCGTACGGTAAGT 60.050 44.000 16.52 0.33 33.94 2.24
2383 2486 5.377358 CGAATAGGTATGTCGTACGGTAAG 58.623 45.833 16.52 0.00 33.94 2.34
2384 2487 4.319477 GCGAATAGGTATGTCGTACGGTAA 60.319 45.833 16.52 1.42 37.12 2.85
2385 2488 3.186409 GCGAATAGGTATGTCGTACGGTA 59.814 47.826 16.52 5.07 37.12 4.02
2386 2489 2.031682 GCGAATAGGTATGTCGTACGGT 60.032 50.000 16.52 4.73 37.12 4.83
2387 2490 2.225019 AGCGAATAGGTATGTCGTACGG 59.775 50.000 16.52 0.00 37.12 4.02
2388 2491 3.532892 AGCGAATAGGTATGTCGTACG 57.467 47.619 9.53 9.53 37.12 3.67


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

AutoCloner maintained by Alex Coulton.