Multiple sequence alignment - TraesCS1D01G254500

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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 TraesCS1D01G254500 chr1D 100.000 3705 0 0 1 3705 346661682 346665386 0.000000e+00 6842
1 TraesCS1D01G254500 chr1B 92.978 3318 101 49 386 3654 466935880 466939114 0.000000e+00 4715
2 TraesCS1D01G254500 chr1B 81.760 784 56 29 127 870 466898429 466899165 3.210000e-160 575
3 TraesCS1D01G254500 chr1B 88.557 201 13 4 1 198 466935173 466935366 6.190000e-58 235
4 TraesCS1D01G254500 chr1B 84.685 222 21 10 231 448 466935364 466935576 3.750000e-50 209
5 TraesCS1D01G254500 chr1A 91.108 3104 133 61 636 3654 447004961 447008006 0.000000e+00 4071
6 TraesCS1D01G254500 chr1A 82.316 475 36 28 148 595 447004162 447004615 5.850000e-98 368
7 TraesCS1D01G254500 chr1A 89.032 155 11 3 1 150 447002641 447002794 1.760000e-43 187


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 TraesCS1D01G254500 chr1D 346661682 346665386 3704 False 6842.000000 6842 100.000000 1 3705 1 chr1D.!!$F1 3704
1 TraesCS1D01G254500 chr1B 466935173 466939114 3941 False 1719.666667 4715 88.740000 1 3654 3 chr1B.!!$F2 3653
2 TraesCS1D01G254500 chr1B 466898429 466899165 736 False 575.000000 575 81.760000 127 870 1 chr1B.!!$F1 743
3 TraesCS1D01G254500 chr1A 447002641 447008006 5365 False 1542.000000 4071 87.485333 1 3654 3 chr1A.!!$F1 3653

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
311 1696 0.516439 AGTTCGTCGTCGAGTTCCTC 59.484 55.0 4.73 0.0 46.81 3.71 F
1266 3395 0.679505 TGAGTTGAGACGGTGGAAGG 59.320 55.0 0.00 0.0 0.00 3.46 F
1607 3746 0.249155 TTCGTTTCGTTGAGCCGAGT 60.249 50.0 0.00 0.0 38.23 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 3725 0.878961 ACCACTCGGCTCAACGAAAC 60.879 55.0 0.00 0.00 42.98 2.78 R
2494 4643 0.107993 TGATGAGGCTCTTGGCGAAG 60.108 55.0 16.72 1.39 44.18 3.79 R
2724 4873 0.248296 GAGCTCATCCACGACGAGAC 60.248 60.0 9.40 0.00 0.00 3.36 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
31 32 2.052104 CGGGGCCTGGAAAATCCAC 61.052 63.158 3.77 0.00 42.67 4.02
146 1521 9.252962 TCAAGCCTTATTATAGTACTAAAACGC 57.747 33.333 6.70 3.07 0.00 4.84
176 1551 6.140968 AGTAATCTAACCTGGGCTTTTTCT 57.859 37.500 0.00 0.00 0.00 2.52
180 1555 3.650942 TCTAACCTGGGCTTTTTCTCTCA 59.349 43.478 0.00 0.00 0.00 3.27
185 1560 2.490903 CTGGGCTTTTTCTCTCACATGG 59.509 50.000 0.00 0.00 0.00 3.66
209 1584 2.775032 TAAACCGCTGGTGACTCGGC 62.775 60.000 10.30 3.69 46.21 5.54
