Multiple sequence alignment - TraesCS3D01G379400

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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 TraesCS3D01G379400 chr3D 100.000 4179 0 0 1 4179 496401507 496405685 0.000000e+00 7718.0
1 TraesCS3D01G379400 chr3B 93.339 3543 138 47 708 4179 655418121 655421636 0.000000e+00 5145.0
2 TraesCS3D01G379400 chr3A 91.510 3569 113 63 735 4179 635726929 635730431 0.000000e+00 4737.0
3 TraesCS3D01G379400 chr3A 86.887 755 83 6 1 739 635725738 635726492 0.000000e+00 832.0
4 TraesCS3D01G379400 chr6A 91.416 897 43 15 977 1868 617760997 617760130 0.000000e+00 1199.0
5 TraesCS3D01G379400 chr1D 78.733 442 89 5 2538 2975 363509235 363508795 1.470000e-74 291.0
6 TraesCS3D01G379400 chr1D 83.408 223 25 11 1489 1704 363510694 363510477 3.300000e-46 196.0
7 TraesCS3D01G379400 chr1A 76.943 386 62 22 1333 1704 462619238 462618866 1.190000e-45 195.0
8 TraesCS3D01G379400 chr1A 93.023 43 2 1 301 343 431029501 431029460 1.250000e-05 62.1
9 TraesCS3D01G379400 chr2D 88.710 124 8 3 3404 3527 526253433 526253316 3.370000e-31 147.0
10 TraesCS3D01G379400 chr4D 86.154 65 6 3 1324 1386 69209859 69209922 2.700000e-07 67.6
11 TraesCS3D01G379400 chr6D 81.609 87 8 7 273 355 22239461 22239543 9.700000e-07 65.8
12 TraesCS3D01G379400 chr6D 85.714 56 6 2 307 362 186858606 186858553 1.620000e-04 58.4
13 TraesCS3D01G379400 chr5A 89.362 47 4 1 318 364 337631179 337631224 1.620000e-04 58.4


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 TraesCS3D01G379400 chr3D 496401507 496405685 4178 False 7718.0 7718 100.0000 1 4179 1 chr3D.!!$F1 4178
1 TraesCS3D01G379400 chr3B 655418121 655421636 3515 False 5145.0 5145 93.3390 708 4179 1 chr3B.!!$F1 3471
2 TraesCS3D01G379400 chr3A 635725738 635730431 4693 False 2784.5 4737 89.1985 1 4179 2 chr3A.!!$F1 4178
3 TraesCS3D01G379400 chr6A 617760130 617760997 867 True 1199.0 1199 91.4160 977 1868 1 chr6A.!!$R1 891
4 TraesCS3D01G379400 chr1D 363508795 363510694 1899 True 243.5 291 81.0705 1489 2975 2 chr1D.!!$R1 1486

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
601 617 0.038159 GTGAGTCGGGGACAAGACAG 60.038 60.0 0.00 0.0 39.37 3.51 F
871 1344 0.039764 TCCCTCTCTCTCGCTCCAAA 59.960 55.0 0.00 0.0 0.00 3.28 F
