Multiple sequence alignment - TraesCS6D01G036600

Loading Multiple Alignment...

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 TraesCS6D01G036600 chr6D 100.000 3742 0 0 1 3742 14987104 14990845 0.000000e+00 6911
1 TraesCS6D01G036600 chr6D 96.078 102 4 0 1180 1281 14988127 14988228 2.310000e-37 167
2 TraesCS6D01G036600 chr6D 96.078 102 4 0 1024 1125 14988283 14988384 2.310000e-37 167
3 TraesCS6D01G036600 chr1A 95.302 2980 120 13 592 3557 61089289 61086316 0.000000e+00 4710
4 TraesCS6D01G036600 chr1A 85.455 605 53 23 1 580 61089978 61089384 6.920000e-167 597
5 TraesCS6D01G036600 chr1A 92.903 155 3 2 3592 3742 61085907 61085757 6.290000e-53 219
6 TraesCS6D01G036600 chr1A 97.059 102 3 0 1180 1281 61088856 61088755 4.970000e-39 172
7 TraesCS6D01G036600 chr1A 95.146 103 5 0 1023 1125 61088698 61088596 2.990000e-36 163


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 TraesCS6D01G036600 chr6D 14987104 14990845 3741 False 2415.0 6911 97.385333 1 3742 3 chr6D.!!$F1 3741
1 TraesCS6D01G036600 chr1A 61085757 61089978 4221 True 1172.2 4710 93.173000 1 3742 5 chr1A.!!$R1 3741

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
318 342 0.179081 GACATTGAGGCGGACTACCC 60.179 60.0 0.00 0.0 0.0 3.69 F
931 1045 0.673644 AACGATTTCCCTCCACTGCG 60.674 55.0 0.00 0.0 0.0 5.18 F
2091 2208 0.329596 AGACAGGCCAATGGAGTTCC 59.670 55.0 5.01 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2191 0.038744 CTGGAACTCCATTGGCCTGT 59.961 55.000 3.32 0.00 46.46 4.00 R
2165 2282 1.344438 TCGGCTGCAGGAACCATATAG 59.656 52.381 17.12 0.00 0.00 1.31 R
3578 3702 0.236711 CTTCTTTCTGTGCCACAGCG 59.763 55.000 20.05 10.55 45.54 5.18 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
66 67 0.467384 ATGACATCGCAAGGAGGAGG 59.533 55.000 0.00 0.00 38.47 4.30
70 71 1.687146 ATCGCAAGGAGGAGGAGCA 60.687 57.895 0.00 0.00 38.47 4.26
73 74 0.465705 CGCAAGGAGGAGGAGCATTA 59.534 55.000 0.00 0.00 0.00 1.90
82 83 0.839946 GAGGAGCATTAGAGGGCCAA 59.160 55.000 6.18 0.00 0.00 4.52
117 118 6.905076 GCTCGCGATGATAATTGTTAGAAAAA 59.095 34.615 10.36 0.00 0.00 1.94
118 119 7.587757 GCTCGCGATGATAATTGTTAGAAAAAT 59.412 33.333 10.36 0.00 0.00 1.82
172 176 2.489040 TCGATAGAGGCAACGAGCA 58.511 52.632 6.91 0.00 43.70 4.26
173 177 0.815095 TCGATAGAGGCAACGAGCAA 59.185 50.000 6.91 0.00 43.70 3.91
175 179 1.735700 CGATAGAGGCAACGAGCAACA 60.736 52.381 6.91 0.00 42.82 3.33
176 180 3.610610 CGATAGAGGCAACGAGCAACAG 61.611 54.545 6.91 0.00 42.82 3.16
186 191 1.505353 GAGCAACAGCCACATGAGC 59.495 57.895 0.00 1.38 0.00 4.26
209 214 5.441709 TGGACGATATGCAATACGAGTAA 57.558 39.130 14.57 0.00 31.19 2.24
212 217 5.568296 GGACGATATGCAATACGAGTAAGAC 59.432 44.000 14.57 0.00 31.19 3.01
213 218 6.068473 ACGATATGCAATACGAGTAAGACA 57.932 37.500 14.57 0.00 31.19 3.41
214 219 6.500910 ACGATATGCAATACGAGTAAGACAA 58.499 36.000 14.57 0.00 31.19 3.18
