Multiple sequence alignment - TraesCS5B01G180100

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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 TraesCS5B01G180100 chr5B 100.000 4329 0 0 1 4329 327793071 327788743 0.000000e+00 7995.0
1 TraesCS5B01G180100 chr5B 87.912 91 11 0 519 609 50469123 50469213 1.650000e-19 108.0
2 TraesCS5B01G180100 chr5D 96.431 3558 107 7 1 3540 288382793 288379238 0.000000e+00 5849.0
3 TraesCS5B01G180100 chr5D 91.364 579 30 9 3761 4329 288379156 288378588 0.000000e+00 774.0
4 TraesCS5B01G180100 chr5A 95.339 3690 137 18 1 3659 381764310 381760625 0.000000e+00 5829.0
5 TraesCS5B01G180100 chr5A 84.536 388 45 12 3945 4324 381760183 381759803 1.900000e-98 370.0
6 TraesCS5B01G180100 chr5A 91.892 74 5 1 536 609 33929230 33929158 7.660000e-18 102.0
7 TraesCS5B01G180100 chr2A 95.588 68 3 0 536 603 102688052 102688119 4.580000e-20 110.0
8 TraesCS5B01G180100 chr2A 91.139 79 7 0 531 609 102688119 102688041 1.650000e-19 108.0
9 TraesCS5B01G180100 chr2D 87.640 89 10 1 522 610 234147933 234147846 7.660000e-18 102.0
10 TraesCS5B01G180100 chr1B 89.873 79 8 0 531 609 411570494 411570416 7.660000e-18 102.0
11 TraesCS5B01G180100 chr3B 87.059 85 11 0 525 609 113517573 113517657 3.560000e-16 97.1


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 TraesCS5B01G180100 chr5B 327788743 327793071 4328 True 7995.0 7995 100.0000 1 4329 1 chr5B.!!$R1 4328
1 TraesCS5B01G180100 chr5D 288378588 288382793 4205 True 3311.5 5849 93.8975 1 4329 2 chr5D.!!$R1 4328
2 TraesCS5B01G180100 chr5A 381759803 381764310 4507 True 3099.5 5829 89.9375 1 4324 2 chr5A.!!$R2 4323

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
245 249 1.153289 GAGCATGGTGGCGTCTCAT 60.153 57.895 0.00 0.0 39.27 2.90 F
1211 1241 1.472082 CATGCAACACCCGCTCATTTA 59.528 47.619 0.00 0.0 0.00 1.40 F
2471 2502 0.322008 GTTTCTGCCTGGGAGTGAGG 60.322 60.000 15.24 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1414 1444 1.280998 GGTATAGGTGTTGCTGTGGGT 59.719 52.381 0.00 0.00 0.00 4.51 R
2866 2897 0.032540 CCTGTTGCTTCAGTTTGGCC 59.967 55.000 0.00 0.00 34.02 5.36 R
3879 3986 0.031178 CCAAATGATAAGCAGGCCGC 59.969 55.000 11.02 11.02 42.91 6.53 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
34 38 8.084073 TGCTAAATTTCCTTGCAGATTATATGC 58.916 33.333 4.71 4.71 44.11 3.14
43 47 7.443879 TCCTTGCAGATTATATGCGTTGAATTA 59.556 33.333 7.33 0.00 46.87 1.40
86 90 3.367292 CGGGTTCTGGTGATTTGGAATTG 60.367 47.826 0.00 0.00 0.00 2.32
97 101 6.322201 GGTGATTTGGAATTGTGATGGTATCT 59.678 38.462 0.00 0.00 0.00 1.98
245 249 1.153289 GAGCATGGTGGCGTCTCAT 60.153 57.895 0.00 0.00 39.27 2.90
325 329 1.532868 GACAGCACTGTGATGTTGGTC 59.467 52.381 29.50 15.10 45.71 4.02
