Multiple sequence alignment - TraesCS5B01G562300

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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 TraesCS5B01G562300 chr5B 100.000 3614 0 0 1 3614 708240769 708237156 0.000000e+00 6674.0
1 TraesCS5B01G562300 chr4A 91.419 3030 132 47 672 3611 606523164 606526155 0.000000e+00 4037.0
2 TraesCS5B01G562300 chr4A 90.476 630 40 8 1 618 606522535 606523156 0.000000e+00 813.0
3 TraesCS5B01G562300 chr5D 96.002 2051 55 7 798 2828 565050038 565052081 0.000000e+00 3308.0
4 TraesCS5B01G562300 chr5D 91.983 711 41 10 1 704 565049180 565049881 0.000000e+00 983.0
5 TraesCS5B01G562300 chr5D 89.050 621 32 16 2992 3611 565052145 565052730 0.000000e+00 737.0
6 TraesCS5B01G562300 chr5D 100.000 28 0 0 2953 2980 565052118 565052145 7.000000e-03 52.8
7 TraesCS5B01G562300 chr6D 91.398 93 7 1 2825 2917 122992104 122992195 3.790000e-25 126.0
8 TraesCS5B01G562300 chr2A 89.899 99 9 1 2815 2913 385002800 385002703 3.790000e-25 126.0
9 TraesCS5B01G562300 chr6A 91.860 86 7 0 2827 2912 548408145 548408060 1.760000e-23 121.0
10 TraesCS5B01G562300 chr6B 94.737 76 4 0 2827 2902 602828620 602828545 6.340000e-23 119.0
11 TraesCS5B01G562300 chr3D 88.660 97 9 2 2820 2914 496737779 496737683 2.280000e-22 117.0
12 TraesCS5B01G562300 chr3D 91.566 83 4 3 2823 2905 516868176 516868097 1.060000e-20 111.0
13 TraesCS5B01G562300 chr2B 90.110 91 8 1 2824 2913 394722947 394723037 2.280000e-22 117.0
14 TraesCS5B01G562300 chr7B 87.500 96 11 1 2825 2919 552011765 552011860 3.820000e-20 110.0


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 TraesCS5B01G562300 chr5B 708237156 708240769 3613 True 6674.0 6674 100.00000 1 3614 1 chr5B.!!$R1 3613
1 TraesCS5B01G562300 chr4A 606522535 606526155 3620 False 2425.0 4037 90.94750 1 3611 2 chr4A.!!$F1 3610
2 TraesCS5B01G562300 chr5D 565049180 565052730 3550 False 1270.2 3308 94.25875 1 3611 4 chr5D.!!$F1 3610

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
22 23 0.317160 AAGATTCAGCCGACGTCACA 59.683 50.000 17.16 0.00 0.00 3.58 F
140 146 1.071542 TCACTCTCCGGATTTGTGCAA 59.928 47.619 20.12 7.47 0.00 4.08 F
942 1027 1.455587 ACACACCAAGGCAAGTGGG 60.456 57.895 6.80 4.81 43.25 4.61 F
1071 1156 1.585006 GAAGCCGTCGTCTTCTGGA 59.415 57.895 8.71 0.00 37.53 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1140 1225 3.640407 TGGAGCAGCCTGGACACC 61.640 66.667 0.0 0.0 37.63 4.16 R
