Multiple sequence alignment - TraesCS4B01G118500

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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 TraesCS4B01G118500 chr4B 100.000 3385 0 0 1 3385 139021418 139024802 0.000000e+00 6252.0
1 TraesCS4B01G118500 chr4D 91.339 3429 194 42 1 3385 97375240 97378609 0.000000e+00 4591.0
2 TraesCS4B01G118500 chr4D 80.273 806 121 23 2601 3374 97382701 97383500 1.050000e-159 573.0
3 TraesCS4B01G118500 chr4A 91.406 2362 133 36 152 2467 478869158 478866821 0.000000e+00 3173.0
4 TraesCS4B01G118500 chr4A 79.116 747 112 21 2652 3374 478752732 478752006 3.060000e-130 475.0
5 TraesCS4B01G118500 chr4A 93.780 209 13 0 3175 3383 478866582 478866374 7.050000e-82 315.0
6 TraesCS4B01G118500 chr4A 96.250 160 6 0 5 164 478869339 478869180 2.590000e-66 263.0
7 TraesCS4B01G118500 chr4A 97.638 127 3 0 3061 3187 478866730 478866604 5.690000e-53 219.0
8 TraesCS4B01G118500 chr2B 96.875 32 0 1 264 294 625237273 625237242 6.000000e-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 TraesCS4B01G118500 chr4B 139021418 139024802 3384 False 6252.0 6252 100.0000 1 3385 1 chr4B.!!$F1 3384
1 TraesCS4B01G118500 chr4D 97375240 97378609 3369 False 4591.0 4591 91.3390 1 3385 1 chr4D.!!$F1 3384
2 TraesCS4B01G118500 chr4D 97382701 97383500 799 False 573.0 573 80.2730 2601 3374 1 chr4D.!!$F2 773
3 TraesCS4B01G118500 chr4A 478866374 478869339 2965 True 992.5 3173 94.7685 5 3383 4 chr4A.!!$R2 3378
4 TraesCS4B01G118500 chr4A 478752006 478752732 726 True 475.0 475 79.1160 2652 3374 1 chr4A.!!$R1 722

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
667 720 0.250901 AATGGCAGGTCAGTGTGGAC 60.251 55.0 0.0 0.0 37.06 4.02 F
1861 1945 0.103937 CGGCCTTTGAAGTTTTGGCA 59.896 50.0 0.0 0.0 44.85 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2098 0.036306 GGAACGCCAAGAAGAGGGAA 59.964 55.0 0.00 0.00 0.00 3.97 R
3212 3386 0.319555 TGGCGGAGAAAAGACGTCTG 60.320 55.0 20.85 5.59 32.73 3.51 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
28 29 9.611284 TGTTGTCTGAATTTAATTTTCTGATCG 57.389 29.630 9.78 0.00 34.79 3.69
150 151 3.439293 CTGTCTACCTCACAAGCATACG 58.561 50.000 0.00 0.00 0.00 3.06
206 241 2.291465 GCTGATCACAAAACTGCACAGA 59.709 45.455 4.31 0.00 0.00 3.41
220 255 5.140454 ACTGCACAGAAAACCTTAAGGAAT 58.860 37.500 28.52 13.23 38.94 3.01
