Multiple sequence alignment - TraesCS2B01G243000

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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 TraesCS2B01G243000 chr2B 100.000 5386 0 0 1 5386 247388817 247383432 0.000000e+00 9947
1 TraesCS2B01G243000 chr2D 93.796 2289 113 13 1 2285 190353613 190351350 0.000000e+00 3413
2 TraesCS2B01G243000 chr2D 97.170 1555 39 2 3836 5386 190349811 190348258 0.000000e+00 2623
3 TraesCS2B01G243000 chr2D 97.825 1517 32 1 2326 3841 190351354 190349838 0.000000e+00 2617
4 TraesCS2B01G243000 chr2D 94.048 168 10 0 2187 2354 56540995 56541162 6.920000e-64 255
5 TraesCS2B01G243000 chr2A 92.660 1771 108 8 1 1766 204884860 204883107 0.000000e+00 2531
6 TraesCS2B01G243000 chr2A 95.464 1433 51 8 2413 3841 204873921 204872499 0.000000e+00 2274
7 TraesCS2B01G243000 chr2A 93.584 904 44 6 3832 4724 204872477 204871577 0.000000e+00 1336
8 TraesCS2B01G243000 chr2A 92.258 775 51 7 1415 2188 204654491 204653725 0.000000e+00 1090
9 TraesCS2B01G243000 chr2A 91.444 561 35 9 4792 5341 204857184 204856626 0.000000e+00 758
10 TraesCS2B01G243000 chr3D 95.152 165 8 0 2185 2349 571465530 571465366 1.490000e-65 261
11 TraesCS2B01G243000 chr3D 95.152 165 8 0 2185 2349 579494790 579494954 1.490000e-65 261
12 TraesCS2B01G243000 chr3D 95.122 164 8 0 2185 2348 410670226 410670063 5.350000e-65 259
13 TraesCS2B01G243000 chr7A 94.578 166 9 0 2184 2349 105168360 105168195 1.920000e-64 257
14 TraesCS2B01G243000 chr6A 94.578 166 9 0 2183 2348 73573746 73573911 1.920000e-64 257
15 TraesCS2B01G243000 chr4D 94.048 168 10 0 2182 2349 230542716 230542549 6.920000e-64 255
16 TraesCS2B01G243000 chr3A 93.567 171 9 2 2182 2351 151465640 151465471 2.490000e-63 254


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 TraesCS2B01G243000 chr2B 247383432 247388817 5385 True 9947.000000 9947 100.000000 1 5386 1 chr2B.!!$R1 5385
1 TraesCS2B01G243000 chr2D 190348258 190353613 5355 True 2884.333333 3413 96.263667 1 5386 3 chr2D.!!$R1 5385
2 TraesCS2B01G243000 chr2A 204883107 204884860 1753 True 2531.000000 2531 92.660000 1 1766 1 chr2A.!!$R3 1765
3 TraesCS2B01G243000 chr2A 204871577 204873921 2344 True 1805.000000 2274 94.524000 2413 4724 2 chr2A.!!$R4 2311
4 TraesCS2B01G243000 chr2A 204653725 204654491 766 True 1090.000000 1090 92.258000 1415 2188 1 chr2A.!!$R1 773
5 TraesCS2B01G243000 chr2A 204856626 204857184 558 True 758.000000 758 91.444000 4792 5341 1 chr2A.!!$R2 549

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
320 322 0.307760 CCAAAACACTCACGAGCACC 59.692 55.000 0.00 0.00 0.00 5.01 F
