Multiple sequence alignment - TraesCS2B01G244400

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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 TraesCS2B01G244400 chr2B 100.000 2633 0 0 1 2633 248155445 248158077 0.000000e+00 4863.0
1 TraesCS2B01G244400 chr2B 90.769 130 10 2 2336 2463 180426754 180426625 3.480000e-39 172.0
2 TraesCS2B01G244400 chr2A 91.854 2406 112 34 1 2358 206116084 206118453 0.000000e+00 3280.0
3 TraesCS2B01G244400 chr2A 89.385 179 12 3 2462 2633 206118452 206118630 4.410000e-53 219.0
4 TraesCS2B01G244400 chr2A 98.148 108 2 0 2356 2463 729833118 729833011 3.460000e-44 189.0
5 TraesCS2B01G244400 chr2D 91.256 2356 102 35 1 2325 192157906 192155624 0.000000e+00 3114.0
6 TraesCS2B01G244400 chr2D 91.061 179 9 2 2462 2633 192155603 192155425 4.380000e-58 235.0
7 TraesCS2B01G244400 chr2D 95.690 116 5 0 2349 2464 627971627 627971512 1.240000e-43 187.0
8 TraesCS2B01G244400 chr1B 98.131 107 2 0 2357 2463 250409544 250409438 1.240000e-43 187.0
9 TraesCS2B01G244400 chr1B 89.286 140 11 4 2345 2481 658701360 658701498 3.480000e-39 172.0
10 TraesCS2B01G244400 chr7A 94.958 119 4 2 2355 2472 46523039 46522922 4.480000e-43 185.0
11 TraesCS2B01G244400 chr7A 94.167 120 6 1 2345 2463 192671843 192671962 5.790000e-42 182.0
12 TraesCS2B01G244400 chr6A 96.396 111 4 0 2353 2463 408886187 408886077 1.610000e-42 183.0
13 TraesCS2B01G244400 chr1A 94.068 118 6 1 2357 2474 56105811 56105927 7.490000e-41 178.0
14 TraesCS2B01G244400 chr7D 96.774 31 1 0 2559 2589 611359896 611359926 5.000000e-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 TraesCS2B01G244400 chr2B 248155445 248158077 2632 False 4863.0 4863 100.0000 1 2633 1 chr2B.!!$F1 2632
1 TraesCS2B01G244400 chr2A 206116084 206118630 2546 False 1749.5 3280 90.6195 1 2633 2 chr2A.!!$F1 2632
2 TraesCS2B01G244400 chr2D 192155425 192157906 2481 True 1674.5 3114 91.1585 1 2633 2 chr2D.!!$R2 2632

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
132 150 0.108804 GCGATCCTGTTCGTCTTCCA 60.109 55.0 0.0 0.0 41.16 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1959 0.804933 GTATCGACACCGGCTGGAAC 60.805 60.0 21.41 7.93 39.21 3.62 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
132 150 0.108804 GCGATCCTGTTCGTCTTCCA 60.109 55.000 0.00 0.00 41.16 3.53
144 162 3.664107 TCGTCTTCCATGGTTCTTTCTG 58.336 45.455 12.58 0.00 0.00 3.02
162 182 0.974010 TGAGGCCGTTTAGGGTCGAT 60.974 55.000 0.00 0.00 41.48 3.59
186 206 4.341235 CCGTGTAGGTATTCTTGGATCTCA 59.659 45.833 0.00 0.00 34.51 3.27
195 215 7.992033 AGGTATTCTTGGATCTCATTCTCTTTG 59.008 37.037 0.00 0.00 0.00 2.77
229 249 9.698309 ATTGATAAGGTCGTCTGTTCTTATATG 57.302 33.333 0.00 0.00 33.95 1.78
263 283 6.465439 TCGGGTATTGATTGCGATATCTAT 57.535 37.500 0.34 0.00 0.00 1.98
267 287 8.082242 CGGGTATTGATTGCGATATCTATGATA 58.918 37.037 0.34 0.00 0.00 2.15
269 289 9.750125 GGTATTGATTGCGATATCTATGATACA 57.250 33.333 0.34 0.00 0.00 2.29
339 362 9.973450 CTGTACAAACATAGTATGATTAGCTCT 57.027 33.333 17.13 0.00 34.37 4.09
