Multiple sequence alignment - TraesCS5B01G090000

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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 TraesCS5B01G090000 chr5B 100.000 1998 0 0 459 2456 115655655 115653658 0.000000e+00 3690
1 TraesCS5B01G090000 chr5B 98.462 325 4 1 470 793 107835400 107835076 2.740000e-159 571
2 TraesCS5B01G090000 chr5B 98.754 321 2 2 474 793 21688578 21688259 9.850000e-159 569
3 TraesCS5B01G090000 chr5B 100.000 286 0 0 1 286 115656113 115655828 1.670000e-146 529
4 TraesCS5B01G090000 chr5B 99.550 222 1 0 1 222 21689092 21688871 2.940000e-109 405
5 TraesCS5B01G090000 chr5B 81.720 186 34 0 1205 1390 115871187 115871372 3.270000e-34 156
6 TraesCS5B01G090000 chr5B 87.368 95 12 0 1292 1386 114452346 114452440 2.580000e-20 110
7 TraesCS5B01G090000 chr5D 96.787 1245 25 6 813 2056 105620669 105619439 0.000000e+00 2063
8 TraesCS5B01G090000 chr5D 92.568 296 13 3 2170 2456 105619440 105619145 1.360000e-112 416
9 TraesCS5B01G090000 chr5D 81.720 186 34 0 1205 1390 107012763 107012948 3.270000e-34 156
10 TraesCS5B01G090000 chr5A 99.405 336 0 2 459 793 21571119 21571453 2.090000e-170 608
11 TraesCS5B01G090000 chr5A 99.650 286 1 0 1 286 21570782 21571067 7.780000e-145 523
12 TraesCS5B01G090000 chr5A 95.736 258 11 0 1 258 8230874 8230617 1.360000e-112 416
13 TraesCS5B01G090000 chr5A 83.019 159 27 0 1232 1390 136644386 136644544 7.080000e-31 145
14 TraesCS5B01G090000 chr3A 99.096 332 2 1 463 793 315975746 315976077 1.630000e-166 595
15 TraesCS5B01G090000 chr3A 98.951 286 3 0 1 286 315974643 315974928 1.680000e-141 512
16 TraesCS5B01G090000 chr4B 98.788 330 3 1 465 793 78230149 78230478 9.790000e-164 586
17 TraesCS5B01G090000 chr4B 99.288 281 1 1 514 793 408966167 408965887 7.840000e-140 507
18 TraesCS5B01G090000 chr4B 99.573 234 1 0 1 234 408966790 408966557 6.280000e-116 427
19 TraesCS5B01G090000 chr4B 99.145 117 1 0 2055 2171 604533764 604533648 6.880000e-51 211
20 TraesCS5B01G090000 chr4B 93.701 127 8 0 2045 2171 457415441 457415567 8.960000e-45 191
21 TraesCS5B01G090000 chr1A 98.780 328 3 1 467 793 256980476 256980803 1.270000e-162 582
22 TraesCS5B01G090000 chr1A 96.512 258 9 0 1 258 508582242 508581985 6.280000e-116 427
23 TraesCS5B01G090000 chr1A 96.512 258 8 1 1 258 480553274 480553530 2.260000e-115 425
24 TraesCS5B01G090000 chr3B 98.447 322 4 1 473 793 627903915 627904236 1.270000e-157 566
25 TraesCS5B01G090000 chr3B 99.301 286 2 0 1 286 627903379 627903664 3.620000e-143 518
26 TraesCS5B01G090000 chr3B 95.082 122 6 0 2051 2172 475817009 475816888 2.490000e-45 193
27 TraesCS5B01G090000 chr3B 94.262 122 6 1 2055 2175 556520782 556520661 4.170000e-43 185
28 TraesCS5B01G090000 chr4A 97.552 286 7 0 1 286 28590483 28590768 7.890000e-135 490
29 TraesCS5B01G090000 chr2A 95.333 300 13 1 495 793 1234265 1234564 2.210000e-130 475
30 TraesCS5B01G090000 chr2A 95.736 258 11 0 1 258 537156238 537156495 1.360000e-112 416
