Multiple sequence alignment - TraesCS3B01G139000

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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 TraesCS3B01G139000 chr3B 100.000 3466 0 0 1 3466 125550731 125554196 0.000000e+00 6401.0
1 TraesCS3B01G139000 chr3B 91.827 1505 95 19 1060 2557 125778973 125780456 0.000000e+00 2073.0
2 TraesCS3B01G139000 chr3B 91.829 1334 99 8 1057 2385 125524360 125523032 0.000000e+00 1851.0
3 TraesCS3B01G139000 chr3B 87.027 555 26 19 2906 3459 726438349 726438858 4.980000e-163 584.0
4 TraesCS3B01G139000 chr3B 80.814 172 14 6 835 1001 125778727 125778884 2.190000e-22 117.0
5 TraesCS3B01G139000 chr3B 90.000 60 6 0 745 804 125778663 125778722 1.030000e-10 78.7
6 TraesCS3B01G139000 chr3D 89.744 2974 219 40 1 2905 79426969 79429925 0.000000e+00 3723.0
7 TraesCS3B01G139000 chr3D 91.413 1514 83 23 1060 2557 79504249 79505731 0.000000e+00 2032.0
8 TraesCS3B01G139000 chr3D 91.742 1332 104 3 1057 2385 79421376 79420048 0.000000e+00 1845.0
9 TraesCS3B01G139000 chr3D 91.667 60 5 0 745 804 79503945 79504004 2.220000e-12 84.2
10 TraesCS3B01G139000 chr3A 88.392 2481 206 53 1 2425 93262662 93265116 0.000000e+00 2911.0
11 TraesCS3B01G139000 chr3A 87.161 2547 240 66 413 2907 93336708 93339219 0.000000e+00 2811.0
12 TraesCS3B01G139000 chr3A 92.042 1332 100 3 1057 2385 93042878 93041550 0.000000e+00 1868.0
13 TraesCS3B01G139000 chr3A 92.795 347 25 0 2113 2459 93265663 93266009 1.440000e-138 503.0
14 TraesCS3B01G139000 chr3A 90.909 176 8 4 2451 2622 93309888 93310059 2.690000e-56 230.0
15 TraesCS3B01G139000 chr3A 94.444 90 5 0 1902 1991 468728529 468728440 4.660000e-29 139.0
16 TraesCS3B01G139000 chr3A 91.579 95 8 0 2618 2712 93319510 93319604 7.810000e-27 132.0
17 TraesCS3B01G139000 chrUn 87.543 578 42 12 2907 3459 67438059 67437487 2.920000e-180 641.0
18 TraesCS3B01G139000 chrUn 84.076 157 17 3 3304 3459 35361572 35361423 1.000000e-30 145.0
19 TraesCS3B01G139000 chrUn 84.076 157 17 3 3304 3459 263319811 263319662 1.000000e-30 145.0
20 TraesCS3B01G139000 chr4D 85.802 486 51 12 2951 3421 401625200 401624718 1.860000e-137 499.0
21 TraesCS3B01G139000 chr6A 75.871 402 68 19 7 390 449807582 449807192 9.890000e-41 178.0
22 TraesCS3B01G139000 chr2D 81.152 191 31 3 14 201 28560891 28560703 7.750000e-32 148.0
23 TraesCS3B01G139000 chr2D 72.917 384 82 18 20 385 145737133 145736754 2.830000e-21 113.0
