Multiple sequence alignment - TraesCS7D01G138200

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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 TraesCS7D01G138200 chr7D 100.000 2432 0 0 1 2432 88621542 88623973 0 4492
1 TraesCS7D01G138200 chr7D 95.706 1048 41 3 781 1824 231555098 231554051 0 1683
2 TraesCS7D01G138200 chr7B 95.710 1049 40 4 781 1824 662725731 662726779 0 1683
3 TraesCS7D01G138200 chr7B 95.615 1049 41 4 781 1824 663100098 663099050 0 1677
4 TraesCS7D01G138200 chr7B 96.211 607 23 0 1826 2432 662727482 662728088 0 994
5 TraesCS7D01G138200 chr6D 95.710 1049 40 4 781 1824 389246495 389245447 0 1683
6 TraesCS7D01G138200 chr6D 96.046 607 24 0 1826 2432 389244744 389244138 0 989
7 TraesCS7D01G138200 chr5D 95.710 1049 40 4 781 1824 503244599 503245647 0 1683
8 TraesCS7D01G138200 chr5D 95.706 1048 40 4 781 1824 503265976 503264930 0 1681
9 TraesCS7D01G138200 chr5D 93.324 749 45 2 1 749 432356596 432357339 0 1101
10 TraesCS7D01G138200 chr5D 96.211 607 23 0 1826 2432 503246350 503246956 0 994
11 TraesCS7D01G138200 chr5D 96.211 607 23 0 1826 2432 503263698 503263092 0 994
12 TraesCS7D01G138200 chr3A 95.706 1048 41 3 781 1824 66005805 66004758 0 1683
13 TraesCS7D01G138200 chr3A 93.057 749 43 3 1 749 650014645 650015384 0 1086
14 TraesCS7D01G138200 chr2D 95.710 1049 40 4 781 1824 591983936 591984984 0 1683
15 TraesCS7D01G138200 chr2D 96.211 607 23 0 1826 2432 272811168 272810562 0 994
16 TraesCS7D01G138200 chr2A 95.710 1049 40 4 781 1824 726907128 726906080 0 1683
17 TraesCS7D01G138200 chr2A 93.048 748 48 2 2 749 335847183 335846440 0 1090
18 TraesCS7D01G138200 chr2A 96.211 607 23 0 1826 2432 726905377 726904771 0 994
19 TraesCS7D01G138200 chrUn 94.126 749 39 2 1 749 388830620 388831363 0 1134
20 TraesCS7D01G138200 chr2B 93.992 749 39 2 1 749 474920800 474920058 0 1129
21 TraesCS7D01G138200 chr4A 93.725 749 42 2 1 749 583869042 583869785 0 1118
22 TraesCS7D01G138200 chr3B 93.591 749 42 2 1 749 201539391 201538649 0 1112
23 TraesCS7D01G138200 chr1B 93.591 749 42 2 1 749 633739759 633740501 0 1112
24 TraesCS7D01G138200 chr1D 93.324 749 46 2 1 749 51914417 51915161 0 1103
25 TraesCS7D01G138200 chr1D 96.211 607 23 0 1826 2432 459903639 459903033 0 994
26 TraesCS7D01G138200 chr5B 96.211 607 23 0 1826 2432 599755456 599756062 0 994
27 TraesCS7D01G138200 chr3D 96.046 607 24 0 1826 2432 589262448 589261842 0 989


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 TraesCS7D01G138200 chr7D 88621542 88623973 2431 False 4492.0 4492 100.0000 1 2432 1 chr7D.!!$F1 2431
