Multiple sequence alignment - TraesCS6A01G244400

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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 TraesCS6A01G244400 chr6A 100.000 5312 0 0 1 5312 455709415 455704104 0.000000e+00 9810.0
1 TraesCS6A01G244400 chr6D 94.629 1750 52 17 917 2624 318151673 318149924 0.000000e+00 2673.0
2 TraesCS6A01G244400 chr6D 98.046 1177 18 2 2624 3800 318149816 318148645 0.000000e+00 2041.0
3 TraesCS6A01G244400 chr6D 92.482 1104 51 12 3801 4881 318148613 318147519 0.000000e+00 1550.0
4 TraesCS6A01G244400 chr6D 88.261 690 62 9 244 915 6387636 6388324 0.000000e+00 808.0
5 TraesCS6A01G244400 chr6D 92.829 251 18 0 1 251 6387444 6387694 1.090000e-96 364.0
6 TraesCS6A01G244400 chr6D 89.928 139 13 1 5175 5312 318147013 318146875 1.520000e-40 178.0
7 TraesCS6A01G244400 chr6D 100.000 28 0 0 3826 3853 157659493 157659520 1.000000e-02 52.8
8 TraesCS6A01G244400 chr6B 93.504 1755 64 21 912 2624 506126237 506127983 0.000000e+00 2564.0
9 TraesCS6A01G244400 chr6B 98.467 1174 18 0 2624 3797 506128091 506129264 0.000000e+00 2069.0
10 TraesCS6A01G244400 chr6B 96.213 713 15 3 3801 4511 506129299 506130001 0.000000e+00 1157.0
11 TraesCS6A01G244400 chr6B 87.324 639 43 19 4544 5148 506130297 506130931 0.000000e+00 697.0
12 TraesCS6A01G244400 chr6B 90.000 140 13 1 5174 5312 506130927 506131066 4.230000e-41 180.0
13 TraesCS6A01G244400 chr5D 81.559 808 93 31 123 915 469404565 469403799 2.720000e-172 616.0
14 TraesCS6A01G244400 chr5D 88.889 99 9 1 1 99 469404610 469404514 2.600000e-23 121.0
15 TraesCS6A01G244400 chr5D 94.444 36 2 0 3826 3861 536420364 536420329 7.430000e-04 56.5
16 TraesCS6A01G244400 chr5B 81.222 671 94 16 244 900 576867128 576866476 3.670000e-141 512.0
17 TraesCS6A01G244400 chr5B 86.869 99 9 2 1 99 576867242 576867148 2.020000e-19 108.0
18 TraesCS6A01G244400 chr5B 100.000 29 0 0 3821 3849 284835384 284835412 3.000000e-03 54.7
19 TraesCS6A01G244400 chr7B 81.743 482 67 13 437 915 533383663 533383200 3.000000e-102 383.0
20 TraesCS6A01G244400 chr3D 96.970 33 1 0 3826 3858 429043529 429043497 7.430000e-04 56.5
21 TraesCS6A01G244400 chr3D 96.970 33 1 0 3821 3853 564658110 564658078 7.430000e-04 56.5
22 TraesCS6A01G244400 chr7D 100.000 29 0 0 3828 3856 310990281 310990309 3.000000e-03 54.7
23 TraesCS6A01G244400 chr7A 100.000 29 0 0 3828 3856 368242192 368242220 3.000000e-03 54.7


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 TraesCS6A01G244400 chr6A 455704104 455709415 5311 True 9810.0 9810 100.00000 1 5312 1 chr6A.!!$R1 5311
1 TraesCS6A01G244400 chr6D 318146875 318151673 4798 True 1610.5 2673 93.77125 917 5312 4 chr6D.!!$R1 4395
2 TraesCS6A01G244400 chr6D 6387444 6388324 880 False 586.0 808 90.54500 1 915 2 chr6D.!!$F2 914
3 TraesCS6A01G244400 chr6B 506126237 506131066 4829 False 1333.4 2564 93.10160 912 5312 5 chr6B.!!$F1 4400
4 TraesCS6A01G244400 chr5D 469403799 469404610 811 True 368.5 616 85.22400 1 915 2 chr5D.!!$R2 914
5 TraesCS6A01G244400 chr5B 576866476 576867242 766 True 310.0 512 84.04550 1 900 2 chr5B.!!$R1 899

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
558 591 0.026803 GCTAAAATGGAGCAGTCGCG 59.973 55.000 0.00 0.00 45.49 5.87 F
788 840 0.321346 TGAGATGGTGATGCGTGTGT 59.679 50.000 0.00 0.00 0.00 3.72 F
1357 1420 0.536460 CGCCGGCCCAGGTTATTAAT 60.536 55.000 23.46 0.00 0.00 1.40 F
1359 1422 1.477923 GCCGGCCCAGGTTATTAATCA 60.478 52.381 18.11 0.00 0.00 2.57 F
1483 1565 1.957113 GCAAGAGCCAATTGGTAGCCT 60.957 52.381 25.19 13.74 37.57 4.58 F
