Multiple sequence alignment - TraesCS4B01G258200

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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 TraesCS4B01G258200 chr4B 100.000 3039 0 0 1 3039 524708794 524705756 0.000000e+00 5613
1 TraesCS4B01G258200 chr4D 92.590 1579 35 22 831 2356 428119086 428117537 0.000000e+00 2193
2 TraesCS4B01G258200 chr4D 95.577 407 11 5 363 765 428119500 428119097 0.000000e+00 645
3 TraesCS4B01G258200 chr4D 85.505 614 45 22 2384 2976 428117539 428116949 4.340000e-168 601
4 TraesCS4B01G258200 chr4D 89.078 293 20 9 1 287 428119778 428119492 1.340000e-93 353
5 TraesCS4B01G258200 chr4A 91.645 1137 39 21 363 1469 38328846 38329956 0.000000e+00 1522
6 TraesCS4B01G258200 chr4A 95.345 580 8 6 1510 2077 38329955 38330527 0.000000e+00 904
7 TraesCS4B01G258200 chr4A 82.410 307 29 12 1 284 38328546 38328850 8.420000e-61 244
8 TraesCS4B01G258200 chr4A 91.429 140 9 3 2677 2815 38330534 38330671 4.000000e-44 189
9 TraesCS4B01G258200 chr5B 96.667 90 3 0 281 370 62940322 62940411 1.890000e-32 150
10 TraesCS4B01G258200 chr7A 96.629 89 2 1 278 366 666152363 666152276 2.440000e-31 147
11 TraesCS4B01G258200 chr5D 95.604 91 4 0 280 370 350331951 350331861 2.440000e-31 147
12 TraesCS4B01G258200 chr5A 95.604 91 4 0 280 370 450750794 450750704 2.440000e-31 147
13 TraesCS4B01G258200 chr1B 96.552 87 3 0 280 366 151363743 151363657 8.780000e-31 145
14 TraesCS4B01G258200 chr6B 94.565 92 4 1 276 366 359864726 359864635 1.140000e-29 141
15 TraesCS4B01G258200 chr3D 94.565 92 4 1 282 373 450878870 450878780 1.140000e-29 141
16 TraesCS4B01G258200 chr1D 95.455 88 4 0 280 367 406664977 406665064 1.140000e-29 141
17 TraesCS4B01G258200 chr7B 93.548 93 6 0 275 367 639796192 639796284 4.090000e-29 139


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 TraesCS4B01G258200 chr4B 524705756 524708794 3038 True 5613.00 5613 100.00000 1 3039 1 chr4B.!!$R1 3038
1 TraesCS4B01G258200 chr4D 428116949 428119778 2829 True 948.00 2193 90.68750 1 2976 4 chr4D.!!$R1 2975
2 TraesCS4B01G258200 chr4A 38328546 38330671 2125 False 714.75 1522 90.20725 1 2815 4 chr4A.!!$F1 2814

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
808 839 1.106944 CACCACACCAAACCAGACCC 61.107 60.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2588 2719 0.092351 GTCACACGTATCCAAACGCG 59.908 55.0 3.53 3.53 46.71 6.01 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
44 46 7.256012 GGATGGTTTGTAAAGGTTGGACAATTA 60.256 37.037 0.00 0.00 33.33 1.40
284 307 4.448720 ACAACCCCTGCTAAAAAGTACT 57.551 40.909 0.00 0.00 0.00 2.73
285 308 4.395625 ACAACCCCTGCTAAAAAGTACTC 58.604 43.478 0.00 0.00 0.00 2.59
286 309 3.715638 ACCCCTGCTAAAAAGTACTCC 57.284 47.619 0.00 0.00 0.00 3.85
