Multiple sequence alignment - TraesCS7A01G103600

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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 TraesCS7A01G103600 chr7A 100.000 3346 0 0 1 3346 63385411 63382066 0.000000e+00 6180.0
1 TraesCS7A01G103600 chr7A 91.966 585 47 0 1414 1998 63378416 63379000 0.000000e+00 821.0
2 TraesCS7A01G103600 chr7A 89.590 586 58 1 1415 1997 31592096 31592681 0.000000e+00 741.0
3 TraesCS7A01G103600 chr7A 85.642 397 40 11 1012 1393 63377965 63378359 5.200000e-108 401.0
4 TraesCS7A01G103600 chr7A 100.000 30 0 0 3239 3268 430757427 430757398 4.660000e-04 56.5
5 TraesCS7A01G103600 chr7D 92.965 1322 56 14 864 2160 58843443 58842134 0.000000e+00 1892.0
6 TraesCS7A01G103600 chr7D 92.637 584 43 0 1414 1997 58829830 58830413 0.000000e+00 841.0
7 TraesCS7A01G103600 chr7D 87.563 595 62 3 1415 1997 31119637 31120231 0.000000e+00 678.0
8 TraesCS7A01G103600 chr7D 86.395 588 48 14 2 581 58846171 58845608 6.140000e-172 614.0
9 TraesCS7A01G103600 chr7D 93.069 303 13 6 559 860 58843790 58843495 1.430000e-118 436.0
10 TraesCS7A01G103600 chr7D 85.219 433 31 13 2400 2805 58834627 58834201 6.680000e-112 414.0
11 TraesCS7A01G103600 chr7D 80.916 524 57 24 2730 3228 58832679 58832174 1.130000e-99 374.0
12 TraesCS7A01G103600 chr7D 84.615 364 28 16 1022 1360 58829385 58829745 1.490000e-88 337.0
13 TraesCS7A01G103600 chr7D 89.370 254 12 3 2146 2384 58842116 58841863 4.190000e-79 305.0
14 TraesCS7A01G103600 chr7D 85.345 116 16 1 2271 2385 58833551 58833436 5.860000e-23 119.0
15 TraesCS7A01G103600 chr7D 96.970 33 1 0 798 830 58829011 58829043 4.660000e-04 56.5
16 TraesCS7A01G103600 chr4A 90.470 808 44 14 1413 2199 675955098 675954303 0.000000e+00 1035.0
17 TraesCS7A01G103600 chr4A 93.857 586 36 0 1413 1998 675932608 675933193 0.000000e+00 883.0
18 TraesCS7A01G103600 chr4A 84.161 846 74 28 2540 3345 675951468 675950643 0.000000e+00 765.0
19 TraesCS7A01G103600 chr4A 89.273 550 36 9 873 1401 675955694 675955147 0.000000e+00 667.0
20 TraesCS7A01G103600 chr4A 83.184 446 53 14 2791 3228 675960241 675959810 4.050000e-104 388.0
21 TraesCS7A01G103600 chr4A 80.906 508 76 14 16 516 675957460 675956967 6.770000e-102 381.0
22 TraesCS7A01G103600 chr4A 85.759 323 19 18 534 852 675956065 675955766 1.940000e-82 316.0
23 TraesCS7A01G103600 chr4A 89.712 243 19 2 1124 1360 675932278 675932520 4.190000e-79 305.0
24 TraesCS7A01G103600 chr4A 88.793 116 9 4 2271 2385 675962239 675962127 4.500000e-29 139.0
