Multiple sequence alignment - TraesCS5B01G408100

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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 TraesCS5B01G408100 chr5B 100.000 4323 0 0 1 4323 583713899 583709577 0.000000e+00 7984.0
1 TraesCS5B01G408100 chr5A 90.949 3458 207 54 700 4116 595554564 595551172 0.000000e+00 4554.0
2 TraesCS5B01G408100 chr5A 90.844 699 49 11 1 687 595555649 595554954 0.000000e+00 922.0
3 TraesCS5B01G408100 chr5A 81.250 112 19 1 295 406 595555136 595555027 5.950000e-14 89.8
4 TraesCS5B01G408100 chr5D 89.861 2081 123 30 2286 4322 476196372 476194336 0.000000e+00 2593.0
5 TraesCS5B01G408100 chr5D 89.103 1248 91 21 698 1906 476197814 476196573 0.000000e+00 1509.0
6 TraesCS5B01G408100 chr5D 96.861 669 18 3 22 687 476198738 476198070 0.000000e+00 1116.0
7 TraesCS5B01G408100 chr5D 90.055 181 12 5 1982 2160 476196569 476196393 3.360000e-56 230.0
8 TraesCS5B01G408100 chr6B 96.143 700 19 3 1212 1911 426742896 426743587 0.000000e+00 1136.0
9 TraesCS5B01G408100 chr2A 83.434 332 38 9 1640 1959 663652079 663652405 4.230000e-75 292.0
10 TraesCS5B01G408100 chr6A 76.627 415 73 17 286 687 66752276 66751873 1.580000e-49 207.0
11 TraesCS5B01G408100 chr7B 79.464 224 26 13 466 687 478015786 478015581 1.620000e-29 141.0
12 TraesCS5B01G408100 chr7B 88.679 53 4 2 221 273 478016620 478016570 3.610000e-06 63.9


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 TraesCS5B01G408100 chr5B 583709577 583713899 4322 True 7984.000000 7984 100.000 1 4323 1 chr5B.!!$R1 4322
1 TraesCS5B01G408100 chr5A 595551172 595555649 4477 True 1855.266667 4554 87.681 1 4116 3 chr5A.!!$R1 4115
2 TraesCS5B01G408100 chr5D 476194336 476198738 4402 True 1362.000000 2593 91.470 22 4322 4 chr5D.!!$R1 4300
3 TraesCS5B01G408100 chr6B 426742896 426743587 691 False 1136.000000 1136 96.143 1212 1911 1 chr6B.!!$F1 699

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
358 367 0.109597 CTGCATGGTCGCTTTTGGAC 60.110 55.000 0.00 0.00 0.00 4.02 F
1965 2410 1.410882 GTCATGGGTCTCTACCTCTGC 59.589 57.143 0.00 0.00 45.95 4.26 F
2351 2808 1.242665 TGCATGCATGTTCGCCTTCA 61.243 50.000 26.79 11.44 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2466 1.131693 GGATTAACGGACAAAAGGGCG 59.868 52.381 0.00 0.0 0.00 6.13 R
3235 3711 0.530650 CGGCTCGTGCATGAGGTATT 60.531 55.000 31.82 0.0 41.91 1.89 R
3879 4362 1.070758 ACGAAGCACTGATCCTGTTGT 59.929 47.619 0.00 0.0 0.00 3.32 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
26 27 2.145397 ATCGGAGACTCTAGCAACCA 57.855 50.000 1.74 0.00 42.51 3.67
38 39 6.418101 ACTCTAGCAACCATAACATGACATT 58.582 36.000 0.00 0.00 0.00 2.71
41 42 3.378112 AGCAACCATAACATGACATTCCG 59.622 43.478 0.00 0.00 0.00 4.30
