Multiple sequence alignment - TraesCS1D01G241300

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 TraesCS1D01G241300 chr1D 100.000 3763 0 0 1 3763 332073359 332069597 0.000000e+00 6950.0
1 TraesCS1D01G241300 chr1D 100.000 35 0 0 3039 3073 332070200 332070166 8.720000e-07 65.8
2 TraesCS1D01G241300 chr1D 100.000 35 0 0 3160 3194 332070321 332070287 8.720000e-07 65.8
3 TraesCS1D01G241300 chr1A 91.070 3102 102 60 1 3009 429004920 429001901 0.000000e+00 4032.0
4 TraesCS1D01G241300 chr1A 89.494 514 20 7 3282 3763 429001671 429001160 1.480000e-173 619.0
5 TraesCS1D01G241300 chr1A 91.111 180 14 1 3121 3298 429001861 429001682 3.760000e-60 243.0
6 TraesCS1D01G241300 chr1B 93.617 2256 68 30 1 2233 446260080 446257878 0.000000e+00 3299.0
7 TraesCS1D01G241300 chr1B 95.549 719 15 10 2272 2980 446257882 446257171 0.000000e+00 1134.0
8 TraesCS1D01G241300 chr1B 86.035 401 22 8 3121 3518 446257104 446256735 2.110000e-107 399.0
9 TraesCS1D01G241300 chr1B 97.959 147 3 0 3617 3763 446256653 446256507 4.820000e-64 255.0
10 TraesCS1D01G241300 chr1B 96.491 57 2 0 3516 3572 446256711 446256655 1.110000e-15 95.3
11 TraesCS1D01G241300 chr5D 90.654 535 27 16 2232 2756 315913388 315912867 0.000000e+00 689.0
12 TraesCS1D01G241300 chr4D 89.346 535 35 12 2232 2756 1741968 1741446 0.000000e+00 652.0
13 TraesCS1D01G241300 chr4D 91.563 403 22 8 2356 2756 130857888 130858280 2.560000e-151 545.0
14 TraesCS1D01G241300 chr2D 91.584 404 21 7 2356 2756 52740477 52740870 2.560000e-151 545.0
15 TraesCS1D01G241300 chr2D 80.838 334 28 19 1932 2252 381865092 381865402 2.920000e-56 230.0


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 TraesCS1D01G241300 chr1D 332069597 332073359 3762 True 2360.533333 6950 100.000000 1 3763 3 chr1D.!!$R1 3762
1 TraesCS1D01G241300 chr1A 429001160 429004920 3760 True 1631.333333 4032 90.558333 1 3763 3 chr1A.!!$R1 3762
2 TraesCS1D01G241300 chr1B 446256507 446260080 3573 True 1036.460000 3299 93.930200 1 3763 5 chr1B.!!$R1 3762
3 TraesCS1D01G241300 chr5D 315912867 315913388 521 True 689.000000 689 90.654000 2232 2756 1 chr5D.!!$R1 524
4 TraesCS1D01G241300 chr4D 1741446 1741968 522 True 652.000000 652 89.346000 2232 2756 1 chr4D.!!$R1 524

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
272 303 0.032217 CCCCTCTCTCCTTCTCTGCT 60.032 60.0 0.00 0.0 0.0 4.24 F
336 370 0.038159 CTCTCACACTCCGTTGTCCC 60.038 60.0 0.00 0.0 0.0 4.46 F
1799 1884 0.171007 CATCAACGGCCACATGTTCC 59.829 55.0 2.24 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2234 0.472044 TGGAAGTTAGCTGTGGCACA 59.528 50.000 20.76 20.76 41.70 4.57 R
2258 2355 2.488937 CACAACAGCATCAGCCACATAA 59.511 45.455 0.00 0.00 43.56 1.90 R
3115 3244 0.116342 TGGCCACTCCTTAGTCCTCA 59.884 55.000 0.00 0.00 31.97 3.86 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
23 24 3.478274 GGCAGAGCAGGAGGGGAG 61.478 72.222 0.00 0.00 0.00 4.30
