Multiple sequence alignment - TraesCS2D01G268200

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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 TraesCS2D01G268200 chr2D 100.000 2251 0 0 626 2876 328369139 328371389 0.000000e+00 4157.0
1 TraesCS2D01G268200 chr2D 100.000 307 0 0 1 307 328368514 328368820 4.160000e-158 568.0
2 TraesCS2D01G268200 chr2A 94.211 1382 41 10 682 2031 434578585 434579959 0.000000e+00 2073.0
3 TraesCS2D01G268200 chr2A 92.547 738 24 12 2086 2811 434611174 434611892 0.000000e+00 1029.0
4 TraesCS2D01G268200 chr2A 89.015 264 28 1 39 301 464955897 464955634 2.760000e-85 326.0
5 TraesCS2D01G268200 chr2A 97.297 74 2 0 2014 2087 434580264 434580337 3.010000e-25 126.0
6 TraesCS2D01G268200 chr2A 98.333 60 0 1 626 684 432581708 432581767 1.410000e-18 104.0
7 TraesCS2D01G268200 chr2B 91.804 1391 51 23 682 2055 397452704 397454048 0.000000e+00 1879.0
8 TraesCS2D01G268200 chr2B 91.516 719 23 13 2105 2814 397454046 397454735 0.000000e+00 955.0
9 TraesCS2D01G268200 chr2B 90.262 267 26 0 39 305 136974771 136974505 1.640000e-92 350.0
10 TraesCS2D01G268200 chr2B 91.935 62 2 2 626 684 396927465 396927526 1.840000e-12 84.2
11 TraesCS2D01G268200 chrUn 88.525 305 23 10 1 293 92147158 92146854 2.720000e-95 359.0
12 TraesCS2D01G268200 chr3D 87.619 315 28 6 2 305 186943473 186943787 3.520000e-94 355.0
13 TraesCS2D01G268200 chr5D 90.370 270 25 1 39 307 78793158 78793427 1.270000e-93 353.0
14 TraesCS2D01G268200 chr5D 86.709 316 31 6 1 305 481736470 481736155 9.870000e-90 340.0
15 TraesCS2D01G268200 chr5A 87.987 308 26 7 9 305 428401364 428401671 1.270000e-93 353.0
16 TraesCS2D01G268200 chr1B 89.552 268 27 1 39 305 100554923 100555190 3.550000e-89 339.0
17 TraesCS2D01G268200 chr6B 88.433 268 28 3 39 304 474766965 474767231 1.290000e-83 320.0


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 TraesCS2D01G268200 chr2D 328368514 328371389 2875 False 2362.5 4157 100.000 1 2876 2 chr2D.!!$F1 2875
1 TraesCS2D01G268200 chr2A 434578585 434580337 1752 False 1099.5 2073 95.754 682 2087 2 chr2A.!!$F3 1405
2 TraesCS2D01G268200 chr2A 434611174 434611892 718 False 1029.0 1029 92.547 2086 2811 1 chr2A.!!$F2 725
3 TraesCS2D01G268200 chr2B 397452704 397454735 2031 False 1417.0 1879 91.660 682 2814 2 chr2B.!!$F2 2132

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
143 144 0.101040 CAACACTGCCACCACAACTG 59.899 55.0 0.00 0.0 0.0 3.16 F
201 202 0.178767 CAGATCTGGGCCGTCATGAA 59.821 55.0 15.38 0.0 0.0 2.57 F
202 203 0.179000 AGATCTGGGCCGTCATGAAC 59.821 55.0 0.00 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1147 0.039180 TCTGACTGAGGAGGCCGTTA 59.961 55.0 0.00 0.00 0.00 3.18 R
1437 1465 0.320374 TCACCATCTGGGACGTCAAC 59.680 55.0 18.91 10.22 41.15 3.18 R
2044 2410 0.826256 ACACACTCGACTAGGCACCA 60.826 55.0 0.00 0.00 0.00 4.17 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
30 31 4.315941 GGCCATCCGACCCGATCC 62.316 72.222 0.00 0.00 0.00 3.36
31 32 4.315941 GCCATCCGACCCGATCCC 62.316 72.222 0.00 0.00 0.00 3.85
32 33 2.524394 CCATCCGACCCGATCCCT 60.524 66.667 0.00 0.00 0.00 4.20
33 34 2.737180 CATCCGACCCGATCCCTG 59.263 66.667 0.00 0.00 0.00 4.45
34 35 1.832608 CATCCGACCCGATCCCTGA 60.833 63.158 0.00 0.00 0.00 3.86
35 36 1.833049 ATCCGACCCGATCCCTGAC 60.833 63.158 0.00 0.00 0.00 3.51
