Multiple sequence alignment - TraesCS5B01G131600

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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 TraesCS5B01G131600 chr5B 100.000 4322 0 0 1 4322 244975080 244979401 0.000000e+00 7982
1 TraesCS5B01G131600 chr5D 93.327 4271 113 69 96 4322 226942894 226938752 0.000000e+00 6150
2 TraesCS5B01G131600 chr5D 85.714 154 9 6 1 143 226943035 226942884 2.690000e-32 150
3 TraesCS5B01G131600 chr5A 92.426 3565 98 57 501 4006 300966221 300962770 0.000000e+00 4929
4 TraesCS5B01G131600 chr5A 90.421 428 19 11 1 413 300966678 300966258 1.060000e-150 544
5 TraesCS5B01G131600 chr5A 91.713 181 11 3 4143 4322 300962768 300962591 9.280000e-62 248
6 TraesCS5B01G131600 chr4A 75.381 1247 142 80 1853 3040 463924498 463923358 2.370000e-122 449
7 TraesCS5B01G131600 chr4D 74.800 1250 131 82 1857 3040 113236131 113237262 1.130000e-105 394
8 TraesCS5B01G131600 chr4D 75.967 362 58 16 1556 1907 113235569 113235911 4.470000e-35 159
9 TraesCS5B01G131600 chr4B 78.194 720 63 34 1857 2532 173968041 173968710 1.470000e-99 374
10 TraesCS5B01G131600 chr4B 76.567 367 47 18 1556 1907 173967533 173967875 9.620000e-37 165
11 TraesCS5B01G131600 chr4B 78.365 208 34 10 2841 3040 173968968 173969172 1.630000e-24 124


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 TraesCS5B01G131600 chr5B 244975080 244979401 4321 False 7982.0 7982 100.000000 1 4322 1 chr5B.!!$F1 4321
1 TraesCS5B01G131600 chr5D 226938752 226943035 4283 True 3150.0 6150 89.520500 1 4322 2 chr5D.!!$R1 4321
2 TraesCS5B01G131600 chr5A 300962591 300966678 4087 True 1907.0 4929 91.520000 1 4322 3 chr5A.!!$R1 4321
3 TraesCS5B01G131600 chr4A 463923358 463924498 1140 True 449.0 449 75.381000 1853 3040 1 chr4A.!!$R1 1187
4 TraesCS5B01G131600 chr4D 113235569 113237262 1693 False 276.5 394 75.383500 1556 3040 2 chr4D.!!$F1 1484
5 TraesCS5B01G131600 chr4B 173967533 173969172 1639 False 221.0 374 77.708667 1556 3040 3 chr4B.!!$F1 1484

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
781 838 0.610687 CTTCCTCCTCTGGACCACAC 59.389 60.0 0.00 0.0 35.58 3.82 F
1325 1407 0.817654 GCTATTTTGGTCACCCTGCC 59.182 55.0 0.00 0.0 0.00 4.85 F
2800 3350 0.312729 CAGCAGCAGCAACAACATCA 59.687 50.0 3.17 0.0 45.49 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2476 1.376037 GGAGGCTGAACTTGACGGG 60.376 63.158 0.00 0.00 0.0 5.28 R
3133 3714 0.179086 GTTGGTTGGTTGGTTGGCTG 60.179 55.000 0.00 0.00 0.0 4.85 R
4139 4761 0.465097 AAGCAAGATCCATGGAGCCG 60.465 55.000 26.11 18.34 0.0 5.52 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
44 45 4.261801 AGGATCGTAACATTTCTGGTTGG 58.738 43.478 0.00 0.00 0.00 3.77
45 46 3.377172 GGATCGTAACATTTCTGGTTGGG 59.623 47.826 0.00 0.00 0.00 4.12
46 47 3.495434 TCGTAACATTTCTGGTTGGGT 57.505 42.857 0.00 0.00 0.00 4.51
47 48 3.404899 TCGTAACATTTCTGGTTGGGTC 58.595 45.455 0.00 0.00 0.00 4.46
49 50 2.649531 AACATTTCTGGTTGGGTCGA 57.350 45.000 0.00 0.00 0.00 4.20
50 51 2.649531 ACATTTCTGGTTGGGTCGAA 57.350 45.000 0.00 0.00 0.00 3.71
51 52 2.227194 ACATTTCTGGTTGGGTCGAAC 58.773 47.619 0.00 0.00 0.00 3.95