24 TraesCS3B01G139000 chr5A 87.288 118 15 0 14 131 476636944 476637061 6.030000e-28 135.0
25 TraesCS3B01G139000 chr7D 74.084 382 73 23 1086 1458 452998127 452997763 2.170000e-27 134.0
26 TraesCS3B01G139000 chr4B 74.324 370 65 18 42 384 387391312 387390946 2.810000e-26 130.0
27 TraesCS3B01G139000 chr5D 84.921 126 19 0 14 139 420980888 420980763 1.010000e-25 128.0
28 TraesCS3B01G139000 chr5D 74.044 366 59 19 42 383 534016768 534016415 2.190000e-22 117.0
29 TraesCS3B01G139000 chr7A 87.619 105 11 2 3110 3213 2720819 2720716 1.690000e-23 121.0
30 TraesCS3B01G139000 chr1D 79.268 164 29 4 42 201 364609495 364609333 3.660000e-20 110.0
31 TraesCS3B01G139000 chr6B 77.174 184 33 7 14 192 522528316 522528137 7.920000e-17 99.0
32 TraesCS3B01G139000 chr7B 77.692 130 22 4 257 379 527861589 527861718 4.800000e-09 73.1


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 TraesCS3B01G139000 chr3B 125550731 125554196 3465 False 6401.000000 6401 100.0000 1 3466 1 chr3B.!!$F1 3465
1 TraesCS3B01G139000 chr3B 125523032 125524360 1328 True 1851.000000 1851 91.8290 1057 2385 1 chr3B.!!$R1 1328
2 TraesCS3B01G139000 chr3B 125778663 125780456 1793 False 756.233333 2073 87.5470 745 2557 3 chr3B.!!$F3 1812
3 TraesCS3B01G139000 chr3B 726438349 726438858 509 False 584.000000 584 87.0270 2906 3459 1 chr3B.!!$F2 553
4 TraesCS3B01G139000 chr3D 79426969 79429925 2956 False 3723.000000 3723 89.7440 1 2905 1 chr3D.!!$F1 2904
5 TraesCS3B01G139000 chr3D 79420048 79421376 1328 True 1845.000000 1845 91.7420 1057 2385 1 chr3D.!!$R1 1328
6 TraesCS3B01G139000 chr3D 79503945 79505731 1786 False 1058.100000 2032 91.5400 745 2557 2 chr3D.!!$F2 1812
7 TraesCS3B01G139000 chr3A 93336708 93339219 2511 False 2811.000000 2811 87.1610 413 2907 1 chr3A.!!$F3 2494
8 TraesCS3B01G139000 chr3A 93041550 93042878 1328 True 1868.000000 1868 92.0420 1057 2385 1 chr3A.!!$R1 1328
9 TraesCS3B01G139000 chr3A 93262662 93266009 3347 False 1707.000000 2911 90.5935 1 2459 2 chr3A.!!$F4 2458
10 TraesCS3B01G139000 chrUn 67437487 67438059 572 True 641.000000 641 87.5430 2907 3459 1 chrUn.!!$R2 552

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
357 365 0.108329 CAGAGGTCGGGCGTGTATTT 60.108 55.0 0.0 0.0 0.00 1.40 F
358 366 0.108329 AGAGGTCGGGCGTGTATTTG 60.108 55.0 0.0 0.0 0.00 2.32 F
