Multiple sequence alignment - TraesCS2B01G336300

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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 TraesCS2B01G336300 chr2B 100.000 3143 0 0 1 3143 480411093 480414235 0.000000e+00 5805
1 TraesCS2B01G336300 chr2D 92.796 2471 91 34 1 2439 405274603 405277018 0.000000e+00 3496
2 TraesCS2B01G336300 chr2D 85.426 693 52 27 2437 3109 405277233 405277896 0.000000e+00 675
3 TraesCS2B01G336300 chr2A 89.049 2712 145 66 512 3136 543307642 543310288 0.000000e+00 3223
4 TraesCS2B01G336300 chr2A 85.612 278 26 7 251 516 543307220 543307495 2.390000e-71 279
5 TraesCS2B01G336300 chr2A 91.411 163 13 1 1 163 543306843 543307004 4.080000e-54 222
6 TraesCS2B01G336300 chr3A 88.071 394 38 8 1165 1555 27543690 27544077 2.860000e-125 459
7 TraesCS2B01G336300 chr3A 83.168 202 19 9 1665 1866 27544148 27544334 1.500000e-38 171
8 TraesCS2B01G336300 chr3D 87.817 394 39 8 1165 1555 19880725 19881112 1.330000e-123 453
9 TraesCS2B01G336300 chr3D 80.080 251 26 15 1625 1866 19881134 19881369 6.970000e-37 165
10 TraesCS2B01G336300 chr3B 85.445 371 35 7 1185 1555 31799301 31799652 4.950000e-98 368
11 TraesCS2B01G336300 chr1B 89.781 137 14 0 1372 1508 657470888 657470752 3.220000e-40 176
12 TraesCS2B01G336300 chr7D 85.714 161 22 1 1400 1559 629248233 629248393 5.390000e-38 169
13 TraesCS2B01G336300 chr7D 77.455 275 44 13 1299 1559 628987348 628987078 7.020000e-32 148
14 TraesCS2B01G336300 chr7B 75.134 374 71 20 1196 1552 731243384 731243752 4.200000e-34 156


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 TraesCS2B01G336300 chr2B 480411093 480414235 3142 False 5805.000000 5805 100.000000 1 3143 1 chr2B.!!$F1 3142
1 TraesCS2B01G336300 chr2D 405274603 405277896 3293 False 2085.500000 3496 89.111000 1 3109 2 chr2D.!!$F1 3108
2 TraesCS2B01G336300 chr2A 543306843 543310288 3445 False 1241.333333 3223 88.690667 1 3136 3 chr2A.!!$F1 3135
3 TraesCS2B01G336300 chr3A 27543690 27544334 644 False 315.000000 459 85.619500 1165 1866 2 chr3A.!!$F1 701
4 TraesCS2B01G336300 chr3D 19880725 19881369 644 False 309.000000 453 83.948500 1165 1866 2 chr3D.!!$F1 701

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
270 435 0.387239 GCTGCGGCGAACATTTTCTT 60.387 50.0 12.98 0.0 0.0 2.52 F
542 869 0.682292 TGCACCGGTGAGACAATACA 59.318 50.0 38.30 20.1 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1071 1430 2.436646 AAAGACTGCGCCATCCCG 60.437 61.111 4.18 0.0 0.00 5.14 R
2279 2668 0.808125 ACAAGAGCACACGCAAACAA 59.192 45.000 0.00 0.0 42.27 2.83 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