480 501 5.646467 CAAAGAAATTGTGGAACTTGCAG 57.354 39.130 0.00 0.00 38.04 4.41
513 534 8.030692 TGAAGAAAATGATGTGGCTTTCTATTG 58.969 33.333 0.00 0.00 37.18 1.90
768 798 5.705905 ACTCTAGGTTGCATCCTTTTGTTAC 59.294 40.000 21.19 0.00 38.86 2.50
784 814 8.911662 CCTTTTGTTACGGTATCTGAAATTTTG 58.088 33.333 0.00 0.00 0.00 2.44
793 823 5.245075 GGTATCTGAAATTTTGGGTGTTCCA 59.755 40.000 0.00 0.00 45.43 3.53
842 872 9.635520 CTGTTTAGTTTAATCTAGTTCTCCGAA 57.364 33.333 0.00 0.00 0.00 4.30
870 900 3.179443 TCGGAAGATAGCACCACATTC 57.821 47.619 0.00 0.00 33.31 2.67
910 940 7.100458 AGGTTTGGTTGAACTGATATATTGC 57.900 36.000 0.00 0.00 0.00 3.56
1211 1241 1.472082 CATGCAACACCCGCTCATTTA 59.528 47.619 0.00 0.00 0.00 1.40
1215 1245 2.791158 GCAACACCCGCTCATTTAATCG 60.791 50.000 0.00 0.00 0.00 3.34
1277 1307 4.954118 AGTCCACGCCCACCTGGA 62.954 66.667 0.00 0.00 37.39 3.86
1382 1412 3.573538 AGCATATGCAACTTTCACAACCA 59.426 39.130 28.62 0.00 45.16 3.67
1414 1444 6.314120 CCATGAATATCCCTTTCCACCAATA 58.686 40.000 0.00 0.00 0.00 1.90
1460 1490 3.362596 CGAATGTCCAGTACGTTGTTGTG 60.363 47.826 0.00 0.00 37.44 3.33
1592 1622 6.085555 ACTCGTCAAGAAGAACAAGACATA 57.914 37.500 0.00 0.00 0.00 2.29
1656 1686 1.135083 AGCGATTACACTGGACGGAAG 60.135 52.381 0.00 0.00 0.00 3.46
1679 1709 3.039011 GGAGGACATAAGGCTGGTAAGA 58.961 50.000 0.00 0.00 0.00 2.10
1772 1803 7.272978 ACTGTAGATACGTATTTGGCTGAATT 58.727 34.615 9.92 0.00 0.00 2.17
2362 2393 4.853924 TCAAAATCTTGAACCTTCCAGC 57.146 40.909 0.00 0.00 38.65 4.85
2426 2457 3.571401 AGAGAAGCAACCAGAATTGTTGG 59.429 43.478 8.67 6.64 42.58 3.77
2471 2502 0.322008 GTTTCTGCCTGGGAGTGAGG 60.322 60.000 15.24 0.00 0.00 3.86
2590 2621 4.442052 GCACTAGACCATGATAGAGCAACA 60.442 45.833 0.00 0.00 36.16 3.33
3060 3091 7.190920 AGCATTAATCGTTGATTTAGTAGGC 57.809 36.000 0.00 0.00 33.95 3.93
3078 3109 7.787725 AGTAGGCTATATTAAACACTTGTGC 57.212 36.000 0.00 0.00 0.00 4.57
3114 3145 2.580962 TGCAGCACTAATGTTGGAACA 58.419 42.857 0.00 0.00 44.06 3.18
3154 3185 2.694109 ACCTGTCGATTTAGCCTACTCC 59.306 50.000 0.00 0.00 0.00 3.85
3167 3204 2.038033 GCCTACTCCAAGTAACACCACA 59.962 50.000 0.00 0.00 29.00 4.17
3188 3225 6.072008 CCACATGTGTTGTTTATCCTTCATCA 60.072 38.462 23.79 0.00 36.00 3.07
3198 3235 2.978156 TCCTTCATCAGCCCTTGTTT 57.022 45.000 0.00 0.00 0.00 2.83
3283 3320 4.523173 ACATGATTTGATGGCTGATGGATC 59.477 41.667 0.00 0.00 0.00 3.36
3385 3424 7.971168 CCGTTGCAAATAAATAGTGTTAATCCA 59.029 33.333 0.00 0.00 0.00 3.41
3393 3432 2.736670 AGTGTTAATCCATCTGGGCC 57.263 50.000 0.00 0.00 36.21 5.80
3483 3522 5.897377 TTCTAGCTTAATGGCTCCAAAAC 57.103 39.130 0.00 0.00 42.97 2.43
3525 3565 5.511888 CCAAACAATCTTTGCTCAGGGAAAT 60.512 40.000 0.00 0.00 32.61 2.17