36 37 2.583298 ATCCGACCCGATCCCTGACA 62.583 60.000 0.00 0.00 0.00 3.58
37 38 2.786495 CCGACCCGATCCCTGACAG 61.786 68.421 0.00 0.00 0.00 3.51
38 39 2.501610 GACCCGATCCCTGACAGC 59.498 66.667 0.00 0.00 0.00 4.40
39 40 3.083997 ACCCGATCCCTGACAGCC 61.084 66.667 0.00 0.00 0.00 4.85
40 41 3.866582 CCCGATCCCTGACAGCCC 61.867 72.222 0.00 0.00 0.00 5.19
41 42 4.227134 CCGATCCCTGACAGCCCG 62.227 72.222 0.00 0.00 0.00 6.13
42 43 4.899239 CGATCCCTGACAGCCCGC 62.899 72.222 0.00 0.00 0.00 6.13
43 44 4.554036 GATCCCTGACAGCCCGCC 62.554 72.222 0.00 0.00 0.00 6.13
97 98 3.420482 CCCGGGATCCAAGGCCTT 61.420 66.667 18.48 13.78 0.00 4.35
98 99 2.193248 CCGGGATCCAAGGCCTTC 59.807 66.667 17.29 3.91 0.00 3.46
99 100 2.193248 CGGGATCCAAGGCCTTCC 59.807 66.667 17.29 14.36 0.00 3.46
100 101 2.193248 GGGATCCAAGGCCTTCCG 59.807 66.667 17.29 9.05 37.47 4.30
101 102 2.517166 GGATCCAAGGCCTTCCGC 60.517 66.667 17.29 5.29 37.47 5.54
110 111 2.340443 GCCTTCCGCCCTAGATCG 59.660 66.667 0.00 0.00 0.00 3.69
111 112 3.052081 CCTTCCGCCCTAGATCGG 58.948 66.667 14.11 14.11 46.52 4.18
119 120 4.932060 CCTAGATCGGGAGGAGCA 57.068 61.111 5.66 0.00 34.46 4.26
120 121 2.652313 CCTAGATCGGGAGGAGCAG 58.348 63.158 5.66 0.00 34.46 4.24
121 122 1.531739 CCTAGATCGGGAGGAGCAGC 61.532 65.000 5.66 0.00 34.46 5.25
122 123 1.861542 CTAGATCGGGAGGAGCAGCG 61.862 65.000 0.00 0.00 32.03 5.18
123 124 4.959596 GATCGGGAGGAGCAGCGC 62.960 72.222 0.00 0.00 0.00 5.92
128 129 4.704833 GGAGGAGCAGCGCCAACA 62.705 66.667 18.51 0.00 0.00 3.33
129 130 3.426568 GAGGAGCAGCGCCAACAC 61.427 66.667 18.51 2.17 0.00 3.32
130 131 3.890936 GAGGAGCAGCGCCAACACT 62.891 63.158 18.51 0.00 0.00 3.55
131 132 3.730761 GGAGCAGCGCCAACACTG 61.731 66.667 10.86 0.00 36.96 3.66
135 136 4.332637 CAGCGCCAACACTGCCAC 62.333 66.667 2.29 0.00 0.00 5.01
138 139 3.964875 CGCCAACACTGCCACCAC 61.965 66.667 0.00 0.00 0.00 4.16
139 140 2.832661 GCCAACACTGCCACCACA 60.833 61.111 0.00 0.00 0.00 4.17
140 141 2.422231 GCCAACACTGCCACCACAA 61.422 57.895 0.00 0.00 0.00 3.33
141 142 1.437160 CCAACACTGCCACCACAAC 59.563 57.895 0.00 0.00 0.00 3.32
142 143 1.037030 CCAACACTGCCACCACAACT 61.037 55.000 0.00 0.00 0.00 3.16
143 144 0.101040 CAACACTGCCACCACAACTG 59.899 55.000 0.00 0.00 0.00 3.16
144 145 1.666209 AACACTGCCACCACAACTGC 61.666 55.000 0.00 0.00 0.00 4.40
145 146 2.519302 ACTGCCACCACAACTGCC 60.519 61.111 0.00 0.00 0.00 4.85
146 147 3.663176 CTGCCACCACAACTGCCG 61.663 66.667 0.00 0.00 0.00 5.69
147 148 4.182433 TGCCACCACAACTGCCGA 62.182 61.111 0.00 0.00 0.00 5.54
148 149 2.672996 GCCACCACAACTGCCGAT 60.673 61.111 0.00 0.00 0.00 4.18
149 150 1.376683 GCCACCACAACTGCCGATA 60.377 57.895 0.00 0.00 0.00 2.92
150 151 1.369091 GCCACCACAACTGCCGATAG 61.369 60.000 0.00 0.00 0.00 2.08
162 163 4.647615 CGATAGGACGCCGGCCAG 62.648 72.222 23.46 10.83 0.00 4.85
163 164 4.971125 GATAGGACGCCGGCCAGC 62.971 72.222 23.46 10.29 0.00 4.85
183 184 4.308458 CCACACCGCCGAAGTCCA 62.308 66.667 0.00 0.00 0.00 4.02
184 185 2.738521 CACACCGCCGAAGTCCAG 60.739 66.667 0.00 0.00 0.00 3.86
185 186 2.915659 ACACCGCCGAAGTCCAGA 60.916 61.111 0.00 0.00 0.00 3.86
186 187 2.283529 ACACCGCCGAAGTCCAGAT 61.284 57.895 0.00 0.00 0.00 2.90
187 188 1.519455 CACCGCCGAAGTCCAGATC 60.519 63.158 0.00 0.00 0.00 2.75
188 189 1.682684 ACCGCCGAAGTCCAGATCT 60.683 57.895 0.00 0.00 0.00 2.75
