Multiple sequence alignment - TraesCS5B01G396300

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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 TraesCS5B01G396300 chr5B 100.000 5928 0 0 1 5928 573220684 573226611 0.000000e+00 10948
1 TraesCS5B01G396300 chr5D 93.193 6023 267 56 1 5928 466224925 466230899 0.000000e+00 8719
2 TraesCS5B01G396300 chr5A 92.748 6012 264 61 1 5928 586598964 586604887 0.000000e+00 8528
3 TraesCS5B01G396300 chr5A 88.104 538 42 11 5045 5576 538233016 538232495 2.350000e-173 619
4 TraesCS5B01G396300 chr6A 87.146 529 46 11 5049 5571 218851046 218850534 1.110000e-161 580
5 TraesCS5B01G396300 chr3A 86.803 538 47 13 5045 5576 380636011 380636530 3.980000e-161 579


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 TraesCS5B01G396300 chr5B 573220684 573226611 5927 False 10948 10948 100.000 1 5928 1 chr5B.!!$F1 5927
1 TraesCS5B01G396300 chr5D 466224925 466230899 5974 False 8719 8719 93.193 1 5928 1 chr5D.!!$F1 5927
2 TraesCS5B01G396300 chr5A 586598964 586604887 5923 False 8528 8528 92.748 1 5928 1 chr5A.!!$F1 5927
3 TraesCS5B01G396300 chr5A 538232495 538233016 521 True 619 619 88.104 5045 5576 1 chr5A.!!$R1 531
4 TraesCS5B01G396300 chr6A 218850534 218851046 512 True 580 580 87.146 5049 5571 1 chr6A.!!$R1 522
5 TraesCS5B01G396300 chr3A 380636011 380636530 519 False 579 579 86.803 5045 5576 1 chr3A.!!$F1 531

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
541 543 0.108041 GGCCATTGATTGGGTTGCTG 60.108 55.000 0.0 0.0 46.55 4.41 F
542 544 0.108041 GCCATTGATTGGGTTGCTGG 60.108 55.000 0.0 0.0 46.55 4.85 F
1570 1634 0.108615 AACTGGCTCGGTTCTCATCG 60.109 55.000 0.0 0.0 0.00 3.84 F
1739 1803 0.319555 TGTTCGTAGGTCTGTGCTGC 60.320 55.000 0.0 0.0 0.00 5.25 F
2519 2613 0.878416 TTCCGAACATTTTCCCGCTG 59.122 50.000 0.0 0.0 0.00 5.18 F
3200 3311 1.222936 GGAGGCAGGTGTGAGGATG 59.777 63.158 0.0 0.0 0.00 3.51 F
4620 4766 0.940126 CCATATCTGCGTCACCTTGC 59.060 55.000 0.0 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2503 2597 0.591170 ACACAGCGGGAAAATGTTCG 59.409 50.000 0.00 0.00 34.28 3.95 R
2519 2613 6.946229 ACAATAAAGACATGACGAGTACAC 57.054 37.500 0.00 0.00 0.00 2.90 R
3200 3311 2.361737 GCAGACAGGGGGCCTTTC 60.362 66.667 0.84 0.00 31.03 2.62 R
3510 3621 6.000840 TCTGCAACATTACAAGGAATGTACA 58.999 36.000 10.86 11.07 46.84 2.90 R
3866 4010 0.251354 ATCTCAGGCACACGCAGAAT 59.749 50.000 0.00 0.00 41.24 2.40 R
4885 5032 1.580059 TCTGTTGGGGGATGTACTCC 58.420 55.000 0.00 0.00 44.11 3.85 R
5614 5781 1.134521 TCAGTGACGAACATATGGGCC 60.135 52.381 7.80 0.00 0.00 5.80 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 0.473755 ATGGTGACTGTGCAAGACCA 59.526 50.000 10.00 10.00 37.24 4.02
77 78 0.250901 AGTGGGCAGCTTGTAAGTGG 60.251 55.000 0.00 0.00 0.00 4.00
84 85 2.872038 GCAGCTTGTAAGTGGCAGTAGT 60.872 50.000 0.00 0.00 0.00 2.73
103 104 1.352622 TGACAGGAGGTTGCCCTTGT 61.353 55.000 0.00 0.00 42.86 3.16
153 154 4.773674 TGATGAGTTTTCTGGGATGCAATT 59.226 37.500 0.00 0.00 0.00 2.32
201 202 1.459450 GTTTGCTGGATAGGCCGAAA 58.541 50.000 0.00 0.00 40.66 3.46
