Multiple sequence alignment - TraesCS3D01G278200

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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 TraesCS3D01G278200 chr3D 100.000 4476 0 0 1 4476 385431817 385427342 0 8266
1 TraesCS3D01G278200 chr3B 95.451 2814 95 17 949 3734 501394508 501391700 0 4457
2 TraesCS3D01G278200 chr3B 92.228 965 48 16 5 957 501396478 501395529 0 1341
3 TraesCS3D01G278200 chr3B 87.198 703 43 26 3807 4476 501391584 501390896 0 756
4 TraesCS3D01G278200 chr3A 94.380 2740 124 17 949 3659 507472440 507469702 0 4180
5 TraesCS3D01G278200 chr3A 92.662 954 42 13 25 959 507474401 507473457 0 1349
6 TraesCS3D01G278200 chr3A 88.698 699 47 16 3800 4476 507469573 507468885 0 824


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 TraesCS3D01G278200 chr3D 385427342 385431817 4475 True 8266.000000 8266 100.000000 1 4476 1 chr3D.!!$R1 4475
1 TraesCS3D01G278200 chr3B 501390896 501396478 5582 True 2184.666667 4457 91.625667 5 4476 3 chr3B.!!$R1 4471
2 TraesCS3D01G278200 chr3A 507468885 507474401 5516 True 2117.666667 4180 91.913333 25 4476 3 chr3A.!!$R1 4451


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
388 389 0.318441 TGTGTGTGCTCTGGTCTAGC 59.682 55.0 0.0 0.0 40.5 3.42 F
1536 2591 0.398318 AGAGACCCACAGCTTTCACC 59.602 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 3103 0.173708 GGATGTCTGTCTCCACGACC 59.826 60.0 0.0 0.0 42.13 4.79 R
3484 4555 0.034960 TGTCTCTCCTGACTCCGAGG 60.035 60.0 0.0 0.0 37.79 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
74 75 2.282180 TGTTTGGGCTCGGCTTCC 60.282 61.111 0.00 0.00 0.00 3.46
117 118 1.398960 CGCTCTTTCTTTGTTGCGGAG 60.399 52.381 0.00 0.00 39.76 4.63
386 387 2.289631 CCATTGTGTGTGCTCTGGTCTA 60.290 50.000 0.00 0.00 0.00 2.59
388 389 0.318441 TGTGTGTGCTCTGGTCTAGC 59.682 55.000 0.00 0.00 40.50 3.42
403 404 2.406691 GTCTAGCGCGCAGATTATTCAG 59.593 50.000 35.10 14.40 0.00 3.02
459 460 6.271391 ACGGATAACTTGATATGTAATGGGGA 59.729 38.462 0.00 0.00 0.00 4.81
647 668 3.326747 ACATGTTTACGAGTTGCTCTCC 58.673 45.455 0.00 0.00 39.84 3.71
659 680 5.053978 AGTTGCTCTCCCCATAAATAAGG 57.946 43.478 0.00 0.00 0.00 2.69
732 753 1.238439 CGTGGAGCAACATTTGGAGT 58.762 50.000 0.00 0.00 0.00 3.85
755 776 6.601613 AGTGGAAAATAACTCACAGTTGACAA 59.398 34.615 0.00 0.00 39.11 3.18
778 800 6.679327 AATTAGACCGTGCTAAAGATTTCC 57.321 37.500 0.00 0.00 34.33 3.13
802 824 8.045507 TCCAATAGAAGATGAATGCCATATCTC 58.954 37.037 0.00 0.00 34.91 2.75
923 945 2.742372 GCTCACGCCGTCCATTGT 60.742 61.111 0.00 0.00 0.00 2.71
925 947 0.810031 GCTCACGCCGTCCATTGTAT 60.810 55.000 0.00 0.00 0.00 2.29
926 948 1.651987 CTCACGCCGTCCATTGTATT 58.348 50.000 0.00 0.00 0.00 1.89
1086 2137 5.107133 GTGGCAGAAAATGAAATGGATCAG 58.893 41.667 0.00 0.00 31.76 2.90
1141 2192 6.436027 ACCACTTCTGATAGAGAGGACAATA 58.564 40.000 0.00 0.00 32.06 1.90
1146 2197 6.924913 TCTGATAGAGAGGACAATATTGGG 57.075 41.667 19.37 0.00 0.00 4.12
1151 2202 5.983333 AGAGAGGACAATATTGGGTTCAT 57.017 39.130 19.37 5.96 0.00 2.57
1187 2238 2.580962 TGTTGCTTGTTATGCAGGACA 58.419 42.857 0.00 0.00 41.71 4.02
1257 2308 0.991344 CGGATGCAATTTTTGGCGAC 59.009 50.000 0.00 0.00 0.00 5.19
