Multiple sequence alignment - TraesCS2B01G302500

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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 TraesCS2B01G302500 chr2B 100.000 4173 0 0 1 4173 426149594 426145422 0.000000e+00 7707
1 TraesCS2B01G302500 chr2B 92.105 342 24 3 3834 4173 458842721 458842381 2.920000e-131 479
2 TraesCS2B01G302500 chr2A 92.980 3903 202 26 298 4173 481806080 481809937 0.000000e+00 5624
3 TraesCS2B01G302500 chr2A 88.502 287 33 0 1 287 481805811 481806097 8.590000e-92 348
4 TraesCS2B01G302500 chr2D 92.516 3915 177 26 297 4173 359938672 359942508 0.000000e+00 5500
5 TraesCS2B01G302500 chr2D 92.082 341 26 1 3834 4173 353164374 353164034 2.920000e-131 479
6 TraesCS2B01G302500 chr2D 90.196 204 20 0 2 205 359938454 359938657 2.470000e-67 267
7 TraesCS2B01G302500 chr7D 91.931 347 22 6 3830 4173 480459919 480459576 8.110000e-132 481
8 TraesCS2B01G302500 chr7D 91.254 343 26 4 3834 4173 239760981 239761322 8.170000e-127 464
9 TraesCS2B01G302500 chr4B 91.117 349 24 6 3830 4173 300425173 300425519 2.270000e-127 466
10 TraesCS2B01G302500 chr6D 90.751 346 30 2 3830 4173 404619288 404618943 1.060000e-125 460
11 TraesCS2B01G302500 chr5D 90.725 345 28 3 3830 4171 12964361 12964704 1.370000e-124 457


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 TraesCS2B01G302500 chr2B 426145422 426149594 4172 True 7707.0 7707 100.000 1 4173 1 chr2B.!!$R1 4172
1 TraesCS2B01G302500 chr2A 481805811 481809937 4126 False 2986.0 5624 90.741 1 4173 2 chr2A.!!$F1 4172
2 TraesCS2B01G302500 chr2D 359938454 359942508 4054 False 2883.5 5500 91.356 2 4173 2 chr2D.!!$F1 4171

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
668 670 0.035598 TGGTCGAAAATCTTGGCGGA 59.964 50.0 0.0 0.0 0.00 5.54 F
2469 2497 0.248539 GAGGACACCTACATCGACGC 60.249 60.0 0.0 0.0 31.76 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2516 2544 0.038599 TGCTTCATCATGGTGGCTGT 59.961 50.0 6.03 0.0 0.00 4.40 R
3646 3708 0.248907 CACGATTGGAGCGGACGTAT 60.249 55.0 0.00 0.0 35.78 3.06 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
28 29 9.730705 TGTCATCTTGAAACTCTGATTTAGATT 57.269 29.630 0.00 0.00 34.21 2.40
38 39 5.104318 ACTCTGATTTAGATTTGAGTCCCCC 60.104 44.000 0.00 0.00 34.21 5.40
108 109 2.789208 CAATTGCGTGGAAGTATGCAG 58.211 47.619 0.00 0.00 42.91 4.41
171 172 6.043411 GCACTAGATTTTCTCGTCCTTGTAT 58.957 40.000 0.00 0.00 0.00 2.29
177 178 8.302515 AGATTTTCTCGTCCTTGTATAGGTTA 57.697 34.615 0.00 0.00 45.03 2.85
