Multiple sequence alignment - TraesCS1B01G139900

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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 TraesCS1B01G139900 chr1B 100.000 2411 0 0 1 2411 184740953 184743363 0.000000e+00 4453.0
1 TraesCS1B01G139900 chr1B 79.255 564 97 14 67 618 197341949 197341394 2.260000e-100 375.0
2 TraesCS1B01G139900 chr1A 94.160 1524 68 8 897 2411 133126382 133127893 0.000000e+00 2302.0
3 TraesCS1B01G139900 chr1A 89.216 102 10 1 624 725 133126015 133126115 2.520000e-25 126.0
4 TraesCS1B01G139900 chr1D 93.194 1528 69 8 897 2411 121309095 121310600 0.000000e+00 2213.0
5 TraesCS1B01G139900 chr1D 80.466 558 92 12 73 618 140810685 140811237 6.200000e-111 411.0
6 TraesCS1B01G139900 chr1D 91.089 101 8 1 626 725 121308730 121308830 4.180000e-28 135.0
7 TraesCS1B01G139900 chr1D 78.788 132 22 4 730 859 299262994 299263121 1.540000e-12 84.2
8 TraesCS1B01G139900 chr1D 95.556 45 2 0 809 853 65905171 65905127 3.320000e-09 73.1
9 TraesCS1B01G139900 chr6B 83.780 635 87 13 1 624 343256617 343255988 2.670000e-164 588.0
10 TraesCS1B01G139900 chr5B 81.359 633 102 11 1 620 114878666 114879295 3.580000e-138 501.0
11 TraesCS1B01G139900 chr5B 79.894 567 97 13 66 618 114736063 114736626 1.340000e-107 399.0
12 TraesCS1B01G139900 chr5B 94.595 37 2 0 817 853 121004817 121004853 9.310000e-05 58.4
13 TraesCS1B01G139900 chr2A 82.740 562 83 8 68 618 212598506 212597948 2.790000e-134 488.0
14 TraesCS1B01G139900 chr2A 80.000 125 22 2 729 853 653390899 653391020 3.300000e-14 89.8
15 TraesCS1B01G139900 chr2D 80.317 630 108 11 1 618 15110246 15110871 1.690000e-126 462.0
16 TraesCS1B01G139900 chr2D 77.686 121 24 2 733 853 509751350 509751467 1.200000e-08 71.3
17 TraesCS1B01G139900 chr3D 82.028 562 81 13 71 618 375219351 375219906 6.070000e-126 460.0
18 TraesCS1B01G139900 chr3B 80.249 562 96 13 68 618 487701089 487701646 2.230000e-110 409.0
19 TraesCS1B01G139900 chr2B 79.890 547 88 16 87 618 103436858 103437397 4.860000e-102 381.0
20 TraesCS1B01G139900 chr3A 83.916 143 18 4 732 872 515827618 515827479 5.410000e-27 132.0
21 TraesCS1B01G139900 chr5A 84.956 113 15 2 13 123 96767341 96767229 1.960000e-21 113.0
22 TraesCS1B01G139900 chr5D 81.250 128 23 1 726 853 370360065 370360191 4.240000e-18 102.0
23 TraesCS1B01G139900 chr7B 79.231 130 17 8 726 853 733539650 733539771 5.520000e-12 82.4
24 TraesCS1B01G139900 chr6A 79.661 118 18 5 737 853 6585422 6585310 1.990000e-11 80.5


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 TraesCS1B01G139900 chr1B 184740953 184743363 2410 False 4453 4453 100.0000 1 2411 1 chr1B.!!$F1 2410
