Multiple sequence alignment - TraesCS4B01G255600

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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 TraesCS4B01G255600 chr4B 100.000 6395 0 0 1 6395 520404915 520398521 0.000000e+00 11810
1 TraesCS4B01G255600 chr4D 93.003 4645 212 52 1832 6395 424472667 424468055 0.000000e+00 6673
2 TraesCS4B01G255600 chr4D 93.991 932 33 14 927 1837 424473621 424472692 0.000000e+00 1389
3 TraesCS4B01G255600 chr4D 94.429 359 18 2 533 889 424474203 424473845 9.370000e-153 551
4 TraesCS4B01G255600 chr4D 85.546 339 20 11 1 321 424477005 424476678 1.720000e-85 327
5 TraesCS4B01G255600 chr4A 92.056 3663 183 45 491 4105 40245030 40248632 0.000000e+00 5053
6 TraesCS4B01G255600 chr4A 92.463 2335 104 22 4101 6395 40248790 40251092 0.000000e+00 3271
7 TraesCS4B01G255600 chr4A 86.052 423 28 14 1 395 40244578 40244997 5.930000e-115 425
8 TraesCS4B01G255600 chr1A 81.591 1081 145 33 2680 3714 395197356 395196284 0.000000e+00 845
9 TraesCS4B01G255600 chr2D 81.981 1060 129 32 2682 3715 337544578 337543555 0.000000e+00 843
10 TraesCS4B01G255600 chr2D 84.861 251 31 5 2679 2923 403342771 403343020 4.950000e-61 246
11 TraesCS4B01G255600 chr2A 81.151 1077 147 36 2682 3712 473412703 473413769 0.000000e+00 813
12 TraesCS4B01G255600 chr2A 80.425 1083 150 36 2680 3715 10336765 10337832 0.000000e+00 769
13 TraesCS4B01G255600 chr2B 87.200 250 30 2 2672 2921 154933541 154933294 3.770000e-72 283
14 TraesCS4B01G255600 chr6A 88.839 224 25 0 2680 2903 479887549 479887326 6.320000e-70 276
15 TraesCS4B01G255600 chr6A 85.892 241 31 2 2680 2918 445970173 445970412 2.960000e-63 254
16 TraesCS4B01G255600 chr3D 86.066 244 33 1 2680 2923 253508228 253507986 1.770000e-65 261
17 TraesCS4B01G255600 chr3D 84.800 250 34 3 2682 2931 68883680 68883925 1.380000e-61 248
18 TraesCS4B01G255600 chr5D 86.957 138 9 4 2875 3011 9947775 9947904 5.170000e-31 147
19 TraesCS4B01G255600 chr1D 83.478 115 14 5 3535 3647 48792106 48791995 1.130000e-17 102


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 TraesCS4B01G255600 chr4B 520398521 520404915 6394 True 11810.000000 11810 100.000000 1 6395 1 chr4B.!!$R1 6394
1 TraesCS4B01G255600 chr4D 424468055 424477005 8950 True 2235.000000 6673 91.742250 1 6395 4 chr4D.!!$R1 6394
2 TraesCS4B01G255600 chr4A 40244578 40251092 6514 False 2916.333333 5053 90.190333 1 6395 3 chr4A.!!$F1 6394
3 TraesCS4B01G255600 chr1A 395196284 395197356 1072 True 845.000000 845 81.591000 2680 3714 1 chr1A.!!$R1 1034
4 TraesCS4B01G255600 chr2D 337543555 337544578 1023 True 843.000000 843 81.981000 2682 3715 1 chr2D.!!$R1 1033
5 TraesCS4B01G255600 chr2A 473412703 473413769 1066 False 813.000000 813 81.151000 2682 3712 1 chr2A.!!$F2 1030
