Multiple sequence alignment - TraesCS4A01G108900

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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 TraesCS4A01G108900 chr4A 100.000 2768 0 0 1 2768 127805906 127808673 0.000000e+00 5112
1 TraesCS4A01G108900 chr4B 94.658 1666 73 10 170 1820 421742841 421741177 0.000000e+00 2569
2 TraesCS4A01G108900 chr4B 89.571 815 73 11 1 810 421743663 421742856 0.000000e+00 1024
3 TraesCS4A01G108900 chr4B 87.542 594 37 16 1817 2408 421741143 421740585 0.000000e+00 652
4 TraesCS4A01G108900 chr4B 88.401 319 16 13 2469 2768 421740220 421739904 5.630000e-97 364
5 TraesCS4A01G108900 chr4B 86.709 158 9 6 2542 2687 421739984 421739827 6.130000e-37 165
6 TraesCS4A01G108900 chr4D 96.905 1163 22 10 668 1820 340302362 340301204 0.000000e+00 1936
7 TraesCS4A01G108900 chr4D 89.160 655 66 4 1 652 340306185 340305533 0.000000e+00 811
8 TraesCS4A01G108900 chr4D 91.000 600 22 13 1817 2408 340301170 340300595 0.000000e+00 780
9 TraesCS4A01G108900 chr4D 90.260 308 11 12 2480 2768 340300293 340299986 4.320000e-103 385
10 TraesCS4A01G108900 chr4D 88.750 160 6 6 2542 2689 340300066 340299907 4.710000e-43 185


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 TraesCS4A01G108900 chr4A 127805906 127808673 2767 False 5112.0 5112 100.0000 1 2768 1 chr4A.!!$F1 2767
1 TraesCS4A01G108900 chr4B 421739827 421743663 3836 True 954.8 2569 89.3762 1 2768 5 chr4B.!!$R1 2767
2 TraesCS4A01G108900 chr4D 340299907 340306185 6278 True 819.4 1936 91.2150 1 2768 5 chr4D.!!$R1 2767

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
390 395 0.792729 ATAAAATGTGCGTGCGTGCG 60.793 50.0 0.0 0.0 37.81 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 5810 0.994247 AGCATCCATCCTCACAACCA 59.006 50.0 0.0 0.0 0.0 3.67 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
85 86 3.010420 TCGGACAAACAATGTTCACACA 58.990 40.909 0.00 0.00 44.12 3.72
125 126 4.320788 CCAAGCATTTTCACAAGACTCCTC 60.321 45.833 0.00 0.00 0.00 3.71
208 211 2.180159 TAGCCCGACCAGGTTCAAGC 62.180 60.000 0.00 0.00 38.74 4.01
253 256 8.275015 TCGCATATTTCCTGAAGTTATTTCAA 57.725 30.769 0.00 0.00 44.84 2.69
278 281 1.000394 TCTGATGAAGTTCGTTCGGCA 60.000 47.619 0.00 0.00 38.09 5.69
279 282 2.002586 CTGATGAAGTTCGTTCGGCAT 58.997 47.619 0.00 0.00 38.09 4.40
293 296 3.768633 GGCATGAGATGACGTTCCT 57.231 52.632 0.00 0.00 0.00 3.36
349 353 7.599998 GTCAATTTTATGATTTGCCAACTCAGT 59.400 33.333 3.80 0.00 0.00 3.41
