Multiple sequence alignment - TraesCS1B01G420300

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 TraesCS1B01G420300 chr1B 100.000 2681 0 0 1 2681 643280326 643277646 0.000000e+00 4951
1 TraesCS1B01G420300 chr1D 93.797 1983 85 22 179 2145 466495499 466493539 0.000000e+00 2946
2 TraesCS1B01G420300 chr1D 84.397 282 35 7 2401 2681 466493058 466492785 4.400000e-68 268
3 TraesCS1B01G420300 chr1A 90.851 2197 109 41 530 2681 558705665 558703516 0.000000e+00 2859
4 TraesCS1B01G420300 chr1A 84.944 445 47 9 100 529 558707702 558707263 1.470000e-117 433


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 TraesCS1B01G420300 chr1B 643277646 643280326 2680 True 4951 4951 100.0000 1 2681 1 chr1B.!!$R1 2680
1 TraesCS1B01G420300 chr1D 466492785 466495499 2714 True 1607 2946 89.0970 179 2681 2 chr1D.!!$R1 2502
2 TraesCS1B01G420300 chr1A 558703516 558707702 4186 True 1646 2859 87.8975 100 2681 2 chr1A.!!$R1 2581

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
179 180 0.108329 CCTCCTACGACCGCAATGTT 60.108 55.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 3751 0.510359 CGCGAAATCCTAGCATGAGC 59.49 55.0 0.0 0.0 42.56 4.26 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
18 19 2.647356 CACTCGTCTCTCCCACAGT 58.353 57.895 0.00 0.00 0.00 3.55
19 20 0.523966 CACTCGTCTCTCCCACAGTC 59.476 60.000 0.00 0.00 0.00 3.51
20 21 0.956410 ACTCGTCTCTCCCACAGTCG 60.956 60.000 0.00 0.00 0.00 4.18
21 22 0.956410 CTCGTCTCTCCCACAGTCGT 60.956 60.000 0.00 0.00 0.00 4.34
22 23 0.322648 TCGTCTCTCCCACAGTCGTA 59.677 55.000 0.00 0.00 0.00 3.43
23 24 1.065636 TCGTCTCTCCCACAGTCGTAT 60.066 52.381 0.00 0.00 0.00 3.06
24 25 1.331138 CGTCTCTCCCACAGTCGTATC 59.669 57.143 0.00 0.00 0.00 2.24
25 26 2.366533 GTCTCTCCCACAGTCGTATCA 58.633 52.381 0.00 0.00 0.00 2.15
26 27 2.952978 GTCTCTCCCACAGTCGTATCAT 59.047 50.000 0.00 0.00 0.00 2.45
27 28 4.135306 GTCTCTCCCACAGTCGTATCATA 58.865 47.826 0.00 0.00 0.00 2.15
28 29 4.762765 GTCTCTCCCACAGTCGTATCATAT 59.237 45.833 0.00 0.00 0.00 1.78
29 30 5.004448 TCTCTCCCACAGTCGTATCATATC 58.996 45.833 0.00 0.00 0.00 1.63
30 31 3.751698 TCTCCCACAGTCGTATCATATCG 59.248 47.826 0.00 0.00 0.00 2.92
31 32 3.483421 TCCCACAGTCGTATCATATCGT 58.517 45.455 0.00 0.00 0.00 3.73
32 33 4.644498 TCCCACAGTCGTATCATATCGTA 58.356 43.478 0.00 0.00 0.00 3.43
33 34 5.250982 TCCCACAGTCGTATCATATCGTAT 58.749 41.667 0.00 0.00 0.00 3.06
34 35 5.123344 TCCCACAGTCGTATCATATCGTATG 59.877 44.000 0.28 0.28 0.00 2.39
35 36 5.332707 CCACAGTCGTATCATATCGTATGG 58.667 45.833 5.54 0.00 0.00 2.74
36 37 5.106277 CCACAGTCGTATCATATCGTATGGT 60.106 44.000 5.54 2.00 0.00 3.55
37 38 6.379386 CACAGTCGTATCATATCGTATGGTT 58.621 40.000 5.54 0.00 0.00 3.67
38 39 7.361457 CCACAGTCGTATCATATCGTATGGTTA 60.361 40.741 5.54 0.00 0.00 2.85
39 40 8.019094 CACAGTCGTATCATATCGTATGGTTAA 58.981 37.037 5.54 0.00 0.00 2.01
40 41 8.570488 ACAGTCGTATCATATCGTATGGTTAAA 58.430 33.333 5.54 0.00 0.00 1.52
