Multiple sequence alignment - TraesCS2B01G111900

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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 TraesCS2B01G111900 chr2B 100.000 2606 0 0 1 2606 74203226 74205831 0.000000e+00 4813.0
1 TraesCS2B01G111900 chr2D 84.618 2698 161 93 3 2606 46825028 46827565 0.000000e+00 2449.0
2 TraesCS2B01G111900 chr2A 85.869 2130 131 56 549 2606 50132949 50134980 0.000000e+00 2109.0
3 TraesCS2B01G111900 chr2A 80.579 484 33 26 3 478 50132515 50132945 1.510000e-82 316.0
4 TraesCS2B01G111900 chr7D 80.156 257 29 15 1319 1563 605168645 605168891 3.450000e-39 172.0
5 TraesCS2B01G111900 chr1B 87.952 83 10 0 1433 1515 27674478 27674396 5.940000e-17 99.0
6 TraesCS2B01G111900 chrUn 89.474 76 8 0 1433 1508 23302263 23302338 2.130000e-16 97.1
7 TraesCS2B01G111900 chr7A 90.741 54 3 1 913 966 701127238 701127187 1.290000e-08 71.3


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 TraesCS2B01G111900 chr2B 74203226 74205831 2605 False 4813.0 4813 100.000 1 2606 1 chr2B.!!$F1 2605
1 TraesCS2B01G111900 chr2D 46825028 46827565 2537 False 2449.0 2449 84.618 3 2606 1 chr2D.!!$F1 2603
2 TraesCS2B01G111900 chr2A 50132515 50134980 2465 False 1212.5 2109 83.224 3 2606 2 chr2A.!!$F1 2603

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
120 131 0.039798 CGTACGTATATGCCGGCAGT 60.04 55.0 35.36 27.13 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1924 0.905357 CACACCCCCAAACCAAAACA 59.095 50.0 0.0 0.0 0.0 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
67 75 1.266989 CTTTTGGTGGAAAGCGAGACC 59.733 52.381 0.00 0.00 30.66 3.85
112 123 2.717519 CGTTCACTGGCGTACGTATATG 59.282 50.000 17.90 10.78 0.00 1.78
113 124 2.410785 TCACTGGCGTACGTATATGC 57.589 50.000 17.90 3.65 41.87 3.14
117 128 3.455685 GCGTACGTATATGCCGGC 58.544 61.111 22.73 22.73 37.35 6.13
118 129 1.372004 GCGTACGTATATGCCGGCA 60.372 57.895 34.80 34.80 37.35 5.69
119 130 1.342082 GCGTACGTATATGCCGGCAG 61.342 60.000 35.36 22.70 37.35 4.85
120 131 0.039798 CGTACGTATATGCCGGCAGT 60.040 55.000 35.36 27.13 0.00 4.40
121 132 1.197492 CGTACGTATATGCCGGCAGTA 59.803 52.381 35.36 26.03 0.00 2.74
122 133 2.589014 GTACGTATATGCCGGCAGTAC 58.411 52.381 35.36 31.59 0.00 2.73
123 134 1.325355 ACGTATATGCCGGCAGTACT 58.675 50.000 33.69 23.53 0.00 2.73
124 135 1.000607 ACGTATATGCCGGCAGTACTG 60.001 52.381 33.69 29.58 0.00 2.74
125 136 1.000607 CGTATATGCCGGCAGTACTGT 60.001 52.381 33.69 22.63 0.00 3.55
126 137 2.227149 CGTATATGCCGGCAGTACTGTA 59.773 50.000 33.69 23.76 0.00 2.74
