Multiple sequence alignment - TraesCS1D01G039200

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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 TraesCS1D01G039200 chr1D 100.000 3461 0 0 1 3461 18996458 18992998 0.000000e+00 6392.0
1 TraesCS1D01G039200 chr1A 91.799 3158 201 30 1 3125 20920538 20917406 0.000000e+00 4344.0
2 TraesCS1D01G039200 chr1A 86.527 334 29 11 3140 3459 20917369 20917038 1.530000e-93 353.0
3 TraesCS1D01G039200 chr1B 86.592 3110 309 60 419 3456 28163845 28160772 0.000000e+00 3334.0
4 TraesCS1D01G039200 chr1B 89.583 2592 218 33 513 3084 28166724 28164165 0.000000e+00 3243.0
5 TraesCS1D01G039200 chr7D 86.944 1440 174 8 1006 2438 167058350 167056918 0.000000e+00 1605.0
6 TraesCS1D01G039200 chr7D 82.322 1318 216 12 1006 2310 166928013 166926700 0.000000e+00 1127.0
7 TraesCS1D01G039200 chr7D 83.907 1162 177 7 1278 2431 166887093 166885934 0.000000e+00 1101.0
8 TraesCS1D01G039200 chr6A 82.491 1445 225 20 1016 2446 12433908 12432478 0.000000e+00 1242.0
9 TraesCS1D01G039200 chr7A 82.312 1436 241 8 1006 2430 167987329 167985896 0.000000e+00 1232.0
10 TraesCS1D01G039200 chr7B 82.062 1455 237 17 995 2431 130898368 130896920 0.000000e+00 1219.0
11 TraesCS1D01G039200 chr4D 80.806 422 55 16 4 411 108053114 108053523 1.210000e-79 307.0
12 TraesCS1D01G039200 chr4D 77.577 388 65 17 1 378 215457747 215458122 7.520000e-52 215.0
13 TraesCS1D01G039200 chr2D 78.964 309 56 9 107 406 54868552 54868244 5.860000e-48 202.0
14 TraesCS1D01G039200 chr2D 84.615 91 12 2 4 93 539020507 539020418 4.760000e-14 89.8
15 TraesCS1D01G039200 chr3B 81.673 251 34 10 167 411 716299019 716298775 7.580000e-47 198.0
16 TraesCS1D01G039200 chr5D 79.344 305 44 12 1 297 232006262 232006555 2.730000e-46 196.0
17 TraesCS1D01G039200 chr3A 79.079 239 38 6 11 245 497662552 497662782 1.660000e-33 154.0
18 TraesCS1D01G039200 chr2B 74.083 409 77 20 1 398 569241178 569241568 1.300000e-29 141.0
19 TraesCS1D01G039200 chr5A 77.202 193 34 7 1 191 398890569 398890753 1.700000e-18 104.0
20 TraesCS1D01G039200 chr5A 80.952 105 17 3 1 104 664980462 664980564 2.860000e-11 80.5
21 TraesCS1D01G039200 chr5B 88.095 84 10 0 1 84 17551048 17551131 2.200000e-17 100.0


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 TraesCS1D01G039200 chr1D 18992998 18996458 3460 True 6392.0 6392 100.0000 1 3461 1 chr1D.!!$R1 3460
