Multiple sequence alignment - TraesCS4D01G130100

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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 TraesCS4D01G130100 chr4D 100.000 5892 0 0 1 5892 116146870 116152761 0.000000e+00 10881.0
1 TraesCS4D01G130100 chr4D 93.827 81 5 0 3417 3497 281196238 281196158 8.020000e-24 122.0
2 TraesCS4D01G130100 chr4B 93.842 2923 110 23 2985 5891 177858065 177860933 0.000000e+00 4337.0
3 TraesCS4D01G130100 chr4B 94.002 1734 55 12 937 2654 177854669 177856369 0.000000e+00 2580.0
4 TraesCS4D01G130100 chr4B 97.361 341 9 0 2661 3001 177856483 177856823 1.100000e-161 580.0
5 TraesCS4D01G130100 chr4B 93.827 81 4 1 3417 3497 285601291 285601370 2.880000e-23 121.0
6 TraesCS4D01G130100 chr4B 74.324 296 57 15 1821 2110 311362768 311362486 2.250000e-19 108.0
7 TraesCS4D01G130100 chr4A 95.450 2747 78 17 2661 5400 460453207 460450501 0.000000e+00 4337.0
8 TraesCS4D01G130100 chr4A 95.359 1896 57 10 791 2664 460455186 460453300 0.000000e+00 2985.0
9 TraesCS4D01G130100 chr4A 96.635 208 6 1 5685 5892 460450074 460449868 1.570000e-90 344.0
10 TraesCS4D01G130100 chr4A 95.122 82 2 2 5619 5700 460450331 460450252 1.720000e-25 128.0
11 TraesCS4D01G130100 chr4A 100.000 56 0 0 738 793 460455266 460455211 2.900000e-18 104.0
12 TraesCS4D01G130100 chr4A 88.889 54 6 0 1821 1874 690132824 690132771 3.810000e-07 67.6
13 TraesCS4D01G130100 chr4A 100.000 28 0 0 5654 5681 76903599 76903572 1.100000e-02 52.8
14 TraesCS4D01G130100 chr5A 89.605 760 55 11 1 740 291736987 291737742 0.000000e+00 944.0
15 TraesCS4D01G130100 chr5A 95.556 45 2 0 5584 5628 55159064 55159020 8.190000e-09 73.1
16 TraesCS4D01G130100 chr2B 87.664 762 59 20 1 741 89317511 89316764 0.000000e+00 854.0
17 TraesCS4D01G130100 chr2B 80.769 78 9 5 5582 5653 72603675 72603598 8.250000e-04 56.5
18 TraesCS4D01G130100 chr3A 88.435 441 34 7 313 740 745529874 745529438 3.150000e-142 516.0
19 TraesCS4D01G130100 chr3A 90.881 318 27 2 1 317 745535531 745535215 5.460000e-115 425.0
20 TraesCS4D01G130100 chr7B 91.667 324 21 5 1 323 93866767 93867085 1.510000e-120 444.0
21 TraesCS4D01G130100 chr7B 95.556 45 2 0 5584 5628 727607037 727606993 8.190000e-09 73.1
22 TraesCS4D01G130100 chr7B 88.679 53 4 2 5571 5623 659404291 659404241 4.930000e-06 63.9
23 TraesCS4D01G130100 chr3B 76.207 290 51 11 1825 2110 8848787 8848512 2.860000e-28 137.0
24 TraesCS4D01G130100 chr3B 93.750 64 4 0 2591 2654 764843453 764843390 4.860000e-16 97.1
25 TraesCS4D01G130100 chr3B 92.188 64 4 1 2591 2654 794977223 794977285 8.130000e-14 89.8
26 TraesCS4D01G130100 chr6D 81.761 159 24 4 3348 3505 309586303 309586149 1.720000e-25 128.0
27 TraesCS4D01G130100 chr6B 81.132 159 27 3 3348 3505 477223832 477223676 2.230000e-24 124.0
28 TraesCS4D01G130100 chr6B 95.745 47 2 0 5582 5628 143769944 143769990 6.330000e-10 76.8
29 TraesCS4D01G130100 chr6B 95.349 43 2 0 5586 5628 700090390 700090432 1.060000e-07 69.4
