Multiple sequence alignment - TraesCS4B01G150200

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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 TraesCS4B01G150200 chr4B 100.000 4244 0 0 628 4871 230011787 230007544 0.000000e+00 7838
1 TraesCS4B01G150200 chr4B 100.000 334 0 0 1 334 230012414 230012081 6.930000e-173 617
2 TraesCS4B01G150200 chr4A 93.373 4255 193 48 679 4871 423894626 423890399 0.000000e+00 6213
3 TraesCS4B01G150200 chr4A 93.750 288 13 3 1 288 423895364 423895082 1.250000e-115 427
4 TraesCS4B01G150200 chr4D 95.536 3853 142 15 653 4488 137768159 137764320 0.000000e+00 6135
5 TraesCS4B01G150200 chr4D 94.627 335 9 6 1 334 137768856 137768530 1.210000e-140 510


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 TraesCS4B01G150200 chr4B 230007544 230012414 4870 True 4227.5 7838 100.0000 1 4871 2 chr4B.!!$R1 4870
1 TraesCS4B01G150200 chr4A 423890399 423895364 4965 True 3320.0 6213 93.5615 1 4871 2 chr4A.!!$R1 4870
2 TraesCS4B01G150200 chr4D 137764320 137768856 4536 True 3322.5 6135 95.0815 1 4488 2 chr4D.!!$R1 4487


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
899 968 2.051256 ACTGCGACGCGGATATCG 60.051 61.111 33.96 12.15 38.46 2.92 F
1023 1092 2.119495 GGGAGGGTGAAGCTCAAGATA 58.881 52.381 0.00 0.00 0.00 1.98 F
2731 2808 2.224185 ACACTGTGTTCAGCATAACCGA 60.224 45.455 7.80 0.00 44.77 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2821 2898 3.192212 GCTGCTTTGCAAAGTTCTCCTAT 59.808 43.478 33.47 0.0 38.41 2.57 R
2936 3013 1.780503 AATAGCAAGGGCCAACATCC 58.219 50.000 6.18 0.0 42.56 3.51 R
4158 4247 0.175760 GCTCGTGCTTGGAGGATGTA 59.824 55.000 1.41 0.0 36.03 2.29 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
157 158 9.395707 GTATAGATACATAAAGGTGTGAACGAG 57.604 37.037 0.00 0.00 33.62 4.18
159 160 6.565234 AGATACATAAAGGTGTGAACGAGAG 58.435 40.000 0.00 0.00 33.62 3.20
648 649 3.917300 TCTCTCCTTCTTGACCCCTATC 58.083 50.000 0.00 0.00 0.00 2.08
649 650 3.533907 TCTCTCCTTCTTGACCCCTATCT 59.466 47.826 0.00 0.00 0.00 1.98
650 651 3.895041 CTCTCCTTCTTGACCCCTATCTC 59.105 52.174 0.00 0.00 0.00 2.75
651 652 3.533907 TCTCCTTCTTGACCCCTATCTCT 59.466 47.826 0.00 0.00 0.00 3.10
899 968 2.051256 ACTGCGACGCGGATATCG 60.051 61.111 33.96 12.15 38.46 2.92
912 981 5.006649 GCGGATATCGTGAATAACAACAG 57.993 43.478 0.00 0.00 41.72 3.16
940 1009 3.341823 CCATCCAGATTCCATCGGATTC 58.658 50.000 7.14 0.00 39.18 2.52
958 1027 8.972458 TCGGATTCTATCATAATTGGTGAAAA 57.028 30.769 0.31 0.00 0.00 2.29
