Multiple sequence alignment - TraesCS2D01G175900

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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 TraesCS2D01G175900 chr2D 100.000 4653 0 0 1 4653 119302998 119298346 0.000000e+00 8593.0
1 TraesCS2D01G175900 chr2A 93.752 3345 116 38 668 3960 121228115 121224812 0.000000e+00 4933.0
2 TraesCS2D01G175900 chr2A 94.737 570 26 4 4049 4616 121224662 121224095 0.000000e+00 883.0
3 TraesCS2D01G175900 chr2A 97.561 41 1 0 3976 4016 121224815 121224775 2.320000e-08 71.3
4 TraesCS2D01G175900 chr2B 92.445 2568 100 31 2162 4653 171462854 171460305 0.000000e+00 3581.0
5 TraesCS2D01G175900 chr2B 94.051 1412 70 8 675 2080 171464522 171463119 0.000000e+00 2130.0
6 TraesCS2D01G175900 chr5D 84.489 1154 128 29 814 1952 377474953 377476070 0.000000e+00 1092.0
7 TraesCS2D01G175900 chr5D 92.973 185 12 1 3469 3653 377482493 377482676 7.670000e-68 268.0
8 TraesCS2D01G175900 chr5D 93.162 117 8 0 3359 3475 377482144 377482260 6.190000e-39 172.0
9 TraesCS2D01G175900 chr5D 89.412 85 9 0 3182 3266 488863899 488863983 1.770000e-19 108.0
10 TraesCS2D01G175900 chr3D 95.982 672 23 3 1 670 1312799 1312130 0.000000e+00 1088.0
11 TraesCS2D01G175900 chr3D 95.104 674 28 5 1 670 578178794 578179466 0.000000e+00 1057.0
12 TraesCS2D01G175900 chr6B 95.815 669 21 6 1 665 28020238 28019573 0.000000e+00 1074.0
13 TraesCS2D01G175900 chr6B 95.401 674 25 5 1 670 171394881 171394210 0.000000e+00 1068.0
14 TraesCS2D01G175900 chr6B 95.252 674 24 7 1 670 51505183 51504514 0.000000e+00 1061.0
15 TraesCS2D01G175900 chr7D 95.394 673 25 5 1 670 549750113 549750782 0.000000e+00 1066.0
16 TraesCS2D01G175900 chr4D 95.111 675 27 5 1 670 499491887 499492560 0.000000e+00 1059.0
17 TraesCS2D01G175900 chr5A 85.868 1019 115 18 904 1909 478005454 478006456 0.000000e+00 1057.0
18 TraesCS2D01G175900 chr5A 94.054 185 10 1 3469 3653 478013298 478013481 3.550000e-71 279.0
19 TraesCS2D01G175900 chr5A 91.538 130 8 2 3346 3475 478012990 478013116 4.780000e-40 176.0
20 TraesCS2D01G175900 chr5A 84.211 152 19 3 2039 2188 478006506 478006654 4.850000e-30 143.0
21 TraesCS2D01G175900 chr1B 95.097 673 27 5 1 670 492308606 492309275 0.000000e+00 1055.0
22 TraesCS2D01G175900 chr7B 94.955 674 26 7 1 670 589942914 589942245 0.000000e+00 1050.0
23 TraesCS2D01G175900 chr5B 83.170 1123 131 33 843 1952 450758732 450759809 0.000000e+00 974.0
