Multiple sequence alignment - TraesCS5D01G519000

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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 TraesCS5D01G519000 chr5D 100.000 3210 0 0 1 3210 539997084 539993875 0.000000e+00 5928.0
1 TraesCS5D01G519000 chr5D 96.608 973 26 3 1 973 529803466 529804431 0.000000e+00 1607.0
2 TraesCS5D01G519000 chr5D 96.146 986 25 6 1 980 559114358 559113380 0.000000e+00 1598.0
3 TraesCS5D01G519000 chr5D 96.300 973 31 3 1 973 267621220 267620253 0.000000e+00 1592.0
4 TraesCS5D01G519000 chr5B 89.524 1575 81 34 972 2502 682204107 682202573 0.000000e+00 1917.0
5 TraesCS5D01G519000 chr5B 94.863 292 6 6 2899 3190 682198621 682198339 6.320000e-122 448.0
6 TraesCS5D01G519000 chr5B 74.302 179 37 9 1769 1942 276189252 276189426 2.070000e-07 67.6
7 TraesCS5D01G519000 chr1D 96.414 976 29 5 1 976 470207786 470206817 0.000000e+00 1604.0
8 TraesCS5D01G519000 chr3D 96.201 974 32 4 1 973 336809833 336808864 0.000000e+00 1589.0
9 TraesCS5D01G519000 chr3D 96.111 977 31 4 1 975 602048853 602047882 0.000000e+00 1587.0
10 TraesCS5D01G519000 chr3D 95.902 976 30 4 1 973 80219452 80220420 0.000000e+00 1572.0
11 TraesCS5D01G519000 chr3A 95.803 977 38 2 1 977 697433827 697434800 0.000000e+00 1574.0
12 TraesCS5D01G519000 chr6D 95.590 975 36 6 1 973 451667371 451668340 0.000000e+00 1555.0
13 TraesCS5D01G519000 chr6D 100.000 28 0 0 1806 1833 9065646 9065673 6.000000e-03 52.8
14 TraesCS5D01G519000 chr4A 83.357 1400 130 51 1504 2840 627943795 627942436 0.000000e+00 1199.0
15 TraesCS5D01G519000 chr4A 88.048 251 16 8 2948 3190 627920057 627919813 5.240000e-73 285.0
16 TraesCS5D01G519000 chr4A 74.373 359 89 3 1103 1460 55647040 55646684 1.990000e-32 150.0
17 TraesCS5D01G519000 chr4A 95.652 46 2 0 2901 2946 627920138 627920093 1.240000e-09 75.0
18 TraesCS5D01G519000 chr4A 96.875 32 1 0 1806 1837 595773595 595773626 2.000000e-03 54.7
19 TraesCS5D01G519000 chr2B 74.372 199 27 20 1633 1819 206291203 206291017 2.670000e-06 63.9
20 TraesCS5D01G519000 chr5A 85.484 62 6 3 1603 1664 566776251 566776309 9.620000e-06 62.1
21 TraesCS5D01G519000 chr5A 100.000 28 0 0 1904 1931 554245252 554245279 6.000000e-03 52.8
22 TraesCS5D01G519000 chr6B 92.500 40 2 1 1624 1662 593549588 593549549 4.470000e-04 56.5
23 TraesCS5D01G519000 chr6B 100.000 28 0 0 1806 1833 16611144 16611171 6.000000e-03 52.8
