Multiple sequence alignment - TraesCS3D01G108700

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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 TraesCS3D01G108700 chr3D 100.000 3541 0 0 1 3541 61801751 61805291 0.000000e+00 6540.0
1 TraesCS3D01G108700 chr3D 91.018 167 15 0 180 346 512608862 512609028 3.560000e-55 226.0
2 TraesCS3D01G108700 chr3D 100.000 80 0 0 2781 2860 61804610 61804531 7.920000e-32 148.0
3 TraesCS3D01G108700 chr3B 95.188 2473 68 22 344 2782 99500095 99502550 0.000000e+00 3860.0
4 TraesCS3D01G108700 chr3B 94.413 358 18 2 2962 3318 99502709 99503065 1.860000e-152 549.0
5 TraesCS3D01G108700 chr3B 91.111 180 14 2 3364 3541 99503071 99503250 3.530000e-60 243.0
6 TraesCS3D01G108700 chr3B 92.638 163 11 1 2857 3018 99502547 99502709 2.130000e-57 233.0
7 TraesCS3D01G108700 chr3B 86.957 184 10 4 1 182 99499925 99500096 1.000000e-45 195.0
8 TraesCS3D01G108700 chr3A 93.155 2469 99 33 344 2771 70847821 70850260 0.000000e+00 3559.0
9 TraesCS3D01G108700 chr3A 86.667 705 63 17 2859 3541 70850254 70850949 0.000000e+00 752.0
10 TraesCS3D01G108700 chr3A 90.217 184 15 3 1 182 70847640 70847822 1.640000e-58 237.0
11 TraesCS3D01G108700 chr3A 86.735 196 22 4 180 374 264047579 264047771 7.700000e-52 215.0
12 TraesCS3D01G108700 chr2B 91.515 165 14 0 181 345 741379459 741379623 9.890000e-56 228.0
13 TraesCS3D01G108700 chr1B 90.588 170 15 1 180 349 28563396 28563564 1.280000e-54 224.0
14 TraesCS3D01G108700 chr1B 93.258 89 4 2 2773 2861 392878900 392878986 2.870000e-26 130.0
15 TraesCS3D01G108700 chr7A 90.058 171 17 0 180 350 323712196 323712026 4.600000e-54 222.0
16 TraesCS3D01G108700 chr4D 89.266 177 18 1 181 357 503151639 503151464 1.650000e-53 220.0
17 TraesCS3D01G108700 chr4D 71.135 828 191 37 1651 2451 34089867 34090673 1.020000e-35 161.0
18 TraesCS3D01G108700 chr4D 95.402 87 4 0 2774 2860 384974372 384974286 4.770000e-29 139.0
19 TraesCS3D01G108700 chr4D 97.531 81 2 0 2781 2861 384974286 384974366 4.770000e-29 139.0
20 TraesCS3D01G108700 chr1A 89.941 169 17 0 178 346 233421339 233421507 5.950000e-53 219.0
21 TraesCS3D01G108700 chr7D 88.764 178 19 1 181 358 593193273 593193097 2.140000e-52 217.0
22 TraesCS3D01G108700 chr7D 96.386 83 3 0 2781 2863 104640722 104640640 1.710000e-28 137.0
23 TraesCS3D01G108700 chr6B 87.568 185 22 1 176 360 208179053 208178870 2.770000e-51 213.0
24 TraesCS3D01G108700 chr5D 94.505 91 3 2 2777 2866 40190751 40190840 4.770000e-29 139.0
25 TraesCS3D01G108700 chr5D 94.565 92 0 2 2778 2865 500118293 500118383 1.710000e-28 137.0
26 TraesCS3D01G108700 chr4A 71.366 681 153 31 1795 2451 568193853 568194515 4.770000e-29 139.0
27 TraesCS3D01G108700 chr1D 91.262 103 3 5 2766 2864 23423844 23423944 6.170000e-28 135.0
28 TraesCS3D01G108700 chr1D 92.632 95 3 3 2773 2865 476449363 476449455 2.220000e-27 134.0
29 TraesCS3D01G108700 chr4B 93.103 58 4 0 495 552 553952937 553952880 6.300000e-13 86.1