25 26 1.992277 GCAGAGCAGGAGGGGAGAA 60.992 63.158 0.00 0.00 0.00 2.87
26 27 1.970352 GCAGAGCAGGAGGGGAGAAG 61.970 65.000 0.00 0.00 0.00 2.85
27 28 0.325110 CAGAGCAGGAGGGGAGAAGA 60.325 60.000 0.00 0.00 0.00 2.87
226 244 2.328099 CCCGCAGCCACTTCTTCAC 61.328 63.158 0.00 0.00 0.00 3.18
227 245 2.671177 CCGCAGCCACTTCTTCACG 61.671 63.158 0.00 0.00 0.00 4.35
229 247 1.963338 GCAGCCACTTCTTCACGCT 60.963 57.895 0.00 0.00 0.00 5.07
230 248 1.864862 CAGCCACTTCTTCACGCTG 59.135 57.895 0.00 0.00 40.81 5.18
231 249 1.748403 AGCCACTTCTTCACGCTGA 59.252 52.632 0.00 0.00 0.00 4.26
266 297 3.157949 CCGGCCCCTCTCTCCTTC 61.158 72.222 0.00 0.00 0.00 3.46
267 298 2.042435 CGGCCCCTCTCTCCTTCT 60.042 66.667 0.00 0.00 0.00 2.85
268 299 2.131067 CGGCCCCTCTCTCCTTCTC 61.131 68.421 0.00 0.00 0.00 2.87
269 300 1.313129 GGCCCCTCTCTCCTTCTCT 59.687 63.158 0.00 0.00 0.00 3.10
270 301 1.048160 GGCCCCTCTCTCCTTCTCTG 61.048 65.000 0.00 0.00 0.00 3.35
271 302 1.685355 GCCCCTCTCTCCTTCTCTGC 61.685 65.000 0.00 0.00 0.00 4.26
272 303 0.032217 CCCCTCTCTCCTTCTCTGCT 60.032 60.000 0.00 0.00 0.00 4.24
273 304 1.622173 CCCCTCTCTCCTTCTCTGCTT 60.622 57.143 0.00 0.00 0.00 3.91
284 318 4.079500 TCCTTCTCTGCTTCTCTCCTATCA 60.080 45.833 0.00 0.00 0.00 2.15
299 333 2.093288 CCTATCATCACCAGCACACAGT 60.093 50.000 0.00 0.00 0.00 3.55
326 360 0.679640 CGCTCTCTCCCTCTCACACT 60.680 60.000 0.00 0.00 0.00 3.55
328 362 1.762708 CTCTCTCCCTCTCACACTCC 58.237 60.000 0.00 0.00 0.00 3.85
336 370 0.038159 CTCTCACACTCCGTTGTCCC 60.038 60.000 0.00 0.00 0.00 4.46
389 426 0.708209 TAGCCCCTGTGTCCTGTAGA 59.292 55.000 0.00 0.00 0.00 2.59
440 481 1.994399 AAGGGAGGAGGAGAGAGAGA 58.006 55.000 0.00 0.00 0.00 3.10
498 551 4.800914 GCTCTAGAGACTAGAGAGAGGCTG 60.801 54.167 28.67 10.04 42.68 4.85
534 587 2.752075 AGGTGGTAGTAGGGTAGAGC 57.248 55.000 0.00 0.00 0.00 4.09
624 686 2.368011 GGAGAGGAGGGGTTTCCGG 61.368 68.421 0.00 0.00 42.29 5.14
798 873 3.015145 GGGAAGCTACTGCCCCCA 61.015 66.667 0.00 0.00 43.71 4.96
1225 1303 1.301716 GCCGACAAGAAGCAGGTCA 60.302 57.895 0.00 0.00 0.00 4.02
1513 1591 4.596585 CCACCACCACCACCACCC 62.597 72.222 0.00 0.00 0.00 4.61
1601 1679 0.391130 GCACGCACATCCCAAGTCTA 60.391 55.000 0.00 0.00 0.00 2.59
1607 1692 2.359900 CACATCCCAAGTCTAAGCACC 58.640 52.381 0.00 0.00 0.00 5.01
1610 1695 0.690762 TCCCAAGTCTAAGCACCCAC 59.309 55.000 0.00 0.00 0.00 4.61
1632 1717 5.745294 CACAATTCAAGAAACTTGGACACTG 59.255 40.000 10.84 4.84 0.00 3.66
1646 1731 5.330455 TGGACACTGATCACATCTTCTAC 57.670 43.478 0.00 0.00 0.00 2.59
1647 1732 4.160439 TGGACACTGATCACATCTTCTACC 59.840 45.833 0.00 0.00 0.00 3.18
1799 1884 0.171007 CATCAACGGCCACATGTTCC 59.829 55.000 2.24 0.00 0.00 3.62
2010 2101 6.942576 ACCATGAACTGAAAACTATTAGTGCT 59.057 34.615 0.00 0.00 0.00 4.40
2011 2102 8.100791 ACCATGAACTGAAAACTATTAGTGCTA 58.899 33.333 0.00 0.00 0.00 3.49
2012 2103 8.607459 CCATGAACTGAAAACTATTAGTGCTAG 58.393 37.037 0.00 0.00 0.00 3.42
