Multiple sequence alignment - TraesCS4A01G051300

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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 TraesCS4A01G051300 chr4A 100.000 5176 0 0 1 5176 42116752 42121927 0.000000e+00 9559.0
1 TraesCS4A01G051300 chr4A 86.538 156 21 0 2173 2328 321899378 321899533 6.890000e-39 172.0
2 TraesCS4A01G051300 chr4B 94.188 2013 108 6 2338 4346 518879204 518877197 0.000000e+00 3061.0
3 TraesCS4A01G051300 chr4B 93.966 812 33 6 732 1532 518880301 518879495 0.000000e+00 1214.0
4 TraesCS4A01G051300 chr4B 95.143 350 11 3 4311 4659 518877197 518876853 9.800000e-152 547.0
5 TraesCS4A01G051300 chr4B 88.204 373 28 7 1721 2077 564390429 564390801 1.030000e-116 431.0
6 TraesCS4A01G051300 chr4B 85.407 418 50 9 4712 5122 168565230 168565643 1.720000e-114 424.0
7 TraesCS4A01G051300 chr4B 81.412 425 53 20 4712 5124 99578188 99577778 1.800000e-84 324.0
8 TraesCS4A01G051300 chr4B 90.517 232 18 3 2104 2333 564390855 564391084 2.340000e-78 303.0
9 TraesCS4A01G051300 chr4B 94.737 190 9 1 1532 1720 518879397 518879208 1.410000e-75 294.0
10 TraesCS4A01G051300 chr4B 91.667 120 10 0 2112 2231 462737175 462737294 3.210000e-37 167.0
11 TraesCS4A01G051300 chr4B 92.000 50 4 0 5127 5176 518876834 518876785 2.590000e-08 71.3
12 TraesCS4A01G051300 chr4D 90.612 2237 156 31 2411 4635 421952460 421950266 0.000000e+00 2918.0
13 TraesCS4A01G051300 chr4D 87.006 1593 155 24 2527 4089 421925658 421924088 0.000000e+00 1748.0
14 TraesCS4A01G051300 chr4D 92.692 780 39 4 760 1524 421953545 421952769 0.000000e+00 1109.0
15 TraesCS4A01G051300 chr4D 92.453 583 32 6 4080 4659 421897875 421897302 0.000000e+00 822.0
16 TraesCS4A01G051300 chr4D 90.979 521 29 10 4671 5176 421897320 421896803 0.000000e+00 686.0
17 TraesCS4A01G051300 chr4D 93.085 188 11 1 1533 1720 421952687 421952502 1.840000e-69 274.0
18 TraesCS4A01G051300 chr4D 97.561 41 1 0 2338 2378 421952498 421952458 2.590000e-08 71.3
19 TraesCS4A01G051300 chr4D 100.000 31 0 0 732 762 421962615 421962585 2.010000e-04 58.4
20 TraesCS4A01G051300 chr7A 96.585 615 18 2 1721 2333 380031491 380032104 0.000000e+00 1016.0
21 TraesCS4A01G051300 chr7A 88.283 734 76 10 1 731 267890007 267890733 0.000000e+00 870.0
22 TraesCS4A01G051300 chr5D 90.822 730 57 10 1 727 409442713 409443435 0.000000e+00 968.0
23 TraesCS4A01G051300 chr5D 88.315 736 76 9 1 731 247566604 247565874 0.000000e+00 874.0
24 TraesCS4A01G051300 chr7B 89.698 728 63 11 1 725 94262019 94261301 0.000000e+00 918.0
25 TraesCS4A01G051300 chr3A 94.127 613 21 1 1721 2333 542926507 542925910 0.000000e+00 918.0
