Multiple sequence alignment - TraesCS3A01G096700

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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 TraesCS3A01G096700 chr3A 100.000 3878 0 0 1 3878 61481555 61485432 0.000000e+00 7162.0
1 TraesCS3A01G096700 chr3D 95.436 3155 104 17 2 3135 49008380 49011515 0.000000e+00 4992.0
2 TraesCS3A01G096700 chr3D 84.211 76 4 2 3131 3198 588675016 588675091 2.500000e-07 67.6
3 TraesCS3A01G096700 chr3D 81.395 86 8 2 3121 3198 585095740 585095825 3.230000e-06 63.9
4 TraesCS3A01G096700 chr3B 96.066 2135 78 3 768 2902 78606125 78608253 0.000000e+00 3472.0
5 TraesCS3A01G096700 chr3B 88.430 605 42 13 1 594 78598133 78598720 0.000000e+00 704.0
6 TraesCS3A01G096700 chr1A 97.357 681 12 3 3204 3878 269352670 269353350 0.000000e+00 1153.0
7 TraesCS3A01G096700 chr1A 97.210 681 13 1 3204 3878 22112951 22113631 0.000000e+00 1147.0
8 TraesCS3A01G096700 chr1A 97.063 681 14 1 3204 3878 284441768 284441088 0.000000e+00 1142.0
9 TraesCS3A01G096700 chr1A 97.063 681 14 1 3204 3878 563740304 563740984 0.000000e+00 1142.0
10 TraesCS3A01G096700 chr1A 91.946 298 24 0 1811 2108 456474548 456474251 5.990000e-113 418.0
11 TraesCS3A01G096700 chr1A 87.054 224 29 0 1589 1812 456650142 456649919 1.790000e-63 254.0
12 TraesCS3A01G096700 chr4A 97.210 681 13 1 3204 3878 570544475 570545155 0.000000e+00 1147.0
13 TraesCS3A01G096700 chr4A 97.210 681 13 1 3204 3878 595155380 595156060 0.000000e+00 1147.0
14 TraesCS3A01G096700 chr4A 97.063 681 14 1 3204 3878 16522192 16521512 0.000000e+00 1142.0
15 TraesCS3A01G096700 chr4A 97.063 681 14 1 3204 3878 559923759 559924439 0.000000e+00 1142.0
16 TraesCS3A01G096700 chr5A 97.063 681 14 1 3204 3878 689069531 689068851 0.000000e+00 1142.0
17 TraesCS3A01G096700 chr1D 91.139 553 49 0 1556 2108 429581 429029 0.000000e+00 750.0
18 TraesCS3A01G096700 chr1D 91.765 510 42 0 1599 2108 355824362 355823853 0.000000e+00 710.0
19 TraesCS3A01G096700 chr2A 89.199 287 30 1 1848 2134 773404356 773404071 1.320000e-94 357.0
20 TraesCS3A01G096700 chr2A 83.417 199 24 2 1589 1786 773404542 773404352 3.980000e-40 176.0
21 TraesCS3A01G096700 chr7D 96.154 52 1 1 1546 1597 572183354 572183304 2.480000e-12 84.2
22 TraesCS3A01G096700 chr7B 86.420 81 2 2 3131 3203 13251293 13251214 3.210000e-11 80.5
23 TraesCS3A01G096700 chr7B 83.544 79 4 2 3133 3203 325978671 325978594 8.990000e-07 65.8