30 TraesCS3D01G108700 chr2A 82.353 68 6 6 2744 2806 12214171 12214237 2.000000e-03 54.7


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 TraesCS3D01G108700 chr3D 61801751 61805291 3540 False 6540 6540 100.0000 1 3541 1 chr3D.!!$F1 3540
1 TraesCS3D01G108700 chr3B 99499925 99503250 3325 False 1016 3860 92.0614 1 3541 5 chr3B.!!$F1 3540
2 TraesCS3D01G108700 chr3A 70847640 70850949 3309 False 1516 3559 90.0130 1 3541 3 chr3A.!!$F2 3540

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
182 185 0.110192 GAAAACCTGCACGCTGCTAC 60.110 55.0 10.54 0.0 45.31 3.58 F
901 951 0.167470 CACATTCTTGAGCTGTGCCG 59.833 55.0 0.00 0.0 34.47 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 1645 0.105964 ACAGTAGTGGCTTGCGTTGA 59.894 50.0 1.92 0.0 0.0 3.18 R
2849 2920 0.175989 GAACCAAGCTACTCCCTCCG 59.824 60.0 0.00 0.0 0.0 4.63 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
49 50 7.121020 TGTCTAACAAATGCTGCAATCTTCATA 59.879 33.333 6.36 0.00 0.00 2.15
182 185 0.110192 GAAAACCTGCACGCTGCTAC 60.110 55.000 10.54 0.00 45.31 3.58
183 186 0.535102 AAAACCTGCACGCTGCTACT 60.535 50.000 10.54 0.00 45.31 2.57
184 187 0.951040 AAACCTGCACGCTGCTACTC 60.951 55.000 10.54 0.00 45.31 2.59
185 188 2.510238 CCTGCACGCTGCTACTCC 60.510 66.667 10.54 0.00 45.31 3.85
186 189 2.510238 CTGCACGCTGCTACTCCC 60.510 66.667 10.54 0.00 45.31 4.30
187 190 2.997315 TGCACGCTGCTACTCCCT 60.997 61.111 10.54 0.00 45.31 4.20
188 191 2.202810 GCACGCTGCTACTCCCTC 60.203 66.667 0.00 0.00 40.96 4.30
189 192 2.496817 CACGCTGCTACTCCCTCC 59.503 66.667 0.00 0.00 0.00 4.30
190 193 3.141488 ACGCTGCTACTCCCTCCG 61.141 66.667 0.00 0.00 0.00 4.63
191 194 3.141488 CGCTGCTACTCCCTCCGT 61.141 66.667 0.00 0.00 0.00 4.69
192 195 2.711922 CGCTGCTACTCCCTCCGTT 61.712 63.158 0.00 0.00 0.00 4.44
193 196 1.142097 GCTGCTACTCCCTCCGTTC 59.858 63.158 0.00 0.00 0.00 3.95
194 197 1.817209 CTGCTACTCCCTCCGTTCC 59.183 63.158 0.00 0.00 0.00 3.62
195 198 0.684805 CTGCTACTCCCTCCGTTCCT 60.685 60.000 0.00 0.00 0.00 3.36
196 199 0.627451 TGCTACTCCCTCCGTTCCTA 59.373 55.000 0.00 0.00 0.00 2.94
197 200 1.006281 TGCTACTCCCTCCGTTCCTAA 59.994 52.381 0.00 0.00 0.00 2.69
198 201 2.105766 GCTACTCCCTCCGTTCCTAAA 58.894 52.381 0.00 0.00 0.00 1.85
199 202 2.699321 GCTACTCCCTCCGTTCCTAAAT 59.301 50.000 0.00 0.00 0.00 1.40
200 203 3.893813 GCTACTCCCTCCGTTCCTAAATA 59.106 47.826 0.00 0.00 0.00 1.40
201 204 4.527427 GCTACTCCCTCCGTTCCTAAATAT 59.473 45.833 0.00 0.00 0.00 1.28
202 205 5.011840 GCTACTCCCTCCGTTCCTAAATATT 59.988 44.000 0.00 0.00 0.00 1.28
203 206 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
204 207 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
205 208 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
206 209 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
207 210 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
208 211 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
