Multiple sequence alignment - TraesCS3B01G043900

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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 TraesCS3B01G043900 chr3B 100.000 3134 0 0 1 3134 22455274 22452141 0.000000e+00 5788.0
1 TraesCS3B01G043900 chr3B 99.457 368 2 0 2718 3085 101913386 101913753 0.000000e+00 669.0
2 TraesCS3B01G043900 chr3D 91.260 2723 158 32 4 2678 15337255 15334565 0.000000e+00 3637.0
3 TraesCS3B01G043900 chr3D 89.584 2189 152 36 525 2657 489744239 489746407 0.000000e+00 2710.0
4 TraesCS3B01G043900 chr3D 85.532 864 107 9 1096 1944 15338363 15337503 0.000000e+00 887.0
5 TraesCS3B01G043900 chr3D 99.457 368 2 0 2718 3085 589277334 589276967 0.000000e+00 669.0
6 TraesCS3B01G043900 chr3D 91.892 74 6 0 39 112 453813611 453813538 1.540000e-18 104.0
7 TraesCS3B01G043900 chr3D 100.000 50 0 0 3085 3134 202632127 202632078 3.330000e-15 93.5
8 TraesCS3B01G043900 chr3A 90.264 2609 161 39 115 2675 20950028 20952591 0.000000e+00 3325.0
9 TraesCS3B01G043900 chr3A 93.162 117 7 1 9 124 20943974 20944090 1.490000e-38 171.0
10 TraesCS3B01G043900 chr5D 99.457 368 2 0 2718 3085 446175995 446176362 0.000000e+00 669.0
11 TraesCS3B01G043900 chr5D 99.185 368 3 0 2718 3085 446176509 446176876 0.000000e+00 664.0
12 TraesCS3B01G043900 chr5D 90.244 82 8 0 39 120 549026475 549026394 1.190000e-19 108.0
13 TraesCS3B01G043900 chrUn 99.185 368 3 0 2718 3085 216516392 216516025 0.000000e+00 664.0
14 TraesCS3B01G043900 chrUn 99.185 368 3 0 2718 3085 286266991 286267358 0.000000e+00 664.0
15 TraesCS3B01G043900 chrUn 99.185 368 3 0 2718 3085 389361346 389361713 0.000000e+00 664.0
16 TraesCS3B01G043900 chrUn 79.845 387 68 9 150 529 412734258 412733875 1.110000e-69 274.0
17 TraesCS3B01G043900 chrUn 79.452 365 67 7 170 529 12994047 12994408 5.190000e-63 252.0
18 TraesCS3B01G043900 chrUn 98.000 50 1 0 3085 3134 206792260 206792211 1.550000e-13 87.9
19 TraesCS3B01G043900 chrUn 98.000 50 1 0 3085 3134 246704904 246704855 1.550000e-13 87.9
20 TraesCS3B01G043900 chrUn 98.000 50 1 0 3085 3134 266185061 266185012 1.550000e-13 87.9
21 TraesCS3B01G043900 chr6D 99.185 368 3 0 2718 3085 168257137 168257504 0.000000e+00 664.0
22 TraesCS3B01G043900 chr1A 99.185 368 3 0 2718 3085 554514459 554514826 0.000000e+00 664.0
23 TraesCS3B01G043900 chr2A 74.950 1497 280 75 1113 2559 415063763 415062312 1.610000e-167 599.0
24 TraesCS3B01G043900 chr2A 75.685 876 166 36 1113 1959 750148319 750149176 8.150000e-106 394.0
25 TraesCS3B01G043900 chr2D 74.766 1498 283 75 1113 2559 317940863 317942316 4.500000e-163 584.0
26 TraesCS3B01G043900 chr2D 98.000 50 1 0 3085 3134 634989525 634989476 1.550000e-13 87.9
27 TraesCS3B01G043900 chr4B 89.869 306 29 2 150 453 644487431 644487736 2.930000e-105 392.0