6 TraesCS4B01G255600 chr2A 10336765 10337832 1067 False 769.000000 769 80.425000 2680 3715 1 chr2A.!!$F1 1035

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
512 559 0.179067 TCAAACCAAACGGCTCGTCT 60.179 50.000 0.69 0.0 39.99 4.18 F
731 3053 0.921256 CCCATTTCCCTCCCACTCCT 60.921 60.000 0.00 0.0 0.00 3.69 F
2451 5040 2.192624 CGGTTTTGCTTTGTGGTTCAG 58.807 47.619 0.00 0.0 0.00 3.02 F
3110 5760 0.678048 GCCAAAGCTCCCTGACGATT 60.678 55.000 0.00 0.0 35.50 3.34 F
3840 6522 0.326595 AAGGGTGTGTGTGTGTGTGA 59.673 50.000 0.00 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 3888 0.253044 TTGATGCTCAGGCCCTACAC 59.747 55.0 0.0 0.0 37.74 2.90 R
2696 5293 0.179012 TCCGTTCCACTTTGTTCCCC 60.179 55.0 0.0 0.0 0.00 4.81 R
3343 6002 0.611618 TCCCTCCGTAACCTTGCGTA 60.612 55.0 0.0 0.0 34.39 4.42 R
4323 7181 0.962356 GAAGTGCCCACCCATGTCTG 60.962 60.0 0.0 0.0 0.00 3.51 R
5538 8429 0.037326 GGATCAGTCGGCAACACTCA 60.037 55.0 0.0 0.0 0.00 3.41 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 3.681593 GGAATAGCCTTGTGTGGTTGTA 58.318 45.455 0.00 0.00 0.00 2.41
129 132 1.135972 CACTGATTTTTCCTCCGCACG 60.136 52.381 0.00 0.00 0.00 5.34
136 139 2.107041 TTTCCTCCGCACGGTGTGAT 62.107 55.000 22.43 0.00 35.23 3.06
137 140 2.779951 TTCCTCCGCACGGTGTGATG 62.780 60.000 22.43 13.57 35.23 3.07
157 160 3.252484 GACGGCCGAACGAATCCG 61.252 66.667 35.90 15.80 46.61 4.18
363 396 1.205657 CGCGGCAAAGATACGTACAT 58.794 50.000 0.00 0.00 0.00 2.29
374 407 1.646624 TACGTACATGAGGCGCGTCA 61.647 55.000 32.16 32.16 37.05 4.35
414 447 0.882927 TTGGACTGTACGCTTGCACC 60.883 55.000 0.00 0.00 0.00 5.01
459 504 3.322466 CCACCTCCGTTCTGGCCT 61.322 66.667 3.32 0.00 37.80 5.19
460 505 2.750350 CACCTCCGTTCTGGCCTT 59.250 61.111 3.32 0.00 37.80 4.35
461 506 1.376037 CACCTCCGTTCTGGCCTTC 60.376 63.158 3.32 0.00 37.80 3.46
462 507 1.536662 ACCTCCGTTCTGGCCTTCT 60.537 57.895 3.32 0.00 37.80 2.85
463 508 1.078848 CCTCCGTTCTGGCCTTCTG 60.079 63.158 3.32 0.00 37.80 3.02
464 509 1.078848 CTCCGTTCTGGCCTTCTGG 60.079 63.158 3.32 0.00 37.80 3.86
486 533 1.008424 AGCTCGTGACACGACACAG 60.008 57.895 26.04 17.18 46.73 3.66
488 535 1.652563 CTCGTGACACGACACAGGA 59.347 57.895 26.04 4.87 46.73 3.86
489 536 0.241213 CTCGTGACACGACACAGGAT 59.759 55.000 26.04 0.00 46.73 3.24
512 559 0.179067 TCAAACCAAACGGCTCGTCT 60.179 50.000 0.69 0.00 39.99 4.18
555 2877 1.105759 GCTAGTGATCCGTACGGGGT 61.106 60.000 32.80 22.02 36.01 4.95
557 2879 2.575532 CTAGTGATCCGTACGGGGTAA 58.424 52.381 32.80 15.26 36.01 2.85
604 2926 2.488545 AGTACTGGCAGAGTTACAGACG 59.511 50.000 23.66 0.00 35.96 4.18
611 2933 4.078516 AGTTACAGACGGGCGGGC 62.079 66.667 0.00 0.00 0.00 6.13
637 2959 1.003718 AAAAGAAGGACGGGCGGAG 60.004 57.895 0.00 0.00 0.00 4.63
