Multiple sequence alignment - TraesCS4B01G201600

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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 TraesCS4B01G201600 chr4B 100.000 4547 0 0 1 4547 431798630 431794084 0.000000e+00 8397
1 TraesCS4B01G201600 chr4B 78.984 866 149 27 2503 3350 1244574 1243724 1.100000e-155 560
2 TraesCS4B01G201600 chr4B 80.976 615 91 20 2532 3125 654125471 654126080 8.910000e-127 464
3 TraesCS4B01G201600 chr4B 77.299 859 149 29 2532 3355 654130706 654131553 8.910000e-127 464
4 TraesCS4B01G201600 chr4B 80.620 387 69 6 2532 2915 638987543 638987926 1.240000e-75 294
5 TraesCS4B01G201600 chr4D 93.965 4590 171 39 1 4547 349192853 349188327 0.000000e+00 6844
6 TraesCS4B01G201600 chr4D 78.753 866 151 27 2503 3350 630149 630999 2.390000e-152 549
7 TraesCS4B01G201600 chr4A 93.503 4602 187 46 3 4547 115785766 115790312 0.000000e+00 6739
8 TraesCS4B01G201600 chr4A 78.431 867 155 25 2503 3350 900679 901532 1.860000e-148 536
9 TraesCS4B01G201600 chr2D 77.739 849 147 27 2532 3350 602008663 602009499 2.460000e-132 483
10 TraesCS4B01G201600 chr5A 76.513 826 174 20 2535 3350 540053610 540054425 2.510000e-117 433
11 TraesCS4B01G201600 chr3A 76.202 853 176 20 2516 3353 546572733 546571893 4.200000e-115 425
12 TraesCS4B01G201600 chr3B 75.793 851 183 17 2516 3353 142722734 142721894 4.230000e-110 409
13 TraesCS4B01G201600 chr5B 91.429 105 7 1 2313 2417 383038333 383038231 4.740000e-30 143
14 TraesCS4B01G201600 chr6D 92.857 98 4 1 2312 2409 468063517 468063611 6.130000e-29 139
15 TraesCS4B01G201600 chr7A 89.899 99 10 0 2319 2417 465376653 465376751 1.330000e-25 128


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 TraesCS4B01G201600 chr4B 431794084 431798630 4546 True 8397 8397 100.000 1 4547 1 chr4B.!!$R2 4546
1 TraesCS4B01G201600 chr4B 1243724 1244574 850 True 560 560 78.984 2503 3350 1 chr4B.!!$R1 847
2 TraesCS4B01G201600 chr4B 654125471 654126080 609 False 464 464 80.976 2532 3125 1 chr4B.!!$F2 593
3 TraesCS4B01G201600 chr4B 654130706 654131553 847 False 464 464 77.299 2532 3355 1 chr4B.!!$F3 823
4 TraesCS4B01G201600 chr4D 349188327 349192853 4526 True 6844 6844 93.965 1 4547 1 chr4D.!!$R1 4546
5 TraesCS4B01G201600 chr4D 630149 630999 850 False 549 549 78.753 2503 3350 1 chr4D.!!$F1 847
