Multiple sequence alignment - TraesCS2A01G466800

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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 TraesCS2A01G466800 chr2A 100.000 5946 0 0 1 5946 711080285 711074340 0.000000e+00 10981.0
1 TraesCS2A01G466800 chr2D 91.965 6024 290 93 1 5946 572084715 572078808 0.000000e+00 8264.0
2 TraesCS2A01G466800 chr2D 81.041 269 32 8 1 253 651715050 651714785 4.700000e-46 196.0
3 TraesCS2A01G466800 chr2B 92.716 3089 154 32 608 3665 686838887 686835839 0.000000e+00 4392.0
4 TraesCS2A01G466800 chr2B 93.355 1249 44 13 4148 5374 686835196 686833965 0.000000e+00 1810.0
5 TraesCS2A01G466800 chr2B 85.434 611 40 22 5374 5946 686833884 686833285 1.850000e-164 590.0
6 TraesCS2A01G466800 chr2B 91.057 369 19 5 3774 4137 686835662 686835303 2.490000e-133 486.0
7 TraesCS2A01G466800 chr2B 78.788 594 71 27 1 569 687202133 687201570 1.230000e-91 348.0
8 TraesCS2A01G466800 chr2B 95.200 125 6 0 3654 3778 686835819 686835695 1.310000e-46 198.0
9 TraesCS2A01G466800 chr7B 78.072 415 73 10 1 404 3187251 3186844 4.600000e-61 246.0
10 TraesCS2A01G466800 chr7B 78.884 251 32 14 13 250 296583941 296584183 3.710000e-32 150.0
11 TraesCS2A01G466800 chr5D 78.177 362 50 15 69 404 401359585 401359227 2.810000e-48 204.0
12 TraesCS2A01G466800 chr5D 80.632 253 29 13 13 249 510104603 510104851 1.700000e-40 178.0
13 TraesCS2A01G466800 chr7D 79.757 247 35 10 13 250 313744634 313744394 1.330000e-36 165.0
14 TraesCS2A01G466800 chr4B 82.902 193 24 6 69 253 178856736 178856545 1.330000e-36 165.0
15 TraesCS2A01G466800 chr7A 82.199 191 22 7 69 253 611735799 611735983 2.870000e-33 154.0
16 TraesCS2A01G466800 chr4D 85.507 69 4 5 29 92 251967444 251967377 3.850000e-07 67.6
17 TraesCS2A01G466800 chr3A 94.444 36 2 0 1990 2025 70697966 70697931 8.320000e-04 56.5
18 TraesCS2A01G466800 chr5A 100.000 28 0 0 1998 2025 589001854 589001881 1.100000e-02 52.8


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 TraesCS2A01G466800 chr2A 711074340 711080285 5945 True 10981.0 10981 100.0000 1 5946 1 chr2A.!!$R1 5945
1 TraesCS2A01G466800 chr2D 572078808 572084715 5907 True 8264.0 8264 91.9650 1 5946 1 chr2D.!!$R1 5945
2 TraesCS2A01G466800 chr2B 686833285 686838887 5602 True 1495.2 4392 91.5524 608 5946 5 chr2B.!!$R2 5338
3 TraesCS2A01G466800 chr2B 687201570 687202133 563 True 348.0 348 78.7880 1 569 1 chr2B.!!$R1 568

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
604 636 0.391263 CTCTAAGCACAACGGGGGTC 60.391 60.0 0.00 0.0 0.00 4.46 F
912 968 0.604243 ACAAGCGGCATAAACCACGA 60.604 50.0 1.45 0.0 0.00 4.35 F
2397 2497 0.244994 AGTAGCTGAACCTGACGCTG 59.755 55.0 0.00 0.0 34.14 5.18 F
2683 2783 0.169009 GCCTTGATGAGCGGTTTGAC 59.831 55.0 0.00 0.0 0.00 3.18 F
4555 4837 1.195115 TCCGTGGAATCCCTTCTCTG 58.805 55.0 0.00 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 2457 1.153329 AGTTTGGTCCGTGCGAACA 60.153 52.632 0.00 0.0 35.97 3.18 R
2683 2783 1.073177 GGTGTGGAATACCGTTGACG 58.927 55.000 0.00 0.0 38.73 4.35 R