2038 2129 4.580580 GCTAGTAAGCCTGGTGCAATAATT 59.419 41.667 0.00 0.00 43.40 1.40
2141 2234 3.371063 GCTGCATGCTGTGTGCCT 61.371 61.111 23.42 0.00 41.83 4.75
2245 2342 6.796705 AAACTTGCTGTACAACATACTACC 57.203 37.500 0.00 0.00 33.68 3.18
2248 2345 7.177832 ACTTGCTGTACAACATACTACCATA 57.822 36.000 0.00 0.00 33.68 2.74
2252 2349 5.408604 GCTGTACAACATACTACCATATGGC 59.591 44.000 22.18 1.03 36.95 4.40
2258 2355 7.346471 ACAACATACTACCATATGGCTTTTCT 58.654 34.615 22.18 3.50 36.95 2.52
2329 2435 6.127758 TGTTGGGAACTGCAAATCATATACAC 60.128 38.462 0.00 0.00 0.00 2.90
2349 2455 5.772521 ACACTTAAAATCACCATGTTCTGC 58.227 37.500 0.00 0.00 0.00 4.26
2371 2477 3.939592 CGGGTCCTTCTTTGGAGTAATTC 59.060 47.826 0.00 0.00 36.69 2.17
2388 2494 9.894783 GGAGTAATTCTTTTTAGACAAAACCTC 57.105 33.333 0.00 0.00 33.39 3.85
2443 2552 9.880157 GAGGTTGATGGTAGTACTATTGTTAAA 57.120 33.333 5.75 0.00 0.00 1.52
2484 2593 5.745312 TGACTCTTTGATGCTCTTCCTAA 57.255 39.130 0.00 0.00 0.00 2.69
2569 2681 5.758784 GTCTTGTTTACCTTGTTCAGCTAGT 59.241 40.000 0.00 0.00 0.00 2.57
2570 2682 6.927381 GTCTTGTTTACCTTGTTCAGCTAGTA 59.073 38.462 0.00 0.00 0.00 1.82
2571 2683 6.927381 TCTTGTTTACCTTGTTCAGCTAGTAC 59.073 38.462 0.00 0.00 0.00 2.73
2624 2742 2.555732 ACGGGGTTGGTAGGAATAGA 57.444 50.000 0.00 0.00 0.00 1.98
2960 3085 2.224769 GCCGGATCCCAAATCCAGAATA 60.225 50.000 5.05 0.00 38.08 1.75
2961 3086 3.562176 GCCGGATCCCAAATCCAGAATAT 60.562 47.826 5.05 0.00 38.08 1.28
2963 3088 5.186198 CCGGATCCCAAATCCAGAATATAC 58.814 45.833 6.06 0.00 38.08 1.47
2965 3090 6.418101 CGGATCCCAAATCCAGAATATACAT 58.582 40.000 6.06 0.00 38.08 2.29
2966 3091 6.317140 CGGATCCCAAATCCAGAATATACATG 59.683 42.308 6.06 0.00 38.08 3.21
2980 3108 2.483014 TACATGACCCCTTTGTTCCG 57.517 50.000 0.00 0.00 0.00 4.30
3014 3143 9.860898 AGATGTTTTCCAAGCTAACATAATTTC 57.139 29.630 10.95 1.50 41.24 2.17
3016 3145 7.087639 TGTTTTCCAAGCTAACATAATTTCCG 58.912 34.615 0.00 0.00 0.00 4.30
3018 3147 7.639113 TTTCCAAGCTAACATAATTTCCGAT 57.361 32.000 0.00 0.00 0.00 4.18
3019 3148 6.861065 TCCAAGCTAACATAATTTCCGATC 57.139 37.500 0.00 0.00 0.00 3.69
3021 3150 6.826231 TCCAAGCTAACATAATTTCCGATCAA 59.174 34.615 0.00 0.00 0.00 2.57
3022 3151 7.012327 TCCAAGCTAACATAATTTCCGATCAAG 59.988 37.037 0.00 0.00 0.00 3.02
3024 3153 8.562892 CAAGCTAACATAATTTCCGATCAAGAT 58.437 33.333 0.00 0.00 0.00 2.40
3025 3154 8.682936 AGCTAACATAATTTCCGATCAAGATT 57.317 30.769 0.00 0.00 0.00 2.40
3026 3155 9.125026 AGCTAACATAATTTCCGATCAAGATTT 57.875 29.630 0.00 0.00 0.00 2.17
3027 3156 9.736023 GCTAACATAATTTCCGATCAAGATTTT 57.264 29.630 0.00 0.00 0.00 1.82
3057 3186 4.607293 ATTCTGTCTGAGCAAGTACACA 57.393 40.909 0.00 0.00 0.00 3.72
3058 3187 4.607293 TTCTGTCTGAGCAAGTACACAT 57.393 40.909 0.00 0.00 0.00 3.21
3059 3188 5.722021 TTCTGTCTGAGCAAGTACACATA 57.278 39.130 0.00 0.00 0.00 2.29
3060 3189 5.316327 TCTGTCTGAGCAAGTACACATAG 57.684 43.478 0.00 0.00 0.00 2.23
