Multiple sequence alignment - TraesCS4B01G170800

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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 TraesCS4B01G170800 chr4B 100.000 2507 0 0 1 2507 373995593 373993087 0.000000e+00 4630.0
1 TraesCS4B01G170800 chr4D 93.340 976 36 16 781 1745 300788171 300787214 0.000000e+00 1415.0
2 TraesCS4B01G170800 chr4D 87.823 657 52 11 1735 2363 300786947 300786291 0.000000e+00 745.0
3 TraesCS4B01G170800 chr4D 96.319 326 9 2 373 698 300788641 300788319 1.320000e-147 532.0
4 TraesCS4B01G170800 chr4D 85.714 336 21 12 35 365 300789471 300789158 1.860000e-86 329.0
5 TraesCS4B01G170800 chr4D 87.013 154 12 1 2354 2507 300786344 300786199 1.540000e-37 167.0
6 TraesCS4B01G170800 chr4A 89.632 1032 56 21 768 1779 182128480 182129480 0.000000e+00 1266.0
7 TraesCS4B01G170800 chr4A 88.950 362 24 8 1 354 182127216 182127569 1.380000e-117 433.0
8 TraesCS4B01G170800 chr4A 93.605 172 8 2 373 544 182128025 182128193 1.150000e-63 254.0
9 TraesCS4B01G170800 chr4A 98.438 128 2 0 570 697 182128187 182128314 2.510000e-55 226.0
10 TraesCS4B01G170800 chr2A 76.749 486 78 20 1861 2323 553049762 553049289 3.220000e-59 239.0
11 TraesCS4B01G170800 chr2A 75.304 494 92 19 1853 2323 169337011 169337497 2.530000e-50 209.0
12 TraesCS4B01G170800 chr6B 75.720 486 91 15 1852 2318 582869163 582868686 4.200000e-53 219.0
13 TraesCS4B01G170800 chr5B 77.354 393 70 13 1947 2320 589664865 589664473 5.430000e-52 215.0
14 TraesCS4B01G170800 chr5B 81.197 117 13 7 1330 1445 480241290 480241182 4.440000e-13 86.1
15 TraesCS4B01G170800 chr7A 82.305 243 41 2 2079 2320 646552928 646553169 2.530000e-50 209.0
16 TraesCS4B01G170800 chr3A 80.827 266 46 5 2064 2326 725161566 725161303 1.180000e-48 204.0
17 TraesCS4B01G170800 chr3A 80.075 266 48 4 2064 2326 725176959 725176696 2.540000e-45 193.0
18 TraesCS4B01G170800 chr1D 80.000 260 51 1 2065 2323 17049775 17050034 9.150000e-45 191.0


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 TraesCS4B01G170800 chr4B 373993087 373995593 2506 True 4630.00 4630 100.00000 1 2507 1 chr4B.!!$R1 2506
1 TraesCS4B01G170800 chr4D 300786199 300789471 3272 True 637.60 1415 90.04180 35 2507 5 chr4D.!!$R1 2472
2 TraesCS4B01G170800 chr4A 182127216 182129480 2264 False 544.75 1266 92.65625 1 1779 4 chr4A.!!$F1 1778

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
179 183 0.036732 TGGTGTCCTTGGCTGCTTAG 59.963 55.0 0.0 0.0 0.0 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 2326 0.036105 TGCTGCTAGTGTGGATGTGG 60.036 55.0 0.0 0.0 0.0 4.17 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
76 77 8.735692 TGTGATAATAATTGCAACATCTGAGA 57.264 30.769 0.00 0.00 0.00 3.27
77 78 8.833493 TGTGATAATAATTGCAACATCTGAGAG 58.167 33.333 0.00 0.00 0.00 3.20
141 142 5.982890 AGCTAAACATGGTGTTATTTGCT 57.017 34.783 0.00 0.00 40.14 3.91
176 180 1.303888 CATGGTGTCCTTGGCTGCT 60.304 57.895 0.00 0.00 0.00 4.24
179 183 0.036732 TGGTGTCCTTGGCTGCTTAG 59.963 55.000 0.00 0.00 0.00 2.18
180 184 0.036875 GGTGTCCTTGGCTGCTTAGT 59.963 55.000 0.00 0.00 0.00 2.24
