Multiple sequence alignment - TraesCS2D01G372000

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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 TraesCS2D01G372000 chr2D 100.000 3248 0 0 1 3248 476261845 476258598 0.000000e+00 5999
1 TraesCS2D01G372000 chr2D 86.267 1034 139 1 1019 2052 476039728 476038698 0.000000e+00 1120
2 TraesCS2D01G372000 chr2D 82.109 844 138 11 1205 2038 16492746 16491906 0.000000e+00 710
3 TraesCS2D01G372000 chr2D 85.251 339 32 10 176 509 476275004 476274679 1.870000e-87 333
4 TraesCS2D01G372000 chr2A 91.620 1945 112 28 159 2085 618042534 618040623 0.000000e+00 2641
5 TraesCS2D01G372000 chr2A 85.354 1031 146 3 1019 2048 617956320 617955294 0.000000e+00 1062
6 TraesCS2D01G372000 chr2A 85.599 993 104 17 2232 3213 618039997 618039033 0.000000e+00 1005
7 TraesCS2D01G372000 chr2A 85.349 587 64 14 153 728 618114322 618113747 3.610000e-164 588
8 TraesCS2D01G372000 chr2A 81.140 456 49 16 155 603 618103108 618102683 6.720000e-87 331
9 TraesCS2D01G372000 chr2A 84.146 246 34 4 1 244 618113684 618113442 1.950000e-57 233
10 TraesCS2D01G372000 chr2A 91.026 156 7 3 2104 2253 618040160 618040006 1.530000e-48 204
11 TraesCS2D01G372000 chr2A 82.381 210 27 9 152 355 754347684 754347889 1.200000e-39 174
12 TraesCS2D01G372000 chr2A 81.905 210 27 10 152 355 527377979 527378183 2.000000e-37 167
13 TraesCS2D01G372000 chr2A 83.429 175 19 10 69 241 618114480 618114314 1.560000e-33 154
14 TraesCS2D01G372000 chr2B 91.088 1986 109 35 402 2347 556982532 556980575 0.000000e+00 2625
15 TraesCS2D01G372000 chr2B 85.378 1019 144 3 1031 2048 556847368 556846354 0.000000e+00 1051
16 TraesCS2D01G372000 chr2B 88.187 728 77 7 2528 3248 556969567 556968842 0.000000e+00 859
17 TraesCS2D01G372000 chr2B 85.333 150 20 2 2344 2491 556980266 556980117 1.560000e-33 154
18 TraesCS2D01G372000 chr4B 79.639 388 38 22 264 619 139758313 139757935 1.160000e-59 241
19 TraesCS2D01G372000 chr5A 79.667 300 41 15 155 448 316097276 316096991 7.110000e-47 198
20 TraesCS2D01G372000 chr3D 78.405 301 42 19 152 445 460450437 460450721 1.200000e-39 174
21 TraesCS2D01G372000 chr3D 81.773 203 25 12 152 349 460451602 460451797 3.350000e-35 159


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 TraesCS2D01G372000 chr2D 476258598 476261845 3247 True 5999.000000 5999 100.0000 1 3248 1 chr2D.!!$R3 3247
1 TraesCS2D01G372000 chr2D 476038698 476039728 1030 True 1120.000000 1120 86.2670 1019 2052 1 chr2D.!!$R2 1033
2 TraesCS2D01G372000 chr2D 16491906 16492746 840 True 710.000000 710 82.1090 1205 2038 1 chr2D.!!$R1 833
3 TraesCS2D01G372000 chr2A 618039033 618042534 3501 True 1283.333333 2641 89.4150 159 3213 3 chr2A.!!$R3 3054
4 TraesCS2D01G372000 chr2A 617955294 617956320 1026 True 1062.000000 1062 85.3540 1019 2048 1 chr2A.!!$R1 1029
5 TraesCS2D01G372000 chr2A 618113442 618114480 1038 True 325.000000 588 84.3080 1 728 3 chr2A.!!$R4 727
6 TraesCS2D01G372000 chr2B 556980117 556982532 2415 True 1389.500000 2625 88.2105 402 2491 2 chr2B.!!$R3 2089