26 TraesCS4A01G051300 chr3A 89.062 64 7 0 1721 1784 589400711 589400774 4.300000e-11 80.5
27 TraesCS4A01G051300 chr6D 89.466 731 69 8 3 730 7153797 7154522 0.000000e+00 917.0
28 TraesCS4A01G051300 chr5B 89.148 728 73 6 1 726 655140842 655140119 0.000000e+00 902.0
29 TraesCS4A01G051300 chr5B 88.528 462 42 5 1881 2333 605630309 605629850 2.720000e-152 549.0
30 TraesCS4A01G051300 chr5B 79.469 414 73 11 4712 5116 61649897 61650307 3.050000e-72 283.0
31 TraesCS4A01G051300 chr3D 88.950 733 71 7 1 728 357731135 357731862 0.000000e+00 896.0
32 TraesCS4A01G051300 chr3D 84.670 424 49 12 4712 5126 570566281 570565865 4.820000e-110 409.0
33 TraesCS4A01G051300 chr5A 88.587 736 74 8 1 732 456611214 456610485 0.000000e+00 885.0
34 TraesCS4A01G051300 chr2A 88.602 737 70 12 1 731 674497112 674497840 0.000000e+00 883.0
35 TraesCS4A01G051300 chr2A 79.854 412 68 9 4711 5115 70662815 70662412 2.360000e-73 287.0
36 TraesCS4A01G051300 chr2B 88.204 373 28 7 1721 2077 382733953 382733581 1.030000e-116 431.0
37 TraesCS4A01G051300 chr2B 90.435 230 22 0 2104 2333 382733527 382733298 2.340000e-78 303.0
38 TraesCS4A01G051300 chr7D 84.382 429 49 12 4712 5124 45814823 45815249 6.240000e-109 405.0
39 TraesCS4A01G051300 chr6B 82.904 427 46 14 4711 5125 658193612 658194023 4.930000e-95 359.0
40 TraesCS4A01G051300 chr6B 88.312 231 25 2 2104 2333 533282263 533282034 5.110000e-70 276.0
41 TraesCS4A01G051300 chr6B 91.667 120 10 0 2112 2231 622014828 622014947 3.210000e-37 167.0
42 TraesCS4A01G051300 chr6B 91.379 116 10 0 2112 2227 621582347 621582232 5.360000e-35 159.0
43 TraesCS4A01G051300 chr1D 81.295 417 56 17 4709 5115 62690855 62690451 8.360000e-83 318.0
44 TraesCS4A01G051300 chr2D 86.538 156 21 0 2173 2328 81159689 81159534 6.890000e-39 172.0


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 TraesCS4A01G051300 chr4A 42116752 42121927 5175 False 9559.000 9559 100.0000 1 5176 1 chr4A.!!$F1 5175
1 TraesCS4A01G051300 chr4B 518876785 518880301 3516 True 1037.460 3061 94.0068 732 5176 5 chr4B.!!$R2 4444
2 TraesCS4A01G051300 chr4B 564390429 564391084 655 False 367.000 431 89.3605 1721 2333 2 chr4B.!!$F3 612
3 TraesCS4A01G051300 chr4D 421924088 421925658 1570 True 1748.000 1748 87.0060 2527 4089 1 chr4D.!!$R1 1562
4 TraesCS4A01G051300 chr4D 421950266 421953545 3279 True 1093.075 2918 93.4875 760 4635 4 chr4D.!!$R4 3875
5 TraesCS4A01G051300 chr4D 421896803 421897875 1072 True 754.000 822 91.7160 4080 5176 2 chr4D.!!$R3 1096
6 TraesCS4A01G051300 chr7A 380031491 380032104 613 False 1016.000 1016 96.5850 1721 2333 1 chr7A.!!$F2 612
7 TraesCS4A01G051300 chr7A 267890007 267890733 726 False 870.000 870 88.2830 1 731 1 chr7A.!!$F1 730