30 TraesCS4D01G130100 chr2A 81.890 127 22 1 2240 2365 488856940 488857066 8.080000e-19 106.0
31 TraesCS4D01G130100 chr2A 93.878 49 3 0 5580 5628 615347633 615347681 2.280000e-09 75.0
32 TraesCS4D01G130100 chr5D 79.739 153 23 4 3348 3499 528827060 528826915 2.900000e-18 104.0
33 TraesCS4D01G130100 chr5B 79.221 154 27 4 3348 3499 665974696 665974546 1.040000e-17 102.0
34 TraesCS4D01G130100 chr5B 93.750 64 4 0 2591 2654 456671812 456671875 4.860000e-16 97.1
35 TraesCS4D01G130100 chr1D 100.000 28 0 0 5581 5608 98834887 98834914 1.100000e-02 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 TraesCS4D01G130100 chr4D 116146870 116152761 5891 False 10881.0 10881 100.000000 1 5892 1 chr4D.!!$F1 5891
1 TraesCS4D01G130100 chr4B 177854669 177860933 6264 False 2499.0 4337 95.068333 937 5891 3 chr4B.!!$F2 4954
2 TraesCS4D01G130100 chr4A 460449868 460455266 5398 True 1579.6 4337 96.513200 738 5892 5 chr4A.!!$R3 5154
3 TraesCS4D01G130100 chr5A 291736987 291737742 755 False 944.0 944 89.605000 1 740 1 chr5A.!!$F1 739
4 TraesCS4D01G130100 chr2B 89316764 89317511 747 True 854.0 854 87.664000 1 741 1 chr2B.!!$R2 740

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
447 467 1.079127 CCTCGACCGCTCCATGTTT 60.079 57.895 0.00 0.0 0.00 2.83 F
1257 1325 0.627986 CCCTGCTCTTTCCTTCCCAT 59.372 55.000 0.00 0.0 0.00 4.00 F
1911 1979 0.391927 TTTGGGTCGGCTTCGTATGG 60.392 55.000 0.00 0.0 35.06 2.74 F
2654 2736 0.467804 TATTGCAGGCGCTATGTCCA 59.532 50.000 7.64 0.0 39.64 4.02 F
3322 4777 1.757699 GCAAGATTAGGTCGAGAGGGT 59.242 52.381 0.00 0.0 0.00 4.34 F
4337 5793 0.873054 GCGCATCTGCAGCTTCATAT 59.127 50.000 9.47 0.0 42.21 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1847 1.206849 TGAGCAACCGCATACTGATGA 59.793 47.619 0.00 0.00 42.27 2.92 R
3159 4611 2.496817 GCTGCTACTCCCGTCCAG 59.503 66.667 0.00 0.00 0.00 3.86 R
3322 4777 1.370609 TTTTTGGACGTCGCAACTCA 58.629 45.000 16.00 2.85 0.00 3.41 R
3670 5126 2.283298 CAGAGAACCAACATCATCCCG 58.717 52.381 0.00 0.00 0.00 5.14 R
4828 6288 0.970427 TCGATGACAGTGGGCTAGCA 60.970 55.000 18.24 0.00 0.00 3.49 R
5442 6907 1.052287 CCTTTCGACAAAATGCACGC 58.948 50.000 0.00 0.00 0.00 5.34 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
41 42 6.045955 TGAGGCAGTTGGTTTGATTTTTAAC 58.954 36.000 0.00 0.00 0.00 2.01
54 55 3.821421 TTTTTAACACCCCAACGCATT 57.179 38.095 0.00 0.00 0.00 3.56
105 106 5.491070 CACACCATCTCTATCCTCAAAACA 58.509 41.667 0.00 0.00 0.00 2.83
198 199 6.982852 TGGAAATAAACATTTACGCCTGAAA 58.017 32.000 0.00 0.00 0.00 2.69
294 302 1.134946 GCCATGACCCTTTTCCAATCG 59.865 52.381 0.00 0.00 0.00 3.34
331 339 4.664677 GTGCCACCGAGCTCGTGT 62.665 66.667 32.41 25.76 37.74 4.49
334 342 2.029073 CCACCGAGCTCGTGTTGT 59.971 61.111 32.41 20.92 37.74 3.32
337 345 1.143183 ACCGAGCTCGTGTTGTTGT 59.857 52.632 32.41 19.14 37.74 3.32
408 428 2.125106 GAGCACTTCGGGCGGAAT 60.125 61.111 8.00 0.00 33.26 3.01
447 467 1.079127 CCTCGACCGCTCCATGTTT 60.079 57.895 0.00 0.00 0.00 2.83