262 263 2.669569 CTTGTCCACCCAGCACCG 60.670 66.667 0.00 0.00 0.00 4.94
494 495 4.184629 CAAGAGTAACTTCTGAATCCCGG 58.815 47.826 0.00 0.00 36.61 5.73
540 542 1.266867 GGGCCATTGATTGGGTTGCT 61.267 55.000 4.39 0.00 46.55 3.91
541 543 0.108041 GGCCATTGATTGGGTTGCTG 60.108 55.000 0.00 0.00 46.55 4.41
542 544 0.108041 GCCATTGATTGGGTTGCTGG 60.108 55.000 0.00 0.00 46.55 4.85
602 604 1.357137 TGTGTAGCTGGGAACATGGA 58.643 50.000 0.00 0.00 41.51 3.41
695 700 1.135373 CACGGCAACTCTACGAGTGAT 60.135 52.381 0.00 0.00 42.59 3.06
708 713 8.353684 ACTCTACGAGTGATCGATGAATAAAAT 58.646 33.333 0.54 0.00 41.76 1.82
753 759 0.109532 TCAATTCTCGGGTGGTTGCA 59.890 50.000 0.00 0.00 0.00 4.08
757 763 1.243902 TTCTCGGGTGGTTGCAAATC 58.756 50.000 0.00 0.00 0.00 2.17
787 793 6.367149 CGTTCAGTCTGATTTGAGATTCTTGA 59.633 38.462 2.68 0.00 0.00 3.02
827 849 2.724977 TGCAGTGCAGAGTACACTAC 57.275 50.000 15.37 0.00 46.44 2.73
828 850 2.239400 TGCAGTGCAGAGTACACTACT 58.761 47.619 15.37 0.00 46.44 2.57
829 851 3.418047 TGCAGTGCAGAGTACACTACTA 58.582 45.455 15.37 0.00 46.44 1.82
830 852 4.017126 TGCAGTGCAGAGTACACTACTAT 58.983 43.478 15.37 0.00 46.44 2.12
831 853 4.462834 TGCAGTGCAGAGTACACTACTATT 59.537 41.667 15.37 0.00 46.44 1.73
832 854 5.047306 TGCAGTGCAGAGTACACTACTATTT 60.047 40.000 15.37 0.00 46.44 1.40
833 855 5.869888 GCAGTGCAGAGTACACTACTATTTT 59.130 40.000 11.09 0.00 46.44 1.82
834 856 7.033791 GCAGTGCAGAGTACACTACTATTTTA 58.966 38.462 11.09 0.00 46.44 1.52
835 857 7.707035 GCAGTGCAGAGTACACTACTATTTTAT 59.293 37.037 11.09 0.00 46.44 1.40
836 858 9.587772 CAGTGCAGAGTACACTACTATTTTATT 57.412 33.333 0.00 0.00 46.44 1.40
852 874 9.110502 ACTATTTTATTTAGGCTTGCAGAGTAC 57.889 33.333 0.00 0.00 0.00 2.73
861 883 3.192844 GGCTTGCAGAGTACACTACACTA 59.807 47.826 0.00 0.00 0.00 2.74
862 884 4.167268 GCTTGCAGAGTACACTACACTAC 58.833 47.826 0.00 0.00 0.00 2.73
863 885 4.321008 GCTTGCAGAGTACACTACACTACA 60.321 45.833 0.00 0.00 0.00 2.74
864 886 5.769367 CTTGCAGAGTACACTACACTACAA 58.231 41.667 0.00 0.00 33.57 2.41
874 896 8.082852 AGTACACTACACTACAATTGTGAAGAG 58.917 37.037 21.42 12.49 38.65 2.85
875 897 6.223852 ACACTACACTACAATTGTGAAGAGG 58.776 40.000 21.42 11.13 38.65 3.69
880 902 7.639113 ACACTACAATTGTGAAGAGGAAAAA 57.361 32.000 21.42 0.00 38.65 1.94
903 963 1.165270 CCGTTCTAAACAGGCCTTGG 58.835 55.000 0.00 0.00 0.00 3.61
913 973 1.539869 AGGCCTTGGAGCAGAGGAA 60.540 57.895 0.00 0.00 34.91 3.36
1110 1170 2.507484 CTCCACAAGATCAAAGGTGCA 58.493 47.619 0.00 0.00 0.00 4.57
1111 1171 2.486982 CTCCACAAGATCAAAGGTGCAG 59.513 50.000 0.00 0.00 0.00 4.41
1114 1174 3.128242 CCACAAGATCAAAGGTGCAGATC 59.872 47.826 5.05 5.05 38.70 2.75
1152 1212 3.689346 GATCGACTGTAAACCCTCGTAC 58.311 50.000 0.00 0.00 0.00 3.67
1191 1252 2.003672 CAATCGGAGTTAACGCGGG 58.996 57.895 12.47 0.00 0.00 6.13
1194 1255 0.459063 ATCGGAGTTAACGCGGGTTC 60.459 55.000 22.08 8.53 37.58 3.62
1357 1421 1.076549 TCCACATGGTTTGGCTCCC 59.923 57.895 0.00 0.00 33.71 4.30
1358 1422 1.077265 CCACATGGTTTGGCTCCCT 59.923 57.895 0.00 0.00 0.00 4.20
