Multiple sequence alignment - TraesCS1B01G215700

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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 TraesCS1B01G215700 chr1B 100.000 4694 0 0 1 4694 391267263 391271956 0.000000e+00 8669.0
1 TraesCS1B01G215700 chr1D 96.294 3832 110 16 43 3858 289959836 289963651 0.000000e+00 6261.0
2 TraesCS1B01G215700 chr1D 87.376 404 38 5 3858 4259 289965396 289965788 7.160000e-123 451.0
3 TraesCS1B01G215700 chr1A 94.278 3565 130 23 45 3579 362402080 362405600 0.000000e+00 5385.0
4 TraesCS1B01G215700 chr1A 90.353 425 41 0 4270 4694 362406984 362407408 4.100000e-155 558.0
5 TraesCS1B01G215700 chr1A 86.866 434 42 5 3841 4268 362406379 362406803 5.500000e-129 472.0
6 TraesCS1B01G215700 chr1A 87.946 224 15 9 3574 3785 362405641 362405864 2.170000e-63 254.0
7 TraesCS1B01G215700 chr1A 82.308 130 16 4 4336 4464 532758590 532758713 6.420000e-19 106.0
8 TraesCS1B01G215700 chr1A 97.059 34 1 0 3803 3836 362406235 362406268 1.820000e-04 58.4
9 TraesCS1B01G215700 chrUn 91.398 93 6 2 4599 4690 22382391 22382482 4.930000e-25 126.0
10 TraesCS1B01G215700 chr5A 91.954 87 5 2 4609 4694 494282236 494282151 2.290000e-23 121.0
11 TraesCS1B01G215700 chr2B 90.805 87 8 0 4608 4694 400821802 400821888 2.970000e-22 117.0
12 TraesCS1B01G215700 chr2B 91.463 82 7 0 4603 4684 177661415 177661496 3.840000e-21 113.0
13 TraesCS1B01G215700 chr5D 89.130 92 10 0 4603 4694 69071353 69071444 1.070000e-21 115.0
14 TraesCS1B01G215700 chr3A 89.773 88 7 2 4608 4694 504627336 504627250 1.380000e-20 111.0
15 TraesCS1B01G215700 chr5B 89.655 87 8 1 4609 4694 372822203 372822289 4.970000e-20 110.0
16 TraesCS1B01G215700 chr2D 88.506 87 8 2 4609 4694 422515393 422515308 2.310000e-18 104.0


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 TraesCS1B01G215700 chr1B 391267263 391271956 4693 False 8669.00 8669 100.0000 1 4694 1 chr1B.!!$F1 4693
1 TraesCS1B01G215700 chr1D 289959836 289965788 5952 False 3356.00 6261 91.8350 43 4259 2 chr1D.!!$F1 4216
2 TraesCS1B01G215700 chr1A 362402080 362407408 5328 False 1345.48 5385 91.3004 45 4694 5 chr1A.!!$F2 4649

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
467 478 0.038892 ACCACACCGACGTCATGTAC 60.039 55.000 19.00 0.00 0.00 2.90 F
930 944 0.539438 TCAACTTCCTTGGCGCCAAT 60.539 50.000 40.03 23.82 35.20 3.16 F
1059 1073 1.279840 GCGCGGAATTGTGGATAGC 59.720 57.895 8.83 0.00 0.00 2.97 F
1473 1493 1.612146 TTCTCCATCGAGGTGGCCA 60.612 57.895 0.00 0.00 39.19 5.36 F
2426 2452 2.401766 GCAGCCGATGACACCAAGG 61.402 63.158 0.00 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 1877 0.260230 TGGAACCCCAGTTTGAGCAA 59.740 50.000 0.00 0.0 37.58 3.91 R
2666 2692 0.882474 CCTTGTCTCGAACCTCGTCT 59.118 55.000 0.00 0.0 41.35 4.18 R
