Multiple sequence alignment - TraesCS7A01G052700

Loading Multiple Alignment...

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 TraesCS7A01G052700 chr7A 100.000 3662 0 0 1 3662 25688173 25691834 0.000000e+00 6763.0
1 TraesCS7A01G052700 chr7A 92.855 2743 138 20 909 3609 25746244 25748970 0.000000e+00 3927.0
2 TraesCS7A01G052700 chr7A 88.470 3235 268 47 1 3191 37727569 37724396 0.000000e+00 3810.0
3 TraesCS7A01G052700 chr7A 89.924 397 30 6 3273 3662 37724329 37723936 1.520000e-138 503.0
4 TraesCS7A01G052700 chr7A 94.118 51 3 0 3193 3243 37724374 37724324 1.090000e-10 78.7
5 TraesCS7A01G052700 chr7D 92.238 2319 135 16 1380 3662 24942102 24944411 0.000000e+00 3243.0
6 TraesCS7A01G052700 chr7D 91.756 1031 76 6 325 1349 24940982 24942009 0.000000e+00 1424.0
7 TraesCS7A01G052700 chr4A 91.681 2332 151 22 1363 3662 708618148 708615828 0.000000e+00 3192.0
8 TraesCS7A01G052700 chr4A 97.143 35 1 0 836 870 611267196 611267162 3.950000e-05 60.2
9 TraesCS7A01G052700 chr3A 85.915 71 9 1 694 763 696235936 696236006 1.410000e-09 75.0


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 TraesCS7A01G052700 chr7A 25688173 25691834 3661 False 6763.0 6763 100.000000 1 3662 1 chr7A.!!$F1 3661
1 TraesCS7A01G052700 chr7A 25746244 25748970 2726 False 3927.0 3927 92.855000 909 3609 1 chr7A.!!$F2 2700
2 TraesCS7A01G052700 chr7A 37723936 37727569 3633 True 1463.9 3810 90.837333 1 3662 3 chr7A.!!$R1 3661
3 TraesCS7A01G052700 chr7D 24940982 24944411 3429 False 2333.5 3243 91.997000 325 3662 2 chr7D.!!$F1 3337
4 TraesCS7A01G052700 chr4A 708615828 708618148 2320 True 3192.0 3192 91.681000 1363 3662 1 chr4A.!!$R2 2299

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
259 266 0.249489 ATATGCAACGCCGAGGAGAC 60.249 55.000 0.0 0.0 0.00 3.36 F
1651 1754 1.078918 TCCTGCAACATCCTGCTCG 60.079 57.895 0.0 0.0 43.07 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1928 0.108377 ATCGTAACATCTGGCACGCA 60.108 50.0 0.00 0.0 34.50 5.24 R
3483 3634 0.395686 AAGAGCTGAGCTGCTGACAA 59.604 50.0 13.71 0.0 44.17 3.18 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
44 45 4.566545 TTCAAACATGAGTGCACGAAAT 57.433 36.364 12.01 3.59 0.00 2.17
71 72 5.588958 TCCAAATCACACATGTTCACAAA 57.411 34.783 0.00 0.00 0.00 2.83
84 85 7.008266 CACATGTTCACAAATTATACCGAAAGC 59.992 37.037 0.00 0.00 0.00 3.51
87 88 6.858993 TGTTCACAAATTATACCGAAAGCAAC 59.141 34.615 0.00 0.00 0.00 4.17