214 1589 4.742201 CTGGTGACTCGGCCCACG 62.742 72.222 0.00 0.00 46.11 4.94
311 1696 0.516439 AGTTCGTCGTCGAGTTCCTC 59.484 55.000 4.73 0.00 46.81 3.71
317 1706 2.507324 GTCGAGTTCCTCTGCCGC 60.507 66.667 0.00 0.00 0.00 6.53
318 1707 3.760035 TCGAGTTCCTCTGCCGCC 61.760 66.667 0.00 0.00 0.00 6.13
319 1708 4.821589 CGAGTTCCTCTGCCGCCC 62.822 72.222 0.00 0.00 0.00 6.13
320 1709 3.394836 GAGTTCCTCTGCCGCCCT 61.395 66.667 0.00 0.00 0.00 5.19
321 1710 2.038975 AGTTCCTCTGCCGCCCTA 59.961 61.111 0.00 0.00 0.00 3.53
354 1748 2.623718 GGCCAAAAACGCAAACGC 59.376 55.556 0.00 0.00 45.53 4.84
396 1803 2.592574 CCACGCGCATCCATCCAT 60.593 61.111 5.73 0.00 0.00 3.41
398 1805 2.281070 ACGCGCATCCATCCATCC 60.281 61.111 5.73 0.00 0.00 3.51
399 1806 3.052082 CGCGCATCCATCCATCCC 61.052 66.667 8.75 0.00 0.00 3.85
400 1807 2.674380 GCGCATCCATCCATCCCC 60.674 66.667 0.30 0.00 0.00 4.81
401 1808 2.034687 CGCATCCATCCATCCCCC 59.965 66.667 0.00 0.00 0.00 5.40
402 1809 2.034687 GCATCCATCCATCCCCCG 59.965 66.667 0.00 0.00 0.00 5.73
403 1810 2.528818 GCATCCATCCATCCCCCGA 61.529 63.158 0.00 0.00 0.00 5.14
404 1811 2.067932 GCATCCATCCATCCCCCGAA 62.068 60.000 0.00 0.00 0.00 4.30
446 2217 3.760580 AACAAACAGACCAGGAGAGAG 57.239 47.619 0.00 0.00 0.00 3.20
447 2218 2.964209 ACAAACAGACCAGGAGAGAGA 58.036 47.619 0.00 0.00 0.00 3.10
448 2219 3.309296 ACAAACAGACCAGGAGAGAGAA 58.691 45.455 0.00 0.00 0.00 2.87
449 2220 3.906846 ACAAACAGACCAGGAGAGAGAAT 59.093 43.478 0.00 0.00 0.00 2.40
450 2221 5.087323 ACAAACAGACCAGGAGAGAGAATA 58.913 41.667 0.00 0.00 0.00 1.75
453 2224 5.199982 ACAGACCAGGAGAGAGAATAGAA 57.800 43.478 0.00 0.00 0.00 2.10
487 2265 8.704849 AAAATACTAACTATATTGGCATGGCA 57.295 30.769 19.43 19.43 0.00 4.92
488 2266 7.928307 AATACTAACTATATTGGCATGGCAG 57.072 36.000 22.17 12.65 0.00 4.85
489 2267 4.074970 ACTAACTATATTGGCATGGCAGC 58.925 43.478 22.17 0.00 0.00 5.25
608 2387 2.158264 CCATCCCCTATTTCCATTGCCT 60.158 50.000 0.00 0.00 0.00 4.75
698 2798 2.074124 CGCTCTCGCTCAACCTTTC 58.926 57.895 0.00 0.00 0.00 2.62
699 2799 1.678269 CGCTCTCGCTCAACCTTTCG 61.678 60.000 0.00 0.00 0.00 3.46
700 2800 1.960994 GCTCTCGCTCAACCTTTCGC 61.961 60.000 0.00 0.00 0.00 4.70
704 2804 2.861006 GCTCAACCTTTCGCGACC 59.139 61.111 9.15 0.00 0.00 4.79
705 2805 2.677979 GCTCAACCTTTCGCGACCC 61.678 63.158 9.15 0.00 0.00 4.46
706 2806 2.356553 TCAACCTTTCGCGACCCG 60.357 61.111 9.15 0.20 38.61 5.28
