Multiple sequence alignment - TraesCS4D01G053100

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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 TraesCS4D01G053100 chr4D 100.000 2959 0 0 1 2959 29175589 29178547 0.000000e+00 5465
1 TraesCS4D01G053100 chr4B 89.306 1945 127 27 202 2112 41742779 41744676 0.000000e+00 2364
2 TraesCS4D01G053100 chr4B 95.844 385 13 1 2578 2959 41745030 41745414 1.170000e-173 619
3 TraesCS4D01G053100 chr4B 87.619 210 24 2 1 209 41742506 41742714 2.950000e-60 243
4 TraesCS4D01G053100 chr4B 93.878 147 9 0 1060 1206 609819070 609818924 3.840000e-54 222
5 TraesCS4D01G053100 chr4B 96.104 77 3 0 2439 2515 41744954 41745030 3.100000e-25 126
6 TraesCS4D01G053100 chr4A 86.766 1277 63 45 1008 2255 574385353 574384154 0.000000e+00 1325
7 TraesCS4D01G053100 chr4A 95.352 667 21 3 2303 2959 574384148 574383482 0.000000e+00 1051
8 TraesCS4D01G053100 chr4A 85.814 1001 102 17 1 976 574386329 574385344 0.000000e+00 1026
9 TraesCS4D01G053100 chr7B 87.615 218 22 3 1442 1655 677538443 677538227 6.330000e-62 248
10 TraesCS4D01G053100 chr7B 84.932 219 26 4 1442 1655 677667653 677667437 6.420000e-52 215
11 TraesCS4D01G053100 chr7B 91.026 156 13 1 1112 1267 677538724 677538570 2.990000e-50 209
12 TraesCS4D01G053100 chr5B 96.000 150 6 0 1057 1206 691533829 691533680 8.190000e-61 244
13 TraesCS4D01G053100 chr5B 94.667 150 8 0 1057 1206 499900154 499900005 1.770000e-57 233
14 TraesCS4D01G053100 chr3B 95.333 150 7 0 1057 1206 811659071 811658922 3.810000e-59 239
15 TraesCS4D01G053100 chr7A 86.758 219 22 4 1442 1655 690918206 690917990 1.370000e-58 237
16 TraesCS4D01G053100 chr7A 86.301 219 23 4 1442 1655 690929976 690929760 6.380000e-57 231
17 TraesCS4D01G053100 chr2D 95.333 150 5 1 1057 1206 283963813 283963960 1.370000e-58 237
18 TraesCS4D01G053100 chr1A 95.302 149 7 0 1057 1205 481247750 481247898 1.370000e-58 237
19 TraesCS4D01G053100 chr7D 85.253 217 25 4 1442 1653 598485345 598485131 1.790000e-52 217
20 TraesCS4D01G053100 chr7D 85.253 217 25 4 1442 1653 598496770 598496556 1.790000e-52 217
21 TraesCS4D01G053100 chr7D 84.828 145 20 2 1124 1267 617735738 617735595 8.550000e-31 145
22 TraesCS4D01G053100 chr5D 83.406 229 30 5 1436 1658 125737678 125737452 3.870000e-49 206


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 TraesCS4D01G053100 chr4D 29175589 29178547 2958 False 5465 5465 100.000000 1 2959 1 chr4D.!!$F1 2958
1 TraesCS4D01G053100 chr4B 41742506 41745414 2908 False 838 2364 92.218250 1 2959 4 chr4B.!!$F1 2958
2 TraesCS4D01G053100 chr4A 574383482 574386329 2847 True 1134 1325 89.310667 1 2959 3 chr4A.!!$R1 2958

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
31 32 0.035056 GTGCAGGTGGGTAAGATGCT 60.035 55.0 0.00 0.0 37.76 3.79 F