3061 3190 5.010282 TCTGTCTGAGCAAGTACACATAGA 58.990 41.667 0.00 0.00 0.00 1.98
3062 3191 5.124617 TCTGTCTGAGCAAGTACACATAGAG 59.875 44.000 0.00 0.00 0.00 2.43
3063 3192 5.010282 TGTCTGAGCAAGTACACATAGAGA 58.990 41.667 0.00 0.00 0.00 3.10
3064 3193 5.654209 TGTCTGAGCAAGTACACATAGAGAT 59.346 40.000 0.00 0.00 0.00 2.75
3065 3194 6.828785 TGTCTGAGCAAGTACACATAGAGATA 59.171 38.462 0.00 0.00 0.00 1.98
3066 3195 7.503902 TGTCTGAGCAAGTACACATAGAGATAT 59.496 37.037 0.00 0.00 0.00 1.63
3067 3196 9.004717 GTCTGAGCAAGTACACATAGAGATATA 57.995 37.037 0.00 0.00 0.00 0.86
3068 3197 9.746457 TCTGAGCAAGTACACATAGAGATATAT 57.254 33.333 0.00 0.00 0.00 0.86
3073 3202 9.929180 GCAAGTACACATAGAGATATATTTCCA 57.071 33.333 0.00 0.00 0.00 3.53
3085 3214 9.566432 AGAGATATATTTCCAAGCTAACAAAGG 57.434 33.333 0.00 0.00 0.00 3.11
3086 3215 8.697507 AGATATATTTCCAAGCTAACAAAGGG 57.302 34.615 0.00 0.00 0.00 3.95
3087 3216 7.725844 AGATATATTTCCAAGCTAACAAAGGGG 59.274 37.037 0.00 0.00 0.00 4.79
3088 3217 3.322191 TTTCCAAGCTAACAAAGGGGT 57.678 42.857 0.00 0.00 0.00 4.95
3089 3218 4.456662 TTTCCAAGCTAACAAAGGGGTA 57.543 40.909 0.00 0.00 0.00 3.69
3090 3219 3.428413 TCCAAGCTAACAAAGGGGTAC 57.572 47.619 0.00 0.00 0.00 3.34
3091 3220 2.712087 TCCAAGCTAACAAAGGGGTACA 59.288 45.455 0.00 0.00 0.00 2.90
3092 3221 2.817844 CCAAGCTAACAAAGGGGTACAC 59.182 50.000 0.00 0.00 0.00 2.90
3093 3222 3.482436 CAAGCTAACAAAGGGGTACACA 58.518 45.455 0.00 0.00 0.00 3.72
3094 3223 4.079253 CAAGCTAACAAAGGGGTACACAT 58.921 43.478 0.00 0.00 0.00 3.21
3095 3224 5.250200 CAAGCTAACAAAGGGGTACACATA 58.750 41.667 0.00 0.00 0.00 2.29
3096 3225 5.099042 AGCTAACAAAGGGGTACACATAG 57.901 43.478 0.00 0.00 0.00 2.23
3097 3226 4.781087 AGCTAACAAAGGGGTACACATAGA 59.219 41.667 0.00 0.00 0.00 1.98
3098 3227 5.104900 AGCTAACAAAGGGGTACACATAGAG 60.105 44.000 0.00 0.00 0.00 2.43
3099 3228 5.105064 GCTAACAAAGGGGTACACATAGAGA 60.105 44.000 0.00 0.00 0.00 3.10
3100 3229 6.408206 GCTAACAAAGGGGTACACATAGAGAT 60.408 42.308 0.00 0.00 0.00 2.75
3101 3230 7.201974 GCTAACAAAGGGGTACACATAGAGATA 60.202 40.741 0.00 0.00 0.00 1.98
3102 3231 7.691993 AACAAAGGGGTACACATAGAGATAT 57.308 36.000 0.00 0.00 0.00 1.63
3103 3232 8.792830 AACAAAGGGGTACACATAGAGATATA 57.207 34.615 0.00 0.00 0.00 0.86
3104 3233 8.974292 ACAAAGGGGTACACATAGAGATATAT 57.026 34.615 0.00 0.00 0.00 0.86
3105 3234 9.393786 ACAAAGGGGTACACATAGAGATATATT 57.606 33.333 0.00 0.00 0.00 1.28
3106 3235 9.877178 CAAAGGGGTACACATAGAGATATATTC 57.123 37.037 0.00 0.00 0.00 1.75
3107 3236 8.611051 AAGGGGTACACATAGAGATATATTCC 57.389 38.462 0.00 0.00 0.00 3.01
3108 3237 7.133483 AGGGGTACACATAGAGATATATTCCC 58.867 42.308 0.00 0.00 0.00 3.97
3109 3238 6.326843 GGGGTACACATAGAGATATATTCCCC 59.673 46.154 0.00 0.00 40.97 4.81
3110 3239 6.326843 GGGTACACATAGAGATATATTCCCCC 59.673 46.154 0.00 0.00 0.00 5.40
3111 3240 7.133483 GGTACACATAGAGATATATTCCCCCT 58.867 42.308 0.00 0.00 0.00 4.79
3112 3241 7.070074 GGTACACATAGAGATATATTCCCCCTG 59.930 44.444 0.00 0.00 0.00 4.45