420 443 8.417780 TTGTCAGGACAACAAAATTATGTTTG 57.582 30.769 10.63 0.00 45.42 2.93
425 448 7.382218 CAGGACAACAAAATTATGTTTGAGACC 59.618 37.037 4.76 6.50 41.44 3.85
440 463 2.908940 ACCAGCACTGCACTTGCC 60.909 61.111 11.20 0.00 41.18 4.52
455 478 5.584649 TGCACTTGCCTGTACATATTAAGAC 59.415 40.000 0.00 0.00 41.18 3.01
485 512 7.257722 TGTGATCTTGAAGTTGAAAGAAAACC 58.742 34.615 0.00 0.00 36.09 3.27
487 514 7.645735 GTGATCTTGAAGTTGAAAGAAAACCTC 59.354 37.037 0.00 0.00 36.09 3.85
503 530 8.547481 AGAAAACCTCTTTTTAGGAAATTCCA 57.453 30.769 15.21 0.00 36.91 3.53
504 531 8.642432 AGAAAACCTCTTTTTAGGAAATTCCAG 58.358 33.333 15.21 2.37 36.91 3.86
505 532 7.914427 AAACCTCTTTTTAGGAAATTCCAGT 57.086 32.000 15.21 0.00 39.61 4.00
506 533 7.526142 AACCTCTTTTTAGGAAATTCCAGTC 57.474 36.000 15.21 0.00 39.61 3.51
507 534 6.010850 ACCTCTTTTTAGGAAATTCCAGTCC 58.989 40.000 15.21 0.00 39.61 3.85
508 535 5.123979 CCTCTTTTTAGGAAATTCCAGTCCG 59.876 44.000 15.21 0.00 39.61 4.79
509 536 5.007682 TCTTTTTAGGAAATTCCAGTCCGG 58.992 41.667 15.21 0.00 39.61 5.14
531 558 4.405036 GGACTCCGGACTACCTAAGAAAAT 59.595 45.833 0.00 0.00 0.00 1.82
546 573 9.936759 ACCTAAGAAAATTTGAAGAAAACAACA 57.063 25.926 0.00 0.00 0.00 3.33
668 696 7.573283 GCTCCACTAGTTTTGTGAAATAGTTCC 60.573 40.741 0.00 0.00 37.60 3.62
692 720 7.725397 TCCTCCATAATCATTTAGGTCCAATTG 59.275 37.037 0.00 0.00 0.00 2.32
763 791 4.712122 TTGACTGTTGTTCCTTGGTTTC 57.288 40.909 0.00 0.00 0.00 2.78
897 925 7.271511 TGCTTGGTTGTACAAATGAGAAATTT 58.728 30.769 10.51 0.00 0.00 1.82
1047 1075 1.203050 ACTGCCTTTGGTATGCCTGTT 60.203 47.619 0.16 0.00 35.27 3.16
1059 1087 1.337118 TGCCTGTTGTTTTCCATCCC 58.663 50.000 0.00 0.00 0.00 3.85
1083 1111 7.012894 CCCAATTATCATTGAAATTGCTTGCAT 59.987 33.333 18.67 0.00 42.35 3.96
1092 1120 4.512198 TGAAATTGCTTGCATTGTTTGGAG 59.488 37.500 0.00 0.00 0.00 3.86
1097 1125 2.863704 GCTTGCATTGTTTGGAGTGTCC 60.864 50.000 0.00 0.00 36.96 4.02
1104 1132 3.788227 TGTTTGGAGTGTCCTGCTTAT 57.212 42.857 0.00 0.00 37.46 1.73
1107 1135 5.626142 TGTTTGGAGTGTCCTGCTTATTTA 58.374 37.500 0.00 0.00 37.46 1.40
1115 1143 7.232118 AGTGTCCTGCTTATTTATTTTGCTT 57.768 32.000 0.00 0.00 0.00 3.91
1367 1398 2.038387 ACAACAAGCAAACTCGTCCT 57.962 45.000 0.00 0.00 0.00 3.85
1415 1446 2.977914 TCTCATGCAAGCTAGTTGTCC 58.022 47.619 0.00 0.00 38.55 4.02
1827 1858 4.373156 AACTTTGTAAGGAGCACCATCT 57.627 40.909 2.07 0.00 38.94 2.90
1924 1958 3.320541 TCCATTTTGGTTTGACATTCGCT 59.679 39.130 0.00 0.00 39.03 4.93
1925 1959 3.429543 CCATTTTGGTTTGACATTCGCTG 59.570 43.478 0.00 0.00 31.35 5.18
1952 1986 2.034305 GCCGGTGTCGATACATCTAGTT 59.966 50.000 14.58 0.00 38.08 2.24
1959 1993 6.035758 GGTGTCGATACATCTAGTTTTGAACC 59.964 42.308 14.58 0.00 38.08 3.62
1985 2025 7.223582 CGTATCTGCTTGATGACTGAATTAAGT 59.776 37.037 0.00 0.00 36.65 2.24
2009 2049 2.602878 CTGCTTGACATGCACCAATTC 58.397 47.619 11.69 0.00 36.37 2.17
2016 2056 3.084039 GACATGCACCAATTCTTCTGGA 58.916 45.455 0.00 0.00 37.40 3.86