57 66 2.435069 TCTGGTTGGGTCGAACTTTACA 59.565 45.455 0.00 0.00 0.00 2.41
76 85 2.291282 ACATGGATTTCGCCCTAACCAA 60.291 45.455 0.00 0.00 0.00 3.67
106 115 2.033492 GCATTTTGCATAATCAAGCCGC 60.033 45.455 0.00 0.00 44.26 6.53
111 120 2.153645 TGCATAATCAAGCCGCCATAG 58.846 47.619 0.00 0.00 0.00 2.23
127 174 4.420168 GCCATAGCGCATTCAACTAAAAA 58.580 39.130 11.47 0.00 0.00 1.94
143 190 7.711772 TCAACTAAAAAGTCACTAAACATCCGA 59.288 33.333 0.00 0.00 0.00 4.55
179 227 9.095065 GTTTGTATATGTAGTCGAGGTTCAAAT 57.905 33.333 0.00 0.00 0.00 2.32
271 319 7.361457 ACTTAACGGAATATTCCTCTGATGA 57.639 36.000 27.86 7.46 45.33 2.92
276 324 4.002316 GGAATATTCCTCTGATGAGCAGC 58.998 47.826 24.74 0.00 44.11 5.25
299 347 1.372499 CGCACGTCCCGAGAGAAAA 60.372 57.895 0.00 0.00 0.00 2.29
310 363 3.892588 CCCGAGAGAAAATAGTAGGCTCT 59.107 47.826 0.00 0.00 38.55 4.09
311 364 5.071370 CCCGAGAGAAAATAGTAGGCTCTA 58.929 45.833 0.00 0.00 36.17 2.43
312 365 5.048573 CCCGAGAGAAAATAGTAGGCTCTAC 60.049 48.000 0.00 4.67 36.17 2.59
313 366 5.531659 CCGAGAGAAAATAGTAGGCTCTACA 59.468 44.000 12.89 2.64 36.17 2.74
314 367 6.039493 CCGAGAGAAAATAGTAGGCTCTACAA 59.961 42.308 12.89 0.00 36.17 2.41
345 400 4.700213 AGTCTAACTGAAGTCAGAGAGAGC 59.300 45.833 15.15 10.26 46.59 4.09
458 514 1.488261 GGCATCGGTAAGCGCAGTAC 61.488 60.000 11.47 11.59 0.00 2.73
459 515 0.804544 GCATCGGTAAGCGCAGTACA 60.805 55.000 11.47 0.00 0.00 2.90
460 516 0.921347 CATCGGTAAGCGCAGTACAC 59.079 55.000 11.47 5.10 0.00 2.90
461 517 0.815734 ATCGGTAAGCGCAGTACACT 59.184 50.000 11.47 0.00 0.00 3.55
463 519 1.399440 TCGGTAAGCGCAGTACACTAG 59.601 52.381 11.47 4.82 0.00 2.57
545 601 8.606830 AGTGACAAAGGGTATTTAATTCTCTCT 58.393 33.333 0.00 0.00 0.00 3.10
575 631 8.041919 GCTAGTCTTTTGTAGGAGTAGGATTTT 58.958 37.037 0.00 0.00 36.52 1.82
576 632 9.589111 CTAGTCTTTTGTAGGAGTAGGATTTTC 57.411 37.037 0.00 0.00 33.96 2.29
577 633 7.974504 AGTCTTTTGTAGGAGTAGGATTTTCA 58.025 34.615 0.00 0.00 0.00 2.69
598 654 2.742372 ACACACAATCGGCCGAGC 60.742 61.111 33.87 0.00 0.00 5.03
600 656 4.063967 ACACAATCGGCCGAGCGA 62.064 61.111 33.87 10.92 0.00 4.93
601 657 3.257561 CACAATCGGCCGAGCGAG 61.258 66.667 33.87 23.05 0.00 5.03
781 838 0.610687 CTTCCTCCTCTGGACCACAC 59.389 60.000 0.00 0.00 35.58 3.82
782 839 1.185618 TTCCTCCTCTGGACCACACG 61.186 60.000 0.00 0.00 35.58 4.49
786 843 3.314331 CTCTGGACCACACGGGCT 61.314 66.667 0.00 0.00 41.90 5.19
944 1017 2.271800 CACCAAGTTATCTCCAGCGAC 58.728 52.381 0.00 0.00 0.00 5.19
1018 1100 2.160417 CGAGAGCAATGTTTTCCTGGTC 59.840 50.000 0.00 0.00 37.75 4.02
1028 1110 4.008330 TGTTTTCCTGGTCGTTGTTGTTA 58.992 39.130 0.00 0.00 0.00 2.41
1041 1123 7.380320 GTCGTTGTTGTTATTGTTTGTTCTTG 58.620 34.615 0.00 0.00 0.00 3.02
1085 1167 2.045926 GATCTGGGCAGTTGCGGT 60.046 61.111 0.00 0.00 43.26 5.68
1101 1183 2.280797 GTGCACTTGAGGCGGTCA 60.281 61.111 10.32 0.00 0.00 4.02
1162 1244 3.792401 TCTTGCTTCGTCTCAACTCAAA 58.208 40.909 0.00 0.00 0.00 2.69
1230 1312 4.318021 CACGCACGCAGCTTTGCT 62.318 61.111 12.65 0.00 42.61 3.91
1246 1328 7.860872 GCAGCTTTGCTTTACTTTACTTTTCTA 59.139 33.333 0.00 0.00 36.40 2.10
1274 1356 2.206036 TTTCCTCCCGTGTCCCCT 59.794 61.111 0.00 0.00 0.00 4.79