25 TraesCS7A01G103600 chr4A 84.211 114 17 1 2271 2383 675961229 675961116 3.530000e-20 110.0
26 TraesCS7A01G103600 chr5B 87.100 876 93 13 1140 1997 27813040 27813913 0.000000e+00 974.0
27 TraesCS7A01G103600 chr5B 95.122 41 1 1 3241 3280 34747227 34747267 2.790000e-06 63.9
28 TraesCS7A01G103600 chr5D 86.740 905 80 20 1140 2010 37201806 37202704 0.000000e+00 970.0
29 TraesCS7A01G103600 chr5D 78.673 211 29 9 3 207 539864803 539864603 3.500000e-25 126.0
30 TraesCS7A01G103600 chr2D 88.608 158 16 2 55 211 391105433 391105277 1.230000e-44 191.0
31 TraesCS7A01G103600 chr2D 81.340 209 27 10 4 204 59656562 59656358 3.460000e-35 159.0
32 TraesCS7A01G103600 chr6D 81.019 216 24 12 2 207 81104660 81104452 4.470000e-34 156.0
33 TraesCS7A01G103600 chr6D 90.000 50 5 0 3222 3271 89164064 89164015 7.750000e-07 65.8
34 TraesCS7A01G103600 chr2A 81.714 175 22 9 16 182 535338690 535338862 1.620000e-28 137.0
35 TraesCS7A01G103600 chr1A 80.000 205 23 15 2 196 553948674 553948478 5.820000e-28 135.0
36 TraesCS7A01G103600 chr3A 78.818 203 36 5 17 212 745890286 745890084 2.710000e-26 130.0
37 TraesCS7A01G103600 chr4B 82.400 125 17 4 2594 2714 38366513 38366390 1.640000e-18 104.0
38 TraesCS7A01G103600 chr6B 90.000 50 5 0 3218 3267 661073187 661073236 7.750000e-07 65.8


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 TraesCS7A01G103600 chr7A 63382066 63385411 3345 True 6180.000000 6180 100.000000 1 3346 1 chr7A.!!$R1 3345
1 TraesCS7A01G103600 chr7A 31592096 31592681 585 False 741.000000 741 89.590000 1415 1997 1 chr7A.!!$F1 582
2 TraesCS7A01G103600 chr7A 63377965 63379000 1035 False 611.000000 821 88.804000 1012 1998 2 chr7A.!!$F2 986
3 TraesCS7A01G103600 chr7D 58841863 58846171 4308 True 811.750000 1892 90.449750 2 2384 4 chr7D.!!$R2 2382
4 TraesCS7A01G103600 chr7D 31119637 31120231 594 False 678.000000 678 87.563000 1415 1997 1 chr7D.!!$F1 582
5 TraesCS7A01G103600 chr7D 58829011 58830413 1402 False 411.500000 841 91.407333 798 1997 3 chr7D.!!$F2 1199
6 TraesCS7A01G103600 chr7D 58832174 58834627 2453 True 302.333333 414 83.826667 2271 3228 3 chr7D.!!$R1 957
7 TraesCS7A01G103600 chr4A 675932278 675933193 915 False 594.000000 883 91.784500 1124 1998 2 chr4A.!!$F1 874
8 TraesCS7A01G103600 chr4A 675950643 675962239 11596 True 475.125000 1035 85.844625 16 3345 8 chr4A.!!$R1 3329
9 TraesCS7A01G103600 chr5B 27813040 27813913 873 False 974.000000 974 87.100000 1140 1997 1 chr5B.!!$F1 857
10 TraesCS7A01G103600 chr5D 37201806 37202704 898 False 970.000000 970 86.740000 1140 2010 1 chr5D.!!$F1 870

