Multiple sequence alignment - TraesCS7A01G023800

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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 TraesCS7A01G023800 chr7A 100.000 3751 0 0 1 3751 9410302 9414052 0.000000e+00 6927
1 TraesCS7A01G023800 chr7A 75.399 313 62 13 92 398 418500453 418500150 1.820000e-28 137
2 TraesCS7A01G023800 chr4A 90.359 2811 226 15 974 3751 730279756 730282554 0.000000e+00 3648
3 TraesCS7A01G023800 chr4A 91.086 2255 161 17 974 3201 730886641 730888882 0.000000e+00 3014
4 TraesCS7A01G023800 chr4A 90.192 2131 161 21 974 3088 730786958 730784860 0.000000e+00 2734
5 TraesCS7A01G023800 chr4A 87.452 2327 223 25 1461 3751 730193841 730191548 0.000000e+00 2615
6 TraesCS7A01G023800 chr4A 92.693 1218 80 5 1576 2787 728851006 728852220 0.000000e+00 1748
7 TraesCS7A01G023800 chr4A 93.089 492 28 3 974 1461 730199112 730198623 0.000000e+00 715
8 TraesCS7A01G023800 chr4A 91.964 448 33 2 1076 1522 728850474 728850919 3.180000e-175 625
9 TraesCS7A01G023800 chr4A 91.204 216 17 1 3536 3751 730888925 730889138 3.660000e-75 292
10 TraesCS7A01G023800 chr4A 85.204 196 17 6 3556 3751 728852212 728852395 1.380000e-44 191
11 TraesCS7A01G023800 chr7D 89.745 2155 151 27 1630 3751 9378345 9380462 0.000000e+00 2691
12 TraesCS7A01G023800 chr7D 87.608 2316 215 30 1473 3750 8982152 8984433 0.000000e+00 2621
13 TraesCS7A01G023800 chr7D 87.605 2146 194 24 1643 3751 8988517 8990627 0.000000e+00 2423
14 TraesCS7A01G023800 chr7D 94.925 867 34 3 2 866 9374334 9375192 0.000000e+00 1349
15 TraesCS7A01G023800 chr7D 95.527 626 20 4 960 1578 9377723 9378347 0.000000e+00 994
16 TraesCS7A01G023800 chr7D 93.069 505 35 0 974 1478 8981158 8981662 0.000000e+00 739
17 TraesCS7A01G023800 chr7D 91.991 462 33 4 1136 1597 8985509 8985966 0.000000e+00 645
18 TraesCS7A01G023800 chr7D 84.167 480 47 19 4 460 9625253 9625726 4.450000e-119 438
19 TraesCS7A01G023800 chr7D 83.333 480 47 19 4 460 9444027 9444496 2.700000e-111 412
20 TraesCS7A01G023800 chr7D 88.446 251 24 3 547 796 9625772 9626018 7.880000e-77 298
21 TraesCS7A01G023800 chr7D 87.649 251 26 3 547 796 9444542 9444788 1.700000e-73 287
22 TraesCS7A01G023800 chr7D 100.000 89 0 0 871 959 9375230 9375318 8.330000e-37 165
23 TraesCS7A01G023800 chr7D 83.453 139 19 3 212 347 369907585 369907448 3.930000e-25 126
24 TraesCS7A01G023800 chr5D 88.017 968 107 7 1632 2593 445719892 445718928 0.000000e+00 1136
25 TraesCS7A01G023800 chr5D 90.546 476 45 0 987 1462 445720670 445720195 6.840000e-177 630
26 TraesCS7A01G023800 chr6A 86.923 780 86 6 2790 3555 604452116 604452893 0.000000e+00 861
