Multiple sequence alignment - TraesCS4D01G148200

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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 TraesCS4D01G148200 chr4D 100.000 1594 0 0 992 2585 145625252 145623659 0.000000e+00 2944.0
1 TraesCS4D01G148200 chr4D 89.577 662 54 12 1864 2518 7224189 7223536 0.000000e+00 826.0
2 TraesCS4D01G148200 chr4D 100.000 378 0 0 1 378 145626243 145625866 0.000000e+00 699.0
3 TraesCS4D01G148200 chr5D 96.914 875 25 1 992 1864 326744050 326744924 0.000000e+00 1465.0
4 TraesCS4D01G148200 chr5D 84.536 194 17 4 58 238 292683267 292683460 2.040000e-41 180.0
5 TraesCS4D01G148200 chrUn 95.439 877 37 2 992 1866 79926012 79925137 0.000000e+00 1395.0
6 TraesCS4D01G148200 chrUn 94.785 882 39 3 992 1866 108949053 108948172 0.000000e+00 1367.0
7 TraesCS4D01G148200 chr3D 94.886 880 40 3 992 1866 526482023 526481144 0.000000e+00 1371.0
8 TraesCS4D01G148200 chr3D 86.792 265 12 9 58 300 104700383 104700120 9.110000e-70 274.0
9 TraesCS4D01G148200 chr3D 80.290 345 25 14 58 378 104693262 104692937 1.200000e-53 220.0
10 TraesCS4D01G148200 chr3D 78.656 253 21 10 58 285 181651334 181651090 1.250000e-28 137.0
11 TraesCS4D01G148200 chr3D 83.721 86 11 3 156 238 608182365 608182450 7.670000e-11 78.7
12 TraesCS4D01G148200 chr2D 94.767 879 37 3 992 1868 489651467 489652338 0.000000e+00 1360.0
13 TraesCS4D01G148200 chr2D 94.400 875 44 2 992 1864 54889997 54889126 0.000000e+00 1339.0
14 TraesCS4D01G148200 chr2D 92.237 541 37 5 2049 2585 623766261 623766800 0.000000e+00 761.0
15 TraesCS4D01G148200 chr2D 83.965 343 21 5 58 367 109401114 109401455 5.410000e-77 298.0
16 TraesCS4D01G148200 chr2D 85.075 268 13 6 58 299 6719983 6719717 5.520000e-62 248.0
17 TraesCS4D01G148200 chr6D 94.647 878 39 5 992 1864 18023140 18022266 0.000000e+00 1354.0
18 TraesCS4D01G148200 chr6D 81.600 250 24 4 58 285 46861960 46862209 1.220000e-43 187.0
19 TraesCS4D01G148200 chr1D 94.539 879 43 2 994 1867 479343118 479342240 0.000000e+00 1352.0
20 TraesCS4D01G148200 chr1D 82.812 320 23 7 54 348 479343751 479343439 9.180000e-65 257.0
21 TraesCS4D01G148200 chr1D 81.009 337 26 12 58 367 13229704 13229379 1.550000e-57 233.0
22 TraesCS4D01G148200 chr1D 80.178 338 34 13 60 378 396219898 396219575 3.350000e-54 222.0
23 TraesCS4D01G148200 chr1D 82.700 237 15 5 57 267 365895910 365896146 1.220000e-43 187.0
24 TraesCS4D01G148200 chr1D 93.578 109 6 1 51 158 422067264 422067156 7.400000e-36 161.0