48 49 0.461961 GCTCAAGTCCGGAGTGCTAT 59.538 55.0 13.86 0.0 34.83 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1418 0.365859 GCGATCGACTGACGGAAAAC 59.634 55.0 21.57 0.0 42.82 2.43 R
2024 2159 0.980231 CCACAGGGCTAAGAGGAGCT 60.980 60.0 0.00 0.0 42.43 4.09 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
24 25 4.730966 TGAAATTAAAGTGCAGGTGGGTA 58.269 39.130 0.00 0.00 0.00 3.69
31 32 0.035056 GTGCAGGTGGGTAAGATGCT 60.035 55.000 0.00 0.00 37.76 3.79
38 39 2.633488 GTGGGTAAGATGCTCAAGTCC 58.367 52.381 0.00 0.00 0.00 3.85
45 46 1.078848 ATGCTCAAGTCCGGAGTGC 60.079 57.895 13.86 12.81 34.83 4.40
48 49 0.461961 GCTCAAGTCCGGAGTGCTAT 59.538 55.000 13.86 0.00 34.83 2.97
52 53 2.429610 TCAAGTCCGGAGTGCTATTACC 59.570 50.000 13.86 0.00 0.00 2.85
81 83 3.567478 ATCCCTTTGCTCACCTATCAC 57.433 47.619 0.00 0.00 0.00 3.06
84 86 1.009829 CTTTGCTCACCTATCACGGC 58.990 55.000 0.00 0.00 0.00 5.68
153 155 8.562892 ACATTTGAACTTATTGACTCTCAAGTG 58.437 33.333 0.00 0.00 40.05 3.16
167 169 6.064717 ACTCTCAAGTGCAAGTTTCCTTTAT 58.935 36.000 0.00 0.00 33.32 1.40
172 174 5.948992 AGTGCAAGTTTCCTTTATCTGTC 57.051 39.130 0.00 0.00 0.00 3.51
198 200 4.227982 TGATGAACTCCTGGATGAATTGGA 59.772 41.667 0.00 0.00 0.00 3.53
223 296 4.804665 GGTACATCCTAGTTTTCGAAGCTC 59.195 45.833 7.45 0.00 0.00 4.09
224 297 3.512680 ACATCCTAGTTTTCGAAGCTCG 58.487 45.455 7.45 0.00 42.10 5.03
244 317 2.789092 CGATTTGCGAGCAGATTTCCAC 60.789 50.000 2.62 0.00 44.57 4.02
253 326 2.237143 AGCAGATTTCCACCAGATTCGA 59.763 45.455 0.00 0.00 0.00 3.71
254 327 2.352960 GCAGATTTCCACCAGATTCGAC 59.647 50.000 0.00 0.00 0.00 4.20
274 348 2.187163 GCCCAGGCGAAGAGTACC 59.813 66.667 0.00 0.00 0.00 3.34
279 353 1.002087 CCAGGCGAAGAGTACCAAACT 59.998 52.381 0.00 0.00 42.80 2.66
281 355 0.796927 GGCGAAGAGTACCAAACTGC 59.203 55.000 0.00 0.00 39.07 4.40
289 363 3.746492 AGAGTACCAAACTGCGTTTCATC 59.254 43.478 4.11 0.68 39.07 2.92
297 371 2.783135 ACTGCGTTTCATCCTCACAAT 58.217 42.857 0.00 0.00 0.00 2.71
306 380 3.554934 TCATCCTCACAATATTGCCACC 58.445 45.455 15.48 0.00 0.00 4.61
307 381 2.036958 TCCTCACAATATTGCCACCG 57.963 50.000 15.48 0.13 0.00 4.94
314 388 1.132262 CAATATTGCCACCGCGAGTTT 59.868 47.619 8.23 0.00 38.08 2.66
321 395 1.434555 CCACCGCGAGTTTAATGTCA 58.565 50.000 8.23 0.00 0.00 3.58
331 405 3.331150 AGTTTAATGTCATGGCGTTCGA 58.669 40.909 8.31 0.00 0.00 3.71
336 410 4.536364 AATGTCATGGCGTTCGATTAAG 57.464 40.909 0.00 0.00 0.00 1.85
358 433 1.659794 CGCCCAACAACCTTCCAAG 59.340 57.895 0.00 0.00 0.00 3.61
368 443 6.239176 CCAACAACCTTCCAAGCAGTTATTTA 60.239 38.462 0.00 0.00 0.00 1.40
371 446 6.775629 ACAACCTTCCAAGCAGTTATTTAGAA 59.224 34.615 0.00 0.00 0.00 2.10
378 453 9.515226 TTCCAAGCAGTTATTTAGAAATGTACT 57.485 29.630 0.00 0.00 0.00 2.73