315 324 7.683437 ATCTGATGTATGCAACCATTAGATG 57.317 36.000 23.70 4.71 40.70 2.90
358 367 0.109597 CTGCATGGTCGCTTTTGGAC 60.110 55.000 0.00 0.00 0.00 4.02
576 586 8.845413 ATTGCATGGTAGCTTTTCAATAAAAA 57.155 26.923 0.00 0.00 34.26 1.94
642 652 7.241376 AGTACGCATAGAAATAACAACAAAGC 58.759 34.615 0.00 0.00 0.00 3.51
689 702 9.811995 AACGTTAATAGATCATGCTTAAGTACA 57.188 29.630 0.00 0.00 0.00 2.90
690 703 9.982651 ACGTTAATAGATCATGCTTAAGTACAT 57.017 29.630 4.02 0.00 0.00 2.29
719 1110 7.526041 TGATTAACCACTGGAATATATGGCTT 58.474 34.615 0.71 0.00 35.49 4.35
752 1144 6.647212 GCATGGGCATTTTTCTAGTTTTAC 57.353 37.500 0.00 0.00 40.72 2.01
828 1226 3.793559 TGCTCCTCCTTATTTAGCGAAC 58.206 45.455 0.00 0.00 35.95 3.95
967 1365 2.039137 GTTCGTCCCTCCCTCCCT 59.961 66.667 0.00 0.00 0.00 4.20
968 1366 1.612739 GTTCGTCCCTCCCTCCCTT 60.613 63.158 0.00 0.00 0.00 3.95
985 1383 3.189376 TTGTGCTGTGCCATCCCGA 62.189 57.895 0.00 0.00 0.00 5.14
1008 1406 2.095919 ACGTAACTGAAAAATGGCGAGC 60.096 45.455 0.00 0.00 0.00 5.03
1197 1595 1.448540 GGTGAGTCCTCGTGGCATG 60.449 63.158 0.00 0.00 0.00 4.06
1209 1607 2.009051 CGTGGCATGCTCAAACTGATA 58.991 47.619 18.92 0.00 0.00 2.15
1233 1640 3.231818 GGGCAGTGGATAGACTAGCTAA 58.768 50.000 0.00 0.00 31.66 3.09
1235 1642 3.892588 GGCAGTGGATAGACTAGCTAACT 59.107 47.826 0.00 0.08 31.66 2.24
1252 1659 5.932661 GCTAACTCTTCTTTAGCTTTGTGG 58.067 41.667 0.00 0.00 45.40 4.17
1265 1672 7.575414 TTAGCTTTGTGGTCATAAAAACAGA 57.425 32.000 0.00 0.00 0.00 3.41
1389 1799 2.601905 AGAAAAACCTCAGCCAAGCAT 58.398 42.857 0.00 0.00 0.00 3.79
1498 1908 4.408821 CTTGCTGCGGTGGGCCTA 62.409 66.667 4.53 0.00 42.61 3.93
1637 2049 4.256920 CCCCTACACTGAACAAAGAGATG 58.743 47.826 0.00 0.00 0.00 2.90
1898 2343 4.551126 GCTTCATTTCGTCAAACTTCATCG 59.449 41.667 0.00 0.00 0.00 3.84
1912 2357 9.008965 TCAAACTTCATCGGAATTTTCTATGAA 57.991 29.630 14.85 14.85 34.73 2.57
1918 2363 9.955208 TTCATCGGAATTTTCTATGAATCAATG 57.045 29.630 13.06 0.00 36.05 2.82
1961 2406 2.930109 ACTGTCATGGGTCTCTACCT 57.070 50.000 0.00 0.00 45.95 3.08
1962 2407 2.741145 ACTGTCATGGGTCTCTACCTC 58.259 52.381 0.00 0.00 45.95 3.85
1964 2409 2.692557 CTGTCATGGGTCTCTACCTCTG 59.307 54.545 0.00 0.00 45.95 3.35
1965 2410 1.410882 GTCATGGGTCTCTACCTCTGC 59.589 57.143 0.00 0.00 45.95 4.26
1967 2412 1.833630 CATGGGTCTCTACCTCTGCAA 59.166 52.381 0.00 0.00 45.95 4.08
1969 2414 1.902508 TGGGTCTCTACCTCTGCAAAG 59.097 52.381 0.00 0.00 45.95 2.77
1970 2415 1.903183 GGGTCTCTACCTCTGCAAAGT 59.097 52.381 0.00 0.00 45.95 2.66
1971 2416 2.093921 GGGTCTCTACCTCTGCAAAGTC 60.094 54.545 0.00 0.00 45.95 3.01
1972 2417 2.563179 GGTCTCTACCTCTGCAAAGTCA 59.437 50.000 0.00 0.00 43.08 3.41
1973 2418 3.196685 GGTCTCTACCTCTGCAAAGTCAT 59.803 47.826 0.00 0.00 43.08 3.06
