Multiple sequence alignment - TraesCS3A01G240200

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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 TraesCS3A01G240200 chr3A 100.000 2624 0 0 1 2624 450953425 450950802 0.000000e+00 4846.0
1 TraesCS3A01G240200 chr3D 88.704 2222 88 60 1 2140 333285213 333283073 0.000000e+00 2562.0
2 TraesCS3A01G240200 chr3D 92.132 394 25 4 2137 2530 333283048 333282661 3.820000e-153 551.0
3 TraesCS3A01G240200 chr3D 93.684 95 6 0 2530 2624 333282614 333282520 2.720000e-30 143.0
4 TraesCS3A01G240200 chr3B 88.454 2174 128 53 33 2132 432335830 432333706 0.000000e+00 2510.0
5 TraesCS3A01G240200 chr3B 91.718 326 23 2 2137 2461 432333350 432333028 1.430000e-122 449.0
6 TraesCS3A01G240200 chr3B 94.792 96 4 1 2530 2624 432332830 432332735 5.850000e-32 148.0
7 TraesCS3A01G240200 chr3B 97.222 72 1 1 2459 2530 432332947 432332877 1.280000e-23 121.0
8 TraesCS3A01G240200 chr3B 100.000 46 0 0 1 46 432337703 432337658 4.650000e-13 86.1


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 TraesCS3A01G240200 chr3A 450950802 450953425 2623 True 4846.000000 4846 100.000000 1 2624 1 chr3A.!!$R1 2623
1 TraesCS3A01G240200 chr3D 333282520 333285213 2693 True 1085.333333 2562 91.506667 1 2624 3 chr3D.!!$R1 2623
2 TraesCS3A01G240200 chr3B 432332735 432337703 4968 True 662.820000 2510 94.437200 1 2624 5 chr3B.!!$R1 2623


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
312 2202 0.163146 GCAAGTGAACGAACGTAGCC 59.837 55.0 0.0 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 3743 0.304705 CAACGCGCCATGGAAGTATC 59.695 55.0 18.4 0.0 0.0 2.24 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 1971 1.480954 AGCCTCGTCGTCCAATAATGT 59.519 47.619 0.00 0.00 0.00 2.71
138 1980 4.809426 GTCGTCCAATAATGTAACAGAGGG 59.191 45.833 0.00 0.00 0.00 4.30
139 1981 4.712829 TCGTCCAATAATGTAACAGAGGGA 59.287 41.667 0.00 0.00 0.00 4.20
140 1982 5.365605 TCGTCCAATAATGTAACAGAGGGAT 59.634 40.000 0.00 0.00 0.00 3.85
142 1984 5.765182 GTCCAATAATGTAACAGAGGGATGG 59.235 44.000 0.00 0.00 0.00 3.51
143 1985 5.431731 TCCAATAATGTAACAGAGGGATGGT 59.568 40.000 0.00 0.00 0.00 3.55
144 1986 5.765182 CCAATAATGTAACAGAGGGATGGTC 59.235 44.000 0.00 0.00 0.00 4.02
145 1987 6.409695 CCAATAATGTAACAGAGGGATGGTCT 60.410 42.308 0.00 0.00 0.00 3.85
147 1989 5.878406 AATGTAACAGAGGGATGGTCTAG 57.122 43.478 0.00 0.00 0.00 2.43
148 1990 4.603094 TGTAACAGAGGGATGGTCTAGA 57.397 45.455 0.00 0.00 0.00 2.43
149 1991 4.537751 TGTAACAGAGGGATGGTCTAGAG 58.462 47.826 0.00 0.00 0.00 2.43
150 1992 2.765689 ACAGAGGGATGGTCTAGAGG 57.234 55.000 0.00 0.00 0.00 3.69
151 1993 1.337118 CAGAGGGATGGTCTAGAGGC 58.663 60.000 0.00 0.00 0.00 4.70
