Multiple sequence alignment - TraesCS3B01G174400

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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 TraesCS3B01G174400 chr3B 100.000 5638 0 0 1 5638 175763306 175757669 0.000000e+00 10412.0
1 TraesCS3B01G174400 chr3A 92.598 2756 149 19 2908 5638 130838830 130836105 0.000000e+00 3908.0
2 TraesCS3B01G174400 chr3A 87.741 1974 118 49 2 1899 130841961 130840036 0.000000e+00 2191.0
3 TraesCS3B01G174400 chr3A 95.817 765 27 3 1901 2661 130839951 130839188 0.000000e+00 1230.0
4 TraesCS3B01G174400 chr3A 95.349 258 11 1 2655 2911 130839157 130838900 5.260000e-110 409.0
5 TraesCS3B01G174400 chr3D 93.364 2426 100 24 2909 5319 123299039 123296660 0.000000e+00 3531.0
6 TraesCS3B01G174400 chr3D 92.953 1490 64 7 426 1899 123301707 123300243 0.000000e+00 2132.0
7 TraesCS3B01G174400 chr3D 93.161 775 39 7 1901 2661 123300157 123299383 0.000000e+00 1125.0
8 TraesCS3B01G174400 chr3D 96.129 310 12 0 89 398 123303730 123303421 1.810000e-139 507.0
9 TraesCS3B01G174400 chr3D 93.103 319 16 2 5320 5638 123296611 123296299 3.980000e-126 462.0
10 TraesCS3B01G174400 chr3D 93.411 258 16 1 2655 2911 123299352 123299095 1.150000e-101 381.0
11 TraesCS3B01G174400 chr3D 95.506 89 4 0 1 89 123304002 123303914 5.890000e-30 143.0
12 TraesCS3B01G174400 chr3D 100.000 38 0 0 385 422 123301774 123301737 2.820000e-08 71.3


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 TraesCS3B01G174400 chr3B 175757669 175763306 5637 True 10412.0000 10412 100.000000 1 5638 1 chr3B.!!$R1 5637
1 TraesCS3B01G174400 chr3A 130836105 130841961 5856 True 1934.5000 3908 92.876250 2 5638 4 chr3A.!!$R1 5636
2 TraesCS3B01G174400 chr3D 123296299 123304002 7703 True 1044.0375 3531 94.703375 1 5638 8 chr3D.!!$R1 5637

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
499 2393 0.171007 CATGGCGCACGGAAGAAAAT 59.829 50.000 10.83 0.0 0.00 1.82 F
1037 2955 0.033504 TGCTCTTCCACCGTCTTCAC 59.966 55.000 0.00 0.0 0.00 3.18 F
1038 2956 0.670854 GCTCTTCCACCGTCTTCACC 60.671 60.000 0.00 0.0 0.00 4.02 F
1753 3687 0.878416 TTCGTACACAATGCTTGCCC 59.122 50.000 0.00 0.0 0.00 5.36 F
1841 3775 2.095919 CCAGTTCAAAATCCGGTTCGAC 60.096 50.000 0.00 0.0 0.00 4.20 F
2695 4768 2.760634 TGCCTGACGAGCTTAATTGA 57.239 45.000 0.00 0.0 0.00 2.57 F
3110 5256 1.063174 CGATAGCCTTTGCAGTTGCTC 59.937 52.381 8.91 0.0 42.66 4.26 F
3832 5983 2.029380 TGAGCAGCAACTATGTACACGT 60.029 45.455 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 3712 0.179234 TCAGTCTGCCGGTTTCAACA 59.821 50.000 1.90 0.00 0.00 3.33 R