3540 3580 7.503902 GCTCAGGGAAATAGAATTAGGTCATTT 59.496 37.037 0.00 0.00 0.00 2.32
3542 3582 9.768215 TCAGGGAAATAGAATTAGGTCATTTTT 57.232 29.630 0.00 0.00 0.00 1.94
3543 3583 9.807649 CAGGGAAATAGAATTAGGTCATTTTTG 57.192 33.333 0.00 0.00 0.00 2.44
3553 3593 9.815936 GAATTAGGTCATTTTTGAAAAAGCATG 57.184 29.630 9.13 3.09 0.00 4.06
3554 3594 7.727331 TTAGGTCATTTTTGAAAAAGCATGG 57.273 32.000 9.13 0.00 0.00 3.66
3558 3598 5.526846 GTCATTTTTGAAAAAGCATGGACCA 59.473 36.000 9.13 0.00 0.00 4.02
3560 3600 6.427547 TCATTTTTGAAAAAGCATGGACCATC 59.572 34.615 3.21 0.00 0.00 3.51
3561 3601 3.959535 TTGAAAAAGCATGGACCATCC 57.040 42.857 3.21 0.00 36.96 3.51
3588 3628 4.217118 ACAATCTTTGTTCATGCTGGTCTC 59.783 41.667 0.00 0.00 42.22 3.36
3589 3629 2.416747 TCTTTGTTCATGCTGGTCTCG 58.583 47.619 0.00 0.00 0.00 4.04
3590 3630 1.466167 CTTTGTTCATGCTGGTCTCGG 59.534 52.381 0.00 0.00 0.00 4.63
3591 3631 0.396435 TTGTTCATGCTGGTCTCGGT 59.604 50.000 0.00 0.00 0.00 4.69
3604 3644 3.500680 TGGTCTCGGTTATTTTGCTCAAC 59.499 43.478 0.00 0.00 0.00 3.18
3610 3650 5.218885 TCGGTTATTTTGCTCAACAACATG 58.781 37.500 0.00 0.00 38.23 3.21
3634 3674 5.707764 GGTATTTCCTGATGCTTCCTATTCC 59.292 44.000 0.00 0.00 0.00 3.01
3639 3679 3.181461 CCTGATGCTTCCTATTCCGAACT 60.181 47.826 0.00 0.00 0.00 3.01
3647 3687 2.821378 TCCTATTCCGAACTTGTGACGA 59.179 45.455 0.00 0.00 0.00 4.20
3649 3689 2.814280 ATTCCGAACTTGTGACGAGT 57.186 45.000 0.00 0.00 0.00 4.18
3656 3696 4.288531 CGAACTTGTGACGAGTTAGAAGT 58.711 43.478 17.66 5.03 37.46 3.01
3657 3697 5.446709 CGAACTTGTGACGAGTTAGAAGTA 58.553 41.667 17.66 0.00 37.46 2.24
3658 3698 5.911280 CGAACTTGTGACGAGTTAGAAGTAA 59.089 40.000 17.66 0.00 37.46 2.24
3659 3699 6.415867 CGAACTTGTGACGAGTTAGAAGTAAA 59.584 38.462 17.66 0.00 37.46 2.01
3660 3700 7.043854 CGAACTTGTGACGAGTTAGAAGTAAAA 60.044 37.037 17.66 0.00 37.46 1.52
3661 3701 8.658499 AACTTGTGACGAGTTAGAAGTAAAAT 57.342 30.769 16.28 0.00 32.82 1.82
3662 3702 8.295569 ACTTGTGACGAGTTAGAAGTAAAATC 57.704 34.615 8.40 0.00 32.35 2.17
3663 3703 8.142551 ACTTGTGACGAGTTAGAAGTAAAATCT 58.857 33.333 8.40 0.00 32.35 2.40
3664 3704 8.516811 TTGTGACGAGTTAGAAGTAAAATCTC 57.483 34.615 0.00 0.00 0.00 2.75
3665 3705 7.883217 TGTGACGAGTTAGAAGTAAAATCTCT 58.117 34.615 0.00 0.00 0.00 3.10
3666 3706 9.006839 TGTGACGAGTTAGAAGTAAAATCTCTA 57.993 33.333 0.00 0.00 0.00 2.43
3667 3707 9.837525 GTGACGAGTTAGAAGTAAAATCTCTAA 57.162 33.333 0.00 0.00 0.00 2.10
3677 3717 9.931210 AGAAGTAAAATCTCTAAACAAAACACG 57.069 29.630 0.00 0.00 0.00 4.49
3678 3718 9.712359 GAAGTAAAATCTCTAAACAAAACACGT 57.288 29.630 0.00 0.00 0.00 4.49
3683 3723 5.600908 TCTCTAAACAAAACACGTATGGC 57.399 39.130 0.00 0.00 0.00 4.40
