Multiple sequence alignment - TraesCS5D01G337000

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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 TraesCS5D01G337000 chr5D 100.000 4269 0 0 1 4269 426035548 426031280 0.000000e+00 7884.0
1 TraesCS5D01G337000 chr5D 91.025 2741 199 21 1563 4269 426043283 426040556 0.000000e+00 3655.0
2 TraesCS5D01G337000 chr5D 90.753 1568 121 8 6 1570 426045123 426043577 0.000000e+00 2071.0
3 TraesCS5D01G337000 chr5B 90.854 2296 181 16 1563 3840 515714891 515712607 0.000000e+00 3049.0
4 TraesCS5D01G337000 chr5B 87.171 1598 141 19 8 1570 515716752 515715184 0.000000e+00 1757.0
5 TraesCS5D01G337000 chr5B 89.931 437 40 2 3837 4269 515702609 515702173 1.040000e-155 560.0
6 TraesCS5D01G337000 chr5A 86.229 1111 115 20 707 1804 540354196 540353111 0.000000e+00 1170.0
7 TraesCS5D01G337000 chr5A 83.590 1103 138 19 3172 4267 540349921 540348855 0.000000e+00 994.0
8 TraesCS5D01G337000 chr5A 85.619 904 96 21 2000 2888 540351680 540350796 0.000000e+00 918.0
9 TraesCS5D01G337000 chr5A 83.524 437 54 8 462 894 540354621 540354199 4.000000e-105 392.0
10 TraesCS5D01G337000 chr3D 82.509 566 79 13 920 1468 5802732 5803294 2.990000e-131 479.0
11 TraesCS5D01G337000 chr3B 81.104 598 81 18 920 1491 11944343 11943752 2.340000e-122 449.0
12 TraesCS5D01G337000 chr3B 85.714 392 39 9 3094 3483 11934453 11934077 8.600000e-107 398.0
13 TraesCS5D01G337000 chr3A 88.608 79 3 2 1362 1434 588384852 588384930 1.630000e-14 91.6
14 TraesCS5D01G337000 chr2B 88.608 79 3 2 1362 1434 76549493 76549571 1.630000e-14 91.6
15 TraesCS5D01G337000 chr7B 86.076 79 5 5 1362 1434 701399671 701399749 3.540000e-11 80.5
16 TraesCS5D01G337000 chr2A 84.615 65 8 2 4020 4084 682487238 682487176 3.560000e-06 63.9


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 TraesCS5D01G337000 chr5D 426031280 426035548 4268 True 7884.0 7884 100.0000 1 4269 1 chr5D.!!$R1 4268
1 TraesCS5D01G337000 chr5D 426040556 426045123 4567 True 2863.0 3655 90.8890 6 4269 2 chr5D.!!$R2 4263
2 TraesCS5D01G337000 chr5B 515712607 515716752 4145 True 2403.0 3049 89.0125 8 3840 2 chr5B.!!$R2 3832
3 TraesCS5D01G337000 chr5A 540348855 540354621 5766 True 868.5 1170 84.7405 462 4267 4 chr5A.!!$R1 3805
4 TraesCS5D01G337000 chr3D 5802732 5803294 562 False 479.0 479 82.5090 920 1468 1 chr3D.!!$F1 548
5 TraesCS5D01G337000 chr3B 11943752 11944343 591 True 449.0 449 81.1040 920 1491 1 chr3B.!!$R2 571

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
816 1040 0.178978 TTGCATTGGTGGGTGTAGCA 60.179 50.0 0.00 0.0 0.0 3.49 F
1146 1382 0.755698 TGGAGGAGACGGTGGCTATC 60.756 60.0 0.00 0.0 0.0 2.08 F
2931 5025 0.181350 CTACCTGGACATCAAGGGGC 59.819 60.0 7.26 0.0 0.0 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 4026 1.537202 AGCAAAGGACGAAATGCAGAC 59.463 47.619 0.00 0.0 41.18 3.51 R
3121 5216 0.114954 TCCTTCCTTGCTGGCCATTT 59.885 50.000 5.51 0.0 35.26 2.32 R