4079 4254 0.699577 TCCCTTTGTTCCTGGACCCA 60.700 55.000 0.00 0.0 0.00 4.51 R
4643 4925 0.467290 AGCTCCTGGATCCTCTCGTC 60.467 60.000 14.23 0.0 0.00 4.20 R
5465 5857 1.067582 GGCGAGATGGAACTACCGG 59.932 63.158 0.00 0.0 42.61 5.28 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
27 28 6.458503 CATGTGTTCGAGACTTGTAATAACG 58.541 40.000 0.00 0.00 0.00 3.18
96 97 7.389607 TCATTATGATGATGAGGCTATGTTGTG 59.610 37.037 0.00 0.00 37.37 3.33
98 99 3.200605 TGATGATGAGGCTATGTTGTGGT 59.799 43.478 0.00 0.00 0.00 4.16
104 105 3.580895 TGAGGCTATGTTGTGGTACTTCA 59.419 43.478 0.00 0.00 0.00 3.02
105 106 4.041075 TGAGGCTATGTTGTGGTACTTCAA 59.959 41.667 0.00 0.00 0.00 2.69
106 107 5.179452 AGGCTATGTTGTGGTACTTCAAT 57.821 39.130 0.00 0.00 0.00 2.57
107 108 4.943705 AGGCTATGTTGTGGTACTTCAATG 59.056 41.667 0.00 0.00 0.00 2.82
108 109 4.941263 GGCTATGTTGTGGTACTTCAATGA 59.059 41.667 0.00 0.00 0.00 2.57
109 110 5.590259 GGCTATGTTGTGGTACTTCAATGAT 59.410 40.000 0.00 0.00 0.00 2.45
122 123 9.662947 GGTACTTCAATGATGATGATGATGATA 57.337 33.333 3.02 0.00 34.96 2.15
254 279 2.998480 TGGCGCGGGGTAAGAGAA 60.998 61.111 8.83 0.00 0.00 2.87
278 303 2.862541 TGCTACACAGACTTGGCAATT 58.137 42.857 0.00 0.00 0.00 2.32
279 304 3.221771 TGCTACACAGACTTGGCAATTT 58.778 40.909 0.00 0.00 0.00 1.82
285 310 0.598065 AGACTTGGCAATTTCACGGC 59.402 50.000 0.00 0.00 0.00 5.68
299 324 0.809636 CACGGCATTCATACCAGCGA 60.810 55.000 0.00 0.00 0.00 4.93
364 389 4.451096 GCTAAGTTTGTGTAGCAGTAGCAA 59.549 41.667 0.00 0.00 45.49 3.91
404 429 3.754188 CTGCTAAAAGTTAGCTGCAGG 57.246 47.619 17.12 0.00 42.64 4.85
442 467 0.533491 ACACCCGCGTTATTGCTAGA 59.467 50.000 4.92 0.00 0.00 2.43
459 484 1.497161 AGACCTTTACCCTGCGCTAT 58.503 50.000 9.73 0.00 0.00 2.97
460 485 1.139058 AGACCTTTACCCTGCGCTATG 59.861 52.381 9.73 0.00 0.00 2.23
466 491 3.678056 TTACCCTGCGCTATGAATAGG 57.322 47.619 9.73 4.61 0.00 2.57
603 635 1.677552 CTCTAAGCACAACGGGGGT 59.322 57.895 0.00 0.00 0.00 4.95
604 636 0.391263 CTCTAAGCACAACGGGGGTC 60.391 60.000 0.00 0.00 0.00 4.46
605 637 0.834687 TCTAAGCACAACGGGGGTCT 60.835 55.000 0.00 0.00 0.00 3.85
638 690 9.596677 TTTTATTTATTTTCTCGTGTACAACCG 57.403 29.630 0.00 0.00 0.00 4.44
680 733 1.214175 ACACCCACTCCATTTCACACA 59.786 47.619 0.00 0.00 0.00 3.72
702 755 1.555477 GACGGCGCAATAATTTTGGG 58.445 50.000 10.83 10.79 35.73 4.12
855 908 5.544948 ACCGCCTTGTATATAAACCCTATCA 59.455 40.000 0.00 0.00 0.00 2.15
856 909 6.214819 ACCGCCTTGTATATAAACCCTATCAT 59.785 38.462 0.00 0.00 0.00 2.45
859 912 9.314321 CGCCTTGTATATAAACCCTATCATTAG 57.686 37.037 0.00 0.00 0.00 1.73
897 953 3.259123 CCAAATCCCTCTCCCAAAACAAG 59.741 47.826 0.00 0.00 0.00 3.16
912 968 0.604243 ACAAGCGGCATAAACCACGA 60.604 50.000 1.45 0.00 0.00 4.35
959 1016 1.920835 GCTTCCAGTCCACTCCCCT 60.921 63.158 0.00 0.00 0.00 4.79
960 1017 1.492993 GCTTCCAGTCCACTCCCCTT 61.493 60.000 0.00 0.00 0.00 3.95
961 1018 0.615850 CTTCCAGTCCACTCCCCTTC 59.384 60.000 0.00 0.00 0.00 3.46