1271 2322 4.497291 TTGGCGACCAGGTTAATCTAAT 57.503 40.909 0.00 0.00 33.81 1.73
1536 2591 0.398318 AGAGACCCACAGCTTTCACC 59.602 55.000 0.00 0.00 0.00 4.02
1937 2992 2.217510 TCCTCTACCGAGCTCTTTGT 57.782 50.000 12.85 8.76 35.90 2.83
2047 3102 1.748591 GCCATTGGCTCGATCTTCCTT 60.749 52.381 20.66 0.00 46.69 3.36
2048 3103 1.945394 CCATTGGCTCGATCTTCCTTG 59.055 52.381 0.00 0.00 0.00 3.61
2381 3436 3.021695 TCGACCTACCCTACAGACATTG 58.978 50.000 0.00 0.00 0.00 2.82
2569 3624 1.107945 TATCTTGTGCCATCGACCGA 58.892 50.000 0.00 0.00 0.00 4.69
2610 3665 3.204382 ACTTTTATCCCCACCCGATGATT 59.796 43.478 0.00 0.00 0.00 2.57
2611 3666 3.502123 TTTATCCCCACCCGATGATTC 57.498 47.619 0.00 0.00 0.00 2.52
2612 3667 1.358152 TATCCCCACCCGATGATTCC 58.642 55.000 0.00 0.00 0.00 3.01
2651 3709 1.606737 GCCAAGTCTCCTATGATCCGC 60.607 57.143 0.00 0.00 0.00 5.54
2679 3737 4.211374 CGGTAAACCTAGCTTATGCATCAC 59.789 45.833 0.19 0.00 42.74 3.06
2772 3831 4.127171 TGAAGCTTGTCCAAGTAGTTCAC 58.873 43.478 2.10 0.00 40.45 3.18
2848 3907 4.314522 TGGTATGATGAAGAAGGCCAAA 57.685 40.909 5.01 0.00 0.00 3.28
2866 3925 0.542467 AAACAGCCATGGCATCCACA 60.542 50.000 37.18 0.00 44.88 4.17
2875 3934 0.911053 TGGCATCCACAGCTGATACA 59.089 50.000 23.35 6.32 0.00 2.29
2893 3952 1.160137 CAGCCACACAAGCCTTAGTC 58.840 55.000 0.00 0.00 0.00 2.59
3243 4302 0.181114 TGTGAGGCAGCAGACTTTGT 59.819 50.000 0.00 0.00 28.39 2.83
3249 4308 4.006319 GAGGCAGCAGACTTTGTTATTCT 58.994 43.478 0.00 0.00 28.39 2.40
3274 4333 2.417933 GCACACTGAGGATGTTGATCAC 59.582 50.000 0.00 0.00 0.00 3.06
3279 4338 1.550072 TGAGGATGTTGATCACGCTGA 59.450 47.619 0.00 0.00 0.00 4.26
3307 4375 0.823356 AACATGGTGCACAGGTGGTC 60.823 55.000 20.43 0.00 44.50 4.02
3325 4393 1.933853 GTCGAACCTATGTCCACATGC 59.066 52.381 2.26 0.00 37.15 4.06
3352 4420 3.724508 AACAATGGTTTCGATGTTGCA 57.275 38.095 0.00 0.00 34.88 4.08
3403 4474 2.840038 ACTGGAAGGTGATGATGTAGCA 59.160 45.455 0.00 0.00 39.30 3.49
3418 4489 0.666274 TAGCAACGGCAGAACACGAG 60.666 55.000 0.00 0.00 44.61 4.18
3440 4511 1.866925 GCGGAGGAGGAAAACAACG 59.133 57.895 0.00 0.00 0.00 4.10
3445 4516 1.895231 GGAGGAAAACAACGGCGGT 60.895 57.895 13.24 0.00 0.00 5.68
3458 4529 2.667199 GCGGTTGTAACGGTGCCT 60.667 61.111 4.59 0.00 0.00 4.75
3470 4541 1.754745 GGTGCCTCTTCCTCACACA 59.245 57.895 0.00 0.00 32.89 3.72
3484 4555 3.620374 CCTCACACACATAGTTCATCTGC 59.380 47.826 0.00 0.00 0.00 4.26
3488 4559 2.862536 CACACATAGTTCATCTGCCTCG 59.137 50.000 0.00 0.00 0.00 4.63
3496 4567 1.039785 TCATCTGCCTCGGAGTCAGG 61.040 60.000 15.33 1.58 0.00 3.86
3521 4600 2.357009 GACATGATGCGATTCCAGCTTT 59.643 45.455 0.00 0.00 35.28 3.51
3522 4601 2.098607 ACATGATGCGATTCCAGCTTTG 59.901 45.455 0.00 0.00 35.28 2.77
3524 4603 1.469703 TGATGCGATTCCAGCTTTGTG 59.530 47.619 0.00 0.00 35.28 3.33
3525 4604 1.470098 GATGCGATTCCAGCTTTGTGT 59.530 47.619 0.00 0.00 35.28 3.72
3528 4611 1.400242 GCGATTCCAGCTTTGTGTCAC 60.400 52.381 0.00 0.00 0.00 3.67
3533 4616 5.503031 CGATTCCAGCTTTGTGTCACATATC 60.503 44.000 6.48 0.00 0.00 1.63
3539 4622 4.130118 GCTTTGTGTCACATATCTAGGGG 58.870 47.826 6.48 0.00 0.00 4.79