28 TraesCS3B01G043900 chr4B 98.000 50 1 0 3085 3134 70585389 70585340 1.550000e-13 87.9
29 TraesCS3B01G043900 chr7D 74.543 876 154 50 1113 1959 498273591 498274426 5.040000e-83 318.0
30 TraesCS3B01G043900 chr2B 85.304 313 41 4 220 529 716043985 716044295 5.040000e-83 318.0
31 TraesCS3B01G043900 chr2B 80.481 374 70 3 151 522 741918128 741918500 1.840000e-72 283.0
32 TraesCS3B01G043900 chr2B 79.839 372 71 4 153 522 558039900 558040269 5.150000e-68 268.0
33 TraesCS3B01G043900 chr1D 80.282 355 64 6 170 521 475700813 475700462 2.400000e-66 263.0
34 TraesCS3B01G043900 chr1D 98.000 50 1 0 3085 3134 141350517 141350566 1.550000e-13 87.9
35 TraesCS3B01G043900 chr4A 85.849 106 14 1 9 113 449406482 449406587 9.190000e-21 111.0
36 TraesCS3B01G043900 chr4A 86.408 103 10 2 22 120 623361026 623361128 3.300000e-20 110.0
37 TraesCS3B01G043900 chr6A 88.636 88 10 0 29 116 593571007 593571094 1.190000e-19 108.0
38 TraesCS3B01G043900 chr6A 98.000 50 1 0 3085 3134 597220799 597220848 1.550000e-13 87.9
39 TraesCS3B01G043900 chr4D 83.186 113 16 3 9 120 283853406 283853516 1.990000e-17 100.0
40 TraesCS3B01G043900 chr4D 98.000 50 1 0 3085 3134 135041599 135041648 1.550000e-13 87.9
41 TraesCS3B01G043900 chr7B 86.747 83 11 0 25 107 523094953 523095035 3.330000e-15 93.5


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 TraesCS3B01G043900 chr3B 22452141 22455274 3133 True 5788.0 5788 100.000 1 3134 1 chr3B.!!$R1 3133
1 TraesCS3B01G043900 chr3D 489744239 489746407 2168 False 2710.0 2710 89.584 525 2657 1 chr3D.!!$F1 2132
2 TraesCS3B01G043900 chr3D 15334565 15338363 3798 True 2262.0 3637 88.396 4 2678 2 chr3D.!!$R4 2674
3 TraesCS3B01G043900 chr3A 20950028 20952591 2563 False 3325.0 3325 90.264 115 2675 1 chr3A.!!$F2 2560
4 TraesCS3B01G043900 chr5D 446175995 446176876 881 False 666.5 669 99.321 2718 3085 2 chr5D.!!$F1 367
5 TraesCS3B01G043900 chr2A 415062312 415063763 1451 True 599.0 599 74.950 1113 2559 1 chr2A.!!$R1 1446
6 TraesCS3B01G043900 chr2A 750148319 750149176 857 False 394.0 394 75.685 1113 1959 1 chr2A.!!$F1 846
7 TraesCS3B01G043900 chr2D 317940863 317942316 1453 False 584.0 584 74.766 1113 2559 1 chr2D.!!$F1 1446
8 TraesCS3B01G043900 chr7D 498273591 498274426 835 False 318.0 318 74.543 1113 1959 1 chr7D.!!$F1 846

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
41 1147 1.089920 GGCTCTGCAGTGTGTATTGG 58.910 55.000 14.67 0.0 0.00 3.16 F
922 2053 1.140852 TCTGCCAACAGTGCAAGTACT 59.859 47.619 0.00 0.0 44.77 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 2152 1.208535 CCATGCCGTAGTAAACTCCCA 59.791 52.381 0.00 0.0 0.00 4.37 R
2715 4039 0.175760 GATCTTGCGTGGCAGGTCTA 59.824 55.000 9.16 0.0 40.61 2.59 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