192 2059 3.463329 AGAAGGCTAGGGCATTATTTGGA 59.537 43.478 0.00 0.00 42.73 3.53
193 2060 3.515602 AGGCTAGGGCATTATTTGGAG 57.484 47.619 0.00 0.00 40.87 3.86
194 2061 2.785857 AGGCTAGGGCATTATTTGGAGT 59.214 45.455 0.00 0.00 40.87 3.85
195 2062 3.205282 AGGCTAGGGCATTATTTGGAGTT 59.795 43.478 0.00 0.00 40.87 3.01
196 2063 3.319122 GGCTAGGGCATTATTTGGAGTTG 59.681 47.826 0.00 0.00 40.87 3.16
197 2064 3.319122 GCTAGGGCATTATTTGGAGTTGG 59.681 47.826 0.00 0.00 38.54 3.77
278 2165 1.739067 GCCTTTGAATGGCTCGTACT 58.261 50.000 14.17 0.00 46.38 2.73
279 2166 1.666189 GCCTTTGAATGGCTCGTACTC 59.334 52.381 14.17 0.00 46.38 2.59
280 2167 1.927174 CCTTTGAATGGCTCGTACTCG 59.073 52.381 0.00 0.00 38.55 4.18
281 2168 2.607187 CTTTGAATGGCTCGTACTCGT 58.393 47.619 0.00 0.00 38.33 4.18
282 2169 3.428452 CCTTTGAATGGCTCGTACTCGTA 60.428 47.826 0.00 0.00 38.33 3.43
285 2172 2.032290 TGAATGGCTCGTACTCGTATCG 60.032 50.000 0.00 0.00 38.33 2.92
287 2174 1.082235 GGCTCGTACTCGTATCGGC 60.082 63.158 0.00 0.00 38.33 5.54
310 2200 2.096909 CCAAGCAAGTGAACGAACGTAG 60.097 50.000 0.00 0.00 0.00 3.51
312 2202 0.163146 GCAAGTGAACGAACGTAGCC 59.837 55.000 0.00 0.00 0.00 3.93
473 2373 0.811616 CAGTAGCCAGACCGGATTGC 60.812 60.000 9.46 5.03 36.56 3.56
561 2474 2.066999 GGGAGCGTGGGGATTCTCT 61.067 63.158 0.00 0.00 0.00 3.10
565 2478 1.139853 GAGCGTGGGGATTCTCTTCAT 59.860 52.381 0.00 0.00 0.00 2.57
577 2490 6.803807 GGGATTCTCTTCATTTTTGAAACTCG 59.196 38.462 0.00 0.00 0.00 4.18
578 2491 6.306596 GGATTCTCTTCATTTTTGAAACTCGC 59.693 38.462 0.00 0.00 0.00 5.03
590 2503 0.668535 AAACTCGCCAGGCAGTTTTC 59.331 50.000 24.89 0.00 36.94 2.29
615 2528 0.744874 CTGCTTGGCTTGATCATGGG 59.255 55.000 10.35 0.00 0.00 4.00
623 2536 2.310538 GCTTGATCATGGGGTTTAGGG 58.689 52.381 10.35 0.00 0.00 3.53
633 2546 7.240390 TCATGGGGTTTAGGGGATTTATTAA 57.760 36.000 0.00 0.00 0.00 1.40
639 2552 5.537295 GGTTTAGGGGATTTATTAACGCCAT 59.463 40.000 0.00 0.00 38.75 4.40
640 2553 6.041182 GGTTTAGGGGATTTATTAACGCCATT 59.959 38.462 0.00 0.00 38.75 3.16
641 2554 7.418139 GGTTTAGGGGATTTATTAACGCCATTT 60.418 37.037 0.00 0.00 38.75 2.32
642 2555 5.529581 AGGGGATTTATTAACGCCATTTG 57.470 39.130 0.00 0.00 38.75 2.32
643 2556 4.959839 AGGGGATTTATTAACGCCATTTGT 59.040 37.500 0.00 0.00 38.75 2.83
644 2557 5.423931 AGGGGATTTATTAACGCCATTTGTT 59.576 36.000 0.00 0.00 38.75 2.83
645 2558 6.070481 AGGGGATTTATTAACGCCATTTGTTT 60.070 34.615 0.00 0.00 38.75 2.83
646 2559 6.596106 GGGGATTTATTAACGCCATTTGTTTT 59.404 34.615 0.00 0.00 36.78 2.43
647 2560 7.119992 GGGGATTTATTAACGCCATTTGTTTTT 59.880 33.333 0.00 0.00 36.78 1.94
668 2581 5.579384 TTTAACATAGTACACGCACACAC 57.421 39.130 0.00 0.00 0.00 3.82