638 2960 2.465055 AAAAGAAGGACGGGCGGAGG 62.465 60.000 0.00 0.00 0.00 4.30
731 3053 0.921256 CCCATTTCCCTCCCACTCCT 60.921 60.000 0.00 0.00 0.00 3.69
1218 3751 4.735132 CAGTTCGCCTTCGCCGGA 62.735 66.667 5.05 0.00 35.26 5.14
1305 3842 3.797353 CCAGTCCCCATCCCGGTG 61.797 72.222 0.00 0.00 0.00 4.94
1340 3877 2.650765 CGCGCTAGTACTAGTATTTGCG 59.349 50.000 33.26 33.26 44.55 4.85
1428 3965 8.465201 GTTGCTCAAGAAAGGAAATATGATCTT 58.535 33.333 0.00 0.00 0.00 2.40
1455 3992 2.542907 CGGTGGGTCAAGTGTGTGC 61.543 63.158 0.00 0.00 0.00 4.57
1749 4303 5.308237 ACACTTACCTTCTGATCTTTCTGGT 59.692 40.000 0.00 0.00 0.00 4.00
1786 4341 9.550406 CATTTTGAATGTAATGGATTGCCTAAT 57.450 29.630 0.00 0.00 34.31 1.73
1838 4423 2.901338 AGTGACCTACTACTGCCTGA 57.099 50.000 0.00 0.00 38.04 3.86
1940 4526 9.793252 AATGACAAGAATGTGCTTAAATGTATC 57.207 29.630 0.00 0.00 40.74 2.24
1942 4528 8.236586 TGACAAGAATGTGCTTAAATGTATCAC 58.763 33.333 0.00 0.00 40.74 3.06
1983 4569 5.528690 TGGCATGCATAGAAAGTAGCTTTAG 59.471 40.000 21.36 0.00 33.49 1.85
2081 4667 7.454225 AGACTATTGTTATCCAGAAATAGGGC 58.546 38.462 0.00 0.00 37.07 5.19
2283 4872 3.674410 GCCAAGGATTGTAGAAGCAAAGC 60.674 47.826 0.00 0.00 46.99 3.51
2347 4936 6.902224 CATGCAATTTCATGTCACATCATT 57.098 33.333 9.61 0.00 39.10 2.57
2412 5001 6.779860 ACTGGTGAACTACAATAGGAAACAT 58.220 36.000 0.00 0.00 0.00 2.71
2451 5040 2.192624 CGGTTTTGCTTTGTGGTTCAG 58.807 47.619 0.00 0.00 0.00 3.02
2696 5293 4.993029 TCTTTTAGGGTGTGTTTGGTTG 57.007 40.909 0.00 0.00 0.00 3.77
2703 5300 1.187087 GTGTGTTTGGTTGGGGAACA 58.813 50.000 0.00 0.00 0.00 3.18
2726 5323 1.737793 GTGGAACGGAATGTCATGGTC 59.262 52.381 0.00 0.00 0.00 4.02
2779 5376 3.788227 ATGTTTGGTAGGAGCAGTTCA 57.212 42.857 0.00 0.00 0.00 3.18
2978 5607 2.037144 AGTACAGAAGAACACCCACGT 58.963 47.619 0.00 0.00 0.00 4.49
2990 5626 1.196808 CACCCACGTAACACTGAATGC 59.803 52.381 0.00 0.00 0.00 3.56
3042 5692 5.170021 GCTGCAGTATATTGATCTGGAGAG 58.830 45.833 16.64 0.00 45.74 3.20
3050 5700 2.557555 TGATCTGGAGAGACACCCAT 57.442 50.000 0.00 0.00 0.00 4.00
3110 5760 0.678048 GCCAAAGCTCCCTGACGATT 60.678 55.000 0.00 0.00 35.50 3.34
3197 5856 3.181457 CCCTGCTCTGCTGAAGATGATTA 60.181 47.826 0.00 0.00 33.29 1.75
3389 6048 2.609610 CAGGGGAGGGGGAAACGA 60.610 66.667 0.00 0.00 0.00 3.85
3607 6283 3.515602 ACAGGGAATATGCCATTCTCC 57.484 47.619 0.98 6.16 0.00 3.71
3617 6293 1.303309 GCCATTCTCCAGAATCGGTG 58.697 55.000 14.28 1.99 42.41 4.94
3649 6328 4.082845 TCCTTTGACAAACCAAACACTGA 58.917 39.130 0.00 0.00 33.07 3.41
3668 6347 4.741239 ATGGGCTCTGGGGACGGT 62.741 66.667 0.00 0.00 38.16 4.83
3840 6522 0.326595 AAGGGTGTGTGTGTGTGTGA 59.673 50.000 0.00 0.00 0.00 3.58
3891 6574 4.666105 GGCCACCCCTTCTGATTC 57.334 61.111 0.00 0.00 0.00 2.52