379 454 9.515226 TCCAAGCAGTTATTTAGAAATGTACTT 57.485 29.630 0.00 0.00 0.00 2.24
422 498 7.401484 TTTTCGGCATTTAGAATGTGTTTTC 57.599 32.000 2.97 0.00 0.00 2.29
442 518 7.822334 TGTTTTCTGAAGTGGGTACATATGTAG 59.178 37.037 15.93 3.17 0.00 2.74
462 538 3.559069 AGCAAGGGTTCATCCATGTATG 58.441 45.455 0.00 0.00 38.11 2.39
503 581 4.680237 CTGGTTCCGACTGCGCCA 62.680 66.667 4.18 0.00 35.83 5.69
515 593 0.813184 CTGCGCCATTTGACAATCCT 59.187 50.000 4.18 0.00 0.00 3.24
516 594 1.203052 CTGCGCCATTTGACAATCCTT 59.797 47.619 4.18 0.00 0.00 3.36
517 595 2.423185 CTGCGCCATTTGACAATCCTTA 59.577 45.455 4.18 0.00 0.00 2.69
522 600 5.458779 GCGCCATTTGACAATCCTTATAAAC 59.541 40.000 0.00 0.00 0.00 2.01
611 689 8.830580 CCATCAGTTTCGTATGAGTGAAATATT 58.169 33.333 0.00 0.00 36.57 1.28
617 695 8.818057 GTTTCGTATGAGTGAAATATTAGCACT 58.182 33.333 18.54 18.54 44.87 4.40
620 698 7.648112 TCGTATGAGTGAAATATTAGCACTGTC 59.352 37.037 21.75 12.81 42.47 3.51
622 700 9.967346 GTATGAGTGAAATATTAGCACTGTCTA 57.033 33.333 21.75 11.37 42.47 2.59
679 762 7.596749 ACAACAATATAAAGTTCAGAGGACG 57.403 36.000 0.00 0.00 0.00 4.79
686 769 9.575868 AATATAAAGTTCAGAGGACGAGATCTA 57.424 33.333 0.00 0.00 0.00 1.98
767 863 3.201290 GCTACACATGACCCTCAGATTG 58.799 50.000 0.00 0.00 0.00 2.67
795 891 9.268268 CTATAAAACGAACAGCCTCCATATAAA 57.732 33.333 0.00 0.00 0.00 1.40
797 893 3.805207 ACGAACAGCCTCCATATAAACC 58.195 45.455 0.00 0.00 0.00 3.27
801 897 3.805207 ACAGCCTCCATATAAACCGTTC 58.195 45.455 0.00 0.00 0.00 3.95
809 907 6.183360 CCTCCATATAAACCGTTCTTTTTCCC 60.183 42.308 0.00 0.00 0.00 3.97
853 951 8.603181 CAAAACAAAAACATTCTCCGAAAAGAT 58.397 29.630 0.00 0.00 0.00 2.40
934 1037 4.424711 GCCCGTCCCAGCCAATCA 62.425 66.667 0.00 0.00 0.00 2.57
1292 1411 1.974236 GACATCATCGATCCCCCTTCT 59.026 52.381 0.00 0.00 0.00 2.85
1298 1417 3.134804 TCATCGATCCCCCTTCTCTTTTC 59.865 47.826 0.00 0.00 0.00 2.29
1299 1418 1.480954 TCGATCCCCCTTCTCTTTTCG 59.519 52.381 0.00 0.00 0.00 3.46
1301 1420 2.354805 CGATCCCCCTTCTCTTTTCGTT 60.355 50.000 0.00 0.00 0.00 3.85
1302 1421 3.687125 GATCCCCCTTCTCTTTTCGTTT 58.313 45.455 0.00 0.00 0.00 3.60
1303 1422 3.588210 TCCCCCTTCTCTTTTCGTTTT 57.412 42.857 0.00 0.00 0.00 2.43
1304 1423 3.483421 TCCCCCTTCTCTTTTCGTTTTC 58.517 45.455 0.00 0.00 0.00 2.29
1305 1424 2.557056 CCCCCTTCTCTTTTCGTTTTCC 59.443 50.000 0.00 0.00 0.00 3.13
1306 1425 2.225727 CCCCTTCTCTTTTCGTTTTCCG 59.774 50.000 0.00 0.00 38.13 4.30
1318 1437 0.365859 GTTTTCCGTCAGTCGATCGC 59.634 55.000 11.09 5.80 42.86 4.58
1385 1504 2.462927 CGTTCGTTATCCGTGATTCGAG 59.537 50.000 0.00 0.00 42.86 4.04
1483 1607 1.235281 GCGGGACAACAAGAAGACCC 61.235 60.000 0.00 0.00 0.00 4.46
1703 1827 1.448540 GAGGCCGTCCTGTCATGTG 60.449 63.158 0.00 0.00 44.46 3.21