6 TraesCS4B01G201600 chr4A 115785766 115790312 4546 False 6739 6739 93.503 3 4547 1 chr4A.!!$F2 4544
7 TraesCS4B01G201600 chr4A 900679 901532 853 False 536 536 78.431 2503 3350 1 chr4A.!!$F1 847
8 TraesCS4B01G201600 chr2D 602008663 602009499 836 False 483 483 77.739 2532 3350 1 chr2D.!!$F1 818
9 TraesCS4B01G201600 chr5A 540053610 540054425 815 False 433 433 76.513 2535 3350 1 chr5A.!!$F1 815
10 TraesCS4B01G201600 chr3A 546571893 546572733 840 True 425 425 76.202 2516 3353 1 chr3A.!!$R1 837
11 TraesCS4B01G201600 chr3B 142721894 142722734 840 True 409 409 75.793 2516 3353 1 chr3B.!!$R1 837

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
304 325 0.110823 GTCACCGTGCGATTTGACAC 60.111 55.0 12.60 0.00 38.60 3.67 F
768 817 0.179179 GCTCATCGAAACCAAGCAGC 60.179 55.0 0.00 0.00 33.21 5.25 F
2074 2130 0.316204 ACCGGTGTACAAGGACTTCG 59.684 55.0 21.41 7.22 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1331 0.038526 CGAACGTGTAGGAAGCTGGT 60.039 55.0 0.00 0.0 0.00 4.00 R
2418 2474 0.181587 TGTTCCCGTTGCTCTTGGAA 59.818 50.0 0.00 0.0 34.59 3.53 R
3779 3891 0.394565 ATCCTGGAGTATTGAGCCGC 59.605 55.0 1.52 0.0 0.00 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
36 37 2.746277 CACCGGCCGGGAAAAGAG 60.746 66.667 44.99 22.24 39.97 2.85
52 53 5.699458 GGAAAAGAGAAGGAATGTACGAACA 59.301 40.000 0.00 0.00 40.69 3.18
53 54 6.347483 GGAAAAGAGAAGGAATGTACGAACAC 60.347 42.308 0.00 0.00 38.78 3.32
55 56 2.921754 GAGAAGGAATGTACGAACACCG 59.078 50.000 0.00 0.00 38.78 4.94
228 241 2.167662 CGTTCCTAAACAAAGGGCCAT 58.832 47.619 6.18 0.00 37.24 4.40
235 250 4.406649 CCTAAACAAAGGGCCATGATTCAT 59.593 41.667 15.29 0.00 32.55 2.57
294 315 2.173382 GCGAATGTGTCACCGTGC 59.827 61.111 0.00 0.00 0.00 5.34
304 325 0.110823 GTCACCGTGCGATTTGACAC 60.111 55.000 12.60 0.00 38.60 3.67
347 378 2.618709 CGTGCTCTCTTGGAACCTTTTT 59.381 45.455 0.00 0.00 0.00 1.94
351 382 3.504134 GCTCTCTTGGAACCTTTTTCTCC 59.496 47.826 0.00 0.00 0.00 3.71
414 450 5.705441 GGAACATGACAATGAGAACCAGTTA 59.295 40.000 0.00 0.00 37.24 2.24
441 485 4.082136 ACAGTAAAAGAGACCTAAGAGGCG 60.082 45.833 0.00 0.00 39.63 5.52
466 510 1.206578 CCGTTCATCACACGTTGCC 59.793 57.895 0.00 0.00 35.81 4.52
474 518 3.628032 TCATCACACGTTGCCAAAAACTA 59.372 39.130 0.00 0.00 0.00 2.24
477 521 3.880490 TCACACGTTGCCAAAAACTATCT 59.120 39.130 0.00 0.00 0.00 1.98
