Multiple sequence alignment - TraesCS6D01G159100

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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 TraesCS6D01G159100 chr6D 100.000 3192 0 0 1 3192 136130512 136127321 0.000000e+00 5895.0
1 TraesCS6D01G159100 chr6D 80.514 1206 221 12 994 2195 322586945 322585750 0.000000e+00 913.0
2 TraesCS6D01G159100 chr6D 82.212 208 31 6 2977 3179 389599259 389599053 1.180000e-39 174.0
3 TraesCS6D01G159100 chr6A 96.246 2504 80 11 1 2497 177264001 177266497 0.000000e+00 4091.0
4 TraesCS6D01G159100 chr6A 80.824 1189 216 11 1012 2195 460006357 460005176 0.000000e+00 922.0
5 TraesCS6D01G159100 chr6A 91.946 149 12 0 2750 2898 177267617 177267765 3.230000e-50 209.0
6 TraesCS6D01G159100 chr6A 94.915 59 2 1 2561 2619 177266585 177266528 1.220000e-14 91.6
7 TraesCS6D01G159100 chr6B 95.784 2514 75 13 1 2497 234558097 234560596 0.000000e+00 4026.0
8 TraesCS6D01G159100 chr6B 85.135 296 25 14 2618 2898 234560721 234561012 5.210000e-73 285.0
9 TraesCS6D01G159100 chr6B 81.944 288 36 12 2897 3178 234561092 234561369 2.480000e-56 230.0
10 TraesCS6D01G159100 chr6B 80.952 210 33 7 2975 3179 508533430 508533223 3.300000e-35 159.0
11 TraesCS6D01G159100 chr3A 83.193 1184 191 7 1012 2193 279436878 279435701 0.000000e+00 1077.0
12 TraesCS6D01G159100 chr3D 82.764 1201 195 10 995 2193 213996921 213998111 0.000000e+00 1061.0
13 TraesCS6D01G159100 chr3B 82.855 1184 195 7 1012 2193 330800908 330799731 0.000000e+00 1055.0
14 TraesCS6D01G159100 chr2D 78.553 1189 232 16 1013 2193 15133824 15134997 0.000000e+00 761.0
15 TraesCS6D01G159100 chr2A 78.068 383 74 10 1814 2193 17239095 17239470 1.910000e-57 233.0
16 TraesCS6D01G159100 chr2A 81.522 184 27 6 3002 3179 777533790 777533608 9.230000e-31 145.0
17 TraesCS6D01G159100 chr1B 84.360 211 25 8 2975 3179 678869083 678868875 1.940000e-47 200.0
18 TraesCS6D01G159100 chr1D 83.077 195 27 6 2975 3164 377966565 377966372 4.230000e-39 172.0
19 TraesCS6D01G159100 chr4D 86.076 158 18 4 3026 3179 42574061 42574218 1.970000e-37 167.0
20 TraesCS6D01G159100 chr2B 81.347 193 28 8 2992 3179 734683649 734683460 1.980000e-32 150.0
21 TraesCS6D01G159100 chr5A 79.524 210 37 4 2975 3179 40056711 40056919 9.230000e-31 145.0


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 TraesCS6D01G159100 chr6D 136127321 136130512 3191 True 5895.000000 5895 100.000 1 3192 1 chr6D.!!$R1 3191
1 TraesCS6D01G159100 chr6D 322585750 322586945 1195 True 913.000000 913 80.514 994 2195 1 chr6D.!!$R2 1201
2 TraesCS6D01G159100 chr6A 177264001 177267765 3764 False 2150.000000 4091 94.096 1 2898 2 chr6A.!!$F1 2897
3 TraesCS6D01G159100 chr6A 460005176 460006357 1181 True 922.000000 922 80.824 1012 2195 1 chr6A.!!$R2 1183
4 TraesCS6D01G159100 chr6B 234558097 234561369 3272 False 1513.666667 4026 87.621 1 3178 3 chr6B.!!$F1 3177