1913 1998 4.069232 CGCTCTGGGCAACGAGGA 62.069 66.667 0.0 0.0 43.61 3.71 R
2581 2684 0.451783 CTTACTGTTCCATTGCCGCC 59.548 55.000 0.0 0.0 0.00 6.13 R
2999 3137 1.071314 TGTGGTGATGGAGGGGGTTT 61.071 55.000 0.0 0.0 0.00 3.27 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
22 23 0.317160 AAGATTCAGCCGACGTCACA 59.683 50.000 17.16 0.00 0.00 3.58
73 74 1.267261 CCCTCCTCGTCGACATGATAC 59.733 57.143 17.16 0.00 0.00 2.24
85 86 5.119279 GTCGACATGATACAGAACATATGCC 59.881 44.000 11.55 0.00 0.00 4.40
140 146 1.071542 TCACTCTCCGGATTTGTGCAA 59.928 47.619 20.12 7.47 0.00 4.08
158 164 5.401972 TGTGCAACTATTTTTCGCTGATTTG 59.598 36.000 0.00 0.00 38.04 2.32
169 175 8.736751 TTTTTCGCTGATTTGGTAGTATTTTC 57.263 30.769 0.00 0.00 0.00 2.29
170 176 7.441890 TTTCGCTGATTTGGTAGTATTTTCA 57.558 32.000 0.00 0.00 0.00 2.69
314 324 2.036387 CCCGGTGGTATGATCTACACA 58.964 52.381 0.00 0.00 35.62 3.72
361 371 1.701847 AGCAGAGGTTGACACTCCATT 59.298 47.619 0.00 0.00 35.58 3.16
517 528 2.997986 CCTACCACGCGTTTACAAATCT 59.002 45.455 10.22 0.00 0.00 2.40
525 536 5.907391 CACGCGTTTACAAATCTTTCTTTCT 59.093 36.000 10.22 0.00 0.00 2.52
526 537 6.413818 CACGCGTTTACAAATCTTTCTTTCTT 59.586 34.615 10.22 0.00 0.00 2.52
527 538 6.970613 ACGCGTTTACAAATCTTTCTTTCTTT 59.029 30.769 5.58 0.00 0.00 2.52
528 539 7.165318 ACGCGTTTACAAATCTTTCTTTCTTTC 59.835 33.333 5.58 0.00 0.00 2.62
647 661 2.097954 TCAATCGGTTCATGCTTCATGC 59.902 45.455 2.12 0.00 41.18 4.06
664 678 6.441093 TTCATGCTCACATTTAGGAATGAC 57.559 37.500 6.17 0.00 44.37 3.06
667 681 2.032178 GCTCACATTTAGGAATGACGCC 59.968 50.000 6.17 0.00 44.37 5.68
668 682 3.270027 CTCACATTTAGGAATGACGCCA 58.730 45.455 6.17 0.00 44.37 5.69
687 701 3.825308 CCATCATCAACCTTTTCACACG 58.175 45.455 0.00 0.00 0.00 4.49
698 712 2.473451 TTTCACACGTGCGCGATTCG 62.473 55.000 28.73 13.49 42.00 3.34
714 728 4.854399 CGATTCGCACTCTAGATCTTTCT 58.146 43.478 0.00 0.00 35.90 2.52
848 928 5.786457 TCCTTCCCCAATAGTGTTGTACTAA 59.214 40.000 0.00 0.00 44.64 2.24
942 1027 1.455587 ACACACCAAGGCAAGTGGG 60.456 57.895 6.80 4.81 43.25 4.61
1071 1156 1.585006 GAAGCCGTCGTCTTCTGGA 59.415 57.895 8.71 0.00 37.53 3.86
1140 1225 3.965539 CTTCGAGGTGGCCAGCCTG 62.966 68.421 30.76 22.71 36.29 4.85
1260 1345 2.202453 GACGACGACGCCTTCCTC 60.202 66.667 7.30 0.00 43.96 3.71
1377 1462 4.742201 TTCAGGGACGCGCTGCTC 62.742 66.667 5.73 0.00 42.87 4.26
