Multiple sequence alignment - TraesCS2D01G182800

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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 TraesCS2D01G182800 chr2D 100.000 3095 0 0 355 3449 127089406 127086312 0.000000e+00 5716
1 TraesCS2D01G182800 chr2D 100.000 71 0 0 1 71 127089760 127089690 7.770000e-27 132
2 TraesCS2D01G182800 chr2B 97.202 3038 50 5 413 3449 180824192 180821189 0.000000e+00 5107
3 TraesCS2D01G182800 chr2A 96.920 2695 58 8 763 3449 133963135 133960458 0.000000e+00 4494


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 TraesCS2D01G182800 chr2D 127086312 127089760 3448 True 2924 5716 100.000 1 3449 2 chr2D.!!$R1 3448
1 TraesCS2D01G182800 chr2B 180821189 180824192 3003 True 5107 5107 97.202 413 3449 1 chr2B.!!$R1 3036
2 TraesCS2D01G182800 chr2A 133960458 133963135 2677 True 4494 4494 96.920 763 3449 1 chr2A.!!$R1 2686

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
37 38 0.317938 CTAGTGCGGCGTCATCCTAC 60.318 60.0 9.37 0.0 0.00 3.18 F
42 43 0.319900 GCGGCGTCATCCTACATGAT 60.320 55.0 9.37 0.0 0.00 2.45 F
402 403 0.322906 GTGGGCAGGGAGGAGAAAAG 60.323 60.0 0.00 0.0 0.00 2.27 F
953 963 0.467290 GGCACCCAGTGGAAGTGAAA 60.467 55.0 19.38 0.0 40.62 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 1936 1.883021 GCCCATTTGTCGGAACAGG 59.117 57.895 0.0 0.0 36.57 4.00 R
2031 2041 2.684881 AGACCGCATCCAAATCATCAAC 59.315 45.455 0.0 0.0 0.00 3.18 R
2073 2083 4.713824 TCCATAATACGCCTTCCTATCG 57.286 45.455 0.0 0.0 0.00 2.92 R
2802 2815 4.568359 CGTTTCTCACATAGATGAAGGTGG 59.432 45.833 0.0 0.0 33.05 4.61 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
26 27 1.742768 GGACAGATCCCTAGTGCGG 59.257 63.158 0.00 0.00 39.39 5.69
27 28 1.068250 GACAGATCCCTAGTGCGGC 59.932 63.158 0.00 0.00 0.00 6.53
28 29 2.028190 CAGATCCCTAGTGCGGCG 59.972 66.667 0.51 0.51 0.00 6.46
29 30 2.442272 AGATCCCTAGTGCGGCGT 60.442 61.111 9.37 0.00 0.00 5.68
30 31 2.027751 GATCCCTAGTGCGGCGTC 59.972 66.667 9.37 0.91 0.00 5.19
31 32 2.758327 ATCCCTAGTGCGGCGTCA 60.758 61.111 9.37 4.08 0.00 4.35
32 33 2.088674 GATCCCTAGTGCGGCGTCAT 62.089 60.000 9.37 0.00 0.00 3.06
33 34 2.088674 ATCCCTAGTGCGGCGTCATC 62.089 60.000 9.37 2.74 0.00 2.92
34 35 2.279517 CCTAGTGCGGCGTCATCC 60.280 66.667 9.37 0.00 0.00 3.51
35 36 2.786495 CCTAGTGCGGCGTCATCCT 61.786 63.158 9.37 4.41 0.00 3.24