41 42 8.847567 CAGTCGTATCATATCGTATGGTTAAAC 58.152 37.037 5.54 0.00 0.00 2.01
42 43 8.790718 AGTCGTATCATATCGTATGGTTAAACT 58.209 33.333 0.00 0.00 0.00 2.66
52 53 8.967664 ATCGTATGGTTAAACTATAAAAGCCA 57.032 30.769 0.00 0.00 0.00 4.75
53 54 8.789825 TCGTATGGTTAAACTATAAAAGCCAA 57.210 30.769 0.00 0.00 0.00 4.52
54 55 9.398538 TCGTATGGTTAAACTATAAAAGCCAAT 57.601 29.630 0.00 0.00 0.00 3.16
71 72 9.595823 AAAAGCCAATTAATCATCAGATTGAAG 57.404 29.630 1.21 0.00 44.03 3.02
72 73 7.286215 AGCCAATTAATCATCAGATTGAAGG 57.714 36.000 1.21 2.01 44.03 3.46
73 74 6.837568 AGCCAATTAATCATCAGATTGAAGGT 59.162 34.615 1.21 0.00 44.03 3.50
74 75 7.343833 AGCCAATTAATCATCAGATTGAAGGTT 59.656 33.333 1.21 0.00 44.03 3.50
75 76 8.632679 GCCAATTAATCATCAGATTGAAGGTTA 58.367 33.333 1.21 0.00 44.03 2.85
80 81 6.668541 ATCATCAGATTGAAGGTTAACACG 57.331 37.500 8.10 0.00 0.00 4.49
81 82 4.391830 TCATCAGATTGAAGGTTAACACGC 59.608 41.667 8.10 0.00 0.00 5.34
82 83 4.002906 TCAGATTGAAGGTTAACACGCT 57.997 40.909 8.10 0.00 0.00 5.07
83 84 5.142061 TCAGATTGAAGGTTAACACGCTA 57.858 39.130 8.10 0.00 0.00 4.26
84 85 5.543714 TCAGATTGAAGGTTAACACGCTAA 58.456 37.500 8.10 0.00 0.00 3.09
85 86 5.992829 TCAGATTGAAGGTTAACACGCTAAA 59.007 36.000 8.10 0.00 0.00 1.85
86 87 6.147164 TCAGATTGAAGGTTAACACGCTAAAG 59.853 38.462 8.10 0.00 0.00 1.85
87 88 4.477302 TTGAAGGTTAACACGCTAAAGC 57.523 40.909 8.10 0.00 37.78 3.51
88 89 3.468770 TGAAGGTTAACACGCTAAAGCA 58.531 40.909 8.10 0.00 42.21 3.91
89 90 3.878103 TGAAGGTTAACACGCTAAAGCAA 59.122 39.130 8.10 0.00 42.21 3.91
90 91 4.335874 TGAAGGTTAACACGCTAAAGCAAA 59.664 37.500 8.10 0.00 42.21 3.68
91 92 4.904253 AGGTTAACACGCTAAAGCAAAA 57.096 36.364 8.10 0.00 42.21 2.44
92 93 5.251601 AGGTTAACACGCTAAAGCAAAAA 57.748 34.783 8.10 0.00 42.21 1.94
93 94 5.038683 AGGTTAACACGCTAAAGCAAAAAC 58.961 37.500 8.10 0.00 42.21 2.43
94 95 4.799428 GGTTAACACGCTAAAGCAAAAACA 59.201 37.500 8.10 0.00 42.21 2.83
95 96 5.460748 GGTTAACACGCTAAAGCAAAAACAT 59.539 36.000 8.10 0.00 42.21 2.71
96 97 6.019398 GGTTAACACGCTAAAGCAAAAACATT 60.019 34.615 8.10 0.00 42.21 2.71
97 98 5.388225 AACACGCTAAAGCAAAAACATTG 57.612 34.783 2.44 0.00 42.21 2.82
98 99 4.429108 ACACGCTAAAGCAAAAACATTGT 58.571 34.783 2.44 0.00 42.21 2.71
132 133 4.574828 ACAAATATTCACCTTTCGATCGGG 59.425 41.667 16.41 11.33 0.00 5.14
148 149 2.727103 GGGATCCGAGACCTGAGAG 58.273 63.158 5.45 0.00 0.00 3.20
155 156 1.671901 CGAGACCTGAGAGCCCTTCC 61.672 65.000 0.00 0.00 0.00 3.46
156 157 1.306568 AGACCTGAGAGCCCTTCCC 60.307 63.158 0.00 0.00 0.00 3.97
157 158 2.285743 ACCTGAGAGCCCTTCCCC 60.286 66.667 0.00 0.00 0.00 4.81
158 159 3.093172 CCTGAGAGCCCTTCCCCC 61.093 72.222 0.00 0.00 0.00 5.40
178 179 0.968901 TCCTCCTACGACCGCAATGT 60.969 55.000 0.00 0.00 0.00 2.71
179 180 0.108329 CCTCCTACGACCGCAATGTT 60.108 55.000 0.00 0.00 0.00 2.71
180 181 0.999406 CTCCTACGACCGCAATGTTG 59.001 55.000 0.00 0.00 0.00 3.33