241 288 9.956640 AGGAATAAAATAACATTTTGGCATCAA 57.043 25.926 7.04 0.00 0.00 2.57
248 295 2.568509 ACATTTTGGCATCAAGGGGAAG 59.431 45.455 0.00 0.00 33.98 3.46
260 309 6.689946 GCATCAAGGGGAAGAGAAGATGATTA 60.690 42.308 0.00 0.00 34.79 1.75
262 311 7.072263 TCAAGGGGAAGAGAAGATGATTATC 57.928 40.000 0.00 0.00 0.00 1.75
497 550 6.183361 ACCATTAAAGAAAATTCCAACAGCCA 60.183 34.615 0.00 0.00 0.00 4.75
546 599 3.652869 AGACATCCTTTCTTTCTGGTGGA 59.347 43.478 0.00 0.00 0.00 4.02
601 654 2.380064 TGCCCATGATTGGTTATCCC 57.620 50.000 0.00 0.00 41.91 3.85
604 657 0.874390 CCATGATTGGTTATCCCGCG 59.126 55.000 0.00 0.00 38.30 6.46
665 718 1.270550 GAAAATGGCAGGTCAGTGTGG 59.729 52.381 0.00 0.00 0.00 4.17
666 719 0.478072 AAATGGCAGGTCAGTGTGGA 59.522 50.000 0.00 0.00 0.00 4.02
667 720 0.250901 AATGGCAGGTCAGTGTGGAC 60.251 55.000 0.00 0.00 37.06 4.02
757 810 7.609056 ACATTCGTTAAGAGAGTTAAGCCTAA 58.391 34.615 0.00 0.00 0.00 2.69
899 956 1.152139 CCATCCTCCTCCCTCCCTC 60.152 68.421 0.00 0.00 0.00 4.30
920 977 4.747583 TCCTCCCGGACATCTTTATATCA 58.252 43.478 0.73 0.00 33.30 2.15
984 1041 0.903924 CCACCACCATTGCCAATCCA 60.904 55.000 0.00 0.00 0.00 3.41
1080 1142 2.283388 TCCCCGTGCTACGAAGGT 60.283 61.111 9.75 0.00 46.05 3.50
1181 1243 0.247814 CGCGGATTGATCAAGCACAC 60.248 55.000 23.99 11.92 33.53 3.82
1185 1247 2.083774 GGATTGATCAAGCACACCGAA 58.916 47.619 23.99 0.00 0.00 4.30
1187 1249 3.057596 GGATTGATCAAGCACACCGAAAA 60.058 43.478 23.99 0.00 0.00 2.29
1210 1272 1.151668 CACCAAGGCAAGAACTCTCG 58.848 55.000 0.00 0.00 0.00 4.04
1290 1352 1.203523 ACGAACTGTGATGGAGCTCTC 59.796 52.381 14.64 4.74 0.00 3.20
1291 1353 1.203287 CGAACTGTGATGGAGCTCTCA 59.797 52.381 14.64 10.46 0.00 3.27
1292 1354 2.734809 CGAACTGTGATGGAGCTCTCAG 60.735 54.545 14.64 15.31 40.74 3.35
1293 1355 0.536260 ACTGTGATGGAGCTCTCAGC 59.464 55.000 14.64 13.04 39.32 4.26
1415 1480 4.517952 TTAGTTCGTCCATCGTGGTTTA 57.482 40.909 4.33 0.00 39.03 2.01
1501 1566 1.170442 TGCATGCATGTCTGAACAGG 58.830 50.000 26.79 0.00 39.20 4.00
1619 1687 3.588396 ACCGGGAAGTCATTACCCTAAAA 59.412 43.478 6.32 0.00 41.28 1.52
1620 1688 3.943381 CCGGGAAGTCATTACCCTAAAAC 59.057 47.826 0.00 0.00 41.28 2.43
1833 1901 4.864334 CATCCTGGTGAGCCGCCC 62.864 72.222 0.00 0.00 37.67 6.13