1915 2021 3.117169 TGCTTGATTACCATATTGGGGCT 60.117 43.478 0.00 0.00 43.37 5.19 F
3818 4063 0.460109 CGTCATGCACTCCATCCGAA 60.460 55.000 0.00 0.00 30.70 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1458 1.618861 CGAGTAGTAGTGTGCAGTGC 58.381 55.000 8.58 8.58 0.00 4.40 R
1625 1727 1.878953 ACAACCAAACGCTACTGAGG 58.121 50.000 0.00 0.00 0.00 3.86 R
2322 2428 4.143473 GCAAATCATGAAAAGTTGCTCACG 60.143 41.667 20.65 0.00 41.04 4.35 R
3124 3338 5.512942 TGGATCAAAAGGAGGTGATGTTA 57.487 39.130 0.00 0.00 34.61 2.41 R
3412 3626 0.542232 ACCGAGTAGCCTGTCTGGTT 60.542 55.000 0.00 0.00 38.35 3.67 R
3862 4107 0.604780 GCGGGATCTGACATCCATGG 60.605 60.000 4.97 4.97 39.93 3.66 R
5287 6051 0.032515 TGATCCTCCCGCCTACAGAA 60.033 55.000 0.00 0.00 0.00 3.02 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
89 90 3.451556 GATGCTGCTCTGGGCGCTA 62.452 63.158 7.64 0.00 45.43 4.26
96 97 1.522092 CTCTGGGCGCTACAATGGA 59.478 57.895 7.64 0.34 0.00 3.41
176 177 2.674033 TGCTGCAATGGAGCGCTT 60.674 55.556 21.18 0.00 39.47 4.68
241 246 4.742201 GCTGCGACGGAGCTTCCA 62.742 66.667 30.91 1.47 35.91 3.53
242 247 2.507992 CTGCGACGGAGCTTCCAG 60.508 66.667 2.61 0.00 35.91 3.86
243 248 4.742201 TGCGACGGAGCTTCCAGC 62.742 66.667 0.00 0.00 42.84 4.85
252 257 2.202570 GCTTCCAGCGCTGCAATG 60.203 61.111 31.96 21.98 0.00 2.82
253 258 2.488355 CTTCCAGCGCTGCAATGG 59.512 61.111 31.96 19.05 35.30 3.16
254 259 3.695022 CTTCCAGCGCTGCAATGGC 62.695 63.158 31.96 2.47 41.68 4.40
261 266 4.527157 GCTGCAATGGCGCTCGAC 62.527 66.667 7.64 0.00 45.35 4.20
262 267 3.120385 CTGCAATGGCGCTCGACA 61.120 61.111 7.64 0.00 45.35 4.35
263 268 3.092192 CTGCAATGGCGCTCGACAG 62.092 63.158 7.64 5.47 45.35 3.51
264 269 3.121030 GCAATGGCGCTCGACAGT 61.121 61.111 7.64 0.00 36.12 3.55
265 270 2.780643 CAATGGCGCTCGACAGTG 59.219 61.111 11.14 11.14 42.86 3.66
266 271 2.434884 AATGGCGCTCGACAGTGG 60.435 61.111 7.64 0.00 36.12 4.00
271 276 4.803426 CGCTCGACAGTGGCTCCC 62.803 72.222 0.00 0.00 0.00 4.30
272 277 4.803426 GCTCGACAGTGGCTCCCG 62.803 72.222 0.00 0.00 0.00 5.14
273 278 3.062466 CTCGACAGTGGCTCCCGA 61.062 66.667 0.00 0.00 0.00 5.14
274 279 3.343788 CTCGACAGTGGCTCCCGAC 62.344 68.421 0.00 0.00 0.00 4.79
275 280 4.778415 CGACAGTGGCTCCCGACG 62.778 72.222 0.00 0.00 0.00 5.12
291 296 2.430921 CGCTGCGACGGAACTTCT 60.431 61.111 18.66 0.00 0.00 2.85
374 407 0.730494 GAACGCTGCAATGGAGCAAC 60.730 55.000 25.49 12.33 45.13 4.17
447 480 1.974875 CAGGTGCTGCAATGGAGCA 60.975 57.895 25.19 25.19 44.22 4.26
454 487 0.671472 CTGCAATGGAGCACTCGACA 60.671 55.000 0.00 0.00 40.11 4.35
464 497 2.673341 ACTCGACAGCGGCTCTCA 60.673 61.111 0.00 0.00 38.28 3.27
500 533 2.324330 CCGACGTTGCAATGGAGCA 61.324 57.895 22.20 0.00 43.99 4.26
513 546 2.048127 GAGCACTCGCCGAGGTTT 60.048 61.111 19.61 2.49 39.83 3.27
558 591 0.026803 GCTAAAATGGAGCAGTCGCG 59.973 55.000 0.00 0.00 45.49 5.87
585 619 1.089920 GTCCAATGCTGCGATGAAGT 58.910 50.000 6.11 0.00 0.00 3.01
668 712 1.674322 GGCCCGTTACAGCACACAT 60.674 57.895 0.00 0.00 0.00 3.21
697 741 2.849880 TGAGTGTTTCTTTGCAGCAC 57.150 45.000 0.00 0.00 0.00 4.40
708 752 4.008933 GCAGCACCACCGGAGAGT 62.009 66.667 9.46 0.00 0.00 3.24
711 755 1.610673 AGCACCACCGGAGAGTGAT 60.611 57.895 21.72 15.30 40.34 3.06
715 759 2.362369 CCACCGGAGAGTGATGGCT 61.362 63.158 9.46 0.00 40.34 4.75
718 762 1.414181 CACCGGAGAGTGATGGCTAAT 59.586 52.381 9.46 0.00 40.34 1.73
760 811 1.224592 GATTGCCGATGTGAGGGGT 59.775 57.895 0.00 0.00 0.00 4.95