3684 3724 5.302360 TCTCTAAACAAAACACGTATGGCT 58.698 37.500 0.00 0.00 0.00 4.75
3685 3725 5.178623 TCTCTAAACAAAACACGTATGGCTG 59.821 40.000 0.00 0.00 0.00 4.85
3686 3726 4.817464 TCTAAACAAAACACGTATGGCTGT 59.183 37.500 0.00 0.00 0.00 4.40
3687 3727 4.379339 AAACAAAACACGTATGGCTGTT 57.621 36.364 0.00 0.00 31.23 3.16
3688 3728 3.619233 ACAAAACACGTATGGCTGTTC 57.381 42.857 0.00 0.00 30.11 3.18
3689 3729 2.946329 ACAAAACACGTATGGCTGTTCA 59.054 40.909 0.00 0.00 30.11 3.18
3690 3730 3.242936 ACAAAACACGTATGGCTGTTCAC 60.243 43.478 0.00 0.00 30.11 3.18
3691 3731 1.144969 AACACGTATGGCTGTTCACG 58.855 50.000 0.00 0.00 40.15 4.35
3692 3732 0.315886 ACACGTATGGCTGTTCACGA 59.684 50.000 0.00 0.00 37.80 4.35
3693 3733 0.992072 CACGTATGGCTGTTCACGAG 59.008 55.000 0.00 0.00 37.80 4.18
3694 3734 0.108804 ACGTATGGCTGTTCACGAGG 60.109 55.000 0.00 0.00 37.80 4.63
3695 3735 0.172578 CGTATGGCTGTTCACGAGGA 59.827 55.000 0.00 0.00 36.53 3.71
3696 3736 1.403647 CGTATGGCTGTTCACGAGGAA 60.404 52.381 0.00 0.00 36.53 3.36
3697 3737 2.695359 GTATGGCTGTTCACGAGGAAA 58.305 47.619 0.00 0.00 37.23 3.13
3698 3738 1.813513 ATGGCTGTTCACGAGGAAAG 58.186 50.000 0.00 0.00 37.23 2.62
3699 3739 0.250295 TGGCTGTTCACGAGGAAAGG 60.250 55.000 0.00 0.00 37.23 3.11
3710 3750 3.002348 CACGAGGAAAGGAAGAACACAAC 59.998 47.826 0.00 0.00 0.00 3.32
3715 3755 3.565902 GGAAAGGAAGAACACAACCTCTG 59.434 47.826 0.00 0.00 31.89 3.35
3737 3777 6.039717 TCTGGCTAAGCATGGTTTGATATTTC 59.960 38.462 20.70 3.96 0.00 2.17
3742 3782 5.490139 AGCATGGTTTGATATTTCTCACG 57.510 39.130 0.00 0.00 0.00 4.35
3793 3875 7.181569 TGGTTTGAATAATGGGATCCTTTTC 57.818 36.000 12.58 8.39 0.00 2.29
3827 3910 7.950496 GTGATGTGAATCTTGTTTACGACTTAC 59.050 37.037 0.00 0.00 0.00 2.34
3836 3942 6.415867 TCTTGTTTACGACTTACGAAGACTTG 59.584 38.462 0.00 0.00 45.77 3.16
3877 3984 3.363341 AATGGTTTGTTTACTGTGCGG 57.637 42.857 0.00 0.00 0.00 5.69
3878 3985 1.752683 TGGTTTGTTTACTGTGCGGT 58.247 45.000 0.00 0.00 0.00 5.68
3879 3986 1.402259 TGGTTTGTTTACTGTGCGGTG 59.598 47.619 0.00 0.00 0.00 4.94
3880 3987 1.472990 GTTTGTTTACTGTGCGGTGC 58.527 50.000 0.00 0.00 0.00 5.01
3881 3988 0.028242 TTTGTTTACTGTGCGGTGCG 59.972 50.000 0.00 0.00 0.00 5.34
3984 4247 6.044682 GCAGATGGATAAAAGGAAATTGTGG 58.955 40.000 0.00 0.00 0.00 4.17
3986 4249 7.579339 GCAGATGGATAAAAGGAAATTGTGGAA 60.579 37.037 0.00 0.00 0.00 3.53
4024 4288 7.877097 AGCTAATGTGCTTCAGAAGATTATAGG 59.123 37.037 14.86 0.30 40.93 2.57
4056 4320 2.855963 CGTGTGACGTCTAACTGTTTGT 59.144 45.455 17.92 0.00 36.74 2.83
4057 4321 3.305094 CGTGTGACGTCTAACTGTTTGTT 59.695 43.478 17.92 0.00 38.50 2.83
4058 4322 4.500117 CGTGTGACGTCTAACTGTTTGTTA 59.500 41.667 17.92 0.00 37.17 2.41