24 TraesCS3A01G096700 chr6B 86.486 74 2 1 3133 3198 37648160 37648087 1.490000e-09 75.0
25 TraesCS3A01G096700 chr6B 85.714 63 1 1 3133 3187 518675371 518675433 4.180000e-05 60.2
26 TraesCS3A01G096700 chr5D 87.500 64 5 2 3135 3197 285130511 285130450 1.930000e-08 71.3
27 TraesCS3A01G096700 chr2B 85.333 75 2 4 3133 3199 105849056 105849129 6.950000e-08 69.4
28 TraesCS3A01G096700 chr5B 83.544 79 3 3 3130 3198 216654616 216654694 8.990000e-07 65.8


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 TraesCS3A01G096700 chr3A 61481555 61485432 3877 False 7162 7162 100.000 1 3878 1 chr3A.!!$F1 3877
1 TraesCS3A01G096700 chr3D 49008380 49011515 3135 False 4992 4992 95.436 2 3135 1 chr3D.!!$F1 3133
2 TraesCS3A01G096700 chr3B 78606125 78608253 2128 False 3472 3472 96.066 768 2902 1 chr3B.!!$F2 2134
3 TraesCS3A01G096700 chr3B 78598133 78598720 587 False 704 704 88.430 1 594 1 chr3B.!!$F1 593
4 TraesCS3A01G096700 chr1A 269352670 269353350 680 False 1153 1153 97.357 3204 3878 1 chr1A.!!$F2 674
5 TraesCS3A01G096700 chr1A 22112951 22113631 680 False 1147 1147 97.210 3204 3878 1 chr1A.!!$F1 674
6 TraesCS3A01G096700 chr1A 284441088 284441768 680 True 1142 1142 97.063 3204 3878 1 chr1A.!!$R1 674
7 TraesCS3A01G096700 chr1A 563740304 563740984 680 False 1142 1142 97.063 3204 3878 1 chr1A.!!$F3 674
8 TraesCS3A01G096700 chr4A 570544475 570545155 680 False 1147 1147 97.210 3204 3878 1 chr4A.!!$F2 674
9 TraesCS3A01G096700 chr4A 595155380 595156060 680 False 1147 1147 97.210 3204 3878 1 chr4A.!!$F3 674
10 TraesCS3A01G096700 chr4A 16521512 16522192 680 True 1142 1142 97.063 3204 3878 1 chr4A.!!$R1 674
11 TraesCS3A01G096700 chr4A 559923759 559924439 680 False 1142 1142 97.063 3204 3878 1 chr4A.!!$F1 674
12 TraesCS3A01G096700 chr5A 689068851 689069531 680 True 1142 1142 97.063 3204 3878 1 chr5A.!!$R1 674
13 TraesCS3A01G096700 chr1D 429029 429581 552 True 750 750 91.139 1556 2108 1 chr1D.!!$R1 552
14 TraesCS3A01G096700 chr1D 355823853 355824362 509 True 710 710 91.765 1599 2108 1 chr1D.!!$R2 509

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
440 457 0.458543 GATCAGCTTCGCTTCGACCA 60.459 55.000 0.00 0.0 36.4 4.02 F
617 635 1.216064 TGCATCTCCTTGGCCATAGT 58.784 50.000 6.09 0.0 0.0 2.12 F
1418 1442 1.807165 CGCACACCCTCGTCATCAG 60.807 63.158 0.00 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1866 1.118838 CATCCTCTTCCTCCTCGCTT 58.881 55.000 0.00 0.0 0.00 4.68 R
