Multiple sequence alignment - TraesCS3D01G418900

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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 TraesCS3D01G418900 chr3D 100.000 7038 0 0 1 7038 531375620 531368583 0.000000e+00 12997.0
1 TraesCS3D01G418900 chr3D 88.816 3040 254 48 1085 4072 426407744 426410749 0.000000e+00 3651.0
2 TraesCS3D01G418900 chr3D 85.972 2495 223 66 1416 3816 531356653 531359114 0.000000e+00 2551.0
3 TraesCS3D01G418900 chr3D 91.626 1027 70 7 6018 7038 426438365 426439381 0.000000e+00 1406.0
4 TraesCS3D01G418900 chr3D 88.043 1104 83 22 4507 5595 531359809 531360878 0.000000e+00 1262.0
5 TraesCS3D01G418900 chr3D 89.009 646 55 12 4066 4705 426412148 426412783 0.000000e+00 785.0
6 TraesCS3D01G418900 chr3D 81.897 917 123 23 481 1382 531355760 531356648 0.000000e+00 734.0
7 TraesCS3D01G418900 chr3D 87.284 637 60 11 3866 4491 531359121 531359747 0.000000e+00 708.0
8 TraesCS3D01G418900 chr3D 90.037 542 38 8 4702 5230 426413040 426413578 0.000000e+00 688.0
9 TraesCS3D01G418900 chr3D 82.444 581 66 16 175 744 531355210 531355765 6.390000e-130 475.0
10 TraesCS3D01G418900 chr3D 88.189 381 45 0 5597 5977 426434472 426434852 8.320000e-124 455.0
11 TraesCS3D01G418900 chr3D 88.462 286 28 2 5223 5507 426434081 426434362 2.430000e-89 340.0
12 TraesCS3D01G418900 chr3D 97.531 81 2 0 6958 7038 426439545 426439625 9.520000e-29 139.0
13 TraesCS3D01G418900 chr3D 100.000 31 0 0 4945 4975 560082234 560082204 2.740000e-04 58.4
14 TraesCS3D01G418900 chr3A 95.724 4537 149 19 173 4703 665986297 665981800 0.000000e+00 7262.0
15 TraesCS3D01G418900 chr3A 90.317 1136 71 15 4908 6019 665981798 665980678 0.000000e+00 1452.0
16 TraesCS3D01G418900 chr3A 84.615 871 78 20 6209 7038 665968825 665967970 0.000000e+00 815.0
17 TraesCS3D01G418900 chr3A 90.741 162 13 1 1 160 665986707 665986546 1.540000e-51 215.0
18 TraesCS3D01G418900 chr3B 90.600 4298 275 49 2549 6761 702697763 702693510 0.000000e+00 5579.0
19 TraesCS3D01G418900 chr3B 84.427 3018 313 91 177 3075 702849785 702846806 0.000000e+00 2824.0
20 TraesCS3D01G418900 chr3B 89.418 1616 148 12 3083 4682 702846727 702845119 0.000000e+00 2015.0
21 TraesCS3D01G418900 chr3B 85.335 1732 173 38 840 2538 702699513 702697830 0.000000e+00 1716.0
22 TraesCS3D01G418900 chr3B 87.805 1312 115 18 4731 6020 702828089 702826801 0.000000e+00 1495.0
23 TraesCS3D01G418900 chr3B 85.162 1112 110 30 2042 3104 702830843 702829738 0.000000e+00 1088.0
