Multiple sequence alignment - TraesCS7A01G254100

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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 TraesCS7A01G254100 chr7A 100.000 4422 0 0 1 4422 240081352 240085773 0.000000e+00 8167.0
1 TraesCS7A01G254100 chr7B 94.104 3816 148 39 653 4422 199491573 199495357 0.000000e+00 5729.0
2 TraesCS7A01G254100 chr7D 94.940 3340 132 23 662 3991 228005148 228008460 0.000000e+00 5197.0
3 TraesCS7A01G254100 chr7D 90.745 443 27 8 3987 4422 228009954 228010389 2.970000e-161 579.0
4 TraesCS7A01G254100 chr7D 73.072 713 143 33 1 677 212215038 212215737 1.610000e-49 207.0
5 TraesCS7A01G254100 chr5A 77.727 651 112 22 40 671 687220079 687220715 6.990000e-98 368.0
6 TraesCS7A01G254100 chr6A 78.141 581 114 9 100 671 80642701 80643277 1.510000e-94 357.0
7 TraesCS7A01G254100 chr1A 76.087 598 114 22 91 673 405872835 405872252 7.240000e-73 285.0
8 TraesCS7A01G254100 chr2D 76.938 516 87 20 2 492 560969117 560968609 9.430000e-67 265.0
9 TraesCS7A01G254100 chr2D 88.889 45 4 1 681 725 641020909 641020952 2.000000e-03 54.7
10 TraesCS7A01G254100 chr3B 75.410 488 92 18 183 666 62791854 62791391 1.250000e-50 211.0
11 TraesCS7A01G254100 chr3D 73.558 624 124 29 89 677 88353880 88353263 2.700000e-47 200.0
12 TraesCS7A01G254100 chr3D 77.015 335 53 9 1 313 434906524 434906856 2.110000e-38 171.0
13 TraesCS7A01G254100 chr1B 72.046 694 129 32 2 677 671616636 671615990 3.560000e-31 147.0
14 TraesCS7A01G254100 chr1B 72.852 512 98 17 2 496 672127517 672128004 2.150000e-28 137.0


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 TraesCS7A01G254100 chr7A 240081352 240085773 4421 False 8167 8167 100.0000 1 4422 1 chr7A.!!$F1 4421
1 TraesCS7A01G254100 chr7B 199491573 199495357 3784 False 5729 5729 94.1040 653 4422 1 chr7B.!!$F1 3769
2 TraesCS7A01G254100 chr7D 228005148 228010389 5241 False 2888 5197 92.8425 662 4422 2 chr7D.!!$F2 3760
3 TraesCS7A01G254100 chr7D 212215038 212215737 699 False 207 207 73.0720 1 677 1 chr7D.!!$F1 676
4 TraesCS7A01G254100 chr5A 687220079 687220715 636 False 368 368 77.7270 40 671 1 chr5A.!!$F1 631
5 TraesCS7A01G254100 chr6A 80642701 80643277 576 False 357 357 78.1410 100 671 1 chr6A.!!$F1 571
6 TraesCS7A01G254100 chr1A 405872252 405872835 583 True 285 285 76.0870 91 673 1 chr1A.!!$R1 582
