Multiple sequence alignment - TraesCS7B01G443800

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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 TraesCS7B01G443800 chr7B 100.000 2888 0 0 1 2888 708510615 708513502 0.000000e+00 5334
1 TraesCS7B01G443800 chr7B 89.729 1587 89 30 322 1893 708445436 708446963 0.000000e+00 1960
2 TraesCS7B01G443800 chr7B 85.430 1812 183 50 830 2579 708529259 708531051 0.000000e+00 1808
3 TraesCS7B01G443800 chr7B 81.340 1672 169 72 710 2292 708552163 708553780 0.000000e+00 1227
4 TraesCS7B01G443800 chr7B 96.063 127 4 1 713 839 708518208 708518333 3.770000e-49 206
5 TraesCS7B01G443800 chr7B 91.026 78 5 2 2554 2631 708513126 708513201 1.420000e-18 104
6 TraesCS7B01G443800 chr7B 91.026 78 5 2 2512 2587 708513168 708513245 1.420000e-18 104
7 TraesCS7B01G443800 chr7A 87.969 1546 103 36 626 2110 708318719 708320242 0.000000e+00 1748
8 TraesCS7B01G443800 chr7A 80.292 1710 193 75 710 2310 708326197 708327871 0.000000e+00 1158
9 TraesCS7B01G443800 chr7A 81.507 584 91 10 28 602 708318149 708318724 5.640000e-127 464
10 TraesCS7B01G443800 chr7A 87.190 242 27 4 2358 2597 708320255 708320494 3.670000e-69 272
11 TraesCS7B01G443800 chr7D 85.455 1650 154 45 1001 2605 615765512 615767120 0.000000e+00 1639
12 TraesCS7B01G443800 chr7D 87.889 1445 88 29 728 2115 615559725 615558311 0.000000e+00 1618
13 TraesCS7B01G443800 chr7D 82.603 1460 131 71 710 2077 615774599 615776027 0.000000e+00 1175
14 TraesCS7B01G443800 chr7D 86.589 343 30 13 2554 2887 615767025 615767360 5.880000e-97 364
15 TraesCS7B01G443800 chr6B 84.049 326 52 0 1009 1334 245985739 245985414 6.010000e-82 315
16 TraesCS7B01G443800 chr6D 79.287 449 62 13 26 467 88482928 88482504 4.710000e-73 285


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 TraesCS7B01G443800 chr7B 708510615 708513502 2887 False 1847.333333 5334 94.017333 1 2888 3 chr7B.!!$F5 2887
1 TraesCS7B01G443800 chr7B 708445436 708446963 1527 False 1960.000000 1960 89.729000 322 1893 1 chr7B.!!$F1 1571
2 TraesCS7B01G443800 chr7B 708529259 708531051 1792 False 1808.000000 1808 85.430000 830 2579 1 chr7B.!!$F3 1749
3 TraesCS7B01G443800 chr7B 708552163 708553780 1617 False 1227.000000 1227 81.340000 710 2292 1 chr7B.!!$F4 1582
4 TraesCS7B01G443800 chr7A 708326197 708327871 1674 False 1158.000000 1158 80.292000 710 2310 1 chr7A.!!$F1 1600
5 TraesCS7B01G443800 chr7A 708318149 708320494 2345 False 828.000000 1748 85.555333 28 2597 3 chr7A.!!$F2 2569
6 TraesCS7B01G443800 chr7D 615558311 615559725 1414 True 1618.000000 1618 87.889000 728 2115 1 chr7D.!!$R1 1387
7 TraesCS7B01G443800 chr7D 615774599 615776027 1428 False 1175.000000 1175 82.603000 710 2077 1 chr7D.!!$F1 1367
8 TraesCS7B01G443800 chr7D 615765512 615767360 1848 False 1001.500000 1639 86.022000 1001 2887 2 chr7D.!!$F2 1886

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
256 262 0.033504 TGGTCGAGACACTGCCTTTC 59.966 55.0 5.55 0.0 0.0 2.62 F
374 380 0.250467 GTGTGGAGTGGAGTGTGCAT 60.250 55.0 0.00 0.0 0.0 3.96 F
