Multiple sequence alignment - TraesCS7D01G131100

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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 TraesCS7D01G131100 chr7D 100.000 6329 0 0 1 6329 83094552 83100880 0.000000e+00 11688.0
1 TraesCS7D01G131100 chr7D 95.358 754 28 4 4943 5690 83346645 83347397 0.000000e+00 1192.0
2 TraesCS7D01G131100 chr7D 94.245 278 12 2 5906 6182 83348545 83348819 7.590000e-114 422.0
3 TraesCS7D01G131100 chr7D 93.970 199 12 0 5692 5890 83347561 83347759 1.030000e-77 302.0
4 TraesCS7D01G131100 chr7D 91.892 37 3 0 4820 4856 377210412 377210448 1.100000e-02 52.8
5 TraesCS7D01G131100 chr7A 91.566 3557 163 58 1 3485 85076866 85080357 0.000000e+00 4780.0
6 TraesCS7D01G131100 chr7A 96.623 1362 41 3 4821 6182 85081767 85083123 0.000000e+00 2255.0
7 TraesCS7D01G131100 chr7A 96.122 1341 33 5 3484 4823 85080419 85081741 0.000000e+00 2170.0
8 TraesCS7D01G131100 chr7B 93.402 2607 98 17 922 3485 32470935 32473510 0.000000e+00 3794.0
9 TraesCS7D01G131100 chr7B 95.709 1305 41 2 4878 6182 32475184 32476473 0.000000e+00 2085.0
10 TraesCS7D01G131100 chr7B 96.949 1147 31 4 3484 4628 32473607 32474751 0.000000e+00 1921.0
11 TraesCS7D01G131100 chr7B 88.073 981 63 20 1 937 32469949 32470919 0.000000e+00 1114.0
12 TraesCS7D01G131100 chr7B 95.556 135 6 0 4689 4823 32475036 32475170 3.840000e-52 217.0
13 TraesCS7D01G131100 chr3A 79.524 840 112 30 5083 5886 203414614 203413799 1.550000e-150 544.0
14 TraesCS7D01G131100 chr3A 100.000 29 0 0 4837 4865 712148009 712147981 3.000000e-03 54.7
15 TraesCS7D01G131100 chr3D 83.455 550 63 16 5335 5875 165588450 165587920 2.650000e-133 486.0
16 TraesCS7D01G131100 chr3D 87.719 171 15 1 6129 6293 165587911 165587741 1.800000e-45 195.0
17 TraesCS7D01G131100 chr3D 100.000 28 0 0 4829 4856 500343973 500343946 1.100000e-02 52.8
18 TraesCS7D01G131100 chr3B 82.056 574 70 19 5326 5886 240805139 240804586 5.780000e-125 459.0
19 TraesCS7D01G131100 chr3B 85.463 454 50 8 252 700 433936951 433937393 5.780000e-125 459.0
20 TraesCS7D01G131100 chr3B 88.304 171 14 3 6129 6293 240804588 240804418 3.870000e-47 200.0
21 TraesCS7D01G131100 chr3B 91.892 37 3 0 4820 4856 527936949 527936985 1.100000e-02 52.8
22 TraesCS7D01G131100 chr4B 100.000 28 0 0 4829 4856 392962551 392962524 1.100000e-02 52.8
23 TraesCS7D01G131100 chr2D 100.000 28 0 0 4792 4819 608796759 608796786 1.100000e-02 52.8
24 TraesCS7D01G131100 chr1D 100.000 28 0 0 4829 4856 157328249 157328222 1.100000e-02 52.8


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 TraesCS7D01G131100 chr7D 83094552 83100880 6328 False 11688.000000 11688 100.000000 1 6329 1 chr7D.!!$F1 6328
1 TraesCS7D01G131100 chr7D 83346645 83348819 2174 False 638.666667 1192 94.524333 4943 6182 3 chr7D.!!$F3 1239