59 60 9.421806 CTTTATTTTGGCAAATACAATCTGACA 57.578 29.630 14.29 0.00 35.05 3.58
83 84 4.617520 TCAGGTCAAGCGCCGCAA 62.618 61.111 13.36 0.00 0.00 4.85
127 128 2.260481 GTCCAGCGTAACTAAGAGCAC 58.740 52.381 0.00 0.00 0.00 4.40
164 165 1.072332 TGTGGCAGCGGTGTATGTT 59.928 52.632 17.07 0.00 0.00 2.71
177 178 5.465935 CGGTGTATGTTTTATTGGTTGCTT 58.534 37.500 0.00 0.00 0.00 3.91
188 189 1.026182 TGGTTGCTTCGCTGCCATAG 61.026 55.000 0.00 0.00 31.13 2.23
270 435 0.387239 GCTGCGGCGAACATTTTCTT 60.387 50.000 12.98 0.00 0.00 2.52
346 511 1.741770 GCCTCAGGTGCCAACTACG 60.742 63.158 0.00 0.00 0.00 3.51
379 549 5.412904 GCTAAAGCTGAAGTTGGTAACTGAT 59.587 40.000 0.00 0.00 38.88 2.90
380 550 6.072452 GCTAAAGCTGAAGTTGGTAACTGATT 60.072 38.462 0.00 0.00 38.88 2.57
390 560 1.519408 GTAACTGATTGCACCCGTGT 58.481 50.000 0.00 0.00 0.00 4.49
402 572 1.125093 ACCCGTGTTCATCCTGTGGA 61.125 55.000 0.00 0.00 35.55 4.02
429 599 4.753610 CACGAATTGAGTGGCATATGATCT 59.246 41.667 6.97 0.61 36.06 2.75
445 615 2.263077 GATCTGTACAACTGCTCCACG 58.737 52.381 0.00 0.00 0.00 4.94
446 616 1.324383 TCTGTACAACTGCTCCACGA 58.676 50.000 0.00 0.00 0.00 4.35
461 635 2.331805 CGAGGGTAGGCGACATCG 59.668 66.667 9.42 9.42 43.27 3.84
485 659 1.929836 GATCGGTCACACTTCAGCATC 59.070 52.381 0.00 0.00 0.00 3.91
505 680 2.104622 TCTTGTTCTCATGCTCCACACA 59.895 45.455 0.00 0.00 0.00 3.72
506 681 2.865119 TGTTCTCATGCTCCACACAT 57.135 45.000 0.00 0.00 0.00 3.21
538 865 1.965930 GCATGCACCGGTGAGACAA 60.966 57.895 38.30 16.84 0.00 3.18
539 866 1.308069 GCATGCACCGGTGAGACAAT 61.308 55.000 38.30 18.30 0.00 2.71
541 868 1.665679 CATGCACCGGTGAGACAATAC 59.334 52.381 38.30 17.61 0.00 1.89
542 869 0.682292 TGCACCGGTGAGACAATACA 59.318 50.000 38.30 20.10 0.00 2.29
543 870 1.277842 TGCACCGGTGAGACAATACAT 59.722 47.619 38.30 0.00 0.00 2.29
544 871 1.665679 GCACCGGTGAGACAATACATG 59.334 52.381 38.30 7.17 0.00 3.21
545 872 2.676750 GCACCGGTGAGACAATACATGA 60.677 50.000 38.30 0.00 0.00 3.07
572 900 5.647658 GTCCATGTCATATGAAAACCAGTCA 59.352 40.000 7.07 0.00 0.00 3.41
619 947 3.364442 TTGGCGTCATTGGGCAAG 58.636 55.556 0.00 0.00 43.85 4.01
639 967 1.480212 CCTCAGCTACCACACCCACA 61.480 60.000 0.00 0.00 0.00 4.17
710 1044 4.807443 TGTATGACATTTACGGTCGACAA 58.193 39.130 18.91 2.89 38.10 3.18
711 1045 5.228665 TGTATGACATTTACGGTCGACAAA 58.771 37.500 18.91 9.90 38.10 2.83
713 1047 4.718858 TGACATTTACGGTCGACAAAAG 57.281 40.909 18.91 8.98 38.10 2.27
868 1214 5.520376 TTCTGCCCAAGAAAGAAAGAAAG 57.480 39.130 0.00 0.00 42.09 2.62
869 1215 4.792068 TCTGCCCAAGAAAGAAAGAAAGA 58.208 39.130 0.00 0.00 29.54 2.52
1903 2271 2.187946 CCACCAGCCTGATCGACC 59.812 66.667 0.00 0.00 0.00 4.79