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
233 5006 0.091678 GCAATGACAATTTGCACGCG 59.908 50.000 3.53 3.53 46.78 6.01 F
234 5007 0.091678 CAATGACAATTTGCACGCGC 59.908 50.000 5.73 0.00 39.24 6.86 F
256 5029 0.387622 GCGCACACAGACAAATGCAT 60.388 50.000 0.30 0.00 37.97 3.96 F
2045 9849 1.002576 TGCGTGCTCATTGTTGTTCTG 60.003 47.619 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 8991 0.324460 ACTGGCCGTAGAGGTAGCTT 60.324 55.000 0.0 0.0 43.70 3.74 R
2158 10004 1.053424 TTTGTACCTGGCCGAGACTT 58.947 50.000 0.0 0.0 0.00 3.01 R
2196 10042 1.998315 CAAGAGTCAATCGACAGCCAG 59.002 52.381 0.0 0.0 45.23 4.85 R
3198 14954 2.249309 CACGTCGGCACAAGCAAG 59.751 61.111 0.0 0.0 44.61 4.01 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
183 4956 3.070878 AGTGGCATTGGTTTTACCCTTTG 59.929 43.478 0.00 0.00 37.50 2.77
233 5006 0.091678 GCAATGACAATTTGCACGCG 59.908 50.000 3.53 3.53 46.78 6.01
234 5007 0.091678 CAATGACAATTTGCACGCGC 59.908 50.000 5.73 0.00 39.24 6.86
235 5008 1.336403 AATGACAATTTGCACGCGCG 61.336 50.000 30.96 30.96 42.97 6.86
256 5029 0.387622 GCGCACACAGACAAATGCAT 60.388 50.000 0.30 0.00 37.97 3.96
288 5061 9.450807 AAAAATATGCAAGAATAAGCGTATGAC 57.549 29.630 0.00 0.00 40.90 3.06
345 5118 7.503566 AGGAATGGATTAGTGTCATTGGTATTG 59.496 37.037 0.00 0.00 32.05 1.90
357 5130 9.289303 GTGTCATTGGTATTGCACTTAAATAAG 57.711 33.333 0.00 0.00 39.18 1.73
363 5136 9.921637 TTGGTATTGCACTTAAATAAGGAAAAG 57.078 29.630 5.27 0.00 37.62 2.27
388 5161 7.865889 AGAAAAAGTAAAGCGGAACCAAAATAG 59.134 33.333 0.00 0.00 0.00 1.73
447 5221 9.830975 ATGGCATTTGTATTACCCTTTAAAATC 57.169 29.630 0.00 0.00 0.00 2.17
485 5260 9.603298 AAAGAAATCGAAATAACGAGGTTTTAC 57.397 29.630 0.00 0.00 45.22 2.01
505 5280 7.831691 TTTACAAGGAAGAATGAATTGGTGA 57.168 32.000 0.00 0.00 0.00 4.02
507 6130 4.216257 ACAAGGAAGAATGAATTGGTGACG 59.784 41.667 0.00 0.00 0.00 4.35
542 6165 9.454859 ACTCTTCAAGAAGAAAGAAAGAAAGAA 57.545 29.630 13.04 0.00 45.75 2.52
724 8225 4.995487 TCTGAAAGCGAGCGAGAGTATATA 59.005 41.667 0.00 0.00 0.00 0.86
726 8227 5.631992 TGAAAGCGAGCGAGAGTATATATG 58.368 41.667 0.00 0.00 0.00 1.78
727 8228 4.624336 AAGCGAGCGAGAGTATATATGG 57.376 45.455 0.00 0.00 0.00 2.74
860 8361 1.219664 CCTCGGTTATGGCAACGGA 59.780 57.895 0.00 0.00 42.51 4.69
862 8363 1.429148 CTCGGTTATGGCAACGGAGC 61.429 60.000 12.18 0.00 39.54 4.70
1070 8750 1.222387 CCTCCTCGTCCTCGTCTCT 59.778 63.158 0.00 0.00 38.33 3.10
1323 9042 3.717294 AAGCTCGTCCCCGGCAAT 61.717 61.111 0.00 0.00 34.17 3.56
1369 9093 1.134226 CGTACGTATTCCATTCCCGC 58.866 55.000 7.22 0.00 0.00 6.13