4129 4399 6.590068 ACTATTTCTGGTGATGAAGATGAGG 58.410 40.000 0.00 0.00 0.00 3.86
4137 4407 7.935755 TCTGGTGATGAAGATGAGGATATTTTC 59.064 37.037 0.00 0.00 0.00 2.29
4138 4408 7.576403 TGGTGATGAAGATGAGGATATTTTCA 58.424 34.615 0.00 0.00 36.16 2.69
4151 4421 7.067372 TGAGGATATTTTCAATGCCTTAGTGTG 59.933 37.037 0.00 0.00 0.00 3.82
4161 4431 8.039603 TCAATGCCTTAGTGTGTTGTATAAAG 57.960 34.615 0.00 0.00 0.00 1.85
4162 4432 5.873179 TGCCTTAGTGTGTTGTATAAAGC 57.127 39.130 0.00 0.00 0.00 3.51
4188 4458 7.467675 CGCACATGCATTACATATGGCTATTAT 60.468 37.037 7.80 0.00 42.21 1.28
4211 4481 3.371166 GGATGTTTGGGAACTTCGGGATA 60.371 47.826 0.00 0.00 39.54 2.59
4278 4549 3.950395 GCTTGATAATATGAGCATCCCCC 59.050 47.826 0.00 0.00 35.29 5.40
4294 4565 1.373570 CCCCTGCGTTCAAAGATCTC 58.626 55.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 38 9.093970 TCAAAGTATGGTGACTATAATTCAACG 57.906 33.333 2.27 0.00 32.96 4.10
43 47 5.011125 CCCGAGATCAAAGTATGGTGACTAT 59.989 44.000 0.00 0.00 0.00 2.12
86 90 8.972127 TGCTAGAAGGAATATAGATACCATCAC 58.028 37.037 0.00 0.00 0.00 3.06
97 101 8.486210 AGACACATTGTTGCTAGAAGGAATATA 58.514 33.333 0.00 0.00 0.00 0.86
196 200 5.515534 GCATCCTCCATACCTTCCATGTATT 60.516 44.000 0.00 0.00 0.00 1.89
245 249 0.827089 CCCACACAAACATCCTGCCA 60.827 55.000 0.00 0.00 0.00 4.92
480 501 5.349543 GCCACATCATTTTCTTCAATGGAAC 59.650 40.000 0.00 0.00 35.22 3.62
768 798 5.385509 AACACCCAAAATTTCAGATACCG 57.614 39.130 0.00 0.00 0.00 4.02
784 814 4.331968 TGTGAATGTATTCTGGAACACCC 58.668 43.478 6.21 0.00 37.67 4.61
793 823 4.082571 GCAACTTGGCTGTGAATGTATTCT 60.083 41.667 6.21 0.00 37.67 2.40
842 872 4.161565 TGGTGCTATCTTCCGAATTAGTGT 59.838 41.667 0.00 0.00 0.00 3.55
870 900 7.239763 ACCAAACCTCCCAATACATAAAAAG 57.760 36.000 0.00 0.00 0.00 2.27
939 969 2.964464 ACCCATTGTCAAGCAAACATGA 59.036 40.909 0.00 0.00 40.91 3.07
1211 1241 4.823442 TCTGCTGAAATATCCAATGCGATT 59.177 37.500 0.00 0.00 0.00 3.34
1215 1245 5.759963 CTCTTCTGCTGAAATATCCAATGC 58.240 41.667 7.48 0.00 0.00 3.56
1277 1307 8.674607 GGACAATTCTTACGATTTAATGAACCT 58.325 33.333 0.00 0.00 0.00 3.50
1352 1382 4.708726 AAGTTGCATATGCTGAGGAAAC 57.291 40.909 27.13 20.43 42.66 2.78
1382 1412 2.912956 AGGGATATTCATGGCATACGGT 59.087 45.455 0.00 0.00 0.00 4.83
1414 1444 1.280998 GGTATAGGTGTTGCTGTGGGT 59.719 52.381 0.00 0.00 0.00 4.51
1460 1490 3.885297 AGTATGGAGCATATTGTGGTTGC 59.115 43.478 0.00 0.00 39.00 4.17
1592 1622 7.450944 TCAGCAGTCTCATCATTGACTATATCT 59.549 37.037 0.00 0.00 41.06 1.98
1656 1686 1.501582 ACCAGCCTTATGTCCTCCTC 58.498 55.000 0.00 0.00 0.00 3.71
1679 1709 7.049754 ACATGAAAAGAAAAGGAGCAAACAAT 58.950 30.769 0.00 0.00 0.00 2.71
1772 1803 3.450817 TCATACTTCTTGATCTTCGGGCA 59.549 43.478 0.00 0.00 0.00 5.36
