Multiple sequence alignment - TraesCS3B01G547400

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 TraesCS3B01G547400 chr3B 100.000 2626 0 0 1 2626 783217691 783220316 0.000000e+00 4850
1 TraesCS3B01G547400 chr6A 92.669 2087 137 13 1 2083 135434867 135432793 0.000000e+00 2992
2 TraesCS3B01G547400 chr6A 91.383 499 41 2 2129 2626 135432802 135432305 0.000000e+00 682
3 TraesCS3B01G547400 chr3A 79.508 1259 237 16 449 1699 175860929 175862174 0.000000e+00 876
4 TraesCS3B01G547400 chr3A 78.638 1292 244 22 421 1699 102076900 102075628 0.000000e+00 828
5 TraesCS3B01G547400 chr2B 79.365 1260 235 20 449 1699 495227726 495228969 0.000000e+00 863
6 TraesCS3B01G547400 chr7A 78.909 1247 239 19 462 1699 16994404 16995635 0.000000e+00 824
7 TraesCS3B01G547400 chr7A 77.666 694 123 18 449 1135 67818149 67817481 6.810000e-106 394
8 TraesCS3B01G547400 chr4A 78.396 1259 239 22 449 1699 70770483 70769250 0.000000e+00 787
9 TraesCS3B01G547400 chr1A 78.219 1258 255 13 449 1699 255725571 255724326 0.000000e+00 787


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 TraesCS3B01G547400 chr3B 783217691 783220316 2625 False 4850 4850 100.000 1 2626 1 chr3B.!!$F1 2625
1 TraesCS3B01G547400 chr6A 135432305 135434867 2562 True 1837 2992 92.026 1 2626 2 chr6A.!!$R1 2625
2 TraesCS3B01G547400 chr3A 175860929 175862174 1245 False 876 876 79.508 449 1699 1 chr3A.!!$F1 1250
3 TraesCS3B01G547400 chr3A 102075628 102076900 1272 True 828 828 78.638 421 1699 1 chr3A.!!$R1 1278
4 TraesCS3B01G547400 chr2B 495227726 495228969 1243 False 863 863 79.365 449 1699 1 chr2B.!!$F1 1250
5 TraesCS3B01G547400 chr7A 16994404 16995635 1231 False 824 824 78.909 462 1699 1 chr7A.!!$F1 1237
6 TraesCS3B01G547400 chr7A 67817481 67818149 668 True 394 394 77.666 449 1135 1 chr7A.!!$R1 686
7 TraesCS3B01G547400 chr4A 70769250 70770483 1233 True 787 787 78.396 449 1699 1 chr4A.!!$R1 1250
8 TraesCS3B01G547400 chr1A 255724326 255725571 1245 True 787 787 78.219 449 1699 1 chr1A.!!$R1 1250

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
199 200 0.034767 AGCTAGCTTGCAGGCATTCA 60.035 50.0 23.85 4.02 34.99 2.57 F
984 1003 0.034896 CCATGTCCCCGTACCTATGC 59.965 60.0 0.00 0.00 0.00 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1043 1062 0.526954 CTTCGGATTGCTGCCATTGC 60.527 55.0 0.0 0.0 38.26 3.56 R
2557 2586 2.026262 TCCAATGAAGAACTACCTGGCC 60.026 50.0 0.0 0.0 0.00 5.36 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
71 72 7.935338 ATTGTCATGTGTTTTTCAGTGAATC 57.065 32.000 6.36 1.73 0.00 2.52
76 77 8.819974 GTCATGTGTTTTTCAGTGAATCAAAAT 58.180 29.630 6.36 2.69 0.00 1.82