543 565 0.320421 ACAAACACTCTATGCCGCGT 60.320 50.0 4.92 0.0 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 1891 1.038280 GGGAGAACGGGTATGACGAT 58.962 55.000 0.00 0.0 34.93 3.73 R
1819 2021 2.124983 GCCATCCAGAAGCTGCGA 60.125 61.111 0.00 0.0 0.00 5.10 R
2210 2541 3.471620 TCCATCCCGGAGCATAGC 58.528 61.111 0.73 0.0 39.64 2.97 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
30 31 8.939926 CAGTGTTTATTTTACTGTTACGTGTTG 58.060 33.333 0.00 0.00 37.59 3.33
31 32 8.881743 AGTGTTTATTTTACTGTTACGTGTTGA 58.118 29.630 0.00 0.00 0.00 3.18
32 33 9.488124 GTGTTTATTTTACTGTTACGTGTTGAA 57.512 29.630 0.00 0.00 0.00 2.69
37 38 5.579384 TTACTGTTACGTGTTGAATTCCG 57.421 39.130 2.27 1.54 0.00 4.30
44 45 0.110373 GTGTTGAATTCCGTCGGTGC 60.110 55.000 11.88 0.02 0.00 5.01
45 46 0.250124 TGTTGAATTCCGTCGGTGCT 60.250 50.000 11.88 0.00 0.00 4.40
46 47 0.872388 GTTGAATTCCGTCGGTGCTT 59.128 50.000 11.88 3.35 0.00 3.91
74 75 2.040412 GTCCAGGTTGATCTTCAAGGGT 59.960 50.000 0.00 0.00 37.00 4.34
75 76 2.040278 TCCAGGTTGATCTTCAAGGGTG 59.960 50.000 0.00 0.00 37.00 4.61
76 77 1.815003 CAGGTTGATCTTCAAGGGTGC 59.185 52.381 0.00 0.00 37.00 5.01
83 84 5.023533 TGATCTTCAAGGGTGCTATGTAC 57.976 43.478 0.00 0.00 0.00 2.90
111 112 0.324614 TGGTGCGTCCAAGATGATGT 59.675 50.000 0.00 0.00 44.12 3.06
125 126 2.347697 TGATGTCTTTCTCGTGACCG 57.652 50.000 0.00 0.00 32.67 4.79
131 132 1.409790 TCTTTCTCGTGACCGTCCAAA 59.590 47.619 0.00 0.00 35.01 3.28
132 133 2.159071 TCTTTCTCGTGACCGTCCAAAA 60.159 45.455 0.00 0.00 35.01 2.44
133 134 1.860676 TTCTCGTGACCGTCCAAAAG 58.139 50.000 0.00 0.00 35.01 2.27
135 136 1.137479 TCTCGTGACCGTCCAAAAGTT 59.863 47.619 0.00 0.00 35.01 2.66
136 137 1.525619 CTCGTGACCGTCCAAAAGTTC 59.474 52.381 0.00 0.00 35.01 3.01
137 138 1.137479 TCGTGACCGTCCAAAAGTTCT 59.863 47.619 0.00 0.00 35.01 3.01
138 139 1.260561 CGTGACCGTCCAAAAGTTCTG 59.739 52.381 0.00 0.00 0.00 3.02
139 140 1.002792 GTGACCGTCCAAAAGTTCTGC 60.003 52.381 0.00 0.00 0.00 4.26
141 142 0.106918 ACCGTCCAAAAGTTCTGCCA 60.107 50.000 0.00 0.00 0.00 4.92
142 143 0.310854 CCGTCCAAAAGTTCTGCCAC 59.689 55.000 0.00 0.00 0.00 5.01
143 144 1.021202 CGTCCAAAAGTTCTGCCACA 58.979 50.000 0.00 0.00 0.00 4.17
147 148 3.568007 GTCCAAAAGTTCTGCCACATACA 59.432 43.478 0.00 0.00 0.00 2.29
163 164 4.327357 CACATACACGCCAGTCTCTTTTAG 59.673 45.833 0.00 0.00 0.00 1.85
175 176 4.228210 AGTCTCTTTTAGGCATTCATGGGA 59.772 41.667 0.00 0.00 29.52 4.37
183 184 1.481802 GGCATTCATGGGATGGATGGT 60.482 52.381 6.91 0.00 44.76 3.55
185 186 1.616865 CATTCATGGGATGGATGGTGC 59.383 52.381 0.00 0.00 41.62 5.01
186 187 0.630134 TTCATGGGATGGATGGTGCA 59.370 50.000 0.00 0.00 0.00 4.57
187 188 0.106569 TCATGGGATGGATGGTGCAC 60.107 55.000 8.80 8.80 0.00 4.57
188 189 1.111116 CATGGGATGGATGGTGCACC 61.111 60.000 29.67 29.67 0.00 5.01
204 205 0.242825 CACCGGCGAGTGAAGTCTAA 59.757 55.000 19.35 0.00 40.34 2.10
209 210 2.338500 GGCGAGTGAAGTCTAACTTGG 58.662 52.381 0.00 0.00 38.80 3.61
