Multiple sequence alignment - TraesCS2D01G134700

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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 TraesCS2D01G134700 chr2D 100.000 3614 0 0 1 3614 79235079 79231466 0.000000e+00 6674.0
1 TraesCS2D01G134700 chr2D 84.135 208 24 7 978 1176 79332906 79332699 3.680000e-45 193.0
2 TraesCS2D01G134700 chr2D 90.909 66 6 0 1050 1115 79260110 79260045 4.970000e-14 89.8
3 TraesCS2D01G134700 chr2B 92.586 3318 146 48 326 3614 123102658 123099412 0.000000e+00 4673.0
4 TraesCS2D01G134700 chr2B 88.786 651 60 6 321 965 128260180 128259537 0.000000e+00 785.0
5 TraesCS2D01G134700 chr2B 87.569 362 44 1 1 362 128260672 128260312 5.580000e-113 418.0
6 TraesCS2D01G134700 chr2B 87.324 355 44 1 1 355 123103156 123102803 4.350000e-109 405.0
7 TraesCS2D01G134700 chr2B 88.053 226 22 3 980 1201 128312186 128311962 2.770000e-66 263.0
8 TraesCS2D01G134700 chr2B 85.350 157 13 5 1050 1198 123130275 123130121 1.740000e-33 154.0
9 TraesCS2D01G134700 chr2A 91.504 3237 143 40 344 3521 79443652 79440489 0.000000e+00 4333.0
10 TraesCS2D01G134700 chr2A 83.651 367 50 9 6 362 79444206 79443840 1.610000e-88 337.0
11 TraesCS2D01G134700 chr2A 80.556 288 31 15 978 1250 79498147 79497870 7.910000e-47 198.0
12 TraesCS2D01G134700 chr2A 89.677 155 12 3 1048 1198 79541133 79540979 1.020000e-45 195.0
13 TraesCS2D01G134700 chr1B 76.636 1070 195 53 1496 2542 20836132 20835095 1.140000e-149 540.0
14 TraesCS2D01G134700 chr1B 81.117 376 65 5 2204 2578 401603918 401604288 2.730000e-76 296.0
15 TraesCS2D01G134700 chr1D 76.323 1077 192 55 1496 2542 15049761 15048718 5.350000e-143 518.0
16 TraesCS2D01G134700 chr1D 82.692 364 56 5 2218 2578 298548130 298548489 2.090000e-82 316.0
17 TraesCS2D01G134700 chr1A 76.297 983 185 44 1571 2533 15517199 15518153 7.020000e-132 481.0
18 TraesCS2D01G134700 chr1A 82.748 313 53 1 2218 2530 372195254 372195565 9.880000e-71 278.0
19 TraesCS2D01G134700 chr1A 81.448 221 40 1 2288 2508 372197321 372197540 2.870000e-41 180.0


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 TraesCS2D01G134700 chr2D 79231466 79235079 3613 True 6674.0 6674 100.0000 1 3614 1 chr2D.!!$R1 3613
1 TraesCS2D01G134700 chr2B 123099412 123103156 3744 True 2539.0 4673 89.9550 1 3614 2 chr2B.!!$R3 3613
2 TraesCS2D01G134700 chr2B 128259537 128260672 1135 True 601.5 785 88.1775 1 965 2 chr2B.!!$R4 964
3 TraesCS2D01G134700 chr2A 79440489 79444206 3717 True 2335.0 4333 87.5775 6 3521 2 chr2A.!!$R3 3515