8 TraesCS4A01G051300 chr5D 409442713 409443435 722 False 968.000 968 90.8220 1 727 1 chr5D.!!$F1 726
9 TraesCS4A01G051300 chr5D 247565874 247566604 730 True 874.000 874 88.3150 1 731 1 chr5D.!!$R1 730
10 TraesCS4A01G051300 chr7B 94261301 94262019 718 True 918.000 918 89.6980 1 725 1 chr7B.!!$R1 724
11 TraesCS4A01G051300 chr3A 542925910 542926507 597 True 918.000 918 94.1270 1721 2333 1 chr3A.!!$R1 612
12 TraesCS4A01G051300 chr6D 7153797 7154522 725 False 917.000 917 89.4660 3 730 1 chr6D.!!$F1 727
13 TraesCS4A01G051300 chr5B 655140119 655140842 723 True 902.000 902 89.1480 1 726 1 chr5B.!!$R2 725
14 TraesCS4A01G051300 chr3D 357731135 357731862 727 False 896.000 896 88.9500 1 728 1 chr3D.!!$F1 727
15 TraesCS4A01G051300 chr5A 456610485 456611214 729 True 885.000 885 88.5870 1 732 1 chr5A.!!$R1 731
16 TraesCS4A01G051300 chr2A 674497112 674497840 728 False 883.000 883 88.6020 1 731 1 chr2A.!!$F1 730
17 TraesCS4A01G051300 chr2B 382733298 382733953 655 True 367.000 431 89.3195 1721 2333 2 chr2B.!!$R1 612

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
866 886 0.743345 CGTCTTCCCGCCCCTTAAAG 60.743 60.0 0.00 0.0 0.00 1.85 F
1350 1370 0.393402 GGGGTCGGGTTTACATGGTC 60.393 60.0 0.00 0.0 0.00 4.02 F
2903 3094 0.318869 TACTGGCAACACGTACACCG 60.319 55.0 0.00 0.0 46.17 4.94 F
3756 3975 0.108396 TCAGTTGTTGCTGCTGCCTA 59.892 50.0 13.47 0.0 38.71 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2709 2897 2.553602 CACACCAAGTAATTGCAGCTCA 59.446 45.455 0.00 0.00 0.00 4.26 R
2945 3138 1.829222 AGCATTCAAGCCCTGGAAATG 59.171 47.619 0.00 0.00 34.23 2.32 R
4096 4317 1.070758 ACACACCCTCAAGCTGTACAG 59.929 52.381 18.93 18.93 0.00 2.74 R
5081 5355 0.107643 GCTCCATGGAGGCCTCTAAC 59.892 60.000 36.92 17.91 42.19 2.34 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
116 121 6.770076 GTGCAAACACTTTTTGAAGCATAAA 58.230 32.000 0.91 0.00 43.85 1.40
239 245 5.959527 CAGAATATACGTGACATGTGTTTGC 59.040 40.000 1.15 0.00 0.00 3.68
600 620 3.013921 GACCCAATTCAGCAAATACCGA 58.986 45.455 0.00 0.00 0.00 4.69
632 652 5.761205 TCCCAAGATTTAAAATGGATCGGA 58.239 37.500 15.75 5.59 34.82 4.55
648 668 7.762588 TGGATCGGAATTAAAAAGTTTGGTA 57.237 32.000 0.00 0.00 0.00 3.25
660 680 7.713764 AAAAAGTTTGGTATGCTGATTTCAC 57.286 32.000 0.00 0.00 0.00 3.18
666 686 6.993786 TTGGTATGCTGATTTCACGAATTA 57.006 33.333 0.00 0.00 0.00 1.40
674 694 6.650807 TGCTGATTTCACGAATTAAGAGTTCT 59.349 34.615 0.00 0.00 0.00 3.01
677 697 7.158697 TGATTTCACGAATTAAGAGTTCTGGA 58.841 34.615 0.00 0.00 0.00 3.86
693 713 6.071320 AGTTCTGGATTTGGTTTAGCTTTCT 58.929 36.000 0.00 0.00 0.00 2.52
