Multiple sequence alignment - TraesCS3B01G343000

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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 TraesCS3B01G343000 chr3B 100.000 3545 0 0 1 3545 550982193 550978649 0.000000e+00 6547.0
1 TraesCS3B01G343000 chr3D 93.698 2888 129 27 1 2864 422732406 422729548 0.000000e+00 4276.0
2 TraesCS3B01G343000 chr3D 89.147 258 23 5 3290 3545 422728549 422728295 2.050000e-82 316.0
3 TraesCS3B01G343000 chr3A 92.054 1850 75 31 1 1808 566138201 566140020 0.000000e+00 2536.0
4 TraesCS3B01G343000 chr3A 89.479 1017 80 18 1829 2830 566140111 566141115 0.000000e+00 1260.0
5 TraesCS3B01G343000 chr3A 89.541 545 49 4 2508 3045 566202983 566203526 0.000000e+00 684.0
6 TraesCS3B01G343000 chr3A 88.396 293 22 8 3254 3535 566244207 566244498 3.390000e-90 342.0
7 TraesCS3B01G343000 chr3A 87.365 277 23 8 3254 3519 566142601 566142876 1.240000e-79 307.0
8 TraesCS3B01G343000 chr2B 89.831 59 4 2 2928 2984 767484963 767484905 1.360000e-09 75.0
9 TraesCS3B01G343000 chr4D 96.970 33 1 0 2951 2983 474938827 474938859 4.940000e-04 56.5


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 TraesCS3B01G343000 chr3B 550978649 550982193 3544 True 6547.000000 6547 100.000000 1 3545 1 chr3B.!!$R1 3544
1 TraesCS3B01G343000 chr3D 422728295 422732406 4111 True 2296.000000 4276 91.422500 1 3545 2 chr3D.!!$R1 3544
2 TraesCS3B01G343000 chr3A 566138201 566142876 4675 False 1367.666667 2536 89.632667 1 3519 3 chr3A.!!$F3 3518
3 TraesCS3B01G343000 chr3A 566202983 566203526 543 False 684.000000 684 89.541000 2508 3045 1 chr3A.!!$F1 537

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
365 369 0.037326 GACCGGAGCTGTTCATCACA 60.037 55.0 9.46 0.0 0.00 3.58 F
1866 1987 0.109342 ACTGACCAACTCCTTGCTGG 59.891 55.0 0.00 0.0 37.89 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2195 0.095245 CGCACGTATTCACCTTGCTG 59.905 55.0 0.0 0.0 31.04 4.41 R
2901 3663 0.099436 CCATAGCAACAAAGCCGAGC 59.901 55.0 0.0 0.0 34.23 5.03 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
119 120 7.867403 AGGCAGTTTTGTTTTGTATGAACTATG 59.133 33.333 0.00 0.00 0.00 2.23
222 226 3.253677 AGGTATCGTCGAAGATTGCTAGG 59.746 47.826 18.90 0.00 40.67 3.02
263 267 4.817318 AGAGGTTTTTGCCACAGAAAAA 57.183 36.364 0.00 0.00 31.43 1.94
309 313 1.344114 GCAAAAACAGGCCAATCTCCA 59.656 47.619 5.01 0.00 0.00 3.86
