Multiple sequence alignment - TraesCS6A01G032100

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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 TraesCS6A01G032100 chr6A 100.000 3161 0 0 1 3161 15926234 15923074 0.000000e+00 5838.0
1 TraesCS6A01G032100 chr6A 82.717 1244 203 10 979 2215 15873210 15871972 0.000000e+00 1096.0
2 TraesCS6A01G032100 chr6A 87.020 963 91 20 2222 3158 15686064 15687018 0.000000e+00 1055.0
3 TraesCS6A01G032100 chr6A 84.286 490 36 15 2392 2850 15688331 15688810 1.040000e-119 440.0
4 TraesCS6A01G032100 chr6A 85.096 208 20 10 2953 3158 16652588 16652786 5.350000e-48 202.0
5 TraesCS6A01G032100 chr6D 94.660 1985 56 12 242 2209 14941898 14939947 0.000000e+00 3033.0
6 TraesCS6A01G032100 chr6D 83.780 1270 183 20 971 2226 14727356 14726096 0.000000e+00 1182.0
7 TraesCS6A01G032100 chr6D 83.280 1250 190 16 987 2226 14503347 14504587 0.000000e+00 1133.0
8 TraesCS6A01G032100 chr6D 82.931 1242 204 7 979 2215 14689272 14688034 0.000000e+00 1112.0
9 TraesCS6A01G032100 chr6D 82.129 1259 204 20 979 2226 14732952 14731704 0.000000e+00 1059.0
10 TraesCS6A01G032100 chr6D 86.861 959 93 20 2222 3158 14484899 14485846 0.000000e+00 1042.0
11 TraesCS6A01G032100 chr6D 86.798 962 92 20 2222 3158 14438874 14439825 0.000000e+00 1040.0
12 TraesCS6A01G032100 chr6D 87.866 717 76 6 1 714 387868836 387868128 0.000000e+00 832.0
13 TraesCS6A01G032100 chr6D 83.333 942 76 37 2236 3158 16376583 16377462 0.000000e+00 795.0
14 TraesCS6A01G032100 chr1A 94.720 1534 57 7 1 1519 61151641 61153165 0.000000e+00 2362.0
15 TraesCS6A01G032100 chr6B 82.618 1398 203 18 851 2226 27066120 27064741 0.000000e+00 1199.0
16 TraesCS6A01G032100 chr6B 85.141 1097 144 10 1102 2183 28730901 28729809 0.000000e+00 1105.0
17 TraesCS6A01G032100 chr6B 84.680 953 79 35 2227 3161 28729791 28728888 0.000000e+00 889.0
18 TraesCS6A01G032100 chr6B 84.122 951 106 24 2223 3158 26501716 26502636 0.000000e+00 878.0
19 TraesCS6A01G032100 chr6B 87.840 699 62 14 2222 2899 26489810 26490506 0.000000e+00 798.0
20 TraesCS6A01G032100 chr6B 83.920 398 32 8 2428 2819 28502197 28502568 5.020000e-93 351.0
21 TraesCS6A01G032100 chr6B 90.500 200 17 2 2222 2420 28496422 28496620 2.420000e-66 263.0
22 TraesCS6A01G032100 chr6B 87.248 149 11 4 853 994 26494882 26495029 2.520000e-36 163.0
23 TraesCS6A01G032100 chr6B 80.193 207 33 5 2222 2421 26292504 26292709 7.060000e-32 148.0
24 TraesCS6A01G032100 chr6B 88.889 45 5 0 2222 2266 16542807 16542763 4.400000e-04 56.5
25 TraesCS6A01G032100 chr5D 85.952 1082 145 7 1066 2145 27979237 27978161 0.000000e+00 1149.0
26 TraesCS6A01G032100 chr5D 87.544 859 90 12 2222 3066 27984291 27983436 0.000000e+00 977.0
27 TraesCS6A01G032100 chr5D 90.782 716 55 6 1 714 30492541 30493247 0.000000e+00 946.0