1509 1594 3.095163 AGGGCCATGGAGGAGCTG 61.095 66.667 18.40 0.00 41.22 4.24
1921 2006 4.695231 ACGTCGCCGTCCTCGTTG 62.695 66.667 0.00 0.00 46.28 4.10
2641 2744 0.322546 ATCAGAAACCAACGGCCCTC 60.323 55.000 0.00 0.00 0.00 4.30
2643 2746 0.609131 CAGAAACCAACGGCCCTCAT 60.609 55.000 0.00 0.00 0.00 2.90
2644 2747 0.322546 AGAAACCAACGGCCCTCATC 60.323 55.000 0.00 0.00 0.00 2.92
2645 2748 0.608035 GAAACCAACGGCCCTCATCA 60.608 55.000 0.00 0.00 0.00 3.07
2646 2749 0.609131 AAACCAACGGCCCTCATCAG 60.609 55.000 0.00 0.00 0.00 2.90
2672 2775 4.753107 AGACATCCGTGTGTTTAATCGTTT 59.247 37.500 0.00 0.00 39.09 3.60
2678 2781 5.050634 TCCGTGTGTTTAATCGTTTCTCTTG 60.051 40.000 0.00 0.00 0.00 3.02
2771 2891 6.711277 TCTTGATGTGAGTGGTTAATTAGCT 58.289 36.000 0.00 0.00 0.00 3.32
2778 2898 8.039603 TGTGAGTGGTTAATTAGCTTGTAATG 57.960 34.615 0.00 0.00 0.00 1.90
2851 2978 6.708285 ACTACCTTCGATCCATAAAAAGTGT 58.292 36.000 0.00 0.00 0.00 3.55
2855 2982 3.591023 TCGATCCATAAAAAGTGTCGCA 58.409 40.909 0.00 0.00 0.00 5.10
2858 2985 4.651994 GATCCATAAAAAGTGTCGCAGTG 58.348 43.478 0.00 0.00 0.00 3.66
2861 2988 3.974401 CCATAAAAAGTGTCGCAGTGTTG 59.026 43.478 0.00 0.00 0.00 3.33
2870 2997 1.529865 GTCGCAGTGTTGAACTAACCC 59.470 52.381 0.00 0.00 36.83 4.11
2902 3040 1.326245 TGCGACGCTTATTTTGGATCG 59.674 47.619 22.08 0.00 0.00 3.69
2905 3043 2.800544 CGACGCTTATTTTGGATCGGAT 59.199 45.455 0.00 0.00 0.00 4.18
2910 3048 4.273480 CGCTTATTTTGGATCGGATGAAGT 59.727 41.667 0.00 0.00 0.00 3.01
2988 3126 3.831333 TGGTGAACCAACATACATGCATT 59.169 39.130 0.00 0.00 44.35 3.56
2999 3137 7.415429 CCAACATACATGCATTTGTGTCTGATA 60.415 37.037 14.56 0.00 0.00 2.15
3002 3140 7.970061 ACATACATGCATTTGTGTCTGATAAAC 59.030 33.333 9.19 0.00 0.00 2.01
3032 3170 0.687354 ACCACAGACAGCAACCCTAG 59.313 55.000 0.00 0.00 0.00 3.02
3086 3224 0.328926 TGATGCATCTGTGAGCCCAA 59.671 50.000 26.32 0.00 0.00 4.12
3147 3285 3.066342 CCAAGGATGTAGATTTGCTGCTG 59.934 47.826 0.00 0.00 0.00 4.41
3150 3288 2.033049 GGATGTAGATTTGCTGCTGCTG 59.967 50.000 17.00 0.77 40.48 4.41
3151 3289 0.806868 TGTAGATTTGCTGCTGCTGC 59.193 50.000 22.51 22.51 40.48 5.25
3152 3290 1.093159 GTAGATTTGCTGCTGCTGCT 58.907 50.000 27.67 11.62 40.48 4.24
3153 3291 1.092348 TAGATTTGCTGCTGCTGCTG 58.908 50.000 27.67 16.73 40.48 4.41
3177 3322 6.652900 TGCTGCTCAACAAGTTGTTACATATA 59.347 34.615 20.47 5.42 38.77 0.86
