Multiple sequence alignment - TraesCS3D01G495800

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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 TraesCS3D01G495800 chr3D 100.000 3221 0 0 1 3221 587753228 587750008 0.000000e+00 5949
1 TraesCS3D01G495800 chr3A 90.765 2848 156 36 402 3221 717306032 717303264 0.000000e+00 3703
2 TraesCS3D01G495800 chr3B 87.389 2585 181 67 4 2509 785291896 785289378 0.000000e+00 2833
3 TraesCS3D01G495800 chr3B 86.560 439 34 12 2520 2942 785289306 785288877 8.140000e-126 460
4 TraesCS3D01G495800 chr3B 92.523 107 8 0 3018 3124 785288878 785288772 1.550000e-33 154


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 TraesCS3D01G495800 chr3D 587750008 587753228 3220 True 5949 5949 100.000 1 3221 1 chr3D.!!$R1 3220
1 TraesCS3D01G495800 chr3A 717303264 717306032 2768 True 3703 3703 90.765 402 3221 1 chr3A.!!$R1 2819
2 TraesCS3D01G495800 chr3B 785288772 785291896 3124 True 1149 2833 88.824 4 3124 3 chr3B.!!$R1 3120

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
33 34 0.176680 ATCACGACCACAGATGCTCC 59.823 55.0 0.0 0.0 0.0 4.70 F
1735 1793 0.033228 GGAGATGATCACGAGCCCAG 59.967 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2026 1.026718 CCGTGGCCATTGGAGACTTC 61.027 60.0 19.58 0.0 0.00 3.01 R
3078 3276 0.035458 AGTGGTAGAACACAGCAGGC 59.965 55.0 0.00 0.0 43.72 4.85 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
31 32 0.897621 TCATCACGACCACAGATGCT 59.102 50.000 0.00 0.00 39.12 3.79
33 34 0.176680 ATCACGACCACAGATGCTCC 59.823 55.000 0.00 0.00 0.00 4.70
118 119 5.300792 AGAACAAGTTTTCTAATGGCGGAAA 59.699 36.000 0.00 0.00 33.89 3.13
182 183 4.813750 AAGGGAAATCATTGCTCCAAAG 57.186 40.909 0.00 0.00 0.00 2.77
184 185 3.766051 AGGGAAATCATTGCTCCAAAGTC 59.234 43.478 0.00 0.00 0.00 3.01
185 186 3.428045 GGGAAATCATTGCTCCAAAGTCG 60.428 47.826 0.00 0.00 0.00 4.18
187 188 4.096984 GGAAATCATTGCTCCAAAGTCGAT 59.903 41.667 0.00 0.00 0.00 3.59
219 221 5.212194 CCTTTCACGAAACATCGATTTTGT 58.788 37.500 5.11 0.00 36.75 2.83
227 229 6.020201 ACGAAACATCGATTTTGTTTTTGTCC 60.020 34.615 14.86 3.79 44.90 4.02
234 236 5.043248 CGATTTTGTTTTTGTCCAGAGCTT 58.957 37.500 0.00 0.00 0.00 3.74
237 239 4.799564 TTGTTTTTGTCCAGAGCTTGTT 57.200 36.364 0.00 0.00 0.00 2.83
244 247 2.671177 CCAGAGCTTGTTGACGCCG 61.671 63.158 0.00 0.00 0.00 6.46
249 252 0.602638 AGCTTGTTGACGCCGAATCA 60.603 50.000 0.00 0.00 0.00 2.57