216 217 2.093341 TGCTCATCTGCATTGCTACTCA 60.093 45.455 10.49 0.00 38.12 3.41
229 230 5.710513 TTGCTACTCATGCTTTGACAAAT 57.289 34.783 0.05 0.00 0.00 2.32
231 232 4.156556 TGCTACTCATGCTTTGACAAATCC 59.843 41.667 0.05 0.00 0.00 3.01
236 237 5.244402 ACTCATGCTTTGACAAATCCATCAA 59.756 36.000 0.05 0.00 33.03 2.57
241 242 4.560035 GCTTTGACAAATCCATCAACATCG 59.440 41.667 0.05 0.00 34.61 3.84
248 249 1.031571 TCCATCAACATCGGCCTTGC 61.032 55.000 0.00 0.00 0.00 4.01
249 250 1.063006 CATCAACATCGGCCTTGCG 59.937 57.895 0.00 0.00 0.00 4.85
280 281 8.908903 AGATAGACAATCTCGTGAAAAGTATCT 58.091 33.333 0.00 0.00 41.32 1.98
282 283 9.953697 ATAGACAATCTCGTGAAAAGTATCTAC 57.046 33.333 0.00 0.00 0.00 2.59
283 284 8.057536 AGACAATCTCGTGAAAAGTATCTACT 57.942 34.615 0.00 0.00 38.39 2.57
309 310 6.956102 TTTTAGGGGTGTGAAAGGTATCTA 57.044 37.500 0.00 0.00 0.00 1.98
333 334 5.712446 ACTTTTAAGATCTTCTTGCCCCTTC 59.288 40.000 12.24 0.00 37.29 3.46
341 342 3.200825 TCTTCTTGCCCCTTCCTCTATTG 59.799 47.826 0.00 0.00 0.00 1.90
348 349 0.183731 CCTTCCTCTATTGGCACCCC 59.816 60.000 0.00 0.00 0.00 4.95
350 351 1.632018 TTCCTCTATTGGCACCCCGG 61.632 60.000 0.00 0.00 0.00 5.73
473 475 5.519722 TGTTTCCGCAAAAATCTCTTCTTC 58.480 37.500 0.00 0.00 0.00 2.87
490 492 3.572584 TCTTCGAACCTCTTAACTTCGC 58.427 45.455 0.00 0.00 37.34 4.70
506 508 3.131400 ACTTCGCAGAAGAATCTAGGGTC 59.869 47.826 20.18 0.00 45.90 4.46
524 526 2.921126 GTCACGCTTGACCATTTTCTG 58.079 47.619 12.13 0.00 45.77 3.02
526 528 0.598065 ACGCTTGACCATTTTCTGCC 59.402 50.000 0.00 0.00 0.00 4.85
527 529 0.597568 CGCTTGACCATTTTCTGCCA 59.402 50.000 0.00 0.00 0.00 4.92
533 535 2.557924 TGACCATTTTCTGCCACATGAC 59.442 45.455 0.00 0.00 0.00 3.06
545 547 5.124617 TCTGCCACATGACGCAAATAAATAA 59.875 36.000 0.00 0.00 33.87 1.40
596 598 6.425577 TTCCGTTACGAATTTCTTATTGGG 57.574 37.500 6.24 0.00 0.00 4.12
663 665 4.568152 AAGGTGTTGGTCGAAAATCTTG 57.432 40.909 0.00 0.00 0.00 3.02
664 666 2.884639 AGGTGTTGGTCGAAAATCTTGG 59.115 45.455 0.00 0.00 0.00 3.61
668 670 0.035598 TGGTCGAAAATCTTGGCGGA 59.964 50.000 0.00 0.00 0.00 5.54
877 886 0.845102 ATGGGGAGACGGGAAAACCT 60.845 55.000 0.00 0.00 36.97 3.50
1273 1282 0.600557 CGATCTCGATCCTCCCCTTG 59.399 60.000 1.57 0.00 43.02 3.61
1316 1325 3.276846 GTGTGGCGCGTGTTTCCT 61.277 61.111 8.43 0.00 0.00 3.36
1436 1445 2.202851 AGCTCTGCGGCGAGATTG 60.203 61.111 12.98 1.36 37.29 2.67
1536 1545 3.007516 CGTGCCGTTGTTCGACAA 58.992 55.556 0.00 0.00 42.86 3.18
1576 1585 3.053842 AGTCTGATGGCAGGTTGATTGAT 60.054 43.478 0.00 0.00 42.53 2.57