2678 2704 2.214181 CTAGCGACGCCACCTTGTCT 62.214 60.000 17.79 0.0 32.93 3.41 R
3470 3496 1.450312 CGTCTTGAGCCACATCCCC 60.450 63.158 0.00 0.0 0.00 4.81 R
3935 6118 0.620556 CCAATGTCTAGCCAGGGTGT 59.379 55.000 0.00 0.0 0.00 4.16 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
20 21 2.699954 GACTGCCAGCTTTACTTAGCA 58.300 47.619 0.00 0.00 43.68 3.49
23 24 2.699954 TGCCAGCTTTACTTAGCAGAC 58.300 47.619 0.00 0.00 43.68 3.51
24 25 2.038426 TGCCAGCTTTACTTAGCAGACA 59.962 45.455 0.00 0.00 43.68 3.41
25 26 3.074412 GCCAGCTTTACTTAGCAGACAA 58.926 45.455 0.00 0.00 43.68 3.18
26 27 3.126000 GCCAGCTTTACTTAGCAGACAAG 59.874 47.826 0.00 0.00 43.68 3.16
27 28 4.569943 CCAGCTTTACTTAGCAGACAAGA 58.430 43.478 0.00 0.00 43.68 3.02
28 29 5.181748 CCAGCTTTACTTAGCAGACAAGAT 58.818 41.667 0.00 0.00 43.68 2.40
29 30 5.645497 CCAGCTTTACTTAGCAGACAAGATT 59.355 40.000 0.00 0.00 43.68 2.40
30 31 6.402983 CCAGCTTTACTTAGCAGACAAGATTG 60.403 42.308 0.00 0.00 43.68 2.67
31 32 6.148480 CAGCTTTACTTAGCAGACAAGATTGT 59.852 38.462 0.00 0.00 43.68 2.71
32 33 6.370166 AGCTTTACTTAGCAGACAAGATTGTC 59.630 38.462 16.21 16.21 46.13 3.18
60 61 3.778954 AAACTTAGCAGGCAAGAGAGT 57.221 42.857 9.39 0.00 0.00 3.24
76 77 4.489810 AGAGAGTAGAATTTGTCGTGCTG 58.510 43.478 0.00 0.00 0.00 4.41
84 85 5.890334 AGAATTTGTCGTGCTGAAAAAGAA 58.110 33.333 2.19 0.00 37.23 2.52
90 91 4.873827 TGTCGTGCTGAAAAAGAAAGTAGT 59.126 37.500 0.00 0.00 0.00 2.73
91 92 6.044046 TGTCGTGCTGAAAAAGAAAGTAGTA 58.956 36.000 0.00 0.00 0.00 1.82
92 93 6.200286 TGTCGTGCTGAAAAAGAAAGTAGTAG 59.800 38.462 0.00 0.00 0.00 2.57
93 94 6.420008 GTCGTGCTGAAAAAGAAAGTAGTAGA 59.580 38.462 0.00 0.00 0.00 2.59
94 95 6.982141 TCGTGCTGAAAAAGAAAGTAGTAGAA 59.018 34.615 0.00 0.00 0.00 2.10
95 96 7.042925 TCGTGCTGAAAAAGAAAGTAGTAGAAC 60.043 37.037 0.00 0.00 0.00 3.01
96 97 7.042658 CGTGCTGAAAAAGAAAGTAGTAGAACT 60.043 37.037 0.00 0.00 0.00 3.01
97 98 8.613482 GTGCTGAAAAAGAAAGTAGTAGAACTT 58.387 33.333 0.00 0.00 41.46 2.66
99 100 9.439537 GCTGAAAAAGAAAGTAGTAGAACTTTG 57.560 33.333 6.71 0.00 46.92 2.77
148 156 2.609459 AGTGATTAGCAATAGCACACGC 59.391 45.455 0.00 0.00 45.49 5.34
193 201 5.163713 CGTTCTTCTTTGGATCAAATCTCCC 60.164 44.000 0.00 0.00 32.70 4.30
197 205 0.623194 TTGGATCAAATCTCCCGCCA 59.377 50.000 0.00 0.00 31.32 5.69
199 207 0.181350 GGATCAAATCTCCCGCCACT 59.819 55.000 0.00 0.00 0.00 4.00
204 212 2.826777 AAATCTCCCGCCACTGCCAG 62.827 60.000 0.00 0.00 0.00 4.85
272 280 0.757188 AGATCCCCGATCTCGTTGCT 60.757 55.000 0.00 0.00 45.03 3.91
320 330 4.704540 ACGGGCTAATCAATCAATCAAACA 59.295 37.500 0.00 0.00 0.00 2.83
321 331 5.036737 CGGGCTAATCAATCAATCAAACAC 58.963 41.667 0.00 0.00 0.00 3.32
322 332 5.163622 CGGGCTAATCAATCAATCAAACACT 60.164 40.000 0.00 0.00 0.00 3.55
323 333 6.038161 CGGGCTAATCAATCAATCAAACACTA 59.962 38.462 0.00 0.00 0.00 2.74