189 190 1.227089 CCGCCGAAGTCCAGATCTG 60.227 63.158 16.24 16.24 0.00 2.90
198 199 3.234349 CCAGATCTGGGCCGTCAT 58.766 61.111 31.14 0.00 46.81 3.06
199 200 1.227764 CCAGATCTGGGCCGTCATG 60.228 63.158 31.14 4.72 46.81 3.07
200 201 1.689243 CCAGATCTGGGCCGTCATGA 61.689 60.000 31.14 0.00 46.81 3.07
201 202 0.178767 CAGATCTGGGCCGTCATGAA 59.821 55.000 15.38 0.00 0.00 2.57
202 203 0.179000 AGATCTGGGCCGTCATGAAC 59.821 55.000 0.00 0.00 0.00 3.18
203 204 0.815615 GATCTGGGCCGTCATGAACC 60.816 60.000 0.00 0.00 0.00 3.62
204 205 1.561769 ATCTGGGCCGTCATGAACCA 61.562 55.000 0.00 3.23 0.00 3.67
205 206 1.746615 CTGGGCCGTCATGAACCAG 60.747 63.158 17.37 17.37 42.28 4.00
206 207 2.220586 TGGGCCGTCATGAACCAGA 61.221 57.895 0.00 0.00 0.00 3.86
207 208 1.224592 GGGCCGTCATGAACCAGAT 59.775 57.895 0.00 0.00 0.00 2.90
208 209 0.394352 GGGCCGTCATGAACCAGATT 60.394 55.000 0.00 0.00 0.00 2.40
209 210 0.734889 GGCCGTCATGAACCAGATTG 59.265 55.000 0.00 0.00 0.00 2.67
210 211 0.734889 GCCGTCATGAACCAGATTGG 59.265 55.000 0.00 0.00 45.02 3.16
230 231 3.790437 CCGCCACAGCCCAGATCT 61.790 66.667 0.00 0.00 34.57 2.75
231 232 2.513204 CGCCACAGCCCAGATCTG 60.513 66.667 16.24 16.24 37.56 2.90
243 244 2.906691 CAGATCTGGATCACACCCTC 57.093 55.000 15.38 0.00 40.22 4.30
244 245 1.068281 CAGATCTGGATCACACCCTCG 59.932 57.143 15.38 0.00 40.22 4.63
245 246 1.063642 AGATCTGGATCACACCCTCGA 60.064 52.381 12.34 0.00 40.22 4.04
246 247 1.339610 GATCTGGATCACACCCTCGAG 59.660 57.143 5.13 5.13 37.74 4.04
247 248 1.142748 CTGGATCACACCCTCGAGC 59.857 63.158 6.99 0.00 0.00 5.03
248 249 2.303549 CTGGATCACACCCTCGAGCC 62.304 65.000 6.99 0.25 38.22 4.70
249 250 2.359169 GGATCACACCCTCGAGCCA 61.359 63.158 6.99 0.00 37.64 4.75
250 251 1.142748 GATCACACCCTCGAGCCAG 59.857 63.158 6.99 0.00 0.00 4.85
251 252 2.303549 GATCACACCCTCGAGCCAGG 62.304 65.000 6.99 5.72 0.00 4.45
293 294 4.200283 GCGAGAGGGAGGAGTGCG 62.200 72.222 0.00 0.00 0.00 5.34
294 295 2.752238 CGAGAGGGAGGAGTGCGT 60.752 66.667 0.00 0.00 0.00 5.24
295 296 2.766400 CGAGAGGGAGGAGTGCGTC 61.766 68.421 0.00 0.00 0.00 5.19
649 650 7.830940 GGAGTAGATATCATTCAGAATGCAG 57.169 40.000 17.26 0.00 38.77 4.41
650 651 7.609960 GGAGTAGATATCATTCAGAATGCAGA 58.390 38.462 17.26 6.17 38.77 4.26
651 652 8.259411 GGAGTAGATATCATTCAGAATGCAGAT 58.741 37.037 17.26 10.23 38.77 2.90
656 657 9.217278 AGATATCATTCAGAATGCAGATAACAC 57.783 33.333 17.26 7.45 38.77 3.32
657 658 6.630444 ATCATTCAGAATGCAGATAACACC 57.370 37.500 17.26 0.00 38.77 4.16
658 659 4.571984 TCATTCAGAATGCAGATAACACCG 59.428 41.667 17.26 0.00 38.77 4.94
659 660 3.610040 TCAGAATGCAGATAACACCGT 57.390 42.857 0.00 0.00 34.76 4.83
660 661 3.261580 TCAGAATGCAGATAACACCGTG 58.738 45.455 0.00 0.00 34.76 4.94
661 662 2.352651 CAGAATGCAGATAACACCGTGG 59.647 50.000 3.03 0.00 0.00 4.94
662 663 2.236146 AGAATGCAGATAACACCGTGGA 59.764 45.455 3.03 0.00 0.00 4.02
663 664 3.118261 AGAATGCAGATAACACCGTGGAT 60.118 43.478 3.03 0.00 0.00 3.41
664 665 2.022764 TGCAGATAACACCGTGGATG 57.977 50.000 3.03 0.00 0.00 3.51
665 666 1.299541 GCAGATAACACCGTGGATGG 58.700 55.000 3.03 0.00 0.00 3.51
666 667 1.406887 GCAGATAACACCGTGGATGGT 60.407 52.381 3.03 0.00 45.21 3.55
673 674 3.030415 ACCGTGGATGGTGTTTTCC 57.970 52.632 0.00 0.00 41.85 3.13
674 675 0.476771 ACCGTGGATGGTGTTTTCCT 59.523 50.000 0.00 0.00 41.85 3.36