341 345 8.729805 TTGTTGTTTTGCTATTCCTTTTGATT 57.270 26.923 0.00 0.00 0.00 2.57
353 357 5.333566 TCCTTTTGATTTTACTGGGAGGT 57.666 39.130 0.00 0.00 0.00 3.85
422 426 5.055265 TCCATTGGAAGTTTTGTAGGACA 57.945 39.130 1.94 0.00 0.00 4.02
452 456 1.346395 TCACGGCTTACCATGTGAACT 59.654 47.619 0.00 0.00 34.52 3.01
505 524 2.623416 CCCCTTTCCACTGTGAAACTTC 59.377 50.000 9.86 0.00 38.04 3.01
511 530 2.167693 TCCACTGTGAAACTTCGACACT 59.832 45.455 9.86 0.00 38.04 3.55
550 570 4.214971 ACACTGCTTACTGCTGAATTTCTG 59.785 41.667 0.00 0.00 42.27 3.02
610 631 4.162509 AGACAGACCCAGCTATACTTTTCC 59.837 45.833 0.00 0.00 0.00 3.13
757 779 1.609208 CAAGGGTGTGGACAAGAAGG 58.391 55.000 0.00 0.00 0.00 3.46
767 789 2.152016 GGACAAGAAGGAACGGGAAAG 58.848 52.381 0.00 0.00 0.00 2.62
794 816 6.350629 CACACATAGTGGAGATGGATGATA 57.649 41.667 1.93 0.00 44.69 2.15
810 839 3.659089 ATACCCCGTGTGCACTCGC 62.659 63.158 30.30 14.55 39.24 5.03
854 884 1.038130 CACCACCTACTCTCTCCCCG 61.038 65.000 0.00 0.00 0.00 5.73
855 885 1.212934 ACCACCTACTCTCTCCCCGA 61.213 60.000 0.00 0.00 0.00 5.14
940 995 5.525378 CACACTAGAAATCTAAGGTCCATGC 59.475 44.000 0.00 0.00 0.00 4.06
941 996 5.426833 ACACTAGAAATCTAAGGTCCATGCT 59.573 40.000 0.00 0.00 0.00 3.79
942 997 6.611642 ACACTAGAAATCTAAGGTCCATGCTA 59.388 38.462 0.00 0.00 0.00 3.49
943 998 7.125811 ACACTAGAAATCTAAGGTCCATGCTAA 59.874 37.037 0.00 0.00 0.00 3.09
944 999 7.655328 CACTAGAAATCTAAGGTCCATGCTAAG 59.345 40.741 0.00 0.00 0.00 2.18
945 1000 5.934781 AGAAATCTAAGGTCCATGCTAAGG 58.065 41.667 0.00 0.00 0.00 2.69
946 1001 5.430089 AGAAATCTAAGGTCCATGCTAAGGT 59.570 40.000 0.00 0.00 0.00 3.50
947 1002 4.965200 ATCTAAGGTCCATGCTAAGGTC 57.035 45.455 0.00 0.00 0.00 3.85
948 1003 3.039011 TCTAAGGTCCATGCTAAGGTCC 58.961 50.000 0.00 0.00 34.97 4.46
949 1004 1.668826 AAGGTCCATGCTAAGGTCCA 58.331 50.000 8.15 0.00 36.89 4.02
950 1005 1.898863 AGGTCCATGCTAAGGTCCAT 58.101 50.000 8.15 0.00 36.89 3.41
951 1006 1.492176 AGGTCCATGCTAAGGTCCATG 59.508 52.381 8.15 0.00 36.89 3.66
1062 1120 3.787001 GGCGGAGGGTTGGAGGAG 61.787 72.222 0.00 0.00 0.00 3.69
1149 1207 1.328680 CACAACATCTGCATCTACGCC 59.671 52.381 0.00 0.00 0.00 5.68
1539 1597 1.368950 CATCACGGAGCCATCGGAT 59.631 57.895 0.00 0.00 0.00 4.18
1593 1651 2.892425 GTCATCCTTGAGCCGCCG 60.892 66.667 0.00 0.00 30.85 6.46
1695 1753 2.342279 CCGTTCTTGCACCTCGGA 59.658 61.111 11.65 0.00 43.22 4.55