4 TraesCS2D01G134700 chr1B 20835095 20836132 1037 True 540.0 540 76.6360 1496 2542 1 chr1B.!!$R1 1046
5 TraesCS2D01G134700 chr1D 15048718 15049761 1043 True 518.0 518 76.3230 1496 2542 1 chr1D.!!$R1 1046
6 TraesCS2D01G134700 chr1A 15517199 15518153 954 False 481.0 481 76.2970 1571 2533 1 chr1A.!!$F1 962
7 TraesCS2D01G134700 chr1A 372195254 372197540 2286 False 229.0 278 82.0980 2218 2530 2 chr1A.!!$F2 312


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
63 64 0.307760 GCACCATACATAAGCCACGC 59.692 55.0 0.00 0.0 0.00 5.34 F
603 838 0.389296 TGGCGTACGATGGAAGTGTG 60.389 55.0 21.65 0.0 0.00 3.82 F
1328 1581 0.320508 CAGCAGCAGCAGAGTGAGAA 60.321 55.0 3.17 0.0 45.49 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1576 1.667154 CGATCCCGGAGCACTTCTCA 61.667 60.000 0.73 0.00 43.70 3.27 R
2361 4654 1.137404 CTTGTACCCGACGTACCGG 59.863 63.158 8.64 8.64 45.89 5.28 R
2897 5254 0.108898 CTTCCTCCGCTCACTGTCTG 60.109 60.000 0.00 0.00 0.00 3.51 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
52 53 3.056107 TGTCTGGTCAACTAGCACCATAC 60.056 47.826 13.63 13.63 41.97 2.39
63 64 0.307760 GCACCATACATAAGCCACGC 59.692 55.000 0.00 0.00 0.00 5.34
107 114 3.689649 ACCAGCCTCATAAAAGTAAAGCG 59.310 43.478 0.00 0.00 0.00 4.68
112 119 3.308866 CCTCATAAAAGTAAAGCGTCCGG 59.691 47.826 0.00 0.00 0.00 5.14
120 127 4.942761 AGTAAAGCGTCCGGGATATAAA 57.057 40.909 0.00 0.00 0.00 1.40
130 137 3.139077 CCGGGATATAAAGGCTTCACAC 58.861 50.000 0.00 0.00 0.00 3.82
153 160 9.944376 ACACAAATTGTCTATGTATACTTCTGT 57.056 29.630 4.17 0.00 29.79 3.41
209 216 3.060602 GCACACTAGAAGGACACAAGAC 58.939 50.000 0.00 0.00 0.00 3.01
213 220 2.288273 ACTAGAAGGACACAAGACGCAC 60.288 50.000 0.00 0.00 0.00 5.34
221 228 1.333619 ACACAAGACGCACATTTGGTC 59.666 47.619 0.00 0.00 0.00 4.02
276 287 9.445786 AAAAGAACATTTATACAACGAACACAG 57.554 29.630 0.00 0.00 0.00 3.66
293 304 3.381590 ACACAGATCTAGCATCTAACGCA 59.618 43.478 0.00 0.00 0.00 5.24
317 368 1.436195 GCGGCGCAACAAGATATGGA 61.436 55.000 29.21 0.00 0.00 3.41
324 375 4.032217 GCGCAACAAGATATGGATCTATCG 59.968 45.833 0.30 0.00 41.87 2.92
342 393 2.362736 TCGTCTAATGCGACACTAGGT 58.637 47.619 0.00 0.00 33.54 3.08
355 406 4.870426 CGACACTAGGTGCAACAAGATATT 59.130 41.667 3.64 0.00 39.98 1.28
402 518 1.064060 ACTCTGAAGTGTTGCGTTTGC 59.936 47.619 0.00 0.00 36.47 3.68
416 651 4.084447 GCGTTTGCGAGTTGTTTTAAAG 57.916 40.909 0.00 0.00 41.33 1.85