3550 4633 8.305317 GTCACATATCTAGGGGTTAGATTGTAC 58.695 40.741 2.37 0.00 44.92 2.90
3564 4647 3.758554 AGATTGTACTTGATGCCGCTTTT 59.241 39.130 0.00 0.00 0.00 2.27
3583 4666 2.539003 CGGAGTTTGCCGTGATTGA 58.461 52.632 0.00 0.00 46.07 2.57
3624 4707 2.939460 ATTCGGTTTGTTATGCAGCC 57.061 45.000 0.00 0.00 0.00 4.85
3631 4714 3.193267 GGTTTGTTATGCAGCCTGATTCA 59.807 43.478 0.00 0.00 0.00 2.57
3633 4716 4.642445 TTGTTATGCAGCCTGATTCATG 57.358 40.909 0.00 0.00 0.00 3.07
3641 4724 0.178970 GCCTGATTCATGGCTGGGAT 60.179 55.000 15.64 0.00 45.26 3.85
3651 4734 4.401022 TCATGGCTGGGATAAATAGCTTG 58.599 43.478 0.00 0.00 37.58 4.01
3665 4748 6.780457 AAATAGCTTGTTGATGTTGGCTAT 57.220 33.333 0.00 0.00 42.41 2.97
3667 4750 7.880160 AATAGCTTGTTGATGTTGGCTATAA 57.120 32.000 0.00 0.00 40.59 0.98
3668 4751 5.824904 AGCTTGTTGATGTTGGCTATAAG 57.175 39.130 0.00 0.00 0.00 1.73
3708 4791 1.394618 TGTTTAGCCGTGCAGGTTTT 58.605 45.000 5.57 0.00 43.70 2.43
3714 4797 0.318360 GCCGTGCAGGTTTTGTTACC 60.318 55.000 5.57 0.00 43.70 2.85
3718 4801 1.406180 GTGCAGGTTTTGTTACCGGTT 59.594 47.619 15.04 0.00 43.21 4.44
3724 4807 5.463286 CAGGTTTTGTTACCGGTTTAATCC 58.537 41.667 15.04 10.52 43.21 3.01
3734 4817 2.357952 CCGGTTTAATCCTTTAGCTGGC 59.642 50.000 0.00 0.00 0.00 4.85
3736 4819 3.632145 CGGTTTAATCCTTTAGCTGGCAT 59.368 43.478 0.00 0.00 0.00 4.40
3737 4820 4.819630 CGGTTTAATCCTTTAGCTGGCATA 59.180 41.667 0.00 0.00 0.00 3.14
3738 4821 5.473504 CGGTTTAATCCTTTAGCTGGCATAT 59.526 40.000 0.00 0.00 0.00 1.78
3739 4822 6.348540 CGGTTTAATCCTTTAGCTGGCATATC 60.349 42.308 0.00 0.00 0.00 1.63
3740 4823 6.717084 GGTTTAATCCTTTAGCTGGCATATCT 59.283 38.462 0.00 0.00 0.00 1.98
3743 4826 5.839517 ATCCTTTAGCTGGCATATCTCTT 57.160 39.130 0.00 0.00 0.00 2.85
3744 4827 5.636903 TCCTTTAGCTGGCATATCTCTTT 57.363 39.130 0.00 0.00 0.00 2.52
3745 4828 5.371526 TCCTTTAGCTGGCATATCTCTTTG 58.628 41.667 0.00 0.00 0.00 2.77
3747 4830 4.428294 TTAGCTGGCATATCTCTTTGCT 57.572 40.909 0.00 0.00 38.88 3.91
3748 4831 5.551305 TTAGCTGGCATATCTCTTTGCTA 57.449 39.130 0.00 0.00 38.88 3.49
3749 4832 4.428294 AGCTGGCATATCTCTTTGCTAA 57.572 40.909 0.00 0.00 38.88 3.09
3751 4834 3.879295 GCTGGCATATCTCTTTGCTAACA 59.121 43.478 0.00 0.00 38.88 2.41
3752 4835 4.336433 GCTGGCATATCTCTTTGCTAACAA 59.664 41.667 0.00 0.00 38.88 2.83
3753 4836 5.163622 GCTGGCATATCTCTTTGCTAACAAA 60.164 40.000 0.00 0.00 43.45 2.83
3754 4837 6.460676 GCTGGCATATCTCTTTGCTAACAAAT 60.461 38.462 0.00 0.00 44.54 2.32
3755 4838 6.798482 TGGCATATCTCTTTGCTAACAAATG 58.202 36.000 0.00 0.00 44.54 2.32
3756 4839 6.377996 TGGCATATCTCTTTGCTAACAAATGT 59.622 34.615 0.00 0.00 44.54 2.71
3757 4840 6.914757 GGCATATCTCTTTGCTAACAAATGTC 59.085 38.462 0.00 0.00 44.54 3.06
3759 4842 7.854916 GCATATCTCTTTGCTAACAAATGTCTC 59.145 37.037 0.00 0.00 44.54 3.36
3761 4844 7.750229 ATCTCTTTGCTAACAAATGTCTCAA 57.250 32.000 0.00 0.00 44.54 3.02
3762 4845 7.194607 TCTCTTTGCTAACAAATGTCTCAAG 57.805 36.000 0.00 0.00 44.54 3.02
3764 4847 6.959361 TCTTTGCTAACAAATGTCTCAAGTC 58.041 36.000 0.00 0.00 44.54 3.01
3765 4848 6.767902 TCTTTGCTAACAAATGTCTCAAGTCT 59.232 34.615 0.00 0.00 44.54 3.24