324 334 7.415095 CGGGCTAATCAATCAATCAAACACTAA 60.415 37.037 0.00 0.00 0.00 2.24
325 335 7.702348 GGGCTAATCAATCAATCAAACACTAAC 59.298 37.037 0.00 0.00 0.00 2.34
326 336 8.462016 GGCTAATCAATCAATCAAACACTAACT 58.538 33.333 0.00 0.00 0.00 2.24
352 362 0.976641 CTAGCCCTGACCACAGTTCA 59.023 55.000 0.00 0.00 42.05 3.18
369 379 1.444933 TCACAACCCAATCAGACCCT 58.555 50.000 0.00 0.00 0.00 4.34
371 381 1.149101 ACAACCCAATCAGACCCTGT 58.851 50.000 0.00 0.00 32.61 4.00
463 474 2.357034 GCACCACACCGACGTCAT 60.357 61.111 17.16 0.00 0.00 3.06
466 477 0.038983 CACCACACCGACGTCATGTA 60.039 55.000 19.00 0.00 0.00 2.29
467 478 0.038892 ACCACACCGACGTCATGTAC 60.039 55.000 19.00 0.00 0.00 2.90
669 681 1.024579 AACGCCGGATCACATCAACC 61.025 55.000 5.05 0.00 0.00 3.77
672 684 1.463674 GCCGGATCACATCAACCTTT 58.536 50.000 5.05 0.00 0.00 3.11
673 685 1.818674 GCCGGATCACATCAACCTTTT 59.181 47.619 5.05 0.00 0.00 2.27
674 686 2.415893 GCCGGATCACATCAACCTTTTG 60.416 50.000 5.05 0.00 0.00 2.44
888 901 1.072266 TGATTGGCTGGTAGGTTGGT 58.928 50.000 0.00 0.00 0.00 3.67
914 928 2.739913 CGGGTTATTCGCTCAACTTCAA 59.260 45.455 0.00 0.00 0.00 2.69
930 944 0.539438 TCAACTTCCTTGGCGCCAAT 60.539 50.000 40.03 23.82 35.20 3.16
1059 1073 1.279840 GCGCGGAATTGTGGATAGC 59.720 57.895 8.83 0.00 0.00 2.97
1238 1252 4.839706 ATGGATGGGGTTGGGCGC 62.840 66.667 0.00 0.00 0.00 6.53
1381 1401 3.785859 TAGCAGCGCCAAGGGGAG 61.786 66.667 2.29 0.00 35.59 4.30
1389 1409 3.322466 CCAAGGGGAGGCAGTCGT 61.322 66.667 0.00 0.00 35.59 4.34
1473 1493 1.612146 TTCTCCATCGAGGTGGCCA 60.612 57.895 0.00 0.00 39.19 5.36
1475 1495 3.723235 CTCCATCGAGGTGGCCACG 62.723 68.421 29.08 18.56 39.19 4.94
2079 2099 3.425578 CTGGTAGACAGGCTCAACG 57.574 57.895 0.00 0.00 43.70 4.10
2426 2452 2.401766 GCAGCCGATGACACCAAGG 61.402 63.158 0.00 0.00 0.00 3.61
2678 2704 3.677527 GGACCAGACGAGGTTCGA 58.322 61.111 5.38 0.00 43.74 3.71
2912 2938 4.829588 GGAAACGATCCGGAGACC 57.170 61.111 11.34 3.00 38.79 3.85
3003 3029 2.835431 AGATGGCCGACGAGGAGG 60.835 66.667 0.00 0.00 45.00 4.30
3137 3163 2.515523 GCCATCCAGCTGCGTGAT 60.516 61.111 8.66 2.87 0.00 3.06
3521 3547 3.918220 GTGAAGATCAGCGCCGCG 61.918 66.667 8.83 8.83 0.00 6.46
3558 3584 2.512515 GGTGGTCGAGCTGATGCC 60.513 66.667 16.64 6.58 40.80 4.40
3587 3659 4.631813 GTGGATGTGTTGGTAGACTTCATC 59.368 45.833 0.00 0.00 34.36 2.92
3682 3756 4.725556 TCGTGCAGTGTTTACAGAATTC 57.274 40.909 0.00 0.00 0.00 2.17
3872 6055 8.786826 TTTTACCACAATTACCAGTCTATCAG 57.213 34.615 0.00 0.00 0.00 2.90
3954 6137 0.620556 ACACCCTGGCTAGACATTGG 59.379 55.000 11.81 11.81 0.00 3.16
3961 6144 0.680921 GGCTAGACATTGGCTTGGCA 60.681 55.000 19.91 0.00 34.71 4.92
3971 6154 0.752054 TGGCTTGGCAGGACTTTTTG 59.248 50.000 3.40 0.00 0.00 2.44
4057 6246 1.068333 CCTTGTTCATTGCTTCCACCG 60.068 52.381 0.00 0.00 0.00 4.94