115 116 5.303747 TGTTTACCATATTCCAGCAAACG 57.696 39.130 0.00 0.00 0.00 3.60
126 127 3.734463 TCCAGCAAACGATTGTAACAGA 58.266 40.909 7.29 0.00 38.85 3.41
166 167 6.437928 TCAATAACTTCACATGTTTCACTGC 58.562 36.000 0.00 0.00 0.00 4.40
171 172 3.969117 TCACATGTTTCACTGCAGAAC 57.031 42.857 23.35 15.08 0.00 3.01
177 178 5.348451 ACATGTTTCACTGCAGAACAAAAAC 59.652 36.000 23.35 19.90 0.00 2.43
185 186 6.017934 TCACTGCAGAACAAAAACTAAGCTAG 60.018 38.462 23.35 0.00 0.00 3.42
195 196 0.615331 ACTAAGCTAGCTTGCAGGCA 59.385 50.000 34.98 16.41 37.47 4.75
197 198 2.295885 CTAAGCTAGCTTGCAGGCATT 58.704 47.619 34.98 12.21 37.47 3.56
199 200 0.034767 AGCTAGCTTGCAGGCATTCA 60.035 50.000 23.85 4.02 34.99 2.57
201 202 1.468736 GCTAGCTTGCAGGCATTCAAC 60.469 52.381 23.85 2.18 34.17 3.18
202 203 1.814394 CTAGCTTGCAGGCATTCAACA 59.186 47.619 23.85 0.00 34.17 3.33
209 212 1.273048 GCAGGCATTCAACAATGGTCA 59.727 47.619 0.00 0.00 40.03 4.02
245 248 5.675538 AGGTATGTAGCAGATTGGAAGAAC 58.324 41.667 0.00 0.00 0.00 3.01
248 251 6.543831 GGTATGTAGCAGATTGGAAGAACATT 59.456 38.462 0.00 0.00 0.00 2.71
255 258 6.072286 AGCAGATTGGAAGAACATTGTAAGTG 60.072 38.462 0.00 0.00 0.00 3.16
256 259 6.294176 GCAGATTGGAAGAACATTGTAAGTGT 60.294 38.462 0.00 0.00 0.00 3.55
259 262 5.766150 TGGAAGAACATTGTAAGTGTTGG 57.234 39.130 0.00 0.00 39.72 3.77
262 265 5.298276 GGAAGAACATTGTAAGTGTTGGTCA 59.702 40.000 0.00 0.00 39.72 4.02
265 268 6.560711 AGAACATTGTAAGTGTTGGTCAAAC 58.439 36.000 0.00 0.00 39.72 2.93
326 329 6.787085 AAGAGATTGAACTTACTGAAACCG 57.213 37.500 0.00 0.00 0.00 4.44
372 375 7.712797 TGTTAAAGAATCTTGGGTTTCTTCAC 58.287 34.615 0.00 0.00 39.28 3.18
378 381 3.149196 TCTTGGGTTTCTTCACATCAGC 58.851 45.455 0.00 0.00 0.00 4.26
411 414 1.354040 CCATCATAAGCGCCGAGATC 58.646 55.000 2.29 0.00 0.00 2.75
414 417 3.367395 CCATCATAAGCGCCGAGATCTTA 60.367 47.826 2.29 0.00 0.00 2.10
435 438 8.150827 TCTTAGGATTGAGATTGGAAGAGAAA 57.849 34.615 0.00 0.00 0.00 2.52
454 457 7.436118 AGAGAAATATCACTCTTGAGCTGATC 58.564 38.462 14.30 0.00 40.02 2.92
460 463 1.830477 ACTCTTGAGCTGATCCAGTCC 59.170 52.381 0.00 0.00 33.43 3.85
473 476 4.078922 TGATCCAGTCCAGAGGTAGAAGAT 60.079 45.833 0.00 0.00 0.00 2.40
480 483 5.128499 AGTCCAGAGGTAGAAGATGAACATG 59.872 44.000 0.00 0.00 0.00 3.21
503 506 0.459489 GGCGATTGAGTGAGAGCTCT 59.541 55.000 18.28 18.28 36.51 4.09
534 537 1.012841 GTGCTTCTATGGCTGTGAGC 58.987 55.000 0.00 0.00 41.46 4.26
592 595 0.797249 CTAGTACCACGCGTGCTGTC 60.797 60.000 33.17 20.76 38.01 3.51
610 613 2.104622 TGTCACAGAAGTCATTGCCTCA 59.895 45.455 0.00 0.00 0.00 3.86
622 625 3.701542 TCATTGCCTCAGTCTACGAGATT 59.298 43.478 0.00 0.00 31.84 2.40
643 657 6.713903 AGATTGATTGGACATGGATATGACAC 59.286 38.462 0.00 0.00 37.73 3.67