24 TraesCS2D01G175900 chr5B 94.054 185 10 1 3469 3653 450767235 450767418 3.550000e-71 279.0
25 TraesCS2D01G175900 chr5B 93.578 109 7 0 3367 3475 450767048 450767156 3.730000e-36 163.0


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 TraesCS2D01G175900 chr2D 119298346 119302998 4652 True 8593.000000 8593 100.0000 1 4653 1 chr2D.!!$R1 4652
1 TraesCS2D01G175900 chr2A 121224095 121228115 4020 True 1962.433333 4933 95.3500 668 4616 3 chr2A.!!$R1 3948
2 TraesCS2D01G175900 chr2B 171460305 171464522 4217 True 2855.500000 3581 93.2480 675 4653 2 chr2B.!!$R1 3978
3 TraesCS2D01G175900 chr5D 377474953 377476070 1117 False 1092.000000 1092 84.4890 814 1952 1 chr5D.!!$F1 1138
4 TraesCS2D01G175900 chr5D 377482144 377482676 532 False 220.000000 268 93.0675 3359 3653 2 chr5D.!!$F3 294
5 TraesCS2D01G175900 chr3D 1312130 1312799 669 True 1088.000000 1088 95.9820 1 670 1 chr3D.!!$R1 669
6 TraesCS2D01G175900 chr3D 578178794 578179466 672 False 1057.000000 1057 95.1040 1 670 1 chr3D.!!$F1 669
7 TraesCS2D01G175900 chr6B 28019573 28020238 665 True 1074.000000 1074 95.8150 1 665 1 chr6B.!!$R1 664
8 TraesCS2D01G175900 chr6B 171394210 171394881 671 True 1068.000000 1068 95.4010 1 670 1 chr6B.!!$R3 669
9 TraesCS2D01G175900 chr6B 51504514 51505183 669 True 1061.000000 1061 95.2520 1 670 1 chr6B.!!$R2 669
10 TraesCS2D01G175900 chr7D 549750113 549750782 669 False 1066.000000 1066 95.3940 1 670 1 chr7D.!!$F1 669
11 TraesCS2D01G175900 chr4D 499491887 499492560 673 False 1059.000000 1059 95.1110 1 670 1 chr4D.!!$F1 669
12 TraesCS2D01G175900 chr5A 478005454 478006654 1200 False 600.000000 1057 85.0395 904 2188 2 chr5A.!!$F1 1284
13 TraesCS2D01G175900 chr1B 492308606 492309275 669 False 1055.000000 1055 95.0970 1 670 1 chr1B.!!$F1 669
14 TraesCS2D01G175900 chr7B 589942245 589942914 669 True 1050.000000 1050 94.9550 1 670 1 chr7B.!!$R1 669
15 TraesCS2D01G175900 chr5B 450758732 450759809 1077 False 974.000000 974 83.1700 843 1952 1 chr5B.!!$F1 1109

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
521 528 0.313672 GCATGGTCCGCACAAAGAAA 59.686 50.0 0.00 0.00 0.00 2.52 F
1310 1329 1.067295 TGGGATATGACATGCCCTCC 58.933 55.0 21.87 12.19 41.28 4.30 F
3173 3512 0.385390 AACAAACAGCCAGGAAAGCG 59.615 50.0 0.00 0.00 34.64 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2673 0.379669 CATTCGCAGGAGCAACCATC 59.620 55.0 2.96 0.0 42.27 3.51 R