4073 6262 0.034896 ACCGCATTCTTCTTCACCGT 59.965 50.000 0.00 0.00 0.00 4.83
4078 6267 4.569162 CCGCATTCTTCTTCACCGTATTTA 59.431 41.667 0.00 0.00 0.00 1.40
4084 6273 9.893305 CATTCTTCTTCACCGTATTTACTTTTT 57.107 29.630 0.00 0.00 0.00 1.94
4089 6278 7.222872 TCTTCACCGTATTTACTTTTTGGGTA 58.777 34.615 0.00 0.00 0.00 3.69
4090 6279 7.884354 TCTTCACCGTATTTACTTTTTGGGTAT 59.116 33.333 0.00 0.00 0.00 2.73
4117 6306 6.534079 GCACCGTACTAGACATAACTTTCATT 59.466 38.462 0.00 0.00 0.00 2.57
4129 6318 4.734398 AACTTTCATTGGCACTTTGTCA 57.266 36.364 0.00 0.00 0.00 3.58
4130 6319 4.942761 ACTTTCATTGGCACTTTGTCAT 57.057 36.364 0.00 0.00 29.04 3.06
4179 6368 4.939439 ACGCACCTAACATACTTTAAAGGG 59.061 41.667 19.14 10.79 0.00 3.95
4187 6377 9.311676 CCTAACATACTTTAAAGGGGGTAAAAA 57.688 33.333 19.14 1.62 0.00 1.94
4191 6381 8.598916 ACATACTTTAAAGGGGGTAAAAATTGG 58.401 33.333 19.14 0.00 0.00 3.16
4196 6386 5.811796 AAAGGGGGTAAAAATTGGTACAC 57.188 39.130 0.00 0.00 39.29 2.90
4220 6410 8.087750 CACCTTTTGCTAAATGGAGTAATTCAA 58.912 33.333 15.54 0.00 38.63 2.69
4232 6422 9.696917 AATGGAGTAATTCAAATGAAAACTGTC 57.303 29.630 15.23 9.93 37.61 3.51
4340 6709 2.539476 GGCACAATAATGGCGGAAAAG 58.461 47.619 0.00 0.00 35.20 2.27
4356 6725 4.436986 CGGAAAAGAAATTCTAGCGGAACC 60.437 45.833 0.00 0.00 36.70 3.62
4358 6727 2.311124 AGAAATTCTAGCGGAACCGG 57.689 50.000 15.01 0.00 40.19 5.28
4367 6736 1.004679 GCGGAACCGGTTTCTACCA 60.005 57.895 23.22 0.00 45.31 3.25
4378 6747 3.130516 CGGTTTCTACCAGATAGACTGCA 59.869 47.826 0.00 0.00 45.31 4.41
4394 6763 0.445829 TGCAATTGTACGATGGTGCG 59.554 50.000 12.90 0.00 34.73 5.34
4406 6775 2.253603 GATGGTGCGTTGATTTGAAGC 58.746 47.619 0.00 0.00 0.00 3.86
4407 6776 1.028130 TGGTGCGTTGATTTGAAGCA 58.972 45.000 0.00 0.00 35.27 3.91
4410 6779 3.171277 GGTGCGTTGATTTGAAGCATAC 58.829 45.455 0.00 0.00 40.11 2.39
4457 6826 2.409975 GCGTGTATTGTGTGTAGTGGT 58.590 47.619 0.00 0.00 0.00 4.16
4476 6845 3.373748 TGGTACACATTGCTTTGCTATCG 59.626 43.478 0.00 0.00 0.00 2.92
4478 6847 4.142687 GGTACACATTGCTTTGCTATCGTT 60.143 41.667 0.00 0.00 0.00 3.85
4529 6898 3.433598 GCAGAAATCCACCCACTAGCATA 60.434 47.826 0.00 0.00 0.00 3.14
4534 6903 3.328535 TCCACCCACTAGCATAGATCA 57.671 47.619 0.00 0.00 42.77 2.92
4554 6923 4.785453 CTCGCCACCTGCTTCCCC 62.785 72.222 0.00 0.00 38.05 4.81
4582 6951 0.905357 CACCTCCCTCTTCCATCGTT 59.095 55.000 0.00 0.00 0.00 3.85
4583 6952 0.905357 ACCTCCCTCTTCCATCGTTG 59.095 55.000 0.00 0.00 0.00 4.10
4593 6962 3.803082 CATCGTTGCCACCGCCTG 61.803 66.667 0.00 0.00 0.00 4.85
4605 6974 0.908910 ACCGCCTGGATCACATTGTA 59.091 50.000 0.00 0.00 39.21 2.41
4606 6975 1.134401 ACCGCCTGGATCACATTGTAG 60.134 52.381 0.00 0.00 39.21 2.74
4608 6977 1.134401 CGCCTGGATCACATTGTAGGT 60.134 52.381 0.00 0.00 0.00 3.08
