Multiple sequence alignment - TraesCS1D01G227900

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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 TraesCS1D01G227900 chr1D 100.000 3420 0 0 2820 6239 316021682 316018263 0.000000e+00 6316.0
1 TraesCS1D01G227900 chr1D 100.000 2602 0 0 1 2602 316024501 316021900 0.000000e+00 4806.0
2 TraesCS1D01G227900 chr1D 100.000 399 0 0 6515 6913 316017987 316017589 0.000000e+00 737.0
3 TraesCS1D01G227900 chr1A 95.245 3428 116 23 2835 6239 396466166 396462763 0.000000e+00 5384.0
4 TraesCS1D01G227900 chr1A 96.090 2609 83 9 1 2600 396469266 396466668 0.000000e+00 4235.0
5 TraesCS1D01G227900 chr1A 95.098 408 10 2 6515 6913 396462597 396462191 9.780000e-178 634.0
6 TraesCS1D01G227900 chr1A 87.970 133 13 3 245 375 396468970 396468839 3.340000e-33 154.0
7 TraesCS1D01G227900 chr1B 93.198 3440 178 30 2826 6239 428114326 428110917 0.000000e+00 5005.0
8 TraesCS1D01G227900 chr1B 95.608 2550 88 10 1 2536 428117239 428114700 0.000000e+00 4067.0
9 TraesCS1D01G227900 chr1B 84.211 95 8 4 332 419 428116988 428116894 1.240000e-12 86.1
10 TraesCS1D01G227900 chr3A 89.344 122 12 1 545 665 519234124 519234003 1.200000e-32 152.0
11 TraesCS1D01G227900 chr3D 89.286 112 11 1 545 655 400282101 400281990 9.350000e-29 139.0
12 TraesCS1D01G227900 chr3B 90.323 62 5 1 545 605 525987869 525987808 5.750000e-11 80.5


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 TraesCS1D01G227900 chr1D 316017589 316024501 6912 True 3953.00 6316 100.000000 1 6913 3 chr1D.!!$R1 6912
1 TraesCS1D01G227900 chr1A 396462191 396469266 7075 True 2601.75 5384 93.600750 1 6913 4 chr1A.!!$R1 6912
2 TraesCS1D01G227900 chr1B 428110917 428117239 6322 True 3052.70 5005 91.005667 1 6239 3 chr1B.!!$R1 6238

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
707 724 0.693049 AAGCTCCCGGTTCATCTTGT 59.307 50.000 0.0 0.0 0.00 3.16 F
865 882 1.407437 CCATTCTCAAGTTCGAGGGGG 60.407 57.143 0.0 0.0 33.59 5.40 F
2277 2294 3.256383 TGTTGCTCAATGGGAAGTGATTG 59.744 43.478 0.0 0.0 0.00 2.67 F
2589 2606 1.444933 TGAAGTGGGTGGGAGAATGT 58.555 50.000 0.0 0.0 0.00 2.71 F
4150 4436 1.463674 CCCGCCTCTATGTTTGCTTT 58.536 50.000 0.0 0.0 0.00 3.51 F
5169 5469 0.107456 ATCCTTATGAGCTGGTGCCG 59.893 55.000 0.0 0.0 40.80 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2018 2.042831 GTCATCAGGGCCACAGCAC 61.043 63.158 6.18 0.0 45.63 4.40 R