700 720 9.920946 TGGATTTGGTTTAGCTTTCTTCTATAT 57.079 29.630 0.00 0.00 0.00 0.86
744 764 6.712998 ACTTTTTCCTTTAGCTTTCCTCTCTC 59.287 38.462 0.00 0.00 0.00 3.20
745 765 4.828072 TTCCTTTAGCTTTCCTCTCTCC 57.172 45.455 0.00 0.00 0.00 3.71
755 775 2.018086 CCTCTCTCCCTCTCCCCCT 61.018 68.421 0.00 0.00 0.00 4.79
756 776 1.541672 CTCTCTCCCTCTCCCCCTC 59.458 68.421 0.00 0.00 0.00 4.30
758 778 2.204624 TCTCCCTCTCCCCCTCCA 60.205 66.667 0.00 0.00 0.00 3.86
785 805 2.032030 CCAGCACGAAGAAACGAAATGT 60.032 45.455 0.00 0.00 37.03 2.71
787 807 4.386230 CAGCACGAAGAAACGAAATGTAG 58.614 43.478 0.00 0.00 37.03 2.74
815 835 2.604686 AGCGGCAACAGAGGAGGA 60.605 61.111 1.45 0.00 0.00 3.71
866 886 0.743345 CGTCTTCCCGCCCCTTAAAG 60.743 60.000 0.00 0.00 0.00 1.85
1029 1049 2.392181 CGACGAGGAGAGCGTGACT 61.392 63.158 0.00 0.00 42.77 3.41
1323 1343 0.966920 AGTTCGTTCTCCATGTCGGT 59.033 50.000 0.00 0.00 35.57 4.69
1350 1370 0.393402 GGGGTCGGGTTTACATGGTC 60.393 60.000 0.00 0.00 0.00 4.02
1370 1390 3.022914 GCGGTCGGATTAGTCGCG 61.023 66.667 0.00 0.00 37.12 5.87
1454 1485 3.701542 GAGTTTCTGGAATTTGGGGGATC 59.298 47.826 0.00 0.00 0.00 3.36
1468 1499 1.400494 GGGGATCGTATTGTGTTGTGC 59.600 52.381 0.00 0.00 0.00 4.57
2401 2589 1.528129 GAAGCTGTGGGTTCTTCAGG 58.472 55.000 0.00 0.00 43.96 3.86
2405 2593 0.890996 CTGTGGGTTCTTCAGGGTGC 60.891 60.000 0.00 0.00 0.00 5.01
2409 2597 0.967380 GGGTTCTTCAGGGTGCATGG 60.967 60.000 0.00 0.00 0.00 3.66
2445 2633 8.899427 ATCTGAAGATACAATTGTGACTATGG 57.101 34.615 21.42 11.76 32.01 2.74
2477 2665 4.864704 ATATGTTTTCGCTGTTTGGGTT 57.135 36.364 0.00 0.00 0.00 4.11
2481 2669 3.632604 TGTTTTCGCTGTTTGGGTTGATA 59.367 39.130 0.00 0.00 0.00 2.15
2505 2693 1.466856 TAGGCTCTTTCGGCGACTTA 58.533 50.000 10.16 0.00 34.19 2.24
2506 2694 0.606604 AGGCTCTTTCGGCGACTTAA 59.393 50.000 10.16 0.00 34.19 1.85
2509 2697 3.118884 AGGCTCTTTCGGCGACTTAATTA 60.119 43.478 10.16 0.00 34.19 1.40
2689 2877 1.006571 GTCGACCGCTTCCTCACAA 60.007 57.895 3.51 0.00 0.00 3.33
2709 2897 4.037446 ACAACAAGTGTCATTAAACGGCAT 59.963 37.500 0.00 0.00 34.38 4.40
2889 3080 1.120530 AGATACAGGGGCGTTACTGG 58.879 55.000 7.17 0.00 39.00 4.00
2903 3094 0.318869 TACTGGCAACACGTACACCG 60.319 55.000 0.00 0.00 46.17 4.94
2945 3138 5.524281 GCTTCTGCTTAACTTCCCATAGTAC 59.476 44.000 0.00 0.00 36.03 2.73
2964 3157 1.551883 ACATTTCCAGGGCTTGAATGC 59.448 47.619 9.89 0.00 0.00 3.56
3073 3270 6.827727 AGTCCTACTGCAAGAACTTTTCTAA 58.172 36.000 0.00 0.00 39.61 2.10
3089 3286 6.968070 ACTTTTCTAAGGTATGTGCTTGAGCA 60.968 38.462 0.68 0.68 41.28 4.26
3216 3425 7.608761 TCAAATACATTCCTAAGCCTAACGTTT 59.391 33.333 5.91 0.00 0.00 3.60