1 TraesCS1D01G039200 chr1A 20917038 20920538 3500 True 2348.5 4344 89.1630 1 3459 2 chr1A.!!$R1 3458
2 TraesCS1D01G039200 chr1B 28160772 28166724 5952 True 3288.5 3334 88.0875 419 3456 2 chr1B.!!$R1 3037
3 TraesCS1D01G039200 chr7D 167056918 167058350 1432 True 1605.0 1605 86.9440 1006 2438 1 chr7D.!!$R3 1432
4 TraesCS1D01G039200 chr7D 166926700 166928013 1313 True 1127.0 1127 82.3220 1006 2310 1 chr7D.!!$R2 1304
5 TraesCS1D01G039200 chr7D 166885934 166887093 1159 True 1101.0 1101 83.9070 1278 2431 1 chr7D.!!$R1 1153
6 TraesCS1D01G039200 chr6A 12432478 12433908 1430 True 1242.0 1242 82.4910 1016 2446 1 chr6A.!!$R1 1430
7 TraesCS1D01G039200 chr7A 167985896 167987329 1433 True 1232.0 1232 82.3120 1006 2430 1 chr7A.!!$R1 1424
8 TraesCS1D01G039200 chr7B 130896920 130898368 1448 True 1219.0 1219 82.0620 995 2431 1 chr7B.!!$R1 1436

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
609 628 0.026285 GTGCCATCAACGATGTACGC 59.974 55.0 3.47 0.99 46.94 4.42 F
1782 4828 0.255890 GCAAGAACAGGGGGATGCTA 59.744 55.0 0.00 0.00 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 4993 0.107165 GGTCCTTGGACAGGTATGCC 60.107 60.0 19.9 0.0 44.37 4.40 R
3117 6191 0.039978 CGTCCGCCTACTATGAGCTG 60.040 60.0 0.0 0.0 0.00 4.24 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 3.157252 GGAGGCCGAGCTCCATGA 61.157 66.667 8.47 0.00 39.45 3.07
51 52 5.835113 TGAAGGCCTCTATTTGCAATTAC 57.165 39.130 5.23 0.00 0.00 1.89
148 155 3.002451 GGCACAATGTACGTGTGTGTTAA 59.998 43.478 23.09 0.00 46.58 2.01
179 186 4.946160 TGGAATAGGTTGAAATGAGGGT 57.054 40.909 0.00 0.00 0.00 4.34
181 188 6.395780 TGGAATAGGTTGAAATGAGGGTTA 57.604 37.500 0.00 0.00 0.00 2.85
241 248 6.002704 GCTATTCATCCTCAAAGTCCATGAT 58.997 40.000 0.00 0.00 0.00 2.45
366 382 8.950208 TGAAACCGGAAAGTTTGAATTTTAAT 57.050 26.923 9.46 0.00 40.01 1.40
414 433 1.890041 CGGTCACCAAAACGCTCCA 60.890 57.895 0.00 0.00 0.00 3.86
420 439 1.021968 ACCAAAACGCTCCAAGTCAC 58.978 50.000 0.00 0.00 0.00 3.67
435 454 6.449956 TCCAAGTCACCTAGGGAGTATAATT 58.550 40.000 14.81 0.00 0.00 1.40
507 526 6.701340 AGTAATTCGCATATATTCTGAGGCA 58.299 36.000 0.00 0.00 0.00 4.75
512 531 4.526650 TCGCATATATTCTGAGGCACCTAA 59.473 41.667 0.00 0.00 0.00 2.69
588 607 1.791103 ATGGGCGGTCGTGTTGTTTG 61.791 55.000 0.00 0.00 0.00 2.93
589 608 2.330041 GGCGGTCGTGTTGTTTGG 59.670 61.111 0.00 0.00 0.00 3.28