1 TraesCS7D01G138200 chr7D 231554051 231555098 1047 True 1683.0 1683 95.7060 781 1824 1 chr7D.!!$R1 1043
2 TraesCS7D01G138200 chr7B 663099050 663100098 1048 True 1677.0 1677 95.6150 781 1824 1 chr7B.!!$R1 1043
3 TraesCS7D01G138200 chr7B 662725731 662728088 2357 False 1338.5 1683 95.9605 781 2432 2 chr7B.!!$F1 1651
4 TraesCS7D01G138200 chr6D 389244138 389246495 2357 True 1336.0 1683 95.8780 781 2432 2 chr6D.!!$R1 1651
5 TraesCS7D01G138200 chr5D 503244599 503246956 2357 False 1338.5 1683 95.9605 781 2432 2 chr5D.!!$F2 1651
6 TraesCS7D01G138200 chr5D 503263092 503265976 2884 True 1337.5 1681 95.9585 781 2432 2 chr5D.!!$R1 1651
7 TraesCS7D01G138200 chr5D 432356596 432357339 743 False 1101.0 1101 93.3240 1 749 1 chr5D.!!$F1 748
8 TraesCS7D01G138200 chr3A 66004758 66005805 1047 True 1683.0 1683 95.7060 781 1824 1 chr3A.!!$R1 1043
9 TraesCS7D01G138200 chr3A 650014645 650015384 739 False 1086.0 1086 93.0570 1 749 1 chr3A.!!$F1 748
10 TraesCS7D01G138200 chr2D 591983936 591984984 1048 False 1683.0 1683 95.7100 781 1824 1 chr2D.!!$F1 1043
11 TraesCS7D01G138200 chr2D 272810562 272811168 606 True 994.0 994 96.2110 1826 2432 1 chr2D.!!$R1 606
12 TraesCS7D01G138200 chr2A 726904771 726907128 2357 True 1338.5 1683 95.9605 781 2432 2 chr2A.!!$R2 1651
13 TraesCS7D01G138200 chr2A 335846440 335847183 743 True 1090.0 1090 93.0480 2 749 1 chr2A.!!$R1 747
14 TraesCS7D01G138200 chrUn 388830620 388831363 743 False 1134.0 1134 94.1260 1 749 1 chrUn.!!$F1 748
15 TraesCS7D01G138200 chr2B 474920058 474920800 742 True 1129.0 1129 93.9920 1 749 1 chr2B.!!$R1 748
16 TraesCS7D01G138200 chr4A 583869042 583869785 743 False 1118.0 1118 93.7250 1 749 1 chr4A.!!$F1 748
17 TraesCS7D01G138200 chr3B 201538649 201539391 742 True 1112.0 1112 93.5910 1 749 1 chr3B.!!$R1 748
18 TraesCS7D01G138200 chr1B 633739759 633740501 742 False 1112.0 1112 93.5910 1 749 1 chr1B.!!$F1 748
19 TraesCS7D01G138200 chr1D 51914417 51915161 744 False 1103.0 1103 93.3240 1 749 1 chr1D.!!$F1 748
20 TraesCS7D01G138200 chr1D 459903033 459903639 606 True 994.0 994 96.2110 1826 2432 1 chr1D.!!$R1 606
21 TraesCS7D01G138200 chr5B 599755456 599756062 606 False 994.0 994 96.2110 1826 2432 1 chr5B.!!$F1 606
22 TraesCS7D01G138200 chr3D 589261842 589262448 606 True 989.0 989 96.0460 1826 2432 1 chr3D.!!$R1 606

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
444 447 0.254462 TGACGCAATTATCAGGGGCA 59.746 50.0 0.0 0.0 32.84 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 2248 0.038166 GGCCATCCTGGACTTGAACA 59.962 55.0 0.0 0.0 44.12 3.18 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