976 1452 0.042881 ACTAACCACCTCCCTCCTCC 59.957 60.0 0.00 0.0 0.00 4.30 F
1227 1740 0.463295 CGAGGCCTACGAGGTGAGTA 60.463 60.0 4.42 0.0 37.80 2.59 F
2793 3881 1.174712 GGCAAGAAGGTGAGCTGCAA 61.175 55.0 1.02 0.0 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 3551 1.439543 ACATTCCCAGGGGATAGAGC 58.560 55.000 8.12 0.0 44.74 4.09 R
2793 3881 0.447011 GATGACCTCGTCGTCGAACT 59.553 55.000 6.19 0.0 45.61 3.01 R
2818 3906 1.481871 TGATCACCTTCTCGTACCCC 58.518 55.000 0.00 0.0 0.00 4.95 R
3119 4210 4.511454 GCTTGCCTCACGTTTCATCATATA 59.489 41.667 0.00 0.0 0.00 0.86 R
3773 4891 0.027979 CACACACACAAGTTGCTCCG 59.972 55.000 1.81 0.0 0.00 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
44 46 4.540824 ACGTACGAAGGTCTAAAGACAAC 58.459 43.478 24.41 2.35 46.47 3.32
46 48 4.977963 CGTACGAAGGTCTAAAGACAACAA 59.022 41.667 10.44 0.00 46.47 2.83
49 51 4.569564 ACGAAGGTCTAAAGACAACAACAC 59.430 41.667 11.98 0.00 46.47 3.32
50 52 4.569162 CGAAGGTCTAAAGACAACAACACA 59.431 41.667 11.98 0.00 46.47 3.72
51 53 5.501897 CGAAGGTCTAAAGACAACAACACAC 60.502 44.000 11.98 0.00 46.47 3.82
58 60 2.331019 GACAACAACACACCACGCCC 62.331 60.000 0.00 0.00 0.00 6.13
67 69 1.375523 CACCACGCCCTAGAACACC 60.376 63.158 0.00 0.00 0.00 4.16
81 83 2.028930 AGAACACCTAAGCCACGAGAAG 60.029 50.000 0.00 0.00 0.00 2.85
154 166 5.347907 GTCTTCACCCGAAACTATAACACAG 59.652 44.000 0.00 0.00 0.00 3.66
170 182 2.103263 ACACAGAGAGGAGAACCACAAC 59.897 50.000 0.00 0.00 38.94 3.32
183 195 2.912771 ACCACAACGATGTTCACAAGA 58.087 42.857 0.00 0.00 37.82 3.02
250 264 2.360852 CCAGCACAAGGCCTCCAG 60.361 66.667 5.23 1.18 46.50 3.86
251 265 2.360852 CAGCACAAGGCCTCCAGG 60.361 66.667 5.23 0.00 46.50 4.45
253 267 1.927527 AGCACAAGGCCTCCAGGAT 60.928 57.895 5.23 0.00 46.50 3.24
254 268 1.000396 GCACAAGGCCTCCAGGATT 60.000 57.895 5.23 0.00 37.39 3.01
259 273 1.984288 AAGGCCTCCAGGATTACCGC 61.984 60.000 5.23 0.00 41.83 5.68
265 279 1.140161 CCAGGATTACCGCGACGAA 59.860 57.895 8.23 0.00 41.83 3.85
283 297 1.993370 GAACACAAACCTCGAGATCCG 59.007 52.381 15.71 0.00 40.25 4.18
284 298 0.389948 ACACAAACCTCGAGATCCGC 60.390 55.000 15.71 0.00 38.37 5.54
356 371 4.096003 CACCCCCTCGTCGCCAAT 62.096 66.667 0.00 0.00 0.00 3.16
382 397 2.248248 CATCCTTACCTATCCGGAGCA 58.752 52.381 11.34 0.00 36.31 4.26
