Multiple sequence alignment - TraesCS2B01G194800

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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 TraesCS2B01G194800 chr2B 100.000 3095 0 0 1 3095 171796535 171793441 0.000000e+00 5716
1 TraesCS2B01G194800 chr2D 93.579 1978 71 13 38 1963 119380752 119378779 0.000000e+00 2898
2 TraesCS2B01G194800 chr2D 89.854 1025 47 20 2100 3090 119378503 119377502 0.000000e+00 1264
3 TraesCS2B01G194800 chr2D 96.377 138 4 1 1965 2101 119378740 119378603 3.110000e-55 226
4 TraesCS2B01G194800 chr2A 90.916 1233 81 21 899 2114 121596806 121595588 0.000000e+00 1628
5 TraesCS2B01G194800 chr2A 90.231 952 45 19 2169 3090 121595505 121594572 0.000000e+00 1199
6 TraesCS2B01G194800 chr6B 78.404 426 75 14 326 742 578777431 578777014 8.510000e-66 261


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 TraesCS2B01G194800 chr2B 171793441 171796535 3094 True 5716.000000 5716 100.0000 1 3095 1 chr2B.!!$R1 3094
1 TraesCS2B01G194800 chr2D 119377502 119380752 3250 True 1462.666667 2898 93.2700 38 3090 3 chr2D.!!$R1 3052
2 TraesCS2B01G194800 chr2A 121594572 121596806 2234 True 1413.500000 1628 90.5735 899 3090 2 chr2A.!!$R1 2191

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
190 191 0.250513 GCTCCGATCAAGGTGAAGGT 59.749 55.0 0.0 0.0 32.44 3.50 F
245 246 0.460284 CACTGGTGGATCGTGTAGCC 60.460 60.0 0.0 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1435 1.682257 GAAGCTGAGGTTGAGGCCT 59.318 57.895 3.86 3.86 42.53 5.19 R
2208 2434 1.610522 GCTCAGGCACATTGAAACAGT 59.389 47.619 0.00 0.00 38.54 3.55 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 5.628797 TGGTCATAATGCTTGTATGGAGA 57.371 39.130 0.00 0.00 31.13 3.71
23 24 6.000246 TGGTCATAATGCTTGTATGGAGAA 58.000 37.500 0.00 0.00 31.13 2.87
24 25 6.604171 TGGTCATAATGCTTGTATGGAGAAT 58.396 36.000 0.00 0.00 31.13 2.40
25 26 7.062322 TGGTCATAATGCTTGTATGGAGAATT 58.938 34.615 0.00 0.00 31.13 2.17
26 27 7.560991 TGGTCATAATGCTTGTATGGAGAATTT 59.439 33.333 0.00 0.00 31.13 1.82
27 28 9.066892 GGTCATAATGCTTGTATGGAGAATTTA 57.933 33.333 0.00 0.00 31.13 1.40
32 33 8.814038 AATGCTTGTATGGAGAATTTAGAGTT 57.186 30.769 0.00 0.00 0.00 3.01
33 34 7.615582 TGCTTGTATGGAGAATTTAGAGTTG 57.384 36.000 0.00 0.00 0.00 3.16
34 35 7.168219 TGCTTGTATGGAGAATTTAGAGTTGT 58.832 34.615 0.00 0.00 0.00 3.32
35 36 7.119699 TGCTTGTATGGAGAATTTAGAGTTGTG 59.880 37.037 0.00 0.00 0.00 3.33
36 37 7.414540 GCTTGTATGGAGAATTTAGAGTTGTGG 60.415 40.741 0.00 0.00 0.00 4.17