1628 1637 8.477256 GGATCAATAATTTTCCCTGTGAATTGA 58.523 33.333 0.00 0.00 33.70 2.57
1629 1638 9.305925 GATCAATAATTTTCCCTGTGAATTGAC 57.694 33.333 0.00 0.00 32.62 3.18
1633 1643 8.831715 ATAATTTTCCCTGTGAATTGACAAAC 57.168 30.769 0.00 0.00 31.67 2.93
1658 1668 6.670695 AAAACTGTCATAAGCAGGGAAAAT 57.329 33.333 0.00 0.00 38.22 1.82
1811 1823 1.479709 TGGTTGATTATTTGCCCCGG 58.520 50.000 0.00 0.00 0.00 5.73
1935 1947 4.471904 TCAATATGCTCTTCGAACCTGT 57.528 40.909 0.00 0.00 0.00 4.00
1969 1981 6.104665 CCATATCGTCAGATACATTGCATCT 58.895 40.000 0.00 0.00 41.66 2.90
1970 1982 7.093771 ACCATATCGTCAGATACATTGCATCTA 60.094 37.037 0.00 0.00 41.66 1.98
1998 2010 8.827177 TGATCTAGTACTTCGTTGTTGAAATT 57.173 30.769 0.00 0.00 0.00 1.82
2129 2156 2.759795 GGCTCAGGGTCCTTGCTT 59.240 61.111 0.00 0.00 0.00 3.91
2141 2168 3.371285 GGTCCTTGCTTCTTATGTTCGAC 59.629 47.826 0.00 0.00 0.00 4.20
2435 2463 0.535335 GCTCCCGTACCATGTCTTCA 59.465 55.000 0.00 0.00 0.00 3.02
2469 2497 0.248539 GAGGACACCTACATCGACGC 60.249 60.000 0.00 0.00 31.76 5.19
2516 2544 2.418356 GGTGGGACAACGACGTGA 59.582 61.111 0.00 0.00 44.16 4.35
2517 2545 1.952635 GGTGGGACAACGACGTGAC 60.953 63.158 0.00 0.00 44.16 3.67
2578 2606 1.873591 GTGCTGACCTTCAACGTCATT 59.126 47.619 0.00 0.00 39.43 2.57
2707 2735 3.128188 CAGCAGCAGCAGCAGGAG 61.128 66.667 12.92 0.00 45.49 3.69
2708 2736 4.411981 AGCAGCAGCAGCAGGAGG 62.412 66.667 12.92 0.00 45.49 4.30
2709 2737 4.405671 GCAGCAGCAGCAGGAGGA 62.406 66.667 4.63 0.00 45.49 3.71
2710 2738 2.125065 CAGCAGCAGCAGGAGGAG 60.125 66.667 3.17 0.00 45.49 3.69
2711 2739 3.400928 AGCAGCAGCAGGAGGAGG 61.401 66.667 3.17 0.00 45.49 4.30
2712 2740 3.397439 GCAGCAGCAGGAGGAGGA 61.397 66.667 0.00 0.00 41.58 3.71
2713 2741 2.901813 CAGCAGCAGGAGGAGGAG 59.098 66.667 0.00 0.00 0.00 3.69
2714 2742 2.365370 AGCAGCAGGAGGAGGAGG 60.365 66.667 0.00 0.00 0.00 4.30
2715 2743 2.364842 GCAGCAGGAGGAGGAGGA 60.365 66.667 0.00 0.00 0.00 3.71
2945 2973 2.891936 GCGCGTGGCTGATGATGA 60.892 61.111 8.43 0.00 39.11 2.92
2946 2974 2.463620 GCGCGTGGCTGATGATGAA 61.464 57.895 8.43 0.00 39.11 2.57
2947 2975 1.640069 CGCGTGGCTGATGATGAAG 59.360 57.895 0.00 0.00 0.00 3.02
2948 2976 1.354506 GCGTGGCTGATGATGAAGC 59.645 57.895 0.00 0.00 38.76 3.86
2949 2977 1.371337 GCGTGGCTGATGATGAAGCA 61.371 55.000 0.00 0.00 41.36 3.91
2950 2978 0.656259 CGTGGCTGATGATGAAGCAG 59.344 55.000 0.00 0.00 41.36 4.24
2955 2983 1.379527 CTGATGATGAAGCAGCAGCA 58.620 50.000 3.17 3.59 43.70 4.41