2380 4402 1.072331 TGGCAGACAAGGTCCTCTTTC 59.928 52.381 0.00 0.00 32.41 2.62 R
2393 4415 1.809684 GTCAACTAAGGGTGGCAGAC 58.190 55.000 0.00 0.00 0.00 3.51 R
2734 4807 3.328931 TCTTTTCTCCATCACCTGAAGCT 59.671 43.478 0.00 0.00 0.00 3.74 R
3110 5256 4.333649 ACAAGAATATCATCAAGTGCACCG 59.666 41.667 14.63 5.24 0.00 4.94 R
3889 6041 0.907486 TGCAATCTGTGGGAGGAGAG 59.093 55.000 0.00 0.00 0.00 3.20 R
3920 6072 1.005215 AGGAATGTCCCCAGCAAAGAG 59.995 52.381 0.00 0.00 37.19 2.85 R
5441 7666 2.012902 TTAGCTTAGTCCTCGCCGCC 62.013 60.000 0.00 0.00 0.00 6.13 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
50 51 9.270640 AGCATCATTTATTTCTCTGTAGTCATC 57.729 33.333 0.00 0.00 0.00 2.92
91 297 6.126623 TGGGGCTTTAACATACATACATCTGA 60.127 38.462 0.00 0.00 0.00 3.27
146 352 7.772332 TCACACTTCTTCTCTGTTAAAACTC 57.228 36.000 0.00 0.00 0.00 3.01
154 360 7.861630 TCTTCTCTGTTAAAACTCAATTTCCG 58.138 34.615 0.00 0.00 0.00 4.30
299 505 2.797156 CTGTTCATCCTACATAGTGCGC 59.203 50.000 0.00 0.00 0.00 6.09
376 584 1.332195 CATCGTCCTATCTGCCCAGA 58.668 55.000 0.00 0.00 42.37 3.86
379 587 0.757188 CGTCCTATCTGCCCAGAGGT 60.757 60.000 4.16 0.00 41.33 3.85
422 2290 0.255890 CCAGGGTCGTCCAATCCAAT 59.744 55.000 0.04 0.00 38.24 3.16
423 2291 1.382522 CAGGGTCGTCCAATCCAATG 58.617 55.000 0.04 0.00 38.24 2.82
428 2322 2.421388 GGTCGTCCAATCCAATGATCCA 60.421 50.000 0.00 0.00 0.00 3.41
436 2330 2.353357 TCCAATGATCCATGACCAGC 57.647 50.000 0.00 0.00 0.00 4.85
469 2363 1.167781 AAACCTTAACCACCACGGCG 61.168 55.000 4.80 4.80 39.03 6.46
470 2364 2.042404 AACCTTAACCACCACGGCGA 62.042 55.000 16.62 0.00 39.03 5.54
471 2365 1.301874 CCTTAACCACCACGGCGAA 60.302 57.895 16.62 0.00 39.03 4.70
472 2366 1.571215 CCTTAACCACCACGGCGAAC 61.571 60.000 16.62 0.00 39.03 3.95
473 2367 0.881159 CTTAACCACCACGGCGAACA 60.881 55.000 16.62 0.00 39.03 3.18
474 2368 0.250381 TTAACCACCACGGCGAACAT 60.250 50.000 16.62 0.00 39.03 2.71
475 2369 0.671163 TAACCACCACGGCGAACATC 60.671 55.000 16.62 0.00 39.03 3.06
476 2370 2.358125 CCACCACGGCGAACATCA 60.358 61.111 16.62 0.00 0.00 3.07
499 2393 0.171007 CATGGCGCACGGAAGAAAAT 59.829 50.000 10.83 0.00 0.00 1.82
610 2510 4.657824 CAGGCGAACACGGACGGT 62.658 66.667 0.00 0.00 0.00 4.83
631 2531 4.537433 CCTCGCAGGGGCTAGCAC 62.537 72.222 18.24 14.02 38.10 4.40
632 2532 4.880537 CTCGCAGGGGCTAGCACG 62.881 72.222 18.24 11.55 38.10 5.34
742 2642 2.982744 GCGAGCTCCTGGCAAAACC 61.983 63.158 8.47 0.00 44.79 3.27
