Multiple sequence alignment - TraesCS1D01G280300

Loading Multiple Alignment...

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 TraesCS1D01G280300 chr1D 100.000 5098 0 0 892 5989 378699220 378704317 0.000000e+00 9415.0
1 TraesCS1D01G280300 chr1D 100.000 335 0 0 1 335 378698329 378698663 2.370000e-173 619.0
2 TraesCS1D01G280300 chr1A 94.121 5154 158 47 892 5989 479540978 479546042 0.000000e+00 7705.0
3 TraesCS1D01G280300 chr1A 94.675 338 7 2 1 335 479540602 479540931 1.150000e-141 514.0
4 TraesCS1D01G280300 chr1A 91.489 47 3 1 3657 3703 356477244 356477289 5.010000e-06 63.9
5 TraesCS1D01G280300 chr1B 92.816 2798 121 21 892 3661 507306167 507308912 0.000000e+00 3980.0
6 TraesCS1D01G280300 chr1B 88.743 2283 126 60 3795 5989 507309149 507311388 0.000000e+00 2671.0
7 TraesCS1D01G280300 chr1B 96.119 335 5 1 1 335 507305798 507306124 1.900000e-149 540.0
8 TraesCS1D01G280300 chr3A 74.618 524 71 39 1206 1686 612527718 612527214 2.220000e-39 174.0
9 TraesCS1D01G280300 chr3A 81.900 221 19 9 4778 4992 612523805 612523600 3.710000e-37 167.0
10 TraesCS1D01G280300 chr3A 91.667 72 3 2 1094 1162 612527869 612527798 4.940000e-16 97.1
11 TraesCS1D01G280300 chr3B 81.553 206 30 5 1394 1592 624320692 624320488 4.800000e-36 163.0
12 TraesCS1D01G280300 chr3D 73.975 561 75 48 1173 1689 470490593 470490060 1.730000e-35 161.0
13 TraesCS1D01G280300 chr3D 92.958 71 2 2 1094 1161 470490718 470490648 3.820000e-17 100.0
14 TraesCS1D01G280300 chr7A 90.566 53 3 2 3656 3707 12096788 12096839 1.080000e-07 69.4
15 TraesCS1D01G280300 chr7D 93.333 45 2 1 3663 3707 12458110 12458153 1.390000e-06 65.8
16 TraesCS1D01G280300 chr7D 92.683 41 2 1 3655 3695 60438349 60438310 2.330000e-04 58.4
17 TraesCS1D01G280300 chr7B 100.000 35 0 0 3662 3696 157208749 157208783 1.390000e-06 65.8
18 TraesCS1D01G280300 chr4A 91.489 47 3 1 3662 3708 24215368 24215413 5.010000e-06 63.9
19 TraesCS1D01G280300 chr4A 94.872 39 2 0 3656 3694 485014039 485014077 1.800000e-05 62.1
20 TraesCS1D01G280300 chr4D 92.857 42 1 2 3654 3695 488607120 488607159 6.480000e-05 60.2


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 TraesCS1D01G280300 chr1D 378698329 378704317 5988 False 5017.0 9415 100.000000 1 5989 2 chr1D.!!$F1 5988
1 TraesCS1D01G280300 chr1A 479540602 479546042 5440 False 4109.5 7705 94.398000 1 5989 2 chr1A.!!$F2 5988
2 TraesCS1D01G280300 chr1B 507305798 507311388 5590 False 2397.0 3980 92.559333 1 5989 3 chr1B.!!$F1 5988