4616 6985 5.414454 TGGATCACATTGTAGGTGCTAAAAC 59.586 40.000 0.00 0.00 36.22 2.43
4617 6986 5.648092 GGATCACATTGTAGGTGCTAAAACT 59.352 40.000 0.00 0.00 36.22 2.66
4619 6988 4.759693 TCACATTGTAGGTGCTAAAACTGG 59.240 41.667 0.00 0.00 36.22 4.00
4625 6994 3.160679 AGGTGCTAAAACTGGCAGATT 57.839 42.857 23.66 13.62 39.22 2.40
4634 7003 0.541863 ACTGGCAGATTTCGGGTAGG 59.458 55.000 23.66 0.00 0.00 3.18
4670 7039 6.406692 TGGTGATCTAAGCTAGATGGTAAC 57.593 41.667 9.53 4.55 45.16 2.50
4685 7054 4.563140 TGGTAACATGGAAAGTAGGGAC 57.437 45.455 0.00 0.00 46.17 4.46
4687 7056 4.259356 GGTAACATGGAAAGTAGGGACAC 58.741 47.826 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.675348 CTGCTAAGTAAAGCTGGCAGTC 59.325 50.000 17.16 8.57 43.43 3.51
1 2 2.303022 TCTGCTAAGTAAAGCTGGCAGT 59.697 45.455 17.16 0.00 45.90 4.40
2 3 2.675348 GTCTGCTAAGTAAAGCTGGCAG 59.325 50.000 10.94 10.94 46.50 4.85
4 5 2.699954 TGTCTGCTAAGTAAAGCTGGC 58.300 47.619 0.00 1.02 43.83 4.85
5 6 4.569943 TCTTGTCTGCTAAGTAAAGCTGG 58.430 43.478 0.00 0.00 43.19 4.85
38 39 4.464947 ACTCTCTTGCCTGCTAAGTTTTT 58.535 39.130 0.00 0.00 0.00 1.94
39 40 4.092116 ACTCTCTTGCCTGCTAAGTTTT 57.908 40.909 0.00 0.00 0.00 2.43
40 41 3.778954 ACTCTCTTGCCTGCTAAGTTT 57.221 42.857 0.00 0.00 0.00 2.66
41 42 4.090090 TCTACTCTCTTGCCTGCTAAGTT 58.910 43.478 0.00 0.00 0.00 2.66
42 43 3.702792 TCTACTCTCTTGCCTGCTAAGT 58.297 45.455 0.00 0.00 0.00 2.24
43 44 4.727507 TTCTACTCTCTTGCCTGCTAAG 57.272 45.455 0.00 0.00 0.00 2.18
44 45 5.683876 AATTCTACTCTCTTGCCTGCTAA 57.316 39.130 0.00 0.00 0.00 3.09
45 46 5.046304 ACAAATTCTACTCTCTTGCCTGCTA 60.046 40.000 0.00 0.00 0.00 3.49
46 47 4.260170 CAAATTCTACTCTCTTGCCTGCT 58.740 43.478 0.00 0.00 0.00 4.24
47 48 4.006319 ACAAATTCTACTCTCTTGCCTGC 58.994 43.478 0.00 0.00 0.00 4.85
48 49 4.328440 CGACAAATTCTACTCTCTTGCCTG 59.672 45.833 0.00 0.00 0.00 4.85
49 50 4.021016 ACGACAAATTCTACTCTCTTGCCT 60.021 41.667 0.00 0.00 0.00 4.75
50 51 4.092091 CACGACAAATTCTACTCTCTTGCC 59.908 45.833 0.00 0.00 0.00 4.52
51 52 4.434857 GCACGACAAATTCTACTCTCTTGC 60.435 45.833 0.00 0.00 0.00 4.01
52 53 4.926238 AGCACGACAAATTCTACTCTCTTG 59.074 41.667 0.00 0.00 0.00 3.02
60 61 6.612247 TCTTTTTCAGCACGACAAATTCTA 57.388 33.333 0.00 0.00 0.00 2.10
84 85 7.282450 CCCTGTTTTGTCAAAGTTCTACTACTT 59.718 37.037 0.00 0.00 39.97 2.24
90 91 6.016610 GCATACCCTGTTTTGTCAAAGTTCTA 60.017 38.462 0.00 0.00 0.00 2.10
91 92 5.221244 GCATACCCTGTTTTGTCAAAGTTCT 60.221 40.000 0.00 0.00 0.00 3.01
92 93 4.982295 GCATACCCTGTTTTGTCAAAGTTC 59.018 41.667 0.00 0.00 0.00 3.01
93 94 4.404073 TGCATACCCTGTTTTGTCAAAGTT 59.596 37.500 0.00 0.00 0.00 2.66
94 95 3.957497 TGCATACCCTGTTTTGTCAAAGT 59.043 39.130 0.00 0.00 0.00 2.66
95 96 4.582701 TGCATACCCTGTTTTGTCAAAG 57.417 40.909 0.00 0.00 0.00 2.77
96 97 4.798924 GCATGCATACCCTGTTTTGTCAAA 60.799 41.667 14.21 0.00 0.00 2.69