669 2582 1.693467 ACATAGTACACGCACACACG 58.307 50.000 0.00 0.00 39.50 4.49
677 2590 1.300388 ACGCACACACGTCTTACCC 60.300 57.895 0.00 0.00 44.43 3.69
679 2592 1.670083 GCACACACGTCTTACCCCC 60.670 63.158 0.00 0.00 0.00 5.40
680 2593 2.055299 CACACACGTCTTACCCCCT 58.945 57.895 0.00 0.00 0.00 4.79
681 2594 0.320421 CACACACGTCTTACCCCCTG 60.320 60.000 0.00 0.00 0.00 4.45
682 2595 0.761702 ACACACGTCTTACCCCCTGT 60.762 55.000 0.00 0.00 0.00 4.00
683 2596 0.320421 CACACGTCTTACCCCCTGTG 60.320 60.000 0.00 0.00 0.00 3.66
684 2597 0.470456 ACACGTCTTACCCCCTGTGA 60.470 55.000 0.00 0.00 0.00 3.58
685 2598 0.682852 CACGTCTTACCCCCTGTGAA 59.317 55.000 0.00 0.00 0.00 3.18
686 2599 0.683412 ACGTCTTACCCCCTGTGAAC 59.317 55.000 0.00 0.00 0.00 3.18
687 2600 0.682852 CGTCTTACCCCCTGTGAACA 59.317 55.000 0.00 0.00 0.00 3.18
688 2601 1.278127 CGTCTTACCCCCTGTGAACAT 59.722 52.381 0.00 0.00 0.00 2.71
689 2602 2.711542 GTCTTACCCCCTGTGAACATG 58.288 52.381 0.00 0.00 0.00 3.21
691 2604 2.304761 TCTTACCCCCTGTGAACATGTC 59.695 50.000 0.00 0.00 0.00 3.06
694 2607 2.040544 CCCCTGTGAACATGTCCGC 61.041 63.158 0.00 0.00 0.00 5.54
715 2628 1.299468 GACTGAGCCGGCGTATCAG 60.299 63.158 31.73 31.73 44.81 2.90
716 2629 2.028190 CTGAGCCGGCGTATCAGG 59.972 66.667 28.05 14.62 37.41 3.86
719 2632 1.883084 GAGCCGGCGTATCAGGTTG 60.883 63.158 23.20 0.00 32.16 3.77
723 2636 1.539496 GCCGGCGTATCAGGTTGAATA 60.539 52.381 12.58 0.00 32.16 1.75
744 2676 4.976224 ATTAACGGGTATGCCAAACTTC 57.024 40.909 1.04 0.00 36.17 3.01
747 2679 1.807226 GGGTATGCCAAACTTCCGC 59.193 57.895 1.04 0.00 36.17 5.54
758 2690 4.403453 CCAAACTTCCGCTTTCTATTTCG 58.597 43.478 0.00 0.00 0.00 3.46
786 2718 2.094675 GCATTTACTGGCATGTGTCCT 58.905 47.619 0.00 0.00 0.00 3.85
847 2779 1.280746 CAGTTTGCTCGCCACTGTG 59.719 57.895 0.00 0.00 34.39 3.66
848 2780 2.050985 GTTTGCTCGCCACTGTGC 60.051 61.111 1.29 0.00 0.00 4.57
849 2781 2.515757 TTTGCTCGCCACTGTGCA 60.516 55.556 1.29 0.00 36.65 4.57
871 2803 4.496895 CAGCTCAATCGCCTTTTTATTTCG 59.503 41.667 0.00 0.00 0.00 3.46
927 2859 6.378582 CGTTTCAATTGCCACAAGTATTACT 58.621 36.000 0.00 0.00 0.00 2.24
928 2860 6.861055 CGTTTCAATTGCCACAAGTATTACTT 59.139 34.615 3.16 3.16 39.39 2.24
964 2897 0.327924 TGACCATGTCGGCCATTTCT 59.672 50.000 2.24 0.00 39.03 2.52
965 2898 1.271871 TGACCATGTCGGCCATTTCTT 60.272 47.619 2.24 0.00 39.03 2.52
966 2899 1.818674 GACCATGTCGGCCATTTCTTT 59.181 47.619 2.24 0.00 39.03 2.52
967 2900 1.818674 ACCATGTCGGCCATTTCTTTC 59.181 47.619 2.24 0.00 39.03 2.62
1350 3298 3.188786 GTGCGCGACATGGACCTC 61.189 66.667 12.10 0.00 0.00 3.85
1634 3582 0.517316 GACGTGTGAGATGGCCAAAC 59.483 55.000 10.96 7.46 0.00 2.93
1635 3583 0.889186 ACGTGTGAGATGGCCAAACC 60.889 55.000 10.96 1.57 39.84 3.27
