Multiple sequence alignment - TraesCS7D01G013300

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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 TraesCS7D01G013300 chr7D 100.000 4616 0 0 1 4616 5637799 5633184 0.000000e+00 8525.0
1 TraesCS7D01G013300 chr7D 84.085 3726 493 59 6 3687 5448826 5445157 0.000000e+00 3504.0
2 TraesCS7D01G013300 chr7D 72.973 666 104 41 3755 4352 5523245 5522588 3.700000e-36 163.0
3 TraesCS7D01G013300 chr7D 90.141 71 5 1 4389 4459 5804796 5804728 1.770000e-14 91.6
4 TraesCS7D01G013300 chr7D 93.548 62 3 1 4298 4358 5804926 5804865 1.770000e-14 91.6
5 TraesCS7D01G013300 chr4A 90.080 4627 374 44 1 4565 735776695 735781298 0.000000e+00 5923.0
6 TraesCS7D01G013300 chr4A 90.737 3703 312 15 1 3696 735367639 735363961 0.000000e+00 4909.0
7 TraesCS7D01G013300 chr4A 85.544 3701 482 33 1 3685 735316601 735320264 0.000000e+00 3821.0
8 TraesCS7D01G013300 chr4A 94.047 2486 140 6 2 2485 734997039 734999518 0.000000e+00 3764.0
9 TraesCS7D01G013300 chr4A 85.171 3709 496 40 1 3687 735562419 735558743 0.000000e+00 3753.0
10 TraesCS7D01G013300 chr4A 83.288 4051 566 65 4 3996 736470405 736466408 0.000000e+00 3627.0
11 TraesCS7D01G013300 chr4A 82.834 4136 620 56 1 4097 734385469 734389553 0.000000e+00 3622.0
12 TraesCS7D01G013300 chr4A 84.431 3719 517 39 1 3701 736413009 736409335 0.000000e+00 3603.0
13 TraesCS7D01G013300 chr4A 84.499 3716 500 45 1 3698 736756615 736760272 0.000000e+00 3602.0
14 TraesCS7D01G013300 chr4A 84.179 3704 504 49 1 3680 736147577 736151222 0.000000e+00 3518.0
15 TraesCS7D01G013300 chr4A 83.949 3545 518 37 158 3688 735689506 735693013 0.000000e+00 3347.0
16 TraesCS7D01G013300 chr4A 85.502 2359 313 21 1 2349 736056220 736058559 0.000000e+00 2435.0
17 TraesCS7D01G013300 chr4A 85.176 2361 317 20 1 2346 735767399 735769741 0.000000e+00 2390.0
18 TraesCS7D01G013300 chr4A 86.619 1958 230 24 1 1949 734480431 734482365 0.000000e+00 2135.0
19 TraesCS7D01G013300 chr4A 86.686 1735 195 21 1 1723 735487662 735485952 0.000000e+00 1892.0
20 TraesCS7D01G013300 chr4A 86.493 1725 210 11 1 1721 734917741 734919446 0.000000e+00 1873.0
21 TraesCS7D01G013300 chr4A 86.169 723 49 19 3684 4358 735000842 735001561 0.000000e+00 734.0
22 TraesCS7D01G013300 chr4A 86.792 265 10 7 4352 4616 735001683 735001922 5.880000e-69 272.0
23 TraesCS7D01G013300 chr4A 75.869 518 74 35 3877 4354 736907747 736908253 2.800000e-52 217.0
24 TraesCS7D01G013300 chr4A 75.432 521 74 40 3877 4354 735836163 735836672 2.180000e-48 204.0
25 TraesCS7D01G013300 chr4A 75.000 464 68 34 3931 4354 734389592 734390047 2.210000e-38 171.0