1974 2419 4.180057 GTCTCTACCTCTGCAAAGTCATG 58.820 47.826 0.00 0.00 0.00 3.07
1975 2420 2.935201 CTCTACCTCTGCAAAGTCATGC 59.065 50.000 0.00 0.00 46.58 4.06
2000 2445 8.734030 GCGTAAAATTCAGCATATTAAGTTGAC 58.266 33.333 0.00 0.00 0.00 3.18
2004 2449 9.590451 AAAATTCAGCATATTAAGTTGACCATG 57.410 29.630 0.00 0.00 0.00 3.66
2005 2450 7.886629 ATTCAGCATATTAAGTTGACCATGT 57.113 32.000 0.00 0.00 0.00 3.21
2020 2466 6.698008 TGACCATGTAATCATTGTTCATCC 57.302 37.500 0.00 0.00 31.46 3.51
2025 2471 2.442236 AATCATTGTTCATCCGCCCT 57.558 45.000 0.00 0.00 0.00 5.19
2049 2495 5.776173 TTGTCCGTTAATCCAACAAATGT 57.224 34.783 0.00 0.00 36.92 2.71
2050 2496 5.114785 TGTCCGTTAATCCAACAAATGTG 57.885 39.130 0.00 0.00 36.92 3.21
2051 2497 3.917985 GTCCGTTAATCCAACAAATGTGC 59.082 43.478 0.00 0.00 36.92 4.57
2055 2501 5.123186 CCGTTAATCCAACAAATGTGCTCTA 59.877 40.000 0.00 0.00 36.92 2.43
2056 2502 6.183360 CCGTTAATCCAACAAATGTGCTCTAT 60.183 38.462 0.00 0.00 36.92 1.98
2058 2504 7.201644 CGTTAATCCAACAAATGTGCTCTATCT 60.202 37.037 0.00 0.00 36.92 1.98
2112 2566 3.878778 TGGCTTTTCTAGAGAAGATGGC 58.121 45.455 23.50 12.29 35.21 4.40
2157 2612 4.759693 TCTGCGGTTCATTGATTTGTACTT 59.240 37.500 0.00 0.00 0.00 2.24
2172 2627 9.959749 TGATTTGTACTTCTTTATGTGAAAACC 57.040 29.630 0.00 0.00 0.00 3.27
2214 2669 7.092802 TGCCCATTGGTAAACTAGTACTCATAA 60.093 37.037 0.00 0.00 0.00 1.90
2215 2670 7.441458 GCCCATTGGTAAACTAGTACTCATAAG 59.559 40.741 0.00 0.00 0.00 1.73
2222 2677 9.570488 GGTAAACTAGTACTCATAAGTTCTGTG 57.430 37.037 8.79 0.00 34.41 3.66
2226 2681 9.517868 AACTAGTACTCATAAGTTCTGTGTACT 57.482 33.333 26.06 26.06 46.93 2.73
2227 2682 9.517868 ACTAGTACTCATAAGTTCTGTGTACTT 57.482 33.333 27.12 15.81 44.92 2.24
2228 2683 9.776158 CTAGTACTCATAAGTTCTGTGTACTTG 57.224 37.037 27.12 23.31 44.92 3.16
2229 2684 8.405418 AGTACTCATAAGTTCTGTGTACTTGA 57.595 34.615 21.26 0.00 44.92 3.02
2246 2701 8.119226 GTGTACTTGATGAATAGCTTTCATGTC 58.881 37.037 21.25 13.25 39.08 3.06
2277 2732 7.100458 ACAAGCAACCCTATTATGATTGAAC 57.900 36.000 9.61 0.00 41.60 3.18
2281 2736 5.827797 GCAACCCTATTATGATTGAACCTCA 59.172 40.000 0.00 0.00 0.00 3.86
2295 2750 9.699410 TGATTGAACCTCATCTTTATATGGTTT 57.301 29.630 0.00 0.00 37.83 3.27
2351 2808 1.242665 TGCATGCATGTTCGCCTTCA 61.243 50.000 26.79 11.44 0.00 3.02
2458 2915 2.231721 AGTTTGTCGAGAGTTAGCTCCC 59.768 50.000 2.55 0.00 42.59 4.30
2609 3073 6.491062 TGATCCTAAAATATGCACCTTCCATG 59.509 38.462 0.00 0.00 0.00 3.66
2657 3121 5.629849 GCTACACTAATCCTGTATAAGTGCG 59.370 44.000 0.00 0.00 40.94 5.34
2662 3126 2.753055 TCCTGTATAAGTGCGTGCAA 57.247 45.000 0.00 0.00 0.00 4.08
2676 3140 3.938334 TGCGTGCAATATCATACACTTGT 59.062 39.130 0.00 0.00 0.00 3.16