1723 1781 1.737838 GTTTGACGCCATGGAGATGA 58.262 50.000 23.45 3.98 0.00 2.92
1735 1793 0.033228 GGAGATGATCACGAGCCCAG 59.967 60.000 0.00 0.00 0.00 4.45
1748 1806 2.438434 CCCAGGCGGCGAGAATTT 60.438 61.111 12.98 0.00 0.00 1.82
1803 1861 2.836360 ACGACCACCACGACCAGT 60.836 61.111 0.00 0.00 34.70 4.00
1968 2026 0.602905 AGGAGAAGGTCGGCGTTTTG 60.603 55.000 6.85 0.00 0.00 2.44
1977 2035 0.105224 TCGGCGTTTTGAAGTCTCCA 59.895 50.000 6.85 0.00 0.00 3.86
2109 2167 2.124819 AAGCTGCCGATGGAGCTG 60.125 61.111 9.37 0.00 44.97 4.24
2280 2338 9.593134 GACTAGAATTATTCAGAGTGTTGTGAT 57.407 33.333 14.47 0.00 30.95 3.06
2281 2339 9.950496 ACTAGAATTATTCAGAGTGTTGTGATT 57.050 29.630 7.74 0.00 30.01 2.57
2283 2341 8.627208 AGAATTATTCAGAGTGTTGTGATTGT 57.373 30.769 7.74 0.00 0.00 2.71
2284 2342 9.071276 AGAATTATTCAGAGTGTTGTGATTGTT 57.929 29.630 7.74 0.00 0.00 2.83
2288 2396 5.929697 TCAGAGTGTTGTGATTGTTCATC 57.070 39.130 0.00 0.00 33.56 2.92
2293 2401 6.873605 AGAGTGTTGTGATTGTTCATCGATTA 59.126 34.615 0.00 0.00 34.08 1.75
2294 2402 7.550551 AGAGTGTTGTGATTGTTCATCGATTAT 59.449 33.333 0.00 0.00 34.08 1.28
2299 2407 7.250445 TGTGATTGTTCATCGATTATTCAGG 57.750 36.000 0.00 0.00 34.08 3.86
2315 2423 0.462047 CAGGGTGCGGTTAGATGGTC 60.462 60.000 0.00 0.00 0.00 4.02
2330 2438 7.148239 GGTTAGATGGTCACTAGGTTTTGATTG 60.148 40.741 0.00 0.00 0.00 2.67
2354 2462 3.673338 TCATCGTCGTTGTTGACTTGATC 59.327 43.478 3.38 0.00 36.71 2.92
2403 2523 2.841442 AGACTAACTTGTGGAGTGGC 57.159 50.000 0.00 0.00 39.00 5.01
2453 2576 4.996758 AGCAGAGCTTTCTTTCTTCTTCTC 59.003 41.667 0.00 0.00 33.89 2.87
2477 2600 9.658799 CTCCTGAAGAAGACTACAATTATTCAA 57.341 33.333 0.00 0.00 36.51 2.69
2518 2651 3.190874 GCGGTTATTCAGAGTGAGGAAG 58.809 50.000 0.00 0.00 0.00 3.46
2546 2727 1.408702 GTCTGCCTGCAAAGGTTTTGA 59.591 47.619 5.77 0.00 0.00 2.69
2551 2732 2.802247 GCCTGCAAAGGTTTTGATTGTC 59.198 45.455 5.77 0.00 0.00 3.18
2559 2740 6.400303 GCAAAGGTTTTGATTGTCAATCATCG 60.400 38.462 25.19 11.03 46.50 3.84
2588 2775 4.218417 GCACTCAATTACAAACTCCCACAT 59.782 41.667 0.00 0.00 0.00 3.21
2689 2876 3.134442 AGATTGCTTGGTCAGATCTCCTC 59.866 47.826 0.00 0.00 0.00 3.71
2690 2877 2.244486 TGCTTGGTCAGATCTCCTCT 57.756 50.000 0.00 0.00 33.14 3.69
2691 2878 8.534326 AAGATTGCTTGGTCAGATCTCCTCTG 62.534 46.154 0.00 0.00 41.88 3.35
2816 3005 3.254166 CACTGCAGAAATAGTTGGCTTGT 59.746 43.478 23.35 0.00 0.00 3.16