739 2839 4.367023 GTACGCCCTCGCACCACA 62.367 66.667 0.00 0.00 39.84 4.17
914 3040 3.207669 CAGCCAGCGCCATCCTTC 61.208 66.667 2.29 0.00 34.57 3.46
937 3064 1.764054 CCCGGGGAGATCTTGCTCT 60.764 63.158 14.71 0.00 35.26 4.09
939 3066 1.414158 CCGGGGAGATCTTGCTCTTA 58.586 55.000 0.00 0.00 35.26 2.10
940 3067 1.069358 CCGGGGAGATCTTGCTCTTAC 59.931 57.143 0.00 0.00 35.26 2.34
941 3068 2.035632 CGGGGAGATCTTGCTCTTACT 58.964 52.381 0.00 0.00 35.26 2.24
1031 3158 4.072088 CGAGGTCAACCGCAACGC 62.072 66.667 3.80 0.00 42.08 4.84
1066 3195 4.150454 CCGCCCTCCTCCTCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
1263 3392 1.666011 GCTGAGTTGAGACGGTGGA 59.334 57.895 0.00 0.00 0.00 4.02
1265 3394 1.937108 GCTGAGTTGAGACGGTGGAAG 60.937 57.143 0.00 0.00 0.00 3.46
1266 3395 0.679505 TGAGTTGAGACGGTGGAAGG 59.320 55.000 0.00 0.00 0.00 3.46
1591 3725 5.118990 TCAGCAAAGAAATAGGAGGATTCG 58.881 41.667 0.00 0.00 0.00 3.34
1599 3733 5.581085 AGAAATAGGAGGATTCGTTTCGTTG 59.419 40.000 0.00 0.00 0.00 4.10
1600 3734 4.730949 ATAGGAGGATTCGTTTCGTTGA 57.269 40.909 0.00 0.00 0.00 3.18
1602 3736 1.393883 GGAGGATTCGTTTCGTTGAGC 59.606 52.381 0.00 0.00 0.00 4.26
1603 3737 1.393883 GAGGATTCGTTTCGTTGAGCC 59.606 52.381 0.00 0.00 0.00 4.70
1607 3746 0.249155 TTCGTTTCGTTGAGCCGAGT 60.249 50.000 0.00 0.00 38.23 4.18
1620 3763 0.951558 GCCGAGTGGTTTGATTGTGT 59.048 50.000 0.00 0.00 37.67 3.72
1854 3997 2.202570 CGACCACGTCATCGACCC 60.203 66.667 11.63 0.00 40.86 4.46
2705 4854 0.386113 CCGAGCTAACCTCCTGTAGC 59.614 60.000 0.00 0.00 37.27 3.58
2722 4871 1.002134 GCACATACACCAGCCCAGT 60.002 57.895 0.00 0.00 0.00 4.00
2723 4872 1.026718 GCACATACACCAGCCCAGTC 61.027 60.000 0.00 0.00 0.00 3.51
2724 4873 0.740868 CACATACACCAGCCCAGTCG 60.741 60.000 0.00 0.00 0.00 4.18
2725 4874 1.192146 ACATACACCAGCCCAGTCGT 61.192 55.000 0.00 0.00 0.00 4.34
2726 4875 0.460284 CATACACCAGCCCAGTCGTC 60.460 60.000 0.00 0.00 0.00 4.20
2947 5108 1.839894 GGGATCCCCATGTCTGTCC 59.160 63.158 21.42 0.00 44.65 4.02
2953 5114 1.544825 CCCCATGTCTGTCCGTCTGT 61.545 60.000 0.00 0.00 0.00 3.41
2954 5115 0.108615 CCCATGTCTGTCCGTCTGTC 60.109 60.000 0.00 0.00 0.00 3.51
2955 5116 0.108615 CCATGTCTGTCCGTCTGTCC 60.109 60.000 0.00 0.00 0.00 4.02
2956 5117 0.891373 CATGTCTGTCCGTCTGTCCT 59.109 55.000 0.00 0.00 0.00 3.85
2981 5142 6.656902 TCTGATGATAAAACTCAATGGCTCT 58.343 36.000 0.00 0.00 0.00 4.09
2996 5157 3.743091 CTCTTCCTCGTCGGAGCGC 62.743 68.421 0.00 0.00 44.28 5.92