36 37 1.452953 CCTAGTGCGGCGTCATCCTA 61.453 60.000 9.37 5.32 0.00 2.94
37 38 0.317938 CTAGTGCGGCGTCATCCTAC 60.318 60.000 9.37 0.00 0.00 3.18
38 39 1.033202 TAGTGCGGCGTCATCCTACA 61.033 55.000 9.37 0.00 0.00 2.74
39 40 1.227263 GTGCGGCGTCATCCTACAT 60.227 57.895 9.37 0.00 0.00 2.29
40 41 1.227234 TGCGGCGTCATCCTACATG 60.227 57.895 9.37 0.00 0.00 3.21
41 42 1.067416 GCGGCGTCATCCTACATGA 59.933 57.895 9.37 0.00 0.00 3.07
42 43 0.319900 GCGGCGTCATCCTACATGAT 60.320 55.000 9.37 0.00 0.00 2.45
43 44 1.873903 GCGGCGTCATCCTACATGATT 60.874 52.381 9.37 0.00 0.00 2.57
44 45 1.794701 CGGCGTCATCCTACATGATTG 59.205 52.381 0.00 0.00 0.00 2.67
45 46 1.532868 GGCGTCATCCTACATGATTGC 59.467 52.381 0.00 0.00 34.01 3.56
46 47 1.532868 GCGTCATCCTACATGATTGCC 59.467 52.381 0.00 0.00 0.00 4.52
47 48 2.837498 CGTCATCCTACATGATTGCCA 58.163 47.619 0.00 0.00 0.00 4.92
48 49 3.405831 CGTCATCCTACATGATTGCCAT 58.594 45.455 0.00 0.00 35.44 4.40
49 50 3.817084 CGTCATCCTACATGATTGCCATT 59.183 43.478 0.00 0.00 31.94 3.16
50 51 4.319984 CGTCATCCTACATGATTGCCATTG 60.320 45.833 0.00 0.00 31.94 2.82
51 52 4.581824 GTCATCCTACATGATTGCCATTGT 59.418 41.667 0.00 0.00 31.94 2.71
52 53 5.068198 GTCATCCTACATGATTGCCATTGTT 59.932 40.000 0.00 0.00 31.94 2.83
53 54 4.987408 TCCTACATGATTGCCATTGTTG 57.013 40.909 0.00 0.00 31.94 3.33
54 55 3.130869 TCCTACATGATTGCCATTGTTGC 59.869 43.478 0.00 0.00 31.94 4.17
55 56 3.131577 CCTACATGATTGCCATTGTTGCT 59.868 43.478 0.00 0.00 31.94 3.91
56 57 3.241067 ACATGATTGCCATTGTTGCTC 57.759 42.857 0.00 0.00 31.94 4.26
57 58 2.563620 ACATGATTGCCATTGTTGCTCA 59.436 40.909 0.00 0.00 31.94 4.26
58 59 3.196901 ACATGATTGCCATTGTTGCTCAT 59.803 39.130 0.00 0.00 31.94 2.90
59 60 3.965379 TGATTGCCATTGTTGCTCATT 57.035 38.095 0.00 0.00 0.00 2.57
60 61 4.274602 TGATTGCCATTGTTGCTCATTT 57.725 36.364 0.00 0.00 0.00 2.32
61 62 3.997681 TGATTGCCATTGTTGCTCATTTG 59.002 39.130 0.00 0.00 0.00 2.32
62 63 3.472283 TTGCCATTGTTGCTCATTTGT 57.528 38.095 0.00 0.00 0.00 2.83
63 64 3.472283 TGCCATTGTTGCTCATTTGTT 57.528 38.095 0.00 0.00 0.00 2.83
64 65 3.806380 TGCCATTGTTGCTCATTTGTTT 58.194 36.364 0.00 0.00 0.00 2.83
65 66 3.560481 TGCCATTGTTGCTCATTTGTTTG 59.440 39.130 0.00 0.00 0.00 2.93
66 67 3.607542 GCCATTGTTGCTCATTTGTTTGC 60.608 43.478 0.00 0.00 0.00 3.68
67 68 3.058777 CCATTGTTGCTCATTTGTTTGCC 60.059 43.478 0.00 0.00 0.00 4.52