2525 2542 6.201044 CGGTGTATAGGAAGCAATGTCTTAAG 59.799 42.308 0.00 0.0 0.00 1.85 R
3511 3797 1.003580 TCTTCAGGGTTGGTGATGCTC 59.996 52.381 0.00 0.0 0.00 4.26 R
4300 4592 2.574006 TGAAGTGAAAGCATGAGCCT 57.426 45.000 0.00 0.0 43.56 4.58 R
5717 6028 0.468029 CACCAAACTGAGGTTGCCCT 60.468 55.000 4.33 0.0 46.66 5.19 R
6716 7040 0.323178 CCTGGAGGCTCTTGCATGTT 60.323 55.000 15.23 0.0 41.91 2.71 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
129 131 2.168728 GTCCTAGGAGCTCAACGGAATT 59.831 50.000 13.15 0.00 0.00 2.17
151 153 5.420725 TGTTGTCCTAGTAGTGATTGCAT 57.579 39.130 0.00 0.00 0.00 3.96
190 195 2.031258 GCTAGGAAGCTCTGAAACCC 57.969 55.000 0.00 0.00 45.85 4.11
199 204 3.019564 AGCTCTGAAACCCATAACATGC 58.980 45.455 0.00 0.00 0.00 4.06
266 276 5.244626 CAGATTTTGATATTAAGGCAGGGGG 59.755 44.000 0.00 0.00 0.00 5.40
305 321 7.471721 TCTGTTGTGATTTTGATATTAAGGCG 58.528 34.615 0.00 0.00 0.00 5.52
309 325 4.583073 GTGATTTTGATATTAAGGCGGGGT 59.417 41.667 0.00 0.00 0.00 4.95
312 328 3.655615 TTGATATTAAGGCGGGGTGTT 57.344 42.857 0.00 0.00 0.00 3.32
313 329 4.774660 TTGATATTAAGGCGGGGTGTTA 57.225 40.909 0.00 0.00 0.00 2.41
317 333 6.130569 TGATATTAAGGCGGGGTGTTAAAAT 58.869 36.000 0.00 0.00 0.00 1.82
318 334 7.288560 TGATATTAAGGCGGGGTGTTAAAATA 58.711 34.615 0.00 0.00 0.00 1.40
367 384 7.408013 AAGGCAGGGGATCTAAATAGTATTT 57.592 36.000 12.61 12.61 0.00 1.40
400 417 2.571653 TGATATTAAGGCGGGGGATCTG 59.428 50.000 0.00 0.00 0.00 2.90
411 428 4.506802 GGCGGGGGATCTGAAATAGTATTT 60.507 45.833 7.87 7.87 0.00 1.40
414 431 5.473504 CGGGGGATCTGAAATAGTATTTTGG 59.526 44.000 9.47 6.12 0.00 3.28
444 461 5.049129 GCTTCTTGTTTACTGAAGATGTGCT 60.049 40.000 15.17 0.00 39.42 4.40
455 472 1.522668 AGATGTGCTAACGCTTGCAA 58.477 45.000 0.00 0.00 41.10 4.08
478 495 2.162906 ATGTCACTTGGGCCCCTGT 61.163 57.895 22.27 15.60 0.00 4.00
700 717 2.467566 TCTTTACAAGCTCCCGGTTC 57.532 50.000 0.00 0.00 0.00 3.62
706 723 1.089920 CAAGCTCCCGGTTCATCTTG 58.910 55.000 0.00 2.87 0.00 3.02
707 724 0.693049 AAGCTCCCGGTTCATCTTGT 59.307 50.000 0.00 0.00 0.00 3.16
724 741 5.973899 TCTTGTTTAGCAATTGCATGGTA 57.026 34.783 30.89 12.72 45.16 3.25
781 798 5.437060 CACATGGCCATTAGTTACTACCTT 58.563 41.667 17.92 0.00 0.00 3.50
865 882 1.407437 CCATTCTCAAGTTCGAGGGGG 60.407 57.143 0.00 0.00 33.59 5.40
939 956 4.553330 TGGTCTTGGGAATAGTTCACTC 57.447 45.455 0.00 0.00 33.11 3.51
