Multiple sequence alignment - TraesCS3D01G348500

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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 TraesCS3D01G348500 chr3D 100.000 2463 0 0 987 3449 460252183 460249721 0.000000e+00 4549
1 TraesCS3D01G348500 chr3D 100.000 707 0 0 1 707 460253169 460252463 0.000000e+00 1306
2 TraesCS3D01G348500 chr3B 95.211 2422 71 8 1028 3449 610178847 610176471 0.000000e+00 3788
3 TraesCS3D01G348500 chr3B 87.473 463 34 14 251 707 610179623 610179179 2.370000e-141 512
4 TraesCS3D01G348500 chr3B 90.576 191 12 2 1052 1236 807534654 807534844 7.390000e-62 248
5 TraesCS3D01G348500 chr3B 91.061 179 8 5 29 205 610179806 610179634 5.750000e-58 235
6 TraesCS3D01G348500 chr3B 93.694 111 6 1 3340 3449 610176456 610176346 7.660000e-37 165
7 TraesCS3D01G348500 chr3A 96.604 2032 51 9 1029 3052 602241532 602239511 0.000000e+00 3354
8 TraesCS3D01G348500 chr3A 89.811 687 44 16 29 707 602242422 602241754 0.000000e+00 857
9 TraesCS3D01G348500 chr3A 98.824 255 3 0 3084 3338 602239512 602239258 4.060000e-124 455
10 TraesCS3D01G348500 chr1D 78.541 1398 246 36 987 2345 384832124 384833506 0.000000e+00 870
11 TraesCS3D01G348500 chr1B 78.183 1398 247 36 987 2343 516948122 516949502 0.000000e+00 839
12 TraesCS3D01G348500 chr1A 77.778 1404 253 37 987 2349 484998875 485000260 0.000000e+00 809
13 TraesCS3D01G348500 chr2D 95.833 192 8 0 2359 2550 640153864 640154055 9.290000e-81 311
14 TraesCS3D01G348500 chr2D 94.565 184 10 0 2578 2761 640154053 640154236 5.630000e-73 285
15 TraesCS3D01G348500 chr4B 90.052 191 13 2 1052 1236 669306222 669306412 3.440000e-60 243
16 TraesCS3D01G348500 chr4B 89.529 191 14 2 1052 1236 668989305 668989115 1.600000e-58 237
17 TraesCS3D01G348500 chr4B 89.529 191 14 2 1052 1236 669144757 669144947 1.600000e-58 237


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 TraesCS3D01G348500 chr3D 460249721 460253169 3448 True 2927.500000 4549 100.000000 1 3449 2 chr3D.!!$R1 3448
1 TraesCS3D01G348500 chr3B 610176346 610179806 3460 True 1175.000000 3788 91.859750 29 3449 4 chr3B.!!$R1 3420
2 TraesCS3D01G348500 chr3A 602239258 602242422 3164 True 1555.333333 3354 95.079667 29 3338 3 chr3A.!!$R1 3309
3 TraesCS3D01G348500 chr1D 384832124 384833506 1382 False 870.000000 870 78.541000 987 2345 1 chr1D.!!$F1 1358
4 TraesCS3D01G348500 chr1B 516948122 516949502 1380 False 839.000000 839 78.183000 987 2343 1 chr1B.!!$F1 1356