1842 1910 2.436824 GAGCCGCCCTCCTTTGTC 60.437 66.667 0.00 0.00 34.35 3.18
1851 1935 0.250727 CCTCCTTTGTCGGCCTTTGA 60.251 55.000 0.00 0.00 0.00 2.69
1852 1936 1.604604 CTCCTTTGTCGGCCTTTGAA 58.395 50.000 0.00 0.00 0.00 2.69
1857 1941 3.430236 CCTTTGTCGGCCTTTGAAGTTTT 60.430 43.478 0.00 0.00 0.00 2.43
1861 1945 0.103937 CGGCCTTTGAAGTTTTGGCA 59.896 50.000 0.00 0.00 44.85 4.92
1865 1949 2.825205 CCTTTGAAGTTTTGGCACTGG 58.175 47.619 0.00 0.00 0.00 4.00
1866 1950 2.168313 CCTTTGAAGTTTTGGCACTGGT 59.832 45.455 0.00 0.00 0.00 4.00
1867 1951 2.957491 TTGAAGTTTTGGCACTGGTG 57.043 45.000 0.00 0.00 0.00 4.17
1880 1972 1.937223 CACTGGTGCAAGACGTTAACA 59.063 47.619 6.39 0.00 0.00 2.41
1944 2036 2.046892 ACATGCTGTGCTCCGACC 60.047 61.111 0.00 0.00 0.00 4.79
2006 2098 4.379243 CTGGCCCACGACGAGCTT 62.379 66.667 0.00 0.00 0.00 3.74
2016 2108 0.528470 CGACGAGCTTTCCCTCTTCT 59.472 55.000 0.00 0.00 30.41 2.85
2021 2113 0.322008 AGCTTTCCCTCTTCTTGGCG 60.322 55.000 0.00 0.00 0.00 5.69
2185 2277 0.882042 GCGATGGATCCTGCGAATGT 60.882 55.000 24.50 0.00 0.00 2.71
2222 2314 4.357947 GCCGACCGTGTCAGCTCA 62.358 66.667 5.36 0.00 33.67 4.26
2393 2485 3.466881 AGGGCGTGAAGTGCACTA 58.533 55.556 22.01 1.56 46.22 2.74
2394 2486 1.983224 AGGGCGTGAAGTGCACTAT 59.017 52.632 22.01 10.57 46.22 2.12
2395 2487 0.391661 AGGGCGTGAAGTGCACTATG 60.392 55.000 22.01 12.19 46.22 2.23
2396 2488 1.425428 GGCGTGAAGTGCACTATGC 59.575 57.895 22.01 21.33 45.49 3.14
2421 2520 8.140628 GCACATGTAGTATATAGCTAGATGCAT 58.859 37.037 17.12 0.00 41.23 3.96
2441 2540 4.607955 CATACATGCATCTTTTCTGGCAG 58.392 43.478 8.58 8.58 39.95 4.85
2455 2554 2.158957 TCTGGCAGAGAAAAGTCGTTGT 60.159 45.455 14.43 0.00 0.00 3.32
2463 2562 6.090898 GCAGAGAAAAGTCGTTGTATGTACAT 59.909 38.462 13.93 13.93 35.89 2.29
2468 2568 4.025015 AGTCGTTGTATGTACATCCGTC 57.975 45.455 12.68 8.56 35.89 4.79
2469 2569 3.441222 AGTCGTTGTATGTACATCCGTCA 59.559 43.478 12.68 5.36 35.89 4.35
2470 2570 4.097437 AGTCGTTGTATGTACATCCGTCAT 59.903 41.667 12.68 0.00 35.89 3.06
2471 2571 4.206404 GTCGTTGTATGTACATCCGTCATG 59.794 45.833 12.68 0.00 35.89 3.07
2472 2572 3.060540 CGTTGTATGTACATCCGTCATGC 60.061 47.826 12.68 0.00 35.65 4.06
2473 2573 2.738135 TGTATGTACATCCGTCATGCG 58.262 47.619 12.68 3.02 35.65 4.73
2474 2574 2.100087 TGTATGTACATCCGTCATGCGT 59.900 45.455 12.68 0.00 39.32 5.24
