Multiple sequence alignment - TraesCS6D01G231200

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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 TraesCS6D01G231200 chr6D 100.000 3167 0 0 1 3167 324600417 324597251 0.000000e+00 5849
1 TraesCS6D01G231200 chr6D 76.252 1238 206 53 981 2169 324783127 324784325 7.620000e-161 577
2 TraesCS6D01G231200 chr6A 93.525 2749 125 22 446 3167 461988261 461985539 0.000000e+00 4041
3 TraesCS6D01G231200 chr6A 76.504 1230 206 46 994 2176 462225848 462227041 7.560000e-166 593
4 TraesCS6D01G231200 chr6B 94.621 1320 60 5 1497 2807 498852226 498853543 0.000000e+00 2034
5 TraesCS6D01G231200 chr6B 95.542 673 22 4 783 1450 498851469 498852138 0.000000e+00 1070
6 TraesCS6D01G231200 chr6B 76.547 1228 210 44 994 2176 498544056 498542862 4.520000e-168 601
7 TraesCS6D01G231200 chr6B 92.359 301 11 9 2873 3167 498854124 498854418 4.890000e-113 418
8 TraesCS6D01G231200 chr6B 85.079 315 26 10 468 781 498851090 498851384 5.130000e-78 302
9 TraesCS6D01G231200 chr3B 80.861 674 111 14 7 663 172225002 172224330 6.060000e-142 514
10 TraesCS6D01G231200 chr3B 75.248 505 73 27 981 1450 775735525 775736012 3.220000e-45 193
11 TraesCS6D01G231200 chr3B 82.547 212 32 4 1525 1735 775736098 775736305 6.980000e-42 182
12 TraesCS6D01G231200 chr3A 75.338 1257 206 65 981 2176 715973758 715974971 2.820000e-140 508
13 TraesCS6D01G231200 chr5B 80.678 678 107 18 7 664 579144565 579143892 3.650000e-139 505
14 TraesCS6D01G231200 chr1D 80.626 671 115 13 7 665 449127483 449128150 3.650000e-139 505
15 TraesCS6D01G231200 chr1D 80.535 673 107 20 7 663 449122319 449122983 2.190000e-136 496
16 TraesCS6D01G231200 chr1B 80.626 671 114 14 7 665 614611506 614612172 3.650000e-139 505
17 TraesCS6D01G231200 chr3D 80.650 677 105 18 7 663 610803146 610803816 4.720000e-138 501
18 TraesCS6D01G231200 chr3D 80.355 677 113 16 7 663 583547333 583548009 2.190000e-136 496
19 TraesCS6D01G231200 chr3D 79.728 661 103 22 1525 2173 580522320 580522961 1.730000e-122 449
20 TraesCS6D01G231200 chr3D 75.654 497 76 26 981 1449 580521754 580522233 4.140000e-49 206
21 TraesCS6D01G231200 chr4A 80.694 663 108 18 18 663 733564716 733565375 6.100000e-137 497
22 TraesCS6D01G231200 chr7D 80.207 677 111 17 7 663 57072490 57071817 1.320000e-133 486


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 TraesCS6D01G231200 chr6D 324597251 324600417 3166 True 5849.0 5849 100.00000 1 3167 1 chr6D.!!$R1 3166
1 TraesCS6D01G231200 chr6D 324783127 324784325 1198 False 577.0 577 76.25200 981 2169 1 chr6D.!!$F1 1188