2562 2586 2.202932 CGCTCCCGCTTGCAGTAT 60.203 61.111 0.00 0.0 0.00 2.12 R
3143 3169 0.249657 GGAGCTCGGGTGCAGATTAG 60.250 60.000 7.83 0.0 34.99 1.73 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
209 219 1.755179 GCACAGCCATATGGTGAACT 58.245 50.000 22.79 8.61 45.48 3.01
211 221 3.480470 GCACAGCCATATGGTGAACTAT 58.520 45.455 22.79 0.00 45.48 2.12
256 269 5.119694 GGACTGAAACTTGAAGTGAACTCT 58.880 41.667 0.00 0.00 0.00 3.24
257 270 5.235401 GGACTGAAACTTGAAGTGAACTCTC 59.765 44.000 0.00 0.00 0.00 3.20
262 277 4.875561 ACTTGAAGTGAACTCTCTACCC 57.124 45.455 0.00 0.00 0.00 3.69
287 302 1.631898 GGTGGTTACTCCCAGGCTTTA 59.368 52.381 0.00 0.00 34.43 1.85
288 303 2.617276 GGTGGTTACTCCCAGGCTTTAC 60.617 54.545 0.00 0.00 34.43 2.01
301 316 1.009829 GCTTTACTGTCCCTGATGCG 58.990 55.000 0.00 0.00 0.00 4.73
440 457 0.458543 GATCAGCTTCGCTTCGACCA 60.459 55.000 0.00 0.00 36.40 4.02
504 522 2.933573 TGTTCCCGCTTTTCTGGTTTA 58.066 42.857 0.00 0.00 0.00 2.01
512 530 4.100529 CGCTTTTCTGGTTTATGCATCAG 58.899 43.478 0.19 4.42 0.00 2.90
594 612 3.505680 TGTACTGAATTGGGCATGTTGAC 59.494 43.478 0.00 0.00 0.00 3.18
595 613 2.880443 ACTGAATTGGGCATGTTGACT 58.120 42.857 0.00 0.00 0.00 3.41
596 614 2.821969 ACTGAATTGGGCATGTTGACTC 59.178 45.455 0.00 0.00 0.00 3.36
617 635 1.216064 TGCATCTCCTTGGCCATAGT 58.784 50.000 6.09 0.00 0.00 2.12
641 659 5.921004 GCAATTTGCAAAACCAATACTGA 57.079 34.783 17.19 0.00 44.26 3.41
644 662 6.369615 GCAATTTGCAAAACCAATACTGATCT 59.630 34.615 17.19 0.00 44.26 2.75
645 663 7.622672 GCAATTTGCAAAACCAATACTGATCTG 60.623 37.037 17.19 0.00 44.26 2.90
656 674 6.989169 ACCAATACTGATCTGCAAGTATCTTC 59.011 38.462 8.80 0.00 33.76 2.87
657 675 6.426328 CCAATACTGATCTGCAAGTATCTTCC 59.574 42.308 8.80 0.00 33.76 3.46
678 696 1.975407 CCCAAACTGGCTGCTCCTG 60.975 63.158 0.00 0.00 35.79 3.86
693 711 5.055265 TGCTCCTGCTAGTATCTTAGACT 57.945 43.478 0.00 0.00 40.48 3.24
697 715 6.039941 GCTCCTGCTAGTATCTTAGACTGAAA 59.960 42.308 0.00 0.00 36.03 2.69
727 745 5.639757 TGTGCTAAATGATGTGTAATGTGC 58.360 37.500 0.00 0.00 0.00 4.57
729 747 6.597280 TGTGCTAAATGATGTGTAATGTGCTA 59.403 34.615 0.00 0.00 0.00 3.49
732 750 7.128331 GCTAAATGATGTGTAATGTGCTACTG 58.872 38.462 0.00 0.00 0.00 2.74
775 794 6.015434 ACAGGGAAAACATGGTAGAATTGAAC 60.015 38.462 0.00 0.00 34.56 3.18