424 659 3.545228 CGAGTTGTTTTAAAGCGAGCACA 60.545 43.478 0.00 0.00 0.00 4.57
431 666 6.244999 TGTTTTAAAGCGAGCACAATATACG 58.755 36.000 0.00 0.00 0.00 3.06
466 701 5.099042 AGACCACACCGCTTTATCTAAAT 57.901 39.130 0.00 0.00 0.00 1.40
485 720 3.972950 ATGACTATTCTCCGTCACTCG 57.027 47.619 0.00 0.00 42.32 4.18
523 758 3.366374 GGAGTGGCTACAAATCAAGCAAC 60.366 47.826 2.02 0.00 42.06 4.17
525 760 1.539388 TGGCTACAAATCAAGCAACGG 59.461 47.619 0.00 0.00 40.61 4.44
547 782 2.082354 GCGGGAAAAGCGAGAAGAG 58.918 57.895 0.00 0.00 0.00 2.85
603 838 0.389296 TGGCGTACGATGGAAGTGTG 60.389 55.000 21.65 0.00 0.00 3.82
634 869 9.768662 CTGAATATATGGCTGGCTTTAATTTTT 57.231 29.630 2.00 0.00 0.00 1.94
666 902 8.491331 AGAGAAAAGAATGTGAGAAGATAAGC 57.509 34.615 0.00 0.00 0.00 3.09
667 903 7.552330 AGAGAAAAGAATGTGAGAAGATAAGCC 59.448 37.037 0.00 0.00 0.00 4.35
737 973 2.617274 GCTTTGCGCCGATATCCCC 61.617 63.158 4.18 0.00 0.00 4.81
738 974 1.227823 CTTTGCGCCGATATCCCCA 60.228 57.895 4.18 0.00 0.00 4.96
740 976 2.951475 TTTGCGCCGATATCCCCACC 62.951 60.000 4.18 0.00 0.00 4.61
777 1014 4.821260 GCAATCAAAGGACCCACAATTTTT 59.179 37.500 0.00 0.00 0.00 1.94
800 1037 1.710244 TCAAGGATGTTCCATGGGTGT 59.290 47.619 13.02 0.00 39.61 4.16
854 1091 2.031683 CCTCTAACCGCCGCTAATTTTG 59.968 50.000 0.00 0.00 0.00 2.44
868 1107 4.096532 GCTAATTTTGTACTCCCTTCTGCC 59.903 45.833 0.00 0.00 0.00 4.85
887 1126 1.523758 CGTGCCATTTATAGCTCCCC 58.476 55.000 0.00 0.00 0.00 4.81
931 1170 2.158519 ACAATCCAAAACCCCGAGAACT 60.159 45.455 0.00 0.00 0.00 3.01
973 1217 2.169769 TCCCTTCGACTCTCTCTCTCTC 59.830 54.545 0.00 0.00 0.00 3.20
974 1218 2.170607 CCCTTCGACTCTCTCTCTCTCT 59.829 54.545 0.00 0.00 0.00 3.10
1204 1448 4.760047 TGAGCGGCTTCTTCGGCC 62.760 66.667 2.97 0.00 45.57 6.13
1323 1576 4.311445 ACGCAGCAGCAGCAGAGT 62.311 61.111 10.77 0.00 45.49 3.24
1327 1580 1.292541 CAGCAGCAGCAGAGTGAGA 59.707 57.895 3.17 0.00 45.49 3.27
1328 1581 0.320508 CAGCAGCAGCAGAGTGAGAA 60.321 55.000 3.17 0.00 45.49 2.87
2602 4895 0.890090 CCGGCCGAAAACCAAACCTA 60.890 55.000 30.73 0.00 0.00 3.08
2692 4993 8.697507 AGATCAAAATTTACAGACACCTTTCT 57.302 30.769 0.00 0.00 0.00 2.52
2693 4994 8.787852 AGATCAAAATTTACAGACACCTTTCTC 58.212 33.333 0.00 0.00 0.00 2.87
2694 4995 8.697507 ATCAAAATTTACAGACACCTTTCTCT 57.302 30.769 0.00 0.00 0.00 3.10
2698 4999 5.470047 TTTACAGACACCTTTCTCTCTCC 57.530 43.478 0.00 0.00 0.00 3.71
2763 5096 8.681486 TCATACCTGACCATTCATTTCATTAG 57.319 34.615 0.00 0.00 0.00 1.73