1361 1425 0.779997 ACATGGTTTGGCTCCCTCTT 59.220 50.000 0.00 0.00 0.00 2.85
1364 1428 1.000771 GGTTTGGCTCCCTCTTCCC 60.001 63.158 0.00 0.00 0.00 3.97
1366 1430 1.465188 TTTGGCTCCCTCTTCCCCA 60.465 57.895 0.00 0.00 0.00 4.96
1380 1444 1.984570 CCCCACTCTCTCGCCTTCA 60.985 63.158 0.00 0.00 0.00 3.02
1418 1482 1.142748 CTGTCAGATCCTCACCGGC 59.857 63.158 0.00 0.00 0.00 6.13
1561 1625 1.376812 GTACCCCAAACTGGCTCGG 60.377 63.158 0.00 0.00 35.79 4.63
1570 1634 0.108615 AACTGGCTCGGTTCTCATCG 60.109 55.000 0.00 0.00 0.00 3.84
1739 1803 0.319555 TGTTCGTAGGTCTGTGCTGC 60.320 55.000 0.00 0.00 0.00 5.25
1933 1997 3.188786 GCTACCGCTTGTCTGCCG 61.189 66.667 0.00 0.00 0.00 5.69
2012 2076 5.766222 GCCTCTGGCTGTTATTTCATTATG 58.234 41.667 0.73 0.00 46.69 1.90
2013 2077 5.278660 GCCTCTGGCTGTTATTTCATTATGG 60.279 44.000 0.73 0.00 46.69 2.74
2014 2078 5.829924 CCTCTGGCTGTTATTTCATTATGGT 59.170 40.000 0.00 0.00 0.00 3.55
2015 2079 6.238842 CCTCTGGCTGTTATTTCATTATGGTG 60.239 42.308 0.00 0.00 0.00 4.17
2016 2080 6.186957 TCTGGCTGTTATTTCATTATGGTGT 58.813 36.000 0.00 0.00 0.00 4.16
2017 2081 7.342581 TCTGGCTGTTATTTCATTATGGTGTA 58.657 34.615 0.00 0.00 0.00 2.90
2018 2082 7.498900 TCTGGCTGTTATTTCATTATGGTGTAG 59.501 37.037 0.00 0.00 0.00 2.74
2019 2083 7.116075 TGGCTGTTATTTCATTATGGTGTAGT 58.884 34.615 0.00 0.00 0.00 2.73
2020 2084 7.066887 TGGCTGTTATTTCATTATGGTGTAGTG 59.933 37.037 0.00 0.00 0.00 2.74
2021 2085 7.417612 GCTGTTATTTCATTATGGTGTAGTGG 58.582 38.462 0.00 0.00 0.00 4.00
2022 2086 7.067008 GCTGTTATTTCATTATGGTGTAGTGGT 59.933 37.037 0.00 0.00 0.00 4.16
2023 2087 8.275015 TGTTATTTCATTATGGTGTAGTGGTG 57.725 34.615 0.00 0.00 0.00 4.17
2024 2088 7.885922 TGTTATTTCATTATGGTGTAGTGGTGT 59.114 33.333 0.00 0.00 0.00 4.16
2025 2089 9.386010 GTTATTTCATTATGGTGTAGTGGTGTA 57.614 33.333 0.00 0.00 0.00 2.90
2026 2090 7.859325 ATTTCATTATGGTGTAGTGGTGTAC 57.141 36.000 0.00 0.00 0.00 2.90
2044 2108 1.007038 CACAATGTGCCACACTGCC 60.007 57.895 6.14 0.00 35.11 4.85
2067 2131 3.458487 ACTTGTTACTCCCTGGTTGTTCT 59.542 43.478 0.00 0.00 0.00 3.01
2088 2169 5.875224 TCTCTGTCCTATCTGATGTAGGAG 58.125 45.833 9.02 5.52 46.23 3.69
2089 2170 4.402829 TCTGTCCTATCTGATGTAGGAGC 58.597 47.826 9.02 6.00 46.23 4.70
2123 2204 8.922058 AATCTGTCTTTTGTGATGCATTATTC 57.078 30.769 0.00 0.00 0.00 1.75
2124 2205 7.451501 TCTGTCTTTTGTGATGCATTATTCA 57.548 32.000 0.00 0.00 0.00 2.57
2133 2214 5.300034 TGTGATGCATTATTCATTGAGGTCC 59.700 40.000 0.00 0.00 0.00 4.46
2152 2233 4.878397 GGTCCTCATTTCTTCATGAATCGT 59.122 41.667 8.96 0.00 32.63 3.73
2153 2234 5.007136 GGTCCTCATTTCTTCATGAATCGTC 59.993 44.000 8.96 0.00 32.63 4.20
2181 2264 5.411053 AGCTGTTTTCATTAGTTCTCTCAGC 59.589 40.000 0.00 0.00 42.88 4.26
2182 2265 5.180117 GCTGTTTTCATTAGTTCTCTCAGCA 59.820 40.000 0.00 0.00 42.36 4.41
2183 2266 6.620303 GCTGTTTTCATTAGTTCTCTCAGCAG 60.620 42.308 0.00 0.00 42.36 4.24
2218 2302 3.536158 TTTCATCGCCTTTTCACTTCG 57.464 42.857 0.00 0.00 0.00 3.79
2225 2309 3.059188 TCGCCTTTTCACTTCGCTTTTAG 60.059 43.478 0.00 0.00 0.00 1.85
2232 2316 6.870971 TTTCACTTCGCTTTTAGTAACCAT 57.129 33.333 0.00 0.00 0.00 3.55