1636 3584 1.875963 GTGTGAGATGGCCAAACCG 59.124 57.895 10.96 0.00 43.94 4.44
1637 3585 0.889186 GTGTGAGATGGCCAAACCGT 60.889 55.000 10.96 0.00 43.94 4.83
1795 3743 2.493973 GGAGCAGAGCACCGAGAG 59.506 66.667 0.00 0.00 28.62 3.20
1809 3757 1.336332 CCGAGAGATACTTCCATGGCG 60.336 57.143 6.96 2.80 0.00 5.69
1812 3760 0.249489 GAGATACTTCCATGGCGCGT 60.249 55.000 6.96 6.26 0.00 6.01
1817 3765 0.960364 ACTTCCATGGCGCGTTGATT 60.960 50.000 6.96 0.00 0.00 2.57
1843 3792 2.855963 GCAGATGATCCAACGCAAATTG 59.144 45.455 0.00 0.00 0.00 2.32
1856 3805 2.739287 CGCAAATTGGTTGGGGATGATG 60.739 50.000 0.00 0.00 44.40 3.07
1912 3861 1.527844 GGGAGCCTCATGGTCATGC 60.528 63.158 6.10 0.00 43.44 4.06
1927 3876 3.090219 ATGCGCCCCCGAGTAGAAC 62.090 63.158 4.18 0.00 36.29 3.01
1929 3878 2.183555 CGCCCCCGAGTAGAACAC 59.816 66.667 0.00 0.00 36.29 3.32
1981 3930 0.609957 TCGGCTCCTACCTTGTCGAA 60.610 55.000 0.00 0.00 0.00 3.71
1993 3942 5.362556 ACCTTGTCGAATGTTCATTCTTG 57.637 39.130 19.00 8.37 0.00 3.02
1994 3943 5.063204 ACCTTGTCGAATGTTCATTCTTGA 58.937 37.500 19.00 10.11 0.00 3.02
1995 3944 5.707298 ACCTTGTCGAATGTTCATTCTTGAT 59.293 36.000 19.00 1.41 0.00 2.57
1996 3945 6.207417 ACCTTGTCGAATGTTCATTCTTGATT 59.793 34.615 19.00 0.00 0.00 2.57
2008 3957 6.808008 TCATTCTTGATTTCTTCTGTGTCC 57.192 37.500 0.00 0.00 0.00 4.02
2085 4036 4.277423 CGAGGTCTCTAGATTTCTCCCTTC 59.723 50.000 0.00 0.00 0.00 3.46
2086 4037 5.205056 GAGGTCTCTAGATTTCTCCCTTCA 58.795 45.833 0.00 0.00 0.00 3.02
2088 4039 4.202212 GGTCTCTAGATTTCTCCCTTCAGC 60.202 50.000 0.00 0.00 0.00 4.26
2193 4495 5.523188 GCAACATTTGACAAAATCAGTTCCA 59.477 36.000 4.41 0.00 38.99 3.53
2200 4502 6.713762 TGACAAAATCAGTTCCATTGAAGT 57.286 33.333 0.00 0.00 34.39 3.01
2204 4506 7.555087 ACAAAATCAGTTCCATTGAAGTTTCA 58.445 30.769 0.00 0.00 31.64 2.69
2249 4551 2.305635 TGACCTGCTGCTTAGGAAATGA 59.694 45.455 12.51 0.00 38.71 2.57
2281 4583 5.287274 CGTGCAGTAGATTTAGTGTTCAGAG 59.713 44.000 0.00 0.00 33.55 3.35
2287 4589 7.062839 CAGTAGATTTAGTGTTCAGAGACTTGC 59.937 40.741 0.00 0.00 31.03 4.01
2300 4602 1.276421 AGACTTGCGCTGGACTATGTT 59.724 47.619 9.73 0.00 0.00 2.71
2304 4606 0.894835 TGCGCTGGACTATGTTCAGA 59.105 50.000 9.73 0.00 41.40 3.27
2305 4607 1.275010 TGCGCTGGACTATGTTCAGAA 59.725 47.619 9.73 0.00 41.40 3.02
2307 4609 2.094417 GCGCTGGACTATGTTCAGAAAC 59.906 50.000 9.94 0.00 41.40 2.78
2385 4690 5.182001 GTGCTATGGCTTTAATCATGTAGGG 59.818 44.000 1.68 0.00 39.59 3.53
2388 4693 6.490040 GCTATGGCTTTAATCATGTAGGGAAA 59.510 38.462 0.00 0.00 35.22 3.13
2500 4888 5.178809 ACACAAAAGACTTGCGTATTACTCC 59.821 40.000 0.00 0.00 0.00 3.85
2551 4986 6.296145 GGTTATCCCCAATGGAAAACATTCAA 60.296 38.462 0.00 0.00 46.67 2.69