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
82 83 1.380515 CGCTCTCCTCCCTCCTTCA 60.381 63.158 0.00 0.0 0.00 3.02 F
1356 1372 1.826487 GCTCTCCTCGTCCTCCTCC 60.826 68.421 0.00 0.0 0.00 4.30 F
1455 1471 2.579738 GGTCGCTCCAGGTTCCTC 59.420 66.667 0.00 0.0 35.97 3.71 F
2813 2842 0.110238 CTCACAACATTTGGCGACCG 60.110 55.000 0.00 0.0 34.12 4.79 F
4268 4534 1.022735 CTCTTCATGACATGCTGGCC 58.977 55.000 10.76 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1552 0.674581 TGGCATCCAAGTCGAGCAAG 60.675 55.000 0.00 0.0 0.00 4.01 R
2597 2626 1.365633 GAGAGCGATGGAGGCGAAT 59.634 57.895 0.00 0.0 35.00 3.34 R
3013 3048 1.598924 CGTCGTAATTACTCCCTCCGC 60.599 57.143 13.56 0.0 0.00 5.54 R
4375 4643 0.038744 CCAGTTTGAGACCTGCCCAT 59.961 55.000 0.00 0.0 0.00 4.00 R
5140 5429 0.251653 AGGGTCTACACGAGAGGCAA 60.252 55.000 0.00 0.0 33.72 4.52 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
82 83 1.380515 CGCTCTCCTCCCTCCTTCA 60.381 63.158 0.00 0.00 0.00 3.02
1233 1249 2.513204 TACGCGTCCTCCTCCTCG 60.513 66.667 18.63 0.00 0.00 4.63
1356 1372 1.826487 GCTCTCCTCGTCCTCCTCC 60.826 68.421 0.00 0.00 0.00 4.30
1455 1471 2.579738 GGTCGCTCCAGGTTCCTC 59.420 66.667 0.00 0.00 35.97 3.71
1695 1711 7.050377 TCATGGAAGAAGTGAGTTATCAATCC 58.950 38.462 0.00 0.00 37.14 3.01
1700 1716 7.172361 GGAAGAAGTGAGTTATCAATCCTATGC 59.828 40.741 0.00 0.00 37.14 3.14
1722 1741 4.702831 CAGCCTCTAAATTCCCTTCTCTC 58.297 47.826 0.00 0.00 0.00 3.20
1741 1760 3.779183 TCTCCATGCATCTTTCTCTTCCT 59.221 43.478 0.00 0.00 0.00 3.36
1750 1769 3.690460 TCTTTCTCTTCCTTTCCCATGC 58.310 45.455 0.00 0.00 0.00 4.06
1861 1880 4.518970 TGGTTCCACAGCTTATTTCTTGTC 59.481 41.667 0.00 0.00 0.00 3.18
1893 1912 5.645056 TGATGGTGGTTGATATGTATGGT 57.355 39.130 0.00 0.00 0.00 3.55
1894 1913 5.375773 TGATGGTGGTTGATATGTATGGTG 58.624 41.667 0.00 0.00 0.00 4.17
1895 1914 4.163441 TGGTGGTTGATATGTATGGTGG 57.837 45.455 0.00 0.00 0.00 4.61
1989 2008 6.120157 GCGTTGAACAGTTATTTTCTTTTGC 58.880 36.000 0.00 0.00 0.00 3.68
2061 2080 5.230942 AGTTGCACACAGTAGTAGTTCATC 58.769 41.667 0.00 0.00 0.00 2.92
2318 2338 9.851686 TTTCATGTAATCATAGCTAGGTCAATT 57.148 29.630 5.15 0.99 32.47 2.32
2347 2367 4.727507 AGTGACACATGATCTGGTAGTC 57.272 45.455 8.59 4.22 0.00 2.59
2372 2392 6.196571 TGTACACATCTACACACGATAATCG 58.803 40.000 0.00 0.00 46.93 3.34
2455 2484 5.185454 TGCAACAGTCCCACTTATTATCTG 58.815 41.667 0.00 0.00 0.00 2.90
2456 2485 5.186198 GCAACAGTCCCACTTATTATCTGT 58.814 41.667 0.00 0.00 36.45 3.41