2838 3027 0.865769 ACTCAAGTACGCCGCTTTTG 59.134 50.000 0.00 0.00 0.00 2.44
2861 3057 3.290710 TGCCAAATTCTTGCTCCTATCC 58.709 45.455 0.00 0.00 0.00 2.59
2886 3082 3.647771 GGTCCCACTCCCACCCAC 61.648 72.222 0.00 0.00 0.00 4.61
2912 3108 4.385358 TTGTTTCAGAAGCAAAGGAACC 57.615 40.909 9.81 0.00 0.00 3.62
2915 3111 0.850100 TCAGAAGCAAAGGAACCCCA 59.150 50.000 0.00 0.00 33.88 4.96
2927 3123 4.850193 ACCCCATGGTTCAGCTTG 57.150 55.556 11.73 0.00 44.75 4.01
2955 3151 2.729882 GAGCGACGATATAAATTGCGGT 59.270 45.455 0.00 0.00 32.90 5.68
2956 3152 2.475111 AGCGACGATATAAATTGCGGTG 59.525 45.455 0.00 0.00 30.72 4.94
2981 3179 0.741221 GGTGTGAGCACTCGGGATTC 60.741 60.000 0.00 0.00 44.65 2.52
2985 3183 1.519455 GAGCACTCGGGATTCCACG 60.519 63.158 4.80 6.17 0.00 4.94
3013 3211 2.027897 ACGCTTCCACGTACGCAA 59.972 55.556 16.72 4.94 46.19 4.85
3014 3212 2.019951 ACGCTTCCACGTACGCAAG 61.020 57.895 16.72 15.46 46.19 4.01
3015 3213 2.474712 GCTTCCACGTACGCAAGC 59.525 61.111 23.35 23.35 45.62 4.01
3016 3214 2.314647 GCTTCCACGTACGCAAGCA 61.315 57.895 28.61 7.02 40.86 3.91
3078 3276 4.191485 GCATGAACGCGACCGACG 62.191 66.667 15.93 0.00 45.66 5.12
3099 3297 2.146342 CCTGCTGTGTTCTACCACTTG 58.854 52.381 0.00 0.00 36.30 3.16
3109 3307 3.746045 TCTACCACTTGTCCTCACAAC 57.254 47.619 0.00 0.00 37.61 3.32
3199 3397 1.011242 CACGCACGTGTTGTTGAGG 60.011 57.895 18.38 1.00 40.91 3.86
3204 3402 1.531058 GCACGTGTTGTTGAGGTTGAC 60.531 52.381 18.38 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.367498 GGTCGTGATGAGCTATGGATACC 60.367 52.174 0.00 0.00 41.93 2.73
1 2 3.255888 TGGTCGTGATGAGCTATGGATAC 59.744 47.826 5.39 0.00 45.46 2.24
2 3 3.255888 GTGGTCGTGATGAGCTATGGATA 59.744 47.826 5.39 0.00 45.46 2.59
9 10 1.134877 CATCTGTGGTCGTGATGAGCT 60.135 52.381 5.39 0.00 45.46 4.09
31 32 1.543871 GCTTTTACTGTTCACCCGGGA 60.544 52.381 32.02 1.07 0.00 5.14
33 34 0.879090 GGCTTTTACTGTTCACCCGG 59.121 55.000 0.00 0.00 0.00 5.73
110 111 1.134965 CCGCCATAAAATTTTCCGCCA 60.135 47.619 6.72 0.00 0.00 5.69
118 119 4.934602 CCAATGTCAAACCGCCATAAAATT 59.065 37.500 0.00 0.00 0.00 1.82
192 193 6.548441 AATCGATGTTTCGTGAAAGGTTAA 57.452 33.333 0.00 0.00 45.65 2.01
210 212 4.338118 AGCTCTGGACAAAAACAAAATCGA 59.662 37.500 0.00 0.00 0.00 3.59
211 213 4.610945 AGCTCTGGACAAAAACAAAATCG 58.389 39.130 0.00 0.00 0.00 3.34
219 221 3.181501 CGTCAACAAGCTCTGGACAAAAA 60.182 43.478 0.00 0.00 0.00 1.94