2678 3142 4.271049 GCGTGCAATATCATACACTTGTCT 59.729 41.667 0.00 0.00 0.00 3.41
2764 3228 3.609853 TGATGGACCACAGTTCATTAGC 58.390 45.455 0.00 0.00 42.67 3.09
2892 3368 8.627208 TTATGTTATAAGAGTAGTAGTCCCGG 57.373 38.462 0.00 0.00 0.00 5.73
2893 3369 6.006275 TGTTATAAGAGTAGTAGTCCCGGT 57.994 41.667 0.00 0.00 0.00 5.28
2894 3370 6.426587 TGTTATAAGAGTAGTAGTCCCGGTT 58.573 40.000 0.00 0.00 0.00 4.44
2895 3371 6.543831 TGTTATAAGAGTAGTAGTCCCGGTTC 59.456 42.308 0.00 0.00 0.00 3.62
2896 3372 2.433662 AGAGTAGTAGTCCCGGTTCC 57.566 55.000 0.00 0.00 0.00 3.62
2987 3463 4.307432 ACTACTGACTGAACCAATGAACG 58.693 43.478 0.00 0.00 0.00 3.95
3009 3485 6.913170 ACGCATTCAATGTTTCTTTAGATGT 58.087 32.000 0.00 0.00 0.00 3.06
3130 3606 5.132144 TGGGGTAGAAGGTATTCCTCATTTC 59.868 44.000 0.00 0.00 44.35 2.17
3178 3654 2.103941 GGAAGGCAATGTTGTTGGGAAA 59.896 45.455 0.00 0.00 0.00 3.13
3212 3688 7.657336 ACAATATTTTCTCGACAATGTGGTTT 58.343 30.769 0.00 0.00 0.00 3.27
3218 3694 2.738846 CTCGACAATGTGGTTTCTCTGG 59.261 50.000 0.00 0.00 0.00 3.86
3235 3711 0.770499 TGGCTTCTGGTGATCCAACA 59.230 50.000 0.00 0.00 43.81 3.33
3466 3942 9.270640 GAAGAAGTTCATATAGCAGTTGATCAT 57.729 33.333 5.50 0.00 32.36 2.45
3535 4011 2.041620 AGCAATGTCCTTTTGAGGGCTA 59.958 45.455 0.00 0.00 34.00 3.93
3767 4247 2.504175 GCCCCTGACACTACTGGATTTA 59.496 50.000 0.00 0.00 0.00 1.40
3872 4355 3.149196 ACCGAGTGCAGAAATCACATTT 58.851 40.909 0.00 0.00 36.93 2.32
3879 4362 7.591057 CGAGTGCAGAAATCACATTTAAAAGAA 59.409 33.333 0.00 0.00 36.93 2.52
3894 4377 4.574599 AAAAGAACAACAGGATCAGTGC 57.425 40.909 0.00 0.00 0.00 4.40
3999 4485 6.093404 CGAGAATCAGTGTATTGTGTACAGT 58.907 40.000 0.00 0.00 33.17 3.55
4023 4509 1.119684 ACAGATGTATGCTACGGCCA 58.880 50.000 2.24 0.00 37.74 5.36
4030 4516 1.037493 TATGCTACGGCCACGAGAAT 58.963 50.000 2.24 0.00 44.60 2.40
4043 4529 4.174009 CCACGAGAATGTACTGGTGTTAG 58.826 47.826 0.00 0.00 42.25 2.34
4106 4596 6.042777 GGTATTTATCTTTTTGCAAGGAGGC 58.957 40.000 0.00 0.00 0.00 4.70
4110 4600 1.133513 TCTTTTTGCAAGGAGGCTCCA 60.134 47.619 33.86 11.94 39.61 3.86
4166 4656 3.730761 GCGTTGGCTCCTGCACTG 61.731 66.667 0.00 0.00 41.91 3.66
4176 4666 1.602888 CCTGCACTGCTCTGGCTTT 60.603 57.895 1.98 0.00 39.59 3.51
4177 4667 1.177256 CCTGCACTGCTCTGGCTTTT 61.177 55.000 1.98 0.00 39.59 2.27
4178 4668 1.527034 CTGCACTGCTCTGGCTTTTA 58.473 50.000 1.98 0.00 39.59 1.52
4179 4669 1.467734 CTGCACTGCTCTGGCTTTTAG 59.532 52.381 1.98 0.00 39.59 1.85
4180 4670 1.202806 TGCACTGCTCTGGCTTTTAGT 60.203 47.619 1.98 0.00 39.59 2.24
4235 4725 7.982354 GCTGGTGTTATACTAACAAGAAGAGAT 59.018 37.037 1.53 0.00 31.20 2.75
4257 4747 6.647067 AGATATTAGCAAAAGTAGATGACCGC 59.353 38.462 0.00 0.00 0.00 5.68
4258 4748 2.472695 AGCAAAAGTAGATGACCGCA 57.527 45.000 0.00 0.00 0.00 5.69
