Multiple sequence alignment - TraesCS2B01G403700

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 TraesCS2B01G403700 chr2B 100.000 2531 0 0 1 2531 572078793 572081323 0.000000e+00 4674.0
1 TraesCS2B01G403700 chr2B 79.384 422 75 12 1116 1531 653808489 653808904 1.150000e-73 287.0
2 TraesCS2B01G403700 chr2B 91.935 62 5 0 2338 2399 572081069 572081130 1.250000e-13 87.9
3 TraesCS2B01G403700 chr2B 91.935 62 5 0 2277 2338 572081130 572081191 1.250000e-13 87.9
4 TraesCS2B01G403700 chr2B 93.617 47 3 0 2447 2493 142542712 142542666 1.260000e-08 71.3
5 TraesCS2B01G403700 chr2A 89.907 2051 133 28 8 2030 632389733 632391737 0.000000e+00 2573.0
6 TraesCS2B01G403700 chr2A 78.622 421 80 10 1116 1531 691391850 691391435 1.150000e-68 270.0
7 TraesCS2B01G403700 chr2D 94.472 1592 66 11 31 1604 487314957 487316544 0.000000e+00 2433.0
8 TraesCS2B01G403700 chr2D 85.294 476 51 11 1628 2100 487316530 487316989 8.190000e-130 473.0
9 TraesCS2B01G403700 chr2D 76.649 561 103 22 991 1531 547559495 547560047 4.120000e-73 285.0
10 TraesCS2B01G403700 chr2D 76.960 421 87 9 1116 1531 547574744 547575159 5.450000e-57 231.0
11 TraesCS2B01G403700 chr2D 87.500 152 16 1 2342 2493 487317131 487317279 3.350000e-39 172.0
12 TraesCS2B01G403700 chr2D 93.023 43 2 1 2443 2484 61764035 61764077 7.560000e-06 62.1
13 TraesCS2B01G403700 chr6A 88.406 69 6 1 2427 2493 373134861 373134929 5.800000e-12 82.4
14 TraesCS2B01G403700 chr6A 97.059 34 1 0 2303 2336 5344752 5344719 9.780000e-05 58.4
15 TraesCS2B01G403700 chr5D 95.000 40 1 1 1944 1983 547444688 547444650 7.560000e-06 62.1
16 TraesCS2B01G403700 chr7B 97.143 35 1 0 2492 2526 499642451 499642485 2.720000e-05 60.2
17 TraesCS2B01G403700 chr3B 97.143 35 1 0 2492 2526 794837458 794837424 2.720000e-05 60.2
18 TraesCS2B01G403700 chr1B 92.857 42 2 1 2485 2526 620454801 620454761 2.720000e-05 60.2
19 TraesCS2B01G403700 chr1B 97.059 34 1 0 2493 2526 593616363 593616396 9.780000e-05 58.4
20 TraesCS2B01G403700 chrUn 97.059 34 1 0 2493 2526 468826981 468827014 9.780000e-05 58.4
21 TraesCS2B01G403700 chr4B 97.059 34 1 0 2493 2526 80960179 80960212 9.780000e-05 58.4
22 TraesCS2B01G403700 chr4B 97.059 34 1 0 2493 2526 123459602 123459635 9.780000e-05 58.4
23 TraesCS2B01G403700 chr4B 97.059 34 1 0 2493 2526 617917050 617917017 9.780000e-05 58.4
24 TraesCS2B01G403700 chr4B 97.059 34 1 0 2493 2526 669575365 669575332 9.780000e-05 58.4


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 TraesCS2B01G403700 chr2B 572078793 572081323 2530 False 1616.6 4674 94.623333 1 2531 3 chr2B.!!$F2 2530
1 TraesCS2B01G403700 chr2A 632389733 632391737 2004 False 2573.0 2573 89.907000 8 2030 1 chr2A.!!$F1 2022
2 TraesCS2B01G403700 chr2D 487314957 487317279 2322 False 1026.0 2433 89.088667 31 2493 3 chr2D.!!$F4 2462
3 TraesCS2B01G403700 chr2D 547559495 547560047 552 False 285.0 285 76.649000 991 1531 1 chr2D.!!$F2 540

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
86 90 0.107643 TGGCGAACACAAGGATGACA 59.892 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1762 0.523072 AACCATGCGCAAGTGATCAC 59.477 50.0 17.11 18.47 41.68 3.06 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