386 401 2.224066 CCTTACCTATCCGGAGCAACAG 60.224 54.545 11.34 1.18 36.31 3.16
388 403 1.227674 CCTATCCGGAGCAACAGCC 60.228 63.158 11.34 0.00 33.16 4.85
389 404 1.227674 CTATCCGGAGCAACAGCCC 60.228 63.158 11.34 0.00 0.00 5.19
414 429 3.554342 CCCTCGGGCCCAGATCTG 61.554 72.222 24.92 16.24 0.00 2.90
430 445 4.007644 TGGCTGACCAGAGCACGG 62.008 66.667 0.47 0.00 42.67 4.94
454 469 4.309950 GGTCAGAACCACCGCCGT 62.310 66.667 0.00 0.00 45.68 5.68
468 483 2.868331 CCGTCGCGTGTGTAGTCG 60.868 66.667 5.77 0.00 0.00 4.18
472 487 1.082561 TCGCGTGTGTAGTCGTCAC 60.083 57.895 5.77 0.00 36.48 3.67
477 492 1.003223 CGTGTGTAGTCGTCACTGTCA 60.003 52.381 0.00 0.00 36.83 3.58
480 495 2.034179 TGTGTAGTCGTCACTGTCAAGG 59.966 50.000 0.00 0.00 36.83 3.61
503 518 4.579384 CCCGCCCACCACACTGTT 62.579 66.667 0.00 0.00 0.00 3.16
509 524 1.437160 CCACCACACTGTTTGCCAC 59.563 57.895 0.00 0.00 0.00 5.01
512 527 2.026014 CACACTGTTTGCCACGGC 59.974 61.111 0.00 0.00 42.35 5.68
514 529 4.980903 CACTGTTTGCCACGGCGC 62.981 66.667 6.90 0.00 45.51 6.53
601 617 0.038159 GTGAGTCGGGGACAAGACAG 60.038 60.000 0.00 0.00 39.37 3.51
611 627 2.507992 CAAGACAGAGCCTCGCCG 60.508 66.667 0.00 0.00 0.00 6.46
667 683 4.135153 GGCGAGCGAGCAAGAGGA 62.135 66.667 8.59 0.00 39.27 3.71
691 707 2.913060 GCGGCGGAGATCTAGGGT 60.913 66.667 9.78 0.00 0.00 4.34
761 1219 5.384063 TTTTTCACTTTCACAAGCAGACA 57.616 34.783 0.00 0.00 32.57 3.41
802 1262 4.278170 TCCATTGACAATTCAACCTCACAC 59.722 41.667 0.00 0.00 44.66 3.82
827 1288 3.740397 CCACATGCACCACCGCTG 61.740 66.667 0.00 0.00 0.00 5.18
842 1303 2.080693 CCGCTGGTAGTAACAAATGCA 58.919 47.619 0.00 0.00 0.00 3.96
843 1304 2.095853 CCGCTGGTAGTAACAAATGCAG 59.904 50.000 0.00 0.00 0.00 4.41
844 1305 2.742053 CGCTGGTAGTAACAAATGCAGT 59.258 45.455 0.00 0.00 0.00 4.40
845 1306 3.930229 CGCTGGTAGTAACAAATGCAGTA 59.070 43.478 0.00 0.00 0.00 2.74
846 1307 4.032900 CGCTGGTAGTAACAAATGCAGTAG 59.967 45.833 0.00 0.00 0.00 2.57
847 1308 5.175859 GCTGGTAGTAACAAATGCAGTAGA 58.824 41.667 0.00 0.00 0.00 2.59
854 1327 6.578023 AGTAACAAATGCAGTAGATCTCTCC 58.422 40.000 0.00 0.00 0.00 3.71
856 1329 4.036518 ACAAATGCAGTAGATCTCTCCCT 58.963 43.478 0.00 0.00 0.00 4.20
860 1333 2.782925 TGCAGTAGATCTCTCCCTCTCT 59.217 50.000 0.00 0.00 0.00 3.10
871 1344 0.039764 TCCCTCTCTCTCGCTCCAAA 59.960 55.000 0.00 0.00 0.00 3.28
