Multiple sequence alignment - TraesCS5B01G289100

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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 TraesCS5B01G289100 chr5B 100.000 3314 0 0 1 3314 474521122 474524435 0.000000e+00 6120.0
1 TraesCS5B01G289100 chr5D 91.969 2677 120 44 1 2617 394826215 394828856 0.000000e+00 3664.0
2 TraesCS5B01G289100 chr5D 81.511 503 40 32 2675 3170 394828845 394829301 6.760000e-97 364.0
3 TraesCS5B01G289100 chr5D 84.146 164 3 4 3170 3312 394829335 394829496 1.600000e-28 137.0
4 TraesCS5B01G289100 chr5A 91.779 1703 71 25 949 2620 496608412 496610076 0.000000e+00 2305.0
5 TraesCS5B01G289100 chr5A 84.940 923 60 33 47 927 496607464 496608349 0.000000e+00 861.0
6 TraesCS5B01G289100 chr5A 86.627 501 41 9 2675 3170 496610062 496610541 6.300000e-147 531.0
7 TraesCS5B01G289100 chr5A 96.667 60 2 0 3167 3226 496610573 496610632 2.100000e-17 100.0
8 TraesCS5B01G289100 chr2B 86.313 358 39 6 1582 1930 98404758 98404402 6.710000e-102 381.0
9 TraesCS5B01G289100 chr1B 95.000 80 4 0 1063 1142 552947874 552947953 3.470000e-25 126.0
10 TraesCS5B01G289100 chr4B 94.521 73 3 1 1071 1142 182233242 182233314 9.720000e-21 111.0
11 TraesCS5B01G289100 chr4A 97.959 49 1 0 1094 1142 95365266 95365218 5.890000e-13 86.1


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 TraesCS5B01G289100 chr5B 474521122 474524435 3313 False 6120.000000 6120 100.000000 1 3314 1 chr5B.!!$F1 3313
1 TraesCS5B01G289100 chr5D 394826215 394829496 3281 False 1388.333333 3664 85.875333 1 3312 3 chr5D.!!$F1 3311
2 TraesCS5B01G289100 chr5A 496607464 496610632 3168 False 949.250000 2305 90.003250 47 3226 4 chr5A.!!$F1 3179

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
861 922 0.250295 CTCCTTCGCCAAGAACACCA 60.25 55.0 0.0 0.0 34.66 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2614 2782 0.035176 GCATGCAGCCCCAAAAAGAA 59.965 50.0 14.21 0.0 37.23 2.52 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
91 102 1.965414 TCAAATGGGCTCCTCCTACA 58.035 50.000 0.00 0.00 34.39 2.74
97 108 2.134287 GGCTCCTCCTACATCGCCA 61.134 63.158 0.00 0.00 37.48 5.69
138 150 2.792599 GACGGATCGACGAGCAGT 59.207 61.111 18.43 18.43 37.61 4.40
139 151 1.297745 GACGGATCGACGAGCAGTC 60.298 63.158 25.79 25.79 46.16 3.51
189 201 3.917760 GGGAGGGCCGTCGATCAG 61.918 72.222 18.78 0.00 33.83 2.90
277 294 4.977963 CACCCACGAAACGAATATATACGT 59.022 41.667 0.00 0.00 44.57 3.57
449 475 2.507992 CGGTTGCGGCAGAGAGAG 60.508 66.667 1.67 0.00 0.00 3.20
450 476 2.973899 GGTTGCGGCAGAGAGAGA 59.026 61.111 1.67 0.00 0.00 3.10
664 707 1.133450 CCACTCTACCCTGGCTAGCTA 60.133 57.143 15.72 7.83 0.00 3.32
