Multiple sequence alignment - TraesCS6A01G046100

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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 TraesCS6A01G046100 chr6A 100.000 2447 0 0 1 2447 23647324 23649770 0.000000e+00 4519.0
1 TraesCS6A01G046100 chr6A 91.959 1256 84 10 803 2051 23630588 23631833 0.000000e+00 1744.0
2 TraesCS6A01G046100 chr6A 92.795 458 32 1 1 458 600762217 600761761 0.000000e+00 662.0
3 TraesCS6A01G046100 chr6A 93.421 152 9 1 2210 2361 23631903 23632053 8.810000e-55 224.0
4 TraesCS6A01G046100 chr6A 88.158 76 9 0 1951 2026 23631828 23631903 9.320000e-15 91.6
5 TraesCS6A01G046100 chr6A 94.340 53 3 0 2395 2447 23632052 23632104 5.610000e-12 82.4
6 TraesCS6A01G046100 chr6B 93.900 918 49 4 803 1719 41442630 41443541 0.000000e+00 1378.0
7 TraesCS6A01G046100 chr6B 91.928 223 17 1 2139 2361 41445702 41445923 6.570000e-81 311.0
8 TraesCS6A01G046100 chr6B 96.226 53 2 0 2395 2447 41445922 41445974 1.210000e-13 87.9
9 TraesCS6A01G046100 chr3D 93.540 805 50 2 1 805 552414424 552413622 0.000000e+00 1197.0
10 TraesCS6A01G046100 chr3D 88.710 806 85 5 1 805 51733225 51732425 0.000000e+00 979.0
11 TraesCS6A01G046100 chr1D 93.292 805 53 1 1 805 383698511 383697708 0.000000e+00 1186.0
12 TraesCS6A01G046100 chr2B 91.553 805 67 1 1 805 110541478 110540675 0.000000e+00 1109.0
13 TraesCS6A01G046100 chr2B 91.758 364 27 3 1 364 506365116 506364756 1.010000e-138 503.0
14 TraesCS6A01G046100 chr2B 90.000 370 37 0 436 805 506364758 506364389 1.700000e-131 479.0
15 TraesCS6A01G046100 chr2B 73.974 780 186 16 22 793 17210742 17211512 1.420000e-77 300.0
16 TraesCS6A01G046100 chr6D 93.093 666 42 1 803 1468 25636234 25636895 0.000000e+00 972.0
17 TraesCS6A01G046100 chr6D 85.681 433 41 11 1477 1900 25636973 25637393 1.040000e-118 436.0
18 TraesCS6A01G046100 chr6D 91.667 228 18 1 2134 2361 25637738 25637964 5.080000e-82 315.0
19 TraesCS6A01G046100 chr6D 96.226 53 2 0 2395 2447 25637963 25638015 1.210000e-13 87.9
20 TraesCS6A01G046100 chr1B 88.089 806 93 3 1 805 205876049 205876852 0.000000e+00 953.0
21 TraesCS6A01G046100 chr5A 79.058 807 158 9 2 805 554597997 554597199 5.950000e-151 544.0
22 TraesCS6A01G046100 chr2D 77.586 812 167 11 1 805 194802185 194801382 6.120000e-131 477.0


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 TraesCS6A01G046100 chr6A 23647324 23649770 2446 False 4519.000 4519 100.00000 1 2447 1 chr6A.!!$F1 2446
1 TraesCS6A01G046100 chr6A 23630588 23632104 1516 False 535.500 1744 91.96950 803 2447 4 chr6A.!!$F2 1644
2 TraesCS6A01G046100 chr6B 41442630 41445974 3344 False 592.300 1378 94.01800 803 2447 3 chr6B.!!$F1 1644
3 TraesCS6A01G046100 chr3D 552413622 552414424 802 True 1197.000 1197 93.54000 1 805 1 chr3D.!!$R2 804
4 TraesCS6A01G046100 chr3D 51732425 51733225 800 True 979.000 979 88.71000 1 805 1 chr3D.!!$R1 804
5 TraesCS6A01G046100 chr1D 383697708 383698511 803 True 1186.000 1186 93.29200 1 805 1 chr1D.!!$R1 804