127 138 3.119602 CGTATATGCCGGCAGTACTGTAT 60.120 47.826 33.69 27.26 0.00 2.29
136 147 2.460918 GCAGTACTGTATACCAGCACG 58.539 52.381 23.44 0.00 45.68 5.34
151 167 1.418342 GCACGGTATGTACAGGTGCG 61.418 60.000 20.74 3.40 43.23 5.34
172 189 2.596452 GCATGATGGGACGATACGTAG 58.404 52.381 0.08 0.00 41.37 3.51
230 250 2.500369 GCAGAATGTGCGTGCGTG 60.500 61.111 0.00 0.00 43.99 5.34
231 251 2.500369 CAGAATGTGCGTGCGTGC 60.500 61.111 0.00 0.00 0.00 5.34
232 252 4.075910 AGAATGTGCGTGCGTGCG 62.076 61.111 0.00 0.00 37.81 5.34
233 253 4.368808 GAATGTGCGTGCGTGCGT 62.369 61.111 3.11 0.00 37.81 5.24
340 360 3.495806 GCATGTAGGAAAGCTATGCCTCT 60.496 47.826 5.32 0.00 38.48 3.69
341 361 3.827008 TGTAGGAAAGCTATGCCTCTG 57.173 47.619 5.32 0.00 33.28 3.35
342 362 2.158900 TGTAGGAAAGCTATGCCTCTGC 60.159 50.000 5.32 0.00 33.28 4.26
344 364 0.182299 GGAAAGCTATGCCTCTGCCT 59.818 55.000 0.00 0.00 36.33 4.75
345 365 1.592064 GAAAGCTATGCCTCTGCCTC 58.408 55.000 0.00 0.00 36.33 4.70
346 366 0.914644 AAAGCTATGCCTCTGCCTCA 59.085 50.000 0.00 0.00 36.33 3.86
347 367 1.138568 AAGCTATGCCTCTGCCTCAT 58.861 50.000 0.00 0.00 36.33 2.90
348 368 0.397187 AGCTATGCCTCTGCCTCATG 59.603 55.000 0.00 0.00 36.33 3.07
349 369 0.605860 GCTATGCCTCTGCCTCATGG 60.606 60.000 0.00 0.00 36.33 3.66
391 415 4.767255 CTGGCCCGGCTCACTCAC 62.767 72.222 9.86 0.00 0.00 3.51
393 417 4.459089 GGCCCGGCTCACTCACTC 62.459 72.222 9.86 0.00 0.00 3.51
394 418 4.803426 GCCCGGCTCACTCACTCG 62.803 72.222 0.71 0.00 0.00 4.18
395 419 4.803426 CCCGGCTCACTCACTCGC 62.803 72.222 0.00 0.00 0.00 5.03
396 420 3.753434 CCGGCTCACTCACTCGCT 61.753 66.667 0.00 0.00 0.00 4.93
397 421 2.202544 CGGCTCACTCACTCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
398 422 2.183046 GGCTCACTCACTCGCTCC 59.817 66.667 0.00 0.00 0.00 4.70
399 423 2.640302 GGCTCACTCACTCGCTCCA 61.640 63.158 0.00 0.00 0.00 3.86
400 424 1.445238 GCTCACTCACTCGCTCCAC 60.445 63.158 0.00 0.00 0.00 4.02
401 425 1.214062 CTCACTCACTCGCTCCACC 59.786 63.158 0.00 0.00 0.00 4.61
406 430 4.135153 CACTCGCTCCACCCCTCG 62.135 72.222 0.00 0.00 0.00 4.63
431 455 4.477975 GCTCACGTACGGCGCTCT 62.478 66.667 21.06 0.00 46.11 4.09
487 511 2.696759 GGCGAAACCCCATCAACGG 61.697 63.158 0.00 0.00 0.00 4.44
488 512 2.874751 CGAAACCCCATCAACGGC 59.125 61.111 0.00 0.00 0.00 5.68
489 513 1.969064 CGAAACCCCATCAACGGCA 60.969 57.895 0.00 0.00 0.00 5.69
490 514 1.584495 GAAACCCCATCAACGGCAC 59.416 57.895 0.00 0.00 0.00 5.01
510 534 3.652581 GCCAGTAGCCTTTGTCCTT 57.347 52.632 0.00 0.00 34.35 3.36
