Multiple sequence alignment - TraesCS6A01G083800

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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 TraesCS6A01G083800 chr6A 100.000 3851 0 0 1 3851 52290239 52286389 0.000000e+00 7112
1 TraesCS6A01G083800 chr6A 94.532 3676 130 15 9 3659 52185794 52182165 0.000000e+00 5609
2 TraesCS6A01G083800 chr6A 90.705 3303 244 30 1 3255 74148277 74151564 0.000000e+00 4340
3 TraesCS6A01G083800 chr6A 94.271 192 11 0 3660 3851 606568184 606567993 1.050000e-75 294
4 TraesCS6A01G083800 chr6D 93.914 3664 163 16 22 3659 41624470 41620841 0.000000e+00 5476
5 TraesCS6A01G083800 chr6B 92.362 3705 171 31 10 3659 95553319 95556966 0.000000e+00 5171
6 TraesCS6A01G083800 chr6B 92.564 511 27 5 3152 3659 95514562 95515064 0.000000e+00 723
7 TraesCS6A01G083800 chr7D 91.415 3704 250 29 1 3659 562196617 562200297 0.000000e+00 5016
8 TraesCS6A01G083800 chr7D 90.667 3686 273 32 15 3659 524303801 524307456 0.000000e+00 4835
9 TraesCS6A01G083800 chr7D 90.027 3690 285 36 13 3659 524249071 524252720 0.000000e+00 4698
10 TraesCS6A01G083800 chr7D 91.175 3286 234 27 14 3255 524311448 524314721 0.000000e+00 4410
11 TraesCS6A01G083800 chr7D 94.241 191 11 0 3658 3848 32737162 32737352 3.760000e-75 292
12 TraesCS6A01G083800 chr7D 94.709 189 9 1 3660 3848 474022616 474022803 3.760000e-75 292
13 TraesCS6A01G083800 chr7D 93.229 192 13 0 3660 3851 637227786 637227595 2.260000e-72 283
14 TraesCS6A01G083800 chr7D 90.476 210 20 0 3450 3659 524299956 524300165 1.050000e-70 278
15 TraesCS6A01G083800 chr7A 89.837 3690 308 25 13 3659 604249936 604253601 0.000000e+00 4674
16 TraesCS6A01G083800 chr7A 89.756 3690 313 26 12 3659 604260715 604264381 0.000000e+00 4660
17 TraesCS6A01G083800 chr7A 89.430 3699 326 28 1 3659 604255328 604259001 0.000000e+00 4604
18 TraesCS6A01G083800 chr7A 89.427 3509 297 31 193 3659 604221838 604225314 0.000000e+00 4357
19 TraesCS6A01G083800 chr7A 89.417 2060 170 20 1627 3659 604303811 604305849 0.000000e+00 2553
20 TraesCS6A01G083800 chr7A 94.271 192 10 1 3660 3851 718377089 718377279 3.760000e-75 292
21 TraesCS6A01G083800 chr7B 89.844 3397 260 43 328 3659 560501435 560504811 0.000000e+00 4283
22 TraesCS6A01G083800 chr4D 95.238 189 9 0 3660 3848 496310062 496310250 2.250000e-77 300
23 TraesCS6A01G083800 chr3D 94.709 189 10 0 3660 3848 608130634 608130822 1.050000e-75 294
24 TraesCS6A01G083800 chr2A 94.271 192 11 0 3660 3851 716151398 716151207 1.050000e-75 294
25 TraesCS6A01G083800 chrUn 94.271 192 10 1 3660 3851 324288434 324288624 3.760000e-75 292


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 TraesCS6A01G083800 chr6A 52286389 52290239 3850 True 7112.000000 7112 100.000000 1 3851 1 chr6A.!!$R2 3850
1 TraesCS6A01G083800 chr6A 52182165 52185794 3629 True 5609.000000 5609 94.532000 9 3659 1 chr6A.!!$R1 3650