573 617 7.761249 TCGAATATATATGCCAGACAATCTGTG 59.239 37.037 5.18 0.00 42.80 3.66
627 671 0.825840 TTTCCCCCGCAAACAAGGAG 60.826 55.000 0.00 0.00 0.00 3.69
709 758 3.124921 ACCGCAATACGCAGTGCC 61.125 61.111 10.11 0.00 45.73 5.01
756 805 1.134580 ACCACATCCAAGAGCTCATCG 60.135 52.381 17.77 3.14 0.00 3.84
765 814 1.731720 AGAGCTCATCGAAACCAAGC 58.268 50.000 17.77 0.00 0.00 4.01
766 815 1.002430 AGAGCTCATCGAAACCAAGCA 59.998 47.619 17.77 0.00 35.42 3.91
767 816 1.396301 GAGCTCATCGAAACCAAGCAG 59.604 52.381 9.40 0.00 35.42 4.24
768 817 0.179179 GCTCATCGAAACCAAGCAGC 60.179 55.000 0.00 0.00 33.21 5.25
801 850 4.850386 ACTTTCCTTCCTGTGGGTATTAGT 59.150 41.667 0.00 0.00 0.00 2.24
809 858 3.704566 CCTGTGGGTATTAGTAGCAGTCA 59.295 47.826 0.00 0.00 0.00 3.41
810 859 4.202161 CCTGTGGGTATTAGTAGCAGTCAG 60.202 50.000 0.00 2.51 0.00 3.51
811 860 4.350245 TGTGGGTATTAGTAGCAGTCAGT 58.650 43.478 0.00 0.00 0.00 3.41
812 861 4.775780 TGTGGGTATTAGTAGCAGTCAGTT 59.224 41.667 0.00 0.00 0.00 3.16
830 879 1.276421 GTTGCTAACTCCCTCTGCTCA 59.724 52.381 0.00 0.00 0.00 4.26
831 880 1.871418 TGCTAACTCCCTCTGCTCAT 58.129 50.000 0.00 0.00 0.00 2.90
874 929 3.808174 GTCTCAACACCACCTCTACAAAC 59.192 47.826 0.00 0.00 0.00 2.93
887 943 4.081862 CCTCTACAAACCAATCGTCCACTA 60.082 45.833 0.00 0.00 0.00 2.74
888 944 4.813027 TCTACAAACCAATCGTCCACTAC 58.187 43.478 0.00 0.00 0.00 2.73
919 975 2.988684 GGTTTGTGCCGCCATCCA 60.989 61.111 0.00 0.00 0.00 3.41
921 977 1.139520 GTTTGTGCCGCCATCCATC 59.860 57.895 0.00 0.00 0.00 3.51
922 978 2.051518 TTTGTGCCGCCATCCATCC 61.052 57.895 0.00 0.00 0.00 3.51
923 979 2.497792 TTTGTGCCGCCATCCATCCT 62.498 55.000 0.00 0.00 0.00 3.24
924 980 2.124151 GTGCCGCCATCCATCCTT 60.124 61.111 0.00 0.00 0.00 3.36
925 981 2.124193 TGCCGCCATCCATCCTTG 60.124 61.111 0.00 0.00 0.00 3.61
926 982 2.124151 GCCGCCATCCATCCTTGT 60.124 61.111 0.00 0.00 0.00 3.16
927 983 2.189499 GCCGCCATCCATCCTTGTC 61.189 63.158 0.00 0.00 0.00 3.18
928 984 1.526917 CCGCCATCCATCCTTGTCC 60.527 63.158 0.00 0.00 0.00 4.02
934 990 2.954318 CCATCCATCCTTGTCCATGAAC 59.046 50.000 0.00 0.00 0.00 3.18
938 994 1.739466 CATCCTTGTCCATGAACACCG 59.261 52.381 0.00 0.00 0.00 4.94
939 995 0.762418 TCCTTGTCCATGAACACCGT 59.238 50.000 0.00 0.00 0.00 4.83
947 1003 3.894547 ATGAACACCGTCGTGGCCC 62.895 63.158 0.00 0.00 44.86 5.80
