Multiple sequence alignment - TraesCS6D01G365200

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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 TraesCS6D01G365200 chr6D 100.000 2906 0 0 965 3870 454633515 454636420 0.000000e+00 5367.0
1 TraesCS6D01G365200 chr6D 100.000 408 0 0 1 408 454632551 454632958 0.000000e+00 754.0
2 TraesCS6D01G365200 chr6A 92.286 2437 101 37 1026 3417 600816163 600818557 0.000000e+00 3378.0
3 TraesCS6D01G365200 chr6A 86.905 84 5 3 322 405 600815501 600815578 5.330000e-14 89.8
4 TraesCS6D01G365200 chr6A 85.294 68 6 4 3741 3808 600818774 600818837 2.500000e-07 67.6
5 TraesCS6D01G365200 chr6B 93.573 2116 66 30 967 3039 691136555 691138643 0.000000e+00 3090.0
6 TraesCS6D01G365200 chr6B 87.928 671 40 16 2935 3600 691138670 691139304 0.000000e+00 752.0
7 TraesCS6D01G365200 chr6B 86.738 558 43 14 3034 3583 691266062 691266596 3.330000e-165 592.0
8 TraesCS6D01G365200 chr6B 91.860 344 15 7 2704 3039 691265624 691265962 5.850000e-128 468.0
9 TraesCS6D01G365200 chr6B 86.387 191 11 10 96 286 691135886 691136061 1.100000e-45 195.0
10 TraesCS6D01G365200 chr4B 88.934 976 53 23 2733 3682 18656360 18657306 0.000000e+00 1153.0
11 TraesCS6D01G365200 chr4B 92.535 643 32 6 2000 2630 18655732 18656370 0.000000e+00 907.0
12 TraesCS6D01G365200 chr4B 90.205 633 51 6 2935 3561 128090250 128090877 0.000000e+00 815.0
13 TraesCS6D01G365200 chr4B 85.152 559 36 16 1160 1717 18655229 18655741 2.650000e-146 529.0
14 TraesCS6D01G365200 chr3B 90.179 336 22 9 2707 3039 313799496 313799823 9.940000e-116 427.0
15 TraesCS6D01G365200 chr4A 87.805 164 15 5 2876 3039 721670780 721670622 1.840000e-43 187.0
16 TraesCS6D01G365200 chr4A 83.756 197 13 9 2935 3130 721670595 721670417 6.650000e-38 169.0


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 TraesCS6D01G365200 chr6D 454632551 454636420 3869 False 3060.500000 5367 100.000000 1 3870 2 chr6D.!!$F1 3869
1 TraesCS6D01G365200 chr6A 600815501 600818837 3336 False 1178.466667 3378 88.161667 322 3808 3 chr6A.!!$F1 3486
2 TraesCS6D01G365200 chr6B 691135886 691139304 3418 False 1345.666667 3090 89.296000 96 3600 3 chr6B.!!$F1 3504
3 TraesCS6D01G365200 chr6B 691265624 691266596 972 False 530.000000 592 89.299000 2704 3583 2 chr6B.!!$F2 879
4 TraesCS6D01G365200 chr4B 18655229 18657306 2077 False 863.000000 1153 88.873667 1160 3682 3 chr4B.!!$F2 2522
5 TraesCS6D01G365200 chr4B 128090250 128090877 627 False 815.000000 815 90.205000 2935 3561 1 chr4B.!!$F1 626

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
78 79 0.183971 TTTTGCAACCCTTCGGAGGA 59.816 50.0 12.85 0.00 46.74 3.71 F
80 81 0.183971 TTGCAACCCTTCGGAGGAAA 59.816 50.0 12.85 0.00 46.74 3.13 F
1843 2275 0.383949 ACAACAACAACGCCATGGTC 59.616 50.0 14.67 4.79 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 2215 0.768622 TGGGGTGTCGGTCTTCATTT 59.231 50.000 0.0 0.00 0.00 2.32 R
2098 2533 3.832490 ACTTGGTGACATAGTACTCTGCA 59.168 43.478 8.1 5.04 42.32 4.41 R
3844 4631 0.033228 GAGCAGTGGAGATCGGGATG 59.967 60.000 0.0 0.00 0.00 3.51 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
23 24 2.232750 ATGAGAAGCATCGCATCGC 58.767 52.632 2.11 0.00 41.54 4.58
