Multiple sequence alignment - TraesCS4D01G082400

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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 TraesCS4D01G082400 chr4D 100.000 2466 0 0 1 2466 55646176 55643711 0.000000e+00 4554.0
1 TraesCS4D01G082400 chr4D 93.590 156 6 1 1528 1679 55597722 55597567 1.910000e-56 230.0
2 TraesCS4D01G082400 chr4B 88.808 1644 92 24 101 1679 82919882 82918266 0.000000e+00 1932.0
3 TraesCS4D01G082400 chr4B 87.647 170 14 3 1510 1679 82664773 82664611 9.000000e-45 191.0
4 TraesCS4D01G082400 chr4A 87.751 1445 108 23 959 2367 541172379 541173790 0.000000e+00 1624.0
5 TraesCS4D01G082400 chr4A 90.949 906 46 15 1 892 541171497 541172380 0.000000e+00 1186.0
6 TraesCS4D01G082400 chr4A 86.822 258 22 8 1870 2118 738092001 738091747 6.720000e-71 278.0
7 TraesCS4D01G082400 chr1B 87.692 260 21 8 1869 2118 4787551 4787809 2.400000e-75 292.0
8 TraesCS4D01G082400 chr1B 75.460 163 24 12 2148 2296 456997954 456997794 5.690000e-07 65.8
9 TraesCS4D01G082400 chr1D 88.189 254 17 8 1869 2112 139116150 139115900 8.630000e-75 291.0
10 TraesCS4D01G082400 chr5B 87.402 254 19 9 1869 2112 578439656 578439906 1.870000e-71 279.0
11 TraesCS4D01G082400 chr5B 78.008 241 32 5 2144 2363 712876418 712876178 5.530000e-27 132.0
12 TraesCS4D01G082400 chr5B 78.531 177 25 2 2145 2308 595065968 595065792 1.210000e-18 104.0
13 TraesCS4D01G082400 chr2D 86.538 260 24 7 1869 2119 522609020 522609277 2.420000e-70 276.0
14 TraesCS4D01G082400 chr2D 82.063 223 29 6 2150 2363 178610698 178610478 1.950000e-41 180.0
15 TraesCS4D01G082400 chr5D 87.008 254 20 9 1869 2112 459115679 459115429 8.690000e-70 274.0
16 TraesCS4D01G082400 chr5D 79.885 348 34 15 2143 2454 544488212 544488559 3.190000e-54 222.0
17 TraesCS4D01G082400 chr5D 80.913 241 26 5 2145 2365 530732662 530732422 3.260000e-39 172.0
18 TraesCS4D01G082400 chr3D 88.444 225 22 4 1892 2114 593206695 593206473 4.040000e-68 268.0
19 TraesCS4D01G082400 chr3B 85.992 257 25 7 1869 2116 133085441 133085187 5.230000e-67 265.0
20 TraesCS4D01G082400 chr7A 79.023 348 42 16 2144 2461 77591416 77591762 2.490000e-50 209.0
21 TraesCS4D01G082400 chr1A 79.916 239 27 4 2144 2361 71300375 71300613 3.280000e-34 156.0
22 TraesCS4D01G082400 chr3A 77.959 245 33 4 2144 2367 26210254 26210010 1.540000e-27 134.0
23 TraesCS4D01G082400 chr6A 100.000 30 0 0 1836 1865 552995282 552995311 3.430000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G082400 chr4D 55643711 55646176 2465 True 4554 4554 100.000 1 2466 1 chr4D.!!$R2 2465
1 TraesCS4D01G082400 chr4B 82918266 82919882 1616 True 1932 1932 88.808 101 1679 1 chr4B.!!$R2 1578
2 TraesCS4D01G082400 chr4A 541171497 541173790 2293 False 1405 1624 89.350 1 2367 2 chr4A.!!$F1 2366

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
320 328 0.746659 GCCACATGGATTAGGTTGCC 59.253 55.0 0.87 0.0 37.39 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1516 1597 0.512952 AGAACACACGCAGCGAATTC 59.487 50.0 24.65 17.52 0.0 2.17 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
21 22 1.195115 GGACTCCAGGAGCACATACA 58.805 55.000 17.31 0.00 32.04 2.29
22 23 1.134670 GGACTCCAGGAGCACATACAC 60.135 57.143 17.31 0.00 32.04 2.90