685 699 3.877508 GGTTAGTACTATTTGGCAGCAGG 59.122 47.826 2.79 0.00 0.00 4.85
975 994 0.108138 GAGACTTGTCCATGTCCCCG 60.108 60.000 9.06 0.00 36.49 5.73
984 1003 0.034896 CCATGTCCCCGTACCTATGC 59.965 60.000 0.00 0.00 0.00 3.14
1022 1041 0.036022 AGCCAGGAAGAGAACAGTGC 59.964 55.000 0.00 0.00 0.00 4.40
1029 1048 0.181114 AAGAGAACAGTGCTGTGGCA 59.819 50.000 5.53 0.00 44.13 4.92
1057 1076 1.470979 CCTTCAGCAATGGCAGCAATC 60.471 52.381 0.00 0.00 44.61 2.67
1058 1077 0.533491 TTCAGCAATGGCAGCAATCC 59.467 50.000 0.00 0.00 44.61 3.01
1059 1078 1.226859 CAGCAATGGCAGCAATCCG 60.227 57.895 0.00 0.00 44.61 4.18
1060 1079 1.378911 AGCAATGGCAGCAATCCGA 60.379 52.632 0.00 0.00 44.61 4.55
1061 1080 0.966875 AGCAATGGCAGCAATCCGAA 60.967 50.000 0.00 0.00 44.61 4.30
1063 1082 3.803421 GCAATGGCAGCAATCCGAAGG 62.803 57.143 0.00 0.00 46.27 3.46
1082 1101 3.282885 AGGAAGAAAATCCGATGGAAGC 58.717 45.455 0.00 0.00 44.60 3.86
1085 1104 4.098501 GGAAGAAAATCCGATGGAAGCAAT 59.901 41.667 0.00 0.00 34.34 3.56
1098 1117 6.314896 CGATGGAAGCAATTCTTAGTTTCTCT 59.685 38.462 0.00 0.00 34.56 3.10
1140 1159 5.802064 TGTTCGTTGTTATGTTCTGTTCAC 58.198 37.500 0.00 0.00 0.00 3.18
1147 1166 7.095816 CGTTGTTATGTTCTGTTCACTGACATA 60.096 37.037 0.00 0.00 0.00 2.29
1152 1171 9.671279 TTATGTTCTGTTCACTGACATATGAAT 57.329 29.630 10.38 0.00 37.19 2.57
1158 1177 6.841119 TGTTCACTGACATATGAATTTTCCG 58.159 36.000 10.38 0.00 37.19 4.30
1185 1204 7.712264 TTCACTTTCATTTGGTATGCTTTTG 57.288 32.000 0.00 0.00 0.00 2.44
1235 1254 7.483307 TCAATTTCTCTTTCACTTCTGTTTGG 58.517 34.615 0.00 0.00 0.00 3.28
1291 1316 1.363744 GCTGACTCTAGCATGCGTTT 58.636 50.000 13.01 0.00 43.17 3.60
1389 1414 9.785982 TTCCATTCGTGGATGATTAATATGTTA 57.214 29.630 0.00 0.00 37.87 2.41
1536 1562 8.450578 TGATGTTGAAGTTGAAAGACTACATT 57.549 30.769 0.00 0.00 30.47 2.71
1554 1580 4.005650 ACATTGTGTACATGAAGAGCCAG 58.994 43.478 0.00 0.00 0.00 4.85
1578 1604 0.753262 ATACTTCCAGCTGCGTAGGG 59.247 55.000 8.66 0.00 0.00 3.53
1613 1639 5.104610 TGGAAGATTGATGAAGAGGAGAAGG 60.105 44.000 0.00 0.00 0.00 3.46
1656 1682 4.885907 ACATGGAAATTGCAGATGGTAGAG 59.114 41.667 0.00 0.00 0.00 2.43
1782 1808 9.860650 TTGTGGGCAATATATGTTAGTTCTTAT 57.139 29.630 0.00 0.00 0.00 1.73
1863 1889 4.508461 TCAATGAAATGGCTGAGTTGTG 57.492 40.909 0.00 0.00 0.00 3.33
1876 1902 4.913924 GCTGAGTTGTGTGTCATTTCATTC 59.086 41.667 0.00 0.00 0.00 2.67
1882 1908 9.462174 GAGTTGTGTGTCATTTCATTCAAATTA 57.538 29.630 0.00 0.00 31.79 1.40
1910 1936 5.238650 ACCTCTAACATTATTTGTATGCGGC 59.761 40.000 0.00 0.00 37.68 6.53
1948 1975 9.370126 GTATTATGTATTTTAACGCAGCTCTTG 57.630 33.333 0.00 0.00 0.00 3.02