181 185 1.160137 GTGTCCTTGGCTGCTTAGTG 58.840 55.000 0.00 0.00 0.00 2.74
182 186 0.606401 TGTCCTTGGCTGCTTAGTGC 60.606 55.000 0.00 0.00 43.25 4.40
255 420 1.696336 TGAGAAGCTTCTGCAAGGACT 59.304 47.619 33.07 6.22 42.74 3.85
343 510 3.500343 ACTTGGCTTGTGGCTTTTCTAT 58.500 40.909 0.00 0.00 41.46 1.98
362 529 2.214387 TCTATGATGAGCTGCACACG 57.786 50.000 0.90 0.00 0.00 4.49
365 532 0.800631 ATGATGAGCTGCACACGTTG 59.199 50.000 0.90 0.00 0.00 4.10
366 533 0.249826 TGATGAGCTGCACACGTTGA 60.250 50.000 0.90 0.00 0.00 3.18
367 534 0.867746 GATGAGCTGCACACGTTGAA 59.132 50.000 0.90 0.00 0.00 2.69
368 535 1.264020 GATGAGCTGCACACGTTGAAA 59.736 47.619 0.90 0.00 0.00 2.69
369 536 1.090728 TGAGCTGCACACGTTGAAAA 58.909 45.000 1.02 0.00 0.00 2.29
370 537 1.470494 TGAGCTGCACACGTTGAAAAA 59.530 42.857 1.02 0.00 0.00 1.94
397 1074 6.071051 TGCAATTTAGGATTTTCTTGTACCCC 60.071 38.462 0.00 0.00 0.00 4.95
430 1107 3.807622 ACCATACGCTAACCGATTGATTG 59.192 43.478 0.00 0.00 41.02 2.67
522 1199 0.245539 CGTCGGAAGGCTGGAACTTA 59.754 55.000 0.00 0.00 0.00 2.24
523 1200 1.337447 CGTCGGAAGGCTGGAACTTAA 60.337 52.381 0.00 0.00 0.00 1.85
563 1240 4.926238 GGATGCTCTATCAACGTAATCCAG 59.074 45.833 0.00 0.00 37.54 3.86
698 1375 2.026822 TCTCAGAGGATCCAAGTTTGCC 60.027 50.000 15.82 0.00 33.66 4.52
699 1376 1.988107 TCAGAGGATCCAAGTTTGCCT 59.012 47.619 15.82 0.00 33.66 4.75
700 1377 2.376518 TCAGAGGATCCAAGTTTGCCTT 59.623 45.455 15.82 0.00 33.66 4.35
701 1378 3.160269 CAGAGGATCCAAGTTTGCCTTT 58.840 45.455 15.82 0.00 33.66 3.11
703 1380 4.039609 CAGAGGATCCAAGTTTGCCTTTTT 59.960 41.667 15.82 0.00 33.66 1.94
734 1435 6.593382 AGTTTTAGTCATCTGCATGAGAAGAC 59.407 38.462 16.22 16.22 45.85 3.01
750 1451 4.331968 AGAAGACTCTACCTGTCTGACTG 58.668 47.826 9.51 8.50 43.16 3.51
752 1453 3.681593 AGACTCTACCTGTCTGACTGAC 58.318 50.000 15.25 5.57 42.46 3.51
762 1494 3.153130 TGTCTGACTGACTGAAGAGAGG 58.847 50.000 9.51 0.00 45.54 3.69
779 1551 1.602377 GAGGTGTGGTTGTTCCGAAAG 59.398 52.381 0.00 0.00 39.52 2.62
819 1591 2.813908 CGACGGGCGAGAAAAGGG 60.814 66.667 0.00 0.00 44.57 3.95
885 1657 4.392047 TGATAAGAGGATAAGCCGACGTA 58.608 43.478 0.00 0.00 43.43 3.57
918 1690 1.276622 TTCTCCCTGACCCAAGCTAC 58.723 55.000 0.00 0.00 0.00 3.58
926 1698 1.349688 TGACCCAAGCTACCAAACGAT 59.650 47.619 0.00 0.00 0.00 3.73
941 1713 1.093159 ACGATTCGACCTAAGCTCGT 58.907 50.000 13.95 0.00 34.80 4.18
1521 2312 1.338105 CGCTGAAGACTTCCATCCACA 60.338 52.381 12.66 0.00 0.00 4.17
1528 2319 2.848694 AGACTTCCATCCACATCCACAT 59.151 45.455 0.00 0.00 0.00 3.21
1529 2320 3.118112 AGACTTCCATCCACATCCACATC 60.118 47.826 0.00 0.00 0.00 3.06
1530 2321 2.092212 ACTTCCATCCACATCCACATCC 60.092 50.000 0.00 0.00 0.00 3.51
1531 2322 1.594129 TCCATCCACATCCACATCCA 58.406 50.000 0.00 0.00 0.00 3.41
1534 2325 2.423803 CCATCCACATCCACATCCACAT 60.424 50.000 0.00 0.00 0.00 3.21
1535 2326 2.715749 TCCACATCCACATCCACATC 57.284 50.000 0.00 0.00 0.00 3.06
1536 2327 1.212688 TCCACATCCACATCCACATCC 59.787 52.381 0.00 0.00 0.00 3.51
1537 2328 1.064537 CCACATCCACATCCACATCCA 60.065 52.381 0.00 0.00 0.00 3.41