68 69 2.237393 TGTTGCTCATTTGTTTGCCC 57.763 45.000 0.00 0.00 0.00 5.36
69 70 1.483827 TGTTGCTCATTTGTTTGCCCA 59.516 42.857 0.00 0.00 0.00 5.36
70 71 2.104451 TGTTGCTCATTTGTTTGCCCAT 59.896 40.909 0.00 0.00 0.00 4.00
398 399 4.741239 GGGTGGGCAGGGAGGAGA 62.741 72.222 0.00 0.00 0.00 3.71
399 400 2.610859 GGTGGGCAGGGAGGAGAA 60.611 66.667 0.00 0.00 0.00 2.87
400 401 2.231380 GGTGGGCAGGGAGGAGAAA 61.231 63.158 0.00 0.00 0.00 2.52
401 402 1.767692 GTGGGCAGGGAGGAGAAAA 59.232 57.895 0.00 0.00 0.00 2.29
402 403 0.322906 GTGGGCAGGGAGGAGAAAAG 60.323 60.000 0.00 0.00 0.00 2.27
403 404 1.304617 GGGCAGGGAGGAGAAAAGG 59.695 63.158 0.00 0.00 0.00 3.11
404 405 1.208165 GGGCAGGGAGGAGAAAAGGA 61.208 60.000 0.00 0.00 0.00 3.36
405 406 0.698818 GGCAGGGAGGAGAAAAGGAA 59.301 55.000 0.00 0.00 0.00 3.36
406 407 1.286257 GGCAGGGAGGAGAAAAGGAAT 59.714 52.381 0.00 0.00 0.00 3.01
407 408 2.373224 GCAGGGAGGAGAAAAGGAATG 58.627 52.381 0.00 0.00 0.00 2.67
408 409 2.291217 GCAGGGAGGAGAAAAGGAATGT 60.291 50.000 0.00 0.00 0.00 2.71
409 410 3.350833 CAGGGAGGAGAAAAGGAATGTG 58.649 50.000 0.00 0.00 0.00 3.21
410 411 3.009473 CAGGGAGGAGAAAAGGAATGTGA 59.991 47.826 0.00 0.00 0.00 3.58
411 412 3.265479 AGGGAGGAGAAAAGGAATGTGAG 59.735 47.826 0.00 0.00 0.00 3.51
474 475 4.774660 AAGTACTAGAGGGATCGAGACA 57.225 45.455 0.00 0.00 0.00 3.41
475 476 4.345859 AGTACTAGAGGGATCGAGACAG 57.654 50.000 0.00 0.00 0.00 3.51
476 477 2.649531 ACTAGAGGGATCGAGACAGG 57.350 55.000 0.00 0.00 0.00 4.00
477 478 1.847737 ACTAGAGGGATCGAGACAGGT 59.152 52.381 0.00 0.00 0.00 4.00
478 479 2.242708 ACTAGAGGGATCGAGACAGGTT 59.757 50.000 0.00 0.00 0.00 3.50
518 519 5.587043 CACTAACTCACTTCGAGATACTCCT 59.413 44.000 0.00 0.00 45.45 3.69
519 520 6.762187 CACTAACTCACTTCGAGATACTCCTA 59.238 42.308 0.00 0.00 45.45 2.94
520 521 7.442969 CACTAACTCACTTCGAGATACTCCTAT 59.557 40.741 0.00 0.00 45.45 2.57
547 548 4.819769 TGGCTATTTCAAATGTTCAAGCC 58.180 39.130 12.35 12.35 46.71 4.35
559 560 1.820519 GTTCAAGCCTGCCATCATTCA 59.179 47.619 0.00 0.00 0.00 2.57
605 606 8.430431 GGCTAAGGTTAGATGTAGAAATAAGGT 58.570 37.037 0.71 0.00 32.47 3.50
614 615 7.907389 AGATGTAGAAATAAGGTCACACTTCA 58.093 34.615 0.00 0.00 32.02 3.02
618 619 5.063880 AGAAATAAGGTCACACTTCACCAC 58.936 41.667 0.00 0.00 34.80 4.16
623 624 2.769663 AGGTCACACTTCACCACACTTA 59.230 45.455 0.00 0.00 34.80 2.24