2204 2585 4.694509 CAGAGCTTGACTGTAGAAAATGCT 59.305 41.667 0.00 0.00 0.00 3.79
2214 2595 7.594758 TGACTGTAGAAAATGCTTGTAATTTGC 59.405 33.333 0.00 0.00 0.00 3.68
2215 2596 6.868339 ACTGTAGAAAATGCTTGTAATTTGCC 59.132 34.615 0.00 0.00 0.00 4.52
2279 2668 6.276832 TCGTGTTTTTAGCTACAGTAGGAT 57.723 37.500 9.74 0.00 0.00 3.24
2308 2697 0.250467 GTGCTCTTGTGAGGCCTGAA 60.250 55.000 12.00 0.00 40.53 3.02
2309 2698 0.250467 TGCTCTTGTGAGGCCTGAAC 60.250 55.000 12.00 9.46 40.53 3.18
2322 2711 2.616842 GGCCTGAACTTTTCTCGTTTCA 59.383 45.455 0.00 0.00 0.00 2.69
2332 2721 6.949449 ACTTTTCTCGTTTCATTTGACTCTC 58.051 36.000 0.00 0.00 0.00 3.20
2356 2747 4.455124 CGAAGTGAACTTTTTGTCGATCC 58.545 43.478 0.00 0.00 36.11 3.36
2358 2749 2.223377 AGTGAACTTTTTGTCGATCCGC 59.777 45.455 0.00 0.00 0.00 5.54
2428 2819 2.822561 TGTTCACTTTTGGACTTGTGCA 59.177 40.909 0.00 0.00 31.54 4.57
2463 3072 4.682859 GCTTACAGATGAGATGACAGCCTT 60.683 45.833 0.00 0.00 0.00 4.35
2524 3142 8.362639 AGTAATACAACTTTGGTTAAGAGACGA 58.637 33.333 0.00 0.00 37.30 4.20
2565 3189 2.012673 GCAAATCTCATTCTCGTGGCT 58.987 47.619 0.00 0.00 0.00 4.75
2606 3237 4.584055 GCGTAAGGCAGAGCAAATTGCA 62.584 50.000 20.82 0.00 43.81 4.08
2607 3238 5.993405 GCGTAAGGCAGAGCAAATTGCAA 62.993 47.826 20.82 0.00 43.81 4.08
2614 3245 4.749540 GCAAATTGCAATTGCGCC 57.250 50.000 24.74 10.02 44.26 6.53
2616 3247 1.225799 CAAATTGCAATTGCGCCGC 60.226 52.632 24.74 0.00 45.83 6.53
2628 3259 2.421314 CGCCGCTGGTGATGGATA 59.579 61.111 2.49 0.00 34.74 2.59
2648 3279 2.932261 ACCTCTTTAATCATTCCCGGC 58.068 47.619 0.00 0.00 0.00 6.13
2682 3313 4.133820 TCTTTGCGAGATTCCTGTTTTGA 58.866 39.130 0.00 0.00 0.00 2.69
2751 3388 5.102953 TGTCTCCCTCATGGTCAATTTAG 57.897 43.478 0.00 0.00 34.77 1.85
2757 3394 7.069578 TCTCCCTCATGGTCAATTTAGTAGTAC 59.930 40.741 0.00 0.00 34.77 2.73
2759 3396 7.069578 TCCCTCATGGTCAATTTAGTAGTACTC 59.930 40.741 5.96 0.00 34.77 2.59
2762 3399 9.132923 CTCATGGTCAATTTAGTAGTACTCCTA 57.867 37.037 5.96 0.00 0.00 2.94
2780 3418 6.059787 CTCCTATATGAATTGGAAGGAGGG 57.940 45.833 8.08 0.00 44.17 4.30
2802 3440 5.335661 GGGTTCATTCATGTGTAGAACAACC 60.336 44.000 17.74 0.00 43.61 3.77
2857 3499 6.262601 CGGATAAGTTTCGCCATACAAAAAT 58.737 36.000 0.00 0.00 0.00 1.82
2924 3566 4.662961 TGCGTCCTGACCTGCGTG 62.663 66.667 0.00 0.00 0.00 5.34
2943 3589 0.317479 GGTGGCGGTGCTATAGTAGG 59.683 60.000 0.84 0.00 0.00 3.18
2946 3592 1.133575 TGGCGGTGCTATAGTAGGAGT 60.134 52.381 0.84 0.00 0.00 3.85
2949 3595 3.410508 GCGGTGCTATAGTAGGAGTAGT 58.589 50.000 0.84 0.00 0.00 2.73
2950 3596 3.188873 GCGGTGCTATAGTAGGAGTAGTG 59.811 52.174 0.84 0.00 0.00 2.74