31 TraesCS5B01G090000 chr2A 92.308 286 4 2 1 286 1233427 1233694 8.230000e-105 390
32 TraesCS5B01G090000 chr2A 98.198 222 4 0 1 222 769246627 769246848 2.960000e-104 388
33 TraesCS5B01G090000 chr7A 96.124 258 10 0 1 258 585306205 585305948 2.920000e-114 422
34 TraesCS5B01G090000 chr3D 94.186 172 10 0 2283 2454 282949852 282949681 1.870000e-66 263
35 TraesCS5B01G090000 chr3D 91.848 184 11 3 2277 2456 25112631 25112448 1.130000e-63 254
36 TraesCS5B01G090000 chr1B 91.667 168 12 2 2290 2456 120636327 120636161 5.280000e-57 231
37 TraesCS5B01G090000 chr1B 94.400 125 6 1 2051 2175 630918561 630918438 8.960000e-45 191
38 TraesCS5B01G090000 chr2D 95.763 118 5 0 2055 2172 95519658 95519541 8.960000e-45 191
39 TraesCS5B01G090000 chr6D 94.309 123 7 0 2052 2174 319246252 319246374 3.220000e-44 189
40 TraesCS5B01G090000 chr6B 92.537 134 7 3 2045 2178 563489355 563489225 3.220000e-44 189
41 TraesCS5B01G090000 chr2B 93.023 129 7 1 2045 2171 608215787 608215915 1.160000e-43 187


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 TraesCS5B01G090000 chr5B 115653658 115656113 2455 True 2109.5 3690 100.0000 1 2456 2 chr5B.!!$R3 2455
1 TraesCS5B01G090000 chr5B 21688259 21689092 833 True 487.0 569 99.1520 1 793 2 chr5B.!!$R2 792
2 TraesCS5B01G090000 chr5D 105619145 105620669 1524 True 1239.5 2063 94.6775 813 2456 2 chr5D.!!$R1 1643
3 TraesCS5B01G090000 chr5A 21570782 21571453 671 False 565.5 608 99.5275 1 793 2 chr5A.!!$F2 792
4 TraesCS5B01G090000 chr3A 315974643 315976077 1434 False 553.5 595 99.0235 1 793 2 chr3A.!!$F1 792
5 TraesCS5B01G090000 chr4B 408965887 408966790 903 True 467.0 507 99.4305 1 793 2 chr4B.!!$R2 792
6 TraesCS5B01G090000 chr3B 627903379 627904236 857 False 542.0 566 98.8740 1 793 2 chr3B.!!$F1 792
7 TraesCS5B01G090000 chr2A 1233427 1234564 1137 False 432.5 475 93.8205 1 793 2 chr2A.!!$F3 792

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
809 1896 0.102663 GGGCACTACTCTTAGGCGTC 59.897 60.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 3145 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.2 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
793 1880 5.484715 GGTTATTTTTAAGGGTTTGAGGGC 58.515 41.667 0.00 0.00 0.00 5.19
794 1881 5.012251 GGTTATTTTTAAGGGTTTGAGGGCA 59.988 40.000 0.00 0.00 0.00 5.36
795 1882 4.617253 ATTTTTAAGGGTTTGAGGGCAC 57.383 40.909 0.00 0.00 0.00 5.01
796 1883 3.322191 TTTTAAGGGTTTGAGGGCACT 57.678 42.857 0.00 0.00 0.00 4.40
797 1884 4.456662 TTTTAAGGGTTTGAGGGCACTA 57.543 40.909 0.00 0.00 0.00 2.74
798 1885 3.428413 TTAAGGGTTTGAGGGCACTAC 57.572 47.619 0.00 0.00 0.00 2.73
799 1886 1.446016 AAGGGTTTGAGGGCACTACT 58.554 50.000 0.00 0.00 0.00 2.57
800 1887 0.984995 AGGGTTTGAGGGCACTACTC 59.015 55.000 0.00 0.00 35.55 2.59
801 1888 0.984995 GGGTTTGAGGGCACTACTCT 59.015 55.000 0.00 0.00 35.98 3.24
802 1889 1.351350 GGGTTTGAGGGCACTACTCTT 59.649 52.381 0.00 0.00 35.98 2.85
803 1890 2.570302 GGGTTTGAGGGCACTACTCTTA 59.430 50.000 0.00 0.00 35.98 2.10