2 TraesCS7D01G131100 chr7A 85076866 85083123 6257 False 3068.333333 4780 94.770333 1 6182 3 chr7A.!!$F1 6181
3 TraesCS7D01G131100 chr7B 32469949 32476473 6524 False 1826.200000 3794 93.937800 1 6182 5 chr7B.!!$F1 6181
4 TraesCS7D01G131100 chr3A 203413799 203414614 815 True 544.000000 544 79.524000 5083 5886 1 chr3A.!!$R1 803
5 TraesCS7D01G131100 chr3D 165587741 165588450 709 True 340.500000 486 85.587000 5335 6293 2 chr3D.!!$R2 958
6 TraesCS7D01G131100 chr3B 240804418 240805139 721 True 329.500000 459 85.180000 5326 6293 2 chr3B.!!$R1 967

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
465 489 0.036164 ACAACCGTGCCAAGCAGATA 59.964 50.00 0.00 0.00 40.08 1.98 F
858 920 0.462759 GCCTTAGTCGGCTTCTGCAT 60.463 55.00 0.00 0.00 46.63 3.96 F
1784 1920 0.464036 TCGGGGTGTTAGCTATGCAG 59.536 55.00 0.00 0.00 0.00 4.41 F
3327 3478 0.519999 GAATGCTGCTCTTTGACGCG 60.520 55.00 3.53 3.53 0.00 6.01 F
3567 3816 3.645212 TCATTTGCATTTTGGACAAGGGA 59.355 39.13 0.00 0.00 0.00 4.20 F
4654 4905 0.324943 TCTTTTTCGGGAGAGCCTGG 59.675 55.00 0.00 0.00 41.20 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 1452 0.248565 TGTCACATCAGAGAGCAGGC 59.751 55.000 0.00 0.0 0.00 4.85 R
2474 2621 0.110295 TGGCAGAAGGCTTGCTAACA 59.890 50.000 3.46 0.0 44.01 2.41 R
3577 3826 1.002888 CACTGAGGACTGGACAGCAAT 59.997 52.381 0.00 0.0 35.38 3.56 R
4645 4896 0.392193 CATGTGACACCCAGGCTCTC 60.392 60.000 2.45 0.0 0.00 3.20 R
4823 5326 0.944386 TCCAAAAGAAGTGTCGCTGC 59.056 50.000 0.00 0.0 0.00 5.25 R
5575 6103 0.038618 CACCTCGACGATGACAACCA 60.039 55.000 7.16 0.0 0.00 3.67 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
95 96 5.464057 ATGTTTTCACATCAACTGCATGTTG 59.536 36.000 17.67 17.67 44.75 3.33
119 120 2.747177 TGTACCCCTACACCATCTGAG 58.253 52.381 0.00 0.00 0.00 3.35
203 211 2.951101 AACGGCGGGGACAGGTAAG 61.951 63.158 13.24 0.00 0.00 2.34
224 245 3.888323 AGCAACCACACATGTAATTCACA 59.112 39.130 0.00 0.00 42.69 3.58
227 248 3.826524 ACCACACATGTAATTCACACCA 58.173 40.909 0.00 0.00 40.86 4.17
245 267 2.628657 ACCAAGCTACCGATGGATACTC 59.371 50.000 8.39 0.00 37.66 2.59
260 282 7.703621 CGATGGATACTCGGTAAAAACTTCTAA 59.296 37.037 0.00 0.00 34.82 2.10
306 328 0.688749 AATCTGCCCAATTCAGCCCC 60.689 55.000 0.00 0.00 0.00 5.80
325 347 3.433615 CCCCGAGCTATTGATTTCGATTC 59.566 47.826 0.00 0.00 35.19 2.52
339 361 8.737168 TGATTTCGATTCTATTTCATCAAGGT 57.263 30.769 0.00 0.00 0.00 3.50
340 362 9.830975 TGATTTCGATTCTATTTCATCAAGGTA 57.169 29.630 0.00 0.00 0.00 3.08
369 391 2.036217 TCCTAAAACGCGGAGAAGTTCA 59.964 45.455 12.47 0.00 0.00 3.18
392 414 1.509787 CACAAATCGAAGCGCACGG 60.510 57.895 22.26 11.61 0.00 4.94
453 477 2.466846 CAACGTAGAGACAACAACCGT 58.533 47.619 0.00 0.00 0.00 4.83
465 489 0.036164 ACAACCGTGCCAAGCAGATA 59.964 50.000 0.00 0.00 40.08 1.98