3767 4850 5.610398 TGCTAACAAATGTCTCAAGTCTGA 58.390 37.500 0.00 0.00 0.00 3.27
3768 4851 6.233434 TGCTAACAAATGTCTCAAGTCTGAT 58.767 36.000 0.00 0.00 0.00 2.90
3769 4852 6.712095 TGCTAACAAATGTCTCAAGTCTGATT 59.288 34.615 0.00 0.00 0.00 2.57
3770 4853 7.095060 TGCTAACAAATGTCTCAAGTCTGATTC 60.095 37.037 0.00 0.00 0.00 2.52
3772 4855 9.645059 CTAACAAATGTCTCAAGTCTGATTCTA 57.355 33.333 0.00 0.00 0.00 2.10
3773 4856 7.897575 ACAAATGTCTCAAGTCTGATTCTAC 57.102 36.000 0.00 0.00 0.00 2.59
3774 4857 7.675062 ACAAATGTCTCAAGTCTGATTCTACT 58.325 34.615 0.00 0.00 0.00 2.57
3775 4858 7.601886 ACAAATGTCTCAAGTCTGATTCTACTG 59.398 37.037 0.00 0.00 0.00 2.74
3776 4859 5.651387 TGTCTCAAGTCTGATTCTACTGG 57.349 43.478 0.00 0.00 0.00 4.00
3779 4876 6.151312 TGTCTCAAGTCTGATTCTACTGGTAC 59.849 42.308 0.00 0.00 0.00 3.34
3782 4879 8.275758 TCTCAAGTCTGATTCTACTGGTACTAT 58.724 37.037 0.00 0.00 0.00 2.12
3788 4885 9.733219 GTCTGATTCTACTGGTACTATTTACAC 57.267 37.037 0.00 0.00 0.00 2.90
3793 4890 4.119442 ACTGGTACTATTTACACAGGCG 57.881 45.455 0.00 0.00 0.00 5.52
3805 4902 2.086869 ACACAGGCGAAATTGGAGATG 58.913 47.619 0.00 0.00 0.00 2.90
3812 4909 2.415893 GCGAAATTGGAGATGGGTGTTG 60.416 50.000 0.00 0.00 0.00 3.33
3813 4910 2.819608 CGAAATTGGAGATGGGTGTTGT 59.180 45.455 0.00 0.00 0.00 3.32
3814 4911 4.006989 CGAAATTGGAGATGGGTGTTGTA 58.993 43.478 0.00 0.00 0.00 2.41
3838 4967 2.169832 ACACCTTCCACGTCTGAATG 57.830 50.000 0.00 0.00 0.00 2.67
3912 5051 6.670027 AGATGTCTAGGAGTAGAAAATGTGGT 59.330 38.462 0.00 0.00 37.02 4.16
3940 5079 1.024579 AGTTGGGCTTTCATACCGCG 61.025 55.000 0.00 0.00 0.00 6.46
3991 5132 1.203523 GAGTCAGAGTCCAGTGCGATT 59.796 52.381 0.00 0.00 0.00 3.34
4006 5147 0.943673 CGATTGCCACACAGACACAA 59.056 50.000 0.00 0.00 0.00 3.33
4204 5355 4.589908 AGATGTAAGGCCCTACTTTTGTG 58.410 43.478 12.73 0.00 32.02 3.33
4207 5358 4.538738 TGTAAGGCCCTACTTTTGTGTTT 58.461 39.130 12.73 0.00 32.02 2.83
4209 5360 5.422650 TGTAAGGCCCTACTTTTGTGTTTTT 59.577 36.000 12.73 0.00 32.02 1.94
4210 5361 4.665833 AGGCCCTACTTTTGTGTTTTTC 57.334 40.909 0.00 0.00 0.00 2.29
4211 5362 3.067601 AGGCCCTACTTTTGTGTTTTTCG 59.932 43.478 0.00 0.00 0.00 3.46
4212 5363 3.181484 GGCCCTACTTTTGTGTTTTTCGT 60.181 43.478 0.00 0.00 0.00 3.85
4213 5364 4.426416 GCCCTACTTTTGTGTTTTTCGTT 58.574 39.130 0.00 0.00 0.00 3.85
4214 5365 4.865925 GCCCTACTTTTGTGTTTTTCGTTT 59.134 37.500 0.00 0.00 0.00 3.60
4215 5366 5.349270 GCCCTACTTTTGTGTTTTTCGTTTT 59.651 36.000 0.00 0.00 0.00 2.43
4216 5367 6.671164 GCCCTACTTTTGTGTTTTTCGTTTTG 60.671 38.462 0.00 0.00 0.00 2.44
4217 5368 6.586844 CCCTACTTTTGTGTTTTTCGTTTTGA 59.413 34.615 0.00 0.00 0.00 2.69
4240 5391 0.040958 GATTTGATGATCGTGCCCGC 60.041 55.000 0.00 0.00 0.00 6.13
4262 5416 1.954382 GCTCTTTTCTTTTCCCCGTGT 59.046 47.619 0.00 0.00 0.00 4.49
4283 5437 4.933064 CTGACCTCGGGCGCGATC 62.933 72.222 26.78 21.32 0.00 3.69
4301 5456 2.668212 CCCCGTTGCGCAGAAAGA 60.668 61.111 11.31 0.00 0.00 2.52
4398 5561 0.322997 TGTGTAATTTGGCCTCGGGG 60.323 55.000 3.32 0.00 0.00 5.73
4422 5585 5.831103 AGGAAGAAATGTCCATGGTGTATT 58.169 37.500 12.58 8.20 37.65 1.89
4427 5590 5.774690 AGAAATGTCCATGGTGTATTTGTGT 59.225 36.000 20.35 8.59 0.00 3.72