5 TraesCS3D01G348500 chr1A 484998875 485000260 1385 False 809.000000 809 77.778000 987 2349 1 chr1A.!!$F1 1362

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
239 244 0.320683 AAAAATGAAAGGGGCAGCGC 60.321 50.000 0.0 0.0 0.0 5.92 F
382 389 0.387929 TCTGCGTATTTAGCCCCTCG 59.612 55.000 0.0 0.0 0.0 4.63 F
383 390 0.600255 CTGCGTATTTAGCCCCTCGG 60.600 60.000 0.0 0.0 0.0 4.63 F
462 475 1.250840 AATCTCCCCCGTTGCAAAGC 61.251 55.000 0.0 0.0 0.0 3.51 F
1368 1433 1.374252 GCTCTTCACCTTCGCCGAA 60.374 57.895 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1224 1265 0.972983 CGGAGAGGAGGAAGAAGCCA 60.973 60.0 0.0 0.0 0.0 4.75 R
1701 1766 1.195115 GGATGTAGTGCTGGTCCTCA 58.805 55.0 0.0 0.0 0.0 3.86 R
2154 2219 1.291184 TGGTGATTGTCTTGAGCGCG 61.291 55.0 0.0 0.0 0.0 6.86 R
2357 2422 2.974794 CCTGTCATCATGTATCCCCTCA 59.025 50.0 0.0 0.0 0.0 3.86 R
2766 2842 0.660488 GCACGAACAATCACACACCA 59.340 50.0 0.0 0.0 0.0 4.17 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
20 21 3.651803 GATGAATCCTACTCTGGACGG 57.348 52.381 0.00 0.00 39.17 4.79
21 22 1.112113 TGAATCCTACTCTGGACGGC 58.888 55.000 0.00 0.00 39.17 5.68
22 23 1.112113 GAATCCTACTCTGGACGGCA 58.888 55.000 0.00 0.00 39.17 5.69
23 24 1.480954 GAATCCTACTCTGGACGGCAA 59.519 52.381 0.00 0.00 39.17 4.52
24 25 0.824759 ATCCTACTCTGGACGGCAAC 59.175 55.000 0.00 0.00 39.17 4.17
65 70 0.735632 CAGAGCAGAGCTGTTCGGTC 60.736 60.000 8.38 0.00 44.12 4.79
170 175 3.627577 ACAAGGATCGCACCATTATTGTC 59.372 43.478 0.00 0.00 0.00 3.18
178 183 5.730550 TCGCACCATTATTGTCTTAGAAGT 58.269 37.500 0.00 0.00 0.00 3.01
179 184 6.869695 TCGCACCATTATTGTCTTAGAAGTA 58.130 36.000 0.00 0.00 0.00 2.24
233 238 3.658757 TCTTCGCAAAAATGAAAGGGG 57.341 42.857 0.00 0.00 0.00 4.79
234 239 2.068519 CTTCGCAAAAATGAAAGGGGC 58.931 47.619 0.00 0.00 0.00 5.80
235 240 1.043816 TCGCAAAAATGAAAGGGGCA 58.956 45.000 0.00 0.00 0.00 5.36
236 241 1.000731 TCGCAAAAATGAAAGGGGCAG 59.999 47.619 0.00 0.00 0.00 4.85
237 242 1.159285 GCAAAAATGAAAGGGGCAGC 58.841 50.000 0.00 0.00 0.00 5.25
238 243 1.431496 CAAAAATGAAAGGGGCAGCG 58.569 50.000 0.00 0.00 0.00 5.18
239 244 0.320683 AAAAATGAAAGGGGCAGCGC 60.321 50.000 0.00 0.00 0.00 5.92
256 261 2.906458 CCCACTCTGGCTAGCAGG 59.094 66.667 18.24 8.44 35.79 4.85
301 307 5.828299 TTTCGGCGAATATTTCCATTCTT 57.172 34.783 24.33 0.00 33.54 2.52
381 388 1.874320 GCTCTGCGTATTTAGCCCCTC 60.874 57.143 0.00 0.00 0.00 4.30
382 389 0.387929 TCTGCGTATTTAGCCCCTCG 59.612 55.000 0.00 0.00 0.00 4.63
383 390 0.600255 CTGCGTATTTAGCCCCTCGG 60.600 60.000 0.00 0.00 0.00 4.63