810 829 6.260050 ACGCTGAACTAAACTGAATTGAAGAA 59.740 34.615 0.00 0.00 0.00 2.52
813 832 8.962111 GCTGAACTAAACTGAATTGAAGAAAAG 58.038 33.333 0.00 0.00 0.00 2.27
820 839 6.645790 ACTGAATTGAAGAAAAGTCATGCT 57.354 33.333 0.00 0.00 34.03 3.79
846 865 7.967854 TGAAATTATGGTGTCTGCTTTAAATCG 59.032 33.333 0.00 0.00 0.00 3.34
918 942 2.305635 TGTACTGTTGGGTGCAGATGAT 59.694 45.455 0.00 0.00 37.40 2.45
926 950 3.499338 TGGGTGCAGATGATTTGAGTTT 58.501 40.909 0.00 0.00 0.00 2.66
1068 1092 3.532155 ATCGACTCCCTGCGCCTC 61.532 66.667 4.18 0.00 0.00 4.70
1088 1112 3.157949 CCTCCGCTCCCCTTCCTC 61.158 72.222 0.00 0.00 0.00 3.71
1089 1113 3.157949 CTCCGCTCCCCTTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
1090 1114 3.684628 TCCGCTCCCCTTCCTCCT 61.685 66.667 0.00 0.00 0.00 3.69
1417 1441 2.261361 CGCACACCCTCGTCATCA 59.739 61.111 0.00 0.00 0.00 3.07
1418 1442 1.807165 CGCACACCCTCGTCATCAG 60.807 63.158 0.00 0.00 0.00 2.90
2738 2762 3.978491 GGAGATGATCGCGGCGGA 61.978 66.667 23.46 9.74 0.00 5.54
2739 2763 2.731348 GAGATGATCGCGGCGGAC 60.731 66.667 23.46 16.43 0.00 4.79
2850 2874 1.524165 GGAGCCTGATGCAGAGCAG 60.524 63.158 6.95 6.95 43.65 4.24
2864 2888 4.487412 GCAGTTGGCGGCTGATGC 62.487 66.667 11.43 13.44 36.12 3.91
2867 2891 3.058160 GTTGGCGGCTGATGCAGT 61.058 61.111 11.43 0.00 41.91 4.40
2892 2916 0.445436 GTTGATGCTGCTCCACTTCG 59.555 55.000 0.00 0.00 0.00 3.79
2893 2917 0.674581 TTGATGCTGCTCCACTTCGG 60.675 55.000 0.00 0.00 0.00 4.30
2894 2918 1.219124 GATGCTGCTCCACTTCGGA 59.781 57.895 0.00 0.00 43.61 4.55
2895 2919 1.078848 ATGCTGCTCCACTTCGGAC 60.079 57.895 0.00 0.00 39.64 4.79
2896 2920 1.548357 ATGCTGCTCCACTTCGGACT 61.548 55.000 0.00 0.00 39.64 3.85
2897 2921 1.004440 GCTGCTCCACTTCGGACTT 60.004 57.895 0.00 0.00 39.64 3.01
2898 2922 0.603975 GCTGCTCCACTTCGGACTTT 60.604 55.000 0.00 0.00 39.64 2.66
2934 2958 1.651240 ATTGACATGCTCGTGGCTGC 61.651 55.000 0.00 0.00 42.39 5.25
2939 2963 3.997064 ATGCTCGTGGCTGCTCGAC 62.997 63.158 13.92 11.86 42.39 4.20
2985 3009 3.004106 AGAAGTTTCAGTGTCATTGCAGC 59.996 43.478 0.00 0.00 0.00 5.25
3008 3032 0.465824 AGGAGAAGCATGGCAGCATC 60.466 55.000 10.71 8.38 36.85 3.91
3012 3036 0.812811 GAAGCATGGCAGCATCGAGA 60.813 55.000 10.71 0.00 36.85 4.04
3013 3037 0.179026 AAGCATGGCAGCATCGAGAT 60.179 50.000 10.71 0.00 36.85 2.75
3114 3140 6.479001 TCTCAAACTAATAATACCGCAGAAGC 59.521 38.462 0.00 0.00 37.42 3.86