2020 2060 1.547675 GCACCAATTCTTCTGGACCCA 60.548 52.381 0.00 0.00 37.40 4.51
2066 2110 7.230913 GGTCTACTGAATACTGTAGCCTCATTA 59.769 40.741 0.00 0.00 43.45 1.90
2164 2209 4.517285 TGGATCTCATTACTGTTTGAGGC 58.483 43.478 15.91 10.64 39.84 4.70
2192 2239 2.787994 AGCTTTATTCTGCACTGTGCT 58.212 42.857 30.43 14.96 45.31 4.40
2212 2259 3.438434 GCTGCTCTCTAAAAACAGGGAAG 59.562 47.826 0.00 0.00 0.00 3.46
2236 2283 3.380637 GCTTCCTATCTTACGTCAGACCA 59.619 47.826 0.61 0.00 0.00 4.02
2278 2326 1.271127 TTGATCCACGGAGGGCATCA 61.271 55.000 0.08 0.00 38.24 3.07
2338 2395 1.179814 GGACTGCCGGACCGAGATAT 61.180 60.000 17.49 0.00 0.00 1.63
2356 2413 7.440556 CCGAGATATTTTTGTGATCAGACATCT 59.559 37.037 0.00 0.00 0.00 2.90
2357 2414 9.468532 CGAGATATTTTTGTGATCAGACATCTA 57.531 33.333 0.00 0.00 0.00 1.98
2361 2418 7.856145 ATTTTTGTGATCAGACATCTACTCC 57.144 36.000 0.00 0.00 0.00 3.85
2362 2419 5.344743 TTTGTGATCAGACATCTACTCCC 57.655 43.478 0.00 0.00 0.00 4.30
2363 2420 4.256983 TGTGATCAGACATCTACTCCCT 57.743 45.455 0.00 0.00 0.00 4.20
2364 2421 4.211125 TGTGATCAGACATCTACTCCCTC 58.789 47.826 0.00 0.00 0.00 4.30
2365 2422 4.079500 TGTGATCAGACATCTACTCCCTCT 60.080 45.833 0.00 0.00 0.00 3.69
2366 2423 4.278170 GTGATCAGACATCTACTCCCTCTG 59.722 50.000 0.00 0.00 0.00 3.35
2367 2424 4.079500 TGATCAGACATCTACTCCCTCTGT 60.080 45.833 0.00 0.00 31.94 3.41
2368 2425 4.323569 TCAGACATCTACTCCCTCTGTT 57.676 45.455 0.00 0.00 31.94 3.16
2369 2426 4.274147 TCAGACATCTACTCCCTCTGTTC 58.726 47.826 0.00 0.00 31.94 3.18
2370 2427 3.066064 CAGACATCTACTCCCTCTGTTCG 59.934 52.174 0.00 0.00 0.00 3.95
2371 2428 2.359531 GACATCTACTCCCTCTGTTCGG 59.640 54.545 0.00 0.00 0.00 4.30
2372 2429 2.025226 ACATCTACTCCCTCTGTTCGGA 60.025 50.000 0.00 0.00 0.00 4.55
2373 2430 2.893215 TCTACTCCCTCTGTTCGGAA 57.107 50.000 0.00 0.00 0.00 4.30
2374 2431 3.383698 TCTACTCCCTCTGTTCGGAAT 57.616 47.619 0.00 0.00 0.00 3.01
2375 2432 3.709587 TCTACTCCCTCTGTTCGGAATT 58.290 45.455 0.00 0.00 0.00 2.17
2376 2433 4.863548 TCTACTCCCTCTGTTCGGAATTA 58.136 43.478 0.00 0.00 0.00 1.40
2377 2434 3.889520 ACTCCCTCTGTTCGGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2378 2435 3.442076 ACTCCCTCTGTTCGGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2379 2436 3.838903 ACTCCCTCTGTTCGGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
2380 2437 4.184629 CTCCCTCTGTTCGGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2381 2438 3.581332 TCCCTCTGTTCGGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2382 2439 3.933332 CCCTCTGTTCGGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2383 2440 3.612860 CCTCTGTTCGGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
2384 2441 2.991190 TCTGTTCGGAATTACTTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
2385 2442 2.734606 CTGTTCGGAATTACTTGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
2386 2443 3.132160 TGTTCGGAATTACTTGTCGCAA 58.868 40.909 0.00 0.00 0.00 4.85
2387 2444 3.560481 TGTTCGGAATTACTTGTCGCAAA 59.440 39.130 0.00 0.00 0.00 3.68