23 24 1.827969 GACTCCAGGAGCACATACACT 59.172 52.381 17.31 0.00 32.04 3.55
35 36 3.612004 GCACATACACTATACTCCCGAGC 60.612 52.174 0.00 0.00 0.00 5.03
73 75 3.378742 AGTTACACGACTCCTGCTCTATG 59.621 47.826 0.00 0.00 0.00 2.23
155 162 4.201523 CGCTTTTATTTAGTTTGCTGCAGC 60.202 41.667 31.89 31.89 42.50 5.25
206 213 2.368439 GCTACCTTGATGTCCATGCAA 58.632 47.619 0.00 0.00 0.00 4.08
246 254 1.472201 GCAGCACATGGAAGATCGAGA 60.472 52.381 0.00 0.00 0.00 4.04
320 328 0.746659 GCCACATGGATTAGGTTGCC 59.253 55.000 0.87 0.00 37.39 4.52
330 342 3.481453 GATTAGGTTGCCAGAGGAATCC 58.519 50.000 0.00 0.00 0.00 3.01
334 346 1.683319 GGTTGCCAGAGGAATCCCTTC 60.683 57.143 0.00 0.00 44.53 3.46
392 404 4.982295 CGAGTGTCAAATCCGATTAGCATA 59.018 41.667 0.00 0.00 0.00 3.14
393 405 5.635280 CGAGTGTCAAATCCGATTAGCATAT 59.365 40.000 0.00 0.00 0.00 1.78
416 428 3.431486 GCTCCTAGTTTCAGATCAGGTGG 60.431 52.174 0.00 0.00 0.00 4.61
433 445 2.887152 GGTGGCTGAAACTTGTGAGATT 59.113 45.455 0.00 0.00 0.00 2.40
453 469 4.519906 TTGGAAGATTGGATACCCCTTC 57.480 45.455 0.00 0.00 35.70 3.46
523 539 4.320788 GCTTCTTGCTGTGATATATTGGCC 60.321 45.833 0.00 0.00 38.95 5.36
530 546 1.194547 GTGATATATTGGCCGTGTGCG 59.805 52.381 0.00 0.00 42.61 5.34
607 624 6.052840 CTGTCATATGGGAATTTTCGACAG 57.947 41.667 2.13 0.00 42.02 3.51
691 708 4.137543 CTCCTACATTAAGGCCAATGGTC 58.862 47.826 17.54 0.00 39.71 4.02
695 712 1.102978 ATTAAGGCCAATGGTCGCAC 58.897 50.000 5.01 0.00 29.39 5.34
757 806 2.497107 ACAAACAGAGTTGCATGCAC 57.503 45.000 22.58 15.59 31.29 4.57
811 863 4.521146 GGGCATCTCCAATAATCGATGAT 58.479 43.478 0.00 0.00 36.29 2.45
908 969 1.312371 ACTGCCACGCACAACAGTTT 61.312 50.000 0.00 0.00 40.35 2.66
950 1011 7.286775 AGCTAGCTAGGGAAATATATACAGCTC 59.713 40.741 17.69 0.00 38.88 4.09
951 1012 7.286775 GCTAGCTAGGGAAATATATACAGCTCT 59.713 40.741 22.10 0.00 38.88 4.09
952 1013 7.654022 AGCTAGGGAAATATATACAGCTCTC 57.346 40.000 0.00 0.00 32.93 3.20
953 1014 7.418378 AGCTAGGGAAATATATACAGCTCTCT 58.582 38.462 0.00 0.00 32.93 3.10
954 1015 8.561769 AGCTAGGGAAATATATACAGCTCTCTA 58.438 37.037 0.00 0.00 32.93 2.43
973 1034 1.265236 ACTCCTTCTCTGCCTCTGTG 58.735 55.000 0.00 0.00 0.00 3.66
1036 1097 1.736612 GCTTCAGCTGGAGAAGAAGG 58.263 55.000 26.96 0.00 44.00 3.46
1222 1283 2.060980 CCTCCCGCAGCTACCTCTT 61.061 63.158 0.00 0.00 0.00 2.85
1238 1299 0.750546 TCTTCCCAGCTGCATGATGC 60.751 55.000 11.12 11.12 45.29 3.91
1250 1311 3.472943 ATGATGCAGAGGCCGGAGC 62.473 63.158 5.05 9.06 40.13 4.70
1283 1344 2.337583 ACACGCTGCACATGTAAGTAG 58.662 47.619 0.00 0.00 0.00 2.57
1284 1345 2.029380 ACACGCTGCACATGTAAGTAGA 60.029 45.455 0.00 0.00 0.00 2.59
1285 1346 2.993220 CACGCTGCACATGTAAGTAGAA 59.007 45.455 0.00 0.00 0.00 2.10
1317 1386 9.190317 TCTATCTTGATCTTGTTAGCTCTGTTA 57.810 33.333 0.00 0.00 0.00 2.41
1327 1396 5.171476 TGTTAGCTCTGTTAGAGTTCATGC 58.829 41.667 7.59 0.00 44.12 4.06
1328 1397 3.969287 AGCTCTGTTAGAGTTCATGCA 57.031 42.857 7.59 0.00 44.12 3.96
1348 1423 3.594134 CAGTGGACTGACTTCAATCTCC 58.406 50.000 0.04 0.00 46.59 3.71
1354 1429 2.005451 CTGACTTCAATCTCCTTGCGG 58.995 52.381 0.00 0.00 34.66 5.69
1357 1432 1.339151 ACTTCAATCTCCTTGCGGTCC 60.339 52.381 0.00 0.00 34.66 4.46