6 TraesCS6A01G046100 chr2B 110540675 110541478 803 True 1109.000 1109 91.55300 1 805 1 chr2B.!!$R1 804
7 TraesCS6A01G046100 chr2B 506364389 506365116 727 True 491.000 503 90.87900 1 805 2 chr2B.!!$R2 804
8 TraesCS6A01G046100 chr2B 17210742 17211512 770 False 300.000 300 73.97400 22 793 1 chr2B.!!$F1 771
9 TraesCS6A01G046100 chr6D 25636234 25638015 1781 False 452.725 972 91.66675 803 2447 4 chr6D.!!$F1 1644
10 TraesCS6A01G046100 chr1B 205876049 205876852 803 False 953.000 953 88.08900 1 805 1 chr1B.!!$F1 804
11 TraesCS6A01G046100 chr5A 554597199 554597997 798 True 544.000 544 79.05800 2 805 1 chr5A.!!$R1 803
12 TraesCS6A01G046100 chr2D 194801382 194802185 803 True 477.000 477 77.58600 1 805 1 chr2D.!!$R1 804

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
96 97 0.915364 GGGGGCATGAAGAAGACTCT 59.085 55.0 0.0 0.0 0.0 3.24 F
389 390 1.009829 GCTACGCAAACCCAGATCAG 58.990 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1221 1226 0.179059 ACGCATAATGGACGATGGCA 60.179 50.0 0.0 0.0 0.0 4.92 R
2117 4013 0.041535 TACCCCCACACGACCATAGT 59.958 55.0 0.0 0.0 0.0 2.12 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
96 97 0.915364 GGGGGCATGAAGAAGACTCT 59.085 55.000 0.00 0.00 0.00 3.24
146 147 2.152016 GGTGTTTAGCCTGTTGAGGTC 58.848 52.381 0.00 0.00 42.15 3.85
285 286 3.512516 GCCATTGAGCAGCGTCCC 61.513 66.667 0.00 0.00 0.00 4.46
389 390 1.009829 GCTACGCAAACCCAGATCAG 58.990 55.000 0.00 0.00 0.00 2.90
545 547 3.288964 ACGGAAACCTATGAGATCTCGT 58.711 45.455 20.91 20.91 0.00 4.18
593 595 1.889170 CTTTCCCAAGGAAGGAAGCAC 59.111 52.381 0.00 0.00 44.07 4.40
673 676 3.057946 AGAGAGGAGCGTGCAAAAATTTC 60.058 43.478 0.00 0.00 0.00 2.17
678 681 3.740321 GGAGCGTGCAAAAATTTCAATGA 59.260 39.130 0.00 0.00 0.00 2.57
842 845 1.209504 TCTCTTATTTCCCTGCCACCG 59.790 52.381 0.00 0.00 0.00 4.94
861 864 4.565564 CACCGTAAGTCCACATTAACTAGC 59.434 45.833 0.00 0.00 0.00 3.42
867 870 9.395707 CGTAAGTCCACATTAACTAGCTATTAG 57.604 37.037 0.00 0.00 35.39 1.73
885 890 7.339212 AGCTATTAGTTGGCACATTTCACATTA 59.661 33.333 0.00 0.00 39.30 1.90
886 891 8.137437 GCTATTAGTTGGCACATTTCACATTAT 58.863 33.333 0.00 0.00 39.30 1.28
892 897 7.546667 AGTTGGCACATTTCACATTATTGAATC 59.453 33.333 0.00 0.00 39.30 2.52
918 923 5.972107 ACTGATTTGCTTATGCTTGTTCT 57.028 34.783 1.96 0.00 40.48 3.01
933 938 4.697352 GCTTGTTCTCTATGGTGTGAATGT 59.303 41.667 0.00 0.00 0.00 2.71
934 939 5.874810 GCTTGTTCTCTATGGTGTGAATGTA 59.125 40.000 0.00 0.00 0.00 2.29
935 940 6.540189 GCTTGTTCTCTATGGTGTGAATGTAT 59.460 38.462 0.00 0.00 0.00 2.29
936 941 7.710907 GCTTGTTCTCTATGGTGTGAATGTATA 59.289 37.037 0.00 0.00 0.00 1.47
967 972 6.751514 TTGTTAAGCTGTGTTTCTCTTTCA 57.248 33.333 0.00 0.00 0.00 2.69
1010 1015 2.950975 TGTTCAGAGCAATGCTTGACAA 59.049 40.909 9.91 3.67 39.88 3.18
1073 1078 2.031870 CGTGTCCTATGATGTCCTCCA 58.968 52.381 0.00 0.00 0.00 3.86
1081 1086 4.891756 CCTATGATGTCCTCCATGCTTTTT 59.108 41.667 0.00 0.00 32.56 1.94