41 1147 1.089920 GGCTCTGCAGTGTGTATTGG 58.910 55.000 14.67 0.00 0.00 3.16
48 1154 1.346365 CAGTGTGTATTGGGTCGACG 58.654 55.000 9.92 0.00 0.00 5.12
77 1183 1.499049 GGCGAAGTCAGAGTCGTTTT 58.501 50.000 5.54 0.00 39.46 2.43
145 1251 8.628882 ACTGTTTGCAAGAACAATTTAAGTAC 57.371 30.769 5.52 0.00 38.90 2.73
148 1254 4.789784 TGCAAGAACAATTTAAGTACGGC 58.210 39.130 0.00 0.00 0.00 5.68
150 1256 5.009210 TGCAAGAACAATTTAAGTACGGCTT 59.991 36.000 0.00 0.00 41.05 4.35
218 1324 2.569404 AGTCGAGAGGCAAAAGATCCTT 59.431 45.455 0.00 0.00 38.99 3.36
220 1326 4.116238 GTCGAGAGGCAAAAGATCCTTAG 58.884 47.826 0.00 0.00 34.40 2.18
281 1387 6.866770 GCACACTCAGTACAACTATACTTTGA 59.133 38.462 0.00 0.00 32.92 2.69
286 1392 7.450634 ACTCAGTACAACTATACTTTGACAGGA 59.549 37.037 0.00 0.00 32.92 3.86
364 1470 8.786898 TGACTTTCATCAACTCCTTAATTTCAG 58.213 33.333 0.00 0.00 0.00 3.02
386 1493 3.726607 CCAGAGATGACCATAAGCAGAC 58.273 50.000 0.00 0.00 0.00 3.51
442 1549 2.092538 CCTCACTTGAGCCAGATTGGAT 60.093 50.000 0.26 0.00 39.95 3.41
445 1552 4.517285 TCACTTGAGCCAGATTGGATAAC 58.483 43.478 0.00 0.00 35.51 1.89
587 1697 3.443681 AGTTTGATTTATGTCTTGGCCCG 59.556 43.478 0.00 0.00 0.00 6.13
751 1861 9.853555 TGATCAATCAAACACCAATATAACAAC 57.146 29.630 0.00 0.00 33.08 3.32
802 1912 4.998051 ACAAGTCACCAACCTAATCCAAT 58.002 39.130 0.00 0.00 0.00 3.16
833 1943 8.357402 ACAACACCTAATGATTGTACCTTTTTC 58.643 33.333 0.00 0.00 33.51 2.29
834 1944 8.356657 CAACACCTAATGATTGTACCTTTTTCA 58.643 33.333 0.00 0.00 0.00 2.69
922 2053 1.140852 TCTGCCAACAGTGCAAGTACT 59.859 47.619 0.00 0.00 44.77 2.73
938 2069 6.893958 CAAGTACTTTGCTGAACGATAGAT 57.106 37.500 5.07 0.00 41.38 1.98
940 2071 4.806247 AGTACTTTGCTGAACGATAGATGC 59.194 41.667 0.00 0.00 41.38 3.91
941 2072 2.939103 ACTTTGCTGAACGATAGATGCC 59.061 45.455 0.00 0.00 41.38 4.40
942 2073 2.689553 TTGCTGAACGATAGATGCCA 57.310 45.000 0.00 0.00 41.38 4.92
943 2074 2.229675 TGCTGAACGATAGATGCCAG 57.770 50.000 0.00 0.00 41.38 4.85
944 2075 1.756538 TGCTGAACGATAGATGCCAGA 59.243 47.619 0.00 0.00 41.38 3.86
945 2076 2.366590 TGCTGAACGATAGATGCCAGAT 59.633 45.455 0.00 0.00 41.38 2.90
946 2077 2.992543 GCTGAACGATAGATGCCAGATC 59.007 50.000 0.00 0.00 41.38 2.75
998 2143 6.054860 AGCTAAACTGAGAGCTTAATTGGA 57.945 37.500 0.00 0.00 46.99 3.53
999 2144 6.112058 AGCTAAACTGAGAGCTTAATTGGAG 58.888 40.000 0.00 0.00 46.99 3.86
1000 2145 6.070538 AGCTAAACTGAGAGCTTAATTGGAGA 60.071 38.462 0.00 0.00 46.99 3.71
1001 2146 6.765512 GCTAAACTGAGAGCTTAATTGGAGAT 59.234 38.462 0.00 0.00 35.73 2.75
1002 2147 6.998968 AAACTGAGAGCTTAATTGGAGATG 57.001 37.500 0.00 0.00 0.00 2.90
1003 2148 5.033589 ACTGAGAGCTTAATTGGAGATGG 57.966 43.478 0.00 0.00 0.00 3.51
1004 2149 4.718774 ACTGAGAGCTTAATTGGAGATGGA 59.281 41.667 0.00 0.00 0.00 3.41