2958 3604 6.592607 GCTATAGTAGGAGTAGTGTCTAGCAG 59.407 46.154 0.84 0.00 0.00 4.24
2959 3605 4.847990 AGTAGGAGTAGTGTCTAGCAGT 57.152 45.455 0.00 0.00 34.61 4.40
2960 3606 5.954153 AGTAGGAGTAGTGTCTAGCAGTA 57.046 43.478 0.00 0.00 32.14 2.74
2961 3607 5.920903 AGTAGGAGTAGTGTCTAGCAGTAG 58.079 45.833 2.99 0.00 33.97 2.57
2962 3608 3.547746 AGGAGTAGTGTCTAGCAGTAGC 58.452 50.000 2.99 0.00 42.56 3.58
2972 3618 4.326153 GCAGTAGCGCATCGATCA 57.674 55.556 11.47 0.00 0.00 2.92
2973 3619 2.819667 GCAGTAGCGCATCGATCAT 58.180 52.632 11.47 0.00 0.00 2.45
2974 3620 0.712775 GCAGTAGCGCATCGATCATC 59.287 55.000 11.47 0.00 0.00 2.92
2975 3621 1.668337 GCAGTAGCGCATCGATCATCT 60.668 52.381 11.47 0.00 0.00 2.90
2976 3622 2.414691 GCAGTAGCGCATCGATCATCTA 60.415 50.000 11.47 0.00 0.00 1.98
2977 3623 3.733380 GCAGTAGCGCATCGATCATCTAT 60.733 47.826 11.47 0.00 0.00 1.98
2978 3624 4.034350 CAGTAGCGCATCGATCATCTATC 58.966 47.826 11.47 0.00 0.00 2.08
2979 3625 2.575694 AGCGCATCGATCATCTATCC 57.424 50.000 11.47 0.00 0.00 2.59
2980 3626 1.195347 GCGCATCGATCATCTATCCG 58.805 55.000 0.30 0.00 0.00 4.18
2981 3627 1.202188 GCGCATCGATCATCTATCCGA 60.202 52.381 0.30 0.00 0.00 4.55
2982 3628 2.714139 CGCATCGATCATCTATCCGAG 58.286 52.381 0.00 0.00 0.00 4.63
2983 3629 2.352960 CGCATCGATCATCTATCCGAGA 59.647 50.000 0.00 0.00 39.01 4.04
2984 3630 3.690422 GCATCGATCATCTATCCGAGAC 58.310 50.000 0.00 0.00 36.87 3.36
2988 3634 2.997303 CGATCATCTATCCGAGACGAGT 59.003 50.000 0.00 0.00 36.87 4.18
2991 3637 3.394719 TCATCTATCCGAGACGAGTGAG 58.605 50.000 0.00 0.00 36.87 3.51
2992 3638 2.242047 TCTATCCGAGACGAGTGAGG 57.758 55.000 0.00 0.00 0.00 3.86
3015 3661 4.088762 GTGTGTCATGGCGCGGTG 62.089 66.667 8.83 2.27 0.00 4.94
3027 3682 3.423154 GCGGTGCCTTGGAAGACG 61.423 66.667 0.00 0.00 0.00 4.18
3077 3739 2.848887 CACACGAGAAGCAACTAGATCG 59.151 50.000 0.00 0.00 36.32 3.69
3078 3740 2.488545 ACACGAGAAGCAACTAGATCGT 59.511 45.455 0.00 0.00 43.50 3.73
3079 3741 3.102276 CACGAGAAGCAACTAGATCGTC 58.898 50.000 0.00 0.00 41.04 4.20
3104 3766 0.884704 TTGCTCGTGAAGAACAGGGC 60.885 55.000 0.00 0.00 35.42 5.19
3109 3771 2.093890 TCGTGAAGAACAGGGCGTATA 58.906 47.619 0.00 0.00 35.42 1.47
3111 3773 3.050619 CGTGAAGAACAGGGCGTATATC 58.949 50.000 0.00 0.00 0.00 1.63
3112 3774 3.391049 GTGAAGAACAGGGCGTATATCC 58.609 50.000 0.00 0.00 0.00 2.59
3125 3787 3.483248 GCGTATATCCGTACGTCTGCTAG 60.483 52.174 15.21 2.01 46.74 3.42
3127 3789 4.151335 CGTATATCCGTACGTCTGCTAGTT 59.849 45.833 15.21 0.00 41.75 2.24
3136 3798 1.662629 CGTCTGCTAGTTCATGCCAAG 59.337 52.381 0.00 0.00 0.00 3.61
3137 3799 2.675032 CGTCTGCTAGTTCATGCCAAGA 60.675 50.000 0.00 0.00 0.00 3.02
