Multiple sequence alignment - TraesCS1D01G259300

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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 TraesCS1D01G259300 chr1D 100.000 5333 0 0 1 5333 352190451 352195783 0.000000e+00 9849.0
1 TraesCS1D01G259300 chr1D 95.520 692 30 1 4642 5333 318136470 318135780 0.000000e+00 1105.0
2 TraesCS1D01G259300 chr1D 94.798 692 35 1 4642 5333 437286687 437287377 0.000000e+00 1077.0
3 TraesCS1D01G259300 chr1D 90.409 709 37 12 2 680 201528044 201527337 0.000000e+00 904.0
4 TraesCS1D01G259300 chr1D 82.474 97 10 5 4641 4733 470864513 470864420 1.590000e-10 78.7
5 TraesCS1D01G259300 chr1A 95.227 3981 134 17 677 4640 452753265 452757206 0.000000e+00 6248.0
6 TraesCS1D01G259300 chr1A 92.637 747 42 4 1007 1753 452743942 452744675 0.000000e+00 1062.0
7 TraesCS1D01G259300 chr1A 93.922 691 30 4 1 679 265642833 265642143 0.000000e+00 1033.0
8 TraesCS1D01G259300 chr1A 93.266 698 30 7 1 681 549500992 549500295 0.000000e+00 1013.0
9 TraesCS1D01G259300 chr1A 93.590 78 4 1 829 905 452743845 452743922 1.210000e-21 115.0
10 TraesCS1D01G259300 chr1B 95.888 3721 142 7 680 4392 474444750 474448467 0.000000e+00 6013.0
11 TraesCS1D01G259300 chr1B 92.098 696 54 1 4638 5333 16601255 16600561 0.000000e+00 979.0
12 TraesCS1D01G259300 chr5D 96.243 692 24 2 4643 5333 352815508 352816198 0.000000e+00 1133.0
13 TraesCS1D01G259300 chr5D 94.101 695 23 3 1 677 318819249 318818555 0.000000e+00 1040.0
14 TraesCS1D01G259300 chr5D 93.553 698 26 4 1 680 539720357 539721053 0.000000e+00 1022.0
15 TraesCS1D01G259300 chr5D 93.400 697 28 7 1 679 478458476 478459172 0.000000e+00 1016.0
16 TraesCS1D01G259300 chr5D 92.176 703 28 4 1 685 560286816 560286123 0.000000e+00 968.0
17 TraesCS1D01G259300 chr5D 90.485 557 51 2 4643 5198 548470651 548471206 0.000000e+00 734.0
18 TraesCS1D01G259300 chr5D 86.553 647 87 0 4687 5333 57084849 57085495 0.000000e+00 713.0
19 TraesCS1D01G259300 chr5D 88.416 423 31 9 273 677 477026759 477027181 1.330000e-135 494.0
20 TraesCS1D01G259300 chr4D 94.567 681 24 6 1 681 499680782 499680115 0.000000e+00 1040.0
21 TraesCS1D01G259300 chr4D 91.684 493 24 3 210 685 426600786 426600294 0.000000e+00 667.0
22 TraesCS1D01G259300 chr4D 73.263 475 115 11 4803 5271 254486966 254486498 4.270000e-36 163.0
23 TraesCS1D01G259300 chr6A 93.286 700 45 2 4636 5333 609746315 609745616 0.000000e+00 1031.0
24 TraesCS1D01G259300 chr6A 82.667 75 8 5 4643 4714 498051917 498051845 1.600000e-05 62.1