452 465 2.514824 GCTGCGACAATCTCCCCC 60.515 66.667 0.00 0.00 0.00 5.40
456 469 2.106683 GCGACAATCTCCCCCGTTG 61.107 63.158 0.00 0.00 0.00 4.10
462 475 1.250840 AATCTCCCCCGTTGCAAAGC 61.251 55.000 0.00 0.00 0.00 3.51
463 476 2.142292 ATCTCCCCCGTTGCAAAGCT 62.142 55.000 0.00 0.00 0.00 3.74
465 478 1.866853 CTCCCCCGTTGCAAAGCTTC 61.867 60.000 0.00 0.00 0.00 3.86
466 479 2.255252 CCCCGTTGCAAAGCTTCG 59.745 61.111 0.00 0.00 0.00 3.79
467 480 2.429069 CCCGTTGCAAAGCTTCGC 60.429 61.111 1.34 1.34 0.00 4.70
469 482 2.429069 CGTTGCAAAGCTTCGCCC 60.429 61.111 6.97 0.00 0.00 6.13
550 572 4.084888 CAGCCGAACCGCGAAACC 62.085 66.667 8.23 0.00 44.57 3.27
569 591 2.203394 CCCATGATGCTTCCCGGG 60.203 66.667 16.85 16.85 0.00 5.73
1003 1027 2.732468 CAGATCTCGCCGCGATGG 60.732 66.667 17.22 5.76 42.50 3.51
1368 1433 1.374252 GCTCTTCACCTTCGCCGAA 60.374 57.895 0.00 0.00 0.00 4.30
1701 1766 3.144120 CTACTGCATCTCGGCCGCT 62.144 63.158 23.51 4.26 0.00 5.52
1914 1979 2.187073 AGCTAACATTGCTGCAGCC 58.813 52.632 34.64 17.04 39.56 4.85
1986 2051 6.147581 CCAGATCTTCTTGTTTGTTGATGTG 58.852 40.000 0.00 0.00 0.00 3.21
2079 2144 1.898574 CAAGGCTGCACGAACCCTT 60.899 57.895 0.50 0.00 38.17 3.95
2154 2219 7.097192 TGTACTTCACAAGGATCATTGTCTAC 58.903 38.462 22.08 17.19 41.41 2.59
2357 2422 1.201181 CGAGCTCTAGAGTGTTGCTGT 59.799 52.381 20.75 0.00 33.83 4.40
2595 2667 2.694628 TGCTGTCATTTTGCCAAGTCTT 59.305 40.909 0.00 0.00 0.00 3.01
2607 2679 4.207165 TGCCAAGTCTTAGTTTTGCTTCT 58.793 39.130 0.00 0.00 0.00 2.85
2690 2763 9.193806 AGAACATTGATTAACATCTTAATGCCT 57.806 29.630 0.00 0.00 36.26 4.75
2691 2764 9.455847 GAACATTGATTAACATCTTAATGCCTC 57.544 33.333 0.00 0.00 36.26 4.70
2692 2765 8.523915 ACATTGATTAACATCTTAATGCCTCA 57.476 30.769 0.00 0.00 36.26 3.86
2724 2800 7.661437 TGACAGCAAGATCTGTTAGTGTATTTT 59.339 33.333 0.00 0.00 46.40 1.82
2749 2825 5.977489 TGAAGAAACTTGACGAGGATCTA 57.023 39.130 0.00 0.00 0.00 1.98
2766 2842 7.385894 AGGATCTAGGAATTTGCATAGAACT 57.614 36.000 0.00 0.00 35.17 3.01
2798 2897 1.468520 GTTCGTGCATTGCCATGTACT 59.531 47.619 15.30 0.00 42.31 2.73
2799 2898 1.819928 TCGTGCATTGCCATGTACTT 58.180 45.000 15.30 0.00 42.31 2.24
2800 2899 1.468127 TCGTGCATTGCCATGTACTTG 59.532 47.619 15.30 1.78 42.31 3.16
2801 2900 1.467883 CGTGCATTGCCATGTACTTGG 60.468 52.381 20.77 20.77 42.31 3.61
2809 2908 2.642139 CCATGTACTTGGCTGCAAAG 57.358 50.000 15.13 15.13 0.00 2.77
2810 2909 2.161855 CCATGTACTTGGCTGCAAAGA 58.838 47.619 23.05 1.31 0.00 2.52