1317 1399 5.221441 ACCTCCTTGTTTTGCTATTTTGGTC 60.221 40.000 0.00 0.00 0.00 4.02
1325 1407 0.817654 GCTATTTTGGTCACCCTGCC 59.182 55.000 0.00 0.00 0.00 4.85
1422 1504 4.699257 GTCAAGAAGATCCTGCACAAGATT 59.301 41.667 0.00 0.00 0.00 2.40
1431 1513 2.227388 CCTGCACAAGATTGAAGGTGAC 59.773 50.000 0.00 0.00 33.16 3.67
1441 1523 6.059787 AGATTGAAGGTGACAAGATAAGCT 57.940 37.500 0.00 0.00 0.00 3.74
1442 1524 6.112058 AGATTGAAGGTGACAAGATAAGCTC 58.888 40.000 0.00 0.00 0.00 4.09
1446 1528 6.299141 TGAAGGTGACAAGATAAGCTCTTTT 58.701 36.000 0.00 0.00 41.60 2.27
1714 1799 1.884235 AACCAGTTTCAGAAGCTCCG 58.116 50.000 0.00 0.00 0.00 4.63
1977 2476 1.452108 CCGATCAAGGACCCCAAGC 60.452 63.158 0.00 0.00 0.00 4.01
1990 2489 1.237285 CCCAAGCCCGTCAAGTTCAG 61.237 60.000 0.00 0.00 0.00 3.02
2354 2883 0.882927 CGAACAACGCCAAAGGAGGA 60.883 55.000 0.00 0.00 34.51 3.71
2355 2884 0.875059 GAACAACGCCAAAGGAGGAG 59.125 55.000 0.00 0.00 34.32 3.69
2356 2885 0.537371 AACAACGCCAAAGGAGGAGG 60.537 55.000 0.00 0.00 32.16 4.30
2795 3345 2.725641 CAGCAGCAGCAGCAACAA 59.274 55.556 12.92 0.00 45.49 2.83
2796 3346 1.660575 CAGCAGCAGCAGCAACAAC 60.661 57.895 12.92 0.00 45.49 3.32
2797 3347 2.122797 AGCAGCAGCAGCAACAACA 61.123 52.632 12.92 0.00 45.49 3.33
2798 3348 1.006571 GCAGCAGCAGCAACAACAT 60.007 52.632 4.63 0.00 45.49 2.71
2799 3349 1.007336 GCAGCAGCAGCAACAACATC 61.007 55.000 4.63 0.00 45.49 3.06
2800 3350 0.312729 CAGCAGCAGCAACAACATCA 59.687 50.000 3.17 0.00 45.49 3.07
2898 3466 2.927201 GATGGGGTACGGGTACGGGA 62.927 65.000 3.13 0.00 46.48 5.14
3053 3630 4.742201 CGCTGCGCTGTACCCACT 62.742 66.667 9.88 0.00 0.00 4.00
3054 3631 2.577059 GCTGCGCTGTACCCACTA 59.423 61.111 16.05 0.00 0.00 2.74
3055 3632 1.810030 GCTGCGCTGTACCCACTAC 60.810 63.158 16.05 0.00 0.00 2.73
3056 3633 1.153628 CTGCGCTGTACCCACTACC 60.154 63.158 9.73 0.00 0.00 3.18
3057 3634 2.186125 GCGCTGTACCCACTACCC 59.814 66.667 0.00 0.00 0.00 3.69
3058 3635 2.652095 GCGCTGTACCCACTACCCA 61.652 63.158 0.00 0.00 0.00 4.51
3059 3636 1.515954 CGCTGTACCCACTACCCAG 59.484 63.158 0.00 0.00 0.00 4.45
3060 3637 1.255667 CGCTGTACCCACTACCCAGT 61.256 60.000 0.00 0.00 34.42 4.00
3112 3689 6.739331 TTTCCTTTCTCTTCTCTTCTCACT 57.261 37.500 0.00 0.00 0.00 3.41
3132 3713 2.174349 CGCCGCTCTGTTCAAAGC 59.826 61.111 0.00 0.00 35.13 3.51
3133 3714 2.563427 GCCGCTCTGTTCAAAGCC 59.437 61.111 0.00 0.00 35.00 4.35
3134 3715 2.260869 GCCGCTCTGTTCAAAGCCA 61.261 57.895 0.00 0.00 35.00 4.75
3135 3716 1.871772 CCGCTCTGTTCAAAGCCAG 59.128 57.895 0.00 0.00 35.00 4.85
3136 3717 1.208614 CGCTCTGTTCAAAGCCAGC 59.791 57.895 0.00 0.00 35.00 4.85
3137 3718 1.583477 GCTCTGTTCAAAGCCAGCC 59.417 57.895 0.00 0.00 32.22 4.85
3138 3719 1.174712 GCTCTGTTCAAAGCCAGCCA 61.175 55.000 0.00 0.00 32.22 4.75
3139 3720 1.321474 CTCTGTTCAAAGCCAGCCAA 58.679 50.000 0.00 0.00 0.00 4.52
3204 3789 1.141881 GTCATCGCCGTCCATCACT 59.858 57.895 0.00 0.00 0.00 3.41
3235 3824 4.119862 CAGTCAGTATACATGGGAAACGG 58.880 47.826 5.50 0.00 0.00 4.44
3236 3825 2.870411 GTCAGTATACATGGGAAACGGC 59.130 50.000 5.50 0.00 0.00 5.68
3237 3826 1.864711 CAGTATACATGGGAAACGGCG 59.135 52.381 4.80 4.80 0.00 6.46