24 TraesCS3D01G418900 chr3B 89.367 837 79 8 3090 3920 702829721 702828889 0.000000e+00 1044.0
25 TraesCS3D01G418900 chr3B 84.109 1139 118 23 518 1623 702834651 702833543 0.000000e+00 1042.0
26 TraesCS3D01G418900 chr3B 92.026 627 37 3 4683 5296 702845078 702844452 0.000000e+00 869.0
27 TraesCS3D01G418900 chr3B 86.881 747 75 10 5282 6020 702844432 702843701 0.000000e+00 815.0
28 TraesCS3D01G418900 chr3B 85.067 750 79 19 4034 4754 702828841 702828096 0.000000e+00 734.0
29 TraesCS3D01G418900 chr3B 83.439 628 82 11 173 780 702700264 702699639 1.330000e-156 564.0
30 TraesCS3D01G418900 chr3B 91.622 370 30 1 1627 1995 702831215 702830846 1.750000e-140 510.0
31 TraesCS3D01G418900 chr3B 88.500 200 19 4 285 481 702834846 702834648 9.120000e-59 239.0
32 TraesCS3D01G418900 chr3B 96.748 123 4 0 6916 7038 702693492 702693370 9.250000e-49 206.0
33 TraesCS3D01G418900 chr3B 93.750 96 6 0 1 96 702700664 702700569 2.050000e-30 145.0
34 TraesCS3D01G418900 chr3B 90.566 53 5 0 6021 6073 702843674 702843622 3.520000e-08 71.3
35 TraesCS3D01G418900 chr3B 100.000 28 0 0 6046 6073 702826741 702826714 1.300000e-02 52.8
36 TraesCS3D01G418900 chr2D 86.341 2211 188 61 1416 3543 46686227 46688406 0.000000e+00 2305.0
37 TraesCS3D01G418900 chr2D 87.863 585 50 10 3771 4344 46693969 46694543 0.000000e+00 667.0
38 TraesCS3D01G418900 chr2D 83.805 636 75 18 764 1380 46685597 46686223 4.730000e-161 579.0
39 TraesCS3D01G418900 chr2D 82.632 570 62 18 186 744 46684845 46685388 2.970000e-128 470.0
40 TraesCS3D01G418900 chr2D 89.706 204 19 2 3537 3739 46693765 46693967 7.000000e-65 259.0
41 TraesCS3D01G418900 chr4B 87.645 518 55 4 2030 2538 622125216 622124699 1.690000e-165 593.0


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 TraesCS3D01G418900 chr3D 531368583 531375620 7037 True 12997.000000 12997 100.000000 1 7038 1 chr3D.!!$R1 7037
1 TraesCS3D01G418900 chr3D 426407744 426413578 5834 False 1708.000000 3651 89.287333 1085 5230 3 chr3D.!!$F1 4145
2 TraesCS3D01G418900 chr3D 531355210 531360878 5668 False 1146.000000 2551 85.128000 175 5595 5 chr3D.!!$F3 5420
3 TraesCS3D01G418900 chr3D 426434081 426439625 5544 False 585.000000 1406 91.452000 5223 7038 4 chr3D.!!$F2 1815
4 TraesCS3D01G418900 chr3A 665980678 665986707 6029 True 2976.333333 7262 92.260667 1 6019 3 chr3A.!!$R2 6018
5 TraesCS3D01G418900 chr3A 665967970 665968825 855 True 815.000000 815 84.615000 6209 7038 1 chr3A.!!$R1 829
