Multiple sequence alignment - TraesCS1B01G095000

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 TraesCS1B01G095000 chr1B 100.000 3410 0 0 1 3410 98166883 98170292 0.000000e+00 6298
1 TraesCS1B01G095000 chr1B 88.950 181 12 4 1826 2006 243757721 243757893 2.060000e-52 217
2 TraesCS1B01G095000 chr1A 95.044 2704 97 18 1 2683 59613530 59616217 0.000000e+00 4217
3 TraesCS1B01G095000 chr1D 95.305 2577 74 11 732 3295 61485263 61487805 0.000000e+00 4045
4 TraesCS1B01G095000 chr1D 88.601 386 21 6 1 369 61484880 61485259 6.710000e-122 448
5 TraesCS1B01G095000 chr1D 95.349 86 4 0 3322 3407 61487806 61487891 1.650000e-28 137
6 TraesCS1B01G095000 chr3A 86.275 255 26 2 2625 2870 247795229 247794975 5.610000e-68 268
7 TraesCS1B01G095000 chr3A 86.607 112 13 2 3296 3407 476302611 476302502 4.620000e-24 122
8 TraesCS1B01G095000 chr7B 91.160 181 16 0 1826 2006 312427260 312427440 2.630000e-61 246
9 TraesCS1B01G095000 chr7B 89.503 181 15 3 1826 2006 379919855 379920031 3.420000e-55 226
10 TraesCS1B01G095000 chr6A 91.160 181 15 1 1826 2006 222568611 222568790 9.450000e-61 244
11 TraesCS1B01G095000 chr6A 81.111 270 45 3 2949 3216 377775531 377775266 9.590000e-51 211
12 TraesCS1B01G095000 chr4D 91.111 180 16 0 1826 2005 286960775 286960954 9.450000e-61 244
13 TraesCS1B01G095000 chr2A 89.444 180 19 0 1826 2005 138874916 138875095 9.520000e-56 228
14 TraesCS1B01G095000 chr5B 83.401 247 38 3 2971 3214 160127981 160128227 3.420000e-55 226
15 TraesCS1B01G095000 chr5B 81.343 268 44 3 2949 3214 630156836 630156573 2.670000e-51 213
16 TraesCS1B01G095000 chr4B 88.950 181 16 3 1826 2006 207149136 207149312 1.590000e-53 220
17 TraesCS1B01G095000 chr3B 81.818 264 42 3 2949 3210 488441404 488441145 2.060000e-52 217
18 TraesCS1B01G095000 chr5A 81.343 268 44 5 2949 3214 42894334 42894071 2.670000e-51 213
19 TraesCS1B01G095000 chr4A 81.550 271 38 8 2949 3214 348935219 348934956 2.670000e-51 213
20 TraesCS1B01G095000 chr4A 81.111 270 45 3 2947 3214 238416564 238416299 9.590000e-51 211
21 TraesCS1B01G095000 chr4A 80.287 279 53 2 2938 3214 500908762 500909040 3.450000e-50 209


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 TraesCS1B01G095000 chr1B 98166883 98170292 3409 False 6298.000000 6298 100.000 1 3410 1 chr1B.!!$F1 3409
1 TraesCS1B01G095000 chr1A 59613530 59616217 2687 False 4217.000000 4217 95.044 1 2683 1 chr1A.!!$F1 2682
2 TraesCS1B01G095000 chr1D 61484880 61487891 3011 False 1543.333333 4045 93.085 1 3407 3 chr1D.!!$F1 3406

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
23 24 0.610174 TCTCCGCTCAATTGCTCTGT 59.390 50.0 0.0 0.0 0.00 3.41 F
24 25 0.725686 CTCCGCTCAATTGCTCTGTG 59.274 55.0 0.0 0.0 0.00 3.66 F