1005 2150 5.190528 ACTGAGAGCTTAATTGGAGATGGAA 59.809 40.000 0.00 0.00 0.00 3.53
1006 2151 6.126536 ACTGAGAGCTTAATTGGAGATGGAAT 60.127 38.462 0.00 0.00 0.00 3.01
1007 2152 6.666678 TGAGAGCTTAATTGGAGATGGAATT 58.333 36.000 0.00 0.00 0.00 2.17
1008 2153 6.544931 TGAGAGCTTAATTGGAGATGGAATTG 59.455 38.462 0.00 0.00 0.00 2.32
1009 2154 5.832060 AGAGCTTAATTGGAGATGGAATTGG 59.168 40.000 0.00 0.00 0.00 3.16
1010 2155 4.897670 AGCTTAATTGGAGATGGAATTGGG 59.102 41.667 0.00 0.00 0.00 4.12
1011 2156 4.895297 GCTTAATTGGAGATGGAATTGGGA 59.105 41.667 0.00 0.00 0.00 4.37
1012 2157 5.010415 GCTTAATTGGAGATGGAATTGGGAG 59.990 44.000 0.00 0.00 0.00 4.30
1013 2158 4.614967 AATTGGAGATGGAATTGGGAGT 57.385 40.909 0.00 0.00 0.00 3.85
1058 2227 2.995466 TTGATGCTTGTGCTAACTGC 57.005 45.000 0.00 0.00 40.48 4.40
1086 2258 4.017808 TGGTCTCTGCTACTTACCTCTTC 58.982 47.826 0.00 0.00 0.00 2.87
1109 2281 2.328319 GAGGAGGATGAGAGGCAAGAT 58.672 52.381 0.00 0.00 0.00 2.40
1190 2362 1.965754 GAGAAGCCGCTCCACCTCAT 61.966 60.000 0.00 0.00 0.00 2.90
1194 2366 2.513204 CCGCTCCACCTCATGCTG 60.513 66.667 0.00 0.00 0.00 4.41
1326 2498 2.241880 CGTCAACTTCGCCAACCGT 61.242 57.895 0.00 0.00 38.35 4.83
1377 2549 3.702048 GGCTACACGGGGCTGTCA 61.702 66.667 0.00 0.00 0.00 3.58
1599 2805 2.815945 CCTCATGGAGGCCATCGCT 61.816 63.158 5.01 0.00 43.15 4.93
1677 2883 3.181454 ACGAGTTCAAGAAAGTGGTGGAT 60.181 43.478 0.00 0.00 29.12 3.41
1891 3130 2.669808 GATCGGCGTGATGCTCTCGT 62.670 60.000 6.85 0.00 45.43 4.18
1939 3178 0.320771 AGACACTTTCATCGCCGCTT 60.321 50.000 0.00 0.00 0.00 4.68
1958 3197 1.617322 TTAGTCACCGTGAGTGCTCT 58.383 50.000 17.62 6.49 46.81 4.09
2339 3655 4.157120 GCCTACGCCATCCACCGT 62.157 66.667 0.00 0.00 41.11 4.83
2388 3707 2.291043 TTCAGGCCGGAGAGGTTCC 61.291 63.158 5.05 0.00 43.70 3.62
2438 3760 1.754234 GGGGATGATGCTGCCGTTT 60.754 57.895 0.00 0.00 0.00 3.60
2626 3948 2.483106 CTCTCTGCAAACCACATGACAG 59.517 50.000 0.00 0.00 0.00 3.51
2657 3981 5.279910 GGCTATGCTTCAATCAGGATCTAGT 60.280 44.000 0.00 0.00 0.00 2.57
2675 3999 6.080969 TCTAGTTAGTCCATCAAGTCTCCT 57.919 41.667 0.00 0.00 0.00 3.69
2678 4002 0.908198 AGTCCATCAAGTCTCCTGCC 59.092 55.000 0.00 0.00 0.00 4.85
2679 4003 0.107459 GTCCATCAAGTCTCCTGCCC 60.107 60.000 0.00 0.00 0.00 5.36
2680 4004 1.225704 CCATCAAGTCTCCTGCCCC 59.774 63.158 0.00 0.00 0.00 5.80
2681 4005 1.153289 CATCAAGTCTCCTGCCCCG 60.153 63.158 0.00 0.00 0.00 5.73
2682 4006 1.613630 ATCAAGTCTCCTGCCCCGT 60.614 57.895 0.00 0.00 0.00 5.28
2683 4007 0.325296 ATCAAGTCTCCTGCCCCGTA 60.325 55.000 0.00 0.00 0.00 4.02
2684 4008 1.218316 CAAGTCTCCTGCCCCGTAC 59.782 63.158 0.00 0.00 0.00 3.67
2685 4009 1.229082 AAGTCTCCTGCCCCGTACA 60.229 57.895 0.00 0.00 0.00 2.90
2686 4010 0.834687 AAGTCTCCTGCCCCGTACAA 60.835 55.000 0.00 0.00 0.00 2.41