1382 1460 6.900324 CATGTCTATGATCGGTCAGGATGATC 60.900 46.154 3.97 7.25 41.65 2.92
1459 1537 1.550976 GAAGGACGAGGAGGAACACAT 59.449 52.381 0.00 0.00 0.00 3.21
1466 1544 3.769844 ACGAGGAGGAACACATCATTAGT 59.230 43.478 0.00 0.00 28.65 2.24
1475 1553 6.820656 AGGAACACATCATTAGTCTTAGCTTG 59.179 38.462 0.00 0.00 0.00 4.01
1509 1590 7.609056 ACTGTAGACTATAACATTGAAACGGT 58.391 34.615 0.00 0.00 0.00 4.83
1516 1597 1.544724 ACATTGAAACGGTCATGGGG 58.455 50.000 0.00 0.00 35.70 4.96
1545 1626 1.002792 GCGTGTGTTCTTTCTGGAACC 60.003 52.381 5.15 0.00 43.31 3.62
1619 1709 7.539034 AGCAATACAAGTTTAAATTCCAGGT 57.461 32.000 0.00 0.00 0.00 4.00
1631 1721 3.443045 CCAGGTCGGGCATGTTGC 61.443 66.667 0.00 0.00 44.08 4.17
1667 1757 6.467047 CACTTCAGCTTACAATGCTAATTTCG 59.533 38.462 0.00 0.00 38.92 3.46
1690 1780 0.930726 ACCTGGGTGGAAACAAGGAA 59.069 50.000 0.00 0.00 46.06 3.36
1692 1782 2.171003 CCTGGGTGGAAACAAGGAATC 58.829 52.381 0.00 0.00 46.06 2.52
1693 1783 2.490718 CCTGGGTGGAAACAAGGAATCA 60.491 50.000 0.00 0.00 46.06 2.57
1696 1786 3.831911 TGGGTGGAAACAAGGAATCATTC 59.168 43.478 0.00 0.00 46.06 2.67
1743 1833 3.438087 CACATCTTACTTGTGAGCTTGGG 59.562 47.826 0.00 0.00 45.83 4.12
1764 1856 5.832060 TGGGACTATTACACTAGGCTTCTAC 59.168 44.000 0.00 0.00 0.00 2.59
1786 1878 6.963083 ACGGAGTAAAGAGTATGCTAATCT 57.037 37.500 0.00 0.00 41.94 2.40
1801 1893 6.885952 TGCTAATCTGTATAGAGGACACTC 57.114 41.667 0.00 0.00 44.31 3.51
1818 1910 2.738846 CACTCTGTCCGATTGTTTCCTG 59.261 50.000 0.00 0.00 0.00 3.86
1821 1913 2.086869 CTGTCCGATTGTTTCCTGCAT 58.913 47.619 0.00 0.00 0.00 3.96
1841 1933 5.721000 TGCATTGTTATTTCCTCCTTTCCAT 59.279 36.000 0.00 0.00 0.00 3.41
1843 1935 7.105588 GCATTGTTATTTCCTCCTTTCCATTT 58.894 34.615 0.00 0.00 0.00 2.32
1853 1945 6.985225 TCCTCCTTTCCATTTCCATTTATCT 58.015 36.000 0.00 0.00 0.00 1.98
1859 1951 9.506018 CCTTTCCATTTCCATTTATCTGTTTTT 57.494 29.630 0.00 0.00 0.00 1.94
1861 1953 9.844257 TTTCCATTTCCATTTATCTGTTTTTGT 57.156 25.926 0.00 0.00 0.00 2.83
1910 2009 6.526222 GTGCAGACACGAGTTTAAATTCTAG 58.474 40.000 8.82 4.06 36.98 2.43
1934 2033 7.056635 AGAATTGACAAGTGATGTATAAGGGG 58.943 38.462 0.00 0.00 44.12 4.79
1942 2041 6.002653 AGTGATGTATAAGGGGGTTTTCTC 57.997 41.667 0.00 0.00 0.00 2.87
1945 2044 6.100714 GTGATGTATAAGGGGGTTTTCTCCTA 59.899 42.308 0.00 0.00 41.08 2.94
1955 2054 5.302059 GGGGGTTTTCTCCTATTTATTGAGC 59.698 44.000 0.00 0.00 41.08 4.26
1976 2075 4.974721 AAGCTTGGTGTGGGGCGG 62.975 66.667 0.00 0.00 0.00 6.13
2000 2099 6.261826 GGGACCACTCATGAAGAAATATCTTG 59.738 42.308 0.00 0.00 45.91 3.02
2077 2177 2.548067 GGTCGTATGCATCCCTAGTTGG 60.548 54.545 0.19 0.00 0.00 3.77
2082 2182 0.403655 TGCATCCCTAGTTGGTGCAA 59.596 50.000 13.38 0.60 38.55 4.08
2085 2185 2.879756 GCATCCCTAGTTGGTGCAAAGA 60.880 50.000 9.27 0.00 34.56 2.52
2086 2186 2.859165 TCCCTAGTTGGTGCAAAGAG 57.141 50.000 0.00 0.00 0.00 2.85
2088 2188 1.614317 CCCTAGTTGGTGCAAAGAGGG 60.614 57.143 0.00 0.00 39.60 4.30
2100 2200 3.573967 TGCAAAGAGGGGAAGTGAAAATC 59.426 43.478 0.00 0.00 0.00 2.17
2112 2212 6.014242 GGGAAGTGAAAATCTCTCCCATTTTT 60.014 38.462 0.00 0.00 34.30 1.94
2123 2223 7.733773 TCTCTCCCATTTTTATGAGAGTACA 57.266 36.000 13.34 0.00 46.93 2.90