1822 1946 1.728971 GCTCTGTCGTGGTTGAATGAG 59.271 52.381 0.00 0.00 0.00 2.90
1847 1971 4.699637 AGTCGATCGATCAGTAGAAGAGT 58.300 43.478 22.50 11.56 0.00 3.24
1849 1973 4.508492 GTCGATCGATCAGTAGAAGAGTGA 59.492 45.833 22.50 6.67 41.84 3.41
1851 1975 5.585047 TCGATCGATCAGTAGAAGAGTGAAA 59.415 40.000 24.40 0.00 40.96 2.69
1852 1976 6.093633 TCGATCGATCAGTAGAAGAGTGAAAA 59.906 38.462 24.40 0.00 40.96 2.29
1853 1978 6.915300 CGATCGATCAGTAGAAGAGTGAAAAT 59.085 38.462 24.40 0.00 40.96 1.82
1893 2026 2.753989 TATGCGAAAATGATGGTGCG 57.246 45.000 0.00 0.00 0.00 5.34
1968 2103 9.626045 GAATTCCCTGTGAAATTTTAGTTACAG 57.374 33.333 0.00 0.00 36.33 2.74
1985 2120 7.164230 AGTTACAGGAATCTGACTAGTCTTG 57.836 40.000 23.01 15.46 43.49 3.02
2010 2145 5.668471 TCTGAAAGAAATGATCATCTCGCT 58.332 37.500 9.06 1.45 42.31 4.93
2024 2159 5.000591 TCATCTCGCTGTGGAAATAAAACA 58.999 37.500 0.00 0.00 0.00 2.83
2039 2174 1.662686 AAACAGCTCCTCTTAGCCCT 58.337 50.000 0.00 0.00 43.86 5.19
2047 2182 2.507471 CTCCTCTTAGCCCTGTGGAAAT 59.493 50.000 0.00 0.00 0.00 2.17
2094 2229 6.183360 CCTCTTTCAGAAATCAGCCAACATAG 60.183 42.308 0.00 0.00 0.00 2.23
2159 2351 7.582435 TTAACAAACGAAAATGCAGACAAAA 57.418 28.000 0.00 0.00 0.00 2.44
2214 2414 4.482386 CAACTGCAATGTCTGAATTCCTG 58.518 43.478 2.27 0.00 0.00 3.86
2222 2422 4.974645 TGTCTGAATTCCTGGTTACTGT 57.025 40.909 2.27 0.00 0.00 3.55
2223 2423 5.304686 TGTCTGAATTCCTGGTTACTGTT 57.695 39.130 2.27 0.00 0.00 3.16
2225 2425 6.833041 TGTCTGAATTCCTGGTTACTGTTTA 58.167 36.000 2.27 0.00 0.00 2.01
2227 2427 7.942341 TGTCTGAATTCCTGGTTACTGTTTAAT 59.058 33.333 2.27 0.00 0.00 1.40
2228 2428 8.451748 GTCTGAATTCCTGGTTACTGTTTAATC 58.548 37.037 2.27 0.00 0.00 1.75
2252 2462 3.309410 GCTTGCTTGCTTGTTGCTTTTTA 59.691 39.130 0.00 0.00 43.37 1.52
2255 2465 5.655893 TGCTTGCTTGTTGCTTTTTAATC 57.344 34.783 0.00 0.00 43.37 1.75
2256 2466 5.114780 TGCTTGCTTGTTGCTTTTTAATCA 58.885 33.333 0.00 0.00 43.37 2.57
2257 2467 5.234757 TGCTTGCTTGTTGCTTTTTAATCAG 59.765 36.000 0.00 0.00 43.37 2.90
2258 2468 5.655893 TTGCTTGTTGCTTTTTAATCAGC 57.344 34.783 0.36 0.36 43.37 4.26
2259 2469 4.947645 TGCTTGTTGCTTTTTAATCAGCT 58.052 34.783 7.67 0.00 43.37 4.24
2260 2470 5.358922 TGCTTGTTGCTTTTTAATCAGCTT 58.641 33.333 7.67 0.00 43.37 3.74
2261 2471 5.816777 TGCTTGTTGCTTTTTAATCAGCTTT 59.183 32.000 7.67 0.00 43.37 3.51
2262 2472 6.131389 GCTTGTTGCTTTTTAATCAGCTTTG 58.869 36.000 7.67 0.00 36.92 2.77
2263 2473 6.601741 TTGTTGCTTTTTAATCAGCTTTGG 57.398 33.333 7.67 0.00 36.92 3.28
2264 2474 5.911752 TGTTGCTTTTTAATCAGCTTTGGA 58.088 33.333 7.67 0.00 36.92 3.53
2265 2475 6.344500 TGTTGCTTTTTAATCAGCTTTGGAA 58.656 32.000 7.67 0.00 36.92 3.53
2266 2476 6.257630 TGTTGCTTTTTAATCAGCTTTGGAAC 59.742 34.615 7.67 0.00 36.92 3.62