215 220 6.637254 ACGATATGCAATACGAGTAAGACAAG 59.363 38.462 14.57 0.00 31.19 3.16
216 221 6.399039 CGATATGCAATACGAGTAAGACAAGC 60.399 42.308 0.00 0.00 0.00 4.01
217 222 4.188247 TGCAATACGAGTAAGACAAGCT 57.812 40.909 0.00 0.00 0.00 3.74
218 223 4.174009 TGCAATACGAGTAAGACAAGCTC 58.826 43.478 0.00 0.00 0.00 4.09
223 228 1.467713 CGAGTAAGACAAGCTCGTCCC 60.468 57.143 0.00 0.00 44.69 4.46
225 230 2.231721 GAGTAAGACAAGCTCGTCCCTT 59.768 50.000 0.00 0.00 36.52 3.95
229 253 3.983044 AGACAAGCTCGTCCCTTTTAT 57.017 42.857 0.00 0.00 36.52 1.40
243 267 3.128349 CCTTTTATGGTACGGTCCATCG 58.872 50.000 15.11 5.32 45.67 3.84
247 271 1.030457 ATGGTACGGTCCATCGAGAC 58.970 55.000 7.64 0.00 43.85 3.36
253 277 1.076533 CGGTCCATCGAGACAAACCG 61.077 60.000 11.50 11.50 42.97 4.44
272 296 3.435105 CGTGAGGGAAGATGAAGAGAG 57.565 52.381 0.00 0.00 0.00 3.20
278 302 1.115467 GAAGATGAAGAGAGGGCGGA 58.885 55.000 0.00 0.00 0.00 5.54
281 305 0.757188 GATGAAGAGAGGGCGGAGGA 60.757 60.000 0.00 0.00 0.00 3.71
286 310 4.851214 AGAGGGCGGAGGAGGAGC 62.851 72.222 0.00 0.00 0.00 4.70
304 328 1.079819 CGGACTGTGGCGAGACATT 60.080 57.895 0.00 0.00 0.00 2.71
310 334 2.125552 TGGCGAGACATTGAGGCG 60.126 61.111 0.00 0.00 0.00 5.52
318 342 0.179081 GACATTGAGGCGGACTACCC 60.179 60.000 0.00 0.00 0.00 3.69
319 343 1.146263 CATTGAGGCGGACTACCCC 59.854 63.158 0.00 0.00 0.00 4.95
325 349 4.468689 GCGGACTACCCCTGCCAC 62.469 72.222 0.00 0.00 0.00 5.01
326 350 2.683933 CGGACTACCCCTGCCACT 60.684 66.667 0.00 0.00 0.00 4.00
327 351 2.722201 CGGACTACCCCTGCCACTC 61.722 68.421 0.00 0.00 0.00 3.51
540 568 9.777297 AATAAATTTGTTTTATGGCAAGTCACT 57.223 25.926 0.00 0.00 39.15 3.41
548 576 3.928727 ATGGCAAGTCACTTCATTGTG 57.071 42.857 0.00 0.00 39.15 3.33
556 584 7.072030 GCAAGTCACTTCATTGTGTAACTAAG 58.928 38.462 0.00 0.00 38.90 2.18
557 585 7.042051 GCAAGTCACTTCATTGTGTAACTAAGA 60.042 37.037 0.00 0.00 38.90 2.10
580 608 6.704493 AGAGCAGACTTAAATTGTTTCGTACA 59.296 34.615 0.00 0.00 34.12 2.90
581 609 6.888430 AGCAGACTTAAATTGTTTCGTACAG 58.112 36.000 0.00 0.00 38.19 2.74
582 610 6.704493 AGCAGACTTAAATTGTTTCGTACAGA 59.296 34.615 0.00 0.00 38.19 3.41
583 611 7.225931 AGCAGACTTAAATTGTTTCGTACAGAA 59.774 33.333 0.00 0.00 38.19 3.02
633 744 2.358615 CTGCAGGCGTGGTTAGCA 60.359 61.111 5.57 0.00 36.08 3.49
654 765 7.747155 AGCAATCTCCAGATCATCATTAAAG 57.253 36.000 0.00 0.00 32.75 1.85
674 785 8.713708 TTAAAGAAATTAATCTCCCCACACAA 57.286 30.769 0.00 0.00 0.00 3.33
734 845 6.428799 TGTTTTCCTTACCGTACATTTTTCG 58.571 36.000 0.00 0.00 0.00 3.46
799 910 7.545362 TTTAGAGAAGACAATCTGCTTATGC 57.455 36.000 0.00 0.00 30.83 3.14
839 953 1.138036 GTTAATGGCGAAACGGGGC 59.862 57.895 0.00 0.00 0.00 5.80
870 984 1.521681 GGATCCGGCGAAACAGAGG 60.522 63.158 9.30 0.00 0.00 3.69
876 990 2.174319 GGCGAAACAGAGGCCGATC 61.174 63.158 0.00 0.00 37.06 3.69
877 991 2.517450 GCGAAACAGAGGCCGATCG 61.517 63.158 8.51 8.51 0.00 3.69