511 535 1.168714 GCCAGTAGCCTTTGTCCTTG 58.831 55.000 0.00 0.00 34.35 3.61
512 536 1.168714 CCAGTAGCCTTTGTCCTTGC 58.831 55.000 0.00 0.00 0.00 4.01
513 537 1.271597 CCAGTAGCCTTTGTCCTTGCT 60.272 52.381 0.00 0.00 37.84 3.91
514 538 2.508526 CAGTAGCCTTTGTCCTTGCTT 58.491 47.619 0.00 0.00 35.34 3.91
515 539 2.227388 CAGTAGCCTTTGTCCTTGCTTG 59.773 50.000 0.00 0.00 35.34 4.01
516 540 1.541588 GTAGCCTTTGTCCTTGCTTGG 59.458 52.381 0.00 0.00 35.34 3.61
517 541 1.005748 GCCTTTGTCCTTGCTTGGC 60.006 57.895 0.00 0.00 0.00 4.52
518 542 1.747325 GCCTTTGTCCTTGCTTGGCA 61.747 55.000 0.00 0.00 38.79 4.92
519 543 0.316204 CCTTTGTCCTTGCTTGGCAG 59.684 55.000 0.00 0.00 40.61 4.85
533 557 0.592637 TGGCAGCACGAGAACAATTG 59.407 50.000 3.24 3.24 0.00 2.32
564 588 1.816835 AGATGGACATGTACACGTCGT 59.183 47.619 14.44 7.10 32.74 4.34
569 593 0.312729 ACATGTACACGTCGTCTGCA 59.687 50.000 0.00 0.00 0.00 4.41
578 602 3.381983 TCGTCTGCAGGCGTCCAT 61.382 61.111 36.80 0.00 0.00 3.41
593 617 2.611473 CGTCCATGGGCTGATGATCTAC 60.611 54.545 15.80 0.00 0.00 2.59
594 618 2.369860 GTCCATGGGCTGATGATCTACA 59.630 50.000 9.76 0.00 0.00 2.74
660 685 2.172851 GGTGACGGTGTGTGGATTAA 57.827 50.000 0.00 0.00 0.00 1.40
662 687 3.078837 GGTGACGGTGTGTGGATTAATT 58.921 45.455 0.00 0.00 0.00 1.40
741 806 3.902881 ACAACAAAACAAATGGGAGCA 57.097 38.095 0.00 0.00 0.00 4.26
743 808 3.450457 ACAACAAAACAAATGGGAGCAGA 59.550 39.130 0.00 0.00 0.00 4.26
744 809 4.053295 CAACAAAACAAATGGGAGCAGAG 58.947 43.478 0.00 0.00 0.00 3.35
745 810 3.299503 ACAAAACAAATGGGAGCAGAGT 58.700 40.909 0.00 0.00 0.00 3.24
746 811 4.469657 ACAAAACAAATGGGAGCAGAGTA 58.530 39.130 0.00 0.00 0.00 2.59
747 812 4.278419 ACAAAACAAATGGGAGCAGAGTAC 59.722 41.667 0.00 0.00 0.00 2.73
748 813 3.788227 AACAAATGGGAGCAGAGTACA 57.212 42.857 0.00 0.00 0.00 2.90
749 814 4.307032 AACAAATGGGAGCAGAGTACAT 57.693 40.909 0.00 0.00 0.00 2.29
750 815 3.878778 ACAAATGGGAGCAGAGTACATC 58.121 45.455 0.00 0.00 0.00 3.06
751 816 3.209410 CAAATGGGAGCAGAGTACATCC 58.791 50.000 0.00 0.00 0.00 3.51
752 817 2.180946 ATGGGAGCAGAGTACATCCA 57.819 50.000 0.00 0.00 33.24 3.41
753 818 2.180946 TGGGAGCAGAGTACATCCAT 57.819 50.000 0.00 0.00 33.24 3.41
754 819 2.042464 TGGGAGCAGAGTACATCCATC 58.958 52.381 0.00 0.00 33.24 3.51
755 820 1.346068 GGGAGCAGAGTACATCCATCC 59.654 57.143 0.00 0.00 33.24 3.51
756 821 2.042464 GGAGCAGAGTACATCCATCCA 58.958 52.381 0.00 0.00 0.00 3.41
757 822 2.036992 GGAGCAGAGTACATCCATCCAG 59.963 54.545 0.00 0.00 0.00 3.86