221 222 5.497474 AGTCTAACTTGGTGTGTTGTCTTT 58.503 37.500 0.00 0.00 0.00 2.52
223 224 5.353123 GTCTAACTTGGTGTGTTGTCTTTGA 59.647 40.000 0.00 0.00 0.00 2.69
229 230 1.668751 GTGTGTTGTCTTTGAAGGCGA 59.331 47.619 0.00 0.00 31.96 5.54
256 262 0.033504 TGGTCGAGACACTGCCTTTC 59.966 55.000 5.55 0.00 0.00 2.62
268 274 4.019321 ACACTGCCTTTCAGCTTAGGATAA 60.019 41.667 9.88 0.00 46.76 1.75
270 276 4.226168 ACTGCCTTTCAGCTTAGGATAAGT 59.774 41.667 9.88 7.02 46.76 2.24
278 284 4.162320 TCAGCTTAGGATAAGTCCCTTGTG 59.838 45.833 0.00 0.00 46.34 3.33
285 291 3.497942 GGATAAGTCCCTTGTGTTGTGGT 60.498 47.826 0.00 0.00 38.69 4.16
303 309 1.479757 GGTTGTAATGGGTGTGGTGGT 60.480 52.381 0.00 0.00 0.00 4.16
312 318 0.591170 GGTGTGGTGGTTTGTCATCG 59.409 55.000 0.00 0.00 0.00 3.84
313 319 1.588674 GTGTGGTGGTTTGTCATCGA 58.411 50.000 0.00 0.00 0.00 3.59
317 323 3.181464 TGTGGTGGTTTGTCATCGAACTA 60.181 43.478 0.00 0.00 37.89 2.24
318 324 3.185797 GTGGTGGTTTGTCATCGAACTAC 59.814 47.826 0.00 6.37 43.86 2.73
320 326 2.740447 GTGGTTTGTCATCGAACTACCC 59.260 50.000 0.00 0.00 40.93 3.69
323 329 3.000727 GTTTGTCATCGAACTACCCTGG 58.999 50.000 0.00 0.00 35.64 4.45
341 347 0.755327 GGTGGGTGTTGGCTTGTCTT 60.755 55.000 0.00 0.00 0.00 3.01
374 380 0.250467 GTGTGGAGTGGAGTGTGCAT 60.250 55.000 0.00 0.00 0.00 3.96
391 397 1.518102 GCATTGCACTTGTTGTTCACG 59.482 47.619 3.15 0.00 0.00 4.35
406 413 1.996798 TCACGACAAGGGAGTCTTCT 58.003 50.000 0.00 0.00 36.38 2.85
408 415 2.035961 TCACGACAAGGGAGTCTTCTTG 59.964 50.000 18.47 18.47 44.14 3.02
454 461 7.986085 AAAAGTATGATATGCCTGGATGTAC 57.014 36.000 0.00 0.00 0.00 2.90
519 541 1.326852 GATCGAAGTACACGAGCGAGA 59.673 52.381 17.16 0.00 42.81 4.04
535 557 3.047796 GCGAGAACGAACAAACACTCTA 58.952 45.455 0.00 0.00 42.66 2.43
543 565 0.320421 ACAAACACTCTATGCCGCGT 60.320 50.000 4.92 0.00 0.00 6.01
554 576 0.951558 ATGCCGCGTTTTCACTTTCT 59.048 45.000 4.92 0.00 0.00 2.52
571 593 3.936372 TTCTGAACTACCTCTCCAACG 57.064 47.619 0.00 0.00 0.00 4.10
589 611 1.202359 ACGGCAAACTCGCAAACAAAT 60.202 42.857 0.00 0.00 0.00 2.32
594 616 3.305629 GCAAACTCGCAAACAAATCAACA 59.694 39.130 0.00 0.00 0.00 3.33
602 624 4.264145 CGCAAACAAATCAACAGAAACGAA 59.736 37.500 0.00 0.00 0.00 3.85
604 626 6.529696 GCAAACAAATCAACAGAAACGAAAA 58.470 32.000 0.00 0.00 0.00 2.29
609 631 9.743057 AACAAATCAACAGAAACGAAAATATGA 57.257 25.926 0.00 0.00 0.00 2.15
614 636 9.994432 ATCAACAGAAACGAAAATATGATTCTC 57.006 29.630 0.00 0.00 0.00 2.87
615 637 8.450964 TCAACAGAAACGAAAATATGATTCTCC 58.549 33.333 0.00 0.00 0.00 3.71
616 638 7.321745 ACAGAAACGAAAATATGATTCTCCC 57.678 36.000 0.00 0.00 0.00 4.30
617 639 7.112779 ACAGAAACGAAAATATGATTCTCCCT 58.887 34.615 0.00 0.00 0.00 4.20
618 640 7.281100 ACAGAAACGAAAATATGATTCTCCCTC 59.719 37.037 0.00 0.00 0.00 4.30
619 641 7.280876 CAGAAACGAAAATATGATTCTCCCTCA 59.719 37.037 0.00 0.00 0.00 3.86
620 642 7.829211 AGAAACGAAAATATGATTCTCCCTCAA 59.171 33.333 0.00 0.00 0.00 3.02
621 643 7.559590 AACGAAAATATGATTCTCCCTCAAG 57.440 36.000 0.00 0.00 0.00 3.02