2 TraesCS6A01G083800 chr6A 74148277 74151564 3287 False 4340.000000 4340 90.705000 1 3255 1 chr6A.!!$F1 3254
3 TraesCS6A01G083800 chr6D 41620841 41624470 3629 True 5476.000000 5476 93.914000 22 3659 1 chr6D.!!$R1 3637
4 TraesCS6A01G083800 chr6B 95553319 95556966 3647 False 5171.000000 5171 92.362000 10 3659 1 chr6B.!!$F2 3649
5 TraesCS6A01G083800 chr6B 95514562 95515064 502 False 723.000000 723 92.564000 3152 3659 1 chr6B.!!$F1 507
6 TraesCS6A01G083800 chr7D 562196617 562200297 3680 False 5016.000000 5016 91.415000 1 3659 1 chr7D.!!$F4 3658
7 TraesCS6A01G083800 chr7D 524249071 524252720 3649 False 4698.000000 4698 90.027000 13 3659 1 chr7D.!!$F3 3646
8 TraesCS6A01G083800 chr7D 524299956 524314721 14765 False 3174.333333 4835 90.772667 14 3659 3 chr7D.!!$F5 3645
9 TraesCS6A01G083800 chr7A 604249936 604264381 14445 False 4646.000000 4674 89.674333 1 3659 3 chr7A.!!$F4 3658
10 TraesCS6A01G083800 chr7A 604221838 604225314 3476 False 4357.000000 4357 89.427000 193 3659 1 chr7A.!!$F1 3466
11 TraesCS6A01G083800 chr7A 604303811 604305849 2038 False 2553.000000 2553 89.417000 1627 3659 1 chr7A.!!$F2 2032
12 TraesCS6A01G083800 chr7B 560501435 560504811 3376 False 4283.000000 4283 89.844000 328 3659 1 chr7B.!!$F1 3331

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
898 4872 0.399454 AGCAGCAGTCTCCACAATGT 59.601 50.0 0.0 0.0 0.0 2.71 F
1018 4995 0.322546 GATGGTCCCGCTTCCACTTT 60.323 55.0 0.0 0.0 36.5 2.66 F
1746 5759 0.179032 TTGAAGAGCGTTGGAGGCAA 60.179 50.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 5759 0.389948 GTCTCTCGCCGTTGTTCCAT 60.390 55.000 0.00 0.00 0.0 3.41 R
2247 6283 1.302192 GCCCACTCCACTGCGTTTA 60.302 57.895 0.00 0.00 0.0 2.01 R
3668 18555 0.032815 CGGGACAAATGGCCGTTTTT 59.967 50.000 20.59 14.72 47.0 1.94 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
83 3914 2.277737 CATGAGGCAGCATGGGGT 59.722 61.111 11.22 0.00 41.45 4.95
163 3994 4.056740 CGATGTAGCAGCTCATTGAATCT 58.943 43.478 0.00 0.00 0.00 2.40
177 4008 1.764723 TGAATCTCGGATGCATGGTCT 59.235 47.619 2.46 0.00 0.00 3.85
240 4078 3.596214 TCCTGGCGTCTGAAATACTTTC 58.404 45.455 0.00 0.00 40.08 2.62
264 4102 8.036273 TCGGAAAGACAATTATGGTTAGTTTC 57.964 34.615 0.00 0.00 0.00 2.78
284 4125 5.375417 TTCGGATAATACGCTCGGAAATA 57.625 39.130 0.00 0.00 30.64 1.40
823 4790 1.066454 ACACGTAAAGCAAAGTTGGCC 59.934 47.619 0.00 0.00 0.00 5.36
898 4872 0.399454 AGCAGCAGTCTCCACAATGT 59.601 50.000 0.00 0.00 0.00 2.71
1018 4995 0.322546 GATGGTCCCGCTTCCACTTT 60.323 55.000 0.00 0.00 36.50 2.66
1073 5050 2.202987 GCCCGAGATGGTGCTCAG 60.203 66.667 0.00 0.00 34.56 3.35
1191 5168 1.602237 TCCCAAGATCGCAAGGGAC 59.398 57.895 11.81 0.00 45.15 4.46
1401 5378 0.810031 AAGCTGACAACTTGACGCGT 60.810 50.000 13.85 13.85 0.00 6.01
1476 5465 2.153645 GTCAATGTCAGGCATGTCACA 58.846 47.619 0.00 0.00 37.96 3.58
1543 5544 0.683504 GTACTTCGGGGAGCCTCAGA 60.684 60.000 0.00 0.00 0.00 3.27