64 65 3.812577 GGTACACCCAGCATTTTGC 57.187 52.632 0.00 0.00 45.46 3.68
74 75 2.826277 GCATTTTGCAACCCTTCGG 58.174 52.632 0.00 0.00 44.26 4.30
75 76 0.316841 GCATTTTGCAACCCTTCGGA 59.683 50.000 0.00 0.00 44.26 4.55
76 77 1.669795 GCATTTTGCAACCCTTCGGAG 60.670 52.381 0.00 0.00 44.26 4.63
77 78 1.067635 CATTTTGCAACCCTTCGGAGG 60.068 52.381 1.30 1.30 43.15 4.30
78 79 0.183971 TTTTGCAACCCTTCGGAGGA 59.816 50.000 12.85 0.00 46.74 3.71
79 80 0.183971 TTTGCAACCCTTCGGAGGAA 59.816 50.000 12.85 0.00 46.74 3.36
80 81 0.183971 TTGCAACCCTTCGGAGGAAA 59.816 50.000 12.85 0.00 46.74 3.13
81 82 0.183971 TGCAACCCTTCGGAGGAAAA 59.816 50.000 12.85 0.00 46.74 2.29
82 83 1.324383 GCAACCCTTCGGAGGAAAAA 58.676 50.000 12.85 0.00 46.74 1.94
110 111 9.754382 AGACTATACAGAAAGAAAACGTACAAA 57.246 29.630 0.00 0.00 0.00 2.83
133 134 1.021968 ACCGAAAAGCAGCGAAAAGT 58.978 45.000 0.00 0.00 0.00 2.66
137 138 0.594796 AAAAGCAGCGAAAAGTGGCG 60.595 50.000 0.00 0.00 32.92 5.69
139 140 3.660111 GCAGCGAAAAGTGGCGGT 61.660 61.111 0.00 0.00 38.96 5.68
168 169 3.673484 GGCACCAGCACACGCATT 61.673 61.111 0.00 0.00 44.61 3.56
251 252 4.794439 CACGCATCTCCCGACGCA 62.794 66.667 0.00 0.00 0.00 5.24
252 253 4.063967 ACGCATCTCCCGACGCAA 62.064 61.111 0.00 0.00 0.00 4.85
253 254 3.554692 CGCATCTCCCGACGCAAC 61.555 66.667 0.00 0.00 0.00 4.17
257 258 3.989698 ATCTCCCGACGCAACGCAG 62.990 63.158 0.00 0.00 0.00 5.18
281 282 4.366684 CCACAGCCCAACTCCCCC 62.367 72.222 0.00 0.00 0.00 5.40
333 345 1.452108 CCCGCTTCCAGAATCCCAC 60.452 63.158 0.00 0.00 0.00 4.61
334 346 1.452108 CCGCTTCCAGAATCCCACC 60.452 63.158 0.00 0.00 0.00 4.61
370 382 2.611172 TAATCCCACCCGCACCCA 60.611 61.111 0.00 0.00 0.00 4.51
388 400 1.508632 CACCCGCATCCCTTATAACG 58.491 55.000 0.00 0.00 0.00 3.18
394 406 1.610886 GCATCCCTTATAACGCCTCCC 60.611 57.143 0.00 0.00 0.00 4.30
396 408 0.765519 TCCCTTATAACGCCTCCCCC 60.766 60.000 0.00 0.00 0.00 5.40
397 409 1.370064 CCTTATAACGCCTCCCCCG 59.630 63.158 0.00 0.00 0.00 5.73
398 410 1.301479 CTTATAACGCCTCCCCCGC 60.301 63.158 0.00 0.00 0.00 6.13
1789 2215 2.582436 GTCGAGATCCCGCCCAAA 59.418 61.111 0.00 0.00 0.00 3.28
1843 2275 0.383949 ACAACAACAACGCCATGGTC 59.616 50.000 14.67 4.79 0.00 4.02
2485 2930 3.390521 ATGTCGGCTTCCTCGGCA 61.391 61.111 0.00 0.00 46.29 5.69
2635 3081 1.125566 GTTCGTTCGTTCGTTGGATCC 59.874 52.381 4.20 4.20 0.00 3.36
3085 3790 1.747924 TGGAAGCTCTCGTCTGATGAG 59.252 52.381 18.70 18.70 32.57 2.90
3092 3797 0.529833 CTCGTCTGATGAGGCACAGT 59.470 55.000 17.33 0.00 35.84 3.55
3093 3798 0.244721 TCGTCTGATGAGGCACAGTG 59.755 55.000 0.00 0.00 35.84 3.66
3094 3799 0.244721 CGTCTGATGAGGCACAGTGA 59.755 55.000 4.15 0.00 35.84 3.41
3095 3800 1.735038 CGTCTGATGAGGCACAGTGAG 60.735 57.143 4.15 0.00 35.84 3.51
3146 3867 4.717877 AGGCTGCTGCATTTATGTATGTA 58.282 39.130 17.89 0.00 41.91 2.29
3166 3887 1.593196 TATGAGCAGCCGTAAATGCC 58.407 50.000 0.00 0.00 43.60 4.40
3215 3936 7.708322 CACGGGAGATAACCATGATTATCTATG 59.292 40.741 20.35 15.16 47.00 2.23
3216 3937 6.703607 CGGGAGATAACCATGATTATCTATGC 59.296 42.308 20.35 9.72 47.00 3.14
3233 3958 2.328099 GCCGGCTGTGGTTTCTGAG 61.328 63.158 22.15 0.00 0.00 3.35
