Multiple sequence alignment - TraesCS1A01G111600

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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 TraesCS1A01G111600 chr1A 100.000 7872 0 0 1 7872 112934716 112942587 0.000000e+00 14537.0
1 TraesCS1A01G111600 chr1A 88.307 573 54 10 2662 3225 112936468 112937036 0.000000e+00 675.0
2 TraesCS1A01G111600 chr1A 88.307 573 54 10 1753 2321 112937377 112937940 0.000000e+00 675.0
3 TraesCS1A01G111600 chr1A 86.207 290 33 6 6189 6477 112937076 112937359 2.760000e-79 307.0
4 TraesCS1A01G111600 chr1A 86.207 290 33 6 2361 2644 112940904 112941192 2.760000e-79 307.0
5 TraesCS1A01G111600 chr1D 94.845 3317 119 20 1 3291 109471586 109474876 0.000000e+00 5131.0
6 TraesCS1A01G111600 chr1D 98.215 2857 41 5 3288 6138 94053498 94050646 0.000000e+00 4985.0
7 TraesCS1A01G111600 chr1D 98.207 2845 47 3 3288 6132 493217871 493220711 0.000000e+00 4968.0
8 TraesCS1A01G111600 chr1D 89.467 1576 88 27 6211 7761 109474913 109476435 0.000000e+00 1919.0
9 TraesCS1A01G111600 chr1D 83.605 921 102 26 1753 2631 109474250 109475163 0.000000e+00 819.0
10 TraesCS1A01G111600 chr1D 88.287 572 55 9 2662 3225 109473341 109473908 0.000000e+00 675.0
11 TraesCS1A01G111600 chr1D 87.625 299 29 7 6189 6485 109473948 109474240 2.720000e-89 340.0
12 TraesCS1A01G111600 chr1D 92.793 111 8 0 7762 7872 109476634 109476744 2.270000e-35 161.0
13 TraesCS1A01G111600 chr1D 92.857 56 0 1 6126 6181 109474860 109474911 2.360000e-10 78.7
14 TraesCS1A01G111600 chr1B 95.440 3224 118 17 83 3291 165071029 165074238 0.000000e+00 5112.0
15 TraesCS1A01G111600 chr1B 91.745 1490 85 13 6211 7676 165074275 165075750 0.000000e+00 2036.0
16 TraesCS1A01G111600 chr1B 87.695 577 63 7 1753 2325 165073612 165074184 0.000000e+00 665.0
17 TraesCS1A01G111600 chr1B 87.958 573 55 11 2662 3225 165072703 165073270 0.000000e+00 664.0
18 TraesCS1A01G111600 chr1B 85.953 299 34 7 6189 6485 165073310 165073602 5.930000e-81 313.0
19 TraesCS1A01G111600 chr1B 93.694 111 7 0 7762 7872 165075940 165076050 4.890000e-37 167.0
20 TraesCS1A01G111600 chr2D 98.560 2848 38 3 3288 6135 106329860 106332704 0.000000e+00 5029.0
21 TraesCS1A01G111600 chr2D 98.207 2845 45 5 3288 6132 463076984 463079822 0.000000e+00 4966.0
22 TraesCS1A01G111600 chr7A 98.383 2845 39 5 3288 6132 438512052 438514889 0.000000e+00 4992.0
23 TraesCS1A01G111600 chr7A 98.314 2847 41 5 3288 6131 109349118 109351960 0.000000e+00 4985.0
24 TraesCS1A01G111600 chr7A 98.240 2841 45 3 3288 6125 232386859 232384021 0.000000e+00 4964.0