7 TraesCS2D01G372000 chr2B 556846354 556847368 1014 True 1051.000000 1051 85.3780 1031 2048 1 chr2B.!!$R1 1017
8 TraesCS2D01G372000 chr2B 556968842 556969567 725 True 859.000000 859 88.1870 2528 3248 1 chr2B.!!$R2 720

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
555 636 0.03779 GACTCAAGAGAGCGGCTTGT 60.038 55.0 2.97 0.0 46.09 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 3408 0.034477 CTAAAACGCCCTGACCCCAT 60.034 55.0 0.0 0.0 0.0 4.0 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
19 20 4.125695 GCCGCCTCCTACGTCGTT 62.126 66.667 1.78 0.00 0.00 3.85
20 21 2.764314 GCCGCCTCCTACGTCGTTA 61.764 63.158 1.78 0.00 0.00 3.18
22 23 1.091771 CCGCCTCCTACGTCGTTAGA 61.092 60.000 1.78 0.00 0.00 2.10
24 25 1.332997 CGCCTCCTACGTCGTTAGATT 59.667 52.381 1.78 0.00 0.00 2.40
25 26 2.728922 GCCTCCTACGTCGTTAGATTG 58.271 52.381 1.78 0.00 0.00 2.67
26 27 2.357009 GCCTCCTACGTCGTTAGATTGA 59.643 50.000 1.78 0.00 0.00 2.57
27 28 3.548415 GCCTCCTACGTCGTTAGATTGAG 60.548 52.174 1.78 1.35 0.00 3.02
28 29 3.548415 CCTCCTACGTCGTTAGATTGAGC 60.548 52.174 1.78 0.00 0.00 4.26
29 30 2.357009 TCCTACGTCGTTAGATTGAGCC 59.643 50.000 1.78 0.00 0.00 4.70
30 31 2.098607 CCTACGTCGTTAGATTGAGCCA 59.901 50.000 1.78 0.00 0.00 4.75
31 32 1.992170 ACGTCGTTAGATTGAGCCAC 58.008 50.000 0.00 0.00 0.00 5.01
32 33 1.271379 ACGTCGTTAGATTGAGCCACA 59.729 47.619 0.00 0.00 0.00 4.17
33 34 2.288579 ACGTCGTTAGATTGAGCCACAA 60.289 45.455 0.00 0.00 42.95 3.33
34 35 2.734606 CGTCGTTAGATTGAGCCACAAA 59.265 45.455 0.00 0.00 42.03 2.83
35 36 3.370978 CGTCGTTAGATTGAGCCACAAAT 59.629 43.478 0.00 0.00 42.03 2.32
36 37 4.565166 CGTCGTTAGATTGAGCCACAAATA 59.435 41.667 0.00 0.00 42.03 1.40
37 38 5.276395 CGTCGTTAGATTGAGCCACAAATAG 60.276 44.000 0.00 0.00 42.03 1.73
38 39 4.570772 TCGTTAGATTGAGCCACAAATAGC 59.429 41.667 0.00 0.00 42.03 2.97
39 40 4.260784 CGTTAGATTGAGCCACAAATAGCC 60.261 45.833 0.00 0.00 42.03 3.93
40 41 3.370840 AGATTGAGCCACAAATAGCCA 57.629 42.857 0.00 0.00 42.03 4.75
41 42 3.907221 AGATTGAGCCACAAATAGCCAT 58.093 40.909 0.00 0.00 42.03 4.40
42 43 3.887716 AGATTGAGCCACAAATAGCCATC 59.112 43.478 0.00 0.00 42.03 3.51
43 44 1.667236 TGAGCCACAAATAGCCATCG 58.333 50.000 0.00 0.00 0.00 3.84
44 45 0.947244 GAGCCACAAATAGCCATCGG 59.053 55.000 0.00 0.00 0.00 4.18
45 46 0.546122 AGCCACAAATAGCCATCGGA 59.454 50.000 0.00 0.00 0.00 4.55
46 47 1.143684 AGCCACAAATAGCCATCGGAT 59.856 47.619 0.00 0.00 0.00 4.18
47 48 1.537202 GCCACAAATAGCCATCGGATC 59.463 52.381 0.00 0.00 0.00 3.36
48 49 2.811873 GCCACAAATAGCCATCGGATCT 60.812 50.000 0.00 0.00 0.00 2.75
49 50 3.070018 CCACAAATAGCCATCGGATCTC 58.930 50.000 0.00 0.00 0.00 2.75
50 51 3.070018 CACAAATAGCCATCGGATCTCC 58.930 50.000 0.00 0.00 0.00 3.71
51 52 2.039084 ACAAATAGCCATCGGATCTCCC 59.961 50.000 0.00 0.00 0.00 4.30
52 53 1.280457 AATAGCCATCGGATCTCCCC 58.720 55.000 0.00 0.00 0.00 4.81
63 64 4.705482 TCTCCCCGATGAGATGCA 57.295 55.556 0.00 0.00 36.48 3.96