983 1052 7.075741 AGTGTGACGTTAAGACATAATTTTGC 58.924 34.615 0.00 0.00 0.00 3.68
1023 1092 2.119495 GGGAGGGTGAAGCTCAAGATA 58.881 52.381 0.00 0.00 0.00 1.98
1071 1140 3.492656 GGCAGGTGACATATTCTAAGCGA 60.493 47.826 0.00 0.00 0.00 4.93
1104 1173 3.480470 TCTCAAGAAGGCCAAAGAGTTG 58.520 45.455 5.01 0.00 34.25 3.16
1113 1182 3.330701 AGGCCAAAGAGTTGTCCATTCTA 59.669 43.478 5.01 0.00 35.09 2.10
1146 1215 7.326454 TCGATCTCATTCTTCTCATGTTTTCT 58.674 34.615 0.00 0.00 0.00 2.52
1201 1270 5.353111 ACAAAAGGTAATGGTTTTGGTTCG 58.647 37.500 11.16 0.00 44.48 3.95
1207 1276 4.457949 GGTAATGGTTTTGGTTCGTCTGAT 59.542 41.667 0.00 0.00 0.00 2.90
1210 1279 6.642707 AATGGTTTTGGTTCGTCTGATTTA 57.357 33.333 0.00 0.00 0.00 1.40
1214 1283 8.167605 TGGTTTTGGTTCGTCTGATTTAATTA 57.832 30.769 0.00 0.00 0.00 1.40
1252 1321 6.992715 GTCAACAAGCCCATAATATGACTACT 59.007 38.462 1.10 0.00 34.58 2.57
1389 1461 8.392612 GGAAATCGATTTTTCAATGCATTTCAT 58.607 29.630 23.49 0.00 37.34 2.57
1441 1513 2.270352 TTCCGACTGAAGCACCATTT 57.730 45.000 0.00 0.00 0.00 2.32
1514 1590 8.210265 TCTATGCTTTTTCTTTTGGGTGAAATT 58.790 29.630 0.00 0.00 33.04 1.82
1558 1634 9.658799 TGCTTTAGCCATATATCTATCTTGTTC 57.341 33.333 0.00 0.00 41.18 3.18
1578 1654 5.132648 TGTTCTCAGATATGGGGTGCTAATT 59.867 40.000 0.00 0.00 0.00 1.40
1714 1791 8.715190 AAAGGGCTAAAAGGTATTTGAGTTAA 57.285 30.769 0.00 0.00 30.36 2.01
1886 1963 7.992754 AAGTTTGAGAATGAGCTGACTAATT 57.007 32.000 0.00 0.00 28.65 1.40
1978 2055 5.190330 ACTTCTTAGGCTCCGGGTAATTTTA 59.810 40.000 0.00 0.00 0.00 1.52
2175 2252 5.092554 TGGTTTTCGGTATCTAATGCTCA 57.907 39.130 0.00 0.00 0.00 4.26
2535 2612 5.902613 TGAAAATTGAGGAGCATAACAGG 57.097 39.130 0.00 0.00 0.00 4.00
2537 2614 5.774690 TGAAAATTGAGGAGCATAACAGGTT 59.225 36.000 0.00 0.00 0.00 3.50
2573 2650 3.450817 TCTTCAGTTATTGGAGCGATCCA 59.549 43.478 20.59 20.59 38.14 3.41
2664 2741 6.268825 TCGGCATTCATAAGGTAGAGATAC 57.731 41.667 0.00 0.00 0.00 2.24
2697 2774 5.201713 TCTTATTAACTCCAGCCGATCTG 57.798 43.478 0.00 0.00 42.49 2.90
2731 2808 2.224185 ACACTGTGTTCAGCATAACCGA 60.224 45.455 7.80 0.00 44.77 4.69
2803 2880 6.975197 GTCACTCAGAATTCGATCTCATGTTA 59.025 38.462 0.00 0.00 0.00 2.41
2821 2898 5.638530 TGTTATACCCTGTTGGATATGCA 57.361 39.130 0.00 0.00 38.00 3.96
2898 2975 5.066505 AGGTAACAGTTTTCAGCTTCACAAG 59.933 40.000 0.00 0.00 41.41 3.16
3006 3083 0.909623 CTCTGGGGTTAACCGGTGAT 59.090 55.000 18.39 0.00 41.60 3.06
3032 3109 0.531090 CCTTCGTCGTGGTTCCACAA 60.531 55.000 19.90 0.47 36.82 3.33