362 366 1.519455 CCGACCGGAGCTGTTCATC 60.519 63.158 9.46 0.00 37.50 2.92
364 368 1.078759 CGACCGGAGCTGTTCATCAC 61.079 60.000 9.46 0.00 0.00 3.06
365 369 0.037326 GACCGGAGCTGTTCATCACA 60.037 55.000 9.46 0.00 0.00 3.58
381 385 9.154847 TGTTCATCACAAGTGACTATAATTCTG 57.845 33.333 4.84 0.00 43.11 3.02
382 386 8.607459 GTTCATCACAAGTGACTATAATTCTGG 58.393 37.037 4.84 0.00 43.11 3.86
555 567 0.951558 AAACGTAGGTGCCTTGCAAG 59.048 50.000 19.93 19.93 41.47 4.01
561 573 3.225798 GTGCCTTGCAAGCCCACA 61.226 61.111 28.72 18.76 41.47 4.17
578 590 2.779282 CATGTACCCATGCAAGCGA 58.221 52.632 0.00 0.00 41.88 4.93
579 591 1.093972 CATGTACCCATGCAAGCGAA 58.906 50.000 0.00 0.00 41.88 4.70
861 882 0.885879 CCGGACCCAGCCTTAAAAAC 59.114 55.000 0.00 0.00 0.00 2.43
936 965 4.140994 ACTTGTCCCCTTCTCGATATCCTA 60.141 45.833 0.00 0.00 0.00 2.94
975 1004 2.490217 CGTGCGTGCTAGCTAGGT 59.510 61.111 22.10 0.00 38.13 3.08
1241 1276 3.294214 CCTCCTACCAGGTACGTACATT 58.706 50.000 26.02 11.66 36.53 2.71
1246 1282 2.250031 ACCAGGTACGTACATTCCACA 58.750 47.619 26.02 0.00 0.00 4.17
1248 1284 3.118884 ACCAGGTACGTACATTCCACATC 60.119 47.826 26.02 6.40 0.00 3.06
1258 1294 2.305927 ACATTCCACATCTCCTCCGTTT 59.694 45.455 0.00 0.00 0.00 3.60
1710 1756 2.079925 GAAGCGCTCAAGAACTTCCAT 58.920 47.619 12.06 0.00 33.90 3.41
1852 1973 2.917971 GAGCACTACGTGATGAACTGAC 59.082 50.000 0.00 0.00 35.23 3.51
1866 1987 0.109342 ACTGACCAACTCCTTGCTGG 59.891 55.000 0.00 0.00 37.89 4.85
2017 2138 2.611800 TCATGCAGGAGGGTGGCT 60.612 61.111 0.00 0.00 0.00 4.75
2074 2195 1.003349 CATGGCCTGATCCTCTCCATC 59.997 57.143 3.32 0.00 35.51 3.51
2090 2214 2.236146 TCCATCAGCAAGGTGAATACGT 59.764 45.455 6.02 0.00 0.00 3.57
2096 2220 1.004320 AAGGTGAATACGTGCGGCA 60.004 52.632 0.00 0.00 0.00 5.69
2097 2221 1.296056 AAGGTGAATACGTGCGGCAC 61.296 55.000 22.78 22.78 0.00 5.01
2110 2234 2.482374 GGCACGCGACGTACTACT 59.518 61.111 15.93 0.00 38.32 2.57
2111 2235 1.866496 GGCACGCGACGTACTACTG 60.866 63.158 15.93 0.00 38.32 2.74
2112 2236 1.866496 GCACGCGACGTACTACTGG 60.866 63.158 15.93 0.00 38.32 4.00
2113 2237 1.499056 CACGCGACGTACTACTGGT 59.501 57.895 15.93 0.00 38.32 4.00
2114 2238 0.110056 CACGCGACGTACTACTGGTT 60.110 55.000 15.93 0.00 38.32 3.67
2115 2239 0.166814 ACGCGACGTACTACTGGTTC 59.833 55.000 15.93 0.00 38.73 3.62