1951 1978 5.685841 TGTATTTTAACGCAGCTCTTGAAC 58.314 37.500 0.00 0.00 0.00 3.18
2115 2143 9.569122 TTTTACAAATACAATAGATAGGGGAGC 57.431 33.333 0.00 0.00 0.00 4.70
2116 2144 6.763715 ACAAATACAATAGATAGGGGAGCA 57.236 37.500 0.00 0.00 0.00 4.26
2117 2145 6.534634 ACAAATACAATAGATAGGGGAGCAC 58.465 40.000 0.00 0.00 0.00 4.40
2118 2146 5.763876 AATACAATAGATAGGGGAGCACC 57.236 43.478 0.00 0.00 39.11 5.01
2119 2147 3.352611 ACAATAGATAGGGGAGCACCT 57.647 47.619 0.00 0.00 44.75 4.00
2120 2148 3.669949 ACAATAGATAGGGGAGCACCTT 58.330 45.455 0.00 0.00 42.09 3.50
2121 2149 4.827789 ACAATAGATAGGGGAGCACCTTA 58.172 43.478 0.00 0.00 42.09 2.69
2122 2150 5.224441 ACAATAGATAGGGGAGCACCTTAA 58.776 41.667 0.00 0.00 42.09 1.85
2123 2151 5.852250 ACAATAGATAGGGGAGCACCTTAAT 59.148 40.000 0.00 0.00 42.09 1.40
2124 2152 6.332901 ACAATAGATAGGGGAGCACCTTAATT 59.667 38.462 0.00 0.00 42.09 1.40
2125 2153 7.147123 ACAATAGATAGGGGAGCACCTTAATTT 60.147 37.037 0.00 0.00 42.09 1.82
2126 2154 8.383175 CAATAGATAGGGGAGCACCTTAATTTA 58.617 37.037 0.00 0.00 42.09 1.40
2127 2155 6.189036 AGATAGGGGAGCACCTTAATTTAC 57.811 41.667 0.00 0.00 42.09 2.01
2128 2156 5.670361 AGATAGGGGAGCACCTTAATTTACA 59.330 40.000 0.00 0.00 42.09 2.41
2129 2157 4.668138 AGGGGAGCACCTTAATTTACAA 57.332 40.909 0.00 0.00 37.69 2.41
2130 2158 4.341487 AGGGGAGCACCTTAATTTACAAC 58.659 43.478 0.00 0.00 37.69 3.32
2131 2159 4.044191 AGGGGAGCACCTTAATTTACAACT 59.956 41.667 0.00 0.00 37.69 3.16
2132 2160 4.770531 GGGGAGCACCTTAATTTACAACTT 59.229 41.667 0.00 0.00 40.03 2.66
2133 2161 5.105877 GGGGAGCACCTTAATTTACAACTTC 60.106 44.000 0.00 0.00 40.03 3.01
2134 2162 5.710567 GGGAGCACCTTAATTTACAACTTCT 59.289 40.000 0.00 0.00 35.85 2.85
2135 2163 6.208797 GGGAGCACCTTAATTTACAACTTCTT 59.791 38.462 0.00 0.00 35.85 2.52
2136 2164 7.255836 GGGAGCACCTTAATTTACAACTTCTTT 60.256 37.037 0.00 0.00 35.85 2.52
2137 2165 8.789762 GGAGCACCTTAATTTACAACTTCTTTA 58.210 33.333 0.00 0.00 0.00 1.85
2138 2166 9.608617 GAGCACCTTAATTTACAACTTCTTTAC 57.391 33.333 0.00 0.00 0.00 2.01
2179 2207 8.649841 CGTTAGTGAAATAATACCGAAACTCAA 58.350 33.333 0.00 0.00 0.00 3.02
2214 2242 9.627123 TCCAACCAAGTTAAGATAATATGGAAG 57.373 33.333 9.66 4.03 0.00 3.46
2294 2323 7.222805 TGAAATGTATTGATACTGAAGCGAGTC 59.777 37.037 3.11 0.00 34.41 3.36
2295 2324 4.598062 TGTATTGATACTGAAGCGAGTCG 58.402 43.478 8.54 8.54 34.41 4.18
2324 2353 4.337555 AGCATGAAATCAGGTGCTGAATAC 59.662 41.667 9.97 0.00 45.44 1.89
2337 2366 6.381420 AGGTGCTGAATACTAGTACAATGAGT 59.619 38.462 4.31 0.00 33.18 3.41
2338 2367 6.477033 GGTGCTGAATACTAGTACAATGAGTG 59.523 42.308 4.31 0.00 33.18 3.51