1126 1143 8.425577 TTCTGCAGCTACTTTTATGTATCTTC 57.574 34.615 9.47 0.00 0.00 2.87
1275 1292 6.993308 TGCCACAACTTGTTCTGTAAACTATA 59.007 34.615 0.00 0.00 0.00 1.31
1410 1427 4.918810 TCCTTTGCTTTCCAAACTCTTC 57.081 40.909 0.00 0.00 38.46 2.87
1478 1495 4.397417 AGATGTGCTATTGCCTTGTTCTTC 59.603 41.667 0.00 0.00 38.71 2.87
2277 2294 3.256383 TGTTGCTCAATGGGAAGTGATTG 59.744 43.478 0.00 0.00 0.00 2.67
2437 2454 5.103940 ACCTGGTAACTTGCATCCATCTTAT 60.104 40.000 0.00 0.00 37.61 1.73
2500 2517 7.405292 TGCCCTAGATCATTATTCTATTTGGG 58.595 38.462 0.00 0.00 34.26 4.12
2589 2606 1.444933 TGAAGTGGGTGGGAGAATGT 58.555 50.000 0.00 0.00 0.00 2.71
3046 3329 6.072838 GCACACCTATGATGTTATTGATCCAG 60.073 42.308 0.00 0.00 0.00 3.86
3123 3409 7.985184 TGTTATCGATCCAACATTAAGCTAACT 59.015 33.333 0.00 0.00 29.93 2.24
3232 3518 7.202016 TGTTCATATTTCCTTCGGATTATGC 57.798 36.000 7.80 0.00 32.71 3.14
3511 3797 5.182001 CACTTGTACAAAGAAATGAGGAGGG 59.818 44.000 10.03 0.00 0.00 4.30
3660 3946 4.230745 TCTCATGGATCATGGCATATGG 57.769 45.455 0.00 0.00 41.66 2.74
3665 3951 5.430745 TCATGGATCATGGCATATGGATACT 59.569 40.000 0.00 0.00 41.66 2.12
3682 3968 5.899547 TGGATACTATGTGACTCTGGTCAAT 59.100 40.000 0.22 1.22 45.78 2.57
3693 3979 6.038997 GACTCTGGTCAATTGGTAGTAGTT 57.961 41.667 5.42 0.00 41.75 2.24
3734 4020 1.555992 TCGAACATTCCCGGGTGTAAT 59.444 47.619 22.86 10.55 0.00 1.89
3796 4082 4.123745 TCACCCCCTCACCCTAATTTATT 58.876 43.478 0.00 0.00 0.00 1.40
3803 4089 6.045577 CCCCTCACCCTAATTTATTGACCTAT 59.954 42.308 0.00 0.00 0.00 2.57
3804 4090 7.238933 CCCCTCACCCTAATTTATTGACCTATA 59.761 40.741 0.00 0.00 0.00 1.31
3805 4091 8.665906 CCCTCACCCTAATTTATTGACCTATAA 58.334 37.037 0.00 0.00 0.00 0.98
3882 4168 8.877195 TGGAACTAACTTTATTCCACTAGTTCT 58.123 33.333 15.54 0.00 45.46 3.01
3883 4169 9.152595 GGAACTAACTTTATTCCACTAGTTCTG 57.847 37.037 15.54 0.00 42.23 3.02
3928 4214 8.777865 TTTATTATGACACAGTTCCAGAAGAG 57.222 34.615 0.00 0.00 0.00 2.85
4150 4436 1.463674 CCCGCCTCTATGTTTGCTTT 58.536 50.000 0.00 0.00 0.00 3.51
4173 4461 6.620877 TGTTTTCTAGTATGACCATGGTCT 57.379 37.500 37.92 27.06 44.80 3.85
4184 4472 9.830186 AGTATGACCATGGTCTCTAATATAGTT 57.170 33.333 37.92 17.87 44.80 2.24
4269 4557 5.598417 AGTGCTCTTCAAAAAGGTATGGTTT 59.402 36.000 0.00 0.00 33.03 3.27
4354 4650 4.883083 ACAATACGTCATAGGCGATCATT 58.117 39.130 0.00 0.00 0.00 2.57