2291 2375 2.430694 GTGGCAAAAGGGTATGGATTCC 59.569 50.000 0.00 0.00 0.00 3.01
2297 2381 5.509670 GCAAAAGGGTATGGATTCCTATTGC 60.510 44.000 3.95 5.67 33.52 3.56
2311 2395 4.633175 TCCTATTGCGTTGTGAGTGTTTA 58.367 39.130 0.00 0.00 0.00 2.01
2342 2436 7.498900 TGATAACATGTTTAATCCTTCGATGCT 59.501 33.333 17.78 0.00 0.00 3.79
2387 2481 1.413077 GTTCCTTCATCCTCCCTACCG 59.587 57.143 0.00 0.00 0.00 4.02
2409 2503 5.506649 CCGCTTGTCCTGCTTTACTTAAAAA 60.507 40.000 0.00 0.00 0.00 1.94
2440 2534 1.073763 TGTAAACAGTGGGATGCTGCT 59.926 47.619 0.00 0.00 37.47 4.24
2466 2560 7.493971 TCTTTTAGCAGAGATTTAGAGCATCAC 59.506 37.037 0.00 0.00 37.82 3.06
2475 2569 7.609097 AGATTTAGAGCATCACAATCTCCTA 57.391 36.000 0.00 0.00 40.21 2.94
2519 2613 0.878416 TTCCGAACATTTTCCCGCTG 59.122 50.000 0.00 0.00 0.00 5.18
2596 2691 4.275196 GTGGAGGGTGAAAAGAAAGTGTAC 59.725 45.833 0.00 0.00 0.00 2.90
2599 2694 3.883489 AGGGTGAAAAGAAAGTGTACTGC 59.117 43.478 0.00 0.00 0.00 4.40
2615 2710 6.647481 AGTGTACTGCATAACAAACGTCAATA 59.353 34.615 3.07 0.00 0.00 1.90
2635 2730 8.983724 GTCAATACTGTAAGCTTCTATGATTCC 58.016 37.037 0.00 0.00 37.60 3.01
2643 2748 9.935241 TGTAAGCTTCTATGATTCCATCTAATC 57.065 33.333 0.00 0.00 36.57 1.75
2646 2751 7.393216 AGCTTCTATGATTCCATCTAATCACC 58.607 38.462 1.63 0.00 45.90 4.02
2649 2754 7.250032 TCTATGATTCCATCTAATCACCCAG 57.750 40.000 1.63 1.41 45.90 4.45
2656 2761 8.685257 ATTCCATCTAATCACCCAGTATGATA 57.315 34.615 0.00 0.00 39.69 2.15
2662 2767 9.950496 ATCTAATCACCCAGTATGATATGTTTC 57.050 33.333 0.00 0.00 39.69 2.78
2734 2839 3.011144 TCCCCATTCCAGTTAGCATTGAA 59.989 43.478 0.00 0.00 0.00 2.69
2790 2896 9.950496 ACTCATAACAATCTTTGTCTTCATAGT 57.050 29.630 0.00 0.00 44.59 2.12
2941 3047 4.204012 AGAAAGTGGGATTTCGACAAACA 58.796 39.130 0.00 0.00 42.73 2.83
2977 3083 5.481200 CAGCATGTGAAAGAGTAATGAGG 57.519 43.478 0.00 0.00 0.00 3.86
3041 3147 7.607991 AGAGTATCCTTGTTATTCCACAAACTG 59.392 37.037 0.00 0.00 36.22 3.16
3200 3311 1.222936 GGAGGCAGGTGTGAGGATG 59.777 63.158 0.00 0.00 0.00 3.51
3212 3323 1.228510 GAGGATGAAAGGCCCCCTG 59.771 63.158 0.00 0.00 32.13 4.45
3256 3367 5.437060 TCTTTGCAGTCTTCCTACAGTTTT 58.563 37.500 0.00 0.00 0.00 2.43
3464 3575 2.555325 CAAGAAGGCATGTGCTCTTTCA 59.445 45.455 4.84 0.00 41.70 2.69
3695 3836 6.588719 AATAGCATCAAAGGCAGTGTAAAA 57.411 33.333 0.00 0.00 0.00 1.52
3752 3895 6.857964 CCAAGTGAAGTGTGATTTTGTACATC 59.142 38.462 0.00 0.00 0.00 3.06
3817 3961 1.771255 ACTGACCAACTCTTCCTGCTT 59.229 47.619 0.00 0.00 0.00 3.91
4174 4318 8.007716 CCTATTACGCGTATTCCAATAACTTTG 58.992 37.037 21.30 4.21 0.00 2.77
4176 4320 7.824704 TTACGCGTATTCCAATAACTTTGTA 57.175 32.000 21.30 0.00 0.00 2.41
4311 4455 5.009410 AGTGAAATCTTCTTCCAAGCACAAG 59.991 40.000 0.00 0.00 0.00 3.16
4408 4554 8.429641 AGTTCAAGTCCAACTCTAGAATTTGTA 58.570 33.333 11.15 0.00 27.00 2.41
4620 4766 0.940126 CCATATCTGCGTCACCTTGC 59.060 55.000 0.00 0.00 0.00 4.01
4630 4777 1.135083 CGTCACCTTGCCGACTCTAAT 60.135 52.381 0.00 0.00 0.00 1.73
4691 4838 4.134563 GCTTTCACCTGGTCAGTTCTAAA 58.865 43.478 0.00 0.00 0.00 1.85