3138 3800 3.539604 GTCTGCTAGTTCATGCCAAGAT 58.460 45.455 0.00 0.00 0.00 2.40
3139 3801 3.559242 GTCTGCTAGTTCATGCCAAGATC 59.441 47.826 0.00 0.00 0.00 2.75
3140 3802 2.877168 CTGCTAGTTCATGCCAAGATCC 59.123 50.000 0.00 0.00 0.00 3.36
3141 3803 2.239402 TGCTAGTTCATGCCAAGATCCA 59.761 45.455 0.00 0.00 0.00 3.41
3142 3804 2.877168 GCTAGTTCATGCCAAGATCCAG 59.123 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.183360 GCCAAAATAAAGCATAAACTGTTCCG 60.183 38.462 0.00 0.00 0.00 4.30
59 60 2.017049 GGCGCTTGACCTGACAATATT 58.983 47.619 7.64 0.00 0.00 1.28
73 74 0.304705 CTTTCGATATTGCGGCGCTT 59.695 50.000 33.26 21.91 0.00 4.68
188 189 0.527565 AAATTGTGACATGGCTCGGC 59.472 50.000 0.00 0.00 0.00 5.54
270 435 2.586635 GAACCGTGGCACGTCACA 60.587 61.111 34.74 0.00 40.58 3.58
346 511 0.108329 TCAGCTTTAGCCGTACCTGC 60.108 55.000 0.00 0.00 43.38 4.85
379 549 0.888736 CAGGATGAACACGGGTGCAA 60.889 55.000 0.43 0.00 39.69 4.08
380 550 1.302431 CAGGATGAACACGGGTGCA 60.302 57.895 0.00 0.00 39.69 4.57
390 560 0.247460 CGTGAGCTCCACAGGATGAA 59.753 55.000 12.15 0.00 45.98 2.57
411 581 6.178607 TGTACAGATCATATGCCACTCAAT 57.821 37.500 0.00 0.00 0.00 2.57
412 582 5.612725 TGTACAGATCATATGCCACTCAA 57.387 39.130 0.00 0.00 0.00 3.02
429 599 0.317160 CCTCGTGGAGCAGTTGTACA 59.683 55.000 0.00 0.00 34.57 2.90
461 635 0.037326 TGAAGTGTGACCGATCAGGC 60.037 55.000 3.85 0.00 46.52 4.85
470 644 3.812053 AGAACAAGATGCTGAAGTGTGAC 59.188 43.478 0.00 0.00 0.00 3.67
485 659 2.497138 TGTGTGGAGCATGAGAACAAG 58.503 47.619 0.00 0.00 0.00 3.16
505 680 1.477553 CATGCTACACCTGGCCAAAT 58.522 50.000 7.01 0.00 0.00 2.32
506 681 1.250154 GCATGCTACACCTGGCCAAA 61.250 55.000 11.37 0.00 0.00 3.28
542 869 7.342541 TGGTTTTCATATGACATGGACAATCAT 59.657 33.333 4.48 0.00 36.95 2.45
543 870 6.662663 TGGTTTTCATATGACATGGACAATCA 59.337 34.615 4.48 0.00 0.00 2.57
544 871 7.099266 TGGTTTTCATATGACATGGACAATC 57.901 36.000 4.48 0.00 0.00 2.67
545 872 6.664816 ACTGGTTTTCATATGACATGGACAAT 59.335 34.615 4.48 0.00 0.00 2.71
572 900 6.096987 TCCTTAAACAAGCTCATCTAGATCGT 59.903 38.462 1.03 0.00 0.00 3.73
619 947 2.269241 GGGTGTGGTAGCTGAGGC 59.731 66.667 0.00 0.00 39.06 4.70
658 986 7.501892 TGCCATAATTGTAGAATGCAGTATCAA 59.498 33.333 0.00 0.00 27.68 2.57
710 1044 8.503196 TGAATGCGATGCGATTATTAATACTTT 58.497 29.630 0.00 0.00 0.00 2.66
711 1045 8.028540 TGAATGCGATGCGATTATTAATACTT 57.971 30.769 0.00 0.00 0.00 2.24
713 1047 7.423598 CACTGAATGCGATGCGATTATTAATAC 59.576 37.037 0.00 0.00 0.00 1.89
804 1149 5.182001 CACTTGCCTTTTGCTCTTGTAGTAT 59.818 40.000 0.00 0.00 42.00 2.12