675 676 0.881118 CCGTGGATGGTGTTTTCCTG 59.119 55.000 0.00 0.00 32.95 3.86
676 677 0.240945 CGTGGATGGTGTTTTCCTGC 59.759 55.000 0.00 0.00 32.95 4.85
677 678 1.620822 GTGGATGGTGTTTTCCTGCT 58.379 50.000 0.00 0.00 32.95 4.24
678 679 2.790433 GTGGATGGTGTTTTCCTGCTA 58.210 47.619 0.00 0.00 32.95 3.49
679 680 2.749621 GTGGATGGTGTTTTCCTGCTAG 59.250 50.000 0.00 0.00 32.95 3.42
680 681 2.642311 TGGATGGTGTTTTCCTGCTAGA 59.358 45.455 0.00 0.00 32.95 2.43
685 686 2.351455 GTGTTTTCCTGCTAGAGCTCC 58.649 52.381 10.93 0.00 42.66 4.70
688 689 1.656587 TTTCCTGCTAGAGCTCCCAA 58.343 50.000 10.93 0.00 42.66 4.12
933 961 3.906720 TTAGCATCCTAACCACACCTC 57.093 47.619 0.00 0.00 0.00 3.85
1119 1147 0.754472 TTCCCGACTTCTCCACGTTT 59.246 50.000 0.00 0.00 0.00 3.60
1592 1620 0.900647 ACTAAGACTCCTGCGCCAGT 60.901 55.000 4.18 3.82 0.00 4.00
1608 1636 4.825252 GTACCGGCGCCGTCCAAT 62.825 66.667 43.12 25.97 37.81 3.16
1776 1804 3.643978 GCGCCGGCAGATGATGAC 61.644 66.667 28.98 0.68 39.62 3.06
1856 1887 2.202878 TATCGTGGCGCTTCTGGC 60.203 61.111 7.64 0.00 37.64 4.85
1876 1907 3.729526 CGATTGTTGTTTCGCTCTGAT 57.270 42.857 0.00 0.00 0.00 2.90
1921 1958 2.185004 ACGGTTCAAAGCAGCACTAT 57.815 45.000 0.00 0.00 0.00 2.12
1950 1989 2.070783 GTAGGCAAAACGTGATCGGAA 58.929 47.619 0.00 0.00 41.85 4.30
1989 2033 0.839946 ACCAAGAGAAGGCACACTGT 59.160 50.000 0.00 0.00 0.00 3.55
2044 2410 4.267928 GCGATTTACTGCTCAGTATCGTTT 59.732 41.667 24.24 7.02 44.98 3.60
2050 2416 0.727398 GCTCAGTATCGTTTGGTGCC 59.273 55.000 0.00 0.00 0.00 5.01
2101 2467 0.179056 TAGGATTTAGCCTGCCACGC 60.179 55.000 0.00 0.00 39.08 5.34
2244 2617 1.323534 GTCCAGTATGCAGTTTACGCG 59.676 52.381 3.53 3.53 31.97 6.01
2289 2668 1.745115 GCTATGGTGCCACTGCGAA 60.745 57.895 0.00 0.00 41.78 4.70
2291 2670 1.164411 CTATGGTGCCACTGCGAAAA 58.836 50.000 0.00 0.00 41.78 2.29
2300 2679 2.801342 GCCACTGCGAAAACATGGAAAA 60.801 45.455 0.00 0.00 31.69 2.29
2301 2680 2.794350 CCACTGCGAAAACATGGAAAAC 59.206 45.455 0.00 0.00 31.69 2.43
2302 2681 3.490761 CCACTGCGAAAACATGGAAAACT 60.491 43.478 0.00 0.00 31.69 2.66
2303 2682 4.111916 CACTGCGAAAACATGGAAAACTT 58.888 39.130 0.00 0.00 0.00 2.66
2304 2683 4.026640 CACTGCGAAAACATGGAAAACTTG 60.027 41.667 0.00 0.00 0.00 3.16
2399 2786 7.882791 TCACATGATTTACAAGTATGACCACTT 59.117 33.333 0.00 0.00 39.34 3.16
2668 3055 0.177836 GCTGAGGAAGAGAGGGAAGC 59.822 60.000 0.00 0.00 0.00 3.86
2814 3201 8.462811 TCAAATTACATGTGCCACGTTAATTAT 58.537 29.630 9.11 0.00 0.00 1.28
2815 3202 9.081997 CAAATTACATGTGCCACGTTAATTATT 57.918 29.630 9.11 0.00 0.00 1.40
2816 3203 9.646427 AAATTACATGTGCCACGTTAATTATTT 57.354 25.926 9.11 2.83 0.00 1.40
2817 3204 9.646427 AATTACATGTGCCACGTTAATTATTTT 57.354 25.926 9.11 0.00 0.00 1.82
2818 3205 9.646427 ATTACATGTGCCACGTTAATTATTTTT 57.354 25.926 9.11 0.00 0.00 1.94
2842 3229 7.892445 TTTCATTTCTTTCTCTTTTTCGACG 57.108 32.000 0.00 0.00 0.00 5.12
2843 3230 5.985781 TCATTTCTTTCTCTTTTTCGACGG 58.014 37.500 0.00 0.00 0.00 4.79
2844 3231 4.806342 TTTCTTTCTCTTTTTCGACGGG 57.194 40.909 0.00 0.00 0.00 5.28
2845 3232 3.738830 TCTTTCTCTTTTTCGACGGGA 57.261 42.857 0.00 0.00 0.00 5.14
2846 3233 4.062677 TCTTTCTCTTTTTCGACGGGAA 57.937 40.909 0.00 0.00 0.00 3.97
2847 3234 4.444536 TCTTTCTCTTTTTCGACGGGAAA 58.555 39.130 0.00 0.41 42.75 3.13
2867 3254 2.094762 AAAGGTGTATCGACTGTGGC 57.905 50.000 0.00 0.00 0.00 5.01