804 1891 3.369576 GGGTTTGAGGGCACTACTCTTAG 60.370 52.174 0.00 0.00 35.98 2.18
805 1892 3.369576 GGTTTGAGGGCACTACTCTTAGG 60.370 52.174 0.00 0.00 35.98 2.69
806 1893 1.486211 TGAGGGCACTACTCTTAGGC 58.514 55.000 0.00 0.00 35.98 3.93
807 1894 0.386113 GAGGGCACTACTCTTAGGCG 59.614 60.000 0.00 0.00 32.28 5.52
808 1895 0.324460 AGGGCACTACTCTTAGGCGT 60.324 55.000 0.00 0.00 0.00 5.68
809 1896 0.102663 GGGCACTACTCTTAGGCGTC 59.897 60.000 0.00 0.00 0.00 5.19
810 1897 1.104630 GGCACTACTCTTAGGCGTCT 58.895 55.000 0.00 0.00 0.00 4.18
811 1898 1.202313 GGCACTACTCTTAGGCGTCTG 60.202 57.143 0.00 0.00 0.00 3.51
860 1947 2.418910 CGACCGATCTGCCTCCACT 61.419 63.158 0.00 0.00 0.00 4.00
894 1981 1.638529 CAGAGTTCTCAGAGGTGGGT 58.361 55.000 0.00 0.00 0.00 4.51
1240 2327 1.070786 GTGCTGACCGTGGGAGAAA 59.929 57.895 0.00 0.00 0.00 2.52
1279 2366 1.068588 CCGTATGCCTCGAGGAATTCA 59.931 52.381 35.69 22.66 34.53 2.57
1302 2389 2.046892 GGCGGCAAGAAGCTCAGA 60.047 61.111 3.07 0.00 44.79 3.27
1428 2515 3.739300 ACGACGACAACAATAACAAGGAG 59.261 43.478 0.00 0.00 0.00 3.69
1483 2570 2.035832 AGTTTGCCGGAAGTTGAATTGG 59.964 45.455 5.05 0.00 0.00 3.16
1498 2585 0.178953 ATTGGAGTGTGCAGCCCTTT 60.179 50.000 0.00 0.00 0.00 3.11
1628 2715 6.787085 TTCTCAGCTTGAAAACTTAGTAGC 57.213 37.500 0.00 0.00 0.00 3.58
1653 2740 8.191446 GCTCTTCTCTCTGTTATGTACAATACA 58.809 37.037 0.00 6.45 43.80 2.29
1896 2984 4.760204 TGCTTGAGCTACCCTAAGTTTTTC 59.240 41.667 4.44 0.00 42.66 2.29
1919 3007 1.140312 TTCTGTTCTGCTTGGACCCT 58.860 50.000 0.00 0.00 0.00 4.34
1955 3043 7.576666 GCCTTCCTTTGTTTTGTTTTGGAATTT 60.577 33.333 0.00 0.00 32.61 1.82
2056 3144 8.102047 TCTTAGGCTGGTCTGTATCTATACTAC 58.898 40.741 0.00 1.08 34.41 2.73
2057 3145 6.457159 AGGCTGGTCTGTATCTATACTACT 57.543 41.667 2.07 0.00 34.41 2.57
2058 3146 6.478129 AGGCTGGTCTGTATCTATACTACTC 58.522 44.000 2.07 0.00 34.41 2.59
2059 3147 5.648960 GGCTGGTCTGTATCTATACTACTCC 59.351 48.000 2.07 1.29 34.41 3.85
2060 3148 5.648960 GCTGGTCTGTATCTATACTACTCCC 59.351 48.000 2.07 0.00 34.41 4.30
2061 3149 6.522804 GCTGGTCTGTATCTATACTACTCCCT 60.523 46.154 2.07 0.00 34.41 4.20
2062 3150 7.018487 TGGTCTGTATCTATACTACTCCCTC 57.982 44.000 2.07 0.00 34.41 4.30
2063 3151 6.012683 TGGTCTGTATCTATACTACTCCCTCC 60.013 46.154 2.07 0.00 34.41 4.30
2064 3152 6.108015 GTCTGTATCTATACTACTCCCTCCG 58.892 48.000 2.07 0.00 34.41 4.63
2065 3153 5.784390 TCTGTATCTATACTACTCCCTCCGT 59.216 44.000 2.07 0.00 34.41 4.69
2066 3154 6.047511 TGTATCTATACTACTCCCTCCGTC 57.952 45.833 2.07 0.00 34.41 4.79
2067 3155 4.573021 ATCTATACTACTCCCTCCGTCC 57.427 50.000 0.00 0.00 0.00 4.79
2068 3156 2.301296 TCTATACTACTCCCTCCGTCCG 59.699 54.545 0.00 0.00 0.00 4.79
2069 3157 0.110104 ATACTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
2070 3158 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
2071 3159 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
2072 3160 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