29 30 0.827368 GCACTACCCTCCCTCTCAAG 59.173 60.000 0.00 0.00 0.00 3.02
39 40 3.067461 CCTCCCTCTCAAGTCTCAATACG 59.933 52.174 0.00 0.00 0.00 3.06
54 58 2.403252 ATACGACCAAGCTTTCTGGG 57.597 50.000 7.81 3.54 39.46 4.45
86 90 0.107643 TGGCGAACACAAGGATGACA 59.892 50.000 0.00 0.00 0.00 3.58
87 91 1.271325 TGGCGAACACAAGGATGACAT 60.271 47.619 0.00 0.00 0.00 3.06
110 114 3.541996 CACATGTGCTACCTCACCATA 57.458 47.619 13.94 0.00 36.17 2.74
170 174 3.285215 AGCGACACTGACGACGGT 61.285 61.111 5.05 0.00 35.84 4.83
172 176 1.511464 GCGACACTGACGACGGTAG 60.511 63.158 5.05 0.00 33.89 3.18
377 381 0.109873 CGTCGCTGTTCTACTTCGGT 60.110 55.000 0.00 0.00 0.00 4.69
388 392 6.192234 GTTCTACTTCGGTGAGAACATAGA 57.808 41.667 8.70 0.00 45.49 1.98
389 393 6.618811 GTTCTACTTCGGTGAGAACATAGAA 58.381 40.000 8.70 0.00 45.49 2.10
401 405 2.514458 ACATAGAAGTGGGCAAAGGG 57.486 50.000 0.00 0.00 0.00 3.95
566 570 0.747644 TCGGGTGCGGTAAGATCGTA 60.748 55.000 0.00 0.00 0.00 3.43
648 660 2.280119 GGCCATACTGATCGCGCA 60.280 61.111 8.75 0.00 0.00 6.09
656 668 2.356433 TGATCGCGCACCGTTGAA 60.356 55.556 8.75 0.00 38.35 2.69
668 680 1.296867 CGTTGAATGATCACGCCGC 60.297 57.895 0.00 0.00 34.61 6.53
683 695 1.208870 CCGCGCATGCAAGTTAACA 59.791 52.632 19.57 0.00 42.97 2.41
700 712 4.101448 AGCATCCCTCCACGTGGC 62.101 66.667 30.25 15.83 34.44 5.01
761 773 6.869421 ACTTGTAATTCGCAAATTGTATGC 57.131 33.333 0.00 0.00 40.41 3.14
769 781 6.834959 TTCGCAAATTGTATGCTTCAAAAA 57.165 29.167 0.00 0.00 41.64 1.94
802 814 7.425577 TTCACATTTTCATCACTGACAGTAG 57.574 36.000 8.02 3.36 0.00 2.57
803 815 6.524734 TCACATTTTCATCACTGACAGTAGT 58.475 36.000 8.02 0.00 0.00 2.73
804 816 7.666623 TCACATTTTCATCACTGACAGTAGTA 58.333 34.615 8.02 0.00 0.00 1.82
805 817 8.314021 TCACATTTTCATCACTGACAGTAGTAT 58.686 33.333 8.02 0.00 0.00 2.12
806 818 9.586435 CACATTTTCATCACTGACAGTAGTATA 57.414 33.333 8.02 0.00 0.00 1.47
849 875 5.705441 TGAACGCTTCAAATTAACTCTCCAT 59.295 36.000 0.00 0.00 36.59 3.41
922 948 2.514013 GCATACGAGAACCCGCACG 61.514 63.158 0.00 0.00 0.00 5.34
962 988 7.072454 TCCTATATAATGACTGCACTTCCCTTT 59.928 37.037 0.00 0.00 0.00 3.11
984 1010 2.293399 GCAAACTTCACCAAATCGACCT 59.707 45.455 0.00 0.00 0.00 3.85
985 1011 3.500680 GCAAACTTCACCAAATCGACCTA 59.499 43.478 0.00 0.00 0.00 3.08
1020 1046 2.048222 TCTCCTTTCGCCTGCGTG 60.048 61.111 11.68 3.57 40.74 5.34
1539 1580 1.068741 CCGCCCTACTGATTCTGTACC 59.931 57.143 0.00 0.00 0.00 3.34
1540 1581 1.068741 CGCCCTACTGATTCTGTACCC 59.931 57.143 0.00 0.00 0.00 3.69
1541 1582 2.116238 GCCCTACTGATTCTGTACCCA 58.884 52.381 0.00 0.00 0.00 4.51
1551 1594 3.756933 TTCTGTACCCAAAGCTAACGT 57.243 42.857 0.00 0.00 0.00 3.99
1613 1656 4.273480 CCATAGTTCATAACAAAGCGGGAG 59.727 45.833 0.00 0.00 0.00 4.30
1649 1696 8.142994 GGTACCATAGTTCATAACTTCATGTG 57.857 38.462 7.15 0.00 42.81 3.21
1650 1697 7.985184 GGTACCATAGTTCATAACTTCATGTGA 59.015 37.037 7.15 0.00 42.81 3.58
1651 1698 9.378551 GTACCATAGTTCATAACTTCATGTGAA 57.621 33.333 0.00 0.00 42.81 3.18
1653 1700 9.466497 ACCATAGTTCATAACTTCATGTGAATT 57.534 29.630 0.00 0.00 42.81 2.17
1657 1704 8.281212 AGTTCATAACTTCATGTGAATTACCC 57.719 34.615 0.00 0.00 39.04 3.69