181 182 0.390603 TCCTACGACCGCAATGTTGG 60.391 55.000 0.00 0.00 0.00 3.77
183 184 1.295357 CTACGACCGCAATGTTGGCA 61.295 55.000 0.00 0.00 0.00 4.92
184 185 0.885150 TACGACCGCAATGTTGGCAA 60.885 50.000 0.00 0.00 0.00 4.52
185 186 1.007964 CGACCGCAATGTTGGCAAA 60.008 52.632 0.00 0.00 0.00 3.68
186 187 0.596083 CGACCGCAATGTTGGCAAAA 60.596 50.000 0.00 0.00 0.00 2.44
187 188 1.576356 GACCGCAATGTTGGCAAAAA 58.424 45.000 0.00 0.00 0.00 1.94
230 244 2.982130 GGAGGTGCCGTCACTCAT 59.018 61.111 0.00 0.00 42.72 2.90
242 256 0.820226 TCACTCATGCCTCTTCTCCG 59.180 55.000 0.00 0.00 0.00 4.63
271 285 2.305607 GCACCCCTACCCACCATCA 61.306 63.158 0.00 0.00 0.00 3.07
317 331 1.105167 ACTGGTGACGACGAGACCAA 61.105 55.000 18.77 7.61 39.28 3.67
331 345 4.323477 CCAACCGCTTCGTCCCCA 62.323 66.667 0.00 0.00 0.00 4.96
332 346 2.046314 CAACCGCTTCGTCCCCAT 60.046 61.111 0.00 0.00 0.00 4.00
336 350 0.325602 ACCGCTTCGTCCCCATTTTA 59.674 50.000 0.00 0.00 0.00 1.52
353 368 5.412640 CATTTTATGGCATGTTCAAGCTCA 58.587 37.500 10.98 0.00 0.00 4.26
373 388 3.575687 TCACCTCATCGATGATGCTATGT 59.424 43.478 27.43 14.61 39.63 2.29
385 400 0.963856 TGCTATGTCGTGACGTCCCT 60.964 55.000 14.12 0.00 0.00 4.20
406 422 0.898326 TCTTGGACTCAGGCTACGCA 60.898 55.000 0.00 0.00 0.00 5.24
497 514 5.779241 TCCCATTTCCTTGTAGACTCATT 57.221 39.130 0.00 0.00 0.00 2.57
526 543 6.034577 GCTTCCATAAACCGCATTTTAGAAAC 59.965 38.462 0.00 0.00 0.00 2.78
527 544 6.827586 TCCATAAACCGCATTTTAGAAACT 57.172 33.333 0.00 0.00 0.00 2.66
528 545 7.925043 TCCATAAACCGCATTTTAGAAACTA 57.075 32.000 0.00 0.00 0.00 2.24
548 2163 9.482627 GAAACTATAAACACTATCTCATCAGGG 57.517 37.037 0.00 0.00 0.00 4.45
582 2197 3.079578 CCGTTTTCTTAAGTTCTCCCCC 58.920 50.000 1.63 0.00 0.00 5.40
583 2198 3.497227 CCGTTTTCTTAAGTTCTCCCCCA 60.497 47.826 1.63 0.00 0.00 4.96
607 2226 6.470556 CACACACATCGTTTTACATTTTGTCA 59.529 34.615 0.00 0.00 0.00 3.58
608 2227 6.690957 ACACACATCGTTTTACATTTTGTCAG 59.309 34.615 0.00 0.00 0.00 3.51
612 2231 7.643764 CACATCGTTTTACATTTTGTCAGAAGT 59.356 33.333 0.00 0.00 0.00 3.01
617 2236 3.733443 ACATTTTGTCAGAAGTTGGCC 57.267 42.857 0.00 0.00 0.00 5.36
900 2520 1.674057 CTTCCTCTGGCTCAACGGT 59.326 57.895 0.00 0.00 0.00 4.83
932 2552 2.102757 TCGCCGCCATTTATAAGTACCA 59.897 45.455 0.00 0.00 0.00 3.25
940 2560 3.977134 TTTATAAGTACCACCGGCACA 57.023 42.857 0.00 0.00 0.00 4.57
1143 2768 1.800315 CTACGTGTCCCACTTCGCG 60.800 63.158 0.00 0.00 42.16 5.87
1820 3445 1.065764 CGATTGTCCGCCAGATCGA 59.934 57.895 0.00 0.00 42.82 3.59
1914 3539 7.254252 CGAGAGACAAGTAATAAAATGCAGAGG 60.254 40.741 0.00 0.00 0.00 3.69
1934 3559 0.505231 CACACGCTGCATGCTTTTTG 59.495 50.000 20.33 13.06 40.11 2.44
1948 3573 6.294508 GCATGCTTTTTGGGACTAAGAAAGTA 60.295 38.462 11.37 0.00 39.07 2.24
1949 3574 6.628919 TGCTTTTTGGGACTAAGAAAGTAC 57.371 37.500 0.00 0.00 39.07 2.73
1950 3575 6.362248 TGCTTTTTGGGACTAAGAAAGTACT 58.638 36.000 0.00 0.00 39.28 2.73