3113 3242 5.426833 ACACATAGAGATATATTCCCCCTGC 59.573 44.000 0.00 0.00 0.00 4.85
3114 3243 5.664908 CACATAGAGATATATTCCCCCTGCT 59.335 44.000 0.00 0.00 0.00 4.24
3115 3244 6.157645 CACATAGAGATATATTCCCCCTGCTT 59.842 42.308 0.00 0.00 0.00 3.91
3116 3245 6.157645 ACATAGAGATATATTCCCCCTGCTTG 59.842 42.308 0.00 0.00 0.00 4.01
3117 3246 4.767908 AGAGATATATTCCCCCTGCTTGA 58.232 43.478 0.00 0.00 0.00 3.02
3118 3247 4.782156 AGAGATATATTCCCCCTGCTTGAG 59.218 45.833 0.00 0.00 0.00 3.02
3119 3248 3.848975 AGATATATTCCCCCTGCTTGAGG 59.151 47.826 0.00 0.00 42.38 3.86
3276 3407 5.577164 TCTTAGCAGCGAGAAATAACAAGAC 59.423 40.000 0.00 0.00 0.00 3.01
3370 3531 3.047796 CAACAAAGTCATCTTGTGCTGC 58.952 45.455 0.00 0.00 33.79 5.25
3384 3545 1.863454 GTGCTGCGGATCTATTGACTG 59.137 52.381 0.00 0.00 0.00 3.51
3389 3550 4.570772 GCTGCGGATCTATTGACTGTAAAA 59.429 41.667 0.00 0.00 0.00 1.52
3704 3894 3.214328 AGTTTGGTCGATTTGCTTGAGT 58.786 40.909 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.176910 CCGGCTCCCTTCTTCTTCTC 59.823 60.000 0.00 0.00 0.00 2.87
22 23 1.268283 CCCGGCTCCCTTCTTCTTCT 61.268 60.000 0.00 0.00 0.00 2.85
23 24 1.222113 CCCGGCTCCCTTCTTCTTC 59.778 63.158 0.00 0.00 0.00 2.87
25 26 3.403558 GCCCGGCTCCCTTCTTCT 61.404 66.667 0.71 0.00 0.00 2.85
26 27 4.840005 CGCCCGGCTCCCTTCTTC 62.840 72.222 8.05 0.00 0.00 2.87
263 294 5.535783 TGATGATAGGAGAGAAGCAGAGAAG 59.464 44.000 0.00 0.00 0.00 2.85
264 295 5.301551 GTGATGATAGGAGAGAAGCAGAGAA 59.698 44.000 0.00 0.00 0.00 2.87
265 296 4.826733 GTGATGATAGGAGAGAAGCAGAGA 59.173 45.833 0.00 0.00 0.00 3.10
266 297 4.022068 GGTGATGATAGGAGAGAAGCAGAG 60.022 50.000 0.00 0.00 0.00 3.35
267 298 3.894427 GGTGATGATAGGAGAGAAGCAGA 59.106 47.826 0.00 0.00 0.00 4.26
268 299 3.640498 TGGTGATGATAGGAGAGAAGCAG 59.360 47.826 0.00 0.00 0.00 4.24
269 300 3.640498 CTGGTGATGATAGGAGAGAAGCA 59.360 47.826 0.00 0.00 0.00 3.91
270 301 3.554752 GCTGGTGATGATAGGAGAGAAGC 60.555 52.174 0.00 0.00 0.00 3.86
271 302 3.640498 TGCTGGTGATGATAGGAGAGAAG 59.360 47.826 0.00 0.00 0.00 2.85
272 303 3.386078 GTGCTGGTGATGATAGGAGAGAA 59.614 47.826 0.00 0.00 0.00 2.87
273 304 2.961741 GTGCTGGTGATGATAGGAGAGA 59.038 50.000 0.00 0.00 0.00 3.10
284 318 3.260632 TGTGTATACTGTGTGCTGGTGAT 59.739 43.478 4.17 0.00 0.00 3.06
299 333 2.172930 AGAGGGAGAGAGCGTGTGTATA 59.827 50.000 0.00 0.00 0.00 1.47
328 362 1.349259 CTACTTTCCGCGGGACAACG 61.349 60.000 27.83 12.65 0.00 4.10
336 370 3.067742 TCTTTATCCCTCTACTTTCCGCG 59.932 47.826 0.00 0.00 0.00 6.46
534 587 9.639601 AGAGTAAAGAAAAGAAAACACAAAAGG 57.360 29.630 0.00 0.00 0.00 3.11
721 793 1.831580 AAGCTTAGCTCCAAAGGCAG 58.168 50.000 7.36 0.00 38.25 4.85
722 794 2.991250 CTAAGCTTAGCTCCAAAGGCA 58.009 47.619 20.13 0.00 38.25 4.75
769 843 3.415087 CTTCCCCTCCCTGGCTGG 61.415 72.222 2.96 2.96 0.00 4.85
770 844 4.120755 GCTTCCCCTCCCTGGCTG 62.121 72.222 0.00 0.00 0.00 4.85