1099 1155 1.582968 GCGGACAACTACCTCGTCA 59.417 57.895 0.00 0.00 0.00 4.35
1263 1319 4.781959 CTTTACCGGTCCGCGCGA 62.782 66.667 34.63 15.16 0.00 5.87
1345 1401 1.662686 CCTCCACTTCTTCCCCTTCT 58.337 55.000 0.00 0.00 0.00 2.85
1479 1535 3.618750 GTGAACGTCACCGGGGGA 61.619 66.667 2.42 0.00 41.37 4.81
1545 1601 2.202756 GCCATCGAGGTCGTGTCC 60.203 66.667 0.00 0.00 40.61 4.02
1654 1710 0.323633 CCACAGGATCAACATGGGCA 60.324 55.000 0.00 0.00 31.83 5.36
1732 1788 1.972872 CTTCCAGCTCAACACCAACT 58.027 50.000 0.00 0.00 0.00 3.16
1734 1790 1.679139 TCCAGCTCAACACCAACTTG 58.321 50.000 0.00 0.00 0.00 3.16
1794 1850 1.133407 GACGAGAAATCGGCACTCTCT 59.867 52.381 0.00 0.00 41.52 3.10
1798 1854 1.208293 AGAAATCGGCACTCTCTTCCC 59.792 52.381 0.00 0.00 0.00 3.97
1802 1858 2.943978 CGGCACTCTCTTCCCCGTT 61.944 63.158 0.00 0.00 34.56 4.44
1848 1904 4.724602 GCGACGAGGCTGAGCACA 62.725 66.667 6.82 0.00 0.00 4.57
1890 1946 1.953559 ACGTGCAGTTCAACATCAGT 58.046 45.000 0.00 0.00 0.00 3.41
1968 2024 3.512516 GTCAGCAAGGCGGCCATC 61.513 66.667 23.09 9.39 0.00 3.51
2074 2130 0.316204 ACCGGTGTACAAGGACTTCG 59.684 55.000 21.41 7.22 0.00 3.79
2140 2196 1.893335 TCGTCGACCGAGGACAACA 60.893 57.895 10.58 0.00 41.60 3.33
2142 2198 1.361271 GTCGACCGAGGACAACACA 59.639 57.895 3.51 0.00 34.56 3.72
2860 2919 0.250234 GCTGCACTATCTCCACACCA 59.750 55.000 0.00 0.00 0.00 4.17
3156 3249 2.673200 GGAGATGGTGAGCCTGGCA 61.673 63.158 22.65 0.00 35.27 4.92
3388 3481 1.666553 GACGCCGACACCATGTTGA 60.667 57.895 0.00 0.00 33.58 3.18
3414 3513 4.337060 GTGCCCGTGAAAACGCCC 62.337 66.667 0.00 0.00 0.00 6.13
3698 3808 5.753921 GTGATGTACAGTACCAATAAGGAGC 59.246 44.000 8.30 0.00 41.22 4.70
3732 3842 5.768164 TCCTGATTTCACAAAAGTAACCTCC 59.232 40.000 0.00 0.00 0.00 4.30
3738 3848 5.836024 TCACAAAAGTAACCTCCCTATGT 57.164 39.130 0.00 0.00 0.00 2.29
3740 3850 6.704310 TCACAAAAGTAACCTCCCTATGTAC 58.296 40.000 0.00 0.00 0.00 2.90
3741 3851 6.499350 TCACAAAAGTAACCTCCCTATGTACT 59.501 38.462 0.00 0.00 0.00 2.73
3742 3852 7.675195 TCACAAAAGTAACCTCCCTATGTACTA 59.325 37.037 0.00 0.00 0.00 1.82
3743 3853 7.980099 CACAAAAGTAACCTCCCTATGTACTAG 59.020 40.741 0.00 0.00 0.00 2.57
3744 3854 7.677319 ACAAAAGTAACCTCCCTATGTACTAGT 59.323 37.037 0.00 0.00 0.00 2.57
3745 3855 9.193806 CAAAAGTAACCTCCCTATGTACTAGTA 57.806 37.037 0.00 0.00 0.00 1.82