3989 6672 8.162085 TGGTACAAGTATGTTGGGTTTGTATAA 58.838 33.333 0.00 0.00 41.05 0.98
4093 6776 4.119862 ACTACAATGTGGAAATCCGATCG 58.880 43.478 8.51 8.51 39.43 3.69
4128 6973 8.837389 ACTTCAGTGTAACATTTTAAGAGGAAC 58.163 33.333 0.00 0.00 41.43 3.62
4169 7018 6.442513 AAACTATCATGCTGCTCCTTTTAC 57.557 37.500 0.00 0.00 0.00 2.01
4283 7141 6.430616 TCAACATTTGCATTAGTGATGAGTGA 59.569 34.615 0.00 0.00 38.03 3.41
4284 7142 6.432607 ACATTTGCATTAGTGATGAGTGAG 57.567 37.500 0.00 0.00 38.03 3.51
4285 7143 5.942236 ACATTTGCATTAGTGATGAGTGAGT 59.058 36.000 0.00 0.00 38.03 3.41
4286 7144 5.868043 TTTGCATTAGTGATGAGTGAGTG 57.132 39.130 0.00 0.00 38.03 3.51
4287 7145 4.806640 TGCATTAGTGATGAGTGAGTGA 57.193 40.909 0.00 0.00 38.03 3.41
4288 7146 5.349061 TGCATTAGTGATGAGTGAGTGAT 57.651 39.130 0.00 0.00 38.03 3.06
4289 7147 5.114081 TGCATTAGTGATGAGTGAGTGATG 58.886 41.667 0.00 0.00 38.03 3.07
4290 7148 5.105228 TGCATTAGTGATGAGTGAGTGATGA 60.105 40.000 0.00 0.00 38.03 2.92
4291 7149 5.462729 GCATTAGTGATGAGTGAGTGATGAG 59.537 44.000 0.00 0.00 38.03 2.90
4292 7150 6.571605 CATTAGTGATGAGTGAGTGATGAGT 58.428 40.000 0.00 0.00 38.03 3.41
4293 7151 4.453177 AGTGATGAGTGAGTGATGAGTG 57.547 45.455 0.00 0.00 0.00 3.51
4303 7161 5.301551 AGTGAGTGATGAGTGGATGATCTAC 59.698 44.000 0.11 0.11 0.00 2.59
4323 7181 9.937175 GATCTACATTTTGTATTTTAGTGAGGC 57.063 33.333 0.00 0.00 31.66 4.70
4361 7219 1.950909 TCTTTGTTGGCCCAGTTTACG 59.049 47.619 0.00 0.00 0.00 3.18
4395 7253 4.384846 CAGATTGTGTTCATGCTTTTGAGC 59.615 41.667 0.00 0.00 0.00 4.26
4451 7309 3.947196 TGCTTGTTTCTTCTGCTCTCAAA 59.053 39.130 0.00 0.00 0.00 2.69
4474 7332 2.687700 ACTCTGGCAGTGCTATTCTG 57.312 50.000 16.11 2.40 32.26 3.02
4480 7338 5.500234 TCTGGCAGTGCTATTCTGTATTTT 58.500 37.500 16.11 0.00 35.60 1.82
4552 7410 3.731652 GCAACCATATTGCAATGCCTA 57.268 42.857 22.27 1.73 44.34 3.93
4576 7434 1.168714 GCTTCTCGCTTGGGATTGTT 58.831 50.000 0.00 0.00 35.14 2.83
4639 7497 2.721231 GCTGTTTGCCTGTTCGCA 59.279 55.556 0.00 0.00 36.85 5.10
4788 7668 1.796459 CTACCCGTGTGAACTTTTCCG 59.204 52.381 0.00 0.00 0.00 4.30
4824 7704 3.772060 AGCGCTTTTCCATCATTCTTC 57.228 42.857 2.64 0.00 0.00 2.87
4828 7708 5.030936 GCGCTTTTCCATCATTCTTCTTAC 58.969 41.667 0.00 0.00 0.00 2.34
4829 7709 5.163713 GCGCTTTTCCATCATTCTTCTTACT 60.164 40.000 0.00 0.00 0.00 2.24
4830 7710 6.037172 GCGCTTTTCCATCATTCTTCTTACTA 59.963 38.462 0.00 0.00 0.00 1.82
4993 7882 4.023107 TGACTGCGTGAGGTCTAATATAGC 60.023 45.833 0.00 0.00 34.01 2.97
4995 7884 3.143728 TGCGTGAGGTCTAATATAGCGA 58.856 45.455 0.00 0.00 0.00 4.93
5001 7890 7.030165 CGTGAGGTCTAATATAGCGAATCATT 58.970 38.462 0.00 0.00 0.00 2.57
5067 7956 4.794439 TCGTCGGCAGGCATCACG 62.794 66.667 4.23 4.23 0.00 4.35
5268 8158 1.325338 CCCAATTACGGTTTAGCGACG 59.675 52.381 8.45 0.00 0.00 5.12