777 828 1.153289 GTGCGATGCCTGAGATGGT 60.153 57.895 0.00 0.00 0.00 3.55
788 840 0.321346 TGAGATGGTGATGCGTGTGT 59.679 50.000 0.00 0.00 0.00 3.72
806 858 3.351416 TGCTCAGTGCAGCAAGCG 61.351 61.111 12.00 0.00 46.65 4.68
807 859 3.812865 TGCTCAGTGCAGCAAGCGA 62.813 57.895 12.00 1.94 46.65 4.93
817 876 1.153086 AGCAAGCGATGTGGGATCC 60.153 57.895 1.92 1.92 0.00 3.36
945 1004 1.972660 AATACCACGCTGAGGGAGGC 61.973 60.000 12.62 0.00 30.21 4.70
1356 1419 1.153127 CGCCGGCCCAGGTTATTAA 60.153 57.895 23.46 0.00 0.00 1.40
1357 1420 0.536460 CGCCGGCCCAGGTTATTAAT 60.536 55.000 23.46 0.00 0.00 1.40
1359 1422 1.477923 GCCGGCCCAGGTTATTAATCA 60.478 52.381 18.11 0.00 0.00 2.57
1360 1423 2.817839 GCCGGCCCAGGTTATTAATCAT 60.818 50.000 18.11 0.00 0.00 2.45
1362 1425 3.506067 CCGGCCCAGGTTATTAATCATTC 59.494 47.826 0.00 0.00 0.00 2.67
1363 1426 3.506067 CGGCCCAGGTTATTAATCATTCC 59.494 47.826 0.00 0.00 0.00 3.01
1370 1452 8.873144 CCCAGGTTATTAATCATTCCAATCAAT 58.127 33.333 0.00 0.00 0.00 2.57
1452 1534 3.902881 TGTTGGTTTGGCTCAAATGTT 57.097 38.095 4.07 0.00 35.74 2.71
1483 1565 1.957113 GCAAGAGCCAATTGGTAGCCT 60.957 52.381 25.19 13.74 37.57 4.58
1491 1575 6.213397 AGAGCCAATTGGTAGCCTTTTATTTT 59.787 34.615 25.19 0.00 37.57 1.82
1492 1576 7.398904 AGAGCCAATTGGTAGCCTTTTATTTTA 59.601 33.333 25.19 0.00 37.57 1.52
1493 1577 8.089625 AGCCAATTGGTAGCCTTTTATTTTAT 57.910 30.769 25.19 0.00 37.57 1.40
1494 1578 9.207868 AGCCAATTGGTAGCCTTTTATTTTATA 57.792 29.630 25.19 0.00 37.57 0.98
1569 1667 5.871524 GCGAGCTCAAATATTCTGATCCATA 59.128 40.000 15.40 0.00 0.00 2.74
1575 1676 8.457261 GCTCAAATATTCTGATCCATATTGTCC 58.543 37.037 0.00 0.00 0.00 4.02
1625 1727 8.433421 TTTCTACCATCGAATAGGTTGATTTC 57.567 34.615 15.69 0.00 38.94 2.17
1725 1831 6.016024 TCTGCTCAAATAACATGTTTGCTTCT 60.016 34.615 17.78 0.00 36.69 2.85
1915 2021 3.117169 TGCTTGATTACCATATTGGGGCT 60.117 43.478 0.00 0.00 43.37 5.19
2312 2418 7.537715 TCCATGATTTATAACTTGCAACACAG 58.462 34.615 0.00 0.00 0.00 3.66
2322 2428 3.308866 ACTTGCAACACAGTACGAGTTTC 59.691 43.478 0.00 0.00 0.00 2.78
2706 2920 6.834168 TTAAATGTTCTCCCTTTGTCATCC 57.166 37.500 0.00 0.00 0.00 3.51
2737 2951 8.450964 TCATTGGCTTCTTAGAATTTAGAAACG 58.549 33.333 0.00 0.00 30.55 3.60
3499 3713 2.879103 TTCTCGCTCCCTTGGAAAAT 57.121 45.000 0.00 0.00 0.00 1.82
3797 4011 7.432869 AGCTATTACATGAATCAGAGTCTGAC 58.567 38.462 24.93 13.77 43.63 3.51
3818 4063 0.460109 CGTCATGCACTCCATCCGAA 60.460 55.000 0.00 0.00 30.70 4.30
3819 4064 1.807755 CGTCATGCACTCCATCCGAAT 60.808 52.381 0.00 0.00 30.70 3.34
3858 4103 2.423538 CGGAGGGAGTAGCAAAATTTGG 59.576 50.000 7.89 0.00 0.00 3.28
3862 4107 3.448660 AGGGAGTAGCAAAATTTGGCATC 59.551 43.478 19.63 13.19 0.00 3.91
3948 4193 1.349688 GTGTATGTTCCTGTGGACCCA 59.650 52.381 0.00 0.00 0.00 4.51
4104 4349 9.329913 CATTACAAAAATGTGCTGTAGTAGTTC 57.670 33.333 0.00 0.00 0.00 3.01
4281 4526 2.022129 GGACCACTCGTCTGTTGCG 61.022 63.158 0.00 0.00 41.64 4.85
4284 4529 0.601558 ACCACTCGTCTGTTGCGTAT 59.398 50.000 0.00 0.00 0.00 3.06
4419 4666 3.304525 GCTCGAAGCCGTATGTGTAGTAT 60.305 47.826 0.00 0.00 34.48 2.12
4519 4766 3.550842 GCGAAAGTTTTGTTGAGCAGGAT 60.551 43.478 4.76 0.00 0.00 3.24
4531 4778 2.289010 TGAGCAGGATACACACACACAG 60.289 50.000 0.00 0.00 41.41 3.66
4737 5248 6.317789 TGACAGGAACATGATTTTGAGTTC 57.682 37.500 0.00 0.00 39.59 3.01
4774 5285 2.679996 TGGGCTCTGCTCGCTGTA 60.680 61.111 0.00 0.00 0.00 2.74
4824 5341 2.426651 GGCTCAGCCTCCACGTATA 58.573 57.895 9.09 0.00 46.69 1.47