28 TraesCS6A01G032100 chr4B 83.547 1246 181 17 987 2216 575726091 575727328 0.000000e+00 1144.0
29 TraesCS6A01G032100 chr1B 90.542 719 54 9 1 714 585966327 585967036 0.000000e+00 939.0
30 TraesCS6A01G032100 chr7D 89.819 717 60 8 1 714 423617984 423617278 0.000000e+00 907.0
31 TraesCS6A01G032100 chr7D 88.531 715 70 9 2 714 534718719 534718015 0.000000e+00 856.0
32 TraesCS6A01G032100 chr7D 90.909 55 4 1 753 806 11663396 11663450 4.370000e-09 73.1
33 TraesCS6A01G032100 chr7A 89.636 714 63 7 1 712 36636090 36636794 0.000000e+00 898.0
34 TraesCS6A01G032100 chr5A 89.216 714 53 8 1 712 691088227 691087536 0.000000e+00 870.0
35 TraesCS6A01G032100 chr7B 88.936 714 59 7 1 712 667154330 667153635 0.000000e+00 863.0
36 TraesCS6A01G032100 chr7B 94.545 55 2 1 736 789 518401551 518401497 2.020000e-12 84.2
37 TraesCS6A01G032100 chr7B 94.545 55 2 1 736 789 518409659 518409605 2.020000e-12 84.2
38 TraesCS6A01G032100 chrUn 88.531 715 69 8 2 714 141488646 141487943 0.000000e+00 854.0
39 TraesCS6A01G032100 chr4D 88.424 717 70 10 1 714 64146662 64147368 0.000000e+00 852.0
40 TraesCS6A01G032100 chr1D 87.727 717 75 8 1 714 18704240 18703534 0.000000e+00 824.0
41 TraesCS6A01G032100 chr2D 87.133 715 80 7 2 714 602443173 602442469 0.000000e+00 800.0
42 TraesCS6A01G032100 chr2D 90.411 73 5 2 716 787 135380269 135380198 9.330000e-16 95.3
43 TraesCS6A01G032100 chr2D 94.828 58 2 1 732 788 107366129 107366072 4.340000e-14 89.8
44 TraesCS6A01G032100 chr2D 96.364 55 1 1 736 789 648237179 648237125 4.340000e-14 89.8
45 TraesCS6A01G032100 chr3B 84.800 500 65 6 216 714 145473730 145473241 2.830000e-135 492.0
46 TraesCS6A01G032100 chr2B 84.722 72 9 2 715 784 21751808 21751737 1.570000e-08 71.3


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 TraesCS6A01G032100 chr6A 15923074 15926234 3160 True 5838.0 5838 100.0000 1 3161 1 chr6A.!!$R2 3160
1 TraesCS6A01G032100 chr6A 15871972 15873210 1238 True 1096.0 1096 82.7170 979 2215 1 chr6A.!!$R1 1236
2 TraesCS6A01G032100 chr6A 15686064 15688810 2746 False 747.5 1055 85.6530 2222 3158 2 chr6A.!!$F2 936
3 TraesCS6A01G032100 chr6D 14939947 14941898 1951 True 3033.0 3033 94.6600 242 2209 1 chr6D.!!$R4 1967
4 TraesCS6A01G032100 chr6D 14726096 14727356 1260 True 1182.0 1182 83.7800 971 2226 1 chr6D.!!$R2 1255
5 TraesCS6A01G032100 chr6D 14503347 14504587 1240 False 1133.0 1133 83.2800 987 2226 1 chr6D.!!$F3 1239
6 TraesCS6A01G032100 chr6D 14688034 14689272 1238 True 1112.0 1112 82.9310 979 2215 1 chr6D.!!$R1 1236
7 TraesCS6A01G032100 chr6D 14731704 14732952 1248 True 1059.0 1059 82.1290 979 2226 1 chr6D.!!$R3 1247
8 TraesCS6A01G032100 chr6D 14484899 14485846 947 False 1042.0 1042 86.8610 2222 3158 1 chr6D.!!$F2 936