962 1019 0.840722 TTCCAGTCCACTCCCCTTCC 60.841 60.000 0.00 0.00 0.00 3.46
963 1020 1.229658 CCAGTCCACTCCCCTTCCT 60.230 63.158 0.00 0.00 0.00 3.36
964 1021 1.268283 CCAGTCCACTCCCCTTCCTC 61.268 65.000 0.00 0.00 0.00 3.71
965 1022 1.081277 AGTCCACTCCCCTTCCTCC 59.919 63.158 0.00 0.00 0.00 4.30
966 1023 1.996187 GTCCACTCCCCTTCCTCCC 60.996 68.421 0.00 0.00 0.00 4.30
967 1024 2.692741 CCACTCCCCTTCCTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
1112 1174 2.040359 CCCCTTCCCCCTCTCTCC 60.040 72.222 0.00 0.00 0.00 3.71
1226 1289 7.596749 TCTCTCCTGTTTATTTCGTTTGATC 57.403 36.000 0.00 0.00 0.00 2.92
1236 1300 3.715618 TTCGTTTGATCGGTCGATTTG 57.284 42.857 7.32 0.00 34.60 2.32
1261 1338 3.857052 CTCGGGCTGTAGTTATCAACAA 58.143 45.455 0.00 0.00 0.00 2.83
1263 1340 3.007074 TCGGGCTGTAGTTATCAACAACA 59.993 43.478 0.00 0.00 0.00 3.33
1264 1341 3.370978 CGGGCTGTAGTTATCAACAACAG 59.629 47.826 0.00 0.00 0.00 3.16
1265 1342 3.127030 GGGCTGTAGTTATCAACAACAGC 59.873 47.826 15.46 15.46 45.63 4.40
1277 1354 1.148157 ACAACAGCATAGCTAGCGCG 61.148 55.000 9.55 0.00 42.32 6.86
1360 1437 1.360551 CGATTCGGCCTGATCGAGT 59.639 57.895 24.89 4.61 38.67 4.18
1373 1450 5.566623 CCTGATCGAGTTGTCAATTGATTG 58.433 41.667 12.12 0.00 39.10 2.67
1404 1481 0.875908 CTGCGATGATACCGGTGGTG 60.876 60.000 19.93 1.85 36.19 4.17
1479 1556 5.175859 TGATTGGTCCATTTAGAGTTCGAC 58.824 41.667 0.00 0.00 0.00 4.20
1534 1612 5.003804 TGAGATGGGCTCTTTTGTTTAGAC 58.996 41.667 0.00 0.00 44.27 2.59
1652 1730 3.359033 TGATTGGCTTGAAATAGCTGCT 58.641 40.909 7.57 7.57 40.99 4.24
1715 1794 5.814764 TCCTTCGTGTCTGTCTATCTTAC 57.185 43.478 0.00 0.00 0.00 2.34
1763 1842 7.254795 CCAAAGTTGACTCGATTTGTCTAAAGT 60.255 37.037 5.08 0.00 35.63 2.66
1764 1843 8.761497 CAAAGTTGACTCGATTTGTCTAAAGTA 58.239 33.333 5.08 0.00 35.63 2.24
1766 1845 9.490379 AAGTTGACTCGATTTGTCTAAAGTAAT 57.510 29.630 5.08 0.00 35.63 1.89
1795 1881 6.950545 TCACGAAACTGTAAGGTGTATTTTG 58.049 36.000 0.00 0.00 39.30 2.44
1849 1938 4.213482 CCAACAAGGCAACAACTACTAGAC 59.787 45.833 0.00 0.00 41.41 2.59
2035 2124 5.534654 TGGAGGGAGTAACATGTTTTTCTTG 59.465 40.000 17.78 0.00 0.00 3.02
2365 2465 5.146482 TGTGTAACTAACTTTGTTCGCAC 57.854 39.130 12.40 12.40 38.04 5.34
2372 2472 0.745128 ACTTTGTTCGCACGGACCAA 60.745 50.000 0.00 0.00 0.00 3.67
2397 2497 0.244994 AGTAGCTGAACCTGACGCTG 59.755 55.000 0.00 0.00 34.14 5.18
2506 2606 2.339556 GCCATGCCAGCGGTTTACA 61.340 57.895 0.00 0.00 0.00 2.41
2543 2643 5.483685 AGCATACACAGAACTTACCTCAA 57.516 39.130 0.00 0.00 0.00 3.02
2583 2683 1.128692 GATCTTTGTTTCAGGCGACCG 59.871 52.381 0.00 0.00 0.00 4.79
2643 2743 2.808933 CGTGGTTGGCAGTTCCTTTCTA 60.809 50.000 6.91 0.00 35.26 2.10
2650 2750 2.608268 GCAGTTCCTTTCTACGACTCC 58.392 52.381 0.00 0.00 0.00 3.85
2683 2783 0.169009 GCCTTGATGAGCGGTTTGAC 59.831 55.000 0.00 0.00 0.00 3.18
2743 2843 3.027974 ACTGGCGAAGTTCTTACTGAC 57.972 47.619 0.56 0.00 34.57 3.51
2944 3044 8.918202 ATCAACCACAGTTCTTTTATTGTCTA 57.082 30.769 0.00 0.00 32.45 2.59