572 603 0.322456 TTCCCCTCGGAAATGTGCAG 60.322 55.0 0.0 0.0 45.54 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 2032 1.079750 GAAGCAGAGGTGGACGGTC 60.080 63.158 0.00 0.0 0.00 4.79 R
1972 2116 1.208259 CGCGCATGATGTAGTAGCAA 58.792 50.000 8.75 0.0 0.00 3.91 R
2565 2772 1.892474 GAGCCCCTTGCATTGTACAAA 59.108 47.619 13.23 0.0 44.83 2.83 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
37 38 2.011947 CTTGATGAAGGCATTGCTCGA 58.988 47.619 8.82 0.00 34.11 4.04
46 47 1.336240 GGCATTGCTCGAAGTTTGCTT 60.336 47.619 8.82 0.00 37.71 3.91
49 50 1.674359 TTGCTCGAAGTTTGCTTGGA 58.326 45.000 0.00 0.00 37.16 3.53
94 95 5.243954 CCCATGATCTGACCTTCGATAGTTA 59.756 44.000 0.00 0.00 37.40 2.24
102 103 3.819902 GACCTTCGATAGTTAGATCCGGT 59.180 47.826 0.00 0.00 37.40 5.28
105 106 4.320348 CCTTCGATAGTTAGATCCGGTGAC 60.320 50.000 0.00 0.00 37.40 3.67
131 132 1.893168 GCTTGCGCGTCGTTTCCTTA 61.893 55.000 8.43 0.00 0.00 2.69
159 164 3.388024 GGCCTTTTGGAGAACCTTTTCTT 59.612 43.478 0.00 0.00 42.53 2.52
160 165 4.587262 GGCCTTTTGGAGAACCTTTTCTTA 59.413 41.667 0.00 0.00 42.53 2.10
225 230 4.393062 CCACTGTCACTGTATTTCATCACC 59.607 45.833 0.00 0.00 0.00 4.02
236 244 0.895530 TTCATCACCTCGGGAGTGTC 59.104 55.000 4.19 0.00 0.00 3.67
266 274 1.146041 ATTCGCGGGCATAGCTTCA 59.854 52.632 6.13 0.00 0.00 3.02
307 315 3.551454 CCTTGCAGGTGTGATCTTTTGTG 60.551 47.826 0.00 0.00 0.00 3.33
311 319 3.563808 GCAGGTGTGATCTTTTGTGTGTA 59.436 43.478 0.00 0.00 0.00 2.90
318 326 3.496884 TGATCTTTTGTGTGTAGGTTCGC 59.503 43.478 0.00 0.00 0.00 4.70
319 327 2.215196 TCTTTTGTGTGTAGGTTCGCC 58.785 47.619 0.00 0.00 37.60 5.54
348 356 4.336889 TTCTAATTATGCAGAGGTCGGG 57.663 45.455 0.00 0.00 0.00 5.14
349 357 2.037251 TCTAATTATGCAGAGGTCGGGC 59.963 50.000 0.00 0.00 0.00 6.13
355 363 3.077519 GCAGAGGTCGGGCGTGTAT 62.078 63.158 0.00 0.00 0.00 2.29
357 365 0.108329 CAGAGGTCGGGCGTGTATTT 60.108 55.000 0.00 0.00 0.00 1.40
358 366 0.108329 AGAGGTCGGGCGTGTATTTG 60.108 55.000 0.00 0.00 0.00 2.32
387 395 8.420374 TGATTGTATTCCTTGATTCTACGTTC 57.580 34.615 0.00 0.00 0.00 3.95
396 421 6.535150 TCCTTGATTCTACGTTCTGCTTTATG 59.465 38.462 0.00 0.00 0.00 1.90
397 422 6.535150 CCTTGATTCTACGTTCTGCTTTATGA 59.465 38.462 0.00 0.00 0.00 2.15
398 423 7.064609 CCTTGATTCTACGTTCTGCTTTATGAA 59.935 37.037 0.00 0.00 0.00 2.57
469 497 2.555199 CTTGTCCCAATCGAGTGGATC 58.445 52.381 32.29 22.64 41.65 3.36
570 601 4.734652 TTCCCCTCGGAAATGTGC 57.265 55.556 0.00 0.00 45.54 4.57