2362 2393 2.315925 TTCTTTCTGGCGGCTCTATG 57.684 50.000 11.43 0.00 0.00 2.23
2426 2457 0.319555 TACCACGAAGCAGCAGTCAC 60.320 55.000 0.00 0.00 0.00 3.67
2471 2502 2.812011 ACTTCGAATTACCAGCCAACAC 59.188 45.455 0.00 0.00 0.00 3.32
2866 2897 0.032540 CCTGTTGCTTCAGTTTGGCC 59.967 55.000 0.00 0.00 34.02 5.36
3013 3044 9.040259 TGCTAGCTATCATCTCTACCAAATAAT 57.960 33.333 17.23 0.00 0.00 1.28
3075 3106 3.873361 TGCATAAGATAGCACTTCAGCAC 59.127 43.478 0.00 0.00 36.04 4.40
3078 3109 4.124970 TGCTGCATAAGATAGCACTTCAG 58.875 43.478 0.00 0.00 42.05 3.02
3114 3145 7.120923 ACAGGTTATAACAACATCGACCTAT 57.879 36.000 17.16 0.00 34.46 2.57
3123 3154 6.314400 GGCTAAATCGACAGGTTATAACAACA 59.686 38.462 17.16 0.00 0.00 3.33
3132 3163 3.132467 GGAGTAGGCTAAATCGACAGGTT 59.868 47.826 0.00 0.00 0.00 3.50
3167 3204 5.126061 GGCTGATGAAGGATAAACAACACAT 59.874 40.000 0.00 0.00 0.00 3.21
3181 3218 3.129988 GGATCAAACAAGGGCTGATGAAG 59.870 47.826 0.00 0.00 31.45 3.02
3188 3225 0.407139 AGCTGGATCAAACAAGGGCT 59.593 50.000 0.00 0.00 0.00 5.19
3198 3235 3.609256 ATCTAGGTGAGAGCTGGATCA 57.391 47.619 0.00 0.00 39.25 2.92
3283 3320 3.691049 TGCTTCCAAACTTCAACTTCG 57.309 42.857 0.00 0.00 0.00 3.79
3385 3424 5.717119 AAAGACTATAAACAGGCCCAGAT 57.283 39.130 0.00 0.00 0.00 2.90
3483 3522 1.885887 TGGAAGGTCCATGCTTTTTCG 59.114 47.619 0.00 0.00 42.67 3.46
3540 3580 3.645212 TGGATGGTCCATGCTTTTTCAAA 59.355 39.130 22.46 0.00 42.67 2.69
3542 3582 2.886913 TGGATGGTCCATGCTTTTTCA 58.113 42.857 22.46 0.00 42.67 2.69
3550 3590 6.742082 ACAAAGATTGTTTTGGATGGTCCATG 60.742 38.462 9.76 0.00 43.57 3.66
3551 3591 5.307716 ACAAAGATTGTTTTGGATGGTCCAT 59.692 36.000 3.26 3.26 43.57 3.41
3553 3593 5.213891 ACAAAGATTGTTTTGGATGGTCC 57.786 39.130 3.85 0.00 42.22 4.46
3566 3606 4.670992 CGAGACCAGCATGAACAAAGATTG 60.671 45.833 0.00 0.00 39.69 2.67
3567 3607 3.438087 CGAGACCAGCATGAACAAAGATT 59.562 43.478 0.00 0.00 39.69 2.40
3568 3608 3.005554 CGAGACCAGCATGAACAAAGAT 58.994 45.455 0.00 0.00 39.69 2.40
3570 3610 1.466167 CCGAGACCAGCATGAACAAAG 59.534 52.381 0.00 0.00 39.69 2.77
3572 3612 0.396435 ACCGAGACCAGCATGAACAA 59.604 50.000 0.00 0.00 39.69 2.83
3573 3613 0.396435 AACCGAGACCAGCATGAACA 59.604 50.000 0.00 0.00 39.69 3.18
3588 3628 4.385447 CCATGTTGTTGAGCAAAATAACCG 59.615 41.667 8.02 1.76 39.03 4.44
3589 3629 5.296748 ACCATGTTGTTGAGCAAAATAACC 58.703 37.500 8.02 0.00 39.03 2.85
3590 3630 8.532977 AATACCATGTTGTTGAGCAAAATAAC 57.467 30.769 0.00 4.68 39.03 1.89
3591 3631 9.202273 GAAATACCATGTTGTTGAGCAAAATAA 57.798 29.630 0.00 0.00 39.03 1.40
3604 3644 5.450965 GGAAGCATCAGGAAATACCATGTTG 60.451 44.000 0.00 0.00 42.04 3.33
3610 3650 5.707764 GGAATAGGAAGCATCAGGAAATACC 59.292 44.000 0.00 0.00 39.35 2.73