3179 3324 7.852945 GCTGCTCAACAAGTTGTTACATATATC 59.147 37.037 20.47 5.69 38.77 1.63
3180 3325 9.102757 CTGCTCAACAAGTTGTTACATATATCT 57.897 33.333 20.47 0.00 38.77 1.98
3201 3364 6.732896 TCTAATCTACCCTTTCCATCTCAC 57.267 41.667 0.00 0.00 0.00 3.51
3205 3368 0.905357 ACCCTTTCCATCTCACCTCG 59.095 55.000 0.00 0.00 0.00 4.63
3221 3389 0.997932 CTCGTCTCATCAGCAGCAAC 59.002 55.000 0.00 0.00 0.00 4.17
3222 3390 0.605083 TCGTCTCATCAGCAGCAACT 59.395 50.000 0.00 0.00 0.00 3.16
3223 3391 1.001293 TCGTCTCATCAGCAGCAACTT 59.999 47.619 0.00 0.00 0.00 2.66
3224 3392 1.802960 CGTCTCATCAGCAGCAACTTT 59.197 47.619 0.00 0.00 0.00 2.66
3225 3393 2.412455 CGTCTCATCAGCAGCAACTTTG 60.412 50.000 0.00 0.00 0.00 2.77
3226 3394 2.551459 GTCTCATCAGCAGCAACTTTGT 59.449 45.455 0.00 0.00 0.00 2.83
3243 3411 6.391227 ACTTTGTAAGTTGCTGCTAATTGT 57.609 33.333 7.01 0.00 39.04 2.71
3244 3412 6.805713 ACTTTGTAAGTTGCTGCTAATTGTT 58.194 32.000 7.01 0.00 39.04 2.83
3245 3413 7.936584 ACTTTGTAAGTTGCTGCTAATTGTTA 58.063 30.769 7.01 0.00 39.04 2.41
3246 3414 8.410141 ACTTTGTAAGTTGCTGCTAATTGTTAA 58.590 29.630 7.01 0.00 39.04 2.01
3247 3415 9.243637 CTTTGTAAGTTGCTGCTAATTGTTAAA 57.756 29.630 7.01 5.16 0.00 1.52
3280 3448 2.361610 GAGGGTGCATGTGGTGGG 60.362 66.667 0.00 0.00 0.00 4.61
3286 3458 1.228215 TGCATGTGGTGGGTGTGAG 60.228 57.895 0.00 0.00 0.00 3.51
3287 3459 1.228245 GCATGTGGTGGGTGTGAGT 60.228 57.895 0.00 0.00 0.00 3.41
3288 3460 1.518056 GCATGTGGTGGGTGTGAGTG 61.518 60.000 0.00 0.00 0.00 3.51
3289 3461 0.108396 CATGTGGTGGGTGTGAGTGA 59.892 55.000 0.00 0.00 0.00 3.41
3290 3462 0.397941 ATGTGGTGGGTGTGAGTGAG 59.602 55.000 0.00 0.00 0.00 3.51
3451 3637 6.485984 ACTTGCAAGAGCCTGATTAATCTATG 59.514 38.462 32.50 6.13 41.13 2.23
3452 3638 5.933617 TGCAAGAGCCTGATTAATCTATGT 58.066 37.500 16.24 0.00 41.13 2.29
3453 3639 5.761726 TGCAAGAGCCTGATTAATCTATGTG 59.238 40.000 16.24 6.78 41.13 3.21
3454 3640 5.762218 GCAAGAGCCTGATTAATCTATGTGT 59.238 40.000 16.24 0.00 33.58 3.72
3455 3641 6.293298 GCAAGAGCCTGATTAATCTATGTGTG 60.293 42.308 16.24 7.75 33.58 3.82
3474 3660 1.946081 TGTGTGTGTATGTGGCAGTTG 59.054 47.619 0.00 0.00 0.00 3.16
3491 3677 4.757149 GCAGTTGAGTTGGAAGAACTATGT 59.243 41.667 0.00 0.00 0.00 2.29
3503 3689 6.326323 TGGAAGAACTATGTATACCTGATGCA 59.674 38.462 0.00 0.00 34.35 3.96
3512 3698 3.862877 ATACCTGATGCAATGCACCTA 57.137 42.857 11.23 0.00 43.04 3.08