7 TraesCS7A01G254100 chr2D 560968609 560969117 508 True 265 265 76.9380 2 492 1 chr2D.!!$R1 490

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
174 182 0.250124 TTGTCATTGACGTCGGCCTT 60.250 50.000 11.62 0.0 34.95 4.35 F
559 596 0.463833 AGCCGGGAATGGATCGAAAC 60.464 55.000 2.18 0.0 0.00 2.78 F
653 691 0.615544 ACGGGACCGGACCATTTAGA 60.616 55.000 24.44 0.0 44.69 2.10 F
673 711 1.073025 TCGTGCATTGGAGTTGGCT 59.927 52.632 0.00 0.0 0.00 4.75 F
1887 1930 0.182061 TGAAGCATGATGGCCTCCTC 59.818 55.000 3.32 0.0 0.00 3.71 F
1919 1962 0.687920 TGCACCGTCTTGGGTTCATA 59.312 50.000 0.00 0.0 44.64 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 1570 0.466739 GGTAATGGGGTAAAGGGCCG 60.467 60.000 0.00 0.00 0.00 6.13 R
1876 1919 0.689623 AATGGATCGAGGAGGCCATC 59.310 55.000 5.01 0.00 40.09 3.51 R
1887 1930 0.937304 CGGTGCACCTAAATGGATCG 59.063 55.000 32.28 12.05 38.21 3.69 R
1945 1988 3.067106 ACTGTGTAACTCGCCAATTCTG 58.933 45.455 0.00 0.00 38.04 3.02 R
3382 3428 1.376037 CTCGGCCTTCAAGTCCACC 60.376 63.158 0.00 0.00 0.00 4.61 R
3643 3690 3.827898 CACTCCGAGCGGGTCCTC 61.828 72.222 9.29 0.00 37.00 3.71 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
26 27 2.197605 TGTGACGGACAAGCTCGGA 61.198 57.895 0.00 0.00 0.00 4.55
30 31 1.587933 GACGGACAAGCTCGGAGACT 61.588 60.000 9.69 2.61 0.00 3.24
31 32 0.322277 ACGGACAAGCTCGGAGACTA 60.322 55.000 9.69 0.00 0.00 2.59
34 35 2.641305 GGACAAGCTCGGAGACTAGTA 58.359 52.381 9.69 0.00 0.00 1.82
36 37 2.355444 GACAAGCTCGGAGACTAGTACC 59.645 54.545 9.69 1.66 0.00 3.34
38 39 2.952978 CAAGCTCGGAGACTAGTACCAT 59.047 50.000 9.69 0.00 0.00 3.55
45 46 3.498841 CGGAGACTAGTACCATGGAGGAT 60.499 52.174 21.47 3.67 41.22 3.24
49 50 5.144100 AGACTAGTACCATGGAGGATGAAG 58.856 45.833 21.47 8.50 41.22 3.02
61 62 3.077556 ATGAAGGGCCGACGAGCT 61.078 61.111 0.00 0.00 0.00 4.09
63 64 2.509561 GAAGGGCCGACGAGCTTC 60.510 66.667 0.00 0.00 0.00 3.86
81 82 3.430565 CTGCTAGCCGCGACCATGA 62.431 63.158 13.29 0.00 43.27 3.07
90 91 1.666553 GCGACCATGACAACGACCA 60.667 57.895 0.00 0.00 0.00 4.02
91 92 1.019278 GCGACCATGACAACGACCAT 61.019 55.000 0.00 0.00 0.00 3.55
95 96 2.858622 CATGACAACGACCATGGCT 58.141 52.632 13.04 0.00 37.19 4.75
96 97 0.448990 CATGACAACGACCATGGCTG 59.551 55.000 13.04 7.00 37.19 4.85
149 157 2.742372 GCGCCTTGGTGACGATGT 60.742 61.111 0.00 0.00 0.00 3.06