2 TraesCS6D01G231200 chr6A 461985539 461988261 2722 True 4041.0 4041 93.52500 446 3167 1 chr6A.!!$R1 2721
3 TraesCS6D01G231200 chr6A 462225848 462227041 1193 False 593.0 593 76.50400 994 2176 1 chr6A.!!$F1 1182
4 TraesCS6D01G231200 chr6B 498851090 498854418 3328 False 956.0 2034 91.90025 468 3167 4 chr6B.!!$F1 2699
5 TraesCS6D01G231200 chr6B 498542862 498544056 1194 True 601.0 601 76.54700 994 2176 1 chr6B.!!$R1 1182
6 TraesCS6D01G231200 chr3B 172224330 172225002 672 True 514.0 514 80.86100 7 663 1 chr3B.!!$R1 656
7 TraesCS6D01G231200 chr3A 715973758 715974971 1213 False 508.0 508 75.33800 981 2176 1 chr3A.!!$F1 1195
8 TraesCS6D01G231200 chr5B 579143892 579144565 673 True 505.0 505 80.67800 7 664 1 chr5B.!!$R1 657
9 TraesCS6D01G231200 chr1D 449127483 449128150 667 False 505.0 505 80.62600 7 665 1 chr1D.!!$F2 658
10 TraesCS6D01G231200 chr1D 449122319 449122983 664 False 496.0 496 80.53500 7 663 1 chr1D.!!$F1 656
11 TraesCS6D01G231200 chr1B 614611506 614612172 666 False 505.0 505 80.62600 7 665 1 chr1B.!!$F1 658
12 TraesCS6D01G231200 chr3D 610803146 610803816 670 False 501.0 501 80.65000 7 663 1 chr3D.!!$F2 656
13 TraesCS6D01G231200 chr3D 583547333 583548009 676 False 496.0 496 80.35500 7 663 1 chr3D.!!$F1 656
14 TraesCS6D01G231200 chr3D 580521754 580522961 1207 False 327.5 449 77.69100 981 2173 2 chr3D.!!$F3 1192
15 TraesCS6D01G231200 chr4A 733564716 733565375 659 False 497.0 497 80.69400 18 663 1 chr4A.!!$F1 645
16 TraesCS6D01G231200 chr7D 57071817 57072490 673 True 486.0 486 80.20700 7 663 1 chr7D.!!$R1 656

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
359 360 0.035820 GCTCACCAAATCCGGTACCA 60.036 55.0 13.54 0.0 37.07 3.25 F
503 530 0.883833 CTCACAATGGAAGCCACCAC 59.116 55.0 1.49 0.0 43.03 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1664 3.128938 AGTGGAGCTATACACGAAGTCAC 59.871 47.826 9.26 0.00 45.79 3.67 R
2491 2753 1.599071 CTTGATACATCGGCGTGCAAT 59.401 47.619 6.85 2.52 0.00 3.56 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
24 25 1.514003 TCGGCAATAGCGACAACAAA 58.486 45.000 0.00 0.00 43.41 2.83
27 28 2.414029 CGGCAATAGCGACAACAAACAT 60.414 45.455 0.00 0.00 43.41 2.71
54 55 3.368116 GGCAAGATTTCAGCAAAGCAGAT 60.368 43.478 0.00 0.00 29.69 2.90
55 56 4.142315 GGCAAGATTTCAGCAAAGCAGATA 60.142 41.667 0.00 0.00 29.69 1.98
67 68 6.037500 CAGCAAAGCAGATATTACACAGCTTA 59.962 38.462 0.00 0.00 41.01 3.09
70 71 6.551385 AAGCAGATATTACACAGCTTATGC 57.449 37.500 0.00 0.00 40.19 3.14