2764 5097 8.493607 TCATACCTGACCATTCATTTCATTAGA 58.506 33.333 0.00 0.00 0.00 2.10
2765 5098 9.293404 CATACCTGACCATTCATTTCATTAGAT 57.707 33.333 0.00 0.00 0.00 1.98
2766 5099 9.872684 ATACCTGACCATTCATTTCATTAGATT 57.127 29.630 0.00 0.00 0.00 2.40
2767 5100 8.004087 ACCTGACCATTCATTTCATTAGATTG 57.996 34.615 0.00 0.00 0.00 2.67
2768 5101 7.616935 ACCTGACCATTCATTTCATTAGATTGT 59.383 33.333 0.00 0.00 0.00 2.71
2769 5102 8.472413 CCTGACCATTCATTTCATTAGATTGTT 58.528 33.333 0.00 0.00 0.00 2.83
2783 5116 9.996554 TCATTAGATTGTTACTCTCTGTTTTGA 57.003 29.630 0.00 0.00 0.00 2.69
2785 5118 6.771188 AGATTGTTACTCTCTGTTTTGACG 57.229 37.500 0.00 0.00 0.00 4.35
2786 5119 4.789095 TTGTTACTCTCTGTTTTGACGC 57.211 40.909 0.00 0.00 0.00 5.19
2787 5120 4.054780 TGTTACTCTCTGTTTTGACGCT 57.945 40.909 0.00 0.00 0.00 5.07
2788 5121 4.439057 TGTTACTCTCTGTTTTGACGCTT 58.561 39.130 0.00 0.00 0.00 4.68
2789 5122 4.506654 TGTTACTCTCTGTTTTGACGCTTC 59.493 41.667 0.00 0.00 0.00 3.86
2790 5123 3.179443 ACTCTCTGTTTTGACGCTTCA 57.821 42.857 0.00 0.00 0.00 3.02
2791 5124 3.733337 ACTCTCTGTTTTGACGCTTCAT 58.267 40.909 0.00 0.00 0.00 2.57
2792 5125 4.130118 ACTCTCTGTTTTGACGCTTCATT 58.870 39.130 0.00 0.00 0.00 2.57
2793 5126 5.297547 ACTCTCTGTTTTGACGCTTCATTA 58.702 37.500 0.00 0.00 0.00 1.90
2834 5167 0.249447 GATGTGCCCGTGATCGATCA 60.249 55.000 23.99 23.99 39.71 2.92
2895 5252 4.481930 TCAGTTACAATTTTGCGTCCTG 57.518 40.909 0.00 0.00 0.00 3.86
2896 5253 4.130857 TCAGTTACAATTTTGCGTCCTGA 58.869 39.130 0.00 0.00 0.00 3.86
2897 5254 4.024387 TCAGTTACAATTTTGCGTCCTGAC 60.024 41.667 0.00 0.00 0.00 3.51
2898 5255 3.880490 AGTTACAATTTTGCGTCCTGACA 59.120 39.130 0.00 0.00 0.00 3.58
2929 5291 3.093278 GGAAGATTCCTGCGTGCG 58.907 61.111 4.29 0.00 44.11 5.34
3013 5375 0.320421 GTGAACCGCCTCTGCTGTTA 60.320 55.000 0.00 0.00 43.76 2.41
3015 5377 0.320421 GAACCGCCTCTGCTGTTACA 60.320 55.000 0.00 0.00 43.76 2.41
3181 5576 4.263156 GGGTTGGTTGGAACATACTAGTCA 60.263 45.833 0.00 0.00 39.30 3.41
3231 5626 5.556915 TGATAATTAGTGGGCCGATAAAGG 58.443 41.667 0.00 0.00 0.00 3.11
3233 5628 3.945640 ATTAGTGGGCCGATAAAGGTT 57.054 42.857 0.00 0.00 0.00 3.50
3234 5629 2.702592 TAGTGGGCCGATAAAGGTTG 57.297 50.000 0.00 0.00 0.00 3.77
3257 5652 4.007644 CCACCAGCAGTGCTCGGA 62.008 66.667 29.06 0.00 45.83 4.55
3287 5688 3.423154 GGCTGCAGGTGCGTGTAC 61.423 66.667 17.12 0.00 45.83 2.90
3328 5729 1.632589 TCTACTGCTGCCACTGAAGA 58.367 50.000 0.00 0.00 0.00 2.87