1538 2329 2.019249 CACATCCACATCCACATCCAC 58.981 52.381 0.00 0.00 0.00 4.02
1539 2330 1.634973 ACATCCACATCCACATCCACA 59.365 47.619 0.00 0.00 0.00 4.17
1540 2331 2.242965 ACATCCACATCCACATCCACAT 59.757 45.455 0.00 0.00 0.00 3.21
1542 2333 1.212688 TCCACATCCACATCCACATCC 59.787 52.381 0.00 0.00 0.00 3.51
1543 2334 1.064537 CCACATCCACATCCACATCCA 60.065 52.381 0.00 0.00 0.00 3.41
1544 2335 2.019249 CACATCCACATCCACATCCAC 58.981 52.381 0.00 0.00 0.00 4.02
1545 2336 1.634973 ACATCCACATCCACATCCACA 59.365 47.619 0.00 0.00 0.00 4.17
1546 2337 2.019249 CATCCACATCCACATCCACAC 58.981 52.381 0.00 0.00 0.00 3.82
1548 2339 2.545810 TCCACATCCACATCCACACTA 58.454 47.619 0.00 0.00 0.00 2.74
1549 2340 2.501316 TCCACATCCACATCCACACTAG 59.499 50.000 0.00 0.00 0.00 2.57
1550 2341 2.283298 CACATCCACATCCACACTAGC 58.717 52.381 0.00 0.00 0.00 3.42
1551 2342 1.908619 ACATCCACATCCACACTAGCA 59.091 47.619 0.00 0.00 0.00 3.49
1552 2343 2.093288 ACATCCACATCCACACTAGCAG 60.093 50.000 0.00 0.00 0.00 4.24
1553 2344 0.250234 TCCACATCCACACTAGCAGC 59.750 55.000 0.00 0.00 0.00 5.25
1554 2345 0.036105 CCACATCCACACTAGCAGCA 60.036 55.000 0.00 0.00 0.00 4.41
1555 2346 1.611410 CCACATCCACACTAGCAGCAA 60.611 52.381 0.00 0.00 0.00 3.91
1556 2347 2.153645 CACATCCACACTAGCAGCAAA 58.846 47.619 0.00 0.00 0.00 3.68
1557 2348 2.553602 CACATCCACACTAGCAGCAAAA 59.446 45.455 0.00 0.00 0.00 2.44
1558 2349 3.192001 CACATCCACACTAGCAGCAAAAT 59.808 43.478 0.00 0.00 0.00 1.82
1616 2419 2.230940 CGTGGGTCATAAGCGCTCG 61.231 63.158 12.06 1.92 0.00 5.03
1626 2429 2.380084 TAAGCGCTCGGATTTTGAGT 57.620 45.000 12.06 0.00 35.85 3.41
1636 2439 5.381174 TCGGATTTTGAGTCTCGAGTTTA 57.619 39.130 13.13 0.00 0.00 2.01
1637 2440 5.159209 TCGGATTTTGAGTCTCGAGTTTAC 58.841 41.667 13.13 3.25 0.00 2.01
1653 2456 7.577979 TCGAGTTTACATCAATTGTTTGTACC 58.422 34.615 17.65 13.24 39.87 3.34
1678 2482 2.697229 TGTCTGAATCGGCTGATGATCT 59.303 45.455 9.28 0.00 34.24 2.75
1698 2502 9.857656 ATGATCTACATGGTGAGAATATTGTTT 57.142 29.630 0.00 0.00 37.87 2.83
1701 2505 7.629157 TCTACATGGTGAGAATATTGTTTGGA 58.371 34.615 0.00 0.00 0.00 3.53
1724 2528 6.446781 AGCATCCTTGATTTTGTGTATCAG 57.553 37.500 0.00 0.00 33.83 2.90
1787 2868 1.156736 CCAGGTGCTAAACAGAACGG 58.843 55.000 0.00 0.00 0.00 4.44
1800 2881 1.603802 CAGAACGGCTTTGCTTTCTGA 59.396 47.619 19.77 0.00 43.96 3.27
1819 2900 2.168521 TGAATGGCTAGTGCTAGTGGTC 59.831 50.000 7.90 2.62 39.59 4.02
1827 2908 0.977395 GTGCTAGTGGTCTCAAGGGT 59.023 55.000 0.00 0.00 0.00 4.34
1866 2955 1.132500 GCTGCCTATGGACTTAGGGT 58.868 55.000 11.78 0.00 39.39 4.34
1874 2963 2.642171 TGGACTTAGGGTCATGGAGT 57.358 50.000 0.00 0.00 46.16 3.85
1887 2976 0.462047 ATGGAGTCGCGGTGGATTTC 60.462 55.000 6.13 0.00 0.00 2.17
1910 2999 1.365028 TCCTTACCAGTAGGAGGGCTT 59.635 52.381 0.00 0.00 38.69 4.35
1912 3001 2.467880 CTTACCAGTAGGAGGGCTTCA 58.532 52.381 0.00 0.00 38.69 3.02
1917 3006 3.076032 ACCAGTAGGAGGGCTTCATTTTT 59.924 43.478 0.00 0.00 38.69 1.94
1954 3043 8.541234 TGTTGTTTTGAATTTAGGTAGGGTTTT 58.459 29.630 0.00 0.00 0.00 2.43
1969 3058 4.542697 AGGGTTTTTGTCCTGCTTAGAAA 58.457 39.130 0.00 0.00 31.11 2.52