491 515 2.560861 GCGCACCAAATCGCTCAA 59.439 55.556 0.30 0.00 46.92 3.02
492 516 1.081509 GCGCACCAAATCGCTCAAA 60.082 52.632 0.30 0.00 46.92 2.69
495 519 1.337110 GCACCAAATCGCTCAAACGC 61.337 55.000 0.00 0.00 0.00 4.84
600 643 4.778143 GGGTTGTCGCCGAGGCAT 62.778 66.667 15.03 0.00 42.06 4.40
776 822 4.748679 ACGACCACGACGCGCTAC 62.749 66.667 5.73 0.00 42.66 3.58
787 833 3.839432 GCGCTACCGGGCTCTCTT 61.839 66.667 6.32 0.00 44.85 2.85
789 835 1.227002 CGCTACCGGGCTCTCTTTC 60.227 63.158 6.32 0.00 0.00 2.62
858 920 0.462759 GCCTTAGTCGGCTTCTGCAT 60.463 55.000 0.00 0.00 46.63 3.96
992 1093 1.134159 GGGTAGAGAGGTGTCGAGCTA 60.134 57.143 0.00 0.00 0.00 3.32
1003 1104 1.523032 TCGAGCTACGGCGAGATGA 60.523 57.895 16.62 0.02 44.37 2.92
1348 1483 0.822811 GAGCCTGCTCTCTGATGTGA 59.177 55.000 11.82 0.00 39.80 3.58
1357 1492 0.743701 CTCTGATGTGACAGGCCAGC 60.744 60.000 5.01 0.00 38.31 4.85
1467 1603 3.791586 GCTCCTGCCCTGTCCCTC 61.792 72.222 0.00 0.00 0.00 4.30
1498 1634 3.050275 GAAGCCGTGTGCAGGGTC 61.050 66.667 11.83 5.35 44.83 4.46
1539 1675 1.812571 CGCATTGCTTTCCTGTAACCT 59.187 47.619 7.12 0.00 0.00 3.50
1655 1791 7.682787 TTTGCTCCTCTTATCTCCTATTCTT 57.317 36.000 0.00 0.00 0.00 2.52
1715 1851 5.298026 GGCGATCATGCTATCTGTCTATCTA 59.702 44.000 0.00 0.00 34.52 1.98
1748 1884 9.941325 ATATCTGAATGATAGAAGTAGGCAAAG 57.059 33.333 0.00 0.00 40.58 2.77
1767 1903 6.524586 GGCAAAGTATTCTCATTCACTTTTCG 59.475 38.462 0.00 0.00 38.75 3.46
1781 1917 3.374058 CACTTTTCGGGGTGTTAGCTATG 59.626 47.826 0.00 0.00 0.00 2.23
1782 1918 2.032680 TTTCGGGGTGTTAGCTATGC 57.967 50.000 0.00 0.00 0.00 3.14
1784 1920 0.464036 TCGGGGTGTTAGCTATGCAG 59.536 55.000 0.00 0.00 0.00 4.41
1973 2115 1.817099 AGCAGCTGATACTTGCCGC 60.817 57.895 20.43 0.00 38.58 6.53
1995 2137 4.259451 GCGCGTAAGATACTGTTCTTTCAG 60.259 45.833 8.43 0.00 37.20 3.02
2020 2162 5.890985 CCATTCTTTGTATGGTTGTATCCCA 59.109 40.000 0.00 0.00 38.18 4.37
2069 2212 9.890915 ATCCCCTTTTAAATAGTATTTATGGCA 57.109 29.630 14.61 0.00 0.00 4.92
2070 2213 9.716556 TCCCCTTTTAAATAGTATTTATGGCAA 57.283 29.630 14.61 5.15 0.00 4.52
2300 2446 4.039124 ACCCCTGTTTTCAGCACTAAATTG 59.961 41.667 0.00 0.00 45.76 2.32
2461 2608 8.100164 TCACAATGTAATCCTGATTGTCTGTTA 58.900 33.333 2.66 0.00 38.06 2.41
2462 2609 8.729756 CACAATGTAATCCTGATTGTCTGTTAA 58.270 33.333 2.66 0.00 38.06 2.01
2502 2649 1.228367 CCTTCTGCCAGGCTGTTGT 60.228 57.895 14.15 0.00 0.00 3.32
2646 2793 5.048921 GGTTTAGAAGGACAGGTAAAGTTGC 60.049 44.000 0.00 0.00 0.00 4.17
2871 3021 3.614630 GCTTCATGGCATAACAACAGCAA 60.615 43.478 0.00 0.00 0.00 3.91
3327 3478 0.519999 GAATGCTGCTCTTTGACGCG 60.520 55.000 3.53 3.53 0.00 6.01
3401 3552 6.368791 CAGCTTATGCGCCTGTAAATCTATTA 59.631 38.462 4.18 0.00 45.42 0.98
3467 3618 7.543520 GCTACTTGTAATACCCGTTCCATATAC 59.456 40.741 0.00 0.00 0.00 1.47