3111 5276 1.573108 CCTCTGGGGCTAAGACAAGA 58.427 55.000 0.00 0.00 0.00 3.02
3112 5277 1.484240 CCTCTGGGGCTAAGACAAGAG 59.516 57.143 0.00 0.00 0.00 2.85
3128 5293 0.258774 AGAGAGAGAGAGTGCCTCCC 59.741 60.000 0.00 0.00 42.97 4.30
3202 5367 2.434428 CTTCATCCTCTGTTGCTGCTT 58.566 47.619 0.00 0.00 0.00 3.91
3325 5509 0.320421 TTCTTGTGTCAGCTACGGGC 60.320 55.000 0.00 0.00 42.19 6.13
3347 5531 1.539929 GGATTGGATGGTGCTCTCTCG 60.540 57.143 0.00 0.00 0.00 4.04
3439 5639 2.171840 TGCTTCTAGTCCAGTCCAGAC 58.828 52.381 0.00 0.00 34.31 3.51
3548 5761 8.908786 ATCCTTATGTATACACATGTTTGGAG 57.091 34.615 7.96 0.00 45.17 3.86
3559 5772 2.435372 TGTTTGGAGTTTGGACTGCT 57.565 45.000 0.02 0.00 43.87 4.24
3561 5774 3.211045 TGTTTGGAGTTTGGACTGCTAC 58.789 45.455 0.02 0.00 43.87 3.58
3568 5793 4.487019 GAGTTTGGACTGCTACTGTACTC 58.513 47.826 0.00 0.00 35.88 2.59
3570 5795 5.322754 AGTTTGGACTGCTACTGTACTCTA 58.677 41.667 0.00 0.00 33.99 2.43
3573 5798 5.688814 TGGACTGCTACTGTACTCTACTA 57.311 43.478 0.00 0.00 0.00 1.82
3574 5799 6.058553 TGGACTGCTACTGTACTCTACTAA 57.941 41.667 0.00 0.00 0.00 2.24
3591 5816 7.566879 ACTCTACTAAGTTGATCCATCCATTCT 59.433 37.037 0.00 0.00 0.00 2.40
3592 5817 7.957002 TCTACTAAGTTGATCCATCCATTCTC 58.043 38.462 0.00 0.00 0.00 2.87
3624 5851 1.375908 CCACATGGGTGTCGGTGAG 60.376 63.158 0.00 0.00 43.71 3.51
3636 5863 0.899720 TCGGTGAGGAATGTGGTACC 59.100 55.000 4.43 4.43 0.00 3.34
3644 5871 3.678289 AGGAATGTGGTACCGGTAAAAC 58.322 45.455 17.78 17.44 0.00 2.43
3647 5874 4.277921 GGAATGTGGTACCGGTAAAACAAA 59.722 41.667 25.99 17.28 0.00 2.83
3648 5875 5.441709 AATGTGGTACCGGTAAAACAAAG 57.558 39.130 25.99 0.00 0.00 2.77
3649 5876 4.148128 TGTGGTACCGGTAAAACAAAGA 57.852 40.909 22.16 5.27 0.00 2.52
3650 5877 4.716794 TGTGGTACCGGTAAAACAAAGAT 58.283 39.130 22.16 0.00 0.00 2.40
3651 5878 4.515944 TGTGGTACCGGTAAAACAAAGATG 59.484 41.667 22.16 0.00 0.00 2.90
3652 5879 4.756135 GTGGTACCGGTAAAACAAAGATGA 59.244 41.667 17.78 0.00 0.00 2.92
3653 5880 5.413523 GTGGTACCGGTAAAACAAAGATGAT 59.586 40.000 17.78 0.00 0.00 2.45
3654 5881 6.594937 GTGGTACCGGTAAAACAAAGATGATA 59.405 38.462 17.78 0.00 0.00 2.15
3655 5882 7.281549 GTGGTACCGGTAAAACAAAGATGATAT 59.718 37.037 17.78 0.00 0.00 1.63
3656 5883 7.281324 TGGTACCGGTAAAACAAAGATGATATG 59.719 37.037 17.78 0.00 0.00 1.78
3657 5884 6.131544 ACCGGTAAAACAAAGATGATATGC 57.868 37.500 4.49 0.00 0.00 3.14
3658 5885 5.650266 ACCGGTAAAACAAAGATGATATGCA 59.350 36.000 4.49 0.00 0.00 3.96