1 TraesCS1B01G139900 chr1B 197341394 197341949 555 True 375 375 79.2550 67 618 1 chr1B.!!$R1 551
2 TraesCS1B01G139900 chr1A 133126015 133127893 1878 False 1214 2302 91.6880 624 2411 2 chr1A.!!$F1 1787
3 TraesCS1B01G139900 chr1D 121308730 121310600 1870 False 1174 2213 92.1415 626 2411 2 chr1D.!!$F3 1785
4 TraesCS1B01G139900 chr1D 140810685 140811237 552 False 411 411 80.4660 73 618 1 chr1D.!!$F1 545
5 TraesCS1B01G139900 chr6B 343255988 343256617 629 True 588 588 83.7800 1 624 1 chr6B.!!$R1 623
6 TraesCS1B01G139900 chr5B 114878666 114879295 629 False 501 501 81.3590 1 620 1 chr5B.!!$F2 619
7 TraesCS1B01G139900 chr5B 114736063 114736626 563 False 399 399 79.8940 66 618 1 chr5B.!!$F1 552
8 TraesCS1B01G139900 chr2A 212597948 212598506 558 True 488 488 82.7400 68 618 1 chr2A.!!$R1 550
9 TraesCS1B01G139900 chr2D 15110246 15110871 625 False 462 462 80.3170 1 618 1 chr2D.!!$F1 617
10 TraesCS1B01G139900 chr3D 375219351 375219906 555 False 460 460 82.0280 71 618 1 chr3D.!!$F1 547
11 TraesCS1B01G139900 chr3B 487701089 487701646 557 False 409 409 80.2490 68 618 1 chr3B.!!$F1 550
12 TraesCS1B01G139900 chr2B 103436858 103437397 539 False 381 381 79.8900 87 618 1 chr2B.!!$F1 531

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
626 647 0.10852 TATCCCCAACAACGCTCGAC 60.109 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2102 0.389025 AAAAGCTGCCAGTTTTCCCG 59.611 50.0 7.01 0.0 28.25 5.14 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
34 35 2.553028 GCTCCCTCCATGAACTCAACAA 60.553 50.000 0.00 0.00 0.00 2.83
70 71 0.320771 CACAGAGGGCGCTAACTGTT 60.321 55.000 22.86 0.00 40.84 3.16
154 156 1.698506 TTGCTTGAACGGGGTTGATT 58.301 45.000 0.00 0.00 0.00 2.57
283 293 3.641434 TGGCTAACCTAGTACTCGAGT 57.359 47.619 23.66 23.66 36.63 4.18
293 303 3.572604 AGTACTCGAGTGCTTGTAACC 57.427 47.619 27.85 5.40 37.74 2.85
303 314 5.465724 CGAGTGCTTGTAACCTAGTCTTTTT 59.534 40.000 0.00 0.00 0.00 1.94
309 320 5.562298 TGTAACCTAGTCTTTTTGCCTCT 57.438 39.130 0.00 0.00 0.00 3.69
329 340 1.608154 GGGCTCCCCTTTACAGGTC 59.392 63.158 0.00 0.00 41.34 3.85
331 347 0.696501 GGCTCCCCTTTACAGGTCAA 59.303 55.000 0.00 0.00 38.79 3.18
333 349 1.340114 GCTCCCCTTTACAGGTCAAGG 60.340 57.143 5.58 5.58 38.79 3.61
351 367 1.699634 AGGCCTGAGCTTACAACAGAA 59.300 47.619 3.11 0.00 39.73 3.02
352 368 1.807142 GGCCTGAGCTTACAACAGAAC 59.193 52.381 0.00 0.00 39.73 3.01
367 383 1.477700 CAGAACCCGGGTCGTATTACA 59.522 52.381 30.40 0.00 0.00 2.41
377 393 3.181483 GGGTCGTATTACAATCCGTGACT 60.181 47.826 0.00 0.00 0.00 3.41