24 TraesCS5D01G519000 chrUn 100.000 28 0 0 1806 1833 351892274 351892247 6.000000e-03 52.8
25 TraesCS5D01G519000 chr4B 100.000 28 0 0 1808 1835 30744291 30744318 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 TraesCS5D01G519000 chr5D 539993875 539997084 3209 True 5928.0 5928 100.0000 1 3210 1 chr5D.!!$R2 3209
1 TraesCS5D01G519000 chr5D 529803466 529804431 965 False 1607.0 1607 96.6080 1 973 1 chr5D.!!$F1 972
2 TraesCS5D01G519000 chr5D 559113380 559114358 978 True 1598.0 1598 96.1460 1 980 1 chr5D.!!$R3 979
3 TraesCS5D01G519000 chr5D 267620253 267621220 967 True 1592.0 1592 96.3000 1 973 1 chr5D.!!$R1 972
4 TraesCS5D01G519000 chr5B 682198339 682204107 5768 True 1182.5 1917 92.1935 972 3190 2 chr5B.!!$R1 2218
5 TraesCS5D01G519000 chr1D 470206817 470207786 969 True 1604.0 1604 96.4140 1 976 1 chr1D.!!$R1 975
6 TraesCS5D01G519000 chr3D 336808864 336809833 969 True 1589.0 1589 96.2010 1 973 1 chr3D.!!$R1 972
7 TraesCS5D01G519000 chr3D 602047882 602048853 971 True 1587.0 1587 96.1110 1 975 1 chr3D.!!$R2 974
8 TraesCS5D01G519000 chr3D 80219452 80220420 968 False 1572.0 1572 95.9020 1 973 1 chr3D.!!$F1 972
9 TraesCS5D01G519000 chr3A 697433827 697434800 973 False 1574.0 1574 95.8030 1 977 1 chr3A.!!$F1 976
10 TraesCS5D01G519000 chr6D 451667371 451668340 969 False 1555.0 1555 95.5900 1 973 1 chr6D.!!$F2 972
11 TraesCS5D01G519000 chr4A 627942436 627943795 1359 True 1199.0 1199 83.3570 1504 2840 1 chr4A.!!$R2 1336

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
867 885 0.526954 CAACTCCTTATACCGCGCGT 60.527 55.0 29.95 18.85 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2616 2713 0.319383 AAGCTATCTGCCGCGATCTG 60.319 55.0 8.23 3.06 44.23 2.9 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
120 121 2.483877 TGGTCTTCGAAATGCATGTCAC 59.516 45.455 17.08 7.06 0.00 3.67
569 578 3.640000 CATAAAGAGGCCGCGCGG 61.640 66.667 43.13 43.13 38.57 6.46
769 787 0.801836 GAGAAGAGAGAGTGCAGCGC 60.802 60.000 0.00 0.00 0.00 5.92
770 788 2.126149 AAGAGAGAGTGCAGCGCG 60.126 61.111 0.00 0.00 0.00 6.86
867 885 0.526954 CAACTCCTTATACCGCGCGT 60.527 55.000 29.95 18.85 0.00 6.01
997 1015 1.755395 CCAGGTGATGGGCATGGTG 60.755 63.158 0.00 0.00 46.36 4.17
1089 1107 4.747108 GTCGCTGATGCATTTAGTACTGAT 59.253 41.667 5.39 0.00 39.64 2.90
1099 1117 5.763088 CATTTAGTACTGATCTGCGAGCTA 58.237 41.667 5.39 0.00 0.00 3.32