3234 3443 3.807622 CGTTTGGTACATGTCTGTTCTGT 59.192 43.478 0.00 0.00 39.30 3.41
3390 3600 1.494824 GTACGCCGAACACAGTTTCT 58.505 50.000 0.00 0.00 0.00 2.52
3662 3881 1.154225 CCTTAGCGTGCAAAAGCGG 60.154 57.895 0.00 0.00 38.61 5.52
3756 3975 0.108396 TCAGTTGTTGCTGCTGCCTA 59.892 50.000 13.47 0.00 38.71 3.93
3795 4014 1.607178 CAATCAGCCCAACTGCCCA 60.607 57.895 0.00 0.00 46.76 5.36
3834 4053 6.652481 AGACATGAGTACTCCTTTGTTGAATG 59.348 38.462 20.11 14.66 0.00 2.67
3839 4058 6.704493 TGAGTACTCCTTTGTTGAATGTACAC 59.296 38.462 20.11 0.00 33.45 2.90
3998 4217 2.391389 GGCCTGAAAGAAGACGCCG 61.391 63.158 0.00 0.00 34.07 6.46
4033 4252 8.453238 AGTATAATGATCGCGAGGTAAGATAT 57.547 34.615 16.66 8.99 0.00 1.63
4096 4317 9.535270 TTTTGTTTGAATTTGTTTTTCGATCAC 57.465 25.926 0.00 0.00 0.00 3.06
4392 4654 4.319766 CGGCTACCTTCATTGATATGTTGC 60.320 45.833 7.89 7.89 33.34 4.17
4487 4749 4.934356 TGAAGTTTCAGGGCAAATCCTAT 58.066 39.130 0.00 0.00 34.92 2.57
4513 4775 8.705134 TCGTGTTACAACATTTCATTACTACTG 58.295 33.333 0.00 0.00 41.59 2.74
4514 4776 8.492748 CGTGTTACAACATTTCATTACTACTGT 58.507 33.333 0.00 0.00 41.59 3.55
4518 4780 7.591006 ACAACATTTCATTACTACTGTACCG 57.409 36.000 0.00 0.00 0.00 4.02
4602 4865 6.743575 AAGTGAAATGGATACTGCAACTAC 57.256 37.500 0.00 0.00 37.61 2.73
4628 4891 5.287752 GCACATGTCATCAGCAAAATAGTTG 59.712 40.000 0.00 0.00 0.00 3.16
4656 4919 6.848562 ACTCCCTCCAATCCATATTACTTT 57.151 37.500 0.00 0.00 0.00 2.66
4657 4920 7.226059 ACTCCCTCCAATCCATATTACTTTT 57.774 36.000 0.00 0.00 0.00 2.27
4658 4921 7.652554 ACTCCCTCCAATCCATATTACTTTTT 58.347 34.615 0.00 0.00 0.00 1.94
4678 4941 3.611025 TTTTTCAGTGGACCAATCCCT 57.389 42.857 0.00 0.00 45.59 4.20
4679 4942 4.733077 TTTTTCAGTGGACCAATCCCTA 57.267 40.909 0.00 0.00 45.59 3.53
4680 4943 4.946160 TTTTCAGTGGACCAATCCCTAT 57.054 40.909 0.00 0.00 45.59 2.57
4681 4944 4.946160 TTTCAGTGGACCAATCCCTATT 57.054 40.909 0.00 0.00 45.59 1.73
4682 4945 6.395780 TTTTCAGTGGACCAATCCCTATTA 57.604 37.500 0.00 0.00 45.59 0.98
4683 4946 5.367945 TTCAGTGGACCAATCCCTATTAC 57.632 43.478 0.00 0.00 45.59 1.89
4687 4950 4.788617 AGTGGACCAATCCCTATTACTTGT 59.211 41.667 0.00 0.00 45.59 3.16
4756 5019 4.926140 CTCCATGGAGCCCTTTATTTTC 57.074 45.455 28.45 0.00 35.31 2.29
4763 5026 6.353404 TGGAGCCCTTTATTTTCGAAAAAT 57.647 33.333 25.77 16.39 0.00 1.82
4921 5190 9.551734 TTGACTTTGAGGATGAATAGTATCATG 57.448 33.333 0.00 0.00 40.08 3.07
4924 5193 8.708378 ACTTTGAGGATGAATAGTATCATGTGA 58.292 33.333 0.00 0.00 40.08 3.58
4945 5214 6.127647 TGTGATCAAAAGCCTCATATTTGTCC 60.128 38.462 0.00 0.00 35.92 4.02
4958 5227 6.397272 TCATATTTGTCCTTTTTGCACATCC 58.603 36.000 0.00 0.00 0.00 3.51