1971 3060 5.602561 AGGGTTTTTGTCCTGCTTAGAAAAT 59.397 36.000 0.00 0.00 31.11 1.82
1978 3067 3.619038 GTCCTGCTTAGAAAATGAGACGG 59.381 47.826 0.00 0.00 0.00 4.79
2008 3097 5.050023 GCTTCCCGAAGATGTAATAAGCTTC 60.050 44.000 0.00 0.00 40.79 3.86
2011 3100 5.362717 TCCCGAAGATGTAATAAGCTTCTCA 59.637 40.000 0.00 0.00 35.72 3.27
2020 3109 4.414337 AATAAGCTTCTCACTGCCTAGG 57.586 45.455 0.00 3.67 0.00 3.02
2023 3112 1.524482 CTTCTCACTGCCTAGGCCC 59.476 63.158 30.81 5.27 41.09 5.80
2039 3128 2.819595 CCCGTTCCGGTGATGCTG 60.820 66.667 0.00 0.00 46.80 4.41
2057 3146 2.045131 GCTAGTGTCGTCGGAGGGT 61.045 63.158 0.00 0.00 0.00 4.34
2071 3177 2.509336 GGGTGTGTGGATCTCGCG 60.509 66.667 0.00 0.00 0.00 5.87
2075 3181 2.105128 GTGTGGATCTCGCGGGAG 59.895 66.667 22.60 22.60 41.89 4.30
2077 3183 1.982395 TGTGGATCTCGCGGGAGTT 60.982 57.895 26.49 19.70 41.26 3.01
2079 3185 1.680989 TGGATCTCGCGGGAGTTGA 60.681 57.895 26.49 10.61 41.26 3.18
2093 3199 3.557264 GGGAGTTGATCGACCTTTGTCTT 60.557 47.826 9.62 0.00 39.47 3.01
2095 3201 3.318017 AGTTGATCGACCTTTGTCTTCG 58.682 45.455 9.62 0.00 39.47 3.79
2096 3202 2.363788 TGATCGACCTTTGTCTTCGG 57.636 50.000 0.00 0.00 39.47 4.30
2103 3209 1.003233 ACCTTTGTCTTCGGTGGATCC 59.997 52.381 4.20 4.20 0.00 3.36
2121 3227 0.940126 CCGCTTGGATCCAATCTTCG 59.060 55.000 27.20 23.67 35.20 3.79
2125 3231 3.009723 GCTTGGATCCAATCTTCGTTCA 58.990 45.455 27.20 1.21 35.20 3.18
2144 3250 4.332186 TCATCTACGTTCGTGTGTCTAC 57.668 45.455 8.14 0.00 0.00 2.59
2158 3264 5.467705 GTGTGTCTACAGGTTAGATCGTTT 58.532 41.667 0.00 0.00 37.52 3.60
2179 3285 6.534934 GTTTCGATCTACGCTTTTCTTCATT 58.465 36.000 0.00 0.00 42.26 2.57
2205 3311 3.429822 GGCGGTTACTGTTCTAGTGCATA 60.430 47.826 0.00 0.00 40.65 3.14
2212 3318 3.702045 ACTGTTCTAGTGCATAGGTCCTC 59.298 47.826 0.00 0.00 38.49 3.71
2213 3319 3.031736 TGTTCTAGTGCATAGGTCCTCC 58.968 50.000 0.00 0.00 31.83 4.30
2214 3320 1.982660 TCTAGTGCATAGGTCCTCCG 58.017 55.000 0.00 0.00 39.05 4.63
2220 3326 2.201771 ATAGGTCCTCCGAGGCCC 59.798 66.667 18.92 14.10 32.29 5.80
2235 3341 1.080025 GCCCTAGCACGACGACTTT 60.080 57.895 0.00 0.00 39.53 2.66
2251 3357 3.434641 CGACTTTCCGACTGTCTACTACA 59.565 47.826 6.21 0.00 36.42 2.74
2253 3359 5.118642 ACTTTCCGACTGTCTACTACAAC 57.881 43.478 6.21 0.00 37.74 3.32
2257 3363 4.392047 TCCGACTGTCTACTACAACAAGA 58.608 43.478 6.21 0.00 37.74 3.02
2262 3368 6.400091 CGACTGTCTACTACAACAAGATTTGC 60.400 42.308 6.21 0.00 37.74 3.68
2321 3427 2.105930 GGCTCGCTCCAGTGCTAG 59.894 66.667 0.00 0.00 0.00 3.42
2354 3460 9.294030 CACAATGACAATCTAATTTAAGAAGCC 57.706 33.333 0.00 0.00 0.00 4.35
2355 3461 9.023962 ACAATGACAATCTAATTTAAGAAGCCA 57.976 29.630 0.00 0.00 0.00 4.75
2356 3462 9.512435 CAATGACAATCTAATTTAAGAAGCCAG 57.488 33.333 0.00 0.00 0.00 4.85
2357 3463 8.814038 ATGACAATCTAATTTAAGAAGCCAGT 57.186 30.769 0.00 0.00 0.00 4.00
2358 3464 8.044060 TGACAATCTAATTTAAGAAGCCAGTG 57.956 34.615 0.00 0.00 0.00 3.66
2359 3465 6.856895 ACAATCTAATTTAAGAAGCCAGTGC 58.143 36.000 0.00 0.00 37.95 4.40
2370 3476 3.861341 GCCAGTGCTAGTGGATTCA 57.139 52.632 12.53 0.00 41.28 2.57