360 364 1.801178 CCAACTCAGTCTTTCGAAGGC 59.199 52.381 1.73 0.00 0.00 4.35
369 373 2.671396 GTCTTTCGAAGGCGCTCATAAA 59.329 45.455 7.64 0.96 37.46 1.40
374 378 5.804692 TTCGAAGGCGCTCATAAAAATAA 57.195 34.783 7.64 0.00 37.46 1.40
375 379 5.804692 TCGAAGGCGCTCATAAAAATAAA 57.195 34.783 7.64 0.00 37.46 1.40
386 390 6.311332 TCATAAAAATAAAATGTGCGTGCG 57.689 33.333 0.00 0.00 0.00 5.34
390 395 0.792729 ATAAAATGTGCGTGCGTGCG 60.793 50.000 0.00 0.00 37.81 5.34
396 401 2.137395 GTGCGTGCGTGCGTTTATG 61.137 57.895 3.11 0.00 37.81 1.90
445 450 8.557029 ACTTCTACCGTGTTTCTTAGAAAAATG 58.443 33.333 9.14 9.36 31.73 2.32
476 481 7.770433 TGATAACCATCAAACATTCACTAGGAG 59.230 37.037 0.00 0.00 38.25 3.69
508 513 2.200170 GAACACCCGCACAGCCATTC 62.200 60.000 0.00 0.00 0.00 2.67
563 568 9.581099 GAAAAATACCTTGAAAGACTGAAAACA 57.419 29.630 0.00 0.00 0.00 2.83
577 582 2.916934 TGAAAACAGCCTACCCTACCAT 59.083 45.455 0.00 0.00 0.00 3.55
599 1257 1.928868 AAGTTGCCATCCCTCTTTGG 58.071 50.000 0.00 0.00 36.03 3.28
610 1268 5.514834 CCATCCCTCTTTGGACTAAAACTGA 60.515 44.000 0.00 0.00 37.20 3.41
620 1278 6.463995 TGGACTAAAACTGACAGCAAATTT 57.536 33.333 1.25 2.30 0.00 1.82
640 1298 1.549620 TGTTCGCAAATGCCATCCATT 59.450 42.857 0.00 0.00 45.90 3.16
675 4241 3.873952 GGCAGCTATTTGGAGTTCTACAG 59.126 47.826 0.00 0.00 0.00 2.74
714 4280 3.859961 CACGAGTCATGTAGCCAGTAAAG 59.140 47.826 0.00 0.00 0.00 1.85
789 4361 3.072211 GTCACCTAAGCAACCTGGTAAC 58.928 50.000 0.00 0.00 0.00 2.50
793 4365 3.516700 ACCTAAGCAACCTGGTAACGTAT 59.483 43.478 0.00 0.00 42.51 3.06
1581 5161 1.227002 GGTCATCTTCTCCGCCGTC 60.227 63.158 0.00 0.00 0.00 4.79
1725 5305 0.736325 GACTCATTGCCTACGCGTGT 60.736 55.000 24.59 6.91 38.08 4.49
1758 5338 0.525311 TGCTCTTCTCTCTGCTCGTG 59.475 55.000 0.00 0.00 0.00 4.35
1802 5383 7.345691 TGAGATGGAAGGTATGCTTTCATAAA 58.654 34.615 7.89 0.00 36.96 1.40
1902 5520 5.772672 ACCTTTTGCCAACACAACTATGATA 59.227 36.000 0.00 0.00 0.00 2.15
1903 5521 6.266558 ACCTTTTGCCAACACAACTATGATAA 59.733 34.615 0.00 0.00 0.00 1.75
2043 5668 8.599792 TGGATGATATTATTGAGAGAATGCTGA 58.400 33.333 0.00 0.00 0.00 4.26
2076 5701 7.678194 TTTTCACTTATGCTTTTCAAGTTCG 57.322 32.000 0.00 0.00 30.20 3.95
2112 5737 6.753744 GGAAATTATTCTTTGCTGCCTTAGTG 59.246 38.462 0.00 0.00 35.79 2.74
2113 5738 6.840780 AATTATTCTTTGCTGCCTTAGTGT 57.159 33.333 0.00 0.00 0.00 3.55
2114 5739 7.938140 AATTATTCTTTGCTGCCTTAGTGTA 57.062 32.000 0.00 0.00 0.00 2.90
2116 5741 3.762407 TCTTTGCTGCCTTAGTGTACA 57.238 42.857 0.00 0.00 0.00 2.90