3309 3649 1.452110 TATGATGCTGCACACACACC 58.548 50.0 3.57 0.0 0.00 4.16 R
3974 4600 0.178903 ACCAGAGTGCTAGGGTTGGA 60.179 55.0 0.00 0.0 0.00 3.53 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
144 146 4.364409 GCCAACAACGGCGTCGAC 62.364 66.667 20.03 5.18 43.52 4.20
246 252 0.768221 AGCACCTCCAAGAAGGGACA 60.768 55.000 0.00 0.00 41.04 4.02
342 348 0.543410 TCAGGAAGGTCAGGCGGTAA 60.543 55.000 0.00 0.00 0.00 2.85
411 417 1.522569 GATCCCAACCTCCACCTCG 59.477 63.158 0.00 0.00 0.00 4.63
448 454 0.474184 CACCAAACAGACCCTCACCT 59.526 55.000 0.00 0.00 0.00 4.00
521 528 0.313672 GCATGGTCCGCACAAAGAAA 59.686 50.000 0.00 0.00 0.00 2.52
608 615 4.849329 GGTAGCTGACCGGACGCG 62.849 72.222 9.46 3.53 38.87 6.01
688 695 8.238631 GGCCACGTTCTTTTCTAATATAAAACA 58.761 33.333 0.00 0.00 0.00 2.83
731 739 2.290514 TGGCTCAAAGATCAGGGAACAG 60.291 50.000 0.00 0.00 0.00 3.16
756 764 9.220767 AGAAGCAATAGGTTGTCTACTAAAAAG 57.779 33.333 0.00 0.00 37.65 2.27
1171 1190 6.344232 ACTGTTCCTATACTACCTCTTCCT 57.656 41.667 0.00 0.00 0.00 3.36
1225 1244 5.639506 GGACTTGAAGATTTTCTCGATGTGA 59.360 40.000 0.00 0.00 34.31 3.58
1226 1245 6.314896 GGACTTGAAGATTTTCTCGATGTGAT 59.685 38.462 0.00 0.00 34.31 3.06
1268 1287 4.265073 GGGTTCTTGTAGATGTCAGCAAT 58.735 43.478 0.00 0.00 0.00 3.56
1310 1329 1.067295 TGGGATATGACATGCCCTCC 58.933 55.000 21.87 12.19 41.28 4.30
1372 1391 4.927978 ATCCAGAAGGTCTCATAGTTCG 57.072 45.455 0.00 0.00 35.89 3.95
1373 1392 3.024547 TCCAGAAGGTCTCATAGTTCGG 58.975 50.000 0.00 0.00 35.89 4.30
1547 1569 8.067784 TGATCTTTCAGTCGTGTTTTATTTCAC 58.932 33.333 0.00 0.00 0.00 3.18
1574 1597 8.906693 CCGTCGATTGCTATATATGTTCATATC 58.093 37.037 8.35 0.00 0.00 1.63
1643 1666 1.885887 GTTGCCTCCAGTTGTAATGCA 59.114 47.619 0.00 0.00 0.00 3.96
1689 1712 5.929058 ATGACATCTAGACTTCAAGCTCA 57.071 39.130 8.76 0.00 0.00 4.26
2034 2064 8.712285 TTTACGGGTGAAAGATAGAGTTTATG 57.288 34.615 0.00 0.00 0.00 1.90
2138 2432 8.256356 CCACCAAAATAACCATATGGGAATTA 57.744 34.615 25.55 14.98 41.15 1.40
2282 2576 4.768448 ACAAATGTCTCATGCCTGAAATCA 59.232 37.500 0.00 0.00 0.00 2.57
2323 2617 2.224549 TGGCCTTTGAATGTCGTAAACG 59.775 45.455 3.32 0.00 41.45 3.60
2374 2668 6.012658 TGGTTTGCTGATCTTATTGTTCAC 57.987 37.500 0.00 0.00 0.00 3.18
2379 2673 3.242543 GCTGATCTTATTGTTCACGCAGG 60.243 47.826 0.00 0.00 0.00 4.85
