Multiple sequence alignment - TraesCS3D01G109900

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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 TraesCS3D01G109900 chr3D 100.000 3620 0 0 1 3620 63778061 63781680 0.000000e+00 6685
1 TraesCS3D01G109900 chr3D 88.800 625 56 6 3006 3620 173583065 173582445 0.000000e+00 754
2 TraesCS3D01G109900 chr3B 90.551 3069 129 56 1 2990 104969521 104972507 0.000000e+00 3912
3 TraesCS3D01G109900 chr3A 90.585 2974 146 55 75 2990 73511643 73514540 0.000000e+00 3818
4 TraesCS3D01G109900 chr4D 90.909 616 46 8 3014 3620 21138576 21137962 0.000000e+00 819
5 TraesCS3D01G109900 chr1B 90.032 622 51 6 3010 3620 221330991 221330370 0.000000e+00 795
6 TraesCS3D01G109900 chr1B 77.280 669 92 31 1937 2566 190631309 190631956 4.480000e-89 339
7 TraesCS3D01G109900 chr2B 89.951 617 58 2 3007 3619 664233695 664233079 0.000000e+00 793
8 TraesCS3D01G109900 chr2B 89.633 627 51 6 3007 3620 508412549 508413174 0.000000e+00 785
9 TraesCS3D01G109900 chr2B 89.372 621 56 4 3010 3620 78419565 78420185 0.000000e+00 773
10 TraesCS3D01G109900 chr6A 89.593 615 51 8 3010 3620 596755633 596755028 0.000000e+00 769
11 TraesCS3D01G109900 chr6A 90.210 143 10 3 2161 2300 485155775 485155634 2.220000e-42 183
12 TraesCS3D01G109900 chr5B 89.137 626 56 4 3007 3620 631783387 631784012 0.000000e+00 769
13 TraesCS3D01G109900 chr5B 82.171 129 21 2 1551 1678 558871600 558871473 3.820000e-20 110
14 TraesCS3D01G109900 chr4B 89.176 619 58 7 3009 3620 445842808 445842192 0.000000e+00 763
15 TraesCS3D01G109900 chr1A 77.467 679 93 28 1937 2576 140961884 140962541 5.750000e-93 351
16 TraesCS3D01G109900 chr1D 77.545 668 90 28 1938 2566 126473853 126474499 7.440000e-92 348
17 TraesCS3D01G109900 chr5D 82.946 129 20 2 1551 1678 457008363 457008236 8.210000e-22 115
18 TraesCS3D01G109900 chr5A 82.443 131 19 2 1551 1679 574933247 574933119 1.060000e-20 111
19 TraesCS3D01G109900 chr7B 82.906 117 18 2 1565 1680 408567872 408567987 1.780000e-18 104
20 TraesCS3D01G109900 chrUn 82.051 117 19 2 1565 1680 92481505 92481390 8.270000e-17 99
21 TraesCS3D01G109900 chr7A 82.051 117 19 2 1565 1680 457569559 457569674 8.270000e-17 99


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 TraesCS3D01G109900 chr3D 63778061 63781680 3619 False 6685 6685 100.000 1 3620 1 chr3D.!!$F1 3619
1 TraesCS3D01G109900 chr3D 173582445 173583065 620 True 754 754 88.800 3006 3620 1 chr3D.!!$R1 614
2 TraesCS3D01G109900 chr3B 104969521 104972507 2986 False 3912 3912 90.551 1 2990 1 chr3B.!!$F1 2989