2868 3255 0.249398 AAGGTGTATCGACTGTGGCC 59.751 55.000 0.00 0.00 0.00 5.36
2869 3256 1.518572 GGTGTATCGACTGTGGCCG 60.519 63.158 0.00 0.00 0.00 6.13
2870 3257 1.518572 GTGTATCGACTGTGGCCGG 60.519 63.158 0.00 0.00 0.00 6.13
2871 3258 2.106332 GTATCGACTGTGGCCGGG 59.894 66.667 2.18 0.00 0.00 5.73
2872 3259 3.151710 TATCGACTGTGGCCGGGG 61.152 66.667 2.18 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.315941 GGATCGGGTCGGATGGCC 62.316 72.222 0.00 0.00 0.00 5.36
14 15 4.315941 GGGATCGGGTCGGATGGC 62.316 72.222 0.00 0.00 0.00 4.40
15 16 2.524394 AGGGATCGGGTCGGATGG 60.524 66.667 0.00 0.00 0.00 3.51
16 17 1.832608 TCAGGGATCGGGTCGGATG 60.833 63.158 0.00 0.00 0.00 3.51
17 18 1.833049 GTCAGGGATCGGGTCGGAT 60.833 63.158 0.00 0.00 0.00 4.18
18 19 2.441532 GTCAGGGATCGGGTCGGA 60.442 66.667 0.00 0.00 0.00 4.55
19 20 2.758327 TGTCAGGGATCGGGTCGG 60.758 66.667 0.00 0.00 0.00 4.79
20 21 2.808315 CTGTCAGGGATCGGGTCG 59.192 66.667 0.00 0.00 0.00 4.79
21 22 2.501610 GCTGTCAGGGATCGGGTC 59.498 66.667 1.14 0.00 0.00 4.46
22 23 3.083997 GGCTGTCAGGGATCGGGT 61.084 66.667 1.14 0.00 0.00 5.28
23 24 3.866582 GGGCTGTCAGGGATCGGG 61.867 72.222 1.14 0.00 0.00 5.14
24 25 4.227134 CGGGCTGTCAGGGATCGG 62.227 72.222 1.14 0.00 0.00 4.18
25 26 4.899239 GCGGGCTGTCAGGGATCG 62.899 72.222 1.14 0.00 0.00 3.69
26 27 4.554036 GGCGGGCTGTCAGGGATC 62.554 72.222 1.14 0.00 0.00 3.36
80 81 3.420482 AAGGCCTTGGATCCCGGG 61.420 66.667 19.73 16.85 0.00 5.73
81 82 2.193248 GAAGGCCTTGGATCCCGG 59.807 66.667 26.25 11.05 0.00 5.73
82 83 2.193248 GGAAGGCCTTGGATCCCG 59.807 66.667 26.25 0.00 0.00 5.14
83 84 2.193248 CGGAAGGCCTTGGATCCC 59.807 66.667 26.25 16.57 0.00 3.85
84 85 2.517166 GCGGAAGGCCTTGGATCC 60.517 66.667 26.25 17.44 34.80 3.36
102 103 1.531739 GCTGCTCCTCCCGATCTAGG 61.532 65.000 0.00 0.00 0.00 3.02
103 104 1.861542 CGCTGCTCCTCCCGATCTAG 61.862 65.000 0.00 0.00 0.00 2.43
104 105 1.899054 CGCTGCTCCTCCCGATCTA 60.899 63.158 0.00 0.00 0.00 1.98
105 106 3.222855 CGCTGCTCCTCCCGATCT 61.223 66.667 0.00 0.00 0.00 2.75
106 107 4.959596 GCGCTGCTCCTCCCGATC 62.960 72.222 0.00 0.00 0.00 3.69
111 112 4.704833 TGTTGGCGCTGCTCCTCC 62.705 66.667 7.64 0.99 0.00 4.30
112 113 3.426568 GTGTTGGCGCTGCTCCTC 61.427 66.667 7.64 4.11 0.00 3.71
113 114 3.946201 AGTGTTGGCGCTGCTCCT 61.946 61.111 7.64 0.00 33.62 3.69
114 115 3.730761 CAGTGTTGGCGCTGCTCC 61.731 66.667 7.64 0.71 44.83 4.70
123 124 1.037030 AGTTGTGGTGGCAGTGTTGG 61.037 55.000 0.00 0.00 0.00 3.77
124 125 0.101040 CAGTTGTGGTGGCAGTGTTG 59.899 55.000 0.00 0.00 0.00 3.33
125 126 1.666209 GCAGTTGTGGTGGCAGTGTT 61.666 55.000 0.00 0.00 0.00 3.32
126 127 2.120909 GCAGTTGTGGTGGCAGTGT 61.121 57.895 0.00 0.00 0.00 3.55
127 128 2.723746 GCAGTTGTGGTGGCAGTG 59.276 61.111 0.00 0.00 0.00 3.66
128 129 2.519302 GGCAGTTGTGGTGGCAGT 60.519 61.111 0.00 0.00 40.16 4.40
129 130 3.663176 CGGCAGTTGTGGTGGCAG 61.663 66.667 0.00 0.00 40.44 4.85
130 131 2.118233 TATCGGCAGTTGTGGTGGCA 62.118 55.000 0.00 0.00 40.44 4.92
131 132 1.369091 CTATCGGCAGTTGTGGTGGC 61.369 60.000 0.00 0.00 37.13 5.01
132 133 0.744414 CCTATCGGCAGTTGTGGTGG 60.744 60.000 0.00 0.00 0.00 4.61
133 134 0.249120 TCCTATCGGCAGTTGTGGTG 59.751 55.000 0.00 0.00 0.00 4.17
134 135 0.249398 GTCCTATCGGCAGTTGTGGT 59.751 55.000 0.00 0.00 0.00 4.16
135 136 0.806102 CGTCCTATCGGCAGTTGTGG 60.806 60.000 0.00 0.00 0.00 4.17
