Multiple sequence alignment - TraesCS5D01G185500

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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 TraesCS5D01G185500 chr5D 100.000 2966 0 0 1 2966 287779783 287776818 0.000000e+00 5478.0
1 TraesCS5D01G185500 chr5D 80.829 193 20 10 474 660 502884315 502884134 5.160000e-28 135.0
2 TraesCS5D01G185500 chr5B 92.967 1692 82 19 341 2017 326867175 326865506 0.000000e+00 2431.0
3 TraesCS5D01G185500 chr5B 90.335 538 31 14 2414 2947 326865225 326864705 0.000000e+00 686.0
4 TraesCS5D01G185500 chr5B 98.225 169 3 0 2097 2265 326865471 326865303 2.240000e-76 296.0
5 TraesCS5D01G185500 chr5B 89.000 200 20 2 4 202 326879465 326879267 2.280000e-61 246.0
6 TraesCS5D01G185500 chr5A 91.238 1518 97 21 823 2316 380161599 380160094 0.000000e+00 2034.0
7 TraesCS5D01G185500 chr5A 83.662 710 78 11 2 691 380163611 380162920 4.170000e-178 634.0
8 TraesCS5D01G185500 chr5A 89.366 489 30 10 2485 2955 380150618 380150134 1.970000e-166 595.0
9 TraesCS5D01G185500 chr5A 86.179 123 9 5 717 832 380162934 380162813 3.100000e-25 126.0
10 TraesCS5D01G185500 chr5A 100.000 52 0 0 2430 2481 380159836 380159785 2.430000e-16 97.1
11 TraesCS5D01G185500 chr3B 75.970 541 80 22 342 870 728813972 728814474 1.780000e-57 233.0
12 TraesCS5D01G185500 chr3B 77.959 245 40 7 384 617 780878233 780877992 1.110000e-29 141.0
13 TraesCS5D01G185500 chr6D 82.530 166 18 5 458 614 321997138 321997301 5.160000e-28 135.0
14 TraesCS5D01G185500 chr7A 90.909 44 4 0 609 652 126365104 126365061 3.190000e-05 60.2


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 TraesCS5D01G185500 chr5D 287776818 287779783 2965 True 5478.000000 5478 100.000000 1 2966 1 chr5D.!!$R1 2965
1 TraesCS5D01G185500 chr5B 326864705 326867175 2470 True 1137.666667 2431 93.842333 341 2947 3 chr5B.!!$R2 2606
2 TraesCS5D01G185500 chr5A 380159785 380163611 3826 True 722.775000 2034 90.269750 2 2481 4 chr5A.!!$R2 2479
3 TraesCS5D01G185500 chr3B 728813972 728814474 502 False 233.000000 233 75.970000 342 870 1 chr3B.!!$F1 528

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
98 100 0.252103 TCGCTACTGGAGGGGAGTTT 60.252 55.0 3.91 0.0 38.64 2.66 F
100 102 0.393132 GCTACTGGAGGGGAGTTTGC 60.393 60.0 0.00 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 3235 1.004044 CAGCAGGTTGATCTTCCCACT 59.996 52.381 0.0 0.0 0.0 4.00 R
2002 3298 5.212194 CGGTGGACAATTCAAAACTAACAG 58.788 41.667 0.0 0.0 0.0 3.16 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
24 25 3.062763 CACTGCTGAAGTCAAGACGATT 58.937 45.455 0.00 0.00 36.83 3.34
73 75 7.404671 AAGCCTAAAATGAATTACCAACGAT 57.595 32.000 0.00 0.00 0.00 3.73
92 94 0.970937 TTGAGGTCGCTACTGGAGGG 60.971 60.000 0.00 0.00 39.49 4.30
96 98 1.380112 GTCGCTACTGGAGGGGAGT 60.380 63.158 3.91 0.00 38.64 3.85
98 100 0.252103 TCGCTACTGGAGGGGAGTTT 60.252 55.000 3.91 0.00 38.64 2.66
100 102 0.393132 GCTACTGGAGGGGAGTTTGC 60.393 60.000 0.00 0.00 0.00 3.68