2945 3045 8.918202 TCAACCACAGTTCTTTTATTGTCTAT 57.082 30.769 0.00 0.00 32.45 1.98
3067 3167 2.409975 TGCTTTGTAGTGAACGGCTAC 58.590 47.619 0.00 0.00 39.26 3.58
3169 3269 3.110705 AGCTGTATCCTTGGACAGTGAT 58.889 45.455 0.00 0.00 44.10 3.06
3223 3323 2.916527 CTTGGCTCGCCATTCCCCAT 62.917 60.000 12.00 0.00 46.64 4.00
3466 3566 2.404215 CTTCTGGTTACTGGTGACGTG 58.596 52.381 0.00 0.00 0.00 4.49
3556 3656 7.597386 AGACTCTTTTTGTTGGCAAGAATATC 58.403 34.615 10.84 1.42 35.82 1.63
3557 3657 7.231317 AGACTCTTTTTGTTGGCAAGAATATCA 59.769 33.333 10.84 0.00 35.82 2.15
3559 3659 7.653311 ACTCTTTTTGTTGGCAAGAATATCAAC 59.347 33.333 10.84 0.00 39.68 3.18
3635 3737 9.499585 CATATTGATCTGAATGTTGACTTTCAC 57.500 33.333 7.99 1.88 35.81 3.18
3735 3868 5.534654 GCCTGGCCATCTTATTTATGTTACA 59.465 40.000 5.51 0.00 0.00 2.41
3773 3906 7.251321 AGACATTTAGACCCTCCATATCATC 57.749 40.000 0.00 0.00 0.00 2.92
4106 4281 3.633986 CCAGGAACAAAGGGAATGATAGC 59.366 47.826 0.00 0.00 0.00 2.97
4121 4296 4.871933 TGATAGCGAGCCATTTATCAGA 57.128 40.909 0.00 0.00 31.07 3.27
4207 4478 5.682234 TCAGAATGAGCATCTGGTTTAGA 57.318 39.130 3.92 0.00 42.56 2.10
4208 4479 5.423015 TCAGAATGAGCATCTGGTTTAGAC 58.577 41.667 3.92 0.00 42.56 2.59
4209 4480 5.188555 TCAGAATGAGCATCTGGTTTAGACT 59.811 40.000 3.92 0.00 42.56 3.24
4211 4482 6.036953 CAGAATGAGCATCTGGTTTAGACTTC 59.963 42.308 0.00 0.00 40.48 3.01
4212 4483 5.690464 ATGAGCATCTGGTTTAGACTTCT 57.310 39.130 0.00 0.00 38.49 2.85
4213 4484 4.825422 TGAGCATCTGGTTTAGACTTCTG 58.175 43.478 0.00 0.00 38.49 3.02
4215 4486 5.188555 TGAGCATCTGGTTTAGACTTCTGAT 59.811 40.000 0.00 0.00 38.49 2.90
4216 4487 5.426504 AGCATCTGGTTTAGACTTCTGATG 58.573 41.667 0.00 0.00 38.49 3.07
4217 4488 5.046014 AGCATCTGGTTTAGACTTCTGATGT 60.046 40.000 0.00 0.00 38.49 3.06
4218 4489 5.064452 GCATCTGGTTTAGACTTCTGATGTG 59.936 44.000 0.43 0.00 38.49 3.21
4220 4491 6.174720 TCTGGTTTAGACTTCTGATGTGTT 57.825 37.500 0.43 0.00 0.00 3.32
4221 4492 7.297936 TCTGGTTTAGACTTCTGATGTGTTA 57.702 36.000 0.43 0.00 0.00 2.41
4222 4493 7.907389 TCTGGTTTAGACTTCTGATGTGTTAT 58.093 34.615 0.43 0.00 0.00 1.89
4223 4494 8.035394 TCTGGTTTAGACTTCTGATGTGTTATC 58.965 37.037 0.43 0.00 0.00 1.75
4224 4495 7.907389 TGGTTTAGACTTCTGATGTGTTATCT 58.093 34.615 0.43 0.00 0.00 1.98
4225 4496 9.031537 TGGTTTAGACTTCTGATGTGTTATCTA 57.968 33.333 0.43 0.00 0.00 1.98
4226 4497 9.871238 GGTTTAGACTTCTGATGTGTTATCTAA 57.129 33.333 0.43 0.52 0.00 2.10
4378 4660 2.350522 CTGCCTACACTTGTGGATGTC 58.649 52.381 5.72 0.00 0.00 3.06
4540 4822 5.239525 CCTGAAAAAGAAGTTCAAGATCCGT 59.760 40.000 5.50 0.00 34.68 4.69
4555 4837 1.195115 TCCGTGGAATCCCTTCTCTG 58.805 55.000 0.00 0.00 0.00 3.35
4567 4849 1.372087 CTTCTCTGGTCGCCATTGGC 61.372 60.000 18.10 18.10 46.75 4.52
4643 4925 3.272420 GACGCGTTTCCGTTCACCG 62.272 63.158 15.53 0.00 42.24 4.94
4644 4926 3.031457 CGCGTTTCCGTTCACCGA 61.031 61.111 0.00 0.00 39.56 4.69
4678 4960 2.034558 GGAGCTGGAGAAGAAGATCGAG 59.965 54.545 0.00 0.00 29.46 4.04