3115 3141 6.110033 TCAAACTAATAATACCGCAGAAGCA 58.890 36.000 0.00 0.00 42.27 3.91
3116 3142 6.257849 TCAAACTAATAATACCGCAGAAGCAG 59.742 38.462 0.00 0.00 42.27 4.24
3117 3143 5.531122 ACTAATAATACCGCAGAAGCAGA 57.469 39.130 0.00 0.00 42.27 4.26
3118 3144 5.914033 ACTAATAATACCGCAGAAGCAGAA 58.086 37.500 0.00 0.00 42.27 3.02
3119 3145 5.986135 ACTAATAATACCGCAGAAGCAGAAG 59.014 40.000 0.00 0.00 42.27 2.85
3135 3161 6.595772 AGCAGAAGTATAGCTTTTTCATCG 57.404 37.500 0.00 0.00 37.59 3.84
3136 3162 5.525378 AGCAGAAGTATAGCTTTTTCATCGG 59.475 40.000 0.00 0.00 37.59 4.18
3137 3163 5.523916 GCAGAAGTATAGCTTTTTCATCGGA 59.476 40.000 0.00 0.00 37.59 4.55
3138 3164 6.510317 GCAGAAGTATAGCTTTTTCATCGGAC 60.510 42.308 0.00 0.00 37.59 4.79
3139 3165 5.749109 AGAAGTATAGCTTTTTCATCGGACG 59.251 40.000 0.00 0.00 37.59 4.79
3140 3166 3.802685 AGTATAGCTTTTTCATCGGACGC 59.197 43.478 0.00 0.00 0.00 5.19
3141 3167 0.996462 TAGCTTTTTCATCGGACGCG 59.004 50.000 3.53 3.53 0.00 6.01
3142 3168 1.226018 GCTTTTTCATCGGACGCGG 60.226 57.895 12.47 0.00 0.00 6.46
3143 3169 1.226018 CTTTTTCATCGGACGCGGC 60.226 57.895 12.47 7.53 0.00 6.53
3144 3170 1.635663 CTTTTTCATCGGACGCGGCT 61.636 55.000 13.91 0.00 0.00 5.52
3145 3171 0.390078 TTTTTCATCGGACGCGGCTA 60.390 50.000 13.91 0.00 0.00 3.93
3146 3172 0.390078 TTTTCATCGGACGCGGCTAA 60.390 50.000 13.91 0.00 0.00 3.09
3147 3173 0.179094 TTTCATCGGACGCGGCTAAT 60.179 50.000 13.91 2.12 0.00 1.73
3148 3174 0.596600 TTCATCGGACGCGGCTAATC 60.597 55.000 13.91 0.00 0.00 1.75
3149 3175 1.007271 CATCGGACGCGGCTAATCT 60.007 57.895 13.91 0.00 0.00 2.40
3150 3176 1.007271 ATCGGACGCGGCTAATCTG 60.007 57.895 13.91 3.65 0.00 2.90
3151 3177 3.330853 CGGACGCGGCTAATCTGC 61.331 66.667 13.91 0.00 43.66 4.26
3156 3182 3.272334 GCGGCTAATCTGCACCCG 61.272 66.667 0.00 0.00 46.35 5.28
3157 3183 2.499205 CGGCTAATCTGCACCCGA 59.501 61.111 0.00 0.00 41.34 5.14
3158 3184 1.592669 CGGCTAATCTGCACCCGAG 60.593 63.158 0.00 0.00 41.34 4.63
3159 3185 1.889573 GGCTAATCTGCACCCGAGC 60.890 63.158 0.00 0.00 34.04 5.03
3160 3186 1.144936 GCTAATCTGCACCCGAGCT 59.855 57.895 0.00 0.00 34.99 4.09
3161 3187 0.878086 GCTAATCTGCACCCGAGCTC 60.878 60.000 2.73 2.73 34.99 4.09
3162 3188 0.249657 CTAATCTGCACCCGAGCTCC 60.250 60.000 8.47 0.00 34.99 4.70
3163 3189 1.686325 TAATCTGCACCCGAGCTCCC 61.686 60.000 8.47 0.00 34.99 4.30
3170 3196 4.161295 CCCGAGCTCCCGCATGAA 62.161 66.667 8.47 0.00 39.10 2.57
