Multiple sequence alignment - TraesCS1A01G291200

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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 TraesCS1A01G291200 chr1A 100.000 5037 0 0 1 5037 487467276 487462240 0.000000e+00 9302.0
1 TraesCS1A01G291200 chr1A 94.737 703 26 6 1 692 58020994 58020292 0.000000e+00 1083.0
2 TraesCS1A01G291200 chr1A 93.635 707 34 6 1 696 58027846 58028552 0.000000e+00 1046.0
3 TraesCS1A01G291200 chr1A 86.251 851 91 19 1605 2444 487332943 487332108 0.000000e+00 900.0
4 TraesCS1A01G291200 chr1A 88.219 365 32 8 1086 1440 487333850 487333487 4.660000e-115 425.0
5 TraesCS1A01G291200 chr1A 81.835 545 59 17 2537 3042 487332085 487331542 6.030000e-114 422.0
6 TraesCS1A01G291200 chr1A 95.455 154 7 0 3891 4044 487330777 487330624 3.890000e-61 246.0
7 TraesCS1A01G291200 chr1A 82.313 147 23 3 4081 4226 487330403 487330259 1.900000e-24 124.0
8 TraesCS1A01G291200 chr1A 78.740 127 9 6 993 1110 487333874 487333757 9.050000e-08 69.4
9 TraesCS1A01G291200 chr1B 92.834 2819 152 21 1577 4366 521001547 520998750 0.000000e+00 4041.0
10 TraesCS1A01G291200 chr1B 83.000 1500 164 58 1605 3042 520928546 520927076 0.000000e+00 1273.0
11 TraesCS1A01G291200 chr1B 90.332 693 62 5 1 691 499021518 499022207 0.000000e+00 904.0
12 TraesCS1A01G291200 chr1B 92.261 491 23 6 1076 1557 521002014 521001530 0.000000e+00 682.0
13 TraesCS1A01G291200 chr1B 89.135 451 38 5 694 1144 521002489 521002050 7.370000e-153 551.0
14 TraesCS1A01G291200 chr1B 78.032 742 130 21 3125 3847 520927035 520926308 2.150000e-118 436.0
15 TraesCS1A01G291200 chr1B 82.946 516 51 21 1017 1505 520929104 520928599 1.000000e-116 431.0
16 TraesCS1A01G291200 chr1B 94.156 154 9 0 3891 4044 520926210 520926057 8.430000e-58 235.0
17 TraesCS1A01G291200 chr1D 95.020 2048 78 15 2588 4629 387896387 387894358 0.000000e+00 3195.0
18 TraesCS1A01G291200 chr1D 94.583 1569 62 15 1028 2586 387898027 387896472 0.000000e+00 2405.0
19 TraesCS1A01G291200 chr1D 85.272 1066 109 29 1605 2662 387800153 387799128 0.000000e+00 1055.0
20 TraesCS1A01G291200 chr1D 93.709 461 25 2 697 1156 387898434 387897977 0.000000e+00 688.0
21 TraesCS1A01G291200 chr1D 93.639 393 24 1 4646 5037 387894202 387893810 2.020000e-163 586.0
22 TraesCS1A01G291200 chr1D 82.021 584 44 31 1017 1555 387800737 387800170 1.660000e-119 440.0
23 TraesCS1A01G291200 chr1D 85.753 365 34 11 2695 3042 387798726 387798363 2.220000e-98 370.0
24 TraesCS1A01G291200 chr1D 94.156 154 9 0 3891 4044 387797018 387796865 8.430000e-58 235.0
25 TraesCS1A01G291200 chr1D 82.979 141 20 4 4087 4226 387796643 387796506 1.900000e-24 124.0