607 626 1.014352 GGGTGCCATCAACGATGTAC 58.986 55.000 3.47 2.61 38.28 2.90
609 628 0.026285 GTGCCATCAACGATGTACGC 59.974 55.000 3.47 0.99 46.94 4.42
610 629 0.390472 TGCCATCAACGATGTACGCA 60.390 50.000 3.47 3.37 46.94 5.24
757 779 9.535878 ACCAACAACAAATTAACGAACAATAAT 57.464 25.926 0.00 0.00 0.00 1.28
785 807 9.053472 TGGTTTGTTAGGAGAGAGGAATTAATA 57.947 33.333 0.00 0.00 0.00 0.98
803 825 8.780846 AATTAATATCCTGTACACGTCAACAA 57.219 30.769 0.00 0.00 0.00 2.83
817 839 3.559655 CGTCAACAACTCATCCAAGACAA 59.440 43.478 0.00 0.00 0.00 3.18
868 891 9.214953 GAAACATGAGAATTAGCAAATAAGTCG 57.785 33.333 0.00 0.00 42.08 4.18
933 956 4.681978 ACTCACCAACGAGGCGGC 62.682 66.667 0.00 0.00 43.14 6.53
1065 1095 2.096909 CCAGCTCGTCGTAAACAACTTG 60.097 50.000 0.00 0.00 0.00 3.16
1071 1101 4.111198 TCGTCGTAAACAACTTGCTTGTA 58.889 39.130 0.00 0.00 42.70 2.41
1161 1191 2.108168 CTCTCCCGTCTCCATGGTTTA 58.892 52.381 12.58 0.00 0.00 2.01
1182 1212 4.268687 CAGGTCCACGTTCTGCTC 57.731 61.111 0.00 0.00 0.00 4.26
1184 1214 2.201022 AGGTCCACGTTCTGCTCGT 61.201 57.895 0.00 0.00 42.33 4.18
1200 1230 2.971452 GTCGTCTTCCTCCCGCTT 59.029 61.111 0.00 0.00 0.00 4.68
1201 1231 1.292541 GTCGTCTTCCTCCCGCTTT 59.707 57.895 0.00 0.00 0.00 3.51
1252 1282 1.002684 CTCGTAGCGTGTACCTCATCC 60.003 57.143 0.00 0.00 0.00 3.51
1321 1351 1.140407 CTCCGTCGAGAATGTTCGCC 61.140 60.000 0.00 0.00 40.29 5.54
1407 4441 1.622725 GGTGACCAGACCTACCTCCAT 60.623 57.143 0.00 0.00 32.69 3.41
1734 4780 2.756400 GCCCTGATGGTGTCCACA 59.244 61.111 0.00 0.00 35.80 4.17
1740 4786 0.473694 TGATGGTGTCCACAGAGGGT 60.474 55.000 0.00 0.00 35.80 4.34
1771 4817 1.164411 CAACTATGCCGGCAAGAACA 58.836 50.000 36.33 15.11 0.00 3.18
1782 4828 0.255890 GCAAGAACAGGGGGATGCTA 59.744 55.000 0.00 0.00 0.00 3.49
1906 4952 1.672737 CCGCACATGACAGAGCTTACA 60.673 52.381 0.00 0.00 0.00 2.41
1930 4976 3.091545 TGCATTTCCATGAAAGAGGACC 58.908 45.455 0.00 0.00 34.92 4.46
1947 4993 0.995024 ACCATGAGGGAGAAACAGGG 59.005 55.000 0.00 0.00 41.15 4.45
2006 5052 1.074405 AGCTCTCAAGGCCAACATCAA 59.926 47.619 5.01 0.00 0.00 2.57
2009 5055 1.704628 TCTCAAGGCCAACATCAAGGA 59.295 47.619 5.01 0.00 0.00 3.36
2011 5057 2.490903 CTCAAGGCCAACATCAAGGAAG 59.509 50.000 5.01 0.00 0.00 3.46
2100 5146 3.197265 GCTGAGAAGGAAGATCAAGCTC 58.803 50.000 0.00 0.00 0.00 4.09