3036 3113 2.109387 TCGTGGTTCCACAACGGG 59.891 61.111 19.90 5.37 36.82 5.28
3040 3117 4.589675 GGTTCCACAACGGGGGCA 62.590 66.667 0.00 0.00 32.68 5.36
3108 3185 2.298729 GCTCCATCAGAGGTGAGTATCC 59.701 54.545 3.50 0.00 43.46 2.59
3149 3226 4.037089 GGTTGGTCAGGAATTTTGTTACGT 59.963 41.667 0.00 0.00 0.00 3.57
3151 3228 6.368213 GTTGGTCAGGAATTTTGTTACGTAG 58.632 40.000 0.00 0.00 0.00 3.51
3152 3229 4.453136 TGGTCAGGAATTTTGTTACGTAGC 59.547 41.667 2.00 2.00 0.00 3.58
3154 3231 5.390567 GGTCAGGAATTTTGTTACGTAGCAG 60.391 44.000 12.03 0.00 0.00 4.24
3156 3233 5.761234 TCAGGAATTTTGTTACGTAGCAGTT 59.239 36.000 12.03 8.86 0.00 3.16
3157 3234 6.930164 TCAGGAATTTTGTTACGTAGCAGTTA 59.070 34.615 12.03 2.97 0.00 2.24
3523 3610 4.424566 TTCGTCGGCGGCCACTAC 62.425 66.667 20.71 12.50 38.89 2.73
3538 3625 1.144057 CTACGAAATGCCGAGGCCT 59.856 57.895 3.86 3.86 41.09 5.19
3637 3724 4.758674 CCATCTGCCCAAGTGAGTAATATG 59.241 45.833 0.00 0.00 0.00 1.78
3742 3829 6.238211 CGAACGAGCATTTCTTCCAAATATCT 60.238 38.462 0.00 0.00 0.00 1.98
3749 3836 6.020360 GCATTTCTTCCAAATATCTGCGAAAC 60.020 38.462 0.00 0.00 0.00 2.78
3828 3917 8.632679 TCTTTTCAGCTTATTGTTCAGAACATT 58.367 29.630 16.89 15.13 41.79 2.71
3898 3987 2.279918 GTTCGACCACGCCACTGT 60.280 61.111 0.00 0.00 39.58 3.55
3900 3989 3.509137 TTCGACCACGCCACTGTCC 62.509 63.158 0.00 0.00 39.58 4.02
3937 4026 6.962686 TCATGATTTGATGATTCTTTAGCCG 58.037 36.000 0.00 0.00 0.00 5.52
4006 4095 5.997746 CCTTCTCAGTCAGTTTGTTATTCCA 59.002 40.000 0.00 0.00 0.00 3.53
4158 4247 1.494960 TGAAAAAGGTTGGGCAGCTT 58.505 45.000 0.00 0.00 45.60 3.74
4224 4313 3.807622 TCTCAAAATGTTGACGTCCTGAC 59.192 43.478 14.12 9.78 38.88 3.51
4246 4335 2.358322 TTGACAGGGTCTCCAAAACC 57.642 50.000 0.00 0.00 35.97 3.27
4411 4502 1.081094 CTAAAATTTCGGCCGGTCGT 58.919 50.000 29.96 10.67 0.00 4.34
4429 4520 1.328680 CGTCTGCCAGATGTGCATAAC 59.671 52.381 5.73 0.00 38.22 1.89
4441 4532 1.817941 GCATAACGGTCATGCGGGT 60.818 57.895 0.00 0.00 39.43 5.28
4443 4534 0.461163 CATAACGGTCATGCGGGTCA 60.461 55.000 0.00 0.00 0.00 4.02
4459 4550 1.004745 GGTCATGTGATTCCTGGGTGT 59.995 52.381 0.00 0.00 0.00 4.16
4460 4551 2.555227 GGTCATGTGATTCCTGGGTGTT 60.555 50.000 0.00 0.00 0.00 3.32
4467 4558 0.324943 ATTCCTGGGTGTTGTCCTCG 59.675 55.000 0.00 0.00 0.00 4.63
4471 4562 0.038159 CTGGGTGTTGTCCTCGTCTC 60.038 60.000 0.00 0.00 0.00 3.36
4495 4589 0.249955 TACTCCGCGGTAAAAAGGGG 59.750 55.000 27.15 0.00 41.23 4.79
4500 4594 1.022982 CGCGGTAAAAAGGGGAGGAC 61.023 60.000 0.00 0.00 0.00 3.85
