Multiple sequence alignment - TraesCS3B01G016200

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 TraesCS3B01G016200 chr3B 100.000 3690 0 0 1 3690 6660055 6656366 0.000000e+00 6815.0
1 TraesCS3B01G016200 chr3B 75.823 790 142 30 1373 2142 6221246 6220486 4.530000e-94 355.0
2 TraesCS3B01G016200 chr3B 78.761 113 11 10 828 932 6222341 6222234 3.080000e-06 63.9
3 TraesCS3B01G016200 chr3A 93.753 2225 85 16 727 2911 9772490 9770280 0.000000e+00 3290.0
4 TraesCS3B01G016200 chr3A 80.636 1761 289 38 1364 3087 9509701 9507956 0.000000e+00 1315.0
5 TraesCS3B01G016200 chr3A 93.493 753 42 3 2942 3690 9770279 9769530 0.000000e+00 1112.0
6 TraesCS3B01G016200 chr3A 93.976 581 32 2 169 749 9773292 9772715 0.000000e+00 876.0
7 TraesCS3B01G016200 chr3A 94.915 118 6 0 1 118 9774443 9774326 6.290000e-43 185.0
8 TraesCS3B01G016200 chrUn 76.680 759 141 17 1396 2142 276880910 276881644 4.470000e-104 388.0
9 TraesCS3B01G016200 chrUn 75.919 789 142 29 1373 2142 35925897 35925138 9.740000e-96 361.0
10 TraesCS3B01G016200 chrUn 75.919 789 142 29 1373 2142 318764565 318763806 9.740000e-96 361.0
11 TraesCS3B01G016200 chrUn 78.761 113 11 10 828 932 35926992 35926885 3.080000e-06 63.9
12 TraesCS3B01G016200 chrUn 78.761 113 11 10 828 932 318765660 318765553 3.080000e-06 63.9
13 TraesCS3B01G016200 chrUn 77.586 116 13 11 825 932 276879814 276879924 1.430000e-04 58.4
14 TraesCS3B01G016200 chr4A 73.141 659 136 30 1489 2132 615446455 615447087 8.080000e-47 198.0
15 TraesCS3B01G016200 chr1D 85.714 91 12 1 314 403 45085362 45085272 1.090000e-15 95.3
16 TraesCS3B01G016200 chr1D 84.615 91 13 1 314 403 45132690 45132600 5.080000e-14 89.8


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 TraesCS3B01G016200 chr3B 6656366 6660055 3689 True 6815.00 6815 100.00000 1 3690 1 chr3B.!!$R1 3689
1 TraesCS3B01G016200 chr3B 6220486 6222341 1855 True 209.45 355 77.29200 828 2142 2 chr3B.!!$R2 1314
2 TraesCS3B01G016200 chr3A 9769530 9774443 4913 True 1365.75 3290 94.03425 1 3690 4 chr3A.!!$R2 3689
3 TraesCS3B01G016200 chr3A 9507956 9509701 1745 True 1315.00 1315 80.63600 1364 3087 1 chr3A.!!$R1 1723
4 TraesCS3B01G016200 chrUn 276879814 276881644 1830 False 223.20 388 77.13300 825 2142 2 chrUn.!!$F1 1317
5 TraesCS3B01G016200 chrUn 35925138 35926992 1854 True 212.45 361 77.34000 828 2142 2 chrUn.!!$R1 1314
6 TraesCS3B01G016200 chrUn 318763806 318765660 1854 True 212.45 361 77.34000 828 2142 2 chrUn.!!$R2 1314

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
159 852 0.178891 TCACAGAGGAAGAAGGGGCT 60.179 55.0 0.00 0.0 0.0 5.19 F
774 2005 0.179189 CTCTTTCCGCGTGATTTGCC 60.179 55.0 4.92 0.0 0.0 4.52 F
783 2014 0.374758 CGTGATTTGCCGTCCATCTG 59.625 55.0 0.00 0.0 0.0 2.90 F
1250 2594 0.736325 CGTCTACCTTGAACTGGCGG 60.736 60.0 0.00 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 3629 0.250338 AAAGGGTTGCCAGACTCGTC 60.250 55.000 0.00 0.00 0.00 4.20 R