40 41 9.178758 GTATGGAGAATTTAGAGTTGTGGAATT 57.821 33.333 0.00 0.00 0.00 2.17
72 73 7.381766 TGATAAACATGTTCCACAAGAGATG 57.618 36.000 12.39 0.00 0.00 2.90
75 76 8.862325 ATAAACATGTTCCACAAGAGATGTTA 57.138 30.769 12.39 0.00 41.46 2.41
105 106 8.655651 TGAGTTTTTGGACAATTATTGGAAAC 57.344 30.769 9.88 10.83 34.12 2.78
133 134 1.063174 GCAAGCAAAGCGATACTCCAG 59.937 52.381 0.00 0.00 0.00 3.86
136 137 0.654683 GCAAAGCGATACTCCAGCAG 59.345 55.000 0.00 0.00 0.00 4.24
190 191 0.250513 GCTCCGATCAAGGTGAAGGT 59.749 55.000 0.00 0.00 32.44 3.50
201 202 2.357034 TGAAGGTGAAGCCGTCGC 60.357 61.111 0.00 0.00 46.77 5.19
218 219 2.910360 CTGATCCCCGTGGCATGA 59.090 61.111 8.63 0.00 0.00 3.07
245 246 0.460284 CACTGGTGGATCGTGTAGCC 60.460 60.000 0.00 0.00 0.00 3.93
251 252 1.068472 GTGGATCGTGTAGCCCTATCG 60.068 57.143 0.00 0.00 30.06 2.92
294 295 1.689984 TGATGGTTCAGCTGCAAACA 58.310 45.000 17.28 16.51 0.00 2.83
295 296 2.241160 TGATGGTTCAGCTGCAAACAT 58.759 42.857 21.71 21.71 0.00 2.71
303 304 4.794278 TCAGCTGCAAACATCATGATTT 57.206 36.364 9.47 0.00 0.00 2.17
348 349 0.527565 GTTTGCAGCCTACCATGTGG 59.472 55.000 0.00 0.00 42.17 4.17
367 368 3.742369 GTGGTTTTCAAGTGCAATGATGG 59.258 43.478 4.44 0.00 0.00 3.51
372 373 1.894466 TCAAGTGCAATGATGGGTTGG 59.106 47.619 0.00 0.00 0.00 3.77
431 432 2.165030 GGCCATCCAACACTCAGAATTG 59.835 50.000 0.00 0.00 0.00 2.32
449 450 1.107945 TGCCGATTATCGTCCAGTCA 58.892 50.000 13.73 0.00 38.40 3.41
470 471 4.277174 TCAGATTCTTCTAAGGCTCTAGCG 59.723 45.833 0.00 0.00 43.26 4.26
475 476 1.524848 TCTAAGGCTCTAGCGATCCG 58.475 55.000 0.00 0.00 43.26 4.18
478 479 0.885196 AAGGCTCTAGCGATCCGATC 59.115 55.000 0.00 0.00 43.26 3.69
537 538 2.352342 GCAGCAGAGATCAAAGCTCTTC 59.648 50.000 0.00 0.00 40.60 2.87
572 573 5.106515 GGAGTTTATTCCACAGAAGCTCAAC 60.107 44.000 0.00 0.00 37.20 3.18
586 587 6.599244 CAGAAGCTCAACAGGGAACATAATAA 59.401 38.462 0.00 0.00 0.00 1.40
597 603 5.375655 AGGGAACATAATAAGGTAGCCCATT 59.624 40.000 0.00 0.00 36.88 3.16
629 635 7.545965 GCTTGTACATATGAAGTCTTGTACTGT 59.454 37.037 10.38 4.02 42.98 3.55
654 660 3.121019 CTCCTTAGAGGTCCGCCG 58.879 66.667 0.00 0.00 40.50 6.46
663 669 0.527817 GAGGTCCGCCGTGTATCAAG 60.528 60.000 0.00 0.00 40.50 3.02
725 731 4.082408 GGAACAAAACTCCTATTTTCCCCG 60.082 45.833 0.00 0.00 29.17 5.73
729 735 0.988832 ACTCCTATTTTCCCCGCACA 59.011 50.000 0.00 0.00 0.00 4.57
730 736 1.353022 ACTCCTATTTTCCCCGCACAA 59.647 47.619 0.00 0.00 0.00 3.33