2497 2791 4.933330 TGAGCATGTTTACTCGAGGATAC 58.067 43.478 18.41 14.41 35.61 2.24
2576 2893 3.752222 GGCTCATATTTCTCATCTGCAGG 59.248 47.826 15.13 0.00 0.00 4.85
2716 3044 4.217767 TGCGCCAGTACTCCATAAGTATAG 59.782 45.833 4.18 0.00 42.38 1.31
2737 3065 5.924475 AGTCAACAGTAATTTCAAGGACG 57.076 39.130 0.00 0.00 0.00 4.79
2979 3309 1.375523 CTCCGGTAACCCTGTGTGC 60.376 63.158 0.00 0.00 0.00 4.57
3008 3338 3.266772 TGGAGTGGCTGAAATCCATAACT 59.733 43.478 0.65 0.00 36.92 2.24
3075 3405 2.023223 TCGGTAAACGCTGTTCGGC 61.023 57.895 0.00 0.00 43.86 5.54
3173 3512 0.385390 AACAAACAGCCAGGAAAGCG 59.615 50.000 0.00 0.00 34.64 4.68
3282 3622 3.641454 TACACCGCACCATGCCCA 61.641 61.111 0.00 0.00 41.12 5.36
3287 3627 3.133464 CGCACCATGCCCATCGTT 61.133 61.111 0.00 0.00 41.12 3.85
3307 3647 4.272261 CGTTTTCCATTTTGTTCAAAGGGG 59.728 41.667 13.81 11.71 45.07 4.79
3335 3693 1.818850 GTGCAGCATCATAAAGCACG 58.181 50.000 0.00 0.00 44.84 5.34
3373 3737 2.689471 TCGTGTGTGTGTGTAGGTAGTT 59.311 45.455 0.00 0.00 0.00 2.24
3657 4259 1.227205 GGTCGCTGCTCTGATGAGG 60.227 63.158 0.00 0.00 40.53 3.86
3660 4262 0.758310 TCGCTGCTCTGATGAGGGAT 60.758 55.000 0.00 0.00 40.53 3.85
3665 4267 1.664017 CTCTGATGAGGGATGCGCG 60.664 63.158 0.00 0.00 36.70 6.86
3753 4355 5.509840 GGTCATTCGAGATGCTGGTAGTAAT 60.510 44.000 3.57 0.00 0.00 1.89
3785 4388 8.071177 AGGATCTGTAAAATGGAAAATTGGAG 57.929 34.615 0.00 0.00 0.00 3.86
3787 4390 8.966868 GGATCTGTAAAATGGAAAATTGGAGTA 58.033 33.333 0.00 0.00 0.00 2.59
3960 4586 5.392595 GCGCTTGTATTTATCTGTTCCCAAA 60.393 40.000 0.00 0.00 0.00 3.28
3961 4587 6.616947 CGCTTGTATTTATCTGTTCCCAAAA 58.383 36.000 0.00 0.00 0.00 2.44
3962 4588 7.087639 CGCTTGTATTTATCTGTTCCCAAAAA 58.912 34.615 0.00 0.00 0.00 1.94
3963 4589 7.061789 CGCTTGTATTTATCTGTTCCCAAAAAC 59.938 37.037 0.00 0.00 0.00 2.43
3964 4590 8.088365 GCTTGTATTTATCTGTTCCCAAAAACT 58.912 33.333 0.00 0.00 0.00 2.66
3965 4591 9.981114 CTTGTATTTATCTGTTCCCAAAAACTT 57.019 29.630 0.00 0.00 0.00 2.66
3966 4592 9.974980 TTGTATTTATCTGTTCCCAAAAACTTC 57.025 29.630 0.00 0.00 0.00 3.01
3967 4593 8.581578 TGTATTTATCTGTTCCCAAAAACTTCC 58.418 33.333 0.00 0.00 0.00 3.46
3968 4594 6.413783 TTTATCTGTTCCCAAAAACTTCCC 57.586 37.500 0.00 0.00 0.00 3.97
3969 4595 3.390175 TCTGTTCCCAAAAACTTCCCA 57.610 42.857 0.00 0.00 0.00 4.37
3970 4596 3.028130 TCTGTTCCCAAAAACTTCCCAC 58.972 45.455 0.00 0.00 0.00 4.61
3971 4597 3.031013 CTGTTCCCAAAAACTTCCCACT 58.969 45.455 0.00 0.00 0.00 4.00