1101 1106 1.927487 TCCACTACATGTACACGGGT 58.073 50.000 0.08 0.00 0.00 5.28
1200 1205 2.820059 ACTGCGAGAAGTTCATCACA 57.180 45.000 5.50 0.11 0.00 3.58
1221 1226 2.925724 TCCAAGGTGAACAACGACAAT 58.074 42.857 0.00 0.00 0.00 2.71
1236 1241 2.807967 CGACAATGCCATCGTCCATTAT 59.192 45.455 0.00 0.00 33.63 1.28
1341 1346 1.574263 GGGGAGAGTACAAGGAGCTT 58.426 55.000 0.00 0.00 0.00 3.74
1414 1419 1.078497 CAGGACAATACTGCCGCCA 60.078 57.895 0.00 0.00 0.00 5.69
1475 1533 7.363443 GCTGAGGGTAAAATAAAGCCATAACAA 60.363 37.037 0.00 0.00 36.95 2.83
1694 1769 7.331687 GCTTTCAAATTGTACATGCCTACAAAT 59.668 33.333 11.60 2.85 39.49 2.32
1752 3630 2.029623 GACGGTGAAGCCTATCCACTA 58.970 52.381 0.00 0.00 34.25 2.74
1761 3639 3.123273 AGCCTATCCACTACCCAAACAT 58.877 45.455 0.00 0.00 0.00 2.71
1814 3700 9.965824 AAACTACATTCAGTTTTTCGAAATGAT 57.034 25.926 12.12 1.16 44.40 2.45
1854 3740 4.340666 ACCACAATGTGTTGCAACTGAATA 59.659 37.500 28.61 9.08 38.96 1.75
1861 3747 7.686438 ATGTGTTGCAACTGAATAATGTAGA 57.314 32.000 28.61 4.93 0.00 2.59
1876 3762 1.911357 TGTAGACCGAGGAGGAGTACA 59.089 52.381 0.00 0.00 45.00 2.90
1887 3773 1.177256 AGGAGTACACGTCGTTGGCT 61.177 55.000 0.00 0.00 0.00 4.75
1900 3786 1.535028 CGTTGGCTGTTTGCATAGACA 59.465 47.619 0.00 0.00 45.15 3.41
1952 3847 1.423721 CTGCATCATGTGGTCGACCG 61.424 60.000 28.70 15.04 39.43 4.79
1958 3853 0.721154 CATGTGGTCGACCGACATTG 59.279 55.000 32.25 25.86 46.20 2.82
1970 3865 1.431488 CGACATTGCCATGGAGACGG 61.431 60.000 18.40 2.40 34.27 4.79
2061 3957 0.106918 TGGCCAACACGAGGTCTTTT 60.107 50.000 0.61 0.00 0.00 2.27
2065 3961 2.504367 CCAACACGAGGTCTTTTGGAT 58.496 47.619 0.00 0.00 39.33 3.41
2071 3967 2.749621 ACGAGGTCTTTTGGATGCATTC 59.250 45.455 0.00 0.00 0.00 2.67
2072 3968 2.098117 CGAGGTCTTTTGGATGCATTCC 59.902 50.000 1.51 5.41 45.69 3.01
2073 3969 2.428530 GAGGTCTTTTGGATGCATTCCC 59.571 50.000 1.51 0.00 44.77 3.97
2074 3970 2.178580 GGTCTTTTGGATGCATTCCCA 58.821 47.619 1.51 2.35 44.77 4.37
2076 3972 1.818060 TCTTTTGGATGCATTCCCACG 59.182 47.619 6.62 0.17 44.77 4.94
2078 3974 1.916506 TTTGGATGCATTCCCACGAA 58.083 45.000 6.62 0.00 44.77 3.85
2082 3978 1.392589 GATGCATTCCCACGAACCAT 58.607 50.000 0.00 0.00 0.00 3.55
2084 3980 0.964860 TGCATTCCCACGAACCATGG 60.965 55.000 11.19 11.19 36.94 3.66
2085 3981 1.809207 CATTCCCACGAACCATGGC 59.191 57.895 13.04 0.00 35.74 4.40
2086 3982 0.964860 CATTCCCACGAACCATGGCA 60.965 55.000 13.04 0.00 35.74 4.92
2089 3985 2.491152 CCACGAACCATGGCATGC 59.509 61.111 22.02 9.90 0.00 4.06
2093 3989 1.750018 CGAACCATGGCATGCTCCA 60.750 57.895 22.02 8.51 40.97 3.86
2094 3990 1.314534 CGAACCATGGCATGCTCCAA 61.315 55.000 22.02 1.32 39.96 3.53
2098 3994 0.177141 CCATGGCATGCTCCAAAAGG 59.823 55.000 22.02 8.12 39.96 3.11
2103 3999 0.671472 GCATGCTCCAAAAGGTTGCC 60.671 55.000 11.37 0.00 33.01 4.52
2105 4001 1.070445 CATGCTCCAAAAGGTTGCCAA 59.930 47.619 0.00 0.00 33.01 4.52
2107 4003 1.134551 TGCTCCAAAAGGTTGCCAAAC 60.135 47.619 0.00 0.00 33.01 2.93