64 65 3.154278 TCTCCCCGATGAGATGCAT 57.846 52.632 0.00 0.00 40.77 3.96
85 86 1.269448 CGCCAATTGCAACAAGGTAGT 59.731 47.619 0.00 0.00 41.33 2.73
137 138 1.006086 GTTGCAAACCACCAAAGTGC 58.994 50.000 0.00 0.00 42.21 4.40
140 141 2.103373 TGCAAACCACCAAAGTGCTAA 58.897 42.857 0.00 0.00 43.09 3.09
144 145 4.024977 GCAAACCACCAAAGTGCTAATTTG 60.025 41.667 0.00 0.00 43.09 2.32
145 146 3.385193 ACCACCAAAGTGCTAATTTGC 57.615 42.857 4.83 4.83 43.09 3.68
147 148 2.612721 CCACCAAAGTGCTAATTTGCCC 60.613 50.000 9.41 0.00 43.09 5.36
148 149 1.272212 ACCAAAGTGCTAATTTGCCCG 59.728 47.619 9.41 0.00 36.52 6.13
149 150 1.543802 CCAAAGTGCTAATTTGCCCGA 59.456 47.619 9.41 0.00 36.52 5.14
157 158 6.459923 AGTGCTAATTTGCCCGAAATTTTTA 58.540 32.000 9.41 0.00 40.73 1.52
161 162 8.787852 TGCTAATTTGCCCGAAATTTTTATTTT 58.212 25.926 9.41 0.00 40.73 1.82
165 166 9.457110 AATTTGCCCGAAATTTTTATTTTTGTC 57.543 25.926 0.00 0.00 40.73 3.18
166 167 7.793927 TTGCCCGAAATTTTTATTTTTGTCT 57.206 28.000 0.00 0.00 0.00 3.41
167 168 7.793927 TGCCCGAAATTTTTATTTTTGTCTT 57.206 28.000 0.00 0.00 0.00 3.01
168 169 7.856556 TGCCCGAAATTTTTATTTTTGTCTTC 58.143 30.769 0.00 0.00 0.00 2.87
169 170 7.495934 TGCCCGAAATTTTTATTTTTGTCTTCA 59.504 29.630 0.00 0.00 0.00 3.02
170 171 8.338986 GCCCGAAATTTTTATTTTTGTCTTCAA 58.661 29.630 0.00 0.00 0.00 2.69
330 407 1.138661 CTTTTGCAACAAGGCCCTTGA 59.861 47.619 29.74 4.34 43.42 3.02
343 421 2.486548 GGCCCTTGATGCGGAAAGTATA 60.487 50.000 0.00 0.00 0.00 1.47
378 456 2.202492 CGAAGCGAGGACGGACAG 60.202 66.667 0.00 0.00 40.15 3.51
379 457 2.507324 GAAGCGAGGACGGACAGC 60.507 66.667 0.00 0.00 40.15 4.40
509 590 2.347490 GAGAAAGGACGGCCAGCA 59.653 61.111 11.69 0.00 36.29 4.41
516 597 4.314440 GACGGCCAGCAGTGTCCA 62.314 66.667 2.24 0.00 0.00 4.02
529 610 1.904378 TGTCCACCGACGATCACCA 60.904 57.895 0.00 0.00 42.37 4.17
555 636 0.037790 GACTCAAGAGAGCGGCTTGT 60.038 55.000 2.97 0.00 46.09 3.16
636 720 2.029828 GCTGAGAGGAAGACACGAAGAA 60.030 50.000 0.00 0.00 0.00 2.52
689 773 1.234821 GCTCGGTCCATTTCACACAA 58.765 50.000 0.00 0.00 0.00 3.33
768 866 9.675464 TTCCCATTAAACTACGAAATACAAGAT 57.325 29.630 0.00 0.00 0.00 2.40
858 956 5.653507 TGATGTGGCAATAAGAAAATGAGC 58.346 37.500 0.00 0.00 0.00 4.26
866 968 6.385033 GCAATAAGAAAATGAGCTGTTGAGT 58.615 36.000 0.00 0.00 0.00 3.41
945 1047 0.894835 TGTGCATCGCCACTCTTCTA 59.105 50.000 0.00 0.00 36.68 2.10
946 1048 1.281899 GTGCATCGCCACTCTTCTAC 58.718 55.000 0.00 0.00 33.02 2.59
1167 1279 0.460284 CGAAACTGCTCTACCGCCAT 60.460 55.000 0.00 0.00 0.00 4.40
2048 2168 1.752683 TTCGGTCTCTCTGTCTAGCC 58.247 55.000 0.00 0.00 0.00 3.93
2067 2187 2.609491 GCCAGCATTCGATATCCACGTA 60.609 50.000 0.00 0.00 0.00 3.57
2117 2679 5.221263 CGCTAGTATATGTCAACAAGGGAGT 60.221 44.000 0.00 0.00 0.00 3.85
2195 2771 2.432146 CCAGGCAGTACTGATTAGAGCA 59.568 50.000 27.08 0.00 40.97 4.26
2281 2893 8.200792 AGCCTCTAAATATTACACTCAACTCTG 58.799 37.037 0.00 0.00 0.00 3.35
2302 2914 6.810911 TCTGATAGCAACCTTCATCTTCTAC 58.189 40.000 0.00 0.00 0.00 2.59