2117 2241 1.202110 CGCGACGTACTACTGGTTCAT 60.202 52.381 0.00 0.00 0.00 2.57
2133 2259 2.800544 GTTCATGTTCACGTGTACTGCT 59.199 45.455 23.25 8.02 32.57 4.24
2135 2261 3.571571 TCATGTTCACGTGTACTGCTAC 58.428 45.455 23.25 9.08 34.59 3.58
2136 2262 3.254903 TCATGTTCACGTGTACTGCTACT 59.745 43.478 23.25 2.18 34.59 2.57
2138 2264 3.635331 TGTTCACGTGTACTGCTACTTC 58.365 45.455 23.25 0.00 0.00 3.01
2139 2265 2.985139 GTTCACGTGTACTGCTACTTCC 59.015 50.000 16.51 0.00 0.00 3.46
2141 2267 2.624364 TCACGTGTACTGCTACTTCCAA 59.376 45.455 16.51 0.00 0.00 3.53
2143 2269 2.288640 ACGTGTACTGCTACTTCCAACC 60.289 50.000 0.00 0.00 0.00 3.77
2145 2271 3.554337 CGTGTACTGCTACTTCCAACCTT 60.554 47.826 0.00 0.00 0.00 3.50
2146 2272 4.321452 CGTGTACTGCTACTTCCAACCTTA 60.321 45.833 0.00 0.00 0.00 2.69
2147 2273 4.928020 GTGTACTGCTACTTCCAACCTTAC 59.072 45.833 0.00 0.00 0.00 2.34
2149 2275 3.248888 ACTGCTACTTCCAACCTTACCT 58.751 45.455 0.00 0.00 0.00 3.08
2150 2276 3.651423 ACTGCTACTTCCAACCTTACCTT 59.349 43.478 0.00 0.00 0.00 3.50
2151 2277 4.003648 CTGCTACTTCCAACCTTACCTTG 58.996 47.826 0.00 0.00 0.00 3.61
2167 2301 0.861837 CTTGACTTGCAGGTGACGAC 59.138 55.000 6.05 0.00 0.00 4.34
2238 2372 1.348064 CAAGGAGTGGGTGGTGAGTA 58.652 55.000 0.00 0.00 0.00 2.59
2242 2376 0.526662 GAGTGGGTGGTGAGTACTCG 59.473 60.000 17.85 0.00 0.00 4.18
2243 2377 0.111832 AGTGGGTGGTGAGTACTCGA 59.888 55.000 17.85 4.78 0.00 4.04
2249 2383 2.614983 GGTGGTGAGTACTCGATCTCTC 59.385 54.545 17.85 6.39 0.00 3.20
2284 2418 5.566429 GCAGATAGATGTCCTCGATCATGTT 60.566 44.000 0.00 0.00 38.18 2.71
2290 2424 3.073678 TGTCCTCGATCATGTTGGTTTG 58.926 45.455 0.00 0.00 0.00 2.93
2291 2425 2.083774 TCCTCGATCATGTTGGTTTGC 58.916 47.619 0.00 0.00 0.00 3.68
2292 2426 1.202065 CCTCGATCATGTTGGTTTGCG 60.202 52.381 0.00 0.00 0.00 4.85
2293 2427 1.464608 CTCGATCATGTTGGTTTGCGT 59.535 47.619 0.00 0.00 0.00 5.24
2294 2428 1.876799 TCGATCATGTTGGTTTGCGTT 59.123 42.857 0.00 0.00 0.00 4.84
2349 2483 4.383861 CAGGACTCGGCTGCTGCA 62.384 66.667 17.89 0.88 41.91 4.41
2493 2627 4.218578 CGAGAGGCGGATGCTGCT 62.219 66.667 0.00 0.00 42.25 4.24
2496 2630 4.853050 GAGGCGGATGCTGCTGCT 62.853 66.667 17.00 2.26 42.25 4.24
2612 2746 4.427312 AGGTGTATGTAAATCGTCGTTCC 58.573 43.478 0.00 0.00 0.00 3.62
2674 2811 4.385825 TCTGTTATGACGAAGCTTGGTTT 58.614 39.130 15.69 9.04 0.00 3.27