2195 2295 2.907179 GCAACCCTAGCCACCAGGT 61.907 63.158 0.00 0.00 37.19 4.00
2290 2390 0.966370 AACTCCGGTTCTCCCTCTCG 60.966 60.000 0.00 0.00 0.00 4.04
2310 2410 4.643387 GGGCTCTGGTGTTGCCGT 62.643 66.667 0.00 0.00 46.97 5.68
2311 2411 2.594592 GGCTCTGGTGTTGCCGTT 60.595 61.111 0.00 0.00 41.21 4.44
2320 2428 4.025401 GTTGCCGTTGTGGGAGCG 62.025 66.667 0.00 0.00 40.31 5.03
2383 2491 3.499737 GCGGACGGAAGCATGGTG 61.500 66.667 0.00 0.00 0.00 4.17
2384 2492 2.819595 CGGACGGAAGCATGGTGG 60.820 66.667 0.00 0.00 0.00 4.61
2385 2493 2.438434 GGACGGAAGCATGGTGGG 60.438 66.667 0.00 0.00 0.00 4.61
2386 2494 3.134127 GACGGAAGCATGGTGGGC 61.134 66.667 0.00 0.00 0.00 5.36
2387 2495 3.628646 GACGGAAGCATGGTGGGCT 62.629 63.158 0.00 0.00 45.15 5.19
2388 2496 2.825836 CGGAAGCATGGTGGGCTC 60.826 66.667 0.00 0.00 41.66 4.70
2389 2497 2.679716 GGAAGCATGGTGGGCTCT 59.320 61.111 0.00 0.00 41.66 4.09
2390 2498 1.751927 GGAAGCATGGTGGGCTCTG 60.752 63.158 0.00 0.00 41.66 3.35
2391 2499 1.751927 GAAGCATGGTGGGCTCTGG 60.752 63.158 0.00 0.00 41.66 3.86
2392 2500 3.951769 AAGCATGGTGGGCTCTGGC 62.952 63.158 0.00 0.00 41.66 4.85
2393 2501 4.437587 GCATGGTGGGCTCTGGCT 62.438 66.667 0.00 0.00 38.73 4.75
2394 2502 2.124403 CATGGTGGGCTCTGGCTC 60.124 66.667 0.00 0.00 39.89 4.70
2395 2503 2.285969 ATGGTGGGCTCTGGCTCT 60.286 61.111 0.00 0.00 40.19 4.09
2396 2504 2.373707 ATGGTGGGCTCTGGCTCTC 61.374 63.158 0.00 0.00 40.19 3.20
2397 2505 3.005539 GGTGGGCTCTGGCTCTCA 61.006 66.667 0.00 0.00 40.19 3.27
2398 2506 2.373707 GGTGGGCTCTGGCTCTCAT 61.374 63.158 0.00 0.00 40.19 2.90
2399 2507 1.153208 GTGGGCTCTGGCTCTCATG 60.153 63.158 0.00 0.00 40.19 3.07
2400 2508 2.372890 TGGGCTCTGGCTCTCATGG 61.373 63.158 0.00 0.00 40.19 3.66
2401 2509 2.373707 GGGCTCTGGCTCTCATGGT 61.374 63.158 0.00 0.00 35.73 3.55
2402 2510 1.153208 GGCTCTGGCTCTCATGGTG 60.153 63.158 0.00 0.00 38.73 4.17
2403 2511 1.818785 GCTCTGGCTCTCATGGTGC 60.819 63.158 0.00 0.00 35.22 5.01
2407 2515 4.783621 GGCTCTCATGGTGCCGCA 62.784 66.667 10.26 0.00 43.37 5.69
2408 2516 3.200593 GCTCTCATGGTGCCGCAG 61.201 66.667 0.00 0.00 0.00 5.18
2409 2517 3.200593 CTCTCATGGTGCCGCAGC 61.201 66.667 15.72 15.72 40.48 5.25
2425 2533 4.615815 GCGGCTGGCAGATCGGAT 62.616 66.667 20.86 0.00 42.87 4.18
2426 2534 2.356793 CGGCTGGCAGATCGGATC 60.357 66.667 20.86 10.02 0.00 3.36
2427 2535 2.865598 CGGCTGGCAGATCGGATCT 61.866 63.158 20.86 14.68 41.15 2.75
2428 2536 1.005156 GGCTGGCAGATCGGATCTC 60.005 63.158 20.86 11.97 37.58 2.75
2429 2537 1.372748 GCTGGCAGATCGGATCTCG 60.373 63.158 20.86 13.57 37.58 4.04
2430 2538 1.288439 CTGGCAGATCGGATCTCGG 59.712 63.158 17.41 9.01 37.58 4.63
2431 2539 2.152297 CTGGCAGATCGGATCTCGGG 62.152 65.000 17.41 8.31 37.58 5.14
2432 2540 2.653702 GCAGATCGGATCTCGGGG 59.346 66.667 17.41 7.96 37.58 5.73
2433 2541 2.653702 CAGATCGGATCTCGGGGC 59.346 66.667 17.41 0.00 37.58 5.80
2434 2542 2.986413 AGATCGGATCTCGGGGCG 60.986 66.667 14.68 0.00 39.77 6.13
2435 2543 2.984155 GATCGGATCTCGGGGCGA 60.984 66.667 10.73 0.00 39.77 5.54
2436 2544 3.270335 GATCGGATCTCGGGGCGAC 62.270 68.421 10.73 0.00 39.77 5.19
2449 2557 4.515404 GCGACGGCCTCAATAGTT 57.485 55.556 0.00 0.00 0.00 2.24
2450 2558 2.006772 GCGACGGCCTCAATAGTTG 58.993 57.895 0.00 0.00 0.00 3.16