927 1041 0.804989 CTGCAACGATTTCCCTCCAC 59.195 55.000 0.00 0.00 0.00 4.02
931 1045 0.673644 AACGATTTCCCTCCACTGCG 60.674 55.000 0.00 0.00 0.00 5.18
967 1081 2.375174 TCCCAAATTCTCCATATCCCCG 59.625 50.000 0.00 0.00 0.00 5.73
969 1083 3.560025 CCCAAATTCTCCATATCCCCGAG 60.560 52.174 0.00 0.00 0.00 4.63
1149 1263 2.202492 CGAGTCAAGAGACCGCGG 60.202 66.667 26.86 26.86 46.15 6.46
1189 1303 1.134965 ACGAGCAAGATTCTTCCTCCG 60.135 52.381 11.00 8.93 0.00 4.63
1342 1459 1.222113 GAGCTGTCCCCAAGCCTAC 59.778 63.158 0.00 0.00 0.00 3.18
1347 1464 2.286121 TCCCCAAGCCTACCCCTG 60.286 66.667 0.00 0.00 0.00 4.45
1535 1652 1.825474 AGACGCAACCATAGCTACACT 59.175 47.619 0.00 0.00 0.00 3.55
1541 1658 2.932614 CAACCATAGCTACACTGAGCAC 59.067 50.000 0.00 0.00 45.43 4.40
1593 1710 0.681175 ACCCTTTTGCAATGTCAGCC 59.319 50.000 0.00 0.00 0.00 4.85
1737 1854 6.632672 GCCCATATCCTGTTCTACTTTCTTCA 60.633 42.308 0.00 0.00 0.00 3.02
1786 1903 0.798776 CGATCTGTTCGCTGCCTTTT 59.201 50.000 0.00 0.00 41.69 2.27
1810 1927 1.936547 GTAGATTCGCAGCAGAAAGGG 59.063 52.381 4.19 0.00 33.43 3.95
1821 1938 2.119495 GCAGAAAGGGTGATAGGGAGA 58.881 52.381 0.00 0.00 0.00 3.71
1839 1956 5.610982 AGGGAGAGTAGAGATATCAGACTGT 59.389 44.000 5.32 3.50 0.00 3.55
1840 1957 6.790461 AGGGAGAGTAGAGATATCAGACTGTA 59.210 42.308 5.32 0.00 0.00 2.74
1892 2009 2.118683 CATCAGGCGTTTTGTTGTGTG 58.881 47.619 0.00 0.00 0.00 3.82
1941 2058 1.153469 GCTACTGCCACAGCTCTCC 60.153 63.158 0.00 0.00 40.80 3.71
1986 2103 3.256879 TGTCTGCTTCAGTTCTTCGAGAT 59.743 43.478 0.00 0.00 32.61 2.75
2000 2117 2.042464 TCGAGATAAGAAGGCTGCCAT 58.958 47.619 22.65 9.32 0.00 4.40
2022 2139 6.350277 CCATAGAGTTCTCGGTTACTGTTCTT 60.350 42.308 0.00 0.00 0.00 2.52
2035 2152 4.762289 ACTGTTCTTATGGGTGATCTCC 57.238 45.455 5.18 5.18 0.00 3.71
2037 2154 4.163078 ACTGTTCTTATGGGTGATCTCCAG 59.837 45.833 15.46 4.58 37.75 3.86
2052 2169 2.661537 CAGAGCGCCAACGTGACA 60.662 61.111 2.29 0.00 42.83 3.58
2057 2174 1.195900 GAGCGCCAACGTGACAATTAA 59.804 47.619 2.29 0.00 42.83 1.40
2074 2191 7.721842 TGACAATTAACCAGTACCAATCAAAGA 59.278 33.333 0.00 0.00 0.00 2.52
2085 2202 2.093869 CCAATCAAAGACAGGCCAATGG 60.094 50.000 5.01 0.00 0.00 3.16
2091 2208 0.329596 AGACAGGCCAATGGAGTTCC 59.670 55.000 5.01 0.00 0.00 3.62
2154 2271 3.997021 AGATTAAGCAACCGTCTGTTCTG 59.003 43.478 0.00 0.00 34.00 3.02
2165 2282 2.845967 CGTCTGTTCTGTGCAAAAACAC 59.154 45.455 5.87 0.00 41.10 3.32
2173 2290 6.264292 TGTTCTGTGCAAAAACACTATATGGT 59.736 34.615 5.87 0.00 41.30 3.55
2212 2329 1.468985 ACTGATCTCTGTCGACCCAG 58.531 55.000 14.12 8.80 0.00 4.45
2223 2340 2.431419 TGTCGACCCAGACAAGTTAACA 59.569 45.455 14.12 0.00 46.81 2.41
2224 2341 3.057734 GTCGACCCAGACAAGTTAACAG 58.942 50.000 3.51 2.39 40.65 3.16
2298 2415 1.456518 CCTGGAGCGATCTCAGGGA 60.457 63.158 22.87 0.00 41.13 4.20