26 TraesCS7D01G013300 chr4A 88.372 86 5 4 4279 4362 734449548 734449630 1.060000e-16 99.0
27 TraesCS7D01G013300 chr4A 88.372 86 5 4 4279 4362 736255532 736255450 1.060000e-16 99.0
28 TraesCS7D01G013300 chr4A 90.667 75 4 3 4279 4352 734851313 734851385 3.800000e-16 97.1
29 TraesCS7D01G013300 chr4A 93.478 46 3 0 3684 3729 735363867 735363822 8.290000e-08 69.4
30 TraesCS7D01G013300 chr4A 90.909 44 4 0 4312 4355 735482251 735482208 4.990000e-05 60.2
31 TraesCS7D01G013300 chr4A 87.500 48 5 1 4534 4581 736728473 736728519 2.000000e-03 54.7
32 TraesCS7D01G013300 chr7A 84.209 4053 533 59 1 3996 6928369 6924367 0.000000e+00 3840.0
33 TraesCS7D01G013300 chr7A 89.448 417 25 9 4193 4608 6968580 6968182 4.120000e-140 508.0
34 TraesCS7D01G013300 chr7A 94.040 151 5 4 3987 4137 6968728 6968582 4.650000e-55 226.0
35 TraesCS7D01G013300 chr7A 86.250 80 8 2 4279 4357 6923795 6923718 2.960000e-12 84.2


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 TraesCS7D01G013300 chr7D 5633184 5637799 4615 True 8525.0 8525 100.000000 1 4616 1 chr7D.!!$R3 4615
1 TraesCS7D01G013300 chr7D 5445157 5448826 3669 True 3504.0 3504 84.085000 6 3687 1 chr7D.!!$R1 3681
2 TraesCS7D01G013300 chr4A 735776695 735781298 4603 False 5923.0 5923 90.080000 1 4565 1 chr4A.!!$F8 4564
3 TraesCS7D01G013300 chr4A 735316601 735320264 3663 False 3821.0 3821 85.544000 1 3685 1 chr4A.!!$F5 3684
4 TraesCS7D01G013300 chr4A 735558743 735562419 3676 True 3753.0 3753 85.171000 1 3687 1 chr4A.!!$R1 3686
5 TraesCS7D01G013300 chr4A 736466408 736470405 3997 True 3627.0 3627 83.288000 4 3996 1 chr4A.!!$R4 3992
6 TraesCS7D01G013300 chr4A 736409335 736413009 3674 True 3603.0 3603 84.431000 1 3701 1 chr4A.!!$R3 3700
7 TraesCS7D01G013300 chr4A 736756615 736760272 3657 False 3602.0 3602 84.499000 1 3698 1 chr4A.!!$F13 3697
8 TraesCS7D01G013300 chr4A 736147577 736151222 3645 False 3518.0 3518 84.179000 1 3680 1 chr4A.!!$F11 3679
9 TraesCS7D01G013300 chr4A 735689506 735693013 3507 False 3347.0 3347 83.949000 158 3688 1 chr4A.!!$F6 3530
10 TraesCS7D01G013300 chr4A 735363822 735367639 3817 True 2489.2 4909 92.107500 1 3729 2 chr4A.!!$R5 3728
11 TraesCS7D01G013300 chr4A 736056220 736058559 2339 False 2435.0 2435 85.502000 1 2349 1 chr4A.!!$F10 2348
12 TraesCS7D01G013300 chr4A 735767399 735769741 2342 False 2390.0 2390 85.176000 1 2346 1 chr4A.!!$F7 2345
13 TraesCS7D01G013300 chr4A 734480431 734482365 1934 False 2135.0 2135 86.619000 1 1949 1 chr4A.!!$F2 1948
14 TraesCS7D01G013300 chr4A 734385469 734390047 4578 False 1896.5 3622 78.917000 1 4354 2 chr4A.!!$F15 4353