3972 4598 2.763448 TGTTCCCAAAAACTTCCCACTG 59.237 45.455 0.00 0.00 0.00 3.66
3973 4599 3.028130 GTTCCCAAAAACTTCCCACTGA 58.972 45.455 0.00 0.00 0.00 3.41
3974 4600 3.611025 TCCCAAAAACTTCCCACTGAT 57.389 42.857 0.00 0.00 0.00 2.90
3975 4601 3.496331 TCCCAAAAACTTCCCACTGATC 58.504 45.455 0.00 0.00 0.00 2.92
3976 4602 2.562738 CCCAAAAACTTCCCACTGATCC 59.437 50.000 0.00 0.00 0.00 3.36
3977 4603 3.230134 CCAAAAACTTCCCACTGATCCA 58.770 45.455 0.00 0.00 0.00 3.41
3978 4604 3.640967 CCAAAAACTTCCCACTGATCCAA 59.359 43.478 0.00 0.00 0.00 3.53
4018 4644 9.388346 GTTGATCTATTCAAGTCATCTACTACG 57.612 37.037 0.00 0.00 44.89 3.51
4032 4735 9.953697 GTCATCTACTACGAAACAATCTCTAAT 57.046 33.333 0.00 0.00 0.00 1.73
4044 4747 3.651803 ATCTCTAATGCTACACCGAGC 57.348 47.619 0.00 0.00 43.16 5.03
4070 4776 7.534085 AGAAATGCGAACACTAAATAATCGA 57.466 32.000 0.00 0.00 35.65 3.59
4089 4795 1.227527 CAGAACGTCCTGCACCACA 60.228 57.895 0.00 0.00 0.00 4.17
4091 4797 2.203153 AACGTCCTGCACCACACC 60.203 61.111 0.00 0.00 0.00 4.16
4099 4805 0.534412 CTGCACCACACCCACAAAAA 59.466 50.000 0.00 0.00 0.00 1.94
4108 4814 3.317993 CACACCCACAAAAAGAGGTTAGG 59.682 47.826 0.00 0.00 0.00 2.69
4109 4815 3.203487 ACACCCACAAAAAGAGGTTAGGA 59.797 43.478 0.00 0.00 0.00 2.94
4115 4822 5.648092 CCACAAAAAGAGGTTAGGATAGGTG 59.352 44.000 0.00 0.00 0.00 4.00
4142 4849 0.457337 GCAACTTGTAGCTGCATGCC 60.457 55.000 16.68 0.00 44.23 4.40
4233 4940 2.235155 ACATAGCCCACACATGTTACGA 59.765 45.455 0.00 0.00 28.56 3.43
4236 4943 3.179443 AGCCCACACATGTTACGATAG 57.821 47.619 0.00 0.00 46.19 2.08
4312 5019 1.134946 GGTTTTGTTGCAGCACAGAGT 59.865 47.619 1.37 0.00 0.00 3.24
4446 5154 6.051717 AGTAAAAGTGAGGCTATAGCACATG 58.948 40.000 25.53 0.00 44.36 3.21
4449 5157 6.425210 AAAGTGAGGCTATAGCACATGATA 57.575 37.500 25.53 2.45 44.36 2.15
4483 5191 2.428530 GAGGTGATGATTGGCTTTTCCC 59.571 50.000 0.00 0.00 0.00 3.97
4486 5194 3.261643 GGTGATGATTGGCTTTTCCCTTT 59.738 43.478 0.00 0.00 0.00 3.11
4487 5195 4.498241 GTGATGATTGGCTTTTCCCTTTC 58.502 43.478 0.00 0.00 0.00 2.62
4637 5345 5.028549 AGAAATGAGTCAAGCGATGGTAT 57.971 39.130 0.00 0.00 0.00 2.73
4648 5356 6.145696 GTCAAGCGATGGTATTACTATGTTCC 59.854 42.308 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
246 252 2.372690 GCAGCGTCGTCATCGTTGT 61.373 57.895 0.00 0.00 40.51 3.32
411 417 4.828925 GCGAGCTCTGGAGTGCCC 62.829 72.222 12.85 0.00 35.33 5.36