4687 4969 2.079170 AGAAGATCGAGGAGATGGCA 57.921 50.000 0.00 0.00 40.26 4.92
4706 4988 2.432174 AAAGGGGTGGCCTGAGAAGC 62.432 60.000 3.32 0.00 0.00 3.86
4981 5274 0.535780 TGTGTTCCTTGCCAGCTGAG 60.536 55.000 17.39 4.38 0.00 3.35
5086 5382 4.562394 GGTGACATTTATGTGCAAAATCGG 59.438 41.667 0.00 0.00 41.95 4.18
5087 5383 5.160641 GTGACATTTATGTGCAAAATCGGT 58.839 37.500 0.00 0.00 41.95 4.69
5088 5384 5.286082 GTGACATTTATGTGCAAAATCGGTC 59.714 40.000 0.00 0.00 41.95 4.79
5094 5392 6.811253 TTATGTGCAAAATCGGTCTAAGTT 57.189 33.333 0.00 0.00 0.00 2.66
5114 5412 6.272822 AGTTTATGGTTTCAGATCTTTGCC 57.727 37.500 0.00 0.00 0.00 4.52
5187 5490 2.114616 ACCCAGCAAGTAGAGAGATGG 58.885 52.381 0.00 0.00 0.00 3.51
5203 5506 1.462432 TGGCTGTCCCAGTTACCCA 60.462 57.895 0.00 0.00 39.18 4.51
5207 5510 0.394352 CTGTCCCAGTTACCCATGCC 60.394 60.000 0.00 0.00 0.00 4.40
5210 5513 2.278738 CCAGTTACCCATGCCCCC 59.721 66.667 0.00 0.00 0.00 5.40
5215 5518 0.261696 GTTACCCATGCCCCCATTCT 59.738 55.000 0.00 0.00 0.00 2.40
5274 5578 7.383843 GGAAATTCAGAAGCGGTTTGAAAATTA 59.616 33.333 20.52 6.32 34.80 1.40
5282 5586 9.010029 AGAAGCGGTTTGAAAATTATAGAGAAA 57.990 29.630 0.00 0.00 0.00 2.52
5284 5588 7.251281 AGCGGTTTGAAAATTATAGAGAAAGC 58.749 34.615 0.00 0.00 0.00 3.51
5322 5626 7.765819 GGGGATGAACATTTTGGAAATTAGAAG 59.234 37.037 0.00 0.00 0.00 2.85
5465 5857 0.598065 ATTTCTTGCCCGTTGTGAGC 59.402 50.000 0.00 0.00 0.00 4.26
5488 5880 0.747255 TAGTTCCATCTCGCCTCTGC 59.253 55.000 0.00 0.00 0.00 4.26
5568 5960 3.312973 TCACTGTTTGCGTCGGTTTTTAT 59.687 39.130 0.00 0.00 0.00 1.40
5650 6067 9.112725 CAATTTTCTTGGTTTTCCTCATTTTCT 57.887 29.630 0.00 0.00 41.38 2.52
5682 6099 6.927416 ACACATGTCTACATTTTTCATGCAT 58.073 32.000 0.00 0.00 39.27 3.96
5875 6296 9.726232 CATGATTAACATTTTCTCCAGTACATG 57.274 33.333 0.00 0.00 37.07 3.21
5922 6344 8.949953 ACAAGTTAAACATTTTCGAAATACACG 58.050 29.630 12.12 1.59 0.00 4.49
5928 6350 7.603297 AACATTTTCGAAATACACGTTGAAG 57.397 32.000 12.12 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.482743 TGATACACGTTATTACAAGTCTCGAAC 59.517 37.037 0.00 0.00 0.00 3.95
27 28 8.483218 CGTCATCATCTCAAAATAGTGATACAC 58.517 37.037 0.00 0.00 34.10 2.90
41 42 5.077134 ACAAATGTCTCGTCATCATCTCA 57.923 39.130 0.00 0.00 0.00 3.27
96 97 7.974482 TCATCATCATCATCATTGAAGTACC 57.026 36.000 0.00 0.00 34.96 3.34
218 220 5.049405 GCGCCACTGCTAAGATTTTATGTAT 60.049 40.000 0.00 0.00 34.43 2.29
223 225 1.663643 CGCGCCACTGCTAAGATTTTA 59.336 47.619 0.00 0.00 34.43 1.52
254 279 2.567169 TGCCAAGTCTGTGTAGCAGTAT 59.433 45.455 0.00 0.00 45.23 2.12
272 297 2.298411 ATGAATGCCGTGAAATTGCC 57.702 45.000 0.00 0.00 0.00 4.52
278 303 1.378531 GCTGGTATGAATGCCGTGAA 58.621 50.000 0.00 0.00 35.05 3.18
279 304 0.809636 CGCTGGTATGAATGCCGTGA 60.810 55.000 0.00 0.00 35.05 4.35
285 310 2.486918 TCTGCATCGCTGGTATGAATG 58.513 47.619 0.00 0.00 0.00 2.67
299 324 3.858877 GCGCTACTGCTAACTATCTGCAT 60.859 47.826 0.00 0.00 36.07 3.96