2371 3477 1.373570 GCCAGTGCTAGTGGATTCAC 58.626 55.000 12.53 0.00 41.28 3.18
2372 3478 1.339055 GCCAGTGCTAGTGGATTCACA 60.339 52.381 6.96 0.00 41.28 3.58
2373 3479 2.875672 GCCAGTGCTAGTGGATTCACAA 60.876 50.000 6.96 0.00 41.28 3.33
2374 3480 3.614092 CCAGTGCTAGTGGATTCACAAT 58.386 45.455 6.96 0.00 45.91 2.71
2375 3481 3.376234 CCAGTGCTAGTGGATTCACAATG 59.624 47.826 6.96 0.00 45.91 2.82
2376 3482 4.256110 CAGTGCTAGTGGATTCACAATGA 58.744 43.478 6.96 0.00 45.91 2.57
2377 3483 4.880120 CAGTGCTAGTGGATTCACAATGAT 59.120 41.667 6.96 0.00 45.91 2.45
2378 3484 6.051074 CAGTGCTAGTGGATTCACAATGATA 58.949 40.000 6.96 0.00 45.91 2.15
2379 3485 6.539826 CAGTGCTAGTGGATTCACAATGATAA 59.460 38.462 6.96 0.00 45.91 1.75
2380 3486 7.228108 CAGTGCTAGTGGATTCACAATGATAAT 59.772 37.037 6.96 0.00 45.91 1.28
2381 3487 7.443575 AGTGCTAGTGGATTCACAATGATAATC 59.556 37.037 6.96 0.00 45.91 1.75
2382 3488 7.443575 GTGCTAGTGGATTCACAATGATAATCT 59.556 37.037 6.96 0.00 45.91 2.40
2383 3489 8.650490 TGCTAGTGGATTCACAATGATAATCTA 58.350 33.333 6.96 4.23 45.91 1.98
2384 3490 9.494271 GCTAGTGGATTCACAATGATAATCTAA 57.506 33.333 6.96 1.06 45.91 2.10
2435 3541 7.147724 TGCTAGCTGCTAGACTTTCCTTAAATA 60.148 37.037 34.43 7.71 43.37 1.40
2461 3567 4.079980 TCACATTTCCAAGTCTTCGGAA 57.920 40.909 10.63 10.63 39.54 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.221402 TGTCAAACAATGCAAGGCTAAATGA 60.221 36.000 0.00 0.00 0.00 2.57
76 77 6.091437 CGGAAGAACTATCGTACTGAAAACT 58.909 40.000 0.00 0.00 0.00 2.66
77 78 5.860716 ACGGAAGAACTATCGTACTGAAAAC 59.139 40.000 0.00 0.00 33.89 2.43
151 152 2.795329 CCAAGGACACCATGTTTAGCT 58.205 47.619 0.00 0.00 0.00 3.32
152 153 1.202348 GCCAAGGACACCATGTTTAGC 59.798 52.381 0.00 0.00 0.00 3.09
153 154 2.489329 CAGCCAAGGACACCATGTTTAG 59.511 50.000 0.00 0.00 0.00 1.85
156 157 1.181098 GCAGCCAAGGACACCATGTT 61.181 55.000 0.00 0.00 0.00 2.71
157 158 1.604593 GCAGCCAAGGACACCATGT 60.605 57.895 0.00 0.00 0.00 3.21
158 159 0.896940 AAGCAGCCAAGGACACCATG 60.897 55.000 0.00 0.00 0.00 3.66
160 161 0.036732 CTAAGCAGCCAAGGACACCA 59.963 55.000 0.00 0.00 0.00 4.17
162 163 1.160137 CACTAAGCAGCCAAGGACAC 58.840 55.000 0.00 0.00 0.00 3.67
163 164 0.606401 GCACTAAGCAGCCAAGGACA 60.606 55.000 0.00 0.00 44.79 4.02
176 180 5.674525 CAACTCATCATAGGAAGGCACTAA 58.325 41.667 0.00 0.00 38.49 2.24
179 183 2.615912 GCAACTCATCATAGGAAGGCAC 59.384 50.000 0.00 0.00 0.00 5.01
180 184 2.239402 TGCAACTCATCATAGGAAGGCA 59.761 45.455 0.00 0.00 0.00 4.75
181 185 2.923121 TGCAACTCATCATAGGAAGGC 58.077 47.619 0.00 0.00 0.00 4.35
182 186 4.946157 AGTTTGCAACTCATCATAGGAAGG 59.054 41.667 0.00 0.00 37.02 3.46
183 187 6.506500 AAGTTTGCAACTCATCATAGGAAG 57.493 37.500 0.00 0.00 41.91 3.46
184 188 6.899393 AAAGTTTGCAACTCATCATAGGAA 57.101 33.333 0.00 0.00 41.91 3.36
185 189 8.461222 CAATAAAGTTTGCAACTCATCATAGGA 58.539 33.333 0.00 0.00 41.91 2.94
223 227 6.346758 GCAGAAGCTTCTCATAAGATTGATCG 60.347 42.308 26.18 10.70 34.74 3.69
343 510 1.478105 ACGTGTGCAGCTCATCATAGA 59.522 47.619 0.00 0.00 0.00 1.98
369 536 9.435688 GGTACAAGAAAATCCTAAATTGCATTT 57.564 29.630 0.00 0.00 36.29 2.32