27 TraesCS7A01G023800 chr7B 77.419 682 99 26 2884 3516 713228584 713229259 4.610000e-94 355
28 TraesCS7A01G023800 chrUn 95.918 196 8 0 974 1169 475916913 475917108 6.050000e-83 318
29 TraesCS7A01G023800 chr1A 77.018 570 76 25 2904 3432 13826966 13827521 3.690000e-70 276
30 TraesCS7A01G023800 chr1A 82.540 126 20 2 262 387 20903881 20903758 3.960000e-20 110
31 TraesCS7A01G023800 chr2D 81.319 273 37 7 3293 3555 566842984 566843252 3.800000e-50 209
32 TraesCS7A01G023800 chr5B 81.295 278 32 11 3293 3555 45652470 45652742 1.370000e-49 207
33 TraesCS7A01G023800 chr4B 85.484 124 16 2 274 396 655481250 655481128 1.090000e-25 128
34 TraesCS7A01G023800 chr1B 78.756 193 29 9 212 398 15202022 15201836 6.580000e-23 119
35 TraesCS7A01G023800 chr3D 79.518 166 32 2 230 393 48454143 48454308 2.370000e-22 117


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 TraesCS7A01G023800 chr7A 9410302 9414052 3750 False 6927.000000 6927 100.000000 1 3751 1 chr7A.!!$F1 3750
1 TraesCS7A01G023800 chr4A 730279756 730282554 2798 False 3648.000000 3648 90.359000 974 3751 1 chr4A.!!$F1 2777
2 TraesCS7A01G023800 chr4A 730784860 730786958 2098 True 2734.000000 2734 90.192000 974 3088 1 chr4A.!!$R3 2114
3 TraesCS7A01G023800 chr4A 730191548 730193841 2293 True 2615.000000 2615 87.452000 1461 3751 1 chr4A.!!$R1 2290
4 TraesCS7A01G023800 chr4A 730886641 730889138 2497 False 1653.000000 3014 91.145000 974 3751 2 chr4A.!!$F3 2777
5 TraesCS7A01G023800 chr4A 728850474 728852395 1921 False 854.666667 1748 89.953667 1076 3751 3 chr4A.!!$F2 2675
6 TraesCS7A01G023800 chr7D 8981158 8990627 9469 False 1607.000000 2621 90.068250 974 3751 4 chr7D.!!$F1 2777
7 TraesCS7A01G023800 chr7D 9374334 9380462 6128 False 1299.750000 2691 95.049250 2 3751 4 chr7D.!!$F2 3749
8 TraesCS7A01G023800 chr7D 9625253 9626018 765 False 368.000000 438 86.306500 4 796 2 chr7D.!!$F4 792
9 TraesCS7A01G023800 chr7D 9444027 9444788 761 False 349.500000 412 85.491000 4 796 2 chr7D.!!$F3 792
10 TraesCS7A01G023800 chr5D 445718928 445720670 1742 True 883.000000 1136 89.281500 987 2593 2 chr5D.!!$R1 1606
11 TraesCS7A01G023800 chr6A 604452116 604452893 777 False 861.000000 861 86.923000 2790 3555 1 chr6A.!!$F1 765
12 TraesCS7A01G023800 chr7B 713228584 713229259 675 False 355.000000 355 77.419000 2884 3516 1 chr7B.!!$F1 632
13 TraesCS7A01G023800 chr1A 13826966 13827521 555 False 276.000000 276 77.018000 2904 3432 1 chr1A.!!$F1 528

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
73 74 0.179179 GCAAAGTCGCTGGATCTTGC 60.179 55.0 0.0 0.0 36.26 4.01 F