2252 4140 1.929836 GAGCTTAAGCATGACGACCAG 59.070 52.381 28.39 0.00 45.16 4.00 R
2332 4220 2.035626 AATGCAACCAGGACCGGG 59.964 61.111 9.42 9.42 0.00 5.73 R
3095 5016 2.158871 GGCCGTTAACTCCATATCACCA 60.159 50.000 3.71 0.00 0.00 4.17 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
78 79 2.341846 TTTTAGCTAGCCCCCAATCG 57.658 50.000 12.13 0.00 0.00 3.34
109 110 2.291465 CACATATTTCTGCATGGTCCGG 59.709 50.000 0.00 0.00 0.00 5.14
113 114 0.400213 TTTCTGCATGGTCCGGAAGT 59.600 50.000 5.23 0.00 0.00 3.01
120 121 2.046604 GGTCCGGAAGTTTCGGGG 60.047 66.667 22.52 0.00 46.78 5.73
121 122 2.586293 GGTCCGGAAGTTTCGGGGA 61.586 63.158 22.52 0.77 46.78 4.81
122 123 1.372307 GTCCGGAAGTTTCGGGGAA 59.628 57.895 22.52 0.00 46.78 3.97
123 124 0.672711 GTCCGGAAGTTTCGGGGAAG 60.673 60.000 22.52 0.00 46.78 3.46
124 125 2.038837 CCGGAAGTTTCGGGGAAGC 61.039 63.158 15.38 0.00 43.45 3.86
131 824 2.188817 AGTTTCGGGGAAGCATAGAGT 58.811 47.619 0.00 0.00 0.00 3.24
138 831 3.127030 CGGGGAAGCATAGAGTTTCAAAC 59.873 47.826 0.00 0.00 39.01 2.93
139 832 4.079253 GGGGAAGCATAGAGTTTCAAACA 58.921 43.478 2.41 0.00 39.01 2.83
141 834 5.163612 GGGGAAGCATAGAGTTTCAAACATC 60.164 44.000 2.41 0.00 39.01 3.06
142 835 5.415701 GGGAAGCATAGAGTTTCAAACATCA 59.584 40.000 2.41 0.00 39.01 3.07
145 838 6.492007 AGCATAGAGTTTCAAACATCACAG 57.508 37.500 2.41 0.00 0.00 3.66
146 839 6.233434 AGCATAGAGTTTCAAACATCACAGA 58.767 36.000 2.41 0.00 0.00 3.41
147 840 6.370994 AGCATAGAGTTTCAAACATCACAGAG 59.629 38.462 2.41 0.00 0.00 3.35
148 841 6.402983 GCATAGAGTTTCAAACATCACAGAGG 60.403 42.308 2.41 0.00 0.00 3.69
150 843 5.684704 AGAGTTTCAAACATCACAGAGGAA 58.315 37.500 2.41 0.00 0.00 3.36
152 845 5.684704 AGTTTCAAACATCACAGAGGAAGA 58.315 37.500 2.41 0.00 0.00 2.87
153 846 6.122277 AGTTTCAAACATCACAGAGGAAGAA 58.878 36.000 2.41 0.00 0.00 2.52
154 847 6.261826 AGTTTCAAACATCACAGAGGAAGAAG 59.738 38.462 2.41 0.00 0.00 2.85
156 849 3.710209 AACATCACAGAGGAAGAAGGG 57.290 47.619 0.00 0.00 0.00 3.95
157 850 1.912043 ACATCACAGAGGAAGAAGGGG 59.088 52.381 0.00 0.00 0.00 4.79
158 851 0.915364 ATCACAGAGGAAGAAGGGGC 59.085 55.000 0.00 0.00 0.00 5.80
159 852 0.178891 TCACAGAGGAAGAAGGGGCT 60.179 55.000 0.00 0.00 0.00 5.19
160 853 1.078823 TCACAGAGGAAGAAGGGGCTA 59.921 52.381 0.00 0.00 0.00 3.93
161 854 2.122768 CACAGAGGAAGAAGGGGCTAT 58.877 52.381 0.00 0.00 0.00 2.97
162 855 2.507471 CACAGAGGAAGAAGGGGCTATT 59.493 50.000 0.00 0.00 0.00 1.73
163 856 3.054065 CACAGAGGAAGAAGGGGCTATTT 60.054 47.826 0.00 0.00 0.00 1.40
164 857 3.593780 ACAGAGGAAGAAGGGGCTATTTT 59.406 43.478 0.00 0.00 0.00 1.82
166 859 5.253096 ACAGAGGAAGAAGGGGCTATTTTTA 59.747 40.000 0.00 0.00 0.00 1.52
167 860 5.825151 CAGAGGAAGAAGGGGCTATTTTTAG 59.175 44.000 0.00 0.00 0.00 1.85
211 1195 6.514048 GCATGAGAGGGTTATAAGCAAACATC 60.514 42.308 16.07 7.17 0.00 3.06
212 1196 6.061022 TGAGAGGGTTATAAGCAAACATCA 57.939 37.500 16.07 9.31 0.00 3.07