1746 5759 0.179032 TTGAAGAGCGTTGGAGGCAA 60.179 50.000 0.00 0.00 0.00 4.52
1764 5777 3.450507 TGGAACAACGGCGAGAGA 58.549 55.556 16.62 0.00 31.92 3.10
1960 5982 6.323203 TCATAGTCCTACAAGGTAATACGC 57.677 41.667 0.00 0.00 36.53 4.42
2247 6283 0.250166 GCGGCCATAGATAACCCGTT 60.250 55.000 2.24 0.00 40.94 4.44
2453 6489 1.427419 GTGCCGCATGTCGCAATTA 59.573 52.632 9.95 0.00 42.60 1.40
2731 6768 1.450211 CTCACCTGGACCAAACCGT 59.550 57.895 0.00 0.00 0.00 4.83
3064 12536 1.695242 TCGTCCTAGGCTTGTCCAAAA 59.305 47.619 2.96 0.00 37.29 2.44
3228 18082 4.204012 TCCGTTTGAGTTGTTTCTTCCAT 58.796 39.130 0.00 0.00 0.00 3.41
3303 18183 7.658525 TGGTTCATCAATTAAATAGTGCCAT 57.341 32.000 0.00 0.00 0.00 4.40
3304 18184 7.715657 TGGTTCATCAATTAAATAGTGCCATC 58.284 34.615 0.00 0.00 0.00 3.51
3659 18546 1.134367 AGCTCATGTTGATGTGCATGC 59.866 47.619 11.82 11.82 46.90 4.06
3660 18547 1.135228 GCTCATGTTGATGTGCATGCA 60.135 47.619 18.46 18.46 44.85 3.96
3661 18548 2.526077 CTCATGTTGATGTGCATGCAC 58.474 47.619 38.00 38.00 46.33 4.57
3662 18549 2.163613 CTCATGTTGATGTGCATGCACT 59.836 45.455 41.43 30.03 46.30 4.40
3664 18551 3.375922 TCATGTTGATGTGCATGCACTAG 59.624 43.478 41.43 24.62 46.30 2.57
3665 18552 2.781923 TGTTGATGTGCATGCACTAGT 58.218 42.857 41.43 30.02 46.30 2.57
3667 18554 3.934579 TGTTGATGTGCATGCACTAGTAG 59.065 43.478 41.43 0.00 46.30 2.57
3668 18555 4.183865 GTTGATGTGCATGCACTAGTAGA 58.816 43.478 41.43 26.29 46.30 2.59
3672 18559 5.704978 TGATGTGCATGCACTAGTAGAAAAA 59.295 36.000 41.43 23.63 46.30 1.94
3673 18560 5.356882 TGTGCATGCACTAGTAGAAAAAC 57.643 39.130 41.43 18.52 46.30 2.43
3674 18561 4.084066 TGTGCATGCACTAGTAGAAAAACG 60.084 41.667 41.43 0.00 46.30 3.60
3675 18562 3.435327 TGCATGCACTAGTAGAAAAACGG 59.565 43.478 18.46 0.00 0.00 4.44
3676 18563 3.727970 GCATGCACTAGTAGAAAAACGGC 60.728 47.826 14.21 0.00 0.00 5.68
3678 18565 2.224329 TGCACTAGTAGAAAAACGGCCA 60.224 45.455 2.24 0.00 0.00 5.36
3680 18567 3.439129 GCACTAGTAGAAAAACGGCCATT 59.561 43.478 2.24 0.00 0.00 3.16
3681 18568 4.082949 GCACTAGTAGAAAAACGGCCATTT 60.083 41.667 2.24 0.00 0.00 2.32
3683 18570 5.048991 CACTAGTAGAAAAACGGCCATTTGT 60.049 40.000 2.24 0.00 0.00 2.83
3684 18571 4.499037 AGTAGAAAAACGGCCATTTGTC 57.501 40.909 6.34 6.34 0.00 3.18
3685 18572 2.812358 AGAAAAACGGCCATTTGTCC 57.188 45.000 10.85 0.00 0.00 4.02
3686 18573 1.343142 AGAAAAACGGCCATTTGTCCC 59.657 47.619 10.85 0.00 0.00 4.46
3687 18574 0.032815 AAAAACGGCCATTTGTCCCG 59.967 50.000 2.24 0.00 46.97 5.14
3688 18575 1.811645 AAAACGGCCATTTGTCCCGG 61.812 55.000 2.24 0.00 45.93 5.73
3689 18576 2.987355 AAACGGCCATTTGTCCCGGT 62.987 55.000 2.24 2.68 45.30 5.28
3690 18577 2.675075 CGGCCATTTGTCCCGGTT 60.675 61.111 2.24 0.00 38.42 4.44
3692 18579 1.291906 GGCCATTTGTCCCGGTTTG 59.708 57.895 0.00 0.00 0.00 2.93
3693 18580 1.468506 GGCCATTTGTCCCGGTTTGT 61.469 55.000 0.00 0.00 0.00 2.83