2326 2938 5.827756 CCCCCATTTTTCTTACCTAAGAGT 58.172 41.667 0.00 0.00 42.66 3.24
2357 3281 0.457851 ATCTGCTATATCCTCGCCGC 59.542 55.000 0.00 0.00 0.00 6.53
2403 3328 2.764010 AGTTTTTGACCTTTTTCGGGCT 59.236 40.909 0.00 0.00 31.45 5.19
2429 3354 2.234908 CAAATCCCGTAAAAATGGCCCA 59.765 45.455 0.00 0.00 0.00 5.36
2456 3381 0.975040 AAAAATATGCAGGCGGCCCA 60.975 50.000 17.02 8.04 43.89 5.36
2480 3405 4.109675 CCCCCTCCGCCGTTGAAT 62.110 66.667 0.00 0.00 0.00 2.57
2481 3406 2.824041 CCCCTCCGCCGTTGAATG 60.824 66.667 0.00 0.00 0.00 2.67
2482 3407 2.046314 CCCTCCGCCGTTGAATGT 60.046 61.111 0.00 0.00 0.00 2.71
2483 3408 1.219664 CCCTCCGCCGTTGAATGTA 59.780 57.895 0.00 0.00 0.00 2.29
2484 3409 0.179056 CCCTCCGCCGTTGAATGTAT 60.179 55.000 0.00 0.00 0.00 2.29
2485 3410 0.937304 CCTCCGCCGTTGAATGTATG 59.063 55.000 0.00 0.00 0.00 2.39
2515 3440 2.486918 CGTTTTAGGGTTCACGTCCTT 58.513 47.619 0.00 0.00 34.75 3.36
2519 3444 5.240121 GTTTTAGGGTTCACGTCCTTGATA 58.760 41.667 0.00 0.00 34.75 2.15
2526 3451 4.382685 GGTTCACGTCCTTGATATTCTCCA 60.383 45.833 0.00 0.00 0.00 3.86
2538 3463 2.498820 ATTCTCCACCCCCTCCAGCT 62.499 60.000 0.00 0.00 0.00 4.24
2551 3476 2.571202 CCTCCAGCTTCTCCTTTCTCTT 59.429 50.000 0.00 0.00 0.00 2.85
2559 3484 2.780714 TCTCCTTTCTCTTCGACGAGT 58.219 47.619 17.45 0.00 32.83 4.18
2754 3688 4.643387 GTTGGAGCGTGTGGGCCT 62.643 66.667 4.53 0.00 0.00 5.19
2759 3693 3.605749 GAGCGTGTGGGCCTGCTTA 62.606 63.158 4.53 0.00 37.91 3.09
2763 3697 0.107897 CGTGTGGGCCTGCTTATACA 60.108 55.000 4.53 0.00 0.00 2.29
2764 3698 1.475034 CGTGTGGGCCTGCTTATACAT 60.475 52.381 4.53 0.00 0.00 2.29
2765 3699 2.654863 GTGTGGGCCTGCTTATACATT 58.345 47.619 4.53 0.00 0.00 2.71
2766 3700 3.023832 GTGTGGGCCTGCTTATACATTT 58.976 45.455 4.53 0.00 0.00 2.32
2768 3702 4.642885 GTGTGGGCCTGCTTATACATTTTA 59.357 41.667 4.53 0.00 0.00 1.52
2771 3705 5.592688 GTGGGCCTGCTTATACATTTTAGAA 59.407 40.000 4.53 0.00 0.00 2.10
2772 3706 5.592688 TGGGCCTGCTTATACATTTTAGAAC 59.407 40.000 4.53 0.00 0.00 3.01
2773 3707 5.277828 GGGCCTGCTTATACATTTTAGAACG 60.278 44.000 0.84 0.00 0.00 3.95
2776 3710 6.292919 GCCTGCTTATACATTTTAGAACGAGG 60.293 42.308 0.00 0.00 0.00 4.63
2777 3711 6.292919 CCTGCTTATACATTTTAGAACGAGGC 60.293 42.308 0.00 0.00 0.00 4.70
2778 3712 5.233476 TGCTTATACATTTTAGAACGAGGCG 59.767 40.000 0.00 0.00 0.00 5.52
2797 3736 2.338620 CCGCACACGAAGAGGTGA 59.661 61.111 0.00 0.00 43.93 4.02
2805 3744 1.446272 CGAAGAGGTGACGGGAAGC 60.446 63.158 0.00 0.00 0.00 3.86
2839 3778 2.719354 GCGGCAAAGAACACGGTT 59.281 55.556 0.00 0.00 0.00 4.44
2894 3833 2.742372 CCGCAAAGGAGGACCACG 60.742 66.667 0.00 0.00 45.00 4.94
2897 3856 2.030562 CAAAGGAGGACCACGCGT 59.969 61.111 5.58 5.58 38.94 6.01
2898 3857 1.290955 CAAAGGAGGACCACGCGTA 59.709 57.895 13.44 0.00 38.94 4.42
2899 3858 1.012486 CAAAGGAGGACCACGCGTAC 61.012 60.000 13.44 6.57 38.94 3.67
2905 3864 4.807039 GACCACGCGTACGCCCAT 62.807 66.667 32.64 16.92 45.53 4.00