751 2651 2.968697 GGCAAAACCGACGACCGT 60.969 61.111 0.00 0.00 36.31 4.83
908 2815 2.385803 ACCCGTTCGAACTCTATCCAT 58.614 47.619 24.80 0.49 0.00 3.41
1037 2955 0.033504 TGCTCTTCCACCGTCTTCAC 59.966 55.000 0.00 0.00 0.00 3.18
1038 2956 0.670854 GCTCTTCCACCGTCTTCACC 60.671 60.000 0.00 0.00 0.00 4.02
1039 2957 0.969894 CTCTTCCACCGTCTTCACCT 59.030 55.000 0.00 0.00 0.00 4.00
1177 3101 3.013921 GGACAGAGATAGATAGCTCCCG 58.986 54.545 0.00 0.00 39.44 5.14
1179 3103 2.645297 ACAGAGATAGATAGCTCCCGGA 59.355 50.000 0.73 0.00 39.44 5.14
1183 3107 3.360867 AGATAGATAGCTCCCGGATGTG 58.639 50.000 0.73 0.00 0.00 3.21
1184 3108 2.677542 TAGATAGCTCCCGGATGTGT 57.322 50.000 0.73 0.00 0.00 3.72
1236 3160 4.341783 GCAGGTGCTGAGGTGCCT 62.342 66.667 0.00 0.00 38.21 4.75
1349 3276 4.814294 GGCTCGCACCGTCCGATT 62.814 66.667 0.00 0.00 33.83 3.34
1541 3469 3.848019 CCTTTCAATTTGATGCTTCGTCG 59.152 43.478 0.00 0.00 0.00 5.12
1563 3491 6.147656 GTCGGTTCCTTTTATTTCTTTCCGTA 59.852 38.462 0.00 0.00 36.36 4.02
1596 3524 1.004927 GTCGCGTACATTTCTGATGCC 60.005 52.381 5.77 0.00 0.00 4.40
1689 3620 4.450976 GGTGAGTATATCCATGCACACAA 58.549 43.478 0.00 0.00 39.13 3.33
1753 3687 0.878416 TTCGTACACAATGCTTGCCC 59.122 50.000 0.00 0.00 0.00 5.36
1778 3712 6.265577 GCATTTTCTATTCCGCAAACTACAT 58.734 36.000 0.00 0.00 0.00 2.29
1805 3739 2.699954 ACCGGCAGACTGAACTAAATG 58.300 47.619 6.65 0.00 0.00 2.32
1814 3748 3.825308 ACTGAACTAAATGTTGCATGCG 58.175 40.909 14.09 0.00 39.30 4.73
1815 3749 3.173599 CTGAACTAAATGTTGCATGCGG 58.826 45.455 14.09 0.00 39.30 5.69
1841 3775 2.095919 CCAGTTCAAAATCCGGTTCGAC 60.096 50.000 0.00 0.00 0.00 4.20
1889 3824 3.434309 TGAACACCCCTACCACTAGTAC 58.566 50.000 0.00 0.00 0.00 2.73
1899 3834 5.775701 CCCTACCACTAGTACTGCATTCTAT 59.224 44.000 5.39 0.00 0.00 1.98
1914 3933 9.448438 ACTGCATTCTATTTCACAAGTTATGTA 57.552 29.630 0.00 0.00 41.46 2.29
1931 3950 9.530633 AAGTTATGTAGCTTCCTATTTACTTCG 57.469 33.333 0.00 0.00 0.00 3.79
1957 3976 5.470098 ACTCTGTGCTACACAAGTAATTTGG 59.530 40.000 1.64 0.00 44.08 3.28
2042 4061 5.335935 GCACTTTTAGCAGCTAGAAATTCC 58.664 41.667 6.84 0.00 0.00 3.01
2094 4113 4.235360 AGCACTTGCGTAAGTACTACAAG 58.765 43.478 18.77 18.76 45.12 3.16
2254 4276 9.974750 GCTTTTACTTGAACATATCAGACTTAC 57.025 33.333 0.00 0.00 39.77 2.34
2380 4402 7.009174 GGTGATTGTACTTGTTGTTGAAGTTTG 59.991 37.037 0.00 0.00 35.30 2.93
2393 4415 5.125417 TGTTGAAGTTTGAAAGAGGACCTTG 59.875 40.000 0.00 0.00 34.79 3.61
2451 4475 7.246171 TGCTCTTAGTGAAGAACCTTCTAAT 57.754 36.000 8.02 0.00 41.23 1.73