1860 1896 0.251354 TGAGCACCATGAAGAGGAGC 59.749 55.0 0.0 0.0 42.18 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1352 1.673920 TCGTTTGTTTCCTTGGAGTGC 59.326 47.619 0.00 0.0 0.00 4.40 R
1870 1906 2.025793 TGGAGGAGCTCTCTATATCGGG 60.026 54.545 14.64 0.0 42.10 5.14 R
2966 3012 0.106719 AATGGCCAGTAACCGATGGG 60.107 55.000 13.05 0.0 37.05 4.00 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
22 23 1.396301 GTTCTCCGCTCAATTGCTCTG 59.604 52.381 0.00 0.00 0.00 3.35
23 24 0.610174 TCTCCGCTCAATTGCTCTGT 59.390 50.000 0.00 0.00 0.00 3.41
24 25 0.725686 CTCCGCTCAATTGCTCTGTG 59.274 55.000 0.00 0.00 0.00 3.66
28 29 1.451067 GCTCAATTGCTCTGTGCTCT 58.549 50.000 0.00 0.00 43.37 4.09
40 41 2.203832 TGCTCTGTGCTCTCCCCA 60.204 61.111 3.20 0.00 43.37 4.96
126 130 3.980022 TCCCTCATATGGAATAGTTGCCA 59.020 43.478 2.13 0.00 38.78 4.92
191 195 2.050350 GGATCGAGGGTCGGTGTCA 61.050 63.158 0.00 0.00 40.88 3.58
273 291 3.197790 CCAACTCGCCATCGCCAG 61.198 66.667 0.00 0.00 35.26 4.85
369 387 4.426313 CCTTCCCCCGGCCTGAAC 62.426 72.222 0.00 0.00 0.00 3.18
506 530 4.025401 GGTTGTGCCGAAGTGCCG 62.025 66.667 0.00 0.00 0.00 5.69
511 535 4.243008 TGCCGAAGTGCCGAACCA 62.243 61.111 0.00 0.00 0.00 3.67
571 595 7.416817 CCGTGAATTGATATGTTGATGCTTTA 58.583 34.615 0.00 0.00 0.00 1.85
629 653 1.798813 GCCATGTAGTATGCCTAACGC 59.201 52.381 0.00 0.00 38.31 4.84
650 674 4.666237 GCAGATAACGGACTTAACTACGT 58.334 43.478 0.00 0.00 41.88 3.57
656 680 2.162408 ACGGACTTAACTACGTGGCTAC 59.838 50.000 0.00 0.00 38.24 3.58
670 694 1.301479 GCTACGATTAAGCCGGGGG 60.301 63.158 2.18 0.00 33.73 5.40
671 695 1.751349 GCTACGATTAAGCCGGGGGA 61.751 60.000 2.18 0.00 33.73 4.81
672 696 0.974383 CTACGATTAAGCCGGGGGAT 59.026 55.000 2.18 0.00 0.00 3.85
698 730 5.638783 ACTCGCGGTTAGAGTATAATATGC 58.361 41.667 6.13 0.00 46.06 3.14
699 731 5.415077 ACTCGCGGTTAGAGTATAATATGCT 59.585 40.000 6.13 0.00 46.06 3.79
757 789 5.478332 AGTTCTGCCTTTTGCTTAGCTTTAT 59.522 36.000 5.60 0.00 42.00 1.40
758 790 5.982890 TCTGCCTTTTGCTTAGCTTTATT 57.017 34.783 5.60 0.00 42.00 1.40
759 791 7.176690 AGTTCTGCCTTTTGCTTAGCTTTATTA 59.823 33.333 5.60 0.00 42.00 0.98
838 870 2.416202 TCGAATACGCACGAGTGACTTA 59.584 45.455 7.50 0.00 39.58 2.24
873 905 3.917985 CGGCTATTTGCAAACTGGTTAAC 59.082 43.478 15.41 0.00 45.15 2.01
915 947 9.868277 GATCCTGAATCGATGAATTATAACTCT 57.132 33.333 0.00 0.00 0.00 3.24
955 987 7.878477 ATACAAAATTTGCTTGTCTGACATG 57.122 32.000 11.86 14.72 38.05 3.21
1067 1099 1.874019 CATCTGGCGACGAACTCGG 60.874 63.158 0.00 0.00 43.18 4.63
1103 1135 5.045286 AGACAGAGCAAGGAAATTACTGGAT 60.045 40.000 0.00 0.00 0.00 3.41
1259 1294 2.260844 TGTGCCAGAGTTTCTTCAGG 57.739 50.000 0.00 0.00 0.00 3.86
1317 1352 1.374252 AGCGCCGTTGGAACTACAG 60.374 57.895 2.29 0.00 0.00 2.74
1367 1403 4.196626 TGTATGTACCAACACTAGTGCC 57.803 45.455 22.90 4.78 38.78 5.01
1611 1647 6.653526 TCTCAAAATCAAGAAGCAAATCCA 57.346 33.333 0.00 0.00 0.00 3.41