3 TraesCS3D01G109900 chr3A 73511643 73514540 2897 False 3818 3818 90.585 75 2990 1 chr3A.!!$F1 2915
4 TraesCS3D01G109900 chr4D 21137962 21138576 614 True 819 819 90.909 3014 3620 1 chr4D.!!$R1 606
5 TraesCS3D01G109900 chr1B 221330370 221330991 621 True 795 795 90.032 3010 3620 1 chr1B.!!$R1 610
6 TraesCS3D01G109900 chr1B 190631309 190631956 647 False 339 339 77.280 1937 2566 1 chr1B.!!$F1 629
7 TraesCS3D01G109900 chr2B 664233079 664233695 616 True 793 793 89.951 3007 3619 1 chr2B.!!$R1 612
8 TraesCS3D01G109900 chr2B 508412549 508413174 625 False 785 785 89.633 3007 3620 1 chr2B.!!$F2 613
9 TraesCS3D01G109900 chr2B 78419565 78420185 620 False 773 773 89.372 3010 3620 1 chr2B.!!$F1 610
10 TraesCS3D01G109900 chr6A 596755028 596755633 605 True 769 769 89.593 3010 3620 1 chr6A.!!$R2 610
11 TraesCS3D01G109900 chr5B 631783387 631784012 625 False 769 769 89.137 3007 3620 1 chr5B.!!$F1 613
12 TraesCS3D01G109900 chr4B 445842192 445842808 616 True 763 763 89.176 3009 3620 1 chr4B.!!$R1 611
13 TraesCS3D01G109900 chr1A 140961884 140962541 657 False 351 351 77.467 1937 2576 1 chr1A.!!$F1 639
14 TraesCS3D01G109900 chr1D 126473853 126474499 646 False 348 348 77.545 1938 2566 1 chr1D.!!$F1 628

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
976 1041 0.03563 CTGAGTTGCCTTCTCTGGGG 60.036 60.0 0.0 0.0 33.59 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2753 2882 1.202758 CCACAGCCACAGAGGTTAACA 60.203 52.381 8.1 0.0 40.61 2.41 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
17 18 4.227134 CATGGCGAGGACGAGGGG 62.227 72.222 0.00 0.00 42.66 4.79
68 69 1.061570 CGTCACGTACGCCTCTACC 59.938 63.158 16.72 0.00 46.10 3.18
69 70 1.364626 CGTCACGTACGCCTCTACCT 61.365 60.000 16.72 0.00 46.10 3.08
70 71 0.098376 GTCACGTACGCCTCTACCTG 59.902 60.000 16.72 3.37 0.00 4.00
131 136 2.863401 AGTCCAAACCTTTGCGTTTC 57.137 45.000 0.00 0.00 36.86 2.78
188 193 2.446848 CGGCAGGGATCTCCACCAT 61.447 63.158 2.60 0.00 38.24 3.55
216 221 1.794151 TACCCGAAACTGCGTCACGA 61.794 55.000 0.00 0.00 0.00 4.35
259 267 0.937699 TCACCACTCGTTCGCTTTCG 60.938 55.000 0.00 0.00 0.00 3.46
267 275 2.358247 TTCGCTTTCGGGCCAGAC 60.358 61.111 4.56 0.00 36.13 3.51
320 328 9.832445 TTTTGTTTCTTTCTCATCAGTACTACT 57.168 29.630 0.00 0.00 0.00 2.57
321 329 9.477484 TTTGTTTCTTTCTCATCAGTACTACTC 57.523 33.333 0.00 0.00 0.00 2.59
322 330 8.178313 TGTTTCTTTCTCATCAGTACTACTCA 57.822 34.615 0.00 0.00 0.00 3.41