104 106 1.151810 TGGAGGGGAGTTTGCCTCT 60.152 57.895 0.00 0.00 42.97 3.69
105 107 1.301293 GGAGGGGAGTTTGCCTCTG 59.699 63.158 0.00 0.00 39.42 3.35
106 108 1.377856 GAGGGGAGTTTGCCTCTGC 60.378 63.158 0.00 0.00 39.42 4.26
107 109 1.846712 GAGGGGAGTTTGCCTCTGCT 61.847 60.000 0.00 0.00 39.42 4.24
108 110 1.075659 GGGGAGTTTGCCTCTGCTT 59.924 57.895 0.00 0.00 40.30 3.91
109 111 0.540597 GGGGAGTTTGCCTCTGCTTT 60.541 55.000 0.00 0.00 40.30 3.51
110 112 0.884514 GGGAGTTTGCCTCTGCTTTC 59.115 55.000 0.00 0.00 40.30 2.62
111 113 1.546548 GGGAGTTTGCCTCTGCTTTCT 60.547 52.381 0.00 0.00 40.30 2.52
112 114 2.234143 GGAGTTTGCCTCTGCTTTCTT 58.766 47.619 0.00 0.00 40.30 2.52
113 115 2.227626 GGAGTTTGCCTCTGCTTTCTTC 59.772 50.000 0.00 0.00 40.30 2.87
114 116 3.145286 GAGTTTGCCTCTGCTTTCTTCT 58.855 45.455 0.00 0.00 37.22 2.85
115 117 3.560105 AGTTTGCCTCTGCTTTCTTCTT 58.440 40.909 0.00 0.00 38.71 2.52
116 118 3.567585 AGTTTGCCTCTGCTTTCTTCTTC 59.432 43.478 0.00 0.00 38.71 2.87
117 119 2.936919 TGCCTCTGCTTTCTTCTTCA 57.063 45.000 0.00 0.00 38.71 3.02
118 120 3.213206 TGCCTCTGCTTTCTTCTTCAA 57.787 42.857 0.00 0.00 38.71 2.69
119 121 3.144506 TGCCTCTGCTTTCTTCTTCAAG 58.855 45.455 0.00 0.00 38.71 3.02
120 122 3.181451 TGCCTCTGCTTTCTTCTTCAAGA 60.181 43.478 0.00 0.00 36.15 3.02
121 123 3.817647 GCCTCTGCTTTCTTCTTCAAGAA 59.182 43.478 0.00 0.00 45.30 2.52
145 147 2.997485 ATGAAAGCGAAAACTGGAGC 57.003 45.000 0.00 0.00 0.00 4.70
152 154 1.927895 CGAAAACTGGAGCGCTCTAT 58.072 50.000 34.46 15.80 0.00 1.98
163 165 4.266070 GCTCTATGCGTCGGCCGA 62.266 66.667 27.28 27.28 39.56 5.54
182 184 5.469084 GGCCGACGGATAATTAGAAAAGATT 59.531 40.000 20.50 0.00 0.00 2.40
183 185 6.017357 GGCCGACGGATAATTAGAAAAGATTT 60.017 38.462 20.50 0.00 0.00 2.17
184 186 6.851330 GCCGACGGATAATTAGAAAAGATTTG 59.149 38.462 20.50 0.00 0.00 2.32
186 188 6.851330 CGACGGATAATTAGAAAAGATTTGCC 59.149 38.462 0.00 0.00 0.00 4.52
197 199 3.100862 GATTTGCCGGCTCGCTGAC 62.101 63.158 29.70 8.76 0.00 3.51
202 204 2.436646 CCGGCTCGCTGACCATTT 60.437 61.111 0.00 0.00 0.00 2.32
203 205 2.040544 CCGGCTCGCTGACCATTTT 61.041 57.895 0.00 0.00 0.00 1.82
212 214 3.435327 TCGCTGACCATTTTGATGTACAC 59.565 43.478 0.00 0.00 0.00 2.90
225 227 2.222007 TGTACACGTTAACGGCTGTT 57.778 45.000 29.81 16.59 44.95 3.16
230 232 2.252747 CACGTTAACGGCTGTTCGATA 58.747 47.619 29.81 0.65 44.95 2.92
240 242 2.494870 GGCTGTTCGATATACCCCGTAT 59.505 50.000 0.00 0.00 33.05 3.06
248 250 4.397103 TCGATATACCCCGTATGTAAGCAG 59.603 45.833 0.00 0.00 30.79 4.24
267 269 1.410153 AGCCACTTCTTTGCAACAAGG 59.590 47.619 17.65 8.20 0.00 3.61
270 272 2.955660 CCACTTCTTTGCAACAAGGGTA 59.044 45.455 17.65 0.00 0.00 3.69
274 276 1.953686 TCTTTGCAACAAGGGTAGTGC 59.046 47.619 0.00 0.00 0.00 4.40
301 303 1.363807 GCCCTTCACAACAACCAGC 59.636 57.895 0.00 0.00 0.00 4.85
304 306 2.582052 CCCTTCACAACAACCAGCTTA 58.418 47.619 0.00 0.00 0.00 3.09
308 310 4.037923 CCTTCACAACAACCAGCTTATTGT 59.962 41.667 6.54 6.54 40.76 2.71