6 TraesCS3D01G418900 chr3B 702693370 702700664 7294 True 1642.000000 5579 89.974400 1 7038 5 chr3B.!!$R1 7037
7 TraesCS3D01G418900 chr3B 702843622 702849785 6163 True 1318.860000 2824 88.663600 177 6073 5 chr3B.!!$R3 5896
8 TraesCS3D01G418900 chr3B 702826714 702834846 8132 True 775.600000 1495 88.954000 285 6073 8 chr3B.!!$R2 5788
9 TraesCS3D01G418900 chr2D 46684845 46688406 3561 False 1118.000000 2305 84.259333 186 3543 3 chr2D.!!$F1 3357
10 TraesCS3D01G418900 chr2D 46693765 46694543 778 False 463.000000 667 88.784500 3537 4344 2 chr2D.!!$F2 807
11 TraesCS3D01G418900 chr4B 622124699 622125216 517 True 593.000000 593 87.645000 2030 2538 1 chr4B.!!$R1 508

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
421 700 1.774254 TGTGGTTGGTCAGATTCCTGT 59.226 47.619 0.00 0.00 41.16 4.00 F
1154 1814 2.776312 ATGGTATCTCGTGTAGTGCG 57.224 50.000 0.00 0.00 0.00 5.34 F
1957 4980 4.110482 GCCAAGAAATGATTCACATCTGC 58.890 43.478 4.34 2.07 38.38 4.26 F
3252 6502 4.274950 TCGAACAACAGGTTTTTCTCCATC 59.725 41.667 8.80 0.00 40.63 3.51 F
4305 8984 0.988832 TAGCAACGGTGAAGGGGATT 59.011 50.000 3.55 0.00 0.00 3.01 F
5836 11036 0.032678 CCATGAGGCCTAGCTACGTG 59.967 60.000 4.42 4.17 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 5151 5.074115 ACCGTCAAAGTTATTTCCATGGAA 58.926 37.500 23.63 23.63 0.00 3.53 R
2969 6106 4.876679 CAGATCACTGCAAAGACAGATGAT 59.123 41.667 0.00 4.37 40.25 2.45 R
3810 7065 0.804989 CCCACGCTTTTCCATGTCTC 59.195 55.000 0.00 0.00 0.00 3.36 R
4392 9071 1.456705 AAACAAAGGCCCCAGCGAA 60.457 52.632 0.00 0.00 41.24 4.70 R
5928 11128 0.037882 CTTCTTGCTCGAGCTGGACA 60.038 55.000 35.27 14.66 42.66 4.02 R
6645 15345 1.661498 TTGTTTGCACTGCGGCTTCA 61.661 50.000 0.00 0.00 34.04 3.02 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 2.159198 CCCAAGCAACATTAGTGCCATC 60.159 50.000 0.00 0.00 0.00 3.51
102 103 2.098443 TGCCGGTTGAAACTTGAAAGTC 59.902 45.455 1.90 0.00 38.57 3.01
160 163 5.706916 AGCTTGAAGTTGCAATTAGTGATG 58.293 37.500 0.59 0.00 0.00 3.07
161 164 5.242393 AGCTTGAAGTTGCAATTAGTGATGT 59.758 36.000 0.59 0.00 0.00 3.06
165 168 8.795786 TTGAAGTTGCAATTAGTGATGTTAAC 57.204 30.769 0.59 0.00 0.00 2.01
166 169 7.367285 TGAAGTTGCAATTAGTGATGTTAACC 58.633 34.615 0.59 0.00 0.00 2.85
169 172 8.807948 AGTTGCAATTAGTGATGTTAACCTAT 57.192 30.769 0.59 0.00 0.00 2.57
170 173 9.899661 AGTTGCAATTAGTGATGTTAACCTATA 57.100 29.630 0.59 0.00 0.00 1.31
348 627 6.403866 AGTCCATGCTTTCAATTTGTTACA 57.596 33.333 0.00 0.00 0.00 2.41
392 671 5.600908 TTTGTTCACGCAGGAAAGTATAC 57.399 39.130 0.00 0.00 0.00 1.47