987 1062 1.221840 GACCATGCCGACATCACCT 59.778 57.895 0.00 0.00 32.87 4.00
1513 1591 3.775654 GGTGGAGGTGCGAGAGGG 61.776 72.222 0.00 0.00 0.00 4.30
1601 1679 3.706086 AGTTTCTTGAATTGTGGGTGCTT 59.294 39.130 0.00 0.00 0.00 3.91
1607 1692 5.043248 GTGTCCAAGTTTCTTGAATTGTGG 58.957 41.667 10.54 0.00 0.00 4.17
1610 1695 6.135290 TCAGTGTCCAAGTTTCTTGAATTG 57.865 37.500 10.54 4.38 0.00 2.32
1632 1717 3.008485 GGATGGGGGTAGAAGATGTGATC 59.992 52.174 0.00 0.00 0.00 2.92
1646 1731 2.914289 GTCTGCAGAGGATGGGGG 59.086 66.667 18.89 0.00 0.00 5.40
1647 1732 2.503061 CGTCTGCAGAGGATGGGG 59.497 66.667 28.24 3.93 32.08 4.96
1799 1884 1.252904 TGGTCGTAGAGAAACCCCCG 61.253 60.000 0.00 0.00 36.95 5.73
2010 2101 2.957006 GCACCAGGCTTACTAGCTACTA 59.043 50.000 0.00 0.00 46.90 1.82
2011 2102 1.757699 GCACCAGGCTTACTAGCTACT 59.242 52.381 0.00 0.00 46.90 2.57
2012 2103 1.480954 TGCACCAGGCTTACTAGCTAC 59.519 52.381 0.00 0.00 46.90 3.58
2038 2129 7.712204 TGTAGTAACAAGATGGATGTCTACA 57.288 36.000 0.00 0.00 36.53 2.74
2141 2234 0.472044 TGGAAGTTAGCTGTGGCACA 59.528 50.000 20.76 20.76 41.70 4.57
2196 2293 5.770162 CCTTGGAAATACTGACTGGTTTTCT 59.230 40.000 0.00 0.00 0.00 2.52
2240 2337 6.772716 CCACATAAGAAAAGCCATATGGTAGT 59.227 38.462 22.79 5.64 37.57 2.73
2245 2342 5.300034 TCAGCCACATAAGAAAAGCCATATG 59.700 40.000 0.00 0.00 33.12 1.78
2248 2345 3.700538 TCAGCCACATAAGAAAAGCCAT 58.299 40.909 0.00 0.00 0.00 4.40
2252 2349 4.157289 ACAGCATCAGCCACATAAGAAAAG 59.843 41.667 0.00 0.00 43.56 2.27
2258 2355 2.488937 CACAACAGCATCAGCCACATAA 59.511 45.455 0.00 0.00 43.56 1.90
2293 2390 4.937015 GCAGTTCCCAACATATGCAAAATT 59.063 37.500 1.58 0.00 32.31 1.82
2295 2392 3.323115 TGCAGTTCCCAACATATGCAAAA 59.677 39.130 1.58 0.00 37.22 2.44
2329 2435 4.414852 CCGCAGAACATGGTGATTTTAAG 58.585 43.478 0.00 0.00 0.00 1.85
2349 2455 3.629142 ATTACTCCAAAGAAGGACCCG 57.371 47.619 0.00 0.00 33.19 5.28
2388 2494 5.121611 TGGCGTCAAGTGATTACTACAAATG 59.878 40.000 0.00 0.00 35.69 2.32
2443 2552 4.122046 GTCAAACTTTTCAGCTGCCAAAT 58.878 39.130 9.47 0.00 0.00 2.32
2484 2593 1.456892 TGGTCGATAGCGTGGGGAT 60.457 57.895 0.00 0.00 38.98 3.85
2569 2681 9.775854 AAAGAGATAAGAGTATACGTGCTAGTA 57.224 33.333 0.00 0.00 0.00 1.82
2570 2682 8.680039 AAAGAGATAAGAGTATACGTGCTAGT 57.320 34.615 0.00 0.00 0.00 2.57
2571 2683 8.231837 GGAAAGAGATAAGAGTATACGTGCTAG 58.768 40.741 0.00 0.00 0.00 3.42
2828 2953 0.897621 AAACAGGCCAAGGCTAATGC 59.102 50.000 5.01 0.00 41.60 3.56
2960 3085 2.307686 ACGGAACAAAGGGGTCATGTAT 59.692 45.455 0.00 0.00 0.00 2.29
2961 3086 1.700739 ACGGAACAAAGGGGTCATGTA 59.299 47.619 0.00 0.00 0.00 2.29
2963 3088 2.483014 TACGGAACAAAGGGGTCATG 57.517 50.000 0.00 0.00 0.00 3.07
2965 3090 4.847990 ATATTACGGAACAAAGGGGTCA 57.152 40.909 0.00 0.00 0.00 4.02
2966 3091 6.585416 TCTTATATTACGGAACAAAGGGGTC 58.415 40.000 0.00 0.00 0.00 4.46
3036 3165 4.607293 TGTGTACTTGCTCAGACAGAAT 57.393 40.909 0.00 0.00 0.00 2.40