2687 4011 0.834687 AGTCTCCTGCCCCGTACAAA 60.835 55.000 0.00 0.00 0.00 2.83
2688 4012 0.391263 GTCTCCTGCCCCGTACAAAG 60.391 60.000 0.00 0.00 0.00 2.77
2689 4013 0.834687 TCTCCTGCCCCGTACAAAGT 60.835 55.000 0.00 0.00 0.00 2.66
2690 4014 0.036306 CTCCTGCCCCGTACAAAGTT 59.964 55.000 0.00 0.00 0.00 2.66
2691 4015 0.250553 TCCTGCCCCGTACAAAGTTG 60.251 55.000 0.00 0.00 0.00 3.16
2692 4016 0.536460 CCTGCCCCGTACAAAGTTGT 60.536 55.000 1.75 1.75 44.86 3.32
2693 4017 1.270947 CCTGCCCCGTACAAAGTTGTA 60.271 52.381 0.00 0.00 42.35 2.41
2707 4031 7.690952 ACAAAGTTGTACTAAACCAAAGACA 57.309 32.000 0.00 0.00 40.16 3.41
2708 4032 8.288689 ACAAAGTTGTACTAAACCAAAGACAT 57.711 30.769 0.00 0.00 40.16 3.06
2709 4033 8.403236 ACAAAGTTGTACTAAACCAAAGACATC 58.597 33.333 0.00 0.00 40.16 3.06
2710 4034 8.621286 CAAAGTTGTACTAAACCAAAGACATCT 58.379 33.333 0.00 0.00 0.00 2.90
2711 4035 9.841295 AAAGTTGTACTAAACCAAAGACATCTA 57.159 29.630 0.00 0.00 0.00 1.98
2725 4049 5.957771 AGACATCTATTTTAGACCTGCCA 57.042 39.130 0.00 0.00 37.69 4.92
3033 4357 1.153353 GAACGGAATGCTCAAACCGA 58.847 50.000 19.02 0.00 46.94 4.69
3085 4409 5.877564 GCATAACTTGGGCTCCTAGAATATC 59.122 44.000 9.06 0.00 31.18 1.63
3086 4410 4.984146 AACTTGGGCTCCTAGAATATCC 57.016 45.455 9.06 0.00 31.18 2.59
3088 4412 2.344093 TGGGCTCCTAGAATATCCCC 57.656 55.000 0.00 0.00 32.88 4.81
3090 4414 1.196012 GGCTCCTAGAATATCCCCCG 58.804 60.000 0.00 0.00 0.00 5.73
3092 4416 1.196012 CTCCTAGAATATCCCCCGCC 58.804 60.000 0.00 0.00 0.00 6.13
3093 4417 0.252558 TCCTAGAATATCCCCCGCCC 60.253 60.000 0.00 0.00 0.00 6.13
3094 4418 1.272554 CCTAGAATATCCCCCGCCCC 61.273 65.000 0.00 0.00 0.00 5.80
3097 4855 0.996762 AGAATATCCCCCGCCCCAAA 60.997 55.000 0.00 0.00 0.00 3.28
3099 4857 2.656698 AATATCCCCCGCCCCAAAGC 62.657 60.000 0.00 0.00 0.00 3.51
3107 4865 2.665603 GCCCCAAAGCGAGACTCT 59.334 61.111 0.03 0.00 0.00 3.24
3109 4867 0.466124 GCCCCAAAGCGAGACTCTAT 59.534 55.000 0.03 0.00 0.00 1.98
3112 4870 1.757118 CCCAAAGCGAGACTCTATCCA 59.243 52.381 0.03 0.00 0.00 3.41
3115 4873 3.320541 CCAAAGCGAGACTCTATCCAGAT 59.679 47.826 0.03 0.00 0.00 2.90
3118 4876 3.674997 AGCGAGACTCTATCCAGATCTC 58.325 50.000 0.03 0.00 34.94 2.75
3119 4877 3.072330 AGCGAGACTCTATCCAGATCTCA 59.928 47.826 0.03 0.00 36.38 3.27
3120 4878 3.818210 GCGAGACTCTATCCAGATCTCAA 59.182 47.826 0.03 0.00 36.38 3.02
3124 4882 6.262049 CGAGACTCTATCCAGATCTCAAAGAA 59.738 42.308 0.03 0.00 36.38 2.52
3125 4883 7.040478 CGAGACTCTATCCAGATCTCAAAGAAT 60.040 40.741 0.03 0.00 36.38 2.40
3131 4889 8.572185 TCTATCCAGATCTCAAAGAATAACGAG 58.428 37.037 0.00 0.00 0.00 4.18
3132 4890 5.352284 TCCAGATCTCAAAGAATAACGAGC 58.648 41.667 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.179000 AGCCACGTGGAGATGAATCC 59.821 55.000 38.30 16.47 40.03 3.01