3694 18581 1.249407 GCCATTTGTCCCGGTTTGTA 58.751 50.000 0.00 0.00 0.00 2.41
3696 18583 2.352323 GCCATTTGTCCCGGTTTGTAAG 60.352 50.000 0.00 0.00 0.00 2.34
3697 18584 2.230266 CCATTTGTCCCGGTTTGTAAGG 59.770 50.000 0.00 0.00 0.00 2.69
3698 18585 1.320507 TTTGTCCCGGTTTGTAAGGC 58.679 50.000 0.00 0.00 0.00 4.35
3699 18586 0.537828 TTGTCCCGGTTTGTAAGGCC 60.538 55.000 0.00 0.00 0.00 5.19
3700 18587 1.676635 GTCCCGGTTTGTAAGGCCC 60.677 63.158 0.00 0.00 0.00 5.80
3701 18588 2.154747 TCCCGGTTTGTAAGGCCCA 61.155 57.895 0.00 0.00 0.00 5.36
3702 18589 1.000145 CCCGGTTTGTAAGGCCCAT 60.000 57.895 0.00 0.00 0.00 4.00
3703 18590 0.613572 CCCGGTTTGTAAGGCCCATT 60.614 55.000 0.00 0.00 0.00 3.16
3704 18591 1.262417 CCGGTTTGTAAGGCCCATTT 58.738 50.000 0.00 0.00 0.00 2.32
3705 18592 1.067213 CCGGTTTGTAAGGCCCATTTG 60.067 52.381 0.00 0.00 0.00 2.32
3706 18593 1.616374 CGGTTTGTAAGGCCCATTTGT 59.384 47.619 0.00 0.00 0.00 2.83
3707 18594 2.352323 CGGTTTGTAAGGCCCATTTGTC 60.352 50.000 0.00 0.00 0.00 3.18
3708 18595 2.028476 GGTTTGTAAGGCCCATTTGTCC 60.028 50.000 0.00 0.00 0.00 4.02
3709 18596 1.931635 TTGTAAGGCCCATTTGTCCC 58.068 50.000 0.00 0.00 0.00 4.46
3710 18597 0.322997 TGTAAGGCCCATTTGTCCCG 60.323 55.000 0.00 0.00 0.00 5.14
3712 18599 1.502527 TAAGGCCCATTTGTCCCGGT 61.503 55.000 0.00 0.00 0.00 5.28
3713 18600 2.283604 GGCCCATTTGTCCCGGTT 60.284 61.111 0.00 0.00 0.00 4.44
3714 18601 2.645192 GGCCCATTTGTCCCGGTTG 61.645 63.158 0.00 0.00 0.00 3.77
3715 18602 2.645192 GCCCATTTGTCCCGGTTGG 61.645 63.158 0.00 0.00 0.00 3.77
3733 18620 0.034767 GGGAAACCGGGACTAAAGGG 60.035 60.000 6.32 0.00 43.64 3.95
3734 18621 0.694771 GGAAACCGGGACTAAAGGGT 59.305 55.000 6.32 0.00 0.00 4.34
3735 18622 1.339438 GGAAACCGGGACTAAAGGGTC 60.339 57.143 6.32 0.00 35.66 4.46
3737 18624 0.833409 AACCGGGACTAAAGGGTCGT 60.833 55.000 6.32 0.00 37.12 4.34
3738 18625 0.833409 ACCGGGACTAAAGGGTCGTT 60.833 55.000 6.32 0.00 37.12 3.85
3739 18626 1.185315 CCGGGACTAAAGGGTCGTTA 58.815 55.000 0.00 0.00 37.12 3.18
3740 18627 1.134995 CCGGGACTAAAGGGTCGTTAC 60.135 57.143 0.00 0.00 37.12 2.50
3741 18628 1.821136 CGGGACTAAAGGGTCGTTACT 59.179 52.381 0.00 0.00 37.12 2.24
3742 18629 3.016736 CGGGACTAAAGGGTCGTTACTA 58.983 50.000 0.00 0.00 37.12 1.82
3743 18630 3.443681 CGGGACTAAAGGGTCGTTACTAA 59.556 47.826 0.00 0.00 37.12 2.24
3746 18633 6.045318 GGGACTAAAGGGTCGTTACTAAATC 58.955 44.000 0.00 0.00 37.12 2.17
3747 18634 6.045318 GGACTAAAGGGTCGTTACTAAATCC 58.955 44.000 0.00 0.00 37.12 3.01
3748 18635 5.982356 ACTAAAGGGTCGTTACTAAATCCC 58.018 41.667 0.00 0.00 35.56 3.85
3749 18636 5.723405 ACTAAAGGGTCGTTACTAAATCCCT 59.277 40.000 0.00 0.00 45.96 4.20
3750 18637 6.897413 ACTAAAGGGTCGTTACTAAATCCCTA 59.103 38.462 0.00 0.00 43.62 3.53
3751 18638 6.625532 AAAGGGTCGTTACTAAATCCCTAA 57.374 37.500 0.00 0.00 43.62 2.69
3753 18640 5.982356 AGGGTCGTTACTAAATCCCTAAAC 58.018 41.667 0.00 0.00 42.75 2.01