3513 3699 1.755179 ACCTGATGCAATGCACCTAC 58.245 50.000 11.23 3.33 43.04 3.18
3561 3747 5.481824 TGTGTTCATACAGTGGAAGATCTCT 59.518 40.000 0.00 0.00 34.24 3.10
3612 3798 3.077907 GCTCCCCACAGCTGGTTA 58.922 61.111 19.93 0.00 35.46 2.85
3613 3799 1.377333 GCTCCCCACAGCTGGTTAC 60.377 63.158 19.93 0.00 35.46 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.097722 AAGAGAGGAGAAGAGGGGGT 58.902 55.000 0.00 0.00 0.00 4.95
73 74 8.886719 ACGATATGATTTATGGCATATGTTCTG 58.113 33.333 8.24 0.00 37.71 3.02
127 133 4.323336 CGAAAAATAGTTGCACAAATCCGG 59.677 41.667 0.00 0.00 0.00 5.14
128 134 4.201485 GCGAAAAATAGTTGCACAAATCCG 60.201 41.667 0.00 0.00 0.00 4.18
140 146 8.732746 ATACTACCAAATCAGCGAAAAATAGT 57.267 30.769 0.00 0.00 0.00 2.12
184 190 0.664767 GAGGCGTAGGTGATCATCGC 60.665 60.000 20.62 20.62 44.95 4.58
185 191 0.955178 AGAGGCGTAGGTGATCATCG 59.045 55.000 0.00 3.58 0.00 3.84
249 259 3.638160 GCAAATCTTGGGGCTAATCATCA 59.362 43.478 0.00 0.00 0.00 3.07
250 260 3.893813 AGCAAATCTTGGGGCTAATCATC 59.106 43.478 0.00 0.00 34.25 2.92
294 304 2.036387 TGTGTAGATCATACCACCGGG 58.964 52.381 6.32 0.00 41.29 5.73
314 324 2.297033 GGACAATGACATGCCTTGTGTT 59.703 45.455 11.52 0.00 39.18 3.32
361 371 0.120377 AGTTGTAGGATGGTGGGGGA 59.880 55.000 0.00 0.00 0.00 4.81
453 463 7.812690 TGGTGCGTTATAGTAAGATCTAGAA 57.187 36.000 0.00 0.00 0.00 2.10
613 627 9.916397 CATGAACCGATTGATAGTTTTAGTAAC 57.084 33.333 0.00 0.00 0.00 2.50
618 632 7.335673 TGAAGCATGAACCGATTGATAGTTTTA 59.664 33.333 0.00 0.00 0.00 1.52
647 661 3.270027 TGGCGTCATTCCTAAATGTGAG 58.730 45.455 0.00 0.00 42.46 3.51
664 678 2.228582 TGTGAAAAGGTTGATGATGGCG 59.771 45.455 0.00 0.00 0.00 5.69
667 681 4.221342 CACGTGTGAAAAGGTTGATGATG 58.779 43.478 7.58 0.00 0.00 3.07
668 682 3.304659 GCACGTGTGAAAAGGTTGATGAT 60.305 43.478 18.38 0.00 0.00 2.45
698 712 7.761704 TGAATGTTGTAGAAAGATCTAGAGTGC 59.238 37.037 0.00 0.00 38.82 4.40
714 728 8.777865 TGGTTTGAAATGTTTTGAATGTTGTA 57.222 26.923 0.00 0.00 0.00 2.41
848 928 7.667219 TCAAAATGTTTCAAGAGCTTCCTATCT 59.333 33.333 0.00 0.00 0.00 1.98
930 1015 0.326264 AGAGCTACCCACTTGCCTTG 59.674 55.000 0.00 0.00 0.00 3.61
1140 1225 3.640407 TGGAGCAGCCTGGACACC 61.640 66.667 0.00 0.00 37.63 4.16
1913 1998 4.069232 CGCTCTGGGCAACGAGGA 62.069 66.667 0.00 0.00 43.61 3.71
2307 2392 1.009900 GGCTATGTCCGTCGTCGAG 60.010 63.158 2.98 0.00 39.71 4.04