3549 3798 8.139350 CCATGAATATGTGCATTGTACTTCATT 58.861 33.333 14.09 7.88 31.61 2.57
3567 3816 3.645212 TCATTTGCATTTTGGACAAGGGA 59.355 39.130 0.00 0.00 0.00 4.20
3577 3826 7.443879 GCATTTTGGACAAGGGAAAAATTAGAA 59.556 33.333 0.00 0.00 31.57 2.10
3701 3950 5.499004 ACTGTCTGCCTCCAACTTAAATA 57.501 39.130 0.00 0.00 0.00 1.40
3763 4012 9.243105 GTCATATTTATAATATGGCAAGTGGGT 57.757 33.333 15.48 0.00 36.79 4.51
3789 4038 4.101585 TGTTCATCTGGCCAATCCTACTAG 59.898 45.833 7.01 0.00 35.26 2.57
3947 4196 6.183360 GCAAACTGTCATTAGCCTTGTATGAT 60.183 38.462 0.00 0.00 31.58 2.45
3951 4200 6.989169 ACTGTCATTAGCCTTGTATGATCTTC 59.011 38.462 0.00 0.00 31.58 2.87
3978 4227 8.298854 TGAAGTTGTATCAATTGTTTGAGGATG 58.701 33.333 5.13 0.00 44.75 3.51
3979 4228 8.408043 AAGTTGTATCAATTGTTTGAGGATGA 57.592 30.769 5.13 0.00 44.75 2.92
4654 4905 0.324943 TCTTTTTCGGGAGAGCCTGG 59.675 55.000 0.00 0.00 41.20 4.45
4729 5204 1.993956 TGCCATGTTGCCAGTAAGTT 58.006 45.000 0.00 0.00 0.00 2.66
4823 5326 1.497161 ATACTCCCTCCGTCCCAAAG 58.503 55.000 0.00 0.00 0.00 2.77
4835 5338 0.884704 TCCCAAAGCAGCGACACTTC 60.885 55.000 0.00 0.00 0.00 3.01
4842 5345 0.944386 GCAGCGACACTTCTTTTGGA 59.056 50.000 0.00 0.00 0.00 3.53
4910 5413 4.072131 GTTCCAGGTTGTGAAGCTATGAA 58.928 43.478 0.00 0.00 37.49 2.57
5551 6079 0.040067 CGCCTTGGTGAAGTTTCTGC 60.040 55.000 0.00 0.00 0.00 4.26
5593 6121 0.243907 CTGGTTGTCATCGTCGAGGT 59.756 55.000 6.80 0.00 0.00 3.85
5634 6162 0.034059 CTGAAGTGAGGCGTTCCTGT 59.966 55.000 0.00 0.00 44.46 4.00
5728 6425 0.181587 TTGAAACCTGGTCCAGCGAA 59.818 50.000 13.99 0.00 0.00 4.70
5764 6468 4.111016 CATGTGGTGCTGCTGCCG 62.111 66.667 13.47 0.00 38.71 5.69
5791 6495 2.359900 CGCAGCCTAAAGAGTTTGGAT 58.640 47.619 0.00 0.00 31.87 3.41
5792 6496 2.096496 CGCAGCCTAAAGAGTTTGGATG 59.904 50.000 1.59 1.59 45.34 3.51
5958 7434 8.023706 GTCCATCTCAAAAATTTCTTGTAGGTC 58.976 37.037 0.00 0.00 0.00 3.85
5998 7474 7.282224 GTGGAATTTTGTAGCATGGTAGATACA 59.718 37.037 4.51 0.00 38.48 2.29
6013 7489 4.224715 AGATACACACCATGTCGATACG 57.775 45.455 0.00 0.00 42.09 3.06
6046 7522 7.509141 TGTATGCACTTTTGAATTCTTCTCA 57.491 32.000 7.05 0.00 0.00 3.27
6148 7624 8.430801 ACTTACTGAGATTAGCATCATTTGTC 57.569 34.615 0.00 0.00 0.00 3.18
6193 7675 3.565764 TGTGTCCAATCCTCATGATCC 57.434 47.619 0.00 0.00 31.61 3.36
6198 7680 4.721274 TGTCCAATCCTCATGATCCTGTAA 59.279 41.667 0.00 0.00 31.61 2.41
6274 7756 0.460109 TGTGCGCTACATGGCTACAG 60.460 55.000 9.73 0.00 33.42 2.74
6280 7762 2.668556 CGCTACATGGCTACAGGTATCG 60.669 54.545 0.00 2.32 43.63 2.92
6282 7764 3.193691 GCTACATGGCTACAGGTATCGAT 59.806 47.826 2.16 2.16 42.28 3.59
6293 7775 8.033038 GGCTACAGGTATCGATGTTCATTTATA 58.967 37.037 8.54 0.00 0.00 0.98
6294 7776 8.861101 GCTACAGGTATCGATGTTCATTTATAC 58.139 37.037 8.54 0.00 0.00 1.47