2073 3161 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2074 3162 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2075 3163 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2076 3164 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2077 3165 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2078 3166 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2079 3167 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2080 3168 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2081 3169 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2082 3170 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
2083 3171 1.004595 GTCCGGAAATACTTGTCGGC 58.995 55.000 5.23 0.00 40.42 5.54
2084 3172 0.108041 TCCGGAAATACTTGTCGGCC 60.108 55.000 0.00 0.00 40.42 6.13
2085 3173 1.426041 CCGGAAATACTTGTCGGCCG 61.426 60.000 22.12 22.12 37.20 6.13
2086 3174 0.458889 CGGAAATACTTGTCGGCCGA 60.459 55.000 27.28 27.28 39.62 5.54
2087 3175 1.729284 GGAAATACTTGTCGGCCGAA 58.271 50.000 32.93 15.31 0.00 4.30
2088 3176 2.285977 GGAAATACTTGTCGGCCGAAT 58.714 47.619 32.93 17.21 0.00 3.34
2089 3177 2.031683 GGAAATACTTGTCGGCCGAATG 59.968 50.000 32.93 23.84 0.00 2.67
2090 3178 1.663695 AATACTTGTCGGCCGAATGG 58.336 50.000 32.93 23.34 38.77 3.16
2091 3179 0.828022 ATACTTGTCGGCCGAATGGA 59.172 50.000 32.93 19.80 37.49 3.41
2092 3180 0.828022 TACTTGTCGGCCGAATGGAT 59.172 50.000 32.93 16.99 37.49 3.41
2093 3181 0.744414 ACTTGTCGGCCGAATGGATG 60.744 55.000 32.93 18.41 37.49 3.51
2094 3182 0.744414 CTTGTCGGCCGAATGGATGT 60.744 55.000 32.93 0.00 37.49 3.06
2095 3183 0.537653 TTGTCGGCCGAATGGATGTA 59.462 50.000 32.93 0.00 37.49 2.29
2096 3184 0.756294 TGTCGGCCGAATGGATGTAT 59.244 50.000 32.93 0.00 37.49 2.29
2097 3185 1.270094 TGTCGGCCGAATGGATGTATC 60.270 52.381 32.93 14.01 37.49 2.24
2098 3186 1.000955 GTCGGCCGAATGGATGTATCT 59.999 52.381 32.93 0.00 37.49 1.98
2099 3187 2.230508 GTCGGCCGAATGGATGTATCTA 59.769 50.000 32.93 0.00 37.49 1.98
2100 3188 2.492088 TCGGCCGAATGGATGTATCTAG 59.508 50.000 28.99 0.00 37.49 2.43
2101 3189 2.492088 CGGCCGAATGGATGTATCTAGA 59.508 50.000 24.07 0.00 37.49 2.43
2102 3190 3.673594 CGGCCGAATGGATGTATCTAGAC 60.674 52.174 24.07 0.00 37.49 2.59
2103 3191 3.258372 GGCCGAATGGATGTATCTAGACA 59.742 47.826 0.00 0.00 37.49 3.41
2104 3192 4.081420 GGCCGAATGGATGTATCTAGACAT 60.081 45.833 0.00 0.00 42.82 3.06
2105 3193 5.127194 GGCCGAATGGATGTATCTAGACATA 59.873 44.000 0.00 0.00 40.18 2.29
2106 3194 6.183360 GGCCGAATGGATGTATCTAGACATAT 60.183 42.308 0.00 0.00 40.18 1.78
2107 3195 7.268586 GCCGAATGGATGTATCTAGACATATT 58.731 38.462 0.00 0.00 40.18 1.28
2108 3196 7.766278 GCCGAATGGATGTATCTAGACATATTT 59.234 37.037 0.00 0.00 40.18 1.40
2109 3197 9.658799 CCGAATGGATGTATCTAGACATATTTT 57.341 33.333 0.00 0.00 40.18 1.82
2136 3224 9.851686 AGTTCTAGATACATCCATTTTTATGCA 57.148 29.630 0.00 0.00 0.00 3.96
2142 3230 9.976511 AGATACATCCATTTTTATGCATTTCTG 57.023 29.630 3.54 0.00 0.00 3.02