2457 2486 5.065218 GCAACAGTCCCACTTATTATCTGTG 59.935 44.000 0.00 0.00 35.36 3.66
2458 2487 6.173339 CAACAGTCCCACTTATTATCTGTGT 58.827 40.000 0.00 0.00 35.36 3.72
2459 2488 6.374417 ACAGTCCCACTTATTATCTGTGTT 57.626 37.500 0.00 0.00 34.18 3.32
2460 2489 6.779860 ACAGTCCCACTTATTATCTGTGTTT 58.220 36.000 0.00 0.00 34.18 2.83
2461 2490 7.231467 ACAGTCCCACTTATTATCTGTGTTTT 58.769 34.615 0.00 0.00 34.18 2.43
2462 2491 7.724061 ACAGTCCCACTTATTATCTGTGTTTTT 59.276 33.333 0.00 0.00 34.18 1.94
2645 2674 4.385825 TGTCGAAGCATTTCAAGTACCTT 58.614 39.130 0.00 0.00 32.67 3.50
2743 2772 2.409870 CCAACTTCGGGCTCATGGC 61.410 63.158 0.00 0.00 40.90 4.40
2744 2773 2.436646 AACTTCGGGCTCATGGCG 60.437 61.111 0.00 0.00 42.94 5.69
2795 2824 4.626081 AACGCGTTCAGCCAGCCT 62.626 61.111 20.79 0.00 44.76 4.58
2810 2839 1.956043 GCCTCACAACATTTGGCGA 59.044 52.632 0.00 0.00 33.96 5.54
2813 2842 0.110238 CTCACAACATTTGGCGACCG 60.110 55.000 0.00 0.00 34.12 4.79
2889 2918 3.525537 CACTTCTTGCATCCGTGAGTAT 58.474 45.455 0.00 0.00 0.00 2.12
2960 2995 8.709308 ACTATGCAGTTCTTGAAATATACTCCT 58.291 33.333 0.00 0.00 0.00 3.69
3001 3036 4.033129 TGTCTTTGAACTAAAACCACGACG 59.967 41.667 0.00 0.00 0.00 5.12
3003 3038 4.268405 TCTTTGAACTAAAACCACGACGAC 59.732 41.667 0.00 0.00 0.00 4.34
3013 3048 3.984508 ACCACGACGACTATTATGGAG 57.015 47.619 0.00 0.00 0.00 3.86
3414 3458 1.730501 TCGACTGTCGATTCGGTACT 58.269 50.000 27.26 0.00 44.82 2.73
3417 3461 2.783333 GACTGTCGATTCGGTACTGTC 58.217 52.381 16.42 16.42 35.75 3.51
3429 3473 6.438259 TTCGGTACTGTCTGATAAGAAGAG 57.562 41.667 0.64 0.00 0.00 2.85
3442 3486 5.971792 TGATAAGAAGAGCGTTCAACTATCG 59.028 40.000 1.01 0.00 0.00 2.92
3456 3500 6.358118 TCAACTATCGTTAAATGCATGTCC 57.642 37.500 0.00 0.00 0.00 4.02
3459 3504 7.120579 TCAACTATCGTTAAATGCATGTCCTTT 59.879 33.333 0.00 0.00 0.00 3.11
3574 3619 4.499037 AGGCACCAAATCTAAAAACGAC 57.501 40.909 0.00 0.00 0.00 4.34
3630 3675 3.733224 GTCAATTCTCGTCGATCTGATGG 59.267 47.826 0.00 0.00 34.17 3.51
3676 3721 8.642432 CAAATAACATATACTCCCTCTGTCTCA 58.358 37.037 0.00 0.00 0.00 3.27
3882 4106 9.113838 CTTCTATACCTGTGTTCATAAAATGCT 57.886 33.333 0.00 0.00 0.00 3.79
4004 4256 5.907207 TGACATGCTAGCTTTTAGGTCTAG 58.093 41.667 17.23 0.00 34.45 2.43
4037 4289 6.142818 TGTAACTTCAAAACAATGTCCAGG 57.857 37.500 0.00 0.00 0.00 4.45
4066 4322 8.561738 TTTAGGAAGCTTCTAATTAACCTGTG 57.438 34.615 25.05 0.00 0.00 3.66
4073 4329 7.624549 AGCTTCTAATTAACCTGTGAAGATGA 58.375 34.615 11.90 0.00 34.57 2.92