71 72 4.999950 AGCAGATATTACACAGCTTATGCC 59.000 41.667 0.00 0.00 40.80 4.40
77 78 0.409484 ACACAGCTTATGCCCCCTTT 59.591 50.000 0.00 0.00 40.80 3.11
85 86 5.241728 CAGCTTATGCCCCCTTTAGTATTTC 59.758 44.000 0.00 0.00 40.80 2.17
98 99 5.779806 TTAGTATTTCGCAAACTGCTCTC 57.220 39.130 0.00 0.00 42.25 3.20
117 118 4.082845 TCTCAAACCACTGAACCAAACAA 58.917 39.130 0.00 0.00 0.00 2.83
124 125 3.510719 CACTGAACCAAACAACACCAAG 58.489 45.455 0.00 0.00 0.00 3.61
162 163 2.975489 ACACACAAGTTCCTGAGATCCT 59.025 45.455 0.00 0.00 0.00 3.24
164 165 2.569404 ACACAAGTTCCTGAGATCCTCC 59.431 50.000 0.00 0.00 0.00 4.30
182 183 4.840115 TCCTCCCAAAATTTCAGCTCAATT 59.160 37.500 0.00 0.00 0.00 2.32
188 189 5.178067 CCAAAATTTCAGCTCAATTGGACAC 59.822 40.000 5.42 0.00 38.44 3.67
203 204 2.238646 TGGACACTATTTGCCTACCCAG 59.761 50.000 0.00 0.00 0.00 4.45
204 205 2.238898 GGACACTATTTGCCTACCCAGT 59.761 50.000 0.00 0.00 0.00 4.00
210 211 3.525800 ATTTGCCTACCCAGTCTGTTT 57.474 42.857 0.00 0.00 0.00 2.83
222 223 5.130350 CCCAGTCTGTTTGTCTCCTAAAAA 58.870 41.667 0.00 0.00 0.00 1.94
226 227 7.444183 CCAGTCTGTTTGTCTCCTAAAAATACA 59.556 37.037 0.00 0.00 0.00 2.29
227 228 9.003658 CAGTCTGTTTGTCTCCTAAAAATACAT 57.996 33.333 0.00 0.00 0.00 2.29
231 232 9.398170 CTGTTTGTCTCCTAAAAATACATTGTG 57.602 33.333 0.00 0.00 0.00 3.33
254 255 2.878406 TGAAACTGCAGCAGTCTAAACC 59.122 45.455 28.38 13.54 44.62 3.27
289 290 4.163649 TCTCAAATCTGATGCTCCACTGAT 59.836 41.667 0.00 0.00 0.00 2.90
302 303 4.789807 CTCCACTGATCCAATCCTCAAAT 58.210 43.478 0.00 0.00 0.00 2.32
310 311 7.870509 TGATCCAATCCTCAAATCAGTTAAG 57.129 36.000 0.00 0.00 0.00 1.85
312 313 4.635765 TCCAATCCTCAAATCAGTTAAGCG 59.364 41.667 0.00 0.00 0.00 4.68
349 350 4.640771 AGTAAGGAATGAGCTCACCAAA 57.359 40.909 20.97 6.09 0.00 3.28
351 352 5.189180 AGTAAGGAATGAGCTCACCAAATC 58.811 41.667 20.97 12.02 0.00 2.17
352 353 3.010200 AGGAATGAGCTCACCAAATCC 57.990 47.619 20.97 19.76 0.00 3.01
355 356 0.620556 ATGAGCTCACCAAATCCGGT 59.379 50.000 20.97 0.00 41.07 5.28
356 357 1.271856 TGAGCTCACCAAATCCGGTA 58.728 50.000 13.74 0.00 37.07 4.02
357 358 1.066430 TGAGCTCACCAAATCCGGTAC 60.066 52.381 13.74 0.00 37.07 3.34
359 360 0.035820 GCTCACCAAATCCGGTACCA 60.036 55.000 13.54 0.00 37.07 3.25
375 377 3.572255 GGTACCAATCCAAGCACTTTGAA 59.428 43.478 7.15 0.00 39.21 2.69
377 379 3.299503 ACCAATCCAAGCACTTTGAACT 58.700 40.909 0.00 0.00 39.21 3.01
387 389 4.210331 AGCACTTTGAACTTCCAATCACT 58.790 39.130 0.00 0.00 0.00 3.41
390 392 5.239525 GCACTTTGAACTTCCAATCACTAGT 59.760 40.000 0.00 0.00 0.00 2.57