4259 4749 2.778299 AGCAAAAGTAGATGACCGCAA 58.222 42.857 0.00 0.00 0.00 4.85
4260 4750 3.347216 AGCAAAAGTAGATGACCGCAAT 58.653 40.909 0.00 0.00 0.00 3.56
4261 4751 3.375299 AGCAAAAGTAGATGACCGCAATC 59.625 43.478 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.292492 TGGTTGCTAGAGTCTCCGATA 57.708 47.619 0.00 0.00 0.00 2.92
7 8 2.145397 TGGTTGCTAGAGTCTCCGAT 57.855 50.000 0.00 0.00 0.00 4.18
15 16 6.017605 GGAATGTCATGTTATGGTTGCTAGAG 60.018 42.308 0.00 0.00 0.00 2.43
17 18 5.277490 CGGAATGTCATGTTATGGTTGCTAG 60.277 44.000 0.00 0.00 0.00 3.42
26 27 5.342433 CAAATGCACGGAATGTCATGTTAT 58.658 37.500 0.00 0.00 0.00 1.89
315 324 9.573133 CAGTTCCATCTTATATTGTTTTCAACC 57.427 33.333 0.00 0.00 42.94 3.77
358 367 9.866936 CATATTTTGGCCATTTCATAAATTTCG 57.133 29.630 6.09 0.00 0.00 3.46
417 426 4.762251 GGCAGTCTGTTACCTGAAAATCTT 59.238 41.667 0.93 0.00 0.00 2.40
691 704 9.632638 GCCATATATTCCAGTGGTTAATCATAT 57.367 33.333 9.54 5.73 34.23 1.78
692 705 8.835734 AGCCATATATTCCAGTGGTTAATCATA 58.164 33.333 9.54 3.08 34.23 2.15
693 706 7.702785 AGCCATATATTCCAGTGGTTAATCAT 58.297 34.615 9.54 0.00 34.23 2.45
719 1110 1.752833 TGCCCATGCATTGCAACAA 59.247 47.368 16.46 0.00 44.23 2.83
808 1206 3.793559 TGTTCGCTAAATAAGGAGGAGC 58.206 45.455 0.00 0.00 0.00 4.70
828 1226 3.122157 CGTGCACGTTTTTCTTCGATTTG 60.122 43.478 30.50 0.00 34.11 2.32
834 1232 1.385999 GAGCGTGCACGTTTTTCTTC 58.614 50.000 36.80 19.49 42.22 2.87
985 1383 4.533222 CTCGCCATTTTTCAGTTACGTTT 58.467 39.130 0.00 0.00 0.00 3.60
1192 1590 2.295349 CCCATATCAGTTTGAGCATGCC 59.705 50.000 15.66 6.65 0.00 4.40
1197 1595 1.952296 CTGCCCCATATCAGTTTGAGC 59.048 52.381 0.00 0.00 0.00 4.26
1209 1607 2.614259 CTAGTCTATCCACTGCCCCAT 58.386 52.381 0.00 0.00 0.00 4.00
1233 1640 5.036117 TGACCACAAAGCTAAAGAAGAGT 57.964 39.130 0.00 0.00 0.00 3.24
1235 1642 8.458573 TTTTATGACCACAAAGCTAAAGAAGA 57.541 30.769 0.00 0.00 0.00 2.87
1279 1686 7.601886 ACAGTTCATGCTATATTGCTATCTGAC 59.398 37.037 10.48 2.79 0.00 3.51
1411 1821 2.605601 TCTGCAGCAGCCTCCTGA 60.606 61.111 18.43 0.00 41.77 3.86
1498 1908 2.438763 CTGGAGCCTCTGAGATCCAAAT 59.561 50.000 23.27 0.00 41.17 2.32
1637 2049 6.609237 TTAGCTGAACATTATGCATCAGTC 57.391 37.500 21.50 16.13 37.13 3.51
1727 2169 4.766373 TGCAACTGGAAGCATCAAATCTAA 59.234 37.500 0.00 0.00 37.60 2.10
1880 2325 5.880054 ATTCCGATGAAGTTTGACGAAAT 57.120 34.783 0.00 0.00 33.05 2.17
1961 2406 4.764679 ATTTTACGCATGACTTTGCAGA 57.235 36.364 0.00 0.00 42.91 4.26
1962 2407 4.916831 TGAATTTTACGCATGACTTTGCAG 59.083 37.500 0.00 0.00 42.91 4.41
1964 2409 4.201523 GCTGAATTTTACGCATGACTTTGC 60.202 41.667 0.00 0.00 39.29 3.68
1965 2410 4.916831 TGCTGAATTTTACGCATGACTTTG 59.083 37.500 0.00 0.00 0.00 2.77