806 1151 3.316308 CACTTGCCTTTTGCTCTTGTAGT 59.684 43.478 0.00 0.00 42.00 2.73
866 1212 4.262036 GGAAATTCGCACCTTCCTTTTCTT 60.262 41.667 0.00 0.00 36.48 2.52
867 1213 3.255888 GGAAATTCGCACCTTCCTTTTCT 59.744 43.478 0.00 0.00 36.48 2.52
868 1214 3.575630 GGAAATTCGCACCTTCCTTTTC 58.424 45.455 0.00 0.00 36.48 2.29
869 1215 2.299013 GGGAAATTCGCACCTTCCTTTT 59.701 45.455 5.11 0.00 38.94 2.27
928 1274 4.935495 CTGGCGGTGTGGTGTGCT 62.935 66.667 0.00 0.00 0.00 4.40
1071 1430 2.436646 AAAGACTGCGCCATCCCG 60.437 61.111 4.18 0.00 0.00 5.14
1601 1963 3.687321 GAAGGCGAGGGCTGATGCA 62.687 63.158 0.00 0.00 38.81 3.96
2052 2426 4.029809 GACCCGTCCCACCCCTTG 62.030 72.222 0.00 0.00 0.00 3.61
2143 2523 4.337060 TGTGGACTGCCGACGTCG 62.337 66.667 30.33 30.33 36.79 5.12
2272 2659 1.535462 GCACACGCAAACAATCCTACT 59.465 47.619 0.00 0.00 38.36 2.57
2273 2660 1.535462 AGCACACGCAAACAATCCTAC 59.465 47.619 0.00 0.00 42.27 3.18
2279 2668 0.808125 ACAAGAGCACACGCAAACAA 59.192 45.000 0.00 0.00 42.27 2.83
2308 2697 6.292381 CGAGAGTCAAATGAAACGAGAAAAGT 60.292 38.462 0.00 0.00 0.00 2.66
2309 2698 6.067669 CGAGAGTCAAATGAAACGAGAAAAG 58.932 40.000 0.00 0.00 0.00 2.27
2322 2711 2.724977 TCACTTCGCGAGAGTCAAAT 57.275 45.000 9.59 0.00 43.69 2.32
2332 2721 2.026990 CGACAAAAAGTTCACTTCGCG 58.973 47.619 0.00 0.00 34.61 5.87
2343 2732 1.006832 ATCCGCGGATCGACAAAAAG 58.993 50.000 34.60 0.00 41.67 2.27
2344 2733 1.395608 GAATCCGCGGATCGACAAAAA 59.604 47.619 38.94 9.99 41.67 1.94
2428 2819 0.953960 CTGTAAGCGAAAAGGCGGGT 60.954 55.000 0.00 0.00 38.18 5.28
2463 3072 7.601705 AAAATTGATCTCTTGACAAAAGGGA 57.398 32.000 0.00 0.00 0.00 4.20
2497 3106 8.433126 CGTCTCTTAACCAAAGTTGTATTACTG 58.567 37.037 0.00 0.00 36.68 2.74
2524 3142 3.624777 CAAATGCTCCTCCCACTAACAT 58.375 45.455 0.00 0.00 0.00 2.71
2600 3231 2.095847 CAGCGGCGCAATTGCAATT 61.096 52.632 35.02 18.99 42.21 2.32
2606 3237 2.751436 ATCACCAGCGGCGCAATT 60.751 55.556 35.02 14.28 0.00 2.32
2607 3238 3.511595 CATCACCAGCGGCGCAAT 61.512 61.111 35.02 15.98 0.00 3.56
2610 3241 3.807631 TATCCATCACCAGCGGCGC 62.808 63.158 26.86 26.86 0.00 6.53
2611 3242 1.956170 GTATCCATCACCAGCGGCG 60.956 63.158 0.51 0.51 0.00 6.46
2613 3244 0.034059 GAGGTATCCATCACCAGCGG 59.966 60.000 0.00 0.00 38.62 5.52
2614 3245 1.043816 AGAGGTATCCATCACCAGCG 58.956 55.000 0.00 0.00 38.62 5.18
2616 3247 6.830912 TGATTAAAGAGGTATCCATCACCAG 58.169 40.000 0.00 0.00 38.62 4.00
2628 3259 2.509964 AGCCGGGAATGATTAAAGAGGT 59.490 45.455 2.18 0.00 0.00 3.85
2648 3279 1.798223 TCGCAAAGAACGATGGACAAG 59.202 47.619 0.00 0.00 33.96 3.16
2682 3313 1.956629 AAGATCGACCGACGCCCAAT 61.957 55.000 0.00 0.00 42.26 3.16