421 700 1.774254 TGTGGTTGGTCAGATTCCTGT 59.226 47.619 0.00 0.00 41.16 4.00
451 730 7.041098 ACTGCAAAATCTAACTTACCTGACAAG 60.041 37.037 0.00 0.00 0.00 3.16
471 750 6.245408 ACAAGCCTGTATGAACTATTTCCAA 58.755 36.000 0.00 0.00 32.54 3.53
473 752 5.193679 AGCCTGTATGAACTATTTCCAACC 58.806 41.667 0.00 0.00 0.00 3.77
540 819 4.574013 AGCTCATAATTACAAGCTGCAGTC 59.426 41.667 16.64 7.83 43.21 3.51
980 1600 8.517878 TTTCTGCAATTGAAAATTTGGAAACAA 58.482 25.926 10.34 0.00 38.25 2.83
1154 1814 2.776312 ATGGTATCTCGTGTAGTGCG 57.224 50.000 0.00 0.00 0.00 5.34
1438 2106 7.863722 TGTAGGCTCCATAAATTAAACACCTA 58.136 34.615 0.00 0.00 0.00 3.08
1858 4869 5.454897 GGGTTTACTGGGAAGATACCTGATC 60.455 48.000 0.00 0.00 34.40 2.92
1957 4980 4.110482 GCCAAGAAATGATTCACATCTGC 58.890 43.478 4.34 2.07 38.38 4.26
1981 5004 5.530171 CCTTCAATGTTCATGATAGGACTGG 59.470 44.000 0.00 0.00 31.95 4.00
2048 5084 7.990886 TCTTTTATATCACATTTTAGAGCCCGT 59.009 33.333 0.00 0.00 0.00 5.28
2059 5095 8.145122 ACATTTTAGAGCCCGTTTTCAAAATTA 58.855 29.630 0.00 0.00 0.00 1.40
2066 5102 8.364894 AGAGCCCGTTTTCAAAATTAGTAAAAT 58.635 29.630 0.00 0.00 0.00 1.82
2115 5151 5.307456 AGATGTATCTGTCAATGCAGGAGAT 59.693 40.000 0.00 0.00 37.12 2.75
2213 5249 6.395629 TCTTCCTACTTTAGATTTGGTGACG 58.604 40.000 0.00 0.00 0.00 4.35
2419 5458 7.547722 ACAACTTTGTATGTCTTCGCATATGTA 59.452 33.333 4.29 0.00 40.16 2.29
2517 5564 8.926715 ACTTCTCAAAATTTGTTAACCTCAAC 57.073 30.769 5.56 0.00 0.00 3.18
2881 5997 9.524106 TTTCTTCCTTCGTTTTAATTTCCTTTC 57.476 29.630 0.00 0.00 0.00 2.62
2967 6104 5.598005 TCTTCATCCTTTTGGTCAACATGTT 59.402 36.000 4.92 4.92 41.38 2.71
2969 6106 6.968263 TCATCCTTTTGGTCAACATGTTTA 57.032 33.333 8.77 0.00 41.38 2.01
3252 6502 4.274950 TCGAACAACAGGTTTTTCTCCATC 59.725 41.667 8.80 0.00 40.63 3.51
3318 6568 8.667076 TTCACCATGTGATCAAACTATCTATG 57.333 34.615 0.00 0.00 42.40 2.23
3342 6592 6.016610 TGTTGTTCCTAGTATTTTGCCTTCAC 60.017 38.462 0.00 0.00 0.00 3.18
3588 6843 5.177511 CCAGTTGCATCATACTATGTTACGG 59.822 44.000 0.00 0.00 0.00 4.02
4168 8835 1.496429 CAAGGGTTCTATGGGCCATCT 59.504 52.381 25.07 10.01 0.00 2.90
4177 8844 3.969976 TCTATGGGCCATCTATATCAGCC 59.030 47.826 25.07 0.00 43.09 4.85
4305 8984 0.988832 TAGCAACGGTGAAGGGGATT 59.011 50.000 3.55 0.00 0.00 3.01
4330 9009 4.319177 GGTTCACAGAGAAACAGCACTAT 58.681 43.478 0.00 0.00 43.64 2.12
4392 9071 4.523083 TGCGGTTTTAGGATTTCTAGCAT 58.477 39.130 0.00 0.00 0.00 3.79