521 528 1.534697 CTAGTCCCGGCTCCTCTCT 59.465 63.158 0.00 0.00 0.00 3.10
608 615 2.551071 GGCCTGGTATGTTCCTGCTATC 60.551 54.545 0.00 0.00 0.00 2.08
666 673 9.801714 CACGTGTTTTATATTAGAAAAGAACGT 57.198 29.630 20.48 20.48 43.67 3.99
731 739 8.451748 CCTTTTTAGTAGACAACCTATTGCTTC 58.548 37.037 0.00 0.00 39.66 3.86
756 764 1.543358 CTTTCAGAGCTGCCCTTTTCC 59.457 52.381 0.00 0.00 0.00 3.13
1162 1178 5.843019 TGAAGATTTTACCAGGAAGAGGT 57.157 39.130 0.00 0.00 43.14 3.85
1225 1244 2.257353 GGTCGCAACCTGCAGAAAT 58.743 52.632 17.39 0.00 45.36 2.17
1226 1245 3.744559 GGTCGCAACCTGCAGAAA 58.255 55.556 17.39 0.00 45.36 2.52
1268 1287 7.709182 CCCAATAAGTTTGTCGACATGTCTATA 59.291 37.037 20.80 8.48 0.00 1.31
1310 1329 2.971307 GTTGGTGCAACAATTATGGGG 58.029 47.619 22.12 0.00 43.09 4.96
1435 1457 4.078980 ACCTCCCCTGAAATTAGCATTGAT 60.079 41.667 0.00 0.00 0.00 2.57
1547 1569 5.407502 TGAACATATATAGCAATCGACGGG 58.592 41.667 0.00 0.00 0.00 5.28
1695 1722 7.278646 CAGAGATCACATTATCACGAAAGGAAA 59.721 37.037 0.00 0.00 0.00 3.13
1958 1987 6.405065 GCATATTGTCTTGTCATGTGGTTGAT 60.405 38.462 0.00 0.00 0.00 2.57
1959 1988 5.106197 GCATATTGTCTTGTCATGTGGTTGA 60.106 40.000 0.00 0.00 0.00 3.18
2007 2037 9.729281 ATAAACTCTATCTTTCACCCGTAAAAA 57.271 29.630 0.00 0.00 0.00 1.94
2008 2038 9.158233 CATAAACTCTATCTTTCACCCGTAAAA 57.842 33.333 0.00 0.00 0.00 1.52
2009 2039 7.279313 GCATAAACTCTATCTTTCACCCGTAAA 59.721 37.037 0.00 0.00 0.00 2.01
2010 2040 6.759827 GCATAAACTCTATCTTTCACCCGTAA 59.240 38.462 0.00 0.00 0.00 3.18
2011 2041 6.278363 GCATAAACTCTATCTTTCACCCGTA 58.722 40.000 0.00 0.00 0.00 4.02
2012 2042 5.116882 GCATAAACTCTATCTTTCACCCGT 58.883 41.667 0.00 0.00 0.00 5.28
2013 2043 4.209288 CGCATAAACTCTATCTTTCACCCG 59.791 45.833 0.00 0.00 0.00 5.28
2014 2044 5.116882 ACGCATAAACTCTATCTTTCACCC 58.883 41.667 0.00 0.00 0.00 4.61
2015 2045 6.663944 AACGCATAAACTCTATCTTTCACC 57.336 37.500 0.00 0.00 0.00 4.02
2016 2046 8.630278 TCTAACGCATAAACTCTATCTTTCAC 57.370 34.615 0.00 0.00 0.00 3.18
2017 2047 9.084164 GTTCTAACGCATAAACTCTATCTTTCA 57.916 33.333 0.00 0.00 0.00 2.69
2018 2048 9.303537 AGTTCTAACGCATAAACTCTATCTTTC 57.696 33.333 0.00 0.00 0.00 2.62
2019 2049 9.654663 AAGTTCTAACGCATAAACTCTATCTTT 57.345 29.630 0.00 0.00 30.99 2.52
2025 2055 9.216117 ACATTTAAGTTCTAACGCATAAACTCT 57.784 29.630 0.00 0.00 30.99 3.24