209 212 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
210 213 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
211 214 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
212 215 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
213 216 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
214 217 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
227 230 9.507329 TTTGTCTTTCTAGATATTTCAGCAAGT 57.493 29.630 0.00 0.00 31.86 3.16
228 231 8.484641 TGTCTTTCTAGATATTTCAGCAAGTG 57.515 34.615 0.00 0.00 31.86 3.16
229 232 8.314021 TGTCTTTCTAGATATTTCAGCAAGTGA 58.686 33.333 0.00 0.00 31.86 3.41
230 233 8.599774 GTCTTTCTAGATATTTCAGCAAGTGAC 58.400 37.037 0.00 0.00 31.01 3.67
231 234 8.535335 TCTTTCTAGATATTTCAGCAAGTGACT 58.465 33.333 0.00 0.00 33.71 3.41
232 235 9.809096 CTTTCTAGATATTTCAGCAAGTGACTA 57.191 33.333 0.00 0.00 33.71 2.59
233 236 9.587772 TTTCTAGATATTTCAGCAAGTGACTAC 57.412 33.333 0.00 0.00 33.71 2.73
234 237 8.293699 TCTAGATATTTCAGCAAGTGACTACA 57.706 34.615 0.00 0.00 33.71 2.74
235 238 8.918116 TCTAGATATTTCAGCAAGTGACTACAT 58.082 33.333 0.00 0.00 33.71 2.29
237 240 8.879342 AGATATTTCAGCAAGTGACTACATAC 57.121 34.615 0.00 0.00 33.71 2.39
238 241 7.649705 AGATATTTCAGCAAGTGACTACATACG 59.350 37.037 0.00 0.00 33.71 3.06
239 242 3.503827 TCAGCAAGTGACTACATACGG 57.496 47.619 0.00 0.00 0.00 4.02
240 243 3.086282 TCAGCAAGTGACTACATACGGA 58.914 45.455 0.00 0.00 0.00 4.69
241 244 3.508402 TCAGCAAGTGACTACATACGGAA 59.492 43.478 0.00 0.00 0.00 4.30
242 245 3.612860 CAGCAAGTGACTACATACGGAAC 59.387 47.826 0.00 0.00 0.00 3.62
243 246 3.257375 AGCAAGTGACTACATACGGAACA 59.743 43.478 0.00 0.00 0.00 3.18
244 247 3.991773 GCAAGTGACTACATACGGAACAA 59.008 43.478 0.00 0.00 0.00 2.83
245 248 4.449743 GCAAGTGACTACATACGGAACAAA 59.550 41.667 0.00 0.00 0.00 2.83
246 249 5.049954 GCAAGTGACTACATACGGAACAAAA 60.050 40.000 0.00 0.00 0.00 2.44
247 250 6.348213 GCAAGTGACTACATACGGAACAAAAT 60.348 38.462 0.00 0.00 0.00 1.82
248 251 7.148540 GCAAGTGACTACATACGGAACAAAATA 60.149 37.037 0.00 0.00 0.00 1.40
249 252 8.714179 CAAGTGACTACATACGGAACAAAATAA 58.286 33.333 0.00 0.00 0.00 1.40
250 253 8.836268 AGTGACTACATACGGAACAAAATAAA 57.164 30.769 0.00 0.00 0.00 1.40
251 254 9.444600 AGTGACTACATACGGAACAAAATAAAT 57.555 29.630 0.00 0.00 0.00 1.40
252 255 9.485591 GTGACTACATACGGAACAAAATAAATG 57.514 33.333 0.00 0.00 0.00 2.32
253 256 9.438228 TGACTACATACGGAACAAAATAAATGA 57.562 29.630 0.00 0.00 0.00 2.57
320 323 8.341892 ACTCCATTTAAAATCTCTGAAAGGAC 57.658 34.615 0.00 0.00 0.00 3.85
321 324 7.944554 ACTCCATTTAAAATCTCTGAAAGGACA 59.055 33.333 0.00 0.00 0.00 4.02
322 325 8.704849 TCCATTTAAAATCTCTGAAAGGACAA 57.295 30.769 0.00 0.00 0.00 3.18
323 326 9.142014 TCCATTTAAAATCTCTGAAAGGACAAA 57.858 29.630 0.00 0.00 0.00 2.83
324 327 9.933723 CCATTTAAAATCTCTGAAAGGACAAAT 57.066 29.630 0.00 0.00 0.00 2.32
342 345 9.853177 AGGACAAATATATAGAAACAAAGGGAG 57.147 33.333 0.00 0.00 0.00 4.30
