Multiple sequence alignment - TraesCS2D01G183400

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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 TraesCS2D01G183400 chr2D 100.000 6717 0 0 1 6717 128393940 128400656 0.000000e+00 12405
1 TraesCS2D01G183400 chr2B 94.699 5905 160 59 20 5851 182017350 182011526 0.000000e+00 9029
2 TraesCS2D01G183400 chr2B 91.508 577 18 8 6152 6717 182011111 182010555 0.000000e+00 765
3 TraesCS2D01G183400 chr2B 91.241 274 11 8 5887 6153 182011540 182011273 1.780000e-95 361
4 TraesCS2D01G183400 chr2A 95.169 5485 159 43 451 5851 135191593 135197055 0.000000e+00 8564
5 TraesCS2D01G183400 chr2A 92.598 635 31 6 6097 6717 135197211 135197843 0.000000e+00 898
6 TraesCS2D01G183400 chr2A 88.506 435 18 17 16 438 135188364 135188778 1.300000e-136 497
7 TraesCS2D01G183400 chr2A 93.258 178 10 2 5887 6062 135197041 135197218 1.860000e-65 261


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 TraesCS2D01G183400 chr2D 128393940 128400656 6716 False 12405 12405 100.000000 1 6717 1 chr2D.!!$F1 6716
1 TraesCS2D01G183400 chr2B 182010555 182017350 6795 True 3385 9029 92.482667 20 6717 3 chr2B.!!$R1 6697
2 TraesCS2D01G183400 chr2A 135188364 135197843 9479 False 2555 8564 92.382750 16 6717 4 chr2A.!!$F1 6701

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
849 3744 0.321122 CACCGCTGCCTCTTCTTCTT 60.321 55.000 0.00 0.00 0.00 2.52 F
1220 4128 0.257039 ACCATCTCCACCATTGGCTC 59.743 55.000 1.54 0.00 43.56 4.70 F
1926 4848 0.318441 TTCAGTGAAGAGGACAGCCG 59.682 55.000 0.08 0.00 39.96 5.52 F
2269 5195 0.604780 TTCCAGTGCAGAGCTCAAGC 60.605 55.000 17.77 19.35 42.49 4.01 F
3015 5941 1.040339 ATGACTCTCTCCTGGACGCC 61.040 60.000 0.00 0.00 0.00 5.68 F
3423 6349 1.118965 TTGGTGGGCTCGAGTTCTCA 61.119 55.000 15.13 0.78 0.00 3.27 F
3582 6508 1.836802 AGAAGCTTCCAGTCTCCCATC 59.163 52.381 22.81 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 5256 0.036875 AGCCTCTCCTTGGTTTTCCG 59.963 55.000 0.00 0.00 44.36 4.30 R
3015 5941 0.251634 GGGAGTCTTGAGGCTTCAGG 59.748 60.000 1.05 1.05 34.15 3.86 R
3056 5982 0.656259 CATGAGCTTGGCGATGACAG 59.344 55.000 0.00 0.00 0.00 3.51 R
4068 6994 1.156736 CTACCTTTTGGCTCGGTGTG 58.843 55.000 0.00 0.00 45.59 3.82 R
4872 7839 0.667993 ACCAATGCTTGACACAACCG 59.332 50.000 0.00 0.00 0.00 4.44 R
5389 8356 2.996621 CCTTGATCGAAGAAGTTTCGCT 59.003 45.455 4.55 0.00 43.58 4.93 R