846 907 1.319799 CCCCCTCCCATCTTCTCCT 59.680 63.158 0.00 0.00 0.00 3.69
861 922 0.250295 CTCCTTCGCCAAGAACACCA 60.250 55.000 0.00 0.00 34.66 4.17
885 946 1.658717 GCCACCACGATCGATCTCG 60.659 63.158 24.34 14.86 44.14 4.04
891 952 3.445149 CGATCGATCTCGTGCGCG 61.445 66.667 22.43 14.79 40.80 6.86
892 953 2.352457 GATCGATCTCGTGCGCGT 60.352 61.111 20.50 0.00 40.80 6.01
893 954 2.630714 GATCGATCTCGTGCGCGTG 61.631 63.158 20.50 17.67 40.80 5.34
979 1092 1.509961 AGGGGATAGATAGGTGGCTGT 59.490 52.381 0.00 0.00 0.00 4.40
1068 1181 2.353723 CCGTCGTACGTGTGCACA 60.354 61.111 17.42 17.42 40.58 4.57
1262 1375 2.563179 TCCTCGTAAGCTGCTTCTTCTT 59.437 45.455 19.62 0.00 37.18 2.52
1273 1392 3.092301 TGCTTCTTCTTCTCCTCGATGA 58.908 45.455 0.00 0.00 0.00 2.92
1313 1432 0.324614 TCGTTGATGATGCCAGTGGT 59.675 50.000 11.74 0.00 0.00 4.16
1314 1433 0.448990 CGTTGATGATGCCAGTGGTG 59.551 55.000 11.74 0.00 0.00 4.17
1315 1434 1.538047 GTTGATGATGCCAGTGGTGT 58.462 50.000 11.74 0.00 0.00 4.16
1316 1435 2.710377 GTTGATGATGCCAGTGGTGTA 58.290 47.619 11.74 0.00 0.00 2.90
1317 1436 2.401583 TGATGATGCCAGTGGTGTAC 57.598 50.000 11.74 1.15 0.00 2.90
1318 1437 1.908619 TGATGATGCCAGTGGTGTACT 59.091 47.619 11.74 0.00 41.36 2.73
1319 1438 2.093500 TGATGATGCCAGTGGTGTACTC 60.093 50.000 11.74 3.82 37.60 2.59
1326 1450 2.404215 CCAGTGGTGTACTCAAACTCG 58.596 52.381 0.00 0.00 37.60 4.18
1357 1481 0.250684 TGGTGTGTCGTTGATGCCAT 60.251 50.000 0.00 0.00 0.00 4.40
1595 1719 2.284190 GCCCTTAAGCAGAGTAAGCAG 58.716 52.381 0.00 0.00 0.00 4.24
1596 1720 2.355209 GCCCTTAAGCAGAGTAAGCAGT 60.355 50.000 0.00 0.00 0.00 4.40
1604 1728 2.806745 GCAGAGTAAGCAGTTCACCACA 60.807 50.000 0.00 0.00 0.00 4.17
1833 1957 2.580867 CTCGCCGGCTCTTCTTCG 60.581 66.667 26.68 6.06 0.00 3.79
1863 1987 1.516603 GAACCCGTCGCTCTACAGC 60.517 63.158 0.00 0.00 42.96 4.40
1899 2023 2.045242 AGCTCCCATGCTGCACAG 60.045 61.111 3.57 0.00 42.33 3.66
2225 2355 2.663188 GATCCCGATGTGCTCCGC 60.663 66.667 0.00 0.00 0.00 5.54
2226 2356 4.592192 ATCCCGATGTGCTCCGCG 62.592 66.667 0.00 0.00 0.00 6.46
2269 2399 2.438434 CGGCCACCAAGGATGACC 60.438 66.667 2.24 0.00 41.22 4.02
2270 2400 2.763215 GGCCACCAAGGATGACCA 59.237 61.111 0.00 0.00 41.22 4.02
2271 2401 1.307647 GGCCACCAAGGATGACCAT 59.692 57.895 0.00 0.00 41.22 3.55
2272 2402 1.039233 GGCCACCAAGGATGACCATG 61.039 60.000 0.00 0.00 41.22 3.66
2273 2403 0.034186 GCCACCAAGGATGACCATGA 60.034 55.000 0.00 0.00 41.22 3.07
2274 2404 1.410648 GCCACCAAGGATGACCATGAT 60.411 52.381 0.00 0.00 41.22 2.45
2354 2497 1.203287 GGCTGCCAGGTTTTGAAGATC 59.797 52.381 15.17 0.00 0.00 2.75
2368 2511 5.468540 TTGAAGATCAAGAAGACGAGGAA 57.531 39.130 0.00 0.00 31.83 3.36