6295 7777 9.355215 CTACAGGTATCGATGTTCATTTATACC 57.645 37.037 8.54 18.96 39.31 2.73
6296 7778 7.732025 ACAGGTATCGATGTTCATTTATACCA 58.268 34.615 23.58 0.00 40.75 3.25
6297 7779 7.656137 ACAGGTATCGATGTTCATTTATACCAC 59.344 37.037 23.58 0.00 40.75 4.16
6298 7780 6.866770 AGGTATCGATGTTCATTTATACCACG 59.133 38.462 23.58 8.82 40.75 4.94
6299 7781 6.090358 GGTATCGATGTTCATTTATACCACGG 59.910 42.308 20.31 0.00 39.00 4.94
6300 7782 4.373527 TCGATGTTCATTTATACCACGGG 58.626 43.478 0.00 0.00 0.00 5.28
6301 7783 4.099727 TCGATGTTCATTTATACCACGGGA 59.900 41.667 0.00 0.00 0.00 5.14
6302 7784 4.812091 CGATGTTCATTTATACCACGGGAA 59.188 41.667 0.00 0.00 0.00 3.97
6303 7785 5.468746 CGATGTTCATTTATACCACGGGAAT 59.531 40.000 0.00 0.00 0.00 3.01
6304 7786 6.565811 CGATGTTCATTTATACCACGGGAATG 60.566 42.308 0.00 0.00 0.00 2.67
6305 7787 5.746284 TGTTCATTTATACCACGGGAATGA 58.254 37.500 0.00 0.00 35.57 2.57
6306 7788 5.820423 TGTTCATTTATACCACGGGAATGAG 59.180 40.000 0.00 0.00 37.82 2.90
6307 7789 4.385825 TCATTTATACCACGGGAATGAGC 58.614 43.478 0.00 0.00 33.26 4.26
6308 7790 3.916359 TTTATACCACGGGAATGAGCA 57.084 42.857 0.00 0.00 0.00 4.26
6309 7791 4.431416 TTTATACCACGGGAATGAGCAT 57.569 40.909 0.00 0.00 0.00 3.79
6310 7792 2.260844 ATACCACGGGAATGAGCATG 57.739 50.000 0.00 0.00 0.00 4.06
6311 7793 1.199615 TACCACGGGAATGAGCATGA 58.800 50.000 0.00 0.00 0.00 3.07
6312 7794 0.327924 ACCACGGGAATGAGCATGAA 59.672 50.000 0.00 0.00 0.00 2.57
6313 7795 0.734889 CCACGGGAATGAGCATGAAC 59.265 55.000 0.00 0.00 0.00 3.18
6314 7796 1.452110 CACGGGAATGAGCATGAACA 58.548 50.000 0.00 0.00 0.00 3.18
6315 7797 1.811965 CACGGGAATGAGCATGAACAA 59.188 47.619 0.00 0.00 0.00 2.83
6316 7798 2.086869 ACGGGAATGAGCATGAACAAG 58.913 47.619 0.00 0.00 0.00 3.16
6317 7799 1.402968 CGGGAATGAGCATGAACAAGG 59.597 52.381 0.00 0.00 0.00 3.61
6318 7800 2.726821 GGGAATGAGCATGAACAAGGA 58.273 47.619 0.00 0.00 0.00 3.36
6319 7801 3.091545 GGGAATGAGCATGAACAAGGAA 58.908 45.455 0.00 0.00 0.00 3.36
6320 7802 3.511146 GGGAATGAGCATGAACAAGGAAA 59.489 43.478 0.00 0.00 0.00 3.13
6321 7803 4.488879 GGAATGAGCATGAACAAGGAAAC 58.511 43.478 0.00 0.00 0.00 2.78
6322 7804 4.022068 GGAATGAGCATGAACAAGGAAACA 60.022 41.667 0.00 0.00 0.00 2.83
6323 7805 5.509501 GGAATGAGCATGAACAAGGAAACAA 60.510 40.000 0.00 0.00 0.00 2.83
6324 7806 4.305989 TGAGCATGAACAAGGAAACAAC 57.694 40.909 0.00 0.00 0.00 3.32
6325 7807 3.243035 TGAGCATGAACAAGGAAACAACG 60.243 43.478 0.00 0.00 0.00 4.10
6326 7808 2.948979 AGCATGAACAAGGAAACAACGA 59.051 40.909 0.00 0.00 0.00 3.85
6327 7809 3.042887 GCATGAACAAGGAAACAACGAC 58.957 45.455 0.00 0.00 0.00 4.34
6328 7810 3.488384 GCATGAACAAGGAAACAACGACA 60.488 43.478 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.239306 CCTTGTTCTGTATTGCTTCAGTTCA 59.761 40.000 0.00 0.00 33.89 3.18