1665 1712 5.816955 TCATGTGAATTACCCGATATCCA 57.183 39.130 0.00 0.00 0.00 3.41
1691 1738 4.039124 ACAAGGTTCTTTGTTAATGGGCAG 59.961 41.667 0.00 0.00 38.05 4.85
1715 1762 2.609427 TCGATTCAGATTCAGCTGGG 57.391 50.000 15.13 0.00 36.55 4.45
1721 1768 2.190538 TCAGATTCAGCTGGGTGATCA 58.809 47.619 15.13 0.00 36.55 2.92
1724 1771 2.575279 AGATTCAGCTGGGTGATCACTT 59.425 45.455 24.50 4.01 0.00 3.16
1737 1784 2.253603 GATCACTTGCGCATGGTTTTC 58.746 47.619 24.99 14.68 0.00 2.29
1752 1799 5.855740 TGGTTTTCCGGTTAGTTTTGAAT 57.144 34.783 0.00 0.00 44.36 2.57
1859 1908 4.590226 TGAACTTCTTTTAAACCGCGAAC 58.410 39.130 8.23 0.00 0.00 3.95
1860 1909 3.614159 ACTTCTTTTAAACCGCGAACC 57.386 42.857 8.23 0.00 0.00 3.62
1868 1917 2.388106 AAACCGCGAACCGTTTTTAG 57.612 45.000 8.23 0.00 34.38 1.85
2171 2222 9.908152 ATACCAGCAAAAAGAAACAAATACTAC 57.092 29.630 0.00 0.00 0.00 2.73
2186 2239 8.706322 ACAAATACTACAAAAGGTTCAGGAAT 57.294 30.769 0.00 0.00 0.00 3.01
2193 2246 8.847196 ACTACAAAAGGTTCAGGAATTTTCTAC 58.153 33.333 0.00 0.00 0.00 2.59
2207 2260 6.704493 GGAATTTTCTACAAGGTTCCCAAAAC 59.296 38.462 0.00 0.00 31.23 2.43
2221 2274 5.009854 TCCCAAAACAGAAAGAAAAGCAG 57.990 39.130 0.00 0.00 0.00 4.24
2229 2282 9.705290 AAAACAGAAAGAAAAGCAGACTAAAAA 57.295 25.926 0.00 0.00 0.00 1.94
2253 2306 6.838198 ATCTACGCTAGAGCTAGATAATCG 57.162 41.667 15.78 4.69 38.49 3.34
2254 2307 5.963594 TCTACGCTAGAGCTAGATAATCGA 58.036 41.667 8.65 0.00 39.32 3.59
2256 2309 4.316645 ACGCTAGAGCTAGATAATCGACA 58.683 43.478 8.65 0.00 39.32 4.35
2258 2311 4.627900 CGCTAGAGCTAGATAATCGACAGA 59.372 45.833 8.65 0.00 39.32 3.41
2262 2315 3.821600 GAGCTAGATAATCGACAGACCCA 59.178 47.826 0.00 0.00 0.00 4.51
2265 2318 4.320641 GCTAGATAATCGACAGACCCAGTC 60.321 50.000 0.00 0.00 0.00 3.51
2278 2331 4.135153 CAGTCCGTCGCTCCCTGG 62.135 72.222 0.00 0.00 0.00 4.45
2279 2332 4.680537 AGTCCGTCGCTCCCTGGT 62.681 66.667 0.00 0.00 0.00 4.00
2321 2374 4.457466 GGCCGAAATCACTAATTAAGGGA 58.543 43.478 0.00 0.00 43.47 4.20
2346 2399 3.160679 CCTTTCAAAGGTGGTCATCCT 57.839 47.619 8.18 0.00 43.95 3.24
2347 2400 3.500343 CCTTTCAAAGGTGGTCATCCTT 58.500 45.455 8.18 0.00 45.84 3.36
2348 2401 3.256631 CCTTTCAAAGGTGGTCATCCTTG 59.743 47.826 8.18 0.00 43.50 3.61
2349 2402 3.593442 TTCAAAGGTGGTCATCCTTGT 57.407 42.857 0.00 0.00 43.50 3.16
2350 2403 2.862541 TCAAAGGTGGTCATCCTTGTG 58.137 47.619 0.00 0.00 43.50 3.33
2351 2404 1.270550 CAAAGGTGGTCATCCTTGTGC 59.729 52.381 0.00 0.00 43.50 4.57
2352 2405 0.478072 AAGGTGGTCATCCTTGTGCA 59.522 50.000 0.00 0.00 42.79 4.57
2353 2406 0.478072 AGGTGGTCATCCTTGTGCAA 59.522 50.000 0.00 0.00 34.23 4.08
2354 2407 1.133513 AGGTGGTCATCCTTGTGCAAA 60.134 47.619 0.00 0.00 34.23 3.68
2355 2408 1.270550 GGTGGTCATCCTTGTGCAAAG 59.729 52.381 0.00 0.00 34.23 2.77
2356 2409 1.270550 GTGGTCATCCTTGTGCAAAGG 59.729 52.381 16.92 16.92 38.78 3.11
2357 2410 0.890683 GGTCATCCTTGTGCAAAGGG 59.109 55.000 20.54 12.40 37.99 3.95
2358 2411 1.547675 GGTCATCCTTGTGCAAAGGGA 60.548 52.381 10.67 10.67 37.99 4.20
2359 2412 2.450476 GTCATCCTTGTGCAAAGGGAT 58.550 47.619 14.73 14.73 38.92 3.85
2360 2413 2.953466 CATCCTTGTGCAAAGGGATG 57.047 50.000 28.15 28.15 45.75 3.51