453 473 2.481276 CGACCGCTCCATGTTTCTGATA 60.481 50.000 0.00 0.00 0.00 2.15
519 539 3.832237 CTGCAGCTCCGGGTGTGTT 62.832 63.158 0.00 0.00 42.33 3.32
524 544 2.193536 GCTCCGGGTGTGTTGCTTT 61.194 57.895 0.00 0.00 0.00 3.51
583 610 2.037772 TCCTTTTCACAGGCACTCTCTC 59.962 50.000 0.00 0.00 34.60 3.20
614 641 6.360618 TCCTCTCTTTTCTTGCTTTTCTCTT 58.639 36.000 0.00 0.00 0.00 2.85
625 652 2.772287 CTTTTCTCTTGAGGAAGCCGT 58.228 47.619 0.00 0.00 0.00 5.68
684 712 1.822990 CTTTTGCACCAGATGGCATCT 59.177 47.619 24.01 24.01 40.17 2.90
811 866 1.758862 CCAATTCCCCTGGCTTTGATC 59.241 52.381 0.00 0.00 0.00 2.92
840 895 1.461268 TCTCAACACTGGGCCTCCA 60.461 57.895 4.53 0.00 41.58 3.86
882 937 6.352516 CCCATGATCTGCTTTCTACTAGTTT 58.647 40.000 0.00 0.00 0.00 2.66
883 938 6.481644 CCCATGATCTGCTTTCTACTAGTTTC 59.518 42.308 0.00 0.00 0.00 2.78
885 940 8.417106 CCATGATCTGCTTTCTACTAGTTTCTA 58.583 37.037 0.00 0.00 0.00 2.10
890 956 8.859236 TCTGCTTTCTACTAGTTTCTACTACA 57.141 34.615 0.00 0.00 35.78 2.74
911 977 3.193691 CAGTCGTAGTTCCCTTGTCTCAT 59.806 47.826 0.00 0.00 0.00 2.90
912 978 3.444388 AGTCGTAGTTCCCTTGTCTCATC 59.556 47.826 0.00 0.00 0.00 2.92
913 979 3.444388 GTCGTAGTTCCCTTGTCTCATCT 59.556 47.826 0.00 0.00 0.00 2.90
914 980 3.695060 TCGTAGTTCCCTTGTCTCATCTC 59.305 47.826 0.00 0.00 0.00 2.75
994 1062 2.203938 AAACCCTCTCTGGCCGGA 60.204 61.111 15.16 15.16 0.00 5.14
1012 1080 3.591254 AAGCGCGACAACCTCCCTC 62.591 63.158 12.10 0.00 0.00 4.30
1035 1103 1.746991 CTTTGGGGGCTCTCTTCGC 60.747 63.158 0.00 0.00 0.00 4.70
1257 1325 0.627986 CCCTGCTCTTTCCTTCCCAT 59.372 55.000 0.00 0.00 0.00 4.00
1275 1343 1.045911 ATTGCTCCTCCCTCTCCGTC 61.046 60.000 0.00 0.00 0.00 4.79
1469 1537 1.812571 CCACCTCCTGTTTGCATGTAC 59.187 52.381 0.00 0.00 0.00 2.90
1562 1630 1.531423 AGCTTCTTGTCCAGCATGTG 58.469 50.000 0.00 0.00 38.61 3.21
1663 1731 4.509616 TCTTTCTTGTGAAACTGGTCGAA 58.490 39.130 0.00 0.00 37.27 3.71
1674 1742 1.686587 ACTGGTCGAACATCACACAGA 59.313 47.619 2.20 0.00 0.00 3.41
1679 1747 4.578516 TGGTCGAACATCACACAGATTTTT 59.421 37.500 0.00 0.00 33.72 1.94
1880 1948 2.609491 GGTCCGACCCAAAATTTCAAGC 60.609 50.000 6.25 0.00 30.04 4.01
1911 1979 0.391927 TTTGGGTCGGCTTCGTATGG 60.392 55.000 0.00 0.00 35.06 2.74
1968 2036 2.668632 GTCATCGGGGCAAGTGGA 59.331 61.111 0.00 0.00 0.00 4.02
2577 2647 1.306141 TGCTCGTCCCCCTGAGAAT 60.306 57.895 0.00 0.00 34.04 2.40
2654 2736 0.467804 TATTGCAGGCGCTATGTCCA 59.532 50.000 7.64 0.00 39.64 4.02
2657 2739 2.176273 GCAGGCGCTATGTCCACAG 61.176 63.158 7.64 0.00 34.30 3.66
2683 2872 3.014604 GCAATAGCGTCCGTTATCTCT 57.985 47.619 0.00 0.00 0.00 3.10
2764 2953 2.083774 TGAGCGTTTGAATGATCCACC 58.916 47.619 0.00 0.00 29.55 4.61
2771 2960 2.028420 TGAATGATCCACCGCTGAAG 57.972 50.000 0.00 0.00 0.00 3.02
3118 4570 5.294552 GTGCAACTTACCTATTGGATCAGAC 59.705 44.000 0.00 0.00 37.04 3.51
3322 4777 1.757699 GCAAGATTAGGTCGAGAGGGT 59.242 52.381 0.00 0.00 0.00 4.34
3360 4816 1.847328 AAAATCCCTAAACCTGGGCG 58.153 50.000 0.00 0.00 44.23 6.13