3746 3856 8.759481 AAAGTAACCTCCCTATGTACTAGTAC 57.241 38.462 23.58 23.58 36.63 2.73
3766 3878 5.946377 AGTACATGTATATGATCGGCAGAGA 59.054 40.000 9.18 0.00 37.73 3.10
3770 3882 4.398319 TGTATATGATCGGCAGAGACAGA 58.602 43.478 0.00 0.00 35.26 3.41
3772 3884 2.064434 ATGATCGGCAGAGACAGAGA 57.936 50.000 0.00 0.00 0.00 3.10
3773 3885 1.387539 TGATCGGCAGAGACAGAGAG 58.612 55.000 0.00 0.00 0.00 3.20
3774 3886 0.667993 GATCGGCAGAGACAGAGAGG 59.332 60.000 0.00 0.00 0.00 3.69
3775 3887 1.391157 ATCGGCAGAGACAGAGAGGC 61.391 60.000 0.00 0.00 0.00 4.70
3776 3888 2.051518 CGGCAGAGACAGAGAGGCT 61.052 63.158 0.00 0.00 39.48 4.58
3781 3893 3.602103 AGACAGAGAGGCTCAGCG 58.398 61.111 18.26 6.40 32.06 5.18
3782 3894 2.051518 AGACAGAGAGGCTCAGCGG 61.052 63.158 18.26 11.23 32.06 5.52
3783 3895 3.714871 GACAGAGAGGCTCAGCGGC 62.715 68.421 18.26 1.89 38.75 6.53
3902 4014 7.506328 TTCAGAGCAGAATAATTCATGGATG 57.494 36.000 0.00 0.00 0.00 3.51
4079 4191 0.110486 AAAGAGCAAAGCCCTCGGAA 59.890 50.000 0.00 0.00 34.56 4.30
4098 4213 4.338400 CGGAAGAGAAAAATAATGGGGTCC 59.662 45.833 0.00 0.00 0.00 4.46
4108 4223 4.242586 TGGGGTCCCACCAGACGA 62.243 66.667 10.98 0.00 41.02 4.20
4124 4239 2.682494 GACTACTCCCCCGTGGCA 60.682 66.667 0.00 0.00 0.00 4.92
4166 4281 3.429684 CCTTCTACTCTTCCTTCCGCTTC 60.430 52.174 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.997606 CCGGTGTTCGTACATTCCTTC 59.002 52.381 0.00 0.00 36.50 3.46
126 127 1.353091 GAAGTCTCCAACCACCTCCT 58.647 55.000 0.00 0.00 0.00 3.69
228 241 4.436718 CCACGCATTTTGTCGTATGAATCA 60.437 41.667 0.00 0.00 37.14 2.57
235 250 3.694535 AAAACCACGCATTTTGTCGTA 57.305 38.095 0.00 0.00 37.14 3.43
294 315 1.063412 TCTCGCGACGTGTCAAATCG 61.063 55.000 3.71 3.21 38.87 3.34
335 366 1.324383 GCCGGAGAAAAAGGTTCCAA 58.676 50.000 5.05 0.00 0.00 3.53
347 378 2.583441 CCAACACTGAGGCCGGAGA 61.583 63.158 5.05 0.00 0.00 3.71
351 382 0.892755 TAGTACCAACACTGAGGCCG 59.107 55.000 0.00 0.00 0.00 6.13
414 450 7.616313 CCTCTTAGGTCTCTTTTACTGTCAAT 58.384 38.462 0.00 0.00 0.00 2.57
441 485 2.818274 GTGATGAACGGACCGGGC 60.818 66.667 20.00 0.21 0.00 6.13
573 617 3.575965 ATGCCGTCATTTTCTTGGTTC 57.424 42.857 0.00 0.00 0.00 3.62
645 689 6.545298 GTGGAGAGATAGGCTTGAATTTCATT 59.455 38.462 0.00 0.00 0.00 2.57
709 758 4.524328 GGTATTTGATTGATTAGCTGGGGG 59.476 45.833 0.00 0.00 0.00 5.40