1161 1169 0.112995 TTGCCAAAGCCACAGAGGAT 59.887 50.000 0.00 0.00 41.22 3.24 F
1456 1464 1.271379 CTGTGACGGCCACTGTAGTAA 59.729 52.381 2.24 0.00 45.86 2.24 F
1658 1666 2.747467 GCATAATCTCTGGCAGGCAGAA 60.747 50.000 25.74 17.11 0.00 3.02 F
2481 2490 4.424061 TCAACAATGCAGCACATAACTC 57.576 40.909 0.00 0.00 38.34 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1256 1264 0.552615 ATCAAGGGCCCTGGTTAGGT 60.553 55.000 29.5 3.98 42.96 3.08 R
2179 2188 2.603953 GAACGGAGGGAGTAGTTTTCG 58.396 52.381 0.0 0.00 0.00 3.46 R
2294 2303 5.719563 TGTAGAGATTCCACTATGAACCACA 59.280 40.000 0.0 0.00 0.00 4.17 R
3388 3401 5.947228 TCTGGCACATCAAAACTAGAAAG 57.053 39.130 0.0 0.00 38.20 2.62 R
4385 4434 1.740380 GCGCTGATGACTATGTGGTGT 60.740 52.381 0.0 0.00 0.00 4.16 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
36 37 7.245419 ACAAAAATTGGCAATACAGACAAAC 57.755 32.000 14.05 0.00 40.49 2.93
127 129 9.956720 AAAATGACAAATATAGCTGTGAATAGC 57.043 29.630 0.00 0.00 44.01 2.97
145 147 2.110578 AGCACTAATCCAATTTGGGCC 58.889 47.619 15.37 0.00 43.84 5.80
160 162 0.749454 GGGCCGTGAATTCAGCTCAT 60.749 55.000 8.80 0.00 0.00 2.90
169 171 7.642669 CCGTGAATTCAGCTCATTAACAATAT 58.357 34.615 8.80 0.00 0.00 1.28
210 212 6.861065 TTTTTGTTTCTCGAGCTACAGATT 57.139 33.333 7.81 0.00 0.00 2.40
211 213 7.956420 TTTTTGTTTCTCGAGCTACAGATTA 57.044 32.000 7.81 0.00 0.00 1.75
212 214 7.956420 TTTTGTTTCTCGAGCTACAGATTAA 57.044 32.000 7.81 2.99 0.00 1.40
213 215 7.582435 TTTGTTTCTCGAGCTACAGATTAAG 57.418 36.000 7.81 0.00 0.00 1.85
214 216 6.268825 TGTTTCTCGAGCTACAGATTAAGT 57.731 37.500 7.81 0.00 0.00 2.24
215 217 6.688578 TGTTTCTCGAGCTACAGATTAAGTT 58.311 36.000 7.81 0.00 0.00 2.66
216 218 7.152645 TGTTTCTCGAGCTACAGATTAAGTTT 58.847 34.615 7.81 0.00 0.00 2.66
217 219 7.656137 TGTTTCTCGAGCTACAGATTAAGTTTT 59.344 33.333 7.81 0.00 0.00 2.43
218 220 7.582435 TTCTCGAGCTACAGATTAAGTTTTG 57.418 36.000 7.81 0.00 0.00 2.44
219 221 6.100004 TCTCGAGCTACAGATTAAGTTTTGG 58.900 40.000 7.81 0.00 0.00 3.28
240 242 4.037446 TGGTTTGGAACTTTGTGACATAGC 59.963 41.667 2.89 0.00 0.00 2.97
250 252 9.265901 GAACTTTGTGACATAGCAGATACATAT 57.734 33.333 2.89 0.00 0.00 1.78
312 314 5.860941 TTTTTGATAGGCCAAAACACTCA 57.139 34.783 5.01 0.00 43.28 3.41
313 315 4.846779 TTTGATAGGCCAAAACACTCAC 57.153 40.909 5.01 0.00 33.56 3.51
320 322 0.307760 CCAAAACACTCACGAGCACC 59.692 55.000 0.00 0.00 0.00 5.01
321 323 1.013596 CAAAACACTCACGAGCACCA 58.986 50.000 0.00 0.00 0.00 4.17
365 367 3.181489 ACTCCATACATTCTCGTCCGTTC 60.181 47.826 0.00 0.00 0.00 3.95
420 422 8.846943 TGATAAAGTGAAAGTGCAATCTAGAA 57.153 30.769 0.00 0.00 0.00 2.10