3988 6553 0.250727 GAGTAGTGTTGGCAAGGGCA 60.251 55.000 0.00 0.0 43.71 5.36 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
90 91 8.433421 AATTGTCGGTAGTACCTTTATTCATG 57.567 34.615 17.29 0.00 35.66 3.07
115 116 4.318760 CCAACTACAACATCCATATTCGCG 60.319 45.833 0.00 0.00 0.00 5.87
118 119 0.874390 CAACATCCATATTCGCGGGG 59.126 55.000 6.13 0.39 0.00 5.73
129 130 2.050442 CGCGGGGTTCAGCAAAAC 60.050 61.111 0.00 0.00 0.00 2.43
148 149 1.663739 GTGTAGCTCGTGGTCACCA 59.336 57.895 0.00 0.00 0.00 4.17
182 183 3.242091 CCTCTGCATTTGTAACATCGACG 60.242 47.826 0.00 0.00 0.00 5.12
239 240 2.358615 TTGCGGCTCTGCGTGAAT 60.359 55.556 0.00 0.00 37.81 2.57
240 241 2.390599 TTGCGGCTCTGCGTGAATC 61.391 57.895 0.00 0.00 37.81 2.52
241 242 3.567797 GCGGCTCTGCGTGAATCC 61.568 66.667 0.00 0.00 0.00 3.01
270 273 3.328505 GCTTTTGCTAGGTACGGTTGTA 58.671 45.455 0.00 0.00 43.35 2.41
271 274 3.747529 GCTTTTGCTAGGTACGGTTGTAA 59.252 43.478 0.00 0.00 43.35 2.41
272 275 4.213906 GCTTTTGCTAGGTACGGTTGTAAA 59.786 41.667 0.00 0.00 43.35 2.01
273 276 5.840772 GCTTTTGCTAGGTACGGTTGTAAAC 60.841 44.000 0.00 0.00 44.33 2.01
274 277 8.158669 GCTTTTGCTAGGTACGGTTGTAAACA 62.159 42.308 0.00 0.00 45.89 2.83
275 278 9.528211 GCTTTTGCTAGGTACGGTTGTAAACAA 62.528 40.741 0.00 0.00 45.89 2.83
303 315 1.418264 TGGTGTTGCTGGCTACAACTA 59.582 47.619 21.13 9.05 46.03 2.24
309 321 2.985896 TGCTGGCTACAACTATGGTTC 58.014 47.619 0.00 0.00 32.73 3.62
350 365 2.578981 GCCGTCTACCTCGCGTTC 60.579 66.667 5.77 0.00 0.00 3.95
351 366 2.277120 CCGTCTACCTCGCGTTCG 60.277 66.667 5.77 0.00 0.00 3.95
352 367 2.743752 CCGTCTACCTCGCGTTCGA 61.744 63.158 5.77 0.00 43.28 3.71
361 376 1.495509 TCGCGTTCGAGCAAAATGG 59.504 52.632 5.77 0.00 40.21 3.16
368 383 2.396590 TCGAGCAAAATGGGTAGTCC 57.603 50.000 0.00 0.00 0.00 3.85
383 398 1.534729 AGTCCGTTCCAGGAAATTGC 58.465 50.000 2.45 0.00 42.77 3.56
388 403 1.001815 CGTTCCAGGAAATTGCGTTGT 60.002 47.619 2.45 0.00 0.00 3.32
395 410 2.131972 GGAAATTGCGTTGTTGGTTCC 58.868 47.619 0.00 0.00 0.00 3.62
413 428 5.126384 TGGTTCCAGAAAAAGAATGTTCGTT 59.874 36.000 0.00 0.00 0.00 3.85
415 430 6.262601 GTTCCAGAAAAAGAATGTTCGTTGA 58.737 36.000 0.00 0.00 0.00 3.18
432 447 1.163420 TGAAACACGCGGTTGCATCT 61.163 50.000 12.47 0.00 40.23 2.90
445 460 4.507388 CGGTTGCATCTTGTCAACAAAAAT 59.493 37.500 7.31 0.00 43.06 1.82
457 472 4.020662 GTCAACAAAAATTATGCCCCCTCA 60.021 41.667 0.00 0.00 0.00 3.86
458 473 4.222588 TCAACAAAAATTATGCCCCCTCAG 59.777 41.667 0.00 0.00 0.00 3.35
478 493 1.449070 CAAGAGCTCGCAGCCATGA 60.449 57.895 8.37 0.00 43.77 3.07
493 508 0.179192 CATGACCGTGGAATGTTGCG 60.179 55.000 0.00 0.00 0.00 4.85
498 513 2.050533 GTGGAATGTTGCGCGCAA 60.051 55.556 40.23 40.23 0.00 4.85
518 533 1.299850 CACGTGAGTTCCAGCGACA 60.300 57.895 10.90 0.00 46.40 4.35
570 585 0.827507 GGGAAAAAGCTCACTGGCCA 60.828 55.000 4.71 4.71 0.00 5.36
636 653 1.036707 CATCGGGGAAGAGGAGAGAC 58.963 60.000 0.00 0.00 0.00 3.36
638 655 0.408309 TCGGGGAAGAGGAGAGACAA 59.592 55.000 0.00 0.00 0.00 3.18