9 TraesCS6A01G032100 chr6D 14438874 14439825 951 False 1040.0 1040 86.7980 2222 3158 1 chr6D.!!$F1 936
10 TraesCS6A01G032100 chr6D 387868128 387868836 708 True 832.0 832 87.8660 1 714 1 chr6D.!!$R5 713
11 TraesCS6A01G032100 chr6D 16376583 16377462 879 False 795.0 795 83.3330 2236 3158 1 chr6D.!!$F4 922
12 TraesCS6A01G032100 chr1A 61151641 61153165 1524 False 2362.0 2362 94.7200 1 1519 1 chr1A.!!$F1 1518
13 TraesCS6A01G032100 chr6B 27064741 27066120 1379 True 1199.0 1199 82.6180 851 2226 1 chr6B.!!$R2 1375
14 TraesCS6A01G032100 chr6B 28728888 28730901 2013 True 997.0 1105 84.9105 1102 3161 2 chr6B.!!$R3 2059
15 TraesCS6A01G032100 chr6B 26501716 26502636 920 False 878.0 878 84.1220 2223 3158 1 chr6B.!!$F4 935
16 TraesCS6A01G032100 chr6B 26489810 26490506 696 False 798.0 798 87.8400 2222 2899 1 chr6B.!!$F2 677
17 TraesCS6A01G032100 chr5D 27978161 27979237 1076 True 1149.0 1149 85.9520 1066 2145 1 chr5D.!!$R1 1079
18 TraesCS6A01G032100 chr5D 27983436 27984291 855 True 977.0 977 87.5440 2222 3066 1 chr5D.!!$R2 844
19 TraesCS6A01G032100 chr5D 30492541 30493247 706 False 946.0 946 90.7820 1 714 1 chr5D.!!$F1 713
20 TraesCS6A01G032100 chr4B 575726091 575727328 1237 False 1144.0 1144 83.5470 987 2216 1 chr4B.!!$F1 1229
21 TraesCS6A01G032100 chr1B 585966327 585967036 709 False 939.0 939 90.5420 1 714 1 chr1B.!!$F1 713
22 TraesCS6A01G032100 chr7D 423617278 423617984 706 True 907.0 907 89.8190 1 714 1 chr7D.!!$R1 713
23 TraesCS6A01G032100 chr7D 534718015 534718719 704 True 856.0 856 88.5310 2 714 1 chr7D.!!$R2 712
24 TraesCS6A01G032100 chr7A 36636090 36636794 704 False 898.0 898 89.6360 1 712 1 chr7A.!!$F1 711
25 TraesCS6A01G032100 chr5A 691087536 691088227 691 True 870.0 870 89.2160 1 712 1 chr5A.!!$R1 711
26 TraesCS6A01G032100 chr7B 667153635 667154330 695 True 863.0 863 88.9360 1 712 1 chr7B.!!$R3 711
27 TraesCS6A01G032100 chrUn 141487943 141488646 703 True 854.0 854 88.5310 2 714 1 chrUn.!!$R1 712
28 TraesCS6A01G032100 chr4D 64146662 64147368 706 False 852.0 852 88.4240 1 714 1 chr4D.!!$F1 713
29 TraesCS6A01G032100 chr1D 18703534 18704240 706 True 824.0 824 87.7270 1 714 1 chr1D.!!$R1 713
30 TraesCS6A01G032100 chr2D 602442469 602443173 704 True 800.0 800 87.1330 2 714 1 chr2D.!!$R3 712

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
358 363 0.110238 CATGCGGCCGTATAATGTGC 60.11 55.0 28.67 7.52 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2283 2364 1.67968 CCAGCATCCAGTTAAGGCATG 59.32 52.381 0.0 0.0 0.0 4.06 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
48 51 3.822735 CAGCACATTTTCAGGGAGAAGAA 59.177 43.478 0.00 0.00 37.57 2.52
352 357 0.682292 TCCATTCATGCGGCCGTATA 59.318 50.000 28.67 14.95 0.00 1.47