25 TraesCS4D01G148200 chr7D 94.299 877 45 2 992 1866 147577041 147576168 0.000000e+00 1338.0
26 TraesCS4D01G148200 chr7D 82.471 348 20 14 60 374 376527805 376528144 1.520000e-67 267.0
27 TraesCS4D01G148200 chr1B 86.364 704 56 11 1864 2534 640571379 640572075 0.000000e+00 732.0
28 TraesCS4D01G148200 chr1B 80.137 146 19 8 64 204 475466568 475466428 1.640000e-17 100.0
29 TraesCS4D01G148200 chr5A 94.097 288 15 2 1864 2151 19986882 19986597 1.100000e-118 436.0
30 TraesCS4D01G148200 chr5A 93.403 288 17 2 1864 2151 303997868 303997583 2.380000e-115 425.0
31 TraesCS4D01G148200 chr5A 80.357 336 29 15 58 363 131801274 131800946 1.200000e-53 220.0
32 TraesCS4D01G148200 chr3B 86.119 353 33 8 2173 2518 645328115 645328458 1.460000e-97 366.0
33 TraesCS4D01G148200 chr3B 89.888 267 22 3 1864 2126 645327850 645328115 3.190000e-89 339.0
34 TraesCS4D01G148200 chr5B 83.891 329 16 5 58 349 697574814 697575142 1.960000e-71 279.0
35 TraesCS4D01G148200 chr7B 80.347 346 32 13 60 378 518467895 518467559 2.000000e-56 230.0
36 TraesCS4D01G148200 chr7B 80.460 261 26 14 60 301 123403982 123403728 2.640000e-40 176.0
37 TraesCS4D01G148200 chr7A 79.872 313 19 8 62 330 48115273 48115585 3.400000e-44 189.0
38 TraesCS4D01G148200 chr1A 78.700 277 26 15 60 309 304685549 304685279 1.240000e-33 154.0
39 TraesCS4D01G148200 chr1A 78.339 277 27 16 60 309 304523853 304523583 5.760000e-32 148.0
40 TraesCS4D01G148200 chr2B 94.444 54 3 0 7 60 631209678 631209625 1.650000e-12 84.2
41 TraesCS4D01G148200 chr2B 92.593 54 4 0 7 60 177203645 177203698 7.670000e-11 78.7


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 TraesCS4D01G148200 chr4D 145623659 145626243 2584 True 1821.5 2944 100.0000 1 2585 2 chr4D.!!$R2 2584
1 TraesCS4D01G148200 chr4D 7223536 7224189 653 True 826.0 826 89.5770 1864 2518 1 chr4D.!!$R1 654
2 TraesCS4D01G148200 chr5D 326744050 326744924 874 False 1465.0 1465 96.9140 992 1864 1 chr5D.!!$F2 872
3 TraesCS4D01G148200 chrUn 79925137 79926012 875 True 1395.0 1395 95.4390 992 1866 1 chrUn.!!$R1 874
4 TraesCS4D01G148200 chrUn 108948172 108949053 881 True 1367.0 1367 94.7850 992 1866 1 chrUn.!!$R2 874
5 TraesCS4D01G148200 chr3D 526481144 526482023 879 True 1371.0 1371 94.8860 992 1866 1 chr3D.!!$R4 874
6 TraesCS4D01G148200 chr2D 489651467 489652338 871 False 1360.0 1360 94.7670 992 1868 1 chr2D.!!$F2 876
7 TraesCS4D01G148200 chr2D 54889126 54889997 871 True 1339.0 1339 94.4000 992 1864 1 chr2D.!!$R2 872