3329 5730 1.273606 TCTACTGCTGCCACTGAAGAC 59.726 52.381 0.00 0.00 0.00 3.01
3330 5731 1.274728 CTACTGCTGCCACTGAAGACT 59.725 52.381 0.00 0.00 0.00 3.24
3331 5732 0.250209 ACTGCTGCCACTGAAGACTG 60.250 55.000 0.00 0.00 0.00 3.51
3428 5831 2.046507 CAGGCCAGTCACTGCCTC 60.047 66.667 15.57 0.85 36.43 4.70
3436 5839 1.476085 CAGTCACTGCCTCACCTAGAG 59.524 57.143 0.00 0.00 44.31 2.43
3508 5914 3.952323 CTGGGTAAGTCTAGAACCGATGA 59.048 47.826 6.09 0.00 33.89 2.92
3521 5927 1.337728 ACCGATGAACACGCTTGATCA 60.338 47.619 5.63 5.63 38.74 2.92
3533 5939 4.327357 CACGCTTGATCAGATCGTTACTTT 59.673 41.667 13.73 0.00 0.00 2.66
3536 5942 4.494855 GCTTGATCAGATCGTTACTTTGGC 60.495 45.833 5.91 0.00 0.00 4.52
3567 5973 6.145696 GCCAGTGAGTAAAAACAGTACTGTAG 59.854 42.308 28.13 2.79 44.13 2.74
3596 6002 5.173664 GGATTTGCCTTGGATTTGAAGAAG 58.826 41.667 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.316071 TTCAACGCCGGTATAACTCAA 57.684 42.857 1.90 0.00 0.00 3.02
13 14 2.936498 AGACATCTTTATTCAACGCCGG 59.064 45.455 0.00 0.00 0.00 6.13
17 18 6.147821 AGTTGACCAGACATCTTTATTCAACG 59.852 38.462 0.00 0.00 44.01 4.10
76 83 1.067295 ATGAGGCTGGTGGTCTTCAA 58.933 50.000 0.00 0.00 0.00 2.69
77 84 1.951209 TATGAGGCTGGTGGTCTTCA 58.049 50.000 0.00 0.00 0.00 3.02
82 89 4.650972 TTACTTTTATGAGGCTGGTGGT 57.349 40.909 0.00 0.00 0.00 4.16
90 97 3.308866 CCGGACGCTTTACTTTTATGAGG 59.691 47.826 0.00 0.00 0.00 3.86
107 114 3.181458 TGTGAAGCCTTTATATCCCGGAC 60.181 47.826 0.73 0.00 0.00 4.79
112 119 7.547227 ACAATTTGTGTGAAGCCTTTATATCC 58.453 34.615 0.15 0.00 39.72 2.59
120 127 5.072741 ACATAGACAATTTGTGTGAAGCCT 58.927 37.500 6.80 0.00 41.96 4.58
153 160 7.362574 CCTCAAAACAAACACCTACAAAGAAGA 60.363 37.037 0.00 0.00 0.00 2.87
209 216 6.949578 AAATTAAGAATGACCAAATGTGCG 57.050 33.333 0.00 0.00 0.00 5.34
253 262 7.956420 TCTGTGTTCGTTGTATAAATGTTCT 57.044 32.000 0.00 0.00 0.00 3.01
268 279 4.672862 CGTTAGATGCTAGATCTGTGTTCG 59.327 45.833 5.18 0.00 0.00 3.95
276 287 4.376819 GCATGTTGCGTTAGATGCTAGATC 60.377 45.833 11.79 0.00 38.53 2.75
293 304 1.865788 ATCTTGTTGCGCCGCATGTT 61.866 50.000 14.63 0.00 38.76 2.71
317 368 5.122554 CCTAGTGTCGCATTAGACGATAGAT 59.877 44.000 9.73 0.00 43.70 1.98
324 375 2.194271 GCACCTAGTGTCGCATTAGAC 58.806 52.381 9.73 0.00 41.30 2.59
355 406 6.127535 ACGCTAGTTGGTTTTATAGTAGAGCA 60.128 38.462 0.00 0.00 0.00 4.26
357 408 7.431668 GTGACGCTAGTTGGTTTTATAGTAGAG 59.568 40.741 0.00 0.00 0.00 2.43