215 1199 5.648092 AGAGGGTTATAAGCAAACATCACAC 59.352 40.000 16.07 0.00 0.00 3.82
235 1219 5.048713 CACACAGAGATAAAACCAAGGGAAC 60.049 44.000 0.00 0.00 0.00 3.62
254 1238 5.497474 GGAACCCATACCAATAATATCGCT 58.503 41.667 0.00 0.00 0.00 4.93
312 1296 4.184649 ACAACTTCAAATTCCTCACCCT 57.815 40.909 0.00 0.00 0.00 4.34
344 1328 3.420893 CCTGCCAAGTTTAGGACATGAA 58.579 45.455 0.00 0.00 33.33 2.57
347 1331 4.922206 TGCCAAGTTTAGGACATGAATCT 58.078 39.130 0.00 0.00 0.00 2.40
379 1363 2.943036 TCCACCACAAGGAACTAACC 57.057 50.000 0.00 0.00 38.49 2.85
389 1373 4.042187 ACAAGGAACTAACCATCTGAGCTT 59.958 41.667 0.00 0.00 38.49 3.74
442 1426 1.990160 TTCCTTCCACACGCCTTGGT 61.990 55.000 0.00 0.00 35.42 3.67
445 1429 2.709125 CTTCCACACGCCTTGGTCGA 62.709 60.000 9.64 0.00 35.42 4.20
446 1430 2.981977 TTCCACACGCCTTGGTCGAC 62.982 60.000 7.13 7.13 35.42 4.20
451 1435 0.661020 CACGCCTTGGTCGACTTTTT 59.339 50.000 16.46 0.00 0.00 1.94
452 1436 1.868498 CACGCCTTGGTCGACTTTTTA 59.132 47.619 16.46 0.00 0.00 1.52
453 1437 2.482721 CACGCCTTGGTCGACTTTTTAT 59.517 45.455 16.46 0.00 0.00 1.40
455 1439 3.058501 ACGCCTTGGTCGACTTTTTATTG 60.059 43.478 16.46 1.92 0.00 1.90
464 1448 5.123979 GGTCGACTTTTTATTGAAGGCAGAT 59.876 40.000 16.46 0.00 31.40 2.90
471 1455 8.248945 ACTTTTTATTGAAGGCAGATCAATCAG 58.751 33.333 13.96 9.96 44.25 2.90
481 1465 3.185330 CAGATCAATCAGTCTCCACACG 58.815 50.000 0.00 0.00 0.00 4.49
482 1466 2.167281 AGATCAATCAGTCTCCACACGG 59.833 50.000 0.00 0.00 0.00 4.94
494 1478 0.958091 CCACACGGCCAAATCTTTGA 59.042 50.000 2.24 0.00 40.55 2.69
531 1515 1.276705 GGAACCTGGTCTTCTCCACTC 59.723 57.143 9.86 0.00 33.55 3.51
568 1552 9.614792 GGATGTTTCTACTGTACATTATTCCTT 57.385 33.333 0.00 0.00 32.94 3.36
660 1644 5.365403 TTGTGAAATAAAGATTCCGCGTT 57.635 34.783 4.92 0.00 0.00 4.84
676 1660 4.082625 TCCGCGTTATTTGAGACTGTTCTA 60.083 41.667 4.92 0.00 29.47 2.10
695 1679 7.117397 TGTTCTAGACCTACAATACTGCTACT 58.883 38.462 0.00 0.00 0.00 2.57
705 1689 2.691409 TACTGCTACTGGTGCCAATC 57.309 50.000 0.00 0.00 0.00 2.67
755 1986 1.523758 CTGGTCCCTTGTTGCAGTAC 58.476 55.000 0.00 0.00 0.00 2.73
756 1987 1.072331 CTGGTCCCTTGTTGCAGTACT 59.928 52.381 0.00 0.00 0.00 2.73
774 2005 0.179189 CTCTTTCCGCGTGATTTGCC 60.179 55.000 4.92 0.00 0.00 4.52
775 2006 1.511887 CTTTCCGCGTGATTTGCCG 60.512 57.895 4.92 0.00 0.00 5.69
783 2014 0.374758 CGTGATTTGCCGTCCATCTG 59.625 55.000 0.00 0.00 0.00 2.90
795 2026 3.118738 CCGTCCATCTGGCTAGTTTAAGT 60.119 47.826 0.00 0.00 34.44 2.24
811 2042 5.128663 AGTTTAAGTGTTCCAAACCTGCAAT 59.871 36.000 0.00 0.00 33.58 3.56
857 2096 1.867363 TCCACCCTTAGAGAAGAGCC 58.133 55.000 0.00 0.00 34.25 4.70
858 2097 1.078823 TCCACCCTTAGAGAAGAGCCA 59.921 52.381 0.00 0.00 34.25 4.75
859 2098 1.909302 CCACCCTTAGAGAAGAGCCAA 59.091 52.381 0.00 0.00 34.25 4.52
866 2105 4.468153 CCTTAGAGAAGAGCCAAGGTAAGT 59.532 45.833 0.00 0.00 34.25 2.24
867 2106 3.971245 AGAGAAGAGCCAAGGTAAGTG 57.029 47.619 0.00 0.00 0.00 3.16