1654 9433 4.379243 CTCCGCTGCTTCACCCGT 62.379 66.667 0.00 0.00 0.00 5.28
1661 9440 4.681978 GCTTCACCCGTCACGCCT 62.682 66.667 0.00 0.00 0.00 5.52
2035 9839 3.381983 TCGTCCCTGCGTGCTCAT 61.382 61.111 0.00 0.00 0.00 2.90
2036 9840 2.434884 CGTCCCTGCGTGCTCATT 60.435 61.111 0.00 0.00 0.00 2.57
2037 9841 2.743752 CGTCCCTGCGTGCTCATTG 61.744 63.158 0.00 0.00 0.00 2.82
2045 9849 1.002576 TGCGTGCTCATTGTTGTTCTG 60.003 47.619 0.00 0.00 0.00 3.02
2050 9854 4.232221 GTGCTCATTGTTGTTCTGATTGG 58.768 43.478 0.00 0.00 0.00 3.16
2072 9876 2.654863 CTGTGGTTTCTTGGTTCACCT 58.345 47.619 0.00 0.00 36.82 4.00
2078 9882 4.349636 TGGTTTCTTGGTTCACCTCTGATA 59.650 41.667 0.00 0.00 36.82 2.15
2079 9883 5.014123 TGGTTTCTTGGTTCACCTCTGATAT 59.986 40.000 0.00 0.00 36.82 1.63
2108 9912 2.097036 CTGATCTGCCATTTTGCCTCA 58.903 47.619 0.00 0.00 0.00 3.86
2184 10030 1.495951 GCCAGGTACAAACGAAGCG 59.504 57.895 0.00 0.00 0.00 4.68
2196 10042 4.153256 CAAACGAAGCGTAAACAATACCC 58.847 43.478 0.00 0.00 39.99 3.69
2321 13017 5.957798 TCTAGTGAACAAATACCCTACACG 58.042 41.667 0.00 0.00 33.00 4.49
2337 13033 5.391950 CCCTACACGTTCCATCATTTTCAAG 60.392 44.000 0.00 0.00 0.00 3.02
2342 13038 6.207417 ACACGTTCCATCATTTTCAAGAGAAT 59.793 34.615 0.00 0.00 32.89 2.40
2347 13043 9.525409 GTTCCATCATTTTCAAGAGAATAATGG 57.475 33.333 8.51 8.51 35.43 3.16
2385 13666 9.565213 CCATGTGCAAAATGAAAAACTTTTTAA 57.435 25.926 11.33 0.00 31.34 1.52
2409 14064 6.018469 AGATGTCCTTTGAATTTTCCATGGA 58.982 36.000 11.44 11.44 0.00 3.41
2422 14077 9.921637 GAATTTTCCATGGAAACTACAAATACA 57.078 29.630 34.50 18.89 42.88 2.29
2434 14089 9.357652 GAAACTACAAATACAATGTCATTGCAT 57.642 29.630 22.79 14.39 43.98 3.96
2444 14099 7.876936 ACAATGTCATTGCATCTTAAGATCT 57.123 32.000 22.79 0.00 43.98 2.75
2446 14101 9.399797 ACAATGTCATTGCATCTTAAGATCTAA 57.600 29.630 22.79 12.93 43.98 2.10
2451 14106 9.890352 GTCATTGCATCTTAAGATCTAATTTCC 57.110 33.333 15.24 5.72 31.21 3.13
2455 14110 8.442632 TGCATCTTAAGATCTAATTTCCTGTG 57.557 34.615 15.24 2.54 31.21 3.66
2470 14125 7.736447 ATTTCCTGTGTCTAGAGAAACAAAG 57.264 36.000 4.16 0.52 41.37 2.77
2473 14128 6.650120 TCCTGTGTCTAGAGAAACAAAGTTT 58.350 36.000 4.16 0.00 41.37 2.66
2478 14133 7.556275 TGTGTCTAGAGAAACAAAGTTTCCATT 59.444 33.333 16.49 7.40 39.20 3.16
2500 14155 9.316730 CCATTCTTTGTTCAAAATATACCATGG 57.683 33.333 11.19 11.19 0.00 3.66
2515 14170 8.725606 ATATACCATGGCATAAACTTTTCCAT 57.274 30.769 13.04 0.00 37.99 3.41
2521 14176 4.754114 TGGCATAAACTTTTCCATGTTTGC 59.246 37.500 0.00 0.00 37.06 3.68