4438 5601 6.565234 TGGTGTATTTGTGTTGTTTTACCAG 58.435 36.000 0.00 0.00 31.48 4.00
4441 5604 6.198216 GTGTATTTGTGTTGTTTTACCAGCTG 59.802 38.462 6.78 6.78 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.953686 GCCAGCCGCTCCAAAAATATA 59.046 47.619 0.00 0.00 0.00 0.86
1 2 0.746659 GCCAGCCGCTCCAAAAATAT 59.253 50.000 0.00 0.00 0.00 1.28
2 3 1.319614 GGCCAGCCGCTCCAAAAATA 61.320 55.000 0.00 0.00 37.74 1.40
3 4 2.649129 GGCCAGCCGCTCCAAAAAT 61.649 57.895 0.00 0.00 37.74 1.82
117 118 4.645921 GCACGCACCCTGTTTGCC 62.646 66.667 0.00 0.00 36.57 4.52
386 387 0.179073 ACCTGAATAATCTGCGCGCT 60.179 50.000 33.29 14.83 0.00 5.92
388 389 0.041839 GCACCTGAATAATCTGCGCG 60.042 55.000 0.00 0.00 0.00 6.86
459 460 4.040461 ACAAGAACATAGTAGTGCCACTGT 59.960 41.667 7.83 0.00 0.00 3.55
625 645 4.491676 GGAGAGCAACTCGTAAACATGTA 58.508 43.478 0.00 0.00 45.76 2.29
635 655 2.691409 TTTATGGGGAGAGCAACTCG 57.309 50.000 5.17 0.00 45.76 4.18
672 693 3.631250 ACCAACTGAAACACCACATCTT 58.369 40.909 0.00 0.00 0.00 2.40
677 698 3.705604 CAATGACCAACTGAAACACCAC 58.294 45.455 0.00 0.00 0.00 4.16
679 700 2.100584 TGCAATGACCAACTGAAACACC 59.899 45.455 0.00 0.00 0.00 4.16
732 753 7.397892 TTTGTCAACTGTGAGTTATTTTCCA 57.602 32.000 0.00 0.00 36.03 3.53
755 776 6.177610 TGGAAATCTTTAGCACGGTCTAATT 58.822 36.000 0.00 0.00 0.00 1.40
778 800 9.451002 AAGAGATATGGCATTCATCTTCTATTG 57.549 33.333 4.78 0.00 37.30 1.90
837 859 5.796424 AGGAACTCTGCACAAAATGAAAT 57.204 34.783 0.00 0.00 0.00 2.17
1072 2123 6.288941 TGTTTCATGCTGATCCATTTCATT 57.711 33.333 0.00 0.00 0.00 2.57
1086 2137 2.490903 AGAAGGTGCAGATGTTTCATGC 59.509 45.455 0.00 0.00 40.40 4.06
1101 2152 0.896940 TGGTACTCGGCGAAGAAGGT 60.897 55.000 12.13 7.56 0.00 3.50
1146 2197 2.500229 TGGACTTGTTCGGGAATGAAC 58.500 47.619 0.00 0.00 46.63 3.18
1151 2202 2.226330 CAACATGGACTTGTTCGGGAA 58.774 47.619 0.00 0.00 37.73 3.97
1187 2238 3.264193 TGTACTGGATGAAGGTTCTGCAT 59.736 43.478 0.00 0.00 31.37 3.96
1536 2591 0.179936 GTCATCTCCCCAGAAGCCAG 59.820 60.000 0.00 0.00 30.24 4.85
1937 2992 2.203983 TGGGAGGAGGCAGCAGAA 60.204 61.111 0.00 0.00 0.00 3.02
2047 3102 0.888619 GATGTCTGTCTCCACGACCA 59.111 55.000 0.00 0.00 42.13 4.02
2048 3103 0.173708 GGATGTCTGTCTCCACGACC 59.826 60.000 0.00 0.00 42.13 4.79
2381 3436 2.041966 CCACGTCGACTAATACGATGC 58.958 52.381 14.70 0.00 46.40 3.91
2651 3709 4.495844 GCATAAGCTAGGTTTACCGCTTTG 60.496 45.833 13.21 14.24 41.09 2.77
2692 3750 7.285401 ACATTAGTTCAGTCAACTGTGGAATTT 59.715 33.333 9.82 0.00 45.60 1.82
2693 3751 6.772716 ACATTAGTTCAGTCAACTGTGGAATT 59.227 34.615 9.82 0.00 45.60 2.17
2694 3752 6.299141 ACATTAGTTCAGTCAACTGTGGAAT 58.701 36.000 9.82 4.05 45.60 3.01
2772 3831 5.582550 TCTTCAGTACTGATTCAGTATGCG 58.417 41.667 25.68 17.36 46.56 4.73
2848 3907 0.968901 CTGTGGATGCCATGGCTGTT 60.969 55.000 35.53 21.10 42.51 3.16
2875 3934 1.059913 AGACTAAGGCTTGTGTGGCT 58.940 50.000 10.69 1.98 45.04 4.75
2893 3952 4.992319 TCAAAGCCATGCAGAAATTCAAAG 59.008 37.500 0.00 0.00 0.00 2.77
3180 4239 3.863424 TGAGTCACAGTTTTCGTTCACTC 59.137 43.478 0.00 0.00 0.00 3.51
3211 4270 1.612726 GCCTCACAGTTCTCAATGGCT 60.613 52.381 0.00 0.00 36.52 4.75