2154 5200 0.251564 TTTGCATCCATTCCGGTGGT 60.252 50.000 10.70 0.00 40.27 4.16
2180 5226 2.379634 TGATCGACGCGGTGCAAAG 61.380 57.895 12.47 0.00 0.00 2.77
2393 5445 4.645921 GGCCAACAACACCGCTGC 62.646 66.667 0.00 0.00 0.00 5.25
2452 5504 3.323691 TCTCAACAACATCTCGGAGGAAA 59.676 43.478 4.96 0.00 0.00 3.13
2453 5505 3.399330 TCAACAACATCTCGGAGGAAAC 58.601 45.455 4.96 0.00 0.00 2.78
2468 5520 2.551032 AGGAAACGGGCTAAAAACTTCG 59.449 45.455 0.00 0.00 0.00 3.79
2479 5531 1.085501 AAAACTTCGTGCACGGACGT 61.086 50.000 36.41 26.36 40.34 4.34
2480 5532 1.485032 AAACTTCGTGCACGGACGTC 61.485 55.000 36.41 7.13 40.34 4.34
2559 5615 2.975851 GCACGCTGAGACAAAGAAAATG 59.024 45.455 0.00 0.00 0.00 2.32
2609 5665 5.550290 AGGAAAATAAAGCATGTTTGTGGG 58.450 37.500 0.00 0.00 0.00 4.61
2610 5666 5.071653 AGGAAAATAAAGCATGTTTGTGGGT 59.928 36.000 0.00 0.00 0.00 4.51
2652 5714 6.683974 AACACATTTAGACATGTATCTGGC 57.316 37.500 0.00 0.00 35.51 4.85
2654 5716 5.586243 ACACATTTAGACATGTATCTGGCAC 59.414 40.000 0.00 0.00 35.51 5.01
2658 5720 3.046283 AGACATGTATCTGGCACCCTA 57.954 47.619 0.00 0.00 0.00 3.53
2668 5730 5.717119 ATCTGGCACCCTATTTTCTACTT 57.283 39.130 0.00 0.00 0.00 2.24
2688 5753 4.885270 CGGCCACACCCACAACCA 62.885 66.667 2.24 0.00 33.26 3.67
2772 5845 4.579869 TCTCAGTCCCAATCAAAAGTAGC 58.420 43.478 0.00 0.00 0.00 3.58
2859 5932 7.747155 TTTCCATTTTTGTTAGGATCACGTA 57.253 32.000 0.00 0.00 0.00 3.57
2949 6023 7.384524 AATAATTACTAGGTGGAGTAACCCC 57.615 40.000 0.00 0.00 43.04 4.95
2950 6024 2.442236 TACTAGGTGGAGTAACCCCG 57.558 55.000 0.00 0.00 41.54 5.73
2951 6025 0.974525 ACTAGGTGGAGTAACCCCGC 60.975 60.000 0.00 0.00 41.54 6.13
2954 6028 1.073548 GGTGGAGTAACCCCGCAAA 59.926 57.895 0.00 0.00 38.00 3.68
2956 6030 1.320507 GTGGAGTAACCCCGCAAAAA 58.679 50.000 0.00 0.00 38.00 1.94
2957 6031 1.890489 GTGGAGTAACCCCGCAAAAAT 59.110 47.619 0.00 0.00 38.00 1.82
2958 6032 1.889829 TGGAGTAACCCCGCAAAAATG 59.110 47.619 0.00 0.00 38.00 2.32
2959 6033 1.890489 GGAGTAACCCCGCAAAAATGT 59.110 47.619 0.00 0.00 0.00 2.71
2960 6034 2.297880 GGAGTAACCCCGCAAAAATGTT 59.702 45.455 0.00 0.00 0.00 2.71
2962 6036 4.373527 GAGTAACCCCGCAAAAATGTTTT 58.626 39.130 0.00 0.00 0.00 2.43
2963 6037 4.771903 AGTAACCCCGCAAAAATGTTTTT 58.228 34.783 0.00 0.00 40.75 1.94
2995 6069 0.737219 CATGAGCTGGGTTGCTAAGC 59.263 55.000 0.00 0.00 44.17 3.09