387 403 8.644318 ATTACAATCCGTGACTTAGTATGTTC 57.356 34.615 0.00 0.00 0.00 3.18
401 417 9.780186 ACTTAGTATGTTCCCTATTTATCTTGC 57.220 33.333 0.00 0.00 0.00 4.01
443 460 1.746787 TGCGGCGACTTATACTTCTGA 59.253 47.619 12.98 0.00 0.00 3.27
446 463 2.033550 CGGCGACTTATACTTCTGAGCT 59.966 50.000 0.00 0.00 0.00 4.09
452 470 6.293735 GCGACTTATACTTCTGAGCTATGAGT 60.294 42.308 0.00 0.00 0.00 3.41
456 474 3.773860 ACTTCTGAGCTATGAGTCACG 57.226 47.619 0.00 0.00 0.00 4.35
471 489 3.220110 AGTCACGGTCTTCAAGTACTGA 58.780 45.455 0.00 0.00 0.00 3.41
479 498 4.496360 GTCTTCAAGTACTGAGCCCTAAC 58.504 47.826 0.00 0.00 34.81 2.34
484 503 1.361543 AGTACTGAGCCCTAACCCAGA 59.638 52.381 0.00 0.00 0.00 3.86
494 513 2.502538 CCCTAACCCAGACCATTTCGTA 59.497 50.000 0.00 0.00 0.00 3.43
517 536 3.400188 CCCTACCGGCTTTGAGGT 58.600 61.111 0.00 0.00 44.08 3.85
518 537 1.221021 CCCTACCGGCTTTGAGGTC 59.779 63.158 0.00 0.00 41.63 3.85
519 538 1.265454 CCCTACCGGCTTTGAGGTCT 61.265 60.000 0.00 0.00 41.63 3.85
533 554 0.249741 AGGTCTTTGAACGTCACGGG 60.250 55.000 0.35 0.00 0.00 5.28
538 559 1.511318 TTTGAACGTCACGGGCCATG 61.511 55.000 4.39 0.00 0.00 3.66
555 576 3.944015 GCCATGTTGAGTCTTGCTTATCT 59.056 43.478 0.00 0.00 0.00 1.98
562 583 3.834813 TGAGTCTTGCTTATCTGTCACCT 59.165 43.478 0.00 0.00 0.00 4.00
621 642 1.951602 GGGTTATATCCCCAACAACGC 59.048 52.381 7.58 0.00 42.15 4.84
622 643 2.422377 GGGTTATATCCCCAACAACGCT 60.422 50.000 7.58 0.00 42.15 5.07
623 644 2.876550 GGTTATATCCCCAACAACGCTC 59.123 50.000 0.00 0.00 0.00 5.03
624 645 2.519377 TATATCCCCAACAACGCTCG 57.481 50.000 0.00 0.00 0.00 5.03
625 646 0.828022 ATATCCCCAACAACGCTCGA 59.172 50.000 0.00 0.00 0.00 4.04
626 647 0.108520 TATCCCCAACAACGCTCGAC 60.109 55.000 0.00 0.00 0.00 4.20
702 724 6.629128 TGTCCATTTTTATTTGATGCATCGT 58.371 32.000 21.34 12.38 0.00 3.73
733 825 4.499183 ACCAATTCTCTTAAGAGCGTCAG 58.501 43.478 25.04 15.98 41.80 3.51
747 839 3.050703 GTCAGGTACGAGCACATGG 57.949 57.895 0.00 0.00 31.29 3.66
770 862 4.081531 GCAACTCCAATCATTTTGGATGGA 60.082 41.667 7.48 0.00 46.47 3.41
777 869 7.516452 TCCAATCATTTTGGATGGAAAGTTTT 58.484 30.769 2.98 0.00 43.17 2.43
779 871 6.806388 ATCATTTTGGATGGAAAGTTTTGC 57.194 33.333 0.00 0.00 0.00 3.68
785 877 0.951558 ATGGAAAGTTTTGCGAGCGT 59.048 45.000 0.00 0.00 0.00 5.07
788 880 1.268335 GGAAAGTTTTGCGAGCGTGAA 60.268 47.619 0.00 0.00 0.00 3.18
790 882 1.295792 AAGTTTTGCGAGCGTGAAGA 58.704 45.000 0.00 0.00 0.00 2.87
798 890 1.702886 CGAGCGTGAAGATGACAACT 58.297 50.000 0.00 0.00 0.00 3.16
807 899 5.349817 CGTGAAGATGACAACTTTAGATGCT 59.650 40.000 0.00 0.00 0.00 3.79