2157 3245 5.997732 CATTTCTGCAACAACTATTTCCG 57.002 39.130 0.00 0.00 0.00 4.30
2158 3246 4.497473 TTTCTGCAACAACTATTTCCGG 57.503 40.909 0.00 0.00 0.00 5.14
2159 3247 3.410631 TCTGCAACAACTATTTCCGGA 57.589 42.857 0.00 0.00 0.00 5.14
2160 3248 3.071479 TCTGCAACAACTATTTCCGGAC 58.929 45.455 1.83 0.00 0.00 4.79
2161 3249 1.801771 TGCAACAACTATTTCCGGACG 59.198 47.619 1.83 0.00 0.00 4.79
2162 3250 1.129811 GCAACAACTATTTCCGGACGG 59.870 52.381 1.83 3.96 0.00 4.79
2163 3251 2.690786 CAACAACTATTTCCGGACGGA 58.309 47.619 1.83 9.76 43.52 4.69
2164 3252 2.667473 ACAACTATTTCCGGACGGAG 57.333 50.000 13.64 3.57 46.06 4.63
2165 3253 1.206371 ACAACTATTTCCGGACGGAGG 59.794 52.381 13.64 8.21 46.06 4.30
2166 3254 0.828677 AACTATTTCCGGACGGAGGG 59.171 55.000 13.64 7.89 46.06 4.30
2167 3255 0.032813 ACTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2168 3256 0.674534 CTATTTCCGGACGGAGGGAG 59.325 60.000 13.64 8.24 46.06 4.30
2169 3257 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2170 3258 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2187 3275 7.311109 GGAGGGAGTATCTAAAAAGAACCAAGA 60.311 40.741 0.00 0.00 33.73 3.02
2202 3290 4.607293 ACCAAGATTCCTTTTTCTTGCC 57.393 40.909 7.06 0.00 44.79 4.52
2256 3344 1.003118 TCCCGGACAATCAGTTTCCTG 59.997 52.381 0.73 0.00 40.25 3.86
2275 3363 4.489771 CCCCCTCACCCACGCATC 62.490 72.222 0.00 0.00 0.00 3.91
2276 3364 3.402681 CCCCTCACCCACGCATCT 61.403 66.667 0.00 0.00 0.00 2.90
2279 3367 0.469917 CCCTCACCCACGCATCTATT 59.530 55.000 0.00 0.00 0.00 1.73
2281 3369 2.643551 CCTCACCCACGCATCTATTTT 58.356 47.619 0.00 0.00 0.00 1.82
2285 3381 5.029807 TCACCCACGCATCTATTTTATCA 57.970 39.130 0.00 0.00 0.00 2.15
2295 3391 8.395633 ACGCATCTATTTTATCACCTTAAACAC 58.604 33.333 0.00 0.00 0.00 3.32
2299 3395 8.570068 TCTATTTTATCACCTTAAACACCCAC 57.430 34.615 0.00 0.00 0.00 4.61
2369 3465 5.239525 AGAACTGCCTGAACAAGTATCAAAC 59.760 40.000 0.00 0.00 0.00 2.93
2397 3493 1.138247 GCTGGAGAAAGCCAATGCG 59.862 57.895 0.00 0.00 44.33 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
793 1880 2.732597 GCACAGACGCCTAAGAGTAGTG 60.733 54.545 0.00 0.00 36.01 2.74
794 1881 1.473278 GCACAGACGCCTAAGAGTAGT 59.527 52.381 0.00 0.00 0.00 2.73
795 1882 2.196295 GCACAGACGCCTAAGAGTAG 57.804 55.000 0.00 0.00 0.00 2.57
874 1961 0.248843 CCCACCTCTGAGAACTCTGC 59.751 60.000 6.17 0.00 0.00 4.26
945 2032 2.698797 CCGAGGGAGAAGTAATTGCCTA 59.301 50.000 0.00 0.00 35.04 3.93
1240 2327 1.071471 CGCAGTCCTGTTCCCTTGT 59.929 57.895 0.00 0.00 0.00 3.16
1279 2366 2.509336 CTTCTTGCCGCCGTCGAT 60.509 61.111 0.00 0.00 38.10 3.59
1302 2389 0.921896 AGTGGTAGCAGGGCATCATT 59.078 50.000 0.00 0.00 0.00 2.57
1362 2449 2.580815 CAGACAGGGCAGATGCGA 59.419 61.111 0.00 0.00 43.26 5.10
1415 2502 2.644798 AGTCCCAGCTCCTTGTTATTGT 59.355 45.455 0.00 0.00 0.00 2.71
1417 2504 2.619074 GCAGTCCCAGCTCCTTGTTATT 60.619 50.000 0.00 0.00 0.00 1.40
1418 2505 1.065126 GCAGTCCCAGCTCCTTGTTAT 60.065 52.381 0.00 0.00 0.00 1.89