724 773 1.286553 GGATGTGGTGGGGGTATTTGA 59.713 52.381 0.00 0.00 0.00 2.69
725 774 1.006519 TGGATGTGGTGGGGGTATTTG 59.993 52.381 0.00 0.00 0.00 2.32
726 775 1.388174 TGGATGTGGTGGGGGTATTT 58.612 50.000 0.00 0.00 0.00 1.40
727 776 1.287739 CTTGGATGTGGTGGGGGTATT 59.712 52.381 0.00 0.00 0.00 1.89
756 805 1.098050 ATCGATGGCTGCTTGGTTTC 58.902 50.000 0.00 0.00 0.00 2.78
765 814 2.636830 AGGAAAGTGAATCGATGGCTG 58.363 47.619 0.00 0.00 0.00 4.85
766 815 3.274288 GAAGGAAAGTGAATCGATGGCT 58.726 45.455 0.00 0.00 0.00 4.75
767 816 2.356069 GGAAGGAAAGTGAATCGATGGC 59.644 50.000 0.00 0.00 0.00 4.40
768 817 3.624861 CAGGAAGGAAAGTGAATCGATGG 59.375 47.826 0.00 0.00 0.00 3.51
809 858 1.552792 GAGCAGAGGGAGTTAGCAACT 59.447 52.381 1.82 1.82 46.38 3.16
810 859 1.276421 TGAGCAGAGGGAGTTAGCAAC 59.724 52.381 0.00 0.00 0.00 4.17
811 860 1.644509 TGAGCAGAGGGAGTTAGCAA 58.355 50.000 0.00 0.00 0.00 3.91
812 861 1.759445 GATGAGCAGAGGGAGTTAGCA 59.241 52.381 0.00 0.00 0.00 3.49
830 879 3.434641 CACTTGTTGCTTGACGATGAGAT 59.565 43.478 0.00 0.00 0.00 2.75
831 880 2.802247 CACTTGTTGCTTGACGATGAGA 59.198 45.455 0.00 0.00 0.00 3.27
888 944 3.530910 AAACCGGAGAGCACCACCG 62.531 63.158 9.46 9.60 45.24 4.94
893 949 2.617274 GGCACAAACCGGAGAGCAC 61.617 63.158 9.46 0.00 0.00 4.40
919 975 1.351017 ACGGTGTTCATGGACAAGGAT 59.649 47.619 8.85 0.00 0.00 3.24
921 977 1.156736 GACGGTGTTCATGGACAAGG 58.843 55.000 8.85 6.26 0.00 3.61
922 978 0.790207 CGACGGTGTTCATGGACAAG 59.210 55.000 8.85 8.82 0.00 3.16
923 979 0.105224 ACGACGGTGTTCATGGACAA 59.895 50.000 8.85 0.00 0.00 3.18
924 980 0.598942 CACGACGGTGTTCATGGACA 60.599 55.000 1.52 1.52 39.38 4.02
925 981 1.289109 CCACGACGGTGTTCATGGAC 61.289 60.000 0.00 0.00 42.80 4.02
926 982 1.005512 CCACGACGGTGTTCATGGA 60.006 57.895 0.00 0.00 42.80 3.41
927 983 2.677003 GCCACGACGGTGTTCATGG 61.677 63.158 0.00 0.00 42.80 3.66
928 984 2.677003 GGCCACGACGGTGTTCATG 61.677 63.158 0.00 0.00 42.80 3.07
934 990 4.436998 GAGAGGGCCACGACGGTG 62.437 72.222 6.18 0.00 43.99 4.94
938 994 1.076923 TCTAGGAGAGGGCCACGAC 60.077 63.158 6.18 0.00 0.00 4.34
939 995 1.227664 CTCTAGGAGAGGGCCACGA 59.772 63.158 6.18 0.00 38.67 4.35
947 1003 2.494530 GCACGGGGCTCTAGGAGAG 61.495 68.421 0.00 0.00 45.04 3.20
1009 1065 1.291184 CGCACGAGCATGTCAGGAAA 61.291 55.000 5.50 0.00 42.27 3.13