2412 2555 6.812656 GCTATATGATGAGATCAGTCTGGTTG 59.187 42.308 0.00 0.00 43.53 3.77
2468 2621 0.865769 GCTTGTGTAAGTGACCACCG 59.134 55.000 0.00 0.00 36.27 4.94
2469 2622 1.808891 GCTTGTGTAAGTGACCACCGT 60.809 52.381 0.00 0.00 36.27 4.83
2470 2623 2.546373 GCTTGTGTAAGTGACCACCGTA 60.546 50.000 0.00 0.00 36.27 4.02
2471 2624 2.798976 TGTGTAAGTGACCACCGTAC 57.201 50.000 0.00 1.41 0.00 3.67
2472 2625 1.340889 TGTGTAAGTGACCACCGTACC 59.659 52.381 0.00 0.00 0.00 3.34
2538 2697 7.166851 AGATGGAGATGGACATATGAATGAAC 58.833 38.462 10.38 0.00 36.54 3.18
2583 2747 0.689623 AGCCATGATCGATCCTTCCC 59.310 55.000 22.31 7.40 0.00 3.97
2590 2758 0.747255 ATCGATCCTTCCCGTGTCAG 59.253 55.000 0.00 0.00 0.00 3.51
2600 2768 0.039978 CCCGTGTCAGATAGCTAGCG 60.040 60.000 9.55 0.00 0.00 4.26
2601 2769 0.039978 CCGTGTCAGATAGCTAGCGG 60.040 60.000 9.55 2.63 0.00 5.52
2602 2770 0.661780 CGTGTCAGATAGCTAGCGGC 60.662 60.000 9.55 2.62 42.19 6.53
2611 2779 2.501128 GCTAGCGGCTCATCACCA 59.499 61.111 5.39 0.00 38.06 4.17
2612 2780 1.070445 GCTAGCGGCTCATCACCAT 59.930 57.895 5.39 0.00 38.06 3.55
2613 2781 0.533755 GCTAGCGGCTCATCACCATT 60.534 55.000 5.39 0.00 38.06 3.16
2614 2782 1.959042 CTAGCGGCTCATCACCATTT 58.041 50.000 5.39 0.00 0.00 2.32
2615 2783 2.292267 CTAGCGGCTCATCACCATTTT 58.708 47.619 5.39 0.00 0.00 1.82
2616 2784 1.098050 AGCGGCTCATCACCATTTTC 58.902 50.000 0.00 0.00 0.00 2.29
2617 2785 1.098050 GCGGCTCATCACCATTTTCT 58.902 50.000 0.00 0.00 0.00 2.52
2618 2786 1.474077 GCGGCTCATCACCATTTTCTT 59.526 47.619 0.00 0.00 0.00 2.52
2619 2787 2.094545 GCGGCTCATCACCATTTTCTTT 60.095 45.455 0.00 0.00 0.00 2.52
2620 2788 3.614870 GCGGCTCATCACCATTTTCTTTT 60.615 43.478 0.00 0.00 0.00 2.27
2621 2789 4.559153 CGGCTCATCACCATTTTCTTTTT 58.441 39.130 0.00 0.00 0.00 1.94
2622 2790 4.386652 CGGCTCATCACCATTTTCTTTTTG 59.613 41.667 0.00 0.00 0.00 2.44
2623 2791 4.692155 GGCTCATCACCATTTTCTTTTTGG 59.308 41.667 0.00 0.00 36.56 3.28
2624 2792 4.692155 GCTCATCACCATTTTCTTTTTGGG 59.308 41.667 0.00 0.00 34.72 4.12
2625 2793 5.226194 TCATCACCATTTTCTTTTTGGGG 57.774 39.130 0.00 0.00 35.13 4.96
2626 2794 3.483808 TCACCATTTTCTTTTTGGGGC 57.516 42.857 0.00 0.00 33.77 5.80
2627 2795 3.044894 TCACCATTTTCTTTTTGGGGCT 58.955 40.909 0.00 0.00 33.77 5.19
2628 2796 3.140623 CACCATTTTCTTTTTGGGGCTG 58.859 45.455 0.00 0.00 34.72 4.85
2629 2797 2.153645 CCATTTTCTTTTTGGGGCTGC 58.846 47.619 0.00 0.00 0.00 5.25
2630 2798 2.486907 CCATTTTCTTTTTGGGGCTGCA 60.487 45.455 0.50 0.00 0.00 4.41
2631 2799 3.414269 CATTTTCTTTTTGGGGCTGCAT 58.586 40.909 0.50 0.00 0.00 3.96
2632 2800 2.547299 TTTCTTTTTGGGGCTGCATG 57.453 45.000 0.50 0.00 0.00 4.06