5298 8188 0.734889 GTGGCACAGCTAATCGCATT 59.265 50.000 13.86 0.00 41.80 3.56
5349 8239 5.220624 GGAGACACACACGTATCTAGTACTG 60.221 48.000 5.39 0.00 0.00 2.74
5442 8333 2.555227 GGATTCTTTTGACCCAGGCAGA 60.555 50.000 0.00 0.00 0.00 4.26
5444 8335 0.250295 TCTTTTGACCCAGGCAGACG 60.250 55.000 0.00 0.00 0.00 4.18
5445 8336 0.535102 CTTTTGACCCAGGCAGACGT 60.535 55.000 0.00 0.00 0.00 4.34
5534 8425 1.950216 TGCATACAGAGAGCCTAGACG 59.050 52.381 0.00 0.00 0.00 4.18
5538 8429 1.912417 ACAGAGAGCCTAGACGTGTT 58.088 50.000 0.00 0.00 0.00 3.32
5539 8430 1.542030 ACAGAGAGCCTAGACGTGTTG 59.458 52.381 0.00 0.00 0.00 3.33
5540 8431 1.813178 CAGAGAGCCTAGACGTGTTGA 59.187 52.381 0.00 0.00 0.00 3.18
5642 8533 3.149981 CTCCTTTCCTTTTCGCCTCTTT 58.850 45.455 0.00 0.00 0.00 2.52
5651 8542 3.859411 TTTCGCCTCTTTGTTTGTTGT 57.141 38.095 0.00 0.00 0.00 3.32
5657 8548 4.607955 GCCTCTTTGTTTGTTGTAAGGAC 58.392 43.478 0.00 0.00 0.00 3.85
5658 8549 4.097286 GCCTCTTTGTTTGTTGTAAGGACA 59.903 41.667 0.00 0.00 0.00 4.02
5700 8591 3.487372 GGTTATCTACCAGGGCCAAATC 58.513 50.000 6.18 0.00 46.92 2.17
5710 8601 2.283821 GCCAAATCCCAGGCCACA 60.284 61.111 5.01 0.00 45.18 4.17
5712 8603 1.266867 GCCAAATCCCAGGCCACATT 61.267 55.000 5.01 0.00 45.18 2.71
5736 8635 1.098712 TGCTGGTTGTCGTTTGTCCC 61.099 55.000 0.00 0.00 0.00 4.46
5781 8682 1.374560 CAACGTTATCGCAATCCCCA 58.625 50.000 0.00 0.00 41.18 4.96
5806 8707 1.104630 GAAACGGGAGAGGATCGTCT 58.895 55.000 17.54 17.54 42.67 4.18
5943 8848 1.613437 CTGAACCCCGAGTTGCAAAAT 59.387 47.619 0.00 0.00 39.40 1.82
5974 8879 3.228188 TGGCCTGAGTTTCTTCATTGT 57.772 42.857 3.32 0.00 0.00 2.71
5994 8899 3.382227 TGTAGGAACTTGACACGAACTGA 59.618 43.478 0.00 0.00 41.75 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.499633 CCACCGGCCGGCCTAAAT 62.500 66.667 43.58 21.49 39.32 1.40
61 62 0.979187 AGGTCGGCCCGGAGAATTTA 60.979 55.000 0.08 0.00 38.74 1.40
265 284 2.034066 ATGGGTGGTGGAAGCGTG 59.966 61.111 0.00 0.00 36.92 5.34
393 426 1.227999 TGCAAGCGTACAGTCCAAGC 61.228 55.000 0.00 0.00 0.00 4.01
457 502 3.710722 ACGAGCTGGCCCAGAAGG 61.711 66.667 16.85 4.28 39.47 3.46
459 504 2.922503 TCACGAGCTGGCCCAGAA 60.923 61.111 16.85 0.00 32.44 3.02
460 505 3.695606 GTCACGAGCTGGCCCAGA 61.696 66.667 16.85 0.00 32.44 3.86
461 506 4.007644 TGTCACGAGCTGGCCCAG 62.008 66.667 6.32 6.32 34.12 4.45
462 507 4.314440 GTGTCACGAGCTGGCCCA 62.314 66.667 0.00 0.00 0.00 5.36
464 509 4.357947 TCGTGTCACGAGCTGGCC 62.358 66.667 23.70 0.00 46.73 5.36
480 527 1.079503 GGTTTGAGCGATCCTGTGTC 58.920 55.000 0.00 0.00 0.00 3.67
486 533 0.168128 CCGTTTGGTTTGAGCGATCC 59.832 55.000 0.00 0.00 0.00 3.36
488 535 0.889186 AGCCGTTTGGTTTGAGCGAT 60.889 50.000 0.00 0.00 37.67 4.58