2267 2477 4.981674 TGCTTTTTAATCAGCTTTGGAACG 59.018 37.500 7.67 0.00 36.92 3.95
2268 2478 4.982295 GCTTTTTAATCAGCTTTGGAACGT 59.018 37.500 0.00 0.00 32.87 3.99
2269 2479 5.117135 GCTTTTTAATCAGCTTTGGAACGTC 59.883 40.000 0.00 0.00 32.87 4.34
2270 2480 6.385649 TTTTTAATCAGCTTTGGAACGTCT 57.614 33.333 0.00 0.00 0.00 4.18
2271 2481 5.356882 TTTAATCAGCTTTGGAACGTCTG 57.643 39.130 0.00 0.00 0.00 3.51
2272 2482 2.839486 ATCAGCTTTGGAACGTCTGA 57.161 45.000 3.68 3.68 38.05 3.27
2273 2483 2.613026 TCAGCTTTGGAACGTCTGAA 57.387 45.000 0.00 0.00 31.62 3.02
2274 2484 3.126001 TCAGCTTTGGAACGTCTGAAT 57.874 42.857 0.00 0.00 31.62 2.57
2275 2485 3.476552 TCAGCTTTGGAACGTCTGAATT 58.523 40.909 0.00 0.00 31.62 2.17
2276 2486 3.498397 TCAGCTTTGGAACGTCTGAATTC 59.502 43.478 0.00 0.00 31.62 2.17
2277 2487 3.250762 CAGCTTTGGAACGTCTGAATTCA 59.749 43.478 8.12 8.12 0.00 2.57
2278 2488 4.074970 AGCTTTGGAACGTCTGAATTCAT 58.925 39.130 8.96 0.00 0.00 2.57
2279 2489 4.083110 AGCTTTGGAACGTCTGAATTCATG 60.083 41.667 8.96 4.85 0.00 3.07
2280 2490 4.320494 GCTTTGGAACGTCTGAATTCATGT 60.320 41.667 8.96 5.50 0.00 3.21
2281 2491 5.106712 GCTTTGGAACGTCTGAATTCATGTA 60.107 40.000 8.96 0.00 0.00 2.29
2282 2492 6.403636 GCTTTGGAACGTCTGAATTCATGTAT 60.404 38.462 8.96 0.00 0.00 2.29
2283 2493 7.201609 GCTTTGGAACGTCTGAATTCATGTATA 60.202 37.037 8.96 0.00 0.00 1.47
2284 2494 8.731275 TTTGGAACGTCTGAATTCATGTATAT 57.269 30.769 8.96 0.00 0.00 0.86
2285 2495 9.825109 TTTGGAACGTCTGAATTCATGTATATA 57.175 29.630 8.96 0.00 0.00 0.86
2286 2496 9.996554 TTGGAACGTCTGAATTCATGTATATAT 57.003 29.630 8.96 0.00 0.00 0.86
2300 2510 9.599866 TTCATGTATATATATAGCTGTGGTTGC 57.400 33.333 2.53 0.00 0.00 4.17
2301 2511 8.981659 TCATGTATATATATAGCTGTGGTTGCT 58.018 33.333 2.53 0.00 43.79 3.91
2394 2604 6.016610 ACTCTGTCTCTACTCTTGTCTGAAAC 60.017 42.308 0.00 0.00 0.00 2.78
2397 2607 5.148568 GTCTCTACTCTTGTCTGAAACGAC 58.851 45.833 0.00 0.00 34.52 4.34
2530 2740 3.205815 CTCTGTCCCTCTCCCAGAG 57.794 63.158 0.00 0.00 44.30 3.35
2536 2746 1.532794 CCCTCTCCCAGAGATCCGG 60.533 68.421 0.00 0.00 45.07 5.14
2545 2755 3.388024 TCCCAGAGATCCGGAAACATTAG 59.612 47.826 9.01 0.00 0.00 1.73
2573 2783 0.961019 TGCAGAGCCAAAATCCACAC 59.039 50.000 0.00 0.00 0.00 3.82
2617 2830 2.034939 TGCTCAGCAAGTTTCACCATTG 59.965 45.455 0.00 0.00 34.76 2.82
2635 2848 6.002704 ACCATTGGATTCTTCTCATCATAGC 58.997 40.000 10.37 0.00 0.00 2.97
2701 2917 4.220693 TGCTATACATCAACAGCCTTGT 57.779 40.909 0.00 0.00 39.87 3.16
2736 2952 6.170506 TGAATTACACACCCTGATCAGTAAC 58.829 40.000 21.11 3.66 0.00 2.50
2775 2995 2.280183 GCTCGTCAAGTGTTGATCGATC 59.720 50.000 18.72 18.72 42.47 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.795329 CATCTTACCCACCTGCACTTT 58.205 47.619 0.00 0.00 0.00 2.66