4885 5032 1.798223 TCCATTTCGTTTCTGTCGCAG 59.202 47.619 1.02 1.02 0.00 5.18
4971 5118 3.274288 GCAGAATTGTGCTAGGCTAAGT 58.726 45.455 19.63 0.00 40.54 2.24
4990 5137 4.983671 AGTGTCTCCTTTTGTTTTGGTC 57.016 40.909 0.00 0.00 0.00 4.02
5047 5201 5.441500 TCACCTTGGTATTCACAACAAGAA 58.558 37.500 2.52 0.00 42.07 2.52
5162 5326 2.360801 GTGCAAGGCAACCTGTTAGAAA 59.639 45.455 0.00 0.00 41.47 2.52
5218 5383 6.127793 TCTTAGTTCTACTAGGTCACCATCC 58.872 44.000 0.00 0.00 31.47 3.51
5251 5416 7.051000 GCAAGTTCCTATTTACCTGAGATCTT 58.949 38.462 0.00 0.00 0.00 2.40
5359 5524 3.321968 TGCATCTACACAGGCTACCATAG 59.678 47.826 0.00 0.00 0.00 2.23
5471 5636 3.674997 TCTTTCTTACACATGTCCAGGC 58.325 45.455 0.00 0.00 0.00 4.85
5483 5648 0.604780 GTCCAGGCGCATATGAGCAT 60.605 55.000 28.92 21.83 42.80 3.79
5584 5751 5.305585 ACAGTGTTAATCGACCATTCAACT 58.694 37.500 0.00 0.00 0.00 3.16
5670 5837 5.519808 TGAGTAAGGTCATATGTGGAGAGT 58.480 41.667 1.90 0.00 0.00 3.24
5821 5996 7.936847 AGTTCACAAATCAACACTCATTACCTA 59.063 33.333 0.00 0.00 0.00 3.08
5830 6005 8.918202 TCAACACTCATTACCTACAAAATCTT 57.082 30.769 0.00 0.00 0.00 2.40
5892 6069 2.421529 GCTTACCCCACTTTCCGATCAT 60.422 50.000 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.250038 GCTCTGGTCTTGCACAGTCA 60.250 55.000 2.37 0.48 36.17 3.41
63 64 1.734465 CTACTGCCACTTACAAGCTGC 59.266 52.381 0.00 0.00 0.00 5.25
77 78 1.941668 GCAACCTCCTGTCACTACTGC 60.942 57.143 0.00 0.00 0.00 4.40
103 104 8.730680 GGCAATCTAAACACTATCAAAGAAGAA 58.269 33.333 0.00 0.00 0.00 2.52
153 154 7.566760 TTCAGATTGCTTTCAGTTAAGTGAA 57.433 32.000 19.59 19.59 34.56 3.18
201 202 6.715347 AAACAGCTGTTATTTTCAAGGAGT 57.285 33.333 31.31 9.07 37.25 3.85
271 272 2.836636 TCTCCTGTATCAGTGCCTCT 57.163 50.000 0.00 0.00 0.00 3.69
503 505 0.176680 CCTGGTTCACATCTCGAGGG 59.823 60.000 13.56 8.03 0.00 4.30
540 542 0.540365 CCAAAGGGCTTGCTCTTCCA 60.540 55.000 8.28 0.00 33.27 3.53
541 543 1.253593 CCCAAAGGGCTTGCTCTTCC 61.254 60.000 8.28 0.00 35.35 3.46
542 544 0.251341 TCCCAAAGGGCTTGCTCTTC 60.251 55.000 8.28 0.00 43.94 2.87
613 615 1.280421 AGCTCCTCCTCAACCATCAAC 59.720 52.381 0.00 0.00 0.00 3.18
731 737 2.710377 CAACCACCCGAGAATTGATCA 58.290 47.619 0.00 0.00 0.00 2.92
743 749 0.603065 GTCTGGATTTGCAACCACCC 59.397 55.000 0.00 0.00 32.44 4.61
820 842 9.893634 TGCAAGCCTAAATAAAATAGTAGTGTA 57.106 29.630 0.00 0.00 0.00 2.90
821 843 8.801882 TGCAAGCCTAAATAAAATAGTAGTGT 57.198 30.769 0.00 0.00 0.00 3.55
822 844 9.109393 TCTGCAAGCCTAAATAAAATAGTAGTG 57.891 33.333 0.00 0.00 0.00 2.74
823 845 9.331282 CTCTGCAAGCCTAAATAAAATAGTAGT 57.669 33.333 0.00 0.00 0.00 2.73
824 846 9.331282 ACTCTGCAAGCCTAAATAAAATAGTAG 57.669 33.333 0.00 0.00 0.00 2.57
826 848 9.110502 GTACTCTGCAAGCCTAAATAAAATAGT 57.889 33.333 0.00 0.00 0.00 2.12
827 849 9.109393 TGTACTCTGCAAGCCTAAATAAAATAG 57.891 33.333 0.00 0.00 0.00 1.73
828 850 8.889717 GTGTACTCTGCAAGCCTAAATAAAATA 58.110 33.333 0.00 0.00 0.00 1.40
829 851 7.611855 AGTGTACTCTGCAAGCCTAAATAAAAT 59.388 33.333 0.00 0.00 0.00 1.82
830 852 6.940298 AGTGTACTCTGCAAGCCTAAATAAAA 59.060 34.615 0.00 0.00 0.00 1.52