1419 2506 0.324943 GCAGTCCCAGCTCCTTGTTA 59.675 55.000 0.00 0.00 0.00 2.41
1428 2515 0.676151 CTTTCTCAGGCAGTCCCAGC 60.676 60.000 0.00 0.00 35.39 4.85
1483 2570 0.595095 CTTGAAAGGGCTGCACACTC 59.405 55.000 4.01 0.00 0.00 3.51
1498 2585 0.038251 CTAGCACAGTCGTGGCTTGA 60.038 55.000 0.00 0.00 43.81 3.02
1559 2646 6.601613 ACAAGCTTTTGATCGGTAATCCAATA 59.398 34.615 0.00 0.00 33.01 1.90
1569 2656 5.356882 TCAAACTACAAGCTTTTGATCGG 57.643 39.130 6.45 0.00 34.96 4.18
1607 2694 6.162777 AGAGCTACTAAGTTTTCAAGCTGAG 58.837 40.000 0.00 0.00 40.24 3.35
1653 2740 6.935771 TGATGCATAAAGGTGAAATTTTGCTT 59.064 30.769 0.00 3.03 31.20 3.91
1666 2753 7.820872 AGAAAATGAAGGTTTGATGCATAAAGG 59.179 33.333 0.00 0.00 0.00 3.11
1785 2873 8.905702 CATGCTCTGCGGATAATTAATAAAAAC 58.094 33.333 0.00 0.00 0.00 2.43
1786 2874 8.845227 TCATGCTCTGCGGATAATTAATAAAAA 58.155 29.630 0.00 0.00 0.00 1.94
1787 2875 8.389779 TCATGCTCTGCGGATAATTAATAAAA 57.610 30.769 0.00 0.00 0.00 1.52
1788 2876 7.977789 TCATGCTCTGCGGATAATTAATAAA 57.022 32.000 0.00 0.00 0.00 1.40
1789 2877 7.280876 GGATCATGCTCTGCGGATAATTAATAA 59.719 37.037 0.00 0.00 0.00 1.40
1790 2878 6.763135 GGATCATGCTCTGCGGATAATTAATA 59.237 38.462 0.00 0.00 0.00 0.98
1791 2879 5.587844 GGATCATGCTCTGCGGATAATTAAT 59.412 40.000 0.00 0.00 0.00 1.40
1792 2880 4.937620 GGATCATGCTCTGCGGATAATTAA 59.062 41.667 0.00 0.00 0.00 1.40
1802 2890 5.392811 GCCATAAATAAGGATCATGCTCTGC 60.393 44.000 0.00 0.00 0.00 4.26
1847 2935 3.055891 GGCTTATGTGTGGCCAAAGAAAT 60.056 43.478 16.66 4.84 44.69 2.17
1896 2984 3.243535 GGGTCCAAGCAGAACAGAAAAAG 60.244 47.826 0.00 0.00 0.00 2.27
2056 3144 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2057 3145 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2058 3146 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2059 3147 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2060 3148 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2061 3149 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2062 3150 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2063 3151 1.274596 CCGACAAGTATTTCCGGACG 58.725 55.000 1.83 0.00 42.49 4.79
2064 3152 1.004595 GCCGACAAGTATTTCCGGAC 58.995 55.000 1.83 0.00 42.49 4.79
2065 3153 0.108041 GGCCGACAAGTATTTCCGGA 60.108 55.000 0.00 0.00 42.49 5.14
2066 3154 1.426041 CGGCCGACAAGTATTTCCGG 61.426 60.000 24.07 0.00 42.74 5.14
2067 3155 0.458889 TCGGCCGACAAGTATTTCCG 60.459 55.000 27.28 0.00 37.00 4.30
2068 3156 1.729284 TTCGGCCGACAAGTATTTCC 58.271 50.000 31.19 0.00 0.00 3.13
2069 3157 2.031683 CCATTCGGCCGACAAGTATTTC 59.968 50.000 31.19 0.00 0.00 2.17
2070 3158 2.014128 CCATTCGGCCGACAAGTATTT 58.986 47.619 31.19 2.14 0.00 1.40
2071 3159 1.208535 TCCATTCGGCCGACAAGTATT 59.791 47.619 31.19 3.70 0.00 1.89
2072 3160 0.828022 TCCATTCGGCCGACAAGTAT 59.172 50.000 31.19 16.21 0.00 2.12
2073 3161 0.828022 ATCCATTCGGCCGACAAGTA 59.172 50.000 31.19 14.22 0.00 2.24
2074 3162 0.744414 CATCCATTCGGCCGACAAGT 60.744 55.000 31.19 11.77 0.00 3.16