2956 2984 1.379527 TGATGATGAAGCAGCAGCAG 58.620 50.000 3.17 0.00 41.14 4.24
2957 2985 0.029567 GATGATGAAGCAGCAGCAGC 59.970 55.000 3.17 0.46 45.49 5.25
2958 2986 0.679960 ATGATGAAGCAGCAGCAGCA 60.680 50.000 12.92 7.75 45.49 4.41
2959 2987 1.136984 GATGAAGCAGCAGCAGCAC 59.863 57.895 12.92 6.32 45.49 4.40
2960 2988 2.267681 GATGAAGCAGCAGCAGCACC 62.268 60.000 12.92 3.65 45.49 5.01
2961 2989 2.981909 GAAGCAGCAGCAGCACCA 60.982 61.111 12.92 0.00 45.49 4.17
2962 2990 3.264866 GAAGCAGCAGCAGCACCAC 62.265 63.158 12.92 0.00 45.49 4.16
2965 2993 3.667282 CAGCAGCAGCACCACCAC 61.667 66.667 3.17 0.00 45.49 4.16
2966 2994 4.962836 AGCAGCAGCACCACCACC 62.963 66.667 3.17 0.00 45.49 4.61
2968 2996 3.289834 CAGCAGCACCACCACCAC 61.290 66.667 0.00 0.00 0.00 4.16
3192 3247 6.266558 CAGTAGGGCTTAGTATCATCAGACTT 59.733 42.308 0.00 0.00 0.00 3.01
3243 3303 3.016031 TGTGCATGTGTTCTGTGAACTT 58.984 40.909 11.06 0.00 0.00 2.66
3351 3411 1.269166 GATAAGTGCGACACGTCAGG 58.731 55.000 2.27 0.00 39.64 3.86
3352 3412 0.601558 ATAAGTGCGACACGTCAGGT 59.398 50.000 2.27 0.00 39.64 4.00
3413 3473 4.437390 GCAATTCGAGTTACACAAGGATGG 60.437 45.833 0.00 0.00 0.00 3.51
3414 3474 4.819105 ATTCGAGTTACACAAGGATGGA 57.181 40.909 0.00 0.00 0.00 3.41
3431 3491 6.708285 AGGATGGAAATTTCTAGTAACACGT 58.292 36.000 17.42 0.20 0.00 4.49
3465 3526 9.770097 TTTTGTCAAAATAAAATGCTCATACCA 57.230 25.926 6.65 0.00 0.00 3.25
3483 3544 1.136085 CCAAACGTGTGGCACTTATCG 60.136 52.381 19.83 18.40 31.34 2.92
3510 3572 2.340809 CCACCTAACGCCGTGTGA 59.659 61.111 7.66 0.00 0.00 3.58
3533 3595 4.388499 GTCCACGGACACGGCCAT 62.388 66.667 11.43 0.00 46.48 4.40
3540 3602 2.340328 GGACACGGCCATTTCCACC 61.340 63.158 2.24 0.00 0.00 4.61
3577 3639 4.202111 GCAAACCAACACTAAACTGTGGAT 60.202 41.667 0.00 0.00 41.84 3.41
3646 3708 1.725169 CCACCCAAAACCCTCTCCCA 61.725 60.000 0.00 0.00 0.00 4.37
3669 3731 2.055633 TCCGCTCCAATCGTGCCTA 61.056 57.895 0.00 0.00 0.00 3.93
3715 3782 2.486636 TTAGAGCGGACGTGCCACTG 62.487 60.000 0.00 0.00 35.94 3.66
3769 3836 2.434359 GGCGTGGCTTAGAGCGTT 60.434 61.111 0.00 0.00 43.62 4.84
3772 3839 1.566018 GCGTGGCTTAGAGCGTTGTT 61.566 55.000 0.00 0.00 43.62 2.83
3864 3931 1.373570 CTCAAATGCCCGAGGTCTTC 58.626 55.000 0.00 0.00 0.00 2.87
3865 3932 0.690192 TCAAATGCCCGAGGTCTTCA 59.310 50.000 0.00 0.00 0.00 3.02
3981 4048 6.713903 ACTCCTCGCATTGATATCAATTGATT 59.286 34.615 25.16 13.38 43.48 2.57
3987 4054 6.367695 CGCATTGATATCAATTGATTGGCATT 59.632 34.615 25.16 13.81 43.48 3.56