3634 3674 4.288531 ACTTCTAACTCGTCACAAGTTCG 58.711 43.478 0.00 0.00 38.00 3.95
3639 3679 8.358148 AGAGATTTTACTTCTAACTCGTCACAA 58.642 33.333 0.00 0.00 0.00 3.33
3657 3697 7.593644 GCCATACGTGTTTTGTTTAGAGATTTT 59.406 33.333 0.00 0.00 0.00 1.82
3658 3698 7.040686 AGCCATACGTGTTTTGTTTAGAGATTT 60.041 33.333 0.00 0.00 0.00 2.17
3659 3699 6.430000 AGCCATACGTGTTTTGTTTAGAGATT 59.570 34.615 0.00 0.00 0.00 2.40
3660 3700 5.938125 AGCCATACGTGTTTTGTTTAGAGAT 59.062 36.000 0.00 0.00 0.00 2.75
3661 3701 5.178623 CAGCCATACGTGTTTTGTTTAGAGA 59.821 40.000 0.00 0.00 0.00 3.10
3662 3702 5.049680 ACAGCCATACGTGTTTTGTTTAGAG 60.050 40.000 0.00 0.00 0.00 2.43
3663 3703 4.817464 ACAGCCATACGTGTTTTGTTTAGA 59.183 37.500 0.00 0.00 0.00 2.10
3664 3704 5.103290 ACAGCCATACGTGTTTTGTTTAG 57.897 39.130 0.00 0.00 0.00 1.85
3665 3705 5.066117 TGAACAGCCATACGTGTTTTGTTTA 59.934 36.000 0.00 0.00 37.02 2.01
3666 3706 4.142359 TGAACAGCCATACGTGTTTTGTTT 60.142 37.500 0.00 0.00 37.02 2.83
3667 3707 3.378742 TGAACAGCCATACGTGTTTTGTT 59.621 39.130 0.00 1.84 37.02 2.83
3668 3708 2.946329 TGAACAGCCATACGTGTTTTGT 59.054 40.909 0.00 0.00 37.02 2.83
3669 3709 3.296628 GTGAACAGCCATACGTGTTTTG 58.703 45.455 0.00 0.00 37.02 2.44
3670 3710 2.032377 CGTGAACAGCCATACGTGTTTT 60.032 45.455 0.00 0.00 37.02 2.43
3671 3711 1.529438 CGTGAACAGCCATACGTGTTT 59.471 47.619 0.00 0.00 37.02 2.83
3672 3712 1.144969 CGTGAACAGCCATACGTGTT 58.855 50.000 0.00 0.00 39.62 3.32
3673 3713 0.315886 TCGTGAACAGCCATACGTGT 59.684 50.000 0.00 0.00 37.74 4.49
3674 3714 0.992072 CTCGTGAACAGCCATACGTG 59.008 55.000 0.00 0.00 37.74 4.49
3675 3715 0.108804 CCTCGTGAACAGCCATACGT 60.109 55.000 0.00 0.00 37.74 3.57
3676 3716 0.172578 TCCTCGTGAACAGCCATACG 59.827 55.000 0.00 0.00 37.85 3.06
3677 3717 2.380084 TTCCTCGTGAACAGCCATAC 57.620 50.000 0.00 0.00 0.00 2.39
3678 3718 2.354704 CCTTTCCTCGTGAACAGCCATA 60.355 50.000 0.00 0.00 31.05 2.74
3679 3719 1.611673 CCTTTCCTCGTGAACAGCCAT 60.612 52.381 0.00 0.00 31.05 4.40
3680 3720 0.250295 CCTTTCCTCGTGAACAGCCA 60.250 55.000 0.00 0.00 31.05 4.75
3681 3721 0.034896 TCCTTTCCTCGTGAACAGCC 59.965 55.000 0.00 0.00 31.05 4.85
3682 3722 1.801178 CTTCCTTTCCTCGTGAACAGC 59.199 52.381 0.00 0.00 31.05 4.40
3683 3723 3.386768 TCTTCCTTTCCTCGTGAACAG 57.613 47.619 0.00 0.00 31.05 3.16
3684 3724 3.118555 TGTTCTTCCTTTCCTCGTGAACA 60.119 43.478 0.00 0.00 39.57 3.18
3685 3725 3.247886 GTGTTCTTCCTTTCCTCGTGAAC 59.752 47.826 0.00 0.00 34.66 3.18
3686 3726 3.118555 TGTGTTCTTCCTTTCCTCGTGAA 60.119 43.478 0.00 0.00 0.00 3.18
3687 3727 2.432874 TGTGTTCTTCCTTTCCTCGTGA 59.567 45.455 0.00 0.00 0.00 4.35
3688 3728 2.833794 TGTGTTCTTCCTTTCCTCGTG 58.166 47.619 0.00 0.00 0.00 4.35