2633 2801 0.035176 TTCTTTTTGGGGCTGCATGC 59.965 50.000 11.82 11.82 41.94 4.06
2634 2802 1.120184 TCTTTTTGGGGCTGCATGCA 61.120 50.000 21.29 21.29 45.15 3.96
2635 2803 0.035820 CTTTTTGGGGCTGCATGCAT 60.036 50.000 22.97 0.00 45.15 3.96
2636 2804 0.036199 TTTTTGGGGCTGCATGCATC 60.036 50.000 22.97 17.75 45.15 3.91
2637 2805 1.192803 TTTTGGGGCTGCATGCATCA 61.193 50.000 22.97 14.16 45.15 3.07
2638 2806 0.978667 TTTGGGGCTGCATGCATCAT 60.979 50.000 22.97 0.00 45.15 2.45
2639 2807 1.681486 TTGGGGCTGCATGCATCATG 61.681 55.000 22.97 10.78 45.15 3.07
2650 2818 2.593725 CATCATGCAGAGGCCGGG 60.594 66.667 2.18 0.00 40.13 5.73
2651 2819 3.882326 ATCATGCAGAGGCCGGGG 61.882 66.667 2.18 0.00 40.13 5.73
2671 2839 4.635699 GGTGACCCTCCTTTTCTAAGAA 57.364 45.455 0.00 0.00 32.92 2.52
2672 2840 4.981812 GGTGACCCTCCTTTTCTAAGAAA 58.018 43.478 0.00 0.00 32.92 2.52
2673 2841 5.382616 GGTGACCCTCCTTTTCTAAGAAAA 58.617 41.667 0.00 0.00 32.92 2.29
2741 2917 1.204704 TCGTTGCTCGATCAGTCCATT 59.795 47.619 0.00 0.00 44.01 3.16
2742 2918 2.425668 TCGTTGCTCGATCAGTCCATTA 59.574 45.455 0.00 0.00 44.01 1.90
2783 2959 1.352156 CCGCGTCAGAAGCCAAGTAC 61.352 60.000 4.92 0.00 0.00 2.73
2784 2960 0.388649 CGCGTCAGAAGCCAAGTACT 60.389 55.000 0.00 0.00 0.00 2.73
2854 3032 1.292061 TACAACCGCACTGACACAAC 58.708 50.000 0.00 0.00 0.00 3.32
2859 3037 1.617755 CCGCACTGACACAACGCTAG 61.618 60.000 0.00 0.00 0.00 3.42
2866 3044 2.025359 GACACAACGCTAGCCGATGC 62.025 60.000 9.66 0.00 42.69 3.91
2928 3121 2.146073 AACCAGCCGTGCATTGCTTC 62.146 55.000 10.49 2.54 35.12 3.86
2934 3127 1.919918 GCCGTGCATTGCTTCATAAAC 59.080 47.619 10.49 0.00 0.00 2.01
2974 3168 4.950974 CGCGCGCATGAATGAGGC 62.951 66.667 32.61 0.00 0.00 4.70
2996 3190 2.502510 GTTGCAAGCACGCATCCG 60.503 61.111 0.00 0.00 42.62 4.18
2997 3191 2.667874 TTGCAAGCACGCATCCGA 60.668 55.556 0.00 0.00 42.62 4.55
2998 3192 2.679934 TTGCAAGCACGCATCCGAG 61.680 57.895 0.00 0.00 42.62 4.63
2999 3193 3.869272 GCAAGCACGCATCCGAGG 61.869 66.667 0.00 0.00 38.29 4.63
3065 3268 4.083961 CGTACTCGTCGACATCCTTATCAT 60.084 45.833 17.16 0.00 0.00 2.45
3078 3281 0.850217 TTATCATGAGTTACGCGCGC 59.150 50.000 32.58 23.91 0.00 6.86
3109 3312 3.285371 GCTGCTTGCTGGAATGCT 58.715 55.556 0.00 0.00 38.95 3.79
3110 3313 1.153823 GCTGCTTGCTGGAATGCTG 60.154 57.895 0.00 5.76 38.95 4.41
3111 3314 1.511305 CTGCTTGCTGGAATGCTGG 59.489 57.895 0.00 0.00 0.00 4.85
3112 3315 1.228644 TGCTTGCTGGAATGCTGGT 60.229 52.632 0.00 0.00 0.00 4.00
3113 3316 1.214589 GCTTGCTGGAATGCTGGTG 59.785 57.895 0.00 0.00 0.00 4.17
3114 3317 1.214589 CTTGCTGGAATGCTGGTGC 59.785 57.895 0.00 0.00 40.20 5.01
3274 3530 1.626356 CGGCCATGAAGGAAGAGGGA 61.626 60.000 2.24 0.00 41.22 4.20