876 2115 2.427506 CCAAGGTAAGTGCAGGTCTTC 58.572 52.381 0.00 0.00 0.00 2.87
904 2145 6.315714 TCCTCTTCTGGTTTCTCTCTTTCTA 58.684 40.000 0.00 0.00 0.00 2.10
905 2146 6.209788 TCCTCTTCTGGTTTCTCTCTTTCTAC 59.790 42.308 0.00 0.00 0.00 2.59
906 2147 6.015010 CCTCTTCTGGTTTCTCTCTTTCTACA 60.015 42.308 0.00 0.00 0.00 2.74
907 2148 6.987386 TCTTCTGGTTTCTCTCTTTCTACAG 58.013 40.000 0.00 0.00 0.00 2.74
922 2164 8.281212 TCTTTCTACAGATTCCTTAATTTGCC 57.719 34.615 0.00 0.00 31.87 4.52
924 2166 7.391148 TTCTACAGATTCCTTAATTTGCCAC 57.609 36.000 0.00 0.00 31.87 5.01
1010 2270 2.684881 ACGGTTTCGAGATGGTACGTAT 59.315 45.455 0.00 0.00 40.11 3.06
1026 2286 2.095008 ACGTATGCATGCCTCTCTATCG 60.095 50.000 16.68 10.69 0.00 2.92
1212 2556 3.502051 AGTAAACCAGTAGATCCCCCA 57.498 47.619 0.00 0.00 0.00 4.96
1247 2591 5.413833 TCTTAGTACGTCTACCTTGAACTGG 59.586 44.000 0.00 0.00 0.00 4.00
1250 2594 0.736325 CGTCTACCTTGAACTGGCGG 60.736 60.000 0.00 0.00 0.00 6.13
1270 2939 2.689983 GGGGTGCAACATCCTCATTTAG 59.310 50.000 3.06 0.00 39.98 1.85
1300 3141 9.595823 AAAATGATATTTGAAATTGCCTCTCTG 57.404 29.630 0.00 0.00 0.00 3.35
1558 3434 0.957888 GCTTGGCAGAAGGAGTGGTC 60.958 60.000 0.00 0.00 0.00 4.02
1603 3479 2.342179 GCACTGGCTCTCAACTTAGTC 58.658 52.381 0.00 0.00 36.96 2.59
1660 3536 2.363306 TACCATTGATCACCATGGCC 57.637 50.000 21.52 0.00 37.69 5.36
1753 3629 3.549625 GCGTAAGTCCTATCCCTGTAACG 60.550 52.174 0.00 0.00 41.68 3.18
1849 3725 3.451141 TCCATTTTTGTCACTGTTGGC 57.549 42.857 0.00 0.00 0.00 4.52
1855 3731 2.535012 TTGTCACTGTTGGCGTCATA 57.465 45.000 0.00 0.00 0.00 2.15
2252 4140 4.443394 CGGTTGGTATCTTCGTACTATTGC 59.557 45.833 0.00 0.00 0.00 3.56
2567 4455 0.249073 CATAAGGAGTGGTCTCGCCG 60.249 60.000 0.00 0.00 41.26 6.46
2748 4650 6.183360 GCATAAGTAGGCTATCTTTGCACAAA 60.183 38.462 21.27 0.00 33.04 2.83
2800 4709 6.143915 TGAGAGAAGTGTATAATAGGCCCTT 58.856 40.000 0.00 0.00 0.00 3.95
2917 4835 2.995480 CCAATGAGGCCCAAACCAT 58.005 52.632 0.00 0.00 0.00 3.55
2918 4836 2.157640 CCAATGAGGCCCAAACCATA 57.842 50.000 0.00 0.00 0.00 2.74
2921 4839 2.830923 CAATGAGGCCCAAACCATAACA 59.169 45.455 0.00 0.00 0.00 2.41
2923 4841 1.145945 TGAGGCCCAAACCATAACACA 59.854 47.619 0.00 0.00 0.00 3.72
2925 4843 2.166254 GAGGCCCAAACCATAACACATG 59.834 50.000 0.00 0.00 0.00 3.21
3045 4966 3.306571 GGGCTTTAGTTTCTCGTGGTACT 60.307 47.826 0.00 0.00 0.00 2.73
3109 5030 7.448469 GGCAATTATACTTGGTGATATGGAGTT 59.552 37.037 5.12 0.00 0.00 3.01
3119 5040 3.498397 GTGATATGGAGTTAACGGCCATG 59.502 47.826 30.25 0.00 42.15 3.66
3128 5049 5.354792 GGAGTTAACGGCCATGTGTAATAAA 59.645 40.000 2.24 0.00 0.00 1.40
3129 5050 6.127952 GGAGTTAACGGCCATGTGTAATAAAA 60.128 38.462 2.24 0.00 0.00 1.52
3130 5051 6.848451 AGTTAACGGCCATGTGTAATAAAAG 58.152 36.000 2.24 0.00 0.00 2.27
3132 5053 3.020984 ACGGCCATGTGTAATAAAAGGG 58.979 45.455 2.24 0.00 0.00 3.95
3142 5063 9.184523 CATGTGTAATAAAAGGGTCCTAATTGA 57.815 33.333 0.00 0.00 0.00 2.57
