Multiple sequence alignment - TraesCS3D01G456800

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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 TraesCS3D01G456800 chr3D 100.000 3359 0 0 1 3359 562503056 562506414 0.000000e+00 6204
1 TraesCS3D01G456800 chr3D 87.065 2211 218 41 1125 3298 562538243 562540422 0.000000e+00 2436
2 TraesCS3D01G456800 chr3D 80.974 1314 197 39 1125 2423 562545149 562546424 0.000000e+00 992
3 TraesCS3D01G456800 chr3D 78.131 1573 261 56 1124 2649 561462584 561461048 0.000000e+00 922
4 TraesCS3D01G456800 chr3D 78.210 1207 197 36 1071 2235 562348008 562349190 0.000000e+00 712
5 TraesCS3D01G456800 chr3D 76.014 1159 211 47 1125 2245 561711664 561710535 3.810000e-149 538
6 TraesCS3D01G456800 chr3D 81.529 471 61 6 1071 1518 562433110 562433577 6.850000e-97 364
7 TraesCS3D01G456800 chr3D 77.946 331 40 15 2614 2916 562565293 562565618 3.440000e-40 176
8 TraesCS3D01G456800 chr3B 92.506 2095 113 15 1018 3075 749725639 749727726 0.000000e+00 2959
9 TraesCS3D01G456800 chr3B 88.091 1587 143 23 1128 2694 749859919 749861479 0.000000e+00 1842
10 TraesCS3D01G456800 chr3B 80.501 1318 210 32 1125 2423 749979333 749980622 0.000000e+00 966
11 TraesCS3D01G456800 chr3B 78.180 1132 179 30 989 2070 749648099 749649212 0.000000e+00 660
12 TraesCS3D01G456800 chr3B 87.354 514 62 3 5 516 749719846 749720358 1.340000e-163 586
13 TraesCS3D01G456800 chr3B 88.018 434 42 6 2868 3298 749861582 749862008 3.870000e-139 505
14 TraesCS3D01G456800 chr3B 96.169 261 8 2 3097 3356 749727812 749728071 3.100000e-115 425
15 TraesCS3D01G456800 chr3B 90.667 300 22 3 545 844 749720358 749720651 8.740000e-106 394
16 TraesCS3D01G456800 chr3B 94.949 99 4 1 2805 2902 749981572 749981670 1.610000e-33 154
17 TraesCS3D01G456800 chr3A 93.092 1549 77 10 1325 2872 697617717 697619236 0.000000e+00 2241
18 TraesCS3D01G456800 chr3A 85.721 2031 206 48 1126 3116 697673471 697675457 0.000000e+00 2067
19 TraesCS3D01G456800 chr3A 80.687 1310 203 35 1125 2423 697679941 697681211 0.000000e+00 972
20 TraesCS3D01G456800 chr3A 92.418 488 19 9 2871 3357 697619318 697619788 0.000000e+00 680
21 TraesCS3D01G456800 chr3A 90.496 242 23 0 603 844 697617196 697617437 1.500000e-83 320
22 TraesCS3D01G456800 chr3A 78.378 333 39 15 2612 2916 697681656 697681983 5.720000e-43 185
23 TraesCS3D01G456800 chr3A 88.462 130 12 2 437 566 697617075 697617201 1.610000e-33 154