403 414 3.753272 GTGTGTTAGTGTCCATGCAGATT 59.247 43.478 0.00 0.00 0.00 2.40
404 415 4.935205 GTGTGTTAGTGTCCATGCAGATTA 59.065 41.667 0.00 0.00 0.00 1.75
405 416 5.063944 GTGTGTTAGTGTCCATGCAGATTAG 59.936 44.000 0.00 0.00 0.00 1.73
406 417 5.178797 GTGTTAGTGTCCATGCAGATTAGT 58.821 41.667 0.00 0.00 0.00 2.24
408 419 6.477033 GTGTTAGTGTCCATGCAGATTAGTAG 59.523 42.308 0.00 0.00 0.00 2.57
454 477 2.126071 GCAGTTGCAGCAGCCATG 60.126 61.111 6.67 0.00 41.13 3.66
477 500 1.221523 AGAGGAGGACATGGCTCCATA 59.778 52.381 16.49 0.00 39.60 2.74
491 514 1.819632 CCATACACTCCCTTGCGCC 60.820 63.158 4.18 0.00 0.00 6.53
492 515 1.078497 CATACACTCCCTTGCGCCA 60.078 57.895 4.18 0.00 0.00 5.69
586 625 0.674895 GCTTGTTCTCATGCTCCCGT 60.675 55.000 0.00 0.00 40.22 5.28
587 626 1.081892 CTTGTTCTCATGCTCCCGTG 58.918 55.000 0.00 0.00 0.00 4.94
588 627 0.321564 TTGTTCTCATGCTCCCGTGG 60.322 55.000 0.00 0.00 0.00 4.94
589 628 2.109126 GTTCTCATGCTCCCGTGGC 61.109 63.158 0.00 0.00 0.00 5.01
590 629 2.592032 TTCTCATGCTCCCGTGGCA 61.592 57.895 0.00 0.00 44.05 4.92
614 653 0.731417 AGAGAGCGTTGCATGCATTC 59.269 50.000 23.37 16.37 31.07 2.67
689 733 3.500642 CGACTCGCTCGCTCCTCA 61.501 66.667 0.00 0.00 35.06 3.86
690 734 2.101380 GACTCGCTCGCTCCTCAC 59.899 66.667 0.00 0.00 0.00 3.51
691 735 2.360600 ACTCGCTCGCTCCTCACT 60.361 61.111 0.00 0.00 0.00 3.41
692 736 2.317685 GACTCGCTCGCTCCTCACTC 62.318 65.000 0.00 0.00 0.00 3.51
693 737 2.359975 TCGCTCGCTCCTCACTCA 60.360 61.111 0.00 0.00 0.00 3.41
694 738 2.101965 CGCTCGCTCCTCACTCAG 59.898 66.667 0.00 0.00 0.00 3.35
741 785 9.151471 GCATTAATGAGTAAGACTTGTGAGTAA 57.849 33.333 19.73 0.00 35.88 2.24
766 814 5.871465 TTTTTGTTTGTTTTCTTGGAGGC 57.129 34.783 0.00 0.00 0.00 4.70
803 851 0.750546 GTAATGCCCCTCCCGTTTCC 60.751 60.000 0.00 0.00 0.00 3.13
841 889 4.351054 CCACCCACTGGCCTCCAC 62.351 72.222 3.32 0.00 31.36 4.02
842 890 3.252284 CACCCACTGGCCTCCACT 61.252 66.667 3.32 0.00 33.59 4.00
843 891 2.930562 ACCCACTGGCCTCCACTC 60.931 66.667 3.32 0.00 33.59 3.51
844 892 3.721706 CCCACTGGCCTCCACTCC 61.722 72.222 3.32 0.00 0.00 3.85
845 893 2.930019 CCACTGGCCTCCACTCCA 60.930 66.667 3.32 0.00 0.00 3.86
876 924 3.587061 TCCCTCTCTTATTCAAACCTGCA 59.413 43.478 0.00 0.00 0.00 4.41
912 960 1.219393 CGCCTCCTTCCTCTTCCAC 59.781 63.158 0.00 0.00 0.00 4.02
976 1041 0.035630 CTGAGTTGCCTTCTCTGGGG 60.036 60.000 0.00 0.00 33.59 4.96
1071 1136 2.381941 GGAGCAGGGGAAGGAGCAT 61.382 63.158 0.00 0.00 0.00 3.79
1440 1505 1.215382 CGCGGTCAAGATCCAGACA 59.785 57.895 14.80 0.00 36.50 3.41