2361 2414 2.905415 ATCCTTGTGCAAAGGGATGA 57.095 45.000 19.37 4.85 37.22 2.92
2362 2415 1.909700 TCCTTGTGCAAAGGGATGAC 58.090 50.000 20.54 0.00 37.99 3.06
2363 2416 0.890683 CCTTGTGCAAAGGGATGACC 59.109 55.000 15.81 0.00 40.67 4.02
2364 2417 0.523072 CTTGTGCAAAGGGATGACCG 59.477 55.000 0.00 0.00 46.96 4.79
2365 2418 0.893270 TTGTGCAAAGGGATGACCGG 60.893 55.000 0.00 0.00 46.96 5.28
2366 2419 1.002624 GTGCAAAGGGATGACCGGA 60.003 57.895 9.46 0.00 46.96 5.14
2367 2420 0.608035 GTGCAAAGGGATGACCGGAA 60.608 55.000 9.46 0.00 46.96 4.30
2368 2421 0.331278 TGCAAAGGGATGACCGGAAT 59.669 50.000 9.46 0.00 46.96 3.01
2369 2422 1.025041 GCAAAGGGATGACCGGAATC 58.975 55.000 9.46 11.07 46.96 2.52
2370 2423 1.299541 CAAAGGGATGACCGGAATCG 58.700 55.000 9.46 0.00 46.96 3.34
2371 2424 0.463833 AAAGGGATGACCGGAATCGC 60.464 55.000 22.38 22.38 46.96 4.58
2372 2425 1.338136 AAGGGATGACCGGAATCGCT 61.338 55.000 25.02 25.02 46.03 4.93
2373 2426 0.469331 AGGGATGACCGGAATCGCTA 60.469 55.000 27.49 2.61 43.30 4.26
2374 2427 0.391597 GGGATGACCGGAATCGCTAA 59.608 55.000 22.50 0.00 34.93 3.09
2375 2428 1.002087 GGGATGACCGGAATCGCTAAT 59.998 52.381 22.50 0.00 34.93 1.73
2376 2429 2.550208 GGGATGACCGGAATCGCTAATT 60.550 50.000 22.50 0.00 34.93 1.40
2377 2430 3.306502 GGGATGACCGGAATCGCTAATTA 60.307 47.826 22.50 0.00 34.93 1.40
2378 2431 4.312443 GGATGACCGGAATCGCTAATTAA 58.688 43.478 9.46 0.00 34.56 1.40
2379 2432 4.389077 GGATGACCGGAATCGCTAATTAAG 59.611 45.833 9.46 0.00 34.56 1.85
2380 2433 3.724374 TGACCGGAATCGCTAATTAAGG 58.276 45.455 9.46 0.00 34.56 2.69
2381 2434 3.064931 GACCGGAATCGCTAATTAAGGG 58.935 50.000 9.46 0.00 39.48 3.95
2414 2467 2.599408 AGGTCACTCCTAAACCTCGA 57.401 50.000 0.00 0.00 46.10 4.04
2445 2498 2.084546 GTGGCGCAATCTAGGAGTTTT 58.915 47.619 10.83 0.00 0.00 2.43
2451 2504 5.461526 GCGCAATCTAGGAGTTTTCTTTTT 58.538 37.500 0.30 0.00 0.00 1.94
2475 2528 8.874745 TTTCGTAGATTCGCTTATTCAAAAAG 57.125 30.769 0.00 0.00 35.04 2.27
2476 2529 7.591006 TCGTAGATTCGCTTATTCAAAAAGT 57.409 32.000 0.00 0.00 0.00 2.66
2477 2530 8.025243 TCGTAGATTCGCTTATTCAAAAAGTT 57.975 30.769 0.00 0.00 0.00 2.66
2478 2531 8.500773 TCGTAGATTCGCTTATTCAAAAAGTTT 58.499 29.630 0.00 0.00 0.00 2.66
2479 2532 9.113876 CGTAGATTCGCTTATTCAAAAAGTTTT 57.886 29.630 0.00 0.00 0.00 2.43
2496 2549 9.830294 AAAAAGTTTTATCTATTAAACCGGACG 57.170 29.630 9.46 0.00 35.39 4.79
2497 2550 8.552083 AAAGTTTTATCTATTAAACCGGACGT 57.448 30.769 9.46 0.00 35.39 4.34
2498 2551 7.529880 AGTTTTATCTATTAAACCGGACGTG 57.470 36.000 9.46 0.00 35.39 4.49
2499 2552 6.536224 AGTTTTATCTATTAAACCGGACGTGG 59.464 38.462 9.46 0.00 35.39 4.94
2500 2553 5.850557 TTATCTATTAAACCGGACGTGGA 57.149 39.130 9.46 0.00 0.00 4.02
2501 2554 3.788333 TCTATTAAACCGGACGTGGAG 57.212 47.619 9.46 0.00 0.00 3.86
2502 2555 3.091545 TCTATTAAACCGGACGTGGAGT 58.908 45.455 9.46 0.00 0.00 3.85
2503 2556 2.845363 ATTAAACCGGACGTGGAGTT 57.155 45.000 9.46 0.00 0.00 3.01
2504 2557 2.618442 TTAAACCGGACGTGGAGTTT 57.382 45.000 9.46 1.89 36.47 2.66
2505 2558 2.618442 TAAACCGGACGTGGAGTTTT 57.382 45.000 9.46 0.00 34.46 2.43
2506 2559 1.018910 AAACCGGACGTGGAGTTTTG 58.981 50.000 9.46 0.00 0.00 2.44
2507 2560 0.816421 AACCGGACGTGGAGTTTTGG 60.816 55.000 9.46 0.00 0.00 3.28