17 18 2.044551 GGTACGACCCCTCCGTCT 60.045 66.667 0.00 0.00 40.95 4.18
18 19 1.680314 GGTACGACCCCTCCGTCTT 60.680 63.158 0.00 0.00 40.95 3.01
34 35 2.290323 CGTCTTCCCAGAATGAAAGGGT 60.290 50.000 0.00 0.00 43.31 4.34
38 39 3.154827 TCCCAGAATGAAAGGGTTGAC 57.845 47.619 0.00 0.00 43.31 3.18
56 57 4.025040 TGACCTCGTAGTTCTTGGTCTA 57.975 45.455 11.07 0.00 45.22 2.59
76 77 5.581085 GTCTATGAAGATGCGTTGTTAGGTT 59.419 40.000 0.00 0.00 33.30 3.50
82 83 2.851263 TGCGTTGTTAGGTTCTCCAT 57.149 45.000 0.00 0.00 35.89 3.41
257 260 4.971282 TCTACATGGGATCTCACCTGAATT 59.029 41.667 0.00 0.00 0.00 2.17
278 281 1.203237 GCCCCATCTATCCTCCTGAGA 60.203 57.143 0.00 0.00 0.00 3.27
323 326 4.030913 TCCGAATCAAACAGGAGGAGTAT 58.969 43.478 0.00 0.00 0.00 2.12
377 380 2.581354 GGTCAGGCGCTGATGAGT 59.419 61.111 7.64 0.00 42.73 3.41
383 386 1.863454 CAGGCGCTGATGAGTACATTC 59.137 52.381 7.64 0.00 36.82 2.67
444 447 0.254462 TGACGCAATTATCAGGGGCA 59.746 50.000 0.00 0.00 32.84 5.36
447 450 1.321474 CGCAATTATCAGGGGCACAT 58.679 50.000 0.00 0.00 0.00 3.21
488 491 4.373116 TCGCGCGGCCTTCTCTTT 62.373 61.111 31.69 0.00 0.00 2.52
496 499 1.746991 GCCTTCTCTTTGGGAGGCG 60.747 63.158 0.00 0.00 42.10 5.52
527 530 4.261572 CCAAAAGCGAGAAAAACTCCATCA 60.262 41.667 0.00 0.00 42.18 3.07
663 667 2.303311 AGCTTGGTCTTACTTCACCCTC 59.697 50.000 0.00 0.00 0.00 4.30
680 684 2.731976 CCCTCAACGAAAGAAGACTTCG 59.268 50.000 9.53 1.16 35.05 3.79
695 699 8.294954 AGAAGACTTCGATATCCAAGTTTAGA 57.705 34.615 15.66 0.00 32.83 2.10
701 705 8.865090 ACTTCGATATCCAAGTTTAGATCAGAT 58.135 33.333 9.65 0.00 27.81 2.90
720 724 4.456911 CAGATGTAGCTGCCTTCTTTTTGA 59.543 41.667 0.00 0.00 0.00 2.69
723 727 1.696063 AGCTGCCTTCTTTTTGAGCA 58.304 45.000 0.00 0.00 0.00 4.26
749 753 6.378564 TGAAGAAGTGTCAAACCAAAATACCA 59.621 34.615 0.00 0.00 0.00 3.25
750 754 6.783708 AGAAGTGTCAAACCAAAATACCAA 57.216 33.333 0.00 0.00 0.00 3.67
751 755 6.805713 AGAAGTGTCAAACCAAAATACCAAG 58.194 36.000 0.00 0.00 0.00 3.61
752 756 4.944048 AGTGTCAAACCAAAATACCAAGC 58.056 39.130 0.00 0.00 0.00 4.01
753 757 4.649218 AGTGTCAAACCAAAATACCAAGCT 59.351 37.500 0.00 0.00 0.00 3.74
754 758 4.982295 GTGTCAAACCAAAATACCAAGCTC 59.018 41.667 0.00 0.00 0.00 4.09
755 759 4.226761 GTCAAACCAAAATACCAAGCTCG 58.773 43.478 0.00 0.00 0.00 5.03
756 760 3.886505 TCAAACCAAAATACCAAGCTCGT 59.113 39.130 0.00 0.00 0.00 4.18
757 761 3.915437 AACCAAAATACCAAGCTCGTG 57.085 42.857 0.00 0.00 0.00 4.35
758 762 2.858745 ACCAAAATACCAAGCTCGTGT 58.141 42.857 0.00 0.00 0.00 4.49