758 823 2.697751 GAGCAGAGTACATCCATCCAGT 59.302 50.000 0.00 0.00 0.00 4.00
759 824 2.433604 AGCAGAGTACATCCATCCAGTG 59.566 50.000 0.00 0.00 0.00 3.66
760 825 2.432146 GCAGAGTACATCCATCCAGTGA 59.568 50.000 0.00 0.00 0.00 3.41
761 826 3.070734 GCAGAGTACATCCATCCAGTGAT 59.929 47.826 0.00 0.00 0.00 3.06
762 827 4.281941 GCAGAGTACATCCATCCAGTGATA 59.718 45.833 0.00 0.00 0.00 2.15
763 828 5.221521 GCAGAGTACATCCATCCAGTGATAA 60.222 44.000 0.00 0.00 0.00 1.75
764 829 6.686378 GCAGAGTACATCCATCCAGTGATAAA 60.686 42.308 0.00 0.00 0.00 1.40
765 830 7.275183 CAGAGTACATCCATCCAGTGATAAAA 58.725 38.462 0.00 0.00 0.00 1.52
766 831 7.770433 CAGAGTACATCCATCCAGTGATAAAAA 59.230 37.037 0.00 0.00 0.00 1.94
767 832 7.770897 AGAGTACATCCATCCAGTGATAAAAAC 59.229 37.037 0.00 0.00 0.00 2.43
768 833 6.828785 AGTACATCCATCCAGTGATAAAAACC 59.171 38.462 0.00 0.00 0.00 3.27
769 834 5.579047 ACATCCATCCAGTGATAAAAACCA 58.421 37.500 0.00 0.00 0.00 3.67
780 845 5.773176 AGTGATAAAAACCACCGGAATCTTT 59.227 36.000 9.46 3.48 34.00 2.52
783 848 6.492087 TGATAAAAACCACCGGAATCTTTCTT 59.508 34.615 9.46 0.00 0.00 2.52
808 873 1.001633 GCAAGTTAACTCCGTCCCTCA 59.998 52.381 8.95 0.00 0.00 3.86
883 949 1.302285 CAGCCCCTGCATCTGACTT 59.698 57.895 0.00 0.00 41.13 3.01
915 981 2.279120 CATCGAGACCAGAGCGCC 60.279 66.667 2.29 0.00 0.00 6.53
916 982 2.755876 ATCGAGACCAGAGCGCCA 60.756 61.111 2.29 0.00 0.00 5.69
917 983 2.780094 ATCGAGACCAGAGCGCCAG 61.780 63.158 2.29 0.00 0.00 4.85
919 985 4.828925 GAGACCAGAGCGCCAGCC 62.829 72.222 2.29 0.00 46.67 4.85
929 995 3.760035 CGCCAGCCCACGACTAGT 61.760 66.667 0.00 0.00 0.00 2.57
956 1022 4.312231 GCGCGCAACAACAGAGCA 62.312 61.111 29.10 0.00 0.00 4.26
961 1027 1.735360 GCAACAACAGAGCAAGCCA 59.265 52.632 0.00 0.00 0.00 4.75
1424 1490 3.827898 CGGCTCGACCACCTCCTC 61.828 72.222 5.15 0.00 39.03 3.71
1425 1491 3.462678 GGCTCGACCACCTCCTCC 61.463 72.222 0.00 0.00 38.86 4.30
1426 1492 2.363147 GCTCGACCACCTCCTCCT 60.363 66.667 0.00 0.00 0.00 3.69
1428 1494 1.755008 CTCGACCACCTCCTCCTCC 60.755 68.421 0.00 0.00 0.00 4.30
1429 1495 3.141488 CGACCACCTCCTCCTCCG 61.141 72.222 0.00 0.00 0.00 4.63
1616 1682 4.832608 GCCGTGATCCGTCCACCC 62.833 72.222 0.00 0.00 33.66 4.61
1617 1683 3.387091 CCGTGATCCGTCCACCCA 61.387 66.667 0.00 0.00 33.66 4.51
1618 1684 2.731571 CCGTGATCCGTCCACCCAT 61.732 63.158 0.00 0.00 33.66 4.00
1619 1685 1.227263 CGTGATCCGTCCACCCATC 60.227 63.158 0.00 0.00 0.00 3.51
1719 1804 1.080501 CGCTCCAGTGTGTGACGAT 60.081 57.895 0.00 0.00 0.00 3.73
1807 1898 2.689646 AGAAGAAGAAACAGTAGCCGC 58.310 47.619 0.00 0.00 0.00 6.53