25 TraesCS1A01G111600 chr3A 98.207 2845 49 2 3288 6132 77484823 77487665 0.000000e+00 4970.0
26 TraesCS1A01G111600 chr7D 98.137 2845 51 2 3288 6132 231421366 231424208 0.000000e+00 4959.0


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 TraesCS1A01G111600 chr1A 112934716 112942587 7871 False 14537.000000 14537 100.000000 1 7872 1 chr1A.!!$F1 7871
1 TraesCS1A01G111600 chr1A 112936468 112941192 4724 False 491.000000 675 87.257000 1753 6477 4 chr1A.!!$F2 4724
2 TraesCS1A01G111600 chr1D 94050646 94053498 2852 True 4985.000000 4985 98.215000 3288 6138 1 chr1D.!!$R1 2850
3 TraesCS1A01G111600 chr1D 493217871 493220711 2840 False 4968.000000 4968 98.207000 3288 6132 1 chr1D.!!$F1 2844
4 TraesCS1A01G111600 chr1D 109471586 109476744 5158 False 1303.385714 5131 89.925571 1 7872 7 chr1D.!!$F2 7871
5 TraesCS1A01G111600 chr1B 165071029 165076050 5021 False 1492.833333 5112 90.414167 83 7872 6 chr1B.!!$F1 7789
6 TraesCS1A01G111600 chr2D 106329860 106332704 2844 False 5029.000000 5029 98.560000 3288 6135 1 chr2D.!!$F1 2847
7 TraesCS1A01G111600 chr2D 463076984 463079822 2838 False 4966.000000 4966 98.207000 3288 6132 1 chr2D.!!$F2 2844
8 TraesCS1A01G111600 chr7A 438512052 438514889 2837 False 4992.000000 4992 98.383000 3288 6132 1 chr7A.!!$F2 2844
9 TraesCS1A01G111600 chr7A 109349118 109351960 2842 False 4985.000000 4985 98.314000 3288 6131 1 chr7A.!!$F1 2843
10 TraesCS1A01G111600 chr7A 232384021 232386859 2838 True 4964.000000 4964 98.240000 3288 6125 1 chr7A.!!$R1 2837
11 TraesCS1A01G111600 chr3A 77484823 77487665 2842 False 4970.000000 4970 98.207000 3288 6132 1 chr3A.!!$F1 2844
12 TraesCS1A01G111600 chr7D 231421366 231424208 2842 False 4959.000000 4959 98.137000 3288 6132 1 chr7D.!!$F1 2844

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
162 173 1.324740 CGAGGGTAATGGTGGTCCGA 61.325 60.000 0.00 0.0 36.30 4.55 F
719 740 1.379576 GCCTCTGATGCTGCCCTTT 60.380 57.895 0.00 0.0 0.00 3.11 F
1607 1629 1.613437 ACCTTTGGAATTCTGGTTGCG 59.387 47.619 5.23 0.0 0.00 4.85 F
1698 1720 6.976934 TCTGCATATTGTAGACATGGTCTA 57.023 37.500 0.00 2.1 41.51 2.59 F
6513 6553 3.118408 TGGTTACAGCTGTTGTTCTCACT 60.118 43.478 27.06 0.0 41.29 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1591 2.365617 AGGTAACACTCCACACTGACTG 59.634 50.000 0.00 0.0 41.41 3.51 R
1698 1720 6.254157 GCGATCTAAATGTGCAAATCAACAAT 59.746 34.615 0.00 0.0 0.00 2.71 R
6477 6517 4.217550 GCTGTAACCAAATTTCCAGTAGCA 59.782 41.667 0.00 0.0 0.00 3.49 R
6526 6567 4.327627 GTCAACTCTTCCGCTAAGAATCAC 59.672 45.833 0.76 0.0 43.66 3.06 R