25 TraesCS1D01G259300 chr6D 93.544 697 27 3 1 679 68858842 68859538 0.000000e+00 1022.0
26 TraesCS1D01G259300 chr6D 80.000 100 12 6 4648 4742 104318358 104318454 3.450000e-07 67.6
27 TraesCS1D01G259300 chr7D 93.410 698 28 5 1 680 94404466 94403769 0.000000e+00 1018.0
28 TraesCS1D01G259300 chr7D 81.132 106 11 7 4640 4740 106352546 106352445 5.730000e-10 76.8
29 TraesCS1D01G259300 chr3D 93.400 697 28 3 1 679 551075004 551075700 0.000000e+00 1016.0
30 TraesCS1D01G259300 chr2D 95.687 626 24 3 1 624 131274641 131274017 0.000000e+00 1003.0
31 TraesCS1D01G259300 chr2D 85.928 469 66 0 4737 5205 410021663 410021195 7.970000e-138 501.0
32 TraesCS1D01G259300 chr7A 92.132 699 34 7 2 680 43173628 43172931 0.000000e+00 966.0
33 TraesCS1D01G259300 chr7A 88.201 517 58 3 4643 5158 681485941 681485427 9.820000e-172 614.0
34 TraesCS1D01G259300 chr3B 91.486 693 58 1 4641 5333 605500205 605499514 0.000000e+00 952.0
35 TraesCS1D01G259300 chr3A 90.421 689 65 1 4643 5331 608365757 608365070 0.000000e+00 905.0
36 TraesCS1D01G259300 chr3A 87.822 698 82 3 4637 5333 749458230 749458925 0.000000e+00 815.0
37 TraesCS1D01G259300 chr4A 89.625 694 69 3 4639 5331 88769994 88769303 0.000000e+00 880.0
38 TraesCS1D01G259300 chr7B 89.423 104 8 2 4640 4742 593523498 593523397 1.560000e-25 128.0
39 TraesCS1D01G259300 chr7B 98.148 54 1 0 627 680 631318469 631318522 1.580000e-15 95.3
40 TraesCS1D01G259300 chr7B 84.158 101 8 7 4644 4740 535512525 535512429 2.050000e-14 91.6
41 TraesCS1D01G259300 chr5B 73.684 342 54 20 367 681 639921089 639920757 3.400000e-17 100.0
42 TraesCS1D01G259300 chr5A 95.082 61 2 1 623 682 10215430 10215490 1.580000e-15 95.3
43 TraesCS1D01G259300 chr4B 82.653 98 9 5 4641 4733 184898033 184898127 4.430000e-11 80.5


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 TraesCS1D01G259300 chr1D 352190451 352195783 5332 False 9849.0 9849 100.0000 1 5333 1 chr1D.!!$F1 5332
1 TraesCS1D01G259300 chr1D 318135780 318136470 690 True 1105.0 1105 95.5200 4642 5333 1 chr1D.!!$R2 691
2 TraesCS1D01G259300 chr1D 437286687 437287377 690 False 1077.0 1077 94.7980 4642 5333 1 chr1D.!!$F2 691
3 TraesCS1D01G259300 chr1D 201527337 201528044 707 True 904.0 904 90.4090 2 680 1 chr1D.!!$R1 678
4 TraesCS1D01G259300 chr1A 452753265 452757206 3941 False 6248.0 6248 95.2270 677 4640 1 chr1A.!!$F1 3963
5 TraesCS1D01G259300 chr1A 265642143 265642833 690 True 1033.0 1033 93.9220 1 679 1 chr1A.!!$R1 678