15 TraesCS7D01G013300 chr4A 734917741 734919446 1705 False 1873.0 1873 86.493000 1 1721 1 chr4A.!!$F4 1720
16 TraesCS7D01G013300 chr4A 734997039 735001922 4883 False 1590.0 3764 89.002667 2 4616 3 chr4A.!!$F16 4614
17 TraesCS7D01G013300 chr4A 735482208 735487662 5454 True 976.1 1892 88.797500 1 4355 2 chr4A.!!$R6 4354
18 TraesCS7D01G013300 chr4A 736907747 736908253 506 False 217.0 217 75.869000 3877 4354 1 chr4A.!!$F14 477
19 TraesCS7D01G013300 chr4A 735836163 735836672 509 False 204.0 204 75.432000 3877 4354 1 chr4A.!!$F9 477
20 TraesCS7D01G013300 chr7A 6923718 6928369 4651 True 1962.1 3840 85.229500 1 4357 2 chr7A.!!$R1 4356
21 TraesCS7D01G013300 chr7A 6968182 6968728 546 True 367.0 508 91.744000 3987 4608 2 chr7A.!!$R2 621

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
823 845 0.321564 CCACGCATTCTCTGGACCAA 60.322 55.000 0.00 0.0 0.00 3.67 F
1745 1838 1.299620 GCGTGGATTGGCATCATGC 60.300 57.895 0.00 0.0 44.08 4.06 F
2832 2935 1.129998 CTTGACCGCTTGAGCATCTTG 59.870 52.381 3.65 0.0 42.21 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 1956 1.967779 TCGTTCATGTCCCTCAGTTGA 59.032 47.619 0.00 0.0 0.0 3.18 R
3519 3628 0.389166 AACTCTCCTTCAAGCGCTCG 60.389 55.000 12.06 0.0 0.0 5.03 R
3874 4164 0.674895 CAAAGAAGGAGACCGGCCAG 60.675 60.000 0.00 0.0 0.0 4.85 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
129 133 6.959361 TGAGAACAGAAAGCTAATTCAACAC 58.041 36.000 1.17 0.00 0.00 3.32
803 825 3.629398 CAGTTCTTGGCACTCTTCAAACT 59.371 43.478 0.00 0.00 0.00 2.66
823 845 0.321564 CCACGCATTCTCTGGACCAA 60.322 55.000 0.00 0.00 0.00 3.67
849 884 2.096069 CAGAAATCCACAGTTGCGTGAG 60.096 50.000 0.00 0.00 39.34 3.51
972 1007 3.978718 GCATGGAAGGATGCTCTTAAC 57.021 47.619 0.00 0.00 44.57 2.01
983 1018 7.814264 AGGATGCTCTTAACATAAAGATTGG 57.186 36.000 0.00 0.00 35.04 3.16
1029 1064 4.997395 GCTCTGTTGTGGAGTTATGAGAAA 59.003 41.667 0.00 0.00 33.73 2.52
1040 1075 9.213799 GTGGAGTTATGAGAAATTAGATCCATC 57.786 37.037 0.00 0.00 35.70 3.51
1162 1197 6.540914 AGATTCGTACAACCAAAACAAGAGAA 59.459 34.615 0.00 0.00 0.00 2.87
1163 1198 6.497785 TTCGTACAACCAAAACAAGAGAAA 57.502 33.333 0.00 0.00 0.00 2.52
1172 1207 6.218746 ACCAAAACAAGAGAAATGAAGATGC 58.781 36.000 0.00 0.00 0.00 3.91
1218 1260 6.589523 AGATGATCTCTGTTTCGTTCTTTCAG 59.410 38.462 0.00 0.00 31.12 3.02
1731 1824 2.096406 CATCTTGAACGGCGCGTG 59.904 61.111 6.90 2.96 39.99 5.34
1741 1834 4.256090 GGCGCGTGGATTGGCATC 62.256 66.667 8.43 0.00 0.00 3.91
1745 1838 1.299620 GCGTGGATTGGCATCATGC 60.300 57.895 0.00 0.00 44.08 4.06
2023 2117 5.153513 GCAAAAATAACACGAATGCAGAGA 58.846 37.500 0.00 0.00 32.80 3.10