2475 2575 1.570813 ATGTACATCCGTCATGCGTG 58.429 50.000 1.41 0.00 39.32 5.34
2476 2576 0.245266 TGTACATCCGTCATGCGTGT 59.755 50.000 5.68 8.97 39.32 4.49
2477 2577 0.645355 GTACATCCGTCATGCGTGTG 59.355 55.000 5.68 0.00 39.32 3.82
2478 2578 0.245266 TACATCCGTCATGCGTGTGT 59.755 50.000 5.68 5.12 38.88 3.72
2479 2579 1.014044 ACATCCGTCATGCGTGTGTC 61.014 55.000 5.68 0.00 39.32 3.67
2480 2580 0.737367 CATCCGTCATGCGTGTGTCT 60.737 55.000 5.68 0.00 39.32 3.41
2481 2581 0.737367 ATCCGTCATGCGTGTGTCTG 60.737 55.000 5.68 0.00 39.32 3.51
2482 2582 1.372872 CCGTCATGCGTGTGTCTGA 60.373 57.895 5.68 0.00 39.32 3.27
2483 2583 0.943835 CCGTCATGCGTGTGTCTGAA 60.944 55.000 5.68 0.00 39.32 3.02
2484 2584 0.858583 CGTCATGCGTGTGTCTGAAA 59.141 50.000 5.68 0.00 35.54 2.69
2485 2585 1.397190 CGTCATGCGTGTGTCTGAAAC 60.397 52.381 5.68 0.00 35.54 2.78
2486 2586 0.858583 TCATGCGTGTGTCTGAAACG 59.141 50.000 5.68 4.89 40.22 3.60
2491 2591 3.929095 GTGTGTCTGAAACGCGATC 57.071 52.632 15.93 11.71 41.49 3.69
2501 2601 2.419673 TGAAACGCGATCAATGCAAGAT 59.580 40.909 15.93 4.84 0.00 2.40
2521 2636 0.679640 TAATTCAGGGCTGGGCAACG 60.680 55.000 0.00 0.00 37.60 4.10
2532 2647 1.303317 GGGCAACGTGGGACAAGAT 60.303 57.895 0.00 0.00 44.16 2.40
2540 2655 2.758979 ACGTGGGACAAGATTAGTCGAT 59.241 45.455 0.00 0.00 44.16 3.59
2549 2664 4.037565 ACAAGATTAGTCGATGCGTCCATA 59.962 41.667 0.00 0.00 0.00 2.74
2567 2682 7.142680 CGTCCATATAAAGTCTTTCTCCTCTC 58.857 42.308 0.00 0.00 0.00 3.20
2569 2684 8.357402 GTCCATATAAAGTCTTTCTCCTCTCTC 58.643 40.741 0.00 0.00 0.00 3.20
2572 2687 8.576442 CATATAAAGTCTTTCTCCTCTCTCCTC 58.424 40.741 0.00 0.00 0.00 3.71
2578 2693 0.107606 TCTCCTCTCTCCTCGAACCG 60.108 60.000 0.00 0.00 0.00 4.44
2583 2698 0.964358 TCTCTCCTCGAACCGAACCC 60.964 60.000 0.00 0.00 34.74 4.11
2590 2705 1.515736 CGAACCGAACCCTAGACGC 60.516 63.158 0.00 0.00 0.00 5.19
2591 2706 1.515736 GAACCGAACCCTAGACGCG 60.516 63.158 3.53 3.53 0.00 6.01
2592 2707 3.637926 AACCGAACCCTAGACGCGC 62.638 63.158 5.73 0.00 0.00 6.86
2593 2708 4.867599 CCGAACCCTAGACGCGCC 62.868 72.222 5.73 0.00 0.00 6.53
2599 2714 3.896133 CCTAGACGCGCCGCCTAA 61.896 66.667 5.73 0.00 0.00 2.69
2638 2753 2.203181 GCTGATCTGGGCCTCTGC 60.203 66.667 4.53 6.22 0.00 4.26
2769 2894 4.634133 GGTGTGCCGTCGTCGACA 62.634 66.667 24.13 3.01 39.71 4.35