97 98 3.305950 GCATGCATACCCTGTTTTGTCAA 60.306 43.478 14.21 0.00 0.00 3.18
98 99 2.230992 GCATGCATACCCTGTTTTGTCA 59.769 45.455 14.21 0.00 0.00 3.58
99 100 2.493278 AGCATGCATACCCTGTTTTGTC 59.507 45.455 21.98 0.00 0.00 3.18
101 102 2.756760 AGAGCATGCATACCCTGTTTTG 59.243 45.455 21.98 0.00 0.00 2.44
148 156 1.135083 AGTCCACGGCAAATCTCTACG 60.135 52.381 0.00 0.00 0.00 3.51
197 205 2.661866 GTTCGTCACGCTGGCAGT 60.662 61.111 17.16 0.00 0.00 4.40
272 280 1.942223 CGTGTCGACTCGTGTGCAA 60.942 57.895 26.93 0.00 0.00 4.08
320 330 5.655974 GGTCAGGGCTAGTTAGTTAGTTAGT 59.344 44.000 0.00 0.00 0.00 2.24
321 331 5.655532 TGGTCAGGGCTAGTTAGTTAGTTAG 59.344 44.000 0.00 0.00 0.00 2.34
322 332 5.420104 GTGGTCAGGGCTAGTTAGTTAGTTA 59.580 44.000 0.00 0.00 0.00 2.24
323 333 4.222366 GTGGTCAGGGCTAGTTAGTTAGTT 59.778 45.833 0.00 0.00 0.00 2.24
324 334 3.768215 GTGGTCAGGGCTAGTTAGTTAGT 59.232 47.826 0.00 0.00 0.00 2.24
325 335 3.767673 TGTGGTCAGGGCTAGTTAGTTAG 59.232 47.826 0.00 0.00 0.00 2.34
326 336 3.767673 CTGTGGTCAGGGCTAGTTAGTTA 59.232 47.826 0.00 0.00 37.97 2.24
327 337 2.567615 CTGTGGTCAGGGCTAGTTAGTT 59.432 50.000 0.00 0.00 37.97 2.24
328 338 2.180276 CTGTGGTCAGGGCTAGTTAGT 58.820 52.381 0.00 0.00 37.97 2.24
329 339 2.180276 ACTGTGGTCAGGGCTAGTTAG 58.820 52.381 0.00 0.00 45.14 2.34
330 340 2.320681 ACTGTGGTCAGGGCTAGTTA 57.679 50.000 0.00 0.00 45.14 2.24
331 341 1.348036 GAACTGTGGTCAGGGCTAGTT 59.652 52.381 0.00 0.00 45.14 2.24
332 342 0.977395 GAACTGTGGTCAGGGCTAGT 59.023 55.000 0.00 0.00 45.14 2.57
333 343 0.976641 TGAACTGTGGTCAGGGCTAG 59.023 55.000 0.47 0.00 45.14 3.42
352 362 1.149101 ACAGGGTCTGATTGGGTTGT 58.851 50.000 1.59 0.00 35.18 3.32
369 379 1.764571 GAGCAGTGGTGGTGGGTACA 61.765 60.000 0.00 0.00 33.41 2.90
371 381 2.221299 GGAGCAGTGGTGGTGGGTA 61.221 63.158 0.00 0.00 33.41 3.69
463 474 2.477694 CGCCTGGATTACGTTACGTACA 60.478 50.000 17.53 11.25 42.13 2.90
466 477 0.810648 TCGCCTGGATTACGTTACGT 59.189 50.000 16.31 16.31 44.35 3.57
467 478 1.850441 CTTCGCCTGGATTACGTTACG 59.150 52.381 2.19 2.19 0.00 3.18
468 479 1.591619 GCTTCGCCTGGATTACGTTAC 59.408 52.381 0.00 0.00 0.00 2.50
469 480 1.205179 TGCTTCGCCTGGATTACGTTA 59.795 47.619 0.00 0.00 0.00 3.18
470 481 0.036765 TGCTTCGCCTGGATTACGTT 60.037 50.000 0.00 0.00 0.00 3.99
669 681 2.499303 ATCGGGGGTCAGGGCAAAAG 62.499 60.000 0.00 0.00 0.00 2.27
672 684 3.407967 GATCGGGGGTCAGGGCAA 61.408 66.667 0.00 0.00 0.00 4.52
673 685 4.731853 TGATCGGGGGTCAGGGCA 62.732 66.667 0.00 0.00 0.00 5.36
674 686 2.978946 TTTGATCGGGGGTCAGGGC 61.979 63.158 0.00 0.00 0.00 5.19
743 756 0.937304 GACTTGTCAGCGCTCAACAA 59.063 50.000 25.32 25.32 0.00 2.83
888 901 0.614294 TGAGCGAATAACCCGGGAAA 59.386 50.000 32.02 15.55 0.00 3.13
914 928 3.685435 CATTGGCGCCAAGGAAGT 58.315 55.556 42.54 25.79 39.72 3.01