2525 14180 6.402442 GCATAAACTTTTCCATGTTTGCCATC 60.402 38.462 0.00 0.00 37.06 3.51
2535 14190 6.632909 TCCATGTTTGCCATCATTTTTAGAG 58.367 36.000 0.00 0.00 0.00 2.43
2537 14192 7.039152 TCCATGTTTGCCATCATTTTTAGAGAA 60.039 33.333 0.00 0.00 0.00 2.87
2604 14259 9.943163 GTGTAACATGGCAAATTTTATTTTTGT 57.057 25.926 0.00 0.00 35.16 2.83
2657 14328 6.039717 GGCAAGGTTATTTTATCTGAGCATGA 59.960 38.462 0.00 0.00 0.00 3.07
2708 14401 4.412796 TCATTGTTTGGACATGGCAAAA 57.587 36.364 0.00 0.00 35.29 2.44
2709 14402 4.774124 TCATTGTTTGGACATGGCAAAAA 58.226 34.783 1.57 0.00 35.29 1.94
2827 14574 5.649782 AATGAACCATGGCTACTTTTCTG 57.350 39.130 13.04 0.00 0.00 3.02
2834 14581 6.775708 ACCATGGCTACTTTTCTGTAGTTTA 58.224 36.000 13.04 0.00 41.27 2.01
2891 14638 9.333497 GGACATTTTATTAGTTTAAACACGGTC 57.667 33.333 20.06 12.28 0.00 4.79
2902 14652 7.932335 AGTTTAAACACGGTCAAAATGTATGA 58.068 30.769 20.06 0.00 0.00 2.15
2918 14668 9.438163 AAAATGTATGATTAGACCATGGGAAAT 57.562 29.630 18.09 12.11 0.00 2.17
3007 14761 7.793927 TCGCACACACCATCATAAATTATTA 57.206 32.000 0.00 0.00 0.00 0.98
3048 14802 7.953158 TTGAAACATGACAACTTTGTTGAAA 57.047 28.000 16.04 5.19 42.43 2.69
3052 14806 8.600449 AAACATGACAACTTTGTTGAAAAGAA 57.400 26.923 16.04 0.00 42.43 2.52
3060 14814 7.812669 ACAACTTTGTTGAAAAGAACCTTGTAG 59.187 33.333 16.04 0.00 38.47 2.74
3173 14929 9.859427 TTGCCATCTTTCTTTTATATGAAACAG 57.141 29.630 0.00 0.00 0.00 3.16
3180 14936 9.474920 CTTTCTTTTATATGAAACAGTGGCAAA 57.525 29.630 0.00 0.00 0.00 3.68
3198 14954 7.651704 AGTGGCAAACATAAGTTGAAACATAAC 59.348 33.333 0.00 0.00 38.17 1.89
3207 14963 8.693504 CATAAGTTGAAACATAACTTGCTTGTG 58.306 33.333 12.02 0.00 45.22 3.33
3212 14968 1.535462 ACATAACTTGCTTGTGCCGAC 59.465 47.619 0.00 0.00 38.71 4.79
3213 14969 0.796312 ATAACTTGCTTGTGCCGACG 59.204 50.000 0.00 0.00 38.71 5.12
3232 14988 3.340928 ACGTGGCTTAAAACATACTCCC 58.659 45.455 0.00 0.00 0.00 4.30
3237 14993 3.128764 GGCTTAAAACATACTCCCTGTGC 59.871 47.826 0.00 0.00 0.00 4.57
3240 14996 5.449177 GCTTAAAACATACTCCCTGTGCATC 60.449 44.000 0.00 0.00 0.00 3.91
3250 15006 6.949352 ACTCCCTGTGCATCAAAATATAAG 57.051 37.500 0.00 0.00 0.00 1.73
3253 15009 6.422333 TCCCTGTGCATCAAAATATAAGACA 58.578 36.000 0.00 0.00 0.00 3.41
3292 15048 7.011950 TGGTAGTGTCAAAAGGCGAATTATATG 59.988 37.037 0.00 0.00 0.00 1.78
3297 15053 7.218204 GTGTCAAAAGGCGAATTATATGTTGAC 59.782 37.037 0.00 0.00 41.56 3.18
3304 15060 5.106555 GGCGAATTATATGTTGACATGGAGG 60.107 44.000 6.87 0.00 37.15 4.30