325 327 0.250338 GCCCTCGTCACCAGAAACTT 60.250 55.0 0.0 0.0 0.00 2.66 F
1481 4441 0.110192 GCTTTCCTCAACTTTCCGCG 60.110 55.0 0.0 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 3789 0.955428 GCATCAAACTGGTCGAGGCA 60.955 55.0 0.0 0.0 36.52 4.75 R
1944 5083 1.825281 CGGATGGCAGAGATCTCCCC 61.825 65.0 19.3 18.9 0.00 4.81 R
2822 5965 0.036388 TGTTGAGCGGGTGGATCTTC 60.036 55.0 0.0 0.0 30.59 2.87 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
63 64 0.368227 CTCACGATCTGCAAAGTCGC 59.632 55.000 13.06 0.00 38.85 5.19
73 74 0.179179 GCAAAGTCGCTGGATCTTGC 60.179 55.000 0.00 0.00 36.26 4.01
90 91 5.452078 TCTTGCACAAAGGATAAACAAGG 57.548 39.130 0.00 0.00 36.46 3.61
91 92 4.892934 TCTTGCACAAAGGATAAACAAGGT 59.107 37.500 0.00 0.00 36.46 3.50
138 139 4.336993 ACAATTTTGTTGCTCGTAGGTTCA 59.663 37.500 0.00 0.00 38.47 3.18
184 185 4.684703 GCTCGTACTAAGTTTCAAAGCTGA 59.315 41.667 0.00 0.00 0.00 4.26
219 221 4.778904 TGATTTTGTCGGACGATTTTGTC 58.221 39.130 3.34 0.00 38.17 3.18
234 236 4.339872 TTTTGTCGGTTGCTCCTACTAA 57.660 40.909 5.24 2.11 33.65 2.24
296 298 9.689976 TCATCAAAACGTATTCAAAATGAATGT 57.310 25.926 14.23 3.69 45.77 2.71
312 314 5.309323 TGAATGTTATTTGAAAGCCCTCG 57.691 39.130 0.00 0.00 0.00 4.63
325 327 0.250338 GCCCTCGTCACCAGAAACTT 60.250 55.000 0.00 0.00 0.00 2.66
347 349 9.777297 AACTTGAATATGCAAACCAAACTTAAT 57.223 25.926 0.00 0.00 0.00 1.40
525 527 6.566079 TTCAATCTCTCTCTCTCTCTCTCT 57.434 41.667 0.00 0.00 0.00 3.10
526 528 6.166984 TCAATCTCTCTCTCTCTCTCTCTC 57.833 45.833 0.00 0.00 0.00 3.20
527 529 5.662657 TCAATCTCTCTCTCTCTCTCTCTCA 59.337 44.000 0.00 0.00 0.00 3.27
528 530 5.543507 ATCTCTCTCTCTCTCTCTCTCAC 57.456 47.826 0.00 0.00 0.00 3.51
529 531 4.352893 TCTCTCTCTCTCTCTCTCTCACA 58.647 47.826 0.00 0.00 0.00 3.58
530 532 4.160439 TCTCTCTCTCTCTCTCTCTCACAC 59.840 50.000 0.00 0.00 0.00 3.82
531 533 3.837731 TCTCTCTCTCTCTCTCTCACACA 59.162 47.826 0.00 0.00 0.00 3.72
532 534 3.935203 CTCTCTCTCTCTCTCTCACACAC 59.065 52.174 0.00 0.00 0.00 3.82
533 535 3.326297 TCTCTCTCTCTCTCTCACACACA 59.674 47.826 0.00 0.00 0.00 3.72
574 576 1.700523 TGCGACAAATTTGATGCAGC 58.299 45.000 26.54 20.81 37.10 5.25
674 676 3.247648 ACATCACAAGCAAACGTACAGTC 59.752 43.478 0.00 0.00 0.00 3.51
694 696 6.179040 CAGTCCCTTTCTCTCTCATTTTCAT 58.821 40.000 0.00 0.00 0.00 2.57
710 712 1.186200 TCATGGCTATAGCTAGGGCG 58.814 55.000 23.53 8.63 44.37 6.13
776 778 1.370051 GCGTTTTGCTTCGTGGACC 60.370 57.895 0.00 0.00 41.73 4.46
839 842 9.715121 AATTTTAGGTGTGAGAATCGTACTAAA 57.285 29.630 0.00 0.00 38.61 1.85