2078 2172 3.175710 ACCGCCTCAACTTGGGGT 61.176 61.111 9.55 0.00 41.16 4.95
2106 2200 7.136289 TGTAATTGACGGTTACAAATCTTCC 57.864 36.000 0.00 0.00 38.65 3.46
2137 2231 2.162408 GGCTGGTTACTTGATGCTTCAC 59.838 50.000 1.02 0.00 0.00 3.18
2191 2285 3.663995 ATTGCACTGCATTACAAAGCA 57.336 38.095 4.10 0.00 38.76 3.91
2240 2334 6.613271 AGGAATTGCTCTTCACTTATCCTCTA 59.387 38.462 0.00 0.00 0.00 2.43
2303 2397 7.337184 GCTAGGCCTTCAAAAGTTAGAAATAGT 59.663 37.037 12.58 0.00 0.00 2.12
2486 2589 6.427242 TCATTTCTGAAGCAGCTGATGATATC 59.573 38.462 20.43 6.12 0.00 1.63
2490 2593 5.416952 TCTGAAGCAGCTGATGATATCGATA 59.583 40.000 20.43 7.75 0.00 2.92
2541 2644 5.540337 TCTTGAAAGTGCTCTAGAAGGAGAA 59.460 40.000 0.00 0.00 35.52 2.87
2611 2714 3.849911 TGTCACGAGCAAAGGATAAGAG 58.150 45.455 0.00 0.00 0.00 2.85
2671 2774 3.304928 GCCATCAGGTCTTTGTGAACTTG 60.305 47.826 0.00 0.00 40.40 3.16
2673 2776 4.580167 CCATCAGGTCTTTGTGAACTTGAA 59.420 41.667 0.00 0.00 40.40 2.69
2688 2791 4.234530 ACTTGAACTTTCTTCATGCAGC 57.765 40.909 0.00 0.00 0.00 5.25
2753 2856 7.595130 GGCTTCACTGAAAAGGTTGTTATTAAG 59.405 37.037 0.00 0.00 0.00 1.85
2832 2935 1.129998 CTTGACCGCTTGAGCATCTTG 59.870 52.381 3.65 0.00 42.21 3.02
2852 2955 1.901591 CATTGCTGGTGTCTCAGGTT 58.098 50.000 0.00 0.00 35.43 3.50
2887 2990 2.094494 CGAGCTGCTACCTCTCTTTCAA 60.094 50.000 0.15 0.00 0.00 2.69
2888 2991 3.258228 GAGCTGCTACCTCTCTTTCAAC 58.742 50.000 0.15 0.00 0.00 3.18
2890 2993 4.090090 AGCTGCTACCTCTCTTTCAACTA 58.910 43.478 0.00 0.00 0.00 2.24
2919 3022 1.853963 TGTCCTGCCCTTCTCTAGAC 58.146 55.000 0.00 0.00 0.00 2.59
2960 3063 6.715347 ATGTTTGCCATTATCCCTTAAGAC 57.285 37.500 3.36 0.00 0.00 3.01
2962 3065 3.485463 TGCCATTATCCCTTAAGACGG 57.515 47.619 3.36 0.00 0.00 4.79
2965 3068 3.650139 CCATTATCCCTTAAGACGGTCG 58.350 50.000 3.36 0.00 0.00 4.79
3015 3118 2.310779 TCTTCTGTACTGAGTGGCCT 57.689 50.000 3.32 0.00 0.00 5.19
3016 3119 2.609747 TCTTCTGTACTGAGTGGCCTT 58.390 47.619 3.32 0.00 0.00 4.35
3076 3179 2.031682 GCTTGCTTGTCTGTTGGTAGTG 60.032 50.000 0.00 0.00 0.00 2.74
3098 3201 5.637810 GTGTCACCTCTGTTAAATCATTCGA 59.362 40.000 0.00 0.00 0.00 3.71
3289 3392 2.887152 GCTGAAGGTTTCACAGTTCCAT 59.113 45.455 0.00 0.00 35.46 3.41
3301 3404 5.624159 TCACAGTTCCATCATTTCTCTGTT 58.376 37.500 0.00 0.00 33.35 3.16
3326 3429 3.967332 AAGATGCAAGGAACCATTTGG 57.033 42.857 0.00 0.00 42.17 3.28
3381 3484 3.020274 CCAGAGACTGAGATTCTCGGAA 58.980 50.000 25.80 1.09 43.75 4.30
3399 3502 3.758554 CGGAATGTCAAATGACTTCCCTT 59.241 43.478 23.76 10.13 42.59 3.95
3484 3587 4.412796 TCATCTTTACCAGATCTGCCAG 57.587 45.455 17.76 6.56 40.67 4.85