6 TraesCS1D01G259300 chr1A 549500295 549500992 697 True 1013.0 1013 93.2660 1 681 1 chr1A.!!$R2 680
7 TraesCS1D01G259300 chr1A 452743845 452744675 830 False 588.5 1062 93.1135 829 1753 2 chr1A.!!$F2 924
8 TraesCS1D01G259300 chr1B 474444750 474448467 3717 False 6013.0 6013 95.8880 680 4392 1 chr1B.!!$F1 3712
9 TraesCS1D01G259300 chr1B 16600561 16601255 694 True 979.0 979 92.0980 4638 5333 1 chr1B.!!$R1 695
10 TraesCS1D01G259300 chr5D 352815508 352816198 690 False 1133.0 1133 96.2430 4643 5333 1 chr5D.!!$F2 690
11 TraesCS1D01G259300 chr5D 318818555 318819249 694 True 1040.0 1040 94.1010 1 677 1 chr5D.!!$R1 676
12 TraesCS1D01G259300 chr5D 539720357 539721053 696 False 1022.0 1022 93.5530 1 680 1 chr5D.!!$F5 679
13 TraesCS1D01G259300 chr5D 478458476 478459172 696 False 1016.0 1016 93.4000 1 679 1 chr5D.!!$F4 678
14 TraesCS1D01G259300 chr5D 560286123 560286816 693 True 968.0 968 92.1760 1 685 1 chr5D.!!$R2 684
15 TraesCS1D01G259300 chr5D 548470651 548471206 555 False 734.0 734 90.4850 4643 5198 1 chr5D.!!$F6 555
16 TraesCS1D01G259300 chr5D 57084849 57085495 646 False 713.0 713 86.5530 4687 5333 1 chr5D.!!$F1 646
17 TraesCS1D01G259300 chr4D 499680115 499680782 667 True 1040.0 1040 94.5670 1 681 1 chr4D.!!$R3 680
18 TraesCS1D01G259300 chr6A 609745616 609746315 699 True 1031.0 1031 93.2860 4636 5333 1 chr6A.!!$R2 697
19 TraesCS1D01G259300 chr6D 68858842 68859538 696 False 1022.0 1022 93.5440 1 679 1 chr6D.!!$F1 678
20 TraesCS1D01G259300 chr7D 94403769 94404466 697 True 1018.0 1018 93.4100 1 680 1 chr7D.!!$R1 679
21 TraesCS1D01G259300 chr3D 551075004 551075700 696 False 1016.0 1016 93.4000 1 679 1 chr3D.!!$F1 678
22 TraesCS1D01G259300 chr2D 131274017 131274641 624 True 1003.0 1003 95.6870 1 624 1 chr2D.!!$R1 623
23 TraesCS1D01G259300 chr7A 43172931 43173628 697 True 966.0 966 92.1320 2 680 1 chr7A.!!$R1 678
24 TraesCS1D01G259300 chr7A 681485427 681485941 514 True 614.0 614 88.2010 4643 5158 1 chr7A.!!$R2 515
25 TraesCS1D01G259300 chr3B 605499514 605500205 691 True 952.0 952 91.4860 4641 5333 1 chr3B.!!$R1 692
26 TraesCS1D01G259300 chr3A 608365070 608365757 687 True 905.0 905 90.4210 4643 5331 1 chr3A.!!$R1 688
27 TraesCS1D01G259300 chr3A 749458230 749458925 695 False 815.0 815 87.8220 4637 5333 1 chr3A.!!$F1 696
28 TraesCS1D01G259300 chr4A 88769303 88769994 691 True 880.0 880 89.6250 4639 5331 1 chr4A.!!$R1 692

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