7682 7744 0.247736 CTAGCCGAGTCCAACAAGCT 59.752 55.000 0.00 0.0 0.00 3.74 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
133 143 6.894103 AGAGTACTTCGTAGAAAGGGGAAATA 59.106 38.462 0.00 0.00 45.90 1.40
134 144 7.398332 AGAGTACTTCGTAGAAAGGGGAAATAA 59.602 37.037 0.00 0.00 45.90 1.40
135 145 7.910584 AGTACTTCGTAGAAAGGGGAAATAAA 58.089 34.615 0.00 0.00 45.90 1.40
138 149 8.051901 ACTTCGTAGAAAGGGGAAATAAATTG 57.948 34.615 0.00 0.00 45.90 2.32
149 160 5.046878 GGGGAAATAAATTGTTTTCGAGGGT 60.047 40.000 7.08 0.00 33.58 4.34
162 173 1.324740 CGAGGGTAATGGTGGTCCGA 61.325 60.000 0.00 0.00 36.30 4.55
208 219 4.696479 AATGACTTATCAGGTAGCTGGG 57.304 45.455 21.22 11.57 38.57 4.45
245 256 3.054361 CCAGGGCCTGATAACAACTAGTT 60.054 47.826 34.84 1.12 37.70 2.24
284 296 3.767044 AAGCCCAACCCACCAACCC 62.767 63.158 0.00 0.00 0.00 4.11
417 438 2.589159 GATCTTTCCCTCCGCGCC 60.589 66.667 0.00 0.00 0.00 6.53
688 709 3.052869 AGGGGTAGATTTGATGGTTTCCC 60.053 47.826 0.00 0.00 0.00 3.97
703 724 3.444034 GGTTTCCCTAAAGTTGATGAGCC 59.556 47.826 0.00 0.00 0.00 4.70
717 738 2.691623 AGCCTCTGATGCTGCCCT 60.692 61.111 6.65 0.00 37.76 5.19
719 740 1.379576 GCCTCTGATGCTGCCCTTT 60.380 57.895 0.00 0.00 0.00 3.11
727 748 2.773661 TGATGCTGCCCTTTGATAGAGA 59.226 45.455 0.00 0.00 0.00 3.10
807 828 6.943146 TGGCAATAATAAACAGTCTGTACCAA 59.057 34.615 5.77 0.00 0.00 3.67
1181 1202 3.065371 CGATCATTGCTGGGAAAGGTAAC 59.935 47.826 0.00 0.00 0.00 2.50
1258 1279 7.584122 AGAGCAGTTTAGTCGATATTTCCTA 57.416 36.000 0.00 0.00 0.00 2.94
1349 1370 7.174946 CCAATTGTGTATTGTGTTCTAGGAAGT 59.825 37.037 4.43 0.00 41.74 3.01
1493 1515 4.683832 CTTAGTTGACCACCCTAGATTCG 58.316 47.826 0.00 0.00 0.00 3.34
1569 1591 4.370364 TTGCAGGAAAAGTTGTGTCTTC 57.630 40.909 0.00 0.00 0.00 2.87
1607 1629 1.613437 ACCTTTGGAATTCTGGTTGCG 59.387 47.619 5.23 0.00 0.00 4.85
1698 1720 6.976934 TCTGCATATTGTAGACATGGTCTA 57.023 37.500 0.00 2.10 41.51 2.59
6477 6517 9.920946 TTTCTTTGCTTAGGAAATAGTATCCAT 57.079 29.630 0.00 0.00 39.55 3.41
6513 6553 3.118408 TGGTTACAGCTGTTGTTCTCACT 60.118 43.478 27.06 0.00 41.29 3.41
6549 6590 4.327627 GTGATTCTTAGCGGAAGAGTTGAC 59.672 45.833 4.58 1.31 45.05 3.18
6635 6676 0.320421 TGTTACTGGAGCTTGGCGTC 60.320 55.000 0.00 0.00 0.00 5.19
6737 6779 5.163933 CCGACAAAATTTCAGCAATCCAATG 60.164 40.000 0.00 0.00 0.00 2.82
6738 6780 5.634439 CGACAAAATTTCAGCAATCCAATGA 59.366 36.000 0.00 0.00 0.00 2.57
6740 6782 7.429636 ACAAAATTTCAGCAATCCAATGAAG 57.570 32.000 0.00 0.00 34.64 3.02
6741 6783 6.072893 ACAAAATTTCAGCAATCCAATGAAGC 60.073 34.615 0.00 0.00 34.64 3.86