136 137 1.421410 GCGTCCTATCGGCAGTTGTG 61.421 60.000 0.00 0.00 0.00 3.33
137 138 1.153628 GCGTCCTATCGGCAGTTGT 60.154 57.895 0.00 0.00 0.00 3.32
138 139 3.706140 GCGTCCTATCGGCAGTTG 58.294 61.111 0.00 0.00 0.00 3.16
145 146 4.647615 CTGGCCGGCGTCCTATCG 62.648 72.222 22.54 0.00 0.00 2.92
146 147 4.971125 GCTGGCCGGCGTCCTATC 62.971 72.222 23.45 4.79 0.00 2.08
166 167 4.308458 TGGACTTCGGCGGTGTGG 62.308 66.667 7.21 0.00 0.00 4.17
167 168 2.507110 ATCTGGACTTCGGCGGTGTG 62.507 60.000 7.21 0.00 0.00 3.82
168 169 2.227089 GATCTGGACTTCGGCGGTGT 62.227 60.000 7.21 6.19 0.00 4.16
169 170 1.519455 GATCTGGACTTCGGCGGTG 60.519 63.158 7.21 2.39 0.00 4.94
170 171 1.682684 AGATCTGGACTTCGGCGGT 60.683 57.895 7.21 0.00 0.00 5.68
171 172 1.227089 CAGATCTGGACTTCGGCGG 60.227 63.158 15.38 0.00 0.00 6.13
172 173 4.409342 CAGATCTGGACTTCGGCG 57.591 61.111 15.38 0.00 0.00 6.46
182 183 0.178767 TTCATGACGGCCCAGATCTG 59.821 55.000 16.24 16.24 0.00 2.90
183 184 0.179000 GTTCATGACGGCCCAGATCT 59.821 55.000 0.00 0.00 0.00 2.75
184 185 0.815615 GGTTCATGACGGCCCAGATC 60.816 60.000 0.00 0.00 0.00 2.75
185 186 1.224592 GGTTCATGACGGCCCAGAT 59.775 57.895 0.00 0.00 0.00 2.90
186 187 2.184020 CTGGTTCATGACGGCCCAGA 62.184 60.000 18.51 0.00 44.39 3.86
187 188 1.746615 CTGGTTCATGACGGCCCAG 60.747 63.158 12.82 12.82 37.00 4.45
188 189 1.561769 ATCTGGTTCATGACGGCCCA 61.562 55.000 0.00 0.00 0.00 5.36
189 190 0.394352 AATCTGGTTCATGACGGCCC 60.394 55.000 0.00 0.00 0.00 5.80
190 191 0.734889 CAATCTGGTTCATGACGGCC 59.265 55.000 0.00 0.00 0.00 6.13
191 192 0.734889 CCAATCTGGTTCATGACGGC 59.265 55.000 0.00 0.00 31.35 5.68
213 214 3.790437 AGATCTGGGCTGTGGCGG 61.790 66.667 0.00 0.00 39.81 6.13
214 215 2.513204 CAGATCTGGGCTGTGGCG 60.513 66.667 15.38 0.00 39.81 5.69
215 216 2.124403 CCAGATCTGGGCTGTGGC 60.124 66.667 31.14 0.00 46.81 5.01
224 225 1.068281 CGAGGGTGTGATCCAGATCTG 59.932 57.143 16.24 16.24 38.60 2.90
225 226 1.063642 TCGAGGGTGTGATCCAGATCT 60.064 52.381 8.99 0.00 38.60 2.75
226 227 1.339610 CTCGAGGGTGTGATCCAGATC 59.660 57.143 3.91 0.47 38.29 2.75
227 228 1.407936 CTCGAGGGTGTGATCCAGAT 58.592 55.000 3.91 0.00 0.00 2.90
228 229 1.323271 GCTCGAGGGTGTGATCCAGA 61.323 60.000 15.58 0.00 0.00 3.86
229 230 1.142748 GCTCGAGGGTGTGATCCAG 59.857 63.158 15.58 0.00 0.00 3.86
230 231 2.359169 GGCTCGAGGGTGTGATCCA 61.359 63.158 15.58 0.00 0.00 3.41
231 232 2.303549 CTGGCTCGAGGGTGTGATCC 62.304 65.000 15.58 4.49 0.00 3.36
232 233 1.142748 CTGGCTCGAGGGTGTGATC 59.857 63.158 15.58 0.00 0.00 2.92
233 234 2.362369 CCTGGCTCGAGGGTGTGAT 61.362 63.158 15.58 0.00 0.00 3.06
234 235 2.997315 CCTGGCTCGAGGGTGTGA 60.997 66.667 15.58 0.00 0.00 3.58
271 272 4.816984 TCCTCCCTCTCGCGGGTC 62.817 72.222 5.57 0.00 44.95 4.46
272 273 4.824515 CTCCTCCCTCTCGCGGGT 62.825 72.222 5.57 0.00 44.95 5.28
273 274 4.824515 ACTCCTCCCTCTCGCGGG 62.825 72.222 6.13 1.01 46.13 6.13
274 275 3.522731 CACTCCTCCCTCTCGCGG 61.523 72.222 6.13 0.00 0.00 6.46
275 276 4.200283 GCACTCCTCCCTCTCGCG 62.200 72.222 0.00 0.00 0.00 5.87
276 277 4.200283 CGCACTCCTCCCTCTCGC 62.200 72.222 0.00 0.00 0.00 5.03
277 278 2.752238 ACGCACTCCTCCCTCTCG 60.752 66.667 0.00 0.00 0.00 4.04
278 279 2.419739 GGACGCACTCCTCCCTCTC 61.420 68.421 0.00 0.00 35.89 3.20
279 280 2.363147 GGACGCACTCCTCCCTCT 60.363 66.667 0.00 0.00 35.89 3.69