2550 4574 3.876914 TGTGTGTCTCTTGGTAAGCAAAG 59.123 43.478 0.00 0.00 0.00 2.77
2558 4585 3.813166 TCTTGGTAAGCAAAGAAACCTCG 59.187 43.478 0.00 0.00 32.02 4.63
2562 4589 4.933400 TGGTAAGCAAAGAAACCTCGTATC 59.067 41.667 0.00 0.00 32.99 2.24
2684 4757 6.345723 GTTTAAAAACATTGTCATGCCTGACG 60.346 38.462 16.02 5.93 44.67 4.35
2695 4768 2.760634 TGCCTGACGAGCTTAATTGA 57.239 45.000 0.00 0.00 0.00 2.57
2734 4807 6.941857 TGGAGTTACTACATTACTTGATGCA 58.058 36.000 0.00 0.00 0.00 3.96
2767 4840 6.600822 GTGATGGAGAAAAGATGAATGAGGAA 59.399 38.462 0.00 0.00 0.00 3.36
2849 4922 9.811995 CAAATTTCAGGTCACAATATTCATGAT 57.188 29.630 0.00 0.00 0.00 2.45
2957 5103 7.298507 TCGTGTGCTTATATTGTAAACCTTC 57.701 36.000 0.00 0.00 0.00 3.46
3028 5174 7.632462 TCTTCAAAAGAAGTATGCAAAAAGGCA 60.632 33.333 0.00 0.00 40.62 4.75
3044 5190 4.913335 AAGGCAATGCATACAAGATCAG 57.087 40.909 7.79 0.00 0.00 2.90
3068 5214 8.892723 CAGTGACATTAAGGAATATACTGCAAA 58.107 33.333 0.00 0.00 29.94 3.68
3110 5256 1.063174 CGATAGCCTTTGCAGTTGCTC 59.937 52.381 8.91 0.00 42.66 4.26
3158 5304 3.181329 TGGCCCTCTTTCTGTCTGATAA 58.819 45.455 0.00 0.00 0.00 1.75
3160 5306 4.968719 TGGCCCTCTTTCTGTCTGATAATA 59.031 41.667 0.00 0.00 0.00 0.98
3494 5643 4.355437 TGCAACATTGGTAAGAAACAACG 58.645 39.130 0.00 0.00 0.00 4.10
3524 5673 6.222389 TGACAAAAATGGTCCTAATTTGCAG 58.778 36.000 11.39 0.00 35.05 4.41
3566 5716 8.457261 AGTTATCTGTAGTCAACGTACTAAAGG 58.543 37.037 13.41 2.99 37.73 3.11
3595 5746 4.746535 ATTGCAATTGATGGAATGCTGA 57.253 36.364 10.34 0.00 46.88 4.26
3688 5839 4.298103 ACTGCCTTCTCTTGTTGATCAT 57.702 40.909 0.00 0.00 0.00 2.45
3832 5983 2.029380 TGAGCAGCAACTATGTACACGT 60.029 45.455 0.00 0.00 0.00 4.49
3889 6041 9.160496 CTCTTATGGAGATTGGCATTAACTATC 57.840 37.037 0.00 0.00 44.45 2.08
3899 6051 3.904339 GGCATTAACTATCTCTCCTCCCA 59.096 47.826 0.00 0.00 0.00 4.37
3920 6072 1.068055 CAGATTGCAGTTCTTGGTGGC 60.068 52.381 0.00 0.00 0.00 5.01
3973 6125 7.604657 AGGTAAATCAGTACTATCAAGGGAG 57.395 40.000 0.00 0.00 0.00 4.30
4054 6221 2.322339 AGAAGAAACTACCGGGGAGT 57.678 50.000 5.94 5.94 0.00 3.85
4056 6223 2.177734 GAAGAAACTACCGGGGAGTCT 58.822 52.381 13.50 0.00 0.00 3.24
4057 6224 1.558233 AGAAACTACCGGGGAGTCTG 58.442 55.000 13.50 0.00 0.00 3.51
4143 6310 4.759693 TGCTCCGTGTAAATGAATTTGACT 59.240 37.500 0.00 0.00 0.00 3.41
4184 6351 9.853555 CCATGTTTAAATTGCTACAGATTTGTA 57.146 29.630 0.00 0.00 38.76 2.41
4217 6384 6.317789 ACATTTGTTTGTCACTCGATCAAT 57.682 33.333 0.00 0.00 0.00 2.57