1713 1749 2.553602 TGATGGCAGCTTACAAACACTG 59.446 45.455 3.69 0.00 0.00 3.66
1758 1794 5.482175 GGTATAATCCTGCTCCAGTACAGAT 59.518 44.000 0.00 0.00 35.90 2.90
1860 1896 0.251354 TGAGCACCATGAAGAGGAGC 59.749 55.000 0.00 0.00 42.18 4.70
1870 1906 1.206610 TGAAGAGGAGCAGATCAGTGC 59.793 52.381 0.00 0.00 44.35 4.40
1961 1997 0.178926 TGTTCACCGGAAGAGGGGTA 60.179 55.000 9.46 0.00 35.77 3.69
2130 2166 1.135575 GTGCACTGCTGTAAATGGAGC 60.136 52.381 10.32 0.00 35.65 4.70
2137 2173 4.002982 CTGCTGTAAATGGAGCAACACTA 58.997 43.478 0.00 0.00 44.44 2.74
2198 2234 4.519730 GCACCGAATCTAGGTACATAGTCT 59.480 45.833 13.85 3.07 40.59 3.24
2232 2268 7.508687 TGTAGAATGTTCACCATATGCTATGT 58.491 34.615 0.00 0.00 31.97 2.29
2490 2527 3.332034 GAGGCTTAGCGTTTGGAAGTAA 58.668 45.455 0.00 0.00 0.00 2.24
2756 2793 4.984161 GGTTTGAAATGGCATAATGATCCG 59.016 41.667 0.00 0.00 0.00 4.18
2832 2878 0.105760 AATCACCAACCCTGTTGCCA 60.106 50.000 1.46 0.00 0.00 4.92
2870 2916 9.902684 ATTCAGTTGATAAATCTCTGAATCAGT 57.097 29.630 22.63 12.34 44.71 3.41
2871 2917 9.730705 TTCAGTTGATAAATCTCTGAATCAGTT 57.269 29.630 10.36 0.00 40.09 3.16
2872 2918 9.159364 TCAGTTGATAAATCTCTGAATCAGTTG 57.841 33.333 10.36 5.07 36.45 3.16
2873 2919 9.159364 CAGTTGATAAATCTCTGAATCAGTTGA 57.841 33.333 10.36 10.12 34.24 3.18
2874 2920 9.902684 AGTTGATAAATCTCTGAATCAGTTGAT 57.097 29.630 10.36 11.82 36.07 2.57
2883 2929 9.767228 ATCTCTGAATCAGTTGATAAATCTCAG 57.233 33.333 10.36 11.75 36.48 3.35
2884 2930 8.975295 TCTCTGAATCAGTTGATAAATCTCAGA 58.025 33.333 10.36 16.57 39.32 3.27
2885 2931 9.597170 CTCTGAATCAGTTGATAAATCTCAGAA 57.403 33.333 17.49 7.88 40.23 3.02
2886 2932 9.948964 TCTGAATCAGTTGATAAATCTCAGAAA 57.051 29.630 15.75 1.83 38.99 2.52
2920 2966 5.292834 TCGTGAAGATGCTGATCATTTTCTC 59.707 40.000 0.00 5.46 43.14 2.87
2950 2996 1.202758 TCGGTGATCCTTTGCTTGTGT 60.203 47.619 0.00 0.00 0.00 3.72
2951 2997 1.069022 CGGTGATCCTTTGCTTGTGTG 60.069 52.381 0.00 0.00 0.00 3.82
2952 2998 2.229792 GGTGATCCTTTGCTTGTGTGA 58.770 47.619 0.00 0.00 0.00 3.58
2953 2999 2.030805 GGTGATCCTTTGCTTGTGTGAC 60.031 50.000 0.00 0.00 0.00 3.67
2954 3000 1.872952 TGATCCTTTGCTTGTGTGACG 59.127 47.619 0.00 0.00 0.00 4.35
2955 3001 0.593128 ATCCTTTGCTTGTGTGACGC 59.407 50.000 0.00 0.00 0.00 5.19
2957 3003 1.447317 CCTTTGCTTGTGTGACGCCT 61.447 55.000 0.00 0.00 0.00 5.52
2958 3004 0.381801 CTTTGCTTGTGTGACGCCTT 59.618 50.000 0.00 0.00 0.00 4.35
2960 3006 0.746204 TTGCTTGTGTGACGCCTTGA 60.746 50.000 0.00 0.00 0.00 3.02
2961 3007 0.746204 TGCTTGTGTGACGCCTTGAA 60.746 50.000 0.00 0.00 0.00 2.69
2962 3008 0.317020 GCTTGTGTGACGCCTTGAAC 60.317 55.000 0.00 0.00 0.00 3.18
2963 3009 1.013596 CTTGTGTGACGCCTTGAACA 58.986 50.000 0.00 0.00 0.00 3.18
2964 3010 0.730265 TTGTGTGACGCCTTGAACAC 59.270 50.000 0.00 0.00 42.55 3.32