4461 9141 4.956700 TGGAAATGGAAGGTAACACAAACA 59.043 37.500 0.00 0.00 41.41 2.83
4462 9142 5.068460 TGGAAATGGAAGGTAACACAAACAG 59.932 40.000 0.00 0.00 41.41 3.16
4468 9148 7.648039 TGGAAGGTAACACAAACAGTTAAAT 57.352 32.000 0.00 0.00 41.41 1.40
4470 9150 7.976734 TGGAAGGTAACACAAACAGTTAAATTG 59.023 33.333 0.00 0.00 41.41 2.32
4472 9152 9.744468 GAAGGTAACACAAACAGTTAAATTGAT 57.256 29.630 0.00 0.00 41.41 2.57
4475 9156 9.953697 GGTAACACAAACAGTTAAATTGATGTA 57.046 29.630 0.00 0.00 33.64 2.29
4525 9274 4.270325 ACTTCGTTTTACAGAGCTGTTCAC 59.730 41.667 8.60 3.04 41.83 3.18
4547 9296 6.157994 TCACTATAGTTGGAAGGCCTAACATT 59.842 38.462 17.23 7.87 34.31 2.71
4591 9340 3.825014 TCTGCTACGGACAGTTTTAGTCT 59.175 43.478 0.00 0.00 36.50 3.24
4604 9353 8.451908 ACAGTTTTAGTCTTAGCAACATTCTT 57.548 30.769 0.00 0.00 0.00 2.52
4616 9366 1.760405 ACATTCTTGGAAGAGGGGGT 58.240 50.000 0.00 0.00 36.22 4.95
4849 9933 3.760684 AGGAGTTCATGACAGAAATTGCC 59.239 43.478 0.00 0.00 0.00 4.52
4954 10038 1.068352 ACCTGGAACAAGGGAGCCTT 61.068 55.000 0.00 0.00 45.88 4.35
5290 10444 2.730672 CGCTGGCACGCTGTAAGAC 61.731 63.158 7.22 0.00 34.07 3.01
5575 10763 6.993079 ACCTCAAAATAAACCATCAACTTCC 58.007 36.000 0.00 0.00 0.00 3.46
5725 10921 5.105063 CGACTCATCAATGTTGCTCTTCTA 58.895 41.667 0.00 0.00 0.00 2.10
5791 10987 0.904649 TGTCCATGCTCACGGAAGAT 59.095 50.000 0.00 0.00 31.67 2.40
5836 11036 0.032678 CCATGAGGCCTAGCTACGTG 59.967 60.000 4.42 4.17 0.00 4.49
5909 11109 2.125753 CGGCTCAGCAGTCCTCAC 60.126 66.667 0.00 0.00 0.00 3.51
5928 11128 3.031964 GCAGTCAAATCAGCGCGCT 62.032 57.895 31.32 31.32 0.00 5.92
5998 14647 0.741221 CCCTGTCGCCTTGTTCTAGC 60.741 60.000 0.00 0.00 0.00 3.42
6085 14768 7.272144 ACATTGGGTCCTAGTAATTTCTTCT 57.728 36.000 0.00 0.00 0.00 2.85
6120 14803 8.515414 GTTCATATTTGGTTAGTTCTTCTGCTT 58.485 33.333 0.00 0.00 0.00 3.91
6161 14844 8.492673 TTGTTTTCTCTCGCAAATACATAGAT 57.507 30.769 0.00 0.00 0.00 1.98
6162 14845 7.909267 TGTTTTCTCTCGCAAATACATAGATG 58.091 34.615 0.00 0.00 0.00 2.90
6179 14862 3.443037 AGATGTCTCGCTCTTTGATTCG 58.557 45.455 0.00 0.00 0.00 3.34
6182 14865 4.371855 TGTCTCGCTCTTTGATTCGTAT 57.628 40.909 0.00 0.00 0.00 3.06
6191 14874 8.114290 TCGCTCTTTGATTCGTATAATTTTCAC 58.886 33.333 0.00 0.00 0.00 3.18
6193 14876 9.000018 GCTCTTTGATTCGTATAATTTTCACAC 58.000 33.333 0.00 0.00 0.00 3.82
6204 14887 7.799447 CGTATAATTTTCACACGACCTTTTGAA 59.201 33.333 0.00 0.00 34.66 2.69
6220 14903 6.152661 ACCTTTTGAACACTCTGTGAATTGAA 59.847 34.615 4.61 0.00 36.96 2.69