2340 2369 7.433719 GTGCTGAATACTAGTACAATGAGTGAG 59.566 40.741 4.31 0.00 32.04 3.51
2351 2380 8.738645 AGTACAATGAGTGAGAAAAGAAGTTT 57.261 30.769 0.00 0.00 0.00 2.66
2429 2458 6.570692 ACGTAGTCTTTCTTCTTTGACTCAA 58.429 36.000 0.00 0.00 29.74 3.02
2432 2461 6.670077 AGTCTTTCTTCTTTGACTCAACAC 57.330 37.500 0.00 0.00 35.13 3.32
2440 2469 6.706270 TCTTCTTTGACTCAACACTAATGGAC 59.294 38.462 0.00 0.00 0.00 4.02
2445 2474 5.056480 TGACTCAACACTAATGGACAACAG 58.944 41.667 0.00 0.00 0.00 3.16
2452 2481 3.865745 CACTAATGGACAACAGTCGATCC 59.134 47.826 0.00 0.00 30.73 3.36
2455 2484 3.703001 ATGGACAACAGTCGATCCTTT 57.297 42.857 2.40 0.00 33.01 3.11
2467 2496 5.525378 CAGTCGATCCTTTAGCAGCTTATTT 59.475 40.000 0.00 0.00 0.00 1.40
2510 2539 5.408604 TCTCGGTTACTTTTCTCTTCATTGC 59.591 40.000 0.00 0.00 0.00 3.56
2527 2556 5.809001 TCATTGCCATCTTCTAGTTTGACT 58.191 37.500 0.00 0.00 0.00 3.41
2557 2586 2.995283 TCCATGTCAAGATGAAGGCTG 58.005 47.619 0.00 0.00 0.00 4.85
2572 2601 0.393132 GGCTGGCCAGGTAGTTCTTC 60.393 60.000 33.46 13.43 35.81 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 9.428363 CAATTTTGATTCACTGAAAAACACATG 57.572 29.630 0.00 0.00 0.00 3.21
145 146 5.764686 TCTGCAGTGAAACATGTGAAGTTAT 59.235 36.000 14.67 0.00 41.43 1.89
152 153 3.696281 TGTTCTGCAGTGAAACATGTG 57.304 42.857 14.67 0.00 41.43 3.21
157 158 6.237569 GCTTAGTTTTTGTTCTGCAGTGAAAC 60.238 38.462 14.67 16.32 31.94 2.78
163 164 5.049129 AGCTAGCTTAGTTTTTGTTCTGCAG 60.049 40.000 12.68 7.63 0.00 4.41
166 167 5.626955 GCAAGCTAGCTTAGTTTTTGTTCTG 59.373 40.000 28.87 13.97 34.50 3.02
171 172 4.479619 CCTGCAAGCTAGCTTAGTTTTTG 58.520 43.478 28.87 16.83 34.50 2.44
177 178 1.964552 ATGCCTGCAAGCTAGCTTAG 58.035 50.000 28.87 22.32 34.50 2.18
185 186 1.730064 CATTGTTGAATGCCTGCAAGC 59.270 47.619 0.00 0.00 32.83 4.01
199 200 9.088987 ACCTCTATGTTTATTTTGACCATTGTT 57.911 29.630 0.00 0.00 0.00 2.83
245 248 4.035792 TCCGTTTGACCAACACTTACAATG 59.964 41.667 0.00 0.00 34.68 2.82
248 251 3.199677 CTCCGTTTGACCAACACTTACA 58.800 45.455 0.00 0.00 34.68 2.41
255 258 1.305201 TTCTGCTCCGTTTGACCAAC 58.695 50.000 0.00 0.00 0.00 3.77
256 259 2.045561 TTTCTGCTCCGTTTGACCAA 57.954 45.000 0.00 0.00 0.00 3.67
259 262 4.946784 ACATATTTCTGCTCCGTTTGAC 57.053 40.909 0.00 0.00 0.00 3.18
262 265 5.705609 ACAAACATATTTCTGCTCCGTTT 57.294 34.783 0.00 0.00 0.00 3.60
265 268 5.295431 TGAACAAACATATTTCTGCTCCG 57.705 39.130 0.00 0.00 0.00 4.63
300 303 8.936864 CGGTTTCAGTAAGTTCAATCTCTTAAT 58.063 33.333 0.00 0.00 0.00 1.40
316 319 6.438425 AGGTTAGTAAGGATTCGGTTTCAGTA 59.562 38.462 0.00 0.00 0.00 2.74
325 328 7.668525 ACAAAAAGAGGTTAGTAAGGATTCG 57.331 36.000 0.00 0.00 0.00 3.34