2965 3011 2.389386 GTGTGACGCCTTGAACACA 58.611 52.632 0.00 0.00 41.97 3.72
2966 3012 2.389386 TGTGACGCCTTGAACACAC 58.611 52.632 0.00 0.00 38.14 3.82
2967 3013 1.092921 TGTGACGCCTTGAACACACC 61.093 55.000 0.00 0.00 38.14 4.16
2968 3014 1.525077 TGACGCCTTGAACACACCC 60.525 57.895 0.00 0.00 0.00 4.61
2969 3015 1.525077 GACGCCTTGAACACACCCA 60.525 57.895 0.00 0.00 0.00 4.51
2970 3016 0.889186 GACGCCTTGAACACACCCAT 60.889 55.000 0.00 0.00 0.00 4.00
2971 3017 0.889186 ACGCCTTGAACACACCCATC 60.889 55.000 0.00 0.00 0.00 3.51
2987 3033 2.218603 CCATCGGTTACTGGCCATTAC 58.781 52.381 5.51 4.53 0.00 1.89
3001 3047 2.856222 CCATTACTCCTGGCAGAATCC 58.144 52.381 17.94 0.00 0.00 3.01
3012 3058 1.213926 GGCAGAATCCAGATTGGTCCT 59.786 52.381 0.00 0.00 39.03 3.85
3033 3079 6.699642 GTCCTGCAGATCAATACTAGTCTTTC 59.300 42.308 17.39 0.00 0.00 2.62
3037 3083 5.465056 GCAGATCAATACTAGTCTTTCCTGC 59.535 44.000 16.19 16.19 35.96 4.85
3047 3093 0.944386 TCTTTCCTGCGCACTTTGTC 59.056 50.000 5.66 0.00 0.00 3.18
3051 3097 2.671177 CCTGCGCACTTTGTCCTCG 61.671 63.158 5.66 0.00 0.00 4.63
3077 3123 2.002586 ACGCATCTGGAATCAACTTCG 58.997 47.619 0.00 0.00 34.45 3.79
3094 3140 1.212751 CGCAGTCGGTCACTCATCA 59.787 57.895 0.00 0.00 30.26 3.07
3117 3163 5.142061 TGAAATTGCTTCATGTTGAGCAT 57.858 34.783 17.32 7.17 39.20 3.79
3130 3176 5.921004 TGTTGAGCATGTTTAATTTTGGC 57.079 34.783 0.00 0.00 0.00 4.52
3149 3195 0.108615 CGTTCTCCTGAATGGACGCT 60.109 55.000 0.00 0.00 40.56 5.07
3204 3250 6.865834 AGTCTATCATCCCTAATAAGCCAG 57.134 41.667 0.00 0.00 0.00 4.85
3210 3256 5.599751 TCATCCCTAATAAGCCAGGCTATA 58.400 41.667 16.56 9.99 38.25 1.31
3213 3259 5.159637 TCCCTAATAAGCCAGGCTATAACA 58.840 41.667 16.56 0.00 38.25 2.41
3234 3280 2.830704 GATTGGACGCCGACGGTCTT 62.831 60.000 16.73 1.14 46.04 3.01
3235 3281 2.830704 ATTGGACGCCGACGGTCTTC 62.831 60.000 16.73 10.54 46.04 2.87
3251 3297 3.825160 TTCCCTGCACTGTGCCGTC 62.825 63.158 28.17 3.28 44.23 4.79
3276 3322 3.257393 CTCTTTCTCTCATTGGTGGTCG 58.743 50.000 0.00 0.00 0.00 4.79
3281 3327 0.247460 TCTCATTGGTGGTCGAGCAG 59.753 55.000 19.24 5.98 32.41 4.24
3282 3328 0.036952 CTCATTGGTGGTCGAGCAGT 60.037 55.000 19.24 1.61 32.41 4.40
3295 3341 2.028130 CGAGCAGTAGGAATGGAGTCT 58.972 52.381 0.00 0.00 0.00 3.24
3296 3342 2.223688 CGAGCAGTAGGAATGGAGTCTG 60.224 54.545 0.00 0.00 0.00 3.51
3297 3343 2.763448 GAGCAGTAGGAATGGAGTCTGT 59.237 50.000 0.00 0.00 0.00 3.41
3298 3344 2.763448 AGCAGTAGGAATGGAGTCTGTC 59.237 50.000 0.00 0.00 0.00 3.51
3299 3345 2.763448 GCAGTAGGAATGGAGTCTGTCT 59.237 50.000 0.00 0.00 0.00 3.41
3300 3346 3.196685 GCAGTAGGAATGGAGTCTGTCTT 59.803 47.826 0.00 0.00 0.00 3.01
3301 3347 4.753233 CAGTAGGAATGGAGTCTGTCTTG 58.247 47.826 0.00 0.00 0.00 3.02
3302 3348 3.772025 AGTAGGAATGGAGTCTGTCTTGG 59.228 47.826 0.00 0.00 0.00 3.61