227 229 1.221466 TTCGGCGTCAACAAGCTCTG 61.221 55.000 6.85 0.00 0.00 3.35
234 236 0.321210 ATGGTGATTCGGCGTCAACA 60.321 50.000 18.65 18.65 46.33 3.33
237 239 0.036858 TTCATGGTGATTCGGCGTCA 60.037 50.000 6.85 0.40 0.00 4.35
244 247 4.685628 ACGTGCAAAATTTCATGGTGATTC 59.314 37.500 0.00 0.00 0.00 2.52
249 252 2.288763 GGGACGTGCAAAATTTCATGGT 60.289 45.455 9.96 0.00 0.00 3.55
309 313 8.504812 AGGAATAGCAAAACAACAAACAAATT 57.495 26.923 0.00 0.00 0.00 1.82
341 345 1.559682 GGAGCATCACCTCCCAGTAAA 59.440 52.381 0.00 0.00 44.60 2.01
353 357 3.494924 CGATTTGGTGATAGGGAGCATCA 60.495 47.826 0.00 0.00 36.25 3.07
452 456 1.218047 GTCGGTGGTGCATAGCTCA 59.782 57.895 0.00 0.00 0.00 4.26
505 524 0.528901 TGGGTCGTGTCAAAGTGTCG 60.529 55.000 0.00 0.00 0.00 4.35
511 530 1.140052 AGTGTCATGGGTCGTGTCAAA 59.860 47.619 0.00 0.00 0.00 2.69
550 570 5.673337 TGACTTGACAGCAACATTTCTAC 57.327 39.130 0.00 0.00 0.00 2.59
610 631 2.163010 ACGCATGATGGCTCAAGAAAAG 59.837 45.455 0.00 0.00 34.37 2.27
757 779 0.534203 TGTGTGCTCCTTTCCCGTTC 60.534 55.000 0.00 0.00 0.00 3.95
767 789 2.484417 CCATCTCCACTATGTGTGCTCC 60.484 54.545 0.00 0.00 44.92 4.70
784 806 1.878102 GCACACGGGGTATCATCCATC 60.878 57.143 0.00 0.00 0.00 3.51
810 839 2.019156 GCGAGGGAGGAAAAATGGAGG 61.019 57.143 0.00 0.00 0.00 4.30
854 884 4.403734 TGGAATTGTTAGGACTTTGGGTC 58.596 43.478 0.00 0.00 43.79 4.46
855 885 4.463050 TGGAATTGTTAGGACTTTGGGT 57.537 40.909 0.00 0.00 0.00 4.51
940 995 4.862902 AGACGATCATCATGGACCTTAG 57.137 45.455 0.00 0.00 0.00 2.18
941 996 5.241728 CACTAGACGATCATCATGGACCTTA 59.758 44.000 0.00 0.00 0.00 2.69
942 997 4.038522 CACTAGACGATCATCATGGACCTT 59.961 45.833 0.00 0.00 0.00 3.50
943 998 3.571828 CACTAGACGATCATCATGGACCT 59.428 47.826 0.00 0.00 0.00 3.85
944 999 3.570125 TCACTAGACGATCATCATGGACC 59.430 47.826 0.00 0.00 0.00 4.46
945 1000 4.837896 TCACTAGACGATCATCATGGAC 57.162 45.455 0.00 0.00 0.00 4.02
946 1001 5.072741 TGATCACTAGACGATCATCATGGA 58.927 41.667 19.20 2.77 43.30 3.41
947 1002 5.382618 TGATCACTAGACGATCATCATGG 57.617 43.478 19.20 0.00 43.30 3.66
948 1003 6.250951 CGATTGATCACTAGACGATCATCATG 59.749 42.308 21.92 13.04 46.44 3.07
949 1004 6.320944 CGATTGATCACTAGACGATCATCAT 58.679 40.000 21.92 16.25 46.44 2.45
950 1005 5.335191 CCGATTGATCACTAGACGATCATCA 60.335 44.000 21.92 13.40 46.44 3.07
951 1006 5.092105 CCGATTGATCACTAGACGATCATC 58.908 45.833 21.92 19.18 46.44 2.92