2320 2437 5.766670 GGATCAATTTGCCTAGTGATGATCA 59.233 40.000 13.06 0.00 42.01 2.92
2364 2482 2.447887 GCTGACACTGATGGCGACG 61.448 63.158 0.00 0.00 36.14 5.12
2375 2493 2.202878 GGCGACGCATGGAGCTTA 60.203 61.111 23.09 0.00 42.61 3.09
2410 2528 1.070445 GTCCTCCTGATGGATGCCG 59.930 63.158 0.00 0.00 42.29 5.69
2430 2548 3.366985 CCGGCTTATTGGAACAGGTTTTC 60.367 47.826 0.00 0.00 42.39 2.29
2431 2549 3.254657 CGGCTTATTGGAACAGGTTTTCA 59.745 43.478 0.00 0.00 42.39 2.69
2435 2553 6.540551 GGCTTATTGGAACAGGTTTTCAAAAA 59.459 34.615 6.16 0.00 42.39 1.94
2459 2577 1.542915 CTGGTGCATTCTGGTGAAAGG 59.457 52.381 0.00 0.00 35.63 3.11
2460 2578 0.244721 GGTGCATTCTGGTGAAAGGC 59.755 55.000 0.00 0.00 37.20 4.35
2549 2667 2.147958 GCTTGGTGTTACGATGTTCCA 58.852 47.619 0.00 0.00 0.00 3.53
2560 2678 2.698797 ACGATGTTCCATACCCACCTAG 59.301 50.000 0.00 0.00 0.00 3.02
2585 2703 3.921021 CAGACTTGTTTCGTAGGCTACAG 59.079 47.826 23.46 15.82 0.00 2.74
2586 2704 3.825014 AGACTTGTTTCGTAGGCTACAGA 59.175 43.478 23.46 17.65 0.00 3.41
2722 2840 1.994463 AGGGACTGCATTGGAGGTC 59.006 57.895 10.12 4.96 37.18 3.85
2739 2857 2.217038 TCAAGGAGCACGAAGGGCT 61.217 57.895 0.00 0.00 46.07 5.19
2783 2901 3.415457 AACAGAAGCCTCTTGAGAAGG 57.585 47.619 0.00 0.00 0.00 3.46
2815 2933 9.250246 AGCAGTTCTATCTCCTATTATTAGTCC 57.750 37.037 0.00 0.00 0.00 3.85
2840 2958 1.133790 GATACTGTAACTCGGCACCGT 59.866 52.381 9.23 0.00 40.74 4.83
2868 2986 6.677027 TGTTGTTTTGACTGTTGTTAAACG 57.323 33.333 0.00 0.00 39.30 3.60
2925 3044 2.074579 TGTGTCCCTTATTTTGGGGGA 58.925 47.619 0.00 0.00 45.93 4.81
2931 3050 3.706389 CCTTATTTTGGGGGAGGGATT 57.294 47.619 0.00 0.00 0.00 3.01
2958 3077 9.979578 ATTAATAGAGCTATCAAGTCTCAACTG 57.020 33.333 0.00 0.00 35.36 3.16
2960 3079 5.581126 AGAGCTATCAAGTCTCAACTGAG 57.419 43.478 0.00 0.00 43.36 3.35
3028 3152 6.389830 TCTCATGCTGTAAATTTTGTGTGT 57.610 33.333 0.00 0.00 0.00 3.72
3034 3158 8.976471 CATGCTGTAAATTTTGTGTGTTGATTA 58.024 29.630 0.00 0.00 0.00 1.75
3063 3187 9.585099 GTGATTTTGATTACAATGCTAAATCCA 57.415 29.630 0.00 0.00 35.85 3.41
3077 3201 9.435688 AATGCTAAATCCAAATGTAAGTTTTCC 57.564 29.630 0.00 0.00 0.00 3.13
3087 3211 5.869649 ATGTAAGTTTTCCAGCAAAGGTT 57.130 34.783 0.00 0.00 0.00 3.50
3231 3355 3.049708 TCTCAGCAAAGGTGATGTCTG 57.950 47.619 0.00 0.00 42.00 3.51
3274 3398 9.702494 TCATATACAAGCTTAGATGATCACAAG 57.298 33.333 0.00 3.35 27.20 3.16
3295 3419 0.325296 TATTCAGCCTGGGGTCGAGT 60.325 55.000 0.00 0.00 0.00 4.18
3446 3570 8.410673 TGTACAGCCAAAAGACCAAAATATTA 57.589 30.769 0.00 0.00 0.00 0.98
3455 3579 5.582689 AGACCAAAATATTAGCCAGTTGC 57.417 39.130 0.00 0.00 41.71 4.17
3484 3608 1.072965 CTCTTCCCCTGTTCTTGTGCT 59.927 52.381 0.00 0.00 0.00 4.40
3498 3622 2.215942 TGTGCTCTACAGACTGGCTA 57.784 50.000 7.51 0.00 33.42 3.93
3518 3642 4.166888 GCCATCAGCTCCGAGCCA 62.167 66.667 16.99 4.41 43.77 4.75
3557 3681 3.824510 GAAACCGAGTCGTCGCGC 61.825 66.667 12.31 0.00 45.41 6.86