3377 4117 2.026356 TGCTAGCTTTGGGCAGTGATTA 60.026 45.455 17.23 0.00 44.79 1.75
3379 4119 3.004106 GCTAGCTTTGGGCAGTGATTATG 59.996 47.826 7.70 0.00 44.79 1.90
3407 4151 3.521126 ACTTGGTGGAGAGCATATGAAGT 59.479 43.478 6.97 0.92 0.00 3.01
3423 4167 2.356793 GTGAGCAGAGCACGCTGT 60.357 61.111 0.00 0.00 40.63 4.40
3507 4253 0.931702 TGACCGTGCGTGTTAACTTG 59.068 50.000 7.22 0.24 0.00 3.16
3600 4349 2.372504 AGGCCTGATCTTCCTGATGATG 59.627 50.000 3.11 0.00 35.14 3.07
3603 4352 3.403968 CCTGATCTTCCTGATGATGCTG 58.596 50.000 0.00 0.00 35.14 4.41
3604 4353 3.181453 CCTGATCTTCCTGATGATGCTGT 60.181 47.826 0.00 0.00 35.14 4.40
3605 4354 4.040095 CCTGATCTTCCTGATGATGCTGTA 59.960 45.833 0.00 0.00 35.14 2.74
3606 4355 5.280062 CCTGATCTTCCTGATGATGCTGTAT 60.280 44.000 0.00 0.00 35.14 2.29
3657 4442 5.694006 CAGTCTTTGTCTCTCTGAAACGAAT 59.306 40.000 0.00 0.00 0.00 3.34
3659 4444 6.422400 AGTCTTTGTCTCTCTGAAACGAATTC 59.578 38.462 0.00 0.00 38.60 2.17
3664 4449 5.243060 TGTCTCTCTGAAACGAATTCTACCA 59.757 40.000 3.52 0.00 38.92 3.25
3686 4473 6.209192 ACCATGTTTTATCACTTGCTTCATCA 59.791 34.615 0.00 0.00 0.00 3.07
3696 4483 6.829849 TCACTTGCTTCATCATCCATGTATA 58.170 36.000 0.00 0.00 33.66 1.47
3699 4486 7.174426 CACTTGCTTCATCATCCATGTATATGT 59.826 37.037 0.00 0.00 33.66 2.29
3700 4487 8.377799 ACTTGCTTCATCATCCATGTATATGTA 58.622 33.333 0.00 0.00 33.66 2.29
3701 4488 9.392259 CTTGCTTCATCATCCATGTATATGTAT 57.608 33.333 0.00 0.00 33.66 2.29
3702 4489 8.726870 TGCTTCATCATCCATGTATATGTATG 57.273 34.615 0.00 0.00 33.35 2.39
3703 4490 8.323567 TGCTTCATCATCCATGTATATGTATGT 58.676 33.333 5.20 0.00 33.68 2.29
3704 4491 9.822185 GCTTCATCATCCATGTATATGTATGTA 57.178 33.333 5.20 0.00 33.68 2.29
3710 4497 9.265862 TCATCCATGTATATGTATGTATGTCCA 57.734 33.333 5.20 0.00 33.68 4.02
3711 4498 9.317936 CATCCATGTATATGTATGTATGTCCAC 57.682 37.037 0.00 0.00 29.01 4.02
3712 4499 8.664669 TCCATGTATATGTATGTATGTCCACT 57.335 34.615 0.00 0.00 32.21 4.00
3713 4500 8.531146 TCCATGTATATGTATGTATGTCCACTG 58.469 37.037 0.00 0.00 32.21 3.66
3714 4501 7.765819 CCATGTATATGTATGTATGTCCACTGG 59.234 40.741 0.00 0.00 32.21 4.00
3715 4502 7.239763 TGTATATGTATGTATGTCCACTGGG 57.760 40.000 0.00 0.00 0.00 4.45
3716 4503 7.013834 TGTATATGTATGTATGTCCACTGGGA 58.986 38.462 0.00 0.00 42.29 4.37
3724 4511 2.122729 TCCACTGGGACTGGGAGG 59.877 66.667 0.00 0.00 38.64 4.30
3725 4512 3.721706 CCACTGGGACTGGGAGGC 61.722 72.222 0.00 0.00 35.59 4.70
3726 4513 2.930019 CACTGGGACTGGGAGGCA 60.930 66.667 0.00 0.00 29.74 4.75
3727 4514 2.608988 ACTGGGACTGGGAGGCAG 60.609 66.667 0.00 0.00 0.00 4.85
3728 4515 4.106925 CTGGGACTGGGAGGCAGC 62.107 72.222 0.00 0.00 0.00 5.25
3729 4516 4.980592 TGGGACTGGGAGGCAGCA 62.981 66.667 0.00 0.00 0.00 4.41
3730 4517 3.415087 GGGACTGGGAGGCAGCAT 61.415 66.667 0.00 0.00 0.00 3.79
3731 4518 2.124403 GGACTGGGAGGCAGCATG 60.124 66.667 0.00 0.00 40.87 4.06
3732 4519 2.124403 GACTGGGAGGCAGCATGG 60.124 66.667 0.00 0.00 35.86 3.66
3733 4520 2.937689 ACTGGGAGGCAGCATGGT 60.938 61.111 0.00 0.00 35.86 3.55
3734 4521 2.357836 CTGGGAGGCAGCATGGTT 59.642 61.111 0.00 0.00 35.86 3.67
