Multiple sequence alignment - TraesCS4B01G325700

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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 TraesCS4B01G325700 chr4B 100.000 3011 0 0 1 3011 616966513 616969523 0.000000e+00 5561.0
1 TraesCS4B01G325700 chr5A 95.256 1328 58 3 713 2036 665443363 665444689 0.000000e+00 2098.0
2 TraesCS4B01G325700 chr5A 89.130 460 28 11 2522 2975 665445145 665445588 1.220000e-153 553.0
3 TraesCS4B01G325700 chr5A 83.986 281 8 7 2188 2455 665444892 665445148 5.020000e-58 235.0
4 TraesCS4B01G325700 chr5A 100.000 34 0 0 2151 2184 665444694 665444727 2.510000e-06 63.9
5 TraesCS4B01G325700 chr4D 95.389 1171 36 3 908 2072 484620688 484621846 0.000000e+00 1847.0
6 TraesCS4B01G325700 chr4D 91.347 913 52 10 2 898 484619338 484620239 0.000000e+00 1223.0
7 TraesCS4B01G325700 chr4D 89.818 825 47 8 2159 2979 484624407 484625198 0.000000e+00 1024.0
8 TraesCS4B01G325700 chr4D 86.652 457 30 6 2159 2615 250766518 250766943 7.550000e-131 477.0
9 TraesCS4B01G325700 chr4D 85.933 327 21 3 2159 2485 250701523 250701824 2.890000e-85 326.0
10 TraesCS4B01G325700 chr4D 93.617 47 3 0 908 954 484620642 484620688 1.500000e-08 71.3
11 TraesCS4B01G325700 chr3D 86.648 1056 105 21 979 2010 21793036 21794079 0.000000e+00 1136.0
12 TraesCS4B01G325700 chr3D 86.248 1018 127 8 978 1991 21888415 21889423 0.000000e+00 1092.0
13 TraesCS4B01G325700 chr3D 87.800 459 24 10 2159 2617 245677563 245677137 2.680000e-140 508.0
14 TraesCS4B01G325700 chr3D 86.493 422 25 7 2159 2580 499434986 499434597 4.610000e-118 435.0
15 TraesCS4B01G325700 chr3D 96.078 51 2 0 2567 2617 499433641 499433591 1.920000e-12 84.2
16 TraesCS4B01G325700 chr3D 97.059 34 1 0 327 360 452424887 452424920 1.170000e-04 58.4
17 TraesCS4B01G325700 chr3A 86.282 1057 109 20 978 2010 31559186 31560230 0.000000e+00 1116.0
18 TraesCS4B01G325700 chr3A 85.996 1014 130 7 978 1988 31603483 31604487 0.000000e+00 1075.0
19 TraesCS4B01G325700 chr3B 86.161 1055 114 19 978 2010 37970718 37971762 0.000000e+00 1110.0
20 TraesCS4B01G325700 chrUn 84.980 1012 126 15 981 1988 336370761 336369772 0.000000e+00 1003.0
21 TraesCS4B01G325700 chrUn 84.881 1012 127 15 981 1988 336373427 336372438 0.000000e+00 998.0
22 TraesCS4B01G325700 chr2D 88.641 449 20 8 2169 2617 330426891 330427308 4.450000e-143 518.0


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 TraesCS4B01G325700 chr4B 616966513 616969523 3010 False 5561.000 5561 100.00000 1 3011 1 chr4B.!!$F1 3010
1 TraesCS4B01G325700 chr5A 665443363 665445588 2225 False 737.475 2098 92.09300 713 2975 4 chr5A.!!$F1 2262
2 TraesCS4B01G325700 chr4D 484619338 484625198 5860 False 1041.325 1847 92.54275 2 2979 4 chr4D.!!$F3 2977