2117 5742 4.079980 TCTTTGCTGCCTTAGTGTACAA 57.920 40.909 0.00 0.00 0.00 2.41
2118 5743 3.813166 TCTTTGCTGCCTTAGTGTACAAC 59.187 43.478 0.00 0.00 0.00 3.32
2119 5744 3.485463 TTGCTGCCTTAGTGTACAACT 57.515 42.857 0.00 0.00 43.40 3.16
2120 5745 3.485463 TGCTGCCTTAGTGTACAACTT 57.515 42.857 0.00 0.00 40.56 2.66
2121 5746 3.138304 TGCTGCCTTAGTGTACAACTTG 58.862 45.455 0.00 0.00 40.56 3.16
2122 5747 3.139077 GCTGCCTTAGTGTACAACTTGT 58.861 45.455 0.00 0.00 40.56 3.16
2123 5748 3.564225 GCTGCCTTAGTGTACAACTTGTT 59.436 43.478 0.00 0.00 40.56 2.83
2124 5749 4.554723 GCTGCCTTAGTGTACAACTTGTTG 60.555 45.833 11.44 11.44 40.56 3.33
2125 5750 3.880490 TGCCTTAGTGTACAACTTGTTGG 59.120 43.478 16.48 0.00 40.56 3.77
2126 5751 3.881089 GCCTTAGTGTACAACTTGTTGGT 59.119 43.478 16.48 6.24 40.56 3.67
2127 5752 4.261031 GCCTTAGTGTACAACTTGTTGGTG 60.261 45.833 16.48 0.00 40.56 4.17
2128 5753 4.274950 CCTTAGTGTACAACTTGTTGGTGG 59.725 45.833 16.48 4.50 40.56 4.61
2129 5754 3.637911 AGTGTACAACTTGTTGGTGGA 57.362 42.857 16.48 0.00 37.78 4.02
2130 5755 4.164843 AGTGTACAACTTGTTGGTGGAT 57.835 40.909 16.48 0.00 37.78 3.41
2131 5756 5.298989 AGTGTACAACTTGTTGGTGGATA 57.701 39.130 16.48 0.00 37.78 2.59
2132 5757 5.876357 AGTGTACAACTTGTTGGTGGATAT 58.124 37.500 16.48 0.00 37.78 1.63
2133 5758 7.011499 AGTGTACAACTTGTTGGTGGATATA 57.989 36.000 16.48 0.00 37.78 0.86
2134 5759 6.877322 AGTGTACAACTTGTTGGTGGATATAC 59.123 38.462 16.48 9.00 37.78 1.47
2135 5760 6.877322 GTGTACAACTTGTTGGTGGATATACT 59.123 38.462 16.48 0.00 37.78 2.12
2136 5761 7.389607 GTGTACAACTTGTTGGTGGATATACTT 59.610 37.037 16.48 0.00 37.78 2.24
2137 5762 7.940137 TGTACAACTTGTTGGTGGATATACTTT 59.060 33.333 16.48 0.00 37.78 2.66
2138 5763 9.439500 GTACAACTTGTTGGTGGATATACTTTA 57.561 33.333 16.48 0.00 37.78 1.85
2139 5764 8.561738 ACAACTTGTTGGTGGATATACTTTAG 57.438 34.615 16.48 0.00 37.78 1.85
2140 5765 8.161425 ACAACTTGTTGGTGGATATACTTTAGT 58.839 33.333 16.48 0.00 37.78 2.24
2141 5766 8.450964 CAACTTGTTGGTGGATATACTTTAGTG 58.549 37.037 5.65 0.00 0.00 2.74
2142 5767 7.686434 ACTTGTTGGTGGATATACTTTAGTGT 58.314 34.615 0.00 0.00 0.00 3.55
2143 5768 8.818860 ACTTGTTGGTGGATATACTTTAGTGTA 58.181 33.333 0.00 0.00 0.00 2.90
2144 5769 9.095065 CTTGTTGGTGGATATACTTTAGTGTAC 57.905 37.037 0.00 0.00 0.00 2.90
2145 5770 8.136563 TGTTGGTGGATATACTTTAGTGTACA 57.863 34.615 0.00 0.00 0.00 2.90
2182 5808 9.647797 TGTGGATATACTTTAGTGTACAACTTG 57.352 33.333 0.00 0.00 40.56 3.16
2183 5809 9.649167 GTGGATATACTTTAGTGTACAACTTGT 57.351 33.333 0.00 0.00 40.56 3.16