4979 5248 6.007936 TCCCTCATTTCAACGTATTTTGTG 57.992 37.500 0.00 0.00 0.00 3.33
4981 5250 5.460646 CCTCATTTCAACGTATTTTGTGCT 58.539 37.500 0.00 0.00 0.00 4.40
4994 5264 8.536407 ACGTATTTTGTGCTAAAAATTTCACAC 58.464 29.630 9.30 7.59 39.73 3.82
5004 5274 7.166638 TGCTAAAAATTTCACACGTGTACATTG 59.833 33.333 22.90 8.95 0.00 2.82
5012 5282 3.553917 CACACGTGTACATTGTGTCTTCA 59.446 43.478 25.25 0.00 44.49 3.02
5107 5381 3.160047 CTCCATGGAGCTCGGCCT 61.160 66.667 28.45 0.00 35.31 5.19
5167 5441 7.038154 TGACAAACTTATTTCCCAAAGTGAG 57.962 36.000 0.00 0.00 36.12 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
270 277 3.250040 ACACGAACACTCTTTTACATGGC 59.750 43.478 0.00 0.00 0.00 4.40
534 552 2.974536 GCACGCGCACTAATTTGTTTTA 59.025 40.909 5.73 0.00 38.36 1.52
600 620 4.903045 TTAAATCTTGGGAGGACTTCGT 57.097 40.909 0.00 0.00 0.00 3.85
639 659 4.759693 TCGTGAAATCAGCATACCAAACTT 59.240 37.500 0.00 0.00 0.00 2.66
648 668 6.992063 ACTCTTAATTCGTGAAATCAGCAT 57.008 33.333 0.00 0.00 0.00 3.79
660 680 6.743575 ACCAAATCCAGAACTCTTAATTCG 57.256 37.500 0.00 0.00 0.00 3.34
666 686 5.635120 AGCTAAACCAAATCCAGAACTCTT 58.365 37.500 0.00 0.00 0.00 2.85
674 694 9.920946 ATATAGAAGAAAGCTAAACCAAATCCA 57.079 29.630 0.00 0.00 0.00 3.41
700 720 9.157104 GAAAAAGTCCAAAACAAACCTTGAATA 57.843 29.630 0.00 0.00 0.00 1.75
744 764 0.039764 GTTTTTGGAGGGGGAGAGGG 59.960 60.000 0.00 0.00 0.00 4.30
745 765 0.039764 GGTTTTTGGAGGGGGAGAGG 59.960 60.000 0.00 0.00 0.00 3.69
755 775 1.028905 CTTCGTGCTGGGTTTTTGGA 58.971 50.000 0.00 0.00 0.00 3.53
756 776 1.028905 TCTTCGTGCTGGGTTTTTGG 58.971 50.000 0.00 0.00 0.00 3.28
758 778 2.478879 CGTTTCTTCGTGCTGGGTTTTT 60.479 45.455 0.00 0.00 0.00 1.94
981 1001 2.434359 CTCTTCCGGTTGCGGGTC 60.434 66.667 0.00 0.00 0.00 4.46
988 1008 0.252742 ACCTCCATCCTCTTCCGGTT 60.253 55.000 0.00 0.00 0.00 4.44
1113 1133 3.122250 CTCGTCGTCGATGTCCCCC 62.122 68.421 13.91 0.00 45.21 5.40
1317 1337 1.540797 CGACCCCTAACAAAACCGACA 60.541 52.381 0.00 0.00 0.00 4.35
1323 1343 2.752075 AAACCCGACCCCTAACAAAA 57.248 45.000 0.00 0.00 0.00 2.44
1350 1370 1.480219 GCGACTAATCCGACCGCAAG 61.480 60.000 0.00 0.00 44.55 4.01
1370 1390 1.823610 ACCTCGCCTTAACTACCAGAC 59.176 52.381 0.00 0.00 0.00 3.51
1454 1485 5.469373 AGATGTATGCACAACACAATACG 57.531 39.130 5.89 0.00 38.42 3.06
1468 1499 6.846350 TCACTGCAGTATATCGAGATGTATG 58.154 40.000 21.20 0.94 0.00 2.39
1529 1564 9.189723 CACAAGTAACTAAACAACTACTCCTAC 57.810 37.037 0.00 0.00 0.00 3.18
1640 1774 9.742144 TGTAACCTGCTTCTGGTTTATTAATAA 57.258 29.630 12.23 3.71 41.70 1.40
1642 1776 7.668052 TGTGTAACCTGCTTCTGGTTTATTAAT 59.332 33.333 12.23 0.00 41.70 1.40