992 1047 0.886490 GGCAGGCTCCATTACCGATG 60.886 60.000 0.00 0.00 35.42 3.84
993 1048 1.344953 TGGCAGGCTCCATTACCGAT 61.345 55.000 0.00 0.00 0.00 4.18
997 1052 2.225467 GAATCTGGCAGGCTCCATTAC 58.775 52.381 15.73 0.00 35.22 1.89
1062 1120 3.878519 CTCTCCTCGCCGTCGTCC 61.879 72.222 0.00 0.00 36.96 4.79
1149 1207 2.503375 GCGTACACGTCCTGGTCG 60.503 66.667 11.71 11.71 42.22 4.79
1356 1414 3.760035 GCGAACCCGAGGAGCTGA 61.760 66.667 0.00 0.00 38.22 4.26
1417 1475 4.821589 GAACTCCCGCCGCTCCAG 62.822 72.222 0.00 0.00 0.00 3.86
1476 1534 2.413765 GCGAGGGAGAGGCTTACG 59.586 66.667 0.00 0.00 0.00 3.18
1479 1537 4.406763 AGGGCGAGGGAGAGGCTT 62.407 66.667 0.00 0.00 0.00 4.35
1525 1583 4.286320 GCGATCCGATGGCTCCGT 62.286 66.667 8.04 0.00 0.00 4.69
1735 1793 1.298638 GCATCAAATTCTCGCCGCC 60.299 57.895 0.00 0.00 0.00 6.13
1748 1806 3.770040 CCGAGGACACCGGCATCA 61.770 66.667 0.00 0.00 40.54 3.07
1803 1861 2.119029 ATCGATCGCCCTGTCGTCA 61.119 57.895 11.09 0.00 38.85 4.35
1968 2026 1.026718 CCGTGGCCATTGGAGACTTC 61.027 60.000 19.58 0.00 0.00 3.01
2167 2225 2.711922 CCCCGTCCTTCCTCGACTG 61.712 68.421 0.00 0.00 0.00 3.51
2280 2338 4.335315 GCACCCTGAATAATCGATGAACAA 59.665 41.667 0.00 0.00 0.00 2.83
2281 2339 3.876914 GCACCCTGAATAATCGATGAACA 59.123 43.478 0.00 0.00 0.00 3.18
2282 2340 3.059597 CGCACCCTGAATAATCGATGAAC 60.060 47.826 0.00 0.00 0.00 3.18
2283 2341 3.130633 CGCACCCTGAATAATCGATGAA 58.869 45.455 0.00 0.00 0.00 2.57
2284 2342 2.547855 CCGCACCCTGAATAATCGATGA 60.548 50.000 0.00 0.00 0.00 2.92
2288 2396 1.663695 AACCGCACCCTGAATAATCG 58.336 50.000 0.00 0.00 0.00 3.34
2293 2401 1.134098 CCATCTAACCGCACCCTGAAT 60.134 52.381 0.00 0.00 0.00 2.57
2294 2402 0.251916 CCATCTAACCGCACCCTGAA 59.748 55.000 0.00 0.00 0.00 3.02
2299 2407 0.249398 AGTGACCATCTAACCGCACC 59.751 55.000 0.00 0.00 0.00 5.01
2315 2423 6.241207 ACGATGAACAATCAAAACCTAGTG 57.759 37.500 0.00 0.00 39.49 2.74
2330 2438 3.244345 TCAAGTCAACAACGACGATGAAC 59.756 43.478 12.41 6.96 40.98 3.18
2368 2488 5.771165 AGTTAGTCTTAGCTAGAGGTATGCC 59.229 44.000 0.00 0.00 32.23 4.40
2370 2490 8.132362 CACAAGTTAGTCTTAGCTAGAGGTATG 58.868 40.741 0.00 0.00 34.66 2.39
2372 2492 6.602406 CCACAAGTTAGTCTTAGCTAGAGGTA 59.398 42.308 0.00 0.00 34.66 3.08
2403 2523 1.334960 GGACACACGCAAAACTCCATG 60.335 52.381 0.00 0.00 0.00 3.66
2477 2600 5.529800 ACCGCAGTTTTTATACAGAACACTT 59.470 36.000 0.00 0.00 0.00 3.16