403 405 5.527214 CCAATCACTAGTTTGAACACTGTCA 59.473 40.000 8.58 0.00 0.00 3.58
404 406 6.422223 CAATCACTAGTTTGAACACTGTCAC 58.578 40.000 1.66 0.00 0.00 3.67
410 417 1.443802 TTGAACACTGTCACGTGCAA 58.556 45.000 11.67 3.68 38.45 4.08
442 452 9.243637 CTGAATATAACCTCTTCTTCTTCTTCG 57.756 37.037 0.00 0.00 0.00 3.79
451 461 4.390603 TCTTCTTCTTCTTCGTCTCTCTCG 59.609 45.833 0.00 0.00 0.00 4.04
466 485 4.082190 TCTCTCTCGTGGGTTGTATTCTTG 60.082 45.833 0.00 0.00 0.00 3.02
503 530 0.883833 CTCACAATGGAAGCCACCAC 59.116 55.000 1.49 0.00 43.03 4.16
505 532 1.603455 ACAATGGAAGCCACCACCG 60.603 57.895 1.49 0.00 43.03 4.94
506 533 2.035626 AATGGAAGCCACCACCGG 59.964 61.111 0.00 0.00 43.03 5.28
509 537 3.728373 GGAAGCCACCACCGGGAT 61.728 66.667 6.32 0.00 38.05 3.85
545 575 1.633774 TTCTCCTTGTCTCGCTTCCT 58.366 50.000 0.00 0.00 0.00 3.36
550 580 1.134670 CCTTGTCTCGCTTCCTTAGGG 60.135 57.143 0.00 0.00 38.13 3.53
600 630 1.163420 TCAACGGCTCACATGCGTTT 61.163 50.000 5.47 0.00 31.40 3.60
611 644 5.006649 GCTCACATGCGTTTGTCTTATATGA 59.993 40.000 0.00 0.00 0.00 2.15
613 646 6.106003 TCACATGCGTTTGTCTTATATGAGT 58.894 36.000 0.00 0.00 0.00 3.41
672 706 4.395625 ACTTAGCCCAACACCTACTTTTC 58.604 43.478 0.00 0.00 0.00 2.29
673 707 2.287977 AGCCCAACACCTACTTTTCC 57.712 50.000 0.00 0.00 0.00 3.13
718 752 7.075741 GTGTTGTAAAATGTACTTCGCAATCT 58.924 34.615 0.00 0.00 0.00 2.40
733 767 7.744715 ACTTCGCAATCTATTTTCGTTACAAAG 59.255 33.333 0.00 0.00 0.00 2.77
735 769 6.369340 TCGCAATCTATTTTCGTTACAAAGGA 59.631 34.615 0.00 0.00 0.00 3.36
736 770 6.682863 CGCAATCTATTTTCGTTACAAAGGAG 59.317 38.462 0.00 0.00 0.00 3.69
737 771 7.412563 CGCAATCTATTTTCGTTACAAAGGAGA 60.413 37.037 0.00 0.00 0.00 3.71
738 772 7.905493 GCAATCTATTTTCGTTACAAAGGAGAG 59.095 37.037 0.00 0.00 0.00 3.20
739 773 9.151471 CAATCTATTTTCGTTACAAAGGAGAGA 57.849 33.333 0.00 0.00 0.00 3.10
838 963 4.806247 CCAGTCACGTTCTCCTCAATAATC 59.194 45.833 0.00 0.00 0.00 1.75
965 1091 5.939764 ACACTTGAGCTCACCATATCTAA 57.060 39.130 18.03 0.00 0.00 2.10
990 1116 1.422531 ATCCTCTCCCAAGCTAGCTG 58.577 55.000 20.16 12.30 0.00 4.24
1021 1147 5.242838 ACAATGGCGAAATCTTTCACCTTAA 59.757 36.000 10.23 0.00 39.51 1.85
1464 1664 2.285977 GATAACCCCTAAACAGCGTGG 58.714 52.381 0.00 0.00 0.00 4.94
1792 2050 6.524586 GCACAAATTAACAGAGACTGCATTAC 59.475 38.462 0.00 0.00 34.37 1.89
2181 2442 3.041946 CCCCTAAGTTACAGCCTCATCT 58.958 50.000 0.00 0.00 0.00 2.90
2299 2560 4.202284 ACTGCGGGGATTGTATTTATACGT 60.202 41.667 0.00 0.00 36.06 3.57
2526 2790 4.570369 TGTATCAAGTTGTGTGAGTGTGTG 59.430 41.667 2.11 0.00 0.00 3.82