839 871 0.034059 ATGCGAGAAATAGCCCCGAG 59.966 55.0 0.00 0.0 0.00 4.63 F
1869 1936 0.033504 TCCTGCTGGTTCTCGACAAC 59.966 55.0 9.73 0.0 34.23 3.32 F
3223 3296 0.247460 TGACCCTTCTGTCGATGCTG 59.753 55.0 0.00 0.0 38.11 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 2323 0.035439 CCTGCAGGTTCCGGTAACAT 60.035 55.0 25.53 8.18 40.08 2.71 R
3307 3380 0.907486 TCCCTCAAGCTCATGTCCAG 59.093 55.0 0.00 0.00 0.00 3.86 R
4786 4869 0.392863 TGGGCAATGGACGAGACATG 60.393 55.0 0.00 0.00 0.00 3.21 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
170 171 3.121929 ACTATGGGAGGTGATGACTGT 57.878 47.619 0.00 0.00 0.00 3.55
202 203 5.344884 TCATGCACAATACGATCGTAGAAA 58.655 37.500 29.63 12.31 43.58 2.52
337 338 1.234821 GCGTGATTGGGAAACTCACA 58.765 50.000 0.00 0.00 39.36 3.58
384 385 3.054139 AGCATATGTGGACTCATGTTGGT 60.054 43.478 4.29 0.00 0.00 3.67
537 551 3.833545 TGAATGCAATGCAAAATTGGC 57.166 38.095 13.45 0.00 43.62 4.52
580 594 3.961838 TATGGGTCGGCGTGTTGGC 62.962 63.158 6.85 0.00 40.44 4.52
610 624 4.261801 CCGACTCATATGAAAAACAGGGT 58.738 43.478 6.90 0.00 0.00 4.34
692 724 0.107945 CTCTAAGGGTCCAGCAGCAC 60.108 60.000 0.00 0.00 0.00 4.40
839 871 0.034059 ATGCGAGAAATAGCCCCGAG 59.966 55.000 0.00 0.00 0.00 4.63
921 955 1.050988 GGAGGAGGCTCCACATAGCA 61.051 60.000 33.86 0.00 44.64 3.49
962 1011 3.878667 CCTCCCAATCCCCTCGGC 61.879 72.222 0.00 0.00 0.00 5.54
963 1012 4.241555 CTCCCAATCCCCTCGGCG 62.242 72.222 0.00 0.00 0.00 6.46
1548 1615 1.450312 GGAGCGGAAGGACATGGTG 60.450 63.158 0.00 0.00 0.00 4.17
1780 1847 0.543749 GCAGTCTGCTGGGGTAGAAT 59.456 55.000 17.89 0.00 42.78 2.40
1869 1936 0.033504 TCCTGCTGGTTCTCGACAAC 59.966 55.000 9.73 0.00 34.23 3.32
2196 2263 1.127343 AGGCTTCCCAGAGTATCAGC 58.873 55.000 0.00 0.00 37.82 4.26
2256 2323 3.349927 TGTAACCTCAACGCTAGAGCTA 58.650 45.455 0.00 0.00 39.32 3.32
2321 2388 3.461061 TCTGCAGCATATTTCCGAAGAG 58.539 45.455 9.47 0.00 0.00 2.85
2344 2411 1.082756 CGGTTCAAGCGTGACAAGC 60.083 57.895 0.40 5.10 33.95 4.01
2437 2510 5.308825 AGGAGTACTTTGATCAACTTGTGG 58.691 41.667 7.89 0.00 0.00 4.17
2528 2601 0.964700 CTGGCAGAGAGTGTCTCACA 59.035 55.000 9.42 2.23 45.73 3.58
2540 2613 2.609459 GTGTCTCACAAGTTGACTGTGG 59.391 50.000 10.54 0.00 34.08 4.17
2628 2701 0.882042 CTGTCACGCAGCTCAAAGGT 60.882 55.000 0.00 0.00 38.52 3.50
2655 2728 2.031769 CGAGCTCAAAAGATTGCACACA 60.032 45.455 15.40 0.00 36.45 3.72
2694 2767 3.141767 TCCTCGTCTTCTCTCAGTCAA 57.858 47.619 0.00 0.00 0.00 3.18