872 1345 0.174617 CCCTCTCTCTCGCTCCAAAC 59.825 60.000 0.00 0.00 0.00 2.93
973 1449 1.911702 GCCACTAACCACCTCCCTCC 61.912 65.000 0.00 0.00 0.00 4.30
974 1450 0.252742 CCACTAACCACCTCCCTCCT 60.253 60.000 0.00 0.00 0.00 3.69
976 1452 0.042881 ACTAACCACCTCCCTCCTCC 59.957 60.000 0.00 0.00 0.00 4.30
977 1453 0.691413 CTAACCACCTCCCTCCTCCC 60.691 65.000 0.00 0.00 0.00 4.30
978 1454 1.160289 TAACCACCTCCCTCCTCCCT 61.160 60.000 0.00 0.00 0.00 4.20
979 1455 2.041405 CCACCTCCCTCCTCCCTC 60.041 72.222 0.00 0.00 0.00 4.30
980 1456 2.041405 CACCTCCCTCCTCCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
1227 1740 0.463295 CGAGGCCTACGAGGTGAGTA 60.463 60.000 4.42 0.00 37.80 2.59
1228 1741 1.310904 GAGGCCTACGAGGTGAGTAG 58.689 60.000 4.42 0.00 40.77 2.57
1390 1924 2.358247 GGGGTGTGCAACGACGAT 60.358 61.111 0.00 0.00 42.39 3.73
1783 2348 8.764287 CGCCTGAATTCTTAAAGAAAACAAAAT 58.236 29.630 7.05 0.00 37.82 1.82
1972 2960 1.453155 CACTGTTCCCAAATCCTCGG 58.547 55.000 0.00 0.00 0.00 4.63
1982 2970 2.422597 CAAATCCTCGGTGCACAGTAA 58.577 47.619 20.43 5.24 0.00 2.24
2068 3068 2.276732 TTATAGCCTGCCTGCATTCC 57.723 50.000 0.00 0.00 0.00 3.01
2309 3310 3.819368 TCCTTGCCACATATGTGTATGG 58.181 45.455 29.25 25.55 44.21 2.74
2323 3324 3.007398 TGTGTATGGAAATTTGTTGGGGC 59.993 43.478 0.00 0.00 0.00 5.80
2466 3551 2.797177 AGCTTCCTTGCTCCTTTAGG 57.203 50.000 0.00 0.00 39.34 2.69
2792 3880 1.601759 GGCAAGAAGGTGAGCTGCA 60.602 57.895 1.02 0.00 0.00 4.41
2793 3881 1.174712 GGCAAGAAGGTGAGCTGCAA 61.175 55.000 1.02 0.00 0.00 4.08
2818 3906 2.105128 GACGAGGTCATCTGCCCG 59.895 66.667 0.00 0.00 32.09 6.13
2995 4086 2.033801 AGTGAGTCTGCAATGTTGTTGC 59.966 45.455 5.85 5.85 45.11 4.17
3107 4198 7.954788 ACATACAGTTCAGTTTTTCTCTCTC 57.045 36.000 0.00 0.00 0.00 3.20
3109 4200 7.870445 ACATACAGTTCAGTTTTTCTCTCTCTC 59.130 37.037 0.00 0.00 0.00 3.20
3256 4347 9.347240 CCAGTTCATTCATTCCATTAACTATCT 57.653 33.333 0.00 0.00 0.00 1.98
3352 4455 3.630312 GCTTGGCCGAGGAATTTACATTA 59.370 43.478 22.06 0.00 0.00 1.90
3597 4715 9.967346 CAAATTGAATGAAATGATCTAGCTGAT 57.033 29.630 0.00 0.00 38.27 2.90
3599 4717 7.506328 TTGAATGAAATGATCTAGCTGATGG 57.494 36.000 0.00 0.00 35.14 3.51
3600 4718 6.002082 TGAATGAAATGATCTAGCTGATGGG 58.998 40.000 0.00 0.00 35.14 4.00