6757 6800 6.197842 CCAATGAAGCTTTATCGCAGAAATTC 59.802 38.462 3.93 0.00 43.58 2.17
6802 6845 1.888512 CCTATCTGGAGAGCTCTCTGC 59.111 57.143 36.09 24.03 46.53 4.26
6814 6857 1.937278 CTCTCTGCGCATTCACAGAT 58.063 50.000 12.24 0.00 41.84 2.90
6856 6899 4.806342 TTCTGCAGTTTCTAAACCGAAC 57.194 40.909 14.67 0.00 39.71 3.95
6874 6917 0.318784 ACCGTTCAGAAGCGTGACTC 60.319 55.000 4.98 0.00 0.00 3.36
6877 6920 1.600663 CGTTCAGAAGCGTGACTCTGT 60.601 52.381 1.08 0.00 0.00 3.41
6888 6931 0.247460 TGACTCTGTTGGCGATCTGG 59.753 55.000 0.00 0.00 0.00 3.86
6902 6945 0.740868 ATCTGGTGTGATTGCGACGG 60.741 55.000 0.00 0.00 0.00 4.79
6921 6964 2.361610 CGGCAAAGGGGATGCAGT 60.362 61.111 0.00 0.00 45.60 4.40
6963 7006 5.038651 GAGCTAGAGGTAGGTCTCACTAA 57.961 47.826 0.00 0.00 46.27 2.24
6966 7009 4.022676 GCTAGAGGTAGGTCTCACTAATGC 60.023 50.000 0.00 0.00 36.30 3.56
6974 7017 1.592669 CTCACTAATGCGAGGGCCG 60.593 63.158 0.00 0.00 38.85 6.13
6987 7030 0.112412 AGGGCCGCTAATTATTGGGG 59.888 55.000 0.00 4.05 39.01 4.96
7010 7053 2.119801 ACGCCTGCAGATTTTCAGAT 57.880 45.000 17.39 0.00 32.26 2.90
7014 7057 2.751259 GCCTGCAGATTTTCAGATGTGA 59.249 45.455 17.39 0.00 32.26 3.58
7015 7058 3.192001 GCCTGCAGATTTTCAGATGTGAA 59.808 43.478 17.39 0.23 41.13 3.18
7044 7087 4.557205 GTGTACTGCACTTAACAGCTAGT 58.443 43.478 0.00 0.00 44.41 2.57
7045 7088 5.706916 GTGTACTGCACTTAACAGCTAGTA 58.293 41.667 0.00 0.00 44.41 1.82
7059 7104 4.817464 ACAGCTAGTACCGATAGTTCTCAG 59.183 45.833 0.00 0.00 0.00 3.35
7062 7107 5.703592 AGCTAGTACCGATAGTTCTCAGATG 59.296 44.000 0.00 0.00 0.00 2.90
7067 7112 3.564644 ACCGATAGTTCTCAGATGGTACG 59.435 47.826 0.00 0.00 0.00 3.67
7070 7115 5.206299 CGATAGTTCTCAGATGGTACGAAC 58.794 45.833 0.00 0.00 35.44 3.95
7174 7219 8.258007 TCAAATCTTGACCAGTGGTATAGTTAG 58.742 37.037 16.72 6.63 35.25 2.34
7207 7252 6.597672 TGGTTGTCTATATGAAAACGATTGCT 59.402 34.615 0.00 0.00 42.42 3.91
7213 7258 8.012241 GTCTATATGAAAACGATTGCTGGATTC 58.988 37.037 0.00 0.00 0.00 2.52
7217 7262 5.841810 TGAAAACGATTGCTGGATTCTTTT 58.158 33.333 0.00 0.00 0.00 2.27
7249 7294 3.555586 GCCATGGTTTTGTTTGCTGAGAT 60.556 43.478 14.67 0.00 0.00 2.75
7312 7357 7.944729 ATGGCATTACTAGTCAAAATCTTGT 57.055 32.000 0.00 0.00 33.94 3.16
7323 7368 6.591935 AGTCAAAATCTTGTACTGAGGACAA 58.408 36.000 10.28 10.28 35.55 3.18
7382 7427 3.127548 CAGTAGTACTGCCTTGCCATTTG 59.872 47.826 17.11 0.00 39.62 2.32
7389 7434 1.081094 GCCTTGCCATTTGAATGTGC 58.919 50.000 3.30 6.60 34.60 4.57
7429 7474 6.422776 AGACAAACGGTTCACATGATATTC 57.577 37.500 0.00 0.00 0.00 1.75