2784 2909 3.901797 GACACCCACCGCCTCTTGG 62.902 68.421 0.00 0.00 0.00 3.61
2825 2950 1.742900 CGCTGCACACGGTATCTTCG 61.743 60.000 0.00 0.00 0.00 3.79
2845 2970 5.556355 TCGTCAACTACATCGACTACAAT 57.444 39.130 0.00 0.00 0.00 2.71
2856 2981 2.027024 CTACAATCGCCCGCGCTA 59.973 61.111 5.56 0.00 39.59 4.26
2988 3113 0.396695 TATGGGGGTCAGACGGACTC 60.397 60.000 5.70 1.03 46.92 3.36
3018 3146 3.353836 CAACCCCGCCACAAGACG 61.354 66.667 0.00 0.00 0.00 4.18
3056 3184 2.818169 AAGGGTGGCGACTGCAAGA 61.818 57.895 0.00 0.00 45.35 3.02
3150 3290 2.019984 GGATCCTGCACAAGATTCCAC 58.980 52.381 3.84 0.00 30.83 4.02
3212 3386 4.439968 GTCTAGTACAAGGCAATGGTACC 58.560 47.826 4.43 4.43 38.47 3.34
3216 3390 2.200373 ACAAGGCAATGGTACCAGAC 57.800 50.000 21.41 10.00 0.00 3.51
3347 3530 5.065090 CGAGGATCACTTTATGTTCATTGCA 59.935 40.000 0.00 0.00 33.17 4.08
3378 3561 3.703286 TGTCGTGAGGTAATACATCGG 57.297 47.619 0.53 0.00 30.36 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.612620 ACGATCAGAAAATTAAATTCAGACAAC 57.387 29.630 0.00 1.55 0.00 3.32
17 18 8.322906 TCATAAGAACACAACGATCAGAAAAT 57.677 30.769 0.00 0.00 0.00 1.82
28 29 5.700832 TGAGTGGACATCATAAGAACACAAC 59.299 40.000 0.00 0.00 0.00 3.32
150 151 6.881065 TGCAGTAATATAATCCTGATTCTGCC 59.119 38.462 18.47 8.02 42.20 4.85
160 161 8.660373 GCTGTCACTAATGCAGTAATATAATCC 58.340 37.037 0.00 0.00 34.98 3.01
220 255 7.038017 TCCCCTTGATGCCAAAATGTTATTTTA 60.038 33.333 0.00 0.00 0.00 1.52
230 277 2.109834 TCTCTTCCCCTTGATGCCAAAA 59.890 45.455 0.00 0.00 0.00 2.44
241 288 5.012975 GCAGATAATCATCTTCTCTTCCCCT 59.987 44.000 0.00 0.00 39.62 4.79
248 295 8.593842 CATTACGATGCAGATAATCATCTTCTC 58.406 37.037 0.00 0.00 39.62 2.87
312 361 4.440880 GCAGAAGAGAGCAGTCATACATT 58.559 43.478 0.00 0.00 0.00 2.71
315 364 2.797792 CGGCAGAAGAGAGCAGTCATAC 60.798 54.545 0.00 0.00 0.00 2.39
497 550 6.238484 GCCTGTAAAGAAATCGTGCAGATATT 60.238 38.462 0.00 0.00 38.98 1.28
546 599 7.361286 GCAGTTGGTTCTCGAGATTTTAATTCT 60.361 37.037 17.44 5.18 0.00 2.40
742 795 8.817876 ACAGTATTCTTTTAGGCTTAACTCTCT 58.182 33.333 0.00 0.00 0.00 3.10
781 834 9.439500 AAGCAGTACGTGGAACTAATTAATTAA 57.561 29.630 9.15 0.00 31.75 1.40
782 835 8.875803 CAAGCAGTACGTGGAACTAATTAATTA 58.124 33.333 7.66 7.66 31.75 1.40
783 836 7.389607 ACAAGCAGTACGTGGAACTAATTAATT 59.610 33.333 5.89 5.89 31.20 1.40