288 311 2.576648 CCCCTGCTAAAAAGTACTCCCT 59.423 50.000 0.00 0.00 0.00 4.20
289 312 3.370633 CCCCTGCTAAAAAGTACTCCCTC 60.371 52.174 0.00 0.00 0.00 4.30
290 313 3.370633 CCCTGCTAAAAAGTACTCCCTCC 60.371 52.174 0.00 0.00 0.00 4.30
291 314 3.519913 CCTGCTAAAAAGTACTCCCTCCT 59.480 47.826 0.00 0.00 0.00 3.69
292 315 4.019231 CCTGCTAAAAAGTACTCCCTCCTT 60.019 45.833 0.00 0.00 0.00 3.36
293 316 5.189145 CCTGCTAAAAAGTACTCCCTCCTTA 59.811 44.000 0.00 0.00 0.00 2.69
294 317 6.296259 CCTGCTAAAAAGTACTCCCTCCTTAA 60.296 42.308 0.00 0.00 0.00 1.85
295 318 7.081857 TGCTAAAAAGTACTCCCTCCTTAAA 57.918 36.000 0.00 0.00 0.00 1.52
296 319 7.696017 TGCTAAAAAGTACTCCCTCCTTAAAT 58.304 34.615 0.00 0.00 0.00 1.40
297 320 8.828751 TGCTAAAAAGTACTCCCTCCTTAAATA 58.171 33.333 0.00 0.00 0.00 1.40
298 321 9.676861 GCTAAAAAGTACTCCCTCCTTAAATAA 57.323 33.333 0.00 0.00 0.00 1.40
309 332 9.372369 CTCCCTCCTTAAATAAATATAAGAGCG 57.628 37.037 0.00 0.00 32.10 5.03
310 333 8.877195 TCCCTCCTTAAATAAATATAAGAGCGT 58.123 33.333 0.00 0.00 32.10 5.07
311 334 9.503399 CCCTCCTTAAATAAATATAAGAGCGTT 57.497 33.333 0.00 0.00 32.10 4.84
323 346 9.601217 AAATATAAGAGCGTTTTGATCACTACT 57.399 29.630 0.00 0.00 34.70 2.57
324 347 9.601217 AATATAAGAGCGTTTTGATCACTACTT 57.399 29.630 0.00 0.00 34.70 2.24
325 348 7.907214 ATAAGAGCGTTTTGATCACTACTTT 57.093 32.000 0.00 0.00 34.70 2.66
326 349 8.997621 ATAAGAGCGTTTTGATCACTACTTTA 57.002 30.769 0.00 0.00 34.70 1.85
327 350 6.952935 AGAGCGTTTTGATCACTACTTTAG 57.047 37.500 0.00 0.00 34.70 1.85
328 351 6.456501 AGAGCGTTTTGATCACTACTTTAGT 58.543 36.000 0.00 0.00 40.28 2.24
361 384 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
362 385 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
363 386 9.757227 CACTCTTATATTTCTTTACAGAGGGAG 57.243 37.037 0.00 0.00 32.92 4.30
364 387 9.495382 ACTCTTATATTTCTTTACAGAGGGAGT 57.505 33.333 0.00 0.00 32.21 3.85
477 504 7.027778 AGGTAAAAATAAAATAGCTCGCCAG 57.972 36.000 0.00 0.00 0.00 4.85
530 557 3.450578 ACAGTGTTACACAACTGTACGG 58.549 45.455 18.19 0.00 38.08 4.02
626 655 6.656902 ACAATGACATATTGACATCTCTGGT 58.343 36.000 6.63 0.00 31.98 4.00
677 707 2.793278 AAAACAAAACCTAGCGGCTG 57.207 45.000 13.86 0.00 0.00 4.85
773 804 5.352846 CCTCCAAAACGGAAACAAAACAAAT 59.647 36.000 0.00 0.00 45.75 2.32
783 814 6.495706 GGAAACAAAACAAATCTCTCTCGTT 58.504 36.000 0.00 0.00 0.00 3.85
808 839 1.106944 CACCACACCAAACCAGACCC 61.107 60.000 0.00 0.00 0.00 4.46
809 840 1.228793 CCACACCAAACCAGACCCA 59.771 57.895 0.00 0.00 0.00 4.51
820 851 4.453480 AACCAGACCCAGAAAGAAATCA 57.547 40.909 0.00 0.00 0.00 2.57
824 855 4.457257 CCAGACCCAGAAAGAAATCAAGAC 59.543 45.833 0.00 0.00 0.00 3.01
878 909 1.996187 GGGAGGGGGAGACAAGACC 60.996 68.421 0.00 0.00 0.00 3.85