2909 3868 4.752879 ACGCGTACGCCCATGCTT 62.753 61.111 32.64 7.05 45.53 3.91
2910 3869 4.222589 CGCGTACGCCCATGCTTG 62.223 66.667 32.64 13.53 37.98 4.01
2911 3870 4.536687 GCGTACGCCCATGCTTGC 62.537 66.667 29.51 0.00 34.43 4.01
2912 3871 3.876198 CGTACGCCCATGCTTGCC 61.876 66.667 0.52 0.00 34.43 4.52
2913 3872 3.876198 GTACGCCCATGCTTGCCG 61.876 66.667 8.59 8.59 34.43 5.69
2945 3904 2.277120 CGTTCTACCTCGGCGTCG 60.277 66.667 1.15 1.15 37.82 5.12
2958 3917 2.403987 CGTCGACTACTGAGCCGG 59.596 66.667 14.70 0.00 0.00 6.13
2985 3944 9.475620 CCTTCCCTAGGTTTAAATTAGTTTGAT 57.524 33.333 8.29 0.00 39.39 2.57
3044 4003 3.427503 CGGTTGTGTTGCTCTGAACTTTT 60.428 43.478 0.00 0.00 0.00 2.27
3055 4014 4.839174 GCTCTGAACTTTTTAGCGTAAACG 59.161 41.667 0.00 0.00 43.27 3.60
3097 4056 3.557595 CGTTTGAGTGGATCTATTCTGCC 59.442 47.826 3.32 0.00 0.00 4.85
3106 4065 1.204146 TCTATTCTGCCGGGAGCTTT 58.796 50.000 19.71 7.71 44.23 3.51
3154 4113 3.381949 GCAGTACCGGTTTATAGCAGAG 58.618 50.000 15.04 0.00 0.00 3.35
3181 4140 1.133976 GGGATGCTCTAACACTGCCAT 60.134 52.381 0.00 0.00 0.00 4.40
3205 4164 1.102978 GACCCACCCATCCGAATTTG 58.897 55.000 0.00 0.00 0.00 2.32
3244 4203 3.055530 TCCTCTTTTCTGATGCCTCACTC 60.056 47.826 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.659017 CTAACGACGTAGGAGGCGGC 62.659 65.000 0.00 0.00 0.00 6.53
3 4 1.091771 TCTAACGACGTAGGAGGCGG 61.092 60.000 0.00 0.00 0.00 6.13
5 6 2.357009 TCAATCTAACGACGTAGGAGGC 59.643 50.000 0.00 0.00 0.00 4.70
6 7 3.548415 GCTCAATCTAACGACGTAGGAGG 60.548 52.174 0.00 0.27 0.00 4.30
7 8 3.548415 GGCTCAATCTAACGACGTAGGAG 60.548 52.174 0.00 3.78 0.00 3.69
9 10 2.098607 TGGCTCAATCTAACGACGTAGG 59.901 50.000 0.00 0.00 0.00 3.18
12 13 1.271379 TGTGGCTCAATCTAACGACGT 59.729 47.619 0.00 0.00 0.00 4.34
13 14 1.990799 TGTGGCTCAATCTAACGACG 58.009 50.000 0.00 0.00 0.00 5.12
14 15 4.946784 ATTTGTGGCTCAATCTAACGAC 57.053 40.909 2.46 0.00 35.84 4.34
15 16 4.570772 GCTATTTGTGGCTCAATCTAACGA 59.429 41.667 2.46 0.00 35.84 3.85
16 17 4.260784 GGCTATTTGTGGCTCAATCTAACG 60.261 45.833 2.46 0.00 35.84 3.18
17 18 4.640201 TGGCTATTTGTGGCTCAATCTAAC 59.360 41.667 2.46 0.00 35.84 2.34
18 19 4.854173 TGGCTATTTGTGGCTCAATCTAA 58.146 39.130 2.46 0.00 35.84 2.10
19 20 4.502105 TGGCTATTTGTGGCTCAATCTA 57.498 40.909 2.46 0.00 35.84 1.98
20 21 3.370840 TGGCTATTTGTGGCTCAATCT 57.629 42.857 2.46 0.00 35.84 2.40
22 23 2.620115 CGATGGCTATTTGTGGCTCAAT 59.380 45.455 2.46 0.00 35.84 2.57
24 25 1.667236 CGATGGCTATTTGTGGCTCA 58.333 50.000 0.00 0.00 0.00 4.26
25 26 0.947244 CCGATGGCTATTTGTGGCTC 59.053 55.000 0.00 0.00 0.00 4.70
26 27 0.546122 TCCGATGGCTATTTGTGGCT 59.454 50.000 0.00 0.00 0.00 4.75
27 28 1.537202 GATCCGATGGCTATTTGTGGC 59.463 52.381 0.00 0.00 0.00 5.01
28 29 3.070018 GAGATCCGATGGCTATTTGTGG 58.930 50.000 0.00 0.00 0.00 4.17
29 30 3.070018 GGAGATCCGATGGCTATTTGTG 58.930 50.000 0.00 0.00 0.00 3.33
30 31 2.039084 GGGAGATCCGATGGCTATTTGT 59.961 50.000 0.00 0.00 36.71 2.83
31 32 2.616510 GGGGAGATCCGATGGCTATTTG 60.617 54.545 0.00 0.00 36.71 2.32