5 TraesCS6D01G159100 chr3A 279435701 279436878 1177 True 1077.000000 1077 83.193 1012 2193 1 chr3A.!!$R1 1181
6 TraesCS6D01G159100 chr3D 213996921 213998111 1190 False 1061.000000 1061 82.764 995 2193 1 chr3D.!!$F1 1198
7 TraesCS6D01G159100 chr3B 330799731 330800908 1177 True 1055.000000 1055 82.855 1012 2193 1 chr3B.!!$R1 1181
8 TraesCS6D01G159100 chr2D 15133824 15134997 1173 False 761.000000 761 78.553 1013 2193 1 chr2D.!!$F1 1180

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
627 635 1.216122 GAGATGCTGATTCGCAGGTC 58.784 55.0 8.64 3.79 45.03 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2574 2599 0.460987 CACCCTCTGCGAAGGCTAAG 60.461 60.0 0.0 0.0 40.82 2.18 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
140 147 5.277601 TGCGCTTATTTACTTGACAACTC 57.722 39.130 9.73 0.00 0.00 3.01
356 363 1.745653 GTGCCCTGTCCTTTTATCTGC 59.254 52.381 0.00 0.00 0.00 4.26
406 413 2.942376 CAGTAGTTTGGTCACAGTGCAA 59.058 45.455 0.00 0.00 0.00 4.08
407 414 3.565482 CAGTAGTTTGGTCACAGTGCAAT 59.435 43.478 0.00 0.00 0.00 3.56
447 455 2.291153 ACAGTGCAATTGGATAGGTGCT 60.291 45.455 7.72 0.00 37.87 4.40
487 495 1.656652 CTGGGATTTAGTGCTGGACG 58.343 55.000 0.00 0.00 0.00 4.79
503 511 2.227194 GGACGGTGGATGAACTGTTTT 58.773 47.619 0.00 0.00 39.79 2.43
555 563 7.382898 TGTGCTGCGAATAATACTGGATTATA 58.617 34.615 5.57 0.00 39.41 0.98
580 588 1.628846 TCTTAGAACCTTGTCCTGGGC 59.371 52.381 0.00 0.00 0.00 5.36
593 601 4.272489 TGTCCTGGGCAGAATAGAATTTG 58.728 43.478 0.00 0.00 0.00 2.32
627 635 1.216122 GAGATGCTGATTCGCAGGTC 58.784 55.000 8.64 3.79 45.03 3.85
672 680 5.452302 GCAACGGATGATTCTTTTATTCGTG 59.548 40.000 0.00 0.00 0.00 4.35
673 681 6.674519 GCAACGGATGATTCTTTTATTCGTGA 60.675 38.462 0.00 0.00 0.00 4.35
674 682 6.589830 ACGGATGATTCTTTTATTCGTGAG 57.410 37.500 0.00 0.00 0.00 3.51
777 785 5.279256 GCTGCCAACTTTTTACAATAGGGAA 60.279 40.000 0.00 0.00 0.00 3.97
902 910 7.716560 TGGATGTATGTCAGATCTGGTAATTTG 59.283 37.037 22.42 0.00 0.00 2.32
991 1005 5.445964 ACACTGATCACCTTTTGTTTAGGT 58.554 37.500 0.00 0.00 46.87 3.08
1188 1206 4.610605 TTTCGGTGAGATCACTACCAAA 57.389 40.909 12.43 4.60 45.73 3.28
1677 1695 2.370189 GCCTGTTATCCCAGAGCAGTAT 59.630 50.000 0.00 0.00 34.23 2.12
1692 1710 6.581919 CAGAGCAGTATCTTGATGAGAATACG 59.418 42.308 0.00 0.00 38.06 3.06
1953 1971 1.705337 CTATTGGCGTGCCTGAACCG 61.705 60.000 12.84 0.00 36.94 4.44
2116 2134 4.524318 AAGACGGCGGCATACGGG 62.524 66.667 18.30 0.00 44.51 5.28
2226 2244 7.492669 TGAGCGAAGTCTCTGAATAAATTTAGG 59.507 37.037 3.94 0.00 33.17 2.69
2269 2291 7.947332 AGTAATATCTCTATTCACTGCTCCAGA 59.053 37.037 0.00 0.00 35.18 3.86
2497 2522 2.753296 GCAGTAGAGAGCATCCACATC 58.247 52.381 0.00 0.00 33.66 3.06
2499 2524 3.715495 CAGTAGAGAGCATCCACATCAC 58.285 50.000 0.00 0.00 33.66 3.06