2115 4011 2.818841 GTTGCCAAACCACCACCC 59.181 61.111 0.00 0.00 0.00 4.61
2116 4012 2.444895 TTGCCAAACCACCACCCC 60.445 61.111 0.00 0.00 0.00 4.95
2117 4013 3.317436 TTGCCAAACCACCACCCCA 62.317 57.895 0.00 0.00 0.00 4.96
2120 4016 1.847686 CCAAACCACCACCCCACTA 59.152 57.895 0.00 0.00 0.00 2.74
2121 4017 0.407918 CCAAACCACCACCCCACTAT 59.592 55.000 0.00 0.00 0.00 2.12
2122 4018 1.544724 CAAACCACCACCCCACTATG 58.455 55.000 0.00 0.00 0.00 2.23
2123 4019 0.407918 AAACCACCACCCCACTATGG 59.592 55.000 0.00 0.00 42.13 2.74
2125 4021 1.205460 ACCACCACCCCACTATGGTC 61.205 60.000 0.00 0.00 46.62 4.02
2126 4022 1.220749 CACCACCCCACTATGGTCG 59.779 63.158 0.00 0.00 46.62 4.79
2127 4023 1.229400 ACCACCCCACTATGGTCGT 60.229 57.895 0.00 0.00 46.62 4.34
2128 4024 1.220749 CCACCCCACTATGGTCGTG 59.779 63.158 5.67 5.67 36.31 4.35
2129 4025 1.550130 CCACCCCACTATGGTCGTGT 61.550 60.000 9.99 0.00 35.36 4.49
2130 4026 0.391130 CACCCCACTATGGTCGTGTG 60.391 60.000 4.80 0.00 35.17 3.82
2132 4028 4.932789 CCACTATGGTCGTGTGGG 57.067 61.111 0.00 0.00 45.29 4.61
2145 4241 1.811176 CGTGTGGGGGTAGAAACGTTT 60.811 52.381 14.57 14.57 0.00 3.60
2155 4251 5.163332 GGGGTAGAAACGTTTCATATCCTCT 60.163 44.000 35.29 19.06 39.61 3.69
2168 4264 5.363101 TCATATCCTCTTTGTCACATGAGC 58.637 41.667 0.00 0.00 0.00 4.26
2195 4291 1.070758 AGTCTCCACATGCTTTGACGT 59.929 47.619 0.00 0.00 0.00 4.34
2221 4317 1.104577 TGTGAGCCCGTTTTGTTCCC 61.105 55.000 0.00 0.00 0.00 3.97
2233 4329 2.922740 TTGTTCCCAGTCACTACACC 57.077 50.000 0.00 0.00 0.00 4.16
2254 4350 3.580731 CCGAGACCTCTTCAAGAAACTC 58.419 50.000 0.00 0.00 0.00 3.01
2307 4403 7.115378 GTGTCAAAGAGTAATGCAAAGAAATGG 59.885 37.037 0.00 0.00 0.00 3.16
2311 4407 8.490355 CAAAGAGTAATGCAAAGAAATGGAAAC 58.510 33.333 0.00 0.00 0.00 2.78
2345 4441 1.873486 GCAAACATGACCAAGGCCAAC 60.873 52.381 5.01 0.00 0.00 3.77
2353 4449 1.339929 GACCAAGGCCAACGAACAAAT 59.660 47.619 5.01 0.00 0.00 2.32
2361 4457 2.155539 GCCAACGAACAAATCATTGCAC 59.844 45.455 0.00 0.00 40.34 4.57
2362 4458 2.404693 CCAACGAACAAATCATTGCACG 59.595 45.455 0.00 0.00 40.34 5.34
2363 4459 3.042189 CAACGAACAAATCATTGCACGT 58.958 40.909 0.00 7.44 45.92 4.49
2364 4460 3.347958 ACGAACAAATCATTGCACGTT 57.652 38.095 0.00 0.00 43.59 3.99
2365 4461 3.701241 ACGAACAAATCATTGCACGTTT 58.299 36.364 0.00 0.00 43.59 3.60
2366 4462 3.728718 ACGAACAAATCATTGCACGTTTC 59.271 39.130 0.00 0.00 43.59 2.78
2367 4463 3.119463 CGAACAAATCATTGCACGTTTCC 59.881 43.478 0.00 0.00 40.34 3.13
2368 4464 4.298332 GAACAAATCATTGCACGTTTCCT 58.702 39.130 0.00 0.00 40.34 3.36
2369 4465 3.900941 ACAAATCATTGCACGTTTCCTC 58.099 40.909 0.00 0.00 40.34 3.71
2370 4466 3.317711 ACAAATCATTGCACGTTTCCTCA 59.682 39.130 0.00 0.00 40.34 3.86
2371 4467 4.202101 ACAAATCATTGCACGTTTCCTCAA 60.202 37.500 0.00 0.00 40.34 3.02
2372 4468 4.789012 AATCATTGCACGTTTCCTCAAT 57.211 36.364 0.00 0.00 0.00 2.57
2373 4469 3.557577 TCATTGCACGTTTCCTCAATG 57.442 42.857 13.52 13.52 44.12 2.82