4314 6481 0.179145 ATGAGCTCATGCAAAAGCGC 60.179 50.000 28.21 16.88 43.37 5.92
4365 6532 7.220300 AGCGAAATCTACTCATACTTAAACACG 59.780 37.037 0.00 0.00 0.00 4.49
4381 6548 8.886719 ACTTAAACACGGGCTATTATAGAAAAC 58.113 33.333 3.04 0.00 0.00 2.43
4445 6612 9.984190 AATAATATCGACTTTAGGGACTTCTTC 57.016 33.333 0.00 0.00 41.75 2.87
4534 6701 5.797051 ACAAATTCCTGCACAATTTATGCT 58.203 33.333 11.69 0.00 43.77 3.79
4540 6707 4.082625 TCCTGCACAATTTATGCTCAACAG 60.083 41.667 11.69 2.20 43.77 3.16
4688 6855 3.342719 TGGTACATAACAGGTGTGCATG 58.657 45.455 0.00 0.00 34.42 4.06
4839 7006 5.821470 ACTGATATGCTGAAGGTCTTGATTG 59.179 40.000 0.00 0.00 0.00 2.67
4842 7009 3.777106 TGCTGAAGGTCTTGATTGTCT 57.223 42.857 0.00 0.00 0.00 3.41
4977 7144 2.720659 TGAGACTCAGAGCACGTGT 58.279 52.632 18.38 3.69 0.00 4.49
4981 7148 3.067601 TGAGACTCAGAGCACGTGTAAAA 59.932 43.478 18.38 0.00 0.00 1.52
5113 7283 3.733443 AACATTGTTCAGGGAAAGCAC 57.267 42.857 0.00 0.00 0.00 4.40
5114 7284 2.665165 ACATTGTTCAGGGAAAGCACA 58.335 42.857 0.00 0.00 0.00 4.57
5115 7285 2.362077 ACATTGTTCAGGGAAAGCACAC 59.638 45.455 0.00 0.00 0.00 3.82
5116 7286 2.435372 TTGTTCAGGGAAAGCACACT 57.565 45.000 0.00 0.00 0.00 3.55
5179 7349 3.071602 ACAGAAAGTCTATGGCACTGTGT 59.928 43.478 9.86 0.00 36.11 3.72
5344 7569 8.706035 GGCAAAAATGATCATGCTCAATTATAC 58.294 33.333 16.39 0.00 38.79 1.47
5381 7606 4.870363 ACAACATCCAAAAATCTGAACCG 58.130 39.130 0.00 0.00 0.00 4.44
5405 7630 9.655769 CCGATCTTTTGAATTACAATCATAGTG 57.344 33.333 0.00 0.00 38.36 2.74
5430 7655 7.526142 CTACTGTAGCAATTAGGGATACTGA 57.474 40.000 1.26 0.00 32.60 3.41
5441 7666 4.408182 AGGGATACTGACCAATTTCTCG 57.592 45.455 0.00 0.00 0.00 4.04
5594 7819 3.634910 TGCATAGAGTATACAGCGTTGGA 59.365 43.478 5.50 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.749621 GCCCCACTTCATTTCACTACTG 59.250 50.000 0.00 0.00 0.00 2.74
91 297 8.224389 TCATTCCATACAATTTGATTGATCGT 57.776 30.769 2.79 0.00 42.83 3.73
146 352 3.176708 CTCAATCAGCAAGCGGAAATTG 58.823 45.455 0.00 1.12 0.00 2.32
268 474 0.108424 GGATGAACAGCGAGCAGAGT 60.108 55.000 0.00 0.00 0.00 3.24
299 505 7.819415 TGTTCTAGTGTTCTGGATTTGATAGTG 59.181 37.037 0.00 0.00 31.53 2.74
376 584 1.129058 CTCCGGGCTTATTGGTACCT 58.871 55.000 14.36 0.00 0.00 3.08
379 587 1.125633 GTCCTCCGGGCTTATTGGTA 58.874 55.000 0.00 0.00 0.00 3.25
422 2290 1.565288 TGAATGGCTGGTCATGGATCA 59.435 47.619 0.00 0.00 0.00 2.92
423 2291 2.228059 CTGAATGGCTGGTCATGGATC 58.772 52.381 0.00 0.00 0.00 3.36
428 2322 2.719739 CTTGACTGAATGGCTGGTCAT 58.280 47.619 0.00 0.00 38.29 3.06