2558 4993 5.338219 CCAATGGAAAACATTCAATAGGGCA 60.338 40.000 0.00 0.00 46.67 5.36
2572 5007 2.288025 GGGCAGTGACCCGGTAAGA 61.288 63.158 2.42 0.00 40.98 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 1971 3.691603 GCCTCTAGACCATCCCTCTGTTA 60.692 52.174 0.00 0.00 0.00 2.41
138 1980 1.693627 TTCCTCGCCTCTAGACCATC 58.306 55.000 0.00 0.00 0.00 3.51
139 1981 1.757699 GTTTCCTCGCCTCTAGACCAT 59.242 52.381 0.00 0.00 0.00 3.55
140 1982 1.183549 GTTTCCTCGCCTCTAGACCA 58.816 55.000 0.00 0.00 0.00 4.02
142 1984 3.254892 CTTTGTTTCCTCGCCTCTAGAC 58.745 50.000 0.00 0.00 0.00 2.59
143 1985 2.353803 GCTTTGTTTCCTCGCCTCTAGA 60.354 50.000 0.00 0.00 0.00 2.43
144 1986 2.003301 GCTTTGTTTCCTCGCCTCTAG 58.997 52.381 0.00 0.00 0.00 2.43
145 1987 1.671850 CGCTTTGTTTCCTCGCCTCTA 60.672 52.381 0.00 0.00 0.00 2.43
147 1989 1.228657 ACGCTTTGTTTCCTCGCCTC 61.229 55.000 0.00 0.00 0.00 4.70
148 1990 1.227853 ACGCTTTGTTTCCTCGCCT 60.228 52.632 0.00 0.00 0.00 5.52
149 1991 1.082104 CACGCTTTGTTTCCTCGCC 60.082 57.895 0.00 0.00 0.00 5.54
150 1992 0.306533 TTCACGCTTTGTTTCCTCGC 59.693 50.000 0.00 0.00 0.00 5.03
151 1993 2.286833 TCTTTCACGCTTTGTTTCCTCG 59.713 45.455 0.00 0.00 0.00 4.63
192 2059 3.517901 TGATGATAAAGACGGGTCCAACT 59.482 43.478 0.00 0.00 0.00 3.16
193 2060 3.869065 TGATGATAAAGACGGGTCCAAC 58.131 45.455 0.00 0.00 0.00 3.77
194 2061 4.408921 AGATGATGATAAAGACGGGTCCAA 59.591 41.667 0.00 0.00 0.00 3.53
195 2062 3.967326 AGATGATGATAAAGACGGGTCCA 59.033 43.478 0.00 0.00 0.00 4.02
196 2063 4.310769 CAGATGATGATAAAGACGGGTCC 58.689 47.826 0.00 0.00 0.00 4.46
197 2064 4.202264 ACCAGATGATGATAAAGACGGGTC 60.202 45.833 0.00 0.00 0.00 4.46
238 2105 2.509422 GGGTCCGGATAGGTTGCC 59.491 66.667 7.81 1.00 41.99 4.52
277 2164 3.330853 GCTTGGCGCCGATACGAG 61.331 66.667 23.90 8.87 34.06 4.18
278 2165 3.650907 TTGCTTGGCGCCGATACGA 62.651 57.895 23.90 12.25 38.05 3.43
279 2166 3.155470 CTTGCTTGGCGCCGATACG 62.155 63.158 23.90 9.70 38.05 3.06
280 2167 2.106683 ACTTGCTTGGCGCCGATAC 61.107 57.895 23.90 15.69 38.05 2.24
281 2168 2.106074 CACTTGCTTGGCGCCGATA 61.106 57.895 23.90 9.45 38.05 2.92
282 2169 3.434319 CACTTGCTTGGCGCCGAT 61.434 61.111 23.90 0.29 38.05 4.18
285 2172 2.050077 GTTCACTTGCTTGGCGCC 60.050 61.111 22.73 22.73 38.05 6.53
287 2174 0.657368 GTTCGTTCACTTGCTTGGCG 60.657 55.000 0.00 0.00 0.00 5.69
299 2189 0.165295 GCCTTTGGCTACGTTCGTTC 59.835 55.000 2.62 0.00 46.69 3.95
300 2190 2.241171 GCCTTTGGCTACGTTCGTT 58.759 52.632 2.62 0.00 46.69 3.85
301 2191 3.961729 GCCTTTGGCTACGTTCGT 58.038 55.556 0.00 2.91 46.69 3.85
312 2202 1.875963 CAGTAACTGCCGGCCTTTG 59.124 57.895 26.77 13.99 0.00 2.77
368 2268 0.464554 CTCTTTCCCGATTCCTGCCC 60.465 60.000 0.00 0.00 0.00 5.36