24 TraesCS3D01G456800 chr3A 87.402 127 15 1 911 1036 697617558 697617684 9.710000e-31 145


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 TraesCS3D01G456800 chr3D 562503056 562506414 3358 False 6204.0 6204 100.0000 1 3359 1 chr3D.!!$F3 3358
1 TraesCS3D01G456800 chr3D 562538243 562540422 2179 False 2436.0 2436 87.0650 1125 3298 1 chr3D.!!$F4 2173
2 TraesCS3D01G456800 chr3D 562545149 562546424 1275 False 992.0 992 80.9740 1125 2423 1 chr3D.!!$F5 1298
3 TraesCS3D01G456800 chr3D 561461048 561462584 1536 True 922.0 922 78.1310 1124 2649 1 chr3D.!!$R1 1525
4 TraesCS3D01G456800 chr3D 562348008 562349190 1182 False 712.0 712 78.2100 1071 2235 1 chr3D.!!$F1 1164
5 TraesCS3D01G456800 chr3D 561710535 561711664 1129 True 538.0 538 76.0140 1125 2245 1 chr3D.!!$R2 1120
6 TraesCS3D01G456800 chr3B 749725639 749728071 2432 False 1692.0 2959 94.3375 1018 3356 2 chr3B.!!$F3 2338
7 TraesCS3D01G456800 chr3B 749859919 749862008 2089 False 1173.5 1842 88.0545 1128 3298 2 chr3B.!!$F4 2170
8 TraesCS3D01G456800 chr3B 749648099 749649212 1113 False 660.0 660 78.1800 989 2070 1 chr3B.!!$F1 1081
9 TraesCS3D01G456800 chr3B 749979333 749981670 2337 False 560.0 966 87.7250 1125 2902 2 chr3B.!!$F5 1777
10 TraesCS3D01G456800 chr3B 749719846 749720651 805 False 490.0 586 89.0105 5 844 2 chr3B.!!$F2 839
11 TraesCS3D01G456800 chr3A 697673471 697675457 1986 False 2067.0 2067 85.7210 1126 3116 1 chr3A.!!$F1 1990
12 TraesCS3D01G456800 chr3A 697617075 697619788 2713 False 708.0 2241 90.3740 437 3357 5 chr3A.!!$F2 2920
13 TraesCS3D01G456800 chr3A 697679941 697681983 2042 False 578.5 972 79.5325 1125 2916 2 chr3A.!!$F3 1791

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
228 229 0.105913 GGGGTGTTGGAACCAGGAAA 60.106 55.0 0.00 0.0 42.47 3.13 F
1127 1200 0.039035 CTCCCACCGGAAAATCCCAA 59.961 55.0 9.46 0.0 37.86 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1130 1203 0.517755 CCGTCGATCTCCGTCCATAG 59.482 60.0 0.00 0.0 39.75 2.23 R
2765 3394 0.388907 GGGCATCACAACACATGCAC 60.389 55.0 6.26 0.0 46.19 4.57 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
21 22 3.733337 TGCCACTTGTTTTTGTTGTTGT 58.267 36.364 0.00 0.00 0.00 3.32
22 23 4.130118 TGCCACTTGTTTTTGTTGTTGTT 58.870 34.783 0.00 0.00 0.00 2.83
26 27 5.406780 CCACTTGTTTTTGTTGTTGTTGCTA 59.593 36.000 0.00 0.00 0.00 3.49
29 30 6.145371 ACTTGTTTTTGTTGTTGTTGCTACTG 59.855 34.615 0.00 0.00 0.00 2.74