930 944 4.710695 CTGCCGTCGTGTACCGCA 62.711 66.667 0.00 0.00 39.56 5.69
1059 1073 2.124693 GCTCTCCTCCTCGACCAGG 61.125 68.421 0.00 0.00 45.15 4.45
1381 1401 4.357947 TGCTCCACGACGACTGCC 62.358 66.667 0.00 0.00 0.00 4.85
1384 1404 2.986413 AGCTGCTCCACGACGACT 60.986 61.111 0.00 0.00 0.00 4.18
1389 1409 2.659016 CTTCCAGCTGCTCCACGA 59.341 61.111 8.66 0.00 0.00 4.35
1448 1468 0.388659 CCTCGATGGAGAAGAGGCAG 59.611 60.000 6.27 0.00 44.09 4.85
1485 1505 4.195334 GTCCATGGAGGCCGGCAT 62.195 66.667 30.85 24.69 37.29 4.40
1622 1642 1.429463 CGGTGAAGTAGAGGTTGCAC 58.571 55.000 0.00 0.00 0.00 4.57
1857 1877 0.260230 TGGAACCCCAGTTTGAGCAA 59.740 50.000 0.00 0.00 37.58 3.91
2300 2326 3.083349 TGATGACCGGCTCCCCTG 61.083 66.667 0.00 0.00 0.00 4.45
2666 2692 0.882474 CCTTGTCTCGAACCTCGTCT 59.118 55.000 0.00 0.00 41.35 4.18
2678 2704 2.214181 CTAGCGACGCCACCTTGTCT 62.214 60.000 17.79 0.00 32.93 3.41
2912 2938 2.898729 ATGCGAGTACCTCATCCAAG 57.101 50.000 0.00 0.00 0.00 3.61
3003 3029 3.330853 CGCTACCTCGAATGGCGC 61.331 66.667 12.93 0.00 39.42 6.53
3008 3034 4.587189 GCCGGCGCTACCTCGAAT 62.587 66.667 12.58 0.00 35.61 3.34
3236 3262 2.919856 ACGTGCAGGCTCCTCACT 60.920 61.111 6.26 0.00 0.00 3.41
3275 3301 4.367023 CCGCCGACTCCCGACAAA 62.367 66.667 0.00 0.00 41.76 2.83
3470 3496 1.450312 CGTCTTGAGCCACATCCCC 60.450 63.158 0.00 0.00 0.00 4.81
3521 3547 3.434319 CCATGTCACGTGCTGCCC 61.434 66.667 11.67 0.00 0.00 5.36
3542 3568 2.103042 GTGGCATCAGCTCGACCAC 61.103 63.158 8.50 8.50 43.57 4.16
3792 3877 9.378551 AGAACGAGTAAATATTTTGCTACATGA 57.621 29.630 5.91 0.00 0.00 3.07
3935 6118 0.620556 CCAATGTCTAGCCAGGGTGT 59.379 55.000 0.00 0.00 0.00 4.16
3941 6124 0.680921 GCCAAGCCAATGTCTAGCCA 60.681 55.000 0.00 0.00 0.00 4.75
3954 6137 2.101415 AGAACAAAAAGTCCTGCCAAGC 59.899 45.455 0.00 0.00 0.00 4.01
3961 6144 8.157476 ACATACACTATGAGAACAAAAAGTCCT 58.843 33.333 0.00 0.00 39.45 3.85
4023 6212 1.595311 ACAAGGACCTGCATATCCCA 58.405 50.000 11.80 0.00 35.38 4.37
4033 6222 2.158475 TGGAAGCAATGAACAAGGACCT 60.158 45.455 0.00 0.00 0.00 3.85
4057 6246 6.663944 AGTAAATACGGTGAAGAAGAATGC 57.336 37.500 0.00 0.00 0.00 3.56
4089 6278 5.593679 AGTTATGTCTAGTACGGTGCAAT 57.406 39.130 0.00 0.00 0.00 3.56
4090 6279 5.395682 AAGTTATGTCTAGTACGGTGCAA 57.604 39.130 0.00 0.00 0.00 4.08
4096 6285 6.533723 TGCCAATGAAAGTTATGTCTAGTACG 59.466 38.462 0.00 0.00 0.00 3.67
4117 6306 5.451242 GGTTCTTTTACATGACAAAGTGCCA 60.451 40.000 16.10 1.17 32.67 4.92
4129 6318 4.631813 GCATCTCGAGTGGTTCTTTTACAT 59.368 41.667 13.13 0.00 0.00 2.29
4130 6319 3.994392 GCATCTCGAGTGGTTCTTTTACA 59.006 43.478 13.13 0.00 0.00 2.41
4166 6355 8.598916 ACCAATTTTTACCCCCTTTAAAGTATG 58.401 33.333 14.03 4.35 0.00 2.39
4179 6368 5.467399 GCAAAAGGTGTACCAATTTTTACCC 59.533 40.000 3.56 0.00 38.89 3.69