4536 4630 2.047560 CCCCCAACCTCGTCGAAC 60.048 66.667 0.00 0.00 0.00 3.95
4544 4638 2.507102 CTCGTCGAACTGCCGCAT 60.507 61.111 0.00 0.00 0.00 4.73
4579 4706 3.969250 ATCGCCGCCACATTTCCGT 62.969 57.895 0.00 0.00 0.00 4.69
4580 4707 4.459331 CGCCGCCACATTTCCGTG 62.459 66.667 0.00 0.00 36.61 4.94
4583 4710 2.480555 CGCCACATTTCCGTGCTC 59.519 61.111 0.00 0.00 35.47 4.26
4587 4714 2.357034 ACATTTCCGTGCTCGCGT 60.357 55.556 5.77 0.00 35.54 6.01
4635 4764 1.807742 GTGTGCCACCGTTTAAGCATA 59.192 47.619 0.00 0.00 37.60 3.14
4659 4788 5.594317 AGAATCTGGTTTGTAGCACTTTGTT 59.406 36.000 0.00 0.00 0.00 2.83
4662 4791 2.493675 TGGTTTGTAGCACTTTGTTGCA 59.506 40.909 0.00 0.00 45.62 4.08
4681 4810 2.356553 TTGCCGTGCTACGACCAC 60.357 61.111 9.75 0.00 46.05 4.16
4682 4811 3.153270 TTGCCGTGCTACGACCACA 62.153 57.895 9.75 1.54 46.05 4.17
4687 4816 0.791983 CGTGCTACGACCACACTACG 60.792 60.000 3.04 0.00 46.05 3.51
4694 4823 2.599578 ACCACACTACGGGCGAGT 60.600 61.111 0.00 0.00 0.00 4.18
4733 4862 3.777925 GTCACAGCACGCGCGATT 61.778 61.111 39.36 18.25 45.49 3.34
4753 4882 2.548587 GAACTCATGGCGCACGTTCG 62.549 60.000 10.83 2.39 0.00 3.95
4761 4890 3.636043 CGCACGTTCGCTGTGGTT 61.636 61.111 0.00 0.00 37.80 3.67
4763 4892 1.063488 GCACGTTCGCTGTGGTTTT 59.937 52.632 0.00 0.00 37.80 2.43
4764 4893 0.928451 GCACGTTCGCTGTGGTTTTC 60.928 55.000 0.00 0.00 37.80 2.29
4785 4914 0.673644 AGCGTACACCATGGCTTGTC 60.674 55.000 13.04 3.63 30.04 3.18
4825 4954 4.147219 ACACTAGACGCAGCAAAAATTC 57.853 40.909 0.00 0.00 0.00 2.17
4826 4955 3.815401 ACACTAGACGCAGCAAAAATTCT 59.185 39.130 0.00 0.00 0.00 2.40
4857 4986 1.463674 AGCACTAAAGGATTTGGCCG 58.536 50.000 0.00 0.00 40.57 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.959030 AGAAAACCAAGGAGGCTTCAAC 59.041 45.455 0.00 0.00 43.14 3.18
143 144 4.618965 GTTCTACTCTCGTTCACACCTTT 58.381 43.478 0.00 0.00 0.00 3.11
157 158 8.027771 TGTTTATTTTCTCCTCTCGTTCTACTC 58.972 37.037 0.00 0.00 0.00 2.59
159 160 8.530269 TTGTTTATTTTCTCCTCTCGTTCTAC 57.470 34.615 0.00 0.00 0.00 2.59
207 208 6.529829 CAGTTGGAAATGTTTTTCGTTTCTCA 59.470 34.615 10.80 6.24 45.87 3.27
627 628 3.533907 AGATAGGGGTCAAGAAGGAGAGA 59.466 47.826 0.00 0.00 0.00 3.10
628 629 3.895041 GAGATAGGGGTCAAGAAGGAGAG 59.105 52.174 0.00 0.00 0.00 3.20
629 630 3.533907 AGAGATAGGGGTCAAGAAGGAGA 59.466 47.826 0.00 0.00 0.00 3.71
630 631 3.895041 GAGAGATAGGGGTCAAGAAGGAG 59.105 52.174 0.00 0.00 0.00 3.69
631 632 3.533907 AGAGAGATAGGGGTCAAGAAGGA 59.466 47.826 0.00 0.00 0.00 3.36