2743 2880 2.155539 GCTTGTTTTGGCTGCGTATTTG 59.844 45.455 0.00 0.00 0.00 2.32
2746 2883 1.000394 GTTTTGGCTGCGTATTTGGGT 60.000 47.619 0.00 0.00 0.00 4.51
2762 2899 1.111277 GGGTGGTGCTTTGAGTTTGT 58.889 50.000 0.00 0.00 0.00 2.83
2872 3634 2.448931 AAGTGGGGGTCGGGTCAA 60.449 61.111 0.00 0.00 0.00 3.18
3000 3762 8.953223 AATAGATATAACCTACTTCCTCCGTT 57.047 34.615 0.00 0.00 0.00 4.44
3003 3765 8.773033 AGATATAACCTACTTCCTCCGTTTTA 57.227 34.615 0.00 0.00 0.00 1.52
3036 3798 8.567285 AAGTCCTTTTGAAGATTTCGATACAT 57.433 30.769 0.00 0.00 0.00 2.29
3038 3800 9.319143 AGTCCTTTTGAAGATTTCGATACATAG 57.681 33.333 0.00 0.00 0.00 2.23
3039 3801 9.314321 GTCCTTTTGAAGATTTCGATACATAGA 57.686 33.333 0.00 0.00 0.00 1.98
3040 3802 9.314321 TCCTTTTGAAGATTTCGATACATAGAC 57.686 33.333 0.00 0.00 0.00 2.59
3041 3803 9.098355 CCTTTTGAAGATTTCGATACATAGACA 57.902 33.333 0.00 0.00 0.00 3.41
3080 3853 8.492673 AATTCATTTTGCTTCGTATCTAGTCA 57.507 30.769 0.00 0.00 0.00 3.41
3081 3854 8.668510 ATTCATTTTGCTTCGTATCTAGTCAT 57.331 30.769 0.00 0.00 0.00 3.06
3083 3856 9.594478 TTCATTTTGCTTCGTATCTAGTCATTA 57.406 29.630 0.00 0.00 0.00 1.90
3084 3857 9.764363 TCATTTTGCTTCGTATCTAGTCATTAT 57.236 29.630 0.00 0.00 0.00 1.28
3089 3862 7.145985 TGCTTCGTATCTAGTCATTATTGGAC 58.854 38.462 0.00 0.00 35.50 4.02
3090 3863 7.014326 TGCTTCGTATCTAGTCATTATTGGACT 59.986 37.037 0.00 0.00 46.71 3.85
3091 3864 8.512956 GCTTCGTATCTAGTCATTATTGGACTA 58.487 37.037 0.00 0.00 43.50 2.59
3102 3875 9.427821 AGTCATTATTGGACTAGAGAGTATGTT 57.572 33.333 0.00 0.00 43.50 2.71
3247 4083 8.675040 GCTAGTTTAGCCTGAAAAATGTTTAG 57.325 34.615 0.00 0.00 45.95 1.85
3248 4084 7.755373 GCTAGTTTAGCCTGAAAAATGTTTAGG 59.245 37.037 0.00 0.00 45.95 2.69
3249 4085 6.993079 AGTTTAGCCTGAAAAATGTTTAGGG 58.007 36.000 0.00 0.14 0.00 3.53
3251 4087 7.726738 AGTTTAGCCTGAAAAATGTTTAGGGTA 59.273 33.333 2.21 2.21 39.68 3.69
3257 4733 8.691797 GCCTGAAAAATGTTTAGGGTATGATAA 58.308 33.333 0.00 0.00 0.00 1.75
3284 4760 8.375493 TGTTTAGGGTAACTAGATGATGTCTT 57.625 34.615 0.00 0.00 38.42 3.01
3285 4761 8.475639 TGTTTAGGGTAACTAGATGATGTCTTC 58.524 37.037 0.00 0.00 38.42 2.87
3286 4762 8.697292 GTTTAGGGTAACTAGATGATGTCTTCT 58.303 37.037 0.00 4.19 38.42 2.85
3287 4763 6.723298 AGGGTAACTAGATGATGTCTTCTG 57.277 41.667 0.00 2.80 38.42 3.02
3288 4764 6.436027 AGGGTAACTAGATGATGTCTTCTGA 58.564 40.000 0.00 0.00 38.42 3.27