4826 5343 1.344763 GGCTCAGCCTCCACGTATATT 59.655 52.381 9.09 0.00 46.69 1.28
4835 5352 6.481976 CAGCCTCCACGTATATTTATCAACAA 59.518 38.462 0.00 0.00 0.00 2.83
4842 5359 9.916397 CCACGTATATTTATCAACAAAAGAGAC 57.084 33.333 0.00 0.00 0.00 3.36
4883 5647 9.941664 CAATGAGACAAATAATATGGAACTGTC 57.058 33.333 0.00 0.00 33.51 3.51
4912 5676 3.171949 CGAAGGACGGTAGGACTCT 57.828 57.895 0.00 0.00 38.46 3.24
4913 5677 1.461559 CGAAGGACGGTAGGACTCTT 58.538 55.000 0.00 0.00 38.46 2.85
4915 5679 3.012518 CGAAGGACGGTAGGACTCTTAA 58.987 50.000 0.00 0.00 38.46 1.85
4916 5680 3.181502 CGAAGGACGGTAGGACTCTTAAC 60.182 52.174 0.00 0.00 38.46 2.01
4917 5681 3.446442 AGGACGGTAGGACTCTTAACA 57.554 47.619 0.00 0.00 0.00 2.41
4918 5682 3.087781 AGGACGGTAGGACTCTTAACAC 58.912 50.000 0.00 0.00 0.00 3.32
4928 5692 3.718097 CTTAACACGCGCCGGCAA 61.718 61.111 28.98 10.28 39.92 4.52
4962 5726 4.927978 ATAGAATGGACCTGAAGACGAG 57.072 45.455 0.00 0.00 0.00 4.18
4988 5752 4.861102 ATTCTTGAAAAAGAGCTGTGGG 57.139 40.909 0.00 0.00 0.00 4.61
4990 5754 4.431416 TCTTGAAAAAGAGCTGTGGGTA 57.569 40.909 0.00 0.00 0.00 3.69
5016 5780 6.428159 AGCCCTTCGTAAAATATATCTGCAAG 59.572 38.462 0.00 0.00 0.00 4.01
5028 5792 1.817357 TCTGCAAGCTGTGAAGATGG 58.183 50.000 3.28 0.00 36.94 3.51
5071 5835 4.285517 ACATCATCAAGTGTCACCTTCTCT 59.714 41.667 0.00 0.00 0.00 3.10
5080 5844 3.869246 GTGTCACCTTCTCTCGAACAAAA 59.131 43.478 0.00 0.00 0.00 2.44
5090 5854 8.668353 CCTTCTCTCGAACAAAATGAATATGAA 58.332 33.333 0.00 0.00 0.00 2.57
5094 5858 7.688372 TCTCGAACAAAATGAATATGAAGCTC 58.312 34.615 0.00 0.00 0.00 4.09
5118 5882 1.362717 GCTTAGTCCGGCGATGCTA 59.637 57.895 9.30 4.64 0.00 3.49
5165 5929 2.668632 GGACATTGTCCCGGCAGA 59.331 61.111 23.00 0.00 46.19 4.26
5166 5930 1.745489 GGACATTGTCCCGGCAGAC 60.745 63.158 23.00 0.00 46.19 3.51
5167 5931 1.003839 GACATTGTCCCGGCAGACA 60.004 57.895 9.23 9.23 44.89 3.41
5172 5936 2.678786 TGTCCCGGCAGACAATAGT 58.321 52.632 10.70 0.00 43.65 2.12
5173 5937 1.855295 TGTCCCGGCAGACAATAGTA 58.145 50.000 10.70 0.00 43.65 1.82
5174 5938 1.754803 TGTCCCGGCAGACAATAGTAG 59.245 52.381 10.70 0.00 43.65 2.57
5175 5939 0.750850 TCCCGGCAGACAATAGTAGC 59.249 55.000 0.00 0.00 0.00 3.58
5176 5940 0.464036 CCCGGCAGACAATAGTAGCA 59.536 55.000 0.00 0.00 32.30 3.49
5177 5941 1.571919 CCGGCAGACAATAGTAGCAC 58.428 55.000 0.00 0.00 32.30 4.40
5178 5942 1.137086 CCGGCAGACAATAGTAGCACT 59.863 52.381 0.00 0.00 32.30 4.40
5179 5943 2.464865 CGGCAGACAATAGTAGCACTC 58.535 52.381 0.00 0.00 32.30 3.51
5180 5944 2.464865 GGCAGACAATAGTAGCACTCG 58.535 52.381 0.00 0.00 32.30 4.18
5181 5945 2.099263 GGCAGACAATAGTAGCACTCGA 59.901 50.000 0.00 0.00 32.30 4.04
5182 5946 3.428999 GGCAGACAATAGTAGCACTCGAA 60.429 47.826 0.00 0.00 32.30 3.71
5183 5947 4.174009 GCAGACAATAGTAGCACTCGAAA 58.826 43.478 0.00 0.00 0.00 3.46
5184 5948 4.806247 GCAGACAATAGTAGCACTCGAAAT 59.194 41.667 0.00 0.00 0.00 2.17
5185 5949 5.051374 GCAGACAATAGTAGCACTCGAAATC 60.051 44.000 0.00 0.00 0.00 2.17
5193 5957 1.144969 GCACTCGAAATCGGTTGTCA 58.855 50.000 2.63 0.00 40.29 3.58
5197 5961 3.493129 CACTCGAAATCGGTTGTCAAAGA 59.507 43.478 2.63 0.00 40.29 2.52
5206 5970 4.312443 TCGGTTGTCAAAGATCCTGTAAC 58.688 43.478 0.00 0.00 0.00 2.50
5208 5972 4.152402 CGGTTGTCAAAGATCCTGTAACAG 59.848 45.833 0.00 0.00 0.00 3.16
5237 6001 3.843422 ACCCAACATGATTCTGGAACAA 58.157 40.909 0.00 0.00 38.70 2.83
5243 6007 1.234821 TGATTCTGGAACAACCGCAC 58.765 50.000 0.00 0.00 42.61 5.34
5244 6008 0.521735 GATTCTGGAACAACCGCACC 59.478 55.000 0.00 0.00 42.61 5.01