3313 15069 5.255397 TGTTGACATGGAGGGAGTATTTT 57.745 39.130 0.00 0.00 0.00 1.82
3315 15071 6.785076 TGTTGACATGGAGGGAGTATTTTTA 58.215 36.000 0.00 0.00 0.00 1.52
3317 15073 7.393234 TGTTGACATGGAGGGAGTATTTTTAAG 59.607 37.037 0.00 0.00 0.00 1.85
3321 15080 8.721133 ACATGGAGGGAGTATTTTTAAGTTTT 57.279 30.769 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 4656 2.104281 AGGGTAATACCAAAGCCGCTAG 59.896 50.000 12.03 0.00 41.02 3.42
118 4890 9.937577 GAAACATTATTACGTTCATTTTGCTTC 57.062 29.630 0.00 0.00 0.00 3.86
234 5007 3.578089 ATTTGTCTGTGTGCGCGCG 62.578 57.895 28.44 28.44 0.00 6.86
235 5008 2.076628 CATTTGTCTGTGTGCGCGC 61.077 57.895 27.26 27.26 0.00 6.86
237 5010 0.387622 ATGCATTTGTCTGTGTGCGC 60.388 50.000 0.00 0.00 40.34 6.09
239 5012 4.799419 AAAAATGCATTTGTCTGTGTGC 57.201 36.364 24.74 0.00 38.05 4.57
309 5082 9.442047 GACACTAATCCATTCCTTCTTATATGG 57.558 37.037 0.00 0.00 39.09 2.74
313 5086 9.347240 CAATGACACTAATCCATTCCTTCTTAT 57.653 33.333 0.00 0.00 0.00 1.73
357 5130 5.461078 GGTTCCGCTTTACTTTTTCTTTTCC 59.539 40.000 0.00 0.00 0.00 3.13
363 5136 6.838198 ATTTTGGTTCCGCTTTACTTTTTC 57.162 33.333 0.00 0.00 0.00 2.29
366 5139 5.466819 GCTATTTTGGTTCCGCTTTACTTT 58.533 37.500 0.00 0.00 0.00 2.66
369 5142 3.125658 TCGCTATTTTGGTTCCGCTTTAC 59.874 43.478 0.00 0.00 0.00 2.01
412 5185 9.777297 GGGTAATACAAATGCCATTGATTTATT 57.223 29.630 5.66 0.00 34.38 1.40
413 5186 9.158097 AGGGTAATACAAATGCCATTGATTTAT 57.842 29.630 5.66 0.00 34.38 1.40
419 5192 9.442047 TTTTAAAGGGTAATACAAATGCCATTG 57.558 29.630 0.00 0.00 36.37 2.82
457 5231 7.429636 AACCTCGTTATTTCGATTTCTTTCA 57.570 32.000 0.00 0.00 39.12 2.69
458 5232 8.723777 AAAACCTCGTTATTTCGATTTCTTTC 57.276 30.769 0.00 0.00 39.12 2.62
468 5243 8.091385 TCTTCCTTGTAAAACCTCGTTATTTC 57.909 34.615 0.00 0.00 0.00 2.17
485 5260 4.216257 ACGTCACCAATTCATTCTTCCTTG 59.784 41.667 0.00 0.00 0.00 3.61
505 5280 9.706691 TTTCTTCTTGAAGAGTAATATCAACGT 57.293 29.630 12.11 0.00 35.89 3.99
572 6233 4.384846 GTGACGTGTACATTGACTACAAGG 59.615 45.833 0.00 0.00 42.45 3.61
581 6242 1.225368 GCGCGTGACGTGTACATTG 60.225 57.895 20.13 0.00 46.11 2.82
583 6244 2.758770 AAGGCGCGTGACGTGTACAT 62.759 55.000 20.13 3.99 46.11 2.29
700 8201 0.170116 ACTCTCGCTCGCTTTCAGAG 59.830 55.000 4.18 4.18 37.27 3.35
713 8214 2.479730 GCACGGGCCATATATACTCTCG 60.480 54.545 4.39 0.00 0.00 4.04
724 8225 1.526575 CTGTCTTTTGCACGGGCCAT 61.527 55.000 7.46 0.00 40.13 4.40
726 8227 2.644992 CTGTCTTTTGCACGGGCC 59.355 61.111 7.46 0.00 40.13 5.80
727 8228 2.050077 GCTGTCTTTTGCACGGGC 60.050 61.111 0.34 0.34 41.68 6.13
