Multiple sequence alignment - TraesCS4D01G201700

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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 TraesCS4D01G201700 chr4D 100.000 4526 0 0 1 4526 348562682 348567207 0.000000e+00 8359.0
1 TraesCS4D01G201700 chr4D 80.011 1791 323 27 1745 3522 348698393 348700161 0.000000e+00 1291.0
2 TraesCS4D01G201700 chr4A 94.953 4022 126 23 83 4069 116853695 116849716 0.000000e+00 6231.0
3 TraesCS4D01G201700 chr4A 93.301 209 13 1 4102 4310 116849718 116849511 1.580000e-79 307.0
4 TraesCS4D01G201700 chr4A 85.232 237 32 3 4292 4525 116728981 116728745 1.630000e-59 241.0
5 TraesCS4D01G201700 chr4B 97.255 3060 56 6 1105 4160 428844916 428847951 0.000000e+00 5160.0
6 TraesCS4D01G201700 chr4B 80.305 1899 324 35 1643 3524 428899342 428901207 0.000000e+00 1389.0
7 TraesCS4D01G201700 chr4B 91.766 753 29 11 255 996 428843892 428844622 0.000000e+00 1016.0
8 TraesCS4D01G201700 chr4B 92.000 200 16 0 4327 4526 428848276 428848475 9.590000e-72 281.0
9 TraesCS4D01G201700 chr4B 92.647 68 4 1 4192 4259 428847945 428848011 3.730000e-16 97.1
10 TraesCS4D01G201700 chr3D 79.769 954 173 16 2581 3524 460180973 460181916 0.000000e+00 675.0
11 TraesCS4D01G201700 chr3D 78.367 735 146 12 1644 2372 460180072 460180799 8.870000e-127 464.0
12 TraesCS4D01G201700 chr3B 79.079 956 176 19 2581 3524 609802915 609803858 1.780000e-178 636.0
13 TraesCS4D01G201700 chr3B 79.391 723 131 14 1643 2356 24019141 24018428 1.130000e-135 494.0
14 TraesCS4D01G201700 chr3A 79.036 954 180 16 2581 3524 602225915 602226858 1.780000e-178 636.0
15 TraesCS4D01G201700 chr1B 76.892 991 207 20 2584 3559 50205057 50206040 3.980000e-150 542.0
16 TraesCS4D01G201700 chr1A 76.956 946 205 12 2587 3524 31253366 31252426 1.120000e-145 527.0
17 TraesCS4D01G201700 chr1A 77.531 721 148 12 1643 2356 31254277 31253564 5.410000e-114 422.0
18 TraesCS4D01G201700 chr5B 79.833 719 135 8 1643 2356 112021346 112020633 2.410000e-142 516.0
19 TraesCS4D01G201700 chr1D 79.458 701 132 10 1644 2338 32738195 32738889 1.890000e-133 486.0
20 TraesCS4D01G201700 chr5A 79.057 721 137 13 1643 2356 96983814 96984527 2.450000e-132 483.0


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 TraesCS4D01G201700 chr4D 348562682 348567207 4525 False 8359.000 8359 100.0000 1 4526 1 chr4D.!!$F1 4525
1 TraesCS4D01G201700 chr4D 348698393 348700161 1768 False 1291.000 1291 80.0110 1745 3522 1 chr4D.!!$F2 1777
2 TraesCS4D01G201700 chr4A 116849511 116853695 4184 True 3269.000 6231 94.1270 83 4310 2 chr4A.!!$R2 4227
3 TraesCS4D01G201700 chr4B 428843892 428848475 4583 False 1638.525 5160 93.4170 255 4526 4 chr4B.!!$F2 4271