5851 8819 6.194967 AGAACTTCTTTCCTTCCCTCAAAAA 58.805 36.000 0.00 0.00 34.32 1.94 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
135 137 2.278206 CCGGTGAGCTGTCGATCG 60.278 66.667 9.36 9.36 0.00 3.69
145 147 1.866063 GCTGTCGATCGACCCATTCTC 60.866 57.143 37.58 16.81 43.97 2.87
154 156 2.177016 TCGACCCATTCTCTCCTATCCA 59.823 50.000 0.00 0.00 0.00 3.41
156 158 3.309296 GACCCATTCTCTCCTATCCACA 58.691 50.000 0.00 0.00 0.00 4.17
173 179 1.377994 CAGAGGCCAGCAAGAACCT 59.622 57.895 5.01 0.00 34.43 3.50
385 395 2.171489 GACGAAAACTCCTGTGCGGC 62.171 60.000 0.00 0.00 0.00 6.53
591 3437 2.093658 TCCCTCTCTTATTTCACGCACC 60.094 50.000 0.00 0.00 0.00 5.01
592 3438 2.280628 CCTCTCTTATTTCACGCACCC 58.719 52.381 0.00 0.00 0.00 4.61
593 3439 2.354704 CCTCTCTTATTTCACGCACCCA 60.355 50.000 0.00 0.00 0.00 4.51
594 3440 2.932614 CTCTCTTATTTCACGCACCCAG 59.067 50.000 0.00 0.00 0.00 4.45
595 3441 2.009774 CTCTTATTTCACGCACCCAGG 58.990 52.381 0.00 0.00 0.00 4.45
663 3513 1.229690 TTCCCTCCATCCAACCCGA 60.230 57.895 0.00 0.00 0.00 5.14
664 3514 0.842905 TTCCCTCCATCCAACCCGAA 60.843 55.000 0.00 0.00 0.00 4.30
666 3516 1.077716 CCTCCATCCAACCCGAACC 60.078 63.158 0.00 0.00 0.00 3.62
668 3518 2.437716 CCATCCAACCCGAACCCG 60.438 66.667 0.00 0.00 0.00 5.28
669 3519 2.349755 CATCCAACCCGAACCCGT 59.650 61.111 0.00 0.00 0.00 5.28
671 3521 2.963101 ATCCAACCCGAACCCGTCC 61.963 63.158 0.00 0.00 0.00 4.79
672 3522 3.633116 CCAACCCGAACCCGTCCT 61.633 66.667 0.00 0.00 0.00 3.85
673 3523 2.047560 CAACCCGAACCCGTCCTC 60.048 66.667 0.00 0.00 0.00 3.71
674 3524 2.203743 AACCCGAACCCGTCCTCT 60.204 61.111 0.00 0.00 0.00 3.69
675 3525 2.281295 AACCCGAACCCGTCCTCTC 61.281 63.158 0.00 0.00 0.00 3.20
676 3526 3.459063 CCCGAACCCGTCCTCTCC 61.459 72.222 0.00 0.00 0.00 3.71
677 3527 2.362632 CCGAACCCGTCCTCTCCT 60.363 66.667 0.00 0.00 0.00 3.69
678 3528 2.416432 CCGAACCCGTCCTCTCCTC 61.416 68.421 0.00 0.00 0.00 3.71
679 3529 1.378778 CGAACCCGTCCTCTCCTCT 60.379 63.158 0.00 0.00 0.00 3.69
680 3530 1.378124 CGAACCCGTCCTCTCCTCTC 61.378 65.000 0.00 0.00 0.00 3.20
681 3531 1.000612 AACCCGTCCTCTCCTCTCC 59.999 63.158 0.00 0.00 0.00 3.71
682 3532 1.511316 AACCCGTCCTCTCCTCTCCT 61.511 60.000 0.00 0.00 0.00 3.69
683 3533 1.152839 CCCGTCCTCTCCTCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
684 3534 1.641552 CCCGTCCTCTCCTCTCCTCT 61.642 65.000 0.00 0.00 0.00 3.69