6228 14911 6.122277 ACACTCTGTGAATTGAAAAGGAAGA 58.878 36.000 4.61 0.00 36.96 2.87
6230 14913 7.939039 ACACTCTGTGAATTGAAAAGGAAGATA 59.061 33.333 4.61 0.00 36.96 1.98
6305 14990 6.955963 CACAATATGCGAGAGTTTTACAAGAC 59.044 38.462 0.00 0.00 0.00 3.01
6315 15000 7.042051 CGAGAGTTTTACAAGACCAGAATTCAA 60.042 37.037 8.44 0.00 0.00 2.69
6382 15076 5.454613 CCTTGTTTGTTTGGCCTTTAGGAAT 60.455 40.000 3.32 0.00 37.39 3.01
6453 15147 4.309950 GACGGAGGTGCGGGTTGT 62.310 66.667 0.00 0.00 0.00 3.32
6493 15188 0.550914 GCATTGGTGGGAGGTGGATA 59.449 55.000 0.00 0.00 0.00 2.59
6517 15212 1.814772 CGTGCTTTGGGGCATTTCCA 61.815 55.000 0.00 0.00 44.34 3.53
6538 15234 2.880890 ACATTCTCACCAACTTGCAGTC 59.119 45.455 0.00 0.00 0.00 3.51
6543 15239 2.088423 TCACCAACTTGCAGTCGTTTT 58.912 42.857 0.00 0.00 0.00 2.43
6553 15249 7.197071 ACTTGCAGTCGTTTTCACAATTATA 57.803 32.000 0.00 0.00 0.00 0.98
6645 15345 2.362077 CAAGTTTACAGCTGCTTTGGGT 59.638 45.455 15.27 0.00 0.00 4.51
6728 15433 2.519013 GAACCTCTTTTGGCTGGTCAT 58.481 47.619 0.00 0.00 31.64 3.06
6748 15453 5.642063 GTCATCTCTTTTGGTGGTTATTCGA 59.358 40.000 0.00 0.00 0.00 3.71
6966 15695 5.349543 CCTCCGTACATTTAACTGGTACAAC 59.650 44.000 0.00 0.00 38.70 3.32
6986 15715 3.356290 ACTACATGGGGAAATTGTGCTC 58.644 45.455 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.101790 GCGAACATGCACCCACCG 62.102 66.667 0.00 0.00 34.15 4.94
102 103 1.327303 TTTGTAGCAAACCTGGGCTG 58.673 50.000 6.24 0.07 41.25 4.85
135 138 6.147864 TCACTAATTGCAACTTCAAGCTTT 57.852 33.333 0.00 0.00 0.00 3.51
136 139 5.772825 TCACTAATTGCAACTTCAAGCTT 57.227 34.783 0.00 0.00 0.00 3.74
421 700 6.206634 CAGGTAAGTTAGATTTTGCAGTTCCA 59.793 38.462 0.00 0.00 0.00 3.53
451 730 5.066505 CAGGTTGGAAATAGTTCATACAGGC 59.933 44.000 5.15 0.00 35.25 4.85
508 787 6.967199 GCTTGTAATTATGAGCTTGTGTAACC 59.033 38.462 13.00 0.00 31.41 2.85
540 819 3.646162 TGCATCATACAGTAACTAGGGGG 59.354 47.826 0.00 0.00 0.00 5.40
980 1600 7.389884 AGCGCATCAGAATCAATGTAAATCTAT 59.610 33.333 11.47 0.00 0.00 1.98
984 1604 5.762825 AGCGCATCAGAATCAATGTAAAT 57.237 34.783 11.47 0.00 0.00 1.40
1154 1814 5.656480 TGAAAAGAAAACAGGGCAAGTTAC 58.344 37.500 0.00 0.00 0.00 2.50
1858 4869 6.369340 TGCAAATTTGATAAGCTTCCAATGTG 59.631 34.615 22.31 0.01 0.00 3.21
1957 4980 5.530171 CCAGTCCTATCATGAACATTGAAGG 59.470 44.000 0.00 0.00 0.00 3.46
2028 5064 6.601613 TGAAAACGGGCTCTAAAATGTGATAT 59.398 34.615 0.00 0.00 0.00 1.63
2059 5095 9.875691 GCAGGGAAAAGAATCAATTATTTTACT 57.124 29.630 14.27 10.17 40.11 2.24