427 429 7.281774 AGTGAAAGTGCAATCTAGAACATATGG 59.718 37.037 7.80 0.00 0.00 2.74
428 430 7.066284 GTGAAAGTGCAATCTAGAACATATGGT 59.934 37.037 7.80 0.00 0.00 3.55
464 466 7.145932 AGACATGAAGGTACTGTAAAATTGC 57.854 36.000 0.00 0.00 40.86 3.56
505 507 3.988976 AGGACATGCTACAACAGTGAT 57.011 42.857 0.00 0.00 0.00 3.06
506 508 3.603532 AGGACATGCTACAACAGTGATG 58.396 45.455 0.00 0.00 0.00 3.07
507 509 3.261643 AGGACATGCTACAACAGTGATGA 59.738 43.478 7.47 0.00 0.00 2.92
508 510 4.080695 AGGACATGCTACAACAGTGATGAT 60.081 41.667 7.47 0.00 0.00 2.45
509 511 4.034858 GGACATGCTACAACAGTGATGATG 59.965 45.833 7.47 3.16 0.00 3.07
510 512 3.943381 ACATGCTACAACAGTGATGATGG 59.057 43.478 7.47 0.00 0.00 3.51
511 513 3.701205 TGCTACAACAGTGATGATGGT 57.299 42.857 7.47 0.00 0.00 3.55
512 514 3.599343 TGCTACAACAGTGATGATGGTC 58.401 45.455 7.47 0.00 0.00 4.02
513 515 3.261643 TGCTACAACAGTGATGATGGTCT 59.738 43.478 7.47 0.00 0.00 3.85
514 516 3.868077 GCTACAACAGTGATGATGGTCTC 59.132 47.826 7.47 0.00 0.00 3.36
515 517 4.621510 GCTACAACAGTGATGATGGTCTCA 60.622 45.833 7.47 0.00 38.53 3.27
525 527 1.623311 TGATGGTCTCAAAGGCTCGAA 59.377 47.619 0.00 0.00 0.00 3.71
528 530 1.270305 TGGTCTCAAAGGCTCGAACTG 60.270 52.381 0.00 0.00 0.00 3.16
530 532 2.548067 GGTCTCAAAGGCTCGAACTGAA 60.548 50.000 0.00 0.00 0.00 3.02
545 547 5.241064 TCGAACTGAATAGAGGTGGTATAGC 59.759 44.000 0.00 0.00 0.00 2.97
567 569 2.224769 CCACCGGGGATAGCAACATATT 60.225 50.000 4.41 0.00 40.01 1.28
575 577 4.892934 GGGATAGCAACATATTTCCCAACA 59.107 41.667 0.94 0.00 42.03 3.33
592 594 8.561738 TTCCCAACACAAATAGATAGTTTCTC 57.438 34.615 0.00 0.00 35.79 2.87
596 598 9.653287 CCAACACAAATAGATAGTTTCTCTGTA 57.347 33.333 0.00 0.00 35.79 2.74
642 644 5.126061 GCATGAAAGCAGGATTAGAAGGAAA 59.874 40.000 0.00 0.00 0.00 3.13
643 645 6.350445 GCATGAAAGCAGGATTAGAAGGAAAA 60.350 38.462 0.00 0.00 0.00 2.29
746 750 0.786435 AAATTGGAGGTCAAGCCCCT 59.214 50.000 0.00 0.00 38.95 4.79
794 798 2.308570 ACTTTGCAGGATATGGTGACCA 59.691 45.455 6.84 6.84 38.19 4.02
798 802 2.712627 TGCAGGATATGGTGACCATCAT 59.287 45.455 22.25 12.70 40.74 2.45
819 823 6.053650 TCATCATCAGTCATCCTGTCAATTC 58.946 40.000 0.00 0.00 42.19 2.17
820 824 5.425196 TCATCAGTCATCCTGTCAATTCA 57.575 39.130 0.00 0.00 42.19 2.57
829 834 7.668886 AGTCATCCTGTCAATTCAAAGAGAAAT 59.331 33.333 0.00 0.00 40.22 2.17
833 838 7.000472 TCCTGTCAATTCAAAGAGAAATGTCT 59.000 34.615 0.00 0.00 40.22 3.41
868 873 3.117322 TCTGGTCCCAAAGGTCATTTTCA 60.117 43.478 0.00 0.00 0.00 2.69
958 963 3.999663 AGCTTCATGAGTACTTCTGCAAC 59.000 43.478 0.00 0.00 0.00 4.17