3514 3620 4.975147 TCCATCAGATAAGTGTATGGGGTT 59.025 41.667 0.00 0.00 38.11 4.11
3515 3621 5.065914 CCATCAGATAAGTGTATGGGGTTG 58.934 45.833 0.00 0.00 34.66 3.77
3516 3622 5.397899 CCATCAGATAAGTGTATGGGGTTGT 60.398 44.000 0.00 0.00 34.66 3.32
3519 3628 4.096382 CAGATAAGTGTATGGGGTTGTTGC 59.904 45.833 0.00 0.00 0.00 4.17
3601 3712 7.903431 CACATATTCGCAGGAAGTACTTTTTAC 59.097 37.037 10.02 1.31 35.19 2.01
3813 4101 1.673665 CCTCCAGCAGCAACCTGTC 60.674 63.158 0.00 0.00 41.26 3.51
3822 4110 0.767375 AGCAACCTGTCATGAGGTGT 59.233 50.000 7.37 0.00 46.29 4.16
3827 4115 2.609747 ACCTGTCATGAGGTGTAGTGT 58.390 47.619 5.86 0.00 45.20 3.55
3854 4144 2.093973 AGACCGGCTCATCTTACAGTTG 60.094 50.000 0.00 0.00 0.00 3.16
3857 4147 3.244422 ACCGGCTCATCTTACAGTTGAAA 60.244 43.478 0.00 0.00 0.00 2.69
3874 4164 7.387948 ACAGTTGAAATATGTGTCCTACTTCAC 59.612 37.037 0.00 0.00 35.43 3.18
3875 4165 7.604164 CAGTTGAAATATGTGTCCTACTTCACT 59.396 37.037 0.00 0.00 35.82 3.41
3888 4203 1.831652 CTTCACTGGCCGGTCTCCTT 61.832 60.000 16.42 0.00 0.00 3.36
3894 4209 2.041115 GGCCGGTCTCCTTCTTTGC 61.041 63.158 1.90 0.00 0.00 3.68
3895 4210 1.003233 GCCGGTCTCCTTCTTTGCT 60.003 57.895 1.90 0.00 0.00 3.91
3896 4211 1.301677 GCCGGTCTCCTTCTTTGCTG 61.302 60.000 1.90 0.00 0.00 4.41
3909 4232 1.476891 CTTTGCTGCTGATTGCCTCAT 59.523 47.619 0.00 0.00 42.00 2.90
3937 4260 1.107114 ATCTCGCACTCTACCACCTG 58.893 55.000 0.00 0.00 0.00 4.00
3939 4262 2.125512 CGCACTCTACCACCTGCC 60.126 66.667 0.00 0.00 0.00 4.85
3988 4311 5.067936 TGGTGGATTTTGTATTCGTGTTGTT 59.932 36.000 0.00 0.00 0.00 2.83
4003 4623 4.513692 CGTGTTGTTGGTTATCTTCTCCAA 59.486 41.667 0.00 0.00 38.65 3.53
4106 4732 5.998981 TGGAGTATGTCGTACATTTGGTTTT 59.001 36.000 5.04 0.00 39.88 2.43
4115 4741 5.048921 TCGTACATTTGGTTTTTGCGGATTA 60.049 36.000 0.00 0.00 0.00 1.75
4201 4865 3.245518 TGCGTGATGTATTGCAGTACT 57.754 42.857 18.79 6.08 32.73 2.73
4244 6099 0.804989 GTGCCTTGTGCCATGACTAC 59.195 55.000 0.00 0.00 40.16 2.73
4277 6140 5.667539 TGATGGAACTTTTGTTTTGGTCA 57.332 34.783 0.00 0.00 43.66 4.02
4380 6411 5.131642 ACATATATAGGCCCTGTCATCATGG 59.868 44.000 0.00 0.00 33.44 3.66
4447 6478 1.955778 TCGGTTGAGGTACGTCTGAAA 59.044 47.619 16.00 0.42 0.00 2.69
4516 6547 0.469705 ATTTGGTTCAGCAGCCACCA 60.470 50.000 4.82 4.82 38.89 4.17
4532 6563 2.419297 CCACCAGACAGTTAGAGGATGC 60.419 54.545 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 133 6.543831 CCAGGGTATCCTTCAGTTCATTTAAG 59.456 42.308 0.00 0.00 42.67 1.85
803 825 1.191489 TGGTCCAGAGAATGCGTGGA 61.191 55.000 0.00 0.00 38.07 4.02
823 845 4.037923 ACGCAACTGTGGATTTCTGATTTT 59.962 37.500 0.00 0.00 0.00 1.82