436 2330 5.222631 GTTAAGGTTTGCTTGACTGAATGG 58.777 41.667 0.00 0.00 0.00 3.16
499 2393 0.748367 TTGGTTTGTACTGGCGTGCA 60.748 50.000 0.00 0.00 33.79 4.57
605 2505 4.436998 CCTGCGAGGGACACCGTC 62.437 72.222 0.00 0.00 43.47 4.79
623 2523 2.027751 GATCCGGTCGTGCTAGCC 59.972 66.667 13.29 2.49 0.00 3.93
624 2524 2.353607 CGATCCGGTCGTGCTAGC 60.354 66.667 8.10 8.10 45.19 3.42
632 2532 0.890090 CTAGGAGGGACGATCCGGTC 60.890 65.000 0.00 0.00 42.02 4.79
703 2603 1.658994 GGAGTCGACGAGAGAGTGAT 58.341 55.000 10.46 0.00 0.00 3.06
742 2642 0.388134 ATTGTCTTGGACGGTCGTCG 60.388 55.000 15.85 4.37 45.41 5.12
751 2651 0.251297 CACCCCAGCATTGTCTTGGA 60.251 55.000 5.81 0.00 0.00 3.53
908 2815 2.282180 GCTCTTGGCCGTTGGGAA 60.282 61.111 0.00 0.00 34.06 3.97
936 2843 2.345760 GGGACGGACTGAGCGGTTA 61.346 63.158 0.00 0.00 0.00 2.85
1037 2955 1.162505 TATGGAGGAGGAGGAGGAGG 58.837 60.000 0.00 0.00 0.00 4.30
1038 2956 1.203125 GGTATGGAGGAGGAGGAGGAG 60.203 61.905 0.00 0.00 0.00 3.69
1039 2957 0.861155 GGTATGGAGGAGGAGGAGGA 59.139 60.000 0.00 0.00 0.00 3.71
1118 3036 3.702048 GCTGTACCAGTCGGCCCA 61.702 66.667 0.00 0.00 34.57 5.36
1127 3045 1.445410 GATCGTGTGCGCTGTACCA 60.445 57.895 9.73 0.00 38.14 3.25
1177 3101 1.079127 CAGGTGGTCCGACACATCC 60.079 63.158 0.00 0.00 43.08 3.51
1179 3103 1.671742 GTCAGGTGGTCCGACACAT 59.328 57.895 0.00 0.00 43.08 3.21
1189 3113 3.081133 CGATTTCGCGTCAGGTGG 58.919 61.111 5.77 0.00 0.00 4.61
1236 3160 2.491152 CCGGGTCGCGTTTAGCTA 59.509 61.111 5.77 0.00 45.59 3.32
1263 3190 0.461693 CACAGGAGCTCTAAGCAGCC 60.462 60.000 14.64 2.56 45.56 4.85
1271 3198 1.346068 GTCAGAAACCACAGGAGCTCT 59.654 52.381 14.64 0.00 0.00 4.09
1541 3469 8.355169 ACTTTACGGAAAGAAATAAAAGGAACC 58.645 33.333 26.78 0.00 44.23 3.62
1563 3491 1.508632 ACGCGACATGCACTTACTTT 58.491 45.000 15.93 0.00 46.97 2.66
1596 3524 6.487668 AGAAAAGCCTGAAATTGAATTTTGGG 59.512 34.615 18.40 16.39 31.47 4.12
1753 3687 3.758300 AGTTTGCGGAATAGAAAATGCG 58.242 40.909 0.00 0.00 0.00 4.73
1778 3712 0.179234 TCAGTCTGCCGGTTTCAACA 59.821 50.000 1.90 0.00 0.00 3.33
1814 3748 2.423538 CCGGATTTTGAACTGGATGTCC 59.576 50.000 0.00 0.00 34.76 4.02
1815 3749 3.081804 ACCGGATTTTGAACTGGATGTC 58.918 45.455 9.46 0.00 36.50 3.06
1841 3775 2.873133 TAGTTGGTTTTGCGGTTTGG 57.127 45.000 0.00 0.00 0.00 3.28
1889 3824 9.926751 CTACATAACTTGTGAAATAGAATGCAG 57.073 33.333 0.00 0.00 39.48 4.41
1899 3834 9.515226 AAATAGGAAGCTACATAACTTGTGAAA 57.485 29.630 0.00 0.00 39.48 2.69