381 406 4.878397 CCTGCAGCTAACTTTTAGCAGTAT 59.122 41.667 17.84 0.00 45.80 2.12
432 457 4.682320 CGCAGGGTAAAGGTCTAGCAATAA 60.682 45.833 0.00 0.00 0.00 1.40
442 467 1.200519 TCATAGCGCAGGGTAAAGGT 58.799 50.000 11.47 0.00 0.00 3.50
473 498 5.125417 GTCCATACACCGGTAACACTACTAA 59.875 44.000 6.87 0.00 32.19 2.24
474 499 4.640201 GTCCATACACCGGTAACACTACTA 59.360 45.833 6.87 0.00 32.19 1.82
475 500 3.445096 GTCCATACACCGGTAACACTACT 59.555 47.826 6.87 0.00 32.19 2.57
476 501 3.193267 TGTCCATACACCGGTAACACTAC 59.807 47.826 6.87 2.83 32.19 2.73
477 502 3.429492 TGTCCATACACCGGTAACACTA 58.571 45.455 6.87 0.00 32.19 2.74
478 503 2.250031 TGTCCATACACCGGTAACACT 58.750 47.619 6.87 0.00 32.19 3.55
479 504 2.747396 TGTCCATACACCGGTAACAC 57.253 50.000 6.87 0.00 32.19 3.32
529 556 1.254026 GTTTACTGGAAGGTTGGGGC 58.746 55.000 0.00 0.00 39.30 5.80
530 557 2.626266 GTTGTTTACTGGAAGGTTGGGG 59.374 50.000 0.00 0.00 39.30 4.96
531 558 2.292292 CGTTGTTTACTGGAAGGTTGGG 59.708 50.000 0.00 0.00 39.30 4.12
532 559 2.292292 CCGTTGTTTACTGGAAGGTTGG 59.708 50.000 0.00 0.00 39.30 3.77
533 560 2.946990 ACCGTTGTTTACTGGAAGGTTG 59.053 45.455 0.00 0.00 39.30 3.77
534 561 3.286329 ACCGTTGTTTACTGGAAGGTT 57.714 42.857 0.00 0.00 39.30 3.50
535 562 3.286329 AACCGTTGTTTACTGGAAGGT 57.714 42.857 0.00 0.00 39.30 3.50
680 733 2.481104 CCAAAATTATTGCGCCGTCCAT 60.481 45.455 4.18 0.00 0.00 3.41
731 784 2.356553 TTCGCGTCGAAGGTTGGG 60.357 61.111 5.77 0.00 41.05 4.12
742 795 2.509336 CGGATGCTTCCTTCGCGT 60.509 61.111 16.03 0.00 40.17 6.01
743 796 3.264897 CCGGATGCTTCCTTCGCG 61.265 66.667 16.03 0.00 40.17 5.87
760 813 3.512516 GCTCCGGATGCCAACTGC 61.513 66.667 3.57 0.00 41.77 4.40
763 816 1.451927 TCATGCTCCGGATGCCAAC 60.452 57.895 19.09 1.64 0.00 3.77
774 827 2.951745 CGACTCGGCGTCATGCTC 60.952 66.667 6.85 0.00 42.98 4.26
786 839 4.838486 CCGTCTGCTCGGCGACTC 62.838 72.222 4.99 0.80 43.96 3.36
795 848 2.997897 GGTGGGTCTCCGTCTGCT 60.998 66.667 0.00 0.00 35.24 4.24
796 849 3.311110 TGGTGGGTCTCCGTCTGC 61.311 66.667 0.00 0.00 35.24 4.26
797 850 2.657237 GTGGTGGGTCTCCGTCTG 59.343 66.667 0.00 0.00 35.24 3.51
830 883 6.725369 TGATAGGGTTTATATACAAGGCGGTA 59.275 38.462 0.00 0.00 0.00 4.02
833 886 9.314321 CTAATGATAGGGTTTATATACAAGGCG 57.686 37.037 0.00 0.00 0.00 5.52
834 887 9.110502 GCTAATGATAGGGTTTATATACAAGGC 57.889 37.037 0.00 0.00 0.00 4.35
837 890 8.554011 GGGGCTAATGATAGGGTTTATATACAA 58.446 37.037 0.00 0.00 0.00 2.41
855 908 2.044352 GGCACGGTTGGGGCTAAT 60.044 61.111 0.00 0.00 0.00 1.73
856 909 3.571216 TGGCACGGTTGGGGCTAA 61.571 61.111 0.00 0.00 0.00 3.09
897 953 1.702491 GAGGTCGTGGTTTATGCCGC 61.702 60.000 0.00 0.00 35.78 6.53
941 998 1.492993 AAGGGGAGTGGACTGGAAGC 61.493 60.000 0.00 0.00 37.60 3.86
959 1016 4.798682 GGAGCGGAGGGGGAGGAA 62.799 72.222 0.00 0.00 0.00 3.36
1094 1154 2.788589 GAGAGAGGGGGAAGGGGT 59.211 66.667 0.00 0.00 0.00 4.95
1148 1211 3.738481 CATCGGGCCAAGGGGGAA 61.738 66.667 4.39 0.00 40.01 3.97
1226 1289 1.878522 CCGAGCTCCAAATCGACCG 60.879 63.158 8.47 0.00 41.40 4.79