3068 6142 4.215399 CCACAAATAAACACCACGACTGAT 59.785 41.667 0.00 0.00 0.00 2.90
3069 6143 5.146460 CACAAATAAACACCACGACTGATG 58.854 41.667 0.00 0.00 0.00 3.07
3083 6157 4.256920 CGACTGATGACAAAAGAGGGAAT 58.743 43.478 0.00 0.00 0.00 3.01
3114 6188 8.504005 CACTTTAAACAGAACCCATTAGTAGTG 58.496 37.037 0.00 0.00 0.00 2.74
3115 6189 8.434392 ACTTTAAACAGAACCCATTAGTAGTGA 58.566 33.333 0.00 0.00 0.00 3.41
3117 6191 8.611654 TTAAACAGAACCCATTAGTAGTGAAC 57.388 34.615 0.00 0.00 0.00 3.18
3118 6192 5.818678 ACAGAACCCATTAGTAGTGAACA 57.181 39.130 0.00 0.00 0.00 3.18
3120 6194 4.631813 CAGAACCCATTAGTAGTGAACAGC 59.368 45.833 0.00 0.00 0.00 4.40
3121 6195 4.532521 AGAACCCATTAGTAGTGAACAGCT 59.467 41.667 0.00 0.00 0.00 4.24
3122 6196 4.473477 ACCCATTAGTAGTGAACAGCTC 57.527 45.455 0.00 0.00 0.00 4.09
3123 6197 3.838317 ACCCATTAGTAGTGAACAGCTCA 59.162 43.478 0.00 0.00 0.00 4.26
3124 6198 4.471386 ACCCATTAGTAGTGAACAGCTCAT 59.529 41.667 0.00 0.00 36.14 2.90
3125 6199 5.661312 ACCCATTAGTAGTGAACAGCTCATA 59.339 40.000 0.00 0.00 36.14 2.15
3126 6200 6.183360 ACCCATTAGTAGTGAACAGCTCATAG 60.183 42.308 0.00 0.00 36.14 2.23
3136 6226 0.039978 CAGCTCATAGTAGGCGGACG 60.040 60.000 0.00 0.00 0.00 4.79
3138 6235 1.286260 CTCATAGTAGGCGGACGGC 59.714 63.158 10.47 10.47 42.51 5.68
3460 6570 5.878484 TTCCTTCTCCTTTTATTTCCCCT 57.122 39.130 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 7.954666 TTTAGTAATTGCAAATAGAGGCCTT 57.045 32.000 6.77 0.00 0.00 4.35
148 155 9.880157 CATTTCAACCTATTCCATTCTGAAAAT 57.120 29.630 0.00 0.00 35.59 1.82
192 199 6.832520 TCATGTGCTAAAAAGCCTCAATAA 57.167 33.333 0.00 0.00 0.00 1.40
193 200 6.798482 CATCATGTGCTAAAAAGCCTCAATA 58.202 36.000 0.00 0.00 0.00 1.90
194 201 5.657474 CATCATGTGCTAAAAAGCCTCAAT 58.343 37.500 0.00 0.00 0.00 2.57
195 202 5.063180 CATCATGTGCTAAAAAGCCTCAA 57.937 39.130 0.00 0.00 0.00 3.02
253 269 6.027749 GTGAAATACCTTAAAATGCGACCTG 58.972 40.000 0.00 0.00 0.00 4.00
330 346 5.592688 ACTTTCCGGTTTCAAAAGAATCTGA 59.407 36.000 16.94 0.00 34.76 3.27
339 355 7.674471 AAAATTCAAACTTTCCGGTTTCAAA 57.326 28.000 0.00 0.00 37.32 2.69
369 385 6.102897 TCCATCGAGCCCAATTTTTAAAAA 57.897 33.333 15.38 15.38 0.00 1.94
370 386 5.719173 CTCCATCGAGCCCAATTTTTAAAA 58.281 37.500 0.00 0.00 0.00 1.52
387 406 2.478335 TTTGGTGACCGGGCTCCATC 62.478 60.000 31.04 11.43 32.09 3.51
391 410 2.613506 CGTTTTGGTGACCGGGCTC 61.614 63.158 9.82 4.18 0.00 4.70