362 413 6.253727 CAGAGTGACGCTAGTTGGTTTTATAG 59.746 42.308 0.00 0.00 0.00 1.31
363 414 6.071784 TCAGAGTGACGCTAGTTGGTTTTATA 60.072 38.462 0.00 0.00 0.00 0.98
366 482 3.131396 CAGAGTGACGCTAGTTGGTTTT 58.869 45.455 0.00 0.00 0.00 2.43
392 508 1.264672 AAACAACTCGCAAACGCAAC 58.735 45.000 0.00 0.00 39.84 4.17
402 518 2.964768 GTGCTCGCTTTAAAACAACTCG 59.035 45.455 0.00 0.00 0.00 4.18
412 647 5.401376 GTGATCGTATATTGTGCTCGCTTTA 59.599 40.000 0.00 0.00 0.00 1.85
416 651 3.049912 TGTGATCGTATATTGTGCTCGC 58.950 45.455 0.00 0.00 0.00 5.03
424 659 8.516234 GTGGTCTATCTCTTGTGATCGTATATT 58.484 37.037 0.00 0.00 0.00 1.28
431 666 4.688021 GGTGTGGTCTATCTCTTGTGATC 58.312 47.826 0.00 0.00 0.00 2.92
466 701 2.937149 CTCGAGTGACGGAGAATAGTCA 59.063 50.000 3.62 0.00 44.11 3.41
485 720 3.055591 CACTCCGTGCATGATACATCTC 58.944 50.000 7.72 0.00 0.00 2.75
505 740 1.539388 CCGTTGCTTGATTTGTAGCCA 59.461 47.619 0.00 0.00 0.00 4.75
547 782 3.060895 CGATACAACTCAGAAAAGGCGAC 59.939 47.826 0.00 0.00 0.00 5.19
578 813 1.591594 CCATCGTACGCCATCGCTT 60.592 57.895 11.24 0.00 39.84 4.68
603 838 3.077359 GCCAGCCATATATTCAGACACC 58.923 50.000 0.00 0.00 0.00 4.16
634 869 8.737168 TTCTCACATTCTTTTCTCTCTCAAAA 57.263 30.769 0.00 0.00 0.00 2.44
635 870 8.206867 TCTTCTCACATTCTTTTCTCTCTCAAA 58.793 33.333 0.00 0.00 0.00 2.69
636 871 7.730084 TCTTCTCACATTCTTTTCTCTCTCAA 58.270 34.615 0.00 0.00 0.00 3.02
637 872 7.295322 TCTTCTCACATTCTTTTCTCTCTCA 57.705 36.000 0.00 0.00 0.00 3.27
638 873 9.868277 TTATCTTCTCACATTCTTTTCTCTCTC 57.132 33.333 0.00 0.00 0.00 3.20
639 874 9.874205 CTTATCTTCTCACATTCTTTTCTCTCT 57.126 33.333 0.00 0.00 0.00 3.10
666 902 9.090692 GTCAAATGTCAAAATCATAAATGAGGG 57.909 33.333 0.00 0.00 40.64 4.30
667 903 9.865321 AGTCAAATGTCAAAATCATAAATGAGG 57.135 29.630 0.00 0.00 40.64 3.86
737 973 1.236616 TGCAACGGAGCATCAAGGTG 61.237 55.000 0.00 0.00 40.11 4.00
738 974 0.537143 TTGCAACGGAGCATCAAGGT 60.537 50.000 4.86 0.00 45.19 3.50
740 976 1.469703 TGATTGCAACGGAGCATCAAG 59.530 47.619 0.00 0.00 45.19 3.02
854 1091 1.448013 GCACGGCAGAAGGGAGTAC 60.448 63.158 0.00 0.00 0.00 2.73
868 1107 1.523758 GGGGAGCTATAAATGGCACG 58.476 55.000 1.00 0.00 36.66 5.34
887 1126 2.058829 GAAGCGAGAGGAGAGAGCCG 62.059 65.000 0.00 0.00 0.00 5.52
931 1170 4.164221 GGAGAGAGAGAGAGGAGAGAGAAA 59.836 50.000 0.00 0.00 0.00 2.52
939 1183 1.488812 CGAAGGGAGAGAGAGAGAGGA 59.511 57.143 0.00 0.00 0.00 3.71
940 1184 1.488812 TCGAAGGGAGAGAGAGAGAGG 59.511 57.143 0.00 0.00 0.00 3.69