4074 4330 7.768120 AGCTTCTAATTAACCTGTGAAGATGAG 59.232 37.037 11.90 0.00 34.57 2.90
4075 4331 7.550906 GCTTCTAATTAACCTGTGAAGATGAGT 59.449 37.037 11.90 0.00 34.57 3.41
4082 4340 3.194542 ACCTGTGAAGATGAGTAGTGCTC 59.805 47.826 0.56 0.56 44.36 4.26
4129 4390 3.378427 GGTTCTGTATTTGCCATCACTCC 59.622 47.826 0.00 0.00 0.00 3.85
4164 4425 3.484953 TCCAGGTACCCAACTGATAGT 57.515 47.619 8.74 0.00 36.86 2.12
4258 4524 7.335171 CAGTGATTCCAATGTAACTCTTCATGA 59.665 37.037 0.00 0.00 34.02 3.07
4268 4534 1.022735 CTCTTCATGACATGCTGGCC 58.977 55.000 10.76 0.00 0.00 5.36
4364 4632 1.134189 TGCCTGCCTGATGATCTTGAG 60.134 52.381 0.00 0.00 0.00 3.02
4375 4643 6.766467 CCTGATGATCTTGAGACATTTCATGA 59.234 38.462 0.00 0.00 36.21 3.07
4503 4771 1.424493 CGACAAGAATCAGCTCGGCC 61.424 60.000 0.00 0.00 0.00 6.13
4520 4788 3.604667 CCGCAGCAGCAAACCCAA 61.605 61.111 0.82 0.00 42.27 4.12
4529 4797 0.681175 AGCAAACCCAACAGCATTCC 59.319 50.000 0.00 0.00 0.00 3.01
4566 4834 1.442148 CCCTCGGATCCTTCGAACC 59.558 63.158 10.75 0.00 36.15 3.62
5063 5349 6.829703 GCAACATGCAGATGAGATATTCTAC 58.170 40.000 0.00 0.00 44.26 2.59
5140 5429 1.185315 GCTGGGTGCATTGGTACATT 58.815 50.000 0.00 0.00 39.30 2.71
5192 5481 5.347994 TCAATATTTGACACAGTGGGGCTG 61.348 45.833 0.00 0.00 41.93 4.85
5288 5579 5.129320 TGTTCTGATCCTAGATTAAGCTGCA 59.871 40.000 2.82 0.00 0.00 4.41
5298 5589 8.436778 TCCTAGATTAAGCTGCATTATTAACCA 58.563 33.333 2.82 0.00 0.00 3.67
5303 5594 9.612620 GATTAAGCTGCATTATTAACCATGTAC 57.387 33.333 1.02 0.00 0.00 2.90
5359 5653 0.455972 CGTGGCAAATAAAGGGTGCG 60.456 55.000 0.00 0.00 39.22 5.34
5361 5655 0.897863 TGGCAAATAAAGGGTGCGCT 60.898 50.000 9.73 0.00 39.22 5.92
5362 5656 0.179137 GGCAAATAAAGGGTGCGCTC 60.179 55.000 9.73 4.47 39.22 5.03
5398 5702 6.432472 AGCTAGGCTGCAAATTTTATCTATCC 59.568 38.462 0.50 0.00 37.57 2.59
5468 5772 1.076332 GCCGAAGCTTCAACGTGTAT 58.924 50.000 25.47 0.00 35.50 2.29
5688 6006 2.642311 TGGCATCCTTCCTCTGTTAACA 59.358 45.455 8.28 8.28 0.00 2.41
5708 6026 4.134563 ACAACCCTAACAACATCTGTCAC 58.865 43.478 0.00 0.00 37.23 3.67
5841 6159 4.903045 TTTTACTCCTCCCCAGTGTAAG 57.097 45.455 0.00 0.00 0.00 2.34
5842 6160 2.544844 TACTCCTCCCCAGTGTAAGG 57.455 55.000 0.00 0.00 0.00 2.69
5843 6161 0.790993 ACTCCTCCCCAGTGTAAGGA 59.209 55.000 5.54 5.54 36.50 3.36
5844 6162 1.151413 ACTCCTCCCCAGTGTAAGGAA 59.849 52.381 6.79 0.00 37.46 3.36
5845 6163 2.266279 CTCCTCCCCAGTGTAAGGAAA 58.734 52.381 6.79 0.00 37.46 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 3.842923 CGCGGCAGAGGATGAGGT 61.843 66.667 0.00 0.00 0.00 3.85