1131 1149 2.579201 GACCTTGCGGCTGAGCTA 59.421 61.111 3.72 0.00 38.13 3.32
1141 1159 1.743252 GCTGAGCTAGGTGTGGTGC 60.743 63.158 0.00 0.00 0.00 5.01
1146 1164 1.004918 GCTAGGTGTGGTGCGTCTT 60.005 57.895 0.00 0.00 0.00 3.01
1153 1171 1.588404 GTGTGGTGCGTCTTATGATCG 59.412 52.381 0.00 0.00 0.00 3.69
1154 1172 1.474879 TGTGGTGCGTCTTATGATCGA 59.525 47.619 0.00 0.00 0.00 3.59
1162 1180 4.224433 GCGTCTTATGATCGAAACGGATA 58.776 43.478 0.00 0.00 0.00 2.59
1179 1197 0.036164 ATACGCTCCTGGTTGTGCAA 59.964 50.000 0.00 0.00 0.00 4.08
1180 1198 0.602638 TACGCTCCTGGTTGTGCAAG 60.603 55.000 0.00 0.00 0.00 4.01
1193 1211 0.517316 GTGCAAGCCCTTAACAGACG 59.483 55.000 0.00 0.00 0.00 4.18
1211 1229 2.548057 GACGTGCTCCAGATTGTTCAAA 59.452 45.455 0.00 0.00 0.00 2.69
1280 1298 4.214986 TCTCTTCTTGTGTGTTTGTCCA 57.785 40.909 0.00 0.00 0.00 4.02
1288 1306 2.680841 TGTGTGTTTGTCCACTGTAAGC 59.319 45.455 0.00 0.00 37.60 3.09
1340 1358 0.621082 AAGTTAGGCTTGGCTCTCCC 59.379 55.000 0.00 0.00 35.80 4.30
1348 1366 0.401738 CTTGGCTCTCCCTGTTGGAA 59.598 55.000 0.00 0.00 44.57 3.53
1366 1384 3.244770 TGGAAAAGTCCTTGTAGCCGATT 60.245 43.478 0.00 0.00 45.22 3.34
1369 1387 5.007724 GGAAAAGTCCTTGTAGCCGATTATG 59.992 44.000 0.00 0.00 41.24 1.90
1382 1400 2.575532 CGATTATGTGGTTCCAGCCAT 58.424 47.619 0.00 0.00 41.08 4.40
1433 1451 8.421784 TGTAGCCCAGACTATTGAGTAATAAAG 58.578 37.037 0.00 0.00 35.45 1.85
1437 1455 8.097662 GCCCAGACTATTGAGTAATAAAGCTAT 58.902 37.037 0.00 0.00 35.45 2.97
1633 1654 6.983307 TGAACAATTTTGGAATTCGTGAACAT 59.017 30.769 0.00 0.00 33.25 2.71
1799 1822 6.669125 TTCAGGAACAATTGTGGAATTCAT 57.331 33.333 12.82 0.00 28.65 2.57
1802 1825 7.829725 TCAGGAACAATTGTGGAATTCATAAG 58.170 34.615 12.82 0.00 30.11 1.73
2102 2172 8.433421 AATCTTGTATACAGTAATGTTTCCGG 57.567 34.615 0.00 0.00 0.00 5.14
2323 2412 7.698836 AAAACAGAAAATCAATGAAACCGAG 57.301 32.000 0.00 0.00 0.00 4.63
2327 2416 7.141363 ACAGAAAATCAATGAAACCGAGAAAG 58.859 34.615 0.00 0.00 0.00 2.62
2340 2429 8.856103 TGAAACCGAGAAAGGAAAAATAAGAAT 58.144 29.630 0.00 0.00 34.73 2.40
2370 2459 9.930693 ATAAAATAAAAACCGATAAAGGCAACA 57.069 25.926 0.00 0.00 41.41 3.33
2504 2593 0.526211 GGAGTGAACGAAAATGGGCC 59.474 55.000 0.00 0.00 0.00 5.80
2516 2605 3.615224 AAATGGGCCTGCTTTGTAATG 57.385 42.857 4.53 0.00 0.00 1.90
2521 2610 1.064060 GGCCTGCTTTGTAATGTAGCG 59.936 52.381 0.00 0.00 37.73 4.26
2523 2612 1.737236 CCTGCTTTGTAATGTAGCGCA 59.263 47.619 11.47 0.00 37.73 6.09