2352 2446 0.880278 TCTGCAGCAGGAACGTGTTC 60.880 55.000 22.62 4.15 38.80 3.18
2430 2524 1.006571 CCGCCACACGTAGTTCAGT 60.007 57.895 0.00 0.00 41.61 3.41
2581 2684 0.451783 CTTACTGTTCCATTGCCGCC 59.548 55.000 0.00 0.00 0.00 6.13
2641 2744 2.265683 CACACGGATGTCTGACTGATG 58.734 52.381 9.51 3.47 36.72 3.07
2643 2746 1.328279 ACACACGGATGTCTGACTGA 58.672 50.000 9.51 0.00 36.72 3.41
2644 2747 2.154854 AACACACGGATGTCTGACTG 57.845 50.000 9.51 0.99 36.72 3.51
2645 2748 2.910688 AAACACACGGATGTCTGACT 57.089 45.000 9.51 0.00 36.72 3.41
2646 2749 4.201589 CGATTAAACACACGGATGTCTGAC 60.202 45.833 0.00 0.00 36.72 3.51
2672 2775 1.133606 GGGGGTGGACAAAACAAGAGA 60.134 52.381 0.00 0.00 0.00 3.10
2678 2781 2.670019 AACTAGGGGGTGGACAAAAC 57.330 50.000 0.00 0.00 0.00 2.43
2847 2974 2.864343 GTTAGTTCAACACTGCGACACT 59.136 45.455 0.00 0.00 35.97 3.55
2851 2978 1.541670 GGGGTTAGTTCAACACTGCGA 60.542 52.381 0.00 0.00 40.67 5.10
2855 2982 3.945640 AACTGGGGTTAGTTCAACACT 57.054 42.857 0.00 0.00 40.67 3.55
2888 3026 5.757850 ACTTCATCCGATCCAAAATAAGC 57.242 39.130 0.00 0.00 0.00 3.09
2940 3078 8.131847 TCATCTCTCATCTCTCTTCTTTTCAA 57.868 34.615 0.00 0.00 0.00 2.69
2941 3079 7.715266 TCATCTCTCATCTCTCTTCTTTTCA 57.285 36.000 0.00 0.00 0.00 2.69
2949 3087 5.064314 TCACCATCATCTCTCATCTCTCT 57.936 43.478 0.00 0.00 0.00 3.10
2950 3088 5.509501 GGTTCACCATCATCTCTCATCTCTC 60.510 48.000 0.00 0.00 35.64 3.20
2951 3089 4.344679 GGTTCACCATCATCTCTCATCTCT 59.655 45.833 0.00 0.00 35.64 3.10
2988 3126 2.307686 GGAGGGGGTTTATCAGACACAA 59.692 50.000 0.00 0.00 0.00 3.33
2999 3137 1.071314 TGTGGTGATGGAGGGGGTTT 61.071 55.000 0.00 0.00 0.00 3.27
3002 3140 1.616327 TCTGTGGTGATGGAGGGGG 60.616 63.158 0.00 0.00 0.00 5.40
3032 3170 3.060602 GCTCACTTCAACTGGTGTAGTC 58.939 50.000 1.66 0.00 39.18 2.59
3147 3285 1.081376 CTTGTTGAGCAGCAGCAGC 60.081 57.895 3.17 0.46 45.49 5.25
3150 3288 0.383231 ACAACTTGTTGAGCAGCAGC 59.617 50.000 18.82 0.00 42.56 5.25
3151 3289 2.857592 AACAACTTGTTGAGCAGCAG 57.142 45.000 18.82 0.00 39.45 4.24
3152 3290 3.013219 TGTAACAACTTGTTGAGCAGCA 58.987 40.909 18.82 8.15 41.30 4.41
3153 3291 3.691049 TGTAACAACTTGTTGAGCAGC 57.309 42.857 18.82 6.10 41.30 5.25
3154 3292 9.102757 AGATATATGTAACAACTTGTTGAGCAG 57.897 33.333 18.82 0.00 41.30 4.24
3177 3322 6.271159 GGTGAGATGGAAAGGGTAGATTAGAT 59.729 42.308 0.00 0.00 0.00 1.98
3179 3324 5.604650 AGGTGAGATGGAAAGGGTAGATTAG 59.395 44.000 0.00 0.00 0.00 1.73