8 TraesCS4D01G148200 chr2D 623766261 623766800 539 False 761.0 761 92.2370 2049 2585 1 chr2D.!!$F3 536
9 TraesCS4D01G148200 chr6D 18022266 18023140 874 True 1354.0 1354 94.6470 992 1864 1 chr6D.!!$R1 872
10 TraesCS4D01G148200 chr1D 479342240 479343751 1511 True 804.5 1352 88.6755 54 1867 2 chr1D.!!$R4 1813
11 TraesCS4D01G148200 chr7D 147576168 147577041 873 True 1338.0 1338 94.2990 992 1866 1 chr7D.!!$R1 874
12 TraesCS4D01G148200 chr1B 640571379 640572075 696 False 732.0 732 86.3640 1864 2534 1 chr1B.!!$F1 670
13 TraesCS4D01G148200 chr3B 645327850 645328458 608 False 352.5 366 88.0035 1864 2518 2 chr3B.!!$F1 654

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
222 235 0.103208 CACGAGGTGCATCTAGTCCC 59.897 60.000 10.06 0.0 0.0 4.46 F
1283 1311 1.068748 CCCGACGAAGAAGAAGACGAA 60.069 52.381 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 1319 1.009335 CACTGACGACAACCGACGA 60.009 57.895 0.0 0.0 41.76 4.20 R
2390 2466 1.003580 GGAGTCCATGAGAGGCAACAA 59.996 52.381 3.6 0.0 41.41 2.83 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
24 25 7.067496 TCATTCCCTTCTCCTATGATGTTAC 57.933 40.000 0.00 0.00 0.00 2.50
25 26 6.615316 TCATTCCCTTCTCCTATGATGTTACA 59.385 38.462 0.00 0.00 0.00 2.41
26 27 5.871396 TCCCTTCTCCTATGATGTTACAC 57.129 43.478 0.00 0.00 0.00 2.90
27 28 5.277250 TCCCTTCTCCTATGATGTTACACA 58.723 41.667 0.00 0.00 0.00 3.72
28 29 5.905331 TCCCTTCTCCTATGATGTTACACAT 59.095 40.000 0.00 0.00 42.43 3.21
29 30 6.386927 TCCCTTCTCCTATGATGTTACACATT 59.613 38.462 5.94 0.00 39.27 2.71
30 31 7.567250 TCCCTTCTCCTATGATGTTACACATTA 59.433 37.037 5.94 0.00 39.27 1.90
31 32 8.378565 CCCTTCTCCTATGATGTTACACATTAT 58.621 37.037 5.94 0.46 39.27 1.28
44 45 9.845740 ATGTTACACATTATACTATTTGAGCCA 57.154 29.630 0.00 0.00 34.67 4.75
45 46 9.845740 TGTTACACATTATACTATTTGAGCCAT 57.154 29.630 0.00 0.00 0.00 4.40
47 48 9.845740 TTACACATTATACTATTTGAGCCATGT 57.154 29.630 0.00 0.00 0.00 3.21
48 49 8.752005 ACACATTATACTATTTGAGCCATGTT 57.248 30.769 0.00 0.00 0.00 2.71
49 50 8.623903 ACACATTATACTATTTGAGCCATGTTG 58.376 33.333 0.00 0.00 0.00 3.33
50 51 7.592533 CACATTATACTATTTGAGCCATGTTGC 59.407 37.037 0.00 0.00 0.00 4.17
51 52 6.633500 TTATACTATTTGAGCCATGTTGCC 57.367 37.500 0.00 0.00 0.00 4.52
52 53 3.091633 ACTATTTGAGCCATGTTGCCT 57.908 42.857 0.00 0.00 0.00 4.75
53 54 3.434309 ACTATTTGAGCCATGTTGCCTT 58.566 40.909 0.00 0.00 0.00 4.35
54 55 3.834231 ACTATTTGAGCCATGTTGCCTTT 59.166 39.130 0.00 0.00 0.00 3.11
55 56 2.529780 TTTGAGCCATGTTGCCTTTG 57.470 45.000 0.00 0.00 0.00 2.77