3601 4719 5.837770 ATGAAATGATCTAGCTGATGGGA 57.162 39.130 0.00 0.00 35.14 4.37
3602 4720 5.635278 TGAAATGATCTAGCTGATGGGAA 57.365 39.130 0.00 0.00 35.14 3.97
3603 4721 5.618236 TGAAATGATCTAGCTGATGGGAAG 58.382 41.667 0.00 0.00 35.14 3.46
3604 4722 4.637387 AATGATCTAGCTGATGGGAAGG 57.363 45.455 0.00 0.00 35.14 3.46
3767 4885 1.303561 TTTGGTAGCCCAGCAGCAG 60.304 57.895 0.00 0.00 43.15 4.24
3773 4891 2.809861 TAGCCCAGCAGCAGCAGAAC 62.810 60.000 3.17 0.00 45.49 3.01
3774 4892 3.429141 CCCAGCAGCAGCAGAACG 61.429 66.667 3.17 0.00 45.49 3.95
3893 5011 5.064962 GGAGATATGCTGCTGAATGCTTATC 59.935 44.000 0.00 10.74 42.03 1.75
3912 5030 7.117397 GCTTATCCCTAAACTAACCTTCCTTT 58.883 38.462 0.00 0.00 0.00 3.11
3982 5105 1.508088 GTGCCGGCAAATGAAGAGG 59.492 57.895 34.66 0.00 0.00 3.69
4010 5133 1.634960 TATGTTCACGGGTCACAGGA 58.365 50.000 0.00 0.00 0.00 3.86
4061 5186 8.934023 TCCTAAGTTACAAACATGGAAGAATT 57.066 30.769 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 38 1.135517 GCGTGGTGTGTTGTTGTCTTT 60.136 47.619 0.00 0.00 0.00 2.52
44 46 0.250124 TTCTAGGGCGTGGTGTGTTG 60.250 55.000 0.00 0.00 0.00 3.33
46 48 1.370064 GTTCTAGGGCGTGGTGTGT 59.630 57.895 0.00 0.00 0.00 3.72
49 51 1.375523 GGTGTTCTAGGGCGTGGTG 60.376 63.158 0.00 0.00 0.00 4.17
50 52 0.251922 TAGGTGTTCTAGGGCGTGGT 60.252 55.000 0.00 0.00 0.00 4.16
51 53 0.899720 TTAGGTGTTCTAGGGCGTGG 59.100 55.000 0.00 0.00 0.00 4.94
58 60 2.753452 TCTCGTGGCTTAGGTGTTCTAG 59.247 50.000 0.00 0.00 0.00 2.43
81 83 2.407428 GCTTTGCGTCCTTAGGGCC 61.407 63.158 0.00 0.00 0.00 5.80
107 119 1.226547 GTCTCTTCGAGCTCGGCAG 60.227 63.158 33.98 27.77 40.29 4.85
146 158 4.160329 TGTGGTTCTCCTCTCTGTGTTAT 58.840 43.478 0.00 0.00 34.23 1.89
154 166 2.028930 ACATCGTTGTGGTTCTCCTCTC 60.029 50.000 0.00 0.00 33.85 3.20
170 182 2.343843 CGCTCTTCTCTTGTGAACATCG 59.656 50.000 0.00 0.00 0.00 3.84
183 195 2.337879 TTTGGTGTGGCCGCTCTTCT 62.338 55.000 18.96 0.00 41.21 2.85
209 221 2.076863 GGGTGAGATGTCCAACGAAAG 58.923 52.381 0.00 0.00 0.00 2.62
210 222 1.606994 CGGGTGAGATGTCCAACGAAA 60.607 52.381 0.00 0.00 0.00 3.46
211 223 0.037697 CGGGTGAGATGTCCAACGAA 60.038 55.000 0.00 0.00 0.00 3.85
212 224 1.183030 ACGGGTGAGATGTCCAACGA 61.183 55.000 0.00 0.00 0.00 3.85
213 225 1.014044 CACGGGTGAGATGTCCAACG 61.014 60.000 0.00 0.00 0.00 4.10