1829 1924 6.313905 CCGCTCATTTGTAGATTCTTGTTAGT 59.686 38.462 0.00 0.00 0.00 2.24
1851 1952 0.336737 TTTGGTTTGGGGGTGTGTCT 59.663 50.000 0.00 0.00 0.00 3.41
1887 1988 6.115446 TCCGTAAATGCATGAGAGAGATTTT 58.885 36.000 0.00 0.00 0.00 1.82
1894 1995 6.291648 TGCATGAGAGAGATTTTCAGTACT 57.708 37.500 0.00 0.00 0.00 2.73
1897 1998 9.136323 TGCATGAGAGAGATTTTCAGTACTATA 57.864 33.333 0.00 0.00 0.00 1.31
1943 2048 0.800683 CAAGCACGAGATCGCCGTTA 60.801 55.000 12.35 0.00 44.43 3.18
1945 2050 0.102481 AGCACGAGATCGCCGTTATT 59.898 50.000 12.35 1.10 44.43 1.40
1962 2068 5.751028 CCGTTATTTTTGACAATGTTGGTGT 59.249 36.000 0.00 0.00 0.00 4.16
1963 2069 6.074569 CCGTTATTTTTGACAATGTTGGTGTC 60.075 38.462 0.00 0.00 44.67 3.67
1969 2075 3.885484 GACAATGTTGGTGTCAGACTG 57.115 47.619 1.31 0.00 44.00 3.51
1970 2076 3.206150 GACAATGTTGGTGTCAGACTGT 58.794 45.455 1.59 0.00 44.00 3.55
2051 2165 5.621228 CAGAAAGACAAGTGCAACGTTAATC 59.379 40.000 0.00 0.00 45.86 1.75
2052 2166 5.527582 AGAAAGACAAGTGCAACGTTAATCT 59.472 36.000 0.00 0.00 45.86 2.40
2098 2223 2.033550 CCCTTGACCTAATCGAGACGAG 59.966 54.545 0.00 0.00 40.99 4.18
2100 2225 2.039818 TGACCTAATCGAGACGAGCT 57.960 50.000 0.00 0.00 39.91 4.09
2101 2226 2.366533 TGACCTAATCGAGACGAGCTT 58.633 47.619 0.00 0.00 39.91 3.74
2181 2328 5.180271 GGGAGGATTAAATAACACGTGACA 58.820 41.667 25.01 9.57 0.00 3.58
2188 2335 4.330944 AAATAACACGTGACACCTCTGA 57.669 40.909 25.01 0.00 0.00 3.27
2189 2336 2.787601 TAACACGTGACACCTCTGAC 57.212 50.000 25.01 0.00 0.00 3.51
2263 2410 1.204312 GTCGCGCGCTCTTCTTTTT 59.796 52.632 30.48 0.00 0.00 1.94
2345 2507 3.501445 AGATACGTTGAGGTATACCGCTC 59.499 47.826 23.88 14.35 42.08 5.03
2554 2718 2.666596 GATGGACGGCCCTGATCCAC 62.667 65.000 3.83 6.04 45.15 4.02
2594 2763 0.317519 CGCATACGACGACATGGCTA 60.318 55.000 0.00 0.00 43.93 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.161855 AGAAGGTCAAAAGGAACCAAAATC 57.838 37.500 0.00 0.00 31.73 2.17
1 2 6.560003 AAGAAGGTCAAAAGGAACCAAAAT 57.440 33.333 0.00 0.00 31.73 1.82
6 7 5.131067 AGTGTAAGAAGGTCAAAAGGAACC 58.869 41.667 0.00 0.00 31.73 3.62
73 81 1.227999 CGCTCCACCGCAGAGAAAAA 61.228 55.000 0.00 0.00 32.86 1.94
75 83 2.048222 CGCTCCACCGCAGAGAAA 60.048 61.111 0.00 0.00 32.86 2.52
112 123 0.748450 TGGTATACAGTACTGCCGGC 59.252 55.000 22.73 22.73 0.00 6.13
113 124 2.795175 CTGGTATACAGTACTGCCGG 57.205 55.000 22.90 15.93 42.42 6.13
136 147 0.179056 ATGCCGCACCTGTACATACC 60.179 55.000 0.00 0.00 0.00 2.73