370 537 8.040727 GGGTACAAGAAAATCCTAAATTGCATT 58.959 33.333 0.00 0.00 0.00 3.56
371 538 7.364673 GGGGTACAAGAAAATCCTAAATTGCAT 60.365 37.037 0.00 0.00 0.00 3.96
397 1074 6.025280 GGTTAGCGTATGGTTAAAACATGTG 58.975 40.000 0.00 0.00 0.00 3.21
430 1107 5.163854 CGAACCACACTGATCAAGGTAAATC 60.164 44.000 8.64 3.94 31.10 2.17
522 1199 1.512156 CCGCGCACTACCCAACTTTT 61.512 55.000 8.75 0.00 0.00 2.27
523 1200 1.964373 CCGCGCACTACCCAACTTT 60.964 57.895 8.75 0.00 0.00 2.66
563 1240 4.981389 TTGTTGTAAATCGGCAAATTGC 57.019 36.364 9.87 9.87 44.08 3.56
703 1380 9.371136 CTCATGCAGATGACTAAAACTAGTAAA 57.629 33.333 0.00 0.00 34.71 2.01
718 1419 4.341806 AGGTAGAGTCTTCTCATGCAGATG 59.658 45.833 0.00 0.00 42.66 2.90
750 1451 2.103263 ACAACCACACCTCTCTTCAGTC 59.897 50.000 0.00 0.00 0.00 3.51
752 1453 2.918712 ACAACCACACCTCTCTTCAG 57.081 50.000 0.00 0.00 0.00 3.02
762 1494 0.030235 GGCTTTCGGAACAACCACAC 59.970 55.000 0.00 0.00 38.90 3.82
799 1571 2.429571 TTTTCTCGCCCGTCGACG 60.430 61.111 30.33 30.33 43.16 5.12
801 1573 2.260434 CCTTTTCTCGCCCGTCGA 59.740 61.111 0.00 0.00 46.29 4.20
802 1574 2.775032 TTCCCTTTTCTCGCCCGTCG 62.775 60.000 0.00 0.00 40.15 5.12
803 1575 0.604511 TTTCCCTTTTCTCGCCCGTC 60.605 55.000 0.00 0.00 0.00 4.79
804 1576 0.037734 ATTTCCCTTTTCTCGCCCGT 59.962 50.000 0.00 0.00 0.00 5.28
808 1580 1.745653 CCAGGATTTCCCTTTTCTCGC 59.254 52.381 0.00 0.00 44.85 5.03
819 1591 3.068024 TGTGTTTCAGTTGCCAGGATTTC 59.932 43.478 0.00 0.00 0.00 2.17
885 1657 0.833949 GGAGAAAGGGAAGAGGCGAT 59.166 55.000 0.00 0.00 0.00 4.58
918 1690 2.603560 GAGCTTAGGTCGAATCGTTTGG 59.396 50.000 1.52 0.00 0.00 3.28
941 1713 0.469144 GGTTGTGGAAAGGGAGGCAA 60.469 55.000 0.00 0.00 0.00 4.52
1070 1849 3.611674 TCGTGTTGGAGCGAGCCA 61.612 61.111 0.00 0.00 35.78 4.75
1521 2312 2.158564 GGATGTGGATGTGGATGTGGAT 60.159 50.000 0.00 0.00 0.00 3.41
1528 2319 1.361204 AGTGTGGATGTGGATGTGGA 58.639 50.000 0.00 0.00 0.00 4.02
1529 2320 2.910199 CTAGTGTGGATGTGGATGTGG 58.090 52.381 0.00 0.00 0.00 4.17
1530 2321 2.283298 GCTAGTGTGGATGTGGATGTG 58.717 52.381 0.00 0.00 0.00 3.21
1531 2322 1.908619 TGCTAGTGTGGATGTGGATGT 59.091 47.619 0.00 0.00 0.00 3.06
1534 2325 0.250234 GCTGCTAGTGTGGATGTGGA 59.750 55.000 0.00 0.00 0.00 4.02
1535 2326 0.036105 TGCTGCTAGTGTGGATGTGG 60.036 55.000 0.00 0.00 0.00 4.17
1536 2327 1.812235 TTGCTGCTAGTGTGGATGTG 58.188 50.000 0.00 0.00 0.00 3.21
1537 2328 2.566833 TTTGCTGCTAGTGTGGATGT 57.433 45.000 0.00 0.00 0.00 3.06
1538 2329 3.192001 ACATTTTGCTGCTAGTGTGGATG 59.808 43.478 0.00 0.00 0.00 3.51
1539 2330 3.424703 ACATTTTGCTGCTAGTGTGGAT 58.575 40.909 0.00 0.00 0.00 3.41
1540 2331 2.813754 GACATTTTGCTGCTAGTGTGGA 59.186 45.455 0.00 0.00 0.00 4.02
1542 2333 3.902261 TGACATTTTGCTGCTAGTGTG 57.098 42.857 0.00 0.00 0.00 3.82
1543 2334 4.097741 TGTTTGACATTTTGCTGCTAGTGT 59.902 37.500 0.00 2.66 0.00 3.55
1544 2335 4.609947 TGTTTGACATTTTGCTGCTAGTG 58.390 39.130 0.00 0.00 0.00 2.74
1545 2336 4.261741 CCTGTTTGACATTTTGCTGCTAGT 60.262 41.667 0.00 0.00 0.00 2.57
1546 2337 4.022935 TCCTGTTTGACATTTTGCTGCTAG 60.023 41.667 0.00 0.00 0.00 3.42