2451 2559 1.429148 GCGACGGCCTCAATAGTTGG 61.429 60.000 0.00 0.00 0.00 3.77
2452 2560 1.429148 CGACGGCCTCAATAGTTGGC 61.429 60.000 0.00 0.00 45.42 4.52
2453 2561 3.409856 CGGCCTCAATAGTTGGCG 58.590 61.111 0.00 0.00 46.97 5.69
2454 2562 2.180204 CGGCCTCAATAGTTGGCGG 61.180 63.158 0.00 0.00 46.97 6.13
2455 2563 1.823899 GGCCTCAATAGTTGGCGGG 60.824 63.158 0.00 0.00 46.97 6.13
2456 2564 1.823899 GCCTCAATAGTTGGCGGGG 60.824 63.158 0.00 0.00 37.11 5.73
2457 2565 1.152963 CCTCAATAGTTGGCGGGGG 60.153 63.158 0.00 0.00 0.00 5.40
2458 2566 1.607612 CTCAATAGTTGGCGGGGGT 59.392 57.895 0.00 0.00 0.00 4.95
2459 2567 0.748005 CTCAATAGTTGGCGGGGGTG 60.748 60.000 0.00 0.00 0.00 4.61
2460 2568 2.044352 AATAGTTGGCGGGGGTGC 60.044 61.111 0.00 0.00 0.00 5.01
2461 2569 2.913117 AATAGTTGGCGGGGGTGCA 61.913 57.895 0.00 0.00 36.28 4.57
2462 2570 2.837031 AATAGTTGGCGGGGGTGCAG 62.837 60.000 0.00 0.00 36.28 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.134670 GTGTATGTGCTCCTGGAGTCC 60.135 57.143 23.92 15.06 31.39 3.85
16 17 3.125487 CGAGCTCGGGAGTATAGTGTATG 59.875 52.174 28.40 0.00 35.37 2.39
21 22 1.417145 AGTCGAGCTCGGGAGTATAGT 59.583 52.381 33.98 14.24 40.29 2.12
22 23 2.172851 AGTCGAGCTCGGGAGTATAG 57.827 55.000 33.98 4.66 40.29 1.31
23 24 3.323115 TCTTAGTCGAGCTCGGGAGTATA 59.677 47.826 33.98 11.88 40.29 1.47
35 36 4.617645 GTGTAACTGCAACTCTTAGTCGAG 59.382 45.833 0.00 0.00 37.07 4.04
99 105 2.543012 CTCGCTCACCAGCTAATGATTG 59.457 50.000 0.00 0.00 44.40 2.67
193 200 2.429478 CTCACACTTGCATGGACATCA 58.571 47.619 4.44 0.00 0.00 3.07
276 284 2.627771 AGTGTGTTCCCACTTCCCA 58.372 52.632 0.00 0.00 42.99 4.37
282 290 1.068474 CGATCGAAGTGTGTTCCCAC 58.932 55.000 10.26 0.00 42.19 4.61
320 328 2.027192 TGGAAACGAAGGGATTCCTCTG 60.027 50.000 0.00 0.00 44.07 3.35
330 342 2.281208 TGCCGGTGGAAACGAAGG 60.281 61.111 1.90 0.00 0.00 3.46
334 346 2.686816 GGATGTGCCGGTGGAAACG 61.687 63.158 1.90 0.00 0.00 3.60
392 404 4.036518 ACCTGATCTGAAACTAGGAGCAT 58.963 43.478 0.38 0.00 32.86 3.79
393 405 3.196469 CACCTGATCTGAAACTAGGAGCA 59.804 47.826 0.38 0.00 32.86 4.26
416 428 4.516698 TCTTCCAATCTCACAAGTTTCAGC 59.483 41.667 0.00 0.00 0.00 4.26
433 445 2.438021 CGAAGGGGTATCCAATCTTCCA 59.562 50.000 0.00 0.00 38.24 3.53
453 469 4.506886 AACTTCTCTGAACCTGAGTACG 57.493 45.455 0.00 0.00 32.50 3.67
523 539 1.830368 TGCATCAACTGACGCACACG 61.830 55.000 0.00 0.00 38.41 4.49
530 546 0.321919 TGGCCTCTGCATCAACTGAC 60.322 55.000 3.32 0.00 40.13 3.51
569 585 7.607991 CCCATATGACAGTAAGTTTTCTTCTGT 59.392 37.037 3.65 0.00 43.61 3.41
570 586 7.824289 TCCCATATGACAGTAAGTTTTCTTCTG 59.176 37.037 3.65 0.00 40.91 3.02
572 588 8.561738 TTCCCATATGACAGTAAGTTTTCTTC 57.438 34.615 3.65 0.00 40.91 2.87
573 589 9.533831 AATTCCCATATGACAGTAAGTTTTCTT 57.466 29.630 3.65 0.00 43.24 2.52
574 590 9.533831 AAATTCCCATATGACAGTAAGTTTTCT 57.466 29.630 3.65 0.00 0.00 2.52
587 604 5.739959 TCACTGTCGAAAATTCCCATATGA 58.260 37.500 3.65 0.00 0.00 2.15
607 624 6.642540 GGAACCATTGATTTCTGAGTTTTCAC 59.357 38.462 0.00 0.00 0.00 3.18
691 708 0.927537 TGTTTCTTCAGACGTGTGCG 59.072 50.000 8.02 1.66 44.93 5.34
695 712 3.786048 GCTGTTTTGTTTCTTCAGACGTG 59.214 43.478 0.00 0.00 0.00 4.49