343 346 9.628500 GGACAAATATATAGAAACAAAGGGAGT 57.372 33.333 0.00 0.00 0.00 3.85
567 590 6.866480 ACATGCTCTAACCATTGGTAAAATG 58.134 36.000 9.20 9.80 33.12 2.32
574 597 8.393671 TCTAACCATTGGTAAAATGTTACGTT 57.606 30.769 9.20 1.46 40.57 3.99
597 620 7.709182 CGTTGTGTGAGGTTATAGGAATATCAA 59.291 37.037 0.00 0.00 0.00 2.57
749 775 2.380064 TTTGGGGCTCTTGTGACAAT 57.620 45.000 0.00 0.00 0.00 2.71
797 823 2.542595 GACAACCGAACGATTTCACACT 59.457 45.455 0.00 0.00 0.00 3.55
841 891 3.391626 GCCTATATATAGCCCCAAGACCC 59.608 52.174 13.49 0.00 0.00 4.46
901 951 0.167470 CACATTCTTGAGCTGTGCCG 59.833 55.000 0.00 0.00 34.47 5.69
988 1038 1.600636 TCACTCCAAGGCGCAAAGG 60.601 57.895 10.83 7.39 0.00 3.11
1363 1413 4.005650 CCTCTGCTTTATCTTGCTTGTCA 58.994 43.478 0.00 0.00 0.00 3.58
1615 1673 0.447801 GCCACTACTGTTCCATTGCG 59.552 55.000 0.00 0.00 0.00 4.85
1616 1674 1.808411 CCACTACTGTTCCATTGCGT 58.192 50.000 0.00 0.00 0.00 5.24
1623 1681 1.154413 GTTCCATTGCGTGTGCTCG 60.154 57.895 0.00 0.00 43.34 5.03
1739 1797 2.032071 GGGTTCCAGGTCACGGTG 59.968 66.667 0.56 0.56 0.00 4.94
1862 1920 3.680786 TCGGTGCTGGAGGACGTG 61.681 66.667 0.00 0.00 37.24 4.49
2534 2592 0.235665 CGACAACGCTGCAAGAACAT 59.764 50.000 0.00 0.00 34.07 2.71
2545 2603 3.930336 TGCAAGAACATCACTAGACCAG 58.070 45.455 0.00 0.00 0.00 4.00
2555 2613 6.226787 ACATCACTAGACCAGTTCTTCAAAG 58.773 40.000 0.00 0.00 34.26 2.77
2560 2618 6.538742 CACTAGACCAGTTCTTCAAAGAAACA 59.461 38.462 6.76 0.00 45.77 2.83
2634 2705 4.189231 GCCATTGTGAGGAAGTACGTAAT 58.811 43.478 0.00 0.00 0.00 1.89
2789 2860 5.417811 GTTTGCTAAACTAGTACTCCCTCC 58.582 45.833 0.00 0.00 38.35 4.30
2790 2861 3.285484 TGCTAAACTAGTACTCCCTCCG 58.715 50.000 0.00 0.00 0.00 4.63
2791 2862 3.286353 GCTAAACTAGTACTCCCTCCGT 58.714 50.000 0.00 0.00 0.00 4.69
2792 2863 3.314913 GCTAAACTAGTACTCCCTCCGTC 59.685 52.174 0.00 0.00 0.00 4.79
2793 2864 2.433662 AACTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
2794 2865 0.550432 ACTAGTACTCCCTCCGTCCC 59.450 60.000 0.00 0.00 0.00 4.46
2795 2866 0.549950 CTAGTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
2796 2867 1.145325 CTAGTACTCCCTCCGTCCCAT 59.855 57.143 0.00 0.00 0.00 4.00
2797 2868 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2798 2869 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2799 2870 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2800 2871 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2801 2872 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2802 2873 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2803 2874 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2804 2875 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2805 2876 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2806 2877 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2807 2878 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2808 2879 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2809 