151 167 0.033504 ACGTATCGTCCCATCATGCC 59.966 55.000 0.00 0.00 33.69 4.40
172 189 4.208686 CGCCACCTACCTCCGCTC 62.209 72.222 0.00 0.00 0.00 5.03
200 220 1.565390 ATTCTGCCCCTGCTGTGCTA 61.565 55.000 4.44 0.00 38.71 3.49
342 362 1.162698 CATGATTAGGCGCCATGAGG 58.837 55.000 31.54 6.31 39.86 3.86
344 364 0.890542 GGCATGATTAGGCGCCATGA 60.891 55.000 31.54 14.47 44.25 3.07
345 365 1.582968 GGCATGATTAGGCGCCATG 59.417 57.895 31.54 23.26 44.25 3.66
346 366 1.604593 GGGCATGATTAGGCGCCAT 60.605 57.895 31.54 15.16 46.75 4.40
347 367 2.203337 GGGCATGATTAGGCGCCA 60.203 61.111 31.54 9.64 46.75 5.69
348 368 2.203337 TGGGCATGATTAGGCGCC 60.203 61.111 21.89 21.89 44.67 6.53
349 369 2.555547 GGTGGGCATGATTAGGCGC 61.556 63.158 0.00 0.00 45.37 6.53
462 486 4.941309 GGGGTTTCGCCGTGGTGT 62.941 66.667 0.00 0.00 38.44 4.16
472 496 1.584495 GTGCCGTTGATGGGGTTTC 59.416 57.895 0.00 0.00 0.00 2.78
492 516 1.168714 CAAGGACAAAGGCTACTGGC 58.831 55.000 0.00 0.00 40.90 4.85
499 523 1.005748 GCCAAGCAAGGACAAAGGC 60.006 57.895 0.00 0.00 0.00 4.35
500 524 0.316204 CTGCCAAGCAAGGACAAAGG 59.684 55.000 0.00 0.00 38.41 3.11
512 536 0.877071 ATTGTTCTCGTGCTGCCAAG 59.123 50.000 0.00 0.00 0.00 3.61
513 537 1.001487 CAATTGTTCTCGTGCTGCCAA 60.001 47.619 0.00 0.00 0.00 4.52
514 538 0.592637 CAATTGTTCTCGTGCTGCCA 59.407 50.000 0.00 0.00 0.00 4.92
515 539 0.874390 TCAATTGTTCTCGTGCTGCC 59.126 50.000 5.13 0.00 0.00 4.85
516 540 2.686558 TTCAATTGTTCTCGTGCTGC 57.313 45.000 5.13 0.00 0.00 5.25
517 541 2.966708 CGTTTCAATTGTTCTCGTGCTG 59.033 45.455 5.13 0.00 0.00 4.41
518 542 2.869801 TCGTTTCAATTGTTCTCGTGCT 59.130 40.909 5.13 0.00 0.00 4.40
519 543 3.247563 TCGTTTCAATTGTTCTCGTGC 57.752 42.857 5.13 0.00 0.00 5.34
520 544 4.142364 CGTTTCGTTTCAATTGTTCTCGTG 59.858 41.667 5.13 0.00 0.00 4.35
521 545 4.033129 TCGTTTCGTTTCAATTGTTCTCGT 59.967 37.500 5.13 0.00 0.00 4.18
522 546 4.510812 TCGTTTCGTTTCAATTGTTCTCG 58.489 39.130 5.13 6.98 0.00 4.04
523 547 5.734311 TCTCGTTTCGTTTCAATTGTTCTC 58.266 37.500 5.13 0.00 0.00 2.87
533 557 3.432252 ACATGTCCATCTCGTTTCGTTTC 59.568 43.478 0.00 0.00 0.00 2.78
564 588 4.100084 CCCATGGACGCCTGCAGA 62.100 66.667 17.39 0.00 0.00 4.26
569 593 3.092511 ATCAGCCCATGGACGCCT 61.093 61.111 15.22 0.50 0.00 5.52
585 609 4.492611 CGCTGCATGTAGATGTAGATCAT 58.507 43.478 19.98 0.00 43.14 2.45
593 617 1.143305 GTAGGCGCTGCATGTAGATG 58.857 55.000 15.68 7.04 0.00 2.90
594 618 0.319040 CGTAGGCGCTGCATGTAGAT 60.319 55.000 15.68 0.00 0.00 1.98
647 672 3.829601 TCCACCAAATTAATCCACACACC 59.170 43.478 0.00 0.00 0.00 4.16