315 317 7.485913 CACAACAACCAGCTTATTGTAATCATC 59.514 37.037 11.77 0.00 38.08 2.92
317 319 6.186957 ACAACCAGCTTATTGTAATCATCCA 58.813 36.000 10.05 0.00 37.27 3.41
321 323 7.573710 ACCAGCTTATTGTAATCATCCAAGTA 58.426 34.615 0.00 0.00 0.00 2.24
413 434 5.830912 TGTTTGCAACAAAGATCTAGTTGG 58.169 37.500 28.20 17.19 42.07 3.77
569 598 1.125093 TGACGTGAAGGGGATGGTGT 61.125 55.000 0.00 0.00 0.00 4.16
653 682 2.061220 CAGGAGCTTGAGGTGGTCA 58.939 57.895 0.00 0.00 34.04 4.02
844 2119 1.396543 GACGCGAGCGCTATAATCCG 61.397 60.000 15.93 10.16 44.19 4.18
863 2138 3.627123 TCCGCCTGTTGATGTTAATCATG 59.373 43.478 0.00 0.00 42.41 3.07
923 2203 9.950680 ATGAAGTAAATATGGAAAGTAAATGCG 57.049 29.630 0.00 0.00 0.00 4.73
924 2204 8.402472 TGAAGTAAATATGGAAAGTAAATGCGG 58.598 33.333 0.00 0.00 0.00 5.69
926 2206 8.967664 AGTAAATATGGAAAGTAAATGCGGTA 57.032 30.769 0.00 0.00 0.00 4.02
927 2207 9.569122 AGTAAATATGGAAAGTAAATGCGGTAT 57.431 29.630 0.00 0.00 0.00 2.73
928 2208 9.821662 GTAAATATGGAAAGTAAATGCGGTATC 57.178 33.333 0.00 0.00 0.00 2.24
929 2209 7.448748 AATATGGAAAGTAAATGCGGTATCC 57.551 36.000 0.00 0.00 0.00 2.59
930 2210 3.547746 TGGAAAGTAAATGCGGTATCCC 58.452 45.455 0.00 0.00 0.00 3.85
932 2212 4.409574 TGGAAAGTAAATGCGGTATCCCTA 59.590 41.667 0.00 0.00 0.00 3.53
933 2213 4.995487 GGAAAGTAAATGCGGTATCCCTAG 59.005 45.833 0.00 0.00 0.00 3.02
935 2215 2.969950 AGTAAATGCGGTATCCCTAGCA 59.030 45.455 0.00 0.00 44.13 3.49
939 2219 1.419381 TGCGGTATCCCTAGCATTGA 58.581 50.000 0.00 0.00 34.39 2.57
940 2220 1.977854 TGCGGTATCCCTAGCATTGAT 59.022 47.619 0.00 0.00 34.39 2.57
941 2221 2.289631 TGCGGTATCCCTAGCATTGATG 60.290 50.000 0.00 0.00 34.39 3.07
951 2235 6.296026 TCCCTAGCATTGATGTGGTATAAAC 58.704 40.000 0.00 0.00 32.27 2.01
972 2256 7.813087 AAACCAAAATTATGGGAGAAATCCT 57.187 32.000 0.00 0.00 45.18 3.24
973 2257 7.423844 AACCAAAATTATGGGAGAAATCCTC 57.576 36.000 0.00 0.00 45.18 3.71
990 2278 8.656806 AGAAATCCTCGTATTTATACCATTCCA 58.343 33.333 0.00 0.00 0.00 3.53
991 2279 9.449719 GAAATCCTCGTATTTATACCATTCCAT 57.550 33.333 0.00 0.00 0.00 3.41
1003 2291 2.886523 ACCATTCCATATTCGTGCATGG 59.113 45.455 5.98 0.01 35.81 3.66
1015 2303 2.159014 TCGTGCATGGGTGTTCCTATAC 60.159 50.000 5.98 0.00 33.06 1.47
1085 2381 3.307199 CCTCCACCTACGTACCAACAATT 60.307 47.826 0.00 0.00 0.00 2.32
1728 3024 2.444895 GGGAGAGCGGTGGAGGAT 60.445 66.667 0.00 0.00 0.00 3.24
1785 3081 2.201022 GGAGAAGATCCGGCGGCTA 61.201 63.158 23.83 5.12 38.67 3.93
1876 3172 2.203266 GGGTGCAGGAGCTATGGC 60.203 66.667 0.00 0.00 42.74 4.40
1939 3235 1.139734 GTCATCGCGGAGAAGAGCA 59.860 57.895 6.13 0.00 0.00 4.26
2002 3298 0.724785 GTGTTAGTTTTGGCGCGCTC 60.725 55.000 32.29 21.22 0.00 5.03
2124 3421 5.523438 ACTCCTTTATTGCGTTTCCAAAA 57.477 34.783 0.00 0.00 0.00 2.44
2276 3573 2.034842 CGTCGAATTGTCTTATGCGGTC 60.035 50.000 0.00 0.00 0.00 4.79
2277 3574 2.927477 GTCGAATTGTCTTATGCGGTCA 59.073 45.455 0.00 0.00 0.00 4.02