2880 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2810 2881 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2811 2882 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2812 2883 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2813 2884 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2850 2921 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2851 2922 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2852 2923 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2853 2924 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2854 2925 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2855 2926 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2856 2927 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2857 2928 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2858 2929 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2914 2985 2.904434 TCCTCACTCAACCTCCTAAACC 59.096 50.000 0.00 0.00 0.00 3.27
3024 3152 3.068560 CCTTTGTCCGATTTTGGTACGA 58.931 45.455 0.00 0.00 0.00 3.43
3025 3153 3.687698 CCTTTGTCCGATTTTGGTACGAT 59.312 43.478 0.00 0.00 0.00 3.73
3271 3407 6.530181 GGGTTTTGCTATTTATCAAGAAACCG 59.470 38.462 0.00 0.00 35.48 4.44
3328 3464 7.814264 AATCATTGGATCCAAACATCTAGAC 57.186 36.000 30.28 0.00 39.55 2.59
3331 3467 3.459828 TGGATCCAAACATCTAGACCCA 58.540 45.455 13.46 0.00 0.00 4.51
3379 3527 5.107026 TGTTTTATCAAACGGTATGTGGACG 60.107 40.000 0.00 0.00 44.76 4.79
3413 3561 2.898729 TGAGTTGGCTCAGCTATAGC 57.101 50.000 17.33 17.33 45.94 2.97
3434 3583 6.814954 AGCTACTCCCTATCAAAATGAAGA 57.185 37.500 0.00 0.00 0.00 2.87
3441 3590 7.772757 ACTCCCTATCAAAATGAAGAATCTCAC 59.227 37.037 0.00 0.00 0.00 3.51
3443 3592 8.331740 TCCCTATCAAAATGAAGAATCTCACTT 58.668 33.333 0.00 0.00 0.00 3.16
3452 3601 4.471025 TGAAGAATCTCACTTATGGGCTCA 59.529 41.667 0.00 0.00 0.00 4.26
3460 3609 1.496001 ACTTATGGGCTCATGGCATCA 59.504 47.619 10.07 0.00 44.01 3.07
3522 3672 6.237313 AGAAACAAAAATGCTACGTAGACC 57.763 37.500 26.53 9.89 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.587777 TGGGACAGAGGGAGTAGAAGAT 59.412 50.000 0.00 0.00 0.00 2.40
91 94 8.188531 TCTTTCCTTTCCGTAATATACAAACG 57.811 34.615 0.00 0.00 36.42 3.60
107 110 6.017830 AGTGGTAGCTAGTACTCTTTCCTTT 58.982 40.000 0.00 0.00 0.00 3.11
109 112 5.195185 GAGTGGTAGCTAGTACTCTTTCCT 58.805 45.833 21.61 0.00 37.25 3.36
182 185 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
183 186 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
184 187 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
185 188 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
186 189 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
187 190 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
188 191 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
201 204 9.507329 ACTTGCTGAAATATCTAGAAAGACAAA 57.493 29.630 0.00 0.00 33.57 2.83