5254 6018 2.961893 AACCGCACCAATCGCCCTA 61.962 57.895 0.00 0.00 0.00 3.53
5304 6068 1.209747 GTTTTCTGTAGGCGGGAGGAT 59.790 52.381 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.609957 TTTGTGGCTGCATCTCTGGG 60.610 55.000 0.50 0.00 0.00 4.45
30 31 0.450983 GAGCTTTGTGGCTGCATCTC 59.549 55.000 0.50 0.00 43.20 2.75
31 32 1.303799 CGAGCTTTGTGGCTGCATCT 61.304 55.000 0.50 0.00 43.20 2.90
89 90 1.155859 TTGCCCCTTGCTCCATTGT 59.844 52.632 0.00 0.00 42.00 2.71
96 97 0.974010 CATGATGGTTGCCCCTTGCT 60.974 55.000 0.00 0.00 42.00 3.91
176 177 2.260434 CGCCGGGAGTCTTCGAAA 59.740 61.111 2.18 0.00 0.00 3.46
236 241 2.488355 CCATTGCAGCGCTGGAAG 59.512 61.111 40.13 31.23 43.89 3.46
237 242 3.751246 GCCATTGCAGCGCTGGAA 61.751 61.111 40.16 40.16 44.73 3.53
244 249 4.527157 GTCGAGCGCCATTGCAGC 62.527 66.667 2.29 0.00 37.32 5.25
245 250 3.092192 CTGTCGAGCGCCATTGCAG 62.092 63.158 2.29 2.76 37.32 4.41
246 251 3.120385 CTGTCGAGCGCCATTGCA 61.120 61.111 2.29 0.00 37.32 4.08
247 252 3.121030 ACTGTCGAGCGCCATTGC 61.121 61.111 2.29 0.00 0.00 3.56
248 253 2.743752 CCACTGTCGAGCGCCATTG 61.744 63.158 2.29 0.00 0.00 2.82
249 254 2.434884 CCACTGTCGAGCGCCATT 60.435 61.111 2.29 0.00 0.00 3.16
254 259 4.803426 GGGAGCCACTGTCGAGCG 62.803 72.222 0.00 0.00 0.00 5.03
255 260 4.803426 CGGGAGCCACTGTCGAGC 62.803 72.222 0.00 0.00 0.00 5.03
256 261 3.062466 TCGGGAGCCACTGTCGAG 61.062 66.667 0.00 0.00 0.00 4.04
257 262 3.371063 GTCGGGAGCCACTGTCGA 61.371 66.667 0.00 0.00 0.00 4.20
258 263 4.778415 CGTCGGGAGCCACTGTCG 62.778 72.222 0.00 0.00 0.00 4.35
272 277 2.717809 GAAGTTCCGTCGCAGCGTC 61.718 63.158 15.93 8.55 0.00 5.19
273 278 2.733593 GAAGTTCCGTCGCAGCGT 60.734 61.111 15.93 0.00 0.00 5.07
274 279 2.430921 AGAAGTTCCGTCGCAGCG 60.431 61.111 9.06 9.06 0.00 5.18
275 280 1.372997 TCAGAAGTTCCGTCGCAGC 60.373 57.895 0.00 0.00 0.00 5.25
276 281 1.337817 CGTCAGAAGTTCCGTCGCAG 61.338 60.000 0.00 0.00 0.00 5.18
277 282 1.371267 CGTCAGAAGTTCCGTCGCA 60.371 57.895 0.00 0.00 0.00 5.10
278 283 2.717809 GCGTCAGAAGTTCCGTCGC 61.718 63.158 13.44 13.44 35.86 5.19
279 284 1.081376 AGCGTCAGAAGTTCCGTCG 60.081 57.895 0.00 0.07 0.00 5.12
280 285 1.618640 GCAGCGTCAGAAGTTCCGTC 61.619 60.000 0.00 0.00 0.00 4.79
281 286 1.664965 GCAGCGTCAGAAGTTCCGT 60.665 57.895 0.00 0.00 0.00 4.69
282 287 1.221466 TTGCAGCGTCAGAAGTTCCG 61.221 55.000 0.00 0.00 0.00 4.30
286 291 1.956170 CCGTTGCAGCGTCAGAAGT 60.956 57.895 21.64 0.00 0.00 3.01
348 381 1.362768 CATTGCAGCGTTCAGAGCTA 58.637 50.000 0.00 0.00 44.06 3.32
354 387 1.171549 TTGCTCCATTGCAGCGTTCA 61.172 50.000 0.00 0.00 44.27 3.18
356 389 1.286880 GTTGCTCCATTGCAGCGTT 59.713 52.632 0.00 0.00 44.27 4.84
374 407 1.213537 CTGCTTCAATGGTTGCCCG 59.786 57.895 0.00 0.00 0.00 6.13
430 463 2.437449 TGCTCCATTGCAGCACCT 59.563 55.556 0.00 0.00 42.09 4.00
433 466 2.036571 CGAGTGCTCCATTGCAGCA 61.037 57.895 0.00 0.00 44.80 4.41
447 480 2.673341 TGAGAGCCGCTGTCGAGT 60.673 61.111 12.51 0.00 38.10 4.18
500 533 1.226746 CTTTCAAAACCTCGGCGAGT 58.773 50.000 32.41 19.16 0.00 4.18
511 544 4.036262 AGTGTTGCATCGTAGCTTTCAAAA 59.964 37.500 0.00 0.00 34.99 2.44
513 546 3.138304 AGTGTTGCATCGTAGCTTTCAA 58.862 40.909 0.00 0.00 34.99 2.69
542 575 1.514678 TTGCGCGACTGCTCCATTTT 61.515 50.000 12.10 0.00 39.65 1.82
543 576 1.965930 TTGCGCGACTGCTCCATTT 60.966 52.632 12.10 0.00 39.65 2.32
558 591 3.737172 AGCATTGGACGCCGTTGC 61.737 61.111 3.55 3.55 35.26 4.17
570 603 1.938577 CTAGCACTTCATCGCAGCATT 59.061 47.619 0.00 0.00 0.00 3.56