784 837 6.877322 ACAAGCAGTACGTGGAACTAATTAAT 59.123 34.615 0.00 0.00 31.20 1.40
863 920 0.790814 GGTGTGTTGCTCGCTTCTAC 59.209 55.000 0.00 0.00 0.00 2.59
984 1041 1.995542 TCCATGCTTCCTTCTCCCTTT 59.004 47.619 0.00 0.00 0.00 3.11
1080 1142 4.240881 GCGATGATGGCCTTGGAA 57.759 55.556 3.32 0.00 0.00 3.53
1181 1243 0.821711 TGCCTTGGTGGAGTTTTCGG 60.822 55.000 0.00 0.00 38.35 4.30
1185 1247 2.031870 GTTCTTGCCTTGGTGGAGTTT 58.968 47.619 0.00 0.00 38.35 2.66
1187 1249 0.846693 AGTTCTTGCCTTGGTGGAGT 59.153 50.000 0.00 0.00 38.35 3.85
1210 1272 8.924511 TGGAGACCATGAGGATTAATAAATTC 57.075 34.615 0.00 0.00 38.69 2.17
1290 1352 2.745821 TCTTGCTTTACATGCAGAGCTG 59.254 45.455 9.66 3.57 41.71 4.24
1291 1353 3.063510 TCTTGCTTTACATGCAGAGCT 57.936 42.857 9.66 0.00 41.71 4.09
1292 1354 4.574013 AGTATCTTGCTTTACATGCAGAGC 59.426 41.667 1.46 1.46 41.71 4.09
1293 1355 6.674694 AAGTATCTTGCTTTACATGCAGAG 57.325 37.500 0.00 0.00 41.71 3.35
1294 1356 7.201644 GCTTAAGTATCTTGCTTTACATGCAGA 60.202 37.037 4.02 0.00 41.71 4.26
1295 1357 6.909357 GCTTAAGTATCTTGCTTTACATGCAG 59.091 38.462 4.02 0.00 41.71 4.41
1296 1358 6.599244 AGCTTAAGTATCTTGCTTTACATGCA 59.401 34.615 4.02 0.00 38.80 3.96
1415 1480 3.987404 GGTGACGGCAGAGCAAAT 58.013 55.556 0.00 0.00 0.00 2.32
1456 1521 3.356639 GACGGAGACATGCGGCTCA 62.357 63.158 0.00 0.00 46.28 4.26
1501 1566 3.813166 TCATTCTCACCGACCAAACTTTC 59.187 43.478 0.00 0.00 0.00 2.62
1619 1687 5.807011 GCTTCAACATCACAAACAAAGAAGT 59.193 36.000 0.00 0.00 34.15 3.01
1620 1688 5.806502 TGCTTCAACATCACAAACAAAGAAG 59.193 36.000 0.00 0.00 34.61 2.85
1833 1901 1.537202 CTTCAAAGGCCGACAAAGGAG 59.463 52.381 0.00 0.00 0.00 3.69
1842 1910 0.103937 TGCCAAAACTTCAAAGGCCG 59.896 50.000 0.00 0.00 44.60 6.13
1844 1928 2.204237 CAGTGCCAAAACTTCAAAGGC 58.796 47.619 0.00 0.00 45.41 4.35
1861 1945 1.937899 GTGTTAACGTCTTGCACCAGT 59.062 47.619 0.26 0.00 0.00 4.00
1865 1949 0.233848 CCGGTGTTAACGTCTTGCAC 59.766 55.000 0.26 0.00 0.00 4.57
1866 1950 1.500512 GCCGGTGTTAACGTCTTGCA 61.501 55.000 1.90 0.00 0.00 4.08
1867 1951 1.205820 GCCGGTGTTAACGTCTTGC 59.794 57.895 1.90 0.00 0.00 4.01
1868 1952 1.864176 GGCCGGTGTTAACGTCTTG 59.136 57.895 1.90 0.00 0.00 3.02
1869 1953 1.665599 CGGCCGGTGTTAACGTCTT 60.666 57.895 20.10 0.00 0.00 3.01