3507 4963 6.607600 ACTGATACTCCTTAACATAGAGCACA 59.392 38.462 0.00 0.00 0.00 4.57
3670 5126 3.002791 TCTTCGCATCCATCAAAGACAC 58.997 45.455 0.00 0.00 0.00 3.67
3727 5183 9.073475 TGTTAGTAATAGTTTTTGTCAATGGCT 57.927 29.630 0.00 0.00 0.00 4.75
3831 5287 5.236282 ACACTGAGAGAAATGTGTCATCTG 58.764 41.667 0.00 0.00 39.09 2.90
4337 5793 0.873054 GCGCATCTGCAGCTTCATAT 59.127 50.000 9.47 0.00 42.21 1.78
4417 5873 5.652891 TCTGTCTGACCAGTCTTCTTATACC 59.347 44.000 5.17 0.00 34.02 2.73
4505 5961 7.465916 CGGATGACTCAAATGGTAATTGTACAG 60.466 40.741 0.00 0.00 31.21 2.74
4530 5986 8.186821 AGTCATTCTGCTTCTGTAATTAATTGC 58.813 33.333 11.05 10.05 0.00 3.56
4797 6257 1.138069 TGAGACAACCTCTTGCGTTCA 59.862 47.619 0.00 0.00 42.44 3.18
4805 6265 1.927174 CCTCTTGCGTTCATAACTCGG 59.073 52.381 0.00 0.00 0.00 4.63
4806 6266 2.416836 CCTCTTGCGTTCATAACTCGGA 60.417 50.000 0.00 0.00 0.00 4.55
4807 6267 2.854777 CTCTTGCGTTCATAACTCGGAG 59.145 50.000 2.83 2.83 0.00 4.63
4808 6268 1.927174 CTTGCGTTCATAACTCGGAGG 59.073 52.381 10.23 0.00 0.00 4.30
4809 6269 1.179152 TGCGTTCATAACTCGGAGGA 58.821 50.000 10.23 0.00 0.00 3.71
4810 6270 1.546923 TGCGTTCATAACTCGGAGGAA 59.453 47.619 10.23 0.26 0.00 3.36
4811 6271 2.028839 TGCGTTCATAACTCGGAGGAAA 60.029 45.455 10.23 0.00 0.00 3.13
4812 6272 3.195661 GCGTTCATAACTCGGAGGAAAT 58.804 45.455 10.23 0.00 0.00 2.17
4813 6273 3.621715 GCGTTCATAACTCGGAGGAAATT 59.378 43.478 10.23 0.00 0.00 1.82
4814 6274 4.260253 GCGTTCATAACTCGGAGGAAATTC 60.260 45.833 10.23 0.00 0.00 2.17
4823 6283 3.935828 CTCGGAGGAAATTCAGAGGAAAC 59.064 47.826 0.00 0.00 36.25 2.78
4844 6305 1.561076 TCATTGCTAGCCCACTGTCAT 59.439 47.619 13.29 0.00 0.00 3.06
4885 6346 3.981071 ATGAGGAAAGACCGTTGATCA 57.019 42.857 0.00 0.00 44.74 2.92
4889 6350 3.170717 AGGAAAGACCGTTGATCAGGTA 58.829 45.455 6.62 0.00 44.74 3.08
4913 6374 5.642063 AGACTTCTTTGTGTTTCTTGTTCGA 59.358 36.000 0.00 0.00 0.00 3.71
4914 6375 6.148811 AGACTTCTTTGTGTTTCTTGTTCGAA 59.851 34.615 0.00 0.00 0.00 3.71
4918 6379 4.349663 TTGTGTTTCTTGTTCGAACAGG 57.650 40.909 28.86 28.86 40.50 4.00
5039 6500 4.080356 TGGGTTCCTGGAATCTTAGTGATG 60.080 45.833 18.65 0.00 35.21 3.07
5067 6528 3.801997 AGATGGGCCCCGCTTCAG 61.802 66.667 22.27 0.00 0.00 3.02
5074 6535 2.421739 CCCCGCTTCAGATACCCG 59.578 66.667 0.00 0.00 0.00 5.28
5157 6618 5.447818 GCAGCAAGTGGATATTACAGTGAAC 60.448 44.000 0.00 0.00 0.00 3.18
5158 6619 5.643348 CAGCAAGTGGATATTACAGTGAACA 59.357 40.000 0.00 0.00 0.00 3.18
5159 6620 5.643777 AGCAAGTGGATATTACAGTGAACAC 59.356 40.000 0.00 0.00 0.00 3.32
5161 6622 6.149474 GCAAGTGGATATTACAGTGAACACTT 59.851 38.462 4.63 0.00 45.55 3.16
5162 6623 7.308589 GCAAGTGGATATTACAGTGAACACTTT 60.309 37.037 4.63 1.92 43.10 2.66
5163 6624 8.567948 CAAGTGGATATTACAGTGAACACTTTT 58.432 33.333 4.63 0.00 43.10 2.27
5164 6625 8.691661 AGTGGATATTACAGTGAACACTTTTT 57.308 30.769 4.63 0.00 40.20 1.94
5206 6667 8.615878 AACACTATTGACAATACAGCTTTGTA 57.384 30.769 3.68 0.00 37.43 2.41