648 665 4.079970 AGAGGAGAGACAACACGACATTA 58.920 43.478 0.00 0.00 0.00 1.90
709 728 1.820481 GAGGAGTCCGACGAGAGGG 60.820 68.421 2.76 0.00 0.00 4.30
725 744 5.178797 CGAGAGGGAAAAGAAGATAAGCAA 58.821 41.667 0.00 0.00 0.00 3.91
816 1040 0.178978 TTGCATTGGTGGGTGTAGCA 60.179 50.000 0.00 0.00 0.00 3.49
822 1046 2.046314 GTGGGTGTAGCATGGCGT 60.046 61.111 0.00 0.00 0.00 5.68
950 1175 5.399013 CCTTCGCGATCCAAAAATAAAAGT 58.601 37.500 10.88 0.00 0.00 2.66
951 1176 5.861787 CCTTCGCGATCCAAAAATAAAAGTT 59.138 36.000 10.88 0.00 0.00 2.66
968 1193 3.268647 TTCCTCCCCTCCCCTCCAC 62.269 68.421 0.00 0.00 0.00 4.02
986 1222 3.282838 CCCCCAAACTCCCCCTTT 58.717 61.111 0.00 0.00 0.00 3.11
1031 1267 1.684734 CGTACCACCTAGCCACCCT 60.685 63.158 0.00 0.00 0.00 4.34
1048 1284 4.051167 TAGTCTCCCCGGCGACCA 62.051 66.667 9.30 0.00 30.87 4.02
1060 1296 1.815421 GCGACCAGATCAATGGCGT 60.815 57.895 14.55 0.00 44.80 5.68
1094 1330 1.205893 GACACCGGAGAAGAAGCTCAT 59.794 52.381 9.46 0.00 36.62 2.90
1143 1379 2.997897 GTGGAGGAGACGGTGGCT 60.998 66.667 0.00 0.00 0.00 4.75
1146 1382 0.755698 TGGAGGAGACGGTGGCTATC 60.756 60.000 0.00 0.00 0.00 2.08
1231 1467 1.822990 ACGTCAAAGCCGAGATCCTTA 59.177 47.619 0.00 0.00 0.00 2.69
1405 1647 1.287739 GATTTCCATCCAACCCTCCCA 59.712 52.381 0.00 0.00 0.00 4.37
1407 1649 1.863155 TTCCATCCAACCCTCCCAGC 61.863 60.000 0.00 0.00 0.00 4.85
1439 1693 5.171339 TCTAGTTAGTACTCGTCAAGGGT 57.829 43.478 0.00 0.00 35.78 4.34
1460 1714 5.944007 GGGTTCTTGTTCCTGCTATTTAGAA 59.056 40.000 0.00 0.00 0.00 2.10
1480 1735 6.892310 AGAAGCAGTTTTGTTGTGATTTTC 57.108 33.333 0.00 0.00 0.00 2.29
1554 1816 1.474077 GTCTCATGGCATTGTTGGGTC 59.526 52.381 0.00 0.00 0.00 4.46
1629 2194 4.939509 ATTGTATGTTCGTTGCAGGTAC 57.060 40.909 0.00 0.00 0.00 3.34
1634 2199 1.270094 TGTTCGTTGCAGGTACTCTGG 60.270 52.381 11.72 0.00 43.54 3.86
1786 2352 9.319143 CCTAAGTGTTTGTAATCTCAATAGGAG 57.681 37.037 0.00 0.00 45.49 3.69
1971 3919 8.279970 TCAGTATTGTGCTTAGTTAAATGCAT 57.720 30.769 0.00 0.00 37.76 3.96
1985 3933 6.480320 AGTTAAATGCATCCTAGCTTTCTACG 59.520 38.462 0.00 0.00 32.25 3.51
2071 4026 8.873215 AAGAGTACTGTGATAATATTTGACCG 57.127 34.615 0.00 0.00 0.00 4.79
2223 4178 3.383185 TGGTTTTTCGGACTGCTTTGATT 59.617 39.130 0.00 0.00 0.00 2.57
2228 4183 4.685169 TTCGGACTGCTTTGATTTCATC 57.315 40.909 0.00 0.00 0.00 2.92
2230 4185 5.084818 TCGGACTGCTTTGATTTCATCTA 57.915 39.130 0.00 0.00 0.00 1.98
2322 4277 7.875041 CAGTACCTTTATCCCATCAGATTGTAG 59.125 40.741 0.00 0.00 0.00 2.74
2363 4318 6.403866 TGATGCTTTGTGGTGTCTTTATTT 57.596 33.333 0.00 0.00 0.00 1.40
2364 4319 7.517614 TGATGCTTTGTGGTGTCTTTATTTA 57.482 32.000 0.00 0.00 0.00 1.40
2515 4484 5.941948 AGGTTTGTTGTTGTACATAGCTC 57.058 39.130 0.00 0.00 34.27 4.09
2535 4504 4.220602 GCTCTTTTGGGTTATCCATGTTGT 59.779 41.667 0.00 0.00 46.52 3.32
2588 4557 4.829872 ATTGGAATCCATTTGTGTGCAT 57.170 36.364 1.39 0.00 31.53 3.96
2598 4567 5.038683 CCATTTGTGTGCATAGCTTGTATG 58.961 41.667 0.00 0.00 0.00 2.39