731 737 2.017049 CTCCTATTTTCCCCGCACAAG 58.983 52.381 0.00 0.00 0.00 3.16
756 762 5.941788 AGAAAAAGTGGCTCTTCTCCTTAA 58.058 37.500 1.81 0.00 35.02 1.85
794 800 2.672874 GAGCGAGTACATGAATGCACAA 59.327 45.455 0.00 0.00 0.00 3.33
889 895 3.344515 GCCAAAGGTACGGAGAAAATCT 58.655 45.455 0.00 0.00 0.00 2.40
890 896 3.127030 GCCAAAGGTACGGAGAAAATCTG 59.873 47.826 0.00 0.00 40.48 2.90
891 897 4.575885 CCAAAGGTACGGAGAAAATCTGA 58.424 43.478 0.00 0.00 37.76 3.27
892 898 5.186198 CCAAAGGTACGGAGAAAATCTGAT 58.814 41.667 0.00 0.00 37.76 2.90
894 900 4.308899 AGGTACGGAGAAAATCTGATCG 57.691 45.455 0.00 0.00 37.76 3.69
895 901 3.068307 AGGTACGGAGAAAATCTGATCGG 59.932 47.826 0.00 0.00 37.76 4.18
896 902 3.067742 GGTACGGAGAAAATCTGATCGGA 59.932 47.826 6.72 6.72 37.76 4.55
898 904 2.761208 ACGGAGAAAATCTGATCGGAGT 59.239 45.455 10.61 4.24 37.76 3.85
899 905 3.952323 ACGGAGAAAATCTGATCGGAGTA 59.048 43.478 10.61 0.00 37.76 2.59
900 906 4.036971 ACGGAGAAAATCTGATCGGAGTAG 59.963 45.833 10.61 0.00 37.76 2.57
902 908 4.303282 GAGAAAATCTGATCGGAGTAGCC 58.697 47.826 10.61 0.80 0.00 3.93
903 909 3.964031 AGAAAATCTGATCGGAGTAGCCT 59.036 43.478 10.61 3.05 0.00 4.58
941 976 0.801251 GAACTAGCAGCACAAGCCAG 59.199 55.000 0.00 0.00 43.56 4.85
953 988 3.005791 GCACAAGCCAGGAACTTATGTTT 59.994 43.478 0.00 0.00 34.60 2.83
1310 1347 4.728102 CTCCACGCGGCGTTACCA 62.728 66.667 27.24 8.71 38.32 3.25
1659 1696 2.759795 GAGGCCACCTCCTTGCTT 59.240 61.111 5.01 0.00 44.36 3.91
1844 1881 3.382832 CTCCGGCGACCAAGGAGT 61.383 66.667 9.30 0.00 44.79 3.85
1944 1996 0.738412 GGTAAGCCGTACACGCATGT 60.738 55.000 4.87 0.00 43.30 3.21
1956 2009 5.177142 CGTACACGCATGTATCTAGTAGAGT 59.823 44.000 5.98 0.00 43.21 3.24
1963 2045 7.078851 CGCATGTATCTAGTAGAGTTCGAATT 58.921 38.462 0.00 0.00 0.00 2.17
2020 2114 5.518848 TGCAAAATGTGTTCAAGTGATCT 57.481 34.783 0.00 0.00 0.00 2.75
2056 2150 1.805869 CATGGAGATCGAAGGATGGC 58.194 55.000 0.00 0.00 31.51 4.40
2058 2152 1.427809 TGGAGATCGAAGGATGGCAT 58.572 50.000 0.00 0.00 31.51 4.40
2143 2339 1.640428 GACAATCCGATTCGTCTGCA 58.360 50.000 5.20 0.00 0.00 4.41
2149 2345 0.302890 CCGATTCGTCTGCATCAAGC 59.697 55.000 5.20 0.00 45.96 4.01
2167 2391 0.729116 GCATGTGCTAATGTGCTCGT 59.271 50.000 0.00 0.00 38.21 4.18
2207 2433 4.156556 TCAATTTGGCGAGAAAATCTCCAG 59.843 41.667 1.98 0.00 43.60 3.86
2208 2434 3.417069 TTTGGCGAGAAAATCTCCAGA 57.583 42.857 1.98 0.00 43.60 3.86
2245 2471 5.476752 CTGAGCTTATTTTACAGGACAGC 57.523 43.478 0.00 0.00 0.00 4.40