692 3542 0.465460 CTCCTCTCCTCTCCTCACCG 60.465 65.000 0.00 0.00 0.00 4.94
725 3575 0.532417 GAGCCAGCCTCTGCATGTAG 60.532 60.000 4.14 4.14 41.13 2.74
849 3744 0.321122 CACCGCTGCCTCTTCTTCTT 60.321 55.000 0.00 0.00 0.00 2.52
852 3747 1.639280 CGCTGCCTCTTCTTCTTCTC 58.361 55.000 0.00 0.00 0.00 2.87
857 3753 2.564947 TGCCTCTTCTTCTTCTCTGGTC 59.435 50.000 0.00 0.00 0.00 4.02
860 3756 3.447229 CCTCTTCTTCTTCTCTGGTCTCC 59.553 52.174 0.00 0.00 0.00 3.71
1028 3924 2.932234 CGAGGAGGGTGCTCAACGT 61.932 63.158 0.00 0.00 34.19 3.99
1211 4119 1.137872 CACCTAGCTCACCATCTCCAC 59.862 57.143 0.00 0.00 0.00 4.02
1213 4121 1.489481 CTAGCTCACCATCTCCACCA 58.511 55.000 0.00 0.00 0.00 4.17
1220 4128 0.257039 ACCATCTCCACCATTGGCTC 59.743 55.000 1.54 0.00 43.56 4.70
1402 4315 0.694771 TGACCAGATGCCAGAAAGCT 59.305 50.000 0.00 0.00 0.00 3.74
1419 4333 5.243954 AGAAAGCTATCAAGTGGTTTTTCCC 59.756 40.000 0.00 0.00 34.60 3.97
1473 4387 2.092968 ACACAAGTCCTTTCAGACTGCA 60.093 45.455 0.00 0.00 46.44 4.41
1474 4388 2.945008 CACAAGTCCTTTCAGACTGCAA 59.055 45.455 0.00 0.00 46.44 4.08
1504 4418 1.074727 TGGGTAACATGGACAGTTGGG 59.925 52.381 0.00 0.00 39.74 4.12
1728 4650 5.247110 AGAACTGCAAGGAGAACATCTAGAA 59.753 40.000 0.00 0.00 39.30 2.10
1729 4651 5.489792 ACTGCAAGGAGAACATCTAGAAA 57.510 39.130 0.00 0.00 39.30 2.52
1842 4764 7.497909 GCCTAACCACTTTTAGCACTATATGAA 59.502 37.037 0.00 0.00 0.00 2.57
1926 4848 0.318441 TTCAGTGAAGAGGACAGCCG 59.682 55.000 0.08 0.00 39.96 5.52
2048 4970 7.770897 GGAGATGACAGGTTAACAGTTGAATAT 59.229 37.037 8.10 0.00 0.00 1.28
2269 5195 0.604780 TTCCAGTGCAGAGCTCAAGC 60.605 55.000 17.77 19.35 42.49 4.01
2296 5222 4.467082 CCCAAAATCATTCTGGTGATTCCA 59.533 41.667 2.94 0.00 45.49 3.53
2315 5241 5.512942 TCCACCATCTGGACTAAATCAAA 57.487 39.130 2.55 0.00 44.99 2.69
2460 5386 2.964740 TGTTCTTCCTCTTCATGCTCG 58.035 47.619 0.00 0.00 0.00 5.03
2496 5422 2.890371 GGCAGCAAATCAGCCCAG 59.110 61.111 0.00 0.00 41.10 4.45
2532 5458 6.750501 CGTATATCAACGAAGAACTCTTTCCA 59.249 38.462 0.00 0.00 45.68 3.53
2535 5461 4.509616 TCAACGAAGAACTCTTTCCACAA 58.490 39.130 0.00 0.00 36.11 3.33
2536 5462 4.570772 TCAACGAAGAACTCTTTCCACAAG 59.429 41.667 0.00 0.00 36.11 3.16
2622 5548 2.673833 GTCGGTTTCAGAGACATCGTT 58.326 47.619 0.00 0.00 35.19 3.85
2691 5617 2.019984 GCGAATGGAGCAAGAAGGAAT 58.980 47.619 0.00 0.00 34.19 3.01
2694 5620 2.519771 ATGGAGCAAGAAGGAATGCA 57.480 45.000 0.00 0.00 44.95 3.96