1548 2339 2.694628 TCCTGTTTGACATTTTGCTGCT 59.305 40.909 0.00 0.00 0.00 4.24
1549 2340 3.096489 TCCTGTTTGACATTTTGCTGC 57.904 42.857 0.00 0.00 0.00 5.25
1550 2341 5.404946 CCTATCCTGTTTGACATTTTGCTG 58.595 41.667 0.00 0.00 0.00 4.41
1551 2342 4.463891 CCCTATCCTGTTTGACATTTTGCT 59.536 41.667 0.00 0.00 0.00 3.91
1552 2343 4.220602 ACCCTATCCTGTTTGACATTTTGC 59.779 41.667 0.00 0.00 0.00 3.68
1553 2344 5.476599 TCACCCTATCCTGTTTGACATTTTG 59.523 40.000 0.00 0.00 0.00 2.44
1554 2345 5.640147 TCACCCTATCCTGTTTGACATTTT 58.360 37.500 0.00 0.00 0.00 1.82
1555 2346 5.014123 TCTCACCCTATCCTGTTTGACATTT 59.986 40.000 0.00 0.00 0.00 2.32
1556 2347 4.536090 TCTCACCCTATCCTGTTTGACATT 59.464 41.667 0.00 0.00 0.00 2.71
1557 2348 4.104086 TCTCACCCTATCCTGTTTGACAT 58.896 43.478 0.00 0.00 0.00 3.06
1558 2349 3.516586 TCTCACCCTATCCTGTTTGACA 58.483 45.455 0.00 0.00 0.00 3.58
1616 2419 6.590292 TGATGTAAACTCGAGACTCAAAATCC 59.410 38.462 21.68 0.00 0.00 3.01
1626 2429 7.490962 ACAAACAATTGATGTAAACTCGAGA 57.509 32.000 21.68 0.00 42.99 4.04
1636 2439 6.321181 AGACAAGTGGTACAAACAATTGATGT 59.679 34.615 13.59 17.68 44.10 3.06
1637 2440 6.638063 CAGACAAGTGGTACAAACAATTGATG 59.362 38.462 13.59 12.84 44.10 3.07
1653 2456 2.084610 TCAGCCGATTCAGACAAGTG 57.915 50.000 0.00 0.00 0.00 3.16
1678 2482 6.318648 GCTCCAAACAATATTCTCACCATGTA 59.681 38.462 0.00 0.00 0.00 2.29
1698 2502 3.499338 ACACAAAATCAAGGATGCTCCA 58.501 40.909 5.21 0.00 39.61 3.86
1701 2505 5.163581 GCTGATACACAAAATCAAGGATGCT 60.164 40.000 0.00 0.00 33.13 3.79
1724 2528 0.321996 AGGAGGAACAAGGAAGACGC 59.678 55.000 0.00 0.00 0.00 5.19
1787 2868 2.738013 AGCCATTCAGAAAGCAAAGC 57.262 45.000 10.34 0.00 0.00 3.51
1800 2881 2.432510 GAGACCACTAGCACTAGCCATT 59.567 50.000 4.58 0.00 43.56 3.16
1819 2900 2.232208 GGAGGCAATGAAAACCCTTGAG 59.768 50.000 0.00 0.00 0.00 3.02
1827 2908 2.339556 CCGCGGGAGGCAATGAAAA 61.340 57.895 20.10 0.00 43.84 2.29
1850 2931 2.039084 CCATGACCCTAAGTCCATAGGC 59.961 54.545 0.00 0.00 45.68 3.93
1854 2935 3.041946 GACTCCATGACCCTAAGTCCAT 58.958 50.000 0.00 0.00 45.68 3.41
1866 2955 1.613317 AATCCACCGCGACTCCATGA 61.613 55.000 8.23 0.00 0.00 3.07
1874 2963 2.125832 GACCGAAATCCACCGCGA 60.126 61.111 8.23 0.00 0.00 5.87
1925 3014 7.728532 ACCCTACCTAAATTCAAAACAACATCT 59.271 33.333 0.00 0.00 0.00 2.90
1954 3043 4.690748 CGTCTCATTTTCTAAGCAGGACAA 59.309 41.667 0.00 0.00 0.00 3.18
1969 3058 3.296709 AAGCCGTCGCCGTCTCATT 62.297 57.895 0.00 0.00 34.57 2.57
1971 3060 4.415332 GAAGCCGTCGCCGTCTCA 62.415 66.667 0.00 0.00 34.57 3.27
1978 3067 3.718210 ATCTTCGGGAAGCCGTCGC 62.718 63.158 3.54 0.00 38.28 5.19
1987 3076 5.362717 TGAGAAGCTTATTACATCTTCGGGA 59.637 40.000 0.00 0.00 39.72 5.14
1998 3087 4.202264 GCCTAGGCAGTGAGAAGCTTATTA 60.202 45.833 29.33 0.00 41.49 0.98
2008 3097 3.854669 CGGGGCCTAGGCAGTGAG 61.855 72.222 34.09 16.45 44.11 3.51
2011 3100 3.400054 GAACGGGGCCTAGGCAGT 61.400 66.667 34.09 25.83 44.11 4.40
2039 3128 2.045131 ACCCTCCGACGACACTAGC 61.045 63.158 0.00 0.00 0.00 3.42
2057 3146 2.678580 TCCCGCGAGATCCACACA 60.679 61.111 8.23 0.00 0.00 3.72