150 158 2.740714 GCGCCTTGGTGACGATGTC 61.741 63.158 0.00 0.00 0.00 3.06
174 182 0.250124 TTGTCATTGACGTCGGCCTT 60.250 50.000 11.62 0.00 34.95 4.35
235 255 5.155905 ACTTTCTTCTCCTTCTCCCTTGTA 58.844 41.667 0.00 0.00 0.00 2.41
239 259 1.187087 CTCCTTCTCCCTTGTACGCT 58.813 55.000 0.00 0.00 0.00 5.07
240 260 2.025605 TCTCCTTCTCCCTTGTACGCTA 60.026 50.000 0.00 0.00 0.00 4.26
242 262 1.409427 CCTTCTCCCTTGTACGCTAGG 59.591 57.143 0.00 2.37 37.37 3.02
245 266 2.029307 CTCCCTTGTACGCTAGGCCC 62.029 65.000 0.00 0.00 36.49 5.80
259 280 4.570874 GCCCCCTCTTGGCCGATC 62.571 72.222 0.00 0.00 43.33 3.69
262 283 2.378634 CCCCTCTTGGCCGATCCTT 61.379 63.158 0.00 0.00 35.26 3.36
263 284 1.153086 CCCTCTTGGCCGATCCTTG 60.153 63.158 0.00 0.00 35.26 3.61
314 335 2.325082 CCGACCGCAACTTCTTGGG 61.325 63.158 0.00 0.00 39.50 4.12
318 339 1.073199 CCGCAACTTCTTGGGACCT 59.927 57.895 0.00 0.00 41.76 3.85
322 343 1.613925 GCAACTTCTTGGGACCTTTCC 59.386 52.381 0.00 0.00 41.95 3.13
367 397 3.470888 CCAGGTCGCCGGGATTCT 61.471 66.667 2.18 0.00 41.43 2.40
373 404 2.828549 CGCCGGGATTCTTTGGGG 60.829 66.667 2.18 0.00 0.00 4.96
409 444 2.610859 GAGGGAAGGGGGAGTGCA 60.611 66.667 0.00 0.00 0.00 4.57
423 458 0.698818 AGTGCAGGAGGGTTTTAGGG 59.301 55.000 0.00 0.00 0.00 3.53
424 459 0.965866 GTGCAGGAGGGTTTTAGGGC 60.966 60.000 0.00 0.00 0.00 5.19
446 481 1.488705 ATGGAGGGAAAGTGGACGCA 61.489 55.000 0.00 0.00 0.00 5.24
536 573 0.657368 GACGCAAACACGGCTCAAAG 60.657 55.000 0.00 0.00 38.32 2.77
559 596 0.463833 AGCCGGGAATGGATCGAAAC 60.464 55.000 2.18 0.00 0.00 2.78
573 610 0.869730 CGAAACCGGACCGAAAACAT 59.130 50.000 17.49 0.00 0.00 2.71
574 611 1.399215 CGAAACCGGACCGAAAACATG 60.399 52.381 17.49 0.00 0.00 3.21
579 616 1.067915 CCGGACCGAAAACATGCATTT 60.068 47.619 17.49 0.00 0.00 2.32
628 665 2.092538 TGTTTTCTGTCCGTTTACCCCA 60.093 45.455 0.00 0.00 0.00 4.96
637 675 1.200484 CCGTTTACCCCAAAATGACGG 59.800 52.381 0.00 0.00 0.00 4.79
653 691 0.615544 ACGGGACCGGACCATTTAGA 60.616 55.000 24.44 0.00 44.69 2.10
673 711 1.073025 TCGTGCATTGGAGTTGGCT 59.927 52.632 0.00 0.00 0.00 4.75
679 717 1.539827 GCATTGGAGTTGGCTTTACGT 59.460 47.619 0.00 0.00 0.00 3.57
692 730 3.624410 GGCTTTACGTTATCCAAACGGAT 59.376 43.478 14.01 0.00 46.86 4.18
731 770 5.127031 ACATATTGTCCATTTGGGTAGTTGC 59.873 40.000 0.00 0.00 38.11 4.17