3015 5941 1.040339 ATGACTCTCTCCTGGACGCC 61.040 60.000 0.00 0.00 0.00 5.68
3056 5982 3.030652 CCACAGGCGTTCCAACAC 58.969 61.111 0.00 0.00 33.74 3.32
3087 6013 1.153005 GCTCATGGGGCTGGAAGAG 60.153 63.158 0.00 0.00 34.07 2.85
3279 6205 2.573915 ACCTCCTCCAAGAATTCTCACC 59.426 50.000 8.78 0.00 0.00 4.02
3283 6209 3.003480 CCTCCAAGAATTCTCACCGAAC 58.997 50.000 8.78 0.00 33.72 3.95
3423 6349 1.118965 TTGGTGGGCTCGAGTTCTCA 61.119 55.000 15.13 0.78 0.00 3.27
3516 6442 2.941333 GATGGTGATGCCGCATCG 59.059 61.111 24.73 0.00 43.14 3.84
3582 6508 1.836802 AGAAGCTTCCAGTCTCCCATC 59.163 52.381 22.81 0.00 0.00 3.51
4068 6994 4.396166 AGATCATCGTTCATTGACCCAAAC 59.604 41.667 0.00 0.00 0.00 2.93
4277 7225 5.006746 CGACACATCCTTCTACCATAAAAGC 59.993 44.000 0.00 0.00 0.00 3.51
4348 7298 8.422973 TGCATATTCCTTTGCAATGAAATAAC 57.577 30.769 13.58 7.17 45.30 1.89
4555 7520 3.633094 CTCGTGGTCCTGCGAGTGG 62.633 68.421 20.76 4.75 46.45 4.00
4556 7521 4.742201 CGTGGTCCTGCGAGTGGG 62.742 72.222 1.00 0.00 0.00 4.61
4557 7522 3.311110 GTGGTCCTGCGAGTGGGA 61.311 66.667 0.00 0.00 0.00 4.37
4558 7523 2.997315 TGGTCCTGCGAGTGGGAG 60.997 66.667 0.00 0.00 31.66 4.30
4559 7524 2.997897 GGTCCTGCGAGTGGGAGT 60.998 66.667 0.00 0.00 30.99 3.85
4560 7525 2.262915 GTCCTGCGAGTGGGAGTG 59.737 66.667 0.00 0.00 30.99 3.51
4692 7657 2.612672 CTCTGGTGTCTATGCATTGCTG 59.387 50.000 3.54 0.68 0.00 4.41
4836 7801 5.233476 TGTTTCAGTTTAACTGTCTGTAGCG 59.767 40.000 22.36 0.00 46.03 4.26
4872 7839 7.377766 TCTGTCTGGTACATTATTTTTCTGC 57.622 36.000 0.00 0.00 38.20 4.26
5308 8275 4.597507 AGTTCTGACCCTAACATGGAGAAA 59.402 41.667 0.00 0.00 0.00 2.52
5389 8356 4.760530 ATATAGCTCTGCAAGTGGAACA 57.239 40.909 0.00 0.00 41.43 3.18
5467 8434 0.108898 CAGAGGTCGACAGGCTCTTG 60.109 60.000 18.91 10.53 0.00 3.02
5851 8819 0.670546 CACTGGTCTCGCGGACATTT 60.671 55.000 23.07 8.49 46.16 2.32
5852 8820 0.034896 ACTGGTCTCGCGGACATTTT 59.965 50.000 23.07 7.11 46.16 1.82
5853 8821 1.156736 CTGGTCTCGCGGACATTTTT 58.843 50.000 23.07 0.00 46.16 1.94
5874 8842 6.465439 TTTTTGAGGGAAGGAAAGAAGTTC 57.535 37.500 0.00 0.00 35.28 3.01
5875 8843 5.388599 TTTGAGGGAAGGAAAGAAGTTCT 57.611 39.130 0.00 0.00 36.40 3.01
5876 8844 5.388599 TTGAGGGAAGGAAAGAAGTTCTT 57.611 39.130 12.50 12.50 38.59 2.52
5878 8846 5.766590 TGAGGGAAGGAAAGAAGTTCTTTT 58.233 37.500 27.27 14.90 45.85 2.27
5879 8847 6.194967 TGAGGGAAGGAAAGAAGTTCTTTTT 58.805 36.000 27.27 19.82 45.85 1.94