1967 2412 4.764679 TGCTGAATTTTACGCATGACTT 57.235 36.364 0.00 0.00 0.00 3.01
1969 2414 8.781067 TTAATATGCTGAATTTTACGCATGAC 57.219 30.769 0.00 0.00 42.50 3.06
1970 2415 8.620416 ACTTAATATGCTGAATTTTACGCATGA 58.380 29.630 0.00 0.00 42.50 3.07
1971 2416 8.786937 ACTTAATATGCTGAATTTTACGCATG 57.213 30.769 5.91 0.00 42.50 4.06
1972 2417 9.236691 CAACTTAATATGCTGAATTTTACGCAT 57.763 29.630 0.00 0.00 44.47 4.73
1973 2418 8.454894 TCAACTTAATATGCTGAATTTTACGCA 58.545 29.630 0.00 0.00 36.75 5.24
1974 2419 8.734030 GTCAACTTAATATGCTGAATTTTACGC 58.266 33.333 0.00 0.00 0.00 4.42
1975 2420 9.221775 GGTCAACTTAATATGCTGAATTTTACG 57.778 33.333 0.00 0.00 0.00 3.18
1978 2423 9.590451 CATGGTCAACTTAATATGCTGAATTTT 57.410 29.630 0.00 0.00 0.00 1.82
1979 2424 8.752187 ACATGGTCAACTTAATATGCTGAATTT 58.248 29.630 0.00 0.00 0.00 1.82
1980 2425 8.297470 ACATGGTCAACTTAATATGCTGAATT 57.703 30.769 0.00 0.00 0.00 2.17
2000 2445 4.539870 GCGGATGAACAATGATTACATGG 58.460 43.478 0.00 0.00 36.79 3.66
2004 2449 3.214328 AGGGCGGATGAACAATGATTAC 58.786 45.455 0.00 0.00 0.00 1.89
2005 2450 3.576078 AGGGCGGATGAACAATGATTA 57.424 42.857 0.00 0.00 0.00 1.75
2020 2466 1.131693 GGATTAACGGACAAAAGGGCG 59.868 52.381 0.00 0.00 0.00 6.13
2025 2471 6.477033 CACATTTGTTGGATTAACGGACAAAA 59.523 34.615 10.40 0.00 41.70 2.44
2049 2495 8.094548 AGTAACACAAACATTACAGATAGAGCA 58.905 33.333 0.00 0.00 34.36 4.26
2050 2496 8.480643 AGTAACACAAACATTACAGATAGAGC 57.519 34.615 0.00 0.00 34.36 4.09
2051 2497 9.639601 TGAGTAACACAAACATTACAGATAGAG 57.360 33.333 0.00 0.00 34.36 2.43
2056 2502 9.729023 CAAATTGAGTAACACAAACATTACAGA 57.271 29.630 0.00 0.00 34.36 3.41
2058 2504 7.976175 TGCAAATTGAGTAACACAAACATTACA 59.024 29.630 0.00 0.00 34.36 2.41
2112 2566 9.252962 GCAGATAAATAAACCCATCATTTTCTG 57.747 33.333 0.00 0.00 34.42 3.02
2157 2612 3.058293 CGCAGCAGGTTTTCACATAAAGA 60.058 43.478 0.00 0.00 0.00 2.52
2171 2626 3.760035 ACCTCGTACCGCAGCAGG 61.760 66.667 0.00 0.00 37.30 4.85
2172 2627 2.507102 CACCTCGTACCGCAGCAG 60.507 66.667 0.00 0.00 0.00 4.24
2214 2669 6.940739 AGCTATTCATCAAGTACACAGAACT 58.059 36.000 0.00 0.00 0.00 3.01
2215 2670 7.602517 AAGCTATTCATCAAGTACACAGAAC 57.397 36.000 0.00 0.00 0.00 3.01
2222 2677 8.201554 TGACATGAAAGCTATTCATCAAGTAC 57.798 34.615 16.39 0.00 37.06 2.73
2223 2678 8.791327 TTGACATGAAAGCTATTCATCAAGTA 57.209 30.769 16.39 3.06 37.06 2.24
2226 2681 9.361315 CAATTTGACATGAAAGCTATTCATCAA 57.639 29.630 16.39 16.05 37.06 2.57
2227 2682 8.741841 TCAATTTGACATGAAAGCTATTCATCA 58.258 29.630 16.39 12.58 37.06 3.07
2228 2683 9.017669 GTCAATTTGACATGAAAGCTATTCATC 57.982 33.333 21.75 10.85 46.22 2.92
2229 2684 8.922058 GTCAATTTGACATGAAAGCTATTCAT 57.078 30.769 21.75 14.54 46.22 2.57