759 763 3.219281 ACCAAAATACCAAGCTCGTGTT 58.781 40.909 0.00 0.00 0.00 3.32
760 764 4.391155 ACCAAAATACCAAGCTCGTGTTA 58.609 39.130 0.00 0.00 0.00 2.41
761 765 4.822896 ACCAAAATACCAAGCTCGTGTTAA 59.177 37.500 0.00 0.00 0.00 2.01
762 766 5.299782 ACCAAAATACCAAGCTCGTGTTAAA 59.700 36.000 0.00 0.00 0.00 1.52
763 767 6.015772 ACCAAAATACCAAGCTCGTGTTAAAT 60.016 34.615 0.00 0.00 0.00 1.40
764 768 7.175293 ACCAAAATACCAAGCTCGTGTTAAATA 59.825 33.333 0.00 0.00 0.00 1.40
765 769 7.696453 CCAAAATACCAAGCTCGTGTTAAATAG 59.304 37.037 0.00 0.00 0.00 1.73
766 770 8.447833 CAAAATACCAAGCTCGTGTTAAATAGA 58.552 33.333 0.00 0.00 0.00 1.98
767 771 8.556213 AAATACCAAGCTCGTGTTAAATAGAA 57.444 30.769 0.00 0.00 0.00 2.10
768 772 8.732746 AATACCAAGCTCGTGTTAAATAGAAT 57.267 30.769 0.00 0.00 0.00 2.40
769 773 9.826574 AATACCAAGCTCGTGTTAAATAGAATA 57.173 29.630 0.00 0.00 0.00 1.75
770 774 9.826574 ATACCAAGCTCGTGTTAAATAGAATAA 57.173 29.630 0.00 0.00 0.00 1.40
771 775 8.556213 ACCAAGCTCGTGTTAAATAGAATAAA 57.444 30.769 0.00 0.00 0.00 1.40
772 776 9.005777 ACCAAGCTCGTGTTAAATAGAATAAAA 57.994 29.630 0.00 0.00 0.00 1.52
773 777 9.490663 CCAAGCTCGTGTTAAATAGAATAAAAG 57.509 33.333 0.00 0.00 0.00 2.27
774 778 9.490663 CAAGCTCGTGTTAAATAGAATAAAAGG 57.509 33.333 0.00 0.00 0.00 3.11
775 779 7.694886 AGCTCGTGTTAAATAGAATAAAAGGC 58.305 34.615 0.00 0.00 0.00 4.35
776 780 7.553044 AGCTCGTGTTAAATAGAATAAAAGGCT 59.447 33.333 0.00 0.00 0.00 4.58
777 781 7.851472 GCTCGTGTTAAATAGAATAAAAGGCTC 59.149 37.037 0.00 0.00 0.00 4.70
778 782 8.780846 TCGTGTTAAATAGAATAAAAGGCTCA 57.219 30.769 0.00 0.00 0.00 4.26
779 783 9.221933 TCGTGTTAAATAGAATAAAAGGCTCAA 57.778 29.630 0.00 0.00 0.00 3.02
817 821 4.106341 AGGAAAGGGATGGAGTTTTTCTCA 59.894 41.667 0.00 0.00 44.40 3.27
826 830 3.766591 TGGAGTTTTTCTCACTTTTGGCA 59.233 39.130 0.00 0.00 44.40 4.92
834 838 1.747355 CTCACTTTTGGCATAGCAGGG 59.253 52.381 0.00 0.00 0.00 4.45
840 844 3.492353 GGCATAGCAGGGCTCCCA 61.492 66.667 7.82 0.00 40.44 4.37
841 845 2.597340 GCATAGCAGGGCTCCCAA 59.403 61.111 7.82 0.00 40.44 4.12
842 846 1.076777 GCATAGCAGGGCTCCCAAA 60.077 57.895 7.82 0.00 40.44 3.28
911 915 1.160989 ATAATTGCGTCGTTGTGCCA 58.839 45.000 0.00 0.00 0.00 4.92
917 921 2.345991 GTCGTTGTGCCAGGGCTA 59.654 61.111 12.19 0.00 42.51 3.93
929 933 1.532794 AGGGCTATGAGGGCTCTCG 60.533 63.158 9.55 0.00 42.79 4.04
968 972 2.125391 GCTCATCAGCGCCTGACA 60.125 61.111 2.29 0.00 43.63 3.58
1054 1058 5.261216 TGAAACCAAACAAACTTCTCCTCT 58.739 37.500 0.00 0.00 0.00 3.69
1056 1060 2.952310 ACCAAACAAACTTCTCCTCTGC 59.048 45.455 0.00 0.00 0.00 4.26