3558 3682 4.634133 AAACCGAGTCGTCGCGCA 62.634 61.111 12.31 0.00 45.41 6.09
3563 3687 3.173240 GAGTCGTCGCGCACCTTC 61.173 66.667 8.75 0.00 0.00 3.46
3574 3698 4.452733 CACCTTCGGCCTCGACCC 62.453 72.222 0.00 0.00 45.92 4.46
3577 3701 3.839432 CTTCGGCCTCGACCCTCC 61.839 72.222 0.00 0.00 45.92 4.30
3584 3708 4.135153 CTCGACCCTCCCGCTGTG 62.135 72.222 0.00 0.00 0.00 3.66
3606 4104 0.674534 ACAGAAAGAAGACGACGGCT 59.325 50.000 0.00 0.00 0.00 5.52
3649 4147 1.378762 TTGACCTACAAGCCAGGGC 59.621 57.895 0.97 0.97 42.12 5.19
3690 4192 8.437360 TTCATTCATAAGCACAACACCTATAG 57.563 34.615 0.00 0.00 0.00 1.31
3691 4193 6.992123 TCATTCATAAGCACAACACCTATAGG 59.008 38.462 17.73 17.73 42.17 2.57
3692 4194 5.290493 TCATAAGCACAACACCTATAGGG 57.710 43.478 22.91 13.70 40.27 3.53
3693 4195 4.966168 TCATAAGCACAACACCTATAGGGA 59.034 41.667 22.91 2.82 40.27 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.036428 CTCATCCTCCTCATGCGCCA 62.036 60.000 4.18 0.00 0.00 5.69
10 11 0.319727 GAGCTCATCCTCCTCATGCG 60.320 60.000 9.40 0.00 0.00 4.73
66 67 0.821301 GCCTTGGCCCTCTAATGCTC 60.821 60.000 0.00 0.00 0.00 4.26
70 71 1.692749 TCCGCCTTGGCCCTCTAAT 60.693 57.895 0.00 0.00 37.80 1.73
90 91 1.139989 ACAATTATCATCGCGAGCCG 58.860 50.000 16.66 5.73 38.61 5.52
168 172 0.959372 AGCTCATGTGGCTGTTGCTC 60.959 55.000 13.32 0.00 38.73 4.26
169 173 1.074423 AGCTCATGTGGCTGTTGCT 59.926 52.632 13.32 0.00 38.73 3.91
170 174 3.677527 AGCTCATGTGGCTGTTGC 58.322 55.556 13.32 0.00 38.73 4.17
175 179 1.620739 ATCGTCCAGCTCATGTGGCT 61.621 55.000 9.44 9.44 41.07 4.75
176 180 0.104855 TATCGTCCAGCTCATGTGGC 59.895 55.000 5.53 5.53 34.77 5.01
186 191 3.902150 ACTCGTATTGCATATCGTCCAG 58.098 45.455 0.00 0.00 0.00 3.86
188 193 5.568296 GTCTTACTCGTATTGCATATCGTCC 59.432 44.000 0.00 0.00 0.00 4.79
209 214 3.600388 CATAAAAGGGACGAGCTTGTCT 58.400 45.455 29.01 14.54 38.91 3.41
212 217 2.711542 ACCATAAAAGGGACGAGCTTG 58.288 47.619 0.00 0.00 0.00 4.01
213 218 3.870274 GTACCATAAAAGGGACGAGCTT 58.130 45.455 0.00 0.00 31.60 3.74
214 219 3.538634 GTACCATAAAAGGGACGAGCT 57.461 47.619 0.00 0.00 31.60 4.09
220 225 2.549082 TGGACCGTACCATAAAAGGGA 58.451 47.619 0.00 0.00 34.77 4.20
229 253 0.322726 TGTCTCGATGGACCGTACCA 60.323 55.000 2.68 0.48 44.41 3.25
243 267 1.343465 TCTTCCCTCACGGTTTGTCTC 59.657 52.381 0.00 0.00 0.00 3.36
247 271 2.472695 TCATCTTCCCTCACGGTTTG 57.527 50.000 0.00 0.00 0.00 2.93
253 277 2.433970 CCCTCTCTTCATCTTCCCTCAC 59.566 54.545 0.00 0.00 0.00 3.51
259 283 1.068434 CTCCGCCCTCTCTTCATCTTC 59.932 57.143 0.00 0.00 0.00 2.87
267 291 3.024356 TCCTCCTCCGCCCTCTCT 61.024 66.667 0.00 0.00 0.00 3.10
268 292 2.520741 CTCCTCCTCCGCCCTCTC 60.521 72.222 0.00 0.00 0.00 3.20
278 302 2.681778 CCACAGTCCGCTCCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
286 310 1.079819 AATGTCTCGCCACAGTCCG 60.080 57.895 0.00 0.00 0.00 4.79