1125 1204 3.084579 CAGATCCTGAACGTGCGC 58.915 61.111 0.00 0.00 32.44 6.09
1218 1297 3.077519 GCTGCCGTACCTCATCCGT 62.078 63.158 0.00 0.00 0.00 4.69
1323 1402 2.488820 GCCTACGTGGACGACCTC 59.511 66.667 6.12 0.18 43.02 3.85
1327 1406 0.392729 CTACGTGGACGACCTCCTCT 60.393 60.000 6.12 0.00 43.02 3.69
1469 1548 4.162690 CTCGCCTAGGTGGGTGGC 62.163 72.222 22.11 0.00 42.94 5.01
1490 1569 1.401931 CCCGTAACTCACAGTACACCG 60.402 57.143 0.00 0.00 0.00 4.94
2042 2131 4.124351 TCGCCCGGTTCTAGCACG 62.124 66.667 0.00 0.00 0.00 5.34
2073 2168 6.352016 AGTGAGAGAGAAGAAATTACTGCA 57.648 37.500 0.00 0.00 0.00 4.41
2151 2265 5.815740 TCTTCTCTGTATTTTTACCGCATCC 59.184 40.000 0.00 0.00 0.00 3.51
2152 2266 4.116961 TCTCTGTATTTTTACCGCATCCG 58.883 43.478 0.00 0.00 0.00 4.18
2153 2267 2.610374 TCTGTATTTTTACCGCATCCGC 59.390 45.455 0.00 0.00 0.00 5.54
2154 2268 2.353269 CTGTATTTTTACCGCATCCGCA 59.647 45.455 0.00 0.00 38.40 5.69
2155 2269 2.946329 TGTATTTTTACCGCATCCGCAT 59.054 40.909 0.00 0.00 38.40 4.73
2156 2270 2.490328 ATTTTTACCGCATCCGCATG 57.510 45.000 0.00 0.00 38.40 4.06
2157 2271 1.454201 TTTTTACCGCATCCGCATGA 58.546 45.000 0.00 0.00 38.40 3.07
2162 2276 0.101040 ACCGCATCCGCATGAATTTG 59.899 50.000 0.00 0.00 38.40 2.32
2174 2288 4.439153 CGCATGAATTTGTACTTGCCTCAT 60.439 41.667 0.00 0.00 34.98 2.90
2265 2379 4.491241 CGTACGAGTACTCATCAGTTTTCG 59.509 45.833 22.37 7.87 40.44 3.46
2280 2394 6.444633 TCAGTTTTCGTCTCTATCTTTTCGT 58.555 36.000 0.00 0.00 0.00 3.85
2421 2536 3.976793 TCGAGACTGTACACGAGTTTT 57.023 42.857 2.49 0.00 0.00 2.43
2422 2537 3.624900 TCGAGACTGTACACGAGTTTTG 58.375 45.455 2.49 0.00 0.00 2.44
2423 2538 2.724690 CGAGACTGTACACGAGTTTTGG 59.275 50.000 0.00 0.00 0.00 3.28
2430 2545 1.594331 ACACGAGTTTTGGCTCCTTC 58.406 50.000 0.00 0.00 32.11 3.46
2448 2563 1.201429 TCCTCTTCTTGTCCTGCCCC 61.201 60.000 0.00 0.00 0.00 5.80
2449 2564 1.204113 CCTCTTCTTGTCCTGCCCCT 61.204 60.000 0.00 0.00 0.00 4.79
2450 2565 0.035630 CTCTTCTTGTCCTGCCCCTG 60.036 60.000 0.00 0.00 0.00 4.45
2451 2566 0.768221 TCTTCTTGTCCTGCCCCTGT 60.768 55.000 0.00 0.00 0.00 4.00
2452 2567 0.607489 CTTCTTGTCCTGCCCCTGTG 60.607 60.000 0.00 0.00 0.00 3.66
2453 2568 2.034687 CTTGTCCTGCCCCTGTGG 59.965 66.667 0.00 0.00 37.09 4.17
2468 2583 3.716195 TGGCCCTGTCCATCCGTG 61.716 66.667 0.00 0.00 0.00 4.94
2469 2584 3.399181 GGCCCTGTCCATCCGTGA 61.399 66.667 0.00 0.00 0.00 4.35
2504 2629 2.612567 CGCTGCCGCAGTGGTTTTA 61.613 57.895 23.67 0.00 38.21 1.52
2513 2638 3.504520 CCGCAGTGGTTTTAAGTGGTAAT 59.495 43.478 0.00 0.00 0.00 1.89
2517 2642 6.074569 CGCAGTGGTTTTAAGTGGTAATTTTG 60.075 38.462 0.00 0.00 0.00 2.44
2518 2643 6.292649 GCAGTGGTTTTAAGTGGTAATTTTGC 60.293 38.462 0.00 0.00 0.00 3.68
2520 2645 6.099125 AGTGGTTTTAAGTGGTAATTTTGCCT 59.901 34.615 0.00 0.00 33.70 4.75