867 991 9.990360 TGACAGAAACTTACAGTAATTGTCATA 57.010 29.630 14.39 2.36 41.29 2.15
883 1007 5.168647 TGTCATAAAATAACCGGGTGACT 57.831 39.130 0.00 0.00 36.40 3.41
884 1008 6.297080 TGTCATAAAATAACCGGGTGACTA 57.703 37.500 0.00 0.00 36.40 2.59
885 1009 6.709281 TGTCATAAAATAACCGGGTGACTAA 58.291 36.000 0.00 0.00 36.40 2.24
888 1012 7.964559 GTCATAAAATAACCGGGTGACTAAAAC 59.035 37.037 0.00 0.00 33.57 2.43
889 1013 7.664731 TCATAAAATAACCGGGTGACTAAAACA 59.335 33.333 0.00 0.00 0.00 2.83
890 1014 6.712179 AAAATAACCGGGTGACTAAAACAA 57.288 33.333 0.00 0.00 0.00 2.83
891 1015 5.952526 AATAACCGGGTGACTAAAACAAG 57.047 39.130 0.00 0.00 0.00 3.16
892 1016 3.564053 AACCGGGTGACTAAAACAAGA 57.436 42.857 6.32 0.00 0.00 3.02
893 1017 2.842457 ACCGGGTGACTAAAACAAGAC 58.158 47.619 6.32 0.00 0.00 3.01
894 1018 2.148768 CCGGGTGACTAAAACAAGACC 58.851 52.381 0.00 0.00 0.00 3.85
895 1019 2.148768 CGGGTGACTAAAACAAGACCC 58.851 52.381 0.00 0.00 0.00 4.46
926 1050 7.915397 CACTTGTAATTTGGGTTGATGTATAGC 59.085 37.037 0.00 0.00 0.00 2.97
959 1083 0.688487 TAAACACCGACAGGGAAGGG 59.312 55.000 0.00 0.00 43.47 3.95
964 1088 2.670148 CCGACAGGGAAGGGGAAGG 61.670 68.421 0.00 0.00 38.47 3.46
965 1089 1.612442 CGACAGGGAAGGGGAAGGA 60.612 63.158 0.00 0.00 0.00 3.36
966 1090 1.617947 CGACAGGGAAGGGGAAGGAG 61.618 65.000 0.00 0.00 0.00 3.69
967 1091 0.252742 GACAGGGAAGGGGAAGGAGA 60.253 60.000 0.00 0.00 0.00 3.71
968 1092 0.196118 ACAGGGAAGGGGAAGGAGAA 59.804 55.000 0.00 0.00 0.00 2.87
969 1093 0.915364 CAGGGAAGGGGAAGGAGAAG 59.085 60.000 0.00 0.00 0.00 2.85
1085 1210 2.280592 GCAACCCCTGACGAACGT 60.281 61.111 0.00 0.00 0.00 3.99
1559 1688 6.558488 TGGGAAATAAAATTAAGGCTGCAT 57.442 33.333 0.50 0.00 0.00 3.96
1563 1692 8.183536 GGGAAATAAAATTAAGGCTGCATTTTG 58.816 33.333 19.76 0.00 33.28 2.44
1586 1715 4.487714 TCCTGTTGTGGGAGATTACATC 57.512 45.455 0.00 0.00 0.00 3.06
1637 1772 5.804692 TTGGTAGCATACAATTTGTACGG 57.195 39.130 11.31 8.23 45.43 4.02
1682 1817 2.762887 TCTCGATTGATGAAGCCTCAGT 59.237 45.455 0.00 0.00 34.23 3.41
1688 1823 6.925718 TCGATTGATGAAGCCTCAGTATTAAG 59.074 38.462 0.00 0.00 34.23 1.85
1745 1883 7.649306 GTGCCAATTGTGATATTAATTGAGGTC 59.351 37.037 16.33 7.98 43.51 3.85
1753 1891 9.295825 TGTGATATTAATTGAGGTCAACAGTTT 57.704 29.630 0.00 0.00 38.86 2.66
1767 1905 6.695713 GGTCAACAGTTTAAAAAGATGGTCAC 59.304 38.462 0.00 0.00 0.00 3.67
1797 1935 6.585322 GCATATGCCTTGCTTGATAATTTCTC 59.415 38.462 17.26 0.00 37.14 2.87
1834 1972 2.053244 CAAGGAGCCATGGAGATAGGT 58.947 52.381 18.40 0.00 0.00 3.08
1838 1976 3.116551 AGGAGCCATGGAGATAGGTTAGT 60.117 47.826 18.40 0.00 0.00 2.24