26 TraesCS1A01G291200 chr5B 98.266 692 12 0 1 692 491654923 491655614 0.000000e+00 1212.0
27 TraesCS1A01G291200 chr7B 94.556 698 35 3 1 696 297142567 297143263 0.000000e+00 1075.0
28 TraesCS1A01G291200 chr7B 94.444 702 28 6 1 691 581348374 581349075 0.000000e+00 1070.0
29 TraesCS1A01G291200 chr3B 93.883 703 32 6 1 692 607814505 607813803 0.000000e+00 1050.0
30 TraesCS1A01G291200 chr7A 93.741 703 33 6 1 692 706440331 706439629 0.000000e+00 1044.0
31 TraesCS1A01G291200 chr7A 94.531 640 24 6 1 629 694027416 694026777 0.000000e+00 977.0
32 TraesCS1A01G291200 chrUn 91.810 696 44 5 1 694 94949029 94949713 0.000000e+00 957.0
33 TraesCS1A01G291200 chr3A 100.000 28 0 0 4547 4574 194678998 194679025 9.000000e-03 52.8


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 TraesCS1A01G291200 chr1A 487462240 487467276 5036 True 9302.00 9302 100.000000 1 5037 1 chr1A.!!$R2 5036
1 TraesCS1A01G291200 chr1A 58020292 58020994 702 True 1083.00 1083 94.737000 1 692 1 chr1A.!!$R1 691
2 TraesCS1A01G291200 chr1A 58027846 58028552 706 False 1046.00 1046 93.635000 1 696 1 chr1A.!!$F1 695
3 TraesCS1A01G291200 chr1A 487330259 487333874 3615 True 364.40 900 85.468833 993 4226 6 chr1A.!!$R3 3233
4 TraesCS1A01G291200 chr1B 520998750 521002489 3739 True 1758.00 4041 91.410000 694 4366 3 chr1B.!!$R2 3672
5 TraesCS1A01G291200 chr1B 499021518 499022207 689 False 904.00 904 90.332000 1 691 1 chr1B.!!$F1 690
6 TraesCS1A01G291200 chr1B 520926057 520929104 3047 True 593.75 1273 84.533500 1017 4044 4 chr1B.!!$R1 3027
7 TraesCS1A01G291200 chr1D 387893810 387898434 4624 True 1718.50 3195 94.237750 697 5037 4 chr1D.!!$R2 4340
8 TraesCS1A01G291200 chr1D 387796506 387800737 4231 True 444.80 1055 86.036200 1017 4226 5 chr1D.!!$R1 3209
9 TraesCS1A01G291200 chr5B 491654923 491655614 691 False 1212.00 1212 98.266000 1 692 1 chr5B.!!$F1 691
10 TraesCS1A01G291200 chr7B 297142567 297143263 696 False 1075.00 1075 94.556000 1 696 1 chr7B.!!$F1 695
11 TraesCS1A01G291200 chr7B 581348374 581349075 701 False 1070.00 1070 94.444000 1 691 1 chr7B.!!$F2 690
12 TraesCS1A01G291200 chr3B 607813803 607814505 702 True 1050.00 1050 93.883000 1 692 1 chr3B.!!$R1 691
13 TraesCS1A01G291200 chr7A 706439629 706440331 702 True 1044.00 1044 93.741000 1 692 1 chr7A.!!$R2 691
14 TraesCS1A01G291200 chr7A 694026777 694027416 639 True 977.00 977 94.531000 1 629 1 chr7A.!!$R1 628
15 TraesCS1A01G291200 chrUn 94949029 94949713 684 False 957.00 957 91.810000 1 694 1 chrUn.!!$F1 693

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
633 656 0.037590 ACCAAACGCATGCCTAAGGA 59.962 50.0 13.15 0.0 0.00 3.36 F
984 1014 0.106419 GTCCTCCTCCGACTCCTCAT 60.106 60.0 0.00 0.0 0.00 2.90 F