2521 2646 6.201997 GTGGTTTTAAGTGGTAATTTTGCCTG 59.798 38.462 0.00 0.00 33.70 4.85
2522 2647 6.127026 TGGTTTTAAGTGGTAATTTTGCCTGT 60.127 34.615 0.00 0.00 33.70 4.00
2523 2648 6.201997 GGTTTTAAGTGGTAATTTTGCCTGTG 59.798 38.462 0.00 0.00 33.70 3.66
2524 2649 3.385193 AAGTGGTAATTTTGCCTGTGC 57.615 42.857 0.00 0.00 33.70 4.57
2525 2650 2.597455 AGTGGTAATTTTGCCTGTGCT 58.403 42.857 0.00 0.00 38.71 4.40
2557 2688 3.159213 TCCCATAATCATCACCCATGC 57.841 47.619 0.00 0.00 31.70 4.06
2566 2697 2.696187 TCATCACCCATGCCATCATTTG 59.304 45.455 0.00 0.00 31.70 2.32
2570 2701 2.759535 CACCCATGCCATCATTTGTGTA 59.240 45.455 0.00 0.00 31.76 2.90
2571 2702 2.760092 ACCCATGCCATCATTTGTGTAC 59.240 45.455 0.00 0.00 0.00 2.90
2572 2703 3.025978 CCCATGCCATCATTTGTGTACT 58.974 45.455 0.00 0.00 0.00 2.73
2573 2704 3.181484 CCCATGCCATCATTTGTGTACTG 60.181 47.826 0.00 0.00 0.00 2.74
2579 2710 4.665212 CCATCATTTGTGTACTGTGCATC 58.335 43.478 1.04 0.00 0.00 3.91
2600 2731 3.493129 TCAGCATAATCGCGTTTGGATAC 59.507 43.478 12.54 0.00 36.85 2.24
2606 2737 2.436795 CGCGTTTGGATACGTGTGA 58.563 52.632 0.00 0.00 44.53 3.58
2607 2738 0.092351 CGCGTTTGGATACGTGTGAC 59.908 55.000 0.00 0.00 44.53 3.67
2608 2739 0.441145 GCGTTTGGATACGTGTGACC 59.559 55.000 0.00 0.00 43.22 4.02
2609 2740 1.073177 CGTTTGGATACGTGTGACCC 58.927 55.000 0.00 0.00 42.51 4.46
2614 2745 1.153706 GATACGTGTGACCCCACCG 60.154 63.158 0.00 0.00 42.53 4.94
2672 2803 1.515020 CTGGAGAAGGACGGAGCTG 59.485 63.158 0.00 0.00 0.00 4.24
2674 2805 2.185608 GAGAAGGACGGAGCTGCC 59.814 66.667 0.00 0.00 0.00 4.85
2675 2806 2.604686 AGAAGGACGGAGCTGCCA 60.605 61.111 0.00 0.00 35.94 4.92
2700 2831 4.160329 CTCCTATGGCTGAGTATAACCCA 58.840 47.826 0.00 0.00 0.00 4.51
2838 2971 1.813178 GAGGAAAAAGAAGAAGGCCCG 59.187 52.381 0.00 0.00 0.00 6.13
2840 2973 0.243907 GAAAAAGAAGAAGGCCCGGC 59.756 55.000 0.00 0.00 0.00 6.13
2897 3030 2.503375 CGGTGGTGACTCGTACGC 60.503 66.667 11.24 0.00 0.00 4.42
2902 3035 1.300266 TGGTGACTCGTACGCGATCA 61.300 55.000 15.93 11.56 46.80 2.92
2915 3050 3.116300 ACGCGATCATCTTGTCATGTAC 58.884 45.455 15.93 0.00 0.00 2.90
2936 3071 0.249447 CAGGCGTGACAAGACAGTCA 60.249 55.000 0.00 0.00 45.64 3.41
2976 3111 0.895530 TGCTCCACTGCACCTACTAC 59.104 55.000 0.00 0.00 38.12 2.73
2977 3112 1.187087 GCTCCACTGCACCTACTACT 58.813 55.000 0.00 0.00 0.00 2.57
2978 3113 1.550976 GCTCCACTGCACCTACTACTT 59.449 52.381 0.00 0.00 0.00 2.24
2979 3114 2.028020 GCTCCACTGCACCTACTACTTT 60.028 50.000 0.00 0.00 0.00 2.66
2980 3115 3.194968 GCTCCACTGCACCTACTACTTTA 59.805 47.826 0.00 0.00 0.00 1.85
2981 3116 4.141914 GCTCCACTGCACCTACTACTTTAT 60.142 45.833 0.00 0.00 0.00 1.40
2982 3117 5.627040 GCTCCACTGCACCTACTACTTTATT 60.627 44.000 0.00 0.00 0.00 1.40