2206 5833 3.010027 TGGTTGTGAGGATGGATGCTAAA 59.990 43.478 0.00 0.00 0.00 1.85
2316 5943 1.539827 CCTAAAAACTGGGTTGCTCCG 59.460 52.381 0.00 0.00 37.00 4.63
2404 6031 1.028868 GCTTCAGCAGGGACATGTCC 61.029 60.000 33.14 33.14 44.13 4.02
2413 6040 1.068250 GGACATGTCCGGAGCTAGC 59.932 63.158 28.52 6.62 40.36 3.42
2414 6041 1.676678 GGACATGTCCGGAGCTAGCA 61.677 60.000 28.52 0.00 40.36 3.49
2415 6042 0.390860 GACATGTCCGGAGCTAGCAT 59.609 55.000 18.83 0.43 0.00 3.79
2416 6043 0.390860 ACATGTCCGGAGCTAGCATC 59.609 55.000 18.83 11.25 0.00 3.91
2417 6044 0.320247 CATGTCCGGAGCTAGCATCC 60.320 60.000 18.83 18.43 0.00 3.51
2418 6045 1.476007 ATGTCCGGAGCTAGCATCCC 61.476 60.000 18.83 13.57 32.86 3.85
2419 6046 2.524394 TCCGGAGCTAGCATCCCC 60.524 66.667 18.83 11.05 32.86 4.81
2420 6047 3.631046 CCGGAGCTAGCATCCCCC 61.631 72.222 18.83 8.58 32.86 5.40
2441 6068 3.240491 CCCCCTCCGTGCATATGT 58.760 61.111 4.29 0.00 0.00 2.29
2442 6069 1.071471 CCCCCTCCGTGCATATGTC 59.929 63.158 4.29 0.00 0.00 3.06
2443 6070 1.071471 CCCCTCCGTGCATATGTCC 59.929 63.158 4.29 0.00 0.00 4.02
2444 6071 1.410850 CCCCTCCGTGCATATGTCCT 61.411 60.000 4.29 0.00 0.00 3.85
2445 6072 0.034059 CCCTCCGTGCATATGTCCTC 59.966 60.000 4.29 0.00 0.00 3.71
2446 6073 0.034059 CCTCCGTGCATATGTCCTCC 59.966 60.000 4.29 0.00 0.00 4.30
2447 6074 1.043816 CTCCGTGCATATGTCCTCCT 58.956 55.000 4.29 0.00 0.00 3.69
2449 6076 0.034059 CCGTGCATATGTCCTCCTCC 59.966 60.000 4.29 0.00 0.00 4.30
2450 6077 0.752658 CGTGCATATGTCCTCCTCCA 59.247 55.000 4.29 0.00 0.00 3.86
2451 6078 1.345741 CGTGCATATGTCCTCCTCCAT 59.654 52.381 4.29 0.00 0.00 3.41
2452 6079 2.611473 CGTGCATATGTCCTCCTCCATC 60.611 54.545 4.29 0.00 0.00 3.51
2453 6080 1.620323 TGCATATGTCCTCCTCCATCG 59.380 52.381 4.29 0.00 0.00 3.84
2454 6081 1.620819 GCATATGTCCTCCTCCATCGT 59.379 52.381 4.29 0.00 0.00 3.73
2455 6082 2.353208 GCATATGTCCTCCTCCATCGTC 60.353 54.545 4.29 0.00 0.00 4.20
2456 6083 2.748209 TATGTCCTCCTCCATCGTCA 57.252 50.000 0.00 0.00 0.00 4.35
2457 6084 1.115467 ATGTCCTCCTCCATCGTCAC 58.885 55.000 0.00 0.00 0.00 3.67
2458 6085 0.251608 TGTCCTCCTCCATCGTCACA 60.252 55.000 0.00 0.00 0.00 3.58
2459 6086 1.115467 GTCCTCCTCCATCGTCACAT 58.885 55.000 0.00 0.00 0.00 3.21
2460 6087 1.482593 GTCCTCCTCCATCGTCACATT 59.517 52.381 0.00 0.00 0.00 2.71
2461 6088 1.482182 TCCTCCTCCATCGTCACATTG 59.518 52.381 0.00 0.00 0.00 2.82
2462 6089 1.208052 CCTCCTCCATCGTCACATTGT 59.792 52.381 0.00 0.00 0.00 2.71