3278 3534 1.555075 CCATGAAGGAAGAGGGACGAA 59.445 52.381 0.00 0.00 41.22 3.85
3279 3535 2.622436 CATGAAGGAAGAGGGACGAAC 58.378 52.381 0.00 0.00 0.00 3.95
3280 3536 1.712056 TGAAGGAAGAGGGACGAACA 58.288 50.000 0.00 0.00 0.00 3.18
3298 3554 4.589908 GAACAGAGAGAGAGAGAGAAGGT 58.410 47.826 0.00 0.00 0.00 3.50
3303 3559 4.079253 GAGAGAGAGAGAGAAGGTTGTGT 58.921 47.826 0.00 0.00 0.00 3.72
3304 3560 3.826157 AGAGAGAGAGAGAAGGTTGTGTG 59.174 47.826 0.00 0.00 0.00 3.82
3307 3563 2.630580 AGAGAGAGAAGGTTGTGTGGTC 59.369 50.000 0.00 0.00 0.00 4.02
3308 3564 2.365617 GAGAGAGAAGGTTGTGTGGTCA 59.634 50.000 0.00 0.00 0.00 4.02
3309 3565 2.103263 AGAGAGAAGGTTGTGTGGTCAC 59.897 50.000 0.00 0.00 44.08 3.67
3310 3566 1.202533 AGAGAAGGTTGTGTGGTCACG 60.203 52.381 0.00 0.00 46.49 4.35
3311 3567 0.814010 AGAAGGTTGTGTGGTCACGC 60.814 55.000 7.62 7.62 46.49 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.691342 CGGAAGCACGGTGGAGGA 61.691 66.667 10.60 0.00 0.00 3.71
35 36 7.370383 GGCTTTGTTAAGTTCATTCATCTTCA 58.630 34.615 0.00 0.00 33.74 3.02
37 38 6.381801 CGGCTTTGTTAAGTTCATTCATCTT 58.618 36.000 0.00 0.00 33.74 2.40
40 41 4.218417 AGCGGCTTTGTTAAGTTCATTCAT 59.782 37.500 0.00 0.00 33.74 2.57
41 42 3.568007 AGCGGCTTTGTTAAGTTCATTCA 59.432 39.130 0.00 0.00 33.74 2.57
42 43 4.160736 AGCGGCTTTGTTAAGTTCATTC 57.839 40.909 0.00 0.00 33.74 2.67
43 44 4.298332 CAAGCGGCTTTGTTAAGTTCATT 58.702 39.130 13.53 0.00 33.74 2.57
173 185 4.593864 GCTGATCGACGGCCCTCC 62.594 72.222 0.00 0.00 44.40 4.30
189 201 1.009449 CCTACTACGCTCGAGCAGC 60.009 63.158 34.69 11.75 45.85 5.25
247 264 1.009335 GTTTCGTGGGTGAAACGGC 60.009 57.895 3.89 0.00 45.64 5.68
293 310 2.358369 TGCTCTGCTCTGCTGCAC 60.358 61.111 0.00 0.00 38.12 4.57
449 475 1.142314 CCTCTCTGCTGCTGCTCTC 59.858 63.158 17.00 0.00 40.48 3.20
450 476 2.360767 CCCTCTCTGCTGCTGCTCT 61.361 63.158 17.00 0.00 40.48 4.09
664 707 2.750657 GCAGTCCAGCTAGGGGCAT 61.751 63.158 0.00 0.00 44.79 4.40
837 898 2.303022 TGTTCTTGGCGAAGGAGAAGAT 59.697 45.455 8.73 0.00 30.66 2.40
846 907 1.890041 CGGTGGTGTTCTTGGCGAA 60.890 57.895 0.00 0.00 0.00 4.70
861 922 4.760047 GATCGTGGTGGCTGCGGT 62.760 66.667 0.00 0.00 0.00 5.68
931 996 1.889105 CTTCACGGGATCATGGCGG 60.889 63.158 0.00 0.00 0.00 6.13
943 1008 2.060980 CCTCCCCTCCTCCTTCACG 61.061 68.421 0.00 0.00 0.00 4.35
944 1009 1.690985 CCCTCCCCTCCTCCTTCAC 60.691 68.421 0.00 0.00 0.00 3.18
979 1092 2.478335 GATCCGGCCCCTTTGTCACA 62.478 60.000 0.00 0.00 0.00 3.58
1262 1375 1.134877 CAAGCAAGCTCATCGAGGAGA 60.135 52.381 29.82 8.01 37.05 3.71
1313 1432 4.109766 CAACACAGTCGAGTTTGAGTACA 58.890 43.478 13.21 0.00 0.00 2.90
1314 1433 3.489785 CCAACACAGTCGAGTTTGAGTAC 59.510 47.826 13.21 0.00 0.00 2.73