2554 2643 0.980754 TTCAGGCGAGGGGAGCATAA 60.981 55.000 0.00 0.00 36.08 1.90
2555 2644 1.070445 CAGGCGAGGGGAGCATAAG 59.930 63.158 0.00 0.00 36.08 1.73
2556 2645 2.281139 GGCGAGGGGAGCATAAGC 60.281 66.667 0.00 0.00 42.56 3.09
2640 2737 1.645997 GCGGCAGATAGCTTTGCTC 59.354 57.895 14.58 6.69 44.79 4.26
2643 6382 1.216122 GGCAGATAGCTTTGCTCGAG 58.784 55.000 8.45 8.45 44.79 4.04
2662 6401 1.522580 GAGGAGGCCAGATCGCAAC 60.523 63.158 5.01 0.00 0.00 4.17
2709 6448 4.451150 CTTAGCGGCGGACCAGCA 62.451 66.667 9.78 0.00 37.76 4.41
2719 6458 2.807045 GACCAGCACTGCGTCTCG 60.807 66.667 10.29 0.00 32.09 4.04
2720 6459 3.268965 GACCAGCACTGCGTCTCGA 62.269 63.158 10.29 0.00 32.09 4.04
2725 6464 1.330829 CAGCACTGCGTCTCGACTATA 59.669 52.381 0.00 0.00 0.00 1.31
2758 6497 3.124921 GGCCGGTCGATGTTGGTG 61.125 66.667 1.90 0.00 0.00 4.17
2784 6523 1.463444 AGCCGTTATGTTTCTGCGTTC 59.537 47.619 0.00 0.00 0.00 3.95
2786 6525 2.724839 GCCGTTATGTTTCTGCGTTCAG 60.725 50.000 0.00 0.00 41.67 3.02
2787 6526 2.478894 CCGTTATGTTTCTGCGTTCAGT 59.521 45.455 0.00 0.00 41.10 3.41
2808 6547 6.206634 TCAGTAATGAATGTTCCTGTGGTTTC 59.793 38.462 0.00 0.00 0.00 2.78
2846 6629 1.589993 CGATGAGCCGAGCAACGAT 60.590 57.895 4.96 0.00 45.77 3.73
2858 6641 4.318760 CCGAGCAACGATGGTACAAATATG 60.319 45.833 0.00 0.00 45.77 1.78
2860 6643 8.404137 CCGAGCAACGATGGTACAAATATGAC 62.404 46.154 0.00 0.00 45.77 3.06
2870 6653 6.651086 TGGTACAAATATGACGGGTAATTCA 58.349 36.000 0.00 0.00 31.92 2.57
2871 6654 6.539464 TGGTACAAATATGACGGGTAATTCAC 59.461 38.462 0.00 0.00 31.92 3.18
2872 6655 6.764560 GGTACAAATATGACGGGTAATTCACT 59.235 38.462 0.00 0.00 0.00 3.41
2873 6656 6.920569 ACAAATATGACGGGTAATTCACTC 57.079 37.500 0.00 0.00 0.00 3.51
2874 6657 5.820947 ACAAATATGACGGGTAATTCACTCC 59.179 40.000 0.00 0.00 0.00 3.85
2875 6658 5.888982 AATATGACGGGTAATTCACTCCT 57.111 39.130 0.00 0.00 0.00 3.69
2876 6659 5.888982 ATATGACGGGTAATTCACTCCTT 57.111 39.130 0.00 0.00 0.00 3.36
2877 6660 4.569719 ATGACGGGTAATTCACTCCTTT 57.430 40.909 0.00 0.00 0.00 3.11
2878 6661 4.360951 TGACGGGTAATTCACTCCTTTT 57.639 40.909 0.00 0.00 0.00 2.27
2879 6662 4.721132 TGACGGGTAATTCACTCCTTTTT 58.279 39.130 0.00 0.00 0.00 1.94
2973 6756 4.545610 AGAAACAGTTTGTTGTGTGTGTG 58.454 39.130 2.34 0.00 40.14 3.82
2974 6757 4.037446 AGAAACAGTTTGTTGTGTGTGTGT 59.963 37.500 2.34 0.00 40.14 3.72