2501 2526 2.983907 AGAGAGCATCCACATCACAG 57.016 50.000 0.00 0.00 33.66 3.66
2502 2527 1.134461 AGAGAGCATCCACATCACAGC 60.134 52.381 0.00 0.00 33.66 4.40
2503 2528 0.616891 AGAGCATCCACATCACAGCA 59.383 50.000 0.00 0.00 33.66 4.41
2504 2529 1.212195 AGAGCATCCACATCACAGCAT 59.788 47.619 0.00 0.00 33.66 3.79
2505 2530 2.022195 GAGCATCCACATCACAGCATT 58.978 47.619 0.00 0.00 0.00 3.56
2508 2533 2.164827 GCATCCACATCACAGCATTTCA 59.835 45.455 0.00 0.00 0.00 2.69
2512 2537 4.256110 TCCACATCACAGCATTTCACTAG 58.744 43.478 0.00 0.00 0.00 2.57
2513 2538 4.005650 CCACATCACAGCATTTCACTAGT 58.994 43.478 0.00 0.00 0.00 2.57
2514 2539 4.093998 CCACATCACAGCATTTCACTAGTC 59.906 45.833 0.00 0.00 0.00 2.59
2515 2540 4.934001 CACATCACAGCATTTCACTAGTCT 59.066 41.667 0.00 0.00 0.00 3.24
2516 2541 4.934001 ACATCACAGCATTTCACTAGTCTG 59.066 41.667 0.00 0.00 0.00 3.51
2517 2542 4.607293 TCACAGCATTTCACTAGTCTGT 57.393 40.909 6.79 6.79 35.42 3.41
2518 2543 4.960938 TCACAGCATTTCACTAGTCTGTT 58.039 39.130 9.32 0.00 33.08 3.16
2520 2545 5.822519 TCACAGCATTTCACTAGTCTGTTTT 59.177 36.000 9.32 0.00 33.08 2.43
2521 2546 6.989759 TCACAGCATTTCACTAGTCTGTTTTA 59.010 34.615 9.32 0.00 33.08 1.52
2523 2548 8.292448 CACAGCATTTCACTAGTCTGTTTTATT 58.708 33.333 9.32 0.00 33.08 1.40
2527 2552 9.774742 GCATTTCACTAGTCTGTTTTATTTAGG 57.225 33.333 0.00 0.00 0.00 2.69
2530 2555 7.900782 TCACTAGTCTGTTTTATTTAGGTGC 57.099 36.000 0.00 0.00 0.00 5.01
2531 2556 7.676947 TCACTAGTCTGTTTTATTTAGGTGCT 58.323 34.615 0.00 0.00 0.00 4.40
2532 2557 8.809066 TCACTAGTCTGTTTTATTTAGGTGCTA 58.191 33.333 0.00 0.00 0.00 3.49
2546 2571 4.965119 AGGTGCTAAAATAAAAGGAGCG 57.035 40.909 0.00 0.00 36.76 5.03
2547 2572 4.332828 AGGTGCTAAAATAAAAGGAGCGT 58.667 39.130 0.00 0.00 36.76 5.07
2548 2573 4.156008 AGGTGCTAAAATAAAAGGAGCGTG 59.844 41.667 0.00 0.00 36.76 5.34
2549 2574 4.155280 GGTGCTAAAATAAAAGGAGCGTGA 59.845 41.667 0.00 0.00 35.88 4.35
2550 2575 5.086727 GTGCTAAAATAAAAGGAGCGTGAC 58.913 41.667 0.00 0.00 35.88 3.67
2552 2577 6.091713 GTGCTAAAATAAAAGGAGCGTGACTA 59.908 38.462 0.00 0.00 35.88 2.59
2553 2578 6.651643 TGCTAAAATAAAAGGAGCGTGACTAA 59.348 34.615 0.00 0.00 35.88 2.24
2554 2579 6.959871 GCTAAAATAAAAGGAGCGTGACTAAC 59.040 38.462 0.00 0.00 0.00 2.34
2556 2581 5.857822 AATAAAAGGAGCGTGACTAACAC 57.142 39.130 0.00 0.00 45.11 3.32
2557 2582 3.470645 AAAAGGAGCGTGACTAACACT 57.529 42.857 0.00 0.00 46.24 3.55
2558 2583 3.470645 AAAGGAGCGTGACTAACACTT 57.529 42.857 0.00 0.00 46.24 3.16
2559 2584 2.440539 AGGAGCGTGACTAACACTTG 57.559 50.000 0.00 0.00 46.24 3.16
2560 2585 1.687123 AGGAGCGTGACTAACACTTGT 59.313 47.619 0.00 0.00 46.24 3.16
2561 2586 1.792949 GGAGCGTGACTAACACTTGTG 59.207 52.381 0.00 0.00 46.24 3.33
2562 2587 2.470821 GAGCGTGACTAACACTTGTGT 58.529 47.619 0.00 0.00 46.24 3.72