3247 3836 1.218316 GAAACGGCGAGTCCCATCT 59.782 57.895 16.62 0.00 0.00 2.90
3273 3862 1.899142 AGCTCGCTCCTTTTTCTCTCT 59.101 47.619 0.00 0.00 0.00 3.10
3393 3982 7.072177 TGGTGCTTTTTATAATTCGAGACTG 57.928 36.000 0.00 0.00 0.00 3.51
3437 4026 1.677942 TCTTGCATGCATATCGCCAA 58.322 45.000 23.37 2.30 41.33 4.52
3444 4033 3.708890 CATGCATATCGCCAATGTGTTT 58.291 40.909 0.00 0.00 41.33 2.83
3456 4045 3.356145 CAATGTGTTTGCTTTGCTTTGC 58.644 40.909 0.00 0.00 0.00 3.68
3457 4046 2.090400 TGTGTTTGCTTTGCTTTGCA 57.910 40.000 0.00 0.00 36.47 4.08
3470 4069 1.005294 CTTTGCATGTTCCGTGCTGC 61.005 55.000 9.58 0.00 45.53 5.25
3471 4070 1.454572 TTTGCATGTTCCGTGCTGCT 61.455 50.000 9.58 0.00 45.53 4.24
3472 4071 2.132517 TTGCATGTTCCGTGCTGCTG 62.133 55.000 9.58 0.00 45.53 4.41
3484 4083 1.310216 TGCTGCTGTGGATGCATGAC 61.310 55.000 2.46 0.50 39.86 3.06
3485 4084 1.030488 GCTGCTGTGGATGCATGACT 61.030 55.000 2.46 0.00 39.86 3.41
3487 4086 0.678684 TGCTGTGGATGCATGACTGG 60.679 55.000 2.46 0.00 35.31 4.00
3488 4087 2.001361 GCTGTGGATGCATGACTGGC 62.001 60.000 2.46 6.14 0.00 4.85
3489 4088 0.678684 CTGTGGATGCATGACTGGCA 60.679 55.000 2.46 0.00 46.66 4.92
3490 4089 0.678684 TGTGGATGCATGACTGGCAG 60.679 55.000 14.16 14.16 45.68 4.85
3491 4090 0.679002 GTGGATGCATGACTGGCAGT 60.679 55.000 22.26 22.26 45.68 4.40
3493 4092 1.381928 GGATGCATGACTGGCAGTGG 61.382 60.000 27.45 15.06 45.68 4.00
3494 4093 2.001361 GATGCATGACTGGCAGTGGC 62.001 60.000 27.45 23.94 45.68 5.01
3495 4094 2.674033 GCATGACTGGCAGTGGCA 60.674 61.111 27.45 18.19 43.71 4.92
3535 4134 9.249457 CTACAATTCCACACACATATACTACTG 57.751 37.037 0.00 0.00 0.00 2.74
3536 4135 7.047891 ACAATTCCACACACATATACTACTGG 58.952 38.462 0.00 0.00 0.00 4.00
3537 4136 7.093068 ACAATTCCACACACATATACTACTGGA 60.093 37.037 0.00 0.00 0.00 3.86
3602 4201 1.098869 GCCTTTAGCTTTCTGCCCTC 58.901 55.000 0.00 0.00 44.23 4.30
3603 4202 1.373570 CCTTTAGCTTTCTGCCCTCG 58.626 55.000 0.00 0.00 44.23 4.63
3724 4331 3.260483 CCATGTGAGCGAGCGAGC 61.260 66.667 0.00 0.00 37.41 5.03
3725 4332 3.614659 CATGTGAGCGAGCGAGCG 61.615 66.667 0.00 0.00 43.00 5.03
3726 4333 3.815396 ATGTGAGCGAGCGAGCGA 61.815 61.111 1.41 0.00 43.00 4.93
3727 4334 3.748071 ATGTGAGCGAGCGAGCGAG 62.748 63.158 1.41 0.00 43.00 5.03
3730 4337 4.180946 GAGCGAGCGAGCGAGGAA 62.181 66.667 1.41 0.00 43.00 3.36
3731 4338 4.186433 AGCGAGCGAGCGAGGAAG 62.186 66.667 1.41 0.00 43.00 3.46
3733 4340 3.509757 CGAGCGAGCGAGGAAGGA 61.510 66.667 0.00 0.00 0.00 3.36
3734 4341 2.411290 GAGCGAGCGAGGAAGGAG 59.589 66.667 0.00 0.00 0.00 3.69
3933 4555 3.082701 GCCTCTGCCTCTGCCTCT 61.083 66.667 0.00 0.00 36.33 3.69
4020 4642 1.640670 ACTACTCCCCTACCACGGTAA 59.359 52.381 0.00 0.00 0.00 2.85
4021 4643 2.042979 ACTACTCCCCTACCACGGTAAA 59.957 50.000 0.00 0.00 0.00 2.01
4022 4644 2.028561 ACTCCCCTACCACGGTAAAA 57.971 50.000 0.00 0.00 0.00 1.52
4023 4645 2.337849 ACTCCCCTACCACGGTAAAAA 58.662 47.619 0.00 0.00 0.00 1.94
4061 4683 4.156556 ACATTTGGACCTTTGTCATCGATG 59.843 41.667 19.61 19.61 43.65 3.84
4088 4710 3.608506 CACTGATCAAGTACGTACTGCAC 59.391 47.826 28.00 18.65 36.83 4.57