4 TraesCS4D01G201700 chr4B 428899342 428901207 1865 False 1389.000 1389 80.3050 1643 3524 1 chr4B.!!$F1 1881
5 TraesCS4D01G201700 chr3D 460180072 460181916 1844 False 569.500 675 79.0680 1644 3524 2 chr3D.!!$F1 1880
6 TraesCS4D01G201700 chr3B 609802915 609803858 943 False 636.000 636 79.0790 2581 3524 1 chr3B.!!$F1 943
7 TraesCS4D01G201700 chr3B 24018428 24019141 713 True 494.000 494 79.3910 1643 2356 1 chr3B.!!$R1 713
8 TraesCS4D01G201700 chr3A 602225915 602226858 943 False 636.000 636 79.0360 2581 3524 1 chr3A.!!$F1 943
9 TraesCS4D01G201700 chr1B 50205057 50206040 983 False 542.000 542 76.8920 2584 3559 1 chr1B.!!$F1 975
10 TraesCS4D01G201700 chr1A 31252426 31254277 1851 True 474.500 527 77.2435 1643 3524 2 chr1A.!!$R1 1881
11 TraesCS4D01G201700 chr5B 112020633 112021346 713 True 516.000 516 79.8330 1643 2356 1 chr5B.!!$R1 713
12 TraesCS4D01G201700 chr1D 32738195 32738889 694 False 486.000 486 79.4580 1644 2338 1 chr1D.!!$F1 694
13 TraesCS4D01G201700 chr5A 96983814 96984527 713 False 483.000 483 79.0570 1643 2356 1 chr5A.!!$F1 713

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
140 142 0.251297 CCAAGTGATGAGCCCCACAA 60.251 55.0 0.0 0.0 35.84 3.33 F
1054 1070 0.183971 TCCATCGACCTCTCTCTCCC 59.816 60.0 0.0 0.0 0.00 4.30 F
1055 1071 0.184933 CCATCGACCTCTCTCTCCCT 59.815 60.0 0.0 0.0 0.00 4.20 F
2439 2652 0.999406 CGAAGATGAAACACGCCGAT 59.001 50.0 0.0 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1758 0.393673 GGCCCTTCTTCCTCTGCTTC 60.394 60.000 0.00 0.0 0.00 3.86 R
2385 2598 1.242076 GCCATGACTTGTTGTGCTCT 58.758 50.000 0.00 0.0 0.00 4.09 R
2522 2802 1.374252 GTGACATTGCCGTCGGTCT 60.374 57.895 13.94 0.0 38.84 3.85 R
4316 4615 0.174845 TCACGTAATTGAGCGGGGAG 59.825 55.000 0.00 0.0 31.65 4.30 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
20 21 3.484334 GTCAATGAAGAAAGCAGGCTC 57.516 47.619 0.00 0.00 0.00 4.70
21 22 2.163211 GTCAATGAAGAAAGCAGGCTCC 59.837 50.000 0.00 0.00 0.00 4.70
22 23 2.165167 CAATGAAGAAAGCAGGCTCCA 58.835 47.619 0.00 0.00 0.00 3.86
23 24 1.831580 ATGAAGAAAGCAGGCTCCAC 58.168 50.000 0.00 0.00 0.00 4.02
24 25 0.603707 TGAAGAAAGCAGGCTCCACG 60.604 55.000 0.00 0.00 0.00 4.94
25 26 1.916697 GAAGAAAGCAGGCTCCACGC 61.917 60.000 0.00 0.00 38.13 5.34
35 36 4.511246 CTCCACGCCCCATGCCAT 62.511 66.667 0.00 0.00 36.24 4.40
36 37 4.818863 TCCACGCCCCATGCCATG 62.819 66.667 0.00 0.00 36.24 3.66
73 74 3.127533 GGCTACGCCTTGCCTGTG 61.128 66.667 1.21 0.00 46.69 3.66
74 75 2.358737 GCTACGCCTTGCCTGTGT 60.359 61.111 0.00 0.00 0.00 3.72
75 76 2.680913 GCTACGCCTTGCCTGTGTG 61.681 63.158 0.00 0.00 0.00 3.82