310 334 1.612442 TGAGTGGCAGGGGTAGTCC 60.612 63.158 0.00 0.00 0.00 3.85
319 343 2.061220 TCAGGAACCTGAGTGGCAG 58.939 57.895 18.17 0.00 46.80 4.85
326 350 2.370774 ACGAAGTGCTCAGGAACCTGA 61.371 52.381 20.34 20.34 45.71 3.86
327 351 0.034059 ACGAAGTGCTCAGGAACCTG 59.966 55.000 14.01 14.01 42.51 4.00
531 559 5.424121 AGTTACACAATGAAGTGACTTGC 57.576 39.130 0.90 0.00 42.05 4.01
540 568 6.759272 AGTCTGCTCTTAGTTACACAATGAA 58.241 36.000 0.00 0.00 0.00 2.57
556 584 6.884187 TGTACGAAACAATTTAAGTCTGCTC 58.116 36.000 0.00 0.00 34.29 4.26
557 585 6.704493 TCTGTACGAAACAATTTAAGTCTGCT 59.296 34.615 0.00 0.00 37.74 4.24
585 613 8.422566 GTGCAGGGAGATTACTTATAAGTAGTT 58.577 37.037 21.45 14.90 42.04 2.24
586 614 7.015389 GGTGCAGGGAGATTACTTATAAGTAGT 59.985 40.741 21.45 19.62 42.04 2.73
587 615 7.379750 GGTGCAGGGAGATTACTTATAAGTAG 58.620 42.308 21.45 11.18 42.04 2.57
589 617 5.221461 CGGTGCAGGGAGATTACTTATAAGT 60.221 44.000 21.35 21.35 42.91 2.24
619 730 1.009829 GAGATTGCTAACCACGCCTG 58.990 55.000 0.00 0.00 0.00 4.85
629 740 8.654094 TCTTTAATGATGATCTGGAGATTGCTA 58.346 33.333 0.00 0.00 34.37 3.49
716 827 2.785342 GCGCGAAAAATGTACGGTAAGG 60.785 50.000 12.10 0.00 0.00 2.69
722 833 4.145997 AGTTTTAGCGCGAAAAATGTACG 58.854 39.130 26.44 0.00 30.36 3.67
734 845 8.989980 ACAGATTAAGGATAATAGTTTTAGCGC 58.010 33.333 0.00 0.00 31.83 5.92
775 886 7.545362 GCATAAGCAGATTGTCTTCTCTAAA 57.455 36.000 0.00 0.00 41.58 1.85
792 903 2.263741 CGGCCCATCCTGCATAAGC 61.264 63.158 0.00 0.00 42.57 3.09
795 906 0.762842 AGTACGGCCCATCCTGCATA 60.763 55.000 0.00 0.00 0.00 3.14
796 907 2.072487 AGTACGGCCCATCCTGCAT 61.072 57.895 0.00 0.00 0.00 3.96
798 909 2.203070 CAGTACGGCCCATCCTGC 60.203 66.667 0.00 0.00 0.00 4.85
799 910 2.505982 CCAGTACGGCCCATCCTG 59.494 66.667 0.00 0.00 0.00 3.86
839 953 2.919228 CCGGATCCAACTTCTTTAGGG 58.081 52.381 13.41 0.00 0.00 3.53
870 984 6.305638 GCAGAATTTATAATTTTCCGATCGGC 59.694 38.462 29.62 9.79 34.68 5.54
876 990 6.507023 AGGCTGCAGAATTTATAATTTTCCG 58.493 36.000 20.43 0.00 0.00 4.30
877 991 7.168135 CGAAGGCTGCAGAATTTATAATTTTCC 59.832 37.037 20.43 3.31 0.00 3.13
910 1024 0.804989 CAGTGGAGGGAAATCGTTGC 59.195 55.000 0.00 0.00 0.00 4.17
927 1041 3.617263 GGGAACTACAATCTGTTACGCAG 59.383 47.826 0.00 0.00 46.34 5.18
931 1045 8.336801 AGAATTTGGGAACTACAATCTGTTAC 57.663 34.615 0.00 0.00 0.00 2.50
967 1081 8.992835 ATTATTCTTGCAATTCTTGGTTTCTC 57.007 30.769 0.00 0.00 0.00 2.87
969 1083 8.659491 GGAATTATTCTTGCAATTCTTGGTTTC 58.341 33.333 0.00 0.00 39.83 2.78
989 1103 3.490933 CCAGCTCTTCATCGTCGGAATTA 60.491 47.826 0.00 0.00 0.00 1.40
991 1105 1.202463 CCAGCTCTTCATCGTCGGAAT 60.202 52.381 0.00 0.00 0.00 3.01
992 1106 0.173481 CCAGCTCTTCATCGTCGGAA 59.827 55.000 0.00 0.00 0.00 4.30
1068 1182 2.109126 GTCTTCATCACGCCCCTGC 61.109 63.158 0.00 0.00 0.00 4.85
1149 1263 1.338337 TCTTCCGATTCGATGGAGAGC 59.662 52.381 7.83 0.00 35.26 4.09