3754 18641 5.104776 AGGGTCGTTACTAAATCCCTAAACC 60.105 44.000 0.00 0.00 42.75 3.27
3755 18642 5.104776 GGGTCGTTACTAAATCCCTAAACCT 60.105 44.000 0.00 0.00 32.89 3.50
3756 18643 6.409704 GGTCGTTACTAAATCCCTAAACCTT 58.590 40.000 0.00 0.00 0.00 3.50
3757 18644 6.881065 GGTCGTTACTAAATCCCTAAACCTTT 59.119 38.462 0.00 0.00 0.00 3.11
3760 18647 8.815912 TCGTTACTAAATCCCTAAACCTTTAGT 58.184 33.333 10.36 10.36 43.30 2.24
3761 18648 9.091784 CGTTACTAAATCCCTAAACCTTTAGTC 57.908 37.037 9.17 0.00 41.23 2.59
3762 18649 9.388506 GTTACTAAATCCCTAAACCTTTAGTCC 57.611 37.037 9.17 0.94 41.23 3.85
3764 18651 5.871324 AAATCCCTAAACCTTTAGTCCCA 57.129 39.130 4.50 0.00 38.73 4.37
3765 18652 5.452341 AATCCCTAAACCTTTAGTCCCAG 57.548 43.478 4.50 0.00 38.73 4.45
3766 18653 3.878086 TCCCTAAACCTTTAGTCCCAGT 58.122 45.455 4.50 0.00 38.73 4.00
3767 18654 4.245308 TCCCTAAACCTTTAGTCCCAGTT 58.755 43.478 4.50 0.00 38.73 3.16
3768 18655 4.287845 TCCCTAAACCTTTAGTCCCAGTTC 59.712 45.833 4.50 0.00 38.73 3.01
3769 18656 4.288887 CCCTAAACCTTTAGTCCCAGTTCT 59.711 45.833 4.50 0.00 38.73 3.01
3771 18658 6.013119 CCCTAAACCTTTAGTCCCAGTTCTTA 60.013 42.308 4.50 0.00 38.73 2.10
3772 18659 6.877855 CCTAAACCTTTAGTCCCAGTTCTTAC 59.122 42.308 4.50 0.00 38.73 2.34
3773 18660 5.899631 AACCTTTAGTCCCAGTTCTTACA 57.100 39.130 0.00 0.00 0.00 2.41
3775 18662 4.041321 ACCTTTAGTCCCAGTTCTTACACC 59.959 45.833 0.00 0.00 0.00 4.16
3776 18663 4.041198 CCTTTAGTCCCAGTTCTTACACCA 59.959 45.833 0.00 0.00 0.00 4.17
3779 18666 2.105993 AGTCCCAGTTCTTACACCAACC 59.894 50.000 0.00 0.00 0.00 3.77
3780 18667 1.071071 TCCCAGTTCTTACACCAACCG 59.929 52.381 0.00 0.00 0.00 4.44
3782 18669 1.519408 CAGTTCTTACACCAACCGGG 58.481 55.000 6.32 0.00 44.81 5.73
3783 18670 1.071071 CAGTTCTTACACCAACCGGGA 59.929 52.381 6.32 0.00 41.15 5.14
3784 18671 1.071228 AGTTCTTACACCAACCGGGAC 59.929 52.381 6.32 0.00 41.15 4.46
3785 18672 1.129917 TTCTTACACCAACCGGGACA 58.870 50.000 6.32 0.00 41.15 4.02
3786 18673 0.682852 TCTTACACCAACCGGGACAG 59.317 55.000 6.32 0.00 41.15 3.51
3787 18674 0.682852 CTTACACCAACCGGGACAGA 59.317 55.000 6.32 0.00 41.15 3.41
3788 18675 1.278127 CTTACACCAACCGGGACAGAT 59.722 52.381 6.32 0.00 41.15 2.90
3789 18676 0.611200 TACACCAACCGGGACAGATG 59.389 55.000 6.32 0.00 41.15 2.90
3791 18678 2.272146 CCAACCGGGACAGATGGG 59.728 66.667 6.32 0.00 40.01 4.00
3794 18681 4.741239 ACCGGGACAGATGGGCCT 62.741 66.667 6.32 0.00 0.00 5.19
3795 18682 3.866582 CCGGGACAGATGGGCCTC 61.867 72.222 4.53 0.00 0.00 4.70
3808 18695 3.443045 GCCTCCATGTGGCCGTTG 61.443 66.667 14.04 0.00 44.32 4.10
3809 18696 3.443045 CCTCCATGTGGCCGTTGC 61.443 66.667 0.00 0.00 34.44 4.17
3810 18697 3.803082 CTCCATGTGGCCGTTGCG 61.803 66.667 0.00 0.00 38.85 4.85
3838 18725 4.475135 GCAGGAGGGCCTTCGGTC 62.475 72.222 13.83 2.44 43.90 4.79