866 869 6.150318 GGCATGCTCATCTTATCATTTTCAG 58.850 40.000 18.92 0.00 0.00 3.02
867 870 5.629849 GCATGCTCATCTTATCATTTTCAGC 59.370 40.000 11.37 0.00 0.00 4.26
868 871 6.734871 GCATGCTCATCTTATCATTTTCAGCA 60.735 38.462 11.37 0.00 38.64 4.41
869 872 6.954487 TGCTCATCTTATCATTTTCAGCAT 57.046 33.333 0.00 0.00 29.56 3.79
981 3422 6.001460 TGACCTACAAATAACAACCTTCCTG 58.999 40.000 0.00 0.00 0.00 3.86
1070 3515 1.172812 GGAGGAAACTTGCGGTGCTT 61.173 55.000 0.00 0.00 44.43 3.91
1139 3584 3.692406 GACGACCAGGACGGGCTT 61.692 66.667 15.92 0.00 43.06 4.35
1145 3590 2.358737 CAGGACGGGCTTCGCTTT 60.359 61.111 0.29 0.00 43.89 3.51
1169 3614 2.024941 GGTCCCCATCATCCACTTCTTT 60.025 50.000 0.00 0.00 0.00 2.52
1478 4438 4.156739 CAGGTATGCTTTCCTCAACTTTCC 59.843 45.833 0.00 0.00 30.91 3.13
1481 4441 0.110192 GCTTTCCTCAACTTTCCGCG 60.110 55.000 0.00 0.00 0.00 6.46
1494 4477 2.459060 TTCCGCGTTGATAAACCTCA 57.541 45.000 4.92 0.00 0.00 3.86
1940 5079 2.553028 GCACCACTCCTTCTTCATTGGA 60.553 50.000 0.00 0.00 0.00 3.53
1944 5083 3.285484 CACTCCTTCTTCATTGGATGGG 58.715 50.000 0.00 0.00 0.00 4.00
2168 5307 4.796495 GCTTCCCCGGTCGCCATT 62.796 66.667 0.00 0.00 0.00 3.16
2174 5313 3.496131 CCGGTCGCCATTTCCACG 61.496 66.667 0.00 0.00 0.00 4.94
2207 5346 1.221840 CGCCAACCCTGTGAGCTAT 59.778 57.895 0.00 0.00 0.00 2.97
2478 5617 0.833834 CATGGGCGAGGAGGGTATCT 60.834 60.000 0.00 0.00 0.00 1.98
2595 5734 5.498393 AGATGTGATCTGCAATCTGAGTTT 58.502 37.500 9.34 0.00 38.44 2.66
2612 5751 7.623630 TCTGAGTTTGAATCATCATCTGGTAA 58.376 34.615 0.00 0.00 34.96 2.85
2640 5779 6.089820 CGGTTTCAATTGACCATCAAAATGAG 59.910 38.462 7.89 0.00 40.12 2.90
2707 5848 8.500753 TTAGTCACTTTCTTCTTTAGCAAACA 57.499 30.769 0.00 0.00 0.00 2.83
2715 5856 9.736023 CTTTCTTCTTTAGCAAACAATGTAAGT 57.264 29.630 0.00 0.00 0.00 2.24
2806 5949 1.740296 GGTTGTGCTATGCGTCGGT 60.740 57.895 0.00 0.00 0.00 4.69
2822 5965 2.850647 GTCGGTCGACGGATCTTTTAAG 59.149 50.000 25.92 0.00 44.45 1.85
2842 5986 0.400213 AAGATCCACCCGCTCAACAA 59.600 50.000 0.00 0.00 0.00 2.83
2845 5989 2.063015 ATCCACCCGCTCAACAACCA 62.063 55.000 0.00 0.00 0.00 3.67
2852 5996 3.016736 CCCGCTCAACAACCATTAGATT 58.983 45.455 0.00 0.00 0.00 2.40
2913 6057 1.400494 ACAAAGACGGTGTTGCAGAAC 59.600 47.619 0.00 0.00 0.00 3.01
2985 6132 7.556733 TTTTTCAGCTTCATCTTTTTGCAAT 57.443 28.000 0.00 0.00 0.00 3.56
3007 6154 3.529533 AGAGATGATGTTGCGGAAAGAG 58.470 45.455 0.00 0.00 0.00 2.85
3020 6167 2.159599 CGGAAAGAGCTTCTGCAACATC 60.160 50.000 0.00 0.00 42.74 3.06
3068 6216 3.596066 AAGGATGTCGCAGCGCACT 62.596 57.895 10.87 3.41 0.00 4.40
3106 6286 1.326245 CGTTGTTGCAGAAACTCGTCA 59.674 47.619 10.69 0.00 39.70 4.35