2388 2445 4.035324 TGTTCGGAATTACTTGTCGCAAAA 59.965 37.500 0.00 0.00 0.00 2.44
2389 2446 4.815040 TCGGAATTACTTGTCGCAAAAA 57.185 36.364 0.00 0.00 0.00 1.94
2390 2447 5.365403 TCGGAATTACTTGTCGCAAAAAT 57.635 34.783 0.00 0.00 0.00 1.82
2391 2448 5.150683 TCGGAATTACTTGTCGCAAAAATG 58.849 37.500 0.00 0.00 0.00 2.32
2392 2449 5.049336 TCGGAATTACTTGTCGCAAAAATGA 60.049 36.000 0.00 0.00 0.00 2.57
2393 2450 5.627367 CGGAATTACTTGTCGCAAAAATGAA 59.373 36.000 0.00 0.00 0.00 2.57
2394 2451 6.307800 CGGAATTACTTGTCGCAAAAATGAAT 59.692 34.615 0.00 0.00 0.00 2.57
2395 2452 7.447430 GGAATTACTTGTCGCAAAAATGAATG 58.553 34.615 0.00 0.00 0.00 2.67
2396 2453 7.116233 GGAATTACTTGTCGCAAAAATGAATGT 59.884 33.333 0.00 0.00 0.00 2.71
2397 2454 9.123709 GAATTACTTGTCGCAAAAATGAATGTA 57.876 29.630 0.00 0.00 0.00 2.29
2398 2455 9.638239 AATTACTTGTCGCAAAAATGAATGTAT 57.362 25.926 0.00 0.00 0.00 2.29
2399 2456 8.667987 TTACTTGTCGCAAAAATGAATGTATC 57.332 30.769 0.00 0.00 0.00 2.24
2400 2457 6.913170 ACTTGTCGCAAAAATGAATGTATCT 58.087 32.000 0.00 0.00 0.00 1.98
2401 2458 8.039603 ACTTGTCGCAAAAATGAATGTATCTA 57.960 30.769 0.00 0.00 0.00 1.98
2402 2459 8.177663 ACTTGTCGCAAAAATGAATGTATCTAG 58.822 33.333 0.00 0.00 0.00 2.43
2403 2460 7.841915 TGTCGCAAAAATGAATGTATCTAGA 57.158 32.000 0.00 0.00 0.00 2.43
2404 2461 7.684670 TGTCGCAAAAATGAATGTATCTAGAC 58.315 34.615 0.00 0.00 0.00 2.59
2405 2462 6.841286 GTCGCAAAAATGAATGTATCTAGACG 59.159 38.462 0.00 0.00 0.00 4.18
2406 2463 6.533723 TCGCAAAAATGAATGTATCTAGACGT 59.466 34.615 0.00 0.00 0.00 4.34
2407 2464 7.703197 TCGCAAAAATGAATGTATCTAGACGTA 59.297 33.333 0.00 0.00 0.00 3.57
2408 2465 8.325282 CGCAAAAATGAATGTATCTAGACGTAA 58.675 33.333 0.00 0.00 0.00 3.18
2436 2493 9.967346 TTAGTTCTAGATACATCCATTTTCGAG 57.033 33.333 0.00 0.00 0.00 4.04
2437 2494 8.239038 AGTTCTAGATACATCCATTTTCGAGA 57.761 34.615 0.00 0.00 0.00 4.04
2438 2495 8.138712 AGTTCTAGATACATCCATTTTCGAGAC 58.861 37.037 0.00 0.00 0.00 3.36
2439 2496 7.582667 TCTAGATACATCCATTTTCGAGACA 57.417 36.000 0.00 0.00 0.00 3.41
2440 2497 8.007405 TCTAGATACATCCATTTTCGAGACAA 57.993 34.615 0.00 0.00 0.00 3.18
2441 2498 8.138074 TCTAGATACATCCATTTTCGAGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
2442 2499 6.644347 AGATACATCCATTTTCGAGACAAGT 58.356 36.000 0.00 0.00 0.00 3.16
2443 2500 7.782049 AGATACATCCATTTTCGAGACAAGTA 58.218 34.615 0.00 0.00 0.00 2.24
2444 2501 8.258007 AGATACATCCATTTTCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
2445 2502 8.964476 ATACATCCATTTTCGAGACAAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
2446 2503 7.687941 ACATCCATTTTCGAGACAAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
2447 2504 7.752695 ACATCCATTTTCGAGACAAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2448 2505 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
2449 2506 5.350365 TCCATTTTCGAGACAAGTAATTCCG 59.650 40.000 0.00 0.00 0.00 4.30
2450 2507 5.350365 CCATTTTCGAGACAAGTAATTCCGA 59.650 40.000 0.00 0.00 0.00 4.55