2310 3607 7.945134 TCCCTCGTCCAATACTTTATAGTTAC 58.055 38.462 0.00 0.00 35.78 2.50
2364 3661 9.698309 AAATACTTCGGAATAGTACATGAGATG 57.302 33.333 0.00 0.00 31.37 2.90
2366 3663 7.348080 ACTTCGGAATAGTACATGAGATGAA 57.652 36.000 0.00 0.00 0.00 2.57
2367 3664 7.203910 ACTTCGGAATAGTACATGAGATGAAC 58.796 38.462 0.00 0.00 0.00 3.18
2368 3665 6.709018 TCGGAATAGTACATGAGATGAACA 57.291 37.500 0.00 0.00 0.00 3.18
2369 3666 7.290110 TCGGAATAGTACATGAGATGAACAT 57.710 36.000 0.00 0.00 0.00 2.71
2383 3793 0.736325 GAACATCGGACCCTGTGACG 60.736 60.000 0.00 0.00 0.00 4.35
2403 3860 4.964593 ACGTTTTGCCCCGAAGTATATAT 58.035 39.130 0.00 0.00 0.00 0.86
2405 3862 5.824097 ACGTTTTGCCCCGAAGTATATATTT 59.176 36.000 0.00 0.00 0.00 1.40
2484 3941 3.555795 CCAGGGTGAGAATATGTCCATCG 60.556 52.174 0.00 0.00 0.00 3.84
2485 3942 3.070159 CAGGGTGAGAATATGTCCATCGT 59.930 47.826 0.00 0.00 0.00 3.73
2491 3948 5.850128 GTGAGAATATGTCCATCGTACGTAC 59.150 44.000 15.90 15.90 0.00 3.67
2519 3976 0.668401 GCACTAAGGGTTGTACGCGT 60.668 55.000 19.17 19.17 36.04 6.01
2521 3978 2.926159 GCACTAAGGGTTGTACGCGTTA 60.926 50.000 20.78 3.99 36.04 3.18
2572 4029 2.626785 TGTGGGGAAGGTGATGAAGTA 58.373 47.619 0.00 0.00 0.00 2.24
2574 4031 3.054434 TGTGGGGAAGGTGATGAAGTATG 60.054 47.826 0.00 0.00 0.00 2.39
2579 4036 5.125578 GGGGAAGGTGATGAAGTATGTTTTC 59.874 44.000 0.00 0.00 0.00 2.29
2581 4038 6.434340 GGGAAGGTGATGAAGTATGTTTTCTT 59.566 38.462 0.00 0.00 0.00 2.52
2582 4039 7.039714 GGGAAGGTGATGAAGTATGTTTTCTTT 60.040 37.037 0.00 0.00 0.00 2.52
2583 4040 8.360390 GGAAGGTGATGAAGTATGTTTTCTTTT 58.640 33.333 0.00 0.00 0.00 2.27
2584 4041 9.399403 GAAGGTGATGAAGTATGTTTTCTTTTC 57.601 33.333 0.00 0.00 0.00 2.29
2601 4058 0.801872 TTCCATGATGCGGTGTTTCG 59.198 50.000 0.00 0.00 0.00 3.46
2606 4063 1.669760 GATGCGGTGTTTCGGTGGA 60.670 57.895 0.00 0.00 0.00 4.02
2614 4071 2.032924 GGTGTTTCGGTGGACTTTCTTG 59.967 50.000 0.00 0.00 0.00 3.02
2626 4083 3.564225 GGACTTTCTTGACGGTGTGATTT 59.436 43.478 0.00 0.00 0.00 2.17
2627 4084 4.036380 GGACTTTCTTGACGGTGTGATTTT 59.964 41.667 0.00 0.00 0.00 1.82
2682 4139 2.489938 ACTTTGGTGTCCGCATGTAT 57.510 45.000 0.00 0.00 0.00 2.29
2694 4151 6.687105 GTGTCCGCATGTATTTTATTTGTCTC 59.313 38.462 0.00 0.00 0.00 3.36
2697 4154 6.372937 TCCGCATGTATTTTATTTGTCTCACA 59.627 34.615 0.00 0.00 0.00 3.58
2705 4162 7.807977 ATTTTATTTGTCTCACAGTGTCACT 57.192 32.000 0.00 0.00 0.00 3.41
2712 4169 2.499693 TCTCACAGTGTCACTTGTTGGA 59.500 45.455 1.67 3.70 0.00 3.53
2714 4171 1.331756 CACAGTGTCACTTGTTGGAGC 59.668 52.381 1.67 0.00 0.00 4.70
2775 4233 2.715737 TTTTACGGATTGGTTGCTGC 57.284 45.000 0.00 0.00 0.00 5.25
2789 4248 4.467082 TGGTTGCTGCCATTAATTTGAGAT 59.533 37.500 0.00 0.00 32.81 2.75
2839 4299 8.926092 ATTAAATCCCCTAACTAAATGAGAGC 57.074 34.615 0.00 0.00 0.00 4.09
2840 4300 6.582929 AAATCCCCTAACTAAATGAGAGCT 57.417 37.500 0.00 0.00 0.00 4.09
2841 4301 5.816955 ATCCCCTAACTAAATGAGAGCTC 57.183 43.478 5.27 5.27 0.00 4.09