76 77 2.668212 TACGCCTTGCCTGTGTGC 60.668 61.111 0.00 0.00 0.00 4.57
77 78 3.177194 TACGCCTTGCCTGTGTGCT 62.177 57.895 0.00 0.00 0.00 4.40
78 79 4.034258 CGCCTTGCCTGTGTGCTG 62.034 66.667 0.00 0.00 0.00 4.41
79 80 2.908940 GCCTTGCCTGTGTGCTGT 60.909 61.111 0.00 0.00 0.00 4.40
80 81 2.492773 GCCTTGCCTGTGTGCTGTT 61.493 57.895 0.00 0.00 0.00 3.16
81 82 1.361271 CCTTGCCTGTGTGCTGTTG 59.639 57.895 0.00 0.00 0.00 3.33
92 93 3.788766 GCTGTTGTAGTGCCGCCG 61.789 66.667 0.00 0.00 0.00 6.46
105 107 4.630785 CGCCGGCGATCGATCTGT 62.631 66.667 44.86 0.00 42.83 3.41
108 110 1.226974 CCGGCGATCGATCTGTTGT 60.227 57.895 21.57 0.00 42.43 3.32
126 128 3.788227 TGTCAATAGCCAAGACCAAGT 57.212 42.857 0.00 0.00 0.00 3.16
129 131 4.263462 TGTCAATAGCCAAGACCAAGTGAT 60.263 41.667 0.00 0.00 0.00 3.06
140 142 0.251297 CCAAGTGATGAGCCCCACAA 60.251 55.000 0.00 0.00 35.84 3.33
141 143 1.619654 CAAGTGATGAGCCCCACAAA 58.380 50.000 0.00 0.00 35.84 2.83
142 144 2.173519 CAAGTGATGAGCCCCACAAAT 58.826 47.619 0.00 0.00 35.84 2.32
146 148 1.075212 TGATGAGCCCCACAAATGACA 59.925 47.619 0.00 0.00 0.00 3.58
147 149 1.747355 GATGAGCCCCACAAATGACAG 59.253 52.381 0.00 0.00 0.00 3.51
153 155 2.372264 CCCCACAAATGACAGGATGAG 58.628 52.381 0.00 0.00 39.69 2.90
158 160 2.567169 ACAAATGACAGGATGAGACGGA 59.433 45.455 0.00 0.00 39.69 4.69
171 173 4.473520 ACGGAGCGAGCCCCAATG 62.474 66.667 0.00 0.00 0.00 2.82
194 196 7.482654 TGCATGGAAGAAAATCTTATACGAG 57.517 36.000 0.00 0.00 36.73 4.18
208 210 1.957668 TACGAGCTGGTCATACGCTA 58.042 50.000 4.00 0.00 33.47 4.26
213 215 1.341531 AGCTGGTCATACGCTACATCC 59.658 52.381 0.00 0.00 31.12 3.51
250 252 1.946768 CCAGATGACACGTGGTTTTGT 59.053 47.619 21.57 0.00 0.00 2.83
285 287 4.574599 ACCAAAGAACTCAACTTCATGC 57.425 40.909 0.00 0.00 0.00 4.06
320 322 6.951198 AGTTGACCCAAATGTGATGGTTATTA 59.049 34.615 0.00 0.00 36.14 0.98
344 346 2.167398 TTACCTCGTGGCTGCTGGTC 62.167 60.000 2.76 0.00 36.63 4.02
508 517 4.818546 TGCAAAACAATAAACCCAACATGG 59.181 37.500 0.00 0.00 37.25 3.66
552 561 9.208022 TCAGATATTTCCATCTTAGCAATAACG 57.792 33.333 0.00 0.00 32.83 3.18
559 568 4.212214 CCATCTTAGCAATAACGGAGAAGC 59.788 45.833 0.00 0.00 0.00 3.86
571 580 1.446966 GAGAAGCTGCCGGTGAGAC 60.447 63.158 1.90 0.00 0.00 3.36
632 641 7.158021 ACATTTGATTTAAATTTCGCCTCCAA 58.842 30.769 1.43 0.00 36.87 3.53
879 892 1.235724 GCTTCCGTGGCAACTTAACT 58.764 50.000 0.00 0.00 37.61 2.24
921 934 2.452813 CCCACGAAGACGCCAATCG 61.453 63.158 0.00 0.00 43.96 3.34
980 996 1.305046 TCCTCTCGGGTTGACTCCC 60.305 63.158 0.00 0.00 43.78 4.30
1017 1033 7.328737 GCTATAAGAATGGTTACTGGTACGATG 59.671 40.741 0.00 0.00 0.00 3.84
1019 1035 3.451178 AGAATGGTTACTGGTACGATGCT 59.549 43.478 0.00 0.00 0.00 3.79