2115 5151 5.074115 ACCGTCAAAGTTATTTCCATGGAA 58.926 37.500 23.63 23.63 0.00 3.53
2517 5564 7.820648 ACAGTTCCAAAATTGCTTACAGATAG 58.179 34.615 0.00 0.00 0.00 2.08
2967 6104 6.537660 CAGATCACTGCAAAGACAGATGATAA 59.462 38.462 0.00 0.00 40.25 1.75
2969 6106 4.876679 CAGATCACTGCAAAGACAGATGAT 59.123 41.667 0.00 4.37 40.25 2.45
3252 6502 8.960591 ACATATGAAGGGAAACTAAATGAAGTG 58.039 33.333 10.38 0.00 0.00 3.16
3318 6568 6.379386 GTGAAGGCAAAATACTAGGAACAAC 58.621 40.000 0.00 0.00 0.00 3.32
3342 6592 4.166523 TCTCGCTGAAGACAATTTAGTCG 58.833 43.478 0.00 0.00 43.24 4.18
3588 6843 1.519455 CGCCCCATCTCGTTGAGTC 60.519 63.158 0.00 0.00 0.00 3.36
3670 6925 6.119536 TCAGAATCAAGTGTGTTGGTAAACT 58.880 36.000 0.00 0.00 37.19 2.66
3810 7065 0.804989 CCCACGCTTTTCCATGTCTC 59.195 55.000 0.00 0.00 0.00 3.36
3957 7213 9.895138 AAGCAAGCAAAAGATATTAAAATCCAT 57.105 25.926 0.00 0.00 0.00 3.41
3961 7217 8.542926 AGGGAAGCAAGCAAAAGATATTAAAAT 58.457 29.630 0.00 0.00 0.00 1.82
3962 7218 7.818930 CAGGGAAGCAAGCAAAAGATATTAAAA 59.181 33.333 0.00 0.00 0.00 1.52
3964 7220 6.127366 CCAGGGAAGCAAGCAAAAGATATTAA 60.127 38.462 0.00 0.00 0.00 1.40
4168 8835 7.704578 AGAAGATACGCTTAAGGCTGATATA 57.295 36.000 4.29 0.00 36.83 0.86
4177 8844 8.136165 ACAGTACCATAAGAAGATACGCTTAAG 58.864 37.037 0.00 0.00 36.83 1.85
4243 8911 8.723942 ATAATAGAAAGTGGACTGTTGTCATC 57.276 34.615 0.00 0.00 44.61 2.92
4305 8984 2.170397 TGCTGTTTCTCTGTGAACCAGA 59.830 45.455 17.54 4.09 44.71 3.86
4330 9009 4.497291 ACAACCAAACCTGTTCTACTGA 57.503 40.909 0.00 0.00 0.00 3.41
4392 9071 1.456705 AAACAAAGGCCCCAGCGAA 60.457 52.632 0.00 0.00 41.24 4.70
4475 9156 9.936329 ACATGTAAATTTCTCCCCATAATTAGT 57.064 29.630 0.00 0.00 0.00 2.24
4495 9202 6.584942 CAGCTCTGTAAAACGAAGTACATGTA 59.415 38.462 0.08 0.08 45.00 2.29
4502 9209 4.270325 GTGAACAGCTCTGTAAAACGAAGT 59.730 41.667 2.62 0.00 44.37 3.01
4525 9274 7.556275 TGAAAATGTTAGGCCTTCCAACTATAG 59.444 37.037 12.58 0.00 33.74 1.31
4547 9296 9.638239 GCAGATTTTATTTCACCATAACTGAAA 57.362 29.630 0.00 0.00 40.89 2.69
4591 9340 4.335416 CCCTCTTCCAAGAATGTTGCTAA 58.665 43.478 0.00 0.00 34.03 3.09
4604 9353 1.591768 GTCCATAACCCCCTCTTCCA 58.408 55.000 0.00 0.00 0.00 3.53
4616 9366 4.563993 CCGACCTTGTAAACAGGTCCATAA 60.564 45.833 18.13 0.00 46.82 1.90
4849 9933 4.538233 TGCACCGCAGATATGGTG 57.462 55.556 7.02 7.02 43.93 4.17
4954 10038 5.824624 GGAGATACCAAAGATTGCTTGATCA 59.175 40.000 0.00 0.00 38.79 2.92
4986 10101 7.219484 ACTTTTCATGACACCAAGGAATAAG 57.781 36.000 0.00 0.00 0.00 1.73