1472 1537 2.931320 GCTTCCTGGTGAGTAACTTCCG 60.931 54.545 0.00 0.00 0.00 4.30
1549 1614 5.320723 TCGAATCAATGCGTGTTGAATTAC 58.679 37.500 8.33 1.95 41.09 1.89
1775 1840 0.525668 CGCTACTCGCTGGTAAGTGG 60.526 60.000 0.00 0.00 36.13 4.00
1948 2018 3.000819 ATTCCCGGAGCGACCACA 61.001 61.111 0.73 0.00 38.90 4.17
2005 2075 4.034258 TGGAGTCGTCGTCGTGCC 62.034 66.667 1.33 3.23 38.33 5.01
2628 2752 3.784763 AGAAGGGATGGTGATGAACTGAT 59.215 43.478 0.00 0.00 0.00 2.90
2630 2754 2.848694 AGGGATGGTGATGAACTGATGT 59.151 45.455 0.00 0.00 0.00 3.06
2669 2793 9.016623 TCGATCGTGAAGTACAATTAATTACTG 57.983 33.333 15.94 0.00 0.00 2.74
2672 2800 9.811995 ATCGTGAAGTACAATTAATTACTGCTA 57.188 29.630 9.54 0.00 0.00 3.49
2678 2806 8.086143 AGTACAATTAATTACTGCTACCTCCA 57.914 34.615 0.00 0.00 0.00 3.86
2713 2842 4.808767 AGGGTAGGGGGAATTGTTAATC 57.191 45.455 0.00 0.00 0.00 1.75
2733 2862 3.015327 TCTCTAGTTACCGCTTCTCACC 58.985 50.000 0.00 0.00 0.00 4.02
2741 2870 0.041312 CCGCTTCTCACCGTTGTTTG 60.041 55.000 0.00 0.00 0.00 2.93
2745 2874 3.242478 CGCTTCTCACCGTTGTTTGTTTA 60.242 43.478 0.00 0.00 0.00 2.01
2747 2876 4.675114 GCTTCTCACCGTTGTTTGTTTATG 59.325 41.667 0.00 0.00 0.00 1.90
2748 2877 4.822036 TCTCACCGTTGTTTGTTTATGG 57.178 40.909 0.00 0.00 0.00 2.74
2753 2882 3.816523 ACCGTTGTTTGTTTATGGATCGT 59.183 39.130 0.00 0.00 0.00 3.73
2754 2883 4.155449 CCGTTGTTTGTTTATGGATCGTG 58.845 43.478 0.00 0.00 0.00 4.35
2789 2929 1.302431 TGGCCATGACTCCGTTGTG 60.302 57.895 0.00 0.00 0.00 3.33
2818 2958 4.889409 AGGTTCAGAAATGAAACTCTGCAA 59.111 37.500 2.74 0.00 41.57 4.08
2985 3134 0.328258 ACCAAGTGAGTGGGCATACC 59.672 55.000 0.00 0.00 43.56 2.73
2994 3143 1.922057 TGGGCATACCACCATCAGG 59.078 57.895 0.00 0.00 46.80 3.86
2995 3144 1.529244 GGGCATACCACCATCAGGC 60.529 63.158 0.00 0.00 39.85 4.85
2996 3145 1.533711 GGCATACCACCATCAGGCT 59.466 57.895 0.00 0.00 39.06 4.58
2997 3146 0.764890 GGCATACCACCATCAGGCTA 59.235 55.000 0.00 0.00 39.06 3.93
2998 3147 1.271054 GGCATACCACCATCAGGCTAG 60.271 57.143 0.00 0.00 39.06 3.42
2999 3148 1.879796 GCATACCACCATCAGGCTAGC 60.880 57.143 6.04 6.04 39.06 3.42
3000 3149 1.417517 CATACCACCATCAGGCTAGCA 59.582 52.381 18.24 0.00 39.06 3.49
3001 3150 1.578897 TACCACCATCAGGCTAGCAA 58.421 50.000 18.24 1.14 39.06 3.91
3002 3151 0.698238 ACCACCATCAGGCTAGCAAA 59.302 50.000 18.24 0.74 39.06 3.68
3003 3152 1.075374 ACCACCATCAGGCTAGCAAAA 59.925 47.619 18.24 0.33 39.06 2.44
3004 3153 1.474077 CCACCATCAGGCTAGCAAAAC 59.526 52.381 18.24 0.00 39.06 2.43