1951 3576 6.831868 TGCTTTTTGGGACTAAGAAAGTACTT 59.168 34.615 1.12 1.12 39.28 2.24
1952 3577 7.340999 TGCTTTTTGGGACTAAGAAAGTACTTT 59.659 33.333 20.67 20.67 39.28 2.66
2005 3630 2.761071 GCCTTTGCCTCTCTTCTCG 58.239 57.895 0.00 0.00 0.00 4.04
2010 3635 0.805614 TTGCCTCTCTTCTCGTCTCG 59.194 55.000 0.00 0.00 0.00 4.04
2049 3684 0.457166 TATGACGTGAAAGCGGACGG 60.457 55.000 0.00 0.00 39.94 4.79
2050 3685 2.049802 GACGTGAAAGCGGACGGA 60.050 61.111 0.00 0.00 39.94 4.69
2101 3737 1.002033 ACCGTCGGATCTATAACGTGC 60.002 52.381 20.51 0.00 33.45 5.34
2115 3751 3.944422 AACGTGCGCTATTGATTAAGG 57.056 42.857 9.73 0.00 0.00 2.69
2132 3768 2.540265 AGGCTCATGCTAGGATTTCG 57.460 50.000 0.00 0.00 39.59 3.46
2147 3783 0.739462 TTTCGCGTGGGCTACTGATG 60.739 55.000 5.77 0.00 36.88 3.07
2148 3784 1.884075 TTCGCGTGGGCTACTGATGT 61.884 55.000 5.77 0.00 36.88 3.06
2149 3785 1.447838 CGCGTGGGCTACTGATGTT 60.448 57.895 0.00 0.00 36.88 2.71
2151 3787 1.982073 GCGTGGGCTACTGATGTTGC 61.982 60.000 0.00 0.00 42.61 4.17
2152 3788 1.695893 CGTGGGCTACTGATGTTGCG 61.696 60.000 0.00 0.00 43.88 4.85
2153 3789 3.102097 GGGCTACTGATGTTGCGC 58.898 61.111 0.00 0.00 45.89 6.09
2154 3790 4.208632 GGCTACTGATGTTGCGCT 57.791 55.556 9.73 0.00 43.88 5.92
2156 3792 0.097674 GGCTACTGATGTTGCGCTTG 59.902 55.000 9.73 0.00 43.88 4.01
2157 3793 0.798776 GCTACTGATGTTGCGCTTGT 59.201 50.000 9.73 0.00 35.51 3.16
2158 3794 1.201965 GCTACTGATGTTGCGCTTGTC 60.202 52.381 9.73 2.18 35.51 3.18
2160 3796 1.133253 CTGATGTTGCGCTTGTCGG 59.867 57.895 9.73 3.00 38.94 4.79
2161 3797 1.291184 CTGATGTTGCGCTTGTCGGA 61.291 55.000 9.73 0.00 38.94 4.55
2162 3798 1.291184 TGATGTTGCGCTTGTCGGAG 61.291 55.000 9.73 0.00 40.33 4.63
2163 3799 2.568935 GATGTTGCGCTTGTCGGAGC 62.569 60.000 9.73 0.00 40.33 4.70
2164 3800 3.345808 GTTGCGCTTGTCGGAGCA 61.346 61.111 9.73 0.00 42.83 4.26
2165 3801 2.358615 TTGCGCTTGTCGGAGCAT 60.359 55.556 9.73 0.00 42.83 3.79
2166 3802 2.679934 TTGCGCTTGTCGGAGCATG 61.680 57.895 9.73 0.00 42.83 4.06
2167 3803 3.869272 GCGCTTGTCGGAGCATGG 61.869 66.667 0.00 0.00 42.83 3.66
2168 3804 2.125552 CGCTTGTCGGAGCATGGA 60.126 61.111 0.00 0.00 42.83 3.41
2169 3805 2.456119 CGCTTGTCGGAGCATGGAC 61.456 63.158 0.00 0.00 42.83 4.02
2170 3806 2.456119 GCTTGTCGGAGCATGGACG 61.456 63.158 0.00 0.00 42.25 4.79
2186 3999 1.944709 GGACGTTGCACTTAACCAACT 59.055 47.619 0.00 0.00 39.24 3.16
2195 4008 6.518208 TGCACTTAACCAACTGTAAAAACT 57.482 33.333 0.00 0.00 0.00 2.66
2199 4012 9.356433 GCACTTAACCAACTGTAAAAACTAAAA 57.644 29.630 0.00 0.00 0.00 1.52
2266 4083 9.180678 GCCATTTTAGGATTTATAAATGACGTG 57.819 33.333 15.39 5.35 39.26 4.49
2289 4106 3.137484 GCACTCGCCATTAGACACA 57.863 52.632 0.00 0.00 0.00 3.72
2302 4119 7.265673 GCCATTAGACACAAGATCTAGTAACA 58.734 38.462 0.00 0.00 30.46 2.41
2306 4123 5.960113 AGACACAAGATCTAGTAACAGCTG 58.040 41.667 13.48 13.48 0.00 4.24
2360 4185 3.577667 GCACATGCTTGCAATACTTCAA 58.422 40.909 0.00 0.00 42.49 2.69