3993 4060 9.091220 TGATATCAATTGATTGGCATTTCCATA 57.909 29.630 25.26 3.85 46.04 2.74
4010 4077 2.421107 CCATAGCCTGTTGATCAGCTGT 60.421 50.000 14.67 7.60 42.38 4.40
4019 4086 3.056891 TGTTGATCAGCTGTGTCGATGTA 60.057 43.478 14.67 0.00 0.00 2.29
4076 4146 8.423906 AATCTCTACCACGTATTCTATTCCAT 57.576 34.615 0.00 0.00 0.00 3.41
4077 4147 7.450124 TCTCTACCACGTATTCTATTCCATC 57.550 40.000 0.00 0.00 0.00 3.51
4102 4172 6.600427 CCATAGTGATATATTCATGGCTTGCA 59.400 38.462 0.00 0.00 36.54 4.08
4114 4184 2.794103 TGGCTTGCACTCATGTATTGT 58.206 42.857 0.00 0.00 0.00 2.71
4115 4185 2.749076 TGGCTTGCACTCATGTATTGTC 59.251 45.455 0.00 0.00 0.00 3.18
4125 4195 4.194640 CTCATGTATTGTCTGGGAGTTGG 58.805 47.826 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.119495 GAGCAGGGGGACTCAAATCTA 58.881 52.381 0.00 0.00 32.98 1.98
28 29 2.224159 GGTGAGCAGGGGGACTCAA 61.224 63.158 0.00 0.00 44.14 3.02
38 39 3.264947 TCTCAAATTGATCGGTGAGCAG 58.735 45.455 0.00 0.00 37.90 4.24
70 71 5.617308 GCAATTGCCAATGGTTGTAAACATG 60.617 40.000 20.06 0.00 41.57 3.21
71 72 4.455190 GCAATTGCCAATGGTTGTAAACAT 59.545 37.500 20.06 0.00 41.57 2.71
108 109 2.878406 TGCTTAAAAGGGATGCTATCGC 59.122 45.455 5.46 5.46 42.02 4.58
198 199 2.876550 GCATGAGTAGCAATGCAGATGA 59.123 45.455 8.35 0.00 39.61 2.92
199 200 2.879026 AGCATGAGTAGCAATGCAGATG 59.121 45.455 8.35 3.05 42.06 2.90
216 217 5.471556 TGTTGATGGATTTGTCAAAGCAT 57.528 34.783 15.03 6.97 36.23 3.79
229 230 1.031571 GCAAGGCCGATGTTGATGGA 61.032 55.000 12.38 0.00 0.00 3.41
231 232 1.063006 CGCAAGGCCGATGTTGATG 59.937 57.895 12.38 0.00 0.00 3.07
256 257 9.953697 GTAGATACTTTTCACGAGATTGTCTAT 57.046 33.333 0.00 0.00 0.00 1.98
257 258 9.175312 AGTAGATACTTTTCACGAGATTGTCTA 57.825 33.333 0.00 0.00 31.13 2.59
285 286 6.208840 AGATACCTTTCACACCCCTAAAAA 57.791 37.500 0.00 0.00 0.00 1.94
286 287 5.853572 AGATACCTTTCACACCCCTAAAA 57.146 39.130 0.00 0.00 0.00 1.52
287 288 6.027482 AGTAGATACCTTTCACACCCCTAAA 58.973 40.000 0.00 0.00 0.00 1.85
288 289 5.596763 AGTAGATACCTTTCACACCCCTAA 58.403 41.667 0.00 0.00 0.00 2.69
289 290 5.216665 AGTAGATACCTTTCACACCCCTA 57.783 43.478 0.00 0.00 0.00 3.53
290 291 4.076175 AGTAGATACCTTTCACACCCCT 57.924 45.455 0.00 0.00 0.00 4.79
291 292 4.838904 AAGTAGATACCTTTCACACCCC 57.161 45.455 0.00 0.00 0.00 4.95
292 293 8.098912 TCTTAAAAGTAGATACCTTTCACACCC 58.901 37.037 0.00 0.00 0.00 4.61
293 294 9.668497 ATCTTAAAAGTAGATACCTTTCACACC 57.332 33.333 0.00 0.00 30.74 4.16
309 310 5.262455 AGGGGCAAGAAGATCTTAAAAGT 57.738 39.130 8.25 0.00 33.78 2.66