3165 5086 4.007659 CCTTGGTAGGTGTTATTGTGACC 58.992 47.826 0.00 0.00 36.74 4.02
3233 5158 3.133721 AGGAGCTATTTGGCACTCTACTG 59.866 47.826 0.00 0.00 34.17 2.74
3244 5169 6.852420 TGGCACTCTACTGATAGTTTAAGT 57.148 37.500 0.00 0.00 0.00 2.24
3251 5176 9.323985 ACTCTACTGATAGTTTAAGTACCTACG 57.676 37.037 0.00 0.00 0.00 3.51
3382 5307 7.701501 CGTAGTTTCCCTTCTATTACTCACTTC 59.298 40.741 0.00 0.00 0.00 3.01
3389 5314 7.125356 TCCCTTCTATTACTCACTTCCCTTAAC 59.875 40.741 0.00 0.00 0.00 2.01
3511 5436 8.264347 AGAGAGAAGACTCAGGGAATATTTTTC 58.736 37.037 0.00 0.00 44.79 2.29
3512 5437 8.156822 AGAGAAGACTCAGGGAATATTTTTCT 57.843 34.615 0.00 0.00 44.79 2.52
3521 5446 6.600822 TCAGGGAATATTTTTCTGCTCTTCTG 59.399 38.462 0.00 0.00 0.00 3.02
3610 5535 6.851330 GTGCAAATACACACTAAAAGTCTCAC 59.149 38.462 0.00 0.00 40.40 3.51
3621 5546 2.814280 AAGTCTCACGAATTCACCGT 57.186 45.000 6.22 0.00 41.36 4.83
3631 5556 5.518847 TCACGAATTCACCGTCTAATGAATC 59.481 40.000 6.22 0.00 43.21 2.52
3635 5560 6.682863 CGAATTCACCGTCTAATGAATCAAAC 59.317 38.462 6.22 0.00 43.21 2.93
3637 5562 7.630242 ATTCACCGTCTAATGAATCAAACAT 57.370 32.000 0.00 0.00 40.72 2.71
3638 5563 7.447374 TTCACCGTCTAATGAATCAAACATT 57.553 32.000 0.00 0.00 40.40 2.71
3639 5564 7.447374 TCACCGTCTAATGAATCAAACATTT 57.553 32.000 0.00 0.00 38.61 2.32
3640 5565 7.881142 TCACCGTCTAATGAATCAAACATTTT 58.119 30.769 0.00 0.00 38.61 1.82
3670 5595 5.786401 TGCACCAAACATTTACAAAACAC 57.214 34.783 0.00 0.00 0.00 3.32
3671 5596 5.237815 TGCACCAAACATTTACAAAACACA 58.762 33.333 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.383476 ACTCCATCATCCCTTCATTGATTC 58.617 41.667 0.00 0.00 0.00 2.52
42 43 5.432060 AGCTAAAAATAGCCCCTTCTTCCTA 59.568 40.000 4.32 0.00 43.81 2.94
54 55 3.223674 TGGGGGCTAGCTAAAAATAGC 57.776 47.619 15.72 0.00 42.99 2.97
78 79 4.393680 TGCAGAAATATGTGGTAACGGTTC 59.606 41.667 0.00 0.00 42.51 3.62
109 110 3.198872 CTCTATGCTTCCCCGAAACTTC 58.801 50.000 0.00 0.00 0.00 3.01
113 114 3.008594 TGAAACTCTATGCTTCCCCGAAA 59.991 43.478 0.00 0.00 0.00 3.46
118 119 5.415701 TGATGTTTGAAACTCTATGCTTCCC 59.584 40.000 9.69 0.00 0.00 3.97
120 121 6.902341 TGTGATGTTTGAAACTCTATGCTTC 58.098 36.000 9.69 0.00 0.00 3.86
121 122 6.712095 TCTGTGATGTTTGAAACTCTATGCTT 59.288 34.615 9.69 0.00 0.00 3.91
122 123 6.233434 TCTGTGATGTTTGAAACTCTATGCT 58.767 36.000 9.69 0.00 0.00 3.79
123 124 6.402983 CCTCTGTGATGTTTGAAACTCTATGC 60.403 42.308 9.69 0.00 0.00 3.14
124 125 6.875726 TCCTCTGTGATGTTTGAAACTCTATG 59.124 38.462 9.69 0.00 0.00 2.23
131 824 5.532406 CCTTCTTCCTCTGTGATGTTTGAAA 59.468 40.000 0.00 0.00 0.00 2.69
138 831 1.407989 GCCCCTTCTTCCTCTGTGATG 60.408 57.143 0.00 0.00 0.00 3.07
139 832 0.915364 GCCCCTTCTTCCTCTGTGAT 59.085 55.000 0.00 0.00 0.00 3.06
141 834 1.573108 TAGCCCCTTCTTCCTCTGTG 58.427 55.000 0.00 0.00 0.00 3.66
142 835 2.577772 ATAGCCCCTTCTTCCTCTGT 57.422 50.000 0.00 0.00 0.00 3.41
145 838 4.580995 GCTAAAAATAGCCCCTTCTTCCTC 59.419 45.833 0.00 0.00 37.11 3.71