24 25 1.066573 CACTCCGGACTTGAGCATCTT 60.067 52.381 0.00 0.00 34.92 2.40
31 32 2.429610 GGTAATAGCACTCCGGACTTGA 59.570 50.000 0.00 0.00 0.00 3.02
38 39 2.483188 GGAACTGGGTAATAGCACTCCG 60.483 54.545 0.00 0.00 0.00 4.63
45 46 5.388599 AAGGGATTGGAACTGGGTAATAG 57.611 43.478 0.00 0.00 0.00 1.73
48 49 3.773560 CAAAGGGATTGGAACTGGGTAA 58.226 45.455 0.00 0.00 35.27 2.85
52 53 1.821136 GAGCAAAGGGATTGGAACTGG 59.179 52.381 0.00 0.00 39.54 4.00
84 86 2.435938 TTAGGCCCTTCTTGCGCG 60.436 61.111 0.00 0.00 0.00 6.86
100 102 1.075542 CGACACATACACGCCATGTT 58.924 50.000 0.00 0.00 43.19 2.71
167 169 3.840078 TCCAGGAGTTCATCAATGACAGA 59.160 43.478 0.00 0.00 36.36 3.41
172 174 6.461092 CCAATTCATCCAGGAGTTCATCAATG 60.461 42.308 0.00 0.00 0.00 2.82
198 200 9.906575 CGAGCTTCGAAAACTAGGATGTACCTT 62.907 44.444 0.00 0.00 44.48 3.50
223 296 1.398041 TGGAAATCTGCTCGCAAATCG 59.602 47.619 0.00 0.00 40.15 3.34
224 297 2.478539 GGTGGAAATCTGCTCGCAAATC 60.479 50.000 0.00 0.00 0.00 2.17
230 303 2.322355 ATCTGGTGGAAATCTGCTCG 57.678 50.000 0.00 0.00 0.00 5.03
237 310 2.991250 CCAGTCGAATCTGGTGGAAAT 58.009 47.619 12.79 0.00 46.92 2.17
253 326 3.710722 CTCTTCGCCTGGGCCAGT 61.711 66.667 30.68 0.00 37.98 4.00
254 327 2.359169 TACTCTTCGCCTGGGCCAG 61.359 63.158 27.04 27.04 37.98 4.85
279 353 4.438608 GCAATATTGTGAGGATGAAACGCA 60.439 41.667 16.61 0.00 0.00 5.24
281 355 4.096231 TGGCAATATTGTGAGGATGAAACG 59.904 41.667 16.61 0.00 0.00 3.60
289 363 0.381801 GCGGTGGCAATATTGTGAGG 59.618 55.000 16.61 4.68 39.62 3.86
297 371 2.096220 TTAAACTCGCGGTGGCAATA 57.904 45.000 6.13 0.00 39.92 1.90
306 380 1.592110 CGCCATGACATTAAACTCGCG 60.592 52.381 0.00 0.00 0.00 5.87
307 381 1.396996 ACGCCATGACATTAAACTCGC 59.603 47.619 0.00 0.00 0.00 5.03
314 388 5.353111 TCTTAATCGAACGCCATGACATTA 58.647 37.500 0.00 0.00 0.00 1.90
321 395 1.583054 GCCTCTTAATCGAACGCCAT 58.417 50.000 0.00 0.00 0.00 4.40
331 405 1.173913 GTTGTTGGGCGCCTCTTAAT 58.826 50.000 28.56 0.00 0.00 1.40
336 410 2.597510 AAGGTTGTTGGGCGCCTC 60.598 61.111 28.56 17.27 0.00 4.70
358 433 8.020819 TGCACAAGTACATTTCTAAATAACTGC 58.979 33.333 0.00 0.00 29.45 4.40
402 477 5.698832 TCAGAAAACACATTCTAAATGCCG 58.301 37.500 0.00 0.00 37.56 5.69
404 479 7.115378 CCACTTCAGAAAACACATTCTAAATGC 59.885 37.037 0.00 0.00 37.56 3.56
422 498 5.276461 TGCTACATATGTACCCACTTCAG 57.724 43.478 11.62 2.06 0.00 3.02
442 518 3.290710 ACATACATGGATGAACCCTTGC 58.709 45.455 25.07 0.00 35.46 4.01
462 538 4.196971 AGATTGGGCAAACTATACGGAAC 58.803 43.478 0.00 0.00 0.00 3.62
580 658 4.021456 ACTCATACGAAACTGATGGTGTCA 60.021 41.667 0.00 0.00 31.79 3.58
611 689 7.385205 GTCATTCTGAACTTTTAGACAGTGCTA 59.615 37.037 0.00 0.00 0.00 3.49
617 695 7.606456 GGTATGGTCATTCTGAACTTTTAGACA 59.394 37.037 0.00 0.00 34.53 3.41