396 415 1.440938 TTGGAGCGTTTTGGTGACCG 61.441 55.000 0.00 0.00 0.00 4.79
414 433 7.363031 TGAGAATTATACTCCCTAGGTGACTT 58.637 38.462 8.29 0.00 36.36 3.01
420 439 7.456269 ACAAGGATGAGAATTATACTCCCTAGG 59.544 40.741 0.06 0.06 33.95 3.02
491 510 6.881065 TGAATTAGGTGCCTCAGAATATATGC 59.119 38.462 0.00 0.00 0.00 3.14
495 514 8.773033 AAATTGAATTAGGTGCCTCAGAATAT 57.227 30.769 0.00 0.00 0.00 1.28
500 519 9.903682 CATATAAAATTGAATTAGGTGCCTCAG 57.096 33.333 0.00 0.00 0.00 3.35
501 520 9.420118 ACATATAAAATTGAATTAGGTGCCTCA 57.580 29.630 0.00 0.00 0.00 3.86
567 586 1.512156 AACAACACGACCGCCCATTC 61.512 55.000 0.00 0.00 0.00 2.67
588 607 1.014352 GTACATCGTTGATGGCACCC 58.986 55.000 11.17 0.00 43.60 4.61
589 608 0.650512 CGTACATCGTTGATGGCACC 59.349 55.000 11.17 0.00 43.60 5.01
607 626 5.572126 GTCCTTTTCAAGTACTAGTAGTGCG 59.428 44.000 13.29 6.11 35.89 5.34
608 627 6.689554 AGTCCTTTTCAAGTACTAGTAGTGC 58.310 40.000 13.29 11.67 0.00 4.40
609 628 9.543783 AAAAGTCCTTTTCAAGTACTAGTAGTG 57.456 33.333 13.29 8.79 38.27 2.74
757 779 3.583228 TCCTCTCTCCTAACAAACCACA 58.417 45.455 0.00 0.00 0.00 4.17
785 807 3.069016 TGAGTTGTTGACGTGTACAGGAT 59.931 43.478 21.70 6.47 0.00 3.24
789 811 3.181474 TGGATGAGTTGTTGACGTGTACA 60.181 43.478 0.00 0.00 0.00 2.90
803 825 7.613022 ACACATGATAATTTGTCTTGGATGAGT 59.387 33.333 0.00 2.81 0.00 3.41
933 956 3.154710 GGAGATTTTATAAAGGGCCCGG 58.845 50.000 18.44 0.00 0.00 5.73
935 958 6.611785 ACTTAGGAGATTTTATAAAGGGCCC 58.388 40.000 16.46 16.46 0.00 5.80
990 1013 1.077086 TGAGGCCATGGTTGCATGT 59.923 52.632 14.67 0.00 0.00 3.21
1149 1179 0.251916 CCTGCCGTAAACCATGGAGA 59.748 55.000 21.47 0.00 34.93 3.71
1161 1191 3.231736 AGAACGTGGACCTGCCGT 61.232 61.111 0.00 0.00 40.66 5.68
1182 1212 2.488087 AAAGCGGGAGGAAGACGACG 62.488 60.000 0.00 0.00 0.00 5.12
1184 1214 1.590147 GAAAGCGGGAGGAAGACGA 59.410 57.895 0.00 0.00 0.00 4.20
1200 1230 1.205460 GGTAGAGGGTGGCCAAGGAA 61.205 60.000 7.24 0.00 0.00 3.36
1201 1231 1.615424 GGTAGAGGGTGGCCAAGGA 60.615 63.158 7.24 0.00 0.00 3.36
1321 1351 1.309950 TCATCGAGGTAAGGCGAGAG 58.690 55.000 0.00 0.00 40.14 3.20
1407 4441 3.236896 GGGGATATAGTGGAACGAAGGA 58.763 50.000 0.00 0.00 45.86 3.36
1434 4468 1.176527 GGCCATCACTTAAGCTGCAA 58.823 50.000 1.29 0.00 0.00 4.08
1509 4543 3.056250 CGATAGCTCCAGGACTTATGCAT 60.056 47.826 3.79 3.79 0.00 3.96