2527 2791 3.326836 TCAAGTTGTGTGAGTGTGTGA 57.673 42.857 2.11 0.00 0.00 3.58
2537 2801 2.033801 GTGAGTGTGTGATTTTGCAGCT 59.966 45.455 0.00 0.00 0.00 4.24
2601 2865 3.825585 TGTACTGAAATCTGCAATGCCAA 59.174 39.130 1.53 0.00 0.00 4.52
2659 2932 8.462811 AGTCACTCTCAATGTGTGTATTACTAG 58.537 37.037 0.00 0.00 40.09 2.57
2687 2960 0.469892 TGCACCTGAGTCACTCCTCA 60.470 55.000 1.24 0.00 39.11 3.86
2688 2961 0.901124 GCACCTGAGTCACTCCTCAT 59.099 55.000 1.24 0.00 40.53 2.90
2706 2979 3.289836 TCATTGGGGATGCACTACATTG 58.710 45.455 0.00 0.00 39.84 2.82
2745 3018 3.036819 TGTGCAGAGCTCTTCCTATGAT 58.963 45.455 15.27 0.00 0.00 2.45
2747 3020 2.295629 TGCAGAGCTCTTCCTATGATCG 59.704 50.000 15.27 0.00 0.00 3.69
2757 3030 5.292765 TCTTCCTATGATCGCTGATGTTTC 58.707 41.667 0.00 0.00 0.00 2.78
2798 3071 5.408880 TCTTCATGGACCGTGTAATTGTA 57.591 39.130 13.49 0.00 0.00 2.41
2869 3381 8.312564 AGTACTAGGAACTTTGGTAATCAGTTC 58.687 37.037 0.00 3.17 41.75 3.01
2924 3712 3.144657 TGACACATGCAGTTCTCCAAT 57.855 42.857 0.00 0.00 0.00 3.16
2938 3732 7.361286 GCAGTTCTCCAATAAAAAGTACAGGAG 60.361 40.741 0.00 0.00 41.88 3.69
2960 3754 2.370349 GCAGAGGCAGAGACTGTACTA 58.630 52.381 0.00 0.00 40.72 1.82
2970 3767 6.406400 GGCAGAGACTGTACTACTCATCAATT 60.406 42.308 13.62 0.00 33.43 2.32
2974 3771 8.779303 AGAGACTGTACTACTCATCAATTATCG 58.221 37.037 13.62 0.00 33.69 2.92
3006 3803 4.218852 ACTGTTCTCAGAAGGTACTACTGC 59.781 45.833 2.17 0.00 43.76 4.40
3007 3804 4.408276 TGTTCTCAGAAGGTACTACTGCT 58.592 43.478 0.00 0.00 38.49 4.24
3008 3805 4.218635 TGTTCTCAGAAGGTACTACTGCTG 59.781 45.833 1.59 1.59 44.17 4.41
3021 3818 7.982354 AGGTACTACTGCTGTTATTGAAAGATC 59.018 37.037 0.09 0.00 36.02 2.75
3077 3874 2.224305 ACACCAGAGCTTCAGTTGTACC 60.224 50.000 0.00 0.00 0.00 3.34
3092 3892 6.367695 TCAGTTGTACCATTCGACTTTACATG 59.632 38.462 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.530744 TGTCGCTATTGCCGAAGAGT 59.469 50.000 0.00 0.00 35.36 3.24
1 2 1.324736 GTTGTCGCTATTGCCGAAGAG 59.675 52.381 0.00 0.00 35.36 2.85
2 3 1.337354 TGTTGTCGCTATTGCCGAAGA 60.337 47.619 0.00 0.00 35.36 2.87
3 4 1.075542 TGTTGTCGCTATTGCCGAAG 58.924 50.000 0.00 0.00 35.36 3.79
4 5 1.514003 TTGTTGTCGCTATTGCCGAA 58.486 45.000 0.00 0.00 35.36 4.30
12 13 3.682858 GCCTCTTATGTTTGTTGTCGCTA 59.317 43.478 0.00 0.00 0.00 4.26
16 17 5.689383 TCTTGCCTCTTATGTTTGTTGTC 57.311 39.130 0.00 0.00 0.00 3.18
24 25 4.592942 TGCTGAAATCTTGCCTCTTATGT 58.407 39.130 0.00 0.00 0.00 2.29
27 28 4.082571 GCTTTGCTGAAATCTTGCCTCTTA 60.083 41.667 0.00 0.00 0.00 2.10