3333 4818 2.981302 CATGTCCCGCCTCACTCA 59.019 61.111 0.00 0.00 0.00 3.41
3334 4819 1.448540 CATGTCCCGCCTCACTCAC 60.449 63.158 0.00 0.00 0.00 3.51
3345 4830 4.159321 CCGCCTCACTCACATGATATATCT 59.841 45.833 13.79 0.00 0.00 1.98
3346 4831 5.100943 CGCCTCACTCACATGATATATCTG 58.899 45.833 13.79 11.23 0.00 2.90
3347 4832 5.105997 CGCCTCACTCACATGATATATCTGA 60.106 44.000 13.79 8.31 0.00 3.27
3348 4833 6.405619 CGCCTCACTCACATGATATATCTGAT 60.406 42.308 13.79 0.00 0.00 2.90
3349 4834 6.757478 GCCTCACTCACATGATATATCTGATG 59.243 42.308 13.79 11.75 0.00 3.07
3369 4854 6.632909 TGATGCACCATCAAGAAAATAAAGG 58.367 36.000 5.49 0.00 46.17 3.11
3374 4859 6.372381 GCACCATCAAGAAAATAAAGGCATTT 59.628 34.615 0.53 0.53 0.00 2.32
3529 5015 0.529992 CGAATAAGACGGGGTGAGGC 60.530 60.000 0.00 0.00 0.00 4.70
3536 5022 1.952102 GACGGGGTGAGGCGATTACA 61.952 60.000 0.00 0.00 0.00 2.41
3538 5024 0.179056 CGGGGTGAGGCGATTACATT 60.179 55.000 0.00 0.00 0.00 2.71
3542 5028 3.244422 GGGGTGAGGCGATTACATTGATA 60.244 47.826 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.977627 TGCTCAGTGGGACATCCGAT 60.978 55.000 0.00 0.00 44.52 4.18
119 120 2.295885 CTGATCCAAGCAACATCCCTC 58.704 52.381 0.00 0.00 0.00 4.30
222 226 7.044798 ACCTCTATGAACTGAAAGAAGCATAC 58.955 38.462 0.00 0.00 37.43 2.39
263 267 3.390311 AGTTGGAACTACGAACCCTCTTT 59.610 43.478 0.00 0.00 37.82 2.52
264 268 2.970640 AGTTGGAACTACGAACCCTCTT 59.029 45.455 0.00 0.00 37.82 2.85
281 285 2.746362 TGGCCTGTTTTTGCAAAAGTTG 59.254 40.909 22.78 15.97 0.00 3.16
309 313 0.694771 TGGCCTTGCAAGATCAGAGT 59.305 50.000 28.05 0.00 0.00 3.24
339 343 3.062466 CAGCTCCGGTCGGTCTGA 61.062 66.667 20.48 0.00 38.33 3.27
398 403 8.378172 TCAGACAGGTGTGAATTTTAACTAAG 57.622 34.615 0.00 0.00 29.36 2.18
407 412 8.105829 AGAATCTTTATCAGACAGGTGTGAATT 58.894 33.333 3.25 0.00 36.43 2.17
478 483 4.832248 TGACAAAGTCAACACTGAGAACT 58.168 39.130 0.00 0.00 39.78 3.01
561 573 1.832883 TTTCGCTTGCATGGGTACAT 58.167 45.000 14.99 0.00 37.99 2.29
579 591 2.874849 CCTCGCAGTGTTGTTGTTTTT 58.125 42.857 0.00 0.00 0.00 1.94
584 596 0.602638 TAGGCCTCGCAGTGTTGTTG 60.603 55.000 9.68 0.00 0.00 3.33
586 598 0.324943 AATAGGCCTCGCAGTGTTGT 59.675 50.000 9.68 0.00 0.00 3.32
587 599 1.009829 GAATAGGCCTCGCAGTGTTG 58.990 55.000 9.68 0.00 0.00 3.33