127 131 9.729023 CCTTTCTTTTCTCTCTTTCTTTCTTTC 57.271 33.333 0.00 0.00 0.00 2.62
128 132 8.194104 GCCTTTCTTTTCTCTCTTTCTTTCTTT 58.806 33.333 0.00 0.00 0.00 2.52
129 133 7.340487 TGCCTTTCTTTTCTCTCTTTCTTTCTT 59.660 33.333 0.00 0.00 0.00 2.52
130 134 6.830838 TGCCTTTCTTTTCTCTCTTTCTTTCT 59.169 34.615 0.00 0.00 0.00 2.52
131 135 6.915300 GTGCCTTTCTTTTCTCTCTTTCTTTC 59.085 38.462 0.00 0.00 0.00 2.62
132 136 6.183360 GGTGCCTTTCTTTTCTCTCTTTCTTT 60.183 38.462 0.00 0.00 0.00 2.52
133 137 5.300539 GGTGCCTTTCTTTTCTCTCTTTCTT 59.699 40.000 0.00 0.00 0.00 2.52
929 933 4.527583 CTCAGCTCAGCTCGCCCC 62.528 72.222 0.00 0.00 36.40 5.80
997 1001 3.785859 AGCGGCCGATGACATGGT 61.786 61.111 33.48 0.00 0.00 3.55
1233 1249 2.202623 CTGTGCGGCGAGTAGGAC 60.203 66.667 12.98 0.00 0.00 3.85
1356 1372 4.020617 TGCTGAGGCGGAGGGTTG 62.021 66.667 0.00 0.00 42.25 3.77
1440 1456 3.068691 CCGAGGAACCTGGAGCGA 61.069 66.667 0.00 0.00 0.00 4.93
1536 1552 0.674581 TGGCATCCAAGTCGAGCAAG 60.675 55.000 0.00 0.00 0.00 4.01
1695 1711 4.363991 AGGGAATTTAGAGGCTGCATAG 57.636 45.455 0.50 0.00 0.00 2.23
1700 1716 4.444164 GGAGAGAAGGGAATTTAGAGGCTG 60.444 50.000 0.00 0.00 0.00 4.85
1722 1741 4.097589 GGAAAGGAAGAGAAAGATGCATGG 59.902 45.833 2.46 0.00 0.00 3.66
1741 1760 8.991275 AGAAGAAAATAATTATGGCATGGGAAA 58.009 29.630 10.98 0.00 0.00 3.13
1750 1769 9.109393 TCTCCACGAAGAAGAAAATAATTATGG 57.891 33.333 0.00 0.00 0.00 2.74
1861 1880 2.679837 CAACCACCATCAAATCGAGAGG 59.320 50.000 0.00 0.00 0.00 3.69
1893 1912 6.002082 CCAAAAGAGCAGATATCATGATCCA 58.998 40.000 12.53 0.00 33.58 3.41
1894 1913 6.236409 TCCAAAAGAGCAGATATCATGATCC 58.764 40.000 12.53 5.70 33.58 3.36
1895 1914 7.925043 ATCCAAAAGAGCAGATATCATGATC 57.075 36.000 12.53 8.59 33.29 2.92
1989 2008 6.203723 AGTTGCTGCTAGTTTTACAAGAAGAG 59.796 38.462 0.00 0.00 0.00 2.85
2061 2080 7.894376 ATTTGGCTGTTCTAATTTCATGTTG 57.106 32.000 0.00 0.00 0.00 3.33
2120 2139 6.639632 ATCTTAGAAAGCAGCAACTTGAAA 57.360 33.333 0.00 0.00 0.00 2.69
2260 2280 7.215719 ACTTTCCTGAGCTAAATTAAACCAC 57.784 36.000 0.00 0.00 0.00 4.16
2292 2312 9.851686 AATTGACCTAGCTATGATTACATGAAA 57.148 29.630 0.00 0.00 37.87 2.69
2318 2338 6.942005 ACCAGATCATGTGTCACTTCAAAATA 59.058 34.615 4.27 0.00 0.00 1.40
2333 2353 5.582689 TGTGTACAGACTACCAGATCATG 57.417 43.478 0.00 0.00 0.00 3.07
2347 2367 6.357240 CGATTATCGTGTGTAGATGTGTACAG 59.643 42.308 6.43 0.00 32.69 2.74