2975 6758 3.281341 ACAGTTTGTTGTGTGTGTGTG 57.719 42.857 0.00 0.00 0.00 3.82
2976 6759 2.621055 ACAGTTTGTTGTGTGTGTGTGT 59.379 40.909 0.00 0.00 0.00 3.72
2977 6760 2.979151 CAGTTTGTTGTGTGTGTGTGTG 59.021 45.455 0.00 0.00 0.00 3.82
2978 6761 2.621055 AGTTTGTTGTGTGTGTGTGTGT 59.379 40.909 0.00 0.00 0.00 3.72
2979 6762 2.695613 TTGTTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
3153 6936 1.338769 GCACGGGAACTACAATCAGGT 60.339 52.381 0.00 0.00 0.00 4.00
3176 6959 0.880278 GTGACCTGCTCTGCGAACAA 60.880 55.000 0.00 0.00 0.00 2.83
3177 6960 0.601046 TGACCTGCTCTGCGAACAAG 60.601 55.000 0.00 0.00 0.00 3.16
3178 6961 0.601311 GACCTGCTCTGCGAACAAGT 60.601 55.000 0.00 0.00 0.00 3.16
3179 6962 0.679505 ACCTGCTCTGCGAACAAGTA 59.320 50.000 0.00 0.00 0.00 2.24
3190 6973 5.642063 TCTGCGAACAAGTATAAAAGGGAAG 59.358 40.000 0.00 0.00 0.00 3.46
3191 6974 5.553123 TGCGAACAAGTATAAAAGGGAAGA 58.447 37.500 0.00 0.00 0.00 2.87
3192 6975 5.642063 TGCGAACAAGTATAAAAGGGAAGAG 59.358 40.000 0.00 0.00 0.00 2.85
3193 6976 5.642491 GCGAACAAGTATAAAAGGGAAGAGT 59.358 40.000 0.00 0.00 0.00 3.24
3194 6977 6.183360 GCGAACAAGTATAAAAGGGAAGAGTC 60.183 42.308 0.00 0.00 0.00 3.36
3195 6978 6.872020 CGAACAAGTATAAAAGGGAAGAGTCA 59.128 38.462 0.00 0.00 0.00 3.41
3196 6979 7.386848 CGAACAAGTATAAAAGGGAAGAGTCAA 59.613 37.037 0.00 0.00 0.00 3.18
3197 6980 9.232473 GAACAAGTATAAAAGGGAAGAGTCAAT 57.768 33.333 0.00 0.00 0.00 2.57
3198 6981 9.588096 AACAAGTATAAAAGGGAAGAGTCAATT 57.412 29.630 0.00 0.00 0.00 2.32
3204 6987 8.904099 ATAAAAGGGAAGAGTCAATTATACCG 57.096 34.615 0.00 0.00 0.00 4.02
3205 6988 4.957684 AGGGAAGAGTCAATTATACCGG 57.042 45.455 0.00 0.00 0.00 5.28
3206 6989 4.296056 AGGGAAGAGTCAATTATACCGGT 58.704 43.478 13.98 13.98 0.00 5.28
3207 6990 4.101119 AGGGAAGAGTCAATTATACCGGTG 59.899 45.833 19.93 0.00 0.00 4.94
3208 6991 4.377897 GGAAGAGTCAATTATACCGGTGG 58.622 47.826 19.93 0.00 0.00 4.61
3209 6992 4.141779 GGAAGAGTCAATTATACCGGTGGT 60.142 45.833 19.93 8.60 40.16 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
421 429 1.228657 GCGAAGAAGAACAAGGCGGT 61.229 55.000 0.00 0.00 0.00 5.68
691 709 4.697756 CCCCATGGACGCACGTGT 62.698 66.667 15.22 0.00 0.00 4.49
693 711 4.697756 CACCCCATGGACGCACGT 62.698 66.667 15.22 0.00 34.81 4.49
913 931 3.057174 CCGTAAATTTGGCCAGTTTAGCA 60.057 43.478 19.80 4.72 0.00 3.49
991 1009 1.303561 CCACACCCCAGACACCATG 60.304 63.158 0.00 0.00 0.00 3.66