3303 3349 2.625639 AGGAATGGAGTCTGTCTTGGT 58.374 47.619 0.00 0.00 0.00 3.67
3304 3350 2.569404 AGGAATGGAGTCTGTCTTGGTC 59.431 50.000 0.00 0.00 0.00 4.02
3305 3351 2.611518 GAATGGAGTCTGTCTTGGTCG 58.388 52.381 0.00 0.00 0.00 4.79
3306 3352 1.633774 ATGGAGTCTGTCTTGGTCGT 58.366 50.000 0.00 0.00 0.00 4.34
3307 3353 1.410004 TGGAGTCTGTCTTGGTCGTT 58.590 50.000 0.00 0.00 0.00 3.85
3308 3354 1.760613 TGGAGTCTGTCTTGGTCGTTT 59.239 47.619 0.00 0.00 0.00 3.60
3309 3355 2.135933 GGAGTCTGTCTTGGTCGTTTG 58.864 52.381 0.00 0.00 0.00 2.93
3310 3356 2.135933 GAGTCTGTCTTGGTCGTTTGG 58.864 52.381 0.00 0.00 0.00 3.28
3311 3357 1.760613 AGTCTGTCTTGGTCGTTTGGA 59.239 47.619 0.00 0.00 0.00 3.53
3312 3358 2.368875 AGTCTGTCTTGGTCGTTTGGAT 59.631 45.455 0.00 0.00 0.00 3.41
3313 3359 2.480419 GTCTGTCTTGGTCGTTTGGATG 59.520 50.000 0.00 0.00 0.00 3.51
3314 3360 2.367241 TCTGTCTTGGTCGTTTGGATGA 59.633 45.455 0.00 0.00 0.00 2.92
3315 3361 3.007940 TCTGTCTTGGTCGTTTGGATGAT 59.992 43.478 0.00 0.00 0.00 2.45
3316 3362 3.750371 TGTCTTGGTCGTTTGGATGATT 58.250 40.909 0.00 0.00 0.00 2.57
3317 3363 4.141287 TGTCTTGGTCGTTTGGATGATTT 58.859 39.130 0.00 0.00 0.00 2.17
3318 3364 4.023279 TGTCTTGGTCGTTTGGATGATTTG 60.023 41.667 0.00 0.00 0.00 2.32
3319 3365 3.505680 TCTTGGTCGTTTGGATGATTTGG 59.494 43.478 0.00 0.00 0.00 3.28
3320 3366 3.147553 TGGTCGTTTGGATGATTTGGA 57.852 42.857 0.00 0.00 0.00 3.53
3330 3376 6.398234 TTGGATGATTTGGAAGAAACGAAA 57.602 33.333 0.00 0.00 0.00 3.46
3336 3382 6.568869 TGATTTGGAAGAAACGAAACAACAT 58.431 32.000 0.00 0.00 0.00 2.71
3388 3434 7.318893 TGGATTGCATGATCGAACAAATTAAA 58.681 30.769 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.833287 TTATGGGGAGAGCACAGAGC 59.167 55.000 0.00 0.00 46.19 4.09
28 29 3.432186 CGAAATCTTATGGGGAGAGCACA 60.432 47.826 0.00 0.00 0.00 4.57
40 41 7.521871 ACTATCCTTACGGACGAAATCTTAT 57.478 36.000 0.00 0.00 43.51 1.73
60 61 5.810034 GCAGAGGTTAAAAAGGGGGAACTAT 60.810 44.000 0.00 0.00 0.00 2.12
66 67 1.557099 GGCAGAGGTTAAAAAGGGGG 58.443 55.000 0.00 0.00 0.00 5.40
67 68 1.173913 CGGCAGAGGTTAAAAAGGGG 58.826 55.000 0.00 0.00 0.00 4.79
68 69 1.173913 CCGGCAGAGGTTAAAAAGGG 58.826 55.000 0.00 0.00 0.00 3.95
69 70 1.905637 ACCGGCAGAGGTTAAAAAGG 58.094 50.000 0.00 0.00 43.00 3.11
126 130 3.703127 GCCTCGTTCCCCGTTCCT 61.703 66.667 0.00 0.00 37.94 3.36
273 291 0.035739 TCCCTTCCGTTACCTGTTGC 59.964 55.000 0.00 0.00 0.00 4.17
482 506 3.758973 TTCGGCACAACCTCCGCAA 62.759 57.895 0.00 0.00 44.91 4.85
492 516 2.970324 GTTCGGCACTTCGGCACA 60.970 61.111 0.00 0.00 41.26 4.57
498 522 3.655481 CCACTGGTTCGGCACTTC 58.345 61.111 0.00 0.00 0.00 3.01
506 530 0.322008 CCAGAAGAGGCCACTGGTTC 60.322 60.000 21.83 10.19 44.06 3.62
511 535 1.004044 CATTGACCAGAAGAGGCCACT 59.996 52.381 5.01 0.00 0.00 4.00