2579 2604 8.215899 CACTTGTGTGTTTTATTTAGCTTAGC 57.784 34.615 0.00 0.00 39.24 3.09
2580 2605 7.326063 CACTTGTGTGTTTTATTTAGCTTAGCC 59.674 37.037 0.00 0.00 39.24 3.93
2581 2606 7.230712 ACTTGTGTGTTTTATTTAGCTTAGCCT 59.769 33.333 0.00 0.00 0.00 4.58
2582 2607 7.519032 TGTGTGTTTTATTTAGCTTAGCCTT 57.481 32.000 0.00 0.00 0.00 4.35
2583 2608 7.590279 TGTGTGTTTTATTTAGCTTAGCCTTC 58.410 34.615 0.00 0.00 0.00 3.46
2584 2609 6.741358 GTGTGTTTTATTTAGCTTAGCCTTCG 59.259 38.462 0.00 0.00 0.00 3.79
2585 2610 5.737757 GTGTTTTATTTAGCTTAGCCTTCGC 59.262 40.000 0.00 0.00 0.00 4.70
2586 2611 5.413213 TGTTTTATTTAGCTTAGCCTTCGCA 59.587 36.000 0.00 0.00 37.52 5.10
2587 2612 5.734855 TTTATTTAGCTTAGCCTTCGCAG 57.265 39.130 0.00 0.00 37.52 5.18
2588 2613 3.543680 ATTTAGCTTAGCCTTCGCAGA 57.456 42.857 0.00 0.00 37.52 4.26
2589 2614 2.586258 TTAGCTTAGCCTTCGCAGAG 57.414 50.000 0.00 0.00 38.43 3.35
2590 2615 0.747255 TAGCTTAGCCTTCGCAGAGG 59.253 55.000 0.00 0.00 38.43 3.69
2619 2648 9.750882 GCTACGTTTTTCTTACCTAAATGTTAG 57.249 33.333 0.00 0.00 34.08 2.34
2728 3128 1.159713 CGAATTATGAGCTGGCGGCA 61.160 55.000 22.28 12.58 44.79 5.69
2772 3705 8.229811 TGATAATCTGAACGAACACATTTTCAG 58.770 33.333 4.18 4.18 44.22 3.02
2781 3714 4.560035 CGAACACATTTTCAGATGGCATTC 59.440 41.667 0.00 0.00 0.00 2.67
2898 3831 8.365399 TGACAGTTCTTATACAACAACTTGAG 57.635 34.615 0.00 0.00 0.00 3.02
2908 3922 4.188462 ACAACAACTTGAGTGATCGTTGA 58.812 39.130 13.62 0.00 39.14 3.18
2951 3965 6.374417 AGGGTCAGATATATATTGGCGTTT 57.626 37.500 0.00 0.00 0.00 3.60
2979 3993 2.730094 CTGGCTGGTGTTGTTGCC 59.270 61.111 0.00 0.00 45.10 4.52
2980 3994 2.837291 TGGCTGGTGTTGTTGCCC 60.837 61.111 0.00 0.00 44.32 5.36
2982 3996 2.564721 GGCTGGTGTTGTTGCCCTC 61.565 63.158 0.00 0.00 39.49 4.30
2984 3998 1.227823 CTGGTGTTGTTGCCCTCGA 60.228 57.895 0.00 0.00 0.00 4.04
2989 4003 1.375523 GTTGTTGCCCTCGATCCGT 60.376 57.895 0.00 0.00 0.00 4.69
2993 4007 2.771639 TTGCCCTCGATCCGTCTCG 61.772 63.158 0.00 0.00 39.99 4.04
2998 4012 0.531090 CCTCGATCCGTCTCGTCTCT 60.531 60.000 4.14 0.00 39.62 3.10
3000 4014 0.108281 TCGATCCGTCTCGTCTCTGT 60.108 55.000 4.14 0.00 39.62 3.41
3007 4021 0.318762 GTCTCGTCTCTGTTGGCCTT 59.681 55.000 3.32 0.00 0.00 4.35
3014 4028 2.062636 TCTCTGTTGGCCTTAGGGTTT 58.937 47.619 3.32 0.00 34.45 3.27
3018 4032 3.589735 TCTGTTGGCCTTAGGGTTTATGA 59.410 43.478 3.32 0.00 34.45 2.15
3019 4033 3.947834 CTGTTGGCCTTAGGGTTTATGAG 59.052 47.826 3.32 0.00 34.45 2.90
3020 4034 3.288092 GTTGGCCTTAGGGTTTATGAGG 58.712 50.000 3.32 0.00 34.45 3.86
3025 4039 3.545703 CCTTAGGGTTTATGAGGCACAG 58.454 50.000 0.00 0.00 0.00 3.66
3031 4045 3.356290 GGTTTATGAGGCACAGTGGATT 58.644 45.455 1.84 0.00 0.00 3.01
3032 4046 3.378427 GGTTTATGAGGCACAGTGGATTC 59.622 47.826 1.84 0.00 0.00 2.52