572 603 0.322456 TTCCCCTCGGAAATGTGCAG 60.322 55.000 0.00 0.00 45.54 4.41
607 638 4.756642 TCAAAGTCAAGACGATCTGCAATT 59.243 37.500 0.00 0.00 36.20 2.32
641 692 1.293924 GACGTGCATGATCCCTTCAG 58.706 55.000 14.17 0.00 37.89 3.02
642 693 0.745845 ACGTGCATGATCCCTTCAGC 60.746 55.000 14.17 0.00 37.89 4.26
649 700 2.244486 TGATCCCTTCAGCTGTCTCT 57.756 50.000 14.67 0.00 0.00 3.10
653 704 2.614259 TCCCTTCAGCTGTCTCTTCTT 58.386 47.619 14.67 0.00 0.00 2.52
664 715 1.727335 GTCTCTTCTTCCGCCTTTTCG 59.273 52.381 0.00 0.00 0.00 3.46
709 763 0.893447 GAAGTGGTACTAGGGCACGT 59.107 55.000 0.00 0.00 0.00 4.49
760 814 1.669779 GCAAGCAACTGGATAGAGCTG 59.330 52.381 0.00 0.00 38.28 4.24
761 815 1.669779 CAAGCAACTGGATAGAGCTGC 59.330 52.381 0.00 0.00 38.28 5.25
815 870 2.436646 TCGACGTAGGACCGACCC 60.437 66.667 0.00 0.00 40.05 4.46
817 872 2.361610 GACGTAGGACCGACCCCA 60.362 66.667 0.00 0.00 40.05 4.96
818 873 2.362120 ACGTAGGACCGACCCCAG 60.362 66.667 0.00 0.00 40.05 4.45
922 993 0.875059 GCTAACTCCAGCACCAACAC 59.125 55.000 0.00 0.00 41.40 3.32
977 1055 4.662468 TGCCAAGTCAAGCAAACAAATA 57.338 36.364 0.00 0.00 35.69 1.40
1008 1098 1.200948 CAAGCAAGGAGCAAGCTTACC 59.799 52.381 0.00 3.41 46.01 2.85
1037 1131 1.043116 TACTCCCTCTGCATCCACCG 61.043 60.000 0.00 0.00 0.00 4.94
1038 1132 2.038813 TCCCTCTGCATCCACCGA 59.961 61.111 0.00 0.00 0.00 4.69
1042 1136 1.448540 CTCTGCATCCACCGACCAC 60.449 63.158 0.00 0.00 0.00 4.16
1043 1137 1.892819 CTCTGCATCCACCGACCACT 61.893 60.000 0.00 0.00 0.00 4.00
1044 1138 1.003355 CTGCATCCACCGACCACTT 60.003 57.895 0.00 0.00 0.00 3.16
1171 1297 4.189188 CTCGACCGCTACCCCACG 62.189 72.222 0.00 0.00 0.00 4.94
1840 1984 2.280524 TTCGAGGTGTTGGTGGCG 60.281 61.111 0.00 0.00 0.00 5.69
2562 2769 4.020751 TGACTTTGAGGAGTTGATCAGGAG 60.021 45.833 0.00 0.00 0.00 3.69
2563 2770 3.262915 ACTTTGAGGAGTTGATCAGGAGG 59.737 47.826 0.00 0.00 0.00 4.30
2564 2771 2.928036 TGAGGAGTTGATCAGGAGGA 57.072 50.000 0.00 0.00 0.00 3.71
2565 2772 3.411454 TGAGGAGTTGATCAGGAGGAT 57.589 47.619 0.00 0.00 39.53 3.24
2581 2790 3.131046 GGAGGATTTGTACAATGCAAGGG 59.869 47.826 9.56 0.00 0.00 3.95
2635 2844 7.487484 AGTATCATGTGCTTATCTCCATATCG 58.513 38.462 0.00 0.00 0.00 2.92
2703 2913 1.133199 AGTCAAAAATCAGCACCCCCA 60.133 47.619 0.00 0.00 0.00 4.96
2716 2926 2.509336 CCCCACTAAGCGCGAGTG 60.509 66.667 28.41 28.41 43.32 3.51
2720 2930 1.670674 CCCACTAAGCGCGAGTGTAAA 60.671 52.381 30.83 3.58 42.35 2.01