214 226 1.298859 GCACGGGTGAGATGTCCAAC 61.299 60.000 2.38 0.00 0.00 3.77
250 264 0.733566 TGTGTTCGTCGCGGTAATCC 60.734 55.000 6.13 0.00 0.00 3.01
251 265 1.062258 TTGTGTTCGTCGCGGTAATC 58.938 50.000 6.13 0.00 0.00 1.75
253 267 0.576328 GTTTGTGTTCGTCGCGGTAA 59.424 50.000 6.13 0.00 0.00 2.85
254 268 1.214373 GGTTTGTGTTCGTCGCGGTA 61.214 55.000 6.13 0.00 0.00 4.02
259 273 0.776451 CTCGAGGTTTGTGTTCGTCG 59.224 55.000 3.91 0.00 41.28 5.12
265 279 0.389948 GCGGATCTCGAGGTTTGTGT 60.390 55.000 13.56 0.00 42.43 3.72
295 310 0.311790 TTTTCTGTCGTCGGTAGCGT 59.688 50.000 14.79 0.00 0.00 5.07
303 318 1.627550 GGGCTCGCTTTTCTGTCGTC 61.628 60.000 0.00 0.00 0.00 4.20
305 320 2.730672 CGGGCTCGCTTTTCTGTCG 61.731 63.158 0.00 0.00 0.00 4.35
306 321 1.355066 CTCGGGCTCGCTTTTCTGTC 61.355 60.000 0.00 0.00 36.13 3.51
356 371 3.415212 CGGATAGGTAAGGATGGTCGTA 58.585 50.000 0.00 0.00 0.00 3.43
414 429 3.695606 TCCGTGCTCTGGTCAGCC 61.696 66.667 0.00 0.00 38.80 4.85
417 432 2.435120 TAGGGTCCGTGCTCTGGTCA 62.435 60.000 0.00 0.00 0.00 4.02
419 434 1.682684 CTAGGGTCCGTGCTCTGGT 60.683 63.158 0.00 0.00 0.00 4.00
454 469 1.082561 GTGACGACTACACACGCGA 60.083 57.895 15.93 0.00 38.05 5.87
459 474 2.034179 CCTTGACAGTGACGACTACACA 59.966 50.000 0.00 0.00 40.25 3.72
466 481 2.741092 GGGCCTTGACAGTGACGA 59.259 61.111 0.84 0.00 0.00 4.20
468 483 3.050275 GCGGGCCTTGACAGTGAC 61.050 66.667 0.84 0.00 0.00 3.67
489 504 2.417097 GCAAACAGTGTGGTGGGC 59.583 61.111 0.00 0.00 0.00 5.36
581 597 1.292541 GTCTTGTCCCCGACTCACC 59.707 63.158 0.00 0.00 33.15 4.02
582 598 0.038159 CTGTCTTGTCCCCGACTCAC 60.038 60.000 0.00 0.00 33.15 3.51
583 599 0.178973 TCTGTCTTGTCCCCGACTCA 60.179 55.000 0.00 0.00 33.15 3.41
585 601 1.536943 GCTCTGTCTTGTCCCCGACT 61.537 60.000 0.00 0.00 33.15 4.18
590 606 1.216710 CGAGGCTCTGTCTTGTCCC 59.783 63.158 13.50 0.00 0.00 4.46
634 650 4.087892 CCCTGCCAGAGGACACGG 62.088 72.222 0.00 0.00 46.33 4.94
717 734 1.721664 TTATCACCCCTCTCGCGTCG 61.722 60.000 5.77 0.00 0.00 5.12
721 738 3.477210 AAATCTTATCACCCCTCTCGC 57.523 47.619 0.00 0.00 0.00 5.03
727 744 7.090808 GTGAAAGTGAAAAATCTTATCACCCC 58.909 38.462 1.81 0.00 43.46 4.95
730 747 8.694394 GCTTGTGAAAGTGAAAAATCTTATCAC 58.306 33.333 0.00 0.00 42.91 3.06