997 1015 2.113139 CACCACCACACCCCAGAC 59.887 66.667 0.00 0.00 0.00 3.51
1057 1075 1.212616 GCATCAGCGACATGGTCTAC 58.787 55.000 0.00 0.00 0.00 2.59
1059 1077 0.179702 ATGCATCAGCGACATGGTCT 59.820 50.000 0.00 0.00 46.23 3.85
1089 1107 1.035923 CCTTCTCCATAGCTCGCAGA 58.964 55.000 0.00 0.00 0.00 4.26
1099 1117 1.302907 AGGTCCATTGCCTTCTCCAT 58.697 50.000 0.00 0.00 31.04 3.41
1131 1149 0.973632 TCATAAGACGCACCACACCT 59.026 50.000 0.00 0.00 0.00 4.00
1141 1159 4.317551 CGTATCCGTTTCGATCATAAGACG 59.682 45.833 0.00 0.00 0.00 4.18
1146 1164 3.365666 GGAGCGTATCCGTTTCGATCATA 60.366 47.826 0.00 0.00 40.86 2.15
1162 1180 1.893808 CTTGCACAACCAGGAGCGT 60.894 57.895 0.00 0.00 0.00 5.07
1170 1188 1.000274 CTGTTAAGGGCTTGCACAACC 60.000 52.381 0.00 0.00 0.00 3.77
1179 1197 0.037232 GAGCACGTCTGTTAAGGGCT 60.037 55.000 0.00 0.00 0.00 5.19
1180 1198 1.019805 GGAGCACGTCTGTTAAGGGC 61.020 60.000 0.00 0.00 0.00 5.19
1193 1211 4.320788 CCTCTTTTGAACAATCTGGAGCAC 60.321 45.833 0.00 0.00 0.00 4.40
1211 1229 2.309755 TCTTCAATCACATGGGCCTCTT 59.690 45.455 4.53 0.00 0.00 2.85
1263 1281 3.417101 ACAGTGGACAAACACACAAGAA 58.583 40.909 0.00 0.00 43.72 2.52
1340 1358 3.253432 GGCTACAAGGACTTTTCCAACAG 59.747 47.826 0.00 0.00 45.72 3.16
1348 1366 4.876107 CACATAATCGGCTACAAGGACTTT 59.124 41.667 0.00 0.00 0.00 2.66
1366 1384 2.824936 CAACAATGGCTGGAACCACATA 59.175 45.455 0.00 0.00 44.17 2.29
1369 1387 0.319813 GCAACAATGGCTGGAACCAC 60.320 55.000 0.00 0.00 44.17 4.16
1382 1400 3.411446 CCCATTACAGACTCAGCAACAA 58.589 45.455 0.00 0.00 0.00 2.83
1771 1794 5.867903 TCCACAATTGTTCCTGAATGTTT 57.132 34.783 8.77 0.00 0.00 2.83
1774 1797 6.457355 TGAATTCCACAATTGTTCCTGAATG 58.543 36.000 8.77 0.00 31.94 2.67
1884 1909 8.854979 TGAATTTCAAATATGCTACGGAATTG 57.145 30.769 0.00 0.00 0.00 2.32
2079 2149 6.814644 CACCGGAAACATTACTGTATACAAGA 59.185 38.462 9.46 0.00 33.36 3.02
2081 2151 6.465948 ACACCGGAAACATTACTGTATACAA 58.534 36.000 9.46 0.00 33.36 2.41
2478 2567 3.374220 TTTTCGTTCACTCCTTCGCTA 57.626 42.857 0.00 0.00 0.00 4.26
2489 2578 0.539438 AGCAGGCCCATTTTCGTTCA 60.539 50.000 0.00 0.00 0.00 3.18
2504 2593 2.159430 TGTGCGCTACATTACAAAGCAG 59.841 45.455 9.73 0.00 35.98 4.24
2516 2605 3.186409 TGAAGACTTTTCATGTGCGCTAC 59.814 43.478 9.73 5.95 0.00 3.58
2521 2610 2.666619 CGCCTGAAGACTTTTCATGTGC 60.667 50.000 0.00 0.00 0.00 4.57
2523 2612 3.070018 CTCGCCTGAAGACTTTTCATGT 58.930 45.455 0.00 0.00 0.00 3.21