3849 18736 3.894547 CTTCGGTCCCGGTTGGTGG 62.895 68.421 5.80 0.00 40.25 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 3850 3.923017 AGCGGAACCATCTTTTCTTTG 57.077 42.857 0.00 0.00 0.00 2.77
33 3864 2.045242 GGGGAGGGAAAGCGGAAC 60.045 66.667 0.00 0.00 0.00 3.62
77 3908 1.458967 GTACCCCTCGCTACCCCAT 60.459 63.158 0.00 0.00 0.00 4.00
163 3994 1.264045 TGGTCAGACCATGCATCCGA 61.264 55.000 19.21 0.00 44.79 4.55
177 4008 4.393062 GCTTTCGATTTGAAGAGATGGTCA 59.607 41.667 0.00 0.00 37.99 4.02
240 4078 6.959311 CGAAACTAACCATAATTGTCTTTCCG 59.041 38.462 0.00 0.00 0.00 4.30
264 4102 6.260377 TGTATATTTCCGAGCGTATTATCCG 58.740 40.000 0.00 0.00 0.00 4.18
823 4790 3.795101 CCTTGTTATCGTTGCGTAGGTAG 59.205 47.826 0.00 0.00 0.00 3.18
1353 5330 1.675714 CGCTTGTCATGGAGCCACTTA 60.676 52.381 9.88 0.00 35.49 2.24
1401 5378 2.093869 GGCGGTGAGGTTGTAGATGTAA 60.094 50.000 0.00 0.00 0.00 2.41
1476 5465 2.359354 TTGCCGCAGTAATGCCGT 60.359 55.556 9.95 0.00 0.00 5.68
1746 5759 0.389948 GTCTCTCGCCGTTGTTCCAT 60.390 55.000 0.00 0.00 0.00 3.41
1960 5982 6.302269 AGCTATTACCTTTTCTCATGGATGG 58.698 40.000 0.00 0.00 0.00 3.51
2017 6045 4.862371 TGTTTCCCTTTTCTAACACCTGT 58.138 39.130 0.00 0.00 0.00 4.00
2247 6283 1.302192 GCCCACTCCACTGCGTTTA 60.302 57.895 0.00 0.00 0.00 2.01
2297 6333 3.365265 CTCCACCGCTTTGGCCAC 61.365 66.667 3.88 0.00 43.94 5.01
2453 6489 2.258013 CCGCAACAATGGTGTCGGT 61.258 57.895 20.42 0.00 36.80 4.69
2482 6518 2.203877 ACGTGGCTACCCTTGGGA 60.204 61.111 13.39 0.00 0.00 4.37
2731 6768 3.399181 GATGGCCGACACCCCAGA 61.399 66.667 0.00 0.00 34.01 3.86
3064 12536 2.507407 AGCCGGTATTGTTCCAATGT 57.493 45.000 1.90 0.00 0.00 2.71
3080 12553 1.532604 GGGTGGTTGTTTGGCTAGCC 61.533 60.000 27.71 27.71 0.00 3.93
3190 18044 1.283736 CGGAGTTGCCCAACGTATAC 58.716 55.000 5.59 0.00 45.50 1.47
3228 18082 3.016971 CCTGCCTGGGACATGGGA 61.017 66.667 0.00 0.00 38.20 4.37
3454 18341 3.304928 GCTTTCATTGGCCCATAATCTCG 60.305 47.826 0.00 0.00 0.00 4.04
3503 18390 1.756538 CTGGTTCCATTGGCCCATAAC 59.243 52.381 12.62 0.00 0.00 1.89
3659 18546 5.048991 ACAAATGGCCGTTTTTCTACTAGTG 60.049 40.000 20.59 8.53 0.00 2.74
3660 18547 5.067954 ACAAATGGCCGTTTTTCTACTAGT 58.932 37.500 20.59 9.79 0.00 2.57
3661 18548 5.391629 GGACAAATGGCCGTTTTTCTACTAG 60.392 44.000 27.52 14.88 30.66 2.57
3662 18549 4.456566 GGACAAATGGCCGTTTTTCTACTA 59.543 41.667 27.52 0.00 30.66 1.82
3664 18551 3.571571 GGACAAATGGCCGTTTTTCTAC 58.428 45.455 27.52 14.09 30.66 2.59
3665 18552 2.559231 GGGACAAATGGCCGTTTTTCTA 59.441 45.455 27.52 0.00 47.00 2.10
3667 18554 1.790755 GGGACAAATGGCCGTTTTTC 58.209 50.000 23.03 23.03 47.00 2.29
3668 18555 0.032815 CGGGACAAATGGCCGTTTTT 59.967 50.000 20.59 14.72 47.00 1.94
3672 18559 2.987355 AAACCGGGACAAATGGCCGT 62.987 55.000 6.32 0.00 47.00 5.68
3673 18560 2.272447 AAACCGGGACAAATGGCCG 61.272 57.895 6.32 0.00 47.00 6.13
3674 18561 1.291906 CAAACCGGGACAAATGGCC 59.708 57.895 6.32 0.00 44.61 5.36
3675 18562 1.249407 TACAAACCGGGACAAATGGC 58.751 50.000 6.32 0.00 0.00 4.40