1087 1091 0.755686 GGCGATTCAGGTGAGATCCT 59.244 55.000 0.00 0.00 38.51 3.24
1092 1096 4.554292 CGATTCAGGTGAGATCCTATGTG 58.446 47.826 0.00 0.00 35.87 3.21
1164 1169 0.106918 ACGGCTCCTCTCTTCTCGAT 60.107 55.000 0.00 0.00 0.00 3.59
1213 1218 1.946768 AGAGCTATCTCTCGAGCACAC 59.053 52.381 7.81 0.00 46.32 3.82
1298 1303 3.721087 ACGAGATCACCCCTTTCATTT 57.279 42.857 0.00 0.00 0.00 2.32
1308 1313 2.324541 CCCTTTCATTTTGGGGTGACA 58.675 47.619 0.00 0.00 37.37 3.58
1474 1481 9.490379 TTTGAAAAAGGATCTTAGAGTGTCTAC 57.510 33.333 0.00 0.00 0.00 2.59
1571 1578 1.371415 AGAGGGAGAAGGGGGAAGAAT 59.629 52.381 0.00 0.00 0.00 2.40
1585 1593 4.565652 GGGGAAGAATACACTTGAAGAGCA 60.566 45.833 0.00 0.00 0.00 4.26
1619 1627 1.743623 TTGTATGCTGCGTTCGGGG 60.744 57.895 0.00 0.00 0.00 5.73
1667 2204 7.205515 AGTCTATTGATTCTCTCCCAATTGT 57.794 36.000 4.43 0.00 33.21 2.71
1711 2248 1.878656 CTTCACGGGCGAGGTCTCTT 61.879 60.000 0.00 0.00 0.00 2.85
1764 2301 6.379417 CCAGGGAAAAGAATAGAAGAAGCATT 59.621 38.462 0.00 0.00 0.00 3.56
1782 2319 6.519679 AGCATTTGACTCTTTCATGCATAA 57.480 33.333 0.00 0.00 41.11 1.90
1794 2331 3.634504 TCATGCATAATCCACTTGGCTT 58.365 40.909 0.00 0.00 34.44 4.35
1903 3142 2.772515 GTTGGCCTCTATGGTAGAACCT 59.227 50.000 3.32 0.00 39.58 3.50
1947 3186 1.029947 GTTTACCCTGTGGCGGATGG 61.030 60.000 0.00 0.00 33.59 3.51
1963 3202 4.373116 GGCAGCGGTTCGAGTCCA 62.373 66.667 8.93 0.00 0.00 4.02
1982 3221 2.374504 CCACTTATCTCCAGCCCATGAT 59.625 50.000 0.00 0.00 0.00 2.45
1988 3227 2.333069 TCTCCAGCCCATGATCTTAGG 58.667 52.381 0.00 0.00 0.00 2.69
2062 3301 3.763097 TGATTTCACATTCATGGACGC 57.237 42.857 0.00 0.00 0.00 5.19
2091 3330 4.721776 AGATCCTTCCATTTAGTAGCACCA 59.278 41.667 0.00 0.00 0.00 4.17
2120 3359 3.252458 GGCATAGCCTTAACGTTAATGGG 59.748 47.826 24.98 21.77 46.69 4.00
2121 3360 4.131596 GCATAGCCTTAACGTTAATGGGA 58.868 43.478 23.49 11.25 0.00 4.37
2127 3366 4.219070 GCCTTAACGTTAATGGGAAGGTTT 59.781 41.667 23.49 2.16 38.17 3.27
2228 3467 7.001073 GGGGAGTTGAAAATAAGCATAGATCT 58.999 38.462 0.00 0.00 0.00 2.75
2229 3468 8.157476 GGGGAGTTGAAAATAAGCATAGATCTA 58.843 37.037 4.57 4.57 0.00 1.98
2290 3529 1.210538 TCCATGAGCAGGCAAGAGAT 58.789 50.000 0.00 0.00 0.00 2.75
2321 3560 5.392057 GCAAACTGAAACATCTTAGTAGCCC 60.392 44.000 0.00 0.00 0.00 5.19
2348 3587 4.590850 AAAGAAAGCAAAAGCGATTCCT 57.409 36.364 0.00 0.00 0.00 3.36
2408 3647 1.057851 AAACGGGGTTGTGGGAGAGA 61.058 55.000 0.00 0.00 0.00 3.10
2424 3663 3.746492 GGAGAGAAATACAAGCGTTGTGT 59.254 43.478 11.90 4.54 45.03 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.983378 ATTCTGGGAAGACGGAGGGG 60.983 60.000 0.00 0.0 0.00 4.79