7447 7492 0.596600 TCGCCACTGACGTTGTTCTC 60.597 55.000 0.00 0.00 0.00 2.87
7517 7579 8.359642 TGGAAAGGTTTGTTAAAGAATCATCTG 58.640 33.333 0.00 0.00 35.59 2.90
7552 7614 7.649705 ACGTATGCTACATAAATGAGAAGAGTG 59.350 37.037 0.00 0.00 0.00 3.51
7598 7660 2.028294 ACAGACAAGCATGTGAGGAGAG 60.028 50.000 0.00 0.00 40.74 3.20
7602 7664 1.554160 CAAGCATGTGAGGAGAGGAGT 59.446 52.381 0.00 0.00 0.00 3.85
7676 7738 5.654650 CCTCATATGGAGTAGGGAGTATCAC 59.345 48.000 2.13 0.00 42.40 3.06
7678 7740 8.063163 CTCATATGGAGTAGGGAGTATCACGC 62.063 50.000 2.13 0.00 40.77 5.34
7696 7776 1.687494 GCGCTAGCTTGTTGGACTCG 61.687 60.000 13.93 0.00 41.01 4.18
7699 7779 0.247736 CTAGCTTGTTGGACTCGGCT 59.752 55.000 0.00 0.00 0.00 5.52
7712 7792 0.741221 CTCGGCTAGGGCTTGTGTTC 60.741 60.000 0.00 0.00 38.73 3.18
7714 7794 1.378646 GGCTAGGGCTTGTGTTCCC 60.379 63.158 0.00 0.00 42.94 3.97
7723 7803 3.910314 GGCTTGTGTTCCCAAGACTTGG 61.910 54.545 25.05 25.05 45.31 3.61
7738 7818 4.729868 AGACTTGGACACCTTAGCAAATT 58.270 39.130 0.00 0.00 0.00 1.82
7806 8086 0.254178 GCTTGAATGAGCTCCCCTGA 59.746 55.000 12.15 0.00 39.57 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 109 6.458615 CCCTTTCTACGAAGTACTCTAAGAGC 60.459 46.154 0.00 0.00 45.11 4.09
103 110 6.038492 CCCCTTTCTACGAAGTACTCTAAGAG 59.962 46.154 0.00 0.00 45.11 2.85
104 111 5.884792 CCCCTTTCTACGAAGTACTCTAAGA 59.115 44.000 0.00 0.00 45.11 2.10
133 143 5.279256 CCACCATTACCCTCGAAAACAATTT 60.279 40.000 0.00 0.00 0.00 1.82
134 144 4.219725 CCACCATTACCCTCGAAAACAATT 59.780 41.667 0.00 0.00 0.00 2.32
135 145 3.761752 CCACCATTACCCTCGAAAACAAT 59.238 43.478 0.00 0.00 0.00 2.71
138 149 2.745821 GACCACCATTACCCTCGAAAAC 59.254 50.000 0.00 0.00 0.00 2.43
149 160 1.838112 AGTACGTCGGACCACCATTA 58.162 50.000 3.34 0.00 35.59 1.90
162 173 4.453751 TGGGCTTCTTTTGTTTAGTACGT 58.546 39.130 0.00 0.00 0.00 3.57
208 219 1.893137 CCCTGGTTTGGGCTCTAAAAC 59.107 52.381 0.00 0.00 40.84 2.43
245 256 3.601435 TCTCCACGTGAAAACAAGTTGA 58.399 40.909 19.30 0.01 0.00 3.18
576 597 6.788684 TTTACGCAAGCATAGTTACTCAAA 57.211 33.333 0.00 0.00 45.62 2.69
583 604 2.687935 CCCCATTTACGCAAGCATAGTT 59.312 45.455 0.00 0.00 45.62 2.24
688 709 4.272991 GCATCAGAGGCTCATCAACTTTAG 59.727 45.833 18.26 0.00 0.00 1.85
703 724 2.054232 ATCAAAGGGCAGCATCAGAG 57.946 50.000 0.00 0.00 0.00 3.35
717 738 7.487484 TGTTGTGTGCAATTTTCTCTATCAAA 58.513 30.769 0.00 0.00 36.92 2.69
719 740 6.631971 TGTTGTGTGCAATTTTCTCTATCA 57.368 33.333 0.00 0.00 36.92 2.15
727 748 9.852091 AATTAATTTGTTGTTGTGTGCAATTTT 57.148 22.222 0.00 0.00 36.92 1.82