632 633 3.895041 GAGAGAGATAGGGGTCAAGAAGG 59.105 52.174 0.00 0.00 0.00 3.46
633 634 3.895041 GGAGAGAGATAGGGGTCAAGAAG 59.105 52.174 0.00 0.00 0.00 2.85
634 635 3.533907 AGGAGAGAGATAGGGGTCAAGAA 59.466 47.826 0.00 0.00 0.00 2.52
635 636 3.135279 AGGAGAGAGATAGGGGTCAAGA 58.865 50.000 0.00 0.00 0.00 3.02
636 637 3.496331 GAGGAGAGAGATAGGGGTCAAG 58.504 54.545 0.00 0.00 0.00 3.02
637 638 2.158593 CGAGGAGAGAGATAGGGGTCAA 60.159 54.545 0.00 0.00 0.00 3.18
638 639 1.422024 CGAGGAGAGAGATAGGGGTCA 59.578 57.143 0.00 0.00 0.00 4.02
639 640 1.884928 GCGAGGAGAGAGATAGGGGTC 60.885 61.905 0.00 0.00 0.00 4.46
640 641 0.111639 GCGAGGAGAGAGATAGGGGT 59.888 60.000 0.00 0.00 0.00 4.95
641 642 0.610785 GGCGAGGAGAGAGATAGGGG 60.611 65.000 0.00 0.00 0.00 4.79
642 643 0.610785 GGGCGAGGAGAGAGATAGGG 60.611 65.000 0.00 0.00 0.00 3.53
643 644 0.610785 GGGGCGAGGAGAGAGATAGG 60.611 65.000 0.00 0.00 0.00 2.57
644 645 0.610785 GGGGGCGAGGAGAGAGATAG 60.611 65.000 0.00 0.00 0.00 2.08
645 646 1.068943 AGGGGGCGAGGAGAGAGATA 61.069 60.000 0.00 0.00 0.00 1.98
646 647 1.955458 AAGGGGGCGAGGAGAGAGAT 61.955 60.000 0.00 0.00 0.00 2.75
647 648 2.575455 GAAGGGGGCGAGGAGAGAGA 62.575 65.000 0.00 0.00 0.00 3.10
648 649 2.042435 AAGGGGGCGAGGAGAGAG 60.042 66.667 0.00 0.00 0.00 3.20
649 650 2.042843 GAAGGGGGCGAGGAGAGA 60.043 66.667 0.00 0.00 0.00 3.10
650 651 2.042435 AGAAGGGGGCGAGGAGAG 60.042 66.667 0.00 0.00 0.00 3.20
651 652 2.042843 GAGAAGGGGGCGAGGAGA 60.043 66.667 0.00 0.00 0.00 3.71
899 968 7.122055 TGGATGGGAAATACTGTTGTTATTCAC 59.878 37.037 0.00 0.00 0.00 3.18
910 979 5.052693 TGGAATCTGGATGGGAAATACTG 57.947 43.478 0.00 0.00 0.00 2.74
912 981 4.697352 CGATGGAATCTGGATGGGAAATAC 59.303 45.833 0.00 0.00 42.58 1.89
940 1009 7.904977 CGTCACACTTTTCACCAATTATGATAG 59.095 37.037 0.00 0.00 0.00 2.08
958 1027 7.041372 AGCAAAATTATGTCTTAACGTCACACT 60.041 33.333 0.00 0.00 0.00 3.55
983 1052 2.609459 CCCATGTCGAAGAATTTCCGAG 59.391 50.000 0.00 0.00 39.69 4.63
1023 1092 2.856222 CTGGTGTTCTCCAGCTTCTTT 58.144 47.619 7.78 0.00 46.53 2.52
1071 1140 1.938585 TCTTGAGAATCCCTGACCGT 58.061 50.000 0.00 0.00 0.00 4.83
1104 1173 7.766283 TGAGATCGATATCACATAGAATGGAC 58.234 38.462 18.40 0.00 34.28 4.02
1113 1182 8.120140 TGAGAAGAATGAGATCGATATCACAT 57.880 34.615 23.97 16.03 42.90 3.21
1146 1215 0.714180 TGGTAGGCCTTCCACTAGGA 59.286 55.000 26.14 3.28 43.93 2.94
1210 1279 9.860898 GCTTGTTGACCTAAATCTGAATTAATT 57.139 29.630 0.00 0.00 0.00 1.40