146 839 4.230733 AGCTAAAAATAGCCCCTTCTTCCT 59.769 41.667 4.32 0.00 43.81 3.36
147 840 4.537751 AGCTAAAAATAGCCCCTTCTTCC 58.462 43.478 4.32 0.00 43.81 3.46
148 841 6.207614 CCATAGCTAAAAATAGCCCCTTCTTC 59.792 42.308 0.00 0.00 43.81 2.87
150 843 5.458215 CCCATAGCTAAAAATAGCCCCTTCT 60.458 44.000 0.00 0.00 43.81 2.85
152 845 4.449229 CCCCATAGCTAAAAATAGCCCCTT 60.449 45.833 0.00 0.00 43.81 3.95
153 846 3.076032 CCCCATAGCTAAAAATAGCCCCT 59.924 47.826 0.00 0.00 43.81 4.79
154 847 3.075432 TCCCCATAGCTAAAAATAGCCCC 59.925 47.826 0.00 0.00 43.81 5.80
156 849 6.918067 AATTCCCCATAGCTAAAAATAGCC 57.082 37.500 0.00 0.00 43.81 3.93
157 850 8.637196 AGTAATTCCCCATAGCTAAAAATAGC 57.363 34.615 0.00 0.00 43.12 2.97
158 851 9.793259 TGAGTAATTCCCCATAGCTAAAAATAG 57.207 33.333 0.00 0.00 0.00 1.73
160 853 9.082313 CATGAGTAATTCCCCATAGCTAAAAAT 57.918 33.333 0.00 0.00 0.00 1.82
161 854 7.014230 GCATGAGTAATTCCCCATAGCTAAAAA 59.986 37.037 0.00 0.00 0.00 1.94
162 855 6.490040 GCATGAGTAATTCCCCATAGCTAAAA 59.510 38.462 0.00 0.00 0.00 1.52
163 856 6.003950 GCATGAGTAATTCCCCATAGCTAAA 58.996 40.000 0.00 0.00 0.00 1.85
164 857 5.073008 TGCATGAGTAATTCCCCATAGCTAA 59.927 40.000 0.00 0.00 0.00 3.09
166 859 3.395607 TGCATGAGTAATTCCCCATAGCT 59.604 43.478 0.00 0.00 0.00 3.32
167 860 3.754965 TGCATGAGTAATTCCCCATAGC 58.245 45.455 0.00 0.00 0.00 2.97
203 1187 5.858581 GGTTTTATCTCTGTGTGATGTTTGC 59.141 40.000 0.00 0.00 0.00 3.68
211 1195 4.651778 TCCCTTGGTTTTATCTCTGTGTG 58.348 43.478 0.00 0.00 0.00 3.82
212 1196 4.993705 TCCCTTGGTTTTATCTCTGTGT 57.006 40.909 0.00 0.00 0.00 3.72
215 1199 4.017126 GGGTTCCCTTGGTTTTATCTCTG 58.983 47.826 0.00 0.00 0.00 3.35
235 1219 8.204160 TCATCTTAGCGATATTATTGGTATGGG 58.796 37.037 12.55 8.13 0.00 4.00
251 1235 7.306283 GCAACTCTATTTGTAGTCATCTTAGCG 60.306 40.741 0.00 0.00 0.00 4.26
254 1238 9.719355 TTTGCAACTCTATTTGTAGTCATCTTA 57.281 29.630 0.00 0.00 0.00 2.10
297 1281 2.503765 TCGCATAGGGTGAGGAATTTGA 59.496 45.455 0.00 0.00 0.00 2.69
306 1290 2.731571 GGGTGCTCGCATAGGGTGA 61.732 63.158 0.00 0.00 34.20 4.02
308 1292 2.365635 AGGGTGCTCGCATAGGGT 60.366 61.111 5.59 0.00 0.00 4.34
312 1296 2.874648 CTTGGCAGGGTGCTCGCATA 62.875 60.000 5.59 0.00 44.28 3.14
344 1328 2.616458 GGAACCAGCCCACCCAGAT 61.616 63.158 0.00 0.00 0.00 2.90
347 1331 3.897122 GTGGAACCAGCCCACCCA 61.897 66.667 0.00 0.00 46.30 4.51
366 1350 3.584848 AGCTCAGATGGTTAGTTCCTTGT 59.415 43.478 0.00 0.00 0.00 3.16
389 1373 1.227645 AGCAGTGCGAACTGAGCAA 60.228 52.632 28.26 0.00 46.97 3.91
442 1426 5.937540 TGATCTGCCTTCAATAAAAAGTCGA 59.062 36.000 0.00 0.00 0.00 4.20
445 1429 8.125978 TGATTGATCTGCCTTCAATAAAAAGT 57.874 30.769 6.01 0.00 42.38 2.66
446 1430 8.248945 ACTGATTGATCTGCCTTCAATAAAAAG 58.751 33.333 6.01 5.30 42.38 2.27
451 1435 6.244552 AGACTGATTGATCTGCCTTCAATA 57.755 37.500 6.01 0.00 42.38 1.90
452 1436 5.113446 AGACTGATTGATCTGCCTTCAAT 57.887 39.130 5.78 5.78 44.40 2.57