3659 5886 6.151985 ACCGGTAAAACAAAGATGATATGCAA 59.848 34.615 4.49 0.00 0.00 4.08
3660 5887 6.692681 CCGGTAAAACAAAGATGATATGCAAG 59.307 38.462 0.00 0.00 0.00 4.01
3661 5888 6.692681 CGGTAAAACAAAGATGATATGCAAGG 59.307 38.462 0.00 0.00 0.00 3.61
3662 5889 7.547227 GGTAAAACAAAGATGATATGCAAGGT 58.453 34.615 0.00 0.00 0.00 3.50
3663 5890 8.034804 GGTAAAACAAAGATGATATGCAAGGTT 58.965 33.333 0.00 0.00 0.00 3.50
3664 5891 9.423061 GTAAAACAAAGATGATATGCAAGGTTT 57.577 29.630 0.00 0.00 0.00 3.27
3676 5903 9.639563 TGATATGCAAGGTTTATATTTCTTGGA 57.360 29.630 0.00 0.00 40.68 3.53
3681 5908 9.651913 TGCAAGGTTTATATTTCTTGGATTTTC 57.348 29.630 0.00 0.00 37.61 2.29
3682 5909 9.651913 GCAAGGTTTATATTTCTTGGATTTTCA 57.348 29.630 0.00 0.00 37.61 2.69
3686 5913 9.921637 GGTTTATATTTCTTGGATTTTCACACA 57.078 29.630 0.00 0.00 0.00 3.72
3693 5920 6.012658 TCTTGGATTTTCACACACTAATGC 57.987 37.500 0.00 0.00 0.00 3.56
3694 5921 5.534278 TCTTGGATTTTCACACACTAATGCA 59.466 36.000 0.00 0.00 0.00 3.96
3695 5922 5.375417 TGGATTTTCACACACTAATGCAG 57.625 39.130 0.00 0.00 0.00 4.41
3696 5923 5.069318 TGGATTTTCACACACTAATGCAGA 58.931 37.500 0.00 0.00 0.00 4.26
3697 5924 5.181811 TGGATTTTCACACACTAATGCAGAG 59.818 40.000 0.00 0.00 0.00 3.35
3698 5925 5.182001 GGATTTTCACACACTAATGCAGAGT 59.818 40.000 0.00 0.00 0.00 3.24
3699 5926 6.371548 GGATTTTCACACACTAATGCAGAGTA 59.628 38.462 3.85 0.00 0.00 2.59
3700 5927 6.785488 TTTTCACACACTAATGCAGAGTAG 57.215 37.500 3.85 2.53 0.00 2.57
3701 5928 3.849911 TCACACACTAATGCAGAGTAGC 58.150 45.455 3.85 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.879756 GCCTTGTCCTGTTCATTAGGCA 60.880 50.000 0.00 0.00 44.62 4.75
136 142 6.684686 AGATTACTCACACTGCGTTTTAGTA 58.315 36.000 0.00 0.00 0.00 1.82
146 1521 4.759782 CCCAGGTTAGATTACTCACACTG 58.240 47.826 0.00 0.00 0.00 3.66
176 1551 2.935238 GCGGTTTAGAAGCCATGTGAGA 60.935 50.000 0.00 0.00 0.00 3.27
180 1555 1.453155 CAGCGGTTTAGAAGCCATGT 58.547 50.000 0.00 0.00 0.00 3.21
185 1560 0.796927 GTCACCAGCGGTTTAGAAGC 59.203 55.000 0.00 0.00 31.02 3.86
317 1706 2.928116 CCGCTTTCTTTTAGACGTAGGG 59.072 50.000 0.00 0.00 0.00 3.53
318 1707 2.347755 GCCGCTTTCTTTTAGACGTAGG 59.652 50.000 0.00 0.00 0.00 3.18
319 1708 2.347755 GGCCGCTTTCTTTTAGACGTAG 59.652 50.000 0.00 0.00 0.00 3.51
320 1709 2.288948 TGGCCGCTTTCTTTTAGACGTA 60.289 45.455 0.00 0.00 0.00 3.57
321 1710 1.154197 GGCCGCTTTCTTTTAGACGT 58.846 50.000 0.00 0.00 0.00 4.34