634 635 6.595716 ACTTCACCACACTTAGATAATCTTGC 59.404 38.462 0.00 0.00 0.00 4.01
708 709 3.359654 CTTTTACAAGTGTGGCGACAAC 58.640 45.455 2.03 0.00 46.06 3.32
728 729 2.076863 CCCAAACAGAAGGCTAACTCG 58.923 52.381 0.00 0.00 0.00 4.18
729 730 2.289444 CCCAAACAGAAGGCTAACTCGA 60.289 50.000 0.00 0.00 0.00 4.04
730 731 3.600388 CCAAACAGAAGGCTAACTCGAT 58.400 45.455 0.00 0.00 0.00 3.59
731 732 3.619038 CCAAACAGAAGGCTAACTCGATC 59.381 47.826 0.00 0.00 0.00 3.69
732 733 4.245660 CAAACAGAAGGCTAACTCGATCA 58.754 43.478 0.00 0.00 0.00 2.92
733 734 4.537135 AACAGAAGGCTAACTCGATCAA 57.463 40.909 0.00 0.00 0.00 2.57
734 735 4.537135 ACAGAAGGCTAACTCGATCAAA 57.463 40.909 0.00 0.00 0.00 2.69
735 736 4.246458 ACAGAAGGCTAACTCGATCAAAC 58.754 43.478 0.00 0.00 0.00 2.93
736 737 4.245660 CAGAAGGCTAACTCGATCAAACA 58.754 43.478 0.00 0.00 0.00 2.83
737 738 4.872691 CAGAAGGCTAACTCGATCAAACAT 59.127 41.667 0.00 0.00 0.00 2.71
738 739 4.872691 AGAAGGCTAACTCGATCAAACATG 59.127 41.667 0.00 0.00 0.00 3.21
739 740 2.939103 AGGCTAACTCGATCAAACATGC 59.061 45.455 0.00 0.00 0.00 4.06
740 741 2.939103 GGCTAACTCGATCAAACATGCT 59.061 45.455 0.00 0.00 0.00 3.79
741 742 3.375299 GGCTAACTCGATCAAACATGCTT 59.625 43.478 0.00 0.00 0.00 3.91
742 743 4.570772 GGCTAACTCGATCAAACATGCTTA 59.429 41.667 0.00 0.00 0.00 3.09
743 744 5.064707 GGCTAACTCGATCAAACATGCTTAA 59.935 40.000 0.00 0.00 0.00 1.85
744 745 5.960105 GCTAACTCGATCAAACATGCTTAAC 59.040 40.000 0.00 0.00 0.00 2.01
745 746 6.183360 GCTAACTCGATCAAACATGCTTAACT 60.183 38.462 0.00 0.00 0.00 2.24
746 747 7.010183 GCTAACTCGATCAAACATGCTTAACTA 59.990 37.037 0.00 0.00 0.00 2.24
747 748 6.893958 ACTCGATCAAACATGCTTAACTAG 57.106 37.500 0.00 0.00 0.00 2.57
748 749 6.398918 ACTCGATCAAACATGCTTAACTAGT 58.601 36.000 0.00 0.00 0.00 2.57
749 750 6.311445 ACTCGATCAAACATGCTTAACTAGTG 59.689 38.462 0.00 0.00 0.00 2.74
750 751 5.580691 TCGATCAAACATGCTTAACTAGTGG 59.419 40.000 0.00 0.00 0.00 4.00
751 752 5.580691 CGATCAAACATGCTTAACTAGTGGA 59.419 40.000 0.00 0.00 0.00 4.02
752 753 6.092122 CGATCAAACATGCTTAACTAGTGGAA 59.908 38.462 0.00 0.00 0.00 3.53
786 787 1.299541 CACGCCCATATCACACCTTC 58.700 55.000 0.00 0.00 0.00 3.46
949 959 2.839098 CTGGCACCCAGTGGAAGT 59.161 61.111 11.95 0.00 45.82 3.01
950 960 1.601759 CTGGCACCCAGTGGAAGTG 60.602 63.158 11.95 12.46 45.82 3.16