802 1262 1.829533 GGTGCATGTGGGGCCATAG 60.830 63.158 4.39 0.00 0.00 2.23
824 1285 5.175859 TCTACTGCATTTGTTACTACCAGC 58.824 41.667 0.00 0.00 0.00 4.85
827 1288 7.493367 AGAGATCTACTGCATTTGTTACTACC 58.507 38.462 0.00 0.00 0.00 3.18
842 1303 3.578716 CGAGAGAGAGGGAGAGATCTACT 59.421 52.174 0.00 0.00 0.00 2.57
843 1304 3.864921 GCGAGAGAGAGGGAGAGATCTAC 60.865 56.522 0.00 0.00 0.00 2.59
844 1305 2.301870 GCGAGAGAGAGGGAGAGATCTA 59.698 54.545 0.00 0.00 0.00 1.98
845 1306 1.072331 GCGAGAGAGAGGGAGAGATCT 59.928 57.143 0.00 0.00 0.00 2.75
846 1307 1.072331 AGCGAGAGAGAGGGAGAGATC 59.928 57.143 0.00 0.00 0.00 2.75
847 1308 1.072331 GAGCGAGAGAGAGGGAGAGAT 59.928 57.143 0.00 0.00 0.00 2.75
854 1327 0.179150 CGTTTGGAGCGAGAGAGAGG 60.179 60.000 0.00 0.00 0.00 3.69
856 1329 0.894184 ACCGTTTGGAGCGAGAGAGA 60.894 55.000 0.00 0.00 39.21 3.10
860 1333 0.105224 TGAAACCGTTTGGAGCGAGA 59.895 50.000 0.00 0.00 39.21 4.04
871 1344 2.093128 AGGGCGATCTATTTGAAACCGT 60.093 45.455 0.00 0.00 0.00 4.83
872 1345 2.287915 CAGGGCGATCTATTTGAAACCG 59.712 50.000 0.00 0.00 0.00 4.44
976 1452 3.408853 GAAACGGGGGAGGGGAGG 61.409 72.222 0.00 0.00 0.00 4.30
977 1453 3.782443 CGAAACGGGGGAGGGGAG 61.782 72.222 0.00 0.00 0.00 4.30
980 1456 3.562732 AAAGCGAAACGGGGGAGGG 62.563 63.158 0.00 0.00 0.00 4.30
1035 1548 2.034999 GTTCACCATTGGGGCCGA 59.965 61.111 7.78 0.00 42.05 5.54
1728 2293 2.704464 TCAGTCCTGCTCATGGATTG 57.296 50.000 0.00 0.00 41.04 2.67
1783 2348 4.109766 CTGTTCCGCGTGAATTGATAGTA 58.890 43.478 4.92 0.00 34.90 1.82
1784 2349 2.930040 CTGTTCCGCGTGAATTGATAGT 59.070 45.455 4.92 0.00 34.90 2.12
1785 2350 2.285220 CCTGTTCCGCGTGAATTGATAG 59.715 50.000 4.92 4.12 34.90 2.08
1972 2960 1.949257 GTGCTGGGTTACTGTGCAC 59.051 57.895 10.75 10.75 45.23 4.57
2068 3068 7.229506 CCAAAGTAAGCTAAATATTCCCCTGAG 59.770 40.741 0.00 0.00 0.00 3.35
2309 3310 3.483808 TCAAAGGCCCCAACAAATTTC 57.516 42.857 0.00 0.00 0.00 2.17
2323 3324 5.047306 GGTCCAAAAGAAGGGTAATCAAAGG 60.047 44.000 0.00 0.00 0.00 3.11
2466 3551 1.439543 ACATTCCCAGGGGATAGAGC 58.560 55.000 8.12 0.00 44.74 4.09
2679 3767 2.144078 TCGCCCACCCTCTTGAACA 61.144 57.895 0.00 0.00 0.00 3.18
2792 3880 0.879765 ATGACCTCGTCGTCGAACTT 59.120 50.000 6.19 0.00 45.61 2.66
2793 3881 0.447011 GATGACCTCGTCGTCGAACT 59.553 55.000 6.19 0.00 45.61 3.01