831 853 6.472887 AGTGTACTCTGCAAGCCTAAATAAA 58.527 36.000 0.00 0.00 0.00 1.40
832 854 6.049955 AGTGTACTCTGCAAGCCTAAATAA 57.950 37.500 0.00 0.00 0.00 1.40
833 855 5.677319 AGTGTACTCTGCAAGCCTAAATA 57.323 39.130 0.00 0.00 0.00 1.40
834 856 4.559862 AGTGTACTCTGCAAGCCTAAAT 57.440 40.909 0.00 0.00 0.00 1.40
835 857 4.282449 TGTAGTGTACTCTGCAAGCCTAAA 59.718 41.667 12.47 0.00 0.00 1.85
836 858 3.830178 TGTAGTGTACTCTGCAAGCCTAA 59.170 43.478 12.47 0.00 0.00 2.69
837 859 3.192844 GTGTAGTGTACTCTGCAAGCCTA 59.807 47.826 15.81 0.00 32.48 3.93
838 860 2.028930 GTGTAGTGTACTCTGCAAGCCT 60.029 50.000 15.81 0.00 32.48 4.58
839 861 2.028930 AGTGTAGTGTACTCTGCAAGCC 60.029 50.000 15.81 5.83 32.48 4.35
840 862 3.305398 AGTGTAGTGTACTCTGCAAGC 57.695 47.619 15.81 6.45 32.48 4.01
841 863 5.372547 TGTAGTGTAGTGTACTCTGCAAG 57.627 43.478 15.81 0.00 40.27 4.01
852 874 6.455647 TCCTCTTCACAATTGTAGTGTAGTG 58.544 40.000 11.53 3.94 36.27 2.74
880 902 2.940158 AGGCCTGTTTAGAACGGTTTT 58.060 42.857 3.11 0.00 35.99 2.43
884 936 1.165270 CCAAGGCCTGTTTAGAACGG 58.835 55.000 5.69 0.00 37.52 4.44
889 949 1.003580 TCTGCTCCAAGGCCTGTTTAG 59.996 52.381 5.69 2.82 0.00 1.85
903 963 2.175878 TGTGAAAGCTTCCTCTGCTC 57.824 50.000 0.00 0.00 40.22 4.26
1110 1170 0.938926 AGGAGAGGGAAGGGGGATCT 60.939 60.000 0.00 0.00 0.00 2.75
1111 1171 0.472925 GAGGAGAGGGAAGGGGGATC 60.473 65.000 0.00 0.00 0.00 3.36
1114 1174 2.319410 ATCGAGGAGAGGGAAGGGGG 62.319 65.000 0.00 0.00 0.00 5.40
1357 1421 1.671901 GGCGAGAGAGTGGGGAAGAG 61.672 65.000 0.00 0.00 0.00 2.85
1358 1422 1.682684 GGCGAGAGAGTGGGGAAGA 60.683 63.158 0.00 0.00 0.00 2.87
1361 1425 1.682684 GAAGGCGAGAGAGTGGGGA 60.683 63.158 0.00 0.00 0.00 4.81
1364 1428 2.169832 TTTTGAAGGCGAGAGAGTGG 57.830 50.000 0.00 0.00 0.00 4.00
1366 1430 3.513515 AGAGATTTTGAAGGCGAGAGAGT 59.486 43.478 0.00 0.00 0.00 3.24
1380 1444 1.168714 GCTTGGTCGGCAGAGATTTT 58.831 50.000 0.00 0.00 0.00 1.82
1561 1625 4.022464 ACAACGAGAGATCGATGAGAAC 57.978 45.455 0.54 0.00 38.86 3.01
1570 1634 5.276773 GCATGATCAGAAACAACGAGAGATC 60.277 44.000 0.09 0.00 0.00 2.75
1739 1803 3.869272 GGCATCGCAACCGCAGAG 61.869 66.667 0.00 0.00 38.40 3.35
1751 1815 2.277969 CGCATAGATGGATCAGGCATC 58.722 52.381 0.00 0.00 0.00 3.91
1755 1819 3.256879 ACACTACGCATAGATGGATCAGG 59.743 47.826 0.00 0.00 32.23 3.86
1858 1922 7.087007 TGAAGAGTATGCAGATATCGTTGATC 58.913 38.462 0.00 0.00 0.00 2.92
1933 1997 3.978718 AACTGAAGCTTCTGCAAAGAC 57.021 42.857 27.53 1.44 42.74 3.01
2006 2070 5.483811 TGTGTACACCACTACACCATAATG 58.516 41.667 22.91 0.00 44.08 1.90
2012 2076 3.496884 CACATTGTGTACACCACTACACC 59.503 47.826 22.91 0.00 44.08 4.16
2013 2077 3.059188 GCACATTGTGTACACCACTACAC 60.059 47.826 22.91 4.08 44.68 2.90
2014 2078 3.135225 GCACATTGTGTACACCACTACA 58.865 45.455 22.91 0.15 44.81 2.74
2015 2079 2.482721 GGCACATTGTGTACACCACTAC 59.517 50.000 22.91 8.28 44.81 2.73
2016 2080 2.104963 TGGCACATTGTGTACACCACTA 59.895 45.455 22.91 6.61 44.81 2.74
2017 2081 1.133945 TGGCACATTGTGTACACCACT 60.134 47.619 22.91 4.96 44.81 4.00