5207 6668 8.615878 ACACTATTGACAATACAGCTTTGTAA 57.384 30.769 3.68 0.00 37.43 2.41
5285 6746 8.680001 CAGAACAACATCAATCAATATCTTCCA 58.320 33.333 0.00 0.00 0.00 3.53
5324 6785 0.537143 TTGGCTCGGAATTGCACAGT 60.537 50.000 0.00 0.00 0.00 3.55
5344 6806 5.011943 ACAGTTGATACGTTACCCCTAAACA 59.988 40.000 0.00 0.00 0.00 2.83
5379 6843 9.606631 AAAATACTAACATTTCACAGGCAAAAA 57.393 25.926 0.00 0.00 0.00 1.94
5402 6866 3.388552 TGAGGTTCTCTGAGCTATGGA 57.611 47.619 0.00 0.00 0.00 3.41
5433 6898 6.160576 AGAAAATAAGCAGAGCCAACAAAA 57.839 33.333 0.00 0.00 0.00 2.44
5435 6900 3.942130 ATAAGCAGAGCCAACAAAACC 57.058 42.857 0.00 0.00 0.00 3.27
5438 6903 1.830477 AGCAGAGCCAACAAAACCAAA 59.170 42.857 0.00 0.00 0.00 3.28
5440 6905 3.118298 AGCAGAGCCAACAAAACCAAATT 60.118 39.130 0.00 0.00 0.00 1.82
5441 6906 4.100808 AGCAGAGCCAACAAAACCAAATTA 59.899 37.500 0.00 0.00 0.00 1.40
5442 6907 4.448732 GCAGAGCCAACAAAACCAAATTAG 59.551 41.667 0.00 0.00 0.00 1.73
5443 6908 4.448732 CAGAGCCAACAAAACCAAATTAGC 59.551 41.667 0.00 0.00 0.00 3.09
5444 6909 3.389221 AGCCAACAAAACCAAATTAGCG 58.611 40.909 0.00 0.00 0.00 4.26
5445 6910 3.127589 GCCAACAAAACCAAATTAGCGT 58.872 40.909 0.00 0.00 0.00 5.07
5456 6921 3.059306 CCAAATTAGCGTGCATTTTGTCG 59.941 43.478 0.00 0.00 0.00 4.35
5460 6925 2.036556 AGCGTGCATTTTGTCGAAAG 57.963 45.000 0.00 0.00 0.00 2.62
5486 6951 9.129209 GGTAGAAAAGCAATTCACAAGAATAAC 57.871 33.333 4.59 0.00 43.52 1.89
5490 6955 9.248291 GAAAAGCAATTCACAAGAATAACTCAA 57.752 29.630 0.00 0.00 43.52 3.02
5498 6963 9.956720 ATTCACAAGAATAACTCAAAAGAACTG 57.043 29.630 0.00 0.00 42.54 3.16
5548 7014 3.054655 TGGGCCACTATGGAGTAAAACTC 60.055 47.826 0.00 0.00 44.32 3.01
5644 7193 6.538945 ACAACTTCAACACTTAATTTGGGT 57.461 33.333 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.429130 TGGGGTGTTAAAAATCAAACCAAC 58.571 37.500 0.00 0.00 0.00 3.77
41 42 1.378514 AGGCTAATGCGTTGGGGTG 60.379 57.895 0.08 0.00 40.82 4.61
73 74 2.044946 GATGGTGTGGGTCCCAGC 60.045 66.667 12.21 7.39 32.34 4.85
129 130 2.025887 AGATTGGGGAAGAAGATGCGTT 60.026 45.455 0.00 0.00 0.00 4.84
205 206 1.656652 CTAACAGAGGCGATTGGGTG 58.343 55.000 0.00 0.00 0.00 4.61
245 253 2.203126 GCTCAAGGCCGCAGCTAT 60.203 61.111 14.44 0.00 39.73 2.97
280 288 1.241315 CCGTGCGATTGGAAAAGGGT 61.241 55.000 0.00 0.00 0.00 4.34
294 302 2.436646 CCATGGAGGACACCGTGC 60.437 66.667 5.56 0.00 43.34 5.34
331 339 1.142748 CCAAAGCCGGCAACAACAA 59.857 52.632 31.54 0.00 0.00 2.83
390 410 2.660064 ATTCCGCCCGAAGTGCTCT 61.660 57.895 0.00 0.00 32.78 4.09
416 436 1.217882 GTCGAGGCGGAAATACATGG 58.782 55.000 0.00 0.00 0.00 3.66
447 467 3.701542 AGAAGCACGAGTTCCATATCAGA 59.298 43.478 0.00 0.00 0.00 3.27
453 473 2.563179 AGTACAGAAGCACGAGTTCCAT 59.437 45.455 0.00 0.00 0.00 3.41
546 566 1.376649 AGGATGGGAGAAGTTGGCTT 58.623 50.000 0.00 0.00 37.71 4.35
583 610 3.977579 GCAAGAAAAGAGAGGAAAAAGCG 59.022 43.478 0.00 0.00 0.00 4.68
614 641 0.891373 CAGAAGAGACGGCTTCCTCA 59.109 55.000 0.00 0.00 44.14 3.86