2451 2508 6.128391 CCATTTTCGAGACAAGTAATTCCGAA 60.128 38.462 0.00 0.00 33.57 4.30
2452 2509 5.834239 TTTCGAGACAAGTAATTCCGAAC 57.166 39.130 0.00 0.00 34.86 3.95
2453 2510 3.495193 TCGAGACAAGTAATTCCGAACG 58.505 45.455 0.00 0.00 0.00 3.95
2454 2511 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
2455 2512 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
2456 2513 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2457 2514 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2458 2515 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2459 2516 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2460 2517 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2500 2557 1.871039 CTCGTTTTGGTTGTGATCGGT 59.129 47.619 0.00 0.00 0.00 4.69
2506 2563 1.803334 TGGTTGTGATCGGTTGCTAC 58.197 50.000 0.00 0.00 0.00 3.58
2545 2602 7.630242 TTGAATTTCATATTGGTCTGACCTC 57.370 36.000 26.03 12.35 39.58 3.85
2551 2608 0.526662 ATTGGTCTGACCTCGACGAC 59.473 55.000 26.03 0.00 39.58 4.34
2558 2622 2.360852 ACCTCGACGACGGGATGT 60.361 61.111 9.17 0.00 43.41 3.06
2620 2684 2.096174 CCGTGTTCGTTTTGGAAGTCAA 59.904 45.455 0.00 0.00 35.01 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 112 4.264253 TCGCAAGTCAAGATGAATCCATT 58.736 39.130 0.00 0.00 39.48 3.16
132 150 0.693049 ACGGCCTCAGAAAGAACCAT 59.307 50.000 0.00 0.00 0.00 3.55
144 162 0.249363 GATCGACCCTAAACGGCCTC 60.249 60.000 0.00 0.00 0.00 4.70
162 182 4.543689 AGATCCAAGAATACCTACACGGA 58.456 43.478 0.00 0.00 36.31 4.69
186 206 4.837093 TCAATACGGGTCCAAAGAGAAT 57.163 40.909 0.00 0.00 0.00 2.40
195 215 2.363359 ACGACCTTATCAATACGGGTCC 59.637 50.000 0.00 0.00 42.23 4.46
229 249 7.173863 CAATCAATACCCGATTGTACAGTAC 57.826 40.000 3.49 3.49 44.66 2.73
263 283 9.292195 CCCTAACCTTCTTTAAAAAGTGTATCA 57.708 33.333 2.58 0.00 37.31 2.15
267 287 8.777578 AATCCCTAACCTTCTTTAAAAAGTGT 57.222 30.769 2.58 0.00 37.31 3.55
269 289 8.008332 TGGAATCCCTAACCTTCTTTAAAAAGT 58.992 33.333 0.00 0.00 37.31 2.66
270 290 8.417273 TGGAATCCCTAACCTTCTTTAAAAAG 57.583 34.615 0.00 0.00 37.36 2.27
369 392 2.661718 TCCCCTTCGCTCAAAAAGTTT 58.338 42.857 0.00 0.00 0.00 2.66
419 442 0.533531 CAAGTGCAGTGCTGGTCTCA 60.534 55.000 17.60 0.00 0.00 3.27
420 443 1.849976 GCAAGTGCAGTGCTGGTCTC 61.850 60.000 17.60 0.00 41.59 3.36
425 448 0.886043 TACAGGCAAGTGCAGTGCTG 60.886 55.000 17.60 16.52 44.36 4.41
455 478 5.366829 TTCAACTTCAAGATCACAGCATG 57.633 39.130 0.00 0.00 46.00 4.06
485 512 5.123979 CCGGACTGGAATTTCCTAAAAAGAG 59.876 44.000 16.25 6.14 42.00 2.85
487 514 5.007682 TCCGGACTGGAATTTCCTAAAAAG 58.992 41.667 16.25 7.47 46.38 2.27
508 535 2.725221 TCTTAGGTAGTCCGGAGTCC 57.275 55.000 16.99 16.36 39.05 3.85
509 536 5.595257 ATTTTCTTAGGTAGTCCGGAGTC 57.405 43.478 16.99 7.61 39.05 3.36
668 696 7.725397 TCCAATTGGACCTAAATGATTATGGAG 59.275 37.037 23.63 0.00 39.78 3.86
692 720 3.366679 CCACAAGCAATCATCACTGTTCC 60.367 47.826 0.00 0.00 0.00 3.62
813 841 7.928706 GCATCAGAGGTACTTATTTCATACAGT 59.071 37.037 0.00 0.00 41.55 3.55