620 698 6.456988 GCGGTATGGTCATTCTGAACTTTTAG 60.457 42.308 0.00 0.00 34.53 1.85
622 700 4.156008 GCGGTATGGTCATTCTGAACTTTT 59.844 41.667 0.00 0.00 34.53 2.27
674 757 3.560896 GCGACTAGTTTAGATCTCGTCCT 59.439 47.826 0.00 0.00 0.00 3.85
675 758 3.311871 TGCGACTAGTTTAGATCTCGTCC 59.688 47.826 0.00 0.00 0.00 4.79
676 759 4.533225 TGCGACTAGTTTAGATCTCGTC 57.467 45.455 0.00 0.00 0.00 4.20
679 762 4.611943 TGCATGCGACTAGTTTAGATCTC 58.388 43.478 14.09 0.00 0.00 2.75
767 863 4.501071 TGGAGGCTGTTCGTTTTATAGAC 58.499 43.478 0.00 0.00 0.00 2.59
824 922 7.692908 TTCGGAGAATGTTTTTGTTTTGATC 57.307 32.000 0.00 0.00 45.90 2.92
1267 1386 2.557676 GGGGGATCGATGATGTCTAGGA 60.558 54.545 0.54 0.00 0.00 2.94
1299 1418 0.365859 GCGATCGACTGACGGAAAAC 59.634 55.000 21.57 0.00 42.82 2.43
1301 1420 1.153901 GGCGATCGACTGACGGAAA 60.154 57.895 21.57 0.00 42.82 3.13
1302 1421 2.488355 GGCGATCGACTGACGGAA 59.512 61.111 21.57 0.00 42.82 4.30
1303 1422 3.872728 CGGCGATCGACTGACGGA 61.873 66.667 21.57 0.00 42.43 4.69
1385 1504 2.823154 TCAAATCAAACCCCAATCCGAC 59.177 45.455 0.00 0.00 0.00 4.79
1822 1946 4.508492 TCTTCTACTGATCGATCGACTCAC 59.492 45.833 22.06 12.53 0.00 3.51
1853 1978 9.940166 CGCATATACGAAACCACATAGTATATA 57.060 33.333 0.00 0.00 38.29 0.86
1871 2001 4.151070 CGCACCATCATTTTCGCATATAC 58.849 43.478 0.00 0.00 0.00 1.47
1882 2012 1.651240 GACAGCTGCGCACCATCATT 61.651 55.000 15.27 0.00 0.00 2.57
1885 2015 1.580845 AAAGACAGCTGCGCACCATC 61.581 55.000 15.27 2.03 0.00 3.51
1889 2022 2.619013 ATTAAAAGACAGCTGCGCAC 57.381 45.000 15.27 3.54 0.00 5.34
1893 2026 7.761249 ACCAAATCAATATTAAAAGACAGCTGC 59.239 33.333 15.27 6.85 0.00 5.25
1897 2030 9.289303 CCGAACCAAATCAATATTAAAAGACAG 57.711 33.333 0.00 0.00 0.00 3.51
1908 2043 6.392625 TCAAACAACCGAACCAAATCAATA 57.607 33.333 0.00 0.00 0.00 1.90
1915 2050 4.927978 ATCATTCAAACAACCGAACCAA 57.072 36.364 0.00 0.00 0.00 3.67
1968 2103 4.707448 TCAGACCAAGACTAGTCAGATTCC 59.293 45.833 24.44 8.95 35.38 3.01
1985 2120 5.277250 GCGAGATGATCATTTCTTTCAGACC 60.277 44.000 20.48 0.48 0.00 3.85
2010 2145 4.985538 AGAGGAGCTGTTTTATTTCCACA 58.014 39.130 0.00 0.00 0.00 4.17
2024 2159 0.980231 CCACAGGGCTAAGAGGAGCT 60.980 60.000 0.00 0.00 42.43 4.09
2039 2174 5.689514 CGTTTGATGCTGTTTTATTTCCACA 59.310 36.000 0.00 0.00 0.00 4.17
2094 2229 3.403038 TCACCTTCTGCAACTTAAGAGC 58.597 45.455 10.09 13.01 0.00 4.09
2143 2335 4.977741 AGCATTTTTGTCTGCATTTTCG 57.022 36.364 0.00 0.00 40.88 3.46
2200 2400 5.505181 ACAGTAACCAGGAATTCAGACAT 57.495 39.130 7.93 0.00 0.00 3.06
2214 2414 5.629079 AGCAAGCTGATTAAACAGTAACC 57.371 39.130 13.56 0.00 39.73 2.85
2222 2422 4.589216 ACAAGCAAGCAAGCTGATTAAA 57.411 36.364 3.54 0.00 45.89 1.52
2223 2423 4.300803 CAACAAGCAAGCAAGCTGATTAA 58.699 39.130 3.54 0.00 45.89 1.40