625 652 2.544721 AGGTGATTCCTGCAGAAGAGA 58.455 47.619 17.39 0.00 46.19 3.10
649 676 3.612247 AAAGCGGTCGCCTGCAGAT 62.612 57.895 17.39 0.00 43.17 2.90
714 742 3.060000 GCCAACGGTTAGCCCCAC 61.060 66.667 0.00 0.00 0.00 4.61
840 895 0.743345 GGCCGATTAGAAGCACGGTT 60.743 55.000 0.00 0.00 45.91 4.44
890 956 2.872732 TGAGACAAGGGAACTACGACT 58.127 47.619 0.00 0.00 42.68 4.18
925 991 1.198637 CCGAGACGAACTACGACCTTT 59.801 52.381 0.00 0.00 45.77 3.11
927 993 0.036952 TCCGAGACGAACTACGACCT 60.037 55.000 0.00 0.00 45.77 3.85
928 994 0.096108 GTCCGAGACGAACTACGACC 59.904 60.000 0.00 0.00 45.77 4.79
994 1062 3.591254 GAGGGAGGTTGTCGCGCTT 62.591 63.158 5.56 0.00 43.00 4.68
1012 1080 1.284313 AGAGAGCCCCCAAAGAAGAG 58.716 55.000 0.00 0.00 0.00 2.85
1074 1142 0.317479 CCGGGGAATAACTAGGAGCG 59.683 60.000 0.00 0.00 0.00 5.03
1257 1325 1.682684 GACGGAGAGGGAGGAGCAA 60.683 63.158 0.00 0.00 0.00 3.91
1330 1398 4.503123 GCCCTAACAAAGCACAGGAAAAAT 60.503 41.667 0.00 0.00 0.00 1.82
1469 1537 3.947834 GGGTAAAATCATGAGTGACAGGG 59.052 47.826 0.09 0.00 37.14 4.45
1562 1630 2.158842 CCCAGAATGATGGACTGTCTCC 60.159 54.545 7.85 0.00 43.57 3.71
1635 1703 7.254795 CGACCAGTTTCACAAGAAAGAAATACT 60.255 37.037 0.00 0.00 43.95 2.12
1679 1747 1.617850 GGTTCATCATGTGTGGCCAAA 59.382 47.619 7.24 0.00 0.00 3.28
1779 1847 1.206849 TGAGCAACCGCATACTGATGA 59.793 47.619 0.00 0.00 42.27 2.92
1785 1853 2.613595 TGATCATTGAGCAACCGCATAC 59.386 45.455 1.33 0.00 42.27 2.39
1911 1979 2.060383 GCTCCCCTGGCCCATTTTC 61.060 63.158 0.00 0.00 0.00 2.29
2111 2179 6.317642 AGAAAAACAATGCGTATATACAGCCA 59.682 34.615 19.77 11.63 0.00 4.75
2177 2247 9.347240 ACAAATAGCATCATTAGCAGTAGATTT 57.653 29.630 0.00 0.00 0.00 2.17
2178 2248 8.915057 ACAAATAGCATCATTAGCAGTAGATT 57.085 30.769 0.00 0.00 0.00 2.40
2182 2252 9.830975 TCTTTACAAATAGCATCATTAGCAGTA 57.169 29.630 0.00 0.00 0.00 2.74
2183 2253 8.737168 TCTTTACAAATAGCATCATTAGCAGT 57.263 30.769 0.00 0.00 0.00 4.40
2184 2254 9.608617 CATCTTTACAAATAGCATCATTAGCAG 57.391 33.333 0.00 0.00 0.00 4.24
2185 2255 9.123902 ACATCTTTACAAATAGCATCATTAGCA 57.876 29.630 0.00 0.00 0.00 3.49
2233 2303 4.401202 GGTCGGACCCATTTTAATTGACAT 59.599 41.667 16.55 0.00 30.04 3.06
2272 2342 2.651455 CAATGGTGATCAGCCTCATGT 58.349 47.619 21.58 0.00 0.00 3.21
2577 2647 3.859443 TCCGCTACCGCTATTTAAAACA 58.141 40.909 0.00 0.00 0.00 2.83
2683 2872 5.827797 CCTCAGGGCATAGTTTTAAATAGCA 59.172 40.000 0.00 0.00 0.00 3.49
2764 2953 3.180584 GCTTATGACATCGTACTTCAGCG 59.819 47.826 0.00 0.00 0.00 5.18
2771 2960 3.971150 AGCTCTGCTTATGACATCGTAC 58.029 45.455 0.00 0.00 33.89 3.67
2849 3043 3.680490 TGGTCTTGTTTCTGTTGACACA 58.320 40.909 0.00 0.00 31.81 3.72
2850 3044 3.487544 GCTGGTCTTGTTTCTGTTGACAC 60.488 47.826 0.00 0.00 0.00 3.67
2851 3045 2.682856 GCTGGTCTTGTTTCTGTTGACA 59.317 45.455 0.00 0.00 0.00 3.58
2852 3046 2.945668 AGCTGGTCTTGTTTCTGTTGAC 59.054 45.455 0.00 0.00 0.00 3.18
2853 3047 3.281727 AGCTGGTCTTGTTTCTGTTGA 57.718 42.857 0.00 0.00 0.00 3.18