54 55 3.053077 AGGGGGCATAAGCTGTGTAATA 58.947 45.455 0.00 0.00 41.70 0.98
55 56 1.852965 AGGGGGCATAAGCTGTGTAAT 59.147 47.619 0.00 0.00 41.70 1.89
67 68 2.092103 TGCGAAATACTAAAGGGGGCAT 60.092 45.455 0.00 0.00 0.00 4.40
70 71 4.014406 AGTTTGCGAAATACTAAAGGGGG 58.986 43.478 0.00 0.00 0.00 5.40
71 72 4.674362 GCAGTTTGCGAAATACTAAAGGGG 60.674 45.833 0.00 0.00 31.71 4.79
98 99 3.677596 GTGTTGTTTGGTTCAGTGGTTTG 59.322 43.478 0.00 0.00 0.00 2.93
124 125 6.007936 TGTGTGTCTATTTGTATGCCAAAC 57.992 37.500 0.00 0.00 45.43 2.93
132 133 6.822442 TCAGGAACTTGTGTGTCTATTTGTA 58.178 36.000 0.00 0.00 34.60 2.41
137 138 5.105146 GGATCTCAGGAACTTGTGTGTCTAT 60.105 44.000 0.00 0.00 34.60 1.98
147 148 2.649742 TGGGAGGATCTCAGGAACTT 57.350 50.000 0.00 0.00 43.69 2.66
162 163 4.592351 TCCAATTGAGCTGAAATTTTGGGA 59.408 37.500 14.36 9.61 34.33 4.37
164 165 5.178067 GTGTCCAATTGAGCTGAAATTTTGG 59.822 40.000 7.12 9.70 34.75 3.28
182 183 2.238646 CTGGGTAGGCAAATAGTGTCCA 59.761 50.000 0.00 0.00 29.16 4.02
188 189 3.914426 ACAGACTGGGTAGGCAAATAG 57.086 47.619 7.51 0.00 32.87 1.73
203 204 9.612620 CAATGTATTTTTAGGAGACAAACAGAC 57.387 33.333 0.00 0.00 0.00 3.51
204 205 9.349713 ACAATGTATTTTTAGGAGACAAACAGA 57.650 29.630 0.00 0.00 0.00 3.41
210 211 6.939730 TCAGCACAATGTATTTTTAGGAGACA 59.060 34.615 0.00 0.00 0.00 3.41
222 223 4.430137 CTGCAGTTTCAGCACAATGTAT 57.570 40.909 5.25 0.00 37.02 2.29
249 250 8.912988 AGATTTGAGAGTGATTTTGTTGGTTTA 58.087 29.630 0.00 0.00 0.00 2.01
250 251 7.707893 CAGATTTGAGAGTGATTTTGTTGGTTT 59.292 33.333 0.00 0.00 0.00 3.27
252 253 6.547141 TCAGATTTGAGAGTGATTTTGTTGGT 59.453 34.615 0.00 0.00 0.00 3.67
254 255 7.061905 GCATCAGATTTGAGAGTGATTTTGTTG 59.938 37.037 0.00 0.00 36.61 3.33
289 290 4.635765 CGCTTAACTGATTTGAGGATTGGA 59.364 41.667 0.00 0.00 0.00 3.53
302 303 3.693085 AGTACTTCGATCCGCTTAACTGA 59.307 43.478 0.00 0.00 0.00 3.41
306 307 4.707030 TTGAGTACTTCGATCCGCTTAA 57.293 40.909 0.00 0.00 0.00 1.85
310 311 2.877335 ACTTTGAGTACTTCGATCCGC 58.123 47.619 0.00 0.00 0.00 5.54
312 313 6.205101 TCCTTACTTTGAGTACTTCGATCC 57.795 41.667 0.00 0.00 28.93 3.36
349 350 0.916086 TGCTTGGATTGGTACCGGAT 59.084 50.000 9.46 3.68 0.00 4.18
351 352 0.035439 AGTGCTTGGATTGGTACCGG 60.035 55.000 7.57 0.00 0.00 5.28
352 353 1.821216 AAGTGCTTGGATTGGTACCG 58.179 50.000 7.57 0.00 0.00 4.02
355 356 4.469657 AGTTCAAAGTGCTTGGATTGGTA 58.530 39.130 0.00 0.00 35.56 3.25
356 357 3.299503 AGTTCAAAGTGCTTGGATTGGT 58.700 40.909 0.00 0.00 35.56 3.67
357 358 4.301628 GAAGTTCAAAGTGCTTGGATTGG 58.698 43.478 0.00 0.00 35.56 3.16