3180 3325 5.538877 AGGTGAGATGGAAAGGGTAGATTA 58.461 41.667 0.00 0.00 0.00 1.75
3181 3326 4.375313 AGGTGAGATGGAAAGGGTAGATT 58.625 43.478 0.00 0.00 0.00 2.40
3182 3327 3.970640 GAGGTGAGATGGAAAGGGTAGAT 59.029 47.826 0.00 0.00 0.00 1.98
3184 3329 2.101582 CGAGGTGAGATGGAAAGGGTAG 59.898 54.545 0.00 0.00 0.00 3.18
3185 3330 2.108168 CGAGGTGAGATGGAAAGGGTA 58.892 52.381 0.00 0.00 0.00 3.69
3201 3364 0.108472 TTGCTGCTGATGAGACGAGG 60.108 55.000 0.00 0.00 0.00 4.63
3205 3368 2.551459 ACAAAGTTGCTGCTGATGAGAC 59.449 45.455 0.00 0.00 0.00 3.36
3221 3389 8.795786 TTAACAATTAGCAGCAACTTACAAAG 57.204 30.769 0.00 0.00 0.00 2.77
3222 3390 9.757227 ATTTAACAATTAGCAGCAACTTACAAA 57.243 25.926 0.00 0.00 0.00 2.83
3247 3415 9.985730 CATGCACCCTCATTATTTAACAATTAT 57.014 29.630 0.00 0.00 0.00 1.28
3280 3448 0.320247 CCTCCTGTGCTCACTCACAC 60.320 60.000 1.47 0.00 41.57 3.82
3286 3458 1.294780 CCTCACCTCCTGTGCTCAC 59.705 63.158 0.00 0.00 45.03 3.51
3287 3459 0.764369 AACCTCACCTCCTGTGCTCA 60.764 55.000 0.00 0.00 45.03 4.26
3288 3460 0.398318 AAACCTCACCTCCTGTGCTC 59.602 55.000 0.00 0.00 45.03 4.26
3289 3461 0.109342 CAAACCTCACCTCCTGTGCT 59.891 55.000 0.00 0.00 45.03 4.40
3290 3462 0.108585 TCAAACCTCACCTCCTGTGC 59.891 55.000 0.00 0.00 45.03 4.57
3396 3568 1.583556 TTCAGGGGCAGCTAGATTGA 58.416 50.000 0.00 0.00 0.00 2.57
3397 3569 2.158711 TGATTCAGGGGCAGCTAGATTG 60.159 50.000 0.00 0.00 0.00 2.67
3400 3576 0.833287 GTGATTCAGGGGCAGCTAGA 59.167 55.000 0.00 0.00 0.00 2.43
3409 3585 3.332919 CAAGTGTCTCTGTGATTCAGGG 58.667 50.000 0.00 0.00 45.46 4.45
3451 3637 1.264020 CTGCCACATACACACACACAC 59.736 52.381 0.00 0.00 0.00 3.82
3452 3638 1.134250 ACTGCCACATACACACACACA 60.134 47.619 0.00 0.00 0.00 3.72
3453 3639 1.593196 ACTGCCACATACACACACAC 58.407 50.000 0.00 0.00 0.00 3.82
3454 3640 1.946081 CAACTGCCACATACACACACA 59.054 47.619 0.00 0.00 0.00 3.72
3455 3641 2.217750 TCAACTGCCACATACACACAC 58.782 47.619 0.00 0.00 0.00 3.82
3474 3660 8.008513 TCAGGTATACATAGTTCTTCCAACTC 57.991 38.462 5.01 0.00 0.00 3.01
3491 3677 3.862877 AGGTGCATTGCATCAGGTATA 57.137 42.857 23.14 0.00 42.90 1.47
3503 3689 5.650703 GGTGTAAAATACAGGTAGGTGCATT 59.349 40.000 0.00 0.00 39.77 3.56
3561 3747 8.447200 AGGTACTGTAAATAAACAAAAGGGGTA 58.553 33.333 0.00 0.00 37.18 3.69


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

AutoCloner maintained by Alex Coulton.