973 1217 2.286833 CGCGGTTCTAGAGAGAGAGAAG 59.713 54.545 0.00 0.00 32.43 2.85
974 1218 2.093606 TCGCGGTTCTAGAGAGAGAGAA 60.094 50.000 6.13 0.00 31.77 2.87
1204 1448 2.015587 GAAAAGGCAGATGAGGAGCAG 58.984 52.381 0.00 0.00 0.00 4.24
1323 1576 1.667154 CGATCCCGGAGCACTTCTCA 61.667 60.000 0.73 0.00 43.70 3.27
1788 2050 3.908189 TCGGCGGTGAAGTCGATA 58.092 55.556 7.21 0.00 43.75 2.92
2361 4654 1.137404 CTTGTACCCGACGTACCGG 59.863 63.158 8.64 8.64 45.89 5.28
2691 4992 3.652057 AGGAACTGAGAGAGGAGAGAG 57.348 52.381 0.00 0.00 37.18 3.20
2763 5096 5.177696 AGCGTCAAAACAGAGAGTAACAATC 59.822 40.000 0.00 0.00 0.00 2.67
2764 5097 5.057149 AGCGTCAAAACAGAGAGTAACAAT 58.943 37.500 0.00 0.00 0.00 2.71
2765 5098 4.439057 AGCGTCAAAACAGAGAGTAACAA 58.561 39.130 0.00 0.00 0.00 2.83
2766 5099 4.054780 AGCGTCAAAACAGAGAGTAACA 57.945 40.909 0.00 0.00 0.00 2.41
2767 5100 4.506654 TGAAGCGTCAAAACAGAGAGTAAC 59.493 41.667 0.00 0.00 0.00 2.50
2768 5101 4.689071 TGAAGCGTCAAAACAGAGAGTAA 58.311 39.130 0.00 0.00 0.00 2.24
2769 5102 4.316205 TGAAGCGTCAAAACAGAGAGTA 57.684 40.909 0.00 0.00 0.00 2.59
2770 5103 3.179443 TGAAGCGTCAAAACAGAGAGT 57.821 42.857 0.00 0.00 0.00 3.24
2771 5104 4.739046 AATGAAGCGTCAAAACAGAGAG 57.261 40.909 6.39 0.00 37.30 3.20
2772 5105 5.538118 TCTAATGAAGCGTCAAAACAGAGA 58.462 37.500 6.39 1.07 37.30 3.10
2773 5106 5.845985 TCTAATGAAGCGTCAAAACAGAG 57.154 39.130 6.39 0.00 37.30 3.35
2774 5107 6.204688 ACAATCTAATGAAGCGTCAAAACAGA 59.795 34.615 6.39 7.28 37.30 3.41
2775 5108 6.373779 ACAATCTAATGAAGCGTCAAAACAG 58.626 36.000 6.39 2.02 37.30 3.16
2776 5109 6.312399 ACAATCTAATGAAGCGTCAAAACA 57.688 33.333 6.39 0.00 37.30 2.83
2777 5110 8.015658 AGTAACAATCTAATGAAGCGTCAAAAC 58.984 33.333 6.39 0.00 37.30 2.43
2778 5111 8.094798 AGTAACAATCTAATGAAGCGTCAAAA 57.905 30.769 6.39 0.00 37.30 2.44
2779 5112 7.386573 TGAGTAACAATCTAATGAAGCGTCAAA 59.613 33.333 6.39 0.00 37.30 2.69
2780 5113 6.871492 TGAGTAACAATCTAATGAAGCGTCAA 59.129 34.615 6.39 0.00 37.30 3.18
2781 5114 6.394809 TGAGTAACAATCTAATGAAGCGTCA 58.605 36.000 4.40 4.40 38.41 4.35
2782 5115 6.887376 TGAGTAACAATCTAATGAAGCGTC 57.113 37.500 0.00 0.00 0.00 5.19
2783 5116 6.818644 ACATGAGTAACAATCTAATGAAGCGT 59.181 34.615 0.00 0.00 30.55 5.07
2784 5117 7.121911 CACATGAGTAACAATCTAATGAAGCG 58.878 38.462 0.00 0.00 30.55 4.68
2785 5118 7.978982 ACACATGAGTAACAATCTAATGAAGC 58.021 34.615 0.00 0.00 30.55 3.86
2786 5119 9.764870 CAACACATGAGTAACAATCTAATGAAG 57.235 33.333 0.00 0.00 30.55 3.02