1054 1070 0.183971 TCCATCGACCTCTCTCTCCC 59.816 60.000 0.00 0.00 0.00 4.30
1055 1071 0.184933 CCATCGACCTCTCTCTCCCT 59.815 60.000 0.00 0.00 0.00 4.20
1056 1072 1.604604 CATCGACCTCTCTCTCCCTC 58.395 60.000 0.00 0.00 0.00 4.30
1061 1077 1.143073 GACCTCTCTCTCCCTCTCTCC 59.857 61.905 0.00 0.00 0.00 3.71
1158 1359 1.626654 CGAGCAAGATGTCGCGGTTT 61.627 55.000 6.13 0.00 0.00 3.27
1212 1413 3.142393 CCGATGGAGGAAGCCGAT 58.858 61.111 0.00 0.00 0.00 4.18
1467 1668 4.057428 ACCGGCAGTGAGAGCGAC 62.057 66.667 0.00 0.00 0.00 5.19
1633 1846 1.079819 CCACGGATGAAGACGCTGT 60.080 57.895 0.00 0.00 0.00 4.40
2439 2652 0.999406 CGAAGATGAAACACGCCGAT 59.001 50.000 0.00 0.00 0.00 4.18
2522 2802 2.649034 GAAGCTCGTGTCCGGTGA 59.351 61.111 0.00 0.00 33.95 4.02
2925 3205 2.498941 CGGCTTCCCCTCGCTCATA 61.499 63.158 0.00 0.00 0.00 2.15
3564 3850 1.414181 TCATCTTCTTGGATCCCTCGC 59.586 52.381 9.90 0.00 0.00 5.03
3803 4091 7.013274 TCCCTCTACATTTGAAACTTCAAGTTG 59.987 37.037 2.78 9.34 46.68 3.16
3837 4132 4.588528 ACTTTGTTTGGGTATGATTGTGCT 59.411 37.500 0.00 0.00 0.00 4.40
3868 4163 1.290203 CATGACGAAGAACGATGGGG 58.710 55.000 0.00 0.00 45.77 4.96
3878 4173 2.172717 AGAACGATGGGGAAGGTATTGG 59.827 50.000 0.00 0.00 0.00 3.16
3914 4213 2.228582 GCACACATATGTTTGGTGAGCA 59.771 45.455 22.38 0.00 44.77 4.26
3915 4214 3.671433 GCACACATATGTTTGGTGAGCAG 60.671 47.826 22.38 5.28 44.77 4.24
3916 4215 3.752747 CACACATATGTTTGGTGAGCAGA 59.247 43.478 16.10 0.00 36.72 4.26
4032 4331 2.917933 TGCTCCTGTTGCCATATGTAC 58.082 47.619 1.24 0.00 0.00 2.90
4035 4334 3.792401 CTCCTGTTGCCATATGTACGAA 58.208 45.455 1.24 0.00 0.00 3.85
4051 4350 0.577269 CGAAATTCTCGGCGGATGAC 59.423 55.000 7.21 0.00 44.20 3.06
4085 4384 1.657181 CCTGCGTCGGTTTGTTTGC 60.657 57.895 0.00 0.00 0.00 3.68
4086 4385 1.063327 CTGCGTCGGTTTGTTTGCA 59.937 52.632 0.00 0.00 0.00 4.08
4089 4388 0.305313 GCGTCGGTTTGTTTGCACTA 59.695 50.000 0.00 0.00 0.00 2.74
4122 4421 1.003839 CACAGAAACCCTAGCGCCA 60.004 57.895 2.29 0.00 0.00 5.69
4184 4483 2.772077 TGTTACTAGCAAATCCCGCA 57.228 45.000 0.00 0.00 0.00 5.69
4185 4484 3.275617 TGTTACTAGCAAATCCCGCAT 57.724 42.857 0.00 0.00 0.00 4.73
4212 4511 1.109323 GGTTGCAGCAGGGTTGTTCT 61.109 55.000 2.05 0.00 0.00 3.01
4244 4543 6.391537 TCGCGTATGTATATGCCTATTTTCA 58.608 36.000 5.77 0.00 41.15 2.69
4245 4544 6.869388 TCGCGTATGTATATGCCTATTTTCAA 59.131 34.615 5.77 0.00 41.15 2.69
4268 4567 3.609409 GCTGATCGTTGGTTGTTTTCTCC 60.609 47.826 0.00 0.00 0.00 3.71
4318 4617 4.035102 GTGCCACTCCACCCCCTC 62.035 72.222 0.00 0.00 0.00 4.30
4346 4841 5.582665 GCTCAATTACGTGATTCTCCTCTTT 59.417 40.000 2.04 0.00 0.00 2.52