2634 4603 7.063898 CAGTATCATGTAAGACAACTCACCTTG 59.936 40.741 0.00 0.00 0.00 3.61
2692 4662 5.513233 AGTATGAAATTGTGCTCCCTCATT 58.487 37.500 0.00 0.00 0.00 2.57
2707 4677 6.486657 GCTCCCTCATTATGTTGTATTGCTAA 59.513 38.462 0.00 0.00 0.00 3.09
2831 4802 9.734620 GCAAATATATCTTGTTTATGTTGCTCA 57.265 29.630 0.00 0.00 33.30 4.26
2876 4970 8.258007 TCTCTTTTGTGTAAGTATGATACCTGG 58.742 37.037 0.00 0.00 0.00 4.45
2931 5025 0.181350 CTACCTGGACATCAAGGGGC 59.819 60.000 7.26 0.00 0.00 5.80
2934 5028 1.565390 CCTGGACATCAAGGGGCTGA 61.565 60.000 0.00 0.00 0.00 4.26
2942 5036 1.600058 TCAAGGGGCTGATGGATCTT 58.400 50.000 0.00 0.00 0.00 2.40
2962 5056 2.345244 CTGCCAGAAGGTCGCTGT 59.655 61.111 0.00 0.00 37.19 4.40
2973 5067 4.160439 AGAAGGTCGCTGTCATGATAAAGA 59.840 41.667 0.00 0.00 0.00 2.52
2974 5068 4.471904 AGGTCGCTGTCATGATAAAGAA 57.528 40.909 0.00 0.00 0.00 2.52
3005 5099 4.462133 CAGAGGAGATCCGTAAGACCTTA 58.538 47.826 0.00 0.00 42.08 2.69
3090 5185 0.328258 CGAATGAAGGTCAAGGGGGT 59.672 55.000 0.00 0.00 0.00 4.95
3092 5187 2.172717 CGAATGAAGGTCAAGGGGGTAT 59.827 50.000 0.00 0.00 0.00 2.73
3126 5221 9.241317 GAAACAACTATCTCATAATGCAAATGG 57.759 33.333 11.31 4.37 0.00 3.16
3155 5250 0.750249 AAGGAAACCCGGCTTTGTTG 59.250 50.000 0.00 0.00 0.00 3.33
3186 5281 1.918543 GCAGTCGTTAACCGTTTGTGC 60.919 52.381 0.00 0.00 37.94 4.57
3205 5300 7.921786 TTGTGCTTCAAAACTATGCTAGTAT 57.078 32.000 0.00 0.00 38.26 2.12
3267 5830 3.826729 GAGGTTTACCATTTGGCTGACTT 59.173 43.478 1.13 0.00 39.32 3.01
3274 5837 4.079253 ACCATTTGGCTGACTTCGTTATT 58.921 39.130 0.00 0.00 39.32 1.40
3324 5888 9.003658 ACTCTTGAACTTGGTTATTATGAGTTG 57.996 33.333 0.00 0.00 31.24 3.16
3345 5909 2.367241 GGGTGCTGGTTGTTGGTTATTT 59.633 45.455 0.00 0.00 0.00 1.40
3346 5910 3.389221 GGTGCTGGTTGTTGGTTATTTG 58.611 45.455 0.00 0.00 0.00 2.32
3419 5983 2.105006 TTCTTCCTCTGCATGTGCTC 57.895 50.000 6.55 0.00 42.66 4.26
3457 6021 6.506827 GCGAATTCATGTTGTTATGATGTTGC 60.507 38.462 6.22 0.00 36.97 4.17
3464 6028 2.073056 TGTTATGATGTTGCGACGCTT 58.927 42.857 22.08 3.06 0.00 4.68
3465 6029 2.482336 TGTTATGATGTTGCGACGCTTT 59.518 40.909 22.08 2.67 0.00 3.51
3533 6097 1.415659 GCTACCTCTCCATGTGCTCAT 59.584 52.381 0.00 0.00 34.21 2.90
3563 6127 2.904866 TGCCTTGTTCGGTGGTGC 60.905 61.111 0.00 0.00 0.00 5.01
3638 6202 6.098982 CAGGGAAACTCTAACATAGATCACCT 59.901 42.308 0.00 0.00 33.66 4.00
3645 6209 9.427821 AACTCTAACATAGATCACCTAATCACT 57.572 33.333 0.00 0.00 33.66 3.41
3726 6290 1.272554 GGACCGGTCTGAAATCCCCT 61.273 60.000 32.52 0.00 0.00 4.79
3784 6348 4.870426 GTCCAGATGTTCGTAACACATGAT 59.130 41.667 0.00 0.00 45.50 2.45
3793 6357 6.035220 TGTTCGTAACACATGATTCCGATAAC 59.965 38.462 0.00 0.00 36.25 1.89
3796 6360 1.858458 ACACATGATTCCGATAACGCG 59.142 47.619 3.53 3.53 38.29 6.01
3855 6419 7.784550 TCATATGCTATGTATCCATGCTACCTA 59.215 37.037 0.00 0.00 32.29 3.08
3867 6431 0.318784 GCTACCTAACTCCGGCATCG 60.319 60.000 0.00 0.00 0.00 3.84