2071 3177 2.347731 GACAAAGGTCGATCAACTCCC 58.652 52.381 0.00 0.00 33.68 4.30
2103 3209 1.656652 ACGAAGATTGGATCCAAGCG 58.343 50.000 31.33 28.55 45.72 4.68
2114 3220 4.557690 CACGAACGTAGATGAACGAAGATT 59.442 41.667 3.10 0.00 45.68 2.40
2121 3227 3.562505 AGACACACGAACGTAGATGAAC 58.437 45.455 0.00 1.20 0.00 3.18
2125 3231 3.126514 CCTGTAGACACACGAACGTAGAT 59.873 47.826 0.00 0.00 0.00 1.98
2158 3264 5.288712 GTCAATGAAGAAAAGCGTAGATCGA 59.711 40.000 0.00 0.00 42.86 3.59
2171 3277 2.070783 GTAACCGCCGTCAATGAAGAA 58.929 47.619 0.00 0.00 0.00 2.52
2179 3285 1.200716 CTAGAACAGTAACCGCCGTCA 59.799 52.381 0.00 0.00 0.00 4.35
2212 3318 4.208686 GTCGTGCTAGGGCCTCGG 62.209 72.222 10.74 5.57 37.74 4.63
2213 3319 4.554363 CGTCGTGCTAGGGCCTCG 62.554 72.222 10.74 7.87 37.74 4.63
2214 3320 3.138798 TCGTCGTGCTAGGGCCTC 61.139 66.667 10.74 0.00 37.74 4.70
2220 3326 0.167470 TCGGAAAGTCGTCGTGCTAG 59.833 55.000 0.00 0.00 0.00 3.42
2235 3341 4.392047 TCTTGTTGTAGTAGACAGTCGGA 58.608 43.478 0.00 0.00 39.88 4.55
2251 3357 1.270550 CCGAAGCCAGCAAATCTTGTT 59.729 47.619 0.00 0.00 0.00 2.83
2253 3359 0.883833 ACCGAAGCCAGCAAATCTTG 59.116 50.000 0.00 0.00 0.00 3.02
2257 3363 1.750778 CCATTACCGAAGCCAGCAAAT 59.249 47.619 0.00 0.00 0.00 2.32
2262 3368 0.179045 CCCTCCATTACCGAAGCCAG 60.179 60.000 0.00 0.00 0.00 4.85
2352 3458 1.339055 TGTGAATCCACTAGCACTGGC 60.339 52.381 0.00 0.00 43.55 4.85
2353 3459 2.768253 TGTGAATCCACTAGCACTGG 57.232 50.000 0.00 0.00 43.55 4.00
2354 3460 4.256110 TCATTGTGAATCCACTAGCACTG 58.744 43.478 0.00 0.00 43.55 3.66
2355 3461 4.558226 TCATTGTGAATCCACTAGCACT 57.442 40.909 0.00 0.00 43.55 4.40
2356 3462 6.925610 TTATCATTGTGAATCCACTAGCAC 57.074 37.500 0.00 0.00 43.55 4.40
2357 3463 7.512130 AGATTATCATTGTGAATCCACTAGCA 58.488 34.615 0.00 0.00 43.55 3.49
2358 3464 7.976135 AGATTATCATTGTGAATCCACTAGC 57.024 36.000 0.00 0.00 43.55 3.42
2386 3492 9.517868 AGCACTAGACTAGTAGACTTTTCTTAA 57.482 33.333 14.79 0.00 37.23 1.85
2388 3494 9.169592 CTAGCACTAGACTAGTAGACTTTTCTT 57.830 37.037 14.79 0.00 37.23 2.52
2389 3495 7.281549 GCTAGCACTAGACTAGTAGACTTTTCT 59.718 40.741 14.79 0.48 39.48 2.52
2390 3496 7.281549 AGCTAGCACTAGACTAGTAGACTTTTC 59.718 40.741 18.83 6.19 39.48 2.29
2391 3497 7.066525 CAGCTAGCACTAGACTAGTAGACTTTT 59.933 40.741 18.83 0.00 39.48 2.27
2392 3498 6.540914 CAGCTAGCACTAGACTAGTAGACTTT 59.459 42.308 18.83 0.00 39.48 2.66
2393 3499 6.053005 CAGCTAGCACTAGACTAGTAGACTT 58.947 44.000 18.83 2.60 39.48 3.01
2394 3500 5.607477 CAGCTAGCACTAGACTAGTAGACT 58.393 45.833 18.83 14.02 39.48 3.24
2395 3501 4.212636 GCAGCTAGCACTAGACTAGTAGAC 59.787 50.000 18.83 7.89 44.79 2.59
2396 3502 4.382291 GCAGCTAGCACTAGACTAGTAGA 58.618 47.826 18.83 2.98 44.79 2.59
2397 3503 4.742438 GCAGCTAGCACTAGACTAGTAG 57.258 50.000 18.83 10.16 44.79 2.57
2435 3541 5.182001 CCGAAGACTTGGAAATGTGATTCTT 59.818 40.000 0.00 0.00 0.00 2.52
2447 3553 3.408634 GGATGTTTTCCGAAGACTTGGA 58.591 45.455 0.00 0.93 33.93 3.53
2461 3567 2.315763 AGATGGGGGTGATTGGATGTTT 59.684 45.455 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.