2374 4470 2.228582 TCATTGCACGTTTCCTCAATGG 59.771 45.455 16.89 0.00 43.40 3.16
2375 4471 1.686355 TTGCACGTTTCCTCAATGGT 58.314 45.000 0.00 0.00 37.07 3.55
2376 4472 1.234821 TGCACGTTTCCTCAATGGTC 58.765 50.000 0.00 0.00 37.07 4.02
2377 4473 1.202758 TGCACGTTTCCTCAATGGTCT 60.203 47.619 0.00 0.00 37.07 3.85
2378 4474 1.464997 GCACGTTTCCTCAATGGTCTC 59.535 52.381 0.00 0.00 37.07 3.36
2379 4475 2.766313 CACGTTTCCTCAATGGTCTCA 58.234 47.619 0.00 0.00 37.07 3.27
2380 4476 3.138304 CACGTTTCCTCAATGGTCTCAA 58.862 45.455 0.00 0.00 37.07 3.02
2381 4477 3.058914 CACGTTTCCTCAATGGTCTCAAC 60.059 47.826 0.00 0.00 37.07 3.18
2382 4478 3.181454 ACGTTTCCTCAATGGTCTCAACT 60.181 43.478 0.00 0.00 37.07 3.16
2383 4479 4.039973 ACGTTTCCTCAATGGTCTCAACTA 59.960 41.667 0.00 0.00 37.07 2.24
2384 4480 4.389077 CGTTTCCTCAATGGTCTCAACTAC 59.611 45.833 0.00 0.00 37.07 2.73
2385 4481 4.553330 TTCCTCAATGGTCTCAACTACC 57.447 45.455 0.00 0.00 37.53 3.18
2386 4482 3.791320 TCCTCAATGGTCTCAACTACCT 58.209 45.455 0.00 0.00 37.91 3.08
2387 4483 3.769844 TCCTCAATGGTCTCAACTACCTC 59.230 47.826 0.00 0.00 37.91 3.85
2388 4484 3.515502 CCTCAATGGTCTCAACTACCTCA 59.484 47.826 0.00 0.00 37.91 3.86
2389 4485 4.163078 CCTCAATGGTCTCAACTACCTCAT 59.837 45.833 0.00 0.00 37.91 2.90
2390 4486 5.344743 TCAATGGTCTCAACTACCTCATC 57.655 43.478 0.00 0.00 37.91 2.92
2391 4487 4.777366 TCAATGGTCTCAACTACCTCATCA 59.223 41.667 0.00 0.00 37.91 3.07
2392 4488 5.248248 TCAATGGTCTCAACTACCTCATCAA 59.752 40.000 0.00 0.00 37.91 2.57
2393 4489 5.762179 ATGGTCTCAACTACCTCATCAAA 57.238 39.130 0.00 0.00 37.91 2.69
2394 4490 4.894784 TGGTCTCAACTACCTCATCAAAC 58.105 43.478 0.00 0.00 37.91 2.93
2395 4491 4.346709 TGGTCTCAACTACCTCATCAAACA 59.653 41.667 0.00 0.00 37.91 2.83
2401 4497 6.126409 TCAACTACCTCATCAAACAAACCTT 58.874 36.000 0.00 0.00 0.00 3.50
2437 4533 4.605640 ACACCAATTTGATTGAGTTGGG 57.394 40.909 7.77 0.00 44.15 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 3.452786 TCTTCGGCTGGCTCCTCG 61.453 66.667 0.00 0.00 0.00 4.63
389 390 8.486210 TGTAGCTAATATTATGATGGATGGGAC 58.514 37.037 0.00 0.00 0.00 4.46
426 427 4.265073 CCTCTTCTCCCACCATACAAAAG 58.735 47.826 0.00 0.00 0.00 2.27
545 547 8.514594 CATTTTTAAACACCTCTATGCTCTTCA 58.485 33.333 0.00 0.00 0.00 3.02
593 595 4.890581 ACTGCATGTAGGACTAGGTAGAAG 59.109 45.833 15.65 0.00 0.00 2.85
673 676 9.947669 TTTTGCCTTATGTTGAAATTTTCATTG 57.052 25.926 12.39 1.17 39.84 2.82
721 724 0.840617 TTGCTGGTGGTCTTGGTGTA 59.159 50.000 0.00 0.00 0.00 2.90
867 870 7.331440 TGATTCAATAATGTGAAATGTGCCAAC 59.669 33.333 0.00 0.00 40.76 3.77
869 872 6.932947 TGATTCAATAATGTGAAATGTGCCA 58.067 32.000 0.00 0.00 40.76 4.92
885 890 9.472361 GCATAAGCAAATCAGTAATGATTCAAT 57.528 29.630 17.96 8.32 41.58 2.57
886 891 8.689061 AGCATAAGCAAATCAGTAATGATTCAA 58.311 29.630 17.96 4.03 45.49 2.69
892 897 7.972277 AGAACAAGCATAAGCAAATCAGTAATG 59.028 33.333 0.00 0.00 45.49 1.90
936 941 9.899226 GAGAAACACAGCTTAACAAAAAGATAT 57.101 29.630 0.00 0.00 0.00 1.63