3 TraesCS4B01G325700 chr3D 21793036 21794079 1043 False 1136.000 1136 86.64800 979 2010 1 chr3D.!!$F1 1031
4 TraesCS4B01G325700 chr3D 21888415 21889423 1008 False 1092.000 1092 86.24800 978 1991 1 chr3D.!!$F2 1013
5 TraesCS4B01G325700 chr3D 499433591 499434986 1395 True 259.600 435 91.28550 2159 2617 2 chr3D.!!$R2 458
6 TraesCS4B01G325700 chr3A 31559186 31560230 1044 False 1116.000 1116 86.28200 978 2010 1 chr3A.!!$F1 1032
7 TraesCS4B01G325700 chr3A 31603483 31604487 1004 False 1075.000 1075 85.99600 978 1988 1 chr3A.!!$F2 1010
8 TraesCS4B01G325700 chr3B 37970718 37971762 1044 False 1110.000 1110 86.16100 978 2010 1 chr3B.!!$F1 1032
9 TraesCS4B01G325700 chrUn 336369772 336373427 3655 True 1000.500 1003 84.93050 981 1988 2 chrUn.!!$R1 1007

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
571 585 0.109132 CCCAAAACGCTCAATCCAGC 60.109 55.0 0.0 0.0 35.9 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 5772 0.03759 AGCCGTGCATTGGTTTAGGA 59.962 50.0 9.41 0.0 0.0 2.94 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
35 36 7.593825 AGATTAATCGCAAACTAAATATGGCC 58.406 34.615 9.78 0.00 0.00 5.36
53 54 2.420129 GGCCGAACATATCACTCCACTT 60.420 50.000 0.00 0.00 0.00 3.16
77 78 7.517614 TGGACACATACACAAACAAATGTAT 57.482 32.000 0.00 0.00 41.63 2.29
102 103 7.421599 TGTGCATCCAAAATATAAATACCACG 58.578 34.615 0.00 0.00 0.00 4.94
147 148 2.158534 TGTACCCAATCCAACTGCAACT 60.159 45.455 0.00 0.00 0.00 3.16
151 152 2.165030 CCCAATCCAACTGCAACTCATC 59.835 50.000 0.00 0.00 0.00 2.92
173 174 4.877251 TCTTTACCCTGTAAACACACACAC 59.123 41.667 0.00 0.00 0.00 3.82
176 177 1.673920 CCCTGTAAACACACACACCAC 59.326 52.381 0.00 0.00 0.00 4.16
185 186 3.351740 ACACACACACCACAAGATTTGA 58.648 40.909 0.00 0.00 0.00 2.69
227 228 7.682055 CACAAACACAACACAAGAAAAATAACG 59.318 33.333 0.00 0.00 0.00 3.18
243 244 5.359194 AATAACGCATCCTATATCCCCTG 57.641 43.478 0.00 0.00 0.00 4.45
247 248 2.093973 CGCATCCTATATCCCCTGTGTC 60.094 54.545 0.00 0.00 0.00 3.67
258 259 1.622725 CCCCTGTGTCCCTAGCTTAGT 60.623 57.143 0.00 0.00 0.00 2.24
284 285 2.656947 AGTACAACAGCCCACACAAT 57.343 45.000 0.00 0.00 0.00 2.71
325 328 1.032014 AACCCACACAAGCACACATC 58.968 50.000 0.00 0.00 0.00 3.06
335 338 2.690778 GCACACATCGGGCCAGTTC 61.691 63.158 4.39 0.00 0.00 3.01
359 362 9.435688 TTCTTTTGACTCGATTATGAAGAATCA 57.564 29.630 8.45 0.00 40.57 2.57
361 364 6.812481 TTGACTCGATTATGAAGAATCACG 57.188 37.500 0.00 0.00 38.69 4.35
380 383 5.739959 TCACGGTATGGAGAATCAAAATCA 58.260 37.500 0.00 0.00 36.25 2.57
391 394 7.069826 TGGAGAATCAAAATCACAAAAGACCTT 59.930 33.333 0.00 0.00 36.25 3.50
392 395 8.576442 GGAGAATCAAAATCACAAAAGACCTTA 58.424 33.333 0.00 0.00 36.25 2.69