951 961 2.055689 CTGGCACCCAGTGGAAGTGA 62.056 60.000 19.38 2.25 45.82 3.41
952 962 1.150536 GGCACCCAGTGGAAGTGAA 59.849 57.895 19.38 0.00 40.62 3.18
953 963 0.467290 GGCACCCAGTGGAAGTGAAA 60.467 55.000 19.38 0.00 40.62 2.69
1359 1369 3.488978 CTCGCTCTCGTCGTCCGT 61.489 66.667 0.00 0.00 37.94 4.69
1611 1621 1.719600 GTGCTGTCAAGAAGATCGCT 58.280 50.000 0.00 0.00 0.00 4.93
1926 1936 2.681848 CAGGACTGAGGATGCAATGAAC 59.318 50.000 0.00 0.00 0.00 3.18
2031 2041 2.633967 CAGGATCTCTGAAGGGGATGAG 59.366 54.545 5.53 0.00 46.18 2.90
2094 2104 4.338012 TCGATAGGAAGGCGTATTATGGA 58.662 43.478 0.00 0.00 0.00 3.41
2802 2815 8.169268 CGGATAGGCTGTTAAATCGATAAATTC 58.831 37.037 0.00 0.00 0.00 2.17
2839 2852 3.560068 TGAGAAACGAGAAGGAAGTTTGC 59.440 43.478 0.00 0.00 38.09 3.68
3430 3445 9.923143 AAGTTGCTTAAATATTCTTTACCCAAC 57.077 29.630 0.00 0.00 31.87 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.742768 CCGCACTAGGGATCTGTCC 59.257 63.158 0.00 0.00 44.29 4.02
9 10 1.068250 GCCGCACTAGGGATCTGTC 59.932 63.158 0.00 0.00 0.00 3.51
10 11 2.786495 CGCCGCACTAGGGATCTGT 61.786 63.158 0.00 0.00 0.00 3.41
11 12 2.028190 CGCCGCACTAGGGATCTG 59.972 66.667 0.00 0.00 0.00 2.90
12 13 2.442272 ACGCCGCACTAGGGATCT 60.442 61.111 0.00 0.00 0.00 2.75
13 14 2.027751 GACGCCGCACTAGGGATC 59.972 66.667 0.00 0.00 0.00 3.36
14 15 2.088674 GATGACGCCGCACTAGGGAT 62.089 60.000 0.00 0.00 0.00 3.85
15 16 2.758327 ATGACGCCGCACTAGGGA 60.758 61.111 0.00 0.00 0.00 4.20
16 17 2.279517 GATGACGCCGCACTAGGG 60.280 66.667 0.00 0.00 0.00 3.53
17 18 1.452953 TAGGATGACGCCGCACTAGG 61.453 60.000 0.00 0.00 0.00 3.02
18 19 0.317938 GTAGGATGACGCCGCACTAG 60.318 60.000 0.00 0.00 0.00 2.57
19 20 1.033202 TGTAGGATGACGCCGCACTA 61.033 55.000 0.00 0.00 0.00 2.74
20 21 1.676678 ATGTAGGATGACGCCGCACT 61.677 55.000 0.00 0.00 0.00 4.40
21 22 1.227263 ATGTAGGATGACGCCGCAC 60.227 57.895 0.00 0.00 0.00 5.34
22 23 1.227234 CATGTAGGATGACGCCGCA 60.227 57.895 0.00 0.00 0.00 5.69
23 24 0.319900 ATCATGTAGGATGACGCCGC 60.320 55.000 0.00 0.00 0.00 6.53
24 25 1.794701 CAATCATGTAGGATGACGCCG 59.205 52.381 0.00 0.00 0.00 6.46
25 26 1.532868 GCAATCATGTAGGATGACGCC 59.467 52.381 0.00 0.00 0.00 5.68
26 27 1.532868 GGCAATCATGTAGGATGACGC 59.467 52.381 0.00 0.00 32.27 5.19
27 28 2.837498 TGGCAATCATGTAGGATGACG 58.163 47.619 0.00 0.00 0.00 4.35