4388 4883 2.617788 CGGATTTTGAGTCATCCACCCA 60.618 50.000 11.03 0.00 39.29 4.51
4392 4887 3.304911 TTTGAGTCATCCACCCAAACA 57.695 42.857 0.00 0.00 0.00 2.83
4402 4897 2.102578 CCACCCAAACATCATCTTCCC 58.897 52.381 0.00 0.00 0.00 3.97
4407 4902 2.017049 CAAACATCATCTTCCCCCGTC 58.983 52.381 0.00 0.00 0.00 4.79
4408 4903 0.546598 AACATCATCTTCCCCCGTCC 59.453 55.000 0.00 0.00 0.00 4.79
4443 4938 5.676532 TGCCTTCAAATTCAATGCTTTTG 57.323 34.783 2.64 2.64 0.00 2.44
4468 4963 1.020437 GGATGTAGCTCTTTGGCTGC 58.980 55.000 0.00 0.00 43.01 5.25
4495 4990 2.094675 CCTTCTCCCCGTTTAGTCGTA 58.905 52.381 0.00 0.00 0.00 3.43
4497 4992 2.198827 TCTCCCCGTTTAGTCGTACA 57.801 50.000 0.00 0.00 0.00 2.90
4500 4995 1.541147 TCCCCGTTTAGTCGTACAGTG 59.459 52.381 0.00 0.00 0.00 3.66
4502 4997 1.343506 CCGTTTAGTCGTACAGTGGC 58.656 55.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.163211 GGAGCCTGCTTTCTTCATTGAC 59.837 50.000 0.00 0.00 0.00 3.18
1 2 2.224843 TGGAGCCTGCTTTCTTCATTGA 60.225 45.455 0.00 0.00 0.00 2.57
2 3 2.094854 GTGGAGCCTGCTTTCTTCATTG 60.095 50.000 0.00 0.00 0.00 2.82
3 4 2.165998 GTGGAGCCTGCTTTCTTCATT 58.834 47.619 0.00 0.00 0.00 2.57
4 5 1.831580 GTGGAGCCTGCTTTCTTCAT 58.168 50.000 0.00 0.00 0.00 2.57
5 6 0.603707 CGTGGAGCCTGCTTTCTTCA 60.604 55.000 0.00 0.00 0.00 3.02
6 7 1.916697 GCGTGGAGCCTGCTTTCTTC 61.917 60.000 0.00 0.00 40.81 2.87
7 8 1.968540 GCGTGGAGCCTGCTTTCTT 60.969 57.895 0.00 0.00 40.81 2.52
8 9 2.359230 GCGTGGAGCCTGCTTTCT 60.359 61.111 0.00 0.00 40.81 2.52
18 19 4.511246 ATGGCATGGGGCGTGGAG 62.511 66.667 0.00 0.00 46.16 3.86
58 59 2.680913 GCACACAGGCAAGGCGTAG 61.681 63.158 0.00 0.00 0.00 3.51
59 60 2.668212 GCACACAGGCAAGGCGTA 60.668 61.111 0.00 0.00 0.00 4.42
60 61 4.569180 AGCACACAGGCAAGGCGT 62.569 61.111 0.00 0.00 35.83 5.68
61 62 4.034258 CAGCACACAGGCAAGGCG 62.034 66.667 0.00 0.00 35.83 5.52
62 63 2.492773 AACAGCACACAGGCAAGGC 61.493 57.895 0.00 0.00 35.83 4.35
63 64 1.361271 CAACAGCACACAGGCAAGG 59.639 57.895 0.00 0.00 35.83 3.61
64 65 1.265095 CTACAACAGCACACAGGCAAG 59.735 52.381 0.00 0.00 35.83 4.01
65 66 1.308047 CTACAACAGCACACAGGCAA 58.692 50.000 0.00 0.00 35.83 4.52
66 67 0.180171 ACTACAACAGCACACAGGCA 59.820 50.000 0.00 0.00 35.83 4.75
67 68 0.588252 CACTACAACAGCACACAGGC 59.412 55.000 0.00 0.00 0.00 4.85
68 69 0.588252 GCACTACAACAGCACACAGG 59.412 55.000 0.00 0.00 0.00 4.00
69 70 0.588252 GGCACTACAACAGCACACAG 59.412 55.000 0.00 0.00 0.00 3.66
70 71 1.157257 CGGCACTACAACAGCACACA 61.157 55.000 0.00 0.00 0.00 3.72
71 72 1.569493 CGGCACTACAACAGCACAC 59.431 57.895 0.00 0.00 0.00 3.82
72 73 2.250939 GCGGCACTACAACAGCACA 61.251 57.895 0.00 0.00 0.00 4.57