1879 2017 1.164411 GGTGCGTGGTGAATGAATGA 58.836 50.000 0.00 0.00 0.00 2.57
1889 2027 5.461078 GTGGTGAATGAATGAAGCATAATGC 59.539 40.000 0.00 0.00 45.46 3.56
1906 2044 4.824166 CGACTGGCGCAATGCTGC 62.824 66.667 10.83 12.24 45.43 5.25
1924 2062 4.161189 TGCTGCTATGATAGATAAGAGGGC 59.839 45.833 3.13 0.00 0.00 5.19
1931 2069 8.754080 GCTATGATAGATAAGAGGGCTTTAAGA 58.246 37.037 3.13 0.00 35.56 2.10
1946 2084 7.779798 AGGGCTTTAAGATGCAACTATCATTTA 59.220 33.333 0.00 0.00 0.00 1.40
2002 2140 5.566774 GCTTTTGATGACATCTTTTCTGACG 59.433 40.000 16.25 0.00 0.00 4.35
2117 2255 8.987890 CAAAGAAGGAGAAAAGAAAACAAAACA 58.012 29.630 0.00 0.00 0.00 2.83
2130 2268 4.853468 AACAAAACAAAGGGGGAAACAT 57.147 36.364 0.00 0.00 0.00 2.71
2138 2276 2.629017 AGGGGGAAACATGCAATCTT 57.371 45.000 0.00 0.00 0.00 2.40
2184 2322 1.005037 CGGCAAGCAGTAGGACACA 60.005 57.895 0.00 0.00 0.00 3.72
2222 2360 0.249784 CCACATCTGAGCCTCCATCG 60.250 60.000 0.00 0.00 0.00 3.84
2305 2443 3.140325 TCTTTCCAGATTGACCACCAC 57.860 47.619 0.00 0.00 0.00 4.16
2366 2504 1.754226 GAGTGAGACCCAAGGAGCTAG 59.246 57.143 0.00 0.00 0.00 3.42
2384 2522 3.050275 GGTCGCACCAAGCAGTCC 61.050 66.667 1.01 0.00 46.13 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.295792 GCTCGGTGTTGTTGAGTTCA 58.704 50.000 0.00 0.00 32.32 3.18
34 35 3.537874 GGGGCTATCGCTCGGTGT 61.538 66.667 0.00 0.00 37.57 4.16
54 55 0.320771 CACAACAGTTAGCGCCCTCT 60.321 55.000 2.29 0.00 0.00 3.69
56 57 1.302511 CCACAACAGTTAGCGCCCT 60.303 57.895 2.29 0.00 0.00 5.19
63 64 3.127203 CCGTGACAAAACCACAACAGTTA 59.873 43.478 0.00 0.00 34.36 2.24
70 71 0.393132 TCTGCCGTGACAAAACCACA 60.393 50.000 0.00 0.00 34.36 4.17
105 107 2.419990 CGGTGATGGCCTCATGACTAAA 60.420 50.000 3.32 0.00 37.59 1.85
154 156 1.938585 ACCCTTGTCTCTCGATTCCA 58.061 50.000 0.00 0.00 0.00 3.53
283 293 4.277423 GGCAAAAAGACTAGGTTACAAGCA 59.723 41.667 0.00 0.00 0.00 3.91
293 303 2.716217 CCCCAGAGGCAAAAAGACTAG 58.284 52.381 0.00 0.00 33.72 2.57
326 337 0.324943 TGTAAGCTCAGGCCTTGACC 59.675 55.000 0.00 0.00 39.73 4.02
327 338 1.807142 GTTGTAAGCTCAGGCCTTGAC 59.193 52.381 0.00 0.00 39.73 3.18
329 340 1.808945 CTGTTGTAAGCTCAGGCCTTG 59.191 52.381 0.00 0.00 39.73 3.61
331 347 1.352083 TCTGTTGTAAGCTCAGGCCT 58.648 50.000 0.00 0.00 39.73 5.19
333 349 1.807142 GGTTCTGTTGTAAGCTCAGGC 59.193 52.381 0.00 0.00 39.06 4.85
338 354 0.036306 CCCGGGTTCTGTTGTAAGCT 59.964 55.000 14.18 0.00 0.00 3.74
351 367 1.413812 GGATTGTAATACGACCCGGGT 59.586 52.381 30.81 30.81 0.00 5.28
352 368 1.603678 CGGATTGTAATACGACCCGGG 60.604 57.143 22.25 22.25 45.50 5.73
367 383 4.715297 AGGGAACATACTAAGTCACGGATT 59.285 41.667 0.00 0.00 0.00 3.01