32 33 1.630878 GGGGAGATCCGATGGCTATTT 59.369 52.381 0.00 0.00 36.71 1.40
33 34 1.280457 GGGGAGATCCGATGGCTATT 58.720 55.000 0.00 0.00 36.71 1.73
34 35 2.998493 GGGGAGATCCGATGGCTAT 58.002 57.895 0.00 0.00 36.71 2.97
35 36 4.541213 GGGGAGATCCGATGGCTA 57.459 61.111 0.00 0.00 36.71 3.93
47 48 3.529252 GATGCATCTCATCGGGGAG 57.471 57.895 19.70 0.00 41.82 4.30
53 54 2.921069 GCAATTGGCGATGCATCTCATC 60.921 50.000 23.73 10.91 46.32 2.92
54 55 1.000607 GCAATTGGCGATGCATCTCAT 60.001 47.619 23.73 4.51 42.12 2.90
55 56 0.382873 GCAATTGGCGATGCATCTCA 59.617 50.000 23.73 18.03 42.12 3.27
56 57 0.382873 TGCAATTGGCGATGCATCTC 59.617 50.000 23.73 16.44 46.87 2.75
57 58 2.495809 TGCAATTGGCGATGCATCT 58.504 47.368 23.73 2.16 46.87 2.90
66 67 3.059166 CAACTACCTTGTTGCAATTGGC 58.941 45.455 0.59 0.15 40.40 4.52
93 94 1.226686 AACTGTTGCAGAGCGAGCTG 61.227 55.000 0.84 0.00 38.91 4.24
129 130 1.543802 TCGGGCAAATTAGCACTTTGG 59.456 47.619 7.48 0.00 35.21 3.28
135 136 7.913674 AATAAAAATTTCGGGCAAATTAGCA 57.086 28.000 0.00 0.00 42.86 3.49
140 141 8.845227 AGACAAAAATAAAAATTTCGGGCAAAT 58.155 25.926 0.00 0.00 36.12 2.32
144 145 7.856556 TGAAGACAAAAATAAAAATTTCGGGC 58.143 30.769 0.00 0.00 0.00 6.13
180 253 6.905215 TCCTCCCATAACATCATCTATGCTAT 59.095 38.462 0.00 0.00 39.39 2.97
181 254 6.263754 TCCTCCCATAACATCATCTATGCTA 58.736 40.000 0.00 0.00 39.39 3.49
197 270 3.839490 TCATGTTGCAAAAATCCTCCCAT 59.161 39.130 0.00 0.00 0.00 4.00
198 271 3.237746 TCATGTTGCAAAAATCCTCCCA 58.762 40.909 0.00 0.00 0.00 4.37
236 310 8.469200 CCATAGCCATCATCTTTTCAGTAAAAA 58.531 33.333 0.00 0.00 34.26 1.94
240 314 6.057533 CACCATAGCCATCATCTTTTCAGTA 58.942 40.000 0.00 0.00 0.00 2.74
243 317 4.641541 CACACCATAGCCATCATCTTTTCA 59.358 41.667 0.00 0.00 0.00 2.69
256 330 5.741388 AATTTCTCGATTCACACCATAGC 57.259 39.130 0.00 0.00 0.00 2.97
258 332 6.183360 GCAGAAATTTCTCGATTCACACCATA 60.183 38.462 17.91 0.00 34.74 2.74
259 333 5.392380 GCAGAAATTTCTCGATTCACACCAT 60.392 40.000 17.91 0.00 34.74 3.55
361 439 2.202492 CTGTCCGTCCTCGCTTCG 60.202 66.667 0.00 0.00 35.54 3.79
363 441 4.421479 CGCTGTCCGTCCTCGCTT 62.421 66.667 0.00 0.00 35.54 4.68
375 453 3.753434 CCTCTCGCTGTCCGCTGT 61.753 66.667 0.00 0.00 36.73 4.40
379 457 3.522731 CTCCCCTCTCGCTGTCCG 61.523 72.222 0.00 0.00 38.61 4.79
418 496 1.303888 CTGTGCTCCAGCCACCATT 60.304 57.895 0.00 0.00 41.18 3.16
448 526 1.308069 TTCCCCGTCTCCTTACGTCG 61.308 60.000 0.00 0.00 41.27 5.12
450 528 0.893447 CTTTCCCCGTCTCCTTACGT 59.107 55.000 0.00 0.00 41.27 3.57
509 590 1.585006 GTGATCGTCGGTGGACACT 59.415 57.895 2.13 0.00 43.61 3.55
516 597 4.129737 CCGCTGGTGATCGTCGGT 62.130 66.667 0.00 0.00 35.75 4.69
529 610 2.676822 TCTCTTGAGTCCGCCGCT 60.677 61.111 0.00 0.00 0.00 5.52
541 622 2.164624 CACTACTACAAGCCGCTCTCTT 59.835 50.000 0.00 0.00 0.00 2.85
555 636 2.760650 CCAGTCATCCTGCACACTACTA 59.239 50.000 0.00 0.00 40.06 1.82
636 720 7.011382 ACGTCCTTGTCCTTATCCTTATCTAT 58.989 38.462 0.00 0.00 0.00 1.98