974 979 2.938451 TGCAACGCAGATAGATCAAAGG 59.062 45.455 0.00 0.00 33.32 3.11
993 998 4.766404 AGGCCATTTTCTGAAGTAAACG 57.234 40.909 5.01 0.00 0.00 3.60
1059 1067 2.746697 TTCGTCAGAAGGTCAGGCT 58.253 52.632 0.00 0.00 31.76 4.58
1161 1169 0.112995 TTGCCAAAGCCACAGAGGAT 59.887 50.000 0.00 0.00 41.22 3.24
1398 1406 3.459969 AGGACTTCCTTTCCAACTTCAGT 59.540 43.478 0.00 0.00 46.09 3.41
1456 1464 1.271379 CTGTGACGGCCACTGTAGTAA 59.729 52.381 2.24 0.00 45.86 2.24
1658 1666 2.747467 GCATAATCTCTGGCAGGCAGAA 60.747 50.000 25.74 17.11 0.00 3.02
1757 1765 5.812642 AGTTCTTTACTGATACCAAGATGCG 59.187 40.000 0.00 0.00 35.19 4.73
1981 1990 7.363007 GCAAGTTTCTTTTCCTAGAATTAGGGG 60.363 40.741 0.00 0.00 45.60 4.79
1982 1991 6.732487 AGTTTCTTTTCCTAGAATTAGGGGG 58.268 40.000 0.00 0.00 45.60 5.40
2009 2018 9.476202 GAAAAACTTACCAAAGATGTGCTAAAT 57.524 29.630 0.00 0.00 36.50 1.40
2113 2122 5.295540 GCCTTTTTACAGCCAATTTGTTTCA 59.704 36.000 0.00 0.00 0.00 2.69
2179 2188 8.598075 CAAGCTTGGCAATAAATATGAAAAGTC 58.402 33.333 19.14 0.00 0.00 3.01
2210 2219 7.786464 ACTACTCCCTCCGTTCCTAAATATAAA 59.214 37.037 0.00 0.00 0.00 1.40
2280 2289 8.263640 AGTGAATCTACACTCTAAAATGCATCT 58.736 33.333 0.00 0.00 46.36 2.90
2281 2290 9.534565 GTGAATCTACACTCTAAAATGCATCTA 57.465 33.333 0.00 0.00 37.73 1.98
2298 2307 9.788889 AATGCATCTATATACATCCATATGTGG 57.211 33.333 0.00 1.19 45.99 4.17
2299 2308 8.322905 TGCATCTATATACATCCATATGTGGT 57.677 34.615 8.51 0.00 45.99 4.16
2300 2309 8.771286 TGCATCTATATACATCCATATGTGGTT 58.229 33.333 8.51 0.00 45.99 3.67
2301 2310 9.265901 GCATCTATATACATCCATATGTGGTTC 57.734 37.037 8.51 0.00 45.99 3.62
2308 2317 5.624159 ACATCCATATGTGGTTCATAGTGG 58.376 41.667 8.51 0.00 44.79 4.00
2309 2318 5.369404 ACATCCATATGTGGTTCATAGTGGA 59.631 40.000 8.51 14.65 44.79 4.02
2310 2319 5.966853 TCCATATGTGGTTCATAGTGGAA 57.033 39.130 8.51 0.00 46.16 3.53
2311 2320 6.514012 TCCATATGTGGTTCATAGTGGAAT 57.486 37.500 8.51 0.00 46.16 3.01
2312 2321 6.533730 TCCATATGTGGTTCATAGTGGAATC 58.466 40.000 8.51 0.00 46.16 2.52
2313 2322 6.329986 TCCATATGTGGTTCATAGTGGAATCT 59.670 38.462 8.51 0.00 46.16 2.40
2314 2323 6.652481 CCATATGTGGTTCATAGTGGAATCTC 59.348 42.308 0.00 0.00 41.55 2.75
2315 2324 5.965033 ATGTGGTTCATAGTGGAATCTCT 57.035 39.130 0.00 0.00 34.67 3.10
2316 2325 8.588472 CATATGTGGTTCATAGTGGAATCTCTA 58.412 37.037 0.00 0.00 41.55 2.43
2317 2326 6.222038 TGTGGTTCATAGTGGAATCTCTAC 57.778 41.667 0.00 0.00 0.00 2.59
2318 2327 5.719563 TGTGGTTCATAGTGGAATCTCTACA 59.280 40.000 0.00 0.00 29.47 2.74
2319 2328 6.212589 TGTGGTTCATAGTGGAATCTCTACAA 59.787 38.462 0.00 0.00 29.47 2.41