2715 2788 6.002082 TCAATTGCCAGATGATATCCTCAAG 58.998 40.000 10.21 2.73 37.44 3.02
2769 2842 2.632512 TGGCTGCGATATGGTTGATCTA 59.367 45.455 0.00 0.00 0.00 1.98
2877 2950 3.008049 TGTTCCTTCTTCAGACCCTAAGC 59.992 47.826 0.00 0.00 0.00 3.09
3062 3135 4.935808 AGGTCATACGTTGGAAGATTTGTC 59.064 41.667 0.00 0.00 0.00 3.18
3223 3296 0.247460 TGACCCTTCTGTCGATGCTG 59.753 55.000 0.00 0.00 38.11 4.41
3307 3380 1.803334 TGATAAGTCACCGTGTTGGC 58.197 50.000 0.00 0.00 43.94 4.52
3323 3402 0.035725 TGGCTGGACATGAGCTTGAG 60.036 55.000 0.00 0.00 36.63 3.02
3335 3414 3.189606 TGAGCTTGAGGGAGGGAAATAA 58.810 45.455 0.00 0.00 0.00 1.40
3337 3416 4.230502 TGAGCTTGAGGGAGGGAAATAAAT 59.769 41.667 0.00 0.00 0.00 1.40
3348 3427 5.299531 GGAGGGAAATAAATTGTGCCTACTC 59.700 44.000 0.00 0.00 32.54 2.59
3382 3461 2.684943 TGACCAACTGTAGGAAGTGGA 58.315 47.619 1.19 0.00 0.00 4.02
3747 3826 2.807967 TGTTGCACTAGAGACATGTTGC 59.192 45.455 10.35 10.35 0.00 4.17
3834 3913 2.480555 CGCTGCCAAGGCGTAAAG 59.519 61.111 6.60 0.00 46.37 1.85
3844 3923 3.139077 CAAGGCGTAAAGTTTGAGGACT 58.861 45.455 0.00 0.00 0.00 3.85
3882 3961 6.267242 TCTCACTGAAGAAGCTGCATATATCT 59.733 38.462 1.02 0.00 0.00 1.98
3928 4007 1.154197 GGGTACTTGTTTGCGAGGTC 58.846 55.000 0.00 0.00 0.00 3.85
3936 4015 1.189403 GTTTGCGAGGTCTACGATCG 58.811 55.000 14.88 14.88 39.40 3.69
3990 4069 6.676456 GCAACATAACATCTCTTCCACATGTC 60.676 42.308 0.00 0.00 30.22 3.06
3999 4078 2.890945 TCTTCCACATGTCGAGAGTTCA 59.109 45.455 0.00 0.00 0.00 3.18
4020 4099 0.372334 GCGGATTAACGACGTTGCAT 59.628 50.000 23.00 14.25 35.47 3.96
4080 4159 0.236711 CGAGTTTTGCAGCACTGGAG 59.763 55.000 0.00 0.00 31.08 3.86
4088 4167 1.645704 GCAGCACTGGAGAGCATGTG 61.646 60.000 0.00 0.00 34.00 3.21
4114 4193 0.169672 CAATTGCTCCAAGCTCACCG 59.830 55.000 0.00 0.00 42.97 4.94
4128 4207 1.477295 CTCACCGTAGAGTCTTTCCCC 59.523 57.143 0.00 0.00 0.00 4.81
4130 4209 0.969409 ACCGTAGAGTCTTTCCCCGG 60.969 60.000 0.00 5.72 42.31 5.73
4147 4226 3.184683 GCGACTTCAGCAGCCTCG 61.185 66.667 0.00 0.00 34.19 4.63
4224 4303 1.294659 GCTTCCCGTCTTCACTGCAG 61.295 60.000 13.48 13.48 0.00 4.41
4350 4429 0.667792 GACCAGAGGCTCGTTGTGTC 60.668 60.000 9.22 8.70 0.00 3.67
4351 4430 1.374758 CCAGAGGCTCGTTGTGTCC 60.375 63.158 9.22 0.00 0.00 4.02
4398 4479 1.987770 GTTCGTCGCCGTTCAAGAATA 59.012 47.619 0.00 0.00 35.01 1.75
4401 4482 0.643820 GTCGCCGTTCAAGAATACCG 59.356 55.000 0.00 0.00 0.00 4.02
4422 4503 4.023707 CCGCCTTTCCTATGAAATGATCAC 60.024 45.833 0.00 0.00 41.93 3.06