2018 2082 1.001815 GTGGCACATTGTGTACACCAC 60.002 52.381 22.91 22.61 44.52 4.16
2019 2083 1.313772 GTGGCACATTGTGTACACCA 58.686 50.000 22.91 13.08 44.52 4.17
2020 2084 1.001815 GTGTGGCACATTGTGTACACC 60.002 52.381 29.20 19.30 44.52 4.16
2021 2085 1.946768 AGTGTGGCACATTGTGTACAC 59.053 47.619 30.62 30.62 44.98 2.90
2022 2086 1.946081 CAGTGTGGCACATTGTGTACA 59.054 47.619 28.71 18.21 44.52 2.90
2023 2087 1.334960 GCAGTGTGGCACATTGTGTAC 60.335 52.381 34.00 19.55 44.52 2.90
2024 2088 0.950836 GCAGTGTGGCACATTGTGTA 59.049 50.000 34.00 6.25 44.52 2.90
2025 2089 1.735360 GCAGTGTGGCACATTGTGT 59.265 52.632 34.00 12.74 44.52 3.72
2026 2090 1.007038 GGCAGTGTGGCACATTGTG 60.007 57.895 34.00 25.97 44.52 3.33
2044 2108 3.208747 ACAACCAGGGAGTAACAAGTG 57.791 47.619 0.00 0.00 0.00 3.16
2067 2131 4.141158 TGCTCCTACATCAGATAGGACAGA 60.141 45.833 0.00 0.00 42.74 3.41
2088 2169 8.801715 TCACAAAAGACAGATTAAGAAAATGC 57.198 30.769 0.00 0.00 0.00 3.56
2123 2204 5.884232 TCATGAAGAAATGAGGACCTCAATG 59.116 40.000 27.69 22.13 44.04 2.82
2124 2205 6.070951 TCATGAAGAAATGAGGACCTCAAT 57.929 37.500 27.69 17.48 44.04 2.57
2133 2214 5.814188 TCCTGACGATTCATGAAGAAATGAG 59.186 40.000 14.54 5.43 40.22 2.90
2152 2233 5.869579 AGAACTAATGAAAACAGCTCCTGA 58.130 37.500 0.00 0.00 35.18 3.86
2153 2234 5.936956 AGAGAACTAATGAAAACAGCTCCTG 59.063 40.000 0.00 0.00 37.52 3.86
2182 2265 5.575957 CGATGAAATAAATGCAGCAGAACT 58.424 37.500 0.00 0.00 0.00 3.01
2183 2266 4.205792 GCGATGAAATAAATGCAGCAGAAC 59.794 41.667 0.00 0.00 0.00 3.01
2192 2276 7.253420 CGAAGTGAAAAGGCGATGAAATAAATG 60.253 37.037 0.00 0.00 0.00 2.32
2203 2287 1.305201 AAAGCGAAGTGAAAAGGCGA 58.695 45.000 0.00 0.00 0.00 5.54
2218 2302 9.774742 CAGAAATTGTAGATGGTTACTAAAAGC 57.225 33.333 0.00 0.00 0.00 3.51
2225 2309 6.595716 AGTGAGCAGAAATTGTAGATGGTTAC 59.404 38.462 0.00 0.00 0.00 2.50
2232 2316 3.753272 GCCAAGTGAGCAGAAATTGTAGA 59.247 43.478 0.00 0.00 0.00 2.59
2291 2375 7.851822 AAATTAAACACTCACAACGCAATAG 57.148 32.000 0.00 0.00 0.00 1.73
2297 2381 9.227490 TGTTATCAAAATTAAACACTCACAACG 57.773 29.630 0.00 0.00 0.00 4.10
2409 2503 4.335416 CCACTGTTTACACCCAGATCATT 58.665 43.478 0.00 0.00 32.93 2.57
2419 2513 1.200020 GCAGCATCCCACTGTTTACAC 59.800 52.381 0.00 0.00 37.47 2.90
2420 2514 1.073763 AGCAGCATCCCACTGTTTACA 59.926 47.619 0.00 0.00 37.47 2.41
2421 2515 1.740025 GAGCAGCATCCCACTGTTTAC 59.260 52.381 0.00 0.00 37.47 2.01
2440 2534 7.493971 GTGATGCTCTAAATCTCTGCTAAAAGA 59.506 37.037 0.00 0.00 0.00 2.52
2452 2546 7.877097 ACATAGGAGATTGTGATGCTCTAAATC 59.123 37.037 0.00 0.00 0.00 2.17
2503 2597 0.591170 ACACAGCGGGAAAATGTTCG 59.409 50.000 0.00 0.00 34.28 3.95
2519 2613 6.946229 ACAATAAAGACATGACGAGTACAC 57.054 37.500 0.00 0.00 0.00 2.90
2596 2691 5.927030 ACAGTATTGACGTTTGTTATGCAG 58.073 37.500 0.00 0.00 0.00 4.41
2599 2694 7.739295 AGCTTACAGTATTGACGTTTGTTATG 58.261 34.615 0.00 0.00 0.00 1.90
2635 2730 9.730705 AAACATATCATACTGGGTGATTAGATG 57.269 33.333 3.03 4.28 37.48 2.90
2643 2748 9.645059 CATACTAGAAACATATCATACTGGGTG 57.355 37.037 0.00 0.00 0.00 4.61