4104 4726 2.203938 ACCCCTCCAAAGCCTCGA 60.204 61.111 0.00 0.00 0.00 4.04
4105 4727 2.269241 CCCCTCCAAAGCCTCGAC 59.731 66.667 0.00 0.00 0.00 4.20
4136 4758 0.438830 CGCCTTTTCTCTTTCGTCCG 59.561 55.000 0.00 0.00 0.00 4.79
4138 4760 2.140717 GCCTTTTCTCTTTCGTCCGAA 58.859 47.619 0.00 0.00 0.00 4.30
4139 4761 2.096367 GCCTTTTCTCTTTCGTCCGAAC 60.096 50.000 0.91 0.00 33.41 3.95
4174 4796 1.821753 TGCTTGGTACTGCTCTCTCTC 59.178 52.381 0.00 0.00 0.00 3.20
4175 4797 2.099405 GCTTGGTACTGCTCTCTCTCT 58.901 52.381 0.00 0.00 0.00 3.10
4176 4798 3.283751 GCTTGGTACTGCTCTCTCTCTA 58.716 50.000 0.00 0.00 0.00 2.43
4177 4799 3.888930 GCTTGGTACTGCTCTCTCTCTAT 59.111 47.826 0.00 0.00 0.00 1.98
4178 4800 4.023193 GCTTGGTACTGCTCTCTCTCTATC 60.023 50.000 0.00 0.00 0.00 2.08
4179 4801 5.376625 CTTGGTACTGCTCTCTCTCTATCT 58.623 45.833 0.00 0.00 0.00 1.98
4186 4808 4.562082 TGCTCTCTCTCTATCTACGTAGC 58.438 47.826 18.00 4.43 0.00 3.58
4252 4878 6.872020 GCGTGGTACTGTTGGTATATATTGAT 59.128 38.462 0.00 0.00 32.56 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.404899 TCGACCCAACCAGAAATGTTAC 58.595 45.455 0.00 0.00 0.00 2.50
36 37 2.435069 TGTAAAGTTCGACCCAACCAGA 59.565 45.455 0.00 0.00 0.00 3.86
37 38 2.841215 TGTAAAGTTCGACCCAACCAG 58.159 47.619 0.00 0.00 0.00 4.00
38 39 3.142951 CATGTAAAGTTCGACCCAACCA 58.857 45.455 0.00 0.00 0.00 3.67
40 41 3.404899 TCCATGTAAAGTTCGACCCAAC 58.595 45.455 0.00 0.00 0.00 3.77
42 43 3.992943 ATCCATGTAAAGTTCGACCCA 57.007 42.857 0.00 0.00 0.00 4.51
44 45 4.726876 GCGAAATCCATGTAAAGTTCGACC 60.727 45.833 19.77 5.93 40.06 4.79
45 46 4.331962 GCGAAATCCATGTAAAGTTCGAC 58.668 43.478 19.77 11.18 40.06 4.20
46 47 3.372822 GGCGAAATCCATGTAAAGTTCGA 59.627 43.478 19.77 0.00 40.06 3.71
47 48 3.486875 GGGCGAAATCCATGTAAAGTTCG 60.487 47.826 14.36 14.36 40.48 3.95
49 50 3.697166 AGGGCGAAATCCATGTAAAGTT 58.303 40.909 0.00 0.00 0.00 2.66
50 51 3.366052 AGGGCGAAATCCATGTAAAGT 57.634 42.857 0.00 0.00 0.00 2.66
51 52 4.036380 GGTTAGGGCGAAATCCATGTAAAG 59.964 45.833 0.00 0.00 0.00 1.85
57 66 2.818751 TTGGTTAGGGCGAAATCCAT 57.181 45.000 0.00 0.00 0.00 3.41
106 115 5.640732 ACTTTTTAGTTGAATGCGCTATGG 58.359 37.500 9.73 0.00 0.00 2.74
111 120 4.537015 AGTGACTTTTTAGTTGAATGCGC 58.463 39.130 0.00 0.00 0.00 6.09
127 174 5.120208 CGTTTCATTCGGATGTTTAGTGACT 59.880 40.000 3.00 0.00 34.77 3.41
143 190 8.377681 CGACTACATATACAAACACGTTTCATT 58.622 33.333 0.00 0.00 0.00 2.57
179 227 0.850100 ATGTGGGGTGACAAACTGGA 59.150 50.000 0.00 0.00 0.00 3.86
271 319 2.105128 GACGTGCGGATAGCTGCT 59.895 61.111 13.83 7.57 46.76 4.24
299 347 8.307582 ACTGTTTGTATTGTAGAGCCTACTAT 57.692 34.615 11.92 11.77 0.00 2.12
310 363 9.472361 GACTTCAGTTAGACTGTTTGTATTGTA 57.528 33.333 7.85 0.00 46.03 2.41
311 364 7.985184 TGACTTCAGTTAGACTGTTTGTATTGT 59.015 33.333 7.85 0.00 46.03 2.71
312 365 8.365399 TGACTTCAGTTAGACTGTTTGTATTG 57.635 34.615 7.85 0.00 46.03 1.90
313 366 8.421784 TCTGACTTCAGTTAGACTGTTTGTATT 58.578 33.333 6.15 0.00 46.03 1.89
314 367 7.952671 TCTGACTTCAGTTAGACTGTTTGTAT 58.047 34.615 6.15 0.00 46.03 2.29
343 398 4.384056 CAATTTCATATCAGTCCCTCGCT 58.616 43.478 0.00 0.00 0.00 4.93