3868 6432 1.030457 CTACCTAACTCCGGCATCGT 58.970 55.000 0.00 0.00 33.95 3.73
3910 6474 2.035940 AAGCCTCGTCGGACCTCT 59.964 61.111 1.91 0.00 33.16 3.69
3929 6493 2.801631 CCCTCTCCATCCAGACGCC 61.802 68.421 0.00 0.00 0.00 5.68
3951 6516 2.269241 GCTTTGCCTACGCCTCCT 59.731 61.111 0.00 0.00 0.00 3.69
3977 6542 0.609131 CCTGAAATCAACCACGGCCT 60.609 55.000 0.00 0.00 0.00 5.19
3988 6553 0.178958 CCACGGCCTAGGTATCCTCT 60.179 60.000 11.31 0.00 34.61 3.69
4012 6577 2.553028 CCTTGCCAACACTACTCATGGT 60.553 50.000 0.00 0.00 35.34 3.55
4056 6621 5.167845 GTTCGGTCAAATGTTATTGCCAAT 58.832 37.500 0.00 0.00 31.20 3.16
4101 6666 8.696410 TTTACTTTGAAGAAAACACAATGGAC 57.304 30.769 0.00 0.00 0.00 4.02
4112 6677 3.424703 ACACAATGGACTCAAATGAGGG 58.575 45.455 14.50 0.58 46.13 4.30
4123 6691 3.433343 TCAAATGAGGGGTACTACGTCA 58.567 45.455 13.12 13.12 37.18 4.35
4193 6776 6.617782 AATATCGATGATGAGGGTGATTCT 57.382 37.500 8.54 0.00 0.00 2.40
4221 6804 1.878775 GGAATGTGTGGCAGAGCAC 59.121 57.895 0.00 0.00 36.26 4.40
4256 6839 3.304911 TGGTTCAACAAAGGGACATCA 57.695 42.857 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.589830 ACATCTATTTACAACTTAGCTGCG 57.410 37.500 0.00 0.00 0.00 5.18
15 16 9.379791 AGTTGGTACATCTATTTACAACTTAGC 57.620 33.333 0.00 0.00 36.51 3.09
66 67 6.990349 CCATGAATAAAGGTACTACCGACAAT 59.010 38.462 0.00 0.00 44.90 2.71
79 80 5.184864 TGTTGTAGTTGGCCATGAATAAAGG 59.815 40.000 6.09 0.00 0.00 3.11
90 91 4.024048 CGAATATGGATGTTGTAGTTGGCC 60.024 45.833 0.00 0.00 0.00 5.36
115 116 1.265905 CTACACGTTTTGCTGAACCCC 59.734 52.381 0.00 0.00 0.00 4.95
118 119 2.659291 CGAGCTACACGTTTTGCTGAAC 60.659 50.000 15.19 0.87 35.76 3.18
129 130 1.443872 GGTGACCACGAGCTACACG 60.444 63.158 0.00 0.00 33.08 4.49
148 149 1.045350 TGCAGAGGAGCTTAGGCGAT 61.045 55.000 0.00 0.00 44.37 4.58
182 183 3.711541 AACCGCCGACGACATAGGC 62.712 63.158 0.00 0.00 45.30 3.93
239 240 2.158957 CCTAGCAAAAGCTACATCCGGA 60.159 50.000 6.61 6.61 0.00 5.14
240 241 2.213499 CCTAGCAAAAGCTACATCCGG 58.787 52.381 0.00 0.00 0.00 5.14
241 242 2.906354 ACCTAGCAAAAGCTACATCCG 58.094 47.619 0.00 0.00 0.00 4.18
257 260 4.938080 TCGTTTGTTTACAACCGTACCTA 58.062 39.130 11.39 0.00 41.51 3.08
258 261 3.791245 TCGTTTGTTTACAACCGTACCT 58.209 40.909 11.39 0.00 41.51 3.08
263 266 4.155449 CCATCATCGTTTGTTTACAACCG 58.845 43.478 6.26 6.26 42.02 4.44
266 269 5.759506 ACACCATCATCGTTTGTTTACAA 57.240 34.783 0.00 0.00 0.00 2.41
270 273 3.068024 AGCAACACCATCATCGTTTGTTT 59.932 39.130 0.00 0.00 0.00 2.83
271 274 2.622942 AGCAACACCATCATCGTTTGTT 59.377 40.909 0.00 0.00 0.00 2.83
272 275 2.030893 CAGCAACACCATCATCGTTTGT 60.031 45.455 0.00 0.00 0.00 2.83
273 276 2.587956 CAGCAACACCATCATCGTTTG 58.412 47.619 0.00 0.00 0.00 2.93
274 277 1.541147 CCAGCAACACCATCATCGTTT 59.459 47.619 0.00 0.00 0.00 3.60
275 278 1.167851 CCAGCAACACCATCATCGTT 58.832 50.000 0.00 0.00 0.00 3.85
276 279 1.308069 GCCAGCAACACCATCATCGT 61.308 55.000 0.00 0.00 0.00 3.73