2983 3118 6.406624 GCTCCACTGCACCTACTACTTTATTA 60.407 42.308 0.00 0.00 0.00 0.98
2984 3119 7.108841 TCCACTGCACCTACTACTTTATTAG 57.891 40.000 0.00 0.00 0.00 1.73
2985 3120 6.097839 TCCACTGCACCTACTACTTTATTAGG 59.902 42.308 0.00 0.00 37.18 2.69
2986 3121 6.127140 CCACTGCACCTACTACTTTATTAGGT 60.127 42.308 0.00 0.00 42.88 3.08
2987 3122 7.328737 CACTGCACCTACTACTTTATTAGGTT 58.671 38.462 0.00 0.00 40.25 3.50
2988 3123 7.822822 CACTGCACCTACTACTTTATTAGGTTT 59.177 37.037 0.00 0.00 40.25 3.27
2989 3124 9.039165 ACTGCACCTACTACTTTATTAGGTTTA 57.961 33.333 0.00 0.00 40.25 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 46 8.899887 ACAAAAAGGCCATGGCTATATATTAT 57.100 30.769 34.70 10.58 37.50 1.28
53 55 0.397564 CCAACAAAAAGGCCATGGCT 59.602 50.000 34.70 18.82 41.24 4.75
55 57 1.055040 TCCCAACAAAAAGGCCATGG 58.945 50.000 7.63 7.63 0.00 3.66
58 60 3.721087 TTTTTCCCAACAAAAAGGCCA 57.279 38.095 5.01 0.00 31.65 5.36
83 85 4.067896 AGTGCATTTTCAGACGACTTGAT 58.932 39.130 0.00 0.00 0.00 2.57
125 137 6.037098 CCAAATTGTACGTTTGAAACTCCAA 58.963 36.000 19.39 6.46 38.51 3.53
127 139 5.584442 ACCAAATTGTACGTTTGAAACTCC 58.416 37.500 19.39 0.00 38.51 3.85
129 141 9.589111 AAAATACCAAATTGTACGTTTGAAACT 57.411 25.926 19.39 0.00 38.51 2.66
139 153 7.722795 AACTGCCAAAAATACCAAATTGTAC 57.277 32.000 0.00 0.00 0.00 2.90
245 266 6.980051 GGTTGTAACCTCATTAAGTACAGG 57.020 41.667 6.54 0.00 45.75 4.00
284 307 8.877195 ACGCTCTTATATTTATTTAAGGAGGGA 58.123 33.333 0.00 0.00 0.00 4.20
285 308 9.503399 AACGCTCTTATATTTATTTAAGGAGGG 57.497 33.333 0.00 0.00 0.00 4.30
297 320 9.601217 AGTAGTGATCAAAACGCTCTTATATTT 57.399 29.630 0.00 0.00 0.00 1.40
298 321 9.601217 AAGTAGTGATCAAAACGCTCTTATATT 57.399 29.630 0.00 0.00 0.00 1.28
299 322 9.601217 AAAGTAGTGATCAAAACGCTCTTATAT 57.399 29.630 0.00 0.00 0.00 0.86
300 323 8.997621 AAAGTAGTGATCAAAACGCTCTTATA 57.002 30.769 0.00 0.00 0.00 0.98
301 324 7.907214 AAAGTAGTGATCAAAACGCTCTTAT 57.093 32.000 0.00 0.00 0.00 1.73
302 325 8.086522 ACTAAAGTAGTGATCAAAACGCTCTTA 58.913 33.333 0.00 0.00 37.69 2.10
303 326 6.929606 ACTAAAGTAGTGATCAAAACGCTCTT 59.070 34.615 0.00 0.00 37.69 2.85
304 327 6.456501 ACTAAAGTAGTGATCAAAACGCTCT 58.543 36.000 0.00 0.00 37.69 4.09
305 328 6.707599 ACTAAAGTAGTGATCAAAACGCTC 57.292 37.500 0.00 0.00 37.69 5.03
335 358 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
336 359 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
337 360 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
338 361 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
341 364 9.984190 GGTACTCCCTCTGTAAAGAAATATAAG 57.016 37.037 0.00 0.00 0.00 1.73
342 365 9.725206 AGGTACTCCCTCTGTAAAGAAATATAA 57.275 33.333 0.00 0.00 40.71 0.98
343 366 9.725206 AAGGTACTCCCTCTGTAAAGAAATATA 57.275 33.333 0.00 0.00 45.47 0.86