2075 3163 0.744414 ACATCCATTCGGCCGACAAG 60.744 55.000 31.19 20.07 0.00 3.16
2076 3164 0.537653 TACATCCATTCGGCCGACAA 59.462 50.000 31.19 16.06 0.00 3.18
2077 3165 0.756294 ATACATCCATTCGGCCGACA 59.244 50.000 31.19 19.65 0.00 4.35
2078 3166 1.000955 AGATACATCCATTCGGCCGAC 59.999 52.381 31.19 12.50 0.00 4.79
2079 3167 1.338107 AGATACATCCATTCGGCCGA 58.662 50.000 27.28 27.28 0.00 5.54
2080 3168 2.492088 TCTAGATACATCCATTCGGCCG 59.508 50.000 22.12 22.12 0.00 6.13
2081 3169 3.258372 TGTCTAGATACATCCATTCGGCC 59.742 47.826 0.00 0.00 0.00 6.13
2082 3170 4.521130 TGTCTAGATACATCCATTCGGC 57.479 45.455 0.00 0.00 0.00 5.54
2083 3171 9.658799 AAAATATGTCTAGATACATCCATTCGG 57.341 33.333 0.00 0.00 40.52 4.30
2110 3198 9.851686 TGCATAAAAATGGATGTATCTAGAACT 57.148 29.630 0.00 0.00 0.00 3.01
2116 3204 9.976511 CAGAAATGCATAAAAATGGATGTATCT 57.023 29.630 0.00 0.00 32.82 1.98
2117 3205 8.706035 GCAGAAATGCATAAAAATGGATGTATC 58.294 33.333 0.00 0.00 32.82 2.24
2118 3206 8.205512 TGCAGAAATGCATAAAAATGGATGTAT 58.794 29.630 0.00 0.00 40.23 2.29
2119 3207 7.554211 TGCAGAAATGCATAAAAATGGATGTA 58.446 30.769 0.00 0.00 40.23 2.29
2120 3208 6.408035 TGCAGAAATGCATAAAAATGGATGT 58.592 32.000 0.00 0.00 40.23 3.06
2121 3209 6.912203 TGCAGAAATGCATAAAAATGGATG 57.088 33.333 0.00 0.00 40.23 3.51
2122 3210 6.879993 TGTTGCAGAAATGCATAAAAATGGAT 59.120 30.769 0.00 0.00 44.94 3.41
2123 3211 6.228995 TGTTGCAGAAATGCATAAAAATGGA 58.771 32.000 0.00 0.00 44.94 3.41
2124 3212 6.483385 TGTTGCAGAAATGCATAAAAATGG 57.517 33.333 0.00 0.00 44.94 3.16
2125 3213 7.577979 AGTTGTTGCAGAAATGCATAAAAATG 58.422 30.769 0.00 0.00 44.94 2.32
2126 3214 7.733402 AGTTGTTGCAGAAATGCATAAAAAT 57.267 28.000 0.00 0.00 44.94 1.82
2127 3215 8.830201 ATAGTTGTTGCAGAAATGCATAAAAA 57.170 26.923 0.00 0.00 44.94 1.94
2128 3216 8.830201 AATAGTTGTTGCAGAAATGCATAAAA 57.170 26.923 0.00 0.00 44.94 1.52
2129 3217 8.830201 AAATAGTTGTTGCAGAAATGCATAAA 57.170 26.923 0.00 0.00 44.94 1.40
2130 3218 7.545265 GGAAATAGTTGTTGCAGAAATGCATAA 59.455 33.333 0.00 0.60 44.94 1.90
2131 3219 7.035004 GGAAATAGTTGTTGCAGAAATGCATA 58.965 34.615 0.00 0.00 44.94 3.14
2132 3220 5.870978 GGAAATAGTTGTTGCAGAAATGCAT 59.129 36.000 3.44 0.00 44.94 3.96
2133 3221 5.229423 GGAAATAGTTGTTGCAGAAATGCA 58.771 37.500 0.00 0.00 43.81 3.96
2134 3222 4.324402 CGGAAATAGTTGTTGCAGAAATGC 59.676 41.667 0.00 0.00 0.00 3.56
2135 3223 4.858692 CCGGAAATAGTTGTTGCAGAAATG 59.141 41.667 0.00 0.00 0.00 2.32
2136 3224 4.764823 TCCGGAAATAGTTGTTGCAGAAAT 59.235 37.500 0.00 0.00 0.00 2.17
2137 3225 4.023536 GTCCGGAAATAGTTGTTGCAGAAA 60.024 41.667 5.23 0.00 0.00 2.52
2138 3226 3.500680 GTCCGGAAATAGTTGTTGCAGAA 59.499 43.478 5.23 0.00 0.00 3.02
2139 3227 3.071479 GTCCGGAAATAGTTGTTGCAGA 58.929 45.455 5.23 0.00 0.00 4.26
2140 3228 2.159707 CGTCCGGAAATAGTTGTTGCAG 60.160 50.000 5.23 0.00 0.00 4.41
2141 3229 1.801771 CGTCCGGAAATAGTTGTTGCA 59.198 47.619 5.23 0.00 0.00 4.08
2142 3230 1.129811 CCGTCCGGAAATAGTTGTTGC 59.870 52.381 5.23 0.00 37.50 4.17