2751 3388 9.310449 TCCTTCCAATTCATATAGGAGTACTAC 57.690 37.037 0.00 0.00 33.70 2.73
2757 3394 5.549619 ACCCTCCTTCCAATTCATATAGGAG 59.450 44.000 0.00 0.00 45.32 3.69
2759 3396 5.850046 ACCCTCCTTCCAATTCATATAGG 57.150 43.478 0.00 0.00 0.00 2.57
2762 3399 5.732331 TGAACCCTCCTTCCAATTCATAT 57.268 39.130 0.00 0.00 0.00 1.78
2780 3418 6.373779 CAGGTTGTTCTACACATGAATGAAC 58.626 40.000 0.00 8.88 34.43 3.18
2802 3440 2.673523 CACAAGAGCCTCCCCCAG 59.326 66.667 0.00 0.00 0.00 4.45
2857 3499 7.094506 ACGTTCTTATCCGCTCATGTGTATATA 60.095 37.037 0.00 0.00 0.00 0.86
2862 3504 2.094182 ACGTTCTTATCCGCTCATGTGT 60.094 45.455 0.00 0.00 0.00 3.72
2863 3505 2.282555 CACGTTCTTATCCGCTCATGTG 59.717 50.000 0.00 0.00 0.00 3.21
2864 3506 2.540515 CACGTTCTTATCCGCTCATGT 58.459 47.619 0.00 0.00 0.00 3.21
2865 3507 1.860950 CCACGTTCTTATCCGCTCATG 59.139 52.381 0.00 0.00 0.00 3.07
2907 3549 4.662961 CACGCAGGTCAGGACGCA 62.663 66.667 0.00 0.00 0.00 5.24
2924 3566 0.317479 CCTACTATAGCACCGCCACC 59.683 60.000 0.00 0.00 0.00 4.61
2926 3568 1.133575 ACTCCTACTATAGCACCGCCA 60.134 52.381 0.00 0.00 0.00 5.69
2930 3572 5.623169 AGACACTACTCCTACTATAGCACC 58.377 45.833 0.00 0.00 0.00 5.01
2932 3574 6.042897 TGCTAGACACTACTCCTACTATAGCA 59.957 42.308 0.00 0.00 39.48 3.49
2934 3576 7.673180 ACTGCTAGACACTACTCCTACTATAG 58.327 42.308 0.00 0.00 0.00 1.31
2935 3577 7.615039 ACTGCTAGACACTACTCCTACTATA 57.385 40.000 0.00 0.00 0.00 1.31
2936 3578 6.503560 ACTGCTAGACACTACTCCTACTAT 57.496 41.667 0.00 0.00 0.00 2.12
2943 3589 2.286536 GCGCTACTGCTAGACACTACTC 60.287 54.545 0.00 0.00 36.97 2.59
2946 3592 1.746470 TGCGCTACTGCTAGACACTA 58.254 50.000 9.73 0.00 36.97 2.74
2949 3595 0.029433 CGATGCGCTACTGCTAGACA 59.971 55.000 9.73 0.00 36.97 3.41
2950 3596 0.308068 TCGATGCGCTACTGCTAGAC 59.692 55.000 9.73 0.00 36.97 2.59
2958 3604 3.367607 GGATAGATGATCGATGCGCTAC 58.632 50.000 9.73 1.09 35.12 3.58
2959 3605 2.032178 CGGATAGATGATCGATGCGCTA 59.968 50.000 15.16 1.24 36.70 4.26
2960 3606 1.202234 CGGATAGATGATCGATGCGCT 60.202 52.381 15.16 0.00 36.70 5.92
2961 3607 1.195347 CGGATAGATGATCGATGCGC 58.805 55.000 15.16 0.00 36.70 6.09
2962 3608 2.352960 TCTCGGATAGATGATCGATGCG 59.647 50.000 19.82 19.82 42.57 4.73
2963 3609 3.690422 GTCTCGGATAGATGATCGATGC 58.310 50.000 0.54 0.00 36.36 3.91
2964 3610 3.619038 TCGTCTCGGATAGATGATCGATG 59.381 47.826 0.54 0.00 43.86 3.84
2965 3611 3.863041 TCGTCTCGGATAGATGATCGAT 58.137 45.455 0.00 0.00 43.86 3.59
2966 3612 3.254892 CTCGTCTCGGATAGATGATCGA 58.745 50.000 0.00 0.00 46.77 3.59
2967 3613 2.997303 ACTCGTCTCGGATAGATGATCG 59.003 50.000 0.00 0.00 46.77 3.69
2968 3614 3.997681 TCACTCGTCTCGGATAGATGATC 59.002 47.826 0.00 0.00 46.77 2.92