1871 1955 2.356194 ACGGCCGGTGTTAACGTC 60.356 61.111 31.76 0.00 31.39 4.34
1872 1956 2.662527 CACGGCCGGTGTTAACGT 60.663 61.111 31.76 0.57 41.89 3.99
1991 2083 3.119096 GAAAGCTCGTCGTGGGCC 61.119 66.667 0.00 0.00 0.00 5.80
2006 2098 0.036306 GGAACGCCAAGAAGAGGGAA 59.964 55.000 0.00 0.00 0.00 3.97
2021 2113 1.294459 GGTCCCGGTGTACAGGAAC 59.706 63.158 0.00 3.10 32.68 3.62
2105 2197 4.424566 TCGTACTTGTCCGCGGCC 62.425 66.667 23.51 10.90 0.00 6.13
2108 2200 2.127118 ACGTCGTACTTGTCCGCG 60.127 61.111 0.00 0.00 0.00 6.46
2393 2485 8.140628 GCATCTAGCTATATACTACATGTGCAT 58.859 37.037 9.11 1.29 41.15 3.96
2394 2486 7.122650 TGCATCTAGCTATATACTACATGTGCA 59.877 37.037 9.11 0.00 45.94 4.57
2395 2487 7.484140 TGCATCTAGCTATATACTACATGTGC 58.516 38.462 9.11 0.00 45.94 4.57
2421 2520 3.943381 CTCTGCCAGAAAAGATGCATGTA 59.057 43.478 2.46 0.00 32.53 2.29
2422 2521 2.753452 CTCTGCCAGAAAAGATGCATGT 59.247 45.455 2.46 0.00 32.53 3.21
2423 2522 3.014623 TCTCTGCCAGAAAAGATGCATG 58.985 45.455 2.46 0.00 32.53 4.06
2424 2523 3.361281 TCTCTGCCAGAAAAGATGCAT 57.639 42.857 0.00 0.00 32.53 3.96
2436 2535 2.325583 ACAACGACTTTTCTCTGCCA 57.674 45.000 0.00 0.00 0.00 4.92
2441 2540 6.237490 CGGATGTACATACAACGACTTTTCTC 60.237 42.308 18.24 0.00 40.60 2.87
2468 2568 3.349972 CGTTTCAGACACACGCATG 57.650 52.632 0.00 0.00 0.00 4.06
2472 2572 0.091344 GATCGCGTTTCAGACACACG 59.909 55.000 5.77 0.00 36.98 4.49
2473 2573 1.136690 TGATCGCGTTTCAGACACAC 58.863 50.000 5.77 0.00 0.00 3.82
2474 2574 1.859383 TTGATCGCGTTTCAGACACA 58.141 45.000 5.77 0.00 0.00 3.72
2475 2575 2.762472 CATTGATCGCGTTTCAGACAC 58.238 47.619 5.77 0.00 0.00 3.67
2476 2576 1.128507 GCATTGATCGCGTTTCAGACA 59.871 47.619 5.77 0.00 0.00 3.41
2477 2577 1.128507 TGCATTGATCGCGTTTCAGAC 59.871 47.619 5.77 5.17 0.00 3.51
2478 2578 1.437625 TGCATTGATCGCGTTTCAGA 58.562 45.000 5.77 3.07 0.00 3.27
2479 2579 2.159667 TCTTGCATTGATCGCGTTTCAG 60.160 45.455 5.77 1.64 0.00 3.02
2480 2580 1.803555 TCTTGCATTGATCGCGTTTCA 59.196 42.857 5.77 8.28 0.00 2.69
2481 2581 2.525750 TCTTGCATTGATCGCGTTTC 57.474 45.000 5.77 5.37 0.00 2.78
2482 2582 3.492421 AATCTTGCATTGATCGCGTTT 57.508 38.095 5.77 0.00 0.00 3.60
2483 2583 4.614555 TTAATCTTGCATTGATCGCGTT 57.385 36.364 5.77 0.00 0.00 4.84
2484 2584 4.818534 ATTAATCTTGCATTGATCGCGT 57.181 36.364 5.77 0.00 0.00 6.01