769 809 1.399744 TTCTCCCCATCGTCCATCGG 61.400 60.000 0.00 0.00 40.32 4.18
770 810 3.521529 CTCCCCATCGTCCATCGGC 62.522 68.421 0.00 0.00 40.32 5.54
771 811 4.626081 CCCCATCGTCCATCGGCC 62.626 72.222 0.00 0.00 40.32 6.13
772 812 3.860605 CCCATCGTCCATCGGCCA 61.861 66.667 2.24 0.00 40.32 5.36
773 813 2.427320 CCATCGTCCATCGGCCAT 59.573 61.111 2.24 0.00 40.32 4.40
774 814 1.669115 CCATCGTCCATCGGCCATC 60.669 63.158 2.24 0.00 40.32 3.51
775 815 2.023771 CATCGTCCATCGGCCATCG 61.024 63.158 2.24 0.00 40.32 3.84
1104 1144 2.584608 CAGAAGTACCCCGCCCTG 59.415 66.667 0.00 0.00 0.00 4.45
1320 1360 2.752903 TCACTCGATCGATCAACTGGAA 59.247 45.455 24.40 1.47 0.00 3.53
1355 1395 3.762288 TGTGTGCTCTACGGAGTCTTTAT 59.238 43.478 0.00 0.00 43.93 1.40
1407 1447 4.823989 AGACACAAAGGTTTCCTCAATCAG 59.176 41.667 0.00 0.00 30.89 2.90
1432 1472 3.721035 GCATTTGCTCAATGGTATTCCC 58.279 45.455 10.18 0.00 42.51 3.97
1472 1512 7.796958 GGTAACAATACAATCAAAGCAACTC 57.203 36.000 0.00 0.00 33.45 3.01
1487 1527 2.480419 GCAACTCGTGATGTAGCAAGTT 59.520 45.455 0.00 0.00 0.00 2.66
1530 1570 1.216710 CTGAGACAACCGGCCTCTC 59.783 63.158 11.17 11.17 0.00 3.20
1553 1593 2.948600 GCCCTTTACCCCATTACCACTG 60.949 54.545 0.00 0.00 0.00 3.66
1565 1605 5.009010 CCCATTACCACTGAAAGCATATGAC 59.991 44.000 6.97 0.00 37.60 3.06
1573 1613 7.557358 ACCACTGAAAGCATATGACAAATATGA 59.443 33.333 6.97 0.00 37.60 2.15
1582 1622 3.050273 TGACAAATATGATGCGTTGCG 57.950 42.857 0.00 0.00 0.00 4.85
1638 1679 2.159430 GCAAAGTGACATGCGTGTATGA 59.841 45.455 12.53 0.00 39.09 2.15
1658 1700 1.726791 AGCGACGTTGCTTTATCAGTG 59.273 47.619 24.88 0.00 44.46 3.66
1662 1704 3.421826 CGACGTTGCTTTATCAGTGTCAC 60.422 47.826 0.00 0.00 0.00 3.67
1664 1706 3.247648 ACGTTGCTTTATCAGTGTCACAC 59.752 43.478 0.00 0.00 34.10 3.82
1665 1707 3.661678 CGTTGCTTTATCAGTGTCACACG 60.662 47.826 1.22 0.00 39.64 4.49
1680 1723 4.211389 GTCACACGTATGTCAGCAAAAAG 58.789 43.478 0.00 0.00 36.72 2.27
1702 1745 3.157087 GTGAAATGGGGTTGTGAGACAT 58.843 45.455 0.00 0.00 0.00 3.06
1763 1806 7.001155 CTTGTAGTCAATGGATACGGAGTACG 61.001 46.154 0.00 0.00 40.58 3.67
1764 1807 9.273096 CTTGTAGTCAATGGATACGGAGTACGT 62.273 44.444 5.35 5.35 44.79 3.57
1876 1919 7.010923 GTCCTAGTTGAGAGTTATTGAAGCATG 59.989 40.741 0.00 0.00 0.00 4.06
1887 1930 0.182061 TGAAGCATGATGGCCTCCTC 59.818 55.000 3.32 0.00 0.00 3.71