2320 2329 7.103641 GTGGTTCATAGTGGAATCTCTACAAA 58.896 38.462 0.00 0.00 29.47 2.83
2321 2330 7.278868 GTGGTTCATAGTGGAATCTCTACAAAG 59.721 40.741 0.00 0.00 29.47 2.77
2322 2331 7.180229 TGGTTCATAGTGGAATCTCTACAAAGA 59.820 37.037 0.00 0.00 29.47 2.52
2323 2332 7.492994 GGTTCATAGTGGAATCTCTACAAAGAC 59.507 40.741 0.00 0.00 29.47 3.01
2324 2333 7.962995 TCATAGTGGAATCTCTACAAAGACT 57.037 36.000 0.00 0.00 29.47 3.24
2433 2442 6.375455 GTGTTCCTTCAGTTATGATGAATGGT 59.625 38.462 0.00 0.00 36.16 3.55
2481 2490 4.424061 TCAACAATGCAGCACATAACTC 57.576 40.909 0.00 0.00 38.34 3.01
2697 2706 8.978874 TCACCACTGCATAAGATAATATTTGT 57.021 30.769 0.00 0.00 0.00 2.83
3114 3123 7.296628 ACTATGCACAATTTAACTTTTCCCA 57.703 32.000 0.00 0.00 0.00 4.37
3388 3401 5.346181 AGACTACTTCATCTTTGGTAGCC 57.654 43.478 0.00 0.00 36.19 3.93
3445 3458 9.840427 GCACAGTATTATTTATAATTTGGCGAT 57.160 29.630 0.68 0.00 34.91 4.58
3447 3460 9.840427 ACAGTATTATTTATAATTTGGCGATGC 57.160 29.630 0.68 0.00 34.91 3.91
3452 3465 6.747659 ATTTATAATTTGGCGATGCGTTTC 57.252 33.333 0.00 0.00 0.00 2.78
3457 3470 0.519519 TTGGCGATGCGTTTCGATTT 59.480 45.000 12.34 0.00 41.62 2.17
3990 4039 9.236006 GGGAAACTATACAATCTCATTGCATAT 57.764 33.333 0.00 0.00 43.98 1.78
4149 4198 4.789807 AGATGGAAAATGGAGTGAGATGG 58.210 43.478 0.00 0.00 0.00 3.51
4456 4505 6.916360 AGTTTATTTGCCTCCAGATGAAAA 57.084 33.333 0.00 0.00 0.00 2.29
4518 4575 7.066163 TGTTTATGCACATCTTTCTGTCCTATG 59.934 37.037 0.00 0.00 0.00 2.23
4737 4796 2.301870 TGTCCAGTGACACATTCCTACC 59.698 50.000 8.59 0.00 46.40 3.18
4751 4810 7.924412 ACACATTCCTACCATAAAGTACATACG 59.076 37.037 0.00 0.00 0.00 3.06
4787 4846 4.458989 GGTGAAGTGATACTTGGCAAATGA 59.541 41.667 0.00 0.00 38.80 2.57
4864 4923 5.856126 TGGAAGAACAGTAATTGCTAACG 57.144 39.130 0.00 0.00 0.00 3.18
5058 5124 4.443978 AACAGTATGCAGCATCCCTATT 57.556 40.909 12.38 1.80 42.53 1.73
5115 5181 5.950023 TCTACATAGGGAAACTAGATCGGT 58.050 41.667 0.00 0.00 34.56 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 6.817765 AGACGTGTATTTCAAATCCATTGT 57.182 33.333 0.00 0.00 40.11 2.71
72 74 8.786826 TTCTAGACGTGTATTTCAAATCCATT 57.213 30.769 0.00 0.00 0.00 3.16
85 87 7.773864 TGTCATTTTTGTTTCTAGACGTGTA 57.226 32.000 0.00 0.00 0.00 2.90
127 129 2.099405 ACGGCCCAAATTGGATTAGTG 58.901 47.619 14.62 0.00 40.96 2.74
145 147 8.337532 TCATATTGTTAATGAGCTGAATTCACG 58.662 33.333 3.38 2.41 0.00 4.35
160 162 9.412460 AGAAGAATCCAGCATTCATATTGTTAA 57.588 29.630 0.00 0.00 43.27 2.01
198 200 6.481954 AACCAAAACTTAATCTGTAGCTCG 57.518 37.500 0.00 0.00 0.00 5.03