2842 4302 3.637229 TCCCCTAACTAAATGAGAGCTCG 59.363 47.826 8.37 0.00 0.00 5.03
2843 4303 3.385111 CCCCTAACTAAATGAGAGCTCGT 59.615 47.826 8.37 0.00 0.00 4.18
2844 4304 4.500035 CCCCTAACTAAATGAGAGCTCGTC 60.500 50.000 8.37 7.13 0.00 4.20
2845 4305 4.283678 CCTAACTAAATGAGAGCTCGTCG 58.716 47.826 8.37 0.00 0.00 5.12
2846 4306 2.853731 ACTAAATGAGAGCTCGTCGG 57.146 50.000 8.37 0.00 0.00 4.79
2847 4307 2.093106 ACTAAATGAGAGCTCGTCGGT 58.907 47.619 8.37 0.00 0.00 4.69
2848 4308 2.097791 ACTAAATGAGAGCTCGTCGGTC 59.902 50.000 8.37 0.00 40.43 4.79
2849 4309 0.173708 AAATGAGAGCTCGTCGGTCC 59.826 55.000 8.37 0.00 41.03 4.46
2860 4320 3.560068 GCTCGTCGGTCCAAATCATAAAT 59.440 43.478 0.00 0.00 0.00 1.40
2930 4390 8.364142 AGTAAGGAGCATAGTGAATTAGATGAC 58.636 37.037 0.00 0.00 0.00 3.06
2933 4393 5.403766 GGAGCATAGTGAATTAGATGACACG 59.596 44.000 0.00 0.00 38.15 4.49
2937 4397 6.238211 GCATAGTGAATTAGATGACACGCTTT 60.238 38.462 0.00 0.00 38.15 3.51
2938 4398 7.042725 GCATAGTGAATTAGATGACACGCTTTA 60.043 37.037 0.00 0.00 38.15 1.85
2939 4399 6.893958 AGTGAATTAGATGACACGCTTTAG 57.106 37.500 0.00 0.00 38.15 1.85
2942 4402 7.387948 AGTGAATTAGATGACACGCTTTAGTTT 59.612 33.333 0.00 0.00 38.15 2.66
2943 4403 8.653338 GTGAATTAGATGACACGCTTTAGTTTA 58.347 33.333 0.00 0.00 0.00 2.01
2945 4405 7.772332 ATTAGATGACACGCTTTAGTTTAGG 57.228 36.000 0.00 0.00 0.00 2.69
2946 4406 5.401531 AGATGACACGCTTTAGTTTAGGA 57.598 39.130 0.00 0.00 0.00 2.94
2947 4407 5.978814 AGATGACACGCTTTAGTTTAGGAT 58.021 37.500 0.00 0.00 0.00 3.24
2948 4408 7.108841 AGATGACACGCTTTAGTTTAGGATA 57.891 36.000 0.00 0.00 0.00 2.59
2949 4409 7.727181 AGATGACACGCTTTAGTTTAGGATAT 58.273 34.615 0.00 0.00 0.00 1.63
2950 4410 8.857098 AGATGACACGCTTTAGTTTAGGATATA 58.143 33.333 0.00 0.00 0.00 0.86
2951 4411 9.640963 GATGACACGCTTTAGTTTAGGATATAT 57.359 33.333 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.143094 GGTGTTAATCGTCTTGACTTCAGC 60.143 45.833 0.00 0.00 0.00 4.26
63 65 1.274167 AGCGACCTCAATCGTTGGTAA 59.726 47.619 0.00 0.00 44.13 2.85
64 66 0.892755 AGCGACCTCAATCGTTGGTA 59.107 50.000 0.00 0.00 44.13 3.25
73 75 0.970937 CCCTCCAGTAGCGACCTCAA 60.971 60.000 0.00 0.00 0.00 3.02
96 98 3.554934 TGAAGAAGAAAGCAGAGGCAAA 58.445 40.909 0.00 0.00 44.61 3.68
98 100 2.936919 TGAAGAAGAAAGCAGAGGCA 57.063 45.000 0.00 0.00 44.61 4.75
112 114 6.618287 TCGCTTTCATTTCTTTCTTGAAGA 57.382 33.333 0.00 0.00 42.56 2.87
113 115 7.684062 TTTCGCTTTCATTTCTTTCTTGAAG 57.316 32.000 0.00 0.00 36.67 3.02
114 116 7.759433 AGTTTTCGCTTTCATTTCTTTCTTGAA 59.241 29.630 0.00 0.00 0.00 2.69
115 117 7.220683 CAGTTTTCGCTTTCATTTCTTTCTTGA 59.779 33.333 0.00 0.00 0.00 3.02
116 118 7.332530 CAGTTTTCGCTTTCATTTCTTTCTTG 58.667 34.615 0.00 0.00 0.00 3.02
117 119 6.476706 CCAGTTTTCGCTTTCATTTCTTTCTT 59.523 34.615 0.00 0.00 0.00 2.52
118 120 5.979517 CCAGTTTTCGCTTTCATTTCTTTCT 59.020 36.000 0.00 0.00 0.00 2.52
119 121 5.977129 TCCAGTTTTCGCTTTCATTTCTTTC 59.023 36.000 0.00 0.00 0.00 2.62