28 29 4.581824 ACAATGGCAATCATGTAGGATGAC 59.418 41.667 0.00 0.00 35.99 3.06
29 30 4.795469 ACAATGGCAATCATGTAGGATGA 58.205 39.130 0.00 0.00 35.99 2.92
30 31 5.286438 CAACAATGGCAATCATGTAGGATG 58.714 41.667 0.00 0.00 35.99 3.51
31 32 4.202182 GCAACAATGGCAATCATGTAGGAT 60.202 41.667 0.00 0.00 35.99 3.24
32 33 3.130869 GCAACAATGGCAATCATGTAGGA 59.869 43.478 0.00 0.00 35.99 2.94
33 34 3.131577 AGCAACAATGGCAATCATGTAGG 59.868 43.478 0.00 0.00 35.99 3.18
34 35 4.142337 TGAGCAACAATGGCAATCATGTAG 60.142 41.667 0.00 0.00 35.99 2.74
35 36 3.762823 TGAGCAACAATGGCAATCATGTA 59.237 39.130 0.00 0.00 35.99 2.29
36 37 2.563620 TGAGCAACAATGGCAATCATGT 59.436 40.909 0.00 0.00 35.99 3.21
37 38 3.239587 TGAGCAACAATGGCAATCATG 57.760 42.857 0.00 0.00 35.99 3.07
38 39 4.481368 AATGAGCAACAATGGCAATCAT 57.519 36.364 0.00 0.00 37.79 2.45
39 40 3.965379 AATGAGCAACAATGGCAATCA 57.035 38.095 0.00 0.00 0.00 2.57
40 41 3.998341 ACAAATGAGCAACAATGGCAATC 59.002 39.130 0.00 0.00 0.00 2.67
41 42 4.010667 ACAAATGAGCAACAATGGCAAT 57.989 36.364 0.00 0.00 0.00 3.56
42 43 3.472283 ACAAATGAGCAACAATGGCAA 57.528 38.095 0.00 0.00 0.00 4.52
43 44 3.472283 AACAAATGAGCAACAATGGCA 57.528 38.095 0.00 0.00 0.00 4.92
44 45 3.607542 GCAAACAAATGAGCAACAATGGC 60.608 43.478 0.00 0.00 0.00 4.40
45 46 3.058777 GGCAAACAAATGAGCAACAATGG 60.059 43.478 0.00 0.00 0.00 3.16
46 47 3.058777 GGGCAAACAAATGAGCAACAATG 60.059 43.478 0.00 0.00 0.00 2.82
47 48 3.140623 GGGCAAACAAATGAGCAACAAT 58.859 40.909 0.00 0.00 0.00 2.71
48 49 2.093288 TGGGCAAACAAATGAGCAACAA 60.093 40.909 0.00 0.00 0.00 2.83
49 50 1.483827 TGGGCAAACAAATGAGCAACA 59.516 42.857 0.00 0.00 0.00 3.33
50 51 2.237393 TGGGCAAACAAATGAGCAAC 57.763 45.000 0.00 0.00 0.00 4.17
381 382 4.741239 TCTCCTCCCTGCCCACCC 62.741 72.222 0.00 0.00 0.00 4.61
382 383 1.789576 TTTTCTCCTCCCTGCCCACC 61.790 60.000 0.00 0.00 0.00 4.61
383 384 0.322906 CTTTTCTCCTCCCTGCCCAC 60.323 60.000 0.00 0.00 0.00 4.61
384 385 1.500783 CCTTTTCTCCTCCCTGCCCA 61.501 60.000 0.00 0.00 0.00 5.36
385 386 1.208165 TCCTTTTCTCCTCCCTGCCC 61.208 60.000 0.00 0.00 0.00 5.36
386 387 0.698818 TTCCTTTTCTCCTCCCTGCC 59.301 55.000 0.00 0.00 0.00 4.85
387 388 2.291217 ACATTCCTTTTCTCCTCCCTGC 60.291 50.000 0.00 0.00 0.00 4.85
388 389 3.009473 TCACATTCCTTTTCTCCTCCCTG 59.991 47.826 0.00 0.00 0.00 4.45
389 390 3.260205 TCACATTCCTTTTCTCCTCCCT 58.740 45.455 0.00 0.00 0.00 4.20