2739 2949 0.110486 AGCGGTTCACCAAATGTCCT 59.890 50.000 0.00 0.00 35.14 3.85
2746 2956 5.163447 CGGTTCACCAAATGTCCTCTAGATA 60.163 44.000 0.00 0.00 35.14 1.98
2751 2961 5.931146 CACCAAATGTCCTCTAGATATCTGC 59.069 44.000 15.79 0.00 0.00 4.26
2754 2964 7.166851 CCAAATGTCCTCTAGATATCTGCATT 58.833 38.462 15.79 11.76 0.00 3.56
2756 2966 7.550597 AATGTCCTCTAGATATCTGCATTGA 57.449 36.000 15.79 3.02 0.00 2.57
2768 2978 2.146342 CTGCATTGAACAGTTCGGACT 58.854 47.619 8.80 0.00 36.25 3.85
2769 2979 3.006430 TCTGCATTGAACAGTTCGGACTA 59.994 43.478 8.80 0.00 36.50 2.59
2788 3002 0.172352 ATTTTGCCATACAACGCCCG 59.828 50.000 0.00 0.00 38.23 6.13
2791 3005 2.203153 GCCATACAACGCCCGGAT 60.203 61.111 0.73 0.00 0.00 4.18
2794 3008 1.880646 GCCATACAACGCCCGGATATT 60.881 52.381 0.73 0.00 0.00 1.28
2812 3026 6.293407 CGGATATTAGTTTTGTGCGGATGAAT 60.293 38.462 0.00 0.00 0.00 2.57
2823 3037 1.597937 GCGGATGAATGAAATCCACGC 60.598 52.381 3.54 0.00 43.33 5.34
2852 3066 2.159382 CAAATGTACGGGAGGTTTGCT 58.841 47.619 0.00 0.00 0.00 3.91
2866 3080 2.951475 TTTGCTGGCGTTCGGACCTT 62.951 55.000 0.00 0.00 0.00 3.50
2897 3111 0.944386 CCTCCGAAAATATGTGCCCG 59.056 55.000 0.00 0.00 0.00 6.13
2898 3112 1.663695 CTCCGAAAATATGTGCCCGT 58.336 50.000 0.00 0.00 0.00 5.28
3192 3406 1.020333 CCTCTTCTCGACCGACGTCT 61.020 60.000 14.70 0.00 43.13 4.18
3204 3419 3.991536 GACGTCTGGAAGGGCGAGC 62.992 68.421 8.70 0.00 36.54 5.03
3242 3457 2.351276 GCTGGAACGGGTGTCCAT 59.649 61.111 0.00 0.00 32.54 3.41
3243 3458 2.040544 GCTGGAACGGGTGTCCATG 61.041 63.158 0.00 0.00 32.54 3.66
3244 3459 1.377202 CTGGAACGGGTGTCCATGG 60.377 63.158 4.97 4.97 32.54 3.66
3245 3460 2.045340 GGAACGGGTGTCCATGGG 60.045 66.667 13.02 0.00 0.00 4.00
3246 3461 2.598787 GGAACGGGTGTCCATGGGA 61.599 63.158 13.02 0.00 0.00 4.37
3247 3462 1.078426 GAACGGGTGTCCATGGGAG 60.078 63.158 13.02 0.00 29.39 4.30
3248 3463 3.268103 AACGGGTGTCCATGGGAGC 62.268 63.158 13.02 8.58 29.39 4.70
3249 3464 3.402681 CGGGTGTCCATGGGAGCT 61.403 66.667 13.02 0.00 29.39 4.09
3250 3465 2.273449 GGGTGTCCATGGGAGCTG 59.727 66.667 13.02 0.00 29.39 4.24
3251 3466 2.439156 GGTGTCCATGGGAGCTGC 60.439 66.667 13.02 0.00 29.39 5.25
3252 3467 2.352422 GTGTCCATGGGAGCTGCA 59.648 61.111 13.02 0.00 29.39 4.41
3253 3468 1.303561 GTGTCCATGGGAGCTGCAA 60.304 57.895 13.02 0.00 29.39 4.08
3254 3469 1.303561 TGTCCATGGGAGCTGCAAC 60.304 57.895 13.02 0.00 29.39 4.17