5897 8865 3.520187 TTTTTAGGGTCTCGCGGAC 57.480 52.632 16.40 16.40 43.79 4.79
5898 8866 0.680618 TTTTTAGGGTCTCGCGGACA 59.319 50.000 23.07 6.22 46.16 4.02
5899 8867 0.899720 TTTTAGGGTCTCGCGGACAT 59.100 50.000 23.07 15.65 46.16 3.06
5900 8868 0.899720 TTTAGGGTCTCGCGGACATT 59.100 50.000 23.07 15.08 46.16 2.71
5906 8874 1.443702 TCTCGCGGACATTGACACG 60.444 57.895 6.13 0.00 0.00 4.49
5910 8878 1.674611 CGCGGACATTGACACGAGAC 61.675 60.000 0.00 0.00 0.00 3.36
5943 8911 6.690098 GCAGTTGAATATCAGTTATGCACTTG 59.310 38.462 0.00 0.00 30.92 3.16
6138 9115 1.078848 GCCAGGAAGATCGCACACT 60.079 57.895 0.00 0.00 0.00 3.55
6139 9116 1.364626 GCCAGGAAGATCGCACACTG 61.365 60.000 0.00 0.00 0.00 3.66
6306 9452 0.179084 TCCCTTGAACCGATCATCGC 60.179 55.000 0.00 0.00 38.82 4.58
6376 9525 0.629058 TAGGTTGGAATTGAGGCCCC 59.371 55.000 0.00 0.00 0.00 5.80
6392 9541 1.426041 CCCCGTACAGGCGAAAATCG 61.426 60.000 0.00 0.00 43.89 3.34
6621 9779 1.065854 AGGCATTTCTTGGAGAGGACG 60.066 52.381 0.00 0.00 0.00 4.79
6649 9807 4.791069 GTACCTGGGGAGGGCCGA 62.791 72.222 0.00 0.00 33.83 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.106131 CTGCCTGCCGCGTATGTA 59.894 61.111 4.92 0.00 42.08 2.29
10 11 4.838152 ACCTGCCTGCCGCGTATG 62.838 66.667 4.92 0.00 42.08 2.39
11 12 4.530857 GACCTGCCTGCCGCGTAT 62.531 66.667 4.92 0.00 42.08 3.06
47 48 3.352338 ATGACGGGAGAACGACGGC 62.352 63.158 0.00 0.00 37.61 5.68
135 137 3.309296 TGTGGATAGGAGAGAATGGGTC 58.691 50.000 0.00 0.00 0.00 4.46
145 147 1.047002 CTGGCCTCTGTGGATAGGAG 58.953 60.000 3.32 0.00 38.35 3.69
154 156 1.073897 GGTTCTTGCTGGCCTCTGT 59.926 57.895 3.32 0.00 0.00 3.41
156 158 1.362224 TAAGGTTCTTGCTGGCCTCT 58.638 50.000 3.32 0.00 0.00 3.69
173 179 3.262151 TCTCCATTGGGTGATGTCGTTAA 59.738 43.478 2.09 0.00 31.92 2.01
395 405 1.376543 GGCATGTGATCTGTGTCAGG 58.623 55.000 0.00 0.00 31.51 3.86
663 3513 1.000612 GGAGAGGAGAGGACGGGTT 59.999 63.158 0.00 0.00 0.00 4.11
664 3514 1.928714 GAGGAGAGGAGAGGACGGGT 61.929 65.000 0.00 0.00 0.00 5.28
666 3516 0.179029 GAGAGGAGAGGAGAGGACGG 60.179 65.000 0.00 0.00 0.00 4.79
668 3518 1.143073 GAGGAGAGGAGAGGAGAGGAC 59.857 61.905 0.00 0.00 0.00 3.85
669 3519 1.274708 TGAGGAGAGGAGAGGAGAGGA 60.275 57.143 0.00 0.00 0.00 3.71
671 3521 1.133792 GGTGAGGAGAGGAGAGGAGAG 60.134 61.905 0.00 0.00 0.00 3.20
672 3522 0.923358 GGTGAGGAGAGGAGAGGAGA 59.077 60.000 0.00 0.00 0.00 3.71