2220 2880 0.603975 GGATAGTTCCTGGATGGCGC 60.604 60.0 0.00 0.0 39.14 6.53 F
2489 3178 0.539986 ATGTTGTAGGTAGCCCACGG 59.460 55.0 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2661 0.179179 GAAGAATTCAGCAGGCGCAC 60.179 55.000 10.83 0.0 46.62 5.34 R
2489 3178 1.139520 GCCGGTCATTTGACATGCC 59.860 57.895 12.43 0.0 46.47 4.40 R
3115 4292 2.093890 TGGATGCATTGCAGTTCGAAT 58.906 42.857 17.52 0.0 43.65 3.34 R
4474 6446 0.036952 AGATCCGTGTGACTGCCTTG 60.037 55.000 0.00 0.0 0.00 3.61 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
217 218 4.792068 TCCCACAAATCACAGAAGAAAGT 58.208 39.130 0.00 0.00 0.00 2.66
481 504 4.003648 CAGGAAAGCGGTGACTTTTATCT 58.996 43.478 0.00 0.00 39.93 1.98
633 656 0.037590 ACCAAACGCATGCCTAAGGA 59.962 50.000 13.15 0.00 0.00 3.36
735 758 2.409012 GGTGCATAAAACCAAAACGGG 58.591 47.619 0.00 0.00 40.22 5.28
873 903 4.465512 CCCAGTTCATGTGCGCGC 62.466 66.667 27.26 27.26 0.00 6.86
983 1013 1.208844 AGTCCTCCTCCGACTCCTCA 61.209 60.000 0.00 0.00 35.68 3.86
984 1014 0.106419 GTCCTCCTCCGACTCCTCAT 60.106 60.000 0.00 0.00 0.00 2.90
985 1015 1.143277 GTCCTCCTCCGACTCCTCATA 59.857 57.143 0.00 0.00 0.00 2.15
990 1020 1.231221 CTCCGACTCCTCATACTCCG 58.769 60.000 0.00 0.00 0.00 4.63
991 1021 0.835276 TCCGACTCCTCATACTCCGA 59.165 55.000 0.00 0.00 0.00 4.55
1010 1040 2.361104 TTTCCTCATGGCCACCGC 60.361 61.111 8.16 0.00 0.00 5.68
1444 1660 0.931702 CGCACGAAGGTAACACAACA 59.068 50.000 0.00 0.00 41.41 3.33
1558 2199 6.672147 CGTTCAGAAATTTGACCTTCTTCAT 58.328 36.000 0.00 0.00 29.29 2.57
1559 2200 6.798959 CGTTCAGAAATTTGACCTTCTTCATC 59.201 38.462 0.00 0.00 29.29 2.92
1560 2201 7.520453 CGTTCAGAAATTTGACCTTCTTCATCA 60.520 37.037 0.00 0.00 29.29 3.07
1591 2232 6.656632 AAGGAAGAAGAAATTTGACCTTCC 57.343 37.500 22.24 22.24 45.99 3.46
1593 2234 6.018589 GGAAGAAGAAATTTGACCTTCCTG 57.981 41.667 22.35 0.00 43.67 3.86
1594 2235 5.536538 GGAAGAAGAAATTTGACCTTCCTGT 59.463 40.000 22.35 9.06 43.67 4.00
1961 2602 3.135530 AGCATTTGGCCAAGGTTTTACAA 59.864 39.130 19.48 0.00 46.50 2.41
1963 2604 4.518590 GCATTTGGCCAAGGTTTTACAATT 59.481 37.500 19.48 0.00 36.11 2.32
1964 2605 5.009510 GCATTTGGCCAAGGTTTTACAATTT 59.990 36.000 19.48 0.00 36.11 1.82
2039 2699 2.337583 TCTTGCTAATCGTGTGCTGAC 58.662 47.619 0.00 0.00 0.00 3.51
2220 2880 0.603975 GGATAGTTCCTGGATGGCGC 60.604 60.000 0.00 0.00 39.14 6.53
2489 3178 0.539986 ATGTTGTAGGTAGCCCACGG 59.460 55.000 0.00 0.00 0.00 4.94
2515 3204 3.071479 GTCAAATGACCGGCTTGAAGTA 58.929 45.455 0.00 0.00 39.07 2.24
2522 3211 5.002464 TGACCGGCTTGAAGTAAGTATAC 57.998 43.478 0.00 0.00 38.70 1.47
2973 4148 9.135189 AGGAATCATCAGAGATATGCTATAGAC 57.865 37.037 3.21 0.00 0.00 2.59