1261 1338 0.032678 ATTCGCGCTAGCTATGCTGT 59.967 50.000 13.93 0.00 40.10 4.40
1263 1340 2.229062 TCTTATTCGCGCTAGCTATGCT 59.771 45.455 13.93 0.00 43.41 3.79
1264 1341 2.596452 TCTTATTCGCGCTAGCTATGC 58.404 47.619 13.93 8.11 42.32 3.14
1265 1342 4.415735 TCATCTTATTCGCGCTAGCTATG 58.584 43.478 13.93 2.14 42.32 2.23
1266 1343 4.396478 TCTCATCTTATTCGCGCTAGCTAT 59.604 41.667 13.93 3.67 42.32 2.97
1373 1450 8.540492 CCGGTATCATCGCAGATATTATTTAAC 58.460 37.037 0.00 0.00 45.12 2.01
1396 1473 2.280797 CCAGTCACACACCACCGG 60.281 66.667 0.00 0.00 0.00 5.28
1404 1481 3.467803 AGTTAGAACAAGCCAGTCACAC 58.532 45.455 0.00 0.00 0.00 3.82
1479 1556 4.211374 GCACTAGCGGTTGATAAATACAGG 59.789 45.833 2.41 0.00 0.00 4.00
1652 1730 2.635915 ACCCGTGAAAGTTGACCATAGA 59.364 45.455 0.00 0.00 0.00 1.98
1763 1842 8.742777 ACACCTTACAGTTTCGTGAGTATATTA 58.257 33.333 0.00 0.00 0.00 0.98
1764 1843 7.609056 ACACCTTACAGTTTCGTGAGTATATT 58.391 34.615 0.00 0.00 0.00 1.28
1766 1845 6.579666 ACACCTTACAGTTTCGTGAGTATA 57.420 37.500 0.00 0.00 0.00 1.47
1767 1846 5.464030 ACACCTTACAGTTTCGTGAGTAT 57.536 39.130 0.00 0.00 0.00 2.12
1768 1847 4.924305 ACACCTTACAGTTTCGTGAGTA 57.076 40.909 0.00 0.00 0.00 2.59
1769 1848 3.814005 ACACCTTACAGTTTCGTGAGT 57.186 42.857 0.00 0.00 0.00 3.41
1770 1849 6.780706 AAATACACCTTACAGTTTCGTGAG 57.219 37.500 0.00 0.00 0.00 3.51
1849 1938 6.656314 TGTTTCGCATAAACCACATACTAG 57.344 37.500 8.69 0.00 0.00 2.57
2070 2159 8.887036 ATTGAACAAAACTATTCCCAAAAGAC 57.113 30.769 0.00 0.00 0.00 3.01
2198 2297 4.406456 ACCTGACCAATTTGCATCACTTA 58.594 39.130 0.00 0.00 0.00 2.24
2211 2310 1.358152 CTCCCCTACAACCTGACCAA 58.642 55.000 0.00 0.00 0.00 3.67
2357 2457 1.153329 AGTTTGGTCCGTGCGAACA 60.153 52.632 0.00 0.00 35.97 3.18
2365 2465 2.230508 TCAGCTACTACAGTTTGGTCCG 59.769 50.000 0.00 0.00 0.00 4.79
2372 2472 3.057456 CGTCAGGTTCAGCTACTACAGTT 60.057 47.826 0.00 0.00 0.00 3.16
2397 2497 2.288666 TGACAGAAGGAACAGTTGCAC 58.711 47.619 7.64 1.07 0.00 4.57
2529 2629 5.051891 CTTGCCATTTGAGGTAAGTTCTG 57.948 43.478 3.11 0.00 43.72 3.02
2543 2643 1.891150 CACCTCAAAGCTCTTGCCATT 59.109 47.619 0.00 0.00 40.80 3.16
2643 2743 1.526575 TTTACGGCCTTCGGAGTCGT 61.527 55.000 12.81 12.81 44.45 4.34
2683 2783 1.073177 GGTGTGGAATACCGTTGACG 58.927 55.000 0.00 0.00 38.73 4.35
2743 2843 3.246226 CACTCACAAACTCAACTCCTTCG 59.754 47.826 0.00 0.00 0.00 3.79
2944 3044 8.414003 TGTCTAGATCTGTAAAAGCGTGAATAT 58.586 33.333 5.18 0.00 0.00 1.28
2945 3045 7.768240 TGTCTAGATCTGTAAAAGCGTGAATA 58.232 34.615 5.18 0.00 0.00 1.75
3169 3269 9.912634 GAAAAACTGTTATTGAATGATTCCTCA 57.087 29.630 2.26 0.00 35.41 3.86
3337 3437 2.093921 TGCATCCAAACCATGCTCATTG 60.094 45.455 6.24 0.00 45.90 2.82
3403 3503 2.162681 GCTTTAGCCTTTGCCTTCTCA 58.837 47.619 0.00 0.00 38.69 3.27
3427 3527 1.905215 AGGGACTCCAATGTCTGTGAG 59.095 52.381 0.00 0.00 37.16 3.51
3466 3566 3.053831 TCTTTCCCGATGACAAAGTCC 57.946 47.619 0.00 0.00 0.00 3.85