673 3523 0.465460 CGGTGAGGAGAGGAGAGGAG 60.465 65.000 0.00 0.00 0.00 3.69
674 3524 1.610327 CGGTGAGGAGAGGAGAGGA 59.390 63.158 0.00 0.00 0.00 3.71
675 3525 1.454847 CCGGTGAGGAGAGGAGAGG 60.455 68.421 0.00 0.00 45.00 3.69
676 3526 1.454847 CCCGGTGAGGAGAGGAGAG 60.455 68.421 0.00 0.00 45.00 3.20
677 3527 2.212794 GACCCGGTGAGGAGAGGAGA 62.213 65.000 0.00 0.00 45.00 3.71
678 3528 1.755008 GACCCGGTGAGGAGAGGAG 60.755 68.421 0.00 0.00 45.00 3.69
679 3529 2.359404 GACCCGGTGAGGAGAGGA 59.641 66.667 0.00 0.00 45.00 3.71
680 3530 2.037367 TGACCCGGTGAGGAGAGG 59.963 66.667 0.00 0.00 45.00 3.69
681 3531 2.701780 CGTGACCCGGTGAGGAGAG 61.702 68.421 0.00 0.00 45.00 3.20
682 3532 2.675423 CGTGACCCGGTGAGGAGA 60.675 66.667 0.00 0.00 45.00 3.71
683 3533 2.675423 TCGTGACCCGGTGAGGAG 60.675 66.667 0.00 0.00 45.00 3.69
684 3534 2.675423 CTCGTGACCCGGTGAGGA 60.675 66.667 0.00 0.00 45.00 3.71
692 3542 4.500116 GCTCGGCTCTCGTGACCC 62.500 72.222 0.00 0.00 40.32 4.46
725 3575 1.531423 ATGATGATGATTGCGGCTCC 58.469 50.000 0.00 0.00 0.00 4.70
849 3744 1.075698 AGAAGGTTCGGAGACCAGAGA 59.924 52.381 10.55 0.00 34.32 3.10
852 3747 0.533032 GGAGAAGGTTCGGAGACCAG 59.467 60.000 10.55 0.00 34.32 4.00
857 3753 0.610687 AAGCAGGAGAAGGTTCGGAG 59.389 55.000 0.00 0.00 0.00 4.63
860 3756 1.068954 GCAAAAGCAGGAGAAGGTTCG 60.069 52.381 0.00 0.00 0.00 3.95
1028 3924 2.434185 GCATGTCGTCGGCCAAGA 60.434 61.111 2.24 0.00 0.00 3.02
1220 4128 0.325933 TGGACACAAGATGGCAGGAG 59.674 55.000 0.00 0.00 38.59 3.69
1343 4252 3.326210 CGCGCGATTCAGAGAGCC 61.326 66.667 28.94 0.00 0.00 4.70
1402 4315 5.450453 TGACAAGGGAAAAACCACTTGATA 58.550 37.500 12.23 0.00 43.29 2.15
1419 4333 4.443394 GCAACAAGCAATCTTTCTGACAAG 59.557 41.667 0.00 0.00 44.79 3.16
1473 4387 4.044065 TCCATGTTACCCAACTCTGGATTT 59.956 41.667 7.74 0.00 46.92 2.17
1474 4388 3.591527 TCCATGTTACCCAACTCTGGATT 59.408 43.478 7.74 0.00 46.92 3.01
1728 4650 3.758023 TGCTGTTTATGTACTGCTGCATT 59.242 39.130 1.31 0.00 41.75 3.56
1729 4651 3.346315 TGCTGTTTATGTACTGCTGCAT 58.654 40.909 1.31 0.00 41.75 3.96
1842 4764 1.678635 CACCATGTCAATGCCCGGT 60.679 57.895 0.00 0.00 31.93 5.28
2269 5195 2.234414 CACCAGAATGATTTTGGGGGTG 59.766 50.000 17.72 9.21 39.69 4.61
2315 5241 6.712276 TGGTTTTCCGGCCAATAAAATTAAT 58.288 32.000 2.24 0.00 44.36 1.40
2330 5256 0.036875 AGCCTCTCCTTGGTTTTCCG 59.963 55.000 0.00 0.00 44.36 4.30