344 367 8.625467 AAGGTACTCCCTCTGTAAAGAAATAT 57.375 34.615 0.00 0.00 45.47 1.28
345 368 7.676893 TGAAGGTACTCCCTCTGTAAAGAAATA 59.323 37.037 0.00 0.00 45.47 1.40
346 369 6.500751 TGAAGGTACTCCCTCTGTAAAGAAAT 59.499 38.462 0.00 0.00 45.47 2.17
347 370 5.842328 TGAAGGTACTCCCTCTGTAAAGAAA 59.158 40.000 0.00 0.00 45.47 2.52
348 371 5.399991 TGAAGGTACTCCCTCTGTAAAGAA 58.600 41.667 0.00 0.00 45.47 2.52
349 372 5.006896 TGAAGGTACTCCCTCTGTAAAGA 57.993 43.478 0.00 0.00 45.47 2.52
350 373 5.941555 ATGAAGGTACTCCCTCTGTAAAG 57.058 43.478 0.00 0.00 45.47 1.85
351 374 5.189145 GGAATGAAGGTACTCCCTCTGTAAA 59.811 44.000 0.00 0.00 45.47 2.01
352 375 4.715297 GGAATGAAGGTACTCCCTCTGTAA 59.285 45.833 0.00 0.00 45.47 2.41
353 376 4.264668 TGGAATGAAGGTACTCCCTCTGTA 60.265 45.833 0.00 0.00 45.47 2.74
354 377 3.108376 GGAATGAAGGTACTCCCTCTGT 58.892 50.000 0.00 0.00 45.47 3.41
355 378 3.107601 TGGAATGAAGGTACTCCCTCTG 58.892 50.000 0.00 0.00 45.47 3.35
356 379 3.108376 GTGGAATGAAGGTACTCCCTCT 58.892 50.000 0.00 0.00 45.47 3.69
357 380 2.838202 TGTGGAATGAAGGTACTCCCTC 59.162 50.000 0.00 0.00 45.47 4.30
359 382 3.713826 TTGTGGAATGAAGGTACTCCC 57.286 47.619 0.00 0.00 38.49 4.30
360 383 8.974060 TTATAATTGTGGAATGAAGGTACTCC 57.026 34.615 0.00 0.00 38.49 3.85
363 386 8.504005 CCGATTATAATTGTGGAATGAAGGTAC 58.496 37.037 11.09 0.00 0.00 3.34
364 387 8.433599 TCCGATTATAATTGTGGAATGAAGGTA 58.566 33.333 11.09 0.00 0.00 3.08
365 388 7.287061 TCCGATTATAATTGTGGAATGAAGGT 58.713 34.615 11.09 0.00 0.00 3.50
366 389 7.661437 TCTCCGATTATAATTGTGGAATGAAGG 59.339 37.037 11.09 2.83 0.00 3.46
369 392 8.428852 TCTTCTCCGATTATAATTGTGGAATGA 58.571 33.333 11.09 6.23 0.00 2.57
387 410 6.073003 AGTGCTTGTATTTTCTTTCTTCTCCG 60.073 38.462 0.00 0.00 0.00 4.63
462 488 2.500098 AGGTGACTGGCGAGCTATTTTA 59.500 45.455 0.00 0.00 41.13 1.52
477 504 7.636150 TGGTACAGTACTAGATTAAGGTGAC 57.364 40.000 10.62 0.00 0.00 3.67
541 570 8.531982 ACATCACTGTCTTCTTTATTAGCTGTA 58.468 33.333 0.00 0.00 0.00 2.74
542 571 7.390027 ACATCACTGTCTTCTTTATTAGCTGT 58.610 34.615 0.00 0.00 0.00 4.40
677 707 1.903183 AGGAGAGGCGCCTATAATTCC 59.097 52.381 32.97 27.54 30.33 3.01
773 804 1.666011 GTGTGGGCAACGAGAGAGA 59.334 57.895 0.00 0.00 37.60 3.10
783 814 2.055042 GTTTGGTGTGGTGTGGGCA 61.055 57.895 0.00 0.00 0.00 5.36
808 839 3.126000 GCTCCCGTCTTGATTTCTTTCTG 59.874 47.826 0.00 0.00 0.00 3.02
809 840 3.244561 TGCTCCCGTCTTGATTTCTTTCT 60.245 43.478 0.00 0.00 0.00 2.52
820 851 1.294780 CTTGCTCTGCTCCCGTCTT 59.705 57.895 0.00 0.00 0.00 3.01
824 855 4.441695 TCGCTTGCTCTGCTCCCG 62.442 66.667 0.00 0.00 0.00 5.14
878 909 2.727123 TGGCTACCTCTCTCTCTCTG 57.273 55.000 0.00 0.00 0.00 3.35
973 1028 2.325393 CTGACTTGGGATACGGGGCC 62.325 65.000 0.00 0.00 37.60 5.80