4058 4233 7.684529 ACCCAAGCAAAATAATTTGTCCATTA 58.315 30.769 5.21 0.00 46.19 1.90
4079 4254 0.699577 TCCCTTTGTTCCTGGACCCA 60.700 55.000 0.00 0.00 0.00 4.51
4106 4281 4.199432 AGGCTATCTGATAAATGGCTCG 57.801 45.455 5.88 0.00 31.85 5.03
4198 4469 8.037758 AGATAACACATCAGAAGTCTAAACCAG 58.962 37.037 0.00 0.00 0.00 4.00
4207 4478 9.376075 CACAATCTTAGATAACACATCAGAAGT 57.624 33.333 0.00 0.00 0.00 3.01
4208 4479 9.591792 TCACAATCTTAGATAACACATCAGAAG 57.408 33.333 0.00 0.00 0.00 2.85
4225 4496 9.814899 CAGTCTTCTCATACTTATCACAATCTT 57.185 33.333 0.00 0.00 0.00 2.40
4226 4497 9.194972 TCAGTCTTCTCATACTTATCACAATCT 57.805 33.333 0.00 0.00 0.00 2.40
4227 4498 9.809096 TTCAGTCTTCTCATACTTATCACAATC 57.191 33.333 0.00 0.00 0.00 2.67
4273 4555 2.540383 TCTGCTACAGGAACCTGACAT 58.460 47.619 25.03 7.63 46.30 3.06
4378 4660 6.931281 TGTTCTTCTCCTTGATCTTGTTGTAG 59.069 38.462 0.00 0.00 0.00 2.74
4424 4706 0.680280 TGGTCCCTGTCGCTAGAGAC 60.680 60.000 18.64 18.64 41.30 3.36
4540 4822 1.195115 CGACCAGAGAAGGGATTCCA 58.805 55.000 4.80 0.00 34.83 3.53
4643 4925 0.467290 AGCTCCTGGATCCTCTCGTC 60.467 60.000 14.23 0.00 0.00 4.20
4644 4926 0.754957 CAGCTCCTGGATCCTCTCGT 60.755 60.000 14.23 0.00 0.00 4.18
4678 4960 1.380380 CCACCCCTTTGCCATCTCC 60.380 63.158 0.00 0.00 0.00 3.71
4687 4969 1.770324 CTTCTCAGGCCACCCCTTT 59.230 57.895 5.01 0.00 43.06 3.11
4843 5125 2.922503 TTCTCCTCACCCAGCGCA 60.923 61.111 11.47 0.00 0.00 6.09
4981 5274 0.097674 GCACATGATTCAGACACGCC 59.902 55.000 0.00 0.00 0.00 5.68
5087 5383 8.730680 GCAAAGATCTGAAACCATAAACTTAGA 58.269 33.333 0.00 0.00 0.00 2.10
5088 5384 7.970614 GGCAAAGATCTGAAACCATAAACTTAG 59.029 37.037 0.00 0.00 0.00 2.18
5094 5392 6.916360 AAAGGCAAAGATCTGAAACCATAA 57.084 33.333 0.00 0.00 0.00 1.90
5203 5506 0.325577 GGGTGAAAGAATGGGGGCAT 60.326 55.000 0.00 0.00 0.00 4.40
5207 5510 0.679960 GGACGGGTGAAAGAATGGGG 60.680 60.000 0.00 0.00 0.00 4.96
5210 5513 1.806542 CAGTGGACGGGTGAAAGAATG 59.193 52.381 0.00 0.00 0.00 2.67
5215 5518 0.834612 AGAACAGTGGACGGGTGAAA 59.165 50.000 0.00 0.00 0.00 2.69
5297 5601 8.314021 ACTTCTAATTTCCAAAATGTTCATCCC 58.686 33.333 0.00 0.00 0.00 3.85
5322 5626 8.567948 TGGTGTTTCTAGATGAGAATTTGAAAC 58.432 33.333 0.00 0.00 43.84 2.78
5341 5645 7.503566 TCTCTTCTCTGAAATTTCATGGTGTTT 59.496 33.333 20.76 0.00 36.46 2.83
5411 5803 2.861462 TGGTTCGCCTTTTCTTGTTG 57.139 45.000 0.00 0.00 38.36 3.33
5465 5857 1.067582 GGCGAGATGGAACTACCGG 59.932 63.158 0.00 0.00 42.61 5.28
5517 5909 7.668525 ACGAAAGGAATACTACAAAGGAAAG 57.331 36.000 0.00 0.00 0.00 2.62
5520 5912 8.454570 AAAAACGAAAGGAATACTACAAAGGA 57.545 30.769 0.00 0.00 0.00 3.36
5617 6028 9.161629 GAGGAAAACCAAGAAAATTGAAGAAAA 57.838 29.630 0.00 0.00 0.00 2.29
5624 6035 9.112725 AGAAAATGAGGAAAACCAAGAAAATTG 57.887 29.630 0.00 0.00 0.00 2.32
5625 6036 9.685276 AAGAAAATGAGGAAAACCAAGAAAATT 57.315 25.926 0.00 0.00 0.00 1.82
5903 6325 7.305763 GCTTCAACGTGTATTTCGAAAATGTTT 60.306 33.333 15.66 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.