382 2282 0.464036 TACGCGCCATGGATCTCTTT 59.536 50.000 18.40 0.00 0.00 2.52
473 2373 3.365265 GCGTGGAGTGGGGCTTTG 61.365 66.667 0.00 0.00 0.00 2.77
530 2443 3.625897 CTCCCTGTGGTGGCGTGA 61.626 66.667 0.00 0.00 0.00 4.35
548 2461 4.458989 TCAAAAATGAAGAGAATCCCCACG 59.541 41.667 0.00 0.00 33.66 4.94
550 2463 6.554605 AGTTTCAAAAATGAAGAGAATCCCCA 59.445 34.615 0.00 0.00 33.66 4.96
554 2467 6.306596 GGCGAGTTTCAAAAATGAAGAGAATC 59.693 38.462 0.00 0.00 0.00 2.52
561 2474 3.798548 GCCTGGCGAGTTTCAAAAATGAA 60.799 43.478 1.35 0.00 0.00 2.57
565 2478 1.066908 CTGCCTGGCGAGTTTCAAAAA 59.933 47.619 14.98 0.00 0.00 1.94
577 2490 0.598419 GCAACAGAAAACTGCCTGGC 60.598 55.000 12.87 12.87 34.85 4.85
578 2491 1.035139 AGCAACAGAAAACTGCCTGG 58.965 50.000 0.00 0.00 36.73 4.45
590 2503 0.601558 ATCAAGCCAAGCAGCAACAG 59.398 50.000 0.00 0.00 34.23 3.16
592 2505 0.599558 TGATCAAGCCAAGCAGCAAC 59.400 50.000 0.00 0.00 34.23 4.17
593 2506 1.203758 CATGATCAAGCCAAGCAGCAA 59.796 47.619 0.00 0.00 34.23 3.91
595 2508 0.102481 CCATGATCAAGCCAAGCAGC 59.898 55.000 0.00 0.00 0.00 5.25
596 2509 0.744874 CCCATGATCAAGCCAAGCAG 59.255 55.000 0.00 0.00 0.00 4.24
597 2510 0.685131 CCCCATGATCAAGCCAAGCA 60.685 55.000 0.00 0.00 0.00 3.91
598 2511 0.685458 ACCCCATGATCAAGCCAAGC 60.685 55.000 0.00 0.00 0.00 4.01
599 2512 1.856629 AACCCCATGATCAAGCCAAG 58.143 50.000 0.00 0.00 0.00 3.61
600 2513 2.323999 AAACCCCATGATCAAGCCAA 57.676 45.000 0.00 0.00 0.00 4.52
601 2514 2.358090 CCTAAACCCCATGATCAAGCCA 60.358 50.000 0.00 0.00 0.00 4.75
602 2515 2.310538 CCTAAACCCCATGATCAAGCC 58.689 52.381 0.00 0.00 0.00 4.35
615 2528 4.888823 TGGCGTTAATAAATCCCCTAAACC 59.111 41.667 0.00 0.00 0.00 3.27
644 2557 6.420588 GTGTGTGCGTGTACTATGTTAAAAA 58.579 36.000 0.00 0.00 0.00 1.94
645 2558 5.332430 CGTGTGTGCGTGTACTATGTTAAAA 60.332 40.000 0.00 0.00 0.00 1.52
646 2559 4.148522 CGTGTGTGCGTGTACTATGTTAAA 59.851 41.667 0.00 0.00 0.00 1.52
647 2560 3.669588 CGTGTGTGCGTGTACTATGTTAA 59.330 43.478 0.00 0.00 0.00 2.01
648 2561 3.236005 CGTGTGTGCGTGTACTATGTTA 58.764 45.455 0.00 0.00 0.00 2.41
649 2562 2.055838 CGTGTGTGCGTGTACTATGTT 58.944 47.619 0.00 0.00 0.00 2.71
650 2563 1.001048 ACGTGTGTGCGTGTACTATGT 60.001 47.619 0.00 0.00 43.99 2.29
651 2564 1.647213 GACGTGTGTGCGTGTACTATG 59.353 52.381 0.00 0.00 45.79 2.23
652 2565 1.538512 AGACGTGTGTGCGTGTACTAT 59.461 47.619 0.00 0.00 45.79 2.12
658 2571 1.554042 GGGTAAGACGTGTGTGCGTG 61.554 60.000 0.00 0.00 45.79 5.34
660 2573 2.025418 GGGGTAAGACGTGTGTGCG 61.025 63.158 0.00 0.00 37.94 5.34
665 2578 0.470456 TCACAGGGGGTAAGACGTGT 60.470 55.000 0.00 0.00 36.27 4.49
668 2581 0.682852 TGTTCACAGGGGGTAAGACG 59.317 55.000 0.00 0.00 0.00 4.18