1315 1434 3.131577 ACCAACACAGTCGAGTTTGAGTA 59.868 43.478 13.21 0.00 0.00 2.59
1316 1435 2.093658 ACCAACACAGTCGAGTTTGAGT 60.094 45.455 13.21 4.87 0.00 3.41
1317 1436 2.550978 ACCAACACAGTCGAGTTTGAG 58.449 47.619 13.21 5.27 0.00 3.02
1318 1437 2.675844 CAACCAACACAGTCGAGTTTGA 59.324 45.455 13.21 0.00 0.00 2.69
1319 1438 2.223249 CCAACCAACACAGTCGAGTTTG 60.223 50.000 4.85 4.85 0.00 2.93
1326 1450 1.400494 GACACACCAACCAACACAGTC 59.600 52.381 0.00 0.00 0.00 3.51
1580 1704 3.323691 TGGTGAACTGCTTACTCTGCTTA 59.676 43.478 0.00 0.00 0.00 3.09
1595 1719 2.034221 GGGAGGGCTGTGGTGAAC 59.966 66.667 0.00 0.00 0.00 3.18
1596 1720 1.650242 TTTGGGAGGGCTGTGGTGAA 61.650 55.000 0.00 0.00 0.00 3.18
1604 1728 2.175715 GGTATTGAGATTTGGGAGGGCT 59.824 50.000 0.00 0.00 0.00 5.19
1827 1951 0.608308 TCGGAGCAGAGGACGAAGAA 60.608 55.000 0.00 0.00 31.79 2.52
1833 1957 2.579738 GGGTTCGGAGCAGAGGAC 59.420 66.667 0.00 0.00 0.00 3.85
2269 2399 1.860950 GTCGTTCCGGTCATCATCATG 59.139 52.381 0.00 0.00 0.00 3.07
2270 2400 1.202533 GGTCGTTCCGGTCATCATCAT 60.203 52.381 0.00 0.00 0.00 2.45
2271 2401 0.174845 GGTCGTTCCGGTCATCATCA 59.825 55.000 0.00 0.00 0.00 3.07
2272 2402 0.529992 GGGTCGTTCCGGTCATCATC 60.530 60.000 0.00 0.00 37.00 2.92
2273 2403 1.520666 GGGTCGTTCCGGTCATCAT 59.479 57.895 0.00 0.00 37.00 2.45
2274 2404 2.975536 GGGTCGTTCCGGTCATCA 59.024 61.111 0.00 0.00 37.00 3.07
2337 2480 3.831323 TCTTGATCTTCAAAACCTGGCA 58.169 40.909 0.00 0.00 35.73 4.92
2343 2486 5.696724 TCCTCGTCTTCTTGATCTTCAAAAC 59.303 40.000 0.00 0.00 35.73 2.43
2368 2511 3.100671 AGCTACTGAACCTCGGAATCTT 58.899 45.455 0.00 0.00 0.00 2.40
2378 2521 8.060931 TGATCTCATCATATAGCTACTGAACC 57.939 38.462 10.88 1.03 33.59 3.62
2412 2555 5.123979 ACTTGCGATCAAAATTCCCTTCTAC 59.876 40.000 0.00 0.00 0.00 2.59
2468 2621 0.460459 GAAGAGCGGGCAGAAGGTAC 60.460 60.000 0.00 0.00 0.00 3.34
2469 2622 1.614241 GGAAGAGCGGGCAGAAGGTA 61.614 60.000 0.00 0.00 0.00 3.08
2470 2623 2.665603 GAAGAGCGGGCAGAAGGT 59.334 61.111 0.00 0.00 0.00 3.50
2471 2624 2.124942 GGAAGAGCGGGCAGAAGG 60.125 66.667 0.00 0.00 0.00 3.46
2472 2625 0.322008 AAAGGAAGAGCGGGCAGAAG 60.322 55.000 0.00 0.00 0.00 2.85
2538 2697 4.148838 ACTGAAGCCCTAGTAGAGCTATG 58.851 47.826 6.61 3.27 35.30 2.23
2583 2747 0.661780 GCCGCTAGCTATCTGACACG 60.662 60.000 13.93 0.00 38.99 4.49
2600 2768 4.692155 CCAAAAAGAAAATGGTGATGAGCC 59.308 41.667 0.00 0.00 0.00 4.70
2601 2769 4.692155 CCCAAAAAGAAAATGGTGATGAGC 59.308 41.667 0.00 0.00 32.13 4.26
2602 2770 5.240121 CCCCAAAAAGAAAATGGTGATGAG 58.760 41.667 0.00 0.00 32.13 2.90
2603 2771 4.504689 GCCCCAAAAAGAAAATGGTGATGA 60.505 41.667 0.00 0.00 32.13 2.92