4480 4561 0.804364 TCGATGTCTGCCATTTGTGC 59.196 50.000 0.00 0.00 32.56 4.57
4489 4570 3.254411 TCTGCCATTTGTGCGTGAAATTA 59.746 39.130 0.00 0.00 0.00 1.40
4518 4599 3.583806 CAAGATGAGAGATACCGGATGC 58.416 50.000 9.46 0.00 0.00 3.91
4519 4600 1.815613 AGATGAGAGATACCGGATGCG 59.184 52.381 9.46 0.00 0.00 4.73
4537 4618 2.426024 TGCGTCTGTATCCCTTCTGTAC 59.574 50.000 0.00 0.00 0.00 2.90
4547 4628 8.241497 TGTATCCCTTCTGTACGTATGTAATT 57.759 34.615 0.00 0.00 30.94 1.40
4548 4629 8.698210 TGTATCCCTTCTGTACGTATGTAATTT 58.302 33.333 0.00 0.00 30.94 1.82
4598 4679 9.678941 ACGTTCTGTATGACTATGTATGTAATG 57.321 33.333 0.00 0.00 0.00 1.90
4599 4680 9.678941 CGTTCTGTATGACTATGTATGTAATGT 57.321 33.333 0.00 0.00 0.00 2.71
4603 4684 7.158697 TGTATGACTATGTATGTAATGTGCCC 58.841 38.462 0.00 0.00 0.00 5.36
4629 4710 6.048732 TGGCTGAAGTACATTCTCATTACA 57.951 37.500 0.00 0.00 38.83 2.41
4636 4717 9.208022 TGAAGTACATTCTCATTACACTTTCTG 57.792 33.333 0.00 0.00 38.83 3.02
4786 4869 1.108132 CCGTACCCTAGACTGGCTCC 61.108 65.000 0.00 0.00 0.00 4.70
5212 5295 0.744874 CCTCCTAGCCAAACGATCGA 59.255 55.000 24.34 0.00 0.00 3.59
5284 5369 1.749258 GGGGCACGGTTCTTCCATC 60.749 63.158 0.00 0.00 35.57 3.51
5288 5373 0.389948 GCACGGTTCTTCCATCTCGT 60.390 55.000 0.00 0.00 35.57 4.18
5298 5383 2.202440 CATCTCGTCGTCGCCGTT 60.202 61.111 0.00 0.00 36.96 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
358 359 5.045012 ACATGAGTCCACATATGCTCAAT 57.955 39.130 12.80 4.46 40.71 2.57
474 477 6.394025 TTTAACAAACAAAATAGTCCGCCT 57.606 33.333 0.00 0.00 0.00 5.52
554 568 1.146041 GCCGACCCATATGTGCAGA 59.854 57.895 1.24 0.00 0.00 4.26
580 594 0.729478 CATATGAGTCGGTAGCGCGG 60.729 60.000 8.83 0.00 0.00 6.46
587 601 4.261801 CCCTGTTTTTCATATGAGTCGGT 58.738 43.478 5.39 0.00 0.00 4.69
625 640 2.625488 GCGATTTCGTCCGCTTTTG 58.375 52.632 0.00 0.00 46.96 2.44
667 699 1.831736 GCTGGACCCTTAGAGCAACTA 59.168 52.381 0.00 0.00 0.00 2.24
692 724 0.914551 CGACGGCACTACAGATTTCG 59.085 55.000 0.00 0.00 0.00 3.46
744 776 2.499685 GGGAATGACGGACGGGAG 59.500 66.667 0.00 0.00 0.00 4.30
745 777 3.078836 GGGGAATGACGGACGGGA 61.079 66.667 0.00 0.00 0.00 5.14
916 950 1.381872 ACGAGGGGTCAGCTGCTAT 60.382 57.895 9.47 0.00 0.00 2.97
995 1044 4.933064 CCGCCTCGACCATCTCGC 62.933 72.222 0.00 0.00 42.62 5.03
1084 1139 3.050275 GCCGTTGAGCCACCTGAC 61.050 66.667 0.00 0.00 0.00 3.51
1611 1678 3.941657 GAGCCCTATGATCGCGGCC 62.942 68.421 6.13 0.00 42.66 6.13
1780 1847 3.554934 AGTTGTTCATGCTGTCAGGAAA 58.445 40.909 0.00 0.00 43.48 3.13