669 2582 2.039879 ACATGTTCACAGGGGGTAAGAC 59.960 50.000 0.00 0.00 30.95 3.01
677 2590 2.390599 CGCGGACATGTTCACAGGG 61.391 63.158 4.68 0.00 30.95 4.45
679 2592 0.388520 TCTCGCGGACATGTTCACAG 60.389 55.000 6.13 0.00 0.00 3.66
680 2593 0.666274 GTCTCGCGGACATGTTCACA 60.666 55.000 18.80 0.00 43.94 3.58
681 2594 0.388649 AGTCTCGCGGACATGTTCAC 60.389 55.000 23.47 0.00 46.72 3.18
682 2595 0.388520 CAGTCTCGCGGACATGTTCA 60.389 55.000 23.47 0.00 46.72 3.18
683 2596 0.109272 TCAGTCTCGCGGACATGTTC 60.109 55.000 23.47 0.00 46.72 3.18
684 2597 0.109086 CTCAGTCTCGCGGACATGTT 60.109 55.000 23.47 6.09 46.72 2.71
685 2598 1.508545 CTCAGTCTCGCGGACATGT 59.491 57.895 23.47 0.00 46.72 3.21
686 2599 1.875813 GCTCAGTCTCGCGGACATG 60.876 63.158 23.47 18.55 46.72 3.21
687 2600 2.492090 GCTCAGTCTCGCGGACAT 59.508 61.111 23.47 10.53 46.72 3.06
688 2601 3.749064 GGCTCAGTCTCGCGGACA 61.749 66.667 23.47 8.42 46.72 4.02
689 2602 4.838486 CGGCTCAGTCTCGCGGAC 62.838 72.222 16.80 16.80 44.80 4.79
694 2607 2.718993 GATACGCCGGCTCAGTCTCG 62.719 65.000 26.68 8.67 0.00 4.04
715 2628 4.822896 TGGCATACCCGTTAATATTCAACC 59.177 41.667 0.00 0.00 35.87 3.77
716 2629 6.380095 TTGGCATACCCGTTAATATTCAAC 57.620 37.500 0.00 0.00 35.87 3.18
719 2632 6.628919 AGTTTGGCATACCCGTTAATATTC 57.371 37.500 4.38 0.00 35.87 1.75
723 2636 3.697542 GGAAGTTTGGCATACCCGTTAAT 59.302 43.478 4.38 0.00 35.87 1.40
744 2676 1.641677 CGCCCGAAATAGAAAGCGG 59.358 57.895 0.00 0.00 43.20 5.52
747 2679 0.928229 CGTCCGCCCGAAATAGAAAG 59.072 55.000 0.00 0.00 0.00 2.62
758 2690 2.469516 CCAGTAAATGCGTCCGCCC 61.470 63.158 9.43 0.00 41.09 6.13
786 2718 4.700213 GCTGTAAATTAAGCCTCTGGACAA 59.300 41.667 0.00 0.00 33.12 3.18
847 2779 2.919666 TAAAAAGGCGATTGAGCTGC 57.080 45.000 0.00 0.00 37.29 5.25
848 2780 4.496895 CGAAATAAAAAGGCGATTGAGCTG 59.503 41.667 0.00 0.00 37.29 4.24
849 2781 4.156008 ACGAAATAAAAAGGCGATTGAGCT 59.844 37.500 0.00 0.00 37.29 4.09
871 2803 2.027625 CGAGAGCGGTGTTTGGGAC 61.028 63.158 0.00 0.00 0.00 4.46
927 2859 2.095969 GTCATGGCATCACGACGAAAAA 60.096 45.455 0.00 0.00 0.00 1.94
928 2860 1.463056 GTCATGGCATCACGACGAAAA 59.537 47.619 0.00 0.00 0.00 2.29
1084 3017 4.224274 TTGGTCGCCGTCGTGGTT 62.224 61.111 0.00 0.00 41.21 3.67
1661 3609 0.665369 ACAGACCGTACGGAAAAGCG 60.665 55.000 39.52 21.71 38.96 4.68
1795 3743 0.304705 CAACGCGCCATGGAAGTATC 59.695 55.000 18.40 0.00 0.00 2.24
1809 3757 1.739466 TCATCTGCTGGAAATCAACGC 59.261 47.619 0.00 0.00 0.00 4.84
1812 3760 4.239428 TGGATCATCTGCTGGAAATCAA 57.761 40.909 0.00 0.00 0.00 2.57
1817 3765 2.013563 GCGTTGGATCATCTGCTGGAA 61.014 52.381 0.00 0.00 0.00 3.53
1843 3792 1.511613 TCTCCTCATCATCCCCAACC 58.488 55.000 0.00 0.00 0.00 3.77