978 1033 1.743958 AGACGACTGACTTGGGATACG 59.256 52.381 0.00 0.00 37.60 3.06
1323 1402 2.725008 GCGTCGAGGATGGAGAGG 59.275 66.667 9.75 0.00 0.00 3.69
1327 1406 3.889044 GAGCGCGTCGAGGATGGA 61.889 66.667 8.43 0.00 0.00 3.41
1469 1548 1.067354 GGTGTACTGTGAGTTACGGGG 60.067 57.143 0.00 0.00 40.13 5.73
1470 1549 1.401931 CGGTGTACTGTGAGTTACGGG 60.402 57.143 0.00 0.00 40.13 5.28
1471 1550 1.973138 CGGTGTACTGTGAGTTACGG 58.027 55.000 0.00 0.00 41.64 4.02
1472 1551 1.334054 GCGGTGTACTGTGAGTTACG 58.666 55.000 0.00 0.00 0.00 3.18
1477 1556 0.525668 GATCGGCGGTGTACTGTGAG 60.526 60.000 7.21 0.00 0.00 3.51
1510 1589 8.184848 GCAAGGAAAGGAAAGACTATAATTGAC 58.815 37.037 0.00 0.00 0.00 3.18
1559 1648 4.098807 TCGATTGATTGATTACTCCGGTCA 59.901 41.667 0.00 0.00 0.00 4.02
1592 1681 1.923204 CAAGAACCTGCTCGAAGATCG 59.077 52.381 0.00 0.00 42.10 3.69
1593 1682 3.238108 TCAAGAACCTGCTCGAAGATC 57.762 47.619 0.00 0.00 33.89 2.75
1594 1683 3.330267 GTTCAAGAACCTGCTCGAAGAT 58.670 45.455 1.51 0.00 35.36 2.40
1595 1684 2.755650 GTTCAAGAACCTGCTCGAAGA 58.244 47.619 1.51 0.00 35.36 2.87
1596 1685 1.457303 CGTTCAAGAACCTGCTCGAAG 59.543 52.381 7.32 0.00 38.03 3.79
1597 1686 1.067974 TCGTTCAAGAACCTGCTCGAA 59.932 47.619 7.32 0.00 38.03 3.71
1598 1687 0.671796 TCGTTCAAGAACCTGCTCGA 59.328 50.000 7.32 0.00 38.03 4.04
1912 2001 2.285442 AGGTGGGCCCTGAGGTAC 60.285 66.667 25.70 11.64 44.08 3.34
2112 2209 3.959449 AGAGAAGAAATACGGGGTAGACC 59.041 47.826 0.00 0.00 39.11 3.85
2151 2265 3.119884 TGAGGCAAGTACAAATTCATGCG 60.120 43.478 0.00 0.00 34.73 4.73
2152 2266 4.439305 TGAGGCAAGTACAAATTCATGC 57.561 40.909 0.00 0.00 0.00 4.06
2153 2267 7.281774 AGTCTATGAGGCAAGTACAAATTCATG 59.718 37.037 0.00 0.00 0.00 3.07
2154 2268 7.341805 AGTCTATGAGGCAAGTACAAATTCAT 58.658 34.615 0.00 0.82 0.00 2.57
2155 2269 6.711277 AGTCTATGAGGCAAGTACAAATTCA 58.289 36.000 0.00 0.00 0.00 2.57
2156 2270 6.019479 CGAGTCTATGAGGCAAGTACAAATTC 60.019 42.308 0.00 0.00 0.00 2.17
2157 2271 5.812642 CGAGTCTATGAGGCAAGTACAAATT 59.187 40.000 0.00 0.00 0.00 1.82
2162 2276 2.950309 TCCGAGTCTATGAGGCAAGTAC 59.050 50.000 0.00 0.00 0.00 2.73
2174 2288 3.369471 CCTGGCATTTTCTTCCGAGTCTA 60.369 47.826 0.00 0.00 0.00 2.59
2265 2379 8.522178 TTTCTTCTCAACGAAAAGATAGAGAC 57.478 34.615 0.00 0.00 32.41 3.36
2394 2509 2.472560 CGTGTACAGTCTCGAACTCTCG 60.473 54.545 0.00 0.00 46.87 4.04
2411 2526 1.594331 GAAGGAGCCAAAACTCGTGT 58.406 50.000 0.00 0.00 37.57 4.49
2412 2527 0.875059 GGAAGGAGCCAAAACTCGTG 59.125 55.000 0.00 0.00 37.57 4.35
2421 2536 1.625818 GACAAGAAGAGGAAGGAGCCA 59.374 52.381 0.00 0.00 0.00 4.75
2422 2537 1.065782 GGACAAGAAGAGGAAGGAGCC 60.066 57.143 0.00 0.00 0.00 4.70
2423 2538 1.905894 AGGACAAGAAGAGGAAGGAGC 59.094 52.381 0.00 0.00 0.00 4.70