98 99 7.859325 ATACCGAAAGCAACAACATAGTATT 57.141 32.000 0.00 0.00 0.00 1.89
123 130 2.238847 TAGATCCACGCCACACTGCC 62.239 60.000 0.00 0.00 0.00 4.85
137 144 1.077212 CTGCCCTTGCTGCCATAGT 60.077 57.895 0.00 0.00 38.71 2.12
138 145 1.378911 TGCCCTTGCTGCCATAGTG 60.379 57.895 0.00 0.00 38.71 2.74
183 190 2.583593 GTCGTCGCTCCAGCATCC 60.584 66.667 0.00 0.00 42.21 3.51
184 191 3.068064 TCGTCGCTCCAGCATCCA 61.068 61.111 0.00 0.00 42.21 3.41
185 192 2.125552 CGTCGCTCCAGCATCCAA 60.126 61.111 0.00 0.00 42.21 3.53
190 197 1.224039 GCTCCAGCATCCAAGCTCT 59.776 57.895 0.00 0.00 44.54 4.09
200 207 1.999648 TCCAAGCTCTGCCAAAACAT 58.000 45.000 0.00 0.00 0.00 2.71
209 216 1.274167 CTGCCAAAACATGCACCATCT 59.726 47.619 0.00 0.00 33.17 2.90
213 220 2.428171 CCAAAACATGCACCATCTAGGG 59.572 50.000 0.00 0.00 43.89 3.53
228 235 0.969149 TAGGGCCATCACTATGCTCG 59.031 55.000 6.18 0.00 0.00 5.03
231 238 0.390860 GGCCATCACTATGCTCGAGT 59.609 55.000 15.13 0.00 0.00 4.18
259 266 0.249489 ATATGCAACGCCGAGGAGAC 60.249 55.000 0.00 0.00 0.00 3.36
262 269 2.202492 CAACGCCGAGGAGACGAG 60.202 66.667 0.00 0.00 35.09 4.18
279 286 3.443045 GCCCACCAGCATTGTCGG 61.443 66.667 0.00 0.00 0.00 4.79
280 287 2.350895 CCCACCAGCATTGTCGGA 59.649 61.111 1.11 0.00 0.00 4.55
304 311 1.419387 AGAGGCTTTGTCTGACAGCTT 59.581 47.619 17.92 12.61 0.00 3.74
316 323 1.895798 TGACAGCTTCCTTCGATGACT 59.104 47.619 0.00 0.00 0.00 3.41
326 333 1.273606 CTTCGATGACTGTGAGGTGGT 59.726 52.381 0.00 0.00 0.00 4.16
362 376 2.878406 ACGAGGACAATGACAACTTTGG 59.122 45.455 0.00 0.00 36.09 3.28
365 379 4.554723 CGAGGACAATGACAACTTTGGTTC 60.555 45.833 0.00 0.00 36.09 3.62
367 381 3.550030 GGACAATGACAACTTTGGTTCCG 60.550 47.826 0.00 0.00 36.09 4.30
394 408 3.197790 CAGCCTGAATCCACGCCG 61.198 66.667 0.00 0.00 0.00 6.46
410 424 1.515954 CCGAAGCGAGCCCTTAGAA 59.484 57.895 0.00 0.00 0.00 2.10
419 433 2.232941 CGAGCCCTTAGAACCACAACTA 59.767 50.000 0.00 0.00 0.00 2.24
433 447 5.967088 ACCACAACTACTACAATGAGCTAG 58.033 41.667 0.00 0.00 0.00 3.42
441 455 1.799933 ACAATGAGCTAGCTAGGCCT 58.200 50.000 19.38 11.78 0.00 5.19
442 456 2.122768 ACAATGAGCTAGCTAGGCCTT 58.877 47.619 19.38 1.79 0.00 4.35
475 489 1.697432 CTGGGCCCGATTATTGACCTA 59.303 52.381 19.37 0.00 0.00 3.08
480 494 4.142038 GGCCCGATTATTGACCTAATTGT 58.858 43.478 0.00 0.00 0.00 2.71