387 403 5.934781 ACTCAGGAAGCAAGATAAATAGGG 58.065 41.667 0.00 0.00 0.00 3.53
416 432 2.708386 ATAAGTCGCCGCATAGAGTC 57.292 50.000 0.00 0.00 0.00 3.36
443 460 2.447443 TGAAGACCGTGACTCATAGCT 58.553 47.619 0.00 0.00 0.00 3.32
446 463 5.008331 AGTACTTGAAGACCGTGACTCATA 58.992 41.667 0.00 0.00 0.00 2.15
452 470 2.030185 GCTCAGTACTTGAAGACCGTGA 60.030 50.000 0.00 0.00 34.81 4.35
456 474 1.903183 AGGGCTCAGTACTTGAAGACC 59.097 52.381 12.01 12.01 34.81 3.85
471 489 1.285078 GAAATGGTCTGGGTTAGGGCT 59.715 52.381 0.00 0.00 0.00 5.19
479 498 1.379527 GGCTTACGAAATGGTCTGGG 58.620 55.000 0.00 0.00 0.00 4.45
510 529 2.605818 CGTGACGTTCAAAGACCTCAAA 59.394 45.455 0.00 0.00 0.00 2.69
512 531 1.537348 CCGTGACGTTCAAAGACCTCA 60.537 52.381 3.64 0.00 0.00 3.86
513 532 1.137513 CCGTGACGTTCAAAGACCTC 58.862 55.000 3.64 0.00 0.00 3.85
515 534 1.838568 GCCCGTGACGTTCAAAGACC 61.839 60.000 3.64 0.00 0.00 3.85
517 536 1.595929 GGCCCGTGACGTTCAAAGA 60.596 57.895 3.64 0.00 0.00 2.52
518 537 1.234615 ATGGCCCGTGACGTTCAAAG 61.235 55.000 3.64 0.00 0.00 2.77
519 538 1.228003 ATGGCCCGTGACGTTCAAA 60.228 52.632 3.64 0.00 0.00 2.69
533 554 3.944015 AGATAAGCAAGACTCAACATGGC 59.056 43.478 0.00 0.00 0.00 4.40
538 559 4.390297 GGTGACAGATAAGCAAGACTCAAC 59.610 45.833 0.00 0.00 0.00 3.18
555 576 1.553248 CGGGTTATCCAAGAGGTGACA 59.447 52.381 0.00 0.00 35.89 3.58
562 583 1.208844 TTGGGCCGGGTTATCCAAGA 61.209 55.000 2.18 0.00 34.71 3.02
620 641 1.199558 GGGTCTATATCCACGTCGAGC 59.800 57.143 0.00 0.00 0.00 5.03
621 642 2.780714 AGGGTCTATATCCACGTCGAG 58.219 52.381 0.00 0.00 0.00 4.04
622 643 2.945080 AGGGTCTATATCCACGTCGA 57.055 50.000 0.00 0.00 0.00 4.20
623 644 4.518211 AGTTAAGGGTCTATATCCACGTCG 59.482 45.833 0.00 0.00 0.00 5.12
624 645 6.402456 AAGTTAAGGGTCTATATCCACGTC 57.598 41.667 0.00 0.00 0.00 4.34
625 646 6.803366 AAAGTTAAGGGTCTATATCCACGT 57.197 37.500 0.00 0.00 0.00 4.49
626 647 6.018180 GCAAAAGTTAAGGGTCTATATCCACG 60.018 42.308 0.00 0.00 0.00 4.94
627 648 7.054751 AGCAAAAGTTAAGGGTCTATATCCAC 58.945 38.462 0.00 0.00 0.00 4.02
634 655 7.909518 TGTACATAGCAAAAGTTAAGGGTCTA 58.090 34.615 0.00 0.00 0.00 2.59
684 706 6.450545 TCCAACACGATGCATCAAATAAAAA 58.549 32.000 25.70 2.61 0.00 1.94
733 825 0.673644 AGTTGCCATGTGCTCGTACC 60.674 55.000 7.54 0.00 42.00 3.34
755 847 6.073112 CGCAAAACTTTCCATCCAAAATGATT 60.073 34.615 0.00 0.00 0.00 2.57
757 849 4.749099 CGCAAAACTTTCCATCCAAAATGA 59.251 37.500 0.00 0.00 0.00 2.57
770 862 1.668751 TCTTCACGCTCGCAAAACTTT 59.331 42.857 0.00 0.00 0.00 2.66
777 869 0.319469 TTGTCATCTTCACGCTCGCA 60.319 50.000 0.00 0.00 0.00 5.10