3212 6412 3.033659 GGGACCTCCAGTCTAGATCAA 57.966 52.381 0.00 0.00 45.54 2.57
3218 6418 0.461548 CCAGTCTAGATCAAGCCGCA 59.538 55.000 0.00 0.00 0.00 5.69
3235 6435 4.790962 AGCAGAGGTGGCATGGCG 62.791 66.667 15.27 0.00 0.00 5.69
3255 6455 0.953960 CTTACCGTTGACACCTGGGC 60.954 60.000 0.00 0.00 0.00 5.36
3278 6479 4.812476 CCATGGCGACCGCTCGAA 62.812 66.667 14.25 0.00 43.06 3.71
3291 6492 2.203938 TCGAACCCAGCCTCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
3330 6542 0.250727 CCGGTGGAGGTTGTGTCATT 60.251 55.000 0.00 0.00 0.00 2.57
3331 6543 1.002659 CCGGTGGAGGTTGTGTCATTA 59.997 52.381 0.00 0.00 0.00 1.90
3441 6653 8.210946 AGTTGCAAGAATATACTATGTGGCTAA 58.789 33.333 0.00 0.00 0.00 3.09
3456 6668 3.558418 GTGGCTAACGTTTCAGTGAAGAA 59.442 43.478 5.91 0.00 0.00 2.52
3470 6683 3.265479 AGTGAAGAAAAGGATGAGGGAGG 59.735 47.826 0.00 0.00 0.00 4.30
3480 6697 3.083997 GAGGGAGGGATGCGGTGT 61.084 66.667 0.00 0.00 0.00 4.16
3530 12949 4.615223 CGTAGGACGTCAGACAAAAGATCA 60.615 45.833 18.91 0.00 36.74 2.92
3613 13032 8.902806 GGAATAACTTACATTGTCATCCATTGA 58.097 33.333 0.00 0.00 0.00 2.57
3632 13051 6.538742 CCATTGAATCTACTTCATGTAACGGT 59.461 38.462 0.00 0.00 43.30 4.83
3642 13061 5.763204 ACTTCATGTAACGGTTGAGAATTGT 59.237 36.000 3.07 0.00 0.00 2.71
3682 13101 3.181516 GCCGTCAGATCAATTCTTGTGTC 60.182 47.826 0.00 0.00 29.93 3.67
3700 13119 2.100989 GTCGTACCAGATCCTTCCACT 58.899 52.381 0.00 0.00 0.00 4.00
3711 13130 0.038744 CCTTCCACTTGGTCATGGCT 59.961 55.000 0.00 0.00 35.81 4.75
3718 13137 0.674581 CTTGGTCATGGCTTGCTCGA 60.675 55.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.521681 GTAGATGCGTGCCTCCACC 60.522 63.158 0.00 0.00 38.79 4.61
63 64 5.183713 TGTTTATCCTTTGTGCAAGATCCAG 59.816 40.000 0.00 0.00 33.80 3.86
116 117 4.854399 TGAACCTACGAGCAACAAAATTG 58.146 39.130 0.00 0.00 0.00 2.32
117 118 4.819630 TCTGAACCTACGAGCAACAAAATT 59.180 37.500 0.00 0.00 0.00 1.82
138 139 6.016276 AGCGTCCAACAAAATCATAAGTTTCT 60.016 34.615 0.00 0.00 0.00 2.52
156 157 2.553602 TGAAACTTAGTACGAGCGTCCA 59.446 45.455 0.00 0.00 0.00 4.02
184 185 9.673454 GTCCGACAAAATCATAAGTTTAACTTT 57.327 29.630 15.83 1.65 39.51 2.66
219 221 3.921677 TGAAACTTAGTAGGAGCAACCG 58.078 45.455 0.00 0.00 44.74 4.44
234 236 9.628746 TTTCGCTAAGTTTTAACTTTTGAAACT 57.371 25.926 12.62 3.65 46.52 2.66
296 298 3.078837 GGTGACGAGGGCTTTCAAATAA 58.921 45.455 0.00 0.00 0.00 1.40
307 309 1.070134 TCAAGTTTCTGGTGACGAGGG 59.930 52.381 0.00 0.00 0.00 4.30
312 314 5.627499 TGCATATTCAAGTTTCTGGTGAC 57.373 39.130 0.00 0.00 0.00 3.67