585 619 2.349755 GGAAACCACCGCCTAGCA 59.650 61.111 0.00 0.00 0.00 3.49
668 712 3.599730 AGAAACACTCATCGCATCTCA 57.400 42.857 0.00 0.00 0.00 3.27
697 741 1.043116 TAGCCATCACTCTCCGGTGG 61.043 60.000 0.00 0.00 37.75 4.61
708 752 1.227527 CCGACGCCATTAGCCATCA 60.228 57.895 0.00 0.00 38.78 3.07
711 755 4.169696 CCCCGACGCCATTAGCCA 62.170 66.667 0.00 0.00 38.78 4.75
715 759 3.690685 CTTGCCCCCGACGCCATTA 62.691 63.158 0.00 0.00 0.00 1.90
748 799 1.884464 CATCGCACCCCTCACATCG 60.884 63.158 0.00 0.00 0.00 3.84
760 811 1.153309 CACCATCTCAGGCATCGCA 60.153 57.895 0.00 0.00 0.00 5.10
777 828 0.532640 ACTGAGCAACACACGCATCA 60.533 50.000 0.00 0.00 0.00 3.07
799 851 1.153086 GGATCCCACATCGCTTGCT 60.153 57.895 0.00 0.00 0.00 3.91
801 853 1.889105 CCGGATCCCACATCGCTTG 60.889 63.158 6.06 0.00 0.00 4.01
802 854 1.622607 TTCCGGATCCCACATCGCTT 61.623 55.000 4.15 0.00 0.00 4.68
804 856 1.595382 CTTCCGGATCCCACATCGC 60.595 63.158 4.15 0.00 0.00 4.58
805 857 1.069765 CCTTCCGGATCCCACATCG 59.930 63.158 4.15 0.00 0.00 3.84
806 858 0.106894 GTCCTTCCGGATCCCACATC 59.893 60.000 4.15 0.00 42.43 3.06
807 859 1.345715 GGTCCTTCCGGATCCCACAT 61.346 60.000 4.15 0.00 42.43 3.21
808 860 1.993391 GGTCCTTCCGGATCCCACA 60.993 63.158 4.15 0.00 42.43 4.17
817 876 2.809601 CGTCGCTTGGTCCTTCCG 60.810 66.667 0.00 0.00 39.52 4.30
945 1004 1.657556 GGATCGAGCGAGGAAGAGG 59.342 63.158 0.00 0.00 0.00 3.69
996 1055 2.825836 GGCCCTTGCGTCATGGAG 60.826 66.667 11.56 5.27 38.85 3.86
1134 1193 2.044252 CCGGACGAGGAGGAGGAA 60.044 66.667 0.00 0.00 0.00 3.36
1153 1212 4.491409 GCCGGAGAGAAAGGGGCC 62.491 72.222 5.05 0.00 37.82 5.80
1356 1419 6.713903 CAGTGCCTACTATTGATTGGAATGAT 59.286 38.462 0.00 0.00 34.74 2.45
1357 1420 6.057533 CAGTGCCTACTATTGATTGGAATGA 58.942 40.000 0.00 0.00 34.74 2.57
1359 1422 4.823989 GCAGTGCCTACTATTGATTGGAAT 59.176 41.667 2.85 0.00 34.74 3.01
1360 1423 4.199310 GCAGTGCCTACTATTGATTGGAA 58.801 43.478 2.85 0.00 34.74 3.53
1362 1425 3.313526 GTGCAGTGCCTACTATTGATTGG 59.686 47.826 13.72 0.00 34.74 3.16
1363 1426 3.940852 TGTGCAGTGCCTACTATTGATTG 59.059 43.478 13.72 0.00 34.74 2.67
1370 1452 2.803956 AGTAGTGTGCAGTGCCTACTA 58.196 47.619 23.17 21.11 38.60 1.82
1372 1454 2.492484 AGTAGTAGTGTGCAGTGCCTAC 59.508 50.000 13.72 16.05 0.00 3.18
1376 1458 1.618861 CGAGTAGTAGTGTGCAGTGC 58.381 55.000 8.58 8.58 0.00 4.40
1491 1575 5.504853 TGATGCCAATGGTTGTCAAGTATA 58.495 37.500 0.00 0.00 0.00 1.47
1492 1576 4.343231 TGATGCCAATGGTTGTCAAGTAT 58.657 39.130 0.00 0.00 0.00 2.12
1493 1577 3.758023 CTGATGCCAATGGTTGTCAAGTA 59.242 43.478 0.00 0.00 0.00 2.24
1494 1578 2.559668 CTGATGCCAATGGTTGTCAAGT 59.440 45.455 0.00 0.00 0.00 3.16
1496 1594 2.874014 TCTGATGCCAATGGTTGTCAA 58.126 42.857 0.00 0.00 0.00 3.18
1499 1597 6.549433 AATTAATCTGATGCCAATGGTTGT 57.451 33.333 0.00 0.00 0.00 3.32
1503 1601 5.479375 AGGCTAATTAATCTGATGCCAATGG 59.521 40.000 14.51 0.00 41.12 3.16
1504 1602 6.208007 TGAGGCTAATTAATCTGATGCCAATG 59.792 38.462 14.51 0.00 41.12 2.82
1542 1640 6.105333 GGATCAGAATATTTGAGCTCGCTAT 58.895 40.000 9.64 4.83 31.89 2.97
1546 1644 8.388853 CAATATGGATCAGAATATTTGAGCTCG 58.611 37.037 9.64 0.00 31.89 5.03
1569 1667 9.872684 AGGTATTCAGATTCATTATTGGACAAT 57.127 29.630 2.80 2.80 34.93 2.71
1582 1683 9.886132 TGGTAGAAAAACTAGGTATTCAGATTC 57.114 33.333 0.00 0.00 0.00 2.52
1606 1707 5.368145 TGAGGAAATCAACCTATTCGATGG 58.632 41.667 0.00 0.00 37.93 3.51
1625 1727 1.878953 ACAACCAAACGCTACTGAGG 58.121 50.000 0.00 0.00 0.00 3.86