333 334 2.510906 CCGGGGTGCCAATAGAGG 59.489 66.667 0.00 0.00 0.00 3.69
348 349 1.791103 TTTGCCCTTTCTTCGTGCCG 61.791 55.000 0.00 0.00 0.00 5.69
350 351 0.664466 GCTTTGCCCTTTCTTCGTGC 60.664 55.000 0.00 0.00 0.00 5.34
352 353 2.341452 GGCTTTGCCCTTTCTTCGT 58.659 52.632 0.00 0.00 44.06 3.85
450 452 5.514274 AAGAAGAGATTTTTGCGGAAACA 57.486 34.783 0.00 0.00 0.00 2.83
473 475 2.942710 TCTGCGAAGTTAAGAGGTTCG 58.057 47.619 0.00 0.00 44.63 3.95
490 492 2.428890 AGCGTGACCCTAGATTCTTCTG 59.571 50.000 0.00 0.00 33.17 3.02
506 508 1.666888 GGCAGAAAATGGTCAAGCGTG 60.667 52.381 0.00 0.00 0.00 5.34
524 526 7.922505 TTATTATTTATTTGCGTCATGTGGC 57.077 32.000 0.00 0.00 0.00 5.01
556 558 8.730427 CGTAACGGAAATGAAAATAAATGTAGC 58.270 33.333 0.00 0.00 0.00 3.58
596 598 6.698329 TCATTTATTGCTGTATCAATGCTTGC 59.302 34.615 0.00 0.00 37.27 4.01
622 624 4.262808 CCTTTTGGATTGCAATTGGTGGTA 60.263 41.667 14.33 0.00 44.07 3.25
663 665 0.390860 ACTACTCAGATGCATCCGCC 59.609 55.000 23.06 0.00 37.32 6.13
664 666 1.202463 ACACTACTCAGATGCATCCGC 60.202 52.381 23.06 0.00 39.24 5.54
668 670 5.201243 TGGTACTACACTACTCAGATGCAT 58.799 41.667 0.00 0.00 0.00 3.96
748 753 8.967664 ATTGCATATTTGGCACTTCATATTTT 57.032 26.923 0.00 0.00 41.75 1.82
877 886 0.960364 GGTCAGCCGGAAATGCTTCA 60.960 55.000 5.05 0.00 36.81 3.02
1273 1282 1.513586 CACGAAGACGACGGCTACC 60.514 63.158 2.15 0.00 42.66 3.18
1316 1325 4.466370 TGGAAGATTCTAGAAGAAGGCGAA 59.534 41.667 11.53 0.00 37.69 4.70
1414 1423 3.192954 CTCGCCGCAGAGCTCCTAG 62.193 68.421 10.93 1.71 0.00 3.02
1436 1445 2.857592 ATCGCAATCTGCACCAAATC 57.142 45.000 0.00 0.00 45.36 2.17
1536 1545 0.319900 CTCGCCGCTGCATATAACCT 60.320 55.000 0.00 0.00 37.32 3.50
1576 1585 5.921408 GCAATTTTTCGTGTTTACCATGGTA 59.079 36.000 21.05 21.05 0.00 3.25
1628 1637 6.042143 CCTGCTTATGACAGTTTTTGTTTGT 58.958 36.000 0.00 0.00 41.05 2.83
1629 1638 5.463061 CCCTGCTTATGACAGTTTTTGTTTG 59.537 40.000 0.00 0.00 41.05 2.93
1633 1643 5.452078 TTCCCTGCTTATGACAGTTTTTG 57.548 39.130 0.00 0.00 33.09 2.44
1658 1668 2.650322 GGGGCAATTTTCTATCGGTCA 58.350 47.619 0.00 0.00 0.00 4.02
1811 1823 8.549548 CATCTGACATGAGTCTATCAATTGTTC 58.450 37.037 5.13 0.00 45.20 3.18
1908 1920 7.172190 CAGGTTCGAAGAGCATATTGAACATAT 59.828 37.037 0.00 2.12 40.41 1.78
1909 1921 6.479990 CAGGTTCGAAGAGCATATTGAACATA 59.520 38.462 0.00 0.00 40.41 2.29
1910 1922 5.295292 CAGGTTCGAAGAGCATATTGAACAT 59.705 40.000 0.00 7.31 40.41 2.71
1935 1947 8.856103 TGTATCTGACGATATGGTCTGATTTAA 58.144 33.333 30.78 18.47 46.77 1.52