352 1746 3.748048 TGAGAATTGAGAGTTCCTTTGCG 59.252 43.478 0.00 0.00 0.00 4.85
354 1748 5.642919 CCTCTGAGAATTGAGAGTTCCTTTG 59.357 44.000 6.17 0.00 34.94 2.77
395 1802 1.781153 TTTGGACGGTTTCGGGGGAT 61.781 55.000 0.00 0.00 41.39 3.85
396 1803 1.992519 TTTTGGACGGTTTCGGGGGA 61.993 55.000 0.00 0.00 41.39 4.81
398 1805 1.102222 TGTTTTGGACGGTTTCGGGG 61.102 55.000 0.00 0.00 41.39 5.73
399 1806 0.739561 TTGTTTTGGACGGTTTCGGG 59.260 50.000 0.00 0.00 41.39 5.14
400 1807 2.785713 ATTGTTTTGGACGGTTTCGG 57.214 45.000 0.00 0.00 41.39 4.30
401 1808 5.035443 TGTTTATTGTTTTGGACGGTTTCG 58.965 37.500 0.00 0.00 43.02 3.46
402 1809 6.889019 TTGTTTATTGTTTTGGACGGTTTC 57.111 33.333 0.00 0.00 0.00 2.78
403 1810 7.172703 TGTTTTGTTTATTGTTTTGGACGGTTT 59.827 29.630 0.00 0.00 0.00 3.27
404 1811 6.649557 TGTTTTGTTTATTGTTTTGGACGGTT 59.350 30.769 0.00 0.00 0.00 4.44
468 2246 3.125829 CGCTGCCATGCCAATATAGTTAG 59.874 47.826 0.00 0.00 0.00 2.34
488 2266 2.280457 CCCTAGCTAAGCTGCCGC 60.280 66.667 0.00 0.00 40.10 6.53
489 2267 2.423446 CCCCTAGCTAAGCTGCCG 59.577 66.667 0.00 0.00 40.10 5.69
589 2368 2.110721 GGAGGCAATGGAAATAGGGGAT 59.889 50.000 0.00 0.00 0.00 3.85
687 2787 2.677979 GGGTCGCGAAAGGTTGAGC 61.678 63.158 12.06 0.00 0.00 4.26
689 2789 2.356553 CGGGTCGCGAAAGGTTGA 60.357 61.111 12.06 0.00 0.00 3.18
690 2790 4.084888 GCGGGTCGCGAAAGGTTG 62.085 66.667 12.06 0.00 44.55 3.77
708 2808 4.908877 GTACGAGGCTCGGCTCGC 62.909 72.222 36.81 19.60 45.59 5.03
914 3040 2.064581 AAGATCTCCCCGGGGAACG 61.065 63.158 41.16 30.62 44.66 3.95
937 3064 0.248565 CTCAGCTGCTGCAGGAGTAA 59.751 55.000 32.29 18.55 42.74 2.24
939 3066 1.890625 CTCTCAGCTGCTGCAGGAGT 61.891 60.000 32.29 18.48 40.96 3.85
940 3067 1.153529 CTCTCAGCTGCTGCAGGAG 60.154 63.158 29.15 29.15 42.74 3.69
941 3068 2.979649 CTCTCAGCTGCTGCAGGA 59.020 61.111 29.05 18.05 42.74 3.86
1052 3181 0.908198 CAAACAGAGGAGGAGGAGGG 59.092 60.000 0.00 0.00 0.00 4.30
1062 3191 2.335712 GGGAAGCGCCAAACAGAGG 61.336 63.158 2.29 0.00 38.95 3.69
1063 3192 2.680913 CGGGAAGCGCCAAACAGAG 61.681 63.158 2.29 0.00 38.95 3.35
1064 3193 2.668212 CGGGAAGCGCCAAACAGA 60.668 61.111 2.29 0.00 38.95 3.41
1065 3194 4.404654 GCGGGAAGCGCCAAACAG 62.405 66.667 2.29 0.00 38.95 3.16
1263 3392 3.029981 GCCCCAATCCCCTCCCTT 61.030 66.667 0.00 0.00 0.00 3.95
1468 3602 4.093952 CTCTGCGGCAAAGGCACG 62.094 66.667 3.44 0.00 43.71 5.34
1469 3603 4.410743 GCTCTGCGGCAAAGGCAC 62.411 66.667 5.33 0.00 43.71 5.01
1591 3725 0.878961 ACCACTCGGCTCAACGAAAC 60.879 55.000 0.00 0.00 42.98 2.78