358 363 0.110238 CATGCGGCCGTATAATGTGC 60.110 55.000 28.67 7.52 0.00 4.57
390 395 3.067833 ACGCTTCTTAGCCTCAACTTTC 58.932 45.455 0.00 0.00 44.86 2.62
391 396 3.244249 ACGCTTCTTAGCCTCAACTTTCT 60.244 43.478 0.00 0.00 44.86 2.52
393 398 4.068599 GCTTCTTAGCCTCAACTTTCTGT 58.931 43.478 0.00 0.00 41.74 3.41
395 400 4.273148 TCTTAGCCTCAACTTTCTGTCC 57.727 45.455 0.00 0.00 0.00 4.02
396 401 3.646162 TCTTAGCCTCAACTTTCTGTCCA 59.354 43.478 0.00 0.00 0.00 4.02
397 402 2.557920 AGCCTCAACTTTCTGTCCAG 57.442 50.000 0.00 0.00 0.00 3.86
398 403 1.771255 AGCCTCAACTTTCTGTCCAGT 59.229 47.619 0.00 0.00 0.00 4.00
399 404 2.173569 AGCCTCAACTTTCTGTCCAGTT 59.826 45.455 0.00 0.00 33.29 3.16
400 405 3.391296 AGCCTCAACTTTCTGTCCAGTTA 59.609 43.478 0.00 0.00 31.78 2.24
401 406 4.134563 GCCTCAACTTTCTGTCCAGTTAA 58.865 43.478 0.00 0.00 31.78 2.01
402 407 4.214332 GCCTCAACTTTCTGTCCAGTTAAG 59.786 45.833 9.03 9.03 31.78 1.85
403 408 4.214332 CCTCAACTTTCTGTCCAGTTAAGC 59.786 45.833 9.97 0.00 31.78 3.09
427 432 8.272545 GCATTAAGCATCAGTGGATATTCATA 57.727 34.615 0.00 0.00 44.79 2.15
647 658 1.922135 ATGCCATCGACGCAAACACC 61.922 55.000 12.56 0.00 40.22 4.16
677 688 4.336532 ACGCGTTCCAGTTAAATGATTC 57.663 40.909 5.58 0.00 0.00 2.52
684 695 6.555315 GTTCCAGTTAAATGATTCGATGCTT 58.445 36.000 4.10 0.00 0.00 3.91
697 708 1.303309 GATGCTTTCCACATCCTCCG 58.697 55.000 0.00 0.00 38.38 4.63
751 762 0.668535 GTGCTTCGGGCTCAAAACTT 59.331 50.000 3.33 0.00 42.39 2.66
875 891 2.849943 TGAACACATAGGTAGGCCCATT 59.150 45.455 0.00 0.00 34.66 3.16
876 892 3.268334 TGAACACATAGGTAGGCCCATTT 59.732 43.478 0.00 0.00 34.66 2.32
885 901 1.289830 GTAGGCCCATTTAAACCCCCT 59.710 52.381 0.00 0.00 0.00 4.79
1942 2017 6.544197 TCGATCAGTAATTCTCTGTCTTAGCT 59.456 38.462 0.00 0.00 34.86 3.32
2155 2230 6.259608 AGAGATGCCAACTAATTTCAGATTCG 59.740 38.462 0.00 0.00 0.00 3.34
2188 2264 2.110578 AGGGCTATGGAAATTGGTTGC 58.889 47.619 0.00 0.00 0.00 4.17
2189 2265 1.830477 GGGCTATGGAAATTGGTTGCA 59.170 47.619 0.00 0.00 42.34 4.08
2190 2266 2.159057 GGGCTATGGAAATTGGTTGCAG 60.159 50.000 0.00 0.00 41.33 4.41
2191 2267 2.497273 GGCTATGGAAATTGGTTGCAGT 59.503 45.455 0.00 0.00 41.33 4.40
2192 2268 3.055891 GGCTATGGAAATTGGTTGCAGTT 60.056 43.478 0.00 0.00 41.33 3.16
2193 2269 4.563374 GGCTATGGAAATTGGTTGCAGTTT 60.563 41.667 0.00 0.00 41.33 2.66
2194 2270 5.337169 GGCTATGGAAATTGGTTGCAGTTTA 60.337 40.000 0.00 0.00 41.33 2.01
2195 2271 6.340522 GCTATGGAAATTGGTTGCAGTTTAT 58.659 36.000 0.00 0.00 41.33 1.40
2196 2272 6.256321 GCTATGGAAATTGGTTGCAGTTTATG 59.744 38.462 0.00 0.00 41.33 1.90
2197 2273 4.892433 TGGAAATTGGTTGCAGTTTATGG 58.108 39.130 0.00 0.00 31.74 2.74
2198 2274 3.684305 GGAAATTGGTTGCAGTTTATGGC 59.316 43.478 0.00 0.00 0.00 4.40
2199 2275 4.314121 GAAATTGGTTGCAGTTTATGGCA 58.686 39.130 0.00 0.00 38.46 4.92