280 281 3.827898 CGGACGCACTCCTCCCTC 61.828 72.222 0.00 0.00 36.80 4.30
625 626 7.609960 TCTGCATTCTGAATGATATCTACTCC 58.390 38.462 29.34 11.21 41.46 3.85
630 631 9.217278 GTGTTATCTGCATTCTGAATGATATCT 57.783 33.333 29.34 13.79 41.46 1.98
631 632 8.449397 GGTGTTATCTGCATTCTGAATGATATC 58.551 37.037 29.34 17.66 41.46 1.63
632 633 7.118825 CGGTGTTATCTGCATTCTGAATGATAT 59.881 37.037 29.34 20.25 41.46 1.63
633 634 6.424812 CGGTGTTATCTGCATTCTGAATGATA 59.575 38.462 29.34 17.01 41.46 2.15
634 635 5.237996 CGGTGTTATCTGCATTCTGAATGAT 59.762 40.000 29.34 17.88 41.46 2.45
635 636 4.571984 CGGTGTTATCTGCATTCTGAATGA 59.428 41.667 29.34 15.51 41.46 2.57
636 637 4.333649 ACGGTGTTATCTGCATTCTGAATG 59.666 41.667 22.83 22.83 41.85 2.67
637 638 4.333649 CACGGTGTTATCTGCATTCTGAAT 59.666 41.667 0.00 0.00 0.00 2.57
638 639 3.684305 CACGGTGTTATCTGCATTCTGAA 59.316 43.478 0.00 0.00 0.00 3.02
639 640 3.261580 CACGGTGTTATCTGCATTCTGA 58.738 45.455 0.00 0.00 0.00 3.27
640 641 2.352651 CCACGGTGTTATCTGCATTCTG 59.647 50.000 7.45 0.00 0.00 3.02
641 642 2.236146 TCCACGGTGTTATCTGCATTCT 59.764 45.455 7.45 0.00 0.00 2.40
642 643 2.627945 TCCACGGTGTTATCTGCATTC 58.372 47.619 7.45 0.00 0.00 2.67
643 644 2.779755 TCCACGGTGTTATCTGCATT 57.220 45.000 7.45 0.00 0.00 3.56
644 645 2.564771 CATCCACGGTGTTATCTGCAT 58.435 47.619 7.45 0.00 0.00 3.96
645 646 1.406751 CCATCCACGGTGTTATCTGCA 60.407 52.381 7.45 0.00 0.00 4.41
646 647 1.299541 CCATCCACGGTGTTATCTGC 58.700 55.000 7.45 0.00 0.00 4.26
647 648 2.691409 ACCATCCACGGTGTTATCTG 57.309 50.000 7.45 0.00 38.07 2.90
655 656 0.476771 AGGAAAACACCATCCACGGT 59.523 50.000 0.00 0.00 41.07 4.83
656 657 0.881118 CAGGAAAACACCATCCACGG 59.119 55.000 0.00 0.00 38.23 4.94
657 658 0.240945 GCAGGAAAACACCATCCACG 59.759 55.000 0.00 0.00 38.23 4.94
658 659 1.620822 AGCAGGAAAACACCATCCAC 58.379 50.000 0.00 0.00 38.23 4.02
659 660 2.642311 TCTAGCAGGAAAACACCATCCA 59.358 45.455 0.00 0.00 38.23 3.41
660 661 3.274288 CTCTAGCAGGAAAACACCATCC 58.726 50.000 0.00 0.00 35.88 3.51
661 662 2.680339 GCTCTAGCAGGAAAACACCATC 59.320 50.000 0.00 0.00 41.59 3.51
662 663 2.307098 AGCTCTAGCAGGAAAACACCAT 59.693 45.455 4.54 0.00 45.16 3.55
663 664 1.699634 AGCTCTAGCAGGAAAACACCA 59.300 47.619 4.54 0.00 45.16 4.17
664 665 2.351455 GAGCTCTAGCAGGAAAACACC 58.649 52.381 6.43 0.00 45.16 4.16
665 666 2.351455 GGAGCTCTAGCAGGAAAACAC 58.649 52.381 14.64 0.00 45.16 3.32
666 667 1.279271 GGGAGCTCTAGCAGGAAAACA 59.721 52.381 14.64 0.00 45.16 2.83
667 668 1.279271 TGGGAGCTCTAGCAGGAAAAC 59.721 52.381 14.64 0.00 45.16 2.43
668 669 1.656587 TGGGAGCTCTAGCAGGAAAA 58.343 50.000 14.64 0.00 45.16 2.29
669 670 1.656587 TTGGGAGCTCTAGCAGGAAA 58.343 50.000 14.64 0.00 45.16 3.13
670 671 1.656587 TTTGGGAGCTCTAGCAGGAA 58.343 50.000 14.64 0.00 45.16 3.36
671 672 1.556911 CTTTTGGGAGCTCTAGCAGGA 59.443 52.381 14.64 0.00 45.16 3.86
672 673 1.407989 CCTTTTGGGAGCTCTAGCAGG 60.408 57.143 14.64 9.13 38.75 4.85
673 674 2.016096 GCCTTTTGGGAGCTCTAGCAG 61.016 57.143 14.64 3.80 41.33 4.24
674 675 0.035056 GCCTTTTGGGAGCTCTAGCA 60.035 55.000 14.64 0.00 41.33 3.49
675 676 0.749818 GGCCTTTTGGGAGCTCTAGC 60.750 60.000 14.64 6.18 40.82 3.42
676 677 0.620556 TGGCCTTTTGGGAGCTCTAG 59.379 55.000 14.64 3.83 40.82 2.43
677 678 0.620556 CTGGCCTTTTGGGAGCTCTA 59.379 55.000 14.64 0.00 40.82 2.43