209 211 7.385478 GTCACAAAGTTCCAAACCAAAACTTAA 59.615 33.333 0.63 0.00 41.17 1.85
210 212 6.869388 GTCACAAAGTTCCAAACCAAAACTTA 59.131 34.615 0.63 0.00 41.17 2.24
211 213 5.699001 GTCACAAAGTTCCAAACCAAAACTT 59.301 36.000 0.00 0.00 43.22 2.66
212 214 5.221541 TGTCACAAAGTTCCAAACCAAAACT 60.222 36.000 0.00 0.00 34.81 2.66
213 215 4.991687 TGTCACAAAGTTCCAAACCAAAAC 59.008 37.500 0.00 0.00 0.00 2.43
214 216 5.215252 TGTCACAAAGTTCCAAACCAAAA 57.785 34.783 0.00 0.00 0.00 2.44
215 217 4.873746 TGTCACAAAGTTCCAAACCAAA 57.126 36.364 0.00 0.00 0.00 3.28
216 218 5.451242 GCTATGTCACAAAGTTCCAAACCAA 60.451 40.000 0.00 0.00 0.00 3.67
217 219 4.037446 GCTATGTCACAAAGTTCCAAACCA 59.963 41.667 0.00 0.00 0.00 3.67
218 220 4.037446 TGCTATGTCACAAAGTTCCAAACC 59.963 41.667 0.00 0.00 0.00 3.27
219 221 5.008613 TCTGCTATGTCACAAAGTTCCAAAC 59.991 40.000 0.00 0.00 0.00 2.93
264 266 9.643693 AATTACCAAAACTTATGAGCAGAATTG 57.356 29.630 0.00 0.00 0.00 2.32
295 297 2.673368 CTCGTGAGTGTTTTGGCCTATC 59.327 50.000 3.32 0.00 0.00 2.08
307 309 1.080230 CTCCTGGTGCTCGTGAGTG 60.080 63.158 0.00 0.00 0.00 3.51
308 310 0.251209 TACTCCTGGTGCTCGTGAGT 60.251 55.000 0.00 0.00 39.47 3.41
309 311 1.107114 ATACTCCTGGTGCTCGTGAG 58.893 55.000 0.00 0.00 0.00 3.51
312 314 0.824759 GGAATACTCCTGGTGCTCGT 59.175 55.000 0.00 0.00 38.88 4.18
313 315 0.824109 TGGAATACTCCTGGTGCTCG 59.176 55.000 0.00 0.00 42.94 5.03
320 322 0.178068 CCCGGTGTGGAATACTCCTG 59.822 60.000 0.00 0.00 42.94 3.86
321 323 0.042131 TCCCGGTGTGGAATACTCCT 59.958 55.000 0.00 0.00 42.94 3.69
420 422 6.539173 TGTCTAAAACAAGGTCACCATATGT 58.461 36.000 0.00 0.00 34.03 2.29
427 429 5.531287 ACCTTCATGTCTAAAACAAGGTCAC 59.469 40.000 5.59 0.00 40.95 3.67
428 430 5.690865 ACCTTCATGTCTAAAACAAGGTCA 58.309 37.500 5.59 0.00 40.95 4.02
464 466 8.311836 TGTCCTAGTTTCACATCTTAGTAAAGG 58.688 37.037 0.00 0.00 33.22 3.11
505 507 1.266178 TCGAGCCTTTGAGACCATCA 58.734 50.000 0.00 0.00 35.62 3.07
506 508 2.003301 GTTCGAGCCTTTGAGACCATC 58.997 52.381 0.00 0.00 0.00 3.51
507 509 1.625818 AGTTCGAGCCTTTGAGACCAT 59.374 47.619 0.00 0.00 0.00 3.55
508 510 1.048601 AGTTCGAGCCTTTGAGACCA 58.951 50.000 0.00 0.00 0.00 4.02
509 511 1.000955 TCAGTTCGAGCCTTTGAGACC 59.999 52.381 0.00 0.00 0.00 3.85
510 512 2.440539 TCAGTTCGAGCCTTTGAGAC 57.559 50.000 0.00 0.00 0.00 3.36
511 513 3.685139 ATTCAGTTCGAGCCTTTGAGA 57.315 42.857 0.00 0.00 0.00 3.27
512 514 4.748892 TCTATTCAGTTCGAGCCTTTGAG 58.251 43.478 0.00 0.00 0.00 3.02
513 515 4.382040 CCTCTATTCAGTTCGAGCCTTTGA 60.382 45.833 0.00 0.00 0.00 2.69
514 516 3.868077 CCTCTATTCAGTTCGAGCCTTTG 59.132 47.826 0.00 0.00 0.00 2.77