17 18 3.496331 GTCAACCCTTTCATTCTGGGAA 58.504 45.455 4.11 0.0 43.47 3.97
18 19 2.225017 GGTCAACCCTTTCATTCTGGGA 60.225 50.000 4.11 0.0 43.47 4.37
34 35 3.228453 AGACCAAGAACTACGAGGTCAA 58.772 45.455 11.93 0.0 44.05 3.18
38 39 5.357314 TCTTCATAGACCAAGAACTACGAGG 59.643 44.000 0.00 0.0 0.00 4.63
56 57 4.579869 AGAACCTAACAACGCATCTTCAT 58.420 39.130 0.00 0.0 0.00 2.57
76 77 3.622206 CGTCCTCAATGGGAAAATGGAGA 60.622 47.826 0.00 0.0 37.10 3.71
82 83 2.107552 AGGTTCGTCCTCAATGGGAAAA 59.892 45.455 0.00 0.0 44.42 2.29
137 139 6.256819 TCGAGAATCCATACATCCCTTATCT 58.743 40.000 0.00 0.0 0.00 1.98
217 220 9.703892 CCCATGTAGATCTAACTTTCTATTCAG 57.296 37.037 3.40 0.0 0.00 3.02
257 260 0.567687 TCAGGAGGATAGATGGGGCA 59.432 55.000 0.00 0.0 0.00 5.36
306 309 2.846206 TGGCATACTCCTCCTGTTTGAT 59.154 45.455 0.00 0.0 0.00 2.57
323 326 0.818938 CAAGGCACATTAGCATGGCA 59.181 50.000 0.00 0.0 43.55 4.92
377 380 5.104569 TCAGCCACATGGATAGTTGAATGTA 60.105 40.000 0.87 0.0 37.39 2.29
383 386 3.464907 CTCTCAGCCACATGGATAGTTG 58.535 50.000 0.87 0.0 37.39 3.16
413 416 2.672996 GCGTCATTGTGCCTGGGT 60.673 61.111 0.00 0.0 0.00 4.51
444 447 5.221541 GGCTATTAGCTCAGTGGTAGAATGT 60.222 44.000 15.02 0.0 41.99 2.71
447 450 3.641906 GGGCTATTAGCTCAGTGGTAGAA 59.358 47.826 15.02 0.0 42.59 2.10
479 482 0.674895 CACGCCTCCCAAAGAGAAGG 60.675 60.000 0.00 0.0 46.50 3.46
481 484 1.302511 GCACGCCTCCCAAAGAGAA 60.303 57.895 0.00 0.0 46.50 2.87
484 487 0.036388 CTTAGCACGCCTCCCAAAGA 60.036 55.000 0.00 0.0 0.00 2.52
486 489 1.674322 GCTTAGCACGCCTCCCAAA 60.674 57.895 0.00 0.0 0.00 3.28
487 490 2.046314 GCTTAGCACGCCTCCCAA 60.046 61.111 0.00 0.0 0.00 4.12
488 491 4.096003 GGCTTAGCACGCCTCCCA 62.096 66.667 6.53 0.0 44.17 4.37
496 499 1.156736 TCTCGCTTTTGGCTTAGCAC 58.843 50.000 6.53 0.0 37.23 4.40
527 530 3.611025 TGGGGATGTCAAAAGGAAAGT 57.389 42.857 0.00 0.0 0.00 2.66
568 572 1.182385 TTTTTGGCGTCCCCATGTCC 61.182 55.000 0.00 0.0 44.89 4.02
569 573 2.346597 TTTTTGGCGTCCCCATGTC 58.653 52.632 0.00 0.0 44.89 3.06
663 667 5.805486 TGGATATCGAAGTCTTCTTTCGTTG 59.195 40.000 10.81 0.0 33.64 4.10
680 684 9.364989 GCTACATCTGATCTAAACTTGGATATC 57.635 37.037 0.00 0.0 0.00 1.63
695 699 4.500499 AAAGAAGGCAGCTACATCTGAT 57.500 40.909 0.00 0.0 36.19 2.90
701 705 2.554032 GCTCAAAAAGAAGGCAGCTACA 59.446 45.455 0.00 0.0 0.00 2.74
720 724 3.554934 TGGTTTGACACTTCTTCATGCT 58.445 40.909 0.00 0.0 0.00 3.79
723 727 7.069331 TGGTATTTTGGTTTGACACTTCTTCAT 59.931 33.333 0.00 0.0 0.00 2.57