4364 4661 1.103398 GGCGATCATTTGGGGTCCTG 61.103 60.000 0.00 0.00 0.00 3.86
4528 4825 3.005155 GCCAGGTTGCTATCATCCAAATC 59.995 47.826 0.00 0.00 35.08 2.17
4652 4949 9.257651 CTAACATACTAAAACTGGGTACTATGC 57.742 37.037 0.00 0.00 0.00 3.14
4717 5014 4.281525 TGTAAGAACGTTTCCTTGTTGC 57.718 40.909 0.46 0.00 0.00 4.17
4810 5108 4.219725 TGTCACAGTCGTATGGAGAATTGA 59.780 41.667 0.00 0.00 0.00 2.57
4961 5259 7.066645 CCAGCTGATTTGTTCATCTTTCTATCA 59.933 37.037 17.39 0.00 32.72 2.15
5053 5351 0.606604 ACAAGACACGGCGGAATAGT 59.393 50.000 13.24 0.91 0.00 2.12
5169 5469 0.107456 ATCCTTATGAGCTGGTGCCG 59.893 55.000 0.00 0.00 40.80 5.69
5229 5529 8.463930 ACATTGTCAAATTTTAGAGTCCTCAA 57.536 30.769 0.00 0.00 0.00 3.02
5241 5541 3.262151 AGAGTCCTCAAAGCTTTCCTACC 59.738 47.826 9.23 0.00 0.00 3.18
5383 5683 7.119116 GCAATTTTTACCCTTTTTACATGGAGG 59.881 37.037 0.00 0.00 0.00 4.30
5432 5740 5.420409 GAATACACTCAACTCAAGGGTAGG 58.580 45.833 0.00 0.00 36.14 3.18
5485 5795 6.681729 TGTAAGTTAGTGGAATCTGAAGGT 57.318 37.500 0.00 0.00 0.00 3.50
5493 5803 6.253946 AGTGGAATCTGAAGGTTAATAGGG 57.746 41.667 0.00 0.00 0.00 3.53
5517 5828 6.762661 GGCAATTGTGATATAAGCCACATTTT 59.237 34.615 7.40 0.00 42.13 1.82
5540 5851 9.372699 TTTTCTGGAAAAATGAGCTACTCAGCG 62.373 40.741 6.09 0.00 43.44 5.18
5600 5911 2.550606 TGGGTCAAATGTGCTTTACGTC 59.449 45.455 0.00 0.00 0.00 4.34
5672 5983 5.362430 CCTCCTTCTACAGAAAGAGTATGCT 59.638 44.000 13.83 0.00 39.69 3.79
5717 6028 9.498176 CTTGTTCATATATTCCATCATGTCAGA 57.502 33.333 0.00 0.00 0.00 3.27
5771 6082 2.616510 CCAGGTGGAATGGAAGTCTCAC 60.617 54.545 0.00 0.00 40.51 3.51
5787 6098 5.223382 AGTCTCACATTGTAAGTTCTCACG 58.777 41.667 0.00 0.00 0.00 4.35
5812 6127 7.073265 GCAAAACATCAATGGACTGATTTTTG 58.927 34.615 17.79 17.79 40.74 2.44
5879 6195 2.429250 ACTTTGTTTTCAGGTTTCCCGG 59.571 45.455 0.00 0.00 35.12 5.73
5901 6217 2.845752 GAATCGTGCACGTAGCCCCA 62.846 60.000 35.74 17.61 44.83 4.96
5917 6233 2.169978 GCCCCATACGGTTCTAGAACTT 59.830 50.000 29.66 20.75 40.94 2.66
5991 6308 2.872038 GCTACAAGCAAGCACCTACTGT 60.872 50.000 0.00 0.00 41.89 3.55
6044 6361 6.650807 TGTTGATAGGCTTCTGTAGTTTTCTG 59.349 38.462 0.00 0.00 0.00 3.02
6153 6472 1.173043 CCTCTGCCGCATTTTGGTTA 58.827 50.000 0.00 0.00 0.00 2.85
6154 6473 1.543802 CCTCTGCCGCATTTTGGTTAA 59.456 47.619 0.00 0.00 0.00 2.01
6155 6474 2.166254 CCTCTGCCGCATTTTGGTTAAT 59.834 45.455 0.00 0.00 0.00 1.40