277 280 1.028330 AGCCAGCAACACCATCATCG 61.028 55.000 0.00 0.00 0.00 3.84
278 281 1.672881 GTAGCCAGCAACACCATCATC 59.327 52.381 0.00 0.00 0.00 2.92
283 295 0.182537 AGTTGTAGCCAGCAACACCA 59.817 50.000 15.00 0.00 46.09 4.17
325 340 3.376078 GGTAGACGGCCACGACCA 61.376 66.667 19.09 0.00 44.60 4.02
350 365 1.006832 CGGACTACCCATTTTGCTCG 58.993 55.000 0.00 0.00 34.14 5.03
351 366 2.109425 ACGGACTACCCATTTTGCTC 57.891 50.000 0.00 0.00 34.14 4.26
352 367 2.433436 GAACGGACTACCCATTTTGCT 58.567 47.619 0.00 0.00 34.14 3.91
353 368 1.471287 GGAACGGACTACCCATTTTGC 59.529 52.381 0.00 0.00 34.14 3.68
354 369 2.747446 CTGGAACGGACTACCCATTTTG 59.253 50.000 0.00 0.00 36.31 2.44
355 370 2.290705 CCTGGAACGGACTACCCATTTT 60.291 50.000 0.00 0.00 36.31 1.82
356 371 1.280998 CCTGGAACGGACTACCCATTT 59.719 52.381 0.00 0.00 36.31 2.32
357 372 0.909623 CCTGGAACGGACTACCCATT 59.090 55.000 0.00 0.00 36.31 3.16
361 376 3.007635 CAATTTCCTGGAACGGACTACC 58.992 50.000 9.04 0.00 36.31 3.18
368 383 1.001815 ACAACGCAATTTCCTGGAACG 60.002 47.619 9.04 11.81 0.00 3.95
383 398 4.364415 TCTTTTTCTGGAACCAACAACG 57.636 40.909 0.00 0.00 0.00 4.10
388 403 5.126384 ACGAACATTCTTTTTCTGGAACCAA 59.874 36.000 0.00 0.00 0.00 3.67
395 410 7.383361 GTGTTTCAACGAACATTCTTTTTCTG 58.617 34.615 0.00 0.00 41.18 3.02
413 428 1.163420 AGATGCAACCGCGTGTTTCA 61.163 50.000 13.02 13.02 42.97 2.69
415 430 0.317770 CAAGATGCAACCGCGTGTTT 60.318 50.000 4.92 0.00 38.50 2.83
432 447 4.349342 AGGGGGCATAATTTTTGTTGACAA 59.651 37.500 0.00 0.00 0.00 3.18
445 460 1.839994 CTCTTGTCTGAGGGGGCATAA 59.160 52.381 0.00 0.00 0.00 1.90
457 472 1.897225 ATGGCTGCGAGCTCTTGTCT 61.897 55.000 12.85 0.00 41.99 3.41
458 473 1.449246 ATGGCTGCGAGCTCTTGTC 60.449 57.895 12.85 3.71 41.99 3.18
478 493 3.722295 CGCGCAACATTCCACGGT 61.722 61.111 8.75 0.00 0.00 4.83
493 508 2.248431 GAACTCACGTGGTTGCGC 59.752 61.111 21.85 0.00 34.88 6.09
498 513 2.029073 CGCTGGAACTCACGTGGT 59.971 61.111 17.00 9.81 0.00 4.16
518 533 1.444119 ATGTTGCAACCGACGTGCTT 61.444 50.000 26.14 0.00 42.69 3.91
579 594 4.825679 CTCCTCCACCCCTCCCCC 62.826 77.778 0.00 0.00 0.00 5.40
636 653 1.390123 CTCACCGCTAATGTCGTGTTG 59.610 52.381 0.00 0.00 0.00 3.33
638 655 0.736325 GCTCACCGCTAATGTCGTGT 60.736 55.000 0.00 0.00 35.14 4.49
709 728 7.065683 CCCTTCTCTCTTGCTTATCTTCTTTTC 59.934 40.741 0.00 0.00 0.00 2.29
725 744 1.489649 CCATGCACATCCCTTCTCTCT 59.510 52.381 0.00 0.00 0.00 3.10
816 1040 2.520536 GCTCCCTCCCATACGCCAT 61.521 63.158 0.00 0.00 0.00 4.40
851 1075 4.627284 TCATTTAGGGAAACACCGAAGA 57.373 40.909 0.00 0.00 40.11 2.87
896 1120 7.624879 AGGTGGATTTTCTTTTATGGAATGGAT 59.375 33.333 0.00 0.00 0.00 3.41
950 1175 2.879490 TGGAGGGGAGGGGAGGAA 60.879 66.667 0.00 0.00 0.00 3.36
951 1176 3.695825 GTGGAGGGGAGGGGAGGA 61.696 72.222 0.00 0.00 0.00 3.71
986 1222 3.515901 GAGAAACCTTAGGAGAGAAGGCA 59.484 47.826 4.77 0.00 46.41 4.75
1031 1267 4.051167 TGGTCGCCGGGGAGACTA 62.051 66.667 23.26 11.90 42.99 2.59
1048 1284 1.591594 CCGCGTACGCCATTGATCT 60.592 57.895 32.64 0.00 38.22 2.75