2378 4243 0.034896 AACATCGTTCCAAGTCGCCT 59.965 50.000 0.00 0.00 0.00 5.52
2448 4354 4.724074 AGATCTGAAGAGAGCAACAGAG 57.276 45.455 0.00 0.00 41.55 3.35
2472 4378 1.027357 CAACACCTGCCCTCATATGC 58.973 55.000 0.00 0.00 0.00 3.14
2509 4415 5.084519 TGGATCAAGTGTTGTAGAGGTAGT 58.915 41.667 0.00 0.00 0.00 2.73
2558 4464 2.420372 TCATCGCTGTCTGTCACTAGTC 59.580 50.000 0.00 0.00 0.00 2.59
2650 4556 2.360483 TGCGAGAAACTTGCATTGGAAA 59.640 40.909 9.27 0.00 44.84 3.13
2670 4576 1.613630 AGGAGGAGCATTGGTCGGT 60.614 57.895 9.58 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.523966 GACTGTGGGAGAGACGAGTG 59.476 60.000 0.00 0.00 0.00 3.51
1 2 0.956410 CGACTGTGGGAGAGACGAGT 60.956 60.000 0.00 0.00 0.00 4.18
2 3 0.956410 ACGACTGTGGGAGAGACGAG 60.956 60.000 0.00 0.00 0.00 4.18
3 4 0.322648 TACGACTGTGGGAGAGACGA 59.677 55.000 0.00 0.00 0.00 4.20
5 6 2.366533 TGATACGACTGTGGGAGAGAC 58.633 52.381 0.00 0.00 0.00 3.36
6 7 2.801077 TGATACGACTGTGGGAGAGA 57.199 50.000 0.00 0.00 0.00 3.10
7 8 4.142795 CGATATGATACGACTGTGGGAGAG 60.143 50.000 0.00 0.00 0.00 3.20
9 10 3.502595 ACGATATGATACGACTGTGGGAG 59.497 47.826 0.00 0.00 0.00 4.30
10 11 3.483421 ACGATATGATACGACTGTGGGA 58.517 45.455 0.00 0.00 0.00 4.37
11 12 3.917329 ACGATATGATACGACTGTGGG 57.083 47.619 0.00 0.00 0.00 4.61
12 13 5.106277 ACCATACGATATGATACGACTGTGG 60.106 44.000 0.00 0.00 0.00 4.17
13 14 5.939457 ACCATACGATATGATACGACTGTG 58.061 41.667 0.00 0.00 0.00 3.66
14 15 6.570672 AACCATACGATATGATACGACTGT 57.429 37.500 0.00 0.00 0.00 3.55
15 16 8.847567 GTTTAACCATACGATATGATACGACTG 58.152 37.037 0.00 0.00 0.00 3.51
16 17 8.790718 AGTTTAACCATACGATATGATACGACT 58.209 33.333 0.00 0.00 0.00 4.18
17 18 8.961294 AGTTTAACCATACGATATGATACGAC 57.039 34.615 0.00 0.00 0.00 4.34
27 28 8.967664 TGGCTTTTATAGTTTAACCATACGAT 57.032 30.769 0.00 0.00 0.00 3.73
28 29 8.789825 TTGGCTTTTATAGTTTAACCATACGA 57.210 30.769 0.00 0.00 0.00 3.43
45 46 9.595823 CTTCAATCTGATGATTAATTGGCTTTT 57.404 29.630 0.00 0.00 40.61 2.27
46 47 8.202137 CCTTCAATCTGATGATTAATTGGCTTT 58.798 33.333 0.00 0.00 40.61 3.51
47 48 7.343833 ACCTTCAATCTGATGATTAATTGGCTT 59.656 33.333 0.00 0.00 40.61 4.35
48 49 6.837568 ACCTTCAATCTGATGATTAATTGGCT 59.162 34.615 0.00 0.00 40.61 4.75
49 50 7.047460 ACCTTCAATCTGATGATTAATTGGC 57.953 36.000 0.00 0.00 40.61 4.52
54 55 8.664798 CGTGTTAACCTTCAATCTGATGATTAA 58.335 33.333 2.48 0.00 40.61 1.40
55 56 7.201609 GCGTGTTAACCTTCAATCTGATGATTA 60.202 37.037 2.48 0.00 40.61 1.75
56 57 6.403636 GCGTGTTAACCTTCAATCTGATGATT 60.404 38.462 2.48 0.00 43.10 2.57
57 58 5.065218 GCGTGTTAACCTTCAATCTGATGAT 59.935 40.000 2.48 0.00 33.70 2.45
58 59 4.391830 GCGTGTTAACCTTCAATCTGATGA 59.608 41.667 2.48 0.00 0.00 2.92
59 60 4.393062 AGCGTGTTAACCTTCAATCTGATG 59.607 41.667 2.48 0.00 0.00 3.07
60 61 4.579869 AGCGTGTTAACCTTCAATCTGAT 58.420 39.130 2.48 0.00 0.00 2.90
61 62 4.002906 AGCGTGTTAACCTTCAATCTGA 57.997 40.909 2.48 0.00 0.00 3.27