622 644 6.889198 ACGAAAATATGATTCTCCCTCAAGA 58.111 36.000 0.00 0.00 0.00 3.02
623 645 7.338710 ACGAAAATATGATTCTCCCTCAAGAA 58.661 34.615 0.00 0.00 39.49 2.52
624 646 7.829211 ACGAAAATATGATTCTCCCTCAAGAAA 59.171 33.333 0.00 0.00 38.69 2.52
625 647 8.677300 CGAAAATATGATTCTCCCTCAAGAAAA 58.323 33.333 0.00 0.00 38.69 2.29
802 836 4.020378 CGTTTCCGGTGCCGTTGG 62.020 66.667 9.90 0.00 37.81 3.77
835 877 2.609299 TTGGATGGGGCCTCGTGA 60.609 61.111 0.00 0.00 0.00 4.35
915 975 2.358247 CTTCCCCGACAACCACCG 60.358 66.667 0.00 0.00 0.00 4.94
1634 1815 4.742201 CCACCACGACAGCTCCCG 62.742 72.222 3.01 3.01 0.00 5.14
1819 2021 2.034066 CCAACCTGCCGTCCATGT 59.966 61.111 0.00 0.00 0.00 3.21
1828 2030 2.456119 CCGTCCATGTCGCAGCTTC 61.456 63.158 0.00 0.00 0.00 3.86
1893 2095 0.596083 CGAGGATGCAGTGACCGATC 60.596 60.000 0.00 0.00 0.00 3.69
1895 2097 0.904649 AGGATGCAGTGACCGATCAA 59.095 50.000 0.00 0.00 36.31 2.57
1943 2224 4.127171 GCTGGCTTCATTTCGTTAGGATA 58.873 43.478 0.00 0.00 0.00 2.59
1945 2226 5.932303 GCTGGCTTCATTTCGTTAGGATATA 59.068 40.000 0.00 0.00 0.00 0.86
1951 2232 8.496751 GCTTCATTTCGTTAGGATATAAAGTCC 58.503 37.037 0.00 0.00 35.94 3.85
1991 2294 4.456222 GGGAGAAAGAAGAACTAGGCAAAC 59.544 45.833 0.00 0.00 0.00 2.93
2013 2332 4.214332 ACCTGACGATTTGCTTCTTTCTTC 59.786 41.667 0.00 0.00 0.00 2.87
2014 2333 4.453819 CCTGACGATTTGCTTCTTTCTTCT 59.546 41.667 0.00 0.00 0.00 2.85
2147 2478 3.417069 TCTGAAGCGAAAAATCCCTCA 57.583 42.857 0.00 0.00 0.00 3.86
2152 2483 5.496556 TGAAGCGAAAAATCCCTCATTCTA 58.503 37.500 0.00 0.00 0.00 2.10
2162 2493 4.819105 TCCCTCATTCTACATTTGACGT 57.181 40.909 0.00 0.00 0.00 4.34
2165 2496 5.186215 TCCCTCATTCTACATTTGACGTACA 59.814 40.000 0.00 0.00 0.00 2.90
2166 2497 5.872617 CCCTCATTCTACATTTGACGTACAA 59.127 40.000 0.00 0.00 36.65 2.41
2190 2521 3.046968 TGCCAAGTAACATCAAGCGTA 57.953 42.857 0.00 0.00 0.00 4.42
2210 2541 2.656973 AAACGGCGCGGCAAAAAG 60.657 55.556 32.60 17.84 0.00 2.27
2220 2555 0.248215 CGGCAAAAAGCTATGCTCCG 60.248 55.000 15.89 9.80 44.79 4.63
2245 2580 5.884792 GGATGGAGAAGTTGAACAATCAGAT 59.115 40.000 0.00 0.00 36.78 2.90
2246 2581 6.183360 GGATGGAGAAGTTGAACAATCAGATG 60.183 42.308 0.00 0.00 36.78 2.90
2250 2585 7.080724 GGAGAAGTTGAACAATCAGATGAAAC 58.919 38.462 0.00 0.00 36.78 2.78
2252 2587 6.483307 AGAAGTTGAACAATCAGATGAAACGA 59.517 34.615 0.00 0.00 36.78 3.85
2269 2604 7.227992 TGAAACGATGACCAAAACAAATTTC 57.772 32.000 0.00 0.00 0.00 2.17
2386 2727 5.577835 TGTTCTGGACGTGAATTTCAAAAG 58.422 37.500 0.00 0.00 0.00 2.27
2395 2736 8.020819 GGACGTGAATTTCAAAAGATGTTCATA 58.979 33.333 0.00 0.00 0.00 2.15
2498 2849 7.951530 AAGCATTCGTGAAATTCAAAGATTT 57.048 28.000 0.00 0.00 32.16 2.17
2523 2874 8.598509 TTTTGCAATTTTGAAAAAGTTCATCG 57.401 26.923 0.00 0.00 43.29 3.84
2524 2875 6.900568 TGCAATTTTGAAAAAGTTCATCGT 57.099 29.167 0.00 0.00 43.29 3.73
2525 2876 6.932051 TGCAATTTTGAAAAAGTTCATCGTC 58.068 32.000 0.00 0.00 43.29 4.20
2526 2877 6.019156 TGCAATTTTGAAAAAGTTCATCGTCC 60.019 34.615 0.00 0.00 43.29 4.79