593 605 1.144716 CAGCAGAATAGGCCTCGCA 59.855 57.895 9.68 0.00 0.00 5.10
852 873 0.519961 CGCGGTGGAGGTTTTTAAGG 59.480 55.000 0.00 0.00 0.00 2.69
861 882 2.049985 GATCGATCGCGGTGGAGG 60.050 66.667 10.53 0.00 38.28 4.30
975 1004 2.434185 GGCCGATGTCGTTCAGCA 60.434 61.111 1.44 0.00 37.74 4.41
1241 1276 0.902531 GGAAACGGAGGAGATGTGGA 59.097 55.000 0.00 0.00 0.00 4.02
1258 1294 3.680156 GCATTTGCTTGGACGGGA 58.320 55.556 0.00 0.00 38.21 5.14
1388 1430 4.193334 CGATCTGGACGCTCCGCA 62.193 66.667 0.00 0.00 40.17 5.69
1431 1473 2.813908 CCTTTCGACCGGCCTTCG 60.814 66.667 15.62 15.62 37.85 3.79
1764 1810 1.707989 TCCAGCTTGTTTGGGATGGTA 59.292 47.619 0.00 0.00 39.67 3.25
1838 1959 2.548067 GGAGTTGGTCAGTTCATCACGT 60.548 50.000 0.00 0.00 0.00 4.49
1866 1987 3.165498 CGTAAGCCTGCGGTTGTC 58.835 61.111 0.00 0.00 0.00 3.18
2017 2138 1.448893 GCAGTTTATCCCGACGGCA 60.449 57.895 8.86 0.00 37.03 5.69
2062 2183 1.767681 ACCTTGCTGATGGAGAGGATC 59.232 52.381 0.00 0.00 0.00 3.36
2063 2184 1.489649 CACCTTGCTGATGGAGAGGAT 59.510 52.381 0.00 0.00 0.00 3.24
2074 2195 0.095245 CGCACGTATTCACCTTGCTG 59.905 55.000 0.00 0.00 31.04 4.41
2096 2220 0.166814 GAACCAGTAGTACGTCGCGT 59.833 55.000 5.77 9.64 44.35 6.01
2097 2221 0.166597 TGAACCAGTAGTACGTCGCG 59.833 55.000 0.00 0.00 0.00 5.87
2098 2222 2.182825 CATGAACCAGTAGTACGTCGC 58.817 52.381 0.00 0.00 0.00 5.19
2099 2223 3.482722 ACATGAACCAGTAGTACGTCG 57.517 47.619 0.00 0.00 0.00 5.12
2100 2224 4.620184 GTGAACATGAACCAGTAGTACGTC 59.380 45.833 0.00 0.00 0.00 4.34
2101 2225 4.553323 GTGAACATGAACCAGTAGTACGT 58.447 43.478 0.00 0.00 0.00 3.57
2102 2226 3.606777 CGTGAACATGAACCAGTAGTACG 59.393 47.826 0.00 0.00 0.00 3.67
2103 2227 4.384846 CACGTGAACATGAACCAGTAGTAC 59.615 45.833 10.90 0.00 0.00 2.73
2104 2228 4.038282 ACACGTGAACATGAACCAGTAGTA 59.962 41.667 25.01 0.00 0.00 1.82
2105 2229 3.181469 ACACGTGAACATGAACCAGTAGT 60.181 43.478 25.01 0.00 0.00 2.73
2106 2230 3.390135 ACACGTGAACATGAACCAGTAG 58.610 45.455 25.01 0.00 0.00 2.57
2107 2231 3.462483 ACACGTGAACATGAACCAGTA 57.538 42.857 25.01 0.00 0.00 2.74
2108 2232 2.325583 ACACGTGAACATGAACCAGT 57.674 45.000 25.01 0.00 0.00 4.00
2109 2233 3.184379 CAGTACACGTGAACATGAACCAG 59.816 47.826 25.01 0.00 0.00 4.00
2110 2234 3.127589 CAGTACACGTGAACATGAACCA 58.872 45.455 25.01 0.00 0.00 3.67
2111 2235 2.096417 GCAGTACACGTGAACATGAACC 60.096 50.000 25.01 0.00 0.00 3.62