623 647 5.338365 AGTTAAGTCCGTTATCTGCGTTAG 58.662 41.667 0.00 0.00 0.00 2.34
629 653 5.032863 CCACGTAGTTAAGTCCGTTATCTG 58.967 45.833 0.00 0.00 41.61 2.90
656 680 2.148768 GTTAATCCCCCGGCTTAATCG 58.851 52.381 0.00 0.00 0.00 3.34
667 691 1.410153 TCTAACCGCGAGTTAATCCCC 59.590 52.381 8.23 0.00 40.43 4.81
671 695 9.784680 CATATTATACTCTAACCGCGAGTTAAT 57.215 33.333 8.23 11.29 40.43 1.40
672 696 7.752239 GCATATTATACTCTAACCGCGAGTTAA 59.248 37.037 8.23 5.06 40.43 2.01
698 730 1.914634 CTGGTTGCTGCTACTCGTAG 58.085 55.000 13.54 0.00 36.29 3.51
699 731 0.108804 GCTGGTTGCTGCTACTCGTA 60.109 55.000 13.54 0.00 38.95 3.43
745 777 8.101654 TCCGTTTCTTTTAATAAAGCTAAGCA 57.898 30.769 0.00 0.00 40.47 3.91
759 791 8.069574 GCATCAAAAATGATTTCCGTTTCTTTT 58.930 29.630 0.00 0.00 33.08 2.27
838 870 2.736670 ATAGCCGAGCAAAAAGGGAT 57.263 45.000 0.00 0.00 0.00 3.85
873 905 4.080129 TCAGGATCTCTTTCAATTCAGGGG 60.080 45.833 0.00 0.00 0.00 4.79
955 987 5.376854 AGAACATCAACCAAACTACATGC 57.623 39.130 0.00 0.00 0.00 4.06
1067 1099 3.149196 TGCTCTGTCTTTTGATTCCCAC 58.851 45.455 0.00 0.00 0.00 4.61
1103 1135 6.899089 TCAGATAGCCTTGAATTCCATTGTA 58.101 36.000 2.27 0.00 0.00 2.41
1259 1294 2.914097 AAGGCCCTGTGCTGCAAC 60.914 61.111 2.77 0.00 40.92 4.17
1317 1352 1.673920 TCGTTTGTTTCCTTGGAGTGC 59.326 47.619 0.00 0.00 0.00 4.40
1367 1403 7.145985 TCTATATGAGCCTTTAGTAAAGCACG 58.854 38.462 15.95 5.30 37.18 5.34
1611 1647 5.191727 TGGTGTCCATTTCATTATGACCT 57.808 39.130 0.00 0.00 0.00 3.85
1758 1794 8.565896 ACTATAGATGCTTGAACAAACAATCA 57.434 30.769 6.78 0.00 32.05 2.57
1870 1906 2.025793 TGGAGGAGCTCTCTATATCGGG 60.026 54.545 14.64 0.00 42.10 5.14
2039 2075 2.033407 CACGTGTCTTCTTTGTCAGCTG 60.033 50.000 7.63 7.63 0.00 4.24
2198 2234 4.458989 GGTGAACATTCTACAATTGCTCCA 59.541 41.667 5.05 0.00 0.00 3.86
2232 2268 2.445905 ACGGGACCATACTATCAGGAGA 59.554 50.000 0.00 0.00 0.00 3.71
2490 2527 2.109799 CGAGGCTGCGGATGGAAT 59.890 61.111 0.00 0.00 0.00 3.01
2742 2779 3.609853 GCTTATCCGGATCATTATGCCA 58.390 45.455 23.08 0.00 0.00 4.92
2743 2780 2.945668 GGCTTATCCGGATCATTATGCC 59.054 50.000 23.08 21.24 0.00 4.40
2789 2835 6.140377 TCCAAAACCTCCAAAAATCTTAGGT 58.860 36.000 0.00 0.00 42.35 3.08
2824 2870 9.886657 ACTGAATAGTGGAGTACATGGCAACAG 62.887 44.444 0.00 0.00 43.59 3.16
2867 2913 7.718753 AGGGCTATTTCTGAGATTTATCAACTG 59.281 37.037 0.00 0.00 0.00 3.16
2868 2914 7.718753 CAGGGCTATTTCTGAGATTTATCAACT 59.281 37.037 0.00 0.00 33.11 3.16
2869 2915 7.716998 TCAGGGCTATTTCTGAGATTTATCAAC 59.283 37.037 0.00 0.00 35.37 3.18
2870 2916 7.805163 TCAGGGCTATTTCTGAGATTTATCAA 58.195 34.615 0.00 0.00 35.37 2.57
2871 2917 7.379059 TCAGGGCTATTTCTGAGATTTATCA 57.621 36.000 0.00 0.00 35.37 2.15
2872 2918 7.277539 CGATCAGGGCTATTTCTGAGATTTATC 59.722 40.741 0.00 0.00 42.40 1.75