481 495 4.583073 GGCCCGATTATTGACCTAATTGTT 59.417 41.667 0.00 0.00 0.00 2.83
482 496 5.068591 GGCCCGATTATTGACCTAATTGTTT 59.931 40.000 0.00 0.00 0.00 2.83
495 509 8.474025 TGACCTAATTGTTTGTCAGTTTTCATT 58.526 29.630 0.00 0.00 33.09 2.57
501 515 7.953158 TTGTTTGTCAGTTTTCATTGTTTGA 57.047 28.000 0.00 0.00 0.00 2.69
517 531 7.877612 TCATTGTTTGAGTTGTAGCAAGAGATA 59.122 33.333 0.00 0.00 0.00 1.98
521 535 7.331934 TGTTTGAGTTGTAGCAAGAGATATGAC 59.668 37.037 0.00 0.00 0.00 3.06
537 551 7.558444 AGAGATATGACGAAAAGTACTTCCTCT 59.442 37.037 8.95 1.11 0.00 3.69
541 555 5.075493 TGACGAAAAGTACTTCCTCTACCT 58.925 41.667 8.95 0.00 0.00 3.08
569 584 5.045668 TCATTGTTGATGAAACGGATGTG 57.954 39.130 0.00 0.00 41.73 3.21
571 586 4.909696 TTGTTGATGAAACGGATGTGTT 57.090 36.364 0.00 0.00 42.10 3.32
609 625 8.554835 TTTCAGTGACAATTAATATGGAACGA 57.445 30.769 0.00 0.00 0.00 3.85
627 643 6.183360 TGGAACGAAGAAAATAGATTCCATGC 60.183 38.462 0.00 0.00 39.28 4.06
692 709 2.616842 AGCCGAACGTTTGTTTCTTGAT 59.383 40.909 14.38 0.00 38.78 2.57
702 719 7.202526 ACGTTTGTTTCTTGATCATGACAAAT 58.797 30.769 21.32 11.08 0.00 2.32
741 758 7.552459 TGACATCTTTAATAACGTGAGGATGA 58.448 34.615 14.21 0.39 35.01 2.92
744 761 7.492669 ACATCTTTAATAACGTGAGGATGACAG 59.507 37.037 14.21 0.00 35.01 3.51
776 793 2.799978 CACGCATGATAAATCCGTGCTA 59.200 45.455 0.00 0.00 41.95 3.49
783 800 7.062956 CGCATGATAAATCCGTGCTAAGTATAA 59.937 37.037 0.00 0.00 36.14 0.98
807 824 8.845413 AATTTTTGCTAGAAAATTACCATGCA 57.155 26.923 11.30 0.00 43.61 3.96
890 915 8.948853 TCAAATCATGAACGTTTCAGATTTAC 57.051 30.769 23.23 3.96 43.98 2.01
954 988 4.002982 AGAATGCAGTTCTTATTCGCACA 58.997 39.130 0.00 0.00 44.80 4.57
960 994 4.728882 GCAGTTCTTATTCGCACATCCTTG 60.729 45.833 0.00 0.00 0.00 3.61
981 1016 8.141268 TCCTTGTGATTTCAGTTTGTAATTTCC 58.859 33.333 0.00 0.00 0.00 3.13
983 1018 6.754193 TGTGATTTCAGTTTGTAATTTCCCC 58.246 36.000 0.00 0.00 0.00 4.81
1148 1189 4.394712 CCTCGCGCACCTCCCTTT 62.395 66.667 8.75 0.00 0.00 3.11
1626 1729 1.109920 AGCTCTACATCACGCCCGAT 61.110 55.000 0.00 0.00 0.00 4.18
1651 1754 1.078918 TCCTGCAACATCCTGCTCG 60.079 57.895 0.00 0.00 43.07 5.03
1825 1928 3.686016 GATGATATAATTGCCGGTGGGT 58.314 45.455 1.90 0.00 34.97 4.51
2070 2173 2.203538 CTGGCTGCCAAGGTGGTT 60.204 61.111 23.51 0.00 40.46 3.67
2077 2180 0.184692 TGCCAAGGTGGTTGATGTGA 59.815 50.000 0.00 0.00 40.46 3.58