359 360 3.960102 TGGAAGTTCAAAGTGCTTGGATT 59.040 39.130 5.01 0.00 35.56 3.01
375 377 6.260936 CAGTGTTCAAACTAGTGATTGGAAGT 59.739 38.462 0.00 0.00 0.00 3.01
377 379 6.119536 ACAGTGTTCAAACTAGTGATTGGAA 58.880 36.000 0.00 0.00 0.00 3.53
387 389 2.605818 GCACGTGACAGTGTTCAAACTA 59.394 45.455 22.23 0.00 43.61 2.24
390 392 1.443802 TGCACGTGACAGTGTTCAAA 58.556 45.000 22.23 0.00 43.61 2.69
403 405 2.717580 TATTCAGACTCGTTGCACGT 57.282 45.000 8.22 0.00 43.14 4.49
404 406 4.026804 GGTTATATTCAGACTCGTTGCACG 60.027 45.833 0.00 0.00 44.19 5.34
410 417 7.558444 AGAAGAAGAGGTTATATTCAGACTCGT 59.442 37.037 0.00 0.00 31.22 4.18
412 419 9.744468 GAAGAAGAAGAGGTTATATTCAGACTC 57.256 37.037 0.00 0.00 31.22 3.36
419 426 8.973182 AGACGAAGAAGAAGAAGAGGTTATATT 58.027 33.333 0.00 0.00 0.00 1.28
423 430 6.005198 AGAGACGAAGAAGAAGAAGAGGTTA 58.995 40.000 0.00 0.00 0.00 2.85
442 452 3.444388 AGAATACAACCCACGAGAGAGAC 59.556 47.826 0.00 0.00 0.00 3.36
451 461 3.638484 GCACAACAAGAATACAACCCAC 58.362 45.455 0.00 0.00 0.00 4.61
466 485 0.038709 AGACTGAGAGAGCGCACAAC 60.039 55.000 11.47 1.64 0.00 3.32
503 530 1.683917 CTCTAGTCAGTCCAATCCCGG 59.316 57.143 0.00 0.00 0.00 5.73
505 532 4.828072 AAACTCTAGTCAGTCCAATCCC 57.172 45.455 0.00 0.00 0.00 3.85
506 533 6.043854 AGAAAACTCTAGTCAGTCCAATCC 57.956 41.667 0.00 0.00 0.00 3.01
508 536 5.782845 AGGAGAAAACTCTAGTCAGTCCAAT 59.217 40.000 0.00 0.00 0.00 3.16
509 537 5.148502 AGGAGAAAACTCTAGTCAGTCCAA 58.851 41.667 0.00 0.00 0.00 3.53
535 564 0.324368 TGCTCCCTAAGGAAGCGAGA 60.324 55.000 0.00 0.00 43.40 4.04
545 575 2.752030 ACAGCTGATAGTGCTCCCTAA 58.248 47.619 23.35 0.00 38.92 2.69
550 580 2.568696 TCGAACAGCTGATAGTGCTC 57.431 50.000 23.35 4.04 38.92 4.26
600 630 7.928167 CAGCCTAACATCAACTCATATAAGACA 59.072 37.037 0.00 0.00 0.00 3.41
611 644 2.162681 GTTGGCAGCCTAACATCAACT 58.837 47.619 14.15 0.00 33.77 3.16
613 646 1.885887 GTGTTGGCAGCCTAACATCAA 59.114 47.619 23.81 3.80 38.84 2.57
688 722 6.086241 GCGAAGTACATTTTACAACACACATG 59.914 38.462 0.00 0.00 0.00 3.21
689 723 6.140110 GCGAAGTACATTTTACAACACACAT 58.860 36.000 0.00 0.00 0.00 3.21
690 724 5.064834 TGCGAAGTACATTTTACAACACACA 59.935 36.000 0.00 0.00 0.00 3.72
693 727 7.075741 AGATTGCGAAGTACATTTTACAACAC 58.924 34.615 0.00 0.00 0.00 3.32
700 734 8.234546 ACGAAAATAGATTGCGAAGTACATTTT 58.765 29.630 0.00 0.00 0.00 1.82
718 752 7.095270 GGAGTCTCTCCTTTGTAACGAAAATA 58.905 38.462 8.38 0.00 46.41 1.40
735 769 7.121315 GCACCAACAAAATTTATAGGAGTCTCT 59.879 37.037 0.00 0.00 0.00 3.10