2811 2910 2.756760 CCATGTACTTGGCTGCAAAGAT 59.243 45.455 23.05 9.90 0.00 2.40
2812 2911 3.194116 CCATGTACTTGGCTGCAAAGATT 59.806 43.478 23.05 4.50 0.00 2.40
2813 2912 4.322198 CCATGTACTTGGCTGCAAAGATTT 60.322 41.667 23.05 3.77 0.00 2.17
2814 2913 4.241590 TGTACTTGGCTGCAAAGATTTG 57.758 40.909 23.05 0.84 41.03 2.32
2815 2914 3.636300 TGTACTTGGCTGCAAAGATTTGT 59.364 39.130 23.05 3.90 40.24 2.83
2816 2915 4.824537 TGTACTTGGCTGCAAAGATTTGTA 59.175 37.500 23.05 2.91 40.24 2.41
2817 2916 5.476599 TGTACTTGGCTGCAAAGATTTGTAT 59.523 36.000 23.05 1.58 40.24 2.29
2818 2917 4.813027 ACTTGGCTGCAAAGATTTGTATG 58.187 39.130 23.05 0.00 40.24 2.39
2819 2918 3.235157 TGGCTGCAAAGATTTGTATGC 57.765 42.857 0.50 8.38 40.24 3.14
2820 2919 2.827322 TGGCTGCAAAGATTTGTATGCT 59.173 40.909 0.50 0.00 40.24 3.79
2821 2920 3.258872 TGGCTGCAAAGATTTGTATGCTT 59.741 39.130 0.50 0.00 40.24 3.91
2822 2921 3.615496 GGCTGCAAAGATTTGTATGCTTG 59.385 43.478 0.50 0.00 40.24 4.01
2823 2922 3.061697 GCTGCAAAGATTTGTATGCTTGC 59.938 43.478 7.12 0.00 40.24 4.01
2824 2923 3.587923 TGCAAAGATTTGTATGCTTGCC 58.412 40.909 7.12 0.00 40.24 4.52
2873 2972 6.254281 CCTACATGGTTTGTAAACTTGGAG 57.746 41.667 7.36 10.35 40.27 3.86
2893 2992 2.143925 GTCAACAGTAAGACCCAGTGC 58.856 52.381 0.00 0.00 0.00 4.40
2914 3013 4.221482 TGCTCCAGATTAGCATCGTGATAT 59.779 41.667 0.00 0.00 44.78 1.63
2923 3022 7.600375 AGATTAGCATCGTGATATTTGATCGTT 59.400 33.333 0.00 0.00 34.17 3.85
2948 3047 6.283694 TGTTACTGAGCTATCTGCCTTTATG 58.716 40.000 0.00 0.00 44.23 1.90
2958 3057 5.886960 ATCTGCCTTTATGAGTGTGTTTC 57.113 39.130 0.00 0.00 0.00 2.78
2961 3060 5.239306 TCTGCCTTTATGAGTGTGTTTCTTG 59.761 40.000 0.00 0.00 0.00 3.02
2971 3070 5.810587 TGAGTGTGTTTCTTGTCTGAACTAC 59.189 40.000 0.00 0.00 0.00 2.73
2972 3071 5.730550 AGTGTGTTTCTTGTCTGAACTACA 58.269 37.500 0.00 0.00 0.00 2.74
2973 3072 5.812642 AGTGTGTTTCTTGTCTGAACTACAG 59.187 40.000 0.00 0.00 46.97 2.74
2974 3073 5.581085 GTGTGTTTCTTGTCTGAACTACAGT 59.419 40.000 0.00 0.00 45.86 3.55
2975 3074 6.092259 GTGTGTTTCTTGTCTGAACTACAGTT 59.908 38.462 0.00 0.00 45.86 3.16
2976 3075 6.653320 TGTGTTTCTTGTCTGAACTACAGTTT 59.347 34.615 0.00 0.00 45.86 2.66
3010 3109 8.494433 TCCTGAAGTAAGTTATTATTGCCTGAT 58.506 33.333 0.00 0.00 0.00 2.90
3050 3149 2.851195 CACAAGTACAGGCTTTCAGGT 58.149 47.619 0.00 0.00 0.00 4.00
3061 3160 6.303839 ACAGGCTTTCAGGTAAATTGACTTA 58.696 36.000 0.00 0.00 0.00 2.24
3066 3165 7.755373 GGCTTTCAGGTAAATTGACTTATTGAC 59.245 37.037 0.00 0.00 0.00 3.18