2311 2414 5.309543 TCTGAAAATGGGGAGTTACAAGAGA 59.690 40.000 0.00 0.00 0.00 3.10
2313 2416 4.302559 AAATGGGGAGTTACAAGAGACC 57.697 45.455 0.00 0.00 0.00 3.85
2317 2420 1.553706 GGAGTTACAAGAGACCGGGA 58.446 55.000 6.32 0.00 0.00 5.14
2370 2473 1.067516 GCGCCAAATGCCATGACTTAT 59.932 47.619 0.00 0.00 36.24 1.73
2379 2482 1.952296 GCCATGACTTATGAGGCCTTG 59.048 52.381 6.77 0.00 39.21 3.61
2433 2536 1.940613 GAAGGGGCTGCAGTATTTACG 59.059 52.381 16.64 0.00 0.00 3.18
2446 2549 3.387050 AGTATTTACGGAGATGGTGACCC 59.613 47.826 0.00 0.00 0.00 4.46
2508 2611 2.547211 CGATAGCCTTTCTGAGCCAATG 59.453 50.000 0.00 0.00 0.00 2.82
2653 2756 5.005740 ACAAGCATCTCAATTCAGTGCTAA 58.994 37.500 6.80 0.00 44.66 3.09
2763 2870 1.271543 CCTTGATGGCACCAGTCTTCA 60.272 52.381 0.00 0.00 32.42 3.02
2806 2927 4.764050 TCTTCCACTGAAACTAACACCA 57.236 40.909 0.00 0.00 0.00 4.17
2829 2950 7.027760 CCATCAATAGCACATTGATCTATTGC 58.972 38.462 22.74 12.64 44.30 3.56
2840 2961 8.618677 CACATTGATCTATTGCTTGTGTAAGAT 58.381 33.333 0.00 0.00 35.92 2.40
2862 2983 0.463654 GAATGGCTGTGGCGGTGATA 60.464 55.000 0.00 0.00 39.81 2.15
2901 3022 1.207488 TGGAGGGGTCCACATCAAGG 61.207 60.000 0.00 0.00 34.33 3.61
2929 3051 7.551262 TGTGACTTACAACACACTTACTTTCAT 59.449 33.333 0.00 0.00 41.19 2.57
3033 3159 1.276421 TGAGGAACTGGAGCTGCTAAC 59.724 52.381 6.82 0.00 41.55 2.34
3069 3195 8.454106 CAAAACTTTCTGGATGAATAGTGTAGG 58.546 37.037 0.00 0.00 34.24 3.18
3100 3226 4.261197 GGTGTTCTTGGTTGCTGAACTAAG 60.261 45.833 6.67 6.67 46.74 2.18
3107 3233 4.579869 TGGTTGCTGAACTAAGATCTTCC 58.420 43.478 12.24 3.42 32.15 3.46
3108 3234 4.287067 TGGTTGCTGAACTAAGATCTTCCT 59.713 41.667 12.24 0.00 32.15 3.36
3109 3235 4.633565 GGTTGCTGAACTAAGATCTTCCTG 59.366 45.833 12.24 6.38 32.15 3.86
3110 3236 4.478206 TGCTGAACTAAGATCTTCCTGG 57.522 45.455 12.24 3.89 0.00 4.45
3111 3237 3.198635 TGCTGAACTAAGATCTTCCTGGG 59.801 47.826 12.24 0.96 0.00 4.45
3112 3238 3.452627 GCTGAACTAAGATCTTCCTGGGA 59.547 47.826 12.24 0.00 0.00 4.37
3180 3307 2.172293 GCAACTCAGATCTTCCTGGGAT 59.828 50.000 0.00 0.00 36.78 3.85
3191 3318 8.159447 CAGATCTTCCTGGGATATTGTATTTCA 58.841 37.037 0.00 0.00 0.00 2.69
3272 3419 5.405935 ACATGTAACTCAGTATGTGCTCA 57.594 39.130 0.00 0.00 37.40 4.26
3291 3438 2.257409 ATCCCCATCGTCACTGGTGC 62.257 60.000 0.00 0.00 31.44 5.01
3354 3502 4.102838 AGAGGAAGATGGTGATGATTCTGG 59.897 45.833 0.00 0.00 0.00 3.86