56 57 0.680618 TTGAGCCATGTTGCCTTTGG 59.319 50.000 0.00 0.00 0.00 3.28
57 58 0.469705 TGAGCCATGTTGCCTTTGGT 60.470 50.000 0.00 0.00 32.90 3.67
86 87 9.935241 GAGCATCTCCAATAGATAGTTCAAATA 57.065 33.333 0.00 0.00 43.42 1.40
189 202 2.737783 TGTAAAATACAACACCTCGCGG 59.262 45.455 6.13 0.00 35.38 6.46
209 222 3.727673 CGGTGCAAATTTACATCACGAGG 60.728 47.826 2.67 0.00 0.00 4.63
217 230 4.729227 TTTACATCACGAGGTGCATCTA 57.271 40.909 0.00 0.00 32.98 1.98
222 235 0.103208 CACGAGGTGCATCTAGTCCC 59.897 60.000 10.06 0.00 0.00 4.46
267 291 3.440415 CTTTCCTTTCCCGCCCGC 61.440 66.667 0.00 0.00 0.00 6.13
348 376 4.742201 CGCCCGCATAGGATCCGG 62.742 72.222 5.98 3.02 45.00 5.14
350 378 4.394712 CCCGCATAGGATCCGGCC 62.395 72.222 16.96 0.00 45.00 6.13
351 379 4.394712 CCGCATAGGATCCGGCCC 62.395 72.222 16.96 0.00 45.00 5.80
352 380 4.394712 CGCATAGGATCCGGCCCC 62.395 72.222 16.96 0.00 0.00 5.80
353 381 4.394712 GCATAGGATCCGGCCCCG 62.395 72.222 5.98 0.00 39.44 5.73
354 382 4.394712 CATAGGATCCGGCCCCGC 62.395 72.222 5.98 0.00 38.24 6.13
374 402 4.038080 CGCCCCTGCCGTTGTTTC 62.038 66.667 0.00 0.00 0.00 2.78
375 403 3.680786 GCCCCTGCCGTTGTTTCC 61.681 66.667 0.00 0.00 0.00 3.13
376 404 2.203422 CCCCTGCCGTTGTTTCCA 60.203 61.111 0.00 0.00 0.00 3.53
377 405 2.561037 CCCCTGCCGTTGTTTCCAC 61.561 63.158 0.00 0.00 0.00 4.02
1283 1311 1.068748 CCCGACGAAGAAGAAGACGAA 60.069 52.381 0.00 0.00 0.00 3.85
1291 1319 5.216648 CGAAGAAGAAGACGAAGAAGAAGT 58.783 41.667 0.00 0.00 0.00 3.01
1332 1360 2.750637 GAGACCGACGAGGAGGCA 60.751 66.667 8.56 0.00 45.00 4.75
1509 1543 1.258445 GGGCAGACTTCTCGGAGGAA 61.258 60.000 4.96 0.00 0.00 3.36
1722 1764 7.835682 ACATCTTCATTTTGGACCATCTATTGA 59.164 33.333 0.00 0.00 0.00 2.57
1763 1805 7.016072 ACCATTAATTTGGACCATCTGTTGAAA 59.984 33.333 3.10 0.00 39.25 2.69
1805 1847 2.739379 CAAAACACACTTTTTGGCGGTT 59.261 40.909 1.19 0.00 41.07 4.44
1871 1915 7.365497 TCTATTGGAGATGCTCTTACATTGA 57.635 36.000 0.00 0.00 0.00 2.57
1891 1935 8.216423 ACATTGATCCAGTTTTCATAGCTAGAT 58.784 33.333 0.00 0.00 0.00 1.98
1910 1954 6.037281 GCTAGATTTTAGAGCCAGGTAACAAC 59.963 42.308 0.00 0.00 41.41 3.32
1966 2025 7.044901 CCGACGATATAGTAGATACAAATTGCG 60.045 40.741 0.00 0.00 0.00 4.85
2184 2254 4.574828 ACATGAACACAGTTCTGGTTACAC 59.425 41.667 0.00 0.00 0.00 2.90
2329 2404 2.432456 CGAGCTGCCGCAAGTACA 60.432 61.111 2.05 0.00 39.10 2.90
2390 2466 4.466726 GTCCAGGTTATGACTACTGACCTT 59.533 45.833 0.00 0.00 38.62 3.50