1919 1962 0.687920 TGCACCGTCTTGGGTTCATA 59.312 50.000 0.00 0.00 44.64 2.15
1946 1989 9.502091 AAAACTTACTGTCTGATAATTAGCACA 57.498 29.630 0.00 0.00 0.00 4.57
1980 2023 6.402222 AGTTACACAGTCCATTCTCATCTTC 58.598 40.000 0.00 0.00 0.00 2.87
1989 2032 7.986320 CAGTCCATTCTCATCTTCTATTGTCTT 59.014 37.037 0.00 0.00 0.00 3.01
2074 2118 7.581213 AACTGGTTGTTTGTTGATTGAGATA 57.419 32.000 0.00 0.00 34.84 1.98
2495 2540 7.551262 TGCTGTTATTGACAAAGGTATCGTTAT 59.449 33.333 0.00 0.00 37.93 1.89
2743 2788 4.887655 GGGGAGGTGAACAGGTAAATAATG 59.112 45.833 0.00 0.00 0.00 1.90
2839 2884 3.640029 TCAACGATAAGGGGGTCTACATC 59.360 47.826 0.00 0.00 0.00 3.06
2893 2938 5.010282 ACTCTGTGGTTTTCTTCTTGTGTT 58.990 37.500 0.00 0.00 0.00 3.32
3037 3082 1.620413 GCCACCGGTTCGACTTAACG 61.620 60.000 2.97 0.00 0.00 3.18
3039 3084 1.055338 CACCGGTTCGACTTAACGAC 58.945 55.000 2.97 0.00 41.97 4.34
3068 3113 8.705594 CCTACTCTTGACCCTTTTGATCTATTA 58.294 37.037 0.00 0.00 0.00 0.98
3175 3220 5.397360 AGAAGTTCCAAAAAGACATGGGAT 58.603 37.500 0.00 0.00 37.31 3.85
3382 3428 0.532862 AGGACAACGACAGTGCAAGG 60.533 55.000 0.00 0.00 0.00 3.61
3589 3636 7.701924 TCGAATTTGGAATAGAAATGAATGTGC 59.298 33.333 0.00 0.00 0.00 4.57
3609 3656 4.848299 GTGCTGTTTTCATGTCTTTCGATC 59.152 41.667 0.00 0.00 0.00 3.69
3727 3774 0.613260 CCAGAATCTTGTGGGACGGA 59.387 55.000 0.00 0.00 37.92 4.69
3741 3788 2.237893 GGGACGGAAAAGTATCTTGGGA 59.762 50.000 0.00 0.00 0.00 4.37
3992 5562 3.134623 TGGGAGCATGGTATGTCTAAGTG 59.865 47.826 0.00 0.00 0.00 3.16
4060 5636 1.427435 CGAACCCGCATGCAATTTTT 58.573 45.000 19.57 2.53 0.00 1.94
4065 5641 2.807392 ACCCGCATGCAATTTTTCTTTG 59.193 40.909 19.57 0.00 0.00 2.77
4188 5766 3.006112 GGGAAAGTGGAAGAATCCCTC 57.994 52.381 1.89 0.00 45.95 4.30
4236 5814 1.815421 CCAACGCCTCCAGATTCGG 60.815 63.158 0.00 0.00 0.00 4.30
4260 5838 1.978580 GTCTCCTTCTCTTTCCCACCA 59.021 52.381 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.022129 GAGCTTGTCCGTCACACCG 61.022 63.158 0.00 0.00 33.41 4.94
18 19 2.803030 TGGTACTAGTCTCCGAGCTT 57.197 50.000 0.00 0.00 0.00 3.74
26 27 4.816048 TCATCCTCCATGGTACTAGTCT 57.184 45.455 12.58 0.00 37.07 3.24
30 31 3.587498 CCCTTCATCCTCCATGGTACTA 58.413 50.000 12.58 0.00 37.07 1.82
31 32 2.412591 CCCTTCATCCTCCATGGTACT 58.587 52.381 12.58 0.00 37.07 2.73