1510 4544 2.297315 CGATAGCTCCAGGACTTATGCA 59.703 50.000 0.00 0.00 0.00 3.96
1713 4747 2.359850 GACACCATCAGGGCGCAA 60.360 61.111 10.83 0.00 42.05 4.85
1714 4748 4.408821 GGACACCATCAGGGCGCA 62.409 66.667 10.83 0.00 42.05 6.09
1740 4786 4.462834 CCGGCATAGTTGATGATAGAGGTA 59.537 45.833 0.00 0.00 37.82 3.08
1771 4817 2.599139 TACGGCAGTAGCATCCCCCT 62.599 60.000 0.00 0.00 44.61 4.79
1782 4828 3.584868 GAACAGGGCGTACGGCAGT 62.585 63.158 37.70 31.39 46.16 4.40
1906 4952 4.159135 GTCCTCTTTCATGGAAATGCACAT 59.841 41.667 0.00 0.00 33.72 3.21
1930 4976 0.394899 GCCCCTGTTTCTCCCTCATG 60.395 60.000 0.00 0.00 0.00 3.07
1947 4993 0.107165 GGTCCTTGGACAGGTATGCC 60.107 60.000 19.90 0.00 44.37 4.40
2006 5052 0.324460 CACGAGGGACCCTACTTCCT 60.324 60.000 14.87 0.00 31.76 3.36
2009 5055 0.971447 GAGCACGAGGGACCCTACTT 60.971 60.000 14.87 0.00 31.76 2.24
2011 5057 2.424733 GGAGCACGAGGGACCCTAC 61.425 68.421 14.87 6.47 31.76 3.18
2180 5226 4.877282 GACATCCCTGTCTGATAAGCTAC 58.123 47.826 0.00 0.00 46.84 3.58
2452 5504 0.589708 GCACGAAGTTTTTAGCCCGT 59.410 50.000 0.00 0.00 41.61 5.28
2453 5505 0.589223 TGCACGAAGTTTTTAGCCCG 59.411 50.000 0.00 0.00 41.61 6.13
2468 5520 1.389106 GAATTGTAGACGTCCGTGCAC 59.611 52.381 13.01 6.82 0.00 4.57
2584 5640 7.038373 ACCCACAAACATGCTTTATTTTCCTAT 60.038 33.333 0.00 0.00 0.00 2.57
2597 5653 3.127030 GCTCTACTTACCCACAAACATGC 59.873 47.826 0.00 0.00 0.00 4.06
2652 5714 4.573607 GGCCGTTAAGTAGAAAATAGGGTG 59.426 45.833 0.00 0.00 0.00 4.61
2654 5716 4.573607 GTGGCCGTTAAGTAGAAAATAGGG 59.426 45.833 0.00 0.00 0.00 3.53
2658 5720 3.754850 GGTGTGGCCGTTAAGTAGAAAAT 59.245 43.478 0.00 0.00 0.00 1.82
2668 5730 1.526455 GTTGTGGGTGTGGCCGTTA 60.526 57.895 0.00 0.00 38.44 3.18
2688 5753 1.072159 GTGCACTCCTTGAGGCAGT 59.928 57.895 10.32 0.00 36.86 4.40
2772 5845 6.017605 GCTCATAATGATTTACACTCCACCAG 60.018 42.308 0.00 0.00 0.00 4.00
2838 5911 6.978343 TCTACGTGATCCTAACAAAAATGG 57.022 37.500 0.00 0.00 0.00 3.16
2859 5932 3.028850 CACATGCCATCCTCCATTTTCT 58.971 45.455 0.00 0.00 0.00 2.52
2892 5966 5.066593 AGAAAGAGAAAAAGGCTCACGAAT 58.933 37.500 0.00 0.00 34.85 3.34
2937 6011 1.320507 TTTTTGCGGGGTTACTCCAC 58.679 50.000 0.86 0.00 38.11 4.02
2960 6034 6.599244 CCAGCTCATGTTCCATCTAGTAAAAA 59.401 38.462 0.00 0.00 0.00 1.94
2962 6036 5.396772 CCCAGCTCATGTTCCATCTAGTAAA 60.397 44.000 0.00 0.00 0.00 2.01