3735 4522 1.751927 CTGGGAGGCAGCATGGTTC 60.752 63.158 0.00 0.00 35.86 3.62
3736 4523 2.207501 CTGGGAGGCAGCATGGTTCT 62.208 60.000 0.00 0.00 35.86 3.01
3737 4524 1.452833 GGGAGGCAGCATGGTTCTC 60.453 63.158 13.65 13.65 35.86 2.87
3738 4525 1.300963 GGAGGCAGCATGGTTCTCA 59.699 57.895 20.08 0.00 35.86 3.27
3739 4526 0.322816 GGAGGCAGCATGGTTCTCAA 60.323 55.000 20.08 0.00 35.86 3.02
3758 4545 2.513435 GCACTAGCTGCTGCCTCC 60.513 66.667 13.43 0.00 43.33 4.30
3759 4546 2.188994 CACTAGCTGCTGCCTCCC 59.811 66.667 13.43 0.00 40.80 4.30
3760 4547 2.040278 ACTAGCTGCTGCCTCCCT 59.960 61.111 13.43 0.00 40.80 4.20
3761 4548 2.365586 ACTAGCTGCTGCCTCCCTG 61.366 63.158 13.43 0.00 40.80 4.45
3763 4550 2.590391 CTAGCTGCTGCCTCCCTGTG 62.590 65.000 13.43 0.00 40.80 3.66
3765 4552 4.031129 CTGCTGCCTCCCTGTGCT 62.031 66.667 0.00 0.00 0.00 4.40
3766 4553 4.340246 TGCTGCCTCCCTGTGCTG 62.340 66.667 0.00 0.00 0.00 4.41
3808 4595 6.179504 GCATCTGCATATCTGAATTACTGG 57.820 41.667 0.00 0.00 41.59 4.00
3809 4596 5.123502 GCATCTGCATATCTGAATTACTGGG 59.876 44.000 0.00 0.00 41.59 4.45
3810 4597 6.470278 CATCTGCATATCTGAATTACTGGGA 58.530 40.000 0.00 0.00 0.00 4.37
3811 4598 5.858381 TCTGCATATCTGAATTACTGGGAC 58.142 41.667 0.00 0.00 0.00 4.46
3812 4599 5.604231 TCTGCATATCTGAATTACTGGGACT 59.396 40.000 0.00 0.00 0.00 3.85
3813 4600 5.614308 TGCATATCTGAATTACTGGGACTG 58.386 41.667 0.00 0.00 0.00 3.51
3814 4601 4.453819 GCATATCTGAATTACTGGGACTGC 59.546 45.833 0.00 0.00 0.00 4.40
3815 4602 5.744300 GCATATCTGAATTACTGGGACTGCT 60.744 44.000 0.00 0.00 0.00 4.24
3816 4603 3.616956 TCTGAATTACTGGGACTGCTG 57.383 47.619 0.00 0.00 0.00 4.41
3817 4604 2.012673 CTGAATTACTGGGACTGCTGC 58.987 52.381 0.00 0.00 0.00 5.25
3818 4605 1.630369 TGAATTACTGGGACTGCTGCT 59.370 47.619 0.00 0.00 0.00 4.24
3819 4606 2.012673 GAATTACTGGGACTGCTGCTG 58.987 52.381 4.89 4.89 0.00 4.41
3820 4607 0.393537 ATTACTGGGACTGCTGCTGC 60.394 55.000 8.89 8.89 40.20 5.25
3832 4619 3.063510 TGCTGCTGCATATCCTATTCC 57.936 47.619 14.93 0.00 45.31 3.01
3833 4620 2.641321 TGCTGCTGCATATCCTATTCCT 59.359 45.455 14.93 0.00 45.31 3.36
3834 4621 3.269178 GCTGCTGCATATCCTATTCCTC 58.731 50.000 11.11 0.00 39.41 3.71
3835 4622 3.871485 CTGCTGCATATCCTATTCCTCC 58.129 50.000 1.31 0.00 0.00 4.30
3836 4623 3.518705 CTGCTGCATATCCTATTCCTCCT 59.481 47.826 1.31 0.00 0.00 3.69
3837 4624 4.687976 TGCTGCATATCCTATTCCTCCTA 58.312 43.478 0.00 0.00 0.00 2.94
3838 4625 5.283763 TGCTGCATATCCTATTCCTCCTAT 58.716 41.667 0.00 0.00 0.00 2.57
3839 4626 5.365025 TGCTGCATATCCTATTCCTCCTATC 59.635 44.000 0.00 0.00 0.00 2.08
3840 4627 5.602145 GCTGCATATCCTATTCCTCCTATCT 59.398 44.000 0.00 0.00 0.00 1.98
3841 4628 6.780031 GCTGCATATCCTATTCCTCCTATCTA 59.220 42.308 0.00 0.00 0.00 1.98
3842 4629 7.454380 GCTGCATATCCTATTCCTCCTATCTAT 59.546 40.741 0.00 0.00 0.00 1.98
3843 4630 8.948401 TGCATATCCTATTCCTCCTATCTATC 57.052 38.462 0.00 0.00 0.00 2.08
3844 4631 7.952930 TGCATATCCTATTCCTCCTATCTATCC 59.047 40.741 0.00 0.00 0.00 2.59
3845 4632 7.952930 GCATATCCTATTCCTCCTATCTATCCA 59.047 40.741 0.00 0.00 0.00 3.41
3848 4635 6.928202 TCCTATTCCTCCTATCTATCCATCC 58.072 44.000 0.00 0.00 0.00 3.51