2246 2701 7.546358 TCATAATAGGGTTGCTTGTCAATTTG 58.454 34.615 0.00 0.00 36.99 2.32
2277 2732 8.960591 AGTTTGTGAAACCATATAAAGATGAGG 58.039 33.333 0.00 0.00 42.34 3.86
2281 2736 8.353423 AGCAGTTTGTGAAACCATATAAAGAT 57.647 30.769 0.00 0.00 42.34 2.40
2289 2744 5.343307 AAAGAAGCAGTTTGTGAAACCAT 57.657 34.783 0.00 0.00 42.34 3.55
2295 2750 2.013400 TGCGAAAGAAGCAGTTTGTGA 58.987 42.857 0.00 0.00 40.01 3.58
2351 2808 8.579850 TGCACTTATCAGGTGAATTAGATTTT 57.420 30.769 0.00 0.00 36.89 1.82
2458 2915 8.673626 ACTGTTGCTCAATTTTGTAAATATCG 57.326 30.769 0.00 0.00 0.00 2.92
2534 2991 6.881602 AGTGAAGGAACCAAATCATAGTTCTC 59.118 38.462 0.00 0.00 39.82 2.87
2596 3060 3.668141 TGTATTCCATGGAAGGTGCAT 57.332 42.857 29.98 16.04 37.56 3.96
2609 3073 5.001232 TGTCCAGCTACAAAGTTGTATTCC 58.999 41.667 4.43 0.00 42.26 3.01
2657 3121 5.504665 GCCAGACAAGTGTATGATATTGCAC 60.505 44.000 7.62 0.00 39.44 4.57
2662 3126 6.551227 TCTGTAGCCAGACAAGTGTATGATAT 59.449 38.462 7.62 0.00 42.80 1.63
2676 3140 5.717178 AGAACTTCAGTATTCTGTAGCCAGA 59.283 40.000 5.99 0.00 45.95 3.86
2678 3142 5.337571 CCAGAACTTCAGTATTCTGTAGCCA 60.338 44.000 11.80 0.00 46.93 4.75
2734 3198 5.818678 ACTGTGGTCCATCAGTACTTTAA 57.181 39.130 19.48 0.00 42.13 1.52
2829 3301 9.862585 GTTTATTTCGAAAAAGTTGAAATGCAT 57.137 25.926 15.66 0.00 41.16 3.96
2890 3366 2.624636 AGCATTTTACTACCGGAACCG 58.375 47.619 9.46 6.25 39.44 4.44
2891 3367 3.427098 GCAAGCATTTTACTACCGGAACC 60.427 47.826 9.46 0.00 0.00 3.62
2892 3368 3.439129 AGCAAGCATTTTACTACCGGAAC 59.561 43.478 9.46 0.00 0.00 3.62
2893 3369 3.438781 CAGCAAGCATTTTACTACCGGAA 59.561 43.478 9.46 0.00 0.00 4.30
2894 3370 3.006940 CAGCAAGCATTTTACTACCGGA 58.993 45.455 9.46 0.00 0.00 5.14
2895 3371 2.747446 ACAGCAAGCATTTTACTACCGG 59.253 45.455 0.00 0.00 0.00 5.28
2896 3372 5.539582 TTACAGCAAGCATTTTACTACCG 57.460 39.130 0.00 0.00 0.00 4.02
2949 3425 7.011950 CAGTCAGTAGTTGTATTTGTGTCCAAA 59.988 37.037 0.00 0.00 44.27 3.28
2955 3431 6.481976 TGGTTCAGTCAGTAGTTGTATTTGTG 59.518 38.462 0.00 0.00 0.00 3.33
2956 3432 6.588204 TGGTTCAGTCAGTAGTTGTATTTGT 58.412 36.000 0.00 0.00 0.00 2.83
2957 3433 7.490962 TTGGTTCAGTCAGTAGTTGTATTTG 57.509 36.000 0.00 0.00 0.00 2.32
2958 3434 7.936847 TCATTGGTTCAGTCAGTAGTTGTATTT 59.063 33.333 0.00 0.00 0.00 1.40
2959 3435 7.450074 TCATTGGTTCAGTCAGTAGTTGTATT 58.550 34.615 0.00 0.00 0.00 1.89
2960 3436 7.004555 TCATTGGTTCAGTCAGTAGTTGTAT 57.995 36.000 0.00 0.00 0.00 2.29
2987 3463 9.846248 ACTAACATCTAAAGAAACATTGAATGC 57.154 29.630 4.84 0.00 0.00 3.56
3130 3606 2.170607 TCCTTCCTTATCCAGAAAGGCG 59.829 50.000 0.00 0.00 42.79 5.52
3178 3654 6.934645 TGTCGAGAAAATATTGTCTTGGAAGT 59.065 34.615 19.06 0.00 0.00 3.01
3212 3688 1.198713 GGATCACCAGAAGCCAGAGA 58.801 55.000 0.00 0.00 35.97 3.10