344 399 3.499918 CCAATTTCATATCAGTCCCTCGC 59.500 47.826 0.00 0.00 0.00 5.03
345 400 3.499918 GCCAATTTCATATCAGTCCCTCG 59.500 47.826 0.00 0.00 0.00 4.63
458 514 6.150140 GGTACCCGGATGTTATACTACTAGTG 59.850 46.154 0.73 0.00 0.00 2.74
459 515 6.241645 GGTACCCGGATGTTATACTACTAGT 58.758 44.000 0.73 0.00 0.00 2.57
460 516 6.749923 GGTACCCGGATGTTATACTACTAG 57.250 45.833 0.73 0.00 0.00 2.57
545 601 4.417437 ACTCCTACAAAAGACTAGCCAGA 58.583 43.478 0.00 0.00 0.00 3.86
575 631 1.163420 GGCCGATTGTGTGTGTGTGA 61.163 55.000 0.00 0.00 0.00 3.58
576 632 1.282570 GGCCGATTGTGTGTGTGTG 59.717 57.895 0.00 0.00 0.00 3.82
577 633 2.250939 CGGCCGATTGTGTGTGTGT 61.251 57.895 24.07 0.00 0.00 3.72
604 660 3.224007 TTTGCCTTGCCCTCCCCTC 62.224 63.158 0.00 0.00 0.00 4.30
605 661 3.192630 TTTGCCTTGCCCTCCCCT 61.193 61.111 0.00 0.00 0.00 4.79
606 662 2.681421 CTTTGCCTTGCCCTCCCC 60.681 66.667 0.00 0.00 0.00 4.81
607 663 2.681421 CCTTTGCCTTGCCCTCCC 60.681 66.667 0.00 0.00 0.00 4.30
608 664 2.681421 CCCTTTGCCTTGCCCTCC 60.681 66.667 0.00 0.00 0.00 4.30
609 665 0.831711 TTTCCCTTTGCCTTGCCCTC 60.832 55.000 0.00 0.00 0.00 4.30
610 666 0.833409 CTTTCCCTTTGCCTTGCCCT 60.833 55.000 0.00 0.00 0.00 5.19
611 667 1.673477 CTTTCCCTTTGCCTTGCCC 59.327 57.895 0.00 0.00 0.00 5.36
612 668 1.673477 CCTTTCCCTTTGCCTTGCC 59.327 57.895 0.00 0.00 0.00 4.52
613 669 1.004560 GCCTTTCCCTTTGCCTTGC 60.005 57.895 0.00 0.00 0.00 4.01
614 670 1.001293 GAAGCCTTTCCCTTTGCCTTG 59.999 52.381 0.00 0.00 0.00 3.61
615 671 1.342074 GAAGCCTTTCCCTTTGCCTT 58.658 50.000 0.00 0.00 0.00 4.35
616 672 0.542938 GGAAGCCTTTCCCTTTGCCT 60.543 55.000 0.00 0.00 46.03 4.75
711 768 3.933515 GAGGCTTCCTCTCTCGCT 58.066 61.111 5.65 0.00 46.41 4.93
1018 1100 6.309251 ACCAAGAACAAACAATAACAACAACG 59.691 34.615 0.00 0.00 0.00 4.10
1028 1110 7.111247 TCAAATCAGACCAAGAACAAACAAT 57.889 32.000 0.00 0.00 0.00 2.71
1041 1123 0.462759 CGGAGGCCTCAAATCAGACC 60.463 60.000 33.29 13.04 0.00 3.85
1085 1167 2.031012 CTGACCGCCTCAAGTGCA 59.969 61.111 0.00 0.00 0.00 4.57
1101 1183 1.940957 ACCTCCTCCTTACTCATCCCT 59.059 52.381 0.00 0.00 0.00 4.20
1162 1244 3.181454 ACAAGAAGGAACACGGAATGTCT 60.181 43.478 0.00 0.00 42.31 3.41
1246 1328 1.271379 CGGGAGGAAACACAGGTGAAT 60.271 52.381 6.40 0.00 0.00 2.57
1274 1356 4.469657 AGGTTTGGAAACACAAGATAGCA 58.530 39.130 4.71 0.00 42.67 3.49
1317 1399 0.322008 GGAACAGAGAAGGCAGGGTG 60.322 60.000 0.00 0.00 0.00 4.61
1325 1407 3.935828 GGAATTTCGGAGGAACAGAGAAG 59.064 47.826 0.00 0.00 0.00 2.85
1422 1504 5.489792 AAGAGCTTATCTTGTCACCTTCA 57.510 39.130 0.00 0.00 46.80 3.02
1457 1539 9.900710 CTGAAGCAATTAGATTACTACTCGTAT 57.099 33.333 0.00 0.00 0.00 3.06
1458 1540 8.900781 ACTGAAGCAATTAGATTACTACTCGTA 58.099 33.333 0.00 0.00 0.00 3.43
1459 1541 7.773149 ACTGAAGCAATTAGATTACTACTCGT 58.227 34.615 0.00 0.00 0.00 4.18
1460 1542 8.635877 AACTGAAGCAATTAGATTACTACTCG 57.364 34.615 0.00 0.00 0.00 4.18
1462 1544 9.088512 CGAAACTGAAGCAATTAGATTACTACT 57.911 33.333 0.00 0.00 0.00 2.57
1463 1545 7.846592 GCGAAACTGAAGCAATTAGATTACTAC 59.153 37.037 0.00 0.00 0.00 2.73
1714 1799 1.507141 CTTGCCACCACCGTCAAGTC 61.507 60.000 0.00 0.00 33.27 3.01