362 365 3.316308 AGTTGTGCTGATGTGAAGAAACC 59.684 43.478 0.00 0.00 0.00 3.27
411 414 8.977267 ATTTCTCTTCCAATCTCAATCCTAAG 57.023 34.615 0.00 0.00 0.00 2.18
414 417 8.721479 TGATATTTCTCTTCCAATCTCAATCCT 58.279 33.333 0.00 0.00 0.00 3.24
435 438 4.900652 ACTGGATCAGCTCAAGAGTGATAT 59.099 41.667 12.10 0.00 34.37 1.63
446 449 0.752054 CCTCTGGACTGGATCAGCTC 59.248 60.000 0.00 0.00 34.37 4.09
454 457 3.636679 TCATCTTCTACCTCTGGACTGG 58.363 50.000 0.00 0.00 0.00 4.00
460 463 6.482641 CCATTCATGTTCATCTTCTACCTCTG 59.517 42.308 0.00 0.00 0.00 3.35
473 476 3.127376 CACTCAATCGCCATTCATGTTCA 59.873 43.478 0.00 0.00 0.00 3.18
480 483 1.596727 GCTCTCACTCAATCGCCATTC 59.403 52.381 0.00 0.00 0.00 2.67
503 506 4.323485 CCATAGAAGCACTCTGTAACCCAA 60.323 45.833 0.00 0.00 35.41 4.12
534 537 5.011533 CCACTATCTCTTCCCATACCTCAAG 59.988 48.000 0.00 0.00 0.00 3.02
592 595 2.740981 GACTGAGGCAATGACTTCTGTG 59.259 50.000 0.00 0.00 29.87 3.66
610 613 5.452496 CCATGTCCAATCAATCTCGTAGACT 60.452 44.000 0.00 0.00 0.00 3.24
622 625 4.165758 TGGTGTCATATCCATGTCCAATCA 59.834 41.667 0.00 0.00 33.57 2.57
643 657 3.009723 CCATTAAGGCAGTGTAGTGTGG 58.990 50.000 0.00 0.00 0.00 4.17
685 699 5.641209 TGGCCAATGTGTAAAATTTACATGC 59.359 36.000 19.82 16.06 0.00 4.06
763 777 8.443937 GGTCTCTTATTTCAGTGACATGTAAAC 58.556 37.037 0.00 0.00 38.51 2.01
764 778 7.606456 GGGTCTCTTATTTCAGTGACATGTAAA 59.394 37.037 0.00 0.00 38.51 2.01
781 796 5.130477 AGAAGTTTCACTGTTGGGTCTCTTA 59.870 40.000 0.00 0.00 0.00 2.10
808 825 4.827692 TCACATATAACACCTCCACACAC 58.172 43.478 0.00 0.00 0.00 3.82
975 994 8.671384 TTGTGGACTAATATTTGCATAGGTAC 57.329 34.615 0.00 0.00 0.00 3.34
984 1003 6.238842 CCTGGCTCATTGTGGACTAATATTTG 60.239 42.308 0.00 0.00 0.00 2.32
1029 1048 1.339824 CCATTGCTGAAGGCTGAGAGT 60.340 52.381 0.00 0.00 42.39 3.24
1043 1062 0.526954 CTTCGGATTGCTGCCATTGC 60.527 55.000 0.00 0.00 38.26 3.56
1057 1076 2.614057 CCATCGGATTTTCTTCCTTCGG 59.386 50.000 0.00 0.00 33.30 4.30
1058 1077 3.531538 TCCATCGGATTTTCTTCCTTCG 58.468 45.455 0.00 0.00 33.30 3.79
1059 1078 4.201960 GCTTCCATCGGATTTTCTTCCTTC 60.202 45.833 0.00 0.00 33.30 3.46
1060 1079 3.696548 GCTTCCATCGGATTTTCTTCCTT 59.303 43.478 0.00 0.00 33.30 3.36
1061 1080 3.282885 GCTTCCATCGGATTTTCTTCCT 58.717 45.455 0.00 0.00 33.30 3.36
1063 1082 4.701956 TTGCTTCCATCGGATTTTCTTC 57.298 40.909 0.00 0.00 0.00 2.87
1064 1083 5.420104 AGAATTGCTTCCATCGGATTTTCTT 59.580 36.000 0.00 0.00 31.27 2.52
1065 1084 4.952335 AGAATTGCTTCCATCGGATTTTCT 59.048 37.500 0.00 0.00 31.27 2.52
1066 1085 5.254339 AGAATTGCTTCCATCGGATTTTC 57.746 39.130 0.00 0.00 31.27 2.29
1067 1086 5.665916 AAGAATTGCTTCCATCGGATTTT 57.334 34.783 0.00 0.00 28.17 1.82