34 35 1.649271 GGCCCTTCATCCTCCATGGT 61.649 60.000 12.58 0.00 37.07 3.55
36 37 1.228063 CGGCCCTTCATCCTCCATG 60.228 63.158 0.00 0.00 0.00 3.66
38 39 2.040442 TCGGCCCTTCATCCTCCA 59.960 61.111 0.00 0.00 0.00 3.86
45 46 3.296709 GAAGCTCGTCGGCCCTTCA 62.297 63.158 11.09 0.00 35.10 3.02
149 157 1.067846 CGACGTCAATGACAAGGAGGA 60.068 52.381 17.16 0.00 32.09 3.71
150 158 1.350193 CGACGTCAATGACAAGGAGG 58.650 55.000 17.16 0.00 32.09 4.30
214 234 4.021368 CGTACAAGGGAGAAGGAGAAGAAA 60.021 45.833 0.00 0.00 0.00 2.52
235 255 3.083997 CAAGAGGGGGCCTAGCGT 61.084 66.667 0.84 0.00 31.76 5.07
245 266 1.153086 CAAGGATCGGCCAAGAGGG 60.153 63.158 2.24 0.00 40.02 4.30
259 280 3.121030 CGCCAAGCTCGACCAAGG 61.121 66.667 0.00 0.00 0.00 3.61
284 305 2.649034 GGTCGGAACTCACGCTGA 59.351 61.111 0.00 0.00 0.00 4.26
286 307 4.719369 GCGGTCGGAACTCACGCT 62.719 66.667 0.00 0.00 46.02 5.07
294 315 0.882927 CCAAGAAGTTGCGGTCGGAA 60.883 55.000 0.00 0.00 31.64 4.30
304 325 3.056832 AGAGGAAAGGTCCCAAGAAGTT 58.943 45.455 0.00 0.00 46.30 2.66
314 335 2.101233 GCGGCGAAGAGGAAAGGTC 61.101 63.158 12.98 0.00 0.00 3.85
318 339 4.752879 CCCGCGGCGAAGAGGAAA 62.753 66.667 25.92 0.00 32.51 3.13
340 364 4.189188 CGACCTGGACGCTACCGG 62.189 72.222 5.52 0.00 39.22 5.28
349 379 3.467226 GAATCCCGGCGACCTGGA 61.467 66.667 9.30 6.80 41.02 3.86
352 382 1.078426 CAAAGAATCCCGGCGACCT 60.078 57.895 9.30 0.00 0.00 3.85
373 404 2.892425 CTCCTTCATGGTCGGCGC 60.892 66.667 0.00 0.00 37.07 6.53
385 416 2.461637 CCCCTTCCCTCCCTCCTT 59.538 66.667 0.00 0.00 0.00 3.36
409 444 2.559705 CCATTTGCCCTAAAACCCTCCT 60.560 50.000 0.00 0.00 0.00 3.69
423 458 1.546029 GTCCACTTTCCCTCCATTTGC 59.454 52.381 0.00 0.00 0.00 3.68
424 459 1.812571 CGTCCACTTTCCCTCCATTTG 59.187 52.381 0.00 0.00 0.00 2.32
497 534 1.135527 CAAAATGGACATGGCGCAGAT 59.864 47.619 10.83 0.00 0.00 2.90
500 537 0.243365 GTCAAAATGGACATGGCGCA 59.757 50.000 10.83 0.00 37.73 6.09
505 542 3.182173 GTGTTTGCGTCAAAATGGACATG 59.818 43.478 6.59 0.00 37.66 3.21
506 543 3.380142 GTGTTTGCGTCAAAATGGACAT 58.620 40.909 6.59 0.00 37.66 3.06
536 573 1.160329 CGATCCATTCCCGGCTCAAC 61.160 60.000 0.00 0.00 0.00 3.18
559 596 0.525761 AATGCATGTTTTCGGTCCGG 59.474 50.000 12.29 0.00 0.00 5.14
573 610 3.497118 CGAAAGCAAACGGATAAATGCA 58.503 40.909 0.00 0.00 41.18 3.96
602 639 1.768112 AACGGACAGAAAACACGGCG 61.768 55.000 4.80 4.80 0.00 6.46