2485 2585 5.207033 TGAATTAATCTTGCATTGATCGCG 58.793 37.500 0.00 0.00 0.00 5.87
2486 2586 5.628193 CCTGAATTAATCTTGCATTGATCGC 59.372 40.000 3.64 0.00 0.00 4.58
2487 2587 6.147581 CCCTGAATTAATCTTGCATTGATCG 58.852 40.000 3.64 0.00 0.00 3.69
2488 2588 5.924825 GCCCTGAATTAATCTTGCATTGATC 59.075 40.000 3.64 0.00 0.00 2.92
2489 2589 5.601313 AGCCCTGAATTAATCTTGCATTGAT 59.399 36.000 0.00 0.00 0.00 2.57
2490 2590 4.957954 AGCCCTGAATTAATCTTGCATTGA 59.042 37.500 0.00 0.00 0.00 2.57
2491 2591 5.047847 CAGCCCTGAATTAATCTTGCATTG 58.952 41.667 0.00 0.00 0.00 2.82
2501 2601 1.555967 GTTGCCCAGCCCTGAATTAA 58.444 50.000 0.00 0.00 0.00 1.40
2521 2636 2.866762 GCATCGACTAATCTTGTCCCAC 59.133 50.000 0.00 0.00 0.00 4.61
2532 2647 6.016527 AGACTTTATATGGACGCATCGACTAA 60.017 38.462 0.00 0.00 0.00 2.24
2540 2655 5.128827 AGGAGAAAGACTTTATATGGACGCA 59.871 40.000 0.00 0.00 0.00 5.24
2549 2664 5.592688 CGAGGAGAGAGGAGAAAGACTTTAT 59.407 44.000 0.00 0.00 0.00 1.40
2567 2682 0.739561 CTAGGGTTCGGTTCGAGGAG 59.260 60.000 0.00 0.00 37.14 3.69
2569 2684 0.455005 GTCTAGGGTTCGGTTCGAGG 59.545 60.000 0.00 0.00 37.14 4.63
2572 2687 1.515736 GCGTCTAGGGTTCGGTTCG 60.516 63.158 0.00 0.00 0.00 3.95
2583 2698 2.654404 GTTAGGCGGCGCGTCTAG 60.654 66.667 31.26 0.00 44.72 2.43
2638 2753 2.513204 CCATGCCTCCACGCAGAG 60.513 66.667 0.00 0.00 43.26 3.35
2812 2937 3.503363 TGTAGTTGACGAAGATACCGTGT 59.497 43.478 0.00 0.00 40.67 4.49
2813 2938 4.087510 TGTAGTTGACGAAGATACCGTG 57.912 45.455 0.00 0.00 40.67 4.94
2825 2950 4.204573 GCGATTGTAGTCGATGTAGTTGAC 59.795 45.833 0.78 0.00 44.06 3.18
2892 3017 1.466558 GCAAGAAGTCTAGGTTGCAGC 59.533 52.381 8.25 0.00 43.86 5.25
2988 3113 2.609759 GGGTTGGCCACGTACAACG 61.610 63.158 3.88 0.00 45.91 4.10
3018 3146 1.144936 CGGCAGAGATCTTCCCACC 59.855 63.158 0.00 0.00 0.00 4.61
3150 3290 1.526917 GAGGATGGTGGCCATTCCG 60.527 63.158 9.72 0.00 45.26 4.30
3212 3386 0.319555 TGGCGGAGAAAAGACGTCTG 60.320 55.000 20.85 5.59 32.73 3.51
3216 3390 1.912371 GCCTTGGCGGAGAAAAGACG 61.912 60.000 0.00 0.00 33.16 4.18
3258 3432 4.438608 GCATCATAGGATCTAGTCGAGCAG 60.439 50.000 0.00 0.00 0.00 4.24
3307 3490 4.848562 TCCTCGCCAATACACACTATAG 57.151 45.455 0.00 0.00 0.00 1.31
3347 3530 1.202533 CCTCACGACAAACACACCTCT 60.203 52.381 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.