2527 2878 6.571588 CAATTTTGAAAAAGTTCATCGTCCG 58.428 36.000 0.00 0.00 43.29 4.79
2528 2879 4.886247 TTTGAAAAAGTTCATCGTCCGT 57.114 36.364 0.00 0.00 43.29 4.69
2529 2880 4.886247 TTGAAAAAGTTCATCGTCCGTT 57.114 36.364 0.00 0.00 43.29 4.44
2530 2881 4.886247 TGAAAAAGTTCATCGTCCGTTT 57.114 36.364 0.00 0.00 38.88 3.60
2531 2882 5.987777 TGAAAAAGTTCATCGTCCGTTTA 57.012 34.783 0.00 0.00 38.88 2.01
2532 2883 6.360844 TGAAAAAGTTCATCGTCCGTTTAA 57.639 33.333 0.00 0.00 38.88 1.52
2533 2884 6.423862 TGAAAAAGTTCATCGTCCGTTTAAG 58.576 36.000 0.00 0.00 38.88 1.85
2534 2885 6.258287 TGAAAAAGTTCATCGTCCGTTTAAGA 59.742 34.615 0.00 0.00 38.88 2.10
2535 2886 6.607735 AAAAGTTCATCGTCCGTTTAAGAA 57.392 33.333 0.00 0.00 0.00 2.52
2536 2887 6.607735 AAAGTTCATCGTCCGTTTAAGAAA 57.392 33.333 0.00 0.00 0.00 2.52
2537 2888 6.796705 AAGTTCATCGTCCGTTTAAGAAAT 57.203 33.333 0.00 0.00 0.00 2.17
2538 2889 6.165659 AGTTCATCGTCCGTTTAAGAAATG 57.834 37.500 0.00 0.00 0.00 2.32
2539 2890 5.699458 AGTTCATCGTCCGTTTAAGAAATGT 59.301 36.000 0.00 0.00 0.00 2.71
2540 2891 6.204108 AGTTCATCGTCCGTTTAAGAAATGTT 59.796 34.615 0.00 0.00 0.00 2.71
2541 2892 6.160664 TCATCGTCCGTTTAAGAAATGTTC 57.839 37.500 0.00 0.00 0.00 3.18
2542 2893 5.697178 TCATCGTCCGTTTAAGAAATGTTCA 59.303 36.000 0.00 0.00 0.00 3.18
2543 2894 6.370442 TCATCGTCCGTTTAAGAAATGTTCAT 59.630 34.615 0.00 0.00 0.00 2.57
2544 2895 5.922546 TCGTCCGTTTAAGAAATGTTCATG 58.077 37.500 0.00 0.00 0.00 3.07
2545 2896 4.553429 CGTCCGTTTAAGAAATGTTCATGC 59.447 41.667 0.00 0.00 0.00 4.06
2546 2897 5.457140 GTCCGTTTAAGAAATGTTCATGCA 58.543 37.500 0.00 0.00 0.00 3.96
2547 2898 5.569059 GTCCGTTTAAGAAATGTTCATGCAG 59.431 40.000 0.00 0.00 0.00 4.41
2548 2899 5.240623 TCCGTTTAAGAAATGTTCATGCAGT 59.759 36.000 0.00 0.00 0.00 4.40
2549 2900 5.343058 CCGTTTAAGAAATGTTCATGCAGTG 59.657 40.000 0.00 0.00 0.00 3.66
2616 2969 3.855689 AAAAGTTCATCGGCCATTCAG 57.144 42.857 2.24 0.00 0.00 3.02
2621 2974 4.019174 AGTTCATCGGCCATTCAGAAAAT 58.981 39.130 2.24 0.00 0.00 1.82
2721 3074 9.575783 TCTTTTGTAAAACAACTGTTCCATAAC 57.424 29.630 0.00 0.00 37.90 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.881743 TCAACACGTAACAGTAAAATAAACACT 58.118 29.630 0.00 0.00 0.00 3.55
6 7 9.488124 TTCAACACGTAACAGTAAAATAAACAC 57.512 29.630 0.00 0.00 0.00 3.32
10 11 9.881529 GGAATTCAACACGTAACAGTAAAATAA 57.118 29.630 7.93 0.00 0.00 1.40
11 12 8.222433 CGGAATTCAACACGTAACAGTAAAATA 58.778 33.333 7.93 0.00 0.00 1.40
12 13 7.073265 CGGAATTCAACACGTAACAGTAAAAT 58.927 34.615 7.93 0.00 0.00 1.82
13 14 6.036953 ACGGAATTCAACACGTAACAGTAAAA 59.963 34.615 7.93 0.00 37.85 1.52
14 15 5.523188 ACGGAATTCAACACGTAACAGTAAA 59.477 36.000 7.93 0.00 37.85 2.01
15 16 5.049167 ACGGAATTCAACACGTAACAGTAA 58.951 37.500 7.93 0.00 37.85 2.24
16 17 4.619973 ACGGAATTCAACACGTAACAGTA 58.380 39.130 7.93 0.00 37.85 2.74
17 18 3.460103 ACGGAATTCAACACGTAACAGT 58.540 40.909 7.93 0.00 37.85 3.55
18 19 3.421312 CGACGGAATTCAACACGTAACAG 60.421 47.826 7.93 0.00 39.95 3.16
19 20 2.472115 CGACGGAATTCAACACGTAACA 59.528 45.455 7.93 0.00 39.95 2.41