453 1437 4.511527 GAGACTGATTGATCTGCCTTCAA 58.488 43.478 0.00 0.00 37.49 2.69
455 1439 3.118482 TGGAGACTGATTGATCTGCCTTC 60.118 47.826 0.00 0.00 32.66 3.46
464 1448 0.037326 GCCGTGTGGAGACTGATTGA 60.037 55.000 0.00 0.00 37.49 2.57
471 1455 0.321653 AGATTTGGCCGTGTGGAGAC 60.322 55.000 0.00 0.00 37.49 3.36
481 1465 6.616774 TGTTTTGAATTCAAAGATTTGGCC 57.383 33.333 27.52 13.12 45.34 5.36
482 1466 8.908172 TTTTGTTTTGAATTCAAAGATTTGGC 57.092 26.923 27.52 15.60 45.34 4.52
494 1478 6.767423 CCAGGTTCCTCATTTTGTTTTGAATT 59.233 34.615 0.00 0.00 0.00 2.17
531 1515 6.372659 ACAGTAGAAACATCCTAATTGCACTG 59.627 38.462 0.00 0.00 0.00 3.66
568 1552 8.822805 ACTTTATTTCACTATCAGTACCCAAGA 58.177 33.333 0.00 0.00 0.00 3.02
642 1626 8.120465 TCTCAAATAACGCGGAATCTTTATTTC 58.880 33.333 12.47 0.00 33.74 2.17
660 1644 8.645814 TTGTAGGTCTAGAACAGTCTCAAATA 57.354 34.615 11.14 0.00 35.12 1.40
676 1660 4.402793 CACCAGTAGCAGTATTGTAGGTCT 59.597 45.833 0.00 0.00 0.00 3.85
695 1679 1.452110 CGAGTCAATGATTGGCACCA 58.548 50.000 12.75 0.00 37.85 4.17
755 1986 0.179189 GGCAAATCACGCGGAAAGAG 60.179 55.000 12.47 0.00 0.00 2.85
756 1987 1.873165 GGCAAATCACGCGGAAAGA 59.127 52.632 12.47 2.80 0.00 2.52
774 2005 3.865745 CACTTAAACTAGCCAGATGGACG 59.134 47.826 2.18 0.00 37.39 4.79
775 2006 4.833390 ACACTTAAACTAGCCAGATGGAC 58.167 43.478 2.18 0.00 37.39 4.02
783 2014 4.825634 AGGTTTGGAACACTTAAACTAGCC 59.174 41.667 0.00 0.00 39.29 3.93
795 2026 1.202627 GCCAATTGCAGGTTTGGAACA 60.203 47.619 22.30 0.00 44.23 3.18
857 2096 2.069273 CGAAGACCTGCACTTACCTTG 58.931 52.381 0.00 0.00 0.00 3.61
858 2097 1.608283 GCGAAGACCTGCACTTACCTT 60.608 52.381 0.00 0.00 0.00 3.50
859 2098 0.037232 GCGAAGACCTGCACTTACCT 60.037 55.000 0.00 0.00 0.00 3.08
866 2105 1.219124 GAGGATGCGAAGACCTGCA 59.781 57.895 0.00 0.00 46.51 4.41
867 2106 0.107945 AAGAGGATGCGAAGACCTGC 60.108 55.000 0.00 0.00 33.89 4.85
876 2115 2.093764 AGAGAAACCAGAAGAGGATGCG 60.094 50.000 0.00 0.00 0.00 4.73
904 2145 6.267471 TCAAAGTGGCAAATTAAGGAATCTGT 59.733 34.615 0.00 0.00 0.00 3.41
905 2146 6.690530 TCAAAGTGGCAAATTAAGGAATCTG 58.309 36.000 0.00 0.00 0.00 2.90
906 2147 6.071165 CCTCAAAGTGGCAAATTAAGGAATCT 60.071 38.462 0.00 0.00 0.00 2.40
907 2148 6.071391 TCCTCAAAGTGGCAAATTAAGGAATC 60.071 38.462 3.51 0.00 0.00 2.52
920 2162 6.089417 CGTTTCATTAATTTCCTCAAAGTGGC 59.911 38.462 0.00 0.00 0.00 5.01
922 2164 8.690840 GTTCGTTTCATTAATTTCCTCAAAGTG 58.309 33.333 0.00 0.00 0.00 3.16
924 2166 7.589954 ACGTTCGTTTCATTAATTTCCTCAAAG 59.410 33.333 0.00 0.00 0.00 2.77
1010 2270 0.755079 AAGCGATAGAGAGGCATGCA 59.245 50.000 21.36 0.00 39.76 3.96
1026 2286 8.940952 AGAAAATTCTACTATCTGTGTTCAAGC 58.059 33.333 0.00 0.00 35.34 4.01
1186 2530 5.516062 GGGGATCTACTGGTTTACTTTTGGT 60.516 44.000 0.00 0.00 0.00 3.67
1193 2537 7.147532 GGATATATGGGGGATCTACTGGTTTAC 60.148 44.444 0.00 0.00 0.00 2.01
1247 2591 3.134127 GAGGATGTTGCACCCCGC 61.134 66.667 0.00 0.00 42.89 6.13