1856 3805 2.178890 CATGCTGCCGCTTCTCCTC 61.179 63.158 0.70 0.00 36.97 3.71
1906 3855 3.792053 CTACTCGGGGGCGCATGAC 62.792 68.421 10.83 0.00 0.00 3.06
1912 3861 2.183555 GTGTTCTACTCGGGGGCG 59.816 66.667 0.00 0.00 0.00 6.13
1919 3868 3.664107 TGTGCATTGAGGTGTTCTACTC 58.336 45.455 0.00 0.00 0.00 2.59
1921 3870 4.379813 CCATTGTGCATTGAGGTGTTCTAC 60.380 45.833 0.00 0.00 0.00 2.59
1927 3876 1.887854 TCACCATTGTGCATTGAGGTG 59.112 47.619 19.31 19.31 45.92 4.00
1929 3878 1.135199 GCTCACCATTGTGCATTGAGG 60.135 52.381 0.00 0.00 42.46 3.86
1981 3930 8.174733 ACACAGAAGAAATCAAGAATGAACAT 57.825 30.769 0.00 0.00 39.49 2.71
1993 3942 3.690460 ACCCATGGACACAGAAGAAATC 58.310 45.455 15.22 0.00 0.00 2.17
1994 3943 3.814504 ACCCATGGACACAGAAGAAAT 57.185 42.857 15.22 0.00 0.00 2.17
1995 3944 3.593442 AACCCATGGACACAGAAGAAA 57.407 42.857 15.22 0.00 0.00 2.52
1996 3945 3.221771 CAAACCCATGGACACAGAAGAA 58.778 45.455 15.22 0.00 0.00 2.52
2008 3957 1.750399 CGAGCTCCCCAAACCCATG 60.750 63.158 8.47 0.00 0.00 3.66
2085 4036 1.143813 ATACAGGGAGGGGATTGCTG 58.856 55.000 0.00 0.00 0.00 4.41
2086 4037 2.815357 TATACAGGGAGGGGATTGCT 57.185 50.000 0.00 0.00 0.00 3.91
2088 4039 6.632672 CGGAAATATATACAGGGAGGGGATTG 60.633 46.154 0.00 0.00 0.00 2.67
2229 4531 2.941720 CTCATTTCCTAAGCAGCAGGTC 59.058 50.000 0.00 0.00 34.56 3.85
2230 4532 2.307098 ACTCATTTCCTAAGCAGCAGGT 59.693 45.455 0.00 0.00 34.56 4.00
2281 4583 1.661112 GAACATAGTCCAGCGCAAGTC 59.339 52.381 11.47 0.00 41.68 3.01
2287 4589 3.589988 AGTTTCTGAACATAGTCCAGCG 58.410 45.455 0.00 0.00 38.26 5.18
2314 4618 6.278363 GGTACTCCCCTTTTCAAAAAGAAAC 58.722 40.000 15.15 5.43 45.48 2.78
2393 4698 1.796459 ACGACGAAACACAGGCAATAC 59.204 47.619 0.00 0.00 0.00 1.89
2394 4699 2.157834 ACGACGAAACACAGGCAATA 57.842 45.000 0.00 0.00 0.00 1.90
2395 4700 1.305201 AACGACGAAACACAGGCAAT 58.695 45.000 0.00 0.00 0.00 3.56
2396 4701 1.062880 GAAACGACGAAACACAGGCAA 59.937 47.619 0.00 0.00 0.00 4.52
2397 4702 0.653636 GAAACGACGAAACACAGGCA 59.346 50.000 0.00 0.00 0.00 4.75
2398 4703 0.041576 GGAAACGACGAAACACAGGC 60.042 55.000 0.00 0.00 0.00 4.85
2403 4708 1.202486 AGCTGAGGAAACGACGAAACA 60.202 47.619 0.00 0.00 0.00 2.83
2409 4714 3.485546 CGTACTCTAGCTGAGGAAACGAC 60.486 52.174 20.14 9.20 46.72 4.34
2469 4857 3.181511 CGCAAGTCTTTTGTGTGTTCTCA 60.182 43.478 0.00 0.00 0.00 3.27
2500 4888 5.049405 GTCTTGCATTATACCCCTTCATTCG 60.049 44.000 0.00 0.00 0.00 3.34
2551 4986 0.325860 TTACCGGGTCACTGCCCTAT 60.326 55.000 6.32 0.00 46.47 2.57
2558 4993 1.909700 TTACGTCTTACCGGGTCACT 58.090 50.000 6.32 0.00 0.00 3.41



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

AutoCloner maintained by Alex Coulton.