476 489 4.541973 AGCCAATCCATCAAAGGAAAAC 57.458 40.909 0.00 0.00 41.92 2.43
477 490 3.903090 AGCCAATCCATCAAAGGAAAACA 59.097 39.130 0.00 0.00 41.92 2.83
481 494 6.207221 GCCAATCCATCAAAGGAAAACATTTT 59.793 34.615 0.00 0.00 41.92 1.82
510 523 3.332485 AGCAAGTACCCCTATTGGACAAA 59.668 43.478 0.00 0.00 35.39 2.83
534 547 9.439500 AAAGTATTTAGAACGTAAATGCCACTA 57.561 29.630 5.27 0.00 35.86 2.74
537 550 5.664294 TTAGAACGTAAATGCCACTAGGA 57.336 39.130 0.00 0.00 36.89 2.94
551 565 3.006537 CCACTAGGACAGACCGAAAAAGA 59.993 47.826 0.00 0.00 44.74 2.52
564 578 2.223386 CGAAAAAGACCCAAAACGCTCA 60.223 45.455 0.00 0.00 0.00 4.26
571 585 0.109132 CCCAAAACGCTCAATCCAGC 60.109 55.000 0.00 0.00 35.90 4.85
578 592 1.886777 GCTCAATCCAGCGAGGCTC 60.887 63.158 3.87 3.87 36.40 4.70
612 626 0.676782 CCCACTCATTCGTCCCCAAC 60.677 60.000 0.00 0.00 0.00 3.77
659 676 4.399303 AGCACTTTGTGATATTTGTAGCCC 59.601 41.667 1.52 0.00 35.23 5.19
684 701 7.852945 CCGCTTTTAAATTGCAATGTTAAACAA 59.147 29.630 23.86 16.25 0.00 2.83
805 823 5.445142 GCTGTTAGAGACATTTCATCACACG 60.445 44.000 0.00 0.00 37.69 4.49
812 830 4.628766 AGACATTTCATCACACGACTCATG 59.371 41.667 0.00 0.00 0.00 3.07
827 845 2.954318 ACTCATGCAACAATCATAGGCC 59.046 45.455 0.00 0.00 0.00 5.19
847 865 4.378874 GGCCGAAATCTCAGAAAAGAACTG 60.379 45.833 0.00 0.00 36.80 3.16
861 879 0.879090 GAACTGGACGGCGGATTTTT 59.121 50.000 13.24 0.00 0.00 1.94
1047 1519 2.267324 GAGCACTCCTCCCAGCAC 59.733 66.667 0.00 0.00 34.35 4.40
1048 1520 2.203907 AGCACTCCTCCCAGCACT 60.204 61.111 0.00 0.00 0.00 4.40
1806 2281 0.889638 TCGTCGTGTTCTCCTGCTCT 60.890 55.000 0.00 0.00 0.00 4.09
2028 2908 5.278169 GCAATGAGATTGGCGAGTATGATTT 60.278 40.000 0.00 0.00 40.57 2.17
2068 2951 3.453353 GGTACTGTATTCCCCAAGCAGTA 59.547 47.826 0.00 0.00 40.39 2.74
2072 2955 4.781087 ACTGTATTCCCCAAGCAGTAACTA 59.219 41.667 0.00 0.00 38.46 2.24
2075 2958 0.899720 TCCCCAAGCAGTAACTACCG 59.100 55.000 0.00 0.00 0.00 4.02
2076 2959 0.899720 CCCCAAGCAGTAACTACCGA 59.100 55.000 0.00 0.00 0.00 4.69
2077 2960 1.276989 CCCCAAGCAGTAACTACCGAA 59.723 52.381 0.00 0.00 0.00 4.30
2078 2961 2.289819 CCCCAAGCAGTAACTACCGAAA 60.290 50.000 0.00 0.00 0.00 3.46
2079 2962 3.404899 CCCAAGCAGTAACTACCGAAAA 58.595 45.455 0.00 0.00 0.00 2.29
2080 2963 3.816523 CCCAAGCAGTAACTACCGAAAAA 59.183 43.478 0.00 0.00 0.00 1.94
2081 2964 4.457949 CCCAAGCAGTAACTACCGAAAAAT 59.542 41.667 0.00 0.00 0.00 1.82
2083 2966 5.313623 CAAGCAGTAACTACCGAAAAATCG 58.686 41.667 0.00 0.00 0.00 3.34
2084 2967 4.563061 AGCAGTAACTACCGAAAAATCGT 58.437 39.130 0.00 0.00 0.00 3.73
2085 2968 4.387862 AGCAGTAACTACCGAAAAATCGTG 59.612 41.667 0.00 0.00 0.00 4.35