1869 1936 1.971695 GCCCCCTTTGTTCCAGACG 60.972 63.158 0.00 0.00 0.00 4.18
2186 2253 3.030291 CTCTTCCAGTGGCTGATACTCT 58.970 50.000 3.51 0.00 32.44 3.24
2196 2263 2.694628 CTCTGAGATCCTCTTCCAGTGG 59.305 54.545 1.40 1.40 0.00 4.00
2256 2323 0.035439 CCTGCAGGTTCCGGTAACAT 60.035 55.000 25.53 8.18 40.08 2.71
2321 2388 4.389576 CACGCTTGAACCGCCAGC 62.390 66.667 0.00 0.00 0.00 4.85
2344 2411 2.695147 GGGCCATCCAAATCTTAACCAG 59.305 50.000 4.39 0.00 35.00 4.00
2437 2510 1.488393 CTCATGGAAGAAGGACCCCTC 59.512 57.143 0.00 0.00 30.89 4.30
2528 2601 4.162320 TCTCAACTCTTCCACAGTCAACTT 59.838 41.667 0.00 0.00 0.00 2.66
2540 2613 2.560542 TCCTCAGCACTCTCAACTCTTC 59.439 50.000 0.00 0.00 0.00 2.87
2628 2701 0.037326 ATCTTTTGAGCTCGCACCGA 60.037 50.000 9.64 2.21 0.00 4.69
2651 2724 9.193806 AGGAATGCTTTAGAATTATGAATGTGT 57.806 29.630 0.00 0.00 0.00 3.72
2655 2728 8.682936 ACGAGGAATGCTTTAGAATTATGAAT 57.317 30.769 0.00 0.00 0.00 2.57
2694 2767 4.600547 TCCTTGAGGATATCATCTGGCAAT 59.399 41.667 17.56 0.00 39.78 3.56
2715 2788 2.486592 CACACGGACACCCTTTAATTCC 59.513 50.000 0.00 0.00 0.00 3.01
2721 2794 1.101049 CAAGCACACGGACACCCTTT 61.101 55.000 0.00 0.00 0.00 3.11
2769 2842 6.460123 GCATCAGTTGACCAATTTTATCCGAT 60.460 38.462 0.00 0.00 0.00 4.18
2877 2950 1.227674 GCGGCACCTCTTAGGGATG 60.228 63.158 0.00 0.00 40.58 3.51
3062 3135 5.211174 TCTGCAGAGACCATTCATATCAG 57.789 43.478 13.74 0.00 0.00 2.90
3223 3296 3.502595 GGTTCAAGGCCTTCTAACACTTC 59.497 47.826 28.78 15.57 0.00 3.01
3307 3380 0.907486 TCCCTCAAGCTCATGTCCAG 59.093 55.000 0.00 0.00 0.00 3.86
3323 3402 3.374764 AGGCACAATTTATTTCCCTCCC 58.625 45.455 0.00 0.00 0.00 4.30
3747 3826 3.117888 AGCCTATTGTAAGGATGGTGGTG 60.118 47.826 0.00 0.00 39.15 4.17
3834 3913 2.576615 AGTGCCTGAAAGTCCTCAAAC 58.423 47.619 0.00 0.00 0.00 2.93
3844 3923 2.170397 TCAGTGAGACAAGTGCCTGAAA 59.830 45.455 0.00 0.00 0.00 2.69
3928 4007 2.224549 CCAGAGAGGTAAGCGATCGTAG 59.775 54.545 17.81 0.00 0.00 3.51
3936 4015 4.465886 TGTCTATCTCCAGAGAGGTAAGC 58.534 47.826 3.41 0.00 41.33 3.09
3939 4018 5.441500 CAGTTGTCTATCTCCAGAGAGGTA 58.558 45.833 3.41 0.00 41.33 3.08
3990 4069 2.279136 CGTTAATCCGCTTGAACTCTCG 59.721 50.000 0.00 0.00 0.00 4.04
3999 4078 0.441145 GCAACGTCGTTAATCCGCTT 59.559 50.000 10.86 0.00 0.00 4.68
4020 4099 3.244078 ACAACTTGGAGCACTGTCGAATA 60.244 43.478 0.00 0.00 0.00 1.75
4080 4159 2.540361 GCAATTGTCGATCCACATGCTC 60.540 50.000 10.64 0.00 32.00 4.26