2496 5422 3.576648 GTTGATATACGGTAGCTCCTGC 58.423 50.000 0.00 0.00 40.05 4.85
2511 5437 5.849510 TGTGGAAAGAGTTCTTCGTTGATA 58.150 37.500 0.00 0.00 34.61 2.15
2532 5458 2.750350 CTCTTCGGTGGCCCTTGT 59.250 61.111 0.00 0.00 0.00 3.16
2535 5461 3.394836 GAGCTCTTCGGTGGCCCT 61.395 66.667 6.43 0.00 0.00 5.19
2536 5462 3.706373 TGAGCTCTTCGGTGGCCC 61.706 66.667 16.19 0.00 0.00 5.80
2622 5548 1.200519 CCCGGTTGATGGAGTCCTTA 58.799 55.000 11.33 0.00 0.00 2.69
2691 5617 0.319555 GCGAGTCCTTGTACTGTGCA 60.320 55.000 0.00 0.00 31.19 4.57
2694 5620 1.000955 CTTGGCGAGTCCTTGTACTGT 59.999 52.381 0.00 0.00 35.26 3.55
3015 5941 0.251634 GGGAGTCTTGAGGCTTCAGG 59.748 60.000 1.05 1.05 34.15 3.86
3056 5982 0.656259 CATGAGCTTGGCGATGACAG 59.344 55.000 0.00 0.00 0.00 3.51
3279 6205 2.581354 CTCCAGGGAGCAGGTTCG 59.419 66.667 1.73 0.00 35.31 3.95
3283 6209 3.795041 CTGCCTCCAGGGAGCAGG 61.795 72.222 21.83 5.76 46.55 4.85
3359 6285 2.436646 ATGCGGTTCTTGGCCTCG 60.437 61.111 3.32 0.00 0.00 4.63
3423 6349 4.125703 CTCTGAAGTCTTTGTTGCACTCT 58.874 43.478 0.00 0.00 0.00 3.24
3524 6450 3.584406 TGAATCCTCTTCTTGGCTCTGAA 59.416 43.478 0.00 0.00 0.00 3.02
3582 6508 1.662629 CTTGCTGGCTTCATGACTACG 59.337 52.381 0.00 0.00 0.00 3.51
4068 6994 1.156736 CTACCTTTTGGCTCGGTGTG 58.843 55.000 0.00 0.00 45.59 3.82
4277 7225 6.822170 TCTCACCTTTGAATGAATCTGAGATG 59.178 38.462 0.00 0.00 30.41 2.90
4559 7524 3.785325 TCAATATGATGTGGTTCCTCCCA 59.215 43.478 0.00 0.00 34.77 4.37
4560 7525 4.437682 TCAATATGATGTGGTTCCTCCC 57.562 45.455 0.00 0.00 34.77 4.30
4692 7657 4.637771 GGTGGGCACATCTACACC 57.362 61.111 0.00 0.00 45.56 4.16
4872 7839 0.667993 ACCAATGCTTGACACAACCG 59.332 50.000 0.00 0.00 0.00 4.44
5308 8275 3.120546 CGAACACAATTCTGCGATGAAGT 60.121 43.478 0.00 0.00 0.00 3.01
5368 8335 4.701765 CTGTTCCACTTGCAGAGCTATAT 58.298 43.478 0.00 0.00 32.39 0.86
5389 8356 2.996621 CCTTGATCGAAGAAGTTTCGCT 59.003 45.455 4.55 0.00 43.58 4.93
5851 8819 6.194967 AGAACTTCTTTCCTTCCCTCAAAAA 58.805 36.000 0.00 0.00 34.32 1.94
5852 8820 5.766590 AGAACTTCTTTCCTTCCCTCAAAA 58.233 37.500 0.00 0.00 34.32 2.44
5853 8821 5.388599 AGAACTTCTTTCCTTCCCTCAAA 57.611 39.130 0.00 0.00 34.32 2.69
5854 8822 5.388599 AAGAACTTCTTTCCTTCCCTCAA 57.611 39.130 0.00 0.00 31.57 3.02
5855 8823 5.388599 AAAGAACTTCTTTCCTTCCCTCA 57.611 39.130 10.49 0.00 42.60 3.86
5856 8824 6.716934 AAAAAGAACTTCTTTCCTTCCCTC 57.283 37.500 15.64 0.00 45.19 4.30