1977 2476 1.376037 GGAGGCTGAACTTGACGGG 60.376 63.158 0.00 0.00 0.00 5.28
2096 2595 1.619654 TCTTGGGGTCGTCGAAGTAA 58.380 50.000 0.00 0.00 0.00 2.24
2615 3150 4.051167 CCAGGTGGAGGCATGCCA 62.051 66.667 37.18 15.78 38.92 4.92
2797 3347 0.250038 CCCGTTCATCATCGCCTGAT 60.250 55.000 0.00 0.00 45.78 2.90
2798 3348 1.143838 CCCGTTCATCATCGCCTGA 59.856 57.895 0.00 0.00 38.53 3.86
2799 3349 2.537560 GCCCGTTCATCATCGCCTG 61.538 63.158 0.00 0.00 0.00 4.85
2800 3350 2.203070 GCCCGTTCATCATCGCCT 60.203 61.111 0.00 0.00 0.00 5.52
2906 3474 1.227704 CGCCATTGGGTACGGCATA 60.228 57.895 4.53 0.00 46.60 3.14
3052 3629 2.434884 CTGCACCGCACTGGGTAG 60.435 66.667 0.00 0.00 44.64 3.18
3053 3630 3.238497 ACTGCACCGCACTGGGTA 61.238 61.111 0.00 0.00 44.64 3.69
3054 3631 4.935495 CACTGCACCGCACTGGGT 62.935 66.667 0.00 0.00 44.64 4.51
3057 3634 4.021631 CTGCACTGCACCGCACTG 62.022 66.667 0.00 0.00 33.79 3.66
3058 3635 4.552365 ACTGCACTGCACCGCACT 62.552 61.111 0.00 0.00 33.79 4.40
3059 3636 4.318021 CACTGCACTGCACCGCAC 62.318 66.667 0.00 0.00 33.79 5.34
3078 3655 2.142357 GAAAGGAAAGCACCCACCGC 62.142 60.000 0.00 0.00 0.00 5.68
3112 3689 4.617520 TTGAACAGAGCGGCGGCA 62.618 61.111 19.21 0.00 43.41 5.69
3132 3713 1.333636 TTGGTTGGTTGGTTGGCTGG 61.334 55.000 0.00 0.00 0.00 4.85
3133 3714 0.179086 GTTGGTTGGTTGGTTGGCTG 60.179 55.000 0.00 0.00 0.00 4.85
3134 3715 1.334384 GGTTGGTTGGTTGGTTGGCT 61.334 55.000 0.00 0.00 0.00 4.75
3135 3716 1.145156 GGTTGGTTGGTTGGTTGGC 59.855 57.895 0.00 0.00 0.00 4.52
3136 3717 0.463620 CTGGTTGGTTGGTTGGTTGG 59.536 55.000 0.00 0.00 0.00 3.77
3137 3718 0.179086 GCTGGTTGGTTGGTTGGTTG 60.179 55.000 0.00 0.00 0.00 3.77
3138 3719 1.334384 GGCTGGTTGGTTGGTTGGTT 61.334 55.000 0.00 0.00 0.00 3.67
3139 3720 1.760480 GGCTGGTTGGTTGGTTGGT 60.760 57.895 0.00 0.00 0.00 3.67
3204 3789 5.302823 CCATGTATACTGACTGACTGATCCA 59.697 44.000 4.17 0.00 0.00 3.41
3207 3792 5.458595 TCCCATGTATACTGACTGACTGAT 58.541 41.667 4.17 0.00 0.00 2.90
3235 3824 1.067915 GCTAGATGAGATGGGACTCGC 60.068 57.143 0.00 0.00 39.49 5.03
3236 3825 2.487762 GAGCTAGATGAGATGGGACTCG 59.512 54.545 0.00 0.00 39.49 4.18
3237 3826 2.487762 CGAGCTAGATGAGATGGGACTC 59.512 54.545 0.00 0.00 37.42 3.36
3247 3836 3.449018 AGAAAAAGGAGCGAGCTAGATGA 59.551 43.478 0.00 0.00 0.00 2.92
3393 3982 1.673665 CCACCAGCAGCACCTTCTC 60.674 63.158 0.00 0.00 0.00 2.87
3437 4026 2.630158 TGCAAAGCAAAGCAAACACAT 58.370 38.095 0.00 0.00 37.90 3.21
3444 4033 1.868469 GGAACATGCAAAGCAAAGCA 58.132 45.000 0.00 0.00 43.62 3.91
3456 4045 1.208358 CACAGCAGCACGGAACATG 59.792 57.895 0.00 0.00 0.00 3.21
3457 4046 1.968017 CCACAGCAGCACGGAACAT 60.968 57.895 0.00 0.00 0.00 2.71
3470 4069 0.678684 TGCCAGTCATGCATCCACAG 60.679 55.000 0.00 0.00 32.85 3.66
3471 4070 0.678684 CTGCCAGTCATGCATCCACA 60.679 55.000 0.00 0.00 38.22 4.17
3472 4071 0.679002 ACTGCCAGTCATGCATCCAC 60.679 55.000 0.00 0.00 38.22 4.02
3484 4083 3.362797 CTGCACTGCCACTGCCAG 61.363 66.667 0.00 0.00 36.33 4.85
3487 4086 1.310933 ATAAGCTGCACTGCCACTGC 61.311 55.000 1.02 0.00 38.26 4.40
3488 4087 0.731417 GATAAGCTGCACTGCCACTG 59.269 55.000 1.02 0.00 0.00 3.66