20 21 2.159934 CCGACGGAATTCAACACGTAAC 60.160 50.000 8.64 0.00 39.95 2.50
21 22 2.060284 CCGACGGAATTCAACACGTAA 58.940 47.619 8.64 0.00 39.95 3.18
22 23 1.000385 ACCGACGGAATTCAACACGTA 60.000 47.619 23.38 0.00 39.95 3.57
23 24 0.249573 ACCGACGGAATTCAACACGT 60.250 50.000 23.38 7.47 42.88 4.49
24 25 0.162933 CACCGACGGAATTCAACACG 59.837 55.000 23.38 4.05 0.00 4.49
25 26 0.110373 GCACCGACGGAATTCAACAC 60.110 55.000 23.38 0.00 0.00 3.32
26 27 0.250124 AGCACCGACGGAATTCAACA 60.250 50.000 23.38 0.00 0.00 3.33
27 28 0.872388 AAGCACCGACGGAATTCAAC 59.128 50.000 23.38 1.26 0.00 3.18
28 29 0.871722 CAAGCACCGACGGAATTCAA 59.128 50.000 23.38 0.00 0.00 2.69
29 30 0.250124 ACAAGCACCGACGGAATTCA 60.250 50.000 23.38 0.00 0.00 2.57
30 31 0.872388 AACAAGCACCGACGGAATTC 59.128 50.000 23.38 6.13 0.00 2.17
31 32 0.591170 CAACAAGCACCGACGGAATT 59.409 50.000 23.38 9.00 0.00 2.17
32 33 1.852067 GCAACAAGCACCGACGGAAT 61.852 55.000 23.38 2.30 44.79 3.01
44 45 1.679139 TCAACCTGGACAGCAACAAG 58.321 50.000 0.00 0.00 0.00 3.16
45 46 2.158623 AGATCAACCTGGACAGCAACAA 60.159 45.455 0.00 0.00 0.00 2.83
46 47 1.421268 AGATCAACCTGGACAGCAACA 59.579 47.619 0.00 0.00 0.00 3.33
76 77 2.385315 CACCAGCGATGACGTACATAG 58.615 52.381 0.06 0.00 39.56 2.23
111 112 1.034356 TTGGACGGTCACGAGAAAGA 58.966 50.000 10.76 0.00 44.60 2.52
125 126 3.568007 TGTATGTGGCAGAACTTTTGGAC 59.432 43.478 0.00 0.00 0.00 4.02
131 132 1.156736 GCGTGTATGTGGCAGAACTT 58.843 50.000 0.00 0.00 0.00 2.66
132 133 0.673644 GGCGTGTATGTGGCAGAACT 60.674 55.000 0.00 0.00 0.00 3.01
133 134 0.953471 TGGCGTGTATGTGGCAGAAC 60.953 55.000 0.00 0.00 35.55 3.01
135 136 3.064416 TGGCGTGTATGTGGCAGA 58.936 55.556 0.00 0.00 35.55 4.26
137 138 1.375396 GACTGGCGTGTATGTGGCA 60.375 57.895 0.00 0.00 39.03 4.92
138 139 1.079127 AGACTGGCGTGTATGTGGC 60.079 57.895 0.00 0.00 0.00 5.01
139 140 0.532573 AGAGACTGGCGTGTATGTGG 59.467 55.000 0.00 0.00 0.00 4.17
141 142 3.402628 AAAAGAGACTGGCGTGTATGT 57.597 42.857 0.00 0.00 0.00 2.29
142 143 3.865745 CCTAAAAGAGACTGGCGTGTATG 59.134 47.826 0.00 0.00 0.00 2.39
143 144 3.679083 GCCTAAAAGAGACTGGCGTGTAT 60.679 47.826 0.00 0.00 33.96 2.29
147 148 0.685097 TGCCTAAAAGAGACTGGCGT 59.315 50.000 0.00 0.00 45.90 5.68
163 164 1.263356 CCATCCATCCCATGAATGCC 58.737 55.000 0.00 0.00 0.00 4.40
183 184 3.858868 GACTTCACTCGCCGGTGCA 62.859 63.158 11.05 0.00 37.16 4.57
185 186 0.242825 TTAGACTTCACTCGCCGGTG 59.757 55.000 9.28 9.28 38.44 4.94
186 187 0.243095 GTTAGACTTCACTCGCCGGT 59.757 55.000 1.90 0.00 0.00 5.28
187 188 0.526662 AGTTAGACTTCACTCGCCGG 59.473 55.000 0.00 0.00 0.00 6.13
188 189 1.986378 CAAGTTAGACTTCACTCGCCG 59.014 52.381 0.00 0.00 36.03 6.46
204 205 3.443681 CCTTCAAAGACAACACACCAAGT 59.556 43.478 0.00 0.00 0.00 3.16
209 210 1.668751 TCGCCTTCAAAGACAACACAC 59.331 47.619 0.00 0.00 0.00 3.82
221 222 1.227823 CCAACACCTGTCGCCTTCA 60.228 57.895 0.00 0.00 0.00 3.02
223 224 1.227853 GACCAACACCTGTCGCCTT 60.228 57.895 0.00 0.00 0.00 4.35