84 85 3.258123 GGGGTACAATTCAACATGCAGTT 59.742 43.478 0.00 0.00 42.42 3.16
95 96 4.163458 TCAGATGGTGTAGGGGTACAATTC 59.837 45.833 0.00 0.00 0.00 2.17
119 120 5.218139 CAAAACAGAAGAAGAAGGCATCAC 58.782 41.667 0.00 0.00 0.00 3.06
170 178 3.442625 CCGCCGTTGTATCTATCTATGGA 59.557 47.826 0.00 0.00 0.00 3.41
188 196 3.262448 TTGCTTACCTGTCCCCGCC 62.262 63.158 0.00 0.00 0.00 6.13
203 211 3.980775 GTGTGAATTACATGTGTGGTTGC 59.019 43.478 9.11 0.00 42.24 4.17
224 245 2.628657 GAGTATCCATCGGTAGCTTGGT 59.371 50.000 0.00 0.00 0.00 3.67
245 267 4.671964 GCCACGTTTTAGAAGTTTTTACCG 59.328 41.667 0.00 0.00 0.00 4.02
254 276 5.202640 GTTGTAGTTGCCACGTTTTAGAAG 58.797 41.667 0.00 0.00 0.00 2.85
260 282 2.488545 TGTTGTTGTAGTTGCCACGTTT 59.511 40.909 0.00 0.00 0.00 3.60
306 328 8.703336 TGAAATAGAATCGAAATCAATAGCTCG 58.297 33.333 0.00 0.00 0.00 5.03
369 391 2.533942 GTGCGCTTCGATTTGTGTTTTT 59.466 40.909 9.73 0.00 0.00 1.94
398 420 0.170561 TCGAAGCTAGGCGTCTGTTC 59.829 55.000 0.00 0.00 35.07 3.18
399 421 0.109226 GTCGAAGCTAGGCGTCTGTT 60.109 55.000 0.00 0.00 35.07 3.16
453 477 2.514592 GCCGCTATCTGCTTGGCA 60.515 61.111 0.00 0.00 44.28 4.92
480 504 0.789383 GTCGGCGTTTGAGCGATTTG 60.789 55.000 6.85 0.00 38.18 2.32
514 538 2.277692 CGATTCGCGTGCTCGGTA 60.278 61.111 5.77 0.00 37.56 4.02
600 643 0.687427 TCCCCATCATCTGCGAGTCA 60.687 55.000 0.00 0.00 0.00 3.41
749 795 2.725759 CGTCGTGGTCGTCTAATCGAAA 60.726 50.000 0.00 0.00 41.47 3.46
776 822 1.842381 AACCCAGAAAGAGAGCCCGG 61.842 60.000 0.00 0.00 0.00 5.73
787 833 1.228552 GAAGGCAGCCAACCCAGAA 60.229 57.895 15.80 0.00 0.00 3.02
789 835 2.677875 GGAAGGCAGCCAACCCAG 60.678 66.667 15.80 0.00 0.00 4.45
858 920 2.607411 TATGTCGGTCGGGCCTACGA 62.607 60.000 0.84 5.93 41.13 3.43
916 986 1.084289 GTGGGCCGCTAAACTAACTG 58.916 55.000 10.52 0.00 0.00 3.16
921 991 0.824759 CTCTAGTGGGCCGCTAAACT 59.175 55.000 25.81 13.02 0.00 2.66
972 1073 0.394625 AGCTCGACACCTCTCTACCC 60.395 60.000 0.00 0.00 0.00 3.69
975 1076 1.472904 CCGTAGCTCGACACCTCTCTA 60.473 57.143 7.07 0.00 42.86 2.43
1331 1452 0.248565 TGTCACATCAGAGAGCAGGC 59.751 55.000 0.00 0.00 0.00 4.85
1337 1458 0.900421 CTGGCCTGTCACATCAGAGA 59.100 55.000 3.32 0.00 37.61 3.10
1467 1603 1.584380 GGCTTCAGTCCAGCAGCAAG 61.584 60.000 0.00 0.00 39.21 4.01
1498 1634 2.805099 GTCAGTGACAGCAAGAAGAAGG 59.195 50.000 18.54 0.00 32.09 3.46
1539 1675 1.547099 AGACCCCTAGGAGGATAGCA 58.453 55.000 19.81 0.00 37.67 3.49
1689 1825 2.029200 AGACAGATAGCATGATCGCCAG 60.029 50.000 0.00 0.00 0.00 4.85
1723 1859 8.928448 ACTTTGCCTACTTCTATCATTCAGATA 58.072 33.333 0.00 0.00 38.19 1.98
1748 1884 4.941873 ACCCCGAAAAGTGAATGAGAATAC 59.058 41.667 0.00 0.00 0.00 1.89
1767 1903 2.707902 GCTGCATAGCTAACACCCC 58.292 57.895 0.00 0.00 46.57 4.95
1781 1917 3.302365 TTTATCAAGCAAAGTGGCTGC 57.698 42.857 0.00 0.00 45.07 5.25