62 63 5.856126 TTAGCGTGTTAACCTTCAATCTG 57.144 39.130 2.48 0.00 0.00 2.90
63 64 5.106673 GCTTTAGCGTGTTAACCTTCAATCT 60.107 40.000 2.48 0.00 0.00 2.40
64 65 5.086727 GCTTTAGCGTGTTAACCTTCAATC 58.913 41.667 2.48 0.00 0.00 2.67
65 66 4.517453 TGCTTTAGCGTGTTAACCTTCAAT 59.483 37.500 2.48 0.00 45.83 2.57
66 67 3.878103 TGCTTTAGCGTGTTAACCTTCAA 59.122 39.130 2.48 0.00 45.83 2.69
67 68 3.468770 TGCTTTAGCGTGTTAACCTTCA 58.531 40.909 2.48 0.00 45.83 3.02
68 69 4.477302 TTGCTTTAGCGTGTTAACCTTC 57.523 40.909 2.48 0.00 45.83 3.46
69 70 4.904253 TTTGCTTTAGCGTGTTAACCTT 57.096 36.364 2.48 0.00 45.83 3.50
70 71 4.904253 TTTTGCTTTAGCGTGTTAACCT 57.096 36.364 2.48 0.00 45.83 3.50
71 72 4.799428 TGTTTTTGCTTTAGCGTGTTAACC 59.201 37.500 2.48 0.00 45.83 2.85
72 73 5.935448 TGTTTTTGCTTTAGCGTGTTAAC 57.065 34.783 0.00 0.00 45.83 2.01
73 74 6.531948 ACAATGTTTTTGCTTTAGCGTGTTAA 59.468 30.769 0.00 0.00 45.83 2.01
74 75 6.020281 CACAATGTTTTTGCTTTAGCGTGTTA 60.020 34.615 0.00 0.00 45.83 2.41
75 76 4.867608 ACAATGTTTTTGCTTTAGCGTGTT 59.132 33.333 0.00 0.00 45.83 3.32
76 77 4.267452 CACAATGTTTTTGCTTTAGCGTGT 59.733 37.500 0.00 0.00 45.83 4.49
77 78 4.267452 ACACAATGTTTTTGCTTTAGCGTG 59.733 37.500 0.00 0.00 45.83 5.34
78 79 4.429108 ACACAATGTTTTTGCTTTAGCGT 58.571 34.783 0.00 0.00 45.83 5.07
79 80 5.388225 AACACAATGTTTTTGCTTTAGCG 57.612 34.783 0.00 0.00 39.96 4.26
110 111 4.814234 TCCCGATCGAAAGGTGAATATTTG 59.186 41.667 18.66 0.00 0.00 2.32
111 112 5.031066 TCCCGATCGAAAGGTGAATATTT 57.969 39.130 18.66 0.00 0.00 1.40
115 116 2.224305 GGATCCCGATCGAAAGGTGAAT 60.224 50.000 18.66 0.00 38.69 2.57
132 133 1.460273 GGGCTCTCAGGTCTCGGATC 61.460 65.000 0.00 0.00 0.00 3.36
137 138 1.334384 GGGAAGGGCTCTCAGGTCTC 61.334 65.000 0.00 0.00 0.00 3.36
141 142 3.093172 GGGGGAAGGGCTCTCAGG 61.093 72.222 0.00 0.00 0.00 3.86
144 145 2.770475 GGAGGGGGAAGGGCTCTC 60.770 72.222 0.00 0.00 0.00 3.20
148 149 3.036045 TAGGAGGAGGGGGAAGGGC 62.036 68.421 0.00 0.00 0.00 5.19
155 156 2.518825 CGGTCGTAGGAGGAGGGG 60.519 72.222 0.00 0.00 0.00 4.79
156 157 3.217743 GCGGTCGTAGGAGGAGGG 61.218 72.222 0.00 0.00 0.00 4.30
157 158 1.392710 ATTGCGGTCGTAGGAGGAGG 61.393 60.000 0.00 0.00 0.00 4.30
158 159 0.249073 CATTGCGGTCGTAGGAGGAG 60.249 60.000 0.00 0.00 0.00 3.69
185 186 1.456705 TGGTGGAAGCGGCCTTTTT 60.457 52.632 0.00 0.00 36.92 1.94
186 187 2.197324 TGGTGGAAGCGGCCTTTT 59.803 55.556 0.00 0.00 36.92 2.27
187 188 2.597510 GTGGTGGAAGCGGCCTTT 60.598 61.111 0.00 0.00 36.92 3.11
188 189 4.660938 GGTGGTGGAAGCGGCCTT 62.661 66.667 0.00 0.00 36.92 4.35
227 241 2.481969 CGATTTCGGAGAAGAGGCATGA 60.482 50.000 0.00 0.00 45.90 3.07
230 244 3.741029 CGATTTCGGAGAAGAGGCA 57.259 52.632 0.00 0.00 45.90 4.75
242 256 3.202706 GGGGTGCTCGCCGATTTC 61.203 66.667 6.08 0.00 36.95 2.17
271 285 0.822121 GCGAAGGGGTCACTGGTTTT 60.822 55.000 0.00 0.00 0.00 2.43
317 331 0.325602 TAAAATGGGGACGAAGCGGT 59.674 50.000 0.00 0.00 0.00 5.68