1263 1319 2.031163 GCTGGTGCGGTGAAGACT 59.969 61.111 0.00 0.00 0.00 3.24
1275 1331 0.038526 CGAACGTGTAGGAAGCTGGT 60.039 55.000 0.00 0.00 0.00 4.00
1443 1499 0.682855 CGGAGAACTCCCTGAGCTCT 60.683 60.000 16.19 0.00 46.96 4.09
1654 1710 1.153168 CGGGCGTGATCTTGGGAAT 60.153 57.895 0.00 0.00 0.00 3.01
1732 1788 2.721231 GTCTTTGTGCTGCGCCAA 59.279 55.556 11.12 5.09 0.00 4.52
1890 1946 4.011517 GGGGCGTCGAACCTCCAA 62.012 66.667 0.00 0.00 0.00 3.53
1968 2024 0.673644 AGACGTTGAAGGCCATTCCG 60.674 55.000 5.01 8.51 40.77 4.30
2160 2216 0.385751 TCATGATCTCGAGGCCGTTC 59.614 55.000 13.56 3.26 37.05 3.95
2231 2287 3.305335 CCCGATTTTGACCTTTGAACTGG 60.305 47.826 0.00 0.00 0.00 4.00
2292 2348 1.375523 GATGAACCCGAGCACCGTT 60.376 57.895 0.00 0.00 36.31 4.44
2294 2350 2.885644 CGATGAACCCGAGCACCG 60.886 66.667 0.00 0.00 38.18 4.94
2418 2474 0.181587 TGTTCCCGTTGCTCTTGGAA 59.818 50.000 0.00 0.00 34.59 3.53
3374 3467 2.677003 GGCGTCAACATGGTGTCGG 61.677 63.158 27.20 12.14 31.89 4.79
3414 3513 1.517257 CAGGCTACGCTGAACCTCG 60.517 63.158 0.00 0.00 0.00 4.63
3516 3621 2.788233 CTCGTCGCTCTTGATCATCTTG 59.212 50.000 0.00 0.00 0.00 3.02
3615 3723 8.931775 TGTACATTGTTTGTCATGTACTACATC 58.068 33.333 18.49 0.00 45.58 3.06
3683 3793 5.700402 ATCTGTTGCTCCTTATTGGTACT 57.300 39.130 0.00 0.00 37.07 2.73
3698 3808 6.564709 TTGTGAAATCAGGAGAATCTGTTG 57.435 37.500 0.00 0.00 36.25 3.33
3738 3848 8.044908 TCTGCCGATCATATACATGTACTAGTA 58.955 37.037 7.96 0.00 33.57 1.82
3740 3850 7.281100 TCTCTGCCGATCATATACATGTACTAG 59.719 40.741 7.96 0.84 33.57 2.57
3741 3851 7.065923 GTCTCTGCCGATCATATACATGTACTA 59.934 40.741 7.96 2.87 33.57 1.82
3742 3852 5.946377 TCTCTGCCGATCATATACATGTACT 59.054 40.000 7.96 0.57 33.57 2.73
3743 3853 6.030849 GTCTCTGCCGATCATATACATGTAC 58.969 44.000 7.96 0.00 33.57 2.90
3744 3854 5.710099 TGTCTCTGCCGATCATATACATGTA 59.290 40.000 8.27 8.27 33.57 2.29
3745 3855 4.524328 TGTCTCTGCCGATCATATACATGT 59.476 41.667 2.69 2.69 33.57 3.21
3746 3856 5.064441 TGTCTCTGCCGATCATATACATG 57.936 43.478 0.00 0.00 0.00 3.21
3766 3878 3.768922 GCCGCTGAGCCTCTCTGT 61.769 66.667 0.00 0.00 33.06 3.41
3770 3882 1.045350 TATTGAGCCGCTGAGCCTCT 61.045 55.000 11.13 2.90 0.00 3.69
3772 3884 1.144936 GTATTGAGCCGCTGAGCCT 59.855 57.895 0.00 0.00 0.00 4.58
3773 3885 0.878086 GAGTATTGAGCCGCTGAGCC 60.878 60.000 0.00 0.00 0.00 4.70