1782 1918 4.874970 ACTTTTATCAAGCAAAGTGGCTG 58.125 39.130 0.00 0.00 45.07 4.85
1820 1961 5.291971 ACAACCAATTTTTGATGAGCAGTC 58.708 37.500 3.97 0.00 0.00 3.51
1973 2115 4.259451 GCTGAAAGAACAGTATCTTACGCG 60.259 45.833 3.53 3.53 38.69 6.01
1995 2137 5.221244 GGGATACAACCATACAAAGAATGGC 60.221 44.000 2.03 0.00 43.15 4.40
2095 2241 6.765403 ACTGAAATTAGTTACACAGTAGCCA 58.235 36.000 0.00 0.00 36.94 4.75
2154 2300 6.586344 AGTATGATGATGTTCTACCACCTTG 58.414 40.000 0.00 0.00 0.00 3.61
2222 2368 7.769970 TCATTTGCTGATCACATCACATTACTA 59.230 33.333 0.00 0.00 35.06 1.82
2229 2375 4.855388 GTGTTCATTTGCTGATCACATCAC 59.145 41.667 9.56 0.00 46.78 3.06
2300 2446 8.546244 CATCAACAACTATGTCATATCTGTGAC 58.454 37.037 7.41 0.59 46.75 3.67
2461 2608 6.715264 AGGCTTGCTAACAACTAACATAACTT 59.285 34.615 0.00 0.00 0.00 2.66
2462 2609 6.238648 AGGCTTGCTAACAACTAACATAACT 58.761 36.000 0.00 0.00 0.00 2.24
2474 2621 0.110295 TGGCAGAAGGCTTGCTAACA 59.890 50.000 3.46 0.00 44.01 2.41
2502 2649 8.348285 AGTGGTGCAAGCTAATAAATAAGAAA 57.652 30.769 0.00 0.00 33.76 2.52
2592 2739 3.558746 GCACCAGATATAAGAGGCTGCAT 60.559 47.826 0.50 0.00 32.33 3.96
3067 3217 9.618890 AGTAAATGCATGCTCTATCTAGAAAAA 57.381 29.630 20.33 0.00 0.00 1.94
3377 3528 3.199880 AGATTTACAGGCGCATAAGCT 57.800 42.857 10.83 0.00 39.10 3.74
3418 3569 5.335583 GCAAATAACACCTCACTGTATGCAA 60.336 40.000 0.00 0.00 0.00 4.08
3549 3798 4.494091 TTTTCCCTTGTCCAAAATGCAA 57.506 36.364 0.00 0.00 0.00 4.08
3567 3816 6.494835 AGGACTGGACAGCAATTCTAATTTTT 59.505 34.615 0.00 0.00 0.00 1.94
3577 3826 1.002888 CACTGAGGACTGGACAGCAAT 59.997 52.381 0.00 0.00 35.38 3.56
3763 4012 4.524802 AGGATTGGCCAGATGAACATAA 57.475 40.909 5.11 0.00 40.02 1.90
3906 4155 1.444933 TTGCGGGATCAGGGGAATAT 58.555 50.000 0.00 0.00 0.00 1.28
3912 4161 1.002134 ACAGTTTGCGGGATCAGGG 60.002 57.895 0.00 0.00 0.00 4.45
3913 4162 0.321564 TGACAGTTTGCGGGATCAGG 60.322 55.000 0.00 0.00 0.00 3.86
3947 4196 9.119418 TCAAACAATTGATACAACTTCAGAAGA 57.881 29.630 17.56 0.00 40.59 2.87
3951 4200 7.874940 TCCTCAAACAATTGATACAACTTCAG 58.125 34.615 13.59 0.00 44.29 3.02
4403 4652 6.202954 CACTTGCTAAACACTAAGTGCTAAGT 59.797 38.462 0.00 0.00 42.16 2.24
4590 4841 6.099701 TGCTCAGTACTCACATACCCATATTT 59.900 38.462 0.00 0.00 0.00 1.40
4645 4896 0.392193 CATGTGACACCCAGGCTCTC 60.392 60.000 2.45 0.00 0.00 3.20
4667 4918 2.026641 CTGGTTATCAATGGTGGCCAG 58.973 52.381 5.11 0.00 36.75 4.85
4747 5222 6.935208 GGGAAACTAGAGAAGCACTAAAGAAA 59.065 38.462 0.00 0.00 0.00 2.52
4823 5326 0.944386 TCCAAAAGAAGTGTCGCTGC 59.056 50.000 0.00 0.00 0.00 5.25
4835 5338 2.302157 AGTACTCCCTCCGTTCCAAAAG 59.698 50.000 0.00 0.00 0.00 2.27
4842 5345 4.928263 ACTAGTTTAGTACTCCCTCCGTT 58.072 43.478 0.00 0.00 37.23 4.44
4921 5424 4.776743 GCCGTCTGCATTAATCATAACAG 58.223 43.478 0.00 0.00 40.77 3.16