2463 6090 2.355108 CCTCCTCCATCGTCACATTGTT 60.355 50.000 0.00 0.00 0.00 2.83
2464 6091 2.674852 CTCCTCCATCGTCACATTGTTG 59.325 50.000 0.00 0.00 0.00 3.33
2465 6092 1.131126 CCTCCATCGTCACATTGTTGC 59.869 52.381 0.00 0.00 0.00 4.17
2466 6093 1.805943 CTCCATCGTCACATTGTTGCA 59.194 47.619 0.00 0.00 0.00 4.08
2467 6094 1.535028 TCCATCGTCACATTGTTGCAC 59.465 47.619 0.00 0.00 0.00 4.57
2477 6408 2.079158 CATTGTTGCACGGATCTCTGT 58.921 47.619 0.00 0.00 35.46 3.41
2484 6415 2.202987 CGGATCTCTGTGGCCTGC 60.203 66.667 3.32 0.00 0.00 4.85
2532 6470 2.486907 GCCTCAAATCCCTGATCCAGAG 60.487 54.545 0.00 0.00 32.44 3.35
2533 6471 2.486907 CCTCAAATCCCTGATCCAGAGC 60.487 54.545 0.00 0.00 32.44 4.09
2609 6559 2.359975 GAGGAGCGGGTGGGTTTG 60.360 66.667 0.00 0.00 0.00 2.93
2621 6571 4.344865 GGTTTGGAGCTGGCCGGA 62.345 66.667 18.31 0.00 0.00 5.14
2708 6658 2.586792 GGCTTGTGGATCCGCTCT 59.413 61.111 25.23 0.00 0.00 4.09
2728 6678 4.579384 CACGGTGGTGGCCCAGTT 62.579 66.667 0.00 0.00 42.94 3.16
2755 6705 0.787084 ACAGTGAGGAGGGAGAGGAA 59.213 55.000 0.00 0.00 0.00 3.36
2757 6707 0.787084 AGTGAGGAGGGAGAGGAACA 59.213 55.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 3.950395 GCTTGGCACCAATCTATTTCTCT 59.050 43.478 1.86 0.00 35.20 3.10
142 145 0.816825 AAGCTATGCATGACCAGGCG 60.817 55.000 10.16 0.00 41.64 5.52
147 150 6.931281 TCTAACAATCTAAGCTATGCATGACC 59.069 38.462 10.16 0.00 0.00 4.02
208 211 1.298859 GCACAACGCCAAGTCTAGGG 61.299 60.000 0.00 0.00 32.94 3.53
278 281 2.092323 TCGACAGGAACGTCATCTCAT 58.908 47.619 0.00 0.00 35.54 2.90
279 282 1.530323 TCGACAGGAACGTCATCTCA 58.470 50.000 0.00 0.00 35.54 3.27
293 296 2.063266 GCAAACACCTCGTTATCGACA 58.937 47.619 0.00 0.00 41.35 4.35
349 353 2.665649 TTATGAGCGCCTTCGAAAGA 57.334 45.000 2.29 0.00 38.10 2.52
369 373 1.718711 GCACGCACGCACATTTTATTT 59.281 42.857 0.00 0.00 0.00 1.40
374 378 2.928313 AAACGCACGCACGCACATTT 62.928 50.000 0.00 0.00 36.19 2.32
375 379 2.107151 TAAACGCACGCACGCACATT 62.107 50.000 0.00 0.00 36.19 2.71
386 390 0.100503 GCACATCCCCATAAACGCAC 59.899 55.000 0.00 0.00 0.00 5.34
390 395 2.760092 ACACATGCACATCCCCATAAAC 59.240 45.455 0.00 0.00 0.00 2.01
445 450 8.686334 AGTGAATGTTTGATGGTTATCATTACC 58.314 33.333 0.00 0.00 42.60 2.85
459 464 5.087323 ACCTCTCTCCTAGTGAATGTTTGA 58.913 41.667 0.00 0.00 0.00 2.69
461 466 4.468153 GGACCTCTCTCCTAGTGAATGTTT 59.532 45.833 0.00 0.00 0.00 2.83
476 481 1.079750 GTGTTCGCTGGGACCTCTC 60.080 63.158 0.00 0.00 0.00 3.20