779 871 1.702886 AGTTGTCATCTTCACGCTCG 58.297 50.000 0.00 0.00 0.00 5.03
785 877 7.065085 GCTTAGCATCTAAAGTTGTCATCTTCA 59.935 37.037 0.00 0.00 0.00 3.02
788 880 6.409704 TGCTTAGCATCTAAAGTTGTCATCT 58.590 36.000 1.39 0.00 31.71 2.90
807 899 3.743521 AGCACAGAAGTTGTCATGCTTA 58.256 40.909 3.13 0.00 44.40 3.09
822 914 9.515020 TTCTGTCAAAAATAAACTAAAGCACAG 57.485 29.630 0.00 0.00 0.00 3.66
823 915 9.862371 TTTCTGTCAAAAATAAACTAAAGCACA 57.138 25.926 0.00 0.00 0.00 4.57
855 979 7.830201 TCACCCGGTTATTTTATGACAATTACT 59.170 33.333 0.00 0.00 0.00 2.24
857 981 7.830201 AGTCACCCGGTTATTTTATGACAATTA 59.170 33.333 0.00 0.00 37.93 1.40
860 984 5.562635 AGTCACCCGGTTATTTTATGACAA 58.437 37.500 0.00 0.00 37.93 3.18
867 991 6.546772 TCTTGTTTTAGTCACCCGGTTATTTT 59.453 34.615 0.00 0.00 0.00 1.82
868 992 6.016860 GTCTTGTTTTAGTCACCCGGTTATTT 60.017 38.462 0.00 0.00 0.00 1.40
871 995 4.379652 GTCTTGTTTTAGTCACCCGGTTA 58.620 43.478 0.00 0.00 0.00 2.85
877 1001 2.546789 CACGGGTCTTGTTTTAGTCACC 59.453 50.000 0.00 0.00 0.00 4.02
883 1007 1.134037 AGTGCCACGGGTCTTGTTTTA 60.134 47.619 0.00 0.00 0.00 1.52
884 1008 0.395173 AGTGCCACGGGTCTTGTTTT 60.395 50.000 0.00 0.00 0.00 2.43
885 1009 0.395173 AAGTGCCACGGGTCTTGTTT 60.395 50.000 0.00 0.00 0.00 2.83
888 1012 0.250124 TACAAGTGCCACGGGTCTTG 60.250 55.000 18.17 18.17 39.99 3.02
889 1013 0.470766 TTACAAGTGCCACGGGTCTT 59.529 50.000 0.00 0.00 0.00 3.01
890 1014 0.690762 ATTACAAGTGCCACGGGTCT 59.309 50.000 0.00 0.00 0.00 3.85
891 1015 1.530323 AATTACAAGTGCCACGGGTC 58.470 50.000 0.00 0.00 0.00 4.46
892 1016 1.611491 CAAATTACAAGTGCCACGGGT 59.389 47.619 0.42 0.42 0.00 5.28
893 1017 1.067915 CCAAATTACAAGTGCCACGGG 60.068 52.381 0.00 0.00 0.00 5.28
894 1018 1.067915 CCCAAATTACAAGTGCCACGG 60.068 52.381 0.00 0.00 0.00 4.94
895 1019 1.611491 ACCCAAATTACAAGTGCCACG 59.389 47.619 0.00 0.00 0.00 4.94
926 1050 2.161609 GGTGTTTAGGGCATCTTCAACG 59.838 50.000 0.00 0.00 0.00 4.10
959 1083 5.012664 AGTTTCTCTTTCTCCTTCTCCTTCC 59.987 44.000 0.00 0.00 0.00 3.46
964 1088 5.337733 GGGGTAGTTTCTCTTTCTCCTTCTC 60.338 48.000 0.00 0.00 0.00 2.87
965 1089 4.532916 GGGGTAGTTTCTCTTTCTCCTTCT 59.467 45.833 0.00 0.00 0.00 2.85
966 1090 4.323638 GGGGGTAGTTTCTCTTTCTCCTTC 60.324 50.000 0.00 0.00 0.00 3.46
967 1091 3.587951 GGGGGTAGTTTCTCTTTCTCCTT 59.412 47.826 0.00 0.00 0.00 3.36
968 1092 3.182976 GGGGGTAGTTTCTCTTTCTCCT 58.817 50.000 0.00 0.00 0.00 3.69
969 1093 2.093606 CGGGGGTAGTTTCTCTTTCTCC 60.094 54.545 0.00 0.00 0.00 3.71
1152 1277 1.582968 GACGTCCTTGCCGTAGTCA 59.417 57.895 3.51 0.00 38.92 3.41
1233 1358 2.224606 TCGTTGAAGTACACCGTCTCT 58.775 47.619 0.00 0.00 35.92 3.10