1250 2594 3.378427 GTCTAAATGAGGATGTTGCACCC 59.622 47.826 0.00 0.00 0.00 4.61
1270 2939 9.977762 GAGGCAATTTCAAATATCATTTTTGTC 57.022 29.630 1.11 0.00 35.90 3.18
1458 3331 6.882140 TCATGGCCGAGTAATAAGAAAAAGAA 59.118 34.615 0.00 0.00 0.00 2.52
1459 3332 6.315393 GTCATGGCCGAGTAATAAGAAAAAGA 59.685 38.462 0.00 0.00 0.00 2.52
1460 3333 6.093495 TGTCATGGCCGAGTAATAAGAAAAAG 59.907 38.462 0.00 0.00 0.00 2.27
1465 3338 4.343814 TGATGTCATGGCCGAGTAATAAGA 59.656 41.667 0.00 0.00 0.00 2.10
1537 3412 1.676967 CACTCCTTCTGCCAAGCCC 60.677 63.158 0.00 0.00 0.00 5.19
1558 3434 0.796312 GCACCGGGCATATCATAACG 59.204 55.000 6.32 0.00 43.97 3.18
1645 3521 1.829533 GCCGGCCATGGTGATCAAT 60.830 57.895 18.11 0.00 0.00 2.57
1660 3536 3.438781 TGCCAGTTATCAAAGTAAAGCCG 59.561 43.478 0.00 0.00 0.00 5.52
1753 3629 0.250338 AAAGGGTTGCCAGACTCGTC 60.250 55.000 0.00 0.00 0.00 4.20
1849 3725 4.697514 AGACCAAGATTCCACATATGACG 58.302 43.478 10.38 0.00 0.00 4.35
1855 3731 3.814504 ACCAAGACCAAGATTCCACAT 57.185 42.857 0.00 0.00 0.00 3.21
2252 4140 1.929836 GAGCTTAAGCATGACGACCAG 59.070 52.381 28.39 0.00 45.16 4.00
2332 4220 2.035626 AATGCAACCAGGACCGGG 59.964 61.111 9.42 9.42 0.00 5.73
2567 4455 3.243501 ACATGTGCAGATGAAACACAACC 60.244 43.478 28.81 0.00 46.47 3.77
2796 4705 4.764823 TGGCACTTTGTCAATAGTTAAGGG 59.235 41.667 0.00 0.00 0.00 3.95
2800 4709 7.663905 ACATACTTGGCACTTTGTCAATAGTTA 59.336 33.333 0.00 0.00 41.56 2.24
2925 4843 2.553086 CACCAAATTACATGGCATGCC 58.447 47.619 30.54 30.54 41.89 4.40
3063 4984 7.889589 TTGCCATGTCATCTATCTATAAACG 57.110 36.000 0.00 0.00 0.00 3.60
3094 5015 3.537580 GCCGTTAACTCCATATCACCAA 58.462 45.455 3.71 0.00 0.00 3.67
3095 5016 2.158871 GGCCGTTAACTCCATATCACCA 60.159 50.000 3.71 0.00 0.00 4.17
3109 5030 4.641094 CCCTTTTATTACACATGGCCGTTA 59.359 41.667 0.00 0.00 0.00 3.18
3154 5075 7.448748 AAGTCATTAAGTGGGTCACAATAAC 57.551 36.000 0.78 0.00 36.74 1.89
3157 5078 6.207417 CAGAAAGTCATTAAGTGGGTCACAAT 59.793 38.462 0.78 0.00 36.74 2.71
3165 5086 7.786030 TCTAGATCCAGAAAGTCATTAAGTGG 58.214 38.462 0.00 0.00 0.00 4.00
3219 5144 7.676947 ACTTAAACTATCAGTAGAGTGCCAAA 58.323 34.615 0.00 0.00 0.00 3.28
3315 5240 6.980051 AATTGTACGCCTACCTAAAAGAAG 57.020 37.500 0.00 0.00 0.00 2.85
3389 5314 9.979270 GTCAGTGTGTCTAATCAGAATATTTTG 57.021 33.333 0.00 0.00 30.85 2.44
3481 5406 3.465832 TCCCTGAGTCTTCTCTCTCCTA 58.534 50.000 0.00 0.00 40.98 2.94
3521 5446 8.666573 GGTAAGAAGTTTTAGGTAATCTCTTGC 58.333 37.037 0.00 0.00 0.00 4.01
3604 5529 2.349297 AGACGGTGAATTCGTGAGAC 57.651 50.000 0.04 0.00 41.22 3.36
3610 5535 5.966636 TGATTCATTAGACGGTGAATTCG 57.033 39.130 0.04 0.00 43.16 3.34
3638 5563 9.330063 TGTAAATGTTTGGTGCATAATCAAAAA 57.670 25.926 0.00 0.00 33.05 1.94
3639 5564 8.893219 TGTAAATGTTTGGTGCATAATCAAAA 57.107 26.923 0.00 0.00 33.05 2.44
3640 5565 8.893219 TTGTAAATGTTTGGTGCATAATCAAA 57.107 26.923 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.