2518 2651 2.034104 TTGCAGGCAGACATCAGATC 57.966 50.000 0.00 0.00 0.00 2.75
2546 2727 2.488937 TGCAGCAACGATGATTGACAAT 59.511 40.909 0.00 0.00 0.00 2.71
2551 2732 1.465777 TGAGTGCAGCAACGATGATTG 59.534 47.619 0.00 0.00 0.00 2.67
2559 2740 4.610945 AGTTTGTAATTGAGTGCAGCAAC 58.389 39.130 0.00 0.00 0.00 4.17
2605 2792 7.364762 CCACTCCACATGTTACTCTTATTAGGT 60.365 40.741 0.00 0.00 0.00 3.08
2606 2793 6.986817 CCACTCCACATGTTACTCTTATTAGG 59.013 42.308 0.00 0.00 0.00 2.69
2689 2876 4.039730 TCTCCTCAAGAAGGTTCAGTTCAG 59.960 45.833 0.00 0.00 46.32 3.02
2690 2877 3.967326 TCTCCTCAAGAAGGTTCAGTTCA 59.033 43.478 0.00 0.00 46.32 3.18
2691 2878 4.282195 TCTCTCCTCAAGAAGGTTCAGTTC 59.718 45.833 0.00 0.00 46.32 3.01
2692 2879 4.227197 TCTCTCCTCAAGAAGGTTCAGTT 58.773 43.478 0.00 0.00 46.32 3.16
2693 2880 3.831911 CTCTCTCCTCAAGAAGGTTCAGT 59.168 47.826 0.00 0.00 46.32 3.41
2838 3027 4.440663 GGATAGGAGCAAGAATTTGGCAAC 60.441 45.833 0.00 0.00 34.79 4.17
2861 3057 1.059913 GGGAGTGGGACCATCCATAG 58.940 60.000 16.41 0.00 38.64 2.23
2886 3082 3.739300 CCTTTGCTTCTGAAACAATGCTG 59.261 43.478 7.02 0.22 0.00 4.41
2912 3108 2.242043 AGAAACAAGCTGAACCATGGG 58.758 47.619 18.09 0.00 0.00 4.00
2915 3111 3.005155 GCTCAAGAAACAAGCTGAACCAT 59.995 43.478 0.00 0.00 33.23 3.55
2921 3117 1.397693 CGTCGCTCAAGAAACAAGCTG 60.398 52.381 0.00 0.00 33.83 4.24
2927 3123 6.354622 GCAATTTATATCGTCGCTCAAGAAAC 59.645 38.462 0.00 0.00 0.00 2.78
2985 3183 0.955428 TGGAAGCGTCTGTTCCATGC 60.955 55.000 0.41 0.00 46.96 4.06
3012 3210 4.927782 TTGGCTCCACGCGTGCTT 62.928 61.111 33.17 0.00 40.44 3.91
3078 3276 0.035458 AGTGGTAGAACACAGCAGGC 59.965 55.000 0.00 0.00 43.72 4.85
3109 3307 1.207593 GCTGCTACGTTGCCACTTG 59.792 57.895 19.09 5.76 0.00 3.16
3147 3345 5.186797 TGGAAGTTGCAAAGAAAAGAGGAAA 59.813 36.000 0.00 0.00 0.00 3.13
3149 3347 4.277476 TGGAAGTTGCAAAGAAAAGAGGA 58.723 39.130 0.00 0.00 0.00 3.71
3151 3349 4.986659 CCATGGAAGTTGCAAAGAAAAGAG 59.013 41.667 5.56 0.00 0.00 2.85
3153 3351 4.060205 CCCATGGAAGTTGCAAAGAAAAG 58.940 43.478 15.22 0.00 0.00 2.27
3156 3354 2.676748 ACCCATGGAAGTTGCAAAGAA 58.323 42.857 15.22 0.00 0.00 2.52
3157 3355 2.380064 ACCCATGGAAGTTGCAAAGA 57.620 45.000 15.22 0.00 0.00 2.52
3158 3356 3.473923 AAACCCATGGAAGTTGCAAAG 57.526 42.857 15.22 0.00 0.00 2.77
3199 3397 1.062258 TCGTATCGGCGTTTGTCAAC 58.938 50.000 6.85 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.