860 8361 1.281960 CGACGACGGGATTATCGCT 59.718 57.895 7.64 0.00 42.12 4.93
862 8363 0.305617 TGACGACGACGGGATTATCG 59.694 55.000 12.58 0.32 44.46 2.92
942 8610 2.577112 CGCTCGTTCGATGCTCGT 60.577 61.111 12.00 0.00 41.35 4.18
1008 8682 2.086251 TAGTGCGGTCGGTTCGGTTT 62.086 55.000 0.00 0.00 0.00 3.27
1009 8683 2.086251 TTAGTGCGGTCGGTTCGGTT 62.086 55.000 0.00 0.00 0.00 4.44
1272 8991 0.324460 ACTGGCCGTAGAGGTAGCTT 60.324 55.000 0.00 0.00 43.70 3.74
1386 9111 6.034591 GCAATGGCATCAGAAATCTATATGC 58.965 40.000 16.08 16.08 40.74 3.14
1654 9433 2.056223 GTAGGGCAGGTAGGCGTGA 61.056 63.158 0.00 0.00 45.36 4.35
1743 9528 1.375326 GACCAGTCCACCTTCACCC 59.625 63.158 0.00 0.00 0.00 4.61
2026 9830 1.264020 TCAGAACAACAATGAGCACGC 59.736 47.619 0.00 0.00 0.00 5.34
2030 9834 3.248266 GCCAATCAGAACAACAATGAGC 58.752 45.455 0.00 0.00 0.00 4.26
2032 9836 3.256383 CAGGCCAATCAGAACAACAATGA 59.744 43.478 5.01 0.00 0.00 2.57
2033 9837 3.006110 ACAGGCCAATCAGAACAACAATG 59.994 43.478 5.01 0.00 0.00 2.82
2035 9839 2.361757 CACAGGCCAATCAGAACAACAA 59.638 45.455 5.01 0.00 0.00 2.83
2036 9840 1.955778 CACAGGCCAATCAGAACAACA 59.044 47.619 5.01 0.00 0.00 3.33
2037 9841 1.270550 CCACAGGCCAATCAGAACAAC 59.729 52.381 5.01 0.00 0.00 3.32
2045 9849 1.273327 CCAAGAAACCACAGGCCAATC 59.727 52.381 5.01 0.00 0.00 2.67
2050 9854 1.067060 GTGAACCAAGAAACCACAGGC 59.933 52.381 0.00 0.00 0.00 4.85
2072 9876 5.653330 GCAGATCAGATCAGAGGATATCAGA 59.347 44.000 13.14 0.00 32.67 3.27
2078 9882 2.973710 TGGCAGATCAGATCAGAGGAT 58.026 47.619 13.14 0.00 36.13 3.24
2079 9883 2.466547 TGGCAGATCAGATCAGAGGA 57.533 50.000 13.14 0.00 0.00 3.71
2108 9912 5.241403 TCAAGAACAGTACATGGGAATGT 57.759 39.130 0.00 0.00 38.49 2.71
2158 10004 1.053424 TTTGTACCTGGCCGAGACTT 58.947 50.000 0.00 0.00 0.00 3.01
2184 10030 2.676342 CGACAGCCAGGGTATTGTTTAC 59.324 50.000 0.00 0.00 0.00 2.01
2196 10042 1.998315 CAAGAGTCAATCGACAGCCAG 59.002 52.381 0.00 0.00 45.23 4.85
2280 12976 5.694910 CACTAGAGACAACATAAACAACCGT 59.305 40.000 0.00 0.00 0.00 4.83
2321 13017 9.525409 CCATTATTCTCTTGAAAATGATGGAAC 57.475 33.333 12.41 0.00 45.20 3.62
2337 13033 9.252962 CATGGCAAAATTAAGACCATTATTCTC 57.747 33.333 0.00 0.00 39.08 2.87
2342 13038 6.105333 GCACATGGCAAAATTAAGACCATTA 58.895 36.000 0.00 0.00 43.97 1.90
2385 13666 6.018469 TCCATGGAAAATTCAAAGGACATCT 58.982 36.000 13.46 0.00 0.00 2.90
2387 13668 6.684897 TTCCATGGAAAATTCAAAGGACAT 57.315 33.333 25.13 0.00 0.00 3.06
2388 13669 6.099557 AGTTTCCATGGAAAATTCAAAGGACA 59.900 34.615 35.70 11.58 44.40 4.02