951 956 4.354587 CCTGTTTGAAAGAGAAACACAGC 58.645 43.478 3.38 0.00 38.17 4.40
967 972 1.073897 GAGACCTGCTGGCCTGTTT 59.926 57.895 9.95 0.00 36.63 2.83
986 991 3.358707 CAAGCATTGCTCTGAACACAA 57.641 42.857 12.39 0.00 40.39 3.33
1010 1015 1.388065 CCGGCTCTCTTCCATCTCGT 61.388 60.000 0.00 0.00 0.00 4.18
1041 1046 1.817357 AGGACACGTCGTACATCTCA 58.183 50.000 0.00 0.00 0.00 3.27
1042 1047 3.558829 TCATAGGACACGTCGTACATCTC 59.441 47.826 0.00 0.00 33.48 2.75
1081 1086 2.028839 CACCCGTGTACATGTAGTGGAA 60.029 50.000 20.19 0.00 0.00 3.53
1101 1106 1.379176 CTCGTCCAGGAGAGCCTCA 60.379 63.158 0.00 0.00 44.80 3.86
1200 1205 2.631160 TGTCGTTGTTCACCTTGGAT 57.369 45.000 0.00 0.00 0.00 3.41
1221 1226 0.179059 ACGCATAATGGACGATGGCA 60.179 50.000 0.00 0.00 0.00 4.92
1341 1346 2.045242 CTCGGGTCCCTCTCGACA 60.045 66.667 6.29 0.00 44.69 4.35
1414 1419 2.241685 AGCAGCAATCTGAATCCCTCTT 59.758 45.455 0.00 0.00 42.95 2.85
1475 1533 6.916360 ATCTCACCAAACCACATTTTATGT 57.084 33.333 0.00 0.00 46.22 2.29
1591 1666 8.459911 AAAATGCTGGTATGTATAGGGTAAAC 57.540 34.615 0.00 0.00 0.00 2.01
1622 1697 7.498900 CCAGAGCATCACACCAAGTAATAATTA 59.501 37.037 0.00 0.00 37.82 1.40
1667 1742 4.192429 AGGCATGTACAATTTGAAAGCC 57.808 40.909 0.00 8.76 39.82 4.35
1793 3671 8.103948 AGAGATCATTTCGAAAAACTGAATGT 57.896 30.769 15.66 3.99 0.00 2.71
1803 3689 6.321181 CCCCCATAAAAGAGATCATTTCGAAA 59.679 38.462 13.91 13.91 0.00 3.46
1807 3693 7.417911 GGTTTCCCCCATAAAAGAGATCATTTC 60.418 40.741 0.00 0.00 0.00 2.17
1814 3700 3.399644 TGTGGTTTCCCCCATAAAAGAGA 59.600 43.478 0.00 0.00 36.74 3.10
1841 3727 5.350365 TCGGTCTACATTATTCAGTTGCAAC 59.650 40.000 22.17 22.17 0.00 4.17
1845 3731 5.902681 TCCTCGGTCTACATTATTCAGTTG 58.097 41.667 0.00 0.00 0.00 3.16
1854 3740 2.830651 ACTCCTCCTCGGTCTACATT 57.169 50.000 0.00 0.00 0.00 2.71
1861 3747 0.676151 GACGTGTACTCCTCCTCGGT 60.676 60.000 0.00 0.00 0.00 4.69
1876 3762 1.444119 ATGCAAACAGCCAACGACGT 61.444 50.000 0.00 0.00 44.83 4.34
1887 3773 1.438651 GGACGCTGTCTATGCAAACA 58.561 50.000 0.00 0.00 32.47 2.83
1900 3786 1.482593 CATCTGGAGTTTAGGGACGCT 59.517 52.381 0.00 0.00 0.00 5.07
1952 3847 2.397751 CCGTCTCCATGGCAATGTC 58.602 57.895 6.96 0.00 31.27 3.06
1970 3865 2.401766 CGTGGGTGGCTCAGATTGC 61.402 63.158 0.00 0.00 0.00 3.56
2048 3944 1.202758 TGCATCCAAAAGACCTCGTGT 60.203 47.619 0.00 0.00 0.00 4.49
2050 3946 2.496899 ATGCATCCAAAAGACCTCGT 57.503 45.000 0.00 0.00 0.00 4.18
2065 3961 0.964860 CCATGGTTCGTGGGAATGCA 60.965 55.000 2.57 0.00 36.92 3.96
2071 3967 3.067480 GCATGCCATGGTTCGTGGG 62.067 63.158 14.67 0.00 40.61 4.61
2072 3968 1.996786 GAGCATGCCATGGTTCGTGG 61.997 60.000 15.66 1.98 41.77 4.94
2073 3969 1.430632 GAGCATGCCATGGTTCGTG 59.569 57.895 15.66 10.26 41.77 4.35
2074 3970 1.750399 GGAGCATGCCATGGTTCGT 60.750 57.895 15.66 0.00 41.77 3.85
2076 3972 0.896923 TTTGGAGCATGCCATGGTTC 59.103 50.000 15.66 9.68 41.77 3.62
2078 3974 0.899720 CTTTTGGAGCATGCCATGGT 59.100 50.000 15.66 9.51 44.87 3.55