2200 2276 2.810439 TTGGTTGCAGTTTATGGCAC 57.190 45.000 0.00 0.00 40.23 5.01
2216 2292 3.561143 TGGCACAACAAAGTTATCACCT 58.439 40.909 0.00 0.00 31.92 4.00
2217 2293 3.957497 TGGCACAACAAAGTTATCACCTT 59.043 39.130 0.00 0.00 31.92 3.50
2218 2294 4.404073 TGGCACAACAAAGTTATCACCTTT 59.596 37.500 0.00 0.00 31.92 3.11
2283 2364 0.398318 AACTCCTGCCTCAGTGTTCC 59.602 55.000 0.00 0.00 0.00 3.62
2290 2371 0.610232 GCCTCAGTGTTCCATGCCTT 60.610 55.000 0.00 0.00 0.00 4.35
2317 2398 4.164030 TGGATGCTGGCTATCTTTTGTAGA 59.836 41.667 0.00 0.00 37.28 2.59
2393 2478 3.045634 TGATTCCTGAACCCCGATATGT 58.954 45.455 0.00 0.00 0.00 2.29
2458 2544 0.874390 GTCTGCTTTCATGGCAACGA 59.126 50.000 0.00 0.00 39.30 3.85
2479 2565 5.992217 ACGATTATCTAGCATGTTCCCTTTC 59.008 40.000 0.00 0.00 0.00 2.62
2714 2811 6.200854 CCATAGTTGACCTTTCTTTTGTTTGC 59.799 38.462 0.00 0.00 0.00 3.68
2722 2819 9.003658 TGACCTTTCTTTTGTTTGCAAATTTTA 57.996 25.926 16.21 0.00 43.26 1.52
2760 2857 7.868906 TGAATCAGTCTTATCATTTGCATCA 57.131 32.000 0.00 0.00 0.00 3.07
2794 2891 5.010282 GTCAGAATAAACCAATGGAGGTGT 58.990 41.667 6.16 0.00 42.25 4.16
2799 2896 3.524095 AAACCAATGGAGGTGTCATGA 57.476 42.857 6.16 0.00 42.25 3.07
2802 2899 3.359033 ACCAATGGAGGTGTCATGAATG 58.641 45.455 6.16 0.00 41.30 2.67
2837 2934 7.595130 GTCCAATGAAGGTTGAACTAACATTTC 59.405 37.037 0.00 0.00 42.75 2.17
2850 2947 8.735315 TGAACTAACATTTCTTCTTGTGAACAA 58.265 29.630 0.00 0.00 0.00 2.83
2852 2949 9.520204 AACTAACATTTCTTCTTGTGAACAATG 57.480 29.630 0.00 0.00 35.69 2.82
2855 2952 6.742109 ACATTTCTTCTTGTGAACAATGGAG 58.258 36.000 0.00 0.00 34.82 3.86
2857 2954 4.437682 TCTTCTTGTGAACAATGGAGGT 57.562 40.909 0.00 0.00 35.02 3.85
2858 2955 4.136796 TCTTCTTGTGAACAATGGAGGTG 58.863 43.478 0.00 0.00 35.02 4.00
2859 2956 2.229792 TCTTGTGAACAATGGAGGTGC 58.770 47.619 0.00 0.00 35.02 5.01
2860 2957 1.270550 CTTGTGAACAATGGAGGTGCC 59.729 52.381 0.00 0.00 35.02 5.01
2890 3001 3.517612 TCCCTCTACAACCTACAGCTTT 58.482 45.455 0.00 0.00 0.00 3.51
2899 3010 2.609747 ACCTACAGCTTTCACTGAGGA 58.390 47.619 13.41 0.00 40.25 3.71
2900 3011 3.177228 ACCTACAGCTTTCACTGAGGAT 58.823 45.455 13.41 1.22 40.25 3.24
2904 3015 5.814705 CCTACAGCTTTCACTGAGGATAAAG 59.185 44.000 0.00 0.00 40.25 1.85
2945 3059 6.767902 TGTCTACAATTCAGGGAAATCATAGC 59.232 38.462 0.00 0.00 0.00 2.97
2984 3098 4.098044 TGCAACAAAATTCGTCCCAGTTTA 59.902 37.500 0.00 0.00 0.00 2.01
2997 3111 2.955660 CCCAGTTTACTGCCTTGAAACA 59.044 45.455 4.34 0.00 42.47 2.83
3001 3115 5.406649 CAGTTTACTGCCTTGAAACAACAA 58.593 37.500 0.00 0.00 37.15 2.83
3017 3131 5.304686 ACAACAATGAGACCTTCAACCTA 57.695 39.130 0.00 0.00 39.77 3.08
3030 3146 5.131142 ACCTTCAACCTATTGTCCATCCTAG 59.869 44.000 0.00 0.00 37.11 3.02