563 568 4.627984 GCAACTTTAATGGTAGGGTAGGCT 60.628 45.833 0.00 0.00 0.00 4.58
577 582 3.831911 CCAAAGAGGGATGGCAACTTTAA 59.168 43.478 0.00 0.00 37.61 1.52
599 1257 7.305418 CGAACAAATTTGCTGTCAGTTTTAGTC 60.305 37.037 18.12 0.00 0.00 2.59
620 1278 1.184431 ATGGATGGCATTTGCGAACA 58.816 45.000 0.00 0.00 43.26 3.18
636 1294 4.433102 CGAACGTTCGCCAAATGG 57.567 55.556 34.54 9.32 44.26 3.16
653 1311 3.873910 TGTAGAACTCCAAATAGCTGCC 58.126 45.455 0.00 0.00 0.00 4.85
654 1312 4.759782 TCTGTAGAACTCCAAATAGCTGC 58.240 43.478 0.00 0.00 0.00 5.25
675 4241 8.462143 TGACTCGTGACTCTTACAATATTTTC 57.538 34.615 0.00 0.00 0.00 2.29
694 4260 4.106197 GTCTTTACTGGCTACATGACTCG 58.894 47.826 0.00 0.00 0.00 4.18
789 4361 5.353123 TGCTAAGTAAAGGGAGCAAAATACG 59.647 40.000 0.00 0.00 41.78 3.06
793 4365 3.500680 CGTGCTAAGTAAAGGGAGCAAAA 59.499 43.478 0.00 0.00 45.92 2.44
1581 5161 1.043673 CCCGTGGTAGGAAGAGGGAG 61.044 65.000 0.00 0.00 41.26 4.30
1725 5305 1.186200 AGAGCATGTAGACGAGCCAA 58.814 50.000 0.00 0.00 0.00 4.52
1758 5338 6.492007 TCTCAAGAACAGCATCAAAAGATC 57.508 37.500 0.00 0.00 0.00 2.75
1802 5383 4.368565 AGCATAGCATGATCTGGTGAAT 57.631 40.909 0.00 0.00 36.79 2.57
1873 5491 5.739959 AGTTGTGTTGGCAAAAGGTTTATT 58.260 33.333 0.00 0.00 0.00 1.40
1881 5499 7.601886 CCATTTATCATAGTTGTGTTGGCAAAA 59.398 33.333 0.00 0.00 0.00 2.44
2011 5636 8.138928 TCTCTCAATAATATCATCCAATCGGT 57.861 34.615 0.00 0.00 0.00 4.69
2043 5668 8.611654 AAAAGCATAAGTGAAAATGAGCATTT 57.388 26.923 2.74 2.74 42.35 2.32
2112 5737 7.916914 AAGTATATCCACCAACAAGTTGTAC 57.083 36.000 9.37 0.00 38.85 2.90
2113 5738 9.661563 CTAAAGTATATCCACCAACAAGTTGTA 57.338 33.333 9.37 0.00 38.85 2.41
2114 5739 8.161425 ACTAAAGTATATCCACCAACAAGTTGT 58.839 33.333 1.64 1.64 38.85 3.32
2116 5741 8.161425 ACACTAAAGTATATCCACCAACAAGTT 58.839 33.333 0.00 0.00 0.00 2.66
2117 5742 7.686434 ACACTAAAGTATATCCACCAACAAGT 58.314 34.615 0.00 0.00 0.00 3.16
2118 5743 9.095065 GTACACTAAAGTATATCCACCAACAAG 57.905 37.037 0.00 0.00 0.00 3.16
2119 5744 8.595421 TGTACACTAAAGTATATCCACCAACAA 58.405 33.333 0.00 0.00 0.00 2.83
2120 5745 8.136563 TGTACACTAAAGTATATCCACCAACA 57.863 34.615 0.00 0.00 0.00 3.33
2121 5746 8.876790 GTTGTACACTAAAGTATATCCACCAAC 58.123 37.037 0.00 0.00 0.00 3.77
2122 5747 8.818860 AGTTGTACACTAAAGTATATCCACCAA 58.181 33.333 0.00 0.00 31.97 3.67
2123 5748 8.370266 AGTTGTACACTAAAGTATATCCACCA 57.630 34.615 0.00 0.00 31.97 4.17
2124 5749 9.741647 GTAGTTGTACACTAAAGTATATCCACC 57.258 37.037 0.00 0.00 39.86 4.61