202 205 8.939929 CACTTGCTGAAATATCTAGAAAGACAA 58.060 33.333 0.00 0.00 33.57 3.18
203 206 8.314021 TCACTTGCTGAAATATCTAGAAAGACA 58.686 33.333 0.00 0.00 33.57 3.41
204 207 8.599774 GTCACTTGCTGAAATATCTAGAAAGAC 58.400 37.037 0.00 0.00 33.57 3.01
205 208 8.535335 AGTCACTTGCTGAAATATCTAGAAAGA 58.465 33.333 0.00 0.00 35.80 2.52
206 209 8.715191 AGTCACTTGCTGAAATATCTAGAAAG 57.285 34.615 0.00 0.00 0.00 2.62
207 210 9.587772 GTAGTCACTTGCTGAAATATCTAGAAA 57.412 33.333 0.00 0.00 0.00 2.52
208 211 8.749354 TGTAGTCACTTGCTGAAATATCTAGAA 58.251 33.333 0.00 0.00 0.00 2.10
209 212 8.293699 TGTAGTCACTTGCTGAAATATCTAGA 57.706 34.615 0.00 0.00 0.00 2.43
211 214 9.967346 GTATGTAGTCACTTGCTGAAATATCTA 57.033 33.333 0.00 0.00 0.00 1.98
212 215 7.649705 CGTATGTAGTCACTTGCTGAAATATCT 59.350 37.037 0.00 0.00 0.00 1.98
213 216 7.096023 CCGTATGTAGTCACTTGCTGAAATATC 60.096 40.741 0.00 0.00 0.00 1.63
214 217 6.701841 CCGTATGTAGTCACTTGCTGAAATAT 59.298 38.462 0.00 0.00 0.00 1.28
215 218 6.040247 CCGTATGTAGTCACTTGCTGAAATA 58.960 40.000 0.00 0.00 0.00 1.40
216 219 4.870426 CCGTATGTAGTCACTTGCTGAAAT 59.130 41.667 0.00 0.00 0.00 2.17
217 220 4.021807 TCCGTATGTAGTCACTTGCTGAAA 60.022 41.667 0.00 0.00 0.00 2.69
218 221 3.508402 TCCGTATGTAGTCACTTGCTGAA 59.492 43.478 0.00 0.00 0.00 3.02
219 222 3.086282 TCCGTATGTAGTCACTTGCTGA 58.914 45.455 0.00 0.00 0.00 4.26
220 223 3.503827 TCCGTATGTAGTCACTTGCTG 57.496 47.619 0.00 0.00 0.00 4.41
221 224 3.257375 TGTTCCGTATGTAGTCACTTGCT 59.743 43.478 0.00 0.00 0.00 3.91
222 225 3.581755 TGTTCCGTATGTAGTCACTTGC 58.418 45.455 0.00 0.00 0.00 4.01
223 226 6.533819 TTTTGTTCCGTATGTAGTCACTTG 57.466 37.500 0.00 0.00 0.00 3.16
224 227 8.836268 TTATTTTGTTCCGTATGTAGTCACTT 57.164 30.769 0.00 0.00 0.00 3.16
225 228 8.836268 TTTATTTTGTTCCGTATGTAGTCACT 57.164 30.769 0.00 0.00 0.00 3.41
226 229 9.485591 CATTTATTTTGTTCCGTATGTAGTCAC 57.514 33.333 0.00 0.00 0.00 3.67
227 230 9.438228 TCATTTATTTTGTTCCGTATGTAGTCA 57.562 29.630 0.00 0.00 0.00 3.41
294 297 9.449719 GTCCTTTCAGAGATTTTAAATGGAGTA 57.550 33.333 0.00 0.00 0.00 2.59
295 298 7.944554 TGTCCTTTCAGAGATTTTAAATGGAGT 59.055 33.333 0.00 0.00 0.00 3.85
296 299 8.340618 TGTCCTTTCAGAGATTTTAAATGGAG 57.659 34.615 0.00 0.00 0.00 3.86
297 300 8.704849 TTGTCCTTTCAGAGATTTTAAATGGA 57.295 30.769 0.00 0.00 0.00 3.41
298 301 9.933723 ATTTGTCCTTTCAGAGATTTTAAATGG 57.066 29.630 0.00 0.00 0.00 3.16
316 319 9.853177 CTCCCTTTGTTTCTATATATTTGTCCT 57.147 33.333 0.00 0.00 0.00 3.85
317 320 9.628500 ACTCCCTTTGTTTCTATATATTTGTCC 57.372 33.333 0.00 0.00 0.00 4.02
330 333 7.713942 TCTGTTAGAAACTACTCCCTTTGTTTC 59.286 37.037 8.76 8.76 44.80 2.78
331 334 7.571025 TCTGTTAGAAACTACTCCCTTTGTTT 58.429 34.615 0.00 0.00 35.64 2.83
332 335 7.133133 TCTGTTAGAAACTACTCCCTTTGTT 57.867 36.000 0.00 0.00 0.00 2.83
333 336 6.742559 TCTGTTAGAAACTACTCCCTTTGT 57.257 37.500 0.00 0.00 0.00 2.83
334 337 7.385478 GTCTTCTGTTAGAAACTACTCCCTTTG 59.615 40.741 0.00 0.00 33.19 2.77