3400 3548 6.122850 ACGGTATTGTTGTTGATGATGATG 57.877 37.500 0.00 0.00 0.00 3.07
3411 3559 5.006941 TGTTGATGATGATGCGAGTGTATTG 59.993 40.000 0.00 0.00 0.00 1.90
3474 3625 4.920340 GGTGATCAGAAGCACGTATATGAG 59.080 45.833 0.00 0.00 42.80 2.90
3483 3634 2.294791 GCACGTATATGAGTCTGCTCCT 59.705 50.000 0.00 0.00 40.95 3.69
3579 3732 7.472100 CGGATTTATCTCAACTACAGGAGGAAT 60.472 40.741 0.00 0.00 0.00 3.01
3596 3749 9.189156 CAGGAGGAATTGGTAAAATATCTTTGA 57.811 33.333 0.00 0.00 0.00 2.69
3617 3770 5.476983 TGATCCCTATTTGTACCCTGATCT 58.523 41.667 0.00 0.00 0.00 2.75
3618 3771 5.911178 TGATCCCTATTTGTACCCTGATCTT 59.089 40.000 0.00 0.00 0.00 2.40
3620 3773 5.538877 TCCCTATTTGTACCCTGATCTTCT 58.461 41.667 0.00 0.00 0.00 2.85
3621 3774 5.602978 TCCCTATTTGTACCCTGATCTTCTC 59.397 44.000 0.00 0.00 0.00 2.87
3622 3775 5.604650 CCCTATTTGTACCCTGATCTTCTCT 59.395 44.000 0.00 0.00 0.00 3.10
3623 3776 6.100424 CCCTATTTGTACCCTGATCTTCTCTT 59.900 42.308 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.146984 CTCATGTTTGAAATGTTGCTGAATTAT 57.853 29.630 0.00 0.00 0.00 1.28
31 32 3.145286 TGGATTTCATTTCGTGCACTCA 58.855 40.909 16.19 0.00 0.00 3.41
33 34 4.582701 TTTGGATTTCATTTCGTGCACT 57.417 36.364 16.19 0.00 0.00 4.40
44 45 6.183360 TGTGAACATGTGTGATTTGGATTTCA 60.183 34.615 0.00 0.00 0.00 2.69
71 72 7.859325 ACTATGTTGTTGCTTTCGGTATAAT 57.141 32.000 0.00 0.00 0.00 1.28
84 85 9.915629 GGATCTAGTCCTAATACTATGTTGTTG 57.084 37.037 0.00 0.00 44.16 3.33
137 144 3.765894 CTTGGTGGTGGTCGTGCCA 62.766 63.158 0.00 0.00 46.95 4.92
138 145 2.978010 CTTGGTGGTGGTCGTGCC 60.978 66.667 0.00 0.00 37.90 5.01
149 156 2.232298 GACTCGAGGGCCTCTTGGTG 62.232 65.000 29.81 17.50 35.27 4.17
150 157 1.985116 GACTCGAGGGCCTCTTGGT 60.985 63.158 29.81 23.29 35.27 3.67
183 190 1.269883 TGCATGTTTTGGCAGAGCTTG 60.270 47.619 3.94 3.94 34.58 4.01
184 191 1.042229 TGCATGTTTTGGCAGAGCTT 58.958 45.000 0.00 0.00 34.58 3.74
185 192 0.316204 GTGCATGTTTTGGCAGAGCT 59.684 50.000 0.00 0.00 41.35 4.09
190 197 1.340088 AGATGGTGCATGTTTTGGCA 58.660 45.000 0.00 0.00 37.77 4.92
200 207 0.987613 TGATGGCCCTAGATGGTGCA 60.988 55.000 0.00 0.00 34.87 4.57
209 216 0.969149 CGAGCATAGTGATGGCCCTA 59.031 55.000 0.00 0.00 33.26 3.53
213 220 1.863454 CAACTCGAGCATAGTGATGGC 59.137 52.381 13.61 0.00 33.26 4.40
228 235 3.543460 GCGTTGCATATACCGTTCAACTC 60.543 47.826 0.00 0.00 35.99 3.01
231 238 1.666700 GGCGTTGCATATACCGTTCAA 59.333 47.619 0.00 0.00 0.00 2.69