3849 4636 6.081356 CCTATTCCTCCTATCTATCCATCCC 58.919 48.000 0.00 0.00 0.00 3.85
3850 4637 3.671740 TCCTCCTATCTATCCATCCCG 57.328 52.381 0.00 0.00 0.00 5.14
3851 4638 3.198827 TCCTCCTATCTATCCATCCCGA 58.801 50.000 0.00 0.00 0.00 5.14
3852 4639 3.794399 TCCTCCTATCTATCCATCCCGAT 59.206 47.826 0.00 0.00 0.00 4.18
3853 4640 4.141135 TCCTCCTATCTATCCATCCCGATC 60.141 50.000 0.00 0.00 0.00 3.69
3854 4641 4.141041 CCTCCTATCTATCCATCCCGATCT 60.141 50.000 0.00 0.00 0.00 2.75
3855 4642 5.055265 TCCTATCTATCCATCCCGATCTC 57.945 47.826 0.00 0.00 0.00 2.75
3856 4643 4.141135 TCCTATCTATCCATCCCGATCTCC 60.141 50.000 0.00 0.00 0.00 3.71
3857 4644 3.765432 ATCTATCCATCCCGATCTCCA 57.235 47.619 0.00 0.00 0.00 3.86
3858 4645 2.808919 TCTATCCATCCCGATCTCCAC 58.191 52.381 0.00 0.00 0.00 4.02
3859 4646 2.380249 TCTATCCATCCCGATCTCCACT 59.620 50.000 0.00 0.00 0.00 4.00
3860 4647 1.346062 ATCCATCCCGATCTCCACTG 58.654 55.000 0.00 0.00 0.00 3.66
3861 4648 1.070445 CCATCCCGATCTCCACTGC 59.930 63.158 0.00 0.00 0.00 4.40
3862 4649 1.406065 CCATCCCGATCTCCACTGCT 61.406 60.000 0.00 0.00 0.00 4.24
3863 4650 0.033228 CATCCCGATCTCCACTGCTC 59.967 60.000 0.00 0.00 0.00 4.26
3864 4651 0.105760 ATCCCGATCTCCACTGCTCT 60.106 55.000 0.00 0.00 0.00 4.09
3865 4652 0.324738 TCCCGATCTCCACTGCTCTT 60.325 55.000 0.00 0.00 0.00 2.85
3866 4653 0.103937 CCCGATCTCCACTGCTCTTC 59.896 60.000 0.00 0.00 0.00 2.87
3867 4654 0.248825 CCGATCTCCACTGCTCTTCG 60.249 60.000 0.00 0.00 0.00 3.79
3868 4655 0.248825 CGATCTCCACTGCTCTTCGG 60.249 60.000 0.00 0.00 0.00 4.30
3869 4656 0.103937 GATCTCCACTGCTCTTCGGG 59.896 60.000 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.163360 GCGATGCGATGCTTCTCATC 59.837 55.000 18.03 18.03 46.32 2.92
5 6 2.232750 GCGATGCGATGCTTCTCAT 58.767 52.632 4.87 4.87 38.32 2.90
6 7 3.710044 GCGATGCGATGCTTCTCA 58.290 55.556 0.00 0.00 31.76 3.27
44 45 3.411263 GCAAAATGCTGGGTGTACCCG 62.411 57.143 15.03 10.77 46.73 5.28
45 46 0.246360 GCAAAATGCTGGGTGTACCC 59.754 55.000 13.28 13.28 45.08 3.69
46 47 0.965439 TGCAAAATGCTGGGTGTACC 59.035 50.000 3.78 0.00 45.31 3.34
47 48 2.403259 GTTGCAAAATGCTGGGTGTAC 58.597 47.619 0.00 0.00 45.31 2.90
48 49 1.342819 GGTTGCAAAATGCTGGGTGTA 59.657 47.619 0.00 0.00 45.31 2.90
49 50 0.106521 GGTTGCAAAATGCTGGGTGT 59.893 50.000 0.00 0.00 45.31 4.16
50 51 0.603439 GGGTTGCAAAATGCTGGGTG 60.603 55.000 0.00 0.00 45.31 4.61
51 52 0.763986 AGGGTTGCAAAATGCTGGGT 60.764 50.000 0.00 0.00 45.31 4.51
52 53 0.397564 AAGGGTTGCAAAATGCTGGG 59.602 50.000 0.00 0.00 45.31 4.45
53 54 1.799544 GAAGGGTTGCAAAATGCTGG 58.200 50.000 0.00 0.00 45.31 4.85
54 55 1.421382 CGAAGGGTTGCAAAATGCTG 58.579 50.000 0.00 0.00 45.31 4.41
55 56 3.892200 CGAAGGGTTGCAAAATGCT 57.108 47.368 0.00 0.00 45.31 3.79
82 83 9.754382 TGTACGTTTTCTTTCTGTATAGTCTTT 57.246 29.630 0.00 0.00 0.00 2.52
83 84 9.754382 TTGTACGTTTTCTTTCTGTATAGTCTT 57.246 29.630 0.00 0.00 0.00 3.01
84 85 9.754382 TTTGTACGTTTTCTTTCTGTATAGTCT 57.246 29.630 0.00 0.00 0.00 3.24
85 86 9.789029 GTTTGTACGTTTTCTTTCTGTATAGTC 57.211 33.333 0.00 0.00 0.00 2.59
86 87 8.768019 GGTTTGTACGTTTTCTTTCTGTATAGT 58.232 33.333 0.00 0.00 0.00 2.12