2034 2064 6.927933 ATGCAAACATTTAAGTTCTAACGC 57.072 33.333 0.00 0.00 30.07 4.84
2046 2102 9.927668 AGCTGTTAAAAGTATATGCAAACATTT 57.072 25.926 0.00 0.00 37.74 2.32
2068 2124 7.171167 CAGATTGATCAGGTATACTTTGAGCTG 59.829 40.741 19.41 11.04 41.51 4.24
2323 2617 1.474077 GAATTCTGTGCCATGGTGTCC 59.526 52.381 14.67 0.00 0.00 4.02
2374 2668 2.270205 AGGAGCAACCATCCTGCG 59.730 61.111 2.96 0.00 45.67 5.18
2379 2673 0.379669 CATTCGCAGGAGCAACCATC 59.620 55.000 2.96 0.00 42.27 3.51
2576 2893 2.048127 AAGCTTCGACCCGTCTGC 60.048 61.111 0.00 0.00 0.00 4.26
2716 3044 5.917541 TCGTCCTTGAAATTACTGTTGAC 57.082 39.130 0.00 0.00 0.00 3.18
2826 3154 3.827302 ACTGTCTCCCTATATGTAAGGCG 59.173 47.826 0.00 0.00 32.34 5.52
2979 3309 2.047844 CAGCCACTCCACGTCCTG 60.048 66.667 0.00 0.00 0.00 3.86
3008 3338 2.174685 TCAGTAGAATGGGCAGGCTA 57.825 50.000 0.00 0.00 0.00 3.93
3075 3405 5.082251 TCCTCTGAATGACTGTGAAGATG 57.918 43.478 0.00 0.00 0.00 2.90
3282 3622 5.757808 CCCTTTGAACAAAATGGAAAACGAT 59.242 36.000 8.77 0.00 36.03 3.73
3287 3627 4.429854 CCCCCTTTGAACAAAATGGAAA 57.570 40.909 13.49 0.00 36.03 3.13
3307 3647 2.598394 ATGCTGCACACACACCCC 60.598 61.111 3.57 0.00 0.00 4.95
3309 3649 1.452110 TATGATGCTGCACACACACC 58.548 50.000 3.57 0.00 0.00 4.16
3335 3693 1.869690 GAAGCACCGCCTTCAGAAC 59.130 57.895 0.00 0.00 40.67 3.01
3517 4119 3.665675 GATCACGTGCTTCGCCCCT 62.666 63.158 11.67 0.00 44.19 4.79
3679 4281 4.568359 GTCCTTCACAGTATGCAGTATGTG 59.432 45.833 17.40 17.40 42.53 3.21
3724 4326 3.200483 CAGCATCTCGAATGACCAATGA 58.800 45.455 10.52 0.00 0.00 2.57
3753 4355 9.747898 TTTTCCATTTTACAGATCCTTAGCTAA 57.252 29.630 5.94 5.94 0.00 3.09
3903 4508 9.793259 TCAAACCTTATATGAACTCTCAAAAGT 57.207 29.630 0.00 0.00 34.49 2.66
3917 4523 3.250040 GCGCGTCCATTCAAACCTTATAT 59.750 43.478 8.43 0.00 0.00 0.86
3960 4586 2.490902 GGGTTGGATCAGTGGGAAGTTT 60.491 50.000 0.00 0.00 0.00 2.66
3961 4587 1.075536 GGGTTGGATCAGTGGGAAGTT 59.924 52.381 0.00 0.00 0.00 2.66
3962 4588 0.698818 GGGTTGGATCAGTGGGAAGT 59.301 55.000 0.00 0.00 0.00 3.01
3963 4589 0.995024 AGGGTTGGATCAGTGGGAAG 59.005 55.000 0.00 0.00 0.00 3.46
3964 4590 2.196595 CTAGGGTTGGATCAGTGGGAA 58.803 52.381 0.00 0.00 0.00 3.97
3965 4591 1.879575 CTAGGGTTGGATCAGTGGGA 58.120 55.000 0.00 0.00 0.00 4.37
3966 4592 0.181350 GCTAGGGTTGGATCAGTGGG 59.819 60.000 0.00 0.00 0.00 4.61
3967 4593 0.911769 TGCTAGGGTTGGATCAGTGG 59.088 55.000 0.00 0.00 0.00 4.00