3171 3197 2.109799 CCGAGCTCCCGCATGAAT 59.890 61.111 8.47 0.00 39.10 2.57
3172 3198 1.367471 CCGAGCTCCCGCATGAATA 59.633 57.895 8.47 0.00 39.10 1.75
3173 3199 0.668706 CCGAGCTCCCGCATGAATAG 60.669 60.000 8.47 0.00 39.10 1.73
3174 3200 0.032678 CGAGCTCCCGCATGAATAGT 59.967 55.000 8.47 0.00 39.10 2.12
3175 3201 1.269723 CGAGCTCCCGCATGAATAGTA 59.730 52.381 8.47 0.00 39.10 1.82
3176 3202 2.288213 CGAGCTCCCGCATGAATAGTAA 60.288 50.000 8.47 0.00 39.10 2.24
3177 3203 3.728845 GAGCTCCCGCATGAATAGTAAA 58.271 45.455 0.87 0.00 39.10 2.01
3178 3204 4.127171 GAGCTCCCGCATGAATAGTAAAA 58.873 43.478 0.87 0.00 39.10 1.52
3179 3205 4.718961 AGCTCCCGCATGAATAGTAAAAT 58.281 39.130 0.00 0.00 39.10 1.82
3180 3206 4.757149 AGCTCCCGCATGAATAGTAAAATC 59.243 41.667 0.00 0.00 39.10 2.17
3181 3207 4.377431 GCTCCCGCATGAATAGTAAAATCG 60.377 45.833 0.00 0.00 35.78 3.34
3182 3208 4.951254 TCCCGCATGAATAGTAAAATCGA 58.049 39.130 0.00 0.00 0.00 3.59
3183 3209 5.361427 TCCCGCATGAATAGTAAAATCGAA 58.639 37.500 0.00 0.00 0.00 3.71
3184 3210 5.818336 TCCCGCATGAATAGTAAAATCGAAA 59.182 36.000 0.00 0.00 0.00 3.46
3185 3211 6.316640 TCCCGCATGAATAGTAAAATCGAAAA 59.683 34.615 0.00 0.00 0.00 2.29
3186 3212 6.970043 CCCGCATGAATAGTAAAATCGAAAAA 59.030 34.615 0.00 0.00 0.00 1.94
3221 3247 1.525535 GGATCGCTGGAGCTTGCAT 60.526 57.895 7.80 1.79 39.32 3.96
3299 3325 6.013032 ACTCTTCTTCCAGAAATCCATTCAGA 60.013 38.462 0.00 0.00 40.72 3.27
3347 3373 9.616156 TGCCAAATTTCATAATCATAAAATGCT 57.384 25.926 0.00 0.00 0.00 3.79
3367 3393 4.158949 TGCTGCAATTGCTAACATGATTCT 59.841 37.500 29.37 0.00 42.66 2.40
3491 3517 0.956633 TACCGTCAGCGTCAGTCTTT 59.043 50.000 0.00 0.00 36.15 2.52
3649 3681 6.535508 GCTTCTTCATAGTTCGTAGGTTCATT 59.464 38.462 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 219 5.069383 CCACAAATGGGATGAATGAGCAATA 59.931 40.000 0.00 0.00 43.04 1.90
211 221 3.196039 CCACAAATGGGATGAATGAGCAA 59.804 43.478 0.00 0.00 43.04 3.91
262 277 0.246635 CTGGGAGTAACCACCAGTCG 59.753 60.000 0.00 0.00 45.21 4.18
287 302 4.101448 GGGCGCATCAGGGACAGT 62.101 66.667 10.83 0.00 37.47 3.55
440 457 6.008331 GGTTACAACCTATCTGTTTTTCCCT 58.992 40.000 3.80 0.00 45.75 4.20
470 487 0.928229 GGAACATCGGACCGAATTCG 59.072 55.000 22.55 20.92 39.99 3.34
472 489 3.471354 GGGAACATCGGACCGAATT 57.529 52.632 22.55 18.01 39.99 2.17
504 522 4.471908 TCGCCGCCACTGATGCAT 62.472 61.111 0.00 0.00 0.00 3.96