3689 3729 3.203716 GTTGTGTTCTTCCTTTCCTCGT 58.796 45.455 0.00 0.00 0.00 4.18
3690 3730 2.548480 GGTTGTGTTCTTCCTTTCCTCG 59.452 50.000 0.00 0.00 0.00 4.63
3691 3731 3.815962 GAGGTTGTGTTCTTCCTTTCCTC 59.184 47.826 0.00 0.00 33.49 3.71
3692 3732 3.459969 AGAGGTTGTGTTCTTCCTTTCCT 59.540 43.478 0.00 0.00 0.00 3.36
3693 3733 3.565902 CAGAGGTTGTGTTCTTCCTTTCC 59.434 47.826 0.00 0.00 0.00 3.13
3694 3734 3.565902 CCAGAGGTTGTGTTCTTCCTTTC 59.434 47.826 0.00 0.00 0.00 2.62
3695 3735 3.555966 CCAGAGGTTGTGTTCTTCCTTT 58.444 45.455 0.00 0.00 0.00 3.11
3696 3736 2.749800 GCCAGAGGTTGTGTTCTTCCTT 60.750 50.000 0.00 0.00 0.00 3.36
3697 3737 1.202818 GCCAGAGGTTGTGTTCTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
3698 3738 1.202818 AGCCAGAGGTTGTGTTCTTCC 60.203 52.381 0.00 0.00 0.00 3.46
3699 3739 2.262423 AGCCAGAGGTTGTGTTCTTC 57.738 50.000 0.00 0.00 0.00 2.87
3710 3750 1.747355 CAAACCATGCTTAGCCAGAGG 59.253 52.381 0.29 0.70 0.00 3.69
3715 3755 6.039717 TGAGAAATATCAAACCATGCTTAGCC 59.960 38.462 0.29 0.00 0.00 3.93
3742 3782 3.265791 CTCCAGTCTCACTACAATTGCC 58.734 50.000 5.05 0.00 0.00 4.52
3793 3875 6.309712 ACAAGATTCACATCACAAGTTCAG 57.690 37.500 0.00 0.00 0.00 3.02
3827 3910 1.901650 GCCAAGCGACCAAGTCTTCG 61.902 60.000 0.00 0.00 38.31 3.79
3836 3942 4.947147 TGGTGGTGCCAAGCGACC 62.947 66.667 0.00 0.00 45.94 4.79
3877 3984 0.740737 AAATGATAAGCAGGCCGCAC 59.259 50.000 19.30 3.61 46.13 5.34
3878 3985 0.740149 CAAATGATAAGCAGGCCGCA 59.260 50.000 19.30 2.76 46.13 5.69
3879 3986 0.031178 CCAAATGATAAGCAGGCCGC 59.969 55.000 11.02 11.02 42.91 6.53
3880 3987 1.679139 TCCAAATGATAAGCAGGCCG 58.321 50.000 0.00 0.00 0.00 6.13
3881 3988 3.243975 CCATTCCAAATGATAAGCAGGCC 60.244 47.826 0.00 0.00 0.00 5.19
3984 4247 5.517770 GCACATTAGCTTTCCAATGATGTTC 59.482 40.000 12.76 0.00 36.00 3.18
3986 4249 4.708421 AGCACATTAGCTTTCCAATGATGT 59.292 37.500 12.76 0.00 43.70 3.06
4021 4285 1.616374 TCACACGTCATGCAGAACCTA 59.384 47.619 0.00 0.00 0.00 3.08
4024 4288 0.161658 CGTCACACGTCATGCAGAAC 59.838 55.000 0.00 0.00 36.74 3.01
4129 4399 8.028938 ACAACACACTAAGGCATTGAAAATATC 58.971 33.333 0.00 0.00 0.00 1.63
4137 4407 6.747280 GCTTTATACAACACACTAAGGCATTG 59.253 38.462 0.00 0.00 0.00 2.82
4138 4408 6.403200 CGCTTTATACAACACACTAAGGCATT 60.403 38.462 0.00 0.00 0.00 3.56
4151 4421 3.129852 TGCATGTGCGCTTTATACAAC 57.870 42.857 9.73 1.69 45.83 3.32
4161 4431 2.587956 CCATATGTAATGCATGTGCGC 58.412 47.619 0.00 0.00 42.90 6.09
4162 4432 2.227149 AGCCATATGTAATGCATGTGCG 59.773 45.455 0.00 0.00 42.90 5.34
4188 4458 1.546773 CCCGAAGTTCCCAAACATCCA 60.547 52.381 0.00 0.00 37.88 3.41
4306 4577 2.106938 TAGATGCCAAGCTCCGCG 59.893 61.111 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.