2604 2772 3.752747 GCCCCAAAAAGAAAATGGTGATG 59.247 43.478 0.00 0.00 32.13 3.07
2605 2773 3.652387 AGCCCCAAAAAGAAAATGGTGAT 59.348 39.130 0.00 0.00 32.13 3.06
2606 2774 3.044894 AGCCCCAAAAAGAAAATGGTGA 58.955 40.909 0.00 0.00 32.13 4.02
2607 2775 3.140623 CAGCCCCAAAAAGAAAATGGTG 58.859 45.455 0.00 0.00 32.13 4.17
2608 2776 2.487086 GCAGCCCCAAAAAGAAAATGGT 60.487 45.455 0.00 0.00 32.13 3.55
2609 2777 2.153645 GCAGCCCCAAAAAGAAAATGG 58.846 47.619 0.00 0.00 0.00 3.16
2610 2778 2.848691 TGCAGCCCCAAAAAGAAAATG 58.151 42.857 0.00 0.00 0.00 2.32
2611 2779 3.414269 CATGCAGCCCCAAAAAGAAAAT 58.586 40.909 0.00 0.00 0.00 1.82
2612 2780 2.848691 CATGCAGCCCCAAAAAGAAAA 58.151 42.857 0.00 0.00 0.00 2.29
2613 2781 1.542987 GCATGCAGCCCCAAAAAGAAA 60.543 47.619 14.21 0.00 37.23 2.52
2614 2782 0.035176 GCATGCAGCCCCAAAAAGAA 59.965 50.000 14.21 0.00 37.23 2.52
2615 2783 1.120184 TGCATGCAGCCCCAAAAAGA 61.120 50.000 18.46 0.00 44.83 2.52
2616 2784 0.035820 ATGCATGCAGCCCCAAAAAG 60.036 50.000 26.69 0.00 44.83 2.27
2617 2785 0.036199 GATGCATGCAGCCCCAAAAA 60.036 50.000 25.21 0.00 44.83 1.94
2618 2786 1.192803 TGATGCATGCAGCCCCAAAA 61.193 50.000 31.30 10.43 44.83 2.44
2619 2787 0.978667 ATGATGCATGCAGCCCCAAA 60.979 50.000 31.30 14.27 44.83 3.28
2620 2788 1.382009 ATGATGCATGCAGCCCCAA 60.382 52.632 31.30 14.67 44.83 4.12
2621 2789 2.131067 CATGATGCATGCAGCCCCA 61.131 57.895 31.30 21.80 44.83 4.96
2622 2790 2.734591 CATGATGCATGCAGCCCC 59.265 61.111 31.30 17.29 44.83 5.80
2632 2800 3.285215 CCGGCCTCTGCATGATGC 61.285 66.667 11.12 11.12 45.29 3.91
2633 2801 2.593725 CCCGGCCTCTGCATGATG 60.594 66.667 0.00 0.00 40.13 3.07
2634 2802 3.882326 CCCCGGCCTCTGCATGAT 61.882 66.667 0.00 0.00 40.13 2.45
2648 2816 4.336816 TCTTAGAAAAGGAGGGTCACCCC 61.337 52.174 10.22 0.02 41.24 4.95
2649 2817 2.910977 TCTTAGAAAAGGAGGGTCACCC 59.089 50.000 3.85 3.85 37.34 4.61
2650 2818 4.635699 TTCTTAGAAAAGGAGGGTCACC 57.364 45.455 0.00 0.00 33.22 4.02
2651 2819 6.954487 TTTTTCTTAGAAAAGGAGGGTCAC 57.046 37.500 17.89 0.00 33.22 3.67
2652 2820 7.230712 GTGATTTTTCTTAGAAAAGGAGGGTCA 59.769 37.037 17.89 13.45 32.54 4.02
2653 2821 7.309255 GGTGATTTTTCTTAGAAAAGGAGGGTC 60.309 40.741 17.89 11.65 32.54 4.46
2654 2822 6.493802 GGTGATTTTTCTTAGAAAAGGAGGGT 59.506 38.462 17.89 4.43 32.54 4.34
2655 2823 6.493458 TGGTGATTTTTCTTAGAAAAGGAGGG 59.507 38.462 17.89 0.00 32.54 4.30
2656 2824 7.524717 TGGTGATTTTTCTTAGAAAAGGAGG 57.475 36.000 17.89 0.00 32.54 4.30
2657 2825 9.987272 AAATGGTGATTTTTCTTAGAAAAGGAG 57.013 29.630 17.89 0.00 32.54 3.69
2669 2837 6.707608 AGAGCCAAAGAAAATGGTGATTTTTC 59.292 34.615 0.00 1.62 41.06 2.29