2508 2561 2.613506 CCGGACGTGGAGTTTTGGC 61.614 63.158 0.00 0.00 0.00 4.52
2509 2562 1.597027 CGGACGTGGAGTTTTGGCT 60.597 57.895 0.00 0.00 0.00 4.75
2510 2563 1.566018 CGGACGTGGAGTTTTGGCTC 61.566 60.000 0.00 0.00 34.89 4.70
2516 2569 3.062466 GAGTTTTGGCTCCCGGGC 61.062 66.667 18.49 4.47 41.27 6.13
2517 2570 3.569200 GAGTTTTGGCTCCCGGGCT 62.569 63.158 18.49 3.64 41.48 5.19
2518 2571 3.062466 GTTTTGGCTCCCGGGCTC 61.062 66.667 18.49 9.71 41.48 4.70
2519 2572 3.575247 TTTTGGCTCCCGGGCTCA 61.575 61.111 18.49 11.07 41.48 4.26
2520 2573 2.917897 TTTTGGCTCCCGGGCTCAT 61.918 57.895 18.49 0.00 41.48 2.90
2521 2574 2.837031 TTTTGGCTCCCGGGCTCATC 62.837 60.000 18.49 3.79 41.48 2.92
2522 2575 4.804420 TGGCTCCCGGGCTCATCT 62.804 66.667 18.49 0.00 41.48 2.90
2523 2576 4.247380 GGCTCCCGGGCTCATCTG 62.247 72.222 18.49 0.33 37.53 2.90
2524 2577 4.925861 GCTCCCGGGCTCATCTGC 62.926 72.222 18.49 7.22 0.00 4.26
2525 2578 3.473647 CTCCCGGGCTCATCTGCA 61.474 66.667 18.49 0.00 34.04 4.41
2526 2579 3.457625 CTCCCGGGCTCATCTGCAG 62.458 68.421 18.49 7.63 34.04 4.41
2527 2580 3.790437 CCCGGGCTCATCTGCAGT 61.790 66.667 8.08 0.00 34.04 4.40
2528 2581 2.202987 CCGGGCTCATCTGCAGTC 60.203 66.667 14.67 0.00 34.04 3.51
2529 2582 2.580815 CGGGCTCATCTGCAGTCA 59.419 61.111 14.67 0.00 34.04 3.41
2530 2583 1.145598 CGGGCTCATCTGCAGTCAT 59.854 57.895 14.67 0.00 34.04 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.452108 GGGAGGGTAGTGCATGTGC 60.452 63.158 0.00 0.00 42.50 4.57
5 6 0.179000 GAGGGAGGGTAGTGCATGTG 59.821 60.000 0.00 0.00 0.00 3.21
6 7 0.043334 AGAGGGAGGGTAGTGCATGT 59.957 55.000 0.00 0.00 0.00 3.21
7 8 0.755686 GAGAGGGAGGGTAGTGCATG 59.244 60.000 0.00 0.00 0.00 4.06
8 9 0.339859 TGAGAGGGAGGGTAGTGCAT 59.660 55.000 0.00 0.00 0.00 3.96
9 10 0.116342 TTGAGAGGGAGGGTAGTGCA 59.884 55.000 0.00 0.00 0.00 4.57
11 12 2.104170 GACTTGAGAGGGAGGGTAGTG 58.896 57.143 0.00 0.00 0.00 2.74
12 13 2.004589 AGACTTGAGAGGGAGGGTAGT 58.995 52.381 0.00 0.00 0.00 2.73
13 14 2.024846 TGAGACTTGAGAGGGAGGGTAG 60.025 54.545 0.00 0.00 0.00 3.18
14 15 2.000803 TGAGACTTGAGAGGGAGGGTA 58.999 52.381 0.00 0.00 0.00 3.69
15 16 0.787084 TGAGACTTGAGAGGGAGGGT 59.213 55.000 0.00 0.00 0.00 4.34
16 17 1.944177 TTGAGACTTGAGAGGGAGGG 58.056 55.000 0.00 0.00 0.00 4.30
17 18 3.067461 CGTATTGAGACTTGAGAGGGAGG 59.933 52.174 0.00 0.00 0.00 4.30
18 19 3.948473 TCGTATTGAGACTTGAGAGGGAG 59.052 47.826 0.00 0.00 0.00 4.30
29 30 4.092091 CAGAAAGCTTGGTCGTATTGAGAC 59.908 45.833 0.00 0.00 37.86 3.36
39 40 1.248486 GGTTCCCAGAAAGCTTGGTC 58.752 55.000 0.00 0.00 0.00 4.02
110 114 4.380867 GCCAGTAATGCAAGCAGTAACAAT 60.381 41.667 3.61 0.00 0.00 2.71
292 296 2.989824 CGTATCCCGCGATCCCCT 60.990 66.667 8.23 0.00 0.00 4.79
365 369 6.192234 TCTATGTTCTCACCGAAGTAGAAC 57.808 41.667 7.35 7.35 45.99 3.01
377 381 4.326826 CTTTGCCCACTTCTATGTTCTCA 58.673 43.478 0.00 0.00 0.00 3.27
384 388 0.394352 CGCCCTTTGCCCACTTCTAT 60.394 55.000 0.00 0.00 36.24 1.98
388 392 2.597510 GACGCCCTTTGCCCACTT 60.598 61.111 0.00 0.00 36.24 3.16
566 570 4.796231 GTGTCGCCGGAGTCGCAT 62.796 66.667 5.05 0.00 34.56 4.73
648 660 1.358725 CGGCGTGATCATTCAACGGT 61.359 55.000 0.00 0.00 32.48 4.83