1214 1283 5.185828 GGGCTTGTTGACCTAAATCTGAATT 59.814 40.000 0.00 0.00 41.93 2.17
1361 1432 7.910441 AATGCATTGAAAAATCGATTTCCTT 57.090 28.000 22.93 14.75 38.30 3.36
1363 1434 7.741198 TGAAATGCATTGAAAAATCGATTTCC 58.259 30.769 22.93 17.35 38.30 3.13
1365 1436 8.937884 TGATGAAATGCATTGAAAAATCGATTT 58.062 25.926 17.60 17.60 37.34 2.17
1369 1441 9.205916 GAATTGATGAAATGCATTGAAAAATCG 57.794 29.630 13.82 0.00 37.34 3.34
1408 1480 8.688151 GCTTCAGTCGGAATATAGGACTAATAT 58.312 37.037 3.70 0.00 38.90 1.28
1412 1484 5.241064 GTGCTTCAGTCGGAATATAGGACTA 59.759 44.000 3.70 0.00 38.90 2.59
1413 1485 4.038162 GTGCTTCAGTCGGAATATAGGACT 59.962 45.833 4.29 0.00 41.47 3.85
1421 1493 2.496899 AATGGTGCTTCAGTCGGAAT 57.503 45.000 0.00 0.00 34.32 3.01
1441 1513 8.629158 AGAAGCACAATGACAAACTGTAAATTA 58.371 29.630 0.00 0.00 0.00 1.40
1514 1590 9.405587 GCTAAAGCATTGTTTTGTAATTCTACA 57.594 29.630 8.55 0.00 41.59 2.74
1550 1626 4.445448 GCACCCCATATCTGAGAACAAGAT 60.445 45.833 0.00 0.00 0.00 2.40
1553 1629 2.846206 AGCACCCCATATCTGAGAACAA 59.154 45.455 0.00 0.00 0.00 2.83
1558 1634 9.911788 AAATATAATTAGCACCCCATATCTGAG 57.088 33.333 0.00 0.00 0.00 3.35
1578 1654 9.692749 CTGATTTAACTCTCCGTGCTAAATATA 57.307 33.333 0.00 0.00 0.00 0.86
1587 1663 5.122239 TGCAATTCTGATTTAACTCTCCGTG 59.878 40.000 0.00 0.00 0.00 4.94
1632 1709 2.171659 TCGTCTATGGGGCTGCAAATTA 59.828 45.455 0.50 0.00 0.00 1.40
1714 1791 9.846248 GTTCAGCAGATAAACAGAAAATGTATT 57.154 29.630 0.00 0.00 43.00 1.89
1851 1928 8.454106 GCTCATTCTCAAACTTAATCTGCTAAA 58.546 33.333 0.00 0.00 0.00 1.85
2027 2104 9.490663 CATAGTGAGAAATTTCGTTGGAATTAC 57.509 33.333 12.42 1.07 30.88 1.89
2490 2567 3.194542 TGGTTTCCCTTCAAGTTTGTGTG 59.805 43.478 0.00 0.00 0.00 3.82
2573 2650 9.836179 ATATGGTCTATATTCTCAACCTTCTCT 57.164 33.333 0.00 0.00 0.00 3.10
2606 2683 6.424883 AGATTCTTTGAGAGATTGCTCCATT 58.575 36.000 0.00 0.00 42.30 3.16
2664 2741 6.965607 TGGAGTTAATAAGAAGGTTTAGGGG 58.034 40.000 0.00 0.00 0.00 4.79
2731 2808 5.599999 ACTTCGGATATTGAACAGCTAGT 57.400 39.130 0.00 0.00 0.00 2.57
2803 2880 5.100811 TCCTATGCATATCCAACAGGGTAT 58.899 41.667 6.92 0.00 38.11 2.73
2821 2898 3.192212 GCTGCTTTGCAAAGTTCTCCTAT 59.808 43.478 33.47 0.00 38.41 2.57
2880 2957 4.985413 TGAACTTGTGAAGCTGAAAACTG 58.015 39.130 0.00 0.00 0.00 3.16
2898 2975 5.324784 ACCTGAAACCAAAAGTTCTGAAC 57.675 39.130 12.54 12.54 37.88 3.18
2936 3013 1.780503 AATAGCAAGGGCCAACATCC 58.219 50.000 6.18 0.00 42.56 3.51
3036 3113 4.783621 TGTCCATCGCTGCTGCCC 62.784 66.667 10.24 0.00 35.36 5.36