335 338 7.290481 AGTCTTCTGTTAGAAACTACTCCCTTT 59.710 37.037 0.00 0.00 33.19 3.11
336 339 6.783482 AGTCTTCTGTTAGAAACTACTCCCTT 59.217 38.462 0.00 0.00 33.19 3.95
337 340 6.209788 CAGTCTTCTGTTAGAAACTACTCCCT 59.790 42.308 0.00 0.00 33.19 4.20
338 341 6.208994 TCAGTCTTCTGTTAGAAACTACTCCC 59.791 42.308 0.00 0.00 41.91 4.30
339 342 7.216973 TCAGTCTTCTGTTAGAAACTACTCC 57.783 40.000 0.00 0.00 41.91 3.85
340 343 9.134734 CATTCAGTCTTCTGTTAGAAACTACTC 57.865 37.037 0.00 0.00 41.91 2.59
341 344 8.643324 ACATTCAGTCTTCTGTTAGAAACTACT 58.357 33.333 0.00 0.00 41.91 2.57
342 345 8.704234 CACATTCAGTCTTCTGTTAGAAACTAC 58.296 37.037 0.00 0.00 41.91 2.73
343 346 8.638873 TCACATTCAGTCTTCTGTTAGAAACTA 58.361 33.333 0.00 0.00 41.91 2.24
344 347 7.500992 TCACATTCAGTCTTCTGTTAGAAACT 58.499 34.615 0.00 0.00 41.91 2.66
504 526 1.339097 ATGAGTCCCTATACGCCCAC 58.661 55.000 0.00 0.00 0.00 4.61
567 590 5.713025 TCCTATAACCTCACACAACGTAAC 58.287 41.667 0.00 0.00 0.00 2.50
574 597 7.126573 TGGTTGATATTCCTATAACCTCACACA 59.873 37.037 0.00 0.00 40.99 3.72
678 703 9.967346 TTTTGACGATTCATGGTTAATGTTTAA 57.033 25.926 0.00 0.00 37.56 1.52
765 791 1.104577 TCGGTTGTCAAAGTTGCCCC 61.105 55.000 0.00 0.00 0.00 5.80
797 823 6.812998 GGCAGAAATGCCGGTATATATACTA 58.187 40.000 19.78 7.28 45.79 1.82
841 891 1.002134 GGGTGTGGTGATCCTGGTG 60.002 63.158 0.00 0.00 34.23 4.17
1316 1366 2.967599 TGCTCTTGTGCATCTACGAT 57.032 45.000 0.00 0.00 38.12 3.73
1341 1391 4.005650 TGACAAGCAAGATAAAGCAGAGG 58.994 43.478 0.00 0.00 0.00 3.69
1587 1645 0.105964 ACAGTAGTGGCTTGCGTTGA 59.894 50.000 1.92 0.00 0.00 3.18
1590 1648 0.602905 GGAACAGTAGTGGCTTGCGT 60.603 55.000 1.92 0.00 0.00 5.24
1591 1649 0.602638 TGGAACAGTAGTGGCTTGCG 60.603 55.000 1.92 0.00 0.00 4.85
1615 1673 1.079543 AGGACATGAGCGAGCACAC 60.080 57.895 0.00 0.00 0.00 3.82
1616 1674 1.079612 CAGGACATGAGCGAGCACA 60.080 57.895 0.00 0.00 0.00 4.57
2534 2592 6.479972 TTCTTTGAAGAACTGGTCTAGTGA 57.520 37.500 0.00 0.00 39.95 3.41
2634 2705 1.555967 TGATGTGTCACCAGGATCGA 58.444 50.000 0.00 0.00 0.00 3.59
2781 2852 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2782 2853 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2783 2854 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2784 2855 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2785 2856 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2786 2857 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2787 2858 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2788 2859 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2789 2860 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2826 2897 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2827 2898 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2828 2899 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2829 2900 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2830 2901 