259 266 2.360350 ACAATGCTGGTGGGCTCG 60.360 61.111 0.00 0.00 0.00 5.03
262 269 3.443045 CCGACAATGCTGGTGGGC 61.443 66.667 0.00 0.00 0.00 5.36
280 287 3.209410 CTGTCAGACAAAGCCTCTTTGT 58.791 45.455 20.77 20.77 44.43 2.83
298 305 1.620819 ACAGTCATCGAAGGAAGCTGT 59.379 47.619 0.00 0.00 31.90 4.40
304 311 1.546029 CACCTCACAGTCATCGAAGGA 59.454 52.381 2.61 0.00 0.00 3.36
316 323 2.677914 TCTTCTCTCAACCACCTCACA 58.322 47.619 0.00 0.00 0.00 3.58
326 333 3.692101 GTCCTCGTCTCATCTTCTCTCAA 59.308 47.826 0.00 0.00 0.00 3.02
362 376 2.970974 GCTGCAACTCAGGCGGAAC 61.971 63.158 0.00 0.00 43.06 3.62
394 408 0.249398 TGGTTCTAAGGGCTCGCTTC 59.751 55.000 2.36 0.00 0.00 3.86
410 424 4.891992 AGCTCATTGTAGTAGTTGTGGT 57.108 40.909 0.00 0.00 0.00 4.16
419 433 2.630580 GGCCTAGCTAGCTCATTGTAGT 59.369 50.000 23.26 0.00 0.00 2.73
441 455 2.300967 CCCAGGCTGCTAGGACCAA 61.301 63.158 9.56 0.00 0.00 3.67
442 456 2.688666 CCCAGGCTGCTAGGACCA 60.689 66.667 9.56 0.00 0.00 4.02
462 476 8.450964 ACTGACAAACAATTAGGTCAATAATCG 58.549 33.333 0.00 0.00 39.53 3.34
475 489 8.997323 TCAAACAATGAAAACTGACAAACAATT 58.003 25.926 0.00 0.00 34.30 2.32
480 494 7.655328 ACAACTCAAACAATGAAAACTGACAAA 59.345 29.630 0.00 0.00 37.67 2.83
481 495 7.151308 ACAACTCAAACAATGAAAACTGACAA 58.849 30.769 0.00 0.00 37.67 3.18
482 496 6.686630 ACAACTCAAACAATGAAAACTGACA 58.313 32.000 0.00 0.00 37.67 3.58
495 509 7.331934 GTCATATCTCTTGCTACAACTCAAACA 59.668 37.037 0.00 0.00 0.00 2.83
500 514 5.822278 TCGTCATATCTCTTGCTACAACTC 58.178 41.667 0.00 0.00 0.00 3.01
501 515 5.836821 TCGTCATATCTCTTGCTACAACT 57.163 39.130 0.00 0.00 0.00 3.16
517 531 5.715753 AGGTAGAGGAAGTACTTTTCGTCAT 59.284 40.000 10.02 0.00 41.84 3.06
521 535 5.640189 TGAGGTAGAGGAAGTACTTTTCG 57.360 43.478 10.02 0.00 0.00 3.46
583 599 9.004717 TCGTTCCATATTAATTGTCACTGAAAA 57.995 29.630 0.00 0.00 0.00 2.29
654 670 4.485875 TCGGCTATATCAGGGTCCTAAAA 58.514 43.478 0.00 0.00 0.00 1.52
670 686 3.196463 TCAAGAAACAAACGTTCGGCTA 58.804 40.909 0.00 0.00 0.00 3.93
671 687 2.011222 TCAAGAAACAAACGTTCGGCT 58.989 42.857 0.00 0.00 0.00 5.52
714 731 9.476202 CATCCTCACGTTATTAAAGATGTCATA 57.524 33.333 0.00 0.00 0.00 2.15
722 739 6.106673 ACCTGTCATCCTCACGTTATTAAAG 58.893 40.000 0.00 0.00 0.00 1.85
727 744 4.553330 AAACCTGTCATCCTCACGTTAT 57.447 40.909 0.00 0.00 0.00 1.89