73 74 2.556287 GCGGCACTACAACAGCAC 59.444 61.111 0.00 0.00 0.00 4.40
74 75 2.668212 GGCGGCACTACAACAGCA 60.668 61.111 3.07 0.00 0.00 4.41
75 76 3.788766 CGGCGGCACTACAACAGC 61.789 66.667 10.53 0.00 0.00 4.40
76 77 3.118454 CCGGCGGCACTACAACAG 61.118 66.667 15.42 0.00 0.00 3.16
92 93 1.640428 TTGACAACAGATCGATCGCC 58.360 50.000 19.33 4.66 0.00 5.54
94 95 3.426859 GGCTATTGACAACAGATCGATCG 59.573 47.826 19.33 9.36 0.00 3.69
95 96 4.371786 TGGCTATTGACAACAGATCGATC 58.628 43.478 17.91 17.91 0.00 3.69
96 97 4.406648 TGGCTATTGACAACAGATCGAT 57.593 40.909 0.00 0.00 0.00 3.59
97 98 3.885724 TGGCTATTGACAACAGATCGA 57.114 42.857 0.00 0.00 0.00 3.59
98 99 4.033358 GTCTTGGCTATTGACAACAGATCG 59.967 45.833 0.00 0.00 36.05 3.69
99 100 4.333926 GGTCTTGGCTATTGACAACAGATC 59.666 45.833 0.00 0.00 36.05 2.75
101 102 3.072330 TGGTCTTGGCTATTGACAACAGA 59.928 43.478 0.00 0.00 36.05 3.41
105 107 3.820467 CACTTGGTCTTGGCTATTGACAA 59.180 43.478 0.00 0.00 39.20 3.18
108 110 4.019411 TCATCACTTGGTCTTGGCTATTGA 60.019 41.667 0.00 0.00 0.00 2.57
126 128 1.075212 TGTCATTTGTGGGGCTCATCA 59.925 47.619 0.00 0.00 0.00 3.07
129 131 0.251297 CCTGTCATTTGTGGGGCTCA 60.251 55.000 0.00 0.00 0.00 4.26
140 142 1.137872 GCTCCGTCTCATCCTGTCATT 59.862 52.381 0.00 0.00 0.00 2.57
141 143 0.749649 GCTCCGTCTCATCCTGTCAT 59.250 55.000 0.00 0.00 0.00 3.06
142 144 1.657751 CGCTCCGTCTCATCCTGTCA 61.658 60.000 0.00 0.00 0.00 3.58
146 148 2.485795 GCTCGCTCCGTCTCATCCT 61.486 63.158 0.00 0.00 0.00 3.24
147 149 2.026879 GCTCGCTCCGTCTCATCC 59.973 66.667 0.00 0.00 0.00 3.51
153 155 4.162690 ATTGGGGCTCGCTCCGTC 62.163 66.667 2.94 0.00 40.15 4.79
158 160 2.831742 CATGCATTGGGGCTCGCT 60.832 61.111 0.00 0.00 34.04 4.93
171 173 6.203723 AGCTCGTATAAGATTTTCTTCCATGC 59.796 38.462 0.00 0.00 37.89 4.06
176 178 6.757010 TGACCAGCTCGTATAAGATTTTCTTC 59.243 38.462 0.00 0.00 37.89 2.87
194 196 1.605712 GGGATGTAGCGTATGACCAGC 60.606 57.143 0.00 0.00 0.00 4.85
208 210 1.807814 GATGGGGTCTACTGGGATGT 58.192 55.000 0.00 0.00 0.00 3.06
213 215 0.686441 TGGTCGATGGGGTCTACTGG 60.686 60.000 0.00 0.00 0.00 4.00
250 252 7.068103 TGAGTTCTTTGGTTGCTTTGAGATTTA 59.932 33.333 0.00 0.00 0.00 1.40
285 287 0.179048 TGGGTCAACTCACACTGCAG 60.179 55.000 13.48 13.48 0.00 4.41
320 322 1.831736 AGCAGCCACGAGGTAATTACT 59.168 47.619 15.05 1.79 37.19 2.24
344 346 2.420022 CTGAAAAATCCTGGTAGGTGCG 59.580 50.000 0.00 0.00 36.53 5.34
440 442 7.637631 TGCATAAATAATAAGCTGTTGACCA 57.362 32.000 0.00 0.00 0.00 4.02
548 557 2.280552 ACCGGCAGCTTCTCCGTTA 61.281 57.895 0.00 0.00 43.87 3.18
550 559 4.379243 CACCGGCAGCTTCTCCGT 62.379 66.667 0.00 4.00 43.87 4.69
552 561 2.125350 CTCACCGGCAGCTTCTCC 60.125 66.667 0.00 0.00 0.00 3.71