608 645 2.574450 TGGGGTAAACGGACAGAAAAC 58.426 47.619 0.00 0.00 0.00 2.43
610 647 3.294038 TTTGGGGTAAACGGACAGAAA 57.706 42.857 0.00 0.00 0.00 2.52
628 665 1.002990 GGTCCGGTCCCGTCATTTT 60.003 57.895 6.44 0.00 37.81 1.82
637 675 1.202382 CGACTCTAAATGGTCCGGTCC 60.202 57.143 11.20 11.20 0.00 4.46
653 691 1.237285 GCCAACTCCAATGCACGACT 61.237 55.000 0.00 0.00 0.00 4.18
708 746 5.126869 TGCAACTACCCAAATGGACAATATG 59.873 40.000 0.00 0.00 37.39 1.78
709 747 5.268387 TGCAACTACCCAAATGGACAATAT 58.732 37.500 0.00 0.00 37.39 1.28
710 748 4.667573 TGCAACTACCCAAATGGACAATA 58.332 39.130 0.00 0.00 37.39 1.90
712 750 2.950781 TGCAACTACCCAAATGGACAA 58.049 42.857 0.00 0.00 37.39 3.18
721 760 1.632920 TCATGGTGATGCAACTACCCA 59.367 47.619 12.96 8.46 33.51 4.51
731 770 6.270815 GGAGAACATTTCAATCATGGTGATG 58.729 40.000 0.00 0.00 37.15 3.07
769 809 2.750888 GGAAACGGAGTGCGATGGC 61.751 63.158 12.27 0.00 45.00 4.40
770 810 3.486263 GGAAACGGAGTGCGATGG 58.514 61.111 12.27 0.00 45.00 3.51
981 1021 4.292178 CCTCCGCTCGGATCTGGC 62.292 72.222 11.77 3.40 44.24 4.85
1320 1360 4.267536 AGAGCACACATTCTACATTGCAT 58.732 39.130 0.00 0.00 32.24 3.96
1355 1395 7.538334 CAGCATTCGATTCATTCTACAAAAACA 59.462 33.333 0.00 0.00 0.00 2.83
1407 1447 5.962133 GGAATACCATTGAGCAAATGCTGTC 60.962 44.000 13.50 0.00 43.80 3.51
1432 1472 2.554806 TACCACGTAATCGCACTGAG 57.445 50.000 0.00 0.00 41.18 3.35
1472 1512 9.031360 AGTAACATATTAACTTGCTACATCACG 57.969 33.333 0.00 0.00 0.00 4.35
1530 1570 0.466739 GGTAATGGGGTAAAGGGCCG 60.467 60.000 0.00 0.00 0.00 6.13
1537 1577 3.074687 TGCTTTCAGTGGTAATGGGGTAA 59.925 43.478 0.00 0.00 0.00 2.85
1539 1579 1.427368 TGCTTTCAGTGGTAATGGGGT 59.573 47.619 0.00 0.00 0.00 4.95
1553 1593 7.080099 ACGCATCATATTTGTCATATGCTTTC 58.920 34.615 0.00 0.00 38.02 2.62
1565 1605 2.473530 ACCGCAACGCATCATATTTG 57.526 45.000 0.00 0.00 0.00 2.32
1573 1613 2.876955 CCATGAACCGCAACGCAT 59.123 55.556 0.00 0.00 0.00 4.73
1598 1638 1.273048 GCACATGATGTTTTGGCCAGA 59.727 47.619 5.11 0.00 0.00 3.86
1638 1679 1.726791 CACTGATAAAGCAACGTCGCT 59.273 47.619 0.00 0.00 46.67 4.93
1658 1700 3.870723 TTTTGCTGACATACGTGTGAC 57.129 42.857 19.87 13.48 39.09 3.67
1662 1704 3.249799 TCACCTTTTTGCTGACATACGTG 59.750 43.478 0.00 0.00 0.00 4.49
1664 1706 4.481930 TTCACCTTTTTGCTGACATACG 57.518 40.909 0.00 0.00 0.00 3.06