3052 4227 9.783256 GTTTGTAATGGTAAGCCTGTTTTATAG 57.217 33.333 0.00 0.00 35.27 1.31
3053 4228 9.742144 TTTGTAATGGTAAGCCTGTTTTATAGA 57.258 29.630 0.00 0.00 35.27 1.98
3054 4229 8.958119 TGTAATGGTAAGCCTGTTTTATAGAG 57.042 34.615 0.00 0.00 35.27 2.43
3055 4230 8.545472 TGTAATGGTAAGCCTGTTTTATAGAGT 58.455 33.333 0.00 0.00 35.27 3.24
3142 4319 5.220265 CGAACTGCAATGCATCCAAAATAAC 60.220 40.000 8.91 0.00 38.13 1.89
3275 4460 9.866936 CATTTGTCCATTTTTATTGTTTCTGTG 57.133 29.630 0.00 0.00 0.00 3.66
3768 5480 4.779993 ACTTCTCCTTGTTTCTTGACCT 57.220 40.909 0.00 0.00 0.00 3.85
3894 5671 8.478775 ACAGAACTTATGTATGTATGCCTCTA 57.521 34.615 0.00 0.00 0.00 2.43
4226 6189 6.954944 TGGTGTCGAAGATCTTTAAAGTTTG 58.045 36.000 14.74 6.54 40.67 2.93
4256 6228 4.687948 GGGAACTTTAAGTACACGTTCTCC 59.312 45.833 0.00 0.00 35.53 3.71
4288 6260 4.274459 AGAAAATGCATATCGCCTGACTTC 59.726 41.667 0.00 0.00 41.33 3.01
4298 6270 7.331934 GCATATCGCCTGACTTCATAGATAAAA 59.668 37.037 0.00 0.00 32.94 1.52
4377 6349 1.466167 GTCTTAGTACAGCCGACACGA 59.534 52.381 0.00 0.00 0.00 4.35
4410 6382 5.167845 CGCAGGCCTAACAAAATAAAACAT 58.832 37.500 3.98 0.00 0.00 2.71
4425 6397 4.974368 AAAACATGAGACGAAACACCAA 57.026 36.364 0.00 0.00 0.00 3.67
4440 6412 3.016736 ACACCAAAAGTCACACTCCAAG 58.983 45.455 0.00 0.00 0.00 3.61
4442 6414 1.956477 CCAAAAGTCACACTCCAAGGG 59.044 52.381 0.00 0.00 0.00 3.95
4450 6422 3.655211 ACTCCAAGGGGCTGGCTG 61.655 66.667 0.00 0.00 36.32 4.85
4466 6438 4.108299 TGGAACGGGCGGCATGAT 62.108 61.111 12.47 0.00 0.00 2.45
4474 6446 2.189499 GGCGGCATGATGGAGGTTC 61.189 63.158 3.07 0.00 0.00 3.62
4552 6524 0.744414 TAGACAGCGGCTTCCATTGC 60.744 55.000 0.00 0.00 0.00 3.56
4576 6548 3.683365 AAAAGGGCAGCCATTTTGTAG 57.317 42.857 31.10 0.00 44.21 2.74
4577 6549 2.309136 AAGGGCAGCCATTTTGTAGT 57.691 45.000 15.19 0.00 0.00 2.73
4579 6551 1.203050 AGGGCAGCCATTTTGTAGTGT 60.203 47.619 15.19 0.00 0.00 3.55
4581 6553 1.135689 GGCAGCCATTTTGTAGTGTCG 60.136 52.381 6.55 0.00 0.00 4.35
4582 6554 1.135689 GCAGCCATTTTGTAGTGTCGG 60.136 52.381 0.00 0.00 0.00 4.79
4583 6555 1.135689 CAGCCATTTTGTAGTGTCGGC 60.136 52.381 0.00 0.00 38.36 5.54
4585 6557 1.135689 GCCATTTTGTAGTGTCGGCTG 60.136 52.381 0.00 0.00 35.17 4.85
4586 6558 2.151202 CCATTTTGTAGTGTCGGCTGT 58.849 47.619 0.00 0.00 0.00 4.40
4587 6559 3.331150 CCATTTTGTAGTGTCGGCTGTA 58.669 45.455 0.00 0.00 0.00 2.74
4589 6561 3.738830 TTTTGTAGTGTCGGCTGTACT 57.261 42.857 9.52 9.52 0.00 2.73
4590 6562 4.852134 TTTTGTAGTGTCGGCTGTACTA 57.148 40.909 7.90 7.90 0.00 1.82
4591 6563 4.852134 TTTGTAGTGTCGGCTGTACTAA 57.148 40.909 12.00 0.52 0.00 2.24