2566 2655 2.368105 GCATGATACCTCGCGCGAG 61.368 63.158 44.25 44.25 41.63 5.03
2567 2656 2.354656 GCATGATACCTCGCGCGA 60.355 61.111 32.60 32.60 0.00 5.87
2568 2657 3.756677 CGCATGATACCTCGCGCG 61.757 66.667 26.76 26.76 41.38 6.86
2616 2713 0.319383 AAGCTATCTGCCGCGATCTG 60.319 55.000 8.23 3.06 44.23 2.90
2640 2737 2.560119 CGATCTGGCCTCCTCCTCG 61.560 68.421 3.32 0.15 0.00 4.63
2643 6382 2.735772 TTGCGATCTGGCCTCCTCC 61.736 63.158 3.32 0.00 0.00 4.30
2686 6425 3.838271 TCCGCCGCTAAGCTCCAG 61.838 66.667 0.00 0.00 0.00 3.86
2687 6426 4.143333 GTCCGCCGCTAAGCTCCA 62.143 66.667 0.00 0.00 0.00 3.86
2688 6427 4.893601 GGTCCGCCGCTAAGCTCC 62.894 72.222 0.00 0.00 0.00 4.70
2719 6458 4.201930 CCGACAACACTCACCTCTATAGTC 60.202 50.000 0.00 0.00 0.00 2.59
2720 6459 3.695060 CCGACAACACTCACCTCTATAGT 59.305 47.826 0.00 0.00 0.00 2.12
2725 6464 1.367840 GCCGACAACACTCACCTCT 59.632 57.895 0.00 0.00 0.00 3.69
2758 6497 4.588278 GCAGAAACATAACGGCTAATGAC 58.412 43.478 0.00 0.00 0.00 3.06
2784 6523 5.964958 AACCACAGGAACATTCATTACTG 57.035 39.130 0.00 0.00 44.89 2.74
2786 6525 5.180492 TCGAAACCACAGGAACATTCATTAC 59.820 40.000 0.00 0.00 0.00 1.89
2787 6526 5.180492 GTCGAAACCACAGGAACATTCATTA 59.820 40.000 0.00 0.00 0.00 1.90
2808 6547 2.159653 CGGCTTGATCTTTTTGAGGTCG 60.160 50.000 0.00 0.00 38.42 4.79
2846 6629 6.539464 GTGAATTACCCGTCATATTTGTACCA 59.461 38.462 0.00 0.00 0.00 3.25
2891 6674 4.392138 ACCTAAGAGTGAATTACGCTTTGC 59.608 41.667 0.00 0.00 45.50 3.68
2892 6675 7.544566 TCTTACCTAAGAGTGAATTACGCTTTG 59.455 37.037 0.00 0.00 45.50 2.77
2893 6676 7.609056 TCTTACCTAAGAGTGAATTACGCTTT 58.391 34.615 0.00 0.00 45.50 3.51
2895 6678 6.770746 TCTTACCTAAGAGTGAATTACGCT 57.229 37.500 0.00 0.00 41.50 5.07
2958 6741 2.723658 CACACACACACACACAACAAAC 59.276 45.455 0.00 0.00 0.00 2.93
2973 6756 2.212652 TCTGCATCAACAGACACACAC 58.787 47.619 0.00 0.00 41.72 3.82
2974 6757 2.618442 TCTGCATCAACAGACACACA 57.382 45.000 0.00 0.00 41.72 3.72
3017 6800 5.109210 GGGTGTGTTTCTTTCTGGAAAAAG 58.891 41.667 0.00 0.00 37.02 2.27
3067 6850 6.107343 CCTAGAGAAAGTAAGGCTAAACCAC 58.893 44.000 0.00 0.00 43.14 4.16
3153 6936 1.595109 CGCAGAGCAGGTCACACAA 60.595 57.895 1.66 0.00 0.00 3.33
3178 6961 9.991906 CGGTATAATTGACTCTTCCCTTTTATA 57.008 33.333 0.00 0.00 0.00 0.98
3179 6962 7.937394 CCGGTATAATTGACTCTTCCCTTTTAT 59.063 37.037 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.