2400 2476 2.706190 ACTACTGACCTTTGTTGCCTCT 59.294 45.455 0.00 0.00 0.00 3.69
2455 2546 3.576078 AGGTGATGTGACTTTTGACCA 57.424 42.857 0.00 0.00 0.00 4.02
2490 2583 6.300354 CCACTACTAAATTTGGCTAATCCG 57.700 41.667 0.00 0.00 37.80 4.18
2491 2584 6.053005 CCACTACTAAATTTGGCTAATCCGA 58.947 40.000 0.00 0.00 37.80 4.55
2492 2585 6.202954 CCACTACTAAATTTGGCTAATCCGAG 59.797 42.308 0.00 0.00 37.80 4.63
2493 2586 6.761714 CACTACTAAATTTGGCTAATCCGAGT 59.238 38.462 0.00 2.31 37.80 4.18
2494 2587 6.985059 ACTACTAAATTTGGCTAATCCGAGTC 59.015 38.462 0.00 0.00 37.80 3.36
2495 2588 5.123936 ACTAAATTTGGCTAATCCGAGTCC 58.876 41.667 0.00 0.00 37.80 3.85
2496 2589 3.644966 AATTTGGCTAATCCGAGTCCA 57.355 42.857 0.00 0.00 37.80 4.02
2497 2590 3.644966 ATTTGGCTAATCCGAGTCCAA 57.355 42.857 0.00 0.00 37.80 3.53
2498 2591 3.644966 TTTGGCTAATCCGAGTCCAAT 57.355 42.857 0.00 0.00 34.63 3.16
2499 2592 4.764050 TTTGGCTAATCCGAGTCCAATA 57.236 40.909 0.00 0.00 34.63 1.90
2500 2593 4.336889 TTGGCTAATCCGAGTCCAATAG 57.663 45.455 0.00 0.00 37.80 1.73
2501 2594 3.572642 TGGCTAATCCGAGTCCAATAGA 58.427 45.455 0.00 0.00 37.80 1.98
2502 2595 3.964688 TGGCTAATCCGAGTCCAATAGAA 59.035 43.478 0.00 0.00 37.80 2.10
2503 2596 4.593206 TGGCTAATCCGAGTCCAATAGAAT 59.407 41.667 0.00 0.00 37.80 2.40
2504 2597 5.071788 TGGCTAATCCGAGTCCAATAGAATT 59.928 40.000 0.00 0.00 37.80 2.17
2505 2598 5.998363 GGCTAATCCGAGTCCAATAGAATTT 59.002 40.000 0.00 0.00 0.00 1.82
2506 2599 7.159372 GGCTAATCCGAGTCCAATAGAATTTA 58.841 38.462 0.00 0.00 0.00 1.40
2507 2600 7.824779 GGCTAATCCGAGTCCAATAGAATTTAT 59.175 37.037 0.00 0.00 0.00 1.40
2508 2601 8.660373 GCTAATCCGAGTCCAATAGAATTTATG 58.340 37.037 0.00 0.00 0.00 1.90
2509 2602 7.440523 AATCCGAGTCCAATAGAATTTATGC 57.559 36.000 0.00 0.00 0.00 3.14
2510 2603 5.924356 TCCGAGTCCAATAGAATTTATGCA 58.076 37.500 0.00 0.00 0.00 3.96
2511 2604 6.533730 TCCGAGTCCAATAGAATTTATGCAT 58.466 36.000 3.79 3.79 0.00 3.96
2512 2605 6.650807 TCCGAGTCCAATAGAATTTATGCATC 59.349 38.462 0.19 0.00 0.00 3.91
2513 2606 6.652481 CCGAGTCCAATAGAATTTATGCATCT 59.348 38.462 0.19 0.00 0.00 2.90
2514 2607 7.360691 CCGAGTCCAATAGAATTTATGCATCTG 60.361 40.741 0.19 0.00 0.00 2.90
2515 2608 7.211966 AGTCCAATAGAATTTATGCATCTGC 57.788 36.000 0.19 0.00 42.50 4.26
2531 2624 4.980434 GCATCTGCACATATTCATTGTTCC 59.020 41.667 0.00 0.00 41.59 3.62
2532 2625 5.450826 GCATCTGCACATATTCATTGTTCCA 60.451 40.000 0.00 0.00 41.59 3.53
2533 2626 6.737622 GCATCTGCACATATTCATTGTTCCAT 60.738 38.462 0.00 0.00 41.59 3.41