522 540 0.179089 CTCATCCCCTGAAGCAGTCG 60.179 60.000 0.00 0.00 32.14 4.18
594 612 0.106868 TGGCCAAGGAGATGCATGAG 60.107 55.000 0.61 0.00 0.00 2.90
595 613 0.554305 ATGGCCAAGGAGATGCATGA 59.446 50.000 10.96 0.00 0.00 3.07
596 614 2.160205 CTATGGCCAAGGAGATGCATG 58.840 52.381 10.96 0.00 0.00 4.06
600 618 1.952296 GCAACTATGGCCAAGGAGATG 59.048 52.381 10.96 13.60 0.00 2.90
673 691 7.575414 TTTCAGTCTAAGATACTAGCAGGAG 57.425 40.000 0.00 0.00 0.00 3.69
693 711 9.356433 CACATCATTTAGCACAATACAATTTCA 57.644 29.630 0.00 0.00 0.00 2.69
727 745 8.310406 TGTACATGTGAATTCAAGAACAGTAG 57.690 34.615 10.35 1.70 0.00 2.57
729 747 6.205464 CCTGTACATGTGAATTCAAGAACAGT 59.795 38.462 22.64 14.44 31.05 3.55
732 750 5.705441 TCCCTGTACATGTGAATTCAAGAAC 59.295 40.000 10.35 5.37 0.00 3.01
820 839 7.967854 CGATTTAAAGCAGACACCATAATTTCA 59.032 33.333 4.10 0.00 0.00 2.69
846 865 8.660373 CCATTTCTTCAGTGTTTCATAGTAGAC 58.340 37.037 0.00 0.00 0.00 2.59
926 950 6.223852 CAGCTCAAGAGACAGGTTTTAGTAA 58.776 40.000 0.32 0.00 0.00 2.24
1842 1866 1.118838 CATCCTCTTCCTCCTCGCTT 58.881 55.000 0.00 0.00 0.00 4.68
2562 2586 2.202932 CGCTCCCGCTTGCAGTAT 60.203 61.111 0.00 0.00 0.00 2.12
2593 2617 2.827555 CATTTCGTCGAACAGCTTCAC 58.172 47.619 7.29 0.00 0.00 3.18
2850 2874 3.044059 GACTGCATCAGCCGCCAAC 62.044 63.158 0.00 0.00 41.13 3.77
2864 2888 0.520404 GCAGCATCAACCAGTGACTG 59.480 55.000 5.42 5.42 39.72 3.51
2867 2891 0.321919 GGAGCAGCATCAACCAGTGA 60.322 55.000 0.00 0.00 41.67 3.41
2892 2916 8.669243 CAATTTGGTATCTCAACTCTAAAGTCC 58.331 37.037 0.00 0.00 33.48 3.85
2893 2917 9.436957 TCAATTTGGTATCTCAACTCTAAAGTC 57.563 33.333 0.00 0.00 33.48 3.01
2894 2918 9.220767 GTCAATTTGGTATCTCAACTCTAAAGT 57.779 33.333 0.00 0.00 37.32 2.66
2895 2919 9.219603 TGTCAATTTGGTATCTCAACTCTAAAG 57.780 33.333 0.00 0.00 0.00 1.85
2896 2920 9.739276 ATGTCAATTTGGTATCTCAACTCTAAA 57.261 29.630 0.00 0.00 0.00 1.85
2897 2921 9.166173 CATGTCAATTTGGTATCTCAACTCTAA 57.834 33.333 0.00 0.00 0.00 2.10
2898 2922 7.280876 GCATGTCAATTTGGTATCTCAACTCTA 59.719 37.037 0.00 0.00 0.00 2.43
2934 2958 2.359214 TGGATCAATCTCTTCCGTCGAG 59.641 50.000 0.00 0.00 31.90 4.04
2939 2963 2.611292 GCTGTTGGATCAATCTCTTCCG 59.389 50.000 0.00 0.00 31.90 4.30
2941 2965 4.005650 TGTGCTGTTGGATCAATCTCTTC 58.994 43.478 0.00 0.00 0.00 2.87
2985 3009 1.380524 CTGCCATGCTTCTCCTTCAG 58.619 55.000 0.00 0.00 0.00 3.02