3235 3711 0.530650 CGGCTCGTGCATGAGGTATT 60.531 55.000 31.82 0.00 41.91 1.89
3426 3902 5.360714 TGAACTTCTTCTGCAAAAGGACAAT 59.639 36.000 0.00 0.00 0.00 2.71
3466 3942 8.758829 ACTAAATCTGGTGACATCATGTACTAA 58.241 33.333 0.00 0.00 41.51 2.24
3505 3981 8.133627 CCTCAAAAGGACATTGCTAAAGATATG 58.866 37.037 0.00 0.00 46.67 1.78
3513 3989 2.041620 AGCCCTCAAAAGGACATTGCTA 59.958 45.455 0.00 0.00 46.67 3.49
3637 4117 5.903198 ATCTAGCCTCCATAAAAGCTTCT 57.097 39.130 0.00 0.00 36.79 2.85
3686 4166 5.459762 CAGATGTGTAAAACCAAGCTGTTTG 59.540 40.000 3.17 0.00 38.41 2.93
3767 4247 3.881688 CCTGCAGGAATCAGATCGAAAAT 59.118 43.478 29.88 0.00 37.39 1.82
3795 4276 7.226720 CCAAGACTCAAATGCGTAACCTATATT 59.773 37.037 0.00 0.00 0.00 1.28
3831 4313 2.820037 GCTCTGCCTAACGCCCAC 60.820 66.667 0.00 0.00 36.24 4.61
3840 4323 2.283532 ACTCGGTCAGCTCTGCCT 60.284 61.111 0.00 0.00 0.00 4.75
3872 4355 5.376625 AGCACTGATCCTGTTGTTCTTTTA 58.623 37.500 0.00 0.00 0.00 1.52
3879 4362 1.070758 ACGAAGCACTGATCCTGTTGT 59.929 47.619 0.00 0.00 0.00 3.32
3894 4377 5.929697 ATGCCACAATCATATACACGAAG 57.070 39.130 0.00 0.00 0.00 3.79
3957 4441 1.738350 TCGTAGTCACTAGCAGCTCAC 59.262 52.381 0.00 0.00 0.00 3.51
3999 4485 3.621268 GCCGTAGCATACATCTGTTTCAA 59.379 43.478 0.00 0.00 43.24 2.69
4023 4509 6.579666 TTACTAACACCAGTACATTCTCGT 57.420 37.500 0.00 0.00 30.76 4.18
4079 4569 8.260114 CCTCCTTGCAAAAAGATAAATACCAAT 58.740 33.333 0.00 0.00 0.00 3.16
4080 4570 7.610865 CCTCCTTGCAAAAAGATAAATACCAA 58.389 34.615 0.00 0.00 0.00 3.67
4081 4571 6.350949 GCCTCCTTGCAAAAAGATAAATACCA 60.351 38.462 0.00 0.00 0.00 3.25
4082 4572 6.042777 GCCTCCTTGCAAAAAGATAAATACC 58.957 40.000 0.00 0.00 0.00 2.73
4083 4573 6.867550 AGCCTCCTTGCAAAAAGATAAATAC 58.132 36.000 0.00 0.00 0.00 1.89
4086 4576 4.220602 GGAGCCTCCTTGCAAAAAGATAAA 59.779 41.667 2.64 0.00 32.53 1.40
4133 4623 3.748048 CCAACGCTCAAGAGAATCAGAAA 59.252 43.478 0.32 0.00 37.82 2.52
4136 4626 1.396301 GCCAACGCTCAAGAGAATCAG 59.604 52.381 0.32 0.00 37.82 2.90
4166 4656 1.541588 CAACCCACTAAAAGCCAGAGC 59.458 52.381 0.00 0.00 40.32 4.09
4197 4687 1.364901 CACCAGCCTGCCAAAACAG 59.635 57.895 0.00 0.00 37.42 3.16
4235 4725 5.666462 TGCGGTCATCTACTTTTGCTAATA 58.334 37.500 0.00 0.00 0.00 0.98
4257 4747 4.326826 TCAAGAGTTGCAGTTAGGGATTG 58.673 43.478 0.00 0.00 0.00 2.67
4258 4748 4.042187 ACTCAAGAGTTGCAGTTAGGGATT 59.958 41.667 0.00 0.00 38.83 3.01
4259 4749 3.584848 ACTCAAGAGTTGCAGTTAGGGAT 59.415 43.478 0.00 0.00 38.83 3.85
4260 4750 2.972713 ACTCAAGAGTTGCAGTTAGGGA 59.027 45.455 0.00 0.00 38.83 4.20
4261 4751 3.070018 CACTCAAGAGTTGCAGTTAGGG 58.930 50.000 0.00 0.00 40.20 3.53


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

AutoCloner maintained by Alex Coulton.