728 745 4.757149 GCAACTCTGTTTGTACCTGAAGAT 59.243 41.667 0.00 0.00 0.00 2.40
729 746 4.127171 GCAACTCTGTTTGTACCTGAAGA 58.873 43.478 0.00 0.00 0.00 2.87
730 747 3.876914 TGCAACTCTGTTTGTACCTGAAG 59.123 43.478 0.00 0.00 0.00 3.02
731 748 3.879998 TGCAACTCTGTTTGTACCTGAA 58.120 40.909 0.00 0.00 0.00 3.02
757 806 1.202770 ACCCCTTTCTTTCCGTGTCTG 60.203 52.381 0.00 0.00 0.00 3.51
790 842 5.181009 TCATCATCGATTATTGGAGATGCC 58.819 41.667 12.43 0.00 40.01 4.40
811 863 2.302157 TGAGTACCTCGAGAGTGACTCA 59.698 50.000 23.22 23.22 45.14 3.41
845 897 7.275888 TCCATGTATTTATTGATCAGTTGCC 57.724 36.000 0.00 0.00 0.00 4.52
950 1011 2.951642 CAGAGGCAGAGAAGGAGTAGAG 59.048 54.545 0.00 0.00 0.00 2.43
951 1012 2.310349 ACAGAGGCAGAGAAGGAGTAGA 59.690 50.000 0.00 0.00 0.00 2.59
952 1013 2.426738 CACAGAGGCAGAGAAGGAGTAG 59.573 54.545 0.00 0.00 0.00 2.57
953 1014 2.225142 ACACAGAGGCAGAGAAGGAGTA 60.225 50.000 0.00 0.00 0.00 2.59
954 1015 1.265236 CACAGAGGCAGAGAAGGAGT 58.735 55.000 0.00 0.00 0.00 3.85
973 1034 1.670380 GGCTGGAGTTCAGAGACGAAC 60.670 57.143 1.33 0.00 46.18 3.95
1238 1299 3.847602 CTCCTGCTCCGGCCTCTG 61.848 72.222 0.00 0.00 37.74 3.35
1295 1364 7.177568 ACTCTAACAGAGCTAACAAGATCAAGA 59.822 37.037 3.09 0.00 46.12 3.02
1300 1369 7.233389 TGAACTCTAACAGAGCTAACAAGAT 57.767 36.000 3.09 0.00 46.12 2.40
1301 1370 6.650427 TGAACTCTAACAGAGCTAACAAGA 57.350 37.500 3.09 0.00 46.12 3.02
1302 1371 6.183360 GCATGAACTCTAACAGAGCTAACAAG 60.183 42.308 0.00 0.00 46.12 3.16
1305 1374 5.171476 TGCATGAACTCTAACAGAGCTAAC 58.829 41.667 0.00 0.00 46.12 2.34
1308 1377 3.260380 ACTGCATGAACTCTAACAGAGCT 59.740 43.478 0.00 0.00 46.12 4.09
1317 1386 1.973515 TCAGTCCACTGCATGAACTCT 59.026 47.619 0.00 0.00 43.46 3.24
1327 1396 3.260380 AGGAGATTGAAGTCAGTCCACTG 59.740 47.826 0.00 0.00 45.08 3.66
1328 1397 3.515562 AGGAGATTGAAGTCAGTCCACT 58.484 45.455 0.60 0.00 33.66 4.00
1348 1423 2.602257 TCATAGACATGGACCGCAAG 57.398 50.000 0.00 0.00 32.61 4.01
1354 1429 3.305676 CCTGACCGATCATAGACATGGAC 60.306 52.174 0.00 0.00 33.22 4.02
1357 1432 4.219288 TCATCCTGACCGATCATAGACATG 59.781 45.833 0.00 0.00 33.22 3.21
1459 1537 3.682718 GCAGGCCAAGCTAAGACTAATGA 60.683 47.826 5.01 0.00 0.00 2.57
1466 1544 0.673644 GTTCGCAGGCCAAGCTAAGA 60.674 55.000 16.79 5.59 0.00 2.10
1475 1553 0.815734 TAGTCTACAGTTCGCAGGCC 59.184 55.000 0.00 0.00 0.00 5.19
1509 1590 1.819208 CGCAGCGAATTCCCCATGA 60.819 57.895 9.98 0.00 0.00 3.07
1516 1597 0.512952 AGAACACACGCAGCGAATTC 59.487 50.000 24.65 17.52 0.00 2.17
1545 1626 5.007034 TCACTCTAAGACTCTGAACTCAGG 58.993 45.833 6.87 1.08 43.91 3.86
1619 1709 1.106351 AACACAAGCAACATGCCCGA 61.106 50.000 0.00 0.00 46.52 5.14
1667 1757 1.040339 TTGTTTCCACCCAGGTGTGC 61.040 55.000 15.49 3.69 44.02 4.57
1690 1780 5.999205 TGGCAAATACAAACAGGAATGAT 57.001 34.783 0.00 0.00 0.00 2.45
1692 1782 5.782047 TCTTGGCAAATACAAACAGGAATG 58.218 37.500 0.00 0.00 0.00 2.67
1693 1783 6.418057 TTCTTGGCAAATACAAACAGGAAT 57.582 33.333 0.00 0.00 0.00 3.01
1696 1786 6.924111 AGTATTCTTGGCAAATACAAACAGG 58.076 36.000 19.11 0.00 40.49 4.00
1743 1833 5.762218 TCCGTAGAAGCCTAGTGTAATAGTC 59.238 44.000 0.00 0.00 0.00 2.59
1764 1856 6.740110 ACAGATTAGCATACTCTTTACTCCG 58.260 40.000 0.00 0.00 26.81 4.63