4592 6564 4.430137 TTGTAGTGTCGGCTGTACTAAG 57.570 45.455 12.00 0.00 0.00 2.18
4593 6565 3.678289 TGTAGTGTCGGCTGTACTAAGA 58.322 45.455 12.00 2.90 0.00 2.10
4594 6566 3.438087 TGTAGTGTCGGCTGTACTAAGAC 59.562 47.826 12.00 0.00 0.00 3.01
4622 6594 8.739972 GGACAGTTAGGAAATACATGTTCAATT 58.260 33.333 2.30 0.00 0.00 2.32
4623 6595 9.559958 GACAGTTAGGAAATACATGTTCAATTG 57.440 33.333 2.30 0.00 0.00 2.32
4624 6596 9.077885 ACAGTTAGGAAATACATGTTCAATTGT 57.922 29.630 2.30 0.00 0.00 2.71
4625 6597 9.559958 CAGTTAGGAAATACATGTTCAATTGTC 57.440 33.333 2.30 1.16 0.00 3.18
4627 6599 9.906660 GTTAGGAAATACATGTTCAATTGTCAA 57.093 29.630 2.30 0.00 0.00 3.18
4631 6603 8.711457 GGAAATACATGTTCAATTGTCAAAAGG 58.289 33.333 2.30 0.00 0.00 3.11
4632 6604 8.606040 AAATACATGTTCAATTGTCAAAAGGG 57.394 30.769 2.30 0.12 0.00 3.95
4634 6606 4.141756 ACATGTTCAATTGTCAAAAGGGCA 60.142 37.500 5.13 0.00 0.00 5.36
4635 6607 4.057406 TGTTCAATTGTCAAAAGGGCAG 57.943 40.909 5.13 0.00 0.00 4.85
4636 6608 2.802247 GTTCAATTGTCAAAAGGGCAGC 59.198 45.455 5.13 0.00 0.00 5.25
4637 6609 1.344114 TCAATTGTCAAAAGGGCAGCC 59.656 47.619 1.26 1.26 0.00 4.85
4638 6610 1.070445 CAATTGTCAAAAGGGCAGCCA 59.930 47.619 15.19 0.00 0.00 4.75
4639 6611 1.648116 ATTGTCAAAAGGGCAGCCAT 58.352 45.000 15.19 1.92 0.00 4.40
4640 6612 1.422531 TTGTCAAAAGGGCAGCCATT 58.577 45.000 15.19 10.36 0.00 3.16
4642 6614 1.767681 TGTCAAAAGGGCAGCCATTTT 59.232 42.857 27.45 27.45 46.33 1.82
4658 6767 3.196254 CCATTTTGTAGCTCCAGCCAAAT 59.804 43.478 0.00 0.00 43.38 2.32
4779 6889 5.922544 GTCACTAGCTGGAAGTTTACGTTTA 59.077 40.000 3.17 0.00 35.30 2.01
4801 6911 2.238521 TCGCTTGCCAAAGGAAAATCT 58.761 42.857 0.00 0.00 33.68 2.40
4839 6949 1.047801 AGGAACGCCAAATTGCCTTT 58.952 45.000 0.00 0.00 36.29 3.11
4856 6966 2.224784 CCTTTAAAAGGTTGTCCCGACG 59.775 50.000 0.00 0.00 43.95 5.12
4891 7001 3.757493 ACGGGAGTAGAGTGACTTAACTG 59.243 47.826 5.64 0.00 44.60 3.16
4897 7007 8.312564 GGGAGTAGAGTGACTTAACTGTAAAAT 58.687 37.037 5.64 0.00 28.69 1.82
4918 7028 4.748798 CAGAGGGGGAGTGGGGCT 62.749 72.222 0.00 0.00 0.00 5.19
4919 7029 2.958739 AGAGGGGGAGTGGGGCTA 60.959 66.667 0.00 0.00 0.00 3.93
4974 7084 0.471617 AGCAAGCAGTGAGTTCCTGT 59.528 50.000 0.00 0.00 32.41 4.00
4976 7086 1.143305 CAAGCAGTGAGTTCCTGTCG 58.857 55.000 0.00 0.00 32.41 4.35
4991 7101 2.480416 CCTGTCGACTATCCAACTCTGC 60.480 54.545 17.92 0.00 0.00 4.26
4997 7107 3.736433 CGACTATCCAACTCTGCAGAAGG 60.736 52.174 18.85 18.76 0.00 3.46
5025 7135 2.420129 CCGTCTAAAACCCAGATCCCAG 60.420 54.545 0.00 0.00 0.00 4.45
5029 7139 5.183969 GTCTAAAACCCAGATCCCAGTTAC 58.816 45.833 0.00 0.00 0.00 2.50