2963 6037 4.101585 CCCAGCTCATGTTCCATCTAGTAA 59.898 45.833 0.00 0.00 0.00 2.24
2965 6039 2.437281 CCCAGCTCATGTTCCATCTAGT 59.563 50.000 0.00 0.00 0.00 2.57
2966 6040 2.437281 ACCCAGCTCATGTTCCATCTAG 59.563 50.000 0.00 0.00 0.00 2.43
2967 6041 2.481441 ACCCAGCTCATGTTCCATCTA 58.519 47.619 0.00 0.00 0.00 1.98
2968 6042 1.293062 ACCCAGCTCATGTTCCATCT 58.707 50.000 0.00 0.00 0.00 2.90
2969 6043 1.747355 CAACCCAGCTCATGTTCCATC 59.253 52.381 0.00 0.00 0.00 3.51
2970 6044 1.843368 CAACCCAGCTCATGTTCCAT 58.157 50.000 0.00 0.00 0.00 3.41
2974 6048 2.440409 CTTAGCAACCCAGCTCATGTT 58.560 47.619 0.00 0.00 45.26 2.71
2975 6049 1.952367 GCTTAGCAACCCAGCTCATGT 60.952 52.381 0.00 0.00 45.26 3.21
3025 6099 2.584261 ATTCCACGCTGCTCGCTCAT 62.584 55.000 0.00 0.00 43.23 2.90
3031 6105 3.490890 GTGGATTCCACGCTGCTC 58.509 61.111 19.65 0.00 44.95 4.26
3083 6157 2.696187 GGGTTCTGTTTAAAGTGGGCAA 59.304 45.455 0.00 0.00 0.00 4.52
3099 6173 4.833390 AGCTGTTCACTACTAATGGGTTC 58.167 43.478 0.00 0.00 0.00 3.62
3114 6188 1.681793 TCCGCCTACTATGAGCTGTTC 59.318 52.381 0.00 0.00 0.00 3.18
3115 6189 1.409427 GTCCGCCTACTATGAGCTGTT 59.591 52.381 0.00 0.00 0.00 3.16
3117 6191 0.039978 CGTCCGCCTACTATGAGCTG 60.040 60.000 0.00 0.00 0.00 4.24
3118 6192 1.173444 CCGTCCGCCTACTATGAGCT 61.173 60.000 0.00 0.00 0.00 4.09
3120 6194 1.286260 GCCGTCCGCCTACTATGAG 59.714 63.158 0.00 0.00 0.00 2.90
3121 6195 2.549198 CGCCGTCCGCCTACTATGA 61.549 63.158 0.00 0.00 0.00 2.15
3122 6196 2.050351 CGCCGTCCGCCTACTATG 60.050 66.667 0.00 0.00 0.00 2.23
3138 6235 4.838486 GAGTCCACGAGCGAGGCG 62.838 72.222 1.33 0.00 0.00 5.52
3178 6277 3.857854 GCGCTCTGTGCCGATGTG 61.858 66.667 0.00 0.00 38.78 3.21
3185 6284 2.463675 GAAAACCTGGCGCTCTGTGC 62.464 60.000 7.64 0.00 38.45 4.57
3221 6320 0.321671 TGGACGAAGGGAGCAGAAAG 59.678 55.000 0.00 0.00 0.00 2.62
3298 6406 8.904834 AGCTTTTCTGAGTTTATCTAGATACGA 58.095 33.333 12.12 1.72 0.00 3.43
3312 6421 3.066760 CGTTCCCAAAAGCTTTTCTGAGT 59.933 43.478 21.45 0.00 0.00 3.41
3315 6424 2.360801 TCCGTTCCCAAAAGCTTTTCTG 59.639 45.455 21.45 14.84 0.00 3.02
3328 6437 9.783081 TCCTAATAAAATATTAACTCCGTTCCC 57.217 33.333 0.00 0.00 0.00 3.97
3361 6470 0.319728 CCCAGATGGAGAGGCGTATG 59.680 60.000 0.00 0.00 37.39 2.39
3434 6544 7.016268 AGGGGAAATAAAAGGAGAAGGAAAAAC 59.984 37.037 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.