515 517 3.515901 ACCTCTATTCAGTTCGAGCCTTT 59.484 43.478 0.00 0.00 0.00 3.11
525 527 4.161102 GGGCTATACCACCTCTATTCAGT 58.839 47.826 0.00 0.00 42.05 3.41
557 559 5.543507 TTTGTGTTGGGAAATATGTTGCT 57.456 34.783 0.00 0.00 0.00 3.91
567 569 8.383175 AGAGAAACTATCTATTTGTGTTGGGAA 58.617 33.333 0.00 0.00 38.96 3.97
615 617 5.766670 CCTTCTAATCCTGCTTTCATGCATA 59.233 40.000 0.00 0.00 42.48 3.14
619 621 6.764308 TTTCCTTCTAATCCTGCTTTCATG 57.236 37.500 0.00 0.00 0.00 3.07
648 652 2.980568 TCCCGTTATCTGAAATTGCGT 58.019 42.857 0.00 0.00 0.00 5.24
741 745 2.378634 ATGCCTACTGGACAGGGGC 61.379 63.158 22.57 22.57 45.16 5.80
746 750 2.906389 AGAGAAACATGCCTACTGGACA 59.094 45.455 0.00 0.00 34.57 4.02
868 873 8.164070 AGAGGTAAACATGTTGAAGGTTCTTAT 58.836 33.333 12.82 0.00 0.00 1.73
958 963 2.245159 TGGCCTTTGATCTATCTGCG 57.755 50.000 3.32 0.00 0.00 5.18
974 979 4.454504 TCCTCGTTTACTTCAGAAAATGGC 59.545 41.667 0.00 0.00 0.00 4.40
993 998 5.022787 AGAGATAATAGTGGCATCCTCCTC 58.977 45.833 0.00 0.00 0.00 3.71
1059 1067 2.554142 CCATTATTGTCGCTGCAGAGA 58.446 47.619 20.43 18.51 0.00 3.10
1161 1169 1.586541 CGTGCCAGTAGCTGAGTGA 59.413 57.895 0.00 0.00 44.23 3.41
1256 1264 0.552615 ATCAAGGGCCCTGGTTAGGT 60.553 55.000 29.50 3.98 42.96 3.08
1456 1464 1.183549 AGGTCTTCATAACGCTCGGT 58.816 50.000 0.00 0.00 0.00 4.69
1658 1666 5.322754 CCATCTGGCCAGAAATGATCTTAT 58.677 41.667 38.02 15.81 41.36 1.73
1981 1990 4.988540 GCACATCTTTGGTAAGTTTTTCCC 59.011 41.667 0.00 0.00 32.98 3.97
1982 1991 5.842907 AGCACATCTTTGGTAAGTTTTTCC 58.157 37.500 0.00 0.00 32.98 3.13
1983 1992 8.865590 TTTAGCACATCTTTGGTAAGTTTTTC 57.134 30.769 0.00 0.00 39.82 2.29
1993 2002 7.043565 AGCCATTTAATTTAGCACATCTTTGG 58.956 34.615 0.00 0.00 0.00 3.28
2009 2018 8.658840 AGGTATTTTGGTTTCTAGCCATTTAA 57.341 30.769 0.00 0.00 35.71 1.52
2113 2122 3.525862 AGGGTGGAGAAGACTGATCTTT 58.474 45.455 0.00 0.00 45.60 2.52
2179 2188 2.603953 GAACGGAGGGAGTAGTTTTCG 58.396 52.381 0.00 0.00 0.00 3.46
2210 2219 6.095440 GTCCATAGTGAAATGCCTACAAACAT 59.905 38.462 0.00 0.00 0.00 2.71
2225 2234 3.819337 GCTCCGTATGTAGTCCATAGTGA 59.181 47.826 0.00 0.00 36.71 3.41
2290 2299 7.448420 AGAGATTCCACTATGAACCACATATG 58.552 38.462 0.00 0.00 40.18 1.78
2291 2300 7.623999 AGAGATTCCACTATGAACCACATAT 57.376 36.000 0.00 0.00 40.18 1.78
2292 2301 7.563556 TGTAGAGATTCCACTATGAACCACATA 59.436 37.037 0.00 0.00 40.07 2.29
2293 2302 5.965033 AGAGATTCCACTATGAACCACAT 57.035 39.130 0.00 0.00 42.39 3.21
2294 2303 5.719563 TGTAGAGATTCCACTATGAACCACA 59.280 40.000 0.00 0.00 0.00 4.17
2295 2304 6.222038 TGTAGAGATTCCACTATGAACCAC 57.778 41.667 0.00 0.00 0.00 4.16