3676 18563 2.230266 CCTTACAAACCGGGACAAATGG 59.770 50.000 6.32 0.00 0.00 3.16
3678 18565 1.890489 GCCTTACAAACCGGGACAAAT 59.110 47.619 6.32 0.00 0.00 2.32
3680 18567 0.537828 GGCCTTACAAACCGGGACAA 60.538 55.000 6.32 0.00 0.00 3.18
3681 18568 1.073548 GGCCTTACAAACCGGGACA 59.926 57.895 6.32 0.00 0.00 4.02
3683 18570 1.502527 ATGGGCCTTACAAACCGGGA 61.503 55.000 6.32 0.00 0.00 5.14
3684 18571 0.613572 AATGGGCCTTACAAACCGGG 60.614 55.000 6.32 0.00 0.00 5.73
3685 18572 1.067213 CAAATGGGCCTTACAAACCGG 60.067 52.381 4.53 0.00 0.00 5.28
3686 18573 1.616374 ACAAATGGGCCTTACAAACCG 59.384 47.619 4.53 0.00 0.00 4.44
3687 18574 2.028476 GGACAAATGGGCCTTACAAACC 60.028 50.000 4.53 0.00 0.00 3.27
3688 18575 2.028476 GGGACAAATGGGCCTTACAAAC 60.028 50.000 4.53 0.00 0.00 2.93
3689 18576 2.252714 GGGACAAATGGGCCTTACAAA 58.747 47.619 4.53 0.00 0.00 2.83
3690 18577 1.888826 CGGGACAAATGGGCCTTACAA 60.889 52.381 4.53 0.00 0.00 2.41
3692 18579 1.035385 CCGGGACAAATGGGCCTTAC 61.035 60.000 4.53 0.00 0.00 2.34
3693 18580 1.304952 CCGGGACAAATGGGCCTTA 59.695 57.895 4.53 0.00 0.00 2.69
3694 18581 2.037208 CCGGGACAAATGGGCCTT 59.963 61.111 4.53 0.00 0.00 4.35
3696 18583 2.283604 AACCGGGACAAATGGGCC 60.284 61.111 6.32 0.00 0.00 5.80
3697 18584 2.645192 CCAACCGGGACAAATGGGC 61.645 63.158 6.32 0.00 40.01 5.36
3698 18585 3.693411 CCAACCGGGACAAATGGG 58.307 61.111 6.32 0.00 40.01 4.00
3712 18599 1.074244 CCTTTAGTCCCGGTTTCCCAA 59.926 52.381 0.00 0.00 0.00 4.12
3713 18600 0.694196 CCTTTAGTCCCGGTTTCCCA 59.306 55.000 0.00 0.00 0.00 4.37
3714 18601 0.034767 CCCTTTAGTCCCGGTTTCCC 60.035 60.000 0.00 0.00 0.00 3.97
3715 18602 0.694771 ACCCTTTAGTCCCGGTTTCC 59.305 55.000 0.00 0.00 0.00 3.13
3717 18604 0.322648 CGACCCTTTAGTCCCGGTTT 59.677 55.000 0.00 0.00 32.91 3.27
3719 18606 0.833409 AACGACCCTTTAGTCCCGGT 60.833 55.000 0.00 0.00 32.91 5.28
3720 18607 1.134995 GTAACGACCCTTTAGTCCCGG 60.135 57.143 0.00 0.00 32.91 5.73
3721 18608 1.821136 AGTAACGACCCTTTAGTCCCG 59.179 52.381 0.00 0.00 32.91 5.14
3725 18612 5.723405 AGGGATTTAGTAACGACCCTTTAGT 59.277 40.000 12.37 0.00 44.27 2.24
3726 18613 6.231258 AGGGATTTAGTAACGACCCTTTAG 57.769 41.667 12.37 0.00 44.27 1.85
3727 18614 7.732222 TTAGGGATTTAGTAACGACCCTTTA 57.268 36.000 19.37 10.18 44.27 1.85
3728 18615 6.625532 TTAGGGATTTAGTAACGACCCTTT 57.374 37.500 19.37 5.96 44.27 3.11
3729 18616 6.409704 GTTTAGGGATTTAGTAACGACCCTT 58.590 40.000 19.37 9.15 44.27 3.95
3731 18618 5.104776 AGGTTTAGGGATTTAGTAACGACCC 60.105 44.000 9.11 9.11 37.79 4.46
3733 18620 7.912056 AAAGGTTTAGGGATTTAGTAACGAC 57.088 36.000 0.00 0.00 0.00 4.34
3734 18621 8.815912 ACTAAAGGTTTAGGGATTTAGTAACGA 58.184 33.333 12.90 0.00 43.24 3.85
3735 18622 9.091784 GACTAAAGGTTTAGGGATTTAGTAACG 57.908 37.037 12.90 0.00 44.39 3.18
3737 18624 8.551440 GGGACTAAAGGTTTAGGGATTTAGTAA 58.449 37.037 12.90 0.00 44.39 2.24