2143 3231 2.671396 CTCCGTCCGGAAATAGTTGTTG 59.329 50.000 5.23 0.00 44.66 3.33
2144 3232 2.354403 CCTCCGTCCGGAAATAGTTGTT 60.354 50.000 5.23 0.00 44.66 2.83
2145 3233 1.206371 CCTCCGTCCGGAAATAGTTGT 59.794 52.381 5.23 0.00 44.66 3.32
2146 3234 1.472728 CCCTCCGTCCGGAAATAGTTG 60.473 57.143 5.23 0.00 44.66 3.16
2147 3235 0.828677 CCCTCCGTCCGGAAATAGTT 59.171 55.000 5.23 0.00 44.66 2.24
2148 3236 0.032813 TCCCTCCGTCCGGAAATAGT 60.033 55.000 5.23 0.00 44.66 2.12
2149 3237 0.674534 CTCCCTCCGTCCGGAAATAG 59.325 60.000 5.23 3.15 44.66 1.73
2150 3238 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2151 3239 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2152 3240 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2153 3241 0.466922 GATACTCCCTCCGTCCGGAA 60.467 60.000 5.23 0.00 44.66 4.30
2154 3242 1.150081 GATACTCCCTCCGTCCGGA 59.850 63.158 0.00 0.00 42.90 5.14
2155 3243 0.399454 TAGATACTCCCTCCGTCCGG 59.601 60.000 0.00 0.00 0.00 5.14
2156 3244 2.267174 TTAGATACTCCCTCCGTCCG 57.733 55.000 0.00 0.00 0.00 4.79
2157 3245 4.648307 TCTTTTTAGATACTCCCTCCGTCC 59.352 45.833 0.00 0.00 0.00 4.79
2158 3246 5.848833 TCTTTTTAGATACTCCCTCCGTC 57.151 43.478 0.00 0.00 0.00 4.79
2159 3247 5.105023 GGTTCTTTTTAGATACTCCCTCCGT 60.105 44.000 0.00 0.00 0.00 4.69
2160 3248 5.105064 TGGTTCTTTTTAGATACTCCCTCCG 60.105 44.000 0.00 0.00 0.00 4.63
2161 3249 6.309389 TGGTTCTTTTTAGATACTCCCTCC 57.691 41.667 0.00 0.00 0.00 4.30
2162 3250 7.621796 TCTTGGTTCTTTTTAGATACTCCCTC 58.378 38.462 0.00 0.00 0.00 4.30
2163 3251 7.569599 TCTTGGTTCTTTTTAGATACTCCCT 57.430 36.000 0.00 0.00 0.00 4.20
2164 3252 8.809468 AATCTTGGTTCTTTTTAGATACTCCC 57.191 34.615 0.00 0.00 0.00 4.30
2165 3253 8.894731 GGAATCTTGGTTCTTTTTAGATACTCC 58.105 37.037 0.00 0.00 0.00 3.85
2166 3254 9.674068 AGGAATCTTGGTTCTTTTTAGATACTC 57.326 33.333 0.00 0.00 0.00 2.59
2198 3286 1.962807 CAGAATGTGGTCCTTTGGCAA 59.037 47.619 0.00 0.00 0.00 4.52
2199 3287 1.619654 CAGAATGTGGTCCTTTGGCA 58.380 50.000 0.00 0.00 0.00 4.92
2202 3290 0.890683 GGGCAGAATGTGGTCCTTTG 59.109 55.000 0.00 0.00 39.31 2.77
2274 3362 7.334921 CGTGGGTGTTTAAGGTGATAAAATAGA 59.665 37.037 0.00 0.00 0.00 1.98
2275 3363 7.414762 CCGTGGGTGTTTAAGGTGATAAAATAG 60.415 40.741 0.00 0.00 0.00 1.73
2276 3364 6.374894 CCGTGGGTGTTTAAGGTGATAAAATA 59.625 38.462 0.00 0.00 0.00 1.40
2279 3367 4.073549 CCGTGGGTGTTTAAGGTGATAAA 58.926 43.478 0.00 0.00 0.00 1.40
2281 3369 2.616001 GCCGTGGGTGTTTAAGGTGATA 60.616 50.000 0.00 0.00 0.00 2.15
2285 3381 1.598685 CGCCGTGGGTGTTTAAGGT 60.599 57.895 0.00 0.00 0.00 3.50
2312 3408 5.701224 TCCAATATTCCACTTAATGTCCCC 58.299 41.667 0.00 0.00 0.00 4.81
2369 3465 0.318441 TTTCTCCAGCTGAGTGGTCG 59.682 55.000 17.39 0.00 42.12 4.79
2397 3493 0.393132 GAGCAGGTTAGGTCCTTGGC 60.393 60.000 0.00 0.00 35.37 4.52
2428 3525 3.515562 AGAAGACTCCCAGTGTCTCATT 58.484 45.455 0.26 0.00 43.16 2.57


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

AutoCloner maintained by Alex Coulton.