120 122 5.901552 TCCAGTTTTCGCTTTCATTTCTTT 58.098 33.333 0.00 0.00 0.00 2.52
121 123 5.514274 TCCAGTTTTCGCTTTCATTTCTT 57.486 34.783 0.00 0.00 0.00 2.52
127 129 0.586319 CGCTCCAGTTTTCGCTTTCA 59.414 50.000 0.00 0.00 0.00 2.69
163 165 6.238648 CCGGCAAATCTTTTCTAATTATCCGT 60.239 38.462 0.00 0.00 32.56 4.69
186 188 1.135315 CAAAATGGTCAGCGAGCCG 59.865 57.895 5.53 0.00 0.00 5.52
197 199 5.083389 CCGTTAACGTGTACATCAAAATGG 58.917 41.667 25.15 3.58 35.94 3.16
202 204 2.732500 CAGCCGTTAACGTGTACATCAA 59.267 45.455 25.15 0.00 37.74 2.57
203 205 2.288334 ACAGCCGTTAACGTGTACATCA 60.288 45.455 25.15 0.00 37.74 3.07
212 214 3.423206 GGTATATCGAACAGCCGTTAACG 59.577 47.826 20.99 20.99 34.75 3.18
225 227 4.334552 TGCTTACATACGGGGTATATCGA 58.665 43.478 0.00 0.00 0.00 3.59
230 232 1.346722 GGCTGCTTACATACGGGGTAT 59.653 52.381 0.00 0.00 0.00 2.73
240 242 1.608590 GCAAAGAAGTGGCTGCTTACA 59.391 47.619 0.00 0.00 27.65 2.41
248 250 1.538849 CCCTTGTTGCAAAGAAGTGGC 60.539 52.381 0.00 0.00 44.93 5.01
274 276 0.323629 TTGTGAAGGGCCTTCTACGG 59.676 55.000 38.24 0.00 40.73 4.02
288 290 6.488344 TGATTACAATAAGCTGGTTGTTGTGA 59.512 34.615 31.41 26.75 46.57 3.58
465 486 3.541996 CCTGTTGCAAAAGGGTTTCTT 57.458 42.857 26.01 0.00 37.28 2.52
538 567 3.376234 CCTTCACGTCACGGTCTCTATTA 59.624 47.826 0.35 0.00 0.00 0.98
569 598 2.217038 AAGCTCCTCCTGCCGTCAA 61.217 57.895 0.00 0.00 0.00 3.18
673 702 3.463505 CTCCTGCAGCAACGTACG 58.536 61.111 15.01 15.01 0.00 3.67
721 750 0.254178 CCACCACCATCTCCTTCAGG 59.746 60.000 0.00 0.00 0.00 3.86
763 792 1.132849 TCTTCCTCAACCTCTGTCCCA 60.133 52.381 0.00 0.00 0.00 4.37
844 2119 4.202050 GGGACATGATTAACATCAACAGGC 60.202 45.833 0.00 0.00 42.93 4.85
924 2204 4.357918 ACCACATCAATGCTAGGGATAC 57.642 45.455 0.00 0.00 0.00 2.24
926 2206 6.702449 TTATACCACATCAATGCTAGGGAT 57.298 37.500 0.00 0.00 0.00 3.85
927 2207 6.296026 GTTTATACCACATCAATGCTAGGGA 58.704 40.000 0.00 0.00 0.00 4.20
928 2208 5.473504 GGTTTATACCACATCAATGCTAGGG 59.526 44.000 0.00 0.00 44.36 3.53
929 2209 6.560253 GGTTTATACCACATCAATGCTAGG 57.440 41.667 0.00 0.00 44.36 3.02
951 2235 5.594317 ACGAGGATTTCTCCCATAATTTTGG 59.406 40.000 7.89 7.89 43.21 3.28
963 2247 9.152595 GGAATGGTATAAATACGAGGATTTCTC 57.847 37.037 0.00 0.00 39.10 2.87
971 2255 9.582431 ACGAATATGGAATGGTATAAATACGAG 57.418 33.333 0.00 0.00 34.11 4.18
972 2256 9.361315 CACGAATATGGAATGGTATAAATACGA 57.639 33.333 0.00 0.00 34.11 3.43
973 2257 8.114290 GCACGAATATGGAATGGTATAAATACG 58.886 37.037 0.00 0.00 34.11 3.06
982 2270 2.886523 CCATGCACGAATATGGAATGGT 59.113 45.455 9.82 0.00 45.32 3.55
983 2271 2.229543 CCCATGCACGAATATGGAATGG 59.770 50.000 14.90 0.00 45.32 3.16
990 2278 2.092429 AGGAACACCCATGCACGAATAT 60.092 45.455 0.00 0.00 37.41 1.28
991 2279 1.280710 AGGAACACCCATGCACGAATA 59.719 47.619 0.00 0.00 37.41 1.75
992 2280 0.038166 AGGAACACCCATGCACGAAT 59.962 50.000 0.00 0.00 37.41 3.34
1003 2291 2.289565 GCTGGCTTGTATAGGAACACC 58.710 52.381 0.00 0.00 0.00 4.16