3087 3209 7.331791 AGGATTAAGATTTAAGTTGCTCGACT 58.668 34.615 0.00 0.00 0.00 4.18
3088 3210 8.475639 AGGATTAAGATTTAAGTTGCTCGACTA 58.524 33.333 0.00 0.00 0.00 2.59
3089 3211 8.756864 GGATTAAGATTTAAGTTGCTCGACTAG 58.243 37.037 0.00 0.00 0.00 2.57
3090 3212 9.303537 GATTAAGATTTAAGTTGCTCGACTAGT 57.696 33.333 0.00 0.00 0.00 2.57
3092 3214 9.565213 TTAAGATTTAAGTTGCTCGACTAGTAC 57.435 33.333 0.00 0.00 0.00 2.73
3093 3215 7.154435 AGATTTAAGTTGCTCGACTAGTACA 57.846 36.000 0.00 0.00 0.00 2.90
3094 3216 7.251994 AGATTTAAGTTGCTCGACTAGTACAG 58.748 38.462 0.00 0.00 0.00 2.74
3122 3244 5.123936 ACTTGTCTTCCAACCAAACTAGTC 58.876 41.667 0.00 0.00 0.00 2.59
3123 3245 3.724374 TGTCTTCCAACCAAACTAGTCG 58.276 45.455 0.00 0.00 0.00 4.18
3125 3247 2.367567 TCTTCCAACCAAACTAGTCGCT 59.632 45.455 0.00 0.00 0.00 4.93
3137 3259 2.497675 ACTAGTCGCTCAACATGTCCAT 59.502 45.455 0.00 0.00 0.00 3.41
3142 3264 2.079158 CGCTCAACATGTCCATGAGTT 58.921 47.619 21.40 0.00 42.00 3.01
3147 3269 2.205022 ACATGTCCATGAGTTGGTGG 57.795 50.000 13.93 0.00 46.52 4.61
3154 3276 2.922704 ATGAGTTGGTGGCCTGGGG 61.923 63.158 3.32 0.00 0.00 4.96
3158 3280 3.256960 TTGGTGGCCTGGGGACTC 61.257 66.667 3.32 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
333 338 0.682292 TATACGGCCGCATGAATGGA 59.318 50.000 28.58 0.00 0.00 3.41
340 345 1.234615 GGCACATTATACGGCCGCAT 61.235 55.000 28.58 22.19 36.58 4.73
352 357 1.692148 CGTGACGCGTATGGCACATT 61.692 55.000 23.23 0.00 43.84 2.71
390 395 5.355071 TGATGCTTAATGCTTAACTGGACAG 59.645 40.000 0.00 0.00 43.37 3.51
391 396 5.252547 TGATGCTTAATGCTTAACTGGACA 58.747 37.500 0.00 0.00 43.37 4.02
393 398 5.355071 CACTGATGCTTAATGCTTAACTGGA 59.645 40.000 0.00 0.00 43.37 3.86
395 400 5.355071 TCCACTGATGCTTAATGCTTAACTG 59.645 40.000 0.00 0.00 43.37 3.16
396 401 5.500234 TCCACTGATGCTTAATGCTTAACT 58.500 37.500 0.00 0.00 43.37 2.24
397 402 5.818136 TCCACTGATGCTTAATGCTTAAC 57.182 39.130 0.00 0.00 43.37 2.01
398 403 8.696043 AATATCCACTGATGCTTAATGCTTAA 57.304 30.769 0.00 0.00 43.37 1.85
399 404 7.938490 TGAATATCCACTGATGCTTAATGCTTA 59.062 33.333 0.00 0.00 43.37 3.09
400 405 6.774170 TGAATATCCACTGATGCTTAATGCTT 59.226 34.615 0.00 0.00 43.37 3.91
401 406 6.301486 TGAATATCCACTGATGCTTAATGCT 58.699 36.000 0.00 0.00 43.37 3.79
402 407 6.564709 TGAATATCCACTGATGCTTAATGC 57.435 37.500 0.00 0.00 43.25 3.56
427 432 1.556911 AGACATTCGATCCACTGGCTT 59.443 47.619 0.00 0.00 0.00 4.35
559 570 2.505819 ACCTTGCCCTCATACAGGTAAG 59.494 50.000 0.00 0.00 41.51 2.34
647 658 4.720530 AACTGGAACGCGTTTACTTTAG 57.279 40.909 27.32 18.26 0.00 1.85
677 688 1.303309 GGAGGATGTGGAAAGCATCG 58.697 55.000 0.00 0.00 42.53 3.84
684 695 1.568504 AGTTAGCGGAGGATGTGGAA 58.431 50.000 0.00 0.00 0.00 3.53