2534 2627 7.522562 GCATCTGCACATATTCATTGTTCCATA 60.523 37.037 0.00 0.00 41.59 2.74
2535 2628 8.520351 CATCTGCACATATTCATTGTTCCATAT 58.480 33.333 0.00 0.00 0.00 1.78
2536 2629 8.102800 TCTGCACATATTCATTGTTCCATATC 57.897 34.615 0.00 0.00 0.00 1.63
2537 2630 7.940688 TCTGCACATATTCATTGTTCCATATCT 59.059 33.333 0.00 0.00 0.00 1.98
2538 2631 8.467963 TGCACATATTCATTGTTCCATATCTT 57.532 30.769 0.00 0.00 0.00 2.40
2539 2632 9.571816 TGCACATATTCATTGTTCCATATCTTA 57.428 29.630 0.00 0.00 0.00 2.10
2561 2654 8.876181 TCTTATCCGAGTCCAATGGAATTTATA 58.124 33.333 2.31 0.00 31.22 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.708054 GTGTAACATCATAGGAGAAGGGAATG 59.292 42.308 0.00 0.00 36.32 2.67
2 3 6.386927 TGTGTAACATCATAGGAGAAGGGAAT 59.613 38.462 0.00 0.00 45.67 3.01
4 5 5.277250 TGTGTAACATCATAGGAGAAGGGA 58.723 41.667 0.00 0.00 45.67 4.20
5 6 5.614324 TGTGTAACATCATAGGAGAAGGG 57.386 43.478 0.00 0.00 45.67 3.95
21 22 9.845740 ACATGGCTCAAATAGTATAATGTGTAA 57.154 29.630 0.00 0.00 0.00 2.41
22 23 9.845740 AACATGGCTCAAATAGTATAATGTGTA 57.154 29.630 0.00 0.00 0.00 2.90
23 24 8.623903 CAACATGGCTCAAATAGTATAATGTGT 58.376 33.333 0.00 0.00 0.00 3.72
24 25 7.592533 GCAACATGGCTCAAATAGTATAATGTG 59.407 37.037 0.00 0.00 0.00 3.21
25 26 7.255590 GGCAACATGGCTCAAATAGTATAATGT 60.256 37.037 0.00 0.00 40.14 2.71
26 27 7.086376 GGCAACATGGCTCAAATAGTATAATG 58.914 38.462 0.00 0.00 40.14 1.90
27 28 7.219484 GGCAACATGGCTCAAATAGTATAAT 57.781 36.000 0.00 0.00 40.14 1.28
28 29 6.633500 GGCAACATGGCTCAAATAGTATAA 57.367 37.500 0.00 0.00 40.14 0.98
41 42 1.892474 TCTAACCAAAGGCAACATGGC 59.108 47.619 0.00 0.00 46.57 4.40
43 44 2.557924 TGCTCTAACCAAAGGCAACATG 59.442 45.455 0.00 0.00 41.41 3.21
44 45 2.875296 TGCTCTAACCAAAGGCAACAT 58.125 42.857 0.00 0.00 41.41 2.71
45 46 2.356665 TGCTCTAACCAAAGGCAACA 57.643 45.000 0.00 0.00 41.41 3.33
46 47 3.084786 AGATGCTCTAACCAAAGGCAAC 58.915 45.455 0.00 0.00 36.49 4.17
47 48 3.347216 GAGATGCTCTAACCAAAGGCAA 58.653 45.455 0.00 0.00 36.49 4.52
48 49 2.356125 GGAGATGCTCTAACCAAAGGCA 60.356 50.000 0.00 0.00 37.32 4.75
49 50 2.293170 GGAGATGCTCTAACCAAAGGC 58.707 52.381 0.00 0.00 0.00 4.35
50 51 3.634397 TGGAGATGCTCTAACCAAAGG 57.366 47.619 0.00 0.00 0.00 3.11
51 52 6.586344 TCTATTGGAGATGCTCTAACCAAAG 58.414 40.000 0.00 0.00 42.53 2.77
52 53 6.560003 TCTATTGGAGATGCTCTAACCAAA 57.440 37.500 0.00 0.00 42.53 3.28
53 54 6.753913 ATCTATTGGAGATGCTCTAACCAA 57.246 37.500 0.00 0.00 43.71 3.67
54 55 7.013220 ACTATCTATTGGAGATGCTCTAACCA 58.987 38.462 0.00 0.00 45.05 3.67