2086 2969 4.435121 GCAGTAACTACCGAAAAATCGTGG 60.435 45.833 0.00 0.00 0.00 4.94
2087 2970 4.092383 CAGTAACTACCGAAAAATCGTGGG 59.908 45.833 0.00 0.00 0.00 4.61
2088 2971 1.445871 ACTACCGAAAAATCGTGGGC 58.554 50.000 0.00 0.00 0.00 5.36
2089 2972 0.372334 CTACCGAAAAATCGTGGGCG 59.628 55.000 0.00 0.00 39.92 6.13
2090 2973 1.020333 TACCGAAAAATCGTGGGCGG 61.020 55.000 0.00 0.00 43.95 6.13
2091 2974 2.483288 CGAAAAATCGTGGGCGGG 59.517 61.111 0.00 0.00 38.89 6.13
2092 2975 2.180769 GAAAAATCGTGGGCGGGC 59.819 61.111 0.00 0.00 38.89 6.13
2093 2976 2.282887 AAAAATCGTGGGCGGGCT 60.283 55.556 0.26 0.00 38.89 5.19
2095 2978 2.764637 AAAAATCGTGGGCGGGCTCT 62.765 55.000 0.26 0.00 38.89 4.09
2096 2979 1.906105 AAAATCGTGGGCGGGCTCTA 61.906 55.000 0.26 0.00 38.89 2.43
2097 2980 2.588856 AAATCGTGGGCGGGCTCTAC 62.589 60.000 0.26 0.00 38.89 2.59
2099 2982 3.771160 CGTGGGCGGGCTCTACTT 61.771 66.667 0.26 0.00 0.00 2.24
2100 2983 2.420568 CGTGGGCGGGCTCTACTTA 61.421 63.158 0.26 0.00 0.00 2.24
2101 2984 1.745320 CGTGGGCGGGCTCTACTTAT 61.745 60.000 0.26 0.00 0.00 1.73
2102 2985 1.335145 GTGGGCGGGCTCTACTTATA 58.665 55.000 0.26 0.00 0.00 0.98
2103 2986 1.690352 GTGGGCGGGCTCTACTTATAA 59.310 52.381 0.26 0.00 0.00 0.98
2104 2987 2.103601 GTGGGCGGGCTCTACTTATAAA 59.896 50.000 0.26 0.00 0.00 1.40
2105 2988 2.103601 TGGGCGGGCTCTACTTATAAAC 59.896 50.000 0.26 0.00 0.00 2.01
2107 2990 3.575687 GGGCGGGCTCTACTTATAAACTA 59.424 47.826 0.26 0.00 0.00 2.24
2108 2991 4.554292 GGCGGGCTCTACTTATAAACTAC 58.446 47.826 0.00 0.00 0.00 2.73
2109 2992 4.280425 GGCGGGCTCTACTTATAAACTACT 59.720 45.833 0.00 0.00 0.00 2.57
2110 2993 5.474876 GGCGGGCTCTACTTATAAACTACTA 59.525 44.000 0.00 0.00 0.00 1.82
2111 2994 6.377780 GCGGGCTCTACTTATAAACTACTAC 58.622 44.000 0.00 0.00 0.00 2.73
2113 2996 7.389053 GCGGGCTCTACTTATAAACTACTACTA 59.611 40.741 0.00 0.00 0.00 1.82
2114 2997 9.447157 CGGGCTCTACTTATAAACTACTACTAT 57.553 37.037 0.00 0.00 0.00 2.12
2256 5774 9.649167 ACATGAAGAGAAAATTTGATTTGATCC 57.351 29.630 0.00 0.00 31.77 3.36
2257 5775 9.871238 CATGAAGAGAAAATTTGATTTGATCCT 57.129 29.630 0.00 0.00 31.77 3.24
2263 5781 9.927668 GAGAAAATTTGATTTGATCCTAAACCA 57.072 29.630 0.00 0.00 31.77 3.67
2267 5785 8.496707 AATTTGATTTGATCCTAAACCAATGC 57.503 30.769 0.00 0.00 0.00 3.56
2296 5814 4.148079 TGTTGGTCTTGGATTGCATTACA 58.852 39.130 0.00 0.00 0.00 2.41
2327 5858 8.628280 TGATTTGATTACTTGTTCATTCACACA 58.372 29.630 0.00 0.00 0.00 3.72
2329 5860 6.558771 TGATTACTTGTTCATTCACACAGG 57.441 37.500 0.00 0.00 0.00 4.00
2384 5915 3.902881 TTTTGGGGAAATATTGCGCAT 57.097 38.095 12.75 3.99 42.97 4.73
2415 5946 7.937649 TCTCTTGCTTGAATGGATCATAAATG 58.062 34.615 0.00 0.00 38.03 2.32