397 399 2.597578 ACAACCAACCCCCTTATCAC 57.402 50.000 0.00 0.00 0.00 3.06
521 523 0.527600 GCGTGTGTGTGTGTGAGAGA 60.528 55.000 0.00 0.00 0.00 3.10
523 525 1.876263 CGCGTGTGTGTGTGTGAGA 60.876 57.895 0.00 0.00 0.00 3.27
525 527 3.559344 GCGCGTGTGTGTGTGTGA 61.559 61.111 8.43 0.00 0.00 3.58
526 528 4.918060 CGCGCGTGTGTGTGTGTG 62.918 66.667 24.19 0.00 0.00 3.82
574 576 5.655488 GGATGATATCCCGTCAGAATACTG 58.345 45.833 0.00 0.00 43.88 2.74
666 668 3.082548 TGAGAGAGAAAGGGACTGTACG 58.917 50.000 0.00 0.00 40.86 3.67
674 676 4.097589 GCCATGAAAATGAGAGAGAAAGGG 59.902 45.833 0.00 0.00 0.00 3.95
694 696 0.898789 GTCCGCCCTAGCTATAGCCA 60.899 60.000 21.17 6.92 43.38 4.75
728 730 3.378911 TCTGACTTGTGCGTGATGTTA 57.621 42.857 0.00 0.00 0.00 2.41
805 808 7.504924 TTCTCACACCTAAAATTAACCTGTG 57.495 36.000 0.00 0.00 0.00 3.66
808 811 7.166167 ACGATTCTCACACCTAAAATTAACCT 58.834 34.615 0.00 0.00 0.00 3.50
839 842 3.851458 TGATAAGATGAGCATGCCAGT 57.149 42.857 15.66 0.00 0.00 4.00
866 869 4.574013 GCACTATGCCTCATATTCCTATGC 59.426 45.833 0.00 0.00 37.42 3.14
867 870 5.987098 AGCACTATGCCTCATATTCCTATG 58.013 41.667 0.00 0.00 46.52 2.23
868 871 6.214208 TCAAGCACTATGCCTCATATTCCTAT 59.786 38.462 0.00 0.00 46.52 2.57
869 872 5.543790 TCAAGCACTATGCCTCATATTCCTA 59.456 40.000 0.00 0.00 46.52 2.94
981 3422 7.108841 TGTGAGTATGTATGAGGAGGTAAAC 57.891 40.000 0.00 0.00 0.00 2.01
1058 3503 3.595758 GGCACAAGCACCGCAAGT 61.596 61.111 0.00 0.00 44.61 3.16
1344 3789 0.955428 GCATCAAACTGGTCGAGGCA 60.955 55.000 0.00 0.00 36.52 4.75
1542 4532 9.090692 CGATTCTGAAAATTGCATTATTTTCCT 57.909 29.630 24.00 12.45 46.56 3.36
1924 5063 2.243221 CCCCATCCAATGAAGAAGGAGT 59.757 50.000 0.00 0.00 34.40 3.85
1944 5083 1.825281 CGGATGGCAGAGATCTCCCC 61.825 65.000 19.30 18.90 0.00 4.81
1955 5094 2.366837 AGGTGGGATCGGATGGCA 60.367 61.111 0.00 0.00 0.00 4.92
2168 5307 3.552384 AAGTCACCGGCCGTGGAA 61.552 61.111 26.12 3.21 43.23 3.53
2207 5346 3.321648 ATCACCAGCTCCACGGCA 61.322 61.111 0.00 0.00 34.17 5.69
2338 5477 2.038269 TCGCGGATTCCAACCTTGC 61.038 57.895 6.13 0.00 0.00 4.01
2478 5617 2.347114 CATGCACACGGGGACTGA 59.653 61.111 0.00 0.00 38.67 3.41
2554 5693 0.041312 CTTGGAAAACGTGTCAGCCG 60.041 55.000 0.00 0.00 0.00 5.52
2595 5734 4.081142 ACCGTGTTACCAGATGATGATTCA 60.081 41.667 0.00 0.00 36.00 2.57
2612 5751 3.218453 TGATGGTCAATTGAAACCGTGT 58.782 40.909 10.35 0.00 38.45 4.49
2640 5779 3.368236 GTCGAGATTTCAGGTACAAGCAC 59.632 47.826 0.00 0.00 0.00 4.40
2770 5912 9.998752 AGCACAACCCTAGATATATAGTAATCT 57.001 33.333 3.79 0.00 36.45 2.40
2822 5965 0.036388 TGTTGAGCGGGTGGATCTTC 60.036 55.000 0.00 0.00 30.59 2.87