741 758 2.319136 TGCGTGTCAACTAAACCTGT 57.681 45.000 0.00 0.00 0.00 4.00
744 761 5.539582 TTATCATGCGTGTCAACTAAACC 57.460 39.130 5.68 0.00 0.00 3.27
783 800 8.885722 CATGCATGGTAATTTTCTAGCAAAAAT 58.114 29.630 19.40 0.00 39.83 1.82
807 824 7.177216 TCAGAGGATTGCAAATTTAGTTGACAT 59.823 33.333 1.71 0.00 0.00 3.06
890 915 5.596772 ACCCATCCTAAATAAACCGAAATGG 59.403 40.000 0.00 0.00 46.41 3.16
954 988 9.696917 GAAATTACAAACTGAAATCACAAGGAT 57.303 29.630 0.00 0.00 38.05 3.24
960 994 6.754193 TGGGGAAATTACAAACTGAAATCAC 58.246 36.000 0.00 0.00 0.00 3.06
968 1002 3.567886 GGGGGATGGGGAAATTACAAACT 60.568 47.826 0.00 0.00 0.00 2.66
1626 1729 0.532573 GGATGTTGCAGGAGACGAGA 59.467 55.000 0.00 0.00 0.00 4.04
1680 1783 3.718210 GAGTACCTTGAGGGCGGCG 62.718 68.421 0.51 0.51 40.27 6.46
1825 1928 0.108377 ATCGTAACATCTGGCACGCA 60.108 50.000 0.00 0.00 34.50 5.24
2070 2173 0.391528 CGTCCTGGCACATCACATCA 60.392 55.000 0.00 0.00 38.20 3.07
2077 2180 1.244019 GCTTTTCCGTCCTGGCACAT 61.244 55.000 0.00 0.00 38.20 3.21
2126 2229 1.070289 GTGGGACGTTCTTCTTCACCT 59.930 52.381 0.00 0.00 0.00 4.00
2268 2371 8.731275 TTTCAGATAATCCAGAAATAAGCGAA 57.269 30.769 0.00 0.00 0.00 4.70
2288 2391 5.412904 GTCTCTTGTAACTCCCCATTTTCAG 59.587 44.000 0.00 0.00 0.00 3.02
2313 2416 1.078426 GTCATCCCACACCTTCCCG 60.078 63.158 0.00 0.00 0.00 5.14
2317 2420 1.075601 ACCATGTCATCCCACACCTT 58.924 50.000 0.00 0.00 0.00 3.50
2351 2454 2.358582 TCATAAGTCATGGCATTTGGCG 59.641 45.455 0.00 0.00 46.16 5.69
2379 2482 5.114081 CCAATCTTGCAAAATCCCTTGATC 58.886 41.667 0.00 0.00 0.00 2.92
2397 2500 2.305009 CCTTCATCTGGCTTCCCAATC 58.695 52.381 0.00 0.00 41.58 2.67
2421 2524 3.449377 TCACCATCTCCGTAAATACTGCA 59.551 43.478 0.00 0.00 0.00 4.41
2478 2581 3.751175 CAGAAAGGCTATCGACCAAAACA 59.249 43.478 0.00 0.00 0.00 2.83
2508 2611 3.419264 TTGCCAACAATATCGTCATGC 57.581 42.857 0.00 0.00 0.00 4.06
2678 2781 0.843309 TGGGCTTTCAACCTGTCTGA 59.157 50.000 0.00 0.00 0.00 3.27
2684 2789 2.430694 GTCAGTTTTGGGCTTTCAACCT 59.569 45.455 0.00 0.00 0.00 3.50
2806 2927 8.297426 CAAGCAATAGATCAATGTGCTATTGAT 58.703 33.333 25.94 21.70 46.84 2.57
2829 2950 4.460382 ACAGCCATTCCAATCTTACACAAG 59.540 41.667 0.00 0.00 0.00 3.16
2840 2961 2.676121 CCGCCACAGCCATTCCAA 60.676 61.111 0.00 0.00 34.57 3.53
2862 2983 2.574006 TGAGCTCATCAAACAGCCTT 57.426 45.000 13.74 0.00 36.17 4.35
2929 3051 9.653287 CTCCTGTAACTCTGTTTTCACATAATA 57.347 33.333 0.00 0.00 30.39 0.98