2435 5966 7.876936 AAATGTGAGCATTCATCTTGTCTAT 57.123 32.000 0.00 0.00 43.89 1.98
2436 5967 8.969260 AAATGTGAGCATTCATCTTGTCTATA 57.031 30.769 0.00 0.00 43.89 1.31
2437 5968 8.969260 AATGTGAGCATTCATCTTGTCTATAA 57.031 30.769 0.00 0.00 41.08 0.98
2438 5969 8.969260 ATGTGAGCATTCATCTTGTCTATAAA 57.031 30.769 0.00 0.00 35.39 1.40
2439 5970 8.969260 TGTGAGCATTCATCTTGTCTATAAAT 57.031 30.769 0.00 0.00 35.39 1.40
2548 6079 6.373774 CCAAGTAGCTTCAACTTCATCATTCT 59.626 38.462 0.00 0.00 34.99 2.40
2550 6081 8.939929 CAAGTAGCTTCAACTTCATCATTCTTA 58.060 33.333 0.00 0.00 34.99 2.10
2625 7131 6.656270 TGTAAGAGTTGTCATCATGAAGCATT 59.344 34.615 0.00 0.00 0.00 3.56
2715 7221 4.593206 TGACCCTACTGTTTCAGATCTTGT 59.407 41.667 0.00 0.00 35.18 3.16
2876 8003 9.403583 ACTCAACTTACAAAATTACTTTCTCCA 57.596 29.630 0.00 0.00 0.00 3.86
2914 8041 4.947388 CCCCCTCGAATTTTGAGTTATTCA 59.053 41.667 11.81 0.00 31.70 2.57
2919 8046 7.362920 CCCTCGAATTTTGAGTTATTCACCATT 60.363 37.037 11.81 0.00 34.94 3.16
2933 8060 9.267084 GTTATTCACCATTAAAAGGCTCAAAAA 57.733 29.630 0.00 0.00 0.00 1.94
2975 9023 3.052414 TCATGAGGGGGCAAGTAGTACTA 60.052 47.826 2.50 0.00 0.00 1.82
2979 9027 4.017222 TGAGGGGGCAAGTAGTACTAGTAA 60.017 45.833 10.68 0.00 0.00 2.24
2980 9028 5.146298 GAGGGGGCAAGTAGTACTAGTAAT 58.854 45.833 10.68 8.10 0.00 1.89
2981 9029 5.535990 AGGGGGCAAGTAGTACTAGTAATT 58.464 41.667 8.34 0.96 0.00 1.40
2982 9030 6.686544 AGGGGGCAAGTAGTACTAGTAATTA 58.313 40.000 8.34 0.00 0.00 1.40
2983 9031 7.134842 AGGGGGCAAGTAGTACTAGTAATTAA 58.865 38.462 8.34 0.00 0.00 1.40
2984 9032 7.289549 AGGGGGCAAGTAGTACTAGTAATTAAG 59.710 40.741 8.34 0.00 0.00 1.85
2985 9033 6.927936 GGGGCAAGTAGTACTAGTAATTAAGC 59.072 42.308 8.34 7.93 0.00 3.09
2986 9034 7.201983 GGGGCAAGTAGTACTAGTAATTAAGCT 60.202 40.741 8.34 1.14 0.00 3.74
2987 9035 7.866898 GGGCAAGTAGTACTAGTAATTAAGCTC 59.133 40.741 8.34 4.78 0.00 4.09
2988 9036 8.411683 GGCAAGTAGTACTAGTAATTAAGCTCA 58.588 37.037 8.34 0.00 0.00 4.26
2989 9037 9.968870 GCAAGTAGTACTAGTAATTAAGCTCAT 57.031 33.333 8.34 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.875544 TGCGATTAATCTAAAGTGGTGC 57.124 40.909 13.45 6.57 0.00 5.01
1 2 6.842163 AGTTTGCGATTAATCTAAAGTGGTG 58.158 36.000 13.45 0.00 0.00 4.17
2 3 8.556213 TTAGTTTGCGATTAATCTAAAGTGGT 57.444 30.769 20.98 9.61 0.00 4.16
35 36 3.865745 GTCCAAGTGGAGTGATATGTTCG 59.134 47.826 0.00 0.00 46.49 3.95
53 54 5.843673 ACATTTGTTTGTGTATGTGTCCA 57.156 34.783 0.00 0.00 30.51 4.02
77 78 7.283354 TCGTGGTATTTATATTTTGGATGCACA 59.717 33.333 0.00 0.00 0.00 4.57
78 79 7.589954 GTCGTGGTATTTATATTTTGGATGCAC 59.410 37.037 0.00 0.00 0.00 4.57
82 83 9.793259 AGATGTCGTGGTATTTATATTTTGGAT 57.207 29.630 0.00 0.00 0.00 3.41