3243 4302 5.187772 ACATCCTCAGTGTGCTGTAGAATAA 59.812 40.000 0.00 0.00 43.05 1.40
3249 4308 2.632512 TCAACATCCTCAGTGTGCTGTA 59.367 45.455 0.00 0.00 43.05 2.74
3274 4333 1.202065 CCATGTTCCATTTCGTCAGCG 60.202 52.381 0.00 0.00 39.92 5.18
3279 4338 1.269448 GTGCACCATGTTCCATTTCGT 59.731 47.619 5.22 0.00 0.00 3.85
3307 4375 0.930310 CGCATGTGGACATAGGTTCG 59.070 55.000 0.00 0.00 34.26 3.95
3313 4381 3.006940 GTTTTCCTCGCATGTGGACATA 58.993 45.455 6.39 0.00 37.49 2.29
3325 4393 3.889196 TCGAAACCATTGTTTTCCTCG 57.111 42.857 1.62 0.00 44.57 4.63
3403 4474 1.300697 GTCCTCGTGTTCTGCCGTT 60.301 57.895 0.00 0.00 0.00 4.44
3418 4489 1.740664 GTTTTCCTCCTCCGCGTCC 60.741 63.158 4.92 0.00 0.00 4.79
3440 4511 3.729698 GGCACCGTTACAACCGCC 61.730 66.667 0.00 0.00 0.00 6.13
3445 4516 1.001633 GAGGAAGAGGCACCGTTACAA 59.998 52.381 0.00 0.00 0.00 2.41
3451 4522 1.374758 GTGTGAGGAAGAGGCACCG 60.375 63.158 0.00 0.00 0.00 4.94
3458 4529 5.481824 AGATGAACTATGTGTGTGAGGAAGA 59.518 40.000 0.00 0.00 0.00 2.87
3470 4541 2.363680 CTCCGAGGCAGATGAACTATGT 59.636 50.000 0.00 0.00 0.00 2.29
3484 4555 0.034960 TGTCTCTCCTGACTCCGAGG 60.035 60.000 0.00 0.00 37.79 4.63
3488 4559 2.224018 GCATCATGTCTCTCCTGACTCC 60.224 54.545 0.00 0.00 37.79 3.85
3496 4567 3.058450 CTGGAATCGCATCATGTCTCTC 58.942 50.000 0.00 0.00 0.00 3.20
3521 4600 5.773091 TCTAACCCCTAGATATGTGACACA 58.227 41.667 11.41 11.41 31.28 3.72
3522 4601 6.919775 ATCTAACCCCTAGATATGTGACAC 57.080 41.667 0.00 0.00 44.22 3.67
3524 4603 7.304497 ACAATCTAACCCCTAGATATGTGAC 57.696 40.000 0.00 0.00 45.12 3.67
3525 4604 8.232412 AGTACAATCTAACCCCTAGATATGTGA 58.768 37.037 0.00 0.00 45.12 3.58
3528 4611 9.090103 TCAAGTACAATCTAACCCCTAGATATG 57.910 37.037 0.00 0.61 45.12 1.78
3533 4616 5.992217 GCATCAAGTACAATCTAACCCCTAG 59.008 44.000 0.00 0.00 0.00 3.02
3539 4622 3.871594 AGCGGCATCAAGTACAATCTAAC 59.128 43.478 1.45 0.00 0.00 2.34
3545 4628 2.095969 CGAAAAGCGGCATCAAGTACAA 60.096 45.455 1.45 0.00 36.03 2.41
3583 4666 7.148983 CGAATAATGTCAGCAAAAATGAAACGT 60.149 33.333 0.00 0.00 0.00 3.99
3624 4707 5.125097 GCTATTTATCCCAGCCATGAATCAG 59.875 44.000 0.00 0.00 0.00 2.90
3631 4714 4.459852 ACAAGCTATTTATCCCAGCCAT 57.540 40.909 0.00 0.00 35.88 4.40
3633 4716 4.207165 TCAACAAGCTATTTATCCCAGCC 58.793 43.478 0.00 0.00 35.88 4.85
3641 4724 7.880160 ATAGCCAACATCAACAAGCTATTTA 57.120 32.000 0.00 0.00 39.80 1.40
3651 4734 7.320443 TGAATCACTTATAGCCAACATCAAC 57.680 36.000 0.00 0.00 0.00 3.18
3686 4769 1.616159 ACCTGCACGGCTAAACAAAT 58.384 45.000 2.50 0.00 35.61 2.32
3687 4770 1.394618 AACCTGCACGGCTAAACAAA 58.605 45.000 2.50 0.00 35.61 2.83
3690 4773 1.066454 ACAAAACCTGCACGGCTAAAC 59.934 47.619 2.50 0.00 35.61 2.01
3691 4774 1.394618 ACAAAACCTGCACGGCTAAA 58.605 45.000 2.50 0.00 35.61 1.85
3696 4779 0.040781 CGGTAACAAAACCTGCACGG 60.041 55.000 1.16 1.16 37.39 4.94
3708 4791 5.644636 CAGCTAAAGGATTAAACCGGTAACA 59.355 40.000 8.00 0.00 34.73 2.41
3714 4797 3.013921 TGCCAGCTAAAGGATTAAACCG 58.986 45.455 0.00 0.00 34.73 4.44
3718 4801 7.321717 AGAGATATGCCAGCTAAAGGATTAA 57.678 36.000 0.00 0.00 0.00 1.40
3724 4807 4.820716 AGCAAAGAGATATGCCAGCTAAAG 59.179 41.667 0.00 0.00 43.57 1.85