3070 3169 8.279970 TCAGGTAAATTGACTTATTGACATGG 57.720 34.615 0.00 0.00 33.48 3.66
3354 3453 5.992217 ACATATTTAGGCTCTGTTCGGAATC 59.008 40.000 0.00 0.00 0.00 2.52
3362 3461 1.825474 TCTGTTCGGAATCTCTCCACC 59.175 52.381 0.00 0.00 45.74 4.61
3364 3463 0.178301 GTTCGGAATCTCTCCACCCC 59.822 60.000 0.00 0.00 45.74 4.95
3373 3472 3.322466 CTCCACCCCGCTCCACTT 61.322 66.667 0.00 0.00 0.00 3.16
3380 3479 2.359975 CCGCTCCACTTTGGGGAC 60.360 66.667 0.00 0.00 41.85 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.288518 GCCGTCCAGAGTAGGATTCATC 60.289 54.545 0.00 0.00 40.42 2.92
1 2 1.689273 GCCGTCCAGAGTAGGATTCAT 59.311 52.381 0.00 0.00 40.42 2.57
2 3 1.112113 GCCGTCCAGAGTAGGATTCA 58.888 55.000 0.00 0.00 40.42 2.57
3 4 1.112113 TGCCGTCCAGAGTAGGATTC 58.888 55.000 0.00 0.00 40.42 2.52
4 5 1.207329 GTTGCCGTCCAGAGTAGGATT 59.793 52.381 0.00 0.00 40.42 3.01
5 6 0.824759 GTTGCCGTCCAGAGTAGGAT 59.175 55.000 0.00 0.00 40.42 3.24
6 7 1.592400 CGTTGCCGTCCAGAGTAGGA 61.592 60.000 0.00 0.00 34.64 2.94
7 8 1.153823 CGTTGCCGTCCAGAGTAGG 60.154 63.158 0.00 0.00 0.00 3.18
8 9 0.179161 CTCGTTGCCGTCCAGAGTAG 60.179 60.000 0.00 0.00 35.01 2.57
9 10 0.607217 TCTCGTTGCCGTCCAGAGTA 60.607 55.000 0.00 0.00 35.01 2.59
10 11 1.901948 TCTCGTTGCCGTCCAGAGT 60.902 57.895 0.00 0.00 35.01 3.24
11 12 1.444553 GTCTCGTTGCCGTCCAGAG 60.445 63.158 0.00 0.00 35.01 3.35
12 13 2.649034 GTCTCGTTGCCGTCCAGA 59.351 61.111 0.00 0.00 35.01 3.86
13 14 2.805353 CGTCTCGTTGCCGTCCAG 60.805 66.667 0.00 0.00 35.01 3.86
14 15 4.351938 CCGTCTCGTTGCCGTCCA 62.352 66.667 0.00 0.00 35.01 4.02
43 44 1.077645 CGAACAGCTCTGCTCTGCTC 61.078 60.000 0.00 0.00 36.40 4.26
44 45 1.079956 CGAACAGCTCTGCTCTGCT 60.080 57.895 0.00 0.00 36.40 4.24
47 49 1.589113 GACCGAACAGCTCTGCTCT 59.411 57.895 0.00 0.00 36.40 4.09
65 70 1.654220 CAACAACCGACCAAGCAGG 59.346 57.895 0.00 0.00 45.67 4.85
170 175 8.132362 GTGACAGTGACATCCTATACTTCTAAG 58.868 40.741 0.00 0.00 0.00 2.18
178 183 3.704566 GGTGGTGACAGTGACATCCTATA 59.295 47.826 3.38 0.00 44.46 1.31
179 184 2.501723 GGTGGTGACAGTGACATCCTAT 59.498 50.000 3.38 0.00 44.46 2.57
208 213 3.724508 TTCATTTTTGCGAAGAAGCCA 57.275 38.095 0.00 0.00 36.02 4.75
216 221 1.000731 CTGCCCCTTTCATTTTTGCGA 59.999 47.619 0.00 0.00 0.00 5.10
239 244 2.739996 CCCTGCTAGCCAGAGTGGG 61.740 68.421 13.29 10.03 44.64 4.61
240 245 2.906458 CCCTGCTAGCCAGAGTGG 59.094 66.667 13.29 4.79 44.64 4.00
241 246 2.188994 GCCCTGCTAGCCAGAGTG 59.811 66.667 13.29 0.00 44.64 3.51
242 247 2.284921 TGCCCTGCTAGCCAGAGT 60.285 61.111 13.29 0.00 44.64 3.24