2283 2512 5.819901 TGCCCAAAAATTTGACGAGAAAATT 59.180 32.000 7.44 0.00 40.55 1.82
2325 2560 8.349568 ACTTTAATCCAGTTAACAGGAAATCC 57.650 34.615 21.99 0.00 35.11 3.01
2345 2595 4.085733 TCCCACATGGAAAATCAACGAAT 58.914 39.130 0.00 0.00 41.40 3.34
2349 2599 3.195396 ACATGGAAAATCAACGAATGGGG 59.805 43.478 0.00 0.00 0.00 4.96
2405 2655 3.855950 CGAACCACGGTTACTAGAACATC 59.144 47.826 0.34 0.00 38.60 3.06
2452 2702 2.676232 CCTCTGCAAGGGTCTCTCA 58.324 57.895 6.96 0.00 42.03 3.27
2461 2711 3.875369 GCAAGGGTCTCTCATCACCAAAT 60.875 47.826 0.00 0.00 33.91 2.32
2469 2719 6.045955 GTCTCTCATCACCAAATCTAGGAAC 58.954 44.000 0.00 0.00 0.00 3.62
2510 2760 0.109919 GGCCAAGGCGAAAACTTACG 60.110 55.000 4.80 0.00 43.06 3.18
2514 2764 0.535553 AAGGCGAAAACTTACGGGCA 60.536 50.000 0.00 0.00 0.00 5.36
2533 2783 2.094675 CACAGGAAGGGCAAGTTATGG 58.905 52.381 0.00 0.00 0.00 2.74
2534 2784 1.005924 ACAGGAAGGGCAAGTTATGGG 59.994 52.381 0.00 0.00 0.00 4.00
2535 2785 1.284785 CAGGAAGGGCAAGTTATGGGA 59.715 52.381 0.00 0.00 0.00 4.37
2536 2786 2.000048 AGGAAGGGCAAGTTATGGGAA 59.000 47.619 0.00 0.00 0.00 3.97
2537 2787 2.024941 AGGAAGGGCAAGTTATGGGAAG 60.025 50.000 0.00 0.00 0.00 3.46
2538 2788 2.379005 GAAGGGCAAGTTATGGGAAGG 58.621 52.381 0.00 0.00 0.00 3.46
2539 2789 1.382914 AGGGCAAGTTATGGGAAGGT 58.617 50.000 0.00 0.00 0.00 3.50
2542 2792 1.005450 GGCAAGTTATGGGAAGGTGGA 59.995 52.381 0.00 0.00 0.00 4.02
2549 2799 4.041691 AGTTATGGGAAGGTGGATTATCCG 59.958 45.833 6.77 0.00 40.17 4.18
2562 2812 6.239232 GGTGGATTATCCGACAATACTGTACT 60.239 42.308 6.77 0.00 40.17 2.73
2653 2904 1.426251 TTGACAGGGGATGTGCCTGT 61.426 55.000 0.00 0.00 44.17 4.00
2663 2914 0.393402 ATGTGCCTGTGATGCGATGT 60.393 50.000 0.00 0.00 0.00 3.06
2860 3125 0.107508 ACAAGCAGATCACCATCCCG 60.108 55.000 0.00 0.00 0.00 5.14
2861 3126 0.178767 CAAGCAGATCACCATCCCGA 59.821 55.000 0.00 0.00 0.00 5.14
2912 3177 0.179056 AGTTATGCCCACCGAATCCG 60.179 55.000 0.00 0.00 0.00 4.18
3048 3313 9.868277 GAGCTCTAGTGATATATTACTGCAAAT 57.132 33.333 17.95 3.99 0.00 2.32
3065 3330 8.483307 ACTGCAAATTTTGTTCATTCATATCC 57.517 30.769 10.65 0.00 0.00 2.59
3091 3356 9.482627 CTAGCTTATTTAGTGCTAGCAAATACT 57.517 33.333 21.29 14.75 46.06 2.12
3092 3357 8.371770 AGCTTATTTAGTGCTAGCAAATACTC 57.628 34.615 21.29 12.86 35.05 2.59
3093 3358 7.442666 AGCTTATTTAGTGCTAGCAAATACTCC 59.557 37.037 21.29 4.93 35.05 3.85