2132 5757 9.874205 ACAAACAAGTAGTTGTACACTAAAGTA 57.126 29.630 16.18 0.00 46.68 2.24
2133 5758 8.662141 CACAAACAAGTAGTTGTACACTAAAGT 58.338 33.333 16.18 4.35 46.68 2.66
2134 5759 8.120465 CCACAAACAAGTAGTTGTACACTAAAG 58.880 37.037 16.18 3.81 46.68 1.85
2135 5760 7.823310 TCCACAAACAAGTAGTTGTACACTAAA 59.177 33.333 16.18 0.00 46.68 1.85
2136 5761 7.329499 TCCACAAACAAGTAGTTGTACACTAA 58.671 34.615 16.18 0.00 46.68 2.24
2137 5762 6.876155 TCCACAAACAAGTAGTTGTACACTA 58.124 36.000 16.18 0.00 46.68 2.74
2138 5763 5.736813 TCCACAAACAAGTAGTTGTACACT 58.263 37.500 16.18 0.00 46.68 3.55
2139 5764 6.613755 ATCCACAAACAAGTAGTTGTACAC 57.386 37.500 16.18 0.00 46.68 2.90
2140 5765 9.426837 GTATATCCACAAACAAGTAGTTGTACA 57.573 33.333 16.18 0.00 46.68 2.90
2141 5766 9.649167 AGTATATCCACAAACAAGTAGTTGTAC 57.351 33.333 16.18 6.91 46.68 2.90
2151 5776 9.999660 TGTACACTAAAGTATATCCACAAACAA 57.000 29.630 0.00 0.00 0.00 2.83
2180 5806 3.156293 CATCCATCCTCACAACCAACAA 58.844 45.455 0.00 0.00 0.00 2.83
2181 5807 2.794103 CATCCATCCTCACAACCAACA 58.206 47.619 0.00 0.00 0.00 3.33
2182 5808 1.474077 GCATCCATCCTCACAACCAAC 59.526 52.381 0.00 0.00 0.00 3.77
2183 5809 1.355381 AGCATCCATCCTCACAACCAA 59.645 47.619 0.00 0.00 0.00 3.67
2184 5810 0.994247 AGCATCCATCCTCACAACCA 59.006 50.000 0.00 0.00 0.00 3.67
2206 5833 2.943978 GCCTACGGTGTGGCTGACT 61.944 63.158 16.32 0.00 45.26 3.41
2269 5896 2.697425 CACTCTCGAAATGCCGCG 59.303 61.111 0.00 0.00 0.00 6.46
2272 5899 1.648467 GGCACCACTCTCGAAATGCC 61.648 60.000 0.00 0.00 45.26 4.40
2316 5943 3.781079 TCCGTCAATCAATTTGGCATC 57.219 42.857 0.00 0.00 40.06 3.91
2347 5974 2.027469 ACGTTGGGGATAGGAGTGAAAC 60.027 50.000 0.00 0.00 0.00 2.78
2424 6051 1.071471 GACATATGCACGGAGGGGG 59.929 63.158 1.58 0.00 0.00 5.40
2426 6053 0.034059 GAGGACATATGCACGGAGGG 59.966 60.000 1.58 0.00 0.00 4.30
2429 6056 1.040646 GAGGAGGACATATGCACGGA 58.959 55.000 1.58 0.00 0.00 4.69
2430 6057 0.034059 GGAGGAGGACATATGCACGG 59.966 60.000 1.58 0.00 0.00 4.94
2432 6059 2.611473 CGATGGAGGAGGACATATGCAC 60.611 54.545 1.58 0.00 0.00 4.57
2433 6060 1.620323 CGATGGAGGAGGACATATGCA 59.380 52.381 1.58 0.00 0.00 3.96
2435 6062 2.893489 TGACGATGGAGGAGGACATATG 59.107 50.000 0.00 0.00 0.00 1.78
2436 6063 2.894126 GTGACGATGGAGGAGGACATAT 59.106 50.000 0.00 0.00 0.00 1.78
2437 6064 2.307768 GTGACGATGGAGGAGGACATA 58.692 52.381 0.00 0.00 0.00 2.29
2438 6065 1.115467 GTGACGATGGAGGAGGACAT 58.885 55.000 0.00 0.00 0.00 3.06
2440 6067 1.115467 ATGTGACGATGGAGGAGGAC 58.885 55.000 0.00 0.00 0.00 3.85