243 248 2.188994 GTGCCCTGCTAGCCAGAG 59.811 66.667 13.29 2.59 44.64 3.35
244 249 3.402681 GGTGCCCTGCTAGCCAGA 61.403 66.667 13.29 0.00 44.64 3.86
245 250 2.490270 AAAGGTGCCCTGCTAGCCAG 62.490 60.000 13.29 9.57 41.41 4.85
246 251 2.080336 AAAAGGTGCCCTGCTAGCCA 62.080 55.000 13.29 0.00 32.13 4.75
247 252 1.304464 AAAAGGTGCCCTGCTAGCC 60.304 57.895 13.29 0.00 32.13 3.93
248 253 1.315981 GGAAAAGGTGCCCTGCTAGC 61.316 60.000 8.10 8.10 32.13 3.42
249 254 0.329596 AGGAAAAGGTGCCCTGCTAG 59.670 55.000 0.00 0.00 32.13 3.42
256 261 9.529325 GAAAAATATATGTTAGGAAAAGGTGCC 57.471 33.333 0.00 0.00 0.00 5.01
274 279 8.576442 AGAATGGAAATATTCGCCGAAAAATAT 58.424 29.630 2.60 0.00 40.99 1.28
301 307 2.685897 AGCAGAAAAGTTGTTAACCGCA 59.314 40.909 2.48 0.00 0.00 5.69
469 482 4.147322 GTTGATGCGGCCGTGACG 62.147 66.667 28.70 0.00 36.98 4.35
479 492 3.478394 TGTCGAGCGCGTTGATGC 61.478 61.111 10.30 0.00 38.98 3.91
480 493 1.686566 ATGTGTCGAGCGCGTTGATG 61.687 55.000 10.30 0.00 38.98 3.07
481 494 1.014044 AATGTGTCGAGCGCGTTGAT 61.014 50.000 10.30 0.00 35.68 2.57
482 495 1.218875 AAATGTGTCGAGCGCGTTGA 61.219 50.000 10.30 0.00 36.96 3.18
483 496 0.785708 GAAATGTGTCGAGCGCGTTG 60.786 55.000 10.30 0.00 36.96 4.10
484 497 1.218875 TGAAATGTGTCGAGCGCGTT 61.219 50.000 10.30 0.00 38.35 4.84
550 572 2.203394 CGGGAAGCATCATGGGGG 60.203 66.667 0.00 0.00 0.00 5.40
555 577 0.474184 CCTTACCCGGGAAGCATCAT 59.526 55.000 32.02 3.84 0.00 2.45
569 591 0.320160 ACTTTGACCGGCGACCTTAC 60.320 55.000 9.30 0.00 0.00 2.34
1224 1265 0.972983 CGGAGAGGAGGAAGAAGCCA 60.973 60.000 0.00 0.00 0.00 4.75
1388 1453 1.228154 ACGGGGAAGGTCTTGTTGC 60.228 57.895 0.00 0.00 0.00 4.17
1701 1766 1.195115 GGATGTAGTGCTGGTCCTCA 58.805 55.000 0.00 0.00 0.00 3.86
1914 1979 2.430244 CCGGTCTCACCAACGACG 60.430 66.667 0.00 0.00 38.47 5.12
1951 2016 4.916041 AGAAGATCTGGTTCCATGTCAA 57.084 40.909 0.00 0.00 0.00 3.18
2154 2219 1.291184 TGGTGATTGTCTTGAGCGCG 61.291 55.000 0.00 0.00 0.00 6.86
2357 2422 2.974794 CCTGTCATCATGTATCCCCTCA 59.025 50.000 0.00 0.00 0.00 3.86
2607 2679 6.926630 AAAGGAAATATAACAAGTGGGCAA 57.073 33.333 0.00 0.00 0.00 4.52
2684 2757 6.301486 TCTTGCTGTCATATTATGAGGCATT 58.699 36.000 23.24 0.00 43.55 3.56
2724 2800 4.600692 TCCTCGTCAAGTTTCTTCATCA 57.399 40.909 0.00 0.00 0.00 3.07
2740 2816 6.030548 TCTATGCAAATTCCTAGATCCTCG 57.969 41.667 0.00 0.00 0.00 4.63
2749 2825 4.460382 CACACCAGTTCTATGCAAATTCCT 59.540 41.667 0.00 0.00 0.00 3.36