571 580 0.394352 CCTCCTTGGATGGTTTCGGG 60.394 60.000 0.00 0.00 38.35 5.14
601 610 7.201435 GGCGAAATTTAAATCAAATGTCAGTCC 60.201 37.037 0.10 0.00 39.85 3.85
623 632 1.351017 AGTCAGGAAATTTGGAGGCGA 59.649 47.619 0.00 0.00 0.00 5.54
632 641 2.158475 TGTTGGCCAGAGTCAGGAAATT 60.158 45.455 5.11 0.00 0.00 1.82
879 892 4.737352 GCTTCTTGCTGTTTGTTGGATTCA 60.737 41.667 0.00 0.00 38.95 2.57
980 996 4.768968 CCATTCTTATAGCTCCCCATTTGG 59.231 45.833 0.00 0.00 0.00 3.28
1017 1033 1.406205 GGAGCTGGTTGGACTCTAAGC 60.406 57.143 0.00 0.00 0.00 3.09
1019 1035 2.024176 TGGAGCTGGTTGGACTCTAA 57.976 50.000 0.00 0.00 0.00 2.10
1054 1070 1.891919 CGGCGAGAGAGGGAGAGAG 60.892 68.421 0.00 0.00 0.00 3.20
1055 1071 2.190843 CGGCGAGAGAGGGAGAGA 59.809 66.667 0.00 0.00 0.00 3.10
1056 1072 3.591835 GCGGCGAGAGAGGGAGAG 61.592 72.222 12.98 0.00 0.00 3.20
1099 1115 2.015736 AAATCTAGCTCGCACACTGG 57.984 50.000 0.00 0.00 0.00 4.00
1100 1116 4.380087 CGTATAAATCTAGCTCGCACACTG 59.620 45.833 0.00 0.00 0.00 3.66
1288 1489 4.473520 CTCGGGCGCCATCAAGGT 62.474 66.667 30.85 0.00 40.61 3.50
1467 1668 4.704833 CCGGTGAGGCTGGTGTGG 62.705 72.222 0.00 0.00 38.84 4.17
1545 1758 0.393673 GGCCCTTCTTCCTCTGCTTC 60.394 60.000 0.00 0.00 0.00 3.86
1617 1830 0.670546 CCAACAGCGTCTTCATCCGT 60.671 55.000 0.00 0.00 0.00 4.69
1633 1846 3.450904 CCTCCCCGGAGATATTATCCAA 58.549 50.000 12.54 0.00 44.53 3.53
2385 2598 1.242076 GCCATGACTTGTTGTGCTCT 58.758 50.000 0.00 0.00 0.00 4.09
2522 2802 1.374252 GTGACATTGCCGTCGGTCT 60.374 57.895 13.94 0.00 38.84 3.85
2949 3229 2.107546 ACGGCGAAGAACGTGGTT 59.892 55.556 16.62 0.00 40.71 3.67
3564 3850 1.369091 ATTGCTCGCGCCAGTAAAGG 61.369 55.000 9.79 0.00 34.43 3.11
3646 3932 6.533723 CCATCTTAATCACACGCAGTTAAGTA 59.466 38.462 0.00 0.00 41.61 2.24
3654 3940 1.557371 TCCCCATCTTAATCACACGCA 59.443 47.619 0.00 0.00 0.00 5.24
3803 4091 2.544267 CCAAACAAAGTCGACACCTCTC 59.456 50.000 19.50 0.00 0.00 3.20
3837 4132 1.253100 TCGTCATGGAGCACACTACA 58.747 50.000 0.00 0.00 42.41 2.74
3868 4163 1.803334 TGCGTCACACCAATACCTTC 58.197 50.000 0.00 0.00 0.00 3.46
3878 4173 3.304382 GTGTGCTTATATGCGTCACAC 57.696 47.619 21.87 17.99 46.72 3.82
3914 4213 5.305585 TGGTTGCTAAGTCGAATTTCTTCT 58.694 37.500 2.37 0.00 0.00 2.85
3915 4214 5.607119 TGGTTGCTAAGTCGAATTTCTTC 57.393 39.130 2.37 0.00 0.00 2.87
3916 4215 6.385649 TTTGGTTGCTAAGTCGAATTTCTT 57.614 33.333 2.37 0.00 0.00 2.52
4035 4334 1.207089 TGAAGTCATCCGCCGAGAATT 59.793 47.619 0.00 0.00 0.00 2.17
4051 4350 1.068055 GCAGGTGCCAACTTCATGAAG 60.068 52.381 29.74 29.74 38.56 3.02
4085 4384 0.546598 GGGTCACCTCCCCAATAGTG 59.453 60.000 0.00 0.00 42.15 2.74