3094 3359 7.308049 GCTTATTTAGTGCTAGCAAATACTCCC 60.308 40.741 21.29 4.10 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.516198 AATTCTCCATACAAGCATTATGACC 57.484 36.000 0.00 0.00 0.00 4.02
6 7 9.905713 AACTCTAAATTCTCCATACAAGCATTA 57.094 29.630 0.00 0.00 0.00 1.90
7 8 8.680903 CAACTCTAAATTCTCCATACAAGCATT 58.319 33.333 0.00 0.00 0.00 3.56
8 9 7.831193 ACAACTCTAAATTCTCCATACAAGCAT 59.169 33.333 0.00 0.00 0.00 3.79
9 10 7.119699 CACAACTCTAAATTCTCCATACAAGCA 59.880 37.037 0.00 0.00 0.00 3.91
10 11 7.414540 CCACAACTCTAAATTCTCCATACAAGC 60.415 40.741 0.00 0.00 0.00 4.01
11 12 7.824289 TCCACAACTCTAAATTCTCCATACAAG 59.176 37.037 0.00 0.00 0.00 3.16
12 13 7.685481 TCCACAACTCTAAATTCTCCATACAA 58.315 34.615 0.00 0.00 0.00 2.41
13 14 7.252612 TCCACAACTCTAAATTCTCCATACA 57.747 36.000 0.00 0.00 0.00 2.29
14 15 8.738645 ATTCCACAACTCTAAATTCTCCATAC 57.261 34.615 0.00 0.00 0.00 2.39
15 16 9.753674 AAATTCCACAACTCTAAATTCTCCATA 57.246 29.630 0.00 0.00 0.00 2.74
16 17 8.526147 CAAATTCCACAACTCTAAATTCTCCAT 58.474 33.333 0.00 0.00 0.00 3.41
17 18 7.039784 CCAAATTCCACAACTCTAAATTCTCCA 60.040 37.037 0.00 0.00 0.00 3.86
18 19 7.315890 CCAAATTCCACAACTCTAAATTCTCC 58.684 38.462 0.00 0.00 0.00 3.71
19 20 6.808704 GCCAAATTCCACAACTCTAAATTCTC 59.191 38.462 0.00 0.00 0.00 2.87
20 21 6.494835 AGCCAAATTCCACAACTCTAAATTCT 59.505 34.615 0.00 0.00 0.00 2.40
21 22 6.691508 AGCCAAATTCCACAACTCTAAATTC 58.308 36.000 0.00 0.00 0.00 2.17
22 23 6.267471 TGAGCCAAATTCCACAACTCTAAATT 59.733 34.615 0.00 0.00 0.00 1.82
23 24 5.774690 TGAGCCAAATTCCACAACTCTAAAT 59.225 36.000 0.00 0.00 0.00 1.40
24 25 5.136828 TGAGCCAAATTCCACAACTCTAAA 58.863 37.500 0.00 0.00 0.00 1.85
25 26 4.724399 TGAGCCAAATTCCACAACTCTAA 58.276 39.130 0.00 0.00 0.00 2.10
26 27 4.365514 TGAGCCAAATTCCACAACTCTA 57.634 40.909 0.00 0.00 0.00 2.43
27 28 3.228188 TGAGCCAAATTCCACAACTCT 57.772 42.857 0.00 0.00 0.00 3.24
28 29 3.507233 TCATGAGCCAAATTCCACAACTC 59.493 43.478 0.00 0.00 0.00 3.01
29 30 3.499338 TCATGAGCCAAATTCCACAACT 58.501 40.909 0.00 0.00 0.00 3.16
30 31 3.940209 TCATGAGCCAAATTCCACAAC 57.060 42.857 0.00 0.00 0.00 3.32
31 32 6.014755 TGTTTATCATGAGCCAAATTCCACAA 60.015 34.615 0.09 0.00 0.00 3.33
32 33 5.479724 TGTTTATCATGAGCCAAATTCCACA 59.520 36.000 0.09 0.00 0.00 4.17
33 34 5.964758 TGTTTATCATGAGCCAAATTCCAC 58.035 37.500 0.09 0.00 0.00 4.02
34 35 6.795144 ATGTTTATCATGAGCCAAATTCCA 57.205 33.333 0.09 0.00 35.19 3.53
63 64 7.823745 AAAACTCAACCATAACATCTCTTGT 57.176 32.000 0.00 0.00 41.53 3.16