7 8 1.137872 AGAGCCACGTGGAGATGAATC 59.862 52.381 38.30 20.28 37.39 2.52
61 1167 4.442733 CACTGAGAAAACGACTCTGACTTC 59.557 45.833 0.00 0.00 37.00 3.01
77 1183 1.207089 CGCCATCCCTAAACACTGAGA 59.793 52.381 0.00 0.00 0.00 3.27
218 1324 2.569853 CACCAAGGACCACCATGTACTA 59.430 50.000 0.00 0.00 38.94 1.82
220 1326 1.821216 CACCAAGGACCACCATGTAC 58.179 55.000 0.00 0.00 38.94 2.90
248 1354 1.616865 GTACTGAGTGTGCCACCACTA 59.383 52.381 0.00 0.00 45.46 2.74
251 1357 0.833949 TTGTACTGAGTGTGCCACCA 59.166 50.000 0.00 0.77 34.49 4.17
252 1358 1.202651 AGTTGTACTGAGTGTGCCACC 60.203 52.381 0.00 0.00 34.49 4.61
281 1387 2.005370 TAGGGTTGTCGACTTCCTGT 57.995 50.000 24.63 16.49 0.00 4.00
286 1392 4.941873 GGATCAAAATAGGGTTGTCGACTT 59.058 41.667 17.92 0.00 0.00 3.01
364 1470 2.103771 TCTGCTTATGGTCATCTCTGGC 59.896 50.000 0.00 0.00 0.00 4.85
386 1493 0.319900 CAACGGATGGGCTAGATCGG 60.320 60.000 0.00 0.00 0.00 4.18
442 1549 4.099881 ACACACTAAACCTTCCAGTCGTTA 59.900 41.667 0.00 0.00 0.00 3.18
445 1552 3.107642 ACACACTAAACCTTCCAGTCG 57.892 47.619 0.00 0.00 0.00 4.18
607 1717 1.452145 ATCACGTTTGCTTTGGCGGT 61.452 50.000 0.00 0.00 42.25 5.68
651 1761 9.077885 TCATGTTGATGACTGCTACATAGTATA 57.922 33.333 0.00 0.00 33.40 1.47
652 1762 7.955918 TCATGTTGATGACTGCTACATAGTAT 58.044 34.615 0.00 0.00 33.40 2.12
726 1836 9.009327 CGTTGTTATATTGGTGTTTGATTGATC 57.991 33.333 0.00 0.00 0.00 2.92
861 1978 6.531021 TGGAAAGTAAAAGGACTTCACTAGG 58.469 40.000 0.00 0.00 38.75 3.02
922 2053 2.938451 CTGGCATCTATCGTTCAGCAAA 59.062 45.455 0.00 0.00 0.00 3.68
935 2066 1.039068 CTCCACGAGATCTGGCATCT 58.961 55.000 0.00 0.00 0.00 2.90
936 2067 0.749649 ACTCCACGAGATCTGGCATC 59.250 55.000 0.00 0.00 33.32 3.91
937 2068 1.198713 AACTCCACGAGATCTGGCAT 58.801 50.000 0.00 0.00 33.32 4.40
938 2069 1.847328 TAACTCCACGAGATCTGGCA 58.153 50.000 0.00 0.00 33.32 4.92
940 2071 4.341235 TGGTTATAACTCCACGAGATCTGG 59.659 45.833 15.05 0.00 33.32 3.86
941 2072 5.515797 TGGTTATAACTCCACGAGATCTG 57.484 43.478 15.05 0.00 33.32 2.90
942 2073 6.407074 CCTTTGGTTATAACTCCACGAGATCT 60.407 42.308 15.05 0.00 33.12 2.75
943 2074 5.753921 CCTTTGGTTATAACTCCACGAGATC 59.246 44.000 15.05 0.00 33.12 2.75
944 2075 5.189145 ACCTTTGGTTATAACTCCACGAGAT 59.811 40.000 15.05 0.00 33.12 2.75
945 2076 4.529377 ACCTTTGGTTATAACTCCACGAGA 59.471 41.667 15.05 0.00 33.12 4.04
946 2077 4.828829 ACCTTTGGTTATAACTCCACGAG 58.171 43.478 15.05 6.63 33.12 4.18
990 2135 6.091076 ACTCCCAATTCCATCTCCAATTAA 57.909 37.500 0.00 0.00 0.00 1.40
991 2136 5.732331 ACTCCCAATTCCATCTCCAATTA 57.268 39.130 0.00 0.00 0.00 1.40
992 2137 4.614967 ACTCCCAATTCCATCTCCAATT 57.385 40.909 0.00 0.00 0.00 2.32
993 2138 4.614967 AACTCCCAATTCCATCTCCAAT 57.385 40.909 0.00 0.00 0.00 3.16