489 536 1.503818 GAGCCGTTTGGTTTGAGCGA 61.504 55.000 0.00 0.00 37.67 4.93
555 2877 2.192664 TTTCCTGCCAGTGCGATTTA 57.807 45.000 0.00 0.00 41.78 1.40
557 2879 1.327303 TTTTTCCTGCCAGTGCGATT 58.673 45.000 0.00 0.00 41.78 3.34
611 2933 2.359900 CCGTCCTTCTTTTCATCTGGG 58.640 52.381 0.00 0.00 0.00 4.45
616 2938 0.676782 CCGCCCGTCCTTCTTTTCAT 60.677 55.000 0.00 0.00 0.00 2.57
617 2939 1.302192 CCGCCCGTCCTTCTTTTCA 60.302 57.895 0.00 0.00 0.00 2.69
731 3053 2.732016 CGTGTCCGAGTGGTGGAA 59.268 61.111 0.00 0.00 37.23 3.53
761 3083 1.843851 TCCCAGTCTCTCTCTCTCTCC 59.156 57.143 0.00 0.00 0.00 3.71
858 3202 2.644992 CTGCTTGCCGTTGGTTCC 59.355 61.111 0.00 0.00 0.00 3.62
925 3274 4.890306 GAGGAGGAGGGAGGGGCC 62.890 77.778 0.00 0.00 0.00 5.80
1033 3566 2.281091 CGGTACAGGCTCCCCCTA 59.719 66.667 0.00 0.00 44.09 3.53
1305 3842 0.811616 AGCGCGGATGATGAGAAACC 60.812 55.000 8.83 0.00 0.00 3.27
1351 3888 0.253044 TTGATGCTCAGGCCCTACAC 59.747 55.000 0.00 0.00 37.74 2.90
1356 3893 2.550101 GCGATTGATGCTCAGGCCC 61.550 63.158 0.00 0.00 37.74 5.80
1428 3965 1.769716 TTGACCCACCGGTGCATGTA 61.770 55.000 29.75 10.79 44.88 2.29
1578 4123 3.441222 TGCATTACAAGCATCACTCCAAG 59.559 43.478 0.00 0.00 37.02 3.61
1687 4241 2.432510 AGAAGGTATAGTGTGCTGAGGC 59.567 50.000 0.00 0.00 39.26 4.70
1749 4303 7.737972 TTACATTCAAAATGGAGAAAGTCGA 57.262 32.000 4.82 0.00 29.71 4.20
1784 4339 6.189859 TGATGCCTTTTAGTCCTCATCAATT 58.810 36.000 0.00 0.00 37.81 2.32
1786 4341 5.178096 TGATGCCTTTTAGTCCTCATCAA 57.822 39.130 0.00 0.00 37.81 2.57
1940 4526 2.549754 CCAGAACACAAGTGCCTTAGTG 59.450 50.000 0.00 0.00 37.95 2.74
1942 4528 1.537202 GCCAGAACACAAGTGCCTTAG 59.463 52.381 0.00 0.00 0.00 2.18
1983 4569 7.654520 TGTATACTTATCCGCCTTGTAAATGTC 59.345 37.037 4.17 0.00 0.00 3.06
2032 4618 4.463539 TCACATGATTACATTTGCTTGCCT 59.536 37.500 0.00 0.00 35.10 4.75
2271 4860 8.504005 TCTTACAATTAGTTGCTTTGCTTCTAC 58.496 33.333 0.00 0.00 38.96 2.59
2347 4936 5.009631 GCATGTGGTGGCATTATATTCCTA 58.990 41.667 0.00 0.00 0.00 2.94
2412 5001 3.243771 ACCGTCAACAACAACAAAAACCA 60.244 39.130 0.00 0.00 0.00 3.67
2696 5293 0.179012 TCCGTTCCACTTTGTTCCCC 60.179 55.000 0.00 0.00 0.00 4.81
2703 5300 2.819608 CCATGACATTCCGTTCCACTTT 59.180 45.455 0.00 0.00 0.00 2.66
2779 5376 6.155049 CCAAAATGTAACCATTCCATTCCTCT 59.845 38.462 0.00 0.00 40.42 3.69
2978 5607 7.386059 TCTTCTGTATTCAGCATTCAGTGTTA 58.614 34.615 0.00 0.00 41.10 2.41
2990 5626 8.867935 CAAGTACATCTGTTCTTCTGTATTCAG 58.132 37.037 0.00 0.00 42.54 3.02
3042 5692 1.067635 GTGACATTTGCCATGGGTGTC 60.068 52.381 15.13 5.06 39.58 3.67
3050 5700 0.385029 GTGTGCAGTGACATTTGCCA 59.615 50.000 11.07 7.03 39.54 4.92
3295 5954 4.415150 CCATGACTGGCCACCGCT 62.415 66.667 0.00 0.00 35.23 5.52
3343 6002 0.611618 TCCCTCCGTAACCTTGCGTA 60.612 55.000 0.00 0.00 34.39 4.42