2112 2236 2.800544 AGCAGTACACGTGAACATGAAC 59.199 45.455 25.01 8.08 0.00 3.18
2113 2237 3.106242 AGCAGTACACGTGAACATGAA 57.894 42.857 25.01 0.00 0.00 2.57
2114 2238 2.812358 AGCAGTACACGTGAACATGA 57.188 45.000 25.01 0.00 0.00 3.07
2115 2239 3.575630 AGTAGCAGTACACGTGAACATG 58.424 45.455 25.01 15.39 0.00 3.21
2117 2241 3.551454 GGAAGTAGCAGTACACGTGAACA 60.551 47.826 25.01 3.65 0.00 3.18
2133 2259 5.617252 CAAGTCAAGGTAAGGTTGGAAGTA 58.383 41.667 0.00 0.00 0.00 2.24
2135 2261 3.253432 GCAAGTCAAGGTAAGGTTGGAAG 59.747 47.826 0.00 0.00 0.00 3.46
2136 2262 3.219281 GCAAGTCAAGGTAAGGTTGGAA 58.781 45.455 0.00 0.00 0.00 3.53
2138 2264 2.554032 CTGCAAGTCAAGGTAAGGTTGG 59.446 50.000 0.00 0.00 0.00 3.77
2139 2265 2.554032 CCTGCAAGTCAAGGTAAGGTTG 59.446 50.000 0.00 0.00 0.00 3.77
2141 2267 1.774856 ACCTGCAAGTCAAGGTAAGGT 59.225 47.619 0.00 0.00 32.13 3.50
2143 2269 2.808543 GTCACCTGCAAGTCAAGGTAAG 59.191 50.000 0.00 0.00 32.72 2.34
2145 2271 1.270094 CGTCACCTGCAAGTCAAGGTA 60.270 52.381 0.00 0.00 32.72 3.08
2146 2272 0.532862 CGTCACCTGCAAGTCAAGGT 60.533 55.000 0.00 0.00 34.56 3.50
2147 2273 0.249868 TCGTCACCTGCAAGTCAAGG 60.250 55.000 0.00 0.00 0.00 3.61
2149 2275 0.531974 GGTCGTCACCTGCAAGTCAA 60.532 55.000 0.00 0.00 40.00 3.18
2150 2276 1.069090 GGTCGTCACCTGCAAGTCA 59.931 57.895 0.00 0.00 40.00 3.41
2151 2277 0.531974 TTGGTCGTCACCTGCAAGTC 60.532 55.000 0.00 0.00 44.17 3.01
2167 2301 1.082117 GTACACCACGATCGGCTTGG 61.082 60.000 20.98 19.69 41.50 3.61
2238 2372 0.453793 CTGTTGCCGAGAGATCGAGT 59.546 55.000 0.00 0.00 34.64 4.18
2242 2376 2.675519 CAGCTGTTGCCGAGAGATC 58.324 57.895 5.25 0.00 40.80 2.75
2243 2377 4.928398 CAGCTGTTGCCGAGAGAT 57.072 55.556 5.25 0.00 40.80 2.75
2284 2418 2.580867 GCAACGCAACGCAAACCA 60.581 55.556 0.00 0.00 0.00 3.67
2290 2424 3.158813 CGTGATGCAACGCAACGC 61.159 61.111 8.32 0.55 43.62 4.84
2291 2425 2.499520 CCGTGATGCAACGCAACG 60.500 61.111 8.32 6.28 43.62 4.10
2292 2426 1.440353 GTCCGTGATGCAACGCAAC 60.440 57.895 8.32 4.06 43.62 4.17
2293 2427 2.612567 GGTCCGTGATGCAACGCAA 61.613 57.895 8.32 0.00 43.62 4.85
2294 2428 3.047280 GGTCCGTGATGCAACGCA 61.047 61.111 8.32 0.00 44.86 5.24
2415 2549 4.767255 CAGCACCCTCCCACGAGC 62.767 72.222 0.00 0.00 34.49 5.03
2493 2627 2.202878 GTATCTTCGGCCGCAGCA 60.203 61.111 23.51 9.92 42.56 4.41