3037 3166 4.607293 ATGTGTACTTGCTCAGACAGAA 57.393 40.909 0.00 0.00 0.00 3.02
3039 3168 5.124617 TCTCTATGTGTACTTGCTCAGACAG 59.875 44.000 0.00 0.00 0.00 3.51
3040 3169 5.010282 TCTCTATGTGTACTTGCTCAGACA 58.990 41.667 0.00 0.00 0.00 3.41
3042 3171 9.746457 ATATATCTCTATGTGTACTTGCTCAGA 57.254 33.333 0.00 0.00 0.00 3.27
3047 3176 9.929180 TGGAAATATATCTCTATGTGTACTTGC 57.071 33.333 0.00 0.00 0.00 4.01
3059 3188 9.566432 CCTTTGTTAGCTTGGAAATATATCTCT 57.434 33.333 0.00 0.00 0.00 3.10
3060 3189 8.787852 CCCTTTGTTAGCTTGGAAATATATCTC 58.212 37.037 0.00 0.00 0.00 2.75
3061 3190 7.725844 CCCCTTTGTTAGCTTGGAAATATATCT 59.274 37.037 0.00 0.00 0.00 1.98
3062 3191 7.505923 ACCCCTTTGTTAGCTTGGAAATATATC 59.494 37.037 0.00 0.00 0.00 1.63
3063 3192 7.362234 ACCCCTTTGTTAGCTTGGAAATATAT 58.638 34.615 0.00 0.00 0.00 0.86
3064 3193 6.737608 ACCCCTTTGTTAGCTTGGAAATATA 58.262 36.000 0.00 0.00 0.00 0.86
3065 3194 5.589831 ACCCCTTTGTTAGCTTGGAAATAT 58.410 37.500 0.00 0.00 0.00 1.28
3066 3195 5.005628 ACCCCTTTGTTAGCTTGGAAATA 57.994 39.130 0.00 0.00 0.00 1.40
3067 3196 3.856900 ACCCCTTTGTTAGCTTGGAAAT 58.143 40.909 0.00 0.00 0.00 2.17
3068 3197 3.322191 ACCCCTTTGTTAGCTTGGAAA 57.678 42.857 0.00 0.00 0.00 3.13
3069 3198 3.138653 TGTACCCCTTTGTTAGCTTGGAA 59.861 43.478 0.00 0.00 0.00 3.53
3070 3199 2.712087 TGTACCCCTTTGTTAGCTTGGA 59.288 45.455 0.00 0.00 0.00 3.53
3071 3200 2.817844 GTGTACCCCTTTGTTAGCTTGG 59.182 50.000 0.00 0.00 0.00 3.61
3072 3201 3.482436 TGTGTACCCCTTTGTTAGCTTG 58.518 45.455 0.00 0.00 0.00 4.01
3073 3202 3.868619 TGTGTACCCCTTTGTTAGCTT 57.131 42.857 0.00 0.00 0.00 3.74
3074 3203 4.781087 TCTATGTGTACCCCTTTGTTAGCT 59.219 41.667 0.00 0.00 0.00 3.32
3075 3204 5.093849 TCTATGTGTACCCCTTTGTTAGC 57.906 43.478 0.00 0.00 0.00 3.09
3076 3205 6.540438 TCTCTATGTGTACCCCTTTGTTAG 57.460 41.667 0.00 0.00 0.00 2.34
3077 3206 8.792830 ATATCTCTATGTGTACCCCTTTGTTA 57.207 34.615 0.00 0.00 0.00 2.41
3078 3207 7.691993 ATATCTCTATGTGTACCCCTTTGTT 57.308 36.000 0.00 0.00 0.00 2.83
3079 3208 8.974292 ATATATCTCTATGTGTACCCCTTTGT 57.026 34.615 0.00 0.00 0.00 2.83
3080 3209 9.877178 GAATATATCTCTATGTGTACCCCTTTG 57.123 37.037 0.00 0.00 0.00 2.77
3081 3210 9.047947 GGAATATATCTCTATGTGTACCCCTTT 57.952 37.037 0.00 0.00 0.00 3.11
3082 3211 7.624077 GGGAATATATCTCTATGTGTACCCCTT 59.376 40.741 0.00 0.00 0.00 3.95
3083 3212 7.133483 GGGAATATATCTCTATGTGTACCCCT 58.867 42.308 0.00 0.00 0.00 4.79
3084 3213 6.326843 GGGGAATATATCTCTATGTGTACCCC 59.673 46.154 0.00 0.00 42.86 4.95
3085 3214 6.326843 GGGGGAATATATCTCTATGTGTACCC 59.673 46.154 0.00 0.00 0.00 3.69
3086 3215 7.070074 CAGGGGGAATATATCTCTATGTGTACC 59.930 44.444 0.00 0.00 0.00 3.34
3087 3216 7.418025 GCAGGGGGAATATATCTCTATGTGTAC 60.418 44.444 0.00 0.00 0.00 2.90
3088 3217 6.611642 GCAGGGGGAATATATCTCTATGTGTA 59.388 42.308 0.00 0.00 0.00 2.90
3089 3218 5.426833 GCAGGGGGAATATATCTCTATGTGT 59.573 44.000 0.00 0.00 0.00 3.72