72 73 9.705290 ATAATTGTCCAAAAACTCAACCATAAC 57.295 29.630 0.00 0.00 0.00 1.89
75 76 7.661027 CCAATAATTGTCCAAAAACTCAACCAT 59.339 33.333 0.00 0.00 0.00 3.55
105 106 1.199789 TCGCTTTGCTTGCACAATAGG 59.800 47.619 0.00 0.00 0.00 2.57
133 134 2.838736 TCCCTTTAATCATCTCGCTGC 58.161 47.619 0.00 0.00 0.00 5.25
136 137 3.001330 CACGTTCCCTTTAATCATCTCGC 59.999 47.826 0.00 0.00 0.00 5.03
201 202 1.524621 GTCATGCCACGGGGATCAG 60.525 63.158 8.67 0.00 29.13 2.90
211 212 1.229625 AGTGGAGGAGGTCATGCCA 60.230 57.895 8.58 0.00 40.61 4.92
251 252 6.834168 TTAGAAGAAAATGACCCATCAACC 57.166 37.500 0.00 0.00 38.69 3.77
294 295 5.292834 CACTAGCACGTCTCAAAATCATGAT 59.707 40.000 1.18 1.18 0.00 2.45
295 296 4.627035 CACTAGCACGTCTCAAAATCATGA 59.373 41.667 0.00 0.00 0.00 3.07
303 304 4.988065 GCCACTAGCACGTCTCAA 57.012 55.556 0.00 0.00 42.97 3.02
322 323 1.599518 TAGGCTGCAAACACCACCG 60.600 57.895 0.50 0.00 0.00 4.94
348 349 3.993920 ACCCATCATTGCACTTGAAAAC 58.006 40.909 2.84 0.00 0.00 2.43
367 368 2.098770 GCATGAATCTCTGCTTCCAACC 59.901 50.000 0.00 0.00 35.49 3.77
372 373 3.268330 TGAGTGCATGAATCTCTGCTTC 58.732 45.455 0.00 7.68 39.16 3.86
449 450 4.465886 TCGCTAGAGCCTTAGAAGAATCT 58.534 43.478 0.00 0.00 37.45 2.40
470 471 4.506886 AAGGTTATCACTCGATCGGATC 57.493 45.455 16.41 7.95 32.73 3.36
475 476 5.420409 ACCTGAAAAGGTTATCACTCGATC 58.580 41.667 0.00 0.00 39.57 3.69
478 479 3.933332 GGACCTGAAAAGGTTATCACTCG 59.067 47.826 0.00 0.00 43.24 4.18
479 480 3.933332 CGGACCTGAAAAGGTTATCACTC 59.067 47.826 0.00 0.00 43.24 3.51
537 538 4.471386 TGGAATAAACTCCCTCTCTTCCTG 59.529 45.833 0.00 0.00 34.22 3.86
551 552 5.335191 CCTGTTGAGCTTCTGTGGAATAAAC 60.335 44.000 0.00 0.00 0.00 2.01
572 573 4.104102 TGGGCTACCTTATTATGTTCCCTG 59.896 45.833 0.00 0.00 37.76 4.45
597 603 7.182817 AGACTTCATATGTACAAGCCAACTA 57.817 36.000 0.00 0.00 0.00 2.24
629 635 3.134081 CGGACCTCTAAGGAGCCAAATTA 59.866 47.826 0.00 0.00 37.67 1.40
654 660 5.675538 AGAGGCAATAACTCCTTGATACAC 58.324 41.667 0.00 0.00 35.58 2.90
663 669 7.573968 ATTACAATCAAGAGGCAATAACTCC 57.426 36.000 0.00 0.00 35.58 3.85
706 712 2.823154 TGCGGGGAAAATAGGAGTTTTG 59.177 45.455 0.00 0.00 31.80 2.44
725 731 3.067320 AGAGCCACTTTTTCTTCTTGTGC 59.933 43.478 0.00 0.00 0.00 4.57
731 737 4.393834 AGGAGAAGAGCCACTTTTTCTTC 58.606 43.478 5.55 5.55 44.45 2.87
889 895 1.341089 ACTGTGAGGCTACTCCGATCA 60.341 52.381 0.00 0.00 43.29 2.92
890 896 1.335496 GACTGTGAGGCTACTCCGATC 59.665 57.143 0.00 0.00 43.29 3.69