749 753 8.182227 GCCTTTTATTCTATTTAACACGAGCTT 58.818 33.333 0.00 0.0 0.00 3.74
750 754 7.553044 AGCCTTTTATTCTATTTAACACGAGCT 59.447 33.333 0.00 0.0 0.00 4.09
751 755 7.694886 AGCCTTTTATTCTATTTAACACGAGC 58.305 34.615 0.00 0.0 0.00 5.03
752 756 8.879759 TGAGCCTTTTATTCTATTTAACACGAG 58.120 33.333 0.00 0.0 0.00 4.18
753 757 8.780846 TGAGCCTTTTATTCTATTTAACACGA 57.219 30.769 0.00 0.0 0.00 4.35
754 758 9.834628 TTTGAGCCTTTTATTCTATTTAACACG 57.165 29.630 0.00 0.0 0.00 4.49
759 763 8.923270 CCCCATTTGAGCCTTTTATTCTATTTA 58.077 33.333 0.00 0.0 0.00 1.40
760 764 7.623278 TCCCCATTTGAGCCTTTTATTCTATTT 59.377 33.333 0.00 0.0 0.00 1.40
761 765 7.132128 TCCCCATTTGAGCCTTTTATTCTATT 58.868 34.615 0.00 0.0 0.00 1.73
762 766 6.682537 TCCCCATTTGAGCCTTTTATTCTAT 58.317 36.000 0.00 0.0 0.00 1.98
763 767 6.086011 TCCCCATTTGAGCCTTTTATTCTA 57.914 37.500 0.00 0.0 0.00 2.10
764 768 4.946646 TCCCCATTTGAGCCTTTTATTCT 58.053 39.130 0.00 0.0 0.00 2.40
765 769 5.129320 ACATCCCCATTTGAGCCTTTTATTC 59.871 40.000 0.00 0.0 0.00 1.75
766 770 5.032170 ACATCCCCATTTGAGCCTTTTATT 58.968 37.500 0.00 0.0 0.00 1.40
767 771 4.623863 ACATCCCCATTTGAGCCTTTTAT 58.376 39.130 0.00 0.0 0.00 1.40
768 772 4.023291 GACATCCCCATTTGAGCCTTTTA 58.977 43.478 0.00 0.0 0.00 1.52
769 773 2.833943 GACATCCCCATTTGAGCCTTTT 59.166 45.455 0.00 0.0 0.00 2.27
770 774 2.225343 TGACATCCCCATTTGAGCCTTT 60.225 45.455 0.00 0.0 0.00 3.11
771 775 1.358787 TGACATCCCCATTTGAGCCTT 59.641 47.619 0.00 0.0 0.00 4.35
772 776 1.002069 TGACATCCCCATTTGAGCCT 58.998 50.000 0.00 0.0 0.00 4.58
773 777 1.851304 TTGACATCCCCATTTGAGCC 58.149 50.000 0.00 0.0 0.00 4.70
774 778 3.368739 CCTTTTGACATCCCCATTTGAGC 60.369 47.826 0.00 0.0 0.00 4.26
775 779 4.088634 TCCTTTTGACATCCCCATTTGAG 58.911 43.478 0.00 0.0 0.00 3.02
776 780 4.125124 TCCTTTTGACATCCCCATTTGA 57.875 40.909 0.00 0.0 0.00 2.69
777 781 4.888326 TTCCTTTTGACATCCCCATTTG 57.112 40.909 0.00 0.0 0.00 2.32
778 782 4.286808 CCTTTCCTTTTGACATCCCCATTT 59.713 41.667 0.00 0.0 0.00 2.32
779 783 3.840078 CCTTTCCTTTTGACATCCCCATT 59.160 43.478 0.00 0.0 0.00 3.16
817 821 0.040204 AGCCCTGCTATGCCAAAAGT 59.960 50.000 0.00 0.0 36.99 2.66
826 830 1.925888 CCTTTGGGAGCCCTGCTAT 59.074 57.895 7.16 0.0 39.88 2.97
853 857 1.362717 GAGCTAATAGCCCGTCGCA 59.637 57.895 8.88 0.0 43.77 5.10
911 915 1.532794 CGAGAGCCCTCATAGCCCT 60.533 63.158 0.00 0.0 39.39 5.19
929 933 3.290710 ACATTGAACTATCCATGTGGCC 58.709 45.455 0.00 0.0 39.67 5.36
980 984 2.646930 TGCTAATGTGCCTTGGATGAG 58.353 47.619 0.00 0.0 0.00 2.90
1054 1058 0.837691 ATCGCCCCATCTATCCTGCA 60.838 55.000 0.00 0.0 0.00 4.41