1515 1644 6.726299 TCCCAATCAGAATATCGAGGAACTAT 59.274 38.462 0.00 0.00 41.55 2.12
1559 1688 3.374042 TCTCCCACAACAGGAACAAAA 57.626 42.857 0.00 0.00 31.49 2.44
1563 1692 4.015872 TGTAATCTCCCACAACAGGAAC 57.984 45.455 0.00 0.00 31.49 3.62
1586 1715 2.617308 CAGCATGGACAATTAGCTCCAG 59.383 50.000 0.00 0.00 39.99 3.86
1637 1772 9.382275 AGAATGAACATAAATACCAATTTTGCC 57.618 29.630 0.00 0.00 36.67 4.52
1664 1799 6.703607 ACTTAATACTGAGGCTTCATCAATCG 59.296 38.462 0.00 0.00 31.68 3.34
1673 1808 7.269316 GCTCTTCTAACTTAATACTGAGGCTT 58.731 38.462 0.00 0.00 0.00 4.35
1682 1817 6.466885 AGGCTTCGCTCTTCTAACTTAATA 57.533 37.500 0.00 0.00 0.00 0.98
1688 1823 7.224949 ACAAATTATAGGCTTCGCTCTTCTAAC 59.775 37.037 0.00 0.00 0.00 2.34
1706 1841 5.933463 CACAATTGGCACAGGAACAAATTAT 59.067 36.000 10.83 0.00 42.39 1.28
1745 1883 8.647143 AATGTGACCATCTTTTTAAACTGTTG 57.353 30.769 0.00 0.00 0.00 3.33
1753 1891 7.492020 GCATATGCAAATGTGACCATCTTTTTA 59.508 33.333 22.84 0.00 41.59 1.52
1758 1896 3.319972 GGCATATGCAAATGTGACCATCT 59.680 43.478 28.07 0.00 44.36 2.90
1767 1905 3.787785 TCAAGCAAGGCATATGCAAATG 58.212 40.909 28.07 22.00 46.22 2.32
1813 1951 2.053244 CCTATCTCCATGGCTCCTTGT 58.947 52.381 6.96 0.00 0.00 3.16
1824 1962 7.973048 AGTTAACATGACTAACCTATCTCCA 57.027 36.000 8.61 0.00 30.88 3.86
1838 1976 7.323420 CACCTACAGATCTGAAGTTAACATGA 58.677 38.462 29.27 0.70 0.00 3.07
1855 1993 1.078709 CATTCACCACGCACCTACAG 58.921 55.000 0.00 0.00 0.00 2.74
1879 2017 2.016961 CGCCAGTCGCATTATGCTT 58.983 52.632 15.54 0.00 42.25 3.91
1889 2027 4.824166 GCAGCATTGCGCCAGTCG 62.824 66.667 4.18 0.00 44.04 4.18
1916 2054 5.179452 AGTTGCATCTTAAAGCCCTCTTA 57.821 39.130 0.00 0.00 31.02 2.10
1946 2084 5.864418 TCCCGAGCATTACTACAAATAGT 57.136 39.130 0.00 0.00 44.22 2.12
1951 2089 4.693566 CAGTTTTCCCGAGCATTACTACAA 59.306 41.667 0.00 0.00 0.00 2.41
1964 2102 0.389025 AAAAGCTGCCAGTTTTCCCG 59.611 50.000 7.01 0.00 28.25 5.14
2028 2166 7.902087 ACTCTGTTCCTATCCTATCTATTTGC 58.098 38.462 0.00 0.00 0.00 3.68
2117 2255 2.906568 AGATTGCATGTTTCCCCCTTT 58.093 42.857 0.00 0.00 0.00 3.11
2138 2276 2.938451 CTCGTGAGCCTGATTAAATGCA 59.062 45.455 0.00 0.00 0.00 3.96
2184 2322 1.908340 GACTGAGGCTGGCCAGATGT 61.908 60.000 37.21 23.44 38.92 3.06
2222 2360 1.607148 CACTTTGTTCCGGAAACTCCC 59.393 52.381 20.79 6.63 38.76 4.30
2305 2443 4.829518 TCGATCGTGGCGCTCGTG 62.830 66.667 15.94 13.54 44.06 4.35
2366 2504 3.050275 GACTGCTTGGTGCGACCC 61.050 66.667 3.33 0.00 46.63 4.46


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

AutoCloner maintained by Alex Coulton.