1725 1831 6.320164 AGCAAAACTGATTGTAACACCTGTTA 59.680 34.615 0.00 0.00 39.31 2.41
1825 1931 4.452455 GCATATGTGTACAAGTATGCTCCC 59.548 45.833 28.93 13.10 43.62 4.30
1934 2040 9.674824 CAAGAATTGGATAAAATAGCTTGCTAG 57.325 33.333 8.36 0.00 43.94 3.42
1972 2078 2.293122 CGGAACATTGCCTTTCACAGAA 59.707 45.455 0.00 0.00 0.00 3.02
2032 2138 5.123186 TGGAGCCAATATGTTAACTGAAACG 59.877 40.000 7.22 0.00 31.76 3.60
2322 2428 4.143473 GCAAATCATGAAAAGTTGCTCACG 60.143 41.667 20.65 0.00 41.04 4.35
3124 3338 5.512942 TGGATCAAAAGGAGGTGATGTTA 57.487 39.130 0.00 0.00 34.61 2.41
3407 3621 2.038557 GAGTAGCCTGTCTGGTTCCAAA 59.961 50.000 0.00 0.00 38.35 3.28
3412 3626 0.542232 ACCGAGTAGCCTGTCTGGTT 60.542 55.000 0.00 0.00 38.35 3.67
3499 3713 1.428912 ACCCTCCTGCCAGATTGAAAA 59.571 47.619 0.00 0.00 0.00 2.29
3713 3927 9.793252 CAATTTGGTACATCTGAGATTTTTAGG 57.207 33.333 0.00 0.00 39.30 2.69
3730 3944 4.895889 TGTGAAACCATGGACAATTTGGTA 59.104 37.500 21.47 0.00 42.85 3.25
3797 4011 2.528743 GGATGGAGTGCATGACGCG 61.529 63.158 3.53 3.53 46.97 6.01
3862 4107 0.604780 GCGGGATCTGACATCCATGG 60.605 60.000 4.97 4.97 39.93 3.66
3948 4193 1.543429 CCAGGACAAGAAAAGCGAGGT 60.543 52.381 0.00 0.00 0.00 3.85
4092 4337 0.531200 ACAGGGCGAACTACTACAGC 59.469 55.000 0.00 0.00 0.00 4.40
4104 4349 1.298859 GGCAGTCAGTAAACAGGGCG 61.299 60.000 0.00 0.00 0.00 6.13
4281 4526 1.871080 CCGAAGGCACTCCATGATAC 58.129 55.000 0.00 0.00 46.14 2.24
4384 4629 2.474816 CTTCGAGCAATACAGGTAGGC 58.525 52.381 0.00 0.00 0.00 3.93
4419 4666 7.669089 TGTACATATGGAACTATGGAGAACA 57.331 36.000 7.80 0.00 34.11 3.18
4519 4766 1.550976 TGGTGTGTCTGTGTGTGTGTA 59.449 47.619 0.00 0.00 0.00 2.90
4531 4778 3.882888 TCCAAGTGAATCTTTGGTGTGTC 59.117 43.478 13.79 0.00 33.63 3.67
4642 5152 8.707938 AGTAACAACACTTACGAACTAAGTTT 57.292 30.769 0.00 0.00 42.19 2.66
4643 5153 8.707938 AAGTAACAACACTTACGAACTAAGTT 57.292 30.769 0.00 0.00 42.19 2.66
4644 5154 9.801873 TTAAGTAACAACACTTACGAACTAAGT 57.198 29.630 0.00 0.00 45.20 2.24
4737 5248 2.947652 CAGCCCAACATCAGATGTAAGG 59.052 50.000 16.71 19.08 44.07 2.69
4774 5285 1.416401 TGAGTCGCCCTCTGTTCTTTT 59.584 47.619 4.00 0.00 41.11 2.27
4861 5379 8.594881 ATCGACAGTTCCATATTATTTGTCTC 57.405 34.615 0.00 0.00 33.23 3.36
4897 5661 3.087781 GTGTTAAGAGTCCTACCGTCCT 58.912 50.000 0.00 0.00 0.00 3.85
4910 5674 4.666397 TGCCGGCGCGTGTTAAGA 62.666 61.111 23.90 0.00 38.08 2.10
4911 5675 2.896428 GATTGCCGGCGCGTGTTAAG 62.896 60.000 23.90 0.00 38.08 1.85
4912 5676 3.029564 GATTGCCGGCGCGTGTTAA 62.030 57.895 23.90 8.98 38.08 2.01
4913 5677 3.492545 GATTGCCGGCGCGTGTTA 61.493 61.111 23.90 0.00 38.08 2.41
4918 5682 3.112126 AATTCAGATTGCCGGCGCG 62.112 57.895 23.90 0.00 38.08 6.86
4928 5692 6.103797 AGGTCCATTCTATTCCCAATTCAGAT 59.896 38.462 0.00 0.00 0.00 2.90
4962 5726 4.978580 ACAGCTCTTTTTCAAGAATTTCGC 59.021 37.500 0.00 0.00 38.63 4.70
4988 5752 7.386848 TGCAGATATATTTTACGAAGGGCTTAC 59.613 37.037 0.00 0.00 0.00 2.34
4990 5754 6.296026 TGCAGATATATTTTACGAAGGGCTT 58.704 36.000 0.00 0.00 0.00 4.35
4995 5759 7.795734 CACAGCTTGCAGATATATTTTACGAAG 59.204 37.037 0.00 0.00 0.00 3.79
5016 5780 1.021390 CGTCCCACCATCTTCACAGC 61.021 60.000 0.00 0.00 0.00 4.40
5028 5792 3.256558 GTTCCAGTATTACACGTCCCAC 58.743 50.000 0.00 0.00 0.00 4.61
5071 5835 6.312672 TCGAGCTTCATATTCATTTTGTTCGA 59.687 34.615 0.00 0.00 0.00 3.71
5090 5854 1.542030 CCGGACTAAGCATATCGAGCT 59.458 52.381 0.00 0.00 45.97 4.09
5094 5858 0.240145 TCGCCGGACTAAGCATATCG 59.760 55.000 5.05 0.00 0.00 2.92