3734 4817 8.886719 TGAGACATTTGTTAGCAAAGAGATATG 58.113 33.333 10.59 5.42 46.30 1.78
3736 4819 8.846943 TTGAGACATTTGTTAGCAAAGAGATA 57.153 30.769 10.59 0.00 46.30 1.98
3737 4820 7.446625 ACTTGAGACATTTGTTAGCAAAGAGAT 59.553 33.333 10.59 0.00 46.30 2.75
3738 4821 6.767902 ACTTGAGACATTTGTTAGCAAAGAGA 59.232 34.615 10.59 0.00 46.30 3.10
3739 4822 6.963796 ACTTGAGACATTTGTTAGCAAAGAG 58.036 36.000 10.59 8.02 46.30 2.85
3740 4823 6.767902 AGACTTGAGACATTTGTTAGCAAAGA 59.232 34.615 10.59 0.00 46.30 2.52
3743 4826 6.054941 TCAGACTTGAGACATTTGTTAGCAA 58.945 36.000 0.00 0.00 0.00 3.91
3744 4827 5.610398 TCAGACTTGAGACATTTGTTAGCA 58.390 37.500 0.00 0.00 0.00 3.49
3745 4828 6.734104 ATCAGACTTGAGACATTTGTTAGC 57.266 37.500 0.00 0.00 36.61 3.09
3747 4830 9.424319 GTAGAATCAGACTTGAGACATTTGTTA 57.576 33.333 0.00 0.00 36.61 2.41
3748 4831 8.153550 AGTAGAATCAGACTTGAGACATTTGTT 58.846 33.333 0.00 0.00 36.61 2.83
3749 4832 7.601886 CAGTAGAATCAGACTTGAGACATTTGT 59.398 37.037 0.00 0.00 36.61 2.83
3751 4834 7.102346 CCAGTAGAATCAGACTTGAGACATTT 58.898 38.462 0.00 0.00 36.61 2.32
3752 4835 6.212388 ACCAGTAGAATCAGACTTGAGACATT 59.788 38.462 0.00 0.00 36.61 2.71
3753 4836 5.719085 ACCAGTAGAATCAGACTTGAGACAT 59.281 40.000 0.00 0.00 36.61 3.06
3754 4837 5.080337 ACCAGTAGAATCAGACTTGAGACA 58.920 41.667 0.00 0.00 36.61 3.41
3755 4838 5.652994 ACCAGTAGAATCAGACTTGAGAC 57.347 43.478 0.00 0.00 36.61 3.36
3756 4839 6.486056 AGTACCAGTAGAATCAGACTTGAGA 58.514 40.000 0.00 0.00 36.61 3.27
3757 4840 6.767524 AGTACCAGTAGAATCAGACTTGAG 57.232 41.667 0.00 0.00 36.61 3.02
3761 4844 9.696572 TGTAAATAGTACCAGTAGAATCAGACT 57.303 33.333 0.00 0.00 0.00 3.24
3762 4845 9.733219 GTGTAAATAGTACCAGTAGAATCAGAC 57.267 37.037 0.00 0.00 0.00 3.51
3764 4847 9.737427 CTGTGTAAATAGTACCAGTAGAATCAG 57.263 37.037 0.00 0.00 0.00 2.90
3765 4848 8.692710 CCTGTGTAAATAGTACCAGTAGAATCA 58.307 37.037 0.00 0.00 0.00 2.57
3767 4850 7.498443 GCCTGTGTAAATAGTACCAGTAGAAT 58.502 38.462 0.00 0.00 0.00 2.40
3768 4851 6.405065 CGCCTGTGTAAATAGTACCAGTAGAA 60.405 42.308 0.00 0.00 0.00 2.10
3769 4852 5.066893 CGCCTGTGTAAATAGTACCAGTAGA 59.933 44.000 0.00 0.00 0.00 2.59
3770 4853 5.066893 TCGCCTGTGTAAATAGTACCAGTAG 59.933 44.000 0.00 0.00 0.00 2.57
3772 4855 3.765511 TCGCCTGTGTAAATAGTACCAGT 59.234 43.478 0.00 0.00 0.00 4.00
3773 4856 4.380841 TCGCCTGTGTAAATAGTACCAG 57.619 45.455 0.00 0.00 0.00 4.00
3774 4857 4.804868 TTCGCCTGTGTAAATAGTACCA 57.195 40.909 0.00 0.00 0.00 3.25
3775 4858 6.457799 CCAATTTCGCCTGTGTAAATAGTACC 60.458 42.308 0.00 0.00 0.00 3.34
3776 4859 6.314400 TCCAATTTCGCCTGTGTAAATAGTAC 59.686 38.462 0.00 0.00 0.00 2.73
3779 4876 5.584649 TCTCCAATTTCGCCTGTGTAAATAG 59.415 40.000 0.00 0.00 0.00 1.73
3782 4879 3.745799 TCTCCAATTTCGCCTGTGTAAA 58.254 40.909 0.00 0.00 0.00 2.01
3786 4883 1.402968 CCATCTCCAATTTCGCCTGTG 59.597 52.381 0.00 0.00 0.00 3.66
3788 4885 1.027357 CCCATCTCCAATTTCGCCTG 58.973 55.000 0.00 0.00 0.00 4.85
3793 4890 5.975693 TTACAACACCCATCTCCAATTTC 57.024 39.130 0.00 0.00 0.00 2.17
3812 4909 5.232463 TCAGACGTGGAAGGTGTAAATTAC 58.768 41.667 0.00 0.00 33.50 1.89