3114 3140 6.291849 CGTCCGATGAAAAAGCTATACTTCTG 60.292 42.308 0.00 0.00 37.75 3.02
3115 3141 5.749109 CGTCCGATGAAAAAGCTATACTTCT 59.251 40.000 0.00 0.00 37.75 2.85
3116 3142 5.556570 GCGTCCGATGAAAAAGCTATACTTC 60.557 44.000 0.00 0.00 37.75 3.01
3117 3143 4.270325 GCGTCCGATGAAAAAGCTATACTT 59.730 41.667 0.00 0.00 41.70 2.24
3118 3144 3.802685 GCGTCCGATGAAAAAGCTATACT 59.197 43.478 0.00 0.00 0.00 2.12
3119 3145 3.361724 CGCGTCCGATGAAAAAGCTATAC 60.362 47.826 0.00 0.00 36.29 1.47
3135 3161 2.202878 TGCAGATTAGCCGCGTCC 60.203 61.111 4.92 0.00 0.00 4.79
3136 3162 2.526120 GGTGCAGATTAGCCGCGTC 61.526 63.158 4.92 0.00 0.00 5.19
3137 3163 2.511600 GGTGCAGATTAGCCGCGT 60.512 61.111 4.92 0.00 0.00 6.01
3138 3164 3.272334 GGGTGCAGATTAGCCGCG 61.272 66.667 0.00 0.00 0.00 6.46
3141 3167 1.889573 GCTCGGGTGCAGATTAGCC 60.890 63.158 0.00 0.00 0.00 3.93
3142 3168 0.878086 GAGCTCGGGTGCAGATTAGC 60.878 60.000 0.00 0.00 34.99 3.09
3143 3169 0.249657 GGAGCTCGGGTGCAGATTAG 60.250 60.000 7.83 0.00 34.99 1.73
3144 3170 1.686325 GGGAGCTCGGGTGCAGATTA 61.686 60.000 7.83 0.00 34.99 1.75
3145 3171 2.586792 GGAGCTCGGGTGCAGATT 59.413 61.111 7.83 0.00 34.99 2.40
3146 3172 3.474570 GGGAGCTCGGGTGCAGAT 61.475 66.667 7.83 0.00 34.99 2.90
3159 3185 4.988540 TCGATTTTACTATTCATGCGGGAG 59.011 41.667 0.00 0.00 0.00 4.30
3160 3186 4.951254 TCGATTTTACTATTCATGCGGGA 58.049 39.130 0.00 0.00 0.00 5.14
3161 3187 5.666969 TTCGATTTTACTATTCATGCGGG 57.333 39.130 0.00 0.00 0.00 6.13
3162 3188 7.962934 TTTTTCGATTTTACTATTCATGCGG 57.037 32.000 0.00 0.00 0.00 5.69
3195 3221 1.401905 GCTCCAGCGATCCGAATTTTT 59.598 47.619 0.00 0.00 0.00 1.94
3196 3222 1.017387 GCTCCAGCGATCCGAATTTT 58.983 50.000 0.00 0.00 0.00 1.82
3197 3223 2.695314 GCTCCAGCGATCCGAATTT 58.305 52.632 0.00 0.00 0.00 1.82
3198 3224 4.445699 GCTCCAGCGATCCGAATT 57.554 55.556 0.00 0.00 0.00 2.17
3221 3247 4.986054 TCCAAAGGGAGCTAACAAAGTA 57.014 40.909 0.00 0.00 38.64 2.24
3299 3325 5.475719 CAGATGGATGTCAAAACTGCATTT 58.524 37.500 0.00 0.00 0.00 2.32
3347 3373 5.183522 TGTCAGAATCATGTTAGCAATTGCA 59.816 36.000 30.89 14.94 45.16 4.08
3367 3393 4.363138 CATAGCGATGCTTAAGTCTGTCA 58.637 43.478 4.02 0.00 40.44 3.58
3649 3681 8.697507 TCTGAAAGTCATGCTACTAGATCATA 57.302 34.615 0.00 0.00 33.76 2.15
3670 3702 3.194116 GTGGTACGGTAATCCTGTTCTGA 59.806 47.826 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.