2977 3171 3.159213 ACACATTTGCTTGATCCCAGA 57.841 42.857 0.00 0.00 0.00 3.86
3087 4539 5.833131 CCAATAGGTAAGTTGCACCCATAAT 59.167 40.000 0.00 0.00 36.67 1.28
3159 4611 2.496817 GCTGCTACTCCCGTCCAG 59.503 66.667 0.00 0.00 0.00 3.86
3322 4777 1.370609 TTTTTGGACGTCGCAACTCA 58.629 45.000 16.00 2.85 0.00 3.41
3360 4816 5.689383 AAATCCATAACACGGTATCATGC 57.311 39.130 0.00 0.00 0.00 4.06
3507 4963 9.972106 ATCTCAATCATAAGAAAGGAAAAGAGT 57.028 29.630 0.00 0.00 0.00 3.24
3573 5029 4.063689 CTCACCAGCTATGCAAAGGATAG 58.936 47.826 0.00 1.70 0.00 2.08
3630 5086 5.293079 CGAAGAAAATTGGAACTTGGCAAAA 59.707 36.000 0.00 0.00 0.00 2.44
3631 5087 4.808364 CGAAGAAAATTGGAACTTGGCAAA 59.192 37.500 0.00 0.00 0.00 3.68
3642 5098 4.374843 TGATGGATGCGAAGAAAATTGG 57.625 40.909 0.00 0.00 0.00 3.16
3643 5099 6.034256 GTCTTTGATGGATGCGAAGAAAATTG 59.966 38.462 0.00 0.00 37.48 2.32
3644 5100 6.095377 GTCTTTGATGGATGCGAAGAAAATT 58.905 36.000 0.00 0.00 37.48 1.82
3670 5126 2.283298 CAGAGAACCAACATCATCCCG 58.717 52.381 0.00 0.00 0.00 5.14
3727 5183 9.950496 GGCATTTCTTCCAAGATTCTATATAGA 57.050 33.333 8.44 8.44 34.49 1.98
3831 5287 6.423302 CAGAATCTACTTGGACAGCATCATAC 59.577 42.308 0.00 0.00 0.00 2.39
4337 5793 6.915300 CACGTTTGAATGAAAATTACAGTGGA 59.085 34.615 0.00 0.00 0.00 4.02
4417 5873 3.254060 CTCATCGTCCACTTGTAACCTG 58.746 50.000 0.00 0.00 0.00 4.00
4505 5961 8.186821 AGCAATTAATTACAGAAGCAGAATGAC 58.813 33.333 0.00 0.00 39.69 3.06
4797 6257 4.962995 TCCTCTGAATTTCCTCCGAGTTAT 59.037 41.667 0.00 0.00 0.00 1.89
4805 6265 6.624642 GCAATGAGTTTCCTCTGAATTTCCTC 60.625 42.308 0.00 0.00 38.61 3.71
4806 6266 5.184671 GCAATGAGTTTCCTCTGAATTTCCT 59.815 40.000 0.00 0.00 38.61 3.36
4807 6267 5.184671 AGCAATGAGTTTCCTCTGAATTTCC 59.815 40.000 0.00 0.00 38.61 3.13
4808 6268 6.264841 AGCAATGAGTTTCCTCTGAATTTC 57.735 37.500 0.00 0.00 38.61 2.17
4809 6269 6.127786 GCTAGCAATGAGTTTCCTCTGAATTT 60.128 38.462 10.63 0.00 38.61 1.82
4810 6270 5.356470 GCTAGCAATGAGTTTCCTCTGAATT 59.644 40.000 10.63 0.00 38.61 2.17
4811 6271 4.880696 GCTAGCAATGAGTTTCCTCTGAAT 59.119 41.667 10.63 0.00 38.61 2.57
4812 6272 4.256920 GCTAGCAATGAGTTTCCTCTGAA 58.743 43.478 10.63 0.00 38.61 3.02
4813 6273 3.369892 GGCTAGCAATGAGTTTCCTCTGA 60.370 47.826 18.24 0.00 38.61 3.27
4814 6274 2.941720 GGCTAGCAATGAGTTTCCTCTG 59.058 50.000 18.24 0.00 38.61 3.35
4823 6283 1.065926 TGACAGTGGGCTAGCAATGAG 60.066 52.381 18.24 5.62 0.00 2.90
4828 6288 0.970427 TCGATGACAGTGGGCTAGCA 60.970 55.000 18.24 0.00 0.00 3.49
4844 6305 2.157834 ACGCCAGTACAATGTTTCGA 57.842 45.000 0.00 0.00 0.00 3.71
4885 6346 6.415573 ACAAGAAACACAAAGAAGTCTACCT 58.584 36.000 0.00 0.00 0.00 3.08
4889 6350 5.642063 TCGAACAAGAAACACAAAGAAGTCT 59.358 36.000 0.00 0.00 0.00 3.24
4913 6374 3.521727 ACCCAACTAGATCACTCCTGTT 58.478 45.455 0.00 0.00 0.00 3.16
4914 6375 3.191888 ACCCAACTAGATCACTCCTGT 57.808 47.619 0.00 0.00 0.00 4.00
4918 6379 3.600388 CACCAACCCAACTAGATCACTC 58.400 50.000 0.00 0.00 0.00 3.51