2372 2392 6.564328 ACAGATGAGTTGTTTGAAAGAAACC 58.436 36.000 0.00 0.00 0.00 3.27
2597 2626 1.365633 GAGAGCGATGGAGGCGAAT 59.634 57.895 0.00 0.00 35.00 3.34
2645 2674 2.432146 CTGGCTCTGTATGGTGCTCTTA 59.568 50.000 0.00 0.00 0.00 2.10
2690 2719 3.978571 GAGGCTGTCTTTCCCGCCC 62.979 68.421 0.00 0.00 43.48 6.13
2692 2721 2.815647 CGAGGCTGTCTTTCCCGC 60.816 66.667 0.00 0.00 0.00 6.13
2795 2824 1.945522 CGGTCGCCAAATGTTGTGA 59.054 52.632 0.00 0.00 0.00 3.58
2889 2918 8.729756 CACGAAATCAAATAAGGATATGCCATA 58.270 33.333 0.00 0.00 40.02 2.74
2960 2995 8.092068 TCAAAGACAAGTATTACGGAATCAGAA 58.908 33.333 0.00 0.00 0.00 3.02
3001 3036 2.494073 CTCCCTCCGCTCCATAATAGTC 59.506 54.545 0.00 0.00 0.00 2.59
3003 3038 2.530701 ACTCCCTCCGCTCCATAATAG 58.469 52.381 0.00 0.00 0.00 1.73
3013 3048 1.598924 CGTCGTAATTACTCCCTCCGC 60.599 57.143 13.56 0.00 0.00 5.54
3313 3349 6.743110 TGTTAGATTGCATGCACTAAAACAA 58.257 32.000 24.43 9.20 0.00 2.83
3414 3458 4.783764 TGAACGCTCTTCTTATCAGACA 57.216 40.909 0.00 0.00 0.00 3.41
3417 3461 6.141527 CGATAGTTGAACGCTCTTCTTATCAG 59.858 42.308 0.00 0.00 0.00 2.90
3442 3486 3.369366 CCCCCAAAGGACATGCATTTAAC 60.369 47.826 0.00 0.00 38.24 2.01
3456 3500 1.686115 CCCATGCTAGAACCCCCAAAG 60.686 57.143 0.00 0.00 0.00 2.77
3459 3504 1.230149 ACCCATGCTAGAACCCCCA 60.230 57.895 0.00 0.00 0.00 4.96
3574 3619 2.743938 AGCGGCAAAGATATAGTGACG 58.256 47.619 1.45 4.11 46.63 4.35
3630 3675 1.198637 GCAGTGCAGTCTCCATCAAAC 59.801 52.381 11.09 0.00 0.00 2.93
3695 3740 2.356069 CGTCTCATCTCATCTTCGGTCA 59.644 50.000 0.00 0.00 0.00 4.02
3696 3741 2.287308 CCGTCTCATCTCATCTTCGGTC 60.287 54.545 0.00 0.00 33.39 4.79
3882 4106 5.353394 AACTCAGTAACTCACTCAAACCA 57.647 39.130 0.00 0.00 34.26 3.67
4004 4256 6.375377 TGTTTTGAAGTTACATTACGCCATC 58.625 36.000 0.00 0.00 0.00 3.51
4045 4297 6.879458 TCTTCACAGGTTAATTAGAAGCTTCC 59.121 38.462 22.81 5.63 34.99 3.46
4056 4312 6.070538 AGCACTACTCATCTTCACAGGTTAAT 60.071 38.462 0.00 0.00 0.00 1.40
4066 4322 4.090642 CACAAACGAGCACTACTCATCTTC 59.909 45.833 0.00 0.00 46.63 2.87
4073 4329 3.555956 CAGAAACACAAACGAGCACTACT 59.444 43.478 0.00 0.00 0.00 2.57
4074 4330 3.308866 ACAGAAACACAAACGAGCACTAC 59.691 43.478 0.00 0.00 0.00 2.73
4075 4331 3.527533 ACAGAAACACAAACGAGCACTA 58.472 40.909 0.00 0.00 0.00 2.74
4076 4332 2.351726 GACAGAAACACAAACGAGCACT 59.648 45.455 0.00 0.00 0.00 4.40
4082 4340 2.220133 CGGGTAGACAGAAACACAAACG 59.780 50.000 0.00 0.00 0.00 3.60