31 32 4.448537 TTTTGTTGTTGTTGCTACTGCT 57.551 36.364 0.00 0.00 40.48 4.24
35 36 1.808411 TGTTGTTGCTACTGCTAGGC 58.192 50.000 0.00 0.00 40.48 3.93
68 69 0.530744 TGACCACCAGATGCTACGAC 59.469 55.000 0.00 0.00 0.00 4.34
103 104 3.680786 CGACGGGAGCTGTGACCA 61.681 66.667 0.00 0.00 0.00 4.02
108 109 1.668151 GGGAGCTGTGACCAACGAC 60.668 63.158 0.00 0.00 0.00 4.34
132 133 0.894835 TGTGCTTCTAGCCGTGATGA 59.105 50.000 0.00 0.00 41.51 2.92
138 139 1.834188 TCTAGCCGTGATGACAGTCA 58.166 50.000 5.50 5.50 0.00 3.41
142 143 0.742281 GCCGTGATGACAGTCAGCAT 60.742 55.000 23.82 0.00 45.09 3.79
177 178 1.761244 CGACACACGCAGCTTCAACA 61.761 55.000 0.00 0.00 34.51 3.33
182 183 1.067416 ACGCAGCTTCAACAGACGA 59.933 52.632 0.00 0.00 0.00 4.20
205 206 0.306228 CAAATGTTGCGACCGACACA 59.694 50.000 0.45 0.00 38.15 3.72
206 207 0.306533 AAATGTTGCGACCGACACAC 59.693 50.000 0.45 0.00 38.15 3.82
223 224 3.892162 CCGGGGGTGTTGGAACCA 61.892 66.667 0.00 0.00 42.47 3.67
228 229 0.105913 GGGGTGTTGGAACCAGGAAA 60.106 55.000 0.00 0.00 42.47 3.13
229 230 1.037493 GGGTGTTGGAACCAGGAAAC 58.963 55.000 0.00 0.00 42.47 2.78
243 244 2.173519 AGGAAACCTGACATGGCAATG 58.826 47.619 1.11 0.00 34.25 2.82
250 251 1.754803 CTGACATGGCAATGCTGGAAT 59.245 47.619 1.11 0.00 37.29 3.01
251 252 1.752498 TGACATGGCAATGCTGGAATC 59.248 47.619 0.00 0.00 37.29 2.52
260 261 2.125106 GCTGGAATCGGCGTCCTT 60.125 61.111 16.28 5.14 36.03 3.36
263 264 0.673644 CTGGAATCGGCGTCCTTTGT 60.674 55.000 16.28 0.00 36.03 2.83
264 265 0.953471 TGGAATCGGCGTCCTTTGTG 60.953 55.000 16.28 0.00 36.03 3.33
265 266 1.134694 GAATCGGCGTCCTTTGTGC 59.865 57.895 6.85 0.00 0.00 4.57
266 267 2.563086 GAATCGGCGTCCTTTGTGCG 62.563 60.000 6.85 0.00 0.00 5.34
326 328 3.951680 TGCTTCGACCTATGTCATGACTA 59.048 43.478 25.55 13.07 41.85 2.59
332 334 4.498177 CGACCTATGTCATGACTAGTGGTG 60.498 50.000 25.55 16.47 41.85 4.17
343 345 2.226674 GACTAGTGGTGGAAAAAGCTGC 59.773 50.000 0.00 0.00 0.00 5.25
346 348 1.136891 AGTGGTGGAAAAAGCTGCAAC 59.863 47.619 1.02 0.00 0.00 4.17
348 350 0.597377 GGTGGAAAAAGCTGCAACCG 60.597 55.000 1.02 0.00 0.00 4.44
368 371 1.296056 GCATCGGTTGTGTTACGCCT 61.296 55.000 0.00 0.00 0.00 5.52
396 399 2.048023 GCTGCAACTGGCCATAGCA 61.048 57.895 21.13 21.13 43.89 3.49
417 420 2.897969 AGACTGTAAACATCGGTGACCT 59.102 45.455 0.65 0.00 0.00 3.85
436 439 1.821753 CTGTGTCAGGACTAGAGGTGG 59.178 57.143 0.00 0.00 0.00 4.61