3005 3154 1.131126 CACCATCAGGCTAGCAAAACG 59.869 52.381 18.24 1.23 39.06 3.60
3017 3166 0.666274 GCAAAACGCTAAGGCCAACC 60.666 55.000 5.01 0.00 37.77 3.77
3040 3189 3.484547 GCGCGACCCCAAACGTAG 61.485 66.667 12.10 0.00 0.00 3.51
3052 3201 0.107268 AAACGTAGGTCCGGTTTGCT 59.893 50.000 0.00 0.00 33.05 3.91
3095 3244 3.399181 GATGGGGGCGTGTCTGGA 61.399 66.667 0.00 0.00 0.00 3.86
3182 3344 6.767423 GGGCCAAAAATGCTATTTTCATATGT 59.233 34.615 4.39 0.00 30.31 2.29
3215 3380 5.885881 TGCACGTCCAAATATTAATTGTCC 58.114 37.500 0.00 0.00 0.00 4.02
3259 3424 6.072673 ACAACCCAATCGAAATTGTCTCTAAC 60.073 38.462 0.00 0.00 40.63 2.34
3296 3462 7.973601 ACAACCAAATCAAAATTGTCTTCAAC 58.026 30.769 0.00 0.00 36.33 3.18
3354 3520 5.511373 CCAATATGATCCCACACGTACTCAT 60.511 44.000 0.00 0.00 0.00 2.90
3494 3660 5.824904 AATCAAATCCTTGGTCGAAGATG 57.175 39.130 0.00 0.00 40.67 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 0.098376 CAGGTAGAGGCGTACGTGAC 59.902 60.000 17.90 7.84 39.92 3.67
52 53 0.321919 ACAGGTAGAGGCGTACGTGA 60.322 55.000 17.90 0.00 39.92 4.35
53 54 0.179171 CACAGGTAGAGGCGTACGTG 60.179 60.000 17.90 16.31 42.13 4.49
54 55 1.310933 CCACAGGTAGAGGCGTACGT 61.311 60.000 17.90 0.00 0.00 3.57
55 56 1.432251 CCACAGGTAGAGGCGTACG 59.568 63.158 11.84 11.84 0.00 3.67
61 62 2.125512 GCGTGCCACAGGTAGAGG 60.126 66.667 0.00 0.00 0.00 3.69
70 71 0.592247 CTTTTCACAGTGCGTGCCAC 60.592 55.000 0.00 0.00 45.92 5.01
81 83 3.120792 CGTCTCCTTTCGTCTTTTCACA 58.879 45.455 0.00 0.00 0.00 3.58
178 183 2.515523 GCGCTGCATGGTGGAGAT 60.516 61.111 0.00 0.00 38.14 2.75
188 193 4.010224 TTTCGGGTAGGCGCTGCA 62.010 61.111 7.64 0.00 0.00 4.41
216 221 2.224305 GGGCTGCGATATGGAAGTACTT 60.224 50.000 8.13 8.13 0.00 2.24
250 257 2.358247 GTCTGGCCCGAAAGCGAA 60.358 61.111 0.00 0.00 40.82 4.70
259 267 4.410400 CCCGGTGAAGTCTGGCCC 62.410 72.222 0.00 0.00 32.85 5.80
309 317 5.126384 GGAAAGAGCAGTGAGTAGTACTGAT 59.874 44.000 7.76 2.42 46.36 2.90
320 328 0.241213 CGTCGAGGAAAGAGCAGTGA 59.759 55.000 0.00 0.00 0.00 3.41
321 329 0.241213 TCGTCGAGGAAAGAGCAGTG 59.759 55.000 5.12 0.00 0.00 3.66
322 330 0.241481 GTCGTCGAGGAAAGAGCAGT 59.759 55.000 9.78 0.00 0.00 4.40
403 414 4.437239 GTCAGCTCGTGGTAGTACTACTA 58.563 47.826 27.71 21.66 36.36 1.82
404 415 3.269178 GTCAGCTCGTGGTAGTACTACT 58.731 50.000 27.71 7.78 36.36 2.57
405 416 2.354199 GGTCAGCTCGTGGTAGTACTAC 59.646 54.545 22.53 22.53 35.40 2.73
406 417 2.026915 TGGTCAGCTCGTGGTAGTACTA 60.027 50.000 0.00 0.00 0.00 1.82
408 419 1.135460 GTGGTCAGCTCGTGGTAGTAC 60.135 57.143 0.00 0.00 0.00 2.73