891 897 1.394618 GACTGTGAGGCTACTCCGAT 58.605 55.000 0.00 0.00 43.29 4.18
892 898 0.680280 GGACTGTGAGGCTACTCCGA 60.680 60.000 0.00 0.00 43.29 4.55
894 900 0.533032 GTGGACTGTGAGGCTACTCC 59.467 60.000 0.00 0.00 43.29 3.85
895 901 1.067495 GTGTGGACTGTGAGGCTACTC 60.067 57.143 0.00 0.00 35.50 2.59
896 902 0.969894 GTGTGGACTGTGAGGCTACT 59.030 55.000 0.00 0.00 35.50 2.57
898 904 0.679505 GTGTGTGGACTGTGAGGCTA 59.320 55.000 0.00 0.00 0.00 3.93
899 905 1.447643 GTGTGTGGACTGTGAGGCT 59.552 57.895 0.00 0.00 0.00 4.58
900 906 1.956170 CGTGTGTGGACTGTGAGGC 60.956 63.158 0.00 0.00 0.00 4.70
902 908 1.702886 GATCGTGTGTGGACTGTGAG 58.297 55.000 0.00 0.00 0.00 3.51
903 909 0.039527 CGATCGTGTGTGGACTGTGA 60.040 55.000 7.03 0.00 0.00 3.58
962 999 2.775384 TGGGTGTTCTACTGTTCTTGGT 59.225 45.455 0.00 0.00 0.00 3.67
1310 1347 2.151049 GACCGGAAGTACAGGTGCGT 62.151 60.000 9.46 0.00 46.35 5.24
1398 1435 1.682257 GAAGCTGAGGTTGAGGCCT 59.318 57.895 3.86 3.86 42.53 5.19
1527 1564 2.674754 GCCAATGGGGGAGACGAA 59.325 61.111 0.00 0.00 37.04 3.85
1844 1881 2.747460 GCTTGCCGCTCCATGTGA 60.747 61.111 0.00 0.00 35.14 3.58
1869 1906 3.781770 GAGATGCGTCTCCTGGCCG 62.782 68.421 23.14 0.00 44.20 6.13
1956 2009 6.595326 ACTTAGCAGATGATGAACAATTCGAA 59.405 34.615 0.00 0.00 0.00 3.71
1963 2045 3.273434 GCCACTTAGCAGATGATGAACA 58.727 45.455 0.00 0.00 0.00 3.18
2056 2150 2.620115 CCTCATCGAACCATTTCCCATG 59.380 50.000 0.00 0.00 0.00 3.66
2058 2152 1.912731 TCCTCATCGAACCATTTCCCA 59.087 47.619 0.00 0.00 0.00 4.37
2149 2345 2.674852 AGAACGAGCACATTAGCACATG 59.325 45.455 0.00 0.00 36.85 3.21
2151 2347 2.029020 AGAGAACGAGCACATTAGCACA 60.029 45.455 0.00 0.00 36.85 4.57
2152 2348 2.346847 CAGAGAACGAGCACATTAGCAC 59.653 50.000 0.00 0.00 36.85 4.40
2157 2353 3.686726 GGAATTCAGAGAACGAGCACATT 59.313 43.478 7.93 0.00 0.00 2.71
2167 2391 8.199449 GCCAAATTGATTATGGAATTCAGAGAA 58.801 33.333 7.93 0.00 36.27 2.87
2207 2433 2.351157 GCTCAGGCACATTGAAACAGTC 60.351 50.000 0.00 0.00 38.54 3.51
2208 2434 1.610522 GCTCAGGCACATTGAAACAGT 59.389 47.619 0.00 0.00 38.54 3.55
2273 2502 7.692291 CGTTGTAATCATGCTTAATTTTCTCGT 59.308 33.333 0.00 0.00 0.00 4.18
2274 2503 7.902917 TCGTTGTAATCATGCTTAATTTTCTCG 59.097 33.333 0.00 0.00 0.00 4.04
2283 2512 8.609176 GGATTAAAGTCGTTGTAATCATGCTTA 58.391 33.333 11.83 0.00 36.41 3.09
2325 2560 4.175516 CCATTCGTTGATTTTCCATGTGG 58.824 43.478 0.00 0.00 0.00 4.17
2405 2655 3.056678 TGCTGGGATTTGCTGTTGTATTG 60.057 43.478 0.00 0.00 0.00 1.90