1068 1087 5.888161 ACTAAGAATTGCTTCCATCGGATTT 59.112 36.000 0.00 0.00 38.05 2.17
1122 1141 6.358118 TGTCAGTGAACAGAACATAACAAC 57.642 37.500 0.00 0.00 0.00 3.32
1140 1159 8.400947 AGTGAAATCGGAAAATTCATATGTCAG 58.599 33.333 1.90 0.00 35.70 3.51
1147 1166 9.492973 AAATGAAAGTGAAATCGGAAAATTCAT 57.507 25.926 7.28 0.00 36.77 2.57
1152 1171 6.578023 ACCAAATGAAAGTGAAATCGGAAAA 58.422 32.000 0.00 0.00 0.00 2.29
1158 1177 8.538409 AAAGCATACCAAATGAAAGTGAAATC 57.462 30.769 0.00 0.00 0.00 2.17
1235 1254 5.153950 AGCTCCCATCCGATATTTTCTAC 57.846 43.478 0.00 0.00 0.00 2.59
1410 1436 7.805071 CAGCAAATGGTTTTCTTCAACTACTAG 59.195 37.037 0.00 0.00 0.00 2.57
1536 1562 3.769739 AACTGGCTCTTCATGTACACA 57.230 42.857 0.00 0.00 0.00 3.72
1554 1580 2.618053 ACGCAGCTGGAAGTATGTAAC 58.382 47.619 17.12 0.00 35.30 2.50
1578 1604 1.133025 CAATCTTCCATCCGCACCAAC 59.867 52.381 0.00 0.00 0.00 3.77
1613 1639 7.064609 TCCATGTTTCAAAGTTACTCATCGATC 59.935 37.037 0.00 0.00 0.00 3.69
1656 1682 8.364129 ACACACAAAATGAAATATGAAACACC 57.636 30.769 0.00 0.00 0.00 4.16
1882 1908 9.567848 CGCATACAAATAATGTTAGAGGTTTTT 57.432 29.630 0.00 0.00 43.63 1.94
1901 1927 2.753055 TTTGAGTAGTGCCGCATACA 57.247 45.000 0.00 0.00 0.00 2.29
1941 1968 8.630054 ATTCTATATCGACTAGTTCAAGAGCT 57.370 34.615 0.00 0.00 0.00 4.09
2000 2027 6.259167 ACAGCTTATGTAAGTGAAACGTGAAA 59.741 34.615 0.00 0.00 41.33 2.69
2035 2062 8.572185 TGCATAGTTCATGTAAGCTTTTTGTAA 58.428 29.630 3.20 0.00 36.95 2.41
2042 2069 6.600822 ACTTCATGCATAGTTCATGTAAGCTT 59.399 34.615 3.48 3.48 41.40 3.74
2089 2117 9.569122 GCTCCCCTATCTATTGTATTTGTAAAA 57.431 33.333 0.00 0.00 0.00 1.52
2090 2118 8.719596 TGCTCCCCTATCTATTGTATTTGTAAA 58.280 33.333 0.00 0.00 0.00 2.01
2091 2119 8.154856 GTGCTCCCCTATCTATTGTATTTGTAA 58.845 37.037 0.00 0.00 0.00 2.41
2092 2120 7.256547 GGTGCTCCCCTATCTATTGTATTTGTA 60.257 40.741 0.00 0.00 0.00 2.41
2093 2121 6.465894 GGTGCTCCCCTATCTATTGTATTTGT 60.466 42.308 0.00 0.00 0.00 2.83
2094 2122 5.940470 GGTGCTCCCCTATCTATTGTATTTG 59.060 44.000 0.00 0.00 0.00 2.32
2095 2123 5.852250 AGGTGCTCCCCTATCTATTGTATTT 59.148 40.000 0.00 0.00 31.31 1.40
2096 2124 5.415961 AGGTGCTCCCCTATCTATTGTATT 58.584 41.667 0.00 0.00 31.31 1.89
2097 2125 5.029973 AGGTGCTCCCCTATCTATTGTAT 57.970 43.478 0.00 0.00 31.31 2.29
2098 2126 4.487282 AGGTGCTCCCCTATCTATTGTA 57.513 45.455 0.00 0.00 31.31 2.41
2099 2127 3.352611 AGGTGCTCCCCTATCTATTGT 57.647 47.619 0.00 0.00 31.31 2.71
2100 2128 5.825593 TTAAGGTGCTCCCCTATCTATTG 57.174 43.478 0.00 0.00 33.33 1.90
2101 2129 7.408013 AAATTAAGGTGCTCCCCTATCTATT 57.592 36.000 0.00 0.00 33.33 1.73
2102 2130 7.516209 TGTAAATTAAGGTGCTCCCCTATCTAT 59.484 37.037 0.00 0.00 33.33 1.98