1438 2734 1.517257 CTCCTTCGACGAGCGCATT 60.517 57.895 11.47 0.00 40.61 3.56
1440 2736 3.053896 TCTCCTTCGACGAGCGCA 61.054 61.111 11.47 0.00 40.61 6.09
1728 3024 3.587923 CCCGAACGTGTTAACCTTGATA 58.412 45.455 2.48 0.00 0.00 2.15
1785 3081 4.335647 CACCCCTCCAGCGTGCTT 62.336 66.667 0.00 0.00 0.00 3.91
1876 3172 1.376037 GCTCCCAGACAACCTTCCG 60.376 63.158 0.00 0.00 0.00 4.30
1939 3235 1.004044 CAGCAGGTTGATCTTCCCACT 59.996 52.381 0.00 0.00 0.00 4.00
2002 3298 5.212194 CGGTGGACAATTCAAAACTAACAG 58.788 41.667 0.00 0.00 0.00 3.16
2095 3392 7.011950 TGGAAACGCAATAAAGGAGTATATGTG 59.988 37.037 0.00 0.00 0.00 3.21
2137 3434 6.371825 AGTGAAAGTTCGAAATAGGTCATTCC 59.628 38.462 0.00 0.00 0.00 3.01
2338 3635 9.698309 CATCTCATGTACTATTCCGAAGTATTT 57.302 33.333 0.00 0.00 32.34 1.40
2339 3636 9.078990 TCATCTCATGTACTATTCCGAAGTATT 57.921 33.333 0.00 0.00 32.34 1.89
2340 3637 8.637196 TCATCTCATGTACTATTCCGAAGTAT 57.363 34.615 0.00 0.00 32.34 2.12
2342 3639 6.961360 TCATCTCATGTACTATTCCGAAGT 57.039 37.500 0.00 0.00 0.00 3.01
2343 3640 7.203218 TGTTCATCTCATGTACTATTCCGAAG 58.797 38.462 0.00 0.00 32.55 3.79
2344 3641 7.107639 TGTTCATCTCATGTACTATTCCGAA 57.892 36.000 0.00 0.00 32.55 4.30
2345 3642 6.709018 TGTTCATCTCATGTACTATTCCGA 57.291 37.500 0.00 0.00 32.55 4.55
2346 3643 6.306596 CGATGTTCATCTCATGTACTATTCCG 59.693 42.308 10.44 0.00 32.55 4.30
2347 3644 6.587990 CCGATGTTCATCTCATGTACTATTCC 59.412 42.308 10.44 0.00 32.55 3.01
2348 3645 7.327275 GTCCGATGTTCATCTCATGTACTATTC 59.673 40.741 10.44 0.00 32.55 1.75
2349 3646 7.148641 GTCCGATGTTCATCTCATGTACTATT 58.851 38.462 10.44 0.00 32.55 1.73
2352 3649 4.202161 GGTCCGATGTTCATCTCATGTACT 60.202 45.833 10.44 0.00 32.55 2.73
2353 3650 4.051922 GGTCCGATGTTCATCTCATGTAC 58.948 47.826 10.44 0.00 0.00 2.90
2354 3651 3.069586 GGGTCCGATGTTCATCTCATGTA 59.930 47.826 10.44 0.00 0.00 2.29
2357 3654 2.103771 CAGGGTCCGATGTTCATCTCAT 59.896 50.000 10.44 0.00 0.00 2.90
2358 3655 1.482182 CAGGGTCCGATGTTCATCTCA 59.518 52.381 10.44 0.00 0.00 3.27
2359 3656 1.482593 ACAGGGTCCGATGTTCATCTC 59.517 52.381 10.44 2.47 0.00 2.75
2360 3657 1.208052 CACAGGGTCCGATGTTCATCT 59.792 52.381 10.44 0.00 0.00 2.90
2363 3660 0.320374 GTCACAGGGTCCGATGTTCA 59.680 55.000 0.00 0.00 0.00 3.18
2364 3661 0.736325 CGTCACAGGGTCCGATGTTC 60.736 60.000 0.00 0.00 0.00 3.18
2366 3663 1.469335 AACGTCACAGGGTCCGATGT 61.469 55.000 0.00 0.00 0.00 3.06
2367 3664 0.320421 AAACGTCACAGGGTCCGATG 60.320 55.000 0.00 0.00 0.00 3.84
2368 3665 0.395312 AAAACGTCACAGGGTCCGAT 59.605 50.000 0.00 0.00 0.00 4.18
2369 3666 0.531090 CAAAACGTCACAGGGTCCGA 60.531 55.000 0.00 0.00 0.00 4.55
2484 3941 6.860023 CCCTTAGTGCATATGTAAGTACGTAC 59.140 42.308 18.10 18.10 31.13 3.67
2485 3942 6.547141 ACCCTTAGTGCATATGTAAGTACGTA 59.453 38.462 4.29 0.00 32.73 3.57
2491 3948 6.200286 CGTACAACCCTTAGTGCATATGTAAG 59.800 42.308 4.29 4.79 0.00 2.34
2519 3976 3.375610 ACAACATCAACAACGCAGTGTAA 59.624 39.130 0.00 0.00 45.00 2.41