390 391 3.009584 ACTCACATTCCTTTTCTCCTCCC 59.990 47.826 0.00 0.00 0.00 4.30
391 392 4.006319 CACTCACATTCCTTTTCTCCTCC 58.994 47.826 0.00 0.00 0.00 4.30
392 393 4.899502 TCACTCACATTCCTTTTCTCCTC 58.100 43.478 0.00 0.00 0.00 3.71
393 394 4.982241 TCACTCACATTCCTTTTCTCCT 57.018 40.909 0.00 0.00 0.00 3.69
394 395 6.391227 TTTTCACTCACATTCCTTTTCTCC 57.609 37.500 0.00 0.00 0.00 3.71
395 396 8.137437 TGAATTTTCACTCACATTCCTTTTCTC 58.863 33.333 0.00 0.00 31.01 2.87
396 397 8.010733 TGAATTTTCACTCACATTCCTTTTCT 57.989 30.769 0.00 0.00 31.01 2.52
397 398 8.822652 ATGAATTTTCACTCACATTCCTTTTC 57.177 30.769 0.00 0.00 40.49 2.29
476 477 4.338379 AGTGAGTGGTTCAGGTTCTAAC 57.662 45.455 0.00 0.00 36.21 2.34
477 478 5.601313 AGTTAGTGAGTGGTTCAGGTTCTAA 59.399 40.000 0.00 0.00 36.21 2.10
478 479 5.145564 AGTTAGTGAGTGGTTCAGGTTCTA 58.854 41.667 0.00 0.00 36.21 2.10
518 519 8.669946 TGAACATTTGAAATAGCCATCGTATA 57.330 30.769 0.00 0.00 0.00 1.47
519 520 7.566760 TGAACATTTGAAATAGCCATCGTAT 57.433 32.000 0.00 0.00 0.00 3.06
520 521 6.993786 TGAACATTTGAAATAGCCATCGTA 57.006 33.333 0.00 0.00 0.00 3.43
547 548 5.633830 AAAAGTGTAGTGAATGATGGCAG 57.366 39.130 0.00 0.00 0.00 4.85
605 606 4.955811 ATCTAAGTGTGGTGAAGTGTGA 57.044 40.909 0.00 0.00 0.00 3.58
614 615 5.435686 TGGCAAGATTATCTAAGTGTGGT 57.564 39.130 0.00 0.00 0.00 4.16
708 709 2.076863 CGAGTTAGCCTTCTGTTTGGG 58.923 52.381 0.00 0.00 0.00 4.12
728 729 6.985188 TCCACTAGTTAAGCATGTTTGATC 57.015 37.500 4.89 0.00 0.00 2.92
729 730 6.942576 ACTTCCACTAGTTAAGCATGTTTGAT 59.057 34.615 4.89 0.00 0.00 2.57
730 731 6.296026 ACTTCCACTAGTTAAGCATGTTTGA 58.704 36.000 4.89 0.00 0.00 2.69
731 732 6.560253 ACTTCCACTAGTTAAGCATGTTTG 57.440 37.500 4.89 0.00 0.00 2.93
732 733 7.883311 ACATACTTCCACTAGTTAAGCATGTTT 59.117 33.333 19.24 0.00 34.90 2.83
733 734 7.394816 ACATACTTCCACTAGTTAAGCATGTT 58.605 34.615 19.24 10.01 34.90 2.71
734 735 6.947464 ACATACTTCCACTAGTTAAGCATGT 58.053 36.000 19.24 19.24 34.09 3.21
735 736 7.041721 TGACATACTTCCACTAGTTAAGCATG 58.958 38.462 18.37 18.37 32.57 4.06
736 737 7.182817 TGACATACTTCCACTAGTTAAGCAT 57.817 36.000 12.62 5.10 0.00 3.79
737 738 6.599356 TGACATACTTCCACTAGTTAAGCA 57.401 37.500 12.62 3.23 0.00 3.91
738 739 7.764443 TGATTGACATACTTCCACTAGTTAAGC 59.236 37.037 12.62 0.00 0.00 3.09
739 740 9.653287 TTGATTGACATACTTCCACTAGTTAAG 57.347 33.333 11.53 11.53 0.00 1.85