87 88 8.767085 TGGTTTGTACGTTTTCTTTCTGTATAG 58.233 33.333 0.00 0.00 0.00 1.31
88 89 8.659925 TGGTTTGTACGTTTTCTTTCTGTATA 57.340 30.769 0.00 0.00 0.00 1.47
89 90 7.556733 TGGTTTGTACGTTTTCTTTCTGTAT 57.443 32.000 0.00 0.00 0.00 2.29
90 91 6.981762 TGGTTTGTACGTTTTCTTTCTGTA 57.018 33.333 0.00 0.00 0.00 2.74
91 92 5.883503 TGGTTTGTACGTTTTCTTTCTGT 57.116 34.783 0.00 0.00 0.00 3.41
92 93 5.513849 GGTTGGTTTGTACGTTTTCTTTCTG 59.486 40.000 0.00 0.00 0.00 3.02
93 94 5.643664 GGTTGGTTTGTACGTTTTCTTTCT 58.356 37.500 0.00 0.00 0.00 2.52
94 95 4.496539 CGGTTGGTTTGTACGTTTTCTTTC 59.503 41.667 0.00 0.00 0.00 2.62
107 108 1.208259 GCTGCTTTTCGGTTGGTTTG 58.792 50.000 0.00 0.00 0.00 2.93
110 111 1.098712 TTCGCTGCTTTTCGGTTGGT 61.099 50.000 0.00 0.00 0.00 3.67
151 152 3.615536 GAATGCGTGTGCTGGTGCC 62.616 63.158 0.00 0.00 43.34 5.01
317 329 1.452108 GGGTGGGATTCTGGAAGCG 60.452 63.158 0.00 0.00 0.00 4.68
318 330 1.076705 GGGGTGGGATTCTGGAAGC 60.077 63.158 0.00 0.00 0.00 3.86
319 331 1.615262 GGGGGTGGGATTCTGGAAG 59.385 63.158 0.00 0.00 0.00 3.46
320 332 3.850061 GGGGGTGGGATTCTGGAA 58.150 61.111 0.00 0.00 0.00 3.53
370 382 0.250166 GCGTTATAAGGGATGCGGGT 60.250 55.000 7.25 0.00 0.00 5.28
375 387 1.003233 GGGGAGGCGTTATAAGGGATG 59.997 57.143 7.25 0.00 0.00 3.51
376 388 1.359168 GGGGAGGCGTTATAAGGGAT 58.641 55.000 7.25 0.00 0.00 3.85
377 389 0.765519 GGGGGAGGCGTTATAAGGGA 60.766 60.000 7.25 0.00 0.00 4.20
378 390 1.759236 GGGGGAGGCGTTATAAGGG 59.241 63.158 7.25 0.00 0.00 3.95
1173 1586 3.073101 GGGCGTAGAAGTCGGGGT 61.073 66.667 0.00 0.00 0.00 4.95
1744 2170 3.764160 CTCCCTCATCTTGGGCGGC 62.764 68.421 0.00 0.00 44.23 6.53
1789 2215 0.768622 TGGGGTGTCGGTCTTCATTT 59.231 50.000 0.00 0.00 0.00 2.32
2098 2533 3.832490 ACTTGGTGACATAGTACTCTGCA 59.168 43.478 8.10 5.04 42.32 4.41
2146 2581 3.958860 GGGGGAGCCGATGATGGG 61.959 72.222 0.00 0.00 0.00 4.00
2416 2858 1.814527 CAGGCCGGTGTAGTAGACC 59.185 63.158 6.40 6.40 0.00 3.85
2635 3081 9.354673 ACATATTTAACCCATATTGACTTGGAG 57.645 33.333 0.00 0.00 34.81 3.86
2723 3182 0.394080 AACGAACGAACCCCAAACCA 60.394 50.000 0.14 0.00 0.00 3.67
3085 3790 1.968540 GGAAGCCACTCACTGTGCC 60.969 63.158 2.12 0.00 44.92 5.01
3092 3797 1.131638 AGAACACAGGAAGCCACTCA 58.868 50.000 0.00 0.00 0.00 3.41
3093 3798 2.147150 GAAGAACACAGGAAGCCACTC 58.853 52.381 0.00 0.00 0.00 3.51
3094 3799 1.490490 TGAAGAACACAGGAAGCCACT 59.510 47.619 0.00 0.00 0.00 4.00
3095 3800 1.967319 TGAAGAACACAGGAAGCCAC 58.033 50.000 0.00 0.00 0.00 5.01
3146 3867 2.154462 GGCATTTACGGCTGCTCATAT 58.846 47.619 0.00 0.00 38.45 1.78
3166 3887 1.268335 GCTACACCAACACAACAACCG 60.268 52.381 0.00 0.00 0.00 4.44
3215 3936 2.281484 TCAGAAACCACAGCCGGC 60.281 61.111 21.89 21.89 0.00 6.13
3216 3937 0.951040 GACTCAGAAACCACAGCCGG 60.951 60.000 0.00 0.00 0.00 6.13
3233 3958 7.551035 AACAGCAATTCATAATCTGAGAGAC 57.449 36.000 0.00 0.00 34.68 3.36
3292 4021 4.348857 GCCAAAAGCAACAGCCTG 57.651 55.556 0.00 0.00 42.97 4.85
3377 4117 2.787994 CTCTCCACCAAGTTTCAGCAT 58.212 47.619 0.00 0.00 0.00 3.79
3379 4119 0.877743 GCTCTCCACCAAGTTTCAGC 59.122 55.000 0.00 0.00 0.00 4.26
3407 4151 1.227645 AAACAGCGTGCTCTGCTCA 60.228 52.632 0.00 0.00 41.72 4.26