3345 3606 2.758327 AGCTACATCCGGCGTCCA 60.758 61.111 6.01 0.00 0.00 4.02
3421 3689 3.435262 CGTAGAACGGTGAGCTTTTTC 57.565 47.619 0.00 0.00 38.08 2.29
3423 3691 3.493503 CGTAGAACGGTGAGCTTTTTCTT 59.506 43.478 0.00 0.00 38.08 2.52
3424 3692 4.376109 CGTAGAACGGTGAGCTTTTTCTTC 60.376 45.833 0.00 0.00 38.08 2.87
3459 3727 1.156736 CCGGCAAGTTGAGGTGTTAG 58.843 55.000 7.16 0.00 0.00 2.34
3460 3728 1.270625 CCGGCAAGTTGAGGTGTTAGA 60.271 52.381 7.16 0.00 0.00 2.10
3461 3729 2.069273 CGGCAAGTTGAGGTGTTAGAG 58.931 52.381 7.16 0.00 0.00 2.43
3462 3730 1.807142 GGCAAGTTGAGGTGTTAGAGC 59.193 52.381 7.16 0.00 0.00 4.09
3463 3731 2.494059 GCAAGTTGAGGTGTTAGAGCA 58.506 47.619 7.16 0.00 0.00 4.26
3464 3732 3.077359 GCAAGTTGAGGTGTTAGAGCAT 58.923 45.455 7.16 0.00 0.00 3.79
3465 3733 3.503748 GCAAGTTGAGGTGTTAGAGCATT 59.496 43.478 7.16 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.859205 AAAGATCAAGTCCAAGCAAACTT 57.141 34.783 0.00 0.00 36.16 2.66
46 47 5.576563 TTTCACCCTAAAGATCAAGTCCA 57.423 39.130 0.00 0.00 0.00 4.02
74 75 6.431543 GGATCTAACTATCGAAGGTCAGATCA 59.568 42.308 23.64 0.00 38.44 2.92
75 76 6.402766 CGGATCTAACTATCGAAGGTCAGATC 60.403 46.154 18.40 18.40 37.27 2.75
94 95 2.815308 GCCATCGTCACCGGATCT 59.185 61.111 9.46 0.00 33.95 2.75
131 132 2.529632 GTTCTCCAAAAGGCCTCCAAT 58.470 47.619 5.23 0.00 0.00 3.16
192 197 1.768275 AGTGACAGTGGTGACCATCAA 59.232 47.619 7.94 0.00 35.28 2.57
225 230 3.669251 AAAAAGAGAGACACTCCCGAG 57.331 47.619 0.00 0.00 45.96 4.63
291 299 4.141482 ACCTACACACAAAAGATCACACCT 60.141 41.667 0.00 0.00 0.00 4.00
307 315 2.664436 GCACACGGCGAACCTACAC 61.664 63.158 16.62 0.00 0.00 2.90
348 356 8.342634 AGGAATACAATCATAACAAATACACGC 58.657 33.333 0.00 0.00 0.00 5.34
469 497 1.626654 CGTGCAGGTTAGGCGAGTTG 61.627 60.000 0.00 0.00 0.00 3.16
570 601 0.236711 CTTTGAGTGGCGACTTGCTG 59.763 55.000 1.83 0.00 45.43 4.41
572 603 0.235926 GACTTTGAGTGGCGACTTGC 59.764 55.000 1.83 0.00 45.38 4.01
607 638 3.202906 GCACGTCCATAGGCTTATTTCA 58.797 45.455 0.00 0.00 0.00 2.69
641 692 0.036858 AAGGCGGAAGAAGAGACAGC 60.037 55.000 0.00 0.00 0.00 4.40
642 693 2.464157 AAAGGCGGAAGAAGAGACAG 57.536 50.000 0.00 0.00 0.00 3.51
649 700 2.524300 CGTCGAAAAGGCGGAAGAA 58.476 52.632 0.00 0.00 45.57 2.52
664 715 4.389077 CCTAACAACTCCAAGATTGTCGTC 59.611 45.833 0.00 0.00 38.08 4.20
709 763 3.932710 CCAGCAGCTCACGTTCTTAATTA 59.067 43.478 0.00 0.00 0.00 1.40