668 680 2.179589 GATGCTGTTAACTTGCATGCG 58.820 47.619 29.90 1.59 45.90 4.73
683 695 4.101448 GCCACGTGGAGGGATGCT 62.101 66.667 38.30 0.00 37.39 3.79
700 712 6.043327 TCGATGGTAAATAACTTTGATGCG 57.957 37.500 0.00 0.00 0.00 4.73
794 806 9.433153 CGAGTAATGGAGTATATACTACTGTCA 57.567 37.037 22.91 13.17 38.02 3.58
802 814 8.194433 TCATCGTCGAGTAATGGAGTATATAC 57.806 38.462 4.60 4.60 0.00 1.47
803 815 8.663025 GTTCATCGTCGAGTAATGGAGTATATA 58.337 37.037 0.00 0.00 0.00 0.86
804 816 7.528307 GTTCATCGTCGAGTAATGGAGTATAT 58.472 38.462 0.00 0.00 0.00 0.86
805 817 6.347160 CGTTCATCGTCGAGTAATGGAGTATA 60.347 42.308 0.00 0.00 34.52 1.47
806 818 5.560375 CGTTCATCGTCGAGTAATGGAGTAT 60.560 44.000 0.00 0.00 34.52 2.12
807 819 4.260497 CGTTCATCGTCGAGTAATGGAGTA 60.260 45.833 0.00 0.00 34.52 2.59
808 820 3.487042 CGTTCATCGTCGAGTAATGGAGT 60.487 47.826 0.00 0.00 34.52 3.85
809 821 3.036633 CGTTCATCGTCGAGTAATGGAG 58.963 50.000 0.00 0.00 34.52 3.86
962 988 2.034053 GGTCGATTTGGTGAAGTTTGCA 59.966 45.455 0.00 0.00 0.00 4.08
984 1010 0.901827 ACATGGTGATCTGCGGTGTA 59.098 50.000 0.00 0.00 0.00 2.90
985 1011 0.391661 GACATGGTGATCTGCGGTGT 60.392 55.000 0.00 0.00 0.00 4.16
1374 1415 3.727258 CATGTCTTCCCCGGGGCA 61.727 66.667 36.68 26.85 34.68 5.36
1539 1580 0.669318 TCTCGCCACGTTAGCTTTGG 60.669 55.000 0.00 0.00 0.00 3.28
1540 1581 1.359848 ATCTCGCCACGTTAGCTTTG 58.640 50.000 0.00 0.00 0.00 2.77
1541 1582 2.953466 TATCTCGCCACGTTAGCTTT 57.047 45.000 0.00 0.00 0.00 3.51
1551 1594 6.932400 ACGTTATTTCCAAATATATCTCGCCA 59.068 34.615 0.00 0.00 31.47 5.69
1617 1660 7.471890 AGTTATGAACTATGGTACCCCAAAAA 58.528 34.615 10.07 0.00 40.69 1.94
1618 1661 7.034967 AGTTATGAACTATGGTACCCCAAAA 57.965 36.000 10.07 0.00 40.69 2.44
1619 1662 6.645884 AGTTATGAACTATGGTACCCCAAA 57.354 37.500 10.07 0.00 40.69 3.28
1620 1663 6.215841 TGAAGTTATGAACTATGGTACCCCAA 59.784 38.462 10.07 0.00 42.35 4.12
1621 1664 5.727279 TGAAGTTATGAACTATGGTACCCCA 59.273 40.000 10.07 0.00 42.94 4.96
1622 1665 6.243216 TGAAGTTATGAACTATGGTACCCC 57.757 41.667 10.07 0.00 41.91 4.95
1623 1666 7.226720 CACATGAAGTTATGAACTATGGTACCC 59.773 40.741 10.07 0.00 41.91 3.69
1642 1689 6.181206 TGGATATCGGGTAATTCACATGAA 57.819 37.500 0.00 0.00 38.56 2.57
1643 1690 5.279960 CCTGGATATCGGGTAATTCACATGA 60.280 44.000 0.00 0.00 37.13 3.07
1644 1691 4.937620 CCTGGATATCGGGTAATTCACATG 59.062 45.833 0.00 0.00 37.13 3.21
1645 1692 4.844085 TCCTGGATATCGGGTAATTCACAT 59.156 41.667 11.49 0.00 42.62 3.21
1646 1693 4.039973 GTCCTGGATATCGGGTAATTCACA 59.960 45.833 0.00 0.00 42.62 3.58
1647 1694 4.039973 TGTCCTGGATATCGGGTAATTCAC 59.960 45.833 0.00 4.42 42.62 3.18
1648 1695 4.228010 TGTCCTGGATATCGGGTAATTCA 58.772 43.478 0.00 0.00 42.62 2.57
1649 1696 4.884668 TGTCCTGGATATCGGGTAATTC 57.115 45.455 0.00 0.00 42.62 2.17
1650 1697 4.041691 CCTTGTCCTGGATATCGGGTAATT 59.958 45.833 0.00 0.00 42.62 1.40
1651 1698 3.583086 CCTTGTCCTGGATATCGGGTAAT 59.417 47.826 0.00 0.00 42.62 1.89
1652 1699 2.969950 CCTTGTCCTGGATATCGGGTAA 59.030 50.000 0.00 8.42 42.62 2.85
1653 1700 2.090943 ACCTTGTCCTGGATATCGGGTA 60.091 50.000 0.00 2.72 42.62 3.69
1654 1701 1.344087 ACCTTGTCCTGGATATCGGGT 60.344 52.381 0.00 3.73 42.62 5.28