4949 5452 0.984230 TTCTGGTAGCAGGTTCAGGG 59.016 55.000 21.22 0.00 0.00 4.45
5382 5909 2.811317 CGGTCTCAAGCTGGACGC 60.811 66.667 0.00 0.00 39.57 5.19
5575 6103 0.038618 CACCTCGACGATGACAACCA 60.039 55.000 7.16 0.00 0.00 3.67
5593 6121 7.334858 TCAGGCATAATGACAACAGTAATACA 58.665 34.615 0.00 0.00 30.57 2.29
5703 6400 3.490933 GCTGGACCAGGTTTCAAAGAAAC 60.491 47.826 23.09 12.83 31.21 2.78
5745 6442 2.270257 GGCAGCAGCACCACATGAA 61.270 57.895 2.65 0.00 44.61 2.57
5764 6468 0.673644 TCTTTAGGCTGCGCTCCAAC 60.674 55.000 18.80 1.66 0.00 3.77
5782 6486 2.290960 ACCCACTAAGGCATCCAAACTC 60.291 50.000 0.00 0.00 35.39 3.01
5791 6495 3.799432 ATTGTGTAACCCACTAAGGCA 57.201 42.857 0.00 0.00 44.81 4.75
5792 6496 4.076394 TCAATTGTGTAACCCACTAAGGC 58.924 43.478 5.13 0.00 44.81 4.35
5923 7399 2.636647 TTGAGATGGACACAACAGCA 57.363 45.000 0.00 0.00 0.00 4.41
5958 7434 4.550076 AATTCCACAGAGAAGTCAGGAG 57.450 45.455 0.00 0.00 0.00 3.69
5998 7474 3.306917 TTGAACGTATCGACATGGTGT 57.693 42.857 0.00 0.00 0.00 4.16
6046 7522 7.106239 CACCAATCTCTAGTGTAAGGAAATGT 58.894 38.462 0.00 0.00 0.00 2.71
6213 7695 8.946085 CATGAAAGGTATAAGTACTTTGCTTGA 58.054 33.333 14.49 0.00 34.83 3.02
6221 7703 7.042335 GTGCACTCATGAAAGGTATAAGTACT 58.958 38.462 10.32 0.00 0.00 2.73
6231 7713 3.067180 ACAAACTGTGCACTCATGAAAGG 59.933 43.478 19.41 1.51 0.00 3.11
6274 7756 6.090358 CCGTGGTATAAATGAACATCGATACC 59.910 42.308 19.86 19.86 38.10 2.73
6280 7762 6.485313 TCATTCCCGTGGTATAAATGAACATC 59.515 38.462 0.00 0.00 34.39 3.06
6282 7764 5.746284 TCATTCCCGTGGTATAAATGAACA 58.254 37.500 0.00 0.00 34.39 3.18
6293 7775 0.327924 TTCATGCTCATTCCCGTGGT 59.672 50.000 0.00 0.00 0.00 4.16
6294 7776 0.734889 GTTCATGCTCATTCCCGTGG 59.265 55.000 0.00 0.00 0.00 4.94
6295 7777 1.452110 TGTTCATGCTCATTCCCGTG 58.548 50.000 0.00 0.00 0.00 4.94
6296 7778 2.086869 CTTGTTCATGCTCATTCCCGT 58.913 47.619 0.00 0.00 0.00 5.28
6297 7779 1.402968 CCTTGTTCATGCTCATTCCCG 59.597 52.381 0.00 0.00 0.00 5.14
6298 7780 2.726821 TCCTTGTTCATGCTCATTCCC 58.273 47.619 0.00 0.00 0.00 3.97
6299 7781 4.022068 TGTTTCCTTGTTCATGCTCATTCC 60.022 41.667 0.00 0.00 0.00 3.01
6300 7782 5.125100 TGTTTCCTTGTTCATGCTCATTC 57.875 39.130 0.00 0.00 0.00 2.67
6301 7783 5.291971 GTTGTTTCCTTGTTCATGCTCATT 58.708 37.500 0.00 0.00 0.00 2.57
6302 7784 4.557296 CGTTGTTTCCTTGTTCATGCTCAT 60.557 41.667 0.00 0.00 0.00 2.90
6303 7785 3.243035 CGTTGTTTCCTTGTTCATGCTCA 60.243 43.478 0.00 0.00 0.00 4.26
6304 7786 3.003275 TCGTTGTTTCCTTGTTCATGCTC 59.997 43.478 0.00 0.00 0.00 4.26
6305 7787 2.948979 TCGTTGTTTCCTTGTTCATGCT 59.051 40.909 0.00 0.00 0.00 3.79
6306 7788 3.042887 GTCGTTGTTTCCTTGTTCATGC 58.957 45.455 0.00 0.00 0.00 4.06
6307 7789 4.285807 TGTCGTTGTTTCCTTGTTCATG 57.714 40.909 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.