6156 6475 3.181397 CTCTGCCGCATTTTGGTTAATG 58.819 45.455 0.00 0.00 38.31 1.90
6184 6508 2.620112 CGCTGCCACCTGAAACCTG 61.620 63.158 0.00 0.00 0.00 4.00
6236 6560 7.227049 AGTTAAACCATGGTTTAGGAATGTG 57.773 36.000 36.35 3.05 46.80 3.21
6582 6906 1.065102 CCAAATGAGATGCTCCGCTTG 59.935 52.381 0.00 0.00 0.00 4.01
6618 6942 0.545071 TCATGCAGTGACCTCCCAGA 60.545 55.000 0.00 0.00 0.00 3.86
6624 6948 2.938756 GCAGTGACCTCCCAGATTCTTG 60.939 54.545 0.00 0.00 0.00 3.02
6666 6990 3.069300 CGACCCTCAGACATTCAGATGAT 59.931 47.826 0.00 0.00 36.73 2.45
6667 6991 4.442612 CGACCCTCAGACATTCAGATGATT 60.443 45.833 0.00 0.00 36.73 2.57
6705 7029 2.744494 GCTCATCTCTTCGCCCAAAGAT 60.744 50.000 0.00 0.00 34.85 2.40
6716 7040 5.738619 TCGCCCAAAGATATAGCTTCATA 57.261 39.130 3.25 0.00 0.00 2.15
6796 7129 0.816825 CCTTCCATCCCGTGCTCATG 60.817 60.000 0.00 0.00 0.00 3.07
6868 7201 6.057533 CACCATTGACATTCAGCTTCCTATA 58.942 40.000 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 131 4.882842 TGCAATCACTACTAGGACAACA 57.117 40.909 0.00 0.00 0.00 3.33
151 153 2.811873 GCTCCCAGCAGTTCTTTCTTCA 60.812 50.000 0.00 0.00 41.89 3.02
305 321 8.621286 CACATCAGAATACTATTTTAACACCCC 58.379 37.037 0.00 0.00 0.00 4.95
367 384 7.032580 CCGCCTTAATATCAAAATCACAACAA 58.967 34.615 0.00 0.00 0.00 2.83
400 417 4.981794 AGCGCACACCAAAATACTATTTC 58.018 39.130 11.47 0.00 0.00 2.17
411 428 0.814457 AAACAAGAAGCGCACACCAA 59.186 45.000 11.47 0.00 0.00 3.67
414 431 2.286833 TCAGTAAACAAGAAGCGCACAC 59.713 45.455 11.47 0.00 0.00 3.82
455 472 1.604593 GGCCCAAGTGACATGCTGT 60.605 57.895 0.00 0.00 0.00 4.40
700 717 5.172934 ACCATGCAATTGCTAAACAAGATG 58.827 37.500 29.37 20.45 42.87 2.90
728 745 8.770010 TTGGATCCTCCTGTTTAAACTAAAAA 57.230 30.769 18.72 0.00 37.46 1.94
729 746 8.002459 ACTTGGATCCTCCTGTTTAAACTAAAA 58.998 33.333 18.72 0.00 37.46 1.52
795 812 7.175104 AGAAGTGGGTAAATGCAAAATAGAGA 58.825 34.615 0.00 0.00 0.00 3.10
806 823 7.090173 CCACAAATTGTAGAAGTGGGTAAATG 58.910 38.462 0.00 0.00 44.55 2.32
865 882 2.562912 CACGGCCATGTCACTTGC 59.437 61.111 2.24 0.00 0.00 4.01
895 912 6.403636 CCAAAATAGAGCAGAACACACCATAC 60.404 42.308 0.00 0.00 0.00 2.39
939 956 9.862585 GAAAATTTGCCAACTTAAACAACATAG 57.137 29.630 0.00 0.00 0.00 2.23
1126 1143 4.404073 ACCATAGAAGTAGCAGTCCTTCAG 59.596 45.833 0.00 0.00 39.61 3.02
1167 1184 9.033711 TCACATTCATGGAAATTGAAGGATAAA 57.966 29.630 5.24 0.00 37.12 1.40