2646 2751 9.881649 ATGCATACTAGAAACATATCATACTGG 57.118 33.333 0.00 0.00 0.00 4.00
2662 2767 8.103948 AGGCTAGCAAAATTAATGCATACTAG 57.896 34.615 18.24 10.53 46.22 2.57
2665 2770 8.424274 AAAAGGCTAGCAAAATTAATGCATAC 57.576 30.769 18.24 6.41 46.22 2.39
2679 2784 4.098914 TGAAGAAGGAAAAAGGCTAGCA 57.901 40.909 18.24 0.00 0.00 3.49
2734 2839 8.397148 CAAATTGTTAAACAACCTTTGATTGCT 58.603 29.630 11.95 0.00 41.40 3.91
3200 3311 2.361737 GCAGACAGGGGGCCTTTC 60.362 66.667 0.84 0.00 31.03 2.62
3510 3621 6.000840 TCTGCAACATTACAAGGAATGTACA 58.999 36.000 10.86 11.07 46.84 2.90
3817 3961 9.973661 TTAAATAGAATGAGAATTGGACAAGGA 57.026 29.630 0.00 0.00 0.00 3.36
3866 4010 0.251354 ATCTCAGGCACACGCAGAAT 59.749 50.000 0.00 0.00 41.24 2.40
4042 4186 5.397360 TCCTATCTGAAGCAGGATACATCA 58.603 41.667 2.83 0.00 33.48 3.07
4043 4187 5.105392 CCTCCTATCTGAAGCAGGATACATC 60.105 48.000 6.51 0.00 37.82 3.06
4174 4318 2.917933 TGCAACCCACATCATAGCTAC 58.082 47.619 0.00 0.00 0.00 3.58
4176 4320 2.025981 TCTTGCAACCCACATCATAGCT 60.026 45.455 0.00 0.00 0.00 3.32
4323 4467 5.137551 GCTTGGAATACAGGGGCTAAATAA 58.862 41.667 0.00 0.00 0.00 1.40
4453 4599 9.328721 GCATTTGGCATTTTGTAAGAATAAAAC 57.671 29.630 0.00 0.00 43.97 2.43
4540 4686 5.343249 ACAGATTACGTACACGGGATAAAC 58.657 41.667 6.72 0.00 44.95 2.01
4620 4766 2.032620 ACCTACTGCCATTAGAGTCGG 58.967 52.381 0.00 0.00 32.53 4.79
4647 4794 5.010012 AGCAGTCATAAACCTTTTGGAACAG 59.990 40.000 0.00 0.00 42.39 3.16
4691 4838 5.388408 TTTTAAACACAAACCCGTTGACT 57.612 34.783 0.00 0.00 39.87 3.41
4885 5032 1.580059 TCTGTTGGGGGATGTACTCC 58.420 55.000 0.00 0.00 44.11 3.85
4971 5118 4.082463 GTGTGACCAAAACAAAAGGAGACA 60.082 41.667 0.00 0.00 0.00 3.41
4990 5137 2.682856 ACAAGCAACTACAAGTGGTGTG 59.317 45.455 0.00 0.00 41.89 3.82
5047 5201 5.163663 CGGTATACACCAATTGCAGTCAAAT 60.164 40.000 5.01 0.00 46.14 2.32
5162 5326 4.414846 AGAGTTCCCTATTCAGGCATTCAT 59.585 41.667 0.00 0.00 41.08 2.57
5230 5395 7.015779 AGGCTAAGATCTCAGGTAAATAGGAAC 59.984 40.741 0.00 0.00 0.00 3.62
5251 5416 3.019003 GCTCGGCAAGTGGAGGCTA 62.019 63.158 0.00 0.00 0.00 3.93
5338 5503 2.918712 ATGGTAGCCTGTGTAGATGC 57.081 50.000 0.00 0.00 0.00 3.91
5359 5524 5.594926 CCATGAAATATTTCCAGCTTCCAC 58.405 41.667 22.42 0.00 36.36 4.02
5471 5636 4.393990 ACACAATGGATATGCTCATATGCG 59.606 41.667 13.96 0.00 42.71 4.73
5565 5732 7.972832 ACTTTAGTTGAATGGTCGATTAACA 57.027 32.000 0.00 0.00 0.00 2.41
5571 5738 8.662141 GCTTAAATACTTTAGTTGAATGGTCGA 58.338 33.333 0.00 0.00 0.00 4.20
5603 5770 5.408604 CGAACATATGGGCCTGTACTTAATC 59.591 44.000 4.53 0.00 0.00 1.75
5614 5781 1.134521 TCAGTGACGAACATATGGGCC 60.135 52.381 7.80 0.00 0.00 5.80
5670 5837 2.110213 GTTGACCAGTCCGGCACA 59.890 61.111 0.00 0.00 39.03 4.57
5821 5996 7.295672 TCCCTCCATCATATCCTAAGATTTTGT 59.704 37.037 0.00 0.00 33.67 2.83
5830 6005 7.621285 CAGTATTCTTCCCTCCATCATATCCTA 59.379 40.741 0.00 0.00 0.00 2.94
5892 6069 4.162888 TCTTGAAGCAGCTGATCTGGATAA 59.837 41.667 20.43 3.98 43.06 1.75


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

AutoCloner maintained by Alex Coulton.