3476 6135 2.451493 TCCCTCCCCAACCTTGCA 60.451 61.111 0.00 0.00 0.00 4.08
3517 6176 3.241059 CGCTCGACTTTCGCTCGG 61.241 66.667 0.00 0.00 40.21 4.63
3649 6328 2.677228 CGTCCCCAGAGCCCATTT 59.323 61.111 0.00 0.00 0.00 2.32
3668 6347 4.829872 AGTGAAATGTAATGGGTCGGTA 57.170 40.909 0.00 0.00 0.00 4.02
3757 6439 2.049888 AGAGGAAAATGCCTGCTAGC 57.950 50.000 8.10 8.10 38.73 3.42
3826 6508 2.287769 CCAGAATCACACACACACACA 58.712 47.619 0.00 0.00 0.00 3.72
3886 6569 9.170890 AGACCTTGGTTTCTATATATGGAATCA 57.829 33.333 11.81 10.55 0.00 2.57
3891 6574 7.880195 CAGGAAGACCTTGGTTTCTATATATGG 59.120 40.741 0.00 0.00 45.36 2.74
3989 6672 3.851458 AAGGTTGGGACTAAGTCGTTT 57.149 42.857 0.00 0.00 32.65 3.60
4157 7006 6.089249 ACTTGGAAAATGTAAAAGGAGCAG 57.911 37.500 0.00 0.00 0.00 4.24
4169 7018 7.209475 TCAAGAAGGCTTAAACTTGGAAAATG 58.791 34.615 20.55 2.04 39.74 2.32
4283 7141 6.744175 AATGTAGATCATCCACTCATCACT 57.256 37.500 0.00 0.00 35.48 3.41
4284 7142 7.281774 ACAAAATGTAGATCATCCACTCATCAC 59.718 37.037 0.00 0.00 35.48 3.06
4285 7143 7.341030 ACAAAATGTAGATCATCCACTCATCA 58.659 34.615 0.00 0.00 35.48 3.07
4286 7144 7.798596 ACAAAATGTAGATCATCCACTCATC 57.201 36.000 0.00 0.00 35.48 2.92
4287 7145 9.857656 AATACAAAATGTAGATCATCCACTCAT 57.142 29.630 0.00 0.00 36.14 2.90
4288 7146 9.685276 AAATACAAAATGTAGATCATCCACTCA 57.315 29.630 0.00 0.00 36.14 3.41
4303 7161 7.592938 TGTCTGCCTCACTAAAATACAAAATG 58.407 34.615 0.00 0.00 0.00 2.32
4322 7180 3.064324 GTGCCCACCCATGTCTGC 61.064 66.667 0.00 0.00 0.00 4.26
4323 7181 0.962356 GAAGTGCCCACCCATGTCTG 60.962 60.000 0.00 0.00 0.00 3.51
4361 7219 1.774639 CACAATCTGTGTTGCTTGCC 58.225 50.000 0.00 0.00 43.08 4.52
4395 7253 7.327214 AGACACAAGAGAGCTTCCTTTTATAG 58.673 38.462 0.00 0.00 30.14 1.31
4412 7270 8.856490 AAACAAGCAAATAAACTAGACACAAG 57.144 30.769 0.00 0.00 0.00 3.16
4413 7271 8.682710 AGAAACAAGCAAATAAACTAGACACAA 58.317 29.630 0.00 0.00 0.00 3.33
4451 7309 5.121811 CAGAATAGCACTGCCAGAGTAAAT 58.878 41.667 0.00 0.00 31.73 1.40
4474 7332 9.155053 CGTCAGTTTGTCAGAAACTAAAAATAC 57.845 33.333 0.00 0.00 38.32 1.89
4480 7338 5.013568 TCCGTCAGTTTGTCAGAAACTAA 57.986 39.130 0.00 0.00 38.32 2.24
4513 7371 2.079158 GCTGCAACAAGATAGCTGACA 58.921 47.619 0.00 0.00 33.53 3.58
4569 7427 7.154435 AGCAATGCATAGATATCAACAATCC 57.846 36.000 8.35 0.00 0.00 3.01
4570 7428 8.080417 ACAAGCAATGCATAGATATCAACAATC 58.920 33.333 8.35 0.00 0.00 2.67
4639 7497 4.946160 TTGACTTACCCCATCTCCAATT 57.054 40.909 0.00 0.00 0.00 2.32
4824 7704 6.374333 ACCACACAGCCAATATTGTTAGTAAG 59.626 38.462 14.25 0.00 0.00 2.34
4828 7708 4.458989 ACACCACACAGCCAATATTGTTAG 59.541 41.667 14.25 5.83 0.00 2.34
4829 7709 4.402829 ACACCACACAGCCAATATTGTTA 58.597 39.130 14.25 0.00 0.00 2.41