768 823 1.021202 TCAAAAGGTGGTGAAGCGTG 58.979 50.000 0.00 0.00 0.00 5.34
774 829 1.149627 CGGGGTCAAAAGGTGGTGA 59.850 57.895 0.00 0.00 0.00 4.02
847 909 2.828868 AAGCTGACCGTGGCTTCA 59.171 55.556 0.00 0.00 44.18 3.02
938 1013 1.450312 ATTGAAGGGAGAAGCGCGG 60.450 57.895 8.83 0.00 34.07 6.46
977 1055 0.465287 CCTTGCTTGGCTTGGTTTGT 59.535 50.000 0.00 0.00 0.00 2.83
1008 1098 4.211125 TGCAGAGGGAGTAGATAGTCTTG 58.789 47.826 0.00 0.00 0.00 3.02
1037 1131 3.192633 GGTGAGAGAGAGAAGAAGTGGTC 59.807 52.174 0.00 0.00 0.00 4.02
1038 1132 3.161866 GGTGAGAGAGAGAAGAAGTGGT 58.838 50.000 0.00 0.00 0.00 4.16
1042 1136 4.757594 CCATTGGTGAGAGAGAGAAGAAG 58.242 47.826 0.00 0.00 0.00 2.85
1043 1137 3.055530 GCCATTGGTGAGAGAGAGAAGAA 60.056 47.826 4.26 0.00 0.00 2.52
1044 1138 2.499289 GCCATTGGTGAGAGAGAGAAGA 59.501 50.000 4.26 0.00 0.00 2.87
1623 1764 2.348998 CCAGGCCTTCAACGCTCT 59.651 61.111 0.00 0.00 0.00 4.09
1624 1765 3.435186 GCCAGGCCTTCAACGCTC 61.435 66.667 0.00 0.00 0.00 5.03
1832 1976 2.676121 CCATGCCTTCGCCACCAA 60.676 61.111 0.00 0.00 0.00 3.67
1882 2026 1.970114 GAGGTGGACGGTCGAGTCA 60.970 63.158 7.08 0.00 42.62 3.41
1888 2032 1.079750 GAAGCAGAGGTGGACGGTC 60.080 63.158 0.00 0.00 0.00 4.79
1972 2116 1.208259 CGCGCATGATGTAGTAGCAA 58.792 50.000 8.75 0.00 0.00 3.91
2155 2299 3.923864 TCCGACACCAGCAGCGTT 61.924 61.111 0.00 0.00 0.00 4.84
2394 2541 2.166270 GCCTTCGGCTTCACTTCTG 58.834 57.895 0.00 0.00 46.69 3.02
2461 2658 6.382282 TCAACCAATCCAATGCAACCATATAA 59.618 34.615 0.00 0.00 0.00 0.98
2562 2769 2.418609 GCCCCTTGCATTGTACAAATCC 60.419 50.000 13.23 4.60 40.77 3.01
2563 2770 2.497273 AGCCCCTTGCATTGTACAAATC 59.503 45.455 13.23 7.87 44.83 2.17
2564 2771 2.497273 GAGCCCCTTGCATTGTACAAAT 59.503 45.455 13.23 0.00 44.83 2.32
2565 2772 1.892474 GAGCCCCTTGCATTGTACAAA 59.108 47.619 13.23 0.00 44.83 2.83
2581 2790 9.002600 AGAAAAATTGGTTCATTTTATTGAGCC 57.997 29.630 0.90 0.90 44.66 4.70
2671 2880 6.238484 GCTGATTTTTGACTAAGCACCGATAT 60.238 38.462 0.00 0.00 0.00 1.63
2672 2881 5.064707 GCTGATTTTTGACTAAGCACCGATA 59.935 40.000 0.00 0.00 0.00 2.92
2685 2895 1.133199 AGTGGGGGTGCTGATTTTTGA 60.133 47.619 0.00 0.00 0.00 2.69
2698 2908 3.771160 ACTCGCGCTTAGTGGGGG 61.771 66.667 8.20 8.20 41.74 5.40
2703 2913 1.347320 GCTTTACACTCGCGCTTAGT 58.653 50.000 5.56 6.09 0.00 2.24
2716 2926 3.561503 GACATTTGGTGAACCGCTTTAC 58.438 45.455 0.00 0.00 39.43 2.01