5032 7142 1.946984 ACCCAGATCCCAGTTACGAA 58.053 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 1.531149 GTTGCATGCTTGTACGAGTGT 59.469 47.619 20.33 0.00 0.00 3.55
481 504 4.976996 GCAAAAATCCCCGCGAAA 57.023 50.000 8.23 0.00 0.00 3.46
633 656 3.965539 GATGAGGCGTGCCACAGCT 62.966 63.158 17.42 1.98 39.40 4.24
742 765 3.697166 ACCATTATCCCCGGCATATTTC 58.303 45.455 0.00 0.00 0.00 2.17
858 888 4.799473 CGGCGCGCACATGAACTG 62.799 66.667 34.42 1.37 0.00 3.16
1038 1068 2.252260 CCGTTGCTCTTGCCGTTG 59.748 61.111 0.00 0.00 38.71 4.10
1113 1224 1.954146 GTTGCTCTCGCCGTTCACA 60.954 57.895 0.00 0.00 34.43 3.58
1115 1226 2.733218 CGTTGCTCTCGCCGTTCA 60.733 61.111 0.00 0.00 34.43 3.18
1386 1602 0.673644 CGGGGTAGCAGTTGAACTGG 60.674 60.000 25.00 8.65 46.01 4.00
1444 1660 2.538037 GCACGCGAAAAGGAAATTGTTT 59.462 40.909 15.93 0.00 0.00 2.83
1574 2215 6.004574 AGGTACAGGAAGGTCAAATTTCTTC 58.995 40.000 8.80 8.80 36.95 2.87
1591 2232 4.553938 CGGCACTGTTTTTACAAGGTACAG 60.554 45.833 0.00 0.00 41.42 2.74
1593 2234 3.313249 ACGGCACTGTTTTTACAAGGTAC 59.687 43.478 0.00 0.00 0.00 3.34
1594 2235 3.312973 CACGGCACTGTTTTTACAAGGTA 59.687 43.478 0.00 0.00 0.00 3.08
1961 2602 4.159135 CAGAGCAAGGCAAAGGATGTAAAT 59.841 41.667 0.00 0.00 0.00 1.40
1963 2604 3.084039 CAGAGCAAGGCAAAGGATGTAA 58.916 45.455 0.00 0.00 0.00 2.41
1964 2605 2.040278 ACAGAGCAAGGCAAAGGATGTA 59.960 45.455 0.00 0.00 0.00 2.29
2001 2661 0.179179 GAAGAATTCAGCAGGCGCAC 60.179 55.000 10.83 0.00 46.62 5.34
2039 2699 2.734606 TCTGCGACCTAATTGAACAACG 59.265 45.455 0.00 0.00 0.00 4.10
2173 2833 2.035632 GGACAGAGACCCTATGGACAG 58.964 57.143 0.00 0.00 34.81 3.51
2208 2868 4.113815 CCAAGGCGCCATCCAGGA 62.114 66.667 31.54 0.00 41.22 3.86
2220 2880 1.153168 CACCGCTACCCATCCAAGG 60.153 63.158 0.00 0.00 0.00 3.61
2306 2969 8.154856 GCATAACAGAGTACTAATTAATCCCCA 58.845 37.037 0.00 0.00 0.00 4.96
2489 3178 1.139520 GCCGGTCATTTGACATGCC 59.860 57.895 12.43 0.00 46.47 4.40
2522 3211 9.746711 CGACTTTCAAACTCAGTAAAATCTATG 57.253 33.333 0.00 0.00 0.00 2.23
2634 3415 7.760340 AGTTCTATTCAATAGTCGGTTCAGTTC 59.240 37.037 4.28 0.00 34.47 3.01
2676 3818 5.639506 ACTTGACCGAGAAGAATACAATGTG 59.360 40.000 0.00 0.00 0.00 3.21
2778 3953 2.082231 TGAAGATGCAAGAGAAGCTGC 58.918 47.619 0.00 0.00 0.00 5.25
3056 4231 8.612145 ACACTCCCTAAGGAAACATTTTACTAT 58.388 33.333 0.00 0.00 43.40 2.12
3115 4292 2.093890 TGGATGCATTGCAGTTCGAAT 58.906 42.857 17.52 0.00 43.65 3.34
3123 4300 8.039538 TCAATTAGTTATTTTGGATGCATTGCA 58.960 29.630 14.72 14.72 44.86 4.08
3208 4385 5.711036 TCCTAGAAGAACTTTAGCTCTCGTT 59.289 40.000 0.00 0.00 0.00 3.85
3350 4542 7.940137 ACCTGTTTACATGGAAGTTAATACACA 59.060 33.333 0.00 0.00 0.00 3.72
3894 5671 2.242043 CCAGAACACTCCCTGCATTTT 58.758 47.619 0.00 0.00 0.00 1.82