229 230 0.104304 GTGTCTCGACCAACACCTGT 59.896 55.000 8.95 0.00 39.87 4.00
270 276 3.367646 TTACAACCACAACACAAGGGA 57.632 42.857 0.00 0.00 0.00 4.20
278 284 2.035321 CCACACCCATTACAACCACAAC 59.965 50.000 0.00 0.00 0.00 3.32
285 291 2.695666 CAAACCACCACACCCATTACAA 59.304 45.455 0.00 0.00 0.00 2.41
303 309 2.635915 ACCAGGGTAGTTCGATGACAAA 59.364 45.455 0.00 0.00 0.00 2.83
320 326 1.455383 GACAAGCCAACACCCACCAG 61.455 60.000 0.00 0.00 0.00 4.00
323 329 0.668535 GAAGACAAGCCAACACCCAC 59.331 55.000 0.00 0.00 0.00 4.61
341 347 0.817634 CCACACCGAGGCAAGTTTGA 60.818 55.000 0.00 0.00 0.00 2.69
374 380 1.807142 TGTCGTGAACAACAAGTGCAA 59.193 42.857 0.00 0.00 37.58 4.08
434 441 7.161404 TCAAAGTACATCCAGGCATATCATAC 58.839 38.462 0.00 0.00 0.00 2.39
468 488 3.628832 TCCAAAGGGGGTTTTCAATCT 57.371 42.857 0.00 0.00 37.22 2.40
469 489 6.367374 TTTATCCAAAGGGGGTTTTCAATC 57.633 37.500 0.00 0.00 37.22 2.67
470 490 6.771934 TTTTATCCAAAGGGGGTTTTCAAT 57.228 33.333 0.00 0.00 37.22 2.57
471 491 6.576778 TTTTTATCCAAAGGGGGTTTTCAA 57.423 33.333 0.00 0.00 37.22 2.69
510 532 0.850856 GTTTGTTCGTTCTCGCTCGT 59.149 50.000 0.00 0.00 36.96 4.18
511 533 0.850217 TGTTTGTTCGTTCTCGCTCG 59.150 50.000 0.00 0.00 36.96 5.03
519 541 2.478894 CGGCATAGAGTGTTTGTTCGTT 59.521 45.455 0.00 0.00 0.00 3.85
535 557 0.951558 AGAAAGTGAAAACGCGGCAT 59.048 45.000 12.47 0.00 0.00 4.40
554 576 0.606604 GCCGTTGGAGAGGTAGTTCA 59.393 55.000 0.00 0.00 0.00 3.18
571 593 2.468831 TGATTTGTTTGCGAGTTTGCC 58.531 42.857 0.00 0.00 0.00 4.52
589 611 8.450964 GGAGAATCATATTTTCGTTTCTGTTGA 58.549 33.333 0.00 0.00 36.25 3.18
594 616 7.338710 TGAGGGAGAATCATATTTTCGTTTCT 58.661 34.615 0.00 0.00 36.25 2.52
650 672 7.095982 CGGTGGTACATTTTGTTTAAACCATTC 60.096 37.037 15.59 1.00 44.52 2.67
871 916 3.043418 GGGAGGTGGTATTTGTAGCCTA 58.957 50.000 0.00 0.00 0.00 3.93
1063 1160 2.283101 GCCATGGCACTCCACCAA 60.283 61.111 32.08 0.00 46.92 3.67
1465 1613 1.601419 TAAACCTGACCGAGCCCGAG 61.601 60.000 0.00 0.00 38.22 4.63
1634 1815 2.575461 GCTGGTGGAAATGGCTGC 59.425 61.111 0.00 0.00 0.00 5.25
1707 1891 1.038280 GGGAGAACGGGTATGACGAT 58.962 55.000 0.00 0.00 34.93 3.73
1819 2021 2.124983 GCCATCCAGAAGCTGCGA 60.125 61.111 0.00 0.00 0.00 5.10
1943 2224 7.201732 CCATTGCTAATTCAGTTCGGACTTTAT 60.202 37.037 0.00 0.00 32.54 1.40
1945 2226 5.106157 CCATTGCTAATTCAGTTCGGACTTT 60.106 40.000 0.00 0.00 32.54 2.66
1951 2232 4.191544 TCTCCCATTGCTAATTCAGTTCG 58.808 43.478 0.00 0.00 0.00 3.95
1991 2294 4.453819 AGAAGAAAGAAGCAAATCGTCAGG 59.546 41.667 0.00 0.00 0.00 3.86
2162 2493 7.479980 GCTTGATGTTACTTGGCATATTTGTA 58.520 34.615 0.00 0.00 0.00 2.41
2165 2496 5.125417 ACGCTTGATGTTACTTGGCATATTT 59.875 36.000 0.00 0.00 0.00 1.40
2166 2497 4.640201 ACGCTTGATGTTACTTGGCATATT 59.360 37.500 0.00 0.00 0.00 1.28
2168 2499 3.605634 ACGCTTGATGTTACTTGGCATA 58.394 40.909 0.00 0.00 0.00 3.14
2173 2504 4.661993 TTGCTACGCTTGATGTTACTTG 57.338 40.909 0.00 0.00 0.00 3.16
2174 2505 4.377022 CGTTTGCTACGCTTGATGTTACTT 60.377 41.667 0.00 0.00 44.26 2.24