1914 3933 4.160626 AGAGTGCGAAGTAAATAGGAAGCT 59.839 41.667 0.00 0.00 0.00 3.74
1931 3950 9.830370 CCAAATTACTTGTGTAGCACAGAGTGC 62.830 44.444 13.87 13.87 45.39 4.40
1944 3963 6.744112 ACACATTGGTACCAAATTACTTGTG 58.256 36.000 34.37 34.37 39.55 3.33
1957 3976 9.769093 GACTCATTTTTGTATACACATTGGTAC 57.231 33.333 4.68 0.00 33.76 3.34
2042 4061 2.162408 GCCAAGAAAAATGACTCCTCCG 59.838 50.000 0.00 0.00 0.00 4.63
2254 4276 4.342092 ACCCAAGAAGATCAACCTTGTTTG 59.658 41.667 15.70 9.42 36.47 2.93
2380 4402 1.072331 TGGCAGACAAGGTCCTCTTTC 59.928 52.381 0.00 0.00 32.41 2.62
2393 4415 1.809684 GTCAACTAAGGGTGGCAGAC 58.190 55.000 0.00 0.00 0.00 3.51
2451 4475 5.933617 AGGCACATCAGATAAGAATAGCAA 58.066 37.500 0.00 0.00 0.00 3.91
2550 4574 9.698617 GTAAATGTAACAATGATACGAGGTTTC 57.301 33.333 0.00 0.00 0.00 2.78
2734 4807 3.328931 TCTTTTCTCCATCACCTGAAGCT 59.671 43.478 0.00 0.00 0.00 3.74
2767 4840 5.888982 TTTGAAGTTCTACCTCCTCTTGT 57.111 39.130 4.17 0.00 0.00 3.16
2809 4882 9.921637 GACCTGAAATTTGAGGATATACTAGAG 57.078 37.037 27.84 0.00 34.93 2.43
2814 4887 8.506168 TTGTGACCTGAAATTTGAGGATATAC 57.494 34.615 27.84 18.97 34.93 1.47
2823 4896 9.811995 ATCATGAATATTGTGACCTGAAATTTG 57.188 29.630 0.00 0.00 0.00 2.32
2849 4922 9.958180 TGAATGTGTTTTTCTCTAAGATCCATA 57.042 29.630 0.00 0.00 0.00 2.74
3028 5174 8.510243 TTAATGTCACTGATCTTGTATGCATT 57.490 30.769 3.54 7.18 0.00 3.56
3030 5176 6.539826 CCTTAATGTCACTGATCTTGTATGCA 59.460 38.462 0.00 0.00 0.00 3.96
3044 5190 9.722056 CTTTTGCAGTATATTCCTTAATGTCAC 57.278 33.333 0.00 0.00 0.00 3.67
3110 5256 4.333649 ACAAGAATATCATCAAGTGCACCG 59.666 41.667 14.63 5.24 0.00 4.94
3360 5509 9.696917 GTCAATCTTGGTTGTGAAAATAGAATT 57.303 29.630 0.00 0.00 0.00 2.17
3380 5529 6.136541 AGAACAAGGAAACAAGTGTCAATC 57.863 37.500 0.00 0.00 0.00 2.67
3494 5643 6.887626 TTAGGACCATTTTTGTCAAGTACC 57.112 37.500 0.00 0.00 34.36 3.34
3524 5673 8.635877 ACAGATAACTTATCACGAGAATGTTC 57.364 34.615 10.76 0.00 37.65 3.18
3566 5716 7.327761 GCATTCCATCAATTGCAATGTATAGTC 59.672 37.037 13.82 0.00 0.00 2.59
3595 5746 6.686484 AATGACCAAAGCCCTAAAGAATTT 57.314 33.333 0.00 0.00 43.42 1.82
3889 6041 0.907486 TGCAATCTGTGGGAGGAGAG 59.093 55.000 0.00 0.00 0.00 3.20
3899 6051 2.233271 CCACCAAGAACTGCAATCTGT 58.767 47.619 2.65 0.00 0.00 3.41
3920 6072 1.005215 AGGAATGTCCCCAGCAAAGAG 59.995 52.381 0.00 0.00 37.19 2.85
3965 6117 2.269023 TGAGAAATCAGGCTCCCTTGA 58.731 47.619 0.00 0.00 0.00 3.02
3999 6156 1.410004 TGCTAGGGATGTTAGTCGGG 58.590 55.000 0.00 0.00 0.00 5.14