1801 1893 1.522668 TGCAGGAAACAATCGGACAG 58.477 50.000 0.00 0.00 0.00 3.51
1806 1898 6.034898 GGAAATAACAATGCAGGAAACAATCG 59.965 38.462 0.00 0.00 0.00 3.34
1807 1899 7.099120 AGGAAATAACAATGCAGGAAACAATC 58.901 34.615 0.00 0.00 0.00 2.67
1818 1910 5.659440 TGGAAAGGAGGAAATAACAATGC 57.341 39.130 0.00 0.00 0.00 3.56
1821 1913 6.784969 TGGAAATGGAAAGGAGGAAATAACAA 59.215 34.615 0.00 0.00 0.00 2.83
1841 1933 7.042389 GCCGAAACAAAAACAGATAAATGGAAA 60.042 33.333 0.00 0.00 0.00 3.13
1843 1935 5.923684 GCCGAAACAAAAACAGATAAATGGA 59.076 36.000 0.00 0.00 0.00 3.41
1853 1945 0.526662 ACCACGCCGAAACAAAAACA 59.473 45.000 0.00 0.00 0.00 2.83
1859 1951 2.902846 CCCAACCACGCCGAAACA 60.903 61.111 0.00 0.00 0.00 2.83
1861 1953 4.877619 TGCCCAACCACGCCGAAA 62.878 61.111 0.00 0.00 0.00 3.46
1883 1975 3.936902 TTAAACTCGTGTCTGCACAAC 57.063 42.857 0.00 0.00 45.50 3.32
1910 2009 6.263168 CCCCCTTATACATCACTTGTCAATTC 59.737 42.308 0.00 0.00 39.87 2.17
1919 2018 5.104067 GGAGAAAACCCCCTTATACATCACT 60.104 44.000 0.00 0.00 0.00 3.41
1920 2019 5.104067 AGGAGAAAACCCCCTTATACATCAC 60.104 44.000 0.00 0.00 0.00 3.06
1929 2028 7.051696 TCAATAAATAGGAGAAAACCCCCTT 57.948 36.000 0.00 0.00 0.00 3.95
1934 2033 8.225603 TGATGCTCAATAAATAGGAGAAAACC 57.774 34.615 0.00 0.00 0.00 3.27
1955 2054 1.880819 GCCCCACACCAAGCTTGATG 61.881 60.000 28.05 23.97 0.00 3.07
1976 2075 7.050377 TCAAGATATTTCTTCATGAGTGGTCC 58.950 38.462 0.00 0.00 40.28 4.46
2039 2138 8.861101 GCATACGACCATTTTAGTATGAGTATC 58.139 37.037 15.84 0.00 45.38 2.24
2077 2177 1.981256 TTCACTTCCCCTCTTTGCAC 58.019 50.000 0.00 0.00 0.00 4.57
2082 2182 4.018870 GGAGAGATTTTCACTTCCCCTCTT 60.019 45.833 0.00 0.00 30.59 2.85
2085 2185 2.578480 GGGAGAGATTTTCACTTCCCCT 59.422 50.000 0.00 0.00 27.63 4.79
2086 2186 2.308866 TGGGAGAGATTTTCACTTCCCC 59.691 50.000 5.00 0.00 32.41 4.81
2088 2188 6.596309 AAAATGGGAGAGATTTTCACTTCC 57.404 37.500 0.00 0.00 33.82 3.46
2112 2212 6.325028 CCCTTCTCTTCCAATGTACTCTCATA 59.675 42.308 0.00 0.00 0.00 2.15
2123 2223 4.242336 GGTCAATCCCTTCTCTTCCAAT 57.758 45.455 0.00 0.00 0.00 3.16
2173 2273 4.410400 GTGGCTAGGGTTGCGCCT 62.410 66.667 4.18 0.00 44.09 5.52
2178 2278 1.002134 CACCTGGTGGCTAGGGTTG 60.002 63.158 19.23 0.00 39.71 3.77
2181 2281 1.201429 AGTTCACCTGGTGGCTAGGG 61.201 60.000 25.67 0.00 39.71 3.53
2190 2290 1.608717 CGAGGAGGGAGTTCACCTGG 61.609 65.000 0.00 0.00 38.79 4.45
2195 2295 1.984570 CTGGCGAGGAGGGAGTTCA 60.985 63.158 0.00 0.00 0.00 3.18
2299 2399 2.830827 CCCACAACGGCAACACCA 60.831 61.111 0.00 0.00 39.03 4.17
2302 2402 2.904866 GCTCCCACAACGGCAACA 60.905 61.111 0.00 0.00 0.00 3.33
2310 2410 4.980805 GACCACGCGCTCCCACAA 62.981 66.667 5.73 0.00 0.00 3.33
2367 2475 2.819595 CCACCATGCTTCCGTCCG 60.820 66.667 0.00 0.00 0.00 4.79
2368 2476 2.438434 CCCACCATGCTTCCGTCC 60.438 66.667 0.00 0.00 0.00 4.79
2369 2477 3.134127 GCCCACCATGCTTCCGTC 61.134 66.667 0.00 0.00 0.00 4.79
2370 2478 3.628646 GAGCCCACCATGCTTCCGT 62.629 63.158 0.00 0.00 39.69 4.69
2371 2479 2.825836 GAGCCCACCATGCTTCCG 60.826 66.667 0.00 0.00 39.69 4.30
2372 2480 1.751927 CAGAGCCCACCATGCTTCC 60.752 63.158 0.00 0.00 39.69 3.46
2373 2481 1.751927 CCAGAGCCCACCATGCTTC 60.752 63.158 0.00 0.00 39.69 3.86