1785 1919 7.919091 CAGTATGTTATTACTGTGGTATCGTGT 59.081 37.037 3.94 0.00 42.63 4.49
2365 2551 6.018098 CACAGCTTCTGATATGAAATCAGGAC 60.018 42.308 13.50 5.37 44.15 3.85
2401 2589 5.474532 TCAGATAATTAAGATGCCATGCACC 59.525 40.000 0.00 0.00 43.04 5.01
2445 2633 9.716507 AACAGCGAAAACATATTGTATTATGTC 57.283 29.630 0.00 0.00 40.94 3.06
2453 2641 4.038642 ACCCAAACAGCGAAAACATATTGT 59.961 37.500 0.00 0.00 0.00 2.71
2477 2665 5.047590 TCGCCGAAAGAGCCTATTTATATCA 60.048 40.000 0.00 0.00 0.00 2.15
2481 2669 3.069729 AGTCGCCGAAAGAGCCTATTTAT 59.930 43.478 0.00 0.00 0.00 1.40
2505 2693 9.429359 CTCGATGCCTAGAAAATGTAGATAATT 57.571 33.333 0.00 0.00 0.00 1.40
2506 2694 8.037758 CCTCGATGCCTAGAAAATGTAGATAAT 58.962 37.037 0.00 0.00 0.00 1.28
2509 2697 5.540337 TCCTCGATGCCTAGAAAATGTAGAT 59.460 40.000 0.00 0.00 0.00 1.98
2689 2877 3.818210 TCATGCCGTTTAATGACACTTGT 59.182 39.130 0.00 0.00 0.00 3.16
2709 2897 2.553602 CACACCAAGTAATTGCAGCTCA 59.446 45.455 0.00 0.00 0.00 4.26
2784 2975 8.397575 TCAGATAGTCACGCTAAGAGATAAAT 57.602 34.615 0.00 0.00 32.72 1.40
2945 3138 1.829222 AGCATTCAAGCCCTGGAAATG 59.171 47.619 0.00 0.00 34.23 2.32
3178 3387 6.882140 AGGAATGTATTTGAACACAATACGGA 59.118 34.615 0.00 0.00 30.75 4.69
3181 3390 9.503427 GCTTAGGAATGTATTTGAACACAATAC 57.497 33.333 0.00 0.00 30.75 1.89
3216 3425 4.681074 TTGACAGAACAGACATGTACCA 57.319 40.909 0.00 0.00 39.29 3.25
3357 3567 2.022195 GGCGTACCTCAGTAGATGTCA 58.978 52.381 0.00 0.00 0.00 3.58
3366 3576 0.732880 CTGTGTTCGGCGTACCTCAG 60.733 60.000 14.09 16.51 0.00 3.35
3630 3849 2.092914 CGCTAAGGTTTGAAGAGGGGAT 60.093 50.000 0.00 0.00 0.00 3.85
3662 3881 3.118905 ACACAGAAACTCCAGCTTCTC 57.881 47.619 0.00 0.00 28.83 2.87
3795 4014 4.785376 ACTCATGTCTTCTTACCCAAGGAT 59.215 41.667 0.00 0.00 32.22 3.24
3864 4083 4.982295 GGTTCTGCAGAATAAACACAAACC 59.018 41.667 30.65 19.75 36.33 3.27
3866 4085 5.592282 TCAGGTTCTGCAGAATAAACACAAA 59.408 36.000 30.65 2.63 36.33 2.83
3998 4217 6.198403 TCGCGATCATTATACTTGACTTTGAC 59.802 38.462 3.71 0.00 0.00 3.18
4096 4317 1.070758 ACACACCCTCAAGCTGTACAG 59.929 52.381 18.93 18.93 0.00 2.74
4392 4654 1.270465 TGCTCCAGTCGCATATCATGG 60.270 52.381 0.00 0.00 31.40 3.66
4487 4749 8.705134 CAGTAGTAATGAAATGTTGTAACACGA 58.295 33.333 0.00 0.00 42.51 4.35
4513 4775 7.749126 GGCAATATATTCTGCATAAAACGGTAC 59.251 37.037 10.73 0.00 40.46 3.34
4514 4776 7.663905 AGGCAATATATTCTGCATAAAACGGTA 59.336 33.333 10.73 0.00 40.46 4.02
4516 4778 6.913170 AGGCAATATATTCTGCATAAAACGG 58.087 36.000 10.73 0.00 40.46 4.44
4517 4779 7.747799 CAGAGGCAATATATTCTGCATAAAACG 59.252 37.037 10.73 0.00 40.46 3.60
4518 4780 8.786898 TCAGAGGCAATATATTCTGCATAAAAC 58.213 33.333 10.73 0.00 40.46 2.43