1056 1060 1.625315 TGAATCGCCCCATCTATCCTG 59.375 52.381 0.00 0.0 0.00 3.86
1092 1096 6.697892 CCACGAGTGAATAGAAAGTTAGATCC 59.302 42.308 4.59 0.0 0.00 3.36
1139 1143 3.775654 GAGAGGAGCCGTGGTGGG 61.776 72.222 0.00 0.0 38.63 4.61
1164 1169 7.872061 ACACTGATAAGGGATGTATGGATTA 57.128 36.000 0.00 0.0 0.00 1.75
1298 1303 1.264749 CGATCCCTCTGTCACCCCAA 61.265 60.000 0.00 0.0 0.00 4.12
1308 1313 2.231529 CTCGAATGGTACGATCCCTCT 58.768 52.381 0.00 0.0 39.02 3.69
1349 1356 1.130054 TGCTGCTTTCTCCAGACCCT 61.130 55.000 0.00 0.0 32.03 4.34
1350 1357 0.250901 TTGCTGCTTTCTCCAGACCC 60.251 55.000 0.00 0.0 32.03 4.46
1412 1419 9.948964 CTCCCATTTAAGGAAAAAGAATTTCAT 57.051 29.630 0.00 0.0 37.28 2.57
1571 1578 4.929819 TGTACTGTGCTCTTCAAGTGTA 57.070 40.909 0.00 0.0 0.00 2.90
1619 1627 0.389391 TTCGGGAGCGATTCATCCTC 59.611 55.000 5.22 0.0 35.80 3.71
1667 2204 4.037441 TCGCCCCTACGATCCAAA 57.963 55.556 0.00 0.0 37.09 3.28
1711 2248 0.038166 GGCCATCCTGGACTTGAACA 59.962 55.000 0.00 0.0 44.12 3.18
1764 2301 6.182627 AGTGGATTATGCATGAAAGAGTCAA 58.817 36.000 10.16 0.0 40.50 3.18
1782 2319 2.772924 CCCCCAAGCCAAGTGGAT 59.227 61.111 0.18 0.0 38.54 3.41
1824 2362 3.255888 ACTTTCATCGTACTGTGCTCTCA 59.744 43.478 0.00 0.0 0.00 3.27
1874 3113 2.894126 CCATAGAGGCCAACGATAGACT 59.106 50.000 5.01 0.0 41.38 3.24
1903 3142 3.965026 CTCTCAGGCCTCCCCGACA 62.965 68.421 0.00 0.0 39.21 4.35
1947 3186 3.112709 GTGGACTCGAACCGCTGC 61.113 66.667 12.65 0.0 35.35 5.25
1963 3202 3.596101 AGATCATGGGCTGGAGATAAGT 58.404 45.455 0.00 0.0 0.00 2.24
1982 3221 6.323210 TCGCTATCATAGTATCCCCTAAGA 57.677 41.667 0.00 0.0 0.00 2.10
1988 3227 5.278561 GGTGCTATCGCTATCATAGTATCCC 60.279 48.000 0.00 0.0 36.97 3.85
2062 3301 8.370940 TGCTACTAAATGGAAGGATCTTATCAG 58.629 37.037 0.00 0.0 0.00 2.90
2120 3359 6.216569 CAAGCCTTTCCTCTTTTAAACCTTC 58.783 40.000 0.00 0.0 0.00 3.46
2121 3360 5.453339 GCAAGCCTTTCCTCTTTTAAACCTT 60.453 40.000 0.00 0.0 0.00 3.50
2127 3366 2.159382 CCGCAAGCCTTTCCTCTTTTA 58.841 47.619 0.00 0.0 0.00 1.52
2228 3467 5.970640 AGGTTGACCTATTTGGGAATCTCTA 59.029 40.000 0.00 0.0 46.48 2.43
2229 3468 4.790790 AGGTTGACCTATTTGGGAATCTCT 59.209 41.667 0.00 0.0 46.48 3.10
2290 3529 4.469657 AGATGTTTCAGTTTGCCAGGTTA 58.530 39.130 0.00 0.0 0.00 2.85
2321 3560 4.111916 TCGCTTTTGCTTTCTTTTCCTTG 58.888 39.130 0.00 0.0 44.80 3.61
2348 3587 0.946528 TTTCGCTCGCCGCTACTATA 59.053 50.000 0.00 0.0 36.73 1.31
2408 3647 3.708563 AGCAACACAACGCTTGTATTT 57.291 38.095 3.60 0.0 43.23 1.40


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

AutoCloner maintained by Alex Coulton.