2873 2919 7.102346 CGATCAGGGCTATTTCTGAGATTTAT 58.898 38.462 0.00 0.00 42.40 1.40
2874 2920 6.042093 ACGATCAGGGCTATTTCTGAGATTTA 59.958 38.462 0.00 0.00 42.40 1.40
2875 2921 5.163258 ACGATCAGGGCTATTTCTGAGATTT 60.163 40.000 0.00 0.00 42.40 2.17
2876 2922 4.346418 ACGATCAGGGCTATTTCTGAGATT 59.654 41.667 0.00 0.00 42.40 2.40
2877 2923 3.900601 ACGATCAGGGCTATTTCTGAGAT 59.099 43.478 0.00 0.00 42.40 2.75
2878 2924 3.068732 CACGATCAGGGCTATTTCTGAGA 59.931 47.826 0.00 0.00 42.40 3.27
2879 2925 3.068732 TCACGATCAGGGCTATTTCTGAG 59.931 47.826 0.00 0.00 42.40 3.35
2880 2926 3.031013 TCACGATCAGGGCTATTTCTGA 58.969 45.455 0.00 0.00 43.15 3.27
2881 2927 3.459232 TCACGATCAGGGCTATTTCTG 57.541 47.619 0.00 0.00 0.00 3.02
2882 2928 3.706594 TCTTCACGATCAGGGCTATTTCT 59.293 43.478 0.00 0.00 0.00 2.52
2883 2929 4.060038 TCTTCACGATCAGGGCTATTTC 57.940 45.455 0.00 0.00 0.00 2.17
2884 2930 4.384056 CATCTTCACGATCAGGGCTATTT 58.616 43.478 0.00 0.00 0.00 1.40
2885 2931 3.805108 GCATCTTCACGATCAGGGCTATT 60.805 47.826 0.00 0.00 0.00 1.73
2886 2932 2.289320 GCATCTTCACGATCAGGGCTAT 60.289 50.000 0.00 0.00 0.00 2.97
2920 2966 1.592669 GATCACCGAGCATCCCACG 60.593 63.158 0.00 0.00 0.00 4.94
2950 2996 1.525077 GGGTGTGTTCAAGGCGTCA 60.525 57.895 0.00 0.00 0.00 4.35
2951 2997 0.889186 ATGGGTGTGTTCAAGGCGTC 60.889 55.000 0.00 0.00 0.00 5.19
2952 2998 0.889186 GATGGGTGTGTTCAAGGCGT 60.889 55.000 0.00 0.00 0.00 5.68
2953 2999 1.875963 GATGGGTGTGTTCAAGGCG 59.124 57.895 0.00 0.00 0.00 5.52
2954 3000 1.586154 CCGATGGGTGTGTTCAAGGC 61.586 60.000 0.00 0.00 0.00 4.35
2955 3001 2.555123 CCGATGGGTGTGTTCAAGG 58.445 57.895 0.00 0.00 0.00 3.61
2966 3012 0.106719 AATGGCCAGTAACCGATGGG 60.107 55.000 13.05 0.00 37.05 4.00
2967 3013 2.158813 AGTAATGGCCAGTAACCGATGG 60.159 50.000 15.71 0.00 39.73 3.51
2968 3014 3.131396 GAGTAATGGCCAGTAACCGATG 58.869 50.000 15.71 0.00 0.00 3.84
2969 3015 2.104281 GGAGTAATGGCCAGTAACCGAT 59.896 50.000 15.71 0.00 0.00 4.18
2970 3016 1.483415 GGAGTAATGGCCAGTAACCGA 59.517 52.381 15.71 0.00 0.00 4.69
2971 3017 1.485066 AGGAGTAATGGCCAGTAACCG 59.515 52.381 15.71 0.00 0.00 4.44
3001 3047 2.704464 TGATCTGCAGGACCAATCTG 57.296 50.000 15.13 0.00 35.49 2.90
3012 3058 6.577103 CAGGAAAGACTAGTATTGATCTGCA 58.423 40.000 2.98 0.00 0.00 4.41
3033 3079 2.671177 CGAGGACAAAGTGCGCAGG 61.671 63.158 12.22 3.11 0.00 4.85
3037 3083 1.205064 CAAGCGAGGACAAAGTGCG 59.795 57.895 0.00 0.00 0.00 5.34
3047 3093 1.148157 CCAGATGCGTACAAGCGAGG 61.148 60.000 0.00 0.00 40.67 4.63
3051 3097 2.279741 TGATTCCAGATGCGTACAAGC 58.720 47.619 0.00 0.00 37.71 4.01
3077 3123 1.134995 TCATGATGAGTGACCGACTGC 60.135 52.381 0.00 0.00 33.83 4.40
3110 3156 4.626042 ACGCCAAAATTAAACATGCTCAA 58.374 34.783 0.00 0.00 0.00 3.02
3117 3163 4.580995 TCAGGAGAACGCCAAAATTAAACA 59.419 37.500 0.00 0.00 0.00 2.83