651 676 4.006989 CGTCTCCACCAAATTAATCCACA 58.993 43.478 0.00 0.00 0.00 4.17
660 685 1.299976 GGCCTCGTCTCCACCAAAT 59.700 57.895 0.00 0.00 0.00 2.32
662 687 2.525629 TGGCCTCGTCTCCACCAA 60.526 61.111 3.32 0.00 0.00 3.67
741 806 7.437713 TTTTATCACTGGATGGATGTACTCT 57.562 36.000 0.00 0.00 34.89 3.24
743 808 6.828785 GGTTTTTATCACTGGATGGATGTACT 59.171 38.462 0.00 0.00 34.89 2.73
744 809 6.601613 TGGTTTTTATCACTGGATGGATGTAC 59.398 38.462 0.00 0.00 34.89 2.90
745 810 6.601613 GTGGTTTTTATCACTGGATGGATGTA 59.398 38.462 0.00 0.00 34.89 2.29
746 811 5.418840 GTGGTTTTTATCACTGGATGGATGT 59.581 40.000 0.00 0.00 34.89 3.06
747 812 5.163519 GGTGGTTTTTATCACTGGATGGATG 60.164 44.000 0.00 0.00 34.89 3.51
748 813 4.956075 GGTGGTTTTTATCACTGGATGGAT 59.044 41.667 0.00 0.00 34.89 3.41
749 814 4.340617 GGTGGTTTTTATCACTGGATGGA 58.659 43.478 0.00 0.00 34.89 3.41
750 815 3.128589 CGGTGGTTTTTATCACTGGATGG 59.871 47.826 0.00 0.00 36.81 3.51
751 816 4.355543 CGGTGGTTTTTATCACTGGATG 57.644 45.455 0.00 0.00 36.81 3.51
755 820 4.700213 AGATTCCGGTGGTTTTTATCACTG 59.300 41.667 0.00 0.00 39.32 3.66
756 821 4.918588 AGATTCCGGTGGTTTTTATCACT 58.081 39.130 0.00 0.00 34.57 3.41
757 822 5.638596 AAGATTCCGGTGGTTTTTATCAC 57.361 39.130 0.00 0.00 0.00 3.06
758 823 6.007703 AGAAAGATTCCGGTGGTTTTTATCA 58.992 36.000 0.00 0.00 0.00 2.15
759 824 6.510879 AGAAAGATTCCGGTGGTTTTTATC 57.489 37.500 0.00 0.00 0.00 1.75
760 825 6.687604 CAAGAAAGATTCCGGTGGTTTTTAT 58.312 36.000 0.00 0.00 0.00 1.40
761 826 5.508320 GCAAGAAAGATTCCGGTGGTTTTTA 60.508 40.000 0.00 0.00 0.00 1.52
762 827 4.739436 GCAAGAAAGATTCCGGTGGTTTTT 60.739 41.667 0.00 0.00 0.00 1.94
763 828 3.243737 GCAAGAAAGATTCCGGTGGTTTT 60.244 43.478 0.00 0.00 0.00 2.43
764 829 2.296190 GCAAGAAAGATTCCGGTGGTTT 59.704 45.455 0.00 0.00 0.00 3.27
765 830 1.886542 GCAAGAAAGATTCCGGTGGTT 59.113 47.619 0.00 0.00 0.00 3.67
766 831 1.073923 AGCAAGAAAGATTCCGGTGGT 59.926 47.619 0.00 0.00 0.00 4.16
767 832 1.740025 GAGCAAGAAAGATTCCGGTGG 59.260 52.381 0.00 0.00 0.00 4.61
768 833 1.394917 CGAGCAAGAAAGATTCCGGTG 59.605 52.381 0.00 0.00 0.00 4.94
769 834 1.726853 CGAGCAAGAAAGATTCCGGT 58.273 50.000 0.00 0.00 0.00 5.28
783 848 0.032952 ACGGAGTTAACTTGCGAGCA 59.967 50.000 19.73 0.00 37.78 4.26
808 873 4.038883 GCCGGGATATATATAAAGCGGAGT 59.961 45.833 2.18 0.00 0.00 3.85
841 906 1.314867 GATGAGTGGGAGGGAGGGA 59.685 63.158 0.00 0.00 0.00 4.20
843 908 1.768077 GGGATGAGTGGGAGGGAGG 60.768 68.421 0.00 0.00 0.00 4.30
883 949 1.368345 CGATGGACGATGGCTTTGCA 61.368 55.000 0.00 0.00 45.77 4.08