1176 1193 6.255670 CAGAAGCATCACATTCATGGAAATTG 59.744 38.462 0.00 0.00 0.00 2.32
1275 1292 9.508642 TTGTTTGTTTTGGAAGGTTCTATTTTT 57.491 25.926 0.00 0.00 0.00 1.94
1410 1427 7.169308 ACAGAATTCGGCTACTCATAAATTACG 59.831 37.037 5.43 0.00 0.00 3.18
1478 1495 9.339850 AGAAGATCAAGAATCAAATAGACATGG 57.660 33.333 0.00 0.00 36.79 3.66
2001 2018 2.042831 GTCATCAGGGCCACAGCAC 61.043 63.158 6.18 0.00 45.63 4.40
2437 2454 6.671614 ACACGTCTAAAAAGTTGATTGTGA 57.328 33.333 0.00 0.00 0.00 3.58
2514 2531 9.852091 GAAGCAATGTCTTAAGAAAATGAATCT 57.148 29.630 13.94 0.24 0.00 2.40
2525 2542 6.201044 CGGTGTATAGGAAGCAATGTCTTAAG 59.799 42.308 0.00 0.00 0.00 1.85
2828 2845 9.450807 CCATCTAAAGTGTGTAGTTTCAAAAAG 57.549 33.333 0.00 0.00 32.00 2.27
3232 3518 9.809096 ATCATTGTACTGAGTAACTGAGTATTG 57.191 33.333 0.00 0.00 33.31 1.90
3298 3584 6.065374 TGACCCTTAAATCTGTAGTTTTGCA 58.935 36.000 0.00 0.00 0.00 4.08
3511 3797 1.003580 TCTTCAGGGTTGGTGATGCTC 59.996 52.381 0.00 0.00 0.00 4.26
3682 3968 2.629137 TGAACGGCTCAACTACTACCAA 59.371 45.455 0.00 0.00 0.00 3.67
3693 3979 2.844946 TCAACTGAATTGAACGGCTCA 58.155 42.857 0.00 0.00 44.59 4.26
4111 4397 2.986479 GGCAACAATTTGAACTAAGGCG 59.014 45.455 2.79 0.00 34.24 5.52
4150 4436 6.440647 AGAGACCATGGTCATACTAGAAAACA 59.559 38.462 39.38 0.00 46.76 2.83
4194 4482 6.838198 ACTACATCGCGATAAAATTGCTTA 57.162 33.333 23.22 0.00 37.53 3.09
4196 4484 8.595533 CATATACTACATCGCGATAAAATTGCT 58.404 33.333 23.22 5.46 37.53 3.91
4201 4489 5.513849 CCGCATATACTACATCGCGATAAAA 59.486 40.000 23.22 9.09 45.17 1.52
4300 4592 2.574006 TGAAGTGAAAGCATGAGCCT 57.426 45.000 0.00 0.00 43.56 4.58
4354 4650 5.528600 TTAGAAAATGATCAGGACCCCAA 57.471 39.130 0.09 0.00 0.00 4.12
4528 4825 3.367932 TGAAAGCTTTCTTATCTGACGCG 59.632 43.478 33.03 3.53 38.02 6.01
4639 4936 8.435931 TTGATCATATTAGCATAGTACCCAGT 57.564 34.615 0.00 0.00 0.00 4.00
4652 4949 9.077674 GTAGACAGCGGTAATTGATCATATTAG 57.922 37.037 0.00 0.00 0.00 1.73
4670 4967 2.918712 ACAGGCATATGGTAGACAGC 57.081 50.000 4.56 0.00 0.00 4.40
4717 5014 7.168972 TGGAAAAATGTTAGTTCTTTTCATGCG 59.831 33.333 8.03 0.00 38.80 4.73
4810 5108 7.293073 AGCATTTCATAGGACTGGAAACATAT 58.707 34.615 0.00 0.00 41.51 1.78
4961 5259 8.125733 AGGGATATAGCTTGTCATAGGTTCTAT 58.874 37.037 0.00 0.00 0.00 1.98
5005 5303 4.889409 CCAGCTCCTAATATTTTCTGGCAA 59.111 41.667 0.00 0.00 34.07 4.52