1655 1702 1.424638 ACCTTGTCCTGGATATCGGG 58.575 55.000 0.00 3.10 43.43 5.14
1656 1703 2.700897 AGAACCTTGTCCTGGATATCGG 59.299 50.000 0.00 3.77 0.00 4.18
1657 1704 4.408182 AAGAACCTTGTCCTGGATATCG 57.592 45.455 0.00 0.00 0.00 2.92
1665 1712 4.832823 CCCATTAACAAAGAACCTTGTCCT 59.167 41.667 0.00 0.00 38.59 3.85
1691 1738 2.799412 AGCTGAATCTGAATCGAATCGC 59.201 45.455 0.00 0.00 0.00 4.58
1715 1762 0.523072 AACCATGCGCAAGTGATCAC 59.477 50.000 17.11 18.47 41.68 3.06
1721 1768 1.285641 CGGAAAACCATGCGCAAGT 59.714 52.632 17.11 13.11 41.68 3.16
1724 1771 0.889638 TAACCGGAAAACCATGCGCA 60.890 50.000 14.96 14.96 32.32 6.09
1842 1890 1.939255 ACGGTTCGCGGTTTAAAAGAA 59.061 42.857 6.13 0.00 0.00 2.52
1844 1892 2.388106 AACGGTTCGCGGTTTAAAAG 57.612 45.000 6.13 0.00 37.36 2.27
1928 1978 8.450964 CGTGTTTTTCAATATATCAGTGTTCCT 58.549 33.333 0.00 0.00 0.00 3.36
1933 1983 9.773328 ATGTTCGTGTTTTTCAATATATCAGTG 57.227 29.630 0.00 0.00 0.00 3.66
2127 2178 9.412460 TGCTGGTATTTATGATCTCTTTTGATT 57.588 29.630 0.00 0.00 0.00 2.57
2128 2179 8.985315 TGCTGGTATTTATGATCTCTTTTGAT 57.015 30.769 0.00 0.00 0.00 2.57
2129 2180 8.806429 TTGCTGGTATTTATGATCTCTTTTGA 57.194 30.769 0.00 0.00 0.00 2.69
2130 2181 9.859427 TTTTGCTGGTATTTATGATCTCTTTTG 57.141 29.630 0.00 0.00 0.00 2.44
2168 2219 8.846211 TGTAGAAAATTCCTGAACCTTTTGTAG 58.154 33.333 0.00 0.00 0.00 2.74
2171 2222 7.653311 CCTTGTAGAAAATTCCTGAACCTTTTG 59.347 37.037 0.00 0.00 0.00 2.44
2236 2289 5.163794 GGTCTGTCGATTATCTAGCTCTAGC 60.164 48.000 0.00 0.00 42.49 3.42
2240 2293 3.821600 TGGGTCTGTCGATTATCTAGCTC 59.178 47.826 0.00 0.00 0.00 4.09
2256 2309 3.063084 GAGCGACGGACTGGGTCT 61.063 66.667 0.00 0.00 32.47 3.85
2262 2315 4.680537 ACCAGGGAGCGACGGACT 62.681 66.667 0.00 0.00 0.00 3.85
2265 2318 3.432051 GATGACCAGGGAGCGACGG 62.432 68.421 0.00 0.00 0.00 4.79
2300 2353 6.148976 GGTATCCCTTAATTAGTGATTTCGGC 59.851 42.308 0.00 0.00 0.00 5.54
2327 2380 3.891366 ACAAGGATGACCACCTTTGAAAG 59.109 43.478 0.00 0.00 44.13 2.62
2328 2381 3.636300 CACAAGGATGACCACCTTTGAAA 59.364 43.478 0.00 0.00 44.13 2.69
2329 2382 3.221771 CACAAGGATGACCACCTTTGAA 58.778 45.455 0.00 0.00 44.13 2.69
2330 2383 2.862541 CACAAGGATGACCACCTTTGA 58.137 47.619 0.00 0.00 44.13 2.69
2331 2384 1.270550 GCACAAGGATGACCACCTTTG 59.729 52.381 0.00 0.00 44.13 2.77
2332 2385 1.133513 TGCACAAGGATGACCACCTTT 60.134 47.619 0.00 0.00 44.13 3.11
2333 2386 0.478072 TGCACAAGGATGACCACCTT 59.522 50.000 0.00 0.00 47.00 3.50
2334 2387 0.478072 TTGCACAAGGATGACCACCT 59.522 50.000 0.00 0.00 39.69 4.00
2335 2388 1.270550 CTTTGCACAAGGATGACCACC 59.729 52.381 0.00 0.00 38.94 4.61
2336 2389 1.270550 CCTTTGCACAAGGATGACCAC 59.729 52.381 17.72 0.00 39.81 4.16
2337 2390 1.619654 CCTTTGCACAAGGATGACCA 58.380 50.000 17.72 0.00 39.81 4.02
2338 2391 0.890683 CCCTTTGCACAAGGATGACC 59.109 55.000 21.94 0.00 39.81 4.02
2339 2392 1.909700 TCCCTTTGCACAAGGATGAC 58.090 50.000 21.94 0.00 39.81 3.06
2340 2393 2.905415 ATCCCTTTGCACAAGGATGA 57.095 45.000 21.94 14.72 39.81 2.92
2342 2395 2.450476 GTCATCCCTTTGCACAAGGAT 58.550 47.619 21.94 12.07 39.81 3.24
2343 2396 1.547675 GGTCATCCCTTTGCACAAGGA 60.548 52.381 21.94 10.38 39.81 3.36