2296 2305 6.867519 TTGTAGAGATTCCACTATGAACCA 57.132 37.500 0.00 0.00 0.00 3.67
2297 2306 7.492994 GTCTTTGTAGAGATTCCACTATGAACC 59.507 40.741 0.00 0.00 0.00 3.62
2298 2307 8.254508 AGTCTTTGTAGAGATTCCACTATGAAC 58.745 37.037 0.00 0.00 0.00 3.18
2299 2308 8.367660 AGTCTTTGTAGAGATTCCACTATGAA 57.632 34.615 0.00 0.00 0.00 2.57
2300 2309 7.962995 AGTCTTTGTAGAGATTCCACTATGA 57.037 36.000 0.00 0.00 0.00 2.15
2316 2325 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
2317 2326 8.202137 TCCTCCGTTCCTAAATATAAGTCTTTG 58.798 37.037 0.00 0.00 0.00 2.77
2318 2327 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
2319 2328 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
2320 2329 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2321 2330 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2322 2331 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2323 2332 9.640963 CATACTTCCTCCGTTCCTAAATATAAG 57.359 37.037 0.00 0.00 0.00 1.73
2324 2333 9.151177 ACATACTTCCTCCGTTCCTAAATATAA 57.849 33.333 0.00 0.00 0.00 0.98
2433 2442 8.392372 ACGCTATGTCTTTGATATGACTAGTA 57.608 34.615 0.00 0.00 34.57 1.82
2444 2453 6.456853 GCATTGTTGATACGCTATGTCTTTGA 60.457 38.462 0.00 0.00 0.00 2.69
2481 2490 8.647143 AAATCTATTTTGATAAACCAATGGCG 57.353 30.769 0.00 0.00 0.00 5.69
3388 3401 5.947228 TCTGGCACATCAAAACTAGAAAG 57.053 39.130 0.00 0.00 38.20 2.62
3479 3492 6.265577 CAGTTTAATCGCCTTCCTTTAATGG 58.734 40.000 0.83 0.83 0.00 3.16
3756 3769 2.688364 CTTCCAAAAGAAGCGGACAC 57.312 50.000 0.00 0.00 45.38 3.67
3990 4039 3.830755 GGTCTAGGGTAACTTCACTCACA 59.169 47.826 0.00 0.00 0.00 3.58
4149 4198 2.349886 CGTTCTCTGCTGGACAATAAGC 59.650 50.000 0.00 0.00 39.96 3.09
4252 4301 4.340666 TGGTGTTTAGCATTGTGACAACAT 59.659 37.500 0.00 0.00 33.39 2.71
4385 4434 1.740380 GCGCTGATGACTATGTGGTGT 60.740 52.381 0.00 0.00 0.00 4.16
4456 4505 9.394767 TCGGCATCACTATATTAATGCAAATAT 57.605 29.630 8.35 8.35 44.90 1.28
4751 4810 8.251721 AGTATCACTTCACCTCTATTGTTGTAC 58.748 37.037 0.00 0.00 0.00 2.90
4765 4824 5.048782 TGTCATTTGCCAAGTATCACTTCAC 60.049 40.000 0.00 0.00 36.03 3.18
4787 4846 7.775561 ACTCTTAATTTTGTCAGAGTCCTTTGT 59.224 33.333 0.00 0.00 41.85 2.83
4880 4939 1.164411 TGCTGGCGTACTTGAATTGG 58.836 50.000 0.00 0.00 0.00 3.16
5058 5124 6.306837 CGCAATTCCACTTTTAAATTCGCTTA 59.693 34.615 0.00 0.00 0.00 3.09
5115 5181 7.228906 CCCAGATTCGTCTCTACAACTCTATAA 59.771 40.741 0.00 0.00 0.00 0.98
5188 5254 1.867919 CGGACCGACAAGTCTCAGCT 61.868 60.000 8.64 0.00 36.95 4.24


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

AutoCloner maintained by Alex Coulton.