5118 5882 5.440610 CCTACTTATCAGCCAATCCAGTTT 58.559 41.667 0.00 0.00 0.00 2.66
5149 5913 0.605319 TTGTCTGCCGGGACAATGTC 60.605 55.000 18.81 4.51 46.91 3.06
5150 5914 1.454104 TTGTCTGCCGGGACAATGT 59.546 52.632 18.81 0.00 46.91 2.71
5151 5915 4.395519 TTGTCTGCCGGGACAATG 57.604 55.556 18.81 0.00 46.91 2.82
5155 5919 1.538419 GCTACTATTGTCTGCCGGGAC 60.538 57.143 2.18 3.32 36.81 4.46
5156 5920 0.750850 GCTACTATTGTCTGCCGGGA 59.249 55.000 2.18 0.00 0.00 5.14
5157 5921 0.464036 TGCTACTATTGTCTGCCGGG 59.536 55.000 2.18 0.00 0.00 5.73
5158 5922 1.137086 AGTGCTACTATTGTCTGCCGG 59.863 52.381 0.00 0.00 0.00 6.13
5159 5923 2.464865 GAGTGCTACTATTGTCTGCCG 58.535 52.381 3.65 0.00 0.00 5.69
5160 5924 2.099263 TCGAGTGCTACTATTGTCTGCC 59.901 50.000 3.65 0.00 0.00 4.85
5161 5925 3.422417 TCGAGTGCTACTATTGTCTGC 57.578 47.619 0.00 0.00 0.00 4.26
5162 5926 5.172232 CGATTTCGAGTGCTACTATTGTCTG 59.828 44.000 0.00 0.00 43.02 3.51
5163 5927 5.274718 CGATTTCGAGTGCTACTATTGTCT 58.725 41.667 0.00 0.00 43.02 3.41
5164 5928 4.441415 CCGATTTCGAGTGCTACTATTGTC 59.559 45.833 0.67 0.00 43.02 3.18
5165 5929 4.142227 ACCGATTTCGAGTGCTACTATTGT 60.142 41.667 0.67 0.00 43.02 2.71
5166 5930 4.360563 ACCGATTTCGAGTGCTACTATTG 58.639 43.478 0.67 0.00 43.02 1.90
5167 5931 4.650754 ACCGATTTCGAGTGCTACTATT 57.349 40.909 0.67 0.00 43.02 1.73
5168 5932 4.142227 ACAACCGATTTCGAGTGCTACTAT 60.142 41.667 0.67 0.00 43.02 2.12
5169 5933 3.192001 ACAACCGATTTCGAGTGCTACTA 59.808 43.478 0.67 0.00 43.02 1.82
5170 5934 2.029290 ACAACCGATTTCGAGTGCTACT 60.029 45.455 0.67 0.00 43.02 2.57
5171 5935 2.334838 ACAACCGATTTCGAGTGCTAC 58.665 47.619 0.67 0.00 43.02 3.58
5172 5936 2.029739 TGACAACCGATTTCGAGTGCTA 60.030 45.455 0.67 0.00 43.02 3.49
5173 5937 1.270094 TGACAACCGATTTCGAGTGCT 60.270 47.619 0.67 0.00 43.02 4.40
5174 5938 1.144969 TGACAACCGATTTCGAGTGC 58.855 50.000 0.67 0.00 43.02 4.40
5175 5939 3.493129 TCTTTGACAACCGATTTCGAGTG 59.507 43.478 0.67 1.83 43.02 3.51
5176 5940 3.724374 TCTTTGACAACCGATTTCGAGT 58.276 40.909 0.67 0.00 43.02 4.18
5177 5941 4.201724 GGATCTTTGACAACCGATTTCGAG 60.202 45.833 0.67 0.00 43.02 4.04
5178 5942 3.682858 GGATCTTTGACAACCGATTTCGA 59.317 43.478 0.67 0.00 43.02 3.71
5179 5943 3.684788 AGGATCTTTGACAACCGATTTCG 59.315 43.478 0.00 0.00 39.44 3.46
5180 5944 4.455877 ACAGGATCTTTGACAACCGATTTC 59.544 41.667 5.03 0.00 0.00 2.17
5181 5945 4.398319 ACAGGATCTTTGACAACCGATTT 58.602 39.130 5.03 0.00 0.00 2.17
5182 5946 4.021102 ACAGGATCTTTGACAACCGATT 57.979 40.909 5.03 0.00 0.00 3.34
5183 5947 3.703001 ACAGGATCTTTGACAACCGAT 57.297 42.857 5.03 0.00 0.00 4.18
5184 5948 4.202274 TGTTACAGGATCTTTGACAACCGA 60.202 41.667 5.03 0.00 0.00 4.69
5185 5949 4.062293 TGTTACAGGATCTTTGACAACCG 58.938 43.478 5.03 0.00 0.00 4.44
5193 5957 5.209818 TCGTCAACTGTTACAGGATCTTT 57.790 39.130 17.21 0.00 35.51 2.52
5197 5961 3.556423 GGGTTCGTCAACTGTTACAGGAT 60.556 47.826 17.21 2.18 35.51 3.24
5206 5970 2.217750 TCATGTTGGGTTCGTCAACTG 58.782 47.619 8.17 4.94 43.36 3.16
5208 5972 3.502211 AGAATCATGTTGGGTTCGTCAAC 59.498 43.478 0.00 0.00 43.29 3.18
5237 6001 1.404479 TATAGGGCGATTGGTGCGGT 61.404 55.000 0.00 0.00 0.00 5.68
5243 6007 1.338200 GGCAGAGTATAGGGCGATTGG 60.338 57.143 0.00 0.00 0.00 3.16
5244 6008 1.620819 AGGCAGAGTATAGGGCGATTG 59.379 52.381 0.00 0.00 0.00 2.67
5287 6051 0.032515 TGATCCTCCCGCCTACAGAA 60.033 55.000 0.00 0.00 0.00 3.02
5293 6057 2.123077 CTCCTGATCCTCCCGCCT 60.123 66.667 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.