2720 2930 0.110486 AGGACATTTGGTGAACCGCT 59.890 50.000 0.00 0.00 39.43 5.52
2739 2949 6.920210 CGAACTGTTCAATGCAGATATCTAGA 59.080 38.462 19.56 0.00 37.40 2.43
2746 2956 2.744202 GTCCGAACTGTTCAATGCAGAT 59.256 45.455 19.56 0.00 37.40 2.90
2751 2961 5.569059 GCAAAATAGTCCGAACTGTTCAATG 59.431 40.000 19.56 8.09 35.98 2.82
2754 2964 3.500680 GGCAAAATAGTCCGAACTGTTCA 59.499 43.478 19.56 0.88 35.98 3.18
2756 2966 3.482436 TGGCAAAATAGTCCGAACTGTT 58.518 40.909 0.00 0.00 38.35 3.16
2768 2978 1.402259 CGGGCGTTGTATGGCAAAATA 59.598 47.619 0.00 0.00 39.03 1.40
2769 2979 0.172352 CGGGCGTTGTATGGCAAAAT 59.828 50.000 0.00 0.00 39.03 1.82
2788 3002 6.371809 TTCATCCGCACAAAACTAATATCC 57.628 37.500 0.00 0.00 0.00 2.59
2791 3005 6.993786 TCATTCATCCGCACAAAACTAATA 57.006 33.333 0.00 0.00 0.00 0.98
2794 3008 5.697473 TTTCATTCATCCGCACAAAACTA 57.303 34.783 0.00 0.00 0.00 2.24
2823 3037 1.810151 CCCGTACATTTGGTTCCAGTG 59.190 52.381 0.00 5.27 0.00 3.66
2852 3066 2.029964 GTGAAGGTCCGAACGCCA 59.970 61.111 0.00 0.00 0.00 5.69
2866 3080 3.740397 CGGAGGCGTACGTGGTGA 61.740 66.667 17.90 0.00 0.00 4.02
2969 3183 2.281484 GTGGGTCCATGTGCGTGT 60.281 61.111 0.00 0.00 0.00 4.49
3192 3406 3.952508 TTGCAGCTCGCCCTTCCA 61.953 61.111 5.82 0.00 41.33 3.53
3204 3419 2.449548 CTGCTGTCTACGGTTGCAG 58.550 57.895 0.00 0.00 43.71 4.41
3229 3444 1.078426 CTCCCATGGACACCCGTTC 60.078 63.158 15.22 0.00 34.29 3.95
3233 3448 2.273449 CAGCTCCCATGGACACCC 59.727 66.667 15.22 0.00 0.00 4.61
3234 3449 2.439156 GCAGCTCCCATGGACACC 60.439 66.667 15.22 0.00 0.00 4.16
3235 3450 1.303561 TTGCAGCTCCCATGGACAC 60.304 57.895 15.22 0.98 0.00 3.67
3236 3451 1.303561 GTTGCAGCTCCCATGGACA 60.304 57.895 15.22 0.00 0.00 4.02
3237 3452 2.048603 GGTTGCAGCTCCCATGGAC 61.049 63.158 15.22 1.82 0.00 4.02
3238 3453 2.356278 GGTTGCAGCTCCCATGGA 59.644 61.111 15.22 0.00 0.00 3.41
3239 3454 3.136123 CGGTTGCAGCTCCCATGG 61.136 66.667 4.14 4.14 0.00 3.66
3240 3455 3.136123 CCGGTTGCAGCTCCCATG 61.136 66.667 0.00 0.00 0.00 3.66
3248 3463 3.803082 CATGGACGCCGGTTGCAG 61.803 66.667 1.90 0.00 41.33 4.41
3251 3466 4.402528 TCCCATGGACGCCGGTTG 62.403 66.667 15.22 0.00 0.00 3.77
3252 3467 4.096003 CTCCCATGGACGCCGGTT 62.096 66.667 15.22 0.00 0.00 4.44
3317 3578 2.324541 GGATGTAGCTCCTCCAGATGT 58.675 52.381 0.00 0.00 32.27 3.06
3345 3606 1.304713 CACCATTTGCAGCTCCCCT 60.305 57.895 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.