4164 4425 4.142071 TGTTTAGCCAACATTTGCTTGTCA 60.142 37.500 0.00 0.00 40.71 3.58
4258 4524 3.731547 TGCTAGAGGCCAGCATGT 58.268 55.556 12.02 0.00 43.90 3.21
4268 4534 3.181480 GGTGCTAAGAGACCTTGCTAGAG 60.181 52.174 0.00 0.00 33.94 2.43
4338 4606 1.466856 TCATCAGGCAGGCAATGTTC 58.533 50.000 0.00 0.00 0.00 3.18
4364 4632 2.360165 GACCTGCCCATCATGAAATGTC 59.640 50.000 0.00 0.00 46.80 3.06
4375 4643 0.038744 CCAGTTTGAGACCTGCCCAT 59.961 55.000 0.00 0.00 0.00 4.00
4503 4771 3.604667 TTGGGTTTGCTGCTGCGG 61.605 61.111 11.21 3.55 43.34 5.69
4520 4788 2.671070 CTGTCCGGGGAATGCTGT 59.329 61.111 0.00 0.00 0.00 4.40
4553 4821 1.521681 CTGCGGGTTCGAAGGATCC 60.522 63.158 2.48 2.48 38.37 3.36
4566 4834 4.729856 GCTTTGCCCTTGCTGCGG 62.730 66.667 0.00 0.00 38.71 5.69
4727 4995 4.691506 TGCGACAGTGCAATGCTA 57.308 50.000 15.18 0.00 43.02 3.49
5060 5346 0.249238 GACCAGATCAGCCAGCGTAG 60.249 60.000 0.00 0.00 0.00 3.51
5063 5349 2.202987 GGACCAGATCAGCCAGCG 60.203 66.667 0.00 0.00 0.00 5.18
5140 5429 0.251653 AGGGTCTACACGAGAGGCAA 60.252 55.000 0.00 0.00 33.72 4.52
5288 5579 6.928202 TCAATGGGGGTACATGGTTAATAAT 58.072 36.000 0.00 0.00 0.00 1.28
5298 5589 2.408565 AGTCGATCAATGGGGGTACAT 58.591 47.619 0.00 0.00 0.00 2.29
5303 5594 0.394216 TGCAAGTCGATCAATGGGGG 60.394 55.000 0.00 0.00 0.00 5.40
5359 5653 5.810074 GCAGCCTAGCTAATAAAGATAGAGC 59.190 44.000 0.00 1.93 45.38 4.09
5361 5655 6.918067 TGCAGCCTAGCTAATAAAGATAGA 57.082 37.500 0.00 0.00 45.38 1.98
5362 5656 7.969536 TTTGCAGCCTAGCTAATAAAGATAG 57.030 36.000 0.00 0.00 42.74 2.08
5444 5748 1.493311 GTTGAAGCTTCGGCACTCG 59.507 57.895 21.11 0.00 44.74 4.18
5468 5772 7.041721 CCACAGTCATATTCTAGTGCTACAAA 58.958 38.462 0.00 0.00 0.00 2.83
5688 6006 3.399330 CGTGACAGATGTTGTTAGGGTT 58.601 45.455 0.00 0.00 41.05 4.11
5720 6038 1.320344 TGTCCTACAGTAGGCAGGCG 61.320 60.000 20.77 0.00 45.82 5.52
5721 6039 1.069358 GATGTCCTACAGTAGGCAGGC 59.931 57.143 20.77 13.59 45.82 4.85
5722 6040 2.625790 GAGATGTCCTACAGTAGGCAGG 59.374 54.545 20.77 1.00 45.82 4.85
5723 6041 2.625790 GGAGATGTCCTACAGTAGGCAG 59.374 54.545 20.77 0.00 45.82 4.85
5737 6055 0.387202 CGATCAAGGAGCGGAGATGT 59.613 55.000 0.00 0.00 37.82 3.06
5827 6145 3.518992 TTTTTCCTTACACTGGGGAGG 57.481 47.619 0.00 0.00 0.00 4.30
5844 6162 4.658435 AGGTAACATGGGCCTTTTCTTTTT 59.342 37.500 4.53 0.00 41.41 1.94
5845 6163 4.040339 CAGGTAACATGGGCCTTTTCTTTT 59.960 41.667 4.53 0.00 41.41 2.27


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

AutoCloner maintained by Alex Coulton.