3423 4167 8.539770 TTTGATCAGCAAAACAGTAAAACAAA 57.460 26.923 0.00 0.00 43.18 2.83
3589 4338 9.494271 GTCTTAATAATACAGCATCATCAGGAA 57.506 33.333 0.00 0.00 0.00 3.36
3600 4349 6.201806 CAGCTCAGGTGTCTTAATAATACAGC 59.798 42.308 11.24 11.24 40.90 4.40
3603 4352 6.018669 GCACAGCTCAGGTGTCTTAATAATAC 60.019 42.308 6.51 0.00 42.60 1.89
3604 4353 6.049149 GCACAGCTCAGGTGTCTTAATAATA 58.951 40.000 6.51 0.00 42.60 0.98
3605 4354 4.878397 GCACAGCTCAGGTGTCTTAATAAT 59.122 41.667 6.51 0.00 42.60 1.28
3606 4355 4.253685 GCACAGCTCAGGTGTCTTAATAA 58.746 43.478 6.51 0.00 42.60 1.40
3657 4442 7.446931 TGAAGCAAGTGATAAAACATGGTAGAA 59.553 33.333 0.00 0.00 30.10 2.10
3659 4444 7.144722 TGAAGCAAGTGATAAAACATGGTAG 57.855 36.000 0.00 0.00 30.10 3.18
3664 4449 7.123098 TGGATGATGAAGCAAGTGATAAAACAT 59.877 33.333 0.00 0.00 0.00 2.71
3686 4473 9.271921 AGTGGACATACATACATATACATGGAT 57.728 33.333 0.00 0.00 35.99 3.41
3708 4495 3.721706 GCCTCCCAGTCCCAGTGG 61.722 72.222 0.63 0.63 38.45 4.00
3709 4496 2.930019 TGCCTCCCAGTCCCAGTG 60.930 66.667 0.00 0.00 0.00 3.66
3710 4497 2.608988 CTGCCTCCCAGTCCCAGT 60.609 66.667 0.00 0.00 36.79 4.00
3711 4498 4.106925 GCTGCCTCCCAGTCCCAG 62.107 72.222 0.00 0.00 43.71 4.45
3712 4499 4.980592 TGCTGCCTCCCAGTCCCA 62.981 66.667 0.00 0.00 43.71 4.37
3713 4500 3.415087 ATGCTGCCTCCCAGTCCC 61.415 66.667 0.00 0.00 43.71 4.46
3714 4501 2.124403 CATGCTGCCTCCCAGTCC 60.124 66.667 0.00 0.00 43.71 3.85
3715 4502 2.124403 CCATGCTGCCTCCCAGTC 60.124 66.667 0.00 0.00 43.71 3.51
3716 4503 2.490270 GAACCATGCTGCCTCCCAGT 62.490 60.000 0.00 0.00 43.71 4.00
3717 4504 1.751927 GAACCATGCTGCCTCCCAG 60.752 63.158 0.00 0.00 44.67 4.45
3718 4505 2.202236 GAGAACCATGCTGCCTCCCA 62.202 60.000 0.00 0.00 0.00 4.37
3719 4506 1.452833 GAGAACCATGCTGCCTCCC 60.453 63.158 0.00 0.00 0.00 4.30
3720 4507 0.322816 TTGAGAACCATGCTGCCTCC 60.323 55.000 0.00 0.00 0.00 4.30
3721 4508 1.471684 CTTTGAGAACCATGCTGCCTC 59.528 52.381 0.00 0.00 0.00 4.70
3722 4509 1.542492 CTTTGAGAACCATGCTGCCT 58.458 50.000 0.00 0.00 0.00 4.75
3723 4510 0.108945 GCTTTGAGAACCATGCTGCC 60.109 55.000 0.00 0.00 0.00 4.85
3724 4511 0.599558 TGCTTTGAGAACCATGCTGC 59.400 50.000 0.00 0.00 0.00 5.25
3725 4512 1.884579 AGTGCTTTGAGAACCATGCTG 59.115 47.619 0.00 0.00 0.00 4.41
3726 4513 2.283145 AGTGCTTTGAGAACCATGCT 57.717 45.000 0.00 0.00 0.00 3.79
3727 4514 2.159462 GCTAGTGCTTTGAGAACCATGC 60.159 50.000 0.00 0.00 36.03 4.06
3728 4515 3.754188 GCTAGTGCTTTGAGAACCATG 57.246 47.619 0.00 0.00 36.03 3.66
3758 4545 4.655647 AGCACTGCCCAGCACAGG 62.656 66.667 0.00 0.00 39.55 4.00
3759 4546 3.362797 CAGCACTGCCCAGCACAG 61.363 66.667 0.00 0.00 41.08 3.66
3760 4547 4.960866 CCAGCACTGCCCAGCACA 62.961 66.667 0.00 0.00 33.79 4.57
3765 4552 4.536526 TTTGCCCAGCACTGCCCA 62.537 61.111 0.00 0.00 38.71 5.36
3766 4553 3.688159 CTTTGCCCAGCACTGCCC 61.688 66.667 0.00 0.00 38.71 5.36
3767 4554 2.914097 ACTTTGCCCAGCACTGCC 60.914 61.111 0.00 0.00 38.71 4.85
3768 4555 2.337532 CACTTTGCCCAGCACTGC 59.662 61.111 0.00 0.00 38.71 4.40
3769 4556 1.812686 ATGCACTTTGCCCAGCACTG 61.813 55.000 0.00 0.00 44.23 3.66