55 56 7.475137 ACTATCTATTGGAGATGCTCTAACC 57.525 40.000 0.00 0.00 45.05 2.85
56 57 8.580720 TGAACTATCTATTGGAGATGCTCTAAC 58.419 37.037 0.00 0.00 45.05 2.34
57 58 8.712228 TGAACTATCTATTGGAGATGCTCTAA 57.288 34.615 0.00 0.00 45.05 2.10
92 93 5.291971 TCAGACGGTCCAAAAGTTAGTTAC 58.708 41.667 4.14 0.00 0.00 2.50
97 98 2.549349 GCCTCAGACGGTCCAAAAGTTA 60.549 50.000 4.14 0.00 0.00 2.24
189 202 4.158384 CACCTCGTGATGTAAATTTGCAC 58.842 43.478 11.35 7.90 35.23 4.57
197 210 3.699538 ACTAGATGCACCTCGTGATGTAA 59.300 43.478 0.00 0.00 35.23 2.41
209 222 1.369625 CGGTTTGGGACTAGATGCAC 58.630 55.000 0.00 0.00 0.00 4.57
217 230 2.663852 CGTTCGCGGTTTGGGACT 60.664 61.111 6.13 0.00 39.57 3.85
222 235 3.955101 TTGGGCGTTCGCGGTTTG 61.955 61.111 6.13 0.00 41.67 2.93
242 266 1.257743 GGGAAAGGAAAGGAACTGGC 58.742 55.000 0.00 0.00 40.86 4.85
246 270 1.248785 GGGCGGGAAAGGAAAGGAAC 61.249 60.000 0.00 0.00 0.00 3.62
250 274 3.440415 GCGGGCGGGAAAGGAAAG 61.440 66.667 0.00 0.00 0.00 2.62
326 354 3.499929 ATCCTATGCGGGCGACGTG 62.500 63.158 0.00 0.00 46.52 4.49
327 355 3.208884 GATCCTATGCGGGCGACGT 62.209 63.158 0.00 0.00 46.52 4.34
358 386 3.680786 GGAAACAACGGCAGGGGC 61.681 66.667 0.00 0.00 40.13 5.80
359 387 2.203422 TGGAAACAACGGCAGGGG 60.203 61.111 0.00 0.00 37.44 4.79
360 388 3.039134 GTGGAAACAACGGCAGGG 58.961 61.111 0.00 0.00 46.06 4.45
1020 1048 0.321122 AGAAGCTCGACTTGCCCTTG 60.321 55.000 5.20 0.00 39.29 3.61
1033 1061 2.262915 CCTCACGCCGAAGAAGCT 59.737 61.111 0.00 0.00 0.00 3.74
1283 1311 1.334779 CGACAACCGACGACTTCTTCT 60.335 52.381 0.00 0.00 41.76 2.85
1291 1319 1.009335 CACTGACGACAACCGACGA 60.009 57.895 0.00 0.00 41.76 4.20
1368 1396 2.052690 GTACTCCAGCTCGGCCTGA 61.053 63.158 0.00 0.00 34.77 3.86
1454 1482 1.048724 GGACTCGATGGGGATCACCA 61.049 60.000 21.60 21.60 46.24 4.17
1509 1543 3.673597 TCGCACCCCTCCTCCTCT 61.674 66.667 0.00 0.00 0.00 3.69
1662 1704 7.797038 AAAACGACAAACTACTAGTCCATTT 57.203 32.000 0.00 0.00 0.00 2.32
1742 1784 8.187913 TCAATTTCAACAGATGGTCCAAATTA 57.812 30.769 0.00 0.00 32.75 1.40
1805 1847 6.265649 TCCAAAACCGGAGATGTAAAATTTGA 59.734 34.615 9.46 0.00 0.00 2.69
1891 1935 3.071312 TCCGTTGTTACCTGGCTCTAAAA 59.929 43.478 0.00 0.00 0.00 1.52
1910 1954 2.483876 TCAACTGAAGCTGAAAGTCCG 58.516 47.619 0.00 0.00 35.30 4.79
1966 2025 8.214721 CCAAAGGGATAGATCTAAAAGACAAC 57.785 38.462 6.52 0.00 35.59 3.32
2047 2110 2.751166 ACGTGATGTTAGCTCAGCTT 57.249 45.000 3.31 0.00 40.44 3.74