994 2139 4.402616 AAACTCCCAATTCCATCTCCAA 57.597 40.909 0.00 0.00 0.00 3.53
995 2140 4.540099 AGTAAACTCCCAATTCCATCTCCA 59.460 41.667 0.00 0.00 0.00 3.86
996 2141 5.117406 AGTAAACTCCCAATTCCATCTCC 57.883 43.478 0.00 0.00 0.00 3.71
997 2142 5.753921 CGTAGTAAACTCCCAATTCCATCTC 59.246 44.000 0.00 0.00 0.00 2.75
998 2143 5.396436 CCGTAGTAAACTCCCAATTCCATCT 60.396 44.000 0.00 0.00 0.00 2.90
999 2144 4.814771 CCGTAGTAAACTCCCAATTCCATC 59.185 45.833 0.00 0.00 0.00 3.51
1000 2145 4.777463 CCGTAGTAAACTCCCAATTCCAT 58.223 43.478 0.00 0.00 0.00 3.41
1001 2146 3.620472 GCCGTAGTAAACTCCCAATTCCA 60.620 47.826 0.00 0.00 0.00 3.53
1002 2147 2.941064 GCCGTAGTAAACTCCCAATTCC 59.059 50.000 0.00 0.00 0.00 3.01
1003 2148 3.602483 TGCCGTAGTAAACTCCCAATTC 58.398 45.455 0.00 0.00 0.00 2.17
1004 2149 3.706600 TGCCGTAGTAAACTCCCAATT 57.293 42.857 0.00 0.00 0.00 2.32
1005 2150 3.541632 CATGCCGTAGTAAACTCCCAAT 58.458 45.455 0.00 0.00 0.00 3.16
1006 2151 2.355310 CCATGCCGTAGTAAACTCCCAA 60.355 50.000 0.00 0.00 0.00 4.12
1007 2152 1.208535 CCATGCCGTAGTAAACTCCCA 59.791 52.381 0.00 0.00 0.00 4.37
1008 2153 1.208776 ACCATGCCGTAGTAAACTCCC 59.791 52.381 0.00 0.00 0.00 4.30
1009 2154 2.685850 ACCATGCCGTAGTAAACTCC 57.314 50.000 0.00 0.00 0.00 3.85
1010 2155 5.353938 TCATTACCATGCCGTAGTAAACTC 58.646 41.667 0.00 0.00 30.33 3.01
1011 2156 5.347620 TCATTACCATGCCGTAGTAAACT 57.652 39.130 0.00 0.00 30.33 2.66
1012 2157 4.025145 GCTCATTACCATGCCGTAGTAAAC 60.025 45.833 0.00 0.00 30.33 2.01
1013 2158 4.124238 GCTCATTACCATGCCGTAGTAAA 58.876 43.478 0.00 0.00 30.33 2.01
1058 2227 2.949451 AGTAGCAGAGACCATGAACG 57.051 50.000 0.00 0.00 0.00 3.95
1086 2258 1.421480 TGCCTCTCATCCTCCTCATG 58.579 55.000 0.00 0.00 0.00 3.07
1530 2736 2.925170 AGCTCGACCCTGGCAACT 60.925 61.111 0.00 0.00 37.61 3.16
1774 2980 2.046892 CCTCCGGTTCACCAGCTG 60.047 66.667 6.78 6.78 35.14 4.24
1891 3130 2.892640 CGGATCGGACTCCTGCAA 59.107 61.111 0.00 0.00 32.77 4.08
1958 3197 2.217510 AGACGAAGCAGTAGGAGGAA 57.782 50.000 0.00 0.00 0.00 3.36
2121 3431 4.200283 CGCGCTCACCTCCTCTCC 62.200 72.222 5.56 0.00 0.00 3.71
2267 3583 3.699894 CCGTGGAGGCTGCAGTCT 61.700 66.667 23.48 23.48 0.00 3.24
2339 3655 4.918278 TCCCACACGGACGGGTCA 62.918 66.667 0.00 0.00 43.57 4.02
2388 3707 2.398036 GTCGGCGCCATTAACGTG 59.602 61.111 28.98 7.38 0.00 4.49
2543 3865 0.388649 GCGTCATGTCAACCTCGTCT 60.389 55.000 0.00 0.00 0.00 4.18
2657 3981 2.501723 GGCAGGAGACTTGATGGACTAA 59.498 50.000 0.00 0.00 40.21 2.24
2682 4006 8.789825 TGTCTTTGGTTTAGTACAACTTTGTA 57.210 30.769 0.00 0.00 42.35 2.41
2683 4007 7.690952 TGTCTTTGGTTTAGTACAACTTTGT 57.309 32.000 0.00 0.00 44.86 2.83
2684 4008 8.621286 AGATGTCTTTGGTTTAGTACAACTTTG 58.379 33.333 0.00 0.00 0.00 2.77
2685 4009 8.747538 AGATGTCTTTGGTTTAGTACAACTTT 57.252 30.769 0.00 0.00 0.00 2.66