3090 3219 5.664908 AGCAGGGGGAATATATCTCTATGTG 59.335 44.000 0.00 0.00 0.00 3.21
3091 3220 5.859429 AGCAGGGGGAATATATCTCTATGT 58.141 41.667 0.00 0.00 0.00 2.29
3092 3221 6.385176 TCAAGCAGGGGGAATATATCTCTATG 59.615 42.308 0.00 0.00 0.00 2.23
3093 3222 6.515779 TCAAGCAGGGGGAATATATCTCTAT 58.484 40.000 0.00 0.00 0.00 1.98
3094 3223 5.915628 TCAAGCAGGGGGAATATATCTCTA 58.084 41.667 0.00 0.00 0.00 2.43
3095 3224 4.767908 TCAAGCAGGGGGAATATATCTCT 58.232 43.478 0.00 0.00 0.00 3.10
3096 3225 4.080638 CCTCAAGCAGGGGGAATATATCTC 60.081 50.000 0.00 0.00 38.91 2.75
3097 3226 3.848975 CCTCAAGCAGGGGGAATATATCT 59.151 47.826 0.00 0.00 38.91 1.98
3098 3227 3.846588 TCCTCAAGCAGGGGGAATATATC 59.153 47.826 0.00 0.00 43.67 1.63
3099 3228 3.589288 GTCCTCAAGCAGGGGGAATATAT 59.411 47.826 0.00 0.00 43.67 0.86
3100 3229 2.979678 GTCCTCAAGCAGGGGGAATATA 59.020 50.000 0.00 0.00 43.67 0.86
3101 3230 1.777272 GTCCTCAAGCAGGGGGAATAT 59.223 52.381 0.00 0.00 43.67 1.28
3102 3231 1.213296 GTCCTCAAGCAGGGGGAATA 58.787 55.000 0.00 0.00 43.67 1.75
3103 3232 0.551131 AGTCCTCAAGCAGGGGGAAT 60.551 55.000 0.00 0.00 43.67 3.01
3104 3233 0.118346 TAGTCCTCAAGCAGGGGGAA 59.882 55.000 0.00 0.00 43.67 3.97
3105 3234 0.118346 TTAGTCCTCAAGCAGGGGGA 59.882 55.000 0.00 0.00 43.67 4.81
3106 3235 0.543749 CTTAGTCCTCAAGCAGGGGG 59.456 60.000 0.00 0.00 43.67 5.40
3107 3236 0.543749 CCTTAGTCCTCAAGCAGGGG 59.456 60.000 0.00 0.00 43.67 4.79
3108 3237 1.484240 CTCCTTAGTCCTCAAGCAGGG 59.516 57.143 0.00 0.00 43.67 4.45
3109 3238 2.093764 CACTCCTTAGTCCTCAAGCAGG 60.094 54.545 0.00 0.00 45.15 4.85
3110 3239 2.093764 CCACTCCTTAGTCCTCAAGCAG 60.094 54.545 0.00 0.00 31.97 4.24
3111 3240 1.902508 CCACTCCTTAGTCCTCAAGCA 59.097 52.381 0.00 0.00 31.97 3.91
3112 3241 1.406205 GCCACTCCTTAGTCCTCAAGC 60.406 57.143 0.00 0.00 31.97 4.01
3113 3242 1.208293 GGCCACTCCTTAGTCCTCAAG 59.792 57.143 0.00 0.00 31.97 3.02
3114 3243 1.276622 GGCCACTCCTTAGTCCTCAA 58.723 55.000 0.00 0.00 31.97 3.02
3115 3244 0.116342 TGGCCACTCCTTAGTCCTCA 59.884 55.000 0.00 0.00 31.97 3.86
3116 3245 1.501582 ATGGCCACTCCTTAGTCCTC 58.498 55.000 8.16 0.00 31.97 3.71
3117 3246 2.868964 TATGGCCACTCCTTAGTCCT 57.131 50.000 8.16 0.00 31.97 3.85
3118 3247 3.243724 AGATATGGCCACTCCTTAGTCC 58.756 50.000 8.16 0.00 31.97 3.85
3119 3248 3.898123 TGAGATATGGCCACTCCTTAGTC 59.102 47.826 8.16 2.02 31.97 2.59
3250 3381 6.818644 TCTTGTTATTTCTCGCTGCTAAGAAT 59.181 34.615 12.98 4.87 31.89 2.40
3259 3390 7.865706 AAATATGGTCTTGTTATTTCTCGCT 57.134 32.000 0.00 0.00 0.00 4.93
3370 3531 6.092122 TGCAAGTTTTACAGTCAATAGATCCG 59.908 38.462 0.00 0.00 0.00 4.18
3417 3578 9.260002 CATTTGTAATTTGCACTCCTAAAACTT 57.740 29.630 0.00 0.00 0.00 2.66
3578 3765 4.142609 TGATCACCTGCCAATCTTAGAC 57.857 45.455 0.00 0.00 0.00 2.59
3633 3823 5.163447 GGAAATAGCCACCAAATTAACCCTC 60.163 44.000 0.00 0.00 0.00 4.30
3704 3894 1.300620 CGTCCTCAAGTTGCGGTGA 60.301 57.895 11.57 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.