849 884 0.243095 CTGCAAAAGCTTCCAGCCTC 59.757 55.000 0.00 0.00 43.77 4.70
972 1007 7.223387 GGCTCACTTAATTTGCCAATCTTTATG 59.777 37.037 0.00 0.00 42.79 1.90
983 1018 3.696051 TCTCATGGGCTCACTTAATTTGC 59.304 43.478 0.00 0.00 0.00 3.68
1029 1064 4.283978 CACCTCTGCAGAGATGGATCTAAT 59.716 45.833 39.34 8.98 44.74 1.73
1040 1075 4.613929 GGAAGCACCTCTGCAGAG 57.386 61.111 32.84 32.84 46.97 3.35
1137 1172 6.053005 TCTCTTGTTTTGGTTGTACGAATCT 58.947 36.000 0.00 0.00 0.00 2.40
1162 1197 1.213926 GTCCCTCCCAGCATCTTCATT 59.786 52.381 0.00 0.00 0.00 2.57
1163 1198 0.842635 GTCCCTCCCAGCATCTTCAT 59.157 55.000 0.00 0.00 0.00 2.57
1172 1207 0.035630 CTTGAAGCAGTCCCTCCCAG 60.036 60.000 0.00 0.00 0.00 4.45
1218 1260 7.671495 ATGTTCCATTTTCTTACCAAATTGC 57.329 32.000 0.00 0.00 0.00 3.56
1242 1290 6.987403 TGCATAACATAGTATGTGGGAGTA 57.013 37.500 16.46 5.44 44.07 2.59
1731 1824 6.016024 TGTCTATTAAAGCATGATGCCAATCC 60.016 38.462 14.72 4.62 46.52 3.01
1741 1834 7.463469 TGTATGACGTGTCTATTAAAGCATG 57.537 36.000 0.00 0.00 0.00 4.06
1863 1956 1.967779 TCGTTCATGTCCCTCAGTTGA 59.032 47.619 0.00 0.00 0.00 3.18
2106 2200 5.192927 TCAAGTAACCAGCCAGGATATTTG 58.807 41.667 10.16 10.16 41.06 2.32
2191 2285 8.319146 CCTAAATAGTTCGGTATTGGATGGTAT 58.681 37.037 0.00 0.00 0.00 2.73
2240 2334 2.362077 GTCTTCAGGTTTGGCACATTGT 59.638 45.455 0.00 0.00 39.30 2.71
2277 2371 5.959618 TTTCTAACTTTTGAAGGCCTAGC 57.040 39.130 5.16 1.17 0.00 3.42
2486 2589 3.189285 TGTGACACATCAGCATGTATCG 58.811 45.455 3.56 0.00 39.04 2.92
2490 2593 2.786777 ACATGTGACACATCAGCATGT 58.213 42.857 18.27 10.92 44.19 3.21
2541 2644 6.015940 CCTCTTTTGCCAGTACTTCATCTTTT 60.016 38.462 0.00 0.00 0.00 2.27
2611 2714 3.144506 CCATGCTCCTTCCATATGTGAC 58.855 50.000 1.24 0.00 0.00 3.67
2658 2761 7.447374 TGAAGAAAGTTCAAGTTCACAAAGA 57.553 32.000 0.00 0.00 0.00 2.52
2671 2774 5.702865 TGTAATGCTGCATGAAGAAAGTTC 58.297 37.500 17.00 0.00 0.00 3.01
2673 2776 5.005740 TCTGTAATGCTGCATGAAGAAAGT 58.994 37.500 17.00 0.00 0.00 2.66
2832 2935 0.607489 ACCTGAGACACCAGCAATGC 60.607 55.000 0.00 0.00 32.97 3.56
2887 2990 4.910304 AGGGCAGGACATCAATCTAATAGT 59.090 41.667 0.00 0.00 0.00 2.12
2888 2991 5.495926 AGGGCAGGACATCAATCTAATAG 57.504 43.478 0.00 0.00 0.00 1.73
2890 2993 4.414846 AGAAGGGCAGGACATCAATCTAAT 59.585 41.667 0.00 0.00 0.00 1.73
2919 3022 0.957395 ATTCTGCTCCACGTGCCAAG 60.957 55.000 10.91 8.20 0.00 3.61
2960 3063 3.606777 CACACACTTGACTATAACGACCG 59.393 47.826 0.00 0.00 0.00 4.79
2962 3065 4.235360 AGCACACACTTGACTATAACGAC 58.765 43.478 0.00 0.00 0.00 4.34
2965 3068 4.994852 TGGAAGCACACACTTGACTATAAC 59.005 41.667 0.00 0.00 0.00 1.89