5039 6500 2.224646 GGGGCCCATCTGATAAAGAGAC 60.225 54.545 26.86 0.00 38.67 3.36
5067 6528 2.747446 TCAAAAAGAAGCAGCGGGTATC 59.253 45.455 0.00 0.00 0.00 2.24
5074 6535 2.816672 AGCCTACTCAAAAAGAAGCAGC 59.183 45.455 0.00 0.00 0.00 5.25
5164 6625 9.781834 CAATAGTGTTCACTGTACTTTCAAAAA 57.218 29.630 14.69 0.00 0.00 1.94
5165 6626 9.168451 TCAATAGTGTTCACTGTACTTTCAAAA 57.832 29.630 14.69 0.00 0.00 2.44
5166 6627 8.609176 GTCAATAGTGTTCACTGTACTTTCAAA 58.391 33.333 14.69 0.00 0.00 2.69
5167 6628 7.766738 TGTCAATAGTGTTCACTGTACTTTCAA 59.233 33.333 14.69 0.00 0.00 2.69
5168 6629 7.269316 TGTCAATAGTGTTCACTGTACTTTCA 58.731 34.615 14.69 4.18 0.00 2.69
5169 6630 7.709269 TGTCAATAGTGTTCACTGTACTTTC 57.291 36.000 14.69 2.08 0.00 2.62
5170 6631 8.677148 ATTGTCAATAGTGTTCACTGTACTTT 57.323 30.769 14.69 0.18 0.00 2.66
5180 6641 7.584987 ACAAAGCTGTATTGTCAATAGTGTTC 58.415 34.615 5.49 0.00 36.28 3.18
5187 6648 8.850156 AGTTCTTTACAAAGCTGTATTGTCAAT 58.150 29.630 5.55 3.06 41.11 2.57
5206 6667 9.219603 TCATTGATTCGTCATTAGAAGTTCTTT 57.780 29.630 11.40 0.00 0.00 2.52
5207 6668 8.777865 TCATTGATTCGTCATTAGAAGTTCTT 57.222 30.769 11.40 0.00 0.00 2.52
5285 6746 4.501915 CCAAGGTTTTGATGTGAACAGCAT 60.502 41.667 1.73 0.00 42.26 3.79
5324 6785 6.594937 GTGATTGTTTAGGGGTAACGTATCAA 59.405 38.462 0.00 0.00 34.19 2.57
5379 6843 4.718774 TCCATAGCTCAGAGAACCTCAATT 59.281 41.667 0.00 0.00 32.06 2.32
5380 6844 4.293494 TCCATAGCTCAGAGAACCTCAAT 58.707 43.478 0.00 0.00 32.06 2.57
5389 6853 1.415289 TGTGGCATCCATAGCTCAGAG 59.585 52.381 0.00 0.00 35.28 3.35
5397 6861 5.655974 TGCTTATTTTCTTGTGGCATCCATA 59.344 36.000 0.00 0.00 35.28 2.74
5402 6866 4.381292 GCTCTGCTTATTTTCTTGTGGCAT 60.381 41.667 0.00 0.00 0.00 4.40
5433 6898 3.987220 GACAAAATGCACGCTAATTTGGT 59.013 39.130 14.55 6.97 33.54 3.67
5435 6900 3.911365 TCGACAAAATGCACGCTAATTTG 59.089 39.130 0.00 10.85 37.10 2.32
5438 6903 3.822594 TTCGACAAAATGCACGCTAAT 57.177 38.095 0.00 0.00 0.00 1.73
5440 6905 2.095969 CCTTTCGACAAAATGCACGCTA 60.096 45.455 0.00 0.00 0.00 4.26
5441 6906 1.334960 CCTTTCGACAAAATGCACGCT 60.335 47.619 0.00 0.00 0.00 5.07
5442 6907 1.052287 CCTTTCGACAAAATGCACGC 58.948 50.000 0.00 0.00 0.00 5.34
5443 6908 2.399396 ACCTTTCGACAAAATGCACG 57.601 45.000 0.00 0.00 0.00 5.34
5444 6909 4.742438 TCTACCTTTCGACAAAATGCAC 57.258 40.909 0.00 0.00 0.00 4.57
5445 6910 5.759506 TTTCTACCTTTCGACAAAATGCA 57.240 34.783 0.00 0.00 0.00 3.96
5456 6921 7.425606 TCTTGTGAATTGCTTTTCTACCTTTC 58.574 34.615 0.00 0.00 0.00 2.62
5460 6925 9.129209 GTTATTCTTGTGAATTGCTTTTCTACC 57.871 33.333 0.00 0.00 42.37 3.18
5548 7014 9.855021 CTTTTTATATGGAGGTTAGGTTTGTTG 57.145 33.333 0.00 0.00 0.00 3.33
5579 7045 4.748277 TTTGGAACGGAGGGAGTATTAG 57.252 45.455 0.00 0.00 0.00 1.73
5637 7186 6.389869 TGTCTAATATTCCCTCTGACCCAAAT 59.610 38.462 0.00 0.00 0.00 2.32
5644 7193 7.786943 ACAAGAGATGTCTAATATTCCCTCTGA 59.213 37.037 0.00 0.00 37.96 3.27


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

AutoCloner maintained by Alex Coulton.