331 345 5.413499 GTGAGCTTGAACATGCCATAAAAT 58.587 37.500 8.64 0.00 32.53 1.82
332 346 4.321899 GGTGAGCTTGAACATGCCATAAAA 60.322 41.667 8.64 0.00 32.53 1.52
336 350 1.180029 GGTGAGCTTGAACATGCCAT 58.820 50.000 8.64 0.00 32.53 4.40
344 358 2.497273 TCATCGATGAGGTGAGCTTGAA 59.503 45.455 23.99 0.00 34.48 2.69
346 360 2.591571 TCATCGATGAGGTGAGCTTG 57.408 50.000 23.99 0.00 34.48 4.01
347 361 2.806019 GCATCATCGATGAGGTGAGCTT 60.806 50.000 33.09 13.81 44.28 3.74
353 368 3.366781 CGACATAGCATCATCGATGAGGT 60.367 47.826 33.09 27.66 42.09 3.85
373 388 1.658114 CAAGACAGGGACGTCACGA 59.342 57.895 18.91 0.00 38.43 4.35
385 400 0.888619 CGTAGCCTGAGTCCAAGACA 59.111 55.000 0.00 0.00 34.60 3.41
406 422 2.193127 TGGGTAGGTCGGTCAAATCAT 58.807 47.619 0.00 0.00 0.00 2.45
528 545 9.927081 ATTTTTCCCTGATGAGATAGTGTTTAT 57.073 29.630 0.00 0.00 0.00 1.40
545 2160 2.597578 ACGGTGCCTAATTTTTCCCT 57.402 45.000 0.00 0.00 0.00 4.20
548 2163 7.650504 ACTTAAGAAAACGGTGCCTAATTTTTC 59.349 33.333 10.09 0.00 36.73 2.29
582 2197 6.470556 TGACAAAATGTAAAACGATGTGTGTG 59.529 34.615 0.00 0.00 0.00 3.82
583 2198 6.556212 TGACAAAATGTAAAACGATGTGTGT 58.444 32.000 0.00 0.00 0.00 3.72
607 2226 2.594592 GTGCGGTGGCCAACTTCT 60.595 61.111 20.91 0.00 38.85 2.85
608 2227 2.268076 ATGTGCGGTGGCCAACTTC 61.268 57.895 20.91 11.19 38.85 3.01
612 2231 2.035469 ATCATGTGCGGTGGCCAA 59.965 55.556 7.24 0.00 38.85 4.52
663 2283 2.472695 TCTGCGCATTACTTTGTCCT 57.527 45.000 12.24 0.00 0.00 3.85
900 2520 2.730733 GCGGCGAGATGATCTGGA 59.269 61.111 12.98 0.00 0.00 3.86
981 2606 0.964358 TCGTCCGGTTCTCTCCCTTC 60.964 60.000 0.00 0.00 0.00 3.46
1168 2793 3.931247 CGTCCACACCGGGTCCAA 61.931 66.667 6.32 0.00 34.36 3.53
1746 3371 2.654863 CTGTCCCAGTCAAACCAACTT 58.345 47.619 0.00 0.00 0.00 2.66
1957 3582 6.333416 TGTCAACGAAACCATGATTCAAAAA 58.667 32.000 0.00 0.00 0.00 1.94
1958 3583 5.895928 TGTCAACGAAACCATGATTCAAAA 58.104 33.333 0.00 0.00 0.00 2.44
1959 3584 5.506686 TGTCAACGAAACCATGATTCAAA 57.493 34.783 0.00 0.00 0.00 2.69
1960 3585 5.067153 ACTTGTCAACGAAACCATGATTCAA 59.933 36.000 0.00 0.00 0.00 2.69
1961 3586 4.578516 ACTTGTCAACGAAACCATGATTCA 59.421 37.500 0.00 0.00 0.00 2.57
1962 3587 5.108385 ACTTGTCAACGAAACCATGATTC 57.892 39.130 0.00 0.00 0.00 2.52
1963 3588 4.319477 CGACTTGTCAACGAAACCATGATT 60.319 41.667 0.00 0.00 0.00 2.57
1964 3589 3.186409 CGACTTGTCAACGAAACCATGAT 59.814 43.478 0.00 0.00 0.00 2.45
1965 3590 2.542178 CGACTTGTCAACGAAACCATGA 59.458 45.455 0.00 0.00 0.00 3.07
1966 3591 2.349438 CCGACTTGTCAACGAAACCATG 60.349 50.000 0.00 0.00 0.00 3.66
1967 3592 1.871039 CCGACTTGTCAACGAAACCAT 59.129 47.619 0.00 0.00 0.00 3.55
1995 3620 1.444836 ACCACGAGACGAGAAGAGAG 58.555 55.000 0.00 0.00 0.00 3.20
2005 3630 4.525912 TTTTTACCTCCTACCACGAGAC 57.474 45.455 0.00 0.00 0.00 3.36
2033 3668 1.411493 GATCCGTCCGCTTTCACGTC 61.411 60.000 0.00 0.00 34.06 4.34
2101 3737 3.750130 AGCATGAGCCTTAATCAATAGCG 59.250 43.478 0.00 0.00 43.56 4.26