3040 3117 4.827087 CGGCTGTCCATCGCTGCT 62.827 66.667 0.00 0.00 0.00 4.24
3108 3185 2.681778 ACCCCTGAGCTCAGTCCG 60.682 66.667 35.47 25.32 42.27 4.79
3151 3228 8.391106 ACGATTATGTTTCTTCTTCATAACTGC 58.609 33.333 0.00 0.00 37.04 4.40
3152 3229 9.907576 GACGATTATGTTTCTTCTTCATAACTG 57.092 33.333 0.00 0.00 37.04 3.16
3154 3231 8.879759 TGGACGATTATGTTTCTTCTTCATAAC 58.120 33.333 0.00 0.00 37.04 1.89
3156 3233 7.222031 CGTGGACGATTATGTTTCTTCTTCATA 59.778 37.037 0.00 0.00 43.02 2.15
3157 3234 6.036083 CGTGGACGATTATGTTTCTTCTTCAT 59.964 38.462 0.00 0.00 43.02 2.57
3186 3273 3.567478 CTGCGTGGTGGAGTGCGTA 62.567 63.158 0.00 0.00 0.00 4.42
3232 3319 3.077556 CCCGGGTAGCTCTGCAGT 61.078 66.667 14.18 0.00 0.00 4.40
3318 3405 2.434359 GCTGGTGCTGACGTACCC 60.434 66.667 2.83 0.00 44.39 3.69
3324 3411 3.360340 GCTGGTGCTGGTGCTGAC 61.360 66.667 0.00 0.00 40.48 3.51
3523 3610 3.204827 CCAGGCCTCGGCATTTCG 61.205 66.667 0.00 0.00 44.11 3.46
3637 3724 6.140303 TCAAGATTTTTGCTATCCATGAGC 57.860 37.500 0.00 0.00 40.53 4.26
3742 3829 3.701532 AGGAAAAACAATCGTTTCGCA 57.298 38.095 0.00 0.00 44.65 5.10
3749 3836 7.985634 TTTTCTCAGAAAGGAAAAACAATCG 57.014 32.000 0.00 0.00 38.13 3.34
3828 3917 2.100197 CTGACGGTCAGGGATTCAGTA 58.900 52.381 26.72 0.00 40.71 2.74
3898 3987 2.391678 TCATGAGCTGCTGATGTAGGA 58.608 47.619 24.74 6.56 0.00 2.94
3900 3989 4.814771 TCAAATCATGAGCTGCTGATGTAG 59.185 41.667 24.74 14.65 32.56 2.74
3937 4026 1.356938 CCTTTAGGCTTCGGTTCGTC 58.643 55.000 0.00 0.00 0.00 4.20
4006 4095 7.421382 CCCCTATACACCTTGTTTCATTCCTAT 60.421 40.741 0.00 0.00 0.00 2.57
4107 4196 6.878317 ACTGCAGCATAGTTTACATTAGAGA 58.122 36.000 15.27 0.00 0.00 3.10
4158 4247 0.175760 GCTCGTGCTTGGAGGATGTA 59.824 55.000 1.41 0.00 36.03 2.29
4224 4313 2.558359 GTTTTGGAGACCCTGTCAATGG 59.442 50.000 0.00 0.00 34.60 3.16
4246 4335 9.716507 GTATATTGTAGTACAAACAAATGCTGG 57.283 33.333 19.19 0.00 41.96 4.85
4386 4477 0.528924 GGCCGAAATTTTAGCCGGTT 59.471 50.000 14.47 0.00 43.51 4.44
4411 4502 1.655484 CGTTATGCACATCTGGCAGA 58.345 50.000 21.19 21.19 45.68 4.26
4441 4532 2.108075 ACAACACCCAGGAATCACATGA 59.892 45.455 0.00 0.00 31.40 3.07
4443 4534 2.555227 GGACAACACCCAGGAATCACAT 60.555 50.000 0.00 0.00 0.00 3.21
4446 4537 1.351017 GAGGACAACACCCAGGAATCA 59.649 52.381 0.00 0.00 0.00 2.57
4459 4550 2.740981 GAGTAGTTCGAGACGAGGACAA 59.259 50.000 0.00 0.00 37.14 3.18
4460 4551 2.344950 GAGTAGTTCGAGACGAGGACA 58.655 52.381 0.00 0.00 37.14 4.02