3489 4088 0.393537 GGATAAGCTGCACTGCCACT 60.394 55.000 1.02 0.00 0.00 4.00
3490 4089 1.379642 GGGATAAGCTGCACTGCCAC 61.380 60.000 1.02 0.00 0.00 5.01
3491 4090 1.077501 GGGATAAGCTGCACTGCCA 60.078 57.895 1.02 0.00 0.00 4.92
3493 4092 1.134401 TGTAGGGATAAGCTGCACTGC 60.134 52.381 1.02 0.00 0.00 4.40
3494 4093 2.988010 TGTAGGGATAAGCTGCACTG 57.012 50.000 1.02 0.00 0.00 3.66
3495 4094 4.455606 GAATTGTAGGGATAAGCTGCACT 58.544 43.478 1.02 0.00 0.00 4.40
3496 4095 3.565902 GGAATTGTAGGGATAAGCTGCAC 59.434 47.826 1.02 0.00 0.00 4.57
3497 4096 3.201930 TGGAATTGTAGGGATAAGCTGCA 59.798 43.478 1.02 0.00 0.00 4.41
3535 4134 3.181441 CCACTACTACTACTCCCTCCTCC 60.181 56.522 0.00 0.00 0.00 4.30
3536 4135 3.715834 TCCACTACTACTACTCCCTCCTC 59.284 52.174 0.00 0.00 0.00 3.71
3537 4136 3.745489 TCCACTACTACTACTCCCTCCT 58.255 50.000 0.00 0.00 0.00 3.69
3602 4201 2.410638 TTCCCTCACACCGACGAACG 62.411 60.000 0.00 0.00 42.18 3.95
3603 4202 0.666577 CTTCCCTCACACCGACGAAC 60.667 60.000 0.00 0.00 0.00 3.95
3646 4250 3.687321 CTGTCACCATGGCCGGGAG 62.687 68.421 19.39 11.85 0.00 4.30
3724 4331 0.548989 TCCTCTCCTCTCCTTCCTCG 59.451 60.000 0.00 0.00 0.00 4.63
3725 4332 2.597455 CATCCTCTCCTCTCCTTCCTC 58.403 57.143 0.00 0.00 0.00 3.71
3726 4333 1.412937 GCATCCTCTCCTCTCCTTCCT 60.413 57.143 0.00 0.00 0.00 3.36
3727 4334 1.047801 GCATCCTCTCCTCTCCTTCC 58.952 60.000 0.00 0.00 0.00 3.46
3728 4335 2.086610 AGCATCCTCTCCTCTCCTTC 57.913 55.000 0.00 0.00 0.00 3.46
3729 4336 2.158325 CCTAGCATCCTCTCCTCTCCTT 60.158 54.545 0.00 0.00 0.00 3.36
3730 4337 1.428912 CCTAGCATCCTCTCCTCTCCT 59.571 57.143 0.00 0.00 0.00 3.69
3731 4338 1.146982 ACCTAGCATCCTCTCCTCTCC 59.853 57.143 0.00 0.00 0.00 3.71
3732 4339 2.238521 CACCTAGCATCCTCTCCTCTC 58.761 57.143 0.00 0.00 0.00 3.20
3733 4340 1.757405 GCACCTAGCATCCTCTCCTCT 60.757 57.143 0.00 0.00 44.79 3.69
3734 4341 0.678950 GCACCTAGCATCCTCTCCTC 59.321 60.000 0.00 0.00 44.79 3.71
3761 4383 3.119708 CGCAGGAAAAAGAAAGCATAGCT 60.120 43.478 0.00 0.00 42.56 3.32
3919 4541 3.397439 GGCAGAGGCAGAGGCAGA 61.397 66.667 0.00 0.00 43.71 4.26
3933 4555 1.683943 GGAGAAATAGCATGCAGGCA 58.316 50.000 26.87 11.99 35.83 4.75
4020 4642 8.212317 CCAAATGTTGGTTCATTCTTCTTTTT 57.788 30.769 0.00 0.00 45.93 1.94
4021 4643 7.790823 CCAAATGTTGGTTCATTCTTCTTTT 57.209 32.000 0.00 0.00 45.93 2.27
4036 4658 4.023279 TCGATGACAAAGGTCCAAATGTTG 60.023 41.667 0.00 0.00 43.65 3.33
4061 4683 5.733655 CAGTACGTACTTGATCAGTGGATCC 60.734 48.000 25.35 4.20 40.88 3.36
4088 4710 2.269241 GTCGAGGCTTTGGAGGGG 59.731 66.667 0.00 0.00 0.00 4.79
4104 4726 1.863155 AAAGGCGATGGGTGATGGGT 61.863 55.000 0.00 0.00 0.00 4.51
4105 4727 0.684153 AAAAGGCGATGGGTGATGGG 60.684 55.000 0.00 0.00 0.00 4.00
4136 4758 1.303309 CAAGATCCATGGAGCCGTTC 58.697 55.000 26.11 14.86 0.00 3.95
4138 4760 1.153086 GCAAGATCCATGGAGCCGT 60.153 57.895 26.11 12.15 0.00 5.68
4139 4761 0.465097 AAGCAAGATCCATGGAGCCG 60.465 55.000 26.11 18.34 0.00 5.52
4186 4808 1.073216 CTCTGAGCAAGCACGTACCG 61.073 60.000 0.00 0.00 0.00 4.02
4252 4878 4.398044 GGGCCTCTCAAAACAATCGAATAA 59.602 41.667 0.84 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.