1969 1981 8.502105 TCAACAACGAAGTACTAGATCAGATA 57.498 34.615 0.00 0.00 45.00 1.98
1970 1982 7.392494 TCAACAACGAAGTACTAGATCAGAT 57.608 36.000 0.00 0.00 45.00 2.90
1998 2010 8.984891 CATAAATGTATGCAAGGAAAACAAGA 57.015 30.769 0.00 0.00 31.07 3.02
2435 2463 2.956333 TGTCCTCATCATCGTAATCCGT 59.044 45.455 0.00 0.00 37.94 4.69
2449 2477 1.092348 CGTCGATGTAGGTGTCCTCA 58.908 55.000 0.00 0.00 34.61 3.86
2516 2544 0.038599 TGCTTCATCATGGTGGCTGT 59.961 50.000 6.03 0.00 0.00 4.40
2517 2545 0.738975 CTGCTTCATCATGGTGGCTG 59.261 55.000 6.03 3.02 0.00 4.85
2678 2706 3.857854 CTGCTGGATGTGCGCGAC 61.858 66.667 12.10 5.96 0.00 5.19
2884 2912 3.942377 ATGCATTGCCACGCCCTGA 62.942 57.895 6.12 0.00 0.00 3.86
2945 2973 3.292936 GTGGTGCTGCTGCTGCTT 61.293 61.111 27.67 0.00 40.48 3.91
2948 2976 3.667282 GTGGTGGTGCTGCTGCTG 61.667 66.667 17.00 0.77 40.48 4.41
2949 2977 4.962836 GGTGGTGGTGCTGCTGCT 62.963 66.667 17.00 0.00 40.48 4.24
2951 2979 3.289834 GTGGTGGTGGTGCTGCTG 61.290 66.667 0.00 0.00 0.00 4.41
2952 2980 4.586235 GGTGGTGGTGGTGCTGCT 62.586 66.667 0.00 0.00 0.00 4.24
2953 2981 4.892965 TGGTGGTGGTGGTGCTGC 62.893 66.667 0.00 0.00 0.00 5.25
2954 2982 2.595463 CTGGTGGTGGTGGTGCTG 60.595 66.667 0.00 0.00 0.00 4.41
2955 2983 4.586235 GCTGGTGGTGGTGGTGCT 62.586 66.667 0.00 0.00 0.00 4.40
2956 2984 4.892965 TGCTGGTGGTGGTGGTGC 62.893 66.667 0.00 0.00 0.00 5.01
2957 2985 2.595463 CTGCTGGTGGTGGTGGTG 60.595 66.667 0.00 0.00 0.00 4.17
2958 2986 4.586235 GCTGCTGGTGGTGGTGGT 62.586 66.667 0.00 0.00 0.00 4.16
2959 2987 4.584518 TGCTGCTGGTGGTGGTGG 62.585 66.667 0.00 0.00 0.00 4.61
2960 2988 2.981909 CTGCTGCTGGTGGTGGTG 60.982 66.667 0.00 0.00 0.00 4.17
2961 2989 4.962836 GCTGCTGCTGGTGGTGGT 62.963 66.667 8.53 0.00 36.03 4.16
2962 2990 4.960866 TGCTGCTGCTGGTGGTGG 62.961 66.667 17.00 0.00 40.48 4.61
2963 2991 3.362797 CTGCTGCTGCTGGTGGTG 61.363 66.667 17.00 0.00 40.48 4.17
2966 2994 3.738246 CTGCTGCTGCTGCTGGTG 61.738 66.667 27.67 13.98 40.48 4.17
3243 3303 2.224744 TGGTGCTCTTACATCCAAGCAA 60.225 45.455 0.00 0.00 45.55 3.91
3385 3445 5.123186 CCTTGTGTAACTCGAATTGCCATAA 59.877 40.000 0.00 0.00 38.04 1.90
3386 3446 4.634004 CCTTGTGTAACTCGAATTGCCATA 59.366 41.667 0.00 0.00 38.04 2.74
3397 3457 7.454260 AGAAATTTCCATCCTTGTGTAACTC 57.546 36.000 14.61 0.00 38.04 3.01
3401 3461 9.444600 GTTACTAGAAATTTCCATCCTTGTGTA 57.555 33.333 14.61 3.11 0.00 2.90
3413 3473 5.600908 TGCCACGTGTTACTAGAAATTTC 57.399 39.130 15.65 10.33 0.00 2.17
3414 3474 5.529800 ACTTGCCACGTGTTACTAGAAATTT 59.470 36.000 15.65 0.00 0.00 1.82