2344 2397 0.890683 GGTCATCCCTTTGCACAAGG 59.109 55.000 16.37 16.37 37.17 3.61
2345 2398 0.523072 CGGTCATCCCTTTGCACAAG 59.477 55.000 0.00 0.00 0.00 3.16
2346 2399 0.893270 CCGGTCATCCCTTTGCACAA 60.893 55.000 0.00 0.00 0.00 3.33
2347 2400 1.303236 CCGGTCATCCCTTTGCACA 60.303 57.895 0.00 0.00 0.00 4.57
2348 2401 0.608035 TTCCGGTCATCCCTTTGCAC 60.608 55.000 0.00 0.00 0.00 4.57
2349 2402 0.331278 ATTCCGGTCATCCCTTTGCA 59.669 50.000 0.00 0.00 0.00 4.08
2350 2403 1.025041 GATTCCGGTCATCCCTTTGC 58.975 55.000 0.00 0.00 0.00 3.68
2351 2404 1.299541 CGATTCCGGTCATCCCTTTG 58.700 55.000 0.00 0.00 0.00 2.77
2352 2405 0.463833 GCGATTCCGGTCATCCCTTT 60.464 55.000 0.00 0.00 36.06 3.11
2353 2406 1.146263 GCGATTCCGGTCATCCCTT 59.854 57.895 0.00 0.00 36.06 3.95
2354 2407 0.469331 TAGCGATTCCGGTCATCCCT 60.469 55.000 0.00 5.14 46.09 4.20
2355 2408 0.391597 TTAGCGATTCCGGTCATCCC 59.608 55.000 0.00 0.00 46.09 3.85
2356 2409 2.457366 ATTAGCGATTCCGGTCATCC 57.543 50.000 0.00 0.00 46.09 3.51
2357 2410 4.389077 CCTTAATTAGCGATTCCGGTCATC 59.611 45.833 0.00 3.70 46.09 2.92
2358 2411 4.315803 CCTTAATTAGCGATTCCGGTCAT 58.684 43.478 0.00 0.00 46.09 3.06
2359 2412 3.493699 CCCTTAATTAGCGATTCCGGTCA 60.494 47.826 0.00 0.00 46.09 4.02
2360 2413 3.064931 CCCTTAATTAGCGATTCCGGTC 58.935 50.000 0.00 0.00 46.09 4.79
2362 2415 3.396260 TCCCTTAATTAGCGATTCCGG 57.604 47.619 0.00 0.00 36.06 5.14
2363 2416 4.868734 GGTATCCCTTAATTAGCGATTCCG 59.131 45.833 0.00 0.00 39.16 4.30
2364 2417 5.183969 GGGTATCCCTTAATTAGCGATTCC 58.816 45.833 0.00 6.00 41.34 3.01
2421 2474 0.613260 TCCTAGATTGCGCCACTTGT 59.387 50.000 4.18 0.00 0.00 3.16
2451 2504 8.025243 ACTTTTTGAATAAGCGAATCTACGAA 57.975 30.769 0.00 0.00 35.09 3.85
2475 2528 6.534793 TCCACGTCCGGTTTAATAGATAAAAC 59.465 38.462 0.00 0.00 37.75 2.43
2476 2529 6.638610 TCCACGTCCGGTTTAATAGATAAAA 58.361 36.000 0.00 0.00 35.33 1.52
2477 2530 6.127366 ACTCCACGTCCGGTTTAATAGATAAA 60.127 38.462 0.00 0.00 0.00 1.40
2478 2531 5.360714 ACTCCACGTCCGGTTTAATAGATAA 59.639 40.000 0.00 0.00 0.00 1.75
2479 2532 4.889409 ACTCCACGTCCGGTTTAATAGATA 59.111 41.667 0.00 0.00 0.00 1.98
2499 2552 3.062466 GCCCGGGAGCCAAAACTC 61.062 66.667 29.31 0.00 35.86 3.01
2500 2553 3.569200 GAGCCCGGGAGCCAAAACT 62.569 63.158 29.31 9.07 0.00 2.66
2501 2554 3.062466 GAGCCCGGGAGCCAAAAC 61.062 66.667 29.31 2.84 0.00 2.43
2502 2555 2.837031 GATGAGCCCGGGAGCCAAAA 62.837 60.000 29.31 1.13 0.00 2.44
2503 2556 3.338250 ATGAGCCCGGGAGCCAAA 61.338 61.111 29.31 2.41 0.00 3.28
2504 2557 3.797353 GATGAGCCCGGGAGCCAA 61.797 66.667 29.31 4.14 0.00 4.52
2505 2558 4.804420 AGATGAGCCCGGGAGCCA 62.804 66.667 29.31 18.65 0.00 4.75
2506 2559 4.247380 CAGATGAGCCCGGGAGCC 62.247 72.222 29.31 12.80 0.00 4.70
2507 2560 4.925861 GCAGATGAGCCCGGGAGC 62.926 72.222 29.31 16.09 0.00 4.70
2508 2561 3.457625 CTGCAGATGAGCCCGGGAG 62.458 68.421 29.31 4.89 0.00 4.30
2509 2562 3.473647 CTGCAGATGAGCCCGGGA 61.474 66.667 29.31 2.74 0.00 5.14
2510 2563 3.746949 GACTGCAGATGAGCCCGGG 62.747 68.421 23.35 19.09 0.00 5.73
2511 2564 2.202987 GACTGCAGATGAGCCCGG 60.203 66.667 23.35 0.00 0.00 5.73
2512 2565 1.145598 ATGACTGCAGATGAGCCCG 59.854 57.895 23.35 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.