441 444 3.578716 TGTCAGGACTAGAGGTGGAAAAG 59.421 47.826 0.00 0.00 0.00 2.27
523 526 1.258445 CCTGCTACAACCGGAGACCT 61.258 60.000 9.46 0.00 0.00 3.85
555 558 2.661537 CCTGTGCTGCGACGACAA 60.662 61.111 0.00 0.00 0.00 3.18
569 572 1.202325 ACGACAACGACAAGTGCTACA 60.202 47.619 0.00 0.00 42.66 2.74
581 584 4.528596 ACAAGTGCTACAATAGGAGTGACT 59.471 41.667 0.00 0.00 29.66 3.41
601 604 2.432456 TGCTACAAGCGCAGTCGG 60.432 61.111 11.47 5.91 46.26 4.79
603 606 2.432456 CTACAAGCGCAGTCGGCA 60.432 61.111 11.47 0.00 45.17 5.69
724 731 4.927782 ACCTTCTGCGCAACGGCA 62.928 61.111 13.05 0.00 41.24 5.69
725 732 4.389576 CCTTCTGCGCAACGGCAC 62.390 66.667 13.05 0.00 41.24 5.01
726 733 4.389576 CTTCTGCGCAACGGCACC 62.390 66.667 13.05 0.00 41.24 5.01
818 825 2.291741 GTGCAAGAGGTTGAGAACTTGG 59.708 50.000 0.00 0.00 39.70 3.61
851 890 0.865111 CGTGTGAGGCGAAAATGACA 59.135 50.000 0.00 0.00 0.00 3.58
862 901 4.261197 GGCGAAAATGACATAAGGGATGAC 60.261 45.833 0.00 0.00 39.06 3.06
866 905 1.107945 TGACATAAGGGATGACGCGA 58.892 50.000 15.93 0.00 39.06 5.87
879 919 1.369091 GACGCGAGGCACAATCCAAT 61.369 55.000 15.93 0.00 40.66 3.16
881 921 1.353103 GCGAGGCACAATCCAATCG 59.647 57.895 0.00 0.00 0.00 3.34
886 926 3.303329 CGAGGCACAATCCAATCGTTATG 60.303 47.826 0.00 0.00 0.00 1.90
902 942 5.097529 TCGTTATGAGTGTCGTAATCCAAC 58.902 41.667 0.00 0.00 31.34 3.77
903 943 4.860352 CGTTATGAGTGTCGTAATCCAACA 59.140 41.667 0.00 0.00 31.34 3.33
906 946 5.654603 ATGAGTGTCGTAATCCAACAGTA 57.345 39.130 0.00 0.00 0.00 2.74
908 948 5.224888 TGAGTGTCGTAATCCAACAGTAAC 58.775 41.667 0.00 0.00 0.00 2.50
912 973 4.449743 TGTCGTAATCCAACAGTAACAAGC 59.550 41.667 0.00 0.00 0.00 4.01
933 995 0.249031 TGAGATGCACGTATGAGGCG 60.249 55.000 0.00 0.00 0.00 5.52
940 1002 1.663643 GCACGTATGAGGCGAAAATGA 59.336 47.619 0.00 0.00 0.00 2.57
961 1023 3.706373 AAGGCATGACGCGAGGGT 61.706 61.111 15.93 0.00 43.84 4.34
1000 1062 5.889853 ACTAGTGTCCTGTATAATCCAACGA 59.110 40.000 0.00 0.00 0.00 3.85
1015 1077 3.389687 CAACGATGGAAAACGGATCAG 57.610 47.619 0.00 0.00 0.00 2.90
1022 1084 3.408634 TGGAAAACGGATCAGGAAGAAC 58.591 45.455 0.00 0.00 0.00 3.01
1036 1101 2.547430 GGAAGAACGAGGAAGGAAACGT 60.547 50.000 0.00 0.00 40.64 3.99
1053 1120 2.813474 TTCGATTCAGCCGGCGTG 60.813 61.111 23.20 19.40 0.00 5.34
1067 1134 0.392461 GGCGTGTCCATTCTGCCTAA 60.392 55.000 0.00 0.00 42.44 2.69
1126 1199 1.688811 CTCCCACCGGAAAATCCCA 59.311 57.895 9.46 0.00 37.86 4.37