3038 4052 2.438434 CACAGTGGATTCCGGCCC 60.438 66.667 0.00 0.00 0.00 5.80
3105 4120 6.591935 TGTTAGGGTTTATATTCTGCTCAGG 58.408 40.000 0.00 0.00 0.00 3.86
3109 4124 5.667626 AGGGTTTATATTCTGCTCAGGAAGA 59.332 40.000 0.00 0.00 0.00 2.87
3112 4127 6.273825 GTTTATATTCTGCTCAGGAAGACGA 58.726 40.000 0.00 0.00 0.00 4.20
3134 4152 2.896854 GCGGCGCCATGAAGATGA 60.897 61.111 28.98 0.00 0.00 2.92
3143 4161 4.555511 GCGCCATGAAGATGAAATAAGGTC 60.556 45.833 0.00 0.00 0.00 3.85
3146 4164 5.240403 GCCATGAAGATGAAATAAGGTCCTC 59.760 44.000 0.00 0.00 0.00 3.71
3170 4188 2.363795 TAGCCCCCGTCTCAGTGG 60.364 66.667 0.00 0.00 0.00 4.00
3178 4196 1.583495 CCGTCTCAGTGGTGCGTCTA 61.583 60.000 0.00 0.00 0.00 2.59
3179 4197 0.452184 CGTCTCAGTGGTGCGTCTAT 59.548 55.000 0.00 0.00 0.00 1.98
3180 4198 1.135373 CGTCTCAGTGGTGCGTCTATT 60.135 52.381 0.00 0.00 0.00 1.73
3181 4199 2.671351 CGTCTCAGTGGTGCGTCTATTT 60.671 50.000 0.00 0.00 0.00 1.40
3182 4200 3.326747 GTCTCAGTGGTGCGTCTATTTT 58.673 45.455 0.00 0.00 0.00 1.82
3183 4201 3.368236 GTCTCAGTGGTGCGTCTATTTTC 59.632 47.826 0.00 0.00 0.00 2.29
3184 4202 2.333926 TCAGTGGTGCGTCTATTTTCG 58.666 47.619 0.00 0.00 0.00 3.46
3185 4203 2.066262 CAGTGGTGCGTCTATTTTCGT 58.934 47.619 0.00 0.00 0.00 3.85
3186 4204 2.066262 AGTGGTGCGTCTATTTTCGTG 58.934 47.619 0.00 0.00 0.00 4.35
3187 4205 1.796459 GTGGTGCGTCTATTTTCGTGT 59.204 47.619 0.00 0.00 0.00 4.49
3188 4206 1.795872 TGGTGCGTCTATTTTCGTGTG 59.204 47.619 0.00 0.00 0.00 3.82
3189 4207 1.796459 GGTGCGTCTATTTTCGTGTGT 59.204 47.619 0.00 0.00 0.00 3.72
3190 4208 2.222445 GGTGCGTCTATTTTCGTGTGTT 59.778 45.455 0.00 0.00 0.00 3.32
3191 4209 3.303526 GGTGCGTCTATTTTCGTGTGTTT 60.304 43.478 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 147 2.852748 CGACACTTCCTCTAGACAACG 58.147 52.381 0.00 0.00 0.00 4.10
356 363 4.944962 TCCATTGTTCAGCACTAAATCG 57.055 40.909 0.00 0.00 0.00 3.34
447 455 3.694072 AGCCACTATTTCGCAGCATAAAA 59.306 39.130 0.00 0.00 0.00 1.52
487 495 3.380004 TGTGACAAAACAGTTCATCCACC 59.620 43.478 0.00 0.00 0.00 4.61
503 511 3.244875 ACCTATCCAATTGCACTGTGACA 60.245 43.478 12.86 6.40 0.00 3.58
555 563 5.316987 CCAGGACAAGGTTCTAAGAACAAT 58.683 41.667 0.00 0.00 0.00 2.71
580 588 7.369803 ACACAGCAGTACAAATTCTATTCTG 57.630 36.000 0.00 0.00 0.00 3.02
593 601 0.818296 ATCTCGGGACACAGCAGTAC 59.182 55.000 0.00 0.00 0.00 2.73
655 663 9.388506 ACAAGATCTCACGAATAAAAGAATCAT 57.611 29.630 0.00 0.00 0.00 2.45
672 680 3.141398 TGCACAAACAGGACAAGATCTC 58.859 45.455 0.00 0.00 0.00 2.75
673 681 3.213206 TGCACAAACAGGACAAGATCT 57.787 42.857 0.00 0.00 0.00 2.75
674 682 3.316308 AGTTGCACAAACAGGACAAGATC 59.684 43.478 0.00 0.00 41.61 2.75
724 732 6.879458 AGGGACAAGAAATACACATACAAGAC 59.121 38.462 0.00 0.00 0.00 3.01
777 785 1.953559 ATGTGCACAAGTCGTTCTGT 58.046 45.000 25.72 0.00 0.00 3.41