2225 2425 2.750948 CAACAAGCAAGCAAGCTGATT 58.249 42.857 3.54 0.00 45.89 2.57
2227 2427 0.249155 GCAACAAGCAAGCAAGCTGA 60.249 50.000 3.54 0.00 45.89 4.26
2228 2428 0.249322 AGCAACAAGCAAGCAAGCTG 60.249 50.000 3.54 1.87 45.89 4.24
2252 2462 3.126001 TCAGACGTTCCAAAGCTGATT 57.874 42.857 0.00 0.00 31.24 2.57
2255 2465 3.250762 TGAATTCAGACGTTCCAAAGCTG 59.749 43.478 3.38 0.00 0.00 4.24
2256 2466 3.476552 TGAATTCAGACGTTCCAAAGCT 58.523 40.909 3.38 0.00 0.00 3.74
2257 2467 3.896648 TGAATTCAGACGTTCCAAAGC 57.103 42.857 3.38 0.00 0.00 3.51
2258 2468 5.362556 ACATGAATTCAGACGTTCCAAAG 57.637 39.130 14.54 0.00 0.00 2.77
2259 2469 8.731275 ATATACATGAATTCAGACGTTCCAAA 57.269 30.769 14.54 0.00 0.00 3.28
2260 2470 9.996554 ATATATACATGAATTCAGACGTTCCAA 57.003 29.630 14.54 0.00 0.00 3.53
2274 2484 9.599866 GCAACCACAGCTATATATATACATGAA 57.400 33.333 0.00 0.00 0.00 2.57
2275 2485 8.981659 AGCAACCACAGCTATATATATACATGA 58.018 33.333 0.00 0.00 41.32 3.07
2289 2499 2.867109 ACTGAATAGCAACCACAGCT 57.133 45.000 0.00 0.00 45.77 4.24
2290 2500 3.568538 CAAACTGAATAGCAACCACAGC 58.431 45.455 0.00 0.00 32.67 4.40
2291 2501 3.569701 ACCAAACTGAATAGCAACCACAG 59.430 43.478 0.00 0.00 35.14 3.66
2292 2502 3.561143 ACCAAACTGAATAGCAACCACA 58.439 40.909 0.00 0.00 0.00 4.17
2293 2503 4.584327 AACCAAACTGAATAGCAACCAC 57.416 40.909 0.00 0.00 0.00 4.16
2294 2504 4.646945 TCAAACCAAACTGAATAGCAACCA 59.353 37.500 0.00 0.00 0.00 3.67
2295 2505 5.195001 TCAAACCAAACTGAATAGCAACC 57.805 39.130 0.00 0.00 0.00 3.77
2296 2506 6.446318 TGATCAAACCAAACTGAATAGCAAC 58.554 36.000 0.00 0.00 0.00 4.17
2297 2507 6.647334 TGATCAAACCAAACTGAATAGCAA 57.353 33.333 0.00 0.00 0.00 3.91
2298 2508 6.127647 GGATGATCAAACCAAACTGAATAGCA 60.128 38.462 14.74 0.00 0.00 3.49
2299 2509 6.268566 GGATGATCAAACCAAACTGAATAGC 58.731 40.000 14.74 0.00 0.00 2.97
2300 2510 6.316140 TCGGATGATCAAACCAAACTGAATAG 59.684 38.462 18.14 3.11 0.00 1.73
2301 2511 6.176896 TCGGATGATCAAACCAAACTGAATA 58.823 36.000 18.14 0.00 0.00 1.75
2397 2607 1.651138 GATCTCTTCGACAACACGCAG 59.349 52.381 0.00 0.00 0.00 5.18
2530 2740 3.531538 TGCAGACTAATGTTTCCGGATC 58.468 45.455 4.15 2.09 0.00 3.36
2560 2770 1.372872 GGCACGTGTGGATTTTGGC 60.373 57.895 18.38 0.00 0.00 4.52
2573 2783 1.835483 GCACAGAAGTCACTGGCACG 61.835 60.000 0.00 0.00 41.59 5.34
2617 2830 8.162878 TCATTTTGCTATGATGAGAAGAATCC 57.837 34.615 0.00 0.00 29.82 3.01
2701 2917 3.191162 GTGTGTAATTCAGGCATTGCAGA 59.809 43.478 11.39 4.96 30.40 4.26
2736 2952 1.334054 GCAGCAAGCAAGTTGATTCG 58.666 50.000 7.16 3.18 44.79 3.34
2932 3152 0.691078 TACCTGAGGGCCATGGAGAC 60.691 60.000 18.40 4.25 35.63 3.36


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

AutoCloner maintained by Alex Coulton.