697 708 3.614150 GCCTGGGCTTTTTACAAGTTAGC 60.614 47.826 4.12 0.00 38.26 3.09
836 847 5.807520 GTGTTCACTGTATGTCCACTCATAG 59.192 44.000 0.00 0.00 32.01 2.23
837 848 5.245075 TGTGTTCACTGTATGTCCACTCATA 59.755 40.000 4.59 0.00 33.73 2.15
838 849 4.040339 TGTGTTCACTGTATGTCCACTCAT 59.960 41.667 4.59 0.00 33.73 2.90
845 859 6.273825 CCTACCTATGTGTTCACTGTATGTC 58.726 44.000 4.59 0.00 0.00 3.06
875 891 3.053917 GCTCTATTGGACAGGGGGTTTAA 60.054 47.826 0.00 0.00 0.00 1.52
876 892 2.508300 GCTCTATTGGACAGGGGGTTTA 59.492 50.000 0.00 0.00 0.00 2.01
885 901 1.220749 GCGTGGGCTCTATTGGACA 59.779 57.895 0.00 0.00 35.83 4.02
1003 1039 2.754658 GGACTCTCGGAGCCGGAA 60.755 66.667 5.05 0.00 40.25 4.30
2188 2264 7.114811 GTGATAACTTTGTTGTGCCATAAACTG 59.885 37.037 0.00 0.00 0.00 3.16
2189 2265 7.145323 GTGATAACTTTGTTGTGCCATAAACT 58.855 34.615 0.00 0.00 0.00 2.66
2190 2266 6.364976 GGTGATAACTTTGTTGTGCCATAAAC 59.635 38.462 0.00 0.00 0.00 2.01
2191 2267 6.266558 AGGTGATAACTTTGTTGTGCCATAAA 59.733 34.615 0.00 0.00 0.00 1.40
2192 2268 5.772672 AGGTGATAACTTTGTTGTGCCATAA 59.227 36.000 0.00 0.00 0.00 1.90
2193 2269 5.321102 AGGTGATAACTTTGTTGTGCCATA 58.679 37.500 0.00 0.00 0.00 2.74
2194 2270 4.151883 AGGTGATAACTTTGTTGTGCCAT 58.848 39.130 0.00 0.00 0.00 4.40
2195 2271 3.561143 AGGTGATAACTTTGTTGTGCCA 58.439 40.909 0.00 0.00 0.00 4.92
2196 2272 4.584327 AAGGTGATAACTTTGTTGTGCC 57.416 40.909 0.00 0.00 0.00 5.01
2197 2273 5.587289 TGAAAGGTGATAACTTTGTTGTGC 58.413 37.500 0.00 0.00 38.21 4.57
2198 2274 6.692681 CACTGAAAGGTGATAACTTTGTTGTG 59.307 38.462 0.00 0.50 38.21 3.33
2199 2275 6.377146 ACACTGAAAGGTGATAACTTTGTTGT 59.623 34.615 0.00 0.00 38.21 3.32
2200 2276 6.795399 ACACTGAAAGGTGATAACTTTGTTG 58.205 36.000 0.00 0.00 38.21 3.33
2201 2277 8.567948 CATACACTGAAAGGTGATAACTTTGTT 58.432 33.333 0.00 0.00 38.21 2.83
2202 2278 7.174946 CCATACACTGAAAGGTGATAACTTTGT 59.825 37.037 0.00 0.00 38.21 2.83
2203 2279 7.174946 ACCATACACTGAAAGGTGATAACTTTG 59.825 37.037 0.00 0.00 38.21 2.77
2204 2280 7.231467 ACCATACACTGAAAGGTGATAACTTT 58.769 34.615 1.52 0.00 40.61 2.66
2205 2281 6.779860 ACCATACACTGAAAGGTGATAACTT 58.220 36.000 1.52 0.00 39.30 2.66
2206 2282 6.374417 ACCATACACTGAAAGGTGATAACT 57.626 37.500 1.52 0.00 39.30 2.24
2213 2289 2.884639 GTTGCACCATACACTGAAAGGT 59.115 45.455 0.00 0.00 39.30 3.50
2214 2290 2.884012 TGTTGCACCATACACTGAAAGG 59.116 45.455 0.00 0.00 39.30 3.11
2215 2291 4.566545 TTGTTGCACCATACACTGAAAG 57.433 40.909 0.00 0.00 42.29 2.62
2216 2292 4.400884 ACTTTGTTGCACCATACACTGAAA 59.599 37.500 0.00 0.00 0.00 2.69
2217 2293 3.951037 ACTTTGTTGCACCATACACTGAA 59.049 39.130 0.00 0.00 0.00 3.02
2218 2294 3.550820 ACTTTGTTGCACCATACACTGA 58.449 40.909 0.00 0.00 0.00 3.41
2283 2364 1.679680 CCAGCATCCAGTTAAGGCATG 59.320 52.381 0.00 0.00 0.00 4.06