3968 4594 1.556911 AGTGCTAGGGTTGGATCAGTG 59.443 52.381 0.00 0.00 0.00 3.66
3969 4595 1.834263 GAGTGCTAGGGTTGGATCAGT 59.166 52.381 0.00 0.00 0.00 3.41
3970 4596 2.114616 AGAGTGCTAGGGTTGGATCAG 58.885 52.381 0.00 0.00 0.00 2.90
3971 4597 1.833630 CAGAGTGCTAGGGTTGGATCA 59.166 52.381 0.00 0.00 0.00 2.92
3972 4598 1.139853 CCAGAGTGCTAGGGTTGGATC 59.860 57.143 0.00 0.00 0.00 3.36
3973 4599 1.207791 CCAGAGTGCTAGGGTTGGAT 58.792 55.000 0.00 0.00 0.00 3.41
3974 4600 0.178903 ACCAGAGTGCTAGGGTTGGA 60.179 55.000 0.00 0.00 0.00 3.53
3975 4601 0.693049 AACCAGAGTGCTAGGGTTGG 59.307 55.000 0.00 0.00 41.82 3.77
3977 4603 1.729586 TCAACCAGAGTGCTAGGGTT 58.270 50.000 0.00 0.00 44.11 4.11
3978 4604 1.834263 GATCAACCAGAGTGCTAGGGT 59.166 52.381 0.00 0.00 34.43 4.34
4018 4644 5.810587 TCGGTGTAGCATTAGAGATTGTTTC 59.189 40.000 0.00 0.00 0.00 2.78
4032 4735 2.738643 GCATTTCTAGCTCGGTGTAGCA 60.739 50.000 0.00 0.00 45.30 3.49
4044 4747 8.752254 TCGATTATTTAGTGTTCGCATTTCTAG 58.248 33.333 0.00 0.00 0.00 2.43
4070 4776 1.227556 GTGGTGCAGGACGTTCTGT 60.228 57.895 24.56 0.00 37.12 3.41
4089 4795 4.741928 ATCCTAACCTCTTTTTGTGGGT 57.258 40.909 0.00 0.00 33.83 4.51
4091 4797 5.648092 CACCTATCCTAACCTCTTTTTGTGG 59.352 44.000 0.00 0.00 35.56 4.17
4099 4805 5.069251 CGAATGAACACCTATCCTAACCTCT 59.931 44.000 0.00 0.00 0.00 3.69
4108 4814 4.154195 ACAAGTTGCGAATGAACACCTATC 59.846 41.667 1.81 0.00 0.00 2.08
4109 4815 4.072131 ACAAGTTGCGAATGAACACCTAT 58.928 39.130 1.81 0.00 0.00 2.57
4115 4822 3.482786 CAGCTACAAGTTGCGAATGAAC 58.517 45.455 1.81 0.00 36.47 3.18
4142 4849 1.342174 AGTTTGCTTGGACCATTGCTG 59.658 47.619 17.34 0.00 0.00 4.41
4233 4940 5.188434 ACTGCTGTGACAATGTTATGCTAT 58.812 37.500 0.00 0.00 0.00 2.97
4236 4943 3.837213 ACTGCTGTGACAATGTTATGC 57.163 42.857 0.00 0.00 0.00 3.14
4312 5019 5.551233 CTGGTAGACTGTTTGAATGGAAGA 58.449 41.667 0.00 0.00 0.00 2.87
4429 5136 4.629200 GCTTATCATGTGCTATAGCCTCAC 59.371 45.833 21.84 13.72 41.18 3.51
4446 5154 2.941720 CACCTCTCTTTGCTGGCTTATC 59.058 50.000 0.00 0.00 0.00 1.75
4449 5157 0.767375 TCACCTCTCTTTGCTGGCTT 59.233 50.000 0.00 0.00 0.00 4.35
4483 5191 4.639310 CCTGATGGAAGGTGAGATTGAAAG 59.361 45.833 0.00 0.00 34.57 2.62
4486 5194 3.920231 CCTGATGGAAGGTGAGATTGA 57.080 47.619 0.00 0.00 34.57 2.57


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

AutoCloner maintained by Alex Coulton.