2696 4020 9.014297 CAGGTCTAAAATAGATGTCTTTGGTTT 57.986 33.333 0.00 0.00 37.13 3.27
2697 4021 7.121315 GCAGGTCTAAAATAGATGTCTTTGGTT 59.879 37.037 0.00 0.00 37.13 3.67
2698 4022 6.599638 GCAGGTCTAAAATAGATGTCTTTGGT 59.400 38.462 0.00 0.00 37.13 3.67
2699 4023 6.038714 GGCAGGTCTAAAATAGATGTCTTTGG 59.961 42.308 0.00 0.00 37.13 3.28
2700 4024 6.599244 TGGCAGGTCTAAAATAGATGTCTTTG 59.401 38.462 0.00 0.00 37.13 2.77
2701 4025 6.599638 GTGGCAGGTCTAAAATAGATGTCTTT 59.400 38.462 0.00 0.00 37.13 2.52
2702 4026 6.116126 GTGGCAGGTCTAAAATAGATGTCTT 58.884 40.000 0.00 0.00 37.13 3.01
2703 4027 5.675538 GTGGCAGGTCTAAAATAGATGTCT 58.324 41.667 0.00 0.00 37.13 3.41
2704 4028 4.508124 CGTGGCAGGTCTAAAATAGATGTC 59.492 45.833 0.00 0.00 37.13 3.06
2705 4029 4.442706 CGTGGCAGGTCTAAAATAGATGT 58.557 43.478 0.00 0.00 37.13 3.06
2706 4030 3.248602 GCGTGGCAGGTCTAAAATAGATG 59.751 47.826 9.16 0.00 37.13 2.90
2707 4031 3.118408 TGCGTGGCAGGTCTAAAATAGAT 60.118 43.478 9.16 0.00 33.82 1.98
2708 4032 2.235155 TGCGTGGCAGGTCTAAAATAGA 59.765 45.455 9.16 0.00 33.32 1.98
2709 4033 2.627945 TGCGTGGCAGGTCTAAAATAG 58.372 47.619 9.16 0.00 33.32 1.73
2710 4034 2.772077 TGCGTGGCAGGTCTAAAATA 57.228 45.000 9.16 0.00 33.32 1.40
2711 4035 1.812571 CTTGCGTGGCAGGTCTAAAAT 59.187 47.619 9.16 0.00 40.61 1.82
2712 4036 1.202710 TCTTGCGTGGCAGGTCTAAAA 60.203 47.619 9.16 0.00 40.61 1.52
2713 4037 0.394938 TCTTGCGTGGCAGGTCTAAA 59.605 50.000 9.16 0.00 40.61 1.85
2714 4038 0.613260 ATCTTGCGTGGCAGGTCTAA 59.387 50.000 9.16 1.92 40.61 2.10
2715 4039 0.175760 GATCTTGCGTGGCAGGTCTA 59.824 55.000 9.16 0.00 40.61 2.59
2716 4040 1.078848 GATCTTGCGTGGCAGGTCT 60.079 57.895 9.16 0.00 40.61 3.85
2725 4049 2.427506 GGAAGACCAAAGATCTTGCGT 58.572 47.619 9.17 8.05 36.53 5.24
3033 4357 5.763204 TGAAAATTCGTTCCTCTAGCAGTTT 59.237 36.000 0.00 0.00 0.00 2.66
3090 4414 0.466124 ATAGAGTCTCGCTTTGGGGC 59.534 55.000 0.00 0.00 0.00 5.80
3092 4416 1.757118 TGGATAGAGTCTCGCTTTGGG 59.243 52.381 0.00 0.00 0.00 4.12
3093 4417 2.690497 TCTGGATAGAGTCTCGCTTTGG 59.310 50.000 0.00 0.00 0.00 3.28
3094 4418 4.278170 AGATCTGGATAGAGTCTCGCTTTG 59.722 45.833 0.00 0.00 36.14 2.77
3097 4855 3.072330 TGAGATCTGGATAGAGTCTCGCT 59.928 47.826 0.00 0.00 38.74 4.93
3099 4857 5.762711 TCTTTGAGATCTGGATAGAGTCTCG 59.237 44.000 0.00 0.00 38.74 4.04
3100 4858 7.581213 TTCTTTGAGATCTGGATAGAGTCTC 57.419 40.000 0.00 0.00 37.69 3.36
3102 4860 9.691362 GTTATTCTTTGAGATCTGGATAGAGTC 57.309 37.037 0.00 0.00 36.14 3.36
3103 4861 8.356657 CGTTATTCTTTGAGATCTGGATAGAGT 58.643 37.037 0.00 0.00 36.14 3.24
3107 4865 7.014711 AGCTCGTTATTCTTTGAGATCTGGATA 59.985 37.037 0.00 0.00 0.00 2.59
3109 4867 5.127845 AGCTCGTTATTCTTTGAGATCTGGA 59.872 40.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.