2290 2371 4.778213 AAAGATAGCCAGCATCCAGTTA 57.222 40.909 0.00 0.00 0.00 2.24
2317 2398 4.681744 CAAACTGGCATGTAACAAACACT 58.318 39.130 0.00 0.00 42.09 3.55
2393 2478 7.279615 TCTTCTCTAAGGAATGACAACAACAA 58.720 34.615 0.00 0.00 33.22 2.83
2432 2518 2.233271 CCATGAAAGCAGACCACACTT 58.767 47.619 0.00 0.00 0.00 3.16
2458 2544 6.174720 TCGAAAGGGAACATGCTAGATAAT 57.825 37.500 0.00 0.00 0.00 1.28
2479 2565 7.565450 TGCAACTGAAAATACAATGAAATCG 57.435 32.000 0.00 0.00 0.00 3.34
2619 2712 8.168725 AGAACAGGCATCCATGAGAAATATATT 58.831 33.333 0.00 0.00 0.00 1.28
2794 2891 3.753815 TGGACTTGCTTGTCATTCATGA 58.246 40.909 10.77 0.00 38.61 3.07
2799 2896 4.021719 CCTTCATTGGACTTGCTTGTCATT 60.022 41.667 10.77 0.00 38.61 2.57
2802 2899 2.887152 ACCTTCATTGGACTTGCTTGTC 59.113 45.455 1.86 1.86 36.31 3.18
2837 2934 3.304928 GCACCTCCATTGTTCACAAGAAG 60.305 47.826 0.00 0.00 39.47 2.85
2852 2949 1.482182 GGGAAAAATCATGGCACCTCC 59.518 52.381 0.00 0.00 0.00 4.30
2855 2952 2.460669 AGAGGGAAAAATCATGGCACC 58.539 47.619 0.00 0.00 0.00 5.01
2857 2954 4.314522 TGTAGAGGGAAAAATCATGGCA 57.685 40.909 0.00 0.00 0.00 4.92
2858 2955 4.142160 GGTTGTAGAGGGAAAAATCATGGC 60.142 45.833 0.00 0.00 0.00 4.40
2859 2956 5.264395 AGGTTGTAGAGGGAAAAATCATGG 58.736 41.667 0.00 0.00 0.00 3.66
2860 2957 6.884295 TGTAGGTTGTAGAGGGAAAAATCATG 59.116 38.462 0.00 0.00 0.00 3.07
2862 2959 6.442541 TGTAGGTTGTAGAGGGAAAAATCA 57.557 37.500 0.00 0.00 0.00 2.57
2915 3027 5.416271 TTCCCTGAATTGTAGACAGGTAC 57.584 43.478 0.00 0.00 46.61 3.34
2974 3088 2.561478 TCAAGGCAGTAAACTGGGAC 57.439 50.000 11.86 0.00 43.94 4.46
2984 3098 3.953612 TCTCATTGTTGTTTCAAGGCAGT 59.046 39.130 0.00 0.00 0.00 4.40
2997 3111 6.306987 ACAATAGGTTGAAGGTCTCATTGTT 58.693 36.000 0.00 0.00 38.71 2.83
3001 3115 4.536090 TGGACAATAGGTTGAAGGTCTCAT 59.464 41.667 0.00 0.00 38.71 2.90
3017 3131 7.631377 GCAACTTTTTATGCTAGGATGGACAAT 60.631 37.037 7.05 0.00 39.46 2.71
3089 3211 6.155136 GGTTGGAAGACAAGTACTACTGTAC 58.845 44.000 0.00 0.00 46.89 2.90
3090 3212 5.834742 TGGTTGGAAGACAAGTACTACTGTA 59.165 40.000 0.00 0.00 40.38 2.74
3091 3213 4.652421 TGGTTGGAAGACAAGTACTACTGT 59.348 41.667 0.00 0.00 40.38 3.55
3092 3214 5.209818 TGGTTGGAAGACAAGTACTACTG 57.790 43.478 0.00 0.00 40.38 2.74
3093 3215 5.881923 TTGGTTGGAAGACAAGTACTACT 57.118 39.130 0.00 0.00 40.38 2.57
3094 3216 6.053650 AGTTTGGTTGGAAGACAAGTACTAC 58.946 40.000 0.00 0.00 40.38 2.73
3108 3230 2.163818 TGAGCGACTAGTTTGGTTGG 57.836 50.000 0.00 0.00 0.00 3.77
3122 3244 1.730501 ACTCATGGACATGTTGAGCG 58.269 50.000 20.88 5.21 40.40 5.03
3123 3245 3.482722 CAACTCATGGACATGTTGAGC 57.517 47.619 20.88 0.28 41.35 4.26
3137 3259 3.579302 CCCCAGGCCACCAACTCA 61.579 66.667 5.01 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.