2766 2842 0.660488 GCACGAACAATCACACACCA 59.340 50.000 0.00 0.00 0.00 4.17
2798 2897 3.258872 AGCATACAAATCTTTGCAGCCAA 59.741 39.130 2.63 0.00 41.79 4.52
2799 2898 2.827322 AGCATACAAATCTTTGCAGCCA 59.173 40.909 2.63 0.00 41.79 4.75
2800 2899 3.515330 AGCATACAAATCTTTGCAGCC 57.485 42.857 2.63 0.00 41.79 4.85
2801 2900 3.061697 GCAAGCATACAAATCTTTGCAGC 59.938 43.478 2.63 4.91 41.79 5.25
2802 2901 3.615496 GGCAAGCATACAAATCTTTGCAG 59.385 43.478 8.93 0.00 41.79 4.41
2803 2902 3.258872 AGGCAAGCATACAAATCTTTGCA 59.741 39.130 8.93 0.00 41.79 4.08
2804 2903 3.615496 CAGGCAAGCATACAAATCTTTGC 59.385 43.478 2.63 0.00 41.79 3.68
2805 2904 5.063180 TCAGGCAAGCATACAAATCTTTG 57.937 39.130 1.19 1.19 43.62 2.77
2806 2905 4.768968 ACTCAGGCAAGCATACAAATCTTT 59.231 37.500 0.00 0.00 0.00 2.52
2807 2906 4.338879 ACTCAGGCAAGCATACAAATCTT 58.661 39.130 0.00 0.00 0.00 2.40
2808 2907 3.960571 ACTCAGGCAAGCATACAAATCT 58.039 40.909 0.00 0.00 0.00 2.40
2809 2908 4.260948 GCTACTCAGGCAAGCATACAAATC 60.261 45.833 0.00 0.00 36.26 2.17
2810 2909 3.629398 GCTACTCAGGCAAGCATACAAAT 59.371 43.478 0.00 0.00 36.26 2.32
2811 2910 3.009723 GCTACTCAGGCAAGCATACAAA 58.990 45.455 0.00 0.00 36.26 2.83
2812 2911 2.027285 TGCTACTCAGGCAAGCATACAA 60.027 45.455 0.00 0.00 41.15 2.41
2813 2912 1.554617 TGCTACTCAGGCAAGCATACA 59.445 47.619 0.00 0.00 41.15 2.29
2814 2913 2.315925 TGCTACTCAGGCAAGCATAC 57.684 50.000 0.00 0.00 41.15 2.39
2816 2915 3.963733 TTGCTACTCAGGCAAGCAT 57.036 47.368 0.02 0.00 45.09 3.79
2864 2963 5.123936 GGTCTTACTGTTGACTCCAAGTTT 58.876 41.667 11.46 0.00 34.01 2.66
2873 2972 2.143925 GCACTGGGTCTTACTGTTGAC 58.856 52.381 5.45 5.45 0.00 3.18
2893 2992 6.870439 TCAAATATCACGATGCTAATCTGGAG 59.130 38.462 0.00 0.00 0.00 3.86
2914 3013 7.063426 CAGATAGCTCAGTAACAAACGATCAAA 59.937 37.037 0.00 0.00 0.00 2.69
2923 3022 4.826274 AAGGCAGATAGCTCAGTAACAA 57.174 40.909 0.00 0.00 44.79 2.83
2948 3047 5.810587 TGTAGTTCAGACAAGAAACACACTC 59.189 40.000 0.00 0.00 0.00 3.51
3010 3109 8.100791 ACTTGTGCTAGAAATGTATCTGGTAAA 58.899 33.333 0.00 0.00 31.15 2.01
3354 3453 3.775654 GTGGAGCGGGGTGGAGAG 61.776 72.222 0.00 0.00 0.00 3.20
3362 3461 3.646715 TCCCCAAAGTGGAGCGGG 61.647 66.667 0.00 0.00 40.96 6.13
3364 3463 2.359975 GGTCCCCAAAGTGGAGCG 60.360 66.667 0.00 0.00 40.96 5.03
3373 3472 1.048724 CGAGCTCCATAGGTCCCCAA 61.049 60.000 8.47 0.00 45.60 4.12
3380 3479 2.231215 CTCAAACCGAGCTCCATAGG 57.769 55.000 8.47 5.95 34.18 2.57


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

AutoCloner maintained by Alex Coulton.