2184 2254 2.459934 GTTGACCAACAGCGGAAAAAG 58.540 47.619 7.92 0.00 40.84 2.27
2260 2335 5.516996 CATGTATGGAATGAATGTCTGCAC 58.483 41.667 0.00 0.00 0.00 4.57
2390 2466 1.003580 GGAGTCCATGAGAGGCAACAA 59.996 52.381 3.60 0.00 41.41 2.83
2444 2535 5.163612 GGCATTATTCTCCTGGTCAAAAGTC 60.164 44.000 0.00 0.00 0.00 3.01
2448 2539 4.016444 GTGGCATTATTCTCCTGGTCAAA 58.984 43.478 0.00 0.00 0.00 2.69
2455 2546 9.125026 CAAATTTAGTAGTGGCATTATTCTCCT 57.875 33.333 0.00 0.00 0.00 3.69
2485 2578 6.998074 TGCATAAATTCTATTGGACTCGGATT 59.002 34.615 0.00 0.00 0.00 3.01
2489 2582 7.516481 CAGATGCATAAATTCTATTGGACTCG 58.484 38.462 0.00 0.00 0.00 4.18
2490 2583 7.303998 GCAGATGCATAAATTCTATTGGACTC 58.696 38.462 0.00 0.00 41.59 3.36
2491 2584 7.211966 GCAGATGCATAAATTCTATTGGACT 57.788 36.000 0.00 0.00 41.59 3.85
2506 2599 9.036158 TGGAACAATGAATATGTGCAGATGCAT 62.036 37.037 11.20 0.00 45.89 3.96
2507 2600 7.803110 TGGAACAATGAATATGTGCAGATGCA 61.803 38.462 6.60 2.75 42.94 3.96
2508 2601 4.980434 GGAACAATGAATATGTGCAGATGC 59.020 41.667 6.60 0.00 42.50 3.91
2509 2602 6.139048 TGGAACAATGAATATGTGCAGATG 57.861 37.500 6.60 0.00 31.92 2.90
2527 2620 5.723672 TGGACTCGGATAAGATATGGAAC 57.276 43.478 0.00 0.00 0.00 3.62
2528 2621 6.295859 CCATTGGACTCGGATAAGATATGGAA 60.296 42.308 0.00 0.00 32.51 3.53
2529 2622 5.187772 CCATTGGACTCGGATAAGATATGGA 59.812 44.000 0.00 0.00 32.51 3.41
2530 2623 5.187772 TCCATTGGACTCGGATAAGATATGG 59.812 44.000 0.00 0.00 0.00 2.74
2531 2624 6.286240 TCCATTGGACTCGGATAAGATATG 57.714 41.667 0.00 0.00 0.00 1.78
2532 2625 6.935240 TTCCATTGGACTCGGATAAGATAT 57.065 37.500 4.45 0.00 0.00 1.63
2533 2626 6.935240 ATTCCATTGGACTCGGATAAGATA 57.065 37.500 4.45 0.00 0.00 1.98
2534 2627 5.832539 ATTCCATTGGACTCGGATAAGAT 57.167 39.130 4.45 0.00 0.00 2.40
2535 2628 5.630415 AATTCCATTGGACTCGGATAAGA 57.370 39.130 4.45 0.00 0.00 2.10
2536 2629 7.986085 ATAAATTCCATTGGACTCGGATAAG 57.014 36.000 4.45 0.00 0.00 1.73
2537 2630 8.433599 TGTATAAATTCCATTGGACTCGGATAA 58.566 33.333 4.45 0.00 0.00 1.75
2538 2631 7.969004 TGTATAAATTCCATTGGACTCGGATA 58.031 34.615 4.45 0.00 0.00 2.59
2539 2632 6.837312 TGTATAAATTCCATTGGACTCGGAT 58.163 36.000 4.45 0.00 0.00 4.18
2540 2633 6.241882 TGTATAAATTCCATTGGACTCGGA 57.758 37.500 4.45 0.00 0.00 4.55
2541 2634 6.486657 ACATGTATAAATTCCATTGGACTCGG 59.513 38.462 4.45 0.00 0.00 4.63
2561 2654 6.135290 GGTACAATGAATATGTGCACATGT 57.865 37.500 36.72 29.69 37.15 3.21


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

AutoCloner maintained by Alex Coulton.