741 742 9.431887 GTTTGATTGACATACTTCCACTAGTTA 57.568 33.333 0.00 0.00 0.00 2.24
742 743 7.936847 TGTTTGATTGACATACTTCCACTAGTT 59.063 33.333 0.00 0.00 32.96 2.24
743 744 7.387948 GTGTTTGATTGACATACTTCCACTAGT 59.612 37.037 0.00 0.00 32.96 2.57
744 745 7.411912 CGTGTTTGATTGACATACTTCCACTAG 60.412 40.741 0.00 0.00 32.96 2.57
745 746 6.367695 CGTGTTTGATTGACATACTTCCACTA 59.632 38.462 0.00 0.00 32.96 2.74
746 747 5.179368 CGTGTTTGATTGACATACTTCCACT 59.821 40.000 0.00 0.00 32.96 4.00
747 748 5.382303 CGTGTTTGATTGACATACTTCCAC 58.618 41.667 0.00 0.00 32.96 4.02
748 749 4.083537 GCGTGTTTGATTGACATACTTCCA 60.084 41.667 0.00 0.00 32.96 3.53
749 750 4.403453 GCGTGTTTGATTGACATACTTCC 58.597 43.478 0.00 0.00 32.96 3.46
750 751 4.403453 GGCGTGTTTGATTGACATACTTC 58.597 43.478 0.00 0.00 32.96 3.01
751 752 3.190535 GGGCGTGTTTGATTGACATACTT 59.809 43.478 0.00 0.00 32.96 2.24
752 753 2.747446 GGGCGTGTTTGATTGACATACT 59.253 45.455 0.00 0.00 32.96 2.12
786 787 8.608844 ACTGAATTTTATCCTAGGCTATTTCG 57.391 34.615 2.96 3.42 0.00 3.46
948 958 1.709115 AGGGTTAGGGGAGGTTTTCAC 59.291 52.381 0.00 0.00 0.00 3.18
949 959 1.990327 GAGGGTTAGGGGAGGTTTTCA 59.010 52.381 0.00 0.00 0.00 2.69
950 960 1.990327 TGAGGGTTAGGGGAGGTTTTC 59.010 52.381 0.00 0.00 0.00 2.29
951 961 2.143231 TGAGGGTTAGGGGAGGTTTT 57.857 50.000 0.00 0.00 0.00 2.43
952 962 2.206223 GATGAGGGTTAGGGGAGGTTT 58.794 52.381 0.00 0.00 0.00 3.27
953 963 1.894699 GATGAGGGTTAGGGGAGGTT 58.105 55.000 0.00 0.00 0.00 3.50
1611 1621 2.630098 GTCATCCGGGAAGATCTCATGA 59.370 50.000 5.12 0.00 0.00 3.07
1926 1936 1.883021 GCCCATTTGTCGGAACAGG 59.117 57.895 0.00 0.00 36.57 4.00
2031 2041 2.684881 AGACCGCATCCAAATCATCAAC 59.315 45.455 0.00 0.00 0.00 3.18
2073 2083 4.713824 TCCATAATACGCCTTCCTATCG 57.286 45.455 0.00 0.00 0.00 2.92
2094 2104 7.399765 TCAATCCCACATAAAACCTTGATGAAT 59.600 33.333 0.00 0.00 0.00 2.57
2566 2579 5.008712 GGATATGCTACTGGTTAAAACAGCC 59.991 44.000 1.56 0.00 39.55 4.85
2655 2668 7.040409 AGTGTAAGATTCCATGAAGTTCCAAAC 60.040 37.037 0.00 0.00 0.00 2.93
2802 2815 4.568359 CGTTTCTCACATAGATGAAGGTGG 59.432 45.833 0.00 0.00 33.05 4.61
2839 2852 5.343249 CCCTAGCCAAAATTTCTCATTTCG 58.657 41.667 0.00 0.00 0.00 3.46
3019 3032 3.368248 ACCACAAATAGCAGGCATGAAT 58.632 40.909 0.62 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.