1127 1200 0.039035 CTCCCACCGGAAAATCCCAA 59.961 55.000 9.46 0.00 37.86 4.12
1130 1203 1.001520 CCCACCGGAAAATCCCAAAAC 59.998 52.381 9.46 0.00 31.13 2.43
1131 1204 1.967779 CCACCGGAAAATCCCAAAACT 59.032 47.619 9.46 0.00 31.13 2.66
1224 1335 2.790791 CCTCCTGCGCGAGATCCTT 61.791 63.158 12.10 0.00 30.97 3.36
1229 1340 2.009424 CTGCGCGAGATCCTTCTCCA 62.009 60.000 12.10 0.00 44.76 3.86
1239 1350 0.836400 TCCTTCTCCACCTCGGCTTT 60.836 55.000 0.00 0.00 33.14 3.51
1449 1564 3.532155 GCGACCTCCTCCTGCGAT 61.532 66.667 0.00 0.00 0.00 4.58
1734 1888 1.140161 GTATGCGGAGGTGTGCGTA 59.860 57.895 0.00 0.00 40.19 4.42
1745 1899 0.721718 GTGTGCGTACTTGGATCTGC 59.278 55.000 4.97 0.00 0.00 4.26
2011 2183 0.607489 GCTCAGTGTGTGGCTCCATT 60.607 55.000 0.00 0.00 0.00 3.16
2021 2193 0.617935 TGGCTCCATTCGATGTTGGA 59.382 50.000 10.71 10.71 39.70 3.53
2170 2360 3.550842 GGACAATGCTGACTTTGTGTTCC 60.551 47.826 2.50 0.00 42.42 3.62
2173 2363 2.708216 TGCTGACTTTGTGTTCCTGA 57.292 45.000 0.00 0.00 0.00 3.86
2401 2597 9.999009 CGTTGTACTATCTAAACTGAGTATGAA 57.001 33.333 0.00 0.00 0.00 2.57
2675 3295 5.221601 TGGCCAAATAAAAATGACAAGCAGA 60.222 36.000 0.61 0.00 0.00 4.26
2754 3375 1.300963 GACAGGGATGGCTCAAGCA 59.699 57.895 4.13 0.00 44.36 3.91
2765 3394 1.398390 GGCTCAAGCAATAAGACGGTG 59.602 52.381 4.13 0.00 44.36 4.94
2782 3411 1.411394 GTGTGCATGTGTTGTGATGC 58.589 50.000 0.00 0.00 44.42 3.91
3026 3932 5.362430 AGTCCTAGCTTATCAGAAACCTGAG 59.638 44.000 0.00 0.00 43.23 3.35
3031 3937 8.861086 CCTAGCTTATCAGAAACCTGAGTAATA 58.139 37.037 0.00 0.00 43.23 0.98
3161 4134 4.671377 GCATTCGAGGCATCATTACAAAA 58.329 39.130 0.00 0.00 0.00 2.44
3191 4168 2.826488 AGATTAGCCACACTCCTGACT 58.174 47.619 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.733337 ACAACAACAAAAACAAGTGGCA 58.267 36.364 0.00 0.00 0.00 4.92
1 2 4.462307 CAACAACAACAAAAACAAGTGGC 58.538 39.130 0.00 0.00 0.00 5.01
21 22 1.218047 CACCGCCTAGCAGTAGCAA 59.782 57.895 0.00 0.00 45.49 3.91
22 23 2.892640 CACCGCCTAGCAGTAGCA 59.107 61.111 0.00 0.00 45.49 3.49
26 27 2.893398 GTAGCACCGCCTAGCAGT 59.107 61.111 0.00 0.00 0.00 4.40
29 30 1.146358 CTTTCGTAGCACCGCCTAGC 61.146 60.000 0.00 0.00 0.00 3.42
31 32 0.108992 CACTTTCGTAGCACCGCCTA 60.109 55.000 0.00 0.00 0.00 3.93
35 36 0.319211 TGGTCACTTTCGTAGCACCG 60.319 55.000 0.00 0.00 34.26 4.94
41 42 2.611971 GCATCTGGTGGTCACTTTCGTA 60.612 50.000 0.93 0.00 0.00 3.43
87 88 1.668151 GTTGGTCACAGCTCCCGTC 60.668 63.158 0.00 0.00 0.00 4.79