2670 2838 6.484308 CAGAGCCAAAGAAAATGGTGATTTTT 59.516 34.615 0.00 0.00 41.06 1.94
2671 2839 5.993441 CAGAGCCAAAGAAAATGGTGATTTT 59.007 36.000 0.00 0.00 43.20 1.82
2672 2840 5.544650 CAGAGCCAAAGAAAATGGTGATTT 58.455 37.500 0.00 0.00 40.23 2.17
2673 2841 4.562143 GCAGAGCCAAAGAAAATGGTGATT 60.562 41.667 0.00 0.00 40.23 2.57
2741 2917 7.685641 GCGGTTAAAATGGATGGAAATGGATTA 60.686 37.037 0.00 0.00 0.00 1.75
2742 2918 6.581712 CGGTTAAAATGGATGGAAATGGATT 58.418 36.000 0.00 0.00 0.00 3.01
2765 2941 0.388649 AGTACTTGGCTTCTGACGCG 60.389 55.000 3.53 3.53 0.00 6.01
2783 2959 7.113658 TCAGAAGCCCTCAAGTTTATACTAG 57.886 40.000 0.00 0.00 33.17 2.57
2784 2960 7.202011 GGATCAGAAGCCCTCAAGTTTATACTA 60.202 40.741 0.00 0.00 33.17 1.82
2830 3008 0.673644 GTCAGTGCGGTTGTATGGCT 60.674 55.000 0.00 0.00 0.00 4.75
2859 3037 0.723414 CCATCACATATCGCATCGGC 59.277 55.000 0.00 0.00 0.00 5.54
2866 3044 3.683365 TCCATGGTCCATCACATATCG 57.317 47.619 12.58 0.00 0.00 2.92
2928 3121 6.376978 CAGAGTCAAAGCAAAGAGGTTTATG 58.623 40.000 0.00 0.00 45.55 1.90
2934 3127 2.483491 GAGCAGAGTCAAAGCAAAGAGG 59.517 50.000 0.00 0.00 0.00 3.69
2974 3168 2.353839 GCGTGCTTGCAACAGTGG 60.354 61.111 0.00 0.00 34.15 4.00
2996 3190 2.627839 ATCGGTCGTCTCCCTCCCTC 62.628 65.000 0.00 0.00 0.00 4.30
2997 3191 2.627839 GATCGGTCGTCTCCCTCCCT 62.628 65.000 0.00 0.00 0.00 4.20
2998 3192 2.123812 ATCGGTCGTCTCCCTCCC 60.124 66.667 0.00 0.00 0.00 4.30
2999 3193 2.544698 CGATCGGTCGTCTCCCTCC 61.545 68.421 10.62 0.00 42.78 4.30
3040 3239 1.298190 GGATGTCGACGAGTACGGC 60.298 63.158 11.62 0.00 45.02 5.68
3041 3240 0.731417 AAGGATGTCGACGAGTACGG 59.269 55.000 11.62 0.00 44.46 4.02
3042 3241 3.246936 TGATAAGGATGTCGACGAGTACG 59.753 47.826 11.62 0.00 45.75 3.67
3043 3242 4.808077 TGATAAGGATGTCGACGAGTAC 57.192 45.455 11.62 0.00 0.00 2.73
3078 3281 3.463505 CAGCTTCCTGCACGTACG 58.536 61.111 15.01 15.01 45.94 3.67
3107 3310 2.433664 GCTTTGCCATGCACCAGC 60.434 61.111 0.00 4.25 38.71 4.85
3108 3311 1.940883 ATCGCTTTGCCATGCACCAG 61.941 55.000 0.00 0.00 38.71 4.00
3109 3312 1.534336 AATCGCTTTGCCATGCACCA 61.534 50.000 0.00 0.00 38.71 4.17
3110 3313 0.390209 AAATCGCTTTGCCATGCACC 60.390 50.000 0.00 0.00 38.71 5.01
3111 3314 0.717224 CAAATCGCTTTGCCATGCAC 59.283 50.000 0.00 0.00 38.71 4.57
3112 3315 3.125200 CAAATCGCTTTGCCATGCA 57.875 47.368 0.00 0.00 35.69 3.96
3274 3530 3.973206 TCTCTCTCTCTCTCTGTTCGT 57.027 47.619 0.00 0.00 0.00 3.85
3278 3534 4.202567 ACAACCTTCTCTCTCTCTCTCTGT 60.203 45.833 0.00 0.00 0.00 3.41
3279 3535 4.156556 CACAACCTTCTCTCTCTCTCTCTG 59.843 50.000 0.00 0.00 0.00 3.35
3280 3536 4.202567 ACACAACCTTCTCTCTCTCTCTCT 60.203 45.833 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.