768 866 7.905604 GCAGTGATGTTGCCATACTTATATA 57.094 36.000 0.00 0.00 35.54 0.86
844 942 8.416329 ACAAACTCAACAGCTCATTTTCTTATT 58.584 29.630 0.00 0.00 0.00 1.40
858 956 3.181534 CGGCGTATACACAAACTCAACAG 60.182 47.826 0.00 0.00 0.00 3.16
866 968 1.430479 CACCACGGCGTATACACAAA 58.570 50.000 14.22 0.00 0.00 2.83
976 1080 2.975489 AGGTATGAGCAGGGATAAGGTG 59.025 50.000 0.00 0.00 0.00 4.00
1152 1264 0.684479 TCTCATGGCGGTAGAGCAGT 60.684 55.000 0.00 0.00 39.27 4.40
1729 1845 1.655329 GGCTCATCTCCTCGTACCG 59.345 63.158 0.00 0.00 0.00 4.02
2048 2168 4.485163 TGATACGTGGATATCGAATGCTG 58.515 43.478 0.00 0.00 34.75 4.41
2067 2187 6.593072 CACACGTATGCGAATATTGAATGAT 58.407 36.000 11.07 0.00 42.00 2.45
2117 2679 9.315525 CAATTTCAATATCAACACAATATGCCA 57.684 29.630 0.00 0.00 0.00 4.92
2146 2722 2.165437 TCCATAATTCCAAACTTGCGGC 59.835 45.455 0.00 0.00 0.00 6.53
2195 2771 1.403687 GGGGCTAGCGTTGGAGAGAT 61.404 60.000 9.00 0.00 0.00 2.75
2281 2893 5.301555 GGGTAGAAGATGAAGGTTGCTATC 58.698 45.833 0.00 0.00 0.00 2.08
2317 2929 8.177119 CAGATCTGCTAAAGATACTCTTAGGT 57.823 38.462 10.38 0.00 46.12 3.08
2357 3281 3.480505 AACCGTCGGAATTATAAGGGG 57.519 47.619 20.51 0.00 0.00 4.79
2403 3328 4.991687 GCCATTTTTACGGGATTTGTTCAA 59.008 37.500 0.00 0.00 0.00 2.69
2468 3393 0.462937 CCCATACATTCAACGGCGGA 60.463 55.000 13.24 0.00 0.00 5.54
2471 3396 1.021968 GACCCCATACATTCAACGGC 58.978 55.000 0.00 0.00 0.00 5.68
2472 3397 2.288666 CTGACCCCATACATTCAACGG 58.711 52.381 0.00 0.00 0.00 4.44
2474 3399 2.654863 CCCTGACCCCATACATTCAAC 58.345 52.381 0.00 0.00 0.00 3.18
2475 3400 1.064017 GCCCTGACCCCATACATTCAA 60.064 52.381 0.00 0.00 0.00 2.69
2476 3401 0.550914 GCCCTGACCCCATACATTCA 59.449 55.000 0.00 0.00 0.00 2.57
2477 3402 0.535102 CGCCCTGACCCCATACATTC 60.535 60.000 0.00 0.00 0.00 2.67
2478 3403 1.279025 ACGCCCTGACCCCATACATT 61.279 55.000 0.00 0.00 0.00 2.71
2479 3404 1.279025 AACGCCCTGACCCCATACAT 61.279 55.000 0.00 0.00 0.00 2.29
2480 3405 1.493854 AAACGCCCTGACCCCATACA 61.494 55.000 0.00 0.00 0.00 2.29
2481 3406 0.323087 AAAACGCCCTGACCCCATAC 60.323 55.000 0.00 0.00 0.00 2.39
2482 3407 1.210967 CTAAAACGCCCTGACCCCATA 59.789 52.381 0.00 0.00 0.00 2.74
2483 3408 0.034477 CTAAAACGCCCTGACCCCAT 60.034 55.000 0.00 0.00 0.00 4.00
2484 3409 1.377229 CTAAAACGCCCTGACCCCA 59.623 57.895 0.00 0.00 0.00 4.96
2485 3410 1.378119 CCTAAAACGCCCTGACCCC 60.378 63.158 0.00 0.00 0.00 4.95
2515 3440 1.296832 TGGAGGGGGTGGAGAATATCA 59.703 52.381 0.00 0.00 0.00 2.15
2519 3444 2.003548 GCTGGAGGGGGTGGAGAAT 61.004 63.158 0.00 0.00 0.00 2.40
2526 3451 2.285743 GGAGAAGCTGGAGGGGGT 60.286 66.667 0.00 0.00 0.00 4.95
2538 3463 3.058155 CACTCGTCGAAGAGAAAGGAGAA 60.058 47.826 30.95 0.00 40.57 2.87
2551 3476 2.488355 GGCGGAATCACTCGTCGA 59.512 61.111 0.00 0.00 0.00 4.20
2559 3484 1.161843 GAAAGAAACGGGCGGAATCA 58.838 50.000 0.00 0.00 0.00 2.57
2649 3583 4.828925 GAGCTGCTGGTCTCCGCC 62.829 72.222 7.01 0.00 37.68 6.13
2679 3613 3.195698 GGAACGCCATGGCTCGAC 61.196 66.667 33.07 20.31 39.32 4.20