3149 3195 7.889873 TCAACAAGGAATTTCTTCTTTACCA 57.110 32.000 0.00 0.00 30.26 3.25
3204 3250 2.143925 GCGTCCAATCCTGTTATAGCC 58.856 52.381 0.00 0.00 0.00 3.93
3210 3256 1.375523 GTCGGCGTCCAATCCTGTT 60.376 57.895 6.85 0.00 0.00 3.16
3213 3259 4.143333 CCGTCGGCGTCCAATCCT 62.143 66.667 9.28 0.00 36.15 3.24
3251 3297 3.008330 CACCAATGAGAGAAAGAGCTGG 58.992 50.000 0.00 0.00 0.00 4.85
3276 3322 2.763448 ACAGACTCCATTCCTACTGCTC 59.237 50.000 0.00 0.00 0.00 4.26
3281 3327 3.515901 ACCAAGACAGACTCCATTCCTAC 59.484 47.826 0.00 0.00 0.00 3.18
3282 3328 3.769844 GACCAAGACAGACTCCATTCCTA 59.230 47.826 0.00 0.00 0.00 2.94
3295 3341 2.920724 TCATCCAAACGACCAAGACA 57.079 45.000 0.00 0.00 0.00 3.41
3296 3342 4.475944 CAAATCATCCAAACGACCAAGAC 58.524 43.478 0.00 0.00 0.00 3.01
3297 3343 3.505680 CCAAATCATCCAAACGACCAAGA 59.494 43.478 0.00 0.00 0.00 3.02
3298 3344 3.505680 TCCAAATCATCCAAACGACCAAG 59.494 43.478 0.00 0.00 0.00 3.61
3299 3345 3.491342 TCCAAATCATCCAAACGACCAA 58.509 40.909 0.00 0.00 0.00 3.67
3300 3346 3.147553 TCCAAATCATCCAAACGACCA 57.852 42.857 0.00 0.00 0.00 4.02
3301 3347 3.756434 TCTTCCAAATCATCCAAACGACC 59.244 43.478 0.00 0.00 0.00 4.79
3302 3348 5.371115 TTCTTCCAAATCATCCAAACGAC 57.629 39.130 0.00 0.00 0.00 4.34
3303 3349 5.561919 CGTTTCTTCCAAATCATCCAAACGA 60.562 40.000 7.63 0.00 44.68 3.85
3304 3350 4.616802 CGTTTCTTCCAAATCATCCAAACG 59.383 41.667 0.00 0.00 38.97 3.60
3305 3351 5.768317 TCGTTTCTTCCAAATCATCCAAAC 58.232 37.500 0.00 0.00 0.00 2.93
3306 3352 6.398234 TTCGTTTCTTCCAAATCATCCAAA 57.602 33.333 0.00 0.00 0.00 3.28
3307 3353 6.183360 TGTTTCGTTTCTTCCAAATCATCCAA 60.183 34.615 0.00 0.00 0.00 3.53
3308 3354 5.300539 TGTTTCGTTTCTTCCAAATCATCCA 59.699 36.000 0.00 0.00 0.00 3.41
3309 3355 5.768317 TGTTTCGTTTCTTCCAAATCATCC 58.232 37.500 0.00 0.00 0.00 3.51
3310 3356 6.695278 TGTTGTTTCGTTTCTTCCAAATCATC 59.305 34.615 0.00 0.00 0.00 2.92
3311 3357 6.568869 TGTTGTTTCGTTTCTTCCAAATCAT 58.431 32.000 0.00 0.00 0.00 2.45
3312 3358 5.955488 TGTTGTTTCGTTTCTTCCAAATCA 58.045 33.333 0.00 0.00 0.00 2.57
3313 3359 7.860872 ACTATGTTGTTTCGTTTCTTCCAAATC 59.139 33.333 0.00 0.00 0.00 2.17
3314 3360 7.712797 ACTATGTTGTTTCGTTTCTTCCAAAT 58.287 30.769 0.00 0.00 0.00 2.32
3315 3361 7.090953 ACTATGTTGTTTCGTTTCTTCCAAA 57.909 32.000 0.00 0.00 0.00 3.28
3316 3362 6.687081 ACTATGTTGTTTCGTTTCTTCCAA 57.313 33.333 0.00 0.00 0.00 3.53
3317 3363 6.687081 AACTATGTTGTTTCGTTTCTTCCA 57.313 33.333 0.00 0.00 0.00 3.53
3318 3364 7.980742 AAAACTATGTTGTTTCGTTTCTTCC 57.019 32.000 0.00 0.00 38.98 3.46
3319 3365 9.068008 TCAAAAACTATGTTGTTTCGTTTCTTC 57.932 29.630 0.00 0.00 38.98 2.87
3320 3366 8.973835 TCAAAAACTATGTTGTTTCGTTTCTT 57.026 26.923 0.00 0.00 38.98 2.52


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

AutoCloner maintained by Alex Coulton.