2496 2630 3.142162 TCGGTATCTTCGGCCGCA 61.142 61.111 23.51 9.50 44.58 5.69
2498 2632 2.126417 ATCGTCGGTATCTTCGGCCG 62.126 60.000 22.12 22.12 46.12 6.13
2499 2633 0.663568 CATCGTCGGTATCTTCGGCC 60.664 60.000 0.00 0.00 0.00 6.13
2503 2637 3.058363 GGGTAGTCATCGTCGGTATCTTC 60.058 52.174 0.00 0.00 0.00 2.87
2504 2638 2.883386 GGGTAGTCATCGTCGGTATCTT 59.117 50.000 0.00 0.00 0.00 2.40
2505 2639 2.106166 AGGGTAGTCATCGTCGGTATCT 59.894 50.000 0.00 0.00 0.00 1.98
2612 2746 0.612732 ACATCACAACAGGGCCATGG 60.613 55.000 23.35 7.63 0.00 3.66
2743 2880 1.111277 ACAAACTCAAAGCACCACCC 58.889 50.000 0.00 0.00 0.00 4.61
2746 2883 2.023673 CCTCACAAACTCAAAGCACCA 58.976 47.619 0.00 0.00 0.00 4.17
2762 2899 3.580895 TGCTGAGTATTACAACCACCTCA 59.419 43.478 0.00 0.00 0.00 3.86
2807 2947 3.447586 TCTCAACCCCTCTCAAACTATCG 59.552 47.826 0.00 0.00 0.00 2.92
2872 3634 3.141398 AGTTTCACTGATGCACGATTGT 58.859 40.909 0.00 0.00 0.00 2.71
2901 3663 0.099436 CCATAGCAACAAAGCCGAGC 59.901 55.000 0.00 0.00 34.23 5.03
2905 3667 3.893326 ATTTCCCATAGCAACAAAGCC 57.107 42.857 0.00 0.00 34.23 4.35
3055 3817 8.492673 TGACTAGATACGAAGCAAAATGAATT 57.507 30.769 0.00 0.00 0.00 2.17
3057 3819 8.492673 AATGACTAGATACGAAGCAAAATGAA 57.507 30.769 0.00 0.00 0.00 2.57
3058 3820 9.764363 ATAATGACTAGATACGAAGCAAAATGA 57.236 29.630 0.00 0.00 0.00 2.57
3223 4059 8.244113 CCCTAAACATTTTTCAGGCTAAACTAG 58.756 37.037 0.00 0.00 0.00 2.57
3241 4077 9.635404 CCCTAAACATTTATCATACCCTAAACA 57.365 33.333 0.00 0.00 0.00 2.83
3242 4078 9.636789 ACCCTAAACATTTATCATACCCTAAAC 57.363 33.333 0.00 0.00 0.00 2.01
3257 4733 8.993424 AGACATCATCTAGTTACCCTAAACATT 58.007 33.333 0.00 0.00 35.15 2.71
3322 4807 2.827800 ATATCATGTGAGTGAGGCGG 57.172 50.000 0.00 0.00 0.00 6.13
3324 4809 6.278172 TCAGATATATCATGTGAGTGAGGC 57.722 41.667 15.08 0.00 0.00 4.70
3333 4818 6.954232 TGATGGTGCATCAGATATATCATGT 58.046 36.000 15.08 0.00 44.60 3.21
3346 4831 5.521372 GCCTTTATTTTCTTGATGGTGCATC 59.479 40.000 0.00 0.00 40.88 3.91
3347 4832 5.046448 TGCCTTTATTTTCTTGATGGTGCAT 60.046 36.000 0.00 0.00 0.00 3.96
3348 4833 4.282957 TGCCTTTATTTTCTTGATGGTGCA 59.717 37.500 0.00 0.00 0.00 4.57
3349 4834 4.819769 TGCCTTTATTTTCTTGATGGTGC 58.180 39.130 0.00 0.00 0.00 5.01
3494 4980 8.074370 CGTCTTATTCGAGTAGGATTGATTGTA 58.926 37.037 3.13 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.