1599 3733 1.197721 CACAATCAAACCACTCGGCTC 59.802 52.381 0.00 0.00 34.57 4.70
1600 3734 1.238439 CACAATCAAACCACTCGGCT 58.762 50.000 0.00 0.00 34.57 5.52
1602 3736 3.708563 AAACACAATCAAACCACTCGG 57.291 42.857 0.00 0.00 38.77 4.63
1628 3771 1.214062 GTGAGAGCGAGACCACCAG 59.786 63.158 0.00 0.00 0.00 4.00
2494 4643 0.107993 TGATGAGGCTCTTGGCGAAG 60.108 55.000 16.72 1.39 44.18 3.79
2705 4854 0.740868 CGACTGGGCTGGTGTATGTG 60.741 60.000 0.00 0.00 0.00 3.21
2722 4871 1.978712 GCTCATCCACGACGAGACGA 61.979 60.000 0.00 0.00 37.03 4.20
2723 4872 1.583967 GCTCATCCACGACGAGACG 60.584 63.158 0.00 0.00 39.31 4.18
2724 4873 0.248296 GAGCTCATCCACGACGAGAC 60.248 60.000 9.40 0.00 0.00 3.36
2725 4874 1.706287 CGAGCTCATCCACGACGAGA 61.706 60.000 15.40 0.00 0.00 4.04
2726 4875 1.297967 CGAGCTCATCCACGACGAG 60.298 63.158 15.40 0.00 0.00 4.18
2834 4988 2.018324 GCGGCGGCGGTAGTATAAC 61.018 63.158 33.02 8.86 0.00 1.89
2943 5104 1.546029 CATCAGAAGGACAGACGGACA 59.454 52.381 0.00 0.00 0.00 4.02
2947 5108 6.102663 AGTTTTATCATCAGAAGGACAGACG 58.897 40.000 0.00 0.00 0.00 4.18
2953 5114 6.319658 GCCATTGAGTTTTATCATCAGAAGGA 59.680 38.462 0.00 0.00 0.00 3.36
2954 5115 6.320672 AGCCATTGAGTTTTATCATCAGAAGG 59.679 38.462 0.00 0.00 0.00 3.46
2955 5116 7.282675 AGAGCCATTGAGTTTTATCATCAGAAG 59.717 37.037 0.00 0.00 0.00 2.85
2956 5117 7.114754 AGAGCCATTGAGTTTTATCATCAGAA 58.885 34.615 0.00 0.00 0.00 3.02
2996 5157 3.508840 GACGGCAATGGCTTCCCG 61.509 66.667 5.02 9.78 45.80 5.14
3009 5170 1.365699 CGGAACAATTAGTGGGACGG 58.634 55.000 0.00 0.00 0.00 4.79
3039 5201 4.148825 GATCACACCGGCCGAGCT 62.149 66.667 30.73 5.22 0.00 4.09
3041 5203 3.019003 AAGGATCACACCGGCCGAG 62.019 63.158 30.73 21.50 34.73 4.63
3042 5204 3.000819 AAGGATCACACCGGCCGA 61.001 61.111 30.73 6.25 34.73 5.54
3043 5205 2.819595 CAAGGATCACACCGGCCG 60.820 66.667 21.04 21.04 34.73 6.13
3046 5208 0.324943 AGAACCAAGGATCACACCGG 59.675 55.000 0.00 0.00 34.73 5.28
3202 5367 1.487976 CCCTCAAGGATAAGCAGCAGA 59.512 52.381 0.00 0.00 38.24 4.26
3275 5444 4.046462 CCACATCAACAGCAACAAAAGAG 58.954 43.478 0.00 0.00 0.00 2.85
3325 5509 1.489649 AGAGAGCACCATCCAATCCAG 59.510 52.381 0.00 0.00 0.00 3.86
3439 5639 4.069304 CTGCTAGCCTAGACTACTACTGG 58.931 52.174 13.29 0.00 0.00 4.00
3548 5761 4.522722 AGAGTACAGTAGCAGTCCAAAC 57.477 45.455 0.00 0.00 0.00 2.93
3559 5772 9.339850 GATGGATCAACTTAGTAGAGTACAGTA 57.660 37.037 0.00 0.00 0.00 2.74