3076 3179 6.369065 AGTTCGAATGATTTAACAGAGGTGAC 59.631 38.462 0.00 0.00 0.00 3.67
3098 3201 4.488790 CTGGCAAGTGCTCCAGTT 57.511 55.556 2.85 0.00 43.66 3.16
3162 3265 6.424509 TGAGTTTTGGAACATCAATCAAATGC 59.575 34.615 0.00 0.00 39.30 3.56
3289 3392 7.984422 TGCATCTTAGAAAACAGAGAAATGA 57.016 32.000 0.00 0.00 0.00 2.57
3301 3404 6.295236 CCAAATGGTTCCTTGCATCTTAGAAA 60.295 38.462 0.00 0.00 0.00 2.52
3326 3429 6.710692 AATTTGCGGATTCTTCAAATGAAC 57.289 33.333 13.39 0.00 39.50 3.18
3484 3587 2.038295 CACTTATCTGATGGAGGGAGGC 59.962 54.545 0.00 0.00 0.00 4.70
3514 3620 2.606961 CCTTCAAGCGCTCGCAACA 61.607 57.895 12.06 0.00 44.88 3.33
3515 3621 2.174349 CCTTCAAGCGCTCGCAAC 59.826 61.111 12.06 0.00 44.88 4.17
3516 3622 2.029288 CTCCTTCAAGCGCTCGCAA 61.029 57.895 12.06 2.56 44.88 4.85
3519 3628 0.389166 AACTCTCCTTCAAGCGCTCG 60.389 55.000 12.06 0.00 0.00 5.03
3822 4110 3.694746 CCGGTCTGAGGCACACTA 58.305 61.111 0.00 0.00 0.00 2.74
3854 4144 5.294552 GCCAGTGAAGTAGGACACATATTTC 59.705 44.000 0.00 0.00 39.18 2.17
3857 4147 3.134804 GGCCAGTGAAGTAGGACACATAT 59.865 47.826 0.00 0.00 39.18 1.78
3874 4164 0.674895 CAAAGAAGGAGACCGGCCAG 60.675 60.000 0.00 0.00 0.00 4.85
3875 4165 1.374947 CAAAGAAGGAGACCGGCCA 59.625 57.895 0.00 0.00 0.00 5.36
3909 4232 1.371337 GAGTGCGAGATGGCAATGCA 61.371 55.000 7.79 0.00 45.93 3.96
3918 4241 1.107114 CAGGTGGTAGAGTGCGAGAT 58.893 55.000 0.00 0.00 0.00 2.75
3939 4262 1.003355 ATTGTGGCACCAGAGGACG 60.003 57.895 16.26 0.00 0.00 4.79
3988 4311 4.908601 TGAAGCTTGGAGAAGATAACCA 57.091 40.909 2.10 0.00 0.00 3.67
4106 4732 9.725019 ACAAGAGATCATAATAATAATCCGCAA 57.275 29.630 0.00 0.00 0.00 4.85
4201 4865 7.001674 ACACTGTATCAAGTATGAAACCCAAA 58.998 34.615 0.00 0.00 39.49 3.28
4244 6099 2.731572 AGTTCCATCATGCAAGGGAAG 58.268 47.619 4.80 0.00 39.91 3.46
4277 6140 0.945099 CATGCGCTGCAGATCTGAAT 59.055 50.000 27.04 6.31 43.65 2.57
4380 6411 7.639039 TCATGTTCAACACAGAAAACTGTATC 58.361 34.615 0.00 0.00 39.40 2.24
4447 6478 1.547372 CTTTTTGCCTGCCAGCACTAT 59.453 47.619 0.00 0.00 43.97 2.12
4474 6505 1.490621 GCACCAACAGTTTGTGCATC 58.509 50.000 28.94 7.50 38.53 3.91
4516 6547 6.313905 CGTTTTTATGCATCCTCTAACTGTCT 59.686 38.462 0.19 0.00 0.00 3.41
4532 6563 0.678684 AGGGGACGGCCGTTTTTATG 60.679 55.000 34.65 0.00 33.83 1.90
4580 6611 8.643324 AGATCAGAAAACCCATCTGTATACTAC 58.357 37.037 4.17 0.00 43.77 2.73
4581 6612 8.783660 AGATCAGAAAACCCATCTGTATACTA 57.216 34.615 4.17 0.00 43.77 1.82
4582 6613 7.682787 AGATCAGAAAACCCATCTGTATACT 57.317 36.000 4.17 0.00 43.77 2.12


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

AutoCloner maintained by Alex Coulton.