4033 6200 3.363627 ACTCCCCGGTAGTTTCTTCTAG 58.636 50.000 0.00 0.00 0.00 2.43
4054 6221 3.068691 CCGGGTTCGAGGCTCAGA 61.069 66.667 15.95 9.96 39.00 3.27
4057 6224 4.452733 CACCCGGGTTCGAGGCTC 62.453 72.222 27.83 3.87 39.00 4.70
4082 6249 2.360726 TAGAGGCGACCGTGCTCA 60.361 61.111 0.00 0.00 34.52 4.26
4121 6288 5.296813 AGTCAAATTCATTTACACGGAGC 57.703 39.130 0.00 0.00 0.00 4.70
4143 6310 4.447138 AACATGGGAGTGAAACCACTAA 57.553 40.909 0.00 0.00 44.34 2.24
4184 6351 4.277174 TGACAAACAAATGTAATCCGCACT 59.723 37.500 0.00 0.00 32.57 4.40
4188 6355 5.079406 CGAGTGACAAACAAATGTAATCCG 58.921 41.667 0.00 0.00 32.57 4.18
4341 6508 7.043590 CCCGTGTTTAAGTATGAGTAGATTTCG 60.044 40.741 0.00 0.00 0.00 3.46
4425 6592 5.017490 TGAGAAGAAGTCCCTAAAGTCGAT 58.983 41.667 0.00 0.00 0.00 3.59
4445 6612 4.551388 GAGTATTTATCTCCACGGCTGAG 58.449 47.826 0.00 0.00 0.00 3.35
4477 6644 3.525800 AGTTTCCTACAAATGTGGCCT 57.474 42.857 3.32 0.00 0.00 5.19
4478 6645 3.572255 TCAAGTTTCCTACAAATGTGGCC 59.428 43.478 0.00 0.00 0.00 5.36
4688 6855 8.749499 GCATTTTGCAAGTAAATGATGTATCTC 58.251 33.333 21.14 2.86 44.26 2.75
4829 6996 7.454260 AAATTTCCTGTAGACAATCAAGACC 57.546 36.000 0.00 0.00 0.00 3.85
4842 7009 8.553153 TCCCATATCAACAGTAAATTTCCTGTA 58.447 33.333 15.81 3.18 40.91 2.74
4977 7144 6.959639 AATGCTCTTTGGACTTGAGTTTTA 57.040 33.333 0.00 0.00 0.00 1.52
4981 7148 5.859205 AAAAATGCTCTTTGGACTTGAGT 57.141 34.783 0.00 0.00 0.00 3.41
5113 7283 4.336433 ACTGTTGAACAAATCAGTGGAGTG 59.664 41.667 0.00 0.00 39.77 3.51
5114 7284 4.526970 ACTGTTGAACAAATCAGTGGAGT 58.473 39.130 0.00 0.00 39.77 3.85
5115 7285 4.576053 TGACTGTTGAACAAATCAGTGGAG 59.424 41.667 12.98 0.00 40.53 3.86
5116 7286 4.335315 GTGACTGTTGAACAAATCAGTGGA 59.665 41.667 11.05 1.39 40.53 4.02
5179 7349 4.765273 TGTGCTAGACTGAAACAGTTCAA 58.235 39.130 5.88 0.00 45.44 2.69
5344 7569 6.863275 TGGATGTTGTCACATACTAGTAGTG 58.137 40.000 13.29 18.72 44.01 2.74
5350 7575 8.729756 CAGATTTTTGGATGTTGTCACATACTA 58.270 33.333 0.00 0.00 44.01 1.82
5351 7576 7.448161 TCAGATTTTTGGATGTTGTCACATACT 59.552 33.333 0.00 0.00 44.01 2.12
5352 7577 7.592938 TCAGATTTTTGGATGTTGTCACATAC 58.407 34.615 0.00 0.00 44.22 2.39
5430 7655 3.124921 CGCCGCCGAGAAATTGGT 61.125 61.111 0.00 0.00 36.29 3.67
5441 7666 2.012902 TTAGCTTAGTCCTCGCCGCC 62.013 60.000 0.00 0.00 0.00 6.13
5478 7703 3.304391 CGAGTAGCTCTTCCTATGCTGTC 60.304 52.174 0.00 0.00 37.62 3.51
5594 7819 2.044758 ACCGGTGACTACTTTTCAGGT 58.955 47.619 6.12 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.