4045 5838 7.939782 TGAAAATGATTTACAGCTTCAGTCAA 58.060 30.769 0.00 0.00 32.76 3.18
4232 6195 5.280654 AGAACGTGTACTTAAAGTTCCCA 57.719 39.130 0.00 0.00 41.28 4.37
4234 6197 5.536260 AGGAGAACGTGTACTTAAAGTTCC 58.464 41.667 0.00 1.47 41.28 3.62
4235 6198 7.474398 AAAGGAGAACGTGTACTTAAAGTTC 57.526 36.000 0.00 0.00 40.84 3.01
4236 6199 7.854557 AAAAGGAGAACGTGTACTTAAAGTT 57.145 32.000 0.00 0.00 0.00 2.66
4276 6248 5.992217 GGTTTTATCTATGAAGTCAGGCGAT 59.008 40.000 0.00 0.00 0.00 4.58
4288 6260 5.913137 TGGCTTGTTGGGTTTTATCTATG 57.087 39.130 0.00 0.00 0.00 2.23
4298 6270 4.019174 CTCTATGATTTGGCTTGTTGGGT 58.981 43.478 0.00 0.00 0.00 4.51
4399 6371 7.484975 TGGTGTTTCGTCTCATGTTTTATTTT 58.515 30.769 0.00 0.00 0.00 1.82
4410 6382 3.372822 GTGACTTTTGGTGTTTCGTCTCA 59.627 43.478 0.00 0.00 0.00 3.27
4425 6397 0.178990 GCCCCTTGGAGTGTGACTTT 60.179 55.000 0.00 0.00 0.00 2.66
4450 6422 3.585990 CATCATGCCGCCCGTTCC 61.586 66.667 0.00 0.00 0.00 3.62
4463 6435 1.003580 GACTGCCTTGAACCTCCATCA 59.996 52.381 0.00 0.00 0.00 3.07
4466 6438 0.108585 GTGACTGCCTTGAACCTCCA 59.891 55.000 0.00 0.00 0.00 3.86
4474 6446 0.036952 AGATCCGTGTGACTGCCTTG 60.037 55.000 0.00 0.00 0.00 3.61
4507 6479 1.620819 ACGGACTTCAAGATGCTCACT 59.379 47.619 0.00 0.00 0.00 3.41
4515 6487 1.819288 CTAGGCTGACGGACTTCAAGA 59.181 52.381 0.00 0.00 33.70 3.02
4516 6488 1.819288 TCTAGGCTGACGGACTTCAAG 59.181 52.381 0.00 0.00 33.70 3.02
4552 6524 3.244181 ACAAAATGGCTGCCCTTTTACAG 60.244 43.478 26.87 19.46 37.46 2.74
4576 6548 1.467035 CCGTCTTAGTACAGCCGACAC 60.467 57.143 0.00 0.00 0.00 3.67
4577 6549 0.806868 CCGTCTTAGTACAGCCGACA 59.193 55.000 0.00 0.00 0.00 4.35
4579 6551 0.035152 TCCCGTCTTAGTACAGCCGA 60.035 55.000 0.00 0.00 0.00 5.54
4581 6553 1.134560 CTGTCCCGTCTTAGTACAGCC 59.865 57.143 0.00 0.00 32.02 4.85
4582 6554 1.817447 ACTGTCCCGTCTTAGTACAGC 59.183 52.381 0.00 0.00 40.94 4.40
4583 6555 4.096081 CCTAACTGTCCCGTCTTAGTACAG 59.904 50.000 0.00 0.00 42.53 2.74
4585 6557 4.265073 TCCTAACTGTCCCGTCTTAGTAC 58.735 47.826 0.00 0.00 0.00 2.73
4586 6558 4.574674 TCCTAACTGTCCCGTCTTAGTA 57.425 45.455 0.00 0.00 0.00 1.82
4587 6559 3.446442 TCCTAACTGTCCCGTCTTAGT 57.554 47.619 0.00 0.00 0.00 2.24
4589 6561 5.716228 TGTATTTCCTAACTGTCCCGTCTTA 59.284 40.000 0.00 0.00 0.00 2.10
4590 6562 4.529377 TGTATTTCCTAACTGTCCCGTCTT 59.471 41.667 0.00 0.00 0.00 3.01
4591 6563 4.091549 TGTATTTCCTAACTGTCCCGTCT 58.908 43.478 0.00 0.00 0.00 4.18
4592 6564 4.460948 TGTATTTCCTAACTGTCCCGTC 57.539 45.455 0.00 0.00 0.00 4.79
4593 6565 4.224370 ACATGTATTTCCTAACTGTCCCGT 59.776 41.667 0.00 0.00 0.00 5.28