4187 6377 5.777732 TCCATTTAGCAAAAGGTGTACCAAT 59.222 36.000 3.56 0.00 38.89 3.16
4191 6381 5.959618 ACTCCATTTAGCAAAAGGTGTAC 57.040 39.130 8.04 0.00 0.00 2.90
4196 6386 9.657419 ATTTGAATTACTCCATTTAGCAAAAGG 57.343 29.630 0.00 0.00 0.00 3.11
4220 6410 8.706322 AGTTACCCTATTTGACAGTTTTCATT 57.294 30.769 0.00 0.00 0.00 2.57
4268 6458 6.373759 AGAGTGAATTCCATATTTAACCCCC 58.626 40.000 2.27 0.00 0.00 5.40
4301 6670 5.163457 TGTGCCATAGAGACGATGAATGTAA 60.163 40.000 0.00 0.00 0.00 2.41
4302 6671 4.340950 TGTGCCATAGAGACGATGAATGTA 59.659 41.667 0.00 0.00 0.00 2.29
4317 6686 2.647683 TCCGCCATTATTGTGCCATA 57.352 45.000 0.00 0.00 0.00 2.74
4318 6687 1.774110 TTCCGCCATTATTGTGCCAT 58.226 45.000 0.00 0.00 0.00 4.40
4321 6690 3.502191 TCTTTTCCGCCATTATTGTGC 57.498 42.857 0.00 0.00 0.00 4.57
4326 6695 6.513393 CGCTAGAATTTCTTTTCCGCCATTAT 60.513 38.462 3.86 0.00 0.00 1.28
4327 6696 5.220777 CGCTAGAATTTCTTTTCCGCCATTA 60.221 40.000 3.86 0.00 0.00 1.90
4330 6699 2.418628 CGCTAGAATTTCTTTTCCGCCA 59.581 45.455 3.86 0.00 0.00 5.69
4332 6701 2.676342 TCCGCTAGAATTTCTTTTCCGC 59.324 45.455 3.86 0.33 0.00 5.54
4340 6709 2.019948 ACCGGTTCCGCTAGAATTTC 57.980 50.000 0.00 0.00 36.69 2.17
4358 6727 6.595716 ACAATTGCAGTCTATCTGGTAGAAAC 59.404 38.462 5.05 0.00 41.00 2.78
4367 6736 5.163405 ACCATCGTACAATTGCAGTCTATCT 60.163 40.000 5.05 0.00 0.00 1.98
4378 6747 2.418692 TCAACGCACCATCGTACAATT 58.581 42.857 0.00 0.00 42.46 2.32
4410 6779 9.862371 CCTAGCTATGTTTGACTATGGTATAAG 57.138 37.037 0.00 0.00 0.00 1.73
4457 6826 5.049060 ACAAACGATAGCAAAGCAATGTGTA 60.049 36.000 0.00 0.00 42.67 2.90
4471 6840 1.260561 GCGGGCATGTACAAACGATAG 59.739 52.381 0.00 0.00 46.19 2.08
4476 6845 3.066064 TCAATATGCGGGCATGTACAAAC 59.934 43.478 16.03 0.00 37.82 2.93
4478 6847 2.924421 TCAATATGCGGGCATGTACAA 58.076 42.857 16.03 0.00 37.82 2.41
4529 6898 1.220206 CAGGTGGCGAGCTTGATCT 59.780 57.895 4.70 0.00 0.00 2.75
4554 6923 3.604582 GAAGAGGGAGGTGATGAACTTG 58.395 50.000 0.00 0.00 0.00 3.16
4593 6962 5.648092 AGTTTTAGCACCTACAATGTGATCC 59.352 40.000 0.00 0.00 35.74 3.36
4605 6974 2.887151 ATCTGCCAGTTTTAGCACCT 57.113 45.000 0.00 0.00 34.68 4.00
4606 6975 3.670627 CGAAATCTGCCAGTTTTAGCACC 60.671 47.826 0.87 0.00 34.68 5.01
4608 6977 2.487762 CCGAAATCTGCCAGTTTTAGCA 59.512 45.455 0.87 0.00 37.46 3.49
4616 6985 0.179045 CCCTACCCGAAATCTGCCAG 60.179 60.000 0.00 0.00 0.00 4.85
4617 6986 1.632018 CCCCTACCCGAAATCTGCCA 61.632 60.000 0.00 0.00 0.00 4.92
4619 6988 1.148498 CCCCCTACCCGAAATCTGC 59.852 63.158 0.00 0.00 0.00 4.26
4656 7025 6.067217 ACTTTCCATGTTACCATCTAGCTT 57.933 37.500 0.00 0.00 0.00 3.74
4670 7039 3.198068 CATCGTGTCCCTACTTTCCATG 58.802 50.000 0.00 0.00 0.00 3.66
4672 7041 2.253610 ACATCGTGTCCCTACTTTCCA 58.746 47.619 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.