4086 4385 3.022897 GGGTCACCTCCCCAATAGT 57.977 57.895 0.00 0.00 42.15 2.12
4122 4421 2.228822 GTGAATCAATGTTCTTGGCGGT 59.771 45.455 0.00 0.00 0.00 5.68
4128 4427 3.334881 AGAGGGGGTGAATCAATGTTCTT 59.665 43.478 0.00 0.00 0.00 2.52
4132 4431 1.566231 GGAGAGGGGGTGAATCAATGT 59.434 52.381 0.00 0.00 0.00 2.71
4184 4483 1.471119 CTGCTGCAACCATCCTTCAT 58.529 50.000 3.02 0.00 0.00 2.57
4185 4484 0.609957 CCTGCTGCAACCATCCTTCA 60.610 55.000 3.02 0.00 0.00 3.02
4212 4511 4.860352 GCATATACATACGCGAACATACCA 59.140 41.667 15.93 0.00 0.00 3.25
4244 4543 3.632145 AGAAAACAACCAACGATCAGCTT 59.368 39.130 0.00 0.00 0.00 3.74
4245 4544 3.214328 AGAAAACAACCAACGATCAGCT 58.786 40.909 0.00 0.00 0.00 4.24
4311 4610 2.850851 TAATTGAGCGGGGAGGGGGT 62.851 60.000 0.00 0.00 0.00 4.95
4312 4611 2.076184 TAATTGAGCGGGGAGGGGG 61.076 63.158 0.00 0.00 0.00 5.40
4313 4612 1.148498 GTAATTGAGCGGGGAGGGG 59.852 63.158 0.00 0.00 0.00 4.79
4314 4613 1.227556 CGTAATTGAGCGGGGAGGG 60.228 63.158 0.00 0.00 0.00 4.30
4315 4614 0.810031 CACGTAATTGAGCGGGGAGG 60.810 60.000 0.00 0.00 0.00 4.30
4316 4615 0.174845 TCACGTAATTGAGCGGGGAG 59.825 55.000 0.00 0.00 31.65 4.30
4317 4616 0.828022 ATCACGTAATTGAGCGGGGA 59.172 50.000 0.00 0.00 31.65 4.81
4318 4617 1.597663 GAATCACGTAATTGAGCGGGG 59.402 52.381 0.00 0.00 31.65 5.73
4319 4618 2.540101 GAGAATCACGTAATTGAGCGGG 59.460 50.000 0.00 0.00 33.17 6.13
4320 4619 2.540101 GGAGAATCACGTAATTGAGCGG 59.460 50.000 0.00 0.00 36.25 5.52
4321 4620 3.448686 AGGAGAATCACGTAATTGAGCG 58.551 45.455 0.00 0.00 36.25 5.03
4322 4621 4.688021 AGAGGAGAATCACGTAATTGAGC 58.312 43.478 0.00 0.00 36.25 4.26
4323 4622 6.256757 GGAAAGAGGAGAATCACGTAATTGAG 59.743 42.308 0.00 0.00 36.25 3.02
4324 4623 6.106673 GGAAAGAGGAGAATCACGTAATTGA 58.893 40.000 0.00 0.00 36.25 2.57
4325 4624 5.294552 GGGAAAGAGGAGAATCACGTAATTG 59.705 44.000 0.00 0.00 36.25 2.32
4365 4860 1.401905 GTGGATGACTCAAAATCCGCC 59.598 52.381 4.27 0.00 44.34 6.13
4388 4883 1.064685 GGACGGGGGAAGATGATGTTT 60.065 52.381 0.00 0.00 0.00 2.83
4392 4887 0.471971 ATCGGACGGGGGAAGATGAT 60.472 55.000 0.00 0.00 0.00 2.45
4402 4897 1.800586 CAAAGCATCATATCGGACGGG 59.199 52.381 0.00 0.00 0.00 5.28
4407 4902 2.880268 TGAAGGCAAAGCATCATATCGG 59.120 45.455 0.00 0.00 0.00 4.18
4408 4903 4.556942 TTGAAGGCAAAGCATCATATCG 57.443 40.909 0.00 0.00 0.00 2.92
4443 4938 1.398390 CAAAGAGCTACATCCGGCAAC 59.602 52.381 0.00 0.00 0.00 4.17
4484 4979 1.068055 AGGCCACTGTACGACTAAACG 60.068 52.381 5.01 0.00 39.31 3.60
4502 4997 1.172180 TGGAAGCTTGCCGACAAAGG 61.172 55.000 15.98 0.00 34.74 3.11


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

AutoCloner maintained by Alex Coulton.