2830 5974 1.349688 TCTAATGGTTGTTGAGCGGGT 59.650 47.619 0.00 0.00 0.00 5.28
2842 5986 4.787551 TGGATAACGCCAAATCTAATGGT 58.212 39.130 0.00 0.00 40.23 3.55
2874 6018 4.299586 TGTTGCAATAGTGAGGATGGAA 57.700 40.909 0.59 0.00 0.00 3.53
2913 6057 2.616842 ACACGAGCTTTGTTACAAAGGG 59.383 45.455 30.94 15.43 0.00 3.95
2985 6132 4.686972 CTCTTTCCGCAACATCATCTCTA 58.313 43.478 0.00 0.00 0.00 2.43
3007 6154 2.983166 CATCATCGATGTTGCAGAAGC 58.017 47.619 24.09 0.00 36.97 3.86
3020 6167 5.860182 ACAAAAAGATTCTGCAACATCATCG 59.140 36.000 7.38 0.00 0.00 3.84
3037 6184 6.148948 TGCGACATCCTTTCATTACAAAAAG 58.851 36.000 0.00 0.00 33.26 2.27
3068 6216 3.632107 GCGACGGCAACAACGACA 61.632 61.111 0.00 0.00 39.62 4.35
3140 6320 2.185350 CCTCGTGCATCGGAAGCT 59.815 61.111 6.77 0.00 40.32 3.74
3148 6328 4.129737 CGGGTCGACCTCGTGCAT 62.130 66.667 32.52 0.00 40.80 3.96
3201 6401 0.103937 GCTGCGGCTTGATCTAGACT 59.896 55.000 11.21 0.00 35.22 3.24
3206 6406 1.153409 CTCTGCTGCGGCTTGATCT 60.153 57.895 20.27 0.00 39.59 2.75
3218 6418 4.790962 CGCCATGCCACCTCTGCT 62.791 66.667 0.00 0.00 0.00 4.24
3235 6435 0.953960 CCCAGGTGTCAACGGTAAGC 60.954 60.000 0.00 0.00 0.00 3.09
3277 6478 1.693640 CATGAAGGGAGGCTGGGTT 59.306 57.895 0.00 0.00 0.00 4.11
3278 6479 2.311854 CCATGAAGGGAGGCTGGGT 61.312 63.158 0.00 0.00 0.00 4.51
3291 6492 3.399181 GTGGCCTCCCGACCATGA 61.399 66.667 3.32 0.00 38.46 3.07
3330 6542 0.758734 CGTGAGGGAGGGCAATGATA 59.241 55.000 0.00 0.00 0.00 2.15
3331 6543 1.528824 CGTGAGGGAGGGCAATGAT 59.471 57.895 0.00 0.00 0.00 2.45
3354 6566 2.352805 CAGACCCACCAGGAAGGC 59.647 66.667 0.00 0.00 43.14 4.35
3441 6653 5.123227 TCATCCTTTTCTTCACTGAAACGT 58.877 37.500 0.00 0.00 35.91 3.99
3456 6668 0.849417 GCATCCCTCCCTCATCCTTT 59.151 55.000 0.00 0.00 0.00 3.11
3470 6683 2.594592 GGCCCATACACCGCATCC 60.595 66.667 0.00 0.00 0.00 3.51
3480 6697 0.108396 CACGTCATCATGGGCCCATA 59.892 55.000 36.95 23.98 34.91 2.74
3613 13032 6.931838 TCTCAACCGTTACATGAAGTAGATT 58.068 36.000 0.00 0.00 33.43 2.40
3632 13051 5.200483 ACTCTTGGGTTTGACAATTCTCAA 58.800 37.500 0.00 0.00 0.00 3.02
3642 13061 2.808933 CGGCTACAACTCTTGGGTTTGA 60.809 50.000 0.00 0.00 34.12 2.69
3682 13101 2.418746 CCAAGTGGAAGGATCTGGTACG 60.419 54.545 0.00 0.00 37.39 3.67
3700 13119 0.955428 GTCGAGCAAGCCATGACCAA 60.955 55.000 0.00 0.00 0.00 3.67
3711 13130 2.649034 GGAGTCCACGTCGAGCAA 59.351 61.111 3.60 0.00 0.00 3.91
3718 13137 1.349067 AAGCTTTAGGGAGTCCACGT 58.651 50.000 12.30 0.00 34.83 4.49


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

AutoCloner maintained by Alex Coulton.