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2831 2902 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2832 2903 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2833 2904 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2834 2905 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2835 2906 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2836 2907 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2837 2908 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2838 2909 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2839 2910 3.816842 GCTACTCCCTCCGTCCCATAATA 60.817 52.174 0.00 0.00 0.00 0.98
2840 2911 2.890814 CTACTCCCTCCGTCCCATAAT 58.109 52.381 0.00 0.00 0.00 1.28
2841 2912 1.756690 GCTACTCCCTCCGTCCCATAA 60.757 57.143 0.00 0.00 0.00 1.90
2842 2913 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.00 0.00 2.74
2843 2914 1.457831 GCTACTCCCTCCGTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
2844 2915 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
2845 2916 1.381463 AAGCTACTCCCTCCGTCCC 60.381 63.158 0.00 0.00 0.00 4.46
2846 2917 1.677637 CCAAGCTACTCCCTCCGTCC 61.678 65.000 0.00 0.00 0.00 4.79
2847 2918 0.971447 ACCAAGCTACTCCCTCCGTC 60.971 60.000 0.00 0.00 0.00 4.79
2848 2919 0.544595 AACCAAGCTACTCCCTCCGT 60.545 55.000 0.00 0.00 0.00 4.69
2849 2920 0.175989 GAACCAAGCTACTCCCTCCG 59.824 60.000 0.00 0.00 0.00 4.63
2850 2921 1.066071 GTGAACCAAGCTACTCCCTCC 60.066 57.143 0.00 0.00 0.00 4.30
2851 2922 1.903183 AGTGAACCAAGCTACTCCCTC 59.097 52.381 0.00 0.00 0.00 4.30
2852 2923 2.031495 AGTGAACCAAGCTACTCCCT 57.969 50.000 0.00 0.00 0.00 4.20
2853 2924 2.861147 AAGTGAACCAAGCTACTCCC 57.139 50.000 0.00 0.00 0.00 4.30
3024 3152 1.030457 GACGGTGTGATCGGTAGGAT 58.970 55.000 0.00 0.00 38.35 3.24
3025 3153 1.033746 GGACGGTGTGATCGGTAGGA 61.034 60.000 0.00 0.00 0.00 2.94
3168 3301 3.264104 CAACATTTGGGGTGCATCATTC 58.736 45.455 0.00 0.00 0.00 2.67
3210 3343 9.823647 GAGATCAAAGGATGAACATCTAACTAA 57.176 33.333 13.34 0.00 42.54 2.24
3293 3429 7.156876 TGGATCCAATGATTTGTTACTGTTC 57.843 36.000 13.46 0.00 0.00 3.18
3297 3433 7.537596 TGTTTGGATCCAATGATTTGTTACT 57.462 32.000 27.53 0.00 35.70 2.24
3328 3464 4.955925 TGTGATTTTATACTTGCGTGGG 57.044 40.909 0.00 0.00 0.00 4.61
3331 3467 7.865385 ACATTTGTTGTGATTTTATACTTGCGT 59.135 29.630 0.00 0.00 37.11 5.24
3349 3485 8.973378 CACATACCGTTTGATAAAACATTTGTT 58.027 29.630 6.49 0.00 40.50 2.83
3413 3561 9.487790 GAGATTCTTCATTTTGATAGGGAGTAG 57.512 37.037 0.00 0.00 0.00 2.57
3434 3583 3.749954 GCCATGAGCCCATAAGTGAGATT 60.750 47.826 0.00 0.00 34.35 2.40
3441 3590 2.281539 TGATGCCATGAGCCCATAAG 57.718 50.000 0.00 0.00 42.71 1.73
3443 3592 2.158430 ACATTGATGCCATGAGCCCATA 60.158 45.455 0.00 0.00 42.71 2.74
3452 3601 6.231951 TGTTTTGATTTCACATTGATGCCAT 58.768 32.000 0.00 0.00 0.00 4.40
3522 3672 3.146783 TGCCGGTAAGTTGGATTCG 57.853 52.632 1.90 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.