96 97 6.546772 TGTTGGTGTATATAGATGTCGTGGTA 59.453 38.462 0.00 0.00 0.00 3.25
100 101 8.803235 ACATATGTTGGTGTATATAGATGTCGT 58.197 33.333 1.41 0.00 0.00 4.34
102 103 9.929180 ACACATATGTTGGTGTATATAGATGTC 57.071 33.333 5.37 0.00 45.77 3.06
131 132 3.087031 AGATGAGTTGCAGTTGGATTGG 58.913 45.455 0.00 0.00 0.00 3.16
147 148 5.761234 GTGTGTGTTTACAGGGTAAAGATGA 59.239 40.000 2.04 0.00 37.52 2.92
151 152 4.035909 GGTGTGTGTGTTTACAGGGTAAAG 59.964 45.833 2.04 0.00 37.52 1.85
173 174 6.718454 TGTTTTGTTTGTCAAATCTTGTGG 57.282 33.333 0.40 0.00 44.15 4.17
176 177 8.867935 TGTGTATGTTTTGTTTGTCAAATCTTG 58.132 29.630 0.40 0.00 44.15 3.02
185 186 6.701841 TGTGTTTGTGTGTATGTTTTGTTTGT 59.298 30.769 0.00 0.00 0.00 2.83
227 228 2.237392 GGACACAGGGGATATAGGATGC 59.763 54.545 0.00 0.00 0.00 3.91
258 259 3.325425 TGTGGGCTGTTGTACTAGCTAAA 59.675 43.478 14.07 0.00 39.80 1.85
325 328 0.875059 GAGTCAAAAGAACTGGCCCG 59.125 55.000 0.00 0.00 0.00 6.13
335 338 7.843204 CGTGATTCTTCATAATCGAGTCAAAAG 59.157 37.037 0.00 0.00 38.47 2.27
359 362 5.496556 TGTGATTTTGATTCTCCATACCGT 58.503 37.500 0.00 0.00 0.00 4.83
361 364 8.522830 TCTTTTGTGATTTTGATTCTCCATACC 58.477 33.333 0.00 0.00 0.00 2.73
380 383 2.553247 GGGCAGAGCTAAGGTCTTTTGT 60.553 50.000 0.00 0.00 38.40 2.83
409 412 5.068460 AGAGATTCTGGGTTGATTCTAGACG 59.932 44.000 0.00 0.00 29.95 4.18
457 470 7.229106 ACAAAATGTTTTCCTTTGATGGATTGG 59.771 33.333 1.08 0.00 35.83 3.16
476 489 4.749598 GGGGTACTTGCTGAAAACAAAATG 59.250 41.667 0.00 0.00 0.00 2.32
477 490 4.653801 AGGGGTACTTGCTGAAAACAAAAT 59.346 37.500 0.00 0.00 0.00 1.82
481 494 4.650972 ATAGGGGTACTTGCTGAAAACA 57.349 40.909 0.00 0.00 0.00 2.83
510 523 7.709613 CCTAGTGGCATTTACGTTCTAAATACT 59.290 37.037 0.00 0.00 0.00 2.12
534 547 1.071857 GGGTCTTTTTCGGTCTGTCCT 59.928 52.381 0.00 0.00 0.00 3.85
537 550 2.721425 TTGGGTCTTTTTCGGTCTGT 57.279 45.000 0.00 0.00 0.00 3.41
551 565 1.247567 CTGGATTGAGCGTTTTGGGT 58.752 50.000 0.00 0.00 0.00 4.51
571 585 2.202388 TTACGAACGCGAGCCTCG 60.202 61.111 15.93 17.28 43.89 4.63
656 673 2.741517 ACATTGCAATTTAAAAGCGGGC 59.258 40.909 9.83 3.28 0.00 6.13
659 676 8.759260 TTGTTTAACATTGCAATTTAAAAGCG 57.241 26.923 24.74 11.85 0.00 4.68
699 716 9.325150 CGTCTAATATGAACACGAAAACAAATT 57.675 29.630 0.00 0.00 32.08 1.82
700 717 8.500773 ACGTCTAATATGAACACGAAAACAAAT 58.499 29.630 0.00 0.00 34.55 2.32
701 718 7.794810 CACGTCTAATATGAACACGAAAACAAA 59.205 33.333 0.00 0.00 34.55 2.83
702 719 7.169476 TCACGTCTAATATGAACACGAAAACAA 59.831 33.333 0.00 0.00 34.55 2.83
703 720 6.641723 TCACGTCTAATATGAACACGAAAACA 59.358 34.615 0.00 0.00 34.55 2.83
704 721 7.041187 TCACGTCTAATATGAACACGAAAAC 57.959 36.000 0.00 0.00 34.55 2.43