828 856 9.330063 CTGACTAAATAATTTGCATCAGAGGTA 57.670 33.333 1.29 0.00 35.42 3.08
970 998 0.240411 GCTGAGACTGGCAAAAGCTG 59.760 55.000 0.00 0.00 0.00 4.24
982 1010 8.517861 TCAGACATGAAATCTCCTGCTGAGAC 62.518 46.154 0.00 0.00 41.97 3.36
988 1016 4.706035 AGATCAGACATGAAATCTCCTGC 58.294 43.478 0.00 0.00 39.39 4.85
1047 1075 7.730672 TCAATGATAATTGGGATGGAAAACA 57.269 32.000 2.80 0.00 32.65 2.83
1059 1087 9.220635 CAATGCAAGCAATTTCAATGATAATTG 57.779 29.630 18.03 18.03 42.08 2.32
1083 1111 2.435372 AAGCAGGACACTCCAAACAA 57.565 45.000 0.00 0.00 39.61 2.83
1092 1120 7.315890 AGAAGCAAAATAAATAAGCAGGACAC 58.684 34.615 0.00 0.00 0.00 3.67
1104 1132 7.338449 GGGGTCTGTATGTAGAAGCAAAATAAA 59.662 37.037 0.00 0.00 0.00 1.40
1107 1135 5.044846 AGGGGTCTGTATGTAGAAGCAAAAT 60.045 40.000 0.00 0.00 0.00 1.82
1115 1143 2.504175 GGCAAAGGGGTCTGTATGTAGA 59.496 50.000 0.00 0.00 0.00 2.59
1367 1398 6.018589 TGCGAAACAAATGGACATGATAAA 57.981 33.333 0.00 0.00 0.00 1.40
1415 1446 3.442625 TGGAAAAGAGCAGCAATGATCAG 59.557 43.478 0.09 0.00 0.00 2.90
1827 1858 4.080526 GGAGAGGGTAACAAGCCATCTAAA 60.081 45.833 0.00 0.00 45.74 1.85
1877 1911 2.884827 ACGAAGGATACCACGCTTAAC 58.115 47.619 0.00 0.00 38.81 2.01
1924 1958 1.252215 TATCGACACCGGCTGGAACA 61.252 55.000 21.41 0.00 39.21 3.18
1925 1959 0.804933 GTATCGACACCGGCTGGAAC 60.805 60.000 21.41 7.93 39.21 3.62
1952 1986 4.391830 GTCATCAAGCAGATACGGTTCAAA 59.608 41.667 0.00 0.00 34.43 2.69
1959 1993 5.980698 AATTCAGTCATCAAGCAGATACG 57.019 39.130 0.00 0.00 34.43 3.06
2009 2049 2.633860 GTGCAACTGGGTCCAGAAG 58.366 57.895 22.46 14.50 46.30 2.85
2066 2110 1.132262 CTGCGGTCGTAAATTGCCATT 59.868 47.619 0.00 0.00 0.00 3.16
2107 2151 3.302347 GAGTAGCCGCAGCACCACT 62.302 63.158 0.00 0.00 43.56 4.00
2164 2209 4.154195 AGTGCAGAATAAAGCTAAACCGTG 59.846 41.667 0.00 0.00 0.00 4.94
2192 2239 3.412386 GCTTCCCTGTTTTTAGAGAGCA 58.588 45.455 0.00 0.00 0.00 4.26
2212 2259 2.033049 TCTGACGTAAGATAGGAAGCGC 59.967 50.000 0.00 0.00 43.62 5.92
2236 2283 1.806542 GTGCATCAACGGTCAATGAGT 59.193 47.619 0.00 0.00 0.00 3.41
2278 2326 4.415596 TGGACCAGCTATCCAAAAATGTT 58.584 39.130 15.01 0.00 43.43 2.71
2338 2395 6.013379 AGGGAGTAGATGTCTGATCACAAAAA 60.013 38.462 0.00 0.00 0.00 1.94
2356 2413 4.607239 AGTAATTCCGAACAGAGGGAGTA 58.393 43.478 0.00 0.00 33.01 2.59
2357 2414 3.442076 AGTAATTCCGAACAGAGGGAGT 58.558 45.455 0.00 0.00 33.01 3.85
2358 2415 4.184629 CAAGTAATTCCGAACAGAGGGAG 58.815 47.826 0.00 0.00 33.01 4.30
2359 2416 3.581332 ACAAGTAATTCCGAACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2360 2417 3.933332 GACAAGTAATTCCGAACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2361 2418 3.612860 CGACAAGTAATTCCGAACAGAGG 59.387 47.826 0.00 0.00 0.00 3.69
2362 2419 3.060895 GCGACAAGTAATTCCGAACAGAG 59.939 47.826 0.00 0.00 0.00 3.35
2363 2420 2.991190 GCGACAAGTAATTCCGAACAGA 59.009 45.455 0.00 0.00 0.00 3.41
2364 2421 2.734606 TGCGACAAGTAATTCCGAACAG 59.265 45.455 0.00 0.00 0.00 3.16