4602 4865 3.291809 TTTTGCTGATGACATGTGCAG 57.708 42.857 1.15 9.28 35.02 4.41
4628 4891 6.380079 AATATGGATTGGAGGGAGTACATC 57.620 41.667 0.00 0.00 0.00 3.06
4667 4930 4.338400 GCAACAAGTAATAGGGATTGGTCC 59.662 45.833 0.00 0.00 44.29 4.46
4668 4931 5.193679 AGCAACAAGTAATAGGGATTGGTC 58.806 41.667 0.00 0.00 0.00 4.02
4669 4932 5.193099 AGCAACAAGTAATAGGGATTGGT 57.807 39.130 0.00 0.00 0.00 3.67
4670 4933 6.530019 AAAGCAACAAGTAATAGGGATTGG 57.470 37.500 0.00 0.00 0.00 3.16
4671 4934 8.281212 ACTAAAGCAACAAGTAATAGGGATTG 57.719 34.615 0.00 0.00 0.00 2.67
4672 4935 9.392259 GTACTAAAGCAACAAGTAATAGGGATT 57.608 33.333 0.00 0.00 0.00 3.01
4673 4936 8.545472 TGTACTAAAGCAACAAGTAATAGGGAT 58.455 33.333 0.00 0.00 0.00 3.85
4674 4937 7.909518 TGTACTAAAGCAACAAGTAATAGGGA 58.090 34.615 0.00 0.00 0.00 4.20
4675 4938 8.448615 GTTGTACTAAAGCAACAAGTAATAGGG 58.551 37.037 0.00 0.00 43.03 3.53
4676 4939 9.216117 AGTTGTACTAAAGCAACAAGTAATAGG 57.784 33.333 9.58 0.00 45.16 2.57
4679 4942 9.116067 TGAAGTTGTACTAAAGCAACAAGTAAT 57.884 29.630 9.58 0.00 45.16 1.89
4680 4943 8.495361 TGAAGTTGTACTAAAGCAACAAGTAA 57.505 30.769 9.58 0.00 45.16 2.24
4681 4944 7.767198 ACTGAAGTTGTACTAAAGCAACAAGTA 59.233 33.333 9.58 0.00 45.16 2.24
4682 4945 6.598064 ACTGAAGTTGTACTAAAGCAACAAGT 59.402 34.615 9.58 7.18 45.16 3.16
4683 4946 7.016361 ACTGAAGTTGTACTAAAGCAACAAG 57.984 36.000 9.58 6.68 45.16 3.16
4687 4950 7.502696 TCCTTACTGAAGTTGTACTAAAGCAA 58.497 34.615 0.00 0.00 0.00 3.91
4832 5097 9.906660 TTTCATCCTGAATTTTTACACACATAC 57.093 29.630 0.00 0.00 36.11 2.39
4861 5126 1.955778 TGCACAGGTCACATTTCAAGG 59.044 47.619 0.00 0.00 0.00 3.61
4862 5127 3.713858 TTGCACAGGTCACATTTCAAG 57.286 42.857 0.00 0.00 0.00 3.02
4921 5190 6.096001 AGGACAAATATGAGGCTTTTGATCAC 59.904 38.462 14.52 3.92 35.03 3.06
4924 5193 7.486407 AAAGGACAAATATGAGGCTTTTGAT 57.514 32.000 14.52 1.66 35.03 2.57
4945 5214 4.885413 TGAAATGAGGGATGTGCAAAAAG 58.115 39.130 0.00 0.00 0.00 2.27
4958 5227 5.460646 AGCACAAAATACGTTGAAATGAGG 58.539 37.500 0.00 0.00 32.59 3.86
4979 5248 7.166804 ACAATGTACACGTGTGAAATTTTTAGC 59.833 33.333 30.83 6.79 0.00 3.09
4981 5250 7.968956 ACACAATGTACACGTGTGAAATTTTTA 59.031 29.630 32.74 4.53 42.10 1.52
4994 5264 8.694394 CATATAGATGAAGACACAATGTACACG 58.306 37.037 0.00 0.00 34.73 4.49
5065 5339 6.427853 GGCCTCTAACAGCATTTTTCAAATTT 59.572 34.615 0.00 0.00 0.00 1.82
5081 5355 0.107643 GCTCCATGGAGGCCTCTAAC 59.892 60.000 36.92 17.91 42.19 2.34
5084 5358 1.765657 GAGCTCCATGGAGGCCTCT 60.766 63.158 36.92 26.79 42.19 3.69
5113 5387 1.607148 GCTTACTGGACAAAAACGCCT 59.393 47.619 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.