2441 6068 1.482182 CAATGTGACGATGGAGGAGGA 59.518 52.381 0.00 0.00 0.00 3.71
2442 6069 1.208052 ACAATGTGACGATGGAGGAGG 59.792 52.381 0.00 0.00 0.00 4.30
2443 6070 2.674852 CAACAATGTGACGATGGAGGAG 59.325 50.000 0.00 0.00 0.00 3.69
2444 6071 2.698803 CAACAATGTGACGATGGAGGA 58.301 47.619 0.00 0.00 0.00 3.71
2445 6072 1.131126 GCAACAATGTGACGATGGAGG 59.869 52.381 0.00 0.00 0.00 4.30
2446 6073 1.805943 TGCAACAATGTGACGATGGAG 59.194 47.619 0.00 0.00 0.00 3.86
2447 6074 1.535028 GTGCAACAATGTGACGATGGA 59.465 47.619 0.00 0.00 36.32 3.41
2449 6076 1.594517 CGTGCAACAATGTGACGATG 58.405 50.000 6.94 0.00 36.96 3.84
2450 6077 0.516877 CCGTGCAACAATGTGACGAT 59.483 50.000 12.52 0.00 36.96 3.73
2451 6078 0.530870 TCCGTGCAACAATGTGACGA 60.531 50.000 12.52 0.10 36.96 4.20
2452 6079 0.516877 ATCCGTGCAACAATGTGACG 59.483 50.000 0.00 6.04 35.74 4.35
2453 6080 1.806542 AGATCCGTGCAACAATGTGAC 59.193 47.619 0.00 0.00 35.74 3.67
2454 6081 2.076100 GAGATCCGTGCAACAATGTGA 58.924 47.619 0.00 0.00 35.74 3.58
2455 6082 2.079158 AGAGATCCGTGCAACAATGTG 58.921 47.619 0.00 0.00 35.74 3.21
2456 6083 2.079158 CAGAGATCCGTGCAACAATGT 58.921 47.619 0.00 0.00 35.74 2.71
2457 6084 2.079158 ACAGAGATCCGTGCAACAATG 58.921 47.619 0.00 0.00 35.74 2.82
2458 6085 2.079158 CACAGAGATCCGTGCAACAAT 58.921 47.619 0.00 0.00 35.74 2.71
2459 6086 1.511850 CACAGAGATCCGTGCAACAA 58.488 50.000 0.00 0.00 35.74 2.83
2460 6087 0.320683 CCACAGAGATCCGTGCAACA 60.321 55.000 0.00 0.00 35.74 3.33
2461 6088 1.639298 GCCACAGAGATCCGTGCAAC 61.639 60.000 0.00 0.00 0.00 4.17
2462 6089 1.375908 GCCACAGAGATCCGTGCAA 60.376 57.895 0.00 0.00 0.00 4.08
2463 6090 2.265739 GCCACAGAGATCCGTGCA 59.734 61.111 2.71 0.00 0.00 4.57
2464 6091 2.512515 GGCCACAGAGATCCGTGC 60.513 66.667 0.00 0.00 0.00 5.34
2465 6092 1.153489 CAGGCCACAGAGATCCGTG 60.153 63.158 5.01 0.00 0.00 4.94
2466 6093 3.023949 GCAGGCCACAGAGATCCGT 62.024 63.158 5.01 0.00 0.00 4.69
2467 6094 2.202987 GCAGGCCACAGAGATCCG 60.203 66.667 5.01 0.00 0.00 4.18
2477 6408 3.214190 ATGCTGTTCCTGCAGGCCA 62.214 57.895 28.91 23.57 41.22 5.36
2513 6451 2.486907 GGCTCTGGATCAGGGATTTGAG 60.487 54.545 0.00 0.00 32.95 3.02
2629 6579 3.944250 AAGCCCACTGCCCATTCCG 62.944 63.158 0.00 0.00 42.71 4.30
2632 6582 2.284112 CCAAGCCCACTGCCCATT 60.284 61.111 0.00 0.00 42.71 3.16
2728 6678 1.451504 CTCCTCACTGTTGTGCCCA 59.548 57.895 0.00 0.00 43.49 5.36


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

AutoCloner maintained by Alex Coulton.