2787 5120 8.729756 CCAACACATGAGTAACAATCTAATGAA 58.270 33.333 0.00 0.00 30.55 2.57
2788 5121 7.882791 ACCAACACATGAGTAACAATCTAATGA 59.117 33.333 0.00 0.00 30.55 2.57
2789 5122 7.964559 CACCAACACATGAGTAACAATCTAATG 59.035 37.037 0.00 0.00 31.85 1.90
2790 5123 7.882791 TCACCAACACATGAGTAACAATCTAAT 59.117 33.333 0.00 0.00 0.00 1.73
2791 5124 7.220740 TCACCAACACATGAGTAACAATCTAA 58.779 34.615 0.00 0.00 0.00 2.10
2792 5125 6.764379 TCACCAACACATGAGTAACAATCTA 58.236 36.000 0.00 0.00 0.00 1.98
2793 5126 5.620206 TCACCAACACATGAGTAACAATCT 58.380 37.500 0.00 0.00 0.00 2.40
2834 5167 6.936900 GGTATGTATGTATTCACATCAAGCCT 59.063 38.462 0.00 0.00 44.42 4.58
2895 5252 1.214062 CCTCCGCTCACTGTCTGTC 59.786 63.158 0.00 0.00 0.00 3.51
2896 5253 0.827925 TTCCTCCGCTCACTGTCTGT 60.828 55.000 0.00 0.00 0.00 3.41
2897 5254 0.108898 CTTCCTCCGCTCACTGTCTG 60.109 60.000 0.00 0.00 0.00 3.51
2898 5255 0.251386 TCTTCCTCCGCTCACTGTCT 60.251 55.000 0.00 0.00 0.00 3.41
2970 5332 4.577677 TGCCCTGCAAGCACGGAA 62.578 61.111 13.21 0.65 34.76 4.30
3013 5375 0.687354 GATCCTCCTGGTGTGTGTGT 59.313 55.000 0.00 0.00 34.23 3.72
3015 5377 0.473694 TGGATCCTCCTGGTGTGTGT 60.474 55.000 14.23 0.00 37.46 3.72
3199 5594 5.008712 GGCCCACTAATTATCAGTGCTTTAC 59.991 44.000 0.00 0.00 41.72 2.01
3231 5626 1.806542 CACTGCTGGTGGTGATACAAC 59.193 52.381 0.00 0.00 41.90 3.32
3233 5628 0.321564 GCACTGCTGGTGGTGATACA 60.322 55.000 11.18 0.00 45.44 2.29
3234 5629 2.471255 GCACTGCTGGTGGTGATAC 58.529 57.895 11.18 0.00 45.44 2.24
3257 5652 4.827087 CAGCCGCAGTCGCCATCT 62.827 66.667 0.00 0.00 33.11 2.90
3287 5688 2.990066 AAGAAGCCGGAGTAGGAATG 57.010 50.000 5.05 0.00 0.00 2.67
3328 5729 1.687123 ACAACTAGCCGTTCAGTCAGT 59.313 47.619 0.00 0.00 32.27 3.41
3329 5730 2.440539 ACAACTAGCCGTTCAGTCAG 57.559 50.000 0.00 0.00 32.27 3.51
3330 5731 2.159014 ACAACAACTAGCCGTTCAGTCA 60.159 45.455 0.00 0.00 32.27 3.41
3331 5732 2.480845 ACAACAACTAGCCGTTCAGTC 58.519 47.619 0.00 0.00 32.27 3.51
3508 5914 2.370281 ACGATCTGATCAAGCGTGTT 57.630 45.000 17.19 0.00 33.52 3.32
3521 5927 2.076863 GTGCAGCCAAAGTAACGATCT 58.923 47.619 0.00 0.00 0.00 2.75
3536 5942 1.225855 TTTTACTCACTGGCGTGCAG 58.774 50.000 0.00 0.00 40.99 4.41
3567 5973 5.047377 TCAAATCCAAGGCAAATCCAGTAAC 60.047 40.000 0.00 0.00 37.29 2.50
3596 6002 4.751431 AGGAACCATCTGCCTTGC 57.249 55.556 0.00 0.00 0.00 4.01



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

AutoCloner maintained by Alex Coulton.