1181 1202 7.962964 TTCTGGTAGTGATTTACAACAGAAG 57.037 36.000 0.00 0.00 38.27 2.85
1258 1279 5.948162 TCTTACGAGTATAGGACCAACAACT 59.052 40.000 0.00 0.00 0.00 3.16
1374 1395 6.631971 TGAAATGTGCACTTGTTCTGAATA 57.368 33.333 19.41 0.34 0.00 1.75
1445 1467 8.774586 GCAATGATATTCTTTGATTACTACCGT 58.225 33.333 7.17 0.00 34.56 4.83
1543 1565 6.681777 AGACACAACTTTTCCTGCAATATTC 58.318 36.000 0.00 0.00 0.00 1.75
1569 1591 2.365617 AGGTAACACTCCACACTGACTG 59.634 50.000 0.00 0.00 41.41 3.51
1655 1677 6.377146 TGCAGAAAGACCCTACAAATTTATCC 59.623 38.462 0.00 0.00 0.00 2.59
1698 1720 6.254157 GCGATCTAAATGTGCAAATCAACAAT 59.746 34.615 0.00 0.00 0.00 2.71
6477 6517 4.217550 GCTGTAACCAAATTTCCAGTAGCA 59.782 41.667 0.00 0.00 0.00 3.49
6526 6567 4.327627 GTCAACTCTTCCGCTAAGAATCAC 59.672 45.833 0.76 0.00 43.66 3.06
6609 6650 1.717032 AGCTCCAGTAACAGGTCACA 58.283 50.000 0.00 0.00 0.00 3.58
6711 6753 4.038522 TGGATTGCTGAAATTTTGTCGGAA 59.961 37.500 0.00 0.00 0.00 4.30
6715 6757 7.424227 TTCATTGGATTGCTGAAATTTTGTC 57.576 32.000 0.00 0.00 0.00 3.18
6737 6779 4.274865 CGGAATTTCTGCGATAAAGCTTC 58.725 43.478 0.00 0.00 42.35 3.86
6738 6780 3.487544 GCGGAATTTCTGCGATAAAGCTT 60.488 43.478 14.13 0.00 42.35 3.74
6740 6782 2.376032 GCGGAATTTCTGCGATAAAGC 58.624 47.619 14.13 0.00 42.35 3.51
6757 6800 1.178534 ACATTTTGACAGGTGGGCGG 61.179 55.000 0.00 0.00 0.00 6.13
6814 6857 1.865788 GCCGGCTTGTGCATTCAGAA 61.866 55.000 22.15 0.00 41.91 3.02
6856 6899 0.039074 AGAGTCACGCTTCTGAACGG 60.039 55.000 13.84 0.85 0.00 4.44
6874 6917 0.320683 TCACACCAGATCGCCAACAG 60.321 55.000 0.00 0.00 0.00 3.16
6877 6920 1.452110 CAATCACACCAGATCGCCAA 58.548 50.000 0.00 0.00 0.00 4.52
6888 6931 2.726691 CCGACCGTCGCAATCACAC 61.727 63.158 15.64 0.00 38.82 3.82
6902 6945 2.361104 TGCATCCCCTTTGCCGAC 60.361 61.111 0.00 0.00 39.39 4.79
6912 6955 2.698855 TCTAAGCTCAACTGCATCCC 57.301 50.000 0.00 0.00 34.99 3.85
6921 6964 4.005650 CTCAGTTTGGCATCTAAGCTCAA 58.994 43.478 0.00 0.00 34.17 3.02
6966 7009 1.156736 CCAATAATTAGCGGCCCTCG 58.843 55.000 0.00 0.00 42.76 4.63
6974 7017 2.034179 GGCGTTCACCCCAATAATTAGC 59.966 50.000 0.00 0.00 0.00 3.09
6981 7024 2.676471 GCAGGCGTTCACCCCAAT 60.676 61.111 0.00 0.00 0.00 3.16
6987 7030 1.266718 TGAAAATCTGCAGGCGTTCAC 59.733 47.619 15.13 5.62 0.00 3.18
7010 7053 4.329462 TGCAGTACACTGTACATTCACA 57.671 40.909 19.34 8.33 45.45 3.58
7043 7086 5.333952 CGTACCATCTGAGAACTATCGGTAC 60.334 48.000 0.00 0.00 42.63 3.34
7044 7087 4.753610 CGTACCATCTGAGAACTATCGGTA 59.246 45.833 0.00 0.00 0.00 4.02