4989 10106 6.777580 ACTTACTTTTCATGACACCAAGGAAT 59.222 34.615 0.00 0.00 0.00 3.01
5101 10220 1.679944 GCTAGACCTCTTGCAATGCCA 60.680 52.381 1.53 0.00 42.75 4.92
5290 10444 3.242413 CGATTAAGACGGACAGCAAATGG 60.242 47.826 0.00 0.00 0.00 3.16
5545 10733 5.710099 TGATGGTTTATTTTGAGGTCAGGAC 59.290 40.000 0.00 0.00 0.00 3.85
5582 10775 8.983724 GTGAGCTTAATTTCCTTAGTATGCTAG 58.016 37.037 0.00 0.00 0.00 3.42
5791 10987 1.371337 CCACGTCGGTCACCTCGATA 61.371 60.000 13.87 0.00 38.93 2.92
5928 11128 0.037882 CTTCTTGCTCGAGCTGGACA 60.038 55.000 35.27 14.66 42.66 4.02
5955 11158 3.626924 GCGAGGTGTCCCTGTGGT 61.627 66.667 0.00 0.00 42.86 4.16
5980 11183 2.755929 GCTAGAACAAGGCGACAGG 58.244 57.895 0.00 0.00 0.00 4.00
6161 14844 2.724977 ACGAATCAAAGAGCGAGACA 57.275 45.000 0.00 0.00 0.00 3.41
6162 14845 6.994868 ATTATACGAATCAAAGAGCGAGAC 57.005 37.500 0.00 0.00 0.00 3.36
6179 14862 8.898792 GTTCAAAAGGTCGTGTGAAAATTATAC 58.101 33.333 0.00 0.00 32.12 1.47
6182 14865 6.748198 GTGTTCAAAAGGTCGTGTGAAAATTA 59.252 34.615 0.00 0.00 32.12 1.40
6191 14874 2.936498 ACAGAGTGTTCAAAAGGTCGTG 59.064 45.455 0.00 0.00 0.00 4.35
6193 14876 3.194861 TCACAGAGTGTTCAAAAGGTCG 58.805 45.455 0.00 0.00 34.79 4.79
6204 14887 6.122277 TCTTCCTTTTCAATTCACAGAGTGT 58.878 36.000 0.00 0.00 34.79 3.55
6220 14903 4.957327 AGAGACGCTTACCTATCTTCCTTT 59.043 41.667 0.00 0.00 0.00 3.11
6228 14911 5.198965 TGAAAGGTAGAGACGCTTACCTAT 58.801 41.667 3.81 0.00 41.67 2.57
6230 14913 3.428532 TGAAAGGTAGAGACGCTTACCT 58.571 45.455 0.00 0.00 44.16 3.08
6305 14990 5.591472 TGCACTCCAATCTATTGAATTCTGG 59.409 40.000 7.05 4.23 40.14 3.86
6315 15000 5.755375 CGACTTTACATGCACTCCAATCTAT 59.245 40.000 0.00 0.00 0.00 1.98
6382 15076 1.234821 CTGCGCCTACCAAAAGTTGA 58.765 50.000 4.18 0.00 0.00 3.18
6453 15147 2.284921 CTCCCCTGTCCTCCTGCA 60.285 66.667 0.00 0.00 0.00 4.41
6538 15234 8.012151 TGTTTGGCAATATAATTGTGAAAACG 57.988 30.769 0.00 0.00 0.00 3.60
6543 15239 9.632807 GTTAGTTGTTTGGCAATATAATTGTGA 57.367 29.630 0.00 0.00 39.55 3.58
6553 15249 8.449251 AAAATGAATGTTAGTTGTTTGGCAAT 57.551 26.923 0.00 0.00 39.55 3.56
6645 15345 1.661498 TTGTTTGCACTGCGGCTTCA 61.661 50.000 0.00 0.00 34.04 3.02
6728 15433 4.000988 GCTCGAATAACCACCAAAAGAGA 58.999 43.478 0.00 0.00 0.00 3.10
6781 15487 4.142004 TGGTACTAATTCCGGAGAAGAAGC 60.142 45.833 3.34 0.64 34.86 3.86
6966 15695 2.355756 CGAGCACAATTTCCCCATGTAG 59.644 50.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.