991 1005 3.006859 TCGACTTCAGCCATCTTCTTTGA 59.993 43.478 0.00 0.00 0.00 2.69
1188 1206 5.426689 TCTTCTCATAGTCAACATTGGCT 57.573 39.130 3.88 3.88 46.38 4.75
1677 1695 6.715347 TGGAAGATCGTATTCTCATCAAGA 57.285 37.500 0.00 0.00 0.00 3.02
1692 1710 4.387598 CAGATGGGTTGAGATGGAAGATC 58.612 47.826 0.00 0.00 0.00 2.75
1908 1926 3.381983 ACCTGGACGATGCAGCGA 61.382 61.111 33.25 7.86 34.22 4.93
1953 1971 1.668751 TGTCAGACAAACACCGAAAGC 59.331 47.619 0.00 0.00 0.00 3.51
1956 1974 2.388310 TGTGTCAGACAAACACCGAA 57.612 45.000 4.32 0.00 45.10 4.30
1968 1986 1.361668 GCCAGTGCCGTATGTGTCAG 61.362 60.000 0.00 0.00 0.00 3.51
2011 2029 5.760253 GTCAAAGTTCTCCTTGACAATCTCA 59.240 40.000 9.46 0.00 34.29 3.27
2080 2098 2.849646 AGATAGCGCCCCTTCCCC 60.850 66.667 2.29 0.00 0.00 4.81
2095 2113 1.141019 GTATGCCGCCGTCTTGAGA 59.859 57.895 0.00 0.00 0.00 3.27
2116 2134 4.785453 CCCTCCCTGCCGAAGTGC 62.785 72.222 0.00 0.00 0.00 4.40
2201 2219 7.492994 ACCTAAATTTATTCAGAGACTTCGCTC 59.507 37.037 0.00 0.00 35.11 5.03
2226 2244 5.986004 ATTACTTGCTGCGATAGGTAAAC 57.014 39.130 4.83 0.00 0.00 2.01
2237 2255 7.359933 GCAGTGAATAGAGATATTACTTGCTGC 60.360 40.741 0.00 0.00 35.97 5.25
2303 2327 5.825679 ACAATACAAGCACCTCTAAACACAA 59.174 36.000 0.00 0.00 0.00 3.33
2497 2522 5.679734 AAACAGACTAGTGAAATGCTGTG 57.320 39.130 12.01 0.00 36.77 3.66
2501 2526 9.774742 CCTAAATAAAACAGACTAGTGAAATGC 57.225 33.333 0.00 0.00 0.00 3.56
2504 2529 8.780249 GCACCTAAATAAAACAGACTAGTGAAA 58.220 33.333 0.00 0.00 0.00 2.69
2505 2530 8.154856 AGCACCTAAATAAAACAGACTAGTGAA 58.845 33.333 0.00 0.00 0.00 3.18
2520 2545 8.617809 CGCTCCTTTTATTTTAGCACCTAAATA 58.382 33.333 0.00 0.00 36.10 1.40
2521 2546 7.122204 ACGCTCCTTTTATTTTAGCACCTAAAT 59.878 33.333 0.00 0.00 36.10 1.40
2523 2548 5.941647 ACGCTCCTTTTATTTTAGCACCTAA 59.058 36.000 0.00 0.00 32.69 2.69
2526 2551 4.155280 TCACGCTCCTTTTATTTTAGCACC 59.845 41.667 0.00 0.00 32.69 5.01
2527 2552 5.086727 GTCACGCTCCTTTTATTTTAGCAC 58.913 41.667 0.00 0.00 32.69 4.40
2528 2553 5.001232 AGTCACGCTCCTTTTATTTTAGCA 58.999 37.500 0.00 0.00 32.69 3.49
2529 2554 5.547181 AGTCACGCTCCTTTTATTTTAGC 57.453 39.130 0.00 0.00 0.00 3.09
2530 2555 7.955864 GTGTTAGTCACGCTCCTTTTATTTTAG 59.044 37.037 0.00 0.00 37.31 1.85
2531 2556 7.799784 GTGTTAGTCACGCTCCTTTTATTTTA 58.200 34.615 0.00 0.00 37.31 1.52
2532 2557 6.665465 GTGTTAGTCACGCTCCTTTTATTTT 58.335 36.000 0.00 0.00 37.31 1.82
2534 2559 5.857822 GTGTTAGTCACGCTCCTTTTATT 57.142 39.130 0.00 0.00 37.31 1.40
2536 2561 4.748102 CAAGTGTTAGTCACGCTCCTTTTA 59.252 41.667 0.00 0.00 46.13 1.52
2538 2563 3.131396 CAAGTGTTAGTCACGCTCCTTT 58.869 45.455 0.00 0.00 46.13 3.11
2539 2564 2.102588 ACAAGTGTTAGTCACGCTCCTT 59.897 45.455 0.00 0.00 46.13 3.36
2540 2565 1.687123 ACAAGTGTTAGTCACGCTCCT 59.313 47.619 0.00 0.00 46.13 3.69