4594 6566 4.766375 ACATGTATTTCCTAACTGTCCCG 58.234 43.478 0.00 0.00 0.00 5.14
4595 6567 6.177610 TGAACATGTATTTCCTAACTGTCCC 58.822 40.000 0.00 0.00 0.00 4.46
4622 6594 1.422531 AAATGGCTGCCCTTTTGACA 58.577 45.000 17.53 0.00 37.17 3.58
4623 6595 2.145536 CAAAATGGCTGCCCTTTTGAC 58.854 47.619 37.50 8.48 39.23 3.18
4624 6596 1.767681 ACAAAATGGCTGCCCTTTTGA 59.232 42.857 42.27 19.61 39.23 2.69
4625 6597 2.259266 ACAAAATGGCTGCCCTTTTG 57.741 45.000 37.99 37.99 40.77 2.44
4627 6599 1.276138 GCTACAAAATGGCTGCCCTTT 59.724 47.619 17.53 16.14 0.00 3.11
4628 6600 0.897621 GCTACAAAATGGCTGCCCTT 59.102 50.000 17.53 10.13 0.00 3.95
4629 6601 0.040204 AGCTACAAAATGGCTGCCCT 59.960 50.000 17.53 2.69 44.86 5.19
4631 6603 0.457443 GGAGCTACAAAATGGCTGCC 59.543 55.000 12.87 12.87 46.91 4.85
4635 6607 0.457443 GGCTGGAGCTACAAAATGGC 59.543 55.000 0.00 0.00 41.70 4.40
4636 6608 1.838112 TGGCTGGAGCTACAAAATGG 58.162 50.000 0.00 0.00 41.70 3.16
4637 6609 3.940209 TTTGGCTGGAGCTACAAAATG 57.060 42.857 0.00 0.00 41.70 2.32
4638 6610 5.240121 CAAATTTGGCTGGAGCTACAAAAT 58.760 37.500 10.49 0.08 41.70 1.82
4639 6611 4.502950 CCAAATTTGGCTGGAGCTACAAAA 60.503 41.667 23.81 0.00 42.21 2.44
4640 6612 3.006752 CCAAATTTGGCTGGAGCTACAAA 59.993 43.478 23.81 1.41 42.21 2.83
4642 6614 2.170166 CCAAATTTGGCTGGAGCTACA 58.830 47.619 23.81 0.00 42.21 2.74
4643 6615 2.947448 CCAAATTTGGCTGGAGCTAC 57.053 50.000 23.81 0.00 42.21 3.58
4658 6767 6.832520 TTCTATTTACTGCATCTTGCCAAA 57.167 33.333 0.00 0.00 44.23 3.28
4674 6783 8.041323 ACCGAAGACACTGAACATATTCTATTT 58.959 33.333 0.00 0.00 35.69 1.40
4779 6889 3.259123 AGATTTTCCTTTGGCAAGCGATT 59.741 39.130 0.00 0.00 0.00 3.34
4801 6911 6.187682 GTTCCTGGATCCCTCTGAAAATTAA 58.812 40.000 9.90 0.00 0.00 1.40
4839 6949 0.603439 GGCGTCGGGACAACCTTTTA 60.603 55.000 0.00 0.00 36.97 1.52
4856 6966 3.365265 CCCGTCTTTGTGCTGGGC 61.365 66.667 0.00 0.00 32.09 5.36
4866 6976 2.883122 AGTCACTCTACTCCCGTCTT 57.117 50.000 0.00 0.00 0.00 3.01
4891 7001 4.455606 CACTCCCCCTCTGATCATTTTAC 58.544 47.826 0.00 0.00 0.00 2.01
4897 7007 1.003442 CCCACTCCCCCTCTGATCA 59.997 63.158 0.00 0.00 0.00 2.92
4900 7010 4.741239 GCCCCACTCCCCCTCTGA 62.741 72.222 0.00 0.00 0.00 3.27
4974 7084 2.723273 TCTGCAGAGTTGGATAGTCGA 58.277 47.619 13.74 0.00 0.00 4.20
4976 7086 3.791245 CCTTCTGCAGAGTTGGATAGTC 58.209 50.000 17.43 0.00 0.00 2.59
4991 7101 0.970937 TAGACGGGTCCTGCCTTCTG 60.971 60.000 0.00 0.00 37.43 3.02
4997 7107 0.675837 GGGTTTTAGACGGGTCCTGC 60.676 60.000 0.00 0.00 0.00 4.85
5001 7111 2.419713 GGATCTGGGTTTTAGACGGGTC 60.420 54.545 0.00 0.00 0.00 4.46
5002 7112 1.558294 GGATCTGGGTTTTAGACGGGT 59.442 52.381 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.