1072 1308 1.179814 AGCTTCTTCTCCGGTGTCGT 61.180 55.000 0.00 0.00 33.95 4.34
1094 1330 2.636412 CCGTCGGAGCTCCTCAACA 61.636 63.158 29.73 6.18 31.08 3.33
1143 1379 3.181486 GCTTGATGGTCTGTGACTCGATA 60.181 47.826 0.00 0.00 32.47 2.92
1146 1382 1.337167 TGCTTGATGGTCTGTGACTCG 60.337 52.381 0.00 0.00 32.47 4.18
1231 1467 2.305635 TGCAGTACTTGATGACCATGGT 59.694 45.455 19.89 19.89 0.00 3.55
1278 1514 1.754380 CGGTGGAGTCTGTGGGTTCA 61.754 60.000 0.00 0.00 0.00 3.18
1282 1518 4.394712 GGCGGTGGAGTCTGTGGG 62.395 72.222 0.00 0.00 0.00 4.61
1347 1583 1.371389 GAGGACGCGTTGTTCGACT 60.371 57.895 15.53 3.24 42.86 4.18
1405 1647 1.751924 CTAACTAGAAGGAGCACGGCT 59.248 52.381 0.00 0.00 43.88 5.52
1407 1649 3.946558 AGTACTAACTAGAAGGAGCACGG 59.053 47.826 0.00 0.00 32.84 4.94
1439 1693 6.237901 TGCTTCTAAATAGCAGGAACAAGAA 58.762 36.000 0.00 0.00 43.30 2.52
1460 1714 5.062058 CGTTGAAAATCACAACAAAACTGCT 59.938 36.000 0.00 0.00 45.09 4.24
1463 1717 5.474825 ACCGTTGAAAATCACAACAAAACT 58.525 33.333 0.00 0.00 45.09 2.66
1502 1757 0.593128 AGCACACGAAGCACAAATCC 59.407 50.000 0.00 0.00 0.00 3.01
1554 1816 4.398673 GTCTACACTACTACCCAGTTCCTG 59.601 50.000 0.00 0.00 36.14 3.86
1570 1832 2.228343 AGTACCTGCAACGAGTCTACAC 59.772 50.000 0.00 0.00 0.00 2.90
1629 2194 7.320443 TGAACCATTCGAATATTTTCCAGAG 57.680 36.000 10.97 0.00 0.00 3.35
1709 2275 9.660180 GGCAATTAACCCATAAATTAGAAAACA 57.340 29.630 0.00 0.00 0.00 2.83
1814 3760 6.852853 GCAATACACTTTCACCAATATCATCG 59.147 38.462 0.00 0.00 0.00 3.84
1944 3891 8.236586 TGCATTTAACTAAGCACAATACTGAAG 58.763 33.333 0.00 0.00 31.05 3.02
1971 3919 2.168521 AGCAATGCGTAGAAAGCTAGGA 59.831 45.455 0.00 0.00 35.10 2.94
1985 3933 3.924686 CAGGAAACAGAAATCAGCAATGC 59.075 43.478 0.00 0.00 0.00 3.56
2062 4017 3.331150 ACGAAATGCAGACGGTCAAATA 58.669 40.909 11.27 0.00 0.00 1.40
2070 4025 1.725931 GCAAAGGACGAAATGCAGACG 60.726 52.381 8.09 8.09 38.63 4.18
2071 4026 1.537202 AGCAAAGGACGAAATGCAGAC 59.463 47.619 0.00 0.00 41.18 3.51
2130 4085 8.884323 TGACCATTTCTATAGATAATCTGCCTT 58.116 33.333 2.58 0.00 0.00 4.35
2134 4089 9.716531 TTGCTGACCATTTCTATAGATAATCTG 57.283 33.333 2.58 4.68 0.00 2.90
2223 4178 8.661352 TGCAACAAGAATCGAATATAGATGAA 57.339 30.769 0.00 0.00 0.00 2.57
2228 4183 8.715088 TGATGATGCAACAAGAATCGAATATAG 58.285 33.333 0.00 0.00 34.71 1.31
2230 4185 7.228108 ACTGATGATGCAACAAGAATCGAATAT 59.772 33.333 0.00 0.00 34.71 1.28
2239 4194 4.644498 TCTTGACTGATGATGCAACAAGA 58.356 39.130 0.00 0.00 38.10 3.02
2322 4277 1.888512 TCAAAGAAAGCTCACATGCCC 59.111 47.619 0.00 0.00 0.00 5.36
2535 4504 3.245229 ACAGTGCAGATGAATTACCCCAA 60.245 43.478 5.87 0.00 0.00 4.12
2588 4557 9.542462 GATACTGAAACAATACCATACAAGCTA 57.458 33.333 0.00 0.00 0.00 3.32
2598 4567 9.378551 TGTCTTACATGATACTGAAACAATACC 57.621 33.333 0.00 0.00 0.00 2.73
2680 4650 5.506317 GCAATACAACATAATGAGGGAGCAC 60.506 44.000 0.00 0.00 0.00 4.40
2774 4745 1.722034 AGTGAGGGAGCAGAACTTCA 58.278 50.000 0.00 0.00 0.00 3.02