2430 2545 1.204113 AGGGGCAGGACAAGAAGAGG 61.204 60.000 0.00 0.00 0.00 3.69
2448 2563 2.273449 GGATGGACAGGGCCACAG 59.727 66.667 6.18 0.00 41.56 3.66
2449 2564 3.716195 CGGATGGACAGGGCCACA 61.716 66.667 6.18 0.00 41.56 4.17
2450 2565 3.717294 ACGGATGGACAGGGCCAC 61.717 66.667 6.18 0.00 41.56 5.01
2451 2566 3.716195 CACGGATGGACAGGGCCA 61.716 66.667 6.18 0.00 43.23 5.36
2452 2567 3.399181 TCACGGATGGACAGGGCC 61.399 66.667 0.00 0.00 0.00 5.80
2453 2568 2.125106 GTCACGGATGGACAGGGC 60.125 66.667 0.00 0.00 35.36 5.19
2454 2569 3.387716 TGTCACGGATGGACAGGG 58.612 61.111 0.00 0.00 40.16 4.45
2492 2608 4.759516 ATTACCACTTAAAACCACTGCG 57.240 40.909 0.00 0.00 0.00 5.18
2504 2629 2.965147 AGCACAGGCAAAATTACCACTT 59.035 40.909 0.00 0.00 44.61 3.16
2522 2647 8.257602 TGATTATGGGATACTAGTGTTTAGCA 57.742 34.615 5.39 0.00 0.00 3.49
2523 2648 9.372369 GATGATTATGGGATACTAGTGTTTAGC 57.628 37.037 5.39 0.00 0.00 3.09
2537 2662 2.225091 GGCATGGGTGATGATTATGGGA 60.225 50.000 0.00 0.00 33.31 4.37
2538 2663 2.173519 GGCATGGGTGATGATTATGGG 58.826 52.381 0.00 0.00 33.31 4.00
2539 2664 2.879154 TGGCATGGGTGATGATTATGG 58.121 47.619 0.00 0.00 33.31 2.74
2540 2665 4.083565 TGATGGCATGGGTGATGATTATG 58.916 43.478 3.81 0.00 33.31 1.90
2541 2666 4.391683 TGATGGCATGGGTGATGATTAT 57.608 40.909 3.81 0.00 33.31 1.28
2543 2668 2.759839 TGATGGCATGGGTGATGATT 57.240 45.000 3.81 0.00 33.31 2.57
2544 2669 2.992847 ATGATGGCATGGGTGATGAT 57.007 45.000 3.81 0.00 33.31 2.45
2551 2682 3.025978 AGTACACAAATGATGGCATGGG 58.974 45.455 3.81 0.00 34.26 4.00
2557 2688 4.156373 TGATGCACAGTACACAAATGATGG 59.844 41.667 0.00 0.00 0.00 3.51
2579 2710 3.661678 CGTATCCAAACGCGATTATGCTG 60.662 47.826 15.93 0.00 35.87 4.41
2588 2719 0.092351 GTCACACGTATCCAAACGCG 59.908 55.000 3.53 3.53 46.71 6.01
2589 2720 0.441145 GGTCACACGTATCCAAACGC 59.559 55.000 0.00 0.00 46.71 4.84
2591 2722 1.270947 TGGGGTCACACGTATCCAAAC 60.271 52.381 0.00 0.00 0.00 2.93
2604 2735 2.203422 CTTTTGGCGGTGGGGTCA 60.203 61.111 0.00 0.00 0.00 4.02
2605 2736 1.110518 TTTCTTTTGGCGGTGGGGTC 61.111 55.000 0.00 0.00 0.00 4.46
2606 2737 0.688087 TTTTCTTTTGGCGGTGGGGT 60.688 50.000 0.00 0.00 0.00 4.95
2607 2738 0.466124 TTTTTCTTTTGGCGGTGGGG 59.534 50.000 0.00 0.00 0.00 4.96
2627 2758 9.807649 GACTTATCCAAATGCAATTGTATTTCT 57.192 29.630 25.76 17.40 38.07 2.52
2628 2759 9.034544 GGACTTATCCAAATGCAATTGTATTTC 57.965 33.333 25.76 15.04 45.47 2.17
2629 2760 8.947055 GGACTTATCCAAATGCAATTGTATTT 57.053 30.769 23.71 23.71 45.47 1.40
2897 3030 4.981054 CCTGAGTACATGACAAGATGATCG 59.019 45.833 0.00 0.00 0.00 3.69
2902 3035 2.497675 ACGCCTGAGTACATGACAAGAT 59.502 45.455 0.00 0.00 0.00 2.40
2915 3050 0.032678 ACTGTCTTGTCACGCCTGAG 59.967 55.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.