454 477 1.383803 AGCCATGTCCTCCTCTCCC 60.384 63.158 0.00 0.00 0.00 4.30
477 500 1.675641 GATTGGCGCAAGGGAGTGT 60.676 57.895 10.83 0.00 38.28 3.55
491 514 4.493350 CGCAGCGATAGTTCAAAAAGATTG 59.507 41.667 9.98 0.00 39.35 2.67
492 515 4.154195 ACGCAGCGATAGTTCAAAAAGATT 59.846 37.500 24.65 0.00 39.35 2.40
540 579 0.608130 GAGGGATTTGGTTTGGTGCC 59.392 55.000 0.00 0.00 0.00 5.01
586 625 3.258228 AACGCTCTCTGCCATGCCA 62.258 57.895 0.00 0.00 38.78 4.92
587 626 2.437359 AACGCTCTCTGCCATGCC 60.437 61.111 0.00 0.00 38.78 4.40
588 627 2.789917 CAACGCTCTCTGCCATGC 59.210 61.111 0.00 0.00 38.78 4.06
589 628 1.374343 ATGCAACGCTCTCTGCCATG 61.374 55.000 0.00 0.00 37.79 3.66
590 629 1.077930 ATGCAACGCTCTCTGCCAT 60.078 52.632 0.00 0.00 37.79 4.40
686 730 2.033755 GGTGCTGCTGCTGAGTGAG 61.034 63.158 17.00 0.00 40.48 3.51
687 731 2.031616 GGTGCTGCTGCTGAGTGA 59.968 61.111 17.00 0.00 40.48 3.41
688 732 1.674651 ATGGTGCTGCTGCTGAGTG 60.675 57.895 17.00 0.00 40.48 3.51
689 733 1.674651 CATGGTGCTGCTGCTGAGT 60.675 57.895 17.00 0.00 40.48 3.41
690 734 3.052620 GCATGGTGCTGCTGCTGAG 62.053 63.158 17.00 0.00 40.96 3.35
691 735 3.060000 GCATGGTGCTGCTGCTGA 61.060 61.111 17.00 0.90 40.96 4.26
692 736 2.710902 ATGCATGGTGCTGCTGCTG 61.711 57.895 17.00 7.59 45.31 4.41
693 737 2.362503 ATGCATGGTGCTGCTGCT 60.363 55.556 17.00 0.00 45.31 4.24
694 738 2.202743 CATGCATGGTGCTGCTGC 60.203 61.111 19.40 8.89 45.31 5.25
766 814 6.586082 GGCATTACAGGACAAAAACAATAGTG 59.414 38.462 0.00 0.00 0.00 2.74
803 851 2.623416 GGGAGCGGGATCCAAATAAAAG 59.377 50.000 15.23 0.00 41.52 2.27
841 889 1.069358 GAGAGGGAAACGGCTATGGAG 59.931 57.143 0.00 0.00 0.00 3.86
842 890 1.120530 GAGAGGGAAACGGCTATGGA 58.879 55.000 0.00 0.00 0.00 3.41
843 891 1.123928 AGAGAGGGAAACGGCTATGG 58.876 55.000 0.00 0.00 0.00 2.74
844 892 2.990066 AAGAGAGGGAAACGGCTATG 57.010 50.000 0.00 0.00 0.00 2.23
845 893 4.654262 TGAATAAGAGAGGGAAACGGCTAT 59.346 41.667 0.00 0.00 0.00 2.97
876 924 3.303135 TGAGGCGTGAGAAGCGGT 61.303 61.111 0.00 0.00 35.00 5.68
912 960 1.010797 GCGTGTGTGTGAAGTGCAG 60.011 57.895 0.00 0.00 0.00 4.41
1926 1996 2.043349 TCGCTCCGGGAATCCTCA 60.043 61.111 0.00 0.00 0.00 3.86
2005 2075 4.487412 GCTCCGGTCGTACCCGTG 62.487 72.222 0.00 3.90 46.66 4.94
2628 2752 2.223272 CGATCGAGTGAATCCGAGAACA 60.223 50.000 10.26 0.00 38.25 3.18
2630 2754 2.014857 ACGATCGAGTGAATCCGAGAA 58.985 47.619 24.34 0.00 38.25 2.87
2669 2793 3.231818 TCAGGCTATTACTGGAGGTAGC 58.768 50.000 0.00 0.00 38.98 3.58