89 90 2.738521 CGTTGGTCACAGCTCCCG 60.739 66.667 0.00 0.00 0.00 5.14
93 94 1.299926 GTCGTCGTTGGTCACAGCT 60.300 57.895 0.00 0.00 0.00 4.24
108 109 2.152699 CGGCTAGAAGCACACGTCG 61.153 63.158 0.00 0.00 44.75 5.12
119 120 1.745653 CTGACTGTCATCACGGCTAGA 59.254 52.381 11.45 0.00 31.07 2.43
132 133 3.705502 AGCCTCGATGCTGACTGT 58.294 55.556 14.78 0.00 40.90 3.55
138 139 4.887987 GCTCGCAGCCTCGATGCT 62.888 66.667 9.61 9.61 43.23 3.79
156 157 4.077188 GAAGCTGCGTGTGTCGGC 62.077 66.667 0.00 0.00 40.26 5.54
157 158 2.243957 TTGAAGCTGCGTGTGTCGG 61.244 57.895 0.00 0.00 40.26 4.79
160 161 0.461870 TCTGTTGAAGCTGCGTGTGT 60.462 50.000 0.00 0.00 0.00 3.72
164 165 1.067416 TCGTCTGTTGAAGCTGCGT 59.933 52.632 0.00 0.00 0.00 5.24
177 178 0.586319 CGCAACATTTGGTGTCGTCT 59.414 50.000 0.00 0.00 41.14 4.18
182 183 0.816018 TCGGTCGCAACATTTGGTGT 60.816 50.000 0.00 0.00 44.84 4.16
205 206 3.893399 GGTTCCAACACCCCCGGT 61.893 66.667 0.00 0.00 35.62 5.28
206 207 3.860930 CTGGTTCCAACACCCCCGG 62.861 68.421 0.00 0.00 35.73 5.73
223 224 2.173519 CATTGCCATGTCAGGTTTCCT 58.826 47.619 0.00 0.00 0.00 3.36
228 229 0.968901 CCAGCATTGCCATGTCAGGT 60.969 55.000 4.70 0.00 32.28 4.00
229 230 0.681887 TCCAGCATTGCCATGTCAGG 60.682 55.000 4.70 0.08 32.28 3.86
236 237 2.417257 GCCGATTCCAGCATTGCCA 61.417 57.895 4.70 0.00 0.00 4.92
237 238 2.414594 GCCGATTCCAGCATTGCC 59.585 61.111 4.70 0.00 0.00 4.52
243 244 1.745489 AAAGGACGCCGATTCCAGC 60.745 57.895 0.00 0.00 35.33 4.85
250 251 4.287781 TCGCACAAAGGACGCCGA 62.288 61.111 0.00 0.00 0.00 5.54
251 252 3.777925 CTCGCACAAAGGACGCCG 61.778 66.667 0.00 0.00 0.00 6.46
257 258 2.476619 CACACTAGTTCTCGCACAAAGG 59.523 50.000 0.00 0.00 0.00 3.11
260 261 1.497991 GCACACTAGTTCTCGCACAA 58.502 50.000 0.00 0.00 0.00 3.33
263 264 1.733041 GCGCACACTAGTTCTCGCA 60.733 57.895 20.66 0.00 37.92 5.10
264 265 1.078759 ATGCGCACACTAGTTCTCGC 61.079 55.000 14.90 19.47 38.25 5.03
265 266 0.642291 CATGCGCACACTAGTTCTCG 59.358 55.000 14.90 0.00 0.00 4.04
266 267 1.391485 CACATGCGCACACTAGTTCTC 59.609 52.381 14.90 0.00 0.00 2.87
310 312 4.202161 CCACCACTAGTCATGACATAGGTC 60.202 50.000 27.02 0.00 44.57 3.85
326 328 1.136891 GTTGCAGCTTTTTCCACCACT 59.863 47.619 0.00 0.00 0.00 4.00
332 334 1.664649 GCCGGTTGCAGCTTTTTCC 60.665 57.895 1.90 0.00 40.77 3.13
348 350 1.133869 GCGTAACACAACCGATGCC 59.866 57.895 0.00 0.00 0.00 4.40