5053 5351 3.695606 GGTCGCTGCTCCCAGTCA 61.696 66.667 0.00 0.00 41.26 3.41
5214 5514 6.547402 AGGAAAGCTTTGAGGACTCTAAAAT 58.453 36.000 18.30 0.00 0.00 1.82
5229 5529 4.953579 TGACAAAACAAGGTAGGAAAGCTT 59.046 37.500 0.00 0.00 46.81 3.74
5241 5541 1.199624 GCCGCAACTGACAAAACAAG 58.800 50.000 0.00 0.00 0.00 3.16
5316 5616 5.699097 TTCCCACTAATGCAGTTTACAAC 57.301 39.130 0.00 0.00 34.26 3.32
5432 5740 9.471084 AAAATGTACAAATTTAACCTGCACTAC 57.529 29.630 0.00 0.00 0.00 2.73
5485 5795 7.947332 TGGCTTATATCACAATTGCCCTATTAA 59.053 33.333 5.05 0.00 38.23 1.40
5493 5803 7.707893 AGAAAATGTGGCTTATATCACAATTGC 59.292 33.333 5.05 0.00 45.39 3.56
5517 5828 4.256920 GCTGAGTAGCTCATTTTTCCAGA 58.743 43.478 0.00 0.00 46.57 3.86
5579 5890 2.550606 GACGTAAAGCACATTTGACCCA 59.449 45.455 0.00 0.00 32.01 4.51
5580 5891 2.412325 CGACGTAAAGCACATTTGACCC 60.412 50.000 0.00 0.00 32.01 4.46
5600 5911 5.123186 TGGCACTTTACATCCTTGATAAACG 59.877 40.000 0.00 0.00 0.00 3.60
5672 5983 1.742880 GACCGCAGCATCAAGAGCA 60.743 57.895 0.00 0.00 0.00 4.26
5717 6028 0.468029 CACCAAACTGAGGTTGCCCT 60.468 55.000 4.33 0.00 46.66 5.19
5771 6082 5.270083 TGTTTTGCGTGAGAACTTACAATG 58.730 37.500 0.00 0.00 0.00 2.82
5787 6098 6.790285 AAAATCAGTCCATTGATGTTTTGC 57.210 33.333 0.00 0.00 37.83 3.68
5879 6195 1.693083 GGCTACGTGCACGATTCACC 61.693 60.000 42.94 29.39 45.15 4.02
5901 6217 3.705072 CCCTGGAAGTTCTAGAACCGTAT 59.295 47.826 28.05 14.54 42.06 3.06
5957 6273 3.007290 TGCTTGTAGCTGTCAGAACTCAT 59.993 43.478 3.32 0.00 42.97 2.90
5991 6308 4.074970 GTTCCTTGGAAGATGAAGCTGAA 58.925 43.478 1.83 0.00 0.00 3.02
6044 6361 1.965754 CTGAGACCAGCTAGGGTGCC 61.966 65.000 0.00 0.00 42.53 5.01
6184 6508 1.538047 ACTCACCACCAACATGATGC 58.462 50.000 0.00 0.00 0.00 3.91
6618 6942 4.597507 TGGGAACTCAAGTCTACCAAGAAT 59.402 41.667 0.00 0.00 32.16 2.40
6624 6948 2.094649 CGTCTGGGAACTCAAGTCTACC 60.095 54.545 0.00 0.00 0.00 3.18
6666 6990 3.265737 TGAGCCTTGGGAAGCTATACAAA 59.734 43.478 0.00 0.00 40.11 2.83
6667 6991 2.843730 TGAGCCTTGGGAAGCTATACAA 59.156 45.455 0.00 0.00 40.11 2.41
6705 7029 5.702670 GGCTCTTGCATGTTATGAAGCTATA 59.297 40.000 8.11 0.00 41.91 1.31
6716 7040 0.323178 CCTGGAGGCTCTTGCATGTT 60.323 55.000 15.23 0.00 41.91 2.71
6740 7064 6.349611 GGCGTATAACGGAATCACTAATCCTA 60.350 42.308 1.25 0.00 42.82 2.94
6796 7129 2.607892 GCTGGTGTTGTCTGCCGTC 61.608 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.