1665 1707 5.634859 CCATTTCACCTTTTTGCTGACATAC 59.365 40.000 0.00 0.00 0.00 2.39
1680 1723 1.886542 GTCTCACAACCCCATTTCACC 59.113 52.381 0.00 0.00 0.00 4.02
1702 1745 0.858369 AAGGGAGTCGCTAGGGGATA 59.142 55.000 10.52 0.00 0.00 2.59
1866 1909 1.217183 AGGAGGCCATCATGCTTCAAT 59.783 47.619 5.01 0.00 38.96 2.57
1876 1919 0.689623 AATGGATCGAGGAGGCCATC 59.310 55.000 5.01 0.00 40.09 3.51
1887 1930 0.937304 CGGTGCACCTAAATGGATCG 59.063 55.000 32.28 12.05 38.21 3.69
1945 1988 3.067106 ACTGTGTAACTCGCCAATTCTG 58.933 45.455 0.00 0.00 38.04 3.02
1946 1989 3.326747 GACTGTGTAACTCGCCAATTCT 58.673 45.455 0.00 0.00 38.04 2.40
1989 2032 8.755028 TGCCTAACAGTCAATACAATAAGTAGA 58.245 33.333 0.00 0.00 35.85 2.59
2370 2415 3.205784 AGTAAGCCGTAGATACTCCGT 57.794 47.619 0.00 0.00 0.00 4.69
2418 2463 7.327975 ACATGTTTCTTACATCCATCTTCGTA 58.672 34.615 0.00 0.00 45.71 3.43
2495 2540 5.394005 GCTGGCAACCATTACATTTACATCA 60.394 40.000 0.00 0.00 30.82 3.07
2743 2788 8.986847 CAGAGATATCACAACAAATATCAGTCC 58.013 37.037 5.32 0.00 37.34 3.85
3037 3082 1.836802 AGGGTCAAGAGTAGGACGTC 58.163 55.000 7.13 7.13 34.87 4.34
3039 3084 3.006537 TCAAAAGGGTCAAGAGTAGGACG 59.993 47.826 0.00 0.00 34.87 4.79
3175 3220 3.695606 GGCAGTGGCTCGGTCAGA 61.696 66.667 9.90 0.00 40.87 3.27
3276 3321 4.338327 GACAAGCTTGTCGACGGT 57.662 55.556 36.44 13.15 46.80 4.83
3382 3428 1.376037 CTCGGCCTTCAAGTCCACC 60.376 63.158 0.00 0.00 0.00 4.61
3589 3636 6.576313 CACAAGATCGAAAGACATGAAAACAG 59.424 38.462 0.00 0.00 46.97 3.16
3609 3656 8.286800 TGAACACGGAAATAAATTCTACACAAG 58.713 33.333 0.00 0.00 38.18 3.16
3643 3690 3.827898 CACTCCGAGCGGGTCCTC 61.828 72.222 9.29 0.00 37.00 3.71
3727 3774 8.028652 TCCACAAATTTTCCCAAGATACTTTT 57.971 30.769 0.00 0.00 0.00 2.27
3857 3906 9.449719 AGTTCAAGTTTCTCTTCTGAAGTTTTA 57.550 29.630 16.43 0.00 33.63 1.52
3950 4004 5.049828 CCCAACTCACAAAAGTCAAATTCC 58.950 41.667 0.00 0.00 0.00 3.01
4049 5625 9.557338 TTTCTGAAAACAAAGAAAAATTGCATG 57.443 25.926 0.00 0.00 38.98 4.06
4188 5766 2.102357 CGTCGATCCGTCCCACTG 59.898 66.667 0.00 0.00 0.00 3.66
4210 5788 0.960364 TGGAGGCGTTGGATTGAAGC 60.960 55.000 0.00 0.00 0.00 3.86
4236 5814 1.673329 GGGAAAGAGAAGGAGACGTGC 60.673 57.143 0.00 0.00 0.00 5.34
4260 5838 3.124066 GGAGAGGGATTTTTAGGGAGGT 58.876 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.