762 780 4.018960 ACAGCCATAGATTGAAACTGAGGT 60.019 41.667 0.00 0.00 0.00 3.85
763 781 4.521146 ACAGCCATAGATTGAAACTGAGG 58.479 43.478 0.00 0.00 0.00 3.86
805 823 3.004106 GGCCTATGATTGTTGCATGAGTC 59.996 47.826 0.00 0.00 0.00 3.36
812 830 3.316308 AGATTTCGGCCTATGATTGTTGC 59.684 43.478 0.00 0.00 0.00 4.17
827 845 5.388890 CGTCCAGTTCTTTTCTGAGATTTCG 60.389 44.000 0.00 0.00 35.20 3.46
847 865 1.002792 GCTCATAAAAATCCGCCGTCC 60.003 52.381 0.00 0.00 0.00 4.79
861 879 2.103094 CCCGGAGAATCAACTGCTCATA 59.897 50.000 0.73 0.00 36.25 2.15
914 1325 1.977009 GGCCAGTTCTTTTCCCCCG 60.977 63.158 0.00 0.00 0.00 5.73
1037 1509 2.581354 CGGAAGAGTGCTGGGAGG 59.419 66.667 0.00 0.00 0.00 4.30
1038 1510 2.581354 CCGGAAGAGTGCTGGGAG 59.419 66.667 0.00 0.00 0.00 4.30
1039 1511 3.706373 GCCGGAAGAGTGCTGGGA 61.706 66.667 5.05 0.00 32.24 4.37
1806 2281 1.174783 GCTTCTCCTGTCCGTACTCA 58.825 55.000 0.00 0.00 0.00 3.41
1901 2394 1.332195 GGCTTGTTCTCCTTTGCCTT 58.668 50.000 0.00 0.00 37.58 4.35
2050 2930 4.222124 AGTTACTGCTTGGGGAATACAG 57.778 45.455 0.00 0.00 0.00 2.74
2068 2951 1.808343 GCCCACGATTTTTCGGTAGTT 59.192 47.619 0.00 0.00 37.45 2.24
2072 2955 2.329614 CCGCCCACGATTTTTCGGT 61.330 57.895 0.00 0.00 43.93 4.69
2075 2958 2.180769 GCCCGCCCACGATTTTTC 59.819 61.111 0.00 0.00 43.93 2.29
2076 2959 2.282887 AGCCCGCCCACGATTTTT 60.283 55.556 0.00 0.00 43.93 1.94
2077 2960 1.906105 TAGAGCCCGCCCACGATTTT 61.906 55.000 0.00 0.00 43.93 1.82
2078 2961 2.363975 TAGAGCCCGCCCACGATTT 61.364 57.895 0.00 0.00 43.93 2.17
2079 2962 2.762459 TAGAGCCCGCCCACGATT 60.762 61.111 0.00 0.00 43.93 3.34
2080 2963 3.537874 GTAGAGCCCGCCCACGAT 61.538 66.667 0.00 0.00 43.93 3.73
2081 2964 2.842188 TAAGTAGAGCCCGCCCACGA 62.842 60.000 0.00 0.00 43.93 4.35
2083 2966 1.335145 TATAAGTAGAGCCCGCCCAC 58.665 55.000 0.00 0.00 0.00 4.61
2084 2967 2.091098 TTATAAGTAGAGCCCGCCCA 57.909 50.000 0.00 0.00 0.00 5.36
2085 2968 2.367894 AGTTTATAAGTAGAGCCCGCCC 59.632 50.000 0.00 0.00 0.00 6.13
2086 2969 3.747854 AGTTTATAAGTAGAGCCCGCC 57.252 47.619 0.00 0.00 0.00 6.13
2087 2970 5.450592 AGTAGTTTATAAGTAGAGCCCGC 57.549 43.478 0.00 0.00 0.00 6.13
2088 2971 7.742556 AGTAGTAGTTTATAAGTAGAGCCCG 57.257 40.000 0.00 0.00 0.00 6.13
2145 5502 5.300792 TGGTTTAGCAAAGATTTCTCGGTTT 59.699 36.000 0.00 0.00 0.00 3.27
2146 5503 4.825085 TGGTTTAGCAAAGATTTCTCGGTT 59.175 37.500 0.00 0.00 0.00 4.44
2148 5505 4.455877 ACTGGTTTAGCAAAGATTTCTCGG 59.544 41.667 0.00 0.00 0.00 4.63
2149 5506 5.613358 ACTGGTTTAGCAAAGATTTCTCG 57.387 39.130 0.00 0.00 0.00 4.04
2249 5767 3.192422 CCGTGCATTGGTTTAGGATCAAA 59.808 43.478 0.00 0.00 0.00 2.69
2250 5768 2.752354 CCGTGCATTGGTTTAGGATCAA 59.248 45.455 0.00 0.00 0.00 2.57