3561 5774 7.285629 TGGATGGATCAACTTAGTAGAGTACAG 59.714 40.741 0.00 0.00 0.00 2.74
3568 5793 6.865726 CGAGAATGGATGGATCAACTTAGTAG 59.134 42.308 0.00 0.00 0.00 2.57
3570 5795 5.453903 CCGAGAATGGATGGATCAACTTAGT 60.454 44.000 0.00 0.00 0.00 2.24
3573 5798 3.200825 ACCGAGAATGGATGGATCAACTT 59.799 43.478 0.00 0.00 0.00 2.66
3574 5799 2.774234 ACCGAGAATGGATGGATCAACT 59.226 45.455 0.00 0.00 0.00 3.16
3624 5851 3.410508 TGTTTTACCGGTACCACATTCC 58.589 45.455 15.53 0.00 0.00 3.01
3636 5863 6.692681 CCTTGCATATCATCTTTGTTTTACCG 59.307 38.462 0.00 0.00 0.00 4.02
3650 5877 9.639563 TCCAAGAAATATAAACCTTGCATATCA 57.360 29.630 0.00 0.00 35.83 2.15
3655 5882 9.651913 GAAAATCCAAGAAATATAAACCTTGCA 57.348 29.630 0.00 0.00 35.83 4.08
3656 5883 9.651913 TGAAAATCCAAGAAATATAAACCTTGC 57.348 29.630 0.00 0.00 35.83 4.01
3660 5887 9.921637 TGTGTGAAAATCCAAGAAATATAAACC 57.078 29.630 0.00 0.00 0.00 3.27
3667 5894 7.599998 GCATTAGTGTGTGAAAATCCAAGAAAT 59.400 33.333 0.00 0.00 0.00 2.17
3668 5895 6.922957 GCATTAGTGTGTGAAAATCCAAGAAA 59.077 34.615 0.00 0.00 0.00 2.52
3669 5896 6.040278 TGCATTAGTGTGTGAAAATCCAAGAA 59.960 34.615 0.00 0.00 0.00 2.52
3670 5897 5.534278 TGCATTAGTGTGTGAAAATCCAAGA 59.466 36.000 0.00 0.00 0.00 3.02
3671 5898 5.771469 TGCATTAGTGTGTGAAAATCCAAG 58.229 37.500 0.00 0.00 0.00 3.61
3672 5899 5.534278 TCTGCATTAGTGTGTGAAAATCCAA 59.466 36.000 0.00 0.00 0.00 3.53
3673 5900 5.069318 TCTGCATTAGTGTGTGAAAATCCA 58.931 37.500 0.00 0.00 0.00 3.41
3674 5901 5.182001 ACTCTGCATTAGTGTGTGAAAATCC 59.818 40.000 1.27 0.00 32.21 3.01
3675 5902 6.246420 ACTCTGCATTAGTGTGTGAAAATC 57.754 37.500 1.27 0.00 32.21 2.17
3676 5903 6.128172 GCTACTCTGCATTAGTGTGTGAAAAT 60.128 38.462 11.16 0.00 35.03 1.82
3677 5904 5.179368 GCTACTCTGCATTAGTGTGTGAAAA 59.821 40.000 11.16 0.00 35.03 2.29
3678 5905 4.690748 GCTACTCTGCATTAGTGTGTGAAA 59.309 41.667 11.16 0.00 35.03 2.69
3679 5906 4.245660 GCTACTCTGCATTAGTGTGTGAA 58.754 43.478 11.16 0.00 35.03 3.18
3680 5907 3.258123 TGCTACTCTGCATTAGTGTGTGA 59.742 43.478 11.16 0.00 38.12 3.58
3681 5908 3.369147 GTGCTACTCTGCATTAGTGTGTG 59.631 47.826 11.16 2.28 45.23 3.82
3682 5909 3.589988 GTGCTACTCTGCATTAGTGTGT 58.410 45.455 11.16 0.00 45.23 3.72
3683 5910 2.600420 CGTGCTACTCTGCATTAGTGTG 59.400 50.000 11.16 6.14 45.23 3.82
3684 5911 2.881074 CGTGCTACTCTGCATTAGTGT 58.119 47.619 11.16 0.00 45.23 3.55


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

AutoCloner maintained by Alex Coulton.