2082 3978 0.680618 CAACCTTTTGGAGCATGCCA 59.319 50.000 15.66 2.78 44.07 4.92
2084 3980 0.671472 GGCAACCTTTTGGAGCATGC 60.671 55.000 10.51 10.51 44.07 4.06
2085 3981 0.680618 TGGCAACCTTTTGGAGCATG 59.319 50.000 0.00 0.00 44.07 4.06
2086 3982 1.422531 TTGGCAACCTTTTGGAGCAT 58.577 45.000 0.00 0.00 44.07 3.79
2098 3994 2.802724 GGGGTGGTGGTTTGGCAAC 61.803 63.158 0.00 0.00 0.00 4.17
2103 3999 1.544724 CATAGTGGGGTGGTGGTTTG 58.455 55.000 0.00 0.00 0.00 2.93
2105 4001 0.774491 ACCATAGTGGGGTGGTGGTT 60.774 55.000 0.52 0.00 46.55 3.67
2107 4003 3.835134 ACCATAGTGGGGTGGTGG 58.165 61.111 0.52 0.00 46.55 4.61
2110 4006 1.220749 CACGACCATAGTGGGGTGG 59.779 63.158 12.05 0.00 43.37 4.61
2112 4008 1.980052 CACACGACCATAGTGGGGT 59.020 57.895 0.52 0.00 43.37 4.95
2113 4009 4.932789 CACACGACCATAGTGGGG 57.067 61.111 0.52 0.00 43.37 4.96
2114 4010 4.932789 CCACACGACCATAGTGGG 57.067 61.111 0.00 0.00 46.98 4.61
2116 4012 1.220749 CCCCCACACGACCATAGTG 59.779 63.158 0.00 0.00 44.57 2.74
2117 4013 0.041535 TACCCCCACACGACCATAGT 59.958 55.000 0.00 0.00 0.00 2.12
2120 4016 0.545787 TTCTACCCCCACACGACCAT 60.546 55.000 0.00 0.00 0.00 3.55
2121 4017 0.763604 TTTCTACCCCCACACGACCA 60.764 55.000 0.00 0.00 0.00 4.02
2122 4018 0.321034 GTTTCTACCCCCACACGACC 60.321 60.000 0.00 0.00 0.00 4.79
2123 4019 0.668401 CGTTTCTACCCCCACACGAC 60.668 60.000 0.00 0.00 0.00 4.34
2124 4020 1.114722 ACGTTTCTACCCCCACACGA 61.115 55.000 0.00 0.00 0.00 4.35
2125 4021 0.249996 AACGTTTCTACCCCCACACG 60.250 55.000 0.00 0.00 0.00 4.49
2126 4022 1.875514 GAAACGTTTCTACCCCCACAC 59.124 52.381 29.27 3.23 34.41 3.82
2127 4023 1.489649 TGAAACGTTTCTACCCCCACA 59.510 47.619 33.94 14.36 38.02 4.17
2128 4024 2.259266 TGAAACGTTTCTACCCCCAC 57.741 50.000 33.94 12.09 38.02 4.61
2129 4025 4.384427 GGATATGAAACGTTTCTACCCCCA 60.384 45.833 33.94 18.12 38.02 4.96
2130 4026 4.132336 GGATATGAAACGTTTCTACCCCC 58.868 47.826 33.94 24.67 38.02 5.40
2131 4027 5.032327 AGGATATGAAACGTTTCTACCCC 57.968 43.478 33.94 27.75 38.02 4.95
2132 4028 5.915175 AGAGGATATGAAACGTTTCTACCC 58.085 41.667 33.94 27.48 38.02 3.69
2145 4241 5.129980 AGCTCATGTGACAAAGAGGATATGA 59.870 40.000 16.62 1.09 0.00 2.15
2155 4251 0.178995 TGGGCAGCTCATGTGACAAA 60.179 50.000 0.00 0.00 0.00 2.83
2168 4264 1.310933 GCATGTGGAGACTTGGGCAG 61.311 60.000 0.00 0.00 0.00 4.85
2195 4291 0.319083 AAACGGGCTCACATGACGTA 59.681 50.000 0.00 0.00 36.69 3.57
2208 4304 0.666374 GTGACTGGGAACAAAACGGG 59.334 55.000 0.00 0.00 42.06 5.28
2221 4317 0.526662 GGTCTCGGGTGTAGTGACTG 59.473 60.000 0.00 0.00 33.93 3.51
2233 4329 3.580731 GAGTTTCTTGAAGAGGTCTCGG 58.419 50.000 0.00 0.00 34.09 4.63
2275 4371 5.858381 TGCATTACTCTTTGACACTCTTCT 58.142 37.500 0.00 0.00 0.00 2.85
2307 4403 0.659957 GCTCGGATCATGGCAGTTTC 59.340 55.000 0.00 0.00 0.00 2.78
2311 4407 0.379669 GTTTGCTCGGATCATGGCAG 59.620 55.000 0.00 0.00 36.06 4.85
2345 4441 3.119463 GGAAACGTGCAATGATTTGTTCG 59.881 43.478 0.00 0.00 37.22 3.95
2353 4449 2.228582 CCATTGAGGAAACGTGCAATGA 59.771 45.455 20.31 0.00 44.49 2.57