2374 2482 2.357836 CCAGAGCCCACCATGCTT 59.642 61.111 0.00 0.00 39.69 3.91
2375 2483 4.437587 GCCAGAGCCCACCATGCT 62.438 66.667 0.00 0.00 43.03 3.79
2376 2484 4.437587 AGCCAGAGCCCACCATGC 62.438 66.667 0.00 0.00 41.25 4.06
2377 2485 2.124403 GAGCCAGAGCCCACCATG 60.124 66.667 0.00 0.00 41.25 3.66
2378 2486 2.285969 AGAGCCAGAGCCCACCAT 60.286 61.111 0.00 0.00 41.25 3.55
2379 2487 3.005539 GAGAGCCAGAGCCCACCA 61.006 66.667 0.00 0.00 41.25 4.17
2380 2488 2.373707 ATGAGAGCCAGAGCCCACC 61.374 63.158 0.00 0.00 41.25 4.61
2381 2489 1.153208 CATGAGAGCCAGAGCCCAC 60.153 63.158 0.00 0.00 41.25 4.61
2382 2490 2.372890 CCATGAGAGCCAGAGCCCA 61.373 63.158 0.00 0.00 41.25 5.36
2383 2491 2.373707 ACCATGAGAGCCAGAGCCC 61.374 63.158 0.00 0.00 41.25 5.19
2384 2492 1.153208 CACCATGAGAGCCAGAGCC 60.153 63.158 0.00 0.00 41.25 4.70
2385 2493 1.818785 GCACCATGAGAGCCAGAGC 60.819 63.158 0.00 0.00 40.32 4.09
2386 2494 4.536316 GCACCATGAGAGCCAGAG 57.464 61.111 0.00 0.00 0.00 3.35
2390 2498 4.783621 TGCGGCACCATGAGAGCC 62.784 66.667 0.00 11.56 44.89 4.70
2391 2499 3.200593 CTGCGGCACCATGAGAGC 61.201 66.667 0.00 0.00 0.00 4.09
2392 2500 3.200593 GCTGCGGCACCATGAGAG 61.201 66.667 14.08 0.00 38.54 3.20
2408 2516 4.615815 ATCCGATCTGCCAGCCGC 62.616 66.667 1.62 0.00 38.31 6.53
2409 2517 2.356793 GATCCGATCTGCCAGCCG 60.357 66.667 0.75 0.00 0.00 5.52
2410 2518 1.005156 GAGATCCGATCTGCCAGCC 60.005 63.158 15.85 0.00 40.38 4.85
2411 2519 1.372748 CGAGATCCGATCTGCCAGC 60.373 63.158 15.85 0.13 40.38 4.85
2412 2520 1.288439 CCGAGATCCGATCTGCCAG 59.712 63.158 15.85 4.58 40.38 4.85
2413 2521 2.203082 CCCGAGATCCGATCTGCCA 61.203 63.158 15.85 0.00 40.38 4.92
2414 2522 2.653702 CCCGAGATCCGATCTGCC 59.346 66.667 15.85 1.56 40.38 4.85
2415 2523 2.653702 CCCCGAGATCCGATCTGC 59.346 66.667 15.85 6.68 40.38 4.26
2416 2524 2.653702 GCCCCGAGATCCGATCTG 59.346 66.667 15.85 7.98 40.38 2.90
2417 2525 2.986413 CGCCCCGAGATCCGATCT 60.986 66.667 10.83 10.83 43.70 2.75
2418 2526 2.984155 TCGCCCCGAGATCCGATC 60.984 66.667 0.00 0.00 41.76 3.69
2419 2527 3.296054 GTCGCCCCGAGATCCGAT 61.296 66.667 5.32 0.00 41.76 4.18
2432 2540 1.429148 CCAACTATTGAGGCCGTCGC 61.429 60.000 0.00 0.00 0.00 5.19
2433 2541 1.429148 GCCAACTATTGAGGCCGTCG 61.429 60.000 0.00 0.00 42.58 5.12
2434 2542 1.429148 CGCCAACTATTGAGGCCGTC 61.429 60.000 0.00 0.00 45.56 4.79
2435 2543 1.449601 CGCCAACTATTGAGGCCGT 60.450 57.895 0.00 0.00 45.56 5.68
2436 2544 2.180204 CCGCCAACTATTGAGGCCG 61.180 63.158 0.00 5.55 45.56 6.13
2437 2545 1.823899 CCCGCCAACTATTGAGGCC 60.824 63.158 0.00 0.00 45.56 5.19
2438 2546 1.823899 CCCCGCCAACTATTGAGGC 60.824 63.158 0.00 0.00 44.89 4.70
2439 2547 1.152963 CCCCCGCCAACTATTGAGG 60.153 63.158 0.00 0.00 0.00 3.86
2440 2548 0.748005 CACCCCCGCCAACTATTGAG 60.748 60.000 0.00 0.00 0.00 3.02
2441 2549 1.301623 CACCCCCGCCAACTATTGA 59.698 57.895 0.00 0.00 0.00 2.57
2442 2550 2.414785 GCACCCCCGCCAACTATTG 61.415 63.158 0.00 0.00 0.00 1.90
2443 2551 2.044352 GCACCCCCGCCAACTATT 60.044 61.111 0.00 0.00 0.00 1.73
2444 2552 3.334891 TGCACCCCCGCCAACTAT 61.335 61.111 0.00 0.00 0.00 2.12
2445 2553 4.028490 CTGCACCCCCGCCAACTA 62.028 66.667 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.