2969 3615 4.000325 CTCACTCGTCTCGGATAGATGAT 59.000 47.826 0.00 0.00 46.77 2.45
2970 3616 3.394719 CTCACTCGTCTCGGATAGATGA 58.605 50.000 0.00 0.00 46.03 2.92
2971 3617 2.482336 CCTCACTCGTCTCGGATAGATG 59.518 54.545 0.00 0.00 41.88 2.90
2972 3618 2.551287 CCCTCACTCGTCTCGGATAGAT 60.551 54.545 0.00 0.00 36.36 1.98
2973 3619 1.202663 CCCTCACTCGTCTCGGATAGA 60.203 57.143 0.00 0.00 0.00 1.98
2974 3620 1.202663 TCCCTCACTCGTCTCGGATAG 60.203 57.143 0.00 0.00 0.00 2.08
2975 3621 0.835276 TCCCTCACTCGTCTCGGATA 59.165 55.000 0.00 0.00 0.00 2.59
2976 3622 0.464735 CTCCCTCACTCGTCTCGGAT 60.465 60.000 0.00 0.00 0.00 4.18
2977 3623 1.078356 CTCCCTCACTCGTCTCGGA 60.078 63.158 0.00 0.00 0.00 4.55
2978 3624 2.766400 GCTCCCTCACTCGTCTCGG 61.766 68.421 0.00 0.00 0.00 4.63
2979 3625 2.766400 GGCTCCCTCACTCGTCTCG 61.766 68.421 0.00 0.00 0.00 4.04
2980 3626 2.766400 CGGCTCCCTCACTCGTCTC 61.766 68.421 0.00 0.00 0.00 3.36
2981 3627 2.752238 CGGCTCCCTCACTCGTCT 60.752 66.667 0.00 0.00 0.00 4.18
2982 3628 3.063084 ACGGCTCCCTCACTCGTC 61.063 66.667 0.00 0.00 0.00 4.20
2983 3629 3.374402 CACGGCTCCCTCACTCGT 61.374 66.667 0.00 0.00 34.19 4.18
2984 3630 3.374402 ACACGGCTCCCTCACTCG 61.374 66.667 0.00 0.00 0.00 4.18
2988 3634 1.913262 ATGACACACGGCTCCCTCA 60.913 57.895 0.00 0.00 0.00 3.86
2991 3637 2.436646 CCATGACACACGGCTCCC 60.437 66.667 0.00 0.00 0.00 4.30
2992 3638 3.127533 GCCATGACACACGGCTCC 61.128 66.667 1.56 0.00 42.78 4.70
3009 3655 3.423154 GTCTTCCAAGGCACCGCG 61.423 66.667 0.00 0.00 0.00 6.46
3010 3656 3.423154 CGTCTTCCAAGGCACCGC 61.423 66.667 0.00 0.00 0.00 5.68
3011 3657 3.423154 GCGTCTTCCAAGGCACCG 61.423 66.667 0.00 0.00 0.00 4.94
3012 3658 1.856265 CTTGCGTCTTCCAAGGCACC 61.856 60.000 0.00 0.00 39.54 5.01
3014 3660 4.063529 CTTGCGTCTTCCAAGGCA 57.936 55.556 0.00 0.00 38.19 4.75
3027 3682 3.673484 TTGCCAGCTTCGCCTTGC 61.673 61.111 0.17 0.00 0.00 4.01
3038 3699 1.008538 GGTGCGTTTCTGTTGCCAG 60.009 57.895 0.00 0.00 40.25 4.85
3039 3700 1.750780 TGGTGCGTTTCTGTTGCCA 60.751 52.632 0.00 0.00 0.00 4.92
3077 3739 1.733912 TCTTCACGAGCAATGCATGAC 59.266 47.619 8.35 0.00 0.00 3.06
3078 3740 2.097680 TCTTCACGAGCAATGCATGA 57.902 45.000 8.35 5.35 0.00 3.07
3079 3741 2.095617 TGTTCTTCACGAGCAATGCATG 60.096 45.455 8.35 2.73 29.28 4.06
3109 3771 2.362736 TGAACTAGCAGACGTACGGAT 58.637 47.619 21.06 4.25 0.00 4.18
3111 3773 2.451132 CATGAACTAGCAGACGTACGG 58.549 52.381 21.06 2.64 0.00 4.02
3112 3774 1.846782 GCATGAACTAGCAGACGTACG 59.153 52.381 15.01 15.01 0.00 3.67


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

AutoCloner maintained by Alex Coulton.