4467 4558 1.062206 CCGCGGAGTAGTTCGAGAC 59.938 63.158 24.07 0.00 0.00 3.36
4471 4562 1.981254 TTTTACCGCGGAGTAGTTCG 58.019 50.000 35.90 0.93 0.00 3.95
4512 4606 3.979497 GAGGTTGGGGGTGGGGTG 61.979 72.222 0.00 0.00 0.00 4.61
4515 4609 4.029809 GACGAGGTTGGGGGTGGG 62.030 72.222 0.00 0.00 0.00 4.61
4561 4688 3.202001 CGGAAATGTGGCGGCGAT 61.202 61.111 12.98 0.00 0.00 4.58
4569 4696 2.096406 CGCGAGCACGGAAATGTG 59.904 61.111 0.00 0.00 42.81 3.21
4587 4714 1.225855 CTAAAAGTGCGGTGAGTGCA 58.774 50.000 0.00 0.00 40.70 4.57
4590 4717 0.605589 GGCCTAAAAGTGCGGTGAGT 60.606 55.000 0.00 0.00 0.00 3.41
4594 4721 2.035155 GGGGCCTAAAAGTGCGGT 59.965 61.111 0.84 0.00 0.00 5.68
4595 4722 3.131478 CGGGGCCTAAAAGTGCGG 61.131 66.667 0.84 0.00 0.00 5.69
4597 4724 2.396157 CGTCGGGGCCTAAAAGTGC 61.396 63.158 0.84 0.00 0.00 4.40
4599 4726 1.004200 CACGTCGGGGCCTAAAAGT 60.004 57.895 0.84 0.00 0.00 2.66
4600 4727 1.004200 ACACGTCGGGGCCTAAAAG 60.004 57.895 0.84 0.00 0.00 2.27
4601 4728 1.301874 CACACGTCGGGGCCTAAAA 60.302 57.895 0.84 0.00 0.00 1.52
4602 4729 2.344500 CACACGTCGGGGCCTAAA 59.656 61.111 0.84 0.00 0.00 1.85
4603 4730 4.382320 GCACACGTCGGGGCCTAA 62.382 66.667 0.84 0.00 0.00 2.69
4635 4764 5.133221 ACAAAGTGCTACAAACCAGATTCT 58.867 37.500 0.00 0.00 0.00 2.40
4676 4805 2.151049 AACTCGCCCGTAGTGTGGTC 62.151 60.000 0.00 0.00 0.00 4.02
4681 4810 0.511221 CAACAAACTCGCCCGTAGTG 59.489 55.000 0.00 0.00 0.00 2.74
4682 4811 1.226030 GCAACAAACTCGCCCGTAGT 61.226 55.000 0.00 0.00 0.00 2.73
4694 4823 2.569354 GGCGACATGGGGCAACAAA 61.569 57.895 11.63 0.00 39.74 2.83
4730 4859 0.247814 CGTGCGCCATGAGTTCAATC 60.248 55.000 4.18 0.00 0.00 2.67
4731 4860 0.955428 ACGTGCGCCATGAGTTCAAT 60.955 50.000 4.18 0.00 0.00 2.57
4733 4862 1.565156 GAACGTGCGCCATGAGTTCA 61.565 55.000 18.64 0.00 40.41 3.18
4753 4882 0.163146 GTACGCTCGAAAACCACAGC 59.837 55.000 0.00 0.00 0.00 4.40
4757 4886 0.104487 TGGTGTACGCTCGAAAACCA 59.896 50.000 6.35 0.00 35.39 3.67
4761 4890 1.017177 GCCATGGTGTACGCTCGAAA 61.017 55.000 14.67 0.00 0.00 3.46
4763 4892 1.884075 AAGCCATGGTGTACGCTCGA 61.884 55.000 14.67 0.00 0.00 4.04
4764 4893 1.447838 AAGCCATGGTGTACGCTCG 60.448 57.895 14.67 0.00 0.00 5.03
4785 4914 0.320374 TTTACTGGAGCACGACAGGG 59.680 55.000 0.00 0.00 39.00 4.45
4825 4954 3.520290 TTAGTGCTATGGTCGGTGAAG 57.480 47.619 0.00 0.00 0.00 3.02
4826 4955 3.369052 CCTTTAGTGCTATGGTCGGTGAA 60.369 47.826 0.00 0.00 0.00 3.18



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

AutoCloner maintained by Alex Coulton.