2672 2800 4.421131 CCTATCAGGCTATTACTGGAGGT 58.579 47.826 0.00 0.00 36.01 3.85
2678 2806 4.264895 CCCCTACCCTATCAGGCTATTACT 60.265 50.000 0.00 0.00 32.73 2.24
2713 2842 2.223294 CGGTGAGAAGCGGTAACTAGAG 60.223 54.545 0.00 0.00 0.00 2.43
2733 2862 4.778904 ACACGATCCATAAACAAACAACG 58.221 39.130 0.00 0.00 0.00 4.10
2741 2870 5.873164 ACAGAGGTTAACACGATCCATAAAC 59.127 40.000 8.10 0.00 0.00 2.01
2745 2874 3.369471 CCACAGAGGTTAACACGATCCAT 60.369 47.826 8.10 0.00 0.00 3.41
2747 2876 2.618053 CCACAGAGGTTAACACGATCC 58.382 52.381 8.10 0.00 0.00 3.36
2748 2877 2.000447 GCCACAGAGGTTAACACGATC 59.000 52.381 8.10 0.00 40.61 3.69
2753 2882 1.202758 CCACAGCCACAGAGGTTAACA 60.203 52.381 8.10 0.00 40.61 2.41
2754 2883 1.523758 CCACAGCCACAGAGGTTAAC 58.476 55.000 0.00 0.00 40.61 2.01
2789 2929 6.931840 AGAGTTTCATTTCTGAACCTAGACAC 59.068 38.462 0.00 0.00 41.05 3.67
2818 2958 7.491682 ACATGTTTACACAAAGCAAGAGAAAT 58.508 30.769 0.00 0.00 36.16 2.17
2985 3134 1.131126 CGTTTTGCTAGCCTGATGGTG 59.869 52.381 13.29 0.00 35.27 4.17
2986 3135 1.453155 CGTTTTGCTAGCCTGATGGT 58.547 50.000 13.29 0.00 35.27 3.55
2988 3137 3.611433 GCGTTTTGCTAGCCTGATG 57.389 52.632 13.29 4.31 41.73 3.07
2998 3147 0.666274 GGTTGGCCTTAGCGTTTTGC 60.666 55.000 3.32 0.00 46.98 3.68
2999 3148 0.038618 GGGTTGGCCTTAGCGTTTTG 60.039 55.000 3.32 0.00 41.24 2.44
3000 3149 1.183030 GGGGTTGGCCTTAGCGTTTT 61.183 55.000 3.32 0.00 41.24 2.43
3001 3150 1.605451 GGGGTTGGCCTTAGCGTTT 60.605 57.895 3.32 0.00 41.24 3.60
3002 3151 2.035155 GGGGTTGGCCTTAGCGTT 59.965 61.111 3.32 0.00 41.24 4.84
3003 3152 3.253838 TGGGGTTGGCCTTAGCGT 61.254 61.111 3.32 0.00 41.24 5.07
3004 3153 2.750237 GTGGGGTTGGCCTTAGCG 60.750 66.667 3.32 0.00 41.24 4.26
3005 3154 2.362503 GGTGGGGTTGGCCTTAGC 60.363 66.667 3.32 1.12 38.76 3.09
3085 3234 4.504132 GGACAGATCCAGACACGC 57.496 61.111 0.00 0.00 45.47 5.34
3095 3244 1.690633 ACCGCATCCCAGGACAGAT 60.691 57.895 0.00 0.00 0.00 2.90
3136 3294 2.409870 GCGGACAGGATGGGCAAAG 61.410 63.158 0.00 0.00 43.62 2.77
3182 3344 7.675962 ATATTTGGACGTGCAAACTAGTTTA 57.324 32.000 33.15 21.64 0.00 2.01
3265 3431 9.442047 AGACAATTTTGATTTGGTTGTAAAACA 57.558 25.926 0.00 0.00 45.47 2.83
3354 3520 6.975196 TTTGGATCTTCAAAATGACTTGGA 57.025 33.333 0.00 0.00 34.17 3.53
3494 3660 1.587613 GGACGAGCGTGATGAGAGC 60.588 63.158 0.00 0.00 0.00 4.09
3536 3702 2.072298 GAGGTGATGACTGCTTGTGTC 58.928 52.381 0.00 0.00 35.21 3.67


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

AutoCloner maintained by Alex Coulton.