2103 2131 6.847567 TGTAAATTAAGGTGCTCCCCTATCTA 59.152 38.462 0.00 0.00 33.33 1.98
2104 2132 5.670361 TGTAAATTAAGGTGCTCCCCTATCT 59.330 40.000 0.00 0.00 33.33 1.98
2105 2133 5.937111 TGTAAATTAAGGTGCTCCCCTATC 58.063 41.667 0.00 0.00 33.33 2.08
2106 2134 5.987019 TGTAAATTAAGGTGCTCCCCTAT 57.013 39.130 0.00 0.00 33.33 2.57
2107 2135 5.252164 AGTTGTAAATTAAGGTGCTCCCCTA 59.748 40.000 0.00 0.00 33.33 3.53
2108 2136 4.044191 AGTTGTAAATTAAGGTGCTCCCCT 59.956 41.667 0.00 0.00 35.96 4.79
2109 2137 4.341487 AGTTGTAAATTAAGGTGCTCCCC 58.659 43.478 0.00 0.00 0.00 4.81
2110 2138 5.710567 AGAAGTTGTAAATTAAGGTGCTCCC 59.289 40.000 0.00 0.00 0.00 4.30
2111 2139 6.819397 AGAAGTTGTAAATTAAGGTGCTCC 57.181 37.500 0.00 0.00 0.00 4.70
2112 2140 9.608617 GTAAAGAAGTTGTAAATTAAGGTGCTC 57.391 33.333 0.00 0.00 0.00 4.26
2113 2141 9.350951 AGTAAAGAAGTTGTAAATTAAGGTGCT 57.649 29.630 0.00 0.00 0.00 4.40
2114 2142 9.961265 AAGTAAAGAAGTTGTAAATTAAGGTGC 57.039 29.630 0.00 0.00 0.00 5.01
2149 2177 9.891535 GTTTCGGTATTATTTCACTAACGTTAG 57.108 33.333 29.27 29.27 36.82 2.34
2151 2179 8.538409 AGTTTCGGTATTATTTCACTAACGTT 57.462 30.769 5.88 5.88 0.00 3.99
2154 2182 9.968743 CTTGAGTTTCGGTATTATTTCACTAAC 57.031 33.333 0.00 0.00 0.00 2.34
2158 2186 9.326339 GTTTCTTGAGTTTCGGTATTATTTCAC 57.674 33.333 0.00 0.00 0.00 3.18
2165 2193 7.827236 TGGATATGTTTCTTGAGTTTCGGTATT 59.173 33.333 0.00 0.00 0.00 1.89
2168 2196 5.556915 TGGATATGTTTCTTGAGTTTCGGT 58.443 37.500 0.00 0.00 0.00 4.69
2289 2318 4.978580 TGATTTCATGCTTCTATCGACTCG 59.021 41.667 0.00 0.00 0.00 4.18
2294 2323 4.319333 GCACCTGATTTCATGCTTCTATCG 60.319 45.833 0.00 0.00 35.16 2.92
2295 2324 4.820716 AGCACCTGATTTCATGCTTCTATC 59.179 41.667 3.41 0.00 46.06 2.08
2312 2341 6.381420 ACTCATTGTACTAGTATTCAGCACCT 59.619 38.462 5.75 0.00 0.00 4.00
2324 2353 9.482627 AACTTCTTTTCTCACTCATTGTACTAG 57.517 33.333 0.00 0.00 0.00 2.57
2377 2406 7.992180 ACTGTTGTTGATTTCATTTCTTGTC 57.008 32.000 0.00 0.00 0.00 3.18
2429 2458 4.495422 GATCGACTGTTGTCCATTAGTGT 58.505 43.478 0.00 0.00 39.94 3.55
2432 2461 4.392921 AGGATCGACTGTTGTCCATTAG 57.607 45.455 14.85 0.00 39.94 1.73
2440 2469 2.349886 GCTGCTAAAGGATCGACTGTTG 59.650 50.000 0.00 0.00 0.00 3.33
2445 2474 5.993106 AAATAAGCTGCTAAAGGATCGAC 57.007 39.130 0.90 0.00 0.00 4.20
2472 2501 7.951347 AGTAACCGAGAGAAGTATTTCCTTA 57.049 36.000 0.00 0.00 33.64 2.69
2480 2509 7.230108 TGAAGAGAAAAGTAACCGAGAGAAGTA 59.770 37.037 0.00 0.00 0.00 2.24
2482 2511 6.448006 TGAAGAGAAAAGTAACCGAGAGAAG 58.552 40.000 0.00 0.00 0.00 2.85
2557 2586 2.026262 TCCAATGAAGAACTACCTGGCC 60.026 50.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.