5879 8847 0.680618 TGTCCGCGAGACCCTAAAAA 59.319 50.000 20.21 2.55 45.68 1.94
5880 8848 0.899720 ATGTCCGCGAGACCCTAAAA 59.100 50.000 20.21 5.73 45.68 1.52
5881 8849 0.899720 AATGTCCGCGAGACCCTAAA 59.100 50.000 20.21 6.31 45.68 1.85
5882 8850 0.174845 CAATGTCCGCGAGACCCTAA 59.825 55.000 20.21 6.61 45.68 2.69
5883 8851 0.681887 TCAATGTCCGCGAGACCCTA 60.682 55.000 20.21 6.90 45.68 3.53
5884 8852 1.982395 TCAATGTCCGCGAGACCCT 60.982 57.895 20.21 8.86 45.68 4.34
5885 8853 1.810030 GTCAATGTCCGCGAGACCC 60.810 63.158 20.21 2.75 45.68 4.46
5886 8854 1.080093 TGTCAATGTCCGCGAGACC 60.080 57.895 20.21 8.78 45.68 3.85
5887 8855 1.674611 CGTGTCAATGTCCGCGAGAC 61.675 60.000 8.23 14.35 46.51 3.36
5888 8856 1.443702 CGTGTCAATGTCCGCGAGA 60.444 57.895 8.23 0.00 36.74 4.04
5889 8857 1.443702 TCGTGTCAATGTCCGCGAG 60.444 57.895 8.23 0.00 38.53 5.03
5890 8858 1.443702 CTCGTGTCAATGTCCGCGA 60.444 57.895 8.23 9.85 40.85 5.87
5891 8859 1.443702 TCTCGTGTCAATGTCCGCG 60.444 57.895 0.00 0.00 36.00 6.46
5892 8860 1.674611 CGTCTCGTGTCAATGTCCGC 61.675 60.000 0.00 0.00 0.00 5.54
5893 8861 0.109919 TCGTCTCGTGTCAATGTCCG 60.110 55.000 0.00 0.00 0.00 4.79
5894 8862 1.986378 CTTCGTCTCGTGTCAATGTCC 59.014 52.381 0.00 0.00 0.00 4.02
5895 8863 1.387084 GCTTCGTCTCGTGTCAATGTC 59.613 52.381 0.00 0.00 0.00 3.06
5896 8864 1.269569 TGCTTCGTCTCGTGTCAATGT 60.270 47.619 0.00 0.00 0.00 2.71
5897 8865 1.418373 TGCTTCGTCTCGTGTCAATG 58.582 50.000 0.00 0.00 0.00 2.82
5898 8866 2.061773 CTTGCTTCGTCTCGTGTCAAT 58.938 47.619 0.00 0.00 0.00 2.57
5899 8867 1.487482 CTTGCTTCGTCTCGTGTCAA 58.513 50.000 0.00 0.00 0.00 3.18
5900 8868 0.939577 GCTTGCTTCGTCTCGTGTCA 60.940 55.000 0.00 0.00 0.00 3.58
5906 8874 1.502231 TCAACTGCTTGCTTCGTCTC 58.498 50.000 0.00 0.00 0.00 3.36
5910 8878 4.093998 ACTGATATTCAACTGCTTGCTTCG 59.906 41.667 0.00 0.00 0.00 3.79
6090 9067 2.104963 GCCGAATGGTCCCTTCTTATCT 59.895 50.000 5.48 0.00 37.67 1.98
6280 9420 2.671963 GGTTCAAGGGACACCGCC 60.672 66.667 0.00 0.00 43.47 6.13
6281 9421 3.047877 CGGTTCAAGGGACACCGC 61.048 66.667 0.00 0.00 46.45 5.68
6306 9452 6.198650 TGCATCAATTCATTTACTGTGAGG 57.801 37.500 0.00 0.00 0.00 3.86
6413 9564 1.207085 GAGAGCTCGACGACGTGTT 59.793 57.895 4.58 2.54 40.69 3.32
6560 9718 2.350522 CTAGCTGTTGCCGATGAAACT 58.649 47.619 0.00 0.00 40.80 2.66


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

AutoCloner maintained by Alex Coulton.