2727 3661 2.671177 CGCTCCAACCTTCACTGCG 61.671 63.158 0.00 0.00 36.19 5.18
2738 3672 4.641645 CAGGCCCACACGCTCCAA 62.642 66.667 0.00 0.00 0.00 3.53
2754 3688 5.233476 CGCCTCGTTCTAAAATGTATAAGCA 59.767 40.000 0.00 0.00 0.00 3.91
2759 3693 2.870411 GGCGCCTCGTTCTAAAATGTAT 59.130 45.455 22.15 0.00 0.00 2.29
2763 3697 1.087771 CGGGCGCCTCGTTCTAAAAT 61.088 55.000 28.56 0.00 0.00 1.82
2764 3698 1.738830 CGGGCGCCTCGTTCTAAAA 60.739 57.895 28.56 0.00 0.00 1.52
2765 3699 2.125832 CGGGCGCCTCGTTCTAAA 60.126 61.111 28.56 0.00 0.00 1.85
2766 3700 4.807039 GCGGGCGCCTCGTTCTAA 62.807 66.667 29.37 0.00 34.56 2.10
2778 3712 4.681978 ACCTCTTCGTGTGCGGGC 62.682 66.667 0.00 0.00 38.89 6.13
2788 3727 1.446272 CGCTTCCCGTCACCTCTTC 60.446 63.158 0.00 0.00 0.00 2.87
2797 3736 2.363795 TCCTCATCCGCTTCCCGT 60.364 61.111 0.00 0.00 34.38 5.28
2824 3763 1.657181 CGCAACCGTGTTCTTTGCC 60.657 57.895 0.00 0.00 42.20 4.52
2839 3778 4.082523 CCTTCTTCTCCGGCCGCA 62.083 66.667 22.85 2.88 0.00 5.69
2901 3860 3.944250 AACCTCCGGCAAGCATGGG 62.944 63.158 0.00 0.00 0.00 4.00
2902 3861 2.361610 AACCTCCGGCAAGCATGG 60.362 61.111 0.00 0.00 0.00 3.66
2903 3862 2.703798 CCAACCTCCGGCAAGCATG 61.704 63.158 0.00 0.00 0.00 4.06
2904 3863 2.361610 CCAACCTCCGGCAAGCAT 60.362 61.111 0.00 0.00 0.00 3.79
2905 3864 3.551496 CTCCAACCTCCGGCAAGCA 62.551 63.158 0.00 0.00 0.00 3.91
2906 3865 2.747855 CTCCAACCTCCGGCAAGC 60.748 66.667 0.00 0.00 0.00 4.01
2907 3866 2.045926 CCTCCAACCTCCGGCAAG 60.046 66.667 0.00 0.00 0.00 4.01
2908 3867 2.528127 TCCTCCAACCTCCGGCAA 60.528 61.111 0.00 0.00 0.00 4.52
2909 3868 3.003173 CTCCTCCAACCTCCGGCA 61.003 66.667 0.00 0.00 0.00 5.69
2910 3869 3.787001 CCTCCTCCAACCTCCGGC 61.787 72.222 0.00 0.00 0.00 6.13
2911 3870 3.787001 GCCTCCTCCAACCTCCGG 61.787 72.222 0.00 0.00 0.00 5.14
2912 3871 4.148825 CGCCTCCTCCAACCTCCG 62.149 72.222 0.00 0.00 0.00 4.63
2913 3872 2.523453 GAACGCCTCCTCCAACCTCC 62.523 65.000 0.00 0.00 0.00 4.30
2914 3873 1.079057 GAACGCCTCCTCCAACCTC 60.079 63.158 0.00 0.00 0.00 3.85
2915 3874 0.252103 TAGAACGCCTCCTCCAACCT 60.252 55.000 0.00 0.00 0.00 3.50
2916 3875 0.108281 GTAGAACGCCTCCTCCAACC 60.108 60.000 0.00 0.00 0.00 3.77
2919 3878 0.683504 GAGGTAGAACGCCTCCTCCA 60.684 60.000 0.12 0.00 45.05 3.86
2945 3904 1.142097 GAAGGCCGGCTCAGTAGTC 59.858 63.158 28.56 6.68 0.00 2.59
2985 3944 8.962884 ACATCATACATAGCACAAAACATAGA 57.037 30.769 0.00 0.00 0.00 1.98
3044 4003 9.640974 GCATATTTAAAATCTCGTTTACGCTAA 57.359 29.630 0.00 0.00 39.60 3.09
3055 4014 9.982291 TCAAACGTACTGCATATTTAAAATCTC 57.018 29.630 0.00 0.00 0.00 2.75
3097 4056 4.303257 GGGAACTCAAAGCTCCCG 57.697 61.111 0.00 0.00 40.50 5.14
3106 4065 4.599047 AAAATGATTTTGCGGGAACTCA 57.401 36.364 1.78 0.00 0.00 3.41
3154 4113 1.414181 TGTTAGAGCATCCCTAGCAGC 59.586 52.381 0.00 0.00 33.66 5.25
3222 4181 2.909006 AGTGAGGCATCAGAAAAGAGGA 59.091 45.455 0.00 0.00 35.66 3.71


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

AutoCloner maintained by Alex Coulton.