2541 2566 1.792949 CACAAGTGTTAGTCACGCTCC 59.207 52.381 0.00 0.00 46.13 4.70
2556 2581 7.593825 AGGCTAAGCTAAATAAAACACACAAG 58.406 34.615 0.00 0.00 0.00 3.16
2557 2582 7.519032 AGGCTAAGCTAAATAAAACACACAA 57.481 32.000 0.00 0.00 0.00 3.33
2558 2583 7.519032 AAGGCTAAGCTAAATAAAACACACA 57.481 32.000 0.00 0.00 0.00 3.72
2559 2584 6.741358 CGAAGGCTAAGCTAAATAAAACACAC 59.259 38.462 0.00 0.00 0.00 3.82
2560 2585 6.622028 GCGAAGGCTAAGCTAAATAAAACACA 60.622 38.462 6.84 0.00 35.83 3.72
2561 2586 5.737757 GCGAAGGCTAAGCTAAATAAAACAC 59.262 40.000 6.84 0.00 35.83 3.32
2562 2587 5.413213 TGCGAAGGCTAAGCTAAATAAAACA 59.587 36.000 13.91 0.00 40.82 2.83
2565 2590 5.424757 TCTGCGAAGGCTAAGCTAAATAAA 58.575 37.500 13.91 0.00 40.82 1.40
2566 2591 5.018539 TCTGCGAAGGCTAAGCTAAATAA 57.981 39.130 13.91 0.00 40.82 1.40
2567 2592 4.501571 CCTCTGCGAAGGCTAAGCTAAATA 60.502 45.833 13.91 0.00 40.82 1.40
2569 2594 2.418746 CCTCTGCGAAGGCTAAGCTAAA 60.419 50.000 13.91 1.24 40.82 1.85
2570 2595 1.137086 CCTCTGCGAAGGCTAAGCTAA 59.863 52.381 13.91 3.26 40.82 3.09
2571 2596 0.747255 CCTCTGCGAAGGCTAAGCTA 59.253 55.000 13.91 3.53 40.82 3.32
2572 2597 1.519719 CCTCTGCGAAGGCTAAGCT 59.480 57.895 13.91 0.00 40.82 3.74
2573 2598 1.522580 CCCTCTGCGAAGGCTAAGC 60.523 63.158 7.12 7.12 40.82 3.09
2574 2599 0.460987 CACCCTCTGCGAAGGCTAAG 60.461 60.000 0.00 0.00 40.82 2.18
2575 2600 1.596934 CACCCTCTGCGAAGGCTAA 59.403 57.895 0.00 0.00 40.82 3.09
2576 2601 3.019003 GCACCCTCTGCGAAGGCTA 62.019 63.158 0.00 0.00 40.82 3.93
2577 2602 4.400961 GCACCCTCTGCGAAGGCT 62.401 66.667 0.00 0.00 40.82 4.58
2585 2610 2.767505 AGAAAAACGTAGCACCCTCTG 58.232 47.619 0.00 0.00 0.00 3.35
2586 2611 3.487120 AAGAAAAACGTAGCACCCTCT 57.513 42.857 0.00 0.00 0.00 3.69
2587 2612 3.434641 GGTAAGAAAAACGTAGCACCCTC 59.565 47.826 0.00 0.00 32.82 4.30
2588 2613 3.072038 AGGTAAGAAAAACGTAGCACCCT 59.928 43.478 0.00 0.00 34.44 4.34
2589 2614 3.405831 AGGTAAGAAAAACGTAGCACCC 58.594 45.455 0.00 0.00 34.44 4.61
2590 2615 6.544038 TTTAGGTAAGAAAAACGTAGCACC 57.456 37.500 0.00 0.00 34.44 5.01
2591 2616 7.578852 ACATTTAGGTAAGAAAAACGTAGCAC 58.421 34.615 0.00 0.00 34.44 4.40
2593 2618 9.750882 CTAACATTTAGGTAAGAAAAACGTAGC 57.249 33.333 0.00 0.00 0.00 3.58
2637 2767 0.824109 TGCCTGAGGGTATTCACTCG 59.176 55.000 0.00 0.00 46.28 4.18
2677 2807 3.299340 TGAGAGTGAACGCTTTAGGAC 57.701 47.619 0.00 0.00 0.00 3.85
2728 3128 9.205513 AGATTATCATCCAAGCAAACCTTTAAT 57.794 29.630 0.00 0.00 0.00 1.40
2772 3705 5.105063 GCTCTAAAACCAAAGAATGCCATC 58.895 41.667 0.00 0.00 0.00 3.51
2814 3747 0.250295 CTCGCCAAAGGGAGTCAACA 60.250 55.000 0.00 0.00 45.57 3.33
2878 3811 8.162880 CGATCACTCAAGTTGTTGTATAAGAAC 58.837 37.037 2.11 4.32 39.59 3.01
2898 3831 5.507650 GGGGATAACTAGAGTCAACGATCAC 60.508 48.000 0.00 0.00 0.00 3.06