2115 3751 0.510359 CGCGAAATCCTAGCATGAGC 59.490 55.000 0.00 0.00 42.56 4.26
2132 3768 1.982073 GCAACATCAGTAGCCCACGC 61.982 60.000 0.00 0.00 0.00 5.34
2147 3783 2.680913 ATGCTCCGACAAGCGCAAC 61.681 57.895 11.47 0.00 45.54 4.17
2148 3784 2.358615 ATGCTCCGACAAGCGCAA 60.359 55.556 11.47 0.00 45.54 4.85
2149 3785 3.120385 CATGCTCCGACAAGCGCA 61.120 61.111 11.47 0.00 45.54 6.09
2151 3787 2.125552 TCCATGCTCCGACAAGCG 60.126 61.111 0.00 0.00 45.54 4.68
2152 3788 2.456119 CGTCCATGCTCCGACAAGC 61.456 63.158 1.58 0.00 42.82 4.01
2153 3789 0.670546 AACGTCCATGCTCCGACAAG 60.671 55.000 0.00 0.00 0.00 3.16
2154 3790 0.948623 CAACGTCCATGCTCCGACAA 60.949 55.000 0.00 0.00 0.00 3.18
2156 3792 2.740714 GCAACGTCCATGCTCCGAC 61.741 63.158 3.46 0.00 40.64 4.79
2157 3793 2.434185 GCAACGTCCATGCTCCGA 60.434 61.111 3.46 0.00 40.64 4.55
2158 3794 2.741985 TGCAACGTCCATGCTCCG 60.742 61.111 11.66 0.00 44.14 4.63
2160 3796 1.438651 TAAGTGCAACGTCCATGCTC 58.561 50.000 11.66 8.23 45.86 4.26
2161 3797 1.535462 GTTAAGTGCAACGTCCATGCT 59.465 47.619 11.66 0.00 45.86 3.79
2162 3798 1.401018 GGTTAAGTGCAACGTCCATGC 60.401 52.381 3.73 3.73 45.86 4.06
2163 3799 1.876799 TGGTTAAGTGCAACGTCCATG 59.123 47.619 0.00 0.00 45.86 3.66
2164 3800 2.264005 TGGTTAAGTGCAACGTCCAT 57.736 45.000 0.00 0.00 45.86 3.41
2165 3801 1.671845 GTTGGTTAAGTGCAACGTCCA 59.328 47.619 0.00 0.00 45.86 4.02
2166 3802 1.944709 AGTTGGTTAAGTGCAACGTCC 59.055 47.619 0.00 0.00 45.86 4.79
2167 3803 2.353579 ACAGTTGGTTAAGTGCAACGTC 59.646 45.455 0.00 0.00 45.86 4.34
2168 3804 2.361789 ACAGTTGGTTAAGTGCAACGT 58.638 42.857 0.00 0.00 45.86 3.99
2169 3805 4.539509 TTACAGTTGGTTAAGTGCAACG 57.460 40.909 0.00 0.00 45.86 4.10
2170 3806 6.809689 AGTTTTTACAGTTGGTTAAGTGCAAC 59.190 34.615 0.00 0.00 40.22 4.17
2289 4106 7.671302 TGTTTCTTCAGCTGTTACTAGATCTT 58.329 34.615 14.67 0.00 0.00 2.40
2302 4119 4.457257 GCTCCAACTATTGTTTCTTCAGCT 59.543 41.667 0.00 0.00 33.52 4.24
2306 4123 6.317857 GTGATGCTCCAACTATTGTTTCTTC 58.682 40.000 0.00 0.00 33.52 2.87
2360 4185 0.389948 GAGGCGACTTGGAACGATGT 60.390 55.000 0.00 0.00 44.43 3.06
2394 4259 5.237344 AGTGTGTTAATCAAGTGAAGCAGTC 59.763 40.000 0.00 0.00 0.00 3.51
2472 4378 3.976701 ATCCAGCGCCGACAAAGGG 62.977 63.158 2.29 0.00 0.00 3.95
2484 4390 3.265791 CCTCTACAACACTTGATCCAGC 58.734 50.000 0.00 0.00 0.00 4.85
2509 4415 6.156775 TGTTGGAAGATATCATCAGGTTCTCA 59.843 38.462 9.96 0.54 0.00 3.27
2544 4450 4.675408 GCATTGATCGACTAGTGACAGACA 60.675 45.833 0.00 0.00 0.00 3.41
2545 4451 3.794028 GCATTGATCGACTAGTGACAGAC 59.206 47.826 0.00 0.00 0.00 3.51
2547 4453 3.795639 CAGCATTGATCGACTAGTGACAG 59.204 47.826 0.00 0.00 0.00 3.51
2548 4454 3.193479 ACAGCATTGATCGACTAGTGACA 59.807 43.478 0.00 0.00 0.00 3.58
2558 4464 2.096496 GGTTTCCTGACAGCATTGATCG 59.904 50.000 0.00 0.00 0.00 3.69
2650 4556 1.333636 CCGACCAATGCTCCTCCTCT 61.334 60.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.