2365 2422 2.756829 TGCGACAAGTAATTCCGAACA 58.243 42.857 0.00 0.00 0.00 3.18
2366 2423 3.799137 TTGCGACAAGTAATTCCGAAC 57.201 42.857 0.00 0.00 0.00 3.95
2367 2424 4.815040 TTTTGCGACAAGTAATTCCGAA 57.185 36.364 0.00 0.00 0.00 4.30
2368 2425 4.815040 TTTTTGCGACAAGTAATTCCGA 57.185 36.364 0.00 0.00 0.00 4.55
2369 2426 5.150683 TCATTTTTGCGACAAGTAATTCCG 58.849 37.500 0.00 0.00 0.00 4.30
2370 2427 7.116233 ACATTCATTTTTGCGACAAGTAATTCC 59.884 33.333 0.00 0.00 0.00 3.01
2371 2428 8.006741 ACATTCATTTTTGCGACAAGTAATTC 57.993 30.769 0.00 0.00 0.00 2.17
2372 2429 7.945033 ACATTCATTTTTGCGACAAGTAATT 57.055 28.000 0.00 0.00 0.00 1.40
2373 2430 9.289303 GATACATTCATTTTTGCGACAAGTAAT 57.711 29.630 0.00 0.00 0.00 1.89
2374 2431 8.511321 AGATACATTCATTTTTGCGACAAGTAA 58.489 29.630 0.00 0.00 0.00 2.24
2375 2432 8.039603 AGATACATTCATTTTTGCGACAAGTA 57.960 30.769 0.00 0.00 0.00 2.24
2376 2433 6.913170 AGATACATTCATTTTTGCGACAAGT 58.087 32.000 0.00 0.00 0.00 3.16
2377 2434 8.390354 TCTAGATACATTCATTTTTGCGACAAG 58.610 33.333 0.00 0.00 0.00 3.16
2378 2435 8.175069 GTCTAGATACATTCATTTTTGCGACAA 58.825 33.333 0.00 0.00 0.00 3.18
2379 2436 7.464045 CGTCTAGATACATTCATTTTTGCGACA 60.464 37.037 0.00 0.00 0.00 4.35
2380 2437 6.841286 CGTCTAGATACATTCATTTTTGCGAC 59.159 38.462 0.00 0.00 0.00 5.19
2381 2438 6.533723 ACGTCTAGATACATTCATTTTTGCGA 59.466 34.615 0.00 0.00 0.00 5.10
2382 2439 6.705782 ACGTCTAGATACATTCATTTTTGCG 58.294 36.000 0.00 0.00 0.00 4.85
2410 2467 9.967346 CTCGAAAATGGATGTATCTAGAACTAA 57.033 33.333 0.00 0.00 0.00 2.24
2411 2468 9.350951 TCTCGAAAATGGATGTATCTAGAACTA 57.649 33.333 0.00 0.00 0.00 2.24
2412 2469 8.138712 GTCTCGAAAATGGATGTATCTAGAACT 58.861 37.037 0.00 0.00 0.00 3.01
2413 2470 7.921214 TGTCTCGAAAATGGATGTATCTAGAAC 59.079 37.037 0.00 0.00 0.00 3.01
2414 2471 8.007405 TGTCTCGAAAATGGATGTATCTAGAA 57.993 34.615 0.00 0.00 0.00 2.10
2415 2472 7.582667 TGTCTCGAAAATGGATGTATCTAGA 57.417 36.000 0.00 0.00 0.00 2.43
2416 2473 7.923344 ACTTGTCTCGAAAATGGATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
2417 2474 7.782049 ACTTGTCTCGAAAATGGATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
2418 2475 6.644347 ACTTGTCTCGAAAATGGATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
2419 2476 6.910536 ACTTGTCTCGAAAATGGATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
2420 2477 8.964476 ATTACTTGTCTCGAAAATGGATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
2421 2478 8.786826 AATTACTTGTCTCGAAAATGGATGTA 57.213 30.769 0.00 0.00 0.00 2.29
2422 2479 7.148239 GGAATTACTTGTCTCGAAAATGGATGT 60.148 37.037 0.00 0.00 0.00 3.06
2423 2480 7.189512 GGAATTACTTGTCTCGAAAATGGATG 58.810 38.462 0.00 0.00 0.00 3.51
2424 2481 6.037172 CGGAATTACTTGTCTCGAAAATGGAT 59.963 38.462 0.00 0.00 0.00 3.41
2425 2482 5.350365 CGGAATTACTTGTCTCGAAAATGGA 59.650 40.000 0.00 0.00 0.00 3.41
2426 2483 5.350365 TCGGAATTACTTGTCTCGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
2427 2484 6.403333 TCGGAATTACTTGTCTCGAAAATG 57.597 37.500 0.00 0.00 0.00 2.32