3738 18625 7.683754 TGGGACTAAAGGTTTAGGGATTTAGTA 59.316 37.037 12.90 0.00 44.39 1.82
3739 18626 6.506413 TGGGACTAAAGGTTTAGGGATTTAGT 59.494 38.462 12.90 8.49 46.05 2.24
3740 18627 6.965607 TGGGACTAAAGGTTTAGGGATTTAG 58.034 40.000 12.90 0.00 43.38 1.85
3741 18628 6.506413 ACTGGGACTAAAGGTTTAGGGATTTA 59.494 38.462 12.90 0.00 43.38 1.40
3742 18629 5.315109 ACTGGGACTAAAGGTTTAGGGATTT 59.685 40.000 12.90 0.00 43.38 2.17
3743 18630 4.856182 ACTGGGACTAAAGGTTTAGGGATT 59.144 41.667 12.90 0.00 43.38 3.01
3746 18633 4.288887 AGAACTGGGACTAAAGGTTTAGGG 59.711 45.833 12.90 2.46 43.38 3.53
3747 18634 5.500546 AGAACTGGGACTAAAGGTTTAGG 57.499 43.478 12.90 0.00 43.38 2.69
3748 18635 7.387122 GTGTAAGAACTGGGACTAAAGGTTTAG 59.613 40.741 7.77 7.77 44.37 1.85
3749 18636 7.219322 GTGTAAGAACTGGGACTAAAGGTTTA 58.781 38.462 0.00 0.00 0.00 2.01
3750 18637 6.060136 GTGTAAGAACTGGGACTAAAGGTTT 58.940 40.000 0.00 0.00 0.00 3.27
3751 18638 5.455755 GGTGTAAGAACTGGGACTAAAGGTT 60.456 44.000 0.00 0.00 0.00 3.50
3753 18640 4.041198 TGGTGTAAGAACTGGGACTAAAGG 59.959 45.833 0.00 0.00 0.00 3.11
3754 18641 5.223449 TGGTGTAAGAACTGGGACTAAAG 57.777 43.478 0.00 0.00 0.00 1.85
3755 18642 5.370679 GTTGGTGTAAGAACTGGGACTAAA 58.629 41.667 0.00 0.00 0.00 1.85
3756 18643 4.202388 GGTTGGTGTAAGAACTGGGACTAA 60.202 45.833 0.00 0.00 0.00 2.24
3757 18644 3.325716 GGTTGGTGTAAGAACTGGGACTA 59.674 47.826 0.00 0.00 0.00 2.59
3760 18647 1.071071 CGGTTGGTGTAAGAACTGGGA 59.929 52.381 0.00 0.00 0.00 4.37
3761 18648 1.519408 CGGTTGGTGTAAGAACTGGG 58.481 55.000 0.00 0.00 0.00 4.45
3762 18649 1.519408 CCGGTTGGTGTAAGAACTGG 58.481 55.000 0.00 0.00 41.18 4.00
3764 18651 1.071228 GTCCCGGTTGGTGTAAGAACT 59.929 52.381 0.00 0.00 34.77 3.01
3765 18652 1.202675 TGTCCCGGTTGGTGTAAGAAC 60.203 52.381 0.00 0.00 34.77 3.01
3766 18653 1.071071 CTGTCCCGGTTGGTGTAAGAA 59.929 52.381 0.00 0.00 34.77 2.52
3767 18654 0.682852 CTGTCCCGGTTGGTGTAAGA 59.317 55.000 0.00 0.00 34.77 2.10
3768 18655 0.682852 TCTGTCCCGGTTGGTGTAAG 59.317 55.000 0.00 0.00 34.77 2.34
3769 18656 1.002659 CATCTGTCCCGGTTGGTGTAA 59.997 52.381 0.00 0.00 34.77 2.41
3771 18658 1.374947 CATCTGTCCCGGTTGGTGT 59.625 57.895 0.00 0.00 34.77 4.16
3772 18659 1.377202 CCATCTGTCCCGGTTGGTG 60.377 63.158 0.00 0.00 34.77 4.17
3773 18660 2.602676 CCCATCTGTCCCGGTTGGT 61.603 63.158 0.00 0.00 34.77 3.67
3775 18662 2.438434 GCCCATCTGTCCCGGTTG 60.438 66.667 0.00 0.00 0.00 3.77
3776 18663 3.728373 GGCCCATCTGTCCCGGTT 61.728 66.667 0.00 0.00 0.00 4.44
3779 18666 3.866582 GGAGGCCCATCTGTCCCG 61.867 72.222 0.00 0.00 0.00 5.14
3780 18667 2.692368 TGGAGGCCCATCTGTCCC 60.692 66.667 0.00 0.00 37.58 4.46
3831 18718 2.358247 CACCAACCGGGACCGAAG 60.358 66.667 13.13 0.00 42.83 3.79
3832 18719 3.943691 CCACCAACCGGGACCGAA 61.944 66.667 13.13 0.00 42.83 4.30


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

AutoCloner maintained by Alex Coulton.