1189 1303 4.214327 CTTCTCCGGCGAGCTCCC 62.214 72.222 9.30 9.59 35.94 4.30
1296 1413 1.592223 GTCTCCCTCCGTGTCCAAG 59.408 63.158 0.00 0.00 0.00 3.61
1319 1436 1.218316 CTTGGGGACAGCTCCGTAC 59.782 63.158 0.00 0.00 44.54 3.67
1342 1459 3.117452 GCATCTCCTCCAGCAGGGG 62.117 68.421 0.00 0.00 45.98 4.79
1347 1464 3.092511 TGGGGCATCTCCTCCAGC 61.093 66.667 0.00 0.00 32.90 4.85
1593 1710 1.690219 CCGAACAGGATCCTCCCAGG 61.690 65.000 12.69 9.81 45.00 4.45
1610 1727 0.040067 GAGCAAACACCTGAAAGCCG 60.040 55.000 0.00 0.00 0.00 5.52
1642 1759 1.588674 TCTTCAATCAAACCACGCGT 58.411 45.000 5.58 5.58 0.00 6.01
1810 1927 7.769044 GTCTGATATCTCTACTCTCCCTATCAC 59.231 44.444 3.98 0.00 0.00 3.06
1821 1938 8.321353 CCATCTCTACAGTCTGATATCTCTACT 58.679 40.741 6.91 2.19 0.00 2.57
1839 1956 3.708121 TGAGCAGAATCAAGCCATCTCTA 59.292 43.478 0.00 0.00 0.00 2.43
1840 1957 2.504585 TGAGCAGAATCAAGCCATCTCT 59.495 45.455 0.00 0.00 0.00 3.10
1941 2058 5.544136 TGTAAACATGATCACCGTCATTG 57.456 39.130 0.00 0.00 36.72 2.82
1986 2103 4.033709 AGAACTCTATGGCAGCCTTCTTA 58.966 43.478 14.15 0.00 0.00 2.10
2000 2117 7.148120 CCATAAGAACAGTAACCGAGAACTCTA 60.148 40.741 0.41 0.00 0.00 2.43
2022 2139 1.332195 CGCTCTGGAGATCACCCATA 58.668 55.000 6.73 0.00 32.49 2.74
2035 2152 1.568612 ATTGTCACGTTGGCGCTCTG 61.569 55.000 7.64 0.00 42.83 3.35
2037 2154 0.793861 TAATTGTCACGTTGGCGCTC 59.206 50.000 7.64 0.00 42.83 5.03
2052 2169 7.176690 CCTGTCTTTGATTGGTACTGGTTAATT 59.823 37.037 0.00 0.00 0.00 1.40
2057 2174 3.810743 GCCTGTCTTTGATTGGTACTGGT 60.811 47.826 0.00 0.00 33.22 4.00
2074 2191 0.038744 CTGGAACTCCATTGGCCTGT 59.961 55.000 3.32 0.00 46.46 4.00
2131 2248 4.092091 CAGAACAGACGGTTGCTTAATCTC 59.908 45.833 0.00 0.00 40.63 2.75
2154 2271 6.092748 CAGGAACCATATAGTGTTTTTGCAC 58.907 40.000 0.00 0.00 39.51 4.57
2165 2282 1.344438 TCGGCTGCAGGAACCATATAG 59.656 52.381 17.12 0.00 0.00 1.31
2212 2329 2.853281 GCGTGCCAACTGTTAACTTGTC 60.853 50.000 7.22 0.00 0.00 3.18
2290 2407 3.782523 ACTAGGCAAATTGATCCCTGAGA 59.217 43.478 0.00 0.00 0.00 3.27
2298 2415 6.630444 GTGATCATCACTAGGCAAATTGAT 57.370 37.500 10.81 0.00 43.73 2.57
2320 2437 6.377429 TCGAAGACCATTACTCTGTTATCTGT 59.623 38.462 0.00 0.00 0.00 3.41
2375 2493 1.880027 GGACCGTGAAACTGCTTGAAT 59.120 47.619 0.00 0.00 31.75 2.57
2410 2528 4.864704 TGAAAACCTGTTCCAATAAGCC 57.135 40.909 0.00 0.00 0.00 4.35
2435 2553 1.355381 TCACCAGAATGCACCAGGATT 59.645 47.619 6.40 0.00 38.61 3.01
2459 2577 2.287188 CCCAATGTCAATGTATCGCAGC 60.287 50.000 0.00 0.00 0.00 5.25
2460 2578 2.291465 CCCCAATGTCAATGTATCGCAG 59.709 50.000 0.00 0.00 0.00 5.18
2549 2667 3.246021 ACAAGTCTGTCCTAGGTGGGTAT 60.246 47.826 9.08 0.00 36.20 2.73
2560 2678 2.067013 GCCTACGAAACAAGTCTGTCC 58.933 52.381 0.00 0.00 33.45 4.02
2585 2703 1.899142 AGAAGAGGCTCACCAACTCTC 59.101 52.381 18.26 0.19 40.49 3.20
2586 2704 2.022718 AGAAGAGGCTCACCAACTCT 57.977 50.000 18.26 5.48 43.03 3.24