2428 2485 6.400727 CGTTCGGAATTACTTGTCTCGAAAAT 60.401 38.462 0.00 0.00 37.00 1.82
2429 2486 5.107760 CGTTCGGAATTACTTGTCTCGAAAA 60.108 40.000 0.00 0.00 37.00 2.29
2430 2487 4.383649 CGTTCGGAATTACTTGTCTCGAAA 59.616 41.667 0.00 0.00 37.00 3.46
2431 2488 3.916172 CGTTCGGAATTACTTGTCTCGAA 59.084 43.478 0.00 0.00 33.66 3.71
2432 2489 3.495193 CGTTCGGAATTACTTGTCTCGA 58.505 45.455 0.00 0.00 0.00 4.04
2433 2490 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2434 2491 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2435 2492 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2436 2493 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2437 2494 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2438 2495 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2439 2496 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2440 2497 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2441 2498 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2442 2499 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2443 2500 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2444 2501 1.856629 TTACTCCCTCCGTTCGGAAT 58.143 50.000 14.79 2.09 33.41 3.01
2445 2502 1.631405 TTTACTCCCTCCGTTCGGAA 58.369 50.000 14.79 0.04 33.41 4.30
2446 2503 1.273327 GTTTTACTCCCTCCGTTCGGA 59.727 52.381 13.34 13.34 0.00 4.55
2447 2504 1.274447 AGTTTTACTCCCTCCGTTCGG 59.726 52.381 4.74 4.74 0.00 4.30
2448 2505 2.738013 AGTTTTACTCCCTCCGTTCG 57.262 50.000 0.00 0.00 0.00 3.95
2449 2506 7.099120 TGTTTATAGTTTTACTCCCTCCGTTC 58.901 38.462 0.00 0.00 0.00 3.95
2450 2507 7.008021 TGTTTATAGTTTTACTCCCTCCGTT 57.992 36.000 0.00 0.00 0.00 4.44
2451 2508 6.610075 TGTTTATAGTTTTACTCCCTCCGT 57.390 37.500 0.00 0.00 0.00 4.69
2452 2509 6.420008 CGATGTTTATAGTTTTACTCCCTCCG 59.580 42.308 0.00 0.00 0.00 4.63
2453 2510 6.704937 CCGATGTTTATAGTTTTACTCCCTCC 59.295 42.308 0.00 0.00 0.00 4.30
2454 2511 7.270779 ACCGATGTTTATAGTTTTACTCCCTC 58.729 38.462 0.00 0.00 0.00 4.30
2455 2512 7.125356 AGACCGATGTTTATAGTTTTACTCCCT 59.875 37.037 0.00 0.00 0.00 4.20
2456 2513 7.270779 AGACCGATGTTTATAGTTTTACTCCC 58.729 38.462 0.00 0.00 0.00 4.30
2457 2514 7.167136 CGAGACCGATGTTTATAGTTTTACTCC 59.833 40.741 0.00 0.00 38.22 3.85
2458 2515 7.699812 ACGAGACCGATGTTTATAGTTTTACTC 59.300 37.037 0.00 0.00 39.50 2.59
2459 2516 7.542025 ACGAGACCGATGTTTATAGTTTTACT 58.458 34.615 0.00 0.00 39.50 2.24
2460 2517 7.746526 ACGAGACCGATGTTTATAGTTTTAC 57.253 36.000 0.00 0.00 39.50 2.01
2500 2557 3.862877 ATGCATATCACCCTGTAGCAA 57.137 42.857 0.00 0.00 33.91 3.91
2506 2563 6.575267 TGAAATTCAAATGCATATCACCCTG 58.425 36.000 0.00 0.00 0.00 4.45
2545 2602 1.145759 CCAATCACATCCCGTCGTCG 61.146 60.000 0.00 0.00 0.00 5.12
2551 2608 1.597742 GGTCATCCAATCACATCCCG 58.402 55.000 0.00 0.00 0.00 5.14
2558 2622 1.526887 GGAGCCGGTCATCCAATCA 59.473 57.895 15.18 0.00 35.54 2.57


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

AutoCloner maintained by Alex Coulton.