2908 3922 3.663632 CCTCCTAGGGGGATAACTAGAGT 59.336 52.174 25.17 0.00 44.15 3.24
2939 3953 9.804758 CCAGGTTAAAATAAAAACGCCAATATA 57.195 29.630 0.00 0.00 0.00 0.86
2940 3954 7.279090 GCCAGGTTAAAATAAAAACGCCAATAT 59.721 33.333 0.00 0.00 0.00 1.28
2941 3955 6.590677 GCCAGGTTAAAATAAAAACGCCAATA 59.409 34.615 0.00 0.00 0.00 1.90
2942 3956 5.410132 GCCAGGTTAAAATAAAAACGCCAAT 59.590 36.000 0.00 0.00 0.00 3.16
2943 3957 4.750598 GCCAGGTTAAAATAAAAACGCCAA 59.249 37.500 0.00 0.00 0.00 4.52
2944 3958 4.039366 AGCCAGGTTAAAATAAAAACGCCA 59.961 37.500 0.00 0.00 0.00 5.69
2976 3990 3.209812 CGAGACGGATCGAGGGCA 61.210 66.667 5.70 0.00 45.56 5.36
2977 3991 3.183776 GACGAGACGGATCGAGGGC 62.184 68.421 16.95 1.92 45.56 5.19
2979 3993 0.531090 AGAGACGAGACGGATCGAGG 60.531 60.000 16.95 0.00 45.56 4.63
2980 3994 0.579630 CAGAGACGAGACGGATCGAG 59.420 60.000 16.95 0.00 45.56 4.04
2984 3998 0.811915 CCAACAGAGACGAGACGGAT 59.188 55.000 0.00 0.00 0.00 4.18
2989 4003 1.819288 CTAAGGCCAACAGAGACGAGA 59.181 52.381 5.01 0.00 0.00 4.04
2993 4007 0.984995 ACCCTAAGGCCAACAGAGAC 59.015 55.000 5.01 0.00 36.11 3.36
2998 4012 3.308832 CCTCATAAACCCTAAGGCCAACA 60.309 47.826 5.01 0.00 36.11 3.33
3000 4014 2.357777 GCCTCATAAACCCTAAGGCCAA 60.358 50.000 5.01 0.00 45.45 4.52
3007 4021 2.238646 CCACTGTGCCTCATAAACCCTA 59.761 50.000 1.29 0.00 0.00 3.53
3014 4028 1.138859 CGGAATCCACTGTGCCTCATA 59.861 52.381 1.29 0.00 0.00 2.15
3018 4032 2.671070 CCGGAATCCACTGTGCCT 59.329 61.111 0.00 0.00 0.00 4.75
3019 4033 3.134127 GCCGGAATCCACTGTGCC 61.134 66.667 5.05 0.00 0.00 5.01
3020 4034 3.134127 GGCCGGAATCCACTGTGC 61.134 66.667 5.05 0.00 0.00 4.57
3021 4035 2.438434 GGGCCGGAATCCACTGTG 60.438 66.667 5.05 0.00 0.00 3.66
3022 4036 2.231380 AAGGGCCGGAATCCACTGT 61.231 57.895 5.05 0.00 0.00 3.55
3023 4037 1.750399 CAAGGGCCGGAATCCACTG 60.750 63.158 5.05 1.24 0.00 3.66
3025 4039 3.140814 GCAAGGGCCGGAATCCAC 61.141 66.667 5.05 0.00 0.00 4.02
3043 4057 1.740332 AAAACAAAACCCTCCCGCCG 61.740 55.000 0.00 0.00 0.00 6.46
3053 4067 8.926715 ACTCAAAGAACCATCTAAAACAAAAC 57.073 30.769 0.00 0.00 33.77 2.43
3058 4073 8.926715 ACAAAACTCAAAGAACCATCTAAAAC 57.073 30.769 0.00 0.00 33.77 2.43
3105 4120 2.956964 CGCCGCCATCTCGTCTTC 60.957 66.667 0.00 0.00 0.00 2.87
3123 4138 5.767168 GGAGGACCTTATTTCATCTTCATGG 59.233 44.000 0.00 0.00 0.00 3.66
3125 4140 5.163045 GGGGAGGACCTTATTTCATCTTCAT 60.163 44.000 0.00 0.00 40.03 2.57
3134 4152 0.623617 AGGCGGGGAGGACCTTATTT 60.624 55.000 0.00 0.00 40.03 1.40
3164 4182 2.288579 ACGAAAATAGACGCACCACTGA 60.289 45.455 0.00 0.00 0.00 3.41
3165 4183 2.066262 ACGAAAATAGACGCACCACTG 58.934 47.619 0.00 0.00 0.00 3.66
3166 4184 2.066262 CACGAAAATAGACGCACCACT 58.934 47.619 0.00 0.00 0.00 4.00
3170 4188 3.515071 AACACACGAAAATAGACGCAC 57.485 42.857 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.