2818 3906 1.481871 TGATCACCTTCTCGTACCCC 58.518 55.000 0.00 0.00 0.00 4.95
2995 4086 4.528596 ACTTATACATACAGCTGGGCCTAG 59.471 45.833 19.93 12.68 0.00 3.02
3115 4206 6.466812 TGCCTCACGTTTCATCATATATCAT 58.533 36.000 0.00 0.00 0.00 2.45
3116 4207 5.852827 TGCCTCACGTTTCATCATATATCA 58.147 37.500 0.00 0.00 0.00 2.15
3117 4208 6.619446 GCTTGCCTCACGTTTCATCATATATC 60.619 42.308 0.00 0.00 0.00 1.63
3118 4209 5.180117 GCTTGCCTCACGTTTCATCATATAT 59.820 40.000 0.00 0.00 0.00 0.86
3119 4210 4.511454 GCTTGCCTCACGTTTCATCATATA 59.489 41.667 0.00 0.00 0.00 0.86
3256 4347 2.295909 GCACCAATTAACTGCACCTTCA 59.704 45.455 0.00 0.00 0.00 3.02
3257 4348 2.558359 AGCACCAATTAACTGCACCTTC 59.442 45.455 4.51 0.00 33.06 3.46
3258 4349 2.558359 GAGCACCAATTAACTGCACCTT 59.442 45.455 4.51 0.00 33.06 3.50
3259 4350 2.162681 GAGCACCAATTAACTGCACCT 58.837 47.619 4.51 0.00 33.06 4.00
3260 4351 1.135689 CGAGCACCAATTAACTGCACC 60.136 52.381 4.51 0.00 33.06 5.01
3320 4423 0.550914 TCGGCCAAGCAAGGGATTAT 59.449 50.000 2.24 0.00 0.00 1.28
3524 4642 1.405526 CCATGGTCCAGTTTCGTCGAT 60.406 52.381 2.57 0.00 0.00 3.59
3569 4687 7.704899 CAGCTAGATCATTTCATTCAATTTGCA 59.295 33.333 0.00 0.00 0.00 4.08
3597 4715 4.038804 CCCTCCCCTCCCTTCCCA 62.039 72.222 0.00 0.00 0.00 4.37
3599 4717 3.707189 TCCCCTCCCCTCCCTTCC 61.707 72.222 0.00 0.00 0.00 3.46
3600 4718 2.040359 CTCCCCTCCCCTCCCTTC 60.040 72.222 0.00 0.00 0.00 3.46
3601 4719 3.711782 CCTCCCCTCCCCTCCCTT 61.712 72.222 0.00 0.00 0.00 3.95
3602 4720 4.761304 TCCTCCCCTCCCCTCCCT 62.761 72.222 0.00 0.00 0.00 4.20
3603 4721 4.179599 CTCCTCCCCTCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
3604 4722 4.179599 CCTCCTCCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
3726 4844 1.039068 CAATTGGCACTGAACCACCA 58.961 50.000 0.00 0.00 36.76 4.17
3767 4885 0.040958 CACAAGTTGCTCCGTTCTGC 60.041 55.000 1.81 0.00 0.00 4.26
3773 4891 0.027979 CACACACACAAGTTGCTCCG 59.972 55.000 1.81 0.00 0.00 4.63
3774 4892 0.248621 GCACACACACAAGTTGCTCC 60.249 55.000 1.81 0.00 0.00 4.70
3921 5039 4.910195 ACAGTATGCATGGTCTGAGAAAA 58.090 39.130 24.49 0.00 42.53 2.29
3982 5105 1.129811 CCCGTGAACATAAAACGCCTC 59.870 52.381 0.00 0.00 36.02 4.70
4010 5133 0.694771 TTCAGCAGCCTCTTGACCAT 59.305 50.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.