4830 7710 3.230134 ACACCACACAGCCAATATTGTT 58.770 40.909 14.25 0.00 0.00 2.83
4976 7865 5.939457 TGATTCGCTATATTAGACCTCACG 58.061 41.667 0.00 0.00 0.00 4.35
4993 7882 4.164822 ACCAAGAAACAGCAATGATTCG 57.835 40.909 0.00 0.00 0.00 3.34
4995 7884 6.660521 TGATCTACCAAGAAACAGCAATGATT 59.339 34.615 0.00 0.00 34.73 2.57
5001 7890 3.325870 CGTGATCTACCAAGAAACAGCA 58.674 45.455 0.00 0.00 34.73 4.41
5160 8049 1.984570 CAGGAAGGAGGGCGTGAGA 60.985 63.158 0.00 0.00 0.00 3.27
5268 8158 1.472376 GCTGTGCCACTCTATCCAGAC 60.472 57.143 0.00 0.00 0.00 3.51
5298 8188 2.008543 GCACATCAGCTTCCGATCACA 61.009 52.381 0.00 0.00 0.00 3.58
5349 8239 6.602009 ACCTATTCCACTTTTTACATAGGTGC 59.398 38.462 7.70 0.00 43.16 5.01
5364 8254 7.502561 AGACAAGCCATTAATTACCTATTCCAC 59.497 37.037 0.00 0.00 0.00 4.02
5442 8333 1.081094 GCGTTTTATAGGGCACACGT 58.919 50.000 0.00 0.00 0.00 4.49
5444 8335 2.745281 TCAAGCGTTTTATAGGGCACAC 59.255 45.455 0.00 0.00 0.00 3.82
5445 8336 3.060736 TCAAGCGTTTTATAGGGCACA 57.939 42.857 0.00 0.00 0.00 4.57
5453 8344 4.156008 GGTTCAGGACATCAAGCGTTTTAT 59.844 41.667 0.00 0.00 0.00 1.40
5534 8425 0.304705 CAGTCGGCAACACTCAACAC 59.695 55.000 0.00 0.00 0.00 3.32
5538 8429 0.037326 GGATCAGTCGGCAACACTCA 60.037 55.000 0.00 0.00 0.00 3.41
5539 8430 0.037326 TGGATCAGTCGGCAACACTC 60.037 55.000 0.00 0.00 0.00 3.51
5540 8431 0.615331 ATGGATCAGTCGGCAACACT 59.385 50.000 0.00 0.00 0.00 3.55
5587 8478 9.500785 GATTTCCATTCTCCTATCCTAAGAAAG 57.499 37.037 0.00 0.00 33.10 2.62
5642 8533 3.547746 GGGACTGTCCTTACAACAAACA 58.452 45.455 25.01 0.00 36.57 2.83
5651 8542 2.288025 GGGCACGGGACTGTCCTTA 61.288 63.158 25.01 0.00 36.57 2.69
5657 8548 1.227943 CCATATGGGCACGGGACTG 60.228 63.158 14.52 0.00 0.00 3.51
5658 8549 3.240491 CCATATGGGCACGGGACT 58.760 61.111 14.52 0.00 0.00 3.85
5700 8591 2.035626 ACCGAAATGTGGCCTGGG 59.964 61.111 3.32 0.00 0.00 4.45
5710 8601 0.534203 ACGACAACCAGCACCGAAAT 60.534 50.000 0.00 0.00 0.00 2.17
5712 8603 0.745128 AAACGACAACCAGCACCGAA 60.745 50.000 0.00 0.00 0.00 4.30
5736 8635 0.604780 CTAGCAATGCATCCCCCTCG 60.605 60.000 8.35 0.00 0.00 4.63
5781 8682 1.420430 TCCTCTCCCGTTTCTTGTGT 58.580 50.000 0.00 0.00 0.00 3.72
5806 8707 3.243670 GGAAGCATCTGATGTCGATCTCA 60.244 47.826 18.19 0.00 0.00 3.27
5837 8738 1.587034 GCTCTACGATTACCACAACGC 59.413 52.381 0.00 0.00 0.00 4.84
5943 8848 2.875296 ACTCAGGCCATTGTAGCAAAA 58.125 42.857 5.01 0.00 0.00 2.44
5974 8879 3.887110 TCTCAGTTCGTGTCAAGTTCCTA 59.113 43.478 0.00 0.00 0.00 2.94
5994 8899 5.902681 TGTACAGCTTTATAATCTGCGTCT 58.097 37.500 12.53 0.82 0.00 4.18
6158 9071 4.767255 AAGAAGCTCGGGCGGCTG 62.767 66.667 12.43 12.43 44.37 4.85


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

AutoCloner maintained by Alex Coulton.