7045 7088 3.564644 CGTACCATCTGAGAACTATCGGT 59.435 47.826 0.00 0.00 0.00 4.69
7070 7115 6.238211 GGAACAATTCAGAACATGGACGATAG 60.238 42.308 0.00 0.00 46.19 2.08
7144 7189 5.262588 ACCACTGGTCAAGATTTGAAAAC 57.737 39.130 0.00 0.00 42.15 2.43
7149 7194 8.258007 TCTAACTATACCACTGGTCAAGATTTG 58.742 37.037 3.21 3.24 37.09 2.32
7217 7262 8.940952 GCAAACAAAACCATGGCTTATAATAAA 58.059 29.630 13.04 0.00 0.00 1.40
7312 7357 6.971726 TTTGACTTCTAGTTGTCCTCAGTA 57.028 37.500 12.69 0.00 32.67 2.74
7323 7368 7.015292 TCCACAACTGTAGATTTGACTTCTAGT 59.985 37.037 0.00 0.00 0.00 2.57
7370 7415 1.081094 GCACATTCAAATGGCAAGGC 58.919 50.000 7.58 0.00 40.70 4.35
7389 7434 0.657312 TCTTTGACAACAGCAGCGTG 59.343 50.000 0.00 0.00 0.00 5.34
7429 7474 0.874175 TGAGAACAACGTCAGTGGCG 60.874 55.000 17.03 17.03 0.00 5.69
7468 7513 3.832490 TCTCCCCATACATCGATCGATTT 59.168 43.478 27.45 23.28 31.62 2.17
7470 7515 3.087370 TCTCCCCATACATCGATCGAT 57.913 47.619 24.60 24.60 34.81 3.59
7471 7516 2.579410 TCTCCCCATACATCGATCGA 57.421 50.000 21.86 21.86 0.00 3.59
7472 7517 2.159184 CCATCTCCCCATACATCGATCG 60.159 54.545 9.36 9.36 0.00 3.69
7473 7518 3.099905 TCCATCTCCCCATACATCGATC 58.900 50.000 0.00 0.00 0.00 3.69
7517 7579 4.832590 ATGTAGCATACGTAGGAGACAC 57.167 45.455 12.12 3.05 46.99 3.67
7552 7614 4.091800 CACATTTCATTTCGTTTCCATGCC 59.908 41.667 0.00 0.00 0.00 4.40
7676 7738 1.687494 GAGTCCAACAAGCTAGCGCG 61.687 60.000 9.55 0.00 42.32 6.86
7678 7740 1.078759 CCGAGTCCAACAAGCTAGCG 61.079 60.000 9.55 0.00 0.00 4.26
7681 7743 1.476891 CTAGCCGAGTCCAACAAGCTA 59.523 52.381 0.00 0.00 0.00 3.32
7682 7744 0.247736 CTAGCCGAGTCCAACAAGCT 59.752 55.000 0.00 0.00 0.00 3.74
7696 7776 1.378646 GGGAACACAAGCCCTAGCC 60.379 63.158 0.00 0.00 41.31 3.93
7699 7779 1.073284 GTCTTGGGAACACAAGCCCTA 59.927 52.381 11.41 0.00 45.72 3.53
7714 7794 3.126001 TGCTAAGGTGTCCAAGTCTTG 57.874 47.619 5.53 5.53 0.00 3.02
7723 7803 5.880054 TTGCTCTAATTTGCTAAGGTGTC 57.120 39.130 0.00 0.00 0.00 3.67
7731 7811 9.578439 GTGATTTCTAAATTGCTCTAATTTGCT 57.422 29.630 7.63 0.00 45.90 3.91
7738 7818 9.330063 CATGGTAGTGATTTCTAAATTGCTCTA 57.670 33.333 0.00 0.00 0.00 2.43
7792 8072 1.067295 TGTGTTCAGGGGAGCTCATT 58.933 50.000 17.19 0.00 0.00 2.57
7797 8077 4.809673 CTTTAATTTGTGTTCAGGGGAGC 58.190 43.478 0.00 0.00 0.00 4.70
7832 8112 4.479158 ACTGGAATAACAGGCTTTTTCCA 58.521 39.130 13.49 13.49 42.58 3.53
7833 8113 6.775594 ATACTGGAATAACAGGCTTTTTCC 57.224 37.500 0.00 0.00 42.75 3.13


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

AutoCloner maintained by Alex Coulton.