919 985 3.181967 GCTGCGCACTAGTCGTGG 61.182 66.667 5.66 0.00 43.97 4.94
920 986 3.536394 CGCTGCGCACTAGTCGTG 61.536 66.667 5.66 0.00 46.58 4.35
1017 1083 4.736896 GACGCCGTGGTGGAGGTC 62.737 72.222 0.00 0.00 42.78 3.85
1356 1422 2.285969 AGAGCAGGTGCAGGGGAT 60.286 61.111 4.48 0.00 45.16 3.85
1578 1644 4.816984 GGGGAGACGGCGGAGAGA 62.817 72.222 13.24 0.00 0.00 3.10
1609 1675 2.510906 CCGGATGGATGGGTGGAC 59.489 66.667 0.00 0.00 37.49 4.02
1612 1678 4.935495 CGGCCGGATGGATGGGTG 62.935 72.222 20.10 0.00 37.49 4.61
1616 1682 4.996434 GAGGCGGCCGGATGGATG 62.996 72.222 29.38 0.00 37.49 3.51
1632 1706 2.913117 CGGGGGATGTTGGGGTTGA 61.913 63.158 0.00 0.00 0.00 3.18
1719 1804 4.365505 TGGCGTGGCGTCGATTCA 62.366 61.111 0.00 0.00 32.50 2.57
1829 1924 0.905357 CACACCCCCAAACCAAAACA 59.095 50.000 0.00 0.00 0.00 2.83
1851 1952 4.878971 TGCATTTACGGATTTAGCTTAGCA 59.121 37.500 7.07 0.00 0.00 3.49
1887 1988 6.379133 ACAACACTCCGGAAATATAGTACTGA 59.621 38.462 5.23 0.00 0.00 3.41
1894 1995 6.045072 AGAACACAACACTCCGGAAATATA 57.955 37.500 5.23 0.00 0.00 0.86
1897 1998 3.139077 GAGAACACAACACTCCGGAAAT 58.861 45.455 5.23 0.00 0.00 2.17
1962 2068 1.486310 ACCAAAGCACTGACAGTCTGA 59.514 47.619 14.03 0.00 0.00 3.27
1963 2069 1.959042 ACCAAAGCACTGACAGTCTG 58.041 50.000 4.74 5.91 0.00 3.51
1964 2070 2.684881 CAAACCAAAGCACTGACAGTCT 59.315 45.455 4.74 3.53 0.00 3.24
1965 2071 2.682856 TCAAACCAAAGCACTGACAGTC 59.317 45.455 4.74 1.09 0.00 3.51
1966 2072 2.423538 GTCAAACCAAAGCACTGACAGT 59.576 45.455 1.07 1.07 37.07 3.55
1967 2073 2.423185 TGTCAAACCAAAGCACTGACAG 59.577 45.455 0.00 0.00 40.98 3.51
1968 2074 2.441410 TGTCAAACCAAAGCACTGACA 58.559 42.857 0.00 0.00 42.98 3.58
1969 2075 3.438360 CTTGTCAAACCAAAGCACTGAC 58.562 45.455 0.00 0.00 37.50 3.51
1970 2076 2.159254 GCTTGTCAAACCAAAGCACTGA 60.159 45.455 1.93 0.00 0.00 3.41
2032 2146 5.558273 CGAAAGATTAACGTTGCACTTGTCT 60.558 40.000 11.99 1.05 0.00 3.41
2098 2223 3.428282 CCGGCCACCGTACAAAGC 61.428 66.667 2.24 0.00 46.80 3.51
2281 2428 9.724839 GTATTTCTACAAGTTTACTGCACAAAA 57.275 29.630 0.00 0.00 0.00 2.44
2282 2429 8.894731 TGTATTTCTACAAGTTTACTGCACAAA 58.105 29.630 0.00 0.00 34.92 2.83
2283 2430 8.439993 TGTATTTCTACAAGTTTACTGCACAA 57.560 30.769 0.00 0.00 34.92 3.33
2284 2431 7.929245 TCTGTATTTCTACAAGTTTACTGCACA 59.071 33.333 0.00 0.00 37.41 4.57
2486 2649 3.580193 GCCAGCCATAGCACTGCG 61.580 66.667 0.00 0.00 43.56 5.18


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

AutoCloner maintained by Alex Coulton.