3813 4910 5.471556 TCAGACGTGGAAGGTGTAAATTA 57.528 39.130 0.00 0.00 33.50 1.40
3814 4911 4.345859 TCAGACGTGGAAGGTGTAAATT 57.654 40.909 0.00 0.00 33.50 1.82
3838 4967 1.005340 CATCTTCGCCTGAAGCTGAC 58.995 55.000 3.45 0.00 46.41 3.51
3868 4997 5.777732 ACATCTTCGCCTTCTCCTAATCTAT 59.222 40.000 0.00 0.00 0.00 1.98
3870 4999 3.964031 ACATCTTCGCCTTCTCCTAATCT 59.036 43.478 0.00 0.00 0.00 2.40
3871 5000 4.038642 AGACATCTTCGCCTTCTCCTAATC 59.961 45.833 0.00 0.00 0.00 1.75
3872 5001 3.964031 AGACATCTTCGCCTTCTCCTAAT 59.036 43.478 0.00 0.00 0.00 1.73
3873 5002 3.366396 AGACATCTTCGCCTTCTCCTAA 58.634 45.455 0.00 0.00 0.00 2.69
3874 5003 3.019799 AGACATCTTCGCCTTCTCCTA 57.980 47.619 0.00 0.00 0.00 2.94
3875 5004 1.859302 AGACATCTTCGCCTTCTCCT 58.141 50.000 0.00 0.00 0.00 3.69
3876 5005 2.035321 CCTAGACATCTTCGCCTTCTCC 59.965 54.545 0.00 0.00 0.00 3.71
3877 5006 2.952978 TCCTAGACATCTTCGCCTTCTC 59.047 50.000 0.00 0.00 0.00 2.87
3879 5008 2.691011 ACTCCTAGACATCTTCGCCTTC 59.309 50.000 0.00 0.00 0.00 3.46
3880 5009 2.741145 ACTCCTAGACATCTTCGCCTT 58.259 47.619 0.00 0.00 0.00 4.35
3991 5132 1.308047 GACATTGTGTCTGTGTGGCA 58.692 50.000 0.00 0.00 43.73 4.92
4037 5178 0.433492 CGCCGCGGAATAATAACGAG 59.567 55.000 33.48 0.00 0.00 4.18
4114 5255 3.056328 GAGACTTGCAACCCCCGC 61.056 66.667 0.00 0.00 0.00 6.13
4115 5256 2.359975 GGAGACTTGCAACCCCCG 60.360 66.667 0.00 0.00 0.00 5.73
4116 5257 1.303643 CTGGAGACTTGCAACCCCC 60.304 63.158 0.00 0.00 0.00 5.40
4204 5355 9.913451 TCATCAAATCAAATCAAAACGAAAAAC 57.087 25.926 0.00 0.00 0.00 2.43
4207 5358 8.637704 CGATCATCAAATCAAATCAAAACGAAA 58.362 29.630 0.00 0.00 0.00 3.46
4209 5360 7.271008 CACGATCATCAAATCAAATCAAAACGA 59.729 33.333 0.00 0.00 0.00 3.85
4210 5361 7.378047 CACGATCATCAAATCAAATCAAAACG 58.622 34.615 0.00 0.00 0.00 3.60
4211 5362 7.168796 GCACGATCATCAAATCAAATCAAAAC 58.831 34.615 0.00 0.00 0.00 2.43
4212 5363 6.310956 GGCACGATCATCAAATCAAATCAAAA 59.689 34.615 0.00 0.00 0.00 2.44
4213 5364 5.806502 GGCACGATCATCAAATCAAATCAAA 59.193 36.000 0.00 0.00 0.00 2.69
4214 5365 5.342433 GGCACGATCATCAAATCAAATCAA 58.658 37.500 0.00 0.00 0.00 2.57
4215 5366 4.202040 GGGCACGATCATCAAATCAAATCA 60.202 41.667 0.00 0.00 0.00 2.57
4216 5367 4.293415 GGGCACGATCATCAAATCAAATC 58.707 43.478 0.00 0.00 0.00 2.17
4217 5368 3.243168 CGGGCACGATCATCAAATCAAAT 60.243 43.478 0.00 0.00 44.60 2.32
4240 5391 0.521735 CGGGGAAAAGAAAAGAGCGG 59.478 55.000 0.00 0.00 0.00 5.52
4283 5437 3.737172 CTTTCTGCGCAACGGGGG 61.737 66.667 13.05 0.00 0.00 5.40
4301 5456 2.235898 GCACCTTGAGATTGACCTCTCT 59.764 50.000 3.07 0.00 41.87 3.10
4360 5523 2.884012 ACAGGCGAATGAATGAAACACA 59.116 40.909 0.00 0.00 0.00 3.72
4398 5561 3.690460 ACACCATGGACATTTCTTCCTC 58.310 45.455 21.47 0.00 33.84 3.71
4422 5585 2.159170 GGCAGCTGGTAAAACAACACAA 60.159 45.455 17.12 0.00 0.00 3.33
4427 5590 2.356665 TCAGGCAGCTGGTAAAACAA 57.643 45.000 17.12 0.00 0.00 2.83
4438 5601 2.671070 CGGGTACAAAATTTCAGGCAGC 60.671 50.000 0.00 0.00 0.00 5.25
4441 5604 4.036380 CCTATCGGGTACAAAATTTCAGGC 59.964 45.833 0.00 0.00 0.00 4.85



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

AutoCloner maintained by Alex Coulton.