3774 3886 0.878086 GGAGTATTGAGCCGCTGAGC 60.878 60.000 0.00 0.00 0.00 4.26
3775 3887 0.461548 TGGAGTATTGAGCCGCTGAG 59.538 55.000 0.00 0.00 0.00 3.35
3776 3888 0.461548 CTGGAGTATTGAGCCGCTGA 59.538 55.000 0.00 0.00 0.00 4.26
3777 3889 0.531532 CCTGGAGTATTGAGCCGCTG 60.532 60.000 0.00 0.00 0.00 5.18
3778 3890 0.687757 TCCTGGAGTATTGAGCCGCT 60.688 55.000 0.00 0.00 0.00 5.52
3779 3891 0.394565 ATCCTGGAGTATTGAGCCGC 59.605 55.000 1.52 0.00 0.00 6.53
3780 3892 1.688735 TCATCCTGGAGTATTGAGCCG 59.311 52.381 1.52 0.00 0.00 5.52
3781 3893 2.703007 ACTCATCCTGGAGTATTGAGCC 59.297 50.000 19.91 0.00 45.95 4.70
3804 3916 3.371898 TGTTCACATAGCGATTCTGCTTG 59.628 43.478 8.00 8.63 44.46 4.01
3842 3954 4.783227 ACTGACACCTCCTGGTTTATGTAT 59.217 41.667 0.00 0.00 46.05 2.29
3864 3976 2.475187 GCTCTGAATGCAATGACGTGAC 60.475 50.000 0.00 0.00 0.00 3.67
3865 3977 1.733912 GCTCTGAATGCAATGACGTGA 59.266 47.619 0.00 0.00 0.00 4.35
3866 3978 1.465777 TGCTCTGAATGCAATGACGTG 59.534 47.619 0.00 0.00 37.51 4.49
3867 3979 1.736126 CTGCTCTGAATGCAATGACGT 59.264 47.619 0.00 0.00 40.13 4.34
3868 3980 2.004733 TCTGCTCTGAATGCAATGACG 58.995 47.619 0.00 0.00 40.13 4.35
3869 3981 4.634184 ATTCTGCTCTGAATGCAATGAC 57.366 40.909 0.00 0.00 40.13 3.06
3870 3982 6.954487 ATTATTCTGCTCTGAATGCAATGA 57.046 33.333 10.87 0.00 40.13 2.57
3871 3983 7.200455 TGAATTATTCTGCTCTGAATGCAATG 58.800 34.615 6.50 0.00 40.13 2.82
3872 3984 7.342769 TGAATTATTCTGCTCTGAATGCAAT 57.657 32.000 6.50 0.00 40.13 3.56
3873 3985 6.762702 TGAATTATTCTGCTCTGAATGCAA 57.237 33.333 6.50 1.45 40.13 4.08
3902 4014 8.436200 CACTTACTGCAGTTATCTTTCACTTAC 58.564 37.037 27.06 0.00 0.00 2.34
3915 4027 1.142870 TCTTGCCCACTTACTGCAGTT 59.857 47.619 27.06 3.70 36.21 3.16
4068 4180 2.951229 TTTTTCTCTTCCGAGGGCTT 57.049 45.000 0.00 0.00 37.86 4.35
4079 4191 4.965283 TGGGACCCCATTATTTTTCTCT 57.035 40.909 8.45 0.00 41.89 3.10
4098 4213 1.321074 GGGGAGTAGTCGTCTGGTGG 61.321 65.000 0.00 0.00 0.00 4.61
4108 4223 1.615424 ATTGCCACGGGGGAGTAGT 60.615 57.895 5.47 0.00 40.01 2.73
4166 4281 1.114627 GGGCCAGAAAGCAATTAGGG 58.885 55.000 4.39 0.00 0.00 3.53
4205 4320 4.685924 TCGACGAGGTTCTTAAGTTTGTT 58.314 39.130 1.63 0.00 0.00 2.83
4349 4464 2.935238 GCTTCTTCTGGCAATGTCGGTA 60.935 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.