4088 4167 1.064654 GCTTGGAGCAATTGTCGATCC 59.935 52.381 7.40 10.12 41.89 3.36
4114 4193 1.141234 CGCCGGGGAAAGACTCTAC 59.859 63.158 14.46 0.00 0.00 2.59
4128 4207 4.749310 AGGCTGCTGAAGTCGCCG 62.749 66.667 0.00 0.00 46.85 6.46
4130 4209 3.184683 CGAGGCTGCTGAAGTCGC 61.185 66.667 0.00 0.00 34.84 5.19
4147 4226 9.565213 CATTATGTTCAATTTTCTCAGAGAACC 57.435 33.333 12.75 0.00 33.26 3.62
4224 4303 2.659428 CCCCCAATCAGATCAAGAACC 58.341 52.381 0.00 0.00 0.00 3.62
4329 4408 0.668706 CACAACGAGCCTCTGGTCAG 60.669 60.000 0.00 0.00 38.96 3.51
4398 4479 3.644966 TCATTTCATAGGAAAGGCGGT 57.355 42.857 9.49 0.00 45.58 5.68
4401 4482 6.645790 ATGTGATCATTTCATAGGAAAGGC 57.354 37.500 9.49 0.00 45.58 4.35
4422 4503 2.656897 CACATACCGCGTCGATTCTATG 59.343 50.000 4.92 1.18 0.00 2.23
4480 4561 9.196552 TCTCATCTTGCATACTATAATTTCACG 57.803 33.333 0.00 0.00 0.00 4.35
4489 4570 6.096141 CCGGTATCTCTCATCTTGCATACTAT 59.904 42.308 0.00 0.00 0.00 2.12
4510 4591 1.740285 GGATACAGACGCATCCGGT 59.260 57.895 0.00 0.00 39.22 5.28
4518 4599 2.681848 ACGTACAGAAGGGATACAGACG 59.318 50.000 0.00 0.00 39.74 4.18
4519 4600 5.298777 ACATACGTACAGAAGGGATACAGAC 59.701 44.000 0.00 0.00 39.74 3.51
4548 4629 9.626045 CGTATGAGCATACTAGAATTTCACATA 57.374 33.333 16.12 0.00 41.04 2.29
4549 4630 8.144478 ACGTATGAGCATACTAGAATTTCACAT 58.856 33.333 16.12 0.00 41.04 3.21
4584 4665 5.827797 CCAAAGGGCACATTACATACATAGT 59.172 40.000 0.00 0.00 0.00 2.12
4585 4666 6.317789 CCAAAGGGCACATTACATACATAG 57.682 41.667 0.00 0.00 0.00 2.23
4603 4684 6.506500 AATGAGAATGTACTTCAGCCAAAG 57.493 37.500 0.00 0.00 36.24 2.77
4613 4694 9.561069 AAACAGAAAGTGTAATGAGAATGTACT 57.439 29.630 0.00 0.00 39.03 2.73
4641 4722 7.589395 TGCTATGCGTATTTGAGAAAGAAAAA 58.411 30.769 0.00 0.00 0.00 1.94
4642 4723 7.139896 TGCTATGCGTATTTGAGAAAGAAAA 57.860 32.000 0.00 0.00 0.00 2.29
4643 4724 6.735678 TGCTATGCGTATTTGAGAAAGAAA 57.264 33.333 0.00 0.00 0.00 2.52
4644 4725 6.718388 CATGCTATGCGTATTTGAGAAAGAA 58.282 36.000 0.00 0.00 0.00 2.52
4645 4726 6.291067 CATGCTATGCGTATTTGAGAAAGA 57.709 37.500 0.00 0.00 0.00 2.52
4786 4869 0.392863 TGGGCAATGGACGAGACATG 60.393 55.000 0.00 0.00 0.00 3.21
5212 5295 2.281761 CAACCGCTGCTGGACCTT 60.282 61.111 15.53 0.00 0.00 3.50
5236 5319 2.711542 CCGTTTCTTCCTATGGCTTGT 58.288 47.619 0.00 0.00 0.00 3.16
5298 5383 4.791069 GGTCGGGAGGTAGCCCCA 62.791 72.222 15.91 3.90 45.84 4.96


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

AutoCloner maintained by Alex Coulton.