678 679 1.381851 CTGGCCTTTTGGGAGCTCT 59.618 57.895 14.64 0.00 40.82 4.09
679 680 2.346541 GCTGGCCTTTTGGGAGCTC 61.347 63.158 4.71 4.71 40.82 4.09
680 681 2.283460 GCTGGCCTTTTGGGAGCT 60.283 61.111 3.32 0.00 40.82 4.09
685 686 1.228675 ACTCAGGCTGGCCTTTTGG 60.229 57.895 15.73 0.85 45.70 3.28
688 689 2.177594 CTCGACTCAGGCTGGCCTTT 62.178 60.000 15.73 0.00 45.70 3.11
1119 1147 0.039180 TCTGACTGAGGAGGCCGTTA 59.961 55.000 0.00 0.00 0.00 3.18
1219 1247 3.827898 GACGTCTGAGGGGAGCGG 61.828 72.222 8.70 0.00 0.00 5.52
1437 1465 0.320374 TCACCATCTGGGACGTCAAC 59.680 55.000 18.91 10.22 41.15 3.18
1562 1590 1.762957 GAGTCTTAGTATGGGCAGGCA 59.237 52.381 0.00 0.00 0.00 4.75
1608 1636 1.346395 TCCGTCTTTGGCTTCTTGCTA 59.654 47.619 0.00 0.00 42.39 3.49
1776 1804 2.126850 TCGTCGCTGCTCTTGTCG 60.127 61.111 0.00 0.00 0.00 4.35
1856 1887 3.729526 ATCAGAGCGAAACAACAATCG 57.270 42.857 0.00 0.00 41.81 3.34
1861 1892 4.098416 GGCATAAATCAGAGCGAAACAAC 58.902 43.478 0.00 0.00 0.00 3.32
1876 1907 4.556592 AACCTACTTGTACGGGCATAAA 57.443 40.909 0.00 0.00 0.00 1.40
1921 1958 1.876799 CGTTTTGCCTACACACCATCA 59.123 47.619 0.00 0.00 0.00 3.07
1950 1989 4.704540 TGGTAATTTCGATTTGACAGCCAT 59.295 37.500 0.00 0.00 0.00 4.40
1989 2033 2.234143 CTCCTATCTCGCACATCCTGA 58.766 52.381 0.00 0.00 0.00 3.86
2044 2410 0.826256 ACACACTCGACTAGGCACCA 60.826 55.000 0.00 0.00 0.00 4.17
2101 2467 5.820926 GCATAAGCTTCTATCGAACTCTG 57.179 43.478 0.00 0.00 37.91 3.35
2244 2617 5.234543 GCTCCCTTAGAAAATGATACGTGAC 59.765 44.000 0.00 0.00 0.00 3.67
2291 2670 8.023128 CGACAGAAATTATCAAGTTTTCCATGT 58.977 33.333 0.00 0.00 31.25 3.21
2816 3203 8.794406 CGTCGAAAAAGAGAAAGAAATGAAAAA 58.206 29.630 0.00 0.00 0.00 1.94
2817 3204 7.431084 CCGTCGAAAAAGAGAAAGAAATGAAAA 59.569 33.333 0.00 0.00 0.00 2.29
2818 3205 6.910433 CCGTCGAAAAAGAGAAAGAAATGAAA 59.090 34.615 0.00 0.00 0.00 2.69
2819 3206 6.427150 CCGTCGAAAAAGAGAAAGAAATGAA 58.573 36.000 0.00 0.00 0.00 2.57
2820 3207 5.049680 CCCGTCGAAAAAGAGAAAGAAATGA 60.050 40.000 0.00 0.00 0.00 2.57
2821 3208 5.049680 TCCCGTCGAAAAAGAGAAAGAAATG 60.050 40.000 0.00 0.00 0.00 2.32
2822 3209 5.061179 TCCCGTCGAAAAAGAGAAAGAAAT 58.939 37.500 0.00 0.00 0.00 2.17
2823 3210 4.444536 TCCCGTCGAAAAAGAGAAAGAAA 58.555 39.130 0.00 0.00 0.00 2.52
2824 3211 4.062677 TCCCGTCGAAAAAGAGAAAGAA 57.937 40.909 0.00 0.00 0.00 2.52
2825 3212 3.738830 TCCCGTCGAAAAAGAGAAAGA 57.261 42.857 0.00 0.00 0.00 2.52
2826 3213 4.806342 TTTCCCGTCGAAAAAGAGAAAG 57.194 40.909 0.00 0.00 37.53 2.62
2846 3233 2.812011 GCCACAGTCGATACACCTTTTT 59.188 45.455 0.00 0.00 0.00 1.94
2847 3234 2.423577 GCCACAGTCGATACACCTTTT 58.576 47.619 0.00 0.00 0.00 2.27
2848 3235 1.338769 GGCCACAGTCGATACACCTTT 60.339 52.381 0.00 0.00 0.00 3.11
2849 3236 0.249398 GGCCACAGTCGATACACCTT 59.751 55.000 0.00 0.00 0.00 3.50
2850 3237 1.898154 GGCCACAGTCGATACACCT 59.102 57.895 0.00 0.00 0.00 4.00
2851 3238 1.518572 CGGCCACAGTCGATACACC 60.519 63.158 2.24 0.00 46.55 4.16
2852 3239 1.518572 CCGGCCACAGTCGATACAC 60.519 63.158 2.24 0.00 46.55 2.90
2853 3240 2.717044 CCCGGCCACAGTCGATACA 61.717 63.158 2.24 0.00 46.55 2.29
2854 3241 2.106332 CCCGGCCACAGTCGATAC 59.894 66.667 2.24 0.00 46.55 2.24
2855 3242 3.151710 CCCCGGCCACAGTCGATA 61.152 66.667 2.24 0.00 46.55 2.92


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

AutoCloner maintained by Alex Coulton.