2210 2541 3.471620 TCCATCCCGGAGCATAGC 58.528 61.111 0.73 0.00 39.64 2.97
2220 2555 4.335416 TGATTGTTCAACTTCTCCATCCC 58.665 43.478 0.00 0.00 0.00 3.85
2245 2580 6.256757 GGAAATTTGTTTTGGTCATCGTTTCA 59.743 34.615 0.00 0.00 0.00 2.69
2246 2581 6.256757 TGGAAATTTGTTTTGGTCATCGTTTC 59.743 34.615 0.00 0.00 0.00 2.78
2250 2585 4.150451 GCTGGAAATTTGTTTTGGTCATCG 59.850 41.667 0.00 0.00 0.00 3.84
2252 2587 5.033589 TGCTGGAAATTTGTTTTGGTCAT 57.966 34.783 0.00 0.00 0.00 3.06
2269 2604 5.567224 TTCATACATGAAAGCCTTTTGCTGG 60.567 40.000 0.00 0.00 44.58 4.85
2463 2808 5.687770 TCACGAATGCTTCTTGAATTCAA 57.312 34.783 19.45 19.45 40.07 2.69
2498 2849 8.233190 ACGATGAACTTTTTCAAAATTGCAAAA 58.767 25.926 1.71 4.19 45.01 2.44
2509 2860 4.886247 AAACGGACGATGAACTTTTTCA 57.114 36.364 0.00 0.00 45.93 2.69
2510 2861 6.652245 TCTTAAACGGACGATGAACTTTTTC 58.348 36.000 0.00 0.00 0.00 2.29
2511 2862 6.607735 TCTTAAACGGACGATGAACTTTTT 57.392 33.333 0.00 0.00 0.00 1.94
2512 2863 6.607735 TTCTTAAACGGACGATGAACTTTT 57.392 33.333 0.00 0.00 0.00 2.27
2513 2864 6.607735 TTTCTTAAACGGACGATGAACTTT 57.392 33.333 0.00 0.00 0.00 2.66
2514 2865 6.204108 ACATTTCTTAAACGGACGATGAACTT 59.796 34.615 0.00 0.00 0.00 2.66
2515 2866 5.699458 ACATTTCTTAAACGGACGATGAACT 59.301 36.000 0.00 0.00 0.00 3.01
2516 2867 5.923665 ACATTTCTTAAACGGACGATGAAC 58.076 37.500 0.00 0.00 0.00 3.18
2517 2868 6.203145 TGAACATTTCTTAAACGGACGATGAA 59.797 34.615 0.00 0.00 0.00 2.57
2518 2869 5.697178 TGAACATTTCTTAAACGGACGATGA 59.303 36.000 0.00 0.00 0.00 2.92
2519 2870 5.922546 TGAACATTTCTTAAACGGACGATG 58.077 37.500 0.00 0.00 0.00 3.84
2520 2871 6.542852 CATGAACATTTCTTAAACGGACGAT 58.457 36.000 0.00 0.00 0.00 3.73
2521 2872 5.615984 GCATGAACATTTCTTAAACGGACGA 60.616 40.000 0.00 0.00 0.00 4.20
2522 2873 4.553429 GCATGAACATTTCTTAAACGGACG 59.447 41.667 0.00 0.00 0.00 4.79
2523 2874 5.457140 TGCATGAACATTTCTTAAACGGAC 58.543 37.500 0.00 0.00 0.00 4.79
2524 2875 5.240623 ACTGCATGAACATTTCTTAAACGGA 59.759 36.000 0.00 0.00 0.00 4.69
2525 2876 5.343058 CACTGCATGAACATTTCTTAAACGG 59.657 40.000 0.00 0.00 0.00 4.44
2526 2877 5.914635 ACACTGCATGAACATTTCTTAAACG 59.085 36.000 0.00 0.00 0.00 3.60
2527 2878 8.795786 TTACACTGCATGAACATTTCTTAAAC 57.204 30.769 0.00 0.00 0.00 2.01
2528 2879 9.809096 TTTTACACTGCATGAACATTTCTTAAA 57.191 25.926 0.00 0.00 0.00 1.52
2529 2880 9.809096 TTTTTACACTGCATGAACATTTCTTAA 57.191 25.926 0.00 0.00 0.00 1.85
2566 2917 5.240623 ACTGCATGAACATTTCTTAAACGGA 59.759 36.000 0.00 0.00 0.00 4.69
2691 3044 9.495572 TGGAACAGTTGTTTTACAAAAGATTTT 57.504 25.926 0.00 0.00 40.15 1.82
2753 3108 9.781834 GACATAAACATATTTTGAAATGGACGA 57.218 29.630 0.00 0.00 0.00 4.20
2754 3109 9.566530 TGACATAAACATATTTTGAAATGGACG 57.433 29.630 0.00 0.00 0.00 4.79
2851 3211 9.900710 ATTTTGTTAAATGCGTGAACACTATTA 57.099 25.926 6.23 0.00 32.98 0.98
2854 3214 7.616103 CATTTTGTTAAATGCGTGAACACTA 57.384 32.000 6.23 0.00 42.85 2.74


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

AutoCloner maintained by Alex Coulton.