2361 4457 3.403038 AGTTGAGACCATTGAGGAAACG 58.597 45.455 0.00 0.00 41.22 3.60
2362 4458 4.695928 GGTAGTTGAGACCATTGAGGAAAC 59.304 45.833 0.00 0.00 41.22 2.78
2363 4459 4.597507 AGGTAGTTGAGACCATTGAGGAAA 59.402 41.667 0.00 0.00 41.22 3.13
2364 4460 4.168101 AGGTAGTTGAGACCATTGAGGAA 58.832 43.478 0.00 0.00 41.22 3.36
2365 4461 3.769844 GAGGTAGTTGAGACCATTGAGGA 59.230 47.826 0.00 0.00 41.22 3.71
2366 4462 3.515502 TGAGGTAGTTGAGACCATTGAGG 59.484 47.826 0.00 0.00 45.67 3.86
2367 4463 4.808414 TGAGGTAGTTGAGACCATTGAG 57.192 45.455 0.00 0.00 39.65 3.02
2368 4464 4.777366 TGATGAGGTAGTTGAGACCATTGA 59.223 41.667 0.00 0.00 39.65 2.57
2369 4465 5.089970 TGATGAGGTAGTTGAGACCATTG 57.910 43.478 0.00 0.00 39.65 2.82
2370 4466 5.762179 TTGATGAGGTAGTTGAGACCATT 57.238 39.130 0.00 0.00 39.65 3.16
2371 4467 5.013079 TGTTTGATGAGGTAGTTGAGACCAT 59.987 40.000 0.00 0.00 39.65 3.55
2372 4468 4.346709 TGTTTGATGAGGTAGTTGAGACCA 59.653 41.667 0.00 0.00 39.65 4.02
2373 4469 4.894784 TGTTTGATGAGGTAGTTGAGACC 58.105 43.478 0.00 0.00 37.22 3.85
2374 4470 6.293462 GGTTTGTTTGATGAGGTAGTTGAGAC 60.293 42.308 0.00 0.00 0.00 3.36
2375 4471 5.763204 GGTTTGTTTGATGAGGTAGTTGAGA 59.237 40.000 0.00 0.00 0.00 3.27
2376 4472 5.765182 AGGTTTGTTTGATGAGGTAGTTGAG 59.235 40.000 0.00 0.00 0.00 3.02
2377 4473 5.690865 AGGTTTGTTTGATGAGGTAGTTGA 58.309 37.500 0.00 0.00 0.00 3.18
2378 4474 6.208644 CAAGGTTTGTTTGATGAGGTAGTTG 58.791 40.000 0.00 0.00 0.00 3.16
2379 4475 5.301805 CCAAGGTTTGTTTGATGAGGTAGTT 59.698 40.000 0.00 0.00 0.00 2.24
2380 4476 4.827284 CCAAGGTTTGTTTGATGAGGTAGT 59.173 41.667 0.00 0.00 0.00 2.73
2381 4477 5.070001 TCCAAGGTTTGTTTGATGAGGTAG 58.930 41.667 0.00 0.00 0.00 3.18
2382 4478 5.055265 TCCAAGGTTTGTTTGATGAGGTA 57.945 39.130 0.00 0.00 0.00 3.08
2383 4479 3.909732 TCCAAGGTTTGTTTGATGAGGT 58.090 40.909 0.00 0.00 0.00 3.85
2384 4480 5.473066 AATCCAAGGTTTGTTTGATGAGG 57.527 39.130 0.00 0.00 0.00 3.86
2385 4481 6.985645 TCAAAATCCAAGGTTTGTTTGATGAG 59.014 34.615 0.00 0.00 36.36 2.90
2386 4482 6.882656 TCAAAATCCAAGGTTTGTTTGATGA 58.117 32.000 0.00 0.00 36.36 2.92
2387 4483 7.408910 GTTCAAAATCCAAGGTTTGTTTGATG 58.591 34.615 0.00 0.00 34.92 3.07
2388 4484 6.542005 GGTTCAAAATCCAAGGTTTGTTTGAT 59.458 34.615 0.00 0.00 34.92 2.57
2389 4485 5.877564 GGTTCAAAATCCAAGGTTTGTTTGA 59.122 36.000 0.00 0.00 36.36 2.69
2390 4486 5.220567 CGGTTCAAAATCCAAGGTTTGTTTG 60.221 40.000 3.15 0.00 36.36 2.93
2391 4487 4.873259 CGGTTCAAAATCCAAGGTTTGTTT 59.127 37.500 3.15 0.00 36.36 2.83
2392 4488 4.081365 ACGGTTCAAAATCCAAGGTTTGTT 60.081 37.500 0.00 0.00 36.36 2.83
2393 4489 3.449377 ACGGTTCAAAATCCAAGGTTTGT 59.551 39.130 0.00 0.00 36.36 2.83
2394 4490 4.053469 ACGGTTCAAAATCCAAGGTTTG 57.947 40.909 0.00 0.00 36.30 2.93
2395 4491 4.645588 TGTACGGTTCAAAATCCAAGGTTT 59.354 37.500 0.00 0.00 0.00 3.27
2401 4497 3.210232 TGGTGTACGGTTCAAAATCCA 57.790 42.857 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.