2251 5769 2.364632 CCGTGCATTGGTTTAGGATCA 58.635 47.619 0.00 0.00 0.00 2.92
2252 5770 1.065551 GCCGTGCATTGGTTTAGGATC 59.934 52.381 9.41 0.00 0.00 3.36
2253 5771 1.102978 GCCGTGCATTGGTTTAGGAT 58.897 50.000 9.41 0.00 0.00 3.24
2254 5772 0.037590 AGCCGTGCATTGGTTTAGGA 59.962 50.000 9.41 0.00 0.00 2.94
2255 5773 0.887933 AAGCCGTGCATTGGTTTAGG 59.112 50.000 8.03 0.00 0.00 2.69
2256 5774 1.269448 ACAAGCCGTGCATTGGTTTAG 59.731 47.619 9.20 7.28 0.00 1.85
2257 5775 1.323412 ACAAGCCGTGCATTGGTTTA 58.677 45.000 9.20 0.00 0.00 2.01
2258 5776 0.463620 AACAAGCCGTGCATTGGTTT 59.536 45.000 9.41 6.96 0.00 3.27
2259 5777 0.249405 CAACAAGCCGTGCATTGGTT 60.249 50.000 9.41 3.76 0.00 3.67
2260 5778 1.363443 CAACAAGCCGTGCATTGGT 59.637 52.632 9.41 0.00 0.00 3.67
2261 5779 1.373246 CCAACAAGCCGTGCATTGG 60.373 57.895 3.67 3.67 34.07 3.16
2262 5780 0.664166 GACCAACAAGCCGTGCATTG 60.664 55.000 0.00 0.00 0.00 2.82
2263 5781 0.823356 AGACCAACAAGCCGTGCATT 60.823 50.000 0.00 0.00 0.00 3.56
2264 5782 0.823356 AAGACCAACAAGCCGTGCAT 60.823 50.000 0.00 0.00 0.00 3.96
2265 5783 1.453015 AAGACCAACAAGCCGTGCA 60.453 52.632 0.00 0.00 0.00 4.57
2266 5784 1.008538 CAAGACCAACAAGCCGTGC 60.009 57.895 0.00 0.00 0.00 5.34
2267 5785 0.817634 TCCAAGACCAACAAGCCGTG 60.818 55.000 0.00 0.00 0.00 4.94
2314 5839 5.507149 GCACATTTACCTGTGTGAATGAACA 60.507 40.000 14.62 0.00 46.14 3.18
2384 5915 5.178096 TCCATTCAAGCAAGAGATAACCA 57.822 39.130 0.00 0.00 0.00 3.67
2435 5966 8.778059 ACCCACAGGAGATTTAGTCATTATTTA 58.222 33.333 0.00 0.00 36.73 1.40
2436 5967 7.643123 ACCCACAGGAGATTTAGTCATTATTT 58.357 34.615 0.00 0.00 36.73 1.40
2437 5968 7.213178 ACCCACAGGAGATTTAGTCATTATT 57.787 36.000 0.00 0.00 36.73 1.40
2438 5969 6.831664 ACCCACAGGAGATTTAGTCATTAT 57.168 37.500 0.00 0.00 36.73 1.28
2439 5970 7.743116 TTACCCACAGGAGATTTAGTCATTA 57.257 36.000 0.00 0.00 36.73 1.90
2499 6030 7.999545 TGGAGCAAGATATGACTAGTAGTAGTT 59.000 37.037 11.56 0.00 39.78 2.24
2500 6031 7.519057 TGGAGCAAGATATGACTAGTAGTAGT 58.481 38.462 10.09 10.09 42.59 2.73
2501 6032 7.987750 TGGAGCAAGATATGACTAGTAGTAG 57.012 40.000 1.88 2.87 0.00 2.57
2502 6033 7.999545 ACTTGGAGCAAGATATGACTAGTAGTA 59.000 37.037 1.88 0.00 43.42 1.82
2550 6081 7.944554 CCATCCCTTTTGGTATAACTGATGTAT 59.055 37.037 0.00 0.00 38.10 2.29
2565 6102 5.603170 ATTAATGCACTCCATCCCTTTTG 57.397 39.130 0.00 0.00 31.43 2.44
2745 7251 7.803724 ACTAACTTTTGTTATAGTTTCTGCCG 58.196 34.615 0.00 0.00 43.16 5.69
2912 8039 7.989741 TCAAATTTTTGAGCCTTTTAATGGTGA 59.010 29.630 1.66 0.00 41.88 4.02
2933 8060 3.266772 TGACTCATAAGCACCCCTCAAAT 59.733 43.478 0.00 0.00 0.00 2.32
2949 8076 0.842030 ACTTGCCCCCTCATGACTCA 60.842 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.