2722 2840 2.037136 CAGCCCTTCGTGCTCCTTG 61.037 63.158 0.00 0.00 36.81 3.61
2757 2875 4.021016 TCTCAAGAGGCTTCTGTTTAGGTC 60.021 45.833 0.00 0.00 32.79 3.85
2783 2901 2.093235 AGGAGATAGAACTGCTTGTGGC 60.093 50.000 0.00 0.00 35.11 5.01
2815 2933 4.499357 GGTGCCGAGTTACAGTATCTAAGG 60.499 50.000 7.71 7.71 0.00 2.69
2990 3114 1.674359 TGAGAAAGAAAAGCGCCACA 58.326 45.000 2.29 0.00 0.00 4.17
2991 3115 2.589014 CATGAGAAAGAAAAGCGCCAC 58.411 47.619 2.29 0.00 0.00 5.01
3063 3187 6.233905 ACCTTTGCTGGAAAACTTACATTT 57.766 33.333 0.00 0.00 0.00 2.32
3077 3201 7.481275 AACAAAATTGACATAACCTTTGCTG 57.519 32.000 0.00 0.00 0.00 4.41
3167 3291 2.875296 TCACCTTTGCTGCAATACCTT 58.125 42.857 16.77 0.00 0.00 3.50
3274 3398 1.001406 CTCGACCCCAGGCTGAATATC 59.999 57.143 17.94 6.99 0.00 1.63
3295 3419 0.984961 CTTGGGGAGCCTCATCAGGA 60.985 60.000 0.00 0.00 43.65 3.86
3392 3516 3.761897 AGCCTTGTTACTGTAAATGGCA 58.238 40.909 26.50 11.41 41.33 4.92
3401 3525 3.316308 ACAGCAAAGAAGCCTTGTTACTG 59.684 43.478 12.81 12.81 34.23 2.74
3446 3570 1.065551 GAGAAAACAACGCAACTGGCT 59.934 47.619 0.00 0.00 41.67 4.75
3455 3579 2.572290 ACAGGGGAAGAGAAAACAACG 58.428 47.619 0.00 0.00 0.00 4.10
3484 3608 2.490165 GCGGTAGCCAGTCTGTAGA 58.510 57.895 0.00 0.00 37.42 2.59
3529 3653 3.117046 GACTCGGTTTCAGATCGATTCC 58.883 50.000 0.00 0.00 32.32 3.01
3567 3691 4.135153 CACAGCGGGAGGGTCGAG 62.135 72.222 0.00 0.00 0.00 4.04
3574 3698 3.535629 TTCTGTGCCACAGCGGGAG 62.536 63.158 20.05 0.00 45.54 4.30
3577 3701 1.165907 TTCTTTCTGTGCCACAGCGG 61.166 55.000 20.05 11.67 45.54 5.52
3578 3702 0.236711 CTTCTTTCTGTGCCACAGCG 59.763 55.000 20.05 10.55 45.54 5.18
3579 3703 1.265365 GTCTTCTTTCTGTGCCACAGC 59.735 52.381 20.05 0.00 45.54 4.40
3581 3705 1.138069 TCGTCTTCTTTCTGTGCCACA 59.862 47.619 0.00 0.00 0.00 4.17
3582 3706 1.527311 GTCGTCTTCTTTCTGTGCCAC 59.473 52.381 0.00 0.00 0.00 5.01
3583 3707 1.865865 GTCGTCTTCTTTCTGTGCCA 58.134 50.000 0.00 0.00 0.00 4.92
3584 3708 0.784778 CGTCGTCTTCTTTCTGTGCC 59.215 55.000 0.00 0.00 0.00 5.01
3585 3709 0.784778 CCGTCGTCTTCTTTCTGTGC 59.215 55.000 0.00 0.00 0.00 4.57
3586 3710 0.784778 GCCGTCGTCTTCTTTCTGTG 59.215 55.000 0.00 0.00 0.00 3.66
3587 3711 0.674534 AGCCGTCGTCTTCTTTCTGT 59.325 50.000 0.00 0.00 0.00 3.41
3588 3712 2.631418 TAGCCGTCGTCTTCTTTCTG 57.369 50.000 0.00 0.00 0.00 3.02
3589 3713 3.693085 TGTATAGCCGTCGTCTTCTTTCT 59.307 43.478 0.00 0.00 0.00 2.52
3590 3714 4.025015 TGTATAGCCGTCGTCTTCTTTC 57.975 45.455 0.00 0.00 0.00 2.62
3606 4104 6.483974 AGTTCGACAACAACCACATTTGTATA 59.516 34.615 0.00 0.00 38.82 1.47
3645 4143 0.482446 TGGAGAAAATGGTGTGCCCT 59.518 50.000 0.00 0.00 0.00 5.19
3648 4146 3.940209 TGAATGGAGAAAATGGTGTGC 57.060 42.857 0.00 0.00 0.00 4.57
3649 4147 6.028146 TGAATGAATGGAGAAAATGGTGTG 57.972 37.500 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.