352 354 1.957186 GCAGGCGTAACACAACCGA 60.957 57.895 0.00 0.00 0.00 4.69
355 357 1.082104 GCTGCAGGCGTAACACAAC 60.082 57.895 17.12 0.00 0.00 3.32
356 358 3.339731 GCTGCAGGCGTAACACAA 58.660 55.556 17.12 0.00 0.00 3.33
396 399 2.897969 AGGTCACCGATGTTTACAGTCT 59.102 45.455 0.00 0.00 0.00 3.24
417 420 1.427753 TCCACCTCTAGTCCTGACACA 59.572 52.381 0.00 0.00 0.00 3.72
436 439 3.120442 CCGACACCGATTACAACCTTTTC 60.120 47.826 0.00 0.00 38.22 2.29
441 444 1.363885 GGCCGACACCGATTACAACC 61.364 60.000 0.00 0.00 38.22 3.77
497 500 2.813908 GTTGTAGCAGGGTCGCCG 60.814 66.667 0.00 0.00 0.00 6.46
555 558 3.510360 ACTCCTATTGTAGCACTTGTCGT 59.490 43.478 0.00 0.00 0.00 4.34
569 572 3.441101 TGTAGCACCAGTCACTCCTATT 58.559 45.455 0.00 0.00 0.00 1.73
581 584 1.667830 GACTGCGCTTGTAGCACCA 60.668 57.895 9.73 0.00 42.58 4.17
616 619 3.157252 ATCATCGTCGCCTGCCCT 61.157 61.111 0.00 0.00 0.00 5.19
697 700 0.035056 CGCAGAAGGTCTTCCCCATT 60.035 55.000 7.06 0.00 40.33 3.16
725 732 0.600255 CGCGCATTAGGACCTTAGGG 60.600 60.000 8.75 0.00 38.88 3.53
726 733 0.387929 TCGCGCATTAGGACCTTAGG 59.612 55.000 8.75 0.00 0.00 2.69
727 734 1.488527 GTCGCGCATTAGGACCTTAG 58.511 55.000 8.75 0.00 0.00 2.18
782 789 2.833533 GCACGAGCAAGCACCAACA 61.834 57.895 0.00 0.00 41.58 3.33
840 847 4.552767 CGTCATCCCTTATGTCATTTTCGC 60.553 45.833 0.00 0.00 36.89 4.70
844 851 2.872245 CGCGTCATCCCTTATGTCATTT 59.128 45.455 0.00 0.00 36.89 2.32
845 852 2.102420 TCGCGTCATCCCTTATGTCATT 59.898 45.455 5.77 0.00 36.89 2.57
851 890 1.367840 GCCTCGCGTCATCCCTTAT 59.632 57.895 5.77 0.00 0.00 1.73
862 901 1.353103 GATTGGATTGTGCCTCGCG 59.647 57.895 0.00 0.00 0.00 5.87
866 905 3.879295 CTCATAACGATTGGATTGTGCCT 59.121 43.478 0.00 0.00 0.00 4.75
879 919 4.968812 TGGATTACGACACTCATAACGA 57.031 40.909 0.00 0.00 0.00 3.85
881 921 5.867716 ACTGTTGGATTACGACACTCATAAC 59.132 40.000 0.00 0.00 38.57 1.89
886 926 5.224888 TGTTACTGTTGGATTACGACACTC 58.775 41.667 0.00 0.00 38.57 3.51
912 973 1.797046 GCCTCATACGTGCATCTCATG 59.203 52.381 0.00 0.00 37.70 3.07
933 995 2.253603 GTCATGCCTTGCGTCATTTTC 58.746 47.619 0.00 0.00 0.00 2.29
943 1005 2.572095 TACCCTCGCGTCATGCCTTG 62.572 60.000 5.77 0.00 42.08 3.61
948 1010 0.719465 GTTTGTACCCTCGCGTCATG 59.281 55.000 5.77 0.00 0.00 3.07
954 1016 3.976758 GGTGGTTTGTACCCTCGC 58.023 61.111 0.00 0.00 44.35 5.03
961 1023 3.640967 ACACTAGTAACGGGTGGTTTGTA 59.359 43.478 0.00 0.00 40.09 2.41