736 770 7.121315 AGCACCAACAAAATTTATAGGAGTCTC 59.879 37.037 0.00 0.00 0.00 3.36
737 771 6.948309 AGCACCAACAAAATTTATAGGAGTCT 59.052 34.615 0.00 0.00 0.00 3.24
738 772 7.029563 CAGCACCAACAAAATTTATAGGAGTC 58.970 38.462 0.00 0.00 0.00 3.36
739 773 6.572314 GCAGCACCAACAAAATTTATAGGAGT 60.572 38.462 0.00 0.00 0.00 3.85
838 963 1.839994 TGGGGATTCTGCTTCTGGTAG 59.160 52.381 0.00 0.00 0.00 3.18
965 1091 3.288454 AGCTTGGGAGAGGATATGGAT 57.712 47.619 0.00 0.00 0.00 3.41
990 1116 2.094545 AGATTTCGCCATTGTTGCTTCC 60.095 45.455 0.00 0.00 0.00 3.46
1097 1244 2.367868 CTTGTGGGCCTTGGTTGCAC 62.368 60.000 4.53 0.09 0.00 4.57
1464 1664 3.128938 AGTGGAGCTATACACGAAGTCAC 59.871 47.826 9.26 0.00 45.79 3.67
1575 1816 3.357919 TCGGTGATGACGACGGTT 58.642 55.556 0.00 0.00 35.12 4.44
1967 2228 3.872603 TCCAGGTGCCGCAGTTGT 61.873 61.111 0.00 0.00 0.00 3.32
2491 2753 1.599071 CTTGATACATCGGCGTGCAAT 59.401 47.619 6.85 2.52 0.00 3.56
2597 2861 7.889589 AATTAAACTGAATAAAGTGCTTGGC 57.110 32.000 0.00 0.00 0.00 4.52
2678 2951 0.548031 GCATCCCCAATGAGGAGTGA 59.452 55.000 0.00 0.00 41.22 3.41
2687 2960 2.669781 CCAATGTAGTGCATCCCCAAT 58.330 47.619 0.00 0.00 36.67 3.16
2688 2961 1.959508 GCCAATGTAGTGCATCCCCAA 60.960 52.381 0.00 0.00 36.67 4.12
2718 2991 2.816087 GGAAGAGCTCTGCACATTTTGA 59.184 45.455 23.57 0.00 0.00 2.69
2745 3018 2.297315 AGAGTGTGAGAAACATCAGCGA 59.703 45.455 0.00 0.00 41.97 4.93
2747 3020 3.397482 ACAGAGTGTGAGAAACATCAGC 58.603 45.455 0.00 0.00 41.97 4.26
2757 3030 4.533919 AGAATGAAGGACAGAGTGTGAG 57.466 45.455 0.00 0.00 0.00 3.51
2798 3071 5.350640 GCGCTCCTATAAACACAAGTACTTT 59.649 40.000 5.07 0.00 0.00 2.66
2869 3381 2.175202 ACCAGAGTAACAGAGGAGCAG 58.825 52.381 0.00 0.00 0.00 4.24
2924 3712 3.263425 CCTCTGCCCTCCTGTACTTTTTA 59.737 47.826 0.00 0.00 0.00 1.52
2938 3732 0.972983 TACAGTCTCTGCCTCTGCCC 60.973 60.000 0.00 0.00 34.37 5.36
2960 3754 7.063898 CAGTTCTTGTGTCGATAATTGATGAGT 59.936 37.037 0.00 0.00 0.00 3.41
2970 3767 5.240844 TCTGAGAACAGTTCTTGTGTCGATA 59.759 40.000 17.19 0.00 43.81 2.92
2974 3771 4.509600 CCTTCTGAGAACAGTTCTTGTGTC 59.490 45.833 17.19 5.02 43.81 3.67
3006 3803 4.181578 ACCGACGGATCTTTCAATAACAG 58.818 43.478 23.38 0.00 0.00 3.16
3007 3804 4.196626 ACCGACGGATCTTTCAATAACA 57.803 40.909 23.38 0.00 0.00 2.41
3008 3805 4.390909 ACAACCGACGGATCTTTCAATAAC 59.609 41.667 23.38 0.00 0.00 1.89
3021 3818 2.084681 GTGCTCGTACAACCGACGG 61.085 63.158 13.61 13.61 40.70 4.79
3077 3874 5.812642 ACCTTCTAGCATGTAAAGTCGAATG 59.187 40.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.