3770 4557 1.530013 GATGCACTTTGCCCAGCACT 61.530 55.000 0.00 0.00 44.23 4.40
3800 4587 1.952367 GCAGCAGCAGTCCCAGTAATT 60.952 52.381 0.00 0.00 41.58 1.40
3813 4600 3.269178 GAGGAATAGGATATGCAGCAGC 58.731 50.000 0.00 0.00 42.57 5.25
3814 4601 3.518705 AGGAGGAATAGGATATGCAGCAG 59.481 47.826 0.00 0.00 0.00 4.24
3815 4602 3.524826 AGGAGGAATAGGATATGCAGCA 58.475 45.455 0.00 0.00 0.00 4.41
3816 4603 5.602145 AGATAGGAGGAATAGGATATGCAGC 59.398 44.000 0.00 0.00 0.00 5.25
3817 4604 8.954834 ATAGATAGGAGGAATAGGATATGCAG 57.045 38.462 0.00 0.00 0.00 4.41
3818 4605 7.952930 GGATAGATAGGAGGAATAGGATATGCA 59.047 40.741 0.00 0.00 0.00 3.96
3819 4606 7.952930 TGGATAGATAGGAGGAATAGGATATGC 59.047 40.741 0.00 0.00 0.00 3.14
3822 4609 8.683445 GGATGGATAGATAGGAGGAATAGGATA 58.317 40.741 0.00 0.00 0.00 2.59
3823 4610 7.424836 GGGATGGATAGATAGGAGGAATAGGAT 60.425 44.444 0.00 0.00 0.00 3.24
3824 4611 6.125741 GGGATGGATAGATAGGAGGAATAGGA 60.126 46.154 0.00 0.00 0.00 2.94
3825 4612 6.081356 GGGATGGATAGATAGGAGGAATAGG 58.919 48.000 0.00 0.00 0.00 2.57
3826 4613 5.772672 CGGGATGGATAGATAGGAGGAATAG 59.227 48.000 0.00 0.00 0.00 1.73
3827 4614 5.435373 TCGGGATGGATAGATAGGAGGAATA 59.565 44.000 0.00 0.00 0.00 1.75
3828 4615 4.233053 TCGGGATGGATAGATAGGAGGAAT 59.767 45.833 0.00 0.00 0.00 3.01
3829 4616 3.596500 TCGGGATGGATAGATAGGAGGAA 59.403 47.826 0.00 0.00 0.00 3.36
3830 4617 3.198827 TCGGGATGGATAGATAGGAGGA 58.801 50.000 0.00 0.00 0.00 3.71
3831 4618 3.671740 TCGGGATGGATAGATAGGAGG 57.328 52.381 0.00 0.00 0.00 4.30
3832 4619 5.060427 AGATCGGGATGGATAGATAGGAG 57.940 47.826 0.00 0.00 0.00 3.69
3833 4620 4.141135 GGAGATCGGGATGGATAGATAGGA 60.141 50.000 0.00 0.00 0.00 2.94
3834 4621 4.148838 GGAGATCGGGATGGATAGATAGG 58.851 52.174 0.00 0.00 0.00 2.57
3835 4622 4.582656 GTGGAGATCGGGATGGATAGATAG 59.417 50.000 0.00 0.00 0.00 2.08
3836 4623 4.230733 AGTGGAGATCGGGATGGATAGATA 59.769 45.833 0.00 0.00 0.00 1.98
3837 4624 3.012274 AGTGGAGATCGGGATGGATAGAT 59.988 47.826 0.00 0.00 0.00 1.98
3838 4625 2.380249 AGTGGAGATCGGGATGGATAGA 59.620 50.000 0.00 0.00 0.00 1.98
3839 4626 2.495270 CAGTGGAGATCGGGATGGATAG 59.505 54.545 0.00 0.00 0.00 2.08
3840 4627 2.529632 CAGTGGAGATCGGGATGGATA 58.470 52.381 0.00 0.00 0.00 2.59
3841 4628 1.346062 CAGTGGAGATCGGGATGGAT 58.654 55.000 0.00 0.00 0.00 3.41
3842 4629 1.402896 GCAGTGGAGATCGGGATGGA 61.403 60.000 0.00 0.00 0.00 3.41
3843 4630 1.070445 GCAGTGGAGATCGGGATGG 59.930 63.158 0.00 0.00 0.00 3.51
3844 4631 0.033228 GAGCAGTGGAGATCGGGATG 59.967 60.000 0.00 0.00 0.00 3.51
3845 4632 0.105760 AGAGCAGTGGAGATCGGGAT 60.106 55.000 0.00 0.00 0.00 3.85
3846 4633 0.324738 AAGAGCAGTGGAGATCGGGA 60.325 55.000 0.00 0.00 0.00 5.14
3847 4634 0.103937 GAAGAGCAGTGGAGATCGGG 59.896 60.000 0.00 0.00 0.00 5.14
3848 4635 0.248825 CGAAGAGCAGTGGAGATCGG 60.249 60.000 0.00 0.00 0.00 4.18
3849 4636 0.248825 CCGAAGAGCAGTGGAGATCG 60.249 60.000 0.00 0.00 0.00 3.69
3850 4637 0.103937 CCCGAAGAGCAGTGGAGATC 59.896 60.000 0.00 0.00 0.00 2.75
3851 4638 2.206635 CCCGAAGAGCAGTGGAGAT 58.793 57.895 0.00 0.00 0.00 2.75
3852 4639 3.700109 CCCGAAGAGCAGTGGAGA 58.300 61.111 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.