2876 4970 4.796038 AGGCAAATATAAGCATGATGGC 57.204 40.909 0.00 0.00 0.00 4.40
2931 5025 2.702478 TCTGGCAGGTAAGATCCATCAG 59.298 50.000 15.73 0.00 0.00 2.90
2934 5028 2.441001 CCTTCTGGCAGGTAAGATCCAT 59.559 50.000 15.73 0.00 0.00 3.41
2962 5056 7.201983 CCTCTGGAGTCATCTTCTTTATCATGA 60.202 40.741 0.00 0.00 0.00 3.07
3005 5099 3.139077 GGTGAGGTCGTTCTTGATGTTT 58.861 45.455 0.00 0.00 0.00 2.83
3050 5144 1.068352 AGGCCCACTGGTTCTTCCTT 61.068 55.000 0.00 0.00 37.07 3.36
3083 5177 7.762610 AGTTGTTTCTTTAGTTATACCCCCTT 58.237 34.615 0.00 0.00 0.00 3.95
3114 5209 2.158871 CCTTGCTGGCCATTTGCATTAT 60.159 45.455 17.91 0.00 43.89 1.28
3121 5216 0.114954 TCCTTCCTTGCTGGCCATTT 59.885 50.000 5.51 0.00 35.26 2.32
3126 5221 1.536073 GGGTTTCCTTCCTTGCTGGC 61.536 60.000 0.00 0.00 35.26 4.85
3170 5265 2.676839 TTGAAGCACAAACGGTTAACGA 59.323 40.909 0.00 0.00 39.25 3.85
3205 5300 5.172934 CAGACCAATGTACTTACGGCTTAA 58.827 41.667 0.00 0.00 0.00 1.85
3274 5837 8.804688 GTGTAGCAAAATACACCAACATAAAA 57.195 30.769 5.85 0.00 46.43 1.52
3324 5888 1.627864 ATAACCAACAACCAGCACCC 58.372 50.000 0.00 0.00 0.00 4.61
3366 5930 6.480524 TCATAGGCATGCAAAACGATATAC 57.519 37.500 21.36 0.00 31.73 1.47
3419 5983 5.106555 ACATGAATTCGCTACTCAAACTTGG 60.107 40.000 0.00 0.00 0.00 3.61
3457 6021 1.687494 GCAGCTCACCTAAAGCGTCG 61.687 60.000 0.00 0.00 44.59 5.12
3512 6076 0.105778 GAGCACATGGAGAGGTAGCC 59.894 60.000 0.00 0.00 0.00 3.93
3533 6097 3.508845 ACAAGGCAGAAGGAAAGCTTA 57.491 42.857 0.00 0.00 0.00 3.09
3586 6150 8.609483 AGATGCTAGGGTTGACATATTGAATAT 58.391 33.333 0.00 0.00 0.00 1.28
3638 6202 4.265904 TCTGGACTTTTGCGAGTGATTA 57.734 40.909 0.00 0.00 0.00 1.75
3643 6207 1.673033 CCGATCTGGACTTTTGCGAGT 60.673 52.381 0.00 0.00 42.00 4.18
3645 6209 0.606096 TCCGATCTGGACTTTTGCGA 59.394 50.000 2.65 0.00 43.74 5.10
3755 6319 1.153369 CGAACATCTGGACGCCCAT 60.153 57.895 0.00 0.00 42.59 4.00
3771 6335 4.736307 CGTTATCGGAATCATGTGTTACGA 59.264 41.667 18.36 18.36 45.05 3.43
3793 6357 1.664151 GGAAAAATACAGACTCCCGCG 59.336 52.381 0.00 0.00 0.00 6.46
3796 6360 5.183331 GGAACAAGGAAAAATACAGACTCCC 59.817 44.000 0.00 0.00 0.00 4.30
3855 6419 0.534203 ACAACAACGATGCCGGAGTT 60.534 50.000 5.05 1.93 40.78 3.01
3910 6474 1.758514 GCGTCTGGATGGAGAGGGA 60.759 63.158 0.00 0.00 0.00 4.20
3951 6516 2.962421 GTGGTTGATTTCAGGGTGGAAA 59.038 45.455 0.00 0.00 40.72 3.13
3977 6542 1.424638 GCAAGGGCAGAGGATACCTA 58.575 55.000 0.00 0.00 40.72 3.08
3988 6553 0.250727 GAGTAGTGTTGGCAAGGGCA 60.251 55.000 0.00 0.00 43.71 5.36
4012 6577 2.494471 CACTTGTCGGGTGTAGTATCCA 59.506 50.000 0.00 0.00 0.00 3.41
4075 6640 9.313118 GTCCATTGTGTTTTCTTCAAAGTAAAT 57.687 29.630 0.00 0.00 29.96 1.40
4193 6776 1.811965 CCACACATTCCGCATCTTCAA 59.188 47.619 0.00 0.00 0.00 2.69
4221 6804 5.007234 TGTTGAACCATTGTAGTTGAGAACG 59.993 40.000 0.00 0.00 36.23 3.95


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

AutoCloner maintained by Alex Coulton.