3033 3159 5.890334 TCCAGAAAGTTTTGTTGCTAACAG 58.110 37.500 0.00 0.00 43.27 3.16
3069 3195 4.055360 GCAACCAAGAACACCATTTAACC 58.945 43.478 0.00 0.00 0.00 2.85
3100 3226 5.104259 AGTAACAATGTCCCAGGAAGATC 57.896 43.478 0.00 0.00 0.00 2.75
3102 3228 4.020218 CAGAGTAACAATGTCCCAGGAAGA 60.020 45.833 0.00 0.00 0.00 2.87
3104 3230 3.650942 ACAGAGTAACAATGTCCCAGGAA 59.349 43.478 0.00 0.00 0.00 3.36
3105 3231 3.248024 ACAGAGTAACAATGTCCCAGGA 58.752 45.455 0.00 0.00 0.00 3.86
3106 3232 3.703001 ACAGAGTAACAATGTCCCAGG 57.297 47.619 0.00 0.00 0.00 4.45
3107 3233 6.406370 TGAATACAGAGTAACAATGTCCCAG 58.594 40.000 0.00 0.00 0.00 4.45
3108 3234 6.013725 ACTGAATACAGAGTAACAATGTCCCA 60.014 38.462 0.00 0.00 46.03 4.37
3109 3235 6.407202 ACTGAATACAGAGTAACAATGTCCC 58.593 40.000 0.00 0.00 46.03 4.46
3110 3236 7.819900 AGAACTGAATACAGAGTAACAATGTCC 59.180 37.037 0.00 0.00 46.03 4.02
3111 3237 8.764524 AGAACTGAATACAGAGTAACAATGTC 57.235 34.615 0.00 0.00 46.03 3.06
3112 3238 8.367911 TGAGAACTGAATACAGAGTAACAATGT 58.632 33.333 0.00 0.00 46.03 2.71
3180 3307 5.067674 GCAAGCCATGGACTGAAATACAATA 59.932 40.000 18.40 0.00 0.00 1.90
3191 3318 1.819753 TATAGGGCAAGCCATGGACT 58.180 50.000 18.40 9.58 37.98 3.85
3272 3419 1.907739 CACCAGTGACGATGGGGAT 59.092 57.895 0.00 0.00 44.59 3.85
3291 3438 2.359602 CCACAGCCCAGCAGTCTG 60.360 66.667 0.00 0.00 40.02 3.51
3400 3548 3.813529 AACAAAGAGCAATACACTCGC 57.186 42.857 0.00 0.00 39.23 5.03
3411 3559 9.624697 TCACATATATTTCACAAAACAAAGAGC 57.375 29.630 0.00 0.00 0.00 4.09
3483 3634 0.395686 AAGAGCTGAGCTGCTGACAA 59.604 50.000 13.71 0.00 44.17 3.18
3512 3663 8.798859 ACATAGTTTACAAGAGCAATTCATCT 57.201 30.769 0.00 0.00 0.00 2.90
3596 3749 6.153924 AGAAGATCAGGGTACAAATAGGGAT 58.846 40.000 0.00 0.00 0.00 3.85
3617 3770 8.883731 CAGTTTCAGTCTGAAAAACTAAGAGAA 58.116 33.333 25.87 0.82 46.53 2.87
3618 3771 8.041323 ACAGTTTCAGTCTGAAAAACTAAGAGA 58.959 33.333 25.87 1.31 46.53 3.10
3620 3773 7.822334 TGACAGTTTCAGTCTGAAAAACTAAGA 59.178 33.333 25.87 7.98 46.53 2.10
3621 3774 7.974675 TGACAGTTTCAGTCTGAAAAACTAAG 58.025 34.615 25.87 13.78 46.53 2.18
3622 3775 7.915293 TGACAGTTTCAGTCTGAAAAACTAA 57.085 32.000 25.87 11.87 46.53 2.24
3623 3776 7.389330 TGTTGACAGTTTCAGTCTGAAAAACTA 59.611 33.333 25.87 14.62 46.53 2.24


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

AutoCloner maintained by Alex Coulton.