2452 2702 3.197766 TGCTCGTTCCTAGATTTGGTGAT 59.802 43.478 0.00 0.00 0.00 3.06
2461 2711 0.824109 CATGGGTGCTCGTTCCTAGA 59.176 55.000 0.00 0.00 0.00 2.43
2494 2744 0.109919 GCCCGTAAGTTTTCGCCTTG 60.110 55.000 0.00 0.00 0.00 3.61
2496 2746 1.071814 TGCCCGTAAGTTTTCGCCT 59.928 52.632 0.00 0.00 0.00 5.52
2497 2747 1.208358 GTGCCCGTAAGTTTTCGCC 59.792 57.895 0.00 0.00 0.00 5.54
2498 2748 0.110373 CTGTGCCCGTAAGTTTTCGC 60.110 55.000 0.00 0.00 0.00 4.70
2499 2749 0.515564 CCTGTGCCCGTAAGTTTTCG 59.484 55.000 0.00 0.00 0.00 3.46
2505 2755 1.078426 CCCTTCCTGTGCCCGTAAG 60.078 63.158 0.00 0.00 0.00 2.34
2507 2757 3.712907 GCCCTTCCTGTGCCCGTA 61.713 66.667 0.00 0.00 0.00 4.02
2510 2760 2.677875 CTTGCCCTTCCTGTGCCC 60.678 66.667 0.00 0.00 0.00 5.36
2514 2764 1.005924 CCCATAACTTGCCCTTCCTGT 59.994 52.381 0.00 0.00 0.00 4.00
2525 2775 5.456186 CGGATAATCCACCTTCCCATAACTT 60.456 44.000 0.00 0.00 35.91 2.66
2527 2777 4.041198 TCGGATAATCCACCTTCCCATAAC 59.959 45.833 0.00 0.00 35.91 1.89
2529 2779 3.581332 GTCGGATAATCCACCTTCCCATA 59.419 47.826 0.00 0.00 35.91 2.74
2532 2782 1.766496 TGTCGGATAATCCACCTTCCC 59.234 52.381 0.00 0.00 35.91 3.97
2533 2783 3.553828 TTGTCGGATAATCCACCTTCC 57.446 47.619 0.00 0.00 35.91 3.46
2534 2784 5.696724 CAGTATTGTCGGATAATCCACCTTC 59.303 44.000 3.08 0.00 35.91 3.46
2535 2785 5.130477 ACAGTATTGTCGGATAATCCACCTT 59.870 40.000 3.08 0.00 35.91 3.50
2536 2786 4.654262 ACAGTATTGTCGGATAATCCACCT 59.346 41.667 3.08 0.00 35.91 4.00
2537 2787 4.957296 ACAGTATTGTCGGATAATCCACC 58.043 43.478 3.08 0.00 35.91 4.61
2538 2788 6.746120 AGTACAGTATTGTCGGATAATCCAC 58.254 40.000 3.08 0.00 38.76 4.02
2539 2789 6.971726 AGTACAGTATTGTCGGATAATCCA 57.028 37.500 3.08 0.00 38.76 3.41
2653 2904 4.367450 TCATATTTGTCGACATCGCATCA 58.633 39.130 20.80 0.00 39.60 3.07
2663 2914 3.627123 CCAGCCATGTTCATATTTGTCGA 59.373 43.478 0.00 0.00 0.00 4.20
2706 2957 9.350357 CGTATTACTTACAGTTGAGCTAAGAAA 57.650 33.333 0.00 0.00 0.00 2.52
2707 2958 8.733458 TCGTATTACTTACAGTTGAGCTAAGAA 58.267 33.333 0.00 0.00 0.00 2.52
2717 2968 9.953697 GAGAAGATCATCGTATTACTTACAGTT 57.046 33.333 0.00 0.00 0.00 3.16
2743 2994 3.834489 ATTACATGGAGGTCTGAGCTG 57.166 47.619 14.96 3.20 0.00 4.24
2860 3125 2.579410 TGCCCCCTTCAAGTAAACTC 57.421 50.000 0.00 0.00 0.00 3.01
2861 3126 2.963101 GTTTGCCCCCTTCAAGTAAACT 59.037 45.455 0.00 0.00 34.51 2.66
2912 3177 0.874390 TGGCGCTGTCAAACTCATTC 59.126 50.000 7.64 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.