970 1032 6.294397 GGATTATACAGGACACTAGTAACGGG 60.294 46.154 0.00 0.00 0.00 5.28
1000 1062 4.010349 GTTCTTCCTGATCCGTTTTCCAT 58.990 43.478 0.00 0.00 0.00 3.41
1008 1070 1.103803 TCCTCGTTCTTCCTGATCCG 58.896 55.000 0.00 0.00 0.00 4.18
1015 1077 2.067013 CGTTTCCTTCCTCGTTCTTCC 58.933 52.381 0.00 0.00 0.00 3.46
1022 1084 1.992170 ATCGAACGTTTCCTTCCTCG 58.008 50.000 0.46 0.00 0.00 4.63
1036 1101 2.813474 CACGCCGGCTGAATCGAA 60.813 61.111 26.68 0.00 0.00 3.71
1053 1120 6.515696 GCAGGAAATATTTAGGCAGAATGGAC 60.516 42.308 0.00 0.00 35.86 4.02
1126 1199 3.488721 CGTCGATCTCCGTCCATAGTTTT 60.489 47.826 0.00 0.00 39.75 2.43
1127 1200 2.033049 CGTCGATCTCCGTCCATAGTTT 59.967 50.000 0.00 0.00 39.75 2.66
1130 1203 0.517755 CCGTCGATCTCCGTCCATAG 59.482 60.000 0.00 0.00 39.75 2.23
1131 1204 1.512996 GCCGTCGATCTCCGTCCATA 61.513 60.000 0.00 0.00 39.75 2.74
1224 1335 2.291043 GGGAAAGCCGAGGTGGAGA 61.291 63.158 0.00 0.00 42.00 3.71
1229 1340 2.529389 AGGTGGGAAAGCCGAGGT 60.529 61.111 0.00 0.00 33.83 3.85
1239 1350 4.631740 TGGACGAGGCAGGTGGGA 62.632 66.667 0.00 0.00 0.00 4.37
1632 1780 4.407296 GGTAGGAACATCTCAGTGAATCCT 59.593 45.833 12.78 12.78 39.97 3.24
1734 1888 0.617413 CAGACCTGGCAGATCCAAGT 59.383 55.000 17.94 3.46 46.01 3.16
1870 2042 3.706594 CTCCTGGTGGCTAAATCTAGACA 59.293 47.826 0.00 0.00 41.16 3.41
2011 2183 2.734276 TTGTCATCGTCCAACATCGA 57.266 45.000 0.00 0.00 40.28 3.59
2021 2193 1.308069 GCCTGCACCATTGTCATCGT 61.308 55.000 0.00 0.00 0.00 3.73
2170 2360 1.404391 GCCACTTGCTGGATGATTCAG 59.596 52.381 0.00 0.00 43.95 3.02
2173 2363 1.660560 GCGCCACTTGCTGGATGATT 61.661 55.000 0.00 0.00 43.95 2.57
2284 2474 2.462456 ACAGGAGAGACACGTACGTA 57.538 50.000 22.34 0.00 0.00 3.57
2401 2597 7.847711 AGTACATACCTCTCTATTGCAGAAT 57.152 36.000 0.00 0.00 31.12 2.40
2754 3375 2.778299 ACACATGCACACCGTCTTATT 58.222 42.857 0.00 0.00 0.00 1.40
2765 3394 0.388907 GGGCATCACAACACATGCAC 60.389 55.000 6.26 0.00 46.19 4.57
2782 3411 9.981114 AGACAAGTCAGTTTTAATAAAAATGGG 57.019 29.630 20.90 12.90 44.15 4.00
2916 3816 1.956477 GTGGACACCAAGCATCACTTT 59.044 47.619 0.00 0.00 36.04 2.66
3161 4134 7.836183 AGGAGTGTGGCTAATCTTTGATATTTT 59.164 33.333 0.00 0.00 0.00 1.82
3191 4168 7.434492 GGAGCAAAGTGATACAGTTAGCTATA 58.566 38.462 0.00 0.00 0.00 1.31
3309 4286 7.423844 TTCATCAAGTTCCTGATAAGCTAGA 57.576 36.000 0.00 0.00 34.20 2.43


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

AutoCloner maintained by Alex Coulton.