3431 3491 7.699812 GCATTTTATTTTGACAAAAACTTGCCA 59.300 29.630 16.85 0.00 38.07 4.92
3465 3526 1.153353 CCGATAAGTGCCACACGTTT 58.847 50.000 0.00 0.00 39.64 3.60
3483 3544 0.315886 CGTTAGGTGGCAAAAACCCC 59.684 55.000 0.00 0.00 38.57 4.95
3530 3592 3.929334 TTCGGGCGGGTGGAAATGG 62.929 63.158 0.00 0.00 0.00 3.16
3531 3593 1.319614 ATTTCGGGCGGGTGGAAATG 61.320 55.000 0.00 0.00 38.55 2.32
3532 3594 0.613572 AATTTCGGGCGGGTGGAAAT 60.614 50.000 0.00 0.00 40.92 2.17
3533 3595 1.228613 AATTTCGGGCGGGTGGAAA 60.229 52.632 0.00 0.00 34.52 3.13
3540 3602 2.983930 TTTGCGGAATTTCGGGCGG 61.984 57.895 8.51 0.00 0.00 6.13
3577 3639 1.227321 GTCCGGACGTCCACAAACA 60.227 57.895 32.80 7.65 35.14 2.83
3646 3708 0.248907 CACGATTGGAGCGGACGTAT 60.249 55.000 0.00 0.00 35.78 3.06
3769 3836 1.129624 GTCATTAACATGGCGCGAACA 59.870 47.619 12.10 8.66 0.00 3.18
3780 3847 2.486592 TCGCTCTGAGTCGTCATTAACA 59.513 45.455 16.79 0.00 30.18 2.41
3828 3895 1.854939 TGAGGAAGCCCATCATTGGAT 59.145 47.619 0.00 0.00 46.92 3.41
3832 3899 2.433239 GCATTTGAGGAAGCCCATCATT 59.567 45.455 0.00 0.00 33.88 2.57
3864 3931 1.269883 TGCATCCAACTTGCTTGCTTG 60.270 47.619 12.63 0.00 40.77 4.01
3865 3932 1.042229 TGCATCCAACTTGCTTGCTT 58.958 45.000 12.63 0.00 40.77 3.91
3987 4054 2.507058 AGCTGATCAACAGGCTATGGAA 59.493 45.455 5.44 0.00 45.82 3.53
3993 4060 0.399454 ACACAGCTGATCAACAGGCT 59.601 50.000 23.35 1.52 45.82 4.58
3997 4064 2.289010 ACATCGACACAGCTGATCAACA 60.289 45.455 23.35 4.80 0.00 3.33
4010 4077 5.723672 AGGAAGAAAGTCTTACATCGACA 57.276 39.130 3.15 0.00 39.81 4.35
4019 4086 7.067615 GGAGAAGACAAAAAGGAAGAAAGTCTT 59.932 37.037 0.00 0.00 44.67 3.01
4076 4146 6.825213 GCAAGCCATGAATATATCACTATGGA 59.175 38.462 15.88 0.00 41.93 3.41
4077 4147 6.600427 TGCAAGCCATGAATATATCACTATGG 59.400 38.462 0.00 0.00 41.93 2.74
4096 4166 3.181503 CCAGACAATACATGAGTGCAAGC 60.182 47.826 0.00 0.00 0.00 4.01
4102 4172 4.323792 CCAACTCCCAGACAATACATGAGT 60.324 45.833 0.00 0.00 33.30 3.41
4114 4184 1.774254 TCAGCTTTTCCAACTCCCAGA 59.226 47.619 0.00 0.00 0.00 3.86
4115 4185 2.276732 TCAGCTTTTCCAACTCCCAG 57.723 50.000 0.00 0.00 0.00 4.45
4125 4195 5.175673 ACTTTTTAATGCGCTTCAGCTTTTC 59.824 36.000 9.73 0.00 39.32 2.29
4138 4208 8.255394 AGCAATTGGTTCATACTTTTTAATGC 57.745 30.769 3.82 0.00 0.00 3.56
4140 4210 9.218440 CCAAGCAATTGGTTCATACTTTTTAAT 57.782 29.630 19.59 0.00 37.32 1.40


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

AutoCloner maintained by Alex Coulton.