2389 13670 6.524734 AGTTTCCATGGAAAATTCAAAGGAC 58.475 36.000 35.70 22.05 44.40 3.85
2392 14039 8.885494 TTGTAGTTTCCATGGAAAATTCAAAG 57.115 30.769 36.46 4.46 42.08 2.77
2409 14064 9.357652 GATGCAATGACATTGTATTTGTAGTTT 57.642 29.630 26.18 7.79 43.99 2.66
2443 14098 8.833231 TTGTTTCTCTAGACACAGGAAATTAG 57.167 34.615 7.21 0.00 36.29 1.73
2444 14099 9.273016 CTTTGTTTCTCTAGACACAGGAAATTA 57.727 33.333 7.21 0.00 36.29 1.40
2446 14101 7.283329 ACTTTGTTTCTCTAGACACAGGAAAT 58.717 34.615 7.21 0.00 36.29 2.17
2451 14106 6.538742 TGGAAACTTTGTTTCTCTAGACACAG 59.461 38.462 18.59 0.00 36.29 3.66
2455 14110 8.384607 AGAATGGAAACTTTGTTTCTCTAGAC 57.615 34.615 18.59 5.82 0.00 2.59
2478 14133 7.473735 TGCCATGGTATATTTTGAACAAAGA 57.526 32.000 14.67 0.00 0.00 2.52
2500 14155 4.754114 TGGCAAACATGGAAAAGTTTATGC 59.246 37.500 0.00 0.00 36.28 3.14
2515 14170 7.048629 TGTTCTCTAAAAATGATGGCAAACA 57.951 32.000 0.00 0.00 0.00 2.83
2604 14259 8.871125 TGGTTAAAAAGGTAAATTTGCCATAGA 58.129 29.630 24.85 5.63 35.15 1.98
2606 14261 9.442047 CATGGTTAAAAAGGTAAATTTGCCATA 57.558 29.630 24.85 10.88 35.65 2.74
2657 14328 8.970859 TCCATGGTTCAAACAAATAAAAATGT 57.029 26.923 12.58 0.00 0.00 2.71
2887 14634 6.918892 TGGTCTAATCATACATTTTGACCG 57.081 37.500 10.24 0.00 43.84 4.79
2891 14638 7.822161 TCCCATGGTCTAATCATACATTTTG 57.178 36.000 11.73 0.00 0.00 2.44
2894 14641 9.438163 AAATTTCCCATGGTCTAATCATACATT 57.562 29.630 11.73 0.00 0.00 2.71
2895 14642 9.438163 AAAATTTCCCATGGTCTAATCATACAT 57.562 29.630 11.73 0.00 0.00 2.29
3019 14773 9.609950 CAACAAAGTTGTCATGTTTCAAATTTT 57.390 25.926 16.57 11.19 41.31 1.82
3020 14774 8.997323 TCAACAAAGTTGTCATGTTTCAAATTT 58.003 25.926 9.43 14.82 41.31 1.82
3021 14775 8.545229 TCAACAAAGTTGTCATGTTTCAAATT 57.455 26.923 9.43 0.79 41.31 1.82
3022 14776 8.545229 TTCAACAAAGTTGTCATGTTTCAAAT 57.455 26.923 9.43 0.00 41.31 2.32
3034 14788 6.521162 ACAAGGTTCTTTTCAACAAAGTTGT 58.479 32.000 9.43 0.00 44.72 3.32
3173 14929 7.651704 AGTTATGTTTCAACTTATGTTTGCCAC 59.348 33.333 0.00 0.00 32.28 5.01
3180 14936 8.413229 ACAAGCAAGTTATGTTTCAACTTATGT 58.587 29.630 0.52 4.51 42.79 2.29
3198 14954 2.249309 CACGTCGGCACAAGCAAG 59.751 61.111 0.00 0.00 44.61 4.01
3212 14968 3.374058 CAGGGAGTATGTTTTAAGCCACG 59.626 47.826 0.00 0.00 0.00 4.94
3213 14969 4.156008 CACAGGGAGTATGTTTTAAGCCAC 59.844 45.833 0.00 0.00 0.00 5.01
3268 15024 7.916552 ACATATAATTCGCCTTTTGACACTAC 58.083 34.615 0.00 0.00 0.00 2.73
3292 15048 7.393515 ACTTAAAAATACTCCCTCCATGTCAAC 59.606 37.037 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.