2521 3978 1.742831 ACAACATCAACAACGCAGTGT 59.257 42.857 0.00 0.00 45.00 3.55
2572 4029 4.021192 ACCGCATCATGGAAAAGAAAACAT 60.021 37.500 0.00 0.00 0.00 2.71
2574 4031 3.674753 CACCGCATCATGGAAAAGAAAAC 59.325 43.478 0.00 0.00 0.00 2.43
2579 4036 3.244976 GAAACACCGCATCATGGAAAAG 58.755 45.455 0.00 0.00 0.00 2.27
2581 4038 1.198867 CGAAACACCGCATCATGGAAA 59.801 47.619 0.00 0.00 0.00 3.13
2582 4039 0.801872 CGAAACACCGCATCATGGAA 59.198 50.000 0.00 0.00 0.00 3.53
2583 4040 1.024046 CCGAAACACCGCATCATGGA 61.024 55.000 0.00 0.00 0.00 3.41
2584 4041 1.305219 ACCGAAACACCGCATCATGG 61.305 55.000 0.00 0.00 0.00 3.66
2601 4058 1.226746 CACCGTCAAGAAAGTCCACC 58.773 55.000 0.00 0.00 0.00 4.61
2606 4063 4.398044 ACAAAATCACACCGTCAAGAAAGT 59.602 37.500 0.00 0.00 0.00 2.66
2614 4071 4.022464 TGAAACACAAAATCACACCGTC 57.978 40.909 0.00 0.00 0.00 4.79
2626 4083 8.642432 TCCACATAATTATTGGTTGAAACACAA 58.358 29.630 18.32 0.00 36.02 3.33
2627 4084 8.183104 TCCACATAATTATTGGTTGAAACACA 57.817 30.769 18.32 0.00 0.00 3.72
2682 4139 7.120579 ACAAGTGACACTGTGAGACAAATAAAA 59.879 33.333 15.86 0.00 0.00 1.52
2694 4151 1.331756 GCTCCAACAAGTGACACTGTG 59.668 52.381 9.33 11.74 0.00 3.66
2697 4154 2.717639 AAGCTCCAACAAGTGACACT 57.282 45.000 1.07 1.07 0.00 3.55
2823 4283 4.283678 CGACGAGCTCTCATTTAGTTAGG 58.716 47.826 12.85 0.00 0.00 2.69
2824 4284 4.201930 ACCGACGAGCTCTCATTTAGTTAG 60.202 45.833 12.85 0.00 0.00 2.34
2825 4285 3.693085 ACCGACGAGCTCTCATTTAGTTA 59.307 43.478 12.85 0.00 0.00 2.24
2827 4287 2.093106 ACCGACGAGCTCTCATTTAGT 58.907 47.619 12.85 0.00 0.00 2.24
2828 4288 2.541999 GGACCGACGAGCTCTCATTTAG 60.542 54.545 12.85 0.00 0.00 1.85
2829 4289 1.404391 GGACCGACGAGCTCTCATTTA 59.596 52.381 12.85 0.00 0.00 1.40
2832 4292 0.965866 TTGGACCGACGAGCTCTCAT 60.966 55.000 12.85 0.00 0.00 2.90
2833 4293 1.176619 TTTGGACCGACGAGCTCTCA 61.177 55.000 12.85 0.00 0.00 3.27
2835 4295 0.173708 GATTTGGACCGACGAGCTCT 59.826 55.000 12.85 0.00 0.00 4.09
2836 4296 0.108804 TGATTTGGACCGACGAGCTC 60.109 55.000 2.73 2.73 0.00 4.09
2838 4298 2.218953 TATGATTTGGACCGACGAGC 57.781 50.000 0.00 0.00 0.00 5.03
2839 4299 4.808895 TGATTTATGATTTGGACCGACGAG 59.191 41.667 0.00 0.00 0.00 4.18
2840 4300 4.760878 TGATTTATGATTTGGACCGACGA 58.239 39.130 0.00 0.00 0.00 4.20
2841 4301 5.478233 TTGATTTATGATTTGGACCGACG 57.522 39.130 0.00 0.00 0.00 5.12
2842 4302 6.039270 TGGATTGATTTATGATTTGGACCGAC 59.961 38.462 0.00 0.00 0.00 4.79
2843 4303 6.125719 TGGATTGATTTATGATTTGGACCGA 58.874 36.000 0.00 0.00 0.00 4.69
2844 4304 6.389830 TGGATTGATTTATGATTTGGACCG 57.610 37.500 0.00 0.00 0.00 4.79
2845 4305 9.617523 ATTTTGGATTGATTTATGATTTGGACC 57.382 29.630 0.00 0.00 0.00 4.46
2860 4320 5.302568 ACTGAGCTGTTCAATTTTGGATTGA 59.697 36.000 0.00 0.00 34.81 2.57
2876 4336 2.925306 GCTTTGCCATTCAACTGAGCTG 60.925 50.000 0.00 0.00 34.70 4.24


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

AutoCloner maintained by Alex Coulton.